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#include <cstring> |
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#include <cmath> |
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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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inline double roundMe( double x ){ |
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return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 ); |
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} |
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SimInfo* currentInfo; |
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SimInfo::SimInfo(){ |
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calcHmatI(); |
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calcBoxL(); |
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setFortranBoxSize(Hmat); |
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setFortranBoxSize(Hmat, HmatI, &orthoRhombic); |
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smallestBoxL = boxLx; |
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if (boxLy < smallestBoxL) smallestBoxL = boxLy; |
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calcHmatI(); |
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calcBoxL(); |
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setFortranBoxSize(Hmat); |
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setFortranBoxSize(Hmat, HmatI, &orthoRhombic); |
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smallestBoxL = boxLx; |
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if (boxLy < smallestBoxL) smallestBoxL = boxLy; |
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} |
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void SimInfo::getBox(double theBox[9]) { |
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void SimInfo::getBoxM (double theBox[9]) { |
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int i; |
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for(i=0; i<9; i++) theBox[i] = Hmat[i]; |
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} |
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void SimInfo::scaleBox(double scale) { |
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double theBox[9]; |
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int i; |
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for(i=0; i<9; i++) theBox[i] = Hmat[i]*scale; |
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setBoxM(theBox); |
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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; |
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double tol; |
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double sanity[3][3]; |
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// calculate the adjunct of Hmat; |
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HmatI[i] = C[j][k] / detHmat; |
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i++; |
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} |
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} |
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// sanity check |
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for(i=0; i<3; i++){ |
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for(j=0; j<3; j++){ |
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sanity[i][j] = 0.0; |
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for(k=0; k<3; k++){ |
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sanity[i][j] += Hmat[3*k+i] * HmatI[3*j+k]; |
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} |
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} |
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} |
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cerr << "sanity => \n" |
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<< sanity[0][0] << "\t" << sanity[0][1] << "\t" << sanity [0][2] << "\n" |
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<< sanity[1][0] << "\t" << sanity[1][1] << "\t" << sanity [1][2] << "\n" |
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<< sanity[2][0] << "\t" << sanity[2][1] << "\t" << sanity [2][2] |
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<< "\n"; |
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// check to see if Hmat is orthorhombic |
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smallDiag = Hmat[0]; |
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if(smallDiag > Hmat[4]) smallDiag = Hmat[4]; |
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if(smallDiag > Hmat[8]) smallDiag = Hmat[8]; |
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tol = smallDiag * 1E-6; |
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orthoRhombic = 1; |
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for(i=0; (i<9) && orthoRhombic; i++){ |
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if( (i%4) ){ // ignore the diagonals (0, 4, and 8) |
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orthoRhombic = (Hmat[i] <= tol); |
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} |
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} |
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} |
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void SimInfo::calcBoxL( void ){ |
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int i, j, k; |
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double scaled[3]; |
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// calc the scaled coordinates. |
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for(i=0; i<3; i++) |
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scaled[i] = thePos[0]*Hmat[i] + thePos[1]*Hat[i+3] + thePos[3]*Hmat[i+6]; |
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// wrap the scaled coordinates |
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for(i=0; i<3; i++) |
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scaled[i] -= (copysign(1,scaled[i]) * (int)(fabs(scaled[i]) + 0.5)); |
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if( !orthoRhombic ){ |
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// calc the scaled coordinates. |
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for(i=0; i<3; i++) |
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scaled[i] = |
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thePos[0]*HmatI[i] + thePos[1]*HmatI[i+3] + thePos[3]*HmatI[i+6]; |
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// wrap the scaled coordinates |
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for(i=0; i<3; i++) |
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scaled[i] -= roundMe(scaled[i]); |
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// calc the wrapped real coordinates from the wrapped scaled coordinates |
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for(i=0; i<3; i++) |
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thePos[i] = |
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scaled[0]*Hmat[i] + scaled[1]*Hmat[i+3] + scaled[2]*Hmat[i+6]; |
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} |
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else{ |
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// calc the scaled coordinates. |
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for(i=0; i<3; i++) |
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scaled[i] = thePos[i]*HmatI[i*4]; |
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// wrap the scaled coordinates |
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for(i=0; i<3; i++) |
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scaled[i] -= roundMe(scaled[i]); |
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// calc the wrapped real coordinates from the wrapped scaled coordinates |
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for(i=0; i<3; i++) |
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thePos[i] = scaled[i]*Hmat[i*4]; |
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} |
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} |
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fInfo.rt = 0.0; |
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fInfo.dielect = 0.0; |
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fInfo.box[0] = box_x; |
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fInfo.box[1] = box_y; |
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fInfo.box[2] = box_z; |
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fInfo.rlist = rList; |
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fInfo.rcut = rCut; |
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