CREST Adapter by calvinp0 · Pull Request #807 · ReactionMechanismGenerator/ARC

calvinp0 · 2025-11-27T22:16:29Z

Addition of CREST Adapter that complements the heuristic adapter.

This pull request adds support for the CREST conformer and transition state (TS) search method to the ARC project, along with several related improvements and code cleanups. The most important changes include integrating CREST as a TS search adapter, updating configuration and constants, and enhancing the heuristics TS search logic for better provenance tracking and code clarity.

CREST Integration:

Added CREST as a supported TS search method: updated JobEnum (arc/job/adapter.py), included CREST in the list of adapters and RMG family mapping, and registered it as a default incore adapter (arc/job/adapters/common.py, arc/job/adapters/ts/__init__.py). [1] [2] [3] [4]
Implemented a new test suite for CREST input generation (arc/job/adapters/ts/crest_test.py).
Added a Makefile target and installation script for CREST (Makefile). [1] [2]

Constants and Configuration:

Added the angstrom_to_bohr conversion constant to both Cython and Python constants modules (arc/constants.pxd, arc/constants.py). [1] [2] [3]

Heuristics TS Search Enhancements and Refactoring:

Refactored heuristics TS search logic to track and combine method provenance for TS guesses, allowing for more precise attribution when multiple methods contribute to a guess (arc/job/adapters/ts/heuristics.py). [1] [2] [3] [4]
Improved code readability and maintainability by reformatting imports and function calls, and clarifying data structures and comments in heuristics TS search (arc/job/adapters/ts/heuristics.py). [1] [2] [3] [4] [5] [6] [7]
.

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codecov · 2026-07-06T09:10:36Z

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 64.71%. Comparing base (e7f2c98) to head (8661c5c).
⚠️ Report is 3 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #807      +/-   ##
==========================================
+ Coverage   63.15%   64.71%   +1.55%     
==========================================
  Files         114      127      +13     
  Lines       38178    42499    +4321     
  Branches     9990    10909     +919     
==========================================
+ Hits        24113    27502    +3389     
- Misses      11183    11791     +608     
- Partials     2882     3206     +324

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unittests	`64.71% <ø> (+1.55%)`	⬆️

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+# adapters support (see ts_adapters_by_rmg_family) but that RMG does not list as recommended
+# (e.g. Intra_RH_Add_Endocyclic, XY_Addition_MultipleBond). Useful when running specific
+# reactions across many families (e.g. a benchmark) rather than generating a mechanism.
+rmg_family_set = 'default'


To fix this without changing behavior, explicitly mark rmg_family_set as a public module variable by adding it to __all__ in arc/settings/settings.py. This matches the rule’s own guidance (“not explicitly made public by inclusion in __all__”), preserves existing config semantics, and avoids risky deletion/renaming of a likely externally used setting.

Best concrete change:

In arc/settings/settings.py, add a module-level __all__ definition that includes 'rmg_family_set'.

Place it near the rmg_family_set declaration for clarity.

No new imports, methods, or dependencies are required.

…_Endocyclic)

+        rxn = ARCReaction(r_species=[ARCSpecies(label='R', smiles='C=CCC', multiplicity=1)],
+                          p_species=[ARCSpecies(label='P', smiles='C1CCC1', multiplicity=1)])
+        product_dicts = rxn.get_product_dicts(rmg_family_set=['Intra_RH_Add_Endocyclic'])
+        self.assertTrue(len(product_dicts) > 0)


Replace the imprecise boolean assertion with a specific unittest assertion:

In arc/family/family_test.py, inside test_apply_recipe_coerces_string_bond_order, change:

self.assertTrue(len(product_dicts) > 0)

to

self.assertGreater(len(product_dicts), 0)

This preserves behavior while improving failure diagnostics (it will report actual compared values). No imports, helper methods, or additional definitions are needed.

…product_dict reversal)

…rest/heuristics

… thermo step

…library Fix C: get_reactants_xyz/get_products_xyz now expand each species by get_species_count so a repeated participant (e.g. OH + OH) contributes all its atoms and the combined geometry matches the atom map, instead of failing with an atom-count mismatch. Fix A: skip isomorphic, same-multiplicity duplicates when building the thermo library so identical reactants don't abort it with an Arkane DatabaseError.

…t invalid A submerged/negative barrier (e.g. barrierless radical-radical reactions like OH+OH) raises a ValueError in Arkane's Eckart method and aborted the whole rate calculation. tunneling is now a template parameter; on that specific failure ARC retries once with tunneling disabled so a (tunneling-free) rate coefficient is still produced.

# Conflicts: # arc/statmech/arkane.py

1+2_Cycloaddition, Diels_alder_addition, Retroene, XY_elimination_hydroxyl, and intra_halogen_migration only had linear (or kinbot+linear), which finds spurious H-motion saddles that NMD correctly rejects. Adds the double-ended path finders so the real heavy-atom TS can be located (same fix as XY_Addition).

# Conflicts: # arc/job/adapters/common.py

…t run_arkane's bool run_arkane can wrongly return success when Arkane crashes on an invalid (submerged) barrier: it writes a partial output.py and the error is missed in captured stderr (async tee). So the previous 'if not success' guard never fired (reaction 05 stayed NO_RATE). Now the retry keys off the actual outcome — no kinetics produced AND the invalid-barrier signature present — and re-runs without tunneling. Detector reads both stderr.log and stdout.log for robustness. Validated: a no-tunneling Arkane run produces a rate for 05's -20.8 kJ/mol barrier.

+    for name in ('stderr.log', 'stdout.log'):
+        path = os.path.join(statmech_dir, name)
+        if os.path.isfile(path):
+            content += open(path, encoding='utf-8', errors='ignore').read()


Use a context manager when reading each log file in arkane_failed_on_invalid_barrier so each descriptor is always closed, even if reading fails.

Best fix (no behavior change): in arc/statmech/arkane.py, replace the inline open(...).read() at line 614 with:

with open(path, encoding='utf-8', errors='ignore') as f:

content += f.read()

This preserves existing logic and encoding/error handling while guaranteeing closure on all paths. No new imports or helper methods are needed.

Continuation of the A+A dedup fix: remove_dup_species dedups rxn.reactants to a single label, so AutoTST building the reverse from rxn.products/reactants produced the imbalanced 'P1 + P2 <=> R1' instead of 'P1 + P2 <=> R1 + R1'. Re-expand the reverse labels by get_species_count so the reverse reaction stays atom-balanced.

…cbench

SMILES cannot encode a lone-pair singlet (e.g. singlet carbene [CH2], mult 1, C u0 p1): Arkane re-perceives SMILES('[CH2]') as a u2 biradical, and u2+multiplicity=1 violates Hund's rule when save_thermo_lib writes/reloads the adjacency list, crashing the whole thermo step (reaction 01). When a species' SMILES doesn't round-trip to the same multiplicity, emit the lossless adjacency list instead. Validated: RMG parses the u0 p1 carbene adjlist cleanly (the call that crashed).

github-actions Bot added Module: Converter Module: Species labels Nov 27, 2025

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Comment thread arc/job/adapters/ts/crest.py Fixed

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calvinp0 force-pushed the crest_adapter branch from d6a83b4 to c231a43 Compare January 27, 2026 12:39

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Comment thread arc/job/adapters/ts/heuristics.py Fixed

Comment thread arc/settings/settings.py Fixed

Comment thread arc/settings/settings.py Fixed

calvinp0 force-pushed the crest_adapter branch 2 times, most recently from 3e88c36 to 7674f5f Compare February 2, 2026 09:49

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calvinp0 force-pushed the crest_adapter branch 3 times, most recently from 9c25f3d to 51368be Compare February 2, 2026 14:31

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calvinp0 force-pushed the crest_adapter branch 2 times, most recently from 9be935e to eab7647 Compare February 4, 2026 20:14

calvinp0 requested a review from alongd February 4, 2026 21:30

calvinp0 added 3 commits July 6, 2026 12:44

Include RMG database directory families in the 'all' family set

cead051

Make the RMG family set configurable via settings (default 'default')

916d994

Merge branch 'fix_family_set' into arcbench

2c76e57

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calvinp0 added 2 commits July 6, 2026 13:17

Coerce string bond-order in family recipes to int (fixes Intra_RH_Add…

f10ea72

…_Endocyclic)

Merge branch 'fix_endocyclic_family' into arcbench

8467b15

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calvinp0 added 7 commits July 6, 2026 13:36

Fix H-abstraction heuristics IndexError for symmetric reactants (per-…

48ae9d9

…product_dict reversal)

Merge branch 'fix_habs_heuristics_index' into arcbench

27463a1

Add XY_Addition_MultipleBond TS seed builder (own module); register c…

9aba13a

…rest/heuristics

XY_Addition: register seed + path methods (union of both approaches)

56a704e

Merge branch 'feature_xy_addition_seed' into arcbench

dc3b667

Don't report no-thermo species (e.g. IRC endpoints) as unconverged in…

3688d7d

… thermo step

Merge branch 'fix_irc_species_thermo_report' into arcbench

4694bd8

github-actions Bot added the Module: Processor label Jul 6, 2026

calvinp0 added 4 commits July 7, 2026 04:25

Merge branch 'fix_repeated_reactant_species' into arcbench

7d5a147

Merge branch 'fix_eckart_negative_barrier' into arcbench

68c6ad2

# Conflicts: # arc/statmech/arkane.py

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Comment thread arc/statmech/arkane.py Fixed

calvinp0 added 4 commits July 7, 2026 04:56

Merge branch 'fix_linear_only_ts_adapters' into arcbench

4c641a6

# Conflicts: # arc/job/adapters/common.py

Merge branch 'fix_eckart_retry' into arcbench

286a458

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calvinp0 added 4 commits July 7, 2026 13:32

Merge updated fix_repeated_reactant_species (reverse A+A fix) into ar…

8661c5c

…cbench

Merge branch 'fix_arkane_lonepair_adjlist' into arcbench

70f2062

@@ -366,6 +366,7 @@
             # (e.g. Intra_RH_Add_Endocyclic, XY_Addition_MultipleBond). Useful when running specific
             # reactions across many families (e.g. a benchmark) rather than generating a mechanism.
             rmg_family_set = 'default'
+            __all__ = ['rmg_family_set']
             # Default environment names for sister repos
             TS_GCN_PYTHON, TANI_PYTHON, AUTOTST_PYTHON, KINBOT_PYTHON, ARC_PYTHON, XTB, XTB_PYTHON, OB_PYTHON, RMG_PYTHON, RMG_PATH, RMG_DB_PATH = \

@@ -611,7 +611,8 @@
                 for name in ('stderr.log', 'stdout.log'):
                     path = os.path.join(statmech_dir, name)
                     if os.path.isfile(path):
-                        content += open(path, encoding='utf-8', errors='ignore').read()
+                        with open(path, encoding='utf-8', errors='ignore') as f:
+                            content += f.read()
                 return 'Eckart method are invalid' in content \
                     or ('barrier heights' in content and 'Eckart' in content)

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