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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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#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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rSw = 0.0; |
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|
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haveRcut = 0; |
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haveRsw = 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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ngroup = 0; |
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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); |
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|
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minDist = min(min(distXY, distYZ), distZX); |
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return minDist/2; |
281 |
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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; |
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double scaled[3]; |
288 |
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|
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if( !orthoRhombic ){ |
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// calc the scaled coordinates. |
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|
292 |
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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]); |
297 |
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|
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// calc the wrapped real coordinates from the wrapped scaled coordinates |
299 |
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|
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matVecMul3(Hmat, scaled, thePos); |
301 |
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|
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} |
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else{ |
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// calc the scaled coordinates. |
305 |
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|
306 |
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for(i=0; i<3; i++) |
307 |
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scaled[i] = thePos[i]*HmatInv[i][i]; |
308 |
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|
309 |
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// wrap the scaled coordinates |
310 |
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|
311 |
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for(i=0; i<3; i++) |
312 |
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scaled[i] -= roundMe(scaled[i]); |
313 |
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|
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// calc the wrapped real coordinates from the wrapped scaled coordinates |
315 |
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|
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for(i=0; i<3; i++) |
317 |
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thePos[i] = scaled[i]*Hmat[i][i]; |
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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|
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int SimInfo::getNDF(){ |
324 |
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int ndf_local; |
325 |
+ |
|
326 |
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ndf_local = 0; |
327 |
+ |
|
328 |
+ |
for(int i = 0; i < integrableObjects.size(); i++){ |
329 |
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ndf_local += 3; |
330 |
+ |
if (integrableObjects[i]->isDirectional()) { |
331 |
+ |
if (integrableObjects[i]->isLinear()) |
332 |
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ndf_local += 2; |
333 |
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else |
334 |
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ndf_local += 3; |
335 |
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} |
336 |
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} |
337 |
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|
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// n_constraints is local, so subtract them on each processor: |
339 |
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|
340 |
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ndf_local -= n_constraints; |
341 |
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|
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+ |
#ifdef IS_MPI |
343 |
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MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
344 |
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#else |
345 |
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ndf = ndf_local; |
346 |
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#endif |
347 |
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|
348 |
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// nZconstraints is global, as are the 3 COM translations for the |
349 |
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// entire system: |
350 |
+ |
|
351 |
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ndf = ndf - 3 - nZconstraints; |
352 |
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|
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return ndf; |
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|
} |
355 |
|
|
356 |
+ |
int SimInfo::getNDFraw() { |
357 |
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int ndfRaw_local; |
358 |
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|
359 |
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// Raw degrees of freedom that we have to set |
360 |
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ndfRaw_local = 0; |
361 |
+ |
|
362 |
+ |
for(int i = 0; i < integrableObjects.size(); i++){ |
363 |
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ndfRaw_local += 3; |
364 |
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if (integrableObjects[i]->isDirectional()) { |
365 |
+ |
if (integrableObjects[i]->isLinear()) |
366 |
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ndfRaw_local += 2; |
367 |
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else |
368 |
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ndfRaw_local += 3; |
369 |
+ |
} |
370 |
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} |
371 |
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|
372 |
+ |
#ifdef IS_MPI |
373 |
+ |
MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
374 |
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#else |
375 |
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ndfRaw = ndfRaw_local; |
376 |
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#endif |
377 |
+ |
|
378 |
+ |
return ndfRaw; |
379 |
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} |
380 |
+ |
|
381 |
+ |
int SimInfo::getNDFtranslational() { |
382 |
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int ndfTrans_local; |
383 |
+ |
|
384 |
+ |
ndfTrans_local = 3 * integrableObjects.size() - n_constraints; |
385 |
+ |
|
386 |
+ |
|
387 |
+ |
#ifdef IS_MPI |
388 |
+ |
MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
389 |
+ |
#else |
390 |
+ |
ndfTrans = ndfTrans_local; |
391 |
+ |
#endif |
392 |
+ |
|
393 |
+ |
ndfTrans = ndfTrans - 3 - nZconstraints; |
394 |
+ |
|
395 |
+ |
return ndfTrans; |
396 |
+ |
} |
397 |
+ |
|
398 |
+ |
int SimInfo::getTotIntegrableObjects() { |
399 |
+ |
int nObjs_local; |
400 |
+ |
int nObjs; |
401 |
+ |
|
402 |
+ |
nObjs_local = integrableObjects.size(); |
403 |
+ |
|
404 |
+ |
|
405 |
+ |
#ifdef IS_MPI |
406 |
+ |
MPI_Allreduce(&nObjs_local,&nObjs,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
407 |
+ |
#else |
408 |
+ |
nObjs = nObjs_local; |
409 |
+ |
#endif |
410 |
+ |
|
411 |
+ |
|
412 |
+ |
return nObjs; |
413 |
+ |
} |
414 |
+ |
|
415 |
|
void SimInfo::refreshSim(){ |
416 |
|
|
417 |
|
simtype fInfo; |
418 |
|
int isError; |
419 |
+ |
int n_global; |
420 |
+ |
int* excl; |
421 |
|
|
422 |
< |
fInfo.box[0] = box_x; |
42 |
< |
fInfo.box[1] = box_y; |
43 |
< |
fInfo.box[2] = box_z; |
422 |
> |
fInfo.dielect = 0.0; |
423 |
|
|
424 |
< |
fInfo.rlist = rList; |
425 |
< |
fInfo.rcut = rCut; |
426 |
< |
fInfo.rrf = ecr; |
48 |
< |
fInfo.rt = ecr - est; |
49 |
< |
fInfo.dielect = dielectric; |
424 |
> |
if( useDipoles ){ |
425 |
> |
if( useReactionField )fInfo.dielect = dielectric; |
426 |
> |
} |
427 |
|
|
428 |
|
fInfo.SIM_uses_PBC = usePBC; |
429 |
+ |
//fInfo.SIM_uses_LJ = 0; |
430 |
|
fInfo.SIM_uses_LJ = useLJ; |
431 |
< |
//fInfo.SIM_uses_sticky = useSticky; |
432 |
< |
fInfo.SIM_uses_sticky = 0; |
433 |
< |
fInfo.SIM_uses_dipoles = useDipole; |
431 |
> |
fInfo.SIM_uses_sticky = useSticky; |
432 |
> |
//fInfo.SIM_uses_sticky = 0; |
433 |
> |
fInfo.SIM_uses_charges = useCharges; |
434 |
> |
fInfo.SIM_uses_dipoles = useDipoles; |
435 |
|
//fInfo.SIM_uses_dipoles = 0; |
436 |
|
fInfo.SIM_uses_RF = useReactionField; |
437 |
+ |
//fInfo.SIM_uses_RF = 0; |
438 |
|
fInfo.SIM_uses_GB = useGB; |
439 |
|
fInfo.SIM_uses_EAM = useEAM; |
440 |
|
|
441 |
< |
|
441 |
> |
n_exclude = excludes->getSize(); |
442 |
> |
excl = excludes->getFortranArray(); |
443 |
> |
|
444 |
> |
#ifdef IS_MPI |
445 |
> |
n_global = mpiSim->getTotAtoms(); |
446 |
> |
#else |
447 |
> |
n_global = n_atoms; |
448 |
> |
#endif |
449 |
> |
|
450 |
|
isError = 0; |
451 |
< |
|
452 |
< |
fInfo; |
453 |
< |
n_atoms; |
454 |
< |
identArray; |
455 |
< |
n_exclude; |
456 |
< |
excludes; |
457 |
< |
nGlobalExcludes; |
70 |
< |
globalExcludes; |
71 |
< |
isError; |
72 |
< |
|
73 |
< |
setFsimulation( &fInfo, &n_atoms, identArray, &n_exclude, excludes, &nGlobalExcludes, globalExcludes, &isError ); |
74 |
< |
|
451 |
> |
|
452 |
> |
getFortranGroupArray(this, mfact, ngroup, groupList, groupStart); |
453 |
> |
|
454 |
> |
setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl, |
455 |
> |
&nGlobalExcludes, globalExcludes, molMembershipArray, |
456 |
> |
&mfact[0], &ngroup, &groupList[0], &groupStart[0], &isError); |
457 |
> |
|
458 |
|
if( isError ){ |
459 |
< |
|
459 |
> |
|
460 |
|
sprintf( painCave.errMsg, |
461 |
< |
"There was an error setting the simulation information in fortran.\n" ); |
461 |
> |
"There was an error setting the simulation information in fortran.\n" ); |
462 |
|
painCave.isFatal = 1; |
463 |
|
simError(); |
464 |
|
} |
465 |
< |
|
465 |
> |
|
466 |
|
#ifdef IS_MPI |
467 |
|
sprintf( checkPointMsg, |
468 |
|
"succesfully sent the simulation information to fortran.\n"); |
469 |
|
MPIcheckPoint(); |
470 |
|
#endif // is_mpi |
471 |
+ |
|
472 |
+ |
this->ndf = this->getNDF(); |
473 |
+ |
this->ndfRaw = this->getNDFraw(); |
474 |
+ |
this->ndfTrans = this->getNDFtranslational(); |
475 |
|
} |
476 |
|
|
477 |
+ |
void SimInfo::setDefaultRcut( double theRcut ){ |
478 |
+ |
|
479 |
+ |
haveRcut = 1; |
480 |
+ |
rCut = theRcut; |
481 |
+ |
rList = rCut + 1.0; |
482 |
+ |
|
483 |
+ |
notifyFortranCutOffs( &rCut, &rSw, &rList ); |
484 |
+ |
} |
485 |
+ |
|
486 |
+ |
void SimInfo::setDefaultRcut( double theRcut, double theRsw ){ |
487 |
+ |
|
488 |
+ |
rSw = theRsw; |
489 |
+ |
setDefaultRcut( theRcut ); |
490 |
+ |
} |
491 |
+ |
|
492 |
+ |
|
493 |
+ |
void SimInfo::checkCutOffs( void ){ |
494 |
+ |
|
495 |
+ |
if( boxIsInit ){ |
496 |
+ |
|
497 |
+ |
//we need to check cutOffs against the box |
498 |
+ |
|
499 |
+ |
if( rCut > maxCutoff ){ |
500 |
+ |
sprintf( painCave.errMsg, |
501 |
+ |
"cutoffRadius is too large for the current periodic box.\n" |
502 |
+ |
"\tCurrent Value of cutoffRadius = %G at time %G\n " |
503 |
+ |
"\tThis is larger than half of at least one of the\n" |
504 |
+ |
"\tperiodic box vectors. Right now, the Box matrix is:\n" |
505 |
+ |
"\n" |
506 |
+ |
"\t[ %G %G %G ]\n" |
507 |
+ |
"\t[ %G %G %G ]\n" |
508 |
+ |
"\t[ %G %G %G ]\n", |
509 |
+ |
rCut, currentTime, |
510 |
+ |
Hmat[0][0], Hmat[0][1], Hmat[0][2], |
511 |
+ |
Hmat[1][0], Hmat[1][1], Hmat[1][2], |
512 |
+ |
Hmat[2][0], Hmat[2][1], Hmat[2][2]); |
513 |
+ |
painCave.isFatal = 1; |
514 |
+ |
simError(); |
515 |
+ |
} |
516 |
+ |
} else { |
517 |
+ |
// initialize this stuff before using it, OK? |
518 |
+ |
sprintf( painCave.errMsg, |
519 |
+ |
"Trying to check cutoffs without a box.\n" |
520 |
+ |
"\tOOPSE should have better programmers than that.\n" ); |
521 |
+ |
painCave.isFatal = 1; |
522 |
+ |
simError(); |
523 |
+ |
} |
524 |
+ |
|
525 |
+ |
} |
526 |
+ |
|
527 |
+ |
void SimInfo::addProperty(GenericData* prop){ |
528 |
+ |
|
529 |
+ |
map<string, GenericData*>::iterator result; |
530 |
+ |
result = properties.find(prop->getID()); |
531 |
+ |
|
532 |
+ |
//we can't simply use properties[prop->getID()] = prop, |
533 |
+ |
//it will cause memory leak if we already contain a propery which has the same name of prop |
534 |
+ |
|
535 |
+ |
if(result != properties.end()){ |
536 |
+ |
|
537 |
+ |
delete (*result).second; |
538 |
+ |
(*result).second = prop; |
539 |
+ |
|
540 |
+ |
} |
541 |
+ |
else{ |
542 |
+ |
|
543 |
+ |
properties[prop->getID()] = prop; |
544 |
+ |
|
545 |
+ |
} |
546 |
+ |
|
547 |
+ |
} |
548 |
+ |
|
549 |
+ |
GenericData* SimInfo::getProperty(const string& propName){ |
550 |
+ |
|
551 |
+ |
map<string, GenericData*>::iterator result; |
552 |
+ |
|
553 |
+ |
//string lowerCaseName = (); |
554 |
+ |
|
555 |
+ |
result = properties.find(propName); |
556 |
+ |
|
557 |
+ |
if(result != properties.end()) |
558 |
+ |
return (*result).second; |
559 |
+ |
else |
560 |
+ |
return NULL; |
561 |
+ |
} |
562 |
+ |
|
563 |
+ |
|
564 |
+ |
void getFortranGroupArray(SimInfo* info, vector<double>& mfact, int& ngroup, |
565 |
+ |
vector<int>& groupList, vector<int>& groupStart){ |
566 |
+ |
Molecule* mol; |
567 |
+ |
Atom** myAtoms; |
568 |
+ |
int numAtom; |
569 |
+ |
int curIndex; |
570 |
+ |
double mtot; |
571 |
+ |
|
572 |
+ |
mfact.clear(); |
573 |
+ |
groupList.clear(); |
574 |
+ |
groupStart.clear(); |
575 |
+ |
|
576 |
+ |
//Be careful, fortran array begin at 1 |
577 |
+ |
curIndex = 1; |
578 |
+ |
|
579 |
+ |
if(info->useMolecularCutoffs){ |
580 |
+ |
|
581 |
+ |
#ifdef IS_MPI |
582 |
+ |
ngroup = mpiSim->getMyNMol(); |
583 |
+ |
#else |
584 |
+ |
ngroup = info->n_mol; |
585 |
+ |
#endif |
586 |
+ |
|
587 |
+ |
for(int i = 0; i < ngroup; i ++){ |
588 |
+ |
mol = &(info->molecules[i]); |
589 |
+ |
numAtom = mol->getNAtoms(); |
590 |
+ |
myAtoms = mol->getMyAtoms(); |
591 |
+ |
mtot = 0.0; |
592 |
+ |
|
593 |
+ |
for(int j=0; j < numAtom; j++) |
594 |
+ |
mtot += myAtoms[j]->getMass(); |
595 |
+ |
|
596 |
+ |
for(int j=0; j < numAtom; j++){ |
597 |
+ |
|
598 |
+ |
// We want the local Index: |
599 |
+ |
groupList.push_back(myAtoms[j]->getIndex() + 1); |
600 |
+ |
mfact.push_back(myAtoms[j]->getMass() / mtot); |
601 |
+ |
|
602 |
+ |
} |
603 |
+ |
|
604 |
+ |
groupStart.push_back(curIndex); |
605 |
+ |
curIndex += numAtom; |
606 |
+ |
|
607 |
+ |
} //end for(int i =0 ; i < ngroup; i++) |
608 |
+ |
} |
609 |
+ |
else{ |
610 |
+ |
//using atomic cutoff, every single atom is just a group |
611 |
+ |
|
612 |
+ |
#ifdef IS_MPI |
613 |
+ |
ngroup = mpiSim->getMyNlocal(); |
614 |
+ |
#else |
615 |
+ |
ngroup = info->n_atoms; |
616 |
+ |
#endif |
617 |
+ |
|
618 |
+ |
for(int i =0 ; i < ngroup; i++){ |
619 |
+ |
groupStart.push_back(curIndex++); |
620 |
+ |
groupList.push_back((info->atoms[i])->getIndex() + 1); |
621 |
+ |
mfact.push_back(1.0); |
622 |
+ |
|
623 |
+ |
}//end for(int i =0 ; i < ngroup; i++) |
624 |
+ |
|
625 |
+ |
}//end if (info->useMolecularCutoffs) |
626 |
+ |
|
627 |
+ |
} |