CREST Adapter

Makefile

@@ -36,6 +36,7 @@ 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 ""
@@ -100,6 +101,9 @@ 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
 

arc/constants.pxd

@@ -1 +1 @@
-cdef double pi, Na, kB, R, h, hbar, c, e, m_e, m_p, m_n, amu, a0, E_h, F, E_h_kJmol, bohr_to_angstrom
+cdef double pi, Na, kB, R, h, hbar, c, e, m_e, m_p, m_n, amu, a0, E_h, F, E_h_kJmol, bohr_to_angstrom, angstrom_to_bohr

arc/constants.py

@@ -79,6 +79,7 @@
 epsilon_0 = 8.8541878128
 
 bohr_to_angstrom = 0.529177
+angstrom_to_bohr = 1 / bohr_to_angstrom
 
 # Cython does not automatically place module-level variables into the module
 # symbol table when in compiled mode, so we must do this manually so that we
@@ -102,4 +103,5 @@
     'F': F,
     'epsilon_0': epsilon_0,
     'bohr_to_angstrom': bohr_to_angstrom,
+    'angstrom_to_bohr': angstrom_to_bohr,
 })

arc/job/adapter.py

@@ -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

arc/job/adapter_test.py

@@ -207,6 +207,12 @@ def setUpClass(cls):
                                     server='server3',
                                     testing=True,
                                     )
+        os.makedirs(cls.job_5.local_path, exist_ok=True)
+        fixture_path = os.path.join(ARC_TESTING_PATH, 'trsh', 'wall_exceeded.txt')
+        with open(fixture_path, 'r') as f:
+            log_content = f.read()
+        with open(os.path.join(cls.job_5.local_path, 'out.txt'), 'w') as f:
+            f.write(log_content)
         cls.job_6 = GaussianAdapter(execution_type='queue',
                                     job_name='spc1',
                                     job_type='opt',

arc/job/adapters/common.py

@@ -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'],
@@ -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',

arc/job/adapters/ts/__init__.py

@@ -1,5 +1,7 @@
 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
+import arc.job.adapters.ts.seed_hub
 import arc.job.adapters.ts.xtb_gsm