Skip to content

Repair the Gaussian ESS troubleshooting ladder and route construction #1006

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

Open
calvinp0 wants to merge 4 commits into
base: main
Choose a base branch
from
Open

Repair the Gaussian ESS troubleshooting ladder and route construction #1006

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
4 commits
Select commit Hold shift + click to select a range
724d374
Skip the ~/.arc settings/submit/inputs overlays under pytest
calvinp0 Aug 22, 2026
550401a
Repair and extend the Gaussian ESS troubleshooting ladder
calvinp0 Aug 22, 2026
72ccaf0
Pass is_ts to trsh_ess_job so the opt-cycle ladder is TS-aware
calvinp0 Aug 22, 2026
4cf9fb0
Fix Gaussian route construction: trsh keywords, integration grid, gue…
calvinp0 Aug 22, 2026
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
23 changes: 20 additions & 3 deletions arc/imports.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -56,13 +56,30 @@ def resolve_overridden_dependents(settings: dict, local_settings_dict: dict) ->
queue_deferred_warning(msg)


def _local_overlays_disabled() -> bool:
"""Return True when ~/.arc/{settings,submit,inputs}.py overlays should be skipped.

The repo's arc/settings/settings.py is always loaded as the baseline. This
guard only controls whether a user's personal ~/.arc/*.py files are layered
on top — we want them ignored under pytest (so tests see the same defaults
CI does) and overridable explicitly via env var.

Triggered by either pytest being loaded (`'pytest' in sys.modules`, true
from collection onward) or an explicit ARC_IGNORE_LOCAL_SETTINGS=1 env var.
"""
if os.environ.get('ARC_IGNORE_LOCAL_SETTINGS') == '1':
return True
return 'pytest' in sys.modules


# Common imports where the user can optionally put a modified copy of settings.py or submit.py file under ~/.arc
home = os.getenv("HOME") or os.path.expanduser("~")
local_arc_path = os.path.join(home, '.arc')
_skip_local = _local_overlays_disabled()

local_arc_settings_path = os.path.join(local_arc_path, 'settings.py')
settings = {key: val for key, val in vars(arc_settings).items() if '__' not in key}
if os.path.isfile(local_arc_settings_path):
if not _skip_local and os.path.isfile(local_arc_settings_path):
local_settings = dict()
if local_arc_path not in sys.path:
sys.path.insert(1, local_arc_path)
Expand All @@ -79,7 +96,7 @@ def resolve_overridden_dependents(settings: dict, local_settings_dict: dict) ->
if 'global_ess_settings' in local_settings_dict and local_settings_dict['global_ess_settings'] else None

local_arc_submit_path = os.path.join(local_arc_path, 'submit.py')
if os.path.isfile(local_arc_submit_path):
if not _skip_local and os.path.isfile(local_arc_submit_path):
local_incore_commands, local_pipe_submit, local_submit_scripts = dict(), dict(), dict()
if local_arc_path not in sys.path:
sys.path.insert(1, local_arc_path)
Expand All @@ -103,7 +120,7 @@ def resolve_overridden_dependents(settings: dict, local_settings_dict: dict) ->
submit_scripts.update(local_submit_scripts)

local_arc_inputs_path = os.path.join(local_arc_path, 'inputs.py')
if os.path.isfile(local_arc_inputs_path):
if not _skip_local and os.path.isfile(local_arc_inputs_path):
local_input_files = dict()
if local_arc_path not in sys.path:
sys.path.insert(1, local_arc_path)
Expand Down
65 changes: 49 additions & 16 deletions arc/job/adapters/gaussian.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -250,8 +250,17 @@ def write_input_file(self) -> None:
input_dict['method'] = self.level.method
input_dict['multiplicity'] = self.multiplicity
input_dict['scan_trsh'] = self.args['keyword']['scan_trsh'] if 'scan_trsh' in self.args['keyword'] else ''
integral_algorithm = 'Acc2E=14' if 'Acc2E=14' in input_dict['trsh'] else 'Acc2E=12'
input_dict['trsh'] = input_dict['trsh'].replace('int=(Acc2E=14)', '') if 'Acc2E=14' in input_dict['trsh'] else input_dict['trsh']
acc2e_requested = 'Acc2E=14' in input_dict['trsh'] # troubleshooting asked to tighten integrals
integral_algorithm = 'Acc2E=14' if acc2e_requested else 'Acc2E=12'
input_dict['trsh'] = input_dict['trsh'].replace('int=(Acc2E=14)', '') if acc2e_requested else input_dict['trsh']
# The InaccurateQuadrature remedy escalates to a finer DFT integration grid (recorded as
# 'int=grid=NNNMMM'). Fold that grid into the single integral=() keyword (replacing the
# default ultrafine) rather than emitting a second, conflicting Int keyword - ultrafine is
# (99,590), the remedy grid e.g. 300590 = (300,590) is finer. Sourced from ess_trsh_methods
# so the finer grid persists across retries, and the standalone int=grid= token is dropped.
grid_remedy = next((m for m in (self.ess_trsh_methods or []) if m.startswith('int=grid=')), None)
integration_grid = grid_remedy.split('int=grid=', 1)[1] if grid_remedy else 'ultrafine'
input_dict['trsh'] = re.sub(r'\s*int=grid=\S+', '', input_dict['trsh']) if grid_remedy else input_dict['trsh']
input_dict['xyz'] = [xyz_to_str(xyz) for xyz in self.xyz] if self.run_multi_species else xyz_to_str(self.xyz)

if self.level.basis is not None:
Expand All @@ -267,9 +276,12 @@ def write_input_file(self) -> None:

if self.level.method[:2] == 'ro':
self.add_to_args(val='use=L506')
elif not('no_xqc' in list(self.args['trsh'].values())) and 'qc' in input_dict['trsh']:
elif 'no_xqc' not in self.ess_trsh_methods \
and not('no_xqc' in list(self.args['trsh'].values())) and 'qc' in input_dict['trsh']:
# xqc will do qc (quadratic convergence) if the job fails w/o it, so use it by default.
# replace qc with xqc if it's not already there
# replace qc with xqc if it's not already there.
# 'no_xqc' in ess_trsh_methods records that the xqc algorithm itself already failed
# (Gaussian l508), so don't upgrade qc to xqc in that case (see arc.job.trsh.trsh_keyword_no_qc).
input_dict['trsh'] = input_dict['trsh'].replace('qc', 'xqc')

if self.level.method == 'cbs-qb3-paraskevas':
Expand All @@ -293,7 +305,7 @@ def write_input_file(self) -> None:
if self.fine:
if self.level.method_type in ['dft', 'composite']:
# Note that the Acc2E argument is not available in Gaussian03
input_dict['fine'] = f'integral=(grid=ultrafine, {integral_algorithm})'
input_dict['fine'] = f'integral=(grid={integration_grid}, {integral_algorithm})'
# input_dict['trsh'] may have scf=(...) in it, so we need to add the tight and direct keywords to it
scf_start = input_dict['trsh'].find('scf=(')
scf_end = input_dict['trsh'].find(')', scf_start)
Expand All @@ -317,13 +329,13 @@ def write_input_file(self) -> None:
else f"opt=({', '.join(key for key in keywords)})"

elif self.job_type == 'freq':
input_dict['job_type_2'] = f'freq IOp(7/33=1) scf=(tight, direct) integral=(grid=ultrafine, {integral_algorithm})'
input_dict['job_type_2'] = f'freq IOp(7/33=1) scf=(tight, direct) integral=(grid={integration_grid}, {integral_algorithm})'

elif self.job_type == 'optfreq':
input_dict['job_type_2'] = 'freq IOp(7/33=1)'

elif self.job_type in ['sp', 'conf_sp']:
input_dict['job_type_1'] = f'integral=(grid=ultrafine, {integral_algorithm})'
input_dict['job_type_1'] = f'integral=(grid={integration_grid}, {integral_algorithm})'
if input_dict['trsh']:
input_dict['trsh'] += ' '
input_dict['trsh'] += 'scf=(tight, direct)'
Expand All @@ -344,7 +356,7 @@ def write_input_file(self) -> None:

ts = 'ts, ' if self.is_ts else ''
input_dict['job_type_1'] = f'opt=({ts}modredundant, calcfc, noeigentest, maxStep=5)' \
f'integral=(grid=ultrafine, {integral_algorithm})'
f'integral=(grid={integration_grid}, {integral_algorithm})'
if input_dict['trsh']:
input_dict['trsh'] += ' '
input_dict['trsh'] += 'scf=(tight, direct)'
Expand All @@ -355,7 +367,7 @@ def write_input_file(self) -> None:
elif self.job_type == 'irc':
if self.fine:
# Note that the Acc2E argument is not available in Gaussian03
input_dict['fine'] = f'integral=(grid=ultrafine, {integral_algorithm})'
input_dict['fine'] = f'integral=(grid={integration_grid}, {integral_algorithm})'
# We need to add scf=(direct) to the trsh argument
# But we to check if it's already there, and
if 'direct' not in input_dict['trsh']:
Expand All @@ -376,6 +388,16 @@ def write_input_file(self) -> None:

input_dict['job_type_1'] = f'irc=(CalcAll, {self.irc_direction}, maxpoints=50, stepsize=7)'

if (acc2e_requested or grid_remedy) and not self.fine and not input_dict['fine'] \
and self.job_type in ['opt', 'conf_opt', 'optfreq', 'composite', 'irc']:
# Fine jobs fold Acc2E=14 (and any InaccurateQuadrature grid remedy) into integral=(...).
# A non-fine opt/IRC job would otherwise silently drop those troubleshooting requests
# (no integral= in the route), producing a byte-identical resubmit. Emit the integral=()
# keyword so the tightened accuracy and/or finer grid actually take effect (the default
# ultrafine grid stays a fine-only concern - only an explicit grid remedy is emitted here).
grid_part = f'grid={integration_grid}, ' if grid_remedy else ''
input_dict['fine'] = f'integral=({grid_part}{integral_algorithm})'

for constraint_tuple in self.constraints:
constraint_type = constraint_type_dict[len(constraint_tuple[0])]
constraint_atom_indices = ' '.join([str(atom_index) for atom_index in constraint_tuple[0]])
Expand All @@ -387,21 +409,32 @@ def write_input_file(self) -> None:
input_dict['job_type_1'] += f' SCRF=({self.level.solvation_method}, Solvent={self.level.solvent})'

if self.species[0].number_of_atoms > 1:
if input_dict['job_type_1']:
input_dict['job_type_1'] += ' '
guess_keyword = ''
if 'guess=INDO' in input_dict['trsh']:
input_dict['job_type_1'] += 'guess=INDO'
guess_keyword = '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_keyword = ' guess=read'
elif any(spc.multiplicity == 1 and spc.number_of_radicals is not None and spc.number_of_radicals > 1
for spc in self.species):
guess_keyword = ' guess=mix'
if guess_keyword:
if input_dict['job_type_1']:
input_dict['job_type_1'] += ' '
input_dict['job_type_1'] += guess_keyword

# Fix OPT
terms_opt = [r'opt=\((.*?)\)', r'opt=(\w+)']
input_dict, parameters_opt = combine_parameters(input_dict, terms_opt)
# If 'opt' parameters are found, concatenate and reinsert them
if parameters_opt:
# Remove duplicate parameters
# Keep a single force-constant recompute directive (calcall > recalcfc=* > calcfc) so a
# troubleshot opt=() clause never carries conflicting Hessian options - the base route
# always contributes 'calcfc', while the MaxOptCycles ladder may add recalcfc/calcall.
if 'calcall' in parameters_opt:
parameters_opt = [p for p in parameters_opt if p != 'calcfc' and not p.startswith('recalcfc')]
elif any(p.startswith('recalcfc') for p in parameters_opt):
parameters_opt = [p for p in parameters_opt if p != 'calcfc']
combined_opt_params = ','.join(parameters_opt)
input_dict['job_type_1'] = f"opt=({combined_opt_params}) {input_dict['job_type_1']}"

Expand Down
Loading
Loading