From 91a09247b0cae2421d50e1311648c23cce6dbc0e Mon Sep 17 00:00:00 2001
From: Archis Joglekar <joglekara@users.noreply.github.com>
Date: Fri, 30 Aug 2024 13:53:40 -0700
Subject: [PATCH] can initialize super gaussians (#62)

---
 adept/vfp1d/helpers.py          | 15 +++++++------
 configs/vfp-1d/epp-short.yaml   | 40 ++++++++++++++++++++++++---------
 tests/test_vfp1d/epp-short.yaml |  4 ++--
 3 files changed, 40 insertions(+), 19 deletions(-)

diff --git a/adept/vfp1d/helpers.py b/adept/vfp1d/helpers.py
index 4aa75d4..3ed08c9 100644
--- a/adept/vfp1d/helpers.py
+++ b/adept/vfp1d/helpers.py
@@ -112,16 +112,17 @@ def _initialize_distribution_(
     dv = vmax / nv
     vax = np.linspace(dv / 2.0, vmax - dv / 2.0, nv)
 
-    # alpha = np.sqrt(3.0 * gamma_3_over_m(m) / gamma_5_over_m(m))
-    # cst = m / (4 * np.pi * alpha**3.0 * gamma(3.0 / m))
-
-    # single_dist = np.exp(-3 * (vax**2.0) / (2 * vth**2.0)) / (2 * np.pi * vth**2.0) ** 1.5
-    # norm = 1.0 / np.sum(4 * np.pi * single_dist * vax**2.0 * dv, axis=0)
-
     f = np.zeros([nx, nv])
     for ix, (tn, tt) in enumerate(zip(n_prof, T_prof)):
         # eq 4-51b in Shkarofsky
         single_dist = (2 * np.pi * tt * (vth**2.0 / 2)) ** -1.5 * np.exp(-(vax**2.0) / (2 * tt * (vth**2.0 / 2)))
+
+        # from Ridgers2008
+        vth_x = np.sqrt(tt) * vth
+        alpha = np.sqrt(3.0 * gamma_3_over_m(m) / 2.0 / gamma_5_over_m(m))
+        cst = m / (4 * np.pi * alpha**3.0 * gamma_3_over_m(m))
+        single_dist = cst / vth_x**3.0 * np.exp(-((vax / alpha / vth_x) ** m))
+
         f[ix, :] = tn * single_dist
 
     # if noise_type.casefold() == "uniform":
@@ -164,7 +165,7 @@ def _initialize_total_distribution_(cfg, cfg_grid):
 
             for k in ["n", "T"]:
                 if species_params[k]["basis"] == "uniform":
-                    profs[k] = np.ones_like(prof_total[k])
+                    profs[k] = species_params[k]["baseline"] * np.ones_like(prof_total[k])
 
                 elif species_params[k]["basis"] == "tanh":
                     center = (_Q(species_params[k]["center"]) / cfg["units"]["derived"]["x0"]).to("").value
diff --git a/configs/vfp-1d/epp-short.yaml b/configs/vfp-1d/epp-short.yaml
index 361393b..799f923 100644
--- a/configs/vfp-1d/epp-short.yaml
+++ b/configs/vfp-1d/epp-short.yaml
@@ -1,9 +1,9 @@
 units:
   laser_wavelength: 351nm
-  reference electron temperature: 300eV
+  reference electron temperature: 3000eV
   reference ion temperature: 300eV
-  reference electron density: 1.5e21/cm^3
-  Z: 30
+  reference electron density: 2.275e21/cm^3
+  Z: 6
   Ion: Au+
   logLambda: nrl
 
@@ -16,10 +16,10 @@ density:
     noise_val: 0.0
     v0: 0.0
     T0: 1.0
-    m: 2.0
+    m: 3.4
     n: 
       basis: uniform
-      baseline: 1.0
+      baseline: 0.9
       bump_or_trough: bump
       center: 0m
       rise: 1m
@@ -27,9 +27,29 @@ density:
       width: 1m
     T:
       basis: sine
-      baseline: 1.0
+      baseline: 1.
       amplitude: 1.0e-3
       wavelength: 250um
+  species-hote:
+    noise_seed: 420
+    noise_type: gaussian
+    noise_val: 0.0
+    v0: 0.0
+    T0: 1.0
+    m: 2.0
+    n: 
+      basis: uniform
+      baseline: 0.1
+      bump_or_trough: bump
+      center: 0m
+      rise: 1m
+      bump_height: 0.0
+      width: 1m
+    T:
+      basis: sine
+      baseline: 40.0
+      amplitude: 0.
+      wavelength: 250um
 
 grid:
   dt: 1fs
@@ -46,19 +66,19 @@ save:
   fields:
     t:
       tmin: 0.0ps
-      tmax: 0.5ps
+      tmax: 2.0ps
       nt: 11
   electron:
     t:
       tmin: 0.0ps
-      tmax: 0.5ps
+      tmax: 2.0ps
       nt: 6
 
 solver: vfp-1d
 
 mlflow:
   experiment: vfp1d
-  run: epperlein-short
+  run: epperlein-short-hote-ee
 
 drivers:
   ex: {}
@@ -67,7 +87,7 @@ drivers:
 terms:
   fokker_planck:
     flm:
-      ee: false
+      ee: true
     f00:
       type: Dougherty
   e_solver: oshun
\ No newline at end of file
diff --git a/tests/test_vfp1d/epp-short.yaml b/tests/test_vfp1d/epp-short.yaml
index 361393b..1d13c2c 100644
--- a/tests/test_vfp1d/epp-short.yaml
+++ b/tests/test_vfp1d/epp-short.yaml
@@ -1,9 +1,9 @@
 units:
   laser_wavelength: 351nm
-  reference electron temperature: 300eV
+  reference electron temperature: 2000eV
   reference ion temperature: 300eV
   reference electron density: 1.5e21/cm^3
-  Z: 30
+  Z: 6
   Ion: Au+
   logLambda: nrl