dumpConverter

#!@Python3_EXECUTABLE@
"""Dump File Converter
 
Converts old-style OOPSE md and dump files into new OpenMD style
combined files
 
Usage: dumpConverter 
 
Options:
  -h, --help              show this help
  -m, --meta-data=...     use specified meta-data (.md) file
  -c, --config-file=...   use specified configuration (.in, .eor, .dump) file
  -o, --output-file=...   use specified output (.omd) file
 
 
Example:
   dumpConverter -m Ar.md -c Ar.dump -o Ar.omd
 
"""
 
__author__ = "Dan Gezelter (gezelter@nd.edu)"
__version__ = "$Revision$"
__date__ = "$Date$"
__copyright__ = "Copyright (c) 2004-present The University of Notre Dame. All Rights Reserved."
__license__ = "OpenMD"
 
import sys
import getopt
import string
 
_haveMDFileName = 0
_haveConfFileName = 0
_haveOutputFileName = 0
 
def usage():
    print(__doc__)
 
 
def convertFiles(mdFileName, configFileName, outputFileName):
    mdFile = open(mdFileName, 'r')
    outputFile = open(outputFileName, 'w')
 
    outputFile.write("<OpenMD version=1>\n");
    outputFile.write("  <MetaData>\n")
    
    mdLines = mdFile.readlines()
    for l in mdLines:
        if (l.find('initialConfig') == -1):
            outputFile.write(l)
 
    outputFile.write("  </MetaData>\n")
    mdFile.close()
 
    framePos = 0
    configFile = open(configFileName, 'r')
    for line in configFile.readlines():
        framePos = framePos + 1
        if (framePos == 1):
            L = line.split()
            nStuntDoubles = int(L[0])
            whichSD = 0
            outputFile.write("  <Snapshot>\n")
            continue
        elif (framePos == 2):
            L = line.replace(';', ' ').split()
            time = float(L[0])
            outputFile.write("    <FrameData>\n");
            outputFile.write("        Time: %.10g\n" % (time))
            Hxx = float(L[1])
            Hxy = float(L[2])
            Hxz = float(L[3])
            Hyx = float(L[4])
            Hyy = float(L[5])
            Hyz = float(L[6])
            Hzx = float(L[7])
            Hzy = float(L[8])
            Hzz = float(L[9])
            outputFile.write("        Hmat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n" % (Hxx, Hxy, Hxz, Hyx, Hyy, Hyz, Hzx, Hzy, Hzz))
            if (len(L) >= 12):
                chi = float(L[10])
                integChi = float(L[11])
                outputFile.write("  Thermostat: %.10g , %.10g\n" % (chi, integChi))
            if (len(L) >= 21):
                Nxx = float(L[12])
                Nxy = float(L[13])
                Nxz = float(L[14])
                Nyx = float(L[15])
                Nyy = float(L[16])
                Nyz = float(L[17])
                Nzx = float(L[18])
                Nzy = float(L[19])
                Nzz = float(L[20])
                outputFile.write("    Barostat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n" % (Nxx, Nxy, Nxz, Nyx, Nyy, Nyz, Nzx, Nzy, Nzz))
            
            outputFile.write("    </FrameData>\n")
            outputFile.write("    <StuntDoubles>\n")
        else:
            whichSD = whichSD + 1
            L = line.split()
            x = float(L[1])
            y = float(L[2])
            z = float(L[3])
            vx = float(L[4])
            vy = float(L[5])
            vz = float(L[6])
            sdFormat = 'pv'
            if (len(L) == 10):
                sdFormat = 'pvf'
                fx = float(L[7])
                fy = float(L[8])
                fz = float(L[9])
            if (len(L) >= 14):
                qw = float(L[7])
                qx = float(L[8])
                qy = float(L[9])
                qz = float(L[10])
                jx = float(L[11])
                jy = float(L[12])
                jz = float(L[13])
                if (qw == 0.0 and qx == 0.0 and qy == 0.0 and qz == 0.0):
                    sdFormat = 'pv'
                else:
                    sdFormat = 'pvqj'
            if (len(L) == 20):
                fx = float(L[14])
                fy = float(L[15])
                fz = float(L[16])
                tx = float(L[17])
                ty = float(L[18])
                tz = float(L[19])
                if (qw == 0.0 and qx == 0.0 and qy == 0.0 and qz == 0.0):
                    sdFormat = 'pvf'
                else:
                    sdFormat = 'pvqjft'
            if (sdFormat == 'pv'):
                outputFile.write("%10d %7s %18.10g %18.10g %18.10g %14e %13e %13e\n" % (whichSD-1, sdFormat, x, y, z, vx, vy, vz))
            elif (sdFormat == 'pvf'):
                outputFile.write("%10d %7s %18.10g %18.10g %18.10g %13e %13e %13e %13e %13e %13e\n" % (whichSD-1, sdFormat, x, y, z, vx, vy, vz, fx, fy, fz))
            elif (sdFormat == 'pvqj'):
                outputFile.write("%10d %7s %18.10g %18.10g %18.10g %13e %13e %13e %13e %13e %13e %13e %13e %13e %13e\n" % (whichSD-1, sdFormat, x, y, z, vx, vy, vz, qw, qx, qy, qz, jx, jy, jz))
            elif (sdFormat == 'pvqjft'):
                outputFile.write("%d %s %18.10g %18.10g %18.10g %13e %13e %13e %13e %13e %13e %13e %13e %13e %13e %13e %13e %13e %13e %13e %13e\n" % (whichSD-1, sdFormat, x, y, z, vx, vy, vz, qw, qx, qy, qz, jx, jy, jz, fx, fy, fz, tx, ty, tz))
        if (whichSD == nStuntDoubles):
            outputFile.write("    </StuntDoubles>\n")
            outputFile.write("  </Snapshot>\n")
            framePos = 0
    
 
    configFile.close()
    outputFile.write("</OpenMD>\n")
    outputFile.close()
 
 
def main(argv):                         
    try:                                
        opts, args = getopt.getopt(argv, "hm:c:o:", ["help", "meta-data=", "config-file=", "output-file="]) 
    except getopt.GetoptError:           
        usage()                          
        sys.exit(2)                     
    for opt, arg in opts:                
        if opt in ("-h", "--help"):      
            usage()                     
            sys.exit()                  
        elif opt in ("-m", "--meta-data"): 
            mdFileName = arg
            global _haveMDFileName
            _haveMDFileName = 1
        elif opt in ("-c", "--config-file"): 
            configFileName = arg
            global _haveConfFileName
            _haveConfFileName = 1
        elif opt in ("-o", "--output-file"): 
            outputFileName = arg
            global _haveOutputFileName
            _haveOutputFileName = 1
    if (_haveMDFileName != 1):
        usage() 
        print("No meta-data file was specified")
        sys.exit()
    if (_haveConfFileName != 1):
        usage()
        print("No configuration file was specified")
        sys.exit()
    if (_haveOutputFileName != 1):
        usage()
        print("No output file was specified")
        sys.exit()
    convertFiles(mdFileName, configFileName, outputFileName);
 
if __name__ == "__main__":
    if len(sys.argv) == 1:
        usage()
        sys.exit()
    main(sys.argv[1:])