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root/group/trunk/OOPSE/libmdtools/SimInfo.cpp
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Comparing trunk/OOPSE/libmdtools/SimInfo.cpp (file contents):
Revision 569 by mmeineke, Tue Jul 1 21:33:45 2003 UTC vs.
Revision 1150 by gezelter, Fri May 7 21:35:05 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;
7  
8   #include "SimInfo.hpp"
9   #define __C
# Line 10 | Line 12
12  
13   #include "fortranWrappers.hpp"
14  
15 + #include "MatVec3.h"
16 +
17   #ifdef IS_MPI
18   #include "mpiSimulation.hpp"
19   #endif
20  
21 + 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 <  wrapMeSimInfo( this );
40 < }
68 >  excludes = Exclude::Instance();
69  
70 < void SimInfo::setBox(double newBox[3]) {
70 >  myConfiguration = new SimState();
71  
72 <  double smallestBoxL, maxCutoff;
73 <  int status;
46 <  int i;
72 >  has_minimizer = false;
73 >  the_minimizer =NULL;
74  
75 <  for(i=0; i<9; i++) Hmat[i] = 0.0;;
75 >  ngroup = 0;
76  
77 <  Hmat[0] = newBox[0];
78 <  Hmat[4] = newBox[1];
52 <  Hmat[8] = newBox[2];
77 >  wrapMeSimInfo( this );
78 > }
79  
54 –  calcHmatI();
55 –  calcBoxL();
80  
81 <  setFortranBoxSize(Hmat, HmatI, &orthoRhombic);
81 > SimInfo::~SimInfo(){
82  
83 <  smallestBoxL = boxLx;
60 <  if (boxLy < smallestBoxL) smallestBoxL = boxLy;
61 <  if (boxLz < smallestBoxL) smallestBoxL = boxLz;
83 >  delete myConfiguration;
84  
85 <  maxCutoff = smallestBoxL / 2.0;
85 >  map<string, GenericData*>::iterator i;
86 >  
87 >  for(i = properties.begin(); i != properties.end(); i++)
88 >    delete (*i).second;
89 >  
90 > }
91  
92 <  if (rList > maxCutoff) {
93 <    sprintf( painCave.errMsg,
94 <             "New Box size is forcing neighborlist radius down to %lf\n",
95 <             maxCutoff );
69 <    painCave.isFatal = 0;
70 <    simError();
92 > void SimInfo::setBox(double newBox[3]) {
93 >  
94 >  int i, j;
95 >  double tempMat[3][3];
96  
97 <    rList = maxCutoff;
97 >  for(i=0; i<3; i++)
98 >    for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
99  
100 <    sprintf( painCave.errMsg,
101 <             "New Box size is forcing cutoff radius down to %lf\n",
102 <             maxCutoff - 1.0 );
77 <    painCave.isFatal = 0;
78 <    simError();
100 >  tempMat[0][0] = newBox[0];
101 >  tempMat[1][1] = newBox[1];
102 >  tempMat[2][2] = newBox[2];
103  
104 <    rCut = rList - 1.0;
104 >  setBoxM( tempMat );
105  
82 –    // list radius changed so we have to refresh the simulation structure.
83 –    refreshSim();
84 –  }
85 –
86 –  if (rCut > maxCutoff) {
87 –    sprintf( painCave.errMsg,
88 –             "New Box size is forcing cutoff radius down to %lf\n",
89 –             maxCutoff );
90 –    painCave.isFatal = 0;
91 –    simError();
92 –
93 –    status = 0;
94 –    LJ_new_rcut(&rCut, &status);
95 –    if (status != 0) {
96 –      sprintf( painCave.errMsg,
97 –               "Error in recomputing LJ shifts based on new rcut\n");
98 –      painCave.isFatal = 1;
99 –      simError();
100 –    }
101 –  }
106   }
107  
108 < void SimInfo::setBoxM( double theBox[9] ){
108 > void SimInfo::setBoxM( double theBox[3][3] ){
109    
110 <  int i, status;
111 <  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 ]
114 >                         // [ 1 4 7 ]
115 >                         // [ 2 5 8 ]
116 >  double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
117  
118 <  for(i=0; i<9; i++) Hmat[i] = theBox[i];
119 <  calcHmatI();
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 >  
123    calcBoxL();
124 +  calcHmatInv();
125  
126 <  setFortranBoxSize(Hmat, HmatI, &orthoRhombic);
126 >  for(i=0; i < 3; i++) {
127 >    for (j=0; j < 3; j++) {
128 >      FortranHmat[3*j + i] = Hmat[i][j];
129 >      FortranHmatInv[3*j + i] = HmatInv[i][j];
130 >    }
131 >  }
132 >
133 >  setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic);
134  
135 <  smallestBoxL = boxLx;
136 <  if (boxLy < smallestBoxL) smallestBoxL = boxLy;
117 <  if (boxLz < smallestBoxL) smallestBoxL = boxLz;
135 > }
136 >
137  
138 <  maxCutoff = smallestBoxL / 2.0;
138 > void SimInfo::getBoxM (double theBox[3][3]) {
139  
140 <  if (rList > maxCutoff) {
141 <    sprintf( painCave.errMsg,
142 <             "New Box size is forcing neighborlist radius down to %lf\n",
143 <             maxCutoff );
125 <    painCave.isFatal = 0;
126 <    simError();
140 >  int i, j;
141 >  for(i=0; i<3; i++)
142 >    for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j];
143 > }
144  
128 –    rList = maxCutoff;
145  
146 <    sprintf( painCave.errMsg,
147 <             "New Box size is forcing cutoff radius down to %lf\n",
148 <             maxCutoff - 1.0 );
133 <    painCave.isFatal = 0;
134 <    simError();
146 > void SimInfo::scaleBox(double scale) {
147 >  double theBox[3][3];
148 >  int i, j;
149  
150 <    rCut = rList - 1.0;
150 >  // cerr << "Scaling box by " << scale << "\n";
151  
152 <    // list radius changed so we have to refresh the simulation structure.
153 <    refreshSim();
140 <  }
152 >  for(i=0; i<3; i++)
153 >    for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
154  
155 <  if (rCut > maxCutoff) {
143 <    sprintf( painCave.errMsg,
144 <             "New Box size is forcing cutoff radius down to %lf\n",
145 <             maxCutoff );
146 <    painCave.isFatal = 0;
147 <    simError();
148 <
149 <    status = 0;
150 <    LJ_new_rcut(&rCut, &status);
151 <    if (status != 0) {
152 <      sprintf( painCave.errMsg,
153 <               "Error in recomputing LJ shifts based on new rcut\n");
154 <      painCave.isFatal = 1;
155 <      simError();
156 <    }
157 <  }
158 < }
159 <
155 >  setBoxM(theBox);
156  
161 – void SimInfo::getBox(double theBox[9]) {
162 –
163 –  int i;
164 –  for(i=0; i<9; i++) theBox[i] = Hmat[i];
157   }
166 –
158  
159 < void SimInfo::calcHmatI( void ) {
160 <
161 <  double C[3][3];
162 <  double detHmat;
172 <  int i, j, k;
159 > void SimInfo::calcHmatInv( void ) {
160 >  
161 >  int oldOrtho;
162 >  int i,j;
163    double smallDiag;
164    double tol;
165    double sanity[3][3];
166  
167 <  // calculate the adjunct of Hmat;
167 >  invertMat3( Hmat, HmatInv );
168  
169 <  C[0][0] =  ( Hmat[4]*Hmat[8]) - (Hmat[7]*Hmat[5]);
180 <  C[1][0] = -( Hmat[1]*Hmat[8]) + (Hmat[7]*Hmat[2]);
181 <  C[2][0] =  ( Hmat[1]*Hmat[5]) - (Hmat[4]*Hmat[2]);
182 <
183 <  C[0][1] = -( Hmat[3]*Hmat[8]) + (Hmat[6]*Hmat[5]);
184 <  C[1][1] =  ( Hmat[0]*Hmat[8]) - (Hmat[6]*Hmat[2]);
185 <  C[2][1] = -( Hmat[0]*Hmat[5]) + (Hmat[3]*Hmat[2]);
186 <
187 <  C[0][2] =  ( Hmat[3]*Hmat[7]) - (Hmat[6]*Hmat[4]);
188 <  C[1][2] = -( Hmat[0]*Hmat[7]) + (Hmat[6]*Hmat[1]);
189 <  C[2][2] =  ( Hmat[0]*Hmat[4]) - (Hmat[3]*Hmat[1]);
190 <
191 <  // calcutlate the determinant of Hmat
169 >  // check to see if Hmat is orthorhombic
170    
171 <  detHmat = 0.0;
194 <  for(i=0; i<3; i++) detHmat += Hmat[i] * C[i][0];
171 >  oldOrtho = orthoRhombic;
172  
173 <  
174 <  // H^-1 = C^T / det(H)
175 <  
176 <  i=0;
200 <  for(j=0; j<3; j++){
201 <    for(k=0; k<3; k++){
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 <      HmatI[i] = C[j][k] / detHmat;
179 <      i++;
180 <    }
181 <  }
182 <
183 <  // sanity check
184 <
185 <  for(i=0; i<3; i++){
211 <    for(j=0; j<3; j++){
212 <      
213 <      sanity[i][j] = 0.0;
214 <      for(k=0; k<3; k++){
215 <        sanity[i][j] += Hmat[3*k+i] * HmatI[3*j+k];
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 ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0;
185 >        }        
186        }
187      }
188    }
189  
190 <  cerr << "sanity => \n"
221 <       << sanity[0][0] << "\t" << sanity[0][1] << "\t" << sanity [0][2] << "\n"
222 <       << sanity[1][0] << "\t" << sanity[1][1] << "\t" << sanity [1][2] << "\n"
223 <       << sanity[2][0] << "\t" << sanity[2][1] << "\t" << sanity [2][2]
224 <       << "\n";
190 >  if( oldOrtho != orthoRhombic ){
191      
192 <
193 <  // check to see if Hmat is orthorhombic
194 <  
195 <  smallDiag = Hmat[0];
196 <  if(smallDiag > Hmat[4]) smallDiag = Hmat[4];
197 <  if(smallDiag > Hmat[8]) smallDiag = Hmat[8];
198 <  tol = smallDiag * 1E-6;
199 <
200 <  orthoRhombic = 1;
235 <  for(i=0; (i<9) && orthoRhombic; i++){
236 <    
237 <    if( (i%4) ){ // ignore the diagonals (0, 4, and 8)
238 <      orthoRhombic = (Hmat[i] <= tol);
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    }
241 –    
214   }
215  
216   void SimInfo::calcBoxL( void ){
217  
218    double dx, dy, dz, dsq;
247 –  int i;
219  
220 <  // boxVol = h1 (dot) h2 (cross) h3
220 >  // boxVol = Determinant of Hmat
221  
222 <  boxVol = Hmat[0] * ( (Hmat[4]*Hmat[8]) - (Hmat[7]*Hmat[5]) )
252 <         + Hmat[1] * ( (Hmat[5]*Hmat[6]) - (Hmat[8]*Hmat[3]) )
253 <         + Hmat[2] * ( (Hmat[3]*Hmat[7]) - (Hmat[6]*Hmat[4]) );
222 >  boxVol = matDet3( Hmat );
223  
255 –
224    // boxLx
225    
226 <  dx = Hmat[0]; dy = Hmat[1]; dz = Hmat[2];
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[3]; dy = Hmat[4]; dz = Hmat[5];
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[6]; dy = Hmat[7]; dz = Hmat[8];
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 ){
292      // calc the scaled coordinates.
293 +  
294 +
295 +    matVecMul3(HmatInv, thePos, scaled);
296      
297      for(i=0; i<3; i++)
298 <      scaled[i] =
287 <        thePos[0]*HmatI[i] + thePos[1]*HmatI[i+3] + thePos[3]*HmatI[i+6];
298 >      scaled[i] -= roundMe(scaled[i]);
299      
289 –    // wrap the scaled coordinates
290 –    
291 –    for(i=0; i<3; i++)
292 –      scaled[i] -= round(scaled[i]);
293 –    
300      // calc the wrapped real coordinates from the wrapped scaled coordinates
301      
302 <    for(i=0; i<3; i++)
303 <      thePos[i] =
298 <        scaled[0]*Hmat[i] + scaled[1]*Hmat[i+3] + scaled[3]*Hmat[i+6];
302 >    matVecMul3(Hmat, scaled, thePos);
303 >
304    }
305    else{
306      // calc the scaled coordinates.
307      
308      for(i=0; i<3; i++)
309 <      scaled[i] = thePos[i]*HmatI[i*4];
309 >      scaled[i] = thePos[i]*HmatInv[i][i];
310      
311      // wrap the scaled coordinates
312      
313      for(i=0; i<3; i++)
314 <      scaled[i] -= round(scaled[i]);
314 >      scaled[i] -= roundMe(scaled[i]);
315      
316      // calc the wrapped real coordinates from the wrapped scaled coordinates
317      
318      for(i=0; i<3; i++)
319 <      thePos[i] = scaled[i]*Hmat[i*4];
319 >      thePos[i] = scaled[i]*Hmat[i][i];
320    }
321      
317 –    
322   }
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 348 | 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 <  
359 <  fInfo.rrf = 0.0;
360 <  fInfo.rt = 0.0;
423 >
424    fInfo.dielect = 0.0;
425  
426 <  fInfo.box[0] = box_x;
364 <  fInfo.box[1] = box_y;
365 <  fInfo.box[2] = box_z;
366 <
367 <  fInfo.rlist = rList;
368 <  fInfo.rcut = rCut;
369 <
370 <  if( useDipole ){
371 <    fInfo.rrf = ecr;
372 <    fInfo.rt = ecr - est;
426 >  if( useDipoles ){
427      if( useReactionField )fInfo.dielect = dielectric;
428    }
429  
# Line 378 | 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
449    n_global = n_atoms;
450   #endif
451 <
451 >  
452    isError = 0;
453 <
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 );
459 <
457 >                  &nGlobalExcludes, globalExcludes, molMembershipArray,
458 >                  &mfact[0], &ngroup, &groupList[0], &groupStart[0], &isError);
459 >  
460    if( isError ){
461 <
461 >    
462      sprintf( painCave.errMsg,
463 <             "There was an error setting the simulation information in fortran.\n" );
463 >             "There was an error setting the simulation information in fortran.\n" );
464      painCave.isFatal = 1;
465      simError();
466    }
467 <
467 >  
468   #ifdef IS_MPI
469    sprintf( checkPointMsg,
470             "succesfully sent the simulation information to fortran.\n");
471    MPIcheckPoint();
472   #endif // is_mpi
473 <
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 +  Atom** myAtoms;
602 +  int numAtom;
603 +  int curIndex;
604 +  double mtot;
605 +
606 +  mfact.clear();
607 +  groupList.clear();
608 +  groupStart.clear();
609 +  
610 +  //Be careful, fortran array begin at 1
611 +  curIndex = 1;
612 +  
613 +  if(info->useMolecularCutoffs){
614 +    
615 + #ifdef IS_MPI
616 +    ngroup = mpiSim->getMyNMol();
617 + #else
618 +    ngroup = info->n_mol;
619 + #endif
620 +    
621 +    for(int i = 0; i < ngroup; i ++){
622 +      mol = &(info->molecules[i]);
623 +      numAtom = mol->getNAtoms();
624 +      myAtoms = mol->getMyAtoms();
625 +      mtot = 0.0;
626 +
627 +      for(int j=0; j < numAtom; j++)
628 +        mtot += myAtoms[j]->getMass();                
629 +      
630 +      for(int j=0; j < numAtom; j++){
631 +              
632 +        // We want the local Index:
633 +        groupList.push_back(myAtoms[j]->getIndex() + 1);
634 +        mfact.push_back(myAtoms[j]->getMass() / mtot);
635 +
636 +      }
637 +      
638 +      groupStart.push_back(curIndex);
639 +      curIndex += numAtom;
640 +      
641 +    } //end for(int i =0 ; i < ngroup; i++)    
642 +  }
643 +  else{
644 +    //using atomic cutoff, every single atom is just a group
645 +    
646 + #ifdef IS_MPI
647 +    ngroup = mpiSim->getMyNlocal();
648 + #else
649 +    ngroup = info->n_atoms;
650 + #endif
651 +    
652 +    for(int i =0 ; i < ngroup; i++){
653 +      groupStart.push_back(curIndex++);      
654 +      groupList.push_back((info->atoms[i])->getIndex() + 1);
655 +      mfact.push_back(1.0);
656 +      
657 +    }//end for(int i =0 ; i < ngroup; i++)
658 +    
659 +  }//end if (info->useMolecularCutoffs)
660 +  
661 + }

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