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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 1118 by tim, Mon Apr 19 03:52:27 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  
67 <  wrapMeSimInfo( this );
40 < }
67 >  excludes = Exclude::Instance();
68  
69 < void SimInfo::setBox(double newBox[3]) {
69 >  myConfiguration = new SimState();
70  
71 <  double smallestBoxL, maxCutoff;
72 <  int status;
46 <  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  
50 –  Hmat[0] = newBox[0];
51 –  Hmat[4] = newBox[1];
52 –  Hmat[8] = newBox[2];
77  
78 <  calcHmatI();
55 <  calcBoxL();
78 > SimInfo::~SimInfo(){
79  
80 <  setFortranBoxSize(Hmat);
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,
67 <             "New Box size is forcing neighborlist radius down to %lf\n",
68 <             maxCutoff );
69 <    painCave.isFatal = 0;
70 <    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,
75 <             "New Box size is forcing cutoff radius down to %lf\n",
76 <             maxCutoff - 1.0 );
77 <    painCave.isFatal = 0;
78 <    simError();
101 >  setBoxM( tempMat );
102  
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 –  }
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);
124 <
125 <  smallestBoxL = boxLx;
126 <  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();
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::getBox(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   }
166 –
141  
168 – void SimInfo::calcHmatI( void ) {
142  
143 <  double C[3][3];
144 <  double detHmat;
145 <  int i, j, k;
143 > void SimInfo::scaleBox(double scale) {
144 >  double theBox[3][3];
145 >  int i, j;
146  
147 <  // calculate the adjunct of Hmat;
147 >  // cerr << "Scaling box by " << scale << "\n";
148  
149 <  C[0][0] =  ( Hmat[4]*Hmat[8]) - (Hmat[7]*Hmat[5]);
150 <  C[1][0] = -( Hmat[1]*Hmat[8]) + (Hmat[7]*Hmat[2]);
178 <  C[2][0] =  ( Hmat[1]*Hmat[5]) - (Hmat[4]*Hmat[2]);
149 >  for(i=0; i<3; i++)
150 >    for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
151  
152 <  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]);
152 >  setBoxM(theBox);
153  
154 <  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]);
154 > }
155  
156 <  // calcutlate the determinant of Hmat
156 > void SimInfo::calcHmatInv( void ) {
157    
158 <  detHmat = 0.0;
159 <  for(i=0; i<3; i++) detHmat += Hmat[i] * C[i][0];
158 >  int oldOrtho;
159 >  int i,j;
160 >  double smallDiag;
161 >  double tol;
162 >  double sanity[3][3];
163  
164 +  invertMat3( Hmat, HmatInv );
165 +
166 +  // check to see if Hmat is orthorhombic
167    
168 <  // H^-1 = C^T / det(H)
168 >  oldOrtho = orthoRhombic;
169 >
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 >  orthoRhombic = 1;
176    
177 <  i=0;
178 <  for(j=0; j<3; j++){
179 <    for(k=0; k<3; k++){
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 <      HmatI[i] = C[j][k] / detHmat;
188 <      i++;
187 >  if( oldOrtho != orthoRhombic ){
188 >    
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    }
211   }
212  
213   void SimInfo::calcBoxL( void ){
214  
215    double dx, dy, dz, dsq;
209 –  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]) )
214 <         + Hmat[1] * ( (Hmat[5]*Hmat[6]) - (Hmat[8]*Hmat[3]) )
215 <         + Hmat[2] * ( (Hmat[3]*Hmat[7]) - (Hmat[6]*Hmat[4]) );
219 >  boxVol = matDet3( Hmat );
220  
217 –
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 < void SimInfo::wrapVector( double thePos[3] ){
261 >  rj[0] = Hmat[0][1];
262 >  rj[1] = Hmat[1][1];
263 >  rj[2] = Hmat[2][1];
264  
265 <  int i, j, k;
266 <  double scaled[3];
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 <  // calc the scaled coordinates.
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 <  for(i=0; i<3; i++)
247 <    scaled[i] = thePos[0]*Hmat[i] + thePos[1]*Hat[i+3] + thePos[3]*Hmat[i+6];
281 > }
282  
283 <  // wrap the scaled coordinates
283 > void SimInfo::wrapVector( double thePos[3] ){
284  
285 <  for(i=0; i<3; i++)
286 <    scaled[i] -= (copysign(1,scaled[i]) * (int)(fabs(scaled[i]) + 0.5));
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++)
295 +      scaled[i] -= roundMe(scaled[i]);
296 +    
297 +    // calc the wrapped real coordinates from the wrapped scaled coordinates
298 +    
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]*HmatInv[i][i];
307 +    
308 +    // wrap the scaled coordinates
309 +    
310 +    for(i=0; i<3; i++)
311 +      scaled[i] -= roundMe(scaled[i]);
312 +    
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][i];
317 +  }
318 +    
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 >      if (integrableObjects[i]->isLinear())
331 >        ndf_local += 2;
332 >      else
333 >        ndf_local += 3;
334 >    }
335 >  }
336  
337 +  // n_constraints is local, so subtract them on each processor:
338 +
339 +  ndf_local -= n_constraints;
340 +
341   #ifdef IS_MPI
342    MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
343   #else
344    ndf = ndf_local;
345   #endif
346  
347 <  ndf = ndf - 3;
347 >  // nZconstraints is global, as are the 3 COM translations for the
348 >  // entire system:
349  
350 +  ndf = ndf - 3 - nZconstraints;
351 +
352    return ndf;
353   }
354  
355   int SimInfo::getNDFraw() {
356 <  int ndfRaw_local, ndfRaw;
356 >  int ndfRaw_local;
357  
358    // Raw degrees of freedom that we have to set
359 <  ndfRaw_local = 3 * n_atoms + 3 * n_oriented;
360 <  
359 >  ndfRaw_local = 0;
360 >
361 >  for(int i = 0; i < integrableObjects.size(); i++){
362 >    ndfRaw_local += 3;
363 >    if (integrableObjects[i]->isDirectional()) {
364 >       if (integrableObjects[i]->isLinear())
365 >        ndfRaw_local += 2;
366 >      else
367 >        ndfRaw_local += 3;
368 >    }
369 >  }
370 >    
371   #ifdef IS_MPI
372    MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
373   #else
# Line 285 | Line 376 | int SimInfo::getNDFraw() {
376  
377    return ndfRaw;
378   }
379 <
379 >
380 > int SimInfo::getNDFtranslational() {
381 >  int ndfTrans_local;
382 >
383 >  ndfTrans_local = 3 * integrableObjects.size() - n_constraints;
384 >
385 >
386 > #ifdef IS_MPI
387 >  MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
388 > #else
389 >  ndfTrans = ndfTrans_local;
390 > #endif
391 >
392 >  ndfTrans = ndfTrans - 3 - nZconstraints;
393 >
394 >  return ndfTrans;
395 > }
396 >
397 > int SimInfo::getTotIntegrableObjects() {
398 >  int nObjs_local;
399 >  int nObjs;
400 >
401 >  nObjs_local =  integrableObjects.size();
402 >
403 >
404 > #ifdef IS_MPI
405 >  MPI_Allreduce(&nObjs_local,&nObjs,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
406 > #else
407 >  nObjs = nObjs_local;
408 > #endif
409 >
410 >
411 >  return nObjs;
412 > }
413 >
414   void SimInfo::refreshSim(){
415  
416    simtype fInfo;
417    int isError;
418    int n_global;
419    int* excl;
420 <  
296 <  fInfo.rrf = 0.0;
297 <  fInfo.rt = 0.0;
420 >
421    fInfo.dielect = 0.0;
422  
423 <  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;
423 >  if( useDipoles ){
424      if( useReactionField )fInfo.dielect = dielectric;
425    }
426  
# Line 315 | Line 429 | void SimInfo::refreshSim(){
429    fInfo.SIM_uses_LJ = useLJ;
430    fInfo.SIM_uses_sticky = useSticky;
431    //fInfo.SIM_uses_sticky = 0;
432 <  fInfo.SIM_uses_dipoles = useDipole;
432 >  fInfo.SIM_uses_charges = useCharges;
433 >  fInfo.SIM_uses_dipoles = useDipoles;
434    //fInfo.SIM_uses_dipoles = 0;
435 <  //fInfo.SIM_uses_RF = useReactionField;
436 <  fInfo.SIM_uses_RF = 0;
435 >  fInfo.SIM_uses_RF = useReactionField;
436 >  //fInfo.SIM_uses_RF = 0;
437    fInfo.SIM_uses_GB = useGB;
438    fInfo.SIM_uses_EAM = useEAM;
439  
440 <  excl = Exclude::getArray();
440 >  n_exclude = excludes->getSize();
441 >  excl = excludes->getFortranArray();
442  
443   #ifdef IS_MPI
444    n_global = mpiSim->getTotAtoms();
# Line 352 | Line 468 | void SimInfo::refreshSim(){
468  
469    this->ndf = this->getNDF();
470    this->ndfRaw = this->getNDFraw();
471 +  this->ndfTrans = this->getNDFtranslational();
472 + }
473  
474 + void SimInfo::setDefaultRcut( double theRcut ){
475 +
476 +  haveRcut = 1;
477 +  rCut = theRcut;
478 +
479 +  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
480 +
481 +  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
482   }
483  
484 + void SimInfo::setDefaultEcr( double theEcr ){
485 +
486 +  haveEcr = 1;
487 +  ecr = theEcr;
488 +  
489 +  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
490 +
491 +  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
492 + }
493 +
494 + void SimInfo::setDefaultEcr( double theEcr, double theEst ){
495 +
496 +  est = theEst;
497 +  setDefaultEcr( theEcr );
498 + }
499 +
500 +
501 + void SimInfo::checkCutOffs( void ){
502 +  
503 +  if( boxIsInit ){
504 +    
505 +    //we need to check cutOffs against the box
506 +    
507 +    if( rCut > maxCutoff ){
508 +      sprintf( painCave.errMsg,
509 +               "LJrcut is too large for the current periodic box.\n"
510 +               "\tCurrent Value of LJrcut = %G at time %G\n "
511 +               "\tThis is larger than half of at least one of the\n"
512 +               "\tperiodic box vectors.  Right now, the Box matrix is:\n"
513 +               "\n, %G"
514 +               "\t[ %G %G %G ]\n"
515 +               "\t[ %G %G %G ]\n"
516 +               "\t[ %G %G %G ]\n",
517 +               rCut, currentTime, maxCutoff,
518 +               Hmat[0][0], Hmat[0][1], Hmat[0][2],
519 +               Hmat[1][0], Hmat[1][1], Hmat[1][2],
520 +               Hmat[2][0], Hmat[2][1], Hmat[2][2]);
521 +      painCave.isFatal = 1;
522 +      simError();
523 +    }
524 +    
525 +    if( haveEcr ){
526 +      if( ecr > maxCutoff ){
527 +        sprintf( painCave.errMsg,
528 +                 "electrostaticCutoffRadius is too large for the current\n"
529 +                 "\tperiodic box.\n\n"
530 +                 "\tCurrent Value of ECR = %G at time %G\n "
531 +                 "\tThis is larger than half of at least one of the\n"
532 +                 "\tperiodic box vectors.  Right now, the Box matrix is:\n"
533 +                 "\n"
534 +                 "\t[ %G %G %G ]\n"
535 +                 "\t[ %G %G %G ]\n"
536 +                 "\t[ %G %G %G ]\n",
537 +                 ecr, currentTime,
538 +                 Hmat[0][0], Hmat[0][1], Hmat[0][2],
539 +                 Hmat[1][0], Hmat[1][1], Hmat[1][2],
540 +                 Hmat[2][0], Hmat[2][1], Hmat[2][2]);
541 +        painCave.isFatal = 1;
542 +        simError();
543 +      }
544 +    }
545 +  } else {
546 +    // initialize this stuff before using it, OK?
547 +    sprintf( painCave.errMsg,
548 +             "Trying to check cutoffs without a box.\n"
549 +             "\tOOPSE should have better programmers than that.\n" );
550 +    painCave.isFatal = 1;
551 +    simError();      
552 +  }
553 +  
554 + }
555 +
556 + void SimInfo::addProperty(GenericData* prop){
557 +
558 +  map<string, GenericData*>::iterator result;
559 +  result = properties.find(prop->getID());
560 +  
561 +  //we can't simply use  properties[prop->getID()] = prop,
562 +  //it will cause memory leak if we already contain a propery which has the same name of prop
563 +  
564 +  if(result != properties.end()){
565 +    
566 +    delete (*result).second;
567 +    (*result).second = prop;
568 +      
569 +  }
570 +  else{
571 +
572 +    properties[prop->getID()] = prop;
573 +
574 +  }
575 +    
576 + }
577 +
578 + GenericData* SimInfo::getProperty(const string& propName){
579 +
580 +  map<string, GenericData*>::iterator result;
581 +  
582 +  //string lowerCaseName = ();
583 +  
584 +  result = properties.find(propName);
585 +  
586 +  if(result != properties.end())
587 +    return (*result).second;  
588 +  else  
589 +    return NULL;  
590 + }
591 +

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