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Orca 5 sol (#709)
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Added the option to write Orca v5 input files with solvation methods,
plus fixed the error message when sp file is missing for rate
calculations.
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@alongd
alongd authored Oct 30, 2023
2 parents 6b51ce5 + b895514 commit bdaa2a3
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Showing 3 changed files with 117 additions and 15 deletions.
19 changes: 15 additions & 4 deletions arc/job/adapters/orca.py
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
"""
An adapter for executing Orca jobs
An adapter for executing Orca 5 jobs
https://orcaforum.kofo.mpg.de/app.php/portal
"""
Expand Down Expand Up @@ -47,16 +47,13 @@
# method_class: 'HF' for wavefunction methods (hf, mp, cc, dlpno ...). 'KS' for DFT methods.
# options: additional keywords to control job (e.g., TightSCF, NormalPNO ...)
input_template = """!${restricted}${method_class} ${method} ${basis} ${auxiliary_basis} ${keywords}
! NRSCF # using Newton–Raphson SCF algorithm
!${job_type_1}
${job_type_2}
%%maxcore ${memory}
%%pal # job parallelization settings
nprocs ${cpus}
end
%%scf # recommended SCF settings
NRMaxIt 400
NRStart 0.00005
MaxIter 500
end${scan}
${block}
Expand Down Expand Up @@ -312,6 +309,20 @@ def write_input_file(self) -> None:
input_dict['scan'] += f'\nD {torsion} = {dihedral:.1f}, {dihedral - self.scan_res:.1f}, {self.scan_res:.1f}\n'
input_dict['scan'] += '\nend\nend' if len(self.torsions) > 1 else '\nend'

if self.level.solvation_method:
if self.level.solvation_method.lower() == 'smd':
self.add_to_args(val=f"""
%cpcm SMD true
SMDsolvent "{self.level.solvent}"
end
""",
key1='block')
elif self.level.solvation_method.lower() in ['pcm', 'cpcm']:
self.add_to_args(val=f"""
!CPCM({self.level.solvent})
""",
key1='block')

input_dict = update_input_dict_with_args(args=self.args, input_dict=input_dict)

with open(os.path.join(self.local_path, input_filenames[self.job_adapter]), 'w') as f:
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111 changes: 101 additions & 10 deletions arc/job/adapters/orca_test.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,7 @@

"""
This module contains unit tests of the arc.job.adapters.orca module
Compatible with Orca version 5
"""

import math
Expand Down Expand Up @@ -40,36 +41,59 @@ def setUpClass(cls):
H -0.53338088 -0.77135867 -0.54806440""")],
testing=True,
)

cls.job_2 = OrcaAdapter(execution_type='queue',
job_type='sp',
level=Level(method='DLPNO-CCSD(T)', basis='def2-tzvp', auxiliary_basis='def2-tzvp/c',
solvation_method='SMD', solvent='DMSO'),
project='test',
project_directory=os.path.join(ARC_PATH, 'arc', 'testing', 'test_OrcaAdapter'),
species=[ARCSpecies(label='CH3O',
xyz="""C 0.03807240 0.00035621 -0.00484242
O 1.35198769 0.01264937 -0.17195885
H -0.33965241 -0.14992727 1.02079480
H -0.51702680 0.90828035 -0.29592912
H -0.53338088 -0.77135867 -0.54806440""")],
testing=True,
)
cls.job_3 = OrcaAdapter(execution_type='queue',
job_type='sp',
level=Level(method='DLPNO-CCSD(T)', basis='def2-tzvp', auxiliary_basis='def2-tzvp/c',
solvation_method='cpcm', solvent='water'),
project='test',
project_directory=os.path.join(ARC_PATH, 'arc', 'testing', 'test_OrcaAdapter'),
species=[ARCSpecies(label='CH3O',
xyz="""C 0.03807240 0.00035621 -0.00484242
O 1.35198769 0.01264937 -0.17195885
H -0.33965241 -0.14992727 1.02079480
H -0.51702680 0.90828035 -0.29592912
H -0.53338088 -0.77135867 -0.54806440""")],
testing=True,
)
def test_set_cpu_and_mem(self):
"""Test assigning number of cpu's and memory"""
self.job_1.cpu_cores = 48
self.job_1.input_file_memory = None
self.job_1.submit_script_memory = None
self.job_1.set_cpu_and_mem()
self.assertEqual(self.job_1.cpu_cores, 48)
self.assertEqual(self.job_1.cpu_cores, 8)

def test_set_input_file_memory(self):
"""Test setting the input_file_memory argument"""
expected_memory = math.ceil(14 * 1024 / 48)
expected_memory = math.ceil(14 * 1024 / 8)
self.assertEqual(self.job_1.input_file_memory, expected_memory)

def test_write_input_file(self):
"""Test writing Gaussian input files"""
"""Test writing Orca input files"""
self.job_1.write_input_file()
with open(os.path.join(self.job_1.local_path, input_filenames[self.job_1.job_adapter]), 'r') as f:
content_1 = f.read()
job_1_expected_input_file = """!uHF dlpno-ccsd(t) def2-tzvp def2-tzvp/c tightscf normalpno
! NRSCF # using Newton–Raphson SCF algorithm
!sp
%maxcore 299
%maxcore 1792
%pal # job parallelization settings
nprocs 48
nprocs 8
end
%scf # recommended SCF settings
NRMaxIt 400
NRStart 0.00005
MaxIter 500
end
Expand All @@ -84,6 +108,73 @@ def test_write_input_file(self):
"""
self.assertEqual(content_1, job_1_expected_input_file)

def test_write_input_file_with_SMD_solvation(self):
"""Test writing ORCA input files with SMD solvation"""
self.job_2.write_input_file()
with open(os.path.join(self.job_2.local_path, input_filenames[self.job_2.job_adapter]), 'r') as f:
content_2 = f.read()
job_2_expected_input_file = """!uHF dlpno-ccsd(t) def2-tzvp def2-tzvp/c tightscf normalpno
!sp
%maxcore 1792
%pal # job parallelization settings
nprocs 8
end
%scf # recommended SCF settings
MaxIter 500
end
%cpcm SMD true
SMDsolvent "dmso"
end
* xyz 0 2
C 0.03807240 0.00035621 -0.00484242
O 1.35198769 0.01264937 -0.17195885
H -0.33965241 -0.14992727 1.02079480
H -0.51702680 0.90828035 -0.29592912
H -0.53338088 -0.77135867 -0.54806440
*
"""
self.assertEqual(content_2, job_2_expected_input_file)


def test_write_input_file_with_CPCM_solvation(self):
"""Test writing ORCA input files with CPCM solvation"""
self.job_3.write_input_file()
with open(os.path.join(self.job_3.local_path, input_filenames[self.job_3.job_adapter]), 'r') as f:
content_3 = f.read()
job_3_expected_input_file = """!uHF dlpno-ccsd(t) def2-tzvp def2-tzvp/c tightscf normalpno
!sp
%maxcore 1792
%pal # job parallelization settings
nprocs 8
end
%scf # recommended SCF settings
MaxIter 500
end
!CPCM(water)
* xyz 0 2
C 0.03807240 0.00035621 -0.00484242
O 1.35198769 0.01264937 -0.17195885
H -0.33965241 -0.14992727 1.02079480
H -0.51702680 0.90828035 -0.29592912
H -0.53338088 -0.77135867 -0.54806440
*
"""
self.assertEqual(content_3, job_3_expected_input_file)

def test_set_files(self):
"""Test setting files"""
job_1_files_to_upload = [{'file_name': 'submit.sub',
Expand Down
2 changes: 1 addition & 1 deletion arc/statmech/arkane.py
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Original file line number Diff line number Diff line change
Expand Up @@ -540,7 +540,7 @@ def generate_arkane_species_file(self,
if not os.path.isfile(freq_path):
return_none_text = f'the freq file in path {freq_path}'
if not os.path.isfile(sp_path):
return_none_text = f'the freq file in path {sp_path}'
return_none_text = f'the sp file in path {sp_path}'
if return_none_text is not None:
logger.error(f'Could not find {return_none_text} for species {species.label}. Not calculating properties.')
return None
Expand Down

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