diff --git a/.github/workflows/build_cpu.yml b/.github/workflows/build_cpu.yml deleted file mode 100644 index 3438bc56..00000000 --- a/.github/workflows/build_cpu.yml +++ /dev/null @@ -1,44 +0,0 @@ -name: build_cpu - -on: - push: - branches: [ master ] - # Run when container or environment is changed - paths: - - 'containers/dockerfile_cpu' - - 'environment-cpu.yml' - # Allows workflow to be manually triggered - workflow_dispatch: - -jobs: - build_cpu: - if: github.repository_owner == 'cmelab' - runs-on: ubuntu-latest - - steps: - - - name: Checkout - uses: actions/checkout@v2 - - - name: Set up QEMU - uses: docker/setup-qemu-action@v1 - - - name: Set up Docker Buildx - uses: docker/setup-buildx-action@v1 - - - name: Login to DockerHub - uses: docker/login-action@v1 - with: - username: ${{ secrets.DOCKERHUB_USERNAME }} - password: ${{ secrets.DOCKERHUB_TOKEN }} - - - name: Build and push - uses: docker/build-push-action@v2 - with: - context: . - file: ./containers/dockerfile_cpu - push: true - tags: cmelab/msibi_cpu:latest - - - name: Image digest - run: echo ${{ steps.docker_build.outputs.digest }} diff --git a/.github/workflows/build_gpu.yml b/.github/workflows/build_gpu.yml deleted file mode 100644 index 58d24de9..00000000 --- a/.github/workflows/build_gpu.yml +++ /dev/null @@ -1,45 +0,0 @@ -name: build_gpu - -on: - push: - branches: [ master ] - - # Run when container or environment is changed - paths: - - 'containers/dockerfile_gpu' - - 'environment-nohoomd.yml' - # Allows workflow to be manually triggered - workflow_dispatch: - -jobs: - build_gpu: - if: github.repository_owner == 'cmelab' - runs-on: ubuntu-latest - - steps: - - - name: Checkout - uses: actions/checkout@v2 - - - name: Set up QEMU - uses: docker/setup-qemu-action@v1 - - - name: Set up Docker Buildx - uses: docker/setup-buildx-action@v1 - - - name: Login to DockerHub - uses: docker/login-action@v1 - with: - username: ${{ secrets.DOCKERHUB_USERNAME }} - password: ${{ secrets.DOCKERHUB_TOKEN }} - - - name: Build and push - uses: docker/build-push-action@v2 - with: - context: . - file: ./containers/dockerfile_gpu - push: true - tags: cmelab/msibi_gpu:latest - - - name: Image digest - run: echo ${{ steps.docker_build.outputs.digest }} diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml index 87962a73..0c07cb60 100644 --- a/.github/workflows/pytest.yml +++ b/.github/workflows/pytest.yml @@ -4,15 +4,15 @@ on: push: branches: [ master ] paths: - - '.github/workflows/pytest.yml' - - 'environment-cpu.yml' - - 'msibi/**' + - msibi/** + - environment-dev.yml + - .github/workflows/pytest.yml pull_request: branches: [ master ] paths: - - 'msibi/**' - - 'environment-cpu.yml' - - '.github/workflows/pytest.yml' + - msibi/** + - environment-dev.yml + - .github/workflows/pytest.yml # Allows workflow to be manually triggered workflow_dispatch: @@ -27,9 +27,9 @@ jobs: - name: Build environment uses: conda-incubator/setup-miniconda@v2 with: - environment-file: environment-cpu.yml + environment-file: environment-dev.yml miniforge-variant: Mambaforge - miniforge-version: 4.9.2-4 + miniforge-version: 23.11.0-0 use-mamba: true - name: Install package @@ -38,10 +38,10 @@ jobs: - name: Run pytest with coverage report shell: bash -l {0} - run: python -m pytest --cov=./ --cov-report=xml -v + run: python -m pytest -rs -v --cov=./ --cov-report=xml - name: Upload coverage to Codecov - uses: codecov/codecov-action@v1 + uses: codecov/codecov-action@v3 with: token: ${{ secrets.CODECOV_TOKEN }} file: ./coverage.xml diff --git a/.gitignore b/.gitignore index 43dec6e9..501d19cb 100644 --- a/.gitignore +++ b/.gitignore @@ -10,7 +10,7 @@ msibi/tutorials/lj/state*/run.py *.dcd .DS_Store *.egg-info - +*.idea/ # Byte-compiled / optimized / DLL files __pycache__/ *.py[cod] diff --git a/README.md b/README.md index e46c53b9..bc16ecb1 100644 --- a/README.md +++ b/README.md @@ -2,8 +2,6 @@ # MultiState Iterative Boltzmann Inversion (MS-IBI) ---------------------------------------- -[![build_cpu](https://github.com/cmelab/msibi/actions/workflows/build_cpu.yml/badge.svg)](https://github.com/cmelab/msibi/actions/workflows/build_cpu.yml) -[![build_gpu](https://github.com/cmelab/msibi/actions/workflows/build_gpu.yml/badge.svg)](https://github.com/cmelab/msibi/actions/workflows/build_gpu.yml) [![pytest](https://github.com/cmelab/msibi/actions/workflows/pytest.yml/badge.svg)](https://github.com/cmelab/msibi/actions/workflows/pytest.yml) [![codecov](https://codecov.io/gh/cmelab/msibi/branch/master/graph/badge.svg?token=7NFPBMBN0I)](https://codecov.io/gh/cmelab/msibi) @@ -20,10 +18,6 @@ pip install . ``` -### Tutorials -[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/cmelab/msibi/master?urlpath=tree/msibi/tutorials/lj/LJ_Tutorial.ipynb) - Tutorial showing how to recreate the Lennard Jones potential using MS-IBI - - ### Citation [![Citing MSIBI](https://img.shields.io/badge/DOI-10.1063%2F1.4880555-blue.svg)](http://dx.doi.org/10.1063/1.4880555) Details of the underlying method and its validation can be found [here](http://dx.doi.org/10.1063/1.4880555). diff --git a/Tutorials/README b/Tutorials/README deleted file mode 100644 index 215c73dd..00000000 --- a/Tutorials/README +++ /dev/null @@ -1,18 +0,0 @@ -This directory contains several tests. -It is advisable, at the minimum, to run the LJ test to make sure the -code works as expected. To run plot.py, downloading and installing msibi_utils -is highly recommended to visualize the results. - -LJ : recover known LJ potential - - This test, as described in the original paper, is recovering a - known potential to show that the methodology works. The target - data was derived from LJ fluids at three different states. - -PROPANE : optimize pair potentials for a single-site propane model - - This test, as described in the original 2014 paper, performs further - optimizations on propane using a coarse-graining 3-1 mapping. The 3-site - propane is mapped to the single-site propane and the generated data can be - compared to known LJ potentials from literature [1]. - -[1] Q. Pu et al., “Molecular simulations of stretching gold nanowires in - solvents,” Nanotechnology 18, 424007 (2007). diff --git a/Tutorials/lj/opt.py b/Tutorials/lj/opt.py deleted file mode 100755 index da2369c6..00000000 --- a/Tutorials/lj/opt.py +++ /dev/null @@ -1,58 +0,0 @@ -import itertools -import os - -import numpy as np - -from msibi import MSIBI, Pair, State, mie - -os.system("rm state*/_* rdfs/pair* potentials/* f_fits.log state*/log.txt") -os.system("rm state*/err.txt") -os.system("rm state*/query.dcd") - -# Set up global parameters. -rdf_cutoff = 5.0 -opt = MSIBI( - rdf_cutoff=rdf_cutoff, n_rdf_points=101, pot_cutoff=3.0, smooth_rdfs=True -) - -# Specify states. -state0 = State( - kT=0.5, - state_dir="./state0", - top_file="start.hoomdxml", - name="state0", - backup_trajectory=True, -) -state1 = State( - kT=1.5, - state_dir="./state1", - top_file="start.hoomdxml", - name="state1", - backup_trajectory=True, -) -state2 = State( - kT=2.0, - state_dir="./state2", - top_file="start.hoomdxml", - name="state2", - backup_trajectory=True, -) -states = [state0, state1, state2] - -# Specify pairs. -indices = list(itertools.combinations(range(1468), 2)) # all-all for 1468 atoms -initial_guess = mie(opt.pot_r, 1.0, 1.0) # 1-D array of potential values. -rdf_targets = [ - np.loadtxt("rdfs/rdf.target{0:d}.t1t1.txt".format(i)) for i in range(3) -] - -pair0 = Pair("1", "1", initial_guess) -alphas = [1.0, 1.0, 1.0] - -# Add targets to pair. -for state, target, alpha in zip(states, rdf_targets, alphas): - pair0.add_state(state, target, alpha, indices) -pairs = [pair0] # optimize() expects a list of pairs - -# Do magic. -opt.optimize(states, pairs, n_iterations=5, engine="hoomd") diff --git a/Tutorials/lj/rdfs/rdftarget0.5 b/Tutorials/lj/rdfs/rdftarget0.5 deleted file mode 100644 index 71dcec6e..00000000 --- a/Tutorials/lj/rdfs/rdftarget0.5 +++ /dev/null @@ -1,101 +0,0 @@ -2.475247532129287720e-02 0.000000000000000000e+00 -7.425742596387863159e-02 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files a/Tutorials/lj/trajectory0.5.gsd and /dev/null differ diff --git a/Tutorials/lj/trajectory1.5.gsd b/Tutorials/lj/trajectory1.5.gsd deleted file mode 100644 index d3aedb1d..00000000 Binary files a/Tutorials/lj/trajectory1.5.gsd and /dev/null differ diff --git a/Tutorials/lj/trajectory2.0.gsd b/Tutorials/lj/trajectory2.0.gsd deleted file mode 100644 index 8bbfbb37..00000000 Binary files a/Tutorials/lj/trajectory2.0.gsd and /dev/null differ diff --git a/Tutorials/propane/.gitignore b/Tutorials/propane/.gitignore deleted file mode 100644 index 7c8814b6..00000000 --- a/Tutorials/propane/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -rdfs/pair* -potentials/ -state*/*.txt -state*/run.py diff --git a/Tutorials/propane/opt.py b/Tutorials/propane/opt.py deleted file mode 100644 index 943bd361..00000000 --- a/Tutorials/propane/opt.py +++ /dev/null @@ -1,61 +0,0 @@ -import itertools -import os -import string - -import numpy as np - -from msibi import MSIBI, Pair, State, mie - -os.system("rm rdfs/pair_C3*_state*-step*.txt f_fits.log") -os.system("rm state_*/*.txt state*/run.py state*/*query.dcd") - - -# Set up global parameters. -rdf_cutoff = 5.0 -opt = MSIBI( - rdf_cutoff=rdf_cutoff, n_rdf_points=201, pot_cutoff=3.0, smooth_rdfs=True -) - -# Specify states. -stateA = State( - kT=0.5, - state_dir="./state_A", - top_file="start.hoomdxml", - name="stateA", - backup_trajectory=True, -) -stateB = State( - kT=1.5, - state_dir="./state_B", - top_file="start.hoomdxml", - name="stateB", - backup_trajectory=True, -) -stateC = State( - kT=2.0, - state_dir="./state_C", - top_file="start.hoomdxml", - name="stateC", - backup_trajectory=True, -) -states = [stateA, stateB, stateC] - -# Specify pairs. -indices = list(itertools.combinations(range(1024), 2)) # all-all for 1024 atoms - -initial_guess = mie(opt.pot_r, 1.0, 1.0) # 1-D array of potential values. -alphabet = ["A", "B", "C"] -rdf_targets = [ - np.loadtxt("rdfs/C3-C3-state_{0}.txt".format(i)) for i in alphabet -] - -pair0 = Pair("C3", "C3", initial_guess) -alphas = [1.0, 1.0, 1.0] - -# Add targets to pair. -for state, target, alpha in zip(states, rdf_targets, alphas): - pair0.add_state(state, target, alpha, indices) -pairs = [pair0] # optimize() expects a list of pairs - -# Do magic. -opt.optimize(states, pairs, n_iterations=5, engine="hoomd") diff --git a/Tutorials/propane/plot.py b/Tutorials/propane/plot.py deleted file mode 100644 index ae076647..00000000 --- a/Tutorials/propane/plot.py +++ /dev/null @@ -1,7 +0,0 @@ -from msibi_utils.animate_rdf import animate_all_pairs_states -from msibi_utils.plot_fit import plot_all_fits -from msibi_utils.plot_rdfs import plot_all_rdfs - -plot_all_fits("opt.out", ylims=(0.5, 1)) -plot_all_rdfs("opt.out", "rdfs", step=4) -animate_all_pairs_states("opt.out", "rdfs", step=4, n_skip=0) diff --git a/Tutorials/propane/rdfs/C3-C3-state_A.txt b/Tutorials/propane/rdfs/C3-C3-state_A.txt deleted file mode 100644 index 03865b89..00000000 --- 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1.1242 -2.325 1.10807 -2.35 1.13237 -2.375 1.076 -2.4 1.09375 -2.425 1.06837 -2.45 1.08812 -2.475 1.08134 -2.5 1.06257 -2.525 1.08044 -2.55 1.03609 -2.575 1.06178 -2.6 1.07895 -2.625 1.042 -2.65 1.04652 -2.675 1.0425 -2.7 1.06157 -2.725 1.06052 -2.75 1.03683 -2.775 1.00619 -2.8 1.03141 -2.825 1.04785 -2.85 1.04705 -2.875 1.03301 -2.9 1.02932 -2.925 1.0441 -2.95 1.02118 -2.975 1.02748 -3 1.0331 -3.025 1.01699 -3.05 1.02621 -3.075 1.03373 -3.1 1.04008 -3.125 1.0015 -3.15 1.03343 -3.175 1.03179 -3.2 1.03066 -3.225 1.00205 -3.25 1.00531 -3.275 1.01749 -3.3 1.00607 -3.325 1.02488 -3.35 1.01628 -3.375 1.01974 -3.4 1.01737 -3.425 1.01073 -3.45 1.01659 -3.475 1.00232 -3.5 1.03022 -3.525 0.99543 -3.55 0.995634 -3.575 1.01498 -3.6 1.0281 -3.625 1.01184 -3.65 0.997846 -3.675 1.00738 -3.7 0.998266 -3.725 1.0289 -3.75 0.99316 -3.775 1.00371 -3.8 0.998534 -3.825 1.00424 -3.85 1.0089 -3.875 0.999082 -3.9 1.02278 -3.925 1.00346 -3.95 0.996261 -3.975 0.999478 -4 0.999141 -4.025 1.00629 -4.05 1.0187 -4.075 0.995549 -4.1 1.00899 -4.125 0.99382 -4.15 1.00209 -4.175 1.00246 -4.2 1.00387 -4.225 1.00619 -4.25 1.00914 -4.275 0.998725 -4.3 1.00621 -4.325 1.00305 -4.35 0.989747 -4.375 0.983472 -4.4 1.00607 -4.425 1.00132 -4.45 0.992959 -4.475 1.01233 -4.5 1.01778 -4.525 0.998039 -4.55 0.993919 -4.575 1.01567 -4.6 0.982628 -4.625 0.989017 -4.65 1.00528 -4.675 0.992508 -4.7 0.995893 -4.725 0.995767 -4.75 0.999742 -4.775 0.993372 -4.8 0.992983 -4.825 1.00489 -4.85 0.997149 -4.875 1.00122 -4.9 0.996219 -4.925 0.995193 -4.95 1.00247 -4.975 1.00844 -5 1.0125 diff --git a/Tutorials/propane/state_A/hoomd_run_template.py b/Tutorials/propane/state_A/hoomd_run_template.py deleted file mode 100755 index 0e9a7f31..00000000 --- a/Tutorials/propane/state_A/hoomd_run_template.py +++ /dev/null @@ -1,7 +0,0 @@ -all = hoomd.group.all() -nvt_int = hoomd.md.integrate.langevin(group=all, kT=T_final, seed=1) -hoomd.md.integrate.mode_standard(dt=0.001) - -hoomd.run(1e2) -output_dcd = hoomd.dump.dcd(filename="query.dcd", period=100, overwrite=True) -hoomd.run(1e4) diff --git a/Tutorials/propane/state_A/start.hoomdxml b/Tutorials/propane/state_A/start.hoomdxml deleted file mode 100755 index 04727a84..00000000 --- a/Tutorials/propane/state_A/start.hoomdxml +++ /dev/null @@ -1,4116 +0,0 @@ - - - - - --6.01612 -3.0955 -4.99577 -0.220974 5.24077 5.03659 --5.70426 3.15938 2.71932 -5.76901 -6.30648 3.65493 --3.66534 5.84858 -1.21114 -2.71256 -3.30432 4.31491 --5.06002 3.36388 -2.91929 --1.31727 0.433331 0.456665 --1.45514 2.70539 -1.61655 --5.49077 2.1344 2.22842 -2.20271 0.867396 4.30593 --2.15852 -6.30026 1.52611 -0.973216 3.27374 -4.11579 --1.58572 4.93515 -1.65297 --1.34241 -4.11456 4.36808 --3.07913 0.48815 3.75148 -2.13865 -2.77927 0.683071 -2.26642 5.45902 -0.130551 --0.994597 -2.89972 4.43253 --0.99154 -3.50506 -3.07266 --6.28643 6.31503 0.9468 -4.65868 4.89313 -6.33431 --3.29319 -3.89999 -3.86059 --5.71125 1.45214 -4.55811 -2.04264 -0.025519 -3.86554 --3.96794 4.32649 -2.65945 --0.993918 -4.7269 -6.11152 --1.03233 1.47937 4.48647 -1.76569 1.29366 -4.85505 --4.61486 -1.67588 1.79159 --1.80087 -3.88535 -0.992383 --4.7964 -4.04722 0.685786 -5.66279 4.3154 5.99225 -0.962799 3.86015 1.69311 -0.414324 -1.83811 -2.57762 --4.43975 2.06389 -1.11518 --3.38766 -3.01055 2.71661 -3.60683 0.50622 1.36112 --2.02362 -2.85795 -2.15046 -2.27631 6.03188 4.7797 -3.34931 0.948497 3.78295 --0.737757 6.10005 4.93934 -3.68833 4.103 3.09821 --4.96122 5.41138 -3.01114 -0.164526 5.93348 0.0462726 -2.44686 -6.09788 -2.74129 --1.76268 4.09923 1.76897 --3.4593 -2.23883 1.65692 --1.79358 -1.17876 -3.04282 -1.90542 2.99555 -6.16072 -3.74107 3.8709 -0.160424 -4.32706 3.90173 -5.14763 -2.95917 -0.881434 -2.83139 -1.33071 2.32683 -3.38335 --4.73733 -0.353173 -6.45436 -5.08525 -6.11892 -1.78523 --0.78474 -2.96762 0.773421 -4.86522 -3.5281 0.178994 -2.19895 3.34443 -3.17661 -0.653561 3.96852 5.0262 --3.5435 -4.52532 2.45952 -6.34745 -5.16347 -1.79884 --3.06034 4.62658 5.17225 -5.96897 3.60947 2.85503 -3.13371 -1.62433 -5.04333 -5.31659 1.65998 3.54204 --5.06761 5.94926 4.77502 -3.33549 -0.42812 -0.79081 -0.834086 -6.41363 -4.90031 -4.47299 -0.73911 -1.4426 -6.11899 -2.68688 3.21074 -3.99629 -3.54714 3.75087 --1.67415 5.46194 -3.64536 -1.57286 4.78852 4.61479 -6.41417 0.449628 3.85584 --4.82324 5.25808 3.00396 --2.67648 5.56773 6.26099 -1.47376 -4.16714 -6.42487 -6.01382 4.12661 -5.5272 -5.33592 -2.57472 -2.22984 -2.14754 -1.44735 -3.95026 -0.683049 -4.26636 -5.20018 -6.38473 6.01646 -6.4326 --0.0598788 1.20869 1.20787 -1.98768 -6.09948 2.75338 --1.09323 -4.81498 3.02891 --5.10055 0.909714 1.23022 -3.17638 -5.10978 -3.25619 --4.49809 -2.66642 -5.21763 --4.60771 -2.87659 4.57599 -4.35702 0.491878 0.0636225 -5.53763 1.23565 0.219419 -3.92617 2.00748 -4.17214 -2.37495 -0.172804 -5.10957 --3.46111 5.94698 2.68867 --3.6763 -4.10527 4.80813 -4.22115 -0.614719 5.3439 -6.3962 -1.8728 -0.945171 -1.3639 -1.39025 5.04173 --2.15539 -0.811089 0.361711 -2.36265 -4.23452 -1.31383 -2.18457 6.20704 -5.3216 --1.22158 5.26214 2.30229 --4.62608 6.03754 -3.94002 --0.0446613 -5.99237 -3.0907 --3.21694 -6.29481 -2.40482 -5.78042 -1.16297 0.370149 -1.68515 -5.81025 0.894172 -1.0296 0.583502 3.82442 --6.09873 3.49592 5.67275 --5.2235 -5.36986 1.20153 -1.08034 -1.25098 -3.45048 -1.64914 -4.91509 3.19351 -0.714045 3.15969 6.18164 -0.851042 6.49123 3.14753 --3.42291 5.07279 -0.141787 --3.23547 3.41628 4.04415 --2.49942 -1.70473 2.93386 -2.28232 -2.14412 5.55102 -5.95361 -4.56865 2.95015 --4.67492 -5.30718 -0.0495295 -4.01306 4.64414 1.84082 --4.25995 -5.08134 5.54882 --0.670696 2.72867 -2.93336 --1.32976 -4.66448 -3.24926 -0.147416 -0.664268 4.38209 -1.19393 1.33532 1.08151 --5.98452 3.77302 3.89649 --2.21329 -1.11952 4.99689 --3.97382 -2.16618 -3.67262 -2.3762 3.94508 2.01102 --4.04959 2.9141 0.602355 --0.507425 -5.93492 3.79394 -0.0557174 5.04243 2.22613 --1.25688 -6.11554 -5.18292 -6.14893 -2.38601 -5.87403 --3.68305 -5.33132 -4.69401 --6.47976 3.75168 -2.21312 --1.5146 -4.04591 1.12987 --4.78106 1.17203 2.47296 --3.65057 5.59218 -6.03266 --0.431343 -3.34928 3.15229 --5.99854 -4.49722 5.01084 -3.9392 5.33137 3.15389 --2.57125 6.27066 0.0422787 -4.31022 -6.41007 3.58716 -3.95178 -2.85897 2.10099 -1.96106 -2.4062 -5.20706 -0.602548 4.94387 1.19117 --1.8836 6.48559 -6.23748 -3.28041 -0.479787 -4.24551 --1.48669 -5.25676 1.89311 --3.44217 -6.31968 -5.61047 -2.59759 0.509724 -2.51816 --3.87243 2.51411 4.92474 --1.11053 -3.70705 6.15658 -3.04325 -0.668947 1.45788 --6.18735 -4.97057 2.25191 --0.982362 -5.66987 -2.19071 --0.508532 -2.0414 3.17056 --0.395179 1.53008 -1.75646 --4.40267 0.276855 5.54112 --1.11511 2.37179 6.22271 --5.63902 5.88634 -5.31377 --1.04852 0.464527 -2.50012 --5.54853 -1.37066 6.30796 -3.49581 -5.37505 3.04462 --2.5265 -1.92497 -0.638543 --0.921121 -0.75 0.924951 -3.37411 2.91792 -3.22505 -4.58918 6.31726 -3.01478 -6.46094 -3.82521 -2.67033 -1.02893 2.69201 -5.27729 --2.33059 -4.90584 3.04071 --6.0288 -4.37562 -0.356661 --2.94071 2.31182 -1.66161 -1.93188 -1.23263 0.654091 -3.99707 1.20131 -5.66115 --0.581759 5.22542 0.840171 --5.68498 -6.33649 -2.41538 -4.13335 -2.3642 -5.10512 --3.01972 3.0869 -6.02433 --0.200788 0.887171 3.68048 -5.47352 -0.462574 3.59406 --2.74062 4.52238 0.993979 -4.85292 4.43288 2.65801 -5.41131 -2.6634 1.86438 --2.95932 -6.14978 3.82345 -5.92695 2.356 0.798225 -1.29127 2.84229 2.33023 -4.93115 1.00379 5.92376 -2.02553 3.46097 4.41364 --6.19898 -3.35229 2.42118 -4.38852 -0.650588 0.792572 --2.16821 5.14937 -0.475286 -0.989795 2.65071 -0.0939543 --1.60615 1.74319 -2.75737 --5.20605 2.15423 3.50167 --1.881 3.90096 4.07254 --1.23057 -2.0876 5.48858 --0.515798 -2.50359 -4.85999 -5.52911 5.70253 -2.20443 --5.00214 3.82387 -4.48147 -4.3928 -5.05424 -0.921729 -5.50317 1.97833 -0.991695 -3.15077 2.89305 0.857805 -1.75289 4.56458 -2.47087 --5.85984 -5.13413 -2.76503 --3.41753 -0.898193 -6.18639 -6.49788 -2.87288 4.74793 -2.22493 5.77957 -2.91425 -0.257357 -4.07854 0.17984 --5.43079 0.0929639 3.24578 --0.642237 3.0078 4.09485 -5.61561 0.601912 2.80179 -4.62261 3.03741 -1.20817 -4.4783 -1.20465 -0.282902 -2.08578 2.40797 -2.23422 -6.18842 -4.67787 6.23062 --0.363027 6.26686 -5.74561 -0.101871 -5.3985 -5.75026 -4.6891 2.14967 -2.54446 -3.75885 -1.28326 -6.36573 -2.26752 1.25945 0.938583 --1.73759 -1.09344 6.42287 --4.8024 -4.43215 4.33963 -4.28201 -0.372165 -3.22787 --4.23563 1.75763 1.4672 --0.92952 2.85896 0.51692 -4.26518 -2.65658 -3.6889 --2.38332 -5.32796 -5.66163 -2.89669 -6.12605 1.99424 --4.37874 4.378 4.25882 --1.35228 6.28722 -2.71685 -5.80473 -0.621039 4.75492 -0.0643505 -5.98912 -4.29771 --6.18327 1.45014 0.254725 -4.06514 -1.24542 3.24459 --2.40078 1.31844 0.273312 -1.21406 4.8587 5.98463 -1.89029 6.48993 -4.14039 --2.18269 -3.70847 -3.38856 -4.09664 5.62619 -3.93415 --6.19879 -6.10931 5.71369 -0.13834 1.82506 -3.2032 --4.64683 1.37236 4.49212 --4.39942 4.80835 -5.20288 --5.86287 -3.9128 1.16045 -5.70314 4.47185 -3.01742 --2.47901 3.20804 -4.84603 -6.4794 -0.793043 -5.52481 -0.449064 -1.95168 4.06236 -2.62997 -4.21974 0.546325 -5.00418 0.727203 -0.986634 -0.723978 2.74618 4.59941 -3.08588 -3.0221 -5.58164 --5.54919 -1.54347 -5.36647 -1.43035 0.484136 -1.50061 --0.0771183 -0.286622 0.140749 -2.27925 2.05066 -0.0140352 -6.02389 -3.90782 4.17866 --1.18415 5.82008 3.65669 --0.782665 -0.840195 -2.49142 -6.20607 -3.54607 -0.0758306 --0.748059 -0.868995 5.64016 -4.18663 0.313116 -2.12511 -6.29033 -6.11588 1.96951 --0.247012 3.38065 -6.01134 -5.89288 -5.09684 -3.06834 --2.78508 3.77478 -0.183686 --1.48238 -5.37383 0.627504 -4.49032 6.47882 -4.70425 -6.3202 1.89979 5.87404 --5.94845 -0.595753 -4.27427 --6.1769 -0.0303637 -1.75028 -0.630255 -0.645549 5.75079 --4.77383 -5.3377 -2.28882 -0.0766993 -4.96167 -0.946354 -2.5468 -0.21204 0.345585 --1.0537 -3.91334 -0.0435371 --0.33378 -4.49852 -2.24403 --2.67709 2.69619 2.86473 --6.11697 -2.68182 -2.32437 -1.33709 -5.54117 -3.65794 --5.23903 -5.36994 -5.27306 --2.14006 -0.424073 1.5224 -5.89354 -3.67157 1.28424 -3.65948 -3.98615 -3.61722 -4.78149 5.79617 0.123173 --2.31501 0.746976 1.53051 -3.44483 -5.04752 5.98302 --3.34607 1.85688 -3.19367 --5.01869 -2.65351 2.60515 -5.27302 -5.67922 -4.14272 -5.00409 -6.49286 4.80775 --1.87563 -5.17001 5.86727 --0.0419609 2.63131 -4.52641 --0.571635 -0.98961 -3.64769 --5.68395 2.27521 0.921195 --0.97392 6.45462 1.03486 -1.46925 5.89484 0.521641 --4.06445 2.75406 6.26443 --1.31765 2.44492 -4.28774 -1.23597 -6.4441 5.54868 --5.23553 -6.23956 -6.42278 -3.90143 5.74298 5.69578 -1.73878 -2.13465 2.86692 -5.96976 4.29097 1.73964 -4.56212 -3.18296 -6.02652 --2.14401 -2.98997 6.41267 -2.2081 -3.09209 -6.49093 --3.59398 -0.9932 1.1927 --3.26685 -2.27913 -1.38319 -0.371066 4.41134 -2.29019 --1.51894 4.18581 0.647323 --0.510016 3.78545 1.52904 -3.33961 4.17104 -2.62025 -0.905179 -4.00468 3.54221 --3.36014 6.35113 5.27058 -6.28494 0.863206 -0.839809 --1.11986 -3.67644 -4.37626 --6.0261 4.96945 0.791567 --3.08022 -0.97913 -3.74403 --3.29328 0.350038 -6.37167 -0.784406 -2.83528 -5.45966 -1.16583 -1.95388 -0.137189 --2.27367 2.65908 -3.46441 --1.6444 2.02256 -0.160851 --5.91703 -1.03731 3.9581 -1.83048 -0.327255 6.18797 -3.42176 5.22999 -0.474494 -0.729611 1.2327 2.54564 -1.00378 5.80846 -0.863861 --0.0820037 -2.88218 5.97716 --4.96924 -6.39004 3.60532 --3.94026 3.38362 -1.49208 --4.44058 -4.05023 -0.906831 -4.48375 4.08006 5.36334 -5.91771 -6.31405 -5.19694 --3.89595 -3.4647 1.66024 -0.122764 -4.29163 -3.58928 --2.38982 1.31043 -3.81634 --2.39306 -2.10964 -5.32561 --2.65888 1.47078 -6.31385 --5.95456 2.67361 4.60555 -3.43876 -4.82379 4.22813 --6.06623 0.975162 -2.56118 --3.5155 1.68763 0.328084 -0.685078 6.25254 1.49697 -2.31021 4.22246 -6.18898 --5.66526 -5.48438 -1.14174 -6.30757 -0.383786 2.74042 --6.22615 2.79348 -0.227014 -1.10558 -0.665535 -0.524878 -2.79222 5.04953 -1.8203 -3.53113 4.50231 -6.3401 --1.95388 -4.39325 -4.91523 --5.58595 -2.86501 -6.07968 -1.9297 -1.95791 -2.6466 --0.810616 -0.372193 3.54135 --5.97436 -0.029845 6.03747 --2.27964 -4.50935 0.13603 --2.15282 -3.19297 0.218621 -5.3964 1.92685 5.05388 --5.70944 2.61904 -3.49568 -5.19378 -2.85576 5.6476 -4.52775 4.27443 4.04449 -5.05584 -2.87796 4.44483 -5.00005 -5.02788 -1.99456 -4.105 5.2331 -5.19654 -3.88729 6.28938 2.16324 --2.93974 3.42999 -2.48051 --3.84985 3.20896 -3.69175 --6.14793 -4.06128 -5.79506 --3.08759 4.93678 -1.68636 -4.86531 -6.40262 1.31993 --0.0443516 -4.68613 4.04759 --4.13591 4.71622 -1.40105 -2.63241 1.96753 6.44536 -2.34045 -1.83514 4.01054 --2.83902 -4.5759 -2.67989 --2.01266 4.41375 -4.75339 -6.46974 -1.75407 2.52765 -4.08173 0.172924 6.23606 -6.0175 2.68652 3.70365 --1.84872 0.519483 -0.62777 --4.38215 -2.98091 6.44316 -5.30343 -1.78106 -5.1542 -1.09648 1.59142 -2.24016 -1.32263 1.33181 4.93106 -3.83287 -1.4132 1.98919 --5.94388 4.16103 -3.33891 -2.94206 -0.560597 5.97685 -0.837112 -2.76399 -1.45153 -6.25093 1.05674 -3.67597 --5.53271 4.02831 -5.48654 --3.55645 -5.86943 -0.683272 -1.62756 5.35844 2.00358 --3.06382 1.23934 -5.18582 -5.65517 -5.6154 -0.671965 --6.27772 -0.681853 -0.368902 --3.206 1.26275 2.67708 --5.49594 2.04747 -2.29335 --3.56012 1.82874 3.76206 -0.13551 -1.59471 -0.718695 --3.83919 5.74358 4.03774 -2.99 6.35931 -1.51294 --4.16838 4.62688 -3.83191 -1.82736 -3.67237 -5.02052 --1.70494 2.38136 3.62764 --6.29467 1.24858 2.93116 --2.52165 -0.0566989 -3.21384 --0.458799 -2.93868 1.8886 --1.5939 3.28927 2.84018 --6.38986 -3.48505 5.87048 --3.08404 1.32971 -0.921668 --5.66498 0.87604 -5.98454 -4.56148 -0.771481 -4.91997 -3.50147 0.613312 -3.4618 -5.31565 4.4705 -4.39917 -1.82254 -3.32539 3.28481 -5.28681 -3.60577 2.92651 --1.64507 2.8347 4.90997 -5.46169 5.8286 -3.91396 --5.25199 0.424156 -3.65437 -2.79031 -4.50632 -5.91629 -1.87334 -4.40195 -3.84251 -2.64835 4.90456 5.54691 -5.51775 -0.306974 -2.0554 --1.52252 3.32564 -0.418359 --0.929475 4.25958 2.87429 --5.12829 -0.561194 0.764996 --1.20943 -5.15185 -0.980838 -1.35336 -4.91782 -0.184305 --1.96039 -6.38454 2.90331 --4.13457 3.18479 -5.538 --0.619882 3.63555 -1.76899 -3.6085 2.89275 -2.08488 -3.75607 -4.58719 0.376594 --1.73169 1.52523 5.58677 -3.09657 -5.29724 -0.801387 --2.88842 2.3308 5.70599 --0.181236 5.33554 3.34343 -0.207244 2.52861 1.37333 -5.58541 1.13772 -2.09623 -3.27954 1.4559 2.20809 -5.75083 -4.30629 -1.07106 --2.76898 1.97728 1.57429 --4.87473 -3.36214 -4.13904 --3.83442 0.00512382 -3.2724 -4.29122 1.65378 4.49666 --5.20525 -6.29792 2.29949 --2.96434 2.68842 -0.462881 -4.74822 4.54749 -0.578403 -0.541597 -3.3449 -4.22502 --2.65712 -4.04518 3.90329 --2.35002 4.88443 -2.77225 -2.00077 3.68207 5.65888 --5.65525 -2.71336 -0.995193 -2.57893 3.71785 -1.39583 --5.02426 3.82409 6.32852 --5.48183 -4.25515 -1.55952 -5.21174 -1.82756 -3.73118 -5.7674 5.72829 1.39785 -1.17757 -2.9096 5.9254 -1.78487 4.41821 0.760976 --3.86371 1.20868 -2.20084 --2.4151 -5.29933 -3.97943 -4.55236 -1.56706 -2.55462 --4.53372 -1.8377 0.512544 --3.79966 -4.13527 6.36155 -2.29235 2.2825 2.07366 -5.20958 5.4265 3.87579 --3.86889 -5.80843 2.91849 --2.11833 4.8741 3.15773 --0.193723 -0.0837779 -4.70058 -2.0805 -4.81027 -2.51559 -5.94321 3.66155 0.661105 --1.37172 1.60012 1.07307 --0.0565926 -0.016279 2.73462 -4.2926 5.76053 -1.72654 -1.56425 -4.98211 -5.04423 --0.198969 -3.6659 -5.60759 -4.17583 0.844743 -4.52132 --6.29273 -5.7641 3.12213 --0.168147 -5.69636 1.6218 -5.92884 -0.847615 -4.28672 -1.33192 0.279753 2.4113 -0.0764802 -1.48417 -6.16458 -3.92192 5.40488 0.75196 --4.68489 1.28509 -3.05431 -4.57305 3.33404 0.521583 -4.14255 2.46121 1.64126 --3.23794 -0.955299 -2.17914 --1.34411 -0.390684 -5.50234 -1.83831 -2.63608 -3.66505 --5.37698 5.11135 -4.08593 -1.67047 2.8031 1.07689 --2.83306 0.204765 0.452163 -0.988458 5.61776 -2.25299 -2.31592 -0.0799472 3.06125 --6.2189 4.84963 -1.52619 -5.08468 0.684654 4.46787 -1.83823 6.15248 -1.52242 --4.73307 -0.233818 2.06585 -5.75435 3.3745 -0.678354 --5.39668 0.241149 4.50069 -2.30048 2.51323 -4.29583 --3.74924 -1.14252 -0.83256 --5.865 0.243157 1.84559 --3.02368 -0.0667283 2.61571 -3.05221 4.4871 0.95462 --1.65464 -3.3705 -5.4316 --0.307965 4.43282 6.0826 -3.31881 0.684052 -1.31184 --0.609214 1.80847 2.77918 -4.99806 2.30633 6.48589 -3.50194 3.25443 2.17508 --6.40164 -5.76976 -6.0807 --3.58276 -3.28352 0.4812 -0.124116 -2.55341 -3.52592 --1.81536 0.0539574 2.65819 -1.72474 2.67263 -1.13325 --1.26118 -5.9858 -3.84264 -2.75985 -3.09599 -0.513938 --5.21953 -3.95736 -2.8383 -2.87856 3.17799 -5.39553 -3.96284 4.2246 -1.46381 --3.9039 3.38907 1.86966 -5.12743 0.270085 -5.76795 -2.9024 4.9345 3.88296 -3.1776 3.24608 6.34374 -6.16603 4.73448 -0.374182 -1.59664 -0.43966 -2.57535 --5.56613 -2.36579 1.58909 -0.847239 -5.51743 4.31397 -3.12523 -2.88331 -4.10042 --4.19128 -3.56301 3.5275 --2.85637 3.56276 5.63068 -2.0919 -2.77161 -1.86747 -6.23997 2.63705 -1.88331 --0.579755 3.34004 5.37005 --3.66274 0.0925181 -5.0325 -0.123427 -0.207091 -3.14292 -4.78756 0.984279 -3.13366 --5.39584 3.09054 -1.55592 -1.00907 4.47677 -3.42364 -4.72973 -4.83332 3.88423 --4.77423 -2.18385 -2.6519 -5.81378 3.02096 5.35971 --0.402323 -4.42284 1.90683 --4.88318 -4.07875 2.22673 --4.08812 -6.00015 4.42568 --4.0485 -4.28531 -2.39379 --0.435579 4.90317 -5.27129 -2.90763 -2.55218 2.97035 --3.17629 -3.30197 -0.636348 --1.57321 -5.38937 4.47843 --5.49999 0.385553 -0.327191 -0.623585 2.0984 3.52214 --1.11003 4.50225 -0.533207 --2.93126 -2.01274 0.496216 -5.07888 -4.75834 0.383679 -2.9398 1.65023 4.95858 -4.28645 0.257398 3.55804 -1.23418 5.45235 -5.55589 -5.65684 0.164054 1.32042 -4.82154 -3.64908 -1.30982 -4.36043 -5.13842 5.06395 --4.96344 -6.42741 -0.922661 -5.36367 1.46653 -5.28276 -0.610216 -3.16685 1.04131 -1.14891 -4.07177 -1.49007 -4.24097 -4.22144 2.82921 -0.316906 0.708596 -2.26612 --4.12372 1.54178 5.79893 --1.58704 0.506382 -6.31196 -3.32538 -6.3912 -3.64242 -3.08901 -6.47219 3.52758 --6.31035 3.32986 1.65586 -3.09115 2.56 -0.770601 --0.421879 1.51219 -0.152739 --2.18125 -5.68456 -0.31418 -5.28031 -2.35838 -0.767878 --4.4116 -1.50365 -5.75881 --2.89691 -3.07537 -4.63214 --5.37713 4.06492 -0.817858 --4.2553 -2.62515 -0.35524 -6.09347 5.08804 2.7742 --3.39692 4.14052 -4.83907 -1.28207 3.26007 3.43041 -1.67133 -5.22142 -1.34354 --4.92844 -5.03622 2.89598 --3.51539 -4.03287 -5.27692 -4.70251 1.58174 0.958076 --2.92966 -2.04559 -2.5056 -0.198825 1.39473 4.71766 -4.1171 -5.11576 -4.20646 -1.1482 -0.246041 -4.67529 --6.24278 4.77367 6.45525 -5.5109 -1.2027 -1.1233 --4.55802 6.34741 -5.27496 --3.27851 2.28282 -4.55527 --4.71995 -3.00888 -1.74838 --6.35659 -5.68358 -4.12059 -3.39384 -0.123048 2.75636 -2.77679 4.73686 -5.18491 --1.81692 -1.61039 -1.79997 -0.882813 -4.08637 5.028 -2.4205 0.479517 1.92145 -2.19829 -5.73367 -6.19553 --3.06436 -5.84808 0.62609 -2.57399 -3.70908 -2.87267 -0.263746 4.18751 3.71416 -3.1162 -0.397403 4.05207 -6.1465 -1.32469 -2.29727 --1.32577 3.75623 -3.81956 -5.4938 -1.18357 1.61574 --3.11776 5.88596 1.17727 --2.80509 -0.497357 -0.8465 --4.23178 3.83098 5.38925 --4.15584 4.34357 0.889076 --5.62453 3.67536 0.564403 --0.551294 -1.8669 -1.57666 -1.30597 0.832706 -3.31758 --4.14717 5.22821 5.46235 -5.24636 -3.15321 -4.78003 --5.56247 -4.91186 6.28716 -6.23691 2.19311 -4.31682 --6.0396 -1.61379 -3.18402 --6.3637 0.178015 0.577049 --2.28762 -4.22356 -6.16491 --3.66673 -6.4189 -4.08052 --4.40556 3.92144 3.10731 -5.26265 4.71139 0.719174 -0.0476459 3.77767 -0.768521 -5.20805 -4.1207 5.08002 -4.40264 2.83755 3.09741 -1.92753 0.389183 -0.440487 -2.3567 1.57257 -3.32032 -2.18784 5.59657 6.49967 -5.14409 -3.87813 -2.6076 --3.01288 0.421692 -4.15644 -2.60228 -1.51615 -6.04493 --1.61769 -3.71756 2.41933 -5.84509 3.26754 -3.37773 --0.149578 -2.75449 -0.349346 --4.61159 2.56298 -4.16494 -2.21162 -5.26723 5.33308 -4.84594 6.15083 -6.15468 --1.59665 3.62329 -2.45859 -0.232609 -1.85806 5.3995 --5.90988 -1.87011 0.307409 --6.11628 -1.27213 5.22082 -1.95967 5.88314 3.55777 --0.831103 4.60156 -2.80662 --4.3396 -0.854997 -4.55264 -5.66964 4.01872 4.05454 --0.934284 2.075 -5.7044 -0.00894878 -6.00181 5.05173 -0.614489 -0.634351 -5.71502 --1.46649 2.68241 1.59282 -6.33126 0.325316 -5.04136 --1.48739 -0.784262 -0.680483 -4.45524 -5.87579 0.0639949 --4.4869 -1.27501 -1.64427 -1.66296 4.06984 -4.81176 --6.08276 -6.09938 -0.0657241 --0.568678 5.95297 -4.30206 --0.00508163 3.55949 -3.42569 --0.472887 0.257391 -5.93187 -3.41845 5.65843 -2.79255 -4.86472 -2.08282 -6.33543 -0.0998649 1.64023 -6.05761 --4.78341 1.45958 0.00352717 -1.52246 1.60895 -6.29877 --5.41295 0.839319 -1.47309 -2.84935 -5.66142 0.474771 --2.42943 -0.133788 -5.55579 --1.90201 5.4986 -5.32534 --0.996851 -1.44225 4.41879 -2.98917 -4.28478 -4.72793 -1.48633 -3.40549 -0.185428 -3.37336 2.11221 3.28218 -0.803336 0.715452 -5.52788 -2.23975 0.882902 5.73005 -5.34048 -0.070311 -0.0795594 -4.43111 -3.77016 1.33475 --2.27975 5.4912 4.56873 --1.02395 3.63993 -5.24626 --3.52901 0.216832 -1.86371 --5.04744 -0.994002 5.18697 --3.92569 -1.14494 2.93878 -2.65068 -1.25674 2.78761 --2.80657 -5.20402 4.92065 -4.78653 -4.33883 6.20805 --2.07255 2.07243 -5.41457 -1.70673 -4.2215 1.19518 -6.46324 6.2076 -1.46582 --1.35091 5.5126 5.87622 --4.89654 -5.72726 -3.9068 -6.07219 2.06179 -2.87436 -5.47936 -4.90937 1.63441 -2.10632 -5.68119 4.11712 -2.10157 2.14387 3.90912 --2.80584 -4.53527 1.33626 --5.31177 4.42644 5.28214 -2.21826 -5.10624 1.9898 -5.30491 4.40777 -1.73954 -3.25285 3.38114 -4.31635 --2.5991 2.92461 0.930505 -4.14033 -2.55383 -0.49651 --4.67333 3.06645 4.07258 -4.55072 -2.15746 0.948056 -0.341566 0.526371 -0.473006 -3.89098 5.39681 4.64983 --2.70229 3.99777 -3.61565 --1.92798 -6.43125 5.19465 --5.25556 5.50628 -1.75656 -6.07265 0.988928 -6.41513 --4.48529 6.40059 -2.54734 -2.6195 3.14406 3.2551 --4.78694 -1.05545 -3.42997 --0.61739 -4.63368 5.42505 -3.49704 -6.10229 4.81296 --1.87592 -1.70023 3.83469 --3.43656 1.05079 4.85394 --5.78925 -3.37485 3.66378 --2.08039 -1.64435 1.54082 --6.09594 -4.74908 3.92496 -4.43802 2.83131 5.65424 -1.08133 4.87743 3.15212 --4.99443 -0.13945 -2.55601 -5.87457 -1.26251 6.1147 -0.798267 0.600358 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-0 -0 -0 -0 -0 -0 -0 -0 -0 -0 -0 -0 -0 -0 -0 -0 -0 -0 -0 -0 -0 -0 -0 -0 -0 - - - - - - - - - diff --git a/Tutorials/propane/state_B/hoomd_run_template.py b/Tutorials/propane/state_B/hoomd_run_template.py deleted file mode 100755 index 0e9a7f31..00000000 --- a/Tutorials/propane/state_B/hoomd_run_template.py +++ /dev/null @@ -1,7 +0,0 @@ -all = hoomd.group.all() -nvt_int = hoomd.md.integrate.langevin(group=all, kT=T_final, seed=1) -hoomd.md.integrate.mode_standard(dt=0.001) - -hoomd.run(1e2) -output_dcd = hoomd.dump.dcd(filename="query.dcd", period=100, overwrite=True) -hoomd.run(1e4) diff --git a/Tutorials/propane/state_B/start.hoomdxml b/Tutorials/propane/state_B/start.hoomdxml deleted file mode 100755 index 04727a84..00000000 --- a/Tutorials/propane/state_B/start.hoomdxml +++ /dev/null @@ -1,4116 +0,0 @@ - - - - - --6.01612 -3.0955 -4.99577 -0.220974 5.24077 5.03659 --5.70426 3.15938 2.71932 -5.76901 -6.30648 3.65493 --3.66534 5.84858 -1.21114 -2.71256 -3.30432 4.31491 --5.06002 3.36388 -2.91929 --1.31727 0.433331 0.456665 --1.45514 2.70539 -1.61655 --5.49077 2.1344 2.22842 -2.20271 0.867396 4.30593 --2.15852 -6.30026 1.52611 -0.973216 3.27374 -4.11579 --1.58572 4.93515 -1.65297 --1.34241 -4.11456 4.36808 --3.07913 0.48815 3.75148 -2.13865 -2.77927 0.683071 -2.26642 5.45902 -0.130551 --0.994597 -2.89972 4.43253 --0.99154 -3.50506 -3.07266 --6.28643 6.31503 0.9468 -4.65868 4.89313 -6.33431 --3.29319 -3.89999 -3.86059 --5.71125 1.45214 -4.55811 -2.04264 -0.025519 -3.86554 --3.96794 4.32649 -2.65945 --0.993918 -4.7269 -6.11152 --1.03233 1.47937 4.48647 -1.76569 1.29366 -4.85505 --4.61486 -1.67588 1.79159 --1.80087 -3.88535 -0.992383 --4.7964 -4.04722 0.685786 -5.66279 4.3154 5.99225 -0.962799 3.86015 1.69311 -0.414324 -1.83811 -2.57762 --4.43975 2.06389 -1.11518 --3.38766 -3.01055 2.71661 -3.60683 0.50622 1.36112 --2.02362 -2.85795 -2.15046 -2.27631 6.03188 4.7797 -3.34931 0.948497 3.78295 --0.737757 6.10005 4.93934 -3.68833 4.103 3.09821 --4.96122 5.41138 -3.01114 -0.164526 5.93348 0.0462726 -2.44686 -6.09788 -2.74129 --1.76268 4.09923 1.76897 --3.4593 -2.23883 1.65692 --1.79358 -1.17876 -3.04282 -1.90542 2.99555 -6.16072 -3.74107 3.8709 -0.160424 -4.32706 3.90173 -5.14763 -2.95917 -0.881434 -2.83139 -1.33071 2.32683 -3.38335 --4.73733 -0.353173 -6.45436 -5.08525 -6.11892 -1.78523 --0.78474 -2.96762 0.773421 -4.86522 -3.5281 0.178994 -2.19895 3.34443 -3.17661 -0.653561 3.96852 5.0262 --3.5435 -4.52532 2.45952 -6.34745 -5.16347 -1.79884 --3.06034 4.62658 5.17225 -5.96897 3.60947 2.85503 -3.13371 -1.62433 -5.04333 -5.31659 1.65998 3.54204 --5.06761 5.94926 4.77502 -3.33549 -0.42812 -0.79081 -0.834086 -6.41363 -4.90031 -4.47299 -0.73911 -1.4426 -6.11899 -2.68688 3.21074 -3.99629 -3.54714 3.75087 --1.67415 5.46194 -3.64536 -1.57286 4.78852 4.61479 -6.41417 0.449628 3.85584 --4.82324 5.25808 3.00396 --2.67648 5.56773 6.26099 -1.47376 -4.16714 -6.42487 -6.01382 4.12661 -5.5272 -5.33592 -2.57472 -2.22984 -2.14754 -1.44735 -3.95026 -0.683049 -4.26636 -5.20018 -6.38473 6.01646 -6.4326 --0.0598788 1.20869 1.20787 -1.98768 -6.09948 2.75338 --1.09323 -4.81498 3.02891 --5.10055 0.909714 1.23022 -3.17638 -5.10978 -3.25619 --4.49809 -2.66642 -5.21763 --4.60771 -2.87659 4.57599 -4.35702 0.491878 0.0636225 -5.53763 1.23565 0.219419 -3.92617 2.00748 -4.17214 -2.37495 -0.172804 -5.10957 --3.46111 5.94698 2.68867 --3.6763 -4.10527 4.80813 -4.22115 -0.614719 5.3439 -6.3962 -1.8728 -0.945171 -1.3639 -1.39025 5.04173 --2.15539 -0.811089 0.361711 -2.36265 -4.23452 -1.31383 -2.18457 6.20704 -5.3216 --1.22158 5.26214 2.30229 --4.62608 6.03754 -3.94002 --0.0446613 -5.99237 -3.0907 --3.21694 -6.29481 -2.40482 -5.78042 -1.16297 0.370149 -1.68515 -5.81025 0.894172 -1.0296 0.583502 3.82442 --6.09873 3.49592 5.67275 --5.2235 -5.36986 1.20153 -1.08034 -1.25098 -3.45048 -1.64914 -4.91509 3.19351 -0.714045 3.15969 6.18164 -0.851042 6.49123 3.14753 --3.42291 5.07279 -0.141787 --3.23547 3.41628 4.04415 --2.49942 -1.70473 2.93386 -2.28232 -2.14412 5.55102 -5.95361 -4.56865 2.95015 --4.67492 -5.30718 -0.0495295 -4.01306 4.64414 1.84082 --4.25995 -5.08134 5.54882 --0.670696 2.72867 -2.93336 --1.32976 -4.66448 -3.24926 -0.147416 -0.664268 4.38209 -1.19393 1.33532 1.08151 --5.98452 3.77302 3.89649 --2.21329 -1.11952 4.99689 --3.97382 -2.16618 -3.67262 -2.3762 3.94508 2.01102 --4.04959 2.9141 0.602355 --0.507425 -5.93492 3.79394 -0.0557174 5.04243 2.22613 --1.25688 -6.11554 -5.18292 -6.14893 -2.38601 -5.87403 --3.68305 -5.33132 -4.69401 --6.47976 3.75168 -2.21312 --1.5146 -4.04591 1.12987 --4.78106 1.17203 2.47296 --3.65057 5.59218 -6.03266 --0.431343 -3.34928 3.15229 --5.99854 -4.49722 5.01084 -3.9392 5.33137 3.15389 --2.57125 6.27066 0.0422787 -4.31022 -6.41007 3.58716 -3.95178 -2.85897 2.10099 -1.96106 -2.4062 -5.20706 -0.602548 4.94387 1.19117 --1.8836 6.48559 -6.23748 -3.28041 -0.479787 -4.24551 --1.48669 -5.25676 1.89311 --3.44217 -6.31968 -5.61047 -2.59759 0.509724 -2.51816 --3.87243 2.51411 4.92474 --1.11053 -3.70705 6.15658 -3.04325 -0.668947 1.45788 --6.18735 -4.97057 2.25191 --0.982362 -5.66987 -2.19071 --0.508532 -2.0414 3.17056 --0.395179 1.53008 -1.75646 --4.40267 0.276855 5.54112 --1.11511 2.37179 6.22271 --5.63902 5.88634 -5.31377 --1.04852 0.464527 -2.50012 --5.54853 -1.37066 6.30796 -3.49581 -5.37505 3.04462 --2.5265 -1.92497 -0.638543 --0.921121 -0.75 0.924951 -3.37411 2.91792 -3.22505 -4.58918 6.31726 -3.01478 -6.46094 -3.82521 -2.67033 -1.02893 2.69201 -5.27729 --2.33059 -4.90584 3.04071 --6.0288 -4.37562 -0.356661 --2.94071 2.31182 -1.66161 -1.93188 -1.23263 0.654091 -3.99707 1.20131 -5.66115 --0.581759 5.22542 0.840171 --5.68498 -6.33649 -2.41538 -4.13335 -2.3642 -5.10512 --3.01972 3.0869 -6.02433 --0.200788 0.887171 3.68048 -5.47352 -0.462574 3.59406 --2.74062 4.52238 0.993979 -4.85292 4.43288 2.65801 -5.41131 -2.6634 1.86438 --2.95932 -6.14978 3.82345 -5.92695 2.356 0.798225 -1.29127 2.84229 2.33023 -4.93115 1.00379 5.92376 -2.02553 3.46097 4.41364 --6.19898 -3.35229 2.42118 -4.38852 -0.650588 0.792572 --2.16821 5.14937 -0.475286 -0.989795 2.65071 -0.0939543 --1.60615 1.74319 -2.75737 --5.20605 2.15423 3.50167 --1.881 3.90096 4.07254 --1.23057 -2.0876 5.48858 --0.515798 -2.50359 -4.85999 -5.52911 5.70253 -2.20443 --5.00214 3.82387 -4.48147 -4.3928 -5.05424 -0.921729 -5.50317 1.97833 -0.991695 -3.15077 2.89305 0.857805 -1.75289 4.56458 -2.47087 --5.85984 -5.13413 -2.76503 --3.41753 -0.898193 -6.18639 -6.49788 -2.87288 4.74793 -2.22493 5.77957 -2.91425 -0.257357 -4.07854 0.17984 --5.43079 0.0929639 3.24578 --0.642237 3.0078 4.09485 -5.61561 0.601912 2.80179 -4.62261 3.03741 -1.20817 -4.4783 -1.20465 -0.282902 -2.08578 2.40797 -2.23422 -6.18842 -4.67787 6.23062 --0.363027 6.26686 -5.74561 -0.101871 -5.3985 -5.75026 -4.6891 2.14967 -2.54446 -3.75885 -1.28326 -6.36573 -2.26752 1.25945 0.938583 --1.73759 -1.09344 6.42287 --4.8024 -4.43215 4.33963 -4.28201 -0.372165 -3.22787 --4.23563 1.75763 1.4672 --0.92952 2.85896 0.51692 -4.26518 -2.65658 -3.6889 --2.38332 -5.32796 -5.66163 -2.89669 -6.12605 1.99424 --4.37874 4.378 4.25882 --1.35228 6.28722 -2.71685 -5.80473 -0.621039 4.75492 -0.0643505 -5.98912 -4.29771 --6.18327 1.45014 0.254725 -4.06514 -1.24542 3.24459 --2.40078 1.31844 0.273312 -1.21406 4.8587 5.98463 -1.89029 6.48993 -4.14039 --2.18269 -3.70847 -3.38856 -4.09664 5.62619 -3.93415 --6.19879 -6.10931 5.71369 -0.13834 1.82506 -3.2032 --4.64683 1.37236 4.49212 --4.39942 4.80835 -5.20288 --5.86287 -3.9128 1.16045 -5.70314 4.47185 -3.01742 --2.47901 3.20804 -4.84603 -6.4794 -0.793043 -5.52481 -0.449064 -1.95168 4.06236 -2.62997 -4.21974 0.546325 -5.00418 0.727203 -0.986634 -0.723978 2.74618 4.59941 -3.08588 -3.0221 -5.58164 --5.54919 -1.54347 -5.36647 -1.43035 0.484136 -1.50061 --0.0771183 -0.286622 0.140749 -2.27925 2.05066 -0.0140352 -6.02389 -3.90782 4.17866 --1.18415 5.82008 3.65669 --0.782665 -0.840195 -2.49142 -6.20607 -3.54607 -0.0758306 --0.748059 -0.868995 5.64016 -4.18663 0.313116 -2.12511 -6.29033 -6.11588 1.96951 --0.247012 3.38065 -6.01134 -5.89288 -5.09684 -3.06834 --2.78508 3.77478 -0.183686 --1.48238 -5.37383 0.627504 -4.49032 6.47882 -4.70425 -6.3202 1.89979 5.87404 --5.94845 -0.595753 -4.27427 --6.1769 -0.0303637 -1.75028 -0.630255 -0.645549 5.75079 --4.77383 -5.3377 -2.28882 -0.0766993 -4.96167 -0.946354 -2.5468 -0.21204 0.345585 --1.0537 -3.91334 -0.0435371 --0.33378 -4.49852 -2.24403 --2.67709 2.69619 2.86473 --6.11697 -2.68182 -2.32437 -1.33709 -5.54117 -3.65794 --5.23903 -5.36994 -5.27306 --2.14006 -0.424073 1.5224 -5.89354 -3.67157 1.28424 -3.65948 -3.98615 -3.61722 -4.78149 5.79617 0.123173 --2.31501 0.746976 1.53051 -3.44483 -5.04752 5.98302 --3.34607 1.85688 -3.19367 --5.01869 -2.65351 2.60515 -5.27302 -5.67922 -4.14272 -5.00409 -6.49286 4.80775 --1.87563 -5.17001 5.86727 --0.0419609 2.63131 -4.52641 --0.571635 -0.98961 -3.64769 --5.68395 2.27521 0.921195 --0.97392 6.45462 1.03486 -1.46925 5.89484 0.521641 --4.06445 2.75406 6.26443 --1.31765 2.44492 -4.28774 -1.23597 -6.4441 5.54868 --5.23553 -6.23956 -6.42278 -3.90143 5.74298 5.69578 -1.73878 -2.13465 2.86692 -5.96976 4.29097 1.73964 -4.56212 -3.18296 -6.02652 --2.14401 -2.98997 6.41267 -2.2081 -3.09209 -6.49093 --3.59398 -0.9932 1.1927 --3.26685 -2.27913 -1.38319 -0.371066 4.41134 -2.29019 --1.51894 4.18581 0.647323 --0.510016 3.78545 1.52904 -3.33961 4.17104 -2.62025 -0.905179 -4.00468 3.54221 --3.36014 6.35113 5.27058 -6.28494 0.863206 -0.839809 --1.11986 -3.67644 -4.37626 --6.0261 4.96945 0.791567 --3.08022 -0.97913 -3.74403 --3.29328 0.350038 -6.37167 -0.784406 -2.83528 -5.45966 -1.16583 -1.95388 -0.137189 --2.27367 2.65908 -3.46441 --1.6444 2.02256 -0.160851 --5.91703 -1.03731 3.9581 -1.83048 -0.327255 6.18797 -3.42176 5.22999 -0.474494 -0.729611 1.2327 2.54564 -1.00378 5.80846 -0.863861 --0.0820037 -2.88218 5.97716 --4.96924 -6.39004 3.60532 --3.94026 3.38362 -1.49208 --4.44058 -4.05023 -0.906831 -4.48375 4.08006 5.36334 -5.91771 -6.31405 -5.19694 --3.89595 -3.4647 1.66024 -0.122764 -4.29163 -3.58928 --2.38982 1.31043 -3.81634 --2.39306 -2.10964 -5.32561 --2.65888 1.47078 -6.31385 --5.95456 2.67361 4.60555 -3.43876 -4.82379 4.22813 --6.06623 0.975162 -2.56118 --3.5155 1.68763 0.328084 -0.685078 6.25254 1.49697 -2.31021 4.22246 -6.18898 --5.66526 -5.48438 -1.14174 -6.30757 -0.383786 2.74042 --6.22615 2.79348 -0.227014 -1.10558 -0.665535 -0.524878 -2.79222 5.04953 -1.8203 -3.53113 4.50231 -6.3401 --1.95388 -4.39325 -4.91523 --5.58595 -2.86501 -6.07968 -1.9297 -1.95791 -2.6466 --0.810616 -0.372193 3.54135 --5.97436 -0.029845 6.03747 --2.27964 -4.50935 0.13603 --2.15282 -3.19297 0.218621 -5.3964 1.92685 5.05388 --5.70944 2.61904 -3.49568 -5.19378 -2.85576 5.6476 -4.52775 4.27443 4.04449 -5.05584 -2.87796 4.44483 -5.00005 -5.02788 -1.99456 -4.105 5.2331 -5.19654 -3.88729 6.28938 2.16324 --2.93974 3.42999 -2.48051 --3.84985 3.20896 -3.69175 --6.14793 -4.06128 -5.79506 --3.08759 4.93678 -1.68636 -4.86531 -6.40262 1.31993 --0.0443516 -4.68613 4.04759 --4.13591 4.71622 -1.40105 -2.63241 1.96753 6.44536 -2.34045 -1.83514 4.01054 --2.83902 -4.5759 -2.67989 --2.01266 4.41375 -4.75339 -6.46974 -1.75407 2.52765 -4.08173 0.172924 6.23606 -6.0175 2.68652 3.70365 --1.84872 0.519483 -0.62777 --4.38215 -2.98091 6.44316 -5.30343 -1.78106 -5.1542 -1.09648 1.59142 -2.24016 -1.32263 1.33181 4.93106 -3.83287 -1.4132 1.98919 --5.94388 4.16103 -3.33891 -2.94206 -0.560597 5.97685 -0.837112 -2.76399 -1.45153 -6.25093 1.05674 -3.67597 --5.53271 4.02831 -5.48654 --3.55645 -5.86943 -0.683272 -1.62756 5.35844 2.00358 --3.06382 1.23934 -5.18582 -5.65517 -5.6154 -0.671965 --6.27772 -0.681853 -0.368902 --3.206 1.26275 2.67708 --5.49594 2.04747 -2.29335 --3.56012 1.82874 3.76206 -0.13551 -1.59471 -0.718695 --3.83919 5.74358 4.03774 -2.99 6.35931 -1.51294 --4.16838 4.62688 -3.83191 -1.82736 -3.67237 -5.02052 --1.70494 2.38136 3.62764 --6.29467 1.24858 2.93116 --2.52165 -0.0566989 -3.21384 --0.458799 -2.93868 1.8886 --1.5939 3.28927 2.84018 --6.38986 -3.48505 5.87048 --3.08404 1.32971 -0.921668 --5.66498 0.87604 -5.98454 -4.56148 -0.771481 -4.91997 -3.50147 0.613312 -3.4618 -5.31565 4.4705 -4.39917 -1.82254 -3.32539 3.28481 -5.28681 -3.60577 2.92651 --1.64507 2.8347 4.90997 -5.46169 5.8286 -3.91396 --5.25199 0.424156 -3.65437 -2.79031 -4.50632 -5.91629 -1.87334 -4.40195 -3.84251 -2.64835 4.90456 5.54691 -5.51775 -0.306974 -2.0554 --1.52252 3.32564 -0.418359 --0.929475 4.25958 2.87429 --5.12829 -0.561194 0.764996 --1.20943 -5.15185 -0.980838 -1.35336 -4.91782 -0.184305 --1.96039 -6.38454 2.90331 --4.13457 3.18479 -5.538 --0.619882 3.63555 -1.76899 -3.6085 2.89275 -2.08488 -3.75607 -4.58719 0.376594 --1.73169 1.52523 5.58677 -3.09657 -5.29724 -0.801387 --2.88842 2.3308 5.70599 --0.181236 5.33554 3.34343 -0.207244 2.52861 1.37333 -5.58541 1.13772 -2.09623 -3.27954 1.4559 2.20809 -5.75083 -4.30629 -1.07106 --2.76898 1.97728 1.57429 --4.87473 -3.36214 -4.13904 --3.83442 0.00512382 -3.2724 -4.29122 1.65378 4.49666 --5.20525 -6.29792 2.29949 --2.96434 2.68842 -0.462881 -4.74822 4.54749 -0.578403 -0.541597 -3.3449 -4.22502 --2.65712 -4.04518 3.90329 --2.35002 4.88443 -2.77225 -2.00077 3.68207 5.65888 --5.65525 -2.71336 -0.995193 -2.57893 3.71785 -1.39583 --5.02426 3.82409 6.32852 --5.48183 -4.25515 -1.55952 -5.21174 -1.82756 -3.73118 -5.7674 5.72829 1.39785 -1.17757 -2.9096 5.9254 -1.78487 4.41821 0.760976 --3.86371 1.20868 -2.20084 --2.4151 -5.29933 -3.97943 -4.55236 -1.56706 -2.55462 --4.53372 -1.8377 0.512544 --3.79966 -4.13527 6.36155 -2.29235 2.2825 2.07366 -5.20958 5.4265 3.87579 --3.86889 -5.80843 2.91849 --2.11833 4.8741 3.15773 --0.193723 -0.0837779 -4.70058 -2.0805 -4.81027 -2.51559 -5.94321 3.66155 0.661105 --1.37172 1.60012 1.07307 --0.0565926 -0.016279 2.73462 -4.2926 5.76053 -1.72654 -1.56425 -4.98211 -5.04423 --0.198969 -3.6659 -5.60759 -4.17583 0.844743 -4.52132 --6.29273 -5.7641 3.12213 --0.168147 -5.69636 1.6218 -5.92884 -0.847615 -4.28672 -1.33192 0.279753 2.4113 -0.0764802 -1.48417 -6.16458 -3.92192 5.40488 0.75196 --4.68489 1.28509 -3.05431 -4.57305 3.33404 0.521583 -4.14255 2.46121 1.64126 --3.23794 -0.955299 -2.17914 --1.34411 -0.390684 -5.50234 -1.83831 -2.63608 -3.66505 --5.37698 5.11135 -4.08593 -1.67047 2.8031 1.07689 --2.83306 0.204765 0.452163 -0.988458 5.61776 -2.25299 -2.31592 -0.0799472 3.06125 --6.2189 4.84963 -1.52619 -5.08468 0.684654 4.46787 -1.83823 6.15248 -1.52242 --4.73307 -0.233818 2.06585 -5.75435 3.3745 -0.678354 --5.39668 0.241149 4.50069 -2.30048 2.51323 -4.29583 --3.74924 -1.14252 -0.83256 --5.865 0.243157 1.84559 --3.02368 -0.0667283 2.61571 -3.05221 4.4871 0.95462 --1.65464 -3.3705 -5.4316 --0.307965 4.43282 6.0826 -3.31881 0.684052 -1.31184 --0.609214 1.80847 2.77918 -4.99806 2.30633 6.48589 -3.50194 3.25443 2.17508 --6.40164 -5.76976 -6.0807 --3.58276 -3.28352 0.4812 -0.124116 -2.55341 -3.52592 --1.81536 0.0539574 2.65819 -1.72474 2.67263 -1.13325 --1.26118 -5.9858 -3.84264 -2.75985 -3.09599 -0.513938 --5.21953 -3.95736 -2.8383 -2.87856 3.17799 -5.39553 -3.96284 4.2246 -1.46381 --3.9039 3.38907 1.86966 -5.12743 0.270085 -5.76795 -2.9024 4.9345 3.88296 -3.1776 3.24608 6.34374 -6.16603 4.73448 -0.374182 -1.59664 -0.43966 -2.57535 --5.56613 -2.36579 1.58909 -0.847239 -5.51743 4.31397 -3.12523 -2.88331 -4.10042 --4.19128 -3.56301 3.5275 --2.85637 3.56276 5.63068 -2.0919 -2.77161 -1.86747 -6.23997 2.63705 -1.88331 --0.579755 3.34004 5.37005 --3.66274 0.0925181 -5.0325 -0.123427 -0.207091 -3.14292 -4.78756 0.984279 -3.13366 --5.39584 3.09054 -1.55592 -1.00907 4.47677 -3.42364 -4.72973 -4.83332 3.88423 --4.77423 -2.18385 -2.6519 -5.81378 3.02096 5.35971 --0.402323 -4.42284 1.90683 --4.88318 -4.07875 2.22673 --4.08812 -6.00015 4.42568 --4.0485 -4.28531 -2.39379 --0.435579 4.90317 -5.27129 -2.90763 -2.55218 2.97035 --3.17629 -3.30197 -0.636348 --1.57321 -5.38937 4.47843 --5.49999 0.385553 -0.327191 -0.623585 2.0984 3.52214 --1.11003 4.50225 -0.533207 --2.93126 -2.01274 0.496216 -5.07888 -4.75834 0.383679 -2.9398 1.65023 4.95858 -4.28645 0.257398 3.55804 -1.23418 5.45235 -5.55589 -5.65684 0.164054 1.32042 -4.82154 -3.64908 -1.30982 -4.36043 -5.13842 5.06395 --4.96344 -6.42741 -0.922661 -5.36367 1.46653 -5.28276 -0.610216 -3.16685 1.04131 -1.14891 -4.07177 -1.49007 -4.24097 -4.22144 2.82921 -0.316906 0.708596 -2.26612 --4.12372 1.54178 5.79893 --1.58704 0.506382 -6.31196 -3.32538 -6.3912 -3.64242 -3.08901 -6.47219 3.52758 --6.31035 3.32986 1.65586 -3.09115 2.56 -0.770601 --0.421879 1.51219 -0.152739 --2.18125 -5.68456 -0.31418 -5.28031 -2.35838 -0.767878 --4.4116 -1.50365 -5.75881 --2.89691 -3.07537 -4.63214 --5.37713 4.06492 -0.817858 --4.2553 -2.62515 -0.35524 -6.09347 5.08804 2.7742 --3.39692 4.14052 -4.83907 -1.28207 3.26007 3.43041 -1.67133 -5.22142 -1.34354 --4.92844 -5.03622 2.89598 --3.51539 -4.03287 -5.27692 -4.70251 1.58174 0.958076 --2.92966 -2.04559 -2.5056 -0.198825 1.39473 4.71766 -4.1171 -5.11576 -4.20646 -1.1482 -0.246041 -4.67529 --6.24278 4.77367 6.45525 -5.5109 -1.2027 -1.1233 --4.55802 6.34741 -5.27496 --3.27851 2.28282 -4.55527 --4.71995 -3.00888 -1.74838 --6.35659 -5.68358 -4.12059 -3.39384 -0.123048 2.75636 -2.77679 4.73686 -5.18491 --1.81692 -1.61039 -1.79997 -0.882813 -4.08637 5.028 -2.4205 0.479517 1.92145 -2.19829 -5.73367 -6.19553 --3.06436 -5.84808 0.62609 -2.57399 -3.70908 -2.87267 -0.263746 4.18751 3.71416 -3.1162 -0.397403 4.05207 -6.1465 -1.32469 -2.29727 --1.32577 3.75623 -3.81956 -5.4938 -1.18357 1.61574 --3.11776 5.88596 1.17727 --2.80509 -0.497357 -0.8465 --4.23178 3.83098 5.38925 --4.15584 4.34357 0.889076 --5.62453 3.67536 0.564403 --0.551294 -1.8669 -1.57666 -1.30597 0.832706 -3.31758 --4.14717 5.22821 5.46235 -5.24636 -3.15321 -4.78003 --5.56247 -4.91186 6.28716 -6.23691 2.19311 -4.31682 --6.0396 -1.61379 -3.18402 --6.3637 0.178015 0.577049 --2.28762 -4.22356 -6.16491 --3.66673 -6.4189 -4.08052 --4.40556 3.92144 3.10731 -5.26265 4.71139 0.719174 -0.0476459 3.77767 -0.768521 -5.20805 -4.1207 5.08002 -4.40264 2.83755 3.09741 -1.92753 0.389183 -0.440487 -2.3567 1.57257 -3.32032 -2.18784 5.59657 6.49967 -5.14409 -3.87813 -2.6076 --3.01288 0.421692 -4.15644 -2.60228 -1.51615 -6.04493 --1.61769 -3.71756 2.41933 -5.84509 3.26754 -3.37773 --0.149578 -2.75449 -0.349346 --4.61159 2.56298 -4.16494 -2.21162 -5.26723 5.33308 -4.84594 6.15083 -6.15468 --1.59665 3.62329 -2.45859 -0.232609 -1.85806 5.3995 --5.90988 -1.87011 0.307409 --6.11628 -1.27213 5.22082 -1.95967 5.88314 3.55777 --0.831103 4.60156 -2.80662 --4.3396 -0.854997 -4.55264 -5.66964 4.01872 4.05454 --0.934284 2.075 -5.7044 -0.00894878 -6.00181 5.05173 -0.614489 -0.634351 -5.71502 --1.46649 2.68241 1.59282 -6.33126 0.325316 -5.04136 --1.48739 -0.784262 -0.680483 -4.45524 -5.87579 0.0639949 --4.4869 -1.27501 -1.64427 -1.66296 4.06984 -4.81176 --6.08276 -6.09938 -0.0657241 --0.568678 5.95297 -4.30206 --0.00508163 3.55949 -3.42569 --0.472887 0.257391 -5.93187 -3.41845 5.65843 -2.79255 -4.86472 -2.08282 -6.33543 -0.0998649 1.64023 -6.05761 --4.78341 1.45958 0.00352717 -1.52246 1.60895 -6.29877 --5.41295 0.839319 -1.47309 -2.84935 -5.66142 0.474771 --2.42943 -0.133788 -5.55579 --1.90201 5.4986 -5.32534 --0.996851 -1.44225 4.41879 -2.98917 -4.28478 -4.72793 -1.48633 -3.40549 -0.185428 -3.37336 2.11221 3.28218 -0.803336 0.715452 -5.52788 -2.23975 0.882902 5.73005 -5.34048 -0.070311 -0.0795594 -4.43111 -3.77016 1.33475 --2.27975 5.4912 4.56873 --1.02395 3.63993 -5.24626 --3.52901 0.216832 -1.86371 --5.04744 -0.994002 5.18697 --3.92569 -1.14494 2.93878 -2.65068 -1.25674 2.78761 --2.80657 -5.20402 4.92065 -4.78653 -4.33883 6.20805 --2.07255 2.07243 -5.41457 -1.70673 -4.2215 1.19518 -6.46324 6.2076 -1.46582 --1.35091 5.5126 5.87622 --4.89654 -5.72726 -3.9068 -6.07219 2.06179 -2.87436 -5.47936 -4.90937 1.63441 -2.10632 -5.68119 4.11712 -2.10157 2.14387 3.90912 --2.80584 -4.53527 1.33626 --5.31177 4.42644 5.28214 -2.21826 -5.10624 1.9898 -5.30491 4.40777 -1.73954 -3.25285 3.38114 -4.31635 --2.5991 2.92461 0.930505 -4.14033 -2.55383 -0.49651 --4.67333 3.06645 4.07258 -4.55072 -2.15746 0.948056 -0.341566 0.526371 -0.473006 -3.89098 5.39681 4.64983 --2.70229 3.99777 -3.61565 --1.92798 -6.43125 5.19465 --5.25556 5.50628 -1.75656 -6.07265 0.988928 -6.41513 --4.48529 6.40059 -2.54734 -2.6195 3.14406 3.2551 --4.78694 -1.05545 -3.42997 --0.61739 -4.63368 5.42505 -3.49704 -6.10229 4.81296 --1.87592 -1.70023 3.83469 --3.43656 1.05079 4.85394 --5.78925 -3.37485 3.66378 --2.08039 -1.64435 1.54082 --6.09594 -4.74908 3.92496 -4.43802 2.83131 5.65424 -1.08133 4.87743 3.15212 --4.99443 -0.13945 -2.55601 -5.87457 -1.26251 6.1147 -0.798267 0.600358 6.09537 --3.0105 -4.34369 -1.29356 -3.09447 -2.51345 -2.72838 --3.33393 -3.0325 5.60944 -3.81589 1.62571 6.0763 -5.29082 -1.42969 2.85345 -1.05314 6.0031 4.2955 --4.42496 -4.5405 -4.11964 --0.00141563 -5.12728 0.643285 -3.65856 -0.272157 -5.58798 -3.18845 5.90019 -4.66933 --5.37738 -2.46759 5.48965 -4.44726 -5.35111 -3.16135 -5.92935 -5.4553 4.73984 -5.1123 -4.42707 -5.02013 -0.320563 3.48494 0.560547 -0.197104 -6.26186 -1.90126 --0.484072 -4.91305 -4.67074 -3.33399 1.56993 -2.51386 --1.92862 -0.998583 -4.5603 --3.2104 -0.396661 5.30704 -3.67523 6.49519 -0.46112 -1.33871 -2.89934 4.51402 --5.1638 -1.95821 -4.05637 -0.606286 0.898776 -4.21981 --2.37989 -6.44582 -4.65642 -6.09728 5.77219 4.92846 --5.05631 2.7647 -0.304617 -3.85362 -3.51127 5.19211 --2.35913 0.512256 5.57804 --5.93751 -3.00762 -3.7308 -1.77206 5.25351 -4.28243 --3.34103 -3.42419 -2.10812 --3.79938 4.84495 2.10204 -5.05569 -5.64793 2.68931 -4.75149 3.30558 -2.66528 --4.42869 -1.89949 3.55906 --5.49379 2.74204 -5.14809 --5.59544 1.09599 5.68344 --0.831406 0.233155 4.92746 -0.926872 -6.31695 -6.17169 -6.29116 -5.03831 -5.15761 --3.11702 5.54553 -4.47671 --0.792604 4.63616 4.55607 --4.24898 0.388214 3.32789 --2.26478 -2.87189 1.46232 --2.93952 -5.70155 2.09992 -5.33337 2.8862 -5.02461 -3.90804 2.57268 -5.65665 -4.64205 -1.72221 5.34988 --0.997684 -2.90703 -1.45126 -3.75796 -3.88781 -0.616146 --5.31994 -5.69893 5.08941 -3.53081 -3.10097 0.711947 -6.48623 4.5029 5.00919 --0.428053 0.892921 5.89258 -0.156029 -3.44746 4.38072 --3.40646 -2.42818 3.93862 --2.55085 1.94946 4.46262 --4.18758 -3.08343 -2.89595 -4.97543 -5.60862 -5.4913 -2.91221 1.91508 -5.30136 --5.99016 1.975 -1.1225 -1.12982 1.56014 -0.727533 --0.646761 4.77883 -4.10752 -0.438905 1.9976 5.60321 --0.124723 5.53444 -2.82694 -5.32205 0.255361 -4.19263 --1.94735 4.1388 5.6549 --1.82064 0.957918 3.53148 --1.17585 5.81123 -0.249845 --1.07658 -0.895811 2.36448 -1.52274 -0.185624 4.77061 --3.4453 -1.68081 -4.83836 --3.65714 -4.93038 3.74562 --1.71517 1.79497 2.41263 --5.696 -1.05538 -1.88509 -3.26293 -1.26701 4.85001 -2.34125 -0.755992 -1.56889 --6.18471 6.19331 -4.02282 -0.646165 5.14699 -4.55027 --6.45229 -0.0621779 -3.06483 -0.735896 -5.99021 -0.53175 --0.872907 -2.19178 -2.88078 --4.04583 2.47844 2.85665 -2.20652 1.41113 3.0049 --0.74723 0.0815798 -1.31924 --0.0335299 3.13363 2.77743 -5.03093 5.35891 5.33496 --4.30909 1.14554 -4.36086 -0.312072 -0.0983377 1.43626 --0.288044 2.47342 -0.830117 --5.38035 2.33945 -6.47515 --3.74841 -1.6726 4.80372 --0.758189 1.05287 -3.61908 -1.31987 -6.10991 -2.50246 -6.20923 -4.03951 -4.34135 -3.67965 -2.4541 4.21009 -4.06369 4.26351 -3.73614 -2.89087 -3.94033 2.98995 -1.36461 -0.936629 3.55516 -2.27594 -3.86129 5.41367 --1.73554 5.51498 0.900444 -3.95987 -3.87715 -5.06434 -6.41011 3.24328 -6.25008 --4.23505 0.0987359 0.221397 --1.32141 0.0634173 -3.94881 --6.2011 -1.00005 1.24704 -6.41831 -2.16752 -4.5377 -0.768673 6.14435 -3.52612 -2.90046 -6.48696 5.84874 --0.915046 0.639511 1.68498 -3.62054 -5.98026 -5.6517 --0.372936 1.36712 -4.73817 --4.18774 0.575845 -0.95394 -3.29455 -1.54995 0.550853 -5.51389 5.6829 -1.02404 -5.69366 -6.36136 0.358777 --4.51793 1.81133 -5.44591 -4.6578 3.67012 -6.28145 --2.93697 -5.34189 6.30275 -0.169694 -0.67499 -1.6657 --5.62271 -2.07012 4.02501 --0.393754 -6.18062 -0.669494 -5.43483 -5.90323 5.79289 -0.818169 -5.25027 5.86905 -0.411722 2.69674 -1.79443 --3.84913 -5.31636 -1.5803 -5.75311 -3.63454 -6.06572 -4.35118 2.8839 4.36763 -4.97866 -0.856184 -6.07742 --2.95183 3.86605 2.46218 --6.47376 -5.0676 0.819666 -2.06204 -6.20675 -0.481882 --1.79278 -4.40897 -2.04986 -3.6662 -5.81236 -2.2532 -0.169164 5.52063 6.44145 -2.63791 0.612765 -6.20023 -5.01004 -4.22269 -3.6721 -6.31174 5.3493 -4.46707 --6.4814 -2.29103 5.91304 -0.591146 -1.61557 -4.4651 --1.33113 -1.9045 -0.0893525 --5.6983 4.5115 3.04088 --6.11853 -6.35464 4.25145 --5.69355 -4.64469 -4.13837 --2.60565 -2.41369 -3.65096 --3.63032 -5.35811 -3.07629 -0.197998 -4.17932 6.26366 --4.25428 2.37134 -2.56199 --1.6158 3.49518 -6.34182 -0.142372 3.90524 -4.70712 -1.2261 0.010799 0.708489 --4.25429 -0.311533 4.30024 -5.56188 5.31305 -5.60733 --4.11251 6.4044 0.271825 -6.02878 2.26257 2.38608 --0.223953 -3.81687 -1.09191 -2.01704 -4.41845 4.30794 -4.57406 5.09215 -2.85869 -2.11844 3.36653 -0.0566786 --1.38095 4.73742 -5.98848 --6.05601 1.39022 4.39233 --0.525137 -1.7431 1.58184 -2.83764 5.34665 2.4558 -4.13434 1.73569 -1.51915 --5.88479 5.42178 1.87789 -3.06731 1.02576 -0.154484 -0.295682 -1.23051 2.72897 --2.29691 -3.89282 5.27238 --4.22464 -6.06724 1.68374 --5.39245 -3.10319 0.11962 --5.51982 -1.08017 2.52848 -3.66082 -1.7423 -1.63303 -1.6633 -2.98148 1.94892 -0.339277 -5.15069 3.00335 --4.26815 -5.21809 -6.10575 --5.01604 -1.37163 -0.54626 -4.77413 1.48685 2.22218 --2.52131 6.08149 -1.66338 --0.387018 -6.34942 2.55248 -5.1708 1.86776 -3.97481 -2.69851 5.93086 1.04038 -3.68066 0.535514 4.92246 --5.77945 5.57291 5.58638 -0.948882 -1.85787 1.41492 --1.83511 -0.26107 -1.8412 --4.21788 3.90379 -0.185131 -1.4999 -0.831125 1.8844 -0.992525 -4.04047 2.1901 --5.21978 6.14161 0.578886 --3.1854 -2.8394 -6.0978 -2.76299 4.65235 -3.66972 --0.18927 5.47875 -1.25484 -2.64593 -2.05429 1.60061 --3.64041 -4.38939 -0.0256431 --3.64122 5.59304 -2.83693 -1.27794 -1.43872 -1.5244 -0.085504 -3.31091 -2.36143 --2.38476 -2.68343 4.6936 --1.54074 -2.38713 2.5833 --4.95044 0.188942 -5.22512 -6.23669 0.516036 5.2541 -3.65358 -1.55645 -3.94825 -6.30061 1.26926 1.521 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-hoomd.md.integrate.mode_standard(dt=0.001) - -hoomd.run(1e2) -output_dcd = hoomd.dump.dcd(filename="query.dcd", period=100, overwrite=True) -hoomd.run(1e4) diff --git a/Tutorials/propane/state_C/start.hoomdxml b/Tutorials/propane/state_C/start.hoomdxml deleted file mode 100755 index 04727a84..00000000 --- a/Tutorials/propane/state_C/start.hoomdxml +++ /dev/null @@ -1,4116 +0,0 @@ - - - - - --6.01612 -3.0955 -4.99577 -0.220974 5.24077 5.03659 --5.70426 3.15938 2.71932 -5.76901 -6.30648 3.65493 --3.66534 5.84858 -1.21114 -2.71256 -3.30432 4.31491 --5.06002 3.36388 -2.91929 --1.31727 0.433331 0.456665 --1.45514 2.70539 -1.61655 --5.49077 2.1344 2.22842 -2.20271 0.867396 4.30593 --2.15852 -6.30026 1.52611 -0.973216 3.27374 -4.11579 --1.58572 4.93515 -1.65297 --1.34241 -4.11456 4.36808 --3.07913 0.48815 3.75148 -2.13865 -2.77927 0.683071 -2.26642 5.45902 -0.130551 --0.994597 -2.89972 4.43253 --0.99154 -3.50506 -3.07266 --6.28643 6.31503 0.9468 -4.65868 4.89313 -6.33431 --3.29319 -3.89999 -3.86059 --5.71125 1.45214 -4.55811 -2.04264 -0.025519 -3.86554 --3.96794 4.32649 -2.65945 --0.993918 -4.7269 -6.11152 --1.03233 1.47937 4.48647 -1.76569 1.29366 -4.85505 --4.61486 -1.67588 1.79159 --1.80087 -3.88535 -0.992383 --4.7964 -4.04722 0.685786 -5.66279 4.3154 5.99225 -0.962799 3.86015 1.69311 -0.414324 -1.83811 -2.57762 --4.43975 2.06389 -1.11518 --3.38766 -3.01055 2.71661 -3.60683 0.50622 1.36112 --2.02362 -2.85795 -2.15046 -2.27631 6.03188 4.7797 -3.34931 0.948497 3.78295 --0.737757 6.10005 4.93934 -3.68833 4.103 3.09821 --4.96122 5.41138 -3.01114 -0.164526 5.93348 0.0462726 -2.44686 -6.09788 -2.74129 --1.76268 4.09923 1.76897 --3.4593 -2.23883 1.65692 --1.79358 -1.17876 -3.04282 -1.90542 2.99555 -6.16072 -3.74107 3.8709 -0.160424 -4.32706 3.90173 -5.14763 -2.95917 -0.881434 -2.83139 -1.33071 2.32683 -3.38335 --4.73733 -0.353173 -6.45436 -5.08525 -6.11892 -1.78523 --0.78474 -2.96762 0.773421 -4.86522 -3.5281 0.178994 -2.19895 3.34443 -3.17661 -0.653561 3.96852 5.0262 --3.5435 -4.52532 2.45952 -6.34745 -5.16347 -1.79884 --3.06034 4.62658 5.17225 -5.96897 3.60947 2.85503 -3.13371 -1.62433 -5.04333 -5.31659 1.65998 3.54204 --5.06761 5.94926 4.77502 -3.33549 -0.42812 -0.79081 -0.834086 -6.41363 -4.90031 -4.47299 -0.73911 -1.4426 -6.11899 -2.68688 3.21074 -3.99629 -3.54714 3.75087 --1.67415 5.46194 -3.64536 -1.57286 4.78852 4.61479 -6.41417 0.449628 3.85584 --4.82324 5.25808 3.00396 --2.67648 5.56773 6.26099 -1.47376 -4.16714 -6.42487 -6.01382 4.12661 -5.5272 -5.33592 -2.57472 -2.22984 -2.14754 -1.44735 -3.95026 -0.683049 -4.26636 -5.20018 -6.38473 6.01646 -6.4326 --0.0598788 1.20869 1.20787 -1.98768 -6.09948 2.75338 --1.09323 -4.81498 3.02891 --5.10055 0.909714 1.23022 -3.17638 -5.10978 -3.25619 --4.49809 -2.66642 -5.21763 --4.60771 -2.87659 4.57599 -4.35702 0.491878 0.0636225 -5.53763 1.23565 0.219419 -3.92617 2.00748 -4.17214 -2.37495 -0.172804 -5.10957 --3.46111 5.94698 2.68867 --3.6763 -4.10527 4.80813 -4.22115 -0.614719 5.3439 -6.3962 -1.8728 -0.945171 -1.3639 -1.39025 5.04173 --2.15539 -0.811089 0.361711 -2.36265 -4.23452 -1.31383 -2.18457 6.20704 -5.3216 --1.22158 5.26214 2.30229 --4.62608 6.03754 -3.94002 --0.0446613 -5.99237 -3.0907 --3.21694 -6.29481 -2.40482 -5.78042 -1.16297 0.370149 -1.68515 -5.81025 0.894172 -1.0296 0.583502 3.82442 --6.09873 3.49592 5.67275 --5.2235 -5.36986 1.20153 -1.08034 -1.25098 -3.45048 -1.64914 -4.91509 3.19351 -0.714045 3.15969 6.18164 -0.851042 6.49123 3.14753 --3.42291 5.07279 -0.141787 --3.23547 3.41628 4.04415 --2.49942 -1.70473 2.93386 -2.28232 -2.14412 5.55102 -5.95361 -4.56865 2.95015 --4.67492 -5.30718 -0.0495295 -4.01306 4.64414 1.84082 --4.25995 -5.08134 5.54882 --0.670696 2.72867 -2.93336 --1.32976 -4.66448 -3.24926 -0.147416 -0.664268 4.38209 -1.19393 1.33532 1.08151 --5.98452 3.77302 3.89649 --2.21329 -1.11952 4.99689 --3.97382 -2.16618 -3.67262 -2.3762 3.94508 2.01102 --4.04959 2.9141 0.602355 --0.507425 -5.93492 3.79394 -0.0557174 5.04243 2.22613 --1.25688 -6.11554 -5.18292 -6.14893 -2.38601 -5.87403 --3.68305 -5.33132 -4.69401 --6.47976 3.75168 -2.21312 --1.5146 -4.04591 1.12987 --4.78106 1.17203 2.47296 --3.65057 5.59218 -6.03266 --0.431343 -3.34928 3.15229 --5.99854 -4.49722 5.01084 -3.9392 5.33137 3.15389 --2.57125 6.27066 0.0422787 -4.31022 -6.41007 3.58716 -3.95178 -2.85897 2.10099 -1.96106 -2.4062 -5.20706 -0.602548 4.94387 1.19117 --1.8836 6.48559 -6.23748 -3.28041 -0.479787 -4.24551 --1.48669 -5.25676 1.89311 --3.44217 -6.31968 -5.61047 -2.59759 0.509724 -2.51816 --3.87243 2.51411 4.92474 --1.11053 -3.70705 6.15658 -3.04325 -0.668947 1.45788 --6.18735 -4.97057 2.25191 --0.982362 -5.66987 -2.19071 --0.508532 -2.0414 3.17056 --0.395179 1.53008 -1.75646 --4.40267 0.276855 5.54112 --1.11511 2.37179 6.22271 --5.63902 5.88634 -5.31377 --1.04852 0.464527 -2.50012 --5.54853 -1.37066 6.30796 -3.49581 -5.37505 3.04462 --2.5265 -1.92497 -0.638543 --0.921121 -0.75 0.924951 -3.37411 2.91792 -3.22505 -4.58918 6.31726 -3.01478 -6.46094 -3.82521 -2.67033 -1.02893 2.69201 -5.27729 --2.33059 -4.90584 3.04071 --6.0288 -4.37562 -0.356661 --2.94071 2.31182 -1.66161 -1.93188 -1.23263 0.654091 -3.99707 1.20131 -5.66115 --0.581759 5.22542 0.840171 --5.68498 -6.33649 -2.41538 -4.13335 -2.3642 -5.10512 --3.01972 3.0869 -6.02433 --0.200788 0.887171 3.68048 -5.47352 -0.462574 3.59406 --2.74062 4.52238 0.993979 -4.85292 4.43288 2.65801 -5.41131 -2.6634 1.86438 --2.95932 -6.14978 3.82345 -5.92695 2.356 0.798225 -1.29127 2.84229 2.33023 -4.93115 1.00379 5.92376 -2.02553 3.46097 4.41364 --6.19898 -3.35229 2.42118 -4.38852 -0.650588 0.792572 --2.16821 5.14937 -0.475286 -0.989795 2.65071 -0.0939543 --1.60615 1.74319 -2.75737 --5.20605 2.15423 3.50167 --1.881 3.90096 4.07254 --1.23057 -2.0876 5.48858 --0.515798 -2.50359 -4.85999 -5.52911 5.70253 -2.20443 --5.00214 3.82387 -4.48147 -4.3928 -5.05424 -0.921729 -5.50317 1.97833 -0.991695 -3.15077 2.89305 0.857805 -1.75289 4.56458 -2.47087 --5.85984 -5.13413 -2.76503 --3.41753 -0.898193 -6.18639 -6.49788 -2.87288 4.74793 -2.22493 5.77957 -2.91425 -0.257357 -4.07854 0.17984 --5.43079 0.0929639 3.24578 --0.642237 3.0078 4.09485 -5.61561 0.601912 2.80179 -4.62261 3.03741 -1.20817 -4.4783 -1.20465 -0.282902 -2.08578 2.40797 -2.23422 -6.18842 -4.67787 6.23062 --0.363027 6.26686 -5.74561 -0.101871 -5.3985 -5.75026 -4.6891 2.14967 -2.54446 -3.75885 -1.28326 -6.36573 -2.26752 1.25945 0.938583 --1.73759 -1.09344 6.42287 --4.8024 -4.43215 4.33963 -4.28201 -0.372165 -3.22787 --4.23563 1.75763 1.4672 --0.92952 2.85896 0.51692 -4.26518 -2.65658 -3.6889 --2.38332 -5.32796 -5.66163 -2.89669 -6.12605 1.99424 --4.37874 4.378 4.25882 --1.35228 6.28722 -2.71685 -5.80473 -0.621039 4.75492 -0.0643505 -5.98912 -4.29771 --6.18327 1.45014 0.254725 -4.06514 -1.24542 3.24459 --2.40078 1.31844 0.273312 -1.21406 4.8587 5.98463 -1.89029 6.48993 -4.14039 --2.18269 -3.70847 -3.38856 -4.09664 5.62619 -3.93415 --6.19879 -6.10931 5.71369 -0.13834 1.82506 -3.2032 --4.64683 1.37236 4.49212 --4.39942 4.80835 -5.20288 --5.86287 -3.9128 1.16045 -5.70314 4.47185 -3.01742 --2.47901 3.20804 -4.84603 -6.4794 -0.793043 -5.52481 -0.449064 -1.95168 4.06236 -2.62997 -4.21974 0.546325 -5.00418 0.727203 -0.986634 -0.723978 2.74618 4.59941 -3.08588 -3.0221 -5.58164 --5.54919 -1.54347 -5.36647 -1.43035 0.484136 -1.50061 --0.0771183 -0.286622 0.140749 -2.27925 2.05066 -0.0140352 -6.02389 -3.90782 4.17866 --1.18415 5.82008 3.65669 --0.782665 -0.840195 -2.49142 -6.20607 -3.54607 -0.0758306 --0.748059 -0.868995 5.64016 -4.18663 0.313116 -2.12511 -6.29033 -6.11588 1.96951 --0.247012 3.38065 -6.01134 -5.89288 -5.09684 -3.06834 --2.78508 3.77478 -0.183686 --1.48238 -5.37383 0.627504 -4.49032 6.47882 -4.70425 -6.3202 1.89979 5.87404 --5.94845 -0.595753 -4.27427 --6.1769 -0.0303637 -1.75028 -0.630255 -0.645549 5.75079 --4.77383 -5.3377 -2.28882 -0.0766993 -4.96167 -0.946354 -2.5468 -0.21204 0.345585 --1.0537 -3.91334 -0.0435371 --0.33378 -4.49852 -2.24403 --2.67709 2.69619 2.86473 --6.11697 -2.68182 -2.32437 -1.33709 -5.54117 -3.65794 --5.23903 -5.36994 -5.27306 --2.14006 -0.424073 1.5224 -5.89354 -3.67157 1.28424 -3.65948 -3.98615 -3.61722 -4.78149 5.79617 0.123173 --2.31501 0.746976 1.53051 -3.44483 -5.04752 5.98302 --3.34607 1.85688 -3.19367 --5.01869 -2.65351 2.60515 -5.27302 -5.67922 -4.14272 -5.00409 -6.49286 4.80775 --1.87563 -5.17001 5.86727 --0.0419609 2.63131 -4.52641 --0.571635 -0.98961 -3.64769 --5.68395 2.27521 0.921195 --0.97392 6.45462 1.03486 -1.46925 5.89484 0.521641 --4.06445 2.75406 6.26443 --1.31765 2.44492 -4.28774 -1.23597 -6.4441 5.54868 --5.23553 -6.23956 -6.42278 -3.90143 5.74298 5.69578 -1.73878 -2.13465 2.86692 -5.96976 4.29097 1.73964 -4.56212 -3.18296 -6.02652 --2.14401 -2.98997 6.41267 -2.2081 -3.09209 -6.49093 --3.59398 -0.9932 1.1927 --3.26685 -2.27913 -1.38319 -0.371066 4.41134 -2.29019 --1.51894 4.18581 0.647323 --0.510016 3.78545 1.52904 -3.33961 4.17104 -2.62025 -0.905179 -4.00468 3.54221 --3.36014 6.35113 5.27058 -6.28494 0.863206 -0.839809 --1.11986 -3.67644 -4.37626 --6.0261 4.96945 0.791567 --3.08022 -0.97913 -3.74403 --3.29328 0.350038 -6.37167 -0.784406 -2.83528 -5.45966 -1.16583 -1.95388 -0.137189 --2.27367 2.65908 -3.46441 --1.6444 2.02256 -0.160851 --5.91703 -1.03731 3.9581 -1.83048 -0.327255 6.18797 -3.42176 5.22999 -0.474494 -0.729611 1.2327 2.54564 -1.00378 5.80846 -0.863861 --0.0820037 -2.88218 5.97716 --4.96924 -6.39004 3.60532 --3.94026 3.38362 -1.49208 --4.44058 -4.05023 -0.906831 -4.48375 4.08006 5.36334 -5.91771 -6.31405 -5.19694 --3.89595 -3.4647 1.66024 -0.122764 -4.29163 -3.58928 --2.38982 1.31043 -3.81634 --2.39306 -2.10964 -5.32561 --2.65888 1.47078 -6.31385 --5.95456 2.67361 4.60555 -3.43876 -4.82379 4.22813 --6.06623 0.975162 -2.56118 --3.5155 1.68763 0.328084 -0.685078 6.25254 1.49697 -2.31021 4.22246 -6.18898 --5.66526 -5.48438 -1.14174 -6.30757 -0.383786 2.74042 --6.22615 2.79348 -0.227014 -1.10558 -0.665535 -0.524878 -2.79222 5.04953 -1.8203 -3.53113 4.50231 -6.3401 --1.95388 -4.39325 -4.91523 --5.58595 -2.86501 -6.07968 -1.9297 -1.95791 -2.6466 --0.810616 -0.372193 3.54135 --5.97436 -0.029845 6.03747 --2.27964 -4.50935 0.13603 --2.15282 -3.19297 0.218621 -5.3964 1.92685 5.05388 --5.70944 2.61904 -3.49568 -5.19378 -2.85576 5.6476 -4.52775 4.27443 4.04449 -5.05584 -2.87796 4.44483 -5.00005 -5.02788 -1.99456 -4.105 5.2331 -5.19654 -3.88729 6.28938 2.16324 --2.93974 3.42999 -2.48051 --3.84985 3.20896 -3.69175 --6.14793 -4.06128 -5.79506 --3.08759 4.93678 -1.68636 -4.86531 -6.40262 1.31993 --0.0443516 -4.68613 4.04759 --4.13591 4.71622 -1.40105 -2.63241 1.96753 6.44536 -2.34045 -1.83514 4.01054 --2.83902 -4.5759 -2.67989 --2.01266 4.41375 -4.75339 -6.46974 -1.75407 2.52765 -4.08173 0.172924 6.23606 -6.0175 2.68652 3.70365 --1.84872 0.519483 -0.62777 --4.38215 -2.98091 6.44316 -5.30343 -1.78106 -5.1542 -1.09648 1.59142 -2.24016 -1.32263 1.33181 4.93106 -3.83287 -1.4132 1.98919 --5.94388 4.16103 -3.33891 -2.94206 -0.560597 5.97685 -0.837112 -2.76399 -1.45153 -6.25093 1.05674 -3.67597 --5.53271 4.02831 -5.48654 --3.55645 -5.86943 -0.683272 -1.62756 5.35844 2.00358 --3.06382 1.23934 -5.18582 -5.65517 -5.6154 -0.671965 --6.27772 -0.681853 -0.368902 --3.206 1.26275 2.67708 --5.49594 2.04747 -2.29335 --3.56012 1.82874 3.76206 -0.13551 -1.59471 -0.718695 --3.83919 5.74358 4.03774 -2.99 6.35931 -1.51294 --4.16838 4.62688 -3.83191 -1.82736 -3.67237 -5.02052 --1.70494 2.38136 3.62764 --6.29467 1.24858 2.93116 --2.52165 -0.0566989 -3.21384 --0.458799 -2.93868 1.8886 --1.5939 3.28927 2.84018 --6.38986 -3.48505 5.87048 --3.08404 1.32971 -0.921668 --5.66498 0.87604 -5.98454 -4.56148 -0.771481 -4.91997 -3.50147 0.613312 -3.4618 -5.31565 4.4705 -4.39917 -1.82254 -3.32539 3.28481 -5.28681 -3.60577 2.92651 --1.64507 2.8347 4.90997 -5.46169 5.8286 -3.91396 --5.25199 0.424156 -3.65437 -2.79031 -4.50632 -5.91629 -1.87334 -4.40195 -3.84251 -2.64835 4.90456 5.54691 -5.51775 -0.306974 -2.0554 --1.52252 3.32564 -0.418359 --0.929475 4.25958 2.87429 --5.12829 -0.561194 0.764996 --1.20943 -5.15185 -0.980838 -1.35336 -4.91782 -0.184305 --1.96039 -6.38454 2.90331 --4.13457 3.18479 -5.538 --0.619882 3.63555 -1.76899 -3.6085 2.89275 -2.08488 -3.75607 -4.58719 0.376594 --1.73169 1.52523 5.58677 -3.09657 -5.29724 -0.801387 --2.88842 2.3308 5.70599 --0.181236 5.33554 3.34343 -0.207244 2.52861 1.37333 -5.58541 1.13772 -2.09623 -3.27954 1.4559 2.20809 -5.75083 -4.30629 -1.07106 --2.76898 1.97728 1.57429 --4.87473 -3.36214 -4.13904 --3.83442 0.00512382 -3.2724 -4.29122 1.65378 4.49666 --5.20525 -6.29792 2.29949 --2.96434 2.68842 -0.462881 -4.74822 4.54749 -0.578403 -0.541597 -3.3449 -4.22502 --2.65712 -4.04518 3.90329 --2.35002 4.88443 -2.77225 -2.00077 3.68207 5.65888 --5.65525 -2.71336 -0.995193 -2.57893 3.71785 -1.39583 --5.02426 3.82409 6.32852 --5.48183 -4.25515 -1.55952 -5.21174 -1.82756 -3.73118 -5.7674 5.72829 1.39785 -1.17757 -2.9096 5.9254 -1.78487 4.41821 0.760976 --3.86371 1.20868 -2.20084 --2.4151 -5.29933 -3.97943 -4.55236 -1.56706 -2.55462 --4.53372 -1.8377 0.512544 --3.79966 -4.13527 6.36155 -2.29235 2.2825 2.07366 -5.20958 5.4265 3.87579 --3.86889 -5.80843 2.91849 --2.11833 4.8741 3.15773 --0.193723 -0.0837779 -4.70058 -2.0805 -4.81027 -2.51559 -5.94321 3.66155 0.661105 --1.37172 1.60012 1.07307 --0.0565926 -0.016279 2.73462 -4.2926 5.76053 -1.72654 -1.56425 -4.98211 -5.04423 --0.198969 -3.6659 -5.60759 -4.17583 0.844743 -4.52132 --6.29273 -5.7641 3.12213 --0.168147 -5.69636 1.6218 -5.92884 -0.847615 -4.28672 -1.33192 0.279753 2.4113 -0.0764802 -1.48417 -6.16458 -3.92192 5.40488 0.75196 --4.68489 1.28509 -3.05431 -4.57305 3.33404 0.521583 -4.14255 2.46121 1.64126 --3.23794 -0.955299 -2.17914 --1.34411 -0.390684 -5.50234 -1.83831 -2.63608 -3.66505 --5.37698 5.11135 -4.08593 -1.67047 2.8031 1.07689 --2.83306 0.204765 0.452163 -0.988458 5.61776 -2.25299 -2.31592 -0.0799472 3.06125 --6.2189 4.84963 -1.52619 -5.08468 0.684654 4.46787 -1.83823 6.15248 -1.52242 --4.73307 -0.233818 2.06585 -5.75435 3.3745 -0.678354 --5.39668 0.241149 4.50069 -2.30048 2.51323 -4.29583 --3.74924 -1.14252 -0.83256 --5.865 0.243157 1.84559 --3.02368 -0.0667283 2.61571 -3.05221 4.4871 0.95462 --1.65464 -3.3705 -5.4316 --0.307965 4.43282 6.0826 -3.31881 0.684052 -1.31184 --0.609214 1.80847 2.77918 -4.99806 2.30633 6.48589 -3.50194 3.25443 2.17508 --6.40164 -5.76976 -6.0807 --3.58276 -3.28352 0.4812 -0.124116 -2.55341 -3.52592 --1.81536 0.0539574 2.65819 -1.72474 2.67263 -1.13325 --1.26118 -5.9858 -3.84264 -2.75985 -3.09599 -0.513938 --5.21953 -3.95736 -2.8383 -2.87856 3.17799 -5.39553 -3.96284 4.2246 -1.46381 --3.9039 3.38907 1.86966 -5.12743 0.270085 -5.76795 -2.9024 4.9345 3.88296 -3.1776 3.24608 6.34374 -6.16603 4.73448 -0.374182 -1.59664 -0.43966 -2.57535 --5.56613 -2.36579 1.58909 -0.847239 -5.51743 4.31397 -3.12523 -2.88331 -4.10042 --4.19128 -3.56301 3.5275 --2.85637 3.56276 5.63068 -2.0919 -2.77161 -1.86747 -6.23997 2.63705 -1.88331 --0.579755 3.34004 5.37005 --3.66274 0.0925181 -5.0325 -0.123427 -0.207091 -3.14292 -4.78756 0.984279 -3.13366 --5.39584 3.09054 -1.55592 -1.00907 4.47677 -3.42364 -4.72973 -4.83332 3.88423 --4.77423 -2.18385 -2.6519 -5.81378 3.02096 5.35971 --0.402323 -4.42284 1.90683 --4.88318 -4.07875 2.22673 --4.08812 -6.00015 4.42568 --4.0485 -4.28531 -2.39379 --0.435579 4.90317 -5.27129 -2.90763 -2.55218 2.97035 --3.17629 -3.30197 -0.636348 --1.57321 -5.38937 4.47843 --5.49999 0.385553 -0.327191 -0.623585 2.0984 3.52214 --1.11003 4.50225 -0.533207 --2.93126 -2.01274 0.496216 -5.07888 -4.75834 0.383679 -2.9398 1.65023 4.95858 -4.28645 0.257398 3.55804 -1.23418 5.45235 -5.55589 -5.65684 0.164054 1.32042 -4.82154 -3.64908 -1.30982 -4.36043 -5.13842 5.06395 --4.96344 -6.42741 -0.922661 -5.36367 1.46653 -5.28276 -0.610216 -3.16685 1.04131 -1.14891 -4.07177 -1.49007 -4.24097 -4.22144 2.82921 -0.316906 0.708596 -2.26612 --4.12372 1.54178 5.79893 --1.58704 0.506382 -6.31196 -3.32538 -6.3912 -3.64242 -3.08901 -6.47219 3.52758 --6.31035 3.32986 1.65586 -3.09115 2.56 -0.770601 --0.421879 1.51219 -0.152739 --2.18125 -5.68456 -0.31418 -5.28031 -2.35838 -0.767878 --4.4116 -1.50365 -5.75881 --2.89691 -3.07537 -4.63214 --5.37713 4.06492 -0.817858 --4.2553 -2.62515 -0.35524 -6.09347 5.08804 2.7742 --3.39692 4.14052 -4.83907 -1.28207 3.26007 3.43041 -1.67133 -5.22142 -1.34354 --4.92844 -5.03622 2.89598 --3.51539 -4.03287 -5.27692 -4.70251 1.58174 0.958076 --2.92966 -2.04559 -2.5056 -0.198825 1.39473 4.71766 -4.1171 -5.11576 -4.20646 -1.1482 -0.246041 -4.67529 --6.24278 4.77367 6.45525 -5.5109 -1.2027 -1.1233 --4.55802 6.34741 -5.27496 --3.27851 2.28282 -4.55527 --4.71995 -3.00888 -1.74838 --6.35659 -5.68358 -4.12059 -3.39384 -0.123048 2.75636 -2.77679 4.73686 -5.18491 --1.81692 -1.61039 -1.79997 -0.882813 -4.08637 5.028 -2.4205 0.479517 1.92145 -2.19829 -5.73367 -6.19553 --3.06436 -5.84808 0.62609 -2.57399 -3.70908 -2.87267 -0.263746 4.18751 3.71416 -3.1162 -0.397403 4.05207 -6.1465 -1.32469 -2.29727 --1.32577 3.75623 -3.81956 -5.4938 -1.18357 1.61574 --3.11776 5.88596 1.17727 --2.80509 -0.497357 -0.8465 --4.23178 3.83098 5.38925 --4.15584 4.34357 0.889076 --5.62453 3.67536 0.564403 --0.551294 -1.8669 -1.57666 -1.30597 0.832706 -3.31758 --4.14717 5.22821 5.46235 -5.24636 -3.15321 -4.78003 --5.56247 -4.91186 6.28716 -6.23691 2.19311 -4.31682 --6.0396 -1.61379 -3.18402 --6.3637 0.178015 0.577049 --2.28762 -4.22356 -6.16491 --3.66673 -6.4189 -4.08052 --4.40556 3.92144 3.10731 -5.26265 4.71139 0.719174 -0.0476459 3.77767 -0.768521 -5.20805 -4.1207 5.08002 -4.40264 2.83755 3.09741 -1.92753 0.389183 -0.440487 -2.3567 1.57257 -3.32032 -2.18784 5.59657 6.49967 -5.14409 -3.87813 -2.6076 --3.01288 0.421692 -4.15644 -2.60228 -1.51615 -6.04493 --1.61769 -3.71756 2.41933 -5.84509 3.26754 -3.37773 --0.149578 -2.75449 -0.349346 --4.61159 2.56298 -4.16494 -2.21162 -5.26723 5.33308 -4.84594 6.15083 -6.15468 --1.59665 3.62329 -2.45859 -0.232609 -1.85806 5.3995 --5.90988 -1.87011 0.307409 --6.11628 -1.27213 5.22082 -1.95967 5.88314 3.55777 --0.831103 4.60156 -2.80662 --4.3396 -0.854997 -4.55264 -5.66964 4.01872 4.05454 --0.934284 2.075 -5.7044 -0.00894878 -6.00181 5.05173 -0.614489 -0.634351 -5.71502 --1.46649 2.68241 1.59282 -6.33126 0.325316 -5.04136 --1.48739 -0.784262 -0.680483 -4.45524 -5.87579 0.0639949 --4.4869 -1.27501 -1.64427 -1.66296 4.06984 -4.81176 --6.08276 -6.09938 -0.0657241 --0.568678 5.95297 -4.30206 --0.00508163 3.55949 -3.42569 --0.472887 0.257391 -5.93187 -3.41845 5.65843 -2.79255 -4.86472 -2.08282 -6.33543 -0.0998649 1.64023 -6.05761 --4.78341 1.45958 0.00352717 -1.52246 1.60895 -6.29877 --5.41295 0.839319 -1.47309 -2.84935 -5.66142 0.474771 --2.42943 -0.133788 -5.55579 --1.90201 5.4986 -5.32534 --0.996851 -1.44225 4.41879 -2.98917 -4.28478 -4.72793 -1.48633 -3.40549 -0.185428 -3.37336 2.11221 3.28218 -0.803336 0.715452 -5.52788 -2.23975 0.882902 5.73005 -5.34048 -0.070311 -0.0795594 -4.43111 -3.77016 1.33475 --2.27975 5.4912 4.56873 --1.02395 3.63993 -5.24626 --3.52901 0.216832 -1.86371 --5.04744 -0.994002 5.18697 --3.92569 -1.14494 2.93878 -2.65068 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/home diff --git a/environment-dev.yml b/environment-dev.yml new file mode 100644 index 00000000..7a0dd6a9 --- /dev/null +++ b/environment-dev.yml @@ -0,0 +1,15 @@ +name: msibi-dev +channels: +- conda-forge +dependencies: +- cuda-version=11.8 +- freud >=2.13 +- gsd >=3.0 +- hoomd >=4.0 +- python >=3.9 +- pandas +- cmeutils >=1.2 +- more-itertools +- pytest +- pytest-cov +- pre-commit diff --git a/msibi/forces.py b/msibi/forces.py index 45468398..bdb27196 100644 --- a/msibi/forces.py +++ b/msibi/forces.py @@ -61,7 +61,7 @@ def __init__( nbins: int=None, correction_form: str="linear" ): - if optimize and nbins is None or nbins<=0: + if optimize and nbins is None or nbins and nbins<=0: raise ValueError( "If a force is set to be optimized, nbins must be " "a positive, non-zero integer." @@ -364,7 +364,11 @@ def set_quadratic( self.x_min = x_min self.x_max = x_max self.dx = x_max / self.nbins - self.x_range = np.arange(x_min, x_max + self.dx, self.dx) + if isinstance(self, msibi.forces.Dihedral): + self.dx *= 2 + self.x_range = np.arange(x_min, x_max + self.dx/2, self.dx) + else: + self.x_range = np.arange(x_min, x_max + self.dx, self.dx) self.potential = quadratic_spring(self.x_range, x0, k4, k3, k2) self.force_init = "Table" self.force_entry = self._table_entry() @@ -603,7 +607,7 @@ def set_harmonic(self, r0: Union[float, int], k: Union[float, int]) -> None: "for a force designated for optimization. " "Instead, use set_from_file() or set_quadratic()." ) - self.type = "static" + self.format = "static" self.force_init = "Harmonic" self.force_entry = dict(r0=r0, k=k) @@ -718,7 +722,7 @@ def set_harmonic(self, t0: Union[float, int], k: Union[float, int]) -> None: "for a force designated for optimization. " "Instead, use set_from_file() or set_quadratic()." ) - self.type = "static" + self.format = "static" self.force_init = "Harmonic" self.force_entry = dict(t0=t0, k=k) @@ -941,6 +945,7 @@ def __init__( self.type3 = type3 self.type4 = type4 name = f"{self.type1}-{self.type2}-{self.type3}-{self.type4}" + self._correction_function = bond_correction super(Dihedral, self).__init__( name=name, optimize=optimize, @@ -976,7 +981,7 @@ def set_harmonic( "for a force designated for optimization. " "Instead, use set_from_file() or set_quadratic()." ) - self.type = "static" + self.format = "static" self.force_init = "Periodic" self.force_entry = dict(phi0=phi0, k=k, d=d, n=n) @@ -1000,7 +1005,7 @@ def _get_distribution( """ return dihedral_distribution( - gsd_file=gsd, + gsd_file=gsd_file, A_name=self.type1, B_name=self.type2, C_name=self.type3, diff --git a/msibi/state.py b/msibi/state.py index 7d3341a2..49268292 100644 --- a/msibi/state.py +++ b/msibi/state.py @@ -48,7 +48,7 @@ def __init__( traj_file: str, n_frames: int, alpha: float=1.0, - exclude_bonded: bool=True, + exclude_bonded: bool=True, #TODO: Do we use this here or in Force? _dir=None ): self.name = name diff --git a/msibi/tests/__init__.py b/msibi/tests/__init__.py index e69de29b..9eb4c5fb 100644 --- a/msibi/tests/__init__.py +++ b/msibi/tests/__init__.py @@ -0,0 +1 @@ +from .base_test import BaseTest diff --git a/msibi/tests/assets/AB-1.0kT.gsd b/msibi/tests/assets/AB-1.0kT.gsd new file mode 100644 index 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test_assets = os.path.join(os.path.dirname(__file__), "assets") class BaseTest: @pytest.fixture - def state0(self, tmp_path): - return self.init_state(0, tmp_path) + def msibi(self): + msibi = MSIBI( + nlist=hoomd.md.nlist.Cell, + integrator_method=hoomd.md.methods.ConstantVolume, + thermostat=hoomd.md.methods.thermostats.MTTK, + method_kwargs={}, + thermostat_kwargs={"tau": 0.01}, + dt=0.003, + gsd_period=int(1e3), + ) + return msibi @pytest.fixture - def state1(self, tmp_path): - return self.init_state(1, tmp_path) + def stateX(self, tmp_path): + state = State( + name="X", + alpha=1.0, + kT=1.0, + traj_file=os.path.join(test_assets, "AB-1.0kT.gsd"), + n_frames=10, + _dir=tmp_path + ) + return state @pytest.fixture - def pairs(self): - pair0 = Pair("0", "0") - pair0.set_table_potential( - epsilon=1, sigma=1, r_min=0, r_max=2.5, n_points=len(r) - ) - pair1 = Pair("1", "1") - pair1.set_table_potential( - epsilon=1, sigma=1, r_min=0, r_max=2.5, n_points=len(r) - ) - pair2 = Pair("2", "2") - pair2.set_table_potential( - epsilon=1, sigma=1, r_min=0, r_max=2.5, n_points=len(r) + def stateY(self, tmp_path): + state = State( + name="Y", + alpha=1.0, + kT=4.0, + traj_file=os.path.join(test_assets, "AB-4.0kT.gsd"), + n_frames=100, + _dir=tmp_path ) - pair01 = Pair("0", "1") - pair01.set_table_potential( - epsilon=1, sigma=1, r_min=0, r_max=2.5, n_points=len(r) + return state + + + @pytest.fixture + def pairA(self): + pair = Pair( + type1="A", + type2="A", + r_cut=3.0, + nbins=100, + optimize=False, + exclude_bonded=True ) - pair02 = Pair("0", "2") - pair02.set_table_potential( - epsilon=1, sigma=1, r_min=0, r_max=2.5, n_points=len(r) + pair.set_lj(sigma=2, epsilon=2, r_cut=3.0, r_min=0.1) + return pair + + @pytest.fixture + def pairB(self): + pair = Pair( + type1="B", + type2="B", + r_cut=3.0, + nbins=100, + optimize=False, + exclude_bonded=True ) - pair12 = Pair("1", "2") - pair12.set_table_potential( - epsilon=1, sigma=1, r_min=0, r_max=2.5, n_points=len(r) + pair.set_lj(sigma=1.5, epsilon=1, r_cut=3.0, r_min=0.1) + return pair + + @pytest.fixture + def pairAB(self): + pair = Pair( + type1="A", + type2="B", + r_cut=3.0, + nbins=100, + optimize=False, + exclude_bonded=True ) - return [pair0, pair1, pair2, pair01, pair02, pair12] + pair.set_lj(sigma=1.5, epsilon=1, r_cut=3.0, r_min=0.1) + return pair @pytest.fixture def bond(self): - bond = Bond("0", "1") - bond.set_quadratic(l0=1, k4=1, k3=1, k2=1, l_min=0, l_max=2) + bond = Bond( + type1="A", + type2="B", + optimize=False, + nbins=100 + ) return bond @pytest.fixture def angle(self): - angle = Angle("0", "1", "2") - angle.set_harmonic(k=1, theta0=1) - angle.set_quadratic(theta0=1, k4=1, k3=1, k2=1) + angle = Angle( + type1="A", + type2="B", + type3="A", + optimize=False, + nbins=100 + ) return angle @pytest.fixture - def rdf0(self): - return self.get_rdf(0) + def dihedral(self): + dihedral = Dihedral( + type1="A", + type2="B", + type3="A", + type4="B", + optimize=False, + nbins=100 + ) + return dihedral @pytest.fixture - def rdf1(self): - return self.get_rdf(1) + def rdfAA(self): + return self.get_rdf(0) - def get_rdf(self, state_n): - return np.loadtxt(os.path.join(test_assets, f"target-rdf{state_n}.txt")) + @pytest.fixture + def rdfBB(self): + pass - def init_state(self, state_n, tmp_path): - traj_filename = os.path.join(test_assets, f"query{state_n}.gsd") - state = State( - name=f"state{state_n}", - kT=T, - max_frames=5, - alpha=0.5, - traj_file=traj_filename, - _dir=tmp_path - ) - return state + @pytest.fixture + def rdfAB(self): + pass diff --git a/msibi/tests/test_angles.py b/msibi/tests/test_angles.py deleted file mode 100644 index 32e983fc..00000000 --- a/msibi/tests/test_angles.py +++ /dev/null @@ -1,40 +0,0 @@ -import os - -import numpy as np -import pytest - -from msibi import MSIBI, State, Bond, Angle -from msibi.potentials import save_table_potential - -from .base_test import BaseTest - - -class TestAngle(BaseTest): - def test_angle_name(self, angle): - assert angle.name == "0-1-2" - - def test_set_harmonic(self): - angle = Angle("0", "1", "2") - angle.set_harmonic(k=500, theta0=2) - assert angle.angle_type == "static" - assert "k=500" in angle.angle_entry - assert "t0=2" in angle.angle_entry - - def test_set_quadratic(self): - angle = Angle("0", "1", "2") - angle.set_quadratic(1, 1, 1, 1) - assert angle.angle_type == "table" - - def test_save_table_potential(self, tmp_path): - angle = Angle("0", "1", "2") - angle.set_quadratic(1, 1, 1, 1) - angle.potential_file = os.path.join(tmp_path, "pot.txt") - save_table_potential( - angle.potential, - angle.theta_range, - angle.dtheta, - None, - angle.potential_file - ) - assert os.path.isfile(angle.potential_file) - diff --git a/msibi/tests/test_bonds.py b/msibi/tests/test_bonds.py deleted file mode 100644 index 21b44988..00000000 --- a/msibi/tests/test_bonds.py +++ /dev/null @@ -1,92 +0,0 @@ -import os - -import numpy as np -import pytest - -from msibi import MSIBI, State, Bond, Angle -from msibi.potentials import save_table_potential - -from .base_test import BaseTest - - -class TestBond(BaseTest): - def test_bond_name(self, bond): - assert bond.name == "0-1" - - def test_set_harmonic(self): - bond = Bond("0", "1") - bond.set_harmonic(k=500, l0=2) - assert bond.bond_type == "static" - assert "k=500" in bond.bond_entry - assert "r0=2" in bond.bond_entry - - def test_set_quadratic(self): - bond = Bond("0", "1") - bond.set_quadratic( - theta0=1, - k4=1, - k3=1, - k2=1, - n_points=20 - ) - assert bond.bond_type == "table" - - def test_save_table_potential(self, tmp_path): - bond = Bond("0", "1") - bond.set_quadratic( - theta0=1, - k4=1, - k3=1, - k2=1, - n_points=20 - ) - bond.potential_file = os.path.join(tmp_path, "pot.txt") - save_table_potential( - bond.potential, - bond.l_range, - bond.dl, - None, - bond.potential_file - ) - assert os.path.isfile(bond.potential_file) - - def test_angle_name(self, angle): - assert angle.name == "0-1-2" - - def test_set_harmonic(self): - angle = Angle("0", "1", "2") - angle.set_harmonic(k=500, theta0=2) - assert angle.angle_type == "static" - assert "k=500" in angle.angle_entry - assert "t0=2" in angle.angle_entry - - def test_set_quadratic(self): - angle = Angle("0", "1", "2") - angle.set_quadratic( - theta0=1, - k4=1, - k3=1, - k2=1, - n_points=20 - ) - assert angle.angle_type == "table" - - def test_save_table_potential(self, tmp_path): - angle = Angle("0", "1", "2") - angle.set_quadratic( - theta0=1, - k4=1, - k3=1, - k2=1, - n_points=20 - ) - angle.potential_file = os.path.join(tmp_path, "pot.txt") - save_table_potential( - angle.potential, - angle.theta_range, - angle.dtheta, - None, - angle.potential_file - ) - assert os.path.isfile(angle.potential_file) - diff --git a/msibi/tests/test_error_calculation.py b/msibi/tests/test_error_calculation.py deleted file mode 100644 index 3e933643..00000000 --- a/msibi/tests/test_error_calculation.py +++ /dev/null @@ -1,18 +0,0 @@ -import numpy as np - -from msibi.utils.error_calculation import calc_similarity - - -def test_calc_similarity(): - arr1 = np.ones(10) - arr2 = np.ones(10) - f_fit = calc_similarity(arr1, arr2) - assert f_fit == 1.0 - - arr2 = np.zeros(10) - f_fit = calc_similarity(arr1, arr2) - assert f_fit == 0.0 - - arr1 = np.random.random(10) - arr2 = np.random.random(10) - assert calc_similarity(arr1, arr2) == calc_similarity(arr2, arr1) diff --git a/msibi/tests/test_forces.py b/msibi/tests/test_forces.py new file mode 100644 index 00000000..e1d2c7d8 --- /dev/null +++ b/msibi/tests/test_forces.py @@ -0,0 +1,212 @@ +import os + +import numpy as np +import pytest + +from msibi import Bond, Angle, Dihedral, Pair + +from .base_test import BaseTest + +class TestForce(BaseTest): + def test_dx(self, bond): + bond.set_quadratic( + x0=2, + k4=1, + k3=1, + k2=1, + x_min=1, + x_max=3, + ) + assert bond.dx == 0.03 + + def test_potential_setter(self, bond): + bond.set_quadratic( + x0=2, + k4=0, + k3=0, + k2=100, + x_min=1, + x_max=3, + ) + initial_pot = np.copy(bond.potential) + bond.potential = bond.potential * 2 + assert np.allclose(bond.potential, initial_pot * 2) + + def test_smooth_potential(self, bond): + bond.set_quadratic( + x0=2, + k4=0, + k3=0, + k2=100, + x_min=1, + x_max=3, + ) + bond.potential = bond.potential + np.random.normal(0, 0.5, bond.potential.shape) + noisy_pot = np.copy(bond.potential) + bond.smoothing_window = 5 + bond.smooth_potential() + assert bond.smoothing_window == 5 + for i, j in zip(bond.potential, noisy_pot): + assert i != j + + def test_smoothing_window(self, bond): + bond.smoothing_window = 5 + assert bond.smoothing_window == 5 + + def test_smoothing_order(self, bond): + bond.smoothing_order = 3 + assert bond.smoothing_order == 3 + + def test_nbins(self, bond): + bond.nbins = 60 + assert bond.nbins == 60 + + +class TestBond(BaseTest): + def test_bond_name(self, bond): + assert bond.name == "A-B" + + def test_set_harmonic(self, bond): + bond.set_harmonic(k=500, r0=2) + assert bond.format == "static" + assert bond.force_entry["k"] == 500 + assert bond.force_entry["r0"] == 2 + + def test_set_quadratic(self, bond): + bond.set_quadratic( + x0=1.5, + k4=0, + k3=0, + k2=300, + x_min=0, + x_max=3, + ) + assert bond.format == "table" + assert len(bond.potential) == bond.nbins + 1 + assert bond.x_range[0] == 0 + assert np.around(bond.x_range[-1], 1) == 3.0 + + def test_save_table_potential(self, tmp_path, bond): + bond.set_quadratic( + x0=2, + k4=1, + k3=1, + k2=1, + x_min=1, + x_max=3, + ) + path = os.path.join(tmp_path, "AB_bond.csv") + bond.save_potential(path) + assert os.path.isfile(path) + + +class TestAngle(BaseTest): + def test_angle_name(self, angle): + assert angle.name == "A-B-A" + assert angle.optimize is False + + def test_set_angle_harmonic(self, angle): + angle.set_harmonic(k=500, t0=2) + assert angle.format == "static" + assert angle.force_entry["t0"] == 2 + assert angle.force_entry["k"] == 500 + + def test_set_quadratic(self, angle): + angle.set_quadratic( + x0=2, + k4=0, + k3=0, + k2=100, + x_min=0, + x_max=np.pi + ) + assert angle.format == "table" + assert len(angle.x_range) == angle.nbins + 1 + assert angle.x_range[0] == 0 + assert np.allclose(angle.x_range[-1], np.pi, atol=1e-3) + + def test_save_angle_potential(self, tmp_path, angle): + angle.set_quadratic( + x0=2, + k4=0, + k3=0, + k2=100, + x_min=0, + x_max=np.pi + ) + path = os.path.join(tmp_path, "ABA_angle.csv") + angle.save_potential(path) + assert os.path.isfile(path) + + +class TestPair(BaseTest): + def test_pair_name(self, pairAB): + assert pairAB.name == "A-B" + assert pairAB._pair_name == ("A", "B") + assert pairAB.optimize is False + + def test_set_lj(self, pairAB): + pairAB.set_lj( + r_min=0.1, + r_cut=3.0, + epsilon=1.0, + sigma=1.0 + ) + assert pairAB.format == "table" + assert pairAB._table_entry()["r_min"] == 0.1 + assert len(pairAB._table_entry()["U"]) == len(pairAB.x_range) + assert len(pairAB._table_entry()["F"]) == len(pairAB.x_range) + assert pairAB.x_range[0] == 0.1 + assert pairAB.x_range[-1] == 3.0 + + def test_save_angle_potential(self, tmp_path, pairAB): + pairAB.set_lj( + r_min=0.1, + r_cut=3.0, + epsilon=1.0, + sigma=1.0 + ) + path = os.path.join(tmp_path, "AB_pair.csv") + pairAB.save_potential(path) + assert os.path.isfile(path) + + +class TestDihedral(BaseTest): + def test_dihedral_name(self, dihedral): + assert dihedral.name == "A-B-A-B" + assert dihedral.optimize is False + + def test_set_dihedral_harmonic(self, dihedral): + dihedral.set_harmonic(k=500, phi0=0, d=-1, n=1) + assert dihedral.format == "static" + assert dihedral.force_entry["phi0"] == 0 + assert dihedral.force_entry["k"] == 500 + assert dihedral.force_entry["d"] == -1 + assert dihedral.force_entry["n"] == 1 + + def test_set_dihedral_quadratic(self, dihedral): + dihedral.set_quadratic( + x0=0, + k4=0, + k3=0, + k2=100, + x_min=-np.pi, + x_max=np.pi + ) + assert dihedral.format == "table" + assert len(dihedral.x_range) == dihedral.nbins + 1 + assert np.allclose(dihedral.x_range[0], -np.pi, atol=1e-3) + assert np.allclose(dihedral.x_range[-1], np.pi, atol=1e-3) + + def test_save_angle_potential(self, tmp_path, dihedral): + dihedral.set_quadratic( + x0=0, + k4=0, + k3=0, + k2=100, + x_min=-np.pi, + x_max=np.pi + ) + path = os.path.join(tmp_path, "ABAA_dihedral.csv") + dihedral.save_potential(path) + assert os.path.isfile(path) diff --git a/msibi/tests/test_msibi.py b/msibi/tests/test_msibi.py deleted file mode 100644 index 03b682f6..00000000 --- a/msibi/tests/test_msibi.py +++ /dev/null @@ -1,83 +0,0 @@ -import pytest - -from msibi import MSIBI - -from .base_test import BaseTest - -n_bins = 151 - - -class TestMSIBI(BaseTest): - def test_add_potential_objects(self, state0, pairs, bond, angle): - opt = MSIBI( - integrator="hoomd.md.integrate.nvt", - integrator_kwargs={"tau": 0.1}, - nlist="hoomd.md.nlist.cell", - dt=0.001, - gsd_period=1000, - n_steps=1e6, - ) - opt.add_state(state0) - opt.add_pair(pairs[0]) - opt.add_bond(bond) - opt.add_angle(angle) - assert len(opt.pairs) == len(opt.bonds) == len(opt.angles) == 1 - - def test_opt_pairs(self, state0, pairs, tmp_path): - opt = MSIBI( - integrator="hoomd.md.integrate.nvt", - integrator_kwargs={"tau": 0.1}, - nlist="hoomd.md.nlist.cell", - dt=0.001, - gsd_period=1000, - n_steps=1e6, - ) - opt.add_state(state0) - opt.add_pair(pairs[0]) - opt.optimize_pairs( - n_iterations=0, - r_switch=None, - smooth_rdfs=False, - _dir=tmp_path, - ) - assert opt.optimization == "pairs" - assert pairs[0].r_switch == pairs[0].r_range[-5] - for key in pairs[0]._states.keys(): - assert key == state0 - - def test_opt_bonds(self, state0, bond, tmp_path): - opt = MSIBI( - integrator="hoomd.md.integrate.nvt", - integrator_kwargs={"tau": 0.1}, - nlist="hoomd.md.nlist.cell", - dt=0.001, - gsd_period=1000, - n_steps=1e6, - ) - opt.add_state(state0) - opt.add_bond(bond) - opt.optimize_bonds( - n_iterations=0, - ) - assert opt.optimization == "bonds" - for key in bond._states.keys(): - assert key == state0 - - @pytest.mark.skip(reason="Need better toy system") - def test_opt_angles(self, state0, angle, tmp_path): - opt = MSIBI( - integrator="hoomd.md.integrate.nvt", - integrator_kwargs={"tau": 0.1}, - nlist="hoomd.md.nlist.cell", - dt=0.001, - gsd_period=1000, - n_steps=1e6, - ) - opt.add_state(state0) - opt.add_angle(angle) - opt.optimize_angles( - n_iterations=0, - ) - assert opt.optimization == "angles" - for key in angle._states.keys(): - assert key == state0 diff --git a/msibi/tests/test_optimize.py b/msibi/tests/test_optimize.py new file mode 100644 index 00000000..6d470698 --- /dev/null +++ b/msibi/tests/test_optimize.py @@ -0,0 +1,71 @@ +import numpy as np +import pytest +import hoomd +from msibi import MSIBI, Bond, Angle, Dihedral, Pair + +from .base_test import BaseTest + + + +class TestMSIBI(BaseTest): + def test_init(self, msibi): + assert msibi.n_iterations == 0 + assert isinstance(msibi.nlist(buffer=0.20), hoomd.md.nlist.Cell) + assert isinstance(msibi.integrator_method(filter=hoomd.filter.All()), hoomd.md.methods.ConstantVolume) + assert isinstance(msibi.thermostat(kT=1.0, tau=0.01), hoomd.md.methods.thermostats.MTTK) + + def test_add_state(self, msibi, stateX, stateY): + msibi.add_state(stateX) + msibi.add_state(stateY) + assert msibi.states[0] == stateX + assert msibi.states[1] == stateY + assert len(msibi.states) == 2 + + def test_add_forces(self, msibi, pairA, bond, angle, dihedral): + msibi.add_force(pairA) + msibi.add_force(bond) + msibi.add_force(angle) + msibi.add_force(dihedral) + assert msibi.forces[0] == pairA + assert msibi.forces[1] == bond + assert msibi.forces[2] == angle + assert msibi.forces[3] == dihedral + assert len(msibi.forces) == 4 + assert len(msibi.pairs) == 1 + assert len(msibi.bonds) == 1 + assert len(msibi.angles) == 1 + assert len(msibi.dihedrals) == 1 + + def test_run(self, msibi, stateX, stateY): + msibi.gsd_period = 10 + bond = Bond(type1="A", type2="B", optimize=True, nbins=60) + bond.set_quadratic(x_min=0.0, x_max=3.0, x0=1, k2=200, k3=0, k4=0) + msibi.add_state(stateX) + msibi.add_state(stateY) + msibi.add_force(bond) + init_bond_pot = np.copy(bond.potential) + msibi.run_optimization(n_steps=500, n_iterations=1) + assert not np.array_equal(bond.potential, init_bond_pot) + assert msibi.n_iterations == 1 + ff = msibi._build_force_objects() + assert len(ff) == 1 + + def test_run_with_static_force(self, msibi, stateX, stateY): + msibi.gsd_period = 10 + bond = Bond(type1="A", type2="B", optimize=True, nbins=60) + bond.set_quadratic(x_min=0.0, x_max=3.0, x0=1, k2=200, k3=0, k4=0) + angle = Angle(type1="A", type2="B", type3="A", optimize=False) + angle.set_harmonic(t0=1.9, k=100) + angle2 = Angle(type1="B", type2="A", type3="B", optimize=False) + angle2.set_harmonic(t0=2.3, k=100) + msibi.add_force(angle) + msibi.add_force(angle2) + msibi.add_state(stateX) + msibi.add_state(stateY) + msibi.add_force(bond) + init_bond_pot = np.copy(bond.potential) + msibi.run_optimization(n_steps=500, n_iterations=1) + assert not np.array_equal(bond.potential, init_bond_pot) + assert msibi.n_iterations == 1 + ff = msibi._build_force_objects() + assert len(ff) == 2 \ No newline at end of file diff --git a/msibi/tests/test_pair.py b/msibi/tests/test_pair.py deleted file mode 100644 index b1d0d812..00000000 --- a/msibi/tests/test_pair.py +++ /dev/null @@ -1,154 +0,0 @@ -import os - -import numpy as np -import pytest - -from msibi import MSIBI, State, Pair -from msibi.potentials import save_table_potential - -from .base_test import BaseTest - -dr = 0.1 / 6.0 -r = np.arange(0, 2.5 + dr, dr) -r_range = np.asarray([0.0, 2.5 + dr]) -n_bins = 151 -k_B = 1.9872041e-3 # kcal/mol-K -T = 298.0 # K - - -class TestPair(BaseTest): - def test_pair_name(self, pairs): - assert pairs[0].name == "0-0" - - def test_save_table_potential(self, tmp_path): - pair = Pair("0", "1") - pair.set_table_potential(1, 1, 0, 2.5, 100) - pair.potential_file = os.path.join(tmp_path, "pot.txt") - save_table_potential( - pair.potential, - pair.r_range, - pair.dr, - None, - pair.potential_file - ) - assert os.path.isfile(pair.potential_file) - - def test_add_state(self, pairs, state0, rdf0, tmp_path): - opt = MSIBI( - integrator="hoomd.md.integrate.nvt", - integrator_kwargs={"tau": 0.1}, - nlist="hoomd.md.nlist.cell", - dt=0.001, - gsd_period=1000, - n_steps=1e6, - ) - opt.add_state(state0) - opt.add_pair(pairs[3]) - opt.optimize_pairs( - n_iterations=0, - r_switch=None, - smooth_rdfs=False, - _dir=tmp_path, - ) - assert isinstance(pairs[0]._states, dict) - #assert np.array_equal(pairs[3]._states[state0]["target_distribution"], rdf0) - assert pairs[3]._states[state0]["current_distribution"] is None - assert pairs[3]._states[state0]["alpha"] == 0.5 - assert len(pairs[3]._states[state0]["f_fit"]) == 0 - - @pytest.mark.skip(reason="Need better test GSDs before running IBI in tests") - def test_current_rdf_no_smooth(self, state0, pairs, tmp_path): - opt = MSIBI( - integrator="hoomd.md.integrate.nvt", - integrator_kwargs={"tau": 0.1}, - nlist="hoomd.md.nlist.cell", - dt=0.001, - gsd_period=5000, - n_steps=1e4, - ) - opt.add_state(state0) - for pair in pairs: - opt.add_pair(pair) - opt.optimize_pairs( - n_iterations=1, - r_switch=None, - smooth_rdfs=False, - _dir=tmp_path, - ) - pairs[3]._compute_current_rdf(state0) - assert pairs[3]._states[state0]["current_distribution"] is not None - assert len(pairs[3]._states[state0]["f_fit"]) > 0 - - @pytest.mark.skip(reason="Need better test GSDs before running IBI in tests") - def test_current_rdf_smooth(self, state0, pairs, tmp_path): - opt = MSIBI( - integrator="hoomd.md.integrate.nvt", - integrator_kwargs={"tau": 0.1}, - nlist="hoomd.md.nlist.cell", - dt=0.001, - gsd_period=5000, - n_steps=1e4, - ) - opt.add_state(state0) - for pair in pairs: - opt.add_pair(pair) - opt.optimize_pairs( - n_iterations=1, - r_switch=None, - smooth_rdfs=True, - _dir=tmp_path, - ) - pairs[3]._compute_current_rdf(state0) - assert pairs[3]._states[state0]["current_distribution"] is not None - assert len(pairs[3]._states[state0]["f_fit"]) > 0 - - def test_save_current_rdf(self, state0, pairs, tmp_path): - opt = MSIBI( - integrator="hoomd.md.integrate.nvt", - integrator_kwargs={"tau": 0.1}, - nlist="hoomd.md.nlist.cell", - dt=0.001, - gsd_period=1000, - n_steps=1e6, - ) - opt.add_state(state0) - for pair in pairs: - opt.add_pair(pair) - opt.optimize_pairs( - n_iterations=0, - r_switch=None, - smooth_rdfs=True, - _dir=tmp_path, - ) - target_rdf = pairs[0]._states[state0]["target_distribution"] - pairs[0]._states[state0]["current_distribution"] = target_rdf - pairs[0]._save_current_rdf(state0, 0) - assert os.path.isfile( - os.path.join( - state0.dir, f"pair_rdf_{pairs[0].name}-state_{state0.name}-step0.txt" - ) - ) - - def test_update_potential(self, state0, pairs, tmp_path): - """Make sure the potential changes after calculating RDF""" - opt = MSIBI( - integrator="hoomd.md.integrate.nvt", - integrator_kwargs={"tau": 0.1}, - nlist="hoomd.md.nlist.cell", - dt=0.001, - gsd_period=1000, - n_steps=1e6, - ) - opt.add_state(state0) - for pair in pairs: - opt.add_pair(pair) - opt.optimize_pairs( - n_iterations=0, - r_switch=None, - smooth_rdfs=False, - _dir=tmp_path, - ) - target_rdf = pairs[1]._states[state0]["target_distribution"] - pairs[0]._states[state0]["current_distribution"] = target_rdf - pairs[0]._update_potential(smooth=False, smoothing_window=5) - assert not np.array_equal(pairs[0].potential, pairs[0].previous_potential) diff --git a/msibi/tests/test_state.py b/msibi/tests/test_state.py index 8f1cb002..380a4715 100644 --- a/msibi/tests/test_state.py +++ b/msibi/tests/test_state.py @@ -1,13 +1,20 @@ +import os + +import numpy as np import pytest -from msibi.state import State +from msibi import MSIBI, State, Bond, Angle +from .base_test import BaseTest -@pytest.mark.skipif(True, reason="Needs implementing!") -def test_init(): - pass +class TestState(BaseTest): + def test_state_init(self, tmp_path, stateX): + assert stateX.name == "X" + assert stateX.alpha == 1.0 + assert stateX.kT == 1.0 + assert os.path.exists(os.path.join(tmp_path, "states/X_1.0/")) -@pytest.mark.skipif(True, reason="Needs implementing!") -def test_save_runscript(): - pass + def test_n_frames(self, stateX): + stateX.nframes = 50 + assert stateX.nframes == 50 diff --git a/msibi/tests/test_utils.py b/msibi/tests/test_utils.py index 764b10f9..b0938829 100644 --- a/msibi/tests/test_utils.py +++ b/msibi/tests/test_utils.py @@ -12,7 +12,9 @@ def test_calc_similarity(): assert calc_similarity(a, b) == 1.0 b *= -1 assert calc_similarity(a, b) == 0.0 - + arr1 = np.random.random(10) + arr2 = np.random.random(10) + assert calc_similarity(arr1, arr2) == calc_similarity(arr2, arr1) def test_find_nearest(): a = np.arange(10) diff --git a/msibi/tests/test_workers.py b/msibi/tests/test_workers.py deleted file mode 100644 index dbf6e370..00000000 --- a/msibi/tests/test_workers.py +++ /dev/null @@ -1,22 +0,0 @@ -import os -import pytest -from pathlib import Path - -from msibi.utils.exceptions import UnsupportedEngine -from msibi.workers import _post_query, run_query_simulations - -from .base_test import BaseTest - - -class TestWorkers(BaseTest): - def test_post_query(self, state0): - log_file = os.path.join(state0.dir, "log.txt") - err_file = os.path.join(state0.dir, "err.txt") - Path(log_file).touch() - Path(err_file).touch() - - _post_query(state0) - assert state0.traj_file is not None - assert state0.query_traj is not None - assert os.path.isfile(os.path.join(state0.dir, "_.0.log.txt")) - assert os.path.isfile(os.path.join(state0.dir, "_.0.err.txt")) diff --git a/msibi/utils/general.py b/msibi/utils/general.py index dc4014ce..580399cc 100644 --- a/msibi/utils/general.py +++ b/msibi/utils/general.py @@ -1,48 +1,7 @@ -import glob -import os -import shutil - import numpy as np -from pkg_resources import resource_filename -import gc def find_nearest(array, target): """Find array component whose numeric value is closest to 'target'.""" idx = np.abs(array - target).argmin() return idx, array[idx] - - -def _count_backups(filename): - """Count the number of backups of a file in a directory.""" - head, tail = os.path.split(filename) - backup_files = f"_.*.{tail}" - return len(glob.glob(os.path.join(head, backup_files))) - - -def _backup_name(filename, n_backups): - """Return backup filename based on the number of existing backups. - - Parameters - ---------- - filename : str - Full path to file to make backup of. - n_backups : int - Number of existing backups. - """ - head, tail = os.path.split(filename) - new_backup = f"_.{n_backups:d}.{tail}" - return os.path.join(head, new_backup) - - -def backup_file(filename): - """Backup a file based on the number of backups in the file's directory. - - Parameters - ---------- - filename : str - Full path to file to make backup of. - """ - n_backups = _count_backups(filename) - new_backup = _backup_name(filename, n_backups) - shutil.copy(filename, new_backup) diff --git a/setup.py b/setup.py index f634cae3..b6a84c23 100644 --- a/setup.py +++ b/setup.py @@ -8,7 +8,6 @@ from setuptools.command.test import test as TestCommand import sys -requirements = ["numpy", "networkx"] NAME = "msibi" # Load the package's __version__.py module as a dictionary. @@ -36,15 +35,19 @@ def run_tests(self): description=( "A package for optimizing coarse-grained force fields using " + "multistate iterative Boltzmann inversion." - ), + ), url="http://github.com/cmelab/msibi", - author="Christoph Klein, Timothy C. Moore", - author_email=( - "christoph.klein@vanderbilt.edu, timothy.c.moore@vanderbilt.edu" - ), + author="Chris Jones", + author_email=("chrisjones4@u.boisestate.edu"), + packages=find_packages( + exclude=("tests", "docs") + ), + package_data={ + "msibi":[ + "msibi/**" + ] + }, license="MIT", - packages=find_packages(), - install_requires=requirements, zip_safe=False, test_suite="tests", cmdclass={"test": PyTest},