qchem.py

"""
/******************************************************************************
  This source file is part of the Avogadro project.

  This source code is released under the New BSD License, (the "License").
******************************************************************************/
"""

import argparse
import json
import sys

# Some globals:
targetName = 'Q-Chem'
debug = False


def getOptions():
    userOptions = {}

    userOptions['Title'] = {}
    userOptions['Title']['type'] = 'string'
    userOptions['Title']['default'] = ''

    userOptions['Calculation Type'] = {}
    userOptions['Calculation Type']['type'] = "stringList"
    userOptions['Calculation Type']['default'] = 1
    userOptions['Calculation Type']['values'] = \
        ['Single Point', 'Equilibrium Geometry', 'Frequencies']

    userOptions['Theory'] = {}
    userOptions['Theory']['type'] = "stringList"
    userOptions['Theory']['default'] = 2
    userOptions['Theory']['values'] = \
        ['HF', 'MP2', 'B3LYP', 'B3LYP5', 'EDF1', 'M062X', 'CCSD']

    userOptions['Basis'] = {}
    userOptions['Basis']['type'] = "stringList"
    userOptions['Basis']['default'] = 2
    userOptions['Basis']['values'] = \
        ['STO-3G', '3-21G', '6-31G(d)', '6-31G(d,p)', '6-31+G(d)', '6-311G(d)',
         'cc-pVDZ', 'cc-pVTZ', 'LANL2DZ', 'LACVP']

    userOptions['Filename Base'] = {}
    userOptions['Filename Base']['type'] = 'string'
    userOptions['Filename Base']['default'] = 'job'

    userOptions['Charge'] = {}
    userOptions['Charge']['type'] = "integer"
    userOptions['Charge']['default'] = 0
    userOptions['Charge']['minimum'] = -9
    userOptions['Charge']['maximum'] = 9

    userOptions['Multiplicity'] = {}
    userOptions['Multiplicity']['type'] = "integer"
    userOptions['Multiplicity']['default'] = 1
    userOptions['Multiplicity']['minimum'] = 1
    userOptions['Multiplicity']['maximum'] = 6

    # TODO Coordinate format (need zmatrix)

    opts = {'userOptions': userOptions}

    return opts


def generateInputFile(opts):
    # Extract options:
    title = opts['Title']
    calculate = opts['Calculation Type']
    theory = opts['Theory']
    basis = opts['Basis']
    charge = opts['Charge']
    multiplicity = opts['Multiplicity']

    # Convert to code-specific strings
    calcStr = ''
    if calculate == 'Single Point':
        calcStr = 'SP'
    elif calculate == 'Equilibrium Geometry':
        calcStr = 'Opt'
    elif calculate == 'Frequencies':
        calcStr = 'Freq'
    else:
        raise Exception('Unhandled calculation type: %s' % calculate)

    theoryStr = ''
    if theory in ['HF', 'B3LYP', 'B3LYP5', 'EDF1', 'M062X', 'MP2', 'CCSD']:
        theoryStr = theory
    else:
        raise Exception('Unhandled theory type: %s' % theory)

    basisStr = ''
    if basis in ['STO-3G', '3-21G', '6-31G(d)', '6-31G(d,p)', '6-31+G(d)',
                 '6-311G(d)', 'cc-pVDZ', 'cc-pVTZ']:
        basisStr = 'BASIS %s' % basis
    elif basis in ['LANL2DZ', 'LACVP']:
        basisStr = 'ECP %s' % basis
    else:
        raise Exception('Unhandled basis type: %s' % basis)

    output = ''

    output += '$rem\n'
    output += '   JOBTYPE %s\n' % calcStr
    output += '   METHOD %s\n' % theoryStr
    output += '   %s\n' % basisStr
    output += '   GUI 2\n'
    output += '$end\n\n'

    output += '$comment\n   %s\n$end\n\n' % title

    output += '$molecule\n'
    output += '   %s %s\n' % (charge, multiplicity)
    output += '$$coords:___Sxyz$$\n'
    output += '$end\n'

    return output


def generateInput():
    # Read options from stdin
    stdinStr = sys.stdin.read()

    # Parse the JSON strings
    opts = json.loads(stdinStr)

    # Generate the input file
    inp = generateInputFile(opts['options'])

    # Basename for input files:
    baseName = opts['options']['Filename Base']

    # Prepare the result
    result = {}
    # Input file text -- will appear in the same order in the GUI as they are
    # listed in the array:
    files = []
    files.append({'filename': '%s.qcin' % baseName, 'contents': inp})
    if debug:
        files.append({'filename': 'debug_info', 'contents': stdinStr})
    result['files'] = files
    # Specify the main input file. This will be used by MoleQueue to determine
    # the value of the $$inputFileName$$ and $$inputFileBaseName$$ keywords.
    result['mainFile'] = '%s.qcin' % baseName
    return result

if __name__ == "__main__":
    parser = argparse.ArgumentParser('Generate a %s input file.' % targetName)
    parser.add_argument('--debug', action='store_true')
    parser.add_argument('--print-options', action='store_true')
    parser.add_argument('--generate-input', action='store_true')
    parser.add_argument('--display-name', action='store_true')
    parser.add_argument('--lang', nargs='?', default='en')
    args = vars(parser.parse_args())

    debug = args['debug']

    if args['display_name']:
        print(targetName)
    if args['print_options']:
        print(json.dumps(getOptions()))
    elif args['generate_input']:
        print(json.dumps(generateInput()))