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root/group/trunk/OOPSE/libmdtools/SimInfo.cpp
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Comparing trunk/OOPSE/libmdtools/SimInfo.cpp (file contents):
Revision 572 by mmeineke, Wed Jul 2 21:26:55 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 +  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 <  wrapMeSimInfo( this );
47 < }
68 >  haveCutoffGroups = false;
69  
70 < void SimInfo::setBox(double newBox[3]) {
70 >  excludes = Exclude::Instance();
71  
72 <  double smallestBoxL, maxCutoff;
52 <  int status;
53 <  int i;
72 >  myConfiguration = new SimState();
73  
74 <  for(i=0; i<9; i++) Hmat[i] = 0.0;;
74 >  has_minimizer = false;
75 >  the_minimizer =NULL;
76  
77 <  Hmat[0] = newBox[0];
58 <  Hmat[4] = newBox[1];
59 <  Hmat[8] = newBox[2];
77 >  ngroup = 0;
78  
79 <  calcHmatI();
80 <  calcBoxL();
79 >  wrapMeSimInfo( this );
80 > }
81  
64 –  setFortranBoxSize(Hmat, HmatI, &orthoRhombic);
82  
83 <  smallestBoxL = boxLx;
67 <  if (boxLy < smallestBoxL) smallestBoxL = boxLy;
68 <  if (boxLz < smallestBoxL) smallestBoxL = boxLz;
83 > SimInfo::~SimInfo(){
84  
85 <  maxCutoff = smallestBoxL / 2.0;
85 >  delete myConfiguration;
86  
87 <  if (rList > maxCutoff) {
88 <    sprintf( painCave.errMsg,
89 <             "New Box size is forcing neighborlist radius down to %lf\n",
90 <             maxCutoff );
91 <    painCave.isFatal = 0;
92 <    simError();
87 >  map<string, GenericData*>::iterator i;
88 >  
89 >  for(i = properties.begin(); i != properties.end(); i++)
90 >    delete (*i).second;
91 >  
92 > }
93  
94 <    rList = maxCutoff;
94 > void SimInfo::setBox(double newBox[3]) {
95 >  
96 >  int i, j;
97 >  double tempMat[3][3];
98  
99 <    sprintf( painCave.errMsg,
100 <             "New Box size is forcing cutoff radius down to %lf\n",
83 <             maxCutoff - 1.0 );
84 <    painCave.isFatal = 0;
85 <    simError();
99 >  for(i=0; i<3; i++)
100 >    for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
101  
102 <    rCut = rList - 1.0;
102 >  tempMat[0][0] = newBox[0];
103 >  tempMat[1][1] = newBox[1];
104 >  tempMat[2][2] = newBox[2];
105  
106 <    // list radius changed so we have to refresh the simulation structure.
90 <    refreshSim();
91 <  }
106 >  setBoxM( tempMat );
107  
93 –  if (rCut > maxCutoff) {
94 –    sprintf( painCave.errMsg,
95 –             "New Box size is forcing cutoff radius down to %lf\n",
96 –             maxCutoff );
97 –    painCave.isFatal = 0;
98 –    simError();
99 –
100 –    status = 0;
101 –    LJ_new_rcut(&rCut, &status);
102 –    if (status != 0) {
103 –      sprintf( painCave.errMsg,
104 –               "Error in recomputing LJ shifts based on new rcut\n");
105 –      painCave.isFatal = 1;
106 –      simError();
107 –    }
108 –  }
108   }
109  
110 < void SimInfo::setBoxM( double theBox[9] ){
110 > void SimInfo::setBoxM( double theBox[3][3] ){
111    
112 <  int i, status;
113 <  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 ]
116 >                         // [ 1 4 7 ]
117 >                         // [ 2 5 8 ]
118 >  double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
119  
120 <  for(i=0; i<9; i++) Hmat[i] = theBox[i];
121 <  calcHmatI();
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 >  
125    calcBoxL();
126 +  calcHmatInv();
127  
128 <  setFortranBoxSize(Hmat, HmatI, &orthoRhombic);
128 >  for(i=0; i < 3; i++) {
129 >    for (j=0; j < 3; j++) {
130 >      FortranHmat[3*j + i] = Hmat[i][j];
131 >      FortranHmatInv[3*j + i] = HmatInv[i][j];
132 >    }
133 >  }
134 >
135 >  setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic);
136  
137 <  smallestBoxL = boxLx;
138 <  if (boxLy < smallestBoxL) smallestBoxL = boxLy;
124 <  if (boxLz < smallestBoxL) smallestBoxL = boxLz;
137 > }
138 >
139  
140 <  maxCutoff = smallestBoxL / 2.0;
140 > void SimInfo::getBoxM (double theBox[3][3]) {
141  
142 <  if (rList > maxCutoff) {
143 <    sprintf( painCave.errMsg,
144 <             "New Box size is forcing neighborlist radius down to %lf\n",
145 <             maxCutoff );
132 <    painCave.isFatal = 0;
133 <    simError();
142 >  int i, j;
143 >  for(i=0; i<3; i++)
144 >    for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j];
145 > }
146  
135 –    rList = maxCutoff;
147  
148 <    sprintf( painCave.errMsg,
149 <             "New Box size is forcing cutoff radius down to %lf\n",
150 <             maxCutoff - 1.0 );
140 <    painCave.isFatal = 0;
141 <    simError();
148 > void SimInfo::scaleBox(double scale) {
149 >  double theBox[3][3];
150 >  int i, j;
151  
152 <    rCut = rList - 1.0;
152 >  // cerr << "Scaling box by " << scale << "\n";
153  
154 <    // list radius changed so we have to refresh the simulation structure.
155 <    refreshSim();
147 <  }
154 >  for(i=0; i<3; i++)
155 >    for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
156  
157 <  if (rCut > maxCutoff) {
150 <    sprintf( painCave.errMsg,
151 <             "New Box size is forcing cutoff radius down to %lf\n",
152 <             maxCutoff );
153 <    painCave.isFatal = 0;
154 <    simError();
157 >  setBoxM(theBox);
158  
159 <    status = 0;
157 <    LJ_new_rcut(&rCut, &status);
158 <    if (status != 0) {
159 <      sprintf( painCave.errMsg,
160 <               "Error in recomputing LJ shifts based on new rcut\n");
161 <      painCave.isFatal = 1;
162 <      simError();
163 <    }
164 <  }
165 < }
166 <
159 > }
160  
161 < void SimInfo::getBoxM (double theBox[9]) {
162 <
163 <  int i;
164 <  for(i=0; i<9; i++) theBox[i] = Hmat[i];
172 < }
173 <
174 <
175 < void SimInfo::calcHmatI( void ) {
176 <
177 <  double C[3][3];
178 <  double detHmat;
179 <  int i, j, k;
161 > void SimInfo::calcHmatInv( void ) {
162 >  
163 >  int oldOrtho;
164 >  int i,j;
165    double smallDiag;
166    double tol;
167    double sanity[3][3];
168  
169 <  // calculate the adjunct of Hmat;
169 >  invertMat3( Hmat, HmatInv );
170  
171 <  C[0][0] =  ( Hmat[4]*Hmat[8]) - (Hmat[7]*Hmat[5]);
187 <  C[1][0] = -( Hmat[1]*Hmat[8]) + (Hmat[7]*Hmat[2]);
188 <  C[2][0] =  ( Hmat[1]*Hmat[5]) - (Hmat[4]*Hmat[2]);
189 <
190 <  C[0][1] = -( Hmat[3]*Hmat[8]) + (Hmat[6]*Hmat[5]);
191 <  C[1][1] =  ( Hmat[0]*Hmat[8]) - (Hmat[6]*Hmat[2]);
192 <  C[2][1] = -( Hmat[0]*Hmat[5]) + (Hmat[3]*Hmat[2]);
193 <
194 <  C[0][2] =  ( Hmat[3]*Hmat[7]) - (Hmat[6]*Hmat[4]);
195 <  C[1][2] = -( Hmat[0]*Hmat[7]) + (Hmat[6]*Hmat[1]);
196 <  C[2][2] =  ( Hmat[0]*Hmat[4]) - (Hmat[3]*Hmat[1]);
197 <
198 <  // calcutlate the determinant of Hmat
171 >  // check to see if Hmat is orthorhombic
172    
173 <  detHmat = 0.0;
201 <  for(i=0; i<3; i++) detHmat += Hmat[i] * C[i][0];
173 >  oldOrtho = orthoRhombic;
174  
175 <  
176 <  // H^-1 = C^T / det(H)
177 <  
178 <  i=0;
207 <  for(j=0; j<3; j++){
208 <    for(k=0; k<3; k++){
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 <      HmatI[i] = C[j][k] / detHmat;
181 <      i++;
182 <    }
183 <  }
184 <
185 <  // sanity check
186 <
187 <  for(i=0; i<3; i++){
218 <    for(j=0; j<3; j++){
219 <      
220 <      sanity[i][j] = 0.0;
221 <      for(k=0; k<3; k++){
222 <        sanity[i][j] += Hmat[3*k+i] * HmatI[3*j+k];
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 ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0;
187 >        }        
188        }
189      }
190    }
191  
192 <  cerr << "sanity => \n"
228 <       << sanity[0][0] << "\t" << sanity[0][1] << "\t" << sanity [0][2] << "\n"
229 <       << sanity[1][0] << "\t" << sanity[1][1] << "\t" << sanity [1][2] << "\n"
230 <       << sanity[2][0] << "\t" << sanity[2][1] << "\t" << sanity [2][2]
231 <       << "\n";
192 >  if( oldOrtho != orthoRhombic ){
193      
194 <
195 <  // check to see if Hmat is orthorhombic
196 <  
197 <  smallDiag = Hmat[0];
198 <  if(smallDiag > Hmat[4]) smallDiag = Hmat[4];
199 <  if(smallDiag > Hmat[8]) smallDiag = Hmat[8];
200 <  tol = smallDiag * 1E-6;
201 <
202 <  orthoRhombic = 1;
203 <  for(i=0; (i<9) && orthoRhombic; i++){
243 <    
244 <    if( (i%4) ){ // ignore the diagonals (0, 4, and 8)
245 <      orthoRhombic = (Hmat[i] <= tol);
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 +    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    }
248 –    
218   }
219  
220   void SimInfo::calcBoxL( void ){
221  
222    double dx, dy, dz, dsq;
254 –  int i;
223  
224 <  // boxVol = h1 (dot) h2 (cross) h3
224 >  // boxVol = Determinant of Hmat
225  
226 <  boxVol = Hmat[0] * ( (Hmat[4]*Hmat[8]) - (Hmat[7]*Hmat[5]) )
259 <         + Hmat[1] * ( (Hmat[5]*Hmat[6]) - (Hmat[8]*Hmat[3]) )
260 <         + Hmat[2] * ( (Hmat[3]*Hmat[7]) - (Hmat[6]*Hmat[4]) );
226 >  boxVol = matDet3( Hmat );
227  
262 –
228    // boxLx
229    
230 <  dx = Hmat[0]; dy = Hmat[1]; dz = Hmat[2];
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[3]; dy = Hmat[4]; dz = Hmat[5];
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[6]; dy = Hmat[7]; dz = Hmat[8];
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 ){
296      // calc the scaled coordinates.
297 +  
298 +
299 +    matVecMul3(HmatInv, thePos, scaled);
300      
301      for(i=0; i<3; i++)
293 –      scaled[i] =
294 –        thePos[0]*HmatI[i] + thePos[1]*HmatI[i+3] + thePos[3]*HmatI[i+6];
295 –    
296 –    // wrap the scaled coordinates
297 –    
298 –    for(i=0; i<3; i++)
302        scaled[i] -= roundMe(scaled[i]);
303      
304      // calc the wrapped real coordinates from the wrapped scaled coordinates
305      
306 <    for(i=0; i<3; i++)
307 <      thePos[i] =
305 <        scaled[0]*Hmat[i] + scaled[1]*Hmat[i+3] + scaled[2]*Hmat[i+6];
306 >    matVecMul3(Hmat, scaled, thePos);
307 >
308    }
309    else{
310      // calc the scaled coordinates.
311      
312      for(i=0; i<3; i++)
313 <      scaled[i] = thePos[i]*HmatI[i*4];
313 >      scaled[i] = thePos[i]*HmatInv[i][i];
314      
315      // wrap the scaled coordinates
316      
# Line 318 | Line 320 | void SimInfo::wrapVector( double thePos[3] ){
320      // calc the wrapped real coordinates from the wrapped scaled coordinates
321      
322      for(i=0; i<3; i++)
323 <      thePos[i] = scaled[i]*Hmat[i*4];
323 >      thePos[i] = scaled[i]*Hmat[i][i];
324    }
325      
324 –    
326   }
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 355 | 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 <  
366 <  fInfo.rrf = 0.0;
367 <  fInfo.rt = 0.0;
427 >
428    fInfo.dielect = 0.0;
429  
430 <  fInfo.rlist = rList;
371 <  fInfo.rcut = rCut;
372 <
373 <  if( useDipole ){
374 <    fInfo.rrf = ecr;
375 <    fInfo.rt = ecr - est;
430 >  if( useDipoles ){
431      if( useReactionField )fInfo.dielect = dielectric;
432    }
433  
# Line 381 | 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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