adding mpenergies parser for psi4 (cclib#1459)

cclib/attribute_parsers/__init__.py

@@ -20,6 +20,7 @@
 from cclib.attribute_parsers.mocoeffs import mocoeffs
 from cclib.attribute_parsers.moenergies import moenergies
 from cclib.attribute_parsers.mosyms import mosyms
+from cclib.attribute_parsers.mpenergies import mpenergies
 from cclib.attribute_parsers.mult import mult
 from cclib.attribute_parsers.natom import natom
 from cclib.attribute_parsers.nbasis import nbasis

cclib/attribute_parsers/mpenergies.py

@@ -0,0 +1,50 @@
+# Copyright (c) 2024, the cclib development team
+#
+# This file is part of cclib (http://cclib.github.io) and is distributed under
+# the terms of the BSD 3-Clause License.
+from typing import Optional
+
+from cclib.attribute_parsers import utils
+from cclib.attribute_parsers.base_parser import base_parser
+
+import numpy as np
+
+
+class mpenergies(base_parser):
+    """
+    Docstring? Units?
+    """
+
+    known_codes = ["psi4"]
+
+    @staticmethod
+    def psi4(file_handler, ccdata) -> Optional[dict]:
+        line = file_handler.last_line
+        # This is for the older conventional MP2 code in 4.0b5.
+        mp_trigger = "MP2 Total Energy (a.u.)"
+        if line.strip()[: len(mp_trigger)] == mp_trigger:
+            mpenergy = utils.convertor(float(line.split()[-1]), "hartree", "eV")
+            if getattr(ccdata, "mpenergies") is None:
+                this_mpenergies = []
+            this_mpenergies.append([mpenergy])
+            return {mpenergies.__name__: this_mpenergies}
+        # This is for the newer DF-MP2 code in 4.0.
+        if "DF-MP2 Energies" in line:
+            while "Total Energy" not in line:
+                line = file_handler.virtual_next()
+            mpenergy = utils.convertor(float(line.split()[3]), "hartree", "eV")
+            if getattr(ccdata, "mpenergies") is None:
+                this_mpenergies = []
+            this_mpenergies.append([mpenergy])
+            return {mpenergies.__name__: np.array(this_mpenergies)}
+        return None
+
+    @staticmethod
+    def parse(file_handler, program: str, ccdata) -> Optional[dict]:
+        constructed_data = None
+        if program in mpenergies.known_codes:
+            file_handler.virtual_set()
+            program_parser = getattr(mpenergies, program)
+            constructed_data = program_parser(file_handler, ccdata)
+            file_handler.virtual_reset()
+        return constructed_data

cclib/combinator/combinator.py

@@ -30,6 +30,7 @@ class combinator:
     cprops.aooverlaps,
     cprops.atommasses,
     cprops.mosyms,
+    cprops.mpenergies,
     cprops.nmo,
     cprops.atombasis,
     cprops.scftargets,

pytest.ini

@@ -8,6 +8,7 @@ python_files =
        testBasis.py
        testCC.py
        testSP.py
+       testMP.py
        testSPun.py
        test_code_in_code.py
        test_tree.py

test/data/testMP.py

@@ -15,14 +15,23 @@ class GenericMP2Test:
 
     def testsizeandshape(self, data) -> None:
         """(MP2) Are the dimensions of mpenergies correct?"""
-        assert data.mpenergies.shape == (len(data.scfenergies), self.level - 1)
+        assert data._ccCollection._parsed_data[0].mpenergies.shape == (
+            len(data._ccCollection._parsed_data[0].scfenergies),
+            self.level - 1,
+        )
 
     def testsign(self, data) -> None:
         """Are the Moller-Plesset corrections negative?"""
         if self.level == 2:
-            corrections = data.mpenergies[:, 0] - data.scfenergies
+            corrections = (
+                data._ccCollection._parsed_data[0].mpenergies[:, 0]
+                - data._ccCollection._parsed_data[0].scfenergies
+            )
         else:
-            corrections = data.mpenergies[:, self.level - 2] - data.mpenergies[:, self.level - 3]
+            corrections = (
+                data._ccCollection._parsed_data[0].mpenergies[:, self.level - 2]
+                - data._ccCollection._parsed_data[0].mpenergies[:, self.level - 3]
+            )
         assert numpy.all(corrections < 0.0)
 
 

test/testdata

@@ -223,9 +223,9 @@ CC        Psi4        Psi4CCSDPTTest        basicPsi4-1.7         water_ccsd(t).
 # MP        ORCA        GenericMP3Test        basicORCA4.1          water_mp3.out
 # MP        ORCA        GenericMP3Test        basicORCA4.2          water_mp3.out
 # MP        ORCA        GenericMP3Test        basicORCA5.0          water_mp3.out
-# MP        Psi4        GenericMP2Test        basicPsi4-1.2.1       water_mp2.out
-# MP        Psi4        GenericMP2Test        basicPsi4-1.3.1       water_mp2.out
-# MP        Psi4        GenericMP2Test        basicPsi4-1.7         water_mp2.out
+MP        Psi4        GenericMP2Test        basicPsi4-1.2.1       water_mp2.out
+MP        Psi4        GenericMP2Test        basicPsi4-1.3.1       water_mp2.out
+MP        Psi4        GenericMP2Test        basicPsi4-1.7         water_mp2.out
 # MP        QChem       GenericMP2Test        basicQChem5.1         water_mp2.out
 # MP        QChem       GenericMP3Test        basicQChem5.1         water_mp3.out
 # MP        QChem       QChemMP4SDQTest       basicQChem5.1         water_mp4sdq.out