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#include <cstdlib> |
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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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|
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#include "SimInfo.hpp" |
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#define __C |
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#include "fSimulation.h" |
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#include "simError.h" |
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|
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#include "fortranWrappers.hpp" |
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|
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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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|
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|
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SimInfo* currentInfo; |
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|
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SimInfo::SimInfo(){ |
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excludes = NULL; |
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n_constraints = 0; |
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n_oriented = 0; |
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n_dipoles = 0; |
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ndf = 0; |
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ndfRaw = 0; |
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the_integrator = NULL; |
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setTemp = 0; |
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thermalTime = 0.0; |
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rCut = 0.0; |
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|
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usePBC = 0; |
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useLJ = 0; |
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useSticky = 0; |
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useDipole = 0; |
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useReactionField = 0; |
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useGB = 0; |
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useEAM = 0; |
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|
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wrapMeSimInfo( this ); |
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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; |
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double tempMat[9]; |
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|
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for(i=0; i<9; i++) tempMat[i] = 0.0;; |
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|
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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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|
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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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|
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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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|
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|
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|
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setFortranBoxSize(Hmat, HmatI, &orthoRhombic); |
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|
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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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|
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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 ); |
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painCave.isFatal = 0; |
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simError(); |
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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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} |
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} |
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} |
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|
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|
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void SimInfo::getBoxM (double theBox[9]) { |
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|
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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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|
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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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|
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cerr << "Scaling box by " << scale << "\n"; |
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|
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for(i=0; i<9; i++) theBox[i] = Hmat[i]*scale; |
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|
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setBoxM(theBox); |
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|
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} |
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|
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void SimInfo::calcHmatI( void ) { |
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|
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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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|
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// calculate the adjunct of Hmat; |
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|
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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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|
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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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|
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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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|
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// calcutlate the determinant of Hmat |
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|
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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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|
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|
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// H^-1 = C^T / det(H) |
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|
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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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|
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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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|
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// sanity check |
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|
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for(i=0; i<3; i++){ |
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for(j=0; j<3; j++){ |
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|
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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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|
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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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|
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|
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// check to see if Hmat is orthorhombic |
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|
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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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|
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orthoRhombic = 1; |
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for(i=0; (i<9) && orthoRhombic; i++){ |
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|
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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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} |
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|
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void SimInfo::calcBoxL( void ){ |
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|
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double dx, dy, dz, dsq; |
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int i; |
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|
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// boxVol = h1 (dot) h2 (cross) h3 |
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|
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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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|
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|
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// boxLx |
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|
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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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|
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// boxLy |
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|
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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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|
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// boxLz |
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|
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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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} |
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|
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|
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void SimInfo::wrapVector( double thePos[3] ){ |
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|
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int i, j, k; |
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double scaled[3]; |
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|
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if( !orthoRhombic ){ |
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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] = |
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thePos[0]*HmatI[i] + thePos[1]*HmatI[i+3] + thePos[3]*HmatI[i+6]; |
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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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|
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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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|
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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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|
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} |
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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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|
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ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints; |
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|
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#ifdef IS_MPI |
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MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
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#else |
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ndf = ndf_local; |
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#endif |
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|
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ndf = ndf - 3; |
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|
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return ndf; |
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} |
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|
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int SimInfo::getNDFraw() { |
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int ndfRaw_local, ndfRaw; |
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|
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// Raw degrees of freedom that we have to set |
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ndfRaw_local = 3 * n_atoms + 3 * n_oriented; |
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|
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#ifdef IS_MPI |
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MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
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#else |
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ndfRaw = ndfRaw_local; |
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#endif |
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|
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return ndfRaw; |
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} |
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|
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void SimInfo::refreshSim(){ |
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|
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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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|
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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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|
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fInfo.rlist = rList; |
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fInfo.rcut = rCut; |
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|
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if( useDipole ){ |
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fInfo.rrf = ecr; |
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fInfo.rt = ecr - est; |
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if( useReactionField )fInfo.dielect = dielectric; |
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} |
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|
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fInfo.SIM_uses_PBC = usePBC; |
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//fInfo.SIM_uses_LJ = 0; |
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fInfo.SIM_uses_LJ = useLJ; |
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fInfo.SIM_uses_sticky = useSticky; |
| 357 |
//fInfo.SIM_uses_sticky = 0; |
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fInfo.SIM_uses_dipoles = useDipole; |
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//fInfo.SIM_uses_dipoles = 0; |
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//fInfo.SIM_uses_RF = useReactionField; |
| 361 |
fInfo.SIM_uses_RF = 0; |
| 362 |
fInfo.SIM_uses_GB = useGB; |
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fInfo.SIM_uses_EAM = useEAM; |
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|
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excl = Exclude::getArray(); |
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|
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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; |
| 371 |
#endif |
| 372 |
|
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isError = 0; |
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|
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setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl, |
| 376 |
&nGlobalExcludes, globalExcludes, molMembershipArray, |
| 377 |
&isError ); |
| 378 |
|
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if( isError ){ |
| 380 |
|
| 381 |
sprintf( painCave.errMsg, |
| 382 |
"There was an error setting the simulation information in fortran.\n" ); |
| 383 |
painCave.isFatal = 1; |
| 384 |
simError(); |
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} |
| 386 |
|
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#ifdef IS_MPI |
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sprintf( checkPointMsg, |
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"succesfully sent the simulation information to fortran.\n"); |
| 390 |
MPIcheckPoint(); |
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#endif // is_mpi |
| 392 |
|
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this->ndf = this->getNDF(); |
| 394 |
this->ndfRaw = this->getNDFraw(); |
| 395 |
|
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} |
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|
