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root/group/trunk/OOPSE/libmdtools/SimInfo.cpp
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Comparing trunk/OOPSE/libmdtools/SimInfo.cpp (file contents):
Revision 463 by gezelter, Sat Apr 5 03:39:25 2003 UTC vs.
Revision 1031 by tim, Fri Feb 6 18:58:06 2004 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 | SimInfo* currentInfo;
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 + inline double min( double a, double b ){
24 +  return (a < b ) ? a : b;
25 + }
26 +
27   SimInfo* currentInfo;
28  
29   SimInfo::SimInfo(){
30    excludes = NULL;
31    n_constraints = 0;
32 +  nZconstraints = 0;
33    n_oriented = 0;
34    n_dipoles = 0;
35    ndf = 0;
36    ndfRaw = 0;
37 +  nZconstraints = 0;
38    the_integrator = NULL;
39    setTemp = 0;
40    thermalTime = 0.0;
41 +  currentTime = 0.0;
42    rCut = 0.0;
43 +  ecr = 0.0;
44 +  est = 0.0;
45  
46 +  haveRcut = 0;
47 +  haveEcr = 0;
48 +  boxIsInit = 0;
49 +  
50 +  resetTime = 1e99;
51 +
52 +  orthoTolerance = 1E-6;
53 +  useInitXSstate = true;
54 +
55    usePBC = 0;
56    useLJ = 0;
57    useSticky = 0;
58 <  useDipole = 0;
58 >  useCharges = 0;
59 >  useDipoles = 0;
60    useReactionField = 0;
61    useGB = 0;
62    useEAM = 0;
63  
64 +  myConfiguration = new SimState();
65 +
66 +  has_minimizer = false;
67 +  the_minimizer =NULL;
68 +
69    wrapMeSimInfo( this );
70   }
71  
72 +
73 + SimInfo::~SimInfo(){
74 +
75 +  delete myConfiguration;
76 +
77 +  map<string, GenericData*>::iterator i;
78 +  
79 +  for(i = properties.begin(); i != properties.end(); i++)
80 +    delete (*i).second;
81 +    
82 + }
83 +
84   void SimInfo::setBox(double newBox[3]) {
85 <  double smallestBox, maxCutoff;
86 <  int status;
87 <  box_x = newBox[0];
41 <  box_y = newBox[1];
42 <  box_z = newBox[2];
43 <  setFortranBoxSize(newBox);
85 >  
86 >  int i, j;
87 >  double tempMat[3][3];
88  
89 <  smallestBox = box_x;
90 <  if (box_y < smallestBox) smallestBox = box_y;
47 <  if (box_z < smallestBox) smallestBox = box_z;
89 >  for(i=0; i<3; i++)
90 >    for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
91  
92 <  maxCutoff = smallestBox / 2.0;
92 >  tempMat[0][0] = newBox[0];
93 >  tempMat[1][1] = newBox[1];
94 >  tempMat[2][2] = newBox[2];
95  
96 <  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();
96 >  setBoxM( tempMat );
97  
98 <    rList = maxCutoff;
98 > }
99  
100 <    sprintf( painCave.errMsg,
101 <             "New Box size is forcing cutoff radius down to %lf\n",
102 <             maxCutoff - 1.0 );
103 <    painCave.isFatal = 0;
104 <    simError();
100 > void SimInfo::setBoxM( double theBox[3][3] ){
101 >  
102 >  int i, j;
103 >  double FortranHmat[9]; // to preserve compatibility with Fortran the
104 >                         // ordering in the array is as follows:
105 >                         // [ 0 3 6 ]
106 >                         // [ 1 4 7 ]
107 >                         // [ 2 5 8 ]
108 >  double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
109  
110 <    rCut = rList - 1.0;
110 >  if( !boxIsInit ) boxIsInit = 1;
111  
112 <    // list radius changed so we have to refresh the simulation structure.
113 <    refreshSim();
112 >  for(i=0; i < 3; i++)
113 >    for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
114 >  
115 >  calcBoxL();
116 >  calcHmatInv();
117 >
118 >  for(i=0; i < 3; i++) {
119 >    for (j=0; j < 3; j++) {
120 >      FortranHmat[3*j + i] = Hmat[i][j];
121 >      FortranHmatInv[3*j + i] = HmatInv[i][j];
122 >    }
123    }
124  
125 <  if (rCut > maxCutoff) {
126 <    sprintf( painCave.errMsg,
127 <             "New Box size is forcing cutoff radius down to %lf\n",
128 <             maxCutoff );
76 <    painCave.isFatal = 0;
77 <    simError();
125 >  setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic);
126 >
127 > }
128 >
129  
130 <    status = 0;
131 <    LJ_new_rcut(&rCut, &status);
132 <    if (status != 0) {
130 > void SimInfo::getBoxM (double theBox[3][3]) {
131 >
132 >  int i, j;
133 >  for(i=0; i<3; i++)
134 >    for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j];
135 > }
136 >
137 >
138 > void SimInfo::scaleBox(double scale) {
139 >  double theBox[3][3];
140 >  int i, j;
141 >
142 >  // cerr << "Scaling box by " << scale << "\n";
143 >
144 >  for(i=0; i<3; i++)
145 >    for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
146 >
147 >  setBoxM(theBox);
148 >
149 > }
150 >
151 > void SimInfo::calcHmatInv( void ) {
152 >  
153 >  int oldOrtho;
154 >  int i,j;
155 >  double smallDiag;
156 >  double tol;
157 >  double sanity[3][3];
158 >
159 >  invertMat3( Hmat, HmatInv );
160 >
161 >  // check to see if Hmat is orthorhombic
162 >  
163 >  oldOrtho = orthoRhombic;
164 >
165 >  smallDiag = fabs(Hmat[0][0]);
166 >  if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]);
167 >  if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]);
168 >  tol = smallDiag * orthoTolerance;
169 >
170 >  orthoRhombic = 1;
171 >  
172 >  for (i = 0; i < 3; i++ ) {
173 >    for (j = 0 ; j < 3; j++) {
174 >      if (i != j) {
175 >        if (orthoRhombic) {
176 >          if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0;
177 >        }        
178 >      }
179 >    }
180 >  }
181 >
182 >  if( oldOrtho != orthoRhombic ){
183 >    
184 >    if( orthoRhombic ){
185        sprintf( painCave.errMsg,
186 <               "Error in recomputing LJ shifts based on new rcut\n");
187 <      painCave.isFatal = 1;
186 >               "Hmat is switching from Non-Orthorhombic to Orthorhombic Box.\n"
187 >               "\tIf this is a bad thing, change the orthoBoxTolerance\n"
188 >               "\tvariable ( currently set to %G ).\n",
189 >               orthoTolerance);
190        simError();
191      }
192 +    else {
193 +      sprintf( painCave.errMsg,
194 +               "Hmat is switching from Orthorhombic to Non-Orthorhombic Box.\n"
195 +               "\tIf this is a bad thing, change the orthoBoxTolerance\n"
196 +               "\tvariable ( currently set to %G ).\n",
197 +               orthoTolerance);
198 +      simError();
199 +    }
200    }
201   }
202  
203 < void SimInfo::getBox(double theBox[3]) {
204 <  theBox[0] = box_x;
205 <  theBox[1] = box_y;
206 <  theBox[2] = box_z;
203 > double SimInfo::matDet3(double a[3][3]) {
204 >  int i, j, k;
205 >  double determinant;
206 >
207 >  determinant = 0.0;
208 >
209 >  for(i = 0; i < 3; i++) {
210 >    j = (i+1)%3;
211 >    k = (i+2)%3;
212 >
213 >    determinant += a[0][i] * (a[1][j]*a[2][k] - a[1][k]*a[2][j]);
214 >  }
215 >
216 >  return determinant;
217   }
218 <
218 >
219 > void SimInfo::invertMat3(double a[3][3], double b[3][3]) {
220 >  
221 >  int  i, j, k, l, m, n;
222 >  double determinant;
223 >
224 >  determinant = matDet3( a );
225 >
226 >  if (determinant == 0.0) {
227 >    sprintf( painCave.errMsg,
228 >             "Can't invert a matrix with a zero determinant!\n");
229 >    painCave.isFatal = 1;
230 >    simError();
231 >  }
232 >
233 >  for (i=0; i < 3; i++) {
234 >    j = (i+1)%3;
235 >    k = (i+2)%3;
236 >    for(l = 0; l < 3; l++) {
237 >      m = (l+1)%3;
238 >      n = (l+2)%3;
239 >      
240 >      b[l][i] = (a[j][m]*a[k][n] - a[j][n]*a[k][m]) / determinant;
241 >    }
242 >  }
243 > }
244 >
245 > void SimInfo::matMul3(double a[3][3], double b[3][3], double c[3][3]) {
246 >  double r00, r01, r02, r10, r11, r12, r20, r21, r22;
247 >
248 >  r00 = a[0][0]*b[0][0] + a[0][1]*b[1][0] + a[0][2]*b[2][0];
249 >  r01 = a[0][0]*b[0][1] + a[0][1]*b[1][1] + a[0][2]*b[2][1];
250 >  r02 = a[0][0]*b[0][2] + a[0][1]*b[1][2] + a[0][2]*b[2][2];
251 >  
252 >  r10 = a[1][0]*b[0][0] + a[1][1]*b[1][0] + a[1][2]*b[2][0];
253 >  r11 = a[1][0]*b[0][1] + a[1][1]*b[1][1] + a[1][2]*b[2][1];
254 >  r12 = a[1][0]*b[0][2] + a[1][1]*b[1][2] + a[1][2]*b[2][2];
255 >  
256 >  r20 = a[2][0]*b[0][0] + a[2][1]*b[1][0] + a[2][2]*b[2][0];
257 >  r21 = a[2][0]*b[0][1] + a[2][1]*b[1][1] + a[2][2]*b[2][1];
258 >  r22 = a[2][0]*b[0][2] + a[2][1]*b[1][2] + a[2][2]*b[2][2];
259 >  
260 >  c[0][0] = r00; c[0][1] = r01; c[0][2] = r02;
261 >  c[1][0] = r10; c[1][1] = r11; c[1][2] = r12;
262 >  c[2][0] = r20; c[2][1] = r21; c[2][2] = r22;
263 > }
264 >
265 > void SimInfo::matVecMul3(double m[3][3], double inVec[3], double outVec[3]) {
266 >  double a0, a1, a2;
267 >
268 >  a0 = inVec[0];  a1 = inVec[1];  a2 = inVec[2];
269 >
270 >  outVec[0] = m[0][0]*a0 + m[0][1]*a1 + m[0][2]*a2;
271 >  outVec[1] = m[1][0]*a0 + m[1][1]*a1 + m[1][2]*a2;
272 >  outVec[2] = m[2][0]*a0 + m[2][1]*a1 + m[2][2]*a2;
273 > }
274 >
275 > void SimInfo::transposeMat3(double in[3][3], double out[3][3]) {
276 >  double temp[3][3];
277 >  int i, j;
278 >
279 >  for (i = 0; i < 3; i++) {
280 >    for (j = 0; j < 3; j++) {
281 >      temp[j][i] = in[i][j];
282 >    }
283 >  }
284 >  for (i = 0; i < 3; i++) {
285 >    for (j = 0; j < 3; j++) {
286 >      out[i][j] = temp[i][j];
287 >    }
288 >  }
289 > }
290 >  
291 > void SimInfo::printMat3(double A[3][3] ){
292 >
293 >  std::cerr
294 >            << "[ " << A[0][0] << ", " << A[0][1] << ", " << A[0][2] << " ]\n"
295 >            << "[ " << A[1][0] << ", " << A[1][1] << ", " << A[1][2] << " ]\n"
296 >            << "[ " << A[2][0] << ", " << A[2][1] << ", " << A[2][2] << " ]\n";
297 > }
298 >
299 > void SimInfo::printMat9(double A[9] ){
300 >
301 >  std::cerr
302 >            << "[ " << A[0] << ", " << A[1] << ", " << A[2] << " ]\n"
303 >            << "[ " << A[3] << ", " << A[4] << ", " << A[5] << " ]\n"
304 >            << "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n";
305 > }
306 >
307 >
308 > void SimInfo::crossProduct3(double a[3],double b[3], double out[3]){
309 >
310 >      out[0] = a[1] * b[2] - a[2] * b[1];
311 >      out[1] = a[2] * b[0] - a[0] * b[2] ;
312 >      out[2] = a[0] * b[1] - a[1] * b[0];
313 >      
314 > }
315 >
316 > double SimInfo::dotProduct3(double a[3], double b[3]){
317 >  return a[0]*b[0] + a[1]*b[1]+ a[2]*b[2];
318 > }
319 >
320 > double SimInfo::length3(double a[3]){
321 >  return sqrt(a[0]*a[0] + a[1]*a[1] + a[2]*a[2]);
322 > }
323 >
324 > void SimInfo::calcBoxL( void ){
325 >
326 >  double dx, dy, dz, dsq;
327 >
328 >  // boxVol = Determinant of Hmat
329 >
330 >  boxVol = matDet3( Hmat );
331 >
332 >  // boxLx
333 >  
334 >  dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
335 >  dsq = dx*dx + dy*dy + dz*dz;
336 >  boxL[0] = sqrt( dsq );
337 >  //maxCutoff = 0.5 * boxL[0];
338 >
339 >  // boxLy
340 >  
341 >  dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
342 >  dsq = dx*dx + dy*dy + dz*dz;
343 >  boxL[1] = sqrt( dsq );
344 >  //if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
345 >
346 >
347 >  // boxLz
348 >  
349 >  dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
350 >  dsq = dx*dx + dy*dy + dz*dz;
351 >  boxL[2] = sqrt( dsq );
352 >  //if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
353 >
354 >  //calculate the max cutoff
355 >  maxCutoff =  calcMaxCutOff();
356 >  
357 >  checkCutOffs();
358 >
359 > }
360 >
361 >
362 > double SimInfo::calcMaxCutOff(){
363 >
364 >  double ri[3], rj[3], rk[3];
365 >  double rij[3], rjk[3], rki[3];
366 >  double minDist;
367 >
368 >  ri[0] = Hmat[0][0];
369 >  ri[1] = Hmat[1][0];
370 >  ri[2] = Hmat[2][0];
371 >
372 >  rj[0] = Hmat[0][1];
373 >  rj[1] = Hmat[1][1];
374 >  rj[2] = Hmat[2][1];
375 >
376 >  rk[0] = Hmat[0][2];
377 >  rk[1] = Hmat[1][2];
378 >  rk[2] = Hmat[2][2];
379 >  
380 >  crossProduct3(ri,rj, rij);
381 >  distXY = dotProduct3(rk,rij) / length3(rij);
382 >
383 >  crossProduct3(rj,rk, rjk);
384 >  distYZ = dotProduct3(ri,rjk) / length3(rjk);
385 >
386 >  crossProduct3(rk,ri, rki);
387 >  distZX = dotProduct3(rj,rki) / length3(rki);
388 >
389 >  minDist = min(min(distXY, distYZ), distZX);
390 >  return minDist/2;
391 >  
392 > }
393 >
394 > void SimInfo::wrapVector( double thePos[3] ){
395 >
396 >  int i;
397 >  double scaled[3];
398 >
399 >  if( !orthoRhombic ){
400 >    // calc the scaled coordinates.
401 >  
402 >
403 >    matVecMul3(HmatInv, thePos, scaled);
404 >    
405 >    for(i=0; i<3; i++)
406 >      scaled[i] -= roundMe(scaled[i]);
407 >    
408 >    // calc the wrapped real coordinates from the wrapped scaled coordinates
409 >    
410 >    matVecMul3(Hmat, scaled, thePos);
411 >
412 >  }
413 >  else{
414 >    // calc the scaled coordinates.
415 >    
416 >    for(i=0; i<3; i++)
417 >      scaled[i] = thePos[i]*HmatInv[i][i];
418 >    
419 >    // wrap the scaled coordinates
420 >    
421 >    for(i=0; i<3; i++)
422 >      scaled[i] -= roundMe(scaled[i]);
423 >    
424 >    // calc the wrapped real coordinates from the wrapped scaled coordinates
425 >    
426 >    for(i=0; i<3; i++)
427 >      thePos[i] = scaled[i]*Hmat[i][i];
428 >  }
429 >    
430 > }
431 >
432 >
433   int SimInfo::getNDF(){
434 <  int ndf_local, ndf;
434 >  int ndf_local;
435    
436    ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints;
437  
# Line 104 | Line 441 | int SimInfo::getNDF(){
441    ndf = ndf_local;
442   #endif
443  
444 <  ndf = ndf - 3;
444 >  ndf = ndf - 3 - nZconstraints;
445  
446    return ndf;
447   }
448  
449   int SimInfo::getNDFraw() {
450 <  int ndfRaw_local, ndfRaw;
450 >  int ndfRaw_local;
451  
452    // Raw degrees of freedom that we have to set
453    ndfRaw_local = 3 * n_atoms + 3 * n_oriented;
# Line 123 | Line 460 | int SimInfo::getNDFraw() {
460  
461    return ndfRaw;
462   }
463 <
463 >
464 > int SimInfo::getNDFtranslational() {
465 >  int ndfTrans_local;
466 >
467 >  ndfTrans_local = 3 * n_atoms - n_constraints;
468 >
469 > #ifdef IS_MPI
470 >  MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
471 > #else
472 >  ndfTrans = ndfTrans_local;
473 > #endif
474 >
475 >  ndfTrans = ndfTrans - 3 - nZconstraints;
476 >
477 >  return ndfTrans;
478 > }
479 >
480   void SimInfo::refreshSim(){
481  
482    simtype fInfo;
483    int isError;
484 +  int n_global;
485    int* excl;
486  
487 <  fInfo.box[0] = box_x;
134 <  fInfo.box[1] = box_y;
135 <  fInfo.box[2] = box_z;
487 >  fInfo.dielect = 0.0;
488  
489 <  fInfo.rlist = rList;
490 <  fInfo.rcut = rCut;
491 <  fInfo.rrf = ecr;
140 <  fInfo.rt = ecr - est;
141 <  fInfo.dielect = dielectric;
489 >  if( useDipoles ){
490 >    if( useReactionField )fInfo.dielect = dielectric;
491 >  }
492  
493    fInfo.SIM_uses_PBC = usePBC;
494    //fInfo.SIM_uses_LJ = 0;
495    fInfo.SIM_uses_LJ = useLJ;
496    fInfo.SIM_uses_sticky = useSticky;
497    //fInfo.SIM_uses_sticky = 0;
498 <  fInfo.SIM_uses_dipoles = useDipole;
498 >  fInfo.SIM_uses_charges = useCharges;
499 >  fInfo.SIM_uses_dipoles = useDipoles;
500    //fInfo.SIM_uses_dipoles = 0;
501 <  //fInfo.SIM_uses_RF = useReactionField;
502 <  fInfo.SIM_uses_RF = 0;
501 >  fInfo.SIM_uses_RF = useReactionField;
502 >  //fInfo.SIM_uses_RF = 0;
503    fInfo.SIM_uses_GB = useGB;
504    fInfo.SIM_uses_EAM = useEAM;
505  
506    excl = Exclude::getArray();
507  
508 + #ifdef IS_MPI
509 +  n_global = mpiSim->getTotAtoms();
510 + #else
511 +  n_global = n_atoms;
512 + #endif
513 +
514    isError = 0;
515  
516 < //   fInfo;
517 < //   n_atoms;
518 < //   identArray;
162 < //   n_exclude;
163 < //   excludes;
164 < //   nGlobalExcludes;
165 < //   globalExcludes;
166 < //   isError;
516 >  setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl,
517 >                  &nGlobalExcludes, globalExcludes, molMembershipArray,
518 >                  &isError );
519  
168 –  setFsimulation( &fInfo, &n_atoms, identArray, &n_exclude, excl,
169 –                  &nGlobalExcludes, globalExcludes, &isError );
170 –
520    if( isError ){
521  
522      sprintf( painCave.errMsg,
# Line 182 | Line 531 | void SimInfo::refreshSim(){
531    MPIcheckPoint();
532   #endif // is_mpi
533  
534 <  ndf = this->getNDF();
535 <  ndfRaw = this->getNDFraw();
534 >  this->ndf = this->getNDF();
535 >  this->ndfRaw = this->getNDFraw();
536 >  this->ndfTrans = this->getNDFtranslational();
537 > }
538  
539 + void SimInfo::setDefaultRcut( double theRcut ){
540 +
541 +  haveRcut = 1;
542 +  rCut = theRcut;
543 +
544 +  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
545 +
546 +  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
547   }
548  
549 + void SimInfo::setDefaultEcr( double theEcr ){
550 +
551 +  haveEcr = 1;
552 +  ecr = theEcr;
553 +  
554 +  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
555 +
556 +  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
557 + }
558 +
559 + void SimInfo::setDefaultEcr( double theEcr, double theEst ){
560 +
561 +  est = theEst;
562 +  setDefaultEcr( theEcr );
563 + }
564 +
565 +
566 + void SimInfo::checkCutOffs( void ){
567 +  
568 +  if( boxIsInit ){
569 +    
570 +    //we need to check cutOffs against the box
571 +    
572 +    if( rCut > maxCutoff ){
573 +      sprintf( painCave.errMsg,
574 +               "Box size is too small for the long range cutoff radius, "
575 +               "%G, at time %G\n"
576 +               "\t[ %G %G %G ]\n"
577 +               "\t[ %G %G %G ]\n"
578 +               "\t[ %G %G %G ]\n",
579 +               rCut, currentTime,
580 +               Hmat[0][0], Hmat[0][1], Hmat[0][2],
581 +               Hmat[1][0], Hmat[1][1], Hmat[1][2],
582 +               Hmat[2][0], Hmat[2][1], Hmat[2][2]);
583 +      painCave.isFatal = 1;
584 +      simError();
585 +    }
586 +    
587 +    if( haveEcr ){
588 +      if( ecr > maxCutoff ){
589 +        sprintf( painCave.errMsg,
590 +                 "Box size is too small for the electrostatic cutoff radius, "
591 +                 "%G, at time %G\n"
592 +                 "\t[ %G %G %G ]\n"
593 +                 "\t[ %G %G %G ]\n"
594 +                 "\t[ %G %G %G ]\n",
595 +                 ecr, currentTime,
596 +                 Hmat[0][0], Hmat[0][1], Hmat[0][2],
597 +                 Hmat[1][0], Hmat[1][1], Hmat[1][2],
598 +                 Hmat[2][0], Hmat[2][1], Hmat[2][2]);
599 +        painCave.isFatal = 1;
600 +        simError();
601 +      }
602 +    }
603 +  } else {
604 +    // initialize this stuff before using it, OK?
605 +    sprintf( painCave.errMsg,
606 +             "Trying to check cutoffs without a box.\n"
607 +             "\tOOPSE should have better programmers than that.\n" );
608 +    painCave.isFatal = 1;
609 +    simError();      
610 +  }
611 +  
612 + }
613 +
614 + void SimInfo::addProperty(GenericData* prop){
615 +
616 +  map<string, GenericData*>::iterator result;
617 +  result = properties.find(prop->getID());
618 +  
619 +  //we can't simply use  properties[prop->getID()] = prop,
620 +  //it will cause memory leak if we already contain a propery which has the same name of prop
621 +  
622 +  if(result != properties.end()){
623 +    
624 +    delete (*result).second;
625 +    (*result).second = prop;
626 +      
627 +  }
628 +  else{
629 +
630 +    properties[prop->getID()] = prop;
631 +
632 +  }
633 +    
634 + }
635 +
636 + GenericData* SimInfo::getProperty(const string& propName){
637 +
638 +  map<string, GenericData*>::iterator result;
639 +  
640 +  //string lowerCaseName = ();
641 +  
642 +  result = properties.find(propName);
643 +  
644 +  if(result != properties.end())
645 +    return (*result).second;  
646 +  else  
647 +    return NULL;  
648 + }
649 +
650 + vector<GenericData*> SimInfo::getProperties(){
651 +
652 +  vector<GenericData*> result;
653 +  map<string, GenericData*>::iterator i;
654 +  
655 +  for(i = properties.begin(); i != properties.end(); i++)
656 +    result.push_back((*i).second);
657 +    
658 +  return result;
659 + }
660 +
661 + double SimInfo::matTrace3(double m[3][3]){
662 +  double trace;
663 +  trace = m[0][0] + m[1][1] + m[2][2];
664 +
665 +  return trace;
666 + }

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