Merge 4c6fda2 into e1c075c

materialsproject · Jan 17, 2023 · 8b71c4b · 8b71c4b
2 parents e1c075c + 4c6fda2
commit 8b71c4b
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Showing 23 changed files with 980,709 additions and 301 deletions.
diff --git a/pymatgen/io/qchem/inputs.py b/pymatgen/io/qchem/inputs.py
@@ -18,8 +18,11 @@
 
 from .utils import lower_and_check_unique, read_pattern, read_table_pattern
 
-__author__ = "Brandon Wood, Samuel Blau, Shyam Dwaraknath, Evan Spotte-Smith, Ryan Kingsbury"
+__author__ = "Brandon Wood, Samuel Blau, Shyam Dwaraknath, Julian Self, Evan Spotte-Smith, Ryan Kingsbury"
 __copyright__ = "Copyright 2018-2022, The Materials Project"
+__version__ = "0.1"
+__maintainer__ = "Samuel Blau"
+__email__ = "samblau1@gmail.com"
 __credits__ = "Xiaohui Qu"
 
 logger = logging.getLogger(__name__)
@@ -913,7 +916,7 @@ def read_nbo(string: str) -> dict:
             (dict) nbo parameters.
         """
         header = r"^\s*\$nbo"
-        row = r"\s*([a-zA-Z\_]+)\s*=?\s*(\S+)"
+        row = r"\s*([a-zA-Z\_\d]+)\s*=?\s*(\S+)"
         footer = r"^\s*\$end"
         nbo_table = read_table_pattern(string, header_pattern=header, row_pattern=row, footer_pattern=footer)
         if nbo_table == []:

diff --git a/pymatgen/io/qchem/outputs.py b/pymatgen/io/qchem/outputs.py
diff --git a/pymatgen/io/qchem/sets.py b/pymatgen/io/qchem/sets.py
diff --git a/pymatgen/io/qchem/tests/multi_job.json b/pymatgen/io/qchem/tests/multi_job.json
diff --git a/pymatgen/io/qchem/tests/single_job.json b/pymatgen/io/qchem/tests/single_job.json
diff --git a/pymatgen/io/qchem/tests/test_inputs.py b/pymatgen/io/qchem/tests/test_inputs.py
@@ -16,6 +16,9 @@
 
 __author__ = "Brandon Wood, Samuel Blau, Shyam Dwaraknath, Julian Self, Evan Spotte-Smith, Ryan Kingsbury"
 __copyright__ = "Copyright 2018-2022, The Materials Project"
+__version__ = "0.1"
+__maintainer__ = "Samuel Blau"
+__email__ = "samblau1@gmail.com"
 __credits__ = "Xiaohui Qu"
 
 logger = logging.getLogger(__name__)
@@ -1046,6 +1049,36 @@ def test_read_write_nbo7(self):
         ref_file.close()
         os.remove(os.path.join(os.path.dirname(__file__), "test_nbo7.qin"))
 
+    def test_read_write_nbo_e2pert(self):
+        qcinp = QCInput.from_file(
+            os.path.join(PymatgenTest.TEST_FILES_DIR, "molecules", "new_qchem_files", "e2pert.qin")
+        )
+        qcinp.write_file(os.path.join(os.path.dirname(__file__), "test_e2pert.qin"))
+        test_file = open(os.path.join(PymatgenTest.TEST_FILES_DIR, "molecules", "new_qchem_files", "e2pert.qin"))
+        ref_file = open(os.path.join(os.path.dirname(__file__), "test_e2pert.qin"))
+
+        for l_test, l_ref in zip(test_file, ref_file):
+            assert l_test == l_ref
+
+        test_file.close()
+        ref_file.close()
+        os.remove(os.path.join(os.path.dirname(__file__), "test_e2pert.qin"))
+
+    def test_read_write_custom_smd(self):
+        qcinp = QCInput.from_file(
+            os.path.join(PymatgenTest.TEST_FILES_DIR, "molecules", "new_qchem_files", "custom_smd.qin")
+        )
+        qcinp.write_file(os.path.join(os.path.dirname(__file__), "test_custom_smd.qin"))
+        test_file = open(os.path.join(PymatgenTest.TEST_FILES_DIR, "molecules", "new_qchem_files", "custom_smd.qin"))
+        ref_file = open(os.path.join(os.path.dirname(__file__), "test_custom_smd.qin"))
+
+        for l_test, l_ref in zip(test_file, ref_file):
+            assert l_test == l_ref
+
+        test_file.close()
+        ref_file.close()
+        os.remove(os.path.join(os.path.dirname(__file__), "test_custom_smd.qin"))
+
 
 if __name__ == "__main__":
     unittest.main()
diff --git a/pymatgen/io/qchem/tests/test_outputs.py b/pymatgen/io/qchem/tests/test_outputs.py
@@ -15,14 +15,14 @@
 
 try:
     from openbabel import openbabel
-
-    openbabel  # reference openbabel so it's not unused import
-    have_babel = True
 except ImportError:
-    have_babel = False
+    openbabel = None
 
 __author__ = "Samuel Blau, Brandon Wood, Shyam Dwaraknath, Evan Spotte-Smith, Ryan Kingsbury"
 __copyright__ = "Copyright 2018-2022, The Materials Project"
+__version__ = "0.1"
+__maintainer__ = "Samuel Blau"
+__email__ = "samblau1@gmail.com"
 
 single_job_dict = loadfn(os.path.join(os.path.dirname(__file__), "single_job.json"))
 multi_job_dict = loadfn(os.path.join(os.path.dirname(__file__), "multi_job.json"))
@@ -115,9 +115,13 @@
     "exchange_e",
     "min_neg_field_e",
     "max_pos_field_e",
+    "norm_of_stepsize",
+    "version",
+    "dipoles",
+    "gap_info",
 }
 
-if have_babel:
+if openbabel is not None:
     property_list.add("structure_change")
 
 single_job_out_names = {
@@ -188,6 +192,15 @@
     "new_qchem_files/cmirs_water_single.qcout",
     "new_qchem_files/isosvp_water_single.qcout",
     "new_qchem_files/isosvp_dielst10_single.qcout",
+    "new_qchem_files/custom_gdm_gdmqls_opt.qout",
+    "new_qchem_files/unable.qout",
+    "new_qchem_files/unexpected_ts.out",
+    "new_qchem_files/svd_failed.qout",
+    "new_qchem_files/v6_old_driver.out",
+    "new_qchem_files/gap.qout",
+    "new_qchem_files/3C.qout",
+    "new_qchem_files/hyper.qout",
+    "new_qchem_files/os_gap.qout",
 }
 
 multi_job_out_names = {
@@ -240,15 +253,20 @@ def _test_property(self, key, single_outs, multi_outs):
             try:
                 self.assertEqual(outdata.get(key), single_job_dict[name].get(key))
             except ValueError:
-                self.assertArrayEqual(outdata.get(key), single_job_dict[name].get(key))
+                try:
+                    self.assertArrayEqual(outdata.get(key), single_job_dict[name].get(key))
+                except AssertionError:
+                    raise RuntimeError("Issue with file: " + name + " Exiting...")
+            except AssertionError:
+                raise RuntimeError("Issue with file: " + name + " Exiting...")
         for name, outputs in multi_outs.items():
             for ii, sub_output in enumerate(outputs):
                 try:
                     self.assertEqual(sub_output.data.get(key), multi_job_dict[name][ii].get(key))
                 except ValueError:
                     self.assertArrayEqual(sub_output.data.get(key), multi_job_dict[name][ii].get(key))
 
-    @unittest.skipIf(not have_babel, "OpenBabel not installed.")
+    @unittest.skipIf(openbabel is None, "OpenBabel not installed.")
     def test_all(self):
         self.maxDiff = None
         single_outs = {}
@@ -265,7 +283,7 @@ def test_all(self):
             print("Testing ", key)
             self._test_property(key, single_outs, multi_outs)
 
-    @unittest.skipIf((not have_babel), "OpenBabel not installed.")
+    @unittest.skipIf((openbabel is None), "OpenBabel not installed.")
     def test_structural_change(self):
 
         t1 = Molecule.from_file(os.path.join(PymatgenTest.TEST_FILES_DIR, "molecules", "structural_change", "t1.xyz"))
@@ -302,10 +320,10 @@ def test_structural_change(self):
     def test_NBO_parsing(self):
         data = QCOutput(os.path.join(PymatgenTest.TEST_FILES_DIR, "molecules", "new_qchem_files", "nbo.qout")).data
         self.assertEqual(len(data["nbo_data"]["natural_populations"]), 3)
-        self.assertEqual(len(data["nbo_data"]["hybridization_character"]), 4)
+        self.assertEqual(len(data["nbo_data"]["hybridization_character"]), 6)
         self.assertEqual(len(data["nbo_data"]["perturbation_energy"]), 2)
         self.assertEqual(data["nbo_data"]["natural_populations"][0]["Density"][5], -0.08624)
-        self.assertEqual(data["nbo_data"]["hybridization_character"][-1]["atom 2 pol coeff"][35], "-0.7059")
+        self.assertEqual(data["nbo_data"]["hybridization_character"][4]["atom 2 pol coeff"][35], "-0.7059")
         next_to_last = list(data["nbo_data"]["perturbation_energy"][-1]["fock matrix element"])[-2]
         self.assertEqual(data["nbo_data"]["perturbation_energy"][-1]["fock matrix element"][next_to_last], 0.071)
         self.assertEqual(data["nbo_data"]["perturbation_energy"][0]["acceptor type"][0], "RY*")
@@ -336,8 +354,8 @@ def test_NBO5_vs_NBO7_hybridization_character(self):
             len(data5["nbo_data"]["hybridization_character"]), len(data7["nbo_data"]["hybridization_character"])
         )
         self.assertEqual(
-            data5["nbo_data"]["hybridization_character"][3]["atom 2 pol coeff"][9],
-            data7["nbo_data"]["hybridization_character"][3]["atom 2 pol coeff"][9],
+            data5["nbo_data"]["hybridization_character"][4]["atom 2 pol coeff"][9],
+            data7["nbo_data"]["hybridization_character"][4]["atom 2 pol coeff"][9],
         )
         self.assertEqual(
             data5["nbo_data"]["hybridization_character"][0]["s"][0],
@@ -429,6 +447,28 @@ def test_cmirs_water(self):
         self.assertEqual(data["solvent_data"]["cmirs"]["min_neg_field_e"], 0.0004967767)
         self.assertEqual(data["solvent_data"]["cmirs"]["max_pos_field_e"], 0.0180445935)
 
+    def test_NBO_hyperbonds(self):
+        data = QCOutput(os.path.join(PymatgenTest.TEST_FILES_DIR, "molecules", "new_qchem_files", "hyper.qout")).data
+        self.assertEqual(len(data["nbo_data"]["hyperbonds"][0]["hyperbond index"].keys()), 2)
+        self.assertEqual(data["nbo_data"]["hyperbonds"][0]["BD(A-B)"][1], 106)
+        self.assertEqual(data["nbo_data"]["hyperbonds"][0]["bond atom 2 symbol"][0], "C")
+        self.assertEqual(data["nbo_data"]["hyperbonds"][0]["occ"][1], 3.0802)
+
+    def test_NBO_3C(self):
+        data = QCOutput(os.path.join(PymatgenTest.TEST_FILES_DIR, "molecules", "new_qchem_files", "3C.qout")).data
+        self.assertEqual(len(data["nbo_data"]["hybridization_character"]), 3)
+        self.assertEqual(data["nbo_data"]["hybridization_character"][2]["type"][0], "3C")
+        self.assertEqual(data["nbo_data"]["hybridization_character"][2]["type"][10], "3Cn")
+        self.assertEqual(data["nbo_data"]["hybridization_character"][2]["type"][20], "3C*")
+        self.assertEqual(data["nbo_data"]["hybridization_character"][2]["atom 3 pol coeff"][15], "0.3643")
+        self.assertEqual(data["nbo_data"]["hybridization_character"][2]["atom 3 polarization"][8], "56.72")
+        self.assertEqual(data["nbo_data"]["hybridization_character"][2]["atom 3 symbol"][3], "B")
+        self.assertEqual(data["nbo_data"]["perturbation_energy"][0]["donor atom 2 number"][2592], 36)
+        self.assertEqual(data["nbo_data"]["perturbation_energy"][0]["donor atom 2 symbol"][2125], "B12")
+        self.assertEqual(data["nbo_data"]["perturbation_energy"][0]["donor atom 2 number"][2593], "info_is_from_3C")
+        self.assertEqual(data["nbo_data"]["perturbation_energy"][0]["acceptor type"][723], "3C*")
+        self.assertEqual(data["nbo_data"]["perturbation_energy"][0]["perturbation energy"][3209], 3.94)
+
 
 if __name__ == "__main__":
     unittest.main()
diff --git a/pymatgen/io/qchem/tests/test_ref.qin b/pymatgen/io/qchem/tests/test_ref.qin
@@ -8,7 +8,7 @@ $end
 
 $rem
    job_type = opt
-   basis = def2-tzvppd
+   basis = def2-svpd
    max_scf_cycles = 100
    gen_scfman = true
    xc_grid = 3
@@ -18,6 +18,6 @@ $rem
    resp_charges = true
    symmetry = false
    sym_ignore = true
-   method = wb97xd
+   method = wb97mv
    geom_opt_max_cycles = 200
 $end
diff --git a/pymatgen/io/qchem/tests/test_ref_vdw.qin b/pymatgen/io/qchem/tests/test_ref_vdw.qin
@@ -8,7 +8,7 @@ $end
 
 $rem
    job_type = opt
-   basis = def2-tzvppd
+   basis = def2-svpd
    max_scf_cycles = 100
    gen_scfman = true
    xc_grid = 3
@@ -18,7 +18,7 @@ $rem
    resp_charges = true
    symmetry = false
    sym_ignore = true
-   method = wb97xd
+   method = wb97mv
    geom_opt_max_cycles = 200
 $end