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#include <cstdlib> |
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#include <cstring> |
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#include <cmath> |
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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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wrapMeSimInfo( this ); |
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} |
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excludes = Exclude::Instance(); |
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void SimInfo::setBox(double newBox[3]) { |
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myConfiguration = new SimState(); |
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|
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double smallestBoxL, maxCutoff; |
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int status; |
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int i; |
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has_minimizer = false; |
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the_minimizer =NULL; |
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|
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for(i=0; i<9; i++) Hmat[i] = 0.0;; |
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wrapMeSimInfo( this ); |
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} |
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|
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Hmat[0] = newBox[0]; |
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Hmat[4] = newBox[1]; |
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Hmat[8] = newBox[2]; |
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|
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calcHmatI(); |
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calcBoxL(); |
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SimInfo::~SimInfo(){ |
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|
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setFortranBoxSize(Hmat, HmatI, &orthoRhombic); |
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delete myConfiguration; |
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|
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smallestBoxL = boxLx; |
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if (boxLy < smallestBoxL) smallestBoxL = boxLy; |
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if (boxLz < smallestBoxL) smallestBoxL = boxLz; |
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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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maxCutoff = smallestBoxL / 2.0; |
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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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if (rList > maxCutoff) { |
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sprintf( painCave.errMsg, |
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"New Box size is forcing neighborlist radius down to %lf\n", |
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maxCutoff ); |
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painCave.isFatal = 0; |
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simError(); |
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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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rList = maxCutoff; |
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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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sprintf( painCave.errMsg, |
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"New Box size is forcing cutoff radius down to %lf\n", |
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maxCutoff - 1.0 ); |
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painCave.isFatal = 0; |
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simError(); |
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setBoxM( tempMat ); |
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|
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rCut = rList - 1.0; |
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|
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// list radius changed so we have to refresh the simulation structure. |
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refreshSim(); |
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} |
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|
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if (rCut > maxCutoff) { |
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sprintf( painCave.errMsg, |
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"New Box size is forcing cutoff radius down to %lf\n", |
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maxCutoff ); |
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painCave.isFatal = 0; |
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simError(); |
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|
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status = 0; |
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LJ_new_rcut(&rCut, &status); |
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if (status != 0) { |
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sprintf( painCave.errMsg, |
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"Error in recomputing LJ shifts based on new rcut\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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} |
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|
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void SimInfo::setBoxM( double theBox[9] ){ |
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void SimInfo::setBoxM( double theBox[3][3] ){ |
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|
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int i, status; |
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double smallestBoxL, maxCutoff; |
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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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for(i=0; i<9; i++) Hmat[i] = theBox[i]; |
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calcHmatI(); |
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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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setFortranBoxSize(Hmat, HmatI, &orthoRhombic); |
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for(i=0; i < 3; i++) { |
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for (j=0; j < 3; j++) { |
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FortranHmat[3*j + i] = Hmat[i][j]; |
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FortranHmatInv[3*j + i] = HmatInv[i][j]; |
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} |
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} |
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|
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setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic); |
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|
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smallestBoxL = boxLx; |
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if (boxLy < smallestBoxL) smallestBoxL = boxLy; |
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if (boxLz < smallestBoxL) smallestBoxL = boxLz; |
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} |
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|
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|
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maxCutoff = smallestBoxL / 2.0; |
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> |
void SimInfo::getBoxM (double theBox[3][3]) { |
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|
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if (rList > maxCutoff) { |
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sprintf( painCave.errMsg, |
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"New Box size is forcing neighborlist radius down to %lf\n", |
140 |
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maxCutoff ); |
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painCave.isFatal = 0; |
126 |
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simError(); |
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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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rList = maxCutoff; |
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|
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sprintf( painCave.errMsg, |
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"New Box size is forcing cutoff radius down to %lf\n", |
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maxCutoff - 1.0 ); |
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painCave.isFatal = 0; |
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simError(); |
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> |
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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rCut = rList - 1.0; |
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// cerr << "Scaling box by " << scale << "\n"; |
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|
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// list radius changed so we have to refresh the simulation structure. |
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refreshSim(); |
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} |
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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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if (rCut > maxCutoff) { |
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sprintf( painCave.errMsg, |
144 |
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"New Box size is forcing cutoff radius down to %lf\n", |
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maxCutoff ); |
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painCave.isFatal = 0; |
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simError(); |
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setBoxM(theBox); |
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|
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status = 0; |
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LJ_new_rcut(&rCut, &status); |
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if (status != 0) { |
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sprintf( painCave.errMsg, |
153 |
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"Error in recomputing LJ shifts based on new rcut\n"); |
154 |
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painCave.isFatal = 1; |
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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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|
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< |
void SimInfo::getBox(double theBox[9]) { |
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|
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int i; |
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< |
for(i=0; i<9; i++) theBox[i] = Hmat[i]; |
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} |
166 |
< |
|
167 |
< |
|
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< |
void SimInfo::calcHmatI( void ) { |
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|
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< |
double C[3][3]; |
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< |
double detHmat; |
172 |
< |
int i, j, k; |
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> |
void SimInfo::calcHmatInv( void ) { |
157 |
> |
|
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> |
int oldOrtho; |
159 |
> |
int i,j; |
160 |
|
double smallDiag; |
161 |
|
double tol; |
162 |
|
double sanity[3][3]; |
163 |
|
|
164 |
< |
// calculate the adjunct of Hmat; |
164 |
> |
invertMat3( Hmat, HmatInv ); |
165 |
|
|
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< |
C[0][0] = ( Hmat[4]*Hmat[8]) - (Hmat[7]*Hmat[5]); |
180 |
< |
C[1][0] = -( Hmat[1]*Hmat[8]) + (Hmat[7]*Hmat[2]); |
181 |
< |
C[2][0] = ( Hmat[1]*Hmat[5]) - (Hmat[4]*Hmat[2]); |
182 |
< |
|
183 |
< |
C[0][1] = -( Hmat[3]*Hmat[8]) + (Hmat[6]*Hmat[5]); |
184 |
< |
C[1][1] = ( Hmat[0]*Hmat[8]) - (Hmat[6]*Hmat[2]); |
185 |
< |
C[2][1] = -( Hmat[0]*Hmat[5]) + (Hmat[3]*Hmat[2]); |
186 |
< |
|
187 |
< |
C[0][2] = ( Hmat[3]*Hmat[7]) - (Hmat[6]*Hmat[4]); |
188 |
< |
C[1][2] = -( Hmat[0]*Hmat[7]) + (Hmat[6]*Hmat[1]); |
189 |
< |
C[2][2] = ( Hmat[0]*Hmat[4]) - (Hmat[3]*Hmat[1]); |
190 |
< |
|
191 |
< |
// calcutlate the determinant of Hmat |
166 |
> |
// check to see if Hmat is orthorhombic |
167 |
|
|
168 |
< |
detHmat = 0.0; |
194 |
< |
for(i=0; i<3; i++) detHmat += Hmat[i] * C[i][0]; |
168 |
> |
oldOrtho = orthoRhombic; |
169 |
|
|
170 |
< |
|
171 |
< |
// H^-1 = C^T / det(H) |
172 |
< |
|
173 |
< |
i=0; |
200 |
< |
for(j=0; j<3; j++){ |
201 |
< |
for(k=0; k<3; k++){ |
170 |
> |
smallDiag = fabs(Hmat[0][0]); |
171 |
> |
if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]); |
172 |
> |
if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]); |
173 |
> |
tol = smallDiag * orthoTolerance; |
174 |
|
|
175 |
< |
HmatI[i] = C[j][k] / detHmat; |
176 |
< |
i++; |
177 |
< |
} |
178 |
< |
} |
179 |
< |
|
180 |
< |
// sanity check |
181 |
< |
|
182 |
< |
for(i=0; i<3; i++){ |
211 |
< |
for(j=0; j<3; j++){ |
212 |
< |
|
213 |
< |
sanity[i][j] = 0.0; |
214 |
< |
for(k=0; k<3; k++){ |
215 |
< |
sanity[i][j] += Hmat[3*k+i] * HmatI[3*j+k]; |
175 |
> |
orthoRhombic = 1; |
176 |
> |
|
177 |
> |
for (i = 0; i < 3; i++ ) { |
178 |
> |
for (j = 0 ; j < 3; j++) { |
179 |
> |
if (i != j) { |
180 |
> |
if (orthoRhombic) { |
181 |
> |
if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0; |
182 |
> |
} |
183 |
|
} |
184 |
|
} |
185 |
|
} |
186 |
|
|
187 |
< |
cerr << "sanity => \n" |
221 |
< |
<< sanity[0][0] << "\t" << sanity[0][1] << "\t" << sanity [0][2] << "\n" |
222 |
< |
<< sanity[1][0] << "\t" << sanity[1][1] << "\t" << sanity [1][2] << "\n" |
223 |
< |
<< sanity[2][0] << "\t" << sanity[2][1] << "\t" << sanity [2][2] |
224 |
< |
<< "\n"; |
187 |
> |
if( oldOrtho != orthoRhombic ){ |
188 |
|
|
189 |
< |
|
190 |
< |
// check to see if Hmat is orthorhombic |
191 |
< |
|
192 |
< |
smallDiag = Hmat[0]; |
193 |
< |
if(smallDiag > Hmat[4]) smallDiag = Hmat[4]; |
194 |
< |
if(smallDiag > Hmat[8]) smallDiag = Hmat[8]; |
195 |
< |
tol = smallDiag * 1E-6; |
196 |
< |
|
197 |
< |
orthoRhombic = 1; |
235 |
< |
for(i=0; (i<9) && orthoRhombic; i++){ |
236 |
< |
|
237 |
< |
if( (i%4) ){ // ignore the diagonals (0, 4, and 8) |
238 |
< |
orthoRhombic = (Hmat[i] <= tol); |
189 |
> |
if( orthoRhombic ){ |
190 |
> |
sprintf( painCave.errMsg, |
191 |
> |
"OOPSE is switching from the default Non-Orthorhombic\n" |
192 |
> |
"\tto the faster Orthorhombic periodic boundary computations.\n" |
193 |
> |
"\tThis is usually a good thing, but if you wan't the\n" |
194 |
> |
"\tNon-Orthorhombic computations, make the orthoBoxTolerance\n" |
195 |
> |
"\tvariable ( currently set to %G ) smaller.\n", |
196 |
> |
orthoTolerance); |
197 |
> |
simError(); |
198 |
|
} |
199 |
+ |
else { |
200 |
+ |
sprintf( painCave.errMsg, |
201 |
+ |
"OOPSE is switching from the faster Orthorhombic to the more\n" |
202 |
+ |
"\tflexible Non-Orthorhombic periodic boundary computations.\n" |
203 |
+ |
"\tThis is usually because the box has deformed under\n" |
204 |
+ |
"\tNPTf integration. If you wan't to live on the edge with\n" |
205 |
+ |
"\tthe Orthorhombic computations, make the orthoBoxTolerance\n" |
206 |
+ |
"\tvariable ( currently set to %G ) larger.\n", |
207 |
+ |
orthoTolerance); |
208 |
+ |
simError(); |
209 |
+ |
} |
210 |
|
} |
241 |
– |
|
211 |
|
} |
212 |
|
|
213 |
|
void SimInfo::calcBoxL( void ){ |
214 |
|
|
215 |
|
double dx, dy, dz, dsq; |
247 |
– |
int i; |
216 |
|
|
217 |
< |
// boxVol = h1 (dot) h2 (cross) h3 |
217 |
> |
// boxVol = Determinant of Hmat |
218 |
|
|
219 |
< |
boxVol = Hmat[0] * ( (Hmat[4]*Hmat[8]) - (Hmat[7]*Hmat[5]) ) |
252 |
< |
+ Hmat[1] * ( (Hmat[5]*Hmat[6]) - (Hmat[8]*Hmat[3]) ) |
253 |
< |
+ Hmat[2] * ( (Hmat[3]*Hmat[7]) - (Hmat[6]*Hmat[4]) ); |
219 |
> |
boxVol = matDet3( Hmat ); |
220 |
|
|
255 |
– |
|
221 |
|
// boxLx |
222 |
|
|
223 |
< |
dx = Hmat[0]; dy = Hmat[1]; dz = Hmat[2]; |
223 |
> |
dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0]; |
224 |
|
dsq = dx*dx + dy*dy + dz*dz; |
225 |
< |
boxLx = sqrt( dsq ); |
225 |
> |
boxL[0] = sqrt( dsq ); |
226 |
> |
//maxCutoff = 0.5 * boxL[0]; |
227 |
|
|
228 |
|
// boxLy |
229 |
|
|
230 |
< |
dx = Hmat[3]; dy = Hmat[4]; dz = Hmat[5]; |
230 |
> |
dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1]; |
231 |
|
dsq = dx*dx + dy*dy + dz*dz; |
232 |
< |
boxLy = sqrt( dsq ); |
232 |
> |
boxL[1] = sqrt( dsq ); |
233 |
> |
//if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1]; |
234 |
|
|
235 |
+ |
|
236 |
|
// boxLz |
237 |
|
|
238 |
< |
dx = Hmat[6]; dy = Hmat[7]; dz = Hmat[8]; |
238 |
> |
dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2]; |
239 |
|
dsq = dx*dx + dy*dy + dz*dz; |
240 |
< |
boxLz = sqrt( dsq ); |
240 |
> |
boxL[2] = sqrt( dsq ); |
241 |
> |
//if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2]; |
242 |
> |
|
243 |
> |
//calculate the max cutoff |
244 |
> |
maxCutoff = calcMaxCutOff(); |
245 |
|
|
246 |
+ |
checkCutOffs(); |
247 |
+ |
|
248 |
|
} |
249 |
|
|
250 |
|
|
251 |
+ |
double SimInfo::calcMaxCutOff(){ |
252 |
+ |
|
253 |
+ |
double ri[3], rj[3], rk[3]; |
254 |
+ |
double rij[3], rjk[3], rki[3]; |
255 |
+ |
double minDist; |
256 |
+ |
|
257 |
+ |
ri[0] = Hmat[0][0]; |
258 |
+ |
ri[1] = Hmat[1][0]; |
259 |
+ |
ri[2] = Hmat[2][0]; |
260 |
+ |
|
261 |
+ |
rj[0] = Hmat[0][1]; |
262 |
+ |
rj[1] = Hmat[1][1]; |
263 |
+ |
rj[2] = Hmat[2][1]; |
264 |
+ |
|
265 |
+ |
rk[0] = Hmat[0][2]; |
266 |
+ |
rk[1] = Hmat[1][2]; |
267 |
+ |
rk[2] = Hmat[2][2]; |
268 |
+ |
|
269 |
+ |
crossProduct3(ri, rj, rij); |
270 |
+ |
distXY = dotProduct3(rk,rij) / norm3(rij); |
271 |
+ |
|
272 |
+ |
crossProduct3(rj,rk, rjk); |
273 |
+ |
distYZ = dotProduct3(ri,rjk) / norm3(rjk); |
274 |
+ |
|
275 |
+ |
crossProduct3(rk,ri, rki); |
276 |
+ |
distZX = dotProduct3(rj,rki) / norm3(rki); |
277 |
+ |
|
278 |
+ |
minDist = min(min(distXY, distYZ), distZX); |
279 |
+ |
return minDist/2; |
280 |
+ |
|
281 |
+ |
} |
282 |
+ |
|
283 |
|
void SimInfo::wrapVector( double thePos[3] ){ |
284 |
|
|
285 |
< |
int i, j, k; |
285 |
> |
int i; |
286 |
|
double scaled[3]; |
287 |
|
|
288 |
|
if( !orthoRhombic ){ |
289 |
|
// calc the scaled coordinates. |
290 |
+ |
|
291 |
+ |
|
292 |
+ |
matVecMul3(HmatInv, thePos, scaled); |
293 |
|
|
294 |
|
for(i=0; i<3; i++) |
295 |
< |
scaled[i] = |
287 |
< |
thePos[0]*HmatI[i] + thePos[1]*HmatI[i+3] + thePos[3]*HmatI[i+6]; |
295 |
> |
scaled[i] -= roundMe(scaled[i]); |
296 |
|
|
289 |
– |
// wrap the scaled coordinates |
290 |
– |
|
291 |
– |
for(i=0; i<3; i++) |
292 |
– |
scaled[i] -= round(scaled[i]); |
293 |
– |
|
297 |
|
// calc the wrapped real coordinates from the wrapped scaled coordinates |
298 |
|
|
299 |
< |
for(i=0; i<3; i++) |
300 |
< |
thePos[i] = |
298 |
< |
scaled[0]*Hmat[i] + scaled[1]*Hmat[i+3] + scaled[3]*Hmat[i+6]; |
299 |
> |
matVecMul3(Hmat, scaled, thePos); |
300 |
> |
|
301 |
|
} |
302 |
|
else{ |
303 |
|
// calc the scaled coordinates. |
304 |
|
|
305 |
|
for(i=0; i<3; i++) |
306 |
< |
scaled[i] = thePos[i]*HmatI[i*4]; |
306 |
> |
scaled[i] = thePos[i]*HmatInv[i][i]; |
307 |
|
|
308 |
|
// wrap the scaled coordinates |
309 |
|
|
310 |
|
for(i=0; i<3; i++) |
311 |
< |
scaled[i] -= round(scaled[i]); |
311 |
> |
scaled[i] -= roundMe(scaled[i]); |
312 |
|
|
313 |
|
// calc the wrapped real coordinates from the wrapped scaled coordinates |
314 |
|
|
315 |
|
for(i=0; i<3; i++) |
316 |
< |
thePos[i] = scaled[i]*Hmat[i*4]; |
316 |
> |
thePos[i] = scaled[i]*Hmat[i][i]; |
317 |
|
} |
318 |
|
|
317 |
– |
|
319 |
|
} |
320 |
|
|
321 |
|
|
322 |
|
int SimInfo::getNDF(){ |
323 |
< |
int ndf_local, ndf; |
323 |
< |
|
324 |
< |
ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints; |
323 |
> |
int ndf_local; |
324 |
|
|
325 |
+ |
for(int i = 0; i < integrableObjects.size(); i++){ |
326 |
+ |
ndf_local += 3; |
327 |
+ |
if (integrableObjects[i]->isDirectional()) |
328 |
+ |
ndf_local += 3; |
329 |
+ |
} |
330 |
+ |
|
331 |
+ |
// n_constraints is local, so subtract them on each processor: |
332 |
+ |
|
333 |
+ |
ndf_local -= n_constraints; |
334 |
+ |
|
335 |
|
#ifdef IS_MPI |
336 |
|
MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
337 |
|
#else |
338 |
|
ndf = ndf_local; |
339 |
|
#endif |
340 |
|
|
341 |
< |
ndf = ndf - 3; |
341 |
> |
// nZconstraints is global, as are the 3 COM translations for the |
342 |
> |
// entire system: |
343 |
|
|
344 |
+ |
ndf = ndf - 3 - nZconstraints; |
345 |
+ |
|
346 |
|
return ndf; |
347 |
|
} |
348 |
|
|
349 |
|
int SimInfo::getNDFraw() { |
350 |
< |
int ndfRaw_local, ndfRaw; |
350 |
> |
int ndfRaw_local; |
351 |
|
|
352 |
|
// Raw degrees of freedom that we have to set |
353 |
< |
ndfRaw_local = 3 * n_atoms + 3 * n_oriented; |
354 |
< |
|
353 |
> |
|
354 |
> |
for(int i = 0; i < integrableObjects.size(); i++){ |
355 |
> |
ndfRaw_local += 3; |
356 |
> |
if (integrableObjects[i]->isDirectional()) |
357 |
> |
ndfRaw_local += 3; |
358 |
> |
} |
359 |
> |
|
360 |
|
#ifdef IS_MPI |
361 |
|
MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
362 |
|
#else |
365 |
|
|
366 |
|
return ndfRaw; |
367 |
|
} |
368 |
< |
|
368 |
> |
|
369 |
> |
int SimInfo::getNDFtranslational() { |
370 |
> |
int ndfTrans_local; |
371 |
> |
|
372 |
> |
ndfTrans_local = 3 * integrableObjects.size() - n_constraints; |
373 |
> |
|
374 |
> |
|
375 |
> |
#ifdef IS_MPI |
376 |
> |
MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
377 |
> |
#else |
378 |
> |
ndfTrans = ndfTrans_local; |
379 |
> |
#endif |
380 |
> |
|
381 |
> |
ndfTrans = ndfTrans - 3 - nZconstraints; |
382 |
> |
|
383 |
> |
return ndfTrans; |
384 |
> |
} |
385 |
> |
|
386 |
> |
int SimInfo::getTotIntegrableObjects() { |
387 |
> |
int nObjs_local; |
388 |
> |
int nObjs; |
389 |
> |
|
390 |
> |
nObjs_local = integrableObjects.size(); |
391 |
> |
|
392 |
> |
|
393 |
> |
#ifdef IS_MPI |
394 |
> |
MPI_Allreduce(&nObjs_local,&nObjs,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
395 |
> |
#else |
396 |
> |
nObjs = nObjs_local; |
397 |
> |
#endif |
398 |
> |
|
399 |
> |
|
400 |
> |
return nObjs; |
401 |
> |
} |
402 |
> |
|
403 |
|
void SimInfo::refreshSim(){ |
404 |
|
|
405 |
|
simtype fInfo; |
406 |
|
int isError; |
407 |
|
int n_global; |
408 |
|
int* excl; |
358 |
– |
|
359 |
– |
fInfo.rrf = 0.0; |
360 |
– |
fInfo.rt = 0.0; |
361 |
– |
fInfo.dielect = 0.0; |
409 |
|
|
410 |
< |
fInfo.box[0] = box_x; |
364 |
< |
fInfo.box[1] = box_y; |
365 |
< |
fInfo.box[2] = box_z; |
410 |
> |
fInfo.dielect = 0.0; |
411 |
|
|
412 |
< |
fInfo.rlist = rList; |
368 |
< |
fInfo.rcut = rCut; |
369 |
< |
|
370 |
< |
if( useDipole ){ |
371 |
< |
fInfo.rrf = ecr; |
372 |
< |
fInfo.rt = ecr - est; |
412 |
> |
if( useDipoles ){ |
413 |
|
if( useReactionField )fInfo.dielect = dielectric; |
414 |
|
} |
415 |
|
|
418 |
|
fInfo.SIM_uses_LJ = useLJ; |
419 |
|
fInfo.SIM_uses_sticky = useSticky; |
420 |
|
//fInfo.SIM_uses_sticky = 0; |
421 |
< |
fInfo.SIM_uses_dipoles = useDipole; |
421 |
> |
fInfo.SIM_uses_charges = useCharges; |
422 |
> |
fInfo.SIM_uses_dipoles = useDipoles; |
423 |
|
//fInfo.SIM_uses_dipoles = 0; |
424 |
< |
//fInfo.SIM_uses_RF = useReactionField; |
425 |
< |
fInfo.SIM_uses_RF = 0; |
424 |
> |
fInfo.SIM_uses_RF = useReactionField; |
425 |
> |
//fInfo.SIM_uses_RF = 0; |
426 |
|
fInfo.SIM_uses_GB = useGB; |
427 |
|
fInfo.SIM_uses_EAM = useEAM; |
428 |
|
|
429 |
< |
excl = Exclude::getArray(); |
429 |
> |
n_exclude = excludes->getSize(); |
430 |
> |
excl = excludes->getFortranArray(); |
431 |
|
|
432 |
|
#ifdef IS_MPI |
433 |
|
n_global = mpiSim->getTotAtoms(); |
457 |
|
|
458 |
|
this->ndf = this->getNDF(); |
459 |
|
this->ndfRaw = this->getNDFraw(); |
460 |
+ |
this->ndfTrans = this->getNDFtranslational(); |
461 |
+ |
} |
462 |
|
|
463 |
+ |
void SimInfo::setDefaultRcut( double theRcut ){ |
464 |
+ |
|
465 |
+ |
haveRcut = 1; |
466 |
+ |
rCut = theRcut; |
467 |
+ |
|
468 |
+ |
( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0; |
469 |
+ |
|
470 |
+ |
notifyFortranCutOffs( &rCut, &rList, &ecr, &est ); |
471 |
|
} |
472 |
|
|
473 |
+ |
void SimInfo::setDefaultEcr( double theEcr ){ |
474 |
+ |
|
475 |
+ |
haveEcr = 1; |
476 |
+ |
ecr = theEcr; |
477 |
+ |
|
478 |
+ |
( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0; |
479 |
+ |
|
480 |
+ |
notifyFortranCutOffs( &rCut, &rList, &ecr, &est ); |
481 |
+ |
} |
482 |
+ |
|
483 |
+ |
void SimInfo::setDefaultEcr( double theEcr, double theEst ){ |
484 |
+ |
|
485 |
+ |
est = theEst; |
486 |
+ |
setDefaultEcr( theEcr ); |
487 |
+ |
} |
488 |
+ |
|
489 |
+ |
|
490 |
+ |
void SimInfo::checkCutOffs( void ){ |
491 |
+ |
|
492 |
+ |
if( boxIsInit ){ |
493 |
+ |
|
494 |
+ |
//we need to check cutOffs against the box |
495 |
+ |
|
496 |
+ |
if( rCut > maxCutoff ){ |
497 |
+ |
sprintf( painCave.errMsg, |
498 |
+ |
"LJrcut is too large for the current periodic box.\n" |
499 |
+ |
"\tCurrent Value of LJrcut = %G at time %G\n " |
500 |
+ |
"\tThis is larger than half of at least one of the\n" |
501 |
+ |
"\tperiodic box vectors. Right now, the Box matrix is:\n" |
502 |
+ |
"\n, %G" |
503 |
+ |
"\t[ %G %G %G ]\n" |
504 |
+ |
"\t[ %G %G %G ]\n" |
505 |
+ |
"\t[ %G %G %G ]\n", |
506 |
+ |
rCut, currentTime, maxCutoff, |
507 |
+ |
Hmat[0][0], Hmat[0][1], Hmat[0][2], |
508 |
+ |
Hmat[1][0], Hmat[1][1], Hmat[1][2], |
509 |
+ |
Hmat[2][0], Hmat[2][1], Hmat[2][2]); |
510 |
+ |
painCave.isFatal = 1; |
511 |
+ |
simError(); |
512 |
+ |
} |
513 |
+ |
|
514 |
+ |
if( haveEcr ){ |
515 |
+ |
if( ecr > maxCutoff ){ |
516 |
+ |
sprintf( painCave.errMsg, |
517 |
+ |
"electrostaticCutoffRadius is too large for the current\n" |
518 |
+ |
"\tperiodic box.\n\n" |
519 |
+ |
"\tCurrent Value of ECR = %G at time %G\n " |
520 |
+ |
"\tThis is larger than half of at least one of the\n" |
521 |
+ |
"\tperiodic box vectors. Right now, the Box matrix is:\n" |
522 |
+ |
"\n" |
523 |
+ |
"\t[ %G %G %G ]\n" |
524 |
+ |
"\t[ %G %G %G ]\n" |
525 |
+ |
"\t[ %G %G %G ]\n", |
526 |
+ |
ecr, currentTime, |
527 |
+ |
Hmat[0][0], Hmat[0][1], Hmat[0][2], |
528 |
+ |
Hmat[1][0], Hmat[1][1], Hmat[1][2], |
529 |
+ |
Hmat[2][0], Hmat[2][1], Hmat[2][2]); |
530 |
+ |
painCave.isFatal = 1; |
531 |
+ |
simError(); |
532 |
+ |
} |
533 |
+ |
} |
534 |
+ |
} else { |
535 |
+ |
// initialize this stuff before using it, OK? |
536 |
+ |
sprintf( painCave.errMsg, |
537 |
+ |
"Trying to check cutoffs without a box.\n" |
538 |
+ |
"\tOOPSE should have better programmers than that.\n" ); |
539 |
+ |
painCave.isFatal = 1; |
540 |
+ |
simError(); |
541 |
+ |
} |
542 |
+ |
|
543 |
+ |
} |
544 |
+ |
|
545 |
+ |
void SimInfo::addProperty(GenericData* prop){ |
546 |
+ |
|
547 |
+ |
map<string, GenericData*>::iterator result; |
548 |
+ |
result = properties.find(prop->getID()); |
549 |
+ |
|
550 |
+ |
//we can't simply use properties[prop->getID()] = prop, |
551 |
+ |
//it will cause memory leak if we already contain a propery which has the same name of prop |
552 |
+ |
|
553 |
+ |
if(result != properties.end()){ |
554 |
+ |
|
555 |
+ |
delete (*result).second; |
556 |
+ |
(*result).second = prop; |
557 |
+ |
|
558 |
+ |
} |
559 |
+ |
else{ |
560 |
+ |
|
561 |
+ |
properties[prop->getID()] = prop; |
562 |
+ |
|
563 |
+ |
} |
564 |
+ |
|
565 |
+ |
} |
566 |
+ |
|
567 |
+ |
GenericData* SimInfo::getProperty(const string& propName){ |
568 |
+ |
|
569 |
+ |
map<string, GenericData*>::iterator result; |
570 |
+ |
|
571 |
+ |
//string lowerCaseName = (); |
572 |
+ |
|
573 |
+ |
result = properties.find(propName); |
574 |
+ |
|
575 |
+ |
if(result != properties.end()) |
576 |
+ |
return (*result).second; |
577 |
+ |
else |
578 |
+ |
return NULL; |
579 |
+ |
} |
580 |
+ |
|
581 |
+ |
vector<GenericData*> SimInfo::getProperties(){ |
582 |
+ |
|
583 |
+ |
vector<GenericData*> result; |
584 |
+ |
map<string, GenericData*>::iterator i; |
585 |
+ |
|
586 |
+ |
for(i = properties.begin(); i != properties.end(); i++) |
587 |
+ |
result.push_back((*i).second); |
588 |
+ |
|
589 |
+ |
return result; |
590 |
+ |
} |