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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 "fSimulation.h" |
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#include "simError.h" |
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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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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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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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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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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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wrapMeSimInfo( this ); |
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} |
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|
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void SimInfo::setBox(double newBox[3]) { |
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int i, j; |
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double tempMat[3][3]; |
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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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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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setBoxM( tempMat ); |
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|
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} |
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|
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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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|
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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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// 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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calcBoxL(); |
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calcHmatInv(); |
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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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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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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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maxCutoff = smallestBoxL / 2.0; |
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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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rList = 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 - 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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// list radius changed so we have to refresh the simulation structure. |
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refreshSim(); |
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} |
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if( ecr > maxCutoff ){ |
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sprintf( painCave.errMsg, |
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"New Box size is forcing electrostatic cutoff radius " |
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"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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ecr = maxCutoff; |
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est = 0.05 * ecr; |
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refreshSim(); |
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} |
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} |
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|
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void SimInfo::getBoxM (double theBox[3][3]) { |
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|
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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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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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// cerr << "Scaling box by " << scale << "\n"; |
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mmeineke |
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|
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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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setBoxM(theBox); |
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} |
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void SimInfo::calcHmatInv( void ) { |
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int i,j; |
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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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invertMat3( Hmat, HmatInv ); |
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|
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// Check the inverse to make sure it is sane: |
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|
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matMul3( Hmat, HmatInv, sanity ); |
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// check to see if Hmat is orthorhombic |
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smallDiag = Hmat[0][0]; |
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if(smallDiag > Hmat[1][1]) smallDiag = Hmat[1][1]; |
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if(smallDiag > Hmat[2][2]) smallDiag = Hmat[2][2]; |
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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 < 3; i++ ) { |
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for (j = 0 ; j < 3; j++) { |
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if (i != j) { |
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if (orthoRhombic) { |
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if (Hmat[i][j] >= tol) orthoRhombic = 0; |
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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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double SimInfo::matDet3(double a[3][3]) { |
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int i, j, k; |
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double determinant; |
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|
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determinant = 0.0; |
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for(i = 0; i < 3; i++) { |
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j = (i+1)%3; |
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k = (i+2)%3; |
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determinant += a[0][i] * (a[1][j]*a[2][k] - a[1][k]*a[2][j]); |
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} |
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return determinant; |
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} |
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void SimInfo::invertMat3(double a[3][3], double b[3][3]) { |
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|
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int i, j, k, l, m, n; |
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double determinant; |
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determinant = matDet3( a ); |
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if (determinant == 0.0) { |
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sprintf( painCave.errMsg, |
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"Can't invert a matrix with a zero determinant!\n"); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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for (i=0; i < 3; i++) { |
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j = (i+1)%3; |
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k = (i+2)%3; |
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for(l = 0; l < 3; l++) { |
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m = (l+1)%3; |
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n = (l+2)%3; |
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b[l][i] = (a[j][m]*a[k][n] - a[j][n]*a[k][m]) / determinant; |
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} |
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} |
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mmeineke |
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} |
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void SimInfo::matMul3(double a[3][3], double b[3][3], double c[3][3]) { |
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double r00, r01, r02, r10, r11, r12, r20, r21, r22; |
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r00 = a[0][0]*b[0][0] + a[0][1]*b[1][0] + a[0][2]*b[2][0]; |
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r01 = a[0][0]*b[0][1] + a[0][1]*b[1][1] + a[0][2]*b[2][1]; |
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r02 = a[0][0]*b[0][2] + a[0][1]*b[1][2] + a[0][2]*b[2][2]; |
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r10 = a[1][0]*b[0][0] + a[1][1]*b[1][0] + a[1][2]*b[2][0]; |
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r11 = a[1][0]*b[0][1] + a[1][1]*b[1][1] + a[1][2]*b[2][1]; |
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r12 = a[1][0]*b[0][2] + a[1][1]*b[1][2] + a[1][2]*b[2][2]; |
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r20 = a[2][0]*b[0][0] + a[2][1]*b[1][0] + a[2][2]*b[2][0]; |
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r21 = a[2][0]*b[0][1] + a[2][1]*b[1][1] + a[2][2]*b[2][1]; |
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r22 = a[2][0]*b[0][2] + a[2][1]*b[1][2] + a[2][2]*b[2][2]; |
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c[0][0] = r00; c[0][1] = r01; c[0][2] = r02; |
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c[1][0] = r10; c[1][1] = r11; c[1][2] = r12; |
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c[2][0] = r20; c[2][1] = r21; c[2][2] = r22; |
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} |
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void SimInfo::matVecMul3(double m[3][3], double inVec[3], double outVec[3]) { |
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double a0, a1, a2; |
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a0 = inVec[0]; a1 = inVec[1]; a2 = inVec[2]; |
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outVec[0] = m[0][0]*a0 + m[0][1]*a1 + m[0][2]*a2; |
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outVec[1] = m[1][0]*a0 + m[1][1]*a1 + m[1][2]*a2; |
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outVec[2] = m[2][0]*a0 + m[2][1]*a1 + m[2][2]*a2; |
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} |
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mmeineke |
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void SimInfo::transposeMat3(double in[3][3], double out[3][3]) { |
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double temp[3][3]; |
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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++) { |
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temp[j][i] = in[i][j]; |
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} |
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} |
280 |
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for (i = 0; i < 3; i++) { |
281 |
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for (j = 0; j < 3; j++) { |
282 |
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out[i][j] = temp[i][j]; |
283 |
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} |
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} |
285 |
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} |
286 |
gezelter |
588 |
|
287 |
mmeineke |
597 |
void SimInfo::printMat3(double A[3][3] ){ |
288 |
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289 |
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std::cerr |
290 |
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<< "[ " << A[0][0] << ", " << A[0][1] << ", " << A[0][2] << " ]\n" |
291 |
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<< "[ " << A[1][0] << ", " << A[1][1] << ", " << A[1][2] << " ]\n" |
292 |
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<< "[ " << A[2][0] << ", " << A[2][1] << ", " << A[2][2] << " ]\n"; |
293 |
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} |
294 |
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295 |
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void SimInfo::printMat9(double A[9] ){ |
296 |
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297 |
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std::cerr |
298 |
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<< "[ " << A[0] << ", " << A[1] << ", " << A[2] << " ]\n" |
299 |
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<< "[ " << A[3] << ", " << A[4] << ", " << A[5] << " ]\n" |
300 |
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<< "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n"; |
301 |
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} |
302 |
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303 |
mmeineke |
568 |
void SimInfo::calcBoxL( void ){ |
304 |
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305 |
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double dx, dy, dz, dsq; |
306 |
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int i; |
307 |
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|
308 |
gezelter |
588 |
// boxVol = Determinant of Hmat |
309 |
mmeineke |
568 |
|
310 |
gezelter |
588 |
boxVol = matDet3( Hmat ); |
311 |
mmeineke |
568 |
|
312 |
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// boxLx |
313 |
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|
314 |
gezelter |
588 |
dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0]; |
315 |
mmeineke |
568 |
dsq = dx*dx + dy*dy + dz*dz; |
316 |
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boxLx = sqrt( dsq ); |
317 |
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318 |
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// boxLy |
319 |
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|
320 |
gezelter |
588 |
dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1]; |
321 |
mmeineke |
568 |
dsq = dx*dx + dy*dy + dz*dz; |
322 |
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boxLy = sqrt( dsq ); |
323 |
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324 |
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// boxLz |
325 |
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|
326 |
gezelter |
588 |
dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2]; |
327 |
mmeineke |
568 |
dsq = dx*dx + dy*dy + dz*dz; |
328 |
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boxLz = sqrt( dsq ); |
329 |
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330 |
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} |
331 |
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332 |
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333 |
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void SimInfo::wrapVector( double thePos[3] ){ |
334 |
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335 |
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int i, j, k; |
336 |
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double scaled[3]; |
337 |
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|
338 |
mmeineke |
569 |
if( !orthoRhombic ){ |
339 |
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// calc the scaled coordinates. |
340 |
gezelter |
588 |
|
341 |
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342 |
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matVecMul3(HmatInv, thePos, scaled); |
343 |
mmeineke |
569 |
|
344 |
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for(i=0; i<3; i++) |
345 |
mmeineke |
572 |
scaled[i] -= roundMe(scaled[i]); |
346 |
mmeineke |
569 |
|
347 |
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// calc the wrapped real coordinates from the wrapped scaled coordinates |
348 |
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|
349 |
gezelter |
588 |
matVecMul3(Hmat, scaled, thePos); |
350 |
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|
351 |
mmeineke |
569 |
} |
352 |
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else{ |
353 |
|
|
// calc the scaled coordinates. |
354 |
|
|
|
355 |
|
|
for(i=0; i<3; i++) |
356 |
gezelter |
588 |
scaled[i] = thePos[i]*HmatInv[i][i]; |
357 |
mmeineke |
569 |
|
358 |
|
|
// wrap the scaled coordinates |
359 |
|
|
|
360 |
|
|
for(i=0; i<3; i++) |
361 |
mmeineke |
572 |
scaled[i] -= roundMe(scaled[i]); |
362 |
mmeineke |
569 |
|
363 |
|
|
// calc the wrapped real coordinates from the wrapped scaled coordinates |
364 |
|
|
|
365 |
|
|
for(i=0; i<3; i++) |
366 |
gezelter |
588 |
thePos[i] = scaled[i]*Hmat[i][i]; |
367 |
mmeineke |
569 |
} |
368 |
|
|
|
369 |
mmeineke |
568 |
} |
370 |
|
|
|
371 |
|
|
|
372 |
gezelter |
458 |
int SimInfo::getNDF(){ |
373 |
|
|
int ndf_local, ndf; |
374 |
gezelter |
457 |
|
375 |
gezelter |
458 |
ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints; |
376 |
|
|
|
377 |
|
|
#ifdef IS_MPI |
378 |
|
|
MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
379 |
|
|
#else |
380 |
|
|
ndf = ndf_local; |
381 |
|
|
#endif |
382 |
|
|
|
383 |
|
|
ndf = ndf - 3; |
384 |
|
|
|
385 |
|
|
return ndf; |
386 |
|
|
} |
387 |
|
|
|
388 |
|
|
int SimInfo::getNDFraw() { |
389 |
|
|
int ndfRaw_local, ndfRaw; |
390 |
|
|
|
391 |
|
|
// Raw degrees of freedom that we have to set |
392 |
|
|
ndfRaw_local = 3 * n_atoms + 3 * n_oriented; |
393 |
|
|
|
394 |
|
|
#ifdef IS_MPI |
395 |
|
|
MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
396 |
|
|
#else |
397 |
|
|
ndfRaw = ndfRaw_local; |
398 |
|
|
#endif |
399 |
|
|
|
400 |
|
|
return ndfRaw; |
401 |
|
|
} |
402 |
|
|
|
403 |
mmeineke |
377 |
void SimInfo::refreshSim(){ |
404 |
|
|
|
405 |
|
|
simtype fInfo; |
406 |
|
|
int isError; |
407 |
gezelter |
490 |
int n_global; |
408 |
mmeineke |
424 |
int* excl; |
409 |
mmeineke |
469 |
|
410 |
|
|
fInfo.rrf = 0.0; |
411 |
|
|
fInfo.rt = 0.0; |
412 |
|
|
fInfo.dielect = 0.0; |
413 |
mmeineke |
377 |
|
414 |
|
|
fInfo.rlist = rList; |
415 |
|
|
fInfo.rcut = rCut; |
416 |
|
|
|
417 |
mmeineke |
469 |
if( useDipole ){ |
418 |
|
|
fInfo.rrf = ecr; |
419 |
|
|
fInfo.rt = ecr - est; |
420 |
|
|
if( useReactionField )fInfo.dielect = dielectric; |
421 |
|
|
} |
422 |
|
|
|
423 |
mmeineke |
377 |
fInfo.SIM_uses_PBC = usePBC; |
424 |
mmeineke |
443 |
//fInfo.SIM_uses_LJ = 0; |
425 |
chuckv |
439 |
fInfo.SIM_uses_LJ = useLJ; |
426 |
mmeineke |
443 |
fInfo.SIM_uses_sticky = useSticky; |
427 |
|
|
//fInfo.SIM_uses_sticky = 0; |
428 |
chuckv |
482 |
fInfo.SIM_uses_dipoles = useDipole; |
429 |
|
|
//fInfo.SIM_uses_dipoles = 0; |
430 |
mmeineke |
443 |
//fInfo.SIM_uses_RF = useReactionField; |
431 |
|
|
fInfo.SIM_uses_RF = 0; |
432 |
mmeineke |
377 |
fInfo.SIM_uses_GB = useGB; |
433 |
|
|
fInfo.SIM_uses_EAM = useEAM; |
434 |
|
|
|
435 |
mmeineke |
424 |
excl = Exclude::getArray(); |
436 |
mmeineke |
377 |
|
437 |
gezelter |
490 |
#ifdef IS_MPI |
438 |
|
|
n_global = mpiSim->getTotAtoms(); |
439 |
|
|
#else |
440 |
|
|
n_global = n_atoms; |
441 |
|
|
#endif |
442 |
|
|
|
443 |
mmeineke |
377 |
isError = 0; |
444 |
|
|
|
445 |
gezelter |
490 |
setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl, |
446 |
gezelter |
483 |
&nGlobalExcludes, globalExcludes, molMembershipArray, |
447 |
|
|
&isError ); |
448 |
mmeineke |
377 |
|
449 |
|
|
if( isError ){ |
450 |
|
|
|
451 |
|
|
sprintf( painCave.errMsg, |
452 |
|
|
"There was an error setting the simulation information in fortran.\n" ); |
453 |
|
|
painCave.isFatal = 1; |
454 |
|
|
simError(); |
455 |
|
|
} |
456 |
|
|
|
457 |
|
|
#ifdef IS_MPI |
458 |
|
|
sprintf( checkPointMsg, |
459 |
|
|
"succesfully sent the simulation information to fortran.\n"); |
460 |
|
|
MPIcheckPoint(); |
461 |
|
|
#endif // is_mpi |
462 |
gezelter |
458 |
|
463 |
gezelter |
474 |
this->ndf = this->getNDF(); |
464 |
|
|
this->ndfRaw = this->getNDFraw(); |
465 |
gezelter |
458 |
|
466 |
mmeineke |
377 |
} |
467 |
|
|
|