1 |
kfletch2 |
1262 |
#!/usr/bin/env python |
2 |
|
|
"""Ice Cube Solvator |
3 |
gezelter |
1116 |
|
4 |
kfletch2 |
1262 |
Opens two md files, one with water in an ice structure, |
5 |
|
|
and one with water in a liquid phase. Deletes any overlapping |
6 |
|
|
liquid molecules and merges the two md files. |
7 |
gezelter |
1116 |
|
8 |
kfletch2 |
1262 |
Usage: waterRotator |
9 |
gezelter |
1116 |
|
10 |
kfletch2 |
1262 |
Options: |
11 |
|
|
-h, --help show this help |
12 |
|
|
-u, --solute=... use specified meta-data (.md) file as the solute |
13 |
|
|
-v, --solvent=... use specified meta-data (.md) file as the solvent |
14 |
|
|
-r, --rcut=... specify the cutoff radius for deleting solvent |
15 |
|
|
-o, --output-file=... use specified output (.md) file |
16 |
gezelter |
1116 |
|
17 |
|
|
|
18 |
kfletch2 |
1262 |
Example: |
19 |
|
|
iceCubeSolvator -u frosty.md -v tepid.md -r 4.0 -o lukewarm.md |
20 |
gezelter |
1116 |
|
21 |
kfletch2 |
1262 |
""" |
22 |
gezelter |
1116 |
|
23 |
kfletch2 |
1262 |
__author__ = "Dan Gezelter (gezelter@nd.edu)" |
24 |
chuckv |
1263 |
__version__ = "$Revision: 1.5 $" |
25 |
|
|
__date__ = "$Date: 2008-06-26 14:23:49 $" |
26 |
kfletch2 |
1262 |
__copyright__ = "Copyright (c) 2006 by the University of Notre Dame" |
27 |
|
|
__license__ = "OOPSE" |
28 |
gezelter |
1116 |
|
29 |
kfletch2 |
1262 |
import sys |
30 |
|
|
import getopt |
31 |
|
|
import string |
32 |
|
|
import math |
33 |
|
|
import random |
34 |
|
|
from sets import * |
35 |
|
|
#from Numeric import * |
36 |
gezelter |
1116 |
|
37 |
kfletch2 |
1262 |
_haveMDFileName1 = 0 |
38 |
|
|
_haveMDFileName2 = 0 |
39 |
|
|
_haveRcut = 0 |
40 |
|
|
_haveOutputFileName = 0 |
41 |
gezelter |
1116 |
|
42 |
kfletch2 |
1262 |
metaData1 = [] |
43 |
|
|
frameData1 = [] |
44 |
|
|
positions1 = [] |
45 |
|
|
velocities1 = [] |
46 |
|
|
quaternions1 = [] |
47 |
|
|
angVels1 = [] |
48 |
|
|
indices1 = [] |
49 |
|
|
Hmat1 = [] |
50 |
|
|
BoxInv1 = [] |
51 |
chuckv |
1263 |
pvqj1 = [] |
52 |
gezelter |
1116 |
|
53 |
kfletch2 |
1262 |
metaData2 = [] |
54 |
|
|
frameData2 = [] |
55 |
|
|
positions2 = [] |
56 |
|
|
velocities2 = [] |
57 |
|
|
quaternions2 = [] |
58 |
|
|
angVels2 = [] |
59 |
|
|
indices2 = [] |
60 |
|
|
Hmat2 = [] |
61 |
|
|
BoxInv2 = [] |
62 |
chuckv |
1263 |
pvqj2 = [] |
63 |
gezelter |
1116 |
|
64 |
kfletch2 |
1262 |
keepers = [] |
65 |
gezelter |
1116 |
|
66 |
kfletch2 |
1262 |
def usage(): |
67 |
|
|
print __doc__ |
68 |
gezelter |
1116 |
|
69 |
kfletch2 |
1262 |
def readFile1(mdFileName): |
70 |
|
|
mdFile = open(mdFileName, 'r') |
71 |
|
|
# Find OOPSE version info first |
72 |
|
|
line = mdFile.readline() |
73 |
|
|
while 1: |
74 |
|
|
if '<OOPSE version=' in line: |
75 |
|
|
OOPSEversion = line |
76 |
|
|
break |
77 |
|
|
line = mdFile.readline() |
78 |
|
|
|
79 |
|
|
# Rewind file and find start of MetaData block |
80 |
|
|
|
81 |
|
|
mdFile.seek(0) |
82 |
|
|
line = mdFile.readline() |
83 |
|
|
print "reading MetaData" |
84 |
|
|
while 1: |
85 |
|
|
if '<MetaData>' in line: |
86 |
|
|
while 2: |
87 |
|
|
metaData1.append(line) |
88 |
|
|
line = mdFile.readline() |
89 |
|
|
if '</MetaData>' in line: |
90 |
|
|
metaData1.append(line) |
91 |
|
|
break |
92 |
|
|
break |
93 |
|
|
line = mdFile.readline() |
94 |
gezelter |
1116 |
|
95 |
kfletch2 |
1262 |
mdFile.seek(0) |
96 |
|
|
print "reading Snapshot" |
97 |
|
|
line = mdFile.readline() |
98 |
|
|
while 1: |
99 |
|
|
if '<Snapshot>' in line: |
100 |
|
|
line = mdFile.readline() |
101 |
|
|
while 1: |
102 |
|
|
print "reading FrameData" |
103 |
|
|
if '<FrameData>' in line: |
104 |
|
|
while 2: |
105 |
|
|
frameData1.append(line) |
106 |
|
|
if 'Hmat:' in line: |
107 |
|
|
L = line.split() |
108 |
|
|
Hxx = float(L[2].strip(',')) |
109 |
|
|
Hxy = float(L[3].strip(',')) |
110 |
|
|
Hxz = float(L[4].strip(',')) |
111 |
|
|
Hyx = float(L[7].strip(',')) |
112 |
|
|
Hyy = float(L[8].strip(',')) |
113 |
|
|
Hyz = float(L[9].strip(',')) |
114 |
|
|
Hzx = float(L[12].strip(',')) |
115 |
|
|
Hzy = float(L[13].strip(',')) |
116 |
|
|
Hzz = float(L[14].strip(',')) |
117 |
|
|
Hmat1.append([Hxx, Hxy, Hxz]) |
118 |
|
|
Hmat1.append([Hyx, Hyy, Hyz]) |
119 |
|
|
Hmat1.append([Hzx, Hzy, Hzz]) |
120 |
|
|
print Hmat1 |
121 |
|
|
BoxInv1.append(1.0/Hxx) |
122 |
|
|
BoxInv1.append(1.0/Hyy) |
123 |
|
|
BoxInv1.append(1.0/Hzz) |
124 |
|
|
print BoxInv1 |
125 |
|
|
line = mdFile.readline() |
126 |
|
|
if '</FrameData>' in line: |
127 |
|
|
frameData1.append(line) |
128 |
|
|
break |
129 |
|
|
break |
130 |
gezelter |
1116 |
|
131 |
kfletch2 |
1262 |
line = mdFile.readline() |
132 |
|
|
while 1: |
133 |
|
|
if '<StuntDoubles>' in line: |
134 |
|
|
line = mdFile.readline() |
135 |
|
|
while 2: |
136 |
|
|
L = line.split() |
137 |
|
|
myIndex = int(L[0]) |
138 |
|
|
indices1.append(myIndex) |
139 |
|
|
pvqj1.append(L[1]) |
140 |
|
|
x = float(L[2]) |
141 |
|
|
y = float(L[3]) |
142 |
|
|
z = float(L[4]) |
143 |
|
|
positions1.append([x, y, z]) |
144 |
|
|
vx = float(L[5]) |
145 |
|
|
vy = float(L[6]) |
146 |
|
|
vz = float(L[7]) |
147 |
|
|
velocities1.append([vx, vy, vz]) |
148 |
chuckv |
1263 |
if 'pvqj' in L[1]: |
149 |
|
|
qw = float(L[8]) |
150 |
|
|
qx = float(L[9]) |
151 |
|
|
qy = float(L[10]) |
152 |
|
|
qz = float(L[11]) |
153 |
|
|
quaternions1.append([qw, qx, qy, qz]) |
154 |
|
|
jx = float(L[12]) |
155 |
|
|
jy = float(L[13]) |
156 |
|
|
jz = float(L[14]) |
157 |
|
|
angVels1.append([jx, jy, jz]) |
158 |
|
|
else: |
159 |
|
|
quaternions1.append([0.0, 0.0, 0.0, 0.0]) |
160 |
|
|
angVels1.append([0.0, 0.0, 0.0]) |
161 |
|
|
|
162 |
kfletch2 |
1262 |
line = mdFile.readline() |
163 |
|
|
if '</StuntDoubles>' in line: |
164 |
|
|
break |
165 |
|
|
break |
166 |
|
|
line = mdFile.readline() |
167 |
|
|
if not line: break |
168 |
|
|
|
169 |
|
|
mdFile.close() |
170 |
gezelter |
1116 |
|
171 |
kfletch2 |
1262 |
def readFile2(mdFileName): |
172 |
|
|
mdFile = open(mdFileName, 'r') |
173 |
|
|
# Find OOPSE version info first |
174 |
|
|
line = mdFile.readline() |
175 |
|
|
while 1: |
176 |
|
|
if '<OOPSE version=' in line: |
177 |
|
|
OOPSEversion = line |
178 |
|
|
break |
179 |
|
|
line = mdFile.readline() |
180 |
|
|
|
181 |
|
|
# Rewind file and find start of MetaData block |
182 |
|
|
|
183 |
|
|
mdFile.seek(0) |
184 |
|
|
line = mdFile.readline() |
185 |
|
|
print "reading MetaData" |
186 |
|
|
while 1: |
187 |
|
|
if '<MetaData>' in line: |
188 |
|
|
while 2: |
189 |
|
|
metaData2.append(line) |
190 |
|
|
line = mdFile.readline() |
191 |
|
|
if '</MetaData>' in line: |
192 |
|
|
metaData2.append(line) |
193 |
|
|
break |
194 |
|
|
break |
195 |
|
|
line = mdFile.readline() |
196 |
gezelter |
1116 |
|
197 |
kfletch2 |
1262 |
mdFile.seek(0) |
198 |
|
|
print "reading Snapshot" |
199 |
|
|
line = mdFile.readline() |
200 |
|
|
while 1: |
201 |
|
|
if '<Snapshot>' in line: |
202 |
|
|
line = mdFile.readline() |
203 |
|
|
while 1: |
204 |
|
|
print "reading FrameData" |
205 |
|
|
if '<FrameData>' in line: |
206 |
|
|
while 2: |
207 |
|
|
frameData2.append(line) |
208 |
|
|
if 'Hmat:' in line: |
209 |
|
|
L = line.split() |
210 |
|
|
Hxx = float(L[2].strip(',')) |
211 |
|
|
Hxy = float(L[3].strip(',')) |
212 |
|
|
Hxz = float(L[4].strip(',')) |
213 |
|
|
Hyx = float(L[7].strip(',')) |
214 |
|
|
Hyy = float(L[8].strip(',')) |
215 |
|
|
Hyz = float(L[9].strip(',')) |
216 |
|
|
Hzx = float(L[12].strip(',')) |
217 |
|
|
Hzy = float(L[13].strip(',')) |
218 |
|
|
Hzz = float(L[14].strip(',')) |
219 |
|
|
Hmat2.append([Hxx, Hxy, Hxz]) |
220 |
|
|
Hmat2.append([Hyx, Hyy, Hyz]) |
221 |
|
|
Hmat2.append([Hzx, Hzy, Hzz]) |
222 |
|
|
print Hmat2 |
223 |
|
|
BoxInv2.append(1.0/Hxx) |
224 |
|
|
BoxInv2.append(1.0/Hyy) |
225 |
|
|
BoxInv2.append(1.0/Hzz) |
226 |
|
|
print BoxInv2 |
227 |
|
|
line = mdFile.readline() |
228 |
|
|
if '</FrameData>' in line: |
229 |
|
|
frameData2.append(line) |
230 |
|
|
break |
231 |
|
|
break |
232 |
gezelter |
1116 |
|
233 |
kfletch2 |
1262 |
line = mdFile.readline() |
234 |
|
|
while 1: |
235 |
|
|
if '<StuntDoubles>' in line: |
236 |
|
|
line = mdFile.readline() |
237 |
|
|
while 2: |
238 |
|
|
L = line.split() |
239 |
|
|
myIndex = int(L[0]) |
240 |
|
|
indices2.append(myIndex) |
241 |
|
|
pvqj2.append(L[1]) |
242 |
|
|
x = float(L[2]) |
243 |
|
|
y = float(L[3]) |
244 |
|
|
z = float(L[4]) |
245 |
|
|
positions2.append([x, y, z]) |
246 |
|
|
vx = float(L[5]) |
247 |
|
|
vy = float(L[6]) |
248 |
|
|
vz = float(L[7]) |
249 |
|
|
velocities2.append([vx, vy, vz]) |
250 |
chuckv |
1263 |
if 'pvqj' in L[1]: |
251 |
|
|
qw = float(L[8]) |
252 |
|
|
qx = float(L[9]) |
253 |
|
|
qy = float(L[10]) |
254 |
|
|
qz = float(L[11]) |
255 |
|
|
quaternions2.append([qw, qx, qy, qz]) |
256 |
|
|
jx = float(L[12]) |
257 |
|
|
jy = float(L[13]) |
258 |
|
|
jz = float(L[14]) |
259 |
|
|
angVels2.append([jx, jy, jz]) |
260 |
|
|
else: |
261 |
|
|
quaternions1.append([0.0, 0.0, 0.0, 0.0]) |
262 |
|
|
angVels1.append([0.0, 0.0, 0.0]) |
263 |
|
|
|
264 |
kfletch2 |
1262 |
line = mdFile.readline() |
265 |
|
|
if '</StuntDoubles>' in line: |
266 |
|
|
break |
267 |
|
|
break |
268 |
|
|
line = mdFile.readline() |
269 |
|
|
if not line: break |
270 |
|
|
|
271 |
|
|
mdFile.close() |
272 |
xsun |
1214 |
|
273 |
kfletch2 |
1262 |
def writeFile(outputFileName): |
274 |
|
|
outputFile = open(outputFileName, 'w') |
275 |
gezelter |
1116 |
|
276 |
kfletch2 |
1262 |
outputFile.write("<OOPSE version=4>\n"); |
277 |
|
|
|
278 |
|
|
for metaline in metaData1: |
279 |
|
|
outputFile.write(metaline) |
280 |
gezelter |
1116 |
|
281 |
kfletch2 |
1262 |
outputFile.write(" <Snapshot>\n") |
282 |
gezelter |
1116 |
|
283 |
kfletch2 |
1262 |
for frameline in frameData1: |
284 |
|
|
outputFile.write(frameline) |
285 |
|
|
|
286 |
|
|
outputFile.write(" <StuntDoubles>\n") |
287 |
gezelter |
1116 |
|
288 |
chuckv |
1263 |
|
289 |
kfletch2 |
1262 |
newIndex = 0 |
290 |
|
|
for i in range(len(indices1)): |
291 |
chuckv |
1263 |
if (pvqj[i] == 'pv'): |
292 |
|
|
outputFile.write("%10d %7s %18.10g %18.10g %18.10g %14e %13e %13e\n" % (newIndex, pvqj1[i], positions1[i][0], positions1[i][1], positions1[i][2], velocities1[i][0], velocities1[i][1], velocities1[i][2])) |
293 |
|
|
elif(pvqj[i] == 'pvqj'): |
294 |
|
|
outputFile.write("%10d %7s %18.10g %18.10g %18.10g %13e %13e %13e %13e %13e %13e %13e %13e %13e %13e\n" % (newIndex, pvqj1[i], positions1[i][0], positions1[i][1], positions1[i][2], velocities1[i][0], velocities1[i][1], velocities1[i][2], quaternions1[i][0], quaternions1[i][1], quaternions1[i][2], quaternions1[i][3], angVels1[i][0], angVels1[i][1], angVels1[i][2])) |
295 |
|
|
|
296 |
kfletch2 |
1262 |
newIndex = newIndex + 1 |
297 |
gezelter |
1116 |
|
298 |
kfletch2 |
1262 |
outputFile.write(" </StuntDoubles>\n") |
299 |
|
|
outputFile.write(" </Snapshot>\n") |
300 |
|
|
outputFile.write("</OOPSE>\n") |
301 |
|
|
outputFile.close() |
302 |
|
|
|
303 |
|
|
def roundMe(x): |
304 |
|
|
if (x >= 0.0): |
305 |
|
|
return math.floor(x + 0.5) |
306 |
|
|
else: |
307 |
|
|
return math.ceil(x - 0.5) |
308 |
gezelter |
1116 |
|
309 |
chuckv |
1263 |
def frange(start,stop,step=1.0): |
310 |
|
|
while start < stop: |
311 |
|
|
yield start |
312 |
|
|
start += step |
313 |
|
|
|
314 |
|
|
|
315 |
kfletch2 |
1262 |
def wrapVector(myVect): |
316 |
|
|
scaled = [0.0, 0.0, 0.0] |
317 |
|
|
for i in range(3): |
318 |
|
|
scaled[i] = myVect[i] * BoxInv1[i] |
319 |
|
|
scaled[i] = scaled[i] - roundMe(scaled[i]) |
320 |
|
|
myVect[i] = scaled[i] * Hmat1[i][i] |
321 |
|
|
return myVect |
322 |
gezelter |
1116 |
|
323 |
kfletch2 |
1262 |
def dot(L1, L2): |
324 |
|
|
myDot = 0.0 |
325 |
|
|
for i in range(len(L1)): |
326 |
|
|
myDot = myDot + L1[i]*L2[i] |
327 |
|
|
return myDot |
328 |
gezelter |
1116 |
|
329 |
kfletch2 |
1262 |
def normalize(L1): |
330 |
|
|
L2 = [] |
331 |
|
|
myLength = math.sqrt(dot(L1, L1)) |
332 |
|
|
for i in range(len(L1)): |
333 |
|
|
L2.append(L1[i] / myLength) |
334 |
|
|
return L2 |
335 |
gezelter |
1116 |
|
336 |
kfletch2 |
1262 |
def cross(L1, L2): |
337 |
|
|
# don't call this with anything other than length 3 lists please |
338 |
|
|
# or you'll be sorry |
339 |
|
|
L3 = [0.0, 0.0, 0.0] |
340 |
|
|
L3[0] = L1[1]*L2[2] - L1[2]*L2[1] |
341 |
|
|
L3[1] = L1[2]*L2[0] - L1[0]*L2[2] |
342 |
|
|
L3[2] = L1[0]*L2[1] - L1[1]*L2[0] |
343 |
|
|
return L3 |
344 |
gezelter |
1116 |
|
345 |
chuckv |
1263 |
def removeOverlaps(rcut,nSolventAtoms,nSoluteAtoms: |
346 |
gezelter |
1116 |
|
347 |
kfletch2 |
1262 |
rcut2 = rcut*rcut |
348 |
chuckv |
1263 |
nextMol = 0 |
349 |
|
|
|
350 |
|
|
|
351 |
|
|
for i in range(0,len(indices2),nSolventAtoms): |
352 |
kfletch2 |
1262 |
keepThisMolecule = 1 |
353 |
chuckv |
1263 |
for atom1 in range (i, (i+nSolventAtoms-1)): |
354 |
|
|
iPos = positions2[atom1] |
355 |
kfletch2 |
1262 |
|
356 |
chuckv |
1263 |
for j in range(0,len(indices1),nSoluteAtoms): |
357 |
|
|
for atom2 in range (j, (j+nSoluteAtoms-1)): |
358 |
|
|
jPos = positions1[j] |
359 |
|
|
dpos = [jPos[0]-iPos[0], jPos[1]-iPos[1], jPos[2]-iPos[2]] |
360 |
|
|
dpos = wrapVector(dpos) |
361 |
|
|
dist2 = dot(dpos,dpos) |
362 |
gezelter |
1116 |
|
363 |
chuckv |
1263 |
if (dist2 < rcut2): |
364 |
|
|
keepThisMolecule = 0 |
365 |
|
|
break |
366 |
|
|
|
367 |
kfletch2 |
1262 |
keepers.append(keepThisMolecule) |
368 |
gezelter |
1116 |
|
369 |
chuckv |
1263 |
for i in range(0,len(indices2),nSolventAtoms): |
370 |
kfletch2 |
1262 |
if (keepers[i] == 1): |
371 |
chuckv |
1263 |
for j in range (i, i+nSolventAtoms): |
372 |
|
|
positions1.append(positions2[j]) |
373 |
|
|
velocities1.append(velocities2[j]) |
374 |
|
|
quaternions1.append(quaternions2[j]) |
375 |
|
|
angVels1.append(angVels2[j]) |
376 |
|
|
indices1.append(indices2[j]) |
377 |
gezelter |
1116 |
|
378 |
kfletch2 |
1262 |
def main(argv): |
379 |
|
|
try: |
380 |
chuckv |
1263 |
opts, args = getopt.getopt(argv, "hu:v:n:p:r:o:", ["help", "solute=","solvent=","nSoluteAtoms","nSoluteAtoms", "rcut" "output-file="]) |
381 |
kfletch2 |
1262 |
except getopt.GetoptError: |
382 |
|
|
usage() |
383 |
|
|
sys.exit(2) |
384 |
|
|
for opt, arg in opts: |
385 |
|
|
if opt in ("-h", "--help"): |
386 |
|
|
usage() |
387 |
|
|
sys.exit() |
388 |
|
|
elif opt in ("-u", "--solute"): |
389 |
|
|
mdFileName1 = arg |
390 |
|
|
global _haveMDFileName1 |
391 |
|
|
_haveMDFileName1 = 1 |
392 |
|
|
elif opt in ("-v", "--solvent"): |
393 |
|
|
mdFileName2 = arg |
394 |
|
|
global _haveMDFileName2 |
395 |
|
|
_haveMDFileName2 = 1 |
396 |
chuckv |
1263 |
elif opt in ("-n", "--nSoluteAtoms"): |
397 |
|
|
nSoluteAtoms = arg |
398 |
|
|
global _haveNSoluteAtoms |
399 |
|
|
_haveNSoluteAtoms = 1 |
400 |
|
|
elif opt in ("-p", "--nSolventAtoms"): |
401 |
|
|
mdFileName2 = arg |
402 |
|
|
global _haveNSolventAtoms |
403 |
|
|
_haveNSolventAtoms = 1 |
404 |
kfletch2 |
1262 |
elif opt in ("-r", "--rcut"): |
405 |
|
|
rcut = float(arg) |
406 |
|
|
global _haveRcut |
407 |
|
|
_haveRcut = 1 |
408 |
|
|
elif opt in ("-o", "--output-file"): |
409 |
|
|
outputFileName = arg |
410 |
|
|
global _haveOutputFileName |
411 |
|
|
_haveOutputFileName = 1 |
412 |
gezelter |
1116 |
|
413 |
kfletch2 |
1262 |
if (_haveMDFileName1 != 1): |
414 |
|
|
usage() |
415 |
|
|
print "No meta-data file was specified for the solute" |
416 |
|
|
sys.exit() |
417 |
gezelter |
1116 |
|
418 |
kfletch2 |
1262 |
if (_haveMDFileName2 != 1): |
419 |
|
|
usage() |
420 |
|
|
print "No meta-data file was specified for the solvent" |
421 |
|
|
sys.exit() |
422 |
gezelter |
1116 |
|
423 |
kfletch2 |
1262 |
if (_haveOutputFileName != 1): |
424 |
|
|
usage() |
425 |
|
|
print "No output file was specified" |
426 |
|
|
sys.exit() |
427 |
gezelter |
1116 |
|
428 |
kfletch2 |
1262 |
if (_haveRcut != 1): |
429 |
|
|
print "No cutoff radius was specified, using 4 angstroms" |
430 |
|
|
rcut = 4.0 |
431 |
gezelter |
1116 |
|
432 |
chuckv |
1263 |
if (_haveNSoluteAtoms != 1): |
433 |
|
|
nSoluteAtoms = 1 |
434 |
|
|
|
435 |
|
|
if (_haveNSolventAtoms != 1): |
436 |
|
|
nSolventAtoms = 1 |
437 |
|
|
|
438 |
kfletch2 |
1262 |
readFile1(mdFileName1) |
439 |
|
|
readFile2(mdFileName2) |
440 |
chuckv |
1263 |
removeOverlaps(rcut,nSolventAtoms,nSoluteAtoms) |
441 |
kfletch2 |
1262 |
writeFile(outputFileName) |
442 |
gezelter |
1116 |
|
443 |
kfletch2 |
1262 |
if __name__ == "__main__": |
444 |
|
|
if len(sys.argv) == 1: |
445 |
|
|
usage() |
446 |
|
|
sys.exit() |
447 |
|
|
main(sys.argv[1:]) |