1 |
mmeineke |
1062 |
#define _FILE_OFFSET_BITS 64 |
2 |
|
|
|
3 |
|
|
#include <stdio.h> |
4 |
|
|
#include <stdlib.h> |
5 |
|
|
#include <math.h> |
6 |
|
|
#include <mkl_lapack64.h> |
7 |
|
|
|
8 |
|
|
|
9 |
|
|
#include "params.h" |
10 |
|
|
#include "tcProps.h" |
11 |
|
|
#include "readWrite.h" |
12 |
|
|
#include "directorWhole.h" |
13 |
|
|
|
14 |
|
|
struct directStr{ |
15 |
|
|
double u[3]; |
16 |
|
|
double order; |
17 |
|
|
double time; |
18 |
|
|
}; |
19 |
|
|
|
20 |
|
|
struct directStr* directorWhole; |
21 |
|
|
|
22 |
|
|
void accumDWFrame( int index, struct atomCoord *atoms ); |
23 |
|
|
|
24 |
|
|
void calcDirWholeCorr(double startTime, struct atomCoord* atoms, |
25 |
|
|
char* outPrefix ){ |
26 |
|
|
|
27 |
|
|
// list of 'a priori' constants |
28 |
|
|
|
29 |
|
|
const int nLipAtoms = NL_ATOMS; |
30 |
|
|
const int nBonds = NBONDS; |
31 |
|
|
const int nLipids = NLIPIDS; |
32 |
|
|
const int nSSD = NSSD; |
33 |
|
|
const int nAtoms = nLipAtoms * nLipids + nSSD; |
34 |
|
|
|
35 |
|
|
// variables |
36 |
|
|
|
37 |
|
|
char outName[500]; |
38 |
|
|
FILE* outFile; |
39 |
|
|
int i, j, k; |
40 |
|
|
int startFrame, corrFrames, framesFinished; |
41 |
|
|
int startFound, percentComplete; |
42 |
|
|
|
43 |
|
|
double Hmat[3][3]; |
44 |
|
|
|
45 |
|
|
framesFinished = 0; |
46 |
|
|
|
47 |
|
|
startFound = 0; |
48 |
|
|
startFrame = -1; |
49 |
|
|
while( !startFound ){ |
50 |
|
|
|
51 |
|
|
startFrame++; |
52 |
|
|
|
53 |
|
|
if(startFrame >= nFrames){ |
54 |
|
|
|
55 |
|
|
fprintf( stderr, |
56 |
|
|
"Start Time, %G, was not found in the dump file.\n", |
57 |
|
|
startTime ); |
58 |
|
|
exit(0); |
59 |
|
|
} |
60 |
|
|
|
61 |
|
|
if(startTime <= frameTimes[startFrame]) |
62 |
|
|
startFound = 1; |
63 |
|
|
|
64 |
|
|
|
65 |
|
|
} |
66 |
|
|
|
67 |
|
|
corrFrames = nFrames - startFrame; |
68 |
|
|
directorWhole = (struct directStr*)calloc(corrFrames, |
69 |
|
|
sizeof(struct directStr)); |
70 |
|
|
|
71 |
|
|
|
72 |
|
|
for(i=startFrame; i<nFrames; i++){ |
73 |
|
|
|
74 |
|
|
percentComplete = |
75 |
|
|
(int)( 100.0 * (double)framesFinished / (double) corrFrames ); |
76 |
|
|
|
77 |
mmeineke |
1067 |
fprintf( stdout, |
78 |
|
|
"\rDirector bilayer corr %3d%% complete.", |
79 |
|
|
percentComplete ); |
80 |
|
|
fflush( stdout ); |
81 |
mmeineke |
1062 |
|
82 |
|
|
readFrame( i, atoms, Hmat ); |
83 |
|
|
|
84 |
|
|
directorWhole[i-startFrame].time = frameTimes[i]; |
85 |
|
|
|
86 |
|
|
accumDWFrame( i-startFrame, atoms ); |
87 |
|
|
|
88 |
|
|
framesFinished++; |
89 |
|
|
} |
90 |
|
|
|
91 |
mmeineke |
1067 |
sprintf( outName, "%s.dirWhole", outPrefix ); |
92 |
|
|
outFile = fopen( outName, "w" ); |
93 |
mmeineke |
1062 |
|
94 |
mmeineke |
1067 |
fprintf( outFile, |
95 |
|
|
"#time\torderParam\tx\ty\tz\n"); |
96 |
|
|
|
97 |
|
|
for(i=0;i<corrFrames;i++){ |
98 |
|
|
fprintf( outFile, |
99 |
|
|
"%6G\t%6G\t%6G\t%6G\t%6G\n", |
100 |
|
|
directorWhole[i].time, |
101 |
|
|
directorWhole[i].order, |
102 |
|
|
directorWhole[i].u[0], |
103 |
|
|
directorWhole[i].u[1], |
104 |
|
|
directorWhole[i].u[2]); |
105 |
|
|
} |
106 |
mmeineke |
1062 |
|
107 |
|
|
|
108 |
|
|
|
109 |
mmeineke |
1067 |
fflush(outFile); |
110 |
|
|
fclose(outFile); |
111 |
mmeineke |
1062 |
|
112 |
|
|
percentComplete = |
113 |
|
|
(int)( 100.0 * (double)framesFinished / (double) corrFrames ); |
114 |
|
|
|
115 |
|
|
fprintf( stdout, |
116 |
|
|
"\rDirector bilayer corr %3d%% complete.\n" |
117 |
|
|
"done.\n", |
118 |
|
|
percentComplete ); |
119 |
|
|
fflush( stdout ); |
120 |
mmeineke |
1073 |
|
121 |
|
|
free(directorWhole); |
122 |
|
|
directorWhole = NULL; |
123 |
mmeineke |
1062 |
} |
124 |
|
|
|
125 |
|
|
|
126 |
|
|
void accumDWFrame( int index, struct atomCoord *atoms ){ |
127 |
|
|
|
128 |
|
|
// list of 'a priori' constants |
129 |
|
|
|
130 |
|
|
const int nLipAtoms = NL_ATOMS; |
131 |
|
|
const int nBonds = NBONDS; |
132 |
|
|
const int nLipids = NLIPIDS; |
133 |
|
|
const int nSSD = NSSD; |
134 |
|
|
const int nAtoms = nLipAtoms * nLipids + nSSD; |
135 |
|
|
const double oneThird = 1.0 / 3.0; |
136 |
|
|
|
137 |
|
|
int i,j,k,l,m,n; |
138 |
|
|
int lWork; |
139 |
|
|
int nfilled; |
140 |
|
|
int ndiag; |
141 |
|
|
int ifail; |
142 |
|
|
|
143 |
|
|
double oMat[3][3]; |
144 |
|
|
double iMat[3][3]; |
145 |
mmeineke |
1067 |
double matWrap[9]; |
146 |
mmeineke |
1062 |
double com[3]; |
147 |
|
|
double totMass; |
148 |
|
|
double lenPrinc, distl; |
149 |
|
|
|
150 |
|
|
struct uVect{ |
151 |
|
|
double u[3]; |
152 |
|
|
}; |
153 |
|
|
struct uVect principal[nLipids]; |
154 |
|
|
|
155 |
|
|
|
156 |
|
|
double evals[3]; |
157 |
|
|
double work[9]; |
158 |
|
|
double *u; |
159 |
|
|
double smallest, max; |
160 |
|
|
int which; |
161 |
|
|
|
162 |
|
|
char job, uplo; |
163 |
|
|
|
164 |
|
|
job = 'V'; |
165 |
|
|
uplo = 'U'; |
166 |
|
|
nfilled = 3; |
167 |
|
|
ndiag = 3; |
168 |
|
|
lWork = 9; |
169 |
|
|
|
170 |
|
|
for(i=0;i<3;i++) |
171 |
|
|
for(j=0;j<3;j++) |
172 |
|
|
oMat[i][j] = 0.0; |
173 |
|
|
|
174 |
|
|
for(i=0;i<nLipids;i++){ |
175 |
|
|
|
176 |
|
|
k = i*nLipAtoms; |
177 |
|
|
|
178 |
|
|
// find the moment of inertia |
179 |
|
|
|
180 |
|
|
for(j=0;j<3;j++) |
181 |
|
|
for(l=0;l<3;l++) |
182 |
|
|
iMat[j][l] = 0.0; |
183 |
|
|
|
184 |
|
|
// com calc |
185 |
|
|
|
186 |
|
|
totMass = 0.0; |
187 |
|
|
for(m=0;m<3;m++) com[m] = 0.0; |
188 |
|
|
for(j=0;j<nLipAtoms;j++){ |
189 |
|
|
l=k+j; |
190 |
|
|
|
191 |
mmeineke |
1067 |
for(m=0;m<3;m++) |
192 |
mmeineke |
1062 |
com[m] += atoms[l].mass * atoms[l].pos[m]; |
193 |
mmeineke |
1067 |
|
194 |
|
|
totMass += atoms[l].mass; |
195 |
mmeineke |
1062 |
} |
196 |
|
|
for(m=0;m<3;m++) com[m] /= totMass; |
197 |
|
|
|
198 |
|
|
for(j=0;j<nLipAtoms;j++){ |
199 |
|
|
l=k+j; |
200 |
|
|
|
201 |
|
|
|
202 |
|
|
distl = 0.0; |
203 |
|
|
for(m=0; m<3;m++) |
204 |
|
|
distl += (atoms[l].pos[m]-com[m])*(atoms[l].pos[m]-com[m]); |
205 |
|
|
|
206 |
|
|
for(m=0; m<3; m++) |
207 |
|
|
iMat[m][m] += atoms[l].mass * distl; |
208 |
|
|
|
209 |
|
|
for(m=0;m<3;m++) |
210 |
|
|
for(n=0;n<3;n++) |
211 |
|
|
iMat[m][n] -= atoms[l].mass * ( atoms[l].pos[m] - com[m] ) * |
212 |
|
|
( atoms[l].pos[n] - com[n] ); |
213 |
|
|
|
214 |
|
|
|
215 |
|
|
} |
216 |
mmeineke |
1067 |
|
217 |
|
|
// fprintf(stderr, "iMat (before) = %6G, %6G, %6G\n" |
218 |
|
|
// " %6G, %6G, %6G\n" |
219 |
|
|
// " %6G, %6G, %6G\n\n", |
220 |
|
|
// iMat[0][0], iMat[0][1], iMat[0][2], |
221 |
|
|
// iMat[1][0], iMat[1][1], iMat[1][2], |
222 |
|
|
// iMat[2][0], iMat[2][1], iMat[2][2]); |
223 |
mmeineke |
1062 |
|
224 |
mmeineke |
1067 |
// matWrap to fortran convention |
225 |
|
|
|
226 |
|
|
for(j=0;j<3;j++) |
227 |
|
|
for(l=0;l<3;l++) |
228 |
|
|
matWrap[l+3*j] = iMat[l][j]; |
229 |
|
|
|
230 |
mmeineke |
1062 |
ifail = 0; |
231 |
mmeineke |
1067 |
dsyev(&job, &uplo, &nfilled, matWrap, &ndiag, evals, work, &lWork, &ifail); |
232 |
mmeineke |
1062 |
|
233 |
|
|
if (ifail) { |
234 |
|
|
fprintf(stderr, "dsyev screwed something up!\n"); |
235 |
|
|
exit(0); |
236 |
|
|
} |
237 |
|
|
|
238 |
mmeineke |
1067 |
// matWrap from fortran convention |
239 |
mmeineke |
1062 |
|
240 |
mmeineke |
1067 |
for(j=0;j<3;j++) |
241 |
|
|
for(l=0;l<3;l++) |
242 |
|
|
iMat[l][j] = matWrap[l+3*j]; |
243 |
mmeineke |
1062 |
|
244 |
mmeineke |
1067 |
// fprintf(stderr, "evals = %6G, %6G, %6G\n\n", |
245 |
|
|
// evals[0], evals[1], evals[2]); |
246 |
mmeineke |
1062 |
|
247 |
mmeineke |
1067 |
// fprintf(stderr, "iMat (after) = %6G, %6G, %6G\n" |
248 |
|
|
// " %6G, %6G, %6G\n" |
249 |
|
|
// " %6G, %6G, %6G\n\n", |
250 |
|
|
// iMat[0][0], iMat[0][1], iMat[0][2], |
251 |
|
|
// iMat[1][0], iMat[1][1], iMat[1][2], |
252 |
|
|
// iMat[2][0], iMat[2][1], iMat[2][2]); |
253 |
|
|
|
254 |
|
|
|
255 |
mmeineke |
1062 |
|
256 |
|
|
smallest = fabs(evals[0]); |
257 |
|
|
which = 0; |
258 |
|
|
for(j=0;j<3;j++){ |
259 |
|
|
if( fabs(evals[j]) < smallest ){ |
260 |
|
|
which = j; |
261 |
|
|
smallest = fabs(evals[j]); |
262 |
|
|
} |
263 |
|
|
} |
264 |
|
|
|
265 |
|
|
lenPrinc = 0.0; |
266 |
|
|
for(j=0;j<3;j++) |
267 |
|
|
lenPrinc += iMat[j][which] * iMat[j][which]; |
268 |
mmeineke |
1067 |
lenPrinc = sqrt( lenPrinc ); |
269 |
mmeineke |
1062 |
|
270 |
|
|
for(j=0;j<3;j++) |
271 |
|
|
principal[i].u[j] = iMat[j][which]/lenPrinc; |
272 |
|
|
|
273 |
|
|
|
274 |
|
|
|
275 |
|
|
|
276 |
|
|
|
277 |
|
|
// find the director of the bilayer |
278 |
|
|
|
279 |
|
|
u = principal[i].u; |
280 |
|
|
|
281 |
|
|
oMat[0][0] += u[0] * u[0] - oneThird; |
282 |
|
|
oMat[0][1] += u[0] * u[1]; |
283 |
|
|
oMat[0][2] += u[0] * u[2]; |
284 |
|
|
|
285 |
|
|
oMat[1][0] += u[1] * u[0]; |
286 |
|
|
oMat[1][1] += u[1] * u[1] - oneThird; |
287 |
|
|
oMat[1][2] += u[1] * u[2]; |
288 |
|
|
|
289 |
|
|
oMat[2][0] += u[2] * u[0]; |
290 |
|
|
oMat[2][1] += u[2] * u[1]; |
291 |
|
|
oMat[2][2] += u[2] * u[2] - oneThird; |
292 |
|
|
} |
293 |
|
|
|
294 |
|
|
for(i=0;i<3;i++) |
295 |
|
|
for(j=0;j<3;j++) |
296 |
|
|
oMat[i][j] /= (double)nLipids; |
297 |
|
|
|
298 |
mmeineke |
1067 |
// matWrap to fortran convention |
299 |
|
|
|
300 |
|
|
for(j=0;j<3;j++) |
301 |
|
|
for(l=0;l<3;l++) |
302 |
|
|
matWrap[l+3*j] = oMat[l][j]; |
303 |
|
|
|
304 |
mmeineke |
1062 |
ifail = 0; |
305 |
mmeineke |
1067 |
dsyev(&job, &uplo, &nfilled, matWrap, &ndiag, evals, work, &lWork, &ifail); |
306 |
mmeineke |
1062 |
|
307 |
|
|
if (ifail) { |
308 |
|
|
fprintf(stderr, "dsyev screwed something up!\n"); |
309 |
|
|
exit(0); |
310 |
|
|
} |
311 |
mmeineke |
1067 |
|
312 |
|
|
// matWrap from fortran convention |
313 |
mmeineke |
1062 |
|
314 |
mmeineke |
1067 |
for(j=0;j<3;j++) |
315 |
|
|
for(l=0;l<3;l++) |
316 |
|
|
oMat[l][j] = matWrap[l+3*j]; |
317 |
|
|
|
318 |
mmeineke |
1062 |
max = 0.0; |
319 |
|
|
for (i=0; i<3;i++) { |
320 |
|
|
if (fabs(evals[i]) > max) { |
321 |
|
|
which = i; |
322 |
|
|
max = fabs(evals[i]); |
323 |
|
|
} |
324 |
|
|
} |
325 |
|
|
|
326 |
|
|
for (i = 0; i < 3; i++) { |
327 |
|
|
directorWhole[index].u[i] = oMat[i][which]; |
328 |
|
|
} |
329 |
|
|
|
330 |
|
|
directorWhole[index].order = 1.5 * max; |
331 |
|
|
|
332 |
mmeineke |
1067 |
// fprintf(stderr, |
333 |
|
|
// "frame[%d] => order = %6G; < %6G, %6G, %6G >\n", |
334 |
|
|
// index, |
335 |
|
|
// directorWhole[index].order, |
336 |
|
|
// directorWhole[index].u[0], |
337 |
|
|
// directorWhole[index].u[1], |
338 |
|
|
// directorWhole[index].u[2] ); |
339 |
mmeineke |
1062 |
|
340 |
|
|
// fprintf(stdout, |
341 |
|
|
// "%6g\t%6G\n", |
342 |
|
|
// directorWhole[index].time, |
343 |
|
|
// directorWhole[index].order); |
344 |
|
|
} |