diff --git a/_sources/examples.daisy_chain_mlip_fitting.ipynb b/_sources/examples.daisy_chain_mlip_fitting.ipynb index 6bd46241..6f755f0b 100644 --- a/_sources/examples.daisy_chain_mlip_fitting.ipynb +++ b/_sources/examples.daisy_chain_mlip_fitting.ipynb @@ -1,7 +1,6 @@ { "cells": [ { - "attachments": {}, "cell_type": "markdown", "metadata": {}, "source": [ @@ -22,7 +21,6 @@ ] }, { - "attachments": {}, "cell_type": "markdown", "metadata": {}, "source": [ @@ -88,19 +86,14 @@ { "cell_type": "code", "execution_count": null, - "metadata": { - "nbsphinx": "hidden" - }, + "metadata": {}, "outputs": [], "source": [ "# set random seed, so that MD runs, etc are reproducible and we can check for RMSEs. \n", - "# this cell is hidden from tutorials. \n", - "random_seed = 20230301\n", - "np.random.seed(random_seed)" + "rng = np.random.default_rng(20230301)" ] }, { - "attachments": {}, "cell_type": "markdown", "metadata": {}, "source": [ @@ -127,7 +120,6 @@ ] }, { - "attachments": {}, "cell_type": "markdown", "metadata": {}, "source": [ @@ -157,7 +149,6 @@ ] }, { - "attachments": {}, "cell_type": "markdown", "metadata": {}, "source": [ @@ -196,15 +187,16 @@ "metadata": {}, "outputs": [], "source": [ - "# regenerate smiles_confgis with a random seed set for testing purposes\n", + "# regenerate smiles_configs with a random seed set for testing purposes\n", "# this cell is hidden from docs. \n", "\n", "outputs = OutputSpec(\"1.ch.rdkit.xyz\", overwrite=True)\n", - "smiles_configs = smiles.smiles(all_smiles, outputs=outputs, randomSeed=random_seed)" + "# set seed for smiles generation to a value from our (reproducible) random number generator\n", + "smiles_configs = smiles.smiles(all_smiles, outputs=outputs, randomSeed=int(rng.integers(np.iinfo(np.int32).max,\n", + " dtype=np.int32)))" ] }, { - "attachments": {}, "cell_type": "markdown", "metadata": {}, "source": [ @@ -252,7 +244,7 @@ "# add random seet for testing purposes\n", "# this cell is hidden from tutorials. \n", "\n", - "md_params[\"autopara_rng_seed\"] = random_seed" + "md_params[\"rng\"] = rng" ] }, { @@ -272,7 +264,6 @@ ] }, { - "attachments": {}, "cell_type": "markdown", "metadata": {}, "source": [ @@ -301,7 +292,6 @@ ] }, { - "attachments": {}, "cell_type": "markdown", "metadata": {}, "source": [ @@ -353,7 +343,6 @@ ] }, { - "attachments": {}, "cell_type": "markdown", "metadata": {}, "source": [ @@ -373,7 +362,7 @@ " inputs=md_soap_global,\n", " outputs=outputs,\n", " num=100, # target number of structures to pick\n", - " at_descs_info_key=\"SOAP\")\n", + " at_descs_info_key=\"SOAP\", rng=rng)\n", " \n", "\n", "train_fname = \"6.1.train.xyz\"\n", @@ -402,7 +391,6 @@ ] }, { - "attachments": {}, "cell_type": "markdown", "metadata": {}, "source": [ @@ -482,7 +470,9 @@ "# set to None for github testing purposes\n", "# This cell is hidden from being rendered in the docs. \n", "# remote_info = None\n", - "gap_params[\"rnd_seed\"] = random_seed " + "\n", + "# set seed for gap fitting to a value from our (reproducible) random number generator\n", + "gap_params[\"rnd_seed\"] = rng.integers(2 ** 31) " ] }, { @@ -501,7 +491,6 @@ ] }, { - "attachments": {}, "cell_type": "markdown", "metadata": {}, "source": [ @@ -528,11 +517,14 @@ " num_cores = 2,\n", " partitions = \"standard\")\n", "\n", + "# note - set OMP_NUM_THREADS to prevent GAP evaluation from using OpenMP, \n", + "# as it clashes with multiprocessing.pool, which wfl uses\n", "remote_info = RemoteInfo(\n", " sys_name = \"github\",\n", " job_name = \"gap-eval\",\n", " resources = resources,\n", " check_interval = 10, \n", + " env_vars = [\"OMP_NUM_THREADS=1\"],\n", " input_files = [\"gap.xml*\"])\n", "\n", "gap_calc_autopara_info = AutoparaInfo(\n", @@ -549,7 +541,6 @@ ] }, { - "attachments": {}, "cell_type": "markdown", "metadata": {}, "source": [ @@ -629,13 +620,13 @@ "\n", "ref_errors = {\n", " 'atomization_energy/atom': {\n", - " 'train': {'RMSE': 0.01784008096943666, 'MAE': 0.014956982529185385, 'count': 50}, \n", - " '_ALL_': {'RMSE': 0.01810274269833562, 'MAE': 0.015205129586306461, 'count': 100}, \n", - " 'test': {'RMSE': 0.018361647458989924, 'MAE': 0.015453276643427535, 'count': 50}}, \n", + " 'train': {'RMSE': 0.026086070005729697, 'MAE': 0.02188233965637977, 'count': 50},\n", + " '_ALL_': {'RMSE': 0.02631013293566519, 'MAE': 0.02217457525203221, 'count': 100},\n", + " 'test': {'RMSE': 0.026532303741682858, 'MAE': 0.02246681084768465, 'count': 50}},\n", " 'forces/comp': {\n", - " 'train': {'RMSE': 0.6064186755127647, 'MAE': 0.440771517768513, 'count': 5037}, \n", - " '_ALL_': {'RMSE': 0.6150461768441347, 'MAE': 0.44579797424459006, 'count': 10074}, \n", - " 'test': {'RMSE': 0.6235543194385854, 'MAE': 0.450824430720667, 'count': 5037}}\n", + " 'train': {'RMSE': 0.6700484048236104, 'MAE': 0.48912067870708253, 'count': 5097},\n", + " '_ALL_': {'RMSE': 0.674843619212047, 'MAE': 0.49305958821652923, 'count': 10188},\n", + " 'test': {'RMSE': 0.6796105918104188, 'MAE': 0.49700313992928696, 'count': 5091}}\n", "}\n", "\n", "print(errors)\n", @@ -659,7 +650,7 @@ ], "metadata": { "kernelspec": { - "display_name": "dev", + "display_name": "Python 3 (ipykernel)", "language": "python", "name": "python3" }, @@ -673,9 +664,8 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.8.13" + "version": "3.9.16" }, - "orig_nbformat": 4, "vscode": { "interpreter": { "hash": "793ab331f77558158f2e16fabf356357fde3f61b8f3bb6d95e9b59dbfcb88650" diff --git a/_sources/examples.select_fps.ipynb b/_sources/examples.select_fps.ipynb index e445ec04..c138880c 100644 --- a/_sources/examples.select_fps.ipynb +++ b/_sources/examples.select_fps.ipynb @@ -29,8 +29,10 @@ "metadata": {}, "outputs": [], "source": [ - "import wfl, pathlib\n", + "import numpy as np\n", "import yaml\n", + "import pathlib\n", + "import wfl\n", "from wfl.configset import ConfigSet, OutputSpec\n", "from wfl.descriptors.quippy import calculate as calc_descriptors\n", "from wfl.select.by_descriptor import greedy_fps_conf_global\n", @@ -53,7 +55,7 @@ "# Step 2: Sampling\n", "fps_out = OutputSpec(files=work_dir/\"out_fps.xyz\")\n", "nsamples = 8\n", - "selected_configs = greedy_fps_conf_global(inputs=md_desc, outputs=fps_out, num=nsamples, at_descs_info_key='desc', keep_descriptor_info=False)" + "selected_configs = greedy_fps_conf_global(inputs=md_desc, outputs=fps_out, num=nsamples, at_descs_info_key='desc', keep_descriptor_info=False, rng=np.random.default_rng())" ] }, { diff --git a/_sources/wfl.utils.rst b/_sources/wfl.utils.rst index 2342bfd7..606a0293 100644 --- a/_sources/wfl.utils.rst +++ b/_sources/wfl.utils.rst @@ -132,14 +132,6 @@ wfl.utils.round\_sig\_figs module :undoc-members: :show-inheritance: -wfl.utils.vector\_utils module ------------------------------- - -.. automodule:: wfl.utils.vector_utils - :members: - :undoc-members: - :show-inheritance: - wfl.utils.version module ------------------------ diff --git a/command_line.automatic_docs.html b/command_line.automatic_docs.html index 46b2e895..ebba5d95 100644 --- a/command_line.automatic_docs.html +++ b/command_line.automatic_docs.html @@ -892,7 +892,7 @@

cur
--stochastic-seed <stochastic_seed>#
-

seed for np.random.seed() in stochastic CUR.

+

seed for np.random.default_rng() in stochastic CUR.

diff --git a/examples.daisy_chain_mlip_fitting.html b/examples.daisy_chain_mlip_fitting.html index 1cdfdf00..c0b5bc4f 100644 --- a/examples.daisy_chain_mlip_fitting.html +++ b/examples.daisy_chain_mlip_fitting.html @@ -470,6 +470,15 @@

Imports +
 
+
+
+
# set random seed, so that MD runs, etc are reproducible and we can check for RMSEs.
+rng = np.random.default_rng(20230301)
+
+
+

Reference calculator#

@@ -540,11 +549,13 @@

Generate initial structures

-
# regenerate smiles_confgis with a random seed set for testing purposes
+
# regenerate smiles_configs with a random seed set for testing purposes
 # this cell is hidden from docs.
 
 outputs = OutputSpec("1.ch.rdkit.xyz", overwrite=True)
-smiles_configs = smiles.smiles(all_smiles, outputs=outputs, randomSeed=random_seed)
+# set seed for smiles generation to a value from our (reproducible) random number generator
+smiles_configs = smiles.smiles(all_smiles, outputs=outputs, randomSeed=int(rng.integers(np.iinfo(np.int32).max,
+                                                                                        dtype=np.int32)))
@@ -675,7 +686,7 @@

Sub-select with CURinputs=md_soap_global, outputs=outputs, num=100, # target number of structures to pick - at_descs_info_key="SOAP") + at_descs_info_key="SOAP", rng=rng) train_fname = "6.1.train.xyz" @@ -801,11 +812,14 @@

Evaluate structures with GAPnum_cores = 2, partitions = "standard") +# note - set OMP_NUM_THREADS to prevent GAP evaluation from using OpenMP, +# as it clashes with multiprocessing.pool, which wfl uses remote_info = RemoteInfo( sys_name = "github", job_name = "gap-eval", resources = resources, check_interval = 10, + env_vars = ["OMP_NUM_THREADS=1"], input_files = ["gap.xml*"]) gap_calc_autopara_info = AutoparaInfo( diff --git a/examples.daisy_chain_mlip_fitting.ipynb b/examples.daisy_chain_mlip_fitting.ipynb index 0b245a95..6f755f0b 100644 --- a/examples.daisy_chain_mlip_fitting.ipynb +++ b/examples.daisy_chain_mlip_fitting.ipynb @@ -1,7 +1,6 @@ { "cells": [ { - "attachments": {}, "cell_type": "markdown", "metadata": {}, "source": [ @@ -22,7 +21,6 @@ ] }, { - "attachments": {}, "cell_type": "markdown", "metadata": {}, "source": [ @@ -88,19 +86,14 @@ { "cell_type": "code", "execution_count": null, - "metadata": { - "nbsphinx": "hidden" - }, + "metadata": {}, "outputs": [], "source": [ "# set random seed, so that MD runs, etc are reproducible and we can check for RMSEs. \n", - "# this cell is hidden from tutorials. \n", - "random_seed = 20230301\n", - "np.random.seed(random_seed)" + "rng = np.random.default_rng(20230301)" ] }, { - "attachments": {}, "cell_type": "markdown", "metadata": {}, "source": [ @@ -127,7 +120,6 @@ ] }, { - "attachments": {}, "cell_type": "markdown", "metadata": {}, "source": [ @@ -157,7 +149,6 @@ ] }, { - "attachments": {}, "cell_type": "markdown", "metadata": {}, "source": [ @@ -196,15 +187,16 @@ "metadata": {}, "outputs": [], "source": [ - "# regenerate smiles_confgis with a random seed set for testing purposes\n", + "# regenerate smiles_configs with a random seed set for testing purposes\n", "# this cell is hidden from docs. \n", "\n", "outputs = OutputSpec(\"1.ch.rdkit.xyz\", overwrite=True)\n", - "smiles_configs = smiles.smiles(all_smiles, outputs=outputs, randomSeed=random_seed)" + "# set seed for smiles generation to a value from our (reproducible) random number generator\n", + "smiles_configs = smiles.smiles(all_smiles, outputs=outputs, randomSeed=int(rng.integers(np.iinfo(np.int32).max,\n", + " dtype=np.int32)))" ] }, { - "attachments": {}, "cell_type": "markdown", "metadata": {}, "source": [ @@ -252,7 +244,7 @@ "# add random seet for testing purposes\n", "# this cell is hidden from tutorials. \n", "\n", - "md_params[\"autopara_rng_seed\"] = random_seed" + "md_params[\"rng\"] = rng" ] }, { @@ -272,7 +264,6 @@ ] }, { - "attachments": {}, "cell_type": "markdown", "metadata": {}, "source": [ @@ -301,7 +292,6 @@ ] }, { - "attachments": {}, "cell_type": "markdown", "metadata": {}, "source": [ @@ -353,7 +343,6 @@ ] }, { - "attachments": {}, "cell_type": "markdown", "metadata": {}, "source": [ @@ -373,7 +362,7 @@ " inputs=md_soap_global,\n", " outputs=outputs,\n", " num=100, # target number of structures to pick\n", - " at_descs_info_key=\"SOAP\")\n", + " at_descs_info_key=\"SOAP\", rng=rng)\n", " \n", "\n", "train_fname = \"6.1.train.xyz\"\n", @@ -402,7 +391,6 @@ ] }, { - "attachments": {}, "cell_type": "markdown", "metadata": {}, "source": [ @@ -482,7 +470,9 @@ "# set to None for github testing purposes\n", "# This cell is hidden from being rendered in the docs. \n", "# remote_info = None\n", - "gap_params[\"rnd_seed\"] = random_seed " + "\n", + "# set seed for gap fitting to a value from our (reproducible) random number generator\n", + "gap_params[\"rnd_seed\"] = rng.integers(2 ** 31) " ] }, { @@ -501,7 +491,6 @@ ] }, { - "attachments": {}, "cell_type": "markdown", "metadata": {}, "source": [ @@ -528,11 +517,14 @@ " num_cores = 2,\n", " partitions = \"standard\")\n", "\n", + "# note - set OMP_NUM_THREADS to prevent GAP evaluation from using OpenMP, \n", + "# as it clashes with multiprocessing.pool, which wfl uses\n", "remote_info = RemoteInfo(\n", " sys_name = \"github\",\n", " job_name = \"gap-eval\",\n", " resources = resources,\n", " check_interval = 10, \n", + " env_vars = [\"OMP_NUM_THREADS=1\"],\n", " input_files = [\"gap.xml*\"])\n", "\n", "gap_calc_autopara_info = AutoparaInfo(\n", @@ -549,7 +541,6 @@ ] }, { - "attachments": {}, "cell_type": "markdown", "metadata": {}, "source": [ @@ -629,13 +620,13 @@ "\n", "ref_errors = {\n", " 'atomization_energy/atom': {\n", - " 'train': {'RMSE': 0.01784008096943666, 'MAE': 0.014956982529185385, 'count': 50}, \n", - " '_ALL_': {'RMSE': 0.01810274269833562, 'MAE': 0.015205129586306461, 'count': 100}, \n", - " 'test': {'RMSE': 0.018361647458989924, 'MAE': 0.015453276643427535, 'count': 50}}, \n", + " 'train': {'RMSE': 0.026086070005729697, 'MAE': 0.02188233965637977, 'count': 50},\n", + " '_ALL_': {'RMSE': 0.02631013293566519, 'MAE': 0.02217457525203221, 'count': 100},\n", + " 'test': {'RMSE': 0.026532303741682858, 'MAE': 0.02246681084768465, 'count': 50}},\n", " 'forces/comp': {\n", - " 'train': {'RMSE': 0.6064186755127647, 'MAE': 0.440771517768513, 'count': 5037}, \n", - " '_ALL_': {'RMSE': 0.6150461768441347, 'MAE': 0.44579797424459006, 'count': 10074}, \n", - " 'test': {'RMSE': 0.6235543194385854, 'MAE': 0.450824430720667, 'count': 5037}}\n", + " 'train': {'RMSE': 0.6700484048236104, 'MAE': 0.48912067870708253, 'count': 5097},\n", + " '_ALL_': {'RMSE': 0.674843619212047, 'MAE': 0.49305958821652923, 'count': 10188},\n", + " 'test': {'RMSE': 0.6796105918104188, 'MAE': 0.49700313992928696, 'count': 5091}}\n", "}\n", "\n", "print(errors)\n", @@ -659,7 +650,7 @@ ], "metadata": { "kernelspec": { - "display_name": "dev", + "display_name": "Python 3 (ipykernel)", "language": "python", "name": "python3" }, @@ -673,7 +664,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.8.13" + "version": "3.9.16" }, "vscode": { "interpreter": { diff --git a/examples.select_fps.html b/examples.select_fps.html index beb783d9..f0b83781 100644 --- a/examples.select_fps.html +++ b/examples.select_fps.html @@ -391,8 +391,10 @@

Selection or Sampling of Structures

-
import wfl, pathlib
+
import numpy as np
 import yaml
+import pathlib
+import wfl
 from wfl.configset import ConfigSet, OutputSpec
 from wfl.descriptors.quippy import calculate as calc_descriptors
 from wfl.select.by_descriptor import greedy_fps_conf_global
@@ -415,7 +417,7 @@ 
Selection or Sampling of Structures# Step 2: Sampling
 fps_out          = OutputSpec(files=work_dir/"out_fps.xyz")
 nsamples         = 8
-selected_configs = greedy_fps_conf_global(inputs=md_desc, outputs=fps_out, num=nsamples, at_descs_info_key='desc', keep_descriptor_info=False)
+selected_configs = greedy_fps_conf_global(inputs=md_desc, outputs=fps_out, num=nsamples, at_descs_info_key='desc', keep_descriptor_info=False, rng=np.random.default_rng())
diff --git a/examples.select_fps.ipynb b/examples.select_fps.ipynb index e445ec04..c138880c 100644 --- a/examples.select_fps.ipynb +++ b/examples.select_fps.ipynb @@ -29,8 +29,10 @@ "metadata": {}, "outputs": [], "source": [ - "import wfl, pathlib\n", + "import numpy as np\n", "import yaml\n", + "import pathlib\n", + "import wfl\n", "from wfl.configset import ConfigSet, OutputSpec\n", "from wfl.descriptors.quippy import calculate as calc_descriptors\n", "from wfl.select.by_descriptor import greedy_fps_conf_global\n", @@ -53,7 +55,7 @@ "# Step 2: Sampling\n", "fps_out = OutputSpec(files=work_dir/\"out_fps.xyz\")\n", "nsamples = 8\n", - "selected_configs = greedy_fps_conf_global(inputs=md_desc, outputs=fps_out, num=nsamples, at_descs_info_key='desc', keep_descriptor_info=False)" + "selected_configs = greedy_fps_conf_global(inputs=md_desc, outputs=fps_out, num=nsamples, at_descs_info_key='desc', keep_descriptor_info=False, rng=np.random.default_rng())" ] }, { diff --git a/genindex.html b/genindex.html index 421a1b94..56b2f20b 100644 --- a/genindex.html +++ b/genindex.html @@ -1071,16 +1071,14 @@

G

  • get() (wfl.utils.params.Params method)
  • get_default_multiplicity() (wfl.calculators.orca.ORCA static method) -
    • -
  • get_homo() (wfl.calculators.orca.basinhopping.BasinHoppingORCA method)
    • @@ -1349,8 +1349,6 @@

    M

  • wfl.utils.replace_eval_in_strs
  • wfl.utils.round_sig_figs -
    • -
  • wfl.utils.vector_utils
  • wfl.utils.version
    • @@ -1451,8 +1449,6 @@

    P

    R

    + - - - -
    +
    • wfl.calculators.orca.basinhopping @@ -1972,8 +1970,6 @@

      W

    • module
    -     		    wfl.utils.round_sig_figs
        - wfl.utils.vector_utils -
        diff --git a/searchindex.js b/searchindex.js index f2e8fcea..3d6e09e7 100644 --- a/searchindex.js +++ b/searchindex.js @@ -1 +1 @@ -Search.setIndex({"docnames": ["attic/command_line", "attic/operations.utils", "command_line.automatic_docs", "examples", "examples.buildcell", "examples.contributions", "examples.daisy_chain_mlip_fitting", "examples.dimers", "examples.fhiaims_calculator", "examples.index", "examples.mace", "examples.md", "examples.mlip_fitting", "examples.normal_modes", "examples.orca_python", "examples.select_fps", "examples.smiles", "first_example", "index", "modules", "operations", "operations.ace_fitting", "operations.calculators", "operations.descriptors", "operations.fitting", "operations.gap_fitting", "operations.generate", "operations.multistage_gap_fitting", "operations.select", "overview", "overview.configset", "overview.overall_design", "overview.parallelisation", "overview.queued", "wfl", "wfl.autoparallelize", "wfl.calculators", "wfl.calculators.orca", "wfl.cli", "wfl.cli.commands", "wfl.descriptors", "wfl.fit", "wfl.fit.gap", "wfl.fit.modify_database", "wfl.generate", "wfl.generate.md_PROTECT", "wfl.select", "wfl.utils", "workflows.rss"], "filenames": ["attic/command_line.rst", "attic/operations.utils.md", "command_line.automatic_docs.rst", "examples.rst", "examples.buildcell.ipynb", "examples.contributions.md", "examples.daisy_chain_mlip_fitting.ipynb", "examples.dimers.ipynb", "examples.fhiaims_calculator.ipynb", "examples.index.md", "examples.mace.md", "examples.md.md", "examples.mlip_fitting.md", "examples.normal_modes.md", "examples.orca_python.md", "examples.select_fps.ipynb", "examples.smiles.md", "first_example.md", "index.rst", "modules.rst", "operations.rst", "operations.ace_fitting.md", "operations.calculators.md", "operations.descriptors.md", "operations.fitting.rst", "operations.gap_fitting.md", "operations.generate.md", "operations.multistage_gap_fitting.rst", "operations.select.md", "overview.rst", "overview.configset.rst", "overview.overall_design.rst", "overview.parallelisation.rst", "overview.queued.md", "wfl.rst", "wfl.autoparallelize.rst", "wfl.calculators.rst", "wfl.calculators.orca.rst", "wfl.cli.rst", "wfl.cli.commands.rst", "wfl.descriptors.rst", "wfl.fit.rst", "wfl.fit.gap.rst", "wfl.fit.modify_database.rst", "wfl.generate.rst", "wfl.generate.md_PROTECT.rst", "wfl.select.rst", "wfl.utils.rst", "workflows.rss.rst"], "titles": ["Command line interface", "Utility functions", "wfl", "Examples", "Random Structures via buildcell", "Contributing Examples", "GAP fit workflow with many wfl use-case examples", "Generating Dimer Structures", "FHI-Aims Calculator", "Index", "Parallelize MACE calculator", "Molecular Dynamics", "Iterative GAP fitting", "Normal Modes of molecules", "ORCA via Python script", "Selection or Sampling of Structures", "SMILES to Atoms", "First Example", "Welcome to Workflow\u2019s documentation!", "wfl", "Operations", "Fitting ACE", "Calculators in Workflow", "Descriptors", "Fitting potentials", "Fitting GAP", "Generating Atomic Structures", "Multistage GAP fitting", "Selecting Configs", "Overview", "Input and output of atomic structures", "Overall design", "Automatic parallelization of tasks", "Functions as independently queued jobs", "wfl package", "wfl.autoparallelize package", "wfl.calculators package", "wfl.calculators.orca package", "wfl.cli package", "wfl.cli.commands package", "wfl.descriptors package", "wfl.fit package", "wfl.fit.gap package", "wfl.fit.modify_database package", "wfl.generate package", "wfl.generate.md package", "wfl.select package", "wfl.utils package", "How to do GAP-RSS"], "terms": {"descript": [0, 5, 18], "all": [0, 2, 5, 6, 7, 8, 9, 12, 13, 14, 15, 17, 18, 22, 26, 27, 28, 30, 32, 33, 34, 35, 36, 37, 40, 41, 42, 44, 45, 47, 48], "cli": [0, 19, 34, 47, 48], "tool": [0, 33, 47], "automat": [0, 15, 17, 18, 21, 29, 33, 34, 36, 40, 41, 44, 45, 46, 48], "gener": [0, 3, 4, 8, 10, 11, 14, 15, 16, 17, 18, 19, 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"nbsphinx": 4, "sphinx": 57}, "alltitles": {"Command line interface": [[0, "command-line-interface"]], "Calculators": [[0, "calculators"]], "ORCA (outdated)": [[0, "orca-outdated"]], "CASTEP": [[0, "castep"]], "VASP": [[0, "vasp"]], "Utility functions": [[1, "utility-functions"]], "Find Voids": [[1, "find-voids"]], "e0 from GAP XML": [[1, "e0-from-gap-xml"]], "wfl": [[2, "wfl"], [19, "wfl"]], "descriptor": [[2, "wfl-descriptor"]], "quippy": [[2, "wfl-descriptor-quippy"]], "error": [[2, "wfl-error"]], "eval": [[2, "wfl-eval"]], "ace": [[2, "wfl-eval-ace"]], "atomization-energy": [[2, "wfl-eval-atomization-energy"]], "gap": [[2, "wfl-eval-gap"]], "mace": [[2, "wfl-eval-mace"]], "generate": [[2, "wfl-generate"]], "buildcell": [[2, "wfl-generate-buildcell"]], "smiles": [[2, "wfl-generate-smiles"]], "select": [[2, "wfl-select"]], "cur": [[2, "wfl-select-cur"]], "lambda": [[2, "wfl-select-lambda"]], "Examples": [[3, "examples"]], "Contents:": [[3, null], [20, null], [24, null]], "Random Structures via buildcell": [[4, "Random-Structures-via-buildcell"]], "Contributing Examples": [[5, "contributing-examples"]], "Preparing the Example": [[5, "preparing-the-example"]], "Hiding Tests in the Online Documentation": [[5, "hiding-tests-in-the-online-documentation"]], "Updating Related Files": [[5, "updating-related-files"]], "GAP fit workflow with many wfl use-case examples": [[6, "GAP-fit-workflow-with-many-wfl-use-case-examples"]], "Imports": [[6, "Imports"]], "Reference calculator": [[6, "Reference-calculator"]], "Prepare isolated atoms": [[6, "Prepare-isolated-atoms"]], "Generate initial structures": [[6, "Generate-initial-structures"]], "Run Molecular Dynamics simulation": [[6, "Run-Molecular-Dynamics-simulation"]], "Filter structures": [[6, "Filter-structures"]], "Calculate SOAP descriptor": [[6, "Calculate-SOAP-descriptor"]], "Sub-select with CUR": [[6, "Sub-select-with-CUR"]], "Fit GAP": [[6, "Fit-GAP"]], "Evaluate structures with GAP": [[6, "Evaluate-structures-with-GAP"]], "Evaluate error & plot correlation": [[6, "Evaluate-error-&-plot-correlation"]], "Generating Dimer Structures": [[7, "Generating-Dimer-Structures"]], "FHI-Aims Calculator": [[8, "FHI-Aims-Calculator"]], "Index": [[9, "index"]], "Evaluate structures with a calculator": [[9, "evaluate-structures-with-a-calculator"]], "Generate structures": [[9, "generate-structures"]], "Run MD": [[9, "run-md"]], "Remote execution": [[9, "remote-execution"]], "Get descriptors": [[9, "get-descriptors"]], "Sampling structures": [[9, "sampling-structures"]], "Fit a potential": [[9, "fit-a-potential"]], "Iterative training": [[9, "iterative-training"]], "Command line": [[9, "command-line"], [16, "command-line"]], "Miscellaneous": [[9, "miscellaneous"]], "Parallelize MACE calculator": [[10, "parallelize-mace-calculator"]], "Complete example": [[10, "complete-example"]], "Molecular Dynamics": [[11, "molecular-dynamics"], [26, "molecular-dynamics"]], "Iterative GAP fitting": [[12, "iterative-gap-fitting"]], "Table of contents": [[12, "table-of-contents"]], "General workflow and setup": [[12, "general-workflow-and-setup"]], "Getting started: Parallelization and Imports": [[12, "getting-started-parallelization-and-imports"]], "Fitting the initial GAP": [[12, "fitting-the-initial-gap"]], "Preparing the iterative process": [[12, "preparing-the-iterative-process"]], "The Iterative Process": [[12, "the-iterative-process"]], "Keeping track of training and test errors": [[12, "keeping-track-of-training-and-test-errors"]], "Normal Modes of molecules": [[13, "normal-modes-of-molecules"]], "Generate": [[13, "generate"]], "Visualize": [[13, "visualize"]], "Sample": [[13, "sample"]], "ORCA via Python script": [[14, "orca-via-python-script"]], "Selection or Sampling of Structures": [[15, "Selection-or-Sampling-of-Structures"]], "SMILES to Atoms": [[16, "smiles-to-atoms"], [26, "smiles-to-atoms"]], "Python script": [[16, "python-script"]], "First Example": [[17, "first-example"]], "Complete script": [[17, "complete-script"], [17, "id2"]], "With remote execution": [[17, "with-remote-execution"]], "Welcome to Workflow\u2019s documentation!": [[18, "welcome-to-workflow-s-documentation"]], "Installation": [[18, "installation"]], "Repository": [[18, "repository"]], "Contents": [[18, "contents"]], "Operations": [[20, "operations"]], "Fitting ACE": [[21, "fitting-ace"]], "Calculators in Workflow": [[22, "calculators-in-workflow"]], "Parallelize with generic.calculate()": [[22, "parallelize-with-generic-calculate"]], "File-based calculators": [[22, "file-based-calculators"]], "Special calculators": [[22, "special-calculators"]], "Descriptors": [[23, "descriptors"]], "Fitting potentials": [[24, "fitting-potentials"]], "Fitting GAP": [[25, "fitting-gap"]], "Generating Atomic Structures": [[26, "generating-atomic-structures"]], "Atoms and Dimers": [[26, "atoms-and-dimers"]], "BuildCell": [[26, "buildcell"]], "Super Cells": [[26, "super-cells"]], 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"overall-design"]], "Automatic parallelization of tasks": [[32, "automatic-parallelization-of-tasks"]], "Programming script that use parallelized operations": [[32, "programming-script-that-use-parallelized-operations"]], "MPI with WFL_MPIPOOL": [[32, "mpi-with-wfl-mpipool"]], "Runtime control over parallelization": [[32, "runtime-control-over-parallelization"]], "Single node using python subprocesses": [[32, "single-node-using-python-subprocesses"]], "Multiple nodes using MPI": [[32, "multiple-nodes-using-mpi"]], "Creating auto-parallelized functions": [[32, "creating-auto-parallelized-functions"]], "Functions as independently queued jobs": [[33, "functions-as-independently-queued-jobs"]], "Example": [[33, "example"]], "Restarts": [[33, "restarts"]], "WFL_EXPYRE_INFO syntax": [[33, "wfl-expyre-info-syntax"]], "Keys": [[33, "keys"]], "Values": [[33, "values"]], "Dividing items into and parallelising within jobs": [[33, "dividing-items-into-and-parallelising-within-jobs"]], "Testing": 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"wfl.generate.normal_modes.generate_normal_modes_parallel_hessian"]], "interstitial() (in module wfl.generate.supercells)": [[44, "wfl.generate.supercells.interstitial"]], "isolated_atom_from_e0() (in module wfl.generate.atoms_and_dimers)": [[44, "wfl.generate.atoms_and_dimers.isolated_atom_from_e0"]], "largest_bulk() (in module wfl.generate.supercells)": [[44, "wfl.generate.supercells.largest_bulk"]], "minimahopping() (in module wfl.generate.minimahopping)": [[44, "wfl.generate.minimahopping.minimahopping"]], "modes_to_evecs() (wfl.generate.normal_modes.normalmodes static method)": [[44, "wfl.generate.normal_modes.NormalModes.modes_to_evecs"]], "num_hess_delta (wfl.generate.normal_modes.normalmodes attribute)": [[44, "wfl.generate.normal_modes.NormalModes.num_hess_delta"]], "phonopy() (in module wfl.generate.phonopy)": [[44, "wfl.generate.phonopy.phonopy"]], "prepare() (in module wfl.generate.atoms_and_dimers)": [[44, "wfl.generate.atoms_and_dimers.prepare"]], "sample_normal_modes() 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"module-wfl.generate.buildcell"]], "wfl.generate.minimahopping": [[44, "module-wfl.generate.minimahopping"]], "wfl.generate.normal_modes": [[44, "module-wfl.generate.normal_modes"]], "wfl.generate.phonopy": [[44, "module-wfl.generate.phonopy"]], "wfl.generate.smiles": [[44, "module-wfl.generate.smiles"]], "wfl.generate.supercells": [[44, "module-wfl.generate.supercells"]], "wfl.generate.utils": [[44, "module-wfl.generate.utils"]], "abortoncollision (class in wfl.generate.md.abort)": [[45, "wfl.generate.md.abort.AbortOnCollision"]], "abortsimbase (class in wfl.generate.md.abort_base)": [[45, "wfl.generate.md.abort_base.AbortSimBase"]], "atoms_ok() (wfl.generate.md.abort.abortoncollision method)": [[45, "wfl.generate.md.abort.AbortOnCollision.atoms_ok"]], "atoms_ok() (wfl.generate.md.abort_base.abortsimbase method)": [[45, "wfl.generate.md.abort_base.AbortSimBase.atoms_ok"]], "md() (in module wfl.generate.md)": [[45, "wfl.generate.md.md"]], "stop() 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"wfl.select.by_descriptor.do_svd"]], "greedy_fps_conf_global() (in module wfl.select.by_descriptor)": [[46, "wfl.select.by_descriptor.greedy_fps_conf_global"]], "minima_among_neighbors() (in module wfl.select.selection_space)": [[46, "wfl.select.selection_space.minima_among_neighbors"]], "prep_descs_and_exclude() (in module wfl.select.by_descriptor)": [[46, "wfl.select.by_descriptor.prep_descs_and_exclude"]], "select() (in module wfl.select.convex_hull)": [[46, "wfl.select.convex_hull.select"]], "val_relative_to_nearby_composition_volume_min() (in module wfl.select.selection_space)": [[46, "wfl.select.selection_space.val_relative_to_nearby_composition_volume_min"]], "wfl.select": [[46, "module-wfl.select"]], "wfl.select.by_descriptor": [[46, "module-wfl.select.by_descriptor"]], "wfl.select.convex_hull": [[46, "module-wfl.select.convex_hull"]], "wfl.select.flat_histogram": [[46, "module-wfl.select.flat_histogram"]], "wfl.select.selection_space": [[46, 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"clean_dir() (in module wfl.utils.file_utils)": [[47, "wfl.utils.file_utils.clean_dir"]], "composition_space_zs() (in module wfl.utils.vol_composition_space)": [[47, "wfl.utils.vol_composition_space.composition_space_Zs"]], "composition_space_coord() (in module wfl.utils.vol_composition_space)": [[47, "wfl.utils.vol_composition_space.composition_space_coord"]], "construct_calculator_picklesafe() (in module wfl.utils.parallel)": [[47, "wfl.utils.parallel.construct_calculator_picklesafe"]], "cur_iter (wfl.utils.params.params property)": [[47, "wfl.utils.params.Params.cur_iter"]], "dft_code (wfl.utils.params.params property)": [[47, "wfl.utils.params.Params.dft_code"]], "dft_params (wfl.utils.params.params property)": [[47, "wfl.utils.params.Params.dft_params"]], "dict_to_quip_str() (in module wfl.utils.quip_cli_strings)": [[47, "wfl.utils.quip_cli_strings.dict_to_quip_str"]], "dict_tuple_keys_to_str() (in module wfl.utils.misc)": [[47, "wfl.utils.misc.dict_tuple_keys_to_str"]], "extract_e0() (in module wfl.utils.gap_xml_tools)": [[47, "wfl.utils.gap_xml_tools.extract_e0"]], "find_hull() (in module wfl.utils.convex_hull)": [[47, "wfl.utils.convex_hull.find_hull"]], "find_isolated_atoms() (in module wfl.utils.configs)": [[47, "wfl.utils.configs.find_isolated_atoms"]], "find_voids() (in module wfl.utils.find_voids)": [[47, "wfl.utils.find_voids.find_voids"]], "get() (wfl.utils.params.params method)": [[47, "wfl.utils.params.Params.get"]], "get_wfl_version() (in module wfl.utils.version)": [[47, "wfl.utils.version.get_wfl_version"]], "implemented_calculators (wfl.utils.params.params attribute)": [[47, "wfl.utils.params.Params.implemented_calculators"]], "increment_active_iter() (in module wfl.utils.logging)": [[47, "wfl.utils.logging.increment_active_iter"]], "julia_exec_path() (in module wfl.utils.julia)": [[47, "wfl.utils.julia.julia_exec_path"]], "print_log() (in module wfl.utils.logging)": [[47, "wfl.utils.logging.print_log"]], "process_active_iter() (in 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+Search.setIndex({"docnames": ["attic/command_line", "attic/operations.utils", "command_line.automatic_docs", "examples", "examples.buildcell", "examples.contributions", "examples.daisy_chain_mlip_fitting", "examples.dimers", "examples.fhiaims_calculator", "examples.index", "examples.mace", "examples.md", "examples.mlip_fitting", "examples.normal_modes", "examples.orca_python", "examples.select_fps", "examples.smiles", "first_example", "index", "modules", "operations", "operations.ace_fitting", "operations.calculators", "operations.descriptors", "operations.fitting", "operations.gap_fitting", "operations.generate", "operations.multistage_gap_fitting", "operations.select", "overview", "overview.configset", "overview.overall_design", "overview.parallelisation", "overview.queued", "wfl", "wfl.autoparallelize", "wfl.calculators", "wfl.calculators.orca", "wfl.cli", "wfl.cli.commands", "wfl.descriptors", "wfl.fit", "wfl.fit.gap", "wfl.fit.modify_database", "wfl.generate", "wfl.generate.md_PROTECT", "wfl.select", "wfl.utils", "workflows.rss"], "filenames": ["attic/command_line.rst", "attic/operations.utils.md", "command_line.automatic_docs.rst", "examples.rst", "examples.buildcell.ipynb", "examples.contributions.md", "examples.daisy_chain_mlip_fitting.ipynb", "examples.dimers.ipynb", "examples.fhiaims_calculator.ipynb", "examples.index.md", "examples.mace.md", "examples.md.md", "examples.mlip_fitting.md", "examples.normal_modes.md", "examples.orca_python.md", "examples.select_fps.ipynb", "examples.smiles.md", "first_example.md", "index.rst", "modules.rst", "operations.rst", "operations.ace_fitting.md", "operations.calculators.md", "operations.descriptors.md", "operations.fitting.rst", "operations.gap_fitting.md", "operations.generate.md", "operations.multistage_gap_fitting.rst", "operations.select.md", "overview.rst", "overview.configset.rst", "overview.overall_design.rst", "overview.parallelisation.rst", "overview.queued.md", "wfl.rst", "wfl.autoparallelize.rst", "wfl.calculators.rst", "wfl.calculators.orca.rst", "wfl.cli.rst", "wfl.cli.commands.rst", "wfl.descriptors.rst", "wfl.fit.rst", "wfl.fit.gap.rst", "wfl.fit.modify_database.rst", "wfl.generate.rst", "wfl.generate.md_PROTECT.rst", "wfl.select.rst", "wfl.utils.rst", "workflows.rss.rst"], "titles": ["Command line interface", "Utility functions", "wfl", "Examples", "Random Structures via buildcell", "Contributing Examples", "GAP fit workflow with many wfl use-case examples", "Generating Dimer Structures", "FHI-Aims Calculator", "Index", "Parallelize MACE calculator", "Molecular Dynamics", "Iterative GAP fitting", "Normal Modes of molecules", "ORCA via Python script", "Selection or Sampling of Structures", "SMILES to Atoms", "First Example", "Welcome to Workflow\u2019s documentation!", "wfl", "Operations", "Fitting ACE", "Calculators in Workflow", "Descriptors", "Fitting potentials", "Fitting GAP", "Generating Atomic Structures", "Multistage GAP fitting", "Selecting Configs", "Overview", "Input and output of atomic structures", "Overall design", "Automatic parallelization of tasks", "Functions as independently queued jobs", "wfl package", "wfl.autoparallelize package", "wfl.calculators package", "wfl.calculators.orca package", "wfl.cli package", "wfl.cli.commands package", "wfl.descriptors package", "wfl.fit package", "wfl.fit.gap package", "wfl.fit.modify_database package", "wfl.generate package", "wfl.generate.md package", "wfl.select package", "wfl.utils package", "How to do GAP-RSS"], "terms": {"descript": [0, 5, 18], "all": [0, 2, 5, 6, 7, 8, 9, 12, 13, 14, 15, 17, 18, 22, 26, 27, 28, 30, 32, 33, 34, 35, 36, 37, 40, 41, 42, 44, 45, 47, 48], "cli": [0, 19, 34, 47, 48], "tool": [0, 33, 47], "automat": [0, 15, 17, 18, 21, 29, 33, 34, 36, 40, 41, 44, 45, 46, 48], "gener": [0, 3, 4, 8, 10, 11, 14, 15, 16, 17, 18, 19, 20, 23, 31, 32, 34, 35, 37, 38, 41, 42, 46, 47, 48], "documment": [0, 17, 21], "function": [0, 2, 4, 6, 7, 8, 9, 12, 13, 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"wfl.generate.buildcell.conv_buildcell_out"]], "create_input() (in module wfl.generate.buildcell)": [[44, "wfl.generate.buildcell.create_input"]], "derive_normal_mode_info() (wfl.generate.normal_modes.normalmodes method)": [[44, "wfl.generate.normal_modes.NormalModes.derive_normal_mode_info"]], "evals_to_freqs() (wfl.generate.normal_modes.normalmodes static method)": [[44, "wfl.generate.normal_modes.NormalModes.evals_to_freqs"]], "evecs_to_modes() (wfl.generate.normal_modes.normalmodes static method)": [[44, "wfl.generate.normal_modes.NormalModes.evecs_to_modes"]], "freqs_to_evals() (wfl.generate.normal_modes.normalmodes static method)": [[44, "wfl.generate.normal_modes.NormalModes.freqs_to_evals"]], "generate_normal_modes_parallel_atoms() (in module wfl.generate.normal_modes)": [[44, "wfl.generate.normal_modes.generate_normal_modes_parallel_atoms"]], "generate_normal_modes_parallel_hessian() (in module wfl.generate.normal_modes)": [[44, "wfl.generate.normal_modes.generate_normal_modes_parallel_hessian"]], "interstitial() (in module wfl.generate.supercells)": [[44, "wfl.generate.supercells.interstitial"]], "isolated_atom_from_e0() (in module wfl.generate.atoms_and_dimers)": [[44, "wfl.generate.atoms_and_dimers.isolated_atom_from_e0"]], "largest_bulk() (in module wfl.generate.supercells)": [[44, "wfl.generate.supercells.largest_bulk"]], "minimahopping() (in module wfl.generate.minimahopping)": [[44, "wfl.generate.minimahopping.minimahopping"]], "modes_to_evecs() (wfl.generate.normal_modes.normalmodes static method)": [[44, "wfl.generate.normal_modes.NormalModes.modes_to_evecs"]], "num_hess_delta (wfl.generate.normal_modes.normalmodes attribute)": [[44, "wfl.generate.normal_modes.NormalModes.num_hess_delta"]], "phonopy() (in module wfl.generate.phonopy)": [[44, "wfl.generate.phonopy.phonopy"]], "prepare() (in module wfl.generate.atoms_and_dimers)": [[44, "wfl.generate.atoms_and_dimers.prepare"]], "sample_normal_modes() 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"module-wfl.generate.buildcell"]], "wfl.generate.minimahopping": [[44, "module-wfl.generate.minimahopping"]], "wfl.generate.normal_modes": [[44, "module-wfl.generate.normal_modes"]], "wfl.generate.phonopy": [[44, "module-wfl.generate.phonopy"]], "wfl.generate.smiles": [[44, "module-wfl.generate.smiles"]], "wfl.generate.supercells": [[44, "module-wfl.generate.supercells"]], "wfl.generate.utils": [[44, "module-wfl.generate.utils"]], "abortoncollision (class in wfl.generate.md.abort)": [[45, "wfl.generate.md.abort.AbortOnCollision"]], "abortsimbase (class in wfl.generate.md.abort_base)": [[45, "wfl.generate.md.abort_base.AbortSimBase"]], "atoms_ok() (wfl.generate.md.abort.abortoncollision method)": [[45, "wfl.generate.md.abort.AbortOnCollision.atoms_ok"]], "atoms_ok() (wfl.generate.md.abort_base.abortsimbase method)": [[45, "wfl.generate.md.abort_base.AbortSimBase.atoms_ok"]], "md() (in module wfl.generate.md)": [[45, "wfl.generate.md.md"]], "stop() 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"wfl.select.by_descriptor.do_svd"]], "greedy_fps_conf_global() (in module wfl.select.by_descriptor)": [[46, "wfl.select.by_descriptor.greedy_fps_conf_global"]], "minima_among_neighbors() (in module wfl.select.selection_space)": [[46, "wfl.select.selection_space.minima_among_neighbors"]], "prep_descs_and_exclude() (in module wfl.select.by_descriptor)": [[46, "wfl.select.by_descriptor.prep_descs_and_exclude"]], "select() (in module wfl.select.convex_hull)": [[46, "wfl.select.convex_hull.select"]], "val_relative_to_nearby_composition_volume_min() (in module wfl.select.selection_space)": [[46, "wfl.select.selection_space.val_relative_to_nearby_composition_volume_min"]], "wfl.select": [[46, "module-wfl.select"]], "wfl.select.by_descriptor": [[46, "module-wfl.select.by_descriptor"]], "wfl.select.convex_hull": [[46, "module-wfl.select.convex_hull"]], "wfl.select.flat_histogram": [[46, "module-wfl.select.flat_histogram"]], "wfl.select.selection_space": [[46, "module-wfl.select.selection_space"]], "wfl.select.simple": [[46, "module-wfl.select.simple"]], "write_selected_and_clean() (in module wfl.select.by_descriptor)": [[46, "wfl.select.by_descriptor.write_selected_and_clean"]], "params (class in wfl.utils.params)": [[47, "wfl.utils.params.Params"]], "pressurerecursionerror": [[47, "wfl.utils.pressure.PressureRecursionError"]], "at_copy_save_results() (in module wfl.utils.at_copy_save_results)": [[47, "wfl.utils.at_copy_save_results.at_copy_save_results"]], "atomization_energy() (in module wfl.utils.configs)": [[47, "wfl.utils.configs.atomization_energy"]], "atoms_to_list() (in module wfl.utils.misc)": [[47, "wfl.utils.misc.atoms_to_list"]], "calc_list() (in module wfl.utils.ndim_neighbor_list)": [[47, "wfl.utils.ndim_neighbor_list.calc_list"]], "calc_list_cells() (in module wfl.utils.ndim_neighbor_list)": [[47, "wfl.utils.ndim_neighbor_list.calc_list_cells"]], "chunks() (in module wfl.utils.misc)": [[47, "wfl.utils.misc.chunks"]], "clean_dir() (in module wfl.utils.file_utils)": [[47, "wfl.utils.file_utils.clean_dir"]], "composition_space_zs() (in module wfl.utils.vol_composition_space)": [[47, "wfl.utils.vol_composition_space.composition_space_Zs"]], "composition_space_coord() (in module wfl.utils.vol_composition_space)": [[47, "wfl.utils.vol_composition_space.composition_space_coord"]], "construct_calculator_picklesafe() (in module wfl.utils.parallel)": [[47, "wfl.utils.parallel.construct_calculator_picklesafe"]], "cur_iter (wfl.utils.params.params property)": [[47, "wfl.utils.params.Params.cur_iter"]], "dft_code (wfl.utils.params.params property)": [[47, "wfl.utils.params.Params.dft_code"]], "dft_params (wfl.utils.params.params property)": [[47, "wfl.utils.params.Params.dft_params"]], "dict_to_quip_str() (in module wfl.utils.quip_cli_strings)": [[47, "wfl.utils.quip_cli_strings.dict_to_quip_str"]], "dict_tuple_keys_to_str() (in module wfl.utils.misc)": [[47, "wfl.utils.misc.dict_tuple_keys_to_str"]], "extract_e0() (in module wfl.utils.gap_xml_tools)": [[47, "wfl.utils.gap_xml_tools.extract_e0"]], "find_hull() (in module wfl.utils.convex_hull)": [[47, "wfl.utils.convex_hull.find_hull"]], "find_isolated_atoms() (in module wfl.utils.configs)": [[47, "wfl.utils.configs.find_isolated_atoms"]], "find_voids() (in module wfl.utils.find_voids)": [[47, "wfl.utils.find_voids.find_voids"]], "get() (wfl.utils.params.params method)": [[47, "wfl.utils.params.Params.get"]], "get_wfl_version() (in module wfl.utils.version)": [[47, "wfl.utils.version.get_wfl_version"]], "implemented_calculators (wfl.utils.params.params attribute)": [[47, "wfl.utils.params.Params.implemented_calculators"]], "increment_active_iter() (in module wfl.utils.logging)": [[47, "wfl.utils.logging.increment_active_iter"]], "julia_exec_path() (in module wfl.utils.julia)": [[47, "wfl.utils.julia.julia_exec_path"]], "print_log() (in module wfl.utils.logging)": [[47, "wfl.utils.logging.print_log"]], "process_active_iter() (in module wfl.utils.logging)": [[47, "wfl.utils.logging.process_active_iter"]], "replace_eval_in_strs() (in module wfl.utils.replace_eval_in_strs)": [[47, "wfl.utils.replace_eval_in_strs.replace_eval_in_strs"]], "round_sig_figs() (in module wfl.utils.round_sig_figs)": [[47, "wfl.utils.round_sig_figs.round_sig_figs"]], "sample_pressure() (in module wfl.utils.pressure)": [[47, "wfl.utils.pressure.sample_pressure"]], "vertical_dist_from_hull() (in module wfl.utils.convex_hull)": [[47, "wfl.utils.convex_hull.vertical_dist_from_hull"]], "wfl.utils": [[47, "module-wfl.utils"]], "wfl.utils.at_copy_save_results": [[47, "module-wfl.utils.at_copy_save_results"]], "wfl.utils.configs": [[47, "module-wfl.utils.configs"]], "wfl.utils.convex_hull": [[47, "module-wfl.utils.convex_hull"]], "wfl.utils.file_utils": [[47, "module-wfl.utils.file_utils"]], "wfl.utils.find_voids": [[47, "module-wfl.utils.find_voids"]], "wfl.utils.gap_xml_tools": [[47, "module-wfl.utils.gap_xml_tools"]], "wfl.utils.julia": [[47, "module-wfl.utils.julia"]], "wfl.utils.logging": [[47, "module-wfl.utils.logging"]], "wfl.utils.misc": [[47, "module-wfl.utils.misc"]], "wfl.utils.ndim_neighbor_list": [[47, "module-wfl.utils.ndim_neighbor_list"]], "wfl.utils.parallel": [[47, "module-wfl.utils.parallel"]], "wfl.utils.params": [[47, "module-wfl.utils.params"]], "wfl.utils.pressure": [[47, "module-wfl.utils.pressure"]], "wfl.utils.quip_cli_strings": [[47, "module-wfl.utils.quip_cli_strings"]], "wfl.utils.replace_eval_in_strs": [[47, "module-wfl.utils.replace_eval_in_strs"]], "wfl.utils.round_sig_figs": [[47, "module-wfl.utils.round_sig_figs"]], "wfl.utils.version": [[47, "module-wfl.utils.version"]], "wfl.utils.vol_composition_space": [[47, "module-wfl.utils.vol_composition_space"]]}}) \ No newline at end of file diff --git a/wfl.autoparallelize.html b/wfl.autoparallelize.html index 48b140ac..260953a1 100644 --- a/wfl.autoparallelize.html +++ b/wfl.autoparallelize.html @@ -405,8 +405,8 @@

    Contents

  • wfl.autoparallelize.utils module
    • @@ -484,10 +484,9 @@

    Submodules
    parallelized_op(inputs, outputs, [args of op], autopara_info=AutoparaInfo(arg1=val1, ...), [kwargs of op])
    -

    If the op takes the argument autopara_per_item_info a list of dicts with info for each item will be -passed, currently including rng_seed and item_i.

    -

    If op takes the argument autopara_rng_seed it will be used as a global seed to generate the per-item seeds -from.

    +

    If the op takes the argument _autopara_per_item_info a list of dicts with info for each item will be +passed, always including item_i. If op takes the argument rng, per-item dict will also include key rng +with a numpy.random.Generator with a unique state for each item.

    Parameters
    -
  • wfl.utils.vector_utils module -
  • wfl.utils.version module @@ -805,7 +801,7 @@

    Submodules
    -wfl.utils.pressure.sample_pressure(pressure, at=None)#
    +wfl.utils.pressure.sample_pressure(pressure, at=None, rng=None)#

    Sample pressure for calculation with various modes

    Parameters
    @@ -823,6 +819,7 @@

    SubmodulesReturns @@ -911,36 +908,6 @@

    Submodules -

    wfl.utils.vector_utils module#

    -
    -
    General utilities to supplement the other submodules.
      -
    • -
      Vector operations:
        -

      • random 3D vector

        • -
      -
      -
      -
      • -
    -
    -
    -
    -
    -wfl.utils.vector_utils.random_three_vector()#
    -

    Generates a random 3D unit vector (direction) with a uniform spherical distribution -Algo from http://stackoverflow.com/questions/5408276/python-uniform-spherical-distribution

    -
    -
    Returns
    -

    x, y, z – random vector

    -
    -
    Return type
    -

    float

    -
    -
    -
    -

    wfl.utils.version module#

    @@ -1115,10 +1082,6 @@

    Submodulesround_sig_figs()

    • -
  • wfl.utils.vector_utils module -
  • wfl.utils.version module