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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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|
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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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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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double smallestBoxL, maxCutoff; |
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int status; |
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int i; |
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|
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for(i=0; i<9; i++) Hmat[i] = 0.0;; |
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|
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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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|
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calcHmatI(); |
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calcBoxL(); |
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|
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setFortranBoxSize(Hmat); |
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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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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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calcHmatI(); |
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calcBoxL(); |
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|
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setFortranBoxSize(Hmat); |
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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::getBox(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::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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|
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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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|
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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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// 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[0]*Hmat[i] + thePos[1]*Hat[i+3] + thePos[3]*Hmat[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] -= (copysign(1,scaled[i]) * (int)(fabs(scaled[i]) + 0.5)); |
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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.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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|
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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; |
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//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; |
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fInfo.SIM_uses_RF = 0; |
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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; |
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#endif |
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|
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isError = 0; |
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|
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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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|
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if( isError ){ |
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|
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sprintf( painCave.errMsg, |
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"There was an error setting the simulation information in fortran.\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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#ifdef IS_MPI |
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sprintf( checkPointMsg, |
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"succesfully sent the simulation information to fortran.\n"); |
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MPIcheckPoint(); |
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#endif // is_mpi |
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|
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this->ndf = this->getNDF(); |
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this->ndfRaw = this->getNDFraw(); |
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|
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} |
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|
