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#include <cstring> |
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#include <cmath> |
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|
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#include <iostream> |
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using namespace std; |
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#include "SimInfo.hpp" |
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#define __C |
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#include "mpiSimulation.hpp" |
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#endif |
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|
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inline double roundMe( double x ){ |
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return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 ); |
| 21 |
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} |
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|
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|
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SimInfo* currentInfo; |
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SimInfo::SimInfo(){ |
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} |
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|
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void SimInfo::setBox(double newBox[3]) { |
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|
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int i, j; |
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double tempMat[3][3]; |
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|
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double smallestBoxL, maxCutoff; |
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int status; |
| 46 |
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int i; |
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> |
for(i=0; i<3; i++) |
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for (j=0; j<3; j++) tempMat[i][j] = 0.0;; |
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|
| 57 |
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for(i=0; i<9; i++) Hmat[i] = 0.0;; |
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tempMat[0][0] = newBox[0]; |
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tempMat[1][1] = newBox[1]; |
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tempMat[2][2] = newBox[2]; |
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|
| 61 |
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Hmat[0] = newBox[0]; |
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Hmat[4] = newBox[1]; |
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Hmat[8] = newBox[2]; |
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setBoxM( tempMat ); |
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|
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calcHmatI(); |
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calcBoxL(); |
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} |
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|
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setFortranBoxSize(Hmat, HmatI, &orthoRhombic); |
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void SimInfo::setBoxM( double theBox[3][3] ){ |
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|
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int i, j, status; |
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double smallestBoxL, maxCutoff; |
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double FortranHmat[9]; // to preserve compatibility with Fortran the |
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// ordering in the array is as follows: |
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// [ 0 3 6 ] |
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// [ 1 4 7 ] |
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// [ 2 5 8 ] |
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double FortranHmatInv[9]; // the inverted Hmat (for Fortran); |
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|
| 59 |
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smallestBoxL = boxLx; |
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if (boxLy < smallestBoxL) smallestBoxL = boxLy; |
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if (boxLz < smallestBoxL) smallestBoxL = boxLz; |
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|
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maxCutoff = smallestBoxL / 2.0; |
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for(i=0; i < 3; i++) |
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for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j]; |
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|
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// cerr |
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// << "setting Hmat ->\n" |
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// << "[ " << Hmat[0][0] << ", " << Hmat[0][1] << ", " << Hmat[0][2] << " ]\n" |
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// << "[ " << Hmat[1][0] << ", " << Hmat[1][1] << ", " << Hmat[1][2] << " ]\n" |
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// << "[ " << Hmat[2][0] << ", " << Hmat[2][1] << ", " << Hmat[2][2] << " ]\n"; |
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|
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if (rList > maxCutoff) { |
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sprintf( painCave.errMsg, |
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"New Box size is forcing neighborlist radius down to %lf\n", |
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maxCutoff ); |
| 69 |
< |
painCave.isFatal = 0; |
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< |
simError(); |
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calcBoxL(); |
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> |
calcHmatInv(); |
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|
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< |
rList = maxCutoff; |
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|
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sprintf( painCave.errMsg, |
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"New Box size is forcing cutoff radius down to %lf\n", |
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maxCutoff - 1.0 ); |
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painCave.isFatal = 0; |
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simError(); |
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|
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rCut = rList - 1.0; |
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|
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// list radius changed so we have to refresh the simulation structure. |
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refreshSim(); |
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} |
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|
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< |
if (rCut > maxCutoff) { |
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sprintf( painCave.errMsg, |
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"New Box size is forcing cutoff radius down to %lf\n", |
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maxCutoff ); |
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painCave.isFatal = 0; |
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simError(); |
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|
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status = 0; |
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LJ_new_rcut(&rCut, &status); |
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if (status != 0) { |
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sprintf( painCave.errMsg, |
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"Error in recomputing LJ shifts based on new rcut\n"); |
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painCave.isFatal = 1; |
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simError(); |
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> |
for(i=0; i < 3; i++) { |
| 90 |
> |
for (j=0; j < 3; j++) { |
| 91 |
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FortranHmat[3*j + i] = Hmat[i][j]; |
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FortranHmatInv[3*j + i] = HmatInv[i][j]; |
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} |
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} |
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} |
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|
| 96 |
< |
void SimInfo::setBoxM( double theBox[9] ){ |
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|
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int i, status; |
| 107 |
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double smallestBoxL, maxCutoff; |
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|
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< |
for(i=0; i<9; i++) Hmat[i] = theBox[i]; |
| 110 |
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calcHmatI(); |
| 111 |
< |
calcBoxL(); |
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|
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< |
setFortranBoxSize(Hmat, HmatI, &orthoRhombic); |
| 96 |
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setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic); |
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smallestBoxL = boxLx; |
| 99 |
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if (boxLy < smallestBoxL) smallestBoxL = boxLy; |
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} |
| 142 |
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|
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|
| 144 |
< |
void SimInfo::getBox(double theBox[9]) { |
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> |
void SimInfo::getBoxM (double theBox[3][3]) { |
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|
| 146 |
< |
int i; |
| 147 |
< |
for(i=0; i<9; i++) theBox[i] = Hmat[i]; |
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> |
int i, j; |
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> |
for(i=0; i<3; i++) |
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for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]; |
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} |
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void SimInfo::calcHmatI( void ) { |
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double C[3][3]; |
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double detHmat; |
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< |
int i, j, k; |
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< |
double smallDiag; |
| 174 |
< |
double tol; |
| 175 |
< |
double sanity[3][3]; |
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> |
void SimInfo::scaleBox(double scale) { |
| 153 |
> |
double theBox[3][3]; |
| 154 |
> |
int i, j; |
| 155 |
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|
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< |
// calculate the adjunct of Hmat; |
| 156 |
> |
// cerr << "Scaling box by " << scale << "\n"; |
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|
| 158 |
< |
C[0][0] = ( Hmat[4]*Hmat[8]) - (Hmat[7]*Hmat[5]); |
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< |
C[1][0] = -( Hmat[1]*Hmat[8]) + (Hmat[7]*Hmat[2]); |
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< |
C[2][0] = ( Hmat[1]*Hmat[5]) - (Hmat[4]*Hmat[2]); |
| 158 |
> |
for(i=0; i<3; i++) |
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> |
for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale; |
| 160 |
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|
| 161 |
< |
C[0][1] = -( Hmat[3]*Hmat[8]) + (Hmat[6]*Hmat[5]); |
| 184 |
< |
C[1][1] = ( Hmat[0]*Hmat[8]) - (Hmat[6]*Hmat[2]); |
| 185 |
< |
C[2][1] = -( Hmat[0]*Hmat[5]) + (Hmat[3]*Hmat[2]); |
| 161 |
> |
setBoxM(theBox); |
| 162 |
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|
| 163 |
< |
C[0][2] = ( Hmat[3]*Hmat[7]) - (Hmat[6]*Hmat[4]); |
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< |
C[1][2] = -( Hmat[0]*Hmat[7]) + (Hmat[6]*Hmat[1]); |
| 189 |
< |
C[2][2] = ( Hmat[0]*Hmat[4]) - (Hmat[3]*Hmat[1]); |
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> |
} |
| 164 |
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|
| 165 |
< |
// calcutlate the determinant of Hmat |
| 165 |
> |
void SimInfo::calcHmatInv( void ) { |
| 166 |
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|
| 167 |
< |
detHmat = 0.0; |
| 168 |
< |
for(i=0; i<3; i++) detHmat += Hmat[i] * C[i][0]; |
| 167 |
> |
int i,j; |
| 168 |
> |
double smallDiag; |
| 169 |
> |
double tol; |
| 170 |
> |
double sanity[3][3]; |
| 171 |
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|
| 172 |
< |
|
| 197 |
< |
// H^-1 = C^T / det(H) |
| 198 |
< |
|
| 199 |
< |
i=0; |
| 200 |
< |
for(j=0; j<3; j++){ |
| 201 |
< |
for(k=0; k<3; k++){ |
| 172 |
> |
invertMat3( Hmat, HmatInv ); |
| 173 |
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|
| 174 |
< |
HmatI[i] = C[j][k] / detHmat; |
| 204 |
< |
i++; |
| 205 |
< |
} |
| 206 |
< |
} |
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> |
// Check the inverse to make sure it is sane: |
| 175 |
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|
| 176 |
< |
// 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"; |
| 176 |
> |
matMul3( Hmat, HmatInv, sanity ); |
| 177 |
|
|
| 226 |
– |
|
| 178 |
|
// check to see if Hmat is orthorhombic |
| 179 |
|
|
| 180 |
< |
smallDiag = Hmat[0]; |
| 181 |
< |
if(smallDiag > Hmat[4]) smallDiag = Hmat[4]; |
| 182 |
< |
if(smallDiag > Hmat[8]) smallDiag = Hmat[8]; |
| 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 |
< |
for(i=0; (i<9) && orthoRhombic; i++){ |
| 187 |
< |
|
| 188 |
< |
if( (i%4) ){ // ignore the diagonals (0, 4, and 8) |
| 189 |
< |
orthoRhombic = (Hmat[i] <= tol); |
| 186 |
> |
|
| 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 |
|
} |
| 241 |
– |
|
| 196 |
|
} |
| 197 |
|
|
| 198 |
+ |
double SimInfo::matDet3(double a[3][3]) { |
| 199 |
+ |
int i, j, k; |
| 200 |
+ |
double determinant; |
| 201 |
+ |
|
| 202 |
+ |
determinant = 0.0; |
| 203 |
+ |
|
| 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 |
+ |
} |
| 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]) ) |
| 252 |
< |
+ Hmat[1] * ( (Hmat[5]*Hmat[6]) - (Hmat[8]*Hmat[3]) ) |
| 253 |
< |
+ Hmat[2] * ( (Hmat[3]*Hmat[7]) - (Hmat[6]*Hmat[4]) ); |
| 309 |
> |
boxVol = matDet3( Hmat ); |
| 310 |
|
|
| 255 |
– |
|
| 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++) |
| 344 |
< |
scaled[i] = |
| 287 |
< |
thePos[0]*HmatI[i] + thePos[1]*HmatI[i+3] + thePos[3]*HmatI[i+6]; |
| 344 |
> |
scaled[i] -= roundMe(scaled[i]); |
| 345 |
|
|
| 289 |
– |
// wrap the scaled coordinates |
| 290 |
– |
|
| 291 |
– |
for(i=0; i<3; i++) |
| 292 |
– |
scaled[i] -= round(scaled[i]); |
| 293 |
– |
|
| 346 |
|
// calc the wrapped real coordinates from the wrapped scaled coordinates |
| 347 |
|
|
| 348 |
< |
for(i=0; i<3; i++) |
| 349 |
< |
thePos[i] = |
| 298 |
< |
scaled[0]*Hmat[i] + scaled[1]*Hmat[i+3] + scaled[3]*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 |
|
|
| 359 |
|
for(i=0; i<3; i++) |
| 360 |
< |
scaled[i] -= round(scaled[i]); |
| 360 |
> |
scaled[i] -= roundMe(scaled[i]); |
| 361 |
|
|
| 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 |
|
|
| 317 |
– |
|
| 368 |
|
} |
| 369 |
|
|
| 370 |
|
|
| 410 |
|
fInfo.rt = 0.0; |
| 411 |
|
fInfo.dielect = 0.0; |
| 412 |
|
|
| 363 |
– |
fInfo.box[0] = box_x; |
| 364 |
– |
fInfo.box[1] = box_y; |
| 365 |
– |
fInfo.box[2] = box_z; |
| 366 |
– |
|
| 413 |
|
fInfo.rlist = rList; |
| 414 |
|
fInfo.rcut = rCut; |
| 415 |
|
|
