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 490 by gezelter, Fri Apr 11 15:16:59 2003 UTC vs.
Revision 621 by gezelter, Wed Jul 16 02:11:02 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 13 | 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 26 | 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 39 | Line 49 | void SimInfo::setBox(double newBox[3]) {
49   }
50  
51   void SimInfo::setBox(double newBox[3]) {
52 <  double smallestBox, maxCutoff;
53 <  int status;
54 <  box_x = newBox[0];
45 <  box_y = newBox[1];
46 <  box_z = newBox[2];
47 <  setFortranBoxSize(newBox);
52 >  
53 >  int i, j;
54 >  double tempMat[3][3];
55  
56 <  smallestBox = box_x;
57 <  if (box_y < smallestBox) smallestBox = box_y;
51 <  if (box_z < smallestBox) smallestBox = box_z;
56 >  for(i=0; i<3; i++)
57 >    for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
58  
59 <  maxCutoff = smallestBox / 2.0;
59 >  tempMat[0][0] = newBox[0];
60 >  tempMat[1][1] = newBox[1];
61 >  tempMat[2][2] = newBox[2];
62  
63 +  setBoxM( tempMat );
64 +
65 + }
66 +
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 +
78 +
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 +  calcBoxL();
89 +  calcHmatInv();
90 +
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 +  }
97 +
98 +  setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic);
99 +
100 +  smallestBoxL = boxL[0];
101 +  if (boxL[1] < smallestBoxL) smallestBoxL = boxL[1];
102 +  if (boxL[2] > smallestBoxL) smallestBoxL = boxL[2];
103 +
104 +  maxCutoff = smallestBoxL / 2.0;
105 +
106    if (rList > maxCutoff) {
107      sprintf( painCave.errMsg,
108               "New Box size is forcing neighborlist radius down to %lf\n",
109               maxCutoff );
110      painCave.isFatal = 0;
111      simError();
61 –
112      rList = maxCutoff;
113  
114 <    sprintf( painCave.errMsg,
115 <             "New Box size is forcing cutoff radius down to %lf\n",
116 <             maxCutoff - 1.0 );
117 <    painCave.isFatal = 0;
118 <    simError();
114 >    if (rCut > (rList - 1.0)) {
115 >      sprintf( painCave.errMsg,
116 >               "New Box size is forcing LJ cutoff radius down to %lf\n",
117 >               rList - 1.0 );
118 >      painCave.isFatal = 0;
119 >      simError();
120 >      rCut = rList - 1.0;
121 >    }
122  
123 <    rCut = rList - 1.0;
123 >    if( ecr > (rList - 1.0) ){
124 >      sprintf( painCave.errMsg,
125 >               "New Box size is forcing electrostaticCutoffRadius "
126 >               "down to %lf\n"
127 >               "electrostaticSkinThickness is now %lf\n",
128 >               rList - 1.0, 0.05*(rList-1.0) );
129 >      painCave.isFatal = 0;
130 >      simError();      
131 >      ecr = maxCutoff;
132 >      est = 0.05 * ecr;
133 >    }
134  
135 <    // list radius changed so we have to refresh the simulation structure.
135 >    // At least one of the radii changed, so we need a refresh:
136      refreshSim();
137 +  }    
138 + }
139 +
140 +
141 + void SimInfo::getBoxM (double theBox[3][3]) {
142 +
143 +  int i, j;
144 +  for(i=0; i<3; i++)
145 +    for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j];
146 + }
147 +
148 +
149 + void SimInfo::scaleBox(double scale) {
150 +  double theBox[3][3];
151 +  int i, j;
152 +
153 +  // cerr << "Scaling box by " << scale << "\n";
154 +
155 +  for(i=0; i<3; i++)
156 +    for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
157 +
158 +  setBoxM(theBox);
159 +
160 + }
161 +
162 + void SimInfo::calcHmatInv( void ) {
163 +  
164 +  int i,j;
165 +  double smallDiag;
166 +  double tol;
167 +  double sanity[3][3];
168 +
169 +  invertMat3( Hmat, HmatInv );
170 +
171 +  // Check the inverse to make sure it is sane:
172 +
173 +  matMul3( Hmat, HmatInv, sanity );
174 +    
175 +  // check to see if Hmat is orthorhombic
176 +  
177 +  smallDiag = Hmat[0][0];
178 +  if(smallDiag > Hmat[1][1]) smallDiag = Hmat[1][1];
179 +  if(smallDiag > Hmat[2][2]) smallDiag = Hmat[2][2];
180 +  tol = smallDiag * 1E-6;
181 +
182 +  orthoRhombic = 1;
183 +  
184 +  for (i = 0; i < 3; i++ ) {
185 +    for (j = 0 ; j < 3; j++) {
186 +      if (i != j) {
187 +        if (orthoRhombic) {
188 +          if (Hmat[i][j] >= tol) orthoRhombic = 0;
189 +        }        
190 +      }
191 +    }
192    }
193 + }
194  
195 <  if (rCut > maxCutoff) {
195 > double SimInfo::matDet3(double a[3][3]) {
196 >  int i, j, k;
197 >  double determinant;
198 >
199 >  determinant = 0.0;
200 >
201 >  for(i = 0; i < 3; i++) {
202 >    j = (i+1)%3;
203 >    k = (i+2)%3;
204 >
205 >    determinant += a[0][i] * (a[1][j]*a[2][k] - a[1][k]*a[2][j]);
206 >  }
207 >
208 >  return determinant;
209 > }
210 >
211 > void SimInfo::invertMat3(double a[3][3], double b[3][3]) {
212 >  
213 >  int  i, j, k, l, m, n;
214 >  double determinant;
215 >
216 >  determinant = matDet3( a );
217 >
218 >  if (determinant == 0.0) {
219      sprintf( painCave.errMsg,
220 <             "New Box size is forcing cutoff radius down to %lf\n",
221 <             maxCutoff );
80 <    painCave.isFatal = 0;
220 >             "Can't invert a matrix with a zero determinant!\n");
221 >    painCave.isFatal = 1;
222      simError();
223 +  }
224  
225 <    status = 0;
226 <    LJ_new_rcut(&rCut, &status);
227 <    if (status != 0) {
228 <      sprintf( painCave.errMsg,
229 <               "Error in recomputing LJ shifts based on new rcut\n");
230 <      painCave.isFatal = 1;
231 <      simError();
225 >  for (i=0; i < 3; i++) {
226 >    j = (i+1)%3;
227 >    k = (i+2)%3;
228 >    for(l = 0; l < 3; l++) {
229 >      m = (l+1)%3;
230 >      n = (l+2)%3;
231 >      
232 >      b[l][i] = (a[j][m]*a[k][n] - a[j][n]*a[k][m]) / determinant;
233      }
234    }
235   }
236  
237 < void SimInfo::getBox(double theBox[3]) {
238 <  theBox[0] = box_x;
239 <  theBox[1] = box_y;
240 <  theBox[2] = box_z;
237 > void SimInfo::matMul3(double a[3][3], double b[3][3], double c[3][3]) {
238 >  double r00, r01, r02, r10, r11, r12, r20, r21, r22;
239 >
240 >  r00 = a[0][0]*b[0][0] + a[0][1]*b[1][0] + a[0][2]*b[2][0];
241 >  r01 = a[0][0]*b[0][1] + a[0][1]*b[1][1] + a[0][2]*b[2][1];
242 >  r02 = a[0][0]*b[0][2] + a[0][1]*b[1][2] + a[0][2]*b[2][2];
243 >  
244 >  r10 = a[1][0]*b[0][0] + a[1][1]*b[1][0] + a[1][2]*b[2][0];
245 >  r11 = a[1][0]*b[0][1] + a[1][1]*b[1][1] + a[1][2]*b[2][1];
246 >  r12 = a[1][0]*b[0][2] + a[1][1]*b[1][2] + a[1][2]*b[2][2];
247 >  
248 >  r20 = a[2][0]*b[0][0] + a[2][1]*b[1][0] + a[2][2]*b[2][0];
249 >  r21 = a[2][0]*b[0][1] + a[2][1]*b[1][1] + a[2][2]*b[2][1];
250 >  r22 = a[2][0]*b[0][2] + a[2][1]*b[1][2] + a[2][2]*b[2][2];
251 >  
252 >  c[0][0] = r00; c[0][1] = r01; c[0][2] = r02;
253 >  c[1][0] = r10; c[1][1] = r11; c[1][2] = r12;
254 >  c[2][0] = r20; c[2][1] = r21; c[2][2] = r22;
255   }
256 <
256 >
257 > void SimInfo::matVecMul3(double m[3][3], double inVec[3], double outVec[3]) {
258 >  double a0, a1, a2;
259 >
260 >  a0 = inVec[0];  a1 = inVec[1];  a2 = inVec[2];
261 >
262 >  outVec[0] = m[0][0]*a0 + m[0][1]*a1 + m[0][2]*a2;
263 >  outVec[1] = m[1][0]*a0 + m[1][1]*a1 + m[1][2]*a2;
264 >  outVec[2] = m[2][0]*a0 + m[2][1]*a1 + m[2][2]*a2;
265 > }
266 >
267 > void SimInfo::transposeMat3(double in[3][3], double out[3][3]) {
268 >  double temp[3][3];
269 >  int i, j;
270 >
271 >  for (i = 0; i < 3; i++) {
272 >    for (j = 0; j < 3; j++) {
273 >      temp[j][i] = in[i][j];
274 >    }
275 >  }
276 >  for (i = 0; i < 3; i++) {
277 >    for (j = 0; j < 3; j++) {
278 >      out[i][j] = temp[i][j];
279 >    }
280 >  }
281 > }
282 >  
283 > void SimInfo::printMat3(double A[3][3] ){
284 >
285 >  std::cerr
286 >            << "[ " << A[0][0] << ", " << A[0][1] << ", " << A[0][2] << " ]\n"
287 >            << "[ " << A[1][0] << ", " << A[1][1] << ", " << A[1][2] << " ]\n"
288 >            << "[ " << A[2][0] << ", " << A[2][1] << ", " << A[2][2] << " ]\n";
289 > }
290 >
291 > void SimInfo::printMat9(double A[9] ){
292 >
293 >  std::cerr
294 >            << "[ " << A[0] << ", " << A[1] << ", " << A[2] << " ]\n"
295 >            << "[ " << A[3] << ", " << A[4] << ", " << A[5] << " ]\n"
296 >            << "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n";
297 > }
298 >
299 > void SimInfo::calcBoxL( void ){
300 >
301 >  double dx, dy, dz, dsq;
302 >  int i;
303 >
304 >  // boxVol = Determinant of Hmat
305 >
306 >  boxVol = matDet3( Hmat );
307 >
308 >  // boxLx
309 >  
310 >  dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
311 >  dsq = dx*dx + dy*dy + dz*dz;
312 >  boxL[0] = sqrt( dsq );
313 >
314 >  // boxLy
315 >  
316 >  dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
317 >  dsq = dx*dx + dy*dy + dz*dz;
318 >  boxL[1] = sqrt( dsq );
319 >
320 >  // boxLz
321 >  
322 >  dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
323 >  dsq = dx*dx + dy*dy + dz*dz;
324 >  boxL[2] = sqrt( dsq );
325 >  
326 > }
327 >
328 >
329 > void SimInfo::wrapVector( double thePos[3] ){
330 >
331 >  int i, j, k;
332 >  double scaled[3];
333 >
334 >  if( !orthoRhombic ){
335 >    // calc the scaled coordinates.
336 >  
337 >
338 >    matVecMul3(HmatInv, thePos, scaled);
339 >    
340 >    for(i=0; i<3; i++)
341 >      scaled[i] -= roundMe(scaled[i]);
342 >    
343 >    // calc the wrapped real coordinates from the wrapped scaled coordinates
344 >    
345 >    matVecMul3(Hmat, scaled, thePos);
346 >
347 >  }
348 >  else{
349 >    // calc the scaled coordinates.
350 >    
351 >    for(i=0; i<3; i++)
352 >      scaled[i] = thePos[i]*HmatInv[i][i];
353 >    
354 >    // wrap the scaled coordinates
355 >    
356 >    for(i=0; i<3; i++)
357 >      scaled[i] -= roundMe(scaled[i]);
358 >    
359 >    // calc the wrapped real coordinates from the wrapped scaled coordinates
360 >    
361 >    for(i=0; i<3; i++)
362 >      thePos[i] = scaled[i]*Hmat[i][i];
363 >  }
364 >    
365 > }
366 >
367 >
368   int SimInfo::getNDF(){
369    int ndf_local, ndf;
370    
# Line 139 | Line 407 | void SimInfo::refreshSim(){
407    fInfo.rt = 0.0;
408    fInfo.dielect = 0.0;
409  
142 –  fInfo.box[0] = box_x;
143 –  fInfo.box[1] = box_y;
144 –  fInfo.box[2] = box_z;
145 –
410    fInfo.rlist = rList;
411    fInfo.rcut = rCut;
412  

Diff Legend

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