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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 860 by mmeineke, Tue Nov 11 17:20:12 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 20 | Line 20 | inline double roundMe( double x ){
20    return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 );
21   }
22            
23 + inline double min( double a, double b ){
24 +  return (a < b ) ? a : b;
25 + }
26  
27   SimInfo* currentInfo;
28  
29   SimInfo::SimInfo(){
30    excludes = NULL;
31    n_constraints = 0;
32 +  nZconstraints = 0;
33    n_oriented = 0;
34    n_dipoles = 0;
35    ndf = 0;
36    ndfRaw = 0;
37 +  nZconstraints = 0;
38    the_integrator = NULL;
39    setTemp = 0;
40    thermalTime = 0.0;
41 +  currentTime = 0.0;
42    rCut = 0.0;
43 +  ecr = 0.0;
44 +  est = 0.0;
45  
46 +  haveRcut = 0;
47 +  haveEcr = 0;
48 +  boxIsInit = 0;
49 +  
50 +  resetTime = 1e99;
51 +
52 +  orthoTolerance = 1E-6;
53 +  useInitXSstate = true;
54 +
55    usePBC = 0;
56    useLJ = 0;
57    useSticky = 0;
# Line 43 | Line 60 | SimInfo::SimInfo(){
60    useGB = 0;
61    useEAM = 0;
62  
63 +  myConfiguration = new SimState();
64 +
65    wrapMeSimInfo( this );
66   }
67  
49 – void SimInfo::setBox(double newBox[3]) {
68  
69 <  double smallestBoxL, maxCutoff;
52 <  int status;
53 <  int i;
69 > SimInfo::~SimInfo(){
70  
71 <  for(i=0; i<9; i++) Hmat[i] = 0.0;;
71 >  delete myConfiguration;
72  
73 <  Hmat[0] = newBox[0];
74 <  Hmat[4] = newBox[1];
75 <  Hmat[8] = newBox[2];
73 >  map<string, GenericData*>::iterator i;
74 >  
75 >  for(i = properties.begin(); i != properties.end(); i++)
76 >    delete (*i).second;
77 >    
78 > }
79  
80 <  calcHmatI();
81 <  calcBoxL();
80 > void SimInfo::setBox(double newBox[3]) {
81 >  
82 >  int i, j;
83 >  double tempMat[3][3];
84  
85 <  setFortranBoxSize(Hmat, HmatI, &orthoRhombic);
85 >  for(i=0; i<3; i++)
86 >    for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
87  
88 <  smallestBoxL = boxLx;
89 <  if (boxLy < smallestBoxL) smallestBoxL = boxLy;
90 <  if (boxLz < smallestBoxL) smallestBoxL = boxLz;
88 >  tempMat[0][0] = newBox[0];
89 >  tempMat[1][1] = newBox[1];
90 >  tempMat[2][2] = newBox[2];
91  
92 <  maxCutoff = smallestBoxL / 2.0;
92 >  setBoxM( tempMat );
93  
94 <  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();
94 > }
95  
96 <    rList = maxCutoff;
96 > void SimInfo::setBoxM( double theBox[3][3] ){
97 >  
98 >  int i, j;
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 <    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();
106 >  if( !boxIsInit ) boxIsInit = 1;
107  
108 <    rCut = rList - 1.0;
108 >  for(i=0; i < 3; i++)
109 >    for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
110 >  
111 >  calcBoxL();
112 >  calcHmatInv();
113  
114 <    // list radius changed so we have to refresh the simulation structure.
115 <    refreshSim();
114 >  for(i=0; i < 3; i++) {
115 >    for (j=0; j < 3; j++) {
116 >      FortranHmat[3*j + i] = Hmat[i][j];
117 >      FortranHmatInv[3*j + i] = HmatInv[i][j];
118 >    }
119    }
120  
121 <  if (rCut > maxCutoff) {
122 <    sprintf( painCave.errMsg,
123 <             "New Box size is forcing cutoff radius down to %lf\n",
124 <             maxCutoff );
97 <    painCave.isFatal = 0;
98 <    simError();
121 >  setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic);
122 >
123 > }
124 >
125  
126 <    status = 0;
127 <    LJ_new_rcut(&rCut, &status);
128 <    if (status != 0) {
129 <      sprintf( painCave.errMsg,
130 <               "Error in recomputing LJ shifts based on new rcut\n");
105 <      painCave.isFatal = 1;
106 <      simError();
107 <    }
108 <  }
126 > void SimInfo::getBoxM (double theBox[3][3]) {
127 >
128 >  int i, j;
129 >  for(i=0; i<3; i++)
130 >    for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j];
131   }
132  
111 – void SimInfo::setBoxM( double theBox[9] ){
112 –  
113 –  int i, status;
114 –  double smallestBoxL, maxCutoff;
133  
134 <  for(i=0; i<9; i++) Hmat[i] = theBox[i];
135 <  calcHmatI();
136 <  calcBoxL();
134 > void SimInfo::scaleBox(double scale) {
135 >  double theBox[3][3];
136 >  int i, j;
137  
138 <  setFortranBoxSize(Hmat, HmatI, &orthoRhombic);
121 <
122 <  smallestBoxL = boxLx;
123 <  if (boxLy < smallestBoxL) smallestBoxL = boxLy;
124 <  if (boxLz < smallestBoxL) smallestBoxL = boxLz;
138 >  // cerr << "Scaling box by " << scale << "\n";
139  
140 <  maxCutoff = smallestBoxL / 2.0;
140 >  for(i=0; i<3; i++)
141 >    for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
142  
143 <  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();
143 >  setBoxM(theBox);
144  
145 <    rList = maxCutoff;
145 > }
146  
147 <    sprintf( painCave.errMsg,
148 <             "New Box size is forcing cutoff radius down to %lf\n",
149 <             maxCutoff - 1.0 );
150 <    painCave.isFatal = 0;
151 <    simError();
147 > void SimInfo::calcHmatInv( void ) {
148 >  
149 >  int oldOrtho;
150 >  int i,j;
151 >  double smallDiag;
152 >  double tol;
153 >  double sanity[3][3];
154  
155 <    rCut = rList - 1.0;
155 >  invertMat3( Hmat, HmatInv );
156  
157 <    // list radius changed so we have to refresh the simulation structure.
158 <    refreshSim();
159 <  }
157 >  // check to see if Hmat is orthorhombic
158 >  
159 >  oldOrtho = orthoRhombic;
160  
161 <  if (rCut > maxCutoff) {
162 <    sprintf( painCave.errMsg,
163 <             "New Box size is forcing cutoff radius down to %lf\n",
164 <             maxCutoff );
153 <    painCave.isFatal = 0;
154 <    simError();
161 >  smallDiag = fabs(Hmat[0][0]);
162 >  if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]);
163 >  if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]);
164 >  tol = smallDiag * orthoTolerance;
165  
166 <    status = 0;
167 <    LJ_new_rcut(&rCut, &status);
168 <    if (status != 0) {
166 >  orthoRhombic = 1;
167 >  
168 >  for (i = 0; i < 3; i++ ) {
169 >    for (j = 0 ; j < 3; j++) {
170 >      if (i != j) {
171 >        if (orthoRhombic) {
172 >          if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0;
173 >        }        
174 >      }
175 >    }
176 >  }
177 >
178 >  if( oldOrtho != orthoRhombic ){
179 >    
180 >    if( orthoRhombic ){
181        sprintf( painCave.errMsg,
182 <               "Error in recomputing LJ shifts based on new rcut\n");
183 <      painCave.isFatal = 1;
182 >               "Hmat is switching from Non-Orthorhombic to OrthoRhombic\n"
183 >               "       If this is a bad thing, change the orthoBoxTolerance( currently %G ).\n",
184 >               orthoTolerance);
185        simError();
186      }
187 +    else {
188 +      sprintf( painCave.errMsg,
189 +               "Hmat is switching from Orthorhombic to Non-OrthoRhombic\n"
190 +               "       If this is a bad thing, change the orthoBoxTolerance( currently %G ).\n",
191 +               orthoTolerance);
192 +      simError();
193 +    }
194    }
195   }
166 –
196  
197 < void SimInfo::getBoxM (double theBox[9]) {
197 > double SimInfo::matDet3(double a[3][3]) {
198 >  int i, j, k;
199 >  double determinant;
200  
201 <  int i;
171 <  for(i=0; i<9; i++) theBox[i] = Hmat[i];
172 < }
201 >  determinant = 0.0;
202  
203 +  for(i = 0; i < 3; i++) {
204 +    j = (i+1)%3;
205 +    k = (i+2)%3;
206  
207 < void SimInfo::scaleBox(double scale) {
208 <  double theBox[9];
177 <  int i;
207 >    determinant += a[0][i] * (a[1][j]*a[2][k] - a[1][k]*a[2][j]);
208 >  }
209  
210 <  for(i=0; i<9; i++) theBox[i] = Hmat[i]*scale;
180 <
181 <  setBoxM(theBox);
182 <
210 >  return determinant;
211   }
212  
213 < 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
213 > void SimInfo::invertMat3(double a[3][3], double b[3][3]) {
214    
215 <  detHmat = 0.0;
216 <  for(i=0; i<3; i++) detHmat += Hmat[i] * C[i][0];
215 >  int  i, j, k, l, m, n;
216 >  double determinant;
217  
218 <  
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++){
218 >  determinant = matDet3( a );
219  
220 <      HmatI[i] = C[j][k] / detHmat;
221 <      i++;
222 <    }
220 >  if (determinant == 0.0) {
221 >    sprintf( painCave.errMsg,
222 >             "Can't invert a matrix with a zero determinant!\n");
223 >    painCave.isFatal = 1;
224 >    simError();
225    }
226  
227 <  // sanity check
228 <
229 <  for(i=0; i<3; i++){
230 <    for(j=0; j<3; j++){
227 >  for (i=0; i < 3; i++) {
228 >    j = (i+1)%3;
229 >    k = (i+2)%3;
230 >    for(l = 0; l < 3; l++) {
231 >      m = (l+1)%3;
232 >      n = (l+2)%3;
233        
234 <      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 <      }
234 >      b[l][i] = (a[j][m]*a[k][n] - a[j][n]*a[k][m]) / determinant;
235      }
236    }
237 + }
238  
239 <  cerr << "sanity => \n"
240 <       << 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 <    
239 > void SimInfo::matMul3(double a[3][3], double b[3][3], double c[3][3]) {
240 >  double r00, r01, r02, r10, r11, r12, r20, r21, r22;
241  
242 <  // check to see if Hmat is orthorhombic
242 >  r00 = a[0][0]*b[0][0] + a[0][1]*b[1][0] + a[0][2]*b[2][0];
243 >  r01 = a[0][0]*b[0][1] + a[0][1]*b[1][1] + a[0][2]*b[2][1];
244 >  r02 = a[0][0]*b[0][2] + a[0][1]*b[1][2] + a[0][2]*b[2][2];
245    
246 <  smallDiag = Hmat[0];
247 <  if(smallDiag > Hmat[4]) smallDiag = Hmat[4];
248 <  if(smallDiag > Hmat[8]) smallDiag = Hmat[8];
249 <  tol = smallDiag * 1E-6;
246 >  r10 = a[1][0]*b[0][0] + a[1][1]*b[1][0] + a[1][2]*b[2][0];
247 >  r11 = a[1][0]*b[0][1] + a[1][1]*b[1][1] + a[1][2]*b[2][1];
248 >  r12 = a[1][0]*b[0][2] + a[1][1]*b[1][2] + a[1][2]*b[2][2];
249 >  
250 >  r20 = a[2][0]*b[0][0] + a[2][1]*b[1][0] + a[2][2]*b[2][0];
251 >  r21 = a[2][0]*b[0][1] + a[2][1]*b[1][1] + a[2][2]*b[2][1];
252 >  r22 = a[2][0]*b[0][2] + a[2][1]*b[1][2] + a[2][2]*b[2][2];
253 >  
254 >  c[0][0] = r00; c[0][1] = r01; c[0][2] = r02;
255 >  c[1][0] = r10; c[1][1] = r11; c[1][2] = r12;
256 >  c[2][0] = r20; c[2][1] = r21; c[2][2] = r22;
257 > }
258  
259 <  orthoRhombic = 1;
260 <  for(i=0; (i<9) && orthoRhombic; i++){
261 <    
262 <    if( (i%4) ){ // ignore the diagonals (0, 4, and 8)
263 <      orthoRhombic = (Hmat[i] <= tol);
259 > void SimInfo::matVecMul3(double m[3][3], double inVec[3], double outVec[3]) {
260 >  double a0, a1, a2;
261 >
262 >  a0 = inVec[0];  a1 = inVec[1];  a2 = inVec[2];
263 >
264 >  outVec[0] = m[0][0]*a0 + m[0][1]*a1 + m[0][2]*a2;
265 >  outVec[1] = m[1][0]*a0 + m[1][1]*a1 + m[1][2]*a2;
266 >  outVec[2] = m[2][0]*a0 + m[2][1]*a1 + m[2][2]*a2;
267 > }
268 >
269 > void SimInfo::transposeMat3(double in[3][3], double out[3][3]) {
270 >  double temp[3][3];
271 >  int i, j;
272 >
273 >  for (i = 0; i < 3; i++) {
274 >    for (j = 0; j < 3; j++) {
275 >      temp[j][i] = in[i][j];
276      }
277    }
278 <    
278 >  for (i = 0; i < 3; i++) {
279 >    for (j = 0; j < 3; j++) {
280 >      out[i][j] = temp[i][j];
281 >    }
282 >  }
283   }
284 +  
285 + void SimInfo::printMat3(double A[3][3] ){
286  
287 +  std::cerr
288 +            << "[ " << A[0][0] << ", " << A[0][1] << ", " << A[0][2] << " ]\n"
289 +            << "[ " << A[1][0] << ", " << A[1][1] << ", " << A[1][2] << " ]\n"
290 +            << "[ " << A[2][0] << ", " << A[2][1] << ", " << A[2][2] << " ]\n";
291 + }
292 +
293 + void SimInfo::printMat9(double A[9] ){
294 +
295 +  std::cerr
296 +            << "[ " << A[0] << ", " << A[1] << ", " << A[2] << " ]\n"
297 +            << "[ " << A[3] << ", " << A[4] << ", " << A[5] << " ]\n"
298 +            << "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n";
299 + }
300 +
301 +
302 + void SimInfo::crossProduct3(double a[3],double b[3], double out[3]){
303 +
304 +      out[0] = a[1] * b[2] - a[2] * b[1];
305 +      out[1] = a[2] * b[0] - a[0] * b[2] ;
306 +      out[2] = a[0] * b[1] - a[1] * b[0];
307 +      
308 + }
309 +
310 + double SimInfo::dotProduct3(double a[3], double b[3]){
311 +  return a[0]*b[0] + a[1]*b[1]+ a[2]*b[2];
312 + }
313 +
314 + double SimInfo::length3(double a[3]){
315 +  return sqrt(a[0]*a[0] + a[1]*a[1] + a[2]*a[2]);
316 + }
317 +
318   void SimInfo::calcBoxL( void ){
319  
320    double dx, dy, dz, dsq;
264 –  int i;
321  
322 <  // boxVol = h1 (dot) h2 (cross) h3
322 >  // boxVol = Determinant of Hmat
323  
324 <  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]) );
324 >  boxVol = matDet3( Hmat );
325  
272 –
326    // boxLx
327    
328 <  dx = Hmat[0]; dy = Hmat[1]; dz = Hmat[2];
328 >  dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
329    dsq = dx*dx + dy*dy + dz*dz;
330 <  boxLx = sqrt( dsq );
330 >  boxL[0] = sqrt( dsq );
331 >  //maxCutoff = 0.5 * boxL[0];
332  
333    // boxLy
334    
335 <  dx = Hmat[3]; dy = Hmat[4]; dz = Hmat[5];
335 >  dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
336    dsq = dx*dx + dy*dy + dz*dz;
337 <  boxLy = sqrt( dsq );
337 >  boxL[1] = sqrt( dsq );
338 >  //if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
339  
340 +
341    // boxLz
342    
343 <  dx = Hmat[6]; dy = Hmat[7]; dz = Hmat[8];
343 >  dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
344    dsq = dx*dx + dy*dy + dz*dz;
345 <  boxLz = sqrt( dsq );
345 >  boxL[2] = sqrt( dsq );
346 >  //if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
347 >
348 >  //calculate the max cutoff
349 >  maxCutoff =  calcMaxCutOff();
350    
351 +  checkCutOffs();
352 +
353   }
354  
355  
356 + double SimInfo::calcMaxCutOff(){
357 +
358 +  double ri[3], rj[3], rk[3];
359 +  double rij[3], rjk[3], rki[3];
360 +  double minDist;
361 +
362 +  ri[0] = Hmat[0][0];
363 +  ri[1] = Hmat[1][0];
364 +  ri[2] = Hmat[2][0];
365 +
366 +  rj[0] = Hmat[0][1];
367 +  rj[1] = Hmat[1][1];
368 +  rj[2] = Hmat[2][1];
369 +
370 +  rk[0] = Hmat[0][2];
371 +  rk[1] = Hmat[1][2];
372 +  rk[2] = Hmat[2][2];
373 +  
374 +  crossProduct3(ri,rj, rij);
375 +  distXY = dotProduct3(rk,rij) / length3(rij);
376 +
377 +  crossProduct3(rj,rk, rjk);
378 +  distYZ = dotProduct3(ri,rjk) / length3(rjk);
379 +
380 +  crossProduct3(rk,ri, rki);
381 +  distZX = dotProduct3(rj,rki) / length3(rki);
382 +
383 +  minDist = min(min(distXY, distYZ), distZX);
384 +  return minDist/2;
385 +  
386 + }
387 +
388   void SimInfo::wrapVector( double thePos[3] ){
389  
390 <  int i, j, k;
390 >  int i;
391    double scaled[3];
392  
393    if( !orthoRhombic ){
394      // calc the scaled coordinates.
395 +  
396 +
397 +    matVecMul3(HmatInv, thePos, scaled);
398      
399      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++)
400        scaled[i] -= roundMe(scaled[i]);
401      
402      // calc the wrapped real coordinates from the wrapped scaled coordinates
403      
404 <    for(i=0; i<3; i++)
405 <      thePos[i] =
315 <        scaled[0]*Hmat[i] + scaled[1]*Hmat[i+3] + scaled[2]*Hmat[i+6];
404 >    matVecMul3(Hmat, scaled, thePos);
405 >
406    }
407    else{
408      // calc the scaled coordinates.
409      
410      for(i=0; i<3; i++)
411 <      scaled[i] = thePos[i]*HmatI[i*4];
411 >      scaled[i] = thePos[i]*HmatInv[i][i];
412      
413      // wrap the scaled coordinates
414      
# Line 328 | Line 418 | void SimInfo::wrapVector( double thePos[3] ){
418      // calc the wrapped real coordinates from the wrapped scaled coordinates
419      
420      for(i=0; i<3; i++)
421 <      thePos[i] = scaled[i]*Hmat[i*4];
421 >      thePos[i] = scaled[i]*Hmat[i][i];
422    }
423      
334 –    
424   }
425  
426  
427   int SimInfo::getNDF(){
428 <  int ndf_local, ndf;
428 >  int ndf_local;
429    
430    ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints;
431  
# Line 346 | Line 435 | int SimInfo::getNDF(){
435    ndf = ndf_local;
436   #endif
437  
438 <  ndf = ndf - 3;
438 >  ndf = ndf - 3 - nZconstraints;
439  
440    return ndf;
441   }
442  
443   int SimInfo::getNDFraw() {
444 <  int ndfRaw_local, ndfRaw;
444 >  int ndfRaw_local;
445  
446    // Raw degrees of freedom that we have to set
447    ndfRaw_local = 3 * n_atoms + 3 * n_oriented;
# Line 365 | Line 454 | int SimInfo::getNDFraw() {
454  
455    return ndfRaw;
456   }
457 <
457 >
458 > int SimInfo::getNDFtranslational() {
459 >  int ndfTrans_local;
460 >
461 >  ndfTrans_local = 3 * n_atoms - n_constraints;
462 >
463 > #ifdef IS_MPI
464 >  MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
465 > #else
466 >  ndfTrans = ndfTrans_local;
467 > #endif
468 >
469 >  ndfTrans = ndfTrans - 3 - nZconstraints;
470 >
471 >  return ndfTrans;
472 > }
473 >
474   void SimInfo::refreshSim(){
475  
476    simtype fInfo;
477    int isError;
478    int n_global;
479    int* excl;
480 <  
376 <  fInfo.rrf = 0.0;
377 <  fInfo.rt = 0.0;
480 >
481    fInfo.dielect = 0.0;
482  
380 –  fInfo.rlist = rList;
381 –  fInfo.rcut = rCut;
382 –
483    if( useDipole ){
384 –    fInfo.rrf = ecr;
385 –    fInfo.rt = ecr - est;
484      if( useReactionField )fInfo.dielect = dielectric;
485    }
486  
# Line 428 | Line 526 | void SimInfo::refreshSim(){
526  
527    this->ndf = this->getNDF();
528    this->ndfRaw = this->getNDFraw();
529 +  this->ndfTrans = this->getNDFtranslational();
530 + }
531  
532 + void SimInfo::setDefaultRcut( double theRcut ){
533 +
534 +  haveRcut = 1;
535 +  rCut = theRcut;
536 +
537 +  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
538 +
539 +  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
540   }
541  
542 + void SimInfo::setDefaultEcr( double theEcr ){
543 +
544 +  haveEcr = 1;
545 +  
546 +  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
547 +
548 +  ecr = theEcr;
549 +
550 +  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
551 + }
552 +
553 + void SimInfo::setDefaultEcr( double theEcr, double theEst ){
554 +
555 +  est = theEst;
556 +  setDefaultEcr( theEcr );
557 + }
558 +
559 +
560 + void SimInfo::checkCutOffs( void ){
561 +  
562 +  if( boxIsInit ){
563 +    
564 +    //we need to check cutOffs against the box
565 +    
566 +    if( rCut > maxCutoff ){
567 +      sprintf( painCave.errMsg,
568 +               "Box size is too small for the long range cutoff radius, "
569 +               "%lf, at time %lf\n",
570 +               rCut, currentTime );
571 +      painCave.isFatal = 1;
572 +      simError();
573 +    }
574 +    
575 +    if( haveEcr ){
576 +      if( ecr > maxCutoff ){
577 +        sprintf( painCave.errMsg,
578 +                 "Box size is too small for the electrostatic cutoff radius, "
579 +                 "%lf, at time %lf\n",
580 +                 ecr, currentTime );
581 +        painCave.isFatal = 1;
582 +        simError();
583 +      }
584 +    }
585 +  } else {
586 +    // initialize this stuff before using it, OK?
587 +    sprintf( painCave.errMsg,
588 +             "Trying to check cutoffs without a box. Be smarter.\n" );
589 +    painCave.isFatal = 1;
590 +    simError();      
591 +  }
592 +  
593 + }
594 +
595 + void SimInfo::addProperty(GenericData* prop){
596 +
597 +  map<string, GenericData*>::iterator result;
598 +  result = properties.find(prop->getID());
599 +  
600 +  //we can't simply use  properties[prop->getID()] = prop,
601 +  //it will cause memory leak if we already contain a propery which has the same name of prop
602 +  
603 +  if(result != properties.end()){
604 +    
605 +    delete (*result).second;
606 +    (*result).second = prop;
607 +      
608 +  }
609 +  else{
610 +
611 +    properties[prop->getID()] = prop;
612 +
613 +  }
614 +    
615 + }
616 +
617 + GenericData* SimInfo::getProperty(const string& propName){
618 +
619 +  map<string, GenericData*>::iterator result;
620 +  
621 +  //string lowerCaseName = ();
622 +  
623 +  result = properties.find(propName);
624 +  
625 +  if(result != properties.end())
626 +    return (*result).second;  
627 +  else  
628 +    return NULL;  
629 + }
630 +
631 + vector<GenericData*> SimInfo::getProperties(){
632 +
633 +  vector<GenericData*> result;
634 +  map<string, GenericData*>::iterator i;
635 +  
636 +  for(i = properties.begin(); i != properties.end(); i++)
637 +    result.push_back((*i).second);
638 +    
639 +  return result;
640 + }
641 +
642 + double SimInfo::matTrace3(double m[3][3]){
643 +  double trace;
644 +  trace = m[0][0] + m[1][1] + m[2][2];
645 +
646 +  return trace;
647 + }

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