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root/group/trunk/OOPSE/libmdtools/SimInfo.cpp
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Comparing trunk/OOPSE/libmdtools/SimInfo.cpp (file contents):
Revision 469 by mmeineke, Mon Apr 7 20:06:31 2003 UTC vs.
Revision 853 by mmeineke, Thu Nov 6 19:11:38 2003 UTC

# Line 1 | Line 1
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 31 | 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];
41 <  box_y = newBox[1];
42 <  box_z = newBox[2];
43 <  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;
47 <  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) {
52 <    sprintf( painCave.errMsg,
53 <             "New Box size is forcing neighborlist radius down to %lf\n",
54 <             maxCutoff );
55 <    painCave.isFatal = 0;
56 <    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;
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 <    rCut = rList - 1.0;
105 >  
106 >  if( !boxIsInit ) boxIsInit = 1;
107  
108 <    // list radius changed so we have to refresh the simulation structure.
109 <    refreshSim();
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 <  if (rCut > maxCutoff) {
122 <    sprintf( painCave.errMsg,
123 <             "New Box size is forcing cutoff radius down to %lf\n",
124 <             maxCutoff );
76 <    painCave.isFatal = 0;
77 <    simError();
121 >  setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic);
122 >
123 > }
124 >
125  
126 <    status = 0;
127 <    LJ_new_rcut(&rCut, &status);
128 <    if (status != 0) {
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 <               "Error in recomputing LJ shifts based on new rcut\n");
183 <      painCave.isFatal = 1;
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 < void SimInfo::getBox(double theBox[3]) {
196 <  theBox[0] = box_x;
197 <  theBox[1] = box_y;
198 <  theBox[2] = box_z;
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 <
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, ndf;
426 >  int ndf_local;
427    
428    ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints;
429  
# Line 104 | Line 433 | int SimInfo::getNDF(){
433    ndf = ndf_local;
434   #endif
435  
436 <  ndf = ndf - 3;
436 >  ndf = ndf - 3 - nZconstraints;
437  
438    return ndf;
439   }
440  
441   int SimInfo::getNDFraw() {
442 <  int ndfRaw_local, ndfRaw;
442 >  int ndfRaw_local;
443  
444    // Raw degrees of freedom that we have to set
445    ndfRaw_local = 3 * n_atoms + 3 * n_oriented;
# Line 123 | Line 452 | int SimInfo::getNDFraw() {
452  
453    return ndfRaw;
454   }
455 <
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 <  
133 <  fInfo.rrf = 0.0;
134 <  fInfo.rt = 0.0;
478 >
479    fInfo.dielect = 0.0;
480  
137 –  fInfo.box[0] = box_x;
138 –  fInfo.box[1] = box_y;
139 –  fInfo.box[2] = box_z;
140 –
141 –  fInfo.rlist = rList;
142 –  fInfo.rcut = rCut;
143 –
481    if( useDipole ){
145 –    fInfo.rrf = ecr;
146 –    fInfo.rt = ecr - est;
482      if( useReactionField )fInfo.dielect = dielectric;
483    }
484  
# Line 152 | Line 487 | void SimInfo::refreshSim(){
487    fInfo.SIM_uses_LJ = useLJ;
488    fInfo.SIM_uses_sticky = useSticky;
489    //fInfo.SIM_uses_sticky = 0;
490 <  //fInfo.SIM_uses_dipoles = useDipole;
491 <  fInfo.SIM_uses_dipoles = 0;
490 >  fInfo.SIM_uses_dipoles = useDipole;
491 >  //fInfo.SIM_uses_dipoles = 0;
492    //fInfo.SIM_uses_RF = useReactionField;
493    fInfo.SIM_uses_RF = 0;
494    fInfo.SIM_uses_GB = useGB;
# Line 161 | 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;
169 < //   n_exclude;
170 < //   excludes;
171 < //   nGlobalExcludes;
172 < //   globalExcludes;
173 < //   isError;
507 >  setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl,
508 >                  &nGlobalExcludes, globalExcludes, molMembershipArray,
509 >                  &isError );
510  
175 –  setFsimulation( &fInfo, &n_atoms, identArray, &n_exclude, excl,
176 –                  &nGlobalExcludes, globalExcludes, &isError );
177 –
511    if( isError ){
512  
513      sprintf( painCave.errMsg,
# Line 189 | Line 522 | void SimInfo::refreshSim(){
522    MPIcheckPoint();
523   #endif // is_mpi
524  
525 <  ndf = this->getNDF();
526 <  ndfRaw = this->getNDFraw();
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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