| 1 |
#include <cstdlib> |
| 2 |
#include <cstring> |
| 3 |
#include <cmath> |
| 4 |
|
| 5 |
#include <iostream> |
| 6 |
using namespace std; |
| 7 |
|
| 8 |
#include "SimInfo.hpp" |
| 9 |
#define __C |
| 10 |
#include "fSimulation.h" |
| 11 |
#include "simError.h" |
| 12 |
|
| 13 |
#include "fortranWrappers.hpp" |
| 14 |
|
| 15 |
#ifdef IS_MPI |
| 16 |
#include "mpiSimulation.hpp" |
| 17 |
#endif |
| 18 |
|
| 19 |
inline double roundMe( double x ){ |
| 20 |
return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 ); |
| 21 |
} |
| 22 |
|
| 23 |
|
| 24 |
SimInfo* currentInfo; |
| 25 |
|
| 26 |
SimInfo::SimInfo(){ |
| 27 |
excludes = NULL; |
| 28 |
n_constraints = 0; |
| 29 |
n_oriented = 0; |
| 30 |
n_dipoles = 0; |
| 31 |
ndf = 0; |
| 32 |
ndfRaw = 0; |
| 33 |
the_integrator = NULL; |
| 34 |
setTemp = 0; |
| 35 |
thermalTime = 0.0; |
| 36 |
rCut = 0.0; |
| 37 |
ecr = 0.0; |
| 38 |
est = 0.0; |
| 39 |
|
| 40 |
usePBC = 0; |
| 41 |
useLJ = 0; |
| 42 |
useSticky = 0; |
| 43 |
useDipole = 0; |
| 44 |
useReactionField = 0; |
| 45 |
useGB = 0; |
| 46 |
useEAM = 0; |
| 47 |
|
| 48 |
wrapMeSimInfo( this ); |
| 49 |
} |
| 50 |
|
| 51 |
void SimInfo::setBox(double newBox[3]) { |
| 52 |
|
| 53 |
int i, j; |
| 54 |
double tempMat[3][3]; |
| 55 |
|
| 56 |
for(i=0; i<3; i++) |
| 57 |
for (j=0; j<3; j++) tempMat[i][j] = 0.0;; |
| 58 |
|
| 59 |
tempMat[0][0] = newBox[0]; |
| 60 |
tempMat[1][1] = newBox[1]; |
| 61 |
tempMat[2][2] = newBox[2]; |
| 62 |
|
| 63 |
setBoxM( tempMat ); |
| 64 |
|
| 65 |
} |
| 66 |
|
| 67 |
void SimInfo::setBoxM( double theBox[3][3] ){ |
| 68 |
|
| 69 |
int i, j, status; |
| 70 |
double smallestBoxL, maxCutoff; |
| 71 |
double FortranHmat[9]; // to preserve compatibility with Fortran the |
| 72 |
// ordering in the array is as follows: |
| 73 |
// [ 0 3 6 ] |
| 74 |
// [ 1 4 7 ] |
| 75 |
// [ 2 5 8 ] |
| 76 |
double FortranHmatInv[9]; // the inverted Hmat (for Fortran); |
| 77 |
|
| 78 |
|
| 79 |
for(i=0; i < 3; i++) |
| 80 |
for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j]; |
| 81 |
|
| 82 |
// cerr |
| 83 |
// << "setting Hmat ->\n" |
| 84 |
// << "[ " << Hmat[0][0] << ", " << Hmat[0][1] << ", " << Hmat[0][2] << " ]\n" |
| 85 |
// << "[ " << Hmat[1][0] << ", " << Hmat[1][1] << ", " << Hmat[1][2] << " ]\n" |
| 86 |
// << "[ " << Hmat[2][0] << ", " << Hmat[2][1] << ", " << Hmat[2][2] << " ]\n"; |
| 87 |
|
| 88 |
calcBoxL(); |
| 89 |
calcHmatInv(); |
| 90 |
|
| 91 |
for(i=0; i < 3; i++) { |
| 92 |
for (j=0; j < 3; j++) { |
| 93 |
FortranHmat[3*j + i] = Hmat[i][j]; |
| 94 |
FortranHmatInv[3*j + i] = HmatInv[i][j]; |
| 95 |
} |
| 96 |
} |
| 97 |
|
| 98 |
setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic); |
| 99 |
|
| 100 |
smallestBoxL = boxL[0]; |
| 101 |
if (boxL[1] < smallestBoxL) smallestBoxL = boxL[1]; |
| 102 |
if (boxL[2] > smallestBoxL) smallestBoxL = boxL[2]; |
| 103 |
|
| 104 |
maxCutoff = smallestBoxL / 2.0; |
| 105 |
|
| 106 |
if (rList > maxCutoff) { |
| 107 |
sprintf( painCave.errMsg, |
| 108 |
"New Box size is forcing neighborlist radius down to %lf\n", |
| 109 |
maxCutoff ); |
| 110 |
painCave.isFatal = 0; |
| 111 |
simError(); |
| 112 |
rList = maxCutoff; |
| 113 |
|
| 114 |
if (rCut > (rList - 1.0)) { |
| 115 |
sprintf( painCave.errMsg, |
| 116 |
"New Box size is forcing LJ cutoff radius down to %lf\n", |
| 117 |
rList - 1.0 ); |
| 118 |
painCave.isFatal = 0; |
| 119 |
simError(); |
| 120 |
rCut = rList - 1.0; |
| 121 |
} |
| 122 |
|
| 123 |
if( ecr > (rList - 1.0) ){ |
| 124 |
sprintf( painCave.errMsg, |
| 125 |
"New Box size is forcing electrostaticCutoffRadius " |
| 126 |
"down to %lf\n" |
| 127 |
"electrostaticSkinThickness is now %lf\n", |
| 128 |
rList - 1.0, 0.05*(rList-1.0) ); |
| 129 |
painCave.isFatal = 0; |
| 130 |
simError(); |
| 131 |
ecr = maxCutoff; |
| 132 |
est = 0.05 * ecr; |
| 133 |
} |
| 134 |
|
| 135 |
// At least one of the radii changed, so we need a refresh: |
| 136 |
refreshSim(); |
| 137 |
} |
| 138 |
} |
| 139 |
|
| 140 |
|
| 141 |
void SimInfo::getBoxM (double theBox[3][3]) { |
| 142 |
|
| 143 |
int i, j; |
| 144 |
for(i=0; i<3; i++) |
| 145 |
for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]; |
| 146 |
} |
| 147 |
|
| 148 |
|
| 149 |
void SimInfo::scaleBox(double scale) { |
| 150 |
double theBox[3][3]; |
| 151 |
int i, j; |
| 152 |
|
| 153 |
// cerr << "Scaling box by " << scale << "\n"; |
| 154 |
|
| 155 |
for(i=0; i<3; i++) |
| 156 |
for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale; |
| 157 |
|
| 158 |
setBoxM(theBox); |
| 159 |
|
| 160 |
} |
| 161 |
|
| 162 |
void SimInfo::calcHmatInv( void ) { |
| 163 |
|
| 164 |
int i,j; |
| 165 |
double smallDiag; |
| 166 |
double tol; |
| 167 |
double sanity[3][3]; |
| 168 |
|
| 169 |
invertMat3( Hmat, HmatInv ); |
| 170 |
|
| 171 |
// Check the inverse to make sure it is sane: |
| 172 |
|
| 173 |
matMul3( Hmat, HmatInv, sanity ); |
| 174 |
|
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// check to see if Hmat is orthorhombic |
| 176 |
|
| 177 |
smallDiag = Hmat[0][0]; |
| 178 |
if(smallDiag > Hmat[1][1]) smallDiag = Hmat[1][1]; |
| 179 |
if(smallDiag > Hmat[2][2]) smallDiag = Hmat[2][2]; |
| 180 |
tol = smallDiag * 1E-6; |
| 181 |
|
| 182 |
orthoRhombic = 1; |
| 183 |
|
| 184 |
for (i = 0; i < 3; i++ ) { |
| 185 |
for (j = 0 ; j < 3; j++) { |
| 186 |
if (i != j) { |
| 187 |
if (orthoRhombic) { |
| 188 |
if (Hmat[i][j] >= tol) orthoRhombic = 0; |
| 189 |
} |
| 190 |
} |
| 191 |
} |
| 192 |
} |
| 193 |
} |
| 194 |
|
| 195 |
double SimInfo::matDet3(double a[3][3]) { |
| 196 |
int i, j, k; |
| 197 |
double determinant; |
| 198 |
|
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determinant = 0.0; |
| 200 |
|
| 201 |
for(i = 0; i < 3; i++) { |
| 202 |
j = (i+1)%3; |
| 203 |
k = (i+2)%3; |
| 204 |
|
| 205 |
determinant += a[0][i] * (a[1][j]*a[2][k] - a[1][k]*a[2][j]); |
| 206 |
} |
| 207 |
|
| 208 |
return determinant; |
| 209 |
} |
| 210 |
|
| 211 |
void SimInfo::invertMat3(double a[3][3], double b[3][3]) { |
| 212 |
|
| 213 |
int i, j, k, l, m, n; |
| 214 |
double determinant; |
| 215 |
|
| 216 |
determinant = matDet3( a ); |
| 217 |
|
| 218 |
if (determinant == 0.0) { |
| 219 |
sprintf( painCave.errMsg, |
| 220 |
"Can't invert a matrix with a zero determinant!\n"); |
| 221 |
painCave.isFatal = 1; |
| 222 |
simError(); |
| 223 |
} |
| 224 |
|
| 225 |
for (i=0; i < 3; i++) { |
| 226 |
j = (i+1)%3; |
| 227 |
k = (i+2)%3; |
| 228 |
for(l = 0; l < 3; l++) { |
| 229 |
m = (l+1)%3; |
| 230 |
n = (l+2)%3; |
| 231 |
|
| 232 |
b[l][i] = (a[j][m]*a[k][n] - a[j][n]*a[k][m]) / determinant; |
| 233 |
} |
| 234 |
} |
| 235 |
} |
| 236 |
|
| 237 |
void SimInfo::matMul3(double a[3][3], double b[3][3], double c[3][3]) { |
| 238 |
double r00, r01, r02, r10, r11, r12, r20, r21, r22; |
| 239 |
|
| 240 |
r00 = a[0][0]*b[0][0] + a[0][1]*b[1][0] + a[0][2]*b[2][0]; |
| 241 |
r01 = a[0][0]*b[0][1] + a[0][1]*b[1][1] + a[0][2]*b[2][1]; |
| 242 |
r02 = a[0][0]*b[0][2] + a[0][1]*b[1][2] + a[0][2]*b[2][2]; |
| 243 |
|
| 244 |
r10 = a[1][0]*b[0][0] + a[1][1]*b[1][0] + a[1][2]*b[2][0]; |
| 245 |
r11 = a[1][0]*b[0][1] + a[1][1]*b[1][1] + a[1][2]*b[2][1]; |
| 246 |
r12 = a[1][0]*b[0][2] + a[1][1]*b[1][2] + a[1][2]*b[2][2]; |
| 247 |
|
| 248 |
r20 = a[2][0]*b[0][0] + a[2][1]*b[1][0] + a[2][2]*b[2][0]; |
| 249 |
r21 = a[2][0]*b[0][1] + a[2][1]*b[1][1] + a[2][2]*b[2][1]; |
| 250 |
r22 = a[2][0]*b[0][2] + a[2][1]*b[1][2] + a[2][2]*b[2][2]; |
| 251 |
|
| 252 |
c[0][0] = r00; c[0][1] = r01; c[0][2] = r02; |
| 253 |
c[1][0] = r10; c[1][1] = r11; c[1][2] = r12; |
| 254 |
c[2][0] = r20; c[2][1] = r21; c[2][2] = r22; |
| 255 |
} |
| 256 |
|
| 257 |
void SimInfo::matVecMul3(double m[3][3], double inVec[3], double outVec[3]) { |
| 258 |
double a0, a1, a2; |
| 259 |
|
| 260 |
a0 = inVec[0]; a1 = inVec[1]; a2 = inVec[2]; |
| 261 |
|
| 262 |
outVec[0] = m[0][0]*a0 + m[0][1]*a1 + m[0][2]*a2; |
| 263 |
outVec[1] = m[1][0]*a0 + m[1][1]*a1 + m[1][2]*a2; |
| 264 |
outVec[2] = m[2][0]*a0 + m[2][1]*a1 + m[2][2]*a2; |
| 265 |
} |
| 266 |
|
| 267 |
void SimInfo::transposeMat3(double in[3][3], double out[3][3]) { |
| 268 |
double temp[3][3]; |
| 269 |
int i, j; |
| 270 |
|
| 271 |
for (i = 0; i < 3; i++) { |
| 272 |
for (j = 0; j < 3; j++) { |
| 273 |
temp[j][i] = in[i][j]; |
| 274 |
} |
| 275 |
} |
| 276 |
for (i = 0; i < 3; i++) { |
| 277 |
for (j = 0; j < 3; j++) { |
| 278 |
out[i][j] = temp[i][j]; |
| 279 |
} |
| 280 |
} |
| 281 |
} |
| 282 |
|
| 283 |
void SimInfo::printMat3(double A[3][3] ){ |
| 284 |
|
| 285 |
std::cerr |
| 286 |
<< "[ " << A[0][0] << ", " << A[0][1] << ", " << A[0][2] << " ]\n" |
| 287 |
<< "[ " << A[1][0] << ", " << A[1][1] << ", " << A[1][2] << " ]\n" |
| 288 |
<< "[ " << A[2][0] << ", " << A[2][1] << ", " << A[2][2] << " ]\n"; |
| 289 |
} |
| 290 |
|
| 291 |
void SimInfo::printMat9(double A[9] ){ |
| 292 |
|
| 293 |
std::cerr |
| 294 |
<< "[ " << A[0] << ", " << A[1] << ", " << A[2] << " ]\n" |
| 295 |
<< "[ " << A[3] << ", " << A[4] << ", " << A[5] << " ]\n" |
| 296 |
<< "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n"; |
| 297 |
} |
| 298 |
|
| 299 |
void SimInfo::calcBoxL( void ){ |
| 300 |
|
| 301 |
double dx, dy, dz, dsq; |
| 302 |
int i; |
| 303 |
|
| 304 |
// boxVol = Determinant of Hmat |
| 305 |
|
| 306 |
boxVol = matDet3( Hmat ); |
| 307 |
|
| 308 |
// boxLx |
| 309 |
|
| 310 |
dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0]; |
| 311 |
dsq = dx*dx + dy*dy + dz*dz; |
| 312 |
boxL[0] = sqrt( dsq ); |
| 313 |
|
| 314 |
// boxLy |
| 315 |
|
| 316 |
dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1]; |
| 317 |
dsq = dx*dx + dy*dy + dz*dz; |
| 318 |
boxL[1] = sqrt( dsq ); |
| 319 |
|
| 320 |
// boxLz |
| 321 |
|
| 322 |
dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2]; |
| 323 |
dsq = dx*dx + dy*dy + dz*dz; |
| 324 |
boxL[2] = sqrt( dsq ); |
| 325 |
|
| 326 |
} |
| 327 |
|
| 328 |
|
| 329 |
void SimInfo::wrapVector( double thePos[3] ){ |
| 330 |
|
| 331 |
int i, j, k; |
| 332 |
double scaled[3]; |
| 333 |
|
| 334 |
if( !orthoRhombic ){ |
| 335 |
// calc the scaled coordinates. |
| 336 |
|
| 337 |
|
| 338 |
matVecMul3(HmatInv, thePos, scaled); |
| 339 |
|
| 340 |
for(i=0; i<3; i++) |
| 341 |
scaled[i] -= roundMe(scaled[i]); |
| 342 |
|
| 343 |
// calc the wrapped real coordinates from the wrapped scaled coordinates |
| 344 |
|
| 345 |
matVecMul3(Hmat, scaled, thePos); |
| 346 |
|
| 347 |
} |
| 348 |
else{ |
| 349 |
// calc the scaled coordinates. |
| 350 |
|
| 351 |
for(i=0; i<3; i++) |
| 352 |
scaled[i] = thePos[i]*HmatInv[i][i]; |
| 353 |
|
| 354 |
// wrap the scaled coordinates |
| 355 |
|
| 356 |
for(i=0; i<3; i++) |
| 357 |
scaled[i] -= roundMe(scaled[i]); |
| 358 |
|
| 359 |
// calc the wrapped real coordinates from the wrapped scaled coordinates |
| 360 |
|
| 361 |
for(i=0; i<3; i++) |
| 362 |
thePos[i] = scaled[i]*Hmat[i][i]; |
| 363 |
} |
| 364 |
|
| 365 |
} |
| 366 |
|
| 367 |
|
| 368 |
int SimInfo::getNDF(){ |
| 369 |
int ndf_local, ndf; |
| 370 |
|
| 371 |
ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints; |
| 372 |
|
| 373 |
#ifdef IS_MPI |
| 374 |
MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
| 375 |
#else |
| 376 |
ndf = ndf_local; |
| 377 |
#endif |
| 378 |
|
| 379 |
ndf = ndf - 3; |
| 380 |
|
| 381 |
return ndf; |
| 382 |
} |
| 383 |
|
| 384 |
int SimInfo::getNDFraw() { |
| 385 |
int ndfRaw_local, ndfRaw; |
| 386 |
|
| 387 |
// Raw degrees of freedom that we have to set |
| 388 |
ndfRaw_local = 3 * n_atoms + 3 * n_oriented; |
| 389 |
|
| 390 |
#ifdef IS_MPI |
| 391 |
MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
| 392 |
#else |
| 393 |
ndfRaw = ndfRaw_local; |
| 394 |
#endif |
| 395 |
|
| 396 |
return ndfRaw; |
| 397 |
} |
| 398 |
|
| 399 |
void SimInfo::refreshSim(){ |
| 400 |
|
| 401 |
simtype fInfo; |
| 402 |
int isError; |
| 403 |
int n_global; |
| 404 |
int* excl; |
| 405 |
|
| 406 |
fInfo.rrf = 0.0; |
| 407 |
fInfo.rt = 0.0; |
| 408 |
fInfo.dielect = 0.0; |
| 409 |
|
| 410 |
fInfo.rlist = rList; |
| 411 |
fInfo.rcut = rCut; |
| 412 |
|
| 413 |
if( useDipole ){ |
| 414 |
fInfo.rrf = ecr; |
| 415 |
fInfo.rt = ecr - est; |
| 416 |
if( useReactionField )fInfo.dielect = dielectric; |
| 417 |
} |
| 418 |
|
| 419 |
fInfo.SIM_uses_PBC = usePBC; |
| 420 |
//fInfo.SIM_uses_LJ = 0; |
| 421 |
fInfo.SIM_uses_LJ = useLJ; |
| 422 |
fInfo.SIM_uses_sticky = useSticky; |
| 423 |
//fInfo.SIM_uses_sticky = 0; |
| 424 |
fInfo.SIM_uses_dipoles = useDipole; |
| 425 |
//fInfo.SIM_uses_dipoles = 0; |
| 426 |
//fInfo.SIM_uses_RF = useReactionField; |
| 427 |
fInfo.SIM_uses_RF = 0; |
| 428 |
fInfo.SIM_uses_GB = useGB; |
| 429 |
fInfo.SIM_uses_EAM = useEAM; |
| 430 |
|
| 431 |
excl = Exclude::getArray(); |
| 432 |
|
| 433 |
#ifdef IS_MPI |
| 434 |
n_global = mpiSim->getTotAtoms(); |
| 435 |
#else |
| 436 |
n_global = n_atoms; |
| 437 |
#endif |
| 438 |
|
| 439 |
isError = 0; |
| 440 |
|
| 441 |
setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl, |
| 442 |
&nGlobalExcludes, globalExcludes, molMembershipArray, |
| 443 |
&isError ); |
| 444 |
|
| 445 |
if( isError ){ |
| 446 |
|
| 447 |
sprintf( painCave.errMsg, |
| 448 |
"There was an error setting the simulation information in fortran.\n" ); |
| 449 |
painCave.isFatal = 1; |
| 450 |
simError(); |
| 451 |
} |
| 452 |
|
| 453 |
#ifdef IS_MPI |
| 454 |
sprintf( checkPointMsg, |
| 455 |
"succesfully sent the simulation information to fortran.\n"); |
| 456 |
MPIcheckPoint(); |
| 457 |
#endif // is_mpi |
| 458 |
|
| 459 |
this->ndf = this->getNDF(); |
| 460 |
this->ndfRaw = this->getNDFraw(); |
| 461 |
|
| 462 |
} |
| 463 |
|
