From bdb1c5361889c7ed0e946af4cd848a5d8faacf15 Mon Sep 17 00:00:00 2001 From: Patol75 Date: Thu, 25 Apr 2024 14:42:26 +0000 Subject: [PATCH] deploy: 6e22ee1ea5f80643662f8f047ffaca030c384e48 --- pydrex/cli.html | 2 +- pydrex/diagnostics.html | 153 ++-- pydrex/minerals.html | 1544 +++++++++++++++++++------------------- search.js | 2 +- tests/conftest.html | 339 +++++---- tests/test_doctests.html | 10 +- 6 files changed, 1047 insertions(+), 1003 deletions(-) diff --git a/pydrex/cli.html b/pydrex/cli.html index 14a53524..813acb79 100644 --- a/pydrex/cli.html +++ b/pydrex/cli.html @@ -893,7 +893,7 @@

CLI_HANDLERS = - CLI_HANDLERS(h5part_extractor=<H5partExtractor object>, npz_file_inspector=<NPZFileInspector object>, pole_figure_visualiser=<PoleFigureVisualiser object>, mesh_generator=<MeshGenerator object>) + CLI_HANDLERS(h5part_extractor=<H5partExtractor object>, mesh_generator=<MeshGenerator object>, npz_file_inspector=<NPZFileInspector object>, pole_figure_visualiser=<PoleFigureVisualiser object>)
diff --git a/pydrex/diagnostics.html b/pydrex/diagnostics.html index 79d3a430..4a7fc563 100644 --- a/pydrex/diagnostics.html +++ b/pydrex/diagnostics.html @@ -510,38 +510,39 @@

392 393 Examples: 394 -395 >>> from numpy import asarray as Ŋ -396 >>> smallest_angle(Ŋ([1e0, 0e0, 0e0]), Ŋ([1e0, 0e0, 0e0])) -397 0.0 -398 >>> smallest_angle(Ŋ([1e0, 0e0, 0e0]), Ŋ([0e0, 1e0, 0e0])) -399 90.0 -400 >>> smallest_angle(Ŋ([1e0, 0e0, 0e0]), Ŋ([0e0, -1e0, 0e0])) -401 90.0 -402 >>> smallest_angle(Ŋ([1e0, 0e0, 0e0]), Ŋ([np.sqrt(2), np.sqrt(2), 0e0])) -403 45.0 -404 >>> smallest_angle(Ŋ([1e0, 0e0, 0e0]), Ŋ([-np.sqrt(2), np.sqrt(2), 0e0])) -405 45.0 -406 -407 """ -408 if plane is not None: -409 _vector = vector - plane * np.dot(vector, plane) -410 else: -411 _vector = vector -412 angle = np.rad2deg( -413 np.arccos( -414 np.clip( -415 np.asarray( # https://github.com/numba/numba/issues/3469 -416 np.dot(_vector, axis) -417 / (np.linalg.norm(_vector) * np.linalg.norm(axis)) -418 ), -419 -1, -420 1, -421 ) -422 ) -423 ) -424 if angle > 90: -425 return 180 - angle -426 return angle +395 >>> import numpy as np +396 >>> def f64(x): return np.asarray(x, dtype=np.float64) +397 >>> int(smallest_angle(f64([1e0, 0e0, 0e0]), f64([1e0, 0e0, 0e0]))) +398 0 +399 >>> int(smallest_angle(f64([1e0, 0e0, 0e0]), f64([0e0, 1e0, 0e0]))) +400 90 +401 >>> int(smallest_angle(f64([1e0, 0e0, 0e0]), f64([0e0, -1e0, 0e0]))) +402 90 +403 >>> int(smallest_angle(f64([1e0, 0e0, 0e0]), f64([np.sqrt(2), np.sqrt(2), 0e0]))) +404 45 +405 >>> int(smallest_angle(f64([1e0, 0e0, 0e0]), f64([-np.sqrt(2), np.sqrt(2), 0e0]))) +406 45 +407 +408 """ +409 if plane is not None: +410 _vector = vector - plane * np.dot(vector, plane) +411 else: +412 _vector = vector +413 angle = np.rad2deg( +414 np.arccos( +415 np.clip( +416 np.asarray( # https://github.com/numba/numba/issues/3469 +417 np.dot(_vector, axis) +418 / (np.linalg.norm(_vector) * np.linalg.norm(axis)) +419 ), +420 -1, +421 1, +422 ) +423 ) +424 ) +425 if angle > 90: +426 return 180 - angle +427 return angle @@ -1141,38 +1142,39 @@

393 394 Examples: 395 -396 >>> from numpy import asarray as Ŋ -397 >>> smallest_angle(Ŋ([1e0, 0e0, 0e0]), Ŋ([1e0, 0e0, 0e0])) -398 0.0 -399 >>> smallest_angle(Ŋ([1e0, 0e0, 0e0]), Ŋ([0e0, 1e0, 0e0])) -400 90.0 -401 >>> smallest_angle(Ŋ([1e0, 0e0, 0e0]), Ŋ([0e0, -1e0, 0e0])) -402 90.0 -403 >>> smallest_angle(Ŋ([1e0, 0e0, 0e0]), Ŋ([np.sqrt(2), np.sqrt(2), 0e0])) -404 45.0 -405 >>> smallest_angle(Ŋ([1e0, 0e0, 0e0]), Ŋ([-np.sqrt(2), np.sqrt(2), 0e0])) -406 45.0 -407 -408 """ -409 if plane is not None: -410 _vector = vector - plane * np.dot(vector, plane) -411 else: -412 _vector = vector -413 angle = np.rad2deg( -414 np.arccos( -415 np.clip( -416 np.asarray( # https://github.com/numba/numba/issues/3469 -417 np.dot(_vector, axis) -418 / (np.linalg.norm(_vector) * np.linalg.norm(axis)) -419 ), -420 -1, -421 1, -422 ) -423 ) -424 ) -425 if angle > 90: -426 return 180 - angle -427 return angle +396 >>> import numpy as np +397 >>> def f64(x): return np.asarray(x, dtype=np.float64) +398 >>> int(smallest_angle(f64([1e0, 0e0, 0e0]), f64([1e0, 0e0, 0e0]))) +399 0 +400 >>> int(smallest_angle(f64([1e0, 0e0, 0e0]), f64([0e0, 1e0, 0e0]))) +401 90 +402 >>> int(smallest_angle(f64([1e0, 0e0, 0e0]), f64([0e0, -1e0, 0e0]))) +403 90 +404 >>> int(smallest_angle(f64([1e0, 0e0, 0e0]), f64([np.sqrt(2), np.sqrt(2), 0e0]))) +405 45 +406 >>> int(smallest_angle(f64([1e0, 0e0, 0e0]), f64([-np.sqrt(2), np.sqrt(2), 0e0]))) +407 45 +408 +409 """ +410 if plane is not None: +411 _vector = vector - plane * np.dot(vector, plane) +412 else: +413 _vector = vector +414 angle = np.rad2deg( +415 np.arccos( +416 np.clip( +417 np.asarray( # https://github.com/numba/numba/issues/3469 +418 np.dot(_vector, axis) +419 / (np.linalg.norm(_vector) * np.linalg.norm(axis)) +420 ), +421 -1, +422 1, +423 ) +424 ) +425 ) +426 if angle > 90: +427 return 180 - angle +428 return angle @@ -1185,17 +1187,18 @@

Examples:

-
>>> from numpy import asarray as Ŋ
->>> smallest_angle(Ŋ([1e0, 0e0, 0e0]), Ŋ([1e0, 0e0, 0e0]))
-0.0
->>> smallest_angle(Ŋ([1e0, 0e0, 0e0]), Ŋ([0e0, 1e0, 0e0]))
-90.0
->>> smallest_angle(Ŋ([1e0, 0e0, 0e0]), Ŋ([0e0, -1e0, 0e0]))
-90.0
->>> smallest_angle(Ŋ([1e0, 0e0, 0e0]), Ŋ([np.sqrt(2), np.sqrt(2), 0e0]))
-45.0
->>> smallest_angle(Ŋ([1e0, 0e0, 0e0]), Ŋ([-np.sqrt(2), np.sqrt(2), 0e0]))
-45.0
+
>>> import numpy as np
+>>> def f64(x): return np.asarray(x, dtype=np.float64)
+>>> int(smallest_angle(f64([1e0, 0e0, 0e0]), f64([1e0, 0e0, 0e0])))
+0
+>>> int(smallest_angle(f64([1e0, 0e0, 0e0]), f64([0e0, 1e0, 0e0])))
+90
+>>> int(smallest_angle(f64([1e0, 0e0, 0e0]), f64([0e0, -1e0, 0e0])))
+90
+>>> int(smallest_angle(f64([1e0, 0e0, 0e0]), f64([np.sqrt(2), np.sqrt(2), 0e0])))
+45
+>>> int(smallest_angle(f64([1e0, 0e0, 0e0]), f64([-np.sqrt(2), np.sqrt(2), 0e0])))
+45
diff --git a/pydrex/minerals.html b/pydrex/minerals.html index bc6e5841..4b1a4453 100644 --- a/pydrex/minerals.html +++ b/pydrex/minerals.html @@ -554,264 +554,267 @@

400 ... get_velocity_gradient, 401 ... (t_start, t_end, get_position), 402 ... ) -403 >>> np.all(deformation_gradient == np.eye(3) + get_velocity_gradient(t_end, np.nan)) -404 True -405 -406 """ -407 -408 # ===== Set up callables for the ODE solver and internal processing ===== -409 -410 def eval_rhs(t, y): -411 """Evaluate right hand side of the D-Rex PDE.""" -412 # assert not np.any(np.isnan(y)), y[np.isnan(y)].shape -413 position = get_position(t) -414 velocity_gradient = get_velocity_gradient(t, position) -415 # _log.debug( -416 # "calculating CPO at %s (t=%e) with velocity gradient %s", -417 # position, -418 # t, -419 # velocity_gradient.ravel(), -420 # ) -421 -422 if self.phase == _core.MineralPhase.olivine: -423 volume_fraction = config["olivine_fraction"] -424 elif self.phase == _core.MineralPhase.enstatite: -425 volume_fraction = config["enstatite_fraction"] -426 else: -427 raise ValueError( -428 f"phase must be a valid `MineralPhase`, not {self.phase}" -429 ) -430 -431 strain_rate = (velocity_gradient + velocity_gradient.transpose()) / 2 -432 strain_rate_max = np.abs(la.eigvalsh(strain_rate)).max() -433 deformation_gradient, orientations, fractions = _utils.extract_vars( -434 y, self.n_grains -435 ) -436 # Uses nondimensional values of strain rate and velocity gradient. -437 orientations_diff, fractions_diff = _core.derivatives( -438 phase=self.phase, -439 fabric=self.fabric, -440 n_grains=self.n_grains, -441 orientations=orientations, -442 fractions=fractions, -443 strain_rate=strain_rate / strain_rate_max, -444 velocity_gradient=velocity_gradient / strain_rate_max, -445 stress_exponent=config["stress_exponent"], -446 deformation_exponent=config["deformation_exponent"], -447 nucleation_efficiency=config["nucleation_efficiency"], -448 gbm_mobility=config["gbm_mobility"], -449 volume_fraction=volume_fraction, -450 ) -451 return np.hstack( -452 ( -453 (velocity_gradient @ deformation_gradient).flatten(), -454 orientations_diff.flatten() * strain_rate_max, -455 fractions_diff * strain_rate_max, -456 ) -457 ) -458 -459 def perform_step(solver): -460 """Perform SciPy solver step and appropriate processing.""" -461 message = solver.step() -462 if message is not None and solver.status == "failed": -463 raise _err.IterationError(message) -464 # _log.debug( -465 # "%s step_size=%e", solver.__class__.__qualname__, solver.step_size -466 # ) -467 -468 deformation_gradient, orientations, fractions = _utils.extract_vars( -469 solver.y, self.n_grains -470 ) -471 orientations, fractions = _utils.apply_gbs( -472 orientations, -473 fractions, -474 config["gbs_threshold"], -475 self.orientations[-1], -476 self.n_grains, -477 ) -478 solver.y[9:] = np.hstack((orientations.flatten(), fractions)) -479 -480 # ===== Initialise and run the solver using the above callables ===== -481 -482 time_start, time_end, get_position = pathline -483 if not callable(get_velocity_gradient): -484 raise ValueError( -485 "unable to evaluate velocity gradient callable." -486 + " You must provide a callable with signature f(t, x)" -487 + " that returns a 3x3 matrix." -488 ) -489 if not callable(get_position): -490 raise ValueError( -491 "unable to evaluate position callable." -492 + " You must provide a callable with signature f(t)" -493 + " that returns a 3-component array." -494 ) -495 _log.debug( -496 "calculating CPO from %s (t=%s) to %s (t=%s)", -497 get_position(time_start), -498 time_start, -499 get_position(time_end), -500 time_end, -501 ) -502 _log.debug(" with deformation gradient %s", deformation_gradient.ravel()) -503 _log.debug( -504 " with velocity gradient interpolated between %s and %s", -505 get_velocity_gradient(time_start, get_position(time_start)).ravel(), -506 get_velocity_gradient(time_end, get_position(time_end)).ravel() -507 ) -508 _log.debug( -509 " intermediate velocity gradient = %s", -510 get_velocity_gradient( -511 (time_start + time_end) / 2, get_position((time_start + time_end) / 2) -512 ).ravel(), -513 ) -514 -515 y_start = np.hstack( -516 ( -517 deformation_gradient.flatten(), -518 self.orientations[-1].flatten(), -519 self.fractions[-1], -520 ) -521 ) -522 solver = LSODA( -523 eval_rhs, -524 time_start, -525 y_start, -526 time_end, -527 atol=kwargs.pop("atol", np.abs(y_start * 1e-6) + 1e-12), -528 rtol=kwargs.pop("rtol", 1e-6), -529 first_step=kwargs.pop("first_step", np.abs(time_end - time_start) * 1e-1), -530 # max_step=kwargs.pop("max_step", np.abs(time_end - time_start)), -531 lband=self.lband, -532 uband=self.uband, -533 **kwargs, -534 ) -535 perform_step(solver) -536 while solver.status == "running": -537 perform_step(solver) -538 -539 # Extract final values for this simulation step, append to storage. -540 deformation_gradient, orientations, fractions = _utils.extract_vars( -541 solver.y.squeeze(), self.n_grains -542 ) -543 self.orientations.append(orientations) -544 self.fractions.append(fractions) -545 return deformation_gradient -546 -547 def save(self, filename, postfix=None): -548 """Save CPO data for all stored timesteps to a `numpy` NPZ file. +403 >>> from numpy import testing as nt +404 >>> nt.assert_allclose(deformation_gradient, +405 ... np.eye(3) + get_velocity_gradient(t_end, np.nan), +406 ... atol=1e-15, rtol=0 +407 ... ) +408 +409 """ +410 +411 # ===== Set up callables for the ODE solver and internal processing ===== +412 +413 def eval_rhs(t, y): +414 """Evaluate right hand side of the D-Rex PDE.""" +415 # assert not np.any(np.isnan(y)), y[np.isnan(y)].shape +416 position = get_position(t) +417 velocity_gradient = get_velocity_gradient(t, position) +418 # _log.debug( +419 # "calculating CPO at %s (t=%e) with velocity gradient %s", +420 # position, +421 # t, +422 # velocity_gradient.ravel(), +423 # ) +424 +425 if self.phase == _core.MineralPhase.olivine: +426 volume_fraction = config["olivine_fraction"] +427 elif self.phase == _core.MineralPhase.enstatite: +428 volume_fraction = config["enstatite_fraction"] +429 else: +430 raise ValueError( +431 f"phase must be a valid `MineralPhase`, not {self.phase}" +432 ) +433 +434 strain_rate = (velocity_gradient + velocity_gradient.transpose()) / 2 +435 strain_rate_max = np.abs(la.eigvalsh(strain_rate)).max() +436 deformation_gradient, orientations, fractions = _utils.extract_vars( +437 y, self.n_grains +438 ) +439 # Uses nondimensional values of strain rate and velocity gradient. +440 orientations_diff, fractions_diff = _core.derivatives( +441 phase=self.phase, +442 fabric=self.fabric, +443 n_grains=self.n_grains, +444 orientations=orientations, +445 fractions=fractions, +446 strain_rate=strain_rate / strain_rate_max, +447 velocity_gradient=velocity_gradient / strain_rate_max, +448 stress_exponent=config["stress_exponent"], +449 deformation_exponent=config["deformation_exponent"], +450 nucleation_efficiency=config["nucleation_efficiency"], +451 gbm_mobility=config["gbm_mobility"], +452 volume_fraction=volume_fraction, +453 ) +454 return np.hstack( +455 ( +456 (velocity_gradient @ deformation_gradient).flatten(), +457 orientations_diff.flatten() * strain_rate_max, +458 fractions_diff * strain_rate_max, +459 ) +460 ) +461 +462 def perform_step(solver): +463 """Perform SciPy solver step and appropriate processing.""" +464 message = solver.step() +465 if message is not None and solver.status == "failed": +466 raise _err.IterationError(message) +467 # _log.debug( +468 # "%s step_size=%e", solver.__class__.__qualname__, solver.step_size +469 # ) +470 +471 deformation_gradient, orientations, fractions = _utils.extract_vars( +472 solver.y, self.n_grains +473 ) +474 orientations, fractions = _utils.apply_gbs( +475 orientations, +476 fractions, +477 config["gbs_threshold"], +478 self.orientations[-1], +479 self.n_grains, +480 ) +481 solver.y[9:] = np.hstack((orientations.flatten(), fractions)) +482 +483 # ===== Initialise and run the solver using the above callables ===== +484 +485 time_start, time_end, get_position = pathline +486 if not callable(get_velocity_gradient): +487 raise ValueError( +488 "unable to evaluate velocity gradient callable." +489 + " You must provide a callable with signature f(t, x)" +490 + " that returns a 3x3 matrix." +491 ) +492 if not callable(get_position): +493 raise ValueError( +494 "unable to evaluate position callable." +495 + " You must provide a callable with signature f(t)" +496 + " that returns a 3-component array." +497 ) +498 _log.debug( +499 "calculating CPO from %s (t=%s) to %s (t=%s)", +500 get_position(time_start), +501 time_start, +502 get_position(time_end), +503 time_end, +504 ) +505 _log.debug(" with deformation gradient %s", deformation_gradient.ravel()) +506 _log.debug( +507 " with velocity gradient interpolated between %s and %s", +508 get_velocity_gradient(time_start, get_position(time_start)).ravel(), +509 get_velocity_gradient(time_end, get_position(time_end)).ravel() +510 ) +511 _log.debug( +512 " intermediate velocity gradient = %s", +513 get_velocity_gradient( +514 (time_start + time_end) / 2, get_position((time_start + time_end) / 2) +515 ).ravel(), +516 ) +517 +518 y_start = np.hstack( +519 ( +520 deformation_gradient.flatten(), +521 self.orientations[-1].flatten(), +522 self.fractions[-1], +523 ) +524 ) +525 solver = LSODA( +526 eval_rhs, +527 time_start, +528 y_start, +529 time_end, +530 atol=kwargs.pop("atol", np.abs(y_start * 1e-6) + 1e-12), +531 rtol=kwargs.pop("rtol", 1e-6), +532 first_step=kwargs.pop("first_step", np.abs(time_end - time_start) * 1e-1), +533 # max_step=kwargs.pop("max_step", np.abs(time_end - time_start)), +534 lband=self.lband, +535 uband=self.uband, +536 **kwargs, +537 ) +538 perform_step(solver) +539 while solver.status == "running": +540 perform_step(solver) +541 +542 # Extract final values for this simulation step, append to storage. +543 deformation_gradient, orientations, fractions = _utils.extract_vars( +544 solver.y.squeeze(), self.n_grains +545 ) +546 self.orientations.append(orientations) +547 self.fractions.append(fractions) +548 return deformation_gradient 549 -550 If `postfix` is not `None`, the data is appended to the NPZ file -551 in fields ending with "`_postfix`". +550 def save(self, filename, postfix=None): +551 """Save CPO data for all stored timesteps to a `numpy` NPZ file. 552 -553 Raises a `ValueError` if the data shapes are not compatible. -554 -555 See also: `numpy.savez`, `Mineral.load`, `Mineral.from_file`. -556 -557 """ -558 if len(self.fractions) != len(self.orientations): -559 raise ValueError( -560 "Length of stored results must match." -561 + " You've supplied currupted data with:\n" -562 + f"- {len(self.fractions)} grain size results, and\n" -563 + f"- {len(self.orientations)} orientation results." -564 ) -565 if self.fractions[0].shape[0] == self.orientations[0].shape[0] == self.n_grains: -566 data = { -567 "meta": np.array( -568 [self.phase, self.fabric, self.regime], dtype=np.uint8 -569 ), -570 "fractions": np.stack(self.fractions), -571 "orientations": np.stack(self.orientations), -572 } -573 # Create parent directories, resolve relative paths. -574 _io.resolve_path(filename) -575 # Append to file, requires postfix (unique name). -576 if postfix is not None: -577 _log.info("saving Mineral to file %s (postfix: %s)", filename, postfix) -578 archive = ZipFile(filename, mode="a", allowZip64=True) -579 for key in data.keys(): -580 with archive.open( -581 f"{key}_{postfix}", "w", force_zip64=True -582 ) as file: -583 buffer = io.BytesIO() -584 np.save(buffer, data[key]) -585 file.write(buffer.getvalue()) -586 buffer.close() -587 else: -588 _log.info("saving Mineral to file %s", filename) -589 np.savez(filename, **data) -590 else: -591 raise ValueError( -592 "Size of CPO data arrays must match number of grains." -593 + " You've supplied corrupted data with:\n" -594 + f"- `n_grains = {self.n_grains}`,\n" -595 + f"- `fractions[0].shape = {self.fractions[0].shape}`, and\n" -596 + f"- `orientations[0].shape = {self.orientations[0].shape}`." -597 ) -598 -599 def load(self, filename, postfix=None): -600 """Load CPO data from a `numpy` NPZ file. +553 If `postfix` is not `None`, the data is appended to the NPZ file +554 in fields ending with "`_postfix`". +555 +556 Raises a `ValueError` if the data shapes are not compatible. +557 +558 See also: `numpy.savez`, `Mineral.load`, `Mineral.from_file`. +559 +560 """ +561 if len(self.fractions) != len(self.orientations): +562 raise ValueError( +563 "Length of stored results must match." +564 + " You've supplied currupted data with:\n" +565 + f"- {len(self.fractions)} grain size results, and\n" +566 + f"- {len(self.orientations)} orientation results." +567 ) +568 if self.fractions[0].shape[0] == self.orientations[0].shape[0] == self.n_grains: +569 data = { +570 "meta": np.array( +571 [self.phase, self.fabric, self.regime], dtype=np.uint8 +572 ), +573 "fractions": np.stack(self.fractions), +574 "orientations": np.stack(self.orientations), +575 } +576 # Create parent directories, resolve relative paths. +577 _io.resolve_path(filename) +578 # Append to file, requires postfix (unique name). +579 if postfix is not None: +580 _log.info("saving Mineral to file %s (postfix: %s)", filename, postfix) +581 archive = ZipFile(filename, mode="a", allowZip64=True) +582 for key in data.keys(): +583 with archive.open( +584 f"{key}_{postfix}", "w", force_zip64=True +585 ) as file: +586 buffer = io.BytesIO() +587 np.save(buffer, data[key]) +588 file.write(buffer.getvalue()) +589 buffer.close() +590 else: +591 _log.info("saving Mineral to file %s", filename) +592 np.savez(filename, **data) +593 else: +594 raise ValueError( +595 "Size of CPO data arrays must match number of grains." +596 + " You've supplied corrupted data with:\n" +597 + f"- `n_grains = {self.n_grains}`,\n" +598 + f"- `fractions[0].shape = {self.fractions[0].shape}`, and\n" +599 + f"- `orientations[0].shape = {self.orientations[0].shape}`." +600 ) 601 -602 If `postfix` is not `None`, data is read from fields ending with "`_postfix`". -603 -604 See also: `Mineral.save`, `Mineral.from_file`. -605 -606 """ -607 if not filename.endswith(".npz"): -608 raise ValueError( -609 f"Must only load from numpy NPZ format. Cannot load from {filename}." -610 ) -611 data = np.load(filename) -612 if postfix is not None: -613 phase, fabric, regime = data[f"meta_{postfix}"] -614 self.fractions = list(data[f"fractions_{postfix}"]) -615 self.orientations = list(data[f"orientations_{postfix}"]) -616 else: -617 phase, fabric, regime = data["meta"] -618 self.fractions = list(data["fractions"]) -619 self.orientations = list(data["orientations"]) -620 -621 self.phase = phase -622 self.fabric = fabric -623 self.regime = regime -624 self.orientations_init = self.orientations[0] -625 self.fractions_init = self.fractions[0] -626 -627 @classmethod -628 def from_file(cls, filename, postfix=None): -629 """Construct a `Mineral` instance using data from a `numpy` NPZ file. -630 -631 If `postfix` is not `None`, data is read from fields ending with “`_postfix`”. -632 -633 See also: `Mineral.save`, `Mineral.load`. -634 -635 """ -636 if not filename.endswith(".npz"): -637 raise ValueError( -638 f"Must only load from numpy NPZ format. Cannot load from {filename}." -639 ) -640 data = np.load(filename) -641 if postfix is not None: -642 phase, fabric, regime = data[f"meta_{postfix}"] -643 fractions = list(data[f"fractions_{postfix}"]) -644 orientations = list(data[f"orientations_{postfix}"]) -645 else: -646 phase, fabric, regime = data["meta"] -647 fractions = list(data["fractions"]) -648 orientations = list(data["orientations"]) -649 -650 mineral = cls( -651 phase, -652 fabric, -653 regime, -654 n_grains=len(fractions[0]), -655 fractions_init=fractions[0], -656 orientations_init=orientations[0], -657 ) -658 mineral.fractions = fractions -659 mineral.orientations = orientations -660 return mineral +602 def load(self, filename, postfix=None): +603 """Load CPO data from a `numpy` NPZ file. +604 +605 If `postfix` is not `None`, data is read from fields ending with "`_postfix`". +606 +607 See also: `Mineral.save`, `Mineral.from_file`. +608 +609 """ +610 if not filename.endswith(".npz"): +611 raise ValueError( +612 f"Must only load from numpy NPZ format. Cannot load from {filename}." +613 ) +614 data = np.load(filename) +615 if postfix is not None: +616 phase, fabric, regime = data[f"meta_{postfix}"] +617 self.fractions = list(data[f"fractions_{postfix}"]) +618 self.orientations = list(data[f"orientations_{postfix}"]) +619 else: +620 phase, fabric, regime = data["meta"] +621 self.fractions = list(data["fractions"]) +622 self.orientations = list(data["orientations"]) +623 +624 self.phase = phase +625 self.fabric = fabric +626 self.regime = regime +627 self.orientations_init = self.orientations[0] +628 self.fractions_init = self.fractions[0] +629 +630 @classmethod +631 def from_file(cls, filename, postfix=None): +632 """Construct a `Mineral` instance using data from a `numpy` NPZ file. +633 +634 If `postfix` is not `None`, data is read from fields ending with “`_postfix`”. +635 +636 See also: `Mineral.save`, `Mineral.load`. +637 +638 """ +639 if not filename.endswith(".npz"): +640 raise ValueError( +641 f"Must only load from numpy NPZ format. Cannot load from {filename}." +642 ) +643 data = np.load(filename) +644 if postfix is not None: +645 phase, fabric, regime = data[f"meta_{postfix}"] +646 fractions = list(data[f"fractions_{postfix}"]) +647 orientations = list(data[f"orientations_{postfix}"]) +648 else: +649 phase, fabric, regime = data["meta"] +650 fractions = list(data["fractions"]) +651 orientations = list(data["orientations"]) +652 +653 mineral = cls( +654 phase, +655 fabric, +656 regime, +657 n_grains=len(fractions[0]), +658 fractions_init=fractions[0], +659 orientations_init=orientations[0], +660 ) +661 mineral.fractions = fractions +662 mineral.orientations = orientations +663 return mineral @@ -1251,264 +1254,267 @@

401 ... get_velocity_gradient, 402 ... (t_start, t_end, get_position), 403 ... ) -404 >>> np.all(deformation_gradient == np.eye(3) + get_velocity_gradient(t_end, np.nan)) -405 True -406 -407 """ -408 -409 # ===== Set up callables for the ODE solver and internal processing ===== -410 -411 def eval_rhs(t, y): -412 """Evaluate right hand side of the D-Rex PDE.""" -413 # assert not np.any(np.isnan(y)), y[np.isnan(y)].shape -414 position = get_position(t) -415 velocity_gradient = get_velocity_gradient(t, position) -416 # _log.debug( -417 # "calculating CPO at %s (t=%e) with velocity gradient %s", -418 # position, -419 # t, -420 # velocity_gradient.ravel(), -421 # ) -422 -423 if self.phase == _core.MineralPhase.olivine: -424 volume_fraction = config["olivine_fraction"] -425 elif self.phase == _core.MineralPhase.enstatite: -426 volume_fraction = config["enstatite_fraction"] -427 else: -428 raise ValueError( -429 f"phase must be a valid `MineralPhase`, not {self.phase}" -430 ) -431 -432 strain_rate = (velocity_gradient + velocity_gradient.transpose()) / 2 -433 strain_rate_max = np.abs(la.eigvalsh(strain_rate)).max() -434 deformation_gradient, orientations, fractions = _utils.extract_vars( -435 y, self.n_grains -436 ) -437 # Uses nondimensional values of strain rate and velocity gradient. -438 orientations_diff, fractions_diff = _core.derivatives( -439 phase=self.phase, -440 fabric=self.fabric, -441 n_grains=self.n_grains, -442 orientations=orientations, -443 fractions=fractions, -444 strain_rate=strain_rate / strain_rate_max, -445 velocity_gradient=velocity_gradient / strain_rate_max, -446 stress_exponent=config["stress_exponent"], -447 deformation_exponent=config["deformation_exponent"], -448 nucleation_efficiency=config["nucleation_efficiency"], -449 gbm_mobility=config["gbm_mobility"], -450 volume_fraction=volume_fraction, -451 ) -452 return np.hstack( -453 ( -454 (velocity_gradient @ deformation_gradient).flatten(), -455 orientations_diff.flatten() * strain_rate_max, -456 fractions_diff * strain_rate_max, -457 ) -458 ) -459 -460 def perform_step(solver): -461 """Perform SciPy solver step and appropriate processing.""" -462 message = solver.step() -463 if message is not None and solver.status == "failed": -464 raise _err.IterationError(message) -465 # _log.debug( -466 # "%s step_size=%e", solver.__class__.__qualname__, solver.step_size -467 # ) -468 -469 deformation_gradient, orientations, fractions = _utils.extract_vars( -470 solver.y, self.n_grains -471 ) -472 orientations, fractions = _utils.apply_gbs( -473 orientations, -474 fractions, -475 config["gbs_threshold"], -476 self.orientations[-1], -477 self.n_grains, -478 ) -479 solver.y[9:] = np.hstack((orientations.flatten(), fractions)) -480 -481 # ===== Initialise and run the solver using the above callables ===== -482 -483 time_start, time_end, get_position = pathline -484 if not callable(get_velocity_gradient): -485 raise ValueError( -486 "unable to evaluate velocity gradient callable." -487 + " You must provide a callable with signature f(t, x)" -488 + " that returns a 3x3 matrix." -489 ) -490 if not callable(get_position): -491 raise ValueError( -492 "unable to evaluate position callable." -493 + " You must provide a callable with signature f(t)" -494 + " that returns a 3-component array." -495 ) -496 _log.debug( -497 "calculating CPO from %s (t=%s) to %s (t=%s)", -498 get_position(time_start), -499 time_start, -500 get_position(time_end), -501 time_end, -502 ) -503 _log.debug(" with deformation gradient %s", deformation_gradient.ravel()) -504 _log.debug( -505 " with velocity gradient interpolated between %s and %s", -506 get_velocity_gradient(time_start, get_position(time_start)).ravel(), -507 get_velocity_gradient(time_end, get_position(time_end)).ravel() -508 ) -509 _log.debug( -510 " intermediate velocity gradient = %s", -511 get_velocity_gradient( -512 (time_start + time_end) / 2, get_position((time_start + time_end) / 2) -513 ).ravel(), -514 ) -515 -516 y_start = np.hstack( -517 ( -518 deformation_gradient.flatten(), -519 self.orientations[-1].flatten(), -520 self.fractions[-1], -521 ) -522 ) -523 solver = LSODA( -524 eval_rhs, -525 time_start, -526 y_start, -527 time_end, -528 atol=kwargs.pop("atol", np.abs(y_start * 1e-6) + 1e-12), -529 rtol=kwargs.pop("rtol", 1e-6), -530 first_step=kwargs.pop("first_step", np.abs(time_end - time_start) * 1e-1), -531 # max_step=kwargs.pop("max_step", np.abs(time_end - time_start)), -532 lband=self.lband, -533 uband=self.uband, -534 **kwargs, -535 ) -536 perform_step(solver) -537 while solver.status == "running": -538 perform_step(solver) -539 -540 # Extract final values for this simulation step, append to storage. -541 deformation_gradient, orientations, fractions = _utils.extract_vars( -542 solver.y.squeeze(), self.n_grains -543 ) -544 self.orientations.append(orientations) -545 self.fractions.append(fractions) -546 return deformation_gradient -547 -548 def save(self, filename, postfix=None): -549 """Save CPO data for all stored timesteps to a `numpy` NPZ file. +404 >>> from numpy import testing as nt +405 >>> nt.assert_allclose(deformation_gradient, +406 ... np.eye(3) + get_velocity_gradient(t_end, np.nan), +407 ... atol=1e-15, rtol=0 +408 ... ) +409 +410 """ +411 +412 # ===== Set up callables for the ODE solver and internal processing ===== +413 +414 def eval_rhs(t, y): +415 """Evaluate right hand side of the D-Rex PDE.""" +416 # assert not np.any(np.isnan(y)), y[np.isnan(y)].shape +417 position = get_position(t) +418 velocity_gradient = get_velocity_gradient(t, position) +419 # _log.debug( +420 # "calculating CPO at %s (t=%e) with velocity gradient %s", +421 # position, +422 # t, +423 # velocity_gradient.ravel(), +424 # ) +425 +426 if self.phase == _core.MineralPhase.olivine: +427 volume_fraction = config["olivine_fraction"] +428 elif self.phase == _core.MineralPhase.enstatite: +429 volume_fraction = config["enstatite_fraction"] +430 else: +431 raise ValueError( +432 f"phase must be a valid `MineralPhase`, not {self.phase}" +433 ) +434 +435 strain_rate = (velocity_gradient + velocity_gradient.transpose()) / 2 +436 strain_rate_max = np.abs(la.eigvalsh(strain_rate)).max() +437 deformation_gradient, orientations, fractions = _utils.extract_vars( +438 y, self.n_grains +439 ) +440 # Uses nondimensional values of strain rate and velocity gradient. +441 orientations_diff, fractions_diff = _core.derivatives( +442 phase=self.phase, +443 fabric=self.fabric, +444 n_grains=self.n_grains, +445 orientations=orientations, +446 fractions=fractions, +447 strain_rate=strain_rate / strain_rate_max, +448 velocity_gradient=velocity_gradient / strain_rate_max, +449 stress_exponent=config["stress_exponent"], +450 deformation_exponent=config["deformation_exponent"], +451 nucleation_efficiency=config["nucleation_efficiency"], +452 gbm_mobility=config["gbm_mobility"], +453 volume_fraction=volume_fraction, +454 ) +455 return np.hstack( +456 ( +457 (velocity_gradient @ deformation_gradient).flatten(), +458 orientations_diff.flatten() * strain_rate_max, +459 fractions_diff * strain_rate_max, +460 ) +461 ) +462 +463 def perform_step(solver): +464 """Perform SciPy solver step and appropriate processing.""" +465 message = solver.step() +466 if message is not None and solver.status == "failed": +467 raise _err.IterationError(message) +468 # _log.debug( +469 # "%s step_size=%e", solver.__class__.__qualname__, solver.step_size +470 # ) +471 +472 deformation_gradient, orientations, fractions = _utils.extract_vars( +473 solver.y, self.n_grains +474 ) +475 orientations, fractions = _utils.apply_gbs( +476 orientations, +477 fractions, +478 config["gbs_threshold"], +479 self.orientations[-1], +480 self.n_grains, +481 ) +482 solver.y[9:] = np.hstack((orientations.flatten(), fractions)) +483 +484 # ===== Initialise and run the solver using the above callables ===== +485 +486 time_start, time_end, get_position = pathline +487 if not callable(get_velocity_gradient): +488 raise ValueError( +489 "unable to evaluate velocity gradient callable." +490 + " You must provide a callable with signature f(t, x)" +491 + " that returns a 3x3 matrix." +492 ) +493 if not callable(get_position): +494 raise ValueError( +495 "unable to evaluate position callable." +496 + " You must provide a callable with signature f(t)" +497 + " that returns a 3-component array." +498 ) +499 _log.debug( +500 "calculating CPO from %s (t=%s) to %s (t=%s)", +501 get_position(time_start), +502 time_start, +503 get_position(time_end), +504 time_end, +505 ) +506 _log.debug(" with deformation gradient %s", deformation_gradient.ravel()) +507 _log.debug( +508 " with velocity gradient interpolated between %s and %s", +509 get_velocity_gradient(time_start, get_position(time_start)).ravel(), +510 get_velocity_gradient(time_end, get_position(time_end)).ravel() +511 ) +512 _log.debug( +513 " intermediate velocity gradient = %s", +514 get_velocity_gradient( +515 (time_start + time_end) / 2, get_position((time_start + time_end) / 2) +516 ).ravel(), +517 ) +518 +519 y_start = np.hstack( +520 ( +521 deformation_gradient.flatten(), +522 self.orientations[-1].flatten(), +523 self.fractions[-1], +524 ) +525 ) +526 solver = LSODA( +527 eval_rhs, +528 time_start, +529 y_start, +530 time_end, +531 atol=kwargs.pop("atol", np.abs(y_start * 1e-6) + 1e-12), +532 rtol=kwargs.pop("rtol", 1e-6), +533 first_step=kwargs.pop("first_step", np.abs(time_end - time_start) * 1e-1), +534 # max_step=kwargs.pop("max_step", np.abs(time_end - time_start)), +535 lband=self.lband, +536 uband=self.uband, +537 **kwargs, +538 ) +539 perform_step(solver) +540 while solver.status == "running": +541 perform_step(solver) +542 +543 # Extract final values for this simulation step, append to storage. +544 deformation_gradient, orientations, fractions = _utils.extract_vars( +545 solver.y.squeeze(), self.n_grains +546 ) +547 self.orientations.append(orientations) +548 self.fractions.append(fractions) +549 return deformation_gradient 550 -551 If `postfix` is not `None`, the data is appended to the NPZ file -552 in fields ending with "`_postfix`". +551 def save(self, filename, postfix=None): +552 """Save CPO data for all stored timesteps to a `numpy` NPZ file. 553 -554 Raises a `ValueError` if the data shapes are not compatible. -555 -556 See also: `numpy.savez`, `Mineral.load`, `Mineral.from_file`. -557 -558 """ -559 if len(self.fractions) != len(self.orientations): -560 raise ValueError( -561 "Length of stored results must match." -562 + " You've supplied currupted data with:\n" -563 + f"- {len(self.fractions)} grain size results, and\n" -564 + f"- {len(self.orientations)} orientation results." -565 ) -566 if self.fractions[0].shape[0] == self.orientations[0].shape[0] == self.n_grains: -567 data = { -568 "meta": np.array( -569 [self.phase, self.fabric, self.regime], dtype=np.uint8 -570 ), -571 "fractions": np.stack(self.fractions), -572 "orientations": np.stack(self.orientations), -573 } -574 # Create parent directories, resolve relative paths. -575 _io.resolve_path(filename) -576 # Append to file, requires postfix (unique name). -577 if postfix is not None: -578 _log.info("saving Mineral to file %s (postfix: %s)", filename, postfix) -579 archive = ZipFile(filename, mode="a", allowZip64=True) -580 for key in data.keys(): -581 with archive.open( -582 f"{key}_{postfix}", "w", force_zip64=True -583 ) as file: -584 buffer = io.BytesIO() -585 np.save(buffer, data[key]) -586 file.write(buffer.getvalue()) -587 buffer.close() -588 else: -589 _log.info("saving Mineral to file %s", filename) -590 np.savez(filename, **data) -591 else: -592 raise ValueError( -593 "Size of CPO data arrays must match number of grains." -594 + " You've supplied corrupted data with:\n" -595 + f"- `n_grains = {self.n_grains}`,\n" -596 + f"- `fractions[0].shape = {self.fractions[0].shape}`, and\n" -597 + f"- `orientations[0].shape = {self.orientations[0].shape}`." -598 ) -599 -600 def load(self, filename, postfix=None): -601 """Load CPO data from a `numpy` NPZ file. +554 If `postfix` is not `None`, the data is appended to the NPZ file +555 in fields ending with "`_postfix`". +556 +557 Raises a `ValueError` if the data shapes are not compatible. +558 +559 See also: `numpy.savez`, `Mineral.load`, `Mineral.from_file`. +560 +561 """ +562 if len(self.fractions) != len(self.orientations): +563 raise ValueError( +564 "Length of stored results must match." +565 + " You've supplied currupted data with:\n" +566 + f"- {len(self.fractions)} grain size results, and\n" +567 + f"- {len(self.orientations)} orientation results." +568 ) +569 if self.fractions[0].shape[0] == self.orientations[0].shape[0] == self.n_grains: +570 data = { +571 "meta": np.array( +572 [self.phase, self.fabric, self.regime], dtype=np.uint8 +573 ), +574 "fractions": np.stack(self.fractions), +575 "orientations": np.stack(self.orientations), +576 } +577 # Create parent directories, resolve relative paths. +578 _io.resolve_path(filename) +579 # Append to file, requires postfix (unique name). +580 if postfix is not None: +581 _log.info("saving Mineral to file %s (postfix: %s)", filename, postfix) +582 archive = ZipFile(filename, mode="a", allowZip64=True) +583 for key in data.keys(): +584 with archive.open( +585 f"{key}_{postfix}", "w", force_zip64=True +586 ) as file: +587 buffer = io.BytesIO() +588 np.save(buffer, data[key]) +589 file.write(buffer.getvalue()) +590 buffer.close() +591 else: +592 _log.info("saving Mineral to file %s", filename) +593 np.savez(filename, **data) +594 else: +595 raise ValueError( +596 "Size of CPO data arrays must match number of grains." +597 + " You've supplied corrupted data with:\n" +598 + f"- `n_grains = {self.n_grains}`,\n" +599 + f"- `fractions[0].shape = {self.fractions[0].shape}`, and\n" +600 + f"- `orientations[0].shape = {self.orientations[0].shape}`." +601 ) 602 -603 If `postfix` is not `None`, data is read from fields ending with "`_postfix`". -604 -605 See also: `Mineral.save`, `Mineral.from_file`. -606 -607 """ -608 if not filename.endswith(".npz"): -609 raise ValueError( -610 f"Must only load from numpy NPZ format. Cannot load from {filename}." -611 ) -612 data = np.load(filename) -613 if postfix is not None: -614 phase, fabric, regime = data[f"meta_{postfix}"] -615 self.fractions = list(data[f"fractions_{postfix}"]) -616 self.orientations = list(data[f"orientations_{postfix}"]) -617 else: -618 phase, fabric, regime = data["meta"] -619 self.fractions = list(data["fractions"]) -620 self.orientations = list(data["orientations"]) -621 -622 self.phase = phase -623 self.fabric = fabric -624 self.regime = regime -625 self.orientations_init = self.orientations[0] -626 self.fractions_init = self.fractions[0] -627 -628 @classmethod -629 def from_file(cls, filename, postfix=None): -630 """Construct a `Mineral` instance using data from a `numpy` NPZ file. -631 -632 If `postfix` is not `None`, data is read from fields ending with “`_postfix`”. -633 -634 See also: `Mineral.save`, `Mineral.load`. -635 -636 """ -637 if not filename.endswith(".npz"): -638 raise ValueError( -639 f"Must only load from numpy NPZ format. Cannot load from {filename}." -640 ) -641 data = np.load(filename) -642 if postfix is not None: -643 phase, fabric, regime = data[f"meta_{postfix}"] -644 fractions = list(data[f"fractions_{postfix}"]) -645 orientations = list(data[f"orientations_{postfix}"]) -646 else: -647 phase, fabric, regime = data["meta"] -648 fractions = list(data["fractions"]) -649 orientations = list(data["orientations"]) -650 -651 mineral = cls( -652 phase, -653 fabric, -654 regime, -655 n_grains=len(fractions[0]), -656 fractions_init=fractions[0], -657 orientations_init=orientations[0], -658 ) -659 mineral.fractions = fractions -660 mineral.orientations = orientations -661 return mineral +603 def load(self, filename, postfix=None): +604 """Load CPO data from a `numpy` NPZ file. +605 +606 If `postfix` is not `None`, data is read from fields ending with "`_postfix`". +607 +608 See also: `Mineral.save`, `Mineral.from_file`. +609 +610 """ +611 if not filename.endswith(".npz"): +612 raise ValueError( +613 f"Must only load from numpy NPZ format. Cannot load from {filename}." +614 ) +615 data = np.load(filename) +616 if postfix is not None: +617 phase, fabric, regime = data[f"meta_{postfix}"] +618 self.fractions = list(data[f"fractions_{postfix}"]) +619 self.orientations = list(data[f"orientations_{postfix}"]) +620 else: +621 phase, fabric, regime = data["meta"] +622 self.fractions = list(data["fractions"]) +623 self.orientations = list(data["orientations"]) +624 +625 self.phase = phase +626 self.fabric = fabric +627 self.regime = regime +628 self.orientations_init = self.orientations[0] +629 self.fractions_init = self.fractions[0] +630 +631 @classmethod +632 def from_file(cls, filename, postfix=None): +633 """Construct a `Mineral` instance using data from a `numpy` NPZ file. +634 +635 If `postfix` is not `None`, data is read from fields ending with “`_postfix`”. +636 +637 See also: `Mineral.save`, `Mineral.load`. +638 +639 """ +640 if not filename.endswith(".npz"): +641 raise ValueError( +642 f"Must only load from numpy NPZ format. Cannot load from {filename}." +643 ) +644 data = np.load(filename) +645 if postfix is not None: +646 phase, fabric, regime = data[f"meta_{postfix}"] +647 fractions = list(data[f"fractions_{postfix}"]) +648 orientations = list(data[f"orientations_{postfix}"]) +649 else: +650 phase, fabric, regime = data["meta"] +651 fractions = list(data["fractions"]) +652 orientations = list(data["orientations"]) +653 +654 mineral = cls( +655 phase, +656 fabric, +657 regime, +658 n_grains=len(fractions[0]), +659 fractions_init=fractions[0], +660 orientations_init=orientations[0], +661 ) +662 mineral.fractions = fractions +663 mineral.orientations = orientations +664 return mineral @@ -1819,149 +1825,152 @@

401 ... get_velocity_gradient, 402 ... (t_start, t_end, get_position), 403 ... ) -404 >>> np.all(deformation_gradient == np.eye(3) + get_velocity_gradient(t_end, np.nan)) -405 True -406 -407 """ -408 -409 # ===== Set up callables for the ODE solver and internal processing ===== -410 -411 def eval_rhs(t, y): -412 """Evaluate right hand side of the D-Rex PDE.""" -413 # assert not np.any(np.isnan(y)), y[np.isnan(y)].shape -414 position = get_position(t) -415 velocity_gradient = get_velocity_gradient(t, position) -416 # _log.debug( -417 # "calculating CPO at %s (t=%e) with velocity gradient %s", -418 # position, -419 # t, -420 # velocity_gradient.ravel(), -421 # ) -422 -423 if self.phase == _core.MineralPhase.olivine: -424 volume_fraction = config["olivine_fraction"] -425 elif self.phase == _core.MineralPhase.enstatite: -426 volume_fraction = config["enstatite_fraction"] -427 else: -428 raise ValueError( -429 f"phase must be a valid `MineralPhase`, not {self.phase}" -430 ) -431 -432 strain_rate = (velocity_gradient + velocity_gradient.transpose()) / 2 -433 strain_rate_max = np.abs(la.eigvalsh(strain_rate)).max() -434 deformation_gradient, orientations, fractions = _utils.extract_vars( -435 y, self.n_grains -436 ) -437 # Uses nondimensional values of strain rate and velocity gradient. -438 orientations_diff, fractions_diff = _core.derivatives( -439 phase=self.phase, -440 fabric=self.fabric, -441 n_grains=self.n_grains, -442 orientations=orientations, -443 fractions=fractions, -444 strain_rate=strain_rate / strain_rate_max, -445 velocity_gradient=velocity_gradient / strain_rate_max, -446 stress_exponent=config["stress_exponent"], -447 deformation_exponent=config["deformation_exponent"], -448 nucleation_efficiency=config["nucleation_efficiency"], -449 gbm_mobility=config["gbm_mobility"], -450 volume_fraction=volume_fraction, -451 ) -452 return np.hstack( -453 ( -454 (velocity_gradient @ deformation_gradient).flatten(), -455 orientations_diff.flatten() * strain_rate_max, -456 fractions_diff * strain_rate_max, -457 ) -458 ) -459 -460 def perform_step(solver): -461 """Perform SciPy solver step and appropriate processing.""" -462 message = solver.step() -463 if message is not None and solver.status == "failed": -464 raise _err.IterationError(message) -465 # _log.debug( -466 # "%s step_size=%e", solver.__class__.__qualname__, solver.step_size -467 # ) -468 -469 deformation_gradient, orientations, fractions = _utils.extract_vars( -470 solver.y, self.n_grains -471 ) -472 orientations, fractions = _utils.apply_gbs( -473 orientations, -474 fractions, -475 config["gbs_threshold"], -476 self.orientations[-1], -477 self.n_grains, -478 ) -479 solver.y[9:] = np.hstack((orientations.flatten(), fractions)) -480 -481 # ===== Initialise and run the solver using the above callables ===== -482 -483 time_start, time_end, get_position = pathline -484 if not callable(get_velocity_gradient): -485 raise ValueError( -486 "unable to evaluate velocity gradient callable." -487 + " You must provide a callable with signature f(t, x)" -488 + " that returns a 3x3 matrix." -489 ) -490 if not callable(get_position): -491 raise ValueError( -492 "unable to evaluate position callable." -493 + " You must provide a callable with signature f(t)" -494 + " that returns a 3-component array." -495 ) -496 _log.debug( -497 "calculating CPO from %s (t=%s) to %s (t=%s)", -498 get_position(time_start), -499 time_start, -500 get_position(time_end), -501 time_end, -502 ) -503 _log.debug(" with deformation gradient %s", deformation_gradient.ravel()) -504 _log.debug( -505 " with velocity gradient interpolated between %s and %s", -506 get_velocity_gradient(time_start, get_position(time_start)).ravel(), -507 get_velocity_gradient(time_end, get_position(time_end)).ravel() -508 ) -509 _log.debug( -510 " intermediate velocity gradient = %s", -511 get_velocity_gradient( -512 (time_start + time_end) / 2, get_position((time_start + time_end) / 2) -513 ).ravel(), -514 ) -515 -516 y_start = np.hstack( -517 ( -518 deformation_gradient.flatten(), -519 self.orientations[-1].flatten(), -520 self.fractions[-1], -521 ) -522 ) -523 solver = LSODA( -524 eval_rhs, -525 time_start, -526 y_start, -527 time_end, -528 atol=kwargs.pop("atol", np.abs(y_start * 1e-6) + 1e-12), -529 rtol=kwargs.pop("rtol", 1e-6), -530 first_step=kwargs.pop("first_step", np.abs(time_end - time_start) * 1e-1), -531 # max_step=kwargs.pop("max_step", np.abs(time_end - time_start)), -532 lband=self.lband, -533 uband=self.uband, -534 **kwargs, -535 ) -536 perform_step(solver) -537 while solver.status == "running": -538 perform_step(solver) -539 -540 # Extract final values for this simulation step, append to storage. -541 deformation_gradient, orientations, fractions = _utils.extract_vars( -542 solver.y.squeeze(), self.n_grains -543 ) -544 self.orientations.append(orientations) -545 self.fractions.append(fractions) -546 return deformation_gradient +404 >>> from numpy import testing as nt +405 >>> nt.assert_allclose(deformation_gradient, +406 ... np.eye(3) + get_velocity_gradient(t_end, np.nan), +407 ... atol=1e-15, rtol=0 +408 ... ) +409 +410 """ +411 +412 # ===== Set up callables for the ODE solver and internal processing ===== +413 +414 def eval_rhs(t, y): +415 """Evaluate right hand side of the D-Rex PDE.""" +416 # assert not np.any(np.isnan(y)), y[np.isnan(y)].shape +417 position = get_position(t) +418 velocity_gradient = get_velocity_gradient(t, position) +419 # _log.debug( +420 # "calculating CPO at %s (t=%e) with velocity gradient %s", +421 # position, +422 # t, +423 # velocity_gradient.ravel(), +424 # ) +425 +426 if self.phase == _core.MineralPhase.olivine: +427 volume_fraction = config["olivine_fraction"] +428 elif self.phase == _core.MineralPhase.enstatite: +429 volume_fraction = config["enstatite_fraction"] +430 else: +431 raise ValueError( +432 f"phase must be a valid `MineralPhase`, not {self.phase}" +433 ) +434 +435 strain_rate = (velocity_gradient + velocity_gradient.transpose()) / 2 +436 strain_rate_max = np.abs(la.eigvalsh(strain_rate)).max() +437 deformation_gradient, orientations, fractions = _utils.extract_vars( +438 y, self.n_grains +439 ) +440 # Uses nondimensional values of strain rate and velocity gradient. +441 orientations_diff, fractions_diff = _core.derivatives( +442 phase=self.phase, +443 fabric=self.fabric, +444 n_grains=self.n_grains, +445 orientations=orientations, +446 fractions=fractions, +447 strain_rate=strain_rate / strain_rate_max, +448 velocity_gradient=velocity_gradient / strain_rate_max, +449 stress_exponent=config["stress_exponent"], +450 deformation_exponent=config["deformation_exponent"], +451 nucleation_efficiency=config["nucleation_efficiency"], +452 gbm_mobility=config["gbm_mobility"], +453 volume_fraction=volume_fraction, +454 ) +455 return np.hstack( +456 ( +457 (velocity_gradient @ deformation_gradient).flatten(), +458 orientations_diff.flatten() * strain_rate_max, +459 fractions_diff * strain_rate_max, +460 ) +461 ) +462 +463 def perform_step(solver): +464 """Perform SciPy solver step and appropriate processing.""" +465 message = solver.step() +466 if message is not None and solver.status == "failed": +467 raise _err.IterationError(message) +468 # _log.debug( +469 # "%s step_size=%e", solver.__class__.__qualname__, solver.step_size +470 # ) +471 +472 deformation_gradient, orientations, fractions = _utils.extract_vars( +473 solver.y, self.n_grains +474 ) +475 orientations, fractions = _utils.apply_gbs( +476 orientations, +477 fractions, +478 config["gbs_threshold"], +479 self.orientations[-1], +480 self.n_grains, +481 ) +482 solver.y[9:] = np.hstack((orientations.flatten(), fractions)) +483 +484 # ===== Initialise and run the solver using the above callables ===== +485 +486 time_start, time_end, get_position = pathline +487 if not callable(get_velocity_gradient): +488 raise ValueError( +489 "unable to evaluate velocity gradient callable." +490 + " You must provide a callable with signature f(t, x)" +491 + " that returns a 3x3 matrix." +492 ) +493 if not callable(get_position): +494 raise ValueError( +495 "unable to evaluate position callable." +496 + " You must provide a callable with signature f(t)" +497 + " that returns a 3-component array." +498 ) +499 _log.debug( +500 "calculating CPO from %s (t=%s) to %s (t=%s)", +501 get_position(time_start), +502 time_start, +503 get_position(time_end), +504 time_end, +505 ) +506 _log.debug(" with deformation gradient %s", deformation_gradient.ravel()) +507 _log.debug( +508 " with velocity gradient interpolated between %s and %s", +509 get_velocity_gradient(time_start, get_position(time_start)).ravel(), +510 get_velocity_gradient(time_end, get_position(time_end)).ravel() +511 ) +512 _log.debug( +513 " intermediate velocity gradient = %s", +514 get_velocity_gradient( +515 (time_start + time_end) / 2, get_position((time_start + time_end) / 2) +516 ).ravel(), +517 ) +518 +519 y_start = np.hstack( +520 ( +521 deformation_gradient.flatten(), +522 self.orientations[-1].flatten(), +523 self.fractions[-1], +524 ) +525 ) +526 solver = LSODA( +527 eval_rhs, +528 time_start, +529 y_start, +530 time_end, +531 atol=kwargs.pop("atol", np.abs(y_start * 1e-6) + 1e-12), +532 rtol=kwargs.pop("rtol", 1e-6), +533 first_step=kwargs.pop("first_step", np.abs(time_end - time_start) * 1e-1), +534 # max_step=kwargs.pop("max_step", np.abs(time_end - time_start)), +535 lband=self.lband, +536 uband=self.uband, +537 **kwargs, +538 ) +539 perform_step(solver) +540 while solver.status == "running": +541 perform_step(solver) +542 +543 # Extract final values for this simulation step, append to storage. +544 deformation_gradient, orientations, fractions = _utils.extract_vars( +545 solver.y.squeeze(), self.n_grains +546 ) +547 self.orientations.append(orientations) +548 self.fractions.append(fractions) +549 return deformation_gradient @@ -2020,8 +2029,11 @@

... get_velocity_gradient, ... (t_start, t_end, get_position), ... ) ->>> np.all(deformation_gradient == np.eye(3) + get_velocity_gradient(t_end, np.nan)) -True +>>> from numpy import testing as nt +>>> nt.assert_allclose(deformation_gradient, +... np.eye(3) + get_velocity_gradient(t_end, np.nan), +... atol=1e-15, rtol=0 +... ) @@ -2039,57 +2051,57 @@

- 
548    def save(self, filename, postfix=None):
-549        """Save CPO data for all stored timesteps to a `numpy` NPZ file.
-550
-551        If `postfix` is not `None`, the data is appended to the NPZ file
-552        in fields ending with "`_postfix`".
+            
551    def save(self, filename, postfix=None):
+552        """Save CPO data for all stored timesteps to a `numpy` NPZ file.
 553
-554        Raises a `ValueError` if the data shapes are not compatible.
-555
-556        See also: `numpy.savez`, `Mineral.load`, `Mineral.from_file`.
-557
-558        """
-559        if len(self.fractions) != len(self.orientations):
-560            raise ValueError(
-561                "Length of stored results must match."
-562                + " You've supplied currupted data with:\n"
-563                + f"- {len(self.fractions)} grain size results, and\n"
-564                + f"- {len(self.orientations)} orientation results."
-565            )
-566        if self.fractions[0].shape[0] == self.orientations[0].shape[0] == self.n_grains:
-567            data = {
-568                "meta": np.array(
-569                    [self.phase, self.fabric, self.regime], dtype=np.uint8
-570                ),
-571                "fractions": np.stack(self.fractions),
-572                "orientations": np.stack(self.orientations),
-573            }
-574            # Create parent directories, resolve relative paths.
-575            _io.resolve_path(filename)
-576            # Append to file, requires postfix (unique name).
-577            if postfix is not None:
-578                _log.info("saving Mineral to file %s (postfix: %s)", filename, postfix)
-579                archive = ZipFile(filename, mode="a", allowZip64=True)
-580                for key in data.keys():
-581                    with archive.open(
-582                        f"{key}_{postfix}", "w", force_zip64=True
-583                    ) as file:
-584                        buffer = io.BytesIO()
-585                        np.save(buffer, data[key])
-586                        file.write(buffer.getvalue())
-587                        buffer.close()
-588            else:
-589                _log.info("saving Mineral to file %s", filename)
-590                np.savez(filename, **data)
-591        else:
-592            raise ValueError(
-593                "Size of CPO data arrays must match number of grains."
-594                + " You've supplied corrupted data with:\n"
-595                + f"- `n_grains = {self.n_grains}`,\n"
-596                + f"- `fractions[0].shape = {self.fractions[0].shape}`, and\n"
-597                + f"- `orientations[0].shape = {self.orientations[0].shape}`."
-598            )
+554        If `postfix` is not `None`, the data is appended to the NPZ file
+555        in fields ending with "`_postfix`".
+556
+557        Raises a `ValueError` if the data shapes are not compatible.
+558
+559        See also: `numpy.savez`, `Mineral.load`, `Mineral.from_file`.
+560
+561        """
+562        if len(self.fractions) != len(self.orientations):
+563            raise ValueError(
+564                "Length of stored results must match."
+565                + " You've supplied currupted data with:\n"
+566                + f"- {len(self.fractions)} grain size results, and\n"
+567                + f"- {len(self.orientations)} orientation results."
+568            )
+569        if self.fractions[0].shape[0] == self.orientations[0].shape[0] == self.n_grains:
+570            data = {
+571                "meta": np.array(
+572                    [self.phase, self.fabric, self.regime], dtype=np.uint8
+573                ),
+574                "fractions": np.stack(self.fractions),
+575                "orientations": np.stack(self.orientations),
+576            }
+577            # Create parent directories, resolve relative paths.
+578            _io.resolve_path(filename)
+579            # Append to file, requires postfix (unique name).
+580            if postfix is not None:
+581                _log.info("saving Mineral to file %s (postfix: %s)", filename, postfix)
+582                archive = ZipFile(filename, mode="a", allowZip64=True)
+583                for key in data.keys():
+584                    with archive.open(
+585                        f"{key}_{postfix}", "w", force_zip64=True
+586                    ) as file:
+587                        buffer = io.BytesIO()
+588                        np.save(buffer, data[key])
+589                        file.write(buffer.getvalue())
+590                        buffer.close()
+591            else:
+592                _log.info("saving Mineral to file %s", filename)
+593                np.savez(filename, **data)
+594        else:
+595            raise ValueError(
+596                "Size of CPO data arrays must match number of grains."
+597                + " You've supplied corrupted data with:\n"
+598                + f"- `n_grains = {self.n_grains}`,\n"
+599                + f"- `fractions[0].shape = {self.fractions[0].shape}`, and\n"
+600                + f"- `orientations[0].shape = {self.orientations[0].shape}`."
+601            )
 

 
 
@@ -2116,33 +2128,33 @@
- 
600    def load(self, filename, postfix=None):
-601        """Load CPO data from a `numpy` NPZ file.
-602
-603        If `postfix` is not `None`, data is read from fields ending with "`_postfix`".
-604
-605        See also: `Mineral.save`, `Mineral.from_file`.
-606
-607        """
-608        if not filename.endswith(".npz"):
-609            raise ValueError(
-610                f"Must only load from numpy NPZ format. Cannot load from {filename}."
-611            )
-612        data = np.load(filename)
-613        if postfix is not None:
-614            phase, fabric, regime = data[f"meta_{postfix}"]
-615            self.fractions = list(data[f"fractions_{postfix}"])
-616            self.orientations = list(data[f"orientations_{postfix}"])
-617        else:
-618            phase, fabric, regime = data["meta"]
-619            self.fractions = list(data["fractions"])
-620            self.orientations = list(data["orientations"])
-621
-622        self.phase = phase
-623        self.fabric = fabric
-624        self.regime = regime
-625        self.orientations_init = self.orientations[0]
-626        self.fractions_init = self.fractions[0]
+            
603    def load(self, filename, postfix=None):
+604        """Load CPO data from a `numpy` NPZ file.
+605
+606        If `postfix` is not `None`, data is read from fields ending with "`_postfix`".
+607
+608        See also: `Mineral.save`, `Mineral.from_file`.
+609
+610        """
+611        if not filename.endswith(".npz"):
+612            raise ValueError(
+613                f"Must only load from numpy NPZ format. Cannot load from {filename}."
+614            )
+615        data = np.load(filename)
+616        if postfix is not None:
+617            phase, fabric, regime = data[f"meta_{postfix}"]
+618            self.fractions = list(data[f"fractions_{postfix}"])
+619            self.orientations = list(data[f"orientations_{postfix}"])
+620        else:
+621            phase, fabric, regime = data["meta"]
+622            self.fractions = list(data["fractions"])
+623            self.orientations = list(data["orientations"])
+624
+625        self.phase = phase
+626        self.fabric = fabric
+627        self.regime = regime
+628        self.orientations_init = self.orientations[0]
+629        self.fractions_init = self.fractions[0]
 

 
 
@@ -2167,40 +2179,40 @@
- 
628    @classmethod
-629    def from_file(cls, filename, postfix=None):
-630        """Construct a `Mineral` instance using data from a `numpy` NPZ file.
-631
-632        If `postfix` is not `None`, data is read from fields ending with “`_postfix`”.
-633
-634        See also: `Mineral.save`, `Mineral.load`.
-635
-636        """
-637        if not filename.endswith(".npz"):
-638            raise ValueError(
-639                f"Must only load from numpy NPZ format. Cannot load from {filename}."
-640            )
-641        data = np.load(filename)
-642        if postfix is not None:
-643            phase, fabric, regime = data[f"meta_{postfix}"]
-644            fractions = list(data[f"fractions_{postfix}"])
-645            orientations = list(data[f"orientations_{postfix}"])
-646        else:
-647            phase, fabric, regime = data["meta"]
-648            fractions = list(data["fractions"])
-649            orientations = list(data["orientations"])
-650
-651        mineral = cls(
-652            phase,
-653            fabric,
-654            regime,
-655            n_grains=len(fractions[0]),
-656            fractions_init=fractions[0],
-657            orientations_init=orientations[0],
-658        )
-659        mineral.fractions = fractions
-660        mineral.orientations = orientations
-661        return mineral
+            
631    @classmethod
+632    def from_file(cls, filename, postfix=None):
+633        """Construct a `Mineral` instance using data from a `numpy` NPZ file.
+634
+635        If `postfix` is not `None`, data is read from fields ending with “`_postfix`”.
+636
+637        See also: `Mineral.save`, `Mineral.load`.
+638
+639        """
+640        if not filename.endswith(".npz"):
+641            raise ValueError(
+642                f"Must only load from numpy NPZ format. Cannot load from {filename}."
+643            )
+644        data = np.load(filename)
+645        if postfix is not None:
+646            phase, fabric, regime = data[f"meta_{postfix}"]
+647            fractions = list(data[f"fractions_{postfix}"])
+648            orientations = list(data[f"orientations_{postfix}"])
+649        else:
+650            phase, fabric, regime = data["meta"]
+651            fractions = list(data["fractions"])
+652            orientations = list(data["orientations"])
+653
+654        mineral = cls(
+655            phase,
+656            fabric,
+657            regime,
+658            n_grains=len(fractions[0]),
+659            fractions_init=fractions[0],
+660            orientations_init=orientations[0],
+661        )
+662        mineral.fractions = fractions
+663        mineral.orientations = orientations
+664        return mineral
 

 
 
diff --git a/search.js b/search.js
index 6743b2dd..9d3333ef 100644
--- a/search.js
+++ b/search.js
@@ -1,6 +1,6 @@
 window.pdocSearch = (function(){
 /** elasticlunr - http://weixsong.github.io * Copyright (C) 2017 Oliver Nightingale * Copyright (C) 2017 Wei Song * MIT Licensed */!function(){function e(e){if(null===e||"object"!=typeof e)return e;var t=e.constructor();for(var n in e)e.hasOwnProperty(n)&&(t[n]=e[n]);return t}var t=function(e){var n=new t.Index;return n.pipeline.add(t.trimmer,t.stopWordFilter,t.stemmer),e&&e.call(n,n),n};t.version="0.9.5",lunr=t,t.utils={},t.utils.warn=function(e){return function(t){e.console&&console.warn&&console.warn(t)}}(this),t.utils.toString=function(e){return void 0===e||null===e?"":e.toString()},t.EventEmitter=function(){this.events={}},t.EventEmitter.prototype.addListener=function(){var e=Array.prototype.slice.call(arguments),t=e.pop(),n=e;if("function"!=typeof t)throw new TypeError("last argument must be a function");n.forEach(function(e){this.hasHandler(e)||(this.events[e]=[]),this.events[e].push(t)},this)},t.EventEmitter.prototype.removeListener=function(e,t){if(this.hasHandler(e)){var n=this.events[e].indexOf(t);-1!==n&&(this.events[e].splice(n,1),0==this.events[e].length&&delete this.events[e])}},t.EventEmitter.prototype.emit=function(e){if(this.hasHandler(e)){var t=Array.prototype.slice.call(arguments,1);this.events[e].forEach(function(e){e.apply(void 0,t)},this)}},t.EventEmitter.prototype.hasHandler=function(e){return e in this.events},t.tokenizer=function(e){if(!arguments.length||null===e||void 0===e)return[];if(Array.isArray(e)){var n=e.filter(function(e){return null===e||void 0===e?!1:!0});n=n.map(function(e){return t.utils.toString(e).toLowerCase()});var i=[];return n.forEach(function(e){var n=e.split(t.tokenizer.seperator);i=i.concat(n)},this),i}return e.toString().trim().toLowerCase().split(t.tokenizer.seperator)},t.tokenizer.defaultSeperator=/[\s\-]+/,t.tokenizer.seperator=t.tokenizer.defaultSeperator,t.tokenizer.setSeperator=function(e){null!==e&&void 0!==e&&"object"==typeof e&&(t.tokenizer.seperator=e)},t.tokenizer.resetSeperator=function(){t.tokenizer.seperator=t.tokenizer.defaultSeperator},t.tokenizer.getSeperator=function(){return t.tokenizer.seperator},t.Pipeline=function(){this._queue=[]},t.Pipeline.registeredFunctions={},t.Pipeline.registerFunction=function(e,n){n in t.Pipeline.registeredFunctions&&t.utils.warn("Overwriting existing registered function: "+n),e.label=n,t.Pipeline.registeredFunctions[n]=e},t.Pipeline.getRegisteredFunction=function(e){return e in t.Pipeline.registeredFunctions!=!0?null:t.Pipeline.registeredFunctions[e]},t.Pipeline.warnIfFunctionNotRegistered=function(e){var n=e.label&&e.label in this.registeredFunctions;n||t.utils.warn("Function is not registered with pipeline. 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this.config},t.Configuration.prototype.reset=function(){this.config={}},lunr.SortedSet=function(){this.length=0,this.elements=[]},lunr.SortedSet.load=function(e){var t=new this;return t.elements=e,t.length=e.length,t},lunr.SortedSet.prototype.add=function(){var e,t;for(e=0;e1;){if(r===e)return o;e>r&&(t=o),r>e&&(n=o),i=n-t,o=t+Math.floor(i/2),r=this.elements[o]}return r===e?o:-1},lunr.SortedSet.prototype.locationFor=function(e){for(var t=0,n=this.elements.length,i=n-t,o=t+Math.floor(i/2),r=this.elements[o];i>1;)e>r&&(t=o),r>e&&(n=o),i=n-t,o=t+Math.floor(i/2),r=this.elements[o];return r>e?o:e>r?o+1:void 0},lunr.SortedSet.prototype.intersect=function(e){for(var t=new lunr.SortedSet,n=0,i=0,o=this.length,r=e.length,s=this.elements,u=e.elements;;){if(n>o-1||i>r-1)break;s[n]!==u[i]?s[n]u[i]&&i++:(t.add(s[n]),n++,i++)}return t},lunr.SortedSet.prototype.clone=function(){var e=new lunr.SortedSet;return e.elements=this.toArray(),e.length=e.elements.length,e},lunr.SortedSet.prototype.union=function(e){var t,n,i;this.length>=e.length?(t=this,n=e):(t=e,n=this),i=t.clone();for(var o=0,r=n.toArray();oSimulate crystallographic preferred orientation evolution in polycrystals

\n\n
\n\n
\n\n

This software is currently in early development (alpha)\nand therefore subject to breaking changes without notice.

\n\n
\n\n

About

\n\n

Viscoplastic deformation of minerals, e.g. in Earth's mantle, leads to distinct\nsignatures in the mineral texture. Many minerals naturally occur in\npolycrystalline form, which means that they are composed of many grains with\ndifferent volumes and lattice orientations. Preferential alignment of the\naverage lattice orientation is called crystallographic preferred orientation\n(CPO). PyDRex simulates the development and evolution of CPO in deforming\npolycrystals, as well as tracking macroscopic finite strain measures.\nCurrently, the code supports olivine and enstatite mineral phases. The\nfollowing features are provided:

\n\n\n\n

The core CPO solver is based on the original Fortran 90 implementation by \u00c9douard Kaminski,\nwhich can be downloaded from this link (~90KB).\nThe reference papers are Kaminski & Ribe (2001)\nand Kaminski & Ribe (2004),\nand an open-access paper which discusses the model is Fraters & Billen (2021).

\n\n

Installation

\n\n

The minimum required Python version is set using requires-python in the\npyproject.toml file.\nFor installation instructions,\nsee the README file.

\n\n

Documentation

\n\n

The website menu can be used to discover the public API of this package.\nSome of the tests are also documented and can serve as usage examples.\nTheir docstrings can be viewed in this section.\nDocumentation is also available from the Python REPL via the help() method.

\n\n

The D-Rex kinematic CPO model

\n\n

The D-Rex model is used to compute crystallographic preferred orientation (CPO)\nfor polycrystals deforming by plastic deformation and dynamic recrystallization.\nPolycrystals are discretized into \"grains\" which represent fractional volumes\nof the total crystal that are characterised by a particular crystal lattice\norientation. For numerical efficiency, the number of grains in the model does\nnot change, and should only be interpreted as an approximation of the number\nof (unrecrystallised) physical grains. Dynamic recrystallization is modelled using\nstatistical expressions which approximate the interaction of each grain with an\neffective medium based on the averaged dislocation energy of all other grains. Note that\nthe model is not suited to situations where static recrystallization processes are\nsignificant.

\n\n

The primary microphysical mechanism for plastic deformation of the polycrystal\nis dislocation creep, which involves dislocation glide (\"slip\") along symmetry\nplanes of the mineral and dislocation climb, which allows for dislocations to\nannihilate each other so that the number of dislocations reaches a steady-state.\nThe D-Rex model does not simulate dislocation climb, but implicitly assumes that\nthe dislocations are in steady-state so that the dislocation density of the\ncrystal can be described by

\n\n

$$\n\u03c1 \u221d b^{-2} \\left(\\frac{\u03c3}{\u03bc}\\right)^{p}\n$$

\n\n

where $b$ is the length of the Burgers' vector, $\u03c3$ is the stress\nand $\u03bc$ is the shear modulus. The value of the exponent $p$ is given by the\nstress_exponent input parameter. For an overview of available parameters,\nsee [the pydrex.mock source code, for now...]

\n\n

The effects of dynamic recrystallization are twofold. Grains with a higher than\naverage dislocation density may be affected by either grain nucleation, which is\nthe formation of initially small, strain-free sub-grains, or grain boundary\nmigration, by which process other grains of lower strain energy annex a portion\nof its volume. Nucleation occurs mostly in grains oriented favourably for\ndislocation glide, and the new grains also grow by grain boundary migration.\nIf nucleation is too inefficient, the dislocation density in deformation-aligned\ngrains will remain high and these grains will therefore shrink in volume. On the\nother hand, if grain boundaries are too immobile, then nucleated grains will take\nlonger to grow, reducing the speed of CPO development and re-orientation.\nBecause nucleated grains are assumed to inherit the orientation of the parent,\nthey do not affect the model except by reducing the average dislocation density.\nA grain boundary mobility parameter of $M^{\u2217} = 0$ will therefore disable any\nrecrystallization effects. Finally, the process of grain boundary sliding can\nalso be included, which simply disallows rotation of grains with very small volume.\nThis only affects CPO evolution by introducing a latency for the onset of grain\nboundary migration in nucleated grains. It also manifests as an upper bound on\ntexture strength.

\n\n

Parameter reference

\n\n

Model parameters will eventually be provided in a .toml file.\nFor now just pass a dictionary to config in the Mineral.update_orientations method.\nA draft of the input file spec is shown below:

\n\n
\n
# PyDRex TOML configuration specification.\n# Exactly one valid combination of fields from the [input] section are required,\n# the rest is optional.\n\n# Simulation name is optional but recommended.\nname = "pydrex-spec"\n\n# Input files/options are given in this section:\n[input]\n\n# Input data can be provided in one of three ways:\n# 1. An input mesh with the steady-state numerical velocity gradient field\n#    and a plain text SCSV file specifying the FINAL locations of the polycrystals.\n#    In this case, polycrystals will first be back-propagated along flow pathlines,\n#    and then forward-propagated while the CPO is calculated.\n#    The SCSV file should have column names 'X', 'Y', 'Z' for 3D or any two of those for 2D.\n# 2. A built-in (analytical) velocity gradient function from `pydrex.velocity_gradients`,\n#    its arguments, and INITIAL locations of the polycrystals. In this case,\n#    polycrystals will immediately be forward-advected in the specified field.\n# 3. Pre-computed pathline files with velocity gradients at each point.\n#    These can be either plain text SCSV files or binary NPZ files.\n#    They should have columns/fields called: 'X_id', 'Y_id', 'Z_id', 'L11_id', 'L12_id', 'L13_id', etc.\n#    where 'id' is replaced by an unique identifier of the particle/pathline.\n#    If a field called 't' is also present, it will be used for the timestamps.\n#    Alternatively, a fixed timestep for all paths can be specified using `timestep`.\n# 4. Names of fields to be read from a geodynamics framework during runtime (not implemented yet).\n\n# Example for method 1, not only .vtu but any format supported by meshio should work:\n# mesh = "filename.vtu"\n# locations_final = "filename.scsv"\n# timestep = 1e9\n\n# Example for method 2:\nvelocity_gradient = ["simple_shear_2d", "Y", "X", 5e-6]\nlocations_initial = "start.scsv"\ntimestep = 1e9\n\n# Example for method 3:\n# timestep = 1e9\n# paths = ["path001.npz", "path002.scsv"]\n\n# In cases where the pathlines do not exit the domain,\n# a maximum strain threshold can bee provided, after which advection is halted.\n# max_strain = 10\n\n# Output files/options are given in this section:\n[output]\n\n# Optional output directory, will be created if missing.\n# This is also relative to the parent directory of the TOML file,\n# unless an absolute path is given.\ndirectory = "out"\n\n# Optional choice of mineral phases to include in raw output.\n# Raw output means rotation matrices and grain volumes, so 10 floats per grain per mineral.\n# By default, raw output for all supported minerals is saved.\nraw_output = ["olivine"]\n\n# Optional choice of mineral phases to include in diagnostic output.\n# Diagnostic output includes texture symmetry, strength and mean angle results.\n# By default, diagnostic output for all supported minerals is saved.\ndiagnostics = ["olivine"]\n\n# Should anisotropy postprocessing results be calculated?\n# This uses voigt averaging so the effective values for the multiphase polycrystal are calculated.\nanisotropy = true\n\n# Optional pathline output files (velocity gradients, positions, timestamps, particle ids).\n# Pathline output files use the same format as pathline inputs (by default, they are not produced).\n# They are stored inside the output directory unless absolute paths are given.\n# paths = ["pathline001.scsv"]\n\n# Optional logging level for log files.\n# This sets the log level for all log files, overriding the default value of "WARNING".\n# Supported levels are controlled by Python's logging module.\n# Usually they are "CRITICAL", "ERROR", "WARNING", "INFO" and "DEBUG".\nlog_level = "DEBUG"\n\n# DREX and simulation parameters are given in this section:\n[parameters]\n\n# Optional olivine volume fraction to use for multiphase simulations.\n# If enstatite_fraction is provided, they must sum to 1.\n# Otherwise, the remainder is assumed to be enstatite.\n# olivine_fraction = 1.\n\n# Optional enstatite volume fraction to use for multiphase simulations.\n# If olivine_fraction is provided, they must sum to 1.\n# Otherwise, the remainder is assumed to be olivine.\n# enstatite_fraction = 0.\n\n# Optional initial olivine fabric. A-type by default.\ninitial_olivine_fabric = "A"\n\n# Optional DREX stress_exponent, see documentation for details.\nstress_exponent = 1.5\n\n# Optional DREX deformation_exponent, see documentation for details.\ndeformation_exponent = 3.5\n\n# Optional DREX grain boudary mobility, see documentation for details.\ngbm_mobility = 125\n\n# Optional DREX grain boundary sliding threshold, see documentation for details.\ngbs_threshold = 0.3\n\n# Optional DREX nucleation efficiency, see documentation for details.\nnucleation_efficiency = 5.0\n\n# Optional number of (initial) grains per mineral phase per polycrystal.\nnumber_of_grains = 2000\n
\n
\n"}, "pydrex.axes": {"fullname": "pydrex.axes", "modulename": "pydrex.axes", "kind": "module", "doc": "
\n

PyDRex: Custom Matplotlib Axes subclasses.

\n
\n"}, "pydrex.axes.PoleFigureAxes": {"fullname": "pydrex.axes.PoleFigureAxes", "modulename": "pydrex.axes", "qualname": "PoleFigureAxes", "kind": "class", "doc": "

Axes class designed for crystallographic pole figures.

\n\n

Thin matplotlib Axes wrapper for crystallographic pole figures.

\n\n
\n\n

Projections are not performed automatically using default methods like\nscatter or plot. To actually plot the pole figures, use polefigure.

\n\n
\n", "bases": "matplotlib.axes._axes.Axes"}, "pydrex.axes.PoleFigureAxes.name": {"fullname": "pydrex.axes.PoleFigureAxes.name", "modulename": "pydrex.axes", "qualname": "PoleFigureAxes.name", "kind": "variable", "doc": "

\n", "default_value": "'pydrex.polefigure'"}, "pydrex.axes.PoleFigureAxes.polefigure": {"fullname": "pydrex.axes.PoleFigureAxes.polefigure", "modulename": "pydrex.axes", "qualname": "PoleFigureAxes.polefigure", "kind": "function", "doc": "

Plot pole figure of crystallographic texture.

\n\n

Args:

\n\n\n\n

Any additional keyword arguments are passed to either tripcolor if\ndensity=True or scatter if density=False

\n", "signature": "(\tself,\tdata,\tdensity=False,\tref_axes='xz',\thkl=[1, 0, 0],\tdensity_kwargs=None,\t**kwargs):", "funcdef": "def"}, "pydrex.axes.PoleFigureAxes.set": {"fullname": "pydrex.axes.PoleFigureAxes.set", "modulename": "pydrex.axes", "qualname": "PoleFigureAxes.set", "kind": "function", "doc": "

Set multiple properties at once.

\n\n

Supported properties are

\n\n

Properties:\n adjustable: {'box', 'datalim'}\n agg_filter: a filter function, which takes a (m, n, 3) float array and a dpi value, and returns a (m, n, 3) array and two offsets from the bottom left corner of the image\n alpha: scalar or None\n anchor: (float, float) or {'C', 'SW', 'S', 'SE', 'E', 'NE', ...}\n animated: bool\n aspect: {'auto', 'equal'} or float\n autoscale_on: bool\n autoscalex_on: unknown\n autoscaley_on: unknown\n axes_locator: Callable[[Axes, Renderer], Bbox]\n axisbelow: bool or 'line'\n box_aspect: float or None\n clip_box: ~matplotlib.transforms.BboxBase or None\n clip_on: bool\n clip_path: Patch or (Path, Transform) or None\n facecolor or fc: color\n figure: ~matplotlib.figure.Figure\n frame_on: bool\n gid: str\n in_layout: bool\n label: object\n mouseover: bool\n navigate: bool\n navigate_mode: unknown\n path_effects: list of .AbstractPathEffect\n picker: None or bool or float or callable\n position: [left, bottom, width, height] or ~matplotlib.transforms.Bbox\n prop_cycle: ~cycler.Cycler\n rasterization_zorder: float or None\n rasterized: bool\n sketch_params: (scale: float, length: float, randomness: float)\n snap: bool or None\n subplotspec: unknown\n title: str\n transform: ~matplotlib.transforms.Transform\n url: str\n visible: bool\n xbound: (lower: float, upper: float)\n xlabel: str\n xlim: (left: float, right: float)\n xmargin: float greater than -0.5\n xscale: unknown\n xticklabels: unknown\n xticks: unknown\n ybound: (lower: float, upper: float)\n ylabel: str\n ylim: (bottom: float, top: float)\n ymargin: float greater than -0.5\n yscale: unknown\n yticklabels: unknown\n yticks: unknown\n zorder: float

\n", "signature": "(\tself,\t*,\tadjustable=<UNSET>,\tagg_filter=<UNSET>,\talpha=<UNSET>,\tanchor=<UNSET>,\tanimated=<UNSET>,\taspect=<UNSET>,\tautoscale_on=<UNSET>,\tautoscalex_on=<UNSET>,\tautoscaley_on=<UNSET>,\taxes_locator=<UNSET>,\taxisbelow=<UNSET>,\tbox_aspect=<UNSET>,\tclip_box=<UNSET>,\tclip_on=<UNSET>,\tclip_path=<UNSET>,\tfacecolor=<UNSET>,\tframe_on=<UNSET>,\tgid=<UNSET>,\tin_layout=<UNSET>,\tlabel=<UNSET>,\tmouseover=<UNSET>,\tnavigate=<UNSET>,\tpath_effects=<UNSET>,\tpicker=<UNSET>,\tposition=<UNSET>,\tprop_cycle=<UNSET>,\trasterization_zorder=<UNSET>,\trasterized=<UNSET>,\tsketch_params=<UNSET>,\tsnap=<UNSET>,\tsubplotspec=<UNSET>,\ttitle=<UNSET>,\ttransform=<UNSET>,\turl=<UNSET>,\tvisible=<UNSET>,\txbound=<UNSET>,\txlabel=<UNSET>,\txlim=<UNSET>,\txmargin=<UNSET>,\txscale=<UNSET>,\txticklabels=<UNSET>,\txticks=<UNSET>,\tybound=<UNSET>,\tylabel=<UNSET>,\tylim=<UNSET>,\tymargin=<UNSET>,\tyscale=<UNSET>,\tyticklabels=<UNSET>,\tyticks=<UNSET>,\tzorder=<UNSET>):", "funcdef": "def"}, "pydrex.cli": {"fullname": "pydrex.cli", "modulename": "pydrex.cli", "kind": "module", "doc": "
\n

PyDRex: Entry points and argument handling for command line tools.

\n
\n\n

All CLI handlers should be registered in the CLI_HANDLERS namedtuple,\nwhich ensures that they will be installed as executable scripts alongside the package.

\n"}, "pydrex.cli.CliTool": {"fullname": "pydrex.cli.CliTool", "modulename": "pydrex.cli", "qualname": "CliTool", "kind": "class", "doc": "

Base class for CLI tools defining the required interface.

\n"}, "pydrex.cli.MeshGenerator": {"fullname": "pydrex.cli.MeshGenerator", "modulename": "pydrex.cli", "qualname": "MeshGenerator", "kind": "class", "doc": "

PyDRex script to generate various simple meshes.

\n\n

Only rectangular (2D) meshes are currently supported. The RESOLUTION must be a comma\ndelimited set of directives of the form <LOC>:<RES> where <LOC> is a location\nspecifier, i.e. either \"G\" (global) or a compas direction like \"N\", \"S\", \"NE\", etc.,\nand <RES> is a floating point value to be set as the resolution at that location.

\n", "bases": "CliTool"}, "pydrex.cli.H5partExtractor": {"fullname": "pydrex.cli.H5partExtractor", "modulename": "pydrex.cli", "qualname": "H5partExtractor", "kind": "class", "doc": "

PyDRex script to extract raw CPO data from Fluidity .h5part files.

\n\n

Fluidity saves data stored on model particles to an .h5part file.\nThis script converts that file to canonical serialisation formats:

\n\n\n\n

It is assumed that CPO data is stored in keys called 'CPO_' in the .h5part\ndata, where <N> is an integer in the range 1\u2014n_grains. The accumulated strain is\nread from the attribute CPO_<S> where S=ngrains+1. Particle positions are read\nfrom the attributes x, y, and z.

\n\n

At the moment, dynamic changes in fabric or phase are not supported.

\n", "bases": "CliTool"}, "pydrex.cli.NPZFileInspector": {"fullname": "pydrex.cli.NPZFileInspector", "modulename": "pydrex.cli", "qualname": "NPZFileInspector", "kind": "class", "doc": "

PyDRex script to show information about serialized CPO data.

\n\n

Lists the keys that should be used for the postfix in pydrex.Mineral.load and\npydrex.Mineral.from_file.

\n", "bases": "CliTool"}, "pydrex.cli.PoleFigureVisualiser": {"fullname": "pydrex.cli.PoleFigureVisualiser", "modulename": "pydrex.cli", "qualname": "PoleFigureVisualiser", "kind": "class", "doc": "

PyDRex script to plot pole figures of serialized CPO data.

\n\n

Produces [100], [010] and [001] pole figures for serialized pydrex.Minerals.\nIf the range of indices is not specified,\na maximum of 25 of each pole figure will be produced by default.

\n", "bases": "CliTool"}, "pydrex.cli.CLI_HANDLERS": {"fullname": "pydrex.cli.CLI_HANDLERS", "modulename": "pydrex.cli", "qualname": "CLI_HANDLERS", "kind": "variable", "doc": "

\n", "default_value": "CLI_HANDLERS(h5part_extractor=<pydrex.cli.H5partExtractor object>, npz_file_inspector=<pydrex.cli.NPZFileInspector object>, pole_figure_visualiser=<pydrex.cli.PoleFigureVisualiser object>, mesh_generator=<pydrex.cli.MeshGenerator object>)"}, "pydrex.core": {"fullname": "pydrex.core", "modulename": "pydrex.core", "kind": "module", "doc": "
\n

PyDRex: Core D-Rex functions and enums.

\n
\n\n

The function derivatives implements the core D-Rex solver, which computes the\ncrystallographic rotation rate and changes in fractional grain volumes.

\n\n

Acronyms:

\n\n\n"}, "pydrex.core.PERMUTATION_SYMBOL": {"fullname": "pydrex.core.PERMUTATION_SYMBOL", "modulename": "pydrex.core", "qualname": "PERMUTATION_SYMBOL", "kind": "variable", "doc": "

\n", "default_value": "array([[[ 0., 0., 0.],\n [ 0., 0., 1.],\n [ 0., -1., 0.]],\n\n [[ 0., 0., -1.],\n [ 0., 0., 0.],\n [ 1., 0., 0.]],\n\n [[ 0., 1., 0.],\n [-1., 0., 0.],\n [ 0., 0., 0.]]])"}, "pydrex.core.MineralPhase": {"fullname": "pydrex.core.MineralPhase", "modulename": "pydrex.core", "qualname": "MineralPhase", "kind": "class", "doc": "

Supported mineral phases.

\n", "bases": "enum.IntEnum"}, "pydrex.core.MineralPhase.olivine": {"fullname": "pydrex.core.MineralPhase.olivine", "modulename": "pydrex.core", "qualname": "MineralPhase.olivine", "kind": "variable", "doc": "

\n", "default_value": "<MineralPhase.olivine: 0>"}, "pydrex.core.MineralPhase.enstatite": {"fullname": "pydrex.core.MineralPhase.enstatite", "modulename": "pydrex.core", "qualname": "MineralPhase.enstatite", "kind": "variable", "doc": "

\n", "default_value": "<MineralPhase.enstatite: 1>"}, "pydrex.core.DeformationRegime": {"fullname": "pydrex.core.DeformationRegime", "modulename": "pydrex.core", "qualname": "DeformationRegime", "kind": "class", "doc": "

Deformation mechanism regimes.

\n", "bases": "enum.IntEnum"}, "pydrex.core.DeformationRegime.diffusion": {"fullname": "pydrex.core.DeformationRegime.diffusion", "modulename": "pydrex.core", "qualname": "DeformationRegime.diffusion", "kind": "variable", "doc": "

\n", "default_value": "<DeformationRegime.diffusion: 0>"}, "pydrex.core.DeformationRegime.dislocation": {"fullname": "pydrex.core.DeformationRegime.dislocation", "modulename": "pydrex.core", "qualname": "DeformationRegime.dislocation", "kind": "variable", "doc": "

\n", "default_value": "<DeformationRegime.dislocation: 1>"}, "pydrex.core.DeformationRegime.byerlee": {"fullname": "pydrex.core.DeformationRegime.byerlee", "modulename": "pydrex.core", "qualname": "DeformationRegime.byerlee", "kind": "variable", "doc": "

\n", "default_value": "<DeformationRegime.byerlee: 2>"}, "pydrex.core.DeformationRegime.max_viscosity": {"fullname": "pydrex.core.DeformationRegime.max_viscosity", "modulename": "pydrex.core", "qualname": "DeformationRegime.max_viscosity", "kind": "variable", "doc": "

\n", "default_value": "<DeformationRegime.max_viscosity: 3>"}, "pydrex.core.MineralFabric": {"fullname": "pydrex.core.MineralFabric", "modulename": "pydrex.core", "qualname": "MineralFabric", "kind": "class", "doc": "

Supported mineral fabrics.

\n\n

The following fabric types are supported:

\n\n\n", "bases": "enum.IntEnum"}, "pydrex.core.MineralFabric.olivine_A": {"fullname": "pydrex.core.MineralFabric.olivine_A", "modulename": "pydrex.core", "qualname": "MineralFabric.olivine_A", "kind": "variable", "doc": "

\n", "default_value": "<MineralFabric.olivine_A: 0>"}, "pydrex.core.MineralFabric.olivine_B": {"fullname": "pydrex.core.MineralFabric.olivine_B", "modulename": "pydrex.core", "qualname": "MineralFabric.olivine_B", "kind": "variable", "doc": "

\n", "default_value": "<MineralFabric.olivine_B: 1>"}, "pydrex.core.MineralFabric.olivine_C": {"fullname": "pydrex.core.MineralFabric.olivine_C", "modulename": "pydrex.core", "qualname": "MineralFabric.olivine_C", "kind": "variable", "doc": "

\n", "default_value": "<MineralFabric.olivine_C: 2>"}, "pydrex.core.MineralFabric.olivine_D": {"fullname": "pydrex.core.MineralFabric.olivine_D", "modulename": "pydrex.core", "qualname": "MineralFabric.olivine_D", "kind": "variable", "doc": "

\n", "default_value": "<MineralFabric.olivine_D: 3>"}, "pydrex.core.MineralFabric.olivine_E": {"fullname": "pydrex.core.MineralFabric.olivine_E", "modulename": "pydrex.core", "qualname": "MineralFabric.olivine_E", "kind": "variable", "doc": "

\n", "default_value": "<MineralFabric.olivine_E: 4>"}, "pydrex.core.MineralFabric.enstatite_AB": {"fullname": "pydrex.core.MineralFabric.enstatite_AB", "modulename": "pydrex.core", "qualname": "MineralFabric.enstatite_AB", "kind": "variable", "doc": "

\n", "default_value": "<MineralFabric.enstatite_AB: 5>"}, "pydrex.core.get_crss": {"fullname": "pydrex.core.get_crss", "modulename": "pydrex.core", "qualname": "get_crss", "kind": "function", "doc": "

Get Critical Resolved Shear Stress for the mineral phase and fabric.

\n\n

Returns an array of the normalised threshold stresses required to activate slip on\neach slip system. Olivine slip systems are ordered according to the convention used\nfor pydrex.minerals.OLIVINE_SLIP_SYSTEMS.

\n", "signature": "(phase, fabric):", "funcdef": "def"}, "pydrex.core.derivatives": {"fullname": "pydrex.core.derivatives", "modulename": "pydrex.core", "qualname": "derivatives", "kind": "function", "doc": "

Get derivatives of orientation and volume distribution.

\n\n

Args:

\n\n\n\n

Returns a tuple with the rotation rates and grain volume fraction changes.

\n", "signature": "(\tphase,\tfabric,\tn_grains,\torientations,\tfractions,\tstrain_rate,\tvelocity_gradient,\tstress_exponent,\tdeformation_exponent,\tnucleation_efficiency,\tgbm_mobility,\tvolume_fraction):", "funcdef": "def"}, "pydrex.diagnostics": {"fullname": "pydrex.diagnostics", "modulename": "pydrex.diagnostics", "kind": "module", "doc": "
\n

PyDRex: Methods to calculate texture and strain diagnostics.

\n
\n\n
\n\n

Calculations expect orientation matrices $a$ to represent passive\n(i.e. alias) rotations, which are defined in terms of the extrinsic ZXZ\neuler angles $\u03d5, \u03b8, \u03c6$ as\n$$\na = \\begin{bmatrix}\n \\cos\u03c6\\cos\u03d5 - \\cos\u03b8\\sin\u03d5\\sin\u03c6 & \\cos\u03b8\\cos\u03d5\\sin\u03c6 + \\cos\u03c6\\sin\u03d5 & \\sin\u03c6\\sin\u03b8 \\cr\n -\\sin\u03c6\\cos\u03d5 - \\cos\u03b8\\sin\u03d5\\cos\u03c6 & \\cos\u03b8\\cos\u03d5\\cos\u03c6 - \\sin\u03c6\\sin\u03d5 & \\cos\u03c6\\sin\u03b8 \\cr\n \\sin\u03b8\\sin\u03d5 & -\\sin\u03b8\\cos\u03d5 & \\cos\u03b8\n \\end{bmatrix}\n$$\nsuch that a[i, j] gives the direction cosine of the angle between the i-th\ngrain axis and the j-th external axis (in the global Eulerian frame).

\n\n
\n"}, "pydrex.diagnostics.elasticity_components": {"fullname": "pydrex.diagnostics.elasticity_components", "modulename": "pydrex.diagnostics", "qualname": "elasticity_components", "kind": "function", "doc": "

Calculate elasticity decompositions for the given elasticity tensors.

\n\n

Args:

\n\n\n\n

Returns a dictionary with the following data series:

\n\n\n\n
\n\n

Only 5 symmetry classes are relevant for elasticity decomposition,\ncompared to the usual 6 used to describe crystal families.\nCrystals with cubic symmetry contribute to the isotropic elasticity tensor,\nbecause the lattice spacing is identical in all orthogonal directions.\nNote also that the trigonal crystal system is not a crystal family\n(it belongs to the hexagonal family).

\n\n
\n", "signature": "(voigt_matrices):", "funcdef": "def"}, "pydrex.diagnostics.bingham_average": {"fullname": "pydrex.diagnostics.bingham_average", "modulename": "pydrex.diagnostics", "qualname": "bingham_average", "kind": "function", "doc": "

Compute Bingham average of orientation matrices.

\n\n

Returns the antipodally symmetric average orientation\nof the given crystallographic axis, or the a-axis by default.\nValid axis specifiers are \"a\" for [100], \"b\" for [010] and \"c\" for [001].

\n\n

See also: Watson (1966),\nMardia & Jupp, \u201cDirectional Statistics\u201d.

\n", "signature": "(orientations, axis='a'):", "funcdef": "def"}, "pydrex.diagnostics.finite_strain": {"fullname": "pydrex.diagnostics.finite_strain", "modulename": "pydrex.diagnostics", "qualname": "finite_strain", "kind": "function", "doc": "

Extract measures of finite strain from the deformation gradient.

\n\n

Extracts the largest principal strain value and the vector defining the axis of\nmaximum extension (longest semiaxis of the finite strain ellipsoid) from the 3x3\ndeformation gradient tensor.

\n", "signature": "(deformation_gradient, driver='ev'):", "funcdef": "def"}, "pydrex.diagnostics.symmetry_pgr": {"fullname": "pydrex.diagnostics.symmetry_pgr", "modulename": "pydrex.diagnostics", "qualname": "symmetry_pgr", "kind": "function", "doc": "

Compute texture symmetry eigenvalue diagnostics from grain orientation matrices.

\n\n

Compute Point, Girdle and Random symmetry diagnostics\nfor ternary texture classification.\nReturns the tuple (P, G, R) where\n$$\n\\begin{align*}\nP &= (\u03bb_{1} - \u03bb_{2}) / N \\cr\nG &= 2 (\u03bb_{2} - \u03bb_{3}) / N \\cr\nR &= 3 \u03bb_{3} / N\n\\end{align*}\n$$\nwith $N$ the sum of the eigenvalues $\u03bb_{1} \u2265 \u03bb_{2} \u2265 \u03bb_{3}$\nof the scatter (inertia) matrix.

\n\n

See e.g. Vollmer (1990).

\n", "signature": "(orientations, axis='a'):", "funcdef": "def"}, "pydrex.diagnostics.misorientation_indices": {"fullname": "pydrex.diagnostics.misorientation_indices", "modulename": "pydrex.diagnostics", "qualname": "misorientation_indices", "kind": "function", "doc": "

Calculate M-indices for a series of polycrystal textures.

\n\n

Calculate M-index using misorientation_index for a series of texture snapshots.\nThe orientation_stack is a NxMx3x3 array of orientations where N is the number of\ntexture snapshots and M is the number of grains.

\n\n

Uses either Ray or the Python multiprocessing library to calculate texture indices\nfor multiple snapshots simultaneously. The arguments ncpus and pool are only\nrelevant to the latter option: if ncpus is None the number of CPU cores to use\nis chosen automatically based on the maximum number available to the Python\ninterpreter, otherwise the specified number of cores is requested. Alternatively, an\nexisting instance of multiprocessing.Pool can be provided.

\n\n

If Ray is installed, it will be automatically preferred. In this case, the number of\nparallel workers should be set upon initialisation of the Ray cluster (which can be\ndistributed over the network).

\n\n

See misorientation_index for documentation of the remaining arguments.

\n", "signature": "(\torientation_stack,\tsystem: pydrex.geometry.LatticeSystem,\tbins=None,\tncpus=None,\tpool=None):", "funcdef": "def"}, "pydrex.diagnostics.misorientation_index": {"fullname": "pydrex.diagnostics.misorientation_index", "modulename": "pydrex.diagnostics", "qualname": "misorientation_index", "kind": "function", "doc": "

Calculate M-index for polycrystal orientations.

\n\n

The bins argument is passed to numpy.histogram.\nIf left as None, 1\u00b0 bins will be used as recommended by the reference paper.\nThe symmetry argument specifies the lattice system which determines intrinsic\nsymmetry degeneracies and the maximum allowable misorientation angle.\nSee _geo.LatticeSystem for supported systems.

\n\n
\n\n

This method must be able to allocate an array of shape\n$ \\frac{N!}{2(N-2)!}\u00d7 M^{2} $\nfor N the length of orientations and M the number of symmetry operations for\nthe given system.

\n\n
\n\n

See Skemer et al. (2005).

\n", "signature": "(orientations, system: pydrex.geometry.LatticeSystem, bins=None):", "funcdef": "def"}, "pydrex.diagnostics.coaxial_index": {"fullname": "pydrex.diagnostics.coaxial_index", "modulename": "pydrex.diagnostics", "qualname": "coaxial_index", "kind": "function", "doc": "

Calculate coaxial \u201cBA\u201d index for a combination of two crystal axes.

\n\n

The BA index of Mainprice et al. (2015)\nis derived from the eigenvalue symmetry diagnostics and measures point vs girdle\nsymmetry in the aggregate. $BA \u2208 [0, 1]$ where $BA = 0$ corresponds to a perfect\naxial girdle texture and $BA = 1$ represents a point symmetry texture assuming that\nthe random component $R$ is negligible. May be less susceptible to random\nfluctuations compared to the raw eigenvalue diagnostics.

\n", "signature": "(orientations, axis1='b', axis2='a'):", "funcdef": "def"}, "pydrex.diagnostics.smallest_angle": {"fullname": "pydrex.diagnostics.smallest_angle", "modulename": "pydrex.diagnostics", "qualname": "smallest_angle", "kind": "function", "doc": "

Get smallest angle between a unit vector and a bidirectional axis.

\n\n

The axis is specified using either of its two parallel unit vectors.\nOptionally project the vector onto the plane (given by its unit normal)\nbefore calculating the angle.

\n\n

Examples:

\n\n
\n
>>> from numpy import asarray as \u014a\n>>> smallest_angle(\u014a([1e0, 0e0, 0e0]), \u014a([1e0, 0e0, 0e0]))\n0.0\n>>> smallest_angle(\u014a([1e0, 0e0, 0e0]), \u014a([0e0, 1e0, 0e0]))\n90.0\n>>> smallest_angle(\u014a([1e0, 0e0, 0e0]), \u014a([0e0, -1e0, 0e0]))\n90.0\n>>> smallest_angle(\u014a([1e0, 0e0, 0e0]), \u014a([np.sqrt(2), np.sqrt(2), 0e0]))\n45.0\n>>> smallest_angle(\u014a([1e0, 0e0, 0e0]), \u014a([-np.sqrt(2), np.sqrt(2), 0e0]))\n45.0\n
\n
\n", "signature": "(vector, axis, plane=None):", "funcdef": "def"}, "pydrex.exceptions": {"fullname": "pydrex.exceptions", "modulename": "pydrex.exceptions", "kind": "module", "doc": "
\n

PyDRex: Custom exceptions (subclasses of pydrex.Error).

\n
\n"}, "pydrex.exceptions.Error": {"fullname": "pydrex.exceptions.Error", "modulename": "pydrex.exceptions", "qualname": "Error", "kind": "class", "doc": "

Base class for exceptions in PyDRex.

\n", "bases": "builtins.Exception"}, "pydrex.exceptions.MissingDependencyError": {"fullname": "pydrex.exceptions.MissingDependencyError", "modulename": "pydrex.exceptions", "qualname": "MissingDependencyError", "kind": "class", "doc": "

Exception raised when optional dependencies are missing.

\n\n

Attributes:\n message \u2014 explanation of the error

\n", "bases": "Error"}, "pydrex.exceptions.MissingDependencyError.__init__": {"fullname": "pydrex.exceptions.MissingDependencyError.__init__", "modulename": "pydrex.exceptions", "qualname": "MissingDependencyError.__init__", "kind": "function", "doc": "

\n", "signature": "(message)"}, "pydrex.exceptions.MissingDependencyError.message": {"fullname": "pydrex.exceptions.MissingDependencyError.message", "modulename": "pydrex.exceptions", "qualname": "MissingDependencyError.message", "kind": "variable", "doc": "

\n"}, "pydrex.exceptions.ConfigError": {"fullname": "pydrex.exceptions.ConfigError", "modulename": "pydrex.exceptions", "qualname": "ConfigError", "kind": "class", "doc": "

Exception raised for errors in the input configuration.

\n\n

Attributes:\n message \u2014 explanation of the error

\n", "bases": "Error"}, "pydrex.exceptions.ConfigError.__init__": {"fullname": "pydrex.exceptions.ConfigError.__init__", "modulename": "pydrex.exceptions", "qualname": "ConfigError.__init__", "kind": "function", "doc": "

\n", "signature": "(message)"}, "pydrex.exceptions.ConfigError.message": {"fullname": "pydrex.exceptions.ConfigError.message", "modulename": "pydrex.exceptions", "qualname": "ConfigError.message", "kind": "variable", "doc": "

\n"}, "pydrex.exceptions.MeshError": {"fullname": "pydrex.exceptions.MeshError", "modulename": "pydrex.exceptions", "qualname": "MeshError", "kind": "class", "doc": "

Exception raised for errors in the input mesh.

\n\n

Attributes:\n message \u2014 explanation of the error

\n", "bases": "Error"}, "pydrex.exceptions.MeshError.__init__": {"fullname": "pydrex.exceptions.MeshError.__init__", "modulename": "pydrex.exceptions", "qualname": "MeshError.__init__", "kind": "function", "doc": "

\n", "signature": "(message)"}, "pydrex.exceptions.MeshError.message": {"fullname": "pydrex.exceptions.MeshError.message", "modulename": "pydrex.exceptions", "qualname": "MeshError.message", "kind": "variable", "doc": "

\n"}, "pydrex.exceptions.IterationError": {"fullname": "pydrex.exceptions.IterationError", "modulename": "pydrex.exceptions", "qualname": "IterationError", "kind": "class", "doc": "

Exception raised for errors in numerical iteration schemes.

\n\n

Attributes:\n message \u2014 explanation of the error

\n", "bases": "Error"}, "pydrex.exceptions.IterationError.__init__": {"fullname": "pydrex.exceptions.IterationError.__init__", "modulename": "pydrex.exceptions", "qualname": "IterationError.__init__", "kind": "function", "doc": "

\n", "signature": "(message)"}, "pydrex.exceptions.IterationError.message": {"fullname": "pydrex.exceptions.IterationError.message", "modulename": "pydrex.exceptions", "qualname": "IterationError.message", "kind": "variable", "doc": "

\n"}, "pydrex.exceptions.SCSVError": {"fullname": "pydrex.exceptions.SCSVError", "modulename": "pydrex.exceptions", "qualname": "SCSVError", "kind": "class", "doc": "

Exception raised for errors in SCSV file I/O.

\n\n

Attributes:

\n\n\n", "bases": "Error"}, "pydrex.exceptions.SCSVError.__init__": {"fullname": "pydrex.exceptions.SCSVError.__init__", "modulename": "pydrex.exceptions", "qualname": "SCSVError.__init__", "kind": "function", "doc": "

\n", "signature": "(message)"}, "pydrex.exceptions.SCSVError.message": {"fullname": "pydrex.exceptions.SCSVError.message", "modulename": "pydrex.exceptions", "qualname": "SCSVError.message", "kind": "variable", "doc": "

\n"}, "pydrex.exceptions.ModelContextError": {"fullname": "pydrex.exceptions.ModelContextError", "modulename": "pydrex.exceptions", "qualname": "ModelContextError", "kind": "class", "doc": "

Exception raised for errors in mesh.Model context state.

\n\n

Attributes:\n message \u2014 explanation of the error

\n", "bases": "Error"}, "pydrex.exceptions.ModelContextError.__init__": {"fullname": "pydrex.exceptions.ModelContextError.__init__", "modulename": "pydrex.exceptions", "qualname": "ModelContextError.__init__", "kind": "function", "doc": "

\n", "signature": "(message)"}, "pydrex.exceptions.ModelContextError.message": {"fullname": "pydrex.exceptions.ModelContextError.message", "modulename": "pydrex.exceptions", "qualname": "ModelContextError.message", "kind": "variable", "doc": "

\n"}, "pydrex.geometry": {"fullname": "pydrex.geometry", "modulename": "pydrex.geometry", "kind": "module", "doc": "
\n

PyDRex: Functions for geometric coordinate conversions and projections.

\n
\n"}, "pydrex.geometry.LatticeSystem": {"fullname": "pydrex.geometry.LatticeSystem", "modulename": "pydrex.geometry", "qualname": "LatticeSystem", "kind": "class", "doc": "

Crystallographic lattice systems supported by postprocessing methods.

\n\n

The value of a member is (a, b) with a and b as given in the table below.\nThe additional row lists the maximum misorientation angle between two crystallites\nfor the given lattice system.

\n\n
        triclinic  monoclinic  orthorhombic  rhombohedral tetragonal hexagonal\n------------------------------------------------------------------------------\na       1          2           2             3            4          6\nb       1          2           4             6            8          12\n\u03b8max    180\u00b0       180\u00b0        120\u00b0          120\u00b0         90\u00b0        90\u00b0\n
\n\n

This is identically Table 1 in Grimmer (1979).

\n", "bases": "enum.Enum"}, "pydrex.geometry.LatticeSystem.triclinic": {"fullname": "pydrex.geometry.LatticeSystem.triclinic", "modulename": "pydrex.geometry", "qualname": "LatticeSystem.triclinic", "kind": "variable", "doc": "

\n", "default_value": "<LatticeSystem.triclinic: (1, 1)>"}, "pydrex.geometry.LatticeSystem.monoclinic": {"fullname": "pydrex.geometry.LatticeSystem.monoclinic", "modulename": "pydrex.geometry", "qualname": "LatticeSystem.monoclinic", "kind": "variable", "doc": "

\n", "default_value": "<LatticeSystem.monoclinic: (2, 2)>"}, "pydrex.geometry.LatticeSystem.orthorhombic": {"fullname": "pydrex.geometry.LatticeSystem.orthorhombic", "modulename": "pydrex.geometry", "qualname": "LatticeSystem.orthorhombic", "kind": "variable", "doc": "

\n", "default_value": "<LatticeSystem.orthorhombic: (2, 4)>"}, "pydrex.geometry.LatticeSystem.rhombohedral": {"fullname": "pydrex.geometry.LatticeSystem.rhombohedral", "modulename": "pydrex.geometry", "qualname": "LatticeSystem.rhombohedral", "kind": "variable", "doc": "

\n", "default_value": "<LatticeSystem.rhombohedral: (3, 6)>"}, "pydrex.geometry.LatticeSystem.tetragonal": {"fullname": "pydrex.geometry.LatticeSystem.tetragonal", "modulename": "pydrex.geometry", "qualname": "LatticeSystem.tetragonal", "kind": "variable", "doc": "

\n", "default_value": "<LatticeSystem.tetragonal: (4, 8)>"}, "pydrex.geometry.LatticeSystem.hexagonal": {"fullname": "pydrex.geometry.LatticeSystem.hexagonal", "modulename": "pydrex.geometry", "qualname": "LatticeSystem.hexagonal", "kind": "variable", "doc": "

\n", "default_value": "<LatticeSystem.hexagonal: (6, 12)>"}, "pydrex.geometry.to_cartesian": {"fullname": "pydrex.geometry.to_cartesian", "modulename": "pydrex.geometry", "qualname": "to_cartesian", "kind": "function", "doc": "

Convert spherical to cartesian coordinates in \u211d\u00b3.

\n\n

Spherical coordinate convention:

\n\n\n\n

By default, a radius of r = 1 is used for the sphere.\nReturns a tuple containing arrays of x, y, and z values.

\n", "signature": "(\u03c6, \u03b8, r=1):", "funcdef": "def"}, "pydrex.geometry.to_spherical": {"fullname": "pydrex.geometry.to_spherical", "modulename": "pydrex.geometry", "qualname": "to_spherical", "kind": "function", "doc": "

Convert cartesian coordinates in \u211d\u00b3 to spherical coordinates.

\n\n

Spherical coordinate convention:

\n\n\n\n

Returns a tuple containing arrays of r, \u03d5 and \u03b8 values.

\n", "signature": "(x, y, z):", "funcdef": "def"}, "pydrex.geometry.misorientation_angles": {"fullname": "pydrex.geometry.misorientation_angles", "modulename": "pydrex.geometry", "qualname": "misorientation_angles", "kind": "function", "doc": "

Calculate minimum misorientation angles for collections of rotation quaternions.

\n\n

Calculate the smallest angular distance between any quaternions q1_array[:, i] and\nq2_array[:, j], where i == j and the first dimensions of q1_array and q2_array\nare of equal length (the output will also be this long):

\n\n
q1_array.shape      q2_array.shape      len(output)\n---------------------------------------------------\nNxAx4               NxBx4               N\n
\n\n
\n\n

This method must be able to allocate a floating point array of shape Nx(A*B)

\n\n
\n\n

Uses ~25% less memory than the same operation with rotation matrices.

\n\n

See also:

\n\n\n", "signature": "(q1_array, q2_array):", "funcdef": "def"}, "pydrex.geometry.symmetry_operations": {"fullname": "pydrex.geometry.symmetry_operations", "modulename": "pydrex.geometry", "qualname": "symmetry_operations", "kind": "function", "doc": "

Get sequence of symmetry operations for the given LatticeSystem.

\n\n

Returned transforms are either quaternions (for rotations of the lattice) or 4x4\nmatrices which pre-multiply a quaternion to give a reflected variant (reflections\nare improper rotations and cannot be represented as quaternions or SciPy rotation\nmatrices).

\n", "signature": "(system: pydrex.geometry.LatticeSystem):", "funcdef": "def"}, "pydrex.geometry.poles": {"fullname": "pydrex.geometry.poles", "modulename": "pydrex.geometry", "qualname": "poles", "kind": "function", "doc": "

Extract 3D vectors of crystallographic directions from orientation matrices.

\n\n

Expects orientations to be an array with shape (N, 3, 3).\nThe optional arguments ref_axes and hkl can be used to change\nthe global reference axes and the crystallographic direction respectively.\nThe reference axes should be given as a string of two letters,\ne.g. \"xz\" (default), which specify the second and third axes\nof the global right-handed reference frame. The third letter in the set \"xyz\"\ndetermines the first axis. The ref_axes will therefore become the\nhorizontal and vertical axes of pole figures used to plot the directions.

\n", "signature": "(orientations, ref_axes='xz', hkl=[1, 0, 0]):", "funcdef": "def"}, "pydrex.geometry.lambert_equal_area": {"fullname": "pydrex.geometry.lambert_equal_area", "modulename": "pydrex.geometry", "qualname": "lambert_equal_area", "kind": "function", "doc": "

Project axial data from a 3D sphere onto a 2D disk.

\n\n

Project points from a 3D sphere of radius 1, given in Cartesian coordinates,\nto points on a 2D disk using a Lambert equal area azimuthal projection.\nReturns arrays of the X and Y coordinates in the unit disk.

\n\n

This implementation first maps all points onto the same hemisphere,\nand then projects that hemisphere onto the disk.

\n", "signature": "(xvals, yvals, zvals):", "funcdef": "def"}, "pydrex.geometry.shirley_concentric_squaredisk": {"fullname": "pydrex.geometry.shirley_concentric_squaredisk", "modulename": "pydrex.geometry", "qualname": "shirley_concentric_squaredisk", "kind": "function", "doc": "

Project points from a square onto a disk using the concentric Shirley method.

\n\n

The concentric method of Shirley & Chiu (1997)\nis optimised to preserve area. See also: http://marc-b-reynolds.github.io/math/2017/01/08/SquareDisc.html.

\n\n

This can be used to set up uniform grids on a disk, e.g.

\n\n
\n
>>> a = [x / 5.0 for x in range(-5, 6)]\n>>> x = [[x] * len(a) for x in a]\n>>> y = [a for _ in a]\n>>> x_flat = [j for i in x for j in i]\n>>> y_flat = [j for i in y for j in i]\n>>> x_disk, y_disk = shirley_concentric_squaredisk(x_flat, y_flat)\n>>> r = x_disk**2 + y_disk**2\n>>> r.reshape((len(a), len(a)))\narray([[1.  , 1.  , 1.  , 1.  , 1.  , 1.  , 1.  , 1.  , 1.  , 1.  , 1.  ],\n       [1.  , 0.64, 0.64, 0.64, 0.64, 0.64, 0.64, 0.64, 0.64, 0.64, 1.  ],\n       [1.  , 0.64, 0.36, 0.36, 0.36, 0.36, 0.36, 0.36, 0.36, 0.64, 1.  ],\n       [1.  , 0.64, 0.36, 0.16, 0.16, 0.16, 0.16, 0.16, 0.36, 0.64, 1.  ],\n       [1.  , 0.64, 0.36, 0.16, 0.04, 0.04, 0.04, 0.16, 0.36, 0.64, 1.  ],\n       [1.  , 0.64, 0.36, 0.16, 0.04, 0.  , 0.04, 0.16, 0.36, 0.64, 1.  ],\n       [1.  , 0.64, 0.36, 0.16, 0.04, 0.04, 0.04, 0.16, 0.36, 0.64, 1.  ],\n       [1.  , 0.64, 0.36, 0.16, 0.16, 0.16, 0.16, 0.16, 0.36, 0.64, 1.  ],\n       [1.  , 0.64, 0.36, 0.36, 0.36, 0.36, 0.36, 0.36, 0.36, 0.64, 1.  ],\n       [1.  , 0.64, 0.64, 0.64, 0.64, 0.64, 0.64, 0.64, 0.64, 0.64, 1.  ],\n       [1.  , 1.  , 1.  , 1.  , 1.  , 1.  , 1.  , 1.  , 1.  , 1.  , 1.  ]])\n>>> from math import atan2\n>>> \u03b8 = [atan2(y, x) for y, x in zip(y_disk, x_disk)]\n>>> max(\u03b8)\n3.141592653589793\n>>> min(\u03b8)\n-2.9845130209101467\n
\n
\n", "signature": "(xvals, yvals):", "funcdef": "def"}, "pydrex.geometry.to_indices": {"fullname": "pydrex.geometry.to_indices", "modulename": "pydrex.geometry", "qualname": "to_indices", "kind": "function", "doc": "

\n", "signature": "(horizontal, vertical):", "funcdef": "def"}, "pydrex.io": {"fullname": "pydrex.io", "modulename": "pydrex.io", "kind": "module", "doc": "
\n

PyDRex: Mesh, configuration and supporting data Input/Output functions.

\n
\n\n

PyDRex can read/write three kinds of plain text files:

\n\n\n\n

SCSV files are our custom CSV files with a YAML header. The header is used for data\nattribution and metadata, as well as a column type spec. There is no official spec for\nSCSV files at the moment but they should follow the format of existing SCSV files in\nthe data/ folder of the source repository. For supported cell types, see\nSCSV_TYPEMAP.

\n"}, "pydrex.io.DEFAULT_PARAMS": {"fullname": "pydrex.io.DEFAULT_PARAMS", "modulename": "pydrex.io", "qualname": "DEFAULT_PARAMS", "kind": "variable", "doc": "

Default simulation parameters.

\n", "default_value": "{'olivine_fraction': 1.0, 'enstatite_fraction': 0.0, 'stress_exponent': 1.5, 'deformation_exponent': 3.5, 'gbm_mobility': 125, 'gbs_threshold': 0.3, 'nucleation_efficiency': 5.0, 'number_of_grains': 3500, 'initial_olivine_fabric': 'A'}"}, "pydrex.io.SCSV_TYPEMAP": {"fullname": "pydrex.io.SCSV_TYPEMAP", "modulename": "pydrex.io", "qualname": "SCSV_TYPEMAP", "kind": "variable", "doc": "

Mapping of supported SCSV field types to corresponding Python types.

\n", "default_value": "{'string': <class 'str'>, 'integer': <class 'int'>, 'float': <class 'float'>, 'boolean': <class 'bool'>, 'complex': <class 'complex'>}"}, "pydrex.io.extract_h5part": {"fullname": "pydrex.io.extract_h5part", "modulename": "pydrex.io", "qualname": "extract_h5part", "kind": "function", "doc": "

Extract CPO data from Fluidity h5part file and save to canonical formats.

\n", "signature": "(file, phase, fabric, n_grains, output):", "funcdef": "def"}, "pydrex.io.read_scsv": {"fullname": "pydrex.io.read_scsv", "modulename": "pydrex.io", "qualname": "read_scsv", "kind": "function", "doc": "

Read data from an SCSV file.

\n\n

Prints the YAML header section to output and returns a NamedTuple with columns of\nthe csv data. See also save_scsv.

\n", "signature": "(file):", "funcdef": "def"}, "pydrex.io.write_scsv_header": {"fullname": "pydrex.io.write_scsv_header", "modulename": "pydrex.io", "qualname": "write_scsv_header", "kind": "function", "doc": "

Write YAML header to an SCSV stream.

\n\n

Args:

\n\n\n\n

See also read_scsv, save_scsv.

\n", "signature": "(stream, schema, comments=None):", "funcdef": "def"}, "pydrex.io.save_scsv": {"fullname": "pydrex.io.save_scsv", "modulename": "pydrex.io", "qualname": "save_scsv", "kind": "function", "doc": "

Save data to SCSV file.

\n\n

Args:

\n\n\n\n

Optional keyword arguments are passed to write_scsv_header. See also read_scsv.

\n", "signature": "(file, schema, data, **kwargs):", "funcdef": "def"}, "pydrex.io.parse_config": {"fullname": "pydrex.io.parse_config", "modulename": "pydrex.io", "qualname": "parse_config", "kind": "function", "doc": "

Parse a TOML file containing PyDRex configuration.

\n", "signature": "(path):", "funcdef": "def"}, "pydrex.io.resolve_path": {"fullname": "pydrex.io.resolve_path", "modulename": "pydrex.io", "qualname": "resolve_path", "kind": "function", "doc": "

Resolve relative paths and create parent directories if necessary.

\n\n

Relative paths are interpreted with respect to the current working directory,\ni.e. the directory from whith the current Python process was executed,\nunless a specific reference directory is provided with refdir.

\n", "signature": "(path, refdir=None):", "funcdef": "def"}, "pydrex.io.stringify": {"fullname": "pydrex.io.stringify", "modulename": "pydrex.io", "qualname": "stringify", "kind": "function", "doc": "

Return a cleaned version of a string for use in filenames, etc.

\n", "signature": "(s):", "funcdef": "def"}, "pydrex.io.data": {"fullname": "pydrex.io.data", "modulename": "pydrex.io", "qualname": "data", "kind": "function", "doc": "

Get resolved path to a pydrex data directory.

\n", "signature": "(directory):", "funcdef": "def"}, "pydrex.logger": {"fullname": "pydrex.logger", "modulename": "pydrex.logger", "kind": "module", "doc": "
\n

PyDRex: logger settings and boilerplate.

\n
\n\n

Python's logging module is weird and its methods don't allow us to specify\nwhich logger to use, so just using logging.debug for example always uses\nthe \"root\" logger, which spams a bunch of messages from other imports/modules.\nInstead, the methods in this module are thin wrappers that use custom\nlogging objects (pydrex.logger.LOGGER and pydrex.logger.CONSOLE_LOGGER).\nThe method quiet_aliens can be invoked to suppress most messages\nfrom third-party modules, except critical errors and warnings from Numba.

\n\n

By default, PyDRex emits INFO level messages to the console.\nThis can be changed globally by setting the new level with CONSOLE_LOGGER.setLevel:

\n\n
\n
from pydrex import logger as _log\n_log.info("this message will be printed to the console")\n\n_log.CONSOLE_LOGGER.setLevel("ERROR")\n_log.info("this message will NOT be printed to the console")\n_log.error("this message will be printed to the console")\n
\n
\n\n

To change the console logging level for a particular local context,\nuse the handler_level context manager:

\n\n
\n
_log.CONSOLE_LOGGER.setLevel("INFO")\n_log.info("this message will be printed to the console")\n\nwith handler_level("ERROR"):\n    _log.info("this message will NOT be printed to the console")\n\n_log.info("this message will be printed to the console")\n
\n
\n\n

To save debug logs to a file, the logfile_enable context manager is recommended.\nAlways use the old printf style formatting for log messages, not fstrings,\notherwise compute time will be wasted on string conversions when logging is disabled:

\n\n
\n
_log.quiet_aliens()  # Suppress third-party log messages except CRITICAL from Numba.\nwith _log.logfile_enable("my_log_file.log"):  # Overwrite existing file unless mode="a".\n    value = 42\n    _log.critical("critical error with value: %s", value)\n    _log.error("runtime error with value: %s", value)\n    _log.warning("warning with value: %s", value)\n    _log.info("information message with value: %s", value)\n    _log.debug("verbose debugging message with value: %s", value)\n    ... # Construct Minerals, update orientations, etc.\n
\n
\n"}, "pydrex.logger.ConsoleFormatter": {"fullname": "pydrex.logger.ConsoleFormatter", "modulename": "pydrex.logger", "qualname": "ConsoleFormatter", "kind": "class", "doc": "

Log formatter that uses terminal color codes.

\n", "bases": "logging.Formatter"}, "pydrex.logger.ConsoleFormatter.colorfmt": {"fullname": "pydrex.logger.ConsoleFormatter.colorfmt", "modulename": "pydrex.logger", "qualname": "ConsoleFormatter.colorfmt", "kind": "function", "doc": "

\n", "signature": "(self, code):", "funcdef": "def"}, "pydrex.logger.ConsoleFormatter.format": {"fullname": "pydrex.logger.ConsoleFormatter.format", "modulename": "pydrex.logger", "qualname": "ConsoleFormatter.format", "kind": "function", "doc": "

Format the specified record as text.

\n\n

The record's attribute dictionary is used as the operand to a\nstring formatting operation which yields the returned string.\nBefore formatting the dictionary, a couple of preparatory steps\nare carried out. The message attribute of the record is computed\nusing LogRecord.getMessage(). If the formatting string uses the\ntime (as determined by a call to usesTime(), formatTime() is\ncalled to format the event time. If there is exception information,\nit is formatted using formatException() and appended to the message.

\n", "signature": "(self, record):", "funcdef": "def"}, "pydrex.logger.LOGGER": {"fullname": "pydrex.logger.LOGGER", "modulename": "pydrex.logger", "qualname": "LOGGER", "kind": "variable", "doc": "

\n", "default_value": "<Logger pydrex (DEBUG)>"}, "pydrex.logger.CONSOLE_LOGGER": {"fullname": "pydrex.logger.CONSOLE_LOGGER", "modulename": "pydrex.logger", "qualname": "CONSOLE_LOGGER", "kind": "variable", "doc": "

\n", "default_value": "<StreamHandler (INFO)>"}, "pydrex.logger.handle_exception": {"fullname": "pydrex.logger.handle_exception", "modulename": "pydrex.logger", "qualname": "handle_exception", "kind": "function", "doc": "

\n", "signature": "(exec_type, exec_value, exec_traceback):", "funcdef": "def"}, "pydrex.logger.handler_level": {"fullname": "pydrex.logger.handler_level", "modulename": "pydrex.logger", "qualname": "handler_level", "kind": "function", "doc": "

Set logging handler level for current context.

\n\n

Args:

\n\n\n", "signature": "(level, handler=<StreamHandler (INFO)>):", "funcdef": "def"}, "pydrex.logger.logfile_enable": {"fullname": "pydrex.logger.logfile_enable", "modulename": "pydrex.logger", "qualname": "logfile_enable", "kind": "function", "doc": "

Enable logging to a file at path with given level.

\n", "signature": "(path, level=10, mode='w'):", "funcdef": "def"}, "pydrex.logger.critical": {"fullname": "pydrex.logger.critical", "modulename": "pydrex.logger", "qualname": "critical", "kind": "function", "doc": "

Log a CRITICAL message in PyDRex.

\n", "signature": "(msg, *args, **kwargs):", "funcdef": "def"}, "pydrex.logger.error": {"fullname": "pydrex.logger.error", "modulename": "pydrex.logger", "qualname": "error", "kind": "function", "doc": "

Log an ERROR message in PyDRex.

\n", "signature": "(msg, *args, **kwargs):", "funcdef": "def"}, "pydrex.logger.warning": {"fullname": "pydrex.logger.warning", "modulename": "pydrex.logger", "qualname": "warning", "kind": "function", "doc": "

Log a WARNING message in PyDRex.

\n", "signature": "(msg, *args, **kwargs):", "funcdef": "def"}, "pydrex.logger.info": {"fullname": "pydrex.logger.info", "modulename": "pydrex.logger", "qualname": "info", "kind": "function", "doc": "

Log an INFO message in PyDRex.

\n", "signature": "(msg, *args, **kwargs):", "funcdef": "def"}, "pydrex.logger.debug": {"fullname": "pydrex.logger.debug", "modulename": "pydrex.logger", "qualname": "debug", "kind": "function", "doc": "

Log a DEBUG message in PyDRex.

\n", "signature": "(msg, *args, **kwargs):", "funcdef": "def"}, "pydrex.logger.exception": {"fullname": "pydrex.logger.exception", "modulename": "pydrex.logger", "qualname": "exception", "kind": "function", "doc": "

Log a message with level ERROR but retain exception information.

\n\n

This function should only be called from an exception handler.

\n", "signature": "(msg, *args, **kwargs):", "funcdef": "def"}, "pydrex.logger.quiet_aliens": {"fullname": "pydrex.logger.quiet_aliens", "modulename": "pydrex.logger", "qualname": "quiet_aliens", "kind": "function", "doc": "

Restrict alien loggers \ud83d\udc7d because I'm trying to find MY bugs, thanks.

\n", "signature": "():", "funcdef": "def"}, "pydrex.minerals": {"fullname": "pydrex.minerals", "modulename": "pydrex.minerals", "kind": "module", "doc": "
\n

PyDRex: Computations of mineral texture and elasticity.

\n
\n\n

Acronyms:

\n\n\n"}, "pydrex.minerals.OLIVINE_STIFFNESS": {"fullname": "pydrex.minerals.OLIVINE_STIFFNESS", "modulename": "pydrex.minerals", "qualname": "OLIVINE_STIFFNESS", "kind": "variable", "doc": "

Stiffness tensor for olivine (Voigt representation), with units of GPa.

\n\n

The source of the values used here is unknown, but they are copied\nfrom the original DRex code: http://www.ipgp.fr/~kaminski/web_doudoud/DRex.tar.gz\n[88K download]

\n", "default_value": "array([[320.71, 69.84, 71.22, 0. , 0. , 0. ],\n [ 69.84, 197.25, 74.8 , 0. , 0. , 0. ],\n [ 71.22, 74.8 , 234.32, 0. , 0. , 0. ],\n [ 0. , 0. , 0. , 63.77, 0. , 0. ],\n [ 0. , 0. , 0. , 0. , 77.67, 0. ],\n [ 0. , 0. , 0. , 0. , 0. , 78.36]])"}, "pydrex.minerals.ENSTATITE_STIFFNESS": {"fullname": "pydrex.minerals.ENSTATITE_STIFFNESS", "modulename": "pydrex.minerals", "qualname": "ENSTATITE_STIFFNESS", "kind": "variable", "doc": "

Stiffness tensor for enstatite (Voigt representation), with units of GPa.

\n\n

The source of the values used here is unknown, but they are copied\nfrom the original DRex code: http://www.ipgp.fr/~kaminski/web_doudoud/DRex.tar.gz\n[88K download]

\n", "default_value": "array([[236.9, 79.6, 63.2, 0. , 0. , 0. ],\n [ 79.6, 180.5, 56.8, 0. , 0. , 0. ],\n [ 63.2, 56.8, 230.4, 0. , 0. , 0. ],\n [ 0. , 0. , 0. , 84.3, 0. , 0. ],\n [ 0. , 0. , 0. , 0. , 79.4, 0. ],\n [ 0. , 0. , 0. , 0. , 0. , 80.1]])"}, "pydrex.minerals.OLIVINE_PRIMARY_AXIS": {"fullname": "pydrex.minerals.OLIVINE_PRIMARY_AXIS", "modulename": "pydrex.minerals", "qualname": "OLIVINE_PRIMARY_AXIS", "kind": "variable", "doc": "

Primary slip axis name for for the given olivine fabric.

\n", "default_value": "{<MineralFabric.olivine_A: 0>: 'a', <MineralFabric.olivine_B: 1>: 'c', <MineralFabric.olivine_C: 2>: 'c', <MineralFabric.olivine_D: 3>: 'a', <MineralFabric.olivine_E: 4>: 'a'}"}, "pydrex.minerals.OLIVINE_SLIP_SYSTEMS": {"fullname": "pydrex.minerals.OLIVINE_SLIP_SYSTEMS", "modulename": "pydrex.minerals", "qualname": "OLIVINE_SLIP_SYSTEMS", "kind": "variable", "doc": "

Slip systems for olivine in conventional order.

\n\n

Tuples contain the slip plane normal and slip direction vectors.\nThe order of slip systems returned matches the order of critical shear stresses\nreturned by pydrex.core.get_crss.

\n", "default_value": "(([0, 1, 0], [1, 0, 0]), ([0, 0, 1], [1, 0, 0]), ([0, 1, 0], [0, 0, 1]), ([1, 0, 0], [0, 0, 1]))"}, "pydrex.minerals.voigt_averages": {"fullname": "pydrex.minerals.voigt_averages", "modulename": "pydrex.minerals", "qualname": "voigt_averages", "kind": "function", "doc": "

Calculate elastic tensors as the Voigt averages of a collection of minerals.

\n\n

Args:

\n\n\n\n

Raises a ValueError if the minerals contain an unequal number of grains or stored\ntexture results.

\n", "signature": "(minerals, weights):", "funcdef": "def"}, "pydrex.minerals.Mineral": {"fullname": "pydrex.minerals.Mineral", "modulename": "pydrex.minerals", "qualname": "Mineral", "kind": "class", "doc": "

Class for storing polycrystal texture for a single mineral phase.

\n\n

A Mineral stores texture data for an aggregate of grains*.\nAdditionally, mineral fabric type and deformation regime are also tracked.\nTo provide an initial texture for the mineral, use the constructor arguments\nfractions_init and orientations_init. By default,\na uniform volume distribution of random orientations is generated.

\n\n

The update_orientations method computes new orientations and grain volumes\nfor a given velocity gradient. These results are stored in the .orientations and\n.fractions attributes of the Mineral instance. The method also returns the\nupdated macroscopic deformation gradient based on the provided initial deformation\ngradient.

\n\n

*Note that the \"number of grains\" is a static integer value that\ndoes not track the actual number of physical grains in the deforming polycrystal.\nInstead, this number acts as a \"number of bins\" for the statistical resolution of\nthe crystallographic orientation distribution. The value is roughly equivalent to\n(a multiple of) the number of initial, un-recrystallised grains in the polycrystal.\nIt is assumed that recrystallised grains do not grow large enough to require\nrotation tracking.

\n\n

Examples:

\n\n

Mineral with isotropic initial texture:

\n\n
\n
>>> import pydrex\n>>> olA = pydrex.Mineral(\n...     phase=pydrex.MineralPhase.olivine,\n...     fabric=pydrex.MineralFabric.olivine_A,\n...     regime=pydrex.DeformationRegime.dislocation,\n...     n_grains=2000\n... )\n>>> olA.phase\n<MineralPhase.olivine: 0>\n>>> olA.fabric\n<MineralFabric.olivine_A: 0>\n>>> olA.regime\n<DeformationRegime.dislocation: 1>\n>>> olA.n_grains\n2000\n
\n
\n\n

Mineral with specified initial texture and default phase, fabric and regime settings\nwhich are for an olivine A-type mineral in the dislocation creep regime.\nThe initial grain volume fractions should be normalised.

\n\n
\n
>>> import numpy as np\n>>> from scipy.spatial.transform import Rotation\n>>> import pydrex\n>>> rng = np.random.default_rng()\n>>> n_grains = 2000\n>>> olA = pydrex.Mineral(\n...     n_grains=n_grains,\n...     fractions_init=np.full(n_grains, 1 / n_grains),\n...     orientations_init=Rotation.from_euler(\n...         "zxz", [\n...             [x * np.pi / 2, np.pi / 2, np.pi / 2] for x in rng.random(n_grains)\n...         ]\n...     ).inv().as_matrix(),\n... )\n>>> len(olA.orientations)\n1\n>>> type(olA.orientations)\n<class 'list'>\n>>> olA.orientations[0].shape\n(2000, 3, 3)\n>>> olA.fractions[0].shape\n(2000,)\n
\n
\n\n

Note that minerals can also be constructed from serialized data,\nsee Mineral.load and Mineral.from_file.

\n\n

Attributes:

\n\n\n"}, "pydrex.minerals.Mineral.__init__": {"fullname": "pydrex.minerals.Mineral.__init__", "modulename": "pydrex.minerals", "qualname": "Mineral.__init__", "kind": "function", "doc": "

\n", "signature": "(\tphase: int = <MineralPhase.olivine: 0>,\tfabric: int = <MineralFabric.olivine_A: 0>,\tregime: int = <DeformationRegime.dislocation: 1>,\tn_grains: int = 3500,\tfractions_init: numpy.ndarray = None,\torientations_init: numpy.ndarray = None,\tfractions: list = <factory>,\torientations: list = <factory>,\tseed: int = None,\tlband: int = None,\tuband: int = None)"}, "pydrex.minerals.Mineral.phase": {"fullname": "pydrex.minerals.Mineral.phase", "modulename": "pydrex.minerals", "qualname": "Mineral.phase", "kind": "variable", "doc": "

\n", "annotation": ": int", "default_value": "<MineralPhase.olivine: 0>"}, "pydrex.minerals.Mineral.fabric": {"fullname": "pydrex.minerals.Mineral.fabric", "modulename": "pydrex.minerals", "qualname": "Mineral.fabric", "kind": "variable", "doc": "

\n", "annotation": ": int", "default_value": "<MineralFabric.olivine_A: 0>"}, "pydrex.minerals.Mineral.regime": {"fullname": "pydrex.minerals.Mineral.regime", "modulename": "pydrex.minerals", "qualname": "Mineral.regime", "kind": "variable", "doc": "

\n", "annotation": ": int", "default_value": "<DeformationRegime.dislocation: 1>"}, "pydrex.minerals.Mineral.n_grains": {"fullname": "pydrex.minerals.Mineral.n_grains", "modulename": "pydrex.minerals", "qualname": "Mineral.n_grains", "kind": "variable", "doc": "

\n", "annotation": ": int", "default_value": "3500"}, "pydrex.minerals.Mineral.fractions_init": {"fullname": "pydrex.minerals.Mineral.fractions_init", "modulename": "pydrex.minerals", "qualname": "Mineral.fractions_init", "kind": "variable", "doc": "

\n", "annotation": ": numpy.ndarray", "default_value": "None"}, "pydrex.minerals.Mineral.orientations_init": {"fullname": "pydrex.minerals.Mineral.orientations_init", "modulename": "pydrex.minerals", "qualname": "Mineral.orientations_init", "kind": "variable", "doc": "

\n", "annotation": ": numpy.ndarray", "default_value": "None"}, "pydrex.minerals.Mineral.fractions": {"fullname": "pydrex.minerals.Mineral.fractions", "modulename": "pydrex.minerals", "qualname": "Mineral.fractions", "kind": "variable", "doc": "

\n", "annotation": ": list"}, "pydrex.minerals.Mineral.orientations": {"fullname": "pydrex.minerals.Mineral.orientations", "modulename": "pydrex.minerals", "qualname": "Mineral.orientations", "kind": "variable", "doc": "

\n", "annotation": ": list"}, "pydrex.minerals.Mineral.seed": {"fullname": "pydrex.minerals.Mineral.seed", "modulename": "pydrex.minerals", "qualname": "Mineral.seed", "kind": "variable", "doc": "

\n", "annotation": ": int", "default_value": "None"}, "pydrex.minerals.Mineral.lband": {"fullname": "pydrex.minerals.Mineral.lband", "modulename": "pydrex.minerals", "qualname": "Mineral.lband", "kind": "variable", "doc": "

\n", "annotation": ": int", "default_value": "None"}, "pydrex.minerals.Mineral.uband": {"fullname": "pydrex.minerals.Mineral.uband", "modulename": "pydrex.minerals", "qualname": "Mineral.uband", "kind": "variable", "doc": "

\n", "annotation": ": int", "default_value": "None"}, "pydrex.minerals.Mineral.update_orientations": {"fullname": "pydrex.minerals.Mineral.update_orientations", "modulename": "pydrex.minerals", "qualname": "Mineral.update_orientations", "kind": "function", "doc": "

Update orientations and volume distribution for the Mineral.

\n\n

Update crystalline orientations and grain volume distribution\nfor minerals undergoing plastic deformation. Return the updated deformation\ngradient measuring the corresponding macroscopic deformation.

\n\n

Args:

\n\n\n\n

Any additional (optional) keyword arguments are passed to\nscipy.integrate.LSODA.

\n\n

Array values must provide a NumPy-compatible interface:\nhttps://numpy.org/doc/stable/user/whatisnumpy.html

\n\n

Examples:

\n\n
\n
>>> from itertools import pairwise\n>>> import pydrex\n>>> olA = pydrex.Mineral(\n...           phase=pydrex.MineralPhase.olivine,\n...           fabric=pydrex.MineralFabric.olivine_A,\n...           regime=pydrex.DeformationRegime.dislocation,\n...           n_grains=pydrex.DEFAULT_PARAMS["number_of_grains"],\n... )\n>>> def get_velocity_gradient(t, x):  # Simple L for simple shear.\n...     L = np.zeros((3, 3))\n...     L[0, 2] = 1\n...     return L\n>>> def get_position(t):\n...     return np.zeros(3)  # Stationary polycrystal for this example.\n>>> timestamps = range(2)  # Just 1 timestep for demonstration.\n>>> deformation_gradient = np.eye(3)  # Start with an undeformed polycrystal.\n>>> for t_start, t_end in pairwise(timestamps):\n...     # Update deformation_gradient, olA.orientations and olA.fractions.\n...     deformation_gradient = olA.update_orientations(\n...         pydrex.DEFAULT_PARAMS,\n...         deformation_gradient,\n...         get_velocity_gradient,\n...         (t_start, t_end, get_position),\n...     )\n>>> np.all(deformation_gradient == np.eye(3) + get_velocity_gradient(t_end, np.nan))\nTrue\n
\n
\n", "signature": "(\tself,\tconfig,\tdeformation_gradient,\tget_velocity_gradient,\tpathline,\t**kwargs):", "funcdef": "def"}, "pydrex.minerals.Mineral.save": {"fullname": "pydrex.minerals.Mineral.save", "modulename": "pydrex.minerals", "qualname": "Mineral.save", "kind": "function", "doc": "

Save CPO data for all stored timesteps to a numpy NPZ file.

\n\n

If postfix is not None, the data is appended to the NPZ file\nin fields ending with \"_postfix\".

\n\n

Raises a ValueError if the data shapes are not compatible.

\n\n

See also: numpy.savez, Mineral.load, Mineral.from_file.

\n", "signature": "(self, filename, postfix=None):", "funcdef": "def"}, "pydrex.minerals.Mineral.load": {"fullname": "pydrex.minerals.Mineral.load", "modulename": "pydrex.minerals", "qualname": "Mineral.load", "kind": "function", "doc": "

Load CPO data from a numpy NPZ file.

\n\n

If postfix is not None, data is read from fields ending with \"_postfix\".

\n\n

See also: Mineral.save, Mineral.from_file.

\n", "signature": "(self, filename, postfix=None):", "funcdef": "def"}, "pydrex.minerals.Mineral.from_file": {"fullname": "pydrex.minerals.Mineral.from_file", "modulename": "pydrex.minerals", "qualname": "Mineral.from_file", "kind": "function", "doc": "

Construct a Mineral instance using data from a numpy NPZ file.

\n\n

If postfix is not None, data is read from fields ending with \u201c_postfix\u201d.

\n\n

See also: Mineral.save, Mineral.load.

\n", "signature": "(cls, filename, postfix=None):", "funcdef": "def"}, "pydrex.mock": {"fullname": "pydrex.mock", "modulename": "pydrex.mock", "kind": "module", "doc": "
\n

PyDRex: Mock objects for testing and reproducibility.

\n
\n"}, "pydrex.mock.PARAMS_FRATERS2021": {"fullname": "pydrex.mock.PARAMS_FRATERS2021", "modulename": "pydrex.mock", "qualname": "PARAMS_FRATERS2021", "kind": "variable", "doc": "

Values used for tests 1, 2 and 4 in https://doi.org/10.1029/2021gc009846.

\n", "default_value": "{'olivine_fraction': 0.7, 'enstatite_fraction': 0.3, 'initial_olivine_fabric': <MineralFabric.olivine_A: 0>, 'stress_exponent': 1.5, 'deformation_exponent': 3.5, 'gbm_mobility': 125, 'gbs_threshold': 0.3, 'nucleation_efficiency': 5, 'number_of_grains': 5000}"}, "pydrex.mock.PARAMS_KAMINSKI2001_FIG5_SOLID": {"fullname": "pydrex.mock.PARAMS_KAMINSKI2001_FIG5_SOLID", "modulename": "pydrex.mock", "qualname": "PARAMS_KAMINSKI2001_FIG5_SOLID", "kind": "variable", "doc": "

Values used for the M*=0 test in https://doi.org/10.1016/s0012-821x(01)00356-9.

\n", "default_value": "{'olivine_fraction': 1, 'enstatite_fraction': 0, 'initial_olivine_fabric': <MineralFabric.olivine_A: 0>, 'stress_exponent': 1.5, 'deformation_exponent': 3.5, 'gbm_mobility': 0, 'gbs_threshold': 0, 'nucleation_efficiency': 5, 'number_of_grains': 3375}"}, "pydrex.mock.PARAMS_KAMINSKI2001_FIG5_SHORTDASH": {"fullname": "pydrex.mock.PARAMS_KAMINSKI2001_FIG5_SHORTDASH", "modulename": "pydrex.mock", "qualname": "PARAMS_KAMINSKI2001_FIG5_SHORTDASH", "kind": "variable", "doc": "

Values used for the M*=50 test in https://doi.org/10.1016/s0012-821x(01)00356-9.

\n", "default_value": "{'olivine_fraction': 1, 'enstatite_fraction': 0, 'initial_olivine_fabric': <MineralFabric.olivine_A: 0>, 'stress_exponent': 1.5, 'deformation_exponent': 3.5, 'gbm_mobility': 50, 'gbs_threshold': 0, 'nucleation_efficiency': 5, 'number_of_grains': 3375}"}, "pydrex.mock.PARAMS_KAMINSKI2001_FIG5_LONGDASH": {"fullname": "pydrex.mock.PARAMS_KAMINSKI2001_FIG5_LONGDASH", "modulename": "pydrex.mock", "qualname": "PARAMS_KAMINSKI2001_FIG5_LONGDASH", "kind": "variable", "doc": "

Values used for the M*=200 test in https://doi.org/10.1016/s0012-821x(01)00356-9.

\n", "default_value": "{'olivine_fraction': 1, 'enstatite_fraction': 0, 'initial_olivine_fabric': <MineralFabric.olivine_A: 0>, 'stress_exponent': 1.5, 'deformation_exponent': 3.5, 'gbm_mobility': 200, 'gbs_threshold': 0, 'nucleation_efficiency': 5, 'number_of_grains': 3375}"}, "pydrex.mock.PARAMS_KAMINSKI2004_FIG4_TRIANGLES": {"fullname": "pydrex.mock.PARAMS_KAMINSKI2004_FIG4_TRIANGLES", "modulename": "pydrex.mock", "qualname": "PARAMS_KAMINSKI2004_FIG4_TRIANGLES", "kind": "variable", "doc": "

Values used for the \u03c7=0.4 test in https://doi.org/10.1111/j.1365-246x.2004.02308.x.

\n", "default_value": "{'olivine_fraction': 1, 'enstatite_fraction': 0, 'initial_olivine_fabric': <MineralFabric.olivine_A: 0>, 'stress_exponent': 1.5, 'deformation_exponent': 3.5, 'gbm_mobility': 125, 'gbs_threshold': 0.4, 'nucleation_efficiency': 5, 'number_of_grains': 4394}"}, "pydrex.mock.PARAMS_KAMINSKI2004_FIG4_SQUARES": {"fullname": "pydrex.mock.PARAMS_KAMINSKI2004_FIG4_SQUARES", "modulename": "pydrex.mock", "qualname": "PARAMS_KAMINSKI2004_FIG4_SQUARES", "kind": "variable", "doc": "

Values used for the \u03c7=0.2 test in https://doi.org/10.1111/j.1365-246x.2004.02308.x.

\n", "default_value": "{'olivine_fraction': 1, 'enstatite_fraction': 0, 'initial_olivine_fabric': <MineralFabric.olivine_A: 0>, 'stress_exponent': 1.5, 'deformation_exponent': 3.5, 'gbm_mobility': 125, 'gbs_threshold': 0.2, 'nucleation_efficiency': 5, 'number_of_grains': 4394}"}, "pydrex.mock.PARAMS_KAMINSKI2004_FIG4_CIRCLES": {"fullname": "pydrex.mock.PARAMS_KAMINSKI2004_FIG4_CIRCLES", "modulename": "pydrex.mock", "qualname": "PARAMS_KAMINSKI2004_FIG4_CIRCLES", "kind": "variable", "doc": "

Values used for the \u03c7=0 test in https://doi.org/10.1111/j.1365-246x.2004.02308.x.

\n", "default_value": "{'olivine_fraction': 1, 'enstatite_fraction': 0, 'initial_olivine_fabric': <MineralFabric.olivine_A: 0>, 'stress_exponent': 1.5, 'deformation_exponent': 3.5, 'gbm_mobility': 125, 'gbs_threshold': 0, 'nucleation_efficiency': 5, 'number_of_grains': 4394}"}, "pydrex.mock.PARAMS_HEDJAZIAN2017": {"fullname": "pydrex.mock.PARAMS_HEDJAZIAN2017", "modulename": "pydrex.mock", "qualname": "PARAMS_HEDJAZIAN2017", "kind": "variable", "doc": "

Values used for the MOR model in https://doi.org/10.1016/j.epsl.2016.12.004.

\n", "default_value": "{'olivine_fraction': 0.7, 'enstatite_fraction': 0.3, 'initial_olivine_fabric': <MineralFabric.olivine_A: 0>, 'stress_exponent': 1.5, 'deformation_exponent': 3.5, 'gbm_mobility': 10, 'gbs_threshold': 0.2, 'nucleation_efficiency': 5, 'number_of_grains': 2197}"}, "pydrex.pathlines": {"fullname": "pydrex.pathlines", "modulename": "pydrex.pathlines", "kind": "module", "doc": "
\n

PyDRex: Functions for pathline construction.

\n
\n"}, "pydrex.pathlines.get_pathline": {"fullname": "pydrex.pathlines.get_pathline", "modulename": "pydrex.pathlines", "qualname": "get_pathline", "kind": "function", "doc": "

Determine the pathline for a particle in a steady state flow.

\n\n

The pathline will terminate at the given final_location and follow a curve\ndetermined by the velocity gradient. It works for both 2D (rectangular) and 3D\n(orthopiped\u00b9) domains, so long as the provided callables expect/return arrays of the\nappropriate dimension.

\n\n
\n\n

The pathline is calculated backwards in time (t < 0) from the given endpoint.\nTherefore, the returned position callable should be evaluated at negative times.

\n\n
\n\n

Args:

\n\n\n\n

Optional keyword arguments will be passed to scipy.integrate.solve_ivp. However,\nsome of the arguments to the solve_ivp call may not be modified, and a warning\nwill be raised if they are provided.

\n\n

Returns a tuple containing the time points and an interpolant that can be used\nto evaluate the pathline position (see scipy.integrate.OdeSolution).

\n\n

\u00b9An \u201corthopiped\u201d is a 3D rectangle (called a \u201cbox\u201d when we are in a hurry), see\nhttps://www.whatistoday.net/2020/04/cuboid-dilemma.html.

\n", "signature": "(\tfinal_location,\tget_velocity,\tget_velocity_gradient,\tmin_coords,\tmax_coords,\tmax_strain,\tregular_steps=None,\t**kwargs):", "funcdef": "def"}, "pydrex.stats": {"fullname": "pydrex.stats", "modulename": "pydrex.stats", "kind": "module", "doc": "
\n

PyDRex: Statistical methods for orientation and elasticity data.

\n
\n"}, "pydrex.stats.resample_orientations": {"fullname": "pydrex.stats.resample_orientations", "modulename": "pydrex.stats", "qualname": "resample_orientations", "kind": "function", "doc": "

Return new samples from orientations weighted by the volume distribution.

\n\n

Args:

\n\n\n\n

Returns the Nxn_samplesx3x3 orientations and associated sorted (ascending) grain\nvolumes.

\n", "signature": "(orientations, fractions, n_samples=None, seed=None):", "funcdef": "def"}, "pydrex.stats.misorientation_hist": {"fullname": "pydrex.stats.misorientation_hist", "modulename": "pydrex.stats", "qualname": "misorientation_hist", "kind": "function", "doc": "

Calculate misorientation histogram for polycrystal orientations.

\n\n

The bins argument is passed to numpy.histogram.\nIf left as None, 1\u00b0 bins will be used as recommended by the reference paper.\nThe symmetry argument specifies the lattice system which determines intrinsic\nsymmetry degeneracies and the maximum allowable misorientation angle.\nSee _geo.LatticeSystem for supported systems.

\n\n
\n\n

This method must be able to allocate $ \\frac{N!}{(N-2)!} \u00d7 4M $ floats\nfor N the length of orientations and M the number of symmetry operations for\nthe given system (numpy.float32 values are used to reduce the memory\nrequirements)

\n\n
\n\n

See Skemer et al. (2005).

\n", "signature": "(orientations, system: pydrex.geometry.LatticeSystem, bins=None):", "funcdef": "def"}, "pydrex.stats.misorientations_random": {"fullname": "pydrex.stats.misorientations_random", "modulename": "pydrex.stats", "qualname": "misorientations_random", "kind": "function", "doc": "

Get expected count of misorientation angles for an isotropic aggregate.

\n\n

Estimate the expected number of misorientation angles between grains\nthat would fall within $($low, high$)$ in degrees for an aggregate\nwith randomly oriented grains, where low $\u2208 [0, $high$)$,\nand high is bounded by the maximum theoretical misorientation angle\nfor the given lattice symmetry system.\nSee _geo.LatticeSystem for supported systems.

\n", "signature": "(low, high, system: pydrex.geometry.LatticeSystem):", "funcdef": "def"}, "pydrex.stats.point_density": {"fullname": "pydrex.stats.point_density", "modulename": "pydrex.stats", "qualname": "point_density", "kind": "function", "doc": "

Estimate point density of orientation data on the unit sphere.

\n\n

Estimates the density of orientations on the unit sphere by counting the input data\nthat falls within small areas around a uniform grid of spherical counting locations.\nThe input data is expected in cartesian coordinates, and the contouring is performed\nusing kernel functions defined in Vollmer 1995.\nThe following optional parameters control the contouring method:

\n\n\n\n

Any other keyword arguments are passed to the kernel function calls.\nMost kernels accept a parameter \u03c3 to control the degree of smoothing.

\n", "signature": "(\tx_data,\ty_data,\tz_data,\tgridsteps=101,\tweights=1,\tkernel='linear_inverse_kamb',\taxial=True,\t**kwargs):", "funcdef": "def"}, "pydrex.stats.exponential_kamb": {"fullname": "pydrex.stats.exponential_kamb", "modulename": "pydrex.stats", "qualname": "exponential_kamb", "kind": "function", "doc": "

Kernel function from Vollmer 1995 for exponential smoothing.

\n", "signature": "(cos_dist, \u03c3=10, axial=True):", "funcdef": "def"}, "pydrex.stats.linear_inverse_kamb": {"fullname": "pydrex.stats.linear_inverse_kamb", "modulename": "pydrex.stats", "qualname": "linear_inverse_kamb", "kind": "function", "doc": "

Kernel function from Vollmer 1995 for linear smoothing.

\n", "signature": "(cos_dist, \u03c3=10, axial=True):", "funcdef": "def"}, "pydrex.stats.square_inverse_kamb": {"fullname": "pydrex.stats.square_inverse_kamb", "modulename": "pydrex.stats", "qualname": "square_inverse_kamb", "kind": "function", "doc": "

Kernel function from Vollmer 1995 for inverse square smoothing.

\n", "signature": "(cos_dist, \u03c3=10, axial=True):", "funcdef": "def"}, "pydrex.stats.kamb_count": {"fullname": "pydrex.stats.kamb_count", "modulename": "pydrex.stats", "qualname": "kamb_count", "kind": "function", "doc": "

Original Kamb 1959 kernel function (raw count within radius).

\n", "signature": "(cos_dist, \u03c3=10, axial=True):", "funcdef": "def"}, "pydrex.stats.schmidt_count": {"fullname": "pydrex.stats.schmidt_count", "modulename": "pydrex.stats", "qualname": "schmidt_count", "kind": "function", "doc": "

Schmidt (a.k.a. 1%) counting kernel function.

\n", "signature": "(cos_dist, axial=None):", "funcdef": "def"}, "pydrex.stats.SPHERICAL_COUNTING_KERNELS": {"fullname": "pydrex.stats.SPHERICAL_COUNTING_KERNELS", "modulename": "pydrex.stats", "qualname": "SPHERICAL_COUNTING_KERNELS", "kind": "variable", "doc": "

Kernel functions that return an un-summed distribution and a normalization factor.

\n\n

Supported kernel functions are based on the discussion in\nVollmer 1995.\nKamb methods accept the parameter \u03c3 (default: 10) to control the degree of smoothing.\nValues lower than 3 and higher than 20 are not recommended.

\n", "default_value": "{'kamb_count': <function kamb_count>, 'schmidt_count': <function schmidt_count>, 'exponential_kamb': <function exponential_kamb>, 'linear_inverse_kamb': <function linear_inverse_kamb>, 'square_inverse_kamb': <function square_inverse_kamb>}"}, "pydrex.tensors": {"fullname": "pydrex.tensors", "modulename": "pydrex.tensors", "kind": "module", "doc": "
\n

PyDRex: Tensor operation functions and helpers.

\n
\n\n

For Voigt notation, the symmetric 6x6 matrix representation is used,\nwhich assumes that the fourth order tensor being represented as such is also symmetric.\nThe vectorial notation uses 21 components which are the independent components of the\nsymmetric 6x6 matrix.

\n"}, "pydrex.tensors.PERMUTATION_SYMBOL": {"fullname": "pydrex.tensors.PERMUTATION_SYMBOL", "modulename": "pydrex.tensors", "qualname": "PERMUTATION_SYMBOL", "kind": "variable", "doc": "

\n", "default_value": "array([[[ 0., 0., 0.],\n [ 0., 0., 1.],\n [ 0., -1., 0.]],\n\n [[ 0., 0., -1.],\n [ 0., 0., 0.],\n [ 1., 0., 0.]],\n\n [[ 0., 1., 0.],\n [-1., 0., 0.],\n [ 0., 0., 0.]]])"}, "pydrex.tensors.voigt_decompose": {"fullname": "pydrex.tensors.voigt_decompose", "modulename": "pydrex.tensors", "qualname": "voigt_decompose", "kind": "function", "doc": "

Decompose elastic tensor (as 6x6 Voigt matrix) into distinct contractions.

\n\n

Return the only two independent contractions of the elastic tensor given as a 6x6\nVoigt matrix. With reference to the full 4-th order elastic tensor, the\ncontractions are defined as:

\n\n\n\n

Any vector which is an eigenvector of both $d_{ij}$ and $v_{ij}$ is always normal to\na symmetry plane of the elastic medium.

\n\n

See Equations 3.4 & 3.5 in Browaeys & Chevrot (2004).

\n", "signature": "(matrix):", "funcdef": "def"}, "pydrex.tensors.mono_project": {"fullname": "pydrex.tensors.mono_project", "modulename": "pydrex.tensors", "qualname": "mono_project", "kind": "function", "doc": "

Project 21-component voigt_vector onto monoclinic symmetry subspace.

\n\n

Monoclinic symmetry is characterised by 13 independent elasticity components.

\n\n

See Browaeys & Chevrot (2004).

\n", "signature": "(voigt_vector):", "funcdef": "def"}, "pydrex.tensors.ortho_project": {"fullname": "pydrex.tensors.ortho_project", "modulename": "pydrex.tensors", "qualname": "ortho_project", "kind": "function", "doc": "

Project 21-component voigt_vector onto orthorhombic symmetry subspace.

\n\n

Orthorhombic symmetry is characterised by 9 independent elasticity components.

\n\n

See Browaeys & Chevrot (2004).

\n", "signature": "(voigt_vector):", "funcdef": "def"}, "pydrex.tensors.tetr_project": {"fullname": "pydrex.tensors.tetr_project", "modulename": "pydrex.tensors", "qualname": "tetr_project", "kind": "function", "doc": "

Project 21-component voigt_vector onto tetragonal symmetry subspace.

\n\n

Tetragonal symmetry is characterised by 6 independent elasticity components.

\n\n

See Browaeys & Chevrot (2004).

\n", "signature": "(voigt_vector):", "funcdef": "def"}, "pydrex.tensors.hex_project": {"fullname": "pydrex.tensors.hex_project", "modulename": "pydrex.tensors", "qualname": "hex_project", "kind": "function", "doc": "

Project 21-component voigt_vector onto hexagonal symmetry subspace.

\n\n

Hexagonal symmetry (a.k.a. transverse isotropy) is characterised by 5 independent\nelasticity components.

\n\n

See Browaeys & Chevrot (2004).

\n", "signature": "(voigt_vector):", "funcdef": "def"}, "pydrex.tensors.upper_tri_to_symmetric": {"fullname": "pydrex.tensors.upper_tri_to_symmetric", "modulename": "pydrex.tensors", "qualname": "upper_tri_to_symmetric", "kind": "function", "doc": "

Create symmetric array using upper triangle of input array.

\n\n

Examples:

\n\n
\n
>>> import numpy as np\n>>> upper_tri_to_symmetric(np.array([\n...         [ 1.,  2.,  3.,  4.],\n...         [ 0.,  5.,  6.,  7.],\n...         [ 0.,  0.,  8.,  9.],\n...         [ 9.,  0.,  0., 10.]\n... ]))\narray([[ 1.,  2.,  3.,  4.],\n       [ 2.,  5.,  6.,  7.],\n       [ 3.,  6.,  8.,  9.],\n       [ 4.,  7.,  9., 10.]])\n
\n
\n", "signature": "(arr):", "funcdef": "def"}, "pydrex.tensors.voigt_to_elastic_tensor": {"fullname": "pydrex.tensors.voigt_to_elastic_tensor", "modulename": "pydrex.tensors", "qualname": "voigt_to_elastic_tensor", "kind": "function", "doc": "

Create 4-th order elastic tensor from an equivalent Voigt matrix.

\n\n

See also: elastic_tensor_to_voigt.

\n", "signature": "(matrix):", "funcdef": "def"}, "pydrex.tensors.elastic_tensor_to_voigt": {"fullname": "pydrex.tensors.elastic_tensor_to_voigt", "modulename": "pydrex.tensors", "qualname": "elastic_tensor_to_voigt", "kind": "function", "doc": "

Create a 6x6 Voigt matrix from an equivalent 4-th order elastic tensor.

\n", "signature": "(tensor):", "funcdef": "def"}, "pydrex.tensors.voigt_matrix_to_vector": {"fullname": "pydrex.tensors.voigt_matrix_to_vector", "modulename": "pydrex.tensors", "qualname": "voigt_matrix_to_vector", "kind": "function", "doc": "

Create the 21-component Voigt vector equivalent to the 6x6 Voigt matrix.

\n", "signature": "(matrix):", "funcdef": "def"}, "pydrex.tensors.voigt_vector_to_matrix": {"fullname": "pydrex.tensors.voigt_vector_to_matrix", "modulename": "pydrex.tensors", "qualname": "voigt_vector_to_matrix", "kind": "function", "doc": "

Create the 6x6 matrix representation of the 21-component Voigt vector.

\n\n

See also: voigt_matrix_to_vector.

\n", "signature": "(vector):", "funcdef": "def"}, "pydrex.tensors.rotate": {"fullname": "pydrex.tensors.rotate", "modulename": "pydrex.tensors", "qualname": "rotate", "kind": "function", "doc": "

Rotate 4-th order tensor using a 3x3 rotation matrix.

\n", "signature": "(tensor, rotation):", "funcdef": "def"}, "pydrex.utils": {"fullname": "pydrex.utils", "modulename": "pydrex.utils", "kind": "module", "doc": "
\n

PyDRex: Miscellaneous utility methods.

\n
\n"}, "pydrex.utils.import_proc_pool": {"fullname": "pydrex.utils.import_proc_pool", "modulename": "pydrex.utils", "qualname": "import_proc_pool", "kind": "function", "doc": "

Import either ray.util.multiprocessing.Pool or multiprocessing.Pool.

\n\n

Import a process Pool object either from Ray of from Python's stdlib.\nBoth offer the same API, the Ray implementation will be preferred if available.\nUsing the Pool provided by Ray allows for distributed memory multiprocessing.

\n\n

Returns a tuple containing the Pool object and a boolean flag which is True if\nRay is available.

\n", "signature": "():", "funcdef": "def"}, "pydrex.utils.strain_increment": {"fullname": "pydrex.utils.strain_increment", "modulename": "pydrex.utils", "qualname": "strain_increment", "kind": "function", "doc": "

Calculate strain increment for a given time increment and velocity gradient.

\n\n

Returns \u201ctensorial\u201d strain increment \u03b5, which is equal to \u03b3/2 where \u03b3 is the\n\u201c(engineering) shear strain\u201d increment.

\n", "signature": "(dt, velocity_gradient):", "funcdef": "def"}, "pydrex.utils.apply_gbs": {"fullname": "pydrex.utils.apply_gbs", "modulename": "pydrex.utils", "qualname": "apply_gbs", "kind": "function", "doc": "

Apply grain boundary sliding for small grains.

\n", "signature": "(orientations, fractions, gbs_threshold, orientations_prev, n_grains):", "funcdef": "def"}, "pydrex.utils.extract_vars": {"fullname": "pydrex.utils.extract_vars", "modulename": "pydrex.utils", "qualname": "extract_vars", "kind": "function", "doc": "

Extract deformation gradient, orientation matrices and grain sizes from y.

\n", "signature": "(y, n_grains):", "funcdef": "def"}, "pydrex.utils.remove_nans": {"fullname": "pydrex.utils.remove_nans", "modulename": "pydrex.utils", "qualname": "remove_nans", "kind": "function", "doc": "

Remove NaN values from array.

\n", "signature": "(a):", "funcdef": "def"}, "pydrex.utils.remove_dim": {"fullname": "pydrex.utils.remove_dim", "modulename": "pydrex.utils", "qualname": "remove_dim", "kind": "function", "doc": "

Remove all values corresponding to dimension dim from an array.

\n\n

Note that a dim of 0 refers to the \u201cx\u201d values.

\n\n

Examples:

\n\n
\n
>>> a = [1, 2, 3]\n>>> remove_dim(a, 0)\narray([2, 3])\n>>> remove_dim(a, 1)\narray([1, 3])\n>>> remove_dim(a, 2)\narray([1, 2])\n
\n
\n\n
\n
>>> a = [[1, 2, 3], [4, 5, 6], [7, 8, 9]]\n>>> remove_dim(a, 0)\narray([[5, 6],\n       [8, 9]])\n>>> remove_dim(a, 1)\narray([[1, 3],\n       [7, 9]])\n>>> remove_dim(a, 2)\narray([[1, 2],\n       [4, 5]])\n
\n
\n", "signature": "(a, dim):", "funcdef": "def"}, "pydrex.utils.add_dim": {"fullname": "pydrex.utils.add_dim", "modulename": "pydrex.utils", "qualname": "add_dim", "kind": "function", "doc": "

Add entries of val corresponding to dimension dim to an array.

\n\n

Note that a dim of 0 refers to the \u201cx\u201d values.

\n\n

Examples:

\n\n
\n
>>> a = [1, 2]\n>>> add_dim(a, 0)\narray([0, 1, 2])\n>>> add_dim(a, 1)\narray([1, 0, 2])\n>>> add_dim(a, 2)\narray([1, 2, 0])\n
\n
\n\n
\n
>>> add_dim([1.0, 2.0], 2)\narray([1., 2., 0.])\n
\n
\n\n
\n
>>> a = [[1, 2], [3, 4]]\n>>> add_dim(a, 0)\narray([[0, 0, 0],\n       [0, 1, 2],\n       [0, 3, 4]])\n>>> add_dim(a, 1)\narray([[1, 0, 2],\n       [0, 0, 0],\n       [3, 0, 4]])\n>>> add_dim(a, 2)\narray([[1, 2, 0],\n       [3, 4, 0],\n       [0, 0, 0]])\n
\n
\n", "signature": "(a, dim, val=0):", "funcdef": "def"}, "pydrex.utils.default_ncpus": {"fullname": "pydrex.utils.default_ncpus", "modulename": "pydrex.utils", "qualname": "default_ncpus", "kind": "function", "doc": "

Get a safe default number of CPUs available for multiprocessing.

\n\n

On Linux platforms that support it, the method os.sched_getaffinity() is used.\nOn Mac OS, the command sysctl -n hw.ncpu is used.\nOn Windows, the environment variable NUMBER_OF_PROCESSORS is queried.\nIf any of these fail, a fallback of 1 is used and a warning is logged.

\n", "signature": "():", "funcdef": "def"}, "pydrex.utils.diff_like": {"fullname": "pydrex.utils.diff_like", "modulename": "pydrex.utils", "qualname": "diff_like", "kind": "function", "doc": "

Get forward difference of 2D array a, with repeated last elements.

\n\n

The repeated last elements ensure that output and input arrays have equal shape.

\n\n

Examples:

\n\n
\n
>>> diff_like(np.array([1, 2, 3, 4, 5]))\narray([[1, 1, 1, 1, 1]])\n
\n
\n\n
\n
>>> diff_like(np.array([[1, 2, 3, 4, 5], [1, 3, 6, 9, 10]]))\narray([[1, 1, 1, 1, 1],\n       [2, 3, 3, 1, 1]])\n
\n
\n\n
\n
>>> diff_like(np.array([[1, 2, 3, 4, 5], [1, 3, 6, 9, 10], [1, 0, 0, 0, np.inf]]))\narray([[ 1.,  1.,  1.,  1.,  1.],\n       [ 2.,  3.,  3.,  1.,  1.],\n       [-1.,  0.,  0., inf, nan]])\n
\n
\n", "signature": "(a):", "funcdef": "def"}, "pydrex.utils.angle_fse_simpleshear": {"fullname": "pydrex.utils.angle_fse_simpleshear", "modulename": "pydrex.utils", "qualname": "angle_fse_simpleshear", "kind": "function", "doc": "

Get angle of FSE long axis anticlockwise from the X axis in simple shear.

\n", "signature": "(strain):", "funcdef": "def"}, "pydrex.utils.lag_2d_corner_flow": {"fullname": "pydrex.utils.lag_2d_corner_flow", "modulename": "pydrex.utils", "qualname": "lag_2d_corner_flow", "kind": "function", "doc": "

Get predicted grain orientation lag for 2D corner flow.

\n\n

See eq. 11 in Kaminski & Ribe (2002).

\n", "signature": "(\u03b8):", "funcdef": "def"}, "pydrex.utils.quat_product": {"fullname": "pydrex.utils.quat_product", "modulename": "pydrex.utils", "qualname": "quat_product", "kind": "function", "doc": "

Quaternion product, q1, q2 and output are in scalar-last (x,y,z,w) format.

\n", "signature": "(q1, q2):", "funcdef": "def"}, "pydrex.utils.redraw_legend": {"fullname": "pydrex.utils.redraw_legend", "modulename": "pydrex.utils", "qualname": "redraw_legend", "kind": "function", "doc": "

Redraw legend on matplotlib axis or figure.

\n\n

Transparency is removed from legend symbols.\nIf fig is not None and remove_all is True,\nall legends are first removed from the parent figure.\nOptional keyword arguments are passed to matplotlib.axes.Axes.legend by default,\nor matplotlib.figure.Figure.legend if fig is not None.

\n\n

If legendax is not None, the axis legend will be redrawn using the legendax axes\ninstead of taking up space in the original axes. This option requires fig=None.

\n\n
\n\n

Note that if fig is not None, the legend may be cropped from the saved\nfigure due to a Matplotlib bug. In this case, it is required to add the\narguments bbox_extra_artists=(legend,) and bbox_inches=\"tight\" to savefig,\nwhere legend is the object returned by this function. To prevent the legend\nfrom consuming axes/subplot space, it is further required to add the lines:\nlegend.set_in_layout(False), fig.canvas.draw(), legend.set_layout(True)\nand fig.set_layout_engine(\"none\") before saving the figure.

\n\n
\n", "signature": "(ax, fig=None, legendax=None, remove_all=True, **kwargs):", "funcdef": "def"}, "pydrex.utils.add_subplot_labels": {"fullname": "pydrex.utils.add_subplot_labels", "modulename": "pydrex.utils", "qualname": "add_subplot_labels", "kind": "function", "doc": "

Add subplot labels to axes mosaic.

\n\n

Use labelmap to specify a dictionary that maps keys in mosaic to subplot labels.\nIf labelmap is None, the keys in axs will be used as the labels by default.

\n\n

If internal is False (default), the axes titles will be used.\nOtherwise, internal labels will be drawn with ax.text,\nin which case loc must be a tuple of floats.

\n\n

Any axes in axs corresponding to the special key legend are skipped.

\n", "signature": "(\tmosaic,\tlabelmap=None,\tloc='left',\tfontsize='medium',\tinternal=False,\t**kwargs):", "funcdef": "def"}, "pydrex.velocity": {"fullname": "pydrex.velocity", "modulename": "pydrex.velocity", "kind": "module", "doc": "
\n

PyDRex: Steady-state solutions of velocity (gradients) for various flows.

\n
\n\n

For the sake of consistency, all callables returned from methods in this module expect a\ntime scalar and 3D position vector as inputs. They also return 3D tensors in all cases.\nThis means they can be directly used as arguments to e.g.\npydrex.minerals.Mineral.update_orientations.

\n"}, "pydrex.velocity.simple_shear_2d": {"fullname": "pydrex.velocity.simple_shear_2d", "modulename": "pydrex.velocity", "qualname": "simple_shear_2d", "kind": "function", "doc": "

Return simple shear velocity and velocity gradient callables.

\n\n

The returned callables have signature f(t, x) where x is a 3D position vector.

\n\n

Args:

\n\n\n\n
\n\n

Input arrays to the returned callables must have homogeneous element types.\nArrays with e.g. both floating point and integer values are not supported.

\n\n
\n\n

Examples:

\n\n
\n
>>> import numpy as np\n>>> u, L = simple_shear_2d("X", "Z", 1e-4)\n>>> u(np.nan, np.array([0, 0, 0]))  # Time is not used here.\narray([0., 0., 0.])\n>>> u(np.nan, np.array([0, 0, 1]))\narray([0.0001, 0.    , 0.    ])\n>>> u(np.nan, np.array([0.0, 0.0, 2.0]))\narray([0.0002, 0.    , 0.    ])\n>>> L(np.nan, np.array([0, 0, 0]))\narray([[0.    , 0.    , 0.0002],\n       [0.    , 0.    , 0.    ],\n       [0.    , 0.    , 0.    ]])\n>>> L(np.nan, np.array([0.0, 0.0, 1.0]))\narray([[0.    , 0.    , 0.0002],\n       [0.    , 0.    , 0.    ],\n       [0.    , 0.    , 0.    ]])\n
\n
\n", "signature": "(direction, deformation_plane, strain_rate):", "funcdef": "def"}, "pydrex.velocity.cell_2d": {"fullname": "pydrex.velocity.cell_2d", "modulename": "pydrex.velocity", "qualname": "cell_2d", "kind": "function", "doc": "

Get velocity and velocity gradient callables for a steady-state 2D Stokes cell.

\n\n

The cell is centered at (0,0) and the velocity field is defined by:\n$$\n\\bm{u} = U\\cos(\u03c0 x/d)\\sin(\u03c0 z/d) \\bm{\\hat{h}} - U\\sin(\u03c0 x/d)\\cos(\u03c0 z/d) \\bm{\\hat{v}}\n$$\nwhere $\\bm{\\hat{h}}$ and $\\bm{\\hat{v}}$ are unit vectors in the chosen horizontal\nand vertical directions, respectively. The velocity at the cell edge has a magnitude\nof $U$ and $d$ is the length of a cell edge.

\n\n

The returned callables have signature f(t, x) where x is a 3D position vector.

\n\n

Args:

\n\n\n\n

Examples:

\n\n
\n
>>> import numpy as np\n>>> u, L = cell_2d("X", "Z", 1)\n>>> u(np.nan, np.array([0, 0, 0]))  # Time value is not used for steady flows.\narray([ 0.,  0., -0.])\n>>> u(np.nan, np.array([0, 0, 1]))\narray([ 1.,  0., -0.])\n>>> u(np.nan, np.array([0, 1, 0]))  # Y-value is not used.\narray([ 0.,  0., -0.])\n>>> u(np.nan, np.array([0, 0, -1]))\narray([-1.,  0., -0.])\n>>> u(np.nan, np.array([1, 0, 0]))\narray([ 0.,  0., -1.])\n>>> u(np.nan, np.array([-0.5, 0.0, 0.0]))\narray([0.        , 0.        , 0.70710678])\n>>> L(np.nan, np.array([0, 0, 0]))\narray([[-0.        ,  0.        ,  1.57079633],\n       [ 0.        ,  0.        ,  0.        ],\n       [ 0.        ,  0.        , -1.57079633]])\n>>> L(np.nan, np.array([0.5, 0.0, 0.0]))\narray([[-0.        ,  0.        ,  1.11072073],\n       [ 0.        ,  0.        ,  0.        ],\n       [ 0.        ,  0.        , -1.11072073]])\n>>> L(np.nan, np.array([0, 0, 0])) == L(np.nan, np.array([0, 1, 0]))  # Y-value is not used.\narray([[ True,  True,  True],\n       [ True,  True,  True],\n       [ True,  True,  True]])\n>>> L(np.nan, np.array([1, 0, 0])) == L(np.nan, np.array([0, 0, 1]))\narray([[ True,  True,  True],\n       [ True,  True,  True],\n       [ True,  True,  True]])\n>>> L(np.nan, np.array([1, 0, 0])) == L(np.nan, np.array([-1, 0, 0]))\narray([[ True,  True,  True],\n       [ True,  True,  True],\n       [ True,  True,  True]])\n>>> L(np.nan, np.array([1, 0, 0])) == L(np.nan, np.array([0, 0, -1]))\narray([[ True,  True,  True],\n       [ True,  True,  True],\n       [ True,  True,  True]])\n>>> L(np.nan, np.array([0.5, 0.0, 0.5]))\narray([[-0.78539816,  0.        ,  0.78539816],\n       [ 0.        ,  0.        ,  0.        ],\n       [ 0.78539816,  0.        , -0.78539816]])\n
\n
\n\n
\n
>>> u, L = cell_2d("X", "Z", 6.3e-10, 1e5)\n>>> u(np.nan, np.array([0, 0, 0]))\narray([ 0.,  0., -0.])\n>>> u(np.nan, np.array([0.0, 0.0, -5e4]))\narray([-6.3e-10,  0.0e+00, -0.0e+00])\n>>> u(np.nan, np.array([2e2, 0e0, 0e0]))\narray([ 0.0000000e+00,  0.0000000e+00, -3.9583807e-12])\n
\n
\n", "signature": "(horizontal, vertical, velocity_edge, edge_length=2):", "funcdef": "def"}, "pydrex.velocity.corner_2d": {"fullname": "pydrex.velocity.corner_2d", "modulename": "pydrex.velocity", "qualname": "corner_2d", "kind": "function", "doc": "

Get velocity and velocity gradient callables for a steady-state 2D corner flow.

\n\n

The velocity field is defined by:\n$$\n\\bm{u} = \\frac{dr}{dt} \\bm{\\hat{r}} + r \\frac{d\u03b8}{dt} \\bm{\\hat{\u03b8}}\n= \\frac{2 U}{\u03c0}(\u03b8\\sin\u03b8 - \\cos\u03b8) \u22c5 \\bm{\\hat{r}} + \\frac{2 U}{\u03c0}\u03b8\\cos\u03b8 \u22c5 \\bm{\\hat{\u03b8}}\n$$\nwhere $\u03b8 = 0$ points vertically downwards along the ridge axis\nand $\u03b8 = \u03c0/2$ points along the surface. $U$ is the half spreading velocity.\nStreamlines for the flow obey:\n$$\n\u03c8 = \\frac{2 U r}{\u03c0}\u03b8\\cos\u03b8\n$$\nand are related to the velocity through:\n$$\n\\bm{u} = -\\frac{1}{r} \u22c5 \\frac{d\u03c8}{d\u03b8} \u22c5 \\bm{\\hat{r}} + \\frac{d\u03c8}{dr}\\bm{\\hat{\u03b8}}\n$$\nConversion to Cartesian ($x,y,z$) coordinates yields:\n$$\n\\bm{u} = \\frac{2U}{\u03c0} \\left[\n\\tan^{-1}\\left(\\frac{x}{-z}\\right) + \\frac{xz}{x^{2} + z^{2}} \\right] \\bm{\\hat{x}} +\n\\frac{2U}{\u03c0} \\frac{z^{2}}{x^{2} + z^{2}} \\bm{\\hat{z}}\n$$\nwhere\n\\begin{align*}\nx &= r \\sin\u03b8 \\cr\nz &= -r \\cos\u03b8\n\\end{align*}\nand the velocity gradient is:\n$$\nL = \\frac{4 U}{\u03c0{(x^{2}+z^{2})}^{2}} \u22c5\n\\begin{bmatrix}\n -x^{2}z & 0 & x^{3} \\cr\n 0 & 0 & 0 \\cr\n -xz^{2} & 0 & x^{2}z\n\\end{bmatrix}\n$$\nSee also Fig. 5 in Kaminski & Ribe, 2002.

\n\n

The returned callables have signature f(t, x) where x is a 3D position vector.

\n\n

Args:

\n\n\n", "signature": "(horizontal, vertical, plate_speed):", "funcdef": "def"}, "pydrex.visualisation": {"fullname": "pydrex.visualisation", "modulename": "pydrex.visualisation", "kind": "module", "doc": "
\n

PyDRex: Visualisation functions for test outputs and examples.

\n
\n"}, "pydrex.visualisation.polefigures": {"fullname": "pydrex.visualisation.polefigures", "modulename": "pydrex.visualisation", "qualname": "polefigures", "kind": "function", "doc": "

Plot pole figures of a series of (Nx3x3) orientation matrix stacks.

\n\n

Produces [100], [010] and [001] pole figures for (resampled) orientations.\nFor the argument specification, check the output of pydrex-polefigures --help\non the command line.

\n", "signature": "(\torientations,\tref_axes,\ti_range,\tdensity=False,\tsavefile='polefigures.png',\tstrains=None,\t**kwargs):", "funcdef": "def"}, "pydrex.visualisation.pathline_box2d": {"fullname": "pydrex.visualisation.pathline_box2d", "modulename": "pydrex.visualisation", "qualname": "pathline_box2d", "kind": "function", "doc": "

Plot pathlines and velocity arrows for a 2D box domain.

\n\n

If ax is None, a new figure and axes are created with figure_unless.

\n\n

Args:

\n\n\n\n

Additional keyword arguments are passed to the matplotlib.axes.Axes.quiver call\nused to plot the velocity vectors.

\n\n

Returns the figure handle, the axes handle, the quiver collection (velocities) and\nthe scatter collection (pathline).

\n", "signature": "(\tax,\tget_velocity,\tref_axes,\tcolors,\tpositions,\tmarker,\tmin_coords,\tmax_coords,\tresolution,\taspect='equal',\tcmap=<matplotlib.colors.ListedColormap object>,\tcpo_vectors=None,\tcpo_strengths=None,\ttick_formatter=<function <lambda>>,\t**kwargs):", "funcdef": "def"}, "pydrex.visualisation.alignment": {"fullname": "pydrex.visualisation.alignment", "modulename": "pydrex.visualisation", "qualname": "alignment", "kind": "function", "doc": "

Plot angles (in degrees) versus strains on the given axis.

\n\n

Alignment angles could be either bingham averages or the a-axis in the hexagonal\nsymmetry projection, measured from e.g. the shear direction. In the first case,\nthey should be calculated from resampled grain orientations. Expects as many\nmarkers and labels as there are data series in angles.

\n\n

If ax is None, a new figure and axes are created with figure_unless.

\n\n

Args:

\n\n\n\n

If colors and cmaps are used, then angle values are colored individually within\neach angle series.

\n\n

Additional keyword arguments are passed to matplotlib.axes.Axes.scatter if\ncolors is not None, or to matplotlib.axes.Axes.plot otherwise.

\n\n

Returns a tuple of the figure handle, the axes handle and the set of colors used for\nthe data series plots.

\n", "signature": "(\tax,\tstrains,\tangles,\tmarkers,\tlabels,\terr=None,\t\u03b8_max=90,\t\u03b8_fse=None,\tcolors=None,\tcmaps=None,\t**kwargs):", "funcdef": "def"}, "pydrex.visualisation.strengths": {"fullname": "pydrex.visualisation.strengths", "modulename": "pydrex.visualisation", "qualname": "strengths", "kind": "function", "doc": "

Plot CPO strengths (e.g. M-indices) versus strains on the given axis.

\n\n

If ax is None, a new figure and axes are created with figure_unless.

\n\n

Args:

\n\n\n\n

If colors and cmaps are used, then strength values are colored individually\nwithin each strength series.

\n\n

Additional keyword arguments are passed to matplotlib.axes.Axes.scatter if\ncolors is not None, or to matplotlib.axes.Axes.plot otherwise.

\n\n

Returns a tuple of the figure handle, the axes handle and the set of colors used for\nthe data series plots.

\n", "signature": "(\tax,\tstrains,\tstrengths,\tylabel,\tmarkers,\tlabels,\terr=None,\tcpo_threshold=None,\tcolors=None,\tcmaps=None,\t**kwargs):", "funcdef": "def"}, "pydrex.visualisation.grainsizes": {"fullname": "pydrex.visualisation.grainsizes", "modulename": "pydrex.visualisation", "qualname": "grainsizes", "kind": "function", "doc": "

Plot grain volume fractions versus strains on the given axis.

\n\n

If ax is None, a new figure and axes are created with figure_unless.

\n", "signature": "(ax, strains, fractions):", "funcdef": "def"}, "pydrex.visualisation.show_Skemer2016_ShearStrainAngles": {"fullname": "pydrex.visualisation.show_Skemer2016_ShearStrainAngles", "modulename": "pydrex.visualisation", "qualname": "show_Skemer2016_ShearStrainAngles", "kind": "function", "doc": "

Show data from src/pydrex/data/thirdparty/Skemer2016_ShearStrainAngles.scsv.

\n\n

Plot data from the Skemer 2016 datafile on the axis given by ax. Select the\nstudies from which to plot the data, which must be a list of strings with exact\nmatches in the study column in the datafile.\nAlso filter the data to select only the given fabric\n(see pydrex.core.MineralFabric).

\n\n

If ax is None, a new figure and axes are created with figure_unless.

\n\n

Returns a tuple containing:

\n\n\n", "signature": "(ax, studies, markers, colors, fillstyles, labels, fabric):", "funcdef": "def"}, "pydrex.visualisation.spin": {"fullname": "pydrex.visualisation.spin", "modulename": "pydrex.visualisation", "qualname": "spin", "kind": "function", "doc": "

Plot rotation rates of grains with known, unique initial [100] angles from X.

\n\n

If ax is None, a new figure and axes are created with figure_unless.\nThe default labels (\"target\", \"computed\") can also be overriden.\nIf shear_axis is not None, a dashed line will be drawn at the given x-value\n(and its reflection around 180\u00b0).

\n\n

Returns a tuple of the figure handle, the axes handle and the set of colors used for\nthe data series plots.

\n", "signature": "(\tax,\tinitial_angles,\trotation_rates,\ttarget_initial_angles=None,\ttarget_rotation_rates=None,\tlabels=('target', 'computed'),\tshear_axis=None):", "funcdef": "def"}, "pydrex.visualisation.growth": {"fullname": "pydrex.visualisation.growth", "modulename": "pydrex.visualisation", "qualname": "growth", "kind": "function", "doc": "

Plot grain growth of grains with known, unique initial [100] angles from X.

\n\n

If ax is None, a new figure and axes are created with figure_unless.\nThe default labels (\"target\", \"computed\") can also be overriden.\nIf shear_axis is not None, a dashed line will be drawn at the given x-value\n(and its reflection around 180\u00b0).

\n\n

Returns a tuple of the figure handle, the axes handle and the set of colors used for\nthe data series plots.

\n", "signature": "(\tax,\tinitial_angles,\tfractions_diff,\ttarget_initial_angles=None,\ttarget_fractions_diff=None,\tlabels=('target', 'computed'),\tshear_axis=None):", "funcdef": "def"}, "pydrex.visualisation.figure_unless": {"fullname": "pydrex.visualisation.figure_unless", "modulename": "pydrex.visualisation", "qualname": "figure_unless", "kind": "function", "doc": "

Create figure and axes if ax is None, or return existing figure for ax.

\n\n

If ax is None, a new figure is created for the axes with a few opinionated default\nsettings (grid, constrained layout, high DPI).

\n\n

Returns a tuple containing the figure handle and the axes object.

\n", "signature": "(ax):", "funcdef": "def"}, "pydrex.visualisation.figure": {"fullname": "pydrex.visualisation.figure", "modulename": "pydrex.visualisation", "qualname": "figure", "kind": "function", "doc": "

Create new figure with a few opinionated default settings.

\n\n

(e.g. grid, constrained layout, high DPI).

\n\n

The keyword argument figscale can be used to scale the figure width and height\nrelative to the default values by passing a tuple. Any additional keyword arguments\nare passed to matplotlib.pyplot.figure().

\n", "signature": "(figscale=None, **kwargs):", "funcdef": "def"}, "tests": {"fullname": "tests", "modulename": "tests", "kind": "module", "doc": "

PyDRex tests

\n\n

Running the tests requires pytest.\nFrom the root of the source tree, run pytest.\nTo print more verbose information (including INFO level logging),\nsuch as detailed test progress, use the flag pytest -v.\nThe custom optional flag --outdir=\"OUT\" is recommended\nto produce output figures, data dumps and logs and save them in the directory \"OUT\".\nThe value \".\" can be used to save these in the current directory.

\n\n

Running individual tests or test subsets is possible using the pytest\n-k=\"<pattern>\" command line flag, which accepts a string pattern that is\nmatched against the names of test classes or methods.\nTo see a full list of available tests, use the command pytest --co. This\nproduces a rather long list and it is recommended to view the output with a\npager like less on Linux.

\n\n

In total, the following custom pytest command line flags are defined by PyDRex:

\n\n\n\n

Tests which require a \u201csignificant\u201d amount of memory (> ~16GB RAM) are disabled by default.\nTo fully check the functionality of the code, it is recommended to run these locally\nby using the --runbig flag before moving to larger simulations.

\n\n

Long tests/examples are also disabled by default and can be enabled with --runslow.\nIt is recommended to run these on a HPC cluster infrastructure (>100GB RAM, >32 cores).\nThe number of cores to use for shared memory multiprocessing can be specified with --ncpus.

\n\n

Writing tests

\n\n

For quick sanity checks and inline unit tests, use python doctests.\nThese will also appear as inline examples in the generated documentation.\nMore comprehensive unit tests and larger integration tests should be organised\ninto submodules of the test module.

\n\n\n\n

Tests should not produce persistent output by default.\nIf a test method can produce such output for debugging or visualisation,\nit should accept the outdir positional argument,\nand check if its value is not None.\nIf outdir is None then no persistent output should be produced.\nIf outdir is a directory path (string):

\n\n\n"}, "tests.conftest": {"fullname": "tests.conftest", "modulename": "tests.conftest", "kind": "module", "doc": "
\n

Configuration and fixtures for PyDRex tests.

\n
\n"}, "tests.conftest.pytest_addoption": {"fullname": "tests.conftest.pytest_addoption", "modulename": "tests.conftest", "qualname": "pytest_addoption", "kind": "function", "doc": "

\n", "signature": "(parser):", "funcdef": "def"}, "tests.conftest.PytestConsoleLogger": {"fullname": "tests.conftest.PytestConsoleLogger", "modulename": "tests.conftest", "qualname": "PytestConsoleLogger", "kind": "class", "doc": "

Pytest plugin that allows linking up a custom console logger.

\n", "bases": "_pytest.logging.LoggingPlugin"}, "tests.conftest.PytestConsoleLogger.__init__": {"fullname": "tests.conftest.PytestConsoleLogger.__init__", "modulename": "tests.conftest", "qualname": "PytestConsoleLogger.__init__", "kind": "function", "doc": "

Create a new plugin to capture log messages.

\n\n

The formatter can be safely shared across all handlers so\ncreate a single one for the entire test session here.

\n", "signature": "(config, *args, **kwargs)"}, "tests.conftest.PytestConsoleLogger.name": {"fullname": "tests.conftest.PytestConsoleLogger.name", "modulename": "tests.conftest", "qualname": "PytestConsoleLogger.name", "kind": "variable", "doc": "

\n", "default_value": "'pytest-console-logger'"}, "tests.conftest.PytestConsoleLogger.log_cli_handler": {"fullname": "tests.conftest.PytestConsoleLogger.log_cli_handler", "modulename": "tests.conftest", "qualname": "PytestConsoleLogger.log_cli_handler", "kind": "variable", "doc": "

\n"}, "tests.conftest.PytestConsoleLogger.pytest_runtest_teardown": {"fullname": "tests.conftest.PytestConsoleLogger.pytest_runtest_teardown", "modulename": "tests.conftest", "qualname": "PytestConsoleLogger.pytest_runtest_teardown", "kind": "function", "doc": "

\n", "signature": "(self, item):", "funcdef": "def"}, "tests.conftest.pytest_configure": {"fullname": "tests.conftest.pytest_configure", "modulename": "tests.conftest", "qualname": "pytest_configure", "kind": "function", "doc": "

\n", "signature": "(config):", "funcdef": "def"}, "tests.conftest.pytest_collection_modifyitems": {"fullname": "tests.conftest.pytest_collection_modifyitems", "modulename": "tests.conftest", "qualname": "pytest_collection_modifyitems", "kind": "function", "doc": "

\n", "signature": "(config, items):", "funcdef": "def"}, "tests.conftest.outdir": {"fullname": "tests.conftest.outdir", "modulename": "tests.conftest", "qualname": "outdir", "kind": "function", "doc": "

\n", "signature": "(request):", "funcdef": "def"}, "tests.conftest.ncpus": {"fullname": "tests.conftest.ncpus", "modulename": "tests.conftest", "qualname": "ncpus", "kind": "function", "doc": "

\n", "signature": "(request):", "funcdef": "def"}, "tests.conftest.named_tempfile_kwargs": {"fullname": "tests.conftest.named_tempfile_kwargs", "modulename": "tests.conftest", "qualname": "named_tempfile_kwargs", "kind": "function", "doc": "

\n", "signature": "(request):", "funcdef": "def"}, "tests.conftest.ray_session": {"fullname": "tests.conftest.ray_session", "modulename": "tests.conftest", "qualname": "ray_session", "kind": "function", "doc": "

\n", "signature": "():", "funcdef": "def"}, "tests.conftest.console_handler": {"fullname": "tests.conftest.console_handler", "modulename": "tests.conftest", "qualname": "console_handler", "kind": "function", "doc": "

\n", "signature": "(request):", "funcdef": "def"}, "tests.conftest.params_Fraters2021": {"fullname": "tests.conftest.params_Fraters2021", "modulename": "tests.conftest", "qualname": "params_Fraters2021", "kind": "function", "doc": "

\n", "signature": "():", "funcdef": "def"}, "tests.conftest.params_Kaminski2001_fig5_solid": {"fullname": "tests.conftest.params_Kaminski2001_fig5_solid", "modulename": "tests.conftest", "qualname": "params_Kaminski2001_fig5_solid", "kind": "function", "doc": "

\n", "signature": "():", "funcdef": "def"}, "tests.conftest.params_Kaminski2001_fig5_shortdash": {"fullname": "tests.conftest.params_Kaminski2001_fig5_shortdash", "modulename": "tests.conftest", "qualname": "params_Kaminski2001_fig5_shortdash", "kind": "function", "doc": "

\n", "signature": "():", "funcdef": "def"}, "tests.conftest.params_Kaminski2001_fig5_longdash": {"fullname": "tests.conftest.params_Kaminski2001_fig5_longdash", "modulename": "tests.conftest", "qualname": "params_Kaminski2001_fig5_longdash", "kind": "function", "doc": "

\n", "signature": "():", "funcdef": "def"}, "tests.conftest.params_Kaminski2004_fig4_triangles": {"fullname": "tests.conftest.params_Kaminski2004_fig4_triangles", "modulename": "tests.conftest", "qualname": "params_Kaminski2004_fig4_triangles", "kind": "function", "doc": "

\n", "signature": "():", "funcdef": "def"}, "tests.conftest.params_Kaminski2004_fig4_squares": {"fullname": "tests.conftest.params_Kaminski2004_fig4_squares", "modulename": "tests.conftest", "qualname": "params_Kaminski2004_fig4_squares", "kind": "function", "doc": "

\n", "signature": "():", "funcdef": "def"}, "tests.conftest.params_Kaminski2004_fig4_circles": {"fullname": "tests.conftest.params_Kaminski2004_fig4_circles", "modulename": "tests.conftest", "qualname": "params_Kaminski2004_fig4_circles", "kind": "function", "doc": "

\n", "signature": "():", "funcdef": "def"}, "tests.conftest.params_Hedjazian2017": {"fullname": "tests.conftest.params_Hedjazian2017", "modulename": "tests.conftest", "qualname": "params_Hedjazian2017", "kind": "function", "doc": "

\n", "signature": "():", "funcdef": "def"}, "tests.conftest.n_grains": {"fullname": "tests.conftest.n_grains", "modulename": "tests.conftest", "qualname": "n_grains", "kind": "function", "doc": "

\n", "signature": "(request):", "funcdef": "def"}, "tests.conftest.hkl": {"fullname": "tests.conftest.hkl", "modulename": "tests.conftest", "qualname": "hkl", "kind": "function", "doc": "

\n", "signature": "(request):", "funcdef": "def"}, "tests.conftest.ref_axes": {"fullname": "tests.conftest.ref_axes", "modulename": "tests.conftest", "qualname": "ref_axes", "kind": "function", "doc": "

\n", "signature": "(request):", "funcdef": "def"}, "tests.conftest.seeds": {"fullname": "tests.conftest.seeds", "modulename": "tests.conftest", "qualname": "seeds", "kind": "function", "doc": "

1000 unique seeds for ensemble runs that need an RNG seed.

\n", "signature": "():", "funcdef": "def"}, "tests.conftest.seed": {"fullname": "tests.conftest.seed", "modulename": "tests.conftest", "qualname": "seed", "kind": "function", "doc": "

Default seed for test RNG.

\n", "signature": "():", "funcdef": "def"}, "tests.conftest.seeds_nearX45": {"fullname": "tests.conftest.seeds_nearX45", "modulename": "tests.conftest", "qualname": "seeds_nearX45", "kind": "function", "doc": "

41 seeds which have the initial hexagonal symmetry axis near 45\u00b0 from X.

\n", "signature": "():", "funcdef": "def"}, "tests.test_config": {"fullname": "tests.test_config", "modulename": "tests.test_config", "kind": "module", "doc": "
\n

PyDRex: tests for configuration file format.

\n
\n"}, "tests.test_config.test_specfile": {"fullname": "tests.test_config.test_specfile", "modulename": "tests.test_config", "qualname": "test_specfile", "kind": "function", "doc": "

Test TOML spec file parsing.

\n", "signature": "():", "funcdef": "def"}, "tests.test_core": {"fullname": "tests.test_core", "modulename": "tests.test_core", "kind": "module", "doc": "
\n

PyDRex: Tests for core D-Rex routines.

\n
\n"}, "tests.test_core.SUBDIR": {"fullname": "tests.test_core.SUBDIR", "modulename": "tests.test_core", "qualname": "SUBDIR", "kind": "variable", "doc": "

\n", "default_value": "'core'"}, "tests.test_core.TestDislocationCreepOPX": {"fullname": "tests.test_core.TestDislocationCreepOPX", "modulename": "tests.test_core", "qualname": "TestDislocationCreepOPX", "kind": "class", "doc": "

Single-grain orthopyroxene crystallographic rotation rate tests.

\n"}, "tests.test_core.TestDislocationCreepOPX.class_id": {"fullname": "tests.test_core.TestDislocationCreepOPX.class_id", "modulename": "tests.test_core", "qualname": "TestDislocationCreepOPX.class_id", "kind": "variable", "doc": "

\n", "default_value": "'dislocation_creep_OPX'"}, "tests.test_core.TestDislocationCreepOPX.test_shear_dudz": {"fullname": "tests.test_core.TestDislocationCreepOPX.test_shear_dudz", "modulename": "tests.test_core", "qualname": "TestDislocationCreepOPX.test_shear_dudz", "kind": "function", "doc": "

\n", "signature": "(self, outdir):", "funcdef": "def"}, "tests.test_core.TestDislocationCreepOPX.test_shear_dvdx": {"fullname": "tests.test_core.TestDislocationCreepOPX.test_shear_dvdx", "modulename": "tests.test_core", "qualname": "TestDislocationCreepOPX.test_shear_dvdx", "kind": "function", "doc": "

\n", "signature": "(self, outdir):", "funcdef": "def"}, "tests.test_core.TestDislocationCreepOlivineA": {"fullname": "tests.test_core.TestDislocationCreepOlivineA", "modulename": "tests.test_core", "qualname": "TestDislocationCreepOlivineA", "kind": "class", "doc": "

Single-grain A-type olivine analytical rotation rate tests.

\n"}, "tests.test_core.TestDislocationCreepOlivineA.class_id": {"fullname": "tests.test_core.TestDislocationCreepOlivineA.class_id", "modulename": "tests.test_core", "qualname": "TestDislocationCreepOlivineA.class_id", "kind": "variable", "doc": "

\n", "default_value": "'dislocation_creep_OlA'"}, "tests.test_core.TestDislocationCreepOlivineA.test_shear_dvdx_slip_010_100": {"fullname": "tests.test_core.TestDislocationCreepOlivineA.test_shear_dvdx_slip_010_100", "modulename": "tests.test_core", "qualname": "TestDislocationCreepOlivineA.test_shear_dvdx_slip_010_100", "kind": "function", "doc": "

Single grain of A-type olivine, slip on (010)[100].

\n\n

Velocity gradient:\n$$\\bm{L} = \\begin{bmatrix} 0 & 0 & 0 \\cr 2 & 0 & 0 \\cr 0 & 0 & 0 \\end{bmatrix}$$

\n", "signature": "(self, outdir):", "funcdef": "def"}, "tests.test_core.TestDislocationCreepOlivineA.test_shear_dudz_slip_001_100": {"fullname": "tests.test_core.TestDislocationCreepOlivineA.test_shear_dudz_slip_001_100", "modulename": "tests.test_core", "qualname": "TestDislocationCreepOlivineA.test_shear_dudz_slip_001_100", "kind": "function", "doc": "

Single grain of A-type olivine, slip on (001)[100].

\n\n

Velocity gradient:\n$$\\bm{L} = \\begin{bmatrix} 0 & 0 & 2 \\cr 0 & 0 & 0 \\cr 0 & 0 & 0 \\end{bmatrix}$$

\n", "signature": "(self, outdir):", "funcdef": "def"}, "tests.test_core.TestDislocationCreepOlivineA.test_shear_dwdx_slip_001_100": {"fullname": "tests.test_core.TestDislocationCreepOlivineA.test_shear_dwdx_slip_001_100", "modulename": "tests.test_core", "qualname": "TestDislocationCreepOlivineA.test_shear_dwdx_slip_001_100", "kind": "function", "doc": "

Single grain of A-type olivine, slip on (001)[100].

\n\n

Velocity gradient:\n$$\\bm{L} = \\begin{bmatrix} 0 & 0 & 0 \\cr 0 & 0 & 0 \\cr 2 & 0 & 0 \\end{bmatrix}$$

\n", "signature": "(self, outdir):", "funcdef": "def"}, "tests.test_core.TestDislocationCreepOlivineA.test_shear_dvdz_slip_010_001": {"fullname": "tests.test_core.TestDislocationCreepOlivineA.test_shear_dvdz_slip_010_001", "modulename": "tests.test_core", "qualname": "TestDislocationCreepOlivineA.test_shear_dvdz_slip_010_001", "kind": "function", "doc": "

Single grain of A-type olivine, slip on (010)[001].

\n\n

Velocity gradient:\n$$\\bm{L} = \\begin{bmatrix} 0 & 0 & 0 \\cr 0 & 0 & 2 \\cr 0 & 0 & 0 \\end{bmatrix}$$

\n", "signature": "(self, outdir):", "funcdef": "def"}, "tests.test_core.TestRecrystallisation2D": {"fullname": "tests.test_core.TestRecrystallisation2D", "modulename": "tests.test_core", "qualname": "TestRecrystallisation2D", "kind": "class", "doc": "

Basic recrystallisation tests for 2D simple shear.

\n"}, "tests.test_core.TestRecrystallisation2D.class_id": {"fullname": "tests.test_core.TestRecrystallisation2D.class_id", "modulename": "tests.test_core", "qualname": "TestRecrystallisation2D.class_id", "kind": "variable", "doc": "

\n", "default_value": "'recrystallisation_2D'"}, "tests.test_core.TestRecrystallisation2D.test_shear_dvdx_circle_inplane": {"fullname": "tests.test_core.TestRecrystallisation2D.test_shear_dvdx_circle_inplane", "modulename": "tests.test_core", "qualname": "TestRecrystallisation2D.test_shear_dvdx_circle_inplane", "kind": "function", "doc": "

360000 grains of A-type olivine with uniform spread of a-axes on a circle.

\n\n

Grain growth rates are compared to analytical calculations.\nThe a-axes are distributed in the YX plane (i.e.\\ rotated around Z).

\n\n

Velocity gradient:\n$$\\bm{L} = \\begin{bmatrix} 0 & 0 & 0 \\cr 2 & 0 & 0 \\cr 0 & 0 & 0 \\end{bmatrix}$$

\n", "signature": "(self, outdir):", "funcdef": "def"}, "tests.test_core.TestRecrystallisation2D.test_shear_dvdx_circle_shearplane": {"fullname": "tests.test_core.TestRecrystallisation2D.test_shear_dvdx_circle_shearplane", "modulename": "tests.test_core", "qualname": "TestRecrystallisation2D.test_shear_dvdx_circle_shearplane", "kind": "function", "doc": "

360000 grains of A-type olivine with uniform spread of a-axes on a circle.

\n\n

Unlike test_shear_dvdx_circle_inplane, two slip systems are active here,\nwith cyclical variety in which one is dominant depending on grain orientation.\nThe a-axes are distributed in the YZ plane\n(i.e.\\ extrinsic rotation around Z by 90\u00b0 and then around X).

\n\n

Velocity gradient:\n$$\\bm{L} = \\begin{bmatrix} 0 & 0 & 0 \\cr 2 & 0 & 0 \\cr 0 & 0 & 0 \\end{bmatrix}$$

\n", "signature": "(self, outdir):", "funcdef": "def"}, "tests.test_corner_flow_2d": {"fullname": "tests.test_corner_flow_2d", "modulename": "tests.test_corner_flow_2d", "kind": "module", "doc": "
\n

PyDRex: 2D corner flow tests.

\n
\n"}, "tests.test_corner_flow_2d.SUBDIR": {"fullname": "tests.test_corner_flow_2d.SUBDIR", "modulename": "tests.test_corner_flow_2d", "qualname": "SUBDIR", "kind": "variable", "doc": "

\n", "default_value": "'2d_cornerflow'"}, "tests.test_corner_flow_2d.TestOlivineA": {"fullname": "tests.test_corner_flow_2d.TestOlivineA", "modulename": "tests.test_corner_flow_2d", "qualname": "TestOlivineA", "kind": "class", "doc": "

Tests for pure A-type olivine polycrystals in 2D corner flows.

\n"}, "tests.test_corner_flow_2d.TestOlivineA.class_id": {"fullname": "tests.test_corner_flow_2d.TestOlivineA.class_id", "modulename": "tests.test_corner_flow_2d", "qualname": "TestOlivineA.class_id", "kind": "variable", "doc": "

\n", "default_value": "'corner_olivineA'"}, "tests.test_corner_flow_2d.TestOlivineA.run": {"fullname": "tests.test_corner_flow_2d.TestOlivineA.run", "modulename": "tests.test_corner_flow_2d", "qualname": "TestOlivineA.run", "kind": "function", "doc": "

Run 2D corner flow A-type olivine simulation.

\n", "signature": "(\tcls,\tparams,\tseed,\tget_velocity,\tget_velocity_gradient,\tmin_coords,\tmax_coords,\tmax_strain,\tn_timesteps,\tfinal_location):", "funcdef": "def"}, "tests.test_corner_flow_2d.TestOlivineA.test_steady4": {"fullname": "tests.test_corner_flow_2d.TestOlivineA.test_steady4", "modulename": "tests.test_corner_flow_2d", "qualname": "TestOlivineA.test_steady4", "kind": "function", "doc": "

Test CPO evolution in steady 2D corner flow along 4 pathlines.

\n\n

Initial condition: random orientations and uniform volumes in all Minerals.

\n\n

Plate velocity: 2 cm/yr

\n\n
\n\n

This example takes about 11 CPU hours to run and uses around 60GB of RAM.\nIt is recommended to only use ncpus=4 which matches the number of\npathlines, because higher numbers can lead to redundant cross-core\ncommunication.

\n\n
\n", "signature": "(self, outdir, seed, ncpus):", "funcdef": "def"}, "tests.test_diagnostics": {"fullname": "tests.test_diagnostics", "modulename": "tests.test_diagnostics", "kind": "module", "doc": "
\n

PyDRex: tests for texture diagnostics.

\n
\n"}, "tests.test_diagnostics.TestElasticityComponents": {"fullname": "tests.test_diagnostics.TestElasticityComponents", "modulename": "tests.test_diagnostics", "qualname": "TestElasticityComponents", "kind": "class", "doc": "

Test symmetry decomposition of elastic tensors.

\n"}, "tests.test_diagnostics.TestElasticityComponents.test_olivine_Browaeys2004": {"fullname": "tests.test_diagnostics.TestElasticityComponents.test_olivine_Browaeys2004", "modulename": "tests.test_diagnostics", "qualname": "TestElasticityComponents.test_olivine_Browaeys2004", "kind": "function", "doc": "

\n", "signature": "(self):", "funcdef": "def"}, "tests.test_diagnostics.TestElasticityComponents.test_enstatite_Browaeys2004": {"fullname": "tests.test_diagnostics.TestElasticityComponents.test_enstatite_Browaeys2004", "modulename": "tests.test_diagnostics", "qualname": "TestElasticityComponents.test_enstatite_Browaeys2004", "kind": "function", "doc": "

\n", "signature": "(self):", "funcdef": "def"}, "tests.test_diagnostics.TestSymmetryPGR": {"fullname": "tests.test_diagnostics.TestSymmetryPGR", "modulename": "tests.test_diagnostics", "qualname": "TestSymmetryPGR", "kind": "class", "doc": "

Test Point-Girdle-Random (eigenvalue) symmetry diagnostics.

\n"}, "tests.test_diagnostics.TestSymmetryPGR.test_pointX": {"fullname": "tests.test_diagnostics.TestSymmetryPGR.test_pointX", "modulename": "tests.test_diagnostics", "qualname": "TestSymmetryPGR.test_pointX", "kind": "function", "doc": "

Test diagnostics of point symmetry aligned to the X axis.

\n", "signature": "(self):", "funcdef": "def"}, "tests.test_diagnostics.TestSymmetryPGR.test_random": {"fullname": "tests.test_diagnostics.TestSymmetryPGR.test_random", "modulename": "tests.test_diagnostics", "qualname": "TestSymmetryPGR.test_random", "kind": "function", "doc": "

Test diagnostics of random grain orientations.

\n", "signature": "(self):", "funcdef": "def"}, "tests.test_diagnostics.TestSymmetryPGR.test_girdle": {"fullname": "tests.test_diagnostics.TestSymmetryPGR.test_girdle", "modulename": "tests.test_diagnostics", "qualname": "TestSymmetryPGR.test_girdle", "kind": "function", "doc": "

Test diagnostics of girdled orientations.

\n", "signature": "(self):", "funcdef": "def"}, "tests.test_diagnostics.TestVolumeWeighting": {"fullname": "tests.test_diagnostics.TestVolumeWeighting", "modulename": "tests.test_diagnostics", "qualname": "TestVolumeWeighting", "kind": "class", "doc": "

Tests for volumetric resampling of orientation data.

\n"}, "tests.test_diagnostics.TestVolumeWeighting.test_output_shape": {"fullname": "tests.test_diagnostics.TestVolumeWeighting.test_output_shape", "modulename": "tests.test_diagnostics", "qualname": "TestVolumeWeighting.test_output_shape", "kind": "function", "doc": "

Test that we get the correct output shape.

\n", "signature": "(self):", "funcdef": "def"}, "tests.test_diagnostics.TestVolumeWeighting.test_upsample": {"fullname": "tests.test_diagnostics.TestVolumeWeighting.test_upsample", "modulename": "tests.test_diagnostics", "qualname": "TestVolumeWeighting.test_upsample", "kind": "function", "doc": "

Test upsampling of the raw orientation data.

\n", "signature": "(self):", "funcdef": "def"}, "tests.test_diagnostics.TestVolumeWeighting.test_downsample": {"fullname": "tests.test_diagnostics.TestVolumeWeighting.test_downsample", "modulename": "tests.test_diagnostics", "qualname": "TestVolumeWeighting.test_downsample", "kind": "function", "doc": "

Test downsampling of orientation data.

\n", "signature": "(self):", "funcdef": "def"}, "tests.test_diagnostics.TestVolumeWeighting.test_common_input_errors": {"fullname": "tests.test_diagnostics.TestVolumeWeighting.test_common_input_errors", "modulename": "tests.test_diagnostics", "qualname": "TestVolumeWeighting.test_common_input_errors", "kind": "function", "doc": "

Test that exceptions are raised for bad input data.

\n", "signature": "(self):", "funcdef": "def"}, "tests.test_diagnostics.TestBinghamStats": {"fullname": "tests.test_diagnostics.TestBinghamStats", "modulename": "tests.test_diagnostics", "qualname": "TestBinghamStats", "kind": "class", "doc": "

Tests for antipodally symmetric (bingham) statistics.

\n"}, "tests.test_diagnostics.TestBinghamStats.test_average_0": {"fullname": "tests.test_diagnostics.TestBinghamStats.test_average_0", "modulename": "tests.test_diagnostics", "qualname": "TestBinghamStats.test_average_0", "kind": "function", "doc": "

Test bingham average of vectors aligned to the reference frame.

\n", "signature": "(self):", "funcdef": "def"}, "tests.test_diagnostics.TestBinghamStats.test_average_twopoles90Z": {"fullname": "tests.test_diagnostics.TestBinghamStats.test_average_twopoles90Z", "modulename": "tests.test_diagnostics", "qualname": "TestBinghamStats.test_average_twopoles90Z", "kind": "function", "doc": "

Test bingham average of vectors rotated by \u00b190\u00b0 around Z.

\n", "signature": "(self):", "funcdef": "def"}, "tests.test_diagnostics.TestBinghamStats.test_average_spread10X": {"fullname": "tests.test_diagnostics.TestBinghamStats.test_average_spread10X", "modulename": "tests.test_diagnostics", "qualname": "TestBinghamStats.test_average_spread10X", "kind": "function", "doc": "

Test bingham average of vectors spread within 10\u00b0 of the \u00b1X-axis.

\n", "signature": "(self):", "funcdef": "def"}, "tests.test_diagnostics.TestMIndex": {"fullname": "tests.test_diagnostics.TestMIndex", "modulename": "tests.test_diagnostics", "qualname": "TestMIndex", "kind": "class", "doc": "

Tests for the M-index texture strength diagnostic.

\n"}, "tests.test_diagnostics.TestMIndex.test_texture_uniform_ortho": {"fullname": "tests.test_diagnostics.TestMIndex.test_texture_uniform_ortho", "modulename": "tests.test_diagnostics", "qualname": "TestMIndex.test_texture_uniform_ortho", "kind": "function", "doc": "

Test with random (uniform distribution) orthorhombic grain orientations.

\n", "signature": "(self, seed):", "funcdef": "def"}, "tests.test_diagnostics.TestMIndex.test_texture_spread10X_ortho": {"fullname": "tests.test_diagnostics.TestMIndex.test_texture_spread10X_ortho", "modulename": "tests.test_diagnostics", "qualname": "TestMIndex.test_texture_spread10X_ortho", "kind": "function", "doc": "

Test for orthorhombic grains spread within 10\u00b0 of the \u00b1X axis.

\n", "signature": "(self, seed):", "funcdef": "def"}, "tests.test_diagnostics.TestMIndex.test_texture_spread45X_ortho": {"fullname": "tests.test_diagnostics.TestMIndex.test_texture_spread45X_ortho", "modulename": "tests.test_diagnostics", "qualname": "TestMIndex.test_texture_spread45X_ortho", "kind": "function", "doc": "

Test for orthorhombic grains spread within 45\u00b0 of the \u00b1X axis.

\n", "signature": "(self, seed):", "funcdef": "def"}, "tests.test_diagnostics.TestMIndex.test_textures_increasing_ortho": {"fullname": "tests.test_diagnostics.TestMIndex.test_textures_increasing_ortho", "modulename": "tests.test_diagnostics", "qualname": "TestMIndex.test_textures_increasing_ortho", "kind": "function", "doc": "

Test M-index for textures of increasing strength.

\n", "signature": "(self, seed):", "funcdef": "def"}, "tests.test_diagnostics.TestMIndex.test_texture_girdle_ortho": {"fullname": "tests.test_diagnostics.TestMIndex.test_texture_girdle_ortho", "modulename": "tests.test_diagnostics", "qualname": "TestMIndex.test_texture_girdle_ortho", "kind": "function", "doc": "

Test M-index for girdled texture.

\n", "signature": "(self, seed):", "funcdef": "def"}, "tests.test_doctests": {"fullname": "tests.test_doctests", "modulename": "tests.test_doctests", "kind": "module", "doc": "
\n

PyDRex: Run doctests for all submodules.

\n
\n"}, "tests.test_doctests.test_doctests": {"fullname": "tests.test_doctests.test_doctests", "modulename": "tests.test_doctests", "qualname": "test_doctests", "kind": "function", "doc": "

Run doctests for all submodules.

\n", "signature": "(module, capsys):", "funcdef": "def"}, "tests.test_geometry": {"fullname": "tests.test_geometry", "modulename": "tests.test_geometry", "kind": "module", "doc": "
\n

PyDRex: Tests for geometric conversions and projections.

\n
\n"}, "tests.test_geometry.test_poles_example": {"fullname": "tests.test_geometry.test_poles_example", "modulename": "tests.test_geometry", "qualname": "test_poles_example", "kind": "function", "doc": "

Test poles (directions of crystallographic axes) of example data.

\n", "signature": "(hkl, ref_axes):", "funcdef": "def"}, "tests.test_geometry.test_lambert_equal_area": {"fullname": "tests.test_geometry.test_lambert_equal_area", "modulename": "tests.test_geometry", "qualname": "test_lambert_equal_area", "kind": "function", "doc": "

Test Lambert equal area projection.

\n", "signature": "(seed):", "funcdef": "def"}, "tests.test_scsv": {"fullname": "tests.test_scsv", "modulename": "tests.test_scsv", "kind": "module", "doc": "
\n

PyDRex: tests for the SCSV plain text file format.

\n
\n"}, "tests.test_scsv.test_validate_schema": {"fullname": "tests.test_scsv.test_validate_schema", "modulename": "tests.test_scsv", "qualname": "test_validate_schema", "kind": "function", "doc": "

Test SCSV schema validation.

\n", "signature": "(console_handler):", "funcdef": "def"}, "tests.test_scsv.test_read_specfile": {"fullname": "tests.test_scsv.test_read_specfile", "modulename": "tests.test_scsv", "qualname": "test_read_specfile", "kind": "function", "doc": "

Test SCSV spec file parsing.

\n", "signature": "():", "funcdef": "def"}, "tests.test_scsv.test_save_specfile": {"fullname": "tests.test_scsv.test_save_specfile", "modulename": "tests.test_scsv", "qualname": "test_save_specfile", "kind": "function", "doc": "

Test SCSV spec file reproduction.

\n", "signature": "(outdir, named_tempfile_kwargs):", "funcdef": "def"}, "tests.test_scsv.test_read_Kaminski2002": {"fullname": "tests.test_scsv.test_read_Kaminski2002", "modulename": "tests.test_scsv", "qualname": "test_read_Kaminski2002", "kind": "function", "doc": "

\n", "signature": "():", "funcdef": "def"}, "tests.test_scsv.test_save_scsv_errors": {"fullname": "tests.test_scsv.test_save_scsv_errors", "modulename": "tests.test_scsv", "qualname": "test_save_scsv_errors", "kind": "function", "doc": "

Check that we raise errors when attempting to write bad SCSV data.

\n", "signature": "(named_tempfile_kwargs):", "funcdef": "def"}, "tests.test_scsv.test_read_Kaminski2004": {"fullname": "tests.test_scsv.test_read_Kaminski2004", "modulename": "tests.test_scsv", "qualname": "test_read_Kaminski2004", "kind": "function", "doc": "

\n", "signature": "():", "funcdef": "def"}, "tests.test_scsv.test_read_Skemer2016": {"fullname": "tests.test_scsv.test_read_Skemer2016", "modulename": "tests.test_scsv", "qualname": "test_read_Skemer2016", "kind": "function", "doc": "

\n", "signature": "():", "funcdef": "def"}, "tests.test_simple_shear_2d": {"fullname": "tests.test_simple_shear_2d", "modulename": "tests.test_simple_shear_2d", "kind": "module", "doc": "
\n

PyDRex: 2D simple shear tests.

\n
\n"}, "tests.test_simple_shear_2d.SUBDIR": {"fullname": "tests.test_simple_shear_2d.SUBDIR", "modulename": "tests.test_simple_shear_2d", "qualname": "SUBDIR", "kind": "variable", "doc": "

\n", "default_value": "'2d_simple_shear'"}, "tests.test_simple_shear_2d.TestPreliminaries": {"fullname": "tests.test_simple_shear_2d.TestPreliminaries", "modulename": "tests.test_simple_shear_2d", "qualname": "TestPreliminaries", "kind": "class", "doc": "

Preliminary tests to check that various auxiliary routines are working.

\n"}, "tests.test_simple_shear_2d.TestPreliminaries.test_strain_increment": {"fullname": "tests.test_simple_shear_2d.TestPreliminaries.test_strain_increment", "modulename": "tests.test_simple_shear_2d", "qualname": "TestPreliminaries.test_strain_increment", "kind": "function", "doc": "

Test for accumulating strain via strain increment calculations.

\n", "signature": "(self):", "funcdef": "def"}, "tests.test_simple_shear_2d.TestOlivineA": {"fullname": "tests.test_simple_shear_2d.TestOlivineA", "modulename": "tests.test_simple_shear_2d", "qualname": "TestOlivineA", "kind": "class", "doc": "

Tests for stationary A-type olivine polycrystals in 2D simple shear.

\n"}, "tests.test_simple_shear_2d.TestOlivineA.class_id": {"fullname": "tests.test_simple_shear_2d.TestOlivineA.class_id", "modulename": "tests.test_simple_shear_2d", "qualname": "TestOlivineA.class_id", "kind": "variable", "doc": "

\n", "default_value": "'olivineA'"}, "tests.test_simple_shear_2d.TestOlivineA.run": {"fullname": "tests.test_simple_shear_2d.TestOlivineA.run", "modulename": "tests.test_simple_shear_2d", "qualname": "TestOlivineA.run", "kind": "function", "doc": "

Reusable logic for 2D olivine (A-type) simple shear tests.

\n\n

Returns a tuple with the mineral and the FSE angle (or None if return_fse is\nNone).

\n", "signature": "(\tcls,\tparams,\ttimestamps,\tstrain_rate,\tget_velocity_gradient,\tshear_direction,\tseed=None,\treturn_fse=None,\tget_position=<function TestOlivineA.<lambda>>):", "funcdef": "def"}, "tests.test_simple_shear_2d.TestOlivineA.interp_GBM_Kaminski2001": {"fullname": "tests.test_simple_shear_2d.TestOlivineA.interp_GBM_Kaminski2001", "modulename": "tests.test_simple_shear_2d", "qualname": "TestOlivineA.interp_GBM_Kaminski2001", "kind": "function", "doc": "

Interpolate Kaminski & Ribe, 2001 data to get target angles at strains.

\n", "signature": "(cls, strains):", "funcdef": "def"}, "tests.test_simple_shear_2d.TestOlivineA.interp_GBM_FortranDRex": {"fullname": "tests.test_simple_shear_2d.TestOlivineA.interp_GBM_FortranDRex", "modulename": "tests.test_simple_shear_2d", "qualname": "TestOlivineA.interp_GBM_FortranDRex", "kind": "function", "doc": "

Interpolate angles produced using 'tools/drex_forward_simpleshear.f90'.

\n", "signature": "(cls, strains):", "funcdef": "def"}, "tests.test_simple_shear_2d.TestOlivineA.interp_GBS_FortranDRex": {"fullname": "tests.test_simple_shear_2d.TestOlivineA.interp_GBS_FortranDRex", "modulename": "tests.test_simple_shear_2d", "qualname": "TestOlivineA.interp_GBS_FortranDRex", "kind": "function", "doc": "

Interpolate angles produced using 'tools/drex_forward_simpleshear.f90'.

\n", "signature": "(cls, strains):", "funcdef": "def"}, "tests.test_simple_shear_2d.TestOlivineA.interp_GBS_long_FortranDRex": {"fullname": "tests.test_simple_shear_2d.TestOlivineA.interp_GBS_long_FortranDRex", "modulename": "tests.test_simple_shear_2d", "qualname": "TestOlivineA.interp_GBS_long_FortranDRex", "kind": "function", "doc": "

Interpolate angles produced using 'tools/drex_forward_simpleshear.f90'.

\n", "signature": "(cls, strains):", "funcdef": "def"}, "tests.test_simple_shear_2d.TestOlivineA.interp_GBS_Kaminski2004": {"fullname": "tests.test_simple_shear_2d.TestOlivineA.interp_GBS_Kaminski2004", "modulename": "tests.test_simple_shear_2d", "qualname": "TestOlivineA.interp_GBS_Kaminski2004", "kind": "function", "doc": "

Interpolate Kaminski & Ribe, 2001 data to get target angles at strains.

\n", "signature": "(cls, strains):", "funcdef": "def"}, "tests.test_simple_shear_2d.TestOlivineA.test_zero_recrystallisation": {"fullname": "tests.test_simple_shear_2d.TestOlivineA.test_zero_recrystallisation", "modulename": "tests.test_simple_shear_2d", "qualname": "TestOlivineA.test_zero_recrystallisation", "kind": "function", "doc": "

Check that M*=0 is a reliable switch to turn off recrystallisation.

\n", "signature": "(self, seed):", "funcdef": "def"}, "tests.test_simple_shear_2d.TestOlivineA.test_grainsize_median": {"fullname": "tests.test_simple_shear_2d.TestOlivineA.test_grainsize_median", "modulename": "tests.test_simple_shear_2d", "qualname": "TestOlivineA.test_grainsize_median", "kind": "function", "doc": "

Check that M={50,100,150}, \u03bb=5 causes decreasing grain size median.

\n", "signature": "(self, seed, gbm_mobility):", "funcdef": "def"}, "tests.test_simple_shear_2d.TestOlivineA.test_dvdx_ensemble": {"fullname": "tests.test_simple_shear_2d.TestOlivineA.test_dvdx_ensemble", "modulename": "tests.test_simple_shear_2d", "qualname": "TestOlivineA.test_dvdx_ensemble", "kind": "function", "doc": "

Test a-axis alignment to shear in Y direction (init. SCCS near 45\u00b0 from X).

\n\n

Velocity gradient:\n$$\\bm{L} = \\begin{bmatrix} 0 & 0 & 0 \\cr 2 & 0 & 0 \\cr 0 & 0 & 0 \\end{bmatrix}$$

\n", "signature": "(\tself,\toutdir,\tseeds_nearX45,\tncpus,\tgbs_threshold,\tnucleation_efficiency):", "funcdef": "def"}, "tests.test_simple_shear_2d.TestOlivineA.test_dvdx_GBM": {"fullname": "tests.test_simple_shear_2d.TestOlivineA.test_dvdx_GBM", "modulename": "tests.test_simple_shear_2d", "qualname": "TestOlivineA.test_dvdx_GBM", "kind": "function", "doc": "

Test a-axis alignment to shear in Y direction (init. SCCS near 45\u00b0 from X).

\n\n

Velocity gradient:\n$$\n\\bm{L} = 10^{-4} \u00d7\n \\begin{bmatrix} 0 & 0 & 0 \\cr 2 & 0 & 0 \\cr 0 & 0 & 0 \\end{bmatrix}\n$$

\n\n

Results are compared to the Fortran 90 output.

\n", "signature": "(self, outdir, seeds_nearX45, ncpus):", "funcdef": "def"}, "tests.test_simple_shear_2d.TestOlivineA.test_GBM_calibration": {"fullname": "tests.test_simple_shear_2d.TestOlivineA.test_GBM_calibration", "modulename": "tests.test_simple_shear_2d", "qualname": "TestOlivineA.test_GBM_calibration", "kind": "function", "doc": "

Compare results for various values of $$M^\u2217$$ to A-type olivine data.

\n\n

Velocity gradient:\n$$\n\\bm{L} = 10^{-4} \u00d7\n \\begin{bmatrix} 0 & 0 & 0 \\cr 2 & 0 & 0 \\cr 0 & 0 & 0 \\end{bmatrix}\n$$

\n\n

Unlike test_dvdx_GBM,\ngrain boudary sliding is enabled here (see _io.DEFAULT_PARAMS).\nData are provided by Skemer & Hansen, 2016.

\n", "signature": "(self, outdir, seeds, ncpus):", "funcdef": "def"}, "tests.test_simple_shear_2d.TestOlivineA.test_dudz_pathline": {"fullname": "tests.test_simple_shear_2d.TestOlivineA.test_dudz_pathline", "modulename": "tests.test_simple_shear_2d", "qualname": "TestOlivineA.test_dudz_pathline", "kind": "function", "doc": "

Test alignment of olivine a-axis for a polycrystal advected on a pathline.

\n", "signature": "(self, outdir, seed):", "funcdef": "def"}, "tests.test_simple_shear_3d": {"fullname": "tests.test_simple_shear_3d", "modulename": "tests.test_simple_shear_3d", "kind": "module", "doc": "
\n

PyDRex: Simple shear 3D tests.

\n
\n"}, "tests.test_simple_shear_3d.SUBDIR": {"fullname": "tests.test_simple_shear_3d.SUBDIR", "modulename": "tests.test_simple_shear_3d", "qualname": "SUBDIR", "kind": "variable", "doc": "

\n", "default_value": "'3d_simple_shear'"}, "tests.test_simple_shear_3d.TestFraters2021": {"fullname": "tests.test_simple_shear_3d.TestFraters2021", "modulename": "tests.test_simple_shear_3d", "qualname": "TestFraters2021", "kind": "class", "doc": "

Tests inspired by the benchmarks presented in [Fraters & Billen, 2021].

\n"}, "tests.test_simple_shear_3d.TestFraters2021.class_id": {"fullname": "tests.test_simple_shear_3d.TestFraters2021.class_id", "modulename": "tests.test_simple_shear_3d", "qualname": "TestFraters2021.class_id", "kind": "variable", "doc": "

\n", "default_value": "'Fraters2021'"}, "tests.test_simple_shear_3d.TestFraters2021.run": {"fullname": "tests.test_simple_shear_3d.TestFraters2021.run", "modulename": "tests.test_simple_shear_3d", "qualname": "TestFraters2021.run", "kind": "function", "doc": "

Run simulation with stationary particles in the given velocity gradient.

\n\n

The optional RNG seed is used for the initial pseudorandom orientations.\nA prefix msg will be printed before each timestep log message if given.\nOther keyword args are passed to pydrex.Mineral.update_orientations.

\n\n

Returns a tuple containing one olivine (A-type) and one enstatite mineral.\nIf params[\"enstatite_fraction\"] is zero, then the second tuple element will be\nNone instead.

\n", "signature": "(\tcls,\tparams,\ttimestamps,\tget_velocity_gradient_initial,\tget_velocity_gradient_final,\tswitch_time,\tmsg,\tseed=None):", "funcdef": "def"}, "tests.test_simple_shear_3d.TestFraters2021.test_direction_change": {"fullname": "tests.test_simple_shear_3d.TestFraters2021.test_direction_change", "modulename": "tests.test_simple_shear_3d", "qualname": "TestFraters2021.test_direction_change", "kind": "function", "doc": "

Test a-axis alignment in simple shear with instantaneous geometry change.

\n\n

The simulation runs for 5 Ma with a strain rate of 1.58e-14/s, resulting in an\naccumulated strain invariant of 2.5.

\n\n

The initial shear has nonzero du/dz and the final shear has nonzero dv/dx where\nu is the velocity along X and v the velocity along Y.

\n", "signature": "(\tself,\toutdir,\tseeds,\tparams_Fraters2021,\tswitch_time_Ma,\tncpus,\tray_session):", "funcdef": "def"}, "tests.test_tensors": {"fullname": "tests.test_tensors", "modulename": "tests.test_tensors", "kind": "module", "doc": "
\n

PyDRex: Tests for tensor operations.

\n
\n"}, "tests.test_tensors.test_voigt_decompose": {"fullname": "tests.test_tensors.test_voigt_decompose", "modulename": "tests.test_tensors", "qualname": "test_voigt_decompose", "kind": "function", "doc": "

Test decomposition of Voigt 6x6 matrix into distinct contractions.

\n", "signature": "():", "funcdef": "def"}, "tests.test_tensors.test_voigt_tensor": {"fullname": "tests.test_tensors.test_voigt_tensor", "modulename": "tests.test_tensors", "qualname": "test_voigt_tensor", "kind": "function", "doc": "

Test elasticity tensor <-> 6x6 Voigt matrix conversions.

\n", "signature": "():", "funcdef": "def"}, "tests.test_tensors.test_voigt_to_vector": {"fullname": "tests.test_tensors.test_voigt_to_vector", "modulename": "tests.test_tensors", "qualname": "test_voigt_to_vector", "kind": "function", "doc": "

Test Voigt vector construction.

\n", "signature": "():", "funcdef": "def"}, "tests.test_vortex_2d": {"fullname": "tests.test_vortex_2d", "modulename": "tests.test_vortex_2d", "kind": "module", "doc": "
\n

PyDRex: tests for CPO stability in 2D vortex and Stokes cell flows.

\n
\n"}, "tests.test_vortex_2d.SUBDIR": {"fullname": "tests.test_vortex_2d.SUBDIR", "modulename": "tests.test_vortex_2d", "qualname": "SUBDIR", "kind": "variable", "doc": "

\n", "default_value": "'2d_vortex'"}, "tests.test_vortex_2d.TestCellOlivineA": {"fullname": "tests.test_vortex_2d.TestCellOlivineA", "modulename": "tests.test_vortex_2d", "qualname": "TestCellOlivineA", "kind": "class", "doc": "

Tests for A-type olivine polycrystals in a 2D Stokes cell.

\n"}, "tests.test_vortex_2d.TestCellOlivineA.class_id": {"fullname": "tests.test_vortex_2d.TestCellOlivineA.class_id", "modulename": "tests.test_vortex_2d", "qualname": "TestCellOlivineA.class_id", "kind": "variable", "doc": "

\n", "default_value": "'cell_olivineA'"}, "tests.test_vortex_2d.TestCellOlivineA.run": {"fullname": "tests.test_vortex_2d.TestCellOlivineA.run", "modulename": "tests.test_vortex_2d", "qualname": "TestCellOlivineA.run", "kind": "function", "doc": "

Run 2D Stokes cell A-type olivine simulation.

\n", "signature": "(\tcls,\tparams,\tfinal_location,\tget_velocity,\tget_velocity_gradient,\tmin_coords,\tmax_coords,\tmax_strain,\tseed=None):", "funcdef": "def"}, "tests.test_vortex_2d.TestCellOlivineA.test_xz_10k": {"fullname": "tests.test_vortex_2d.TestCellOlivineA.test_xz_10k", "modulename": "tests.test_vortex_2d", "qualname": "TestCellOlivineA.test_xz_10k", "kind": "function", "doc": "

Run 2D cell test with 10000 grains (~14GiB RAM requirement).

\n", "signature": "(self, outdir, seed):", "funcdef": "def"}, "tests.test_vortex_2d.TestCellOlivineA.test_xz": {"fullname": "tests.test_vortex_2d.TestCellOlivineA.test_xz", "modulename": "tests.test_vortex_2d", "qualname": "TestCellOlivineA.test_xz", "kind": "function", "doc": "

Test to check that 5000 grains is \"enough\" to resolve transient features.

\n", "signature": "(self, outdir, seed, n_grains):", "funcdef": "def"}, "tests.test_vortex_2d.TestCellOlivineA.test_xz_ensemble": {"fullname": "tests.test_vortex_2d.TestCellOlivineA.test_xz_ensemble", "modulename": "tests.test_vortex_2d", "qualname": "TestCellOlivineA.test_xz_ensemble", "kind": "function", "doc": "

Test to demonstrate stability of the dip at \u03b5 \u2248 3.75 for 5000+ grains.

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Simulate crystallographic preferred orientation evolution in polycrystals

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This software is currently in early development (alpha)\nand therefore subject to breaking changes without notice.

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About

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Viscoplastic deformation of minerals, e.g. in Earth's mantle, leads to distinct\nsignatures in the mineral texture. Many minerals naturally occur in\npolycrystalline form, which means that they are composed of many grains with\ndifferent volumes and lattice orientations. Preferential alignment of the\naverage lattice orientation is called crystallographic preferred orientation\n(CPO). PyDRex simulates the development and evolution of CPO in deforming\npolycrystals, as well as tracking macroscopic finite strain measures.\nCurrently, the code supports olivine and enstatite mineral phases. The\nfollowing features are provided:

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The core CPO solver is based on the original Fortran 90 implementation by \u00c9douard Kaminski,\nwhich can be downloaded from this link (~90KB).\nThe reference papers are Kaminski & Ribe (2001)\nand Kaminski & Ribe (2004),\nand an open-access paper which discusses the model is Fraters & Billen (2021).

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Installation

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The minimum required Python version is set using requires-python in the\npyproject.toml file.\nFor installation instructions,\nsee the README file.

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Documentation

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The website menu can be used to discover the public API of this package.\nSome of the tests are also documented and can serve as usage examples.\nTheir docstrings can be viewed in this section.\nDocumentation is also available from the Python REPL via the help() method.

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The D-Rex kinematic CPO model

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The D-Rex model is used to compute crystallographic preferred orientation (CPO)\nfor polycrystals deforming by plastic deformation and dynamic recrystallization.\nPolycrystals are discretized into \"grains\" which represent fractional volumes\nof the total crystal that are characterised by a particular crystal lattice\norientation. For numerical efficiency, the number of grains in the model does\nnot change, and should only be interpreted as an approximation of the number\nof (unrecrystallised) physical grains. Dynamic recrystallization is modelled using\nstatistical expressions which approximate the interaction of each grain with an\neffective medium based on the averaged dislocation energy of all other grains. Note that\nthe model is not suited to situations where static recrystallization processes are\nsignificant.

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The primary microphysical mechanism for plastic deformation of the polycrystal\nis dislocation creep, which involves dislocation glide (\"slip\") along symmetry\nplanes of the mineral and dislocation climb, which allows for dislocations to\nannihilate each other so that the number of dislocations reaches a steady-state.\nThe D-Rex model does not simulate dislocation climb, but implicitly assumes that\nthe dislocations are in steady-state so that the dislocation density of the\ncrystal can be described by

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$$\n\u03c1 \u221d b^{-2} \\left(\\frac{\u03c3}{\u03bc}\\right)^{p}\n$$

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where $b$ is the length of the Burgers' vector, $\u03c3$ is the stress\nand $\u03bc$ is the shear modulus. The value of the exponent $p$ is given by the\nstress_exponent input parameter. For an overview of available parameters,\nsee [the pydrex.mock source code, for now...]

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The effects of dynamic recrystallization are twofold. Grains with a higher than\naverage dislocation density may be affected by either grain nucleation, which is\nthe formation of initially small, strain-free sub-grains, or grain boundary\nmigration, by which process other grains of lower strain energy annex a portion\nof its volume. Nucleation occurs mostly in grains oriented favourably for\ndislocation glide, and the new grains also grow by grain boundary migration.\nIf nucleation is too inefficient, the dislocation density in deformation-aligned\ngrains will remain high and these grains will therefore shrink in volume. On the\nother hand, if grain boundaries are too immobile, then nucleated grains will take\nlonger to grow, reducing the speed of CPO development and re-orientation.\nBecause nucleated grains are assumed to inherit the orientation of the parent,\nthey do not affect the model except by reducing the average dislocation density.\nA grain boundary mobility parameter of $M^{\u2217} = 0$ will therefore disable any\nrecrystallization effects. Finally, the process of grain boundary sliding can\nalso be included, which simply disallows rotation of grains with very small volume.\nThis only affects CPO evolution by introducing a latency for the onset of grain\nboundary migration in nucleated grains. It also manifests as an upper bound on\ntexture strength.

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Parameter reference

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Model parameters will eventually be provided in a .toml file.\nFor now just pass a dictionary to config in the Mineral.update_orientations method.\nA draft of the input file spec is shown below:

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# PyDRex TOML configuration specification.\n# Exactly one valid combination of fields from the [input] section are required,\n# the rest is optional.\n\n# Simulation name is optional but recommended.\nname = "pydrex-spec"\n\n# Input files/options are given in this section:\n[input]\n\n# Input data can be provided in one of three ways:\n# 1. An input mesh with the steady-state numerical velocity gradient field\n#    and a plain text SCSV file specifying the FINAL locations of the polycrystals.\n#    In this case, polycrystals will first be back-propagated along flow pathlines,\n#    and then forward-propagated while the CPO is calculated.\n#    The SCSV file should have column names 'X', 'Y', 'Z' for 3D or any two of those for 2D.\n# 2. A built-in (analytical) velocity gradient function from `pydrex.velocity_gradients`,\n#    its arguments, and INITIAL locations of the polycrystals. In this case,\n#    polycrystals will immediately be forward-advected in the specified field.\n# 3. Pre-computed pathline files with velocity gradients at each point.\n#    These can be either plain text SCSV files or binary NPZ files.\n#    They should have columns/fields called: 'X_id', 'Y_id', 'Z_id', 'L11_id', 'L12_id', 'L13_id', etc.\n#    where 'id' is replaced by an unique identifier of the particle/pathline.\n#    If a field called 't' is also present, it will be used for the timestamps.\n#    Alternatively, a fixed timestep for all paths can be specified using `timestep`.\n# 4. Names of fields to be read from a geodynamics framework during runtime (not implemented yet).\n\n# Example for method 1, not only .vtu but any format supported by meshio should work:\n# mesh = "filename.vtu"\n# locations_final = "filename.scsv"\n# timestep = 1e9\n\n# Example for method 2:\nvelocity_gradient = ["simple_shear_2d", "Y", "X", 5e-6]\nlocations_initial = "start.scsv"\ntimestep = 1e9\n\n# Example for method 3:\n# timestep = 1e9\n# paths = ["path001.npz", "path002.scsv"]\n\n# In cases where the pathlines do not exit the domain,\n# a maximum strain threshold can bee provided, after which advection is halted.\n# max_strain = 10\n\n# Output files/options are given in this section:\n[output]\n\n# Optional output directory, will be created if missing.\n# This is also relative to the parent directory of the TOML file,\n# unless an absolute path is given.\ndirectory = "out"\n\n# Optional choice of mineral phases to include in raw output.\n# Raw output means rotation matrices and grain volumes, so 10 floats per grain per mineral.\n# By default, raw output for all supported minerals is saved.\nraw_output = ["olivine"]\n\n# Optional choice of mineral phases to include in diagnostic output.\n# Diagnostic output includes texture symmetry, strength and mean angle results.\n# By default, diagnostic output for all supported minerals is saved.\ndiagnostics = ["olivine"]\n\n# Should anisotropy postprocessing results be calculated?\n# This uses voigt averaging so the effective values for the multiphase polycrystal are calculated.\nanisotropy = true\n\n# Optional pathline output files (velocity gradients, positions, timestamps, particle ids).\n# Pathline output files use the same format as pathline inputs (by default, they are not produced).\n# They are stored inside the output directory unless absolute paths are given.\n# paths = ["pathline001.scsv"]\n\n# Optional logging level for log files.\n# This sets the log level for all log files, overriding the default value of "WARNING".\n# Supported levels are controlled by Python's logging module.\n# Usually they are "CRITICAL", "ERROR", "WARNING", "INFO" and "DEBUG".\nlog_level = "DEBUG"\n\n# DREX and simulation parameters are given in this section:\n[parameters]\n\n# Optional olivine volume fraction to use for multiphase simulations.\n# If enstatite_fraction is provided, they must sum to 1.\n# Otherwise, the remainder is assumed to be enstatite.\n# olivine_fraction = 1.\n\n# Optional enstatite volume fraction to use for multiphase simulations.\n# If olivine_fraction is provided, they must sum to 1.\n# Otherwise, the remainder is assumed to be olivine.\n# enstatite_fraction = 0.\n\n# Optional initial olivine fabric. A-type by default.\ninitial_olivine_fabric = "A"\n\n# Optional DREX stress_exponent, see documentation for details.\nstress_exponent = 1.5\n\n# Optional DREX deformation_exponent, see documentation for details.\ndeformation_exponent = 3.5\n\n# Optional DREX grain boudary mobility, see documentation for details.\ngbm_mobility = 125\n\n# Optional DREX grain boundary sliding threshold, see documentation for details.\ngbs_threshold = 0.3\n\n# Optional DREX nucleation efficiency, see documentation for details.\nnucleation_efficiency = 5.0\n\n# Optional number of (initial) grains per mineral phase per polycrystal.\nnumber_of_grains = 2000\n
\n
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\n

PyDRex: Custom Matplotlib Axes subclasses.

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Axes class designed for crystallographic pole figures.

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Thin matplotlib Axes wrapper for crystallographic pole figures.

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Projections are not performed automatically using default methods like\nscatter or plot. To actually plot the pole figures, use polefigure.

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Plot pole figure of crystallographic texture.

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Args:

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Any additional keyword arguments are passed to either tripcolor if\ndensity=True or scatter if density=False

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Set multiple properties at once.

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Supported properties are

\n\n

Properties:\n adjustable: {'box', 'datalim'}\n agg_filter: a filter function, which takes a (m, n, 3) float array and a dpi value, and returns a (m, n, 3) array and two offsets from the bottom left corner of the image\n alpha: scalar or None\n anchor: (float, float) or {'C', 'SW', 'S', 'SE', 'E', 'NE', ...}\n animated: bool\n aspect: {'auto', 'equal'} or float\n autoscale_on: bool\n autoscalex_on: unknown\n autoscaley_on: unknown\n axes_locator: Callable[[Axes, Renderer], Bbox]\n axisbelow: bool or 'line'\n box_aspect: float or None\n clip_box: ~matplotlib.transforms.BboxBase or None\n clip_on: bool\n clip_path: Patch or (Path, Transform) or None\n facecolor or fc: color\n figure: ~matplotlib.figure.Figure\n frame_on: bool\n gid: str\n in_layout: bool\n label: object\n mouseover: bool\n navigate: bool\n navigate_mode: unknown\n path_effects: list of .AbstractPathEffect\n picker: None or bool or float or callable\n position: [left, bottom, width, height] or ~matplotlib.transforms.Bbox\n prop_cycle: ~cycler.Cycler\n rasterization_zorder: float or None\n rasterized: bool\n sketch_params: (scale: float, length: float, randomness: float)\n snap: bool or None\n subplotspec: unknown\n title: str\n transform: ~matplotlib.transforms.Transform\n url: str\n visible: bool\n xbound: (lower: float, upper: float)\n xlabel: str\n xlim: (left: float, right: float)\n xmargin: float greater than -0.5\n xscale: unknown\n xticklabels: unknown\n xticks: unknown\n ybound: (lower: float, upper: float)\n ylabel: str\n ylim: (bottom: float, top: float)\n ymargin: float greater than -0.5\n yscale: unknown\n yticklabels: unknown\n yticks: unknown\n zorder: float

\n", "signature": "(\tself,\t*,\tadjustable=<UNSET>,\tagg_filter=<UNSET>,\talpha=<UNSET>,\tanchor=<UNSET>,\tanimated=<UNSET>,\taspect=<UNSET>,\tautoscale_on=<UNSET>,\tautoscalex_on=<UNSET>,\tautoscaley_on=<UNSET>,\taxes_locator=<UNSET>,\taxisbelow=<UNSET>,\tbox_aspect=<UNSET>,\tclip_box=<UNSET>,\tclip_on=<UNSET>,\tclip_path=<UNSET>,\tfacecolor=<UNSET>,\tframe_on=<UNSET>,\tgid=<UNSET>,\tin_layout=<UNSET>,\tlabel=<UNSET>,\tmouseover=<UNSET>,\tnavigate=<UNSET>,\tpath_effects=<UNSET>,\tpicker=<UNSET>,\tposition=<UNSET>,\tprop_cycle=<UNSET>,\trasterization_zorder=<UNSET>,\trasterized=<UNSET>,\tsketch_params=<UNSET>,\tsnap=<UNSET>,\tsubplotspec=<UNSET>,\ttitle=<UNSET>,\ttransform=<UNSET>,\turl=<UNSET>,\tvisible=<UNSET>,\txbound=<UNSET>,\txlabel=<UNSET>,\txlim=<UNSET>,\txmargin=<UNSET>,\txscale=<UNSET>,\txticklabels=<UNSET>,\txticks=<UNSET>,\tybound=<UNSET>,\tylabel=<UNSET>,\tylim=<UNSET>,\tymargin=<UNSET>,\tyscale=<UNSET>,\tyticklabels=<UNSET>,\tyticks=<UNSET>,\tzorder=<UNSET>):", "funcdef": "def"}, "pydrex.cli": {"fullname": "pydrex.cli", "modulename": "pydrex.cli", "kind": "module", "doc": "
\n

PyDRex: Entry points and argument handling for command line tools.

\n
\n\n

All CLI handlers should be registered in the CLI_HANDLERS namedtuple,\nwhich ensures that they will be installed as executable scripts alongside the package.

\n"}, "pydrex.cli.CliTool": {"fullname": "pydrex.cli.CliTool", "modulename": "pydrex.cli", "qualname": "CliTool", "kind": "class", "doc": "

Base class for CLI tools defining the required interface.

\n"}, "pydrex.cli.MeshGenerator": {"fullname": "pydrex.cli.MeshGenerator", "modulename": "pydrex.cli", "qualname": "MeshGenerator", "kind": "class", "doc": "

PyDRex script to generate various simple meshes.

\n\n

Only rectangular (2D) meshes are currently supported. The RESOLUTION must be a comma\ndelimited set of directives of the form <LOC>:<RES> where <LOC> is a location\nspecifier, i.e. either \"G\" (global) or a compas direction like \"N\", \"S\", \"NE\", etc.,\nand <RES> is a floating point value to be set as the resolution at that location.

\n", "bases": "CliTool"}, "pydrex.cli.H5partExtractor": {"fullname": "pydrex.cli.H5partExtractor", "modulename": "pydrex.cli", "qualname": "H5partExtractor", "kind": "class", "doc": "

PyDRex script to extract raw CPO data from Fluidity .h5part files.

\n\n

Fluidity saves data stored on model particles to an .h5part file.\nThis script converts that file to canonical serialisation formats:

\n\n\n\n

It is assumed that CPO data is stored in keys called 'CPO_' in the .h5part\ndata, where <N> is an integer in the range 1\u2014n_grains. The accumulated strain is\nread from the attribute CPO_<S> where S=ngrains+1. Particle positions are read\nfrom the attributes x, y, and z.

\n\n

At the moment, dynamic changes in fabric or phase are not supported.

\n", "bases": "CliTool"}, "pydrex.cli.NPZFileInspector": {"fullname": "pydrex.cli.NPZFileInspector", "modulename": "pydrex.cli", "qualname": "NPZFileInspector", "kind": "class", "doc": "

PyDRex script to show information about serialized CPO data.

\n\n

Lists the keys that should be used for the postfix in pydrex.Mineral.load and\npydrex.Mineral.from_file.

\n", "bases": "CliTool"}, "pydrex.cli.PoleFigureVisualiser": {"fullname": "pydrex.cli.PoleFigureVisualiser", "modulename": "pydrex.cli", "qualname": "PoleFigureVisualiser", "kind": "class", "doc": "

PyDRex script to plot pole figures of serialized CPO data.

\n\n

Produces [100], [010] and [001] pole figures for serialized pydrex.Minerals.\nIf the range of indices is not specified,\na maximum of 25 of each pole figure will be produced by default.

\n", "bases": "CliTool"}, "pydrex.cli.CLI_HANDLERS": {"fullname": "pydrex.cli.CLI_HANDLERS", "modulename": "pydrex.cli", "qualname": "CLI_HANDLERS", "kind": "variable", "doc": "

\n", "default_value": "CLI_HANDLERS(h5part_extractor=<pydrex.cli.H5partExtractor object>, mesh_generator=<pydrex.cli.MeshGenerator object>, npz_file_inspector=<pydrex.cli.NPZFileInspector object>, pole_figure_visualiser=<pydrex.cli.PoleFigureVisualiser object>)"}, "pydrex.core": {"fullname": "pydrex.core", "modulename": "pydrex.core", "kind": "module", "doc": "
\n

PyDRex: Core D-Rex functions and enums.

\n
\n\n

The function derivatives implements the core D-Rex solver, which computes the\ncrystallographic rotation rate and changes in fractional grain volumes.

\n\n

Acronyms:

\n\n\n"}, "pydrex.core.PERMUTATION_SYMBOL": {"fullname": "pydrex.core.PERMUTATION_SYMBOL", "modulename": "pydrex.core", "qualname": "PERMUTATION_SYMBOL", "kind": "variable", "doc": "

\n", "default_value": "array([[[ 0., 0., 0.],\n [ 0., 0., 1.],\n [ 0., -1., 0.]],\n\n [[ 0., 0., -1.],\n [ 0., 0., 0.],\n [ 1., 0., 0.]],\n\n [[ 0., 1., 0.],\n [-1., 0., 0.],\n [ 0., 0., 0.]]])"}, "pydrex.core.MineralPhase": {"fullname": "pydrex.core.MineralPhase", "modulename": "pydrex.core", "qualname": "MineralPhase", "kind": "class", "doc": "

Supported mineral phases.

\n", "bases": "enum.IntEnum"}, "pydrex.core.MineralPhase.olivine": {"fullname": "pydrex.core.MineralPhase.olivine", "modulename": "pydrex.core", "qualname": "MineralPhase.olivine", "kind": "variable", "doc": "

\n", "default_value": "<MineralPhase.olivine: 0>"}, "pydrex.core.MineralPhase.enstatite": {"fullname": "pydrex.core.MineralPhase.enstatite", "modulename": "pydrex.core", "qualname": "MineralPhase.enstatite", "kind": "variable", "doc": "

\n", "default_value": "<MineralPhase.enstatite: 1>"}, "pydrex.core.DeformationRegime": {"fullname": "pydrex.core.DeformationRegime", "modulename": "pydrex.core", "qualname": "DeformationRegime", "kind": "class", "doc": "

Deformation mechanism regimes.

\n", "bases": "enum.IntEnum"}, "pydrex.core.DeformationRegime.diffusion": {"fullname": "pydrex.core.DeformationRegime.diffusion", "modulename": "pydrex.core", "qualname": "DeformationRegime.diffusion", "kind": "variable", "doc": "

\n", "default_value": "<DeformationRegime.diffusion: 0>"}, "pydrex.core.DeformationRegime.dislocation": {"fullname": "pydrex.core.DeformationRegime.dislocation", "modulename": "pydrex.core", "qualname": "DeformationRegime.dislocation", "kind": "variable", "doc": "

\n", "default_value": "<DeformationRegime.dislocation: 1>"}, "pydrex.core.DeformationRegime.byerlee": {"fullname": "pydrex.core.DeformationRegime.byerlee", "modulename": "pydrex.core", "qualname": "DeformationRegime.byerlee", "kind": "variable", "doc": "

\n", "default_value": "<DeformationRegime.byerlee: 2>"}, "pydrex.core.DeformationRegime.max_viscosity": {"fullname": "pydrex.core.DeformationRegime.max_viscosity", "modulename": "pydrex.core", "qualname": "DeformationRegime.max_viscosity", "kind": "variable", "doc": "

\n", "default_value": "<DeformationRegime.max_viscosity: 3>"}, "pydrex.core.MineralFabric": {"fullname": "pydrex.core.MineralFabric", "modulename": "pydrex.core", "qualname": "MineralFabric", "kind": "class", "doc": "

Supported mineral fabrics.

\n\n

The following fabric types are supported:

\n\n\n", "bases": "enum.IntEnum"}, "pydrex.core.MineralFabric.olivine_A": {"fullname": "pydrex.core.MineralFabric.olivine_A", "modulename": "pydrex.core", "qualname": "MineralFabric.olivine_A", "kind": "variable", "doc": "

\n", "default_value": "<MineralFabric.olivine_A: 0>"}, "pydrex.core.MineralFabric.olivine_B": {"fullname": "pydrex.core.MineralFabric.olivine_B", "modulename": "pydrex.core", "qualname": "MineralFabric.olivine_B", "kind": "variable", "doc": "

\n", "default_value": "<MineralFabric.olivine_B: 1>"}, "pydrex.core.MineralFabric.olivine_C": {"fullname": "pydrex.core.MineralFabric.olivine_C", "modulename": "pydrex.core", "qualname": "MineralFabric.olivine_C", "kind": "variable", "doc": "

\n", "default_value": "<MineralFabric.olivine_C: 2>"}, "pydrex.core.MineralFabric.olivine_D": {"fullname": "pydrex.core.MineralFabric.olivine_D", "modulename": "pydrex.core", "qualname": "MineralFabric.olivine_D", "kind": "variable", "doc": "

\n", "default_value": "<MineralFabric.olivine_D: 3>"}, "pydrex.core.MineralFabric.olivine_E": {"fullname": "pydrex.core.MineralFabric.olivine_E", "modulename": "pydrex.core", "qualname": "MineralFabric.olivine_E", "kind": "variable", "doc": "

\n", "default_value": "<MineralFabric.olivine_E: 4>"}, "pydrex.core.MineralFabric.enstatite_AB": {"fullname": "pydrex.core.MineralFabric.enstatite_AB", "modulename": "pydrex.core", "qualname": "MineralFabric.enstatite_AB", "kind": "variable", "doc": "

\n", "default_value": "<MineralFabric.enstatite_AB: 5>"}, "pydrex.core.get_crss": {"fullname": "pydrex.core.get_crss", "modulename": "pydrex.core", "qualname": "get_crss", "kind": "function", "doc": "

Get Critical Resolved Shear Stress for the mineral phase and fabric.

\n\n

Returns an array of the normalised threshold stresses required to activate slip on\neach slip system. Olivine slip systems are ordered according to the convention used\nfor pydrex.minerals.OLIVINE_SLIP_SYSTEMS.

\n", "signature": "(phase, fabric):", "funcdef": "def"}, "pydrex.core.derivatives": {"fullname": "pydrex.core.derivatives", "modulename": "pydrex.core", "qualname": "derivatives", "kind": "function", "doc": "

Get derivatives of orientation and volume distribution.

\n\n

Args:

\n\n\n\n

Returns a tuple with the rotation rates and grain volume fraction changes.

\n", "signature": "(\tphase,\tfabric,\tn_grains,\torientations,\tfractions,\tstrain_rate,\tvelocity_gradient,\tstress_exponent,\tdeformation_exponent,\tnucleation_efficiency,\tgbm_mobility,\tvolume_fraction):", "funcdef": "def"}, "pydrex.diagnostics": {"fullname": "pydrex.diagnostics", "modulename": "pydrex.diagnostics", "kind": "module", "doc": "
\n

PyDRex: Methods to calculate texture and strain diagnostics.

\n
\n\n
\n\n

Calculations expect orientation matrices $a$ to represent passive\n(i.e. alias) rotations, which are defined in terms of the extrinsic ZXZ\neuler angles $\u03d5, \u03b8, \u03c6$ as\n$$\na = \\begin{bmatrix}\n \\cos\u03c6\\cos\u03d5 - \\cos\u03b8\\sin\u03d5\\sin\u03c6 & \\cos\u03b8\\cos\u03d5\\sin\u03c6 + \\cos\u03c6\\sin\u03d5 & \\sin\u03c6\\sin\u03b8 \\cr\n -\\sin\u03c6\\cos\u03d5 - \\cos\u03b8\\sin\u03d5\\cos\u03c6 & \\cos\u03b8\\cos\u03d5\\cos\u03c6 - \\sin\u03c6\\sin\u03d5 & \\cos\u03c6\\sin\u03b8 \\cr\n \\sin\u03b8\\sin\u03d5 & -\\sin\u03b8\\cos\u03d5 & \\cos\u03b8\n \\end{bmatrix}\n$$\nsuch that a[i, j] gives the direction cosine of the angle between the i-th\ngrain axis and the j-th external axis (in the global Eulerian frame).

\n\n
\n"}, "pydrex.diagnostics.elasticity_components": {"fullname": "pydrex.diagnostics.elasticity_components", "modulename": "pydrex.diagnostics", "qualname": "elasticity_components", "kind": "function", "doc": "

Calculate elasticity decompositions for the given elasticity tensors.

\n\n

Args:

\n\n\n\n

Returns a dictionary with the following data series:

\n\n\n\n
\n\n

Only 5 symmetry classes are relevant for elasticity decomposition,\ncompared to the usual 6 used to describe crystal families.\nCrystals with cubic symmetry contribute to the isotropic elasticity tensor,\nbecause the lattice spacing is identical in all orthogonal directions.\nNote also that the trigonal crystal system is not a crystal family\n(it belongs to the hexagonal family).

\n\n
\n", "signature": "(voigt_matrices):", "funcdef": "def"}, "pydrex.diagnostics.bingham_average": {"fullname": "pydrex.diagnostics.bingham_average", "modulename": "pydrex.diagnostics", "qualname": "bingham_average", "kind": "function", "doc": "

Compute Bingham average of orientation matrices.

\n\n

Returns the antipodally symmetric average orientation\nof the given crystallographic axis, or the a-axis by default.\nValid axis specifiers are \"a\" for [100], \"b\" for [010] and \"c\" for [001].

\n\n

See also: Watson (1966),\nMardia & Jupp, \u201cDirectional Statistics\u201d.

\n", "signature": "(orientations, axis='a'):", "funcdef": "def"}, "pydrex.diagnostics.finite_strain": {"fullname": "pydrex.diagnostics.finite_strain", "modulename": "pydrex.diagnostics", "qualname": "finite_strain", "kind": "function", "doc": "

Extract measures of finite strain from the deformation gradient.

\n\n

Extracts the largest principal strain value and the vector defining the axis of\nmaximum extension (longest semiaxis of the finite strain ellipsoid) from the 3x3\ndeformation gradient tensor.

\n", "signature": "(deformation_gradient, driver='ev'):", "funcdef": "def"}, "pydrex.diagnostics.symmetry_pgr": {"fullname": "pydrex.diagnostics.symmetry_pgr", "modulename": "pydrex.diagnostics", "qualname": "symmetry_pgr", "kind": "function", "doc": "

Compute texture symmetry eigenvalue diagnostics from grain orientation matrices.

\n\n

Compute Point, Girdle and Random symmetry diagnostics\nfor ternary texture classification.\nReturns the tuple (P, G, R) where\n$$\n\\begin{align*}\nP &= (\u03bb_{1} - \u03bb_{2}) / N \\cr\nG &= 2 (\u03bb_{2} - \u03bb_{3}) / N \\cr\nR &= 3 \u03bb_{3} / N\n\\end{align*}\n$$\nwith $N$ the sum of the eigenvalues $\u03bb_{1} \u2265 \u03bb_{2} \u2265 \u03bb_{3}$\nof the scatter (inertia) matrix.

\n\n

See e.g. Vollmer (1990).

\n", "signature": "(orientations, axis='a'):", "funcdef": "def"}, "pydrex.diagnostics.misorientation_indices": {"fullname": "pydrex.diagnostics.misorientation_indices", "modulename": "pydrex.diagnostics", "qualname": "misorientation_indices", "kind": "function", "doc": "

Calculate M-indices for a series of polycrystal textures.

\n\n

Calculate M-index using misorientation_index for a series of texture snapshots.\nThe orientation_stack is a NxMx3x3 array of orientations where N is the number of\ntexture snapshots and M is the number of grains.

\n\n

Uses either Ray or the Python multiprocessing library to calculate texture indices\nfor multiple snapshots simultaneously. The arguments ncpus and pool are only\nrelevant to the latter option: if ncpus is None the number of CPU cores to use\nis chosen automatically based on the maximum number available to the Python\ninterpreter, otherwise the specified number of cores is requested. Alternatively, an\nexisting instance of multiprocessing.Pool can be provided.

\n\n

If Ray is installed, it will be automatically preferred. In this case, the number of\nparallel workers should be set upon initialisation of the Ray cluster (which can be\ndistributed over the network).

\n\n

See misorientation_index for documentation of the remaining arguments.

\n", "signature": "(\torientation_stack,\tsystem: pydrex.geometry.LatticeSystem,\tbins=None,\tncpus=None,\tpool=None):", "funcdef": "def"}, "pydrex.diagnostics.misorientation_index": {"fullname": "pydrex.diagnostics.misorientation_index", "modulename": "pydrex.diagnostics", "qualname": "misorientation_index", "kind": "function", "doc": "

Calculate M-index for polycrystal orientations.

\n\n

The bins argument is passed to numpy.histogram.\nIf left as None, 1\u00b0 bins will be used as recommended by the reference paper.\nThe symmetry argument specifies the lattice system which determines intrinsic\nsymmetry degeneracies and the maximum allowable misorientation angle.\nSee _geo.LatticeSystem for supported systems.

\n\n
\n\n

This method must be able to allocate an array of shape\n$ \\frac{N!}{2(N-2)!}\u00d7 M^{2} $\nfor N the length of orientations and M the number of symmetry operations for\nthe given system.

\n\n
\n\n

See Skemer et al. (2005).

\n", "signature": "(orientations, system: pydrex.geometry.LatticeSystem, bins=None):", "funcdef": "def"}, "pydrex.diagnostics.coaxial_index": {"fullname": "pydrex.diagnostics.coaxial_index", "modulename": "pydrex.diagnostics", "qualname": "coaxial_index", "kind": "function", "doc": "

Calculate coaxial \u201cBA\u201d index for a combination of two crystal axes.

\n\n

The BA index of Mainprice et al. (2015)\nis derived from the eigenvalue symmetry diagnostics and measures point vs girdle\nsymmetry in the aggregate. $BA \u2208 [0, 1]$ where $BA = 0$ corresponds to a perfect\naxial girdle texture and $BA = 1$ represents a point symmetry texture assuming that\nthe random component $R$ is negligible. May be less susceptible to random\nfluctuations compared to the raw eigenvalue diagnostics.

\n", "signature": "(orientations, axis1='b', axis2='a'):", "funcdef": "def"}, "pydrex.diagnostics.smallest_angle": {"fullname": "pydrex.diagnostics.smallest_angle", "modulename": "pydrex.diagnostics", "qualname": "smallest_angle", "kind": "function", "doc": "

Get smallest angle between a unit vector and a bidirectional axis.

\n\n

The axis is specified using either of its two parallel unit vectors.\nOptionally project the vector onto the plane (given by its unit normal)\nbefore calculating the angle.

\n\n

Examples:

\n\n
\n
>>> import numpy as np\n>>> def f64(x): return np.asarray(x, dtype=np.float64)\n>>> int(smallest_angle(f64([1e0, 0e0, 0e0]), f64([1e0, 0e0, 0e0])))\n0\n>>> int(smallest_angle(f64([1e0, 0e0, 0e0]), f64([0e0, 1e0, 0e0])))\n90\n>>> int(smallest_angle(f64([1e0, 0e0, 0e0]), f64([0e0, -1e0, 0e0])))\n90\n>>> int(smallest_angle(f64([1e0, 0e0, 0e0]), f64([np.sqrt(2), np.sqrt(2), 0e0])))\n45\n>>> int(smallest_angle(f64([1e0, 0e0, 0e0]), f64([-np.sqrt(2), np.sqrt(2), 0e0])))\n45\n
\n
\n", "signature": "(vector, axis, plane=None):", "funcdef": "def"}, "pydrex.exceptions": {"fullname": "pydrex.exceptions", "modulename": "pydrex.exceptions", "kind": "module", "doc": "
\n

PyDRex: Custom exceptions (subclasses of pydrex.Error).

\n
\n"}, "pydrex.exceptions.Error": {"fullname": "pydrex.exceptions.Error", "modulename": "pydrex.exceptions", "qualname": "Error", "kind": "class", "doc": "

Base class for exceptions in PyDRex.

\n", "bases": "builtins.Exception"}, "pydrex.exceptions.MissingDependencyError": {"fullname": "pydrex.exceptions.MissingDependencyError", "modulename": "pydrex.exceptions", "qualname": "MissingDependencyError", "kind": "class", "doc": "

Exception raised when optional dependencies are missing.

\n\n

Attributes:\n message \u2014 explanation of the error

\n", "bases": "Error"}, "pydrex.exceptions.MissingDependencyError.__init__": {"fullname": "pydrex.exceptions.MissingDependencyError.__init__", "modulename": "pydrex.exceptions", "qualname": "MissingDependencyError.__init__", "kind": "function", "doc": "

\n", "signature": "(message)"}, "pydrex.exceptions.MissingDependencyError.message": {"fullname": "pydrex.exceptions.MissingDependencyError.message", "modulename": "pydrex.exceptions", "qualname": "MissingDependencyError.message", "kind": "variable", "doc": "

\n"}, "pydrex.exceptions.ConfigError": {"fullname": "pydrex.exceptions.ConfigError", "modulename": "pydrex.exceptions", "qualname": "ConfigError", "kind": "class", "doc": "

Exception raised for errors in the input configuration.

\n\n

Attributes:\n message \u2014 explanation of the error

\n", "bases": "Error"}, "pydrex.exceptions.ConfigError.__init__": {"fullname": "pydrex.exceptions.ConfigError.__init__", "modulename": "pydrex.exceptions", "qualname": "ConfigError.__init__", "kind": "function", "doc": "

\n", "signature": "(message)"}, "pydrex.exceptions.ConfigError.message": {"fullname": "pydrex.exceptions.ConfigError.message", "modulename": "pydrex.exceptions", "qualname": "ConfigError.message", "kind": "variable", "doc": "

\n"}, "pydrex.exceptions.MeshError": {"fullname": "pydrex.exceptions.MeshError", "modulename": "pydrex.exceptions", "qualname": "MeshError", "kind": "class", "doc": "

Exception raised for errors in the input mesh.

\n\n

Attributes:\n message \u2014 explanation of the error

\n", "bases": "Error"}, "pydrex.exceptions.MeshError.__init__": {"fullname": "pydrex.exceptions.MeshError.__init__", "modulename": "pydrex.exceptions", "qualname": "MeshError.__init__", "kind": "function", "doc": "

\n", "signature": "(message)"}, "pydrex.exceptions.MeshError.message": {"fullname": "pydrex.exceptions.MeshError.message", "modulename": "pydrex.exceptions", "qualname": "MeshError.message", "kind": "variable", "doc": "

\n"}, "pydrex.exceptions.IterationError": {"fullname": "pydrex.exceptions.IterationError", "modulename": "pydrex.exceptions", "qualname": "IterationError", "kind": "class", "doc": "

Exception raised for errors in numerical iteration schemes.

\n\n

Attributes:\n message \u2014 explanation of the error

\n", "bases": "Error"}, "pydrex.exceptions.IterationError.__init__": {"fullname": "pydrex.exceptions.IterationError.__init__", "modulename": "pydrex.exceptions", "qualname": "IterationError.__init__", "kind": "function", "doc": "

\n", "signature": "(message)"}, "pydrex.exceptions.IterationError.message": {"fullname": "pydrex.exceptions.IterationError.message", "modulename": "pydrex.exceptions", "qualname": "IterationError.message", "kind": "variable", "doc": "

\n"}, "pydrex.exceptions.SCSVError": {"fullname": "pydrex.exceptions.SCSVError", "modulename": "pydrex.exceptions", "qualname": "SCSVError", "kind": "class", "doc": "

Exception raised for errors in SCSV file I/O.

\n\n

Attributes:

\n\n\n", "bases": "Error"}, "pydrex.exceptions.SCSVError.__init__": {"fullname": "pydrex.exceptions.SCSVError.__init__", "modulename": "pydrex.exceptions", "qualname": "SCSVError.__init__", "kind": "function", "doc": "

\n", "signature": "(message)"}, "pydrex.exceptions.SCSVError.message": {"fullname": "pydrex.exceptions.SCSVError.message", "modulename": "pydrex.exceptions", "qualname": "SCSVError.message", "kind": "variable", "doc": "

\n"}, "pydrex.exceptions.ModelContextError": {"fullname": "pydrex.exceptions.ModelContextError", "modulename": "pydrex.exceptions", "qualname": "ModelContextError", "kind": "class", "doc": "

Exception raised for errors in mesh.Model context state.

\n\n

Attributes:\n message \u2014 explanation of the error

\n", "bases": "Error"}, "pydrex.exceptions.ModelContextError.__init__": {"fullname": "pydrex.exceptions.ModelContextError.__init__", "modulename": "pydrex.exceptions", "qualname": "ModelContextError.__init__", "kind": "function", "doc": "

\n", "signature": "(message)"}, "pydrex.exceptions.ModelContextError.message": {"fullname": "pydrex.exceptions.ModelContextError.message", "modulename": "pydrex.exceptions", "qualname": "ModelContextError.message", "kind": "variable", "doc": "

\n"}, "pydrex.geometry": {"fullname": "pydrex.geometry", "modulename": "pydrex.geometry", "kind": "module", "doc": "
\n

PyDRex: Functions for geometric coordinate conversions and projections.

\n
\n"}, "pydrex.geometry.LatticeSystem": {"fullname": "pydrex.geometry.LatticeSystem", "modulename": "pydrex.geometry", "qualname": "LatticeSystem", "kind": "class", "doc": "

Crystallographic lattice systems supported by postprocessing methods.

\n\n

The value of a member is (a, b) with a and b as given in the table below.\nThe additional row lists the maximum misorientation angle between two crystallites\nfor the given lattice system.

\n\n
        triclinic  monoclinic  orthorhombic  rhombohedral tetragonal hexagonal\n------------------------------------------------------------------------------\na       1          2           2             3            4          6\nb       1          2           4             6            8          12\n\u03b8max    180\u00b0       180\u00b0        120\u00b0          120\u00b0         90\u00b0        90\u00b0\n
\n\n

This is identically Table 1 in Grimmer (1979).

\n", "bases": "enum.Enum"}, "pydrex.geometry.LatticeSystem.triclinic": {"fullname": "pydrex.geometry.LatticeSystem.triclinic", "modulename": "pydrex.geometry", "qualname": "LatticeSystem.triclinic", "kind": "variable", "doc": "

\n", "default_value": "<LatticeSystem.triclinic: (1, 1)>"}, "pydrex.geometry.LatticeSystem.monoclinic": {"fullname": "pydrex.geometry.LatticeSystem.monoclinic", "modulename": "pydrex.geometry", "qualname": "LatticeSystem.monoclinic", "kind": "variable", "doc": "

\n", "default_value": "<LatticeSystem.monoclinic: (2, 2)>"}, "pydrex.geometry.LatticeSystem.orthorhombic": {"fullname": "pydrex.geometry.LatticeSystem.orthorhombic", "modulename": "pydrex.geometry", "qualname": "LatticeSystem.orthorhombic", "kind": "variable", "doc": "

\n", "default_value": "<LatticeSystem.orthorhombic: (2, 4)>"}, "pydrex.geometry.LatticeSystem.rhombohedral": {"fullname": "pydrex.geometry.LatticeSystem.rhombohedral", "modulename": "pydrex.geometry", "qualname": "LatticeSystem.rhombohedral", "kind": "variable", "doc": "

\n", "default_value": "<LatticeSystem.rhombohedral: (3, 6)>"}, "pydrex.geometry.LatticeSystem.tetragonal": {"fullname": "pydrex.geometry.LatticeSystem.tetragonal", "modulename": "pydrex.geometry", "qualname": "LatticeSystem.tetragonal", "kind": "variable", "doc": "

\n", "default_value": "<LatticeSystem.tetragonal: (4, 8)>"}, "pydrex.geometry.LatticeSystem.hexagonal": {"fullname": "pydrex.geometry.LatticeSystem.hexagonal", "modulename": "pydrex.geometry", "qualname": "LatticeSystem.hexagonal", "kind": "variable", "doc": "

\n", "default_value": "<LatticeSystem.hexagonal: (6, 12)>"}, "pydrex.geometry.to_cartesian": {"fullname": "pydrex.geometry.to_cartesian", "modulename": "pydrex.geometry", "qualname": "to_cartesian", "kind": "function", "doc": "

Convert spherical to cartesian coordinates in \u211d\u00b3.

\n\n

Spherical coordinate convention:

\n\n\n\n

By default, a radius of r = 1 is used for the sphere.\nReturns a tuple containing arrays of x, y, and z values.

\n", "signature": "(\u03c6, \u03b8, r=1):", "funcdef": "def"}, "pydrex.geometry.to_spherical": {"fullname": "pydrex.geometry.to_spherical", "modulename": "pydrex.geometry", "qualname": "to_spherical", "kind": "function", "doc": "

Convert cartesian coordinates in \u211d\u00b3 to spherical coordinates.

\n\n

Spherical coordinate convention:

\n\n\n\n

Returns a tuple containing arrays of r, \u03d5 and \u03b8 values.

\n", "signature": "(x, y, z):", "funcdef": "def"}, "pydrex.geometry.misorientation_angles": {"fullname": "pydrex.geometry.misorientation_angles", "modulename": "pydrex.geometry", "qualname": "misorientation_angles", "kind": "function", "doc": "

Calculate minimum misorientation angles for collections of rotation quaternions.

\n\n

Calculate the smallest angular distance between any quaternions q1_array[:, i] and\nq2_array[:, j], where i == j and the first dimensions of q1_array and q2_array\nare of equal length (the output will also be this long):

\n\n
q1_array.shape      q2_array.shape      len(output)\n---------------------------------------------------\nNxAx4               NxBx4               N\n
\n\n
\n\n

This method must be able to allocate a floating point array of shape Nx(A*B)

\n\n
\n\n

Uses ~25% less memory than the same operation with rotation matrices.

\n\n

See also:

\n\n\n", "signature": "(q1_array, q2_array):", "funcdef": "def"}, "pydrex.geometry.symmetry_operations": {"fullname": "pydrex.geometry.symmetry_operations", "modulename": "pydrex.geometry", "qualname": "symmetry_operations", "kind": "function", "doc": "

Get sequence of symmetry operations for the given LatticeSystem.

\n\n

Returned transforms are either quaternions (for rotations of the lattice) or 4x4\nmatrices which pre-multiply a quaternion to give a reflected variant (reflections\nare improper rotations and cannot be represented as quaternions or SciPy rotation\nmatrices).

\n", "signature": "(system: pydrex.geometry.LatticeSystem):", "funcdef": "def"}, "pydrex.geometry.poles": {"fullname": "pydrex.geometry.poles", "modulename": "pydrex.geometry", "qualname": "poles", "kind": "function", "doc": "

Extract 3D vectors of crystallographic directions from orientation matrices.

\n\n

Expects orientations to be an array with shape (N, 3, 3).\nThe optional arguments ref_axes and hkl can be used to change\nthe global reference axes and the crystallographic direction respectively.\nThe reference axes should be given as a string of two letters,\ne.g. \"xz\" (default), which specify the second and third axes\nof the global right-handed reference frame. The third letter in the set \"xyz\"\ndetermines the first axis. The ref_axes will therefore become the\nhorizontal and vertical axes of pole figures used to plot the directions.

\n", "signature": "(orientations, ref_axes='xz', hkl=[1, 0, 0]):", "funcdef": "def"}, "pydrex.geometry.lambert_equal_area": {"fullname": "pydrex.geometry.lambert_equal_area", "modulename": "pydrex.geometry", "qualname": "lambert_equal_area", "kind": "function", "doc": "

Project axial data from a 3D sphere onto a 2D disk.

\n\n

Project points from a 3D sphere of radius 1, given in Cartesian coordinates,\nto points on a 2D disk using a Lambert equal area azimuthal projection.\nReturns arrays of the X and Y coordinates in the unit disk.

\n\n

This implementation first maps all points onto the same hemisphere,\nand then projects that hemisphere onto the disk.

\n", "signature": "(xvals, yvals, zvals):", "funcdef": "def"}, "pydrex.geometry.shirley_concentric_squaredisk": {"fullname": "pydrex.geometry.shirley_concentric_squaredisk", "modulename": "pydrex.geometry", "qualname": "shirley_concentric_squaredisk", "kind": "function", "doc": "

Project points from a square onto a disk using the concentric Shirley method.

\n\n

The concentric method of Shirley & Chiu (1997)\nis optimised to preserve area. See also: http://marc-b-reynolds.github.io/math/2017/01/08/SquareDisc.html.

\n\n

This can be used to set up uniform grids on a disk, e.g.

\n\n
\n
>>> a = [x / 5.0 for x in range(-5, 6)]\n>>> x = [[x] * len(a) for x in a]\n>>> y = [a for _ in a]\n>>> x_flat = [j for i in x for j in i]\n>>> y_flat = [j for i in y for j in i]\n>>> x_disk, y_disk = shirley_concentric_squaredisk(x_flat, y_flat)\n>>> r = x_disk**2 + y_disk**2\n>>> r.reshape((len(a), len(a)))\narray([[1.  , 1.  , 1.  , 1.  , 1.  , 1.  , 1.  , 1.  , 1.  , 1.  , 1.  ],\n       [1.  , 0.64, 0.64, 0.64, 0.64, 0.64, 0.64, 0.64, 0.64, 0.64, 1.  ],\n       [1.  , 0.64, 0.36, 0.36, 0.36, 0.36, 0.36, 0.36, 0.36, 0.64, 1.  ],\n       [1.  , 0.64, 0.36, 0.16, 0.16, 0.16, 0.16, 0.16, 0.36, 0.64, 1.  ],\n       [1.  , 0.64, 0.36, 0.16, 0.04, 0.04, 0.04, 0.16, 0.36, 0.64, 1.  ],\n       [1.  , 0.64, 0.36, 0.16, 0.04, 0.  , 0.04, 0.16, 0.36, 0.64, 1.  ],\n       [1.  , 0.64, 0.36, 0.16, 0.04, 0.04, 0.04, 0.16, 0.36, 0.64, 1.  ],\n       [1.  , 0.64, 0.36, 0.16, 0.16, 0.16, 0.16, 0.16, 0.36, 0.64, 1.  ],\n       [1.  , 0.64, 0.36, 0.36, 0.36, 0.36, 0.36, 0.36, 0.36, 0.64, 1.  ],\n       [1.  , 0.64, 0.64, 0.64, 0.64, 0.64, 0.64, 0.64, 0.64, 0.64, 1.  ],\n       [1.  , 1.  , 1.  , 1.  , 1.  , 1.  , 1.  , 1.  , 1.  , 1.  , 1.  ]])\n>>> from math import atan2\n>>> \u03b8 = [atan2(y, x) for y, x in zip(y_disk, x_disk)]\n>>> max(\u03b8)\n3.141592653589793\n>>> min(\u03b8)\n-2.9845130209101467\n
\n
\n", "signature": "(xvals, yvals):", "funcdef": "def"}, "pydrex.geometry.to_indices": {"fullname": "pydrex.geometry.to_indices", "modulename": "pydrex.geometry", "qualname": "to_indices", "kind": "function", "doc": "

\n", "signature": "(horizontal, vertical):", "funcdef": "def"}, "pydrex.io": {"fullname": "pydrex.io", "modulename": "pydrex.io", "kind": "module", "doc": "
\n

PyDRex: Mesh, configuration and supporting data Input/Output functions.

\n
\n\n

PyDRex can read/write three kinds of plain text files:

\n\n\n\n

SCSV files are our custom CSV files with a YAML header. The header is used for data\nattribution and metadata, as well as a column type spec. There is no official spec for\nSCSV files at the moment but they should follow the format of existing SCSV files in\nthe data/ folder of the source repository. For supported cell types, see\nSCSV_TYPEMAP.

\n"}, "pydrex.io.DEFAULT_PARAMS": {"fullname": "pydrex.io.DEFAULT_PARAMS", "modulename": "pydrex.io", "qualname": "DEFAULT_PARAMS", "kind": "variable", "doc": "

Default simulation parameters.

\n", "default_value": "{'olivine_fraction': 1.0, 'enstatite_fraction': 0.0, 'stress_exponent': 1.5, 'deformation_exponent': 3.5, 'gbm_mobility': 125, 'gbs_threshold': 0.3, 'nucleation_efficiency': 5.0, 'number_of_grains': 3500, 'initial_olivine_fabric': 'A'}"}, "pydrex.io.SCSV_TYPEMAP": {"fullname": "pydrex.io.SCSV_TYPEMAP", "modulename": "pydrex.io", "qualname": "SCSV_TYPEMAP", "kind": "variable", "doc": "

Mapping of supported SCSV field types to corresponding Python types.

\n", "default_value": "{'string': <class 'str'>, 'integer': <class 'int'>, 'float': <class 'float'>, 'boolean': <class 'bool'>, 'complex': <class 'complex'>}"}, "pydrex.io.extract_h5part": {"fullname": "pydrex.io.extract_h5part", "modulename": "pydrex.io", "qualname": "extract_h5part", "kind": "function", "doc": "

Extract CPO data from Fluidity h5part file and save to canonical formats.

\n", "signature": "(file, phase, fabric, n_grains, output):", "funcdef": "def"}, "pydrex.io.read_scsv": {"fullname": "pydrex.io.read_scsv", "modulename": "pydrex.io", "qualname": "read_scsv", "kind": "function", "doc": "

Read data from an SCSV file.

\n\n

Prints the YAML header section to output and returns a NamedTuple with columns of\nthe csv data. See also save_scsv.

\n", "signature": "(file):", "funcdef": "def"}, "pydrex.io.write_scsv_header": {"fullname": "pydrex.io.write_scsv_header", "modulename": "pydrex.io", "qualname": "write_scsv_header", "kind": "function", "doc": "

Write YAML header to an SCSV stream.

\n\n

Args:

\n\n\n\n

See also read_scsv, save_scsv.

\n", "signature": "(stream, schema, comments=None):", "funcdef": "def"}, "pydrex.io.save_scsv": {"fullname": "pydrex.io.save_scsv", "modulename": "pydrex.io", "qualname": "save_scsv", "kind": "function", "doc": "

Save data to SCSV file.

\n\n

Args:

\n\n\n\n

Optional keyword arguments are passed to write_scsv_header. See also read_scsv.

\n", "signature": "(file, schema, data, **kwargs):", "funcdef": "def"}, "pydrex.io.parse_config": {"fullname": "pydrex.io.parse_config", "modulename": "pydrex.io", "qualname": "parse_config", "kind": "function", "doc": "

Parse a TOML file containing PyDRex configuration.

\n", "signature": "(path):", "funcdef": "def"}, "pydrex.io.resolve_path": {"fullname": "pydrex.io.resolve_path", "modulename": "pydrex.io", "qualname": "resolve_path", "kind": "function", "doc": "

Resolve relative paths and create parent directories if necessary.

\n\n

Relative paths are interpreted with respect to the current working directory,\ni.e. the directory from whith the current Python process was executed,\nunless a specific reference directory is provided with refdir.

\n", "signature": "(path, refdir=None):", "funcdef": "def"}, "pydrex.io.stringify": {"fullname": "pydrex.io.stringify", "modulename": "pydrex.io", "qualname": "stringify", "kind": "function", "doc": "

Return a cleaned version of a string for use in filenames, etc.

\n", "signature": "(s):", "funcdef": "def"}, "pydrex.io.data": {"fullname": "pydrex.io.data", "modulename": "pydrex.io", "qualname": "data", "kind": "function", "doc": "

Get resolved path to a pydrex data directory.

\n", "signature": "(directory):", "funcdef": "def"}, "pydrex.logger": {"fullname": "pydrex.logger", "modulename": "pydrex.logger", "kind": "module", "doc": "
\n

PyDRex: logger settings and boilerplate.

\n
\n\n

Python's logging module is weird and its methods don't allow us to specify\nwhich logger to use, so just using logging.debug for example always uses\nthe \"root\" logger, which spams a bunch of messages from other imports/modules.\nInstead, the methods in this module are thin wrappers that use custom\nlogging objects (pydrex.logger.LOGGER and pydrex.logger.CONSOLE_LOGGER).\nThe method quiet_aliens can be invoked to suppress most messages\nfrom third-party modules, except critical errors and warnings from Numba.

\n\n

By default, PyDRex emits INFO level messages to the console.\nThis can be changed globally by setting the new level with CONSOLE_LOGGER.setLevel:

\n\n
\n
from pydrex import logger as _log\n_log.info("this message will be printed to the console")\n\n_log.CONSOLE_LOGGER.setLevel("ERROR")\n_log.info("this message will NOT be printed to the console")\n_log.error("this message will be printed to the console")\n
\n
\n\n

To change the console logging level for a particular local context,\nuse the handler_level context manager:

\n\n
\n
_log.CONSOLE_LOGGER.setLevel("INFO")\n_log.info("this message will be printed to the console")\n\nwith handler_level("ERROR"):\n    _log.info("this message will NOT be printed to the console")\n\n_log.info("this message will be printed to the console")\n
\n
\n\n

To save debug logs to a file, the logfile_enable context manager is recommended.\nAlways use the old printf style formatting for log messages, not fstrings,\notherwise compute time will be wasted on string conversions when logging is disabled:

\n\n
\n
_log.quiet_aliens()  # Suppress third-party log messages except CRITICAL from Numba.\nwith _log.logfile_enable("my_log_file.log"):  # Overwrite existing file unless mode="a".\n    value = 42\n    _log.critical("critical error with value: %s", value)\n    _log.error("runtime error with value: %s", value)\n    _log.warning("warning with value: %s", value)\n    _log.info("information message with value: %s", value)\n    _log.debug("verbose debugging message with value: %s", value)\n    ... # Construct Minerals, update orientations, etc.\n
\n
\n"}, "pydrex.logger.ConsoleFormatter": {"fullname": "pydrex.logger.ConsoleFormatter", "modulename": "pydrex.logger", "qualname": "ConsoleFormatter", "kind": "class", "doc": "

Log formatter that uses terminal color codes.

\n", "bases": "logging.Formatter"}, "pydrex.logger.ConsoleFormatter.colorfmt": {"fullname": "pydrex.logger.ConsoleFormatter.colorfmt", "modulename": "pydrex.logger", "qualname": "ConsoleFormatter.colorfmt", "kind": "function", "doc": "

\n", "signature": "(self, code):", "funcdef": "def"}, "pydrex.logger.ConsoleFormatter.format": {"fullname": "pydrex.logger.ConsoleFormatter.format", "modulename": "pydrex.logger", "qualname": "ConsoleFormatter.format", "kind": "function", "doc": "

Format the specified record as text.

\n\n

The record's attribute dictionary is used as the operand to a\nstring formatting operation which yields the returned string.\nBefore formatting the dictionary, a couple of preparatory steps\nare carried out. The message attribute of the record is computed\nusing LogRecord.getMessage(). If the formatting string uses the\ntime (as determined by a call to usesTime(), formatTime() is\ncalled to format the event time. If there is exception information,\nit is formatted using formatException() and appended to the message.

\n", "signature": "(self, record):", "funcdef": "def"}, "pydrex.logger.LOGGER": {"fullname": "pydrex.logger.LOGGER", "modulename": "pydrex.logger", "qualname": "LOGGER", "kind": "variable", "doc": "

\n", "default_value": "<Logger pydrex (DEBUG)>"}, "pydrex.logger.CONSOLE_LOGGER": {"fullname": "pydrex.logger.CONSOLE_LOGGER", "modulename": "pydrex.logger", "qualname": "CONSOLE_LOGGER", "kind": "variable", "doc": "

\n", "default_value": "<StreamHandler (INFO)>"}, "pydrex.logger.handle_exception": {"fullname": "pydrex.logger.handle_exception", "modulename": "pydrex.logger", "qualname": "handle_exception", "kind": "function", "doc": "

\n", "signature": "(exec_type, exec_value, exec_traceback):", "funcdef": "def"}, "pydrex.logger.handler_level": {"fullname": "pydrex.logger.handler_level", "modulename": "pydrex.logger", "qualname": "handler_level", "kind": "function", "doc": "

Set logging handler level for current context.

\n\n

Args:

\n\n\n", "signature": "(level, handler=<StreamHandler (INFO)>):", "funcdef": "def"}, "pydrex.logger.logfile_enable": {"fullname": "pydrex.logger.logfile_enable", "modulename": "pydrex.logger", "qualname": "logfile_enable", "kind": "function", "doc": "

Enable logging to a file at path with given level.

\n", "signature": "(path, level=10, mode='w'):", "funcdef": "def"}, "pydrex.logger.critical": {"fullname": "pydrex.logger.critical", "modulename": "pydrex.logger", "qualname": "critical", "kind": "function", "doc": "

Log a CRITICAL message in PyDRex.

\n", "signature": "(msg, *args, **kwargs):", "funcdef": "def"}, "pydrex.logger.error": {"fullname": "pydrex.logger.error", "modulename": "pydrex.logger", "qualname": "error", "kind": "function", "doc": "

Log an ERROR message in PyDRex.

\n", "signature": "(msg, *args, **kwargs):", "funcdef": "def"}, "pydrex.logger.warning": {"fullname": "pydrex.logger.warning", "modulename": "pydrex.logger", "qualname": "warning", "kind": "function", "doc": "

Log a WARNING message in PyDRex.

\n", "signature": "(msg, *args, **kwargs):", "funcdef": "def"}, "pydrex.logger.info": {"fullname": "pydrex.logger.info", "modulename": "pydrex.logger", "qualname": "info", "kind": "function", "doc": "

Log an INFO message in PyDRex.

\n", "signature": "(msg, *args, **kwargs):", "funcdef": "def"}, "pydrex.logger.debug": {"fullname": "pydrex.logger.debug", "modulename": "pydrex.logger", "qualname": "debug", "kind": "function", "doc": "

Log a DEBUG message in PyDRex.

\n", "signature": "(msg, *args, **kwargs):", "funcdef": "def"}, "pydrex.logger.exception": {"fullname": "pydrex.logger.exception", "modulename": "pydrex.logger", "qualname": "exception", "kind": "function", "doc": "

Log a message with level ERROR but retain exception information.

\n\n

This function should only be called from an exception handler.

\n", "signature": "(msg, *args, **kwargs):", "funcdef": "def"}, "pydrex.logger.quiet_aliens": {"fullname": "pydrex.logger.quiet_aliens", "modulename": "pydrex.logger", "qualname": "quiet_aliens", "kind": "function", "doc": "

Restrict alien loggers \ud83d\udc7d because I'm trying to find MY bugs, thanks.

\n", "signature": "():", "funcdef": "def"}, "pydrex.minerals": {"fullname": "pydrex.minerals", "modulename": "pydrex.minerals", "kind": "module", "doc": "
\n

PyDRex: Computations of mineral texture and elasticity.

\n
\n\n

Acronyms:

\n\n\n"}, "pydrex.minerals.OLIVINE_STIFFNESS": {"fullname": "pydrex.minerals.OLIVINE_STIFFNESS", "modulename": "pydrex.minerals", "qualname": "OLIVINE_STIFFNESS", "kind": "variable", "doc": "

Stiffness tensor for olivine (Voigt representation), with units of GPa.

\n\n

The source of the values used here is unknown, but they are copied\nfrom the original DRex code: http://www.ipgp.fr/~kaminski/web_doudoud/DRex.tar.gz\n[88K download]

\n", "default_value": "array([[320.71, 69.84, 71.22, 0. , 0. , 0. ],\n [ 69.84, 197.25, 74.8 , 0. , 0. , 0. ],\n [ 71.22, 74.8 , 234.32, 0. , 0. , 0. ],\n [ 0. , 0. , 0. , 63.77, 0. , 0. ],\n [ 0. , 0. , 0. , 0. , 77.67, 0. ],\n [ 0. , 0. , 0. , 0. , 0. , 78.36]])"}, "pydrex.minerals.ENSTATITE_STIFFNESS": {"fullname": "pydrex.minerals.ENSTATITE_STIFFNESS", "modulename": "pydrex.minerals", "qualname": "ENSTATITE_STIFFNESS", "kind": "variable", "doc": "

Stiffness tensor for enstatite (Voigt representation), with units of GPa.

\n\n

The source of the values used here is unknown, but they are copied\nfrom the original DRex code: http://www.ipgp.fr/~kaminski/web_doudoud/DRex.tar.gz\n[88K download]

\n", "default_value": "array([[236.9, 79.6, 63.2, 0. , 0. , 0. ],\n [ 79.6, 180.5, 56.8, 0. , 0. , 0. ],\n [ 63.2, 56.8, 230.4, 0. , 0. , 0. ],\n [ 0. , 0. , 0. , 84.3, 0. , 0. ],\n [ 0. , 0. , 0. , 0. , 79.4, 0. ],\n [ 0. , 0. , 0. , 0. , 0. , 80.1]])"}, "pydrex.minerals.OLIVINE_PRIMARY_AXIS": {"fullname": "pydrex.minerals.OLIVINE_PRIMARY_AXIS", "modulename": "pydrex.minerals", "qualname": "OLIVINE_PRIMARY_AXIS", "kind": "variable", "doc": "

Primary slip axis name for for the given olivine fabric.

\n", "default_value": "{<MineralFabric.olivine_A: 0>: 'a', <MineralFabric.olivine_B: 1>: 'c', <MineralFabric.olivine_C: 2>: 'c', <MineralFabric.olivine_D: 3>: 'a', <MineralFabric.olivine_E: 4>: 'a'}"}, "pydrex.minerals.OLIVINE_SLIP_SYSTEMS": {"fullname": "pydrex.minerals.OLIVINE_SLIP_SYSTEMS", "modulename": "pydrex.minerals", "qualname": "OLIVINE_SLIP_SYSTEMS", "kind": "variable", "doc": "

Slip systems for olivine in conventional order.

\n\n

Tuples contain the slip plane normal and slip direction vectors.\nThe order of slip systems returned matches the order of critical shear stresses\nreturned by pydrex.core.get_crss.

\n", "default_value": "(([0, 1, 0], [1, 0, 0]), ([0, 0, 1], [1, 0, 0]), ([0, 1, 0], [0, 0, 1]), ([1, 0, 0], [0, 0, 1]))"}, "pydrex.minerals.voigt_averages": {"fullname": "pydrex.minerals.voigt_averages", "modulename": "pydrex.minerals", "qualname": "voigt_averages", "kind": "function", "doc": "

Calculate elastic tensors as the Voigt averages of a collection of minerals.

\n\n

Args:

\n\n\n\n

Raises a ValueError if the minerals contain an unequal number of grains or stored\ntexture results.

\n", "signature": "(minerals, weights):", "funcdef": "def"}, "pydrex.minerals.Mineral": {"fullname": "pydrex.minerals.Mineral", "modulename": "pydrex.minerals", "qualname": "Mineral", "kind": "class", "doc": "

Class for storing polycrystal texture for a single mineral phase.

\n\n

A Mineral stores texture data for an aggregate of grains*.\nAdditionally, mineral fabric type and deformation regime are also tracked.\nTo provide an initial texture for the mineral, use the constructor arguments\nfractions_init and orientations_init. By default,\na uniform volume distribution of random orientations is generated.

\n\n

The update_orientations method computes new orientations and grain volumes\nfor a given velocity gradient. These results are stored in the .orientations and\n.fractions attributes of the Mineral instance. The method also returns the\nupdated macroscopic deformation gradient based on the provided initial deformation\ngradient.

\n\n

*Note that the \"number of grains\" is a static integer value that\ndoes not track the actual number of physical grains in the deforming polycrystal.\nInstead, this number acts as a \"number of bins\" for the statistical resolution of\nthe crystallographic orientation distribution. The value is roughly equivalent to\n(a multiple of) the number of initial, un-recrystallised grains in the polycrystal.\nIt is assumed that recrystallised grains do not grow large enough to require\nrotation tracking.

\n\n

Examples:

\n\n

Mineral with isotropic initial texture:

\n\n
\n
>>> import pydrex\n>>> olA = pydrex.Mineral(\n...     phase=pydrex.MineralPhase.olivine,\n...     fabric=pydrex.MineralFabric.olivine_A,\n...     regime=pydrex.DeformationRegime.dislocation,\n...     n_grains=2000\n... )\n>>> olA.phase\n<MineralPhase.olivine: 0>\n>>> olA.fabric\n<MineralFabric.olivine_A: 0>\n>>> olA.regime\n<DeformationRegime.dislocation: 1>\n>>> olA.n_grains\n2000\n
\n
\n\n

Mineral with specified initial texture and default phase, fabric and regime settings\nwhich are for an olivine A-type mineral in the dislocation creep regime.\nThe initial grain volume fractions should be normalised.

\n\n
\n
>>> import numpy as np\n>>> from scipy.spatial.transform import Rotation\n>>> import pydrex\n>>> rng = np.random.default_rng()\n>>> n_grains = 2000\n>>> olA = pydrex.Mineral(\n...     n_grains=n_grains,\n...     fractions_init=np.full(n_grains, 1 / n_grains),\n...     orientations_init=Rotation.from_euler(\n...         "zxz", [\n...             [x * np.pi / 2, np.pi / 2, np.pi / 2] for x in rng.random(n_grains)\n...         ]\n...     ).inv().as_matrix(),\n... )\n>>> len(olA.orientations)\n1\n>>> type(olA.orientations)\n<class 'list'>\n>>> olA.orientations[0].shape\n(2000, 3, 3)\n>>> olA.fractions[0].shape\n(2000,)\n
\n
\n\n

Note that minerals can also be constructed from serialized data,\nsee Mineral.load and Mineral.from_file.

\n\n

Attributes:

\n\n\n"}, "pydrex.minerals.Mineral.__init__": {"fullname": "pydrex.minerals.Mineral.__init__", "modulename": "pydrex.minerals", "qualname": "Mineral.__init__", "kind": "function", "doc": "

\n", "signature": "(\tphase: int = <MineralPhase.olivine: 0>,\tfabric: int = <MineralFabric.olivine_A: 0>,\tregime: int = <DeformationRegime.dislocation: 1>,\tn_grains: int = 3500,\tfractions_init: numpy.ndarray = None,\torientations_init: numpy.ndarray = None,\tfractions: list = <factory>,\torientations: list = <factory>,\tseed: int = None,\tlband: int = None,\tuband: int = None)"}, "pydrex.minerals.Mineral.phase": {"fullname": "pydrex.minerals.Mineral.phase", "modulename": "pydrex.minerals", "qualname": "Mineral.phase", "kind": "variable", "doc": "

\n", "annotation": ": int", "default_value": "<MineralPhase.olivine: 0>"}, "pydrex.minerals.Mineral.fabric": {"fullname": "pydrex.minerals.Mineral.fabric", "modulename": "pydrex.minerals", "qualname": "Mineral.fabric", "kind": "variable", "doc": "

\n", "annotation": ": int", "default_value": "<MineralFabric.olivine_A: 0>"}, "pydrex.minerals.Mineral.regime": {"fullname": "pydrex.minerals.Mineral.regime", "modulename": "pydrex.minerals", "qualname": "Mineral.regime", "kind": "variable", "doc": "

\n", "annotation": ": int", "default_value": "<DeformationRegime.dislocation: 1>"}, "pydrex.minerals.Mineral.n_grains": {"fullname": "pydrex.minerals.Mineral.n_grains", "modulename": "pydrex.minerals", "qualname": "Mineral.n_grains", "kind": "variable", "doc": "

\n", "annotation": ": int", "default_value": "3500"}, "pydrex.minerals.Mineral.fractions_init": {"fullname": "pydrex.minerals.Mineral.fractions_init", "modulename": "pydrex.minerals", "qualname": "Mineral.fractions_init", "kind": "variable", "doc": "

\n", "annotation": ": numpy.ndarray", "default_value": "None"}, "pydrex.minerals.Mineral.orientations_init": {"fullname": "pydrex.minerals.Mineral.orientations_init", "modulename": "pydrex.minerals", "qualname": "Mineral.orientations_init", "kind": "variable", "doc": "

\n", "annotation": ": numpy.ndarray", "default_value": "None"}, "pydrex.minerals.Mineral.fractions": {"fullname": "pydrex.minerals.Mineral.fractions", "modulename": "pydrex.minerals", "qualname": "Mineral.fractions", "kind": "variable", "doc": "

\n", "annotation": ": list"}, "pydrex.minerals.Mineral.orientations": {"fullname": "pydrex.minerals.Mineral.orientations", "modulename": "pydrex.minerals", "qualname": "Mineral.orientations", "kind": "variable", "doc": "

\n", "annotation": ": list"}, "pydrex.minerals.Mineral.seed": {"fullname": "pydrex.minerals.Mineral.seed", "modulename": "pydrex.minerals", "qualname": "Mineral.seed", "kind": "variable", "doc": "

\n", "annotation": ": int", "default_value": "None"}, "pydrex.minerals.Mineral.lband": {"fullname": "pydrex.minerals.Mineral.lband", "modulename": "pydrex.minerals", "qualname": "Mineral.lband", "kind": "variable", "doc": "

\n", "annotation": ": int", "default_value": "None"}, "pydrex.minerals.Mineral.uband": {"fullname": "pydrex.minerals.Mineral.uband", "modulename": "pydrex.minerals", "qualname": "Mineral.uband", "kind": "variable", "doc": "

\n", "annotation": ": int", "default_value": "None"}, "pydrex.minerals.Mineral.update_orientations": {"fullname": "pydrex.minerals.Mineral.update_orientations", "modulename": "pydrex.minerals", "qualname": "Mineral.update_orientations", "kind": "function", "doc": "

Update orientations and volume distribution for the Mineral.

\n\n

Update crystalline orientations and grain volume distribution\nfor minerals undergoing plastic deformation. Return the updated deformation\ngradient measuring the corresponding macroscopic deformation.

\n\n

Args:

\n\n\n\n

Any additional (optional) keyword arguments are passed to\nscipy.integrate.LSODA.

\n\n

Array values must provide a NumPy-compatible interface:\nhttps://numpy.org/doc/stable/user/whatisnumpy.html

\n\n

Examples:

\n\n
\n
>>> from itertools import pairwise\n>>> import pydrex\n>>> olA = pydrex.Mineral(\n...           phase=pydrex.MineralPhase.olivine,\n...           fabric=pydrex.MineralFabric.olivine_A,\n...           regime=pydrex.DeformationRegime.dislocation,\n...           n_grains=pydrex.DEFAULT_PARAMS["number_of_grains"],\n... )\n>>> def get_velocity_gradient(t, x):  # Simple L for simple shear.\n...     L = np.zeros((3, 3))\n...     L[0, 2] = 1\n...     return L\n>>> def get_position(t):\n...     return np.zeros(3)  # Stationary polycrystal for this example.\n>>> timestamps = range(2)  # Just 1 timestep for demonstration.\n>>> deformation_gradient = np.eye(3)  # Start with an undeformed polycrystal.\n>>> for t_start, t_end in pairwise(timestamps):\n...     # Update deformation_gradient, olA.orientations and olA.fractions.\n...     deformation_gradient = olA.update_orientations(\n...         pydrex.DEFAULT_PARAMS,\n...         deformation_gradient,\n...         get_velocity_gradient,\n...         (t_start, t_end, get_position),\n...     )\n>>> from numpy import testing as nt\n>>> nt.assert_allclose(deformation_gradient,\n...     np.eye(3) + get_velocity_gradient(t_end, np.nan),\n...     atol=1e-15, rtol=0\n... )\n
\n
\n", "signature": "(\tself,\tconfig,\tdeformation_gradient,\tget_velocity_gradient,\tpathline,\t**kwargs):", "funcdef": "def"}, "pydrex.minerals.Mineral.save": {"fullname": "pydrex.minerals.Mineral.save", "modulename": "pydrex.minerals", "qualname": "Mineral.save", "kind": "function", "doc": "

Save CPO data for all stored timesteps to a numpy NPZ file.

\n\n

If postfix is not None, the data is appended to the NPZ file\nin fields ending with \"_postfix\".

\n\n

Raises a ValueError if the data shapes are not compatible.

\n\n

See also: numpy.savez, Mineral.load, Mineral.from_file.

\n", "signature": "(self, filename, postfix=None):", "funcdef": "def"}, "pydrex.minerals.Mineral.load": {"fullname": "pydrex.minerals.Mineral.load", "modulename": "pydrex.minerals", "qualname": "Mineral.load", "kind": "function", "doc": "

Load CPO data from a numpy NPZ file.

\n\n

If postfix is not None, data is read from fields ending with \"_postfix\".

\n\n

See also: Mineral.save, Mineral.from_file.

\n", "signature": "(self, filename, postfix=None):", "funcdef": "def"}, "pydrex.minerals.Mineral.from_file": {"fullname": "pydrex.minerals.Mineral.from_file", "modulename": "pydrex.minerals", "qualname": "Mineral.from_file", "kind": "function", "doc": "

Construct a Mineral instance using data from a numpy NPZ file.

\n\n

If postfix is not None, data is read from fields ending with \u201c_postfix\u201d.

\n\n

See also: Mineral.save, Mineral.load.

\n", "signature": "(cls, filename, postfix=None):", "funcdef": "def"}, "pydrex.mock": {"fullname": "pydrex.mock", "modulename": "pydrex.mock", "kind": "module", "doc": "
\n

PyDRex: Mock objects for testing and reproducibility.

\n
\n"}, "pydrex.mock.PARAMS_FRATERS2021": {"fullname": "pydrex.mock.PARAMS_FRATERS2021", "modulename": "pydrex.mock", "qualname": "PARAMS_FRATERS2021", "kind": "variable", "doc": "

Values used for tests 1, 2 and 4 in https://doi.org/10.1029/2021gc009846.

\n", "default_value": "{'olivine_fraction': 0.7, 'enstatite_fraction': 0.3, 'initial_olivine_fabric': <MineralFabric.olivine_A: 0>, 'stress_exponent': 1.5, 'deformation_exponent': 3.5, 'gbm_mobility': 125, 'gbs_threshold': 0.3, 'nucleation_efficiency': 5, 'number_of_grains': 5000}"}, "pydrex.mock.PARAMS_KAMINSKI2001_FIG5_SOLID": {"fullname": "pydrex.mock.PARAMS_KAMINSKI2001_FIG5_SOLID", "modulename": "pydrex.mock", "qualname": "PARAMS_KAMINSKI2001_FIG5_SOLID", "kind": "variable", "doc": "

Values used for the M*=0 test in https://doi.org/10.1016/s0012-821x(01)00356-9.

\n", "default_value": "{'olivine_fraction': 1, 'enstatite_fraction': 0, 'initial_olivine_fabric': <MineralFabric.olivine_A: 0>, 'stress_exponent': 1.5, 'deformation_exponent': 3.5, 'gbm_mobility': 0, 'gbs_threshold': 0, 'nucleation_efficiency': 5, 'number_of_grains': 3375}"}, "pydrex.mock.PARAMS_KAMINSKI2001_FIG5_SHORTDASH": {"fullname": "pydrex.mock.PARAMS_KAMINSKI2001_FIG5_SHORTDASH", "modulename": "pydrex.mock", "qualname": "PARAMS_KAMINSKI2001_FIG5_SHORTDASH", "kind": "variable", "doc": "

Values used for the M*=50 test in https://doi.org/10.1016/s0012-821x(01)00356-9.

\n", "default_value": "{'olivine_fraction': 1, 'enstatite_fraction': 0, 'initial_olivine_fabric': <MineralFabric.olivine_A: 0>, 'stress_exponent': 1.5, 'deformation_exponent': 3.5, 'gbm_mobility': 50, 'gbs_threshold': 0, 'nucleation_efficiency': 5, 'number_of_grains': 3375}"}, "pydrex.mock.PARAMS_KAMINSKI2001_FIG5_LONGDASH": {"fullname": "pydrex.mock.PARAMS_KAMINSKI2001_FIG5_LONGDASH", "modulename": "pydrex.mock", "qualname": "PARAMS_KAMINSKI2001_FIG5_LONGDASH", "kind": "variable", "doc": "

Values used for the M*=200 test in https://doi.org/10.1016/s0012-821x(01)00356-9.

\n", "default_value": "{'olivine_fraction': 1, 'enstatite_fraction': 0, 'initial_olivine_fabric': <MineralFabric.olivine_A: 0>, 'stress_exponent': 1.5, 'deformation_exponent': 3.5, 'gbm_mobility': 200, 'gbs_threshold': 0, 'nucleation_efficiency': 5, 'number_of_grains': 3375}"}, "pydrex.mock.PARAMS_KAMINSKI2004_FIG4_TRIANGLES": {"fullname": "pydrex.mock.PARAMS_KAMINSKI2004_FIG4_TRIANGLES", "modulename": "pydrex.mock", "qualname": "PARAMS_KAMINSKI2004_FIG4_TRIANGLES", "kind": "variable", "doc": "

Values used for the \u03c7=0.4 test in https://doi.org/10.1111/j.1365-246x.2004.02308.x.

\n", "default_value": "{'olivine_fraction': 1, 'enstatite_fraction': 0, 'initial_olivine_fabric': <MineralFabric.olivine_A: 0>, 'stress_exponent': 1.5, 'deformation_exponent': 3.5, 'gbm_mobility': 125, 'gbs_threshold': 0.4, 'nucleation_efficiency': 5, 'number_of_grains': 4394}"}, "pydrex.mock.PARAMS_KAMINSKI2004_FIG4_SQUARES": {"fullname": "pydrex.mock.PARAMS_KAMINSKI2004_FIG4_SQUARES", "modulename": "pydrex.mock", "qualname": "PARAMS_KAMINSKI2004_FIG4_SQUARES", "kind": "variable", "doc": "

Values used for the \u03c7=0.2 test in https://doi.org/10.1111/j.1365-246x.2004.02308.x.

\n", "default_value": "{'olivine_fraction': 1, 'enstatite_fraction': 0, 'initial_olivine_fabric': <MineralFabric.olivine_A: 0>, 'stress_exponent': 1.5, 'deformation_exponent': 3.5, 'gbm_mobility': 125, 'gbs_threshold': 0.2, 'nucleation_efficiency': 5, 'number_of_grains': 4394}"}, "pydrex.mock.PARAMS_KAMINSKI2004_FIG4_CIRCLES": {"fullname": "pydrex.mock.PARAMS_KAMINSKI2004_FIG4_CIRCLES", "modulename": "pydrex.mock", "qualname": "PARAMS_KAMINSKI2004_FIG4_CIRCLES", "kind": "variable", "doc": "

Values used for the \u03c7=0 test in https://doi.org/10.1111/j.1365-246x.2004.02308.x.

\n", "default_value": "{'olivine_fraction': 1, 'enstatite_fraction': 0, 'initial_olivine_fabric': <MineralFabric.olivine_A: 0>, 'stress_exponent': 1.5, 'deformation_exponent': 3.5, 'gbm_mobility': 125, 'gbs_threshold': 0, 'nucleation_efficiency': 5, 'number_of_grains': 4394}"}, "pydrex.mock.PARAMS_HEDJAZIAN2017": {"fullname": "pydrex.mock.PARAMS_HEDJAZIAN2017", "modulename": "pydrex.mock", "qualname": "PARAMS_HEDJAZIAN2017", "kind": "variable", "doc": "

Values used for the MOR model in https://doi.org/10.1016/j.epsl.2016.12.004.

\n", "default_value": "{'olivine_fraction': 0.7, 'enstatite_fraction': 0.3, 'initial_olivine_fabric': <MineralFabric.olivine_A: 0>, 'stress_exponent': 1.5, 'deformation_exponent': 3.5, 'gbm_mobility': 10, 'gbs_threshold': 0.2, 'nucleation_efficiency': 5, 'number_of_grains': 2197}"}, "pydrex.pathlines": {"fullname": "pydrex.pathlines", "modulename": "pydrex.pathlines", "kind": "module", "doc": "
\n

PyDRex: Functions for pathline construction.

\n
\n"}, "pydrex.pathlines.get_pathline": {"fullname": "pydrex.pathlines.get_pathline", "modulename": "pydrex.pathlines", "qualname": "get_pathline", "kind": "function", "doc": "

Determine the pathline for a particle in a steady state flow.

\n\n

The pathline will terminate at the given final_location and follow a curve\ndetermined by the velocity gradient. It works for both 2D (rectangular) and 3D\n(orthopiped\u00b9) domains, so long as the provided callables expect/return arrays of the\nappropriate dimension.

\n\n
\n\n

The pathline is calculated backwards in time (t < 0) from the given endpoint.\nTherefore, the returned position callable should be evaluated at negative times.

\n\n
\n\n

Args:

\n\n\n\n

Optional keyword arguments will be passed to scipy.integrate.solve_ivp. However,\nsome of the arguments to the solve_ivp call may not be modified, and a warning\nwill be raised if they are provided.

\n\n

Returns a tuple containing the time points and an interpolant that can be used\nto evaluate the pathline position (see scipy.integrate.OdeSolution).

\n\n

\u00b9An \u201corthopiped\u201d is a 3D rectangle (called a \u201cbox\u201d when we are in a hurry), see\nhttps://www.whatistoday.net/2020/04/cuboid-dilemma.html.

\n", "signature": "(\tfinal_location,\tget_velocity,\tget_velocity_gradient,\tmin_coords,\tmax_coords,\tmax_strain,\tregular_steps=None,\t**kwargs):", "funcdef": "def"}, "pydrex.stats": {"fullname": "pydrex.stats", "modulename": "pydrex.stats", "kind": "module", "doc": "
\n

PyDRex: Statistical methods for orientation and elasticity data.

\n
\n"}, "pydrex.stats.resample_orientations": {"fullname": "pydrex.stats.resample_orientations", "modulename": "pydrex.stats", "qualname": "resample_orientations", "kind": "function", "doc": "

Return new samples from orientations weighted by the volume distribution.

\n\n

Args:

\n\n\n\n

Returns the Nxn_samplesx3x3 orientations and associated sorted (ascending) grain\nvolumes.

\n", "signature": "(orientations, fractions, n_samples=None, seed=None):", "funcdef": "def"}, "pydrex.stats.misorientation_hist": {"fullname": "pydrex.stats.misorientation_hist", "modulename": "pydrex.stats", "qualname": "misorientation_hist", "kind": "function", "doc": "

Calculate misorientation histogram for polycrystal orientations.

\n\n

The bins argument is passed to numpy.histogram.\nIf left as None, 1\u00b0 bins will be used as recommended by the reference paper.\nThe symmetry argument specifies the lattice system which determines intrinsic\nsymmetry degeneracies and the maximum allowable misorientation angle.\nSee _geo.LatticeSystem for supported systems.

\n\n
\n\n

This method must be able to allocate $ \\frac{N!}{(N-2)!} \u00d7 4M $ floats\nfor N the length of orientations and M the number of symmetry operations for\nthe given system (numpy.float32 values are used to reduce the memory\nrequirements)

\n\n
\n\n

See Skemer et al. (2005).

\n", "signature": "(orientations, system: pydrex.geometry.LatticeSystem, bins=None):", "funcdef": "def"}, "pydrex.stats.misorientations_random": {"fullname": "pydrex.stats.misorientations_random", "modulename": "pydrex.stats", "qualname": "misorientations_random", "kind": "function", "doc": "

Get expected count of misorientation angles for an isotropic aggregate.

\n\n

Estimate the expected number of misorientation angles between grains\nthat would fall within $($low, high$)$ in degrees for an aggregate\nwith randomly oriented grains, where low $\u2208 [0, $high$)$,\nand high is bounded by the maximum theoretical misorientation angle\nfor the given lattice symmetry system.\nSee _geo.LatticeSystem for supported systems.

\n", "signature": "(low, high, system: pydrex.geometry.LatticeSystem):", "funcdef": "def"}, "pydrex.stats.point_density": {"fullname": "pydrex.stats.point_density", "modulename": "pydrex.stats", "qualname": "point_density", "kind": "function", "doc": "

Estimate point density of orientation data on the unit sphere.

\n\n

Estimates the density of orientations on the unit sphere by counting the input data\nthat falls within small areas around a uniform grid of spherical counting locations.\nThe input data is expected in cartesian coordinates, and the contouring is performed\nusing kernel functions defined in Vollmer 1995.\nThe following optional parameters control the contouring method:

\n\n\n\n

Any other keyword arguments are passed to the kernel function calls.\nMost kernels accept a parameter \u03c3 to control the degree of smoothing.

\n", "signature": "(\tx_data,\ty_data,\tz_data,\tgridsteps=101,\tweights=1,\tkernel='linear_inverse_kamb',\taxial=True,\t**kwargs):", "funcdef": "def"}, "pydrex.stats.exponential_kamb": {"fullname": "pydrex.stats.exponential_kamb", "modulename": "pydrex.stats", "qualname": "exponential_kamb", "kind": "function", "doc": "

Kernel function from Vollmer 1995 for exponential smoothing.

\n", "signature": "(cos_dist, \u03c3=10, axial=True):", "funcdef": "def"}, "pydrex.stats.linear_inverse_kamb": {"fullname": "pydrex.stats.linear_inverse_kamb", "modulename": "pydrex.stats", "qualname": "linear_inverse_kamb", "kind": "function", "doc": "

Kernel function from Vollmer 1995 for linear smoothing.

\n", "signature": "(cos_dist, \u03c3=10, axial=True):", "funcdef": "def"}, "pydrex.stats.square_inverse_kamb": {"fullname": "pydrex.stats.square_inverse_kamb", "modulename": "pydrex.stats", "qualname": "square_inverse_kamb", "kind": "function", "doc": "

Kernel function from Vollmer 1995 for inverse square smoothing.

\n", "signature": "(cos_dist, \u03c3=10, axial=True):", "funcdef": "def"}, "pydrex.stats.kamb_count": {"fullname": "pydrex.stats.kamb_count", "modulename": "pydrex.stats", "qualname": "kamb_count", "kind": "function", "doc": "

Original Kamb 1959 kernel function (raw count within radius).

\n", "signature": "(cos_dist, \u03c3=10, axial=True):", "funcdef": "def"}, "pydrex.stats.schmidt_count": {"fullname": "pydrex.stats.schmidt_count", "modulename": "pydrex.stats", "qualname": "schmidt_count", "kind": "function", "doc": "

Schmidt (a.k.a. 1%) counting kernel function.

\n", "signature": "(cos_dist, axial=None):", "funcdef": "def"}, "pydrex.stats.SPHERICAL_COUNTING_KERNELS": {"fullname": "pydrex.stats.SPHERICAL_COUNTING_KERNELS", "modulename": "pydrex.stats", "qualname": "SPHERICAL_COUNTING_KERNELS", "kind": "variable", "doc": "

Kernel functions that return an un-summed distribution and a normalization factor.

\n\n

Supported kernel functions are based on the discussion in\nVollmer 1995.\nKamb methods accept the parameter \u03c3 (default: 10) to control the degree of smoothing.\nValues lower than 3 and higher than 20 are not recommended.

\n", "default_value": "{'kamb_count': <function kamb_count>, 'schmidt_count': <function schmidt_count>, 'exponential_kamb': <function exponential_kamb>, 'linear_inverse_kamb': <function linear_inverse_kamb>, 'square_inverse_kamb': <function square_inverse_kamb>}"}, "pydrex.tensors": {"fullname": "pydrex.tensors", "modulename": "pydrex.tensors", "kind": "module", "doc": "
\n

PyDRex: Tensor operation functions and helpers.

\n
\n\n

For Voigt notation, the symmetric 6x6 matrix representation is used,\nwhich assumes that the fourth order tensor being represented as such is also symmetric.\nThe vectorial notation uses 21 components which are the independent components of the\nsymmetric 6x6 matrix.

\n"}, "pydrex.tensors.PERMUTATION_SYMBOL": {"fullname": "pydrex.tensors.PERMUTATION_SYMBOL", "modulename": "pydrex.tensors", "qualname": "PERMUTATION_SYMBOL", "kind": "variable", "doc": "

\n", "default_value": "array([[[ 0., 0., 0.],\n [ 0., 0., 1.],\n [ 0., -1., 0.]],\n\n [[ 0., 0., -1.],\n [ 0., 0., 0.],\n [ 1., 0., 0.]],\n\n [[ 0., 1., 0.],\n [-1., 0., 0.],\n [ 0., 0., 0.]]])"}, "pydrex.tensors.voigt_decompose": {"fullname": "pydrex.tensors.voigt_decompose", "modulename": "pydrex.tensors", "qualname": "voigt_decompose", "kind": "function", "doc": "

Decompose elastic tensor (as 6x6 Voigt matrix) into distinct contractions.

\n\n

Return the only two independent contractions of the elastic tensor given as a 6x6\nVoigt matrix. With reference to the full 4-th order elastic tensor, the\ncontractions are defined as:

\n\n\n\n

Any vector which is an eigenvector of both $d_{ij}$ and $v_{ij}$ is always normal to\na symmetry plane of the elastic medium.

\n\n

See Equations 3.4 & 3.5 in Browaeys & Chevrot (2004).

\n", "signature": "(matrix):", "funcdef": "def"}, "pydrex.tensors.mono_project": {"fullname": "pydrex.tensors.mono_project", "modulename": "pydrex.tensors", "qualname": "mono_project", "kind": "function", "doc": "

Project 21-component voigt_vector onto monoclinic symmetry subspace.

\n\n

Monoclinic symmetry is characterised by 13 independent elasticity components.

\n\n

See Browaeys & Chevrot (2004).

\n", "signature": "(voigt_vector):", "funcdef": "def"}, "pydrex.tensors.ortho_project": {"fullname": "pydrex.tensors.ortho_project", "modulename": "pydrex.tensors", "qualname": "ortho_project", "kind": "function", "doc": "

Project 21-component voigt_vector onto orthorhombic symmetry subspace.

\n\n

Orthorhombic symmetry is characterised by 9 independent elasticity components.

\n\n

See Browaeys & Chevrot (2004).

\n", "signature": "(voigt_vector):", "funcdef": "def"}, "pydrex.tensors.tetr_project": {"fullname": "pydrex.tensors.tetr_project", "modulename": "pydrex.tensors", "qualname": "tetr_project", "kind": "function", "doc": "

Project 21-component voigt_vector onto tetragonal symmetry subspace.

\n\n

Tetragonal symmetry is characterised by 6 independent elasticity components.

\n\n

See Browaeys & Chevrot (2004).

\n", "signature": "(voigt_vector):", "funcdef": "def"}, "pydrex.tensors.hex_project": {"fullname": "pydrex.tensors.hex_project", "modulename": "pydrex.tensors", "qualname": "hex_project", "kind": "function", "doc": "

Project 21-component voigt_vector onto hexagonal symmetry subspace.

\n\n

Hexagonal symmetry (a.k.a. transverse isotropy) is characterised by 5 independent\nelasticity components.

\n\n

See Browaeys & Chevrot (2004).

\n", "signature": "(voigt_vector):", "funcdef": "def"}, "pydrex.tensors.upper_tri_to_symmetric": {"fullname": "pydrex.tensors.upper_tri_to_symmetric", "modulename": "pydrex.tensors", "qualname": "upper_tri_to_symmetric", "kind": "function", "doc": "

Create symmetric array using upper triangle of input array.

\n\n

Examples:

\n\n
\n
>>> import numpy as np\n>>> upper_tri_to_symmetric(np.array([\n...         [ 1.,  2.,  3.,  4.],\n...         [ 0.,  5.,  6.,  7.],\n...         [ 0.,  0.,  8.,  9.],\n...         [ 9.,  0.,  0., 10.]\n... ]))\narray([[ 1.,  2.,  3.,  4.],\n       [ 2.,  5.,  6.,  7.],\n       [ 3.,  6.,  8.,  9.],\n       [ 4.,  7.,  9., 10.]])\n
\n
\n", "signature": "(arr):", "funcdef": "def"}, "pydrex.tensors.voigt_to_elastic_tensor": {"fullname": "pydrex.tensors.voigt_to_elastic_tensor", "modulename": "pydrex.tensors", "qualname": "voigt_to_elastic_tensor", "kind": "function", "doc": "

Create 4-th order elastic tensor from an equivalent Voigt matrix.

\n\n

See also: elastic_tensor_to_voigt.

\n", "signature": "(matrix):", "funcdef": "def"}, "pydrex.tensors.elastic_tensor_to_voigt": {"fullname": "pydrex.tensors.elastic_tensor_to_voigt", "modulename": "pydrex.tensors", "qualname": "elastic_tensor_to_voigt", "kind": "function", "doc": "

Create a 6x6 Voigt matrix from an equivalent 4-th order elastic tensor.

\n", "signature": "(tensor):", "funcdef": "def"}, "pydrex.tensors.voigt_matrix_to_vector": {"fullname": "pydrex.tensors.voigt_matrix_to_vector", "modulename": "pydrex.tensors", "qualname": "voigt_matrix_to_vector", "kind": "function", "doc": "

Create the 21-component Voigt vector equivalent to the 6x6 Voigt matrix.

\n", "signature": "(matrix):", "funcdef": "def"}, "pydrex.tensors.voigt_vector_to_matrix": {"fullname": "pydrex.tensors.voigt_vector_to_matrix", "modulename": "pydrex.tensors", "qualname": "voigt_vector_to_matrix", "kind": "function", "doc": "

Create the 6x6 matrix representation of the 21-component Voigt vector.

\n\n

See also: voigt_matrix_to_vector.

\n", "signature": "(vector):", "funcdef": "def"}, "pydrex.tensors.rotate": {"fullname": "pydrex.tensors.rotate", "modulename": "pydrex.tensors", "qualname": "rotate", "kind": "function", "doc": "

Rotate 4-th order tensor using a 3x3 rotation matrix.

\n", "signature": "(tensor, rotation):", "funcdef": "def"}, "pydrex.utils": {"fullname": "pydrex.utils", "modulename": "pydrex.utils", "kind": "module", "doc": "
\n

PyDRex: Miscellaneous utility methods.

\n
\n"}, "pydrex.utils.import_proc_pool": {"fullname": "pydrex.utils.import_proc_pool", "modulename": "pydrex.utils", "qualname": "import_proc_pool", "kind": "function", "doc": "

Import either ray.util.multiprocessing.Pool or multiprocessing.Pool.

\n\n

Import a process Pool object either from Ray of from Python's stdlib.\nBoth offer the same API, the Ray implementation will be preferred if available.\nUsing the Pool provided by Ray allows for distributed memory multiprocessing.

\n\n

Returns a tuple containing the Pool object and a boolean flag which is True if\nRay is available.

\n", "signature": "():", "funcdef": "def"}, "pydrex.utils.strain_increment": {"fullname": "pydrex.utils.strain_increment", "modulename": "pydrex.utils", "qualname": "strain_increment", "kind": "function", "doc": "

Calculate strain increment for a given time increment and velocity gradient.

\n\n

Returns \u201ctensorial\u201d strain increment \u03b5, which is equal to \u03b3/2 where \u03b3 is the\n\u201c(engineering) shear strain\u201d increment.

\n", "signature": "(dt, velocity_gradient):", "funcdef": "def"}, "pydrex.utils.apply_gbs": {"fullname": "pydrex.utils.apply_gbs", "modulename": "pydrex.utils", "qualname": "apply_gbs", "kind": "function", "doc": "

Apply grain boundary sliding for small grains.

\n", "signature": "(orientations, fractions, gbs_threshold, orientations_prev, n_grains):", "funcdef": "def"}, "pydrex.utils.extract_vars": {"fullname": "pydrex.utils.extract_vars", "modulename": "pydrex.utils", "qualname": "extract_vars", "kind": "function", "doc": "

Extract deformation gradient, orientation matrices and grain sizes from y.

\n", "signature": "(y, n_grains):", "funcdef": "def"}, "pydrex.utils.remove_nans": {"fullname": "pydrex.utils.remove_nans", "modulename": "pydrex.utils", "qualname": "remove_nans", "kind": "function", "doc": "

Remove NaN values from array.

\n", "signature": "(a):", "funcdef": "def"}, "pydrex.utils.remove_dim": {"fullname": "pydrex.utils.remove_dim", "modulename": "pydrex.utils", "qualname": "remove_dim", "kind": "function", "doc": "

Remove all values corresponding to dimension dim from an array.

\n\n

Note that a dim of 0 refers to the \u201cx\u201d values.

\n\n

Examples:

\n\n
\n
>>> a = [1, 2, 3]\n>>> remove_dim(a, 0)\narray([2, 3])\n>>> remove_dim(a, 1)\narray([1, 3])\n>>> remove_dim(a, 2)\narray([1, 2])\n
\n
\n\n
\n
>>> a = [[1, 2, 3], [4, 5, 6], [7, 8, 9]]\n>>> remove_dim(a, 0)\narray([[5, 6],\n       [8, 9]])\n>>> remove_dim(a, 1)\narray([[1, 3],\n       [7, 9]])\n>>> remove_dim(a, 2)\narray([[1, 2],\n       [4, 5]])\n
\n
\n", "signature": "(a, dim):", "funcdef": "def"}, "pydrex.utils.add_dim": {"fullname": "pydrex.utils.add_dim", "modulename": "pydrex.utils", "qualname": "add_dim", "kind": "function", "doc": "

Add entries of val corresponding to dimension dim to an array.

\n\n

Note that a dim of 0 refers to the \u201cx\u201d values.

\n\n

Examples:

\n\n
\n
>>> a = [1, 2]\n>>> add_dim(a, 0)\narray([0, 1, 2])\n>>> add_dim(a, 1)\narray([1, 0, 2])\n>>> add_dim(a, 2)\narray([1, 2, 0])\n
\n
\n\n
\n
>>> add_dim([1.0, 2.0], 2)\narray([1., 2., 0.])\n
\n
\n\n
\n
>>> a = [[1, 2], [3, 4]]\n>>> add_dim(a, 0)\narray([[0, 0, 0],\n       [0, 1, 2],\n       [0, 3, 4]])\n>>> add_dim(a, 1)\narray([[1, 0, 2],\n       [0, 0, 0],\n       [3, 0, 4]])\n>>> add_dim(a, 2)\narray([[1, 2, 0],\n       [3, 4, 0],\n       [0, 0, 0]])\n
\n
\n", "signature": "(a, dim, val=0):", "funcdef": "def"}, "pydrex.utils.default_ncpus": {"fullname": "pydrex.utils.default_ncpus", "modulename": "pydrex.utils", "qualname": "default_ncpus", "kind": "function", "doc": "

Get a safe default number of CPUs available for multiprocessing.

\n\n

On Linux platforms that support it, the method os.sched_getaffinity() is used.\nOn Mac OS, the command sysctl -n hw.ncpu is used.\nOn Windows, the environment variable NUMBER_OF_PROCESSORS is queried.\nIf any of these fail, a fallback of 1 is used and a warning is logged.

\n", "signature": "():", "funcdef": "def"}, "pydrex.utils.diff_like": {"fullname": "pydrex.utils.diff_like", "modulename": "pydrex.utils", "qualname": "diff_like", "kind": "function", "doc": "

Get forward difference of 2D array a, with repeated last elements.

\n\n

The repeated last elements ensure that output and input arrays have equal shape.

\n\n

Examples:

\n\n
\n
>>> diff_like(np.array([1, 2, 3, 4, 5]))\narray([[1, 1, 1, 1, 1]])\n
\n
\n\n
\n
>>> diff_like(np.array([[1, 2, 3, 4, 5], [1, 3, 6, 9, 10]]))\narray([[1, 1, 1, 1, 1],\n       [2, 3, 3, 1, 1]])\n
\n
\n\n
\n
>>> diff_like(np.array([[1, 2, 3, 4, 5], [1, 3, 6, 9, 10], [1, 0, 0, 0, np.inf]]))\narray([[ 1.,  1.,  1.,  1.,  1.],\n       [ 2.,  3.,  3.,  1.,  1.],\n       [-1.,  0.,  0., inf, nan]])\n
\n
\n", "signature": "(a):", "funcdef": "def"}, "pydrex.utils.angle_fse_simpleshear": {"fullname": "pydrex.utils.angle_fse_simpleshear", "modulename": "pydrex.utils", "qualname": "angle_fse_simpleshear", "kind": "function", "doc": "

Get angle of FSE long axis anticlockwise from the X axis in simple shear.

\n", "signature": "(strain):", "funcdef": "def"}, "pydrex.utils.lag_2d_corner_flow": {"fullname": "pydrex.utils.lag_2d_corner_flow", "modulename": "pydrex.utils", "qualname": "lag_2d_corner_flow", "kind": "function", "doc": "

Get predicted grain orientation lag for 2D corner flow.

\n\n

See eq. 11 in Kaminski & Ribe (2002).

\n", "signature": "(\u03b8):", "funcdef": "def"}, "pydrex.utils.quat_product": {"fullname": "pydrex.utils.quat_product", "modulename": "pydrex.utils", "qualname": "quat_product", "kind": "function", "doc": "

Quaternion product, q1, q2 and output are in scalar-last (x,y,z,w) format.

\n", "signature": "(q1, q2):", "funcdef": "def"}, "pydrex.utils.redraw_legend": {"fullname": "pydrex.utils.redraw_legend", "modulename": "pydrex.utils", "qualname": "redraw_legend", "kind": "function", "doc": "

Redraw legend on matplotlib axis or figure.

\n\n

Transparency is removed from legend symbols.\nIf fig is not None and remove_all is True,\nall legends are first removed from the parent figure.\nOptional keyword arguments are passed to matplotlib.axes.Axes.legend by default,\nor matplotlib.figure.Figure.legend if fig is not None.

\n\n

If legendax is not None, the axis legend will be redrawn using the legendax axes\ninstead of taking up space in the original axes. This option requires fig=None.

\n\n
\n\n

Note that if fig is not None, the legend may be cropped from the saved\nfigure due to a Matplotlib bug. In this case, it is required to add the\narguments bbox_extra_artists=(legend,) and bbox_inches=\"tight\" to savefig,\nwhere legend is the object returned by this function. To prevent the legend\nfrom consuming axes/subplot space, it is further required to add the lines:\nlegend.set_in_layout(False), fig.canvas.draw(), legend.set_layout(True)\nand fig.set_layout_engine(\"none\") before saving the figure.

\n\n
\n", "signature": "(ax, fig=None, legendax=None, remove_all=True, **kwargs):", "funcdef": "def"}, "pydrex.utils.add_subplot_labels": {"fullname": "pydrex.utils.add_subplot_labels", "modulename": "pydrex.utils", "qualname": "add_subplot_labels", "kind": "function", "doc": "

Add subplot labels to axes mosaic.

\n\n

Use labelmap to specify a dictionary that maps keys in mosaic to subplot labels.\nIf labelmap is None, the keys in axs will be used as the labels by default.

\n\n

If internal is False (default), the axes titles will be used.\nOtherwise, internal labels will be drawn with ax.text,\nin which case loc must be a tuple of floats.

\n\n

Any axes in axs corresponding to the special key legend are skipped.

\n", "signature": "(\tmosaic,\tlabelmap=None,\tloc='left',\tfontsize='medium',\tinternal=False,\t**kwargs):", "funcdef": "def"}, "pydrex.velocity": {"fullname": "pydrex.velocity", "modulename": "pydrex.velocity", "kind": "module", "doc": "
\n

PyDRex: Steady-state solutions of velocity (gradients) for various flows.

\n
\n\n

For the sake of consistency, all callables returned from methods in this module expect a\ntime scalar and 3D position vector as inputs. They also return 3D tensors in all cases.\nThis means they can be directly used as arguments to e.g.\npydrex.minerals.Mineral.update_orientations.

\n"}, "pydrex.velocity.simple_shear_2d": {"fullname": "pydrex.velocity.simple_shear_2d", "modulename": "pydrex.velocity", "qualname": "simple_shear_2d", "kind": "function", "doc": "

Return simple shear velocity and velocity gradient callables.

\n\n

The returned callables have signature f(t, x) where x is a 3D position vector.

\n\n

Args:

\n\n\n\n
\n\n

Input arrays to the returned callables must have homogeneous element types.\nArrays with e.g. both floating point and integer values are not supported.

\n\n
\n\n

Examples:

\n\n
\n
>>> import numpy as np\n>>> u, L = simple_shear_2d("X", "Z", 1e-4)\n>>> u(np.nan, np.array([0, 0, 0]))  # Time is not used here.\narray([0., 0., 0.])\n>>> u(np.nan, np.array([0, 0, 1]))\narray([0.0001, 0.    , 0.    ])\n>>> u(np.nan, np.array([0.0, 0.0, 2.0]))\narray([0.0002, 0.    , 0.    ])\n>>> L(np.nan, np.array([0, 0, 0]))\narray([[0.    , 0.    , 0.0002],\n       [0.    , 0.    , 0.    ],\n       [0.    , 0.    , 0.    ]])\n>>> L(np.nan, np.array([0.0, 0.0, 1.0]))\narray([[0.    , 0.    , 0.0002],\n       [0.    , 0.    , 0.    ],\n       [0.    , 0.    , 0.    ]])\n
\n
\n", "signature": "(direction, deformation_plane, strain_rate):", "funcdef": "def"}, "pydrex.velocity.cell_2d": {"fullname": "pydrex.velocity.cell_2d", "modulename": "pydrex.velocity", "qualname": "cell_2d", "kind": "function", "doc": "

Get velocity and velocity gradient callables for a steady-state 2D Stokes cell.

\n\n

The cell is centered at (0,0) and the velocity field is defined by:\n$$\n\\bm{u} = U\\cos(\u03c0 x/d)\\sin(\u03c0 z/d) \\bm{\\hat{h}} - U\\sin(\u03c0 x/d)\\cos(\u03c0 z/d) \\bm{\\hat{v}}\n$$\nwhere $\\bm{\\hat{h}}$ and $\\bm{\\hat{v}}$ are unit vectors in the chosen horizontal\nand vertical directions, respectively. The velocity at the cell edge has a magnitude\nof $U$ and $d$ is the length of a cell edge.

\n\n

The returned callables have signature f(t, x) where x is a 3D position vector.

\n\n

Args:

\n\n\n\n

Examples:

\n\n
\n
>>> import numpy as np\n>>> u, L = cell_2d("X", "Z", 1)\n>>> u(np.nan, np.array([0, 0, 0]))  # Time value is not used for steady flows.\narray([ 0.,  0., -0.])\n>>> u(np.nan, np.array([0, 0, 1]))\narray([ 1.,  0., -0.])\n>>> u(np.nan, np.array([0, 1, 0]))  # Y-value is not used.\narray([ 0.,  0., -0.])\n>>> u(np.nan, np.array([0, 0, -1]))\narray([-1.,  0., -0.])\n>>> u(np.nan, np.array([1, 0, 0]))\narray([ 0.,  0., -1.])\n>>> u(np.nan, np.array([-0.5, 0.0, 0.0]))\narray([0.        , 0.        , 0.70710678])\n>>> L(np.nan, np.array([0, 0, 0]))\narray([[-0.        ,  0.        ,  1.57079633],\n       [ 0.        ,  0.        ,  0.        ],\n       [ 0.        ,  0.        , -1.57079633]])\n>>> L(np.nan, np.array([0.5, 0.0, 0.0]))\narray([[-0.        ,  0.        ,  1.11072073],\n       [ 0.        ,  0.        ,  0.        ],\n       [ 0.        ,  0.        , -1.11072073]])\n>>> L(np.nan, np.array([0, 0, 0])) == L(np.nan, np.array([0, 1, 0]))  # Y-value is not used.\narray([[ True,  True,  True],\n       [ True,  True,  True],\n       [ True,  True,  True]])\n>>> L(np.nan, np.array([1, 0, 0])) == L(np.nan, np.array([0, 0, 1]))\narray([[ True,  True,  True],\n       [ True,  True,  True],\n       [ True,  True,  True]])\n>>> L(np.nan, np.array([1, 0, 0])) == L(np.nan, np.array([-1, 0, 0]))\narray([[ True,  True,  True],\n       [ True,  True,  True],\n       [ True,  True,  True]])\n>>> L(np.nan, np.array([1, 0, 0])) == L(np.nan, np.array([0, 0, -1]))\narray([[ True,  True,  True],\n       [ True,  True,  True],\n       [ True,  True,  True]])\n>>> L(np.nan, np.array([0.5, 0.0, 0.5]))\narray([[-0.78539816,  0.        ,  0.78539816],\n       [ 0.        ,  0.        ,  0.        ],\n       [ 0.78539816,  0.        , -0.78539816]])\n
\n
\n\n
\n
>>> u, L = cell_2d("X", "Z", 6.3e-10, 1e5)\n>>> u(np.nan, np.array([0, 0, 0]))\narray([ 0.,  0., -0.])\n>>> u(np.nan, np.array([0.0, 0.0, -5e4]))\narray([-6.3e-10,  0.0e+00, -0.0e+00])\n>>> u(np.nan, np.array([2e2, 0e0, 0e0]))\narray([ 0.0000000e+00,  0.0000000e+00, -3.9583807e-12])\n
\n
\n", "signature": "(horizontal, vertical, velocity_edge, edge_length=2):", "funcdef": "def"}, "pydrex.velocity.corner_2d": {"fullname": "pydrex.velocity.corner_2d", "modulename": "pydrex.velocity", "qualname": "corner_2d", "kind": "function", "doc": "

Get velocity and velocity gradient callables for a steady-state 2D corner flow.

\n\n

The velocity field is defined by:\n$$\n\\bm{u} = \\frac{dr}{dt} \\bm{\\hat{r}} + r \\frac{d\u03b8}{dt} \\bm{\\hat{\u03b8}}\n= \\frac{2 U}{\u03c0}(\u03b8\\sin\u03b8 - \\cos\u03b8) \u22c5 \\bm{\\hat{r}} + \\frac{2 U}{\u03c0}\u03b8\\cos\u03b8 \u22c5 \\bm{\\hat{\u03b8}}\n$$\nwhere $\u03b8 = 0$ points vertically downwards along the ridge axis\nand $\u03b8 = \u03c0/2$ points along the surface. $U$ is the half spreading velocity.\nStreamlines for the flow obey:\n$$\n\u03c8 = \\frac{2 U r}{\u03c0}\u03b8\\cos\u03b8\n$$\nand are related to the velocity through:\n$$\n\\bm{u} = -\\frac{1}{r} \u22c5 \\frac{d\u03c8}{d\u03b8} \u22c5 \\bm{\\hat{r}} + \\frac{d\u03c8}{dr}\\bm{\\hat{\u03b8}}\n$$\nConversion to Cartesian ($x,y,z$) coordinates yields:\n$$\n\\bm{u} = \\frac{2U}{\u03c0} \\left[\n\\tan^{-1}\\left(\\frac{x}{-z}\\right) + \\frac{xz}{x^{2} + z^{2}} \\right] \\bm{\\hat{x}} +\n\\frac{2U}{\u03c0} \\frac{z^{2}}{x^{2} + z^{2}} \\bm{\\hat{z}}\n$$\nwhere\n\\begin{align*}\nx &= r \\sin\u03b8 \\cr\nz &= -r \\cos\u03b8\n\\end{align*}\nand the velocity gradient is:\n$$\nL = \\frac{4 U}{\u03c0{(x^{2}+z^{2})}^{2}} \u22c5\n\\begin{bmatrix}\n -x^{2}z & 0 & x^{3} \\cr\n 0 & 0 & 0 \\cr\n -xz^{2} & 0 & x^{2}z\n\\end{bmatrix}\n$$\nSee also Fig. 5 in Kaminski & Ribe, 2002.

\n\n

The returned callables have signature f(t, x) where x is a 3D position vector.

\n\n

Args:

\n\n\n", "signature": "(horizontal, vertical, plate_speed):", "funcdef": "def"}, "pydrex.visualisation": {"fullname": "pydrex.visualisation", "modulename": "pydrex.visualisation", "kind": "module", "doc": "
\n

PyDRex: Visualisation functions for test outputs and examples.

\n
\n"}, "pydrex.visualisation.polefigures": {"fullname": "pydrex.visualisation.polefigures", "modulename": "pydrex.visualisation", "qualname": "polefigures", "kind": "function", "doc": "

Plot pole figures of a series of (Nx3x3) orientation matrix stacks.

\n\n

Produces [100], [010] and [001] pole figures for (resampled) orientations.\nFor the argument specification, check the output of pydrex-polefigures --help\non the command line.

\n", "signature": "(\torientations,\tref_axes,\ti_range,\tdensity=False,\tsavefile='polefigures.png',\tstrains=None,\t**kwargs):", "funcdef": "def"}, "pydrex.visualisation.pathline_box2d": {"fullname": "pydrex.visualisation.pathline_box2d", "modulename": "pydrex.visualisation", "qualname": "pathline_box2d", "kind": "function", "doc": "

Plot pathlines and velocity arrows for a 2D box domain.

\n\n

If ax is None, a new figure and axes are created with figure_unless.

\n\n

Args:

\n\n\n\n

Additional keyword arguments are passed to the matplotlib.axes.Axes.quiver call\nused to plot the velocity vectors.

\n\n

Returns the figure handle, the axes handle, the quiver collection (velocities) and\nthe scatter collection (pathline).

\n", "signature": "(\tax,\tget_velocity,\tref_axes,\tcolors,\tpositions,\tmarker,\tmin_coords,\tmax_coords,\tresolution,\taspect='equal',\tcmap=<matplotlib.colors.ListedColormap object>,\tcpo_vectors=None,\tcpo_strengths=None,\ttick_formatter=<function <lambda>>,\t**kwargs):", "funcdef": "def"}, "pydrex.visualisation.alignment": {"fullname": "pydrex.visualisation.alignment", "modulename": "pydrex.visualisation", "qualname": "alignment", "kind": "function", "doc": "

Plot angles (in degrees) versus strains on the given axis.

\n\n

Alignment angles could be either bingham averages or the a-axis in the hexagonal\nsymmetry projection, measured from e.g. the shear direction. In the first case,\nthey should be calculated from resampled grain orientations. Expects as many\nmarkers and labels as there are data series in angles.

\n\n

If ax is None, a new figure and axes are created with figure_unless.

\n\n

Args:

\n\n\n\n

If colors and cmaps are used, then angle values are colored individually within\neach angle series.

\n\n

Additional keyword arguments are passed to matplotlib.axes.Axes.scatter if\ncolors is not None, or to matplotlib.axes.Axes.plot otherwise.

\n\n

Returns a tuple of the figure handle, the axes handle and the set of colors used for\nthe data series plots.

\n", "signature": "(\tax,\tstrains,\tangles,\tmarkers,\tlabels,\terr=None,\t\u03b8_max=90,\t\u03b8_fse=None,\tcolors=None,\tcmaps=None,\t**kwargs):", "funcdef": "def"}, "pydrex.visualisation.strengths": {"fullname": "pydrex.visualisation.strengths", "modulename": "pydrex.visualisation", "qualname": "strengths", "kind": "function", "doc": "

Plot CPO strengths (e.g. M-indices) versus strains on the given axis.

\n\n

If ax is None, a new figure and axes are created with figure_unless.

\n\n

Args:

\n\n\n\n

If colors and cmaps are used, then strength values are colored individually\nwithin each strength series.

\n\n

Additional keyword arguments are passed to matplotlib.axes.Axes.scatter if\ncolors is not None, or to matplotlib.axes.Axes.plot otherwise.

\n\n

Returns a tuple of the figure handle, the axes handle and the set of colors used for\nthe data series plots.

\n", "signature": "(\tax,\tstrains,\tstrengths,\tylabel,\tmarkers,\tlabels,\terr=None,\tcpo_threshold=None,\tcolors=None,\tcmaps=None,\t**kwargs):", "funcdef": "def"}, "pydrex.visualisation.grainsizes": {"fullname": "pydrex.visualisation.grainsizes", "modulename": "pydrex.visualisation", "qualname": "grainsizes", "kind": "function", "doc": "

Plot grain volume fractions versus strains on the given axis.

\n\n

If ax is None, a new figure and axes are created with figure_unless.

\n", "signature": "(ax, strains, fractions):", "funcdef": "def"}, "pydrex.visualisation.show_Skemer2016_ShearStrainAngles": {"fullname": "pydrex.visualisation.show_Skemer2016_ShearStrainAngles", "modulename": "pydrex.visualisation", "qualname": "show_Skemer2016_ShearStrainAngles", "kind": "function", "doc": "

Show data from src/pydrex/data/thirdparty/Skemer2016_ShearStrainAngles.scsv.

\n\n

Plot data from the Skemer 2016 datafile on the axis given by ax. Select the\nstudies from which to plot the data, which must be a list of strings with exact\nmatches in the study column in the datafile.\nAlso filter the data to select only the given fabric\n(see pydrex.core.MineralFabric).

\n\n

If ax is None, a new figure and axes are created with figure_unless.

\n\n

Returns a tuple containing:

\n\n\n", "signature": "(ax, studies, markers, colors, fillstyles, labels, fabric):", "funcdef": "def"}, "pydrex.visualisation.spin": {"fullname": "pydrex.visualisation.spin", "modulename": "pydrex.visualisation", "qualname": "spin", "kind": "function", "doc": "

Plot rotation rates of grains with known, unique initial [100] angles from X.

\n\n

If ax is None, a new figure and axes are created with figure_unless.\nThe default labels (\"target\", \"computed\") can also be overriden.\nIf shear_axis is not None, a dashed line will be drawn at the given x-value\n(and its reflection around 180\u00b0).

\n\n

Returns a tuple of the figure handle, the axes handle and the set of colors used for\nthe data series plots.

\n", "signature": "(\tax,\tinitial_angles,\trotation_rates,\ttarget_initial_angles=None,\ttarget_rotation_rates=None,\tlabels=('target', 'computed'),\tshear_axis=None):", "funcdef": "def"}, "pydrex.visualisation.growth": {"fullname": "pydrex.visualisation.growth", "modulename": "pydrex.visualisation", "qualname": "growth", "kind": "function", "doc": "

Plot grain growth of grains with known, unique initial [100] angles from X.

\n\n

If ax is None, a new figure and axes are created with figure_unless.\nThe default labels (\"target\", \"computed\") can also be overriden.\nIf shear_axis is not None, a dashed line will be drawn at the given x-value\n(and its reflection around 180\u00b0).

\n\n

Returns a tuple of the figure handle, the axes handle and the set of colors used for\nthe data series plots.

\n", "signature": "(\tax,\tinitial_angles,\tfractions_diff,\ttarget_initial_angles=None,\ttarget_fractions_diff=None,\tlabels=('target', 'computed'),\tshear_axis=None):", "funcdef": "def"}, "pydrex.visualisation.figure_unless": {"fullname": "pydrex.visualisation.figure_unless", "modulename": "pydrex.visualisation", "qualname": "figure_unless", "kind": "function", "doc": "

Create figure and axes if ax is None, or return existing figure for ax.

\n\n

If ax is None, a new figure is created for the axes with a few opinionated default\nsettings (grid, constrained layout, high DPI).

\n\n

Returns a tuple containing the figure handle and the axes object.

\n", "signature": "(ax):", "funcdef": "def"}, "pydrex.visualisation.figure": {"fullname": "pydrex.visualisation.figure", "modulename": "pydrex.visualisation", "qualname": "figure", "kind": "function", "doc": "

Create new figure with a few opinionated default settings.

\n\n

(e.g. grid, constrained layout, high DPI).

\n\n

The keyword argument figscale can be used to scale the figure width and height\nrelative to the default values by passing a tuple. Any additional keyword arguments\nare passed to matplotlib.pyplot.figure().

\n", "signature": "(figscale=None, **kwargs):", "funcdef": "def"}, "tests": {"fullname": "tests", "modulename": "tests", "kind": "module", "doc": "

PyDRex tests

\n\n

Running the tests requires pytest.\nFrom the root of the source tree, run pytest.\nTo print more verbose information (including INFO level logging),\nsuch as detailed test progress, use the flag pytest -v.\nThe custom optional flag --outdir=\"OUT\" is recommended\nto produce output figures, data dumps and logs and save them in the directory \"OUT\".\nThe value \".\" can be used to save these in the current directory.

\n\n

Running individual tests or test subsets is possible using the pytest\n-k=\"<pattern>\" command line flag, which accepts a string pattern that is\nmatched against the names of test classes or methods.\nTo see a full list of available tests, use the command pytest --co. This\nproduces a rather long list and it is recommended to view the output with a\npager like less on Linux.

\n\n

In total, the following custom pytest command line flags are defined by PyDRex:

\n\n\n\n

Tests which require a \u201csignificant\u201d amount of memory (> ~16GB RAM) are disabled by default.\nTo fully check the functionality of the code, it is recommended to run these locally\nby using the --runbig flag before moving to larger simulations.

\n\n

Long tests/examples are also disabled by default and can be enabled with --runslow.\nIt is recommended to run these on a HPC cluster infrastructure (>100GB RAM, >32 cores).\nThe number of cores to use for shared memory multiprocessing can be specified with --ncpus.

\n\n

Writing tests

\n\n

For quick sanity checks and inline unit tests, use python doctests.\nThese will also appear as inline examples in the generated documentation.\nMore comprehensive unit tests and larger integration tests should be organised\ninto submodules of the test module.

\n\n\n\n

Tests should not produce persistent output by default.\nIf a test method can produce such output for debugging or visualisation,\nit should accept the outdir positional argument,\nand check if its value is not None.\nIf outdir is None then no persistent output should be produced.\nIf outdir is a directory path (string):

\n\n\n"}, "tests.conftest": {"fullname": "tests.conftest", "modulename": "tests.conftest", "kind": "module", "doc": "
\n

Configuration and fixtures for PyDRex tests.

\n
\n"}, "tests.conftest.pytest_addoption": {"fullname": "tests.conftest.pytest_addoption", "modulename": "tests.conftest", "qualname": "pytest_addoption", "kind": "function", "doc": "

\n", "signature": "(parser):", "funcdef": "def"}, "tests.conftest.PytestConsoleLogger": {"fullname": "tests.conftest.PytestConsoleLogger", "modulename": "tests.conftest", "qualname": "PytestConsoleLogger", "kind": "class", "doc": "

Pytest plugin that allows linking up a custom console logger.

\n", "bases": "_pytest.logging.LoggingPlugin"}, "tests.conftest.PytestConsoleLogger.__init__": {"fullname": "tests.conftest.PytestConsoleLogger.__init__", "modulename": "tests.conftest", "qualname": "PytestConsoleLogger.__init__", "kind": "function", "doc": "

Create a new plugin to capture log messages.

\n\n

The formatter can be safely shared across all handlers so\ncreate a single one for the entire test session here.

\n", "signature": "(config, *args, **kwargs)"}, "tests.conftest.PytestConsoleLogger.name": {"fullname": "tests.conftest.PytestConsoleLogger.name", "modulename": "tests.conftest", "qualname": "PytestConsoleLogger.name", "kind": "variable", "doc": "

\n", "default_value": "'pytest-console-logger'"}, "tests.conftest.PytestConsoleLogger.log_cli_handler": {"fullname": "tests.conftest.PytestConsoleLogger.log_cli_handler", "modulename": "tests.conftest", "qualname": "PytestConsoleLogger.log_cli_handler", "kind": "variable", "doc": "

\n"}, "tests.conftest.PytestConsoleLogger.pytest_runtest_teardown": {"fullname": "tests.conftest.PytestConsoleLogger.pytest_runtest_teardown", "modulename": "tests.conftest", "qualname": "PytestConsoleLogger.pytest_runtest_teardown", "kind": "function", "doc": "

\n", "signature": "(self, item):", "funcdef": "def"}, "tests.conftest.pytest_configure": {"fullname": "tests.conftest.pytest_configure", "modulename": "tests.conftest", "qualname": "pytest_configure", "kind": "function", "doc": "

\n", "signature": "(config):", "funcdef": "def"}, "tests.conftest.pytest_collection_modifyitems": {"fullname": "tests.conftest.pytest_collection_modifyitems", "modulename": "tests.conftest", "qualname": "pytest_collection_modifyitems", "kind": "function", "doc": "

\n", "signature": "(config, items):", "funcdef": "def"}, "tests.conftest.verbose": {"fullname": "tests.conftest.verbose", "modulename": "tests.conftest", "qualname": "verbose", "kind": "function", "doc": "

\n", "signature": "(request):", "funcdef": "def"}, "tests.conftest.outdir": {"fullname": "tests.conftest.outdir", "modulename": "tests.conftest", "qualname": "outdir", "kind": "function", "doc": "

\n", "signature": "(request):", "funcdef": "def"}, "tests.conftest.ncpus": {"fullname": "tests.conftest.ncpus", "modulename": "tests.conftest", "qualname": "ncpus", "kind": "function", "doc": "

\n", "signature": "(request):", "funcdef": "def"}, "tests.conftest.named_tempfile_kwargs": {"fullname": "tests.conftest.named_tempfile_kwargs", "modulename": "tests.conftest", "qualname": "named_tempfile_kwargs", "kind": "function", "doc": "

\n", "signature": "(request):", "funcdef": "def"}, "tests.conftest.ray_session": {"fullname": "tests.conftest.ray_session", "modulename": "tests.conftest", "qualname": "ray_session", "kind": "function", "doc": "

\n", "signature": "():", "funcdef": "def"}, "tests.conftest.console_handler": {"fullname": "tests.conftest.console_handler", "modulename": "tests.conftest", "qualname": "console_handler", "kind": "function", "doc": "

\n", "signature": "(request):", "funcdef": "def"}, "tests.conftest.params_Fraters2021": {"fullname": "tests.conftest.params_Fraters2021", "modulename": "tests.conftest", "qualname": "params_Fraters2021", "kind": "function", "doc": "

\n", "signature": "():", "funcdef": "def"}, "tests.conftest.params_Kaminski2001_fig5_solid": {"fullname": "tests.conftest.params_Kaminski2001_fig5_solid", "modulename": "tests.conftest", "qualname": "params_Kaminski2001_fig5_solid", "kind": "function", "doc": "

\n", "signature": "():", "funcdef": "def"}, "tests.conftest.params_Kaminski2001_fig5_shortdash": {"fullname": "tests.conftest.params_Kaminski2001_fig5_shortdash", "modulename": "tests.conftest", "qualname": "params_Kaminski2001_fig5_shortdash", "kind": "function", "doc": "

\n", "signature": "():", "funcdef": "def"}, "tests.conftest.params_Kaminski2001_fig5_longdash": {"fullname": "tests.conftest.params_Kaminski2001_fig5_longdash", "modulename": "tests.conftest", "qualname": "params_Kaminski2001_fig5_longdash", "kind": "function", "doc": "

\n", "signature": "():", "funcdef": "def"}, "tests.conftest.params_Kaminski2004_fig4_triangles": {"fullname": "tests.conftest.params_Kaminski2004_fig4_triangles", "modulename": "tests.conftest", "qualname": "params_Kaminski2004_fig4_triangles", "kind": "function", "doc": "

\n", "signature": "():", "funcdef": "def"}, "tests.conftest.params_Kaminski2004_fig4_squares": {"fullname": "tests.conftest.params_Kaminski2004_fig4_squares", "modulename": "tests.conftest", "qualname": "params_Kaminski2004_fig4_squares", "kind": "function", "doc": "

\n", "signature": "():", "funcdef": "def"}, "tests.conftest.params_Kaminski2004_fig4_circles": {"fullname": "tests.conftest.params_Kaminski2004_fig4_circles", "modulename": "tests.conftest", "qualname": "params_Kaminski2004_fig4_circles", "kind": "function", "doc": "

\n", "signature": "():", "funcdef": "def"}, "tests.conftest.params_Hedjazian2017": {"fullname": "tests.conftest.params_Hedjazian2017", "modulename": "tests.conftest", "qualname": "params_Hedjazian2017", "kind": "function", "doc": "

\n", "signature": "():", "funcdef": "def"}, "tests.conftest.n_grains": {"fullname": "tests.conftest.n_grains", "modulename": "tests.conftest", "qualname": "n_grains", "kind": "function", "doc": "

\n", "signature": "(request):", "funcdef": "def"}, "tests.conftest.hkl": {"fullname": "tests.conftest.hkl", "modulename": "tests.conftest", "qualname": "hkl", "kind": "function", "doc": "

\n", "signature": "(request):", "funcdef": "def"}, "tests.conftest.ref_axes": {"fullname": "tests.conftest.ref_axes", "modulename": "tests.conftest", "qualname": "ref_axes", "kind": "function", "doc": "

\n", "signature": "(request):", "funcdef": "def"}, "tests.conftest.seeds": {"fullname": "tests.conftest.seeds", "modulename": "tests.conftest", "qualname": "seeds", "kind": "function", "doc": "

1000 unique seeds for ensemble runs that need an RNG seed.

\n", "signature": "():", "funcdef": "def"}, "tests.conftest.seed": {"fullname": "tests.conftest.seed", "modulename": "tests.conftest", "qualname": "seed", "kind": "function", "doc": "

Default seed for test RNG.

\n", "signature": "():", "funcdef": "def"}, "tests.conftest.seeds_nearX45": {"fullname": "tests.conftest.seeds_nearX45", "modulename": "tests.conftest", "qualname": "seeds_nearX45", "kind": "function", "doc": "

41 seeds which have the initial hexagonal symmetry axis near 45\u00b0 from X.

\n", "signature": "():", "funcdef": "def"}, "tests.test_config": {"fullname": "tests.test_config", "modulename": "tests.test_config", "kind": "module", "doc": "
\n

PyDRex: tests for configuration file format.

\n
\n"}, "tests.test_config.test_specfile": {"fullname": "tests.test_config.test_specfile", "modulename": "tests.test_config", "qualname": "test_specfile", "kind": "function", "doc": "

Test TOML spec file parsing.

\n", "signature": "():", "funcdef": "def"}, "tests.test_core": {"fullname": "tests.test_core", "modulename": "tests.test_core", "kind": "module", "doc": "
\n

PyDRex: Tests for core D-Rex routines.

\n
\n"}, "tests.test_core.SUBDIR": {"fullname": "tests.test_core.SUBDIR", "modulename": "tests.test_core", "qualname": "SUBDIR", "kind": "variable", "doc": "

\n", "default_value": "'core'"}, "tests.test_core.TestDislocationCreepOPX": {"fullname": "tests.test_core.TestDislocationCreepOPX", "modulename": "tests.test_core", "qualname": "TestDislocationCreepOPX", "kind": "class", "doc": "

Single-grain orthopyroxene crystallographic rotation rate tests.

\n"}, "tests.test_core.TestDislocationCreepOPX.class_id": {"fullname": "tests.test_core.TestDislocationCreepOPX.class_id", "modulename": "tests.test_core", "qualname": "TestDislocationCreepOPX.class_id", "kind": "variable", "doc": "

\n", "default_value": "'dislocation_creep_OPX'"}, "tests.test_core.TestDislocationCreepOPX.test_shear_dudz": {"fullname": "tests.test_core.TestDislocationCreepOPX.test_shear_dudz", "modulename": "tests.test_core", "qualname": "TestDislocationCreepOPX.test_shear_dudz", "kind": "function", "doc": "

\n", "signature": "(self, outdir):", "funcdef": "def"}, "tests.test_core.TestDislocationCreepOPX.test_shear_dvdx": {"fullname": "tests.test_core.TestDislocationCreepOPX.test_shear_dvdx", "modulename": "tests.test_core", "qualname": "TestDislocationCreepOPX.test_shear_dvdx", "kind": "function", "doc": "

\n", "signature": "(self, outdir):", "funcdef": "def"}, "tests.test_core.TestDislocationCreepOlivineA": {"fullname": "tests.test_core.TestDislocationCreepOlivineA", "modulename": "tests.test_core", "qualname": "TestDislocationCreepOlivineA", "kind": "class", "doc": "

Single-grain A-type olivine analytical rotation rate tests.

\n"}, "tests.test_core.TestDislocationCreepOlivineA.class_id": {"fullname": "tests.test_core.TestDislocationCreepOlivineA.class_id", "modulename": "tests.test_core", "qualname": "TestDislocationCreepOlivineA.class_id", "kind": "variable", "doc": "

\n", "default_value": "'dislocation_creep_OlA'"}, "tests.test_core.TestDislocationCreepOlivineA.test_shear_dvdx_slip_010_100": {"fullname": "tests.test_core.TestDislocationCreepOlivineA.test_shear_dvdx_slip_010_100", "modulename": "tests.test_core", "qualname": "TestDislocationCreepOlivineA.test_shear_dvdx_slip_010_100", "kind": "function", "doc": "

Single grain of A-type olivine, slip on (010)[100].

\n\n

Velocity gradient:\n$$\\bm{L} = \\begin{bmatrix} 0 & 0 & 0 \\cr 2 & 0 & 0 \\cr 0 & 0 & 0 \\end{bmatrix}$$

\n", "signature": "(self, outdir):", "funcdef": "def"}, "tests.test_core.TestDislocationCreepOlivineA.test_shear_dudz_slip_001_100": {"fullname": "tests.test_core.TestDislocationCreepOlivineA.test_shear_dudz_slip_001_100", "modulename": "tests.test_core", "qualname": "TestDislocationCreepOlivineA.test_shear_dudz_slip_001_100", "kind": "function", "doc": "

Single grain of A-type olivine, slip on (001)[100].

\n\n

Velocity gradient:\n$$\\bm{L} = \\begin{bmatrix} 0 & 0 & 2 \\cr 0 & 0 & 0 \\cr 0 & 0 & 0 \\end{bmatrix}$$

\n", "signature": "(self, outdir):", "funcdef": "def"}, "tests.test_core.TestDislocationCreepOlivineA.test_shear_dwdx_slip_001_100": {"fullname": "tests.test_core.TestDislocationCreepOlivineA.test_shear_dwdx_slip_001_100", "modulename": "tests.test_core", "qualname": "TestDislocationCreepOlivineA.test_shear_dwdx_slip_001_100", "kind": "function", "doc": "

Single grain of A-type olivine, slip on (001)[100].

\n\n

Velocity gradient:\n$$\\bm{L} = \\begin{bmatrix} 0 & 0 & 0 \\cr 0 & 0 & 0 \\cr 2 & 0 & 0 \\end{bmatrix}$$

\n", "signature": "(self, outdir):", "funcdef": "def"}, "tests.test_core.TestDislocationCreepOlivineA.test_shear_dvdz_slip_010_001": {"fullname": "tests.test_core.TestDislocationCreepOlivineA.test_shear_dvdz_slip_010_001", "modulename": "tests.test_core", "qualname": "TestDislocationCreepOlivineA.test_shear_dvdz_slip_010_001", "kind": "function", "doc": "

Single grain of A-type olivine, slip on (010)[001].

\n\n

Velocity gradient:\n$$\\bm{L} = \\begin{bmatrix} 0 & 0 & 0 \\cr 0 & 0 & 2 \\cr 0 & 0 & 0 \\end{bmatrix}$$

\n", "signature": "(self, outdir):", "funcdef": "def"}, "tests.test_core.TestRecrystallisation2D": {"fullname": "tests.test_core.TestRecrystallisation2D", "modulename": "tests.test_core", "qualname": "TestRecrystallisation2D", "kind": "class", "doc": "

Basic recrystallisation tests for 2D simple shear.

\n"}, "tests.test_core.TestRecrystallisation2D.class_id": {"fullname": "tests.test_core.TestRecrystallisation2D.class_id", "modulename": "tests.test_core", "qualname": "TestRecrystallisation2D.class_id", "kind": "variable", "doc": "

\n", "default_value": "'recrystallisation_2D'"}, "tests.test_core.TestRecrystallisation2D.test_shear_dvdx_circle_inplane": {"fullname": "tests.test_core.TestRecrystallisation2D.test_shear_dvdx_circle_inplane", "modulename": "tests.test_core", "qualname": "TestRecrystallisation2D.test_shear_dvdx_circle_inplane", "kind": "function", "doc": "

360000 grains of A-type olivine with uniform spread of a-axes on a circle.

\n\n

Grain growth rates are compared to analytical calculations.\nThe a-axes are distributed in the YX plane (i.e.\\ rotated around Z).

\n\n

Velocity gradient:\n$$\\bm{L} = \\begin{bmatrix} 0 & 0 & 0 \\cr 2 & 0 & 0 \\cr 0 & 0 & 0 \\end{bmatrix}$$

\n", "signature": "(self, outdir):", "funcdef": "def"}, "tests.test_core.TestRecrystallisation2D.test_shear_dvdx_circle_shearplane": {"fullname": "tests.test_core.TestRecrystallisation2D.test_shear_dvdx_circle_shearplane", "modulename": "tests.test_core", "qualname": "TestRecrystallisation2D.test_shear_dvdx_circle_shearplane", "kind": "function", "doc": "

360000 grains of A-type olivine with uniform spread of a-axes on a circle.

\n\n

Unlike test_shear_dvdx_circle_inplane, two slip systems are active here,\nwith cyclical variety in which one is dominant depending on grain orientation.\nThe a-axes are distributed in the YZ plane\n(i.e.\\ extrinsic rotation around Z by 90\u00b0 and then around X).

\n\n

Velocity gradient:\n$$\\bm{L} = \\begin{bmatrix} 0 & 0 & 0 \\cr 2 & 0 & 0 \\cr 0 & 0 & 0 \\end{bmatrix}$$

\n", "signature": "(self, outdir):", "funcdef": "def"}, "tests.test_corner_flow_2d": {"fullname": "tests.test_corner_flow_2d", "modulename": "tests.test_corner_flow_2d", "kind": "module", "doc": "
\n

PyDRex: 2D corner flow tests.

\n
\n"}, "tests.test_corner_flow_2d.SUBDIR": {"fullname": "tests.test_corner_flow_2d.SUBDIR", "modulename": "tests.test_corner_flow_2d", "qualname": "SUBDIR", "kind": "variable", "doc": "

\n", "default_value": "'2d_cornerflow'"}, "tests.test_corner_flow_2d.TestOlivineA": {"fullname": "tests.test_corner_flow_2d.TestOlivineA", "modulename": "tests.test_corner_flow_2d", "qualname": "TestOlivineA", "kind": "class", "doc": "

Tests for pure A-type olivine polycrystals in 2D corner flows.

\n"}, "tests.test_corner_flow_2d.TestOlivineA.class_id": {"fullname": "tests.test_corner_flow_2d.TestOlivineA.class_id", "modulename": "tests.test_corner_flow_2d", "qualname": "TestOlivineA.class_id", "kind": "variable", "doc": "

\n", "default_value": "'corner_olivineA'"}, "tests.test_corner_flow_2d.TestOlivineA.run": {"fullname": "tests.test_corner_flow_2d.TestOlivineA.run", "modulename": "tests.test_corner_flow_2d", "qualname": "TestOlivineA.run", "kind": "function", "doc": "

Run 2D corner flow A-type olivine simulation.

\n", "signature": "(\tcls,\tparams,\tseed,\tget_velocity,\tget_velocity_gradient,\tmin_coords,\tmax_coords,\tmax_strain,\tn_timesteps,\tfinal_location):", "funcdef": "def"}, "tests.test_corner_flow_2d.TestOlivineA.test_steady4": {"fullname": "tests.test_corner_flow_2d.TestOlivineA.test_steady4", "modulename": "tests.test_corner_flow_2d", "qualname": "TestOlivineA.test_steady4", "kind": "function", "doc": "

Test CPO evolution in steady 2D corner flow along 4 pathlines.

\n\n

Initial condition: random orientations and uniform volumes in all Minerals.

\n\n

Plate velocity: 2 cm/yr

\n\n
\n\n

This example takes about 11 CPU hours to run and uses around 60GB of RAM.\nIt is recommended to only use ncpus=4 which matches the number of\npathlines, because higher numbers can lead to redundant cross-core\ncommunication.

\n\n
\n", "signature": "(self, outdir, seed, ncpus):", "funcdef": "def"}, "tests.test_diagnostics": {"fullname": "tests.test_diagnostics", "modulename": "tests.test_diagnostics", "kind": "module", "doc": "
\n

PyDRex: tests for texture diagnostics.

\n
\n"}, "tests.test_diagnostics.TestElasticityComponents": {"fullname": "tests.test_diagnostics.TestElasticityComponents", "modulename": "tests.test_diagnostics", "qualname": "TestElasticityComponents", "kind": "class", "doc": "

Test symmetry decomposition of elastic tensors.

\n"}, "tests.test_diagnostics.TestElasticityComponents.test_olivine_Browaeys2004": {"fullname": "tests.test_diagnostics.TestElasticityComponents.test_olivine_Browaeys2004", "modulename": "tests.test_diagnostics", "qualname": "TestElasticityComponents.test_olivine_Browaeys2004", "kind": "function", "doc": "

\n", "signature": "(self):", "funcdef": "def"}, "tests.test_diagnostics.TestElasticityComponents.test_enstatite_Browaeys2004": {"fullname": "tests.test_diagnostics.TestElasticityComponents.test_enstatite_Browaeys2004", "modulename": "tests.test_diagnostics", "qualname": "TestElasticityComponents.test_enstatite_Browaeys2004", "kind": "function", "doc": "

\n", "signature": "(self):", "funcdef": "def"}, "tests.test_diagnostics.TestSymmetryPGR": {"fullname": "tests.test_diagnostics.TestSymmetryPGR", "modulename": "tests.test_diagnostics", "qualname": "TestSymmetryPGR", "kind": "class", "doc": "

Test Point-Girdle-Random (eigenvalue) symmetry diagnostics.

\n"}, "tests.test_diagnostics.TestSymmetryPGR.test_pointX": {"fullname": "tests.test_diagnostics.TestSymmetryPGR.test_pointX", "modulename": "tests.test_diagnostics", "qualname": "TestSymmetryPGR.test_pointX", "kind": "function", "doc": "

Test diagnostics of point symmetry aligned to the X axis.

\n", "signature": "(self):", "funcdef": "def"}, "tests.test_diagnostics.TestSymmetryPGR.test_random": {"fullname": "tests.test_diagnostics.TestSymmetryPGR.test_random", "modulename": "tests.test_diagnostics", "qualname": "TestSymmetryPGR.test_random", "kind": "function", "doc": "

Test diagnostics of random grain orientations.

\n", "signature": "(self):", "funcdef": "def"}, "tests.test_diagnostics.TestSymmetryPGR.test_girdle": {"fullname": "tests.test_diagnostics.TestSymmetryPGR.test_girdle", "modulename": "tests.test_diagnostics", "qualname": "TestSymmetryPGR.test_girdle", "kind": "function", "doc": "

Test diagnostics of girdled orientations.

\n", "signature": "(self):", "funcdef": "def"}, "tests.test_diagnostics.TestVolumeWeighting": {"fullname": "tests.test_diagnostics.TestVolumeWeighting", "modulename": "tests.test_diagnostics", "qualname": "TestVolumeWeighting", "kind": "class", "doc": "

Tests for volumetric resampling of orientation data.

\n"}, "tests.test_diagnostics.TestVolumeWeighting.test_output_shape": {"fullname": "tests.test_diagnostics.TestVolumeWeighting.test_output_shape", "modulename": "tests.test_diagnostics", "qualname": "TestVolumeWeighting.test_output_shape", "kind": "function", "doc": "

Test that we get the correct output shape.

\n", "signature": "(self):", "funcdef": "def"}, "tests.test_diagnostics.TestVolumeWeighting.test_upsample": {"fullname": "tests.test_diagnostics.TestVolumeWeighting.test_upsample", "modulename": "tests.test_diagnostics", "qualname": "TestVolumeWeighting.test_upsample", "kind": "function", "doc": "

Test upsampling of the raw orientation data.

\n", "signature": "(self):", "funcdef": "def"}, "tests.test_diagnostics.TestVolumeWeighting.test_downsample": {"fullname": "tests.test_diagnostics.TestVolumeWeighting.test_downsample", "modulename": "tests.test_diagnostics", "qualname": "TestVolumeWeighting.test_downsample", "kind": "function", "doc": "

Test downsampling of orientation data.

\n", "signature": "(self):", "funcdef": "def"}, "tests.test_diagnostics.TestVolumeWeighting.test_common_input_errors": {"fullname": "tests.test_diagnostics.TestVolumeWeighting.test_common_input_errors", "modulename": "tests.test_diagnostics", "qualname": "TestVolumeWeighting.test_common_input_errors", "kind": "function", "doc": "

Test that exceptions are raised for bad input data.

\n", "signature": "(self):", "funcdef": "def"}, "tests.test_diagnostics.TestBinghamStats": {"fullname": "tests.test_diagnostics.TestBinghamStats", "modulename": "tests.test_diagnostics", "qualname": "TestBinghamStats", "kind": "class", "doc": "

Tests for antipodally symmetric (bingham) statistics.

\n"}, "tests.test_diagnostics.TestBinghamStats.test_average_0": {"fullname": "tests.test_diagnostics.TestBinghamStats.test_average_0", "modulename": "tests.test_diagnostics", "qualname": "TestBinghamStats.test_average_0", "kind": "function", "doc": "

Test bingham average of vectors aligned to the reference frame.

\n", "signature": "(self):", "funcdef": "def"}, "tests.test_diagnostics.TestBinghamStats.test_average_twopoles90Z": {"fullname": "tests.test_diagnostics.TestBinghamStats.test_average_twopoles90Z", "modulename": "tests.test_diagnostics", "qualname": "TestBinghamStats.test_average_twopoles90Z", "kind": "function", "doc": "

Test bingham average of vectors rotated by \u00b190\u00b0 around Z.

\n", "signature": "(self):", "funcdef": "def"}, "tests.test_diagnostics.TestBinghamStats.test_average_spread10X": {"fullname": "tests.test_diagnostics.TestBinghamStats.test_average_spread10X", "modulename": "tests.test_diagnostics", "qualname": "TestBinghamStats.test_average_spread10X", "kind": "function", "doc": "

Test bingham average of vectors spread within 10\u00b0 of the \u00b1X-axis.

\n", "signature": "(self):", "funcdef": "def"}, "tests.test_diagnostics.TestMIndex": {"fullname": "tests.test_diagnostics.TestMIndex", "modulename": "tests.test_diagnostics", "qualname": "TestMIndex", "kind": "class", "doc": "

Tests for the M-index texture strength diagnostic.

\n"}, "tests.test_diagnostics.TestMIndex.test_texture_uniform_ortho": {"fullname": "tests.test_diagnostics.TestMIndex.test_texture_uniform_ortho", "modulename": "tests.test_diagnostics", "qualname": "TestMIndex.test_texture_uniform_ortho", "kind": "function", "doc": "

Test with random (uniform distribution) orthorhombic grain orientations.

\n", "signature": "(self, seed):", "funcdef": "def"}, "tests.test_diagnostics.TestMIndex.test_texture_spread10X_ortho": {"fullname": "tests.test_diagnostics.TestMIndex.test_texture_spread10X_ortho", "modulename": "tests.test_diagnostics", "qualname": "TestMIndex.test_texture_spread10X_ortho", "kind": "function", "doc": "

Test for orthorhombic grains spread within 10\u00b0 of the \u00b1X axis.

\n", "signature": "(self, seed):", "funcdef": "def"}, "tests.test_diagnostics.TestMIndex.test_texture_spread45X_ortho": {"fullname": "tests.test_diagnostics.TestMIndex.test_texture_spread45X_ortho", "modulename": "tests.test_diagnostics", "qualname": "TestMIndex.test_texture_spread45X_ortho", "kind": "function", "doc": "

Test for orthorhombic grains spread within 45\u00b0 of the \u00b1X axis.

\n", "signature": "(self, seed):", "funcdef": "def"}, "tests.test_diagnostics.TestMIndex.test_textures_increasing_ortho": {"fullname": "tests.test_diagnostics.TestMIndex.test_textures_increasing_ortho", "modulename": "tests.test_diagnostics", "qualname": "TestMIndex.test_textures_increasing_ortho", "kind": "function", "doc": "

Test M-index for textures of increasing strength.

\n", "signature": "(self, seed):", "funcdef": "def"}, "tests.test_diagnostics.TestMIndex.test_texture_girdle_ortho": {"fullname": "tests.test_diagnostics.TestMIndex.test_texture_girdle_ortho", "modulename": "tests.test_diagnostics", "qualname": "TestMIndex.test_texture_girdle_ortho", "kind": "function", "doc": "

Test M-index for girdled texture.

\n", "signature": "(self, seed):", "funcdef": "def"}, "tests.test_doctests": {"fullname": "tests.test_doctests", "modulename": "tests.test_doctests", "kind": "module", "doc": "
\n

PyDRex: Run doctests for all submodules.

\n
\n"}, "tests.test_doctests.test_doctests": {"fullname": "tests.test_doctests.test_doctests", "modulename": "tests.test_doctests", "qualname": "test_doctests", "kind": "function", "doc": "

Run doctests for all submodules.

\n", "signature": "(module, capsys, verbose):", "funcdef": "def"}, "tests.test_geometry": {"fullname": "tests.test_geometry", "modulename": "tests.test_geometry", "kind": "module", "doc": "
\n

PyDRex: Tests for geometric conversions and projections.

\n
\n"}, "tests.test_geometry.test_poles_example": {"fullname": "tests.test_geometry.test_poles_example", "modulename": "tests.test_geometry", "qualname": "test_poles_example", "kind": "function", "doc": "

Test poles (directions of crystallographic axes) of example data.

\n", "signature": "(hkl, ref_axes):", "funcdef": "def"}, "tests.test_geometry.test_lambert_equal_area": {"fullname": "tests.test_geometry.test_lambert_equal_area", "modulename": "tests.test_geometry", "qualname": "test_lambert_equal_area", "kind": "function", "doc": "

Test Lambert equal area projection.

\n", "signature": "(seed):", "funcdef": "def"}, "tests.test_scsv": {"fullname": "tests.test_scsv", "modulename": "tests.test_scsv", "kind": "module", "doc": "
\n

PyDRex: tests for the SCSV plain text file format.

\n
\n"}, "tests.test_scsv.test_validate_schema": {"fullname": "tests.test_scsv.test_validate_schema", "modulename": "tests.test_scsv", "qualname": "test_validate_schema", "kind": "function", "doc": "

Test SCSV schema validation.

\n", "signature": "(console_handler):", "funcdef": "def"}, "tests.test_scsv.test_read_specfile": {"fullname": "tests.test_scsv.test_read_specfile", "modulename": "tests.test_scsv", "qualname": "test_read_specfile", "kind": "function", "doc": "

Test SCSV spec file parsing.

\n", "signature": "():", "funcdef": "def"}, "tests.test_scsv.test_save_specfile": {"fullname": "tests.test_scsv.test_save_specfile", "modulename": "tests.test_scsv", "qualname": "test_save_specfile", "kind": "function", "doc": "

Test SCSV spec file reproduction.

\n", "signature": "(outdir, named_tempfile_kwargs):", "funcdef": "def"}, "tests.test_scsv.test_read_Kaminski2002": {"fullname": "tests.test_scsv.test_read_Kaminski2002", "modulename": "tests.test_scsv", "qualname": "test_read_Kaminski2002", "kind": "function", "doc": "

\n", "signature": "():", "funcdef": "def"}, "tests.test_scsv.test_save_scsv_errors": {"fullname": "tests.test_scsv.test_save_scsv_errors", "modulename": "tests.test_scsv", "qualname": "test_save_scsv_errors", "kind": "function", "doc": "

Check that we raise errors when attempting to write bad SCSV data.

\n", "signature": "(named_tempfile_kwargs):", "funcdef": "def"}, "tests.test_scsv.test_read_Kaminski2004": {"fullname": "tests.test_scsv.test_read_Kaminski2004", "modulename": "tests.test_scsv", "qualname": "test_read_Kaminski2004", "kind": "function", "doc": "

\n", "signature": "():", "funcdef": "def"}, "tests.test_scsv.test_read_Skemer2016": {"fullname": "tests.test_scsv.test_read_Skemer2016", "modulename": "tests.test_scsv", "qualname": "test_read_Skemer2016", "kind": "function", "doc": "

\n", "signature": "():", "funcdef": "def"}, "tests.test_simple_shear_2d": {"fullname": "tests.test_simple_shear_2d", "modulename": "tests.test_simple_shear_2d", "kind": "module", "doc": "
\n

PyDRex: 2D simple shear tests.

\n
\n"}, "tests.test_simple_shear_2d.SUBDIR": {"fullname": "tests.test_simple_shear_2d.SUBDIR", "modulename": "tests.test_simple_shear_2d", "qualname": "SUBDIR", "kind": "variable", "doc": "

\n", "default_value": "'2d_simple_shear'"}, "tests.test_simple_shear_2d.TestPreliminaries": {"fullname": "tests.test_simple_shear_2d.TestPreliminaries", "modulename": "tests.test_simple_shear_2d", "qualname": "TestPreliminaries", "kind": "class", "doc": "

Preliminary tests to check that various auxiliary routines are working.

\n"}, "tests.test_simple_shear_2d.TestPreliminaries.test_strain_increment": {"fullname": "tests.test_simple_shear_2d.TestPreliminaries.test_strain_increment", "modulename": "tests.test_simple_shear_2d", "qualname": "TestPreliminaries.test_strain_increment", "kind": "function", "doc": "

Test for accumulating strain via strain increment calculations.

\n", "signature": "(self):", "funcdef": "def"}, "tests.test_simple_shear_2d.TestOlivineA": {"fullname": "tests.test_simple_shear_2d.TestOlivineA", "modulename": "tests.test_simple_shear_2d", "qualname": "TestOlivineA", "kind": "class", "doc": "

Tests for stationary A-type olivine polycrystals in 2D simple shear.

\n"}, "tests.test_simple_shear_2d.TestOlivineA.class_id": {"fullname": "tests.test_simple_shear_2d.TestOlivineA.class_id", "modulename": "tests.test_simple_shear_2d", "qualname": "TestOlivineA.class_id", "kind": "variable", "doc": "

\n", "default_value": "'olivineA'"}, "tests.test_simple_shear_2d.TestOlivineA.run": {"fullname": "tests.test_simple_shear_2d.TestOlivineA.run", "modulename": "tests.test_simple_shear_2d", "qualname": "TestOlivineA.run", "kind": "function", "doc": "

Reusable logic for 2D olivine (A-type) simple shear tests.

\n\n

Returns a tuple with the mineral and the FSE angle (or None if return_fse is\nNone).

\n", "signature": "(\tcls,\tparams,\ttimestamps,\tstrain_rate,\tget_velocity_gradient,\tshear_direction,\tseed=None,\treturn_fse=None,\tget_position=<function TestOlivineA.<lambda>>):", "funcdef": "def"}, "tests.test_simple_shear_2d.TestOlivineA.interp_GBM_Kaminski2001": {"fullname": "tests.test_simple_shear_2d.TestOlivineA.interp_GBM_Kaminski2001", "modulename": "tests.test_simple_shear_2d", "qualname": "TestOlivineA.interp_GBM_Kaminski2001", "kind": "function", "doc": "

Interpolate Kaminski & Ribe, 2001 data to get target angles at strains.

\n", "signature": "(cls, strains):", "funcdef": "def"}, "tests.test_simple_shear_2d.TestOlivineA.interp_GBM_FortranDRex": {"fullname": "tests.test_simple_shear_2d.TestOlivineA.interp_GBM_FortranDRex", "modulename": "tests.test_simple_shear_2d", "qualname": "TestOlivineA.interp_GBM_FortranDRex", "kind": "function", "doc": "

Interpolate angles produced using 'tools/drex_forward_simpleshear.f90'.

\n", "signature": "(cls, strains):", "funcdef": "def"}, "tests.test_simple_shear_2d.TestOlivineA.interp_GBS_FortranDRex": {"fullname": "tests.test_simple_shear_2d.TestOlivineA.interp_GBS_FortranDRex", "modulename": "tests.test_simple_shear_2d", "qualname": "TestOlivineA.interp_GBS_FortranDRex", "kind": "function", "doc": "

Interpolate angles produced using 'tools/drex_forward_simpleshear.f90'.

\n", "signature": "(cls, strains):", "funcdef": "def"}, "tests.test_simple_shear_2d.TestOlivineA.interp_GBS_long_FortranDRex": {"fullname": "tests.test_simple_shear_2d.TestOlivineA.interp_GBS_long_FortranDRex", "modulename": "tests.test_simple_shear_2d", "qualname": "TestOlivineA.interp_GBS_long_FortranDRex", "kind": "function", "doc": "

Interpolate angles produced using 'tools/drex_forward_simpleshear.f90'.

\n", "signature": "(cls, strains):", "funcdef": "def"}, "tests.test_simple_shear_2d.TestOlivineA.interp_GBS_Kaminski2004": {"fullname": "tests.test_simple_shear_2d.TestOlivineA.interp_GBS_Kaminski2004", "modulename": "tests.test_simple_shear_2d", "qualname": "TestOlivineA.interp_GBS_Kaminski2004", "kind": "function", "doc": "

Interpolate Kaminski & Ribe, 2001 data to get target angles at strains.

\n", "signature": "(cls, strains):", "funcdef": "def"}, "tests.test_simple_shear_2d.TestOlivineA.test_zero_recrystallisation": {"fullname": "tests.test_simple_shear_2d.TestOlivineA.test_zero_recrystallisation", "modulename": "tests.test_simple_shear_2d", "qualname": "TestOlivineA.test_zero_recrystallisation", "kind": "function", "doc": "

Check that M*=0 is a reliable switch to turn off recrystallisation.

\n", "signature": "(self, seed):", "funcdef": "def"}, "tests.test_simple_shear_2d.TestOlivineA.test_grainsize_median": {"fullname": "tests.test_simple_shear_2d.TestOlivineA.test_grainsize_median", "modulename": "tests.test_simple_shear_2d", "qualname": "TestOlivineA.test_grainsize_median", "kind": "function", "doc": "

Check that M={50,100,150}, \u03bb=5 causes decreasing grain size median.

\n", "signature": "(self, seed, gbm_mobility):", "funcdef": "def"}, "tests.test_simple_shear_2d.TestOlivineA.test_dvdx_ensemble": {"fullname": "tests.test_simple_shear_2d.TestOlivineA.test_dvdx_ensemble", "modulename": "tests.test_simple_shear_2d", "qualname": "TestOlivineA.test_dvdx_ensemble", "kind": "function", "doc": "

Test a-axis alignment to shear in Y direction (init. SCCS near 45\u00b0 from X).

\n\n

Velocity gradient:\n$$\\bm{L} = \\begin{bmatrix} 0 & 0 & 0 \\cr 2 & 0 & 0 \\cr 0 & 0 & 0 \\end{bmatrix}$$

\n", "signature": "(\tself,\toutdir,\tseeds_nearX45,\tncpus,\tgbs_threshold,\tnucleation_efficiency):", "funcdef": "def"}, "tests.test_simple_shear_2d.TestOlivineA.test_dvdx_GBM": {"fullname": "tests.test_simple_shear_2d.TestOlivineA.test_dvdx_GBM", "modulename": "tests.test_simple_shear_2d", "qualname": "TestOlivineA.test_dvdx_GBM", "kind": "function", "doc": "

Test a-axis alignment to shear in Y direction (init. SCCS near 45\u00b0 from X).

\n\n

Velocity gradient:\n$$\n\\bm{L} = 10^{-4} \u00d7\n \\begin{bmatrix} 0 & 0 & 0 \\cr 2 & 0 & 0 \\cr 0 & 0 & 0 \\end{bmatrix}\n$$

\n\n

Results are compared to the Fortran 90 output.

\n", "signature": "(self, outdir, seeds_nearX45, ncpus):", "funcdef": "def"}, "tests.test_simple_shear_2d.TestOlivineA.test_GBM_calibration": {"fullname": "tests.test_simple_shear_2d.TestOlivineA.test_GBM_calibration", "modulename": "tests.test_simple_shear_2d", "qualname": "TestOlivineA.test_GBM_calibration", "kind": "function", "doc": "

Compare results for various values of $$M^\u2217$$ to A-type olivine data.

\n\n

Velocity gradient:\n$$\n\\bm{L} = 10^{-4} \u00d7\n \\begin{bmatrix} 0 & 0 & 0 \\cr 2 & 0 & 0 \\cr 0 & 0 & 0 \\end{bmatrix}\n$$

\n\n

Unlike test_dvdx_GBM,\ngrain boudary sliding is enabled here (see _io.DEFAULT_PARAMS).\nData are provided by Skemer & Hansen, 2016.

\n", "signature": "(self, outdir, seeds, ncpus):", "funcdef": "def"}, "tests.test_simple_shear_2d.TestOlivineA.test_dudz_pathline": {"fullname": "tests.test_simple_shear_2d.TestOlivineA.test_dudz_pathline", "modulename": "tests.test_simple_shear_2d", "qualname": "TestOlivineA.test_dudz_pathline", "kind": "function", "doc": "

Test alignment of olivine a-axis for a polycrystal advected on a pathline.

\n", "signature": "(self, outdir, seed):", "funcdef": "def"}, "tests.test_simple_shear_3d": {"fullname": "tests.test_simple_shear_3d", "modulename": "tests.test_simple_shear_3d", "kind": "module", "doc": "
\n

PyDRex: Simple shear 3D tests.

\n
\n"}, "tests.test_simple_shear_3d.SUBDIR": {"fullname": "tests.test_simple_shear_3d.SUBDIR", "modulename": "tests.test_simple_shear_3d", "qualname": "SUBDIR", "kind": "variable", "doc": "

\n", "default_value": "'3d_simple_shear'"}, "tests.test_simple_shear_3d.TestFraters2021": {"fullname": "tests.test_simple_shear_3d.TestFraters2021", "modulename": "tests.test_simple_shear_3d", "qualname": "TestFraters2021", "kind": "class", "doc": "

Tests inspired by the benchmarks presented in [Fraters & Billen, 2021].

\n"}, "tests.test_simple_shear_3d.TestFraters2021.class_id": {"fullname": "tests.test_simple_shear_3d.TestFraters2021.class_id", "modulename": "tests.test_simple_shear_3d", "qualname": "TestFraters2021.class_id", "kind": "variable", "doc": "

\n", "default_value": "'Fraters2021'"}, "tests.test_simple_shear_3d.TestFraters2021.run": {"fullname": "tests.test_simple_shear_3d.TestFraters2021.run", "modulename": "tests.test_simple_shear_3d", "qualname": "TestFraters2021.run", "kind": "function", "doc": "

Run simulation with stationary particles in the given velocity gradient.

\n\n

The optional RNG seed is used for the initial pseudorandom orientations.\nA prefix msg will be printed before each timestep log message if given.\nOther keyword args are passed to pydrex.Mineral.update_orientations.

\n\n

Returns a tuple containing one olivine (A-type) and one enstatite mineral.\nIf params[\"enstatite_fraction\"] is zero, then the second tuple element will be\nNone instead.

\n", "signature": "(\tcls,\tparams,\ttimestamps,\tget_velocity_gradient_initial,\tget_velocity_gradient_final,\tswitch_time,\tmsg,\tseed=None):", "funcdef": "def"}, "tests.test_simple_shear_3d.TestFraters2021.test_direction_change": {"fullname": "tests.test_simple_shear_3d.TestFraters2021.test_direction_change", "modulename": "tests.test_simple_shear_3d", "qualname": "TestFraters2021.test_direction_change", "kind": "function", "doc": "

Test a-axis alignment in simple shear with instantaneous geometry change.

\n\n

The simulation runs for 5 Ma with a strain rate of 1.58e-14/s, resulting in an\naccumulated strain invariant of 2.5.

\n\n

The initial shear has nonzero du/dz and the final shear has nonzero dv/dx where\nu is the velocity along X and v the velocity along Y.

\n", "signature": "(\tself,\toutdir,\tseeds,\tparams_Fraters2021,\tswitch_time_Ma,\tncpus,\tray_session):", "funcdef": "def"}, "tests.test_tensors": {"fullname": "tests.test_tensors", "modulename": "tests.test_tensors", "kind": "module", "doc": "
\n

PyDRex: Tests for tensor operations.

\n
\n"}, "tests.test_tensors.test_voigt_decompose": {"fullname": "tests.test_tensors.test_voigt_decompose", "modulename": "tests.test_tensors", "qualname": "test_voigt_decompose", "kind": "function", "doc": "

Test decomposition of Voigt 6x6 matrix into distinct contractions.

\n", "signature": "():", "funcdef": "def"}, "tests.test_tensors.test_voigt_tensor": {"fullname": "tests.test_tensors.test_voigt_tensor", "modulename": "tests.test_tensors", "qualname": "test_voigt_tensor", "kind": "function", "doc": "

Test elasticity tensor <-> 6x6 Voigt matrix conversions.

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Test Voigt vector construction.

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\n

PyDRex: tests for CPO stability in 2D vortex and Stokes cell flows.

\n
\n"}, "tests.test_vortex_2d.SUBDIR": {"fullname": "tests.test_vortex_2d.SUBDIR", "modulename": "tests.test_vortex_2d", "qualname": "SUBDIR", "kind": "variable", "doc": "

\n", "default_value": "'2d_vortex'"}, "tests.test_vortex_2d.TestCellOlivineA": {"fullname": "tests.test_vortex_2d.TestCellOlivineA", "modulename": "tests.test_vortex_2d", "qualname": "TestCellOlivineA", "kind": "class", "doc": "

Tests for A-type olivine polycrystals in a 2D Stokes cell.

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\n", "default_value": "'cell_olivineA'"}, "tests.test_vortex_2d.TestCellOlivineA.run": {"fullname": "tests.test_vortex_2d.TestCellOlivineA.run", "modulename": "tests.test_vortex_2d", "qualname": "TestCellOlivineA.run", "kind": "function", "doc": "

Run 2D Stokes cell A-type olivine simulation.

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Run 2D cell test with 10000 grains (~14GiB RAM requirement).

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Test to check that 5000 grains is \"enough\" to resolve transient features.

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Test to demonstrate stability of the dip at \u03b5 \u2248 3.75 for 5000+ grains.

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API Documentation

  • pytest_collection_modifyitems
    • +
  • + verbose +
  • outdir
    • @@ -296,119 +299,124 @@

    135 136 137@pytest.fixture(scope="session") -138def outdir(request): -139 _outdir = request.config.getoption("--outdir") -140 yield _outdir -141 # Create combined ensemble figure for 2D cell tests after they have all finished. -142 _test_vortex_2d.TestCellOlivineA._make_ensemble_figure(_outdir) -143 -144 -145@pytest.fixture(scope="session") -146def ncpus(request): -147 return max(1, request.config.getoption("--ncpus")) +138def verbose(request): +139 return request.config.option.verbose +140 +141 +142@pytest.fixture(scope="session") +143def outdir(request): +144 _outdir = request.config.getoption("--outdir") +145 yield _outdir +146 # Create combined ensemble figure for 2D cell tests after they have all finished. +147 _test_vortex_2d.TestCellOlivineA._make_ensemble_figure(_outdir) 148 149 150@pytest.fixture(scope="session") -151def named_tempfile_kwargs(request): -152 if sys.platform == "win32": -153 return {"delete": False} -154 else: -155 return dict() -156 -157 -158@pytest.fixture(scope="session") -159def ray_session(): -160 if HAS_RAY: -161 # NOTE: Expects a running Ray cluster with a number of CPUS matching --ncpus. -162 if not ray.is_initialized(): -163 ray.init(address="auto") -164 _log.info("using Ray cluster with %s", ray.cluster_resources()) -165 yield -166 if ray.is_initialized(): -167 ray.shutdown() -168 yield -169 -170 -171@pytest.fixture(scope="function") -172def console_handler(request): -173 if request.config.option.verbose > 0: # Show console logs if -v/--verbose given. -174 return request.config.pluginmanager.get_plugin( -175 "pytest-console-logger" -176 ).log_cli_handler -177 return _log.CONSOLE_LOGGER -178 -179 -180@pytest.fixture -181def params_Fraters2021(): -182 return _mock.PARAMS_FRATERS2021 +151def ncpus(request): +152 return max(1, request.config.getoption("--ncpus")) +153 +154 +155@pytest.fixture(scope="session") +156def named_tempfile_kwargs(request): +157 if sys.platform == "win32": +158 return {"delete": False} +159 else: +160 return dict() +161 +162 +163@pytest.fixture(scope="session") +164def ray_session(): +165 if HAS_RAY: +166 # NOTE: Expects a running Ray cluster with a number of CPUS matching --ncpus. +167 if not ray.is_initialized(): +168 ray.init(address="auto") +169 _log.info("using Ray cluster with %s", ray.cluster_resources()) +170 yield +171 if ray.is_initialized(): +172 ray.shutdown() +173 yield +174 +175 +176@pytest.fixture(scope="function") +177def console_handler(request): +178 if request.config.option.verbose > 0: # Show console logs if -v/--verbose given. +179 return request.config.pluginmanager.get_plugin( +180 "pytest-console-logger" +181 ).log_cli_handler +182 return _log.CONSOLE_LOGGER 183 184 185@pytest.fixture -186def params_Kaminski2001_fig5_solid(): -187 return _mock.PARAMS_KAMINSKI2001_FIG5_SOLID +186def params_Fraters2021(): +187 return _mock.PARAMS_FRATERS2021 188 189 190@pytest.fixture -191def params_Kaminski2001_fig5_shortdash(): -192 return _mock.PARAMS_KAMINSKI2001_FIG5_SHORTDASH +191def params_Kaminski2001_fig5_solid(): +192 return _mock.PARAMS_KAMINSKI2001_FIG5_SOLID 193 194 195@pytest.fixture -196def params_Kaminski2001_fig5_longdash(): -197 return _mock.PARAMS_KAMINSKI2001_FIG5_LONGDASH +196def params_Kaminski2001_fig5_shortdash(): +197 return _mock.PARAMS_KAMINSKI2001_FIG5_SHORTDASH 198 199 200@pytest.fixture -201def params_Kaminski2004_fig4_triangles(): -202 return _mock.PARAMS_KAMINSKI2004_FIG4_TRIANGLES +201def params_Kaminski2001_fig5_longdash(): +202 return _mock.PARAMS_KAMINSKI2001_FIG5_LONGDASH 203 204 205@pytest.fixture -206def params_Kaminski2004_fig4_squares(): -207 return _mock.PARAMS_KAMINSKI2004_FIG4_SQUARES +206def params_Kaminski2004_fig4_triangles(): +207 return _mock.PARAMS_KAMINSKI2004_FIG4_TRIANGLES 208 209 210@pytest.fixture -211def params_Kaminski2004_fig4_circles(): -212 return _mock.PARAMS_KAMINSKI2004_FIG4_CIRCLES +211def params_Kaminski2004_fig4_squares(): +212 return _mock.PARAMS_KAMINSKI2004_FIG4_SQUARES 213 214 215@pytest.fixture -216def params_Hedjazian2017(): -217 return _mock.PARAMS_HEDJAZIAN2017 +216def params_Kaminski2004_fig4_circles(): +217 return _mock.PARAMS_KAMINSKI2004_FIG4_CIRCLES 218 219 -220@pytest.fixture(scope="session", params=[100, 500, 1000, 5000, 10000]) -221def n_grains(request): -222 return request.param +220@pytest.fixture +221def params_Hedjazian2017(): +222 return _mock.PARAMS_HEDJAZIAN2017 223 224 -225@pytest.fixture(scope="session", params=[[1, 0, 0], [0, 1, 0], [0, 0, 1]]) -226def hkl(request): +225@pytest.fixture(scope="session", params=[100, 500, 1000, 5000, 10000]) +226def n_grains(request): 227 return request.param 228 229 -230@pytest.fixture(scope="session", params=["xz", "yz", "xy"]) -231def ref_axes(request): +230@pytest.fixture(scope="session", params=[[1, 0, 0], [0, 1, 0], [0, 0, 1]]) +231def hkl(request): 232 return request.param 233 234 -235@pytest.fixture(scope="session") -236def seeds(): -237 """1000 unique seeds for ensemble runs that need an RNG seed.""" -238 return _io.read_scsv(_io.data("rng") / "seeds.scsv").seeds +235@pytest.fixture(scope="session", params=["xz", "yz", "xy"]) +236def ref_axes(request): +237 return request.param +238 239 -240 -241@pytest.fixture(scope="session") -242def seed(): -243 """Default seed for test RNG.""" -244 return 8816 +240@pytest.fixture(scope="session") +241def seeds(): +242 """1000 unique seeds for ensemble runs that need an RNG seed.""" +243 return _io.read_scsv(_io.data("rng") / "seeds.scsv").seeds +244 245 -246 -247@pytest.fixture(scope="session") -248def seeds_nearX45(): -249 """41 seeds which have the initial hexagonal symmetry axis near 45° from X.""" -250 return _io.read_scsv(_io.data("rng") / "hexaxis_nearX45_seeds.scsv").seeds +246@pytest.fixture(scope="session") +247def seed(): +248 """Default seed for test RNG.""" +249 return 8816 +250 +251 +252@pytest.fixture(scope="session") +253def seeds_nearX45(): +254 """41 seeds which have the initial hexagonal symmetry axis near 45° from X.""" +255 return _io.read_scsv(_io.data("rng") / "hexaxis_nearX45_seeds.scsv").seeds @@ -690,6 +698,27 @@

    Inherited Members
    + +
    + +
    +
    @pytest.fixture(scope='session')
    + + def + verbose(request): + + + +
    + + 
    138@pytest.fixture(scope="session")
+139def verbose(request):
+140    return request.config.option.verbose
+
    + + + +
    @@ -703,12 +732,12 @@
    Inherited Members
    - 
    138@pytest.fixture(scope="session")
-139def outdir(request):
-140    _outdir = request.config.getoption("--outdir")
-141    yield _outdir
-142    #  Create combined ensemble figure for 2D cell tests after they have all finished.
-143    _test_vortex_2d.TestCellOlivineA._make_ensemble_figure(_outdir)
+            
    143@pytest.fixture(scope="session")
+144def outdir(request):
+145    _outdir = request.config.getoption("--outdir")
+146    yield _outdir
+147    #  Create combined ensemble figure for 2D cell tests after they have all finished.
+148    _test_vortex_2d.TestCellOlivineA._make_ensemble_figure(_outdir)
 
    
 
 
@@ -727,9 +756,9 @@ 
    Inherited Members
    - 
    146@pytest.fixture(scope="session")
-147def ncpus(request):
-148    return max(1, request.config.getoption("--ncpus"))
+            
    151@pytest.fixture(scope="session")
+152def ncpus(request):
+153    return max(1, request.config.getoption("--ncpus"))
 
    
 
 
@@ -748,12 +777,12 @@ 
    Inherited Members
    - 
    151@pytest.fixture(scope="session")
-152def named_tempfile_kwargs(request):
-153    if sys.platform == "win32":
-154        return {"delete": False}
-155    else:
-156        return dict()
+            
    156@pytest.fixture(scope="session")
+157def named_tempfile_kwargs(request):
+158    if sys.platform == "win32":
+159        return {"delete": False}
+160    else:
+161        return dict()
 
    
 
 
@@ -772,17 +801,17 @@ 
    Inherited Members
    - 
    159@pytest.fixture(scope="session")
-160def ray_session():
-161    if HAS_RAY:
-162        # NOTE: Expects a running Ray cluster with a number of CPUS matching --ncpus.
-163        if not ray.is_initialized():
-164            ray.init(address="auto")
-165            _log.info("using Ray cluster with %s", ray.cluster_resources())
-166        yield
-167        if ray.is_initialized():
-168            ray.shutdown()
-169    yield
+            
    164@pytest.fixture(scope="session")
+165def ray_session():
+166    if HAS_RAY:
+167        # NOTE: Expects a running Ray cluster with a number of CPUS matching --ncpus.
+168        if not ray.is_initialized():
+169            ray.init(address="auto")
+170            _log.info("using Ray cluster with %s", ray.cluster_resources())
+171        yield
+172        if ray.is_initialized():
+173            ray.shutdown()
+174    yield
 
    
 
 
@@ -801,13 +830,13 @@ 
    Inherited Members
    - 
    172@pytest.fixture(scope="function")
-173def console_handler(request):
-174    if request.config.option.verbose > 0:  # Show console logs if -v/--verbose given.
-175        return request.config.pluginmanager.get_plugin(
-176            "pytest-console-logger"
-177        ).log_cli_handler
-178    return _log.CONSOLE_LOGGER
+            
    177@pytest.fixture(scope="function")
+178def console_handler(request):
+179    if request.config.option.verbose > 0:  # Show console logs if -v/--verbose given.
+180        return request.config.pluginmanager.get_plugin(
+181            "pytest-console-logger"
+182        ).log_cli_handler
+183    return _log.CONSOLE_LOGGER
 
    
 
 
@@ -826,9 +855,9 @@ 
    Inherited Members
    - 
    181@pytest.fixture
-182def params_Fraters2021():
-183    return _mock.PARAMS_FRATERS2021
+            
    186@pytest.fixture
+187def params_Fraters2021():
+188    return _mock.PARAMS_FRATERS2021
 
    
 
 
@@ -847,9 +876,9 @@ 
    Inherited Members
    - 
    186@pytest.fixture
-187def params_Kaminski2001_fig5_solid():
-188    return _mock.PARAMS_KAMINSKI2001_FIG5_SOLID
+            
    191@pytest.fixture
+192def params_Kaminski2001_fig5_solid():
+193    return _mock.PARAMS_KAMINSKI2001_FIG5_SOLID
 
    
 
 
@@ -868,9 +897,9 @@ 
    Inherited Members
    - 
    191@pytest.fixture
-192def params_Kaminski2001_fig5_shortdash():
-193    return _mock.PARAMS_KAMINSKI2001_FIG5_SHORTDASH
+            
    196@pytest.fixture
+197def params_Kaminski2001_fig5_shortdash():
+198    return _mock.PARAMS_KAMINSKI2001_FIG5_SHORTDASH
 
    
 
 
@@ -889,9 +918,9 @@ 
    Inherited Members
    - 
    196@pytest.fixture
-197def params_Kaminski2001_fig5_longdash():
-198    return _mock.PARAMS_KAMINSKI2001_FIG5_LONGDASH
+            
    201@pytest.fixture
+202def params_Kaminski2001_fig5_longdash():
+203    return _mock.PARAMS_KAMINSKI2001_FIG5_LONGDASH
 
    
 
 
@@ -910,9 +939,9 @@ 
    Inherited Members
    - 
    201@pytest.fixture
-202def params_Kaminski2004_fig4_triangles():
-203    return _mock.PARAMS_KAMINSKI2004_FIG4_TRIANGLES
+            
    206@pytest.fixture
+207def params_Kaminski2004_fig4_triangles():
+208    return _mock.PARAMS_KAMINSKI2004_FIG4_TRIANGLES
 
    
 
 
@@ -931,9 +960,9 @@ 
    Inherited Members
    - 
    206@pytest.fixture
-207def params_Kaminski2004_fig4_squares():
-208    return _mock.PARAMS_KAMINSKI2004_FIG4_SQUARES
+            
    211@pytest.fixture
+212def params_Kaminski2004_fig4_squares():
+213    return _mock.PARAMS_KAMINSKI2004_FIG4_SQUARES
 
    
 
 
@@ -952,9 +981,9 @@ 
    Inherited Members
    - 
    211@pytest.fixture
-212def params_Kaminski2004_fig4_circles():
-213    return _mock.PARAMS_KAMINSKI2004_FIG4_CIRCLES
+            
    216@pytest.fixture
+217def params_Kaminski2004_fig4_circles():
+218    return _mock.PARAMS_KAMINSKI2004_FIG4_CIRCLES
 
    
 
 
@@ -973,9 +1002,9 @@ 
    Inherited Members
    - 
    216@pytest.fixture
-217def params_Hedjazian2017():
-218    return _mock.PARAMS_HEDJAZIAN2017
+            
    221@pytest.fixture
+222def params_Hedjazian2017():
+223    return _mock.PARAMS_HEDJAZIAN2017
 
    
 
 
@@ -994,9 +1023,9 @@ 
    Inherited Members
    - 
    221@pytest.fixture(scope="session", params=[100, 500, 1000, 5000, 10000])
-222def n_grains(request):
-223    return request.param
+            
    226@pytest.fixture(scope="session", params=[100, 500, 1000, 5000, 10000])
+227def n_grains(request):
+228    return request.param
 
    
 
 
@@ -1015,9 +1044,9 @@ 
    Inherited Members
    - 
    226@pytest.fixture(scope="session", params=[[1, 0, 0], [0, 1, 0], [0, 0, 1]])
-227def hkl(request):
-228    return request.param
+            
    231@pytest.fixture(scope="session", params=[[1, 0, 0], [0, 1, 0], [0, 0, 1]])
+232def hkl(request):
+233    return request.param
 
    
 
 
@@ -1036,9 +1065,9 @@ 
    Inherited Members
    - 
    231@pytest.fixture(scope="session", params=["xz", "yz", "xy"])
-232def ref_axes(request):
-233    return request.param
+            
    236@pytest.fixture(scope="session", params=["xz", "yz", "xy"])
+237def ref_axes(request):
+238    return request.param
 
    
 
 
@@ -1057,10 +1086,10 @@ 
    Inherited Members
    - 
    236@pytest.fixture(scope="session")
-237def seeds():
-238    """1000 unique seeds for ensemble runs that need an RNG seed."""
-239    return _io.read_scsv(_io.data("rng") / "seeds.scsv").seeds
+            
    241@pytest.fixture(scope="session")
+242def seeds():
+243    """1000 unique seeds for ensemble runs that need an RNG seed."""
+244    return _io.read_scsv(_io.data("rng") / "seeds.scsv").seeds
 
    
 
 
@@ -1081,10 +1110,10 @@ 
    Inherited Members
    - 
    242@pytest.fixture(scope="session")
-243def seed():
-244    """Default seed for test RNG."""
-245    return 8816
+            
    247@pytest.fixture(scope="session")
+248def seed():
+249    """Default seed for test RNG."""
+250    return 8816
 
    
 
 
@@ -1105,10 +1134,10 @@ 
    Inherited Members
    - 
    248@pytest.fixture(scope="session")
-249def seeds_nearX45():
-250    """41 seeds which have the initial hexagonal symmetry axis near 45° from X."""
-251    return _io.read_scsv(_io.data("rng") / "hexaxis_nearX45_seeds.scsv").seeds
+            
    253@pytest.fixture(scope="session")
+254def seeds_nearX45():
+255    """41 seeds which have the initial hexagonal symmetry axis near 45° from X."""
+256    return _io.read_scsv(_io.data("rng") / "hexaxis_nearX45_seeds.scsv").seeds
 
    
 
 
diff --git a/tests/test_doctests.html b/tests/test_doctests.html
index bbcc21de..406521fa 100644
--- a/tests/test_doctests.html
+++ b/tests/test_doctests.html
@@ -108,7 +108,7 @@ 
    
 28
 29
 30@pytest.mark.parametrize("module", _get_submodule_list())
-31def test_doctests(module, capsys):
+31def test_doctests(module, capsys, verbose):
 32    """Run doctests for all submodules."""
 33    with capsys.disabled():  # Pytest output capturing messes with doctests.
 34        _log.info("running doctests for %s...", module)
@@ -116,7 +116,7 @@ 
    
 36            n_fails, n_tests = doctest.testmod(
 37                importlib.import_module(module),
 38                raise_on_error=True,
-39                verbose=False,  # Change to True to debug doctest failures.
+39                verbose=verbose > 1,  # Run pytest with -vv to show doctest details.
 40            )
 41            if n_fails > 0:
 42                raise AssertionError(f"there were {n_fails} doctest failures from {module}")
@@ -150,14 +150,14 @@ 
    
                     
    @pytest.mark.parametrize('module', _get_submodule_list())
    
 
         def
-        test_doctests(module, capsys):
+        test_doctests(module, capsys, verbose):
 
                 
 
     
    31@pytest.mark.parametrize("module", _get_submodule_list())
-32def test_doctests(module, capsys):
+32def test_doctests(module, capsys, verbose):
 33    """Run doctests for all submodules."""
 34    with capsys.disabled():  # Pytest output capturing messes with doctests.
 35        _log.info("running doctests for %s...", module)
@@ -165,7 +165,7 @@ 
    
 37            n_fails, n_tests = doctest.testmod(
 38                importlib.import_module(module),
 39                raise_on_error=True,
-40                verbose=False,  # Change to True to debug doctest failures.
+40                verbose=verbose > 1,  # Run pytest with -vv to show doctest details.
 41            )
 42            if n_fails > 0:
 43                raise AssertionError(f"there were {n_fails} doctest failures from {module}")