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root/group/trunk/OOPSE/libmdtools/SimInfo.cpp
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Comparing trunk/OOPSE/libmdtools/SimInfo.cpp (file contents):
Revision 572 by mmeineke, Wed Jul 2 21:26:55 2003 UTC vs.
Revision 781 by tim, Mon Sep 22 23:07:57 2003 UTC

# Line 26 | Line 26 | SimInfo::SimInfo(){
26   SimInfo::SimInfo(){
27    excludes = NULL;
28    n_constraints = 0;
29 +  nZconstraints = 0;
30    n_oriented = 0;
31    n_dipoles = 0;
32    ndf = 0;
33    ndfRaw = 0;
34 +  nZconstraints = 0;
35    the_integrator = NULL;
36    setTemp = 0;
37    thermalTime = 0.0;
38 +  currentTime = 0.0;
39    rCut = 0.0;
40 +  origRcut = -1.0;
41 +  ecr = 0.0;
42 +  origEcr = -1.0;
43 +  est = 0.0;
44 +  oldEcr = 0.0;
45 +  oldRcut = 0.0;
46  
47 +  haveOrigRcut = 0;
48 +  haveOrigEcr = 0;
49 +  boxIsInit = 0;
50 +  
51 +  resetTime = 1e99;
52 +  
53 +
54    usePBC = 0;
55    useLJ = 0;
56    useSticky = 0;
# Line 43 | Line 59 | SimInfo::SimInfo(){
59    useGB = 0;
60    useEAM = 0;
61  
62 +  myConfiguration = new SimState();
63 +
64    wrapMeSimInfo( this );
65   }
66  
49 – void SimInfo::setBox(double newBox[3]) {
67  
68 <  double smallestBoxL, maxCutoff;
52 <  int status;
53 <  int i;
68 > SimInfo::~SimInfo(){
69  
70 <  for(i=0; i<9; i++) Hmat[i] = 0.0;;
70 >  delete myConfiguration;
71  
72 <  Hmat[0] = newBox[0];
73 <  Hmat[4] = newBox[1];
74 <  Hmat[8] = newBox[2];
72 >  map<string, GenericData*>::iterator i;
73 >  
74 >  for(i = properties.begin(); i != properties.end(); i++)
75 >    delete (*i).second;
76 >    
77 > }
78  
79 <  calcHmatI();
80 <  calcBoxL();
79 > void SimInfo::setBox(double newBox[3]) {
80 >  
81 >  int i, j;
82 >  double tempMat[3][3];
83  
84 <  setFortranBoxSize(Hmat, HmatI, &orthoRhombic);
84 >  for(i=0; i<3; i++)
85 >    for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
86  
87 <  smallestBoxL = boxLx;
88 <  if (boxLy < smallestBoxL) smallestBoxL = boxLy;
89 <  if (boxLz < smallestBoxL) smallestBoxL = boxLz;
87 >  tempMat[0][0] = newBox[0];
88 >  tempMat[1][1] = newBox[1];
89 >  tempMat[2][2] = newBox[2];
90  
91 <  maxCutoff = smallestBoxL / 2.0;
91 >  setBoxM( tempMat );
92  
72 –  if (rList > maxCutoff) {
73 –    sprintf( painCave.errMsg,
74 –             "New Box size is forcing neighborlist radius down to %lf\n",
75 –             maxCutoff );
76 –    painCave.isFatal = 0;
77 –    simError();
78 –
79 –    rList = maxCutoff;
80 –
81 –    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();
86 –
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 –  }
93   }
94  
95 < void SimInfo::setBoxM( double theBox[9] ){
95 > void SimInfo::setBoxM( double theBox[3][3] ){
96    
97 <  int i, status;
97 >  int i, j, status;
98    double smallestBoxL, maxCutoff;
99 +  double FortranHmat[9]; // to preserve compatibility with Fortran the
100 +                         // ordering in the array is as follows:
101 +                         // [ 0 3 6 ]
102 +                         // [ 1 4 7 ]
103 +                         // [ 2 5 8 ]
104 +  double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
105  
106 <  for(i=0; i<9; i++) Hmat[i] = theBox[i];
107 <  calcHmatI();
106 >  
107 >  if( !boxIsInit ) boxIsInit = 1;
108 >
109 >  for(i=0; i < 3; i++)
110 >    for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
111 >  
112    calcBoxL();
113 +  calcHmatInv();
114  
115 <  setFortranBoxSize(Hmat, HmatI, &orthoRhombic);
115 >  for(i=0; i < 3; i++) {
116 >    for (j=0; j < 3; j++) {
117 >      FortranHmat[3*j + i] = Hmat[i][j];
118 >      FortranHmatInv[3*j + i] = HmatInv[i][j];
119 >    }
120 >  }
121 >
122 >  setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic);
123  
124 <  smallestBoxL = boxLx;
125 <  if (boxLy < smallestBoxL) smallestBoxL = boxLy;
124 <  if (boxLz < smallestBoxL) smallestBoxL = boxLz;
124 > }
125 >
126  
127 <  maxCutoff = smallestBoxL / 2.0;
127 > void SimInfo::getBoxM (double theBox[3][3]) {
128  
129 <  if (rList > maxCutoff) {
130 <    sprintf( painCave.errMsg,
131 <             "New Box size is forcing neighborlist radius down to %lf\n",
132 <             maxCutoff );
132 <    painCave.isFatal = 0;
133 <    simError();
129 >  int i, j;
130 >  for(i=0; i<3; i++)
131 >    for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j];
132 > }
133  
135 –    rList = maxCutoff;
134  
135 <    sprintf( painCave.errMsg,
136 <             "New Box size is forcing cutoff radius down to %lf\n",
137 <             maxCutoff - 1.0 );
140 <    painCave.isFatal = 0;
141 <    simError();
135 > void SimInfo::scaleBox(double scale) {
136 >  double theBox[3][3];
137 >  int i, j;
138  
139 <    rCut = rList - 1.0;
139 >  // cerr << "Scaling box by " << scale << "\n";
140  
141 <    // list radius changed so we have to refresh the simulation structure.
142 <    refreshSim();
147 <  }
141 >  for(i=0; i<3; i++)
142 >    for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
143  
144 <  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();
144 >  setBoxM(theBox);
145  
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();
163 –    }
164 –  }
146   }
166 –
167 –
168 – void SimInfo::getBoxM (double theBox[9]) {
169 –
170 –  int i;
171 –  for(i=0; i<9; i++) theBox[i] = Hmat[i];
172 – }
173 –
147  
148 < void SimInfo::calcHmatI( void ) {
149 <
150 <  double C[3][3];
178 <  double detHmat;
179 <  int i, j, k;
148 > void SimInfo::calcHmatInv( void ) {
149 >  
150 >  int i,j;
151    double smallDiag;
152    double tol;
153    double sanity[3][3];
154  
155 <  // calculate the adjunct of Hmat;
155 >  invertMat3( Hmat, HmatInv );
156  
157 <  C[0][0] =  ( Hmat[4]*Hmat[8]) - (Hmat[7]*Hmat[5]);
187 <  C[1][0] = -( Hmat[1]*Hmat[8]) + (Hmat[7]*Hmat[2]);
188 <  C[2][0] =  ( Hmat[1]*Hmat[5]) - (Hmat[4]*Hmat[2]);
157 >  // Check the inverse to make sure it is sane:
158  
159 <  C[0][1] = -( Hmat[3]*Hmat[8]) + (Hmat[6]*Hmat[5]);
160 <  C[1][1] =  ( Hmat[0]*Hmat[8]) - (Hmat[6]*Hmat[2]);
161 <  C[2][1] = -( Hmat[0]*Hmat[5]) + (Hmat[3]*Hmat[2]);
193 <
194 <  C[0][2] =  ( Hmat[3]*Hmat[7]) - (Hmat[6]*Hmat[4]);
195 <  C[1][2] = -( Hmat[0]*Hmat[7]) + (Hmat[6]*Hmat[1]);
196 <  C[2][2] =  ( Hmat[0]*Hmat[4]) - (Hmat[3]*Hmat[1]);
197 <
198 <  // calcutlate the determinant of Hmat
159 >  matMul3( Hmat, HmatInv, sanity );
160 >    
161 >  // check to see if Hmat is orthorhombic
162    
163 <  detHmat = 0.0;
164 <  for(i=0; i<3; i++) detHmat += Hmat[i] * C[i][0];
163 >  smallDiag = Hmat[0][0];
164 >  if(smallDiag > Hmat[1][1]) smallDiag = Hmat[1][1];
165 >  if(smallDiag > Hmat[2][2]) smallDiag = Hmat[2][2];
166 >  tol = smallDiag * 1E-6;
167  
168 +  orthoRhombic = 1;
169    
170 <  // H^-1 = C^T / det(H)
171 <  
172 <  i=0;
173 <  for(j=0; j<3; j++){
174 <    for(k=0; k<3; k++){
175 <
176 <      HmatI[i] = C[j][k] / detHmat;
211 <      i++;
170 >  for (i = 0; i < 3; i++ ) {
171 >    for (j = 0 ; j < 3; j++) {
172 >      if (i != j) {
173 >        if (orthoRhombic) {
174 >          if (Hmat[i][j] >= tol) orthoRhombic = 0;
175 >        }        
176 >      }
177      }
178    }
179 + }
180  
181 <  // sanity check
181 > double SimInfo::matDet3(double a[3][3]) {
182 >  int i, j, k;
183 >  double determinant;
184  
185 <  for(i=0; i<3; i++){
186 <    for(j=0; j<3; j++){
185 >  determinant = 0.0;
186 >
187 >  for(i = 0; i < 3; i++) {
188 >    j = (i+1)%3;
189 >    k = (i+2)%3;
190 >
191 >    determinant += a[0][i] * (a[1][j]*a[2][k] - a[1][k]*a[2][j]);
192 >  }
193 >
194 >  return determinant;
195 > }
196 >
197 > void SimInfo::invertMat3(double a[3][3], double b[3][3]) {
198 >  
199 >  int  i, j, k, l, m, n;
200 >  double determinant;
201 >
202 >  determinant = matDet3( a );
203 >
204 >  if (determinant == 0.0) {
205 >    sprintf( painCave.errMsg,
206 >             "Can't invert a matrix with a zero determinant!\n");
207 >    painCave.isFatal = 1;
208 >    simError();
209 >  }
210 >
211 >  for (i=0; i < 3; i++) {
212 >    j = (i+1)%3;
213 >    k = (i+2)%3;
214 >    for(l = 0; l < 3; l++) {
215 >      m = (l+1)%3;
216 >      n = (l+2)%3;
217        
218 <      sanity[i][j] = 0.0;
221 <      for(k=0; k<3; k++){
222 <        sanity[i][j] += Hmat[3*k+i] * HmatI[3*j+k];
223 <      }
218 >      b[l][i] = (a[j][m]*a[k][n] - a[j][n]*a[k][m]) / determinant;
219      }
220    }
221 + }
222  
223 <  cerr << "sanity => \n"
224 <       << sanity[0][0] << "\t" << sanity[0][1] << "\t" << sanity [0][2] << "\n"
229 <       << sanity[1][0] << "\t" << sanity[1][1] << "\t" << sanity [1][2] << "\n"
230 <       << sanity[2][0] << "\t" << sanity[2][1] << "\t" << sanity [2][2]
231 <       << "\n";
232 <    
223 > void SimInfo::matMul3(double a[3][3], double b[3][3], double c[3][3]) {
224 >  double r00, r01, r02, r10, r11, r12, r20, r21, r22;
225  
226 <  // check to see if Hmat is orthorhombic
226 >  r00 = a[0][0]*b[0][0] + a[0][1]*b[1][0] + a[0][2]*b[2][0];
227 >  r01 = a[0][0]*b[0][1] + a[0][1]*b[1][1] + a[0][2]*b[2][1];
228 >  r02 = a[0][0]*b[0][2] + a[0][1]*b[1][2] + a[0][2]*b[2][2];
229    
230 <  smallDiag = Hmat[0];
231 <  if(smallDiag > Hmat[4]) smallDiag = Hmat[4];
232 <  if(smallDiag > Hmat[8]) smallDiag = Hmat[8];
233 <  tol = smallDiag * 1E-6;
230 >  r10 = a[1][0]*b[0][0] + a[1][1]*b[1][0] + a[1][2]*b[2][0];
231 >  r11 = a[1][0]*b[0][1] + a[1][1]*b[1][1] + a[1][2]*b[2][1];
232 >  r12 = a[1][0]*b[0][2] + a[1][1]*b[1][2] + a[1][2]*b[2][2];
233 >  
234 >  r20 = a[2][0]*b[0][0] + a[2][1]*b[1][0] + a[2][2]*b[2][0];
235 >  r21 = a[2][0]*b[0][1] + a[2][1]*b[1][1] + a[2][2]*b[2][1];
236 >  r22 = a[2][0]*b[0][2] + a[2][1]*b[1][2] + a[2][2]*b[2][2];
237 >  
238 >  c[0][0] = r00; c[0][1] = r01; c[0][2] = r02;
239 >  c[1][0] = r10; c[1][1] = r11; c[1][2] = r12;
240 >  c[2][0] = r20; c[2][1] = r21; c[2][2] = r22;
241 > }
242  
243 <  orthoRhombic = 1;
244 <  for(i=0; (i<9) && orthoRhombic; i++){
245 <    
246 <    if( (i%4) ){ // ignore the diagonals (0, 4, and 8)
247 <      orthoRhombic = (Hmat[i] <= tol);
243 > void SimInfo::matVecMul3(double m[3][3], double inVec[3], double outVec[3]) {
244 >  double a0, a1, a2;
245 >
246 >  a0 = inVec[0];  a1 = inVec[1];  a2 = inVec[2];
247 >
248 >  outVec[0] = m[0][0]*a0 + m[0][1]*a1 + m[0][2]*a2;
249 >  outVec[1] = m[1][0]*a0 + m[1][1]*a1 + m[1][2]*a2;
250 >  outVec[2] = m[2][0]*a0 + m[2][1]*a1 + m[2][2]*a2;
251 > }
252 >
253 > void SimInfo::transposeMat3(double in[3][3], double out[3][3]) {
254 >  double temp[3][3];
255 >  int i, j;
256 >
257 >  for (i = 0; i < 3; i++) {
258 >    for (j = 0; j < 3; j++) {
259 >      temp[j][i] = in[i][j];
260      }
261    }
262 <    
262 >  for (i = 0; i < 3; i++) {
263 >    for (j = 0; j < 3; j++) {
264 >      out[i][j] = temp[i][j];
265 >    }
266 >  }
267   }
268 +  
269 + void SimInfo::printMat3(double A[3][3] ){
270  
271 +  std::cerr
272 +            << "[ " << A[0][0] << ", " << A[0][1] << ", " << A[0][2] << " ]\n"
273 +            << "[ " << A[1][0] << ", " << A[1][1] << ", " << A[1][2] << " ]\n"
274 +            << "[ " << A[2][0] << ", " << A[2][1] << ", " << A[2][2] << " ]\n";
275 + }
276 +
277 + void SimInfo::printMat9(double A[9] ){
278 +
279 +  std::cerr
280 +            << "[ " << A[0] << ", " << A[1] << ", " << A[2] << " ]\n"
281 +            << "[ " << A[3] << ", " << A[4] << ", " << A[5] << " ]\n"
282 +            << "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n";
283 + }
284 +
285 +
286 + void SimInfo::crossProduct3(double a[3],double b[3], double out[3]){
287 +
288 +      out[0] = a[1] * b[2] - a[2] * b[1];
289 +      out[1] = a[2] * b[0] - a[0] * b[2] ;
290 +      out[2] = a[0] * b[1] - a[1] * b[0];
291 +      
292 + }
293 +
294 + double SimInfo::dotProduct3(double a[3], double b[3]){
295 +  return a[0]*b[0] + a[1]*b[1]+ a[2]*b[2];
296 + }
297 +
298 + double SimInfo::length3(double a[3]){
299 +  return sqrt(a[0]*a[0] + a[1]*a[1] + a[2]*a[2]);
300 + }
301 +
302   void SimInfo::calcBoxL( void ){
303  
304    double dx, dy, dz, dsq;
305    int i;
306  
307 <  // boxVol = h1 (dot) h2 (cross) h3
307 >  // boxVol = Determinant of Hmat
308  
309 <  boxVol = Hmat[0] * ( (Hmat[4]*Hmat[8]) - (Hmat[7]*Hmat[5]) )
259 <         + Hmat[1] * ( (Hmat[5]*Hmat[6]) - (Hmat[8]*Hmat[3]) )
260 <         + Hmat[2] * ( (Hmat[3]*Hmat[7]) - (Hmat[6]*Hmat[4]) );
309 >  boxVol = matDet3( Hmat );
310  
262 –
311    // boxLx
312    
313 <  dx = Hmat[0]; dy = Hmat[1]; dz = Hmat[2];
313 >  dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
314    dsq = dx*dx + dy*dy + dz*dz;
315 <  boxLx = sqrt( dsq );
315 >  boxL[0] = sqrt( dsq );
316 >  //maxCutoff = 0.5 * boxL[0];
317  
318    // boxLy
319    
320 <  dx = Hmat[3]; dy = Hmat[4]; dz = Hmat[5];
320 >  dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
321    dsq = dx*dx + dy*dy + dz*dz;
322 <  boxLy = sqrt( dsq );
322 >  boxL[1] = sqrt( dsq );
323 >  //if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
324  
325 +
326    // boxLz
327    
328 <  dx = Hmat[6]; dy = Hmat[7]; dz = Hmat[8];
328 >  dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
329    dsq = dx*dx + dy*dy + dz*dz;
330 <  boxLz = sqrt( dsq );
330 >  boxL[2] = sqrt( dsq );
331 >  //if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
332 >
333 >  //calculate the max cutoff
334 >  maxCutoff =  calcMaxCutOff();
335    
336 +  checkCutOffs();
337 +
338   }
339  
340  
341 + double SimInfo::calcMaxCutOff(){
342 +
343 +  double ri[3], rj[3], rk[3];
344 +  double rij[3], rjk[3], rki[3];
345 +  double minDist;
346 +
347 +  ri[0] = Hmat[0][0];
348 +  ri[1] = Hmat[1][0];
349 +  ri[2] = Hmat[2][0];
350 +
351 +  rj[0] = Hmat[0][1];
352 +  rj[1] = Hmat[1][1];
353 +  rj[2] = Hmat[2][1];
354 +
355 +  rk[0] = Hmat[0][2];
356 +  rk[1] = Hmat[1][2];
357 +  rk[2] = Hmat[2][2];
358 +  
359 +  crossProduct3(ri,rj, rij);
360 +  distXY = dotProduct3(rk,rij) / length3(rij);
361 +
362 +  crossProduct3(rj,rk, rjk);
363 +  distYZ = dotProduct3(ri,rjk) / length3(rjk);
364 +
365 +  crossProduct3(rk,ri, rki);
366 +  distZX = dotProduct3(rj,rki) / length3(rki);
367 +
368 +  minDist = min(min(distXY, distYZ), distZX);
369 +  return minDist/2;
370 +  
371 + }
372 +
373   void SimInfo::wrapVector( double thePos[3] ){
374  
375    int i, j, k;
# Line 288 | Line 377 | void SimInfo::wrapVector( double thePos[3] ){
377  
378    if( !orthoRhombic ){
379      // calc the scaled coordinates.
380 +  
381 +
382 +    matVecMul3(HmatInv, thePos, scaled);
383      
384      for(i=0; i<3; i++)
293 –      scaled[i] =
294 –        thePos[0]*HmatI[i] + thePos[1]*HmatI[i+3] + thePos[3]*HmatI[i+6];
295 –    
296 –    // wrap the scaled coordinates
297 –    
298 –    for(i=0; i<3; i++)
385        scaled[i] -= roundMe(scaled[i]);
386      
387      // calc the wrapped real coordinates from the wrapped scaled coordinates
388      
389 <    for(i=0; i<3; i++)
390 <      thePos[i] =
305 <        scaled[0]*Hmat[i] + scaled[1]*Hmat[i+3] + scaled[2]*Hmat[i+6];
389 >    matVecMul3(Hmat, scaled, thePos);
390 >
391    }
392    else{
393      // calc the scaled coordinates.
394      
395      for(i=0; i<3; i++)
396 <      scaled[i] = thePos[i]*HmatI[i*4];
396 >      scaled[i] = thePos[i]*HmatInv[i][i];
397      
398      // wrap the scaled coordinates
399      
# Line 318 | Line 403 | void SimInfo::wrapVector( double thePos[3] ){
403      // calc the wrapped real coordinates from the wrapped scaled coordinates
404      
405      for(i=0; i<3; i++)
406 <      thePos[i] = scaled[i]*Hmat[i*4];
406 >      thePos[i] = scaled[i]*Hmat[i][i];
407    }
408      
324 –    
409   }
410  
411  
# Line 336 | Line 420 | int SimInfo::getNDF(){
420    ndf = ndf_local;
421   #endif
422  
423 <  ndf = ndf - 3;
423 >  ndf = ndf - 3 - nZconstraints;
424  
425    return ndf;
426   }
# Line 355 | Line 439 | int SimInfo::getNDFraw() {
439  
440    return ndfRaw;
441   }
442 <
442 >
443 > int SimInfo::getNDFtranslational() {
444 >  int ndfTrans_local, ndfTrans;
445 >
446 >  ndfTrans_local = 3 * n_atoms - n_constraints;
447 >
448 > #ifdef IS_MPI
449 >  MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
450 > #else
451 >  ndfTrans = ndfTrans_local;
452 > #endif
453 >
454 >  ndfTrans = ndfTrans - 3 - nZconstraints;
455 >
456 >  return ndfTrans;
457 > }
458 >
459   void SimInfo::refreshSim(){
460  
461    simtype fInfo;
462    int isError;
463    int n_global;
464    int* excl;
465 <  
366 <  fInfo.rrf = 0.0;
367 <  fInfo.rt = 0.0;
465 >
466    fInfo.dielect = 0.0;
467  
370 –  fInfo.rlist = rList;
371 –  fInfo.rcut = rCut;
372 –
468    if( useDipole ){
374 –    fInfo.rrf = ecr;
375 –    fInfo.rt = ecr - est;
469      if( useReactionField )fInfo.dielect = dielectric;
470    }
471  
# Line 418 | Line 511 | void SimInfo::refreshSim(){
511  
512    this->ndf = this->getNDF();
513    this->ndfRaw = this->getNDFraw();
514 +  this->ndfTrans = this->getNDFtranslational();
515 + }
516 +
517 +
518 + void SimInfo::setRcut( double theRcut ){
519 +
520 +  if( !haveOrigRcut ){
521 +    haveOrigRcut = 1;
522 +    origRcut = theRcut;
523 +  }
524 +
525 +  rCut = theRcut;
526 +  checkCutOffs();
527 + }
528 +
529 + void SimInfo::setEcr( double theEcr ){
530  
531 +  if( !haveOrigEcr ){
532 +    haveOrigEcr = 1;
533 +    origEcr = theEcr;
534 +  }
535 +
536 +  ecr = theEcr;
537 +  checkCutOffs();
538   }
539  
540 + void SimInfo::setEcr( double theEcr, double theEst ){
541 +
542 +  est = theEst;
543 +  setEcr( theEcr );
544 + }
545 +
546 +
547 + void SimInfo::checkCutOffs( void ){
548 +
549 +  int cutChanged = 0;
550 +  
551 +  if( boxIsInit ){
552 +    
553 +    //we need to check cutOffs against the box
554 +
555 +    //detect the change of rCut
556 +    if(( maxCutoff > rCut )&&(usePBC)){
557 +      if( rCut < origRcut ){
558 +        rCut = origRcut;
559 +        
560 +        if (rCut > maxCutoff)
561 +          rCut = maxCutoff;
562 +  
563 +          sprintf( painCave.errMsg,
564 +                    "New Box size is setting the long range cutoff radius "
565 +                    "to %lf at time %lf\n",
566 +                    rCut, currentTime );
567 +          painCave.isFatal = 0;
568 +          simError();
569 +      }
570 +    }
571 +    else if ((rCut > maxCutoff)&&(usePBC)) {
572 +      sprintf( painCave.errMsg,
573 +               "New Box size is setting the long range cutoff radius "
574 +               "to %lf at time %lf\n",
575 +               maxCutoff, currentTime );
576 +      painCave.isFatal = 0;
577 +      simError();
578 +      rCut = maxCutoff;
579 +    }
580 +
581 +
582 +    //detect the change of ecr
583 +    if( maxCutoff > ecr ){
584 +      if( ecr < origEcr ){
585 +        ecr = origEcr;
586 +        if (ecr > maxCutoff) ecr = maxCutoff;
587 +  
588 +          sprintf( painCave.errMsg,
589 +                    "New Box size is setting the electrostaticCutoffRadius "
590 +                    "to %lf at time %lf\n",
591 +                    ecr, currentTime );
592 +            painCave.isFatal = 0;
593 +            simError();
594 +      }
595 +    }
596 +    else if( ecr > maxCutoff){
597 +      sprintf( painCave.errMsg,
598 +               "New Box size is setting the electrostaticCutoffRadius "
599 +               "to %lf at time %lf\n",
600 +               maxCutoff, currentTime  );
601 +      painCave.isFatal = 0;
602 +      simError();      
603 +      ecr = maxCutoff;
604 +    }
605 +
606 +    if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1;
607 +    
608 +    // rlist is the 1.0 plus max( rcut, ecr )
609 +    
610 +    ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
611 +    
612 +    if( cutChanged ){
613 +      
614 +      notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
615 +    }
616 +    
617 +    oldEcr = ecr;
618 +    oldRcut = rCut;
619 +    
620 +  } else {
621 +    // initialize this stuff before using it, OK?
622 +    sprintf( painCave.errMsg,
623 +             "Trying to check cutoffs without a box. Be smarter.\n" );
624 +    painCave.isFatal = 1;
625 +    simError();      
626 +  }
627 +  
628 + }
629 +
630 + void SimInfo::addProperty(GenericData* prop){
631 +
632 +  map<string, GenericData*>::iterator result;
633 +  result = properties.find(prop->getID());
634 +  
635 +  //we can't simply use  properties[prop->getID()] = prop,
636 +  //it will cause memory leak if we already contain a propery which has the same name of prop
637 +  
638 +  if(result != properties.end()){
639 +    
640 +    delete (*result).second;
641 +    (*result).second = prop;
642 +      
643 +  }
644 +  else{
645 +
646 +    properties[prop->getID()] = prop;
647 +
648 +  }
649 +    
650 + }
651 +
652 + GenericData* SimInfo::getProperty(const string& propName){
653 +
654 +  map<string, GenericData*>::iterator result;
655 +  
656 +  //string lowerCaseName = ();
657 +  
658 +  result = properties.find(propName);
659 +  
660 +  if(result != properties.end())
661 +    return (*result).second;  
662 +  else  
663 +    return NULL;  
664 + }
665 +
666 + vector<GenericData*> SimInfo::getProperties(){
667 +
668 +  vector<GenericData*> result;
669 +  map<string, GenericData*>::iterator i;
670 +  
671 +  for(i = properties.begin(); i != properties.end(); i++)
672 +    result.push_back((*i).second);
673 +    
674 +  return result;
675 + }
676 +
677 + double SimInfo::matTrace3(double m[3][3]){
678 +  double trace;
679 +  trace = m[0][0] + m[1][1] + m[2][2];
680 +
681 +  return trace;
682 + }

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