measure.py

#!/usr/bin/env python
# -*- coding: utf-8 -*-

################################################################################
#
#   MEASURE - Master Equation Automatic Solver for Unimolecular REactions
#
#   Copyright (c) 2010 by Joshua W. Allen (jwallen@mit.edu)
#
#   Permission is hereby granted, free of charge, to any person obtaining a
#   copy of this software and associated documentation files (the 'Software'),
#   to deal in the Software without restriction, including without limitation
#   the rights to use, copy, modify, merge, publish, distribute, sublicense,
#   and/or sell copies of the Software, and to permit persons to whom the
#   Software is furnished to do so, subject to the following conditions:
#
#   The above copyright notice and this permission notice shall be included in
#   all copies or substantial portions of the Software.
#
#   THE SOFTWARE IS PROVIDED 'AS IS', WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
#   IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
#   FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
#   AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
#   LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
#   FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
#   DEALINGS IN THE SOFTWARE.
#
################################################################################

"""
This is the primary MEASURE module. To run MEASURE, invoke this script
via ::

$ python measure.py FILE

where ``FILE`` is the path to a valid MEASURE input file describing the job
to be run and providing the necessary information about the unimolecular
reaction network. Other command-line arguments control the level of 
verbosity of information printed to the console.
"""

import argparse
import logging
import time
import os.path
import numpy

################################################################################

def parseCommandLineArguments():
    """
    Parse the command-line arguments being passed to MEASURE. These are
    described in the module docstring.
    """

    parser = argparse.ArgumentParser(description="""
        Master Equation Automatic Solver for Unimolecular REactions (MEASURE):
        A tool for estimating pressure-dependent phenomenological rate
        coefficients k(T,P) for unimolecular reaction networks of arbitrary
        size and complexity using the master equation. Multiple methods of
        varying accuracy, speed, and robustness are available for determining
        the k(T,P) values. The output is a set of k(T,P) functions suitable for
        use in chemical kinetics mechanisms.
    """)
    parser.add_argument('file', metavar='FILE', type=str, nargs=1,
        help='a file containing information about the network')
    
    group1 = parser.add_mutually_exclusive_group()
    group1.add_argument('-d', '--draw', metavar='IMGFILE', type=str, nargs=1,
        help='draw potential energy surface and exit')
    group1.add_argument('-o', '--output', metavar='OUTFILE', type=str, nargs=1,
        help='specify location of output file')

    # Options for controlling the amount of information printed to the console
    # By default a moderate level of information is printed; you can either
    # ask for less (quiet), more (verbose), or much more (debug)
    group2 = parser.add_mutually_exclusive_group()
    group2.add_argument('-q', '--quiet', action='store_true', help='only print warnings and errors')
    group2.add_argument('-v', '--verbose', action='store_true', help='print more verbose output')

    return parser.parse_args()

################################################################################

def initializeLogging(args):
    """
    Initialize the logging system. The level of information printed is 
    determined by looking at the ``args.quiet`` and ``args.verbose`` attributes
    to see if either of the corresponding flags were set. The parameter `args`
    is an object returned by the ``argparse`` module.
    """

    # Set up logging system
    level = logging.INFO
    if args.quiet: 
        level = logging.WARNING
    elif args.verbose: 
        level = logging.DEBUG

    # Reassign the level names so that they look better on printing
    logging.addLevelName(logging.CRITICAL, 'CRITICAL: ')
    logging.addLevelName(logging.ERROR, 'ERROR: ')
    logging.addLevelName(logging.WARNING, 'Warning: ')
    logging.addLevelName(logging.INFO, '')
    logging.addLevelName(logging.DEBUG, '')

    # Create logger
    logger = logging.getLogger()
    logger.setLevel(level)

    # Create console handler and set level to debug
    # Also send everything to stdout rather than stderr
    import sys
    ch = logging.StreamHandler(sys.stdout)
    ch.setLevel(level)

    # Create formatter and add to console handler
    formatter = logging.Formatter('%(levelname)s%(message)s')
    ch.setFormatter(formatter)

    # Remove any old handlers that might exist
    while logger.handlers:
        logger.removeHandler(logger.handlers[0])

    # Add ch to logger
    logger.addHandler(ch)

################################################################################

def logHeader(level=logging.INFO):
    """
    Output a header containing identifying information about RMG to the log.
    """

    logging.log(level, '###############################################################')
    logging.log(level, '# Master Equation Automatic Solver for Unimolecular REactions #')
    logging.log(level, '# (MEASURE)                                                   #')
    logging.log(level, '# Release: 0.1.0 (7 July 2010)                                #')
    logging.log(level, '# Author: Joshua W. Allen (jwallen@mit.edu)                   #')
    logging.log(level, '# Website: http://jwallen.github.com/MEASURE                  #')
    logging.log(level, '###############################################################\n')

################################################################################

if __name__ == '__main__':
    
    # Parse the command-line arguments
    args = parseCommandLineArguments()
    
    # Initialize the logging system
    initializeLogging(args)
    
    # Log start timestamp
    logging.info('MEASURE execution initiated at ' + time.asctime() + '\n')
    
    # Log header
    logHeader()
    
    # Load input file
    from measure.input import readInput
    params = readInput(args.file[0])

    # Only proceed if the input network is valid
    if params is not None:

        network, Tlist, Plist, Elist, method, model, Tmin, Tmax, Pmin, Pmax = params

        Nisom = len(network.isomers)
        Nreac = len(network.reactants)
        Nprod = len(network.products)

        # We will save our output files to the directory containing the input file,
        # NOT the current working directory
        outputDirectory = os.path.dirname(os.path.abspath(args.file[0]))

        # Draw potential energy surface
        if args.draw:
            logging.info('Drawing potential energy surface...')
            network.drawPotentialEnergySurface(args.draw[0])

        else:
            # Automatically choose a suitable set of energy grains if they were not
            # explicitly specified in the input file
            if len(Elist) == 2:
                logging.info('Automatically determining energy grains...')
                grainSize, Ngrains = Elist
                Elist = network.autoGenerateEnergyGrains(Tmax=Tmax, grainSize=grainSize, Ngrains=Ngrains)
                logging.debug('Using %i energy grains from %g to %g kJ/mol in steps of %g kJ/mol' % (len(Elist), Elist[0] / 1000, Elist[-1] / 1000, (Elist[1] - Elist[0]) / 1000))
                logging.debug('')

            # Calculate the rate coefficients
            K, p0 = network.calculateRateCoefficients(Tlist, Plist, Elist, method)

            # Fit interpolation model
            from chempy.reaction import Reaction
            from measure.reaction import fitInterpolationModel
            if model[0] != '':
                logging.info('Fitting %s interpolation models...' % model[0])
            configurations = []
            configurations.extend([[isom] for isom in network.isomers])
            configurations.extend([reactants for reactants in network.reactants])
            configurations.extend([products for products in network.products])
            for i in range(Nisom+Nreac+Nprod):
                for j in range(min(i, Nisom+Nreac)):

                    # Check that we have nonzero k(T,P) values
                    if (numpy.any(K[:,:,i,j]) and not numpy.all(K[:,:,i,j])):
                        raise NetworkError('Zero rate coefficient encountered while updating network %s.' % network)
                    
                    # Make a new net reaction
                    forward = True
                    netReaction = Reaction(
                        reactants=configurations[j],
                        products=configurations[i],
                        kinetics=None,
                        reversible=(i<Nisom+Nreac),
                    )
                    network.netReactions.append(netReaction)

                    # Set/update the net reaction kinetics using interpolation model
                    netReaction.kinetics = fitInterpolationModel(netReaction, Tlist, Plist,
                        K[:,:,i,j] if forward else K[:,:,j,i],
                        model, Tmin, Tmax, Pmin, Pmax, errorCheck=True)

            # Save results to file
            from measure.output import writeOutput
            if args.output:
                out = os.path.abspath(args.output[0])
            else:
                out = os.path.join(outputDirectory, 'output.py')
            writeOutput(out, network, Tlist, Plist, Elist, method, model)

    # Log end timestamp
    logging.info('')
    logging.info('MEASURE execution terminated at ' + time.asctime())