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root/group/branches/new-templateless/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.
branches/new-templateless/OOPSE/libmdtools/SimInfo.cpp (file contents), Revision 852 by mmeineke, Thu Nov 6 18:20:47 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
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 +
54    usePBC = 0;
55    useLJ = 0;
56    useSticky = 0;
# Line 36 | Line 59 | SimInfo::SimInfo(){
59    useGB = 0;
60    useEAM = 0;
61  
62 +  myConfiguration = new SimState();
63 +
64 +  properties = new GenericData();
65 +
66    wrapMeSimInfo( this );
67   }
68  
69 +
70 + SimInfo::~SimInfo(){
71 +
72 +  delete myConfiguration;
73 +  delete properties;    
74 + }
75 +
76   void SimInfo::setBox(double newBox[3]) {
77 +  
78 +  int i, j;
79 +  double tempMat[3][3];
80  
81 <  double smallestBoxL, maxCutoff;
82 <  int status;
46 <  int i;
81 >  for(i=0; i<3; i++)
82 >    for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
83  
84 <  for(i=0; i<9; i++) Hmat[i] = 0.0;;
84 >  tempMat[0][0] = newBox[0];
85 >  tempMat[1][1] = newBox[1];
86 >  tempMat[2][2] = newBox[2];
87  
88 <  Hmat[0] = newBox[0];
51 <  Hmat[4] = newBox[1];
52 <  Hmat[8] = newBox[2];
88 >  setBoxM( tempMat );
89  
90 <  calcHmatI();
90 > }
91 >
92 > void SimInfo::setBoxM( double theBox[3][3] ){
93 >  
94 >  int i, j;
95 >  double FortranHmat[9]; // to preserve compatibility with Fortran the
96 >                         // ordering in the array is as follows:
97 >                         // [ 0 3 6 ]
98 >                         // [ 1 4 7 ]
99 >                         // [ 2 5 8 ]
100 >  double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
101 >
102 >  
103 >  if( !boxIsInit ) boxIsInit = 1;
104 >
105 >  for(i=0; i < 3; i++)
106 >    for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
107 >  
108    calcBoxL();
109 +  calcHmatInv();
110  
111 <  setFortranBoxSize(Hmat);
111 >  for(i=0; i < 3; i++) {
112 >    for (j=0; j < 3; j++) {
113 >      FortranHmat[3*j + i] = Hmat[i][j];
114 >      FortranHmatInv[3*j + i] = HmatInv[i][j];
115 >    }
116 >  }
117  
118 <  smallestBoxL = boxLx;
119 <  if (boxLy < smallestBoxL) smallestBoxL = boxLy;
120 <  if (boxLz < smallestBoxL) smallestBoxL = boxLz;
118 >  setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic);
119 >
120 > }
121 >
122  
123 <  maxCutoff = smallestBoxL / 2.0;
123 > void SimInfo::getBoxM (double theBox[3][3]) {
124  
125 <  if (rList > maxCutoff) {
126 <    sprintf( painCave.errMsg,
127 <             "New Box size is forcing neighborlist radius down to %lf\n",
128 <             maxCutoff );
69 <    painCave.isFatal = 0;
70 <    simError();
125 >  int i, j;
126 >  for(i=0; i<3; i++)
127 >    for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j];
128 > }
129  
72 –    rList = maxCutoff;
130  
131 <    sprintf( painCave.errMsg,
132 <             "New Box size is forcing cutoff radius down to %lf\n",
133 <             maxCutoff - 1.0 );
77 <    painCave.isFatal = 0;
78 <    simError();
131 > void SimInfo::scaleBox(double scale) {
132 >  double theBox[3][3];
133 >  int i, j;
134  
135 <    rCut = rList - 1.0;
135 >  // cerr << "Scaling box by " << scale << "\n";
136  
137 <    // list radius changed so we have to refresh the simulation structure.
138 <    refreshSim();
84 <  }
137 >  for(i=0; i<3; i++)
138 >    for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
139  
140 <  if (rCut > maxCutoff) {
87 <    sprintf( painCave.errMsg,
88 <             "New Box size is forcing cutoff radius down to %lf\n",
89 <             maxCutoff );
90 <    painCave.isFatal = 0;
91 <    simError();
140 >  setBoxM(theBox);
141  
142 <    status = 0;
143 <    LJ_new_rcut(&rCut, &status);
144 <    if (status != 0) {
142 > }
143 >
144 > void SimInfo::calcHmatInv( void ) {
145 >
146 >  int oldOrtho;
147 >  int i,j;
148 >  double smallDiag;
149 >  double tol;
150 >  double sanity[3][3];
151 >
152 >  invertMat3( Hmat, HmatInv );
153 >
154 >  // Check the inverse to make sure it is sane:
155 >
156 >  // matMul3( Hmat, HmatInv, sanity );
157 >    
158 >  // check to see if Hmat is orthorhombic
159 >
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 * 1E-6;
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( 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 ortho tolerance in SimInfo.\n" );
186        simError();
187      }
188 +    else {
189 +      sprintf( painCave.errMsg,
190 +               "Hmat is switching from Orthorhombic to Non-OrthoRhombic\n"
191 +               "       If this is a bad thing change the ortho tolerance in SimInfo.\n" );
192 +      simError();
193 +    }
194    }
195   }
196  
197 < void SimInfo::setBoxM( double theBox[9] ){
198 <  
199 <  int i, status;
107 <  double smallestBoxL, maxCutoff;
197 > double SimInfo::matDet3(double a[3][3]) {
198 >  int i, j, k;
199 >  double determinant;
200  
201 <  for(i=0; i<9; i++) Hmat[i] = theBox[i];
110 <  calcHmatI();
111 <  calcBoxL();
201 >  determinant = 0.0;
202  
203 <  setFortranBoxSize(Hmat);
204 <
205 <  smallestBoxL = boxLx;
116 <  if (boxLy < smallestBoxL) smallestBoxL = boxLy;
117 <  if (boxLz < smallestBoxL) smallestBoxL = boxLz;
203 >  for(i = 0; i < 3; i++) {
204 >    j = (i+1)%3;
205 >    k = (i+2)%3;
206  
207 <  maxCutoff = smallestBoxL / 2.0;
207 >    determinant += a[0][i] * (a[1][j]*a[2][k] - a[1][k]*a[2][j]);
208 >  }
209  
210 <  if (rList > maxCutoff) {
211 <    sprintf( painCave.errMsg,
123 <             "New Box size is forcing neighborlist radius down to %lf\n",
124 <             maxCutoff );
125 <    painCave.isFatal = 0;
126 <    simError();
210 >  return determinant;
211 > }
212  
213 <    rList = maxCutoff;
213 > void SimInfo::invertMat3(double a[3][3], double b[3][3]) {
214 >  
215 >  int  i, j, k, l, m, n;
216 >  double determinant;
217  
218 +  determinant = matDet3( a );
219 +
220 +  if (determinant == 0.0) {
221      sprintf( painCave.errMsg,
222 <             "New Box size is forcing cutoff radius down to %lf\n",
223 <             maxCutoff - 1.0 );
133 <    painCave.isFatal = 0;
222 >             "Can't invert a matrix with a zero determinant!\n");
223 >    painCave.isFatal = 1;
224      simError();
135 –
136 –    rCut = rList - 1.0;
137 –
138 –    // list radius changed so we have to refresh the simulation structure.
139 –    refreshSim();
225    }
226  
227 <  if (rCut > maxCutoff) {
228 <    sprintf( painCave.errMsg,
229 <             "New Box size is forcing cutoff radius down to %lf\n",
230 <             maxCutoff );
231 <    painCave.isFatal = 0;
232 <    simError();
233 <
234 <    status = 0;
150 <    LJ_new_rcut(&rCut, &status);
151 <    if (status != 0) {
152 <      sprintf( painCave.errMsg,
153 <               "Error in recomputing LJ shifts based on new rcut\n");
154 <      painCave.isFatal = 1;
155 <      simError();
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 >      b[l][i] = (a[j][m]*a[k][n] - a[j][n]*a[k][m]) / determinant;
235      }
236    }
237   }
159 –
238  
239 < void SimInfo::getBox(double theBox[9]) {
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 <  int i;
243 <  for(i=0; i<9; i++) theBox[i] = Hmat[i];
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 >  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   }
166 –
258  
259 < void SimInfo::calcHmatI( void ) {
259 > void SimInfo::matVecMul3(double m[3][3], double inVec[3], double outVec[3]) {
260 >  double a0, a1, a2;
261  
262 <  double C[3][3];
171 <  double detHmat;
172 <  int i, j, k;
262 >  a0 = inVec[0];  a1 = inVec[1];  a2 = inVec[2];
263  
264 <  // calculate the adjunct of Hmat;
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 <  C[0][0] =  ( Hmat[4]*Hmat[8]) - (Hmat[7]*Hmat[5]);
270 <  C[1][0] = -( Hmat[1]*Hmat[8]) + (Hmat[7]*Hmat[2]);
271 <  C[2][0] =  ( Hmat[1]*Hmat[5]) - (Hmat[4]*Hmat[2]);
269 > void SimInfo::transposeMat3(double in[3][3], double out[3][3]) {
270 >  double temp[3][3];
271 >  int i, j;
272  
273 <  C[0][1] = -( Hmat[3]*Hmat[8]) + (Hmat[6]*Hmat[5]);
274 <  C[1][1] =  ( Hmat[0]*Hmat[8]) - (Hmat[6]*Hmat[2]);
275 <  C[2][1] = -( Hmat[0]*Hmat[5]) + (Hmat[3]*Hmat[2]);
273 >  for (i = 0; i < 3; i++) {
274 >    for (j = 0; j < 3; j++) {
275 >      temp[j][i] = in[i][j];
276 >    }
277 >  }
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 <  C[0][2] =  ( Hmat[3]*Hmat[7]) - (Hmat[6]*Hmat[4]);
288 <  C[1][2] = -( Hmat[0]*Hmat[7]) + (Hmat[6]*Hmat[1]);
289 <  C[2][2] =  ( Hmat[0]*Hmat[4]) - (Hmat[3]*Hmat[1]);
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 <  // calcutlate the determinant of Hmat
189 <  
190 <  detHmat = 0.0;
191 <  for(i=0; i<3; i++) detHmat += Hmat[i] * C[i][0];
293 > void SimInfo::printMat9(double A[9] ){
294  
295 <  
296 <  // H^-1 = C^T / det(H)
297 <  
298 <  i=0;
299 <  for(j=0; j<3; j++){
198 <    for(k=0; k<3; k++){
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 <      HmatI[i] = C[j][k] / detHmat;
302 <      i++;
303 <    }
304 <  }
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;
209 –  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]) )
214 <         + Hmat[1] * ( (Hmat[5]*Hmat[6]) - (Hmat[8]*Hmat[3]) )
215 <         + Hmat[2] * ( (Hmat[3]*Hmat[7]) - (Hmat[6]*Hmat[4]) );
324 >  boxVol = matDet3( Hmat );
325  
217 –
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 < void SimInfo::wrapVector( double thePos[3] ){
356 > double SimInfo::calcMaxCutOff(){
357  
358 <  int i, j, k;
359 <  double scaled[3];
358 >  double ri[3], rj[3], rk[3];
359 >  double rij[3], rjk[3], rki[3];
360 >  double minDist;
361  
362 <  // calc the scaled coordinates.
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 <  for(i=0; i<3; i++)
375 <    scaled[i] = thePos[0]*Hmat[i] + thePos[1]*Hat[i+3] + thePos[3]*Hmat[i+6];
374 >  crossProduct3(ri,rj, rij);
375 >  distXY = dotProduct3(rk,rij) / length3(rij);
376  
377 <  // wrap the scaled coordinates
377 >  crossProduct3(rj,rk, rjk);
378 >  distYZ = dotProduct3(ri,rjk) / length3(rjk);
379  
380 <  for(i=0; i<3; i++)
381 <    scaled[i] -= (copysign(1,scaled[i]) * (int)(fabs(scaled[i]) + 0.5));
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;
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++)
400 +      scaled[i] -= roundMe(scaled[i]);
401 +    
402 +    // calc the wrapped real coordinates from the wrapped scaled coordinates
403 +    
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]*HmatInv[i][i];
412 +    
413 +    // wrap the scaled coordinates
414 +    
415 +    for(i=0; i<3; i++)
416 +      scaled[i] -= roundMe(scaled[i]);
417 +    
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][i];
422 +  }
423 +    
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 266 | 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 285 | 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;
295 –  
296 –  fInfo.rrf = 0.0;
297 –  fInfo.rt = 0.0;
298 –  fInfo.dielect = 0.0;
480  
481 <  fInfo.box[0] = box_x;
301 <  fInfo.box[1] = box_y;
302 <  fInfo.box[2] = box_z;
481 >  fInfo.dielect = 0.0;
482  
304 –  fInfo.rlist = rList;
305 –  fInfo.rcut = rCut;
306 –
483    if( useDipole ){
308 –    fInfo.rrf = ecr;
309 –    fInfo.rt = ecr - est;
484      if( useReactionField )fInfo.dielect = dielectric;
485    }
486  
# Line 352 | Line 526 | void SimInfo::refreshSim(){
526  
527    this->ndf = this->getNDF();
528    this->ndfRaw = this->getNDFraw();
529 +  this->ndfTrans = this->getNDFtranslational();
530 + }
531  
532 +
533 + void SimInfo::setRcut( double theRcut ){
534 +
535 +  rCut = theRcut;
536 +  checkCutOffs();
537   }
538  
539 + void SimInfo::setDefaultRcut( double theRcut ){
540 +
541 +  haveOrigRcut = 1;
542 +  origRcut = theRcut;
543 +  rCut = theRcut;
544 +
545 +  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
546 +
547 +  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
548 + }
549 +
550 + void SimInfo::setEcr( double theEcr ){
551 +
552 +  ecr = theEcr;
553 +  checkCutOffs();
554 + }
555 +
556 + void SimInfo::setDefaultEcr( double theEcr ){
557 +
558 +  haveOrigEcr = 1;
559 +  origEcr = theEcr;
560 +  
561 +  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
562 +
563 +  ecr = theEcr;
564 +
565 +  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
566 + }
567 +
568 + void SimInfo::setEcr( double theEcr, double theEst ){
569 +
570 +  est = theEst;
571 +  setEcr( theEcr );
572 + }
573 +
574 + void SimInfo::setDefaultEcr( double theEcr, double theEst ){
575 +
576 +  est = theEst;
577 +  setDefaultEcr( theEcr );
578 + }
579 +
580 +
581 + void SimInfo::checkCutOffs( void ){
582 +
583 +  int cutChanged = 0;
584 +  
585 +  if( boxIsInit ){
586 +    
587 +    //we need to check cutOffs against the box
588 +
589 +    //detect the change of rCut
590 +    if(( maxCutoff > rCut )&&(usePBC)){
591 +      if( rCut < origRcut ){
592 +        rCut = origRcut;
593 +        
594 +        if (rCut > maxCutoff)
595 +          rCut = maxCutoff;
596 +  
597 +          sprintf( painCave.errMsg,
598 +                    "New Box size is setting the long range cutoff radius "
599 +                    "to %lf at time %lf\n",
600 +                    rCut, currentTime );
601 +          painCave.isFatal = 0;
602 +          simError();
603 +      }
604 +    }
605 +    else if ((rCut > maxCutoff)&&(usePBC)) {
606 +      sprintf( painCave.errMsg,
607 +               "New Box size is setting the long range cutoff radius "
608 +               "to %lf at time %lf\n",
609 +               maxCutoff, currentTime );
610 +      painCave.isFatal = 0;
611 +      simError();
612 +      rCut = maxCutoff;
613 +    }
614 +
615 +
616 +    //detect the change of ecr
617 +    if( maxCutoff > ecr ){
618 +      if( ecr < origEcr ){
619 +        ecr = origEcr;
620 +        if (ecr > maxCutoff) ecr = maxCutoff;
621 +  
622 +          sprintf( painCave.errMsg,
623 +                    "New Box size is setting the electrostaticCutoffRadius "
624 +                    "to %lf at time %lf\n",
625 +                    ecr, currentTime );
626 +            painCave.isFatal = 0;
627 +            simError();
628 +      }
629 +    }
630 +    else if( ecr > maxCutoff){
631 +      sprintf( painCave.errMsg,
632 +               "New Box size is setting the electrostaticCutoffRadius "
633 +               "to %lf at time %lf\n",
634 +               maxCutoff, currentTime  );
635 +      painCave.isFatal = 0;
636 +      simError();      
637 +      ecr = maxCutoff;
638 +    }
639 +
640 +    if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1;
641 +    
642 +    // rlist is the 1.0 plus max( rcut, ecr )
643 +    
644 +    ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
645 +    
646 +    if( cutChanged ){
647 +      notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
648 +    }
649 +    
650 +    oldEcr = ecr;
651 +    oldRcut = rCut;
652 +    
653 +  } else {
654 +    // initialize this stuff before using it, OK?
655 +    sprintf( painCave.errMsg,
656 +             "Trying to check cutoffs without a box. Be smarter.\n" );
657 +    painCave.isFatal = 1;
658 +    simError();      
659 +  }
660 +  
661 + }
662 +
663 + GenericData* SimInfo::getProperty(char* propName){
664 +
665 +  return properties->find( propName );
666 + }
667 +
668 + double SimInfo::matTrace3(double m[3][3]){
669 +  double trace;
670 +  trace = m[0][0] + m[1][1] + m[2][2];
671 +
672 +  return trace;
673 + }

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