Incl. geuss=INDO logic and tests

Fix attempted trsh methods
ReactionMechanismGenerator · Nov 27, 2023 · 405c6c9 · 405c6c9
1 parent e7e2f09
commit 405c6c9
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Showing 3 changed files with 17 additions and 11 deletions.
diff --git a/arc/job/adapters/gaussian.py b/arc/job/adapters/gaussian.py
@@ -364,8 +364,15 @@ 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:
-            input_dict['job_type_1'] += ' guess=read' if self.checkfile is not None and os.path.isfile(self.checkfile) \
-                else ' guess=mix'
+            if input_dict['job_type_1']:
+                input_dict['job_type_1'] += ' '
+            if 'guess=INDO' in input_dict['trsh']:
+                input_dict['job_type_1'] += 'guess=INDO'
+                # Remove guess=INDO from trsh
+                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'
 
         # Fix OPT
         terms_opt = [r'opt=\((.*?)\)', r'opt=(\w+)']

diff --git a/arc/job/adapters/gaussian_test.py b/arc/job/adapters/gaussian_test.py
@@ -208,7 +208,7 @@ def setUpClass(cls):
                                             )
 
         # Gaussian: Additional SCF error
-        # Second SCF error - Includes previous SCF error and NDump=30
+        # Second SCF error - Includes previous SCF error and NDamp=30
         job_status = {'keywords': ['SCF']}
         output_errors, ess_trsh_methods, remove_checkfile, level_of_theory, software, job_type, fine, trsh_keyword, \
             memory, shift, cpu_cores, couldnt_trsh = trsh.trsh_ess_job(label, level_of_theory, server, job_status,
@@ -518,7 +518,7 @@ def test_trsh_write_input_file(self):
 %mem=14336mb
 %NProcShared=8
 
-#P opt=(calcfc,maxstep=5,tight) guess=mix wb97xd  integral=(grid=ultrafine, Acc2E=14) IOp(2/9=2000)    scf=(direct,tight)
+#P opt=(calcfc,maxstep=5,tight)  guess=mix wb97xd  integral=(grid=ultrafine, Acc2E=14) IOp(2/9=2000)    scf=(direct,tight)
 
 ethanol
 
@@ -544,7 +544,7 @@ def test_trsh_write_input_file(self):
 %mem=14336mb
 %NProcShared=8
 
-#P opt=(calcfc,maxstep=5,tight) guess=mix wb97xd  integral=(grid=ultrafine, Acc2E=14) IOp(2/9=2000)     nosymm scf=(direct,tight,xqc)
+#P opt=(calcfc,maxstep=5,tight)  guess=mix wb97xd  integral=(grid=ultrafine, Acc2E=14) IOp(2/9=2000)     nosymm scf=(direct,tight,xqc)
 
 ethanol
 
@@ -570,7 +570,7 @@ def test_trsh_write_input_file(self):
 %mem=14336mb
 %NProcShared=8
 
-#P opt=(calcfc,maxstep=5,tight) guess=mix wb97xd  integral=(grid=ultrafine, Acc2E=14) IOp(2/9=2000)     nosymm scf=(NDump=30,direct,tight,xqc)
+#P opt=(calcfc,maxstep=5,tight)  guess=mix wb97xd  integral=(grid=ultrafine, Acc2E=14) IOp(2/9=2000)     nosymm scf=(NDamp=30,direct,tight,xqc)
 
 ethanol
 
@@ -596,7 +596,7 @@ def test_trsh_write_input_file(self):
 %mem=14336mb
 %NProcShared=8
 
-#P opt=(calcfc,maxstep=5,tight) guess=mix wb97xd  integral=(grid=ultrafine, Acc2E=14) IOp(2/9=2000)     nosymm scf=(NDump=30,NoDIIS,direct,tight,xqc)
+#P opt=(calcfc,maxstep=5,tight)  guess=mix wb97xd  integral=(grid=ultrafine, Acc2E=14) IOp(2/9=2000)     nosymm scf=(NDamp=30,NoDIIS,direct,tight,xqc)
 
 ethanol
 
@@ -622,7 +622,7 @@ def test_trsh_write_input_file(self):
 %mem=14336mb
 %NProcShared=8
 
-#P opt=(calcfc,cartesian,maxstep=5,tight) guess=mix wb97xd  integral=(grid=ultrafine, Acc2E=14) IOp(2/9=2000)      nosymm scf=(NDump=30,NoDIIS,direct,tight,xqc)
+#P opt=(calcfc,cartesian,maxstep=5,tight)  guess=mix wb97xd  integral=(grid=ultrafine, Acc2E=14) IOp(2/9=2000)      nosymm scf=(NDamp=30,NoDIIS,direct,tight,xqc)
 
 ethanol
 
@@ -649,7 +649,7 @@ def test_trsh_write_input_file(self):
 %mem=14336mb
 %NProcShared=8
 
-#P opt=(cartesian) integral=(grid=ultrafine, Acc2E=14) guess=mix wb97xd   IOp(2/9=2000)      nosymm  scf=(NDump=30,NoDIIS,direct,tight,xqc)
+#P opt=(cartesian) integral=(grid=ultrafine, Acc2E=14) guess=INDO wb97xd   IOp(2/9=2000)       nosymm  scf=(NDamp=30,NoDIIS,direct,tight,xqc)
 
 ethanol
 

diff --git a/arc/job/trsh.py b/arc/job/trsh.py
@@ -858,8 +858,7 @@ def trsh_ess_job(label: str,
         logger_info = []
         couldnt_trsh = True
         fine = False
-        if ess_trsh_methods:
-            attempted_ess_trsh_methods = ess_trsh_methods.copy()
+        attempted_ess_trsh_methods = ess_trsh_methods.copy() if ess_trsh_methods else None
         # Check if Checkfile removal is in the keywords. Removal occurs when:
         # - Basis Set Mismatch
         # - Corrupt or Incomplete Data