# | Line 1 | Line 1 | |
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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 35 | Line 47 | void SimInfo::setBox(double newBox[3]) { | |
47 | } | |
48 | ||
49 | void SimInfo::setBox(double newBox[3]) { | |
50 | < | box_x = newBox[0]; |
51 | < | box_y = newBox[1]; |
52 | < | box_z = newBox[2]; |
53 | < | setFortranBoxSize(newBox); |
50 | > | |
51 | > | int i, j; |
52 | > | double tempMat[3][3]; |
53 | > | |
54 | > | for(i=0; i<3; i++) |
55 | > | for (j=0; j<3; j++) tempMat[i][j] = 0.0;; |
56 | > | |
57 | > | tempMat[0][0] = newBox[0]; |
58 | > | tempMat[1][1] = newBox[1]; |
59 | > | tempMat[2][2] = newBox[2]; |
60 | > | |
61 | > | setBoxM( tempMat ); |
62 | > | |
63 | } | |
64 | ||
65 | < | void SimInfo::getBox(double theBox[3]) { |
66 | < | theBox[0] = box_x; |
67 | < | theBox[1] = box_y; |
68 | < | theBox[2] = box_z; |
65 | > | void SimInfo::setBoxM( double theBox[3][3] ){ |
66 | > | |
67 | > | int i, j, status; |
68 | > | double smallestBoxL, maxCutoff; |
69 | > | double FortranHmat[9]; // to preserve compatibility with Fortran the |
70 | > | // ordering in the array is as follows: |
71 | > | // [ 0 3 6 ] |
72 | > | // [ 1 4 7 ] |
73 | > | // [ 2 5 8 ] |
74 | > | double FortranHmatInv[9]; // the inverted Hmat (for Fortran); |
75 | > | |
76 | > | |
77 | > | for(i=0; i < 3; i++) |
78 | > | for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j]; |
79 | > | |
80 | > | // cerr |
81 | > | // << "setting Hmat ->\n" |
82 | > | // << "[ " << Hmat[0][0] << ", " << Hmat[0][1] << ", " << Hmat[0][2] << " ]\n" |
83 | > | // << "[ " << Hmat[1][0] << ", " << Hmat[1][1] << ", " << Hmat[1][2] << " ]\n" |
84 | > | // << "[ " << Hmat[2][0] << ", " << Hmat[2][1] << ", " << Hmat[2][2] << " ]\n"; |
85 | > | |
86 | > | calcBoxL(); |
87 | > | calcHmatInv(); |
88 | > | |
89 | > | for(i=0; i < 3; i++) { |
90 | > | for (j=0; j < 3; j++) { |
91 | > | FortranHmat[3*j + i] = Hmat[i][j]; |
92 | > | FortranHmatInv[3*j + i] = HmatInv[i][j]; |
93 | > | } |
94 | > | } |
95 | > | |
96 | > | setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic); |
97 | > | |
98 | > | smallestBoxL = boxLx; |
99 | > | if (boxLy < smallestBoxL) smallestBoxL = boxLy; |
100 | > | if (boxLz < smallestBoxL) smallestBoxL = boxLz; |
101 | > | |
102 | > | maxCutoff = smallestBoxL / 2.0; |
103 | > | |
104 | > | if (rList > maxCutoff) { |
105 | > | sprintf( painCave.errMsg, |
106 | > | "New Box size is forcing neighborlist radius down to %lf\n", |
107 | > | maxCutoff ); |
108 | > | painCave.isFatal = 0; |
109 | > | simError(); |
110 | > | |
111 | > | rList = maxCutoff; |
112 | > | |
113 | > | sprintf( painCave.errMsg, |
114 | > | "New Box size is forcing cutoff radius down to %lf\n", |
115 | > | maxCutoff - 1.0 ); |
116 | > | painCave.isFatal = 0; |
117 | > | simError(); |
118 | > | |
119 | > | rCut = rList - 1.0; |
120 | > | |
121 | > | // list radius changed so we have to refresh the simulation structure. |
122 | > | refreshSim(); |
123 | > | } |
124 | > | |
125 | > | if (rCut > maxCutoff) { |
126 | > | sprintf( painCave.errMsg, |
127 | > | "New Box size is forcing cutoff radius down to %lf\n", |
128 | > | maxCutoff ); |
129 | > | painCave.isFatal = 0; |
130 | > | simError(); |
131 | > | |
132 | > | status = 0; |
133 | > | LJ_new_rcut(&rCut, &status); |
134 | > | if (status != 0) { |
135 | > | sprintf( painCave.errMsg, |
136 | > | "Error in recomputing LJ shifts based on new rcut\n"); |
137 | > | painCave.isFatal = 1; |
138 | > | simError(); |
139 | > | } |
140 | > | } |
141 | } | |
142 | ||
143 | + | |
144 | + | void SimInfo::getBoxM (double theBox[3][3]) { |
145 | + | |
146 | + | int i, j; |
147 | + | for(i=0; i<3; i++) |
148 | + | for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]; |
149 | + | } |
150 | + | |
151 | + | |
152 | + | void SimInfo::scaleBox(double scale) { |
153 | + | double theBox[3][3]; |
154 | + | int i, j; |
155 | + | |
156 | + | // cerr << "Scaling box by " << scale << "\n"; |
157 | + | |
158 | + | for(i=0; i<3; i++) |
159 | + | for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale; |
160 | + | |
161 | + | setBoxM(theBox); |
162 | + | |
163 | + | } |
164 | + | |
165 | + | void SimInfo::calcHmatInv( void ) { |
166 | + | |
167 | + | int i,j; |
168 | + | double smallDiag; |
169 | + | double tol; |
170 | + | double sanity[3][3]; |
171 | + | |
172 | + | invertMat3( Hmat, HmatInv ); |
173 | + | |
174 | + | // Check the inverse to make sure it is sane: |
175 | + | |
176 | + | matMul3( Hmat, HmatInv, sanity ); |
177 | + | |
178 | + | // check to see if Hmat is orthorhombic |
179 | + | |
180 | + | smallDiag = Hmat[0][0]; |
181 | + | if(smallDiag > Hmat[1][1]) smallDiag = Hmat[1][1]; |
182 | + | if(smallDiag > Hmat[2][2]) smallDiag = Hmat[2][2]; |
183 | + | tol = smallDiag * 1E-6; |
184 | + | |
185 | + | orthoRhombic = 1; |
186 | + | |
187 | + | for (i = 0; i < 3; i++ ) { |
188 | + | for (j = 0 ; j < 3; j++) { |
189 | + | if (i != j) { |
190 | + | if (orthoRhombic) { |
191 | + | if (Hmat[i][j] >= tol) orthoRhombic = 0; |
192 | + | } |
193 | + | } |
194 | + | } |
195 | + | } |
196 | + | } |
197 | + | |
198 | + | double SimInfo::matDet3(double a[3][3]) { |
199 | + | int i, j, k; |
200 | + | double determinant; |
201 | + | |
202 | + | determinant = 0.0; |
203 | + | |
204 | + | for(i = 0; i < 3; i++) { |
205 | + | j = (i+1)%3; |
206 | + | k = (i+2)%3; |
207 | + | |
208 | + | determinant += a[0][i] * (a[1][j]*a[2][k] - a[1][k]*a[2][j]); |
209 | + | } |
210 | + | |
211 | + | return determinant; |
212 | + | } |
213 | + | |
214 | + | void SimInfo::invertMat3(double a[3][3], double b[3][3]) { |
215 | + | |
216 | + | int i, j, k, l, m, n; |
217 | + | double determinant; |
218 | + | |
219 | + | determinant = matDet3( a ); |
220 | + | |
221 | + | if (determinant == 0.0) { |
222 | + | sprintf( painCave.errMsg, |
223 | + | "Can't invert a matrix with a zero determinant!\n"); |
224 | + | painCave.isFatal = 1; |
225 | + | simError(); |
226 | + | } |
227 | + | |
228 | + | for (i=0; i < 3; i++) { |
229 | + | j = (i+1)%3; |
230 | + | k = (i+2)%3; |
231 | + | for(l = 0; l < 3; l++) { |
232 | + | m = (l+1)%3; |
233 | + | n = (l+2)%3; |
234 | + | |
235 | + | b[l][i] = (a[j][m]*a[k][n] - a[j][n]*a[k][m]) / determinant; |
236 | + | } |
237 | + | } |
238 | + | } |
239 | + | |
240 | + | void SimInfo::matMul3(double a[3][3], double b[3][3], double c[3][3]) { |
241 | + | double r00, r01, r02, r10, r11, r12, r20, r21, r22; |
242 | + | |
243 | + | r00 = a[0][0]*b[0][0] + a[0][1]*b[1][0] + a[0][2]*b[2][0]; |
244 | + | r01 = a[0][0]*b[0][1] + a[0][1]*b[1][1] + a[0][2]*b[2][1]; |
245 | + | r02 = a[0][0]*b[0][2] + a[0][1]*b[1][2] + a[0][2]*b[2][2]; |
246 | + | |
247 | + | r10 = a[1][0]*b[0][0] + a[1][1]*b[1][0] + a[1][2]*b[2][0]; |
248 | + | r11 = a[1][0]*b[0][1] + a[1][1]*b[1][1] + a[1][2]*b[2][1]; |
249 | + | r12 = a[1][0]*b[0][2] + a[1][1]*b[1][2] + a[1][2]*b[2][2]; |
250 | + | |
251 | + | r20 = a[2][0]*b[0][0] + a[2][1]*b[1][0] + a[2][2]*b[2][0]; |
252 | + | r21 = a[2][0]*b[0][1] + a[2][1]*b[1][1] + a[2][2]*b[2][1]; |
253 | + | r22 = a[2][0]*b[0][2] + a[2][1]*b[1][2] + a[2][2]*b[2][2]; |
254 | + | |
255 | + | c[0][0] = r00; c[0][1] = r01; c[0][2] = r02; |
256 | + | c[1][0] = r10; c[1][1] = r11; c[1][2] = r12; |
257 | + | c[2][0] = r20; c[2][1] = r21; c[2][2] = r22; |
258 | + | } |
259 | + | |
260 | + | void SimInfo::matVecMul3(double m[3][3], double inVec[3], double outVec[3]) { |
261 | + | double a0, a1, a2; |
262 | + | |
263 | + | a0 = inVec[0]; a1 = inVec[1]; a2 = inVec[2]; |
264 | + | |
265 | + | outVec[0] = m[0][0]*a0 + m[0][1]*a1 + m[0][2]*a2; |
266 | + | outVec[1] = m[1][0]*a0 + m[1][1]*a1 + m[1][2]*a2; |
267 | + | outVec[2] = m[2][0]*a0 + m[2][1]*a1 + m[2][2]*a2; |
268 | + | } |
269 | + | |
270 | + | void SimInfo::transposeMat3(double in[3][3], double out[3][3]) { |
271 | + | double temp[3][3]; |
272 | + | int i, j; |
273 | + | |
274 | + | for (i = 0; i < 3; i++) { |
275 | + | for (j = 0; j < 3; j++) { |
276 | + | temp[j][i] = in[i][j]; |
277 | + | } |
278 | + | } |
279 | + | for (i = 0; i < 3; i++) { |
280 | + | for (j = 0; j < 3; j++) { |
281 | + | out[i][j] = temp[i][j]; |
282 | + | } |
283 | + | } |
284 | + | } |
285 | + | |
286 | + | void SimInfo::printMat3(double A[3][3] ){ |
287 | + | |
288 | + | std::cerr |
289 | + | << "[ " << A[0][0] << ", " << A[0][1] << ", " << A[0][2] << " ]\n" |
290 | + | << "[ " << A[1][0] << ", " << A[1][1] << ", " << A[1][2] << " ]\n" |
291 | + | << "[ " << A[2][0] << ", " << A[2][1] << ", " << A[2][2] << " ]\n"; |
292 | + | } |
293 | + | |
294 | + | void SimInfo::printMat9(double A[9] ){ |
295 | + | |
296 | + | std::cerr |
297 | + | << "[ " << A[0] << ", " << A[1] << ", " << A[2] << " ]\n" |
298 | + | << "[ " << A[3] << ", " << A[4] << ", " << A[5] << " ]\n" |
299 | + | << "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n"; |
300 | + | } |
301 | + | |
302 | + | void SimInfo::calcBoxL( void ){ |
303 | + | |
304 | + | double dx, dy, dz, dsq; |
305 | + | int i; |
306 | + | |
307 | + | // boxVol = Determinant of Hmat |
308 | + | |
309 | + | boxVol = matDet3( Hmat ); |
310 | + | |
311 | + | // boxLx |
312 | + | |
313 | + | dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0]; |
314 | + | dsq = dx*dx + dy*dy + dz*dz; |
315 | + | boxLx = sqrt( dsq ); |
316 | + | |
317 | + | // boxLy |
318 | + | |
319 | + | dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1]; |
320 | + | dsq = dx*dx + dy*dy + dz*dz; |
321 | + | boxLy = sqrt( dsq ); |
322 | + | |
323 | + | // boxLz |
324 | + | |
325 | + | dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2]; |
326 | + | dsq = dx*dx + dy*dy + dz*dz; |
327 | + | boxLz = sqrt( dsq ); |
328 | + | |
329 | + | } |
330 | + | |
331 | + | |
332 | + | void SimInfo::wrapVector( double thePos[3] ){ |
333 | + | |
334 | + | int i, j, k; |
335 | + | double scaled[3]; |
336 | + | |
337 | + | if( !orthoRhombic ){ |
338 | + | // calc the scaled coordinates. |
339 | + | |
340 | + | |
341 | + | matVecMul3(HmatInv, thePos, scaled); |
342 | + | |
343 | + | for(i=0; i<3; i++) |
344 | + | scaled[i] -= roundMe(scaled[i]); |
345 | + | |
346 | + | // calc the wrapped real coordinates from the wrapped scaled coordinates |
347 | + | |
348 | + | matVecMul3(Hmat, scaled, thePos); |
349 | + | |
350 | + | } |
351 | + | else{ |
352 | + | // calc the scaled coordinates. |
353 | + | |
354 | + | for(i=0; i<3; i++) |
355 | + | scaled[i] = thePos[i]*HmatInv[i][i]; |
356 | + | |
357 | + | // wrap the scaled coordinates |
358 | + | |
359 | + | for(i=0; i<3; i++) |
360 | + | scaled[i] -= roundMe(scaled[i]); |
361 | + | |
362 | + | // calc the wrapped real coordinates from the wrapped scaled coordinates |
363 | + | |
364 | + | for(i=0; i<3; i++) |
365 | + | thePos[i] = scaled[i]*Hmat[i][i]; |
366 | + | } |
367 | + | |
368 | + | } |
369 | + | |
370 | + | |
371 | int SimInfo::getNDF(){ | |
372 | int ndf_local, ndf; | |
373 | ||
# | Line 82 | Line 403 | void SimInfo::refreshSim(){ | |
403 | ||
404 | simtype fInfo; | |
405 | int isError; | |
406 | + | int n_global; |
407 | int* excl; | |
408 | + | |
409 | + | fInfo.rrf = 0.0; |
410 | + | fInfo.rt = 0.0; |
411 | + | fInfo.dielect = 0.0; |
412 | ||
87 | – | fInfo.box[0] = box_x; |
88 | – | fInfo.box[1] = box_y; |
89 | – | fInfo.box[2] = box_z; |
90 | – | |
413 | fInfo.rlist = rList; | |
414 | fInfo.rcut = rCut; | |
93 | – | fInfo.rrf = ecr; |
94 | – | fInfo.rt = ecr - est; |
95 | – | fInfo.dielect = dielectric; |
415 | ||
416 | + | if( useDipole ){ |
417 | + | fInfo.rrf = ecr; |
418 | + | fInfo.rt = ecr - est; |
419 | + | if( useReactionField )fInfo.dielect = dielectric; |
420 | + | } |
421 | + | |
422 | fInfo.SIM_uses_PBC = usePBC; | |
423 | //fInfo.SIM_uses_LJ = 0; | |
424 | fInfo.SIM_uses_LJ = useLJ; | |
# | Line 108 | Line 433 | void SimInfo::refreshSim(){ | |
433 | ||
434 | excl = Exclude::getArray(); | |
435 | ||
436 | + | #ifdef IS_MPI |
437 | + | n_global = mpiSim->getTotAtoms(); |
438 | + | #else |
439 | + | n_global = n_atoms; |
440 | + | #endif |
441 | + | |
442 | isError = 0; | |
443 | ||
444 | < | // fInfo; |
445 | < | // n_atoms; |
446 | < | // identArray; |
116 | < | // n_exclude; |
117 | < | // excludes; |
118 | < | // nGlobalExcludes; |
119 | < | // globalExcludes; |
120 | < | // isError; |
444 | > | setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl, |
445 | > | &nGlobalExcludes, globalExcludes, molMembershipArray, |
446 | > | &isError ); |
447 | ||
122 | – | setFsimulation( &fInfo, &n_atoms, identArray, &n_exclude, excl, |
123 | – | &nGlobalExcludes, globalExcludes, &isError ); |
124 | – | |
448 | if( isError ){ | |
449 | ||
450 | sprintf( painCave.errMsg, | |
# | Line 136 | Line 459 | void SimInfo::refreshSim(){ | |
459 | MPIcheckPoint(); | |
460 | #endif // is_mpi | |
461 | ||
462 | < | ndf = this->getNDF(); |
463 | < | ndfRaw = this->getNDFraw(); |
462 | > | this->ndf = this->getNDF(); |
463 | > | this->ndfRaw = this->getNDFraw(); |
464 | ||
465 | } | |
466 |
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