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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 ); |
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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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setTemp = 0; |
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thermalTime = 0.0; |
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rCut = 0.0; |
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ecr = 0.0; |
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est = 0.0; |
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|
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usePBC = 0; |
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useLJ = 0; |
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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; |
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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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|
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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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|
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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); |
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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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|
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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 ); |
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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++) { |
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for (j=0; j < 3; j++) { |
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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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|
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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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setFortranBoxSize(FortranHmat, FortranHmatInv, &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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smallestBoxL = boxL[0]; |
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if (boxL[1] < smallestBoxL) smallestBoxL = boxL[1]; |
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if (boxL[2] > smallestBoxL) smallestBoxL = boxL[2]; |
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|
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maxCutoff = smallestBoxL / 2.0; |
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|
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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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if (rCut > (rList - 1.0)) { |
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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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"New Box size is forcing LJ cutoff radius down to %lf\n", |
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rList - 1.0 ); |
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painCave.isFatal = 0; |
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simError(); |
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rCut = rList - 1.0; |
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} |
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} |
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|
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if( ecr > (rList - 1.0) ){ |
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sprintf( painCave.errMsg, |
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"New Box size is forcing electrostaticCutoffRadius " |
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"down to %lf\n" |
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"electrostaticSkinThickness is now %lf\n", |
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rList - 1.0, 0.05*(rList-1.0) ); |
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painCave.isFatal = 0; |
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simError(); |
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ecr = maxCutoff; |
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est = 0.05 * ecr; |
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} |
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|
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// At least one of the radii changed, so we need a refresh: |
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refreshSim(); |
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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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void SimInfo::getBoxM (double theBox[3][3]) { |
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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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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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|
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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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void SimInfo::scaleBox(double scale) { |
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double theBox[3][3]; |
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int i, j; |
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|
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// calculate the adjunct of Hmat; |
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// cerr << "Scaling box by " << scale << "\n"; |
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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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for(i=0; i<3; i++) |
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> |
for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale; |
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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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> |
setBoxM(theBox); |
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|
|
160 |
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C[0][2] = ( Hmat[3]*Hmat[7]) - (Hmat[6]*Hmat[4]); |
185 |
< |
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]); |
160 |
> |
} |
161 |
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|
162 |
< |
// calcutlate the determinant of Hmat |
162 |
> |
void SimInfo::calcHmatInv( void ) { |
163 |
|
|
164 |
< |
detHmat = 0.0; |
165 |
< |
for(i=0; i<3; i++) detHmat += Hmat[i] * C[i][0]; |
164 |
> |
int i,j; |
165 |
> |
double smallDiag; |
166 |
> |
double tol; |
167 |
> |
double sanity[3][3]; |
168 |
|
|
169 |
< |
|
194 |
< |
// H^-1 = C^T / det(H) |
195 |
< |
|
196 |
< |
i=0; |
197 |
< |
for(j=0; j<3; j++){ |
198 |
< |
for(k=0; k<3; k++){ |
169 |
> |
invertMat3( Hmat, HmatInv ); |
170 |
|
|
171 |
< |
HmatI[i] = C[j][k] / detHmat; |
172 |
< |
i++; |
171 |
> |
// Check the inverse to make sure it is sane: |
172 |
> |
|
173 |
> |
matMul3( Hmat, HmatInv, sanity ); |
174 |
> |
|
175 |
> |
// check to see if Hmat is orthorhombic |
176 |
> |
|
177 |
> |
smallDiag = Hmat[0][0]; |
178 |
> |
if(smallDiag > Hmat[1][1]) smallDiag = Hmat[1][1]; |
179 |
> |
if(smallDiag > Hmat[2][2]) smallDiag = Hmat[2][2]; |
180 |
> |
tol = smallDiag * 1E-6; |
181 |
> |
|
182 |
> |
orthoRhombic = 1; |
183 |
> |
|
184 |
> |
for (i = 0; i < 3; i++ ) { |
185 |
> |
for (j = 0 ; j < 3; j++) { |
186 |
> |
if (i != j) { |
187 |
> |
if (orthoRhombic) { |
188 |
> |
if (Hmat[i][j] >= tol) orthoRhombic = 0; |
189 |
> |
} |
190 |
> |
} |
191 |
|
} |
192 |
|
} |
193 |
|
} |
194 |
|
|
195 |
+ |
double SimInfo::matDet3(double a[3][3]) { |
196 |
+ |
int i, j, k; |
197 |
+ |
double determinant; |
198 |
+ |
|
199 |
+ |
determinant = 0.0; |
200 |
+ |
|
201 |
+ |
for(i = 0; i < 3; i++) { |
202 |
+ |
j = (i+1)%3; |
203 |
+ |
k = (i+2)%3; |
204 |
+ |
|
205 |
+ |
determinant += a[0][i] * (a[1][j]*a[2][k] - a[1][k]*a[2][j]); |
206 |
+ |
} |
207 |
+ |
|
208 |
+ |
return determinant; |
209 |
+ |
} |
210 |
+ |
|
211 |
+ |
void SimInfo::invertMat3(double a[3][3], double b[3][3]) { |
212 |
+ |
|
213 |
+ |
int i, j, k, l, m, n; |
214 |
+ |
double determinant; |
215 |
+ |
|
216 |
+ |
determinant = matDet3( a ); |
217 |
+ |
|
218 |
+ |
if (determinant == 0.0) { |
219 |
+ |
sprintf( painCave.errMsg, |
220 |
+ |
"Can't invert a matrix with a zero determinant!\n"); |
221 |
+ |
painCave.isFatal = 1; |
222 |
+ |
simError(); |
223 |
+ |
} |
224 |
+ |
|
225 |
+ |
for (i=0; i < 3; i++) { |
226 |
+ |
j = (i+1)%3; |
227 |
+ |
k = (i+2)%3; |
228 |
+ |
for(l = 0; l < 3; l++) { |
229 |
+ |
m = (l+1)%3; |
230 |
+ |
n = (l+2)%3; |
231 |
+ |
|
232 |
+ |
b[l][i] = (a[j][m]*a[k][n] - a[j][n]*a[k][m]) / determinant; |
233 |
+ |
} |
234 |
+ |
} |
235 |
+ |
} |
236 |
+ |
|
237 |
+ |
void SimInfo::matMul3(double a[3][3], double b[3][3], double c[3][3]) { |
238 |
+ |
double r00, r01, r02, r10, r11, r12, r20, r21, r22; |
239 |
+ |
|
240 |
+ |
r00 = a[0][0]*b[0][0] + a[0][1]*b[1][0] + a[0][2]*b[2][0]; |
241 |
+ |
r01 = a[0][0]*b[0][1] + a[0][1]*b[1][1] + a[0][2]*b[2][1]; |
242 |
+ |
r02 = a[0][0]*b[0][2] + a[0][1]*b[1][2] + a[0][2]*b[2][2]; |
243 |
+ |
|
244 |
+ |
r10 = a[1][0]*b[0][0] + a[1][1]*b[1][0] + a[1][2]*b[2][0]; |
245 |
+ |
r11 = a[1][0]*b[0][1] + a[1][1]*b[1][1] + a[1][2]*b[2][1]; |
246 |
+ |
r12 = a[1][0]*b[0][2] + a[1][1]*b[1][2] + a[1][2]*b[2][2]; |
247 |
+ |
|
248 |
+ |
r20 = a[2][0]*b[0][0] + a[2][1]*b[1][0] + a[2][2]*b[2][0]; |
249 |
+ |
r21 = a[2][0]*b[0][1] + a[2][1]*b[1][1] + a[2][2]*b[2][1]; |
250 |
+ |
r22 = a[2][0]*b[0][2] + a[2][1]*b[1][2] + a[2][2]*b[2][2]; |
251 |
+ |
|
252 |
+ |
c[0][0] = r00; c[0][1] = r01; c[0][2] = r02; |
253 |
+ |
c[1][0] = r10; c[1][1] = r11; c[1][2] = r12; |
254 |
+ |
c[2][0] = r20; c[2][1] = r21; c[2][2] = r22; |
255 |
+ |
} |
256 |
+ |
|
257 |
+ |
void SimInfo::matVecMul3(double m[3][3], double inVec[3], double outVec[3]) { |
258 |
+ |
double a0, a1, a2; |
259 |
+ |
|
260 |
+ |
a0 = inVec[0]; a1 = inVec[1]; a2 = inVec[2]; |
261 |
+ |
|
262 |
+ |
outVec[0] = m[0][0]*a0 + m[0][1]*a1 + m[0][2]*a2; |
263 |
+ |
outVec[1] = m[1][0]*a0 + m[1][1]*a1 + m[1][2]*a2; |
264 |
+ |
outVec[2] = m[2][0]*a0 + m[2][1]*a1 + m[2][2]*a2; |
265 |
+ |
} |
266 |
+ |
|
267 |
+ |
void SimInfo::transposeMat3(double in[3][3], double out[3][3]) { |
268 |
+ |
double temp[3][3]; |
269 |
+ |
int i, j; |
270 |
+ |
|
271 |
+ |
for (i = 0; i < 3; i++) { |
272 |
+ |
for (j = 0; j < 3; j++) { |
273 |
+ |
temp[j][i] = in[i][j]; |
274 |
+ |
} |
275 |
+ |
} |
276 |
+ |
for (i = 0; i < 3; i++) { |
277 |
+ |
for (j = 0; j < 3; j++) { |
278 |
+ |
out[i][j] = temp[i][j]; |
279 |
+ |
} |
280 |
+ |
} |
281 |
+ |
} |
282 |
+ |
|
283 |
+ |
void SimInfo::printMat3(double A[3][3] ){ |
284 |
+ |
|
285 |
+ |
std::cerr |
286 |
+ |
<< "[ " << A[0][0] << ", " << A[0][1] << ", " << A[0][2] << " ]\n" |
287 |
+ |
<< "[ " << A[1][0] << ", " << A[1][1] << ", " << A[1][2] << " ]\n" |
288 |
+ |
<< "[ " << A[2][0] << ", " << A[2][1] << ", " << A[2][2] << " ]\n"; |
289 |
+ |
} |
290 |
+ |
|
291 |
+ |
void SimInfo::printMat9(double A[9] ){ |
292 |
+ |
|
293 |
+ |
std::cerr |
294 |
+ |
<< "[ " << A[0] << ", " << A[1] << ", " << A[2] << " ]\n" |
295 |
+ |
<< "[ " << A[3] << ", " << A[4] << ", " << A[5] << " ]\n" |
296 |
+ |
<< "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n"; |
297 |
+ |
} |
298 |
+ |
|
299 |
|
void SimInfo::calcBoxL( void ){ |
300 |
|
|
301 |
|
double dx, dy, dz, dsq; |
302 |
|
int i; |
303 |
|
|
304 |
< |
// boxVol = h1 (dot) h2 (cross) h3 |
304 |
> |
// boxVol = Determinant of Hmat |
305 |
|
|
306 |
< |
boxVol = Hmat[0] * ( (Hmat[4]*Hmat[8]) - (Hmat[7]*Hmat[5]) ) |
214 |
< |
+ Hmat[1] * ( (Hmat[5]*Hmat[6]) - (Hmat[8]*Hmat[3]) ) |
215 |
< |
+ Hmat[2] * ( (Hmat[3]*Hmat[7]) - (Hmat[6]*Hmat[4]) ); |
306 |
> |
boxVol = matDet3( Hmat ); |
307 |
|
|
217 |
– |
|
308 |
|
// boxLx |
309 |
|
|
310 |
< |
dx = Hmat[0]; dy = Hmat[1]; dz = Hmat[2]; |
310 |
> |
dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0]; |
311 |
|
dsq = dx*dx + dy*dy + dz*dz; |
312 |
< |
boxLx = sqrt( dsq ); |
312 |
> |
boxL[0] = sqrt( dsq ); |
313 |
|
|
314 |
|
// boxLy |
315 |
|
|
316 |
< |
dx = Hmat[3]; dy = Hmat[4]; dz = Hmat[5]; |
316 |
> |
dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1]; |
317 |
|
dsq = dx*dx + dy*dy + dz*dz; |
318 |
< |
boxLy = sqrt( dsq ); |
318 |
> |
boxL[1] = sqrt( dsq ); |
319 |
|
|
320 |
|
// boxLz |
321 |
|
|
322 |
< |
dx = Hmat[6]; dy = Hmat[7]; dz = Hmat[8]; |
322 |
> |
dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2]; |
323 |
|
dsq = dx*dx + dy*dy + dz*dz; |
324 |
< |
boxLz = sqrt( dsq ); |
324 |
> |
boxL[2] = sqrt( dsq ); |
325 |
|
|
326 |
|
} |
327 |
|
|
331 |
|
int i, j, k; |
332 |
|
double scaled[3]; |
333 |
|
|
334 |
< |
// calc the scaled coordinates. |
334 |
> |
if( !orthoRhombic ){ |
335 |
> |
// calc the scaled coordinates. |
336 |
|
|
246 |
– |
for(i=0; i<3; i++) |
247 |
– |
scaled[i] = thePos[0]*Hmat[i] + thePos[1]*Hat[i+3] + thePos[3]*Hmat[i+6]; |
337 |
|
|
338 |
< |
// wrap the scaled coordinates |
338 |
> |
matVecMul3(HmatInv, thePos, scaled); |
339 |
> |
|
340 |
> |
for(i=0; i<3; i++) |
341 |
> |
scaled[i] -= roundMe(scaled[i]); |
342 |
> |
|
343 |
> |
// calc the wrapped real coordinates from the wrapped scaled coordinates |
344 |
> |
|
345 |
> |
matVecMul3(Hmat, scaled, thePos); |
346 |
|
|
347 |
< |
for(i=0; i<3; i++) |
348 |
< |
scaled[i] -= (copysign(1,scaled[i]) * (int)(fabs(scaled[i]) + 0.5)); |
349 |
< |
|
350 |
< |
|
347 |
> |
} |
348 |
> |
else{ |
349 |
> |
// calc the scaled coordinates. |
350 |
> |
|
351 |
> |
for(i=0; i<3; i++) |
352 |
> |
scaled[i] = thePos[i]*HmatInv[i][i]; |
353 |
> |
|
354 |
> |
// wrap the scaled coordinates |
355 |
> |
|
356 |
> |
for(i=0; i<3; i++) |
357 |
> |
scaled[i] -= roundMe(scaled[i]); |
358 |
> |
|
359 |
> |
// calc the wrapped real coordinates from the wrapped scaled coordinates |
360 |
> |
|
361 |
> |
for(i=0; i<3; i++) |
362 |
> |
thePos[i] = scaled[i]*Hmat[i][i]; |
363 |
> |
} |
364 |
> |
|
365 |
|
} |
366 |
|
|
367 |
|
|
407 |
|
fInfo.rt = 0.0; |
408 |
|
fInfo.dielect = 0.0; |
409 |
|
|
300 |
– |
fInfo.box[0] = box_x; |
301 |
– |
fInfo.box[1] = box_y; |
302 |
– |
fInfo.box[2] = box_z; |
303 |
– |
|
410 |
|
fInfo.rlist = rList; |
411 |
|
fInfo.rcut = rCut; |
412 |
|
|