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root/group/trunk/OOPSE/libmdtools/SimInfo.cpp
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Comparing trunk/OOPSE/libmdtools/SimInfo.cpp (file contents):
Revision 618 by mmeineke, Tue Jul 15 21:34:56 2003 UTC vs.
Revision 1218 by gezelter, Wed Jun 2 14:21:54 2004 UTC

# Line 1 | Line 1
1 < #include <cstdlib>
2 < #include <cstring>
3 < #include <cmath>
1 > #include <stdlib.h>
2 > #include <string.h>
3 > #include <math.h>
4  
5   #include <iostream>
6   using namespace std;
# Line 12 | Line 12 | using namespace std;
12  
13   #include "fortranWrappers.hpp"
14  
15 + #include "MatVec3.h"
16 +
17   #ifdef IS_MPI
18   #include "mpiSimulation.hpp"
19   #endif
# Line 20 | Line 22 | inline double roundMe( double x ){
22    return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 );
23   }
24            
25 + inline double min( double a, double b ){
26 +  return (a < b ) ? a : b;
27 + }
28  
29   SimInfo* currentInfo;
30  
31   SimInfo::SimInfo(){
32 <  excludes = NULL;
32 >
33    n_constraints = 0;
34 +  nZconstraints = 0;
35    n_oriented = 0;
36    n_dipoles = 0;
37    ndf = 0;
38    ndfRaw = 0;
39 +  nZconstraints = 0;
40    the_integrator = NULL;
41    setTemp = 0;
42    thermalTime = 0.0;
43 +  currentTime = 0.0;
44    rCut = 0.0;
45 <  ecr = 0.0;
45 >  rSw = 0.0;
46  
47 +  haveRcut = 0;
48 +  haveRsw = 0;
49 +  boxIsInit = 0;
50 +  
51 +  resetTime = 1e99;
52 +
53 +  orthoRhombic = 0;
54 +  orthoTolerance = 1E-6;
55 +  useInitXSstate = true;
56 +
57    usePBC = 0;
58    useLJ = 0;
59    useSticky = 0;
60 <  useDipole = 0;
60 >  useCharges = 0;
61 >  useDipoles = 0;
62    useReactionField = 0;
63    useGB = 0;
64    useEAM = 0;
65 +  useSolidThermInt = 0;
66 +  useLiquidThermInt = 0;
67  
68 +  haveCutoffGroups = false;
69 +
70 +  excludes = Exclude::Instance();
71 +
72 +  myConfiguration = new SimState();
73 +
74 +  has_minimizer = false;
75 +  the_minimizer =NULL;
76 +
77 +  ngroup = 0;
78 +
79    wrapMeSimInfo( this );
80   }
81  
82 +
83 + SimInfo::~SimInfo(){
84 +
85 +  delete myConfiguration;
86 +
87 +  map<string, GenericData*>::iterator i;
88 +  
89 +  for(i = properties.begin(); i != properties.end(); i++)
90 +    delete (*i).second;
91 +  
92 + }
93 +
94   void SimInfo::setBox(double newBox[3]) {
95    
96    int i, j;
# Line 65 | Line 109 | void SimInfo::setBoxM( double theBox[3][3] ){
109  
110   void SimInfo::setBoxM( double theBox[3][3] ){
111    
112 <  int i, j, status;
69 <  double smallestBoxL, maxCutoff;
112 >  int i, j;
113    double FortranHmat[9]; // to preserve compatibility with Fortran the
114                           // ordering in the array is as follows:
115                           // [ 0 3 6 ]
# Line 74 | Line 117 | void SimInfo::setBoxM( double theBox[3][3] ){
117                           // [ 2 5 8 ]
118    double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
119  
120 +  if( !boxIsInit ) boxIsInit = 1;
121  
122    for(i=0; i < 3; i++)
123      for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
124    
81 –  //  cerr
82 –  // << "setting Hmat ->\n"
83 –  // << "[ " << Hmat[0][0] << ", " << Hmat[0][1] << ", " << Hmat[0][2] << " ]\n"
84 –  // << "[ " << Hmat[1][0] << ", " << Hmat[1][1] << ", " << Hmat[1][2] << " ]\n"
85 –  // << "[ " << Hmat[2][0] << ", " << Hmat[2][1] << ", " << Hmat[2][2] << " ]\n";
86 –
125    calcBoxL();
126    calcHmatInv();
127  
# Line 96 | Line 134 | void SimInfo::setBoxM( double theBox[3][3] ){
134  
135    setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic);
136  
99 –  smallestBoxL = boxLx;
100 –  if (boxLy < smallestBoxL) smallestBoxL = boxLy;
101 –  if (boxLz < smallestBoxL) smallestBoxL = boxLz;
102 –
103 –  maxCutoff = smallestBoxL / 2.0;
104 –
105 –  if (rList > maxCutoff) {
106 –    sprintf( painCave.errMsg,
107 –             "New Box size is forcing neighborlist radius down to %lf\n",
108 –             maxCutoff );
109 –    painCave.isFatal = 0;
110 –    simError();
111 –
112 –    rList = maxCutoff;
113 –
114 –    sprintf( painCave.errMsg,
115 –             "New Box size is forcing cutoff radius down to %lf\n",
116 –             maxCutoff - 1.0 );
117 –    painCave.isFatal = 0;
118 –    simError();
119 –
120 –    rCut = rList - 1.0;
121 –
122 –    // list radius changed so we have to refresh the simulation structure.
123 –    refreshSim();
124 –  }
125 –
126 –  if( ecr > maxCutoff ){
127 –
128 –    sprintf( painCave.errMsg,
129 –             "New Box size is forcing electrostatic cutoff radius "
130 –             "down to %lf\n",
131 –             maxCutoff );
132 –    painCave.isFatal = 0;
133 –    simError();
134 –
135 –    ecr = maxCutoff;
136 –    est = 0.05 * ecr;
137 –
138 –    refreshSim();
139 –  }
140 –    
137   }
138  
139  
# Line 164 | Line 160 | void SimInfo::calcHmatInv( void ) {
160  
161   void SimInfo::calcHmatInv( void ) {
162    
163 +  int oldOrtho;
164    int i,j;
165    double smallDiag;
166    double tol;
# Line 171 | Line 168 | void SimInfo::calcHmatInv( void ) {
168  
169    invertMat3( Hmat, HmatInv );
170  
174 –  // Check the inverse to make sure it is sane:
175 –
176 –  matMul3( Hmat, HmatInv, sanity );
177 –    
171    // check to see if Hmat is orthorhombic
172    
173 <  smallDiag = Hmat[0][0];
181 <  if(smallDiag > Hmat[1][1]) smallDiag = Hmat[1][1];
182 <  if(smallDiag > Hmat[2][2]) smallDiag = Hmat[2][2];
183 <  tol = smallDiag * 1E-6;
173 >  oldOrtho = orthoRhombic;
174  
175 +  smallDiag = fabs(Hmat[0][0]);
176 +  if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]);
177 +  if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]);
178 +  tol = smallDiag * orthoTolerance;
179 +
180    orthoRhombic = 1;
181    
182    for (i = 0; i < 3; i++ ) {
183      for (j = 0 ; j < 3; j++) {
184        if (i != j) {
185          if (orthoRhombic) {
186 <          if (Hmat[i][j] >= tol) orthoRhombic = 0;
186 >          if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0;
187          }        
188        }
189      }
190    }
196 – }
191  
192 < double SimInfo::matDet3(double a[3][3]) {
193 <  int i, j, k;
194 <  double determinant;
195 <
196 <  determinant = 0.0;
197 <
198 <  for(i = 0; i < 3; i++) {
199 <    j = (i+1)%3;
200 <    k = (i+2)%3;
201 <
202 <    determinant += a[0][i] * (a[1][j]*a[2][k] - a[1][k]*a[2][j]);
203 <  }
210 <
211 <  return determinant;
212 < }
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;
192 >  if( oldOrtho != orthoRhombic ){
193 >    
194 >    if( orthoRhombic ) {
195 >      sprintf( painCave.errMsg,
196 >               "\n\tOOPSE is switching from the default Non-Orthorhombic\n"
197 >               "\tto the faster Orthorhombic periodic boundary computations.\n"
198 >               "\tThis is usually a good thing, but if you wan't the\n"
199 >               "\tNon-Orthorhombic computations, make the orthoBoxTolerance\n"
200 >               "\tvariable ( currently set to %G ) smaller.\n",
201 >               orthoTolerance);
202 >      painCave.severity = OOPSE_INFO;
203 >      simError();
204      }
205 <  }
206 < }
207 <
208 < void SimInfo::matMul3(double a[3][3], double b[3][3], double c[3][3]) {
209 <  double r00, r01, r02, r10, r11, r12, r20, r21, r22;
210 <
211 <  r00 = a[0][0]*b[0][0] + a[0][1]*b[1][0] + a[0][2]*b[2][0];
212 <  r01 = a[0][0]*b[0][1] + a[0][1]*b[1][1] + a[0][2]*b[2][1];
213 <  r02 = a[0][0]*b[0][2] + a[0][1]*b[1][2] + a[0][2]*b[2][2];
214 <  
215 <  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];
205 >    else {
206 >      sprintf( painCave.errMsg,
207 >               "\n\tOOPSE is switching from the faster Orthorhombic to the more\n"
208 >               "\tflexible Non-Orthorhombic periodic boundary computations.\n"
209 >               "\tThis is usually because the box has deformed under\n"
210 >               "\tNPTf integration. If you wan't to live on the edge with\n"
211 >               "\tthe Orthorhombic computations, make the orthoBoxTolerance\n"
212 >               "\tvariable ( currently set to %G ) larger.\n",
213 >               orthoTolerance);
214 >      painCave.severity = OOPSE_WARNING;
215 >      simError();
216      }
217    }
279 –  for (i = 0; i < 3; i++) {
280 –    for (j = 0; j < 3; j++) {
281 –      out[i][j] = temp[i][j];
282 –    }
283 –  }
218   }
285 –  
286 – void SimInfo::printMat3(double A[3][3] ){
219  
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 –
220   void SimInfo::calcBoxL( void ){
221  
222    double dx, dy, dz, dsq;
305 –  int i;
223  
224    // boxVol = Determinant of Hmat
225  
# Line 312 | Line 229 | void SimInfo::calcBoxL( void ){
229    
230    dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
231    dsq = dx*dx + dy*dy + dz*dz;
232 <  boxLx = sqrt( dsq );
232 >  boxL[0] = sqrt( dsq );
233 >  //maxCutoff = 0.5 * boxL[0];
234  
235    // boxLy
236    
237    dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
238    dsq = dx*dx + dy*dy + dz*dz;
239 <  boxLy = sqrt( dsq );
239 >  boxL[1] = sqrt( dsq );
240 >  //if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
241  
242 +
243    // boxLz
244    
245    dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
246    dsq = dx*dx + dy*dy + dz*dz;
247 <  boxLz = sqrt( dsq );
247 >  boxL[2] = sqrt( dsq );
248 >  //if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
249 >
250 >  //calculate the max cutoff
251 >  maxCutoff =  calcMaxCutOff();
252    
253 +  checkCutOffs();
254 +
255   }
256  
257  
258 + double SimInfo::calcMaxCutOff(){
259 +
260 +  double ri[3], rj[3], rk[3];
261 +  double rij[3], rjk[3], rki[3];
262 +  double minDist;
263 +
264 +  ri[0] = Hmat[0][0];
265 +  ri[1] = Hmat[1][0];
266 +  ri[2] = Hmat[2][0];
267 +
268 +  rj[0] = Hmat[0][1];
269 +  rj[1] = Hmat[1][1];
270 +  rj[2] = Hmat[2][1];
271 +
272 +  rk[0] = Hmat[0][2];
273 +  rk[1] = Hmat[1][2];
274 +  rk[2] = Hmat[2][2];
275 +    
276 +  crossProduct3(ri, rj, rij);
277 +  distXY = dotProduct3(rk,rij) / norm3(rij);
278 +
279 +  crossProduct3(rj,rk, rjk);
280 +  distYZ = dotProduct3(ri,rjk) / norm3(rjk);
281 +
282 +  crossProduct3(rk,ri, rki);
283 +  distZX = dotProduct3(rj,rki) / norm3(rki);
284 +
285 +  minDist = min(min(distXY, distYZ), distZX);
286 +  return minDist/2;
287 +  
288 + }
289 +
290   void SimInfo::wrapVector( double thePos[3] ){
291  
292 <  int i, j, k;
292 >  int i;
293    double scaled[3];
294  
295    if( !orthoRhombic ){
# Line 369 | Line 327 | int SimInfo::getNDF(){
327  
328  
329   int SimInfo::getNDF(){
330 <  int ndf_local, ndf;
330 >  int ndf_local;
331 >
332 >  ndf_local = 0;
333    
334 <  ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints;
334 >  for(int i = 0; i < integrableObjects.size(); i++){
335 >    ndf_local += 3;
336 >    if (integrableObjects[i]->isDirectional()) {
337 >      if (integrableObjects[i]->isLinear())
338 >        ndf_local += 2;
339 >      else
340 >        ndf_local += 3;
341 >    }
342 >  }
343  
344 +  // n_constraints is local, so subtract them on each processor:
345 +
346 +  ndf_local -= n_constraints;
347 +
348   #ifdef IS_MPI
349    MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
350   #else
351    ndf = ndf_local;
352   #endif
353  
354 <  ndf = ndf - 3;
354 >  // nZconstraints is global, as are the 3 COM translations for the
355 >  // entire system:
356  
357 +  ndf = ndf - 3 - nZconstraints;
358 +
359    return ndf;
360   }
361  
362   int SimInfo::getNDFraw() {
363 <  int ndfRaw_local, ndfRaw;
363 >  int ndfRaw_local;
364  
365    // Raw degrees of freedom that we have to set
366 <  ndfRaw_local = 3 * n_atoms + 3 * n_oriented;
367 <  
366 >  ndfRaw_local = 0;
367 >
368 >  for(int i = 0; i < integrableObjects.size(); i++){
369 >    ndfRaw_local += 3;
370 >    if (integrableObjects[i]->isDirectional()) {
371 >       if (integrableObjects[i]->isLinear())
372 >        ndfRaw_local += 2;
373 >      else
374 >        ndfRaw_local += 3;
375 >    }
376 >  }
377 >    
378   #ifdef IS_MPI
379    MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
380   #else
# Line 398 | Line 383 | int SimInfo::getNDFraw() {
383  
384    return ndfRaw;
385   }
386 <
386 >
387 > int SimInfo::getNDFtranslational() {
388 >  int ndfTrans_local;
389 >
390 >  ndfTrans_local = 3 * integrableObjects.size() - n_constraints;
391 >
392 >
393 > #ifdef IS_MPI
394 >  MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
395 > #else
396 >  ndfTrans = ndfTrans_local;
397 > #endif
398 >
399 >  ndfTrans = ndfTrans - 3 - nZconstraints;
400 >
401 >  return ndfTrans;
402 > }
403 >
404 > int SimInfo::getTotIntegrableObjects() {
405 >  int nObjs_local;
406 >  int nObjs;
407 >
408 >  nObjs_local =  integrableObjects.size();
409 >
410 >
411 > #ifdef IS_MPI
412 >  MPI_Allreduce(&nObjs_local,&nObjs,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
413 > #else
414 >  nObjs = nObjs_local;
415 > #endif
416 >
417 >
418 >  return nObjs;
419 > }
420 >
421   void SimInfo::refreshSim(){
422  
423    simtype fInfo;
424    int isError;
425    int n_global;
426    int* excl;
427 <  
409 <  fInfo.rrf = 0.0;
410 <  fInfo.rt = 0.0;
427 >
428    fInfo.dielect = 0.0;
429  
430 <  fInfo.rlist = rList;
414 <  fInfo.rcut = rCut;
415 <
416 <  if( useDipole ){
417 <    fInfo.rrf = ecr;
418 <    fInfo.rt = ecr - est;
430 >  if( useDipoles ){
431      if( useReactionField )fInfo.dielect = dielectric;
432    }
433  
# Line 424 | Line 436 | void SimInfo::refreshSim(){
436    fInfo.SIM_uses_LJ = useLJ;
437    fInfo.SIM_uses_sticky = useSticky;
438    //fInfo.SIM_uses_sticky = 0;
439 <  fInfo.SIM_uses_dipoles = useDipole;
439 >  fInfo.SIM_uses_charges = useCharges;
440 >  fInfo.SIM_uses_dipoles = useDipoles;
441    //fInfo.SIM_uses_dipoles = 0;
442 <  //fInfo.SIM_uses_RF = useReactionField;
443 <  fInfo.SIM_uses_RF = 0;
442 >  fInfo.SIM_uses_RF = useReactionField;
443 >  //fInfo.SIM_uses_RF = 0;
444    fInfo.SIM_uses_GB = useGB;
445    fInfo.SIM_uses_EAM = useEAM;
446  
447 <  excl = Exclude::getArray();
448 <
447 >  n_exclude = excludes->getSize();
448 >  excl = excludes->getFortranArray();
449 >  
450   #ifdef IS_MPI
451 <  n_global = mpiSim->getTotAtoms();
451 >  n_global = mpiSim->getNAtomsGlobal();
452   #else
453    n_global = n_atoms;
454   #endif
455 <
455 >  
456    isError = 0;
457 <
457 >  
458 >  getFortranGroupArrays(this, FglobalGroupMembership, mfact);
459 >  //it may not be a good idea to pass the address of first element in vector
460 >  //since c++ standard does not require vector to be stored continuously in meomory
461 >  //Most of the compilers will organize the memory of vector continuously
462    setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl,
463 <                  &nGlobalExcludes, globalExcludes, molMembershipArray,
464 <                  &isError );
463 >                  &nGlobalExcludes, globalExcludes, molMembershipArray,
464 >                  &mfact[0], &ngroup, &FglobalGroupMembership[0], &isError);
465  
466    if( isError ){
467 <
467 >    
468      sprintf( painCave.errMsg,
469 <             "There was an error setting the simulation information in fortran.\n" );
469 >             "There was an error setting the simulation information in fortran.\n" );
470      painCave.isFatal = 1;
471      simError();
472    }
473 <
473 >  
474   #ifdef IS_MPI
475    sprintf( checkPointMsg,
476             "succesfully sent the simulation information to fortran.\n");
477    MPIcheckPoint();
478   #endif // is_mpi
479 <
479 >  
480    this->ndf = this->getNDF();
481    this->ndfRaw = this->getNDFraw();
482 +  this->ndfTrans = this->getNDFtranslational();
483 + }
484  
485 + void SimInfo::setDefaultRcut( double theRcut ){
486 +  
487 +  haveRcut = 1;
488 +  rCut = theRcut;
489 +  rList = rCut + 1.0;
490 +  
491 +  notifyFortranCutOffs( &rCut, &rSw, &rList );
492   }
493  
494 + void SimInfo::setDefaultRcut( double theRcut, double theRsw ){
495 +
496 +  rSw = theRsw;
497 +  setDefaultRcut( theRcut );
498 + }
499 +
500 +
501 + void SimInfo::checkCutOffs( void ){
502 +  
503 +  if( boxIsInit ){
504 +    
505 +    //we need to check cutOffs against the box
506 +    
507 +    if( rCut > maxCutoff ){
508 +      sprintf( painCave.errMsg,
509 +               "\n\tcutoffRadius is too large for the current periodic box.\n"
510 +               "\tCurrent Value of cutoffRadius = %G at time %G\n "
511 +               "\tThis is larger than half of at least one of the\n"
512 +               "\tperiodic box vectors.  Right now, the Box matrix is:\n"
513 +               "\n"
514 +               "\t[ %G %G %G ]\n"
515 +               "\t[ %G %G %G ]\n"
516 +               "\t[ %G %G %G ]\n",
517 +               rCut, currentTime,
518 +               Hmat[0][0], Hmat[0][1], Hmat[0][2],
519 +               Hmat[1][0], Hmat[1][1], Hmat[1][2],
520 +               Hmat[2][0], Hmat[2][1], Hmat[2][2]);
521 +      painCave.severity = OOPSE_ERROR;
522 +      painCave.isFatal = 1;
523 +      simError();
524 +    }    
525 +  } else {
526 +    // initialize this stuff before using it, OK?
527 +    sprintf( painCave.errMsg,
528 +             "\n\tTrying to check cutoffs without a box.\n"
529 +             "\tOOPSE should have better programmers than that.\n" );
530 +    painCave.severity = OOPSE_ERROR;
531 +    painCave.isFatal = 1;
532 +    simError();      
533 +  }
534 +  
535 + }
536 +
537 + void SimInfo::addProperty(GenericData* prop){
538 +
539 +  map<string, GenericData*>::iterator result;
540 +  result = properties.find(prop->getID());
541 +  
542 +  //we can't simply use  properties[prop->getID()] = prop,
543 +  //it will cause memory leak if we already contain a propery which has the same name of prop
544 +  
545 +  if(result != properties.end()){
546 +    
547 +    delete (*result).second;
548 +    (*result).second = prop;
549 +      
550 +  }
551 +  else{
552 +
553 +    properties[prop->getID()] = prop;
554 +
555 +  }
556 +    
557 + }
558 +
559 + GenericData* SimInfo::getProperty(const string& propName){
560 +
561 +  map<string, GenericData*>::iterator result;
562 +  
563 +  //string lowerCaseName = ();
564 +  
565 +  result = properties.find(propName);
566 +  
567 +  if(result != properties.end())
568 +    return (*result).second;  
569 +  else  
570 +    return NULL;  
571 + }
572 +
573 +
574 + void SimInfo::getFortranGroupArrays(SimInfo* info,
575 +                                    vector<int>& FglobalGroupMembership,
576 +                                    vector<double>& mfact){
577 +  
578 +  Molecule* myMols;
579 +  Atom** myAtoms;
580 +  int numAtom;
581 +  double mtot;
582 +  int numMol;
583 +  int numCutoffGroups;
584 +  CutoffGroup* myCutoffGroup;
585 +  vector<CutoffGroup*>::iterator iterCutoff;
586 +  Atom* cutoffAtom;
587 +  vector<Atom*>::iterator iterAtom;
588 +  int atomIndex;
589 +  double totalMass;
590 +  
591 +  mfact.clear();
592 +  FglobalGroupMembership.clear();
593 +  
594 +
595 +  // Fix the silly fortran indexing problem
596 + #ifdef IS_MPI
597 +  numAtom = mpiSim->getNAtomsGlobal();
598 + #else
599 +  numAtom = n_atoms;
600 + #endif
601 +  for (int i = 0; i < numAtom; i++)
602 +    FglobalGroupMembership.push_back(globalGroupMembership[i] + 1);
603 +  
604 +
605 +  myMols = info->molecules;
606 +  numMol = info->n_mol;
607 +  for(int i  = 0; i < numMol; i++){
608 +    numCutoffGroups = myMols[i].getNCutoffGroups();
609 +    for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff);
610 +        myCutoffGroup != NULL;
611 +        myCutoffGroup =myMols[i].nextCutoffGroup(iterCutoff)){
612 +
613 +      totalMass = myCutoffGroup->getMass();
614 +      
615 +      for(cutoffAtom = myCutoffGroup->beginAtom(iterAtom);
616 +          cutoffAtom != NULL;
617 +          cutoffAtom = myCutoffGroup->nextAtom(iterAtom)){
618 +        mfact.push_back(cutoffAtom->getMass()/totalMass);
619 +      }  
620 +    }
621 +  }
622 +
623 + }

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