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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 1113 by tim, Thu Apr 15 16:18:26 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 +  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  
67 <  wrapMeSimInfo( this );
47 < }
67 >  excludes = Exclude::Instance();
68  
69 < void SimInfo::setBox(double newBox[3]) {
69 >  myConfiguration = new SimState();
70  
71 <  double smallestBoxL, maxCutoff;
72 <  int status;
53 <  int i;
71 >  has_minimizer = false;
72 >  the_minimizer =NULL;
73  
74 <  for(i=0; i<9; i++) Hmat[i] = 0.0;;
74 >  wrapMeSimInfo( this );
75 > }
76  
57 –  Hmat[0] = newBox[0];
58 –  Hmat[4] = newBox[1];
59 –  Hmat[8] = newBox[2];
77  
78 <  calcHmatI();
62 <  calcBoxL();
78 > SimInfo::~SimInfo(){
79  
80 <  setFortranBoxSize(Hmat, HmatI, &orthoRhombic);
80 >  delete myConfiguration;
81  
82 <  smallestBoxL = boxLx;
83 <  if (boxLy < smallestBoxL) smallestBoxL = boxLy;
84 <  if (boxLz < smallestBoxL) smallestBoxL = boxLz;
82 >  map<string, GenericData*>::iterator i;
83 >  
84 >  for(i = properties.begin(); i != properties.end(); i++)
85 >    delete (*i).second;
86 >    
87 > }
88  
89 <  maxCutoff = smallestBoxL / 2.0;
89 > void SimInfo::setBox(double newBox[3]) {
90 >  
91 >  int i, j;
92 >  double tempMat[3][3];
93  
94 <  if (rList > maxCutoff) {
95 <    sprintf( painCave.errMsg,
74 <             "New Box size is forcing neighborlist radius down to %lf\n",
75 <             maxCutoff );
76 <    painCave.isFatal = 0;
77 <    simError();
94 >  for(i=0; i<3; i++)
95 >    for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
96  
97 <    rList = maxCutoff;
97 >  tempMat[0][0] = newBox[0];
98 >  tempMat[1][1] = newBox[1];
99 >  tempMat[2][2] = newBox[2];
100  
101 <    sprintf( painCave.errMsg,
82 <             "New Box size is forcing cutoff radius down to %lf\n",
83 <             maxCutoff - 1.0 );
84 <    painCave.isFatal = 0;
85 <    simError();
101 >  setBoxM( tempMat );
102  
87 –    rCut = rList - 1.0;
88 –
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 –  }
103   }
104  
105 < void SimInfo::setBoxM( double theBox[9] ){
105 > void SimInfo::setBoxM( double theBox[3][3] ){
106    
107 <  int i, status;
108 <  double smallestBoxL, maxCutoff;
107 >  int i, j;
108 >  double FortranHmat[9]; // to preserve compatibility with Fortran the
109 >                         // ordering in the array is as follows:
110 >                         // [ 0 3 6 ]
111 >                         // [ 1 4 7 ]
112 >                         // [ 2 5 8 ]
113 >  double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
114  
115 <  for(i=0; i<9; i++) Hmat[i] = theBox[i];
116 <  calcHmatI();
115 >  if( !boxIsInit ) boxIsInit = 1;
116 >
117 >  for(i=0; i < 3; i++)
118 >    for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
119 >  
120    calcBoxL();
121 +  calcHmatInv();
122  
123 <  setFortranBoxSize(Hmat, HmatI, &orthoRhombic);
124 <
125 <  smallestBoxL = boxLx;
126 <  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();
123 >  for(i=0; i < 3; i++) {
124 >    for (j=0; j < 3; j++) {
125 >      FortranHmat[3*j + i] = Hmat[i][j];
126 >      FortranHmatInv[3*j + i] = HmatInv[i][j];
127      }
128    }
129 +
130 +  setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic);
131 +
132   }
133  
134  
135 < void SimInfo::getBoxM (double theBox[9]) {
135 > void SimInfo::getBoxM (double theBox[3][3]) {
136  
137 <  int i;
138 <  for(i=0; i<9; i++) theBox[i] = Hmat[i];
137 >  int i, j;
138 >  for(i=0; i<3; i++)
139 >    for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j];
140   }
141  
142  
143   void SimInfo::scaleBox(double scale) {
144 <  double theBox[9];
145 <  int i;
144 >  double theBox[3][3];
145 >  int i, j;
146  
147 <  for(i=0; i<9; i++) theBox[i] = Hmat[i]*scale;
147 >  // cerr << "Scaling box by " << scale << "\n";
148  
149 +  for(i=0; i<3; i++)
150 +    for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
151 +
152    setBoxM(theBox);
153  
154   }
155  
156 < void SimInfo::calcHmatI( void ) {
157 <
158 <  double C[3][3];
159 <  double detHmat;
189 <  int i, j, k;
156 > void SimInfo::calcHmatInv( void ) {
157 >  
158 >  int oldOrtho;
159 >  int i,j;
160    double smallDiag;
161    double tol;
162    double sanity[3][3];
163  
164 <  // calculate the adjunct of Hmat;
164 >  invertMat3( Hmat, HmatInv );
165  
166 <  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
166 >  // check to see if Hmat is orthorhombic
167    
168 <  detHmat = 0.0;
211 <  for(i=0; i<3; i++) detHmat += Hmat[i] * C[i][0];
168 >  oldOrtho = orthoRhombic;
169  
170 <  
171 <  // H^-1 = C^T / det(H)
172 <  
173 <  i=0;
217 <  for(j=0; j<3; j++){
218 <    for(k=0; k<3; k++){
170 >  smallDiag = fabs(Hmat[0][0]);
171 >  if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]);
172 >  if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]);
173 >  tol = smallDiag * orthoTolerance;
174  
175 <      HmatI[i] = C[j][k] / detHmat;
176 <      i++;
177 <    }
178 <  }
179 <
180 <  // sanity check
181 <
182 <  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];
175 >  orthoRhombic = 1;
176 >  
177 >  for (i = 0; i < 3; i++ ) {
178 >    for (j = 0 ; j < 3; j++) {
179 >      if (i != j) {
180 >        if (orthoRhombic) {
181 >          if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0;
182 >        }        
183        }
184      }
185    }
186  
187 <  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";
187 >  if( oldOrtho != orthoRhombic ){
188      
189 <
190 <  // check to see if Hmat is orthorhombic
191 <  
192 <  smallDiag = Hmat[0];
193 <  if(smallDiag > Hmat[4]) smallDiag = Hmat[4];
194 <  if(smallDiag > Hmat[8]) smallDiag = Hmat[8];
195 <  tol = smallDiag * 1E-6;
196 <
197 <  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);
189 >    if( orthoRhombic ){
190 >      sprintf( painCave.errMsg,
191 >               "OOPSE is switching from the default Non-Orthorhombic\n"
192 >               "\tto the faster Orthorhombic periodic boundary computations.\n"
193 >               "\tThis is usually a good thing, but if you wan't the\n"
194 >               "\tNon-Orthorhombic computations, make the orthoBoxTolerance\n"
195 >               "\tvariable ( currently set to %G ) smaller.\n",
196 >               orthoTolerance);
197 >      simError();
198      }
199 +    else {
200 +      sprintf( painCave.errMsg,
201 +               "OOPSE is switching from the faster Orthorhombic to the more\n"
202 +               "\tflexible Non-Orthorhombic periodic boundary computations.\n"
203 +               "\tThis is usually because the box has deformed under\n"
204 +               "\tNPTf integration. If you wan't to live on the edge with\n"
205 +               "\tthe Orthorhombic computations, make the orthoBoxTolerance\n"
206 +               "\tvariable ( currently set to %G ) larger.\n",
207 +               orthoTolerance);
208 +      simError();
209 +    }
210    }
258 –    
211   }
212  
213   void SimInfo::calcBoxL( void ){
214  
215    double dx, dy, dz, dsq;
264 –  int i;
216  
217 <  // boxVol = h1 (dot) h2 (cross) h3
217 >  // boxVol = Determinant of Hmat
218  
219 <  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]) );
219 >  boxVol = matDet3( Hmat );
220  
272 –
221    // boxLx
222    
223 <  dx = Hmat[0]; dy = Hmat[1]; dz = Hmat[2];
223 >  dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
224    dsq = dx*dx + dy*dy + dz*dz;
225 <  boxLx = sqrt( dsq );
225 >  boxL[0] = sqrt( dsq );
226 >  //maxCutoff = 0.5 * boxL[0];
227  
228    // boxLy
229    
230 <  dx = Hmat[3]; dy = Hmat[4]; dz = Hmat[5];
230 >  dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
231    dsq = dx*dx + dy*dy + dz*dz;
232 <  boxLy = sqrt( dsq );
232 >  boxL[1] = sqrt( dsq );
233 >  //if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
234  
235 +
236    // boxLz
237    
238 <  dx = Hmat[6]; dy = Hmat[7]; dz = Hmat[8];
238 >  dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
239    dsq = dx*dx + dy*dy + dz*dz;
240 <  boxLz = sqrt( dsq );
240 >  boxL[2] = sqrt( dsq );
241 >  //if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
242 >
243 >  //calculate the max cutoff
244 >  maxCutoff =  calcMaxCutOff();
245    
246 +  checkCutOffs();
247 +
248   }
249  
250  
251 + double SimInfo::calcMaxCutOff(){
252 +
253 +  double ri[3], rj[3], rk[3];
254 +  double rij[3], rjk[3], rki[3];
255 +  double minDist;
256 +
257 +  ri[0] = Hmat[0][0];
258 +  ri[1] = Hmat[1][0];
259 +  ri[2] = Hmat[2][0];
260 +
261 +  rj[0] = Hmat[0][1];
262 +  rj[1] = Hmat[1][1];
263 +  rj[2] = Hmat[2][1];
264 +
265 +  rk[0] = Hmat[0][2];
266 +  rk[1] = Hmat[1][2];
267 +  rk[2] = Hmat[2][2];
268 +    
269 +  crossProduct3(ri, rj, rij);
270 +  distXY = dotProduct3(rk,rij) / norm3(rij);
271 +
272 +  crossProduct3(rj,rk, rjk);
273 +  distYZ = dotProduct3(ri,rjk) / norm3(rjk);
274 +
275 +  crossProduct3(rk,ri, rki);
276 +  distZX = dotProduct3(rj,rki) / norm3(rki);
277 +
278 +  minDist = min(min(distXY, distYZ), distZX);
279 +  return minDist/2;
280 +  
281 + }
282 +
283   void SimInfo::wrapVector( double thePos[3] ){
284  
285 <  int i, j, k;
285 >  int i;
286    double scaled[3];
287  
288    if( !orthoRhombic ){
289      // calc the scaled coordinates.
290 +  
291 +
292 +    matVecMul3(HmatInv, thePos, scaled);
293      
294      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++)
295        scaled[i] -= roundMe(scaled[i]);
296      
297      // calc the wrapped real coordinates from the wrapped scaled coordinates
298      
299 <    for(i=0; i<3; i++)
300 <      thePos[i] =
315 <        scaled[0]*Hmat[i] + scaled[1]*Hmat[i+3] + scaled[2]*Hmat[i+6];
299 >    matVecMul3(Hmat, scaled, thePos);
300 >
301    }
302    else{
303      // calc the scaled coordinates.
304      
305      for(i=0; i<3; i++)
306 <      scaled[i] = thePos[i]*HmatI[i*4];
306 >      scaled[i] = thePos[i]*HmatInv[i][i];
307      
308      // wrap the scaled coordinates
309      
# Line 328 | Line 313 | void SimInfo::wrapVector( double thePos[3] ){
313      // calc the wrapped real coordinates from the wrapped scaled coordinates
314      
315      for(i=0; i<3; i++)
316 <      thePos[i] = scaled[i]*Hmat[i*4];
316 >      thePos[i] = scaled[i]*Hmat[i][i];
317    }
318      
334 –    
319   }
320  
321  
322   int SimInfo::getNDF(){
323 <  int ndf_local, ndf;
323 >  int ndf_local;
324 >
325 >  ndf_local = 0;
326    
327 <  ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints;
327 >  for(int i = 0; i < integrableObjects.size(); i++){
328 >    ndf_local += 3;
329 >    if (integrableObjects[i]->isDirectional())
330 >      ndf_local += 3;
331 >  }
332  
333 +  // n_constraints is local, so subtract them on each processor:
334 +
335 +  ndf_local -= n_constraints;
336 +
337   #ifdef IS_MPI
338    MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
339   #else
340    ndf = ndf_local;
341   #endif
342  
343 <  ndf = ndf - 3;
343 >  // nZconstraints is global, as are the 3 COM translations for the
344 >  // entire system:
345  
346 +  ndf = ndf - 3 - nZconstraints;
347 +
348    return ndf;
349   }
350  
351   int SimInfo::getNDFraw() {
352 <  int ndfRaw_local, ndfRaw;
352 >  int ndfRaw_local;
353  
354    // Raw degrees of freedom that we have to set
355 <  ndfRaw_local = 3 * n_atoms + 3 * n_oriented;
356 <  
355 >  ndfRaw_local = 0;
356 >
357 >  for(int i = 0; i < integrableObjects.size(); i++){
358 >    ndfRaw_local += 3;
359 >    if (integrableObjects[i]->isDirectional())
360 >      ndfRaw_local += 3;
361 >  }
362 >    
363   #ifdef IS_MPI
364    MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
365   #else
# Line 365 | Line 368 | int SimInfo::getNDFraw() {
368  
369    return ndfRaw;
370   }
371 <
371 >
372 > int SimInfo::getNDFtranslational() {
373 >  int ndfTrans_local;
374 >
375 >  ndfTrans_local = 3 * integrableObjects.size() - n_constraints;
376 >
377 >
378 > #ifdef IS_MPI
379 >  MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
380 > #else
381 >  ndfTrans = ndfTrans_local;
382 > #endif
383 >
384 >  ndfTrans = ndfTrans - 3 - nZconstraints;
385 >
386 >  return ndfTrans;
387 > }
388 >
389 > int SimInfo::getTotIntegrableObjects() {
390 >  int nObjs_local;
391 >  int nObjs;
392 >
393 >  nObjs_local =  integrableObjects.size();
394 >
395 >
396 > #ifdef IS_MPI
397 >  MPI_Allreduce(&nObjs_local,&nObjs,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
398 > #else
399 >  nObjs = nObjs_local;
400 > #endif
401 >
402 >
403 >  return nObjs;
404 > }
405 >
406   void SimInfo::refreshSim(){
407  
408    simtype fInfo;
409    int isError;
410    int n_global;
411    int* excl;
375 –  
376 –  fInfo.rrf = 0.0;
377 –  fInfo.rt = 0.0;
378 –  fInfo.dielect = 0.0;
412  
413 <  fInfo.rlist = rList;
381 <  fInfo.rcut = rCut;
413 >  fInfo.dielect = 0.0;
414  
415 <  if( useDipole ){
384 <    fInfo.rrf = ecr;
385 <    fInfo.rt = ecr - est;
415 >  if( useDipoles ){
416      if( useReactionField )fInfo.dielect = dielectric;
417    }
418  
# Line 391 | Line 421 | void SimInfo::refreshSim(){
421    fInfo.SIM_uses_LJ = useLJ;
422    fInfo.SIM_uses_sticky = useSticky;
423    //fInfo.SIM_uses_sticky = 0;
424 <  fInfo.SIM_uses_dipoles = useDipole;
424 >  fInfo.SIM_uses_charges = useCharges;
425 >  fInfo.SIM_uses_dipoles = useDipoles;
426    //fInfo.SIM_uses_dipoles = 0;
427 <  //fInfo.SIM_uses_RF = useReactionField;
428 <  fInfo.SIM_uses_RF = 0;
427 >  fInfo.SIM_uses_RF = useReactionField;
428 >  //fInfo.SIM_uses_RF = 0;
429    fInfo.SIM_uses_GB = useGB;
430    fInfo.SIM_uses_EAM = useEAM;
431  
432 <  excl = Exclude::getArray();
432 >  n_exclude = excludes->getSize();
433 >  excl = excludes->getFortranArray();
434  
435   #ifdef IS_MPI
436    n_global = mpiSim->getTotAtoms();
# Line 428 | Line 460 | void SimInfo::refreshSim(){
460  
461    this->ndf = this->getNDF();
462    this->ndfRaw = this->getNDFraw();
463 +  this->ndfTrans = this->getNDFtranslational();
464 + }
465  
466 + void SimInfo::setDefaultRcut( double theRcut ){
467 +
468 +  haveRcut = 1;
469 +  rCut = theRcut;
470 +
471 +  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
472 +
473 +  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
474   }
475  
476 + void SimInfo::setDefaultEcr( double theEcr ){
477 +
478 +  haveEcr = 1;
479 +  ecr = theEcr;
480 +  
481 +  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
482 +
483 +  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
484 + }
485 +
486 + void SimInfo::setDefaultEcr( double theEcr, double theEst ){
487 +
488 +  est = theEst;
489 +  setDefaultEcr( theEcr );
490 + }
491 +
492 +
493 + void SimInfo::checkCutOffs( void ){
494 +  
495 +  if( boxIsInit ){
496 +    
497 +    //we need to check cutOffs against the box
498 +    
499 +    if( rCut > maxCutoff ){
500 +      sprintf( painCave.errMsg,
501 +               "LJrcut is too large for the current periodic box.\n"
502 +               "\tCurrent Value of LJrcut = %G at time %G\n "
503 +               "\tThis is larger than half of at least one of the\n"
504 +               "\tperiodic box vectors.  Right now, the Box matrix is:\n"
505 +               "\n, %G"
506 +               "\t[ %G %G %G ]\n"
507 +               "\t[ %G %G %G ]\n"
508 +               "\t[ %G %G %G ]\n",
509 +               rCut, currentTime, maxCutoff,
510 +               Hmat[0][0], Hmat[0][1], Hmat[0][2],
511 +               Hmat[1][0], Hmat[1][1], Hmat[1][2],
512 +               Hmat[2][0], Hmat[2][1], Hmat[2][2]);
513 +      painCave.isFatal = 1;
514 +      simError();
515 +    }
516 +    
517 +    if( haveEcr ){
518 +      if( ecr > maxCutoff ){
519 +        sprintf( painCave.errMsg,
520 +                 "electrostaticCutoffRadius is too large for the current\n"
521 +                 "\tperiodic box.\n\n"
522 +                 "\tCurrent Value of ECR = %G at time %G\n "
523 +                 "\tThis is larger than half of at least one of the\n"
524 +                 "\tperiodic box vectors.  Right now, the Box matrix is:\n"
525 +                 "\n"
526 +                 "\t[ %G %G %G ]\n"
527 +                 "\t[ %G %G %G ]\n"
528 +                 "\t[ %G %G %G ]\n",
529 +                 ecr, currentTime,
530 +                 Hmat[0][0], Hmat[0][1], Hmat[0][2],
531 +                 Hmat[1][0], Hmat[1][1], Hmat[1][2],
532 +                 Hmat[2][0], Hmat[2][1], Hmat[2][2]);
533 +        painCave.isFatal = 1;
534 +        simError();
535 +      }
536 +    }
537 +  } else {
538 +    // initialize this stuff before using it, OK?
539 +    sprintf( painCave.errMsg,
540 +             "Trying to check cutoffs without a box.\n"
541 +             "\tOOPSE should have better programmers than that.\n" );
542 +    painCave.isFatal = 1;
543 +    simError();      
544 +  }
545 +  
546 + }
547 +
548 + void SimInfo::addProperty(GenericData* prop){
549 +
550 +  map<string, GenericData*>::iterator result;
551 +  result = properties.find(prop->getID());
552 +  
553 +  //we can't simply use  properties[prop->getID()] = prop,
554 +  //it will cause memory leak if we already contain a propery which has the same name of prop
555 +  
556 +  if(result != properties.end()){
557 +    
558 +    delete (*result).second;
559 +    (*result).second = prop;
560 +      
561 +  }
562 +  else{
563 +
564 +    properties[prop->getID()] = prop;
565 +
566 +  }
567 +    
568 + }
569 +
570 + GenericData* SimInfo::getProperty(const string& propName){
571 +
572 +  map<string, GenericData*>::iterator result;
573 +  
574 +  //string lowerCaseName = ();
575 +  
576 +  result = properties.find(propName);
577 +  
578 +  if(result != properties.end())
579 +    return (*result).second;  
580 +  else  
581 +    return NULL;  
582 + }
583 +
584 + vector<GenericData*> SimInfo::getProperties(){
585 +
586 +  vector<GenericData*> result;
587 +  map<string, GenericData*>::iterator i;
588 +  
589 +  for(i = properties.begin(); i != properties.end(); i++)
590 +    result.push_back((*i).second);
591 +    
592 +  return result;
593 + }

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