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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 1164 by tim, Wed May 12 15:02:03 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 +  haveCutoffGroups = false;
67  
68 <  wrapMeSimInfo( this );
47 < }
68 >  excludes = Exclude::Instance();
69  
70 < void SimInfo::setBox(double newBox[3]) {
70 >  myConfiguration = new SimState();
71  
72 <  double smallestBoxL, maxCutoff;
73 <  int status;
53 <  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];
59 <  Hmat[8] = newBox[2];
77 >  wrapMeSimInfo( this );
78 > }
79  
61 –  calcHmatI();
62 –  calcBoxL();
80  
81 <  setFortranBoxSize(Hmat, HmatI, &orthoRhombic);
81 > SimInfo::~SimInfo(){
82  
83 <  smallestBoxL = boxLx;
67 <  if (boxLy < smallestBoxL) smallestBoxL = boxLy;
68 <  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 );
76 <    painCave.isFatal = 0;
77 <    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 );
84 <    painCave.isFatal = 0;
85 <    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  
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 –  }
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);
127 <
128 <  smallestBoxL = boxLx;
129 <  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();
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   }
136  
137  
138 < void SimInfo::getBoxM (double theBox[9]) {
138 > void SimInfo::getBoxM (double theBox[3][3]) {
139  
140 <  int i;
141 <  for(i=0; i<9; i++) theBox[i] = Hmat[i];
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  
145  
146   void SimInfo::scaleBox(double scale) {
147 <  double theBox[9];
148 <  int i;
147 >  double theBox[3][3];
148 >  int i, j;
149  
150 <  for(i=0; i<9; i++) theBox[i] = Hmat[i]*scale;
150 >  // cerr << "Scaling box by " << scale << "\n";
151  
152 +  for(i=0; i<3; i++)
153 +    for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
154 +
155    setBoxM(theBox);
156  
157   }
158  
159 < void SimInfo::calcHmatI( void ) {
160 <
161 <  double C[3][3];
162 <  double detHmat;
189 <  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]);
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
169 >  // check to see if Hmat is orthorhombic
170    
171 <  detHmat = 0.0;
211 <  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;
217 <  for(j=0; j<3; j++){
218 <    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++){
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];
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"
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";
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;
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);
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    }
258 –    
214   }
215  
216   void SimInfo::calcBoxL( void ){
217  
218    double dx, dy, dz, dsq;
264 –  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]) )
269 <         + Hmat[1] * ( (Hmat[5]*Hmat[6]) - (Hmat[8]*Hmat[3]) )
270 <         + Hmat[2] * ( (Hmat[3]*Hmat[7]) - (Hmat[6]*Hmat[4]) );
222 >  boxVol = matDet3( Hmat );
223  
272 –
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++)
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++)
298        scaled[i] -= roundMe(scaled[i]);
299      
300      // calc the wrapped real coordinates from the wrapped scaled coordinates
301      
302 <    for(i=0; i<3; i++)
303 <      thePos[i] =
315 <        scaled[0]*Hmat[i] + scaled[1]*Hmat[i+3] + scaled[2]*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      
# Line 328 | Line 316 | void SimInfo::wrapVector( double thePos[3] ){
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      
334 –    
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 365 | 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 <  
376 <  fInfo.rrf = 0.0;
377 <  fInfo.rt = 0.0;
423 >
424    fInfo.dielect = 0.0;
425  
426 <  fInfo.rlist = rList;
381 <  fInfo.rcut = rCut;
382 <
383 <  if( useDipole ){
384 <    fInfo.rrf = ecr;
385 <    fInfo.rt = ecr - est;
426 >  if( useDipoles ){
427      if( useReactionField )fInfo.dielect = dielectric;
428    }
429  
# Line 391 | 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 >  //it may not be a good idea to pass the address of first element in vector
456 >  //since c++ standard does not require vector to be stored continuously in meomory
457 >  //Most of the compilers will organize the memory of vector continuously
458    setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl,
459 <                  &nGlobalExcludes, globalExcludes, molMembershipArray,
460 <                  &isError );
461 <
459 >                  &nGlobalExcludes, globalExcludes, molMembershipArray,
460 >                  &mfact[0], &ngroup, &groupList[0], &groupStart[0], &isError);
461 >  
462    if( isError ){
463 <
463 >    
464      sprintf( painCave.errMsg,
465 <             "There was an error setting the simulation information in fortran.\n" );
465 >             "There was an error setting the simulation information in fortran.\n" );
466      painCave.isFatal = 1;
467      simError();
468    }
469 <
469 >  
470   #ifdef IS_MPI
471    sprintf( checkPointMsg,
472             "succesfully sent the simulation information to fortran.\n");
473    MPIcheckPoint();
474   #endif // is_mpi
475 <
475 >  
476    this->ndf = this->getNDF();
477    this->ndfRaw = this->getNDFraw();
478 +  this->ndfTrans = this->getNDFtranslational();
479 + }
480  
481 + void SimInfo::setDefaultRcut( double theRcut ){
482 +  
483 +  haveRcut = 1;
484 +  rCut = theRcut;
485 +  rList = rCut + 1.0;
486 +  
487 +  notifyFortranCutOffs( &rCut, &rSw, &rList );
488   }
489  
490 + void SimInfo::setDefaultRcut( double theRcut, double theRsw ){
491 +
492 +  rSw = theRsw;
493 +  setDefaultRcut( theRcut );
494 + }
495 +
496 +
497 + void SimInfo::checkCutOffs( void ){
498 +  
499 +  if( boxIsInit ){
500 +    
501 +    //we need to check cutOffs against the box
502 +    
503 +    if( rCut > maxCutoff ){
504 +      sprintf( painCave.errMsg,
505 +               "cutoffRadius is too large for the current periodic box.\n"
506 +               "\tCurrent Value of cutoffRadius = %G at time %G\n "
507 +               "\tThis is larger than half of at least one of the\n"
508 +               "\tperiodic box vectors.  Right now, the Box matrix is:\n"
509 +               "\n"
510 +               "\t[ %G %G %G ]\n"
511 +               "\t[ %G %G %G ]\n"
512 +               "\t[ %G %G %G ]\n",
513 +               rCut, currentTime,
514 +               Hmat[0][0], Hmat[0][1], Hmat[0][2],
515 +               Hmat[1][0], Hmat[1][1], Hmat[1][2],
516 +               Hmat[2][0], Hmat[2][1], Hmat[2][2]);
517 +      painCave.isFatal = 1;
518 +      simError();
519 +    }    
520 +  } else {
521 +    // initialize this stuff before using it, OK?
522 +    sprintf( painCave.errMsg,
523 +             "Trying to check cutoffs without a box.\n"
524 +             "\tOOPSE should have better programmers than that.\n" );
525 +    painCave.isFatal = 1;
526 +    simError();      
527 +  }
528 +  
529 + }
530 +
531 + void SimInfo::addProperty(GenericData* prop){
532 +
533 +  map<string, GenericData*>::iterator result;
534 +  result = properties.find(prop->getID());
535 +  
536 +  //we can't simply use  properties[prop->getID()] = prop,
537 +  //it will cause memory leak if we already contain a propery which has the same name of prop
538 +  
539 +  if(result != properties.end()){
540 +    
541 +    delete (*result).second;
542 +    (*result).second = prop;
543 +      
544 +  }
545 +  else{
546 +
547 +    properties[prop->getID()] = prop;
548 +
549 +  }
550 +    
551 + }
552 +
553 + GenericData* SimInfo::getProperty(const string& propName){
554 +
555 +  map<string, GenericData*>::iterator result;
556 +  
557 +  //string lowerCaseName = ();
558 +  
559 +  result = properties.find(propName);
560 +  
561 +  if(result != properties.end())
562 +    return (*result).second;  
563 +  else  
564 +    return NULL;  
565 + }
566 +
567 +
568 + void getFortranGroupArray(SimInfo* info, vector<double>& mfact, int& ngroup,
569 +                          vector<int>& groupList, vector<int>& groupStart){
570 +  Molecule* myMols;
571 +  Atom** myAtoms;
572 +  int numAtom;
573 +  int curIndex;
574 +  double mtot;
575 +  int numMol;
576 +  int numCutoffGroups;
577 +  CutoffGroup* myCutoffGroup;
578 +  vector<CutoffGroup*>::iterator iterCutoff;
579 +  Atom* cutoffAtom;
580 +  vector<Atom*>::iterator iterAtom;
581 +  int atomIndex;
582 +  double totalMass;
583 +  
584 +  mfact.clear();
585 +  groupList.clear();
586 +  groupStart.clear();
587 +  
588 +  //Be careful, fortran array begin at 1
589 +  curIndex = 1;
590 +
591 +  myMols = info->molecules;
592 +  numMol = info->n_mol;
593 +  for(int i  = 0; i < numMol; i++){
594 +    numAtom = myMols[i].getNAtoms();
595 +    myAtoms = myMols[i].getMyAtoms();
596 +
597 +    
598 +    for(int j = 0; j < numAtom; j++){
599 +
600 +    
601 + #ifdef IS_MPI      
602 +      atomIndex = myAtoms[j]->getGlobalIndex();
603 + #else
604 +      atomIndex = myAtoms[j]->getIndex();
605 + #endif
606 +
607 +      if(myMols[i].belongToCutoffGroup(atomIndex))
608 +        continue;
609 +      else{
610 +        // this is a fraction of the cutoff group's mass, not the mass itself!
611 +        mfact.push_back(1.0);
612 +        groupList.push_back(myAtoms[j]->getIndex() + 1);
613 +        groupStart.push_back(curIndex++);  
614 +      }
615 +    }
616 +      
617 +    numCutoffGroups = myMols[i].getNCutoffGroups();
618 +    for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff); myCutoffGroup != NULL;
619 +                                                  myCutoffGroup =myMols[i].nextCutoffGroup(iterCutoff)){
620 +
621 +      totalMass = myCutoffGroup->getMass();
622 +      
623 +      for(cutoffAtom = myCutoffGroup->beginAtom(iterAtom); cutoffAtom != NULL;
624 +                                           cutoffAtom = myCutoffGroup->nextAtom(iterAtom)){
625 +        mfact.push_back(cutoffAtom->getMass()/totalMass);
626 +        groupList.push_back(cutoffAtom->getIndex() + 1);
627 +      }  
628 +                              
629 +      groupStart.push_back(curIndex);
630 +      curIndex += myCutoffGroup->getNumAtom();
631 +
632 +    }//end for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff))
633 +
634 +  }//end for(int i  = 0; i < numMol; i++)
635 +  
636 +  ngroup = groupStart.size();
637 + }

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