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root/group/trunk/OOPSE/libmdtools/SimInfo.cpp
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Comparing trunk/OOPSE/libmdtools/SimInfo.cpp (file contents):
Revision 569 by mmeineke, Tue Jul 1 21:33:45 2003 UTC vs.
Revision 619 by mmeineke, Tue Jul 15 22:22:41 2003 UTC

# Line 2 | Line 2
2   #include <cstring>
3   #include <cmath>
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(){
# Line 27 | Line 34 | SimInfo::SimInfo(){
34    setTemp = 0;
35    thermalTime = 0.0;
36    rCut = 0.0;
37 +  ecr = 0.0;
38 +  est = 0.0;
39  
40    usePBC = 0;
41    useLJ = 0;
# Line 40 | Line 49 | void SimInfo::setBox(double newBox[3]) {
49   }
50  
51   void SimInfo::setBox(double newBox[3]) {
52 +  
53 +  int i, j;
54 +  double tempMat[3][3];
55  
56 <  double smallestBoxL, maxCutoff;
57 <  int status;
46 <  int i;
56 >  for(i=0; i<3; i++)
57 >    for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
58  
59 <  for(i=0; i<9; i++) Hmat[i] = 0.0;;
59 >  tempMat[0][0] = newBox[0];
60 >  tempMat[1][1] = newBox[1];
61 >  tempMat[2][2] = newBox[2];
62  
63 <  Hmat[0] = newBox[0];
51 <  Hmat[4] = newBox[1];
52 <  Hmat[8] = newBox[2];
63 >  setBoxM( tempMat );
64  
65 <  calcHmatI();
55 <  calcBoxL();
65 > }
66  
67 <  setFortranBoxSize(Hmat, HmatI, &orthoRhombic);
67 > void SimInfo::setBoxM( double theBox[3][3] ){
68 >  
69 >  int i, j, status;
70 >  double smallestBoxL, maxCutoff;
71 >  double FortranHmat[9]; // to preserve compatibility with Fortran the
72 >                         // ordering in the array is as follows:
73 >                         // [ 0 3 6 ]
74 >                         // [ 1 4 7 ]
75 >                         // [ 2 5 8 ]
76 >  double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
77  
59 –  smallestBoxL = boxLx;
60 –  if (boxLy < smallestBoxL) smallestBoxL = boxLy;
61 –  if (boxLz < smallestBoxL) smallestBoxL = boxLz;
78  
79 <  maxCutoff = smallestBoxL / 2.0;
79 >  for(i=0; i < 3; i++)
80 >    for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
81 >  
82 >  //  cerr
83 >  // << "setting Hmat ->\n"
84 >  // << "[ " << Hmat[0][0] << ", " << Hmat[0][1] << ", " << Hmat[0][2] << " ]\n"
85 >  // << "[ " << Hmat[1][0] << ", " << Hmat[1][1] << ", " << Hmat[1][2] << " ]\n"
86 >  // << "[ " << Hmat[2][0] << ", " << Hmat[2][1] << ", " << Hmat[2][2] << " ]\n";
87  
88 <  if (rList > maxCutoff) {
89 <    sprintf( painCave.errMsg,
67 <             "New Box size is forcing neighborlist radius down to %lf\n",
68 <             maxCutoff );
69 <    painCave.isFatal = 0;
70 <    simError();
88 >  calcBoxL();
89 >  calcHmatInv();
90  
91 <    rList = maxCutoff;
92 <
93 <    sprintf( painCave.errMsg,
94 <             "New Box size is forcing cutoff radius down to %lf\n",
76 <             maxCutoff - 1.0 );
77 <    painCave.isFatal = 0;
78 <    simError();
79 <
80 <    rCut = rList - 1.0;
81 <
82 <    // list radius changed so we have to refresh the simulation structure.
83 <    refreshSim();
84 <  }
85 <
86 <  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();
92 <
93 <    status = 0;
94 <    LJ_new_rcut(&rCut, &status);
95 <    if (status != 0) {
96 <      sprintf( painCave.errMsg,
97 <               "Error in recomputing LJ shifts based on new rcut\n");
98 <      painCave.isFatal = 1;
99 <      simError();
91 >  for(i=0; i < 3; i++) {
92 >    for (j=0; j < 3; j++) {
93 >      FortranHmat[3*j + i] = Hmat[i][j];
94 >      FortranHmatInv[3*j + i] = HmatInv[i][j];
95      }
96    }
102 – }
97  
98 < void SimInfo::setBoxM( double theBox[9] ){
105 <  
106 <  int i, status;
107 <  double smallestBoxL, maxCutoff;
108 <
109 <  for(i=0; i<9; i++) Hmat[i] = theBox[i];
110 <  calcHmatI();
111 <  calcBoxL();
112 <
113 <  setFortranBoxSize(Hmat, HmatI, &orthoRhombic);
98 >  setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic);
99  
100    smallestBoxL = boxLx;
101    if (boxLy < smallestBoxL) smallestBoxL = boxLy;
# Line 139 | Line 124 | void SimInfo::setBoxM( double theBox[9] ){
124      refreshSim();
125    }
126  
127 <  if (rCut > maxCutoff) {
127 >  if( ecr > maxCutoff ){
128 >
129      sprintf( painCave.errMsg,
130 <             "New Box size is forcing cutoff radius down to %lf\n",
130 >             "New Box size is forcing electrostatic cutoff radius "
131 >             "down to %lf\n",
132               maxCutoff );
133      painCave.isFatal = 0;
134      simError();
135  
136 <    status = 0;
137 <    LJ_new_rcut(&rCut, &status);
138 <    if (status != 0) {
139 <      sprintf( painCave.errMsg,
153 <               "Error in recomputing LJ shifts based on new rcut\n");
154 <      painCave.isFatal = 1;
155 <      simError();
156 <    }
136 >    ecr = maxCutoff;
137 >    est = 0.05 * ecr;
138 >
139 >    refreshSim();
140    }
141 +    
142   }
143  
144  
145 < void SimInfo::getBox(double theBox[9]) {
145 > void SimInfo::getBoxM (double theBox[3][3]) {
146  
147 <  int i;
148 <  for(i=0; i<9; i++) theBox[i] = Hmat[i];
147 >  int i, j;
148 >  for(i=0; i<3; i++)
149 >    for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j];
150   }
166 –
151  
168 – void SimInfo::calcHmatI( void ) {
152  
153 <  double C[3][3];
154 <  double detHmat;
155 <  int i, j, k;
173 <  double smallDiag;
174 <  double tol;
175 <  double sanity[3][3];
153 > void SimInfo::scaleBox(double scale) {
154 >  double theBox[3][3];
155 >  int i, j;
156  
157 <  // calculate the adjunct of Hmat;
157 >  // cerr << "Scaling box by " << scale << "\n";
158  
159 <  C[0][0] =  ( Hmat[4]*Hmat[8]) - (Hmat[7]*Hmat[5]);
160 <  C[1][0] = -( Hmat[1]*Hmat[8]) + (Hmat[7]*Hmat[2]);
181 <  C[2][0] =  ( Hmat[1]*Hmat[5]) - (Hmat[4]*Hmat[2]);
159 >  for(i=0; i<3; i++)
160 >    for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
161  
162 <  C[0][1] = -( Hmat[3]*Hmat[8]) + (Hmat[6]*Hmat[5]);
184 <  C[1][1] =  ( Hmat[0]*Hmat[8]) - (Hmat[6]*Hmat[2]);
185 <  C[2][1] = -( Hmat[0]*Hmat[5]) + (Hmat[3]*Hmat[2]);
162 >  setBoxM(theBox);
163  
164 <  C[0][2] =  ( Hmat[3]*Hmat[7]) - (Hmat[6]*Hmat[4]);
188 <  C[1][2] = -( Hmat[0]*Hmat[7]) + (Hmat[6]*Hmat[1]);
189 <  C[2][2] =  ( Hmat[0]*Hmat[4]) - (Hmat[3]*Hmat[1]);
164 > }
165  
166 <  // calcutlate the determinant of Hmat
166 > void SimInfo::calcHmatInv( void ) {
167    
168 <  detHmat = 0.0;
169 <  for(i=0; i<3; i++) detHmat += Hmat[i] * C[i][0];
168 >  int i,j;
169 >  double smallDiag;
170 >  double tol;
171 >  double sanity[3][3];
172  
173 <  
197 <  // H^-1 = C^T / det(H)
198 <  
199 <  i=0;
200 <  for(j=0; j<3; j++){
201 <    for(k=0; k<3; k++){
173 >  invertMat3( Hmat, HmatInv );
174  
175 <      HmatI[i] = C[j][k] / detHmat;
204 <      i++;
205 <    }
206 <  }
175 >  // Check the inverse to make sure it is sane:
176  
177 <  // sanity check
178 <
179 <  for(i=0; i<3; i++){
180 <    for(j=0; j<3; j++){
181 <      
182 <      sanity[i][j] = 0.0;
183 <      for(k=0; k<3; k++){
184 <        sanity[i][j] += Hmat[3*k+i] * HmatI[3*j+k];
177 >  matMul3( Hmat, HmatInv, sanity );
178 >    
179 >  // check to see if Hmat is orthorhombic
180 >  
181 >  smallDiag = Hmat[0][0];
182 >  if(smallDiag > Hmat[1][1]) smallDiag = Hmat[1][1];
183 >  if(smallDiag > Hmat[2][2]) smallDiag = Hmat[2][2];
184 >  tol = smallDiag * 1E-6;
185 >
186 >  orthoRhombic = 1;
187 >  
188 >  for (i = 0; i < 3; i++ ) {
189 >    for (j = 0 ; j < 3; j++) {
190 >      if (i != j) {
191 >        if (orthoRhombic) {
192 >          if (Hmat[i][j] >= tol) orthoRhombic = 0;
193 >        }        
194        }
195      }
196    }
197 + }
198  
199 <  cerr << "sanity => \n"
200 <       << sanity[0][0] << "\t" << sanity[0][1] << "\t" << sanity [0][2] << "\n"
201 <       << sanity[1][0] << "\t" << sanity[1][1] << "\t" << sanity [1][2] << "\n"
223 <       << sanity[2][0] << "\t" << sanity[2][1] << "\t" << sanity [2][2]
224 <       << "\n";
225 <    
199 > double SimInfo::matDet3(double a[3][3]) {
200 >  int i, j, k;
201 >  double determinant;
202  
203 <  // check to see if Hmat is orthorhombic
203 >  determinant = 0.0;
204 >
205 >  for(i = 0; i < 3; i++) {
206 >    j = (i+1)%3;
207 >    k = (i+2)%3;
208 >
209 >    determinant += a[0][i] * (a[1][j]*a[2][k] - a[1][k]*a[2][j]);
210 >  }
211 >
212 >  return determinant;
213 > }
214 >
215 > void SimInfo::invertMat3(double a[3][3], double b[3][3]) {
216    
217 <  smallDiag = Hmat[0];
218 <  if(smallDiag > Hmat[4]) smallDiag = Hmat[4];
231 <  if(smallDiag > Hmat[8]) smallDiag = Hmat[8];
232 <  tol = smallDiag * 1E-6;
217 >  int  i, j, k, l, m, n;
218 >  double determinant;
219  
220 <  orthoRhombic = 1;
221 <  for(i=0; (i<9) && orthoRhombic; i++){
222 <    
223 <    if( (i%4) ){ // ignore the diagonals (0, 4, and 8)
224 <      orthoRhombic = (Hmat[i] <= tol);
220 >  determinant = matDet3( a );
221 >
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 >  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    }
241 –    
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 +  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 +  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 + 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 +  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 + void SimInfo::printMat9(double A[9] ){
296 +
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 +
303   void SimInfo::calcBoxL( void ){
304  
305    double dx, dy, dz, dsq;
306    int i;
307  
308 <  // boxVol = h1 (dot) h2 (cross) h3
308 >  // boxVol = Determinant of Hmat
309  
310 <  boxVol = Hmat[0] * ( (Hmat[4]*Hmat[8]) - (Hmat[7]*Hmat[5]) )
252 <         + Hmat[1] * ( (Hmat[5]*Hmat[6]) - (Hmat[8]*Hmat[3]) )
253 <         + Hmat[2] * ( (Hmat[3]*Hmat[7]) - (Hmat[6]*Hmat[4]) );
310 >  boxVol = matDet3( Hmat );
311  
255 –
312    // boxLx
313    
314 <  dx = Hmat[0]; dy = Hmat[1]; dz = Hmat[2];
314 >  dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
315    dsq = dx*dx + dy*dy + dz*dz;
316    boxLx = sqrt( dsq );
317  
318    // boxLy
319    
320 <  dx = Hmat[3]; dy = Hmat[4]; dz = Hmat[5];
320 >  dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
321    dsq = dx*dx + dy*dy + dz*dz;
322    boxLy = sqrt( dsq );
323  
324    // boxLz
325    
326 <  dx = Hmat[6]; dy = Hmat[7]; dz = Hmat[8];
326 >  dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
327    dsq = dx*dx + dy*dy + dz*dz;
328    boxLz = sqrt( dsq );
329    
# Line 281 | Line 337 | void SimInfo::wrapVector( double thePos[3] ){
337  
338    if( !orthoRhombic ){
339      // calc the scaled coordinates.
340 +  
341 +
342 +    matVecMul3(HmatInv, thePos, scaled);
343      
344      for(i=0; i<3; i++)
345 <      scaled[i] =
287 <        thePos[0]*HmatI[i] + thePos[1]*HmatI[i+3] + thePos[3]*HmatI[i+6];
345 >      scaled[i] -= roundMe(scaled[i]);
346      
289 –    // wrap the scaled coordinates
290 –    
291 –    for(i=0; i<3; i++)
292 –      scaled[i] -= round(scaled[i]);
293 –    
347      // calc the wrapped real coordinates from the wrapped scaled coordinates
348      
349 <    for(i=0; i<3; i++)
350 <      thePos[i] =
298 <        scaled[0]*Hmat[i] + scaled[1]*Hmat[i+3] + scaled[3]*Hmat[i+6];
349 >    matVecMul3(Hmat, scaled, thePos);
350 >
351    }
352    else{
353      // calc the scaled coordinates.
354      
355      for(i=0; i<3; i++)
356 <      scaled[i] = thePos[i]*HmatI[i*4];
356 >      scaled[i] = thePos[i]*HmatInv[i][i];
357      
358      // wrap the scaled coordinates
359      
360      for(i=0; i<3; i++)
361 <      scaled[i] -= round(scaled[i]);
361 >      scaled[i] -= roundMe(scaled[i]);
362      
363      // calc the wrapped real coordinates from the wrapped scaled coordinates
364      
365      for(i=0; i<3; i++)
366 <      thePos[i] = scaled[i]*Hmat[i*4];
366 >      thePos[i] = scaled[i]*Hmat[i][i];
367    }
368      
317 –    
369   }
370  
371  
# Line 360 | Line 411 | void SimInfo::refreshSim(){
411    fInfo.rt = 0.0;
412    fInfo.dielect = 0.0;
413  
363 –  fInfo.box[0] = box_x;
364 –  fInfo.box[1] = box_y;
365 –  fInfo.box[2] = box_z;
366 –
414    fInfo.rlist = rList;
415    fInfo.rcut = rCut;
416  

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