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janoshjanosh
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redo doc string formatting from #736 lost in git merge main
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‎atomate/qchem/fireworks/core.py‎

Lines changed: 45 additions & 54 deletions
Original file line numberDiff line numberDiff line change
@@ -269,23 +269,20 @@ def __init__(
269269
multimode (str): Parallelization scheme, either openmp or mpi. Defaults to openmp.
270270
max_cores (int): Maximum number of cores to parallelize over. Supports env_chk.
271271
qchem_input_params (dict): Specify kwargs for instantiating the input set parameters.
272-
Basic uses would be to modify the default inputs of the set,
273-
such as dft_rung, basis_set, pcm_dielectric, scf_algorithm,
274-
or max_scf_cycles. See pymatgen/io/qchem/sets.py for default
275-
values of all input parameters. For instance, if a user wanted
276-
to use a more advanced DFT functional, include a pcm with a
277-
dielectric of 30, and use a larger basis, the user would set
278-
qchem_input_params = {"dft_rung": 5, "pcm_dielectric": 30,
279-
"basis_set": "6-311++g**"}. However, more advanced customization
280-
of the input is also possible through the overwrite_inputs key
281-
which allows the user to directly modify the rem, pcm, smd, and
282-
solvent dictionaries that QChemDictSet passes to inputs.py to
283-
print an actual input file. For instance, if a user wanted to
284-
set the sym_ignore flag in the rem section of the input file
285-
to true, then they would set qchem_input_params = {"overwrite_inputs":
286-
"rem": {"sym_ignore": "true"}}. Of course, overwrite_inputs
287-
could be used in conjuction with more typical modifications,
288-
as seen in the test_double_FF_opt workflow test.
272+
Basic uses would be to modify the default inputs of the set, such as dft_rung,
273+
basis_set, pcm_dielectric, scf_algorithm, or max_scf_cycles. See
274+
pymatgen/io/qchem/sets.py for default values of all input parameters. For
275+
instance, if a user wanted to use a more advanced DFT functional, include a pcm
276+
with a dielectric of 30, and use a larger basis, the user would set
277+
qchem_input_params = {"dft_rung": 5, "pcm_dielectric": 30, "basis_set":
278+
"6-311++g**"}. However, more advanced customization of the input is also
279+
possible through the overwrite_inputs key which allows the user to directly
280+
modify the rem, pcm, smd, and solvent dictionaries that QChemDictSet passes to
281+
inputs.py to print an actual input file. For instance, if a user wanted to set
282+
the sym_ignore flag in the rem section of the input file to true, then they
283+
would set qchem_input_params = {"overwrite_inputs": "rem": {"sym_ignore":
284+
"true"}}. Of course, overwrite_inputs could be used in conjunction with more
285+
typical modifications, as seen in the test_double_FF_opt workflow test.
289286
db_file (str): Path to file specifying db credentials to place output parsing.
290287
parents ([Firework]): Parents of this particular Firework.
291288
**kwargs: Other kwargs that are passed to Firework.__init__.
@@ -347,23 +344,20 @@ def __init__(
347344
multimode (str): Parallelization scheme, either openmp or mpi. Defaults to openmp.
348345
max_cores (int): Maximum number of cores to parallelize over. Supports env_chk.
349346
qchem_input_params (dict): Specify kwargs for instantiating the input set parameters.
350-
Basic uses would be to modify the default inputs of the set,
351-
such as dft_rung, basis_set, pcm_dielectric, scf_algorithm,
352-
or max_scf_cycles. See pymatgen/io/qchem/sets.py for default
353-
values of all input parameters. For instance, if a user wanted
354-
to use a more advanced DFT functional, include a pcm with a
355-
dielectric of 30, and use a larger basis, the user would set
356-
qchem_input_params = {"dft_rung": 5, "pcm_dielectric": 30,
357-
"basis_set": "6-311++g**"}. However, more advanced customization
358-
of the input is also possible through the overwrite_inputs key
359-
which allows the user to directly modify the rem, pcm, smd, and
360-
solvent dictionaries that QChemDictSet passes to inputs.py to
361-
print an actual input file. For instance, if a user wanted to
362-
set the sym_ignore flag in the rem section of the input file
363-
to true, then they would set qchem_input_params = {"overwrite_inputs":
364-
"rem": {"sym_ignore": "true"}}. Of course, overwrite_inputs
365-
could be used in conjuction with more typical modifications,
366-
as seen in the test_double_FF_opt workflow test.
347+
Basic uses would be to modify the default inputs of the set, such as dft_rung,
348+
basis_set, pcm_dielectric, scf_algorithm, or max_scf_cycles. See
349+
pymatgen/io/qchem/sets.py for default values of all input parameters. For
350+
instance, if a user wanted to use a more advanced DFT functional, include a pcm
351+
with a dielectric of 30, and use a larger basis, the user would set
352+
qchem_input_params = {"dft_rung": 5, "pcm_dielectric": 30, "basis_set":
353+
"6-311++g**"}. However, more advanced customization of the input is also
354+
possible through the overwrite_inputs key which allows the user to directly
355+
modify the rem, pcm, smd, and solvent dictionaries that QChemDictSet passes to
356+
inputs.py to print an actual input file. For instance, if a user wanted to set
357+
the sym_ignore flag in the rem section of the input file to true, then they
358+
would set qchem_input_params = {"overwrite_inputs": "rem": {"sym_ignore":
359+
"true"}}. Of course, overwrite_inputs could be used in conjunction with more
360+
typical modifications, as seen in the test_double_FF_opt workflow test.
367361
db_file (str): Path to file specifying db credentials to place output parsing.
368362
parents ([Firework]): Parents of this particular Firework.
369363
**kwargs: Other kwargs that are passed to Firework.__init__.
@@ -639,28 +633,25 @@ def __init__(
639633
multimode (str): Parallelization scheme, either openmp or mpi. Supports env_chk.
640634
max_cores (int): Maximum number of cores to parallelize over. Supports env_chk.
641635
qchem_input_params (dict): Specify kwargs for instantiating the input set parameters.
642-
Basic uses would be to modify the default inputs of the set,
643-
such as dft_rung, basis_set, pcm_dielectric, scf_algorithm,
644-
or max_scf_cycles. See pymatgen/io/qchem/sets.py for default
645-
values of all input parameters. For instance, if a user wanted
646-
to use a more advanced DFT functional, include a pcm with a
647-
dielectric of 30, and use a larger basis, the user would set
648-
qchem_input_params = {"dft_rung": 5, "pcm_dielectric": 30,
649-
"basis_set": "6-311++g**"}. However, more advanced customization
650-
of the input is also possible through the overwrite_inputs key
651-
which allows the user to directly modify the rem, pcm, smd, and
652-
solvent dictionaries that QChemDictSet passes to inputs.py to
653-
print an actual input file. For instance, if a user wanted to
654-
set the sym_ignore flag in the rem section of the input file
655-
to true, then they would set qchem_input_params = {"overwrite_inputs":
656-
"rem": {"sym_ignore": "true"}}. Of course, overwrite_inputs
657-
could be used in conjuction with more typical modifications,
658-
as seen in the test_double_FF_opt workflow test.
636+
Basic uses would be to modify the default inputs of the set, such as dft_rung,
637+
basis_set, pcm_dielectric, scf_algorithm, or max_scf_cycles. See
638+
pymatgen/io/qchem/sets.py for default values of all input parameters. For
639+
instance, if a user wanted to use a more advanced DFT functional, include a pcm
640+
with a dielectric of 30, and use a larger basis, the user would set
641+
qchem_input_params = {"dft_rung": 5, "pcm_dielectric": 30, "basis_set":
642+
"6-311++g**"}. However, more advanced customization of the input is also
643+
possible through the overwrite_inputs key which allows the user to directly
644+
modify the rem, pcm, smd, and solvent dictionaries that QChemDictSet passes to
645+
inputs.py to print an actual input file. For instance, if a user wanted to set
646+
the sym_ignore flag in the rem section of the input file to true, then they
647+
would set qchem_input_params = {"overwrite_inputs": "rem": {"sym_ignore":
648+
"true"}}. Of course, overwrite_inputs could be used in conjunction with more
649+
typical modifications, as seen in the test_double_FF_opt workflow test.
659650
max_iterations (int): Number of perturbation -> optimization -> frequency
660-
iterations to perform. Defaults to 3. Higher numbers are not
661-
recommended, as they rarely lead to improved performance.
651+
iterations to perform. Defaults to 3. Higher numbers are not recommended, as
652+
they rarely lead to improved performance.
662653
max_molecule_perturb_scale (float): The maximum scaled perturbation that can be
663-
applied to the molecule. Defaults to 0.3.
654+
applied to the molecule. Defaults to 0.3.
664655
linked (bool): If True (default False), the scratch output from one calculation will be passed
665656
from one calculation to the next, improving convergence behavior.
666657
freq_before_opt (bool): If True (default False), run a frequency

‎atomate/qchem/workflows/base/reaction_path.py‎

Lines changed: 15 additions & 19 deletions
Original file line numberDiff line numberDiff line change
@@ -45,26 +45,22 @@ def get_wf_reaction_path_with_ts(
4545
mode (np.ndarray): a matrix used to perturb the molecule
4646
scale (float): Scaling factor for molecular perturbations.
4747
qchem_cmd (str): Command to run QChem.
48-
max_cores (int): Maximum number of cores to parallelize over.
49-
Defaults to 32.
48+
max_cores (int): Maximum number of cores to parallelize over. Defaults to 32.
5049
qchem_input_params (dict): Specify kwargs for instantiating the input set parameters.
51-
Basic uses would be to modify the default inputs of the set,
52-
such as dft_rung, basis_set, pcm_dielectric, scf_algorithm,
53-
or max_scf_cycles. See pymatgen/io/qchem/sets.py for default
54-
values of all input parameters. For instance, if a user wanted
55-
to use a more advanced DFT functional, include a pcm with a
56-
dielectric of 30, and use a larger basis, the user would set
57-
qchem_input_params = {"dft_rung": 5, "pcm_dielectric": 30,
58-
"basis_set": "6-311++g**"}. However, more advanced customization
59-
of the input is also possible through the overwrite_inputs key
60-
which allows the user to directly modify the rem, pcm, smd, and
61-
solvent dictionaries that QChemDictSet passes to inputs.py to
62-
print an actual input file. For instance, if a user wanted to
63-
set the sym_ignore flag in the rem section of the input file
64-
to true, then they would set qchem_input_params = {"overwrite_inputs":
65-
"rem": {"sym_ignore": "true"}}. Of course, overwrite_inputs
66-
could be used in conjuction with more typical modifications,
67-
as seen in the test_double_FF_opt workflow test.
50+
Basic uses would be to modify the default inputs of the set, such as dft_rung,
51+
basis_set, pcm_dielectric, scf_algorithm, or max_scf_cycles. See
52+
pymatgen/io/qchem/sets.py for default values of all input parameters. For instance,
53+
if a user wanted to use a more advanced DFT functional, include a pcm with a
54+
dielectric of 30, and use a larger basis, the user would set qchem_input_params =
55+
{"dft_rung": 5, "pcm_dielectric": 30, "basis_set": "6-311++g**"}. However, more
56+
advanced customization of the input is also possible through the overwrite_inputs
57+
key which allows the user to directly modify the rem, pcm, smd, and solvent
58+
dictionaries that QChemDictSet passes to inputs.py to print an actual input file.
59+
For instance, if a user wanted to set the sym_ignore flag in the rem section of the
60+
input file to true, then they would set qchem_input_params = {"overwrite_inputs":
61+
"rem": {"sym_ignore": "true"}}. Of course, overwrite_inputs could be used in
62+
conjunction with more typical modifications, as seen in the test_double_FF_opt
63+
workflow test.
6864
name (string): name for the Workflow
6965
db_file (str): path to file containing the database credentials.
7066
kwargs (keyword arguments): additional kwargs to be passed to Workflow

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