ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/group/trunk/OOPSE/libmdtools/SimInfo.cpp
(Generate patch)

Comparing trunk/OOPSE/libmdtools/SimInfo.cpp (file contents):
Revision 483 by gezelter, Wed Apr 9 04:06:43 2003 UTC vs.
Revision 588 by gezelter, Thu Jul 10 17:10:56 2003 UTC

# Line 1 | Line 1
1   #include <cstdlib>
2   #include <cstring>
3 + #include <cmath>
4  
5 + #include <iostream>
6 + using namespace std;
7  
8   #include "SimInfo.hpp"
9   #define __C
# Line 9 | Line 12 | SimInfo* currentInfo;
12  
13   #include "fortranWrappers.hpp"
14  
15 + #ifdef IS_MPI
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 35 | Line 47 | void SimInfo::setBox(double newBox[3]) {
47   }
48  
49   void SimInfo::setBox(double newBox[3]) {
50 <  double smallestBox, maxCutoff;
51 <  int status;
52 <  box_x = newBox[0];
41 <  box_y = newBox[1];
42 <  box_z = newBox[2];
43 <  setFortranBoxSize(newBox);
50 >  
51 >  int i, j;
52 >  double tempMat[3][3];
53  
54 <  smallestBox = box_x;
55 <  if (box_y < smallestBox) smallestBox = box_y;
47 <  if (box_z < smallestBox) smallestBox = box_z;
54 >  for(i=0; i<3; i++)
55 >    for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
56  
57 <  maxCutoff = smallestBox / 2.0;
57 >  tempMat[0][0] = newBox[0];
58 >  tempMat[1][1] = newBox[1];
59 >  tempMat[2][2] = newBox[2];
60  
61 +  setBoxM( tempMat );
62 +
63 + }
64 +
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 +
76 +
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 +  calcBoxL();
87 +  calcHmatInv();
88 +
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 +  }
95 +
96 +  setFortranBoxSize(FortranHmat, FortranHmatI, &orthoRhombic);
97 +
98 +  smallestBoxL = boxLx;
99 +  if (boxLy < smallestBoxL) smallestBoxL = boxLy;
100 +  if (boxLz < smallestBoxL) smallestBoxL = boxLz;
101 +
102 +  maxCutoff = smallestBoxL / 2.0;
103 +
104    if (rList > maxCutoff) {
105      sprintf( painCave.errMsg,
106               "New Box size is forcing neighborlist radius down to %lf\n",
# Line 86 | Line 139 | void SimInfo::setBox(double newBox[3]) {
139      }
140    }
141   }
142 +
143  
144 < void SimInfo::getBox(double theBox[3]) {
145 <  theBox[0] = box_x;
146 <  theBox[1] = box_y;
147 <  theBox[2] = box_z;
144 > void SimInfo::getBoxM (double theBox[3][3]) {
145 >
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   }
150 <
150 >
151 >
152 > void SimInfo::scaleBox(double scale) {
153 >  double theBox[3][3];
154 >  int i, j;
155 >
156 >  cerr << "Scaling box by " << scale << "\n";
157 >
158 >  for(i=0; i<3; i++)
159 >    for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
160 >
161 >  setBoxM(theBox);
162 >
163 > }
164 >
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 >  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 >  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 >  int  i, j, k, l, m, n;
222 >  double determinant;
223 >
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 = Determinant of Hmat
281 >
282 >  boxVol = matDet3( Hmat );
283 >
284 >  // boxLx
285 >  
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[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[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
299 >  dsq = dx*dx + dy*dy + dz*dz;
300 >  boxLz = sqrt( dsq );
301 >  
302 > }
303 >
304 >
305 > void SimInfo::wrapVector( double thePos[3] ){
306 >
307 >  int i, j, k;
308 >  double scaled[3];
309 >
310 >  if( !orthoRhombic ){
311 >    // calc the scaled coordinates.
312 >  
313 >
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 >  }
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 >
344   int SimInfo::getNDF(){
345    int ndf_local, ndf;
346    
# Line 128 | Line 376 | void SimInfo::refreshSim(){
376  
377    simtype fInfo;
378    int isError;
379 +  int n_global;
380    int* excl;
381    
382    fInfo.rrf = 0.0;
383    fInfo.rt = 0.0;
384    fInfo.dielect = 0.0;
385  
137 –  fInfo.box[0] = box_x;
138 –  fInfo.box[1] = box_y;
139 –  fInfo.box[2] = box_z;
140 –
386    fInfo.rlist = rList;
387    fInfo.rcut = rCut;
388  
# Line 161 | Line 406 | void SimInfo::refreshSim(){
406  
407    excl = Exclude::getArray();
408  
409 + #ifdef IS_MPI
410 +  n_global = mpiSim->getTotAtoms();
411 + #else
412 +  n_global = n_atoms;
413 + #endif
414 +
415    isError = 0;
416  
417 <  setFsimulation( &fInfo, &n_atoms, identArray, &n_exclude, excl,
417 >  setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl,
418                    &nGlobalExcludes, globalExcludes, molMembershipArray,
419                    &isError );
420  

Diff Legend

– Removed lines
+ Added lines
< Changed lines
> Changed lines