1 |
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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gezelter |
1154 |
rSw = 0.0; |
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mmeineke |
377 |
|
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mmeineke |
859 |
haveRcut = 0; |
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gezelter |
1154 |
haveRsw = 0; |
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mmeineke |
626 |
boxIsInit = 0; |
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|
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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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chrisfen |
1187 |
useThermInt = 0; |
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tim |
1157 |
haveCutoffGroups = false; |
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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 |
457 |
wrapMeSimInfo( this ); |
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} |
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mmeineke |
377 |
|
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mmeineke |
670 |
|
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tim |
660 |
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 |
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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 |
588 |
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 |
590 |
setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic); |
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mmeineke |
568 |
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mmeineke |
377 |
} |
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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 |
} |
145 |
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146 |
gezelter |
574 |
|
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void SimInfo::scaleBox(double scale) { |
148 |
gezelter |
588 |
double theBox[3][3]; |
149 |
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int i, j; |
150 |
gezelter |
574 |
|
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gezelter |
617 |
// cerr << "Scaling box by " << scale << "\n"; |
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mmeineke |
586 |
|
153 |
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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} |
159 |
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160 |
gezelter |
588 |
void SimInfo::calcHmatInv( void ) { |
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mmeineke |
590 |
|
162 |
mmeineke |
853 |
int oldOrtho; |
163 |
mmeineke |
590 |
int i,j; |
164 |
mmeineke |
569 |
double smallDiag; |
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double tol; |
166 |
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double sanity[3][3]; |
167 |
mmeineke |
568 |
|
168 |
gezelter |
588 |
invertMat3( Hmat, HmatInv ); |
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mmeineke |
568 |
|
170 |
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; |
178 |
mmeineke |
568 |
|
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gezelter |
588 |
orthoRhombic = 1; |
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mmeineke |
568 |
|
181 |
gezelter |
588 |
for (i = 0; i < 3; i++ ) { |
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for (j = 0 ; j < 3; j++) { |
183 |
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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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} |
215 |
gezelter |
588 |
} |
216 |
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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221 |
gezelter |
588 |
// boxVol = Determinant of Hmat |
222 |
mmeineke |
568 |
|
223 |
gezelter |
588 |
boxVol = matDet3( Hmat ); |
224 |
mmeineke |
568 |
|
225 |
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// boxLx |
226 |
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|
227 |
gezelter |
588 |
dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0]; |
228 |
mmeineke |
568 |
dsq = dx*dx + dy*dy + dz*dz; |
229 |
gezelter |
621 |
boxL[0] = sqrt( dsq ); |
230 |
tim |
781 |
//maxCutoff = 0.5 * boxL[0]; |
231 |
mmeineke |
568 |
|
232 |
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// boxLy |
233 |
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|
234 |
gezelter |
588 |
dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1]; |
235 |
mmeineke |
568 |
dsq = dx*dx + dy*dy + dz*dz; |
236 |
gezelter |
621 |
boxL[1] = sqrt( dsq ); |
237 |
tim |
781 |
//if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1]; |
238 |
mmeineke |
568 |
|
239 |
tim |
781 |
|
240 |
mmeineke |
568 |
// boxLz |
241 |
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|
242 |
gezelter |
588 |
dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2]; |
243 |
mmeineke |
568 |
dsq = dx*dx + dy*dy + dz*dz; |
244 |
gezelter |
621 |
boxL[2] = sqrt( dsq ); |
245 |
tim |
781 |
//if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2]; |
246 |
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247 |
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//calculate the max cutoff |
248 |
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maxCutoff = calcMaxCutOff(); |
249 |
chuckv |
669 |
|
250 |
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checkCutOffs(); |
251 |
mmeineke |
626 |
|
252 |
mmeineke |
568 |
} |
253 |
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254 |
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255 |
tim |
781 |
double SimInfo::calcMaxCutOff(){ |
256 |
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257 |
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double ri[3], rj[3], rk[3]; |
258 |
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double rij[3], rjk[3], rki[3]; |
259 |
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double minDist; |
260 |
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261 |
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ri[0] = Hmat[0][0]; |
262 |
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ri[1] = Hmat[1][0]; |
263 |
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ri[2] = Hmat[2][0]; |
264 |
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265 |
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rj[0] = Hmat[0][1]; |
266 |
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rj[1] = Hmat[1][1]; |
267 |
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rj[2] = Hmat[2][1]; |
268 |
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269 |
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rk[0] = Hmat[0][2]; |
270 |
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rk[1] = Hmat[1][2]; |
271 |
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rk[2] = Hmat[2][2]; |
272 |
gezelter |
1097 |
|
273 |
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crossProduct3(ri, rj, rij); |
274 |
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distXY = dotProduct3(rk,rij) / norm3(rij); |
275 |
tim |
781 |
|
276 |
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crossProduct3(rj,rk, rjk); |
277 |
gezelter |
1097 |
distYZ = dotProduct3(ri,rjk) / norm3(rjk); |
278 |
tim |
781 |
|
279 |
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crossProduct3(rk,ri, rki); |
280 |
gezelter |
1097 |
distZX = dotProduct3(rj,rki) / norm3(rki); |
281 |
tim |
781 |
|
282 |
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minDist = min(min(distXY, distYZ), distZX); |
283 |
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return minDist/2; |
284 |
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285 |
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} |
286 |
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287 |
mmeineke |
568 |
void SimInfo::wrapVector( double thePos[3] ){ |
288 |
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|
289 |
mmeineke |
787 |
int i; |
290 |
mmeineke |
568 |
double scaled[3]; |
291 |
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|
292 |
mmeineke |
569 |
if( !orthoRhombic ){ |
293 |
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// calc the scaled coordinates. |
294 |
gezelter |
588 |
|
295 |
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|
296 |
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matVecMul3(HmatInv, thePos, scaled); |
297 |
mmeineke |
569 |
|
298 |
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for(i=0; i<3; i++) |
299 |
mmeineke |
572 |
scaled[i] -= roundMe(scaled[i]); |
300 |
mmeineke |
569 |
|
301 |
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// calc the wrapped real coordinates from the wrapped scaled coordinates |
302 |
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|
303 |
gezelter |
588 |
matVecMul3(Hmat, scaled, thePos); |
304 |
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|
305 |
mmeineke |
569 |
} |
306 |
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else{ |
307 |
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// calc the scaled coordinates. |
308 |
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|
309 |
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for(i=0; i<3; i++) |
310 |
gezelter |
588 |
scaled[i] = thePos[i]*HmatInv[i][i]; |
311 |
mmeineke |
569 |
|
312 |
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// wrap the scaled coordinates |
313 |
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|
314 |
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for(i=0; i<3; i++) |
315 |
mmeineke |
572 |
scaled[i] -= roundMe(scaled[i]); |
316 |
mmeineke |
569 |
|
317 |
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// calc the wrapped real coordinates from the wrapped scaled coordinates |
318 |
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|
319 |
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for(i=0; i<3; i++) |
320 |
gezelter |
588 |
thePos[i] = scaled[i]*Hmat[i][i]; |
321 |
mmeineke |
569 |
} |
322 |
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|
323 |
mmeineke |
568 |
} |
324 |
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325 |
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|
326 |
gezelter |
458 |
int SimInfo::getNDF(){ |
327 |
mmeineke |
790 |
int ndf_local; |
328 |
gezelter |
458 |
|
329 |
tim |
1113 |
ndf_local = 0; |
330 |
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|
331 |
gezelter |
1097 |
for(int i = 0; i < integrableObjects.size(); i++){ |
332 |
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ndf_local += 3; |
333 |
tim |
1118 |
if (integrableObjects[i]->isDirectional()) { |
334 |
|
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if (integrableObjects[i]->isLinear()) |
335 |
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ndf_local += 2; |
336 |
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else |
337 |
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ndf_local += 3; |
338 |
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} |
339 |
gezelter |
1097 |
} |
340 |
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341 |
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// n_constraints is local, so subtract them on each processor: |
342 |
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|
343 |
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ndf_local -= n_constraints; |
344 |
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|
345 |
gezelter |
458 |
#ifdef IS_MPI |
346 |
|
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MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
347 |
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#else |
348 |
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ndf = ndf_local; |
349 |
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#endif |
350 |
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|
351 |
gezelter |
1097 |
// nZconstraints is global, as are the 3 COM translations for the |
352 |
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// entire system: |
353 |
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|
354 |
mmeineke |
674 |
ndf = ndf - 3 - nZconstraints; |
355 |
gezelter |
458 |
|
356 |
|
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return ndf; |
357 |
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} |
358 |
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|
359 |
|
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int SimInfo::getNDFraw() { |
360 |
mmeineke |
790 |
int ndfRaw_local; |
361 |
gezelter |
458 |
|
362 |
|
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// Raw degrees of freedom that we have to set |
363 |
tim |
1113 |
ndfRaw_local = 0; |
364 |
gezelter |
1097 |
|
365 |
|
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for(int i = 0; i < integrableObjects.size(); i++){ |
366 |
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ndfRaw_local += 3; |
367 |
tim |
1118 |
if (integrableObjects[i]->isDirectional()) { |
368 |
|
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if (integrableObjects[i]->isLinear()) |
369 |
|
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ndfRaw_local += 2; |
370 |
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else |
371 |
|
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ndfRaw_local += 3; |
372 |
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} |
373 |
gezelter |
1097 |
} |
374 |
|
|
|
375 |
gezelter |
458 |
#ifdef IS_MPI |
376 |
|
|
MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
377 |
|
|
#else |
378 |
|
|
ndfRaw = ndfRaw_local; |
379 |
|
|
#endif |
380 |
|
|
|
381 |
|
|
return ndfRaw; |
382 |
|
|
} |
383 |
tim |
767 |
|
384 |
|
|
int SimInfo::getNDFtranslational() { |
385 |
mmeineke |
790 |
int ndfTrans_local; |
386 |
tim |
767 |
|
387 |
gezelter |
1097 |
ndfTrans_local = 3 * integrableObjects.size() - n_constraints; |
388 |
tim |
767 |
|
389 |
gezelter |
1097 |
|
390 |
tim |
767 |
#ifdef IS_MPI |
391 |
|
|
MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
392 |
|
|
#else |
393 |
|
|
ndfTrans = ndfTrans_local; |
394 |
|
|
#endif |
395 |
|
|
|
396 |
|
|
ndfTrans = ndfTrans - 3 - nZconstraints; |
397 |
|
|
|
398 |
|
|
return ndfTrans; |
399 |
|
|
} |
400 |
|
|
|
401 |
tim |
1108 |
int SimInfo::getTotIntegrableObjects() { |
402 |
|
|
int nObjs_local; |
403 |
|
|
int nObjs; |
404 |
|
|
|
405 |
|
|
nObjs_local = integrableObjects.size(); |
406 |
|
|
|
407 |
|
|
|
408 |
|
|
#ifdef IS_MPI |
409 |
|
|
MPI_Allreduce(&nObjs_local,&nObjs,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
410 |
|
|
#else |
411 |
|
|
nObjs = nObjs_local; |
412 |
|
|
#endif |
413 |
|
|
|
414 |
|
|
|
415 |
|
|
return nObjs; |
416 |
|
|
} |
417 |
|
|
|
418 |
mmeineke |
377 |
void SimInfo::refreshSim(){ |
419 |
|
|
|
420 |
|
|
simtype fInfo; |
421 |
|
|
int isError; |
422 |
gezelter |
490 |
int n_global; |
423 |
mmeineke |
424 |
int* excl; |
424 |
mmeineke |
626 |
|
425 |
mmeineke |
469 |
fInfo.dielect = 0.0; |
426 |
mmeineke |
377 |
|
427 |
gezelter |
941 |
if( useDipoles ){ |
428 |
mmeineke |
469 |
if( useReactionField )fInfo.dielect = dielectric; |
429 |
|
|
} |
430 |
|
|
|
431 |
mmeineke |
377 |
fInfo.SIM_uses_PBC = usePBC; |
432 |
mmeineke |
443 |
//fInfo.SIM_uses_LJ = 0; |
433 |
chuckv |
439 |
fInfo.SIM_uses_LJ = useLJ; |
434 |
mmeineke |
443 |
fInfo.SIM_uses_sticky = useSticky; |
435 |
|
|
//fInfo.SIM_uses_sticky = 0; |
436 |
gezelter |
941 |
fInfo.SIM_uses_charges = useCharges; |
437 |
|
|
fInfo.SIM_uses_dipoles = useDipoles; |
438 |
chuckv |
482 |
//fInfo.SIM_uses_dipoles = 0; |
439 |
chrisfen |
999 |
fInfo.SIM_uses_RF = useReactionField; |
440 |
|
|
//fInfo.SIM_uses_RF = 0; |
441 |
mmeineke |
377 |
fInfo.SIM_uses_GB = useGB; |
442 |
|
|
fInfo.SIM_uses_EAM = useEAM; |
443 |
|
|
|
444 |
gezelter |
1097 |
n_exclude = excludes->getSize(); |
445 |
|
|
excl = excludes->getFortranArray(); |
446 |
tim |
1144 |
|
447 |
gezelter |
490 |
#ifdef IS_MPI |
448 |
|
|
n_global = mpiSim->getTotAtoms(); |
449 |
|
|
#else |
450 |
|
|
n_global = n_atoms; |
451 |
|
|
#endif |
452 |
gezelter |
1150 |
|
453 |
mmeineke |
377 |
isError = 0; |
454 |
gezelter |
1150 |
|
455 |
|
|
getFortranGroupArray(this, mfact, ngroup, groupList, groupStart); |
456 |
tim |
1157 |
//it may not be a good idea to pass the address of first element in vector |
457 |
tim |
1164 |
//since c++ standard does not require vector to be stored continuously in meomory |
458 |
|
|
//Most of the compilers will organize the memory of vector continuously |
459 |
gezelter |
490 |
setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl, |
460 |
gezelter |
1150 |
&nGlobalExcludes, globalExcludes, molMembershipArray, |
461 |
|
|
&mfact[0], &ngroup, &groupList[0], &groupStart[0], &isError); |
462 |
|
|
|
463 |
mmeineke |
377 |
if( isError ){ |
464 |
gezelter |
1150 |
|
465 |
mmeineke |
377 |
sprintf( painCave.errMsg, |
466 |
gezelter |
1150 |
"There was an error setting the simulation information in fortran.\n" ); |
467 |
mmeineke |
377 |
painCave.isFatal = 1; |
468 |
|
|
simError(); |
469 |
|
|
} |
470 |
gezelter |
1150 |
|
471 |
mmeineke |
377 |
#ifdef IS_MPI |
472 |
|
|
sprintf( checkPointMsg, |
473 |
|
|
"succesfully sent the simulation information to fortran.\n"); |
474 |
|
|
MPIcheckPoint(); |
475 |
|
|
#endif // is_mpi |
476 |
gezelter |
1150 |
|
477 |
gezelter |
474 |
this->ndf = this->getNDF(); |
478 |
|
|
this->ndfRaw = this->getNDFraw(); |
479 |
tim |
767 |
this->ndfTrans = this->getNDFtranslational(); |
480 |
mmeineke |
377 |
} |
481 |
|
|
|
482 |
mmeineke |
841 |
void SimInfo::setDefaultRcut( double theRcut ){ |
483 |
gezelter |
1150 |
|
484 |
mmeineke |
859 |
haveRcut = 1; |
485 |
mmeineke |
841 |
rCut = theRcut; |
486 |
gezelter |
1154 |
rList = rCut + 1.0; |
487 |
gezelter |
1150 |
|
488 |
gezelter |
1154 |
notifyFortranCutOffs( &rCut, &rSw, &rList ); |
489 |
mmeineke |
841 |
} |
490 |
|
|
|
491 |
gezelter |
1154 |
void SimInfo::setDefaultRcut( double theRcut, double theRsw ){ |
492 |
mmeineke |
841 |
|
493 |
gezelter |
1154 |
rSw = theRsw; |
494 |
|
|
setDefaultRcut( theRcut ); |
495 |
mmeineke |
841 |
} |
496 |
|
|
|
497 |
mmeineke |
626 |
|
498 |
|
|
void SimInfo::checkCutOffs( void ){ |
499 |
gezelter |
770 |
|
500 |
mmeineke |
626 |
if( boxIsInit ){ |
501 |
|
|
|
502 |
|
|
//we need to check cutOffs against the box |
503 |
mmeineke |
859 |
|
504 |
|
|
if( rCut > maxCutoff ){ |
505 |
mmeineke |
626 |
sprintf( painCave.errMsg, |
506 |
gezelter |
1154 |
"cutoffRadius is too large for the current periodic box.\n" |
507 |
|
|
"\tCurrent Value of cutoffRadius = %G at time %G\n " |
508 |
gezelter |
1097 |
"\tThis is larger than half of at least one of the\n" |
509 |
|
|
"\tperiodic box vectors. Right now, the Box matrix is:\n" |
510 |
tim |
1131 |
"\n" |
511 |
gezelter |
965 |
"\t[ %G %G %G ]\n" |
512 |
|
|
"\t[ %G %G %G ]\n" |
513 |
|
|
"\t[ %G %G %G ]\n", |
514 |
tim |
1131 |
rCut, currentTime, |
515 |
mmeineke |
874 |
Hmat[0][0], Hmat[0][1], Hmat[0][2], |
516 |
|
|
Hmat[1][0], Hmat[1][1], Hmat[1][2], |
517 |
|
|
Hmat[2][0], Hmat[2][1], Hmat[2][2]); |
518 |
mmeineke |
859 |
painCave.isFatal = 1; |
519 |
mmeineke |
626 |
simError(); |
520 |
gezelter |
1154 |
} |
521 |
tim |
767 |
} else { |
522 |
|
|
// initialize this stuff before using it, OK? |
523 |
gezelter |
770 |
sprintf( painCave.errMsg, |
524 |
gezelter |
965 |
"Trying to check cutoffs without a box.\n" |
525 |
|
|
"\tOOPSE should have better programmers than that.\n" ); |
526 |
gezelter |
770 |
painCave.isFatal = 1; |
527 |
|
|
simError(); |
528 |
mmeineke |
626 |
} |
529 |
gezelter |
770 |
|
530 |
mmeineke |
626 |
} |
531 |
tim |
658 |
|
532 |
|
|
void SimInfo::addProperty(GenericData* prop){ |
533 |
|
|
|
534 |
|
|
map<string, GenericData*>::iterator result; |
535 |
|
|
result = properties.find(prop->getID()); |
536 |
|
|
|
537 |
|
|
//we can't simply use properties[prop->getID()] = prop, |
538 |
|
|
//it will cause memory leak if we already contain a propery which has the same name of prop |
539 |
|
|
|
540 |
|
|
if(result != properties.end()){ |
541 |
|
|
|
542 |
|
|
delete (*result).second; |
543 |
|
|
(*result).second = prop; |
544 |
|
|
|
545 |
|
|
} |
546 |
|
|
else{ |
547 |
|
|
|
548 |
|
|
properties[prop->getID()] = prop; |
549 |
|
|
|
550 |
|
|
} |
551 |
|
|
|
552 |
|
|
} |
553 |
|
|
|
554 |
|
|
GenericData* SimInfo::getProperty(const string& propName){ |
555 |
|
|
|
556 |
|
|
map<string, GenericData*>::iterator result; |
557 |
|
|
|
558 |
|
|
//string lowerCaseName = (); |
559 |
|
|
|
560 |
|
|
result = properties.find(propName); |
561 |
|
|
|
562 |
|
|
if(result != properties.end()) |
563 |
|
|
return (*result).second; |
564 |
|
|
else |
565 |
|
|
return NULL; |
566 |
|
|
} |
567 |
|
|
|
568 |
tim |
1144 |
|
569 |
|
|
void getFortranGroupArray(SimInfo* info, vector<double>& mfact, int& ngroup, |
570 |
gezelter |
1150 |
vector<int>& groupList, vector<int>& groupStart){ |
571 |
tim |
1157 |
Molecule* myMols; |
572 |
gezelter |
1150 |
Atom** myAtoms; |
573 |
tim |
1144 |
int numAtom; |
574 |
|
|
int curIndex; |
575 |
gezelter |
1150 |
double mtot; |
576 |
tim |
1157 |
int numMol; |
577 |
|
|
int numCutoffGroups; |
578 |
|
|
CutoffGroup* myCutoffGroup; |
579 |
|
|
vector<CutoffGroup*>::iterator iterCutoff; |
580 |
|
|
Atom* cutoffAtom; |
581 |
|
|
vector<Atom*>::iterator iterAtom; |
582 |
|
|
int atomIndex; |
583 |
tim |
1158 |
double totalMass; |
584 |
tim |
1157 |
|
585 |
tim |
1144 |
mfact.clear(); |
586 |
|
|
groupList.clear(); |
587 |
|
|
groupStart.clear(); |
588 |
gezelter |
1150 |
|
589 |
tim |
1144 |
//Be careful, fortran array begin at 1 |
590 |
|
|
curIndex = 1; |
591 |
tim |
1157 |
|
592 |
|
|
myMols = info->molecules; |
593 |
|
|
numMol = info->n_mol; |
594 |
|
|
for(int i = 0; i < numMol; i++){ |
595 |
|
|
numCutoffGroups = myMols[i].getNCutoffGroups(); |
596 |
|
|
for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff); myCutoffGroup != NULL; |
597 |
|
|
myCutoffGroup =myMols[i].nextCutoffGroup(iterCutoff)){ |
598 |
tim |
1158 |
|
599 |
|
|
totalMass = myCutoffGroup->getMass(); |
600 |
tim |
1157 |
|
601 |
|
|
for(cutoffAtom = myCutoffGroup->beginAtom(iterAtom); cutoffAtom != NULL; |
602 |
tim |
1158 |
cutoffAtom = myCutoffGroup->nextAtom(iterAtom)){ |
603 |
|
|
mfact.push_back(cutoffAtom->getMass()/totalMass); |
604 |
tim |
1201 |
#ifdef IS_MPI |
605 |
|
|
groupList.push_back(cutoffAtom->getGlobalIndex() + 1); |
606 |
|
|
#else |
607 |
tim |
1157 |
groupList.push_back(cutoffAtom->getIndex() + 1); |
608 |
tim |
1201 |
#endif |
609 |
tim |
1157 |
} |
610 |
|
|
|
611 |
tim |
1144 |
groupStart.push_back(curIndex); |
612 |
tim |
1157 |
curIndex += myCutoffGroup->getNumAtom(); |
613 |
|
|
|
614 |
tim |
1158 |
}//end for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff)) |
615 |
|
|
|
616 |
|
|
}//end for(int i = 0; i < numMol; i++) |
617 |
tim |
1198 |
|
618 |
|
|
|
619 |
|
|
//The last cutoff group need more element to indicate the end of the cutoff |
620 |
tim |
1201 |
ngroup = groupStart.size(); |
621 |
tim |
1144 |
} |