# | Line 1 | Line 1 | |
---|---|---|
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 | |
# | Line 9 | Line 12 | |
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(){ | |
# | Line 16 | Line 28 | SimInfo::SimInfo(){ | |
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 | + | currentTime = 0.0; |
37 | rCut = 0.0; | |
38 | + | ecr = 0.0; |
39 | + | est = 0.0; |
40 | + | oldEcr = 0.0; |
41 | + | oldRcut = 0.0; |
42 | ||
43 | + | haveOrigRcut = 0; |
44 | + | haveOrigEcr = 0; |
45 | + | boxIsInit = 0; |
46 | + | |
47 | + | |
48 | + | |
49 | usePBC = 0; | |
50 | useLJ = 0; | |
51 | useSticky = 0; | |
# | Line 29 | Line 54 | SimInfo::SimInfo(){ | |
54 | useGB = 0; | |
55 | useEAM = 0; | |
56 | ||
57 | + | wrapMeSimInfo( this ); |
58 | + | } |
59 | ||
60 | + | SimInfo::~SimInfo(){ |
61 | ||
62 | < | wrapMeSimInfo( this ); |
62 | > | map<string, GenericData*>::iterator i; |
63 | > | |
64 | > | for(i = properties.begin(); i != properties.end(); i++) |
65 | > | delete (*i).second; |
66 | > | |
67 | > | |
68 | } | |
69 | ||
70 | + | void SimInfo::setBox(double newBox[3]) { |
71 | + | |
72 | + | int i, j; |
73 | + | double tempMat[3][3]; |
74 | + | |
75 | + | for(i=0; i<3; i++) |
76 | + | for (j=0; j<3; j++) tempMat[i][j] = 0.0;; |
77 | + | |
78 | + | tempMat[0][0] = newBox[0]; |
79 | + | tempMat[1][1] = newBox[1]; |
80 | + | tempMat[2][2] = newBox[2]; |
81 | + | |
82 | + | setBoxM( tempMat ); |
83 | + | |
84 | + | } |
85 | + | |
86 | + | void SimInfo::setBoxM( double theBox[3][3] ){ |
87 | + | |
88 | + | int i, j, status; |
89 | + | double smallestBoxL, maxCutoff; |
90 | + | double FortranHmat[9]; // to preserve compatibility with Fortran the |
91 | + | // ordering in the array is as follows: |
92 | + | // [ 0 3 6 ] |
93 | + | // [ 1 4 7 ] |
94 | + | // [ 2 5 8 ] |
95 | + | double FortranHmatInv[9]; // the inverted Hmat (for Fortran); |
96 | + | |
97 | + | |
98 | + | if( !boxIsInit ) boxIsInit = 1; |
99 | + | |
100 | + | for(i=0; i < 3; i++) |
101 | + | for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j]; |
102 | + | |
103 | + | calcBoxL(); |
104 | + | calcHmatInv(); |
105 | + | |
106 | + | for(i=0; i < 3; i++) { |
107 | + | for (j=0; j < 3; j++) { |
108 | + | FortranHmat[3*j + i] = Hmat[i][j]; |
109 | + | FortranHmatInv[3*j + i] = HmatInv[i][j]; |
110 | + | } |
111 | + | } |
112 | + | |
113 | + | setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic); |
114 | + | |
115 | + | } |
116 | + | |
117 | + | |
118 | + | void SimInfo::getBoxM (double theBox[3][3]) { |
119 | + | |
120 | + | int i, j; |
121 | + | for(i=0; i<3; i++) |
122 | + | for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]; |
123 | + | } |
124 | + | |
125 | + | |
126 | + | void SimInfo::scaleBox(double scale) { |
127 | + | double theBox[3][3]; |
128 | + | int i, j; |
129 | + | |
130 | + | // cerr << "Scaling box by " << scale << "\n"; |
131 | + | |
132 | + | for(i=0; i<3; i++) |
133 | + | for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale; |
134 | + | |
135 | + | setBoxM(theBox); |
136 | + | |
137 | + | } |
138 | + | |
139 | + | void SimInfo::calcHmatInv( void ) { |
140 | + | |
141 | + | int i,j; |
142 | + | double smallDiag; |
143 | + | double tol; |
144 | + | double sanity[3][3]; |
145 | + | |
146 | + | invertMat3( Hmat, HmatInv ); |
147 | + | |
148 | + | // Check the inverse to make sure it is sane: |
149 | + | |
150 | + | matMul3( Hmat, HmatInv, sanity ); |
151 | + | |
152 | + | // check to see if Hmat is orthorhombic |
153 | + | |
154 | + | smallDiag = Hmat[0][0]; |
155 | + | if(smallDiag > Hmat[1][1]) smallDiag = Hmat[1][1]; |
156 | + | if(smallDiag > Hmat[2][2]) smallDiag = Hmat[2][2]; |
157 | + | tol = smallDiag * 1E-6; |
158 | + | |
159 | + | orthoRhombic = 1; |
160 | + | |
161 | + | for (i = 0; i < 3; i++ ) { |
162 | + | for (j = 0 ; j < 3; j++) { |
163 | + | if (i != j) { |
164 | + | if (orthoRhombic) { |
165 | + | if (Hmat[i][j] >= tol) orthoRhombic = 0; |
166 | + | } |
167 | + | } |
168 | + | } |
169 | + | } |
170 | + | } |
171 | + | |
172 | + | double SimInfo::matDet3(double a[3][3]) { |
173 | + | int i, j, k; |
174 | + | double determinant; |
175 | + | |
176 | + | determinant = 0.0; |
177 | + | |
178 | + | for(i = 0; i < 3; i++) { |
179 | + | j = (i+1)%3; |
180 | + | k = (i+2)%3; |
181 | + | |
182 | + | determinant += a[0][i] * (a[1][j]*a[2][k] - a[1][k]*a[2][j]); |
183 | + | } |
184 | + | |
185 | + | return determinant; |
186 | + | } |
187 | + | |
188 | + | void SimInfo::invertMat3(double a[3][3], double b[3][3]) { |
189 | + | |
190 | + | int i, j, k, l, m, n; |
191 | + | double determinant; |
192 | + | |
193 | + | determinant = matDet3( a ); |
194 | + | |
195 | + | if (determinant == 0.0) { |
196 | + | sprintf( painCave.errMsg, |
197 | + | "Can't invert a matrix with a zero determinant!\n"); |
198 | + | painCave.isFatal = 1; |
199 | + | simError(); |
200 | + | } |
201 | + | |
202 | + | for (i=0; i < 3; i++) { |
203 | + | j = (i+1)%3; |
204 | + | k = (i+2)%3; |
205 | + | for(l = 0; l < 3; l++) { |
206 | + | m = (l+1)%3; |
207 | + | n = (l+2)%3; |
208 | + | |
209 | + | b[l][i] = (a[j][m]*a[k][n] - a[j][n]*a[k][m]) / determinant; |
210 | + | } |
211 | + | } |
212 | + | } |
213 | + | |
214 | + | void SimInfo::matMul3(double a[3][3], double b[3][3], double c[3][3]) { |
215 | + | double r00, r01, r02, r10, r11, r12, r20, r21, r22; |
216 | + | |
217 | + | r00 = a[0][0]*b[0][0] + a[0][1]*b[1][0] + a[0][2]*b[2][0]; |
218 | + | r01 = a[0][0]*b[0][1] + a[0][1]*b[1][1] + a[0][2]*b[2][1]; |
219 | + | r02 = a[0][0]*b[0][2] + a[0][1]*b[1][2] + a[0][2]*b[2][2]; |
220 | + | |
221 | + | r10 = a[1][0]*b[0][0] + a[1][1]*b[1][0] + a[1][2]*b[2][0]; |
222 | + | r11 = a[1][0]*b[0][1] + a[1][1]*b[1][1] + a[1][2]*b[2][1]; |
223 | + | r12 = a[1][0]*b[0][2] + a[1][1]*b[1][2] + a[1][2]*b[2][2]; |
224 | + | |
225 | + | r20 = a[2][0]*b[0][0] + a[2][1]*b[1][0] + a[2][2]*b[2][0]; |
226 | + | r21 = a[2][0]*b[0][1] + a[2][1]*b[1][1] + a[2][2]*b[2][1]; |
227 | + | r22 = a[2][0]*b[0][2] + a[2][1]*b[1][2] + a[2][2]*b[2][2]; |
228 | + | |
229 | + | c[0][0] = r00; c[0][1] = r01; c[0][2] = r02; |
230 | + | c[1][0] = r10; c[1][1] = r11; c[1][2] = r12; |
231 | + | c[2][0] = r20; c[2][1] = r21; c[2][2] = r22; |
232 | + | } |
233 | + | |
234 | + | void SimInfo::matVecMul3(double m[3][3], double inVec[3], double outVec[3]) { |
235 | + | double a0, a1, a2; |
236 | + | |
237 | + | a0 = inVec[0]; a1 = inVec[1]; a2 = inVec[2]; |
238 | + | |
239 | + | outVec[0] = m[0][0]*a0 + m[0][1]*a1 + m[0][2]*a2; |
240 | + | outVec[1] = m[1][0]*a0 + m[1][1]*a1 + m[1][2]*a2; |
241 | + | outVec[2] = m[2][0]*a0 + m[2][1]*a1 + m[2][2]*a2; |
242 | + | } |
243 | + | |
244 | + | void SimInfo::transposeMat3(double in[3][3], double out[3][3]) { |
245 | + | double temp[3][3]; |
246 | + | int i, j; |
247 | + | |
248 | + | for (i = 0; i < 3; i++) { |
249 | + | for (j = 0; j < 3; j++) { |
250 | + | temp[j][i] = in[i][j]; |
251 | + | } |
252 | + | } |
253 | + | for (i = 0; i < 3; i++) { |
254 | + | for (j = 0; j < 3; j++) { |
255 | + | out[i][j] = temp[i][j]; |
256 | + | } |
257 | + | } |
258 | + | } |
259 | + | |
260 | + | void SimInfo::printMat3(double A[3][3] ){ |
261 | + | |
262 | + | std::cerr |
263 | + | << "[ " << A[0][0] << ", " << A[0][1] << ", " << A[0][2] << " ]\n" |
264 | + | << "[ " << A[1][0] << ", " << A[1][1] << ", " << A[1][2] << " ]\n" |
265 | + | << "[ " << A[2][0] << ", " << A[2][1] << ", " << A[2][2] << " ]\n"; |
266 | + | } |
267 | + | |
268 | + | void SimInfo::printMat9(double A[9] ){ |
269 | + | |
270 | + | std::cerr |
271 | + | << "[ " << A[0] << ", " << A[1] << ", " << A[2] << " ]\n" |
272 | + | << "[ " << A[3] << ", " << A[4] << ", " << A[5] << " ]\n" |
273 | + | << "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n"; |
274 | + | } |
275 | + | |
276 | + | void SimInfo::calcBoxL( void ){ |
277 | + | |
278 | + | double dx, dy, dz, dsq; |
279 | + | int i; |
280 | + | |
281 | + | // boxVol = Determinant of Hmat |
282 | + | |
283 | + | boxVol = matDet3( Hmat ); |
284 | + | |
285 | + | // boxLx |
286 | + | |
287 | + | dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0]; |
288 | + | dsq = dx*dx + dy*dy + dz*dz; |
289 | + | boxL[0] = sqrt( dsq ); |
290 | + | maxCutoff = 0.5 * boxL[0]; |
291 | + | |
292 | + | // boxLy |
293 | + | |
294 | + | dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1]; |
295 | + | dsq = dx*dx + dy*dy + dz*dz; |
296 | + | boxL[1] = sqrt( dsq ); |
297 | + | if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1]; |
298 | + | |
299 | + | // boxLz |
300 | + | |
301 | + | dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2]; |
302 | + | dsq = dx*dx + dy*dy + dz*dz; |
303 | + | boxL[2] = sqrt( dsq ); |
304 | + | if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2]; |
305 | + | |
306 | + | } |
307 | + | |
308 | + | |
309 | + | void SimInfo::wrapVector( double thePos[3] ){ |
310 | + | |
311 | + | int i, j, k; |
312 | + | double scaled[3]; |
313 | + | |
314 | + | if( !orthoRhombic ){ |
315 | + | // calc the scaled coordinates. |
316 | + | |
317 | + | |
318 | + | matVecMul3(HmatInv, thePos, scaled); |
319 | + | |
320 | + | for(i=0; i<3; i++) |
321 | + | scaled[i] -= roundMe(scaled[i]); |
322 | + | |
323 | + | // calc the wrapped real coordinates from the wrapped scaled coordinates |
324 | + | |
325 | + | matVecMul3(Hmat, scaled, thePos); |
326 | + | |
327 | + | } |
328 | + | else{ |
329 | + | // calc the scaled coordinates. |
330 | + | |
331 | + | for(i=0; i<3; i++) |
332 | + | scaled[i] = thePos[i]*HmatInv[i][i]; |
333 | + | |
334 | + | // wrap the scaled coordinates |
335 | + | |
336 | + | for(i=0; i<3; i++) |
337 | + | scaled[i] -= roundMe(scaled[i]); |
338 | + | |
339 | + | // calc the wrapped real coordinates from the wrapped scaled coordinates |
340 | + | |
341 | + | for(i=0; i<3; i++) |
342 | + | thePos[i] = scaled[i]*Hmat[i][i]; |
343 | + | } |
344 | + | |
345 | + | } |
346 | + | |
347 | + | |
348 | + | int SimInfo::getNDF(){ |
349 | + | int ndf_local, ndf; |
350 | + | |
351 | + | ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints; |
352 | + | |
353 | + | #ifdef IS_MPI |
354 | + | MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
355 | + | #else |
356 | + | ndf = ndf_local; |
357 | + | #endif |
358 | + | |
359 | + | ndf = ndf - 3; |
360 | + | |
361 | + | return ndf; |
362 | + | } |
363 | + | |
364 | + | int SimInfo::getNDFraw() { |
365 | + | int ndfRaw_local, ndfRaw; |
366 | + | |
367 | + | // Raw degrees of freedom that we have to set |
368 | + | ndfRaw_local = 3 * n_atoms + 3 * n_oriented; |
369 | + | |
370 | + | #ifdef IS_MPI |
371 | + | MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
372 | + | #else |
373 | + | ndfRaw = ndfRaw_local; |
374 | + | #endif |
375 | + | |
376 | + | return ndfRaw; |
377 | + | } |
378 | + | |
379 | void SimInfo::refreshSim(){ | |
380 | ||
381 | simtype fInfo; | |
382 | int isError; | |
383 | + | int n_global; |
384 | int* excl; | |
385 | ||
386 | < | fInfo.box[0] = box_x; |
44 | < | fInfo.box[1] = box_y; |
45 | < | fInfo.box[2] = box_z; |
386 | > | fInfo.dielect = 0.0; |
387 | ||
388 | < | fInfo.rlist = rList; |
389 | < | fInfo.rcut = rCut; |
390 | < | fInfo.rrf = ecr; |
50 | < | fInfo.rt = ecr - est; |
51 | < | fInfo.dielect = dielectric; |
388 | > | if( useDipole ){ |
389 | > | if( useReactionField )fInfo.dielect = dielectric; |
390 | > | } |
391 | ||
392 | fInfo.SIM_uses_PBC = usePBC; | |
393 | //fInfo.SIM_uses_LJ = 0; | |
# | Line 64 | Line 403 | void SimInfo::refreshSim(){ | |
403 | ||
404 | excl = Exclude::getArray(); | |
405 | ||
406 | + | #ifdef IS_MPI |
407 | + | n_global = mpiSim->getTotAtoms(); |
408 | + | #else |
409 | + | n_global = n_atoms; |
410 | + | #endif |
411 | + | |
412 | isError = 0; | |
413 | ||
414 | < | // fInfo; |
415 | < | // n_atoms; |
416 | < | // identArray; |
72 | < | // n_exclude; |
73 | < | // excludes; |
74 | < | // nGlobalExcludes; |
75 | < | // globalExcludes; |
76 | < | // isError; |
414 | > | setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl, |
415 | > | &nGlobalExcludes, globalExcludes, molMembershipArray, |
416 | > | &isError ); |
417 | ||
78 | – | setFsimulation( &fInfo, &n_atoms, identArray, &n_exclude, excl, |
79 | – | &nGlobalExcludes, globalExcludes, &isError ); |
80 | – | |
418 | if( isError ){ | |
419 | ||
420 | sprintf( painCave.errMsg, | |
# | Line 91 | Line 428 | void SimInfo::refreshSim(){ | |
428 | "succesfully sent the simulation information to fortran.\n"); | |
429 | MPIcheckPoint(); | |
430 | #endif // is_mpi | |
431 | + | |
432 | + | this->ndf = this->getNDF(); |
433 | + | this->ndfRaw = this->getNDFraw(); |
434 | + | |
435 | } | |
436 | ||
437 | + | |
438 | + | void SimInfo::setRcut( double theRcut ){ |
439 | + | |
440 | + | if( !haveOrigRcut ){ |
441 | + | haveOrigRcut = 1; |
442 | + | origRcut = theRcut; |
443 | + | } |
444 | + | |
445 | + | rCut = theRcut; |
446 | + | checkCutOffs(); |
447 | + | } |
448 | + | |
449 | + | void SimInfo::setEcr( double theEcr ){ |
450 | + | |
451 | + | if( !haveOrigEcr ){ |
452 | + | haveOrigEcr = 1; |
453 | + | origEcr = theEcr; |
454 | + | } |
455 | + | |
456 | + | ecr = theEcr; |
457 | + | checkCutOffs(); |
458 | + | } |
459 | + | |
460 | + | void SimInfo::setEcr( double theEcr, double theEst ){ |
461 | + | |
462 | + | est = theEst; |
463 | + | setEcr( theEcr ); |
464 | + | } |
465 | + | |
466 | + | |
467 | + | void SimInfo::checkCutOffs( void ){ |
468 | + | |
469 | + | int cutChanged = 0; |
470 | + | |
471 | + | if( boxIsInit ){ |
472 | + | |
473 | + | //we need to check cutOffs against the box |
474 | + | |
475 | + | if( maxCutoff > rCut ){ |
476 | + | if( rCut < origRcut ){ |
477 | + | rCut = origRcut; |
478 | + | if (rCut > maxCutoff) rCut = maxCutoff; |
479 | + | |
480 | + | sprintf( painCave.errMsg, |
481 | + | "New Box size is setting the long range cutoff radius " |
482 | + | "to %lf\n", |
483 | + | rCut ); |
484 | + | painCave.isFatal = 0; |
485 | + | simError(); |
486 | + | } |
487 | + | } |
488 | + | |
489 | + | if( maxCutoff > ecr ){ |
490 | + | if( ecr < origEcr ){ |
491 | + | rCut = origEcr; |
492 | + | if (ecr > maxCutoff) ecr = maxCutoff; |
493 | + | |
494 | + | sprintf( painCave.errMsg, |
495 | + | "New Box size is setting the electrostaticCutoffRadius " |
496 | + | "to %lf\n", |
497 | + | ecr ); |
498 | + | painCave.isFatal = 0; |
499 | + | simError(); |
500 | + | } |
501 | + | } |
502 | + | |
503 | + | |
504 | + | if (rCut > maxCutoff) { |
505 | + | sprintf( painCave.errMsg, |
506 | + | "New Box size is setting the long range cutoff radius " |
507 | + | "to %lf\n", |
508 | + | maxCutoff ); |
509 | + | painCave.isFatal = 0; |
510 | + | simError(); |
511 | + | rCut = maxCutoff; |
512 | + | } |
513 | + | |
514 | + | if( ecr > maxCutoff){ |
515 | + | sprintf( painCave.errMsg, |
516 | + | "New Box size is setting the electrostaticCutoffRadius " |
517 | + | "to %lf\n", |
518 | + | maxCutoff ); |
519 | + | painCave.isFatal = 0; |
520 | + | simError(); |
521 | + | ecr = maxCutoff; |
522 | + | } |
523 | + | |
524 | + | |
525 | + | } |
526 | + | |
527 | + | |
528 | + | if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1; |
529 | + | |
530 | + | // rlist is the 1.0 plus max( rcut, ecr ) |
531 | + | |
532 | + | ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0; |
533 | + | |
534 | + | if( cutChanged ){ |
535 | + | |
536 | + | notifyFortranCutOffs( &rCut, &rList, &ecr, &est ); |
537 | + | } |
538 | + | |
539 | + | oldEcr = ecr; |
540 | + | oldRcut = rCut; |
541 | + | } |
542 | + | |
543 | + | void SimInfo::addProperty(GenericData* prop){ |
544 | + | |
545 | + | map<string, GenericData*>::iterator result; |
546 | + | result = properties.find(prop->getID()); |
547 | + | |
548 | + | //we can't simply use properties[prop->getID()] = prop, |
549 | + | //it will cause memory leak if we already contain a propery which has the same name of prop |
550 | + | |
551 | + | if(result != properties.end()){ |
552 | + | |
553 | + | delete (*result).second; |
554 | + | (*result).second = prop; |
555 | + | |
556 | + | } |
557 | + | else{ |
558 | + | |
559 | + | properties[prop->getID()] = prop; |
560 | + | |
561 | + | } |
562 | + | |
563 | + | } |
564 | + | |
565 | + | GenericData* SimInfo::getProperty(const string& propName){ |
566 | + | |
567 | + | map<string, GenericData*>::iterator result; |
568 | + | |
569 | + | //string lowerCaseName = (); |
570 | + | |
571 | + | result = properties.find(propName); |
572 | + | |
573 | + | if(result != properties.end()) |
574 | + | return (*result).second; |
575 | + | else |
576 | + | return NULL; |
577 | + | } |
578 | + | |
579 | + | vector<GenericData*> SimInfo::getProperties(){ |
580 | + | |
581 | + | vector<GenericData*> result; |
582 | + | map<string, GenericData*>::iterator i; |
583 | + | |
584 | + | for(i = properties.begin(); i != properties.end(); i++) |
585 | + | result.push_back((*i).second); |
586 | + | |
587 | + | return result; |
588 | + | } |
589 | + | |
590 | + |
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