# | 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; | |
36 | + | rCut = 0.0; |
37 | ||
38 | usePBC = 0; | |
39 | useLJ = 0; | |
# | Line 28 | 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::calcHmatI( void ) { |
176 | + | |
177 | + | double C[3][3]; |
178 | + | double detHmat; |
179 | + | int i, j, k; |
180 | + | double smallDiag; |
181 | + | double tol; |
182 | + | double sanity[3][3]; |
183 | + | |
184 | + | // calculate the adjunct of Hmat; |
185 | + | |
186 | + | C[0][0] = ( Hmat[4]*Hmat[8]) - (Hmat[7]*Hmat[5]); |
187 | + | C[1][0] = -( Hmat[1]*Hmat[8]) + (Hmat[7]*Hmat[2]); |
188 | + | C[2][0] = ( Hmat[1]*Hmat[5]) - (Hmat[4]*Hmat[2]); |
189 | + | |
190 | + | C[0][1] = -( Hmat[3]*Hmat[8]) + (Hmat[6]*Hmat[5]); |
191 | + | C[1][1] = ( Hmat[0]*Hmat[8]) - (Hmat[6]*Hmat[2]); |
192 | + | C[2][1] = -( Hmat[0]*Hmat[5]) + (Hmat[3]*Hmat[2]); |
193 | + | |
194 | + | C[0][2] = ( Hmat[3]*Hmat[7]) - (Hmat[6]*Hmat[4]); |
195 | + | C[1][2] = -( Hmat[0]*Hmat[7]) + (Hmat[6]*Hmat[1]); |
196 | + | C[2][2] = ( Hmat[0]*Hmat[4]) - (Hmat[3]*Hmat[1]); |
197 | + | |
198 | + | // calcutlate the determinant of Hmat |
199 | + | |
200 | + | detHmat = 0.0; |
201 | + | for(i=0; i<3; i++) detHmat += Hmat[i] * C[i][0]; |
202 | + | |
203 | + | |
204 | + | // H^-1 = C^T / det(H) |
205 | + | |
206 | + | i=0; |
207 | + | for(j=0; j<3; j++){ |
208 | + | for(k=0; k<3; k++){ |
209 | + | |
210 | + | HmatI[i] = C[j][k] / detHmat; |
211 | + | i++; |
212 | + | } |
213 | + | } |
214 | + | |
215 | + | // sanity check |
216 | + | |
217 | + | for(i=0; i<3; i++){ |
218 | + | for(j=0; j<3; j++){ |
219 | + | |
220 | + | sanity[i][j] = 0.0; |
221 | + | for(k=0; k<3; k++){ |
222 | + | sanity[i][j] += Hmat[3*k+i] * HmatI[3*j+k]; |
223 | + | } |
224 | + | } |
225 | + | } |
226 | + | |
227 | + | cerr << "sanity => \n" |
228 | + | << sanity[0][0] << "\t" << sanity[0][1] << "\t" << sanity [0][2] << "\n" |
229 | + | << sanity[1][0] << "\t" << sanity[1][1] << "\t" << sanity [1][2] << "\n" |
230 | + | << sanity[2][0] << "\t" << sanity[2][1] << "\t" << sanity [2][2] |
231 | + | << "\n"; |
232 | + | |
233 | + | |
234 | + | // check to see if Hmat is orthorhombic |
235 | + | |
236 | + | smallDiag = Hmat[0]; |
237 | + | if(smallDiag > Hmat[4]) smallDiag = Hmat[4]; |
238 | + | if(smallDiag > Hmat[8]) smallDiag = Hmat[8]; |
239 | + | tol = smallDiag * 1E-6; |
240 | + | |
241 | + | orthoRhombic = 1; |
242 | + | for(i=0; (i<9) && orthoRhombic; i++){ |
243 | + | |
244 | + | if( (i%4) ){ // ignore the diagonals (0, 4, and 8) |
245 | + | orthoRhombic = (Hmat[i] <= tol); |
246 | + | } |
247 | + | } |
248 | + | |
249 | + | } |
250 | + | |
251 | + | void SimInfo::calcBoxL( void ){ |
252 | + | |
253 | + | double dx, dy, dz, dsq; |
254 | + | int i; |
255 | + | |
256 | + | // boxVol = h1 (dot) h2 (cross) h3 |
257 | + | |
258 | + | boxVol = Hmat[0] * ( (Hmat[4]*Hmat[8]) - (Hmat[7]*Hmat[5]) ) |
259 | + | + Hmat[1] * ( (Hmat[5]*Hmat[6]) - (Hmat[8]*Hmat[3]) ) |
260 | + | + Hmat[2] * ( (Hmat[3]*Hmat[7]) - (Hmat[6]*Hmat[4]) ); |
261 | + | |
262 | + | |
263 | + | // boxLx |
264 | + | |
265 | + | dx = Hmat[0]; dy = Hmat[1]; dz = Hmat[2]; |
266 | + | dsq = dx*dx + dy*dy + dz*dz; |
267 | + | boxLx = sqrt( dsq ); |
268 | + | |
269 | + | // boxLy |
270 | + | |
271 | + | dx = Hmat[3]; dy = Hmat[4]; dz = Hmat[5]; |
272 | + | dsq = dx*dx + dy*dy + dz*dz; |
273 | + | boxLy = sqrt( dsq ); |
274 | + | |
275 | + | // boxLz |
276 | + | |
277 | + | dx = Hmat[6]; dy = Hmat[7]; dz = Hmat[8]; |
278 | + | dsq = dx*dx + dy*dy + dz*dz; |
279 | + | boxLz = sqrt( dsq ); |
280 | + | |
281 | + | } |
282 | + | |
283 | + | |
284 | + | void SimInfo::wrapVector( double thePos[3] ){ |
285 | + | |
286 | + | int i, j, k; |
287 | + | double scaled[3]; |
288 | + | |
289 | + | if( !orthoRhombic ){ |
290 | + | // calc the scaled coordinates. |
291 | + | |
292 | + | for(i=0; i<3; i++) |
293 | + | scaled[i] = |
294 | + | thePos[0]*HmatI[i] + thePos[1]*HmatI[i+3] + thePos[3]*HmatI[i+6]; |
295 | + | |
296 | + | // wrap the scaled coordinates |
297 | + | |
298 | + | for(i=0; i<3; i++) |
299 | + | scaled[i] -= roundMe(scaled[i]); |
300 | + | |
301 | + | // calc the wrapped real coordinates from the wrapped scaled coordinates |
302 | + | |
303 | + | for(i=0; i<3; i++) |
304 | + | thePos[i] = |
305 | + | scaled[0]*Hmat[i] + scaled[1]*Hmat[i+3] + scaled[2]*Hmat[i+6]; |
306 | + | } |
307 | + | else{ |
308 | + | // calc the scaled coordinates. |
309 | + | |
310 | + | for(i=0; i<3; i++) |
311 | + | scaled[i] = thePos[i]*HmatI[i*4]; |
312 | + | |
313 | + | // wrap the scaled coordinates |
314 | + | |
315 | + | for(i=0; i<3; i++) |
316 | + | scaled[i] -= roundMe(scaled[i]); |
317 | + | |
318 | + | // calc the wrapped real coordinates from the wrapped scaled coordinates |
319 | + | |
320 | + | for(i=0; i<3; i++) |
321 | + | thePos[i] = scaled[i]*Hmat[i*4]; |
322 | + | } |
323 | + | |
324 | + | |
325 | + | } |
326 | + | |
327 | + | |
328 | + | int SimInfo::getNDF(){ |
329 | + | int ndf_local, ndf; |
330 | + | |
331 | + | ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints; |
332 | + | |
333 | + | #ifdef IS_MPI |
334 | + | MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
335 | + | #else |
336 | + | ndf = ndf_local; |
337 | + | #endif |
338 | + | |
339 | + | ndf = ndf - 3; |
340 | + | |
341 | + | return ndf; |
342 | + | } |
343 | + | |
344 | + | int SimInfo::getNDFraw() { |
345 | + | int ndfRaw_local, ndfRaw; |
346 | + | |
347 | + | // Raw degrees of freedom that we have to set |
348 | + | ndfRaw_local = 3 * n_atoms + 3 * n_oriented; |
349 | + | |
350 | + | #ifdef IS_MPI |
351 | + | MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
352 | + | #else |
353 | + | ndfRaw = ndfRaw_local; |
354 | + | #endif |
355 | + | |
356 | + | return ndfRaw; |
357 | + | } |
358 | + | |
359 | void SimInfo::refreshSim(){ | |
360 | ||
361 | simtype fInfo; | |
362 | int isError; | |
363 | + | int n_global; |
364 | + | int* excl; |
365 | + | |
366 | + | fInfo.rrf = 0.0; |
367 | + | fInfo.rt = 0.0; |
368 | + | fInfo.dielect = 0.0; |
369 | ||
41 | – | fInfo.box[0] = box_x; |
42 | – | fInfo.box[1] = box_y; |
43 | – | fInfo.box[2] = box_z; |
44 | – | |
370 | fInfo.rlist = rList; | |
371 | fInfo.rcut = rCut; | |
47 | – | fInfo.rrf = rRF; |
48 | – | fInfo.rt = 0.95 * rRF; |
49 | – | fInfo.dielect = dielectric; |
50 | – | |
372 | ||
373 | + | if( useDipole ){ |
374 | + | fInfo.rrf = ecr; |
375 | + | fInfo.rt = ecr - est; |
376 | + | if( useReactionField )fInfo.dielect = dielectric; |
377 | + | } |
378 | + | |
379 | fInfo.SIM_uses_PBC = usePBC; | |
380 | + | //fInfo.SIM_uses_LJ = 0; |
381 | fInfo.SIM_uses_LJ = useLJ; | |
382 | fInfo.SIM_uses_sticky = useSticky; | |
383 | + | //fInfo.SIM_uses_sticky = 0; |
384 | fInfo.SIM_uses_dipoles = useDipole; | |
385 | < | fInfo.SIM_uses_RF = useReactionField; |
385 | > | //fInfo.SIM_uses_dipoles = 0; |
386 | > | //fInfo.SIM_uses_RF = useReactionField; |
387 | > | fInfo.SIM_uses_RF = 0; |
388 | fInfo.SIM_uses_GB = useGB; | |
389 | fInfo.SIM_uses_EAM = useEAM; | |
390 | ||
391 | + | excl = Exclude::getArray(); |
392 | ||
393 | + | #ifdef IS_MPI |
394 | + | n_global = mpiSim->getTotAtoms(); |
395 | + | #else |
396 | + | n_global = n_atoms; |
397 | + | #endif |
398 | + | |
399 | isError = 0; | |
400 | ||
401 | < | fInfo; |
402 | < | n_atoms; |
403 | < | identArray; |
66 | < | n_exclude; |
67 | < | excludes; |
68 | < | nGlobalExcludes; |
69 | < | globalExcludes; |
70 | < | isError; |
401 | > | setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl, |
402 | > | &nGlobalExcludes, globalExcludes, molMembershipArray, |
403 | > | &isError ); |
404 | ||
72 | – | setFsimulation( &fInfo, &n_atoms, identArray, &n_exclude, excludes, &nGlobalExcludes, globalExcludes, &isError ); |
73 | – | |
405 | if( isError ){ | |
406 | ||
407 | sprintf( painCave.errMsg, | |
# | Line 84 | Line 415 | void SimInfo::refreshSim(){ | |
415 | "succesfully sent the simulation information to fortran.\n"); | |
416 | MPIcheckPoint(); | |
417 | #endif // is_mpi | |
418 | + | |
419 | + | this->ndf = this->getNDF(); |
420 | + | this->ndfRaw = this->getNDFraw(); |
421 | + | |
422 | } | |
423 |
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