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root/group/trunk/OOPSE/libmdtools/SimInfo.cpp
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Comparing trunk/OOPSE/libmdtools/SimInfo.cpp (file contents):
Revision 588 by gezelter, Thu Jul 10 17:10:56 2003 UTC vs.
Revision 1144 by tim, Sat May 1 18:52:38 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;
46 +  est = 0.0;
47  
48 +  haveRcut = 0;
49 +  haveEcr = 0;
50 +  boxIsInit = 0;
51 +  
52 +  resetTime = 1e99;
53 +
54 +  orthoRhombic = 0;
55 +  orthoTolerance = 1E-6;
56 +  useInitXSstate = true;
57 +
58    usePBC = 0;
59    useLJ = 0;
60    useSticky = 0;
61 <  useDipole = 0;
61 >  useCharges = 0;
62 >  useDipoles = 0;
63    useReactionField = 0;
64    useGB = 0;
65    useEAM = 0;
66 +  useMolecularCutoffs = 0;
67  
68 +  excludes = Exclude::Instance();
69 +
70 +  myConfiguration = new SimState();
71 +
72 +  has_minimizer = false;
73 +  the_minimizer =NULL;
74 +
75 +  ngroup = 0;
76 +
77    wrapMeSimInfo( this );
78   }
79  
80 +
81 + SimInfo::~SimInfo(){
82 +
83 +  delete myConfiguration;
84 +
85 +  map<string, GenericData*>::iterator i;
86 +  
87 +  for(i = properties.begin(); i != properties.end(); i++)
88 +    delete (*i).second;
89 +  
90 + }
91 +
92   void SimInfo::setBox(double newBox[3]) {
93    
94    int i, j;
# Line 64 | Line 107 | void SimInfo::setBoxM( double theBox[3][3] ){
107  
108   void SimInfo::setBoxM( double theBox[3][3] ){
109    
110 <  int i, j, status;
68 <  double smallestBoxL, maxCutoff;
110 >  int i, j;
111    double FortranHmat[9]; // to preserve compatibility with Fortran the
112                           // ordering in the array is as follows:
113                           // [ 0 3 6 ]
# Line 73 | Line 115 | void SimInfo::setBoxM( double theBox[3][3] ){
115                           // [ 2 5 8 ]
116    double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
117  
118 +  if( !boxIsInit ) boxIsInit = 1;
119  
120    for(i=0; i < 3; i++)
121      for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
122    
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 –
123    calcBoxL();
124    calcHmatInv();
125  
# Line 93 | Line 130 | void SimInfo::setBoxM( double theBox[3][3] ){
130      }
131    }
132  
133 <  setFortranBoxSize(FortranHmat, FortranHmatI, &orthoRhombic);
133 >  setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic);
134  
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 –  }
135   }
136  
137  
# Line 153 | Line 147 | void SimInfo::scaleBox(double scale) {
147    double theBox[3][3];
148    int i, j;
149  
150 <  cerr << "Scaling box by " << scale << "\n";
150 >  // cerr << "Scaling box by " << scale << "\n";
151  
152    for(i=0; i<3; i++)
153      for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
# Line 163 | Line 157 | void SimInfo::calcHmatInv( void ) {
157   }
158  
159   void SimInfo::calcHmatInv( void ) {
160 <
160 >  
161 >  int oldOrtho;
162 >  int i,j;
163    double smallDiag;
164    double tol;
165    double sanity[3][3];
166  
167    invertMat3( Hmat, HmatInv );
168  
173 –  // Check the inverse to make sure it is sane:
174 –
175 –  matMul3( Hmat, HmatInv, sanity );
176 –
177 –  cerr << "sanity => \n"
178 –       << sanity[0][0] << "\t" << sanity[0][1] << "\t" << sanity [0][2] << "\n"
179 –       << sanity[1][0] << "\t" << sanity[1][1] << "\t" << sanity [1][2] << "\n"
180 –       << sanity[2][0] << "\t" << sanity[2][1] << "\t" << sanity [2][2]
181 –       << "\n";
182 –    
169    // check to see if Hmat is orthorhombic
170    
171 <  smallDiag = Hmat[0][0];
186 <  if(smallDiag > Hmat[1][1]) smallDiag = Hmat[1][1];
187 <  if(smallDiag > Hmat[2][2]) smallDiag = Hmat[2][2];
188 <  tol = smallDiag * 1E-6;
171 >  oldOrtho = orthoRhombic;
172  
173 +  smallDiag = fabs(Hmat[0][0]);
174 +  if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]);
175 +  if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]);
176 +  tol = smallDiag * orthoTolerance;
177 +
178    orthoRhombic = 1;
179    
180    for (i = 0; i < 3; i++ ) {
181      for (j = 0 ; j < 3; j++) {
182        if (i != j) {
183          if (orthoRhombic) {
184 <          if (Hmat[i][j] >= tol) orthoRhombic = 0;
184 >          if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0;
185          }        
186        }
187      }
200 –  }
201 – }
202 –
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]);
188    }
189  
190 <  return determinant;
191 < }
192 <
193 < void SimInfo::invertMat3(double a[3][3], double b[3][3]) {
194 <  
195 <  int  i, j, k, l, m, n;
196 <  double determinant;
197 <
198 <  determinant = matDet3( a );
199 <
200 <  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;
190 >  if( oldOrtho != orthoRhombic ){
191 >    
192 >    if( orthoRhombic ){
193 >      sprintf( painCave.errMsg,
194 >               "OOPSE is switching from the default Non-Orthorhombic\n"
195 >               "\tto the faster Orthorhombic periodic boundary computations.\n"
196 >               "\tThis is usually a good thing, but if you wan't the\n"
197 >               "\tNon-Orthorhombic computations, make the orthoBoxTolerance\n"
198 >               "\tvariable ( currently set to %G ) smaller.\n",
199 >               orthoTolerance);
200 >      simError();
201      }
202 +    else {
203 +      sprintf( painCave.errMsg,
204 +               "OOPSE is switching from the faster Orthorhombic to the more\n"
205 +               "\tflexible Non-Orthorhombic periodic boundary computations.\n"
206 +               "\tThis is usually because the box has deformed under\n"
207 +               "\tNPTf integration. If you wan't to live on the edge with\n"
208 +               "\tthe Orthorhombic computations, make the orthoBoxTolerance\n"
209 +               "\tvariable ( currently set to %G ) larger.\n",
210 +               orthoTolerance);
211 +      simError();
212 +    }
213    }
214   }
215  
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 –  
216   void SimInfo::calcBoxL( void ){
217  
218    double dx, dy, dz, dsq;
278 –  int i;
219  
220    // boxVol = Determinant of Hmat
221  
# Line 285 | Line 225 | void SimInfo::calcBoxL( void ){
225    
226    dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
227    dsq = dx*dx + dy*dy + dz*dz;
228 <  boxLx = sqrt( dsq );
228 >  boxL[0] = sqrt( dsq );
229 >  //maxCutoff = 0.5 * boxL[0];
230  
231    // boxLy
232    
233    dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
234    dsq = dx*dx + dy*dy + dz*dz;
235 <  boxLy = sqrt( dsq );
235 >  boxL[1] = sqrt( dsq );
236 >  //if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
237  
238 +
239    // boxLz
240    
241    dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
242    dsq = dx*dx + dy*dy + dz*dz;
243 <  boxLz = sqrt( dsq );
243 >  boxL[2] = sqrt( dsq );
244 >  //if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
245 >
246 >  //calculate the max cutoff
247 >  maxCutoff =  calcMaxCutOff();
248    
249 +  checkCutOffs();
250 +
251   }
252  
253  
254 + double SimInfo::calcMaxCutOff(){
255 +
256 +  double ri[3], rj[3], rk[3];
257 +  double rij[3], rjk[3], rki[3];
258 +  double minDist;
259 +
260 +  ri[0] = Hmat[0][0];
261 +  ri[1] = Hmat[1][0];
262 +  ri[2] = Hmat[2][0];
263 +
264 +  rj[0] = Hmat[0][1];
265 +  rj[1] = Hmat[1][1];
266 +  rj[2] = Hmat[2][1];
267 +
268 +  rk[0] = Hmat[0][2];
269 +  rk[1] = Hmat[1][2];
270 +  rk[2] = Hmat[2][2];
271 +    
272 +  crossProduct3(ri, rj, rij);
273 +  distXY = dotProduct3(rk,rij) / norm3(rij);
274 +
275 +  crossProduct3(rj,rk, rjk);
276 +  distYZ = dotProduct3(ri,rjk) / norm3(rjk);
277 +
278 +  crossProduct3(rk,ri, rki);
279 +  distZX = dotProduct3(rj,rki) / norm3(rki);
280 +
281 +  minDist = min(min(distXY, distYZ), distZX);
282 +  return minDist/2;
283 +  
284 + }
285 +
286   void SimInfo::wrapVector( double thePos[3] ){
287  
288 <  int i, j, k;
288 >  int i;
289    double scaled[3];
290  
291    if( !orthoRhombic ){
# Line 342 | Line 323 | int SimInfo::getNDF(){
323  
324  
325   int SimInfo::getNDF(){
326 <  int ndf_local, ndf;
326 >  int ndf_local;
327 >
328 >  ndf_local = 0;
329    
330 <  ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints;
330 >  for(int i = 0; i < integrableObjects.size(); i++){
331 >    ndf_local += 3;
332 >    if (integrableObjects[i]->isDirectional()) {
333 >      if (integrableObjects[i]->isLinear())
334 >        ndf_local += 2;
335 >      else
336 >        ndf_local += 3;
337 >    }
338 >  }
339  
340 +  // n_constraints is local, so subtract them on each processor:
341 +
342 +  ndf_local -= n_constraints;
343 +
344   #ifdef IS_MPI
345    MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
346   #else
347    ndf = ndf_local;
348   #endif
349  
350 <  ndf = ndf - 3;
350 >  // nZconstraints is global, as are the 3 COM translations for the
351 >  // entire system:
352  
353 +  ndf = ndf - 3 - nZconstraints;
354 +
355    return ndf;
356   }
357  
358   int SimInfo::getNDFraw() {
359 <  int ndfRaw_local, ndfRaw;
359 >  int ndfRaw_local;
360  
361    // Raw degrees of freedom that we have to set
362 <  ndfRaw_local = 3 * n_atoms + 3 * n_oriented;
363 <  
362 >  ndfRaw_local = 0;
363 >
364 >  for(int i = 0; i < integrableObjects.size(); i++){
365 >    ndfRaw_local += 3;
366 >    if (integrableObjects[i]->isDirectional()) {
367 >       if (integrableObjects[i]->isLinear())
368 >        ndfRaw_local += 2;
369 >      else
370 >        ndfRaw_local += 3;
371 >    }
372 >  }
373 >    
374   #ifdef IS_MPI
375    MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
376   #else
# Line 371 | Line 379 | int SimInfo::getNDFraw() {
379  
380    return ndfRaw;
381   }
382 <
382 >
383 > int SimInfo::getNDFtranslational() {
384 >  int ndfTrans_local;
385 >
386 >  ndfTrans_local = 3 * integrableObjects.size() - n_constraints;
387 >
388 >
389 > #ifdef IS_MPI
390 >  MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
391 > #else
392 >  ndfTrans = ndfTrans_local;
393 > #endif
394 >
395 >  ndfTrans = ndfTrans - 3 - nZconstraints;
396 >
397 >  return ndfTrans;
398 > }
399 >
400 > int SimInfo::getTotIntegrableObjects() {
401 >  int nObjs_local;
402 >  int nObjs;
403 >
404 >  nObjs_local =  integrableObjects.size();
405 >
406 >
407 > #ifdef IS_MPI
408 >  MPI_Allreduce(&nObjs_local,&nObjs,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
409 > #else
410 >  nObjs = nObjs_local;
411 > #endif
412 >
413 >
414 >  return nObjs;
415 > }
416 >
417   void SimInfo::refreshSim(){
418  
419    simtype fInfo;
420    int isError;
421    int n_global;
422    int* excl;
423 <  
382 <  fInfo.rrf = 0.0;
383 <  fInfo.rt = 0.0;
423 >
424    fInfo.dielect = 0.0;
425  
426 <  fInfo.rlist = rList;
387 <  fInfo.rcut = rCut;
388 <
389 <  if( useDipole ){
390 <    fInfo.rrf = ecr;
391 <    fInfo.rt = ecr - est;
426 >  if( useDipoles ){
427      if( useReactionField )fInfo.dielect = dielectric;
428    }
429  
# Line 397 | Line 432 | void SimInfo::refreshSim(){
432    fInfo.SIM_uses_LJ = useLJ;
433    fInfo.SIM_uses_sticky = useSticky;
434    //fInfo.SIM_uses_sticky = 0;
435 <  fInfo.SIM_uses_dipoles = useDipole;
435 >  fInfo.SIM_uses_charges = useCharges;
436 >  fInfo.SIM_uses_dipoles = useDipoles;
437    //fInfo.SIM_uses_dipoles = 0;
438 <  //fInfo.SIM_uses_RF = useReactionField;
439 <  fInfo.SIM_uses_RF = 0;
438 >  fInfo.SIM_uses_RF = useReactionField;
439 >  //fInfo.SIM_uses_RF = 0;
440    fInfo.SIM_uses_GB = useGB;
441    fInfo.SIM_uses_EAM = useEAM;
442  
443 <  excl = Exclude::getArray();
444 <
443 >  n_exclude = excludes->getSize();
444 >  excl = excludes->getFortranArray();
445 >  
446   #ifdef IS_MPI
447    n_global = mpiSim->getTotAtoms();
448   #else
# Line 414 | Line 451 | void SimInfo::refreshSim(){
451  
452    isError = 0;
453  
454 + getFortranGroupArray(this, mfact, ngroup, groupList, groupStart);
455 +
456    setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl,
457 <                  &nGlobalExcludes, globalExcludes, molMembershipArray,
458 <                  &isError );
457 >                                    &nGlobalExcludes, globalExcludes, molMembershipArray,
458 >                                    &mfact[0], &ngroup, &groupList[0], &groupStart[0], &isError );
459  
460    if( isError ){
461  
# Line 434 | Line 473 | void SimInfo::refreshSim(){
473  
474    this->ndf = this->getNDF();
475    this->ndfRaw = this->getNDFraw();
476 +  this->ndfTrans = this->getNDFtranslational();
477 + }
478  
479 + void SimInfo::setDefaultRcut( double theRcut ){
480 +
481 +  haveRcut = 1;
482 +  rCut = theRcut;
483 +
484 +  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
485 +
486 +  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
487   }
488  
489 + void SimInfo::setDefaultEcr( double theEcr ){
490 +
491 +  haveEcr = 1;
492 +  ecr = theEcr;
493 +  
494 +  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
495 +
496 +  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
497 + }
498 +
499 + void SimInfo::setDefaultEcr( double theEcr, double theEst ){
500 +
501 +  est = theEst;
502 +  setDefaultEcr( theEcr );
503 + }
504 +
505 +
506 + void SimInfo::checkCutOffs( void ){
507 +  
508 +  if( boxIsInit ){
509 +    
510 +    //we need to check cutOffs against the box
511 +    
512 +    if( rCut > maxCutoff ){
513 +      sprintf( painCave.errMsg,
514 +               "LJrcut is too large for the current periodic box.\n"
515 +               "\tCurrent Value of LJrcut = %G at time %G\n "
516 +               "\tThis is larger than half of at least one of the\n"
517 +               "\tperiodic box vectors.  Right now, the Box matrix is:\n"
518 +               "\n"
519 +               "\t[ %G %G %G ]\n"
520 +               "\t[ %G %G %G ]\n"
521 +               "\t[ %G %G %G ]\n",
522 +               rCut, currentTime,
523 +               Hmat[0][0], Hmat[0][1], Hmat[0][2],
524 +               Hmat[1][0], Hmat[1][1], Hmat[1][2],
525 +               Hmat[2][0], Hmat[2][1], Hmat[2][2]);
526 +      painCave.isFatal = 1;
527 +      simError();
528 +    }
529 +    
530 +    if( haveEcr ){
531 +      if( ecr > maxCutoff ){
532 +        sprintf( painCave.errMsg,
533 +                 "electrostaticCutoffRadius is too large for the current\n"
534 +                 "\tperiodic box.\n\n"
535 +                 "\tCurrent Value of ECR = %G at time %G\n "
536 +                 "\tThis is larger than half of at least one of the\n"
537 +                 "\tperiodic box vectors.  Right now, the Box matrix is:\n"
538 +                 "\n"
539 +                 "\t[ %G %G %G ]\n"
540 +                 "\t[ %G %G %G ]\n"
541 +                 "\t[ %G %G %G ]\n",
542 +                 ecr, currentTime,
543 +                 Hmat[0][0], Hmat[0][1], Hmat[0][2],
544 +                 Hmat[1][0], Hmat[1][1], Hmat[1][2],
545 +                 Hmat[2][0], Hmat[2][1], Hmat[2][2]);
546 +        painCave.isFatal = 1;
547 +        simError();
548 +      }
549 +    }
550 +  } else {
551 +    // initialize this stuff before using it, OK?
552 +    sprintf( painCave.errMsg,
553 +             "Trying to check cutoffs without a box.\n"
554 +             "\tOOPSE should have better programmers than that.\n" );
555 +    painCave.isFatal = 1;
556 +    simError();      
557 +  }
558 +  
559 + }
560 +
561 + void SimInfo::addProperty(GenericData* prop){
562 +
563 +  map<string, GenericData*>::iterator result;
564 +  result = properties.find(prop->getID());
565 +  
566 +  //we can't simply use  properties[prop->getID()] = prop,
567 +  //it will cause memory leak if we already contain a propery which has the same name of prop
568 +  
569 +  if(result != properties.end()){
570 +    
571 +    delete (*result).second;
572 +    (*result).second = prop;
573 +      
574 +  }
575 +  else{
576 +
577 +    properties[prop->getID()] = prop;
578 +
579 +  }
580 +    
581 + }
582 +
583 + GenericData* SimInfo::getProperty(const string& propName){
584 +
585 +  map<string, GenericData*>::iterator result;
586 +  
587 +  //string lowerCaseName = ();
588 +  
589 +  result = properties.find(propName);
590 +  
591 +  if(result != properties.end())
592 +    return (*result).second;  
593 +  else  
594 +    return NULL;  
595 + }
596 +
597 +
598 + void getFortranGroupArray(SimInfo* info, vector<double>& mfact, int& ngroup,
599 +                                                          vector<int>& groupList, vector<int>& groupStart){
600 +  Molecule* mol;
601 +  int numAtom;
602 +  int curIndex;
603 +
604 +  mfact.clear();
605 +  groupList.clear();
606 +  groupStart.clear();
607 +
608 +  //Be careful, fortran array begin at 1
609 +  curIndex = 1;
610 +    
611 +  if(info->useMolecularCutoffs){
612 +    //if using molecular cutoff
613 +    ngroup = info->n_mol;
614 +
615 +    for(int i = 0; i < ngroup; i ++){
616 +      mol = &(info->molecules[i]);
617 +      numAtom = mol->getNAtoms();
618 +      
619 +      for(int j=0; j < numAtom; j++){
620 + #ifdef IS_MPI
621 +        groupList.push_back((info->atoms[i])->getGlobalIndex() + 1);
622 + #else
623 +        groupList.push_back((info->atoms[i])->getIndex() + 1);
624 + #endif
625 +      }//for(int j=0; j < numAtom; j++)
626 +            
627 +      groupStart.push_back(curIndex);
628 +      curIndex += numAtom;
629 +      
630 +    }//end for(int i =0 ; i < ngroup; i++)    
631 +  }
632 +  else{
633 +    //using atomic cutoff, every single atom is just a group
634 +    ngroup = info->n_atoms;
635 +    for(int i =0 ; i < ngroup; i++){
636 +      groupStart.push_back(curIndex++);
637 +
638 + #ifdef IS_MPI
639 +      groupList.push_back((info->atoms[i])->getGlobalIndex() + 1);
640 + #else
641 +      groupList.push_back((info->atoms[i])->getIndex() + 1);
642 + #endif
643 +
644 +    }//end for(int i =0 ; i < ngroup; i++)
645 +
646 +  }//end if (info->useMolecularCutoffs)
647 +
648 + }

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