# | Line 1 | Line 1 | |
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1 | < | #include <cstdlib> |
2 | < | #include <cstring> |
1 | > | #include <stdlib.h> |
2 | > | #include <string.h> |
3 | > | #include <math.h> |
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(){ | |
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 29 | Line 59 | SimInfo::SimInfo(){ | |
59 | useGB = 0; | |
60 | useEAM = 0; | |
61 | ||
62 | + | myConfiguration = new SimState(); |
63 | ||
33 | – | |
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 | + | |
81 | + | int i, j; |
82 | + | double tempMat[3][3]; |
83 | + | |
84 | + | for(i=0; i<3; i++) |
85 | + | for (j=0; j<3; j++) tempMat[i][j] = 0.0;; |
86 | + | |
87 | + | tempMat[0][0] = newBox[0]; |
88 | + | tempMat[1][1] = newBox[1]; |
89 | + | tempMat[2][2] = newBox[2]; |
90 | + | |
91 | + | setBoxM( tempMat ); |
92 | + | |
93 | + | } |
94 | + | |
95 | + | void SimInfo::setBoxM( double theBox[3][3] ){ |
96 | + | |
97 | + | int i, j; |
98 | + | double FortranHmat[9]; // to preserve compatibility with Fortran the |
99 | + | // ordering in the array is as follows: |
100 | + | // [ 0 3 6 ] |
101 | + | // [ 1 4 7 ] |
102 | + | // [ 2 5 8 ] |
103 | + | double FortranHmatInv[9]; // the inverted Hmat (for Fortran); |
104 | + | |
105 | + | |
106 | + | if( !boxIsInit ) boxIsInit = 1; |
107 | + | |
108 | + | for(i=0; i < 3; i++) |
109 | + | for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j]; |
110 | + | |
111 | + | calcBoxL(); |
112 | + | calcHmatInv(); |
113 | + | |
114 | + | for(i=0; i < 3; i++) { |
115 | + | for (j=0; j < 3; j++) { |
116 | + | FortranHmat[3*j + i] = Hmat[i][j]; |
117 | + | FortranHmatInv[3*j + i] = HmatInv[i][j]; |
118 | + | } |
119 | + | } |
120 | + | |
121 | + | setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic); |
122 | + | |
123 | + | } |
124 | + | |
125 | + | |
126 | + | void SimInfo::getBoxM (double theBox[3][3]) { |
127 | + | |
128 | + | int i, j; |
129 | + | for(i=0; i<3; i++) |
130 | + | for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]; |
131 | + | } |
132 | + | |
133 | + | |
134 | + | void SimInfo::scaleBox(double scale) { |
135 | + | double theBox[3][3]; |
136 | + | int i, j; |
137 | + | |
138 | + | // cerr << "Scaling box by " << scale << "\n"; |
139 | + | |
140 | + | for(i=0; i<3; i++) |
141 | + | for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale; |
142 | + | |
143 | + | setBoxM(theBox); |
144 | + | |
145 | + | } |
146 | + | |
147 | + | void SimInfo::calcHmatInv( void ) { |
148 | + | |
149 | + | int oldOrtho; |
150 | + | int i,j; |
151 | + | double smallDiag; |
152 | + | double tol; |
153 | + | double sanity[3][3]; |
154 | + | |
155 | + | invertMat3( Hmat, HmatInv ); |
156 | + | |
157 | + | // check to see if Hmat is orthorhombic |
158 | + | |
159 | + | oldOrtho = orthoRhombic; |
160 | + | |
161 | + | smallDiag = fabs(Hmat[0][0]); |
162 | + | if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]); |
163 | + | if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]); |
164 | + | tol = smallDiag * 1E-6; |
165 | + | |
166 | + | orthoRhombic = 1; |
167 | + | |
168 | + | for (i = 0; i < 3; i++ ) { |
169 | + | for (j = 0 ; j < 3; j++) { |
170 | + | if (i != j) { |
171 | + | if (orthoRhombic) { |
172 | + | if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0; |
173 | + | } |
174 | + | } |
175 | + | } |
176 | + | } |
177 | + | |
178 | + | if( oldOrtho != orthoRhombic ){ |
179 | + | |
180 | + | if( orthoRhombic ){ |
181 | + | sprintf( painCave.errMsg, |
182 | + | "Hmat is switching from Non-Orthorhombic to OrthoRhombic\n" |
183 | + | " If this is a bad thing change the ortho tolerance in SimInfo.\n" ); |
184 | + | simError(); |
185 | + | } |
186 | + | else { |
187 | + | sprintf( painCave.errMsg, |
188 | + | "Hmat is switching from Orthorhombic to Non-OrthoRhombic\n" |
189 | + | " If this is a bad thing change the ortho tolerance in SimInfo.\n" ); |
190 | + | simError(); |
191 | + | } |
192 | + | } |
193 | + | } |
194 | + | |
195 | + | double SimInfo::matDet3(double a[3][3]) { |
196 | + | int i, j, k; |
197 | + | double determinant; |
198 | + | |
199 | + | determinant = 0.0; |
200 | + | |
201 | + | for(i = 0; i < 3; i++) { |
202 | + | j = (i+1)%3; |
203 | + | k = (i+2)%3; |
204 | + | |
205 | + | determinant += a[0][i] * (a[1][j]*a[2][k] - a[1][k]*a[2][j]); |
206 | + | } |
207 | + | |
208 | + | return determinant; |
209 | + | } |
210 | + | |
211 | + | void SimInfo::invertMat3(double a[3][3], double b[3][3]) { |
212 | + | |
213 | + | int i, j, k, l, m, n; |
214 | + | double determinant; |
215 | + | |
216 | + | determinant = matDet3( a ); |
217 | + | |
218 | + | if (determinant == 0.0) { |
219 | + | sprintf( painCave.errMsg, |
220 | + | "Can't invert a matrix with a zero determinant!\n"); |
221 | + | painCave.isFatal = 1; |
222 | + | simError(); |
223 | + | } |
224 | + | |
225 | + | for (i=0; i < 3; i++) { |
226 | + | j = (i+1)%3; |
227 | + | k = (i+2)%3; |
228 | + | for(l = 0; l < 3; l++) { |
229 | + | m = (l+1)%3; |
230 | + | n = (l+2)%3; |
231 | + | |
232 | + | b[l][i] = (a[j][m]*a[k][n] - a[j][n]*a[k][m]) / determinant; |
233 | + | } |
234 | + | } |
235 | + | } |
236 | + | |
237 | + | void SimInfo::matMul3(double a[3][3], double b[3][3], double c[3][3]) { |
238 | + | double r00, r01, r02, r10, r11, r12, r20, r21, r22; |
239 | + | |
240 | + | r00 = a[0][0]*b[0][0] + a[0][1]*b[1][0] + a[0][2]*b[2][0]; |
241 | + | r01 = a[0][0]*b[0][1] + a[0][1]*b[1][1] + a[0][2]*b[2][1]; |
242 | + | r02 = a[0][0]*b[0][2] + a[0][1]*b[1][2] + a[0][2]*b[2][2]; |
243 | + | |
244 | + | r10 = a[1][0]*b[0][0] + a[1][1]*b[1][0] + a[1][2]*b[2][0]; |
245 | + | r11 = a[1][0]*b[0][1] + a[1][1]*b[1][1] + a[1][2]*b[2][1]; |
246 | + | r12 = a[1][0]*b[0][2] + a[1][1]*b[1][2] + a[1][2]*b[2][2]; |
247 | + | |
248 | + | r20 = a[2][0]*b[0][0] + a[2][1]*b[1][0] + a[2][2]*b[2][0]; |
249 | + | r21 = a[2][0]*b[0][1] + a[2][1]*b[1][1] + a[2][2]*b[2][1]; |
250 | + | r22 = a[2][0]*b[0][2] + a[2][1]*b[1][2] + a[2][2]*b[2][2]; |
251 | + | |
252 | + | c[0][0] = r00; c[0][1] = r01; c[0][2] = r02; |
253 | + | c[1][0] = r10; c[1][1] = r11; c[1][2] = r12; |
254 | + | c[2][0] = r20; c[2][1] = r21; c[2][2] = r22; |
255 | + | } |
256 | + | |
257 | + | void SimInfo::matVecMul3(double m[3][3], double inVec[3], double outVec[3]) { |
258 | + | double a0, a1, a2; |
259 | + | |
260 | + | a0 = inVec[0]; a1 = inVec[1]; a2 = inVec[2]; |
261 | + | |
262 | + | outVec[0] = m[0][0]*a0 + m[0][1]*a1 + m[0][2]*a2; |
263 | + | outVec[1] = m[1][0]*a0 + m[1][1]*a1 + m[1][2]*a2; |
264 | + | outVec[2] = m[2][0]*a0 + m[2][1]*a1 + m[2][2]*a2; |
265 | + | } |
266 | + | |
267 | + | void SimInfo::transposeMat3(double in[3][3], double out[3][3]) { |
268 | + | double temp[3][3]; |
269 | + | int i, j; |
270 | + | |
271 | + | for (i = 0; i < 3; i++) { |
272 | + | for (j = 0; j < 3; j++) { |
273 | + | temp[j][i] = in[i][j]; |
274 | + | } |
275 | + | } |
276 | + | for (i = 0; i < 3; i++) { |
277 | + | for (j = 0; j < 3; j++) { |
278 | + | out[i][j] = temp[i][j]; |
279 | + | } |
280 | + | } |
281 | + | } |
282 | + | |
283 | + | void SimInfo::printMat3(double A[3][3] ){ |
284 | + | |
285 | + | std::cerr |
286 | + | << "[ " << A[0][0] << ", " << A[0][1] << ", " << A[0][2] << " ]\n" |
287 | + | << "[ " << A[1][0] << ", " << A[1][1] << ", " << A[1][2] << " ]\n" |
288 | + | << "[ " << A[2][0] << ", " << A[2][1] << ", " << A[2][2] << " ]\n"; |
289 | + | } |
290 | + | |
291 | + | void SimInfo::printMat9(double A[9] ){ |
292 | + | |
293 | + | std::cerr |
294 | + | << "[ " << A[0] << ", " << A[1] << ", " << A[2] << " ]\n" |
295 | + | << "[ " << A[3] << ", " << A[4] << ", " << A[5] << " ]\n" |
296 | + | << "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n"; |
297 | + | } |
298 | + | |
299 | + | |
300 | + | void SimInfo::crossProduct3(double a[3],double b[3], double out[3]){ |
301 | + | |
302 | + | out[0] = a[1] * b[2] - a[2] * b[1]; |
303 | + | out[1] = a[2] * b[0] - a[0] * b[2] ; |
304 | + | out[2] = a[0] * b[1] - a[1] * b[0]; |
305 | + | |
306 | + | } |
307 | + | |
308 | + | double SimInfo::dotProduct3(double a[3], double b[3]){ |
309 | + | return a[0]*b[0] + a[1]*b[1]+ a[2]*b[2]; |
310 | + | } |
311 | + | |
312 | + | double SimInfo::length3(double a[3]){ |
313 | + | return sqrt(a[0]*a[0] + a[1]*a[1] + a[2]*a[2]); |
314 | + | } |
315 | + | |
316 | + | void SimInfo::calcBoxL( void ){ |
317 | + | |
318 | + | double dx, dy, dz, dsq; |
319 | + | |
320 | + | // boxVol = Determinant of Hmat |
321 | + | |
322 | + | boxVol = matDet3( Hmat ); |
323 | + | |
324 | + | // boxLx |
325 | + | |
326 | + | dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0]; |
327 | + | dsq = dx*dx + dy*dy + dz*dz; |
328 | + | boxL[0] = sqrt( dsq ); |
329 | + | //maxCutoff = 0.5 * boxL[0]; |
330 | + | |
331 | + | // boxLy |
332 | + | |
333 | + | dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1]; |
334 | + | dsq = dx*dx + dy*dy + dz*dz; |
335 | + | boxL[1] = sqrt( dsq ); |
336 | + | //if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1]; |
337 | + | |
338 | + | |
339 | + | // boxLz |
340 | + | |
341 | + | dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2]; |
342 | + | dsq = dx*dx + dy*dy + dz*dz; |
343 | + | boxL[2] = sqrt( dsq ); |
344 | + | //if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2]; |
345 | + | |
346 | + | //calculate the max cutoff |
347 | + | maxCutoff = calcMaxCutOff(); |
348 | + | |
349 | + | checkCutOffs(); |
350 | + | |
351 | + | } |
352 | + | |
353 | + | |
354 | + | double SimInfo::calcMaxCutOff(){ |
355 | + | |
356 | + | double ri[3], rj[3], rk[3]; |
357 | + | double rij[3], rjk[3], rki[3]; |
358 | + | double minDist; |
359 | + | |
360 | + | ri[0] = Hmat[0][0]; |
361 | + | ri[1] = Hmat[1][0]; |
362 | + | ri[2] = Hmat[2][0]; |
363 | + | |
364 | + | rj[0] = Hmat[0][1]; |
365 | + | rj[1] = Hmat[1][1]; |
366 | + | rj[2] = Hmat[2][1]; |
367 | + | |
368 | + | rk[0] = Hmat[0][2]; |
369 | + | rk[1] = Hmat[1][2]; |
370 | + | rk[2] = Hmat[2][2]; |
371 | + | |
372 | + | crossProduct3(ri,rj, rij); |
373 | + | distXY = dotProduct3(rk,rij) / length3(rij); |
374 | + | |
375 | + | crossProduct3(rj,rk, rjk); |
376 | + | distYZ = dotProduct3(ri,rjk) / length3(rjk); |
377 | + | |
378 | + | crossProduct3(rk,ri, rki); |
379 | + | distZX = dotProduct3(rj,rki) / length3(rki); |
380 | + | |
381 | + | minDist = min(min(distXY, distYZ), distZX); |
382 | + | return minDist/2; |
383 | + | |
384 | } | |
385 | ||
386 | + | void SimInfo::wrapVector( double thePos[3] ){ |
387 | + | |
388 | + | int i; |
389 | + | double scaled[3]; |
390 | + | |
391 | + | if( !orthoRhombic ){ |
392 | + | // calc the scaled coordinates. |
393 | + | |
394 | + | |
395 | + | matVecMul3(HmatInv, thePos, scaled); |
396 | + | |
397 | + | for(i=0; i<3; i++) |
398 | + | scaled[i] -= roundMe(scaled[i]); |
399 | + | |
400 | + | // calc the wrapped real coordinates from the wrapped scaled coordinates |
401 | + | |
402 | + | matVecMul3(Hmat, scaled, thePos); |
403 | + | |
404 | + | } |
405 | + | else{ |
406 | + | // calc the scaled coordinates. |
407 | + | |
408 | + | for(i=0; i<3; i++) |
409 | + | scaled[i] = thePos[i]*HmatInv[i][i]; |
410 | + | |
411 | + | // wrap the scaled coordinates |
412 | + | |
413 | + | for(i=0; i<3; i++) |
414 | + | scaled[i] -= roundMe(scaled[i]); |
415 | + | |
416 | + | // calc the wrapped real coordinates from the wrapped scaled coordinates |
417 | + | |
418 | + | for(i=0; i<3; i++) |
419 | + | thePos[i] = scaled[i]*Hmat[i][i]; |
420 | + | } |
421 | + | |
422 | + | } |
423 | + | |
424 | + | |
425 | + | int SimInfo::getNDF(){ |
426 | + | int ndf_local; |
427 | + | |
428 | + | ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints; |
429 | + | |
430 | + | #ifdef IS_MPI |
431 | + | MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
432 | + | #else |
433 | + | ndf = ndf_local; |
434 | + | #endif |
435 | + | |
436 | + | ndf = ndf - 3 - nZconstraints; |
437 | + | |
438 | + | return ndf; |
439 | + | } |
440 | + | |
441 | + | int SimInfo::getNDFraw() { |
442 | + | int ndfRaw_local; |
443 | + | |
444 | + | // Raw degrees of freedom that we have to set |
445 | + | ndfRaw_local = 3 * n_atoms + 3 * n_oriented; |
446 | + | |
447 | + | #ifdef IS_MPI |
448 | + | MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
449 | + | #else |
450 | + | ndfRaw = ndfRaw_local; |
451 | + | #endif |
452 | + | |
453 | + | return ndfRaw; |
454 | + | } |
455 | + | |
456 | + | int SimInfo::getNDFtranslational() { |
457 | + | int ndfTrans_local; |
458 | + | |
459 | + | ndfTrans_local = 3 * n_atoms - n_constraints; |
460 | + | |
461 | + | #ifdef IS_MPI |
462 | + | MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
463 | + | #else |
464 | + | ndfTrans = ndfTrans_local; |
465 | + | #endif |
466 | + | |
467 | + | ndfTrans = ndfTrans - 3 - nZconstraints; |
468 | + | |
469 | + | return ndfTrans; |
470 | + | } |
471 | + | |
472 | void SimInfo::refreshSim(){ | |
473 | ||
474 | simtype fInfo; | |
475 | int isError; | |
476 | + | int n_global; |
477 | int* excl; | |
478 | ||
479 | < | fInfo.box[0] = box_x; |
44 | < | fInfo.box[1] = box_y; |
45 | < | fInfo.box[2] = box_z; |
479 | > | fInfo.dielect = 0.0; |
480 | ||
481 | < | fInfo.rlist = rList; |
482 | < | fInfo.rcut = rCut; |
483 | < | fInfo.rrf = ecr; |
50 | < | fInfo.rt = ecr - est; |
51 | < | fInfo.dielect = dielectric; |
481 | > | if( useDipole ){ |
482 | > | if( useReactionField )fInfo.dielect = dielectric; |
483 | > | } |
484 | ||
485 | fInfo.SIM_uses_PBC = usePBC; | |
486 | //fInfo.SIM_uses_LJ = 0; | |
# | Line 64 | Line 496 | void SimInfo::refreshSim(){ | |
496 | ||
497 | excl = Exclude::getArray(); | |
498 | ||
499 | + | #ifdef IS_MPI |
500 | + | n_global = mpiSim->getTotAtoms(); |
501 | + | #else |
502 | + | n_global = n_atoms; |
503 | + | #endif |
504 | + | |
505 | isError = 0; | |
506 | ||
507 | < | // fInfo; |
508 | < | // n_atoms; |
509 | < | // identArray; |
72 | < | // n_exclude; |
73 | < | // excludes; |
74 | < | // nGlobalExcludes; |
75 | < | // globalExcludes; |
76 | < | // isError; |
507 | > | setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl, |
508 | > | &nGlobalExcludes, globalExcludes, molMembershipArray, |
509 | > | &isError ); |
510 | ||
78 | – | setFsimulation( &fInfo, &n_atoms, identArray, &n_exclude, excl, |
79 | – | &nGlobalExcludes, globalExcludes, &isError ); |
80 | – | |
511 | if( isError ){ | |
512 | ||
513 | sprintf( painCave.errMsg, | |
# | Line 91 | Line 521 | void SimInfo::refreshSim(){ | |
521 | "succesfully sent the simulation information to fortran.\n"); | |
522 | MPIcheckPoint(); | |
523 | #endif // is_mpi | |
524 | + | |
525 | + | this->ndf = this->getNDF(); |
526 | + | this->ndfRaw = this->getNDFraw(); |
527 | + | this->ndfTrans = this->getNDFtranslational(); |
528 | } | |
529 | ||
530 | + | |
531 | + | void SimInfo::setRcut( double theRcut ){ |
532 | + | |
533 | + | rCut = theRcut; |
534 | + | checkCutOffs(); |
535 | + | } |
536 | + | |
537 | + | void SimInfo::setDefaultRcut( double theRcut ){ |
538 | + | |
539 | + | haveOrigRcut = 1; |
540 | + | origRcut = theRcut; |
541 | + | rCut = theRcut; |
542 | + | |
543 | + | ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0; |
544 | + | |
545 | + | notifyFortranCutOffs( &rCut, &rList, &ecr, &est ); |
546 | + | } |
547 | + | |
548 | + | void SimInfo::setEcr( double theEcr ){ |
549 | + | |
550 | + | ecr = theEcr; |
551 | + | checkCutOffs(); |
552 | + | } |
553 | + | |
554 | + | void SimInfo::setDefaultEcr( double theEcr ){ |
555 | + | |
556 | + | haveOrigEcr = 1; |
557 | + | origEcr = theEcr; |
558 | + | |
559 | + | ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0; |
560 | + | |
561 | + | ecr = theEcr; |
562 | + | |
563 | + | notifyFortranCutOffs( &rCut, &rList, &ecr, &est ); |
564 | + | } |
565 | + | |
566 | + | void SimInfo::setEcr( double theEcr, double theEst ){ |
567 | + | |
568 | + | est = theEst; |
569 | + | setEcr( theEcr ); |
570 | + | } |
571 | + | |
572 | + | void SimInfo::setDefaultEcr( double theEcr, double theEst ){ |
573 | + | |
574 | + | est = theEst; |
575 | + | setDefaultEcr( theEcr ); |
576 | + | } |
577 | + | |
578 | + | |
579 | + | void SimInfo::checkCutOffs( void ){ |
580 | + | |
581 | + | int cutChanged = 0; |
582 | + | |
583 | + | if( boxIsInit ){ |
584 | + | |
585 | + | //we need to check cutOffs against the box |
586 | + | |
587 | + | //detect the change of rCut |
588 | + | if(( maxCutoff > rCut )&&(usePBC)){ |
589 | + | if( rCut < origRcut ){ |
590 | + | rCut = origRcut; |
591 | + | |
592 | + | if (rCut > maxCutoff) |
593 | + | rCut = maxCutoff; |
594 | + | |
595 | + | sprintf( painCave.errMsg, |
596 | + | "New Box size is setting the long range cutoff radius " |
597 | + | "to %lf at time %lf\n", |
598 | + | rCut, currentTime ); |
599 | + | painCave.isFatal = 0; |
600 | + | simError(); |
601 | + | } |
602 | + | } |
603 | + | else if ((rCut > maxCutoff)&&(usePBC)) { |
604 | + | sprintf( painCave.errMsg, |
605 | + | "New Box size is setting the long range cutoff radius " |
606 | + | "to %lf at time %lf\n", |
607 | + | maxCutoff, currentTime ); |
608 | + | painCave.isFatal = 0; |
609 | + | simError(); |
610 | + | rCut = maxCutoff; |
611 | + | } |
612 | + | |
613 | + | |
614 | + | //detect the change of ecr |
615 | + | if( maxCutoff > ecr ){ |
616 | + | if( ecr < origEcr ){ |
617 | + | ecr = origEcr; |
618 | + | if (ecr > maxCutoff) ecr = maxCutoff; |
619 | + | |
620 | + | sprintf( painCave.errMsg, |
621 | + | "New Box size is setting the electrostaticCutoffRadius " |
622 | + | "to %lf at time %lf\n", |
623 | + | ecr, currentTime ); |
624 | + | painCave.isFatal = 0; |
625 | + | simError(); |
626 | + | } |
627 | + | } |
628 | + | else if( ecr > maxCutoff){ |
629 | + | sprintf( painCave.errMsg, |
630 | + | "New Box size is setting the electrostaticCutoffRadius " |
631 | + | "to %lf at time %lf\n", |
632 | + | maxCutoff, currentTime ); |
633 | + | painCave.isFatal = 0; |
634 | + | simError(); |
635 | + | ecr = maxCutoff; |
636 | + | } |
637 | + | |
638 | + | if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1; |
639 | + | |
640 | + | // rlist is the 1.0 plus max( rcut, ecr ) |
641 | + | |
642 | + | ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0; |
643 | + | |
644 | + | if( cutChanged ){ |
645 | + | notifyFortranCutOffs( &rCut, &rList, &ecr, &est ); |
646 | + | } |
647 | + | |
648 | + | oldEcr = ecr; |
649 | + | oldRcut = rCut; |
650 | + | |
651 | + | } else { |
652 | + | // initialize this stuff before using it, OK? |
653 | + | sprintf( painCave.errMsg, |
654 | + | "Trying to check cutoffs without a box. Be smarter.\n" ); |
655 | + | painCave.isFatal = 1; |
656 | + | simError(); |
657 | + | } |
658 | + | |
659 | + | } |
660 | + | |
661 | + | void SimInfo::addProperty(GenericData* prop){ |
662 | + | |
663 | + | map<string, GenericData*>::iterator result; |
664 | + | result = properties.find(prop->getID()); |
665 | + | |
666 | + | //we can't simply use properties[prop->getID()] = prop, |
667 | + | //it will cause memory leak if we already contain a propery which has the same name of prop |
668 | + | |
669 | + | if(result != properties.end()){ |
670 | + | |
671 | + | delete (*result).second; |
672 | + | (*result).second = prop; |
673 | + | |
674 | + | } |
675 | + | else{ |
676 | + | |
677 | + | properties[prop->getID()] = prop; |
678 | + | |
679 | + | } |
680 | + | |
681 | + | } |
682 | + | |
683 | + | GenericData* SimInfo::getProperty(const string& propName){ |
684 | + | |
685 | + | map<string, GenericData*>::iterator result; |
686 | + | |
687 | + | //string lowerCaseName = (); |
688 | + | |
689 | + | result = properties.find(propName); |
690 | + | |
691 | + | if(result != properties.end()) |
692 | + | return (*result).second; |
693 | + | else |
694 | + | return NULL; |
695 | + | } |
696 | + | |
697 | + | vector<GenericData*> SimInfo::getProperties(){ |
698 | + | |
699 | + | vector<GenericData*> result; |
700 | + | map<string, GenericData*>::iterator i; |
701 | + | |
702 | + | for(i = properties.begin(); i != properties.end(); i++) |
703 | + | result.push_back((*i).second); |
704 | + | |
705 | + | return result; |
706 | + | } |
707 | + | |
708 | + | double SimInfo::matTrace3(double m[3][3]){ |
709 | + | double trace; |
710 | + | trace = m[0][0] + m[1][1] + m[2][2]; |
711 | + | |
712 | + | return trace; |
713 | + | } |
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