| 1 |
#!@PYTHON_EXECUTABLE@ |
| 2 |
"""MetaData file remapper |
| 3 |
|
| 4 |
Takes a MetaData file and maps all StuntDoubles back to the periodic box. |
| 5 |
Will optionally replicate the system in the three box directions, or |
| 6 |
translate every object in the box and before writing out a new MetaData file. |
| 7 |
|
| 8 |
Usage: md2md |
| 9 |
|
| 10 |
Options: |
| 11 |
-h, --help show this help |
| 12 |
-m, --meta-data=... use specified meta-data (.md, .eor) file |
| 13 |
-o, --output-file=... use specified output file |
| 14 |
-x, --repeatX=... make the system repeat in the x direction |
| 15 |
-y, --repeatY=... make the system repeat in the y direction |
| 16 |
-z, --repeatZ=... make the system repeat in the z direction |
| 17 |
-t, --translateX=... translate all x coordinates by some amount |
| 18 |
-u, --translateY=... translate all y coordinates by some amount |
| 19 |
-v, --translateZ=... translate all z coordinates by some amount |
| 20 |
|
| 21 |
Example: |
| 22 |
md2md -m lipidSystem.md -o bigLipidSystem.md -x 2 -y 2 -z 1 -v 35.0 |
| 23 |
|
| 24 |
""" |
| 25 |
|
| 26 |
__author__ = "Dan Gezelter (gezelter@nd.edu)" |
| 27 |
__version__ = "$Revision$" |
| 28 |
__date__ = "$Date$" |
| 29 |
__copyright__ = "Copyright (c) 2009 by the University of Notre Dame" |
| 30 |
__license__ = "OpenMD" |
| 31 |
|
| 32 |
import sys |
| 33 |
import getopt |
| 34 |
import string |
| 35 |
import math |
| 36 |
import random |
| 37 |
from sets import * |
| 38 |
|
| 39 |
metaData = [] |
| 40 |
frameData = [] |
| 41 |
indices = [] |
| 42 |
pvqj = [] |
| 43 |
p = [] |
| 44 |
v = [] |
| 45 |
q = [] |
| 46 |
j = [] |
| 47 |
Hmat = [] |
| 48 |
BoxInv = [] |
| 49 |
|
| 50 |
def usage(): |
| 51 |
print __doc__ |
| 52 |
|
| 53 |
def readFile(mdFileName): |
| 54 |
mdFile = open(mdFileName, 'r') |
| 55 |
# Find OpenMD version info first |
| 56 |
line = mdFile.readline() |
| 57 |
while 1: |
| 58 |
if '<OOPSE version=' in line or '<OpenMD version=' in line: |
| 59 |
OpenMDversion = line |
| 60 |
break |
| 61 |
line = mdFile.readline() |
| 62 |
|
| 63 |
# Rewind file and find start of MetaData block |
| 64 |
|
| 65 |
mdFile.seek(0) |
| 66 |
line = mdFile.readline() |
| 67 |
print "reading MetaData" |
| 68 |
while 1: |
| 69 |
if '<MetaData>' in line: |
| 70 |
while 2: |
| 71 |
metaData.append(line) |
| 72 |
line = mdFile.readline() |
| 73 |
if '</MetaData>' in line: |
| 74 |
metaData.append(line) |
| 75 |
break |
| 76 |
break |
| 77 |
line = mdFile.readline() |
| 78 |
|
| 79 |
mdFile.seek(0) |
| 80 |
print "reading Snapshot" |
| 81 |
line = mdFile.readline() |
| 82 |
while 1: |
| 83 |
if '<Snapshot>' in line: |
| 84 |
line = mdFile.readline() |
| 85 |
while 1: |
| 86 |
print "reading FrameData" |
| 87 |
if '<FrameData>' in line: |
| 88 |
while 2: |
| 89 |
frameData.append(line) |
| 90 |
if 'Hmat:' in line: |
| 91 |
L = line.split() |
| 92 |
Hxx = float(L[2].strip(',')) |
| 93 |
Hxy = float(L[3].strip(',')) |
| 94 |
Hxz = float(L[4].strip(',')) |
| 95 |
Hyx = float(L[7].strip(',')) |
| 96 |
Hyy = float(L[8].strip(',')) |
| 97 |
Hyz = float(L[9].strip(',')) |
| 98 |
Hzx = float(L[12].strip(',')) |
| 99 |
Hzy = float(L[13].strip(',')) |
| 100 |
Hzz = float(L[14].strip(',')) |
| 101 |
Hmat.append([Hxx, Hxy, Hxz]) |
| 102 |
Hmat.append([Hyx, Hyy, Hyz]) |
| 103 |
Hmat.append([Hzx, Hzy, Hzz]) |
| 104 |
BoxInv.append(1.0/Hxx) |
| 105 |
BoxInv.append(1.0/Hyy) |
| 106 |
BoxInv.append(1.0/Hzz) |
| 107 |
line = mdFile.readline() |
| 108 |
if '</FrameData>' in line: |
| 109 |
frameData.append(line) |
| 110 |
break |
| 111 |
break |
| 112 |
|
| 113 |
line = mdFile.readline() |
| 114 |
while 1: |
| 115 |
if '<StuntDoubles>' in line: |
| 116 |
line = mdFile.readline() |
| 117 |
while 2: |
| 118 |
L = line.split() |
| 119 |
myIndex = int(L[0]) |
| 120 |
indices.append(myIndex) |
| 121 |
pvqj.append(L[1]) |
| 122 |
x = float(L[2]) |
| 123 |
y = float(L[3]) |
| 124 |
z = float(L[4]) |
| 125 |
p.append([x, y, z]) |
| 126 |
vx = float(L[5]) |
| 127 |
vy = float(L[6]) |
| 128 |
vz = float(L[7]) |
| 129 |
v.append([vx, vy, vz]) |
| 130 |
if 'pvqj' in L[1]: |
| 131 |
qw = float(L[8]) |
| 132 |
qx = float(L[9]) |
| 133 |
qy = float(L[10]) |
| 134 |
qz = float(L[11]) |
| 135 |
q.append([qw, qx, qy, qz]) |
| 136 |
jx = float(L[12]) |
| 137 |
jy = float(L[13]) |
| 138 |
jz = float(L[14]) |
| 139 |
j.append([jx, jy, jz]) |
| 140 |
else: |
| 141 |
q.append([0.0, 0.0, 0.0, 0.0]) |
| 142 |
j.append([0.0, 0.0, 0.0]) |
| 143 |
|
| 144 |
line = mdFile.readline() |
| 145 |
if '</StuntDoubles>' in line: |
| 146 |
break |
| 147 |
break |
| 148 |
line = mdFile.readline() |
| 149 |
if not line: break |
| 150 |
|
| 151 |
mdFile.close() |
| 152 |
|
| 153 |
def writeFile(outputFileName,repeatX,repeatY,repeatZ): |
| 154 |
outputFile = open(outputFileName, 'w') |
| 155 |
|
| 156 |
outputFile.write("<OpenMD version=1>\n"); |
| 157 |
|
| 158 |
print "writing MetaData" |
| 159 |
for metaline in metaData: |
| 160 |
if 'nMol' in metaline: |
| 161 |
metasplit = metaline.split() |
| 162 |
nMol = float(metasplit[2].strip(';')) |
| 163 |
newNmol = nMol * repeatX * repeatY * repeatZ |
| 164 |
outputFile.write(' nMol = %10d;\n' % (newNmol)) |
| 165 |
else: |
| 166 |
outputFile.write(metaline) |
| 167 |
|
| 168 |
print "writing Snapshot" |
| 169 |
outputFile.write(" <Snapshot>\n") |
| 170 |
|
| 171 |
print "writing FrameData" |
| 172 |
for frameline in frameData: |
| 173 |
if 'Hmat:' in frameline: |
| 174 |
myH = [] |
| 175 |
myH.append([repeatX * Hmat[0][0], repeatX * Hmat[0][1], repeatX * Hmat[0][2]]) |
| 176 |
myH.append([repeatY * Hmat[1][0], repeatY * Hmat[1][1], repeatY * Hmat[1][2]]) |
| 177 |
myH.append([repeatZ * Hmat[2][0], repeatZ * Hmat[2][1], repeatZ * Hmat[2][2]]) |
| 178 |
outputFile.write(" Hmat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n" % (myH[0][0], myH[0][1], myH[0][2], myH[1][0], myH[1][1], myH[1][2], myH[2][0], myH[2][1], myH[2][2])) |
| 179 |
else: |
| 180 |
outputFile.write(frameline) |
| 181 |
|
| 182 |
print "writing StuntDoubles" |
| 183 |
outputFile.write(" <StuntDoubles>\n") |
| 184 |
|
| 185 |
print repeatX, repeatY, repeatZ |
| 186 |
|
| 187 |
deco = [ (index, i) for i, index in enumerate(indices) ] |
| 188 |
deco.sort() |
| 189 |
whichSD = 0 |
| 190 |
for ii in range(repeatX): |
| 191 |
for jj in range(repeatY): |
| 192 |
for kk in range(repeatZ): |
| 193 |
for index in range(len(deco)): |
| 194 |
(index,i) = deco[index] |
| 195 |
print i |
| 196 |
myP = [] |
| 197 |
myP.append(p[i][0] + ii*Hmat[0][0] + jj*Hmat[1][0] + kk*Hmat[2][0]) |
| 198 |
myP.append(p[i][1] + ii*Hmat[0][1] + jj*Hmat[1][1] + kk*Hmat[2][1]) |
| 199 |
myP.append(p[i][2] + ii*Hmat[0][2] + jj*Hmat[1][2] + kk*Hmat[2][2]) |
| 200 |
|
| 201 |
if (pvqj[i] == 'pv'): |
| 202 |
outputFile.write("%10d %7s %18.10g %18.10g %18.10g %14e %13e %13e\n" % (whichSD, pvqj[i], myP[0], myP[1], myP[2], v[i][0], v[i][1], v[i][2])) |
| 203 |
elif (pvqj[i] == 'pvqj'): |
| 204 |
outputFile.write("%10d %7s %18.10g %18.10g %18.10g %13e %13e %13e %13e %13e %13e %13e %13e %13e %13e\n" % (whichSD, pvqj[i], myP[0], myP[1], myP[2], v[i][0], v[i][1], v[i][2], q[i][0], q[i][1], q[i][2], q[i][3], j[i][0], j[i][1], j[i][2])) |
| 205 |
whichSD = whichSD + 1 |
| 206 |
|
| 207 |
outputFile.write(" </StuntDoubles>\n") |
| 208 |
outputFile.write(" </Snapshot>\n") |
| 209 |
outputFile.write("</OpenMD>\n") |
| 210 |
outputFile.close() |
| 211 |
|
| 212 |
def roundMe(x): |
| 213 |
if (x >= 0.0): |
| 214 |
return math.floor(x + 0.5) |
| 215 |
else: |
| 216 |
return math.ceil(x - 0.5) |
| 217 |
|
| 218 |
def wrapVector(myVect): |
| 219 |
scaled = [0.0, 0.0, 0.0] |
| 220 |
for i in range(3): |
| 221 |
scaled[i] = myVect[i] * BoxInv[i] |
| 222 |
scaled[i] = scaled[i] - roundMe(scaled[i]) |
| 223 |
myVect[i] = scaled[i] * Hmat[i][i] |
| 224 |
return myVect |
| 225 |
|
| 226 |
def dot(L1, L2): |
| 227 |
myDot = 0.0 |
| 228 |
for i in range(len(L1)): |
| 229 |
myDot = myDot + L1[i]*L2[i] |
| 230 |
return myDot |
| 231 |
|
| 232 |
def normalize(L1): |
| 233 |
L2 = [] |
| 234 |
myLength = math.sqrt(dot(L1, L1)) |
| 235 |
for i in range(len(L1)): |
| 236 |
L2.append(L1[i] / myLength) |
| 237 |
return L2 |
| 238 |
|
| 239 |
def cross(L1, L2): |
| 240 |
# don't call this with anything other than length 3 lists please |
| 241 |
# or you'll be sorry |
| 242 |
L3 = [0.0, 0.0, 0.0] |
| 243 |
L3[0] = L1[1]*L2[2] - L1[2]*L2[1] |
| 244 |
L3[1] = L1[2]*L2[0] - L1[0]*L2[2] |
| 245 |
L3[2] = L1[0]*L2[1] - L1[1]*L2[0] |
| 246 |
return L3 |
| 247 |
|
| 248 |
def mapToBox(translateX, translateY, translateZ): |
| 249 |
print "translating by %f\t%f\t%f" % (translateX, translateY, translateZ) |
| 250 |
for i in range(len(indices)): |
| 251 |
dpos = [] |
| 252 |
dpos.append(p[i][0] + translateX) |
| 253 |
dpos.append(p[i][1] + translateY) |
| 254 |
dpos.append(p[i][2] + translateZ) |
| 255 |
p[i] = wrapVector(dpos) |
| 256 |
|
| 257 |
def main(argv): |
| 258 |
repeatX = 1 |
| 259 |
repeatY = 1 |
| 260 |
repeatZ = 1 |
| 261 |
translateX = 0.0 |
| 262 |
translateY = 0.0 |
| 263 |
translateZ = 0.0 |
| 264 |
_haveMDFileName = 0 |
| 265 |
_haveOutputFileName = 0 |
| 266 |
try: |
| 267 |
opts, args = getopt.getopt(argv, "hm:o:x:y:z:t:u:v:", ["help", "meta-data=", "output-file=", "repeatX=", "repeatY=", "repeatZ=","translateX=","translateY=","translateZ="]) |
| 268 |
except getopt.GetoptError: |
| 269 |
usage() |
| 270 |
sys.exit(2) |
| 271 |
for opt, arg in opts: |
| 272 |
if opt in ("-h", "--help"): |
| 273 |
usage() |
| 274 |
sys.exit() |
| 275 |
elif opt in ("-m", "--meta-data"): |
| 276 |
mdFileName = arg |
| 277 |
_haveMDFileName = 1 |
| 278 |
elif opt in ("-o", "--output-file"): |
| 279 |
outputFileName = arg |
| 280 |
_haveOutputFileName = 1 |
| 281 |
elif opt in ("-x", "--repeatX"): |
| 282 |
repeatX = int(arg) |
| 283 |
elif opt in ("-y", "--repeatY"): |
| 284 |
repeatY = int(arg) |
| 285 |
elif opt in ("-z", "--repeatZ"): |
| 286 |
repeatZ = int(arg) |
| 287 |
elif opt in ("-t", "--translateX"): |
| 288 |
translateX = float(arg) |
| 289 |
elif opt in ("-u", "--translateY"): |
| 290 |
translateY = float(arg) |
| 291 |
elif opt in ("-v", "--translateZ"): |
| 292 |
translateZ = float(arg) |
| 293 |
if (_haveMDFileName != 1): |
| 294 |
usage() |
| 295 |
print "No meta-data file was specified" |
| 296 |
sys.exit() |
| 297 |
if (_haveOutputFileName != 1): |
| 298 |
usage() |
| 299 |
print "No output file was specified" |
| 300 |
sys.exit() |
| 301 |
|
| 302 |
readFile(mdFileName) |
| 303 |
mapToBox(translateX, translateY, translateZ) |
| 304 |
writeFile(outputFileName, repeatX, repeatY, repeatZ) |
| 305 |
|
| 306 |
if __name__ == "__main__": |
| 307 |
if len(sys.argv) == 1: |
| 308 |
usage() |
| 309 |
sys.exit() |
| 310 |
main(sys.argv[1:]) |
