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#include <cstdlib> |
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#include <cstring> |
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#include <stdlib.h> |
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#include <string.h> |
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#include <math.h> |
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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 "fortranWrappers.hpp" |
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|
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#ifdef IS_MPI |
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#include "mpiSimulation.hpp" |
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#endif |
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|
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inline double roundMe( double x ){ |
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return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 ); |
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} |
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|
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|
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SimInfo* currentInfo; |
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|
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SimInfo::SimInfo(){ |
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excludes = NULL; |
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n_constraints = 0; |
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nZconstraints = 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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nZconstraints = 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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origRcut = -1.0; |
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ecr = 0.0; |
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origEcr = -1.0; |
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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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|
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haveOrigRcut = 0; |
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haveOrigEcr = 0; |
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boxIsInit = 0; |
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|
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resetTime = 1e99; |
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|
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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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useGB = 0; |
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useEAM = 0; |
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|
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myConfiguration = new SimState(); |
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|
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wrapMeSimInfo( this ); |
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} |
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|
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|
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SimInfo::~SimInfo(){ |
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|
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delete myConfiguration; |
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|
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map<string, GenericData*>::iterator i; |
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|
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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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} |
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|
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void SimInfo::setBox(double newBox[3]) { |
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box_x = newBox[0]; |
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box_y = newBox[1]; |
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box_z = newBox[2]; |
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setFortranBoxSize(newBox); |
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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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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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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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setBoxM( tempMat ); |
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|
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} |
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|
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void SimInfo::getBox(double theBox[3]) { |
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theBox[0] = box_x; |
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theBox[1] = box_y; |
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theBox[2] = box_z; |
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void SimInfo::setBoxM( double theBox[3][3] ){ |
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|
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int i, j; |
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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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if( !boxIsInit ) boxIsInit = 1; |
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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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|
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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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} |
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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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|
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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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|
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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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setBoxM(theBox); |
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|
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} |
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|
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void SimInfo::calcHmatInv( void ) { |
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|
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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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|
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// check to see if Hmat is orthorhombic |
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|
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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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|
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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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|
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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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|
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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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|
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return determinant; |
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} |
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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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|
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determinant = matDet3( a ); |
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|
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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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|
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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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|
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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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|
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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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|
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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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|
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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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|
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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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|
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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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|
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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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|
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a0 = inVec[0]; a1 = inVec[1]; a2 = inVec[2]; |
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|
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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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} |
251 |
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|
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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; |
255 |
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|
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for (i = 0; i < 3; i++) { |
257 |
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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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|
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void SimInfo::printMat3(double A[3][3] ){ |
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|
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std::cerr |
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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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} |
275 |
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|
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void SimInfo::printMat9(double A[9] ){ |
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|
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std::cerr |
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<< "[ " << A[0] << ", " << A[1] << ", " << A[2] << " ]\n" |
280 |
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<< "[ " << A[3] << ", " << A[4] << ", " << A[5] << " ]\n" |
281 |
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<< "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n"; |
282 |
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} |
283 |
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|
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|
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void SimInfo::crossProduct3(double a[3],double b[3], double out[3]){ |
286 |
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|
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out[0] = a[1] * b[2] - a[2] * b[1]; |
288 |
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out[1] = a[2] * b[0] - a[0] * b[2] ; |
289 |
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out[2] = a[0] * b[1] - a[1] * b[0]; |
290 |
+ |
|
291 |
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} |
292 |
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|
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double SimInfo::dotProduct3(double a[3], double b[3]){ |
294 |
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return a[0]*b[0] + a[1]*b[1]+ a[2]*b[2]; |
295 |
+ |
} |
296 |
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|
297 |
+ |
double SimInfo::length3(double a[3]){ |
298 |
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return sqrt(a[0]*a[0] + a[1]*a[1] + a[2]*a[2]); |
299 |
+ |
} |
300 |
+ |
|
301 |
+ |
void SimInfo::calcBoxL( void ){ |
302 |
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|
303 |
+ |
double dx, dy, dz, dsq; |
304 |
+ |
|
305 |
+ |
// boxVol = Determinant of Hmat |
306 |
+ |
|
307 |
+ |
boxVol = matDet3( Hmat ); |
308 |
+ |
|
309 |
+ |
// boxLx |
310 |
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|
311 |
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dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0]; |
312 |
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dsq = dx*dx + dy*dy + dz*dz; |
313 |
+ |
boxL[0] = sqrt( dsq ); |
314 |
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//maxCutoff = 0.5 * boxL[0]; |
315 |
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|
316 |
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// boxLy |
317 |
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|
318 |
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dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1]; |
319 |
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dsq = dx*dx + dy*dy + dz*dz; |
320 |
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boxL[1] = sqrt( dsq ); |
321 |
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//if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1]; |
322 |
+ |
|
323 |
+ |
|
324 |
+ |
// boxLz |
325 |
+ |
|
326 |
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dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2]; |
327 |
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dsq = dx*dx + dy*dy + dz*dz; |
328 |
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boxL[2] = sqrt( dsq ); |
329 |
+ |
//if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2]; |
330 |
+ |
|
331 |
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//calculate the max cutoff |
332 |
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maxCutoff = calcMaxCutOff(); |
333 |
+ |
|
334 |
+ |
checkCutOffs(); |
335 |
+ |
|
336 |
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} |
337 |
+ |
|
338 |
+ |
|
339 |
+ |
double SimInfo::calcMaxCutOff(){ |
340 |
+ |
|
341 |
+ |
double ri[3], rj[3], rk[3]; |
342 |
+ |
double rij[3], rjk[3], rki[3]; |
343 |
+ |
double minDist; |
344 |
+ |
|
345 |
+ |
ri[0] = Hmat[0][0]; |
346 |
+ |
ri[1] = Hmat[1][0]; |
347 |
+ |
ri[2] = Hmat[2][0]; |
348 |
+ |
|
349 |
+ |
rj[0] = Hmat[0][1]; |
350 |
+ |
rj[1] = Hmat[1][1]; |
351 |
+ |
rj[2] = Hmat[2][1]; |
352 |
+ |
|
353 |
+ |
rk[0] = Hmat[0][2]; |
354 |
+ |
rk[1] = Hmat[1][2]; |
355 |
+ |
rk[2] = Hmat[2][2]; |
356 |
+ |
|
357 |
+ |
crossProduct3(ri,rj, rij); |
358 |
+ |
distXY = dotProduct3(rk,rij) / length3(rij); |
359 |
+ |
|
360 |
+ |
crossProduct3(rj,rk, rjk); |
361 |
+ |
distYZ = dotProduct3(ri,rjk) / length3(rjk); |
362 |
+ |
|
363 |
+ |
crossProduct3(rk,ri, rki); |
364 |
+ |
distZX = dotProduct3(rj,rki) / length3(rki); |
365 |
+ |
|
366 |
+ |
minDist = min(min(distXY, distYZ), distZX); |
367 |
+ |
return minDist/2; |
368 |
+ |
|
369 |
+ |
} |
370 |
+ |
|
371 |
+ |
void SimInfo::wrapVector( double thePos[3] ){ |
372 |
+ |
|
373 |
+ |
int i; |
374 |
+ |
double scaled[3]; |
375 |
+ |
|
376 |
+ |
if( !orthoRhombic ){ |
377 |
+ |
// calc the scaled coordinates. |
378 |
+ |
|
379 |
+ |
|
380 |
+ |
matVecMul3(HmatInv, thePos, scaled); |
381 |
+ |
|
382 |
+ |
for(i=0; i<3; i++) |
383 |
+ |
scaled[i] -= roundMe(scaled[i]); |
384 |
+ |
|
385 |
+ |
// calc the wrapped real coordinates from the wrapped scaled coordinates |
386 |
+ |
|
387 |
+ |
matVecMul3(Hmat, scaled, thePos); |
388 |
+ |
|
389 |
+ |
} |
390 |
+ |
else{ |
391 |
+ |
// calc the scaled coordinates. |
392 |
+ |
|
393 |
+ |
for(i=0; i<3; i++) |
394 |
+ |
scaled[i] = thePos[i]*HmatInv[i][i]; |
395 |
+ |
|
396 |
+ |
// wrap the scaled coordinates |
397 |
+ |
|
398 |
+ |
for(i=0; i<3; i++) |
399 |
+ |
scaled[i] -= roundMe(scaled[i]); |
400 |
+ |
|
401 |
+ |
// calc the wrapped real coordinates from the wrapped scaled coordinates |
402 |
+ |
|
403 |
+ |
for(i=0; i<3; i++) |
404 |
+ |
thePos[i] = scaled[i]*Hmat[i][i]; |
405 |
+ |
} |
406 |
+ |
|
407 |
+ |
} |
408 |
+ |
|
409 |
+ |
|
410 |
|
int SimInfo::getNDF(){ |
411 |
< |
int ndf_local, ndf; |
411 |
> |
int ndf_local; |
412 |
|
|
413 |
|
ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints; |
414 |
|
|
418 |
|
ndf = ndf_local; |
419 |
|
#endif |
420 |
|
|
421 |
< |
ndf = ndf - 3; |
421 |
> |
ndf = ndf - 3 - nZconstraints; |
422 |
|
|
423 |
|
return ndf; |
424 |
|
} |
425 |
|
|
426 |
|
int SimInfo::getNDFraw() { |
427 |
< |
int ndfRaw_local, ndfRaw; |
427 |
> |
int ndfRaw_local; |
428 |
|
|
429 |
|
// Raw degrees of freedom that we have to set |
430 |
|
ndfRaw_local = 3 * n_atoms + 3 * n_oriented; |
437 |
|
|
438 |
|
return ndfRaw; |
439 |
|
} |
440 |
< |
|
440 |
> |
|
441 |
> |
int SimInfo::getNDFtranslational() { |
442 |
> |
int ndfTrans_local; |
443 |
> |
|
444 |
> |
ndfTrans_local = 3 * n_atoms - n_constraints; |
445 |
> |
|
446 |
> |
#ifdef IS_MPI |
447 |
> |
MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
448 |
> |
#else |
449 |
> |
ndfTrans = ndfTrans_local; |
450 |
> |
#endif |
451 |
> |
|
452 |
> |
ndfTrans = ndfTrans - 3 - nZconstraints; |
453 |
> |
|
454 |
> |
return ndfTrans; |
455 |
> |
} |
456 |
> |
|
457 |
|
void SimInfo::refreshSim(){ |
458 |
|
|
459 |
|
simtype fInfo; |
460 |
|
int isError; |
461 |
+ |
int n_global; |
462 |
|
int* excl; |
463 |
|
|
464 |
< |
fInfo.box[0] = box_x; |
88 |
< |
fInfo.box[1] = box_y; |
89 |
< |
fInfo.box[2] = box_z; |
464 |
> |
fInfo.dielect = 0.0; |
465 |
|
|
466 |
< |
fInfo.rlist = rList; |
467 |
< |
fInfo.rcut = rCut; |
468 |
< |
fInfo.rrf = ecr; |
94 |
< |
fInfo.rt = ecr - est; |
95 |
< |
fInfo.dielect = dielectric; |
466 |
> |
if( useDipole ){ |
467 |
> |
if( useReactionField )fInfo.dielect = dielectric; |
468 |
> |
} |
469 |
|
|
470 |
|
fInfo.SIM_uses_PBC = usePBC; |
471 |
|
//fInfo.SIM_uses_LJ = 0; |
481 |
|
|
482 |
|
excl = Exclude::getArray(); |
483 |
|
|
484 |
+ |
#ifdef IS_MPI |
485 |
+ |
n_global = mpiSim->getTotAtoms(); |
486 |
+ |
#else |
487 |
+ |
n_global = n_atoms; |
488 |
+ |
#endif |
489 |
+ |
|
490 |
|
isError = 0; |
491 |
|
|
492 |
< |
// fInfo; |
493 |
< |
// n_atoms; |
494 |
< |
// identArray; |
116 |
< |
// n_exclude; |
117 |
< |
// excludes; |
118 |
< |
// nGlobalExcludes; |
119 |
< |
// globalExcludes; |
120 |
< |
// isError; |
492 |
> |
setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl, |
493 |
> |
&nGlobalExcludes, globalExcludes, molMembershipArray, |
494 |
> |
&isError ); |
495 |
|
|
122 |
– |
setFsimulation( &fInfo, &n_atoms, identArray, &n_exclude, excl, |
123 |
– |
&nGlobalExcludes, globalExcludes, &isError ); |
124 |
– |
|
496 |
|
if( isError ){ |
497 |
|
|
498 |
|
sprintf( painCave.errMsg, |
507 |
|
MPIcheckPoint(); |
508 |
|
#endif // is_mpi |
509 |
|
|
510 |
< |
ndf = this->getNDF(); |
511 |
< |
ndfRaw = this->getNDFraw(); |
510 |
> |
this->ndf = this->getNDF(); |
511 |
> |
this->ndfRaw = this->getNDFraw(); |
512 |
> |
this->ndfTrans = this->getNDFtranslational(); |
513 |
> |
} |
514 |
|
|
515 |
+ |
|
516 |
+ |
void SimInfo::setRcut( double theRcut ){ |
517 |
+ |
|
518 |
+ |
rCut = theRcut; |
519 |
+ |
checkCutOffs(); |
520 |
|
} |
521 |
|
|
522 |
+ |
void SimInfo::setDefaultRcut( double theRcut ){ |
523 |
+ |
|
524 |
+ |
haveOrigRcut = 1; |
525 |
+ |
origRcut = theRcut; |
526 |
+ |
rCut = theRcut; |
527 |
+ |
|
528 |
+ |
notifyFortranCutOffs( &rCut, &rList, &ecr, &est ); |
529 |
+ |
} |
530 |
+ |
|
531 |
+ |
void SimInfo::setEcr( double theEcr ){ |
532 |
+ |
|
533 |
+ |
ecr = theEcr; |
534 |
+ |
checkCutOffs(); |
535 |
+ |
} |
536 |
+ |
|
537 |
+ |
void SimInfo::setDefaultEcr( double theEcr ){ |
538 |
+ |
|
539 |
+ |
haveOrigEcr = 1; |
540 |
+ |
origEcr = theEcr; |
541 |
+ |
|
542 |
+ |
ecr = theEcr; |
543 |
+ |
notifyFortranCutOffs( &rCut, &rList, &ecr, &est ); |
544 |
+ |
} |
545 |
+ |
|
546 |
+ |
void SimInfo::setEcr( double theEcr, double theEst ){ |
547 |
+ |
|
548 |
+ |
est = theEst; |
549 |
+ |
setEcr( theEcr ); |
550 |
+ |
} |
551 |
+ |
|
552 |
+ |
void SimInfo::setDefaultEcr( double theEcr, double theEst ){ |
553 |
+ |
|
554 |
+ |
est = theEst; |
555 |
+ |
setDefaultEcr( theEcr ); |
556 |
+ |
} |
557 |
+ |
|
558 |
+ |
|
559 |
+ |
void SimInfo::checkCutOffs( void ){ |
560 |
+ |
|
561 |
+ |
int cutChanged = 0; |
562 |
+ |
|
563 |
+ |
if( boxIsInit ){ |
564 |
+ |
|
565 |
+ |
//we need to check cutOffs against the box |
566 |
+ |
|
567 |
+ |
//detect the change of rCut |
568 |
+ |
if(( maxCutoff > rCut )&&(usePBC)){ |
569 |
+ |
if( rCut < origRcut ){ |
570 |
+ |
rCut = origRcut; |
571 |
+ |
|
572 |
+ |
if (rCut > maxCutoff) |
573 |
+ |
rCut = maxCutoff; |
574 |
+ |
|
575 |
+ |
sprintf( painCave.errMsg, |
576 |
+ |
"New Box size is setting the long range cutoff radius " |
577 |
+ |
"to %lf at time %lf\n", |
578 |
+ |
rCut, currentTime ); |
579 |
+ |
painCave.isFatal = 0; |
580 |
+ |
simError(); |
581 |
+ |
} |
582 |
+ |
} |
583 |
+ |
else if ((rCut > maxCutoff)&&(usePBC)) { |
584 |
+ |
sprintf( painCave.errMsg, |
585 |
+ |
"New Box size is setting the long range cutoff radius " |
586 |
+ |
"to %lf at time %lf\n", |
587 |
+ |
maxCutoff, currentTime ); |
588 |
+ |
painCave.isFatal = 0; |
589 |
+ |
simError(); |
590 |
+ |
rCut = maxCutoff; |
591 |
+ |
} |
592 |
+ |
|
593 |
+ |
|
594 |
+ |
//detect the change of ecr |
595 |
+ |
if( maxCutoff > ecr ){ |
596 |
+ |
if( ecr < origEcr ){ |
597 |
+ |
ecr = origEcr; |
598 |
+ |
if (ecr > maxCutoff) ecr = maxCutoff; |
599 |
+ |
|
600 |
+ |
sprintf( painCave.errMsg, |
601 |
+ |
"New Box size is setting the electrostaticCutoffRadius " |
602 |
+ |
"to %lf at time %lf\n", |
603 |
+ |
ecr, currentTime ); |
604 |
+ |
painCave.isFatal = 0; |
605 |
+ |
simError(); |
606 |
+ |
} |
607 |
+ |
} |
608 |
+ |
else if( ecr > maxCutoff){ |
609 |
+ |
sprintf( painCave.errMsg, |
610 |
+ |
"New Box size is setting the electrostaticCutoffRadius " |
611 |
+ |
"to %lf at time %lf\n", |
612 |
+ |
maxCutoff, currentTime ); |
613 |
+ |
painCave.isFatal = 0; |
614 |
+ |
simError(); |
615 |
+ |
ecr = maxCutoff; |
616 |
+ |
} |
617 |
+ |
|
618 |
+ |
if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1; |
619 |
+ |
|
620 |
+ |
// rlist is the 1.0 plus max( rcut, ecr ) |
621 |
+ |
|
622 |
+ |
( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0; |
623 |
+ |
|
624 |
+ |
if( cutChanged ){ |
625 |
+ |
|
626 |
+ |
notifyFortranCutOffs( &rCut, &rList, &ecr, &est ); |
627 |
+ |
} |
628 |
+ |
|
629 |
+ |
oldEcr = ecr; |
630 |
+ |
oldRcut = rCut; |
631 |
+ |
|
632 |
+ |
} else { |
633 |
+ |
// initialize this stuff before using it, OK? |
634 |
+ |
sprintf( painCave.errMsg, |
635 |
+ |
"Trying to check cutoffs without a box. Be smarter.\n" ); |
636 |
+ |
painCave.isFatal = 1; |
637 |
+ |
simError(); |
638 |
+ |
} |
639 |
+ |
|
640 |
+ |
} |
641 |
+ |
|
642 |
+ |
void SimInfo::addProperty(GenericData* prop){ |
643 |
+ |
|
644 |
+ |
map<string, GenericData*>::iterator result; |
645 |
+ |
result = properties.find(prop->getID()); |
646 |
+ |
|
647 |
+ |
//we can't simply use properties[prop->getID()] = prop, |
648 |
+ |
//it will cause memory leak if we already contain a propery which has the same name of prop |
649 |
+ |
|
650 |
+ |
if(result != properties.end()){ |
651 |
+ |
|
652 |
+ |
delete (*result).second; |
653 |
+ |
(*result).second = prop; |
654 |
+ |
|
655 |
+ |
} |
656 |
+ |
else{ |
657 |
+ |
|
658 |
+ |
properties[prop->getID()] = prop; |
659 |
+ |
|
660 |
+ |
} |
661 |
+ |
|
662 |
+ |
} |
663 |
+ |
|
664 |
+ |
GenericData* SimInfo::getProperty(const string& propName){ |
665 |
+ |
|
666 |
+ |
map<string, GenericData*>::iterator result; |
667 |
+ |
|
668 |
+ |
//string lowerCaseName = (); |
669 |
+ |
|
670 |
+ |
result = properties.find(propName); |
671 |
+ |
|
672 |
+ |
if(result != properties.end()) |
673 |
+ |
return (*result).second; |
674 |
+ |
else |
675 |
+ |
return NULL; |
676 |
+ |
} |
677 |
+ |
|
678 |
+ |
vector<GenericData*> SimInfo::getProperties(){ |
679 |
+ |
|
680 |
+ |
vector<GenericData*> result; |
681 |
+ |
map<string, GenericData*>::iterator i; |
682 |
+ |
|
683 |
+ |
for(i = properties.begin(); i != properties.end(); i++) |
684 |
+ |
result.push_back((*i).second); |
685 |
+ |
|
686 |
+ |
return result; |
687 |
+ |
} |
688 |
+ |
|
689 |
+ |
double SimInfo::matTrace3(double m[3][3]){ |
690 |
+ |
double trace; |
691 |
+ |
trace = m[0][0] + m[1][1] + m[2][2]; |
692 |
+ |
|
693 |
+ |
return trace; |
694 |
+ |
} |