# | 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 | + | orthoTolerance = 1E-6; |
54 | + | useInitXSstate = true; |
55 | + | |
56 | usePBC = 0; | |
57 | useLJ = 0; | |
58 | useSticky = 0; | |
# | Line 29 | Line 61 | SimInfo::SimInfo(){ | |
61 | useGB = 0; | |
62 | useEAM = 0; | |
63 | ||
64 | + | myConfiguration = new SimState(); |
65 | + | |
66 | wrapMeSimInfo( this ); | |
67 | } | |
68 | ||
69 | + | |
70 | + | SimInfo::~SimInfo(){ |
71 | + | |
72 | + | delete myConfiguration; |
73 | + | |
74 | + | map<string, GenericData*>::iterator i; |
75 | + | |
76 | + | for(i = properties.begin(); i != properties.end(); i++) |
77 | + | delete (*i).second; |
78 | + | |
79 | + | } |
80 | + | |
81 | void SimInfo::setBox(double newBox[3]) { | |
82 | < | box_x = newBox[0]; |
83 | < | box_y = newBox[1]; |
84 | < | box_z = newBox[2]; |
85 | < | setFortranBoxSize(newBox); |
82 | > | |
83 | > | int i, j; |
84 | > | double tempMat[3][3]; |
85 | > | |
86 | > | for(i=0; i<3; i++) |
87 | > | for (j=0; j<3; j++) tempMat[i][j] = 0.0;; |
88 | > | |
89 | > | tempMat[0][0] = newBox[0]; |
90 | > | tempMat[1][1] = newBox[1]; |
91 | > | tempMat[2][2] = newBox[2]; |
92 | > | |
93 | > | setBoxM( tempMat ); |
94 | > | |
95 | } | |
96 | ||
97 | < | void SimInfo::getBox(double theBox[3]) { |
98 | < | theBox[0] = box_x; |
99 | < | theBox[1] = box_y; |
100 | < | theBox[2] = box_z; |
97 | > | void SimInfo::setBoxM( double theBox[3][3] ){ |
98 | > | |
99 | > | int i, j; |
100 | > | double FortranHmat[9]; // to preserve compatibility with Fortran the |
101 | > | // ordering in the array is as follows: |
102 | > | // [ 0 3 6 ] |
103 | > | // [ 1 4 7 ] |
104 | > | // [ 2 5 8 ] |
105 | > | double FortranHmatInv[9]; // the inverted Hmat (for Fortran); |
106 | > | |
107 | > | |
108 | > | if( !boxIsInit ) boxIsInit = 1; |
109 | > | |
110 | > | for(i=0; i < 3; i++) |
111 | > | for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j]; |
112 | > | |
113 | > | calcBoxL(); |
114 | > | calcHmatInv(); |
115 | > | |
116 | > | for(i=0; i < 3; i++) { |
117 | > | for (j=0; j < 3; j++) { |
118 | > | FortranHmat[3*j + i] = Hmat[i][j]; |
119 | > | FortranHmatInv[3*j + i] = HmatInv[i][j]; |
120 | > | } |
121 | > | } |
122 | > | |
123 | > | setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic); |
124 | > | |
125 | } | |
126 | + | |
127 | + | |
128 | + | void SimInfo::getBoxM (double theBox[3][3]) { |
129 | + | |
130 | + | int i, j; |
131 | + | for(i=0; i<3; i++) |
132 | + | for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]; |
133 | + | } |
134 | + | |
135 | + | |
136 | + | void SimInfo::scaleBox(double scale) { |
137 | + | double theBox[3][3]; |
138 | + | int i, j; |
139 | + | |
140 | + | // cerr << "Scaling box by " << scale << "\n"; |
141 | + | |
142 | + | for(i=0; i<3; i++) |
143 | + | for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale; |
144 | + | |
145 | + | setBoxM(theBox); |
146 | + | |
147 | + | } |
148 | + | |
149 | + | void SimInfo::calcHmatInv( void ) { |
150 | ||
151 | + | int oldOrtho; |
152 | + | int i,j; |
153 | + | double smallDiag; |
154 | + | double tol; |
155 | + | double sanity[3][3]; |
156 | + | |
157 | + | invertMat3( Hmat, HmatInv ); |
158 | + | |
159 | + | // check to see if Hmat is orthorhombic |
160 | + | |
161 | + | oldOrtho = orthoRhombic; |
162 | + | |
163 | + | smallDiag = fabs(Hmat[0][0]); |
164 | + | if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]); |
165 | + | if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]); |
166 | + | tol = smallDiag * orthoTolerance; |
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 ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0; |
175 | + | } |
176 | + | } |
177 | + | } |
178 | + | } |
179 | + | |
180 | + | if( oldOrtho != orthoRhombic ){ |
181 | + | |
182 | + | if( orthoRhombic ){ |
183 | + | sprintf( painCave.errMsg, |
184 | + | "Hmat is switching from Non-Orthorhombic to OrthoRhombic\n" |
185 | + | " If this is a bad thing, change the orthoBoxTolerance( currently %G ).\n", |
186 | + | orthoTolerance); |
187 | + | simError(); |
188 | + | } |
189 | + | else { |
190 | + | sprintf( painCave.errMsg, |
191 | + | "Hmat is switching from Orthorhombic to Non-OrthoRhombic\n" |
192 | + | " If this is a bad thing, change the orthoBoxTolerance( currently %G ).\n", |
193 | + | orthoTolerance); |
194 | + | simError(); |
195 | + | } |
196 | + | } |
197 | + | } |
198 | + | |
199 | + | double SimInfo::matDet3(double a[3][3]) { |
200 | + | int i, j, k; |
201 | + | double determinant; |
202 | + | |
203 | + | determinant = 0.0; |
204 | + | |
205 | + | for(i = 0; i < 3; i++) { |
206 | + | j = (i+1)%3; |
207 | + | k = (i+2)%3; |
208 | + | |
209 | + | determinant += a[0][i] * (a[1][j]*a[2][k] - a[1][k]*a[2][j]); |
210 | + | } |
211 | + | |
212 | + | return determinant; |
213 | + | } |
214 | + | |
215 | + | void SimInfo::invertMat3(double a[3][3], double b[3][3]) { |
216 | + | |
217 | + | int i, j, k, l, m, n; |
218 | + | double determinant; |
219 | + | |
220 | + | determinant = matDet3( a ); |
221 | + | |
222 | + | if (determinant == 0.0) { |
223 | + | sprintf( painCave.errMsg, |
224 | + | "Can't invert a matrix with a zero determinant!\n"); |
225 | + | painCave.isFatal = 1; |
226 | + | simError(); |
227 | + | } |
228 | + | |
229 | + | for (i=0; i < 3; i++) { |
230 | + | j = (i+1)%3; |
231 | + | k = (i+2)%3; |
232 | + | for(l = 0; l < 3; l++) { |
233 | + | m = (l+1)%3; |
234 | + | n = (l+2)%3; |
235 | + | |
236 | + | b[l][i] = (a[j][m]*a[k][n] - a[j][n]*a[k][m]) / determinant; |
237 | + | } |
238 | + | } |
239 | + | } |
240 | + | |
241 | + | void SimInfo::matMul3(double a[3][3], double b[3][3], double c[3][3]) { |
242 | + | double r00, r01, r02, r10, r11, r12, r20, r21, r22; |
243 | + | |
244 | + | r00 = a[0][0]*b[0][0] + a[0][1]*b[1][0] + a[0][2]*b[2][0]; |
245 | + | r01 = a[0][0]*b[0][1] + a[0][1]*b[1][1] + a[0][2]*b[2][1]; |
246 | + | r02 = a[0][0]*b[0][2] + a[0][1]*b[1][2] + a[0][2]*b[2][2]; |
247 | + | |
248 | + | r10 = a[1][0]*b[0][0] + a[1][1]*b[1][0] + a[1][2]*b[2][0]; |
249 | + | r11 = a[1][0]*b[0][1] + a[1][1]*b[1][1] + a[1][2]*b[2][1]; |
250 | + | r12 = a[1][0]*b[0][2] + a[1][1]*b[1][2] + a[1][2]*b[2][2]; |
251 | + | |
252 | + | r20 = a[2][0]*b[0][0] + a[2][1]*b[1][0] + a[2][2]*b[2][0]; |
253 | + | r21 = a[2][0]*b[0][1] + a[2][1]*b[1][1] + a[2][2]*b[2][1]; |
254 | + | r22 = a[2][0]*b[0][2] + a[2][1]*b[1][2] + a[2][2]*b[2][2]; |
255 | + | |
256 | + | c[0][0] = r00; c[0][1] = r01; c[0][2] = r02; |
257 | + | c[1][0] = r10; c[1][1] = r11; c[1][2] = r12; |
258 | + | c[2][0] = r20; c[2][1] = r21; c[2][2] = r22; |
259 | + | } |
260 | + | |
261 | + | void SimInfo::matVecMul3(double m[3][3], double inVec[3], double outVec[3]) { |
262 | + | double a0, a1, a2; |
263 | + | |
264 | + | a0 = inVec[0]; a1 = inVec[1]; a2 = inVec[2]; |
265 | + | |
266 | + | outVec[0] = m[0][0]*a0 + m[0][1]*a1 + m[0][2]*a2; |
267 | + | outVec[1] = m[1][0]*a0 + m[1][1]*a1 + m[1][2]*a2; |
268 | + | outVec[2] = m[2][0]*a0 + m[2][1]*a1 + m[2][2]*a2; |
269 | + | } |
270 | + | |
271 | + | void SimInfo::transposeMat3(double in[3][3], double out[3][3]) { |
272 | + | double temp[3][3]; |
273 | + | int i, j; |
274 | + | |
275 | + | for (i = 0; i < 3; i++) { |
276 | + | for (j = 0; j < 3; j++) { |
277 | + | temp[j][i] = in[i][j]; |
278 | + | } |
279 | + | } |
280 | + | for (i = 0; i < 3; i++) { |
281 | + | for (j = 0; j < 3; j++) { |
282 | + | out[i][j] = temp[i][j]; |
283 | + | } |
284 | + | } |
285 | + | } |
286 | + | |
287 | + | void SimInfo::printMat3(double A[3][3] ){ |
288 | + | |
289 | + | std::cerr |
290 | + | << "[ " << A[0][0] << ", " << A[0][1] << ", " << A[0][2] << " ]\n" |
291 | + | << "[ " << A[1][0] << ", " << A[1][1] << ", " << A[1][2] << " ]\n" |
292 | + | << "[ " << A[2][0] << ", " << A[2][1] << ", " << A[2][2] << " ]\n"; |
293 | + | } |
294 | + | |
295 | + | void SimInfo::printMat9(double A[9] ){ |
296 | + | |
297 | + | std::cerr |
298 | + | << "[ " << A[0] << ", " << A[1] << ", " << A[2] << " ]\n" |
299 | + | << "[ " << A[3] << ", " << A[4] << ", " << A[5] << " ]\n" |
300 | + | << "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n"; |
301 | + | } |
302 | + | |
303 | + | |
304 | + | void SimInfo::crossProduct3(double a[3],double b[3], double out[3]){ |
305 | + | |
306 | + | out[0] = a[1] * b[2] - a[2] * b[1]; |
307 | + | out[1] = a[2] * b[0] - a[0] * b[2] ; |
308 | + | out[2] = a[0] * b[1] - a[1] * b[0]; |
309 | + | |
310 | + | } |
311 | + | |
312 | + | double SimInfo::dotProduct3(double a[3], double b[3]){ |
313 | + | return a[0]*b[0] + a[1]*b[1]+ a[2]*b[2]; |
314 | + | } |
315 | + | |
316 | + | double SimInfo::length3(double a[3]){ |
317 | + | return sqrt(a[0]*a[0] + a[1]*a[1] + a[2]*a[2]); |
318 | + | } |
319 | + | |
320 | + | void SimInfo::calcBoxL( void ){ |
321 | + | |
322 | + | double dx, dy, dz, dsq; |
323 | + | |
324 | + | // boxVol = Determinant of Hmat |
325 | + | |
326 | + | boxVol = matDet3( Hmat ); |
327 | + | |
328 | + | // boxLx |
329 | + | |
330 | + | dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0]; |
331 | + | dsq = dx*dx + dy*dy + dz*dz; |
332 | + | boxL[0] = sqrt( dsq ); |
333 | + | //maxCutoff = 0.5 * boxL[0]; |
334 | + | |
335 | + | // boxLy |
336 | + | |
337 | + | dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1]; |
338 | + | dsq = dx*dx + dy*dy + dz*dz; |
339 | + | boxL[1] = sqrt( dsq ); |
340 | + | //if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1]; |
341 | + | |
342 | + | |
343 | + | // boxLz |
344 | + | |
345 | + | dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2]; |
346 | + | dsq = dx*dx + dy*dy + dz*dz; |
347 | + | boxL[2] = sqrt( dsq ); |
348 | + | //if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2]; |
349 | + | |
350 | + | //calculate the max cutoff |
351 | + | maxCutoff = calcMaxCutOff(); |
352 | + | |
353 | + | checkCutOffs(); |
354 | + | |
355 | + | } |
356 | + | |
357 | + | |
358 | + | double SimInfo::calcMaxCutOff(){ |
359 | + | |
360 | + | double ri[3], rj[3], rk[3]; |
361 | + | double rij[3], rjk[3], rki[3]; |
362 | + | double minDist; |
363 | + | |
364 | + | ri[0] = Hmat[0][0]; |
365 | + | ri[1] = Hmat[1][0]; |
366 | + | ri[2] = Hmat[2][0]; |
367 | + | |
368 | + | rj[0] = Hmat[0][1]; |
369 | + | rj[1] = Hmat[1][1]; |
370 | + | rj[2] = Hmat[2][1]; |
371 | + | |
372 | + | rk[0] = Hmat[0][2]; |
373 | + | rk[1] = Hmat[1][2]; |
374 | + | rk[2] = Hmat[2][2]; |
375 | + | |
376 | + | crossProduct3(ri,rj, rij); |
377 | + | distXY = dotProduct3(rk,rij) / length3(rij); |
378 | + | |
379 | + | crossProduct3(rj,rk, rjk); |
380 | + | distYZ = dotProduct3(ri,rjk) / length3(rjk); |
381 | + | |
382 | + | crossProduct3(rk,ri, rki); |
383 | + | distZX = dotProduct3(rj,rki) / length3(rki); |
384 | + | |
385 | + | minDist = min(min(distXY, distYZ), distZX); |
386 | + | return minDist/2; |
387 | + | |
388 | + | } |
389 | + | |
390 | + | void SimInfo::wrapVector( double thePos[3] ){ |
391 | + | |
392 | + | int i; |
393 | + | double scaled[3]; |
394 | + | |
395 | + | if( !orthoRhombic ){ |
396 | + | // calc the scaled coordinates. |
397 | + | |
398 | + | |
399 | + | matVecMul3(HmatInv, thePos, scaled); |
400 | + | |
401 | + | for(i=0; i<3; i++) |
402 | + | scaled[i] -= roundMe(scaled[i]); |
403 | + | |
404 | + | // calc the wrapped real coordinates from the wrapped scaled coordinates |
405 | + | |
406 | + | matVecMul3(Hmat, scaled, thePos); |
407 | + | |
408 | + | } |
409 | + | else{ |
410 | + | // calc the scaled coordinates. |
411 | + | |
412 | + | for(i=0; i<3; i++) |
413 | + | scaled[i] = thePos[i]*HmatInv[i][i]; |
414 | + | |
415 | + | // wrap the scaled coordinates |
416 | + | |
417 | + | for(i=0; i<3; i++) |
418 | + | scaled[i] -= roundMe(scaled[i]); |
419 | + | |
420 | + | // calc the wrapped real coordinates from the wrapped scaled coordinates |
421 | + | |
422 | + | for(i=0; i<3; i++) |
423 | + | thePos[i] = scaled[i]*Hmat[i][i]; |
424 | + | } |
425 | + | |
426 | + | } |
427 | + | |
428 | + | |
429 | + | int SimInfo::getNDF(){ |
430 | + | int ndf_local; |
431 | + | |
432 | + | ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints; |
433 | + | |
434 | + | #ifdef IS_MPI |
435 | + | MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
436 | + | #else |
437 | + | ndf = ndf_local; |
438 | + | #endif |
439 | + | |
440 | + | ndf = ndf - 3 - nZconstraints; |
441 | + | |
442 | + | return ndf; |
443 | + | } |
444 | + | |
445 | + | int SimInfo::getNDFraw() { |
446 | + | int ndfRaw_local; |
447 | + | |
448 | + | // Raw degrees of freedom that we have to set |
449 | + | ndfRaw_local = 3 * n_atoms + 3 * n_oriented; |
450 | + | |
451 | + | #ifdef IS_MPI |
452 | + | MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
453 | + | #else |
454 | + | ndfRaw = ndfRaw_local; |
455 | + | #endif |
456 | + | |
457 | + | return ndfRaw; |
458 | + | } |
459 | + | |
460 | + | int SimInfo::getNDFtranslational() { |
461 | + | int ndfTrans_local; |
462 | + | |
463 | + | ndfTrans_local = 3 * n_atoms - n_constraints; |
464 | + | |
465 | + | #ifdef IS_MPI |
466 | + | MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
467 | + | #else |
468 | + | ndfTrans = ndfTrans_local; |
469 | + | #endif |
470 | + | |
471 | + | ndfTrans = ndfTrans - 3 - nZconstraints; |
472 | + | |
473 | + | return ndfTrans; |
474 | + | } |
475 | + | |
476 | void SimInfo::refreshSim(){ | |
477 | ||
478 | simtype fInfo; | |
479 | int isError; | |
480 | + | int n_global; |
481 | int* excl; | |
482 | ||
483 | < | fInfo.box[0] = box_x; |
55 | < | fInfo.box[1] = box_y; |
56 | < | fInfo.box[2] = box_z; |
483 | > | fInfo.dielect = 0.0; |
484 | ||
485 | < | fInfo.rlist = rList; |
486 | < | fInfo.rcut = rCut; |
487 | < | fInfo.rrf = ecr; |
61 | < | fInfo.rt = ecr - est; |
62 | < | fInfo.dielect = dielectric; |
485 | > | if( useDipole ){ |
486 | > | if( useReactionField )fInfo.dielect = dielectric; |
487 | > | } |
488 | ||
489 | fInfo.SIM_uses_PBC = usePBC; | |
490 | //fInfo.SIM_uses_LJ = 0; | |
# | Line 75 | Line 500 | void SimInfo::refreshSim(){ | |
500 | ||
501 | excl = Exclude::getArray(); | |
502 | ||
503 | + | #ifdef IS_MPI |
504 | + | n_global = mpiSim->getTotAtoms(); |
505 | + | #else |
506 | + | n_global = n_atoms; |
507 | + | #endif |
508 | + | |
509 | isError = 0; | |
510 | ||
511 | < | // fInfo; |
512 | < | // n_atoms; |
513 | < | // identArray; |
83 | < | // n_exclude; |
84 | < | // excludes; |
85 | < | // nGlobalExcludes; |
86 | < | // globalExcludes; |
87 | < | // isError; |
511 | > | setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl, |
512 | > | &nGlobalExcludes, globalExcludes, molMembershipArray, |
513 | > | &isError ); |
514 | ||
89 | – | setFsimulation( &fInfo, &n_atoms, identArray, &n_exclude, excl, |
90 | – | &nGlobalExcludes, globalExcludes, &isError ); |
91 | – | |
515 | if( isError ){ | |
516 | ||
517 | sprintf( painCave.errMsg, | |
# | Line 102 | Line 525 | void SimInfo::refreshSim(){ | |
525 | "succesfully sent the simulation information to fortran.\n"); | |
526 | MPIcheckPoint(); | |
527 | #endif // is_mpi | |
528 | + | |
529 | + | this->ndf = this->getNDF(); |
530 | + | this->ndfRaw = this->getNDFraw(); |
531 | + | this->ndfTrans = this->getNDFtranslational(); |
532 | } | |
533 | ||
534 | + | |
535 | + | void SimInfo::setRcut( double theRcut ){ |
536 | + | |
537 | + | rCut = theRcut; |
538 | + | checkCutOffs(); |
539 | + | } |
540 | + | |
541 | + | void SimInfo::setDefaultRcut( double theRcut ){ |
542 | + | |
543 | + | haveOrigRcut = 1; |
544 | + | origRcut = theRcut; |
545 | + | rCut = theRcut; |
546 | + | |
547 | + | ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0; |
548 | + | |
549 | + | notifyFortranCutOffs( &rCut, &rList, &ecr, &est ); |
550 | + | } |
551 | + | |
552 | + | void SimInfo::setEcr( double theEcr ){ |
553 | + | |
554 | + | ecr = theEcr; |
555 | + | checkCutOffs(); |
556 | + | } |
557 | + | |
558 | + | void SimInfo::setDefaultEcr( double theEcr ){ |
559 | + | |
560 | + | haveOrigEcr = 1; |
561 | + | origEcr = theEcr; |
562 | + | |
563 | + | ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0; |
564 | + | |
565 | + | ecr = theEcr; |
566 | + | |
567 | + | notifyFortranCutOffs( &rCut, &rList, &ecr, &est ); |
568 | + | } |
569 | + | |
570 | + | void SimInfo::setEcr( double theEcr, double theEst ){ |
571 | + | |
572 | + | est = theEst; |
573 | + | setEcr( theEcr ); |
574 | + | } |
575 | + | |
576 | + | void SimInfo::setDefaultEcr( double theEcr, double theEst ){ |
577 | + | |
578 | + | est = theEst; |
579 | + | setDefaultEcr( theEcr ); |
580 | + | } |
581 | + | |
582 | + | |
583 | + | void SimInfo::checkCutOffs( void ){ |
584 | + | |
585 | + | int cutChanged = 0; |
586 | + | |
587 | + | if( boxIsInit ){ |
588 | + | |
589 | + | //we need to check cutOffs against the box |
590 | + | |
591 | + | //detect the change of rCut |
592 | + | if(( maxCutoff > rCut )&&(usePBC)){ |
593 | + | if( rCut < origRcut ){ |
594 | + | rCut = origRcut; |
595 | + | |
596 | + | if (rCut > maxCutoff) |
597 | + | rCut = maxCutoff; |
598 | + | |
599 | + | sprintf( painCave.errMsg, |
600 | + | "New Box size is setting the long range cutoff radius " |
601 | + | "to %lf at time %lf\n", |
602 | + | rCut, currentTime ); |
603 | + | painCave.isFatal = 0; |
604 | + | simError(); |
605 | + | } |
606 | + | } |
607 | + | else if ((rCut > maxCutoff)&&(usePBC)) { |
608 | + | sprintf( painCave.errMsg, |
609 | + | "New Box size is setting the long range cutoff radius " |
610 | + | "to %lf at time %lf\n", |
611 | + | maxCutoff, currentTime ); |
612 | + | painCave.isFatal = 0; |
613 | + | simError(); |
614 | + | rCut = maxCutoff; |
615 | + | } |
616 | + | |
617 | + | |
618 | + | //detect the change of ecr |
619 | + | if( maxCutoff > ecr ){ |
620 | + | if( ecr < origEcr ){ |
621 | + | ecr = origEcr; |
622 | + | if (ecr > maxCutoff) ecr = maxCutoff; |
623 | + | |
624 | + | sprintf( painCave.errMsg, |
625 | + | "New Box size is setting the electrostaticCutoffRadius " |
626 | + | "to %lf at time %lf\n", |
627 | + | ecr, currentTime ); |
628 | + | painCave.isFatal = 0; |
629 | + | simError(); |
630 | + | } |
631 | + | } |
632 | + | else if( ecr > maxCutoff){ |
633 | + | sprintf( painCave.errMsg, |
634 | + | "New Box size is setting the electrostaticCutoffRadius " |
635 | + | "to %lf at time %lf\n", |
636 | + | maxCutoff, currentTime ); |
637 | + | painCave.isFatal = 0; |
638 | + | simError(); |
639 | + | ecr = maxCutoff; |
640 | + | } |
641 | + | |
642 | + | if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1; |
643 | + | |
644 | + | // rlist is the 1.0 plus max( rcut, ecr ) |
645 | + | |
646 | + | ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0; |
647 | + | |
648 | + | if( cutChanged ){ |
649 | + | notifyFortranCutOffs( &rCut, &rList, &ecr, &est ); |
650 | + | } |
651 | + | |
652 | + | oldEcr = ecr; |
653 | + | oldRcut = rCut; |
654 | + | |
655 | + | } else { |
656 | + | // initialize this stuff before using it, OK? |
657 | + | sprintf( painCave.errMsg, |
658 | + | "Trying to check cutoffs without a box. Be smarter.\n" ); |
659 | + | painCave.isFatal = 1; |
660 | + | simError(); |
661 | + | } |
662 | + | |
663 | + | } |
664 | + | |
665 | + | void SimInfo::addProperty(GenericData* prop){ |
666 | + | |
667 | + | map<string, GenericData*>::iterator result; |
668 | + | result = properties.find(prop->getID()); |
669 | + | |
670 | + | //we can't simply use properties[prop->getID()] = prop, |
671 | + | //it will cause memory leak if we already contain a propery which has the same name of prop |
672 | + | |
673 | + | if(result != properties.end()){ |
674 | + | |
675 | + | delete (*result).second; |
676 | + | (*result).second = prop; |
677 | + | |
678 | + | } |
679 | + | else{ |
680 | + | |
681 | + | properties[prop->getID()] = prop; |
682 | + | |
683 | + | } |
684 | + | |
685 | + | } |
686 | + | |
687 | + | GenericData* SimInfo::getProperty(const string& propName){ |
688 | + | |
689 | + | map<string, GenericData*>::iterator result; |
690 | + | |
691 | + | //string lowerCaseName = (); |
692 | + | |
693 | + | result = properties.find(propName); |
694 | + | |
695 | + | if(result != properties.end()) |
696 | + | return (*result).second; |
697 | + | else |
698 | + | return NULL; |
699 | + | } |
700 | + | |
701 | + | vector<GenericData*> SimInfo::getProperties(){ |
702 | + | |
703 | + | vector<GenericData*> result; |
704 | + | map<string, GenericData*>::iterator i; |
705 | + | |
706 | + | for(i = properties.begin(); i != properties.end(); i++) |
707 | + | result.push_back((*i).second); |
708 | + | |
709 | + | return result; |
710 | + | } |
711 | + | |
712 | + | double SimInfo::matTrace3(double m[3][3]){ |
713 | + | double trace; |
714 | + | trace = m[0][0] + m[1][1] + m[2][2]; |
715 | + | |
716 | + | return trace; |
717 | + | } |
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