Révision 13 prepareQMX/prepareQMX.py
| prepareQMX.py (revision 13) | ||
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#!/usr/bin/env python |
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# command line interface for setup of QMX calculations |
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# |
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# Torsten Kerber, ENS LYON: 2011, 07, 11 |
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# |
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# This work is supported by Award No. UK-C0017, made by King Abdullah |
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# University of Science and Technology (KAUST) |
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#--------------------------------------------------------------------------------------------------- |
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import os, sys |
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from copy import deepcopy |
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from optparse import OptionParser |
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class Data: |
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def __init__(self, name): |
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self.__name__ = name |
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self.str_option = "" |
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self.str_import = None |
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self.str_class = None |
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self.str_methods = [] |
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self.str_structure = None |
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def __str__(self): |
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return self.__name__ |
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#--------------------------------------------------------------------------------------------------- |
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from qmxEMBED import embedDefinitions |
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from qmxJOB import jobDefinitions |
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from qmxSTR import strDefinitions |
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from qmxCALC import calcDefinitions, QmxCalcDefinition |
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from qmxWRITE import writeData |
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#--------------------------------------------------------------------------------------------------- |
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#--------------------------------------------------------------------------------------------------- |
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#--------------------------------------------------------------------------------------------------- |
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def getline(section, subsection, lines): |
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nline = -1 |
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for iline in xrange(len(lines)): |
| ... | ... | |
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return None |
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return lines[nline][1].strip() |
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def analyzeAtoms(section, lines):
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data = Data(section)
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#---------------------------------------------------------------------------------------------------
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def analyzeSection(definitions, section, lines):
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line = getline(section, "program", lines) |
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if line is None: |
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line="" |
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if line.lower() == "turbomole": |
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data.str_import = "from ase.io.turbomole import read_turbomole" |
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data.str_class = "read_turbomole" |
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elif line.lower() == "vasp": |
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data.str_import = "from ase.io.vasp import read_vasp" |
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data.str_class = "read_vasp" |
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print "section <" + section + "> does not contain program" |
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sys.exit(1) |
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data.str_structure = getline(section, "structure", lines) |
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return data |
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myDefinition = None |
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for definition in definitions: |
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if definition.name == line: |
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myDefinition = deepcopy(definition) |
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break |
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if myDefinition is None: |
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print "the program <" + line + "> is not defined for the section <" + section + ">" |
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sys.exit(1) |
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myDefinition.system = section |
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def analyzeCalculator(section, lines): |
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data = Data(section) |
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#read programs |
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line = getline(section, "program", lines) |
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if line.lower() == "turbomole": |
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data.str_import = "from ase.calculators.turbomole import Turbomole" |
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data.str_class = "Turbomole" |
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elif line.lower() == "vasp": |
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data.str_import = "from ase.calculators.vasp import Vasp" |
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data.str_class = "Vasp" |
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subsections = [] |
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for line in lines: |
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subsections.append(line[0].strip().lower()) |
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for subsection in subsections: |
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line = getline(section, subsection, lines) |
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if line is None: |
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print "input error in <"+section+"."+subsection+">" |
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sys.exit(1) |
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if subsection == "program": |
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continue |
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if subsection == "options": |
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subsection = 'class.options' |
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myDefinition.keywords[subsection] = line |
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print subsection, myDefinition.keywords[subsection] |
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str = getline(section, "class", lines) |
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if str is not None: |
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data.str_class = str |
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return myDefinition |
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str = getline(section, "import", lines) |
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if str is not None: |
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data.str_import = str |
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str = getline(section, "options", lines) |
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if str is not None: |
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data.str_option = str |
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return data |
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def analyzeDynamics(section, lines): |
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data = Data(section) |
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line = getline(section, "method", lines) |
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if line.lower() == "optimizer": |
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data.str_import = "from ase.optimize import QuasiNewton" |
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data.str_class = "QuasiNewton" |
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return data |
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#--------------------------------------------------------------------------------------------------- |
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#--- setting default values ------------------------------------------------------------------------ |
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#--------------------------------------------------------------------------------------------------- |
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#define separators |
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separator=":" |
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subseparator="." |
| ... | ... | |
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parser.add_option("-f", action="store_true", dest="overwrite")
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(options, args) = parser.parse_args() |
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#--- check wether output file exists --------------------------------------------------------------- |
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if options.outputFile is not None and os.path.exists(options.outputFile) and not options.overwrite: |
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sys.stderr.write(lineseparator+"the output file <"+options.outputFile+"> already exists"+lineseparator) |
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sys.exit(1) |
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#--- read intput file ------------------------------------------------------------------------------ |
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file=open(options.inputFile, "r") |
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lines = file.readlines() |
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file.close() |
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#--- split intput file ----------------------------------------------------------------------------- |
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#--- remove comments ------------------------------------------------------------------------------- |
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for iline in xrange(len(lines)): |
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lines[iline] = lines[iline].split("#")[0]
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#--- collect data in class ------------------------------------------------------------------------- |
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data_collection=[] |
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definitions=[] |
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definitions.append(QmxCalcDefinition()) |
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#--- settings for QMX class ------------------------------------------------------------------------ |
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data = Data("qmx")
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data.str_class = "Qmx" |
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data.str_import = "from ase.calculators.qmx import Qmx" |
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data.str_option = "highLevel, lowLevel" |
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data_collection.append(data) |
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#--- settings for Embed class ---------------------------------------------------------------------- |
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data = Data("embed")
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data.str_class = "Embed" |
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data.str_import = "from ase.embed import Embed" |
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data.str_option = "system, cluster" |
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data.str_methods = ["embed()", "set_calculator(qmx)"] |
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data_collection.append(data) |
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#--- analyze the input file ------------------------------------------------------------------------ |
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for section in "high-level", "low-level", "cluster", "system", "dynamics":
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for section in "high-level", "low-level", "cluster", "system", "job":
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#search lines for section |
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lines_section=[] |
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for line in lines: |
| ... | ... | |
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if line[0].find(section) >= 0: |
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line[0] = line[0].replace(section+subseparator, "") |
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lines_section.append(line) |
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#calculators |
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if section == "high-level" or section == "low-level": |
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data_collection.append(analyzeCalculator(section, lines_section))
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definitions.append(analyzeSection(calcDefinitions, section, lines_section))
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#systems
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#structures (atoms)
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if section == "cluster" or section == "system": |
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data_collection.append(analyzeAtoms(section, lines_section))
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definitions.append(analyzeSection(strDefinitions, section, lines_section))
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#dynamics |
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if section == "dynamics": |
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data_collection.append(analyzeDynamics(section, lines_section)) |
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#job |
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if section == "job": |
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definitions.append(analyzeSection(jobDefinitions, section, lines_section)) |
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#embed |
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if section == "embed": |
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definitions.append(analyzeSection(embedDefinitions, section, lines_section)) |
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#--- write output file ----------------------------------------------------------------------------- |
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if options.outputFile is not None and os.path.exists(options.outputFile) and not options.overwrite: |
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sys.stderr.write(lineseparator+"the output file <"+options.outputFile+"> already exists"+lineseparator) |
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sys.exit(1) |
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output = None |
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if options.outputFile is None: |
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output=sys.stdout |
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else: |
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output=open(options.outputFile, "w") |
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#--- write header ---------------------------------------------------------------------------------- |
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output.write("#!/usr/bin/env python\n")
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#--- write import lines ---------------------------------------------------------------------------- |
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xlines=[] |
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for data in data_collection: |
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value = data.str_import |
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if value is None or value in xlines: |
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continue |
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xlines.append(value) |
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output.write(value+lineseparator) |
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output.write(lineseparator) |
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#--- define the methods ---------------------------------------------------------------------------- |
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for system in 'high', 'low': |
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for data in data_collection: |
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if data.__name__ == system+"-level": |
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output.write(system+"Level = "+data.str_class+"("+data.str_option+")"+lineseparator)
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output.write(lineseparator) |
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#--- qmx class (substraction scheme ---------------------------------------------------------------- |
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for data in data_collection: |
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if data.__name__ == "qmx": |
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output.write("qmx = "+data.str_class+"("+data.str_option+")"+lineseparator)
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output.write(lineseparator) |
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#--- read all the systems -------------------------------------------------------------------------- |
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for system in "cluster", "system": |
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for data in data_collection: |
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if data.__name__ == system: |
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if data.str_structure is None: |
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continue |
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output.write(system+" = "+data.str_class+"(\""+data.str_structure+"\")"+lineseparator) |
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output.write(lineseparator) |
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#--- embeding class -------------------------------------------------------------------------------- |
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for data in data_collection: |
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if data.__name__ == "embed": |
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output.write("embed = "+data.str_class+"("+data.str_option+")"+lineseparator)
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for method in data.str_methods: |
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output.write("embed."+method+lineseparator)
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output.write(lineseparator) |
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#--- dynamics class -------------------------------------------------------------------------------- |
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for data in data_collection: |
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if data.__name__ == "dynamics": |
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output.write("dyn="+data.str_class+"(embed)"+lineseparator)
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output.write("dyn.run("+data.str_option+")"+lineseparator)
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writeData(output, definitions) |
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output.close() |
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sys.exit(0) |
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