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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 618 by mmeineke, Tue Jul 15 21:34:56 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 27 | Line 34 | SimInfo::SimInfo(){
34    setTemp = 0;
35    thermalTime = 0.0;
36    rCut = 0.0;
37 +  ecr = 0.0;
38  
39    usePBC = 0;
40    useLJ = 0;
# Line 40 | Line 48 | void SimInfo::setBox(double newBox[3]) {
48   }
49  
50   void SimInfo::setBox(double newBox[3]) {
51 +  
52 +  int i, j;
53 +  double tempMat[3][3];
54  
55 <  double smallestBoxL, maxCutoff;
56 <  int status;
46 <  int i;
55 >  for(i=0; i<3; i++)
56 >    for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
57  
58 <  for(i=0; i<9; i++) Hmat[i] = 0.0;;
58 >  tempMat[0][0] = newBox[0];
59 >  tempMat[1][1] = newBox[1];
60 >  tempMat[2][2] = newBox[2];
61  
62 <  Hmat[0] = newBox[0];
51 <  Hmat[4] = newBox[1];
52 <  Hmat[8] = newBox[2];
62 >  setBoxM( tempMat );
63  
64 <  calcHmatI();
55 <  calcBoxL();
64 > }
65  
66 <  setFortranBoxSize(Hmat);
66 > void SimInfo::setBoxM( double theBox[3][3] ){
67 >  
68 >  int i, j, status;
69 >  double smallestBoxL, maxCutoff;
70 >  double FortranHmat[9]; // to preserve compatibility with Fortran the
71 >                         // ordering in the array is as follows:
72 >                         // [ 0 3 6 ]
73 >                         // [ 1 4 7 ]
74 >                         // [ 2 5 8 ]
75 >  double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
76  
59 –  smallestBoxL = boxLx;
60 –  if (boxLy < smallestBoxL) smallestBoxL = boxLy;
61 –  if (boxLz < smallestBoxL) smallestBoxL = boxLz;
77  
78 <  maxCutoff = smallestBoxL / 2.0;
78 >  for(i=0; i < 3; i++)
79 >    for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
80 >  
81 >  //  cerr
82 >  // << "setting Hmat ->\n"
83 >  // << "[ " << Hmat[0][0] << ", " << Hmat[0][1] << ", " << Hmat[0][2] << " ]\n"
84 >  // << "[ " << Hmat[1][0] << ", " << Hmat[1][1] << ", " << Hmat[1][2] << " ]\n"
85 >  // << "[ " << Hmat[2][0] << ", " << Hmat[2][1] << ", " << Hmat[2][2] << " ]\n";
86  
87 <  if (rList > maxCutoff) {
88 <    sprintf( painCave.errMsg,
67 <             "New Box size is forcing neighborlist radius down to %lf\n",
68 <             maxCutoff );
69 <    painCave.isFatal = 0;
70 <    simError();
87 >  calcBoxL();
88 >  calcHmatInv();
89  
90 <    rList = maxCutoff;
91 <
92 <    sprintf( painCave.errMsg,
93 <             "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();
90 >  for(i=0; i < 3; i++) {
91 >    for (j=0; j < 3; j++) {
92 >      FortranHmat[3*j + i] = Hmat[i][j];
93 >      FortranHmatInv[3*j + i] = HmatInv[i][j];
94      }
95    }
102 – }
96  
97 < 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);
97 >  setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic);
98  
99    smallestBoxL = boxLx;
100    if (boxLy < smallestBoxL) smallestBoxL = boxLy;
# Line 139 | Line 123 | void SimInfo::setBoxM( double theBox[9] ){
123      refreshSim();
124    }
125  
126 <  if (rCut > maxCutoff) {
126 >  if( ecr > maxCutoff ){
127 >
128      sprintf( painCave.errMsg,
129 <             "New Box size is forcing cutoff radius down to %lf\n",
129 >             "New Box size is forcing electrostatic cutoff radius "
130 >             "down to %lf\n",
131               maxCutoff );
132      painCave.isFatal = 0;
133      simError();
134  
135 <    status = 0;
136 <    LJ_new_rcut(&rCut, &status);
137 <    if (status != 0) {
138 <      sprintf( painCave.errMsg,
153 <               "Error in recomputing LJ shifts based on new rcut\n");
154 <      painCave.isFatal = 1;
155 <      simError();
156 <    }
135 >    ecr = maxCutoff;
136 >    est = 0.05 * ecr;
137 >
138 >    refreshSim();
139    }
140 +    
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 <  detHmat = 0.0;
168 <  for(i=0; i<3; i++) detHmat += Hmat[i] * C[i][0];
167 >  int i,j;
168 >  double smallDiag;
169 >  double tol;
170 >  double sanity[3][3];
171  
172 +  invertMat3( Hmat, HmatInv );
173 +
174 +  // Check the inverse to make sure it is sane:
175 +
176 +  matMul3( Hmat, HmatInv, sanity );
177 +    
178 +  // check to see if Hmat is orthorhombic
179    
180 <  // H^-1 = C^T / det(H)
181 <  
182 <  i=0;
183 <  for(j=0; j<3; j++){
198 <    for(k=0; k<3; k++){
180 >  smallDiag = Hmat[0][0];
181 >  if(smallDiag > Hmat[1][1]) smallDiag = Hmat[1][1];
182 >  if(smallDiag > Hmat[2][2]) smallDiag = Hmat[2][2];
183 >  tol = smallDiag * 1E-6;
184  
185 <      HmatI[i] = C[j][k] / detHmat;
186 <      i++;
185 >  orthoRhombic = 1;
186 >  
187 >  for (i = 0; i < 3; i++ ) {
188 >    for (j = 0 ; j < 3; j++) {
189 >      if (i != j) {
190 >        if (orthoRhombic) {
191 >          if (Hmat[i][j] >= tol) orthoRhombic = 0;
192 >        }        
193 >      }
194      }
195    }
196   }
197  
198 + double SimInfo::matDet3(double a[3][3]) {
199 +  int i, j, k;
200 +  double determinant;
201 +
202 +  determinant = 0.0;
203 +
204 +  for(i = 0; i < 3; i++) {
205 +    j = (i+1)%3;
206 +    k = (i+2)%3;
207 +
208 +    determinant += a[0][i] * (a[1][j]*a[2][k] - a[1][k]*a[2][j]);
209 +  }
210 +
211 +  return determinant;
212 + }
213 +
214 + void SimInfo::invertMat3(double a[3][3], double b[3][3]) {
215 +  
216 +  int  i, j, k, l, m, n;
217 +  double determinant;
218 +
219 +  determinant = matDet3( a );
220 +
221 +  if (determinant == 0.0) {
222 +    sprintf( painCave.errMsg,
223 +             "Can't invert a matrix with a zero determinant!\n");
224 +    painCave.isFatal = 1;
225 +    simError();
226 +  }
227 +
228 +  for (i=0; i < 3; i++) {
229 +    j = (i+1)%3;
230 +    k = (i+2)%3;
231 +    for(l = 0; l < 3; l++) {
232 +      m = (l+1)%3;
233 +      n = (l+2)%3;
234 +      
235 +      b[l][i] = (a[j][m]*a[k][n] - a[j][n]*a[k][m]) / determinant;
236 +    }
237 +  }
238 + }
239 +
240 + void SimInfo::matMul3(double a[3][3], double b[3][3], double c[3][3]) {
241 +  double r00, r01, r02, r10, r11, r12, r20, r21, r22;
242 +
243 +  r00 = a[0][0]*b[0][0] + a[0][1]*b[1][0] + a[0][2]*b[2][0];
244 +  r01 = a[0][0]*b[0][1] + a[0][1]*b[1][1] + a[0][2]*b[2][1];
245 +  r02 = a[0][0]*b[0][2] + a[0][1]*b[1][2] + a[0][2]*b[2][2];
246 +  
247 +  r10 = a[1][0]*b[0][0] + a[1][1]*b[1][0] + a[1][2]*b[2][0];
248 +  r11 = a[1][0]*b[0][1] + a[1][1]*b[1][1] + a[1][2]*b[2][1];
249 +  r12 = a[1][0]*b[0][2] + a[1][1]*b[1][2] + a[1][2]*b[2][2];
250 +  
251 +  r20 = a[2][0]*b[0][0] + a[2][1]*b[1][0] + a[2][2]*b[2][0];
252 +  r21 = a[2][0]*b[0][1] + a[2][1]*b[1][1] + a[2][2]*b[2][1];
253 +  r22 = a[2][0]*b[0][2] + a[2][1]*b[1][2] + a[2][2]*b[2][2];
254 +  
255 +  c[0][0] = r00; c[0][1] = r01; c[0][2] = r02;
256 +  c[1][0] = r10; c[1][1] = r11; c[1][2] = r12;
257 +  c[2][0] = r20; c[2][1] = r21; c[2][2] = r22;
258 + }
259 +
260 + void SimInfo::matVecMul3(double m[3][3], double inVec[3], double outVec[3]) {
261 +  double a0, a1, a2;
262 +
263 +  a0 = inVec[0];  a1 = inVec[1];  a2 = inVec[2];
264 +
265 +  outVec[0] = m[0][0]*a0 + m[0][1]*a1 + m[0][2]*a2;
266 +  outVec[1] = m[1][0]*a0 + m[1][1]*a1 + m[1][2]*a2;
267 +  outVec[2] = m[2][0]*a0 + m[2][1]*a1 + m[2][2]*a2;
268 + }
269 +
270 + void SimInfo::transposeMat3(double in[3][3], double out[3][3]) {
271 +  double temp[3][3];
272 +  int i, j;
273 +
274 +  for (i = 0; i < 3; i++) {
275 +    for (j = 0; j < 3; j++) {
276 +      temp[j][i] = in[i][j];
277 +    }
278 +  }
279 +  for (i = 0; i < 3; i++) {
280 +    for (j = 0; j < 3; j++) {
281 +      out[i][j] = temp[i][j];
282 +    }
283 +  }
284 + }
285 +  
286 + void SimInfo::printMat3(double A[3][3] ){
287 +
288 +  std::cerr
289 +            << "[ " << A[0][0] << ", " << A[0][1] << ", " << A[0][2] << " ]\n"
290 +            << "[ " << A[1][0] << ", " << A[1][1] << ", " << A[1][2] << " ]\n"
291 +            << "[ " << A[2][0] << ", " << A[2][1] << ", " << A[2][2] << " ]\n";
292 + }
293 +
294 + void SimInfo::printMat9(double A[9] ){
295 +
296 +  std::cerr
297 +            << "[ " << A[0] << ", " << A[1] << ", " << A[2] << " ]\n"
298 +            << "[ " << A[3] << ", " << A[4] << ", " << A[5] << " ]\n"
299 +            << "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n";
300 + }
301 +
302   void SimInfo::calcBoxL( void ){
303  
304    double dx, dy, dz, dsq;
305    int i;
306  
307 <  // boxVol = h1 (dot) h2 (cross) h3
307 >  // boxVol = Determinant of Hmat
308  
309 <  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]) );
309 >  boxVol = matDet3( Hmat );
310  
217 –
311    // boxLx
312    
313 <  dx = Hmat[0]; dy = Hmat[1]; dz = Hmat[2];
313 >  dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
314    dsq = dx*dx + dy*dy + dz*dz;
315    boxLx = sqrt( dsq );
316  
317    // boxLy
318    
319 <  dx = Hmat[3]; dy = Hmat[4]; dz = Hmat[5];
319 >  dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
320    dsq = dx*dx + dy*dy + dz*dz;
321    boxLy = sqrt( dsq );
322  
323    // boxLz
324    
325 <  dx = Hmat[6]; dy = Hmat[7]; dz = Hmat[8];
325 >  dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
326    dsq = dx*dx + dy*dy + dz*dz;
327    boxLz = sqrt( dsq );
328    
# Line 241 | Line 334 | void SimInfo::wrapVector( double thePos[3] ){
334    int i, j, k;
335    double scaled[3];
336  
337 <  // calc the scaled coordinates.
337 >  if( !orthoRhombic ){
338 >    // calc the scaled coordinates.
339    
246 –  for(i=0; i<3; i++)
247 –    scaled[i] = thePos[0]*Hmat[i] + thePos[1]*Hat[i+3] + thePos[3]*Hmat[i+6];
340  
341 <  // wrap the scaled coordinates
341 >    matVecMul3(HmatInv, thePos, scaled);
342 >    
343 >    for(i=0; i<3; i++)
344 >      scaled[i] -= roundMe(scaled[i]);
345 >    
346 >    // calc the wrapped real coordinates from the wrapped scaled coordinates
347 >    
348 >    matVecMul3(Hmat, scaled, thePos);
349  
350 <  for(i=0; i<3; i++)
351 <    scaled[i] -= (copysign(1,scaled[i]) * (int)(fabs(scaled[i]) + 0.5));
352 <  
353 <
350 >  }
351 >  else{
352 >    // calc the scaled coordinates.
353 >    
354 >    for(i=0; i<3; i++)
355 >      scaled[i] = thePos[i]*HmatInv[i][i];
356 >    
357 >    // wrap the scaled coordinates
358 >    
359 >    for(i=0; i<3; i++)
360 >      scaled[i] -= roundMe(scaled[i]);
361 >    
362 >    // calc the wrapped real coordinates from the wrapped scaled coordinates
363 >    
364 >    for(i=0; i<3; i++)
365 >      thePos[i] = scaled[i]*Hmat[i][i];
366 >  }
367 >    
368   }
369  
370  
# Line 297 | Line 410 | void SimInfo::refreshSim(){
410    fInfo.rt = 0.0;
411    fInfo.dielect = 0.0;
412  
300 –  fInfo.box[0] = box_x;
301 –  fInfo.box[1] = box_y;
302 –  fInfo.box[2] = box_z;
303 –
413    fInfo.rlist = rList;
414    fInfo.rcut = rCut;
415  

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