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gezelter |
829 |
#include <stdlib.h> |
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#include <string.h> |
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#include <math.h> |
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mmeineke |
377 |
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mmeineke |
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#include <iostream> |
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using namespace std; |
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mmeineke |
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#include "SimInfo.hpp" |
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#define __C |
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#include "fSimulation.h" |
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#include "simError.h" |
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#include "fortranWrappers.hpp" |
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gezelter |
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#ifdef IS_MPI |
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#include "mpiSimulation.hpp" |
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#endif |
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mmeineke |
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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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mmeineke |
860 |
inline double min( double a, double b ){ |
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return (a < b ) ? a : b; |
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} |
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mmeineke |
572 |
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mmeineke |
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SimInfo* currentInfo; |
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SimInfo::SimInfo(){ |
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excludes = NULL; |
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n_constraints = 0; |
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tim |
699 |
nZconstraints = 0; |
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mmeineke |
377 |
n_oriented = 0; |
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n_dipoles = 0; |
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gezelter |
458 |
ndf = 0; |
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ndfRaw = 0; |
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mmeineke |
674 |
nZconstraints = 0; |
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mmeineke |
377 |
the_integrator = NULL; |
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setTemp = 0; |
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thermalTime = 0.0; |
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mmeineke |
642 |
currentTime = 0.0; |
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mmeineke |
420 |
rCut = 0.0; |
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mmeineke |
618 |
ecr = 0.0; |
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mmeineke |
619 |
est = 0.0; |
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mmeineke |
377 |
|
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mmeineke |
859 |
haveRcut = 0; |
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haveEcr = 0; |
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mmeineke |
626 |
boxIsInit = 0; |
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tim |
781 |
resetTime = 1e99; |
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mmeineke |
626 |
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mmeineke |
855 |
orthoTolerance = 1E-6; |
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useInitXSstate = true; |
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mmeineke |
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usePBC = 0; |
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useLJ = 0; |
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useSticky = 0; |
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gezelter |
941 |
useCharges = 0; |
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useDipoles = 0; |
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mmeineke |
377 |
useReactionField = 0; |
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useGB = 0; |
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useEAM = 0; |
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mmeineke |
670 |
myConfiguration = new SimState(); |
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gezelter |
457 |
wrapMeSimInfo( this ); |
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} |
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mmeineke |
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mmeineke |
670 |
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tim |
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SimInfo::~SimInfo(){ |
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mmeineke |
670 |
delete myConfiguration; |
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tim |
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map<string, GenericData*>::iterator i; |
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for(i = properties.begin(); i != properties.end(); i++) |
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delete (*i).second; |
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mmeineke |
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tim |
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} |
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gezelter |
457 |
void SimInfo::setBox(double newBox[3]) { |
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mmeineke |
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gezelter |
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int i, j; |
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double tempMat[3][3]; |
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gezelter |
463 |
|
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gezelter |
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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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gezelter |
463 |
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gezelter |
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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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gezelter |
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mmeineke |
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setBoxM( tempMat ); |
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mmeineke |
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gezelter |
457 |
} |
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mmeineke |
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|
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gezelter |
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void SimInfo::setBoxM( double theBox[3][3] ){ |
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mmeineke |
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|
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mmeineke |
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int i, j; |
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gezelter |
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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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mmeineke |
568 |
|
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mmeineke |
626 |
if( !boxIsInit ) boxIsInit = 1; |
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mmeineke |
586 |
|
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gezelter |
588 |
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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mmeineke |
568 |
calcBoxL(); |
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gezelter |
588 |
calcHmatInv(); |
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mmeineke |
568 |
|
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gezelter |
588 |
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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mmeineke |
586 |
|
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mmeineke |
590 |
setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic); |
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mmeineke |
568 |
|
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mmeineke |
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} |
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gezelter |
458 |
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mmeineke |
568 |
|
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gezelter |
588 |
void SimInfo::getBoxM (double theBox[3][3]) { |
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mmeineke |
568 |
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gezelter |
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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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mmeineke |
568 |
} |
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gezelter |
574 |
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void SimInfo::scaleBox(double scale) { |
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gezelter |
588 |
double theBox[3][3]; |
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int i, j; |
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gezelter |
574 |
|
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gezelter |
617 |
// cerr << "Scaling box by " << scale << "\n"; |
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mmeineke |
586 |
|
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gezelter |
588 |
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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gezelter |
574 |
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setBoxM(theBox); |
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} |
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gezelter |
588 |
void SimInfo::calcHmatInv( void ) { |
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mmeineke |
590 |
|
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mmeineke |
853 |
int oldOrtho; |
151 |
mmeineke |
590 |
int i,j; |
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mmeineke |
569 |
double smallDiag; |
153 |
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double tol; |
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double sanity[3][3]; |
155 |
mmeineke |
568 |
|
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gezelter |
588 |
invertMat3( Hmat, HmatInv ); |
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mmeineke |
568 |
|
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gezelter |
588 |
// check to see if Hmat is orthorhombic |
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mmeineke |
568 |
|
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mmeineke |
853 |
oldOrtho = orthoRhombic; |
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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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mmeineke |
855 |
tol = smallDiag * orthoTolerance; |
166 |
mmeineke |
568 |
|
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gezelter |
588 |
orthoRhombic = 1; |
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mmeineke |
568 |
|
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gezelter |
588 |
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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mmeineke |
853 |
if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0; |
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gezelter |
588 |
} |
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} |
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mmeineke |
568 |
} |
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} |
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mmeineke |
853 |
|
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if( oldOrtho != orthoRhombic ){ |
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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\n" |
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mmeineke |
855 |
" If this is a bad thing, change the orthoBoxTolerance( currently %G ).\n", |
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orthoTolerance); |
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mmeineke |
853 |
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\n" |
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mmeineke |
855 |
" If this is a bad thing, change the orthoBoxTolerance( currently %G ).\n", |
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orthoTolerance); |
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mmeineke |
853 |
simError(); |
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} |
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} |
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gezelter |
588 |
} |
197 |
mmeineke |
569 |
|
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gezelter |
588 |
double SimInfo::matDet3(double a[3][3]) { |
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int i, j, k; |
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double determinant; |
201 |
mmeineke |
569 |
|
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gezelter |
588 |
determinant = 0.0; |
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for(i = 0; i < 3; i++) { |
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j = (i+1)%3; |
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k = (i+2)%3; |
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determinant += a[0][i] * (a[1][j]*a[2][k] - a[1][k]*a[2][j]); |
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mmeineke |
569 |
} |
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gezelter |
588 |
return determinant; |
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} |
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mmeineke |
569 |
|
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gezelter |
588 |
void SimInfo::invertMat3(double a[3][3], double b[3][3]) { |
215 |
mmeineke |
569 |
|
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gezelter |
588 |
int i, j, k, l, m, n; |
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double determinant; |
218 |
mmeineke |
569 |
|
219 |
gezelter |
588 |
determinant = matDet3( a ); |
220 |
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if (determinant == 0.0) { |
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sprintf( painCave.errMsg, |
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"Can't invert a matrix with a zero determinant!\n"); |
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painCave.isFatal = 1; |
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simError(); |
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} |
227 |
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for (i=0; i < 3; i++) { |
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j = (i+1)%3; |
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k = (i+2)%3; |
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for(l = 0; l < 3; l++) { |
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m = (l+1)%3; |
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n = (l+2)%3; |
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b[l][i] = (a[j][m]*a[k][n] - a[j][n]*a[k][m]) / determinant; |
236 |
mmeineke |
569 |
} |
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} |
238 |
mmeineke |
568 |
} |
239 |
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240 |
gezelter |
588 |
void SimInfo::matMul3(double a[3][3], double b[3][3], double c[3][3]) { |
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double r00, r01, r02, r10, r11, r12, r20, r21, r22; |
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r00 = a[0][0]*b[0][0] + a[0][1]*b[1][0] + a[0][2]*b[2][0]; |
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r01 = a[0][0]*b[0][1] + a[0][1]*b[1][1] + a[0][2]*b[2][1]; |
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r02 = a[0][0]*b[0][2] + a[0][1]*b[1][2] + a[0][2]*b[2][2]; |
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r10 = a[1][0]*b[0][0] + a[1][1]*b[1][0] + a[1][2]*b[2][0]; |
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r11 = a[1][0]*b[0][1] + a[1][1]*b[1][1] + a[1][2]*b[2][1]; |
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r12 = a[1][0]*b[0][2] + a[1][1]*b[1][2] + a[1][2]*b[2][2]; |
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r20 = a[2][0]*b[0][0] + a[2][1]*b[1][0] + a[2][2]*b[2][0]; |
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r21 = a[2][0]*b[0][1] + a[2][1]*b[1][1] + a[2][2]*b[2][1]; |
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r22 = a[2][0]*b[0][2] + a[2][1]*b[1][2] + a[2][2]*b[2][2]; |
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255 |
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c[0][0] = r00; c[0][1] = r01; c[0][2] = r02; |
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c[1][0] = r10; c[1][1] = r11; c[1][2] = r12; |
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c[2][0] = r20; c[2][1] = r21; c[2][2] = r22; |
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} |
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void SimInfo::matVecMul3(double m[3][3], double inVec[3], double outVec[3]) { |
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double a0, a1, a2; |
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a0 = inVec[0]; a1 = inVec[1]; a2 = inVec[2]; |
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outVec[0] = m[0][0]*a0 + m[0][1]*a1 + m[0][2]*a2; |
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outVec[1] = m[1][0]*a0 + m[1][1]*a1 + m[1][2]*a2; |
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outVec[2] = m[2][0]*a0 + m[2][1]*a1 + m[2][2]*a2; |
268 |
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} |
269 |
mmeineke |
597 |
|
270 |
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void SimInfo::transposeMat3(double in[3][3], double out[3][3]) { |
271 |
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double temp[3][3]; |
272 |
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int i, j; |
273 |
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274 |
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for (i = 0; i < 3; i++) { |
275 |
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for (j = 0; j < 3; j++) { |
276 |
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temp[j][i] = in[i][j]; |
277 |
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} |
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} |
279 |
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for (i = 0; i < 3; i++) { |
280 |
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for (j = 0; j < 3; j++) { |
281 |
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out[i][j] = temp[i][j]; |
282 |
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} |
283 |
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} |
284 |
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} |
285 |
gezelter |
588 |
|
286 |
mmeineke |
597 |
void SimInfo::printMat3(double A[3][3] ){ |
287 |
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288 |
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std::cerr |
289 |
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<< "[ " << A[0][0] << ", " << A[0][1] << ", " << A[0][2] << " ]\n" |
290 |
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<< "[ " << A[1][0] << ", " << A[1][1] << ", " << A[1][2] << " ]\n" |
291 |
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<< "[ " << A[2][0] << ", " << A[2][1] << ", " << A[2][2] << " ]\n"; |
292 |
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} |
293 |
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294 |
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void SimInfo::printMat9(double A[9] ){ |
295 |
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296 |
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std::cerr |
297 |
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<< "[ " << A[0] << ", " << A[1] << ", " << A[2] << " ]\n" |
298 |
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<< "[ " << A[3] << ", " << A[4] << ", " << A[5] << " ]\n" |
299 |
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<< "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n"; |
300 |
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} |
301 |
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302 |
tim |
781 |
|
303 |
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void SimInfo::crossProduct3(double a[3],double b[3], double out[3]){ |
304 |
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305 |
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out[0] = a[1] * b[2] - a[2] * b[1]; |
306 |
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out[1] = a[2] * b[0] - a[0] * b[2] ; |
307 |
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out[2] = a[0] * b[1] - a[1] * b[0]; |
308 |
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309 |
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} |
310 |
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311 |
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double SimInfo::dotProduct3(double a[3], double b[3]){ |
312 |
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return a[0]*b[0] + a[1]*b[1]+ a[2]*b[2]; |
313 |
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} |
314 |
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315 |
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double SimInfo::length3(double a[3]){ |
316 |
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return sqrt(a[0]*a[0] + a[1]*a[1] + a[2]*a[2]); |
317 |
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} |
318 |
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319 |
mmeineke |
568 |
void SimInfo::calcBoxL( void ){ |
320 |
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321 |
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double dx, dy, dz, dsq; |
322 |
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323 |
gezelter |
588 |
// boxVol = Determinant of Hmat |
324 |
mmeineke |
568 |
|
325 |
gezelter |
588 |
boxVol = matDet3( Hmat ); |
326 |
mmeineke |
568 |
|
327 |
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// boxLx |
328 |
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|
329 |
gezelter |
588 |
dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0]; |
330 |
mmeineke |
568 |
dsq = dx*dx + dy*dy + dz*dz; |
331 |
gezelter |
621 |
boxL[0] = sqrt( dsq ); |
332 |
tim |
781 |
//maxCutoff = 0.5 * boxL[0]; |
333 |
mmeineke |
568 |
|
334 |
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// boxLy |
335 |
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|
336 |
gezelter |
588 |
dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1]; |
337 |
mmeineke |
568 |
dsq = dx*dx + dy*dy + dz*dz; |
338 |
gezelter |
621 |
boxL[1] = sqrt( dsq ); |
339 |
tim |
781 |
//if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1]; |
340 |
mmeineke |
568 |
|
341 |
tim |
781 |
|
342 |
mmeineke |
568 |
// boxLz |
343 |
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|
344 |
gezelter |
588 |
dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2]; |
345 |
mmeineke |
568 |
dsq = dx*dx + dy*dy + dz*dz; |
346 |
gezelter |
621 |
boxL[2] = sqrt( dsq ); |
347 |
tim |
781 |
//if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2]; |
348 |
|
|
|
349 |
|
|
//calculate the max cutoff |
350 |
|
|
maxCutoff = calcMaxCutOff(); |
351 |
chuckv |
669 |
|
352 |
|
|
checkCutOffs(); |
353 |
mmeineke |
626 |
|
354 |
mmeineke |
568 |
} |
355 |
|
|
|
356 |
|
|
|
357 |
tim |
781 |
double SimInfo::calcMaxCutOff(){ |
358 |
|
|
|
359 |
|
|
double ri[3], rj[3], rk[3]; |
360 |
|
|
double rij[3], rjk[3], rki[3]; |
361 |
|
|
double minDist; |
362 |
|
|
|
363 |
|
|
ri[0] = Hmat[0][0]; |
364 |
|
|
ri[1] = Hmat[1][0]; |
365 |
|
|
ri[2] = Hmat[2][0]; |
366 |
|
|
|
367 |
|
|
rj[0] = Hmat[0][1]; |
368 |
|
|
rj[1] = Hmat[1][1]; |
369 |
|
|
rj[2] = Hmat[2][1]; |
370 |
|
|
|
371 |
|
|
rk[0] = Hmat[0][2]; |
372 |
|
|
rk[1] = Hmat[1][2]; |
373 |
|
|
rk[2] = Hmat[2][2]; |
374 |
|
|
|
375 |
|
|
crossProduct3(ri,rj, rij); |
376 |
|
|
distXY = dotProduct3(rk,rij) / length3(rij); |
377 |
|
|
|
378 |
|
|
crossProduct3(rj,rk, rjk); |
379 |
|
|
distYZ = dotProduct3(ri,rjk) / length3(rjk); |
380 |
|
|
|
381 |
|
|
crossProduct3(rk,ri, rki); |
382 |
|
|
distZX = dotProduct3(rj,rki) / length3(rki); |
383 |
|
|
|
384 |
|
|
minDist = min(min(distXY, distYZ), distZX); |
385 |
|
|
return minDist/2; |
386 |
|
|
|
387 |
|
|
} |
388 |
|
|
|
389 |
mmeineke |
568 |
void SimInfo::wrapVector( double thePos[3] ){ |
390 |
|
|
|
391 |
mmeineke |
787 |
int i; |
392 |
mmeineke |
568 |
double scaled[3]; |
393 |
|
|
|
394 |
mmeineke |
569 |
if( !orthoRhombic ){ |
395 |
|
|
// calc the scaled coordinates. |
396 |
gezelter |
588 |
|
397 |
|
|
|
398 |
|
|
matVecMul3(HmatInv, thePos, scaled); |
399 |
mmeineke |
569 |
|
400 |
|
|
for(i=0; i<3; i++) |
401 |
mmeineke |
572 |
scaled[i] -= roundMe(scaled[i]); |
402 |
mmeineke |
569 |
|
403 |
|
|
// calc the wrapped real coordinates from the wrapped scaled coordinates |
404 |
|
|
|
405 |
gezelter |
588 |
matVecMul3(Hmat, scaled, thePos); |
406 |
|
|
|
407 |
mmeineke |
569 |
} |
408 |
|
|
else{ |
409 |
|
|
// calc the scaled coordinates. |
410 |
|
|
|
411 |
|
|
for(i=0; i<3; i++) |
412 |
gezelter |
588 |
scaled[i] = thePos[i]*HmatInv[i][i]; |
413 |
mmeineke |
569 |
|
414 |
|
|
// wrap the scaled coordinates |
415 |
|
|
|
416 |
|
|
for(i=0; i<3; i++) |
417 |
mmeineke |
572 |
scaled[i] -= roundMe(scaled[i]); |
418 |
mmeineke |
569 |
|
419 |
|
|
// calc the wrapped real coordinates from the wrapped scaled coordinates |
420 |
|
|
|
421 |
|
|
for(i=0; i<3; i++) |
422 |
gezelter |
588 |
thePos[i] = scaled[i]*Hmat[i][i]; |
423 |
mmeineke |
569 |
} |
424 |
|
|
|
425 |
mmeineke |
568 |
} |
426 |
|
|
|
427 |
|
|
|
428 |
gezelter |
458 |
int SimInfo::getNDF(){ |
429 |
mmeineke |
790 |
int ndf_local; |
430 |
gezelter |
457 |
|
431 |
gezelter |
458 |
ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints; |
432 |
|
|
|
433 |
|
|
#ifdef IS_MPI |
434 |
|
|
MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
435 |
|
|
#else |
436 |
|
|
ndf = ndf_local; |
437 |
|
|
#endif |
438 |
|
|
|
439 |
mmeineke |
674 |
ndf = ndf - 3 - nZconstraints; |
440 |
gezelter |
458 |
|
441 |
|
|
return ndf; |
442 |
|
|
} |
443 |
|
|
|
444 |
|
|
int SimInfo::getNDFraw() { |
445 |
mmeineke |
790 |
int ndfRaw_local; |
446 |
gezelter |
458 |
|
447 |
|
|
// Raw degrees of freedom that we have to set |
448 |
|
|
ndfRaw_local = 3 * n_atoms + 3 * n_oriented; |
449 |
|
|
|
450 |
|
|
#ifdef IS_MPI |
451 |
|
|
MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
452 |
|
|
#else |
453 |
|
|
ndfRaw = ndfRaw_local; |
454 |
|
|
#endif |
455 |
|
|
|
456 |
|
|
return ndfRaw; |
457 |
|
|
} |
458 |
tim |
767 |
|
459 |
|
|
int SimInfo::getNDFtranslational() { |
460 |
mmeineke |
790 |
int ndfTrans_local; |
461 |
tim |
767 |
|
462 |
|
|
ndfTrans_local = 3 * n_atoms - n_constraints; |
463 |
|
|
|
464 |
|
|
#ifdef IS_MPI |
465 |
|
|
MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
466 |
|
|
#else |
467 |
|
|
ndfTrans = ndfTrans_local; |
468 |
|
|
#endif |
469 |
|
|
|
470 |
|
|
ndfTrans = ndfTrans - 3 - nZconstraints; |
471 |
|
|
|
472 |
|
|
return ndfTrans; |
473 |
|
|
} |
474 |
|
|
|
475 |
mmeineke |
377 |
void SimInfo::refreshSim(){ |
476 |
|
|
|
477 |
|
|
simtype fInfo; |
478 |
|
|
int isError; |
479 |
gezelter |
490 |
int n_global; |
480 |
mmeineke |
424 |
int* excl; |
481 |
mmeineke |
626 |
|
482 |
mmeineke |
469 |
fInfo.dielect = 0.0; |
483 |
mmeineke |
377 |
|
484 |
gezelter |
941 |
if( useDipoles ){ |
485 |
mmeineke |
469 |
if( useReactionField )fInfo.dielect = dielectric; |
486 |
|
|
} |
487 |
|
|
|
488 |
mmeineke |
377 |
fInfo.SIM_uses_PBC = usePBC; |
489 |
mmeineke |
443 |
//fInfo.SIM_uses_LJ = 0; |
490 |
chuckv |
439 |
fInfo.SIM_uses_LJ = useLJ; |
491 |
mmeineke |
443 |
fInfo.SIM_uses_sticky = useSticky; |
492 |
|
|
//fInfo.SIM_uses_sticky = 0; |
493 |
gezelter |
941 |
fInfo.SIM_uses_charges = useCharges; |
494 |
|
|
fInfo.SIM_uses_dipoles = useDipoles; |
495 |
chuckv |
482 |
//fInfo.SIM_uses_dipoles = 0; |
496 |
mmeineke |
443 |
//fInfo.SIM_uses_RF = useReactionField; |
497 |
|
|
fInfo.SIM_uses_RF = 0; |
498 |
mmeineke |
377 |
fInfo.SIM_uses_GB = useGB; |
499 |
|
|
fInfo.SIM_uses_EAM = useEAM; |
500 |
|
|
|
501 |
mmeineke |
424 |
excl = Exclude::getArray(); |
502 |
mmeineke |
377 |
|
503 |
gezelter |
490 |
#ifdef IS_MPI |
504 |
|
|
n_global = mpiSim->getTotAtoms(); |
505 |
|
|
#else |
506 |
|
|
n_global = n_atoms; |
507 |
|
|
#endif |
508 |
|
|
|
509 |
mmeineke |
377 |
isError = 0; |
510 |
|
|
|
511 |
gezelter |
490 |
setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl, |
512 |
gezelter |
483 |
&nGlobalExcludes, globalExcludes, molMembershipArray, |
513 |
|
|
&isError ); |
514 |
mmeineke |
377 |
|
515 |
|
|
if( isError ){ |
516 |
|
|
|
517 |
|
|
sprintf( painCave.errMsg, |
518 |
|
|
"There was an error setting the simulation information in fortran.\n" ); |
519 |
|
|
painCave.isFatal = 1; |
520 |
|
|
simError(); |
521 |
|
|
} |
522 |
|
|
|
523 |
|
|
#ifdef IS_MPI |
524 |
|
|
sprintf( checkPointMsg, |
525 |
|
|
"succesfully sent the simulation information to fortran.\n"); |
526 |
|
|
MPIcheckPoint(); |
527 |
|
|
#endif // is_mpi |
528 |
gezelter |
458 |
|
529 |
gezelter |
474 |
this->ndf = this->getNDF(); |
530 |
|
|
this->ndfRaw = this->getNDFraw(); |
531 |
tim |
767 |
this->ndfTrans = this->getNDFtranslational(); |
532 |
mmeineke |
377 |
} |
533 |
|
|
|
534 |
mmeineke |
841 |
void SimInfo::setDefaultRcut( double theRcut ){ |
535 |
|
|
|
536 |
mmeineke |
859 |
haveRcut = 1; |
537 |
mmeineke |
841 |
rCut = theRcut; |
538 |
mmeineke |
843 |
|
539 |
gezelter |
845 |
( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0; |
540 |
|
|
|
541 |
mmeineke |
843 |
notifyFortranCutOffs( &rCut, &rList, &ecr, &est ); |
542 |
mmeineke |
841 |
} |
543 |
|
|
|
544 |
|
|
void SimInfo::setDefaultEcr( double theEcr ){ |
545 |
|
|
|
546 |
mmeineke |
859 |
haveEcr = 1; |
547 |
chrisfen |
872 |
ecr = theEcr; |
548 |
mmeineke |
841 |
|
549 |
gezelter |
845 |
( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0; |
550 |
|
|
|
551 |
mmeineke |
843 |
notifyFortranCutOffs( &rCut, &rList, &ecr, &est ); |
552 |
mmeineke |
841 |
} |
553 |
|
|
|
554 |
|
|
void SimInfo::setDefaultEcr( double theEcr, double theEst ){ |
555 |
mmeineke |
626 |
|
556 |
mmeineke |
841 |
est = theEst; |
557 |
|
|
setDefaultEcr( theEcr ); |
558 |
|
|
} |
559 |
|
|
|
560 |
|
|
|
561 |
mmeineke |
626 |
void SimInfo::checkCutOffs( void ){ |
562 |
gezelter |
770 |
|
563 |
mmeineke |
626 |
if( boxIsInit ){ |
564 |
|
|
|
565 |
|
|
//we need to check cutOffs against the box |
566 |
mmeineke |
859 |
|
567 |
|
|
if( rCut > maxCutoff ){ |
568 |
mmeineke |
626 |
sprintf( painCave.errMsg, |
569 |
mmeineke |
859 |
"Box size is too small for the long range cutoff radius, " |
570 |
mmeineke |
874 |
"%G, at time %G\n" |
571 |
|
|
" [ %G %G %G ]\n" |
572 |
|
|
" [ %G %G %G ]\n" |
573 |
|
|
" [ %G %G %G ]\n", |
574 |
|
|
rCut, currentTime, |
575 |
|
|
Hmat[0][0], Hmat[0][1], Hmat[0][2], |
576 |
|
|
Hmat[1][0], Hmat[1][1], Hmat[1][2], |
577 |
|
|
Hmat[2][0], Hmat[2][1], Hmat[2][2]); |
578 |
mmeineke |
859 |
painCave.isFatal = 1; |
579 |
mmeineke |
626 |
simError(); |
580 |
|
|
} |
581 |
mmeineke |
859 |
|
582 |
|
|
if( haveEcr ){ |
583 |
|
|
if( ecr > maxCutoff ){ |
584 |
|
|
sprintf( painCave.errMsg, |
585 |
|
|
"Box size is too small for the electrostatic cutoff radius, " |
586 |
mmeineke |
874 |
"%G, at time %G\n" |
587 |
|
|
" [ %G %G %G ]\n" |
588 |
|
|
" [ %G %G %G ]\n" |
589 |
|
|
" [ %G %G %G ]\n", |
590 |
|
|
ecr, currentTime, |
591 |
|
|
Hmat[0][0], Hmat[0][1], Hmat[0][2], |
592 |
|
|
Hmat[1][0], Hmat[1][1], Hmat[1][2], |
593 |
|
|
Hmat[2][0], Hmat[2][1], Hmat[2][2]); |
594 |
mmeineke |
859 |
painCave.isFatal = 1; |
595 |
|
|
simError(); |
596 |
tim |
781 |
} |
597 |
|
|
} |
598 |
tim |
767 |
} else { |
599 |
|
|
// initialize this stuff before using it, OK? |
600 |
gezelter |
770 |
sprintf( painCave.errMsg, |
601 |
|
|
"Trying to check cutoffs without a box. Be smarter.\n" ); |
602 |
|
|
painCave.isFatal = 1; |
603 |
|
|
simError(); |
604 |
mmeineke |
626 |
} |
605 |
gezelter |
770 |
|
606 |
mmeineke |
626 |
} |
607 |
tim |
658 |
|
608 |
|
|
void SimInfo::addProperty(GenericData* prop){ |
609 |
|
|
|
610 |
|
|
map<string, GenericData*>::iterator result; |
611 |
|
|
result = properties.find(prop->getID()); |
612 |
|
|
|
613 |
|
|
//we can't simply use properties[prop->getID()] = prop, |
614 |
|
|
//it will cause memory leak if we already contain a propery which has the same name of prop |
615 |
|
|
|
616 |
|
|
if(result != properties.end()){ |
617 |
|
|
|
618 |
|
|
delete (*result).second; |
619 |
|
|
(*result).second = prop; |
620 |
|
|
|
621 |
|
|
} |
622 |
|
|
else{ |
623 |
|
|
|
624 |
|
|
properties[prop->getID()] = prop; |
625 |
|
|
|
626 |
|
|
} |
627 |
|
|
|
628 |
|
|
} |
629 |
|
|
|
630 |
|
|
GenericData* SimInfo::getProperty(const string& propName){ |
631 |
|
|
|
632 |
|
|
map<string, GenericData*>::iterator result; |
633 |
|
|
|
634 |
|
|
//string lowerCaseName = (); |
635 |
|
|
|
636 |
|
|
result = properties.find(propName); |
637 |
|
|
|
638 |
|
|
if(result != properties.end()) |
639 |
|
|
return (*result).second; |
640 |
|
|
else |
641 |
|
|
return NULL; |
642 |
|
|
} |
643 |
|
|
|
644 |
|
|
vector<GenericData*> SimInfo::getProperties(){ |
645 |
|
|
|
646 |
|
|
vector<GenericData*> result; |
647 |
|
|
map<string, GenericData*>::iterator i; |
648 |
|
|
|
649 |
|
|
for(i = properties.begin(); i != properties.end(); i++) |
650 |
|
|
result.push_back((*i).second); |
651 |
|
|
|
652 |
|
|
return result; |
653 |
|
|
} |
654 |
|
|
|
655 |
tim |
763 |
double SimInfo::matTrace3(double m[3][3]){ |
656 |
|
|
double trace; |
657 |
|
|
trace = m[0][0] + m[1][1] + m[2][2]; |
658 |
tim |
658 |
|
659 |
tim |
763 |
return trace; |
660 |
|
|
} |