Skip to content

Fix guess keyword consistency for restricted TS routes #973

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Closed
calvinp0 wants to merge 1 commit into from
Closed

Fix guess keyword consistency for restricted TS routes #973

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
27 changes: 18 additions & 9 deletions arc/job/adapters/gaussian.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -386,15 +386,26 @@ def write_input_file(self) -> None:
if self.level.solvation_method is not None:
input_dict['job_type_1'] += f' SCRF=({self.level.solvation_method}, Solvent={self.level.solvent})'

restricted_flags = is_restricted(self)
restricted_flags = [restricted_flags] if isinstance(restricted_flags, bool) else restricted_flags

if self.species[0].number_of_atoms > 1:
if input_dict['job_type_1']:
input_dict['job_type_1'] += ' '
guess = ''
if 'guess=INDO' in input_dict['trsh']:
input_dict['job_type_1'] += 'guess=INDO'
guess = 'guess=INDO'
input_dict['trsh'] = input_dict['trsh'].replace('guess=INDO', '')
else:
input_dict['job_type_1'] += ' guess=read' if self.checkfile is not None and os.path.isfile(self.checkfile) \
else ' guess=mix'
elif self.checkfile is not None and os.path.isfile(self.checkfile):
guess = 'guess=read'
elif not all(restricted_flags):
guess = 'guess=mix'
elif self.is_ts:
logger.info(f'Not using guess=mix for TS {self.species_label}, which is computed with a restricted '
f'reference (multiplicity {self.multiplicity}): guess=mix only acts on an unrestricted '
f'reference.')
if guess:
if input_dict['job_type_1']:
input_dict['job_type_1'] += ' '
input_dict['job_type_1'] += guess

# Fix OPT
terms_opt = [r'opt=\((.*?)\)', r'opt=(\w+)']
Expand Down Expand Up @@ -424,9 +435,7 @@ def write_input_file(self) -> None:
input_file = ''
input_dict_origin = input_dict.copy()

restricted_list_bool = is_restricted(self)
restricted_list = ["" if flag else 'u' for flag in ([restricted_list_bool]
if isinstance(restricted_list_bool, bool) else restricted_list_bool)]
restricted_list = ["" if flag else 'u' for flag in restricted_flags]

with open(os.path.join(self.local_path, input_filenames[self.job_adapter]), 'w') as f:
if not self.run_multi_species:
Expand Down
122 changes: 108 additions & 14 deletions arc/job/adapters/gaussian_test.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -174,6 +174,57 @@ def setUpClass(cls):
testing=True,
)

ts_xyz = """O -0.80000000 0.00000000 0.00000000
H 0.00000000 0.00000000 0.00000000
C 1.30000000 0.00000000 0.00000000
H 1.70000000 1.02000000 0.00000000
H 1.70000000 -0.51000000 0.88000000
H 1.70000000 -0.51000000 -0.88000000"""
cls.job_singlet_ts = GaussianAdapter(execution_type='queue',
job_type='opt',
level=Level(method='wb97xd', basis='def2-TZVP'),
project='test',
project_directory=os.path.join(ARC_TESTING_PATH, 'test_GaussianAdapter'),
species=[ARCSpecies(label='TS_singlet', xyz=ts_xyz, is_ts=True, multiplicity=1)],
testing=True,
)
cls.job_doublet_ts = GaussianAdapter(execution_type='queue',
job_type='opt',
level=Level(method='wb97xd', basis='def2-TZVP'),
project='test',
project_directory=os.path.join(ARC_TESTING_PATH, 'test_GaussianAdapter'),
species=[ARCSpecies(label='TS_doublet',
xyz="""C 0.00000000 0.00000000 0.00000000
H 0.00000000 0.00000000 1.09000000
H 1.02000000 0.00000000 -0.36000000
H -0.51000000 0.88000000 -0.36000000
H -0.51000000 -0.88000000 -0.36000000
H -1.30000000 2.24000000 -0.92000000""",
is_ts=True, multiplicity=2)],
testing=True,
)
cls.job_singlet_spc = GaussianAdapter(execution_type='queue',
job_type='opt',
level=Level(method='wb97xd', basis='def2-TZVP'),
project='test',
project_directory=os.path.join(ARC_TESTING_PATH, 'test_GaussianAdapter'),
species=[ARCSpecies(label='methanol', smiles='CO')],
testing=True,
)
checkfile_path = os.path.join(ARC_TESTING_PATH, 'test_GaussianAdapter', 'check.chk')
os.makedirs(os.path.dirname(checkfile_path), exist_ok=True)
with open(checkfile_path, 'w') as f:
f.write('')
cls.job_singlet_ts_with_checkfile = GaussianAdapter(execution_type='queue',
job_type='opt',
level=Level(method='wb97xd', basis='def2-TZVP'),
checkfile=checkfile_path,
project='test',
project_directory=os.path.join(ARC_TESTING_PATH, 'test_GaussianAdapter'),
species=[ARCSpecies(label='TS_singlet_restart', xyz=ts_xyz, is_ts=True, multiplicity=1)],
testing=True,
)

# Setting up for ESS troubleshooting input file writing

label = 'anion'
Expand Down Expand Up @@ -666,7 +717,7 @@ def test_write_input_file(self):
%mem=14193mb
%NProcShared=8

#P opt=(calcfc,maxStep=5,modredundant,noeigentest) integral=(grid=ultrafine, Acc2E=12) guess=mix wb97xd/def2tzvp IOp(2/9=2000) scf=(direct,tight)
#P opt=(calcfc,maxStep=5,modredundant,noeigentest) integral=(grid=ultrafine, Acc2E=12) wb97xd/def2tzvp IOp(2/9=2000) scf=(direct,tight)

ethanol

Expand Down Expand Up @@ -764,6 +815,49 @@ def test_write_input_file(self):
"""
self.assertEqual(content_opt_uff, job_opt_uff_expected_input_file)

def get_route(self, job) -> str:
"""
Write a job's input file and return its route section.

Args:
job (GaussianAdapter): The job adapter object.

Returns:
str: The route section (the line starting with '#P').
"""
job.write_input_file()
with open(os.path.join(job.local_path, input_filenames[job.job_adapter]), 'r') as f:
content = f.read()
return [line for line in content.splitlines() if line.startswith('#P')][0]

def test_guess_mix_requires_an_unrestricted_reference(self):
"""Test that guess=mix is only added to the route of an unrestricted job"""
route_singlet_ts = self.get_route(self.job_singlet_ts)
self.assertNotIn('guess=mix', route_singlet_ts)
self.assertIn(' wb97xd', route_singlet_ts)

route_doublet_ts = self.get_route(self.job_doublet_ts)
self.assertIn('guess=mix', route_doublet_ts)
self.assertIn(' uwb97xd', route_doublet_ts)

route_singlet_spc = self.get_route(self.job_singlet_spc)
self.assertNotIn('guess=mix', route_singlet_spc)

route_with_checkfile = self.get_route(self.job_singlet_ts_with_checkfile)
self.assertIn('guess=read', route_with_checkfile)
self.assertNotIn('guess=mix', route_with_checkfile)

def test_guess_mix_omission_is_logged_once_for_a_ts(self):
"""Test that omitting guess=mix from a restricted TS job is reported once, and is silent for a non-TS"""
with self.assertLogs('arc', level='INFO') as context_manager:
self.job_singlet_ts.write_input_file()
guess_mix_records = [record for record in context_manager.output if 'guess=mix' in record]
self.assertEqual(len(guess_mix_records), 1)
self.assertIn('TS_singlet', guess_mix_records[0])

with self.assertNoLogs('arc', level='INFO'):
self.job_singlet_spc.write_input_file()

def test_set_files(self):
"""Test setting files"""
job_3_files_to_upload = [{'file_name': 'submit.sub',
Expand Down Expand Up @@ -796,7 +890,7 @@ def test_gaussian_def2tzvp(self):
def test_trsh_write_input_file(self):
"""Test writing a trsh input file
10. Create an input file for a job with int=(Acc2E=14) included
11. Create an input file for a job with guess=mix included (removal of Checkfile via ess_trsh_methods)
11. Create an input file for a job whose checkfile was removed via ess_trsh_methods
12. Create an input file for a job with nosymm included, and also the first pass of SCF error troubleshooting
13. Create an input file for a job with NDamp=30 included, and also the previous pass of SCF error troubleshooting
14. Create an input file for a job with NoDIIS included, and also previous passes of SCF error troubleshooting
Expand Down Expand Up @@ -836,7 +930,7 @@ def test_trsh_write_input_file(self):
%mem=14193mb
%NProcShared=8

#P opt=(calcfc,maxcycle=100,maxstep=5,tight) guess=mix wb97xd integral=(grid=ultrafine, Acc2E=14) IOp(2/9=2000) scf=(direct,tight)
#P opt=(calcfc,maxcycle=100,maxstep=5,tight) wb97xd integral=(grid=ultrafine, Acc2E=14) IOp(2/9=2000) scf=(direct,tight)

ethanol

Expand All @@ -862,7 +956,7 @@ def test_trsh_write_input_file(self):
%mem=14193mb
%NProcShared=8

#P opt=(calcfc,maxcycle=100,maxstep=5,tight) guess=mix wb97xd integral=(grid=ultrafine, Acc2E=14) IOp(2/9=2000) nosymm scf=(direct,tight,xqc)
#P opt=(calcfc,maxcycle=100,maxstep=5,tight) wb97xd integral=(grid=ultrafine, Acc2E=14) IOp(2/9=2000) nosymm scf=(direct,tight,xqc)

ethanol

Expand All @@ -888,7 +982,7 @@ def test_trsh_write_input_file(self):
%mem=14193mb
%NProcShared=8

#P opt=(calcfc,maxcycle=100,maxstep=5,tight) guess=mix wb97xd integral=(grid=ultrafine, Acc2E=14) IOp(2/9=2000) nosymm scf=(NDamp=30,direct,tight,xqc)
#P opt=(calcfc,maxcycle=100,maxstep=5,tight) wb97xd integral=(grid=ultrafine, Acc2E=14) IOp(2/9=2000) nosymm scf=(NDamp=30,direct,tight,xqc)

ethanol

Expand All @@ -914,7 +1008,7 @@ def test_trsh_write_input_file(self):
%mem=14193mb
%NProcShared=8

#P opt=(calcfc,maxcycle=100,maxstep=5,tight) guess=mix wb97xd integral=(grid=ultrafine, Acc2E=14) IOp(2/9=2000) nosymm scf=(NDamp=30,NoDIIS,direct,tight,xqc)
#P opt=(calcfc,maxcycle=100,maxstep=5,tight) wb97xd integral=(grid=ultrafine, Acc2E=14) IOp(2/9=2000) nosymm scf=(NDamp=30,NoDIIS,direct,tight,xqc)

ethanol

Expand All @@ -940,7 +1034,7 @@ def test_trsh_write_input_file(self):
%mem=14193mb
%NProcShared=8

#P opt=(calcfc,cartesian,maxcycle=100,maxstep=5,tight) guess=mix wb97xd integral=(grid=ultrafine, Acc2E=14) IOp(2/9=2000) nosymm scf=(NDamp=30,NoDIIS,direct,tight,xqc)
#P opt=(calcfc,cartesian,maxcycle=100,maxstep=5,tight) wb97xd integral=(grid=ultrafine, Acc2E=14) IOp(2/9=2000) nosymm scf=(NDamp=30,NoDIIS,direct,tight,xqc)

ethanol

Expand Down Expand Up @@ -994,7 +1088,7 @@ def test_trsh_write_input_file(self):
%mem=14193mb
%NProcShared=8

#P opt=(calcfc,maxcycle=200,maxstep=5,tight) guess=mix wb97xd integral=(grid=ultrafine, Acc2E=14) IOp(2/9=2000) scf=(direct,tight,xqc)
#P opt=(calcfc,maxcycle=200,maxstep=5,tight) wb97xd integral=(grid=ultrafine, Acc2E=14) IOp(2/9=2000) scf=(direct,tight,xqc)

ethanol

Expand All @@ -1020,7 +1114,7 @@ def test_trsh_write_input_file(self):
%mem=14193mb
%NProcShared=8

#P opt=(calcfc,maxcycle=100,maxstep=5,tight) guess=mix wb97xd integral=(grid=ultrafine, Acc2E=14) IOp(2/9=2000) int=grid=300590 scf=(direct,tight)
#P opt=(calcfc,maxcycle=100,maxstep=5,tight) wb97xd integral=(grid=ultrafine, Acc2E=14) IOp(2/9=2000) int=grid=300590 scf=(direct,tight)

ethanol

Expand All @@ -1046,7 +1140,7 @@ def test_trsh_write_input_file(self):
%mem=14193mb
%NProcShared=8

#P opt=(calcfc,maxcycle=100,maxstep=5,tight) guess=mix wb97xd integral=(grid=ultrafine, Acc2E=14) IOp(2/9=2000) nosymm scf=(Fermi,NDamp=30,NoDIIS,NoVarAcc,Noincfock,direct,tight,xqc)
#P opt=(calcfc,maxcycle=100,maxstep=5,tight) wb97xd integral=(grid=ultrafine, Acc2E=14) IOp(2/9=2000) nosymm scf=(Fermi,NDamp=30,NoDIIS,NoVarAcc,Noincfock,direct,tight,xqc)

ethanol

Expand All @@ -1072,7 +1166,7 @@ def test_trsh_write_input_file(self):
%mem=14193mb
%NProcShared=8

#P opt=(calcfc,maxcycle=100,maxstep=5,tight) guess=mix wb97xd integral=(grid=ultrafine, Acc2E=14) IOp(2/9=2000) scf=(NDamp=30,NoDIIS,NoVarAcc,direct,tight,xqc)
#P opt=(calcfc,maxcycle=100,maxstep=5,tight) wb97xd integral=(grid=ultrafine, Acc2E=14) IOp(2/9=2000) scf=(NDamp=30,NoDIIS,NoVarAcc,direct,tight,xqc)

ethanol

Expand Down Expand Up @@ -1126,7 +1220,7 @@ def test_trsh_write_input_file(self):
%mem=14193mb
%NProcShared=8

#P opt=(calcfc,maxcycle=200,maxstep=5,tight) guess=mix wb97xd integral=(grid=ultrafine, Acc2E=14) IOp(2/9=2000) scf=(direct,tight)
#P opt=(calcfc,maxcycle=200,maxstep=5,tight) wb97xd integral=(grid=ultrafine, Acc2E=14) IOp(2/9=2000) scf=(direct,tight)

ethanol

Expand All @@ -1153,7 +1247,7 @@ def test_trsh_write_input_file(self):
%mem=14193mb
%NProcShared=8

#P opt=(RFO,calcfc,maxcycle=200,maxstep=5,tight) guess=mix wb97xd integral=(grid=ultrafine, Acc2E=14) IOp(2/9=2000) scf=(direct,tight)
#P opt=(RFO,calcfc,maxcycle=200,maxstep=5,tight) wb97xd integral=(grid=ultrafine, Acc2E=14) IOp(2/9=2000) scf=(direct,tight)

ethanol

Expand All @@ -1180,7 +1274,7 @@ def test_trsh_write_input_file(self):
%mem=14193mb
%NProcShared=8

#P opt=(GDIIS,calcfc,maxcycle=200,maxstep=5,tight) guess=mix wb97xd integral=(grid=ultrafine, Acc2E=14) IOp(2/9=2000) scf=(direct,tight)
#P opt=(GDIIS,calcfc,maxcycle=200,maxstep=5,tight) wb97xd integral=(grid=ultrafine, Acc2E=14) IOp(2/9=2000) scf=(direct,tight)

ethanol

Expand Down
Loading