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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 1154 by gezelter, Tue May 11 16:00:22 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  
66 <  wrapMeSimInfo( this );
47 < }
66 >  excludes = Exclude::Instance();
67  
68 < void SimInfo::setBox(double newBox[3]) {
68 >  myConfiguration = new SimState();
69  
70 <  double smallestBoxL, maxCutoff;
71 <  int status;
53 <  int i;
70 >  has_minimizer = false;
71 >  the_minimizer =NULL;
72  
73 <  for(i=0; i<9; i++) Hmat[i] = 0.0;;
73 >  ngroup = 0;
74  
75 <  Hmat[0] = newBox[0];
76 <  Hmat[4] = newBox[1];
59 <  Hmat[8] = newBox[2];
75 >  wrapMeSimInfo( this );
76 > }
77  
61 –  calcHmatI();
62 –  calcBoxL();
78  
79 <  setFortranBoxSize(Hmat, HmatI, &orthoRhombic);
79 > SimInfo::~SimInfo(){
80  
81 <  smallestBoxL = boxLx;
67 <  if (boxLy < smallestBoxL) smallestBoxL = boxLy;
68 <  if (boxLz < smallestBoxL) smallestBoxL = boxLz;
81 >  delete myConfiguration;
82  
83 <  maxCutoff = smallestBoxL / 2.0;
83 >  map<string, GenericData*>::iterator i;
84 >  
85 >  for(i = properties.begin(); i != properties.end(); i++)
86 >    delete (*i).second;
87 >  
88 > }
89  
90 <  if (rList > maxCutoff) {
91 <    sprintf( painCave.errMsg,
92 <             "New Box size is forcing neighborlist radius down to %lf\n",
93 <             maxCutoff );
76 <    painCave.isFatal = 0;
77 <    simError();
90 > void SimInfo::setBox(double newBox[3]) {
91 >  
92 >  int i, j;
93 >  double tempMat[3][3];
94  
95 <    rList = maxCutoff;
95 >  for(i=0; i<3; i++)
96 >    for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
97  
98 <    sprintf( painCave.errMsg,
99 <             "New Box size is forcing cutoff radius down to %lf\n",
100 <             maxCutoff - 1.0 );
84 <    painCave.isFatal = 0;
85 <    simError();
98 >  tempMat[0][0] = newBox[0];
99 >  tempMat[1][1] = newBox[1];
100 >  tempMat[2][2] = newBox[2];
101  
102 <    rCut = rList - 1.0;
102 >  setBoxM( tempMat );
103  
89 –    // list radius changed so we have to refresh the simulation structure.
90 –    refreshSim();
91 –  }
92 –
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 –  }
104   }
105  
106 < void SimInfo::setBoxM( double theBox[9] ){
106 > void SimInfo::setBoxM( double theBox[3][3] ){
107    
108 <  int i, status;
109 <  double smallestBoxL, maxCutoff;
108 >  int i, j;
109 >  double FortranHmat[9]; // to preserve compatibility with Fortran the
110 >                         // ordering in the array is as follows:
111 >                         // [ 0 3 6 ]
112 >                         // [ 1 4 7 ]
113 >                         // [ 2 5 8 ]
114 >  double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
115  
116 <  for(i=0; i<9; i++) Hmat[i] = theBox[i];
117 <  calcHmatI();
116 >  if( !boxIsInit ) boxIsInit = 1;
117 >
118 >  for(i=0; i < 3; i++)
119 >    for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
120 >  
121    calcBoxL();
122 +  calcHmatInv();
123  
124 <  setFortranBoxSize(Hmat, HmatI, &orthoRhombic);
125 <
126 <  smallestBoxL = boxLx;
127 <  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();
124 >  for(i=0; i < 3; i++) {
125 >    for (j=0; j < 3; j++) {
126 >      FortranHmat[3*j + i] = Hmat[i][j];
127 >      FortranHmatInv[3*j + i] = HmatInv[i][j];
128      }
129    }
130 +
131 +  setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic);
132 +
133   }
134  
135  
136 < void SimInfo::getBoxM (double theBox[9]) {
136 > void SimInfo::getBoxM (double theBox[3][3]) {
137  
138 <  int i;
139 <  for(i=0; i<9; i++) theBox[i] = Hmat[i];
138 >  int i, j;
139 >  for(i=0; i<3; i++)
140 >    for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j];
141   }
142  
143  
144   void SimInfo::scaleBox(double scale) {
145 <  double theBox[9];
146 <  int i;
145 >  double theBox[3][3];
146 >  int i, j;
147  
148 <  for(i=0; i<9; i++) theBox[i] = Hmat[i]*scale;
148 >  // cerr << "Scaling box by " << scale << "\n";
149  
150 +  for(i=0; i<3; i++)
151 +    for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
152 +
153    setBoxM(theBox);
154  
155   }
156  
157 < void SimInfo::calcHmatI( void ) {
158 <
159 <  double C[3][3];
160 <  double detHmat;
189 <  int i, j, k;
157 > void SimInfo::calcHmatInv( void ) {
158 >  
159 >  int oldOrtho;
160 >  int i,j;
161    double smallDiag;
162    double tol;
163    double sanity[3][3];
164  
165 <  // calculate the adjunct of Hmat;
165 >  invertMat3( Hmat, HmatInv );
166  
167 <  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
167 >  // check to see if Hmat is orthorhombic
168    
169 <  detHmat = 0.0;
211 <  for(i=0; i<3; i++) detHmat += Hmat[i] * C[i][0];
169 >  oldOrtho = orthoRhombic;
170  
171 <  
172 <  // H^-1 = C^T / det(H)
173 <  
174 <  i=0;
217 <  for(j=0; j<3; j++){
218 <    for(k=0; k<3; k++){
171 >  smallDiag = fabs(Hmat[0][0]);
172 >  if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]);
173 >  if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]);
174 >  tol = smallDiag * orthoTolerance;
175  
176 <      HmatI[i] = C[j][k] / detHmat;
177 <      i++;
178 <    }
179 <  }
180 <
181 <  // sanity check
182 <
183 <  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];
176 >  orthoRhombic = 1;
177 >  
178 >  for (i = 0; i < 3; i++ ) {
179 >    for (j = 0 ; j < 3; j++) {
180 >      if (i != j) {
181 >        if (orthoRhombic) {
182 >          if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0;
183 >        }        
184        }
185      }
186    }
187  
188 <  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";
188 >  if( oldOrtho != orthoRhombic ){
189      
190 <
191 <  // check to see if Hmat is orthorhombic
192 <  
193 <  smallDiag = Hmat[0];
194 <  if(smallDiag > Hmat[4]) smallDiag = Hmat[4];
195 <  if(smallDiag > Hmat[8]) smallDiag = Hmat[8];
196 <  tol = smallDiag * 1E-6;
197 <
198 <  orthoRhombic = 1;
252 <  for(i=0; (i<9) && orthoRhombic; i++){
253 <    
254 <    if( (i%4) ){ // ignore the diagonals (0, 4, and 8)
255 <      orthoRhombic = (Hmat[i] <= tol);
190 >    if( orthoRhombic ){
191 >      sprintf( painCave.errMsg,
192 >               "OOPSE is switching from the default Non-Orthorhombic\n"
193 >               "\tto the faster Orthorhombic periodic boundary computations.\n"
194 >               "\tThis is usually a good thing, but if you wan't the\n"
195 >               "\tNon-Orthorhombic computations, make the orthoBoxTolerance\n"
196 >               "\tvariable ( currently set to %G ) smaller.\n",
197 >               orthoTolerance);
198 >      simError();
199      }
200 +    else {
201 +      sprintf( painCave.errMsg,
202 +               "OOPSE is switching from the faster Orthorhombic to the more\n"
203 +               "\tflexible Non-Orthorhombic periodic boundary computations.\n"
204 +               "\tThis is usually because the box has deformed under\n"
205 +               "\tNPTf integration. If you wan't to live on the edge with\n"
206 +               "\tthe Orthorhombic computations, make the orthoBoxTolerance\n"
207 +               "\tvariable ( currently set to %G ) larger.\n",
208 +               orthoTolerance);
209 +      simError();
210 +    }
211    }
258 –    
212   }
213  
214   void SimInfo::calcBoxL( void ){
215  
216    double dx, dy, dz, dsq;
264 –  int i;
217  
218 <  // boxVol = h1 (dot) h2 (cross) h3
218 >  // boxVol = Determinant of Hmat
219  
220 <  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]) );
220 >  boxVol = matDet3( Hmat );
221  
272 –
222    // boxLx
223    
224 <  dx = Hmat[0]; dy = Hmat[1]; dz = Hmat[2];
224 >  dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
225    dsq = dx*dx + dy*dy + dz*dz;
226 <  boxLx = sqrt( dsq );
226 >  boxL[0] = sqrt( dsq );
227 >  //maxCutoff = 0.5 * boxL[0];
228  
229    // boxLy
230    
231 <  dx = Hmat[3]; dy = Hmat[4]; dz = Hmat[5];
231 >  dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
232    dsq = dx*dx + dy*dy + dz*dz;
233 <  boxLy = sqrt( dsq );
233 >  boxL[1] = sqrt( dsq );
234 >  //if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
235  
236 +
237    // boxLz
238    
239 <  dx = Hmat[6]; dy = Hmat[7]; dz = Hmat[8];
239 >  dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
240    dsq = dx*dx + dy*dy + dz*dz;
241 <  boxLz = sqrt( dsq );
241 >  boxL[2] = sqrt( dsq );
242 >  //if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
243 >
244 >  //calculate the max cutoff
245 >  maxCutoff =  calcMaxCutOff();
246    
247 +  checkCutOffs();
248 +
249   }
250 +
251 +
252 + double SimInfo::calcMaxCutOff(){
253 +
254 +  double ri[3], rj[3], rk[3];
255 +  double rij[3], rjk[3], rki[3];
256 +  double minDist;
257 +
258 +  ri[0] = Hmat[0][0];
259 +  ri[1] = Hmat[1][0];
260 +  ri[2] = Hmat[2][0];
261  
262 +  rj[0] = Hmat[0][1];
263 +  rj[1] = Hmat[1][1];
264 +  rj[2] = Hmat[2][1];
265  
266 +  rk[0] = Hmat[0][2];
267 +  rk[1] = Hmat[1][2];
268 +  rk[2] = Hmat[2][2];
269 +    
270 +  crossProduct3(ri, rj, rij);
271 +  distXY = dotProduct3(rk,rij) / norm3(rij);
272 +
273 +  crossProduct3(rj,rk, rjk);
274 +  distYZ = dotProduct3(ri,rjk) / norm3(rjk);
275 +
276 +  crossProduct3(rk,ri, rki);
277 +  distZX = dotProduct3(rj,rki) / norm3(rki);
278 +
279 +  minDist = min(min(distXY, distYZ), distZX);
280 +  return minDist/2;
281 +  
282 + }
283 +
284   void SimInfo::wrapVector( double thePos[3] ){
285  
286 <  int i, j, k;
286 >  int i;
287    double scaled[3];
288  
289    if( !orthoRhombic ){
290      // calc the scaled coordinates.
291 +  
292 +
293 +    matVecMul3(HmatInv, thePos, scaled);
294      
295      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++)
296        scaled[i] -= roundMe(scaled[i]);
297      
298      // calc the wrapped real coordinates from the wrapped scaled coordinates
299      
300 <    for(i=0; i<3; i++)
301 <      thePos[i] =
315 <        scaled[0]*Hmat[i] + scaled[1]*Hmat[i+3] + scaled[2]*Hmat[i+6];
300 >    matVecMul3(Hmat, scaled, thePos);
301 >
302    }
303    else{
304      // calc the scaled coordinates.
305      
306      for(i=0; i<3; i++)
307 <      scaled[i] = thePos[i]*HmatI[i*4];
307 >      scaled[i] = thePos[i]*HmatInv[i][i];
308      
309      // wrap the scaled coordinates
310      
# Line 328 | Line 314 | void SimInfo::wrapVector( double thePos[3] ){
314      // calc the wrapped real coordinates from the wrapped scaled coordinates
315      
316      for(i=0; i<3; i++)
317 <      thePos[i] = scaled[i]*Hmat[i*4];
317 >      thePos[i] = scaled[i]*Hmat[i][i];
318    }
319      
334 –    
320   }
321  
322  
323   int SimInfo::getNDF(){
324 <  int ndf_local, ndf;
324 >  int ndf_local;
325 >
326 >  ndf_local = 0;
327    
328 <  ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints;
328 >  for(int i = 0; i < integrableObjects.size(); i++){
329 >    ndf_local += 3;
330 >    if (integrableObjects[i]->isDirectional()) {
331 >      if (integrableObjects[i]->isLinear())
332 >        ndf_local += 2;
333 >      else
334 >        ndf_local += 3;
335 >    }
336 >  }
337  
338 +  // n_constraints is local, so subtract them on each processor:
339 +
340 +  ndf_local -= n_constraints;
341 +
342   #ifdef IS_MPI
343    MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
344   #else
345    ndf = ndf_local;
346   #endif
347  
348 <  ndf = ndf - 3;
348 >  // nZconstraints is global, as are the 3 COM translations for the
349 >  // entire system:
350  
351 +  ndf = ndf - 3 - nZconstraints;
352 +
353    return ndf;
354   }
355  
356   int SimInfo::getNDFraw() {
357 <  int ndfRaw_local, ndfRaw;
357 >  int ndfRaw_local;
358  
359    // Raw degrees of freedom that we have to set
360 <  ndfRaw_local = 3 * n_atoms + 3 * n_oriented;
361 <  
360 >  ndfRaw_local = 0;
361 >
362 >  for(int i = 0; i < integrableObjects.size(); i++){
363 >    ndfRaw_local += 3;
364 >    if (integrableObjects[i]->isDirectional()) {
365 >       if (integrableObjects[i]->isLinear())
366 >        ndfRaw_local += 2;
367 >      else
368 >        ndfRaw_local += 3;
369 >    }
370 >  }
371 >    
372   #ifdef IS_MPI
373    MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
374   #else
# Line 365 | Line 377 | int SimInfo::getNDFraw() {
377  
378    return ndfRaw;
379   }
380 <
380 >
381 > int SimInfo::getNDFtranslational() {
382 >  int ndfTrans_local;
383 >
384 >  ndfTrans_local = 3 * integrableObjects.size() - n_constraints;
385 >
386 >
387 > #ifdef IS_MPI
388 >  MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
389 > #else
390 >  ndfTrans = ndfTrans_local;
391 > #endif
392 >
393 >  ndfTrans = ndfTrans - 3 - nZconstraints;
394 >
395 >  return ndfTrans;
396 > }
397 >
398 > int SimInfo::getTotIntegrableObjects() {
399 >  int nObjs_local;
400 >  int nObjs;
401 >
402 >  nObjs_local =  integrableObjects.size();
403 >
404 >
405 > #ifdef IS_MPI
406 >  MPI_Allreduce(&nObjs_local,&nObjs,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
407 > #else
408 >  nObjs = nObjs_local;
409 > #endif
410 >
411 >
412 >  return nObjs;
413 > }
414 >
415   void SimInfo::refreshSim(){
416  
417    simtype fInfo;
418    int isError;
419    int n_global;
420    int* excl;
421 <  
376 <  fInfo.rrf = 0.0;
377 <  fInfo.rt = 0.0;
421 >
422    fInfo.dielect = 0.0;
423  
424 <  fInfo.rlist = rList;
381 <  fInfo.rcut = rCut;
382 <
383 <  if( useDipole ){
384 <    fInfo.rrf = ecr;
385 <    fInfo.rt = ecr - est;
424 >  if( useDipoles ){
425      if( useReactionField )fInfo.dielect = dielectric;
426    }
427  
# Line 391 | Line 430 | void SimInfo::refreshSim(){
430    fInfo.SIM_uses_LJ = useLJ;
431    fInfo.SIM_uses_sticky = useSticky;
432    //fInfo.SIM_uses_sticky = 0;
433 <  fInfo.SIM_uses_dipoles = useDipole;
433 >  fInfo.SIM_uses_charges = useCharges;
434 >  fInfo.SIM_uses_dipoles = useDipoles;
435    //fInfo.SIM_uses_dipoles = 0;
436 <  //fInfo.SIM_uses_RF = useReactionField;
437 <  fInfo.SIM_uses_RF = 0;
436 >  fInfo.SIM_uses_RF = useReactionField;
437 >  //fInfo.SIM_uses_RF = 0;
438    fInfo.SIM_uses_GB = useGB;
439    fInfo.SIM_uses_EAM = useEAM;
440  
441 <  excl = Exclude::getArray();
442 <
441 >  n_exclude = excludes->getSize();
442 >  excl = excludes->getFortranArray();
443 >  
444   #ifdef IS_MPI
445    n_global = mpiSim->getTotAtoms();
446   #else
447    n_global = n_atoms;
448   #endif
449 <
449 >  
450    isError = 0;
451 <
451 >  
452 >  getFortranGroupArray(this, mfact, ngroup, groupList, groupStart);
453 >  
454    setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl,
455 <                  &nGlobalExcludes, globalExcludes, molMembershipArray,
456 <                  &isError );
457 <
455 >                  &nGlobalExcludes, globalExcludes, molMembershipArray,
456 >                  &mfact[0], &ngroup, &groupList[0], &groupStart[0], &isError);
457 >  
458    if( isError ){
459 <
459 >    
460      sprintf( painCave.errMsg,
461 <             "There was an error setting the simulation information in fortran.\n" );
461 >             "There was an error setting the simulation information in fortran.\n" );
462      painCave.isFatal = 1;
463      simError();
464    }
465 <
465 >  
466   #ifdef IS_MPI
467    sprintf( checkPointMsg,
468             "succesfully sent the simulation information to fortran.\n");
469    MPIcheckPoint();
470   #endif // is_mpi
471 <
471 >  
472    this->ndf = this->getNDF();
473    this->ndfRaw = this->getNDFraw();
474 +  this->ndfTrans = this->getNDFtranslational();
475 + }
476  
477 + void SimInfo::setDefaultRcut( double theRcut ){
478 +  
479 +  haveRcut = 1;
480 +  rCut = theRcut;
481 +  rList = rCut + 1.0;
482 +  
483 +  notifyFortranCutOffs( &rCut, &rSw, &rList );
484   }
485  
486 + void SimInfo::setDefaultRcut( double theRcut, double theRsw ){
487 +
488 +  rSw = theRsw;
489 +  setDefaultRcut( theRcut );
490 + }
491 +
492 +
493 + void SimInfo::checkCutOffs( void ){
494 +  
495 +  if( boxIsInit ){
496 +    
497 +    //we need to check cutOffs against the box
498 +    
499 +    if( rCut > maxCutoff ){
500 +      sprintf( painCave.errMsg,
501 +               "cutoffRadius is too large for the current periodic box.\n"
502 +               "\tCurrent Value of cutoffRadius = %G at time %G\n "
503 +               "\tThis is larger than half of at least one of the\n"
504 +               "\tperiodic box vectors.  Right now, the Box matrix is:\n"
505 +               "\n"
506 +               "\t[ %G %G %G ]\n"
507 +               "\t[ %G %G %G ]\n"
508 +               "\t[ %G %G %G ]\n",
509 +               rCut, currentTime,
510 +               Hmat[0][0], Hmat[0][1], Hmat[0][2],
511 +               Hmat[1][0], Hmat[1][1], Hmat[1][2],
512 +               Hmat[2][0], Hmat[2][1], Hmat[2][2]);
513 +      painCave.isFatal = 1;
514 +      simError();
515 +    }    
516 +  } else {
517 +    // initialize this stuff before using it, OK?
518 +    sprintf( painCave.errMsg,
519 +             "Trying to check cutoffs without a box.\n"
520 +             "\tOOPSE should have better programmers than that.\n" );
521 +    painCave.isFatal = 1;
522 +    simError();      
523 +  }
524 +  
525 + }
526 +
527 + void SimInfo::addProperty(GenericData* prop){
528 +
529 +  map<string, GenericData*>::iterator result;
530 +  result = properties.find(prop->getID());
531 +  
532 +  //we can't simply use  properties[prop->getID()] = prop,
533 +  //it will cause memory leak if we already contain a propery which has the same name of prop
534 +  
535 +  if(result != properties.end()){
536 +    
537 +    delete (*result).second;
538 +    (*result).second = prop;
539 +      
540 +  }
541 +  else{
542 +
543 +    properties[prop->getID()] = prop;
544 +
545 +  }
546 +    
547 + }
548 +
549 + GenericData* SimInfo::getProperty(const string& propName){
550 +
551 +  map<string, GenericData*>::iterator result;
552 +  
553 +  //string lowerCaseName = ();
554 +  
555 +  result = properties.find(propName);
556 +  
557 +  if(result != properties.end())
558 +    return (*result).second;  
559 +  else  
560 +    return NULL;  
561 + }
562 +
563 +
564 + void getFortranGroupArray(SimInfo* info, vector<double>& mfact, int& ngroup,
565 +                          vector<int>& groupList, vector<int>& groupStart){
566 +  Molecule* mol;
567 +  Atom** myAtoms;
568 +  int numAtom;
569 +  int curIndex;
570 +  double mtot;
571 +
572 +  mfact.clear();
573 +  groupList.clear();
574 +  groupStart.clear();
575 +  
576 +  //Be careful, fortran array begin at 1
577 +  curIndex = 1;
578 +  
579 +  if(info->useMolecularCutoffs){
580 +    
581 + #ifdef IS_MPI
582 +    ngroup = mpiSim->getMyNMol();
583 + #else
584 +    ngroup = info->n_mol;
585 + #endif
586 +    
587 +    for(int i = 0; i < ngroup; i ++){
588 +      mol = &(info->molecules[i]);
589 +      numAtom = mol->getNAtoms();
590 +      myAtoms = mol->getMyAtoms();
591 +      mtot = 0.0;
592 +
593 +      for(int j=0; j < numAtom; j++)
594 +        mtot += myAtoms[j]->getMass();                
595 +      
596 +      for(int j=0; j < numAtom; j++){
597 +              
598 +        // We want the local Index:
599 +        groupList.push_back(myAtoms[j]->getIndex() + 1);
600 +        mfact.push_back(myAtoms[j]->getMass() / mtot);
601 +
602 +      }
603 +      
604 +      groupStart.push_back(curIndex);
605 +      curIndex += numAtom;
606 +      
607 +    } //end for(int i =0 ; i < ngroup; i++)    
608 +  }
609 +  else{
610 +    //using atomic cutoff, every single atom is just a group
611 +    
612 + #ifdef IS_MPI
613 +    ngroup = mpiSim->getMyNlocal();
614 + #else
615 +    ngroup = info->n_atoms;
616 + #endif
617 +    
618 +    for(int i =0 ; i < ngroup; i++){
619 +      groupStart.push_back(curIndex++);      
620 +      groupList.push_back((info->atoms[i])->getIndex() + 1);
621 +      mfact.push_back(1.0);
622 +      
623 +    }//end for(int i =0 ; i < ngroup; i++)
624 +    
625 +  }//end if (info->useMolecularCutoffs)
626 +  
627 + }

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