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1 | < | #include <cstdlib> |
2 | < | #include <cstring> |
1 | > | #include <stdlib.h> |
2 | > | #include <string.h> |
3 | > | #include <math.h> |
4 | ||
5 | + | #include <iostream> |
6 | + | using namespace std; |
7 | ||
8 | #include "SimInfo.hpp" | |
9 | #define __C | |
# | Line 9 | Line 12 | |
12 | ||
13 | #include "fortranWrappers.hpp" | |
14 | ||
15 | + | #include "MatVec3.h" |
16 | + | |
17 | + | #ifdef IS_MPI |
18 | + | #include "mpiSimulation.hpp" |
19 | + | #endif |
20 | + | |
21 | + | inline double roundMe( double x ){ |
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; | |
36 | n_dipoles = 0; | |
37 | + | ndf = 0; |
38 | + | ndfRaw = 0; |
39 | + | nZconstraints = 0; |
40 | the_integrator = NULL; | |
41 | setTemp = 0; | |
42 | thermalTime = 0.0; | |
43 | + | currentTime = 0.0; |
44 | + | rCut = 0.0; |
45 | + | rSw = 0.0; |
46 | ||
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 | + | useSolidThermInt = 0; |
66 | + | useLiquidThermInt = 0; |
67 | ||
68 | + | haveCutoffGroups = false; |
69 | ||
70 | + | excludes = Exclude::Instance(); |
71 | ||
72 | + | myConfiguration = new SimState(); |
73 | + | |
74 | + | has_minimizer = false; |
75 | + | the_minimizer =NULL; |
76 | + | |
77 | + | ngroup = 0; |
78 | + | |
79 | wrapMeSimInfo( this ); | |
80 | + | } |
81 | + | |
82 | + | |
83 | + | SimInfo::~SimInfo(){ |
84 | + | |
85 | + | delete myConfiguration; |
86 | + | |
87 | + | map<string, GenericData*>::iterator i; |
88 | + | |
89 | + | for(i = properties.begin(); i != properties.end(); i++) |
90 | + | delete (*i).second; |
91 | + | |
92 | + | } |
93 | + | |
94 | + | void SimInfo::setBox(double newBox[3]) { |
95 | + | |
96 | + | int i, j; |
97 | + | double tempMat[3][3]; |
98 | + | |
99 | + | for(i=0; i<3; i++) |
100 | + | for (j=0; j<3; j++) tempMat[i][j] = 0.0;; |
101 | + | |
102 | + | tempMat[0][0] = newBox[0]; |
103 | + | tempMat[1][1] = newBox[1]; |
104 | + | tempMat[2][2] = newBox[2]; |
105 | + | |
106 | + | setBoxM( tempMat ); |
107 | + | |
108 | + | } |
109 | + | |
110 | + | void SimInfo::setBoxM( double theBox[3][3] ){ |
111 | + | |
112 | + | int i, j; |
113 | + | double FortranHmat[9]; // to preserve compatibility with Fortran the |
114 | + | // ordering in the array is as follows: |
115 | + | // [ 0 3 6 ] |
116 | + | // [ 1 4 7 ] |
117 | + | // [ 2 5 8 ] |
118 | + | double FortranHmatInv[9]; // the inverted Hmat (for Fortran); |
119 | + | |
120 | + | if( !boxIsInit ) boxIsInit = 1; |
121 | + | |
122 | + | for(i=0; i < 3; i++) |
123 | + | for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j]; |
124 | + | |
125 | + | calcBoxL(); |
126 | + | calcHmatInv(); |
127 | + | |
128 | + | for(i=0; i < 3; i++) { |
129 | + | for (j=0; j < 3; j++) { |
130 | + | FortranHmat[3*j + i] = Hmat[i][j]; |
131 | + | FortranHmatInv[3*j + i] = HmatInv[i][j]; |
132 | + | } |
133 | + | } |
134 | + | |
135 | + | setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic); |
136 | + | |
137 | + | } |
138 | + | |
139 | + | |
140 | + | void SimInfo::getBoxM (double theBox[3][3]) { |
141 | + | |
142 | + | int i, j; |
143 | + | for(i=0; i<3; i++) |
144 | + | for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]; |
145 | + | } |
146 | + | |
147 | + | |
148 | + | void SimInfo::scaleBox(double scale) { |
149 | + | double theBox[3][3]; |
150 | + | int i, j; |
151 | + | |
152 | + | // cerr << "Scaling box by " << scale << "\n"; |
153 | + | |
154 | + | for(i=0; i<3; i++) |
155 | + | for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale; |
156 | + | |
157 | + | setBoxM(theBox); |
158 | + | |
159 | + | } |
160 | + | |
161 | + | void SimInfo::calcHmatInv( void ) { |
162 | + | |
163 | + | int oldOrtho; |
164 | + | int i,j; |
165 | + | double smallDiag; |
166 | + | double tol; |
167 | + | double sanity[3][3]; |
168 | + | |
169 | + | invertMat3( Hmat, HmatInv ); |
170 | + | |
171 | + | // check to see if Hmat is orthorhombic |
172 | + | |
173 | + | oldOrtho = orthoRhombic; |
174 | + | |
175 | + | smallDiag = fabs(Hmat[0][0]); |
176 | + | if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]); |
177 | + | if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]); |
178 | + | tol = smallDiag * orthoTolerance; |
179 | + | |
180 | + | orthoRhombic = 1; |
181 | + | |
182 | + | for (i = 0; i < 3; i++ ) { |
183 | + | for (j = 0 ; j < 3; j++) { |
184 | + | if (i != j) { |
185 | + | if (orthoRhombic) { |
186 | + | if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0; |
187 | + | } |
188 | + | } |
189 | + | } |
190 | + | } |
191 | + | |
192 | + | if( oldOrtho != orthoRhombic ){ |
193 | + | |
194 | + | if( orthoRhombic ) { |
195 | + | sprintf( painCave.errMsg, |
196 | + | "\n\tOOPSE is switching from the default Non-Orthorhombic\n" |
197 | + | "\tto the faster Orthorhombic periodic boundary computations.\n" |
198 | + | "\tThis is usually a good thing, but if you wan't the\n" |
199 | + | "\tNon-Orthorhombic computations, make the orthoBoxTolerance\n" |
200 | + | "\tvariable ( currently set to %G ) smaller.\n", |
201 | + | orthoTolerance); |
202 | + | painCave.severity = OOPSE_INFO; |
203 | + | simError(); |
204 | + | } |
205 | + | else { |
206 | + | sprintf( painCave.errMsg, |
207 | + | "\n\tOOPSE is switching from the faster Orthorhombic to the more\n" |
208 | + | "\tflexible Non-Orthorhombic periodic boundary computations.\n" |
209 | + | "\tThis is usually because the box has deformed under\n" |
210 | + | "\tNPTf integration. If you wan't to live on the edge with\n" |
211 | + | "\tthe Orthorhombic computations, make the orthoBoxTolerance\n" |
212 | + | "\tvariable ( currently set to %G ) larger.\n", |
213 | + | orthoTolerance); |
214 | + | painCave.severity = OOPSE_WARNING; |
215 | + | simError(); |
216 | + | } |
217 | + | } |
218 | + | } |
219 | + | |
220 | + | void SimInfo::calcBoxL( void ){ |
221 | + | |
222 | + | double dx, dy, dz, dsq; |
223 | + | |
224 | + | // boxVol = Determinant of Hmat |
225 | + | |
226 | + | boxVol = matDet3( Hmat ); |
227 | + | |
228 | + | // boxLx |
229 | + | |
230 | + | dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0]; |
231 | + | dsq = dx*dx + dy*dy + dz*dz; |
232 | + | boxL[0] = sqrt( dsq ); |
233 | + | //maxCutoff = 0.5 * boxL[0]; |
234 | + | |
235 | + | // boxLy |
236 | + | |
237 | + | dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1]; |
238 | + | dsq = dx*dx + dy*dy + dz*dz; |
239 | + | boxL[1] = sqrt( dsq ); |
240 | + | //if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1]; |
241 | + | |
242 | + | |
243 | + | // boxLz |
244 | + | |
245 | + | dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2]; |
246 | + | dsq = dx*dx + dy*dy + dz*dz; |
247 | + | boxL[2] = sqrt( dsq ); |
248 | + | //if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2]; |
249 | + | |
250 | + | //calculate the max cutoff |
251 | + | maxCutoff = calcMaxCutOff(); |
252 | + | |
253 | + | checkCutOffs(); |
254 | + | |
255 | + | } |
256 | + | |
257 | + | |
258 | + | double SimInfo::calcMaxCutOff(){ |
259 | + | |
260 | + | double ri[3], rj[3], rk[3]; |
261 | + | double rij[3], rjk[3], rki[3]; |
262 | + | double minDist; |
263 | + | |
264 | + | ri[0] = Hmat[0][0]; |
265 | + | ri[1] = Hmat[1][0]; |
266 | + | ri[2] = Hmat[2][0]; |
267 | + | |
268 | + | rj[0] = Hmat[0][1]; |
269 | + | rj[1] = Hmat[1][1]; |
270 | + | rj[2] = Hmat[2][1]; |
271 | + | |
272 | + | rk[0] = Hmat[0][2]; |
273 | + | rk[1] = Hmat[1][2]; |
274 | + | rk[2] = Hmat[2][2]; |
275 | + | |
276 | + | crossProduct3(ri, rj, rij); |
277 | + | distXY = dotProduct3(rk,rij) / norm3(rij); |
278 | + | |
279 | + | crossProduct3(rj,rk, rjk); |
280 | + | distYZ = dotProduct3(ri,rjk) / norm3(rjk); |
281 | + | |
282 | + | crossProduct3(rk,ri, rki); |
283 | + | distZX = dotProduct3(rj,rki) / norm3(rki); |
284 | + | |
285 | + | minDist = min(min(distXY, distYZ), distZX); |
286 | + | return minDist/2; |
287 | + | |
288 | + | } |
289 | + | |
290 | + | void SimInfo::wrapVector( double thePos[3] ){ |
291 | + | |
292 | + | int i; |
293 | + | double scaled[3]; |
294 | + | |
295 | + | if( !orthoRhombic ){ |
296 | + | // calc the scaled coordinates. |
297 | + | |
298 | + | |
299 | + | matVecMul3(HmatInv, thePos, scaled); |
300 | + | |
301 | + | for(i=0; i<3; i++) |
302 | + | scaled[i] -= roundMe(scaled[i]); |
303 | + | |
304 | + | // calc the wrapped real coordinates from the wrapped scaled coordinates |
305 | + | |
306 | + | matVecMul3(Hmat, scaled, thePos); |
307 | + | |
308 | + | } |
309 | + | else{ |
310 | + | // calc the scaled coordinates. |
311 | + | |
312 | + | for(i=0; i<3; i++) |
313 | + | scaled[i] = thePos[i]*HmatInv[i][i]; |
314 | + | |
315 | + | // wrap the scaled coordinates |
316 | + | |
317 | + | for(i=0; i<3; i++) |
318 | + | scaled[i] -= roundMe(scaled[i]); |
319 | + | |
320 | + | // calc the wrapped real coordinates from the wrapped scaled coordinates |
321 | + | |
322 | + | for(i=0; i<3; i++) |
323 | + | thePos[i] = scaled[i]*Hmat[i][i]; |
324 | + | } |
325 | + | |
326 | } | |
327 | ||
328 | + | |
329 | + | int SimInfo::getNDF(){ |
330 | + | int ndf_local; |
331 | + | |
332 | + | ndf_local = 0; |
333 | + | |
334 | + | for(int i = 0; i < integrableObjects.size(); i++){ |
335 | + | ndf_local += 3; |
336 | + | if (integrableObjects[i]->isDirectional()) { |
337 | + | if (integrableObjects[i]->isLinear()) |
338 | + | ndf_local += 2; |
339 | + | else |
340 | + | ndf_local += 3; |
341 | + | } |
342 | + | } |
343 | + | |
344 | + | // n_constraints is local, so subtract them on each processor: |
345 | + | |
346 | + | ndf_local -= n_constraints; |
347 | + | |
348 | + | #ifdef IS_MPI |
349 | + | MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
350 | + | #else |
351 | + | ndf = ndf_local; |
352 | + | #endif |
353 | + | |
354 | + | // nZconstraints is global, as are the 3 COM translations for the |
355 | + | // entire system: |
356 | + | |
357 | + | ndf = ndf - 3 - nZconstraints; |
358 | + | |
359 | + | return ndf; |
360 | + | } |
361 | + | |
362 | + | int SimInfo::getNDFraw() { |
363 | + | int ndfRaw_local; |
364 | + | |
365 | + | // Raw degrees of freedom that we have to set |
366 | + | ndfRaw_local = 0; |
367 | + | |
368 | + | for(int i = 0; i < integrableObjects.size(); i++){ |
369 | + | ndfRaw_local += 3; |
370 | + | if (integrableObjects[i]->isDirectional()) { |
371 | + | if (integrableObjects[i]->isLinear()) |
372 | + | ndfRaw_local += 2; |
373 | + | else |
374 | + | ndfRaw_local += 3; |
375 | + | } |
376 | + | } |
377 | + | |
378 | + | #ifdef IS_MPI |
379 | + | MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
380 | + | #else |
381 | + | ndfRaw = ndfRaw_local; |
382 | + | #endif |
383 | + | |
384 | + | return ndfRaw; |
385 | + | } |
386 | + | |
387 | + | int SimInfo::getNDFtranslational() { |
388 | + | int ndfTrans_local; |
389 | + | |
390 | + | ndfTrans_local = 3 * integrableObjects.size() - n_constraints; |
391 | + | |
392 | + | |
393 | + | #ifdef IS_MPI |
394 | + | MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
395 | + | #else |
396 | + | ndfTrans = ndfTrans_local; |
397 | + | #endif |
398 | + | |
399 | + | ndfTrans = ndfTrans - 3 - nZconstraints; |
400 | + | |
401 | + | return ndfTrans; |
402 | + | } |
403 | + | |
404 | + | int SimInfo::getTotIntegrableObjects() { |
405 | + | int nObjs_local; |
406 | + | int nObjs; |
407 | + | |
408 | + | nObjs_local = integrableObjects.size(); |
409 | + | |
410 | + | |
411 | + | #ifdef IS_MPI |
412 | + | MPI_Allreduce(&nObjs_local,&nObjs,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
413 | + | #else |
414 | + | nObjs = nObjs_local; |
415 | + | #endif |
416 | + | |
417 | + | |
418 | + | return nObjs; |
419 | + | } |
420 | + | |
421 | void SimInfo::refreshSim(){ | |
422 | ||
423 | simtype fInfo; | |
424 | int isError; | |
425 | + | int n_global; |
426 | + | int* excl; |
427 | ||
428 | < | fInfo.box[0] = box_x; |
42 | < | fInfo.box[1] = box_y; |
43 | < | fInfo.box[2] = box_z; |
428 | > | fInfo.dielect = 0.0; |
429 | ||
430 | < | fInfo.rlist = rList; |
431 | < | fInfo.rcut = rCut; |
432 | < | fInfo.rrf = ecr; |
48 | < | fInfo.rt = ecr - est; |
49 | < | fInfo.dielect = dielectric; |
430 | > | if( useDipoles ){ |
431 | > | if( useReactionField )fInfo.dielect = dielectric; |
432 | > | } |
433 | ||
434 | fInfo.SIM_uses_PBC = usePBC; | |
435 | + | //fInfo.SIM_uses_LJ = 0; |
436 | fInfo.SIM_uses_LJ = useLJ; | |
437 | < | //fInfo.SIM_uses_sticky = useSticky; |
438 | < | fInfo.SIM_uses_sticky = 0; |
439 | < | fInfo.SIM_uses_dipoles = useDipole; |
437 | > | fInfo.SIM_uses_sticky = useSticky; |
438 | > | //fInfo.SIM_uses_sticky = 0; |
439 | > | fInfo.SIM_uses_charges = useCharges; |
440 | > | fInfo.SIM_uses_dipoles = useDipoles; |
441 | //fInfo.SIM_uses_dipoles = 0; | |
442 | fInfo.SIM_uses_RF = useReactionField; | |
443 | + | //fInfo.SIM_uses_RF = 0; |
444 | fInfo.SIM_uses_GB = useGB; | |
445 | fInfo.SIM_uses_EAM = useEAM; | |
446 | ||
447 | < | |
447 | > | n_exclude = excludes->getSize(); |
448 | > | excl = excludes->getFortranArray(); |
449 | > | |
450 | > | #ifdef IS_MPI |
451 | > | n_global = mpiSim->getNAtomsGlobal(); |
452 | > | #else |
453 | > | n_global = n_atoms; |
454 | > | #endif |
455 | > | |
456 | isError = 0; | |
457 | + | |
458 | + | getFortranGroupArrays(this, FglobalGroupMembership, mfact); |
459 | + | //it may not be a good idea to pass the address of first element in vector |
460 | + | //since c++ standard does not require vector to be stored continuously in meomory |
461 | + | //Most of the compilers will organize the memory of vector continuously |
462 | + | setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl, |
463 | + | &nGlobalExcludes, globalExcludes, molMembershipArray, |
464 | + | &mfact[0], &ngroup, &FglobalGroupMembership[0], &isError); |
465 | ||
64 | – | fInfo; |
65 | – | n_atoms; |
66 | – | identArray; |
67 | – | n_exclude; |
68 | – | excludes; |
69 | – | nGlobalExcludes; |
70 | – | globalExcludes; |
71 | – | isError; |
72 | – | |
73 | – | setFsimulation( &fInfo, &n_atoms, identArray, &n_exclude, excludes, &nGlobalExcludes, globalExcludes, &isError ); |
74 | – | |
466 | if( isError ){ | |
467 | < | |
467 | > | |
468 | sprintf( painCave.errMsg, | |
469 | < | "There was an error setting the simulation information in fortran.\n" ); |
469 | > | "There was an error setting the simulation information in fortran.\n" ); |
470 | painCave.isFatal = 1; | |
471 | simError(); | |
472 | } | |
473 | < | |
473 | > | |
474 | #ifdef IS_MPI | |
475 | sprintf( checkPointMsg, | |
476 | "succesfully sent the simulation information to fortran.\n"); | |
477 | MPIcheckPoint(); | |
478 | #endif // is_mpi | |
479 | + | |
480 | + | this->ndf = this->getNDF(); |
481 | + | this->ndfRaw = this->getNDFraw(); |
482 | + | this->ndfTrans = this->getNDFtranslational(); |
483 | } | |
484 | ||
485 | + | void SimInfo::setDefaultRcut( double theRcut ){ |
486 | + | |
487 | + | haveRcut = 1; |
488 | + | rCut = theRcut; |
489 | + | rList = rCut + 1.0; |
490 | + | |
491 | + | notifyFortranCutOffs( &rCut, &rSw, &rList ); |
492 | + | } |
493 | + | |
494 | + | void SimInfo::setDefaultRcut( double theRcut, double theRsw ){ |
495 | + | |
496 | + | rSw = theRsw; |
497 | + | setDefaultRcut( theRcut ); |
498 | + | } |
499 | + | |
500 | + | |
501 | + | void SimInfo::checkCutOffs( void ){ |
502 | + | |
503 | + | if( boxIsInit ){ |
504 | + | |
505 | + | //we need to check cutOffs against the box |
506 | + | |
507 | + | if( rCut > maxCutoff ){ |
508 | + | sprintf( painCave.errMsg, |
509 | + | "\n\tcutoffRadius is too large for the current periodic box.\n" |
510 | + | "\tCurrent Value of cutoffRadius = %G at time %G\n " |
511 | + | "\tThis is larger than half of at least one of the\n" |
512 | + | "\tperiodic box vectors. Right now, the Box matrix is:\n" |
513 | + | "\n" |
514 | + | "\t[ %G %G %G ]\n" |
515 | + | "\t[ %G %G %G ]\n" |
516 | + | "\t[ %G %G %G ]\n", |
517 | + | rCut, currentTime, |
518 | + | Hmat[0][0], Hmat[0][1], Hmat[0][2], |
519 | + | Hmat[1][0], Hmat[1][1], Hmat[1][2], |
520 | + | Hmat[2][0], Hmat[2][1], Hmat[2][2]); |
521 | + | painCave.severity = OOPSE_ERROR; |
522 | + | painCave.isFatal = 1; |
523 | + | simError(); |
524 | + | } |
525 | + | } else { |
526 | + | // initialize this stuff before using it, OK? |
527 | + | sprintf( painCave.errMsg, |
528 | + | "\n\tTrying to check cutoffs without a box.\n" |
529 | + | "\tOOPSE should have better programmers than that.\n" ); |
530 | + | painCave.severity = OOPSE_ERROR; |
531 | + | painCave.isFatal = 1; |
532 | + | simError(); |
533 | + | } |
534 | + | |
535 | + | } |
536 | + | |
537 | + | void SimInfo::addProperty(GenericData* prop){ |
538 | + | |
539 | + | map<string, GenericData*>::iterator result; |
540 | + | result = properties.find(prop->getID()); |
541 | + | |
542 | + | //we can't simply use properties[prop->getID()] = prop, |
543 | + | //it will cause memory leak if we already contain a propery which has the same name of prop |
544 | + | |
545 | + | if(result != properties.end()){ |
546 | + | |
547 | + | delete (*result).second; |
548 | + | (*result).second = prop; |
549 | + | |
550 | + | } |
551 | + | else{ |
552 | + | |
553 | + | properties[prop->getID()] = prop; |
554 | + | |
555 | + | } |
556 | + | |
557 | + | } |
558 | + | |
559 | + | GenericData* SimInfo::getProperty(const string& propName){ |
560 | + | |
561 | + | map<string, GenericData*>::iterator result; |
562 | + | |
563 | + | //string lowerCaseName = (); |
564 | + | |
565 | + | result = properties.find(propName); |
566 | + | |
567 | + | if(result != properties.end()) |
568 | + | return (*result).second; |
569 | + | else |
570 | + | return NULL; |
571 | + | } |
572 | + | |
573 | + | |
574 | + | void SimInfo::getFortranGroupArrays(SimInfo* info, |
575 | + | vector<int>& FglobalGroupMembership, |
576 | + | vector<double>& mfact){ |
577 | + | |
578 | + | Molecule* myMols; |
579 | + | Atom** myAtoms; |
580 | + | int numAtom; |
581 | + | double mtot; |
582 | + | int numMol; |
583 | + | int numCutoffGroups; |
584 | + | CutoffGroup* myCutoffGroup; |
585 | + | vector<CutoffGroup*>::iterator iterCutoff; |
586 | + | Atom* cutoffAtom; |
587 | + | vector<Atom*>::iterator iterAtom; |
588 | + | int atomIndex; |
589 | + | double totalMass; |
590 | + | |
591 | + | mfact.clear(); |
592 | + | FglobalGroupMembership.clear(); |
593 | + | |
594 | + | |
595 | + | // Fix the silly fortran indexing problem |
596 | + | #ifdef IS_MPI |
597 | + | numAtom = mpiSim->getNAtomsGlobal(); |
598 | + | #else |
599 | + | numAtom = n_atoms; |
600 | + | #endif |
601 | + | for (int i = 0; i < numAtom; i++) |
602 | + | FglobalGroupMembership.push_back(globalGroupMembership[i] + 1); |
603 | + | |
604 | + | |
605 | + | myMols = info->molecules; |
606 | + | numMol = info->n_mol; |
607 | + | for(int i = 0; i < numMol; i++){ |
608 | + | numCutoffGroups = myMols[i].getNCutoffGroups(); |
609 | + | for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff); |
610 | + | myCutoffGroup != NULL; |
611 | + | myCutoffGroup =myMols[i].nextCutoffGroup(iterCutoff)){ |
612 | + | |
613 | + | totalMass = myCutoffGroup->getMass(); |
614 | + | |
615 | + | for(cutoffAtom = myCutoffGroup->beginAtom(iterAtom); |
616 | + | cutoffAtom != NULL; |
617 | + | cutoffAtom = myCutoffGroup->nextAtom(iterAtom)){ |
618 | + | mfact.push_back(cutoffAtom->getMass()/totalMass); |
619 | + | } |
620 | + | } |
621 | + | } |
622 | + | |
623 | + | } |
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