Chimie Théorique » QMX

#!/usr/bin/env python

import os, sys

from optparse import OptionParser

class Data:

    def __init__(self, name):

        self.__name__ = name

        self.str_option = ""

        self.str_import = None

        self.str_class  = None

        self.str_methods = []

        self.str_structure = None

    def __str__(self):

       return self.__name__

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 analyzeAtoms(section, lines):

    data = Data(section)

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

    if line is None:

        line=""

    if line.lower() == "turbomole":

        data.str_import = "from ase.io.turbomole import read_turbomole"

        data.str_class = "read_turbomole"

    elif line.lower() == "vasp":

        data.str_import = "from ase.io.vasp import read_vasp"

        data.str_class = "read_vasp"

    data.str_structure = getline(section, "structure", lines)

    return data

def analyzeCalculator(section, lines):

    data = Data(section)

    #read programs

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

    if line.lower() == "turbomole":

        data.str_import = "from ase.calculators.turbomole import Turbomole"

        data.str_class = "Turbomole"

    elif line.lower() == "vasp":

        data.str_import = "from ase.calculators.vasp import Vasp"

        data.str_class = "Vasp"

    str = getline(section, "class", lines)

    if str is not None:

        data.str_class = str

    str = getline(section, "import", lines)

    if str is not None:

        data.str_import = str

    str = getline(section, "options", lines)

    if str is not None:

        data.str_option = str

    return data

def analyzeDynamics(section, lines):

    data = Data(section)

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

    if line.lower() == "optimizer":

        data.str_import = "from ase.optimize import QuasiNewton"

        data.str_class = "QuasiNewton"

    return data

#--- 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()

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

lines = file.readlines()

file.close()

#--- split intput file -----------------------------------------------------------------------------

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

for iline in xrange(len(lines)):

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

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

data_collection=[]

#--- settings for QMX class ------------------------------------------------------------------------

data = Data("qmx")

data.str_class = "Qmx"

data.str_import = "from ase.calculators.qmx import Qmx"

data.str_option = "highLevel, lowLevel"

data_collection.append(data)

#--- settings for Embed class ----------------------------------------------------------------------

data = Data("embed")

data.str_class = "Embed"

data.str_import = "from ase.embed import Embed"

data.str_option = "system, cluster"

data.str_methods = ["embed()", "set_calculator(qmx)"]

data_collection.append(data)

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

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

    #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":

        data_collection.append(analyzeCalculator(section, lines_section))

    #systems

    if section == "cluster" or section == "system":

        data_collection.append(analyzeAtoms(section, lines_section))

    #dynamics

    if section == "dynamics":

        data_collection.append(analyzeDynamics(section, lines_section))

#--- write output file -----------------------------------------------------------------------------

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)

output = None

if options.outputFile is None:

    output=sys.stdout

else:

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

#--- write header ----------------------------------------------------------------------------------

output.write("#!/usr/bin/env python\n")

#--- write import lines ----------------------------------------------------------------------------

xlines=[]

for data in data_collection:

    value = data.str_import

    if value is None or value in xlines:

        continue

    xlines.append(value)

    output.write(value+lineseparator)

output.write(lineseparator)

#--- define the methods ----------------------------------------------------------------------------

for system in 'high', 'low':

    for data in data_collection:

        if data.__name__ == system+"-level":

            output.write(system+"Level = "+data.str_class+"("+data.str_option+")"+lineseparator)

output.write(lineseparator)

#--- qmx class (substraction scheme ----------------------------------------------------------------

for data in data_collection:

    if data.__name__ == "qmx":

        output.write("qmx = "+data.str_class+"("+data.str_option+")"+lineseparator)

output.write(lineseparator)

#--- read all the systems --------------------------------------------------------------------------

for system in "cluster", "system":

    for data in data_collection:

        if data.__name__ == system:

            if data.str_structure is None:

                continue

            output.write(system+" = "+data.str_class+"(\""+data.str_structure+"\")"+lineseparator)

output.write(lineseparator)

#--- embeding class --------------------------------------------------------------------------------

for data in data_collection:

    if data.__name__ == "embed":

        output.write("embed = "+data.str_class+"("+data.str_option+")"+lineseparator)

        for method in data.str_methods:

            output.write("embed."+method+lineseparator)

output.write(lineseparator)

#--- dynamics class --------------------------------------------------------------------------------

for data in data_collection:

    if data.__name__ == "dynamics":

        output.write("dyn="+data.str_class+"(embed)"+lineseparator)

        output.write("dyn.run("+data.str_option+")"+lineseparator)

output.close()

sys.exit(0)