#!/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 strDefinitions 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 == line: 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 print subsection, myDefinition.keywords[subsection] 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": #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" or section == "system": definitions.append(analyzeSection(strDefinitions, 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() # ##--- 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) # # # # # #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