Added aqme/templates/basis_sets.csv and aqme/templates/functionals.csv to the repository. These files are used by the aqme/qprep.py script to generate the input files for the quantum chemistry calculations. Also added aqme/.DS_Store to the repository. This file is a hidden file that is created by the MacOS operating system. It is not used by the aqme package, but it is added to the repository to keep the directory structure consistent with the local directory structure on the development machine.

Author: bobbypaton

.DS_Store

@@ -62,6 +62,9 @@
 import glob
 import time
 import json
+import pandas as pd
+from pkg_resources import resource_filename
+
 from aqme.utils import (
     cclib_atoms_coords,
     QM_coords,
@@ -73,10 +76,12 @@
     add_prefix_suffix,
     check_files
 )
+
 from aqme.csearch.crest import xyzall_2_xyz
 from pathlib import Path
 from rdkit import Chem
 
+TEMPLATES_PATH = Path(resource_filename("aqme", "templates"))
 
 class qprep:
     """
@@ -531,3 +536,36 @@ def qprep_coords(self, file, mol, file_format):
             mult = 1
 
         return atom_types, cartesians, charge, mult, found_coords
+
+    def check_level_of_theory(functional, basis, program):
+        """
+        Cross check a chosen functional and basis set against a precompiled list of available options.
+        Not necessarily a definitive list!
+        """
+
+        found = True # assume that they exist
+
+        functional_csv = TEMPLATES_PATH / Path('functionals.csv')
+        basis_set_csv = TEMPLATES_PATH / Path('basis_sets.csv')
+        
+        functional_data = pd.read_csv(functional_csv)
+        functional_data.drop_duplicates(inplace=True)
+
+        basis_set_data = pd.read_csv(basis_set_csv)
+        basis_set_data.drop_duplicates(inplace=True)
+
+        if program == 'orca':
+            functional_list = functional_data['orca'].to_numpy().flatten()
+            functional_list = [x for x in functional_list if str(x) != 'nan'] # remove NaN
+            basis_set_list = basis_set_data['orca'].to_numpy().flatten() 
+            basis_set_list = [x for x in basis_set_list if str(x) != 'nan'] # remove NaN
+            
+        if functional.upper() not in (func.upper() for func in functional_list):
+            print('\n!  {} functional requested but unknown in {}!\n'.format(functional, program))
+            found = False
+            
+        if basis.upper() not in (bs.upper() for bs in basis_set_list):
+            print('\n!  {} basis set requested but unknown in {}!\n'.format(basis, program))
+            found = False
+        
+        return found

aqme/.DS_Store

@@ -0,0 +1,61 @@
+basis set,orca
+,STO-3G
+,3-21G
+,3-21GSP
+,4-22GSP
+,6-31G
+,6-31G*
+,6-31G**
+,6-31+G
+,6-31+G*
+,6-31+G**
+,6-31++G
+,6-31++G*
+,6-31++G**
+,m6-31G
+,6-311G
+,6-311G*
+,6-311G**
+,6-311+G
+,6-311+G*
+,6-311+G**
+,6-311++G
+,6-311++G*
+,6-311++G**
+,def2-SVP
+,def2-SV(P)
+,def2-TZVP
+,def2-TZVP(-f)
+,def2-TZVPP
+,def2-QZVP
+,def2-QZVPP
+,SV
+,SV(P)
+,SVP
+,TZV
+,TZV(P)
+,TZVP
+,TZVPP
+,QZVP
+,QZVPP
+,ma-def2-SVP
+,ma-def2-SV(P)
+,ma-def2-TZVP
+,ma-def2-TZVP(-f)
+,ma-def2-TZVPP
+,ma-def2-QZVPP
+,def2-SVPD
+,def2-TZVPD
+,def2-TZVPPD
+,def2-QZVPD
+,def2-QZVPPD
+,cc-pVDZ
+,cc-pVTZ
+,cc-pVQZ
+,cc-pV5Z
+,cc-pV6Z
+,aug-cc-pVDZ
+,aug-cc-pVTZ
+,aug-cc-pVQZ
+,aug-cc-pV5Z
+,aug-cc-pV6Z

aqme/qprep.py

@@ -0,0 +1,165 @@
+functional,orca,gaussian,,,
+Local and GGA,,,,,
+B97-D3,B97-D3,B97D3,,,
+B97D,,B97D,,,
+BLYP,BLYP,BLYP,,,
+BP86,BP86,BP86,,,
+BPBE,BPBE,BPBE,,,
+GLYP,GLYP,,,,
+HCTH,,HCTH,,,
+HCTH147,,HCTH147,,,
+HCTH407,,HCTH407,,,
+HCTH93,,HCTH93,,,
+HFS,HFS,HFS,,,
+LDA,LDA,,,,
+mPWLYP,mPWLYP,mPWLYP,,,
+mPWPW,mPWPW,,,,
+mPWPW91,,mPWPW91,,,
+N12,,N12,,,
+OLYP,OLYP,OLYP,,,
+OPBE,OPBE,OPBE,,,
+PBE,PBE,PBEPBE,,,
+PBEhPBE,,PBEh1PBE,,,
+PW91,PW91,PW91PW91,,,
+PW91P86,,PW91P86,,,
+PWP,PWP,,,,
+revPBE,revPBE,,,,
+RPBE,RPBE,,,,
+RPW86PBE,RPW86PBE,,,,
+VSXC,,VSXC,,,
+VV10,,,,,
+XLYP,XLYP,,,,
+Meta-GGA,,,,,
+M06L,M06L,M06L,,,
+M11L,,M11L,,,
+MN12L,,MN12L,,,
+MN15L,,MN15L,,,
+PKZB,,PKZBPKZB,,,
+revTPSS,revTPSS,revTPSSrevTPSS,,,
+SCAN,SCANfunc ,,,,
+SOGGA11,,SOGGA11,,,
+tHCTH,,tHCTH,,,
+TPSS,TPSS,TPSSTPSS,,,
+Hybrid,,,,,
+APF,,APF,,,
+APFD,,APFD,,,
+B1B95,,B1B95,,,
+B1LYP,B1LYP,B1LYP,,,
+B1P,B1P,,,,
+B1P86,B1P86,,,,
+B3LYP,B3LYP,B3LYP,,,
+B3LYP-NL,B3LYP NL,,,,
+B3P,B3P,,,,
+B3P86,B3P86,B3P86,,,
+B3PW,B3PW,,,,
+B3PW91,B3PW91,B3PW91,,,
+B97-1,,B971,,,
+B97-2,,B972,,,
+B98,,B98,,,
+BHandH,,BHandH,,,
+BHandHLYP,BHANDHLYP,BHandHLYP,,,
+BHLYP,BHLYP,,,,
+BMK,,BMK,,,
+HISS,,HISSbPBE,,,
+HSE03,,,,,
+HSE06,,,,,
+LC-whPBE,,LC-wHPBE,,,
+M05,,M05,,,
+M052X,,M052X,,,
+M06,M06,M06,,,
+M062X,M062X,M062X,,,
+M06HF,,M06HF,,,
+M08HX,,M08HX,,,
+MN15,,MN15,,,
+MPW1B95,,,,,
+MPW1KCIS,,,,,
+mPW1LYP,mPW1LYP,mPW1LYP,,,
+mPW1PBE,,mPW1PBE,,,
+mPW1PW,mPW1PW,,,,
+mPW1PW91,,mPW1PW91,,,
+mPW3PBE,,mPW3PBE,,,
+MPWB1K,,,,,
+MPWKCIS1K,,,,,
+O3LYP,O3LYP,O3LYP,,,
+PBE0,PBE0,PBE1PBE,,,
+PBE1KCIS,,,,,
+PBEh1PBE,,PBEh1PBE,,,
+PW1PW,PW1PW,,,,
+PW6B95,PW6B95,PW6B95,,,
+PW6B95D3,,PW6B95D3,,,
+REVPBE0,REVPBE0,,,,
+REVPBE38,REVPBE38,,,,
+revTPSS0,,,,,
+revTPSSh,,,,,
+SOGGA11X,,SOGGA11X,,,
+tHCTHhyb,,tHCTHhyb,,,
+TPSS0,TPSS0,,,,
+TPSS1KCIS,,,,,
+TPSSh,TPSSh,TPSSh,,,
+wB97X-D3,wB97X-D3,,,,
+wB97X-V,wB97X-V,,,,
+X3LYP,X3LYP,X3LYP,,,
+range-separated,,,,,
+CAM-B3LYP,CAM-B3LYP,CAM-B3LYP,,,
+HISSbPBE,,HISSbPBE,,,
+HSEH1PBE,,HSEH1PBE,,,
+LC-BLYP,LC-BLYP,LC-BLYP,,,
+LC-PBE,LC-PBE,LC-PBEPBE,,,
+LC-wPBE,,LC-wPBE,,,
+LC-wHPBE,,LC-wHPBE,,,
+M11,,M11,,,
+MN12SX,,MN12SX,,,
+N12SX,,N12SX,,,
+OHSE1PBE,,OHSE1PBE,,,
+OHSE2PBE,,OHSE2PBE,,,
+wB97,wB97,wB97,,,
+wB97M-D3BJ,wB97M-D3BJ,,,,
+wB97M-D4,wB97M-D4,,,,
+wB97M-V,wB97M-V,,,,
+wB97X,wB97X,wB97X,,,
+wB97X-D,,wB97XD,,,
+wB97X-D3,wB97X-D3,,,,
+wB97X-D3BJ,wB97X-D3BJ,,,,
+wB97X-D4,wB97X-D4,,,,
+wB97X-V,wB97X-V,,,,
+Double hybrid,,,,,
+B2GP-PLYP,B2GP-PLYP,,,,
+B2K-PLYP,B2K-PLYP,,,,
+B2PLYP,B2PLYP,B2PLYP,,,
+B2PLYP-D,,B2PLYPD,,,
+B2PLYP-D3,,B2PLYPD3,,,
+B2T-PLYP,B2T-PLYP,,,,
+DSD-BLYP,DSD-BLYP,,,,
+DSD-PBEB95,DSD-PBEB95,,,,
+DSD-PBEP86,DSD-PBEP86,DSDPBEP86,,,
+mPW2PLYP,mPW2PLYP,mPW2PLYP,,,
+mPW2PLYPD,,mPW2PLYPD,,,
+PBE-QIDH,PBE-QIDH,PBEQIDH,,,
+PBE0-DH,PBE0-DH,PBE0DH,,,
+PWPB95,PWPB95,,,,
+composite DFT methods,,,,,
+B97-3c,B97-3c,,,,
+HF-3c,HF-3c,,,,
+PBEh-3c,PBEh-3c,,,,
+r2SCAN-3c,r2SCAN-3c,,,,
+Range-separated double-hybrid,,,,,
+RSX-0DH,RSX-0DH,,,,
+RSX-QIDH,RSX-QIDH,,,,
+wB2GP-PLYP ,wB2GP-PLYP ,,,,
+wB2PLYP ,wB2PLYP ,,,,
+wB88PP86,wB88PP86,,,,
+wPBEPP86 ,wPBEPP86 ,,,,
+Global double hybrids,,,,,
+SCS-B2GP-PLYP21,SCS-B2GP-PLYP21,,,,
+SCS-PBE-QIDH,SCS-PBE-QIDH,,,,
+SCS-RSX-QIDH,SCS-RSX-QIDH,,,,
+SCS-wB2GP-PLYP,SCS-wB2GP-PLYP,,,,
+SCS-wB88PP86,SCS-wB88PP86,,,,
+SCS-wPBEPP86,SCS-wPBEPP86,,,,
+SOS-B2GP-PLYP21,SOS-B2GP-PLYP21,,,,
+SOS-PBE-QIDH,SOS-PBE-QIDH,,,,
+SOS-RSX-QIDH,SOS-RSX-QIDH,,,,
+SOS-wB2GP-PLYP,SOS-wB2GP-PLYP,,,,
+SOS-wB88PP86,SOS-wB88PP86,,,,
+SOS-wPBEPP86,SOS-wPBEPP86,,,,
+wB97X-2,wB97X-2,,,,

aqme/templates/basis_sets.csv

@@ -0,0 +1,14 @@
+
+Host: Roberts-MacBook-Pro-5.local
+
+Timers On : Sun Apr 14 16:48:33 2024
+Timers Off: Sun Apr 14 16:48:45 2024
+
+Wall Time:       11.66 seconds
+
+                                                       Time (seconds)
+Module                                       User      System        Wall        Calls
+
+--------------------------------------------------------------------------------------
+
+**************************************************************************************