# | Line 1 | Line 1 | |
---|---|---|
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 13 | Line 16 | |
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(){ | |
27 | excludes = NULL; | |
28 | n_constraints = 0; | |
29 | + | nZconstraints = 0; |
30 | n_oriented = 0; | |
31 | n_dipoles = 0; | |
32 | ndf = 0; | |
33 | ndfRaw = 0; | |
34 | + | nZconstraints = 0; |
35 | the_integrator = NULL; | |
36 | setTemp = 0; | |
37 | thermalTime = 0.0; | |
38 | + | currentTime = 0.0; |
39 | rCut = 0.0; | |
40 | + | origRcut = -1.0; |
41 | + | ecr = 0.0; |
42 | + | origEcr = -1.0; |
43 | + | est = 0.0; |
44 | + | oldEcr = 0.0; |
45 | + | oldRcut = 0.0; |
46 | ||
47 | + | haveOrigRcut = 0; |
48 | + | haveOrigEcr = 0; |
49 | + | boxIsInit = 0; |
50 | + | |
51 | + | resetTime = 1e99; |
52 | + | |
53 | + | |
54 | usePBC = 0; | |
55 | useLJ = 0; | |
56 | useSticky = 0; | |
# | Line 35 | Line 59 | SimInfo::SimInfo(){ | |
59 | useGB = 0; | |
60 | useEAM = 0; | |
61 | ||
62 | + | myConfiguration = new SimState(); |
63 | + | |
64 | wrapMeSimInfo( this ); | |
65 | } | |
66 | ||
67 | + | |
68 | + | SimInfo::~SimInfo(){ |
69 | + | |
70 | + | delete myConfiguration; |
71 | + | |
72 | + | map<string, GenericData*>::iterator i; |
73 | + | |
74 | + | for(i = properties.begin(); i != properties.end(); i++) |
75 | + | delete (*i).second; |
76 | + | |
77 | + | } |
78 | + | |
79 | void SimInfo::setBox(double newBox[3]) { | |
80 | < | double smallestBox, maxCutoff; |
81 | < | int status; |
82 | < | box_x = newBox[0]; |
45 | < | box_y = newBox[1]; |
46 | < | box_z = newBox[2]; |
47 | < | setFortranBoxSize(newBox); |
80 | > | |
81 | > | int i, j; |
82 | > | double tempMat[3][3]; |
83 | ||
84 | < | smallestBox = box_x; |
85 | < | if (box_y < smallestBox) smallestBox = box_y; |
51 | < | if (box_z < smallestBox) smallestBox = box_z; |
84 | > | for(i=0; i<3; i++) |
85 | > | for (j=0; j<3; j++) tempMat[i][j] = 0.0;; |
86 | ||
87 | < | maxCutoff = smallestBox / 2.0; |
87 | > | tempMat[0][0] = newBox[0]; |
88 | > | tempMat[1][1] = newBox[1]; |
89 | > | tempMat[2][2] = newBox[2]; |
90 | ||
91 | < | if (rList > maxCutoff) { |
56 | < | sprintf( painCave.errMsg, |
57 | < | "New Box size is forcing neighborlist radius down to %lf\n", |
58 | < | maxCutoff ); |
59 | < | painCave.isFatal = 0; |
60 | < | simError(); |
91 | > | setBoxM( tempMat ); |
92 | ||
93 | < | rList = maxCutoff; |
93 | > | } |
94 | ||
95 | < | sprintf( painCave.errMsg, |
96 | < | "New Box size is forcing cutoff radius down to %lf\n", |
97 | < | maxCutoff - 1.0 ); |
98 | < | painCave.isFatal = 0; |
99 | < | simError(); |
95 | > | void SimInfo::setBoxM( double theBox[3][3] ){ |
96 | > | |
97 | > | int i, j, status; |
98 | > | double smallestBoxL, maxCutoff; |
99 | > | double FortranHmat[9]; // to preserve compatibility with Fortran the |
100 | > | // ordering in the array is as follows: |
101 | > | // [ 0 3 6 ] |
102 | > | // [ 1 4 7 ] |
103 | > | // [ 2 5 8 ] |
104 | > | double FortranHmatInv[9]; // the inverted Hmat (for Fortran); |
105 | ||
106 | < | rCut = rList - 1.0; |
106 | > | |
107 | > | if( !boxIsInit ) boxIsInit = 1; |
108 | ||
109 | < | // list radius changed so we have to refresh the simulation structure. |
110 | < | refreshSim(); |
109 | > | for(i=0; i < 3; i++) |
110 | > | for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j]; |
111 | > | |
112 | > | calcBoxL(); |
113 | > | calcHmatInv(); |
114 | > | |
115 | > | for(i=0; i < 3; i++) { |
116 | > | for (j=0; j < 3; j++) { |
117 | > | FortranHmat[3*j + i] = Hmat[i][j]; |
118 | > | FortranHmatInv[3*j + i] = HmatInv[i][j]; |
119 | > | } |
120 | } | |
121 | ||
122 | < | if (rCut > maxCutoff) { |
122 | > | setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic); |
123 | > | |
124 | > | } |
125 | > | |
126 | > | |
127 | > | void SimInfo::getBoxM (double theBox[3][3]) { |
128 | > | |
129 | > | int i, j; |
130 | > | for(i=0; i<3; i++) |
131 | > | for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]; |
132 | > | } |
133 | > | |
134 | > | |
135 | > | void SimInfo::scaleBox(double scale) { |
136 | > | double theBox[3][3]; |
137 | > | int i, j; |
138 | > | |
139 | > | // cerr << "Scaling box by " << scale << "\n"; |
140 | > | |
141 | > | for(i=0; i<3; i++) |
142 | > | for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale; |
143 | > | |
144 | > | setBoxM(theBox); |
145 | > | |
146 | > | } |
147 | > | |
148 | > | void SimInfo::calcHmatInv( void ) { |
149 | > | |
150 | > | int i,j; |
151 | > | double smallDiag; |
152 | > | double tol; |
153 | > | double sanity[3][3]; |
154 | > | |
155 | > | invertMat3( Hmat, HmatInv ); |
156 | > | |
157 | > | // Check the inverse to make sure it is sane: |
158 | > | |
159 | > | matMul3( Hmat, HmatInv, sanity ); |
160 | > | |
161 | > | // check to see if Hmat is orthorhombic |
162 | > | |
163 | > | smallDiag = Hmat[0][0]; |
164 | > | if(smallDiag > Hmat[1][1]) smallDiag = Hmat[1][1]; |
165 | > | if(smallDiag > Hmat[2][2]) smallDiag = Hmat[2][2]; |
166 | > | tol = smallDiag * 1E-6; |
167 | > | |
168 | > | orthoRhombic = 1; |
169 | > | |
170 | > | for (i = 0; i < 3; i++ ) { |
171 | > | for (j = 0 ; j < 3; j++) { |
172 | > | if (i != j) { |
173 | > | if (orthoRhombic) { |
174 | > | if (Hmat[i][j] >= tol) orthoRhombic = 0; |
175 | > | } |
176 | > | } |
177 | > | } |
178 | > | } |
179 | > | } |
180 | > | |
181 | > | double SimInfo::matDet3(double a[3][3]) { |
182 | > | int i, j, k; |
183 | > | double determinant; |
184 | > | |
185 | > | determinant = 0.0; |
186 | > | |
187 | > | for(i = 0; i < 3; i++) { |
188 | > | j = (i+1)%3; |
189 | > | k = (i+2)%3; |
190 | > | |
191 | > | determinant += a[0][i] * (a[1][j]*a[2][k] - a[1][k]*a[2][j]); |
192 | > | } |
193 | > | |
194 | > | return determinant; |
195 | > | } |
196 | > | |
197 | > | void SimInfo::invertMat3(double a[3][3], double b[3][3]) { |
198 | > | |
199 | > | int i, j, k, l, m, n; |
200 | > | double determinant; |
201 | > | |
202 | > | determinant = matDet3( a ); |
203 | > | |
204 | > | if (determinant == 0.0) { |
205 | sprintf( painCave.errMsg, | |
206 | < | "New Box size is forcing cutoff radius down to %lf\n", |
207 | < | maxCutoff ); |
80 | < | painCave.isFatal = 0; |
206 | > | "Can't invert a matrix with a zero determinant!\n"); |
207 | > | painCave.isFatal = 1; |
208 | simError(); | |
209 | + | } |
210 | ||
211 | < | status = 0; |
212 | < | LJ_new_rcut(&rCut, &status); |
213 | < | if (status != 0) { |
214 | < | sprintf( painCave.errMsg, |
215 | < | "Error in recomputing LJ shifts based on new rcut\n"); |
216 | < | painCave.isFatal = 1; |
217 | < | simError(); |
211 | > | for (i=0; i < 3; i++) { |
212 | > | j = (i+1)%3; |
213 | > | k = (i+2)%3; |
214 | > | for(l = 0; l < 3; l++) { |
215 | > | m = (l+1)%3; |
216 | > | n = (l+2)%3; |
217 | > | |
218 | > | b[l][i] = (a[j][m]*a[k][n] - a[j][n]*a[k][m]) / determinant; |
219 | } | |
220 | } | |
221 | } | |
222 | ||
223 | < | void SimInfo::getBox(double theBox[3]) { |
224 | < | theBox[0] = box_x; |
225 | < | theBox[1] = box_y; |
226 | < | theBox[2] = box_z; |
223 | > | void SimInfo::matMul3(double a[3][3], double b[3][3], double c[3][3]) { |
224 | > | double r00, r01, r02, r10, r11, r12, r20, r21, r22; |
225 | > | |
226 | > | r00 = a[0][0]*b[0][0] + a[0][1]*b[1][0] + a[0][2]*b[2][0]; |
227 | > | r01 = a[0][0]*b[0][1] + a[0][1]*b[1][1] + a[0][2]*b[2][1]; |
228 | > | r02 = a[0][0]*b[0][2] + a[0][1]*b[1][2] + a[0][2]*b[2][2]; |
229 | > | |
230 | > | r10 = a[1][0]*b[0][0] + a[1][1]*b[1][0] + a[1][2]*b[2][0]; |
231 | > | r11 = a[1][0]*b[0][1] + a[1][1]*b[1][1] + a[1][2]*b[2][1]; |
232 | > | r12 = a[1][0]*b[0][2] + a[1][1]*b[1][2] + a[1][2]*b[2][2]; |
233 | > | |
234 | > | r20 = a[2][0]*b[0][0] + a[2][1]*b[1][0] + a[2][2]*b[2][0]; |
235 | > | r21 = a[2][0]*b[0][1] + a[2][1]*b[1][1] + a[2][2]*b[2][1]; |
236 | > | r22 = a[2][0]*b[0][2] + a[2][1]*b[1][2] + a[2][2]*b[2][2]; |
237 | > | |
238 | > | c[0][0] = r00; c[0][1] = r01; c[0][2] = r02; |
239 | > | c[1][0] = r10; c[1][1] = r11; c[1][2] = r12; |
240 | > | c[2][0] = r20; c[2][1] = r21; c[2][2] = r22; |
241 | } | |
242 | < | |
242 | > | |
243 | > | void SimInfo::matVecMul3(double m[3][3], double inVec[3], double outVec[3]) { |
244 | > | double a0, a1, a2; |
245 | > | |
246 | > | a0 = inVec[0]; a1 = inVec[1]; a2 = inVec[2]; |
247 | > | |
248 | > | outVec[0] = m[0][0]*a0 + m[0][1]*a1 + m[0][2]*a2; |
249 | > | outVec[1] = m[1][0]*a0 + m[1][1]*a1 + m[1][2]*a2; |
250 | > | outVec[2] = m[2][0]*a0 + m[2][1]*a1 + m[2][2]*a2; |
251 | > | } |
252 | > | |
253 | > | void SimInfo::transposeMat3(double in[3][3], double out[3][3]) { |
254 | > | double temp[3][3]; |
255 | > | int i, j; |
256 | > | |
257 | > | for (i = 0; i < 3; i++) { |
258 | > | for (j = 0; j < 3; j++) { |
259 | > | temp[j][i] = in[i][j]; |
260 | > | } |
261 | > | } |
262 | > | for (i = 0; i < 3; i++) { |
263 | > | for (j = 0; j < 3; j++) { |
264 | > | out[i][j] = temp[i][j]; |
265 | > | } |
266 | > | } |
267 | > | } |
268 | > | |
269 | > | void SimInfo::printMat3(double A[3][3] ){ |
270 | > | |
271 | > | std::cerr |
272 | > | << "[ " << A[0][0] << ", " << A[0][1] << ", " << A[0][2] << " ]\n" |
273 | > | << "[ " << A[1][0] << ", " << A[1][1] << ", " << A[1][2] << " ]\n" |
274 | > | << "[ " << A[2][0] << ", " << A[2][1] << ", " << A[2][2] << " ]\n"; |
275 | > | } |
276 | > | |
277 | > | void SimInfo::printMat9(double A[9] ){ |
278 | > | |
279 | > | std::cerr |
280 | > | << "[ " << A[0] << ", " << A[1] << ", " << A[2] << " ]\n" |
281 | > | << "[ " << A[3] << ", " << A[4] << ", " << A[5] << " ]\n" |
282 | > | << "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n"; |
283 | > | } |
284 | > | |
285 | > | |
286 | > | void SimInfo::crossProduct3(double a[3],double b[3], double out[3]){ |
287 | > | |
288 | > | out[0] = a[1] * b[2] - a[2] * b[1]; |
289 | > | out[1] = a[2] * b[0] - a[0] * b[2] ; |
290 | > | out[2] = a[0] * b[1] - a[1] * b[0]; |
291 | > | |
292 | > | } |
293 | > | |
294 | > | double SimInfo::dotProduct3(double a[3], double b[3]){ |
295 | > | return a[0]*b[0] + a[1]*b[1]+ a[2]*b[2]; |
296 | > | } |
297 | > | |
298 | > | double SimInfo::length3(double a[3]){ |
299 | > | return sqrt(a[0]*a[0] + a[1]*a[1] + a[2]*a[2]); |
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 | > | boxL[0] = sqrt( dsq ); |
316 | > | //maxCutoff = 0.5 * boxL[0]; |
317 | > | |
318 | > | // boxLy |
319 | > | |
320 | > | dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1]; |
321 | > | dsq = dx*dx + dy*dy + dz*dz; |
322 | > | boxL[1] = sqrt( dsq ); |
323 | > | //if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1]; |
324 | > | |
325 | > | |
326 | > | // boxLz |
327 | > | |
328 | > | dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2]; |
329 | > | dsq = dx*dx + dy*dy + dz*dz; |
330 | > | boxL[2] = sqrt( dsq ); |
331 | > | //if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2]; |
332 | > | |
333 | > | //calculate the max cutoff |
334 | > | maxCutoff = calcMaxCutOff(); |
335 | > | |
336 | > | checkCutOffs(); |
337 | > | |
338 | > | } |
339 | > | |
340 | > | |
341 | > | double SimInfo::calcMaxCutOff(){ |
342 | > | |
343 | > | double ri[3], rj[3], rk[3]; |
344 | > | double rij[3], rjk[3], rki[3]; |
345 | > | double minDist; |
346 | > | |
347 | > | ri[0] = Hmat[0][0]; |
348 | > | ri[1] = Hmat[1][0]; |
349 | > | ri[2] = Hmat[2][0]; |
350 | > | |
351 | > | rj[0] = Hmat[0][1]; |
352 | > | rj[1] = Hmat[1][1]; |
353 | > | rj[2] = Hmat[2][1]; |
354 | > | |
355 | > | rk[0] = Hmat[0][2]; |
356 | > | rk[1] = Hmat[1][2]; |
357 | > | rk[2] = Hmat[2][2]; |
358 | > | |
359 | > | crossProduct3(ri,rj, rij); |
360 | > | distXY = dotProduct3(rk,rij) / length3(rij); |
361 | > | |
362 | > | crossProduct3(rj,rk, rjk); |
363 | > | distYZ = dotProduct3(ri,rjk) / length3(rjk); |
364 | > | |
365 | > | crossProduct3(rk,ri, rki); |
366 | > | distZX = dotProduct3(rj,rki) / length3(rki); |
367 | > | |
368 | > | minDist = min(min(distXY, distYZ), distZX); |
369 | > | return minDist/2; |
370 | > | |
371 | > | } |
372 | > | |
373 | > | void SimInfo::wrapVector( double thePos[3] ){ |
374 | > | |
375 | > | int i, j, k; |
376 | > | double scaled[3]; |
377 | > | |
378 | > | if( !orthoRhombic ){ |
379 | > | // calc the scaled coordinates. |
380 | > | |
381 | > | |
382 | > | matVecMul3(HmatInv, thePos, scaled); |
383 | > | |
384 | > | for(i=0; i<3; i++) |
385 | > | scaled[i] -= roundMe(scaled[i]); |
386 | > | |
387 | > | // calc the wrapped real coordinates from the wrapped scaled coordinates |
388 | > | |
389 | > | matVecMul3(Hmat, scaled, thePos); |
390 | > | |
391 | > | } |
392 | > | else{ |
393 | > | // calc the scaled coordinates. |
394 | > | |
395 | > | for(i=0; i<3; i++) |
396 | > | scaled[i] = thePos[i]*HmatInv[i][i]; |
397 | > | |
398 | > | // wrap the scaled coordinates |
399 | > | |
400 | > | for(i=0; i<3; i++) |
401 | > | scaled[i] -= roundMe(scaled[i]); |
402 | > | |
403 | > | // calc the wrapped real coordinates from the wrapped scaled coordinates |
404 | > | |
405 | > | for(i=0; i<3; i++) |
406 | > | thePos[i] = scaled[i]*Hmat[i][i]; |
407 | > | } |
408 | > | |
409 | > | } |
410 | > | |
411 | > | |
412 | int SimInfo::getNDF(){ | |
413 | int ndf_local, ndf; | |
414 | ||
# | Line 108 | Line 420 | int SimInfo::getNDF(){ | |
420 | ndf = ndf_local; | |
421 | #endif | |
422 | ||
423 | < | ndf = ndf - 3; |
423 | > | ndf = ndf - 3 - nZconstraints; |
424 | ||
425 | return ndf; | |
426 | } | |
# | Line 127 | Line 439 | int SimInfo::getNDFraw() { | |
439 | ||
440 | return ndfRaw; | |
441 | } | |
442 | < | |
442 | > | |
443 | > | int SimInfo::getNDFtranslational() { |
444 | > | int ndfTrans_local, ndfTrans; |
445 | > | |
446 | > | ndfTrans_local = 3 * n_atoms - n_constraints; |
447 | > | |
448 | > | #ifdef IS_MPI |
449 | > | MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
450 | > | #else |
451 | > | ndfTrans = ndfTrans_local; |
452 | > | #endif |
453 | > | |
454 | > | ndfTrans = ndfTrans - 3 - nZconstraints; |
455 | > | |
456 | > | return ndfTrans; |
457 | > | } |
458 | > | |
459 | void SimInfo::refreshSim(){ | |
460 | ||
461 | simtype fInfo; | |
462 | int isError; | |
463 | int n_global; | |
464 | int* excl; | |
465 | < | |
138 | < | fInfo.rrf = 0.0; |
139 | < | fInfo.rt = 0.0; |
465 | > | |
466 | fInfo.dielect = 0.0; | |
467 | ||
142 | – | fInfo.box[0] = box_x; |
143 | – | fInfo.box[1] = box_y; |
144 | – | fInfo.box[2] = box_z; |
145 | – | |
146 | – | fInfo.rlist = rList; |
147 | – | fInfo.rcut = rCut; |
148 | – | |
468 | if( useDipole ){ | |
150 | – | fInfo.rrf = ecr; |
151 | – | fInfo.rt = ecr - est; |
469 | if( useReactionField )fInfo.dielect = dielectric; | |
470 | } | |
471 | ||
# | Line 194 | Line 511 | void SimInfo::refreshSim(){ | |
511 | ||
512 | this->ndf = this->getNDF(); | |
513 | this->ndfRaw = this->getNDFraw(); | |
514 | + | this->ndfTrans = this->getNDFtranslational(); |
515 | + | } |
516 | ||
517 | + | |
518 | + | void SimInfo::setRcut( double theRcut ){ |
519 | + | |
520 | + | if( !haveOrigRcut ){ |
521 | + | haveOrigRcut = 1; |
522 | + | origRcut = theRcut; |
523 | + | } |
524 | + | |
525 | + | rCut = theRcut; |
526 | + | checkCutOffs(); |
527 | } | |
528 | ||
529 | + | void SimInfo::setEcr( double theEcr ){ |
530 | + | |
531 | + | if( !haveOrigEcr ){ |
532 | + | haveOrigEcr = 1; |
533 | + | origEcr = theEcr; |
534 | + | } |
535 | + | |
536 | + | ecr = theEcr; |
537 | + | checkCutOffs(); |
538 | + | } |
539 | + | |
540 | + | void SimInfo::setEcr( double theEcr, double theEst ){ |
541 | + | |
542 | + | est = theEst; |
543 | + | setEcr( theEcr ); |
544 | + | } |
545 | + | |
546 | + | |
547 | + | void SimInfo::checkCutOffs( void ){ |
548 | + | |
549 | + | int cutChanged = 0; |
550 | + | |
551 | + | if( boxIsInit ){ |
552 | + | |
553 | + | //we need to check cutOffs against the box |
554 | + | |
555 | + | //detect the change of rCut |
556 | + | if(( maxCutoff > rCut )&&(usePBC)){ |
557 | + | if( rCut < origRcut ){ |
558 | + | rCut = origRcut; |
559 | + | |
560 | + | if (rCut > maxCutoff) |
561 | + | rCut = maxCutoff; |
562 | + | |
563 | + | sprintf( painCave.errMsg, |
564 | + | "New Box size is setting the long range cutoff radius " |
565 | + | "to %lf at time %lf\n", |
566 | + | rCut, currentTime ); |
567 | + | painCave.isFatal = 0; |
568 | + | simError(); |
569 | + | } |
570 | + | } |
571 | + | else if ((rCut > maxCutoff)&&(usePBC)) { |
572 | + | sprintf( painCave.errMsg, |
573 | + | "New Box size is setting the long range cutoff radius " |
574 | + | "to %lf at time %lf\n", |
575 | + | maxCutoff, currentTime ); |
576 | + | painCave.isFatal = 0; |
577 | + | simError(); |
578 | + | rCut = maxCutoff; |
579 | + | } |
580 | + | |
581 | + | |
582 | + | //detect the change of ecr |
583 | + | if( maxCutoff > ecr ){ |
584 | + | if( ecr < origEcr ){ |
585 | + | ecr = origEcr; |
586 | + | if (ecr > maxCutoff) ecr = maxCutoff; |
587 | + | |
588 | + | sprintf( painCave.errMsg, |
589 | + | "New Box size is setting the electrostaticCutoffRadius " |
590 | + | "to %lf at time %lf\n", |
591 | + | ecr, currentTime ); |
592 | + | painCave.isFatal = 0; |
593 | + | simError(); |
594 | + | } |
595 | + | } |
596 | + | else if( ecr > maxCutoff){ |
597 | + | sprintf( painCave.errMsg, |
598 | + | "New Box size is setting the electrostaticCutoffRadius " |
599 | + | "to %lf at time %lf\n", |
600 | + | maxCutoff, currentTime ); |
601 | + | painCave.isFatal = 0; |
602 | + | simError(); |
603 | + | ecr = maxCutoff; |
604 | + | } |
605 | + | |
606 | + | if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1; |
607 | + | |
608 | + | // rlist is the 1.0 plus max( rcut, ecr ) |
609 | + | |
610 | + | ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0; |
611 | + | |
612 | + | if( cutChanged ){ |
613 | + | |
614 | + | notifyFortranCutOffs( &rCut, &rList, &ecr, &est ); |
615 | + | } |
616 | + | |
617 | + | oldEcr = ecr; |
618 | + | oldRcut = rCut; |
619 | + | |
620 | + | } else { |
621 | + | // initialize this stuff before using it, OK? |
622 | + | sprintf( painCave.errMsg, |
623 | + | "Trying to check cutoffs without a box. Be smarter.\n" ); |
624 | + | painCave.isFatal = 1; |
625 | + | simError(); |
626 | + | } |
627 | + | |
628 | + | } |
629 | + | |
630 | + | void SimInfo::addProperty(GenericData* prop){ |
631 | + | |
632 | + | map<string, GenericData*>::iterator result; |
633 | + | result = properties.find(prop->getID()); |
634 | + | |
635 | + | //we can't simply use properties[prop->getID()] = prop, |
636 | + | //it will cause memory leak if we already contain a propery which has the same name of prop |
637 | + | |
638 | + | if(result != properties.end()){ |
639 | + | |
640 | + | delete (*result).second; |
641 | + | (*result).second = prop; |
642 | + | |
643 | + | } |
644 | + | else{ |
645 | + | |
646 | + | properties[prop->getID()] = prop; |
647 | + | |
648 | + | } |
649 | + | |
650 | + | } |
651 | + | |
652 | + | GenericData* SimInfo::getProperty(const string& propName){ |
653 | + | |
654 | + | map<string, GenericData*>::iterator result; |
655 | + | |
656 | + | //string lowerCaseName = (); |
657 | + | |
658 | + | result = properties.find(propName); |
659 | + | |
660 | + | if(result != properties.end()) |
661 | + | return (*result).second; |
662 | + | else |
663 | + | return NULL; |
664 | + | } |
665 | + | |
666 | + | vector<GenericData*> SimInfo::getProperties(){ |
667 | + | |
668 | + | vector<GenericData*> result; |
669 | + | map<string, GenericData*>::iterator i; |
670 | + | |
671 | + | for(i = properties.begin(); i != properties.end(); i++) |
672 | + | result.push_back((*i).second); |
673 | + | |
674 | + | return result; |
675 | + | } |
676 | + | |
677 | + | double SimInfo::matTrace3(double m[3][3]){ |
678 | + | double trace; |
679 | + | trace = m[0][0] + m[1][1] + m[2][2]; |
680 | + | |
681 | + | return trace; |
682 | + | } |
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