54 |
|
calcHmatI(); |
55 |
|
calcBoxL(); |
56 |
|
|
57 |
< |
setFortranBoxSize(Hmat); |
57 |
> |
setFortranBoxSize(Hmat, HmatI, &orthoRhombic); |
58 |
|
|
59 |
|
smallestBoxL = boxLx; |
60 |
|
if (boxLy < smallestBoxL) smallestBoxL = boxLy; |
110 |
|
calcHmatI(); |
111 |
|
calcBoxL(); |
112 |
|
|
113 |
< |
setFortranBoxSize(Hmat); |
113 |
> |
setFortranBoxSize(Hmat, HmatI, &orthoRhombic); |
114 |
|
|
115 |
|
smallestBoxL = boxLx; |
116 |
|
if (boxLy < smallestBoxL) smallestBoxL = boxLy; |
170 |
|
double C[3][3]; |
171 |
|
double detHmat; |
172 |
|
int i, j, k; |
173 |
+ |
double smallDiag; |
174 |
+ |
double tol; |
175 |
+ |
double sanity[3][3]; |
176 |
|
|
177 |
|
// calculate the adjunct of Hmat; |
178 |
|
|
202 |
|
|
203 |
|
HmatI[i] = C[j][k] / detHmat; |
204 |
|
i++; |
205 |
+ |
} |
206 |
+ |
} |
207 |
+ |
|
208 |
+ |
// sanity check |
209 |
+ |
|
210 |
+ |
for(i=0; i<3; i++){ |
211 |
+ |
for(j=0; j<3; j++){ |
212 |
+ |
|
213 |
+ |
sanity[i][j] = 0.0; |
214 |
+ |
for(k=0; k<3; k++){ |
215 |
+ |
sanity[i][j] += Hmat[3*k+i] * HmatI[3*j+k]; |
216 |
+ |
} |
217 |
+ |
} |
218 |
+ |
} |
219 |
+ |
|
220 |
+ |
cerr << "sanity => \n" |
221 |
+ |
<< sanity[0][0] << "\t" << sanity[0][1] << "\t" << sanity [0][2] << "\n" |
222 |
+ |
<< sanity[1][0] << "\t" << sanity[1][1] << "\t" << sanity [1][2] << "\n" |
223 |
+ |
<< sanity[2][0] << "\t" << sanity[2][1] << "\t" << sanity [2][2] |
224 |
+ |
<< "\n"; |
225 |
+ |
|
226 |
+ |
|
227 |
+ |
// check to see if Hmat is orthorhombic |
228 |
+ |
|
229 |
+ |
smallDiag = Hmat[0]; |
230 |
+ |
if(smallDiag > Hmat[4]) smallDiag = Hmat[4]; |
231 |
+ |
if(smallDiag > Hmat[8]) smallDiag = Hmat[8]; |
232 |
+ |
tol = smallDiag * 1E-6; |
233 |
+ |
|
234 |
+ |
orthoRhombic = 1; |
235 |
+ |
for(i=0; (i<9) && orthoRhombic; i++){ |
236 |
+ |
|
237 |
+ |
if( (i%4) ){ // ignore the diagonals (0, 4, and 8) |
238 |
+ |
orthoRhombic = (Hmat[i] <= tol); |
239 |
|
} |
240 |
|
} |
241 |
+ |
|
242 |
|
} |
243 |
|
|
244 |
|
void SimInfo::calcBoxL( void ){ |
279 |
|
int i, j, k; |
280 |
|
double scaled[3]; |
281 |
|
|
282 |
< |
// calc the scaled coordinates. |
283 |
< |
|
284 |
< |
for(i=0; i<3; i++) |
285 |
< |
scaled[i] = thePos[0]*Hmat[i] + thePos[1]*Hat[i+3] + thePos[3]*Hmat[i+6]; |
286 |
< |
|
287 |
< |
// wrap the scaled coordinates |
288 |
< |
|
289 |
< |
for(i=0; i<3; i++) |
290 |
< |
scaled[i] -= (copysign(1,scaled[i]) * (int)(fabs(scaled[i]) + 0.5)); |
291 |
< |
|
292 |
< |
|
282 |
> |
if( !orthoRhombic ){ |
283 |
> |
// calc the scaled coordinates. |
284 |
> |
|
285 |
> |
for(i=0; i<3; i++) |
286 |
> |
scaled[i] = |
287 |
> |
thePos[0]*HmatI[i] + thePos[1]*HmatI[i+3] + thePos[3]*HmatI[i+6]; |
288 |
> |
|
289 |
> |
// wrap the scaled coordinates |
290 |
> |
|
291 |
> |
for(i=0; i<3; i++) |
292 |
> |
scaled[i] -= round(scaled[i]); |
293 |
> |
|
294 |
> |
// calc the wrapped real coordinates from the wrapped scaled coordinates |
295 |
> |
|
296 |
> |
for(i=0; i<3; i++) |
297 |
> |
thePos[i] = |
298 |
> |
scaled[0]*Hmat[i] + scaled[1]*Hmat[i+3] + scaled[3]*Hmat[i+6]; |
299 |
> |
} |
300 |
> |
else{ |
301 |
> |
// calc the scaled coordinates. |
302 |
> |
|
303 |
> |
for(i=0; i<3; i++) |
304 |
> |
scaled[i] = thePos[i]*HmatI[i*4]; |
305 |
> |
|
306 |
> |
// wrap the scaled coordinates |
307 |
> |
|
308 |
> |
for(i=0; i<3; i++) |
309 |
> |
scaled[i] -= round(scaled[i]); |
310 |
> |
|
311 |
> |
// calc the wrapped real coordinates from the wrapped scaled coordinates |
312 |
> |
|
313 |
> |
for(i=0; i<3; i++) |
314 |
> |
thePos[i] = scaled[i]*Hmat[i*4]; |
315 |
> |
} |
316 |
> |
|
317 |
> |
|
318 |
|
} |
319 |
|
|
320 |
|
|