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RMG-Py v3.2.0 for review only DO NOT MERGE #2449

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RMG-Py v3.2.0 for review only DO NOT MERGE #2449

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56cd81f
update RMG-Py version to 3.2.0
sevyharris Jun 6, 2022
3115395
update license year to 2023 in headers
sevyharris May 22, 2023
c2cb98f
update version in conda package description
sevyharris Jul 12, 2022
b55393c
add v3.2.0 release notes for RMG-Py and RMG-database
sevyharris May 22, 2023
ae1a163
`make -C documentation latexpdf` now copies results into right place.
rwest May 30, 2023
824cd99
Recompiled LaTeX documentation PDFs.
sevyharris Aug 2, 2023
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4 changes: 2 additions & 2 deletions .conda/meta.yaml
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@@ -1,7 +1,7 @@
# For conda build
package:
name: rmg
version: 3.1.0
version: 3.2.0

source:
path: ../
Expand Down Expand Up @@ -64,7 +64,7 @@ requirements:
- pyzmq
- quantities
- rdkit >=2018
- rmgdatabase >=3.1.0
- rmgdatabase >=3.2.0
- scikit-learn
- scipy
- symmetry
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2 changes: 1 addition & 1 deletion Arkane.py
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# #
# RMG - Reaction Mechanism Generator #
# #
# Copyright (c) 2002-2021 Prof. William H. Green (whgreen@mit.edu), #
# Copyright (c) 2002-2023 Prof. William H. Green (whgreen@mit.edu), #
# Prof. Richard H. West (r.west@neu.edu) and the RMG Team (rmg_dev@mit.edu) #
# #
# Permission is hereby granted, free of charge, to any person obtaining a #
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2 changes: 1 addition & 1 deletion LICENSE.txt
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Copyright (c) 2002-2021 Prof. William H. Green (whgreen@mit.edu),
Copyright (c) 2002-2023 Prof. William H. Green (whgreen@mit.edu),
Prof. Richard H. West (r.west@neu.edu) and the RMG Team (rmg_dev@mit.edu)

Permission is hereby granted, free of charge, to any person obtaining a
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2 changes: 1 addition & 1 deletion arkane/__init__.py
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# #
# RMG - Reaction Mechanism Generator #
# #
# Copyright (c) 2002-2021 Prof. William H. Green (whgreen@mit.edu), #
# Copyright (c) 2002-2023 Prof. William H. Green (whgreen@mit.edu), #
# Prof. Richard H. West (r.west@neu.edu) and the RMG Team (rmg_dev@mit.edu) #
# #
# Permission is hereby granted, free of charge, to any person obtaining a #
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2 changes: 1 addition & 1 deletion arkane/common.py
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# #
# RMG - Reaction Mechanism Generator #
# #
# Copyright (c) 2002-2021 Prof. William H. Green (whgreen@mit.edu), #
# Copyright (c) 2002-2023 Prof. William H. Green (whgreen@mit.edu), #
# Prof. Richard H. West (r.west@neu.edu) and the RMG Team (rmg_dev@mit.edu) #
# #
# Permission is hereby granted, free of charge, to any person obtaining a #
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2 changes: 1 addition & 1 deletion arkane/commonTest.py
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# #
# RMG - Reaction Mechanism Generator #
# #
# Copyright (c) 2002-2021 Prof. William H. Green (whgreen@mit.edu), #
# Copyright (c) 2002-2023 Prof. William H. Green (whgreen@mit.edu), #
# Prof. Richard H. West (r.west@neu.edu) and the RMG Team (rmg_dev@mit.edu) #
# #
# Permission is hereby granted, free of charge, to any person obtaining a #
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2 changes: 1 addition & 1 deletion arkane/encorr/__init__.py
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# #
# RMG - Reaction Mechanism Generator #
# #
# Copyright (c) 2002-2021 Prof. William H. Green (whgreen@mit.edu), #
# Copyright (c) 2002-2023 Prof. William H. Green (whgreen@mit.edu), #
# Prof. Richard H. West (r.west@neu.edu) and the RMG Team (rmg_dev@mit.edu) #
# #
# Permission is hereby granted, free of charge, to any person obtaining a #
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2 changes: 1 addition & 1 deletion arkane/encorr/ae.py
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# #
# RMG - Reaction Mechanism Generator #
# #
# Copyright (c) 2002-2021 Prof. William H. Green (whgreen@mit.edu), #
# Copyright (c) 2002-2023 Prof. William H. Green (whgreen@mit.edu), #
# Prof. Richard H. West (r.west@neu.edu) and the RMG Team (rmg_dev@mit.edu) #
# #
# Permission is hereby granted, free of charge, to any person obtaining a #
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2 changes: 1 addition & 1 deletion arkane/encorr/aeTest.py
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# #
# RMG - Reaction Mechanism Generator #
# #
# Copyright (c) 2002-2021 Prof. William H. Green (whgreen@mit.edu), #
# Copyright (c) 2002-2023 Prof. William H. Green (whgreen@mit.edu), #
# Prof. Richard H. West (r.west@neu.edu) and the RMG Team (rmg_dev@mit.edu) #
# #
# Permission is hereby granted, free of charge, to any person obtaining a #
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2 changes: 1 addition & 1 deletion arkane/encorr/bac.py
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# #
# RMG - Reaction Mechanism Generator #
# #
# Copyright (c) 2002-2021 Prof. William H. Green (whgreen@mit.edu), #
# Copyright (c) 2002-2023 Prof. William H. Green (whgreen@mit.edu), #
# Prof. Richard H. West (r.west@neu.edu) and the RMG Team (rmg_dev@mit.edu) #
# #
# Permission is hereby granted, free of charge, to any person obtaining a #
Expand Down Expand Up @@ -92,14 +92,14 @@
"""
self.level_of_theory = level_of_theory
self.bac_type = bac_type
self.crossval_n_folds = crossval_n_folds

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self.write_to_database = write_to_database
self.overwrite = overwrite
self.kwargs = kwargs
if self.crossval_n_folds != 1:
self.bac = CrossVal(level_of_theory, bac_type=bac_type, n_folds=crossval_n_folds)

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else:
self.bac = BAC(level_of_theory, bac_type=bac_type)

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def execute(self, output_directory: str = None, plot: bool = False, jobnum: int = 1):
"""
Expand Down Expand Up @@ -144,11 +144,11 @@
with open(output_file1, 'a') as f:
stats_before = self.bac.dataset.calculate_stats()
stats_after = self.bac.dataset.calculate_stats(for_bac_data=True)
bac_type_str = f'{"Melius" if self.bac.bac_type == "m" else "Petersson"}-type BACs'
f.write(f'# Job {jobnum}: {bac_type_str}:\n')
f.write(f'# Training RMSE/MAE before fitting: {stats_before.rmse:.2f}/{stats_before.mae:.2f} kcal/mol\n')
f.write(f'# Training RMSE/MAE after fitting: {stats_after.rmse:.2f}/{stats_after.mae:.2f} kcal/mol\n')
f.writelines(self.bac.format_bacs(ci=True))

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f.write('\n')

with open(output_file2, 'w') as f:
Expand Down Expand Up @@ -197,8 +197,8 @@

model_chemistry_formatted = self.level_of_theory.to_model_chem().replace('//', '__').replace('/', '_')
if self.crossval_n_folds == 1:
correlation_path = os.path.join(output_directory, f'{jobnum}_{model_chemistry_formatted}_correlation.pdf')
self.bac.save_correlation_mat(correlation_path)

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plt.rcParams.update({'font.size': 16})
fig_path = os.path.join(output_directory, f'{jobnum}_{model_chemistry_formatted}_errors.pdf')
Expand Down Expand Up @@ -848,7 +848,7 @@
break
else:
# 'pbac' and 'mbac' should both be found at `data_path`
raise RuntimeError(f'Keyword "{keyword} is not found in the data file. '

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f'Please check the database file at {data_path} and '
f'make sure an up-to-date RMG-database branch is used.')

Expand All @@ -867,13 +867,13 @@
del_idx_end = i + j + 1
if (lines[del_idx_start - 1].lstrip().startswith('#')
or lines[del_idx_end + 1].lstrip().startswith('#')):
logging.warning('There may be left over comments from previous BACs')

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lines[del_idx_start:del_idx_end] = bacs_formatted
break

# Check if the entry is successfully inserted to the `lines`
if del_idx_start is None or del_idx_end is None:
raise RuntimeError(f'The script cannot identify the corresponding block for the given BACs. '

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f'It is possible that the database file at {data_path} is not correctly '
f'formatted. Please check the file.')

Expand All @@ -884,8 +884,8 @@
else:
# Either empty BACs dict or adding BACs for a new level of theory
if not has_entries and '}' in lines[i]: # Empty BACs dict
lines[i] = f'{keyword} = {{\n'
lines[(i+1):(i+1)] = ['\n}\n']

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lines[(i+1):(i+1)] = ['\n'] + bacs_formatted

with open(data_path if alternate_path is None else alternate_path, 'w') as f:
Expand Down Expand Up @@ -914,10 +914,10 @@
bacs_formatted = [' ' + e for e in bacs_formatted]

if ci:
ci_formatted = ['95% Confidence interval half-widths:']
ci_formatted += json.dumps(self.confidence_intervals, indent=4).replace('"', "'").split('\n')

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ci_formatted = ['# ' + e + '\n' for e in ci_formatted]
bacs_formatted.extend(ci_formatted)

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return bacs_formatted

Expand Down Expand Up @@ -1085,7 +1085,7 @@
n = len(y) # Ndata
p = len(x.T) # Nparam
if weights is None:
weights = np.eye(n)

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e = y - ypred # Residuals
sigma2 = e.T @ weights @ e / (n - p) # MSE
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2 changes: 1 addition & 1 deletion arkane/encorr/bacTest.py
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# #
# RMG - Reaction Mechanism Generator #
# #
# Copyright (c) 2002-2021 Prof. William H. Green (whgreen@mit.edu), #
# Copyright (c) 2002-2023 Prof. William H. Green (whgreen@mit.edu), #
# Prof. Richard H. West (r.west@neu.edu) and the RMG Team (rmg_dev@mit.edu) #
# #
# Permission is hereby granted, free of charge, to any person obtaining a #
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2 changes: 1 addition & 1 deletion arkane/encorr/corr.py
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# #
# RMG - Reaction Mechanism Generator #
# #
# Copyright (c) 2002-2021 Prof. William H. Green (whgreen@mit.edu), #
# Copyright (c) 2002-2023 Prof. William H. Green (whgreen@mit.edu), #
# Prof. Richard H. West (r.west@neu.edu) and the RMG Team (rmg_dev@mit.edu) #
# #
# Permission is hereby granted, free of charge, to any person obtaining a #
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2 changes: 1 addition & 1 deletion arkane/encorr/corrTest.py
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# #
# RMG - Reaction Mechanism Generator #
# #
# Copyright (c) 2002-2021 Prof. William H. Green (whgreen@mit.edu), #
# Copyright (c) 2002-2023 Prof. William H. Green (whgreen@mit.edu), #
# Prof. Richard H. West (r.west@neu.edu) and the RMG Team (rmg_dev@mit.edu) #
# #
# Permission is hereby granted, free of charge, to any person obtaining a #
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2 changes: 1 addition & 1 deletion arkane/encorr/data.py
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# #
# RMG - Reaction Mechanism Generator #
# #
# Copyright (c) 2002-2021 Prof. William H. Green (whgreen@mit.edu), #
# Copyright (c) 2002-2023 Prof. William H. Green (whgreen@mit.edu), #
# Prof. Richard H. West (r.west@neu.edu) and the RMG Team (rmg_dev@mit.edu) #
# #
# Permission is hereby granted, free of charge, to any person obtaining a #
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2 changes: 1 addition & 1 deletion arkane/encorr/dataTest.py
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# #
# RMG - Reaction Mechanism Generator #
# #
# Copyright (c) 2002-2021 Prof. William H. Green (whgreen@mit.edu), #
# Copyright (c) 2002-2023 Prof. William H. Green (whgreen@mit.edu), #
# Prof. Richard H. West (r.west@neu.edu) and the RMG Team (rmg_dev@mit.edu) #
# #
# Permission is hereby granted, free of charge, to any person obtaining a #
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2 changes: 1 addition & 1 deletion arkane/encorr/decomp.py
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# #
# RMG - Reaction Mechanism Generator #
# #
# Copyright (c) 2002-2021 Prof. William H. Green (whgreen@mit.edu), #
# Copyright (c) 2002-2023 Prof. William H. Green (whgreen@mit.edu), #
# Prof. Richard H. West (r.west@neu.edu) and the RMG Team (rmg_dev@mit.edu) #
# #
# Permission is hereby granted, free of charge, to any person obtaining a #
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2 changes: 1 addition & 1 deletion arkane/encorr/decompTest.py
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# #
# RMG - Reaction Mechanism Generator #
# #
# Copyright (c) 2002-2021 Prof. William H. Green (whgreen@mit.edu), #
# Copyright (c) 2002-2023 Prof. William H. Green (whgreen@mit.edu), #
# Prof. Richard H. West (r.west@neu.edu) and the RMG Team (rmg_dev@mit.edu) #
# #
# Permission is hereby granted, free of charge, to any person obtaining a #
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2 changes: 1 addition & 1 deletion arkane/encorr/isodesmic.py
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# #
# RMG - Reaction Mechanism Generator #
# #
# Copyright (c) 2002-2021 Prof. William H. Green (whgreen@mit.edu), #
# Copyright (c) 2002-2023 Prof. William H. Green (whgreen@mit.edu), #
# Prof. Richard H. West (r.west@neu.edu) and the RMG Team (rmg_dev@mit.edu) #
# #
# Permission is hereby granted, free of charge, to any person obtaining a #
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2 changes: 1 addition & 1 deletion arkane/encorr/isodesmicTest.py
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# #
# RMG - Reaction Mechanism Generator #
# #
# Copyright (c) 2002-2021 Prof. William H. Green (whgreen@mit.edu), #
# Copyright (c) 2002-2023 Prof. William H. Green (whgreen@mit.edu), #
# Prof. Richard H. West (r.west@neu.edu) and the RMG Team (rmg_dev@mit.edu) #
# #
# Permission is hereby granted, free of charge, to any person obtaining a #
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2 changes: 1 addition & 1 deletion arkane/encorr/reference.py
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# #
# RMG - Reaction Mechanism Generator #
# #
# Copyright (c) 2002-2021 Prof. William H. Green (whgreen@mit.edu), #
# Copyright (c) 2002-2023 Prof. William H. Green (whgreen@mit.edu), #
# Prof. Richard H. West (r.west@neu.edu) and the RMG Team (rmg_dev@mit.edu) #
# #
# Permission is hereby granted, free of charge, to any person obtaining a #
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2 changes: 1 addition & 1 deletion arkane/encorr/referenceTest.py
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# #
# RMG - Reaction Mechanism Generator #
# #
# Copyright (c) 2002-2021 Prof. William H. Green (whgreen@mit.edu), #
# Copyright (c) 2002-2023 Prof. William H. Green (whgreen@mit.edu), #
# Prof. Richard H. West (r.west@neu.edu) and the RMG Team (rmg_dev@mit.edu) #
# #
# Permission is hereby granted, free of charge, to any person obtaining a #
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2 changes: 1 addition & 1 deletion arkane/ess/__init__.py
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# #
# RMG - Reaction Mechanism Generator #
# #
# Copyright (c) 2002-2021 Prof. William H. Green (whgreen@mit.edu), #
# Copyright (c) 2002-2023 Prof. William H. Green (whgreen@mit.edu), #
# Prof. Richard H. West (r.west@neu.edu) and the RMG Team (rmg_dev@mit.edu) #
# #
# Permission is hereby granted, free of charge, to any person obtaining a #
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2 changes: 1 addition & 1 deletion arkane/ess/adapter.py
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# #
# RMG - Reaction Mechanism Generator #
# #
# Copyright (c) 2002-2021 Prof. William H. Green (whgreen@mit.edu), #
# Copyright (c) 2002-2023 Prof. William H. Green (whgreen@mit.edu), #
# Prof. Richard H. West (r.west@neu.edu) and the RMG Team (rmg_dev@mit.edu) #
# #
# Permission is hereby granted, free of charge, to any person obtaining a #
Expand Down Expand Up @@ -56,7 +56,7 @@
Checks the log file for common errors.
Optionally runs when the class is initialized to catch errors before parsing relevant information.
"""
pass

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@abstractmethod
def get_number_of_atoms(self):
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2 changes: 1 addition & 1 deletion arkane/ess/factory.py
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# #
# RMG - Reaction Mechanism Generator #
# #
# Copyright (c) 2002-2021 Prof. William H. Green (whgreen@mit.edu), #
# Copyright (c) 2002-2023 Prof. William H. Green (whgreen@mit.edu), #
# Prof. Richard H. West (r.west@neu.edu) and the RMG Team (rmg_dev@mit.edu) #
# #
# Permission is hereby granted, free of charge, to any person obtaining a #
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2 changes: 1 addition & 1 deletion arkane/ess/factoryTest.py
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# #
# RMG - Reaction Mechanism Generator #
# #
# Copyright (c) 2002-2021 Prof. William H. Green (whgreen@mit.edu), #
# Copyright (c) 2002-2023 Prof. William H. Green (whgreen@mit.edu), #
# Prof. Richard H. West (r.west@neu.edu) and the RMG Team (rmg_dev@mit.edu) #
# #
# Permission is hereby granted, free of charge, to any person obtaining a #
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2 changes: 1 addition & 1 deletion arkane/ess/gaussian.py
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# #
# RMG - Reaction Mechanism Generator #
# #
# Copyright (c) 2002-2021 Prof. William H. Green (whgreen@mit.edu), #
# Copyright (c) 2002-2023 Prof. William H. Green (whgreen@mit.edu), #
# Prof. Richard H. West (r.west@neu.edu) and the RMG Team (rmg_dev@mit.edu) #
# #
# Permission is hereby granted, free of charge, to any person obtaining a #
Expand Down Expand Up @@ -73,22 +73,22 @@
if 'l9999.exe' in line or 'link 9999' in line:
error = 'Unconverged'
elif 'l101.exe' in line:
error = 'The blank line after the coordinate section is missing, ' \

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'or charge/multiplicity was not specified correctly.'
elif 'l103.exe' in line:
error = 'Internal coordinate error'

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elif 'l108.exe' in line:
error = 'There are two blank lines between z-matrix and ' \

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'the variables, expected only one.'
elif 'l202.exe' in line:
error = 'During the optimization process, either the standard ' \

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'orientation or the point group of the molecule has changed.'
elif 'l502.exe' in line:
error = 'Unconverged SCF.'

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elif 'l716.exe' in line:
error = 'Angle in z-matrix outside the allowed range 0 < x < 180.'

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elif 'l906.exe' in line:
error = 'The MP2 calculation has failed. It may be related to pseudopotential. ' \

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'Basis sets (CEP-121G*) that are used with polarization functions, ' \
'where no polarization functions actually exist.'
elif 'l913.exe' in line:
Expand All @@ -100,7 +100,7 @@
# no need to continue parsing if terminated without errors
break
if not terminated:
raise LogError(f'Gaussian output file {self.path} did not terminate')

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def get_number_of_atoms(self):
"""
Expand Down Expand Up @@ -330,7 +330,7 @@
elif 'E(CBS-QB3)=' in line:
# CBS-QB3 calculation without opt and freq calculation
# Keyword in Gaussian CBS-QB3(SP), No zero-point or thermal energies are included.
e_elect = float(line.split()[1]) * constants.E_h * constants.Na

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elif 'CBS-4 (0 K)=' in line:
e0_composite = float(line.split()[3]) * constants.E_h * constants.Na
elif 'G3(0 K)' in line:
Expand All @@ -338,19 +338,19 @@
elif 'G3 Energy=' in line:
# G3 calculation without opt and freq calculation
# Keyword in Gaussian G3(SP), No zero-point or thermal energies are included.
e_elect = float(line.split()[2]) * constants.E_h * constants.Na

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elif 'G4(0 K)' in line:
e0_composite = float(line.split()[2]) * constants.E_h * constants.Na
elif 'G4 Energy=' in line:
# G4 calculation without opt and freq calculation
# Keyword in Gaussian G4(SP), No zero-point or thermal energies are included.
e_elect = float(line.split()[2]) * constants.E_h * constants.Na

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elif 'G4MP2(0 K)' in line:
e0_composite = float(line.split()[2]) * constants.E_h * constants.Na
elif 'G4MP2 Energy=' in line:
# G4MP2 calculation without opt and freq calculation
# Keyword in Gaussian G4MP2(SP), No zero-point or thermal energies are included.
e_elect = float(line.split()[2]) * constants.E_h * constants.Na

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# Read the ZPE from the "E(ZPE)=" line, as this is the scaled version.
# Gaussian defines the following as
Expand Down Expand Up @@ -445,8 +445,8 @@
# In some cases, the optimization cannot converge within the given steps.
# Then, the geometry is not optimized. we need to exclude these values.
if 'Optimization stopped' in line:
non_optimized.append(len(vlist))
vlist.append(energy)

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# Read the optimized angle from optimized parameters
if internal_coord in line and 'Scan' not in line:
# EXAMPLE:
Expand All @@ -457,10 +457,10 @@

# give warning in case this assumption is not true
if rigid_scan:
print(f' Assuming {os.path.basename(self.path)} is the output from a rigid scan...')

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# For rigid scans, all of the angles are evenly spaced with a constant step size
scan_res = math.pi / 180 * self._load_scan_angle()
angle = np.arange(0.0, scan_res * (len(vlist) - 1) + 0.00001, scan_res, np.float64)

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else:
angle = np.array(angle, np.float64)
# Convert -180 ~ 180 degrees to 0 ~ 2pi rads
Expand All @@ -485,10 +485,10 @@
angle = angle[:-1]

if non_optimized:
logging.warning(f'Scan results for angles at {angle[non_optimized]} are discarded '

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f'due to non-converged optimization.')
vlist = np.delete(vlist, non_optimized)
angle = np.delete(angle, non_optimized)

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return vlist, angle

Expand Down Expand Up @@ -528,8 +528,8 @@
# It defines a linear bend which is helpful in calculating
# molecules with ~180 degree bond angles. As no other module
# now depends on this information, simply skipping this line.
line = f.readline()
continue

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else:
raise LogError('This file has an option not supported by Arkane. '
'Unable to read scan specs for line: {0}'.format(line))
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2 changes: 1 addition & 1 deletion arkane/ess/gaussianTest.py
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Expand Up @@ -4,7 +4,7 @@
# #
# RMG - Reaction Mechanism Generator #
# #
# Copyright (c) 2002-2021 Prof. William H. Green (whgreen@mit.edu), #
# Copyright (c) 2002-2023 Prof. William H. Green (whgreen@mit.edu), #
# Prof. Richard H. West (r.west@neu.edu) and the RMG Team (rmg_dev@mit.edu) #
# #
# Permission is hereby granted, free of charge, to any person obtaining a #
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2 changes: 1 addition & 1 deletion arkane/ess/molpro.py
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Expand Up @@ -4,7 +4,7 @@
# #
# RMG - Reaction Mechanism Generator #
# #
# Copyright (c) 2002-2021 Prof. William H. Green (whgreen@mit.edu), #
# Copyright (c) 2002-2023 Prof. William H. Green (whgreen@mit.edu), #
# Prof. Richard H. West (r.west@neu.edu) and the RMG Team (rmg_dev@mit.edu) #
# #
# Permission is hereby granted, free of charge, to any person obtaining a #
Expand Down Expand Up @@ -70,11 +70,11 @@
break
# check for common error messages
elif 'No convergence' in line:
error = 'Unconverged'

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elif 'A further' in line and 'Mwords of memory are needed' in line and 'Increase memory to' in line:
# e.g.: `A further 246.03 Mwords of memory are needed for the triples to run.
# Increase memory to 996.31 Mwords.` (w/o the line break)
error = 'Memory'

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elif 'insufficient memory available - require' in line:
# e.g.: `insufficient memory available - require 228765625 have
# 62928590
Expand All @@ -97,7 +97,7 @@
basis_set = None
for line0 in reversed(line):
if 'SETTING BASIS' in line0:
basis_set = line0.split()[-1]

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error = f'Unrecognized basis set {basis_set}'
if error:
raise LogError(f'There was an error ({error}) with Molpro output file {self.path} '
Expand Down Expand Up @@ -435,8 +435,8 @@
if len(freqs) == 1:
return -float(freqs[0])
elif len(freqs) > 1:
logging.info('More than one imaginary frequency in Molpro output file {0}.'.format(self.path))
return -float(freqs[0])

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else:
raise LogError('Unable to find imaginary frequency in Molpro output file {0}'.format(self.path))

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# #
# RMG - Reaction Mechanism Generator #
# #
# Copyright (c) 2002-2021 Prof. William H. Green (whgreen@mit.edu), #
# Copyright (c) 2002-2023 Prof. William H. Green (whgreen@mit.edu), #
# Prof. Richard H. West (r.west@neu.edu) and the RMG Team (rmg_dev@mit.edu) #
# #
# Permission is hereby granted, free of charge, to any person obtaining a #
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2 changes: 1 addition & 1 deletion arkane/ess/orca.py
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Expand Up @@ -4,7 +4,7 @@
# #
# RMG - Reaction Mechanism Generator #
# #
# Copyright (c) 2002-2021 Prof. William H. Green (whgreen@mit.edu), #
# Copyright (c) 2002-2023 Prof. William H. Green (whgreen@mit.edu), #
# Prof. Richard H. West (r.west@neu.edu) and the RMG Team (rmg_dev@mit.edu) #
# #
# Permission is hereby granted, free of charge, to any person obtaining a #
Expand Down Expand Up @@ -67,11 +67,11 @@
error = 'SCF'
break
elif 'ORCA finished by error termination in MDCI' in line:
error = 'MDCI'
break

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elif 'Error : multiplicity' in line:
error = f'The multiplicity and charge combination for species {species_label} are wrong.'
break

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elif 'ORCA TERMINATED NORMALLY' in line:
break
if error:
Expand Down Expand Up @@ -109,42 +109,42 @@
The units of the returned force constants are J/m^2.
If no force constant matrix can be found, ``None`` is returned.
"""
hess_files = list()

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for (_, _, files) in os.walk(os.path.dirname(self.path)):
for file_ in files:
if file_.endswith('.hess'):
hess_files.append(file_)
break

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if len(hess_files) == 1:
hess_file = hess_files[0]

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else:
expected_hess_name = f"{os.path.basename(self.path).split('.')[0]}.hess"

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for hess_file in hess_files:
if hess_file == expected_hess_name:
break

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else:
raise LogError(f'Could not identify the intended .hess file in {os.path.dirname(self.path)}.\n'

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f'Expected to find {expected_hess_name} in that folder.')

force = None
n_atoms = self.get_number_of_atoms()
n_rows = n_atoms * 3
with open(hess_file, 'r') as f:
line = f.readline()

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while line != '':
if '$hessian' in line:
line = f.readline()
force = np.zeros((n_rows, n_rows), np.float64)

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for i in range(int(math.ceil(n_rows / 5.0))):
line = f.readline()

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for j in range(n_rows):
data = f.readline().split()[1:]

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for k in range(len(data)):
force[j, i * 5 + k] = float(data[k])

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# Convert from atomic units (Hartree/Bohr_radius^2) to J/m^2
force *= 4.35974417e-18 / 5.291772108e-11 ** 2
line = f.readline()
return force

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def load_geometry(self):
"""
Expand Down Expand Up @@ -184,7 +184,7 @@
number = np.array(numbers, np.int)
mass = np.array(mass, np.float64)
if len(number) == 0 or len(coord) == 0 or len(mass) == 0:
raise LogError(f'Unable to read atoms from orca geometry output file {self.path}.')

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return coord, number, mass

Expand Down Expand Up @@ -219,7 +219,7 @@
break
frequencies.extend([float(line_.split()[1])])
else:
raise Exception(f'Frequencies not found in {self.path}')

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frequencies = [f for f in frequencies if f > 0.0]
unscaled_frequencies = frequencies
vibration = HarmonicOscillator(frequencies=(frequencies, "cm^-1"))
Expand All @@ -232,8 +232,8 @@
inertia = list(inertia[0])
if len(inertia):
if any(i == 0.0 for i in inertia):
inertia.remove(0.0)
rot.append(LinearRotor(inertia=(inertia, "amu*angstrom^2"), symmetry=symmetry))

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else:
rot.append(NonlinearRotor(inertia=(inertia, "amu*angstrom^2"), symmetry=symmetry))

Expand Down Expand Up @@ -292,10 +292,10 @@
if len(frequencies) == 1:
return frequencies[0]
elif len(frequencies) > 1:
logging.info('More than one imaginary frequency in Orca output file {0}.'.format(self.path))
return frequencies[0]

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else:
raise LogError(f'Unable to find imaginary frequency in Orca output file {self.path}')

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def get_T1_diagnostic(self):
"""
Expand Down
2 changes: 1 addition & 1 deletion arkane/ess/orcaTest.py
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# #
# RMG - Reaction Mechanism Generator #
# #
# Copyright (c) 2002-2021 Prof. William H. Green (whgreen@mit.edu), #
# Copyright (c) 2002-2023 Prof. William H. Green (whgreen@mit.edu), #
# Prof. Richard H. West (r.west@neu.edu) and the RMG Team (rmg_dev@mit.edu) #
# #
# Permission is hereby granted, free of charge, to any person obtaining a #
Expand Down
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