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; |
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"; |
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(); |
95 |
|
} |
96 |
|
} |
97 |
|
|
98 |
< |
setFortranBoxSize(FortranHmat, FortranHmatI, &orthoRhombic); |
98 |
> |
setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic); |
99 |
|
|
100 |
< |
smallestBoxL = boxLx; |
101 |
< |
if (boxLy < smallestBoxL) smallestBoxL = boxLy; |
102 |
< |
if (boxLz < smallestBoxL) smallestBoxL = boxLz; |
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 |
|
|
109 |
|
maxCutoff ); |
110 |
|
painCave.isFatal = 0; |
111 |
|
simError(); |
110 |
– |
|
112 |
|
rList = maxCutoff; |
113 |
|
|
114 |
< |
sprintf( painCave.errMsg, |
114 |
< |
"New Box size is forcing cutoff radius down to %lf\n", |
115 |
< |
maxCutoff - 1.0 ); |
116 |
< |
painCave.isFatal = 0; |
117 |
< |
simError(); |
118 |
< |
|
119 |
< |
rCut = rList - 1.0; |
120 |
< |
|
121 |
< |
// list radius changed so we have to refresh the simulation structure. |
122 |
< |
refreshSim(); |
123 |
< |
} |
124 |
< |
|
125 |
< |
if (rCut > maxCutoff) { |
126 |
< |
sprintf( painCave.errMsg, |
127 |
< |
"New Box size is forcing cutoff radius down to %lf\n", |
128 |
< |
maxCutoff ); |
129 |
< |
painCave.isFatal = 0; |
130 |
< |
simError(); |
131 |
< |
|
132 |
< |
status = 0; |
133 |
< |
LJ_new_rcut(&rCut, &status); |
134 |
< |
if (status != 0) { |
114 |
> |
if (rCut > (rList - 1.0)) { |
115 |
|
sprintf( painCave.errMsg, |
116 |
< |
"Error in recomputing LJ shifts based on new rcut\n"); |
117 |
< |
painCave.isFatal = 1; |
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 |
< |
} |
122 |
> |
|
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 |
> |
// At least one of the radii changed, so we need a refresh: |
136 |
> |
refreshSim(); |
137 |
> |
} |
138 |
|
} |
139 |
|
|
140 |
|
|
150 |
|
double theBox[3][3]; |
151 |
|
int i, j; |
152 |
|
|
153 |
< |
cerr << "Scaling box by " << scale << "\n"; |
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; |
160 |
|
} |
161 |
|
|
162 |
|
void SimInfo::calcHmatInv( void ) { |
163 |
< |
|
163 |
> |
|
164 |
> |
int i,j; |
165 |
|
double smallDiag; |
166 |
|
double tol; |
167 |
|
double sanity[3][3]; |
171 |
|
// Check the inverse to make sure it is sane: |
172 |
|
|
173 |
|
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"; |
174 |
|
|
175 |
|
// check to see if Hmat is orthorhombic |
176 |
|
|
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; |
309 |
|
|
310 |
|
dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0]; |
311 |
|
dsq = dx*dx + dy*dy + dz*dz; |
312 |
< |
boxLx = sqrt( dsq ); |
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 |
< |
boxLy = sqrt( dsq ); |
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 |
< |
boxLz = sqrt( dsq ); |
324 |
> |
boxL[2] = sqrt( dsq ); |
325 |
|
|
326 |
|
} |
327 |
|
|