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root/group/trunk/OOPSE/libmdtools/SimInfo.cpp
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Comparing trunk/OOPSE/libmdtools/SimInfo.cpp (file contents):
Revision 474 by gezelter, Mon Apr 7 21:42:19 2003 UTC vs.
Revision 941 by gezelter, Tue Jan 13 23:01:43 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    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 <  double smallestBox, maxCutoff;
83 <  int status;
84 <  box_x = newBox[0];
41 <  box_y = newBox[1];
42 <  box_z = newBox[2];
43 <  setFortranBoxSize(newBox);
82 >  
83 >  int i, j;
84 >  double tempMat[3][3];
85  
86 <  smallestBox = box_x;
87 <  if (box_y < smallestBox) smallestBox = box_y;
47 <  if (box_z < smallestBox) smallestBox = box_z;
86 >  for(i=0; i<3; i++)
87 >    for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
88  
89 <  maxCutoff = smallestBox / 2.0;
89 >  tempMat[0][0] = newBox[0];
90 >  tempMat[1][1] = newBox[1];
91 >  tempMat[2][2] = newBox[2];
92  
93 <  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();
93 >  setBoxM( tempMat );
94  
95 <    rList = maxCutoff;
95 > }
96  
97 <    sprintf( painCave.errMsg,
98 <             "New Box size is forcing cutoff radius down to %lf\n",
99 <             maxCutoff - 1.0 );
100 <    painCave.isFatal = 0;
101 <    simError();
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 <    rCut = rList - 1.0;
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) {
123 <    sprintf( painCave.errMsg,
124 <             "New Box size is forcing cutoff radius down to %lf\n",
125 <             maxCutoff );
76 <    painCave.isFatal = 0;
77 <    simError();
122 >  setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic);
123 >
124 > }
125 >
126  
127 <    status = 0;
128 <    LJ_new_rcut(&rCut, &status);
129 <    if (status != 0) {
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 oldOrtho;
151 >  int i,j;
152 >  double smallDiag;
153 >  double tol;
154 >  double sanity[3][3];
155 >
156 >  invertMat3( Hmat, HmatInv );
157 >
158 >  // check to see if Hmat is orthorhombic
159 >  
160 >  oldOrtho = orthoRhombic;
161 >
162 >  smallDiag = fabs(Hmat[0][0]);
163 >  if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]);
164 >  if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]);
165 >  tol = smallDiag * orthoTolerance;
166 >
167 >  orthoRhombic = 1;
168 >  
169 >  for (i = 0; i < 3; i++ ) {
170 >    for (j = 0 ; j < 3; j++) {
171 >      if (i != j) {
172 >        if (orthoRhombic) {
173 >          if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0;
174 >        }        
175 >      }
176 >    }
177 >  }
178 >
179 >  if( oldOrtho != orthoRhombic ){
180 >    
181 >    if( orthoRhombic ){
182        sprintf( painCave.errMsg,
183 <               "Error in recomputing LJ shifts based on new rcut\n");
184 <      painCave.isFatal = 1;
183 >               "Hmat is switching from Non-Orthorhombic to OrthoRhombic\n"
184 >               "       If this is a bad thing, change the orthoBoxTolerance( currently %G ).\n",
185 >               orthoTolerance);
186        simError();
187      }
188 +    else {
189 +      sprintf( painCave.errMsg,
190 +               "Hmat is switching from Orthorhombic to Non-OrthoRhombic\n"
191 +               "       If this is a bad thing, change the orthoBoxTolerance( currently %G ).\n",
192 +               orthoTolerance);
193 +      simError();
194 +    }
195    }
196   }
197  
198 < void SimInfo::getBox(double theBox[3]) {
199 <  theBox[0] = box_x;
200 <  theBox[1] = box_y;
201 <  theBox[2] = box_z;
198 > double SimInfo::matDet3(double a[3][3]) {
199 >  int i, j, k;
200 >  double determinant;
201 >
202 >  determinant = 0.0;
203 >
204 >  for(i = 0; i < 3; i++) {
205 >    j = (i+1)%3;
206 >    k = (i+2)%3;
207 >
208 >    determinant += a[0][i] * (a[1][j]*a[2][k] - a[1][k]*a[2][j]);
209 >  }
210 >
211 >  return determinant;
212   }
213 <
213 >
214 > void SimInfo::invertMat3(double a[3][3], double b[3][3]) {
215 >  
216 >  int  i, j, k, l, m, n;
217 >  double determinant;
218 >
219 >  determinant = matDet3( a );
220 >
221 >  if (determinant == 0.0) {
222 >    sprintf( painCave.errMsg,
223 >             "Can't invert a matrix with a zero determinant!\n");
224 >    painCave.isFatal = 1;
225 >    simError();
226 >  }
227 >
228 >  for (i=0; i < 3; i++) {
229 >    j = (i+1)%3;
230 >    k = (i+2)%3;
231 >    for(l = 0; l < 3; l++) {
232 >      m = (l+1)%3;
233 >      n = (l+2)%3;
234 >      
235 >      b[l][i] = (a[j][m]*a[k][n] - a[j][n]*a[k][m]) / determinant;
236 >    }
237 >  }
238 > }
239 >
240 > void SimInfo::matMul3(double a[3][3], double b[3][3], double c[3][3]) {
241 >  double r00, r01, r02, r10, r11, r12, r20, r21, r22;
242 >
243 >  r00 = a[0][0]*b[0][0] + a[0][1]*b[1][0] + a[0][2]*b[2][0];
244 >  r01 = a[0][0]*b[0][1] + a[0][1]*b[1][1] + a[0][2]*b[2][1];
245 >  r02 = a[0][0]*b[0][2] + a[0][1]*b[1][2] + a[0][2]*b[2][2];
246 >  
247 >  r10 = a[1][0]*b[0][0] + a[1][1]*b[1][0] + a[1][2]*b[2][0];
248 >  r11 = a[1][0]*b[0][1] + a[1][1]*b[1][1] + a[1][2]*b[2][1];
249 >  r12 = a[1][0]*b[0][2] + a[1][1]*b[1][2] + a[1][2]*b[2][2];
250 >  
251 >  r20 = a[2][0]*b[0][0] + a[2][1]*b[1][0] + a[2][2]*b[2][0];
252 >  r21 = a[2][0]*b[0][1] + a[2][1]*b[1][1] + a[2][2]*b[2][1];
253 >  r22 = a[2][0]*b[0][2] + a[2][1]*b[1][2] + a[2][2]*b[2][2];
254 >  
255 >  c[0][0] = r00; c[0][1] = r01; c[0][2] = r02;
256 >  c[1][0] = r10; c[1][1] = r11; c[1][2] = r12;
257 >  c[2][0] = r20; c[2][1] = r21; c[2][2] = r22;
258 > }
259 >
260 > void SimInfo::matVecMul3(double m[3][3], double inVec[3], double outVec[3]) {
261 >  double a0, a1, a2;
262 >
263 >  a0 = inVec[0];  a1 = inVec[1];  a2 = inVec[2];
264 >
265 >  outVec[0] = m[0][0]*a0 + m[0][1]*a1 + m[0][2]*a2;
266 >  outVec[1] = m[1][0]*a0 + m[1][1]*a1 + m[1][2]*a2;
267 >  outVec[2] = m[2][0]*a0 + m[2][1]*a1 + m[2][2]*a2;
268 > }
269 >
270 > void SimInfo::transposeMat3(double in[3][3], double out[3][3]) {
271 >  double temp[3][3];
272 >  int i, j;
273 >
274 >  for (i = 0; i < 3; i++) {
275 >    for (j = 0; j < 3; j++) {
276 >      temp[j][i] = in[i][j];
277 >    }
278 >  }
279 >  for (i = 0; i < 3; i++) {
280 >    for (j = 0; j < 3; j++) {
281 >      out[i][j] = temp[i][j];
282 >    }
283 >  }
284 > }
285 >  
286 > void SimInfo::printMat3(double A[3][3] ){
287 >
288 >  std::cerr
289 >            << "[ " << A[0][0] << ", " << A[0][1] << ", " << A[0][2] << " ]\n"
290 >            << "[ " << A[1][0] << ", " << A[1][1] << ", " << A[1][2] << " ]\n"
291 >            << "[ " << A[2][0] << ", " << A[2][1] << ", " << A[2][2] << " ]\n";
292 > }
293 >
294 > void SimInfo::printMat9(double A[9] ){
295 >
296 >  std::cerr
297 >            << "[ " << A[0] << ", " << A[1] << ", " << A[2] << " ]\n"
298 >            << "[ " << A[3] << ", " << A[4] << ", " << A[5] << " ]\n"
299 >            << "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n";
300 > }
301 >
302 >
303 > void SimInfo::crossProduct3(double a[3],double b[3], double out[3]){
304 >
305 >      out[0] = a[1] * b[2] - a[2] * b[1];
306 >      out[1] = a[2] * b[0] - a[0] * b[2] ;
307 >      out[2] = a[0] * b[1] - a[1] * b[0];
308 >      
309 > }
310 >
311 > double SimInfo::dotProduct3(double a[3], double b[3]){
312 >  return a[0]*b[0] + a[1]*b[1]+ a[2]*b[2];
313 > }
314 >
315 > double SimInfo::length3(double a[3]){
316 >  return sqrt(a[0]*a[0] + a[1]*a[1] + a[2]*a[2]);
317 > }
318 >
319 > void SimInfo::calcBoxL( void ){
320 >
321 >  double dx, dy, dz, dsq;
322 >
323 >  // boxVol = Determinant of Hmat
324 >
325 >  boxVol = matDet3( Hmat );
326 >
327 >  // boxLx
328 >  
329 >  dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
330 >  dsq = dx*dx + dy*dy + dz*dz;
331 >  boxL[0] = sqrt( dsq );
332 >  //maxCutoff = 0.5 * boxL[0];
333 >
334 >  // boxLy
335 >  
336 >  dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
337 >  dsq = dx*dx + dy*dy + dz*dz;
338 >  boxL[1] = sqrt( dsq );
339 >  //if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
340 >
341 >
342 >  // boxLz
343 >  
344 >  dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
345 >  dsq = dx*dx + dy*dy + dz*dz;
346 >  boxL[2] = sqrt( dsq );
347 >  //if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
348 >
349 >  //calculate the max cutoff
350 >  maxCutoff =  calcMaxCutOff();
351 >  
352 >  checkCutOffs();
353 >
354 > }
355 >
356 >
357 > double SimInfo::calcMaxCutOff(){
358 >
359 >  double ri[3], rj[3], rk[3];
360 >  double rij[3], rjk[3], rki[3];
361 >  double minDist;
362 >
363 >  ri[0] = Hmat[0][0];
364 >  ri[1] = Hmat[1][0];
365 >  ri[2] = Hmat[2][0];
366 >
367 >  rj[0] = Hmat[0][1];
368 >  rj[1] = Hmat[1][1];
369 >  rj[2] = Hmat[2][1];
370 >
371 >  rk[0] = Hmat[0][2];
372 >  rk[1] = Hmat[1][2];
373 >  rk[2] = Hmat[2][2];
374 >  
375 >  crossProduct3(ri,rj, rij);
376 >  distXY = dotProduct3(rk,rij) / length3(rij);
377 >
378 >  crossProduct3(rj,rk, rjk);
379 >  distYZ = dotProduct3(ri,rjk) / length3(rjk);
380 >
381 >  crossProduct3(rk,ri, rki);
382 >  distZX = dotProduct3(rj,rki) / length3(rki);
383 >
384 >  minDist = min(min(distXY, distYZ), distZX);
385 >  return minDist/2;
386 >  
387 > }
388 >
389 > void SimInfo::wrapVector( double thePos[3] ){
390 >
391 >  int i;
392 >  double scaled[3];
393 >
394 >  if( !orthoRhombic ){
395 >    // calc the scaled coordinates.
396 >  
397 >
398 >    matVecMul3(HmatInv, thePos, scaled);
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 >    matVecMul3(Hmat, scaled, thePos);
406 >
407 >  }
408 >  else{
409 >    // calc the scaled coordinates.
410 >    
411 >    for(i=0; i<3; i++)
412 >      scaled[i] = thePos[i]*HmatInv[i][i];
413 >    
414 >    // wrap the scaled coordinates
415 >    
416 >    for(i=0; i<3; i++)
417 >      scaled[i] -= roundMe(scaled[i]);
418 >    
419 >    // calc the wrapped real coordinates from the wrapped scaled coordinates
420 >    
421 >    for(i=0; i<3; i++)
422 >      thePos[i] = scaled[i]*Hmat[i][i];
423 >  }
424 >    
425 > }
426 >
427 >
428   int SimInfo::getNDF(){
429 <  int ndf_local, ndf;
429 >  int ndf_local;
430    
431    ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints;
432  
# Line 104 | Line 436 | int SimInfo::getNDF(){
436    ndf = ndf_local;
437   #endif
438  
439 <  ndf = ndf - 3;
439 >  ndf = ndf - 3 - nZconstraints;
440  
441    return ndf;
442   }
443  
444   int SimInfo::getNDFraw() {
445 <  int ndfRaw_local, ndfRaw;
445 >  int ndfRaw_local;
446  
447    // Raw degrees of freedom that we have to set
448    ndfRaw_local = 3 * n_atoms + 3 * n_oriented;
# Line 123 | Line 455 | int SimInfo::getNDFraw() {
455  
456    return ndfRaw;
457   }
458 <
458 >
459 > int SimInfo::getNDFtranslational() {
460 >  int ndfTrans_local;
461 >
462 >  ndfTrans_local = 3 * n_atoms - n_constraints;
463 >
464 > #ifdef IS_MPI
465 >  MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
466 > #else
467 >  ndfTrans = ndfTrans_local;
468 > #endif
469 >
470 >  ndfTrans = ndfTrans - 3 - nZconstraints;
471 >
472 >  return ndfTrans;
473 > }
474 >
475   void SimInfo::refreshSim(){
476  
477    simtype fInfo;
478    int isError;
479 +  int n_global;
480    int* excl;
481 <  
133 <  fInfo.rrf = 0.0;
134 <  fInfo.rt = 0.0;
481 >
482    fInfo.dielect = 0.0;
483  
484 <  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 <
144 <  if( useDipole ){
145 <    fInfo.rrf = ecr;
146 <    fInfo.rt = ecr - est;
484 >  if( useDipoles ){
485      if( useReactionField )fInfo.dielect = dielectric;
486    }
487  
# Line 152 | Line 490 | void SimInfo::refreshSim(){
490    fInfo.SIM_uses_LJ = useLJ;
491    fInfo.SIM_uses_sticky = useSticky;
492    //fInfo.SIM_uses_sticky = 0;
493 <  //fInfo.SIM_uses_dipoles = useDipole;
494 <  fInfo.SIM_uses_dipoles = 0;
493 >  fInfo.SIM_uses_charges = useCharges;
494 >  fInfo.SIM_uses_dipoles = useDipoles;
495 >  //fInfo.SIM_uses_dipoles = 0;
496    //fInfo.SIM_uses_RF = useReactionField;
497    fInfo.SIM_uses_RF = 0;
498    fInfo.SIM_uses_GB = useGB;
# Line 161 | 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;
169 < //   n_exclude;
170 < //   excludes;
171 < //   nGlobalExcludes;
172 < //   globalExcludes;
173 < //   isError;
511 >  setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl,
512 >                  &nGlobalExcludes, globalExcludes, molMembershipArray,
513 >                  &isError );
514  
175 –  setFsimulation( &fInfo, &n_atoms, identArray, &n_exclude, excl,
176 –                  &nGlobalExcludes, globalExcludes, &isError );
177 –
515    if( isError ){
516  
517      sprintf( painCave.errMsg,
# Line 191 | Line 528 | void SimInfo::refreshSim(){
528  
529    this->ndf = this->getNDF();
530    this->ndfRaw = this->getNDFraw();
531 +  this->ndfTrans = this->getNDFtranslational();
532 + }
533  
534 + void SimInfo::setDefaultRcut( double theRcut ){
535 +
536 +  haveRcut = 1;
537 +  rCut = theRcut;
538 +
539 +  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
540 +
541 +  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
542   }
543  
544 + void SimInfo::setDefaultEcr( double theEcr ){
545 +
546 +  haveEcr = 1;
547 +  ecr = theEcr;
548 +  
549 +  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
550 +
551 +  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
552 + }
553 +
554 + void SimInfo::setDefaultEcr( double theEcr, double theEst ){
555 +
556 +  est = theEst;
557 +  setDefaultEcr( theEcr );
558 + }
559 +
560 +
561 + void SimInfo::checkCutOffs( void ){
562 +  
563 +  if( boxIsInit ){
564 +    
565 +    //we need to check cutOffs against the box
566 +    
567 +    if( rCut > maxCutoff ){
568 +      sprintf( painCave.errMsg,
569 +               "Box size is too small for the long range cutoff radius, "
570 +               "%G, at time %G\n"
571 +               "  [ %G %G %G ]\n"
572 +               "  [ %G %G %G ]\n"
573 +               "  [ %G %G %G ]\n",
574 +               rCut, currentTime,
575 +               Hmat[0][0], Hmat[0][1], Hmat[0][2],
576 +               Hmat[1][0], Hmat[1][1], Hmat[1][2],
577 +               Hmat[2][0], Hmat[2][1], Hmat[2][2]);
578 +      painCave.isFatal = 1;
579 +      simError();
580 +    }
581 +    
582 +    if( haveEcr ){
583 +      if( ecr > maxCutoff ){
584 +        sprintf( painCave.errMsg,
585 +                 "Box size is too small for the electrostatic cutoff radius, "
586 +                 "%G, at time %G\n"
587 +                 "  [ %G %G %G ]\n"
588 +                 "  [ %G %G %G ]\n"
589 +                 "  [ %G %G %G ]\n",
590 +                 ecr, currentTime,
591 +                 Hmat[0][0], Hmat[0][1], Hmat[0][2],
592 +                 Hmat[1][0], Hmat[1][1], Hmat[1][2],
593 +                 Hmat[2][0], Hmat[2][1], Hmat[2][2]);
594 +        painCave.isFatal = 1;
595 +        simError();
596 +      }
597 +    }
598 +  } else {
599 +    // initialize this stuff before using it, OK?
600 +    sprintf( painCave.errMsg,
601 +             "Trying to check cutoffs without a box. Be smarter.\n" );
602 +    painCave.isFatal = 1;
603 +    simError();      
604 +  }
605 +  
606 + }
607 +
608 + void SimInfo::addProperty(GenericData* prop){
609 +
610 +  map<string, GenericData*>::iterator result;
611 +  result = properties.find(prop->getID());
612 +  
613 +  //we can't simply use  properties[prop->getID()] = prop,
614 +  //it will cause memory leak if we already contain a propery which has the same name of prop
615 +  
616 +  if(result != properties.end()){
617 +    
618 +    delete (*result).second;
619 +    (*result).second = prop;
620 +      
621 +  }
622 +  else{
623 +
624 +    properties[prop->getID()] = prop;
625 +
626 +  }
627 +    
628 + }
629 +
630 + GenericData* SimInfo::getProperty(const string& propName){
631 +
632 +  map<string, GenericData*>::iterator result;
633 +  
634 +  //string lowerCaseName = ();
635 +  
636 +  result = properties.find(propName);
637 +  
638 +  if(result != properties.end())
639 +    return (*result).second;  
640 +  else  
641 +    return NULL;  
642 + }
643 +
644 + vector<GenericData*> SimInfo::getProperties(){
645 +
646 +  vector<GenericData*> result;
647 +  map<string, GenericData*>::iterator i;
648 +  
649 +  for(i = properties.begin(); i != properties.end(); i++)
650 +    result.push_back((*i).second);
651 +    
652 +  return result;
653 + }
654 +
655 + double SimInfo::matTrace3(double m[3][3]){
656 +  double trace;
657 +  trace = m[0][0] + m[1][1] + m[2][2];
658 +
659 +  return trace;
660 + }

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