add hess parsing test

Author: samblau

atomate/qchem/firetasks/tests/test_parse_outputs.py

@@ -16,13 +16,13 @@
 module_dir = os.path.dirname(os.path.abspath(__file__))
 
 
-class TestParseOutputQChem(AtomateTest):
+class TestParseOutputQChem_grads(AtomateTest):
     def setUp(self, lpad=False):
         super().setUp(lpad=False)
 
     def tearDown(self):
         pass
-        
+
     def test_parse_grad_good(self):
         my_calc_dir = os.path.join(module_dir, "..", "..", "test_files","parse_grad_good")
         ft = QChemToDb(calc_dir=my_calc_dir, parse_grad_file=True)
@@ -53,5 +53,33 @@ def test_parse_grad_bad(self):
         self.assertEqual(task_doc["warnings"]["grad_file_missing"], True)
         os.remove(os.path.join(my_calc_dir, "task.json"))
 
+
+class TestParseOutputQChem_hess(AtomateTest):
+    def setUp(self, lpad=False):
+        os.makedirs(os.path.join(module_dir, "..", "..", "test_files", "freq_save_hess", "scratch"))
+        shutil.copyfile(
+            os.path.join(module_dir, "..", "..", "test_files", "freq_save_hess", "BUP_scratch", "132.0"),
+            os.path.join(module_dir, "..", "..", "test_files", "freq_save_hess", "scratch", "132.0"),
+        )
+        shutil.copyfile(
+            os.path.join(module_dir, "..", "..", "test_files", "freq_save_hess", "BUP_scratch", "HESS"),
+            os.path.join(module_dir, "..", "..", "test_files", "freq_save_hess", "scratch", "HESS"),
+        )
+        super().setUp(lpad=False)
+
+    def test_parse_hess(self):
+        my_calc_dir = os.path.join(module_dir, "..", "..", "test_files","freq_save_hess")
+        ft = QChemToDb(calc_dir=my_calc_dir, parse_hess_file=True)
+        ft.run_task({})
+        task_doc = loadfn(os.path.join(my_calc_dir,"task.json"))
+        self.assertEqual(task_doc["output"]["final_energy"], -151.3244603665)
+        self.assertEqual(task_doc["output"]["hess_data"]["scratch/132.0"][0],0.12636293260949633)
+        self.assertEqual(task_doc["output"]["hess_data"]["scratch/132.0"][-2],-0.2025032138024329)
+        self.assertEqual(task_doc["output"]["hess_data"]["scratch/HESS"][-2], ' -0.175476533300377      -0.202503213802433       0.205623571433770     \n')
+        os.remove(os.path.join(my_calc_dir, "task.json"))
+
+    def tearDown(self):
+        pass
+
 if __name__ == "__main__":
     unittest.main()

atomate/qchem/test_files/freq_save_hess/BUP_scratch/132.0

@@ -0,0 +1,33 @@
+$hessian
+Dimension     12
+  0.126362932609496     
+ -4.433736872010650E-002  4.803028695314032E-002
+ -0.232219060220548       0.103994954971091       0.416818534868519     
+ -0.123167531732906       5.620157833111076E-002  0.195627375150984     
+  0.137538029234560     
+  5.610615881394289E-002 -2.601459393545238E-002 -9.539164914755137E-002
+ -5.996060628950006E-002  2.620827496924317E-002
+  0.215614248544132      -0.100471300908688      -0.406356673600227     
+ -0.202878917050539       9.735610631707604E-002  0.405676795542478     
+ -1.120660716146122E-002 -6.742724595369494E-003  4.943141033484526E-003
+ -3.722786556199047E-003  3.996723218112889E-004 -9.222846621205926E-004
+  0.150458723666484     
+  4.621054102109451E-003 -1.969311331572267E-005  7.592908052803240E-004
+  4.718238922954899E-004  7.822854599492641E-004  9.346035240281546E-004
+  0.165896170411460       0.223593900083420     
+ -1.172738217162766E-002 -3.208374969727183E-003  1.948696686335527E-003
+ -8.608658002456569E-004  1.108219767547019E-003 -2.029424866889353E-003
+ -0.143052788123427      -0.207585064161736       0.196003044584296     
+  8.011206286599550E-003 -5.121485015710039E-003  3.164854403636131E-002
+ -1.064771094556473E-002  3.454775153766684E-003 -1.181304683159105E-002
+ -0.135529329948847      -0.170989048405919       0.155641036095526     
+  0.138165834608429     
+ -1.638984419623026E-002 -2.199599990233876E-002 -9.362596628886355E-003
+  3.287204066181141E-003 -9.759664940144342E-004  2.180591067569924E-003
+ -0.159553118137659      -0.224356492429896       0.209685219363836     
+  0.172655758267816       0.247328458826990     
+  2.833219384811784E-002 -3.152790927580822E-004 -1.241055795519516E-002
+  8.112407699843841E-003 -3.072676937038772E-003  2.709302924727442E-003
+  0.139031931752027       0.205891169832389      -0.195922316403627     
+ -0.175476533300377      -0.202503213802433       0.205623571433770     
+$end

atomate/qchem/test_files/freq_save_hess/BUP_scratch/HESS

@@ -0,0 +1,24 @@
+$molecule
+ 0 1
+ O      0.3178678256     -0.1451772019      0.1876900614
+ H     -0.1270774417      0.0644667196      1.0214927440
+ H      2.3658372785      0.0719311463      0.7249943525
+ O      1.8971011149     -0.5514399588      1.2982221472
+$end
+
+$rem
+job_type = freq
+basis = def2-svpd
+max_scf_cycles = 100
+gen_scfman = true
+xc_grid = 3
+thresh = 14
+s2thresh = 16
+scf_algorithm = diis
+resp_charges = true
+symmetry = false
+sym_ignore = true
+method = wb97xd
+geom_opt_max_cycles = 200
+$end
+