# | 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 | + | rCut = 0.0; |
37 | + | ecr = 0.0; |
38 | + | est = 0.0; |
39 | ||
40 | usePBC = 0; | |
41 | useLJ = 0; | |
# | Line 28 | Line 45 | SimInfo::SimInfo(){ | |
45 | useGB = 0; | |
46 | useEAM = 0; | |
47 | ||
48 | + | wrapMeSimInfo( this ); |
49 | + | } |
50 | ||
51 | + | void SimInfo::setBox(double newBox[3]) { |
52 | + | |
53 | + | int i, j; |
54 | + | double tempMat[3][3]; |
55 | ||
56 | < | wrapMeSimInfo( this ); |
56 | > | for(i=0; i<3; i++) |
57 | > | for (j=0; j<3; j++) tempMat[i][j] = 0.0;; |
58 | > | |
59 | > | tempMat[0][0] = newBox[0]; |
60 | > | tempMat[1][1] = newBox[1]; |
61 | > | tempMat[2][2] = newBox[2]; |
62 | > | |
63 | > | setBoxM( tempMat ); |
64 | > | |
65 | } | |
66 | ||
67 | + | void SimInfo::setBoxM( double theBox[3][3] ){ |
68 | + | |
69 | + | int i, j, status; |
70 | + | double smallestBoxL, maxCutoff; |
71 | + | double FortranHmat[9]; // to preserve compatibility with Fortran the |
72 | + | // ordering in the array is as follows: |
73 | + | // [ 0 3 6 ] |
74 | + | // [ 1 4 7 ] |
75 | + | // [ 2 5 8 ] |
76 | + | double FortranHmatInv[9]; // the inverted Hmat (for Fortran); |
77 | + | |
78 | + | |
79 | + | for(i=0; i < 3; i++) |
80 | + | for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j]; |
81 | + | |
82 | + | // cerr |
83 | + | // << "setting Hmat ->\n" |
84 | + | // << "[ " << Hmat[0][0] << ", " << Hmat[0][1] << ", " << Hmat[0][2] << " ]\n" |
85 | + | // << "[ " << Hmat[1][0] << ", " << Hmat[1][1] << ", " << Hmat[1][2] << " ]\n" |
86 | + | // << "[ " << Hmat[2][0] << ", " << Hmat[2][1] << ", " << Hmat[2][2] << " ]\n"; |
87 | + | |
88 | + | calcBoxL(); |
89 | + | calcHmatInv(); |
90 | + | |
91 | + | for(i=0; i < 3; i++) { |
92 | + | for (j=0; j < 3; j++) { |
93 | + | FortranHmat[3*j + i] = Hmat[i][j]; |
94 | + | FortranHmatInv[3*j + i] = HmatInv[i][j]; |
95 | + | } |
96 | + | } |
97 | + | |
98 | + | setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic); |
99 | + | |
100 | + | smallestBoxL = boxL[0]; |
101 | + | if (boxL[1] < smallestBoxL) smallestBoxL = boxL[1]; |
102 | + | if (boxL[2] > smallestBoxL) smallestBoxL = boxL[2]; |
103 | + | |
104 | + | maxCutoff = smallestBoxL / 2.0; |
105 | + | |
106 | + | if (rList > maxCutoff) { |
107 | + | sprintf( painCave.errMsg, |
108 | + | "New Box size is forcing neighborlist radius down to %lf\n", |
109 | + | maxCutoff ); |
110 | + | painCave.isFatal = 0; |
111 | + | simError(); |
112 | + | rList = maxCutoff; |
113 | + | |
114 | + | if (rCut > (rList - 1.0)) { |
115 | + | sprintf( painCave.errMsg, |
116 | + | "New Box size is forcing LJ cutoff radius down to %lf\n", |
117 | + | rList - 1.0 ); |
118 | + | painCave.isFatal = 0; |
119 | + | simError(); |
120 | + | rCut = rList - 1.0; |
121 | + | } |
122 | + | |
123 | + | if( ecr > (rList - 1.0) ){ |
124 | + | sprintf( painCave.errMsg, |
125 | + | "New Box size is forcing electrostaticCutoffRadius " |
126 | + | "down to %lf\n" |
127 | + | "electrostaticSkinThickness is now %lf\n", |
128 | + | rList - 1.0, 0.05*(rList-1.0) ); |
129 | + | painCave.isFatal = 0; |
130 | + | simError(); |
131 | + | ecr = maxCutoff; |
132 | + | est = 0.05 * ecr; |
133 | + | } |
134 | + | |
135 | + | // At least one of the radii changed, so we need a refresh: |
136 | + | refreshSim(); |
137 | + | } |
138 | + | } |
139 | + | |
140 | + | |
141 | + | void SimInfo::getBoxM (double theBox[3][3]) { |
142 | + | |
143 | + | int i, j; |
144 | + | for(i=0; i<3; i++) |
145 | + | for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]; |
146 | + | } |
147 | + | |
148 | + | |
149 | + | void SimInfo::scaleBox(double scale) { |
150 | + | double theBox[3][3]; |
151 | + | int i, j; |
152 | + | |
153 | + | // cerr << "Scaling box by " << scale << "\n"; |
154 | + | |
155 | + | for(i=0; i<3; i++) |
156 | + | for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale; |
157 | + | |
158 | + | setBoxM(theBox); |
159 | + | |
160 | + | } |
161 | + | |
162 | + | void SimInfo::calcHmatInv( void ) { |
163 | + | |
164 | + | int i,j; |
165 | + | double smallDiag; |
166 | + | double tol; |
167 | + | double sanity[3][3]; |
168 | + | |
169 | + | invertMat3( Hmat, HmatInv ); |
170 | + | |
171 | + | // Check the inverse to make sure it is sane: |
172 | + | |
173 | + | matMul3( Hmat, HmatInv, sanity ); |
174 | + | |
175 | + | // check to see if Hmat is orthorhombic |
176 | + | |
177 | + | smallDiag = Hmat[0][0]; |
178 | + | if(smallDiag > Hmat[1][1]) smallDiag = Hmat[1][1]; |
179 | + | if(smallDiag > Hmat[2][2]) smallDiag = Hmat[2][2]; |
180 | + | tol = smallDiag * 1E-6; |
181 | + | |
182 | + | orthoRhombic = 1; |
183 | + | |
184 | + | for (i = 0; i < 3; i++ ) { |
185 | + | for (j = 0 ; j < 3; j++) { |
186 | + | if (i != j) { |
187 | + | if (orthoRhombic) { |
188 | + | if (Hmat[i][j] >= tol) orthoRhombic = 0; |
189 | + | } |
190 | + | } |
191 | + | } |
192 | + | } |
193 | + | } |
194 | + | |
195 | + | double SimInfo::matDet3(double a[3][3]) { |
196 | + | int i, j, k; |
197 | + | double determinant; |
198 | + | |
199 | + | determinant = 0.0; |
200 | + | |
201 | + | for(i = 0; i < 3; i++) { |
202 | + | j = (i+1)%3; |
203 | + | k = (i+2)%3; |
204 | + | |
205 | + | determinant += a[0][i] * (a[1][j]*a[2][k] - a[1][k]*a[2][j]); |
206 | + | } |
207 | + | |
208 | + | return determinant; |
209 | + | } |
210 | + | |
211 | + | void SimInfo::invertMat3(double a[3][3], double b[3][3]) { |
212 | + | |
213 | + | int i, j, k, l, m, n; |
214 | + | double determinant; |
215 | + | |
216 | + | determinant = matDet3( a ); |
217 | + | |
218 | + | if (determinant == 0.0) { |
219 | + | sprintf( painCave.errMsg, |
220 | + | "Can't invert a matrix with a zero determinant!\n"); |
221 | + | painCave.isFatal = 1; |
222 | + | simError(); |
223 | + | } |
224 | + | |
225 | + | for (i=0; i < 3; i++) { |
226 | + | j = (i+1)%3; |
227 | + | k = (i+2)%3; |
228 | + | for(l = 0; l < 3; l++) { |
229 | + | m = (l+1)%3; |
230 | + | n = (l+2)%3; |
231 | + | |
232 | + | b[l][i] = (a[j][m]*a[k][n] - a[j][n]*a[k][m]) / determinant; |
233 | + | } |
234 | + | } |
235 | + | } |
236 | + | |
237 | + | void SimInfo::matMul3(double a[3][3], double b[3][3], double c[3][3]) { |
238 | + | double r00, r01, r02, r10, r11, r12, r20, r21, r22; |
239 | + | |
240 | + | r00 = a[0][0]*b[0][0] + a[0][1]*b[1][0] + a[0][2]*b[2][0]; |
241 | + | r01 = a[0][0]*b[0][1] + a[0][1]*b[1][1] + a[0][2]*b[2][1]; |
242 | + | r02 = a[0][0]*b[0][2] + a[0][1]*b[1][2] + a[0][2]*b[2][2]; |
243 | + | |
244 | + | r10 = a[1][0]*b[0][0] + a[1][1]*b[1][0] + a[1][2]*b[2][0]; |
245 | + | r11 = a[1][0]*b[0][1] + a[1][1]*b[1][1] + a[1][2]*b[2][1]; |
246 | + | r12 = a[1][0]*b[0][2] + a[1][1]*b[1][2] + a[1][2]*b[2][2]; |
247 | + | |
248 | + | r20 = a[2][0]*b[0][0] + a[2][1]*b[1][0] + a[2][2]*b[2][0]; |
249 | + | r21 = a[2][0]*b[0][1] + a[2][1]*b[1][1] + a[2][2]*b[2][1]; |
250 | + | r22 = a[2][0]*b[0][2] + a[2][1]*b[1][2] + a[2][2]*b[2][2]; |
251 | + | |
252 | + | c[0][0] = r00; c[0][1] = r01; c[0][2] = r02; |
253 | + | c[1][0] = r10; c[1][1] = r11; c[1][2] = r12; |
254 | + | c[2][0] = r20; c[2][1] = r21; c[2][2] = r22; |
255 | + | } |
256 | + | |
257 | + | void SimInfo::matVecMul3(double m[3][3], double inVec[3], double outVec[3]) { |
258 | + | double a0, a1, a2; |
259 | + | |
260 | + | a0 = inVec[0]; a1 = inVec[1]; a2 = inVec[2]; |
261 | + | |
262 | + | outVec[0] = m[0][0]*a0 + m[0][1]*a1 + m[0][2]*a2; |
263 | + | outVec[1] = m[1][0]*a0 + m[1][1]*a1 + m[1][2]*a2; |
264 | + | outVec[2] = m[2][0]*a0 + m[2][1]*a1 + m[2][2]*a2; |
265 | + | } |
266 | + | |
267 | + | void SimInfo::transposeMat3(double in[3][3], double out[3][3]) { |
268 | + | double temp[3][3]; |
269 | + | int i, j; |
270 | + | |
271 | + | for (i = 0; i < 3; i++) { |
272 | + | for (j = 0; j < 3; j++) { |
273 | + | temp[j][i] = in[i][j]; |
274 | + | } |
275 | + | } |
276 | + | for (i = 0; i < 3; i++) { |
277 | + | for (j = 0; j < 3; j++) { |
278 | + | out[i][j] = temp[i][j]; |
279 | + | } |
280 | + | } |
281 | + | } |
282 | + | |
283 | + | void SimInfo::printMat3(double A[3][3] ){ |
284 | + | |
285 | + | std::cerr |
286 | + | << "[ " << A[0][0] << ", " << A[0][1] << ", " << A[0][2] << " ]\n" |
287 | + | << "[ " << A[1][0] << ", " << A[1][1] << ", " << A[1][2] << " ]\n" |
288 | + | << "[ " << A[2][0] << ", " << A[2][1] << ", " << A[2][2] << " ]\n"; |
289 | + | } |
290 | + | |
291 | + | void SimInfo::printMat9(double A[9] ){ |
292 | + | |
293 | + | std::cerr |
294 | + | << "[ " << A[0] << ", " << A[1] << ", " << A[2] << " ]\n" |
295 | + | << "[ " << A[3] << ", " << A[4] << ", " << A[5] << " ]\n" |
296 | + | << "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n"; |
297 | + | } |
298 | + | |
299 | + | void SimInfo::calcBoxL( void ){ |
300 | + | |
301 | + | double dx, dy, dz, dsq; |
302 | + | int i; |
303 | + | |
304 | + | // boxVol = Determinant of Hmat |
305 | + | |
306 | + | boxVol = matDet3( Hmat ); |
307 | + | |
308 | + | // boxLx |
309 | + | |
310 | + | dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0]; |
311 | + | dsq = dx*dx + dy*dy + dz*dz; |
312 | + | boxL[0] = sqrt( dsq ); |
313 | + | |
314 | + | // boxLy |
315 | + | |
316 | + | dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1]; |
317 | + | dsq = dx*dx + dy*dy + dz*dz; |
318 | + | boxL[1] = sqrt( dsq ); |
319 | + | |
320 | + | // boxLz |
321 | + | |
322 | + | dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2]; |
323 | + | dsq = dx*dx + dy*dy + dz*dz; |
324 | + | boxL[2] = sqrt( dsq ); |
325 | + | |
326 | + | } |
327 | + | |
328 | + | |
329 | + | void SimInfo::wrapVector( double thePos[3] ){ |
330 | + | |
331 | + | int i, j, k; |
332 | + | double scaled[3]; |
333 | + | |
334 | + | if( !orthoRhombic ){ |
335 | + | // calc the scaled coordinates. |
336 | + | |
337 | + | |
338 | + | matVecMul3(HmatInv, thePos, scaled); |
339 | + | |
340 | + | for(i=0; i<3; i++) |
341 | + | scaled[i] -= roundMe(scaled[i]); |
342 | + | |
343 | + | // calc the wrapped real coordinates from the wrapped scaled coordinates |
344 | + | |
345 | + | matVecMul3(Hmat, scaled, thePos); |
346 | + | |
347 | + | } |
348 | + | else{ |
349 | + | // calc the scaled coordinates. |
350 | + | |
351 | + | for(i=0; i<3; i++) |
352 | + | scaled[i] = thePos[i]*HmatInv[i][i]; |
353 | + | |
354 | + | // wrap the scaled coordinates |
355 | + | |
356 | + | for(i=0; i<3; i++) |
357 | + | scaled[i] -= roundMe(scaled[i]); |
358 | + | |
359 | + | // calc the wrapped real coordinates from the wrapped scaled coordinates |
360 | + | |
361 | + | for(i=0; i<3; i++) |
362 | + | thePos[i] = scaled[i]*Hmat[i][i]; |
363 | + | } |
364 | + | |
365 | + | } |
366 | + | |
367 | + | |
368 | + | int SimInfo::getNDF(){ |
369 | + | int ndf_local, ndf; |
370 | + | |
371 | + | ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints; |
372 | + | |
373 | + | #ifdef IS_MPI |
374 | + | MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
375 | + | #else |
376 | + | ndf = ndf_local; |
377 | + | #endif |
378 | + | |
379 | + | ndf = ndf - 3; |
380 | + | |
381 | + | return ndf; |
382 | + | } |
383 | + | |
384 | + | int SimInfo::getNDFraw() { |
385 | + | int ndfRaw_local, ndfRaw; |
386 | + | |
387 | + | // Raw degrees of freedom that we have to set |
388 | + | ndfRaw_local = 3 * n_atoms + 3 * n_oriented; |
389 | + | |
390 | + | #ifdef IS_MPI |
391 | + | MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
392 | + | #else |
393 | + | ndfRaw = ndfRaw_local; |
394 | + | #endif |
395 | + | |
396 | + | return ndfRaw; |
397 | + | } |
398 | + | |
399 | void SimInfo::refreshSim(){ | |
400 | ||
401 | simtype fInfo; | |
402 | int isError; | |
403 | + | int n_global; |
404 | + | int* excl; |
405 | + | |
406 | + | fInfo.rrf = 0.0; |
407 | + | fInfo.rt = 0.0; |
408 | + | fInfo.dielect = 0.0; |
409 | ||
41 | – | fInfo.box[0] = box_x; |
42 | – | fInfo.box[1] = box_y; |
43 | – | fInfo.box[2] = box_z; |
44 | – | |
410 | fInfo.rlist = rList; | |
411 | fInfo.rcut = rCut; | |
47 | – | fInfo.rrf = rRF; |
48 | – | fInfo.rt = 0.95 * rRF; |
49 | – | fInfo.dielect = dielectric; |
50 | – | |
412 | ||
413 | + | if( useDipole ){ |
414 | + | fInfo.rrf = ecr; |
415 | + | fInfo.rt = ecr - est; |
416 | + | if( useReactionField )fInfo.dielect = dielectric; |
417 | + | } |
418 | + | |
419 | fInfo.SIM_uses_PBC = usePBC; | |
420 | + | //fInfo.SIM_uses_LJ = 0; |
421 | fInfo.SIM_uses_LJ = useLJ; | |
422 | fInfo.SIM_uses_sticky = useSticky; | |
423 | + | //fInfo.SIM_uses_sticky = 0; |
424 | fInfo.SIM_uses_dipoles = useDipole; | |
425 | < | fInfo.SIM_uses_RF = useReactionField; |
425 | > | //fInfo.SIM_uses_dipoles = 0; |
426 | > | //fInfo.SIM_uses_RF = useReactionField; |
427 | > | fInfo.SIM_uses_RF = 0; |
428 | fInfo.SIM_uses_GB = useGB; | |
429 | fInfo.SIM_uses_EAM = useEAM; | |
430 | ||
431 | + | excl = Exclude::getArray(); |
432 | ||
433 | + | #ifdef IS_MPI |
434 | + | n_global = mpiSim->getTotAtoms(); |
435 | + | #else |
436 | + | n_global = n_atoms; |
437 | + | #endif |
438 | + | |
439 | isError = 0; | |
440 | ||
441 | < | fInfo; |
442 | < | n_atoms; |
443 | < | identArray; |
66 | < | n_exclude; |
67 | < | excludes; |
68 | < | nGlobalExcludes; |
69 | < | globalExcludes; |
70 | < | isError; |
441 | > | setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl, |
442 | > | &nGlobalExcludes, globalExcludes, molMembershipArray, |
443 | > | &isError ); |
444 | ||
72 | – | setFsimulation( &fInfo, &n_atoms, identArray, &n_exclude, excludes, &nGlobalExcludes, globalExcludes, &isError ); |
73 | – | |
445 | if( isError ){ | |
446 | ||
447 | sprintf( painCave.errMsg, | |
# | Line 84 | Line 455 | void SimInfo::refreshSim(){ | |
455 | "succesfully sent the simulation information to fortran.\n"); | |
456 | MPIcheckPoint(); | |
457 | #endif // is_mpi | |
458 | + | |
459 | + | this->ndf = this->getNDF(); |
460 | + | this->ndfRaw = this->getNDFraw(); |
461 | + | |
462 | } | |
463 |
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+ | Added lines |
< | Changed lines |
> | Changed lines |