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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 588 by gezelter, Thu Jul 10 17:10:56 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 40 | Line 47 | void SimInfo::setBox(double newBox[3]) {
47   }
48  
49   void SimInfo::setBox(double newBox[3]) {
50 +  
51 +  int i, j;
52 +  double tempMat[3][3];
53  
54 <  double smallestBoxL, maxCutoff;
55 <  int status;
46 <  int i;
54 >  for(i=0; i<3; i++)
55 >    for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
56  
57 <  for(i=0; i<9; i++) Hmat[i] = 0.0;;
57 >  tempMat[0][0] = newBox[0];
58 >  tempMat[1][1] = newBox[1];
59 >  tempMat[2][2] = newBox[2];
60  
61 <  Hmat[0] = newBox[0];
51 <  Hmat[4] = newBox[1];
52 <  Hmat[8] = newBox[2];
61 >  setBoxM( tempMat );
62  
63 <  calcHmatI();
55 <  calcBoxL();
63 > }
64  
65 <  setFortranBoxSize(Hmat);
65 > void SimInfo::setBoxM( double theBox[3][3] ){
66 >  
67 >  int i, j, status;
68 >  double smallestBoxL, maxCutoff;
69 >  double FortranHmat[9]; // to preserve compatibility with Fortran the
70 >                         // ordering in the array is as follows:
71 >                         // [ 0 3 6 ]
72 >                         // [ 1 4 7 ]
73 >                         // [ 2 5 8 ]
74 >  double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
75  
59 –  smallestBoxL = boxLx;
60 –  if (boxLy < smallestBoxL) smallestBoxL = boxLy;
61 –  if (boxLz < smallestBoxL) smallestBoxL = boxLz;
76  
77 <  maxCutoff = smallestBoxL / 2.0;
77 >  for(i=0; i < 3; i++)
78 >    for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
79 >  
80 >  cerr
81 >    << "setting Hmat ->\n"
82 >    << "[ " << Hmat[0][0] << ", " << Hmat[0][1] << ", " << Hmat[0][2] << " ]\n"
83 >    << "[ " << Hmat[1][0] << ", " << Hmat[1][1] << ", " << Hmat[1][2] << " ]\n"
84 >    << "[ " << Hmat[2][0] << ", " << Hmat[2][1] << ", " << Hmat[2][2] << " ]\n";
85  
86 <  if (rList > maxCutoff) {
87 <    sprintf( painCave.errMsg,
67 <             "New Box size is forcing neighborlist radius down to %lf\n",
68 <             maxCutoff );
69 <    painCave.isFatal = 0;
70 <    simError();
86 >  calcBoxL();
87 >  calcHmatInv();
88  
89 <    rList = maxCutoff;
90 <
91 <    sprintf( painCave.errMsg,
92 <             "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();
89 >  for(i=0; i < 3; i++) {
90 >    for (j=0; j < 3; j++) {
91 >      FortranHmat[3*j + i] = Hmat[i][j];
92 >      FortranHmatInv[3*j + i] = HmatInv[i][j];
93      }
94    }
102 – }
95  
96 < 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);
96 >  setFortranBoxSize(FortranHmat, FortranHmatI, &orthoRhombic);
97  
98    smallestBoxL = boxLx;
99    if (boxLy < smallestBoxL) smallestBoxL = boxLy;
# Line 158 | Line 141 | void SimInfo::getBox(double theBox[9]) {
141   }
142  
143  
144 < void SimInfo::getBox(double theBox[9]) {
144 > void SimInfo::getBoxM (double theBox[3][3]) {
145  
146 <  int i;
147 <  for(i=0; i<9; i++) theBox[i] = Hmat[i];
146 >  int i, j;
147 >  for(i=0; i<3; i++)
148 >    for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j];
149   }
166 –
150  
168 – void SimInfo::calcHmatI( void ) {
151  
152 <  double C[3][3];
153 <  double detHmat;
154 <  int i, j, k;
152 > void SimInfo::scaleBox(double scale) {
153 >  double theBox[3][3];
154 >  int i, j;
155  
156 <  // calculate the adjunct of Hmat;
156 >  cerr << "Scaling box by " << scale << "\n";
157  
158 <  C[0][0] =  ( Hmat[4]*Hmat[8]) - (Hmat[7]*Hmat[5]);
159 <  C[1][0] = -( Hmat[1]*Hmat[8]) + (Hmat[7]*Hmat[2]);
178 <  C[2][0] =  ( Hmat[1]*Hmat[5]) - (Hmat[4]*Hmat[2]);
158 >  for(i=0; i<3; i++)
159 >    for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
160  
161 <  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]);
161 >  setBoxM(theBox);
162  
163 <  C[0][2] =  ( Hmat[3]*Hmat[7]) - (Hmat[6]*Hmat[4]);
185 <  C[1][2] = -( Hmat[0]*Hmat[7]) + (Hmat[6]*Hmat[1]);
186 <  C[2][2] =  ( Hmat[0]*Hmat[4]) - (Hmat[3]*Hmat[1]);
163 > }
164  
165 <  // calcutlate the determinant of Hmat
165 > void SimInfo::calcHmatInv( void ) {
166 >
167 >  double smallDiag;
168 >  double tol;
169 >  double sanity[3][3];
170 >
171 >  invertMat3( Hmat, HmatInv );
172 >
173 >  // Check the inverse to make sure it is sane:
174 >
175 >  matMul3( Hmat, HmatInv, sanity );
176 >
177 >  cerr << "sanity => \n"
178 >       << sanity[0][0] << "\t" << sanity[0][1] << "\t" << sanity [0][2] << "\n"
179 >       << sanity[1][0] << "\t" << sanity[1][1] << "\t" << sanity [1][2] << "\n"
180 >       << sanity[2][0] << "\t" << sanity[2][1] << "\t" << sanity [2][2]
181 >       << "\n";
182 >    
183 >  // check to see if Hmat is orthorhombic
184    
185 <  detHmat = 0.0;
186 <  for(i=0; i<3; i++) detHmat += Hmat[i] * C[i][0];
185 >  smallDiag = Hmat[0][0];
186 >  if(smallDiag > Hmat[1][1]) smallDiag = Hmat[1][1];
187 >  if(smallDiag > Hmat[2][2]) smallDiag = Hmat[2][2];
188 >  tol = smallDiag * 1E-6;
189  
190 +  orthoRhombic = 1;
191    
192 <  // H^-1 = C^T / det(H)
192 >  for (i = 0; i < 3; i++ ) {
193 >    for (j = 0 ; j < 3; j++) {
194 >      if (i != j) {
195 >        if (orthoRhombic) {
196 >          if (Hmat[i][j] >= tol) orthoRhombic = 0;
197 >        }        
198 >      }
199 >    }
200 >  }
201 > }
202 >
203 > double SimInfo::matDet3(double a[3][3]) {
204 >  int i, j, k;
205 >  double determinant;
206 >
207 >  determinant = 0.0;
208 >
209 >  for(i = 0; i < 3; i++) {
210 >    j = (i+1)%3;
211 >    k = (i+2)%3;
212 >
213 >    determinant += a[0][i] * (a[1][j]*a[2][k] - a[1][k]*a[2][j]);
214 >  }
215 >
216 >  return determinant;
217 > }
218 >
219 > void SimInfo::invertMat3(double a[3][3], double b[3][3]) {
220    
221 <  i=0;
222 <  for(j=0; j<3; j++){
198 <    for(k=0; k<3; k++){
221 >  int  i, j, k, l, m, n;
222 >  double determinant;
223  
224 <      HmatI[i] = C[j][k] / detHmat;
225 <      i++;
224 >  determinant = matDet3( a );
225 >
226 >  if (determinant == 0.0) {
227 >    sprintf( painCave.errMsg,
228 >             "Can't invert a matrix with a zero determinant!\n");
229 >    painCave.isFatal = 1;
230 >    simError();
231 >  }
232 >
233 >  for (i=0; i < 3; i++) {
234 >    j = (i+1)%3;
235 >    k = (i+2)%3;
236 >    for(l = 0; l < 3; l++) {
237 >      m = (l+1)%3;
238 >      n = (l+2)%3;
239 >      
240 >      b[l][i] = (a[j][m]*a[k][n] - a[j][n]*a[k][m]) / determinant;
241      }
242    }
243   }
244  
245 + void SimInfo::matMul3(double a[3][3], double b[3][3], double c[3][3]) {
246 +  double r00, r01, r02, r10, r11, r12, r20, r21, r22;
247 +
248 +  r00 = a[0][0]*b[0][0] + a[0][1]*b[1][0] + a[0][2]*b[2][0];
249 +  r01 = a[0][0]*b[0][1] + a[0][1]*b[1][1] + a[0][2]*b[2][1];
250 +  r02 = a[0][0]*b[0][2] + a[0][1]*b[1][2] + a[0][2]*b[2][2];
251 +  
252 +  r10 = a[1][0]*b[0][0] + a[1][1]*b[1][0] + a[1][2]*b[2][0];
253 +  r11 = a[1][0]*b[0][1] + a[1][1]*b[1][1] + a[1][2]*b[2][1];
254 +  r12 = a[1][0]*b[0][2] + a[1][1]*b[1][2] + a[1][2]*b[2][2];
255 +  
256 +  r20 = a[2][0]*b[0][0] + a[2][1]*b[1][0] + a[2][2]*b[2][0];
257 +  r21 = a[2][0]*b[0][1] + a[2][1]*b[1][1] + a[2][2]*b[2][1];
258 +  r22 = a[2][0]*b[0][2] + a[2][1]*b[1][2] + a[2][2]*b[2][2];
259 +  
260 +  c[0][0] = r00; c[0][1] = r01; c[0][2] = r02;
261 +  c[1][0] = r10; c[1][1] = r11; c[1][2] = r12;
262 +  c[2][0] = r20; c[2][1] = r21; c[2][2] = r22;
263 + }
264 +
265 + void SimInfo::matVecMul3(double m[3][3], double inVec[3], double outVec[3]) {
266 +  double a0, a1, a2;
267 +
268 +  a0 = inVec[0];  a1 = inVec[1];  a2 = inVec[2];
269 +
270 +  outVec[0] = m[0][0]*a0 + m[0][1]*a1 + m[0][2]*a2;
271 +  outVec[1] = m[1][0]*a0 + m[1][1]*a1 + m[1][2]*a2;
272 +  outVec[2] = m[2][0]*a0 + m[2][1]*a1 + m[2][2]*a2;
273 + }
274 +  
275   void SimInfo::calcBoxL( void ){
276  
277    double dx, dy, dz, dsq;
278    int i;
279  
280 <  // boxVol = h1 (dot) h2 (cross) h3
280 >  // boxVol = Determinant of Hmat
281  
282 <  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]) );
282 >  boxVol = matDet3( Hmat );
283  
217 –
284    // boxLx
285    
286 <  dx = Hmat[0]; dy = Hmat[1]; dz = Hmat[2];
286 >  dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
287    dsq = dx*dx + dy*dy + dz*dz;
288    boxLx = sqrt( dsq );
289  
290    // boxLy
291    
292 <  dx = Hmat[3]; dy = Hmat[4]; dz = Hmat[5];
292 >  dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
293    dsq = dx*dx + dy*dy + dz*dz;
294    boxLy = sqrt( dsq );
295  
296    // boxLz
297    
298 <  dx = Hmat[6]; dy = Hmat[7]; dz = Hmat[8];
298 >  dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
299    dsq = dx*dx + dy*dy + dz*dz;
300    boxLz = sqrt( dsq );
301    
# Line 241 | Line 307 | void SimInfo::wrapVector( double thePos[3] ){
307    int i, j, k;
308    double scaled[3];
309  
310 <  // calc the scaled coordinates.
310 >  if( !orthoRhombic ){
311 >    // calc the scaled coordinates.
312    
246 –  for(i=0; i<3; i++)
247 –    scaled[i] = thePos[0]*Hmat[i] + thePos[1]*Hat[i+3] + thePos[3]*Hmat[i+6];
313  
314 <  // wrap the scaled coordinates
314 >    matVecMul3(HmatInv, thePos, scaled);
315 >    
316 >    for(i=0; i<3; i++)
317 >      scaled[i] -= roundMe(scaled[i]);
318 >    
319 >    // calc the wrapped real coordinates from the wrapped scaled coordinates
320 >    
321 >    matVecMul3(Hmat, scaled, thePos);
322  
323 <  for(i=0; i<3; i++)
324 <    scaled[i] -= (copysign(1,scaled[i]) * (int)(fabs(scaled[i]) + 0.5));
325 <  
326 <
323 >  }
324 >  else{
325 >    // calc the scaled coordinates.
326 >    
327 >    for(i=0; i<3; i++)
328 >      scaled[i] = thePos[i]*HmatInv[i][i];
329 >    
330 >    // wrap the scaled coordinates
331 >    
332 >    for(i=0; i<3; i++)
333 >      scaled[i] -= roundMe(scaled[i]);
334 >    
335 >    // calc the wrapped real coordinates from the wrapped scaled coordinates
336 >    
337 >    for(i=0; i<3; i++)
338 >      thePos[i] = scaled[i]*Hmat[i][i];
339 >  }
340 >    
341   }
342  
343  
# Line 297 | Line 383 | void SimInfo::refreshSim(){
383    fInfo.rt = 0.0;
384    fInfo.dielect = 0.0;
385  
300 –  fInfo.box[0] = box_x;
301 –  fInfo.box[1] = box_y;
302 –  fInfo.box[2] = box_z;
303 –
386    fInfo.rlist = rList;
387    fInfo.rcut = rCut;
388  

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