From 8b126f0bda55113b892330d0b1cd89ed5d488cad Mon Sep 17 00:00:00 2001
From: avcopan <avcopan@gmail.com>
Date: Sat, 21 Sep 2024 16:11:30 -0500
Subject: [PATCH] New: Adds PM3 semi-empirical method for Gaussian 16

Also, makes basis set optional.
---
 elstruct/par.py                               | 35 +++++++++++++++++--
 elstruct/reader/_gaussian16/energ.py          |  2 ++
 .../writer/_gaussian16/templates/all.mako     |  4 ++-
 elstruct/writer/fill.py                       | 29 ++-------------
 4 files changed, 40 insertions(+), 30 deletions(-)

diff --git a/elstruct/par.py b/elstruct/par.py
index 2f15066f..927a1385 100644
--- a/elstruct/par.py
+++ b/elstruct/par.py
@@ -13,7 +13,7 @@ def standard_case(name):
         :type name: str
         :rtype: str
     """
-    return name.lower()
+    return name.lower() if isinstance(name, str) else name
 
 
 class Module():
@@ -101,6 +101,12 @@ class Method():
                'hf', 'hf',
                ('R',), ('U', 'R'))})
 
+    class SemiEmpirical():
+        PM3 = ('pm3',
+            {Program.GAUSSIAN16: (
+                'pm3', 'pm3',
+                ('R',), ('U', 'R'))})
+
     class Corr():
         """ Correlated method names """
         MP2 = ('mp2',
@@ -353,6 +359,21 @@ def contains(cls, name):
 
         return name in names
 
+    @classmethod
+    def is_semi_empirical(cls, name):
+        """ Assess if a method is a semi-empirical method.
+
+            :param cls: class object
+            :type cls: obj
+            :param name: name of method
+            :type name: str
+        """
+
+        name = standard_case(name)
+        semi_emp_names = [row[0] for row in pclass.all_values(cls.SemiEmpirical)]
+
+        return name in semi_emp_names
+
     @classmethod
     def is_correlated(cls, name):
         """ Assess if a method is a single-reference correlated method.
@@ -632,6 +653,16 @@ class Basis():
 
         (name, {program: name})
     """
+    NONE = (None, {Program.CFOUR2: None,
+                     Program.GAUSSIAN09: None,
+                     Program.GAUSSIAN03: None,
+                     Program.GAUSSIAN16: None,
+                     Program.MOLPRO2015: None,
+                     Program.MOLPRO2021: None,
+                     Program.MRCC2018: None,
+                     Program.NWCHEM6: None,
+                     Program.ORCA4: None,
+                     Program.PSI4: None})
 
     STO3G = ('sto-3g', {Program.CFOUR2: None,
                         Program.GAUSSIAN09: None,
@@ -960,7 +991,7 @@ def is_nonstandard_basis(name):
             :param name: name of basis set
             :type name: str
         """
-        return name.lower().startswith('basis:')
+        return isinstance(name, str) and name.lower().startswith('basis:')
 
     @classmethod
     def nonstandard_basis_name(cls, name):
diff --git a/elstruct/reader/_gaussian16/energ.py b/elstruct/reader/_gaussian16/energ.py
index 1245a676..ee273e32 100644
--- a/elstruct/reader/_gaussian16/energ.py
+++ b/elstruct/reader/_gaussian16/energ.py
@@ -106,6 +106,8 @@ def _doub_hyb_dft_energy(output_str):
             ENERGY_READER_DCT[(METHOD, frozenset({}))] = _dft_energy
         else:
             ENERGY_READER_DCT[(METHOD, frozenset({}))] = _doub_hyb_dft_energy
+    elif Method.is_semi_empirical(METHOD):
+        ENERGY_READER_DCT[(METHOD, frozenset({}))] = _dft_energy
 
 # Check if we have added any unsupported methods to the energy reader
 READ_METHODS = set(method[0] for method in ENERGY_READER_DCT)
diff --git a/elstruct/writer/_gaussian16/templates/all.mako b/elstruct/writer/_gaussian16/templates/all.mako
index 75c0aed1..83775783 100644
--- a/elstruct/writer/_gaussian16/templates/all.mako
+++ b/elstruct/writer/_gaussian16/templates/all.mako
@@ -4,8 +4,10 @@ ${machine_options}
 ## 1. theoretical method block
 % if reference:
 #P ${reference} ${method}/${basis}
-% else:
+% elif basis:
 #P ${method}/${basis}
+% else:
+#P ${method}
 % endif
 % if reference != 'rohf' and method != 'rohf':
 # SCF=(xqc)
diff --git a/elstruct/writer/fill.py b/elstruct/writer/fill.py
index 2cfc03b3..56a8a6f1 100644
--- a/elstruct/writer/fill.py
+++ b/elstruct/writer/fill.py
@@ -126,31 +126,6 @@ def _offset_planar_vals(val):
     return geo_str, zmat_vval_str, zmat_cval_str
 
 
-def _name_mat(zma, frozen_coordinates, job_key):
-    """ Build the name matrix for a Z-Matrix data structure:
-
-        used for cfour optimizations
-
-        :param zma: cartesian or z-matrix geometry
-        :type zma: tuple
-        :param frozen_coordinates: only with z-matrix geometries; list of
-            coordinate names to freeze
-        :type fozen_coordinates: tuple[str]
-        :param job_key: job contained in the inpit file
-        :type job_key: str
-    """
-    if job_key == 'optimization':
-        name_mat = [
-            [name+'*'
-             if name is not None and name not in frozen_coordinates else name
-             for name in row]
-            for row in automol.zmat.name_matrix(zma)]
-    else:
-        name_mat = automol.zmat.name_matrix(zma)
-
-    return name_mat
-
-
 def build_gen_lines(gen_lines, line1=None, line2=None, line3=None):
     """ Set three lines for writing in various blocks of files.
         Function either grabs lines from the dictionary and if nothing
@@ -300,7 +275,7 @@ def program_method_names(prog, method, basis, mult, orb_restricted):
     elif method == Method.HF[0]:
         if prog in (Program.GAUSSIAN09, Program.GAUSSIAN03,
                     Program.GAUSSIAN16):
-            prog_method = prog_reference
+            prog_method = prog_reference if prog_reference else method
         else:
             prog_method = program_method_name(prog, method, singlet=singlet)
     else:
@@ -331,7 +306,7 @@ def _reference(prog, method, mult, orb_restricted):
         :rtype: str
     """
     # Need a multiref version
-    if Method.is_dft(method):
+    if Method.is_dft(method) or Method.is_semi_empirical(method):
         reference = _dft_reference(prog, orb_restricted)
     elif method == Method.HF[0]:
         reference = _hf_reference(prog, mult, orb_restricted)