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c7e9c0a
Adds angstrom to bohr conversion factor
calvinp0 Feb 9, 2026
c727294
Adds CREST settings and installation for transition state search
calvinp0 Feb 9, 2026
e265cdd
Adds CREST TS search adapter
calvinp0 Feb 9, 2026
432e594
Adds CREST documentation
calvinp0 Feb 9, 2026
5d1612d
Normalizes TSGuess method sources
calvinp0 Feb 9, 2026
8891252
Adds CREST to available TS search methods
calvinp0 Feb 9, 2026
146a145
Adds CREST as TS adapter option
calvinp0 Feb 9, 2026
abd9201
Adds function to reorder XYZ strings.
calvinp0 Feb 9, 2026
87f3c51
Fixes restart tests for parallel execution
calvinp0 Feb 9, 2026
0baa098
Added the job pipe sub-module
alongd Apr 3, 2026
cab5b28
Updated the pipe submission script
alongd Apr 3, 2026
f8d102b
Added pipe_settings
alongd Apr 3, 2026
24ac9db
Added the pipe_worker script
alongd Apr 3, 2026
9e7cab6
Removed the previous pipe implementation
alongd Apr 3, 2026
96c70ce
Implement pipe into Scheduler
alongd Apr 3, 2026
1b2a9cb
Docs: pipe mode
alongd Apr 3, 2026
1b20560
Merge branch 'main' into crest_adapter
calvinp0 Apr 5, 2026
a18828f
Merge branch 'pipe' into crest_adapter
calvinp0 Apr 5, 2026
42b0798
Fixes
calvinp0 Apr 5, 2026
63207c4
Adjustments
calvinp0 Apr 5, 2026
5c7dc77
Update
calvinp0 Apr 5, 2026
c46792c
Thread back to Scheduler after completion of TS pipeline
calvinp0 Apr 6, 2026
9840d33
Race to condition
calvinp0 Apr 6, 2026
15503d9
Better reporting
calvinp0 Apr 6, 2026
de8e67b
Added troubleshooting of failed indiv. pipe jobs
calvinp0 Apr 6, 2026
6ae8b8c
Further updates
calvinp0 Apr 6, 2026
00b5e2f
Updates
calvinp0 Apr 6, 2026
a9ac64f
Scratch fix
calvinp0 Apr 6, 2026
c26d5b2
Path sep
calvinp0 Apr 6, 2026
7986864
Handle existing pipe directories on fresh start
calvinp0 Apr 7, 2026
b995e05
Handle existing pipe directories on fresh start
calvinp0 Apr 7, 2026
5e67ea4
Add FAILED_ESS task state and document pipe task lifecycle
calvinp0 Apr 7, 2026
3be97bf
Fix premature 'all conformer jobs terminated' when others still running
calvinp0 Apr 7, 2026
c5b659f
Move pipe directories from runs/ into calcs/ with auto-indexing
calvinp0 Apr 7, 2026
a985a3c
Document pipe directory structure in advanced.rst
calvinp0 Apr 7, 2026
b3b54ec
Write task_summary.txt on pipe run completion
calvinp0 Apr 7, 2026
1267ea5
Write task_summary.txt on pipe run completion
calvinp0 Apr 7, 2026
52c558d
Add tests for pipe directory restructure, ESS error classification, a…
calvinp0 Apr 7, 2026
9d86a9a
Add tests for pipe directory restructure, ESS error classification, a…
calvinp0 Apr 7, 2026
86d8f12
Fix premature check_all_done when species has active pipe run
calvinp0 Apr 7, 2026
456bca8
Fix unused variable in pipe_state_test
calvinp0 Apr 7, 2026
41f0454
Fix worker tests: mock _parse_ess_error for mockter adapter
calvinp0 Apr 8, 2026
b948f75
Fix species tests for method_sources in TSGuess
calvinp0 Apr 8, 2026
7a4c61a
Merge remote-tracking branch 'origin/main' into crest_adapter_pipe
calvinp0 Apr 8, 2026
02cddd7
Improve Arkane AEC and BAC validation and logging
calvinp0 Apr 8, 2026
21f1880
Resolve AEC and BAC keys independently for Arkane corrections
calvinp0 Apr 8, 2026
3f21891
Enhance Arkane level of theory identification and AEC validation logging
calvinp0 Apr 8, 2026
591b492
Support independent AEC and BAC keys in the QM corrections script
calvinp0 Apr 8, 2026
7425633
Merge branch 'arkane_m_fix' into crest_adapter_pipe
calvinp0 Apr 8, 2026
254a29f
Improve Arkane AEC and BAC validation and logging
calvinp0 Apr 8, 2026
78fc445
Resolve AEC and BAC keys independently for Arkane corrections
calvinp0 Apr 8, 2026
7261198
Enhance Arkane level of theory identification and AEC validation logging
calvinp0 Apr 8, 2026
938c49b
Support independent AEC and BAC keys in the QM corrections script
calvinp0 Apr 8, 2026
801498b
Merge branch 'arkane_m_fix' into crest_adapter_pipe
calvinp0 Apr 8, 2026
1e71353
Fix stranding species when conformer troubleshooting is exhausted
calvinp0 Apr 9, 2026
94aa7d5
Refine pipe resubmission logic to prevent redundant scheduler jobs
calvinp0 Apr 9, 2026
f3bc145
Handle monoatomic species for DLPNO methods
calvinp0 Apr 10, 2026
dd796ed
Handle monoatomic species for DLPNO methods in Orca
calvinp0 Apr 10, 2026
abeabd2
Handle DLPNO methods for monoatomic species
calvinp0 Apr 10, 2026
a4cf6fb
Fix switch_ts to reset state & clean up IRC when switching TS guesses
calvinp0 Apr 11, 2026
994d6c4
Pass server job IDs to the pipe coordinator during polling
calvinp0 Apr 12, 2026
701f986
Handle task initialization failures in the pipe worker
calvinp0 Apr 12, 2026
58b8fd5
Handle terminated scheduler jobs during pipe reconciliation
calvinp0 Apr 12, 2026
86b8044
Detect terminated scheduler jobs during pipe polling
calvinp0 Apr 12, 2026
d7258d3
Added CANCELLED
calvinp0 Apr 12, 2026
a7e9f63
Merge branch 'main' into crest_adapter_pipe
calvinp0 Apr 12, 2026
5646c5b
Merge branch 'pipe_job_cancel' into crest_adapter_pipe
calvinp0 Apr 12, 2026
2dbae7a
Merge branch 'main' into crest_adapter_pipe
calvinp0 Apr 14, 2026
eb83cc8
Fix pipe jobs immediately failing due to stale server_job_ids snapshot
calvinp0 Apr 14, 2026
b8c6644
Fix switch_ts resetting rotors convergence flag and stale rotors_dict
calvinp0 Apr 15, 2026
9e1b3fa
Wire Level.cabs into ORCA input file generation
calvinp0 Apr 18, 2026
ef121b6
Emit no whitespace when cabs is unset
calvinp0 Apr 18, 2026
885fa2f
Raise before ORCA submission when F12 method lacks a CABS basis
calvinp0 Apr 18, 2026
1a59773
Preserve aux_basis/cabs/solvation when stripping DLPNO for monoatomics
calvinp0 Apr 18, 2026
8c68b90
Auto-retry non-RI F12-CC jobs with /RI on UHF references (ORCA)
calvinp0 Apr 18, 2026
b40f76e
Only strip DLPNO for single-electron monoatomics (H/D/T), not all atoms
calvinp0 Apr 18, 2026
c6b87c4
Stop duplicating scf_convergence / dlpno_threshold keywords
calvinp0 Apr 18, 2026
87ce966
Dedup DFT grid keyword the same way as SCF/DLPNO
calvinp0 Apr 18, 2026
9182a1a
Merge branch 'main' into crest_adapter
calvinp0 Apr 18, 2026
0149310
Fixes
calvinp0 Apr 18, 2026
3e8a7e0
Diagnostics.
calvinp0 Apr 18, 2026
d7a2916
Improve Orca memory troubleshooting for capped total memory
calvinp0 Apr 19, 2026
38a7e0f
Refine memory error detection and ORCA memory troubleshooting logic
calvinp0 Apr 19, 2026
4febdd8
Enable immediate troubleshooting for failed ESS pipe tasks during eje…
calvinp0 Apr 19, 2026
2ac4488
Enhance memory error detection and tracking for capped memory jobs
calvinp0 Apr 19, 2026
3ef6716
.
calvinp0 Apr 20, 2026
2ef5e15
.
calvinp0 Apr 20, 2026
d2d75cb
Skip 2D-graph isomorphism enforcement for TS species
calvinp0 Apr 20, 2026
47e2b1b
mapping/engine: two-pass pairing to reject formula-only matches
calvinp0 Apr 20, 2026
2615bb6
mapping/driver: surface failed pair mappings and retry next product dict
calvinp0 Apr 20, 2026
dc2d4c0
reaction: derive reactive bonds from RMG family when atom_map is absent
calvinp0 Apr 20, 2026
5514eed
perceive: represent inter-fragment contacts in transition states as r…
calvinp0 Apr 22, 2026
a5735a6
Added user option to provide verytight which will replace tight
calvinp0 Apr 29, 2026
2747bf8
level: preserve args through as_dict round-trip when only one slot is…
calvinp0 Apr 29, 2026
8d68edf
common: drop misleading 'When troubleshooting, ARC ignores' warning
calvinp0 Apr 29, 2026
3271067
scheduler: ensure monoatomic species have final_xyz
calvinp0 May 3, 2026
a415613
scheduler: preserve species jobs on duplicate 'change conformer' trsh
calvinp0 May 3, 2026
a63a1fe
Harden remote job lifecycle
calvinp0 May 25, 2026
4ae2bf2
Improve TS adapter troubleshooting
calvinp0 May 25, 2026
ca7ce14
Expand output.yml calculation provenance
calvinp0 May 25, 2026
c4fe12a
Add TCKDB upload package
calvinp0 May 25, 2026
ee0be10
Wire ARC TCKDB upload sweep
calvinp0 May 25, 2026
f31bb29
Merge remote-tracking branch 'origin/main' into tckdb-imp
calvinp0 Jun 16, 2026
e8124ba
Merge branch 'main' into crest_adapter
calvinp0 Jul 3, 2026
452f4c9
Fix pipe coordinator tests for scheduler_job_alive reconciliation
calvinp0 Jul 3, 2026
5d2227d
Install KinBot 2.3.0 into a dedicated kinbot_env environment
calvinp0 Jul 3, 2026
79610b5
Add a standalone KinBot worker script and a KINBOT_PYTHON setting
calvinp0 Jul 3, 2026
a807c42
Run KinBot through the kinbot_env subprocess boundary
calvinp0 Jul 3, 2026
70ddb5f
Test the KinBot adapter across the mocked subprocess boundary
calvinp0 Jul 3, 2026
2b93b77
Adapt the KinBot worker to Parameters validation in KinBot 2.3.0
calvinp0 Jul 3, 2026
de5f433
Fix GCN adapter to work across the ts_gcn conda-env boundary
calvinp0 Jul 3, 2026
d9b92e9
Fix GCN installer hook expansion and CPU env torch stack
calvinp0 Jul 3, 2026
b07f425
Rewrite GCN adapter tests to exercise the subprocess boundary
calvinp0 Jul 3, 2026
6c91833
Merge branch 'tckdb-imp' into crest_adapter
calvinp0 Jul 3, 2026
3825f3e
Apply KinBot constraint templates fully; scaffold opt-in UMA refinement
calvinp0 Jul 3, 2026
3819ea0
Add an optional --uma flag to the KinBot installer
calvinp0 Jul 3, 2026
ada4955
Add a level attribute to TSGuess and populate it in ES-running TS ada…
calvinp0 Jul 3, 2026
383351c
Collect per-job cost records in the Scheduler and pass them to output…
calvinp0 Jul 3, 2026
873447d
Record per-TS-guess provenance and run cost metrics in output.yml
calvinp0 Jul 3, 2026
54dc1b7
Merge branch 'kinbot_env' into crest_adapter
calvinp0 Jul 3, 2026
4645936
Merge branch 'gcn_fix' into crest_adapter
calvinp0 Jul 3, 2026
caa1a66
Merge branch 'ts_guess_recording' into crest_adapter
calvinp0 Jul 3, 2026
ccb2473
Pull Cartesian Hessian through to TCKDB uploads
calvinp0 Jul 3, 2026
7f9feec
Record pipe task costs into output.yml cost metrics
calvinp0 Jul 3, 2026
3f58df6
Fix TS freq payload: represent the imaginary mode in modes
calvinp0 Jul 3, 2026
ed3b588
Merge branch 'tckdb-imp' into crest_adapter
calvinp0 Jul 3, 2026
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8 changes: 6 additions & 2 deletions .gitignore
Original file line number Diff line number Diff line change
Expand Up @@ -72,13 +72,17 @@ build/*

*.log
*.xml
# Test fixtures: real ESS log files / XML are tracked under arc/testing/
!arc/testing/**/*.log
!arc/testing/**/*.xml

# AI Agent files
# AI Agent files and folders
AGENTS.md
spec.md
.vexb/*

# Other AI things
.agents
ARC.egg*
uv*
*graphify*
*graphify*
28 changes: 27 additions & 1 deletion ARC.py
Original file line number Diff line number Diff line change
Expand Up @@ -11,6 +11,8 @@

from arc.common import read_yaml_file
from arc.main import ARC
from arc.tckdb.config import TCKDBConfig
from arc.tckdb.sweep import run_upload_sweep


def parse_command_line_arguments(command_line_args=None):
Expand Down Expand Up @@ -59,8 +61,32 @@ def main():
input_dict['verbose'] = input_dict['verbose'] if 'verbose' in input_dict else verbose
if 'project_directory' not in input_dict or not input_dict['project_directory']:
input_dict['project_directory'] = project_directory

tckdb_config = TCKDBConfig.from_dict(input_dict.pop('tckdb', None))

arc_object = ARC(**input_dict)
arc_object.execute()
arc_object.tckdb_config = tckdb_config
if tckdb_config is not None:
print(f'TCKDB integration enabled: {tckdb_config.base_url}')

# Persistent SSH pool lives for the duration of the run; close it
# explicitly on every exit path (success, error, ctrl-C) so we don't
# leave paramiko Transports orphaned. Lazily instantiated on first
# remote-queue job, so this is a no-op for fully-local runs.
try:
arc_object.execute()

if tckdb_config is not None:
from arc.tckdb.adapter import TCKDBAdapter
adapter = TCKDBAdapter(tckdb_config, project_directory=arc_object.project_directory)
run_upload_sweep(
adapter=adapter,
project_directory=arc_object.project_directory,
tckdb_config=tckdb_config,
)
finally:
from arc.job.ssh_pool import reset_default_pool
reset_default_pool()


if __name__ == '__main__':
Expand Down
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