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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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currentTime = 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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oldEcr = 0.0; |
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oldRcut = 0.0; |
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haveOrigRcut = 0; |
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haveOrigEcr = 0; |
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boxIsInit = 0; |
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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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myConfiguration = new SimState(); |
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wrapMeSimInfo( this ); |
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} |
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SimInfo::~SimInfo(){ |
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delete myConfiguration; |
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map<string, GenericData*>::iterator i; |
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for(i = properties.begin(); i != properties.end(); i++) |
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delete (*i).second; |
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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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void SimInfo::setBoxM( double theBox[3][3] ){ |
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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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if( !boxIsInit ) boxIsInit = 1; |
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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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calcBoxL(); |
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calcHmatInv(); |
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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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setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic); |
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} |
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void SimInfo::getBoxM (double theBox[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++) 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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// cerr << "Scaling box by " << scale << "\n"; |
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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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// 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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mmeineke |
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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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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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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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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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} |
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gezelter |
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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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} |
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for (i = 0; i < 3; i++) { |
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for (j = 0; j < 3; j++) { |
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out[i][j] = temp[i][j]; |
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} |
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} |
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} |
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gezelter |
588 |
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mmeineke |
597 |
void SimInfo::printMat3(double A[3][3] ){ |
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std::cerr |
267 |
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<< "[ " << A[0][0] << ", " << A[0][1] << ", " << A[0][2] << " ]\n" |
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<< "[ " << A[1][0] << ", " << A[1][1] << ", " << A[1][2] << " ]\n" |
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<< "[ " << A[2][0] << ", " << A[2][1] << ", " << A[2][2] << " ]\n"; |
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} |
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void SimInfo::printMat9(double A[9] ){ |
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std::cerr |
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<< "[ " << A[0] << ", " << A[1] << ", " << A[2] << " ]\n" |
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<< "[ " << A[3] << ", " << A[4] << ", " << A[5] << " ]\n" |
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<< "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n"; |
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} |
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mmeineke |
568 |
void SimInfo::calcBoxL( void ){ |
281 |
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double dx, dy, dz, dsq; |
283 |
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int i; |
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|
285 |
gezelter |
588 |
// boxVol = Determinant of Hmat |
286 |
mmeineke |
568 |
|
287 |
gezelter |
588 |
boxVol = matDet3( Hmat ); |
288 |
mmeineke |
568 |
|
289 |
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// boxLx |
290 |
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|
291 |
gezelter |
588 |
dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0]; |
292 |
mmeineke |
568 |
dsq = dx*dx + dy*dy + dz*dz; |
293 |
gezelter |
621 |
boxL[0] = sqrt( dsq ); |
294 |
mmeineke |
626 |
maxCutoff = 0.5 * boxL[0]; |
295 |
mmeineke |
568 |
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// boxLy |
297 |
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|
298 |
gezelter |
588 |
dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1]; |
299 |
mmeineke |
568 |
dsq = dx*dx + dy*dy + dz*dz; |
300 |
gezelter |
621 |
boxL[1] = sqrt( dsq ); |
301 |
mmeineke |
626 |
if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1]; |
302 |
mmeineke |
568 |
|
303 |
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// boxLz |
304 |
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305 |
gezelter |
588 |
dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2]; |
306 |
mmeineke |
568 |
dsq = dx*dx + dy*dy + dz*dz; |
307 |
gezelter |
621 |
boxL[2] = sqrt( dsq ); |
308 |
mmeineke |
626 |
if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2]; |
309 |
chuckv |
669 |
|
310 |
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checkCutOffs(); |
311 |
mmeineke |
626 |
|
312 |
mmeineke |
568 |
} |
313 |
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314 |
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void SimInfo::wrapVector( double thePos[3] ){ |
316 |
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317 |
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int i, j, k; |
318 |
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double scaled[3]; |
319 |
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320 |
mmeineke |
569 |
if( !orthoRhombic ){ |
321 |
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// calc the scaled coordinates. |
322 |
gezelter |
588 |
|
323 |
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324 |
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matVecMul3(HmatInv, thePos, scaled); |
325 |
mmeineke |
569 |
|
326 |
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for(i=0; i<3; i++) |
327 |
mmeineke |
572 |
scaled[i] -= roundMe(scaled[i]); |
328 |
mmeineke |
569 |
|
329 |
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// calc the wrapped real coordinates from the wrapped scaled coordinates |
330 |
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|
331 |
gezelter |
588 |
matVecMul3(Hmat, scaled, thePos); |
332 |
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|
333 |
mmeineke |
569 |
} |
334 |
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else{ |
335 |
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// calc the scaled coordinates. |
336 |
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337 |
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for(i=0; i<3; i++) |
338 |
gezelter |
588 |
scaled[i] = thePos[i]*HmatInv[i][i]; |
339 |
mmeineke |
569 |
|
340 |
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// wrap the scaled coordinates |
341 |
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342 |
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for(i=0; i<3; i++) |
343 |
mmeineke |
572 |
scaled[i] -= roundMe(scaled[i]); |
344 |
mmeineke |
569 |
|
345 |
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// calc the wrapped real coordinates from the wrapped scaled coordinates |
346 |
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|
347 |
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for(i=0; i<3; i++) |
348 |
gezelter |
588 |
thePos[i] = scaled[i]*Hmat[i][i]; |
349 |
mmeineke |
569 |
} |
350 |
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|
351 |
mmeineke |
568 |
} |
352 |
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353 |
|
|
|
354 |
gezelter |
458 |
int SimInfo::getNDF(){ |
355 |
|
|
int ndf_local, ndf; |
356 |
gezelter |
457 |
|
357 |
gezelter |
458 |
ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints; |
358 |
|
|
|
359 |
|
|
#ifdef IS_MPI |
360 |
|
|
MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
361 |
|
|
#else |
362 |
|
|
ndf = ndf_local; |
363 |
|
|
#endif |
364 |
|
|
|
365 |
|
|
ndf = ndf - 3; |
366 |
|
|
|
367 |
|
|
return ndf; |
368 |
|
|
} |
369 |
|
|
|
370 |
|
|
int SimInfo::getNDFraw() { |
371 |
|
|
int ndfRaw_local, ndfRaw; |
372 |
|
|
|
373 |
|
|
// Raw degrees of freedom that we have to set |
374 |
|
|
ndfRaw_local = 3 * n_atoms + 3 * n_oriented; |
375 |
|
|
|
376 |
|
|
#ifdef IS_MPI |
377 |
|
|
MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
378 |
|
|
#else |
379 |
|
|
ndfRaw = ndfRaw_local; |
380 |
|
|
#endif |
381 |
|
|
|
382 |
|
|
return ndfRaw; |
383 |
|
|
} |
384 |
|
|
|
385 |
mmeineke |
377 |
void SimInfo::refreshSim(){ |
386 |
|
|
|
387 |
|
|
simtype fInfo; |
388 |
|
|
int isError; |
389 |
gezelter |
490 |
int n_global; |
390 |
mmeineke |
424 |
int* excl; |
391 |
mmeineke |
626 |
|
392 |
mmeineke |
469 |
fInfo.dielect = 0.0; |
393 |
mmeineke |
377 |
|
394 |
mmeineke |
469 |
if( useDipole ){ |
395 |
|
|
if( useReactionField )fInfo.dielect = dielectric; |
396 |
|
|
} |
397 |
|
|
|
398 |
mmeineke |
377 |
fInfo.SIM_uses_PBC = usePBC; |
399 |
mmeineke |
443 |
//fInfo.SIM_uses_LJ = 0; |
400 |
chuckv |
439 |
fInfo.SIM_uses_LJ = useLJ; |
401 |
mmeineke |
443 |
fInfo.SIM_uses_sticky = useSticky; |
402 |
|
|
//fInfo.SIM_uses_sticky = 0; |
403 |
chuckv |
482 |
fInfo.SIM_uses_dipoles = useDipole; |
404 |
|
|
//fInfo.SIM_uses_dipoles = 0; |
405 |
mmeineke |
443 |
//fInfo.SIM_uses_RF = useReactionField; |
406 |
|
|
fInfo.SIM_uses_RF = 0; |
407 |
mmeineke |
377 |
fInfo.SIM_uses_GB = useGB; |
408 |
|
|
fInfo.SIM_uses_EAM = useEAM; |
409 |
|
|
|
410 |
mmeineke |
424 |
excl = Exclude::getArray(); |
411 |
mmeineke |
377 |
|
412 |
gezelter |
490 |
#ifdef IS_MPI |
413 |
|
|
n_global = mpiSim->getTotAtoms(); |
414 |
|
|
#else |
415 |
|
|
n_global = n_atoms; |
416 |
|
|
#endif |
417 |
|
|
|
418 |
mmeineke |
377 |
isError = 0; |
419 |
|
|
|
420 |
gezelter |
490 |
setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl, |
421 |
gezelter |
483 |
&nGlobalExcludes, globalExcludes, molMembershipArray, |
422 |
|
|
&isError ); |
423 |
mmeineke |
377 |
|
424 |
|
|
if( isError ){ |
425 |
|
|
|
426 |
|
|
sprintf( painCave.errMsg, |
427 |
|
|
"There was an error setting the simulation information in fortran.\n" ); |
428 |
|
|
painCave.isFatal = 1; |
429 |
|
|
simError(); |
430 |
|
|
} |
431 |
|
|
|
432 |
|
|
#ifdef IS_MPI |
433 |
|
|
sprintf( checkPointMsg, |
434 |
|
|
"succesfully sent the simulation information to fortran.\n"); |
435 |
|
|
MPIcheckPoint(); |
436 |
|
|
#endif // is_mpi |
437 |
gezelter |
458 |
|
438 |
gezelter |
474 |
this->ndf = this->getNDF(); |
439 |
|
|
this->ndfRaw = this->getNDFraw(); |
440 |
gezelter |
458 |
|
441 |
mmeineke |
377 |
} |
442 |
|
|
|
443 |
mmeineke |
626 |
|
444 |
|
|
void SimInfo::setRcut( double theRcut ){ |
445 |
|
|
|
446 |
|
|
if( !haveOrigRcut ){ |
447 |
|
|
haveOrigRcut = 1; |
448 |
|
|
origRcut = theRcut; |
449 |
|
|
} |
450 |
|
|
|
451 |
|
|
rCut = theRcut; |
452 |
|
|
checkCutOffs(); |
453 |
|
|
} |
454 |
|
|
|
455 |
|
|
void SimInfo::setEcr( double theEcr ){ |
456 |
|
|
|
457 |
|
|
if( !haveOrigEcr ){ |
458 |
|
|
haveOrigEcr = 1; |
459 |
|
|
origEcr = theEcr; |
460 |
|
|
} |
461 |
|
|
|
462 |
|
|
ecr = theEcr; |
463 |
|
|
checkCutOffs(); |
464 |
|
|
} |
465 |
|
|
|
466 |
|
|
void SimInfo::setEcr( double theEcr, double theEst ){ |
467 |
|
|
|
468 |
|
|
est = theEst; |
469 |
|
|
setEcr( theEcr ); |
470 |
|
|
} |
471 |
|
|
|
472 |
|
|
|
473 |
|
|
void SimInfo::checkCutOffs( void ){ |
474 |
|
|
|
475 |
|
|
int cutChanged = 0; |
476 |
|
|
|
477 |
chuckv |
669 |
|
478 |
|
|
|
479 |
mmeineke |
626 |
if( boxIsInit ){ |
480 |
|
|
|
481 |
|
|
//we need to check cutOffs against the box |
482 |
chuckv |
669 |
|
483 |
|
|
if(( maxCutoff > rCut )&&(usePBC)){ |
484 |
mmeineke |
626 |
if( rCut < origRcut ){ |
485 |
|
|
rCut = origRcut; |
486 |
|
|
if (rCut > maxCutoff) rCut = maxCutoff; |
487 |
|
|
|
488 |
|
|
sprintf( painCave.errMsg, |
489 |
|
|
"New Box size is setting the long range cutoff radius " |
490 |
|
|
"to %lf\n", |
491 |
|
|
rCut ); |
492 |
|
|
painCave.isFatal = 0; |
493 |
|
|
simError(); |
494 |
|
|
} |
495 |
|
|
} |
496 |
|
|
|
497 |
|
|
if( maxCutoff > ecr ){ |
498 |
|
|
if( ecr < origEcr ){ |
499 |
|
|
rCut = origEcr; |
500 |
|
|
if (ecr > maxCutoff) ecr = maxCutoff; |
501 |
|
|
|
502 |
|
|
sprintf( painCave.errMsg, |
503 |
|
|
"New Box size is setting the electrostaticCutoffRadius " |
504 |
|
|
"to %lf\n", |
505 |
|
|
ecr ); |
506 |
|
|
painCave.isFatal = 0; |
507 |
|
|
simError(); |
508 |
|
|
} |
509 |
|
|
} |
510 |
|
|
|
511 |
|
|
|
512 |
chuckv |
669 |
if ((rCut > maxCutoff)&&(usePBC)) { |
513 |
mmeineke |
626 |
sprintf( painCave.errMsg, |
514 |
|
|
"New Box size is setting the long range cutoff radius " |
515 |
|
|
"to %lf\n", |
516 |
|
|
maxCutoff ); |
517 |
|
|
painCave.isFatal = 0; |
518 |
|
|
simError(); |
519 |
|
|
rCut = maxCutoff; |
520 |
|
|
} |
521 |
|
|
|
522 |
|
|
if( ecr > maxCutoff){ |
523 |
|
|
sprintf( painCave.errMsg, |
524 |
|
|
"New Box size is setting the electrostaticCutoffRadius " |
525 |
|
|
"to %lf\n", |
526 |
|
|
maxCutoff ); |
527 |
|
|
painCave.isFatal = 0; |
528 |
|
|
simError(); |
529 |
|
|
ecr = maxCutoff; |
530 |
|
|
} |
531 |
|
|
|
532 |
|
|
|
533 |
|
|
} |
534 |
|
|
|
535 |
|
|
|
536 |
|
|
if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1; |
537 |
|
|
|
538 |
|
|
// rlist is the 1.0 plus max( rcut, ecr ) |
539 |
|
|
|
540 |
|
|
( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0; |
541 |
|
|
|
542 |
|
|
if( cutChanged ){ |
543 |
|
|
|
544 |
|
|
notifyFortranCutOffs( &rCut, &rList, &ecr, &est ); |
545 |
|
|
} |
546 |
|
|
|
547 |
|
|
oldEcr = ecr; |
548 |
|
|
oldRcut = rCut; |
549 |
|
|
} |
550 |
tim |
658 |
|
551 |
|
|
void SimInfo::addProperty(GenericData* prop){ |
552 |
|
|
|
553 |
|
|
map<string, GenericData*>::iterator result; |
554 |
|
|
result = properties.find(prop->getID()); |
555 |
|
|
|
556 |
|
|
//we can't simply use properties[prop->getID()] = prop, |
557 |
|
|
//it will cause memory leak if we already contain a propery which has the same name of prop |
558 |
|
|
|
559 |
|
|
if(result != properties.end()){ |
560 |
|
|
|
561 |
|
|
delete (*result).second; |
562 |
|
|
(*result).second = prop; |
563 |
|
|
|
564 |
|
|
} |
565 |
|
|
else{ |
566 |
|
|
|
567 |
|
|
properties[prop->getID()] = prop; |
568 |
|
|
|
569 |
|
|
} |
570 |
|
|
|
571 |
|
|
} |
572 |
|
|
|
573 |
|
|
GenericData* SimInfo::getProperty(const string& propName){ |
574 |
|
|
|
575 |
|
|
map<string, GenericData*>::iterator result; |
576 |
|
|
|
577 |
|
|
//string lowerCaseName = (); |
578 |
|
|
|
579 |
|
|
result = properties.find(propName); |
580 |
|
|
|
581 |
|
|
if(result != properties.end()) |
582 |
|
|
return (*result).second; |
583 |
|
|
else |
584 |
|
|
return NULL; |
585 |
|
|
} |
586 |
|
|
|
587 |
|
|
vector<GenericData*> SimInfo::getProperties(){ |
588 |
|
|
|
589 |
|
|
vector<GenericData*> result; |
590 |
|
|
map<string, GenericData*>::iterator i; |
591 |
|
|
|
592 |
|
|
for(i = properties.begin(); i != properties.end(); i++) |
593 |
|
|
result.push_back((*i).second); |
594 |
|
|
|
595 |
|
|
return result; |
596 |
|
|
} |
597 |
|
|
|
598 |
|
|
|