12 |
|
|
13 |
|
#include "fortranWrappers.hpp" |
14 |
|
|
15 |
+ |
#include "MatVec3.h" |
16 |
+ |
|
17 |
|
#ifdef IS_MPI |
18 |
|
#include "mpiSimulation.hpp" |
19 |
|
#endif |
22 |
|
return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 ); |
23 |
|
} |
24 |
|
|
25 |
+ |
inline double min( double a, double b ){ |
26 |
+ |
return (a < b ) ? a : b; |
27 |
+ |
} |
28 |
|
|
29 |
|
SimInfo* currentInfo; |
30 |
|
|
31 |
|
SimInfo::SimInfo(){ |
32 |
< |
excludes = NULL; |
32 |
> |
|
33 |
|
n_constraints = 0; |
34 |
|
nZconstraints = 0; |
35 |
|
n_oriented = 0; |
42 |
|
thermalTime = 0.0; |
43 |
|
currentTime = 0.0; |
44 |
|
rCut = 0.0; |
45 |
< |
origRcut = -1.0; |
41 |
< |
ecr = 0.0; |
42 |
< |
origEcr = -1.0; |
43 |
< |
est = 0.0; |
44 |
< |
oldEcr = 0.0; |
45 |
< |
oldRcut = 0.0; |
45 |
> |
rSw = 0.0; |
46 |
|
|
47 |
< |
haveOrigRcut = 0; |
48 |
< |
haveOrigEcr = 0; |
47 |
> |
haveRcut = 0; |
48 |
> |
haveRsw = 0; |
49 |
|
boxIsInit = 0; |
50 |
|
|
51 |
|
resetTime = 1e99; |
52 |
|
|
53 |
+ |
orthoRhombic = 0; |
54 |
|
orthoTolerance = 1E-6; |
55 |
|
useInitXSstate = true; |
56 |
|
|
57 |
|
usePBC = 0; |
58 |
|
useLJ = 0; |
59 |
|
useSticky = 0; |
60 |
< |
useDipole = 0; |
60 |
> |
useCharges = 0; |
61 |
> |
useDipoles = 0; |
62 |
|
useReactionField = 0; |
63 |
|
useGB = 0; |
64 |
|
useEAM = 0; |
65 |
+ |
|
66 |
+ |
haveCutoffGroups = false; |
67 |
|
|
68 |
+ |
excludes = Exclude::Instance(); |
69 |
+ |
|
70 |
|
myConfiguration = new SimState(); |
71 |
|
|
72 |
+ |
has_minimizer = false; |
73 |
+ |
the_minimizer =NULL; |
74 |
+ |
|
75 |
+ |
ngroup = 0; |
76 |
+ |
|
77 |
|
wrapMeSimInfo( this ); |
78 |
|
} |
79 |
|
|
86 |
|
|
87 |
|
for(i = properties.begin(); i != properties.end(); i++) |
88 |
|
delete (*i).second; |
89 |
< |
|
89 |
> |
|
90 |
|
} |
91 |
|
|
92 |
|
void SimInfo::setBox(double newBox[3]) { |
115 |
|
// [ 2 5 8 ] |
116 |
|
double FortranHmatInv[9]; // the inverted Hmat (for Fortran); |
117 |
|
|
107 |
– |
|
118 |
|
if( !boxIsInit ) boxIsInit = 1; |
119 |
|
|
120 |
|
for(i=0; i < 3; i++) |
191 |
|
|
192 |
|
if( orthoRhombic ){ |
193 |
|
sprintf( painCave.errMsg, |
194 |
< |
"Hmat is switching from Non-Orthorhombic to OrthoRhombic\n" |
195 |
< |
" If this is a bad thing, change the orthoBoxTolerance( currently %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\n" |
205 |
< |
" If this is a bad thing, change the orthoBoxTolerance( currently %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(); |
195 |
– |
} |
196 |
– |
} |
197 |
– |
} |
198 |
– |
|
199 |
– |
double SimInfo::matDet3(double a[3][3]) { |
200 |
– |
int i, j, k; |
201 |
– |
double determinant; |
202 |
– |
|
203 |
– |
determinant = 0.0; |
204 |
– |
|
205 |
– |
for(i = 0; i < 3; i++) { |
206 |
– |
j = (i+1)%3; |
207 |
– |
k = (i+2)%3; |
208 |
– |
|
209 |
– |
determinant += a[0][i] * (a[1][j]*a[2][k] - a[1][k]*a[2][j]); |
210 |
– |
} |
211 |
– |
|
212 |
– |
return determinant; |
213 |
– |
} |
214 |
– |
|
215 |
– |
void SimInfo::invertMat3(double a[3][3], double b[3][3]) { |
216 |
– |
|
217 |
– |
int i, j, k, l, m, n; |
218 |
– |
double determinant; |
219 |
– |
|
220 |
– |
determinant = matDet3( a ); |
221 |
– |
|
222 |
– |
if (determinant == 0.0) { |
223 |
– |
sprintf( painCave.errMsg, |
224 |
– |
"Can't invert a matrix with a zero determinant!\n"); |
225 |
– |
painCave.isFatal = 1; |
226 |
– |
simError(); |
227 |
– |
} |
228 |
– |
|
229 |
– |
for (i=0; i < 3; i++) { |
230 |
– |
j = (i+1)%3; |
231 |
– |
k = (i+2)%3; |
232 |
– |
for(l = 0; l < 3; l++) { |
233 |
– |
m = (l+1)%3; |
234 |
– |
n = (l+2)%3; |
235 |
– |
|
236 |
– |
b[l][i] = (a[j][m]*a[k][n] - a[j][n]*a[k][m]) / determinant; |
237 |
– |
} |
238 |
– |
} |
239 |
– |
} |
240 |
– |
|
241 |
– |
void SimInfo::matMul3(double a[3][3], double b[3][3], double c[3][3]) { |
242 |
– |
double r00, r01, r02, r10, r11, r12, r20, r21, r22; |
243 |
– |
|
244 |
– |
r00 = a[0][0]*b[0][0] + a[0][1]*b[1][0] + a[0][2]*b[2][0]; |
245 |
– |
r01 = a[0][0]*b[0][1] + a[0][1]*b[1][1] + a[0][2]*b[2][1]; |
246 |
– |
r02 = a[0][0]*b[0][2] + a[0][1]*b[1][2] + a[0][2]*b[2][2]; |
247 |
– |
|
248 |
– |
r10 = a[1][0]*b[0][0] + a[1][1]*b[1][0] + a[1][2]*b[2][0]; |
249 |
– |
r11 = a[1][0]*b[0][1] + a[1][1]*b[1][1] + a[1][2]*b[2][1]; |
250 |
– |
r12 = a[1][0]*b[0][2] + a[1][1]*b[1][2] + a[1][2]*b[2][2]; |
251 |
– |
|
252 |
– |
r20 = a[2][0]*b[0][0] + a[2][1]*b[1][0] + a[2][2]*b[2][0]; |
253 |
– |
r21 = a[2][0]*b[0][1] + a[2][1]*b[1][1] + a[2][2]*b[2][1]; |
254 |
– |
r22 = a[2][0]*b[0][2] + a[2][1]*b[1][2] + a[2][2]*b[2][2]; |
255 |
– |
|
256 |
– |
c[0][0] = r00; c[0][1] = r01; c[0][2] = r02; |
257 |
– |
c[1][0] = r10; c[1][1] = r11; c[1][2] = r12; |
258 |
– |
c[2][0] = r20; c[2][1] = r21; c[2][2] = r22; |
259 |
– |
} |
260 |
– |
|
261 |
– |
void SimInfo::matVecMul3(double m[3][3], double inVec[3], double outVec[3]) { |
262 |
– |
double a0, a1, a2; |
263 |
– |
|
264 |
– |
a0 = inVec[0]; a1 = inVec[1]; a2 = inVec[2]; |
265 |
– |
|
266 |
– |
outVec[0] = m[0][0]*a0 + m[0][1]*a1 + m[0][2]*a2; |
267 |
– |
outVec[1] = m[1][0]*a0 + m[1][1]*a1 + m[1][2]*a2; |
268 |
– |
outVec[2] = m[2][0]*a0 + m[2][1]*a1 + m[2][2]*a2; |
269 |
– |
} |
270 |
– |
|
271 |
– |
void SimInfo::transposeMat3(double in[3][3], double out[3][3]) { |
272 |
– |
double temp[3][3]; |
273 |
– |
int i, j; |
274 |
– |
|
275 |
– |
for (i = 0; i < 3; i++) { |
276 |
– |
for (j = 0; j < 3; j++) { |
277 |
– |
temp[j][i] = in[i][j]; |
212 |
|
} |
213 |
|
} |
280 |
– |
for (i = 0; i < 3; i++) { |
281 |
– |
for (j = 0; j < 3; j++) { |
282 |
– |
out[i][j] = temp[i][j]; |
283 |
– |
} |
284 |
– |
} |
214 |
|
} |
286 |
– |
|
287 |
– |
void SimInfo::printMat3(double A[3][3] ){ |
215 |
|
|
289 |
– |
std::cerr |
290 |
– |
<< "[ " << A[0][0] << ", " << A[0][1] << ", " << A[0][2] << " ]\n" |
291 |
– |
<< "[ " << A[1][0] << ", " << A[1][1] << ", " << A[1][2] << " ]\n" |
292 |
– |
<< "[ " << A[2][0] << ", " << A[2][1] << ", " << A[2][2] << " ]\n"; |
293 |
– |
} |
294 |
– |
|
295 |
– |
void SimInfo::printMat9(double A[9] ){ |
296 |
– |
|
297 |
– |
std::cerr |
298 |
– |
<< "[ " << A[0] << ", " << A[1] << ", " << A[2] << " ]\n" |
299 |
– |
<< "[ " << A[3] << ", " << A[4] << ", " << A[5] << " ]\n" |
300 |
– |
<< "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n"; |
301 |
– |
} |
302 |
– |
|
303 |
– |
|
304 |
– |
void SimInfo::crossProduct3(double a[3],double b[3], double out[3]){ |
305 |
– |
|
306 |
– |
out[0] = a[1] * b[2] - a[2] * b[1]; |
307 |
– |
out[1] = a[2] * b[0] - a[0] * b[2] ; |
308 |
– |
out[2] = a[0] * b[1] - a[1] * b[0]; |
309 |
– |
|
310 |
– |
} |
311 |
– |
|
312 |
– |
double SimInfo::dotProduct3(double a[3], double b[3]){ |
313 |
– |
return a[0]*b[0] + a[1]*b[1]+ a[2]*b[2]; |
314 |
– |
} |
315 |
– |
|
316 |
– |
double SimInfo::length3(double a[3]){ |
317 |
– |
return sqrt(a[0]*a[0] + a[1]*a[1] + a[2]*a[2]); |
318 |
– |
} |
319 |
– |
|
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; |
423 |
|
|
424 |
|
fInfo.dielect = 0.0; |
425 |
|
|
426 |
< |
if( useDipole ){ |
426 |
> |
if( useDipoles ){ |
427 |
|
if( useReactionField )fInfo.dielect = dielectric; |
428 |
|
} |
429 |
|
|
432 |
|
fInfo.SIM_uses_LJ = useLJ; |
433 |
|
fInfo.SIM_uses_sticky = useSticky; |
434 |
|
//fInfo.SIM_uses_sticky = 0; |
435 |
< |
fInfo.SIM_uses_dipoles = useDipole; |
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 |
449 |
|
n_global = n_atoms; |
450 |
|
#endif |
451 |
< |
|
451 |
> |
|
452 |
|
isError = 0; |
453 |
< |
|
453 |
> |
|
454 |
> |
getFortranGroupArray(this, mfact, ngroup, groupList, groupStart); |
455 |
> |
//it may not be a good idea to pass the address of first element in vector |
456 |
> |
//since c++ standard does not require vector to be stored continously in meomory |
457 |
> |
//Most of the compilers will organize the memory of vector continously |
458 |
|
setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl, |
459 |
< |
&nGlobalExcludes, globalExcludes, molMembershipArray, |
460 |
< |
&isError ); |
461 |
< |
|
459 |
> |
&nGlobalExcludes, globalExcludes, molMembershipArray, |
460 |
> |
&mfact[0], &ngroup, &groupList[0], &groupStart[0], &isError); |
461 |
> |
|
462 |
|
if( isError ){ |
463 |
< |
|
463 |
> |
|
464 |
|
sprintf( painCave.errMsg, |
465 |
< |
"There was an error setting the simulation information in fortran.\n" ); |
465 |
> |
"There was an error setting the simulation information in fortran.\n" ); |
466 |
|
painCave.isFatal = 1; |
467 |
|
simError(); |
468 |
|
} |
469 |
< |
|
469 |
> |
|
470 |
|
#ifdef IS_MPI |
471 |
|
sprintf( checkPointMsg, |
472 |
|
"succesfully sent the simulation information to fortran.\n"); |
473 |
|
MPIcheckPoint(); |
474 |
|
#endif // is_mpi |
475 |
< |
|
475 |
> |
|
476 |
|
this->ndf = this->getNDF(); |
477 |
|
this->ndfRaw = this->getNDFraw(); |
478 |
|
this->ndfTrans = this->getNDFtranslational(); |
479 |
|
} |
480 |
|
|
534 |
– |
|
535 |
– |
void SimInfo::setRcut( double theRcut ){ |
536 |
– |
|
537 |
– |
rCut = theRcut; |
538 |
– |
checkCutOffs(); |
539 |
– |
} |
540 |
– |
|
481 |
|
void SimInfo::setDefaultRcut( double theRcut ){ |
482 |
< |
|
483 |
< |
haveOrigRcut = 1; |
544 |
< |
origRcut = theRcut; |
482 |
> |
|
483 |
> |
haveRcut = 1; |
484 |
|
rCut = theRcut; |
485 |
< |
|
547 |
< |
( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0; |
548 |
< |
|
549 |
< |
notifyFortranCutOffs( &rCut, &rList, &ecr, &est ); |
550 |
< |
} |
551 |
< |
|
552 |
< |
void SimInfo::setEcr( double theEcr ){ |
553 |
< |
|
554 |
< |
ecr = theEcr; |
555 |
< |
checkCutOffs(); |
556 |
< |
} |
557 |
< |
|
558 |
< |
void SimInfo::setDefaultEcr( double theEcr ){ |
559 |
< |
|
560 |
< |
haveOrigEcr = 1; |
561 |
< |
origEcr = theEcr; |
485 |
> |
rList = rCut + 1.0; |
486 |
|
|
487 |
< |
( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0; |
564 |
< |
|
565 |
< |
ecr = theEcr; |
566 |
< |
|
567 |
< |
notifyFortranCutOffs( &rCut, &rList, &ecr, &est ); |
487 |
> |
notifyFortranCutOffs( &rCut, &rSw, &rList ); |
488 |
|
} |
489 |
|
|
490 |
< |
void SimInfo::setEcr( double theEcr, double theEst ){ |
490 |
> |
void SimInfo::setDefaultRcut( double theRcut, double theRsw ){ |
491 |
|
|
492 |
< |
est = theEst; |
493 |
< |
setEcr( theEcr ); |
492 |
> |
rSw = theRsw; |
493 |
> |
setDefaultRcut( theRcut ); |
494 |
|
} |
495 |
|
|
576 |
– |
void SimInfo::setDefaultEcr( double theEcr, double theEst ){ |
496 |
|
|
578 |
– |
est = theEst; |
579 |
– |
setDefaultEcr( theEcr ); |
580 |
– |
} |
581 |
– |
|
582 |
– |
|
497 |
|
void SimInfo::checkCutOffs( void ){ |
584 |
– |
|
585 |
– |
int cutChanged = 0; |
498 |
|
|
499 |
|
if( boxIsInit ){ |
500 |
|
|
501 |
|
//we need to check cutOffs against the box |
502 |
< |
|
503 |
< |
//detect the change of rCut |
592 |
< |
if(( maxCutoff > rCut )&&(usePBC)){ |
593 |
< |
if( rCut < origRcut ){ |
594 |
< |
rCut = origRcut; |
595 |
< |
|
596 |
< |
if (rCut > maxCutoff) |
597 |
< |
rCut = maxCutoff; |
598 |
< |
|
599 |
< |
sprintf( painCave.errMsg, |
600 |
< |
"New Box size is setting the long range cutoff radius " |
601 |
< |
"to %lf at time %lf\n", |
602 |
< |
rCut, currentTime ); |
603 |
< |
painCave.isFatal = 0; |
604 |
< |
simError(); |
605 |
< |
} |
606 |
< |
} |
607 |
< |
else if ((rCut > maxCutoff)&&(usePBC)) { |
502 |
> |
|
503 |
> |
if( rCut > maxCutoff ){ |
504 |
|
sprintf( painCave.errMsg, |
505 |
< |
"New Box size is setting the long range cutoff radius " |
506 |
< |
"to %lf at time %lf\n", |
507 |
< |
maxCutoff, currentTime ); |
508 |
< |
painCave.isFatal = 0; |
505 |
> |
"cutoffRadius is too large for the current periodic box.\n" |
506 |
> |
"\tCurrent Value of cutoffRadius = %G at time %G\n " |
507 |
> |
"\tThis is larger than half of at least one of the\n" |
508 |
> |
"\tperiodic box vectors. Right now, the Box matrix is:\n" |
509 |
> |
"\n" |
510 |
> |
"\t[ %G %G %G ]\n" |
511 |
> |
"\t[ %G %G %G ]\n" |
512 |
> |
"\t[ %G %G %G ]\n", |
513 |
> |
rCut, currentTime, |
514 |
> |
Hmat[0][0], Hmat[0][1], Hmat[0][2], |
515 |
> |
Hmat[1][0], Hmat[1][1], Hmat[1][2], |
516 |
> |
Hmat[2][0], Hmat[2][1], Hmat[2][2]); |
517 |
> |
painCave.isFatal = 1; |
518 |
|
simError(); |
519 |
< |
rCut = maxCutoff; |
615 |
< |
} |
616 |
< |
|
617 |
< |
|
618 |
< |
//detect the change of ecr |
619 |
< |
if( maxCutoff > ecr ){ |
620 |
< |
if( ecr < origEcr ){ |
621 |
< |
ecr = origEcr; |
622 |
< |
if (ecr > maxCutoff) ecr = maxCutoff; |
623 |
< |
|
624 |
< |
sprintf( painCave.errMsg, |
625 |
< |
"New Box size is setting the electrostaticCutoffRadius " |
626 |
< |
"to %lf at time %lf\n", |
627 |
< |
ecr, currentTime ); |
628 |
< |
painCave.isFatal = 0; |
629 |
< |
simError(); |
630 |
< |
} |
631 |
< |
} |
632 |
< |
else if( ecr > maxCutoff){ |
633 |
< |
sprintf( painCave.errMsg, |
634 |
< |
"New Box size is setting the electrostaticCutoffRadius " |
635 |
< |
"to %lf at time %lf\n", |
636 |
< |
maxCutoff, currentTime ); |
637 |
< |
painCave.isFatal = 0; |
638 |
< |
simError(); |
639 |
< |
ecr = maxCutoff; |
640 |
< |
} |
641 |
< |
|
642 |
< |
if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1; |
643 |
< |
|
644 |
< |
// rlist is the 1.0 plus max( rcut, ecr ) |
645 |
< |
|
646 |
< |
( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0; |
647 |
< |
|
648 |
< |
if( cutChanged ){ |
649 |
< |
notifyFortranCutOffs( &rCut, &rList, &ecr, &est ); |
650 |
< |
} |
651 |
< |
|
652 |
< |
oldEcr = ecr; |
653 |
< |
oldRcut = rCut; |
654 |
< |
|
519 |
> |
} |
520 |
|
} else { |
521 |
|
// initialize this stuff before using it, OK? |
522 |
|
sprintf( painCave.errMsg, |
523 |
< |
"Trying to check cutoffs without a box. Be smarter.\n" ); |
523 |
> |
"Trying to check cutoffs without a box.\n" |
524 |
> |
"\tOOPSE should have better programmers than that.\n" ); |
525 |
|
painCave.isFatal = 1; |
526 |
|
simError(); |
527 |
|
} |
564 |
|
return NULL; |
565 |
|
} |
566 |
|
|
701 |
– |
vector<GenericData*> SimInfo::getProperties(){ |
567 |
|
|
568 |
< |
vector<GenericData*> result; |
569 |
< |
map<string, GenericData*>::iterator i; |
568 |
> |
void getFortranGroupArray(SimInfo* info, vector<double>& mfact, int& ngroup, |
569 |
> |
vector<int>& groupList, vector<int>& groupStart){ |
570 |
> |
Molecule* myMols; |
571 |
> |
Atom** myAtoms; |
572 |
> |
int numAtom; |
573 |
> |
int curIndex; |
574 |
> |
double mtot; |
575 |
> |
int numMol; |
576 |
> |
int numCutoffGroups; |
577 |
> |
CutoffGroup* myCutoffGroup; |
578 |
> |
vector<CutoffGroup*>::iterator iterCutoff; |
579 |
> |
Atom* cutoffAtom; |
580 |
> |
vector<Atom*>::iterator iterAtom; |
581 |
> |
int atomIndex; |
582 |
|
|
583 |
< |
for(i = properties.begin(); i != properties.end(); i++) |
584 |
< |
result.push_back((*i).second); |
583 |
> |
mfact.clear(); |
584 |
> |
groupList.clear(); |
585 |
> |
groupStart.clear(); |
586 |
> |
|
587 |
> |
//Be careful, fortran array begin at 1 |
588 |
> |
curIndex = 1; |
589 |
> |
|
590 |
> |
myMols = info->molecules; |
591 |
> |
numMol = info->n_mol; |
592 |
> |
for(int i = 0; i < numMol; i++){ |
593 |
> |
numAtom = myMols[i].getNAtoms(); |
594 |
> |
myAtoms = myMols[i].getMyAtoms(); |
595 |
> |
|
596 |
|
|
597 |
< |
return result; |
710 |
< |
} |
597 |
> |
for(int j = 0; j < numAtom; j++){ |
598 |
|
|
599 |
< |
double SimInfo::matTrace3(double m[3][3]){ |
600 |
< |
double trace; |
601 |
< |
trace = m[0][0] + m[1][1] + m[2][2]; |
599 |
> |
|
600 |
> |
#ifdef IS_MPI |
601 |
> |
atomIndex = myAtoms[j]->getGlobalIndex(); |
602 |
> |
#else |
603 |
> |
atomIndex = myAtoms[j]->getIndex(); |
604 |
> |
#endif |
605 |
|
|
606 |
< |
return trace; |
606 |
> |
if(myMols[i].belongToCutoffGroup(atomIndex)) |
607 |
> |
continue; |
608 |
> |
else{ |
609 |
> |
mfact.push_back(myAtoms[j]->getMass()); |
610 |
> |
groupList.push_back(myAtoms[j]->getIndex() + 1); |
611 |
> |
groupStart.push_back(curIndex++); |
612 |
> |
} |
613 |
> |
} |
614 |
> |
|
615 |
> |
numCutoffGroups = myMols[i].getNCutoffGroups(); |
616 |
> |
for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff); myCutoffGroup != NULL; |
617 |
> |
myCutoffGroup =myMols[i].nextCutoffGroup(iterCutoff)){ |
618 |
> |
|
619 |
> |
for(cutoffAtom = myCutoffGroup->beginAtom(iterAtom); cutoffAtom != NULL; |
620 |
> |
cutoffAtom = myCutoffGroup->beginAtom(iterAtom)){ |
621 |
> |
groupList.push_back(cutoffAtom->getIndex() + 1); |
622 |
> |
} |
623 |
> |
|
624 |
> |
groupStart.push_back(curIndex); |
625 |
> |
curIndex += myCutoffGroup->getNumAtom(); |
626 |
> |
} |
627 |
> |
|
628 |
> |
} |
629 |
> |
|
630 |
> |
ngroup = groupStart.size(); |
631 |
|
} |