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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 853 by mmeineke, Thu Nov 6 19:11:38 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 +  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  
93 <  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();
93 > }
94  
95 <    rList = maxCutoff;
95 > void SimInfo::setBoxM( double theBox[3][3] ){
96 >  
97 >  int i, j;
98 >  double FortranHmat[9]; // to preserve compatibility with Fortran the
99 >                         // ordering in the array is as follows:
100 >                         // [ 0 3 6 ]
101 >                         // [ 1 4 7 ]
102 >                         // [ 2 5 8 ]
103 >  double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
104  
105 <    sprintf( painCave.errMsg,
106 <             "New Box size is forcing cutoff radius down to %lf\n",
83 <             maxCutoff - 1.0 );
84 <    painCave.isFatal = 0;
85 <    simError();
105 >  
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();
157 >  // check to see if Hmat is orthorhombic
158 >  
159 >  oldOrtho = orthoRhombic;
160 >
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 * 1E-6;
165 >
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 (rCut > maxCutoff) {
179 <    sprintf( painCave.errMsg,
180 <             "New Box size is forcing cutoff radius down to %lf\n",
181 <             maxCutoff );
182 <    painCave.isFatal = 0;
183 <    simError();
184 <
185 <    status = 0;
186 <    LJ_new_rcut(&rCut, &status);
158 <    if (status != 0) {
178 >  if( oldOrtho != orthoRhombic ){
179 >    
180 >    if( orthoRhombic ){
181 >      sprintf( painCave.errMsg,
182 >               "Hmat is switching from Non-Orthorhombic to OrthoRhombic\n"
183 >               "       If this is a bad thing change the ortho tolerance in SimInfo.\n" );
184 >      simError();
185 >    }
186 >    else {
187        sprintf( painCave.errMsg,
188 <               "Error in recomputing LJ shifts based on new rcut\n");
189 <      painCave.isFatal = 1;
188 >               "Hmat is switching from Orthorhombic to Non-OrthoRhombic\n"
189 >               "       If this is a bad thing change the ortho tolerance in SimInfo.\n" );
190        simError();
191      }
192    }
193   }
166 –
194  
195 < void SimInfo::getBoxM (double theBox[9]) {
169 <
170 <  int i;
171 <  for(i=0; i<9; i++) theBox[i] = Hmat[i];
172 < }
173 <
174 <
175 < void SimInfo::calcHmatI( void ) {
176 <
177 <  double C[3][3];
178 <  double detHmat;
195 > double SimInfo::matDet3(double a[3][3]) {
196    int i, j, k;
197 <  double smallDiag;
181 <  double tol;
182 <  double sanity[3][3];
197 >  double determinant;
198  
199 <  // calculate the adjunct of Hmat;
199 >  determinant = 0.0;
200  
201 <  C[0][0] =  ( Hmat[4]*Hmat[8]) - (Hmat[7]*Hmat[5]);
202 <  C[1][0] = -( Hmat[1]*Hmat[8]) + (Hmat[7]*Hmat[2]);
203 <  C[2][0] =  ( Hmat[1]*Hmat[5]) - (Hmat[4]*Hmat[2]);
201 >  for(i = 0; i < 3; i++) {
202 >    j = (i+1)%3;
203 >    k = (i+2)%3;
204  
205 <  C[0][1] = -( Hmat[3]*Hmat[8]) + (Hmat[6]*Hmat[5]);
206 <  C[1][1] =  ( Hmat[0]*Hmat[8]) - (Hmat[6]*Hmat[2]);
192 <  C[2][1] = -( Hmat[0]*Hmat[5]) + (Hmat[3]*Hmat[2]);
205 >    determinant += a[0][i] * (a[1][j]*a[2][k] - a[1][k]*a[2][j]);
206 >  }
207  
208 <  C[0][2] =  ( Hmat[3]*Hmat[7]) - (Hmat[6]*Hmat[4]);
209 <  C[1][2] = -( Hmat[0]*Hmat[7]) + (Hmat[6]*Hmat[1]);
196 <  C[2][2] =  ( Hmat[0]*Hmat[4]) - (Hmat[3]*Hmat[1]);
208 >  return determinant;
209 > }
210  
211 <  // calcutlate the determinant of Hmat
211 > void SimInfo::invertMat3(double a[3][3], double b[3][3]) {
212    
213 <  detHmat = 0.0;
214 <  for(i=0; i<3; i++) detHmat += Hmat[i] * C[i][0];
213 >  int  i, j, k, l, m, n;
214 >  double determinant;
215  
216 <  
204 <  // H^-1 = C^T / det(H)
205 <  
206 <  i=0;
207 <  for(j=0; j<3; j++){
208 <    for(k=0; k<3; k++){
216 >  determinant = matDet3( a );
217  
218 <      HmatI[i] = C[j][k] / detHmat;
219 <      i++;
220 <    }
218 >  if (determinant == 0.0) {
219 >    sprintf( painCave.errMsg,
220 >             "Can't invert a matrix with a zero determinant!\n");
221 >    painCave.isFatal = 1;
222 >    simError();
223    }
224  
225 <  // sanity check
226 <
227 <  for(i=0; i<3; i++){
228 <    for(j=0; j<3; j++){
225 >  for (i=0; i < 3; i++) {
226 >    j = (i+1)%3;
227 >    k = (i+2)%3;
228 >    for(l = 0; l < 3; l++) {
229 >      m = (l+1)%3;
230 >      n = (l+2)%3;
231        
232 <      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 <      }
232 >      b[l][i] = (a[j][m]*a[k][n] - a[j][n]*a[k][m]) / determinant;
233      }
234    }
235 + }
236  
237 <  cerr << "sanity => \n"
238 <       << 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 <    
237 > void SimInfo::matMul3(double a[3][3], double b[3][3], double c[3][3]) {
238 >  double r00, r01, r02, r10, r11, r12, r20, r21, r22;
239  
240 <  // check to see if Hmat is orthorhombic
240 >  r00 = a[0][0]*b[0][0] + a[0][1]*b[1][0] + a[0][2]*b[2][0];
241 >  r01 = a[0][0]*b[0][1] + a[0][1]*b[1][1] + a[0][2]*b[2][1];
242 >  r02 = a[0][0]*b[0][2] + a[0][1]*b[1][2] + a[0][2]*b[2][2];
243    
244 <  smallDiag = Hmat[0];
245 <  if(smallDiag > Hmat[4]) smallDiag = Hmat[4];
246 <  if(smallDiag > Hmat[8]) smallDiag = Hmat[8];
247 <  tol = smallDiag * 1E-6;
244 >  r10 = a[1][0]*b[0][0] + a[1][1]*b[1][0] + a[1][2]*b[2][0];
245 >  r11 = a[1][0]*b[0][1] + a[1][1]*b[1][1] + a[1][2]*b[2][1];
246 >  r12 = a[1][0]*b[0][2] + a[1][1]*b[1][2] + a[1][2]*b[2][2];
247 >  
248 >  r20 = a[2][0]*b[0][0] + a[2][1]*b[1][0] + a[2][2]*b[2][0];
249 >  r21 = a[2][0]*b[0][1] + a[2][1]*b[1][1] + a[2][2]*b[2][1];
250 >  r22 = a[2][0]*b[0][2] + a[2][1]*b[1][2] + a[2][2]*b[2][2];
251 >  
252 >  c[0][0] = r00; c[0][1] = r01; c[0][2] = r02;
253 >  c[1][0] = r10; c[1][1] = r11; c[1][2] = r12;
254 >  c[2][0] = r20; c[2][1] = r21; c[2][2] = r22;
255 > }
256  
257 <  orthoRhombic = 1;
258 <  for(i=0; (i<9) && orthoRhombic; i++){
259 <    
260 <    if( (i%4) ){ // ignore the diagonals (0, 4, and 8)
261 <      orthoRhombic = (Hmat[i] <= tol);
257 > void SimInfo::matVecMul3(double m[3][3], double inVec[3], double outVec[3]) {
258 >  double a0, a1, a2;
259 >
260 >  a0 = inVec[0];  a1 = inVec[1];  a2 = inVec[2];
261 >
262 >  outVec[0] = m[0][0]*a0 + m[0][1]*a1 + m[0][2]*a2;
263 >  outVec[1] = m[1][0]*a0 + m[1][1]*a1 + m[1][2]*a2;
264 >  outVec[2] = m[2][0]*a0 + m[2][1]*a1 + m[2][2]*a2;
265 > }
266 >
267 > void SimInfo::transposeMat3(double in[3][3], double out[3][3]) {
268 >  double temp[3][3];
269 >  int i, j;
270 >
271 >  for (i = 0; i < 3; i++) {
272 >    for (j = 0; j < 3; j++) {
273 >      temp[j][i] = in[i][j];
274      }
275    }
276 <    
276 >  for (i = 0; i < 3; i++) {
277 >    for (j = 0; j < 3; j++) {
278 >      out[i][j] = temp[i][j];
279 >    }
280 >  }
281 > }
282 >  
283 > void SimInfo::printMat3(double A[3][3] ){
284 >
285 >  std::cerr
286 >            << "[ " << A[0][0] << ", " << A[0][1] << ", " << A[0][2] << " ]\n"
287 >            << "[ " << A[1][0] << ", " << A[1][1] << ", " << A[1][2] << " ]\n"
288 >            << "[ " << A[2][0] << ", " << A[2][1] << ", " << A[2][2] << " ]\n";
289 > }
290 >
291 > void SimInfo::printMat9(double A[9] ){
292 >
293 >  std::cerr
294 >            << "[ " << A[0] << ", " << A[1] << ", " << A[2] << " ]\n"
295 >            << "[ " << A[3] << ", " << A[4] << ", " << A[5] << " ]\n"
296 >            << "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n";
297   }
298  
299 +
300 + void SimInfo::crossProduct3(double a[3],double b[3], double out[3]){
301 +
302 +      out[0] = a[1] * b[2] - a[2] * b[1];
303 +      out[1] = a[2] * b[0] - a[0] * b[2] ;
304 +      out[2] = a[0] * b[1] - a[1] * b[0];
305 +      
306 + }
307 +
308 + double SimInfo::dotProduct3(double a[3], double b[3]){
309 +  return a[0]*b[0] + a[1]*b[1]+ a[2]*b[2];
310 + }
311 +
312 + double SimInfo::length3(double a[3]){
313 +  return sqrt(a[0]*a[0] + a[1]*a[1] + a[2]*a[2]);
314 + }
315 +
316   void SimInfo::calcBoxL( void ){
317  
318    double dx, dy, dz, dsq;
254 –  int i;
319  
320 <  // boxVol = h1 (dot) h2 (cross) h3
320 >  // boxVol = Determinant of Hmat
321  
322 <  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]) );
322 >  boxVol = matDet3( Hmat );
323  
262 –
324    // boxLx
325    
326 <  dx = Hmat[0]; dy = Hmat[1]; dz = Hmat[2];
326 >  dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
327    dsq = dx*dx + dy*dy + dz*dz;
328 <  boxLx = sqrt( dsq );
328 >  boxL[0] = sqrt( dsq );
329 >  //maxCutoff = 0.5 * boxL[0];
330  
331    // boxLy
332    
333 <  dx = Hmat[3]; dy = Hmat[4]; dz = Hmat[5];
333 >  dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
334    dsq = dx*dx + dy*dy + dz*dz;
335 <  boxLy = sqrt( dsq );
335 >  boxL[1] = sqrt( dsq );
336 >  //if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
337  
338 +
339    // boxLz
340    
341 <  dx = Hmat[6]; dy = Hmat[7]; dz = Hmat[8];
341 >  dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
342    dsq = dx*dx + dy*dy + dz*dz;
343 <  boxLz = sqrt( dsq );
343 >  boxL[2] = sqrt( dsq );
344 >  //if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
345 >
346 >  //calculate the max cutoff
347 >  maxCutoff =  calcMaxCutOff();
348    
349 +  checkCutOffs();
350 +
351   }
352  
353  
354 + double SimInfo::calcMaxCutOff(){
355 +
356 +  double ri[3], rj[3], rk[3];
357 +  double rij[3], rjk[3], rki[3];
358 +  double minDist;
359 +
360 +  ri[0] = Hmat[0][0];
361 +  ri[1] = Hmat[1][0];
362 +  ri[2] = Hmat[2][0];
363 +
364 +  rj[0] = Hmat[0][1];
365 +  rj[1] = Hmat[1][1];
366 +  rj[2] = Hmat[2][1];
367 +
368 +  rk[0] = Hmat[0][2];
369 +  rk[1] = Hmat[1][2];
370 +  rk[2] = Hmat[2][2];
371 +  
372 +  crossProduct3(ri,rj, rij);
373 +  distXY = dotProduct3(rk,rij) / length3(rij);
374 +
375 +  crossProduct3(rj,rk, rjk);
376 +  distYZ = dotProduct3(ri,rjk) / length3(rjk);
377 +
378 +  crossProduct3(rk,ri, rki);
379 +  distZX = dotProduct3(rj,rki) / length3(rki);
380 +
381 +  minDist = min(min(distXY, distYZ), distZX);
382 +  return minDist/2;
383 +  
384 + }
385 +
386   void SimInfo::wrapVector( double thePos[3] ){
387  
388 <  int i, j, k;
388 >  int i;
389    double scaled[3];
390  
391    if( !orthoRhombic ){
392      // calc the scaled coordinates.
393 +  
394 +
395 +    matVecMul3(HmatInv, thePos, scaled);
396      
397      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++)
398        scaled[i] -= roundMe(scaled[i]);
399      
400      // calc the wrapped real coordinates from the wrapped scaled coordinates
401      
402 <    for(i=0; i<3; i++)
403 <      thePos[i] =
305 <        scaled[0]*Hmat[i] + scaled[1]*Hmat[i+3] + scaled[2]*Hmat[i+6];
402 >    matVecMul3(Hmat, scaled, thePos);
403 >
404    }
405    else{
406      // calc the scaled coordinates.
407      
408      for(i=0; i<3; i++)
409 <      scaled[i] = thePos[i]*HmatI[i*4];
409 >      scaled[i] = thePos[i]*HmatInv[i][i];
410      
411      // wrap the scaled coordinates
412      
# Line 318 | Line 416 | void SimInfo::wrapVector( double thePos[3] ){
416      // calc the wrapped real coordinates from the wrapped scaled coordinates
417      
418      for(i=0; i<3; i++)
419 <      thePos[i] = scaled[i]*Hmat[i*4];
419 >      thePos[i] = scaled[i]*Hmat[i][i];
420    }
421      
324 –    
422   }
423  
424  
425   int SimInfo::getNDF(){
426 <  int ndf_local, ndf;
426 >  int ndf_local;
427    
428    ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints;
429  
# Line 336 | Line 433 | int SimInfo::getNDF(){
433    ndf = ndf_local;
434   #endif
435  
436 <  ndf = ndf - 3;
436 >  ndf = ndf - 3 - nZconstraints;
437  
438    return ndf;
439   }
440  
441   int SimInfo::getNDFraw() {
442 <  int ndfRaw_local, ndfRaw;
442 >  int ndfRaw_local;
443  
444    // Raw degrees of freedom that we have to set
445    ndfRaw_local = 3 * n_atoms + 3 * n_oriented;
# Line 355 | Line 452 | int SimInfo::getNDFraw() {
452  
453    return ndfRaw;
454   }
455 <
455 >
456 > int SimInfo::getNDFtranslational() {
457 >  int ndfTrans_local;
458 >
459 >  ndfTrans_local = 3 * n_atoms - n_constraints;
460 >
461 > #ifdef IS_MPI
462 >  MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
463 > #else
464 >  ndfTrans = ndfTrans_local;
465 > #endif
466 >
467 >  ndfTrans = ndfTrans - 3 - nZconstraints;
468 >
469 >  return ndfTrans;
470 > }
471 >
472   void SimInfo::refreshSim(){
473  
474    simtype fInfo;
475    int isError;
476    int n_global;
477    int* excl;
478 <  
366 <  fInfo.rrf = 0.0;
367 <  fInfo.rt = 0.0;
478 >
479    fInfo.dielect = 0.0;
480  
370 –  fInfo.rlist = rList;
371 –  fInfo.rcut = rCut;
372 –
481    if( useDipole ){
374 –    fInfo.rrf = ecr;
375 –    fInfo.rt = ecr - est;
482      if( useReactionField )fInfo.dielect = dielectric;
483    }
484  
# Line 418 | Line 524 | void SimInfo::refreshSim(){
524  
525    this->ndf = this->getNDF();
526    this->ndfRaw = this->getNDFraw();
527 +  this->ndfTrans = this->getNDFtranslational();
528 + }
529  
530 +
531 + void SimInfo::setRcut( double theRcut ){
532 +
533 +  rCut = theRcut;
534 +  checkCutOffs();
535   }
536  
537 + void SimInfo::setDefaultRcut( double theRcut ){
538 +
539 +  haveOrigRcut = 1;
540 +  origRcut = theRcut;
541 +  rCut = theRcut;
542 +
543 +  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
544 +
545 +  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
546 + }
547 +
548 + void SimInfo::setEcr( double theEcr ){
549 +
550 +  ecr = theEcr;
551 +  checkCutOffs();
552 + }
553 +
554 + void SimInfo::setDefaultEcr( double theEcr ){
555 +
556 +  haveOrigEcr = 1;
557 +  origEcr = theEcr;
558 +  
559 +  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
560 +
561 +  ecr = theEcr;
562 +
563 +  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
564 + }
565 +
566 + void SimInfo::setEcr( double theEcr, double theEst ){
567 +
568 +  est = theEst;
569 +  setEcr( theEcr );
570 + }
571 +
572 + void SimInfo::setDefaultEcr( double theEcr, double theEst ){
573 +
574 +  est = theEst;
575 +  setDefaultEcr( theEcr );
576 + }
577 +
578 +
579 + void SimInfo::checkCutOffs( void ){
580 +
581 +  int cutChanged = 0;
582 +  
583 +  if( boxIsInit ){
584 +    
585 +    //we need to check cutOffs against the box
586 +
587 +    //detect the change of rCut
588 +    if(( maxCutoff > rCut )&&(usePBC)){
589 +      if( rCut < origRcut ){
590 +        rCut = origRcut;
591 +        
592 +        if (rCut > maxCutoff)
593 +          rCut = maxCutoff;
594 +  
595 +          sprintf( painCave.errMsg,
596 +                    "New Box size is setting the long range cutoff radius "
597 +                    "to %lf at time %lf\n",
598 +                    rCut, currentTime );
599 +          painCave.isFatal = 0;
600 +          simError();
601 +      }
602 +    }
603 +    else if ((rCut > maxCutoff)&&(usePBC)) {
604 +      sprintf( painCave.errMsg,
605 +               "New Box size is setting the long range cutoff radius "
606 +               "to %lf at time %lf\n",
607 +               maxCutoff, currentTime );
608 +      painCave.isFatal = 0;
609 +      simError();
610 +      rCut = maxCutoff;
611 +    }
612 +
613 +
614 +    //detect the change of ecr
615 +    if( maxCutoff > ecr ){
616 +      if( ecr < origEcr ){
617 +        ecr = origEcr;
618 +        if (ecr > maxCutoff) ecr = maxCutoff;
619 +  
620 +          sprintf( painCave.errMsg,
621 +                    "New Box size is setting the electrostaticCutoffRadius "
622 +                    "to %lf at time %lf\n",
623 +                    ecr, currentTime );
624 +            painCave.isFatal = 0;
625 +            simError();
626 +      }
627 +    }
628 +    else if( ecr > maxCutoff){
629 +      sprintf( painCave.errMsg,
630 +               "New Box size is setting the electrostaticCutoffRadius "
631 +               "to %lf at time %lf\n",
632 +               maxCutoff, currentTime  );
633 +      painCave.isFatal = 0;
634 +      simError();      
635 +      ecr = maxCutoff;
636 +    }
637 +
638 +    if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1;
639 +    
640 +    // rlist is the 1.0 plus max( rcut, ecr )
641 +    
642 +    ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
643 +    
644 +    if( cutChanged ){
645 +      notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
646 +    }
647 +    
648 +    oldEcr = ecr;
649 +    oldRcut = rCut;
650 +    
651 +  } else {
652 +    // initialize this stuff before using it, OK?
653 +    sprintf( painCave.errMsg,
654 +             "Trying to check cutoffs without a box. Be smarter.\n" );
655 +    painCave.isFatal = 1;
656 +    simError();      
657 +  }
658 +  
659 + }
660 +
661 + void SimInfo::addProperty(GenericData* prop){
662 +
663 +  map<string, GenericData*>::iterator result;
664 +  result = properties.find(prop->getID());
665 +  
666 +  //we can't simply use  properties[prop->getID()] = prop,
667 +  //it will cause memory leak if we already contain a propery which has the same name of prop
668 +  
669 +  if(result != properties.end()){
670 +    
671 +    delete (*result).second;
672 +    (*result).second = prop;
673 +      
674 +  }
675 +  else{
676 +
677 +    properties[prop->getID()] = prop;
678 +
679 +  }
680 +    
681 + }
682 +
683 + GenericData* SimInfo::getProperty(const string& propName){
684 +
685 +  map<string, GenericData*>::iterator result;
686 +  
687 +  //string lowerCaseName = ();
688 +  
689 +  result = properties.find(propName);
690 +  
691 +  if(result != properties.end())
692 +    return (*result).second;  
693 +  else  
694 +    return NULL;  
695 + }
696 +
697 + vector<GenericData*> SimInfo::getProperties(){
698 +
699 +  vector<GenericData*> result;
700 +  map<string, GenericData*>::iterator i;
701 +  
702 +  for(i = properties.begin(); i != properties.end(); i++)
703 +    result.push_back((*i).second);
704 +    
705 +  return result;
706 + }
707 +
708 + double SimInfo::matTrace3(double m[3][3]){
709 +  double trace;
710 +  trace = m[0][0] + m[1][1] + m[2][2];
711 +
712 +  return trace;
713 + }

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