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root/group/trunk/OOPSE/libmdtools/SimInfo.cpp
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Comparing trunk/OOPSE/libmdtools/SimInfo.cpp (file contents):
Revision 568 by mmeineke, Mon Jun 30 22:04:01 2003 UTC vs.
Revision 855 by mmeineke, Thu Nov 6 22:01:37 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;
7  
8   #include "SimInfo.hpp"
9   #define __C
# Line 14 | Line 16 | SimInfo* currentInfo;
16   #include "mpiSimulation.hpp"
17   #endif
18  
19 + inline double roundMe( double x ){
20 +  return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 );
21 + }
22 +          
23 +
24   SimInfo* currentInfo;
25  
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 +  orthoTolerance = 1E-6;
54 +  useInitXSstate = true;
55 +
56    usePBC = 0;
57    useLJ = 0;
58    useSticky = 0;
# Line 36 | Line 61 | SimInfo::SimInfo(){
61    useGB = 0;
62    useEAM = 0;
63  
64 +  myConfiguration = new SimState();
65 +
66    wrapMeSimInfo( this );
67   }
68  
42 – void SimInfo::setBox(double newBox[3]) {
69  
70 <  double smallestBoxL, maxCutoff;
45 <  int status;
46 <  int i;
70 > SimInfo::~SimInfo(){
71  
72 <  for(i=0; i<9; i++) Hmat[i] = 0.0;;
72 >  delete myConfiguration;
73  
74 <  Hmat[0] = newBox[0];
75 <  Hmat[4] = newBox[1];
76 <  Hmat[8] = newBox[2];
74 >  map<string, GenericData*>::iterator i;
75 >  
76 >  for(i = properties.begin(); i != properties.end(); i++)
77 >    delete (*i).second;
78 >    
79 > }
80  
81 <  calcHmatI();
82 <  calcBoxL();
81 > void SimInfo::setBox(double newBox[3]) {
82 >  
83 >  int i, j;
84 >  double tempMat[3][3];
85  
86 <  setFortranBoxSize(Hmat);
86 >  for(i=0; i<3; i++)
87 >    for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
88  
89 <  smallestBoxL = boxLx;
90 <  if (boxLy < smallestBoxL) smallestBoxL = boxLy;
91 <  if (boxLz < smallestBoxL) smallestBoxL = boxLz;
89 >  tempMat[0][0] = newBox[0];
90 >  tempMat[1][1] = newBox[1];
91 >  tempMat[2][2] = newBox[2];
92  
93 <  maxCutoff = smallestBoxL / 2.0;
93 >  setBoxM( tempMat );
94  
95 <  if (rList > maxCutoff) {
66 <    sprintf( painCave.errMsg,
67 <             "New Box size is forcing neighborlist radius down to %lf\n",
68 <             maxCutoff );
69 <    painCave.isFatal = 0;
70 <    simError();
95 > }
96  
97 <    rList = maxCutoff;
97 > void SimInfo::setBoxM( double theBox[3][3] ){
98 >  
99 >  int i, j;
100 >  double FortranHmat[9]; // to preserve compatibility with Fortran the
101 >                         // ordering in the array is as follows:
102 >                         // [ 0 3 6 ]
103 >                         // [ 1 4 7 ]
104 >                         // [ 2 5 8 ]
105 >  double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
106  
107 <    sprintf( painCave.errMsg,
108 <             "New Box size is forcing cutoff radius down to %lf\n",
76 <             maxCutoff - 1.0 );
77 <    painCave.isFatal = 0;
78 <    simError();
107 >  
108 >  if( !boxIsInit ) boxIsInit = 1;
109  
110 <    rCut = rList - 1.0;
110 >  for(i=0; i < 3; i++)
111 >    for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
112 >  
113 >  calcBoxL();
114 >  calcHmatInv();
115  
116 <    // list radius changed so we have to refresh the simulation structure.
117 <    refreshSim();
116 >  for(i=0; i < 3; i++) {
117 >    for (j=0; j < 3; j++) {
118 >      FortranHmat[3*j + i] = Hmat[i][j];
119 >      FortranHmatInv[3*j + i] = HmatInv[i][j];
120 >    }
121    }
122  
123 <  if (rCut > maxCutoff) {
124 <    sprintf( painCave.errMsg,
125 <             "New Box size is forcing cutoff radius down to %lf\n",
126 <             maxCutoff );
90 <    painCave.isFatal = 0;
91 <    simError();
123 >  setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic);
124 >
125 > }
126 >
127  
128 <    status = 0;
129 <    LJ_new_rcut(&rCut, &status);
130 <    if (status != 0) {
131 <      sprintf( painCave.errMsg,
132 <               "Error in recomputing LJ shifts based on new rcut\n");
98 <      painCave.isFatal = 1;
99 <      simError();
100 <    }
101 <  }
128 > void SimInfo::getBoxM (double theBox[3][3]) {
129 >
130 >  int i, j;
131 >  for(i=0; i<3; i++)
132 >    for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j];
133   }
134  
104 – void SimInfo::setBoxM( double theBox[9] ){
105 –  
106 –  int i, status;
107 –  double smallestBoxL, maxCutoff;
135  
136 <  for(i=0; i<9; i++) Hmat[i] = theBox[i];
137 <  calcHmatI();
138 <  calcBoxL();
136 > void SimInfo::scaleBox(double scale) {
137 >  double theBox[3][3];
138 >  int i, j;
139  
140 <  setFortranBoxSize(Hmat);
114 <
115 <  smallestBoxL = boxLx;
116 <  if (boxLy < smallestBoxL) smallestBoxL = boxLy;
117 <  if (boxLz < smallestBoxL) smallestBoxL = boxLz;
140 >  // cerr << "Scaling box by " << scale << "\n";
141  
142 <  maxCutoff = smallestBoxL / 2.0;
142 >  for(i=0; i<3; i++)
143 >    for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
144  
145 <  if (rList > maxCutoff) {
122 <    sprintf( painCave.errMsg,
123 <             "New Box size is forcing neighborlist radius down to %lf\n",
124 <             maxCutoff );
125 <    painCave.isFatal = 0;
126 <    simError();
145 >  setBoxM(theBox);
146  
147 <    rList = maxCutoff;
147 > }
148  
149 <    sprintf( painCave.errMsg,
150 <             "New Box size is forcing cutoff radius down to %lf\n",
151 <             maxCutoff - 1.0 );
152 <    painCave.isFatal = 0;
153 <    simError();
149 > void SimInfo::calcHmatInv( void ) {
150 >  
151 >  int oldOrtho;
152 >  int i,j;
153 >  double smallDiag;
154 >  double tol;
155 >  double sanity[3][3];
156  
157 <    rCut = rList - 1.0;
157 >  invertMat3( Hmat, HmatInv );
158  
159 <    // list radius changed so we have to refresh the simulation structure.
160 <    refreshSim();
159 >  // check to see if Hmat is orthorhombic
160 >  
161 >  oldOrtho = orthoRhombic;
162 >
163 >  smallDiag = fabs(Hmat[0][0]);
164 >  if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]);
165 >  if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]);
166 >  tol = smallDiag * orthoTolerance;
167 >
168 >  orthoRhombic = 1;
169 >  
170 >  for (i = 0; i < 3; i++ ) {
171 >    for (j = 0 ; j < 3; j++) {
172 >      if (i != j) {
173 >        if (orthoRhombic) {
174 >          if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0;
175 >        }        
176 >      }
177 >    }
178    }
179  
180 <  if (rCut > maxCutoff) {
181 <    sprintf( painCave.errMsg,
182 <             "New Box size is forcing cutoff radius down to %lf\n",
145 <             maxCutoff );
146 <    painCave.isFatal = 0;
147 <    simError();
148 <
149 <    status = 0;
150 <    LJ_new_rcut(&rCut, &status);
151 <    if (status != 0) {
180 >  if( oldOrtho != orthoRhombic ){
181 >    
182 >    if( orthoRhombic ){
183        sprintf( painCave.errMsg,
184 <               "Error in recomputing LJ shifts based on new rcut\n");
185 <      painCave.isFatal = 1;
184 >               "Hmat is switching from Non-Orthorhombic to OrthoRhombic\n"
185 >               "       If this is a bad thing, change the orthoBoxTolerance( currently %G ).\n",
186 >               orthoTolerance);
187        simError();
188      }
189 +    else {
190 +      sprintf( painCave.errMsg,
191 +               "Hmat is switching from Orthorhombic to Non-OrthoRhombic\n"
192 +               "       If this is a bad thing, change the orthoBoxTolerance( currently %G ).\n",
193 +               orthoTolerance);
194 +      simError();
195 +    }
196    }
197   }
159 –
198  
199 < void SimInfo::getBox(double theBox[9]) {
199 > double SimInfo::matDet3(double a[3][3]) {
200 >  int i, j, k;
201 >  double determinant;
202  
203 <  int i;
164 <  for(i=0; i<9; i++) theBox[i] = Hmat[i];
165 < }
166 <
203 >  determinant = 0.0;
204  
205 < void SimInfo::calcHmatI( void ) {
205 >  for(i = 0; i < 3; i++) {
206 >    j = (i+1)%3;
207 >    k = (i+2)%3;
208  
209 <  double C[3][3];
210 <  double detHmat;
172 <  int i, j, k;
209 >    determinant += a[0][i] * (a[1][j]*a[2][k] - a[1][k]*a[2][j]);
210 >  }
211  
212 <  // calculate the adjunct of Hmat;
212 >  return determinant;
213 > }
214  
215 <  C[0][0] =  ( Hmat[4]*Hmat[8]) - (Hmat[7]*Hmat[5]);
216 <  C[1][0] = -( Hmat[1]*Hmat[8]) + (Hmat[7]*Hmat[2]);
217 <  C[2][0] =  ( Hmat[1]*Hmat[5]) - (Hmat[4]*Hmat[2]);
215 > void SimInfo::invertMat3(double a[3][3], double b[3][3]) {
216 >  
217 >  int  i, j, k, l, m, n;
218 >  double determinant;
219  
220 <  C[0][1] = -( Hmat[3]*Hmat[8]) + (Hmat[6]*Hmat[5]);
181 <  C[1][1] =  ( Hmat[0]*Hmat[8]) - (Hmat[6]*Hmat[2]);
182 <  C[2][1] = -( Hmat[0]*Hmat[5]) + (Hmat[3]*Hmat[2]);
220 >  determinant = matDet3( a );
221  
222 <  C[0][2] =  ( Hmat[3]*Hmat[7]) - (Hmat[6]*Hmat[4]);
223 <  C[1][2] = -( Hmat[0]*Hmat[7]) + (Hmat[6]*Hmat[1]);
224 <  C[2][2] =  ( Hmat[0]*Hmat[4]) - (Hmat[3]*Hmat[1]);
222 >  if (determinant == 0.0) {
223 >    sprintf( painCave.errMsg,
224 >             "Can't invert a matrix with a zero determinant!\n");
225 >    painCave.isFatal = 1;
226 >    simError();
227 >  }
228  
229 <  // calcutlate the determinant of Hmat
230 <  
231 <  detHmat = 0.0;
232 <  for(i=0; i<3; i++) detHmat += Hmat[i] * C[i][0];
229 >  for (i=0; i < 3; i++) {
230 >    j = (i+1)%3;
231 >    k = (i+2)%3;
232 >    for(l = 0; l < 3; l++) {
233 >      m = (l+1)%3;
234 >      n = (l+2)%3;
235 >      
236 >      b[l][i] = (a[j][m]*a[k][n] - a[j][n]*a[k][m]) / determinant;
237 >    }
238 >  }
239 > }
240  
241 + void SimInfo::matMul3(double a[3][3], double b[3][3], double c[3][3]) {
242 +  double r00, r01, r02, r10, r11, r12, r20, r21, r22;
243 +
244 +  r00 = a[0][0]*b[0][0] + a[0][1]*b[1][0] + a[0][2]*b[2][0];
245 +  r01 = a[0][0]*b[0][1] + a[0][1]*b[1][1] + a[0][2]*b[2][1];
246 +  r02 = a[0][0]*b[0][2] + a[0][1]*b[1][2] + a[0][2]*b[2][2];
247    
248 <  // H^-1 = C^T / det(H)
248 >  r10 = a[1][0]*b[0][0] + a[1][1]*b[1][0] + a[1][2]*b[2][0];
249 >  r11 = a[1][0]*b[0][1] + a[1][1]*b[1][1] + a[1][2]*b[2][1];
250 >  r12 = a[1][0]*b[0][2] + a[1][1]*b[1][2] + a[1][2]*b[2][2];
251    
252 <  i=0;
253 <  for(j=0; j<3; j++){
254 <    for(k=0; k<3; k++){
252 >  r20 = a[2][0]*b[0][0] + a[2][1]*b[1][0] + a[2][2]*b[2][0];
253 >  r21 = a[2][0]*b[0][1] + a[2][1]*b[1][1] + a[2][2]*b[2][1];
254 >  r22 = a[2][0]*b[0][2] + a[2][1]*b[1][2] + a[2][2]*b[2][2];
255 >  
256 >  c[0][0] = r00; c[0][1] = r01; c[0][2] = r02;
257 >  c[1][0] = r10; c[1][1] = r11; c[1][2] = r12;
258 >  c[2][0] = r20; c[2][1] = r21; c[2][2] = r22;
259 > }
260  
261 <      HmatI[i] = C[j][k] / detHmat;
262 <      i++;
261 > void SimInfo::matVecMul3(double m[3][3], double inVec[3], double outVec[3]) {
262 >  double a0, a1, a2;
263 >
264 >  a0 = inVec[0];  a1 = inVec[1];  a2 = inVec[2];
265 >
266 >  outVec[0] = m[0][0]*a0 + m[0][1]*a1 + m[0][2]*a2;
267 >  outVec[1] = m[1][0]*a0 + m[1][1]*a1 + m[1][2]*a2;
268 >  outVec[2] = m[2][0]*a0 + m[2][1]*a1 + m[2][2]*a2;
269 > }
270 >
271 > void SimInfo::transposeMat3(double in[3][3], double out[3][3]) {
272 >  double temp[3][3];
273 >  int i, j;
274 >
275 >  for (i = 0; i < 3; i++) {
276 >    for (j = 0; j < 3; j++) {
277 >      temp[j][i] = in[i][j];
278      }
279    }
280 +  for (i = 0; i < 3; i++) {
281 +    for (j = 0; j < 3; j++) {
282 +      out[i][j] = temp[i][j];
283 +    }
284 +  }
285   }
286 +  
287 + void SimInfo::printMat3(double A[3][3] ){
288  
289 < void SimInfo::calcBoxL( void ){
289 >  std::cerr
290 >            << "[ " << A[0][0] << ", " << A[0][1] << ", " << A[0][2] << " ]\n"
291 >            << "[ " << A[1][0] << ", " << A[1][1] << ", " << A[1][2] << " ]\n"
292 >            << "[ " << A[2][0] << ", " << A[2][1] << ", " << A[2][2] << " ]\n";
293 > }
294  
295 <  double dx, dy, dz, dsq;
209 <  int i;
295 > void SimInfo::printMat9(double A[9] ){
296  
297 <  // boxVol = h1 (dot) h2 (cross) h3
297 >  std::cerr
298 >            << "[ " << A[0] << ", " << A[1] << ", " << A[2] << " ]\n"
299 >            << "[ " << A[3] << ", " << A[4] << ", " << A[5] << " ]\n"
300 >            << "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n";
301 > }
302  
213 –  boxVol = Hmat[0] * ( (Hmat[4]*Hmat[8]) - (Hmat[7]*Hmat[5]) )
214 –         + Hmat[1] * ( (Hmat[5]*Hmat[6]) - (Hmat[8]*Hmat[3]) )
215 –         + Hmat[2] * ( (Hmat[3]*Hmat[7]) - (Hmat[6]*Hmat[4]) );
303  
304 + void SimInfo::crossProduct3(double a[3],double b[3], double out[3]){
305  
306 <  // boxLx
307 <  
308 <  dx = Hmat[0]; dy = Hmat[1]; dz = Hmat[2];
306 >      out[0] = a[1] * b[2] - a[2] * b[1];
307 >      out[1] = a[2] * b[0] - a[0] * b[2] ;
308 >      out[2] = a[0] * b[1] - a[1] * b[0];
309 >      
310 > }
311 >
312 > double SimInfo::dotProduct3(double a[3], double b[3]){
313 >  return a[0]*b[0] + a[1]*b[1]+ a[2]*b[2];
314 > }
315 >
316 > double SimInfo::length3(double a[3]){
317 >  return sqrt(a[0]*a[0] + a[1]*a[1] + a[2]*a[2]);
318 > }
319 >
320 > void SimInfo::calcBoxL( void ){
321 >
322 >  double dx, dy, dz, dsq;
323 >
324 >  // boxVol = Determinant of Hmat
325 >
326 >  boxVol = matDet3( Hmat );
327 >
328 >  // boxLx
329 >  
330 >  dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
331    dsq = dx*dx + dy*dy + dz*dz;
332 <  boxLx = sqrt( dsq );
332 >  boxL[0] = sqrt( dsq );
333 >  //maxCutoff = 0.5 * boxL[0];
334  
335    // boxLy
336    
337 <  dx = Hmat[3]; dy = Hmat[4]; dz = Hmat[5];
337 >  dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
338    dsq = dx*dx + dy*dy + dz*dz;
339 <  boxLy = sqrt( dsq );
339 >  boxL[1] = sqrt( dsq );
340 >  //if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
341  
342 +
343    // boxLz
344    
345 <  dx = Hmat[6]; dy = Hmat[7]; dz = Hmat[8];
345 >  dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
346    dsq = dx*dx + dy*dy + dz*dz;
347 <  boxLz = sqrt( dsq );
347 >  boxL[2] = sqrt( dsq );
348 >  //if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
349 >
350 >  //calculate the max cutoff
351 >  maxCutoff =  calcMaxCutOff();
352    
353 +  checkCutOffs();
354 +
355   }
356  
357  
358 < void SimInfo::wrapVector( double thePos[3] ){
358 > double SimInfo::calcMaxCutOff(){
359  
360 <  int i, j, k;
361 <  double scaled[3];
360 >  double ri[3], rj[3], rk[3];
361 >  double rij[3], rjk[3], rki[3];
362 >  double minDist;
363  
364 <  // calc the scaled coordinates.
364 >  ri[0] = Hmat[0][0];
365 >  ri[1] = Hmat[1][0];
366 >  ri[2] = Hmat[2][0];
367 >
368 >  rj[0] = Hmat[0][1];
369 >  rj[1] = Hmat[1][1];
370 >  rj[2] = Hmat[2][1];
371 >
372 >  rk[0] = Hmat[0][2];
373 >  rk[1] = Hmat[1][2];
374 >  rk[2] = Hmat[2][2];
375    
376 <  for(i=0; i<3; i++)
377 <    scaled[i] = thePos[0]*Hmat[i] + thePos[1]*Hat[i+3] + thePos[3]*Hmat[i+6];
376 >  crossProduct3(ri,rj, rij);
377 >  distXY = dotProduct3(rk,rij) / length3(rij);
378  
379 <  // wrap the scaled coordinates
379 >  crossProduct3(rj,rk, rjk);
380 >  distYZ = dotProduct3(ri,rjk) / length3(rjk);
381  
382 <  for(i=0; i<3; i++)
383 <    scaled[i] -= (copysign(1,scaled[i]) * (int)(fabs(scaled[i]) + 0.5));
382 >  crossProduct3(rk,ri, rki);
383 >  distZX = dotProduct3(rj,rki) / length3(rki);
384 >
385 >  minDist = min(min(distXY, distYZ), distZX);
386 >  return minDist/2;
387    
388 + }
389  
390 + void SimInfo::wrapVector( double thePos[3] ){
391 +
392 +  int i;
393 +  double scaled[3];
394 +
395 +  if( !orthoRhombic ){
396 +    // calc the scaled coordinates.
397 +  
398 +
399 +    matVecMul3(HmatInv, thePos, scaled);
400 +    
401 +    for(i=0; i<3; i++)
402 +      scaled[i] -= roundMe(scaled[i]);
403 +    
404 +    // calc the wrapped real coordinates from the wrapped scaled coordinates
405 +    
406 +    matVecMul3(Hmat, scaled, thePos);
407 +
408 +  }
409 +  else{
410 +    // calc the scaled coordinates.
411 +    
412 +    for(i=0; i<3; i++)
413 +      scaled[i] = thePos[i]*HmatInv[i][i];
414 +    
415 +    // wrap the scaled coordinates
416 +    
417 +    for(i=0; i<3; i++)
418 +      scaled[i] -= roundMe(scaled[i]);
419 +    
420 +    // calc the wrapped real coordinates from the wrapped scaled coordinates
421 +    
422 +    for(i=0; i<3; i++)
423 +      thePos[i] = scaled[i]*Hmat[i][i];
424 +  }
425 +    
426   }
427  
428  
429   int SimInfo::getNDF(){
430 <  int ndf_local, ndf;
430 >  int ndf_local;
431    
432    ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints;
433  
# Line 266 | Line 437 | int SimInfo::getNDF(){
437    ndf = ndf_local;
438   #endif
439  
440 <  ndf = ndf - 3;
440 >  ndf = ndf - 3 - nZconstraints;
441  
442    return ndf;
443   }
444  
445   int SimInfo::getNDFraw() {
446 <  int ndfRaw_local, ndfRaw;
446 >  int ndfRaw_local;
447  
448    // Raw degrees of freedom that we have to set
449    ndfRaw_local = 3 * n_atoms + 3 * n_oriented;
# Line 285 | Line 456 | int SimInfo::getNDFraw() {
456  
457    return ndfRaw;
458   }
459 <
459 >
460 > int SimInfo::getNDFtranslational() {
461 >  int ndfTrans_local;
462 >
463 >  ndfTrans_local = 3 * n_atoms - n_constraints;
464 >
465 > #ifdef IS_MPI
466 >  MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
467 > #else
468 >  ndfTrans = ndfTrans_local;
469 > #endif
470 >
471 >  ndfTrans = ndfTrans - 3 - nZconstraints;
472 >
473 >  return ndfTrans;
474 > }
475 >
476   void SimInfo::refreshSim(){
477  
478    simtype fInfo;
479    int isError;
480    int n_global;
481    int* excl;
482 <  
296 <  fInfo.rrf = 0.0;
297 <  fInfo.rt = 0.0;
482 >
483    fInfo.dielect = 0.0;
484  
300 –  fInfo.box[0] = box_x;
301 –  fInfo.box[1] = box_y;
302 –  fInfo.box[2] = box_z;
303 –
304 –  fInfo.rlist = rList;
305 –  fInfo.rcut = rCut;
306 –
485    if( useDipole ){
308 –    fInfo.rrf = ecr;
309 –    fInfo.rt = ecr - est;
486      if( useReactionField )fInfo.dielect = dielectric;
487    }
488  
# Line 352 | Line 528 | void SimInfo::refreshSim(){
528  
529    this->ndf = this->getNDF();
530    this->ndfRaw = this->getNDFraw();
531 +  this->ndfTrans = this->getNDFtranslational();
532 + }
533  
534 +
535 + void SimInfo::setRcut( double theRcut ){
536 +
537 +  rCut = theRcut;
538 +  checkCutOffs();
539   }
540  
541 + void SimInfo::setDefaultRcut( double theRcut ){
542 +
543 +  haveOrigRcut = 1;
544 +  origRcut = theRcut;
545 +  rCut = theRcut;
546 +
547 +  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
548 +
549 +  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
550 + }
551 +
552 + void SimInfo::setEcr( double theEcr ){
553 +
554 +  ecr = theEcr;
555 +  checkCutOffs();
556 + }
557 +
558 + void SimInfo::setDefaultEcr( double theEcr ){
559 +
560 +  haveOrigEcr = 1;
561 +  origEcr = theEcr;
562 +  
563 +  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
564 +
565 +  ecr = theEcr;
566 +
567 +  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
568 + }
569 +
570 + void SimInfo::setEcr( double theEcr, double theEst ){
571 +
572 +  est = theEst;
573 +  setEcr( theEcr );
574 + }
575 +
576 + void SimInfo::setDefaultEcr( double theEcr, double theEst ){
577 +
578 +  est = theEst;
579 +  setDefaultEcr( theEcr );
580 + }
581 +
582 +
583 + void SimInfo::checkCutOffs( void ){
584 +
585 +  int cutChanged = 0;
586 +  
587 +  if( boxIsInit ){
588 +    
589 +    //we need to check cutOffs against the box
590 +
591 +    //detect the change of rCut
592 +    if(( maxCutoff > rCut )&&(usePBC)){
593 +      if( rCut < origRcut ){
594 +        rCut = origRcut;
595 +        
596 +        if (rCut > maxCutoff)
597 +          rCut = maxCutoff;
598 +  
599 +          sprintf( painCave.errMsg,
600 +                    "New Box size is setting the long range cutoff radius "
601 +                    "to %lf at time %lf\n",
602 +                    rCut, currentTime );
603 +          painCave.isFatal = 0;
604 +          simError();
605 +      }
606 +    }
607 +    else if ((rCut > maxCutoff)&&(usePBC)) {
608 +      sprintf( painCave.errMsg,
609 +               "New Box size is setting the long range cutoff radius "
610 +               "to %lf at time %lf\n",
611 +               maxCutoff, currentTime );
612 +      painCave.isFatal = 0;
613 +      simError();
614 +      rCut = maxCutoff;
615 +    }
616 +
617 +
618 +    //detect the change of ecr
619 +    if( maxCutoff > ecr ){
620 +      if( ecr < origEcr ){
621 +        ecr = origEcr;
622 +        if (ecr > maxCutoff) ecr = maxCutoff;
623 +  
624 +          sprintf( painCave.errMsg,
625 +                    "New Box size is setting the electrostaticCutoffRadius "
626 +                    "to %lf at time %lf\n",
627 +                    ecr, currentTime );
628 +            painCave.isFatal = 0;
629 +            simError();
630 +      }
631 +    }
632 +    else if( ecr > maxCutoff){
633 +      sprintf( painCave.errMsg,
634 +               "New Box size is setting the electrostaticCutoffRadius "
635 +               "to %lf at time %lf\n",
636 +               maxCutoff, currentTime  );
637 +      painCave.isFatal = 0;
638 +      simError();      
639 +      ecr = maxCutoff;
640 +    }
641 +
642 +    if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1;
643 +    
644 +    // rlist is the 1.0 plus max( rcut, ecr )
645 +    
646 +    ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
647 +    
648 +    if( cutChanged ){
649 +      notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
650 +    }
651 +    
652 +    oldEcr = ecr;
653 +    oldRcut = rCut;
654 +    
655 +  } else {
656 +    // initialize this stuff before using it, OK?
657 +    sprintf( painCave.errMsg,
658 +             "Trying to check cutoffs without a box. Be smarter.\n" );
659 +    painCave.isFatal = 1;
660 +    simError();      
661 +  }
662 +  
663 + }
664 +
665 + void SimInfo::addProperty(GenericData* prop){
666 +
667 +  map<string, GenericData*>::iterator result;
668 +  result = properties.find(prop->getID());
669 +  
670 +  //we can't simply use  properties[prop->getID()] = prop,
671 +  //it will cause memory leak if we already contain a propery which has the same name of prop
672 +  
673 +  if(result != properties.end()){
674 +    
675 +    delete (*result).second;
676 +    (*result).second = prop;
677 +      
678 +  }
679 +  else{
680 +
681 +    properties[prop->getID()] = prop;
682 +
683 +  }
684 +    
685 + }
686 +
687 + GenericData* SimInfo::getProperty(const string& propName){
688 +
689 +  map<string, GenericData*>::iterator result;
690 +  
691 +  //string lowerCaseName = ();
692 +  
693 +  result = properties.find(propName);
694 +  
695 +  if(result != properties.end())
696 +    return (*result).second;  
697 +  else  
698 +    return NULL;  
699 + }
700 +
701 + vector<GenericData*> SimInfo::getProperties(){
702 +
703 +  vector<GenericData*> result;
704 +  map<string, GenericData*>::iterator i;
705 +  
706 +  for(i = properties.begin(); i != properties.end(); i++)
707 +    result.push_back((*i).second);
708 +    
709 +  return result;
710 + }
711 +
712 + double SimInfo::matTrace3(double m[3][3]){
713 +  double trace;
714 +  trace = m[0][0] + m[1][1] + m[2][2];
715 +
716 +  return trace;
717 + }

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