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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 |
572 |
#include <iostream> |
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using namespace std; |
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mmeineke |
377 |
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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 |
1097 |
#include "MatVec3.h" |
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gezelter |
490 |
#ifdef IS_MPI |
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#include "mpiSimulation.hpp" |
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#endif |
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mmeineke |
572 |
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 |
377 |
SimInfo* currentInfo; |
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SimInfo::SimInfo(){ |
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gezelter |
1097 |
|
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mmeineke |
377 |
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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gezelter |
1097 |
orthoRhombic = 0; |
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mmeineke |
855 |
orthoTolerance = 1E-6; |
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useInitXSstate = true; |
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mmeineke |
377 |
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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gezelter |
1139 |
useMolecularCutoffs = 0; |
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mmeineke |
377 |
|
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gezelter |
1097 |
excludes = Exclude::Instance(); |
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mmeineke |
670 |
myConfiguration = new SimState(); |
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tim |
1031 |
has_minimizer = false; |
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the_minimizer =NULL; |
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tim |
1144 |
ngroup = 0; |
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gezelter |
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wrapMeSimInfo( this ); |
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} |
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mmeineke |
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|
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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 |
660 |
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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tim |
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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 |
586 |
|
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gezelter |
588 |
int i, j; |
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double tempMat[3][3]; |
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gezelter |
463 |
|
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gezelter |
588 |
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 |
463 |
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mmeineke |
586 |
setBoxM( tempMat ); |
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mmeineke |
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gezelter |
457 |
} |
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mmeineke |
377 |
|
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gezelter |
588 |
void SimInfo::setBoxM( double theBox[3][3] ){ |
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mmeineke |
568 |
|
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mmeineke |
787 |
int i, j; |
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gezelter |
588 |
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 |
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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 |
588 |
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 |
} |
144 |
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145 |
gezelter |
574 |
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void SimInfo::scaleBox(double scale) { |
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gezelter |
588 |
double theBox[3][3]; |
148 |
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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 |
|
152 |
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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} |
158 |
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gezelter |
588 |
void SimInfo::calcHmatInv( void ) { |
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mmeineke |
590 |
|
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mmeineke |
853 |
int oldOrtho; |
162 |
mmeineke |
590 |
int i,j; |
163 |
mmeineke |
569 |
double smallDiag; |
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double tol; |
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double sanity[3][3]; |
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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; |
177 |
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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gezelter |
1097 |
"OOPSE is switching from the default Non-Orthorhombic\n" |
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"\tto the faster Orthorhombic periodic boundary computations.\n" |
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"\tThis is usually a good thing, but if you wan't the\n" |
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"\tNon-Orthorhombic computations, make the orthoBoxTolerance\n" |
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"\tvariable ( currently set to %G ) smaller.\n", |
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mmeineke |
855 |
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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gezelter |
1097 |
"OOPSE is switching from the faster Orthorhombic to the more\n" |
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"\tflexible Non-Orthorhombic periodic boundary computations.\n" |
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"\tThis is usually because the box has deformed under\n" |
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"\tNPTf integration. If you wan't to live on the edge with\n" |
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"\tthe Orthorhombic computations, make the orthoBoxTolerance\n" |
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"\tvariable ( currently set to %G ) larger.\n", |
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mmeineke |
855 |
orthoTolerance); |
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mmeineke |
853 |
simError(); |
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} |
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} |
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gezelter |
588 |
} |
215 |
mmeineke |
569 |
|
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mmeineke |
568 |
void SimInfo::calcBoxL( void ){ |
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double dx, dy, dz, dsq; |
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gezelter |
588 |
// boxVol = Determinant of Hmat |
221 |
mmeineke |
568 |
|
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gezelter |
588 |
boxVol = matDet3( Hmat ); |
223 |
mmeineke |
568 |
|
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// boxLx |
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226 |
gezelter |
588 |
dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0]; |
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mmeineke |
568 |
dsq = dx*dx + dy*dy + dz*dz; |
228 |
gezelter |
621 |
boxL[0] = sqrt( dsq ); |
229 |
tim |
781 |
//maxCutoff = 0.5 * boxL[0]; |
230 |
mmeineke |
568 |
|
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// boxLy |
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233 |
gezelter |
588 |
dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1]; |
234 |
mmeineke |
568 |
dsq = dx*dx + dy*dy + dz*dz; |
235 |
gezelter |
621 |
boxL[1] = sqrt( dsq ); |
236 |
tim |
781 |
//if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1]; |
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mmeineke |
568 |
|
238 |
tim |
781 |
|
239 |
mmeineke |
568 |
// boxLz |
240 |
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|
241 |
gezelter |
588 |
dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2]; |
242 |
mmeineke |
568 |
dsq = dx*dx + dy*dy + dz*dz; |
243 |
gezelter |
621 |
boxL[2] = sqrt( dsq ); |
244 |
tim |
781 |
//if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2]; |
245 |
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//calculate the max cutoff |
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maxCutoff = calcMaxCutOff(); |
248 |
chuckv |
669 |
|
249 |
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checkCutOffs(); |
250 |
mmeineke |
626 |
|
251 |
mmeineke |
568 |
} |
252 |
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253 |
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254 |
tim |
781 |
double SimInfo::calcMaxCutOff(){ |
255 |
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256 |
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double ri[3], rj[3], rk[3]; |
257 |
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double rij[3], rjk[3], rki[3]; |
258 |
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double minDist; |
259 |
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260 |
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ri[0] = Hmat[0][0]; |
261 |
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ri[1] = Hmat[1][0]; |
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ri[2] = Hmat[2][0]; |
263 |
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264 |
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rj[0] = Hmat[0][1]; |
265 |
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rj[1] = Hmat[1][1]; |
266 |
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rj[2] = Hmat[2][1]; |
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268 |
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rk[0] = Hmat[0][2]; |
269 |
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rk[1] = Hmat[1][2]; |
270 |
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rk[2] = Hmat[2][2]; |
271 |
gezelter |
1097 |
|
272 |
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crossProduct3(ri, rj, rij); |
273 |
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distXY = dotProduct3(rk,rij) / norm3(rij); |
274 |
tim |
781 |
|
275 |
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crossProduct3(rj,rk, rjk); |
276 |
gezelter |
1097 |
distYZ = dotProduct3(ri,rjk) / norm3(rjk); |
277 |
tim |
781 |
|
278 |
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crossProduct3(rk,ri, rki); |
279 |
gezelter |
1097 |
distZX = dotProduct3(rj,rki) / norm3(rki); |
280 |
tim |
781 |
|
281 |
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minDist = min(min(distXY, distYZ), distZX); |
282 |
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return minDist/2; |
283 |
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} |
285 |
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286 |
mmeineke |
568 |
void SimInfo::wrapVector( double thePos[3] ){ |
287 |
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|
288 |
mmeineke |
787 |
int i; |
289 |
mmeineke |
568 |
double scaled[3]; |
290 |
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|
291 |
mmeineke |
569 |
if( !orthoRhombic ){ |
292 |
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// calc the scaled coordinates. |
293 |
gezelter |
588 |
|
294 |
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|
295 |
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matVecMul3(HmatInv, thePos, scaled); |
296 |
mmeineke |
569 |
|
297 |
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for(i=0; i<3; i++) |
298 |
mmeineke |
572 |
scaled[i] -= roundMe(scaled[i]); |
299 |
mmeineke |
569 |
|
300 |
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// calc the wrapped real coordinates from the wrapped scaled coordinates |
301 |
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|
302 |
gezelter |
588 |
matVecMul3(Hmat, scaled, thePos); |
303 |
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|
304 |
mmeineke |
569 |
} |
305 |
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else{ |
306 |
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// calc the scaled coordinates. |
307 |
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|
308 |
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for(i=0; i<3; i++) |
309 |
gezelter |
588 |
scaled[i] = thePos[i]*HmatInv[i][i]; |
310 |
mmeineke |
569 |
|
311 |
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// wrap the scaled coordinates |
312 |
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|
313 |
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for(i=0; i<3; i++) |
314 |
mmeineke |
572 |
scaled[i] -= roundMe(scaled[i]); |
315 |
mmeineke |
569 |
|
316 |
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// calc the wrapped real coordinates from the wrapped scaled coordinates |
317 |
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|
318 |
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for(i=0; i<3; i++) |
319 |
gezelter |
588 |
thePos[i] = scaled[i]*Hmat[i][i]; |
320 |
mmeineke |
569 |
} |
321 |
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|
322 |
mmeineke |
568 |
} |
323 |
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324 |
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|
325 |
gezelter |
458 |
int SimInfo::getNDF(){ |
326 |
mmeineke |
790 |
int ndf_local; |
327 |
gezelter |
458 |
|
328 |
tim |
1113 |
ndf_local = 0; |
329 |
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|
330 |
gezelter |
1097 |
for(int i = 0; i < integrableObjects.size(); i++){ |
331 |
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ndf_local += 3; |
332 |
tim |
1118 |
if (integrableObjects[i]->isDirectional()) { |
333 |
|
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if (integrableObjects[i]->isLinear()) |
334 |
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ndf_local += 2; |
335 |
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else |
336 |
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ndf_local += 3; |
337 |
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} |
338 |
gezelter |
1097 |
} |
339 |
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340 |
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// n_constraints is local, so subtract them on each processor: |
341 |
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|
342 |
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ndf_local -= n_constraints; |
343 |
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|
344 |
gezelter |
458 |
#ifdef IS_MPI |
345 |
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MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
346 |
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#else |
347 |
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ndf = ndf_local; |
348 |
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#endif |
349 |
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|
350 |
gezelter |
1097 |
// nZconstraints is global, as are the 3 COM translations for the |
351 |
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// entire system: |
352 |
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|
353 |
mmeineke |
674 |
ndf = ndf - 3 - nZconstraints; |
354 |
gezelter |
458 |
|
355 |
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return ndf; |
356 |
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} |
357 |
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|
358 |
|
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int SimInfo::getNDFraw() { |
359 |
mmeineke |
790 |
int ndfRaw_local; |
360 |
gezelter |
458 |
|
361 |
|
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// Raw degrees of freedom that we have to set |
362 |
tim |
1113 |
ndfRaw_local = 0; |
363 |
gezelter |
1097 |
|
364 |
|
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for(int i = 0; i < integrableObjects.size(); i++){ |
365 |
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ndfRaw_local += 3; |
366 |
tim |
1118 |
if (integrableObjects[i]->isDirectional()) { |
367 |
|
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if (integrableObjects[i]->isLinear()) |
368 |
|
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ndfRaw_local += 2; |
369 |
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else |
370 |
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ndfRaw_local += 3; |
371 |
|
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} |
372 |
gezelter |
1097 |
} |
373 |
|
|
|
374 |
gezelter |
458 |
#ifdef IS_MPI |
375 |
|
|
MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
376 |
|
|
#else |
377 |
|
|
ndfRaw = ndfRaw_local; |
378 |
|
|
#endif |
379 |
|
|
|
380 |
|
|
return ndfRaw; |
381 |
|
|
} |
382 |
tim |
767 |
|
383 |
|
|
int SimInfo::getNDFtranslational() { |
384 |
mmeineke |
790 |
int ndfTrans_local; |
385 |
tim |
767 |
|
386 |
gezelter |
1097 |
ndfTrans_local = 3 * integrableObjects.size() - n_constraints; |
387 |
tim |
767 |
|
388 |
gezelter |
1097 |
|
389 |
tim |
767 |
#ifdef IS_MPI |
390 |
|
|
MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
391 |
|
|
#else |
392 |
|
|
ndfTrans = ndfTrans_local; |
393 |
|
|
#endif |
394 |
|
|
|
395 |
|
|
ndfTrans = ndfTrans - 3 - nZconstraints; |
396 |
|
|
|
397 |
|
|
return ndfTrans; |
398 |
|
|
} |
399 |
|
|
|
400 |
tim |
1108 |
int SimInfo::getTotIntegrableObjects() { |
401 |
|
|
int nObjs_local; |
402 |
|
|
int nObjs; |
403 |
|
|
|
404 |
|
|
nObjs_local = integrableObjects.size(); |
405 |
|
|
|
406 |
|
|
|
407 |
|
|
#ifdef IS_MPI |
408 |
|
|
MPI_Allreduce(&nObjs_local,&nObjs,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
409 |
|
|
#else |
410 |
|
|
nObjs = nObjs_local; |
411 |
|
|
#endif |
412 |
|
|
|
413 |
|
|
|
414 |
|
|
return nObjs; |
415 |
|
|
} |
416 |
|
|
|
417 |
mmeineke |
377 |
void SimInfo::refreshSim(){ |
418 |
|
|
|
419 |
|
|
simtype fInfo; |
420 |
|
|
int isError; |
421 |
gezelter |
490 |
int n_global; |
422 |
mmeineke |
424 |
int* excl; |
423 |
mmeineke |
626 |
|
424 |
mmeineke |
469 |
fInfo.dielect = 0.0; |
425 |
mmeineke |
377 |
|
426 |
gezelter |
941 |
if( useDipoles ){ |
427 |
mmeineke |
469 |
if( useReactionField )fInfo.dielect = dielectric; |
428 |
|
|
} |
429 |
|
|
|
430 |
mmeineke |
377 |
fInfo.SIM_uses_PBC = usePBC; |
431 |
mmeineke |
443 |
//fInfo.SIM_uses_LJ = 0; |
432 |
chuckv |
439 |
fInfo.SIM_uses_LJ = useLJ; |
433 |
mmeineke |
443 |
fInfo.SIM_uses_sticky = useSticky; |
434 |
|
|
//fInfo.SIM_uses_sticky = 0; |
435 |
gezelter |
941 |
fInfo.SIM_uses_charges = useCharges; |
436 |
|
|
fInfo.SIM_uses_dipoles = useDipoles; |
437 |
chuckv |
482 |
//fInfo.SIM_uses_dipoles = 0; |
438 |
chrisfen |
999 |
fInfo.SIM_uses_RF = useReactionField; |
439 |
|
|
//fInfo.SIM_uses_RF = 0; |
440 |
mmeineke |
377 |
fInfo.SIM_uses_GB = useGB; |
441 |
|
|
fInfo.SIM_uses_EAM = useEAM; |
442 |
|
|
|
443 |
gezelter |
1097 |
n_exclude = excludes->getSize(); |
444 |
|
|
excl = excludes->getFortranArray(); |
445 |
tim |
1144 |
|
446 |
gezelter |
490 |
#ifdef IS_MPI |
447 |
|
|
n_global = mpiSim->getTotAtoms(); |
448 |
|
|
#else |
449 |
|
|
n_global = n_atoms; |
450 |
|
|
#endif |
451 |
gezelter |
1150 |
|
452 |
mmeineke |
377 |
isError = 0; |
453 |
gezelter |
1150 |
|
454 |
|
|
getFortranGroupArray(this, mfact, ngroup, groupList, groupStart); |
455 |
|
|
|
456 |
gezelter |
490 |
setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl, |
457 |
gezelter |
1150 |
&nGlobalExcludes, globalExcludes, molMembershipArray, |
458 |
|
|
&mfact[0], &ngroup, &groupList[0], &groupStart[0], &isError); |
459 |
|
|
|
460 |
mmeineke |
377 |
if( isError ){ |
461 |
gezelter |
1150 |
|
462 |
mmeineke |
377 |
sprintf( painCave.errMsg, |
463 |
gezelter |
1150 |
"There was an error setting the simulation information in fortran.\n" ); |
464 |
mmeineke |
377 |
painCave.isFatal = 1; |
465 |
|
|
simError(); |
466 |
|
|
} |
467 |
gezelter |
1150 |
|
468 |
mmeineke |
377 |
#ifdef IS_MPI |
469 |
|
|
sprintf( checkPointMsg, |
470 |
|
|
"succesfully sent the simulation information to fortran.\n"); |
471 |
|
|
MPIcheckPoint(); |
472 |
|
|
#endif // is_mpi |
473 |
gezelter |
1150 |
|
474 |
gezelter |
474 |
this->ndf = this->getNDF(); |
475 |
|
|
this->ndfRaw = this->getNDFraw(); |
476 |
tim |
767 |
this->ndfTrans = this->getNDFtranslational(); |
477 |
mmeineke |
377 |
} |
478 |
|
|
|
479 |
mmeineke |
841 |
void SimInfo::setDefaultRcut( double theRcut ){ |
480 |
gezelter |
1150 |
|
481 |
mmeineke |
859 |
haveRcut = 1; |
482 |
mmeineke |
841 |
rCut = theRcut; |
483 |
gezelter |
1150 |
|
484 |
gezelter |
845 |
( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0; |
485 |
gezelter |
1150 |
|
486 |
mmeineke |
843 |
notifyFortranCutOffs( &rCut, &rList, &ecr, &est ); |
487 |
mmeineke |
841 |
} |
488 |
|
|
|
489 |
|
|
void SimInfo::setDefaultEcr( double theEcr ){ |
490 |
|
|
|
491 |
mmeineke |
859 |
haveEcr = 1; |
492 |
chrisfen |
872 |
ecr = theEcr; |
493 |
mmeineke |
841 |
|
494 |
gezelter |
845 |
( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0; |
495 |
|
|
|
496 |
mmeineke |
843 |
notifyFortranCutOffs( &rCut, &rList, &ecr, &est ); |
497 |
mmeineke |
841 |
} |
498 |
|
|
|
499 |
|
|
void SimInfo::setDefaultEcr( double theEcr, double theEst ){ |
500 |
mmeineke |
626 |
|
501 |
mmeineke |
841 |
est = theEst; |
502 |
|
|
setDefaultEcr( theEcr ); |
503 |
|
|
} |
504 |
|
|
|
505 |
|
|
|
506 |
mmeineke |
626 |
void SimInfo::checkCutOffs( void ){ |
507 |
gezelter |
770 |
|
508 |
mmeineke |
626 |
if( boxIsInit ){ |
509 |
|
|
|
510 |
|
|
//we need to check cutOffs against the box |
511 |
mmeineke |
859 |
|
512 |
|
|
if( rCut > maxCutoff ){ |
513 |
mmeineke |
626 |
sprintf( painCave.errMsg, |
514 |
gezelter |
1097 |
"LJrcut is too large for the current periodic box.\n" |
515 |
|
|
"\tCurrent Value of LJrcut = %G at time %G\n " |
516 |
|
|
"\tThis is larger than half of at least one of the\n" |
517 |
|
|
"\tperiodic box vectors. Right now, the Box matrix is:\n" |
518 |
tim |
1131 |
"\n" |
519 |
gezelter |
965 |
"\t[ %G %G %G ]\n" |
520 |
|
|
"\t[ %G %G %G ]\n" |
521 |
|
|
"\t[ %G %G %G ]\n", |
522 |
tim |
1131 |
rCut, currentTime, |
523 |
mmeineke |
874 |
Hmat[0][0], Hmat[0][1], Hmat[0][2], |
524 |
|
|
Hmat[1][0], Hmat[1][1], Hmat[1][2], |
525 |
|
|
Hmat[2][0], Hmat[2][1], Hmat[2][2]); |
526 |
mmeineke |
859 |
painCave.isFatal = 1; |
527 |
mmeineke |
626 |
simError(); |
528 |
|
|
} |
529 |
mmeineke |
859 |
|
530 |
|
|
if( haveEcr ){ |
531 |
|
|
if( ecr > maxCutoff ){ |
532 |
|
|
sprintf( painCave.errMsg, |
533 |
gezelter |
1097 |
"electrostaticCutoffRadius is too large for the current\n" |
534 |
|
|
"\tperiodic box.\n\n" |
535 |
|
|
"\tCurrent Value of ECR = %G at time %G\n " |
536 |
|
|
"\tThis is larger than half of at least one of the\n" |
537 |
|
|
"\tperiodic box vectors. Right now, the Box matrix is:\n" |
538 |
|
|
"\n" |
539 |
|
|
"\t[ %G %G %G ]\n" |
540 |
|
|
"\t[ %G %G %G ]\n" |
541 |
|
|
"\t[ %G %G %G ]\n", |
542 |
mmeineke |
874 |
ecr, currentTime, |
543 |
|
|
Hmat[0][0], Hmat[0][1], Hmat[0][2], |
544 |
|
|
Hmat[1][0], Hmat[1][1], Hmat[1][2], |
545 |
|
|
Hmat[2][0], Hmat[2][1], Hmat[2][2]); |
546 |
mmeineke |
859 |
painCave.isFatal = 1; |
547 |
|
|
simError(); |
548 |
tim |
781 |
} |
549 |
|
|
} |
550 |
tim |
767 |
} else { |
551 |
|
|
// initialize this stuff before using it, OK? |
552 |
gezelter |
770 |
sprintf( painCave.errMsg, |
553 |
gezelter |
965 |
"Trying to check cutoffs without a box.\n" |
554 |
|
|
"\tOOPSE should have better programmers than that.\n" ); |
555 |
gezelter |
770 |
painCave.isFatal = 1; |
556 |
|
|
simError(); |
557 |
mmeineke |
626 |
} |
558 |
gezelter |
770 |
|
559 |
mmeineke |
626 |
} |
560 |
tim |
658 |
|
561 |
|
|
void SimInfo::addProperty(GenericData* prop){ |
562 |
|
|
|
563 |
|
|
map<string, GenericData*>::iterator result; |
564 |
|
|
result = properties.find(prop->getID()); |
565 |
|
|
|
566 |
|
|
//we can't simply use properties[prop->getID()] = prop, |
567 |
|
|
//it will cause memory leak if we already contain a propery which has the same name of prop |
568 |
|
|
|
569 |
|
|
if(result != properties.end()){ |
570 |
|
|
|
571 |
|
|
delete (*result).second; |
572 |
|
|
(*result).second = prop; |
573 |
|
|
|
574 |
|
|
} |
575 |
|
|
else{ |
576 |
|
|
|
577 |
|
|
properties[prop->getID()] = prop; |
578 |
|
|
|
579 |
|
|
} |
580 |
|
|
|
581 |
|
|
} |
582 |
|
|
|
583 |
|
|
GenericData* SimInfo::getProperty(const string& propName){ |
584 |
|
|
|
585 |
|
|
map<string, GenericData*>::iterator result; |
586 |
|
|
|
587 |
|
|
//string lowerCaseName = (); |
588 |
|
|
|
589 |
|
|
result = properties.find(propName); |
590 |
|
|
|
591 |
|
|
if(result != properties.end()) |
592 |
|
|
return (*result).second; |
593 |
|
|
else |
594 |
|
|
return NULL; |
595 |
|
|
} |
596 |
|
|
|
597 |
tim |
1144 |
|
598 |
|
|
void getFortranGroupArray(SimInfo* info, vector<double>& mfact, int& ngroup, |
599 |
gezelter |
1150 |
vector<int>& groupList, vector<int>& groupStart){ |
600 |
tim |
1144 |
Molecule* mol; |
601 |
gezelter |
1150 |
Atom** myAtoms; |
602 |
tim |
1144 |
int numAtom; |
603 |
|
|
int curIndex; |
604 |
gezelter |
1150 |
double mtot; |
605 |
tim |
1144 |
|
606 |
|
|
mfact.clear(); |
607 |
|
|
groupList.clear(); |
608 |
|
|
groupStart.clear(); |
609 |
gezelter |
1150 |
|
610 |
tim |
1144 |
//Be careful, fortran array begin at 1 |
611 |
|
|
curIndex = 1; |
612 |
gezelter |
1150 |
|
613 |
|
|
if(info->useMolecularCutoffs){ |
614 |
tim |
1144 |
|
615 |
gezelter |
1150 |
#ifdef IS_MPI |
616 |
|
|
ngroup = mpiSim->getMyNMol(); |
617 |
|
|
#else |
618 |
tim |
1144 |
ngroup = info->n_mol; |
619 |
gezelter |
1150 |
#endif |
620 |
|
|
|
621 |
tim |
1144 |
for(int i = 0; i < ngroup; i ++){ |
622 |
|
|
mol = &(info->molecules[i]); |
623 |
|
|
numAtom = mol->getNAtoms(); |
624 |
gezelter |
1150 |
myAtoms = mol->getMyAtoms(); |
625 |
|
|
mtot = 0.0; |
626 |
|
|
|
627 |
|
|
for(int j=0; j < numAtom; j++) |
628 |
|
|
mtot += myAtoms[j]->getMass(); |
629 |
tim |
1144 |
|
630 |
gezelter |
1150 |
for(int j=0; j < numAtom; j++){ |
631 |
|
|
|
632 |
|
|
// We want the local Index: |
633 |
|
|
groupList.push_back(myAtoms[j]->getIndex() + 1); |
634 |
|
|
mfact.push_back(myAtoms[j]->getMass() / mtot); |
635 |
|
|
|
636 |
|
|
} |
637 |
|
|
|
638 |
tim |
1144 |
groupStart.push_back(curIndex); |
639 |
|
|
curIndex += numAtom; |
640 |
|
|
|
641 |
gezelter |
1150 |
} //end for(int i =0 ; i < ngroup; i++) |
642 |
tim |
1144 |
} |
643 |
|
|
else{ |
644 |
|
|
//using atomic cutoff, every single atom is just a group |
645 |
gezelter |
1150 |
|
646 |
|
|
#ifdef IS_MPI |
647 |
|
|
ngroup = mpiSim->getMyNlocal(); |
648 |
|
|
#else |
649 |
tim |
1144 |
ngroup = info->n_atoms; |
650 |
gezelter |
1150 |
#endif |
651 |
|
|
|
652 |
tim |
1144 |
for(int i =0 ; i < ngroup; i++){ |
653 |
gezelter |
1150 |
groupStart.push_back(curIndex++); |
654 |
tim |
1144 |
groupList.push_back((info->atoms[i])->getIndex() + 1); |
655 |
gezelter |
1150 |
mfact.push_back(1.0); |
656 |
|
|
|
657 |
tim |
1144 |
}//end for(int i =0 ; i < ngroup; i++) |
658 |
gezelter |
1150 |
|
659 |
tim |
1144 |
}//end if (info->useMolecularCutoffs) |
660 |
gezelter |
1150 |
|
661 |
tim |
1144 |
} |