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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 1031 by tim, Fri Feb 6 18:58:06 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;
# 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;
58 <  useDipole = 0;
58 >  useCharges = 0;
59 >  useDipoles = 0;
60    useReactionField = 0;
61    useGB = 0;
62    useEAM = 0;
63  
64 +  myConfiguration = new SimState();
65 +
66 +  has_minimizer = false;
67 +  the_minimizer =NULL;
68 +
69    wrapMeSimInfo( this );
70   }
71  
49 – void SimInfo::setBox(double newBox[3]) {
72  
73 <  double smallestBoxL, maxCutoff;
52 <  int status;
53 <  int i;
73 > SimInfo::~SimInfo(){
74  
75 <  for(i=0; i<9; i++) Hmat[i] = 0.0;;
75 >  delete myConfiguration;
76  
77 <  Hmat[0] = newBox[0];
78 <  Hmat[4] = newBox[1];
79 <  Hmat[8] = newBox[2];
77 >  map<string, GenericData*>::iterator i;
78 >  
79 >  for(i = properties.begin(); i != properties.end(); i++)
80 >    delete (*i).second;
81 >    
82 > }
83  
84 <  calcHmatI();
85 <  calcBoxL();
84 > void SimInfo::setBox(double newBox[3]) {
85 >  
86 >  int i, j;
87 >  double tempMat[3][3];
88  
89 <  setFortranBoxSize(Hmat, HmatI, &orthoRhombic);
89 >  for(i=0; i<3; i++)
90 >    for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
91  
92 <  smallestBoxL = boxLx;
93 <  if (boxLy < smallestBoxL) smallestBoxL = boxLy;
94 <  if (boxLz < smallestBoxL) smallestBoxL = boxLz;
92 >  tempMat[0][0] = newBox[0];
93 >  tempMat[1][1] = newBox[1];
94 >  tempMat[2][2] = newBox[2];
95  
96 <  maxCutoff = smallestBoxL / 2.0;
96 >  setBoxM( tempMat );
97  
98 <  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();
98 > }
99  
100 <    rList = maxCutoff;
100 > void SimInfo::setBoxM( double theBox[3][3] ){
101 >  
102 >  int i, j;
103 >  double FortranHmat[9]; // to preserve compatibility with Fortran the
104 >                         // ordering in the array is as follows:
105 >                         // [ 0 3 6 ]
106 >                         // [ 1 4 7 ]
107 >                         // [ 2 5 8 ]
108 >  double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
109  
110 <    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();
110 >  if( !boxIsInit ) boxIsInit = 1;
111  
112 <    rCut = rList - 1.0;
112 >  for(i=0; i < 3; i++)
113 >    for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
114 >  
115 >  calcBoxL();
116 >  calcHmatInv();
117  
118 <    // list radius changed so we have to refresh the simulation structure.
119 <    refreshSim();
118 >  for(i=0; i < 3; i++) {
119 >    for (j=0; j < 3; j++) {
120 >      FortranHmat[3*j + i] = Hmat[i][j];
121 >      FortranHmatInv[3*j + i] = HmatInv[i][j];
122 >    }
123    }
124  
125 <  if (rCut > maxCutoff) {
126 <    sprintf( painCave.errMsg,
127 <             "New Box size is forcing cutoff radius down to %lf\n",
128 <             maxCutoff );
97 <    painCave.isFatal = 0;
98 <    simError();
125 >  setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic);
126 >
127 > }
128 >
129  
130 <    status = 0;
131 <    LJ_new_rcut(&rCut, &status);
132 <    if (status != 0) {
133 <      sprintf( painCave.errMsg,
134 <               "Error in recomputing LJ shifts based on new rcut\n");
105 <      painCave.isFatal = 1;
106 <      simError();
107 <    }
108 <  }
130 > void SimInfo::getBoxM (double theBox[3][3]) {
131 >
132 >  int i, j;
133 >  for(i=0; i<3; i++)
134 >    for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j];
135   }
136  
111 – void SimInfo::setBoxM( double theBox[9] ){
112 –  
113 –  int i, status;
114 –  double smallestBoxL, maxCutoff;
137  
138 <  for(i=0; i<9; i++) Hmat[i] = theBox[i];
139 <  calcHmatI();
140 <  calcBoxL();
138 > void SimInfo::scaleBox(double scale) {
139 >  double theBox[3][3];
140 >  int i, j;
141  
142 <  setFortranBoxSize(Hmat, HmatI, &orthoRhombic);
121 <
122 <  smallestBoxL = boxLx;
123 <  if (boxLy < smallestBoxL) smallestBoxL = boxLy;
124 <  if (boxLz < smallestBoxL) smallestBoxL = boxLz;
142 >  // cerr << "Scaling box by " << scale << "\n";
143  
144 <  maxCutoff = smallestBoxL / 2.0;
144 >  for(i=0; i<3; i++)
145 >    for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
146  
147 <  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();
147 >  setBoxM(theBox);
148  
149 <    rList = maxCutoff;
149 > }
150  
151 <    sprintf( painCave.errMsg,
152 <             "New Box size is forcing cutoff radius down to %lf\n",
153 <             maxCutoff - 1.0 );
154 <    painCave.isFatal = 0;
155 <    simError();
151 > void SimInfo::calcHmatInv( void ) {
152 >  
153 >  int oldOrtho;
154 >  int i,j;
155 >  double smallDiag;
156 >  double tol;
157 >  double sanity[3][3];
158  
159 <    rCut = rList - 1.0;
159 >  invertMat3( Hmat, HmatInv );
160  
161 <    // list radius changed so we have to refresh the simulation structure.
162 <    refreshSim();
161 >  // check to see if Hmat is orthorhombic
162 >  
163 >  oldOrtho = orthoRhombic;
164 >
165 >  smallDiag = fabs(Hmat[0][0]);
166 >  if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]);
167 >  if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]);
168 >  tol = smallDiag * orthoTolerance;
169 >
170 >  orthoRhombic = 1;
171 >  
172 >  for (i = 0; i < 3; i++ ) {
173 >    for (j = 0 ; j < 3; j++) {
174 >      if (i != j) {
175 >        if (orthoRhombic) {
176 >          if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0;
177 >        }        
178 >      }
179 >    }
180    }
181  
182 <  if (rCut > maxCutoff) {
183 <    sprintf( painCave.errMsg,
184 <             "New Box size is forcing cutoff radius down to %lf\n",
152 <             maxCutoff );
153 <    painCave.isFatal = 0;
154 <    simError();
155 <
156 <    status = 0;
157 <    LJ_new_rcut(&rCut, &status);
158 <    if (status != 0) {
182 >  if( oldOrtho != orthoRhombic ){
183 >    
184 >    if( orthoRhombic ){
185        sprintf( painCave.errMsg,
186 <               "Error in recomputing LJ shifts based on new rcut\n");
187 <      painCave.isFatal = 1;
186 >               "Hmat is switching from Non-Orthorhombic to Orthorhombic Box.\n"
187 >               "\tIf this is a bad thing, change the orthoBoxTolerance\n"
188 >               "\tvariable ( currently set to %G ).\n",
189 >               orthoTolerance);
190        simError();
191      }
192 +    else {
193 +      sprintf( painCave.errMsg,
194 +               "Hmat is switching from Orthorhombic to Non-Orthorhombic Box.\n"
195 +               "\tIf this is a bad thing, change the orthoBoxTolerance\n"
196 +               "\tvariable ( currently set to %G ).\n",
197 +               orthoTolerance);
198 +      simError();
199 +    }
200    }
201   }
166 –
202  
203 < void SimInfo::getBoxM (double theBox[9]) {
203 > double SimInfo::matDet3(double a[3][3]) {
204 >  int i, j, k;
205 >  double determinant;
206  
207 <  int i;
171 <  for(i=0; i<9; i++) theBox[i] = Hmat[i];
172 < }
207 >  determinant = 0.0;
208  
209 +  for(i = 0; i < 3; i++) {
210 +    j = (i+1)%3;
211 +    k = (i+2)%3;
212  
213 < void SimInfo::scaleBox(double scale) {
214 <  double theBox[9];
177 <  int i;
213 >    determinant += a[0][i] * (a[1][j]*a[2][k] - a[1][k]*a[2][j]);
214 >  }
215  
216 <  for(i=0; i<9; i++) theBox[i] = Hmat[i]*scale;
180 <
181 <  setBoxM(theBox);
182 <
216 >  return determinant;
217   }
218  
219 < 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
219 > void SimInfo::invertMat3(double a[3][3], double b[3][3]) {
220    
221 <  detHmat = 0.0;
222 <  for(i=0; i<3; i++) detHmat += Hmat[i] * C[i][0];
221 >  int  i, j, k, l, m, n;
222 >  double determinant;
223  
224 <  
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++){
224 >  determinant = matDet3( a );
225  
226 <      HmatI[i] = C[j][k] / detHmat;
227 <      i++;
228 <    }
226 >  if (determinant == 0.0) {
227 >    sprintf( painCave.errMsg,
228 >             "Can't invert a matrix with a zero determinant!\n");
229 >    painCave.isFatal = 1;
230 >    simError();
231    }
232  
233 <  // sanity check
234 <
235 <  for(i=0; i<3; i++){
236 <    for(j=0; j<3; j++){
233 >  for (i=0; i < 3; i++) {
234 >    j = (i+1)%3;
235 >    k = (i+2)%3;
236 >    for(l = 0; l < 3; l++) {
237 >      m = (l+1)%3;
238 >      n = (l+2)%3;
239        
240 <      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 <      }
240 >      b[l][i] = (a[j][m]*a[k][n] - a[j][n]*a[k][m]) / determinant;
241      }
242    }
243 + }
244  
245 <  cerr << "sanity => \n"
246 <       << 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 <    
245 > void SimInfo::matMul3(double a[3][3], double b[3][3], double c[3][3]) {
246 >  double r00, r01, r02, r10, r11, r12, r20, r21, r22;
247  
248 <  // check to see if Hmat is orthorhombic
248 >  r00 = a[0][0]*b[0][0] + a[0][1]*b[1][0] + a[0][2]*b[2][0];
249 >  r01 = a[0][0]*b[0][1] + a[0][1]*b[1][1] + a[0][2]*b[2][1];
250 >  r02 = a[0][0]*b[0][2] + a[0][1]*b[1][2] + a[0][2]*b[2][2];
251    
252 <  smallDiag = Hmat[0];
253 <  if(smallDiag > Hmat[4]) smallDiag = Hmat[4];
254 <  if(smallDiag > Hmat[8]) smallDiag = Hmat[8];
255 <  tol = smallDiag * 1E-6;
252 >  r10 = a[1][0]*b[0][0] + a[1][1]*b[1][0] + a[1][2]*b[2][0];
253 >  r11 = a[1][0]*b[0][1] + a[1][1]*b[1][1] + a[1][2]*b[2][1];
254 >  r12 = a[1][0]*b[0][2] + a[1][1]*b[1][2] + a[1][2]*b[2][2];
255 >  
256 >  r20 = a[2][0]*b[0][0] + a[2][1]*b[1][0] + a[2][2]*b[2][0];
257 >  r21 = a[2][0]*b[0][1] + a[2][1]*b[1][1] + a[2][2]*b[2][1];
258 >  r22 = a[2][0]*b[0][2] + a[2][1]*b[1][2] + a[2][2]*b[2][2];
259 >  
260 >  c[0][0] = r00; c[0][1] = r01; c[0][2] = r02;
261 >  c[1][0] = r10; c[1][1] = r11; c[1][2] = r12;
262 >  c[2][0] = r20; c[2][1] = r21; c[2][2] = r22;
263 > }
264  
265 <  orthoRhombic = 1;
266 <  for(i=0; (i<9) && orthoRhombic; i++){
267 <    
268 <    if( (i%4) ){ // ignore the diagonals (0, 4, and 8)
269 <      orthoRhombic = (Hmat[i] <= tol);
265 > void SimInfo::matVecMul3(double m[3][3], double inVec[3], double outVec[3]) {
266 >  double a0, a1, a2;
267 >
268 >  a0 = inVec[0];  a1 = inVec[1];  a2 = inVec[2];
269 >
270 >  outVec[0] = m[0][0]*a0 + m[0][1]*a1 + m[0][2]*a2;
271 >  outVec[1] = m[1][0]*a0 + m[1][1]*a1 + m[1][2]*a2;
272 >  outVec[2] = m[2][0]*a0 + m[2][1]*a1 + m[2][2]*a2;
273 > }
274 >
275 > void SimInfo::transposeMat3(double in[3][3], double out[3][3]) {
276 >  double temp[3][3];
277 >  int i, j;
278 >
279 >  for (i = 0; i < 3; i++) {
280 >    for (j = 0; j < 3; j++) {
281 >      temp[j][i] = in[i][j];
282      }
283    }
284 <    
284 >  for (i = 0; i < 3; i++) {
285 >    for (j = 0; j < 3; j++) {
286 >      out[i][j] = temp[i][j];
287 >    }
288 >  }
289   }
290 +  
291 + void SimInfo::printMat3(double A[3][3] ){
292  
293 +  std::cerr
294 +            << "[ " << A[0][0] << ", " << A[0][1] << ", " << A[0][2] << " ]\n"
295 +            << "[ " << A[1][0] << ", " << A[1][1] << ", " << A[1][2] << " ]\n"
296 +            << "[ " << A[2][0] << ", " << A[2][1] << ", " << A[2][2] << " ]\n";
297 + }
298 +
299 + void SimInfo::printMat9(double A[9] ){
300 +
301 +  std::cerr
302 +            << "[ " << A[0] << ", " << A[1] << ", " << A[2] << " ]\n"
303 +            << "[ " << A[3] << ", " << A[4] << ", " << A[5] << " ]\n"
304 +            << "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n";
305 + }
306 +
307 +
308 + void SimInfo::crossProduct3(double a[3],double b[3], double out[3]){
309 +
310 +      out[0] = a[1] * b[2] - a[2] * b[1];
311 +      out[1] = a[2] * b[0] - a[0] * b[2] ;
312 +      out[2] = a[0] * b[1] - a[1] * b[0];
313 +      
314 + }
315 +
316 + double SimInfo::dotProduct3(double a[3], double b[3]){
317 +  return a[0]*b[0] + a[1]*b[1]+ a[2]*b[2];
318 + }
319 +
320 + double SimInfo::length3(double a[3]){
321 +  return sqrt(a[0]*a[0] + a[1]*a[1] + a[2]*a[2]);
322 + }
323 +
324   void SimInfo::calcBoxL( void ){
325  
326    double dx, dy, dz, dsq;
264 –  int i;
327  
328 <  // boxVol = h1 (dot) h2 (cross) h3
328 >  // boxVol = Determinant of Hmat
329  
330 <  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]) );
330 >  boxVol = matDet3( Hmat );
331  
272 –
332    // boxLx
333    
334 <  dx = Hmat[0]; dy = Hmat[1]; dz = Hmat[2];
334 >  dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
335    dsq = dx*dx + dy*dy + dz*dz;
336 <  boxLx = sqrt( dsq );
336 >  boxL[0] = sqrt( dsq );
337 >  //maxCutoff = 0.5 * boxL[0];
338  
339    // boxLy
340    
341 <  dx = Hmat[3]; dy = Hmat[4]; dz = Hmat[5];
341 >  dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
342    dsq = dx*dx + dy*dy + dz*dz;
343 <  boxLy = sqrt( dsq );
343 >  boxL[1] = sqrt( dsq );
344 >  //if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
345  
346 +
347    // boxLz
348    
349 <  dx = Hmat[6]; dy = Hmat[7]; dz = Hmat[8];
349 >  dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
350    dsq = dx*dx + dy*dy + dz*dz;
351 <  boxLz = sqrt( dsq );
351 >  boxL[2] = sqrt( dsq );
352 >  //if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
353 >
354 >  //calculate the max cutoff
355 >  maxCutoff =  calcMaxCutOff();
356    
357 +  checkCutOffs();
358 +
359   }
360  
361  
362 + double SimInfo::calcMaxCutOff(){
363 +
364 +  double ri[3], rj[3], rk[3];
365 +  double rij[3], rjk[3], rki[3];
366 +  double minDist;
367 +
368 +  ri[0] = Hmat[0][0];
369 +  ri[1] = Hmat[1][0];
370 +  ri[2] = Hmat[2][0];
371 +
372 +  rj[0] = Hmat[0][1];
373 +  rj[1] = Hmat[1][1];
374 +  rj[2] = Hmat[2][1];
375 +
376 +  rk[0] = Hmat[0][2];
377 +  rk[1] = Hmat[1][2];
378 +  rk[2] = Hmat[2][2];
379 +  
380 +  crossProduct3(ri,rj, rij);
381 +  distXY = dotProduct3(rk,rij) / length3(rij);
382 +
383 +  crossProduct3(rj,rk, rjk);
384 +  distYZ = dotProduct3(ri,rjk) / length3(rjk);
385 +
386 +  crossProduct3(rk,ri, rki);
387 +  distZX = dotProduct3(rj,rki) / length3(rki);
388 +
389 +  minDist = min(min(distXY, distYZ), distZX);
390 +  return minDist/2;
391 +  
392 + }
393 +
394   void SimInfo::wrapVector( double thePos[3] ){
395  
396 <  int i, j, k;
396 >  int i;
397    double scaled[3];
398  
399    if( !orthoRhombic ){
400      // calc the scaled coordinates.
401 +  
402 +
403 +    matVecMul3(HmatInv, thePos, scaled);
404      
405      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++)
406        scaled[i] -= roundMe(scaled[i]);
407      
408      // calc the wrapped real coordinates from the wrapped scaled coordinates
409      
410 <    for(i=0; i<3; i++)
411 <      thePos[i] =
315 <        scaled[0]*Hmat[i] + scaled[1]*Hmat[i+3] + scaled[2]*Hmat[i+6];
410 >    matVecMul3(Hmat, scaled, thePos);
411 >
412    }
413    else{
414      // calc the scaled coordinates.
415      
416      for(i=0; i<3; i++)
417 <      scaled[i] = thePos[i]*HmatI[i*4];
417 >      scaled[i] = thePos[i]*HmatInv[i][i];
418      
419      // wrap the scaled coordinates
420      
# Line 328 | Line 424 | void SimInfo::wrapVector( double thePos[3] ){
424      // calc the wrapped real coordinates from the wrapped scaled coordinates
425      
426      for(i=0; i<3; i++)
427 <      thePos[i] = scaled[i]*Hmat[i*4];
427 >      thePos[i] = scaled[i]*Hmat[i][i];
428    }
429      
334 –    
430   }
431  
432  
433   int SimInfo::getNDF(){
434 <  int ndf_local, ndf;
434 >  int ndf_local;
435    
436    ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints;
437  
# Line 346 | Line 441 | int SimInfo::getNDF(){
441    ndf = ndf_local;
442   #endif
443  
444 <  ndf = ndf - 3;
444 >  ndf = ndf - 3 - nZconstraints;
445  
446    return ndf;
447   }
448  
449   int SimInfo::getNDFraw() {
450 <  int ndfRaw_local, ndfRaw;
450 >  int ndfRaw_local;
451  
452    // Raw degrees of freedom that we have to set
453    ndfRaw_local = 3 * n_atoms + 3 * n_oriented;
# Line 365 | Line 460 | int SimInfo::getNDFraw() {
460  
461    return ndfRaw;
462   }
463 <
463 >
464 > int SimInfo::getNDFtranslational() {
465 >  int ndfTrans_local;
466 >
467 >  ndfTrans_local = 3 * n_atoms - n_constraints;
468 >
469 > #ifdef IS_MPI
470 >  MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
471 > #else
472 >  ndfTrans = ndfTrans_local;
473 > #endif
474 >
475 >  ndfTrans = ndfTrans - 3 - nZconstraints;
476 >
477 >  return ndfTrans;
478 > }
479 >
480   void SimInfo::refreshSim(){
481  
482    simtype fInfo;
483    int isError;
484    int n_global;
485    int* excl;
486 <  
376 <  fInfo.rrf = 0.0;
377 <  fInfo.rt = 0.0;
486 >
487    fInfo.dielect = 0.0;
488  
489 <  fInfo.rlist = rList;
381 <  fInfo.rcut = rCut;
382 <
383 <  if( useDipole ){
384 <    fInfo.rrf = ecr;
385 <    fInfo.rt = ecr - est;
489 >  if( useDipoles ){
490      if( useReactionField )fInfo.dielect = dielectric;
491    }
492  
# Line 391 | Line 495 | void SimInfo::refreshSim(){
495    fInfo.SIM_uses_LJ = useLJ;
496    fInfo.SIM_uses_sticky = useSticky;
497    //fInfo.SIM_uses_sticky = 0;
498 <  fInfo.SIM_uses_dipoles = useDipole;
498 >  fInfo.SIM_uses_charges = useCharges;
499 >  fInfo.SIM_uses_dipoles = useDipoles;
500    //fInfo.SIM_uses_dipoles = 0;
501 <  //fInfo.SIM_uses_RF = useReactionField;
502 <  fInfo.SIM_uses_RF = 0;
501 >  fInfo.SIM_uses_RF = useReactionField;
502 >  //fInfo.SIM_uses_RF = 0;
503    fInfo.SIM_uses_GB = useGB;
504    fInfo.SIM_uses_EAM = useEAM;
505  
# Line 428 | Line 533 | void SimInfo::refreshSim(){
533  
534    this->ndf = this->getNDF();
535    this->ndfRaw = this->getNDFraw();
536 +  this->ndfTrans = this->getNDFtranslational();
537 + }
538  
539 + void SimInfo::setDefaultRcut( double theRcut ){
540 +
541 +  haveRcut = 1;
542 +  rCut = theRcut;
543 +
544 +  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
545 +
546 +  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
547   }
548  
549 + void SimInfo::setDefaultEcr( double theEcr ){
550 +
551 +  haveEcr = 1;
552 +  ecr = theEcr;
553 +  
554 +  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
555 +
556 +  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
557 + }
558 +
559 + void SimInfo::setDefaultEcr( double theEcr, double theEst ){
560 +
561 +  est = theEst;
562 +  setDefaultEcr( theEcr );
563 + }
564 +
565 +
566 + void SimInfo::checkCutOffs( void ){
567 +  
568 +  if( boxIsInit ){
569 +    
570 +    //we need to check cutOffs against the box
571 +    
572 +    if( rCut > maxCutoff ){
573 +      sprintf( painCave.errMsg,
574 +               "Box size is too small for the long range cutoff radius, "
575 +               "%G, at time %G\n"
576 +               "\t[ %G %G %G ]\n"
577 +               "\t[ %G %G %G ]\n"
578 +               "\t[ %G %G %G ]\n",
579 +               rCut, currentTime,
580 +               Hmat[0][0], Hmat[0][1], Hmat[0][2],
581 +               Hmat[1][0], Hmat[1][1], Hmat[1][2],
582 +               Hmat[2][0], Hmat[2][1], Hmat[2][2]);
583 +      painCave.isFatal = 1;
584 +      simError();
585 +    }
586 +    
587 +    if( haveEcr ){
588 +      if( ecr > maxCutoff ){
589 +        sprintf( painCave.errMsg,
590 +                 "Box size is too small for the electrostatic cutoff radius, "
591 +                 "%G, at time %G\n"
592 +                 "\t[ %G %G %G ]\n"
593 +                 "\t[ %G %G %G ]\n"
594 +                 "\t[ %G %G %G ]\n",
595 +                 ecr, currentTime,
596 +                 Hmat[0][0], Hmat[0][1], Hmat[0][2],
597 +                 Hmat[1][0], Hmat[1][1], Hmat[1][2],
598 +                 Hmat[2][0], Hmat[2][1], Hmat[2][2]);
599 +        painCave.isFatal = 1;
600 +        simError();
601 +      }
602 +    }
603 +  } else {
604 +    // initialize this stuff before using it, OK?
605 +    sprintf( painCave.errMsg,
606 +             "Trying to check cutoffs without a box.\n"
607 +             "\tOOPSE should have better programmers than that.\n" );
608 +    painCave.isFatal = 1;
609 +    simError();      
610 +  }
611 +  
612 + }
613 +
614 + void SimInfo::addProperty(GenericData* prop){
615 +
616 +  map<string, GenericData*>::iterator result;
617 +  result = properties.find(prop->getID());
618 +  
619 +  //we can't simply use  properties[prop->getID()] = prop,
620 +  //it will cause memory leak if we already contain a propery which has the same name of prop
621 +  
622 +  if(result != properties.end()){
623 +    
624 +    delete (*result).second;
625 +    (*result).second = prop;
626 +      
627 +  }
628 +  else{
629 +
630 +    properties[prop->getID()] = prop;
631 +
632 +  }
633 +    
634 + }
635 +
636 + GenericData* SimInfo::getProperty(const string& propName){
637 +
638 +  map<string, GenericData*>::iterator result;
639 +  
640 +  //string lowerCaseName = ();
641 +  
642 +  result = properties.find(propName);
643 +  
644 +  if(result != properties.end())
645 +    return (*result).second;  
646 +  else  
647 +    return NULL;  
648 + }
649 +
650 + vector<GenericData*> SimInfo::getProperties(){
651 +
652 +  vector<GenericData*> result;
653 +  map<string, GenericData*>::iterator i;
654 +  
655 +  for(i = properties.begin(); i != properties.end(); i++)
656 +    result.push_back((*i).second);
657 +    
658 +  return result;
659 + }
660 +
661 + double SimInfo::matTrace3(double m[3][3]){
662 +  double trace;
663 +  trace = m[0][0] + m[1][1] + m[2][2];
664 +
665 +  return trace;
666 + }

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