# | 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 28 | Line 54 | SimInfo::SimInfo(){ | |
54 | useGB = 0; | |
55 | useEAM = 0; | |
56 | ||
57 | + | wrapMeSimInfo( this ); |
58 | + | } |
59 | ||
60 | + | void SimInfo::setBox(double newBox[3]) { |
61 | + | |
62 | + | int i, j; |
63 | + | double tempMat[3][3]; |
64 | ||
65 | < | wrapMeSimInfo( this ); |
65 | > | for(i=0; i<3; i++) |
66 | > | for (j=0; j<3; j++) tempMat[i][j] = 0.0;; |
67 | > | |
68 | > | tempMat[0][0] = newBox[0]; |
69 | > | tempMat[1][1] = newBox[1]; |
70 | > | tempMat[2][2] = newBox[2]; |
71 | > | |
72 | > | setBoxM( tempMat ); |
73 | > | |
74 | > | } |
75 | > | |
76 | > | void SimInfo::setBoxM( double theBox[3][3] ){ |
77 | > | |
78 | > | int i, j, status; |
79 | > | double smallestBoxL, maxCutoff; |
80 | > | double FortranHmat[9]; // to preserve compatibility with Fortran the |
81 | > | // ordering in the array is as follows: |
82 | > | // [ 0 3 6 ] |
83 | > | // [ 1 4 7 ] |
84 | > | // [ 2 5 8 ] |
85 | > | double FortranHmatInv[9]; // the inverted Hmat (for Fortran); |
86 | > | |
87 | > | |
88 | > | if( !boxIsInit ) boxIsInit = 1; |
89 | > | |
90 | > | for(i=0; i < 3; i++) |
91 | > | for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j]; |
92 | > | |
93 | > | calcBoxL(); |
94 | > | calcHmatInv(); |
95 | > | |
96 | > | for(i=0; i < 3; i++) { |
97 | > | for (j=0; j < 3; j++) { |
98 | > | FortranHmat[3*j + i] = Hmat[i][j]; |
99 | > | FortranHmatInv[3*j + i] = HmatInv[i][j]; |
100 | > | } |
101 | > | } |
102 | > | |
103 | > | setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic); |
104 | > | |
105 | > | } |
106 | > | |
107 | > | |
108 | > | void SimInfo::getBoxM (double theBox[3][3]) { |
109 | > | |
110 | > | int i, j; |
111 | > | for(i=0; i<3; i++) |
112 | > | for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]; |
113 | > | } |
114 | > | |
115 | > | |
116 | > | void SimInfo::scaleBox(double scale) { |
117 | > | double theBox[3][3]; |
118 | > | int i, j; |
119 | > | |
120 | > | // cerr << "Scaling box by " << scale << "\n"; |
121 | > | |
122 | > | for(i=0; i<3; i++) |
123 | > | for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale; |
124 | > | |
125 | > | setBoxM(theBox); |
126 | > | |
127 | > | } |
128 | > | |
129 | > | void SimInfo::calcHmatInv( void ) { |
130 | > | |
131 | > | int i,j; |
132 | > | double smallDiag; |
133 | > | double tol; |
134 | > | double sanity[3][3]; |
135 | > | |
136 | > | invertMat3( Hmat, HmatInv ); |
137 | > | |
138 | > | // Check the inverse to make sure it is sane: |
139 | > | |
140 | > | matMul3( Hmat, HmatInv, sanity ); |
141 | > | |
142 | > | // check to see if Hmat is orthorhombic |
143 | > | |
144 | > | smallDiag = Hmat[0][0]; |
145 | > | if(smallDiag > Hmat[1][1]) smallDiag = Hmat[1][1]; |
146 | > | if(smallDiag > Hmat[2][2]) smallDiag = Hmat[2][2]; |
147 | > | tol = smallDiag * 1E-6; |
148 | > | |
149 | > | orthoRhombic = 1; |
150 | > | |
151 | > | for (i = 0; i < 3; i++ ) { |
152 | > | for (j = 0 ; j < 3; j++) { |
153 | > | if (i != j) { |
154 | > | if (orthoRhombic) { |
155 | > | if (Hmat[i][j] >= tol) orthoRhombic = 0; |
156 | > | } |
157 | > | } |
158 | > | } |
159 | > | } |
160 | > | } |
161 | > | |
162 | > | double SimInfo::matDet3(double a[3][3]) { |
163 | > | int i, j, k; |
164 | > | double determinant; |
165 | > | |
166 | > | determinant = 0.0; |
167 | > | |
168 | > | for(i = 0; i < 3; i++) { |
169 | > | j = (i+1)%3; |
170 | > | k = (i+2)%3; |
171 | > | |
172 | > | determinant += a[0][i] * (a[1][j]*a[2][k] - a[1][k]*a[2][j]); |
173 | > | } |
174 | > | |
175 | > | return determinant; |
176 | > | } |
177 | > | |
178 | > | void SimInfo::invertMat3(double a[3][3], double b[3][3]) { |
179 | > | |
180 | > | int i, j, k, l, m, n; |
181 | > | double determinant; |
182 | > | |
183 | > | determinant = matDet3( a ); |
184 | > | |
185 | > | if (determinant == 0.0) { |
186 | > | sprintf( painCave.errMsg, |
187 | > | "Can't invert a matrix with a zero determinant!\n"); |
188 | > | painCave.isFatal = 1; |
189 | > | simError(); |
190 | > | } |
191 | > | |
192 | > | for (i=0; i < 3; i++) { |
193 | > | j = (i+1)%3; |
194 | > | k = (i+2)%3; |
195 | > | for(l = 0; l < 3; l++) { |
196 | > | m = (l+1)%3; |
197 | > | n = (l+2)%3; |
198 | > | |
199 | > | b[l][i] = (a[j][m]*a[k][n] - a[j][n]*a[k][m]) / determinant; |
200 | > | } |
201 | > | } |
202 | > | } |
203 | > | |
204 | > | void SimInfo::matMul3(double a[3][3], double b[3][3], double c[3][3]) { |
205 | > | double r00, r01, r02, r10, r11, r12, r20, r21, r22; |
206 | > | |
207 | > | r00 = a[0][0]*b[0][0] + a[0][1]*b[1][0] + a[0][2]*b[2][0]; |
208 | > | r01 = a[0][0]*b[0][1] + a[0][1]*b[1][1] + a[0][2]*b[2][1]; |
209 | > | r02 = a[0][0]*b[0][2] + a[0][1]*b[1][2] + a[0][2]*b[2][2]; |
210 | > | |
211 | > | r10 = a[1][0]*b[0][0] + a[1][1]*b[1][0] + a[1][2]*b[2][0]; |
212 | > | r11 = a[1][0]*b[0][1] + a[1][1]*b[1][1] + a[1][2]*b[2][1]; |
213 | > | r12 = a[1][0]*b[0][2] + a[1][1]*b[1][2] + a[1][2]*b[2][2]; |
214 | > | |
215 | > | r20 = a[2][0]*b[0][0] + a[2][1]*b[1][0] + a[2][2]*b[2][0]; |
216 | > | r21 = a[2][0]*b[0][1] + a[2][1]*b[1][1] + a[2][2]*b[2][1]; |
217 | > | r22 = a[2][0]*b[0][2] + a[2][1]*b[1][2] + a[2][2]*b[2][2]; |
218 | > | |
219 | > | c[0][0] = r00; c[0][1] = r01; c[0][2] = r02; |
220 | > | c[1][0] = r10; c[1][1] = r11; c[1][2] = r12; |
221 | > | c[2][0] = r20; c[2][1] = r21; c[2][2] = r22; |
222 | > | } |
223 | > | |
224 | > | void SimInfo::matVecMul3(double m[3][3], double inVec[3], double outVec[3]) { |
225 | > | double a0, a1, a2; |
226 | > | |
227 | > | a0 = inVec[0]; a1 = inVec[1]; a2 = inVec[2]; |
228 | > | |
229 | > | outVec[0] = m[0][0]*a0 + m[0][1]*a1 + m[0][2]*a2; |
230 | > | outVec[1] = m[1][0]*a0 + m[1][1]*a1 + m[1][2]*a2; |
231 | > | outVec[2] = m[2][0]*a0 + m[2][1]*a1 + m[2][2]*a2; |
232 | > | } |
233 | > | |
234 | > | void SimInfo::transposeMat3(double in[3][3], double out[3][3]) { |
235 | > | double temp[3][3]; |
236 | > | int i, j; |
237 | > | |
238 | > | for (i = 0; i < 3; i++) { |
239 | > | for (j = 0; j < 3; j++) { |
240 | > | temp[j][i] = in[i][j]; |
241 | > | } |
242 | > | } |
243 | > | for (i = 0; i < 3; i++) { |
244 | > | for (j = 0; j < 3; j++) { |
245 | > | out[i][j] = temp[i][j]; |
246 | > | } |
247 | > | } |
248 | > | } |
249 | > | |
250 | > | void SimInfo::printMat3(double A[3][3] ){ |
251 | > | |
252 | > | std::cerr |
253 | > | << "[ " << A[0][0] << ", " << A[0][1] << ", " << A[0][2] << " ]\n" |
254 | > | << "[ " << A[1][0] << ", " << A[1][1] << ", " << A[1][2] << " ]\n" |
255 | > | << "[ " << A[2][0] << ", " << A[2][1] << ", " << A[2][2] << " ]\n"; |
256 | > | } |
257 | > | |
258 | > | void SimInfo::printMat9(double A[9] ){ |
259 | > | |
260 | > | std::cerr |
261 | > | << "[ " << A[0] << ", " << A[1] << ", " << A[2] << " ]\n" |
262 | > | << "[ " << A[3] << ", " << A[4] << ", " << A[5] << " ]\n" |
263 | > | << "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n"; |
264 | > | } |
265 | > | |
266 | > | void SimInfo::calcBoxL( void ){ |
267 | > | |
268 | > | double dx, dy, dz, dsq; |
269 | > | int i; |
270 | > | |
271 | > | // boxVol = Determinant of Hmat |
272 | > | |
273 | > | boxVol = matDet3( Hmat ); |
274 | > | |
275 | > | // boxLx |
276 | > | |
277 | > | dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0]; |
278 | > | dsq = dx*dx + dy*dy + dz*dz; |
279 | > | boxL[0] = sqrt( dsq ); |
280 | > | maxCutoff = 0.5 * boxL[0]; |
281 | > | |
282 | > | // boxLy |
283 | > | |
284 | > | dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1]; |
285 | > | dsq = dx*dx + dy*dy + dz*dz; |
286 | > | boxL[1] = sqrt( dsq ); |
287 | > | if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1]; |
288 | > | |
289 | > | // boxLz |
290 | > | |
291 | > | dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2]; |
292 | > | dsq = dx*dx + dy*dy + dz*dz; |
293 | > | boxL[2] = sqrt( dsq ); |
294 | > | if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2]; |
295 | > | |
296 | } | |
297 | ||
298 | + | |
299 | + | void SimInfo::wrapVector( double thePos[3] ){ |
300 | + | |
301 | + | int i, j, k; |
302 | + | double scaled[3]; |
303 | + | |
304 | + | if( !orthoRhombic ){ |
305 | + | // calc the scaled coordinates. |
306 | + | |
307 | + | |
308 | + | matVecMul3(HmatInv, thePos, scaled); |
309 | + | |
310 | + | for(i=0; i<3; i++) |
311 | + | scaled[i] -= roundMe(scaled[i]); |
312 | + | |
313 | + | // calc the wrapped real coordinates from the wrapped scaled coordinates |
314 | + | |
315 | + | matVecMul3(Hmat, scaled, thePos); |
316 | + | |
317 | + | } |
318 | + | else{ |
319 | + | // calc the scaled coordinates. |
320 | + | |
321 | + | for(i=0; i<3; i++) |
322 | + | scaled[i] = thePos[i]*HmatInv[i][i]; |
323 | + | |
324 | + | // wrap the scaled coordinates |
325 | + | |
326 | + | for(i=0; i<3; i++) |
327 | + | scaled[i] -= roundMe(scaled[i]); |
328 | + | |
329 | + | // calc the wrapped real coordinates from the wrapped scaled coordinates |
330 | + | |
331 | + | for(i=0; i<3; i++) |
332 | + | thePos[i] = scaled[i]*Hmat[i][i]; |
333 | + | } |
334 | + | |
335 | + | } |
336 | + | |
337 | + | |
338 | + | int SimInfo::getNDF(){ |
339 | + | int ndf_local, ndf; |
340 | + | |
341 | + | ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints; |
342 | + | |
343 | + | #ifdef IS_MPI |
344 | + | MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
345 | + | #else |
346 | + | ndf = ndf_local; |
347 | + | #endif |
348 | + | |
349 | + | ndf = ndf - 3; |
350 | + | |
351 | + | return ndf; |
352 | + | } |
353 | + | |
354 | + | int SimInfo::getNDFraw() { |
355 | + | int ndfRaw_local, ndfRaw; |
356 | + | |
357 | + | // Raw degrees of freedom that we have to set |
358 | + | ndfRaw_local = 3 * n_atoms + 3 * n_oriented; |
359 | + | |
360 | + | #ifdef IS_MPI |
361 | + | MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
362 | + | #else |
363 | + | ndfRaw = ndfRaw_local; |
364 | + | #endif |
365 | + | |
366 | + | return ndfRaw; |
367 | + | } |
368 | + | |
369 | void SimInfo::refreshSim(){ | |
370 | ||
371 | simtype fInfo; | |
372 | int isError; | |
373 | + | int n_global; |
374 | + | int* excl; |
375 | ||
376 | < | fInfo.box[0] = box_x; |
42 | < | fInfo.box[1] = box_y; |
43 | < | fInfo.box[2] = box_z; |
376 | > | fInfo.dielect = 0.0; |
377 | ||
378 | < | fInfo.rlist = rList; |
379 | < | fInfo.rcut = rCut; |
380 | < | fInfo.rrf = ecr; |
48 | < | fInfo.rt = ecr - est; |
49 | < | fInfo.dielect = dielectric; |
378 | > | if( useDipole ){ |
379 | > | if( useReactionField )fInfo.dielect = dielectric; |
380 | > | } |
381 | ||
382 | fInfo.SIM_uses_PBC = usePBC; | |
383 | + | //fInfo.SIM_uses_LJ = 0; |
384 | fInfo.SIM_uses_LJ = useLJ; | |
385 | < | //fInfo.SIM_uses_sticky = useSticky; |
386 | < | fInfo.SIM_uses_sticky = 0; |
385 | > | fInfo.SIM_uses_sticky = useSticky; |
386 | > | //fInfo.SIM_uses_sticky = 0; |
387 | fInfo.SIM_uses_dipoles = useDipole; | |
388 | //fInfo.SIM_uses_dipoles = 0; | |
389 | < | fInfo.SIM_uses_RF = useReactionField; |
389 | > | //fInfo.SIM_uses_RF = useReactionField; |
390 | > | fInfo.SIM_uses_RF = 0; |
391 | fInfo.SIM_uses_GB = useGB; | |
392 | fInfo.SIM_uses_EAM = useEAM; | |
393 | ||
394 | + | excl = Exclude::getArray(); |
395 | ||
396 | + | #ifdef IS_MPI |
397 | + | n_global = mpiSim->getTotAtoms(); |
398 | + | #else |
399 | + | n_global = n_atoms; |
400 | + | #endif |
401 | + | |
402 | isError = 0; | |
403 | ||
404 | < | fInfo; |
405 | < | n_atoms; |
406 | < | identArray; |
67 | < | n_exclude; |
68 | < | excludes; |
69 | < | nGlobalExcludes; |
70 | < | globalExcludes; |
71 | < | isError; |
404 | > | setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl, |
405 | > | &nGlobalExcludes, globalExcludes, molMembershipArray, |
406 | > | &isError ); |
407 | ||
73 | – | setFsimulation( &fInfo, &n_atoms, identArray, &n_exclude, excludes, &nGlobalExcludes, globalExcludes, &isError ); |
74 | – | |
408 | if( isError ){ | |
409 | ||
410 | sprintf( painCave.errMsg, | |
# | Line 85 | Line 418 | void SimInfo::refreshSim(){ | |
418 | "succesfully sent the simulation information to fortran.\n"); | |
419 | MPIcheckPoint(); | |
420 | #endif // is_mpi | |
421 | + | |
422 | + | this->ndf = this->getNDF(); |
423 | + | this->ndfRaw = this->getNDFraw(); |
424 | + | |
425 | } | |
426 | ||
427 | + | |
428 | + | void SimInfo::setRcut( double theRcut ){ |
429 | + | |
430 | + | if( !haveOrigRcut ){ |
431 | + | haveOrigRcut = 1; |
432 | + | origRcut = theRcut; |
433 | + | } |
434 | + | |
435 | + | rCut = theRcut; |
436 | + | checkCutOffs(); |
437 | + | } |
438 | + | |
439 | + | void SimInfo::setEcr( double theEcr ){ |
440 | + | |
441 | + | if( !haveOrigEcr ){ |
442 | + | haveOrigEcr = 1; |
443 | + | origEcr = theEcr; |
444 | + | } |
445 | + | |
446 | + | ecr = theEcr; |
447 | + | checkCutOffs(); |
448 | + | } |
449 | + | |
450 | + | void SimInfo::setEcr( double theEcr, double theEst ){ |
451 | + | |
452 | + | est = theEst; |
453 | + | setEcr( theEcr ); |
454 | + | } |
455 | + | |
456 | + | |
457 | + | void SimInfo::checkCutOffs( void ){ |
458 | + | |
459 | + | int cutChanged = 0; |
460 | + | |
461 | + | if( boxIsInit ){ |
462 | + | |
463 | + | //we need to check cutOffs against the box |
464 | + | |
465 | + | if( maxCutoff > rCut ){ |
466 | + | if( rCut < origRcut ){ |
467 | + | rCut = origRcut; |
468 | + | if (rCut > maxCutoff) rCut = maxCutoff; |
469 | + | |
470 | + | sprintf( painCave.errMsg, |
471 | + | "New Box size is setting the long range cutoff radius " |
472 | + | "to %lf\n", |
473 | + | rCut ); |
474 | + | painCave.isFatal = 0; |
475 | + | simError(); |
476 | + | } |
477 | + | } |
478 | + | |
479 | + | if( maxCutoff > ecr ){ |
480 | + | if( ecr < origEcr ){ |
481 | + | rCut = origEcr; |
482 | + | if (ecr > maxCutoff) ecr = maxCutoff; |
483 | + | |
484 | + | sprintf( painCave.errMsg, |
485 | + | "New Box size is setting the electrostaticCutoffRadius " |
486 | + | "to %lf\n", |
487 | + | ecr ); |
488 | + | painCave.isFatal = 0; |
489 | + | simError(); |
490 | + | } |
491 | + | } |
492 | + | |
493 | + | |
494 | + | if (rCut > maxCutoff) { |
495 | + | sprintf( painCave.errMsg, |
496 | + | "New Box size is setting the long range cutoff radius " |
497 | + | "to %lf\n", |
498 | + | maxCutoff ); |
499 | + | painCave.isFatal = 0; |
500 | + | simError(); |
501 | + | rCut = maxCutoff; |
502 | + | } |
503 | + | |
504 | + | if( ecr > maxCutoff){ |
505 | + | sprintf( painCave.errMsg, |
506 | + | "New Box size is setting the electrostaticCutoffRadius " |
507 | + | "to %lf\n", |
508 | + | maxCutoff ); |
509 | + | painCave.isFatal = 0; |
510 | + | simError(); |
511 | + | ecr = maxCutoff; |
512 | + | } |
513 | + | |
514 | + | |
515 | + | } |
516 | + | |
517 | + | |
518 | + | if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1; |
519 | + | |
520 | + | // rlist is the 1.0 plus max( rcut, ecr ) |
521 | + | |
522 | + | ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0; |
523 | + | |
524 | + | if( cutChanged ){ |
525 | + | |
526 | + | notifyFortranCutOffs( &rCut, &rList, &ecr, &est ); |
527 | + | } |
528 | + | |
529 | + | oldEcr = ecr; |
530 | + | oldRcut = rCut; |
531 | + | } |
– | Removed lines |
+ | Added lines |
< | Changed lines |
> | Changed lines |