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root/group/trunk/OOPSE/libmdtools/SimInfo.cpp
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Comparing trunk/OOPSE/libmdtools/SimInfo.cpp (file contents):
Revision 586 by mmeineke, Wed Jul 9 22:14:06 2003 UTC vs.
Revision 767 by tim, Tue Sep 16 20:02:11 2003 UTC

# Line 26 | Line 26 | SimInfo::SimInfo(){
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 +  
52 +
53    usePBC = 0;
54    useLJ = 0;
55    useSticky = 0;
# Line 43 | Line 58 | SimInfo::SimInfo(){
58    useGB = 0;
59    useEAM = 0;
60  
61 +  myConfiguration = new SimState();
62 +
63    wrapMeSimInfo( this );
64   }
65  
66 +
67 + SimInfo::~SimInfo(){
68 +
69 +  delete myConfiguration;
70 +
71 +  map<string, GenericData*>::iterator i;
72 +  
73 +  for(i = properties.begin(); i != properties.end(); i++)
74 +    delete (*i).second;
75 +    
76 + }
77 +
78   void SimInfo::setBox(double newBox[3]) {
79    
80 <  int i;
81 <  double tempMat[9];
80 >  int i, j;
81 >  double tempMat[3][3];
82  
83 <  for(i=0; i<9; i++) tempMat[i] = 0.0;;
83 >  for(i=0; i<3; i++)
84 >    for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
85  
86 <  tempMat[0] = newBox[0];
87 <  tempMat[4] = newBox[1];
88 <  tempMat[8] = newBox[2];
86 >  tempMat[0][0] = newBox[0];
87 >  tempMat[1][1] = newBox[1];
88 >  tempMat[2][2] = newBox[2];
89  
90    setBoxM( tempMat );
91  
92   }
93  
94 < void SimInfo::setBoxM( double theBox[9] ){
94 > void SimInfo::setBoxM( double theBox[3][3] ){
95    
96 <  int i, status;
96 >  int i, j, status;
97    double smallestBoxL, maxCutoff;
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 <  for(i=0; i<9; i++) Hmat[i] = theBox[i];
105 >  
106 >  if( !boxIsInit ) boxIsInit = 1;
107  
108 <  cerr
109 <    << "setting Hmat ->\n"
110 <    << "[ " << Hmat[0] << ", " << Hmat[3] << ", " << Hmat[6] << " ]\n"
74 <    << "[ " << Hmat[1] << ", " << Hmat[4] << ", " << Hmat[7] << " ]\n"
75 <    << "[ " << Hmat[2] << ", " << Hmat[5] << ", " << Hmat[8] << " ]\n";
76 <
77 <  calcHmatI();
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 <
115 <
116 <  setFortranBoxSize(Hmat, HmatI, &orthoRhombic);
117 <
84 <  smallestBoxL = boxLx;
85 <  if (boxLy < smallestBoxL) smallestBoxL = boxLy;
86 <  if (boxLz < smallestBoxL) smallestBoxL = boxLz;
87 <
88 <  maxCutoff = smallestBoxL / 2.0;
89 <
90 <  if (rList > maxCutoff) {
91 <    sprintf( painCave.errMsg,
92 <             "New Box size is forcing neighborlist radius down to %lf\n",
93 <             maxCutoff );
94 <    painCave.isFatal = 0;
95 <    simError();
96 <
97 <    rList = maxCutoff;
98 <
99 <    sprintf( painCave.errMsg,
100 <             "New Box size is forcing cutoff radius down to %lf\n",
101 <             maxCutoff - 1.0 );
102 <    painCave.isFatal = 0;
103 <    simError();
104 <
105 <    rCut = rList - 1.0;
106 <
107 <    // list radius changed so we have to refresh the simulation structure.
108 <    refreshSim();
109 <  }
110 <
111 <  if (rCut > maxCutoff) {
112 <    sprintf( painCave.errMsg,
113 <             "New Box size is forcing cutoff radius down to %lf\n",
114 <             maxCutoff );
115 <    painCave.isFatal = 0;
116 <    simError();
117 <
118 <    status = 0;
119 <    LJ_new_rcut(&rCut, &status);
120 <    if (status != 0) {
121 <      sprintf( painCave.errMsg,
122 <               "Error in recomputing LJ shifts based on new rcut\n");
123 <      painCave.isFatal = 1;
124 <      simError();
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[9]) {
126 > void SimInfo::getBoxM (double theBox[3][3]) {
127  
128 <  int i;
129 <  for(i=0; i<9; i++) theBox[i] = Hmat[i];
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[9];
136 <  int i;
135 >  double theBox[3][3];
136 >  int i, j;
137  
138 <  cerr << "Scaling box by " << scale << "\n";
138 >  // cerr << "Scaling box by " << scale << "\n";
139  
140 <  for(i=0; i<9; i++) theBox[i] = Hmat[i]*scale;
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::calcHmatI( void ) {
148 <
149 <  double C[3][3];
152 <  double detHmat;
153 <  int i, j, k;
147 > void SimInfo::calcHmatInv( void ) {
148 >  
149 >  int i,j;
150    double smallDiag;
151    double tol;
152    double sanity[3][3];
153  
154 <  // calculate the adjunct of Hmat;
154 >  invertMat3( Hmat, HmatInv );
155  
156 <  C[0][0] =  ( Hmat[4]*Hmat[8]) - (Hmat[7]*Hmat[5]);
161 <  C[1][0] = -( Hmat[1]*Hmat[8]) + (Hmat[7]*Hmat[2]);
162 <  C[2][0] =  ( Hmat[1]*Hmat[5]) - (Hmat[4]*Hmat[2]);
156 >  // Check the inverse to make sure it is sane:
157  
158 <  C[0][1] = -( Hmat[3]*Hmat[8]) + (Hmat[6]*Hmat[5]);
159 <  C[1][1] =  ( Hmat[0]*Hmat[8]) - (Hmat[6]*Hmat[2]);
160 <  C[2][1] = -( Hmat[0]*Hmat[5]) + (Hmat[3]*Hmat[2]);
167 <
168 <  C[0][2] =  ( Hmat[3]*Hmat[7]) - (Hmat[6]*Hmat[4]);
169 <  C[1][2] = -( Hmat[0]*Hmat[7]) + (Hmat[6]*Hmat[1]);
170 <  C[2][2] =  ( Hmat[0]*Hmat[4]) - (Hmat[3]*Hmat[1]);
171 <
172 <  // calcutlate the determinant of Hmat
158 >  matMul3( Hmat, HmatInv, sanity );
159 >    
160 >  // check to see if Hmat is orthorhombic
161    
162 <  detHmat = 0.0;
163 <  for(i=0; i<3; i++) detHmat += Hmat[i] * C[i][0];
162 >  smallDiag = Hmat[0][0];
163 >  if(smallDiag > Hmat[1][1]) smallDiag = Hmat[1][1];
164 >  if(smallDiag > Hmat[2][2]) smallDiag = Hmat[2][2];
165 >  tol = smallDiag * 1E-6;
166  
167 +  orthoRhombic = 1;
168    
169 <  // H^-1 = C^T / det(H)
170 <  
171 <  i=0;
172 <  for(j=0; j<3; j++){
173 <    for(k=0; k<3; k++){
174 <
175 <      HmatI[i] = C[j][k] / detHmat;
185 <      i++;
169 >  for (i = 0; i < 3; i++ ) {
170 >    for (j = 0 ; j < 3; j++) {
171 >      if (i != j) {
172 >        if (orthoRhombic) {
173 >          if (Hmat[i][j] >= tol) orthoRhombic = 0;
174 >        }        
175 >      }
176      }
177    }
178 + }
179  
180 <  // sanity check
180 > double SimInfo::matDet3(double a[3][3]) {
181 >  int i, j, k;
182 >  double determinant;
183  
184 <  for(i=0; i<3; i++){
185 <    for(j=0; j<3; j++){
184 >  determinant = 0.0;
185 >
186 >  for(i = 0; i < 3; i++) {
187 >    j = (i+1)%3;
188 >    k = (i+2)%3;
189 >
190 >    determinant += a[0][i] * (a[1][j]*a[2][k] - a[1][k]*a[2][j]);
191 >  }
192 >
193 >  return determinant;
194 > }
195 >
196 > void SimInfo::invertMat3(double a[3][3], double b[3][3]) {
197 >  
198 >  int  i, j, k, l, m, n;
199 >  double determinant;
200 >
201 >  determinant = matDet3( a );
202 >
203 >  if (determinant == 0.0) {
204 >    sprintf( painCave.errMsg,
205 >             "Can't invert a matrix with a zero determinant!\n");
206 >    painCave.isFatal = 1;
207 >    simError();
208 >  }
209 >
210 >  for (i=0; i < 3; i++) {
211 >    j = (i+1)%3;
212 >    k = (i+2)%3;
213 >    for(l = 0; l < 3; l++) {
214 >      m = (l+1)%3;
215 >      n = (l+2)%3;
216        
217 <      sanity[i][j] = 0.0;
195 <      for(k=0; k<3; k++){
196 <        sanity[i][j] += Hmat[3*k+i] * HmatI[3*j+k];
197 <      }
217 >      b[l][i] = (a[j][m]*a[k][n] - a[j][n]*a[k][m]) / determinant;
218      }
219    }
220 + }
221  
222 <  cerr << "sanity => \n"
223 <       << sanity[0][0] << "\t" << sanity[0][1] << "\t" << sanity [0][2] << "\n"
203 <       << sanity[1][0] << "\t" << sanity[1][1] << "\t" << sanity [1][2] << "\n"
204 <       << sanity[2][0] << "\t" << sanity[2][1] << "\t" << sanity [2][2]
205 <       << "\n";
206 <    
222 > void SimInfo::matMul3(double a[3][3], double b[3][3], double c[3][3]) {
223 >  double r00, r01, r02, r10, r11, r12, r20, r21, r22;
224  
225 <  // check to see if Hmat is orthorhombic
225 >  r00 = a[0][0]*b[0][0] + a[0][1]*b[1][0] + a[0][2]*b[2][0];
226 >  r01 = a[0][0]*b[0][1] + a[0][1]*b[1][1] + a[0][2]*b[2][1];
227 >  r02 = a[0][0]*b[0][2] + a[0][1]*b[1][2] + a[0][2]*b[2][2];
228    
229 <  smallDiag = Hmat[0];
230 <  if(smallDiag > Hmat[4]) smallDiag = Hmat[4];
231 <  if(smallDiag > Hmat[8]) smallDiag = Hmat[8];
232 <  tol = smallDiag * 1E-6;
229 >  r10 = a[1][0]*b[0][0] + a[1][1]*b[1][0] + a[1][2]*b[2][0];
230 >  r11 = a[1][0]*b[0][1] + a[1][1]*b[1][1] + a[1][2]*b[2][1];
231 >  r12 = a[1][0]*b[0][2] + a[1][1]*b[1][2] + a[1][2]*b[2][2];
232 >  
233 >  r20 = a[2][0]*b[0][0] + a[2][1]*b[1][0] + a[2][2]*b[2][0];
234 >  r21 = a[2][0]*b[0][1] + a[2][1]*b[1][1] + a[2][2]*b[2][1];
235 >  r22 = a[2][0]*b[0][2] + a[2][1]*b[1][2] + a[2][2]*b[2][2];
236 >  
237 >  c[0][0] = r00; c[0][1] = r01; c[0][2] = r02;
238 >  c[1][0] = r10; c[1][1] = r11; c[1][2] = r12;
239 >  c[2][0] = r20; c[2][1] = r21; c[2][2] = r22;
240 > }
241  
242 <  orthoRhombic = 1;
243 <  for(i=0; (i<9) && orthoRhombic; i++){
244 <    
245 <    if( (i%4) ){ // ignore the diagonals (0, 4, and 8)
246 <      orthoRhombic = (Hmat[i] <= tol);
242 > void SimInfo::matVecMul3(double m[3][3], double inVec[3], double outVec[3]) {
243 >  double a0, a1, a2;
244 >
245 >  a0 = inVec[0];  a1 = inVec[1];  a2 = inVec[2];
246 >
247 >  outVec[0] = m[0][0]*a0 + m[0][1]*a1 + m[0][2]*a2;
248 >  outVec[1] = m[1][0]*a0 + m[1][1]*a1 + m[1][2]*a2;
249 >  outVec[2] = m[2][0]*a0 + m[2][1]*a1 + m[2][2]*a2;
250 > }
251 >
252 > void SimInfo::transposeMat3(double in[3][3], double out[3][3]) {
253 >  double temp[3][3];
254 >  int i, j;
255 >
256 >  for (i = 0; i < 3; i++) {
257 >    for (j = 0; j < 3; j++) {
258 >      temp[j][i] = in[i][j];
259      }
260    }
261 <    
261 >  for (i = 0; i < 3; i++) {
262 >    for (j = 0; j < 3; j++) {
263 >      out[i][j] = temp[i][j];
264 >    }
265 >  }
266   }
267 +  
268 + void SimInfo::printMat3(double A[3][3] ){
269  
270 +  std::cerr
271 +            << "[ " << A[0][0] << ", " << A[0][1] << ", " << A[0][2] << " ]\n"
272 +            << "[ " << A[1][0] << ", " << A[1][1] << ", " << A[1][2] << " ]\n"
273 +            << "[ " << A[2][0] << ", " << A[2][1] << ", " << A[2][2] << " ]\n";
274 + }
275 +
276 + void SimInfo::printMat9(double A[9] ){
277 +
278 +  std::cerr
279 +            << "[ " << A[0] << ", " << A[1] << ", " << A[2] << " ]\n"
280 +            << "[ " << A[3] << ", " << A[4] << ", " << A[5] << " ]\n"
281 +            << "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n";
282 + }
283 +
284   void SimInfo::calcBoxL( void ){
285  
286    double dx, dy, dz, dsq;
287    int i;
288  
289 <  // boxVol = h1 (dot) h2 (cross) h3
289 >  // boxVol = Determinant of Hmat
290  
291 <  boxVol = Hmat[0] * ( (Hmat[4]*Hmat[8]) - (Hmat[7]*Hmat[5]) )
233 <         + Hmat[1] * ( (Hmat[5]*Hmat[6]) - (Hmat[8]*Hmat[3]) )
234 <         + Hmat[2] * ( (Hmat[3]*Hmat[7]) - (Hmat[6]*Hmat[4]) );
291 >  boxVol = matDet3( Hmat );
292  
236 –
293    // boxLx
294    
295 <  dx = Hmat[0]; dy = Hmat[1]; dz = Hmat[2];
295 >  dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
296    dsq = dx*dx + dy*dy + dz*dz;
297 <  boxLx = sqrt( dsq );
297 >  boxL[0] = sqrt( dsq );
298 >  maxCutoff = 0.5 * boxL[0];
299  
300    // boxLy
301    
302 <  dx = Hmat[3]; dy = Hmat[4]; dz = Hmat[5];
302 >  dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
303    dsq = dx*dx + dy*dy + dz*dz;
304 <  boxLy = sqrt( dsq );
304 >  boxL[1] = sqrt( dsq );
305 >  if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
306  
307    // boxLz
308    
309 <  dx = Hmat[6]; dy = Hmat[7]; dz = Hmat[8];
309 >  dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
310    dsq = dx*dx + dy*dy + dz*dz;
311 <  boxLz = sqrt( dsq );
311 >  boxL[2] = sqrt( dsq );
312 >  if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
313    
314 +  checkCutOffs();
315 +
316   }
317  
318  
# Line 262 | Line 323 | void SimInfo::wrapVector( double thePos[3] ){
323  
324    if( !orthoRhombic ){
325      // calc the scaled coordinates.
326 +  
327 +
328 +    matVecMul3(HmatInv, thePos, scaled);
329      
330      for(i=0; i<3; i++)
267 –      scaled[i] =
268 –        thePos[0]*HmatI[i] + thePos[1]*HmatI[i+3] + thePos[3]*HmatI[i+6];
269 –    
270 –    // wrap the scaled coordinates
271 –    
272 –    for(i=0; i<3; i++)
331        scaled[i] -= roundMe(scaled[i]);
332      
333      // calc the wrapped real coordinates from the wrapped scaled coordinates
334      
335 <    for(i=0; i<3; i++)
336 <      thePos[i] =
279 <        scaled[0]*Hmat[i] + scaled[1]*Hmat[i+3] + scaled[2]*Hmat[i+6];
335 >    matVecMul3(Hmat, scaled, thePos);
336 >
337    }
338    else{
339      // calc the scaled coordinates.
340      
341      for(i=0; i<3; i++)
342 <      scaled[i] = thePos[i]*HmatI[i*4];
342 >      scaled[i] = thePos[i]*HmatInv[i][i];
343      
344      // wrap the scaled coordinates
345      
# Line 292 | Line 349 | void SimInfo::wrapVector( double thePos[3] ){
349      // calc the wrapped real coordinates from the wrapped scaled coordinates
350      
351      for(i=0; i<3; i++)
352 <      thePos[i] = scaled[i]*Hmat[i*4];
352 >      thePos[i] = scaled[i]*Hmat[i][i];
353    }
354      
298 –    
355   }
356  
357  
# Line 310 | Line 366 | int SimInfo::getNDF(){
366    ndf = ndf_local;
367   #endif
368  
369 <  ndf = ndf - 3;
369 >  ndf = ndf - 3 - nZconstraints;
370  
371    return ndf;
372   }
# Line 329 | Line 385 | int SimInfo::getNDFraw() {
385  
386    return ndfRaw;
387   }
388 <
388 >
389 > int SimInfo::getNDFtranslational() {
390 >  int ndfTrans_local, ndfTrans;
391 >
392 >  ndfTrans_local = 3 * n_atoms - n_constraints;
393 >
394 > #ifdef IS_MPI
395 >  MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
396 > #else
397 >  ndfTrans = ndfTrans_local;
398 > #endif
399 >
400 >  ndfTrans = ndfTrans - 3 - nZconstraints;
401 >
402 >  return ndfTrans;
403 > }
404 >
405   void SimInfo::refreshSim(){
406  
407    simtype fInfo;
408    int isError;
409    int n_global;
410    int* excl;
411 <  
340 <  fInfo.rrf = 0.0;
341 <  fInfo.rt = 0.0;
411 >
412    fInfo.dielect = 0.0;
413  
344 –  fInfo.rlist = rList;
345 –  fInfo.rcut = rCut;
346 –
414    if( useDipole ){
348 –    fInfo.rrf = ecr;
349 –    fInfo.rt = ecr - est;
415      if( useReactionField )fInfo.dielect = dielectric;
416    }
417  
# Line 392 | Line 457 | void SimInfo::refreshSim(){
457  
458    this->ndf = this->getNDF();
459    this->ndfRaw = this->getNDFraw();
460 +  this->ndfTrans = this->getNDFtranslational();
461 + }
462  
463 +
464 + void SimInfo::setRcut( double theRcut ){
465 +
466 +  if( !haveOrigRcut ){
467 +    haveOrigRcut = 1;
468 +    origRcut = theRcut;
469 +  }
470 +
471 +  rCut = theRcut;
472 +  checkCutOffs();
473   }
474  
475 + void SimInfo::setEcr( double theEcr ){
476 +
477 +  if( !haveOrigEcr ){
478 +    haveOrigEcr = 1;
479 +    origEcr = theEcr;
480 +  }
481 +
482 +  ecr = theEcr;
483 +  checkCutOffs();
484 + }
485 +
486 + void SimInfo::setEcr( double theEcr, double theEst ){
487 +
488 +  est = theEst;
489 +  setEcr( theEcr );
490 + }
491 +
492 +
493 + void SimInfo::checkCutOffs( void ){
494 +
495 +  int cutChanged = 0;
496 +
497 +
498 +
499 +  if( boxIsInit ){
500 +    
501 +    //we need to check cutOffs against the box
502 +  
503 +    if(( maxCutoff > rCut )&&(usePBC)){
504 +      if( rCut < origRcut ){
505 +        rCut = origRcut;
506 +        if (rCut > maxCutoff) rCut = maxCutoff;
507 +        
508 +        sprintf( painCave.errMsg,
509 +                 "New Box size is setting the long range cutoff radius "
510 +                 "to %lf\n",
511 +                 rCut );
512 +        painCave.isFatal = 0;
513 +        simError();
514 +      }
515 +    }
516 +
517 +    if( maxCutoff > ecr ){
518 +      if( ecr < origEcr ){
519 +        ecr = origEcr;
520 +        if (ecr > maxCutoff) ecr = maxCutoff;
521 +        
522 +        sprintf( painCave.errMsg,
523 +                 "New Box size is setting the electrostaticCutoffRadius "
524 +                 "to %lf\n",
525 +                 ecr );
526 +        painCave.isFatal = 0;
527 +        simError();
528 +      }
529 +    }
530 +
531 +
532 +    if ((rCut > maxCutoff)&&(usePBC)) {
533 +      sprintf( painCave.errMsg,
534 +               "New Box size is setting the long range cutoff radius "
535 +               "to %lf\n",
536 +               maxCutoff );
537 +      painCave.isFatal = 0;
538 +      simError();
539 +      rCut = maxCutoff;
540 +    }
541 +
542 +    if( ecr > maxCutoff){
543 +      sprintf( painCave.errMsg,
544 +               "New Box size is setting the electrostaticCutoffRadius "
545 +               "to %lf\n",
546 +               maxCutoff  );
547 +      painCave.isFatal = 0;
548 +      simError();      
549 +      ecr = maxCutoff;
550 +    }
551 +
552 +
553 +    if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1;
554 +
555 +    // rlist is the 1.0 plus max( rcut, ecr )
556 +    
557 +    ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
558 +    
559 +    if( cutChanged ){
560 +      
561 +      notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
562 +    }
563 +    
564 +    oldEcr = ecr;
565 +    oldRcut = rCut;
566 +
567 +  } else {
568 +    // initialize this stuff before using it, OK?
569 +      sprintf( painCave.errMsg,
570 +               "Trying to check cutoffs without a box. Be smarter.\n" );
571 +      painCave.isFatal = 1;
572 +      simError();      
573 +  }
574 +
575 + }
576 +
577 + void SimInfo::addProperty(GenericData* prop){
578 +
579 +  map<string, GenericData*>::iterator result;
580 +  result = properties.find(prop->getID());
581 +  
582 +  //we can't simply use  properties[prop->getID()] = prop,
583 +  //it will cause memory leak if we already contain a propery which has the same name of prop
584 +  
585 +  if(result != properties.end()){
586 +    
587 +    delete (*result).second;
588 +    (*result).second = prop;
589 +      
590 +  }
591 +  else{
592 +
593 +    properties[prop->getID()] = prop;
594 +
595 +  }
596 +    
597 + }
598 +
599 + GenericData* SimInfo::getProperty(const string& propName){
600 +
601 +  map<string, GenericData*>::iterator result;
602 +  
603 +  //string lowerCaseName = ();
604 +  
605 +  result = properties.find(propName);
606 +  
607 +  if(result != properties.end())
608 +    return (*result).second;  
609 +  else  
610 +    return NULL;  
611 + }
612 +
613 + vector<GenericData*> SimInfo::getProperties(){
614 +
615 +  vector<GenericData*> result;
616 +  map<string, GenericData*>::iterator i;
617 +  
618 +  for(i = properties.begin(); i != properties.end(); i++)
619 +    result.push_back((*i).second);
620 +    
621 +  return result;
622 + }
623 +
624 + double SimInfo::matTrace3(double m[3][3]){
625 +  double trace;
626 +  trace = m[0][0] + m[1][1] + m[2][2];
627 +
628 +  return trace;
629 + }

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