Chimie Théorique » QMX

#!/usr/bin/env python

# command line interface for setup of QMX calculations

#

# Torsten Kerber, ENS LYON: 2011, 07, 11

#

# This work is supported by Award No. UK-C0017, made by King Abdullah

# University of Science and Technology (KAUST)

#---------------------------------------------------------------------------------------------------

import os, sys

from copy import deepcopy

from optparse import OptionParser

#---------------------------------------------------------------------------------------------------

from qmxEMBED import embedDefinitions

from qmxJOB  import jobDefinitions

from qmxSTR  import strSystemDefinitions, strClusterDefinitions

from qmxCALC import calcDefinitions, QmxCalcDefinition

from qmxWRITE import writeData

#---------------------------------------------------------------------------------------------------

#---------------------------------------------------------------------------------------------------

#---------------------------------------------------------------------------------------------------

def getline(section, subsection, lines):

    nline = -1

    for iline in xrange(len(lines)):

        if lines[iline][0].strip() == subsection:

            if nline != -1:

                sys.stderr.write("section: <"+section+separator+subsection+"> has been definied more than once\n")

                sys.exit(1)

            nline = iline

    if nline == -1:

        return None

    return lines[nline][1].strip()

#---------------------------------------------------------------------------------------------------

def analyzeSection(definitions, section, lines):

    line = getline(section, "program", lines)

    if line is None:

        print "section <" + section + "> does not contain program"

        sys.exit(1)

    myDefinition = None

    for definition in definitions:

        if definition.name.lower() == line.lower():

            myDefinition = deepcopy(definition)

            break

    if myDefinition is None:

        print "the program <" + line + "> is not defined for the section <" + section + ">"

        sys.exit(1)

    myDefinition.system = section

    subsections = []

    for line in lines:

        subsections.append(line[0].strip().lower())

    for subsection in subsections:

        line = getline(section, subsection, lines)

        if line is None:

            print "input error in <"+section+"."+subsection+">"

            sys.exit(1)

        if subsection == "program":

            continue

        if subsection == "options":

            subsection = 'class.options'

        myDefinition.keywords[subsection] = line

    return myDefinition

#---------------------------------------------------------------------------------------------------

#--- setting default values ------------------------------------------------------------------------

#---------------------------------------------------------------------------------------------------

#define separators

separator=":"

subseparator="."

lineseparator="\n"

#--- parse arguments -------------------------------------------------------------------------------

#parse arguments (python 2.6)

parser = OptionParser()

parser.add_option("-i", "--infile",  dest="inputFile",  help="specifies the input file", metavar="FILE", default="qmx.in")

parser.add_option("-o", "--outfile", dest="outputFile", help="specifies the output file", metavar="FILE")

parser.add_option("-f", action="store_true", dest="overwrite")

(options, args) = parser.parse_args()

#--- check wether output file exists ---------------------------------------------------------------

if options.outputFile is not None and os.path.exists(options.outputFile) and not options.overwrite:

    sys.stderr.write(lineseparator+"the output file <"+options.outputFile+"> already exists"+lineseparator)

    sys.exit(1)

#--- read intput file ------------------------------------------------------------------------------

file=open(options.inputFile, "r")

lines = file.readlines()

file.close()

#--- remove comments -------------------------------------------------------------------------------

for iline in xrange(len(lines)):

    lines[iline] = lines[iline].split("#")[0]

#--- collect data in class -------------------------------------------------------------------------

definitions=[]

definitions.append(QmxCalcDefinition())

#--- analyze the input file ------------------------------------------------------------------------

for section in "high-level", "low-level", "cluster", "system", "job", "embed":

    #search lines for section

    lines_section=[]

    for line in lines:

        line = line.split(separator)

        if line[0].find(section) >= 0:

            line[0] = line[0].replace(section+subseparator, "")

            lines_section.append(line)

    #calculators

    if section == "high-level" or section == "low-level":

        definitions.append(analyzeSection(calcDefinitions, section, lines_section))

    #structures (atoms)

    if section == "cluster":

        definitions.append(analyzeSection(strClusterDefinitions, section, lines_section))

    #structures (atoms)

    if section == "system":

        definitions.append(analyzeSection(strSystemDefinitions, section, lines_section))

    #job

    if section == "job":

        definitions.append(analyzeSection(jobDefinitions, section, lines_section))

    #embed

    if section == "embed":

        definitions.append(analyzeSection(embedDefinitions, section, lines_section))

output = None

if options.outputFile is None:

    output=sys.stdout

else:

    output=open(options.outputFile, "w")

writeData(output, definitions)

output.close()