48 |
|
|
49 |
|
void SimInfo::setBox(double newBox[3]) { |
50 |
|
|
51 |
< |
int i; |
52 |
< |
double tempMat[9]; |
51 |
> |
int i, j; |
52 |
> |
double tempMat[3][3]; |
53 |
|
|
54 |
< |
for(i=0; i<9; i++) tempMat[i] = 0.0;; |
54 |
> |
for(i=0; i<3; i++) |
55 |
> |
for (j=0; j<3; j++) tempMat[i][j] = 0.0;; |
56 |
|
|
57 |
< |
tempMat[0] = newBox[0]; |
58 |
< |
tempMat[4] = newBox[1]; |
59 |
< |
tempMat[8] = newBox[2]; |
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[9] ){ |
65 |
> |
void SimInfo::setBoxM( double theBox[3][3] ){ |
66 |
|
|
67 |
< |
int i, status; |
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 |
|
|
69 |
– |
for(i=0; i<9; i++) Hmat[i] = theBox[i]; |
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] << ", " << Hmat[3] << ", " << Hmat[6] << " ]\n" |
83 |
< |
<< "[ " << Hmat[1] << ", " << Hmat[4] << ", " << Hmat[7] << " ]\n" |
84 |
< |
<< "[ " << Hmat[2] << ", " << Hmat[5] << ", " << Hmat[8] << " ]\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 |
|
|
77 |
– |
calcHmatI(); |
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 |
< |
|
82 |
< |
setFortranBoxSize(Hmat, HmatI, &orthoRhombic); |
96 |
> |
setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic); |
97 |
|
|
98 |
|
smallestBoxL = boxLx; |
99 |
|
if (boxLy < smallestBoxL) smallestBoxL = boxLy; |
141 |
|
} |
142 |
|
|
143 |
|
|
144 |
< |
void SimInfo::getBoxM (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 |
|
} |
150 |
|
|
151 |
|
|
152 |
|
void SimInfo::scaleBox(double scale) { |
153 |
< |
double theBox[9]; |
154 |
< |
int i; |
153 |
> |
double theBox[3][3]; |
154 |
> |
int i, j; |
155 |
|
|
156 |
|
cerr << "Scaling box by " << scale << "\n"; |
157 |
|
|
158 |
< |
for(i=0; i<9; i++) theBox[i] = Hmat[i]*scale; |
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::calcHmatI( void ) { |
166 |
< |
|
167 |
< |
double C[3][3]; |
152 |
< |
double detHmat; |
153 |
< |
int i, j, k; |
165 |
> |
void SimInfo::calcHmatInv( void ) { |
166 |
> |
|
167 |
> |
int i,j; |
168 |
|
double smallDiag; |
169 |
|
double tol; |
170 |
|
double sanity[3][3]; |
171 |
|
|
172 |
< |
// calculate the adjunct of Hmat; |
172 |
> |
invertMat3( Hmat, HmatInv ); |
173 |
|
|
174 |
< |
C[0][0] = ( Hmat[4]*Hmat[8]) - (Hmat[7]*Hmat[5]); |
161 |
< |
C[1][0] = -( Hmat[1]*Hmat[8]) + (Hmat[7]*Hmat[2]); |
162 |
< |
C[2][0] = ( Hmat[1]*Hmat[5]) - (Hmat[4]*Hmat[2]); |
174 |
> |
// Check the inverse to make sure it is sane: |
175 |
|
|
176 |
< |
C[0][1] = -( Hmat[3]*Hmat[8]) + (Hmat[6]*Hmat[5]); |
177 |
< |
C[1][1] = ( Hmat[0]*Hmat[8]) - (Hmat[6]*Hmat[2]); |
178 |
< |
C[2][1] = -( Hmat[0]*Hmat[5]) + (Hmat[3]*Hmat[2]); |
167 |
< |
|
168 |
< |
C[0][2] = ( Hmat[3]*Hmat[7]) - (Hmat[6]*Hmat[4]); |
169 |
< |
C[1][2] = -( Hmat[0]*Hmat[7]) + (Hmat[6]*Hmat[1]); |
170 |
< |
C[2][2] = ( Hmat[0]*Hmat[4]) - (Hmat[3]*Hmat[1]); |
171 |
< |
|
172 |
< |
// calcutlate the determinant of Hmat |
176 |
> |
matMul3( Hmat, HmatInv, sanity ); |
177 |
> |
|
178 |
> |
// check to see if Hmat is orthorhombic |
179 |
|
|
180 |
< |
detHmat = 0.0; |
181 |
< |
for(i=0; i<3; i++) detHmat += Hmat[i] * C[i][0]; |
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 |
+ |
orthoRhombic = 1; |
186 |
|
|
187 |
< |
// H^-1 = C^T / det(H) |
188 |
< |
|
189 |
< |
i=0; |
190 |
< |
for(j=0; j<3; j++){ |
191 |
< |
for(k=0; k<3; k++){ |
192 |
< |
|
184 |
< |
HmatI[i] = C[j][k] / detHmat; |
185 |
< |
i++; |
186 |
< |
} |
187 |
< |
} |
188 |
< |
|
189 |
< |
// sanity check |
190 |
< |
|
191 |
< |
for(i=0; i<3; i++){ |
192 |
< |
for(j=0; j<3; j++){ |
193 |
< |
|
194 |
< |
sanity[i][j] = 0.0; |
195 |
< |
for(k=0; k<3; k++){ |
196 |
< |
sanity[i][j] += Hmat[3*k+i] * HmatI[3*j+k]; |
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 |
< |
cerr << "sanity => \n" |
199 |
< |
<< sanity[0][0] << "\t" << sanity[0][1] << "\t" << sanity [0][2] << "\n" |
200 |
< |
<< sanity[1][0] << "\t" << sanity[1][1] << "\t" << sanity [1][2] << "\n" |
204 |
< |
<< sanity[2][0] << "\t" << sanity[2][1] << "\t" << sanity [2][2] |
205 |
< |
<< "\n"; |
206 |
< |
|
198 |
> |
double SimInfo::matDet3(double a[3][3]) { |
199 |
> |
int i, j, k; |
200 |
> |
double determinant; |
201 |
|
|
202 |
< |
// check to see if Hmat is orthorhombic |
209 |
< |
|
210 |
< |
smallDiag = Hmat[0]; |
211 |
< |
if(smallDiag > Hmat[4]) smallDiag = Hmat[4]; |
212 |
< |
if(smallDiag > Hmat[8]) smallDiag = Hmat[8]; |
213 |
< |
tol = smallDiag * 1E-6; |
202 |
> |
determinant = 0.0; |
203 |
|
|
204 |
< |
orthoRhombic = 1; |
205 |
< |
for(i=0; (i<9) && orthoRhombic; i++){ |
206 |
< |
|
207 |
< |
if( (i%4) ){ // ignore the diagonals (0, 4, and 8) |
208 |
< |
orthoRhombic = (Hmat[i] <= tol); |
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 |
|
} |
222 |
– |
|
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]) ) |
233 |
< |
+ Hmat[1] * ( (Hmat[5]*Hmat[6]) - (Hmat[8]*Hmat[3]) ) |
234 |
< |
+ Hmat[2] * ( (Hmat[3]*Hmat[7]) - (Hmat[6]*Hmat[4]) ); |
309 |
> |
boxVol = matDet3( Hmat ); |
310 |
|
|
236 |
– |
|
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 |
|
|
336 |
|
|
337 |
|
if( !orthoRhombic ){ |
338 |
|
// calc the scaled coordinates. |
339 |
+ |
|
340 |
+ |
|
341 |
+ |
matVecMul3(HmatInv, thePos, scaled); |
342 |
|
|
343 |
|
for(i=0; i<3; i++) |
267 |
– |
scaled[i] = |
268 |
– |
thePos[0]*HmatI[i] + thePos[1]*HmatI[i+3] + thePos[3]*HmatI[i+6]; |
269 |
– |
|
270 |
– |
// wrap the scaled coordinates |
271 |
– |
|
272 |
– |
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 |
< |
for(i=0; i<3; i++) |
349 |
< |
thePos[i] = |
279 |
< |
scaled[0]*Hmat[i] + scaled[1]*Hmat[i+3] + scaled[2]*Hmat[i+6]; |
348 |
> |
matVecMul3(Hmat, scaled, thePos); |
349 |
> |
|
350 |
|
} |
351 |
|
else{ |
352 |
|
// calc the scaled coordinates. |
353 |
|
|
354 |
|
for(i=0; i<3; i++) |
355 |
< |
scaled[i] = thePos[i]*HmatI[i*4]; |
355 |
> |
scaled[i] = thePos[i]*HmatInv[i][i]; |
356 |
|
|
357 |
|
// wrap the scaled coordinates |
358 |
|
|
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*4]; |
365 |
> |
thePos[i] = scaled[i]*Hmat[i][i]; |
366 |
|
} |
367 |
|
|
298 |
– |
|
368 |
|
} |
369 |
|
|
370 |
|
|