| 1 |
#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 |
fprintf( stdout, |
| 78 |
"\rDirector bilayer corr %3d%% complete.", |
| 79 |
percentComplete ); |
| 80 |
fflush( stdout ); |
| 81 |
|
| 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 |
sprintf( outName, "%s.dirWhole", outPrefix ); |
| 92 |
outFile = fopen( outName, "w" ); |
| 93 |
|
| 94 |
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 |
|
| 107 |
|
| 108 |
|
| 109 |
fflush(outFile); |
| 110 |
fclose(outFile); |
| 111 |
|
| 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 |
|
| 121 |
free(directorWhole); |
| 122 |
directorWhole = NULL; |
| 123 |
} |
| 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 |
double matWrap[9]; |
| 146 |
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 |
for(m=0;m<3;m++) |
| 192 |
com[m] += atoms[l].mass * atoms[l].pos[m]; |
| 193 |
|
| 194 |
totMass += atoms[l].mass; |
| 195 |
} |
| 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 |
|
| 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 |
|
| 224 |
// 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 |
ifail = 0; |
| 231 |
dsyev(&job, &uplo, &nfilled, matWrap, &ndiag, evals, work, &lWork, &ifail); |
| 232 |
|
| 233 |
if (ifail) { |
| 234 |
fprintf(stderr, "dsyev screwed something up!\n"); |
| 235 |
exit(0); |
| 236 |
} |
| 237 |
|
| 238 |
// matWrap from fortran convention |
| 239 |
|
| 240 |
for(j=0;j<3;j++) |
| 241 |
for(l=0;l<3;l++) |
| 242 |
iMat[l][j] = matWrap[l+3*j]; |
| 243 |
|
| 244 |
// fprintf(stderr, "evals = %6G, %6G, %6G\n\n", |
| 245 |
// evals[0], evals[1], evals[2]); |
| 246 |
|
| 247 |
// 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 |
|
| 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 |
lenPrinc = sqrt( lenPrinc ); |
| 269 |
|
| 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 |
// 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 |
ifail = 0; |
| 305 |
dsyev(&job, &uplo, &nfilled, matWrap, &ndiag, evals, work, &lWork, &ifail); |
| 306 |
|
| 307 |
if (ifail) { |
| 308 |
fprintf(stderr, "dsyev screwed something up!\n"); |
| 309 |
exit(0); |
| 310 |
} |
| 311 |
|
| 312 |
// matWrap from fortran convention |
| 313 |
|
| 314 |
for(j=0;j<3;j++) |
| 315 |
for(l=0;l<3;l++) |
| 316 |
oMat[l][j] = matWrap[l+3*j]; |
| 317 |
|
| 318 |
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 |
// 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 |
|
| 340 |
// fprintf(stdout, |
| 341 |
// "%6g\t%6G\n", |
| 342 |
// directorWhole[index].time, |
| 343 |
// directorWhole[index].order); |
| 344 |
} |
