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""" |
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21 |
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__author__ = "Dan Gezelter (gezelter@nd.edu)" |
22 |
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__version__ = "$Revision: 1.1 $" |
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__date__ = "$Date: 2006-07-27 19:05:16 $" |
22 |
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__version__ = "$Revision: 1.2 $" |
23 |
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__date__ = "$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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45 |
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mdLines = mdFile.readlines() |
47 |
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for l in mdLines: |
48 |
< |
outputFile.write(l) |
48 |
> |
if (l.find('initialConfig') == -1): |
49 |
> |
outputFile.write(l) |
50 |
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|
51 |
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outputFile.write(" </MetaData>\n") |
52 |
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mdFile.close() |
55 |
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configFile = open(configFileName, 'r') |
56 |
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for line in configFile.readlines(): |
57 |
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framePos = framePos + 1 |
57 |
– |
print framePos |
58 |
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if (framePos == 1): |
59 |
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L = line.split() |
60 |
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nStuntDoubles = int(L[0]) |
62 |
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outputFile.write(" <Snapshot>\n") |
63 |
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continue |
64 |
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elif (framePos == 2): |
65 |
< |
L = line.split() |
66 |
< |
time = float(L[0].split(';')[0]) |
65 |
> |
L = line.replace(';',' ').split() |
66 |
> |
time = float(L[0]) |
67 |
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outputFile.write(" <FrameData>\n"); |
68 |
< |
outputFile.write(" Time: %g\n" % (time)) |
68 |
> |
outputFile.write(" Time: %.10g\n" % (time)) |
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Hxx = float(L[1]) |
70 |
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Hxy = float(L[2]) |
71 |
< |
Hxz = float(L[3].split(';')[0]) |
71 |
> |
Hxz = float(L[3]) |
72 |
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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 |
|
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 |
|
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 |
|
if (whichSD == nStuntDoubles): |
134 |
|
outputFile.write(" </StuntDoubles>\n") |
135 |
|
outputFile.write(" </Snapshot>\n") |