# | Line 34 | 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 77 | Line 79 | void SimInfo::setBoxM( double theBox[3][3] ){ | |
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(); | |
# | Line 122 | Line 124 | void SimInfo::setBoxM( double theBox[3][3] ){ | |
124 | refreshSim(); | |
125 | } | |
126 | ||
127 | < | if (rCut > maxCutoff) { |
127 | > | if( ecr > maxCutoff ){ |
128 | > | |
129 | sprintf( painCave.errMsg, | |
130 | < | "New Box size is forcing cutoff radius down to %lf\n", |
130 | > | "New Box size is forcing electrostatic cutoff radius " |
131 | > | "down to %lf\n", |
132 | maxCutoff ); | |
133 | painCave.isFatal = 0; | |
134 | simError(); | |
135 | ||
136 | < | status = 0; |
137 | < | LJ_new_rcut(&rCut, &status); |
138 | < | if (status != 0) { |
139 | < | sprintf( painCave.errMsg, |
136 | < | "Error in recomputing LJ shifts based on new rcut\n"); |
137 | < | painCave.isFatal = 1; |
138 | < | simError(); |
139 | < | } |
136 | > | ecr = maxCutoff; |
137 | > | est = 0.05 * ecr; |
138 | > | |
139 | > | refreshSim(); |
140 | } | |
141 | + | |
142 | } | |
143 | ||
144 | ||
# | Line 153 | Line 154 | void SimInfo::scaleBox(double scale) { | |
154 | double theBox[3][3]; | |
155 | int i, j; | |
156 | ||
157 | < | cerr << "Scaling box by " << scale << "\n"; |
157 | > | // cerr << "Scaling box by " << scale << "\n"; |
158 | ||
159 | for(i=0; i<3; i++) | |
160 | for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale; | |
# | Line 266 | Line 267 | void SimInfo::matVecMul3(double m[3][3], double inVec[ | |
267 | outVec[1] = m[1][0]*a0 + m[1][1]*a1 + m[1][2]*a2; | |
268 | outVec[2] = m[2][0]*a0 + m[2][1]*a1 + m[2][2]*a2; | |
269 | } | |
270 | + | |
271 | + | void SimInfo::transposeMat3(double in[3][3], double out[3][3]) { |
272 | + | double temp[3][3]; |
273 | + | int i, j; |
274 | + | |
275 | + | for (i = 0; i < 3; i++) { |
276 | + | for (j = 0; j < 3; j++) { |
277 | + | temp[j][i] = in[i][j]; |
278 | + | } |
279 | + | } |
280 | + | for (i = 0; i < 3; i++) { |
281 | + | for (j = 0; j < 3; j++) { |
282 | + | out[i][j] = temp[i][j]; |
283 | + | } |
284 | + | } |
285 | + | } |
286 | ||
287 | + | void SimInfo::printMat3(double A[3][3] ){ |
288 | + | |
289 | + | std::cerr |
290 | + | << "[ " << A[0][0] << ", " << A[0][1] << ", " << A[0][2] << " ]\n" |
291 | + | << "[ " << A[1][0] << ", " << A[1][1] << ", " << A[1][2] << " ]\n" |
292 | + | << "[ " << A[2][0] << ", " << A[2][1] << ", " << A[2][2] << " ]\n"; |
293 | + | } |
294 | + | |
295 | + | void SimInfo::printMat9(double A[9] ){ |
296 | + | |
297 | + | std::cerr |
298 | + | << "[ " << A[0] << ", " << A[1] << ", " << A[2] << " ]\n" |
299 | + | << "[ " << A[3] << ", " << A[4] << ", " << A[5] << " ]\n" |
300 | + | << "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n"; |
301 | + | } |
302 | + | |
303 | void SimInfo::calcBoxL( void ){ | |
304 | ||
305 | double dx, dy, dz, dsq; |
– | Removed lines |
+ | Added lines |
< | Changed lines |
> | Changed lines |