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root/group/trunk/OOPSE/libmdtools/SimInfo.cpp
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Comparing trunk/OOPSE/libmdtools/SimInfo.cpp (file contents):
Revision 617 by gezelter, Tue Jul 15 19:56:08 2003 UTC vs.
Revision 1234 by tim, Fri Jun 4 03:15:31 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 + #include "ConstraintManager.hpp"
18 +
19   #ifdef IS_MPI
20   #include "mpiSimulation.hpp"
21   #endif
# Line 20 | Line 24 | inline double roundMe( double x ){
24    return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 );
25   }
26            
27 + inline double min( double a, double b ){
28 +  return (a < b ) ? a : b;
29 + }
30  
31   SimInfo* currentInfo;
32  
33   SimInfo::SimInfo(){
34 <  excludes = NULL;
34 >
35    n_constraints = 0;
36 +  nZconstraints = 0;
37    n_oriented = 0;
38    n_dipoles = 0;
39    ndf = 0;
40    ndfRaw = 0;
41 +  nZconstraints = 0;
42    the_integrator = NULL;
43    setTemp = 0;
44    thermalTime = 0.0;
45 +  currentTime = 0.0;
46    rCut = 0.0;
47 +  rSw = 0.0;
48  
49 +  haveRcut = 0;
50 +  haveRsw = 0;
51 +  boxIsInit = 0;
52 +  
53 +  resetTime = 1e99;
54 +
55 +  orthoRhombic = 0;
56 +  orthoTolerance = 1E-6;
57 +  useInitXSstate = true;
58 +
59    usePBC = 0;
60    useLJ = 0;
61    useSticky = 0;
62 <  useDipole = 0;
62 >  useCharges = 0;
63 >  useDipoles = 0;
64    useReactionField = 0;
65    useGB = 0;
66    useEAM = 0;
67 +  useSolidThermInt = 0;
68 +  useLiquidThermInt = 0;
69  
70 +  haveCutoffGroups = false;
71 +
72 +  excludes = Exclude::Instance();
73 +
74 +  myConfiguration = new SimState();
75 +
76 +  has_minimizer = false;
77 +  the_minimizer =NULL;
78 +
79 +  ngroup = 0;
80 +
81 +  consMan = NULL;
82 +  
83    wrapMeSimInfo( this );
84   }
85  
86 +
87 + SimInfo::~SimInfo(){
88 +
89 +  delete myConfiguration;
90 +
91 +  map<string, GenericData*>::iterator i;
92 +  
93 +  for(i = properties.begin(); i != properties.end(); i++)
94 +    delete (*i).second;
95 +
96 +  if (!consMan)
97 +    delete consMan;  
98 + }
99 +
100   void SimInfo::setBox(double newBox[3]) {
101    
102    int i, j;
# Line 64 | Line 115 | void SimInfo::setBoxM( double theBox[3][3] ){
115  
116   void SimInfo::setBoxM( double theBox[3][3] ){
117    
118 <  int i, j, status;
68 <  double smallestBoxL, maxCutoff;
118 >  int i, j;
119    double FortranHmat[9]; // to preserve compatibility with Fortran the
120                           // ordering in the array is as follows:
121                           // [ 0 3 6 ]
# Line 73 | Line 123 | void SimInfo::setBoxM( double theBox[3][3] ){
123                           // [ 2 5 8 ]
124    double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
125  
126 +  if( !boxIsInit ) boxIsInit = 1;
127  
128    for(i=0; i < 3; i++)
129      for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
130    
80 –  //  cerr
81 –  // << "setting Hmat ->\n"
82 –  // << "[ " << Hmat[0][0] << ", " << Hmat[0][1] << ", " << Hmat[0][2] << " ]\n"
83 –  // << "[ " << Hmat[1][0] << ", " << Hmat[1][1] << ", " << Hmat[1][2] << " ]\n"
84 –  // << "[ " << Hmat[2][0] << ", " << Hmat[2][1] << ", " << Hmat[2][2] << " ]\n";
85 –
131    calcBoxL();
132    calcHmatInv();
133  
# Line 95 | Line 140 | void SimInfo::setBoxM( double theBox[3][3] ){
140  
141    setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic);
142  
98 –  smallestBoxL = boxLx;
99 –  if (boxLy < smallestBoxL) smallestBoxL = boxLy;
100 –  if (boxLz < smallestBoxL) smallestBoxL = boxLz;
101 –
102 –  maxCutoff = smallestBoxL / 2.0;
103 –
104 –  if (rList > maxCutoff) {
105 –    sprintf( painCave.errMsg,
106 –             "New Box size is forcing neighborlist radius down to %lf\n",
107 –             maxCutoff );
108 –    painCave.isFatal = 0;
109 –    simError();
110 –
111 –    rList = maxCutoff;
112 –
113 –    sprintf( painCave.errMsg,
114 –             "New Box size is forcing cutoff radius down to %lf\n",
115 –             maxCutoff - 1.0 );
116 –    painCave.isFatal = 0;
117 –    simError();
118 –
119 –    rCut = rList - 1.0;
120 –
121 –    // list radius changed so we have to refresh the simulation structure.
122 –    refreshSim();
123 –  }
124 –
125 –  if (rCut > maxCutoff) {
126 –    sprintf( painCave.errMsg,
127 –             "New Box size is forcing cutoff radius down to %lf\n",
128 –             maxCutoff );
129 –    painCave.isFatal = 0;
130 –    simError();
131 –
132 –    status = 0;
133 –    LJ_new_rcut(&rCut, &status);
134 –    if (status != 0) {
135 –      sprintf( painCave.errMsg,
136 –               "Error in recomputing LJ shifts based on new rcut\n");
137 –      painCave.isFatal = 1;
138 –      simError();
139 –    }
140 –  }
143   }
144  
145  
# Line 164 | Line 166 | void SimInfo::calcHmatInv( void ) {
166  
167   void SimInfo::calcHmatInv( void ) {
168    
169 +  int oldOrtho;
170    int i,j;
171    double smallDiag;
172    double tol;
# Line 171 | Line 174 | void SimInfo::calcHmatInv( void ) {
174  
175    invertMat3( Hmat, HmatInv );
176  
174 –  // Check the inverse to make sure it is sane:
175 –
176 –  matMul3( Hmat, HmatInv, sanity );
177 –    
177    // check to see if Hmat is orthorhombic
178    
179 <  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;
179 >  oldOrtho = orthoRhombic;
180  
181 +  smallDiag = fabs(Hmat[0][0]);
182 +  if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]);
183 +  if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]);
184 +  tol = smallDiag * orthoTolerance;
185 +
186    orthoRhombic = 1;
187    
188    for (i = 0; i < 3; i++ ) {
189      for (j = 0 ; j < 3; j++) {
190        if (i != j) {
191          if (orthoRhombic) {
192 <          if (Hmat[i][j] >= tol) orthoRhombic = 0;
192 >          if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0;
193          }        
194        }
195      }
195 –  }
196 – }
197 –
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 –
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();
196    }
197  
198 <  for (i=0; i < 3; i++) {
199 <    j = (i+1)%3;
200 <    k = (i+2)%3;
201 <    for(l = 0; l < 3; l++) {
202 <      m = (l+1)%3;
203 <      n = (l+2)%3;
204 <      
205 <      b[l][i] = (a[j][m]*a[k][n] - a[j][n]*a[k][m]) / determinant;
198 >  if( oldOrtho != orthoRhombic ){
199 >    
200 >    if( orthoRhombic ) {
201 >      sprintf( painCave.errMsg,
202 >               "OOPSE is switching from the default Non-Orthorhombic\n"
203 >               "\tto the faster Orthorhombic periodic boundary computations.\n"
204 >               "\tThis is usually a good thing, but if you wan't the\n"
205 >               "\tNon-Orthorhombic computations, make the orthoBoxTolerance\n"
206 >               "\tvariable ( currently set to %G ) smaller.\n",
207 >               orthoTolerance);
208 >      painCave.severity = OOPSE_INFO;
209 >      simError();
210      }
211 <  }
212 < }
213 <
214 < void SimInfo::matMul3(double a[3][3], double b[3][3], double c[3][3]) {
215 <  double r00, r01, r02, r10, r11, r12, r20, r21, r22;
216 <
217 <  r00 = a[0][0]*b[0][0] + a[0][1]*b[1][0] + a[0][2]*b[2][0];
218 <  r01 = a[0][0]*b[0][1] + a[0][1]*b[1][1] + a[0][2]*b[2][1];
219 <  r02 = a[0][0]*b[0][2] + a[0][1]*b[1][2] + a[0][2]*b[2][2];
220 <  
221 <  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];
211 >    else {
212 >      sprintf( painCave.errMsg,
213 >               "OOPSE is switching from the faster Orthorhombic to the more\n"
214 >               "\tflexible Non-Orthorhombic periodic boundary computations.\n"
215 >               "\tThis is usually because the box has deformed under\n"
216 >               "\tNPTf integration. If you wan't to live on the edge with\n"
217 >               "\tthe Orthorhombic computations, make the orthoBoxTolerance\n"
218 >               "\tvariable ( currently set to %G ) larger.\n",
219 >               orthoTolerance);
220 >      painCave.severity = OOPSE_WARNING;
221 >      simError();
222      }
223    }
279 –  for (i = 0; i < 3; i++) {
280 –    for (j = 0; j < 3; j++) {
281 –      out[i][j] = temp[i][j];
282 –    }
283 –  }
224   }
285 –  
286 – void SimInfo::printMat3(double A[3][3] ){
225  
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 –
226   void SimInfo::calcBoxL( void ){
227  
228    double dx, dy, dz, dsq;
305 –  int i;
229  
230    // boxVol = Determinant of Hmat
231  
# Line 312 | Line 235 | void SimInfo::calcBoxL( void ){
235    
236    dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
237    dsq = dx*dx + dy*dy + dz*dz;
238 <  boxLx = sqrt( dsq );
238 >  boxL[0] = sqrt( dsq );
239 >  //maxCutoff = 0.5 * boxL[0];
240  
241    // boxLy
242    
243    dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
244    dsq = dx*dx + dy*dy + dz*dz;
245 <  boxLy = sqrt( dsq );
245 >  boxL[1] = sqrt( dsq );
246 >  //if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
247  
248 +
249    // boxLz
250    
251    dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
252    dsq = dx*dx + dy*dy + dz*dz;
253 <  boxLz = sqrt( dsq );
253 >  boxL[2] = sqrt( dsq );
254 >  //if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
255 >
256 >  //calculate the max cutoff
257 >  maxCutoff =  calcMaxCutOff();
258    
259 +  checkCutOffs();
260 +
261   }
262 +
263 +
264 + double SimInfo::calcMaxCutOff(){
265 +
266 +  double ri[3], rj[3], rk[3];
267 +  double rij[3], rjk[3], rki[3];
268 +  double minDist;
269 +
270 +  ri[0] = Hmat[0][0];
271 +  ri[1] = Hmat[1][0];
272 +  ri[2] = Hmat[2][0];
273 +
274 +  rj[0] = Hmat[0][1];
275 +  rj[1] = Hmat[1][1];
276 +  rj[2] = Hmat[2][1];
277 +
278 +  rk[0] = Hmat[0][2];
279 +  rk[1] = Hmat[1][2];
280 +  rk[2] = Hmat[2][2];
281 +    
282 +  crossProduct3(ri, rj, rij);
283 +  distXY = dotProduct3(rk,rij) / norm3(rij);
284  
285 +  crossProduct3(rj,rk, rjk);
286 +  distYZ = dotProduct3(ri,rjk) / norm3(rjk);
287  
288 +  crossProduct3(rk,ri, rki);
289 +  distZX = dotProduct3(rj,rki) / norm3(rki);
290 +
291 +  minDist = min(min(distXY, distYZ), distZX);
292 +  return minDist/2;
293 +  
294 + }
295 +
296   void SimInfo::wrapVector( double thePos[3] ){
297  
298 <  int i, j, k;
298 >  int i;
299    double scaled[3];
300  
301    if( !orthoRhombic ){
# Line 369 | Line 333 | int SimInfo::getNDF(){
333  
334  
335   int SimInfo::getNDF(){
336 <  int ndf_local, ndf;
336 >  int ndf_local;
337 >
338 >  ndf_local = 0;
339    
340 <  ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints;
340 >  for(int i = 0; i < integrableObjects.size(); i++){
341 >    ndf_local += 3;
342 >    if (integrableObjects[i]->isDirectional()) {
343 >      if (integrableObjects[i]->isLinear())
344 >        ndf_local += 2;
345 >      else
346 >        ndf_local += 3;
347 >    }
348 >  }
349  
350 +  // n_constraints is local, so subtract them on each processor:
351 +
352 +  ndf_local -= n_constraints;
353 +
354   #ifdef IS_MPI
355    MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
356   #else
357    ndf = ndf_local;
358   #endif
359  
360 <  ndf = ndf - 3;
360 >  // nZconstraints is global, as are the 3 COM translations for the
361 >  // entire system:
362  
363 +  ndf = ndf - 3 - nZconstraints;
364 +
365    return ndf;
366   }
367  
368   int SimInfo::getNDFraw() {
369 <  int ndfRaw_local, ndfRaw;
369 >  int ndfRaw_local;
370  
371    // Raw degrees of freedom that we have to set
372 <  ndfRaw_local = 3 * n_atoms + 3 * n_oriented;
373 <  
372 >  ndfRaw_local = 0;
373 >
374 >  for(int i = 0; i < integrableObjects.size(); i++){
375 >    ndfRaw_local += 3;
376 >    if (integrableObjects[i]->isDirectional()) {
377 >       if (integrableObjects[i]->isLinear())
378 >        ndfRaw_local += 2;
379 >      else
380 >        ndfRaw_local += 3;
381 >    }
382 >  }
383 >    
384   #ifdef IS_MPI
385    MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
386   #else
# Line 398 | Line 389 | int SimInfo::getNDFraw() {
389  
390    return ndfRaw;
391   }
392 <
392 >
393 > int SimInfo::getNDFtranslational() {
394 >  int ndfTrans_local;
395 >
396 >  ndfTrans_local = 3 * integrableObjects.size() - n_constraints;
397 >
398 >
399 > #ifdef IS_MPI
400 >  MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
401 > #else
402 >  ndfTrans = ndfTrans_local;
403 > #endif
404 >
405 >  ndfTrans = ndfTrans - 3 - nZconstraints;
406 >
407 >  return ndfTrans;
408 > }
409 >
410 > int SimInfo::getTotIntegrableObjects() {
411 >  int nObjs_local;
412 >  int nObjs;
413 >
414 >  nObjs_local =  integrableObjects.size();
415 >
416 >
417 > #ifdef IS_MPI
418 >  MPI_Allreduce(&nObjs_local,&nObjs,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
419 > #else
420 >  nObjs = nObjs_local;
421 > #endif
422 >
423 >
424 >  return nObjs;
425 > }
426 >
427   void SimInfo::refreshSim(){
428  
429    simtype fInfo;
430    int isError;
431    int n_global;
432    int* excl;
433 <  
409 <  fInfo.rrf = 0.0;
410 <  fInfo.rt = 0.0;
433 >
434    fInfo.dielect = 0.0;
435  
436 <  fInfo.rlist = rList;
414 <  fInfo.rcut = rCut;
415 <
416 <  if( useDipole ){
417 <    fInfo.rrf = ecr;
418 <    fInfo.rt = ecr - est;
436 >  if( useDipoles ){
437      if( useReactionField )fInfo.dielect = dielectric;
438    }
439  
# Line 424 | Line 442 | void SimInfo::refreshSim(){
442    fInfo.SIM_uses_LJ = useLJ;
443    fInfo.SIM_uses_sticky = useSticky;
444    //fInfo.SIM_uses_sticky = 0;
445 <  fInfo.SIM_uses_dipoles = useDipole;
445 >  fInfo.SIM_uses_charges = useCharges;
446 >  fInfo.SIM_uses_dipoles = useDipoles;
447    //fInfo.SIM_uses_dipoles = 0;
448 <  //fInfo.SIM_uses_RF = useReactionField;
449 <  fInfo.SIM_uses_RF = 0;
448 >  fInfo.SIM_uses_RF = useReactionField;
449 >  //fInfo.SIM_uses_RF = 0;
450    fInfo.SIM_uses_GB = useGB;
451    fInfo.SIM_uses_EAM = useEAM;
452  
453 <  excl = Exclude::getArray();
454 <
453 >  n_exclude = excludes->getSize();
454 >  excl = excludes->getFortranArray();
455 >  
456   #ifdef IS_MPI
457 <  n_global = mpiSim->getTotAtoms();
457 >  n_global = mpiSim->getNAtomsGlobal();
458   #else
459    n_global = n_atoms;
460   #endif
461 <
461 >  
462    isError = 0;
463 <
463 >  
464 >  getFortranGroupArrays(this, FglobalGroupMembership, mfact);
465 >  //it may not be a good idea to pass the address of first element in vector
466 >  //since c++ standard does not require vector to be stored continuously in meomory
467 >  //Most of the compilers will organize the memory of vector continuously
468    setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl,
469 <                  &nGlobalExcludes, globalExcludes, molMembershipArray,
470 <                  &isError );
469 >                  &nGlobalExcludes, globalExcludes, molMembershipArray,
470 >                  &mfact[0], &ngroup, &FglobalGroupMembership[0], &isError);
471  
472    if( isError ){
473 <
473 >    
474      sprintf( painCave.errMsg,
475 <             "There was an error setting the simulation information in fortran.\n" );
475 >             "There was an error setting the simulation information in fortran.\n" );
476      painCave.isFatal = 1;
477 +    painCave.severity = OOPSE_ERROR;
478      simError();
479    }
480 <
480 >  
481   #ifdef IS_MPI
482    sprintf( checkPointMsg,
483             "succesfully sent the simulation information to fortran.\n");
484    MPIcheckPoint();
485   #endif // is_mpi
486 <
486 >  
487    this->ndf = this->getNDF();
488    this->ndfRaw = this->getNDFraw();
489 +  this->ndfTrans = this->getNDFtranslational();
490 + }
491  
492 + void SimInfo::setDefaultRcut( double theRcut ){
493 +  
494 +  haveRcut = 1;
495 +  rCut = theRcut;
496 +  rList = rCut + 1.0;
497 +  
498 +  notifyFortranCutOffs( &rCut, &rSw, &rList );
499   }
500  
501 + void SimInfo::setDefaultRcut( double theRcut, double theRsw ){
502 +
503 +  rSw = theRsw;
504 +  setDefaultRcut( theRcut );
505 + }
506 +
507 +
508 + void SimInfo::checkCutOffs( void ){
509 +  
510 +  if( boxIsInit ){
511 +    
512 +    //we need to check cutOffs against the box
513 +    
514 +    if( rCut > maxCutoff ){
515 +      sprintf( painCave.errMsg,
516 +               "cutoffRadius is too large for the current periodic box.\n"
517 +               "\tCurrent Value of cutoffRadius = %G at time %G\n "
518 +               "\tThis is larger than half of at least one of the\n"
519 +               "\tperiodic box vectors.  Right now, the Box matrix is:\n"
520 +               "\n"
521 +               "\t[ %G %G %G ]\n"
522 +               "\t[ %G %G %G ]\n"
523 +               "\t[ %G %G %G ]\n",
524 +               rCut, currentTime,
525 +               Hmat[0][0], Hmat[0][1], Hmat[0][2],
526 +               Hmat[1][0], Hmat[1][1], Hmat[1][2],
527 +               Hmat[2][0], Hmat[2][1], Hmat[2][2]);
528 +      painCave.severity = OOPSE_ERROR;
529 +      painCave.isFatal = 1;
530 +      simError();
531 +    }    
532 +  } else {
533 +    // initialize this stuff before using it, OK?
534 +    sprintf( painCave.errMsg,
535 +             "Trying to check cutoffs without a box.\n"
536 +             "\tOOPSE should have better programmers than that.\n" );
537 +    painCave.severity = OOPSE_ERROR;
538 +    painCave.isFatal = 1;
539 +    simError();      
540 +  }
541 +  
542 + }
543 +
544 + void SimInfo::addProperty(GenericData* prop){
545 +
546 +  map<string, GenericData*>::iterator result;
547 +  result = properties.find(prop->getID());
548 +  
549 +  //we can't simply use  properties[prop->getID()] = prop,
550 +  //it will cause memory leak if we already contain a propery which has the same name of prop
551 +  
552 +  if(result != properties.end()){
553 +    
554 +    delete (*result).second;
555 +    (*result).second = prop;
556 +      
557 +  }
558 +  else{
559 +
560 +    properties[prop->getID()] = prop;
561 +
562 +  }
563 +    
564 + }
565 +
566 + GenericData* SimInfo::getProperty(const string& propName){
567 +
568 +  map<string, GenericData*>::iterator result;
569 +  
570 +  //string lowerCaseName = ();
571 +  
572 +  result = properties.find(propName);
573 +  
574 +  if(result != properties.end())
575 +    return (*result).second;  
576 +  else  
577 +    return NULL;  
578 + }
579 +
580 +
581 + void SimInfo::getFortranGroupArrays(SimInfo* info,
582 +                                    vector<int>& FglobalGroupMembership,
583 +                                    vector<double>& mfact){
584 +  
585 +  Molecule* myMols;
586 +  Atom** myAtoms;
587 +  int numAtom;
588 +  double mtot;
589 +  int numMol;
590 +  int numCutoffGroups;
591 +  CutoffGroup* myCutoffGroup;
592 +  vector<CutoffGroup*>::iterator iterCutoff;
593 +  Atom* cutoffAtom;
594 +  vector<Atom*>::iterator iterAtom;
595 +  int atomIndex;
596 +  double totalMass;
597 +  
598 +  mfact.clear();
599 +  FglobalGroupMembership.clear();
600 +  
601 +
602 +  // Fix the silly fortran indexing problem
603 + #ifdef IS_MPI
604 +  numAtom = mpiSim->getNAtomsGlobal();
605 + #else
606 +  numAtom = n_atoms;
607 + #endif
608 +  for (int i = 0; i < numAtom; i++)
609 +    FglobalGroupMembership.push_back(globalGroupMembership[i] + 1);
610 +  
611 +
612 +  myMols = info->molecules;
613 +  numMol = info->n_mol;
614 +  for(int i  = 0; i < numMol; i++){
615 +    numCutoffGroups = myMols[i].getNCutoffGroups();
616 +    for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff);
617 +        myCutoffGroup != NULL;
618 +        myCutoffGroup =myMols[i].nextCutoffGroup(iterCutoff)){
619 +
620 +      totalMass = myCutoffGroup->getMass();
621 +      
622 +      for(cutoffAtom = myCutoffGroup->beginAtom(iterAtom);
623 +          cutoffAtom != NULL;
624 +          cutoffAtom = myCutoffGroup->nextAtom(iterAtom)){
625 +        mfact.push_back(cutoffAtom->getMass()/totalMass);
626 +      }  
627 +    }
628 +  }
629 +
630 + }

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