| 12 |
|
|
| 13 |
|
#include "fortranWrappers.hpp" |
| 14 |
|
|
| 15 |
+ |
#include "MatVec3.h" |
| 16 |
+ |
|
| 17 |
|
#ifdef IS_MPI |
| 18 |
|
#include "mpiSimulation.hpp" |
| 19 |
|
#endif |
| 29 |
|
SimInfo* currentInfo; |
| 30 |
|
|
| 31 |
|
SimInfo::SimInfo(){ |
| 32 |
< |
excludes = NULL; |
| 32 |
> |
|
| 33 |
|
n_constraints = 0; |
| 34 |
|
nZconstraints = 0; |
| 35 |
|
n_oriented = 0; |
| 51 |
|
|
| 52 |
|
resetTime = 1e99; |
| 53 |
|
|
| 54 |
+ |
orthoRhombic = 0; |
| 55 |
|
orthoTolerance = 1E-6; |
| 56 |
|
useInitXSstate = true; |
| 57 |
|
|
| 58 |
|
usePBC = 0; |
| 59 |
|
useLJ = 0; |
| 60 |
|
useSticky = 0; |
| 61 |
< |
useDipole = 0; |
| 61 |
> |
useCharges = 0; |
| 62 |
> |
useDipoles = 0; |
| 63 |
|
useReactionField = 0; |
| 64 |
|
useGB = 0; |
| 65 |
|
useEAM = 0; |
| 66 |
|
|
| 67 |
+ |
excludes = Exclude::Instance(); |
| 68 |
+ |
|
| 69 |
|
myConfiguration = new SimState(); |
| 70 |
|
|
| 71 |
+ |
has_minimizer = false; |
| 72 |
+ |
the_minimizer =NULL; |
| 73 |
+ |
|
| 74 |
|
wrapMeSimInfo( this ); |
| 75 |
|
} |
| 76 |
|
|
| 188 |
|
|
| 189 |
|
if( orthoRhombic ){ |
| 190 |
|
sprintf( painCave.errMsg, |
| 191 |
< |
"Hmat is switching from Non-Orthorhombic to OrthoRhombic\n" |
| 192 |
< |
" If this is a bad thing, change the orthoBoxTolerance( currently %G ).\n", |
| 191 |
> |
"OOPSE is switching from the default Non-Orthorhombic\n" |
| 192 |
> |
"\tto the faster Orthorhombic periodic boundary computations.\n" |
| 193 |
> |
"\tThis is usually a good thing, but if you wan't the\n" |
| 194 |
> |
"\tNon-Orthorhombic computations, make the orthoBoxTolerance\n" |
| 195 |
> |
"\tvariable ( currently set to %G ) smaller.\n", |
| 196 |
|
orthoTolerance); |
| 197 |
|
simError(); |
| 198 |
|
} |
| 199 |
|
else { |
| 200 |
|
sprintf( painCave.errMsg, |
| 201 |
< |
"Hmat is switching from Orthorhombic to Non-OrthoRhombic\n" |
| 202 |
< |
" If this is a bad thing, change the orthoBoxTolerance( currently %G ).\n", |
| 201 |
> |
"OOPSE is switching from the faster Orthorhombic to the more\n" |
| 202 |
> |
"\tflexible Non-Orthorhombic periodic boundary computations.\n" |
| 203 |
> |
"\tThis is usually because the box has deformed under\n" |
| 204 |
> |
"\tNPTf integration. If you wan't to live on the edge with\n" |
| 205 |
> |
"\tthe Orthorhombic computations, make the orthoBoxTolerance\n" |
| 206 |
> |
"\tvariable ( currently set to %G ) larger.\n", |
| 207 |
|
orthoTolerance); |
| 208 |
|
simError(); |
| 209 |
|
} |
| 210 |
|
} |
| 211 |
|
} |
| 212 |
|
|
| 197 |
– |
double SimInfo::matDet3(double a[3][3]) { |
| 198 |
– |
int i, j, k; |
| 199 |
– |
double determinant; |
| 200 |
– |
|
| 201 |
– |
determinant = 0.0; |
| 202 |
– |
|
| 203 |
– |
for(i = 0; i < 3; i++) { |
| 204 |
– |
j = (i+1)%3; |
| 205 |
– |
k = (i+2)%3; |
| 206 |
– |
|
| 207 |
– |
determinant += a[0][i] * (a[1][j]*a[2][k] - a[1][k]*a[2][j]); |
| 208 |
– |
} |
| 209 |
– |
|
| 210 |
– |
return determinant; |
| 211 |
– |
} |
| 212 |
– |
|
| 213 |
– |
void SimInfo::invertMat3(double a[3][3], double b[3][3]) { |
| 214 |
– |
|
| 215 |
– |
int i, j, k, l, m, n; |
| 216 |
– |
double determinant; |
| 217 |
– |
|
| 218 |
– |
determinant = matDet3( a ); |
| 219 |
– |
|
| 220 |
– |
if (determinant == 0.0) { |
| 221 |
– |
sprintf( painCave.errMsg, |
| 222 |
– |
"Can't invert a matrix with a zero determinant!\n"); |
| 223 |
– |
painCave.isFatal = 1; |
| 224 |
– |
simError(); |
| 225 |
– |
} |
| 226 |
– |
|
| 227 |
– |
for (i=0; i < 3; i++) { |
| 228 |
– |
j = (i+1)%3; |
| 229 |
– |
k = (i+2)%3; |
| 230 |
– |
for(l = 0; l < 3; l++) { |
| 231 |
– |
m = (l+1)%3; |
| 232 |
– |
n = (l+2)%3; |
| 233 |
– |
|
| 234 |
– |
b[l][i] = (a[j][m]*a[k][n] - a[j][n]*a[k][m]) / determinant; |
| 235 |
– |
} |
| 236 |
– |
} |
| 237 |
– |
} |
| 238 |
– |
|
| 239 |
– |
void SimInfo::matMul3(double a[3][3], double b[3][3], double c[3][3]) { |
| 240 |
– |
double r00, r01, r02, r10, r11, r12, r20, r21, r22; |
| 241 |
– |
|
| 242 |
– |
r00 = a[0][0]*b[0][0] + a[0][1]*b[1][0] + a[0][2]*b[2][0]; |
| 243 |
– |
r01 = a[0][0]*b[0][1] + a[0][1]*b[1][1] + a[0][2]*b[2][1]; |
| 244 |
– |
r02 = a[0][0]*b[0][2] + a[0][1]*b[1][2] + a[0][2]*b[2][2]; |
| 245 |
– |
|
| 246 |
– |
r10 = a[1][0]*b[0][0] + a[1][1]*b[1][0] + a[1][2]*b[2][0]; |
| 247 |
– |
r11 = a[1][0]*b[0][1] + a[1][1]*b[1][1] + a[1][2]*b[2][1]; |
| 248 |
– |
r12 = a[1][0]*b[0][2] + a[1][1]*b[1][2] + a[1][2]*b[2][2]; |
| 249 |
– |
|
| 250 |
– |
r20 = a[2][0]*b[0][0] + a[2][1]*b[1][0] + a[2][2]*b[2][0]; |
| 251 |
– |
r21 = a[2][0]*b[0][1] + a[2][1]*b[1][1] + a[2][2]*b[2][1]; |
| 252 |
– |
r22 = a[2][0]*b[0][2] + a[2][1]*b[1][2] + a[2][2]*b[2][2]; |
| 253 |
– |
|
| 254 |
– |
c[0][0] = r00; c[0][1] = r01; c[0][2] = r02; |
| 255 |
– |
c[1][0] = r10; c[1][1] = r11; c[1][2] = r12; |
| 256 |
– |
c[2][0] = r20; c[2][1] = r21; c[2][2] = r22; |
| 257 |
– |
} |
| 258 |
– |
|
| 259 |
– |
void SimInfo::matVecMul3(double m[3][3], double inVec[3], double outVec[3]) { |
| 260 |
– |
double a0, a1, a2; |
| 261 |
– |
|
| 262 |
– |
a0 = inVec[0]; a1 = inVec[1]; a2 = inVec[2]; |
| 263 |
– |
|
| 264 |
– |
outVec[0] = m[0][0]*a0 + m[0][1]*a1 + m[0][2]*a2; |
| 265 |
– |
outVec[1] = m[1][0]*a0 + m[1][1]*a1 + m[1][2]*a2; |
| 266 |
– |
outVec[2] = m[2][0]*a0 + m[2][1]*a1 + m[2][2]*a2; |
| 267 |
– |
} |
| 268 |
– |
|
| 269 |
– |
void SimInfo::transposeMat3(double in[3][3], double out[3][3]) { |
| 270 |
– |
double temp[3][3]; |
| 271 |
– |
int i, j; |
| 272 |
– |
|
| 273 |
– |
for (i = 0; i < 3; i++) { |
| 274 |
– |
for (j = 0; j < 3; j++) { |
| 275 |
– |
temp[j][i] = in[i][j]; |
| 276 |
– |
} |
| 277 |
– |
} |
| 278 |
– |
for (i = 0; i < 3; i++) { |
| 279 |
– |
for (j = 0; j < 3; j++) { |
| 280 |
– |
out[i][j] = temp[i][j]; |
| 281 |
– |
} |
| 282 |
– |
} |
| 283 |
– |
} |
| 284 |
– |
|
| 285 |
– |
void SimInfo::printMat3(double A[3][3] ){ |
| 286 |
– |
|
| 287 |
– |
std::cerr |
| 288 |
– |
<< "[ " << A[0][0] << ", " << A[0][1] << ", " << A[0][2] << " ]\n" |
| 289 |
– |
<< "[ " << A[1][0] << ", " << A[1][1] << ", " << A[1][2] << " ]\n" |
| 290 |
– |
<< "[ " << A[2][0] << ", " << A[2][1] << ", " << A[2][2] << " ]\n"; |
| 291 |
– |
} |
| 292 |
– |
|
| 293 |
– |
void SimInfo::printMat9(double A[9] ){ |
| 294 |
– |
|
| 295 |
– |
std::cerr |
| 296 |
– |
<< "[ " << A[0] << ", " << A[1] << ", " << A[2] << " ]\n" |
| 297 |
– |
<< "[ " << A[3] << ", " << A[4] << ", " << A[5] << " ]\n" |
| 298 |
– |
<< "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n"; |
| 299 |
– |
} |
| 300 |
– |
|
| 301 |
– |
|
| 302 |
– |
void SimInfo::crossProduct3(double a[3],double b[3], double out[3]){ |
| 303 |
– |
|
| 304 |
– |
out[0] = a[1] * b[2] - a[2] * b[1]; |
| 305 |
– |
out[1] = a[2] * b[0] - a[0] * b[2] ; |
| 306 |
– |
out[2] = a[0] * b[1] - a[1] * b[0]; |
| 307 |
– |
|
| 308 |
– |
} |
| 309 |
– |
|
| 310 |
– |
double SimInfo::dotProduct3(double a[3], double b[3]){ |
| 311 |
– |
return a[0]*b[0] + a[1]*b[1]+ a[2]*b[2]; |
| 312 |
– |
} |
| 313 |
– |
|
| 314 |
– |
double SimInfo::length3(double a[3]){ |
| 315 |
– |
return sqrt(a[0]*a[0] + a[1]*a[1] + a[2]*a[2]); |
| 316 |
– |
} |
| 317 |
– |
|
| 213 |
|
void SimInfo::calcBoxL( void ){ |
| 214 |
|
|
| 215 |
|
double dx, dy, dz, dsq; |
| 265 |
|
rk[0] = Hmat[0][2]; |
| 266 |
|
rk[1] = Hmat[1][2]; |
| 267 |
|
rk[2] = Hmat[2][2]; |
| 268 |
< |
|
| 269 |
< |
crossProduct3(ri,rj, rij); |
| 270 |
< |
distXY = dotProduct3(rk,rij) / length3(rij); |
| 268 |
> |
|
| 269 |
> |
crossProduct3(ri, rj, rij); |
| 270 |
> |
distXY = dotProduct3(rk,rij) / norm3(rij); |
| 271 |
|
|
| 272 |
|
crossProduct3(rj,rk, rjk); |
| 273 |
< |
distYZ = dotProduct3(ri,rjk) / length3(rjk); |
| 273 |
> |
distYZ = dotProduct3(ri,rjk) / norm3(rjk); |
| 274 |
|
|
| 275 |
|
crossProduct3(rk,ri, rki); |
| 276 |
< |
distZX = dotProduct3(rj,rki) / length3(rki); |
| 276 |
> |
distZX = dotProduct3(rj,rki) / norm3(rki); |
| 277 |
|
|
| 278 |
|
minDist = min(min(distXY, distYZ), distZX); |
| 279 |
|
return minDist/2; |
| 321 |
|
|
| 322 |
|
int SimInfo::getNDF(){ |
| 323 |
|
int ndf_local; |
| 324 |
+ |
|
| 325 |
+ |
ndf_local = 0; |
| 326 |
|
|
| 327 |
< |
ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints; |
| 327 |
> |
for(int i = 0; i < integrableObjects.size(); i++){ |
| 328 |
> |
ndf_local += 3; |
| 329 |
> |
if (integrableObjects[i]->isDirectional()) |
| 330 |
> |
ndf_local += 3; |
| 331 |
> |
} |
| 332 |
|
|
| 333 |
+ |
// n_constraints is local, so subtract them on each processor: |
| 334 |
+ |
|
| 335 |
+ |
ndf_local -= n_constraints; |
| 336 |
+ |
|
| 337 |
|
#ifdef IS_MPI |
| 338 |
|
MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
| 339 |
|
#else |
| 340 |
|
ndf = ndf_local; |
| 341 |
|
#endif |
| 342 |
|
|
| 343 |
+ |
// nZconstraints is global, as are the 3 COM translations for the |
| 344 |
+ |
// entire system: |
| 345 |
+ |
|
| 346 |
|
ndf = ndf - 3 - nZconstraints; |
| 347 |
|
|
| 348 |
|
return ndf; |
| 352 |
|
int ndfRaw_local; |
| 353 |
|
|
| 354 |
|
// Raw degrees of freedom that we have to set |
| 355 |
< |
ndfRaw_local = 3 * n_atoms + 3 * n_oriented; |
| 356 |
< |
|
| 355 |
> |
ndfRaw_local = 0; |
| 356 |
> |
|
| 357 |
> |
for(int i = 0; i < integrableObjects.size(); i++){ |
| 358 |
> |
ndfRaw_local += 3; |
| 359 |
> |
if (integrableObjects[i]->isDirectional()) |
| 360 |
> |
ndfRaw_local += 3; |
| 361 |
> |
} |
| 362 |
> |
|
| 363 |
|
#ifdef IS_MPI |
| 364 |
|
MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
| 365 |
|
#else |
| 372 |
|
int SimInfo::getNDFtranslational() { |
| 373 |
|
int ndfTrans_local; |
| 374 |
|
|
| 375 |
< |
ndfTrans_local = 3 * n_atoms - n_constraints; |
| 375 |
> |
ndfTrans_local = 3 * integrableObjects.size() - n_constraints; |
| 376 |
|
|
| 377 |
+ |
|
| 378 |
|
#ifdef IS_MPI |
| 379 |
|
MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
| 380 |
|
#else |
| 386 |
|
return ndfTrans; |
| 387 |
|
} |
| 388 |
|
|
| 389 |
+ |
int SimInfo::getTotIntegrableObjects() { |
| 390 |
+ |
int nObjs_local; |
| 391 |
+ |
int nObjs; |
| 392 |
+ |
|
| 393 |
+ |
nObjs_local = integrableObjects.size(); |
| 394 |
+ |
|
| 395 |
+ |
|
| 396 |
+ |
#ifdef IS_MPI |
| 397 |
+ |
MPI_Allreduce(&nObjs_local,&nObjs,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
| 398 |
+ |
#else |
| 399 |
+ |
nObjs = nObjs_local; |
| 400 |
+ |
#endif |
| 401 |
+ |
|
| 402 |
+ |
|
| 403 |
+ |
return nObjs; |
| 404 |
+ |
} |
| 405 |
+ |
|
| 406 |
|
void SimInfo::refreshSim(){ |
| 407 |
|
|
| 408 |
|
simtype fInfo; |
| 412 |
|
|
| 413 |
|
fInfo.dielect = 0.0; |
| 414 |
|
|
| 415 |
< |
if( useDipole ){ |
| 415 |
> |
if( useDipoles ){ |
| 416 |
|
if( useReactionField )fInfo.dielect = dielectric; |
| 417 |
|
} |
| 418 |
|
|
| 421 |
|
fInfo.SIM_uses_LJ = useLJ; |
| 422 |
|
fInfo.SIM_uses_sticky = useSticky; |
| 423 |
|
//fInfo.SIM_uses_sticky = 0; |
| 424 |
< |
fInfo.SIM_uses_dipoles = useDipole; |
| 424 |
> |
fInfo.SIM_uses_charges = useCharges; |
| 425 |
> |
fInfo.SIM_uses_dipoles = useDipoles; |
| 426 |
|
//fInfo.SIM_uses_dipoles = 0; |
| 427 |
< |
//fInfo.SIM_uses_RF = useReactionField; |
| 428 |
< |
fInfo.SIM_uses_RF = 0; |
| 427 |
> |
fInfo.SIM_uses_RF = useReactionField; |
| 428 |
> |
//fInfo.SIM_uses_RF = 0; |
| 429 |
|
fInfo.SIM_uses_GB = useGB; |
| 430 |
|
fInfo.SIM_uses_EAM = useEAM; |
| 431 |
|
|
| 432 |
< |
excl = Exclude::getArray(); |
| 432 |
> |
n_exclude = excludes->getSize(); |
| 433 |
> |
excl = excludes->getFortranArray(); |
| 434 |
|
|
| 435 |
|
#ifdef IS_MPI |
| 436 |
|
n_global = mpiSim->getTotAtoms(); |
| 498 |
|
|
| 499 |
|
if( rCut > maxCutoff ){ |
| 500 |
|
sprintf( painCave.errMsg, |
| 501 |
< |
"Box size is too small for the long range cutoff radius, " |
| 502 |
< |
"%lf, at time %lf\n", |
| 503 |
< |
rCut, currentTime ); |
| 501 |
> |
"LJrcut is too large for the current periodic box.\n" |
| 502 |
> |
"\tCurrent Value of LJrcut = %G at time %G\n " |
| 503 |
> |
"\tThis is larger than half of at least one of the\n" |
| 504 |
> |
"\tperiodic box vectors. Right now, the Box matrix is:\n" |
| 505 |
> |
"\n, %G" |
| 506 |
> |
"\t[ %G %G %G ]\n" |
| 507 |
> |
"\t[ %G %G %G ]\n" |
| 508 |
> |
"\t[ %G %G %G ]\n", |
| 509 |
> |
rCut, currentTime, maxCutoff, |
| 510 |
> |
Hmat[0][0], Hmat[0][1], Hmat[0][2], |
| 511 |
> |
Hmat[1][0], Hmat[1][1], Hmat[1][2], |
| 512 |
> |
Hmat[2][0], Hmat[2][1], Hmat[2][2]); |
| 513 |
|
painCave.isFatal = 1; |
| 514 |
|
simError(); |
| 515 |
|
} |
| 517 |
|
if( haveEcr ){ |
| 518 |
|
if( ecr > maxCutoff ){ |
| 519 |
|
sprintf( painCave.errMsg, |
| 520 |
< |
"Box size is too small for the electrostatic cutoff radius, " |
| 521 |
< |
"%lf, at time %lf\n", |
| 522 |
< |
ecr, currentTime ); |
| 520 |
> |
"electrostaticCutoffRadius is too large for the current\n" |
| 521 |
> |
"\tperiodic box.\n\n" |
| 522 |
> |
"\tCurrent Value of ECR = %G at time %G\n " |
| 523 |
> |
"\tThis is larger than half of at least one of the\n" |
| 524 |
> |
"\tperiodic box vectors. Right now, the Box matrix is:\n" |
| 525 |
> |
"\n" |
| 526 |
> |
"\t[ %G %G %G ]\n" |
| 527 |
> |
"\t[ %G %G %G ]\n" |
| 528 |
> |
"\t[ %G %G %G ]\n", |
| 529 |
> |
ecr, currentTime, |
| 530 |
> |
Hmat[0][0], Hmat[0][1], Hmat[0][2], |
| 531 |
> |
Hmat[1][0], Hmat[1][1], Hmat[1][2], |
| 532 |
> |
Hmat[2][0], Hmat[2][1], Hmat[2][2]); |
| 533 |
|
painCave.isFatal = 1; |
| 534 |
|
simError(); |
| 535 |
|
} |
| 537 |
|
} else { |
| 538 |
|
// initialize this stuff before using it, OK? |
| 539 |
|
sprintf( painCave.errMsg, |
| 540 |
< |
"Trying to check cutoffs without a box. Be smarter.\n" ); |
| 540 |
> |
"Trying to check cutoffs without a box.\n" |
| 541 |
> |
"\tOOPSE should have better programmers than that.\n" ); |
| 542 |
|
painCave.isFatal = 1; |
| 543 |
|
simError(); |
| 544 |
|
} |
| 591 |
|
|
| 592 |
|
return result; |
| 593 |
|
} |
| 640 |
– |
|
| 641 |
– |
double SimInfo::matTrace3(double m[3][3]){ |
| 642 |
– |
double trace; |
| 643 |
– |
trace = m[0][0] + m[1][1] + m[2][2]; |
| 644 |
– |
|
| 645 |
– |
return trace; |
| 646 |
– |
} |
