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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 859 by mmeineke, Mon Nov 10 21:50:36 2003 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 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 +  ecr = 0.0;
41 +  est = 0.0;
42  
43 +  haveRcut = 0;
44 +  haveEcr = 0;
45 +  boxIsInit = 0;
46 +  
47 +  resetTime = 1e99;
48 +
49 +  orthoTolerance = 1E-6;
50 +  useInitXSstate = true;
51 +
52    usePBC = 0;
53    useLJ = 0;
54    useSticky = 0;
# Line 43 | Line 57 | SimInfo::SimInfo(){
57    useGB = 0;
58    useEAM = 0;
59  
60 +  myConfiguration = new SimState();
61 +
62    wrapMeSimInfo( this );
63   }
64  
49 – void SimInfo::setBox(double newBox[3]) {
65  
66 <  double smallestBoxL, maxCutoff;
52 <  int status;
53 <  int i;
66 > SimInfo::~SimInfo(){
67  
68 <  for(i=0; i<9; i++) Hmat[i] = 0.0;;
68 >  delete myConfiguration;
69  
70 <  Hmat[0] = newBox[0];
71 <  Hmat[4] = newBox[1];
72 <  Hmat[8] = newBox[2];
70 >  map<string, GenericData*>::iterator i;
71 >  
72 >  for(i = properties.begin(); i != properties.end(); i++)
73 >    delete (*i).second;
74 >    
75 > }
76  
77 <  calcHmatI();
78 <  calcBoxL();
77 > void SimInfo::setBox(double newBox[3]) {
78 >  
79 >  int i, j;
80 >  double tempMat[3][3];
81  
82 <  setFortranBoxSize(Hmat, HmatI, &orthoRhombic);
82 >  for(i=0; i<3; i++)
83 >    for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
84  
85 <  smallestBoxL = boxLx;
86 <  if (boxLy < smallestBoxL) smallestBoxL = boxLy;
87 <  if (boxLz < smallestBoxL) smallestBoxL = boxLz;
85 >  tempMat[0][0] = newBox[0];
86 >  tempMat[1][1] = newBox[1];
87 >  tempMat[2][2] = newBox[2];
88  
89 <  maxCutoff = smallestBoxL / 2.0;
89 >  setBoxM( tempMat );
90  
91 <  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();
91 > }
92  
93 <    rList = maxCutoff;
93 > void SimInfo::setBoxM( double theBox[3][3] ){
94 >  
95 >  int i, j;
96 >  double FortranHmat[9]; // to preserve compatibility with Fortran the
97 >                         // ordering in the array is as follows:
98 >                         // [ 0 3 6 ]
99 >                         // [ 1 4 7 ]
100 >                         // [ 2 5 8 ]
101 >  double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
102  
103 <    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();
103 >  if( !boxIsInit ) boxIsInit = 1;
104  
105 <    rCut = rList - 1.0;
105 >  for(i=0; i < 3; i++)
106 >    for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
107 >  
108 >  calcBoxL();
109 >  calcHmatInv();
110  
111 <    // list radius changed so we have to refresh the simulation structure.
112 <    refreshSim();
111 >  for(i=0; i < 3; i++) {
112 >    for (j=0; j < 3; j++) {
113 >      FortranHmat[3*j + i] = Hmat[i][j];
114 >      FortranHmatInv[3*j + i] = HmatInv[i][j];
115 >    }
116    }
117  
118 <  if (rCut > maxCutoff) {
119 <    sprintf( painCave.errMsg,
120 <             "New Box size is forcing cutoff radius down to %lf\n",
121 <             maxCutoff );
97 <    painCave.isFatal = 0;
98 <    simError();
118 >  setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic);
119 >
120 > }
121 >
122  
123 <    status = 0;
124 <    LJ_new_rcut(&rCut, &status);
125 <    if (status != 0) {
126 <      sprintf( painCave.errMsg,
127 <               "Error in recomputing LJ shifts based on new rcut\n");
105 <      painCave.isFatal = 1;
106 <      simError();
107 <    }
108 <  }
123 > void SimInfo::getBoxM (double theBox[3][3]) {
124 >
125 >  int i, j;
126 >  for(i=0; i<3; i++)
127 >    for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j];
128   }
129  
111 – void SimInfo::setBoxM( double theBox[9] ){
112 –  
113 –  int i, status;
114 –  double smallestBoxL, maxCutoff;
130  
131 <  for(i=0; i<9; i++) Hmat[i] = theBox[i];
132 <  calcHmatI();
133 <  calcBoxL();
131 > void SimInfo::scaleBox(double scale) {
132 >  double theBox[3][3];
133 >  int i, j;
134  
135 <  setFortranBoxSize(Hmat, HmatI, &orthoRhombic);
121 <
122 <  smallestBoxL = boxLx;
123 <  if (boxLy < smallestBoxL) smallestBoxL = boxLy;
124 <  if (boxLz < smallestBoxL) smallestBoxL = boxLz;
135 >  // cerr << "Scaling box by " << scale << "\n";
136  
137 <  maxCutoff = smallestBoxL / 2.0;
137 >  for(i=0; i<3; i++)
138 >    for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
139  
140 <  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();
140 >  setBoxM(theBox);
141  
142 <    rList = maxCutoff;
142 > }
143  
144 <    sprintf( painCave.errMsg,
145 <             "New Box size is forcing cutoff radius down to %lf\n",
146 <             maxCutoff - 1.0 );
147 <    painCave.isFatal = 0;
148 <    simError();
144 > void SimInfo::calcHmatInv( void ) {
145 >  
146 >  int oldOrtho;
147 >  int i,j;
148 >  double smallDiag;
149 >  double tol;
150 >  double sanity[3][3];
151  
152 <    rCut = rList - 1.0;
152 >  invertMat3( Hmat, HmatInv );
153  
154 <    // list radius changed so we have to refresh the simulation structure.
155 <    refreshSim();
156 <  }
154 >  // check to see if Hmat is orthorhombic
155 >  
156 >  oldOrtho = orthoRhombic;
157  
158 <  if (rCut > maxCutoff) {
159 <    sprintf( painCave.errMsg,
160 <             "New Box size is forcing cutoff radius down to %lf\n",
161 <             maxCutoff );
153 <    painCave.isFatal = 0;
154 <    simError();
158 >  smallDiag = fabs(Hmat[0][0]);
159 >  if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]);
160 >  if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]);
161 >  tol = smallDiag * orthoTolerance;
162  
163 <    status = 0;
164 <    LJ_new_rcut(&rCut, &status);
165 <    if (status != 0) {
163 >  orthoRhombic = 1;
164 >  
165 >  for (i = 0; i < 3; i++ ) {
166 >    for (j = 0 ; j < 3; j++) {
167 >      if (i != j) {
168 >        if (orthoRhombic) {
169 >          if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0;
170 >        }        
171 >      }
172 >    }
173 >  }
174 >
175 >  if( oldOrtho != orthoRhombic ){
176 >    
177 >    if( orthoRhombic ){
178        sprintf( painCave.errMsg,
179 <               "Error in recomputing LJ shifts based on new rcut\n");
180 <      painCave.isFatal = 1;
179 >               "Hmat is switching from Non-Orthorhombic to OrthoRhombic\n"
180 >               "       If this is a bad thing, change the orthoBoxTolerance( currently %G ).\n",
181 >               orthoTolerance);
182        simError();
183      }
184 +    else {
185 +      sprintf( painCave.errMsg,
186 +               "Hmat is switching from Orthorhombic to Non-OrthoRhombic\n"
187 +               "       If this is a bad thing, change the orthoBoxTolerance( currently %G ).\n",
188 +               orthoTolerance);
189 +      simError();
190 +    }
191    }
192   }
166 –
193  
194 < void SimInfo::getBoxM (double theBox[9]) {
194 > double SimInfo::matDet3(double a[3][3]) {
195 >  int i, j, k;
196 >  double determinant;
197  
198 <  int i;
171 <  for(i=0; i<9; i++) theBox[i] = Hmat[i];
172 < }
198 >  determinant = 0.0;
199  
200 +  for(i = 0; i < 3; i++) {
201 +    j = (i+1)%3;
202 +    k = (i+2)%3;
203  
204 < void SimInfo::scaleBox(double scale) {
205 <  double theBox[9];
177 <  int i;
204 >    determinant += a[0][i] * (a[1][j]*a[2][k] - a[1][k]*a[2][j]);
205 >  }
206  
207 <  for(i=0; i<9; i++) theBox[i] = Hmat[i]*scale;
180 <
181 <  setBoxM(theBox);
182 <
207 >  return determinant;
208   }
209  
210 < void SimInfo::calcHmatI( void ) {
186 <
187 <  double C[3][3];
188 <  double detHmat;
189 <  int i, j, k;
190 <  double smallDiag;
191 <  double tol;
192 <  double sanity[3][3];
193 <
194 <  // calculate the adjunct of Hmat;
195 <
196 <  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
210 > void SimInfo::invertMat3(double a[3][3], double b[3][3]) {
211    
212 <  detHmat = 0.0;
213 <  for(i=0; i<3; i++) detHmat += Hmat[i] * C[i][0];
212 >  int  i, j, k, l, m, n;
213 >  double determinant;
214  
215 <  
214 <  // H^-1 = C^T / det(H)
215 <  
216 <  i=0;
217 <  for(j=0; j<3; j++){
218 <    for(k=0; k<3; k++){
215 >  determinant = matDet3( a );
216  
217 <      HmatI[i] = C[j][k] / detHmat;
218 <      i++;
219 <    }
217 >  if (determinant == 0.0) {
218 >    sprintf( painCave.errMsg,
219 >             "Can't invert a matrix with a zero determinant!\n");
220 >    painCave.isFatal = 1;
221 >    simError();
222    }
223  
224 <  // sanity check
225 <
226 <  for(i=0; i<3; i++){
227 <    for(j=0; j<3; j++){
224 >  for (i=0; i < 3; i++) {
225 >    j = (i+1)%3;
226 >    k = (i+2)%3;
227 >    for(l = 0; l < 3; l++) {
228 >      m = (l+1)%3;
229 >      n = (l+2)%3;
230        
231 <      sanity[i][j] = 0.0;
231 <      for(k=0; k<3; k++){
232 <        sanity[i][j] += Hmat[3*k+i] * HmatI[3*j+k];
233 <      }
231 >      b[l][i] = (a[j][m]*a[k][n] - a[j][n]*a[k][m]) / determinant;
232      }
233    }
234 + }
235  
236 <  cerr << "sanity => \n"
237 <       << 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";
242 <    
236 > void SimInfo::matMul3(double a[3][3], double b[3][3], double c[3][3]) {
237 >  double r00, r01, r02, r10, r11, r12, r20, r21, r22;
238  
239 <  // check to see if Hmat is orthorhombic
239 >  r00 = a[0][0]*b[0][0] + a[0][1]*b[1][0] + a[0][2]*b[2][0];
240 >  r01 = a[0][0]*b[0][1] + a[0][1]*b[1][1] + a[0][2]*b[2][1];
241 >  r02 = a[0][0]*b[0][2] + a[0][1]*b[1][2] + a[0][2]*b[2][2];
242    
243 <  smallDiag = Hmat[0];
244 <  if(smallDiag > Hmat[4]) smallDiag = Hmat[4];
245 <  if(smallDiag > Hmat[8]) smallDiag = Hmat[8];
246 <  tol = smallDiag * 1E-6;
243 >  r10 = a[1][0]*b[0][0] + a[1][1]*b[1][0] + a[1][2]*b[2][0];
244 >  r11 = a[1][0]*b[0][1] + a[1][1]*b[1][1] + a[1][2]*b[2][1];
245 >  r12 = a[1][0]*b[0][2] + a[1][1]*b[1][2] + a[1][2]*b[2][2];
246 >  
247 >  r20 = a[2][0]*b[0][0] + a[2][1]*b[1][0] + a[2][2]*b[2][0];
248 >  r21 = a[2][0]*b[0][1] + a[2][1]*b[1][1] + a[2][2]*b[2][1];
249 >  r22 = a[2][0]*b[0][2] + a[2][1]*b[1][2] + a[2][2]*b[2][2];
250 >  
251 >  c[0][0] = r00; c[0][1] = r01; c[0][2] = r02;
252 >  c[1][0] = r10; c[1][1] = r11; c[1][2] = r12;
253 >  c[2][0] = r20; c[2][1] = r21; c[2][2] = r22;
254 > }
255  
256 <  orthoRhombic = 1;
257 <  for(i=0; (i<9) && orthoRhombic; i++){
258 <    
259 <    if( (i%4) ){ // ignore the diagonals (0, 4, and 8)
260 <      orthoRhombic = (Hmat[i] <= tol);
256 > void SimInfo::matVecMul3(double m[3][3], double inVec[3], double outVec[3]) {
257 >  double a0, a1, a2;
258 >
259 >  a0 = inVec[0];  a1 = inVec[1];  a2 = inVec[2];
260 >
261 >  outVec[0] = m[0][0]*a0 + m[0][1]*a1 + m[0][2]*a2;
262 >  outVec[1] = m[1][0]*a0 + m[1][1]*a1 + m[1][2]*a2;
263 >  outVec[2] = m[2][0]*a0 + m[2][1]*a1 + m[2][2]*a2;
264 > }
265 >
266 > void SimInfo::transposeMat3(double in[3][3], double out[3][3]) {
267 >  double temp[3][3];
268 >  int i, j;
269 >
270 >  for (i = 0; i < 3; i++) {
271 >    for (j = 0; j < 3; j++) {
272 >      temp[j][i] = in[i][j];
273      }
274    }
275 <    
275 >  for (i = 0; i < 3; i++) {
276 >    for (j = 0; j < 3; j++) {
277 >      out[i][j] = temp[i][j];
278 >    }
279 >  }
280   }
281 +  
282 + void SimInfo::printMat3(double A[3][3] ){
283  
284 +  std::cerr
285 +            << "[ " << A[0][0] << ", " << A[0][1] << ", " << A[0][2] << " ]\n"
286 +            << "[ " << A[1][0] << ", " << A[1][1] << ", " << A[1][2] << " ]\n"
287 +            << "[ " << A[2][0] << ", " << A[2][1] << ", " << A[2][2] << " ]\n";
288 + }
289 +
290 + void SimInfo::printMat9(double A[9] ){
291 +
292 +  std::cerr
293 +            << "[ " << A[0] << ", " << A[1] << ", " << A[2] << " ]\n"
294 +            << "[ " << A[3] << ", " << A[4] << ", " << A[5] << " ]\n"
295 +            << "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n";
296 + }
297 +
298 +
299 + void SimInfo::crossProduct3(double a[3],double b[3], double out[3]){
300 +
301 +      out[0] = a[1] * b[2] - a[2] * b[1];
302 +      out[1] = a[2] * b[0] - a[0] * b[2] ;
303 +      out[2] = a[0] * b[1] - a[1] * b[0];
304 +      
305 + }
306 +
307 + double SimInfo::dotProduct3(double a[3], double b[3]){
308 +  return a[0]*b[0] + a[1]*b[1]+ a[2]*b[2];
309 + }
310 +
311 + double SimInfo::length3(double a[3]){
312 +  return sqrt(a[0]*a[0] + a[1]*a[1] + a[2]*a[2]);
313 + }
314 +
315   void SimInfo::calcBoxL( void ){
316  
317    double dx, dy, dz, dsq;
264 –  int i;
318  
319 <  // boxVol = h1 (dot) h2 (cross) h3
319 >  // boxVol = Determinant of Hmat
320  
321 <  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]) );
321 >  boxVol = matDet3( Hmat );
322  
272 –
323    // boxLx
324    
325 <  dx = Hmat[0]; dy = Hmat[1]; dz = Hmat[2];
325 >  dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
326    dsq = dx*dx + dy*dy + dz*dz;
327 <  boxLx = sqrt( dsq );
327 >  boxL[0] = sqrt( dsq );
328 >  //maxCutoff = 0.5 * boxL[0];
329  
330    // boxLy
331    
332 <  dx = Hmat[3]; dy = Hmat[4]; dz = Hmat[5];
332 >  dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
333    dsq = dx*dx + dy*dy + dz*dz;
334 <  boxLy = sqrt( dsq );
334 >  boxL[1] = sqrt( dsq );
335 >  //if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
336  
337 +
338    // boxLz
339    
340 <  dx = Hmat[6]; dy = Hmat[7]; dz = Hmat[8];
340 >  dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
341    dsq = dx*dx + dy*dy + dz*dz;
342 <  boxLz = sqrt( dsq );
342 >  boxL[2] = sqrt( dsq );
343 >  //if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
344 >
345 >  //calculate the max cutoff
346 >  maxCutoff =  calcMaxCutOff();
347    
348 +  checkCutOffs();
349 +
350   }
351  
352  
353 + double SimInfo::calcMaxCutOff(){
354 +
355 +  double ri[3], rj[3], rk[3];
356 +  double rij[3], rjk[3], rki[3];
357 +  double minDist;
358 +
359 +  ri[0] = Hmat[0][0];
360 +  ri[1] = Hmat[1][0];
361 +  ri[2] = Hmat[2][0];
362 +
363 +  rj[0] = Hmat[0][1];
364 +  rj[1] = Hmat[1][1];
365 +  rj[2] = Hmat[2][1];
366 +
367 +  rk[0] = Hmat[0][2];
368 +  rk[1] = Hmat[1][2];
369 +  rk[2] = Hmat[2][2];
370 +  
371 +  crossProduct3(ri,rj, rij);
372 +  distXY = dotProduct3(rk,rij) / length3(rij);
373 +
374 +  crossProduct3(rj,rk, rjk);
375 +  distYZ = dotProduct3(ri,rjk) / length3(rjk);
376 +
377 +  crossProduct3(rk,ri, rki);
378 +  distZX = dotProduct3(rj,rki) / length3(rki);
379 +
380 +  minDist = min(min(distXY, distYZ), distZX);
381 +  return minDist/2;
382 +  
383 + }
384 +
385   void SimInfo::wrapVector( double thePos[3] ){
386  
387 <  int i, j, k;
387 >  int i;
388    double scaled[3];
389  
390    if( !orthoRhombic ){
391      // calc the scaled coordinates.
392 +  
393 +
394 +    matVecMul3(HmatInv, thePos, scaled);
395      
396      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++)
397        scaled[i] -= roundMe(scaled[i]);
398      
399      // calc the wrapped real coordinates from the wrapped scaled coordinates
400      
401 <    for(i=0; i<3; i++)
402 <      thePos[i] =
315 <        scaled[0]*Hmat[i] + scaled[1]*Hmat[i+3] + scaled[2]*Hmat[i+6];
401 >    matVecMul3(Hmat, scaled, thePos);
402 >
403    }
404    else{
405      // calc the scaled coordinates.
406      
407      for(i=0; i<3; i++)
408 <      scaled[i] = thePos[i]*HmatI[i*4];
408 >      scaled[i] = thePos[i]*HmatInv[i][i];
409      
410      // wrap the scaled coordinates
411      
# Line 328 | Line 415 | void SimInfo::wrapVector( double thePos[3] ){
415      // calc the wrapped real coordinates from the wrapped scaled coordinates
416      
417      for(i=0; i<3; i++)
418 <      thePos[i] = scaled[i]*Hmat[i*4];
418 >      thePos[i] = scaled[i]*Hmat[i][i];
419    }
420      
334 –    
421   }
422  
423  
424   int SimInfo::getNDF(){
425 <  int ndf_local, ndf;
425 >  int ndf_local;
426    
427    ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints;
428  
# Line 346 | Line 432 | int SimInfo::getNDF(){
432    ndf = ndf_local;
433   #endif
434  
435 <  ndf = ndf - 3;
435 >  ndf = ndf - 3 - nZconstraints;
436  
437    return ndf;
438   }
439  
440   int SimInfo::getNDFraw() {
441 <  int ndfRaw_local, ndfRaw;
441 >  int ndfRaw_local;
442  
443    // Raw degrees of freedom that we have to set
444    ndfRaw_local = 3 * n_atoms + 3 * n_oriented;
# Line 365 | Line 451 | int SimInfo::getNDFraw() {
451  
452    return ndfRaw;
453   }
454 <
454 >
455 > int SimInfo::getNDFtranslational() {
456 >  int ndfTrans_local;
457 >
458 >  ndfTrans_local = 3 * n_atoms - n_constraints;
459 >
460 > #ifdef IS_MPI
461 >  MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
462 > #else
463 >  ndfTrans = ndfTrans_local;
464 > #endif
465 >
466 >  ndfTrans = ndfTrans - 3 - nZconstraints;
467 >
468 >  return ndfTrans;
469 > }
470 >
471   void SimInfo::refreshSim(){
472  
473    simtype fInfo;
474    int isError;
475    int n_global;
476    int* excl;
477 <  
376 <  fInfo.rrf = 0.0;
377 <  fInfo.rt = 0.0;
477 >
478    fInfo.dielect = 0.0;
479  
380 –  fInfo.rlist = rList;
381 –  fInfo.rcut = rCut;
382 –
480    if( useDipole ){
384 –    fInfo.rrf = ecr;
385 –    fInfo.rt = ecr - est;
481      if( useReactionField )fInfo.dielect = dielectric;
482    }
483  
# Line 428 | Line 523 | void SimInfo::refreshSim(){
523  
524    this->ndf = this->getNDF();
525    this->ndfRaw = this->getNDFraw();
526 +  this->ndfTrans = this->getNDFtranslational();
527 + }
528  
529 + void SimInfo::setDefaultRcut( double theRcut ){
530 +
531 +  haveRcut = 1;
532 +  rCut = theRcut;
533 +
534 +  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
535 +
536 +  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
537   }
538  
539 + void SimInfo::setDefaultEcr( double theEcr ){
540 +
541 +  haveEcr = 1;
542 +  
543 +  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
544 +
545 +  ecr = theEcr;
546 +
547 +  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
548 + }
549 +
550 + void SimInfo::setDefaultEcr( double theEcr, double theEst ){
551 +
552 +  est = theEst;
553 +  setDefaultEcr( theEcr );
554 + }
555 +
556 +
557 + void SimInfo::checkCutOffs( void ){
558 +  
559 +  if( boxIsInit ){
560 +    
561 +    //we need to check cutOffs against the box
562 +    
563 +    if( rCut > maxCutoff ){
564 +      sprintf( painCave.errMsg,
565 +               "Box size is too small for the long range cutoff radius, "
566 +               "%lf, at time %lf\n",
567 +               rCut, currentTime );
568 +      painCave.isFatal = 1;
569 +      simError();
570 +    }
571 +    
572 +    if( haveEcr ){
573 +      if( ecr > maxCutoff ){
574 +        sprintf( painCave.errMsg,
575 +                 "Box size is too small for the electrostatic cutoff radius, "
576 +                 "%lf, at time %lf\n",
577 +                 ecr, currentTime );
578 +        painCave.isFatal = 1;
579 +        simError();
580 +      }
581 +    }
582 +  } else {
583 +    // initialize this stuff before using it, OK?
584 +    sprintf( painCave.errMsg,
585 +             "Trying to check cutoffs without a box. Be smarter.\n" );
586 +    painCave.isFatal = 1;
587 +    simError();      
588 +  }
589 +  
590 + }
591 +
592 + void SimInfo::addProperty(GenericData* prop){
593 +
594 +  map<string, GenericData*>::iterator result;
595 +  result = properties.find(prop->getID());
596 +  
597 +  //we can't simply use  properties[prop->getID()] = prop,
598 +  //it will cause memory leak if we already contain a propery which has the same name of prop
599 +  
600 +  if(result != properties.end()){
601 +    
602 +    delete (*result).second;
603 +    (*result).second = prop;
604 +      
605 +  }
606 +  else{
607 +
608 +    properties[prop->getID()] = prop;
609 +
610 +  }
611 +    
612 + }
613 +
614 + GenericData* SimInfo::getProperty(const string& propName){
615 +
616 +  map<string, GenericData*>::iterator result;
617 +  
618 +  //string lowerCaseName = ();
619 +  
620 +  result = properties.find(propName);
621 +  
622 +  if(result != properties.end())
623 +    return (*result).second;  
624 +  else  
625 +    return NULL;  
626 + }
627 +
628 + vector<GenericData*> SimInfo::getProperties(){
629 +
630 +  vector<GenericData*> result;
631 +  map<string, GenericData*>::iterator i;
632 +  
633 +  for(i = properties.begin(); i != properties.end(); i++)
634 +    result.push_back((*i).second);
635 +    
636 +  return result;
637 + }
638 +
639 + double SimInfo::matTrace3(double m[3][3]){
640 +  double trace;
641 +  trace = m[0][0] + m[1][1] + m[2][2];
642 +
643 +  return trace;
644 + }

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