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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 1198 by tim, Thu May 27 00:48:12 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 +  useThermInt = 0;
66  
67 <  wrapMeSimInfo( this );
47 < }
67 >  haveCutoffGroups = false;
68  
69 < void SimInfo::setBox(double newBox[3]) {
69 >  excludes = Exclude::Instance();
70  
71 <  double smallestBoxL, maxCutoff;
52 <  int status;
53 <  int i;
71 >  myConfiguration = new SimState();
72  
73 <  for(i=0; i<9; i++) Hmat[i] = 0.0;;
73 >  has_minimizer = false;
74 >  the_minimizer =NULL;
75  
76 <  Hmat[0] = newBox[0];
58 <  Hmat[4] = newBox[1];
59 <  Hmat[8] = newBox[2];
76 >  ngroup = 0;
77  
78 <  calcHmatI();
79 <  calcBoxL();
78 >  wrapMeSimInfo( this );
79 > }
80  
64 –  setFortranBoxSize(Hmat, HmatI, &orthoRhombic);
81  
82 <  smallestBoxL = boxLx;
67 <  if (boxLy < smallestBoxL) smallestBoxL = boxLy;
68 <  if (boxLz < smallestBoxL) smallestBoxL = boxLz;
82 > SimInfo::~SimInfo(){
83  
84 <  maxCutoff = smallestBoxL / 2.0;
84 >  delete myConfiguration;
85  
86 <  if (rList > maxCutoff) {
87 <    sprintf( painCave.errMsg,
88 <             "New Box size is forcing neighborlist radius down to %lf\n",
89 <             maxCutoff );
90 <    painCave.isFatal = 0;
91 <    simError();
86 >  map<string, GenericData*>::iterator i;
87 >  
88 >  for(i = properties.begin(); i != properties.end(); i++)
89 >    delete (*i).second;
90 >  
91 > }
92  
93 <    rList = maxCutoff;
93 > void SimInfo::setBox(double newBox[3]) {
94 >  
95 >  int i, j;
96 >  double tempMat[3][3];
97  
98 <    sprintf( painCave.errMsg,
99 <             "New Box size is forcing cutoff radius down to %lf\n",
83 <             maxCutoff - 1.0 );
84 <    painCave.isFatal = 0;
85 <    simError();
98 >  for(i=0; i<3; i++)
99 >    for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
100  
101 <    rCut = rList - 1.0;
101 >  tempMat[0][0] = newBox[0];
102 >  tempMat[1][1] = newBox[1];
103 >  tempMat[2][2] = newBox[2];
104  
105 <    // list radius changed so we have to refresh the simulation structure.
90 <    refreshSim();
91 <  }
105 >  setBoxM( tempMat );
106  
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 –  }
107   }
108  
109 < void SimInfo::setBoxM( double theBox[9] ){
109 > void SimInfo::setBoxM( double theBox[3][3] ){
110    
111 <  int i, status;
112 <  double smallestBoxL, maxCutoff;
111 >  int i, j;
112 >  double FortranHmat[9]; // to preserve compatibility with Fortran the
113 >                         // ordering in the array is as follows:
114 >                         // [ 0 3 6 ]
115 >                         // [ 1 4 7 ]
116 >                         // [ 2 5 8 ]
117 >  double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
118  
119 <  for(i=0; i<9; i++) Hmat[i] = theBox[i];
120 <  calcHmatI();
119 >  if( !boxIsInit ) boxIsInit = 1;
120 >
121 >  for(i=0; i < 3; i++)
122 >    for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
123 >  
124    calcBoxL();
125 +  calcHmatInv();
126  
127 <  setFortranBoxSize(Hmat, HmatI, &orthoRhombic);
128 <
129 <  smallestBoxL = boxLx;
130 <  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();
127 >  for(i=0; i < 3; i++) {
128 >    for (j=0; j < 3; j++) {
129 >      FortranHmat[3*j + i] = Hmat[i][j];
130 >      FortranHmatInv[3*j + i] = HmatInv[i][j];
131      }
132    }
133 +
134 +  setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic);
135 +
136   }
137  
138  
139 < void SimInfo::getBoxM (double theBox[9]) {
139 > void SimInfo::getBoxM (double theBox[3][3]) {
140  
141 <  int i;
142 <  for(i=0; i<9; i++) theBox[i] = Hmat[i];
141 >  int i, j;
142 >  for(i=0; i<3; i++)
143 >    for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j];
144   }
145  
146  
147   void SimInfo::scaleBox(double scale) {
148 <  double theBox[9];
149 <  int i;
148 >  double theBox[3][3];
149 >  int i, j;
150  
151 <  for(i=0; i<9; i++) theBox[i] = Hmat[i]*scale;
151 >  // cerr << "Scaling box by " << scale << "\n";
152  
153 +  for(i=0; i<3; i++)
154 +    for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
155 +
156    setBoxM(theBox);
157  
158   }
159  
160 < void SimInfo::calcHmatI( void ) {
161 <
162 <  double C[3][3];
163 <  double detHmat;
189 <  int i, j, k;
160 > void SimInfo::calcHmatInv( void ) {
161 >  
162 >  int oldOrtho;
163 >  int i,j;
164    double smallDiag;
165    double tol;
166    double sanity[3][3];
167  
168 <  // calculate the adjunct of Hmat;
168 >  invertMat3( Hmat, HmatInv );
169  
170 <  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
170 >  // check to see if Hmat is orthorhombic
171    
172 <  detHmat = 0.0;
211 <  for(i=0; i<3; i++) detHmat += Hmat[i] * C[i][0];
172 >  oldOrtho = orthoRhombic;
173  
174 <  
175 <  // H^-1 = C^T / det(H)
176 <  
177 <  i=0;
217 <  for(j=0; j<3; j++){
218 <    for(k=0; k<3; k++){
174 >  smallDiag = fabs(Hmat[0][0]);
175 >  if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]);
176 >  if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]);
177 >  tol = smallDiag * orthoTolerance;
178  
179 <      HmatI[i] = C[j][k] / detHmat;
180 <      i++;
181 <    }
182 <  }
183 <
184 <  // sanity check
185 <
186 <  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];
179 >  orthoRhombic = 1;
180 >  
181 >  for (i = 0; i < 3; i++ ) {
182 >    for (j = 0 ; j < 3; j++) {
183 >      if (i != j) {
184 >        if (orthoRhombic) {
185 >          if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0;
186 >        }        
187        }
188      }
189    }
190  
191 <  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";
191 >  if( oldOrtho != orthoRhombic ){
192      
193 <
194 <  // check to see if Hmat is orthorhombic
195 <  
196 <  smallDiag = Hmat[0];
197 <  if(smallDiag > Hmat[4]) smallDiag = Hmat[4];
198 <  if(smallDiag > Hmat[8]) smallDiag = Hmat[8];
199 <  tol = smallDiag * 1E-6;
200 <
201 <  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);
193 >    if( orthoRhombic ){
194 >      sprintf( painCave.errMsg,
195 >               "OOPSE is switching from the default Non-Orthorhombic\n"
196 >               "\tto the faster Orthorhombic periodic boundary computations.\n"
197 >               "\tThis is usually a good thing, but if you wan't the\n"
198 >               "\tNon-Orthorhombic computations, make the orthoBoxTolerance\n"
199 >               "\tvariable ( currently set to %G ) smaller.\n",
200 >               orthoTolerance);
201 >      simError();
202      }
203 +    else {
204 +      sprintf( painCave.errMsg,
205 +               "OOPSE is switching from the faster Orthorhombic to the more\n"
206 +               "\tflexible Non-Orthorhombic periodic boundary computations.\n"
207 +               "\tThis is usually because the box has deformed under\n"
208 +               "\tNPTf integration. If you wan't to live on the edge with\n"
209 +               "\tthe Orthorhombic computations, make the orthoBoxTolerance\n"
210 +               "\tvariable ( currently set to %G ) larger.\n",
211 +               orthoTolerance);
212 +      simError();
213 +    }
214    }
258 –    
215   }
216  
217   void SimInfo::calcBoxL( void ){
218  
219    double dx, dy, dz, dsq;
264 –  int i;
220  
221 <  // boxVol = h1 (dot) h2 (cross) h3
221 >  // boxVol = Determinant of Hmat
222  
223 <  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]) );
223 >  boxVol = matDet3( Hmat );
224  
272 –
225    // boxLx
226    
227 <  dx = Hmat[0]; dy = Hmat[1]; dz = Hmat[2];
227 >  dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
228    dsq = dx*dx + dy*dy + dz*dz;
229 <  boxLx = sqrt( dsq );
229 >  boxL[0] = sqrt( dsq );
230 >  //maxCutoff = 0.5 * boxL[0];
231  
232    // boxLy
233    
234 <  dx = Hmat[3]; dy = Hmat[4]; dz = Hmat[5];
234 >  dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
235    dsq = dx*dx + dy*dy + dz*dz;
236 <  boxLy = sqrt( dsq );
236 >  boxL[1] = sqrt( dsq );
237 >  //if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
238  
239 +
240    // boxLz
241    
242 <  dx = Hmat[6]; dy = Hmat[7]; dz = Hmat[8];
242 >  dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
243    dsq = dx*dx + dy*dy + dz*dz;
244 <  boxLz = sqrt( dsq );
244 >  boxL[2] = sqrt( dsq );
245 >  //if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
246 >
247 >  //calculate the max cutoff
248 >  maxCutoff =  calcMaxCutOff();
249    
250 +  checkCutOffs();
251 +
252   }
253  
254  
255 + double SimInfo::calcMaxCutOff(){
256 +
257 +  double ri[3], rj[3], rk[3];
258 +  double rij[3], rjk[3], rki[3];
259 +  double minDist;
260 +
261 +  ri[0] = Hmat[0][0];
262 +  ri[1] = Hmat[1][0];
263 +  ri[2] = Hmat[2][0];
264 +
265 +  rj[0] = Hmat[0][1];
266 +  rj[1] = Hmat[1][1];
267 +  rj[2] = Hmat[2][1];
268 +
269 +  rk[0] = Hmat[0][2];
270 +  rk[1] = Hmat[1][2];
271 +  rk[2] = Hmat[2][2];
272 +    
273 +  crossProduct3(ri, rj, rij);
274 +  distXY = dotProduct3(rk,rij) / norm3(rij);
275 +
276 +  crossProduct3(rj,rk, rjk);
277 +  distYZ = dotProduct3(ri,rjk) / norm3(rjk);
278 +
279 +  crossProduct3(rk,ri, rki);
280 +  distZX = dotProduct3(rj,rki) / norm3(rki);
281 +
282 +  minDist = min(min(distXY, distYZ), distZX);
283 +  return minDist/2;
284 +  
285 + }
286 +
287   void SimInfo::wrapVector( double thePos[3] ){
288  
289 <  int i, j, k;
289 >  int i;
290    double scaled[3];
291  
292    if( !orthoRhombic ){
293      // calc the scaled coordinates.
294 +  
295 +
296 +    matVecMul3(HmatInv, thePos, scaled);
297      
298      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++)
299        scaled[i] -= roundMe(scaled[i]);
300      
301      // calc the wrapped real coordinates from the wrapped scaled coordinates
302      
303 <    for(i=0; i<3; i++)
304 <      thePos[i] =
315 <        scaled[0]*Hmat[i] + scaled[1]*Hmat[i+3] + scaled[2]*Hmat[i+6];
303 >    matVecMul3(Hmat, scaled, thePos);
304 >
305    }
306    else{
307      // calc the scaled coordinates.
308      
309      for(i=0; i<3; i++)
310 <      scaled[i] = thePos[i]*HmatI[i*4];
310 >      scaled[i] = thePos[i]*HmatInv[i][i];
311      
312      // wrap the scaled coordinates
313      
# Line 328 | Line 317 | void SimInfo::wrapVector( double thePos[3] ){
317      // calc the wrapped real coordinates from the wrapped scaled coordinates
318      
319      for(i=0; i<3; i++)
320 <      thePos[i] = scaled[i]*Hmat[i*4];
320 >      thePos[i] = scaled[i]*Hmat[i][i];
321    }
322      
334 –    
323   }
324  
325  
326   int SimInfo::getNDF(){
327 <  int ndf_local, ndf;
327 >  int ndf_local;
328 >
329 >  ndf_local = 0;
330    
331 <  ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints;
331 >  for(int i = 0; i < integrableObjects.size(); i++){
332 >    ndf_local += 3;
333 >    if (integrableObjects[i]->isDirectional()) {
334 >      if (integrableObjects[i]->isLinear())
335 >        ndf_local += 2;
336 >      else
337 >        ndf_local += 3;
338 >    }
339 >  }
340  
341 +  // n_constraints is local, so subtract them on each processor:
342 +
343 +  ndf_local -= n_constraints;
344 +
345   #ifdef IS_MPI
346    MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
347   #else
348    ndf = ndf_local;
349   #endif
350  
351 <  ndf = ndf - 3;
351 >  // nZconstraints is global, as are the 3 COM translations for the
352 >  // entire system:
353  
354 +  ndf = ndf - 3 - nZconstraints;
355 +
356    return ndf;
357   }
358  
359   int SimInfo::getNDFraw() {
360 <  int ndfRaw_local, ndfRaw;
360 >  int ndfRaw_local;
361  
362    // Raw degrees of freedom that we have to set
363 <  ndfRaw_local = 3 * n_atoms + 3 * n_oriented;
364 <  
363 >  ndfRaw_local = 0;
364 >
365 >  for(int i = 0; i < integrableObjects.size(); i++){
366 >    ndfRaw_local += 3;
367 >    if (integrableObjects[i]->isDirectional()) {
368 >       if (integrableObjects[i]->isLinear())
369 >        ndfRaw_local += 2;
370 >      else
371 >        ndfRaw_local += 3;
372 >    }
373 >  }
374 >    
375   #ifdef IS_MPI
376    MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
377   #else
# Line 365 | Line 380 | int SimInfo::getNDFraw() {
380  
381    return ndfRaw;
382   }
383 <
383 >
384 > int SimInfo::getNDFtranslational() {
385 >  int ndfTrans_local;
386 >
387 >  ndfTrans_local = 3 * integrableObjects.size() - n_constraints;
388 >
389 >
390 > #ifdef IS_MPI
391 >  MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
392 > #else
393 >  ndfTrans = ndfTrans_local;
394 > #endif
395 >
396 >  ndfTrans = ndfTrans - 3 - nZconstraints;
397 >
398 >  return ndfTrans;
399 > }
400 >
401 > int SimInfo::getTotIntegrableObjects() {
402 >  int nObjs_local;
403 >  int nObjs;
404 >
405 >  nObjs_local =  integrableObjects.size();
406 >
407 >
408 > #ifdef IS_MPI
409 >  MPI_Allreduce(&nObjs_local,&nObjs,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
410 > #else
411 >  nObjs = nObjs_local;
412 > #endif
413 >
414 >
415 >  return nObjs;
416 > }
417 >
418   void SimInfo::refreshSim(){
419  
420    simtype fInfo;
421    int isError;
422    int n_global;
423    int* excl;
424 <  
376 <  fInfo.rrf = 0.0;
377 <  fInfo.rt = 0.0;
424 >
425    fInfo.dielect = 0.0;
426  
427 <  fInfo.rlist = rList;
381 <  fInfo.rcut = rCut;
382 <
383 <  if( useDipole ){
384 <    fInfo.rrf = ecr;
385 <    fInfo.rt = ecr - est;
427 >  if( useDipoles ){
428      if( useReactionField )fInfo.dielect = dielectric;
429    }
430  
# Line 391 | Line 433 | void SimInfo::refreshSim(){
433    fInfo.SIM_uses_LJ = useLJ;
434    fInfo.SIM_uses_sticky = useSticky;
435    //fInfo.SIM_uses_sticky = 0;
436 <  fInfo.SIM_uses_dipoles = useDipole;
436 >  fInfo.SIM_uses_charges = useCharges;
437 >  fInfo.SIM_uses_dipoles = useDipoles;
438    //fInfo.SIM_uses_dipoles = 0;
439 <  //fInfo.SIM_uses_RF = useReactionField;
440 <  fInfo.SIM_uses_RF = 0;
439 >  fInfo.SIM_uses_RF = useReactionField;
440 >  //fInfo.SIM_uses_RF = 0;
441    fInfo.SIM_uses_GB = useGB;
442    fInfo.SIM_uses_EAM = useEAM;
443  
444 <  excl = Exclude::getArray();
445 <
444 >  n_exclude = excludes->getSize();
445 >  excl = excludes->getFortranArray();
446 >  
447   #ifdef IS_MPI
448    n_global = mpiSim->getTotAtoms();
449   #else
450    n_global = n_atoms;
451   #endif
452 <
452 >  
453    isError = 0;
454 <
454 >  
455 >  getFortranGroupArray(this, mfact, ngroup, groupList, groupStart);
456 >  //it may not be a good idea to pass the address of first element in vector
457 >  //since c++ standard does not require vector to be stored continuously in meomory
458 >  //Most of the compilers will organize the memory of vector continuously
459    setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl,
460 <                  &nGlobalExcludes, globalExcludes, molMembershipArray,
461 <                  &isError );
462 <
460 >                  &nGlobalExcludes, globalExcludes, molMembershipArray,
461 >                  &mfact[0], &ngroup, &groupList[0], &groupStart[0], &isError);
462 >  
463    if( isError ){
464 <
464 >    
465      sprintf( painCave.errMsg,
466 <             "There was an error setting the simulation information in fortran.\n" );
466 >             "There was an error setting the simulation information in fortran.\n" );
467      painCave.isFatal = 1;
468      simError();
469    }
470 <
470 >  
471   #ifdef IS_MPI
472    sprintf( checkPointMsg,
473             "succesfully sent the simulation information to fortran.\n");
474    MPIcheckPoint();
475   #endif // is_mpi
476 <
476 >  
477    this->ndf = this->getNDF();
478    this->ndfRaw = this->getNDFraw();
479 +  this->ndfTrans = this->getNDFtranslational();
480 + }
481  
482 + void SimInfo::setDefaultRcut( double theRcut ){
483 +  
484 +  haveRcut = 1;
485 +  rCut = theRcut;
486 +  rList = rCut + 1.0;
487 +  
488 +  notifyFortranCutOffs( &rCut, &rSw, &rList );
489   }
490  
491 + void SimInfo::setDefaultRcut( double theRcut, double theRsw ){
492 +
493 +  rSw = theRsw;
494 +  setDefaultRcut( theRcut );
495 + }
496 +
497 +
498 + void SimInfo::checkCutOffs( void ){
499 +  
500 +  if( boxIsInit ){
501 +    
502 +    //we need to check cutOffs against the box
503 +    
504 +    if( rCut > maxCutoff ){
505 +      sprintf( painCave.errMsg,
506 +               "cutoffRadius is too large for the current periodic box.\n"
507 +               "\tCurrent Value of cutoffRadius = %G at time %G\n "
508 +               "\tThis is larger than half of at least one of the\n"
509 +               "\tperiodic box vectors.  Right now, the Box matrix is:\n"
510 +               "\n"
511 +               "\t[ %G %G %G ]\n"
512 +               "\t[ %G %G %G ]\n"
513 +               "\t[ %G %G %G ]\n",
514 +               rCut, currentTime,
515 +               Hmat[0][0], Hmat[0][1], Hmat[0][2],
516 +               Hmat[1][0], Hmat[1][1], Hmat[1][2],
517 +               Hmat[2][0], Hmat[2][1], Hmat[2][2]);
518 +      painCave.isFatal = 1;
519 +      simError();
520 +    }    
521 +  } else {
522 +    // initialize this stuff before using it, OK?
523 +    sprintf( painCave.errMsg,
524 +             "Trying to check cutoffs without a box.\n"
525 +             "\tOOPSE should have better programmers than that.\n" );
526 +    painCave.isFatal = 1;
527 +    simError();      
528 +  }
529 +  
530 + }
531 +
532 + void SimInfo::addProperty(GenericData* prop){
533 +
534 +  map<string, GenericData*>::iterator result;
535 +  result = properties.find(prop->getID());
536 +  
537 +  //we can't simply use  properties[prop->getID()] = prop,
538 +  //it will cause memory leak if we already contain a propery which has the same name of prop
539 +  
540 +  if(result != properties.end()){
541 +    
542 +    delete (*result).second;
543 +    (*result).second = prop;
544 +      
545 +  }
546 +  else{
547 +
548 +    properties[prop->getID()] = prop;
549 +
550 +  }
551 +    
552 + }
553 +
554 + GenericData* SimInfo::getProperty(const string& propName){
555 +
556 +  map<string, GenericData*>::iterator result;
557 +  
558 +  //string lowerCaseName = ();
559 +  
560 +  result = properties.find(propName);
561 +  
562 +  if(result != properties.end())
563 +    return (*result).second;  
564 +  else  
565 +    return NULL;  
566 + }
567 +
568 +
569 + void getFortranGroupArray(SimInfo* info, vector<double>& mfact, int& ngroup,
570 +                          vector<int>& groupList, vector<int>& groupStart){
571 +  Molecule* myMols;
572 +  Atom** myAtoms;
573 +  int numAtom;
574 +  int curIndex;
575 +  double mtot;
576 +  int numMol;
577 +  int numCutoffGroups;
578 +  CutoffGroup* myCutoffGroup;
579 +  vector<CutoffGroup*>::iterator iterCutoff;
580 +  Atom* cutoffAtom;
581 +  vector<Atom*>::iterator iterAtom;
582 +  int atomIndex;
583 +  double totalMass;
584 +  
585 +  mfact.clear();
586 +  groupList.clear();
587 +  groupStart.clear();
588 +  
589 +  //Be careful, fortran array begin at 1
590 +  curIndex = 1;
591 +
592 +  myMols = info->molecules;
593 +  numMol = info->n_mol;
594 +  for(int i  = 0; i < numMol; i++){
595 +    numCutoffGroups = myMols[i].getNCutoffGroups();
596 +    for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff); myCutoffGroup != NULL;
597 +                                                  myCutoffGroup =myMols[i].nextCutoffGroup(iterCutoff)){
598 +
599 +      totalMass = myCutoffGroup->getMass();
600 +      
601 +      for(cutoffAtom = myCutoffGroup->beginAtom(iterAtom); cutoffAtom != NULL;
602 +                                           cutoffAtom = myCutoffGroup->nextAtom(iterAtom)){
603 +        mfact.push_back(cutoffAtom->getMass()/totalMass);
604 +        groupList.push_back(cutoffAtom->getIndex() + 1);
605 +      }  
606 +                              
607 +      groupStart.push_back(curIndex);
608 +      curIndex += myCutoffGroup->getNumAtom();
609 +
610 +    }//end for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff))
611 +
612 +  }//end for(int i  = 0; i < numMol; i++)
613 +
614 +
615 +  //The last cutoff group need more element to indicate the end of the cutoff
616 +  groupStart.push_back(curIndex);
617 +  ngroup = groupStart.size() - 1;
618 + }

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