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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 1139 by gezelter, Wed Apr 28 22:06:29 2004 UTC

# Line 1 | Line 1
1 < #include <cstdlib>
2 < #include <cstring>
3 < #include <cmath>
1 > #include <stdlib.h>
2 > #include <string.h>
3 > #include <math.h>
4  
5 + #include <iostream>
6 + using namespace std;
7  
8   #include "SimInfo.hpp"
9   #define __C
# Line 10 | Line 12
12  
13   #include "fortranWrappers.hpp"
14  
15 + #include "MatVec3.h"
16 +
17   #ifdef IS_MPI
18   #include "mpiSimulation.hpp"
19   #endif
20  
21 + inline double roundMe( double x ){
22 +  return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 );
23 + }
24 +          
25 + inline double min( double a, double b ){
26 +  return (a < b ) ? a : b;
27 + }
28 +
29   SimInfo* currentInfo;
30  
31   SimInfo::SimInfo(){
32 <  excludes = NULL;
32 >
33    n_constraints = 0;
34 +  nZconstraints = 0;
35    n_oriented = 0;
36    n_dipoles = 0;
37    ndf = 0;
38    ndfRaw = 0;
39 +  nZconstraints = 0;
40    the_integrator = NULL;
41    setTemp = 0;
42    thermalTime = 0.0;
43 +  currentTime = 0.0;
44    rCut = 0.0;
45 +  ecr = 0.0;
46 +  est = 0.0;
47  
48 +  haveRcut = 0;
49 +  haveEcr = 0;
50 +  boxIsInit = 0;
51 +  
52 +  resetTime = 1e99;
53 +
54 +  orthoRhombic = 0;
55 +  orthoTolerance = 1E-6;
56 +  useInitXSstate = true;
57 +
58    usePBC = 0;
59    useLJ = 0;
60    useSticky = 0;
61 <  useDipole = 0;
61 >  useCharges = 0;
62 >  useDipoles = 0;
63    useReactionField = 0;
64    useGB = 0;
65    useEAM = 0;
66 +  useMolecularCutoffs = 0;
67  
68 <  wrapMeSimInfo( this );
40 < }
68 >  excludes = Exclude::Instance();
69  
70 < void SimInfo::setBox(double newBox[3]) {
70 >  myConfiguration = new SimState();
71  
72 <  double smallestBoxL, maxCutoff;
73 <  int status;
46 <  int i;
72 >  has_minimizer = false;
73 >  the_minimizer =NULL;
74  
75 <  for(i=0; i<9; i++) Hmat[i] = 0.0;;
75 >  wrapMeSimInfo( this );
76 > }
77  
50 –  Hmat[0] = newBox[0];
51 –  Hmat[4] = newBox[1];
52 –  Hmat[8] = newBox[2];
78  
79 <  calcHmatI();
55 <  calcBoxL();
79 > SimInfo::~SimInfo(){
80  
81 <  setFortranBoxSize(Hmat);
81 >  delete myConfiguration;
82  
83 <  smallestBoxL = boxLx;
84 <  if (boxLy < smallestBoxL) smallestBoxL = boxLy;
85 <  if (boxLz < smallestBoxL) smallestBoxL = boxLz;
83 >  map<string, GenericData*>::iterator i;
84 >  
85 >  for(i = properties.begin(); i != properties.end(); i++)
86 >    delete (*i).second;
87 >    
88 > }
89  
90 <  maxCutoff = smallestBoxL / 2.0;
90 > void SimInfo::setBox(double newBox[3]) {
91 >  
92 >  int i, j;
93 >  double tempMat[3][3];
94  
95 <  if (rList > maxCutoff) {
96 <    sprintf( painCave.errMsg,
67 <             "New Box size is forcing neighborlist radius down to %lf\n",
68 <             maxCutoff );
69 <    painCave.isFatal = 0;
70 <    simError();
95 >  for(i=0; i<3; i++)
96 >    for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
97  
98 <    rList = maxCutoff;
98 >  tempMat[0][0] = newBox[0];
99 >  tempMat[1][1] = newBox[1];
100 >  tempMat[2][2] = newBox[2];
101  
102 <    sprintf( painCave.errMsg,
75 <             "New Box size is forcing cutoff radius down to %lf\n",
76 <             maxCutoff - 1.0 );
77 <    painCave.isFatal = 0;
78 <    simError();
102 >  setBoxM( tempMat );
103  
80 –    rCut = rList - 1.0;
81 –
82 –    // list radius changed so we have to refresh the simulation structure.
83 –    refreshSim();
84 –  }
85 –
86 –  if (rCut > maxCutoff) {
87 –    sprintf( painCave.errMsg,
88 –             "New Box size is forcing cutoff radius down to %lf\n",
89 –             maxCutoff );
90 –    painCave.isFatal = 0;
91 –    simError();
92 –
93 –    status = 0;
94 –    LJ_new_rcut(&rCut, &status);
95 –    if (status != 0) {
96 –      sprintf( painCave.errMsg,
97 –               "Error in recomputing LJ shifts based on new rcut\n");
98 –      painCave.isFatal = 1;
99 –      simError();
100 –    }
101 –  }
104   }
105  
106 < void SimInfo::setBoxM( double theBox[9] ){
106 > void SimInfo::setBoxM( double theBox[3][3] ){
107    
108 <  int i, status;
109 <  double smallestBoxL, maxCutoff;
108 >  int i, j;
109 >  double FortranHmat[9]; // to preserve compatibility with Fortran the
110 >                         // ordering in the array is as follows:
111 >                         // [ 0 3 6 ]
112 >                         // [ 1 4 7 ]
113 >                         // [ 2 5 8 ]
114 >  double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
115  
116 <  for(i=0; i<9; i++) Hmat[i] = theBox[i];
117 <  calcHmatI();
116 >  if( !boxIsInit ) boxIsInit = 1;
117 >
118 >  for(i=0; i < 3; i++)
119 >    for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
120 >  
121    calcBoxL();
122 +  calcHmatInv();
123  
124 <  setFortranBoxSize(Hmat);
125 <
126 <  smallestBoxL = boxLx;
127 <  if (boxLy < smallestBoxL) smallestBoxL = boxLy;
117 <  if (boxLz < smallestBoxL) smallestBoxL = boxLz;
118 <
119 <  maxCutoff = smallestBoxL / 2.0;
120 <
121 <  if (rList > maxCutoff) {
122 <    sprintf( painCave.errMsg,
123 <             "New Box size is forcing neighborlist radius down to %lf\n",
124 <             maxCutoff );
125 <    painCave.isFatal = 0;
126 <    simError();
127 <
128 <    rList = maxCutoff;
129 <
130 <    sprintf( painCave.errMsg,
131 <             "New Box size is forcing cutoff radius down to %lf\n",
132 <             maxCutoff - 1.0 );
133 <    painCave.isFatal = 0;
134 <    simError();
135 <
136 <    rCut = rList - 1.0;
137 <
138 <    // list radius changed so we have to refresh the simulation structure.
139 <    refreshSim();
140 <  }
141 <
142 <  if (rCut > maxCutoff) {
143 <    sprintf( painCave.errMsg,
144 <             "New Box size is forcing cutoff radius down to %lf\n",
145 <             maxCutoff );
146 <    painCave.isFatal = 0;
147 <    simError();
148 <
149 <    status = 0;
150 <    LJ_new_rcut(&rCut, &status);
151 <    if (status != 0) {
152 <      sprintf( painCave.errMsg,
153 <               "Error in recomputing LJ shifts based on new rcut\n");
154 <      painCave.isFatal = 1;
155 <      simError();
124 >  for(i=0; i < 3; i++) {
125 >    for (j=0; j < 3; j++) {
126 >      FortranHmat[3*j + i] = Hmat[i][j];
127 >      FortranHmatInv[3*j + i] = HmatInv[i][j];
128      }
129    }
130 +
131 +  setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic);
132 +
133   }
134  
135  
136 < void SimInfo::getBox(double theBox[9]) {
136 > void SimInfo::getBoxM (double theBox[3][3]) {
137  
138 <  int i;
139 <  for(i=0; i<9; i++) theBox[i] = Hmat[i];
138 >  int i, j;
139 >  for(i=0; i<3; i++)
140 >    for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j];
141   }
166 –
142  
168 – void SimInfo::calcHmatI( void ) {
143  
144 <  double C[3][3];
145 <  double detHmat;
146 <  int i, j, k;
144 > void SimInfo::scaleBox(double scale) {
145 >  double theBox[3][3];
146 >  int i, j;
147  
148 <  // calculate the adjunct of Hmat;
148 >  // cerr << "Scaling box by " << scale << "\n";
149  
150 <  C[0][0] =  ( Hmat[4]*Hmat[8]) - (Hmat[7]*Hmat[5]);
151 <  C[1][0] = -( Hmat[1]*Hmat[8]) + (Hmat[7]*Hmat[2]);
178 <  C[2][0] =  ( Hmat[1]*Hmat[5]) - (Hmat[4]*Hmat[2]);
150 >  for(i=0; i<3; i++)
151 >    for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
152  
153 <  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]);
153 >  setBoxM(theBox);
154  
155 <  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]);
155 > }
156  
157 <  // calcutlate the determinant of Hmat
157 > void SimInfo::calcHmatInv( void ) {
158    
159 <  detHmat = 0.0;
160 <  for(i=0; i<3; i++) detHmat += Hmat[i] * C[i][0];
159 >  int oldOrtho;
160 >  int i,j;
161 >  double smallDiag;
162 >  double tol;
163 >  double sanity[3][3];
164  
165 +  invertMat3( Hmat, HmatInv );
166 +
167 +  // check to see if Hmat is orthorhombic
168    
169 <  // H^-1 = C^T / det(H)
169 >  oldOrtho = orthoRhombic;
170 >
171 >  smallDiag = fabs(Hmat[0][0]);
172 >  if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]);
173 >  if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]);
174 >  tol = smallDiag * orthoTolerance;
175 >
176 >  orthoRhombic = 1;
177    
178 <  i=0;
179 <  for(j=0; j<3; j++){
180 <    for(k=0; k<3; k++){
178 >  for (i = 0; i < 3; i++ ) {
179 >    for (j = 0 ; j < 3; j++) {
180 >      if (i != j) {
181 >        if (orthoRhombic) {
182 >          if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0;
183 >        }        
184 >      }
185 >    }
186 >  }
187  
188 <      HmatI[i] = C[j][k] / detHmat;
189 <      i++;
188 >  if( oldOrtho != orthoRhombic ){
189 >    
190 >    if( orthoRhombic ){
191 >      sprintf( painCave.errMsg,
192 >               "OOPSE is switching from the default Non-Orthorhombic\n"
193 >               "\tto the faster Orthorhombic periodic boundary computations.\n"
194 >               "\tThis is usually a good thing, but if you wan't the\n"
195 >               "\tNon-Orthorhombic computations, make the orthoBoxTolerance\n"
196 >               "\tvariable ( currently set to %G ) smaller.\n",
197 >               orthoTolerance);
198 >      simError();
199      }
200 +    else {
201 +      sprintf( painCave.errMsg,
202 +               "OOPSE is switching from the faster Orthorhombic to the more\n"
203 +               "\tflexible Non-Orthorhombic periodic boundary computations.\n"
204 +               "\tThis is usually because the box has deformed under\n"
205 +               "\tNPTf integration. If you wan't to live on the edge with\n"
206 +               "\tthe Orthorhombic computations, make the orthoBoxTolerance\n"
207 +               "\tvariable ( currently set to %G ) larger.\n",
208 +               orthoTolerance);
209 +      simError();
210 +    }
211    }
212   }
213  
214   void SimInfo::calcBoxL( void ){
215  
216    double dx, dy, dz, dsq;
209 –  int i;
217  
218 <  // boxVol = h1 (dot) h2 (cross) h3
218 >  // boxVol = Determinant of Hmat
219  
220 <  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]) );
220 >  boxVol = matDet3( Hmat );
221  
217 –
222    // boxLx
223    
224 <  dx = Hmat[0]; dy = Hmat[1]; dz = Hmat[2];
224 >  dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
225    dsq = dx*dx + dy*dy + dz*dz;
226 <  boxLx = sqrt( dsq );
226 >  boxL[0] = sqrt( dsq );
227 >  //maxCutoff = 0.5 * boxL[0];
228  
229    // boxLy
230    
231 <  dx = Hmat[3]; dy = Hmat[4]; dz = Hmat[5];
231 >  dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
232    dsq = dx*dx + dy*dy + dz*dz;
233 <  boxLy = sqrt( dsq );
233 >  boxL[1] = sqrt( dsq );
234 >  //if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
235  
236 +
237    // boxLz
238    
239 <  dx = Hmat[6]; dy = Hmat[7]; dz = Hmat[8];
239 >  dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
240    dsq = dx*dx + dy*dy + dz*dz;
241 <  boxLz = sqrt( dsq );
241 >  boxL[2] = sqrt( dsq );
242 >  //if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
243 >
244 >  //calculate the max cutoff
245 >  maxCutoff =  calcMaxCutOff();
246    
247 +  checkCutOffs();
248 +
249   }
250 +
251 +
252 + double SimInfo::calcMaxCutOff(){
253 +
254 +  double ri[3], rj[3], rk[3];
255 +  double rij[3], rjk[3], rki[3];
256 +  double minDist;
257  
258 +  ri[0] = Hmat[0][0];
259 +  ri[1] = Hmat[1][0];
260 +  ri[2] = Hmat[2][0];
261  
262 < void SimInfo::wrapVector( double thePos[3] ){
262 >  rj[0] = Hmat[0][1];
263 >  rj[1] = Hmat[1][1];
264 >  rj[2] = Hmat[2][1];
265  
266 <  int i, j, k;
267 <  double scaled[3];
266 >  rk[0] = Hmat[0][2];
267 >  rk[1] = Hmat[1][2];
268 >  rk[2] = Hmat[2][2];
269 >    
270 >  crossProduct3(ri, rj, rij);
271 >  distXY = dotProduct3(rk,rij) / norm3(rij);
272  
273 <  // calc the scaled coordinates.
273 >  crossProduct3(rj,rk, rjk);
274 >  distYZ = dotProduct3(ri,rjk) / norm3(rjk);
275 >
276 >  crossProduct3(rk,ri, rki);
277 >  distZX = dotProduct3(rj,rki) / norm3(rki);
278 >
279 >  minDist = min(min(distXY, distYZ), distZX);
280 >  return minDist/2;
281    
282 <  for(i=0; i<3; i++)
247 <    scaled[i] = thePos[0]*Hmat[i] + thePos[1]*Hat[i+3] + thePos[3]*Hmat[i+6];
282 > }
283  
284 <  // wrap the scaled coordinates
284 > void SimInfo::wrapVector( double thePos[3] ){
285  
286 <  for(i=0; i<3; i++)
287 <    scaled[i] -= (copysign(1,scaled[i]) * (int)(fabs(scaled[i]) + 0.5));
286 >  int i;
287 >  double scaled[3];
288 >
289 >  if( !orthoRhombic ){
290 >    // calc the scaled coordinates.
291    
292  
293 +    matVecMul3(HmatInv, thePos, scaled);
294 +    
295 +    for(i=0; i<3; i++)
296 +      scaled[i] -= roundMe(scaled[i]);
297 +    
298 +    // calc the wrapped real coordinates from the wrapped scaled coordinates
299 +    
300 +    matVecMul3(Hmat, scaled, thePos);
301 +
302 +  }
303 +  else{
304 +    // calc the scaled coordinates.
305 +    
306 +    for(i=0; i<3; i++)
307 +      scaled[i] = thePos[i]*HmatInv[i][i];
308 +    
309 +    // wrap the scaled coordinates
310 +    
311 +    for(i=0; i<3; i++)
312 +      scaled[i] -= roundMe(scaled[i]);
313 +    
314 +    // calc the wrapped real coordinates from the wrapped scaled coordinates
315 +    
316 +    for(i=0; i<3; i++)
317 +      thePos[i] = scaled[i]*Hmat[i][i];
318 +  }
319 +    
320   }
321  
322  
323   int SimInfo::getNDF(){
324 <  int ndf_local, ndf;
324 >  int ndf_local;
325 >
326 >  ndf_local = 0;
327    
328 <  ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints;
328 >  for(int i = 0; i < integrableObjects.size(); i++){
329 >    ndf_local += 3;
330 >    if (integrableObjects[i]->isDirectional()) {
331 >      if (integrableObjects[i]->isLinear())
332 >        ndf_local += 2;
333 >      else
334 >        ndf_local += 3;
335 >    }
336 >  }
337  
338 +  // n_constraints is local, so subtract them on each processor:
339 +
340 +  ndf_local -= n_constraints;
341 +
342   #ifdef IS_MPI
343    MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
344   #else
345    ndf = ndf_local;
346   #endif
347  
348 <  ndf = ndf - 3;
348 >  // nZconstraints is global, as are the 3 COM translations for the
349 >  // entire system:
350  
351 +  ndf = ndf - 3 - nZconstraints;
352 +
353    return ndf;
354   }
355  
356   int SimInfo::getNDFraw() {
357 <  int ndfRaw_local, ndfRaw;
357 >  int ndfRaw_local;
358  
359    // Raw degrees of freedom that we have to set
360 <  ndfRaw_local = 3 * n_atoms + 3 * n_oriented;
361 <  
360 >  ndfRaw_local = 0;
361 >
362 >  for(int i = 0; i < integrableObjects.size(); i++){
363 >    ndfRaw_local += 3;
364 >    if (integrableObjects[i]->isDirectional()) {
365 >       if (integrableObjects[i]->isLinear())
366 >        ndfRaw_local += 2;
367 >      else
368 >        ndfRaw_local += 3;
369 >    }
370 >  }
371 >    
372   #ifdef IS_MPI
373    MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
374   #else
# Line 285 | Line 377 | int SimInfo::getNDFraw() {
377  
378    return ndfRaw;
379   }
380 <
380 >
381 > int SimInfo::getNDFtranslational() {
382 >  int ndfTrans_local;
383 >
384 >  ndfTrans_local = 3 * integrableObjects.size() - n_constraints;
385 >
386 >
387 > #ifdef IS_MPI
388 >  MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
389 > #else
390 >  ndfTrans = ndfTrans_local;
391 > #endif
392 >
393 >  ndfTrans = ndfTrans - 3 - nZconstraints;
394 >
395 >  return ndfTrans;
396 > }
397 >
398 > int SimInfo::getTotIntegrableObjects() {
399 >  int nObjs_local;
400 >  int nObjs;
401 >
402 >  nObjs_local =  integrableObjects.size();
403 >
404 >
405 > #ifdef IS_MPI
406 >  MPI_Allreduce(&nObjs_local,&nObjs,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
407 > #else
408 >  nObjs = nObjs_local;
409 > #endif
410 >
411 >
412 >  return nObjs;
413 > }
414 >
415   void SimInfo::refreshSim(){
416  
417    simtype fInfo;
418    int isError;
419    int n_global;
420    int* excl;
421 <  
296 <  fInfo.rrf = 0.0;
297 <  fInfo.rt = 0.0;
421 >
422    fInfo.dielect = 0.0;
423  
424 <  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;
424 >  if( useDipoles ){
425      if( useReactionField )fInfo.dielect = dielectric;
426    }
427  
# Line 315 | Line 430 | void SimInfo::refreshSim(){
430    fInfo.SIM_uses_LJ = useLJ;
431    fInfo.SIM_uses_sticky = useSticky;
432    //fInfo.SIM_uses_sticky = 0;
433 <  fInfo.SIM_uses_dipoles = useDipole;
433 >  fInfo.SIM_uses_charges = useCharges;
434 >  fInfo.SIM_uses_dipoles = useDipoles;
435    //fInfo.SIM_uses_dipoles = 0;
436 <  //fInfo.SIM_uses_RF = useReactionField;
437 <  fInfo.SIM_uses_RF = 0;
436 >  fInfo.SIM_uses_RF = useReactionField;
437 >  //fInfo.SIM_uses_RF = 0;
438    fInfo.SIM_uses_GB = useGB;
439    fInfo.SIM_uses_EAM = useEAM;
440 +  fInfo.SIM_uses_molecular_cutoffs = useMolecularCutoffs;
441  
442 <  excl = Exclude::getArray();
442 >  n_exclude = excludes->getSize();
443 >  excl = excludes->getFortranArray();
444  
445   #ifdef IS_MPI
446    n_global = mpiSim->getTotAtoms();
# Line 352 | Line 470 | void SimInfo::refreshSim(){
470  
471    this->ndf = this->getNDF();
472    this->ndfRaw = this->getNDFraw();
473 +  this->ndfTrans = this->getNDFtranslational();
474 + }
475  
476 + void SimInfo::setDefaultRcut( double theRcut ){
477 +
478 +  haveRcut = 1;
479 +  rCut = theRcut;
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 ){
487 +
488 +  haveEcr = 1;
489 +  ecr = theEcr;
490 +  
491 +  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
492 +
493 +  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
494 + }
495 +
496 + void SimInfo::setDefaultEcr( double theEcr, double theEst ){
497 +
498 +  est = theEst;
499 +  setDefaultEcr( theEcr );
500 + }
501 +
502 +
503 + void SimInfo::checkCutOffs( void ){
504 +  
505 +  if( boxIsInit ){
506 +    
507 +    //we need to check cutOffs against the box
508 +    
509 +    if( rCut > maxCutoff ){
510 +      sprintf( painCave.errMsg,
511 +               "LJrcut is too large for the current periodic box.\n"
512 +               "\tCurrent Value of LJrcut = %G at time %G\n "
513 +               "\tThis is larger than half of at least one of the\n"
514 +               "\tperiodic box vectors.  Right now, the Box matrix is:\n"
515 +               "\n"
516 +               "\t[ %G %G %G ]\n"
517 +               "\t[ %G %G %G ]\n"
518 +               "\t[ %G %G %G ]\n",
519 +               rCut, currentTime,
520 +               Hmat[0][0], Hmat[0][1], Hmat[0][2],
521 +               Hmat[1][0], Hmat[1][1], Hmat[1][2],
522 +               Hmat[2][0], Hmat[2][1], Hmat[2][2]);
523 +      painCave.isFatal = 1;
524 +      simError();
525 +    }
526 +    
527 +    if( haveEcr ){
528 +      if( ecr > maxCutoff ){
529 +        sprintf( painCave.errMsg,
530 +                 "electrostaticCutoffRadius is too large for the current\n"
531 +                 "\tperiodic box.\n\n"
532 +                 "\tCurrent Value of ECR = %G at time %G\n "
533 +                 "\tThis is larger than half of at least one of the\n"
534 +                 "\tperiodic box vectors.  Right now, the Box matrix is:\n"
535 +                 "\n"
536 +                 "\t[ %G %G %G ]\n"
537 +                 "\t[ %G %G %G ]\n"
538 +                 "\t[ %G %G %G ]\n",
539 +                 ecr, currentTime,
540 +                 Hmat[0][0], Hmat[0][1], Hmat[0][2],
541 +                 Hmat[1][0], Hmat[1][1], Hmat[1][2],
542 +                 Hmat[2][0], Hmat[2][1], Hmat[2][2]);
543 +        painCave.isFatal = 1;
544 +        simError();
545 +      }
546 +    }
547 +  } else {
548 +    // initialize this stuff before using it, OK?
549 +    sprintf( painCave.errMsg,
550 +             "Trying to check cutoffs without a box.\n"
551 +             "\tOOPSE should have better programmers than that.\n" );
552 +    painCave.isFatal = 1;
553 +    simError();      
554 +  }
555 +  
556 + }
557 +
558 + void SimInfo::addProperty(GenericData* prop){
559 +
560 +  map<string, GenericData*>::iterator result;
561 +  result = properties.find(prop->getID());
562 +  
563 +  //we can't simply use  properties[prop->getID()] = prop,
564 +  //it will cause memory leak if we already contain a propery which has the same name of prop
565 +  
566 +  if(result != properties.end()){
567 +    
568 +    delete (*result).second;
569 +    (*result).second = prop;
570 +      
571 +  }
572 +  else{
573 +
574 +    properties[prop->getID()] = prop;
575 +
576 +  }
577 +    
578 + }
579 +
580 + GenericData* SimInfo::getProperty(const string& propName){
581 +
582 +  map<string, GenericData*>::iterator result;
583 +  
584 +  //string lowerCaseName = ();
585 +  
586 +  result = properties.find(propName);
587 +  
588 +  if(result != properties.end())
589 +    return (*result).second;  
590 +  else  
591 +    return NULL;  
592 + }
593 +

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