# | 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 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; | |
# | Line 29 | Line 43 | SimInfo::SimInfo(){ | |
43 | useGB = 0; | |
44 | useEAM = 0; | |
45 | ||
46 | + | wrapMeSimInfo( this ); |
47 | + | } |
48 | ||
49 | + | void SimInfo::setBox(double newBox[3]) { |
50 | ||
51 | < | wrapMeSimInfo( this ); |
51 | > | double smallestBoxL, maxCutoff; |
52 | > | int status; |
53 | > | int i; |
54 | > | |
55 | > | for(i=0; i<9; i++) Hmat[i] = 0.0;; |
56 | > | |
57 | > | Hmat[0] = newBox[0]; |
58 | > | Hmat[4] = newBox[1]; |
59 | > | Hmat[8] = newBox[2]; |
60 | > | |
61 | > | calcHmatI(); |
62 | > | calcBoxL(); |
63 | > | |
64 | > | setFortranBoxSize(Hmat, HmatI, &orthoRhombic); |
65 | > | |
66 | > | smallestBoxL = boxLx; |
67 | > | if (boxLy < smallestBoxL) smallestBoxL = boxLy; |
68 | > | if (boxLz < smallestBoxL) smallestBoxL = boxLz; |
69 | > | |
70 | > | maxCutoff = smallestBoxL / 2.0; |
71 | > | |
72 | > | if (rList > maxCutoff) { |
73 | > | sprintf( painCave.errMsg, |
74 | > | "New Box size is forcing neighborlist radius down to %lf\n", |
75 | > | maxCutoff ); |
76 | > | painCave.isFatal = 0; |
77 | > | simError(); |
78 | > | |
79 | > | rList = maxCutoff; |
80 | > | |
81 | > | sprintf( painCave.errMsg, |
82 | > | "New Box size is forcing cutoff radius down to %lf\n", |
83 | > | maxCutoff - 1.0 ); |
84 | > | painCave.isFatal = 0; |
85 | > | simError(); |
86 | > | |
87 | > | rCut = rList - 1.0; |
88 | > | |
89 | > | // list radius changed so we have to refresh the simulation structure. |
90 | > | refreshSim(); |
91 | > | } |
92 | > | |
93 | > | if (rCut > maxCutoff) { |
94 | > | sprintf( painCave.errMsg, |
95 | > | "New Box size is forcing cutoff radius down to %lf\n", |
96 | > | maxCutoff ); |
97 | > | painCave.isFatal = 0; |
98 | > | simError(); |
99 | > | |
100 | > | status = 0; |
101 | > | LJ_new_rcut(&rCut, &status); |
102 | > | if (status != 0) { |
103 | > | sprintf( painCave.errMsg, |
104 | > | "Error in recomputing LJ shifts based on new rcut\n"); |
105 | > | painCave.isFatal = 1; |
106 | > | simError(); |
107 | > | } |
108 | > | } |
109 | > | } |
110 | > | |
111 | > | void SimInfo::setBoxM( double theBox[9] ){ |
112 | > | |
113 | > | int i, status; |
114 | > | double smallestBoxL, maxCutoff; |
115 | > | |
116 | > | for(i=0; i<9; i++) Hmat[i] = theBox[i]; |
117 | > | calcHmatI(); |
118 | > | calcBoxL(); |
119 | > | |
120 | > | setFortranBoxSize(Hmat, HmatI, &orthoRhombic); |
121 | > | |
122 | > | smallestBoxL = boxLx; |
123 | > | if (boxLy < smallestBoxL) smallestBoxL = boxLy; |
124 | > | if (boxLz < smallestBoxL) smallestBoxL = boxLz; |
125 | > | |
126 | > | maxCutoff = smallestBoxL / 2.0; |
127 | > | |
128 | > | if (rList > maxCutoff) { |
129 | > | sprintf( painCave.errMsg, |
130 | > | "New Box size is forcing neighborlist radius down to %lf\n", |
131 | > | maxCutoff ); |
132 | > | painCave.isFatal = 0; |
133 | > | simError(); |
134 | > | |
135 | > | rList = maxCutoff; |
136 | > | |
137 | > | sprintf( painCave.errMsg, |
138 | > | "New Box size is forcing cutoff radius down to %lf\n", |
139 | > | maxCutoff - 1.0 ); |
140 | > | painCave.isFatal = 0; |
141 | > | simError(); |
142 | > | |
143 | > | rCut = rList - 1.0; |
144 | > | |
145 | > | // list radius changed so we have to refresh the simulation structure. |
146 | > | refreshSim(); |
147 | > | } |
148 | > | |
149 | > | if (rCut > maxCutoff) { |
150 | > | sprintf( painCave.errMsg, |
151 | > | "New Box size is forcing cutoff radius down to %lf\n", |
152 | > | maxCutoff ); |
153 | > | painCave.isFatal = 0; |
154 | > | simError(); |
155 | > | |
156 | > | status = 0; |
157 | > | LJ_new_rcut(&rCut, &status); |
158 | > | if (status != 0) { |
159 | > | sprintf( painCave.errMsg, |
160 | > | "Error in recomputing LJ shifts based on new rcut\n"); |
161 | > | painCave.isFatal = 1; |
162 | > | simError(); |
163 | > | } |
164 | > | } |
165 | > | } |
166 | > | |
167 | > | |
168 | > | void SimInfo::getBoxM (double theBox[9]) { |
169 | > | |
170 | > | int i; |
171 | > | for(i=0; i<9; i++) theBox[i] = Hmat[i]; |
172 | > | } |
173 | > | |
174 | > | |
175 | > | void SimInfo::scaleBox(double scale) { |
176 | > | double theBox[9]; |
177 | > | int i; |
178 | > | |
179 | > | for(i=0; i<9; i++) theBox[i] = Hmat[i]*scale; |
180 | > | |
181 | > | setBoxM(theBox); |
182 | > | |
183 | > | } |
184 | > | |
185 | > | void SimInfo::calcHmatI( void ) { |
186 | > | |
187 | > | double C[3][3]; |
188 | > | double detHmat; |
189 | > | int i, j, k; |
190 | > | double smallDiag; |
191 | > | double tol; |
192 | > | double sanity[3][3]; |
193 | > | |
194 | > | // calculate the adjunct of Hmat; |
195 | > | |
196 | > | C[0][0] = ( Hmat[4]*Hmat[8]) - (Hmat[7]*Hmat[5]); |
197 | > | C[1][0] = -( Hmat[1]*Hmat[8]) + (Hmat[7]*Hmat[2]); |
198 | > | C[2][0] = ( Hmat[1]*Hmat[5]) - (Hmat[4]*Hmat[2]); |
199 | > | |
200 | > | C[0][1] = -( Hmat[3]*Hmat[8]) + (Hmat[6]*Hmat[5]); |
201 | > | C[1][1] = ( Hmat[0]*Hmat[8]) - (Hmat[6]*Hmat[2]); |
202 | > | C[2][1] = -( Hmat[0]*Hmat[5]) + (Hmat[3]*Hmat[2]); |
203 | > | |
204 | > | C[0][2] = ( Hmat[3]*Hmat[7]) - (Hmat[6]*Hmat[4]); |
205 | > | C[1][2] = -( Hmat[0]*Hmat[7]) + (Hmat[6]*Hmat[1]); |
206 | > | C[2][2] = ( Hmat[0]*Hmat[4]) - (Hmat[3]*Hmat[1]); |
207 | > | |
208 | > | // calcutlate the determinant of Hmat |
209 | > | |
210 | > | detHmat = 0.0; |
211 | > | for(i=0; i<3; i++) detHmat += Hmat[i] * C[i][0]; |
212 | > | |
213 | > | |
214 | > | // H^-1 = C^T / det(H) |
215 | > | |
216 | > | i=0; |
217 | > | for(j=0; j<3; j++){ |
218 | > | for(k=0; k<3; k++){ |
219 | > | |
220 | > | HmatI[i] = C[j][k] / detHmat; |
221 | > | i++; |
222 | > | } |
223 | > | } |
224 | > | |
225 | > | // sanity check |
226 | > | |
227 | > | for(i=0; i<3; i++){ |
228 | > | for(j=0; j<3; j++){ |
229 | > | |
230 | > | sanity[i][j] = 0.0; |
231 | > | for(k=0; k<3; k++){ |
232 | > | sanity[i][j] += Hmat[3*k+i] * HmatI[3*j+k]; |
233 | > | } |
234 | > | } |
235 | > | } |
236 | > | |
237 | > | cerr << "sanity => \n" |
238 | > | << sanity[0][0] << "\t" << sanity[0][1] << "\t" << sanity [0][2] << "\n" |
239 | > | << sanity[1][0] << "\t" << sanity[1][1] << "\t" << sanity [1][2] << "\n" |
240 | > | << sanity[2][0] << "\t" << sanity[2][1] << "\t" << sanity [2][2] |
241 | > | << "\n"; |
242 | > | |
243 | > | |
244 | > | // check to see if Hmat is orthorhombic |
245 | > | |
246 | > | smallDiag = Hmat[0]; |
247 | > | if(smallDiag > Hmat[4]) smallDiag = Hmat[4]; |
248 | > | if(smallDiag > Hmat[8]) smallDiag = Hmat[8]; |
249 | > | tol = smallDiag * 1E-6; |
250 | > | |
251 | > | orthoRhombic = 1; |
252 | > | for(i=0; (i<9) && orthoRhombic; i++){ |
253 | > | |
254 | > | if( (i%4) ){ // ignore the diagonals (0, 4, and 8) |
255 | > | orthoRhombic = (Hmat[i] <= tol); |
256 | > | } |
257 | > | } |
258 | > | |
259 | } | |
260 | ||
261 | + | void SimInfo::calcBoxL( void ){ |
262 | + | |
263 | + | double dx, dy, dz, dsq; |
264 | + | int i; |
265 | + | |
266 | + | // boxVol = h1 (dot) h2 (cross) h3 |
267 | + | |
268 | + | boxVol = Hmat[0] * ( (Hmat[4]*Hmat[8]) - (Hmat[7]*Hmat[5]) ) |
269 | + | + Hmat[1] * ( (Hmat[5]*Hmat[6]) - (Hmat[8]*Hmat[3]) ) |
270 | + | + Hmat[2] * ( (Hmat[3]*Hmat[7]) - (Hmat[6]*Hmat[4]) ); |
271 | + | |
272 | + | |
273 | + | // boxLx |
274 | + | |
275 | + | dx = Hmat[0]; dy = Hmat[1]; dz = Hmat[2]; |
276 | + | dsq = dx*dx + dy*dy + dz*dz; |
277 | + | boxLx = sqrt( dsq ); |
278 | + | |
279 | + | // boxLy |
280 | + | |
281 | + | dx = Hmat[3]; dy = Hmat[4]; dz = Hmat[5]; |
282 | + | dsq = dx*dx + dy*dy + dz*dz; |
283 | + | boxLy = sqrt( dsq ); |
284 | + | |
285 | + | // boxLz |
286 | + | |
287 | + | dx = Hmat[6]; dy = Hmat[7]; dz = Hmat[8]; |
288 | + | dsq = dx*dx + dy*dy + dz*dz; |
289 | + | boxLz = sqrt( dsq ); |
290 | + | |
291 | + | } |
292 | + | |
293 | + | |
294 | + | void SimInfo::wrapVector( double thePos[3] ){ |
295 | + | |
296 | + | int i, j, k; |
297 | + | double scaled[3]; |
298 | + | |
299 | + | if( !orthoRhombic ){ |
300 | + | // calc the scaled coordinates. |
301 | + | |
302 | + | for(i=0; i<3; i++) |
303 | + | scaled[i] = |
304 | + | thePos[0]*HmatI[i] + thePos[1]*HmatI[i+3] + thePos[3]*HmatI[i+6]; |
305 | + | |
306 | + | // wrap the scaled coordinates |
307 | + | |
308 | + | for(i=0; i<3; i++) |
309 | + | scaled[i] -= roundMe(scaled[i]); |
310 | + | |
311 | + | // calc the wrapped real coordinates from the wrapped scaled coordinates |
312 | + | |
313 | + | for(i=0; i<3; i++) |
314 | + | thePos[i] = |
315 | + | scaled[0]*Hmat[i] + scaled[1]*Hmat[i+3] + scaled[2]*Hmat[i+6]; |
316 | + | } |
317 | + | else{ |
318 | + | // calc the scaled coordinates. |
319 | + | |
320 | + | for(i=0; i<3; i++) |
321 | + | scaled[i] = thePos[i]*HmatI[i*4]; |
322 | + | |
323 | + | // wrap the scaled coordinates |
324 | + | |
325 | + | for(i=0; i<3; i++) |
326 | + | scaled[i] -= roundMe(scaled[i]); |
327 | + | |
328 | + | // calc the wrapped real coordinates from the wrapped scaled coordinates |
329 | + | |
330 | + | for(i=0; i<3; i++) |
331 | + | thePos[i] = scaled[i]*Hmat[i*4]; |
332 | + | } |
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.rrf = 0.0; |
377 | + | fInfo.rt = 0.0; |
378 | + | fInfo.dielect = 0.0; |
379 | ||
43 | – | fInfo.box[0] = box_x; |
44 | – | fInfo.box[1] = box_y; |
45 | – | fInfo.box[2] = box_z; |
46 | – | |
380 | fInfo.rlist = rList; | |
381 | fInfo.rcut = rCut; | |
49 | – | fInfo.rrf = ecr; |
50 | – | fInfo.rt = ecr - est; |
51 | – | fInfo.dielect = dielectric; |
382 | ||
383 | + | if( useDipole ){ |
384 | + | fInfo.rrf = ecr; |
385 | + | fInfo.rt = ecr - est; |
386 | + | if( useReactionField )fInfo.dielect = dielectric; |
387 | + | } |
388 | + | |
389 | fInfo.SIM_uses_PBC = usePBC; | |
390 | + | //fInfo.SIM_uses_LJ = 0; |
391 | fInfo.SIM_uses_LJ = useLJ; | |
392 | < | //fInfo.SIM_uses_sticky = useSticky; |
393 | < | fInfo.SIM_uses_sticky = 0; |
392 | > | fInfo.SIM_uses_sticky = useSticky; |
393 | > | //fInfo.SIM_uses_sticky = 0; |
394 | fInfo.SIM_uses_dipoles = useDipole; | |
395 | //fInfo.SIM_uses_dipoles = 0; | |
396 | < | fInfo.SIM_uses_RF = useReactionField; |
396 | > | //fInfo.SIM_uses_RF = useReactionField; |
397 | > | fInfo.SIM_uses_RF = 0; |
398 | fInfo.SIM_uses_GB = useGB; | |
399 | fInfo.SIM_uses_EAM = useEAM; | |
400 | ||
401 | excl = Exclude::getArray(); | |
402 | ||
403 | + | #ifdef IS_MPI |
404 | + | n_global = mpiSim->getTotAtoms(); |
405 | + | #else |
406 | + | n_global = n_atoms; |
407 | + | #endif |
408 | + | |
409 | isError = 0; | |
410 | ||
411 | < | fInfo; |
412 | < | n_atoms; |
413 | < | identArray; |
70 | < | n_exclude; |
71 | < | excludes; |
72 | < | nGlobalExcludes; |
73 | < | globalExcludes; |
74 | < | isError; |
411 | > | setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl, |
412 | > | &nGlobalExcludes, globalExcludes, molMembershipArray, |
413 | > | &isError ); |
414 | ||
76 | – | setFsimulation( &fInfo, &n_atoms, identArray, &n_exclude, excl, |
77 | – | &nGlobalExcludes, globalExcludes, &isError ); |
78 | – | |
415 | if( isError ){ | |
416 | ||
417 | sprintf( painCave.errMsg, | |
# | Line 89 | Line 425 | void SimInfo::refreshSim(){ | |
425 | "succesfully sent the simulation information to fortran.\n"); | |
426 | MPIcheckPoint(); | |
427 | #endif // is_mpi | |
428 | + | |
429 | + | this->ndf = this->getNDF(); |
430 | + | this->ndfRaw = this->getNDFraw(); |
431 | + | |
432 | } | |
433 |
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