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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 626 by mmeineke, Wed Jul 16 21:30:56 2003 UTC

# Line 34 | Line 34 | SimInfo::SimInfo(){
34    setTemp = 0;
35    thermalTime = 0.0;
36    rCut = 0.0;
37 +  ecr = 0.0;
38 +  est = 0.0;
39 +  oldEcr = 0.0;
40 +  oldRcut = 0.0;
41  
42 +  haveOrigRcut = 0;
43 +  haveOrigEcr = 0;
44 +  boxIsInit = 0;
45 +  
46 +  
47 +
48    usePBC = 0;
49    useLJ = 0;
50    useSticky = 0;
# Line 47 | Line 57 | void SimInfo::setBox(double newBox[3]) {
57   }
58  
59   void SimInfo::setBox(double newBox[3]) {
60 +  
61 +  int i, j;
62 +  double tempMat[3][3];
63  
64 <  double smallestBoxL, maxCutoff;
65 <  int status;
53 <  int i;
64 >  for(i=0; i<3; i++)
65 >    for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
66  
67 <  for(i=0; i<9; i++) Hmat[i] = 0.0;;
67 >  tempMat[0][0] = newBox[0];
68 >  tempMat[1][1] = newBox[1];
69 >  tempMat[2][2] = newBox[2];
70  
71 <  Hmat[0] = newBox[0];
58 <  Hmat[4] = newBox[1];
59 <  Hmat[8] = newBox[2];
71 >  setBoxM( tempMat );
72  
73 <  calcHmatI();
73 > }
74 >
75 > void SimInfo::setBoxM( double theBox[3][3] ){
76 >  
77 >  int i, j, status;
78 >  double smallestBoxL, maxCutoff;
79 >  double FortranHmat[9]; // to preserve compatibility with Fortran the
80 >                         // ordering in the array is as follows:
81 >                         // [ 0 3 6 ]
82 >                         // [ 1 4 7 ]
83 >                         // [ 2 5 8 ]
84 >  double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
85 >
86 >  
87 >  if( !boxIsInit ) boxIsInit = 1;
88 >
89 >  for(i=0; i < 3; i++)
90 >    for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
91 >  
92    calcBoxL();
93 +  calcHmatInv();
94  
95 <  setFortranBoxSize(Hmat, HmatI, &orthoRhombic);
95 >  for(i=0; i < 3; i++) {
96 >    for (j=0; j < 3; j++) {
97 >      FortranHmat[3*j + i] = Hmat[i][j];
98 >      FortranHmatInv[3*j + i] = HmatInv[i][j];
99 >    }
100 >  }
101  
102 <  smallestBoxL = boxLx;
103 <  if (boxLy < smallestBoxL) smallestBoxL = boxLy;
104 <  if (boxLz < smallestBoxL) smallestBoxL = boxLz;
102 >  setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic);
103 >
104 > }
105 >
106  
107 <  maxCutoff = smallestBoxL / 2.0;
107 > void SimInfo::getBoxM (double theBox[3][3]) {
108  
109 <  if (rList > maxCutoff) {
110 <    sprintf( painCave.errMsg,
111 <             "New Box size is forcing neighborlist radius down to %lf\n",
112 <             maxCutoff );
76 <    painCave.isFatal = 0;
77 <    simError();
109 >  int i, j;
110 >  for(i=0; i<3; i++)
111 >    for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j];
112 > }
113  
79 –    rList = maxCutoff;
114  
115 <    sprintf( painCave.errMsg,
116 <             "New Box size is forcing cutoff radius down to %lf\n",
117 <             maxCutoff - 1.0 );
84 <    painCave.isFatal = 0;
85 <    simError();
115 > void SimInfo::scaleBox(double scale) {
116 >  double theBox[3][3];
117 >  int i, j;
118  
119 <    rCut = rList - 1.0;
119 >  // cerr << "Scaling box by " << scale << "\n";
120  
121 <    // list radius changed so we have to refresh the simulation structure.
122 <    refreshSim();
91 <  }
121 >  for(i=0; i<3; i++)
122 >    for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
123  
124 <  if (rCut > maxCutoff) {
94 <    sprintf( painCave.errMsg,
95 <             "New Box size is forcing cutoff radius down to %lf\n",
96 <             maxCutoff );
97 <    painCave.isFatal = 0;
98 <    simError();
124 >  setBoxM(theBox);
125  
100 –    status = 0;
101 –    LJ_new_rcut(&rCut, &status);
102 –    if (status != 0) {
103 –      sprintf( painCave.errMsg,
104 –               "Error in recomputing LJ shifts based on new rcut\n");
105 –      painCave.isFatal = 1;
106 –      simError();
107 –    }
108 –  }
126   }
127  
128 < void SimInfo::setBoxM( double theBox[9] ){
128 > void SimInfo::calcHmatInv( void ) {
129    
130 <  int i, status;
131 <  double smallestBoxL, maxCutoff;
130 >  int i,j;
131 >  double smallDiag;
132 >  double tol;
133 >  double sanity[3][3];
134  
135 <  for(i=0; i<9; i++) Hmat[i] = theBox[i];
117 <  calcHmatI();
118 <  calcBoxL();
135 >  invertMat3( Hmat, HmatInv );
136  
137 <  setFortranBoxSize(Hmat, HmatI, &orthoRhombic);
121 <
122 <  smallestBoxL = boxLx;
123 <  if (boxLy < smallestBoxL) smallestBoxL = boxLy;
124 <  if (boxLz < smallestBoxL) smallestBoxL = boxLz;
137 >  // Check the inverse to make sure it is sane:
138  
139 <  maxCutoff = smallestBoxL / 2.0;
139 >  matMul3( Hmat, HmatInv, sanity );
140 >    
141 >  // check to see if Hmat is orthorhombic
142 >  
143 >  smallDiag = Hmat[0][0];
144 >  if(smallDiag > Hmat[1][1]) smallDiag = Hmat[1][1];
145 >  if(smallDiag > Hmat[2][2]) smallDiag = Hmat[2][2];
146 >  tol = smallDiag * 1E-6;
147  
148 <  if (rList > maxCutoff) {
149 <    sprintf( painCave.errMsg,
150 <             "New Box size is forcing neighborlist radius down to %lf\n",
151 <             maxCutoff );
152 <    painCave.isFatal = 0;
153 <    simError();
148 >  orthoRhombic = 1;
149 >  
150 >  for (i = 0; i < 3; i++ ) {
151 >    for (j = 0 ; j < 3; j++) {
152 >      if (i != j) {
153 >        if (orthoRhombic) {
154 >          if (Hmat[i][j] >= tol) orthoRhombic = 0;
155 >        }        
156 >      }
157 >    }
158 >  }
159 > }
160  
161 <    rList = maxCutoff;
161 > double SimInfo::matDet3(double a[3][3]) {
162 >  int i, j, k;
163 >  double determinant;
164  
165 <    sprintf( painCave.errMsg,
138 <             "New Box size is forcing cutoff radius down to %lf\n",
139 <             maxCutoff - 1.0 );
140 <    painCave.isFatal = 0;
141 <    simError();
165 >  determinant = 0.0;
166  
167 <    rCut = rList - 1.0;
167 >  for(i = 0; i < 3; i++) {
168 >    j = (i+1)%3;
169 >    k = (i+2)%3;
170  
171 <    // list radius changed so we have to refresh the simulation structure.
146 <    refreshSim();
171 >    determinant += a[0][i] * (a[1][j]*a[2][k] - a[1][k]*a[2][j]);
172    }
173  
174 <  if (rCut > maxCutoff) {
174 >  return determinant;
175 > }
176 >
177 > void SimInfo::invertMat3(double a[3][3], double b[3][3]) {
178 >  
179 >  int  i, j, k, l, m, n;
180 >  double determinant;
181 >
182 >  determinant = matDet3( a );
183 >
184 >  if (determinant == 0.0) {
185      sprintf( painCave.errMsg,
186 <             "New Box size is forcing cutoff radius down to %lf\n",
187 <             maxCutoff );
153 <    painCave.isFatal = 0;
186 >             "Can't invert a matrix with a zero determinant!\n");
187 >    painCave.isFatal = 1;
188      simError();
189 +  }
190  
191 <    status = 0;
192 <    LJ_new_rcut(&rCut, &status);
193 <    if (status != 0) {
194 <      sprintf( painCave.errMsg,
195 <               "Error in recomputing LJ shifts based on new rcut\n");
196 <      painCave.isFatal = 1;
197 <      simError();
191 >  for (i=0; i < 3; i++) {
192 >    j = (i+1)%3;
193 >    k = (i+2)%3;
194 >    for(l = 0; l < 3; l++) {
195 >      m = (l+1)%3;
196 >      n = (l+2)%3;
197 >      
198 >      b[l][i] = (a[j][m]*a[k][n] - a[j][n]*a[k][m]) / determinant;
199      }
200    }
201   }
166 –
202  
203 < void SimInfo::getBoxM (double theBox[9]) {
203 > void SimInfo::matMul3(double a[3][3], double b[3][3], double c[3][3]) {
204 >  double r00, r01, r02, r10, r11, r12, r20, r21, r22;
205  
206 <  int i;
207 <  for(i=0; i<9; i++) theBox[i] = Hmat[i];
206 >  r00 = a[0][0]*b[0][0] + a[0][1]*b[1][0] + a[0][2]*b[2][0];
207 >  r01 = a[0][0]*b[0][1] + a[0][1]*b[1][1] + a[0][2]*b[2][1];
208 >  r02 = a[0][0]*b[0][2] + a[0][1]*b[1][2] + a[0][2]*b[2][2];
209 >  
210 >  r10 = a[1][0]*b[0][0] + a[1][1]*b[1][0] + a[1][2]*b[2][0];
211 >  r11 = a[1][0]*b[0][1] + a[1][1]*b[1][1] + a[1][2]*b[2][1];
212 >  r12 = a[1][0]*b[0][2] + a[1][1]*b[1][2] + a[1][2]*b[2][2];
213 >  
214 >  r20 = a[2][0]*b[0][0] + a[2][1]*b[1][0] + a[2][2]*b[2][0];
215 >  r21 = a[2][0]*b[0][1] + a[2][1]*b[1][1] + a[2][2]*b[2][1];
216 >  r22 = a[2][0]*b[0][2] + a[2][1]*b[1][2] + a[2][2]*b[2][2];
217 >  
218 >  c[0][0] = r00; c[0][1] = r01; c[0][2] = r02;
219 >  c[1][0] = r10; c[1][1] = r11; c[1][2] = r12;
220 >  c[2][0] = r20; c[2][1] = r21; c[2][2] = r22;
221   }
222  
223 + void SimInfo::matVecMul3(double m[3][3], double inVec[3], double outVec[3]) {
224 +  double a0, a1, a2;
225  
226 < void SimInfo::scaleBox(double scale) {
176 <  double theBox[9];
177 <  int i;
226 >  a0 = inVec[0];  a1 = inVec[1];  a2 = inVec[2];
227  
228 <  for(i=0; i<9; i++) theBox[i] = Hmat[i]*scale;
229 <
230 <  setBoxM(theBox);
182 <
228 >  outVec[0] = m[0][0]*a0 + m[0][1]*a1 + m[0][2]*a2;
229 >  outVec[1] = m[1][0]*a0 + m[1][1]*a1 + m[1][2]*a2;
230 >  outVec[2] = m[2][0]*a0 + m[2][1]*a1 + m[2][2]*a2;
231   }
232  
233 < void SimInfo::calcHmatI( void ) {
234 <
235 <  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]);
233 > void SimInfo::transposeMat3(double in[3][3], double out[3][3]) {
234 >  double temp[3][3];
235 >  int i, j;
236  
237 <  C[0][1] = -( Hmat[3]*Hmat[8]) + (Hmat[6]*Hmat[5]);
238 <  C[1][1] =  ( Hmat[0]*Hmat[8]) - (Hmat[6]*Hmat[2]);
239 <  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
209 <  
210 <  detHmat = 0.0;
211 <  for(i=0; i<3; i++) detHmat += Hmat[i] * C[i][0];
212 <
213 <  
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++){
219 <
220 <      HmatI[i] = C[j][k] / detHmat;
221 <      i++;
237 >  for (i = 0; i < 3; i++) {
238 >    for (j = 0; j < 3; j++) {
239 >      temp[j][i] = in[i][j];
240      }
241    }
242 <
243 <  // sanity check
244 <
227 <  for(i=0; i<3; i++){
228 <    for(j=0; j<3; j++){
229 <      
230 <      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 <      }
242 >  for (i = 0; i < 3; i++) {
243 >    for (j = 0; j < 3; j++) {
244 >      out[i][j] = temp[i][j];
245      }
246    }
247 + }
248 +  
249 + void SimInfo::printMat3(double A[3][3] ){
250  
251 <  cerr << "sanity => \n"
252 <       << sanity[0][0] << "\t" << sanity[0][1] << "\t" << sanity [0][2] << "\n"
253 <       << sanity[1][0] << "\t" << sanity[1][1] << "\t" << sanity [1][2] << "\n"
254 <       << sanity[2][0] << "\t" << sanity[2][1] << "\t" << sanity [2][2]
255 <       << "\n";
242 <    
251 >  std::cerr
252 >            << "[ " << A[0][0] << ", " << A[0][1] << ", " << A[0][2] << " ]\n"
253 >            << "[ " << A[1][0] << ", " << A[1][1] << ", " << A[1][2] << " ]\n"
254 >            << "[ " << A[2][0] << ", " << A[2][1] << ", " << A[2][2] << " ]\n";
255 > }
256  
257 <  // check to see if Hmat is orthorhombic
245 <  
246 <  smallDiag = Hmat[0];
247 <  if(smallDiag > Hmat[4]) smallDiag = Hmat[4];
248 <  if(smallDiag > Hmat[8]) smallDiag = Hmat[8];
249 <  tol = smallDiag * 1E-6;
257 > void SimInfo::printMat9(double A[9] ){
258  
259 <  orthoRhombic = 1;
260 <  for(i=0; (i<9) && orthoRhombic; i++){
261 <    
262 <    if( (i%4) ){ // ignore the diagonals (0, 4, and 8)
255 <      orthoRhombic = (Hmat[i] <= tol);
256 <    }
257 <  }
258 <    
259 >  std::cerr
260 >            << "[ " << A[0] << ", " << A[1] << ", " << A[2] << " ]\n"
261 >            << "[ " << A[3] << ", " << A[4] << ", " << A[5] << " ]\n"
262 >            << "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n";
263   }
264  
265   void SimInfo::calcBoxL( void ){
# Line 263 | Line 267 | void SimInfo::calcBoxL( void ){
267    double dx, dy, dz, dsq;
268    int i;
269  
270 <  // boxVol = h1 (dot) h2 (cross) h3
270 >  // boxVol = Determinant of Hmat
271  
272 <  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]) );
272 >  boxVol = matDet3( Hmat );
273  
272 –
274    // boxLx
275    
276 <  dx = Hmat[0]; dy = Hmat[1]; dz = Hmat[2];
276 >  dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
277    dsq = dx*dx + dy*dy + dz*dz;
278 <  boxLx = sqrt( dsq );
278 >  boxL[0] = sqrt( dsq );
279 >  maxCutoff = 0.5 * boxL[0];
280  
281    // boxLy
282    
283 <  dx = Hmat[3]; dy = Hmat[4]; dz = Hmat[5];
283 >  dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
284    dsq = dx*dx + dy*dy + dz*dz;
285 <  boxLy = sqrt( dsq );
285 >  boxL[1] = sqrt( dsq );
286 >  if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
287  
288    // boxLz
289    
290 <  dx = Hmat[6]; dy = Hmat[7]; dz = Hmat[8];
290 >  dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
291    dsq = dx*dx + dy*dy + dz*dz;
292 <  boxLz = sqrt( dsq );
293 <  
292 >  boxL[2] = sqrt( dsq );
293 >  if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
294 >
295   }
296  
297  
# Line 298 | Line 302 | void SimInfo::wrapVector( double thePos[3] ){
302  
303    if( !orthoRhombic ){
304      // calc the scaled coordinates.
305 +  
306 +
307 +    matVecMul3(HmatInv, thePos, scaled);
308      
309      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++)
310        scaled[i] -= roundMe(scaled[i]);
311      
312      // calc the wrapped real coordinates from the wrapped scaled coordinates
313      
314 <    for(i=0; i<3; i++)
315 <      thePos[i] =
315 <        scaled[0]*Hmat[i] + scaled[1]*Hmat[i+3] + scaled[2]*Hmat[i+6];
314 >    matVecMul3(Hmat, scaled, thePos);
315 >
316    }
317    else{
318      // calc the scaled coordinates.
319      
320      for(i=0; i<3; i++)
321 <      scaled[i] = thePos[i]*HmatI[i*4];
321 >      scaled[i] = thePos[i]*HmatInv[i][i];
322      
323      // wrap the scaled coordinates
324      
# Line 328 | Line 328 | void SimInfo::wrapVector( double thePos[3] ){
328      // calc the wrapped real coordinates from the wrapped scaled coordinates
329      
330      for(i=0; i<3; i++)
331 <      thePos[i] = scaled[i]*Hmat[i*4];
331 >      thePos[i] = scaled[i]*Hmat[i][i];
332    }
333      
334 –    
334   }
335  
336  
# Line 372 | Line 371 | void SimInfo::refreshSim(){
371    int isError;
372    int n_global;
373    int* excl;
374 <  
376 <  fInfo.rrf = 0.0;
377 <  fInfo.rt = 0.0;
374 >
375    fInfo.dielect = 0.0;
376  
380 –  fInfo.rlist = rList;
381 –  fInfo.rcut = rCut;
382 –
377    if( useDipole ){
384 –    fInfo.rrf = ecr;
385 –    fInfo.rt = ecr - est;
378      if( useReactionField )fInfo.dielect = dielectric;
379    }
380  
# Line 431 | Line 423 | void SimInfo::refreshSim(){
423  
424   }
425  
426 +
427 + void SimInfo::setRcut( double theRcut ){
428 +
429 +  if( !haveOrigRcut ){
430 +    haveOrigRcut = 1;
431 +    origRcut = theRcut;
432 +  }
433 +
434 +  rCut = theRcut;
435 +  checkCutOffs();
436 + }
437 +
438 + void SimInfo::setEcr( double theEcr ){
439 +
440 +  if( !haveOrigEcr ){
441 +    haveOrigEcr = 1;
442 +    origEcr = theEcr;
443 +  }
444 +
445 +  ecr = theEcr;
446 +  checkCutOffs();
447 + }
448 +
449 + void SimInfo::setEcr( double theEcr, double theEst ){
450 +
451 +  est = theEst;
452 +  setEcr( theEcr );
453 + }
454 +
455 +
456 + void SimInfo::checkCutOffs( void ){
457 +
458 +  int cutChanged = 0;
459 +
460 +  if( boxIsInit ){
461 +    
462 +    //we need to check cutOffs against the box
463 +    
464 +    if( maxCutoff > rCut ){
465 +      if( rCut < origRcut ){
466 +        rCut = origRcut;
467 +        if (rCut > maxCutoff) rCut = maxCutoff;
468 +        
469 +        sprintf( painCave.errMsg,
470 +                 "New Box size is setting the long range cutoff radius "
471 +                 "to %lf\n",
472 +                 rCut );
473 +        painCave.isFatal = 0;
474 +        simError();
475 +      }
476 +    }
477 +
478 +    if( maxCutoff > ecr ){
479 +      if( ecr < origEcr ){
480 +        rCut = origEcr;
481 +        if (ecr > maxCutoff) ecr = maxCutoff;
482 +        
483 +        sprintf( painCave.errMsg,
484 +                 "New Box size is setting the electrostaticCutoffRadius "
485 +                 "to %lf\n",
486 +                 ecr );
487 +        painCave.isFatal = 0;
488 +        simError();
489 +      }
490 +    }
491 +
492 +
493 +    if (rCut > maxCutoff) {
494 +      sprintf( painCave.errMsg,
495 +               "New Box size is setting the long range cutoff radius "
496 +               "to %lf\n",
497 +               maxCutoff );
498 +      painCave.isFatal = 0;
499 +      simError();
500 +      rCut = maxCutoff;
501 +    }
502 +
503 +    if( ecr > maxCutoff){
504 +      sprintf( painCave.errMsg,
505 +               "New Box size is setting the electrostaticCutoffRadius "
506 +               "to %lf\n",
507 +               maxCutoff  );
508 +      painCave.isFatal = 0;
509 +      simError();      
510 +      ecr = maxCutoff;
511 +    }
512 +
513 +    
514 +  }
515 +  
516 +
517 +  if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1;
518 +
519 +  // rlist is the 1.0 plus max( rcut, ecr )
520 +  
521 +  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
522 +
523 +  if( cutChanged ){
524 +    
525 +    notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
526 +  }
527 +
528 +  oldEcr = ecr;
529 +  oldRcut = rCut;
530 + }

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