12 |
|
|
13 |
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#include "fortranWrappers.hpp" |
14 |
|
|
15 |
+ |
#include "MatVec3.h" |
16 |
+ |
|
17 |
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#ifdef IS_MPI |
18 |
|
#include "mpiSimulation.hpp" |
19 |
|
#endif |
29 |
|
SimInfo* currentInfo; |
30 |
|
|
31 |
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SimInfo::SimInfo(){ |
32 |
< |
excludes = NULL; |
32 |
> |
|
33 |
|
n_constraints = 0; |
34 |
|
nZconstraints = 0; |
35 |
|
n_oriented = 0; |
51 |
|
|
52 |
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resetTime = 1e99; |
53 |
|
|
54 |
+ |
orthoRhombic = 0; |
55 |
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orthoTolerance = 1E-6; |
56 |
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useInitXSstate = true; |
57 |
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|
63 |
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useReactionField = 0; |
64 |
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useGB = 0; |
65 |
|
useEAM = 0; |
66 |
+ |
useMolecularCutoffs = 0; |
67 |
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|
68 |
+ |
excludes = Exclude::Instance(); |
69 |
+ |
|
70 |
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myConfiguration = new SimState(); |
71 |
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|
72 |
+ |
has_minimizer = false; |
73 |
+ |
the_minimizer =NULL; |
74 |
+ |
|
75 |
+ |
ngroup = 0; |
76 |
+ |
|
77 |
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wrapMeSimInfo( this ); |
78 |
|
} |
79 |
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|
86 |
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|
87 |
|
for(i = properties.begin(); i != properties.end(); i++) |
88 |
|
delete (*i).second; |
89 |
< |
|
89 |
> |
|
90 |
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} |
91 |
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|
92 |
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void SimInfo::setBox(double newBox[3]) { |
191 |
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|
192 |
|
if( orthoRhombic ){ |
193 |
|
sprintf( painCave.errMsg, |
194 |
< |
"Hmat is switching from Non-Orthorhombic to Orthorhombic Box.\n" |
195 |
< |
"\tIf this is a bad thing, change the orthoBoxTolerance\n" |
196 |
< |
"\tvariable ( currently set to %G ).\n", |
194 |
> |
"OOPSE is switching from the default Non-Orthorhombic\n" |
195 |
> |
"\tto the faster Orthorhombic periodic boundary computations.\n" |
196 |
> |
"\tThis is usually a good thing, but if you wan't the\n" |
197 |
> |
"\tNon-Orthorhombic computations, make the orthoBoxTolerance\n" |
198 |
> |
"\tvariable ( currently set to %G ) smaller.\n", |
199 |
|
orthoTolerance); |
200 |
|
simError(); |
201 |
|
} |
202 |
|
else { |
203 |
|
sprintf( painCave.errMsg, |
204 |
< |
"Hmat is switching from Orthorhombic to Non-Orthorhombic Box.\n" |
205 |
< |
"\tIf this is a bad thing, change the orthoBoxTolerance\n" |
206 |
< |
"\tvariable ( currently set to %G ).\n", |
204 |
> |
"OOPSE is switching from the faster Orthorhombic to the more\n" |
205 |
> |
"\tflexible Non-Orthorhombic periodic boundary computations.\n" |
206 |
> |
"\tThis is usually because the box has deformed under\n" |
207 |
> |
"\tNPTf integration. If you wan't to live on the edge with\n" |
208 |
> |
"\tthe Orthorhombic computations, make the orthoBoxTolerance\n" |
209 |
> |
"\tvariable ( currently set to %G ) larger.\n", |
210 |
|
orthoTolerance); |
211 |
|
simError(); |
212 |
|
} |
213 |
|
} |
214 |
|
} |
215 |
|
|
200 |
– |
double SimInfo::matDet3(double a[3][3]) { |
201 |
– |
int i, j, k; |
202 |
– |
double determinant; |
203 |
– |
|
204 |
– |
determinant = 0.0; |
205 |
– |
|
206 |
– |
for(i = 0; i < 3; i++) { |
207 |
– |
j = (i+1)%3; |
208 |
– |
k = (i+2)%3; |
209 |
– |
|
210 |
– |
determinant += a[0][i] * (a[1][j]*a[2][k] - a[1][k]*a[2][j]); |
211 |
– |
} |
212 |
– |
|
213 |
– |
return determinant; |
214 |
– |
} |
215 |
– |
|
216 |
– |
void SimInfo::invertMat3(double a[3][3], double b[3][3]) { |
217 |
– |
|
218 |
– |
int i, j, k, l, m, n; |
219 |
– |
double determinant; |
220 |
– |
|
221 |
– |
determinant = matDet3( a ); |
222 |
– |
|
223 |
– |
if (determinant == 0.0) { |
224 |
– |
sprintf( painCave.errMsg, |
225 |
– |
"Can't invert a matrix with a zero determinant!\n"); |
226 |
– |
painCave.isFatal = 1; |
227 |
– |
simError(); |
228 |
– |
} |
229 |
– |
|
230 |
– |
for (i=0; i < 3; i++) { |
231 |
– |
j = (i+1)%3; |
232 |
– |
k = (i+2)%3; |
233 |
– |
for(l = 0; l < 3; l++) { |
234 |
– |
m = (l+1)%3; |
235 |
– |
n = (l+2)%3; |
236 |
– |
|
237 |
– |
b[l][i] = (a[j][m]*a[k][n] - a[j][n]*a[k][m]) / determinant; |
238 |
– |
} |
239 |
– |
} |
240 |
– |
} |
241 |
– |
|
242 |
– |
void SimInfo::matMul3(double a[3][3], double b[3][3], double c[3][3]) { |
243 |
– |
double r00, r01, r02, r10, r11, r12, r20, r21, r22; |
244 |
– |
|
245 |
– |
r00 = a[0][0]*b[0][0] + a[0][1]*b[1][0] + a[0][2]*b[2][0]; |
246 |
– |
r01 = a[0][0]*b[0][1] + a[0][1]*b[1][1] + a[0][2]*b[2][1]; |
247 |
– |
r02 = a[0][0]*b[0][2] + a[0][1]*b[1][2] + a[0][2]*b[2][2]; |
248 |
– |
|
249 |
– |
r10 = a[1][0]*b[0][0] + a[1][1]*b[1][0] + a[1][2]*b[2][0]; |
250 |
– |
r11 = a[1][0]*b[0][1] + a[1][1]*b[1][1] + a[1][2]*b[2][1]; |
251 |
– |
r12 = a[1][0]*b[0][2] + a[1][1]*b[1][2] + a[1][2]*b[2][2]; |
252 |
– |
|
253 |
– |
r20 = a[2][0]*b[0][0] + a[2][1]*b[1][0] + a[2][2]*b[2][0]; |
254 |
– |
r21 = a[2][0]*b[0][1] + a[2][1]*b[1][1] + a[2][2]*b[2][1]; |
255 |
– |
r22 = a[2][0]*b[0][2] + a[2][1]*b[1][2] + a[2][2]*b[2][2]; |
256 |
– |
|
257 |
– |
c[0][0] = r00; c[0][1] = r01; c[0][2] = r02; |
258 |
– |
c[1][0] = r10; c[1][1] = r11; c[1][2] = r12; |
259 |
– |
c[2][0] = r20; c[2][1] = r21; c[2][2] = r22; |
260 |
– |
} |
261 |
– |
|
262 |
– |
void SimInfo::matVecMul3(double m[3][3], double inVec[3], double outVec[3]) { |
263 |
– |
double a0, a1, a2; |
264 |
– |
|
265 |
– |
a0 = inVec[0]; a1 = inVec[1]; a2 = inVec[2]; |
266 |
– |
|
267 |
– |
outVec[0] = m[0][0]*a0 + m[0][1]*a1 + m[0][2]*a2; |
268 |
– |
outVec[1] = m[1][0]*a0 + m[1][1]*a1 + m[1][2]*a2; |
269 |
– |
outVec[2] = m[2][0]*a0 + m[2][1]*a1 + m[2][2]*a2; |
270 |
– |
} |
271 |
– |
|
272 |
– |
void SimInfo::transposeMat3(double in[3][3], double out[3][3]) { |
273 |
– |
double temp[3][3]; |
274 |
– |
int i, j; |
275 |
– |
|
276 |
– |
for (i = 0; i < 3; i++) { |
277 |
– |
for (j = 0; j < 3; j++) { |
278 |
– |
temp[j][i] = in[i][j]; |
279 |
– |
} |
280 |
– |
} |
281 |
– |
for (i = 0; i < 3; i++) { |
282 |
– |
for (j = 0; j < 3; j++) { |
283 |
– |
out[i][j] = temp[i][j]; |
284 |
– |
} |
285 |
– |
} |
286 |
– |
} |
287 |
– |
|
288 |
– |
void SimInfo::printMat3(double A[3][3] ){ |
289 |
– |
|
290 |
– |
std::cerr |
291 |
– |
<< "[ " << A[0][0] << ", " << A[0][1] << ", " << A[0][2] << " ]\n" |
292 |
– |
<< "[ " << A[1][0] << ", " << A[1][1] << ", " << A[1][2] << " ]\n" |
293 |
– |
<< "[ " << A[2][0] << ", " << A[2][1] << ", " << A[2][2] << " ]\n"; |
294 |
– |
} |
295 |
– |
|
296 |
– |
void SimInfo::printMat9(double A[9] ){ |
297 |
– |
|
298 |
– |
std::cerr |
299 |
– |
<< "[ " << A[0] << ", " << A[1] << ", " << A[2] << " ]\n" |
300 |
– |
<< "[ " << A[3] << ", " << A[4] << ", " << A[5] << " ]\n" |
301 |
– |
<< "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n"; |
302 |
– |
} |
303 |
– |
|
304 |
– |
|
305 |
– |
void SimInfo::crossProduct3(double a[3],double b[3], double out[3]){ |
306 |
– |
|
307 |
– |
out[0] = a[1] * b[2] - a[2] * b[1]; |
308 |
– |
out[1] = a[2] * b[0] - a[0] * b[2] ; |
309 |
– |
out[2] = a[0] * b[1] - a[1] * b[0]; |
310 |
– |
|
311 |
– |
} |
312 |
– |
|
313 |
– |
double SimInfo::dotProduct3(double a[3], double b[3]){ |
314 |
– |
return a[0]*b[0] + a[1]*b[1]+ a[2]*b[2]; |
315 |
– |
} |
316 |
– |
|
317 |
– |
double SimInfo::length3(double a[3]){ |
318 |
– |
return sqrt(a[0]*a[0] + a[1]*a[1] + a[2]*a[2]); |
319 |
– |
} |
320 |
– |
|
216 |
|
void SimInfo::calcBoxL( void ){ |
217 |
|
|
218 |
|
double dx, dy, dz, dsq; |
268 |
|
rk[0] = Hmat[0][2]; |
269 |
|
rk[1] = Hmat[1][2]; |
270 |
|
rk[2] = Hmat[2][2]; |
271 |
< |
|
272 |
< |
crossProduct3(ri,rj, rij); |
273 |
< |
distXY = dotProduct3(rk,rij) / length3(rij); |
271 |
> |
|
272 |
> |
crossProduct3(ri, rj, rij); |
273 |
> |
distXY = dotProduct3(rk,rij) / norm3(rij); |
274 |
|
|
275 |
|
crossProduct3(rj,rk, rjk); |
276 |
< |
distYZ = dotProduct3(ri,rjk) / length3(rjk); |
276 |
> |
distYZ = dotProduct3(ri,rjk) / norm3(rjk); |
277 |
|
|
278 |
|
crossProduct3(rk,ri, rki); |
279 |
< |
distZX = dotProduct3(rj,rki) / length3(rki); |
279 |
> |
distZX = dotProduct3(rj,rki) / norm3(rki); |
280 |
|
|
281 |
|
minDist = min(min(distXY, distYZ), distZX); |
282 |
|
return minDist/2; |
324 |
|
|
325 |
|
int SimInfo::getNDF(){ |
326 |
|
int ndf_local; |
327 |
+ |
|
328 |
+ |
ndf_local = 0; |
329 |
|
|
330 |
< |
ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints; |
330 |
> |
for(int i = 0; i < integrableObjects.size(); i++){ |
331 |
> |
ndf_local += 3; |
332 |
> |
if (integrableObjects[i]->isDirectional()) { |
333 |
> |
if (integrableObjects[i]->isLinear()) |
334 |
> |
ndf_local += 2; |
335 |
> |
else |
336 |
> |
ndf_local += 3; |
337 |
> |
} |
338 |
> |
} |
339 |
|
|
340 |
+ |
// n_constraints is local, so subtract them on each processor: |
341 |
+ |
|
342 |
+ |
ndf_local -= n_constraints; |
343 |
+ |
|
344 |
|
#ifdef IS_MPI |
345 |
|
MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
346 |
|
#else |
347 |
|
ndf = ndf_local; |
348 |
|
#endif |
349 |
|
|
350 |
+ |
// nZconstraints is global, as are the 3 COM translations for the |
351 |
+ |
// entire system: |
352 |
+ |
|
353 |
|
ndf = ndf - 3 - nZconstraints; |
354 |
|
|
355 |
|
return ndf; |
359 |
|
int ndfRaw_local; |
360 |
|
|
361 |
|
// Raw degrees of freedom that we have to set |
362 |
< |
ndfRaw_local = 3 * n_atoms + 3 * n_oriented; |
363 |
< |
|
362 |
> |
ndfRaw_local = 0; |
363 |
> |
|
364 |
> |
for(int i = 0; i < integrableObjects.size(); i++){ |
365 |
> |
ndfRaw_local += 3; |
366 |
> |
if (integrableObjects[i]->isDirectional()) { |
367 |
> |
if (integrableObjects[i]->isLinear()) |
368 |
> |
ndfRaw_local += 2; |
369 |
> |
else |
370 |
> |
ndfRaw_local += 3; |
371 |
> |
} |
372 |
> |
} |
373 |
> |
|
374 |
|
#ifdef IS_MPI |
375 |
|
MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
376 |
|
#else |
383 |
|
int SimInfo::getNDFtranslational() { |
384 |
|
int ndfTrans_local; |
385 |
|
|
386 |
< |
ndfTrans_local = 3 * n_atoms - n_constraints; |
386 |
> |
ndfTrans_local = 3 * integrableObjects.size() - n_constraints; |
387 |
|
|
388 |
+ |
|
389 |
|
#ifdef IS_MPI |
390 |
|
MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
391 |
|
#else |
397 |
|
return ndfTrans; |
398 |
|
} |
399 |
|
|
400 |
+ |
int SimInfo::getTotIntegrableObjects() { |
401 |
+ |
int nObjs_local; |
402 |
+ |
int nObjs; |
403 |
+ |
|
404 |
+ |
nObjs_local = integrableObjects.size(); |
405 |
+ |
|
406 |
+ |
|
407 |
+ |
#ifdef IS_MPI |
408 |
+ |
MPI_Allreduce(&nObjs_local,&nObjs,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
409 |
+ |
#else |
410 |
+ |
nObjs = nObjs_local; |
411 |
+ |
#endif |
412 |
+ |
|
413 |
+ |
|
414 |
+ |
return nObjs; |
415 |
+ |
} |
416 |
+ |
|
417 |
|
void SimInfo::refreshSim(){ |
418 |
|
|
419 |
|
simtype fInfo; |
435 |
|
fInfo.SIM_uses_charges = useCharges; |
436 |
|
fInfo.SIM_uses_dipoles = useDipoles; |
437 |
|
//fInfo.SIM_uses_dipoles = 0; |
438 |
< |
//fInfo.SIM_uses_RF = useReactionField; |
439 |
< |
fInfo.SIM_uses_RF = 0; |
438 |
> |
fInfo.SIM_uses_RF = useReactionField; |
439 |
> |
//fInfo.SIM_uses_RF = 0; |
440 |
|
fInfo.SIM_uses_GB = useGB; |
441 |
|
fInfo.SIM_uses_EAM = useEAM; |
442 |
|
|
443 |
< |
excl = Exclude::getArray(); |
444 |
< |
|
443 |
> |
n_exclude = excludes->getSize(); |
444 |
> |
excl = excludes->getFortranArray(); |
445 |
> |
|
446 |
|
#ifdef IS_MPI |
447 |
|
n_global = mpiSim->getTotAtoms(); |
448 |
|
#else |
451 |
|
|
452 |
|
isError = 0; |
453 |
|
|
454 |
+ |
getFortranGroupArray(this, mfact, ngroup, groupList, groupStart); |
455 |
+ |
|
456 |
|
setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl, |
457 |
< |
&nGlobalExcludes, globalExcludes, molMembershipArray, |
458 |
< |
&isError ); |
457 |
> |
&nGlobalExcludes, globalExcludes, molMembershipArray, |
458 |
> |
&mfact[0], &ngroup, &groupList[0], &groupStart[0], &isError ); |
459 |
|
|
460 |
|
if( isError ){ |
461 |
|
|
511 |
|
|
512 |
|
if( rCut > maxCutoff ){ |
513 |
|
sprintf( painCave.errMsg, |
514 |
< |
"Box size is too small for the long range cutoff radius, " |
515 |
< |
"%G, at time %G\n" |
514 |
> |
"LJrcut is too large for the current periodic box.\n" |
515 |
> |
"\tCurrent Value of LJrcut = %G at time %G\n " |
516 |
> |
"\tThis is larger than half of at least one of the\n" |
517 |
> |
"\tperiodic box vectors. Right now, the Box matrix is:\n" |
518 |
> |
"\n" |
519 |
|
"\t[ %G %G %G ]\n" |
520 |
|
"\t[ %G %G %G ]\n" |
521 |
|
"\t[ %G %G %G ]\n", |
530 |
|
if( haveEcr ){ |
531 |
|
if( ecr > maxCutoff ){ |
532 |
|
sprintf( painCave.errMsg, |
533 |
< |
"Box size is too small for the electrostatic cutoff radius, " |
534 |
< |
"%G, at time %G\n" |
535 |
< |
"\t[ %G %G %G ]\n" |
536 |
< |
"\t[ %G %G %G ]\n" |
537 |
< |
"\t[ %G %G %G ]\n", |
533 |
> |
"electrostaticCutoffRadius is too large for the current\n" |
534 |
> |
"\tperiodic box.\n\n" |
535 |
> |
"\tCurrent Value of ECR = %G at time %G\n " |
536 |
> |
"\tThis is larger than half of at least one of the\n" |
537 |
> |
"\tperiodic box vectors. Right now, the Box matrix is:\n" |
538 |
> |
"\n" |
539 |
> |
"\t[ %G %G %G ]\n" |
540 |
> |
"\t[ %G %G %G ]\n" |
541 |
> |
"\t[ %G %G %G ]\n", |
542 |
|
ecr, currentTime, |
543 |
|
Hmat[0][0], Hmat[0][1], Hmat[0][2], |
544 |
|
Hmat[1][0], Hmat[1][1], Hmat[1][2], |
594 |
|
return NULL; |
595 |
|
} |
596 |
|
|
647 |
– |
vector<GenericData*> SimInfo::getProperties(){ |
597 |
|
|
598 |
< |
vector<GenericData*> result; |
599 |
< |
map<string, GenericData*>::iterator i; |
600 |
< |
|
601 |
< |
for(i = properties.begin(); i != properties.end(); i++) |
602 |
< |
result.push_back((*i).second); |
598 |
> |
void getFortranGroupArray(SimInfo* info, vector<double>& mfact, int& ngroup, |
599 |
> |
vector<int>& groupList, vector<int>& groupStart){ |
600 |
> |
Molecule* mol; |
601 |
> |
int numAtom; |
602 |
> |
int curIndex; |
603 |
> |
|
604 |
> |
mfact.clear(); |
605 |
> |
groupList.clear(); |
606 |
> |
groupStart.clear(); |
607 |
> |
|
608 |
> |
//Be careful, fortran array begin at 1 |
609 |
> |
curIndex = 1; |
610 |
|
|
611 |
< |
return result; |
612 |
< |
} |
611 |
> |
if(info->useMolecularCutoffs){ |
612 |
> |
//if using molecular cutoff |
613 |
> |
ngroup = info->n_mol; |
614 |
|
|
615 |
< |
double SimInfo::matTrace3(double m[3][3]){ |
616 |
< |
double trace; |
617 |
< |
trace = m[0][0] + m[1][1] + m[2][2]; |
615 |
> |
for(int i = 0; i < ngroup; i ++){ |
616 |
> |
mol = &(info->molecules[i]); |
617 |
> |
numAtom = mol->getNAtoms(); |
618 |
> |
|
619 |
> |
for(int j=0; j < numAtom; j++){ |
620 |
> |
#ifdef IS_MPI |
621 |
> |
groupList.push_back((info->atoms[i])->getGlobalIndex() + 1); |
622 |
> |
#else |
623 |
> |
groupList.push_back((info->atoms[i])->getIndex() + 1); |
624 |
> |
#endif |
625 |
> |
}//for(int j=0; j < numAtom; j++) |
626 |
> |
|
627 |
> |
groupStart.push_back(curIndex); |
628 |
> |
curIndex += numAtom; |
629 |
> |
|
630 |
> |
}//end for(int i =0 ; i < ngroup; i++) |
631 |
> |
} |
632 |
> |
else{ |
633 |
> |
//using atomic cutoff, every single atom is just a group |
634 |
> |
ngroup = info->n_atoms; |
635 |
> |
for(int i =0 ; i < ngroup; i++){ |
636 |
> |
groupStart.push_back(curIndex++); |
637 |
|
|
638 |
< |
return trace; |
638 |
> |
#ifdef IS_MPI |
639 |
> |
groupList.push_back((info->atoms[i])->getGlobalIndex() + 1); |
640 |
> |
#else |
641 |
> |
groupList.push_back((info->atoms[i])->getIndex() + 1); |
642 |
> |
#endif |
643 |
> |
|
644 |
> |
}//end for(int i =0 ; i < ngroup; i++) |
645 |
> |
|
646 |
> |
}//end if (info->useMolecularCutoffs) |
647 |
> |
|
648 |
|
} |