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root/group/trunk/OOPSE/libmdtools/SimInfo.cpp
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Comparing trunk/OOPSE/libmdtools/SimInfo.cpp (file contents):
Revision 574 by gezelter, Tue Jul 8 20:56:10 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 <  wrapMeSimInfo( this );
47 < }
70 >  haveCutoffGroups = false;
71  
72 < void SimInfo::setBox(double newBox[3]) {
72 >  excludes = Exclude::Instance();
73  
74 <  double smallestBoxL, maxCutoff;
52 <  int status;
53 <  int i;
74 >  myConfiguration = new SimState();
75  
76 <  for(i=0; i<9; i++) Hmat[i] = 0.0;;
76 >  has_minimizer = false;
77 >  the_minimizer =NULL;
78  
79 <  Hmat[0] = newBox[0];
58 <  Hmat[4] = newBox[1];
59 <  Hmat[8] = newBox[2];
79 >  ngroup = 0;
80  
81 <  calcHmatI();
82 <  calcBoxL();
81 >  consMan = NULL;
82 >  
83 >  wrapMeSimInfo( this );
84 > }
85  
64 –  setFortranBoxSize(Hmat, HmatI, &orthoRhombic);
86  
87 <  smallestBoxL = boxLx;
67 <  if (boxLy < smallestBoxL) smallestBoxL = boxLy;
68 <  if (boxLz < smallestBoxL) smallestBoxL = boxLz;
87 > SimInfo::~SimInfo(){
88  
89 <  maxCutoff = smallestBoxL / 2.0;
89 >  delete myConfiguration;
90  
91 <  if (rList > maxCutoff) {
92 <    sprintf( painCave.errMsg,
93 <             "New Box size is forcing neighborlist radius down to %lf\n",
94 <             maxCutoff );
76 <    painCave.isFatal = 0;
77 <    simError();
91 >  map<string, GenericData*>::iterator i;
92 >  
93 >  for(i = properties.begin(); i != properties.end(); i++)
94 >    delete (*i).second;
95  
96 <    rList = maxCutoff;
96 >  if (!consMan)
97 >    delete consMan;  
98 > }
99  
100 <    sprintf( painCave.errMsg,
101 <             "New Box size is forcing cutoff radius down to %lf\n",
102 <             maxCutoff - 1.0 );
103 <    painCave.isFatal = 0;
85 <    simError();
100 > void SimInfo::setBox(double newBox[3]) {
101 >  
102 >  int i, j;
103 >  double tempMat[3][3];
104  
105 <    rCut = rList - 1.0;
105 >  for(i=0; i<3; i++)
106 >    for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
107  
108 <    // list radius changed so we have to refresh the simulation structure.
109 <    refreshSim();
110 <  }
108 >  tempMat[0][0] = newBox[0];
109 >  tempMat[1][1] = newBox[1];
110 >  tempMat[2][2] = newBox[2];
111  
112 <  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();
112 >  setBoxM( tempMat );
113  
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 –  }
114   }
115  
116 < void SimInfo::setBoxM( double theBox[9] ){
116 > void SimInfo::setBoxM( double theBox[3][3] ){
117    
118 <  int i, status;
119 <  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 ]
122 >                         // [ 1 4 7 ]
123 >                         // [ 2 5 8 ]
124 >  double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
125  
126 <  for(i=0; i<9; i++) Hmat[i] = theBox[i];
127 <  calcHmatI();
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 >  
131    calcBoxL();
132 +  calcHmatInv();
133  
134 <  setFortranBoxSize(Hmat, HmatI, &orthoRhombic);
135 <
136 <  smallestBoxL = boxLx;
137 <  if (boxLy < smallestBoxL) smallestBoxL = boxLy;
124 <  if (boxLz < smallestBoxL) smallestBoxL = boxLz;
125 <
126 <  maxCutoff = smallestBoxL / 2.0;
127 <
128 <  if (rList > maxCutoff) {
129 <    sprintf( painCave.errMsg,
130 <             "New Box size is forcing neighborlist radius down to %lf\n",
131 <             maxCutoff );
132 <    painCave.isFatal = 0;
133 <    simError();
134 <
135 <    rList = maxCutoff;
136 <
137 <    sprintf( painCave.errMsg,
138 <             "New Box size is forcing cutoff radius down to %lf\n",
139 <             maxCutoff - 1.0 );
140 <    painCave.isFatal = 0;
141 <    simError();
142 <
143 <    rCut = rList - 1.0;
144 <
145 <    // list radius changed so we have to refresh the simulation structure.
146 <    refreshSim();
147 <  }
148 <
149 <  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();
155 <
156 <    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();
134 >  for(i=0; i < 3; i++) {
135 >    for (j=0; j < 3; j++) {
136 >      FortranHmat[3*j + i] = Hmat[i][j];
137 >      FortranHmatInv[3*j + i] = HmatInv[i][j];
138      }
139    }
140 +
141 +  setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic);
142 +
143   }
144  
145  
146 < void SimInfo::getBoxM (double theBox[9]) {
146 > void SimInfo::getBoxM (double theBox[3][3]) {
147  
148 <  int i;
149 <  for(i=0; i<9; i++) theBox[i] = Hmat[i];
148 >  int i, j;
149 >  for(i=0; i<3; i++)
150 >    for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j];
151   }
152  
153  
154   void SimInfo::scaleBox(double scale) {
155 <  double theBox[9];
156 <  int i;
155 >  double theBox[3][3];
156 >  int i, j;
157  
158 <  for(i=0; i<9; i++) theBox[i] = Hmat[i]*scale;
158 >  // cerr << "Scaling box by " << scale << "\n";
159  
160 +  for(i=0; i<3; i++)
161 +    for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
162 +
163    setBoxM(theBox);
164  
165   }
166  
167 < void SimInfo::calcHmatI( void ) {
168 <
169 <  double C[3][3];
170 <  double detHmat;
189 <  int i, j, k;
167 > void SimInfo::calcHmatInv( void ) {
168 >  
169 >  int oldOrtho;
170 >  int i,j;
171    double smallDiag;
172    double tol;
173    double sanity[3][3];
174  
175 <  // calculate the adjunct of Hmat;
175 >  invertMat3( Hmat, HmatInv );
176  
177 <  C[0][0] =  ( Hmat[4]*Hmat[8]) - (Hmat[7]*Hmat[5]);
197 <  C[1][0] = -( Hmat[1]*Hmat[8]) + (Hmat[7]*Hmat[2]);
198 <  C[2][0] =  ( Hmat[1]*Hmat[5]) - (Hmat[4]*Hmat[2]);
199 <
200 <  C[0][1] = -( Hmat[3]*Hmat[8]) + (Hmat[6]*Hmat[5]);
201 <  C[1][1] =  ( Hmat[0]*Hmat[8]) - (Hmat[6]*Hmat[2]);
202 <  C[2][1] = -( Hmat[0]*Hmat[5]) + (Hmat[3]*Hmat[2]);
203 <
204 <  C[0][2] =  ( Hmat[3]*Hmat[7]) - (Hmat[6]*Hmat[4]);
205 <  C[1][2] = -( Hmat[0]*Hmat[7]) + (Hmat[6]*Hmat[1]);
206 <  C[2][2] =  ( Hmat[0]*Hmat[4]) - (Hmat[3]*Hmat[1]);
207 <
208 <  // calcutlate the determinant of Hmat
177 >  // check to see if Hmat is orthorhombic
178    
179 <  detHmat = 0.0;
211 <  for(i=0; i<3; i++) detHmat += Hmat[i] * C[i][0];
179 >  oldOrtho = orthoRhombic;
180  
181 <  
182 <  // H^-1 = C^T / det(H)
183 <  
184 <  i=0;
217 <  for(j=0; j<3; j++){
218 <    for(k=0; k<3; k++){
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 <      HmatI[i] = C[j][k] / detHmat;
187 <      i++;
188 <    }
189 <  }
190 <
191 <  // sanity check
192 <
193 <  for(i=0; i<3; i++){
228 <    for(j=0; j<3; j++){
229 <      
230 <      sanity[i][j] = 0.0;
231 <      for(k=0; k<3; k++){
232 <        sanity[i][j] += Hmat[3*k+i] * HmatI[3*j+k];
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 ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0;
193 >        }        
194        }
195      }
196    }
197  
198 <  cerr << "sanity => \n"
238 <       << sanity[0][0] << "\t" << sanity[0][1] << "\t" << sanity [0][2] << "\n"
239 <       << sanity[1][0] << "\t" << sanity[1][1] << "\t" << sanity [1][2] << "\n"
240 <       << sanity[2][0] << "\t" << sanity[2][1] << "\t" << sanity [2][2]
241 <       << "\n";
198 >  if( oldOrtho != orthoRhombic ){
199      
200 <
201 <  // check to see if Hmat is orthorhombic
202 <  
203 <  smallDiag = Hmat[0];
204 <  if(smallDiag > Hmat[4]) smallDiag = Hmat[4];
205 <  if(smallDiag > Hmat[8]) smallDiag = Hmat[8];
206 <  tol = smallDiag * 1E-6;
207 <
208 <  orthoRhombic = 1;
209 <  for(i=0; (i<9) && orthoRhombic; i++){
253 <    
254 <    if( (i%4) ){ // ignore the diagonals (0, 4, and 8)
255 <      orthoRhombic = (Hmat[i] <= tol);
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 +    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    }
258 –    
224   }
225  
226   void SimInfo::calcBoxL( void ){
227  
228    double dx, dy, dz, dsq;
264 –  int i;
229  
230 <  // boxVol = h1 (dot) h2 (cross) h3
230 >  // boxVol = Determinant of Hmat
231  
232 <  boxVol = Hmat[0] * ( (Hmat[4]*Hmat[8]) - (Hmat[7]*Hmat[5]) )
269 <         + Hmat[1] * ( (Hmat[5]*Hmat[6]) - (Hmat[8]*Hmat[3]) )
270 <         + Hmat[2] * ( (Hmat[3]*Hmat[7]) - (Hmat[6]*Hmat[4]) );
232 >  boxVol = matDet3( Hmat );
233  
272 –
234    // boxLx
235    
236 <  dx = Hmat[0]; dy = Hmat[1]; dz = Hmat[2];
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[3]; dy = Hmat[4]; dz = Hmat[5];
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[6]; dy = Hmat[7]; dz = Hmat[8];
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 ){
302      // calc the scaled coordinates.
303 +  
304 +
305 +    matVecMul3(HmatInv, thePos, scaled);
306      
307      for(i=0; i<3; i++)
303 –      scaled[i] =
304 –        thePos[0]*HmatI[i] + thePos[1]*HmatI[i+3] + thePos[3]*HmatI[i+6];
305 –    
306 –    // wrap the scaled coordinates
307 –    
308 –    for(i=0; i<3; i++)
308        scaled[i] -= roundMe(scaled[i]);
309      
310      // calc the wrapped real coordinates from the wrapped scaled coordinates
311      
312 <    for(i=0; i<3; i++)
313 <      thePos[i] =
315 <        scaled[0]*Hmat[i] + scaled[1]*Hmat[i+3] + scaled[2]*Hmat[i+6];
312 >    matVecMul3(Hmat, scaled, thePos);
313 >
314    }
315    else{
316      // calc the scaled coordinates.
317      
318      for(i=0; i<3; i++)
319 <      scaled[i] = thePos[i]*HmatI[i*4];
319 >      scaled[i] = thePos[i]*HmatInv[i][i];
320      
321      // wrap the scaled coordinates
322      
# Line 328 | Line 326 | void SimInfo::wrapVector( double thePos[3] ){
326      // calc the wrapped real coordinates from the wrapped scaled coordinates
327      
328      for(i=0; i<3; i++)
329 <      thePos[i] = scaled[i]*Hmat[i*4];
329 >      thePos[i] = scaled[i]*Hmat[i][i];
330    }
331      
334 –    
332   }
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 365 | 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 <  
376 <  fInfo.rrf = 0.0;
377 <  fInfo.rt = 0.0;
433 >
434    fInfo.dielect = 0.0;
435  
436 <  fInfo.rlist = rList;
381 <  fInfo.rcut = rCut;
382 <
383 <  if( useDipole ){
384 <    fInfo.rrf = ecr;
385 <    fInfo.rt = ecr - est;
436 >  if( useDipoles ){
437      if( useReactionField )fInfo.dielect = dielectric;
438    }
439  
# Line 391 | 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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