terachem.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 = 'TeraChem'
extension = 'tcin'
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'] = 2
    userOptions['Calculation Type']['values'] = \
        ['Single Point', 'Gradient', 'Equilibrium Geometry']

    userOptions['Theory'] = {}
    userOptions['Theory']['type'] = 'stringList'
    userOptions['Theory']['default'] = 2
    userOptions['Theory']['values'] = \
        ['HF', 'BLYP', 'B3LYP', 'B3LYP1', 'B3LYP5', 'PBE', 'REVPBE']

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

    userOptions['Unrestricted'] = {}
    userOptions['Unrestricted']['type'] = 'boolean'
    userOptions['Unrestricted']['default'] = False

    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']

    userOptions['Dispersion'] = {}
    userOptions['Dispersion']['type'] = 'stringList'
    userOptions['Dispersion']['default'] = 0
    userOptions['Dispersion']['values'] = ['Off', 'On', 'D2', 'D3']

    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 (can do pdb, not sure it's necessary though)

    opts = {'userOptions': userOptions}

    return opts


def generateInputFile(opts):
    # Extract options:
    title = opts['Title']
    calculate = opts['Calculation Type']
    theory = opts['Theory']
    unrestricted = opts['Unrestricted']
    basis = opts['Basis']
    dispersion = opts['Dispersion']
    charge = opts['Charge']
    multiplicity = opts['Multiplicity']
    baseName = opts['Filename Base']

    # Convert to code-specific strings
    basisStr = ''
    if basis == 'STO-3G':
        basisStr = basis.lower()
    else:
        basisStr = basis

    calcStr = ''
    if calculate == 'Single Point':
        calcStr = 'energy'
    elif calculate == 'Gradient':
        calcStr = 'gradient'
    elif calculate == 'Equilibrium Geometry':
        calcStr = 'minimize'
    else:
        raise Exception('Unhandled calculation type: %s' % calculate)

    theoryStr = ''
    if unrestricted:
        theoryStr += 'u'
    elif theory == 'HF':
        theoryStr += 'r'
    theoryStr += theory.lower()

    dispStr = ''
    if dispersion == 'Off':
        dispStr = 'no'
    elif dispersion == 'On':
        dispStr = 'yes'
    else:
        dispStr = dispersion.lower()

    # Create input file
    output = ''

    output += '#\n# %s\n#\n\n' % title

    output += f'{"run":<15}{calcStr}\n\n'

    output += f'{"method":<15}{theoryStr}\n'
    if dispersion != 'Off':
        output += f'{"dispersion":<15}{dispStr}\n'
    output += f'{"basis":<15}{basisStr}\n'
    output += f'{"charge":<15}{charge}\n'
    output += f'{"spinmult":<15}{multiplicity}\n\n'

    output += f'{"coordinates":<15}{baseName}.xyz\n\n'

    output += 'end\n'

    # Create XYZ file
    coordFile = '$$atomCount$$\n%s\n$$coords:Sxyz$$\n' % title

    return output, coordFile


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': f'{baseName}.{extension}', 'contents': inp[0]})
    files.append({'filename': f'{baseName}.xyz', 'contents': inp[1]})
    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'] = f'{baseName}.{extension}'
    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()))