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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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#include "MatVec3.h" |
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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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inline double min( double a, double b ){ |
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return (a < b ) ? a : b; |
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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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|
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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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ecr = 0.0; |
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est = 0.0; |
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|
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haveRcut = 0; |
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haveEcr = 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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orthoRhombic = 0; |
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orthoTolerance = 1E-6; |
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useInitXSstate = true; |
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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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useCharges = 0; |
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useDipoles = 0; |
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useReactionField = 0; |
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useGB = 0; |
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useEAM = 0; |
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|
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excludes = Exclude::Instance(); |
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|
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myConfiguration = new SimState(); |
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|
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has_minimizer = false; |
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the_minimizer =NULL; |
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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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|
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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::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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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 oldOrtho; |
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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 to see if Hmat is orthorhombic |
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|
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oldOrtho = orthoRhombic; |
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|
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smallDiag = fabs(Hmat[0][0]); |
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if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]); |
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if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]); |
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tol = smallDiag * orthoTolerance; |
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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 ( fabs(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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if( oldOrtho != orthoRhombic ){ |
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|
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if( orthoRhombic ){ |
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sprintf( painCave.errMsg, |
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"OOPSE is switching from the default Non-Orthorhombic\n" |
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"\tto the faster Orthorhombic periodic boundary computations.\n" |
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"\tThis is usually a good thing, but if you wan't the\n" |
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"\tNon-Orthorhombic computations, make the orthoBoxTolerance\n" |
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"\tvariable ( currently set to %G ) smaller.\n", |
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orthoTolerance); |
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simError(); |
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} |
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else { |
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sprintf( painCave.errMsg, |
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"OOPSE is switching from the faster Orthorhombic to the more\n" |
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"\tflexible Non-Orthorhombic periodic boundary computations.\n" |
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"\tThis is usually because the box has deformed under\n" |
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"\tNPTf integration. If you wan't to live on the edge with\n" |
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"\tthe Orthorhombic computations, make the orthoBoxTolerance\n" |
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"\tvariable ( currently set to %G ) larger.\n", |
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orthoTolerance); |
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simError(); |
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} |
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} |
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} |
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|
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void SimInfo::calcBoxL( void ){ |
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|
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double dx, dy, dz, dsq; |
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|
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// boxVol = Determinant of Hmat |
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|
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boxVol = matDet3( Hmat ); |
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|
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// boxLx |
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|
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dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0]; |
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dsq = dx*dx + dy*dy + dz*dz; |
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boxL[0] = sqrt( dsq ); |
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//maxCutoff = 0.5 * boxL[0]; |
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|
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// boxLy |
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|
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dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1]; |
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dsq = dx*dx + dy*dy + dz*dz; |
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boxL[1] = sqrt( dsq ); |
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//if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1]; |
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|
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|
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// boxLz |
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|
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dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2]; |
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dsq = dx*dx + dy*dy + dz*dz; |
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boxL[2] = sqrt( dsq ); |
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//if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2]; |
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|
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//calculate the max cutoff |
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maxCutoff = calcMaxCutOff(); |
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|
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checkCutOffs(); |
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|
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} |
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|
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|
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double SimInfo::calcMaxCutOff(){ |
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|
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double ri[3], rj[3], rk[3]; |
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double rij[3], rjk[3], rki[3]; |
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double minDist; |
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|
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ri[0] = Hmat[0][0]; |
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ri[1] = Hmat[1][0]; |
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ri[2] = Hmat[2][0]; |
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|
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rj[0] = Hmat[0][1]; |
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rj[1] = Hmat[1][1]; |
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rj[2] = Hmat[2][1]; |
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|
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rk[0] = Hmat[0][2]; |
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rk[1] = Hmat[1][2]; |
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rk[2] = Hmat[2][2]; |
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|
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crossProduct3(ri, rj, rij); |
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distXY = dotProduct3(rk,rij) / norm3(rij); |
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|
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crossProduct3(rj,rk, rjk); |
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distYZ = dotProduct3(ri,rjk) / norm3(rjk); |
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|
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crossProduct3(rk,ri, rki); |
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distZX = dotProduct3(rj,rki) / norm3(rki); |
277 |
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|
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minDist = min(min(distXY, distYZ), distZX); |
279 |
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return minDist/2; |
280 |
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|
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} |
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|
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void SimInfo::wrapVector( double thePos[3] ){ |
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|
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int i; |
286 |
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double scaled[3]; |
287 |
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|
288 |
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if( !orthoRhombic ){ |
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// calc the scaled coordinates. |
290 |
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|
291 |
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|
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matVecMul3(HmatInv, thePos, scaled); |
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|
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for(i=0; i<3; i++) |
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scaled[i] -= roundMe(scaled[i]); |
296 |
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|
297 |
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// calc the wrapped real coordinates from the wrapped scaled coordinates |
298 |
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|
299 |
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matVecMul3(Hmat, scaled, thePos); |
300 |
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|
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} |
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else{ |
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// calc the scaled coordinates. |
304 |
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|
305 |
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for(i=0; i<3; i++) |
306 |
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scaled[i] = thePos[i]*HmatInv[i][i]; |
307 |
+ |
|
308 |
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// wrap the scaled coordinates |
309 |
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|
310 |
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for(i=0; i<3; i++) |
311 |
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scaled[i] -= roundMe(scaled[i]); |
312 |
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|
313 |
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// calc the wrapped real coordinates from the wrapped scaled coordinates |
314 |
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|
315 |
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for(i=0; i<3; i++) |
316 |
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thePos[i] = scaled[i]*Hmat[i][i]; |
317 |
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} |
318 |
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|
319 |
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} |
320 |
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|
321 |
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|
322 |
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int SimInfo::getNDF(){ |
323 |
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int ndf_local; |
324 |
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|
325 |
+ |
ndf_local = 0; |
326 |
+ |
|
327 |
+ |
for(int i = 0; i < integrableObjects.size(); i++){ |
328 |
+ |
ndf_local += 3; |
329 |
+ |
if (integrableObjects[i]->isDirectional()) { |
330 |
+ |
if (integrableObjects[i]->isLinear()) |
331 |
+ |
ndf_local += 2; |
332 |
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else |
333 |
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ndf_local += 3; |
334 |
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} |
335 |
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} |
336 |
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|
337 |
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// n_constraints is local, so subtract them on each processor: |
338 |
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|
339 |
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ndf_local -= n_constraints; |
340 |
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|
341 |
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#ifdef IS_MPI |
342 |
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MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
343 |
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#else |
344 |
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ndf = ndf_local; |
345 |
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#endif |
346 |
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|
347 |
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// nZconstraints is global, as are the 3 COM translations for the |
348 |
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// entire system: |
349 |
+ |
|
350 |
+ |
ndf = ndf - 3 - nZconstraints; |
351 |
+ |
|
352 |
+ |
return ndf; |
353 |
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} |
354 |
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|
355 |
+ |
int SimInfo::getNDFraw() { |
356 |
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int ndfRaw_local; |
357 |
+ |
|
358 |
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// Raw degrees of freedom that we have to set |
359 |
+ |
ndfRaw_local = 0; |
360 |
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|
361 |
+ |
for(int i = 0; i < integrableObjects.size(); i++){ |
362 |
+ |
ndfRaw_local += 3; |
363 |
+ |
if (integrableObjects[i]->isDirectional()) { |
364 |
+ |
if (integrableObjects[i]->isLinear()) |
365 |
+ |
ndfRaw_local += 2; |
366 |
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else |
367 |
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ndfRaw_local += 3; |
368 |
+ |
} |
369 |
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} |
370 |
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|
371 |
+ |
#ifdef IS_MPI |
372 |
+ |
MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
373 |
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#else |
374 |
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ndfRaw = ndfRaw_local; |
375 |
+ |
#endif |
376 |
+ |
|
377 |
+ |
return ndfRaw; |
378 |
+ |
} |
379 |
+ |
|
380 |
+ |
int SimInfo::getNDFtranslational() { |
381 |
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int ndfTrans_local; |
382 |
+ |
|
383 |
+ |
ndfTrans_local = 3 * integrableObjects.size() - n_constraints; |
384 |
+ |
|
385 |
+ |
|
386 |
+ |
#ifdef IS_MPI |
387 |
+ |
MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
388 |
+ |
#else |
389 |
+ |
ndfTrans = ndfTrans_local; |
390 |
+ |
#endif |
391 |
+ |
|
392 |
+ |
ndfTrans = ndfTrans - 3 - nZconstraints; |
393 |
+ |
|
394 |
+ |
return ndfTrans; |
395 |
+ |
} |
396 |
+ |
|
397 |
+ |
int SimInfo::getTotIntegrableObjects() { |
398 |
+ |
int nObjs_local; |
399 |
+ |
int nObjs; |
400 |
+ |
|
401 |
+ |
nObjs_local = integrableObjects.size(); |
402 |
+ |
|
403 |
+ |
|
404 |
+ |
#ifdef IS_MPI |
405 |
+ |
MPI_Allreduce(&nObjs_local,&nObjs,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
406 |
+ |
#else |
407 |
+ |
nObjs = nObjs_local; |
408 |
+ |
#endif |
409 |
+ |
|
410 |
+ |
|
411 |
+ |
return nObjs; |
412 |
+ |
} |
413 |
+ |
|
414 |
|
void SimInfo::refreshSim(){ |
415 |
|
|
416 |
|
simtype fInfo; |
417 |
|
int isError; |
418 |
+ |
int n_global; |
419 |
|
int* excl; |
420 |
|
|
421 |
< |
fInfo.box[0] = box_x; |
44 |
< |
fInfo.box[1] = box_y; |
45 |
< |
fInfo.box[2] = box_z; |
421 |
> |
fInfo.dielect = 0.0; |
422 |
|
|
423 |
< |
fInfo.rlist = rList; |
424 |
< |
fInfo.rcut = rCut; |
425 |
< |
fInfo.rrf = ecr; |
50 |
< |
fInfo.rt = ecr - est; |
51 |
< |
fInfo.dielect = dielectric; |
423 |
> |
if( useDipoles ){ |
424 |
> |
if( useReactionField )fInfo.dielect = dielectric; |
425 |
> |
} |
426 |
|
|
427 |
|
fInfo.SIM_uses_PBC = usePBC; |
428 |
+ |
//fInfo.SIM_uses_LJ = 0; |
429 |
|
fInfo.SIM_uses_LJ = useLJ; |
430 |
< |
|
431 |
< |
//fInfo.SIM_uses_sticky = useSticky; |
432 |
< |
fInfo.SIM_uses_sticky = 0; |
433 |
< |
fInfo.SIM_uses_dipoles = useDipole; |
430 |
> |
fInfo.SIM_uses_sticky = useSticky; |
431 |
> |
//fInfo.SIM_uses_sticky = 0; |
432 |
> |
fInfo.SIM_uses_charges = useCharges; |
433 |
> |
fInfo.SIM_uses_dipoles = useDipoles; |
434 |
|
//fInfo.SIM_uses_dipoles = 0; |
435 |
|
fInfo.SIM_uses_RF = useReactionField; |
436 |
+ |
//fInfo.SIM_uses_RF = 0; |
437 |
|
fInfo.SIM_uses_GB = useGB; |
438 |
|
fInfo.SIM_uses_EAM = useEAM; |
439 |
|
|
440 |
< |
excl = Exclude::getArray(); |
440 |
> |
n_exclude = excludes->getSize(); |
441 |
> |
excl = excludes->getFortranArray(); |
442 |
|
|
443 |
+ |
#ifdef IS_MPI |
444 |
+ |
n_global = mpiSim->getTotAtoms(); |
445 |
+ |
#else |
446 |
+ |
n_global = n_atoms; |
447 |
+ |
#endif |
448 |
+ |
|
449 |
|
isError = 0; |
450 |
|
|
451 |
< |
fInfo; |
452 |
< |
n_atoms; |
453 |
< |
identArray; |
71 |
< |
n_exclude; |
72 |
< |
excludes; |
73 |
< |
nGlobalExcludes; |
74 |
< |
globalExcludes; |
75 |
< |
isError; |
451 |
> |
setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl, |
452 |
> |
&nGlobalExcludes, globalExcludes, molMembershipArray, |
453 |
> |
&isError ); |
454 |
|
|
77 |
– |
setFsimulation( &fInfo, &n_atoms, identArray, &n_exclude, excl, |
78 |
– |
&nGlobalExcludes, globalExcludes, &isError ); |
79 |
– |
|
455 |
|
if( isError ){ |
456 |
|
|
457 |
|
sprintf( painCave.errMsg, |
465 |
|
"succesfully sent the simulation information to fortran.\n"); |
466 |
|
MPIcheckPoint(); |
467 |
|
#endif // is_mpi |
468 |
+ |
|
469 |
+ |
this->ndf = this->getNDF(); |
470 |
+ |
this->ndfRaw = this->getNDFraw(); |
471 |
+ |
this->ndfTrans = this->getNDFtranslational(); |
472 |
|
} |
473 |
|
|
474 |
+ |
void SimInfo::setDefaultRcut( double theRcut ){ |
475 |
+ |
|
476 |
+ |
haveRcut = 1; |
477 |
+ |
rCut = theRcut; |
478 |
+ |
|
479 |
+ |
( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0; |
480 |
+ |
|
481 |
+ |
notifyFortranCutOffs( &rCut, &rList, &ecr, &est ); |
482 |
+ |
} |
483 |
+ |
|
484 |
+ |
void SimInfo::setDefaultEcr( double theEcr ){ |
485 |
+ |
|
486 |
+ |
haveEcr = 1; |
487 |
+ |
ecr = theEcr; |
488 |
+ |
|
489 |
+ |
( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0; |
490 |
+ |
|
491 |
+ |
notifyFortranCutOffs( &rCut, &rList, &ecr, &est ); |
492 |
+ |
} |
493 |
+ |
|
494 |
+ |
void SimInfo::setDefaultEcr( double theEcr, double theEst ){ |
495 |
+ |
|
496 |
+ |
est = theEst; |
497 |
+ |
setDefaultEcr( theEcr ); |
498 |
+ |
} |
499 |
+ |
|
500 |
+ |
|
501 |
+ |
void SimInfo::checkCutOffs( void ){ |
502 |
+ |
|
503 |
+ |
if( boxIsInit ){ |
504 |
+ |
|
505 |
+ |
//we need to check cutOffs against the box |
506 |
+ |
|
507 |
+ |
if( rCut > maxCutoff ){ |
508 |
+ |
sprintf( painCave.errMsg, |
509 |
+ |
"LJrcut is too large for the current periodic box.\n" |
510 |
+ |
"\tCurrent Value of LJrcut = %G at time %G\n " |
511 |
+ |
"\tThis is larger than half of at least one of the\n" |
512 |
+ |
"\tperiodic box vectors. Right now, the Box matrix is:\n" |
513 |
+ |
"\n" |
514 |
+ |
"\t[ %G %G %G ]\n" |
515 |
+ |
"\t[ %G %G %G ]\n" |
516 |
+ |
"\t[ %G %G %G ]\n", |
517 |
+ |
rCut, currentTime, |
518 |
+ |
Hmat[0][0], Hmat[0][1], Hmat[0][2], |
519 |
+ |
Hmat[1][0], Hmat[1][1], Hmat[1][2], |
520 |
+ |
Hmat[2][0], Hmat[2][1], Hmat[2][2]); |
521 |
+ |
painCave.isFatal = 1; |
522 |
+ |
simError(); |
523 |
+ |
} |
524 |
+ |
|
525 |
+ |
if( haveEcr ){ |
526 |
+ |
if( ecr > maxCutoff ){ |
527 |
+ |
sprintf( painCave.errMsg, |
528 |
+ |
"electrostaticCutoffRadius is too large for the current\n" |
529 |
+ |
"\tperiodic box.\n\n" |
530 |
+ |
"\tCurrent Value of ECR = %G at time %G\n " |
531 |
+ |
"\tThis is larger than half of at least one of the\n" |
532 |
+ |
"\tperiodic box vectors. Right now, the Box matrix is:\n" |
533 |
+ |
"\n" |
534 |
+ |
"\t[ %G %G %G ]\n" |
535 |
+ |
"\t[ %G %G %G ]\n" |
536 |
+ |
"\t[ %G %G %G ]\n", |
537 |
+ |
ecr, currentTime, |
538 |
+ |
Hmat[0][0], Hmat[0][1], Hmat[0][2], |
539 |
+ |
Hmat[1][0], Hmat[1][1], Hmat[1][2], |
540 |
+ |
Hmat[2][0], Hmat[2][1], Hmat[2][2]); |
541 |
+ |
painCave.isFatal = 1; |
542 |
+ |
simError(); |
543 |
+ |
} |
544 |
+ |
} |
545 |
+ |
} else { |
546 |
+ |
// initialize this stuff before using it, OK? |
547 |
+ |
sprintf( painCave.errMsg, |
548 |
+ |
"Trying to check cutoffs without a box.\n" |
549 |
+ |
"\tOOPSE should have better programmers than that.\n" ); |
550 |
+ |
painCave.isFatal = 1; |
551 |
+ |
simError(); |
552 |
+ |
} |
553 |
+ |
|
554 |
+ |
} |
555 |
+ |
|
556 |
+ |
void SimInfo::addProperty(GenericData* prop){ |
557 |
+ |
|
558 |
+ |
map<string, GenericData*>::iterator result; |
559 |
+ |
result = properties.find(prop->getID()); |
560 |
+ |
|
561 |
+ |
//we can't simply use properties[prop->getID()] = prop, |
562 |
+ |
//it will cause memory leak if we already contain a propery which has the same name of prop |
563 |
+ |
|
564 |
+ |
if(result != properties.end()){ |
565 |
+ |
|
566 |
+ |
delete (*result).second; |
567 |
+ |
(*result).second = prop; |
568 |
+ |
|
569 |
+ |
} |
570 |
+ |
else{ |
571 |
+ |
|
572 |
+ |
properties[prop->getID()] = prop; |
573 |
+ |
|
574 |
+ |
} |
575 |
+ |
|
576 |
+ |
} |
577 |
+ |
|
578 |
+ |
GenericData* SimInfo::getProperty(const string& propName){ |
579 |
+ |
|
580 |
+ |
map<string, GenericData*>::iterator result; |
581 |
+ |
|
582 |
+ |
//string lowerCaseName = (); |
583 |
+ |
|
584 |
+ |
result = properties.find(propName); |
585 |
+ |
|
586 |
+ |
if(result != properties.end()) |
587 |
+ |
return (*result).second; |
588 |
+ |
else |
589 |
+ |
return NULL; |
590 |
+ |
} |
591 |
+ |
|