# | 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 | + | int i; |
52 | + | double tempMat[9]; |
53 | ||
54 | < | wrapMeSimInfo( this ); |
54 | > | for(i=0; i<9; i++) tempMat[i] = 0.0;; |
55 | > | |
56 | > | tempMat[0] = newBox[0]; |
57 | > | tempMat[4] = newBox[1]; |
58 | > | tempMat[8] = newBox[2]; |
59 | > | |
60 | > | setBoxM( tempMat ); |
61 | > | |
62 | } | |
63 | ||
64 | + | void SimInfo::setBoxM( double theBox[9] ){ |
65 | + | |
66 | + | int i, status; |
67 | + | double smallestBoxL, maxCutoff; |
68 | + | |
69 | + | for(i=0; i<9; i++) Hmat[i] = theBox[i]; |
70 | + | |
71 | + | cerr |
72 | + | << "setting Hmat ->\n" |
73 | + | << "[ " << Hmat[0] << ", " << Hmat[3] << ", " << Hmat[6] << " ]\n" |
74 | + | << "[ " << Hmat[1] << ", " << Hmat[4] << ", " << Hmat[7] << " ]\n" |
75 | + | << "[ " << Hmat[2] << ", " << Hmat[5] << ", " << Hmat[8] << " ]\n"; |
76 | + | |
77 | + | calcHmatI(); |
78 | + | calcBoxL(); |
79 | + | |
80 | + | |
81 | + | |
82 | + | setFortranBoxSize(Hmat, HmatI, &orthoRhombic); |
83 | + | |
84 | + | smallestBoxL = boxLx; |
85 | + | if (boxLy < smallestBoxL) smallestBoxL = boxLy; |
86 | + | if (boxLz < smallestBoxL) smallestBoxL = boxLz; |
87 | + | |
88 | + | maxCutoff = smallestBoxL / 2.0; |
89 | + | |
90 | + | if (rList > maxCutoff) { |
91 | + | sprintf( painCave.errMsg, |
92 | + | "New Box size is forcing neighborlist radius down to %lf\n", |
93 | + | maxCutoff ); |
94 | + | painCave.isFatal = 0; |
95 | + | simError(); |
96 | + | |
97 | + | rList = maxCutoff; |
98 | + | |
99 | + | sprintf( painCave.errMsg, |
100 | + | "New Box size is forcing cutoff radius down to %lf\n", |
101 | + | maxCutoff - 1.0 ); |
102 | + | painCave.isFatal = 0; |
103 | + | simError(); |
104 | + | |
105 | + | rCut = rList - 1.0; |
106 | + | |
107 | + | // list radius changed so we have to refresh the simulation structure. |
108 | + | refreshSim(); |
109 | + | } |
110 | + | |
111 | + | if (rCut > maxCutoff) { |
112 | + | sprintf( painCave.errMsg, |
113 | + | "New Box size is forcing cutoff radius down to %lf\n", |
114 | + | maxCutoff ); |
115 | + | painCave.isFatal = 0; |
116 | + | simError(); |
117 | + | |
118 | + | status = 0; |
119 | + | LJ_new_rcut(&rCut, &status); |
120 | + | if (status != 0) { |
121 | + | sprintf( painCave.errMsg, |
122 | + | "Error in recomputing LJ shifts based on new rcut\n"); |
123 | + | painCave.isFatal = 1; |
124 | + | simError(); |
125 | + | } |
126 | + | } |
127 | + | } |
128 | + | |
129 | + | |
130 | + | void SimInfo::getBoxM (double theBox[9]) { |
131 | + | |
132 | + | int i; |
133 | + | for(i=0; i<9; i++) theBox[i] = Hmat[i]; |
134 | + | } |
135 | + | |
136 | + | |
137 | + | void SimInfo::scaleBox(double scale) { |
138 | + | double theBox[9]; |
139 | + | int i; |
140 | + | |
141 | + | cerr << "Scaling box by " << scale << "\n"; |
142 | + | |
143 | + | for(i=0; i<9; i++) theBox[i] = Hmat[i]*scale; |
144 | + | |
145 | + | setBoxM(theBox); |
146 | + | |
147 | + | } |
148 | + | |
149 | + | void SimInfo::calcHmatI( void ) { |
150 | + | |
151 | + | double C[3][3]; |
152 | + | double detHmat; |
153 | + | int i, j, k; |
154 | + | double smallDiag; |
155 | + | double tol; |
156 | + | double sanity[3][3]; |
157 | + | |
158 | + | // calculate the adjunct of Hmat; |
159 | + | |
160 | + | C[0][0] = ( Hmat[4]*Hmat[8]) - (Hmat[7]*Hmat[5]); |
161 | + | C[1][0] = -( Hmat[1]*Hmat[8]) + (Hmat[7]*Hmat[2]); |
162 | + | C[2][0] = ( Hmat[1]*Hmat[5]) - (Hmat[4]*Hmat[2]); |
163 | + | |
164 | + | C[0][1] = -( Hmat[3]*Hmat[8]) + (Hmat[6]*Hmat[5]); |
165 | + | C[1][1] = ( Hmat[0]*Hmat[8]) - (Hmat[6]*Hmat[2]); |
166 | + | C[2][1] = -( Hmat[0]*Hmat[5]) + (Hmat[3]*Hmat[2]); |
167 | + | |
168 | + | C[0][2] = ( Hmat[3]*Hmat[7]) - (Hmat[6]*Hmat[4]); |
169 | + | C[1][2] = -( Hmat[0]*Hmat[7]) + (Hmat[6]*Hmat[1]); |
170 | + | C[2][2] = ( Hmat[0]*Hmat[4]) - (Hmat[3]*Hmat[1]); |
171 | + | |
172 | + | // calcutlate the determinant of Hmat |
173 | + | |
174 | + | detHmat = 0.0; |
175 | + | for(i=0; i<3; i++) detHmat += Hmat[i] * C[i][0]; |
176 | + | |
177 | + | |
178 | + | // H^-1 = C^T / det(H) |
179 | + | |
180 | + | i=0; |
181 | + | for(j=0; j<3; j++){ |
182 | + | for(k=0; k<3; k++){ |
183 | + | |
184 | + | HmatI[i] = C[j][k] / detHmat; |
185 | + | i++; |
186 | + | } |
187 | + | } |
188 | + | |
189 | + | // sanity check |
190 | + | |
191 | + | for(i=0; i<3; i++){ |
192 | + | for(j=0; j<3; j++){ |
193 | + | |
194 | + | sanity[i][j] = 0.0; |
195 | + | for(k=0; k<3; k++){ |
196 | + | sanity[i][j] += Hmat[3*k+i] * HmatI[3*j+k]; |
197 | + | } |
198 | + | } |
199 | + | } |
200 | + | |
201 | + | cerr << "sanity => \n" |
202 | + | << sanity[0][0] << "\t" << sanity[0][1] << "\t" << sanity [0][2] << "\n" |
203 | + | << sanity[1][0] << "\t" << sanity[1][1] << "\t" << sanity [1][2] << "\n" |
204 | + | << sanity[2][0] << "\t" << sanity[2][1] << "\t" << sanity [2][2] |
205 | + | << "\n"; |
206 | + | |
207 | + | |
208 | + | // check to see if Hmat is orthorhombic |
209 | + | |
210 | + | smallDiag = Hmat[0]; |
211 | + | if(smallDiag > Hmat[4]) smallDiag = Hmat[4]; |
212 | + | if(smallDiag > Hmat[8]) smallDiag = Hmat[8]; |
213 | + | tol = smallDiag * 1E-6; |
214 | + | |
215 | + | orthoRhombic = 1; |
216 | + | for(i=0; (i<9) && orthoRhombic; i++){ |
217 | + | |
218 | + | if( (i%4) ){ // ignore the diagonals (0, 4, and 8) |
219 | + | orthoRhombic = (Hmat[i] <= tol); |
220 | + | } |
221 | + | } |
222 | + | |
223 | + | } |
224 | + | |
225 | + | void SimInfo::calcBoxL( void ){ |
226 | + | |
227 | + | double dx, dy, dz, dsq; |
228 | + | int i; |
229 | + | |
230 | + | // boxVol = h1 (dot) h2 (cross) h3 |
231 | + | |
232 | + | boxVol = Hmat[0] * ( (Hmat[4]*Hmat[8]) - (Hmat[7]*Hmat[5]) ) |
233 | + | + Hmat[1] * ( (Hmat[5]*Hmat[6]) - (Hmat[8]*Hmat[3]) ) |
234 | + | + Hmat[2] * ( (Hmat[3]*Hmat[7]) - (Hmat[6]*Hmat[4]) ); |
235 | + | |
236 | + | |
237 | + | // boxLx |
238 | + | |
239 | + | dx = Hmat[0]; dy = Hmat[1]; dz = Hmat[2]; |
240 | + | dsq = dx*dx + dy*dy + dz*dz; |
241 | + | boxLx = sqrt( dsq ); |
242 | + | |
243 | + | // boxLy |
244 | + | |
245 | + | dx = Hmat[3]; dy = Hmat[4]; dz = Hmat[5]; |
246 | + | dsq = dx*dx + dy*dy + dz*dz; |
247 | + | boxLy = sqrt( dsq ); |
248 | + | |
249 | + | // boxLz |
250 | + | |
251 | + | dx = Hmat[6]; dy = Hmat[7]; dz = Hmat[8]; |
252 | + | dsq = dx*dx + dy*dy + dz*dz; |
253 | + | boxLz = sqrt( dsq ); |
254 | + | |
255 | + | } |
256 | + | |
257 | + | |
258 | + | void SimInfo::wrapVector( double thePos[3] ){ |
259 | + | |
260 | + | int i, j, k; |
261 | + | double scaled[3]; |
262 | + | |
263 | + | if( !orthoRhombic ){ |
264 | + | // calc the scaled coordinates. |
265 | + | |
266 | + | for(i=0; i<3; i++) |
267 | + | scaled[i] = |
268 | + | thePos[0]*HmatI[i] + thePos[1]*HmatI[i+3] + thePos[3]*HmatI[i+6]; |
269 | + | |
270 | + | // wrap the scaled coordinates |
271 | + | |
272 | + | for(i=0; i<3; i++) |
273 | + | scaled[i] -= roundMe(scaled[i]); |
274 | + | |
275 | + | // calc the wrapped real coordinates from the wrapped scaled coordinates |
276 | + | |
277 | + | for(i=0; i<3; i++) |
278 | + | thePos[i] = |
279 | + | scaled[0]*Hmat[i] + scaled[1]*Hmat[i+3] + scaled[2]*Hmat[i+6]; |
280 | + | } |
281 | + | else{ |
282 | + | // calc the scaled coordinates. |
283 | + | |
284 | + | for(i=0; i<3; i++) |
285 | + | scaled[i] = thePos[i]*HmatI[i*4]; |
286 | + | |
287 | + | // wrap the scaled coordinates |
288 | + | |
289 | + | for(i=0; i<3; i++) |
290 | + | scaled[i] -= roundMe(scaled[i]); |
291 | + | |
292 | + | // calc the wrapped real coordinates from the wrapped scaled coordinates |
293 | + | |
294 | + | for(i=0; i<3; i++) |
295 | + | thePos[i] = scaled[i]*Hmat[i*4]; |
296 | + | } |
297 | + | |
298 | + | |
299 | + | } |
300 | + | |
301 | + | |
302 | + | int SimInfo::getNDF(){ |
303 | + | int ndf_local, ndf; |
304 | + | |
305 | + | ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints; |
306 | + | |
307 | + | #ifdef IS_MPI |
308 | + | MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
309 | + | #else |
310 | + | ndf = ndf_local; |
311 | + | #endif |
312 | + | |
313 | + | ndf = ndf - 3; |
314 | + | |
315 | + | return ndf; |
316 | + | } |
317 | + | |
318 | + | int SimInfo::getNDFraw() { |
319 | + | int ndfRaw_local, ndfRaw; |
320 | + | |
321 | + | // Raw degrees of freedom that we have to set |
322 | + | ndfRaw_local = 3 * n_atoms + 3 * n_oriented; |
323 | + | |
324 | + | #ifdef IS_MPI |
325 | + | MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
326 | + | #else |
327 | + | ndfRaw = ndfRaw_local; |
328 | + | #endif |
329 | + | |
330 | + | return ndfRaw; |
331 | + | } |
332 | + | |
333 | void SimInfo::refreshSim(){ | |
334 | ||
335 | simtype fInfo; | |
336 | int isError; | |
337 | + | int n_global; |
338 | + | int* excl; |
339 | + | |
340 | + | fInfo.rrf = 0.0; |
341 | + | fInfo.rt = 0.0; |
342 | + | fInfo.dielect = 0.0; |
343 | ||
41 | – | fInfo.box[0] = box_x; |
42 | – | fInfo.box[1] = box_y; |
43 | – | fInfo.box[2] = box_z; |
44 | – | |
344 | fInfo.rlist = rList; | |
345 | fInfo.rcut = rCut; | |
47 | – | fInfo.rrf = ecr; |
48 | – | fInfo.rt = ecr - est; |
49 | – | fInfo.dielect = dielectric; |
346 | ||
347 | + | if( useDipole ){ |
348 | + | fInfo.rrf = ecr; |
349 | + | fInfo.rt = ecr - est; |
350 | + | if( useReactionField )fInfo.dielect = dielectric; |
351 | + | } |
352 | + | |
353 | fInfo.SIM_uses_PBC = usePBC; | |
354 | + | //fInfo.SIM_uses_LJ = 0; |
355 | fInfo.SIM_uses_LJ = useLJ; | |
356 | < | //fInfo.SIM_uses_sticky = useSticky; |
357 | < | fInfo.SIM_uses_sticky = 0; |
356 | > | fInfo.SIM_uses_sticky = useSticky; |
357 | > | //fInfo.SIM_uses_sticky = 0; |
358 | fInfo.SIM_uses_dipoles = useDipole; | |
359 | //fInfo.SIM_uses_dipoles = 0; | |
360 | < | fInfo.SIM_uses_RF = useReactionField; |
360 | > | //fInfo.SIM_uses_RF = useReactionField; |
361 | > | fInfo.SIM_uses_RF = 0; |
362 | fInfo.SIM_uses_GB = useGB; | |
363 | fInfo.SIM_uses_EAM = useEAM; | |
364 | ||
365 | + | excl = Exclude::getArray(); |
366 | ||
367 | + | #ifdef IS_MPI |
368 | + | n_global = mpiSim->getTotAtoms(); |
369 | + | #else |
370 | + | n_global = n_atoms; |
371 | + | #endif |
372 | + | |
373 | isError = 0; | |
374 | ||
375 | < | fInfo; |
376 | < | n_atoms; |
377 | < | identArray; |
67 | < | n_exclude; |
68 | < | excludes; |
69 | < | nGlobalExcludes; |
70 | < | globalExcludes; |
71 | < | isError; |
375 | > | setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl, |
376 | > | &nGlobalExcludes, globalExcludes, molMembershipArray, |
377 | > | &isError ); |
378 | ||
73 | – | setFsimulation( &fInfo, &n_atoms, identArray, &n_exclude, excludes, &nGlobalExcludes, globalExcludes, &isError ); |
74 | – | |
379 | if( isError ){ | |
380 | ||
381 | sprintf( painCave.errMsg, | |
# | Line 85 | Line 389 | void SimInfo::refreshSim(){ | |
389 | "succesfully sent the simulation information to fortran.\n"); | |
390 | MPIcheckPoint(); | |
391 | #endif // is_mpi | |
392 | + | |
393 | + | this->ndf = this->getNDF(); |
394 | + | this->ndfRaw = this->getNDFraw(); |
395 | + | |
396 | } | |
397 |
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