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#include <cstdlib> |
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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 "fortranWrappers.hpp" |
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#ifdef IS_MPI |
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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 ); |
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} |
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SimInfo* currentInfo; |
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SimInfo::SimInfo(){ |
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} |
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void SimInfo::setBox(double newBox[3]) { |
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double smallestBox, maxCutoff; |
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int status; |
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box_x = newBox[0]; |
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box_y = newBox[1]; |
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box_z = newBox[2]; |
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setFortranBoxSize(newBox); |
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int i; |
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double tempMat[9]; |
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smallestBox = box_x; |
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if (box_y < smallestBox) smallestBox = box_y; |
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if (box_z < smallestBox) smallestBox = box_z; |
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for(i=0; i<9; i++) tempMat[i] = 0.0;; |
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maxCutoff = smallestBox / 2.0; |
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tempMat[0] = newBox[0]; |
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tempMat[4] = newBox[1]; |
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tempMat[8] = newBox[2]; |
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setBoxM( tempMat ); |
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|
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} |
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|
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void SimInfo::setBoxM( double theBox[9] ){ |
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|
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int i, status; |
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double smallestBoxL, maxCutoff; |
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for(i=0; i<9; i++) Hmat[i] = theBox[i]; |
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|
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cerr |
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<< "setting Hmat ->\n" |
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<< "[ " << Hmat[0] << ", " << Hmat[3] << ", " << Hmat[6] << " ]\n" |
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<< "[ " << Hmat[1] << ", " << Hmat[4] << ", " << Hmat[7] << " ]\n" |
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<< "[ " << Hmat[2] << ", " << Hmat[5] << ", " << Hmat[8] << " ]\n"; |
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|
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calcHmatI(); |
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calcBoxL(); |
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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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if (boxLz < smallestBoxL) smallestBoxL = boxLz; |
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maxCutoff = smallestBoxL / 2.0; |
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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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} |
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} |
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} |
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void SimInfo::getBox(double theBox[3]) { |
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theBox[0] = box_x; |
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theBox[1] = box_y; |
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theBox[2] = box_z; |
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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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cerr << "Scaling box by " << scale << "\n"; |
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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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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]); |
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C[0][1] = -( Hmat[3]*Hmat[8]) + (Hmat[6]*Hmat[5]); |
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C[1][1] = ( Hmat[0]*Hmat[8]) - (Hmat[6]*Hmat[2]); |
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C[2][1] = -( Hmat[0]*Hmat[5]) + (Hmat[3]*Hmat[2]); |
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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]); |
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C[2][2] = ( Hmat[0]*Hmat[4]) - (Hmat[3]*Hmat[1]); |
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// calcutlate the determinant of Hmat |
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detHmat = 0.0; |
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for(i=0; i<3; i++) detHmat += Hmat[i] * C[i][0]; |
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// H^-1 = C^T / det(H) |
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i=0; |
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for(j=0; j<3; j++){ |
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for(k=0; k<3; k++){ |
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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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double dx, dy, dz, dsq; |
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int i; |
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// boxVol = h1 (dot) h2 (cross) h3 |
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boxVol = Hmat[0] * ( (Hmat[4]*Hmat[8]) - (Hmat[7]*Hmat[5]) ) |
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+ Hmat[1] * ( (Hmat[5]*Hmat[6]) - (Hmat[8]*Hmat[3]) ) |
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+ Hmat[2] * ( (Hmat[3]*Hmat[7]) - (Hmat[6]*Hmat[4]) ); |
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// boxLx |
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dx = Hmat[0]; dy = Hmat[1]; dz = Hmat[2]; |
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dsq = dx*dx + dy*dy + dz*dz; |
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boxLx = sqrt( dsq ); |
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// boxLy |
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dx = Hmat[3]; dy = Hmat[4]; dz = Hmat[5]; |
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dsq = dx*dx + dy*dy + dz*dz; |
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boxLy = sqrt( dsq ); |
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// boxLz |
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dx = Hmat[6]; dy = Hmat[7]; dz = Hmat[8]; |
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dsq = dx*dx + dy*dy + dz*dz; |
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boxLz = sqrt( dsq ); |
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} |
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void SimInfo::wrapVector( double thePos[3] ){ |
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int i, j, k; |
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double scaled[3]; |
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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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|
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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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|
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// wrap the scaled coordinates |
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|
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for(i=0; i<3; i++) |
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scaled[i] -= roundMe(scaled[i]); |
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|
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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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int SimInfo::getNDF(){ |
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int ndf_local, ndf; |
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simtype fInfo; |
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int isError; |
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int n_global; |
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int* excl; |
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fInfo.rrf = 0.0; |
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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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excl = Exclude::getArray(); |
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#ifdef IS_MPI |
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n_global = mpiSim->getTotAtoms(); |
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#else |
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n_global = n_atoms; |
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#endif |
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|
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isError = 0; |
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setFsimulation( &fInfo, &n_atoms, identArray, &n_exclude, excl, |
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setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl, |
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&nGlobalExcludes, globalExcludes, molMembershipArray, |
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&isError ); |
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