[ViewVC] Annotation of: OpenMD/branches/development/src/applications/utilities/dumpConverter

#!@PYTHON_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 (.opmd) file


Example:
   dumpConverter -m Ar.md -c Ar.dump -o Ar.opmd

"""

__author__ = "Dan Gezelter (gezelter@nd.edu)"
__version__ = "$Revision$"
__date__ = "$Date$"
__copyright__ = "Copyright (c) 2006 by the University of Notre Dame"
__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:])

Revision:	1646
Committed:	Mon Sep 26 13:30:00 2011 UTC (14 years, 1 month ago) by gezelter
File size:	6896 byte(s)
Log Message:	update for cmake build and install
#	User	Rev	Content
1	gezelter	1646	#!@PYTHON_EXECUTABLE@
2	gezelter	1017	"""Dump File Converter
3
4	gezelter	1390	Converts old-style OOPSE md and dump files into new OpenMD style
5	gezelter	1017	combined files
6
7			Usage: dumpConverter
8
9			Options:
10			-h, --help show this help
11			-m, --meta-data=... use specified meta-data (.md) file
12			-c, --config-file=... use specified configuration (.in, .eor, .dump) file
13	gezelter	1390	-o, --output-file=... use specified output (.opmd) file
14	gezelter	1017
15
16			Example:
17	gezelter	1390	dumpConverter -m Ar.md -c Ar.dump -o Ar.opmd
18	gezelter	1017
19			"""
20
21			__author__ = "Dan Gezelter (gezelter@nd.edu)"
22	gezelter	1442	__version__ = "$Revision$"
23			__date__ = "$Date$"
24	gezelter	1017	__copyright__ = "Copyright (c) 2006 by the University of Notre Dame"
25	gezelter	1390	__license__ = "OpenMD"
26	gezelter	1017
27			import sys
28			import getopt
29			import string
30
31			_haveMDFileName = 0
32			_haveConfFileName = 0
33			_haveOutputFileName = 0
34
35			def usage():
36			print __doc__
37
38
39			def convertFiles(mdFileName, configFileName, outputFileName):
40			mdFile = open(mdFileName, 'r')
41			outputFile = open(outputFileName, 'w')
42
43	gezelter	1390	outputFile.write("<OpenMD version=1>\n");
44	gezelter	1017	outputFile.write(" <MetaData>\n")
45
46			mdLines = mdFile.readlines()
47			for l in mdLines:
48	tim	1018	if (l.find('initialConfig') == -1):
49			outputFile.write(l)
50	gezelter	1017
51			outputFile.write(" </MetaData>\n")
52			mdFile.close()
53
54			framePos = 0
55			configFile = open(configFileName, 'r')
56			for line in configFile.readlines():
57			framePos = framePos + 1
58			if (framePos == 1):
59			L = line.split()
60			nStuntDoubles = int(L[0])
61			whichSD = 0
62			outputFile.write(" <Snapshot>\n")
63			continue
64			elif (framePos == 2):
65	tim	1018	L = line.replace(';',' ').split()
66			time = float(L[0])
67	gezelter	1017	outputFile.write(" <FrameData>\n");
68	tim	1018	outputFile.write(" Time: %.10g\n" % (time))
69	gezelter	1017	Hxx = float(L[1])
70			Hxy = float(L[2])
71	tim	1018	Hxz = float(L[3])
72	gezelter	1017	Hyx = float(L[4])
73			Hyy = float(L[5])
74	tim	1018	Hyz = float(L[6])
75	gezelter	1017	Hzx = float(L[7])
76			Hzy = float(L[8])
77	tim	1018	Hzz = float(L[9])
78			outputFile.write(" Hmat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n" % (Hxx, Hxy, Hxz, Hyx, Hyy, Hyz, Hzx, Hzy, Hzz))
79			if (len(L) >= 12):
80			chi = float(L[10])
81	gezelter	1017	integChi = float(L[11])
82	tim	1018	outputFile.write(" Thermostat: %.10g , %.10g\n" % (chi, integChi))
83			if (len(L) >= 21):
84	gezelter	1017	Nxx = float(L[12])
85	tim	1018	Nxy = float(L[13])
86			Nxz = float(L[14])
87			Nyx = float(L[15])
88			Nyy = float(L[16])
89			Nyz = float(L[17])
90			Nzx = float(L[18])
91			Nzy = float(L[19])
92			Nzz = float(L[20])
93			outputFile.write(" Barostat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n" % (Nxx, Nxy, Nxz, Nyx, Nyy, Nyz, Nzx, Nzy, Nzz))
94
95	gezelter	1017	outputFile.write(" </FrameData>\n")
96			outputFile.write(" <StuntDoubles>\n")
97			else:
98			whichSD = whichSD + 1
99			L = line.split()
100			x = float(L[1])
101			y = float(L[2])
102			z = float(L[3])
103			vx = float(L[4])
104			vy = float(L[5])
105			vz = float(L[6])
106			sdFormat = 'pv'
107	chrisfen	1019	if (len(L) == 10):
108			sdFormat = 'pvf'
109			fx = float(L[7])
110			fy = float(L[8])
111			fz = float(L[9])
112			if (len(L) >= 14):
113	gezelter	1017	qw = float(L[7])
114			qx = float(L[8])
115			qy = float(L[9])
116			qz = float(L[10])
117			jx = float(L[11])
118			jy = float(L[12])
119			jz = float(L[13])
120			if (qw == 0.0 and qx == 0.0 and qy == 0.0 and qz == 0.0):
121			sdFormat = 'pv'
122			else:
123			sdFormat = 'pvqj'
124			if (len(L) == 20):
125			fx = float(L[14])
126			fy = float(L[15])
127			fz = float(L[16])
128			tx = float(L[17])
129			ty = float(L[18])
130			tz = float(L[19])
131	chrisfen	1019	if (qw == 0.0 and qx == 0.0 and qy == 0.0 and qz == 0.0):
132			sdFormat = 'pvf'
133			else:
134			sdFormat = 'pvqjft'
135	gezelter	1017	if (sdFormat == 'pv'):
136	gezelter	1026	outputFile.write("%10d %7s %18.10g %18.10g %18.10g %14e %13e %13e\n" % (whichSD-1, sdFormat, x, y, z, vx, vy, vz))
137	chrisfen	1019	elif (sdFormat == 'pvf'):
138	gezelter	1026	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))
139	gezelter	1017	elif (sdFormat == 'pvqj'):
140	gezelter	1026	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))
141	gezelter	1017	elif (sdFormat == 'pvqjft'):
142	gezelter	1026	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))
143	gezelter	1017	if (whichSD == nStuntDoubles):
144			outputFile.write(" </StuntDoubles>\n")
145			outputFile.write(" </Snapshot>\n")
146			framePos = 0
147
148
149			configFile.close()
150	gezelter	1390	outputFile.write("</OpenMD>\n")
151	gezelter	1017	outputFile.close()
152
153
154			def main(argv):
155			try:
156			opts, args = getopt.getopt(argv, "hm:c:o:", ["help", "meta-data=", "config-file=", "output-file="])
157			except getopt.GetoptError:
158			usage()
159			sys.exit(2)
160			for opt, arg in opts:
161			if opt in ("-h", "--help"):
162			usage()
163			sys.exit()
164			elif opt in ("-m", "--meta-data"):
165			mdFileName = arg
166			global _haveMDFileName
167			_haveMDFileName = 1
168			elif opt in ("-c", "--config-file"):
169			configFileName = arg
170			global _haveConfFileName
171			_haveConfFileName = 1
172			elif opt in ("-o", "--output-file"):
173			outputFileName = arg
174			global _haveOutputFileName
175			_haveOutputFileName = 1
176			if (_haveMDFileName != 1):
177			usage()
178			print "No meta-data file was specified"
179			sys.exit()
180			if (_haveConfFileName != 1):
181			usage()
182			print "No configuration file was specified"
183			sys.exit()
184			if (_haveOutputFileName != 1):
185			usage()
186			print "No output file was specified"
187			sys.exit()
188			convertFiles(mdFileName, configFileName, outputFileName);
189
190			if __name__ == "__main__":
191			if len(sys.argv) == 1:
192			usage()
193			sys.exit()
194			main(sys.argv[1:])
195