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""" |
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__author__ = "Dan Gezelter (gezelter@nd.edu)" |
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< |
__version__ = "$Revision: 1.1 $" |
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< |
__date__ = "$Date: 2006-07-27 19:05:16 $" |
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> |
__version__ = "$Revision: 1.2 $" |
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> |
__date__ = "$Date: 2006-07-27 20:36:54 $" |
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__copyright__ = "Copyright (c) 2006 by the University of Notre Dame" |
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__license__ = "OOPSE" |
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mdLines = mdFile.readlines() |
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for l in mdLines: |
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< |
outputFile.write(l) |
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> |
if (l.find('initialConfig') == -1): |
| 49 |
> |
outputFile.write(l) |
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|
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outputFile.write(" </MetaData>\n") |
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mdFile.close() |
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configFile = open(configFileName, 'r') |
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for line in configFile.readlines(): |
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framePos = framePos + 1 |
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print framePos |
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if (framePos == 1): |
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L = line.split() |
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nStuntDoubles = int(L[0]) |
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outputFile.write(" <Snapshot>\n") |
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continue |
| 64 |
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elif (framePos == 2): |
| 65 |
< |
L = line.split() |
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< |
time = float(L[0].split(';')[0]) |
| 65 |
> |
L = line.replace(';',' ').split() |
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> |
time = float(L[0]) |
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outputFile.write(" <FrameData>\n"); |
| 68 |
< |
outputFile.write(" Time: %g\n" % (time)) |
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outputFile.write(" Time: %.10g\n" % (time)) |
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Hxx = float(L[1]) |
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Hxy = float(L[2]) |
| 71 |
< |
Hxz = float(L[3].split(';')[0]) |
| 71 |
> |
Hxz = float(L[3]) |
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Hyx = float(L[4]) |
| 73 |
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Hyy = float(L[5]) |
| 74 |
< |
Hyz = float(L[6].split(';')[0]) |
| 74 |
> |
Hyz = float(L[6]) |
| 75 |
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Hzx = float(L[7]) |
| 76 |
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Hzy = float(L[8]) |
| 77 |
< |
Hzz = float(L[9].split(';')[0]) |
| 78 |
< |
outputFile.write(" Hmat: {{ %g, %g, %g }, { %g, %g, %g }, { %g, %g, %g }}\n" % (Hxx, Hxy, Hxz, Hyx, Hyy, Hyz, Hzx, Hzy, Hzz)) |
| 79 |
< |
chi = float(L[10]) |
| 80 |
< |
if (L[11][-1] == ';'): |
| 81 |
< |
integChi = float(L[11].split(';')[0]) |
| 82 |
< |
else: |
| 77 |
> |
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 |
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integChi = float(L[11]) |
| 82 |
< |
outputFile.write(" Thermostat: %g , %g\n" % (chi, integChi)) |
| 83 |
< |
if (L[12][0] == ';'): |
| 86 |
< |
Nxx = float(L[12].split(';')[1]) |
| 87 |
< |
else: |
| 82 |
> |
outputFile.write(" Thermostat: %.10g , %.10g\n" % (chi, integChi)) |
| 83 |
> |
if (len(L) >= 21): |
| 84 |
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Nxx = float(L[12]) |
| 85 |
< |
Nxy = float(L[13]) |
| 86 |
< |
Nxz = float(L[14].split(';')[0]) |
| 87 |
< |
Nyx = float(L[15]) |
| 88 |
< |
Nyy = float(L[16]) |
| 89 |
< |
Nyz = float(L[17].split(';')[0]) |
| 90 |
< |
Nzx = float(L[18]) |
| 91 |
< |
Nzy = float(L[19]) |
| 92 |
< |
Nzz = float(L[20].split(';')[0]) |
| 93 |
< |
outputFile.write(" Barostat: {{ %g, %g, %g }, { %g, %g, %g }, { %g, %g, %g }}\n" % (Nxx, Nxy, Nxz, Nyx, Nyy, Nyz, Nzx, Nzy, Nzz)) |
| 85 |
> |
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 |
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outputFile.write(" </FrameData>\n") |
| 96 |
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outputFile.write(" <StuntDoubles>\n") |
| 97 |
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else: |
| 125 |
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tz = float(L[19]) |
| 126 |
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sdFormat = 'pvqjft' |
| 127 |
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if (sdFormat == 'pv'): |
| 128 |
< |
outputFile.write("%d\t%s\t%g\t%g\t%g\t%g\t%g\t%g\n" % (whichSD, sdFormat, x, y, z, vx, vy, vz)) |
| 128 |
> |
outputFile.write("%d\t%s\t%18.10g\t%18.10g\t%18.10g\t%14.10g\t%14.10g\t%14.10g\n" % (whichSD-1, sdFormat, x, y, z, vx, vy, vz)) |
| 129 |
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elif (sdFormat == 'pvqj'): |
| 130 |
< |
outputFile.write("%d\t%s\t%g\t%g\t%g\t%g\t%g\t%g\t%g\t%g\t%g\t%g\t%g\t%g\t%g\n" % (whichSD, sdFormat, x, y, z, vx, vy, vz, qw, qx, qy, qz, jx, jy, jz)) |
| 130 |
> |
outputFile.write("%d\t%s\t%18.10g\t%18.10g\t%18.10g\t%14.10g\t%14.10g\t%14.10g\t%14.10g\t%14.10g\t%14.10g\t%14.10g\t%14.10g\t%14.10g\t%14.10g\n" % (whichSD-1, sdFormat, x, y, z, vx, vy, vz, qw, qx, qy, qz, jx, jy, jz)) |
| 131 |
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elif (sdFormat == 'pvqjft'): |
| 132 |
< |
outputFile.write("%d\t%s\t%g\t%g\t%g\t%g\t%g\t%g\t%g\t%g\t%g\t%g\t%g\t%g\t%g\t%g\t%g\t%g\t%g\t%g\t%g\n" % (whichSD, sdFormat, x, y, z, vx, vy, vz, qw, qx, qy, qz, jx, jy, jz, fx, fy, fz, tx, ty, tz)) |
| 132 |
> |
outputFile.write("%d\t%s\t%18.10g\t%18.10g\t%18.10g\t%14.10g\t%14.10g\t%14.10g\t%14.10g\t%14.10g\t%14.10g\t%14.10g\t%14.10g\t%14.10g\t%14.10g\t%14.10g\t%14.10g\t%14.10g\t%14.10g\t%14.10g\t%14.10g\n" % (whichSD-1, sdFormat, x, y, z, vx, vy, vz, qw, qx, qy, qz, jx, jy, jz, fx, fy, fz, tx, ty, tz)) |
| 133 |
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if (whichSD == nStuntDoubles): |
| 134 |
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outputFile.write(" </StuntDoubles>\n") |
| 135 |
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outputFile.write(" </Snapshot>\n") |
