34 |
|
setTemp = 0; |
35 |
|
thermalTime = 0.0; |
36 |
|
rCut = 0.0; |
37 |
+ |
ecr = 0.0; |
38 |
|
|
39 |
|
usePBC = 0; |
40 |
|
useLJ = 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"; |
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 |
|
calcBoxL(); |
88 |
|
calcHmatInv(); |
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, |
136 |
< |
"Error in recomputing LJ shifts based on new rcut\n"); |
137 |
< |
painCave.isFatal = 1; |
138 |
< |
simError(); |
139 |
< |
} |
135 |
> |
ecr = maxCutoff; |
136 |
> |
est = 0.05 * ecr; |
137 |
> |
|
138 |
> |
refreshSim(); |
139 |
|
} |
140 |
+ |
|
141 |
|
} |
142 |
|
|
143 |
|
|
153 |
|
double theBox[3][3]; |
154 |
|
int i, j; |
155 |
|
|
156 |
< |
cerr << "Scaling box by " << scale << "\n"; |
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; |
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; |