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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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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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thermalTime = 0.0; |
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currentTime = 0.0; |
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rCut = 0.0; |
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origRcut = -1.0; |
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ecr = 0.0; |
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origEcr = -1.0; |
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est = 0.0; |
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oldEcr = 0.0; |
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oldRcut = 0.0; |
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|
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haveOrigRcut = 0; |
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haveOrigEcr = 0; |
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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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|
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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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myConfiguration = new SimState(); |
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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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void SimInfo::setBoxM( double theBox[3][3] ){ |
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int i, j, status; |
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double smallestBoxL, maxCutoff; |
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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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// [ 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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for(i=0; i < 3; i++) |
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void SimInfo::calcHmatInv( void ) { |
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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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|
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invertMat3( Hmat, HmatInv ); |
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|
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// Check the inverse to make sure it is sane: |
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|
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matMul3( Hmat, HmatInv, sanity ); |
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|
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// check to see if Hmat is orthorhombic |
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|
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smallDiag = Hmat[0][0]; |
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if(smallDiag > Hmat[1][1]) smallDiag = Hmat[1][1]; |
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if(smallDiag > Hmat[2][2]) smallDiag = Hmat[2][2]; |
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tol = smallDiag * 1E-6; |
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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 (Hmat[i][j] >= tol) orthoRhombic = 0; |
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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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"Hmat is switching from Non-Orthorhombic to Orthorhombic Box.\n" |
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"\tIf this is a bad thing, change the orthoBoxTolerance\n" |
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"\tvariable ( currently set to %G ).\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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"Hmat is switching from Orthorhombic to Non-Orthorhombic Box.\n" |
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"\tIf this is a bad thing, change the orthoBoxTolerance\n" |
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"\tvariable ( currently set to %G ).\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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double SimInfo::matDet3(double a[3][3]) { |
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void SimInfo::calcBoxL( void ){ |
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double dx, dy, dz, dsq; |
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int i; |
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// boxVol = Determinant of Hmat |
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void SimInfo::wrapVector( double thePos[3] ){ |
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int i, j, k; |
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int i; |
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double scaled[3]; |
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if( !orthoRhombic ){ |
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int SimInfo::getNDF(){ |
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int ndf_local, ndf; |
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int ndf_local; |
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ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints; |
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} |
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int SimInfo::getNDFraw() { |
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int ndfRaw_local, ndfRaw; |
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int ndfRaw_local; |
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|
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// Raw degrees of freedom that we have to set |
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ndfRaw_local = 3 * n_atoms + 3 * n_oriented; |
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} |
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int SimInfo::getNDFtranslational() { |
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int ndfTrans_local, ndfTrans; |
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int ndfTrans_local; |
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|
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ndfTrans_local = 3 * n_atoms - n_constraints; |
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fInfo.dielect = 0.0; |
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|
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if( useDipole ){ |
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if( useDipoles ){ |
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if( useReactionField )fInfo.dielect = dielectric; |
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} |
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|
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fInfo.SIM_uses_LJ = useLJ; |
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fInfo.SIM_uses_sticky = useSticky; |
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//fInfo.SIM_uses_sticky = 0; |
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fInfo.SIM_uses_dipoles = useDipole; |
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fInfo.SIM_uses_charges = useCharges; |
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fInfo.SIM_uses_dipoles = useDipoles; |
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//fInfo.SIM_uses_dipoles = 0; |
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//fInfo.SIM_uses_RF = useReactionField; |
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fInfo.SIM_uses_RF = 0; |
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fInfo.SIM_uses_RF = useReactionField; |
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//fInfo.SIM_uses_RF = 0; |
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fInfo.SIM_uses_GB = useGB; |
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fInfo.SIM_uses_EAM = useEAM; |
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this->ndfTrans = this->getNDFtranslational(); |
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} |
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void SimInfo::setDefaultRcut( double theRcut ){ |
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|
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void SimInfo::setRcut( double theRcut ){ |
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haveRcut = 1; |
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rCut = theRcut; |
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|
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if( !haveOrigRcut ){ |
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haveOrigRcut = 1; |
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origRcut = theRcut; |
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} |
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( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0; |
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|
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rCut = theRcut; |
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checkCutOffs(); |
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notifyFortranCutOffs( &rCut, &rList, &ecr, &est ); |
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} |
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|
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void SimInfo::setEcr( double theEcr ){ |
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void SimInfo::setDefaultEcr( double theEcr ){ |
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|
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if( !haveOrigEcr ){ |
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haveOrigEcr = 1; |
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origEcr = theEcr; |
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} |
535 |
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|
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haveEcr = 1; |
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ecr = theEcr; |
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checkCutOffs(); |
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|
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( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0; |
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|
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notifyFortranCutOffs( &rCut, &rList, &ecr, &est ); |
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} |
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void SimInfo::setEcr( double theEcr, double theEst ){ |
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void SimInfo::setDefaultEcr( double theEcr, double theEst ){ |
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|
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est = theEst; |
562 |
< |
setEcr( theEcr ); |
562 |
> |
setDefaultEcr( theEcr ); |
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} |
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|
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void SimInfo::checkCutOffs( void ){ |
548 |
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|
549 |
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int cutChanged = 0; |
567 |
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|
568 |
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if( boxIsInit ){ |
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|
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//we need to check cutOffs against the box |
571 |
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|
572 |
< |
//detect the change of rCut |
556 |
< |
if(( maxCutoff > rCut )&&(usePBC)){ |
557 |
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if( rCut < origRcut ){ |
558 |
< |
rCut = origRcut; |
559 |
< |
|
560 |
< |
if (rCut > maxCutoff) |
561 |
< |
rCut = maxCutoff; |
562 |
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|
563 |
< |
sprintf( painCave.errMsg, |
564 |
< |
"New Box size is setting the long range cutoff radius " |
565 |
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"to %lf at time %lf\n", |
566 |
< |
rCut, currentTime ); |
567 |
< |
painCave.isFatal = 0; |
568 |
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simError(); |
569 |
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} |
570 |
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} |
571 |
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else if ((rCut > maxCutoff)&&(usePBC)) { |
571 |
> |
|
572 |
> |
if( rCut > maxCutoff ){ |
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sprintf( painCave.errMsg, |
574 |
< |
"New Box size is setting the long range cutoff radius " |
575 |
< |
"to %lf at time %lf\n", |
576 |
< |
maxCutoff, currentTime ); |
577 |
< |
painCave.isFatal = 0; |
574 |
> |
"Box size is too small for the long range cutoff radius, " |
575 |
> |
"%G, at time %G\n" |
576 |
> |
"\t[ %G %G %G ]\n" |
577 |
> |
"\t[ %G %G %G ]\n" |
578 |
> |
"\t[ %G %G %G ]\n", |
579 |
> |
rCut, currentTime, |
580 |
> |
Hmat[0][0], Hmat[0][1], Hmat[0][2], |
581 |
> |
Hmat[1][0], Hmat[1][1], Hmat[1][2], |
582 |
> |
Hmat[2][0], Hmat[2][1], Hmat[2][2]); |
583 |
> |
painCave.isFatal = 1; |
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simError(); |
578 |
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rCut = maxCutoff; |
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} |
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|
587 |
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|
588 |
< |
//detect the change of ecr |
589 |
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if( maxCutoff > ecr ){ |
590 |
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if( ecr < origEcr ){ |
591 |
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ecr = origEcr; |
592 |
< |
if (ecr > maxCutoff) ecr = maxCutoff; |
593 |
< |
|
594 |
< |
sprintf( painCave.errMsg, |
595 |
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"New Box size is setting the electrostaticCutoffRadius " |
596 |
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"to %lf at time %lf\n", |
597 |
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ecr, currentTime ); |
598 |
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painCave.isFatal = 0; |
599 |
< |
simError(); |
586 |
> |
|
587 |
> |
if( haveEcr ){ |
588 |
> |
if( ecr > maxCutoff ){ |
589 |
> |
sprintf( painCave.errMsg, |
590 |
> |
"Box size is too small for the electrostatic cutoff radius, " |
591 |
> |
"%G, at time %G\n" |
592 |
> |
"\t[ %G %G %G ]\n" |
593 |
> |
"\t[ %G %G %G ]\n" |
594 |
> |
"\t[ %G %G %G ]\n", |
595 |
> |
ecr, currentTime, |
596 |
> |
Hmat[0][0], Hmat[0][1], Hmat[0][2], |
597 |
> |
Hmat[1][0], Hmat[1][1], Hmat[1][2], |
598 |
> |
Hmat[2][0], Hmat[2][1], Hmat[2][2]); |
599 |
> |
painCave.isFatal = 1; |
600 |
> |
simError(); |
601 |
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} |
602 |
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} |
596 |
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else if( ecr > maxCutoff){ |
597 |
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sprintf( painCave.errMsg, |
598 |
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"New Box size is setting the electrostaticCutoffRadius " |
599 |
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"to %lf at time %lf\n", |
600 |
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maxCutoff, currentTime ); |
601 |
– |
painCave.isFatal = 0; |
602 |
– |
simError(); |
603 |
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ecr = maxCutoff; |
604 |
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} |
605 |
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|
606 |
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if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1; |
607 |
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|
608 |
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// rlist is the 1.0 plus max( rcut, ecr ) |
609 |
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|
610 |
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( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0; |
611 |
– |
|
612 |
– |
if( cutChanged ){ |
613 |
– |
|
614 |
– |
notifyFortranCutOffs( &rCut, &rList, &ecr, &est ); |
615 |
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} |
616 |
– |
|
617 |
– |
oldEcr = ecr; |
618 |
– |
oldRcut = rCut; |
619 |
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|
603 |
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} else { |
604 |
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// initialize this stuff before using it, OK? |
605 |
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sprintf( painCave.errMsg, |
606 |
< |
"Trying to check cutoffs without a box. Be smarter.\n" ); |
606 |
> |
"Trying to check cutoffs without a box.\n" |
607 |
> |
"\tOOPSE should have better programmers than that.\n" ); |
608 |
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painCave.isFatal = 1; |
609 |
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simError(); |
610 |
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} |