# | Line 1 | Line 1 | |
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1 | #include <cstdlib> | |
2 | #include <cstring> | |
3 | + | #include <cmath> |
4 | ||
5 | ||
6 | #include "SimInfo.hpp" | |
# | Line 9 | Line 10 | |
10 | ||
11 | #include "fortranWrappers.hpp" | |
12 | ||
13 | + | #ifdef IS_MPI |
14 | + | #include "mpiSimulation.hpp" |
15 | + | #endif |
16 | + | |
17 | SimInfo* currentInfo; | |
18 | ||
19 | SimInfo::SimInfo(){ | |
# | Line 16 | Line 21 | SimInfo::SimInfo(){ | |
21 | n_constraints = 0; | |
22 | n_oriented = 0; | |
23 | n_dipoles = 0; | |
24 | + | ndf = 0; |
25 | + | ndfRaw = 0; |
26 | the_integrator = NULL; | |
27 | setTemp = 0; | |
28 | thermalTime = 0.0; | |
# | Line 29 | Line 36 | SimInfo::SimInfo(){ | |
36 | useGB = 0; | |
37 | useEAM = 0; | |
38 | ||
39 | + | wrapMeSimInfo( this ); |
40 | + | } |
41 | ||
42 | + | void SimInfo::setBox(double newBox[3]) { |
43 | ||
44 | < | wrapMeSimInfo( this ); |
44 | > | double smallestBoxL, maxCutoff; |
45 | > | int status; |
46 | > | int i; |
47 | > | |
48 | > | for(i=0; i<9; i++) Hmat[i] = 0.0;; |
49 | > | |
50 | > | Hmat[0] = newBox[0]; |
51 | > | Hmat[4] = newBox[1]; |
52 | > | Hmat[8] = newBox[2]; |
53 | > | |
54 | > | calcHmatI(); |
55 | > | calcBoxL(); |
56 | > | |
57 | > | setFortranBoxSize(Hmat); |
58 | > | |
59 | > | smallestBoxL = boxLx; |
60 | > | if (boxLy < smallestBoxL) smallestBoxL = boxLy; |
61 | > | if (boxLz < smallestBoxL) smallestBoxL = boxLz; |
62 | > | |
63 | > | maxCutoff = smallestBoxL / 2.0; |
64 | > | |
65 | > | if (rList > maxCutoff) { |
66 | > | sprintf( painCave.errMsg, |
67 | > | "New Box size is forcing neighborlist radius down to %lf\n", |
68 | > | maxCutoff ); |
69 | > | painCave.isFatal = 0; |
70 | > | simError(); |
71 | > | |
72 | > | rList = maxCutoff; |
73 | > | |
74 | > | sprintf( painCave.errMsg, |
75 | > | "New Box size is forcing cutoff radius down to %lf\n", |
76 | > | maxCutoff - 1.0 ); |
77 | > | painCave.isFatal = 0; |
78 | > | simError(); |
79 | > | |
80 | > | rCut = rList - 1.0; |
81 | > | |
82 | > | // list radius changed so we have to refresh the simulation structure. |
83 | > | refreshSim(); |
84 | > | } |
85 | > | |
86 | > | if (rCut > maxCutoff) { |
87 | > | sprintf( painCave.errMsg, |
88 | > | "New Box size is forcing cutoff radius down to %lf\n", |
89 | > | maxCutoff ); |
90 | > | painCave.isFatal = 0; |
91 | > | simError(); |
92 | > | |
93 | > | status = 0; |
94 | > | LJ_new_rcut(&rCut, &status); |
95 | > | if (status != 0) { |
96 | > | sprintf( painCave.errMsg, |
97 | > | "Error in recomputing LJ shifts based on new rcut\n"); |
98 | > | painCave.isFatal = 1; |
99 | > | simError(); |
100 | > | } |
101 | > | } |
102 | } | |
103 | ||
104 | + | void SimInfo::setBoxM( double theBox[9] ){ |
105 | + | |
106 | + | int i, status; |
107 | + | double smallestBoxL, maxCutoff; |
108 | + | |
109 | + | for(i=0; i<9; i++) Hmat[i] = theBox[i]; |
110 | + | calcHmatI(); |
111 | + | calcBoxL(); |
112 | + | |
113 | + | setFortranBoxSize(Hmat); |
114 | + | |
115 | + | smallestBoxL = boxLx; |
116 | + | if (boxLy < smallestBoxL) smallestBoxL = boxLy; |
117 | + | if (boxLz < smallestBoxL) smallestBoxL = boxLz; |
118 | + | |
119 | + | maxCutoff = smallestBoxL / 2.0; |
120 | + | |
121 | + | if (rList > maxCutoff) { |
122 | + | sprintf( painCave.errMsg, |
123 | + | "New Box size is forcing neighborlist radius down to %lf\n", |
124 | + | maxCutoff ); |
125 | + | painCave.isFatal = 0; |
126 | + | simError(); |
127 | + | |
128 | + | rList = maxCutoff; |
129 | + | |
130 | + | sprintf( painCave.errMsg, |
131 | + | "New Box size is forcing cutoff radius down to %lf\n", |
132 | + | maxCutoff - 1.0 ); |
133 | + | painCave.isFatal = 0; |
134 | + | simError(); |
135 | + | |
136 | + | rCut = rList - 1.0; |
137 | + | |
138 | + | // list radius changed so we have to refresh the simulation structure. |
139 | + | refreshSim(); |
140 | + | } |
141 | + | |
142 | + | if (rCut > maxCutoff) { |
143 | + | sprintf( painCave.errMsg, |
144 | + | "New Box size is forcing cutoff radius down to %lf\n", |
145 | + | maxCutoff ); |
146 | + | painCave.isFatal = 0; |
147 | + | simError(); |
148 | + | |
149 | + | status = 0; |
150 | + | LJ_new_rcut(&rCut, &status); |
151 | + | if (status != 0) { |
152 | + | sprintf( painCave.errMsg, |
153 | + | "Error in recomputing LJ shifts based on new rcut\n"); |
154 | + | painCave.isFatal = 1; |
155 | + | simError(); |
156 | + | } |
157 | + | } |
158 | + | } |
159 | + | |
160 | + | |
161 | + | void SimInfo::getBox(double theBox[9]) { |
162 | + | |
163 | + | int i; |
164 | + | for(i=0; i<9; i++) theBox[i] = Hmat[i]; |
165 | + | } |
166 | + | |
167 | + | |
168 | + | void SimInfo::calcHmatI( void ) { |
169 | + | |
170 | + | double C[3][3]; |
171 | + | double detHmat; |
172 | + | int i, j, k; |
173 | + | |
174 | + | // calculate the adjunct of Hmat; |
175 | + | |
176 | + | C[0][0] = ( Hmat[4]*Hmat[8]) - (Hmat[7]*Hmat[5]); |
177 | + | C[1][0] = -( Hmat[1]*Hmat[8]) + (Hmat[7]*Hmat[2]); |
178 | + | C[2][0] = ( Hmat[1]*Hmat[5]) - (Hmat[4]*Hmat[2]); |
179 | + | |
180 | + | C[0][1] = -( Hmat[3]*Hmat[8]) + (Hmat[6]*Hmat[5]); |
181 | + | C[1][1] = ( Hmat[0]*Hmat[8]) - (Hmat[6]*Hmat[2]); |
182 | + | C[2][1] = -( Hmat[0]*Hmat[5]) + (Hmat[3]*Hmat[2]); |
183 | + | |
184 | + | C[0][2] = ( Hmat[3]*Hmat[7]) - (Hmat[6]*Hmat[4]); |
185 | + | C[1][2] = -( Hmat[0]*Hmat[7]) + (Hmat[6]*Hmat[1]); |
186 | + | C[2][2] = ( Hmat[0]*Hmat[4]) - (Hmat[3]*Hmat[1]); |
187 | + | |
188 | + | // calcutlate the determinant of Hmat |
189 | + | |
190 | + | detHmat = 0.0; |
191 | + | for(i=0; i<3; i++) detHmat += Hmat[i] * C[i][0]; |
192 | + | |
193 | + | |
194 | + | // H^-1 = C^T / det(H) |
195 | + | |
196 | + | i=0; |
197 | + | for(j=0; j<3; j++){ |
198 | + | for(k=0; k<3; k++){ |
199 | + | |
200 | + | HmatI[i] = C[j][k] / detHmat; |
201 | + | i++; |
202 | + | } |
203 | + | } |
204 | + | } |
205 | + | |
206 | + | void SimInfo::calcBoxL( void ){ |
207 | + | |
208 | + | double dx, dy, dz, dsq; |
209 | + | int i; |
210 | + | |
211 | + | // boxVol = h1 (dot) h2 (cross) h3 |
212 | + | |
213 | + | boxVol = Hmat[0] * ( (Hmat[4]*Hmat[8]) - (Hmat[7]*Hmat[5]) ) |
214 | + | + Hmat[1] * ( (Hmat[5]*Hmat[6]) - (Hmat[8]*Hmat[3]) ) |
215 | + | + Hmat[2] * ( (Hmat[3]*Hmat[7]) - (Hmat[6]*Hmat[4]) ); |
216 | + | |
217 | + | |
218 | + | // boxLx |
219 | + | |
220 | + | dx = Hmat[0]; dy = Hmat[1]; dz = Hmat[2]; |
221 | + | dsq = dx*dx + dy*dy + dz*dz; |
222 | + | boxLx = sqrt( dsq ); |
223 | + | |
224 | + | // boxLy |
225 | + | |
226 | + | dx = Hmat[3]; dy = Hmat[4]; dz = Hmat[5]; |
227 | + | dsq = dx*dx + dy*dy + dz*dz; |
228 | + | boxLy = sqrt( dsq ); |
229 | + | |
230 | + | // boxLz |
231 | + | |
232 | + | dx = Hmat[6]; dy = Hmat[7]; dz = Hmat[8]; |
233 | + | dsq = dx*dx + dy*dy + dz*dz; |
234 | + | boxLz = sqrt( dsq ); |
235 | + | |
236 | + | } |
237 | + | |
238 | + | |
239 | + | void SimInfo::wrapVector( double thePos[3] ){ |
240 | + | |
241 | + | int i, j, k; |
242 | + | double scaled[3]; |
243 | + | |
244 | + | // calc the scaled coordinates. |
245 | + | |
246 | + | for(i=0; i<3; i++) |
247 | + | scaled[i] = thePos[0]*Hmat[i] + thePos[1]*Hat[i+3] + thePos[3]*Hmat[i+6]; |
248 | + | |
249 | + | // wrap the scaled coordinates |
250 | + | |
251 | + | for(i=0; i<3; i++) |
252 | + | scaled[i] -= (copysign(1,scaled[i]) * (int)(fabs(scaled[i]) + 0.5)); |
253 | + | |
254 | + | |
255 | + | } |
256 | + | |
257 | + | |
258 | + | int SimInfo::getNDF(){ |
259 | + | int ndf_local, ndf; |
260 | + | |
261 | + | ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints; |
262 | + | |
263 | + | #ifdef IS_MPI |
264 | + | MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
265 | + | #else |
266 | + | ndf = ndf_local; |
267 | + | #endif |
268 | + | |
269 | + | ndf = ndf - 3; |
270 | + | |
271 | + | return ndf; |
272 | + | } |
273 | + | |
274 | + | int SimInfo::getNDFraw() { |
275 | + | int ndfRaw_local, ndfRaw; |
276 | + | |
277 | + | // Raw degrees of freedom that we have to set |
278 | + | ndfRaw_local = 3 * n_atoms + 3 * n_oriented; |
279 | + | |
280 | + | #ifdef IS_MPI |
281 | + | MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
282 | + | #else |
283 | + | ndfRaw = ndfRaw_local; |
284 | + | #endif |
285 | + | |
286 | + | return ndfRaw; |
287 | + | } |
288 | + | |
289 | void SimInfo::refreshSim(){ | |
290 | ||
291 | simtype fInfo; | |
292 | int isError; | |
293 | + | int n_global; |
294 | int* excl; | |
295 | + | |
296 | + | fInfo.rrf = 0.0; |
297 | + | fInfo.rt = 0.0; |
298 | + | fInfo.dielect = 0.0; |
299 | ||
300 | fInfo.box[0] = box_x; | |
301 | fInfo.box[1] = box_y; | |
# | Line 46 | Line 303 | void SimInfo::refreshSim(){ | |
303 | ||
304 | fInfo.rlist = rList; | |
305 | fInfo.rcut = rCut; | |
49 | – | fInfo.rrf = ecr; |
50 | – | fInfo.rt = ecr - est; |
51 | – | fInfo.dielect = dielectric; |
306 | ||
307 | + | if( useDipole ){ |
308 | + | fInfo.rrf = ecr; |
309 | + | fInfo.rt = ecr - est; |
310 | + | if( useReactionField )fInfo.dielect = dielectric; |
311 | + | } |
312 | + | |
313 | fInfo.SIM_uses_PBC = usePBC; | |
314 | < | // fInfo.SIM_uses_LJ = useLJ; |
315 | < | fInfo.SIM_uses_LJ = 0; |
316 | < | //fInfo.SIM_uses_sticky = useSticky; |
317 | < | fInfo.SIM_uses_sticky = 0; |
314 | > | //fInfo.SIM_uses_LJ = 0; |
315 | > | fInfo.SIM_uses_LJ = useLJ; |
316 | > | fInfo.SIM_uses_sticky = useSticky; |
317 | > | //fInfo.SIM_uses_sticky = 0; |
318 | fInfo.SIM_uses_dipoles = useDipole; | |
319 | //fInfo.SIM_uses_dipoles = 0; | |
320 | < | fInfo.SIM_uses_RF = useReactionField; |
320 | > | //fInfo.SIM_uses_RF = useReactionField; |
321 | > | fInfo.SIM_uses_RF = 0; |
322 | fInfo.SIM_uses_GB = useGB; | |
323 | fInfo.SIM_uses_EAM = useEAM; | |
324 | ||
325 | excl = Exclude::getArray(); | |
326 | ||
327 | + | #ifdef IS_MPI |
328 | + | n_global = mpiSim->getTotAtoms(); |
329 | + | #else |
330 | + | n_global = n_atoms; |
331 | + | #endif |
332 | + | |
333 | isError = 0; | |
334 | ||
335 | < | fInfo; |
336 | < | n_atoms; |
337 | < | identArray; |
71 | < | n_exclude; |
72 | < | excludes; |
73 | < | nGlobalExcludes; |
74 | < | globalExcludes; |
75 | < | isError; |
335 | > | setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl, |
336 | > | &nGlobalExcludes, globalExcludes, molMembershipArray, |
337 | > | &isError ); |
338 | ||
77 | – | setFsimulation( &fInfo, &n_atoms, identArray, &n_exclude, excl, |
78 | – | &nGlobalExcludes, globalExcludes, &isError ); |
79 | – | |
339 | if( isError ){ | |
340 | ||
341 | sprintf( painCave.errMsg, | |
# | Line 90 | Line 349 | void SimInfo::refreshSim(){ | |
349 | "succesfully sent the simulation information to fortran.\n"); | |
350 | MPIcheckPoint(); | |
351 | #endif // is_mpi | |
352 | + | |
353 | + | this->ndf = this->getNDF(); |
354 | + | this->ndfRaw = this->getNDFraw(); |
355 | + | |
356 | } | |
357 |
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