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root/group/trunk/OOPSE/libmdtools/SimInfo.cpp
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Comparing trunk/OOPSE/libmdtools/SimInfo.cpp (file contents):
Revision 568 by mmeineke, Mon Jun 30 22:04:01 2003 UTC vs.
Revision 1214 by gezelter, Tue Jun 1 18:42:58 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 +  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 +  useSolidThermInt = 0;
66 +  useLiquidThermInt = 0;
67  
68 <  wrapMeSimInfo( this );
40 < }
68 >  haveCutoffGroups = false;
69  
70 < void SimInfo::setBox(double newBox[3]) {
70 >  excludes = Exclude::Instance();
71  
72 <  double smallestBoxL, maxCutoff;
45 <  int status;
46 <  int i;
72 >  myConfiguration = new SimState();
73  
74 <  for(i=0; i<9; i++) Hmat[i] = 0.0;;
74 >  has_minimizer = false;
75 >  the_minimizer =NULL;
76  
77 <  Hmat[0] = newBox[0];
51 <  Hmat[4] = newBox[1];
52 <  Hmat[8] = newBox[2];
77 >  ngroup = 0;
78  
79 <  calcHmatI();
80 <  calcBoxL();
79 >  wrapMeSimInfo( this );
80 > }
81  
57 –  setFortranBoxSize(Hmat);
82  
83 <  smallestBoxL = boxLx;
60 <  if (boxLy < smallestBoxL) smallestBoxL = boxLy;
61 <  if (boxLz < smallestBoxL) smallestBoxL = boxLz;
83 > SimInfo::~SimInfo(){
84  
85 <  maxCutoff = smallestBoxL / 2.0;
85 >  delete myConfiguration;
86  
87 <  if (rList > maxCutoff) {
88 <    sprintf( painCave.errMsg,
89 <             "New Box size is forcing neighborlist radius down to %lf\n",
90 <             maxCutoff );
91 <    painCave.isFatal = 0;
92 <    simError();
87 >  map<string, GenericData*>::iterator i;
88 >  
89 >  for(i = properties.begin(); i != properties.end(); i++)
90 >    delete (*i).second;
91 >  
92 > }
93  
94 <    rList = maxCutoff;
94 > void SimInfo::setBox(double newBox[3]) {
95 >  
96 >  int i, j;
97 >  double tempMat[3][3];
98  
99 <    sprintf( painCave.errMsg,
100 <             "New Box size is forcing cutoff radius down to %lf\n",
76 <             maxCutoff - 1.0 );
77 <    painCave.isFatal = 0;
78 <    simError();
99 >  for(i=0; i<3; i++)
100 >    for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
101  
102 <    rCut = rList - 1.0;
102 >  tempMat[0][0] = newBox[0];
103 >  tempMat[1][1] = newBox[1];
104 >  tempMat[2][2] = newBox[2];
105  
106 <    // list radius changed so we have to refresh the simulation structure.
83 <    refreshSim();
84 <  }
106 >  setBoxM( tempMat );
107  
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 –  }
108   }
109  
110 < void SimInfo::setBoxM( double theBox[9] ){
110 > void SimInfo::setBoxM( double theBox[3][3] ){
111    
112 <  int i, status;
113 <  double smallestBoxL, maxCutoff;
112 >  int i, j;
113 >  double FortranHmat[9]; // to preserve compatibility with Fortran the
114 >                         // ordering in the array is as follows:
115 >                         // [ 0 3 6 ]
116 >                         // [ 1 4 7 ]
117 >                         // [ 2 5 8 ]
118 >  double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
119  
120 <  for(i=0; i<9; i++) Hmat[i] = theBox[i];
121 <  calcHmatI();
120 >  if( !boxIsInit ) boxIsInit = 1;
121 >
122 >  for(i=0; i < 3; i++)
123 >    for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
124 >  
125    calcBoxL();
126 +  calcHmatInv();
127  
128 <  setFortranBoxSize(Hmat);
128 >  for(i=0; i < 3; i++) {
129 >    for (j=0; j < 3; j++) {
130 >      FortranHmat[3*j + i] = Hmat[i][j];
131 >      FortranHmatInv[3*j + i] = HmatInv[i][j];
132 >    }
133 >  }
134 >
135 >  setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic);
136  
137 <  smallestBoxL = boxLx;
138 <  if (boxLy < smallestBoxL) smallestBoxL = boxLy;
117 <  if (boxLz < smallestBoxL) smallestBoxL = boxLz;
137 > }
138 >
139  
140 <  maxCutoff = smallestBoxL / 2.0;
140 > void SimInfo::getBoxM (double theBox[3][3]) {
141  
142 <  if (rList > maxCutoff) {
143 <    sprintf( painCave.errMsg,
144 <             "New Box size is forcing neighborlist radius down to %lf\n",
145 <             maxCutoff );
125 <    painCave.isFatal = 0;
126 <    simError();
142 >  int i, j;
143 >  for(i=0; i<3; i++)
144 >    for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j];
145 > }
146  
128 –    rList = maxCutoff;
147  
148 <    sprintf( painCave.errMsg,
149 <             "New Box size is forcing cutoff radius down to %lf\n",
150 <             maxCutoff - 1.0 );
133 <    painCave.isFatal = 0;
134 <    simError();
148 > void SimInfo::scaleBox(double scale) {
149 >  double theBox[3][3];
150 >  int i, j;
151  
152 <    rCut = rList - 1.0;
152 >  // cerr << "Scaling box by " << scale << "\n";
153  
154 <    // list radius changed so we have to refresh the simulation structure.
155 <    refreshSim();
140 <  }
154 >  for(i=0; i<3; i++)
155 >    for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
156  
157 <  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();
157 >  setBoxM(theBox);
158  
159 <    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 <
159 > }
160  
161 < void SimInfo::getBox(double theBox[9]) {
161 > void SimInfo::calcHmatInv( void ) {
162 >  
163 >  int oldOrtho;
164 >  int i,j;
165 >  double smallDiag;
166 >  double tol;
167 >  double sanity[3][3];
168  
169 <  int i;
164 <  for(i=0; i<9; i++) theBox[i] = Hmat[i];
165 < }
166 <
169 >  invertMat3( Hmat, HmatInv );
170  
171 < void SimInfo::calcHmatI( void ) {
171 >  // check to see if Hmat is orthorhombic
172 >  
173 >  oldOrtho = orthoRhombic;
174  
175 <  double C[3][3];
176 <  double detHmat;
177 <  int i, j, k;
175 >  smallDiag = fabs(Hmat[0][0]);
176 >  if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]);
177 >  if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]);
178 >  tol = smallDiag * orthoTolerance;
179  
180 <  // calculate the adjunct of Hmat;
175 <
176 <  C[0][0] =  ( Hmat[4]*Hmat[8]) - (Hmat[7]*Hmat[5]);
177 <  C[1][0] = -( Hmat[1]*Hmat[8]) + (Hmat[7]*Hmat[2]);
178 <  C[2][0] =  ( Hmat[1]*Hmat[5]) - (Hmat[4]*Hmat[2]);
179 <
180 <  C[0][1] = -( Hmat[3]*Hmat[8]) + (Hmat[6]*Hmat[5]);
181 <  C[1][1] =  ( Hmat[0]*Hmat[8]) - (Hmat[6]*Hmat[2]);
182 <  C[2][1] = -( Hmat[0]*Hmat[5]) + (Hmat[3]*Hmat[2]);
183 <
184 <  C[0][2] =  ( Hmat[3]*Hmat[7]) - (Hmat[6]*Hmat[4]);
185 <  C[1][2] = -( Hmat[0]*Hmat[7]) + (Hmat[6]*Hmat[1]);
186 <  C[2][2] =  ( Hmat[0]*Hmat[4]) - (Hmat[3]*Hmat[1]);
187 <
188 <  // calcutlate the determinant of Hmat
180 >  orthoRhombic = 1;
181    
182 <  detHmat = 0.0;
183 <  for(i=0; i<3; i++) detHmat += Hmat[i] * C[i][0];
182 >  for (i = 0; i < 3; i++ ) {
183 >    for (j = 0 ; j < 3; j++) {
184 >      if (i != j) {
185 >        if (orthoRhombic) {
186 >          if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0;
187 >        }        
188 >      }
189 >    }
190 >  }
191  
192 <  
193 <  // H^-1 = C^T / det(H)
194 <  
195 <  i=0;
196 <  for(j=0; j<3; j++){
197 <    for(k=0; k<3; k++){
198 <
199 <      HmatI[i] = C[j][k] / detHmat;
200 <      i++;
192 >  if( oldOrtho != orthoRhombic ){
193 >    
194 >    if( orthoRhombic ){
195 >      sprintf( painCave.errMsg,
196 >               "OOPSE is switching from the default Non-Orthorhombic\n"
197 >               "\tto the faster Orthorhombic periodic boundary computations.\n"
198 >               "\tThis is usually a good thing, but if you wan't the\n"
199 >               "\tNon-Orthorhombic computations, make the orthoBoxTolerance\n"
200 >               "\tvariable ( currently set to %G ) smaller.\n",
201 >               orthoTolerance);
202 >      simError();
203      }
204 +    else {
205 +      sprintf( painCave.errMsg,
206 +               "OOPSE is switching from the faster Orthorhombic to the more\n"
207 +               "\tflexible Non-Orthorhombic periodic boundary computations.\n"
208 +               "\tThis is usually because the box has deformed under\n"
209 +               "\tNPTf integration. If you wan't to live on the edge with\n"
210 +               "\tthe Orthorhombic computations, make the orthoBoxTolerance\n"
211 +               "\tvariable ( currently set to %G ) larger.\n",
212 +               orthoTolerance);
213 +      simError();
214 +    }
215    }
216   }
217  
218   void SimInfo::calcBoxL( void ){
219  
220    double dx, dy, dz, dsq;
209 –  int i;
221  
222 <  // boxVol = h1 (dot) h2 (cross) h3
222 >  // boxVol = Determinant of Hmat
223  
224 <  boxVol = Hmat[0] * ( (Hmat[4]*Hmat[8]) - (Hmat[7]*Hmat[5]) )
214 <         + Hmat[1] * ( (Hmat[5]*Hmat[6]) - (Hmat[8]*Hmat[3]) )
215 <         + Hmat[2] * ( (Hmat[3]*Hmat[7]) - (Hmat[6]*Hmat[4]) );
224 >  boxVol = matDet3( Hmat );
225  
217 –
226    // boxLx
227    
228 <  dx = Hmat[0]; dy = Hmat[1]; dz = Hmat[2];
228 >  dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
229    dsq = dx*dx + dy*dy + dz*dz;
230 <  boxLx = sqrt( dsq );
230 >  boxL[0] = sqrt( dsq );
231 >  //maxCutoff = 0.5 * boxL[0];
232  
233    // boxLy
234    
235 <  dx = Hmat[3]; dy = Hmat[4]; dz = Hmat[5];
235 >  dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
236    dsq = dx*dx + dy*dy + dz*dz;
237 <  boxLy = sqrt( dsq );
237 >  boxL[1] = sqrt( dsq );
238 >  //if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
239  
240 +
241    // boxLz
242    
243 <  dx = Hmat[6]; dy = Hmat[7]; dz = Hmat[8];
243 >  dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
244    dsq = dx*dx + dy*dy + dz*dz;
245 <  boxLz = sqrt( dsq );
245 >  boxL[2] = sqrt( dsq );
246 >  //if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
247 >
248 >  //calculate the max cutoff
249 >  maxCutoff =  calcMaxCutOff();
250    
251 +  checkCutOffs();
252 +
253   }
254  
255  
256 < void SimInfo::wrapVector( double thePos[3] ){
256 > double SimInfo::calcMaxCutOff(){
257  
258 <  int i, j, k;
259 <  double scaled[3];
258 >  double ri[3], rj[3], rk[3];
259 >  double rij[3], rjk[3], rki[3];
260 >  double minDist;
261  
262 <  // calc the scaled coordinates.
263 <  
264 <  for(i=0; i<3; i++)
247 <    scaled[i] = thePos[0]*Hmat[i] + thePos[1]*Hat[i+3] + thePos[3]*Hmat[i+6];
262 >  ri[0] = Hmat[0][0];
263 >  ri[1] = Hmat[1][0];
264 >  ri[2] = Hmat[2][0];
265  
266 <  // wrap the scaled coordinates
266 >  rj[0] = Hmat[0][1];
267 >  rj[1] = Hmat[1][1];
268 >  rj[2] = Hmat[2][1];
269  
270 <  for(i=0; i<3; i++)
271 <    scaled[i] -= (copysign(1,scaled[i]) * (int)(fabs(scaled[i]) + 0.5));
270 >  rk[0] = Hmat[0][2];
271 >  rk[1] = Hmat[1][2];
272 >  rk[2] = Hmat[2][2];
273 >    
274 >  crossProduct3(ri, rj, rij);
275 >  distXY = dotProduct3(rk,rij) / norm3(rij);
276 >
277 >  crossProduct3(rj,rk, rjk);
278 >  distYZ = dotProduct3(ri,rjk) / norm3(rjk);
279 >
280 >  crossProduct3(rk,ri, rki);
281 >  distZX = dotProduct3(rj,rki) / norm3(rki);
282 >
283 >  minDist = min(min(distXY, distYZ), distZX);
284 >  return minDist/2;
285    
286 + }
287  
288 + void SimInfo::wrapVector( double thePos[3] ){
289 +
290 +  int i;
291 +  double scaled[3];
292 +
293 +  if( !orthoRhombic ){
294 +    // calc the scaled coordinates.
295 +  
296 +
297 +    matVecMul3(HmatInv, thePos, scaled);
298 +    
299 +    for(i=0; i<3; i++)
300 +      scaled[i] -= roundMe(scaled[i]);
301 +    
302 +    // calc the wrapped real coordinates from the wrapped scaled coordinates
303 +    
304 +    matVecMul3(Hmat, scaled, thePos);
305 +
306 +  }
307 +  else{
308 +    // calc the scaled coordinates.
309 +    
310 +    for(i=0; i<3; i++)
311 +      scaled[i] = thePos[i]*HmatInv[i][i];
312 +    
313 +    // wrap the scaled coordinates
314 +    
315 +    for(i=0; i<3; i++)
316 +      scaled[i] -= roundMe(scaled[i]);
317 +    
318 +    // calc the wrapped real coordinates from the wrapped scaled coordinates
319 +    
320 +    for(i=0; i<3; i++)
321 +      thePos[i] = scaled[i]*Hmat[i][i];
322 +  }
323 +    
324   }
325  
326  
327   int SimInfo::getNDF(){
328 <  int ndf_local, ndf;
328 >  int ndf_local;
329 >
330 >  ndf_local = 0;
331    
332 <  ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints;
332 >  for(int i = 0; i < integrableObjects.size(); i++){
333 >    ndf_local += 3;
334 >    if (integrableObjects[i]->isDirectional()) {
335 >      if (integrableObjects[i]->isLinear())
336 >        ndf_local += 2;
337 >      else
338 >        ndf_local += 3;
339 >    }
340 >  }
341  
342 +  // n_constraints is local, so subtract them on each processor:
343 +
344 +  ndf_local -= n_constraints;
345 +
346   #ifdef IS_MPI
347    MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
348   #else
349    ndf = ndf_local;
350   #endif
351  
352 <  ndf = ndf - 3;
352 >  // nZconstraints is global, as are the 3 COM translations for the
353 >  // entire system:
354  
355 +  ndf = ndf - 3 - nZconstraints;
356 +
357    return ndf;
358   }
359  
360   int SimInfo::getNDFraw() {
361 <  int ndfRaw_local, ndfRaw;
361 >  int ndfRaw_local;
362  
363    // Raw degrees of freedom that we have to set
364 <  ndfRaw_local = 3 * n_atoms + 3 * n_oriented;
365 <  
364 >  ndfRaw_local = 0;
365 >
366 >  for(int i = 0; i < integrableObjects.size(); i++){
367 >    ndfRaw_local += 3;
368 >    if (integrableObjects[i]->isDirectional()) {
369 >       if (integrableObjects[i]->isLinear())
370 >        ndfRaw_local += 2;
371 >      else
372 >        ndfRaw_local += 3;
373 >    }
374 >  }
375 >    
376   #ifdef IS_MPI
377    MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
378   #else
# Line 285 | Line 381 | int SimInfo::getNDFraw() {
381  
382    return ndfRaw;
383   }
384 <
384 >
385 > int SimInfo::getNDFtranslational() {
386 >  int ndfTrans_local;
387 >
388 >  ndfTrans_local = 3 * integrableObjects.size() - n_constraints;
389 >
390 >
391 > #ifdef IS_MPI
392 >  MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
393 > #else
394 >  ndfTrans = ndfTrans_local;
395 > #endif
396 >
397 >  ndfTrans = ndfTrans - 3 - nZconstraints;
398 >
399 >  return ndfTrans;
400 > }
401 >
402 > int SimInfo::getTotIntegrableObjects() {
403 >  int nObjs_local;
404 >  int nObjs;
405 >
406 >  nObjs_local =  integrableObjects.size();
407 >
408 >
409 > #ifdef IS_MPI
410 >  MPI_Allreduce(&nObjs_local,&nObjs,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
411 > #else
412 >  nObjs = nObjs_local;
413 > #endif
414 >
415 >
416 >  return nObjs;
417 > }
418 >
419   void SimInfo::refreshSim(){
420  
421    simtype fInfo;
422    int isError;
423    int n_global;
424    int* excl;
425 <  
296 <  fInfo.rrf = 0.0;
297 <  fInfo.rt = 0.0;
425 >
426    fInfo.dielect = 0.0;
427  
428 <  fInfo.box[0] = box_x;
301 <  fInfo.box[1] = box_y;
302 <  fInfo.box[2] = box_z;
303 <
304 <  fInfo.rlist = rList;
305 <  fInfo.rcut = rCut;
306 <
307 <  if( useDipole ){
308 <    fInfo.rrf = ecr;
309 <    fInfo.rt = ecr - est;
428 >  if( useDipoles ){
429      if( useReactionField )fInfo.dielect = dielectric;
430    }
431  
# Line 315 | Line 434 | void SimInfo::refreshSim(){
434    fInfo.SIM_uses_LJ = useLJ;
435    fInfo.SIM_uses_sticky = useSticky;
436    //fInfo.SIM_uses_sticky = 0;
437 <  fInfo.SIM_uses_dipoles = useDipole;
437 >  fInfo.SIM_uses_charges = useCharges;
438 >  fInfo.SIM_uses_dipoles = useDipoles;
439    //fInfo.SIM_uses_dipoles = 0;
440 <  //fInfo.SIM_uses_RF = useReactionField;
441 <  fInfo.SIM_uses_RF = 0;
440 >  fInfo.SIM_uses_RF = useReactionField;
441 >  //fInfo.SIM_uses_RF = 0;
442    fInfo.SIM_uses_GB = useGB;
443    fInfo.SIM_uses_EAM = useEAM;
444  
445 <  excl = Exclude::getArray();
446 <
445 >  n_exclude = excludes->getSize();
446 >  excl = excludes->getFortranArray();
447 >  
448   #ifdef IS_MPI
449 <  n_global = mpiSim->getTotAtoms();
449 >  n_global = mpiSim->getNAtomsGlobal();
450   #else
451    n_global = n_atoms;
452   #endif
453 <
453 >  
454    isError = 0;
455 <
455 >  
456 >  getFortranGroupArrays(this, FglobalGroupMembership, mfact);
457 >  //it may not be a good idea to pass the address of first element in vector
458 >  //since c++ standard does not require vector to be stored continuously in meomory
459 >  //Most of the compilers will organize the memory of vector continuously
460    setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl,
461 <                  &nGlobalExcludes, globalExcludes, molMembershipArray,
462 <                  &isError );
463 <
461 >                  &nGlobalExcludes, globalExcludes, molMembershipArray,
462 >                  &mfact[0], &ngroup, &FglobalGroupMembership[0], &isError);
463 >  
464    if( isError ){
465 <
465 >    
466      sprintf( painCave.errMsg,
467 <             "There was an error setting the simulation information in fortran.\n" );
467 >             "There was an error setting the simulation information in fortran.\n" );
468      painCave.isFatal = 1;
469      simError();
470    }
471 <
471 >  
472   #ifdef IS_MPI
473    sprintf( checkPointMsg,
474             "succesfully sent the simulation information to fortran.\n");
475    MPIcheckPoint();
476   #endif // is_mpi
477 <
477 >  
478    this->ndf = this->getNDF();
479    this->ndfRaw = this->getNDFraw();
480 +  this->ndfTrans = this->getNDFtranslational();
481 + }
482  
483 + void SimInfo::setDefaultRcut( double theRcut ){
484 +  
485 +  haveRcut = 1;
486 +  rCut = theRcut;
487 +  rList = rCut + 1.0;
488 +  
489 +  notifyFortranCutOffs( &rCut, &rSw, &rList );
490   }
491  
492 + void SimInfo::setDefaultRcut( double theRcut, double theRsw ){
493 +
494 +  rSw = theRsw;
495 +  setDefaultRcut( theRcut );
496 + }
497 +
498 +
499 + void SimInfo::checkCutOffs( void ){
500 +  
501 +  if( boxIsInit ){
502 +    
503 +    //we need to check cutOffs against the box
504 +    
505 +    if( rCut > maxCutoff ){
506 +      sprintf( painCave.errMsg,
507 +               "cutoffRadius is too large for the current periodic box.\n"
508 +               "\tCurrent Value of cutoffRadius = %G at time %G\n "
509 +               "\tThis is larger than half of at least one of the\n"
510 +               "\tperiodic box vectors.  Right now, the Box matrix is:\n"
511 +               "\n"
512 +               "\t[ %G %G %G ]\n"
513 +               "\t[ %G %G %G ]\n"
514 +               "\t[ %G %G %G ]\n",
515 +               rCut, currentTime,
516 +               Hmat[0][0], Hmat[0][1], Hmat[0][2],
517 +               Hmat[1][0], Hmat[1][1], Hmat[1][2],
518 +               Hmat[2][0], Hmat[2][1], Hmat[2][2]);
519 +      painCave.isFatal = 1;
520 +      simError();
521 +    }    
522 +  } else {
523 +    // initialize this stuff before using it, OK?
524 +    sprintf( painCave.errMsg,
525 +             "Trying to check cutoffs without a box.\n"
526 +             "\tOOPSE should have better programmers than that.\n" );
527 +    painCave.isFatal = 1;
528 +    simError();      
529 +  }
530 +  
531 + }
532 +
533 + void SimInfo::addProperty(GenericData* prop){
534 +
535 +  map<string, GenericData*>::iterator result;
536 +  result = properties.find(prop->getID());
537 +  
538 +  //we can't simply use  properties[prop->getID()] = prop,
539 +  //it will cause memory leak if we already contain a propery which has the same name of prop
540 +  
541 +  if(result != properties.end()){
542 +    
543 +    delete (*result).second;
544 +    (*result).second = prop;
545 +      
546 +  }
547 +  else{
548 +
549 +    properties[prop->getID()] = prop;
550 +
551 +  }
552 +    
553 + }
554 +
555 + GenericData* SimInfo::getProperty(const string& propName){
556 +
557 +  map<string, GenericData*>::iterator result;
558 +  
559 +  //string lowerCaseName = ();
560 +  
561 +  result = properties.find(propName);
562 +  
563 +  if(result != properties.end())
564 +    return (*result).second;  
565 +  else  
566 +    return NULL;  
567 + }
568 +
569 +
570 + void SimInfo::getFortranGroupArrays(SimInfo* info,
571 +                                    vector<int>& FglobalGroupMembership,
572 +                                    vector<double>& mfact){
573 +  
574 +  Molecule* myMols;
575 +  Atom** myAtoms;
576 +  int numAtom;
577 +  double mtot;
578 +  int numMol;
579 +  int numCutoffGroups;
580 +  CutoffGroup* myCutoffGroup;
581 +  vector<CutoffGroup*>::iterator iterCutoff;
582 +  Atom* cutoffAtom;
583 +  vector<Atom*>::iterator iterAtom;
584 +  int atomIndex;
585 +  double totalMass;
586 +  
587 +  mfact.clear();
588 +  FglobalGroupMembership.clear();
589 +  
590 +
591 +  // Fix the silly fortran indexing problem
592 + #ifdef IS_MPI
593 +  numAtom = mpiSim->getNAtomsGlobal();
594 + #else
595 +  numAtom = n_atoms;
596 + #endif
597 +  for (int i = 0; i < numAtom; i++)
598 +    FglobalGroupMembership.push_back(globalGroupMembership[i] + 1);
599 +
600 +  myMols = info->molecules;
601 +  numMol = info->n_mol;
602 +  for(int i  = 0; i < numMol; i++){
603 +    numCutoffGroups = myMols[i].getNCutoffGroups();
604 +    for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff);
605 +        myCutoffGroup != NULL;
606 +        myCutoffGroup =myMols[i].nextCutoffGroup(iterCutoff)){
607 +
608 +      totalMass = myCutoffGroup->getMass();
609 +      
610 +      for(cutoffAtom = myCutoffGroup->beginAtom(iterAtom);
611 +          cutoffAtom != NULL;
612 +          cutoffAtom = myCutoffGroup->nextAtom(iterAtom)){
613 +        mfact.push_back(cutoffAtom->getMass()/totalMass);
614 +      }  
615 +    }
616 +  }
617 +
618 + }

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