Add gaussian to base.py

MolSSI · QuChem · Nov 29, 2023 · Nov 29, 2023 · Nov 29, 2023 · Nov 30, 2023
commit ce55302956780a8dae00af28bea2b8a6cda1bf02
diff --git a/qcengine/programs/base.py b/qcengine/programs/base.py
@@ -28,6 +28,7 @@
 from .torchani import TorchANIHarness
 from .turbomole import TurbomoleHarness
 from .xtb import XTBHarness
+from .gaussian import GaussianHarness
 
 __all__ = ["register_program", "get_program", "list_all_programs", "list_available_programs"]
 
@@ -118,6 +119,7 @@ def list_available_programs() -> Set[str]:
 register_program(TurbomoleHarness())
 register_program(TeraChemFrontEndHarness())
 register_program(TeraChemPBSHarness())
+register_program(GaussianHarness())
 
 # Semi-empirical
 register_program(MopacHarness())

diff --git a/qcengine/programs/gaussian.py b/qcengine/programs/gaussian.py
 """

 import os
 import re
 import tempfile
 import warnings
 from collections import defaultdict
 from typing import Any, Dict, List, Optional, Tuple
 import cclib
 from cclib.method import Nuclear

 import numpy as np
 from qcelemental import constants
 from qcelemental.models import AtomicInput, AtomicResult, Molecule, Provenance
 from qcelemental.molparse import regex
 from qcelemental.util import parse_version, safe_version, which

 from qcengine.config import TaskConfig, get_config

 from ..exceptions import InputError, UnknownError
 from ..util import disk_files, execute, temporary_directory
 from .model import ProgramHarness

 class GaussianHarness(ProgramHarness):
        else:
            raise InputError(f"Driver {input_model.driver} not implemented for Gaussian.")

        #if input_model.molecule.fix_com or input_model.molecule.fix_orientation:
        #    keywords["SYM_IGNORE"] = "TRUE"
        if 'SCF_CONVERGENCE' in keywords:
           gaussian_kw.append('SCF=' + keywords["SCF_CONVERGENCE"])
        if 'POPULATION' in keywords:
           gaussian_kw.append('Pop=' + keywords['POPULATION'])   
           
        keywords = {'scf_damp': 'true',
                    'scf_diis': 'false'}
        # Begin input file
        input_file = []
        data = cclib.io.ccread(tmp_output_file)
        cclib_vars = data.getattributes(True)
        
        last_occupied_energy = data.moenergies[0][data.homos[0]]
        #output_data['HOMO ENERGY'] = last_occupied_energy
        
        scf_energy = data.scfenergies[0] / constants.conversion_factor("hartree", "eV") # Change from the eV unit to the Hartree unit
            output_data['return_result'] = scf_energy
        #print (os.system('ccget --list ' + tmp_output_file)) #data available in the output for parsing

        #if input_model.driver == 'energy':
        #   print (cclib.__version__)        
        #   print (output_data)
        #print (input_model)

        properties = {
        output_data['success'] = True
        #print ('output_data: ', output_data)

        provenance = Provenance(creator="Gaussian", version=self.get_version(), routine='g09').dict()

        stdout = outfiles.pop('stdout')
        stderr = outfiles.pop('stderr')
        #print("\nPRINT STDOUT: \n", stdout)
        

        method = input_model.model.method.lower()
        #method = method[4:] if method.startswith("") else method

        # filter unwanted data
	"""

	import os
	import re
Check notice Code scanning / CodeQL Unused import Note Import of 're' is not used.
	import tempfile
Check notice Code scanning / CodeQL Unused import Note Import of 'tempfile' is not used.
	import warnings
Check notice Code scanning / CodeQL Unused import Note Import of 'warnings' is not used.
	from collections import defaultdict
Check notice Code scanning / CodeQL Unused import Note Import of 'defaultdict' is not used.
	from typing import Any, Dict, List, Optional, Tuple
Check notice Code scanning / CodeQL Unused import Note Import of 'Tuple' is not used.
	import cclib
	from cclib.method import Nuclear

	import numpy as np
Check notice Code scanning / CodeQL Unused import Note Import of 'np' is not used.
	from qcelemental import constants
	from qcelemental.models import AtomicInput, AtomicResult, Molecule, Provenance
Check notice Code scanning / CodeQL Unused import Note Import of 'Molecule' is not used.
	from qcelemental.molparse import regex
Check notice Code scanning / CodeQL Unused import Note Import of 'regex' is not used.
	from qcelemental.util import parse_version, safe_version, which
Check notice Code scanning / CodeQL Unused import Note Import of 'parse_version' is not used. Import of 'safe_version' is not used.

	from qcengine.config import TaskConfig, get_config
Check notice Code scanning / CodeQL Unused import Note Import of 'get_config' is not used.

	from ..exceptions import InputError, UnknownError
	from ..util import disk_files, execute, temporary_directory
Check notice Code scanning / CodeQL Unused import Note Import of 'disk_files' is not used. Import of 'temporary_directory' is not used.
	from .model import ProgramHarness

	class GaussianHarness(ProgramHarness):
	else:
	raise InputError(f"Driver {input_model.driver} not implemented for Gaussian.")

	#if input_model.molecule.fix_com or input_model.molecule.fix_orientation:
	# keywords["SYM_IGNORE"] = "TRUE"
Check notice Code scanning / CodeQL Commented-out code Note This comment appears to contain commented-out code.
	if 'SCF_CONVERGENCE' in keywords:
	gaussian_kw.append('SCF=' + keywords["SCF_CONVERGENCE"])
	if 'POPULATION' in keywords:
	gaussian_kw.append('Pop=' + keywords['POPULATION'])

	keywords = {'scf_damp': 'true',
Check notice Code scanning / CodeQL Unused local variable Note Variable keywords is not used.
	'scf_diis': 'false'}
	# Begin input file
	input_file = []
	data = cclib.io.ccread(tmp_output_file)
	cclib_vars = data.getattributes(True)

	last_occupied_energy = data.moenergies[0][data.homos[0]]
Check notice Code scanning / CodeQL Unused local variable Note Variable last_occupied_energy is not used.
	#output_data['HOMO ENERGY'] = last_occupied_energy

	scf_energy = data.scfenergies[0] / constants.conversion_factor("hartree", "eV") # Change from the eV unit to the Hartree unit
	output_data['return_result'] = scf_energy
	#print (os.system('ccget --list ' + tmp_output_file)) #data available in the output for parsing

	#if input_model.driver == 'energy':
	# print (cclib.__version__)
	# print (output_data)
Check notice Code scanning / CodeQL Commented-out code Note This comment appears to contain commented-out code.
	#print (input_model)

	properties = {
	output_data['success'] = True
	#print ('output_data: ', output_data)

	provenance = Provenance(creator="Gaussian", version=self.get_version(), routine='g09').dict()
Check notice Code scanning / CodeQL Unused local variable Note Variable provenance is not used.

	stdout = outfiles.pop('stdout')
Check notice Code scanning / CodeQL Unused local variable Note Variable stdout is not used.
	stderr = outfiles.pop('stderr')
Check notice Code scanning / CodeQL Unused local variable Note Variable stderr is not used.
	#print("\nPRINT STDOUT: \n", stdout)


	method = input_model.model.method.lower()
Check notice Code scanning / CodeQL Unused local variable Note Variable method is not used.
	#method = method[4:] if method.startswith("") else method

	# filter unwanted data