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CREST Adapter #807

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8c1ef14
Added Crest into heuristics
calvinp0 Nov 25, 2025
734db3e
Crest Adapter
calvinp0 Nov 27, 2025
8c11525
Added AGENTS.md to gitignore
calvinp0 Nov 27, 2025
8f2d147
ARC Installation fixes
calvinp0 Nov 27, 2025
d2f5e03
Added CREST test and also fixed CodeQL errors
calvinp0 Nov 28, 2025
f421c04
Minor fixes
calvinp0 Nov 28, 2025
152dcbb
Stop tracking AGENTS.md
calvinp0 Nov 28, 2025
55eb8ec
Installation documentation update
calvinp0 Nov 28, 2025
7b89b6e
Update fixes
calvinp0 Nov 28, 2025
2878c2c
Update crest install
calvinp0 Jan 15, 2026
fc0ddfe
Merge remote-tracking branch 'origin/main' into crest_adapter
calvinp0 Jan 15, 2026
49234f3
Updates
calvinp0 Jan 18, 2026
7730a26
Merge branch 'main' into crest_adapter
calvinp0 Jan 18, 2026
96b4150
updates
calvinp0 Jan 19, 2026
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1 change: 1 addition & 0 deletions .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -67,3 +67,4 @@ build/*

*.log
*.xml
AGENTS.md
6 changes: 5 additions & 1 deletion Makefile
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Expand Up @@ -8,7 +8,7 @@ DEVTOOLS_DIR := devtools

.PHONY: all help clean test test-unittests test-functional test-all \
install-all install-ci install-pyrdl install-rmgdb install-autotst install-gcn \
install-gcn-cpu install-kinbot install-sella install-xtb install-torchani install-ob \
install-gcn-cpu install-kinbot install-sella install-xtb install-crest install-torchani install-ob \
lite check-env compile


Expand All @@ -35,6 +35,7 @@ help:
@echo " install-kinbot Install KinBot"
@echo " install-sella Install Sella"
@echo " install-xtb Install xTB"
@echo " install-crest Install CREST"
@echo " install-torchani Install TorchANI"
@echo " install-ob Install OpenBabel"
@echo ""
Expand Down Expand Up @@ -96,6 +97,9 @@ install-sella:
install-xtb:
bash $(DEVTOOLS_DIR)/install_xtb.sh

install-crest:
bash $(DEVTOOLS_DIR)/install_crest.sh

install-torchani:
bash $(DEVTOOLS_DIR)/install_torchani.sh

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1 change: 1 addition & 0 deletions arc/job/adapter.py
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Expand Up @@ -97,6 +97,7 @@ class JobEnum(str, Enum):
# TS search methods
autotst = 'autotst' # AutoTST, 10.1021/acs.jpca.7b07361, 10.26434/chemrxiv.13277870.v2
heuristics = 'heuristics' # ARC's heuristics
crest = 'crest' # CREST conformer/TS search
kinbot = 'kinbot' # KinBot, 10.1016/j.cpc.2019.106947
gcn = 'gcn' # Graph neural network for isomerization, https://doi.org/10.1021/acs.jpclett.0c00500
user = 'user' # user guesses
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5 changes: 3 additions & 2 deletions arc/job/adapters/common.py
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Expand Up @@ -41,7 +41,7 @@
'Cyclic_Ether_Formation': ['kinbot'],
'Cyclopentadiene_scission': ['gcn', 'xtb_gsm'],
'Diels_alder_addition': ['kinbot'],
'H_Abstraction': ['heuristics', 'autotst'],
'H_Abstraction': ['heuristics', 'autotst', 'crest'],
'carbonyl_based_hydrolysis': ['heuristics'],
'ether_hydrolysis': ['heuristics'],
'nitrile_hydrolysis': ['heuristics'],
Expand Down Expand Up @@ -77,7 +77,8 @@
adapters_that_do_not_require_a_level_arg = ['xtb', 'torchani']

# Default is "queue", "pipe" will be called whenever needed. So just list 'incore'.
default_incore_adapters = ['autotst', 'gcn', 'heuristics', 'kinbot', 'psi4', 'xtb', 'xtb_gsm', 'torchani', 'openbabel']
default_incore_adapters = ['autotst', 'crest', 'gcn', 'heuristics', 'kinbot', 'psi4', 'xtb', 'xtb_gsm', 'torchani',
'openbabel']


def _initialize_adapter(obj: 'JobAdapter',
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1 change: 1 addition & 0 deletions arc/job/adapters/ts/__init__.py
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@@ -1,4 +1,5 @@
import arc.job.adapters.ts.autotst_ts
import arc.job.adapters.ts.crest
import arc.job.adapters.ts.gcn_ts
import arc.job.adapters.ts.heuristics
import arc.job.adapters.ts.kinbot_ts
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131 changes: 90 additions & 41 deletions arc/job/adapters/ts/autotst_ts.py
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Expand Up @@ -24,6 +24,8 @@


AUTOTST_PYTHON = settings['AUTOTST_PYTHON']
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Copilot AI Jan 15, 2026

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The logic for setting HAS_AUTOTST is incomplete. Line 22 sets HAS_AUTOTST = True unconditionally, then lines 29-30 may set it to False if AUTOTST_PYTHON is None. However, there's no check if AUTOTST_PYTHON is defined in settings. If settings doesn't have 'AUTOTST_PYTHON', this will raise a KeyError. Consider wrapping AUTOTST_PYTHON retrieval in a try-except block or using settings.get('AUTOTST_PYTHON').

Suggested change
AUTOTST_PYTHON = settings['AUTOTST_PYTHON']
AUTOTST_PYTHON = settings.get('AUTOTST_PYTHON')

Copilot uses AI. Check for mistakes.
if AUTOTST_PYTHON is None:
HAS_AUTOTST = False

logger = get_logger()

Expand Down Expand Up @@ -229,83 +231,130 @@ def execute_incore(self):
charge=rxn.charge,
multiplicity=rxn.multiplicity,
)

reaction_label_fwd = get_autotst_reaction_string(rxn)
reaction_label_rev = get_autotst_reaction_string(ARCReaction(r_species=rxn.p_species,
p_species=rxn.r_species,
reactants=rxn.products,
products=rxn.reactants))
reaction_label_rev = get_autotst_reaction_string(
ARCReaction(
r_species=rxn.p_species,
p_species=rxn.r_species,
reactants=rxn.products,
products=rxn.reactants,
)
)

i = 0
for reaction_label, direction in zip([reaction_label_fwd, reaction_label_rev], ['F', 'R']):
# run AutoTST as a subprocess in the desired direction
script_path = os.path.join(ARC_PATH, 'arc', 'job', 'adapters', 'scripts', 'autotst_script.py')
commands = ['source ~/.bashrc', f'"{AUTOTST_PYTHON}" "{script_path}" "{reaction_label}" "{self.output_path}"']
for reaction_label, direction in zip(
[reaction_label_fwd, reaction_label_rev],
['F', 'R'],
):
script_path = os.path.join(
ARC_PATH, 'arc', 'job', 'adapters', 'scripts', 'autotst_script.py'
)
# 2) Build the bash command to run tst_env’s Python on the script
commands = [
'source ~/.bashrc',
f'"{AUTOTST_PYTHON}" "{script_path}" "{reaction_label}" "{self.output_path}"',
]
command = '; '.join(commands)

tic = datetime.datetime.now()

output = subprocess.run(command, shell=True, executable='/bin/bash')
# 3) Capture stdout/stderr so we can diagnose missing AutoTST
output = subprocess.run(
command,
shell=True,
executable='/bin/bash',
capture_output=True,
text=True,
)

tok = datetime.datetime.now() - tic

if output.returncode:
direction_str = 'forward' if direction == 'F' else 'reverse'
logger.warning(f'AutoTST subprocess did not give a successful return code for {rxn} '
f'in the {direction_str} direction.\n'
f'Got return code: {output.returncode}\n'
f'stdout: {output.stdout}\n'
f'stderr: {output.stderr}')
stderr = output.stderr or ""
stdout = output.stdout or ""

# Special case: autotst itself is missing in tst_env
if 'No module named' in stderr and 'autotst' in stderr:
logger.error(
f"AutoTST subprocess failed for {rxn} because the 'autotst' "
f"package is not importable in the tst_env used by AUTOTST_PYTHON:\n"
f"{stderr}"
)
else:
direction_str = 'forward' if direction == 'F' else 'reverse'
logger.warning(
f'AutoTST subprocess did not give a successful return code for {rxn} '
f'in the {direction_str} direction.\n'
f'Got return code: {output.returncode}\n'
f'stdout: {stdout}\n'
f'stderr: {stderr}'
)

# 4) Check for the YAML output and add TS guesses as before
if os.path.isfile(self.output_path):
results = read_yaml_file(path=self.output_path)
if results:
for result in results:
xyz = xyz_from_data(coords=result['coords'], numbers=result['numbers'])
xyz = xyz_from_data(
coords=result['coords'],
numbers=result['numbers'],
)
unique = True
for other_tsg in rxn.ts_species.ts_guesses:
if other_tsg.success and almost_equal_coords(xyz, other_tsg.initial_xyz):
if other_tsg.success and almost_equal_coords(
xyz, other_tsg.initial_xyz
):
if 'autotst' not in other_tsg.method.lower():
other_tsg.method += ' and AutoTST'
unique = False
break
if unique and not colliding_atoms(xyz):
ts_guess = TSGuess(method='AutoTST',
method_direction=direction,
method_index=i,
t0=tic,
execution_time=tok,
xyz=xyz,
success=True,
index=len(rxn.ts_species.ts_guesses),
)
ts_guess = TSGuess(
method='AutoTST',
method_direction=direction,
method_index=i,
t0=tic,
execution_time=tok,
xyz=xyz,
success=True,
index=len(rxn.ts_species.ts_guesses),
)
rxn.ts_species.ts_guesses.append(ts_guess)
save_geo(xyz=xyz,
path=self.local_path,
filename=f'AutoTST {direction}',
format_='xyz',
comment=f'AutoTST {direction}',
)
save_geo(
xyz=xyz,
path=self.local_path,
filename=f'AutoTST {direction}',
format_='xyz',
comment=f'AutoTST {direction}',
)
i += 1
else:
ts_guess = TSGuess(method=f'AutoTST',
method_direction=direction,
method_index=i,
t0=tic,
execution_time=tok,
success=False,
index=len(rxn.ts_species.ts_guesses),
)
ts_guess = TSGuess(
method='AutoTST',
method_direction=direction,
method_index=i,
t0=tic,
execution_time=tok,
success=False,
index=len(rxn.ts_species.ts_guesses),
)
rxn.ts_species.ts_guesses.append(ts_guess)
i += 1

if len(self.reactions) < 5:
successes = len([tsg for tsg in rxn.ts_species.ts_guesses if tsg.success and 'autotst' in tsg.method])
successes = len(
[tsg for tsg in rxn.ts_species.ts_guesses
if tsg.success and 'autotst' in tsg.method.lower()]
)
if successes:
logger.info(f'AutoTST successfully found {successes} TS guesses for {rxn.label}.')
else:
logger.info(f'AutoTST did not find any successful TS guesses for {rxn.label}.')

self.final_time = datetime.datetime.now()


def execute_queue(self):
"""
(Execute a job to the server's queue.)
Expand Down
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