1 |
gezelter |
829 |
#include <stdlib.h> |
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#include <string.h> |
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#include <math.h> |
4 |
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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tim |
1234 |
#include "ConstraintManager.hpp" |
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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 |
|
31 |
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; |
42 |
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; |
47 |
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 |
1212 |
useSolidThermInt = 0; |
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useLiquidThermInt = 0; |
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chrisfen |
1187 |
|
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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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tim |
1234 |
consMan = NULL; |
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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 |
1234 |
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if (!consMan) |
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delete consMan; |
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tim |
660 |
} |
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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 |
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 |
568 |
|
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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] ){ |
117 |
mmeineke |
568 |
|
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mmeineke |
787 |
int i, j; |
119 |
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 |
|
126 |
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]; |
130 |
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mmeineke |
568 |
calcBoxL(); |
132 |
gezelter |
588 |
calcHmatInv(); |
133 |
mmeineke |
568 |
|
134 |
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]; |
138 |
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} |
139 |
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} |
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mmeineke |
586 |
|
141 |
mmeineke |
590 |
setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic); |
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mmeineke |
568 |
|
143 |
mmeineke |
377 |
} |
144 |
gezelter |
458 |
|
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mmeineke |
568 |
|
146 |
gezelter |
588 |
void SimInfo::getBoxM (double theBox[3][3]) { |
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mmeineke |
568 |
|
148 |
gezelter |
588 |
int i, j; |
149 |
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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]; |
151 |
mmeineke |
568 |
} |
152 |
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153 |
gezelter |
574 |
|
154 |
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void SimInfo::scaleBox(double scale) { |
155 |
gezelter |
588 |
double theBox[3][3]; |
156 |
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int i, j; |
157 |
gezelter |
574 |
|
158 |
gezelter |
617 |
// cerr << "Scaling box by " << scale << "\n"; |
159 |
mmeineke |
586 |
|
160 |
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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163 |
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setBoxM(theBox); |
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} |
166 |
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167 |
gezelter |
588 |
void SimInfo::calcHmatInv( void ) { |
168 |
mmeineke |
590 |
|
169 |
mmeineke |
853 |
int oldOrtho; |
170 |
mmeineke |
590 |
int i,j; |
171 |
mmeineke |
569 |
double smallDiag; |
172 |
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double tol; |
173 |
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double sanity[3][3]; |
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mmeineke |
568 |
|
175 |
gezelter |
588 |
invertMat3( Hmat, HmatInv ); |
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mmeineke |
568 |
|
177 |
gezelter |
588 |
// check to see if Hmat is orthorhombic |
178 |
mmeineke |
568 |
|
179 |
mmeineke |
853 |
oldOrtho = orthoRhombic; |
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181 |
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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]); |
184 |
mmeineke |
855 |
tol = smallDiag * orthoTolerance; |
185 |
mmeineke |
568 |
|
186 |
gezelter |
588 |
orthoRhombic = 1; |
187 |
mmeineke |
568 |
|
188 |
gezelter |
588 |
for (i = 0; i < 3; i++ ) { |
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for (j = 0 ; j < 3; j++) { |
190 |
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if (i != j) { |
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if (orthoRhombic) { |
192 |
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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} |
197 |
mmeineke |
853 |
|
198 |
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if( oldOrtho != orthoRhombic ){ |
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200 |
gezelter |
1218 |
if( orthoRhombic ) { |
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mmeineke |
853 |
sprintf( painCave.errMsg, |
202 |
chrisfen |
1221 |
"OOPSE is switching from the default Non-Orthorhombic\n" |
203 |
gezelter |
1097 |
"\tto the faster Orthorhombic periodic boundary computations.\n" |
204 |
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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" |
206 |
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"\tvariable ( currently set to %G ) smaller.\n", |
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mmeineke |
855 |
orthoTolerance); |
208 |
gezelter |
1218 |
painCave.severity = OOPSE_INFO; |
209 |
mmeineke |
853 |
simError(); |
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} |
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else { |
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sprintf( painCave.errMsg, |
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chrisfen |
1221 |
"OOPSE is switching from the faster Orthorhombic to the more\n" |
214 |
gezelter |
1097 |
"\tflexible Non-Orthorhombic periodic boundary computations.\n" |
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"\tThis is usually because the box has deformed under\n" |
216 |
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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", |
219 |
mmeineke |
855 |
orthoTolerance); |
220 |
gezelter |
1218 |
painCave.severity = OOPSE_WARNING; |
221 |
mmeineke |
853 |
simError(); |
222 |
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} |
223 |
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} |
224 |
gezelter |
588 |
} |
225 |
mmeineke |
569 |
|
226 |
mmeineke |
568 |
void SimInfo::calcBoxL( void ){ |
227 |
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|
228 |
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double dx, dy, dz, dsq; |
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|
230 |
gezelter |
588 |
// boxVol = Determinant of Hmat |
231 |
mmeineke |
568 |
|
232 |
gezelter |
588 |
boxVol = matDet3( Hmat ); |
233 |
mmeineke |
568 |
|
234 |
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// boxLx |
235 |
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|
236 |
gezelter |
588 |
dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0]; |
237 |
mmeineke |
568 |
dsq = dx*dx + dy*dy + dz*dz; |
238 |
gezelter |
621 |
boxL[0] = sqrt( dsq ); |
239 |
tim |
781 |
//maxCutoff = 0.5 * boxL[0]; |
240 |
mmeineke |
568 |
|
241 |
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// boxLy |
242 |
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|
243 |
gezelter |
588 |
dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1]; |
244 |
mmeineke |
568 |
dsq = dx*dx + dy*dy + dz*dz; |
245 |
gezelter |
621 |
boxL[1] = sqrt( dsq ); |
246 |
tim |
781 |
//if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1]; |
247 |
mmeineke |
568 |
|
248 |
tim |
781 |
|
249 |
mmeineke |
568 |
// boxLz |
250 |
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|
251 |
gezelter |
588 |
dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2]; |
252 |
mmeineke |
568 |
dsq = dx*dx + dy*dy + dz*dz; |
253 |
gezelter |
621 |
boxL[2] = sqrt( dsq ); |
254 |
tim |
781 |
//if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2]; |
255 |
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256 |
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//calculate the max cutoff |
257 |
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maxCutoff = calcMaxCutOff(); |
258 |
chuckv |
669 |
|
259 |
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checkCutOffs(); |
260 |
mmeineke |
626 |
|
261 |
mmeineke |
568 |
} |
262 |
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263 |
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264 |
tim |
781 |
double SimInfo::calcMaxCutOff(){ |
265 |
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266 |
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double ri[3], rj[3], rk[3]; |
267 |
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double rij[3], rjk[3], rki[3]; |
268 |
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double minDist; |
269 |
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270 |
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ri[0] = Hmat[0][0]; |
271 |
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ri[1] = Hmat[1][0]; |
272 |
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ri[2] = Hmat[2][0]; |
273 |
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274 |
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rj[0] = Hmat[0][1]; |
275 |
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rj[1] = Hmat[1][1]; |
276 |
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rj[2] = Hmat[2][1]; |
277 |
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278 |
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rk[0] = Hmat[0][2]; |
279 |
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rk[1] = Hmat[1][2]; |
280 |
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rk[2] = Hmat[2][2]; |
281 |
gezelter |
1097 |
|
282 |
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crossProduct3(ri, rj, rij); |
283 |
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distXY = dotProduct3(rk,rij) / norm3(rij); |
284 |
tim |
781 |
|
285 |
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crossProduct3(rj,rk, rjk); |
286 |
gezelter |
1097 |
distYZ = dotProduct3(ri,rjk) / norm3(rjk); |
287 |
tim |
781 |
|
288 |
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crossProduct3(rk,ri, rki); |
289 |
gezelter |
1097 |
distZX = dotProduct3(rj,rki) / norm3(rki); |
290 |
tim |
781 |
|
291 |
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minDist = min(min(distXY, distYZ), distZX); |
292 |
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return minDist/2; |
293 |
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294 |
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} |
295 |
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296 |
mmeineke |
568 |
void SimInfo::wrapVector( double thePos[3] ){ |
297 |
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|
298 |
mmeineke |
787 |
int i; |
299 |
mmeineke |
568 |
double scaled[3]; |
300 |
|
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|
301 |
mmeineke |
569 |
if( !orthoRhombic ){ |
302 |
|
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// calc the scaled coordinates. |
303 |
gezelter |
588 |
|
304 |
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|
305 |
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matVecMul3(HmatInv, thePos, scaled); |
306 |
mmeineke |
569 |
|
307 |
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for(i=0; i<3; i++) |
308 |
mmeineke |
572 |
scaled[i] -= roundMe(scaled[i]); |
309 |
mmeineke |
569 |
|
310 |
|
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// calc the wrapped real coordinates from the wrapped scaled coordinates |
311 |
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|
312 |
gezelter |
588 |
matVecMul3(Hmat, scaled, thePos); |
313 |
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|
314 |
mmeineke |
569 |
} |
315 |
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else{ |
316 |
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// calc the scaled coordinates. |
317 |
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|
318 |
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for(i=0; i<3; i++) |
319 |
gezelter |
588 |
scaled[i] = thePos[i]*HmatInv[i][i]; |
320 |
mmeineke |
569 |
|
321 |
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// wrap the scaled coordinates |
322 |
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|
323 |
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for(i=0; i<3; i++) |
324 |
mmeineke |
572 |
scaled[i] -= roundMe(scaled[i]); |
325 |
mmeineke |
569 |
|
326 |
|
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// calc the wrapped real coordinates from the wrapped scaled coordinates |
327 |
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|
328 |
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for(i=0; i<3; i++) |
329 |
gezelter |
588 |
thePos[i] = scaled[i]*Hmat[i][i]; |
330 |
mmeineke |
569 |
} |
331 |
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|
332 |
mmeineke |
568 |
} |
333 |
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|
334 |
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|
335 |
gezelter |
458 |
int SimInfo::getNDF(){ |
336 |
mmeineke |
790 |
int ndf_local; |
337 |
gezelter |
458 |
|
338 |
tim |
1113 |
ndf_local = 0; |
339 |
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|
340 |
gezelter |
1097 |
for(int i = 0; i < integrableObjects.size(); i++){ |
341 |
|
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ndf_local += 3; |
342 |
tim |
1118 |
if (integrableObjects[i]->isDirectional()) { |
343 |
|
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if (integrableObjects[i]->isLinear()) |
344 |
|
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ndf_local += 2; |
345 |
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else |
346 |
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ndf_local += 3; |
347 |
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} |
348 |
gezelter |
1097 |
} |
349 |
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|
350 |
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// n_constraints is local, so subtract them on each processor: |
351 |
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|
352 |
|
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ndf_local -= n_constraints; |
353 |
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|
354 |
gezelter |
458 |
#ifdef IS_MPI |
355 |
|
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MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
356 |
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#else |
357 |
|
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ndf = ndf_local; |
358 |
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#endif |
359 |
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|
360 |
gezelter |
1097 |
// nZconstraints is global, as are the 3 COM translations for the |
361 |
|
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// entire system: |
362 |
|
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|
363 |
mmeineke |
674 |
ndf = ndf - 3 - nZconstraints; |
364 |
gezelter |
458 |
|
365 |
|
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return ndf; |
366 |
|
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} |
367 |
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|
368 |
|
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int SimInfo::getNDFraw() { |
369 |
mmeineke |
790 |
int ndfRaw_local; |
370 |
gezelter |
458 |
|
371 |
|
|
// Raw degrees of freedom that we have to set |
372 |
tim |
1113 |
ndfRaw_local = 0; |
373 |
gezelter |
1097 |
|
374 |
|
|
for(int i = 0; i < integrableObjects.size(); i++){ |
375 |
|
|
ndfRaw_local += 3; |
376 |
tim |
1118 |
if (integrableObjects[i]->isDirectional()) { |
377 |
|
|
if (integrableObjects[i]->isLinear()) |
378 |
|
|
ndfRaw_local += 2; |
379 |
|
|
else |
380 |
|
|
ndfRaw_local += 3; |
381 |
|
|
} |
382 |
gezelter |
1097 |
} |
383 |
|
|
|
384 |
gezelter |
458 |
#ifdef IS_MPI |
385 |
|
|
MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
386 |
|
|
#else |
387 |
|
|
ndfRaw = ndfRaw_local; |
388 |
|
|
#endif |
389 |
|
|
|
390 |
|
|
return ndfRaw; |
391 |
|
|
} |
392 |
tim |
767 |
|
393 |
|
|
int SimInfo::getNDFtranslational() { |
394 |
mmeineke |
790 |
int ndfTrans_local; |
395 |
tim |
767 |
|
396 |
gezelter |
1097 |
ndfTrans_local = 3 * integrableObjects.size() - n_constraints; |
397 |
tim |
767 |
|
398 |
gezelter |
1097 |
|
399 |
tim |
767 |
#ifdef IS_MPI |
400 |
|
|
MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
401 |
|
|
#else |
402 |
|
|
ndfTrans = ndfTrans_local; |
403 |
|
|
#endif |
404 |
|
|
|
405 |
|
|
ndfTrans = ndfTrans - 3 - nZconstraints; |
406 |
|
|
|
407 |
|
|
return ndfTrans; |
408 |
|
|
} |
409 |
|
|
|
410 |
tim |
1108 |
int SimInfo::getTotIntegrableObjects() { |
411 |
|
|
int nObjs_local; |
412 |
|
|
int nObjs; |
413 |
|
|
|
414 |
|
|
nObjs_local = integrableObjects.size(); |
415 |
|
|
|
416 |
|
|
|
417 |
|
|
#ifdef IS_MPI |
418 |
|
|
MPI_Allreduce(&nObjs_local,&nObjs,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
419 |
|
|
#else |
420 |
|
|
nObjs = nObjs_local; |
421 |
|
|
#endif |
422 |
|
|
|
423 |
|
|
|
424 |
|
|
return nObjs; |
425 |
|
|
} |
426 |
|
|
|
427 |
mmeineke |
377 |
void SimInfo::refreshSim(){ |
428 |
|
|
|
429 |
|
|
simtype fInfo; |
430 |
|
|
int isError; |
431 |
gezelter |
490 |
int n_global; |
432 |
mmeineke |
424 |
int* excl; |
433 |
mmeineke |
626 |
|
434 |
mmeineke |
469 |
fInfo.dielect = 0.0; |
435 |
mmeineke |
377 |
|
436 |
gezelter |
941 |
if( useDipoles ){ |
437 |
mmeineke |
469 |
if( useReactionField )fInfo.dielect = dielectric; |
438 |
|
|
} |
439 |
|
|
|
440 |
mmeineke |
377 |
fInfo.SIM_uses_PBC = usePBC; |
441 |
mmeineke |
443 |
//fInfo.SIM_uses_LJ = 0; |
442 |
chuckv |
439 |
fInfo.SIM_uses_LJ = useLJ; |
443 |
mmeineke |
443 |
fInfo.SIM_uses_sticky = useSticky; |
444 |
|
|
//fInfo.SIM_uses_sticky = 0; |
445 |
gezelter |
941 |
fInfo.SIM_uses_charges = useCharges; |
446 |
|
|
fInfo.SIM_uses_dipoles = useDipoles; |
447 |
chuckv |
482 |
//fInfo.SIM_uses_dipoles = 0; |
448 |
chrisfen |
999 |
fInfo.SIM_uses_RF = useReactionField; |
449 |
|
|
//fInfo.SIM_uses_RF = 0; |
450 |
mmeineke |
377 |
fInfo.SIM_uses_GB = useGB; |
451 |
|
|
fInfo.SIM_uses_EAM = useEAM; |
452 |
|
|
|
453 |
gezelter |
1097 |
n_exclude = excludes->getSize(); |
454 |
|
|
excl = excludes->getFortranArray(); |
455 |
tim |
1144 |
|
456 |
gezelter |
490 |
#ifdef IS_MPI |
457 |
gezelter |
1203 |
n_global = mpiSim->getNAtomsGlobal(); |
458 |
gezelter |
490 |
#else |
459 |
|
|
n_global = n_atoms; |
460 |
|
|
#endif |
461 |
gezelter |
1150 |
|
462 |
mmeineke |
377 |
isError = 0; |
463 |
gezelter |
1150 |
|
464 |
gezelter |
1214 |
getFortranGroupArrays(this, FglobalGroupMembership, mfact); |
465 |
tim |
1157 |
//it may not be a good idea to pass the address of first element in vector |
466 |
tim |
1164 |
//since c++ standard does not require vector to be stored continuously in meomory |
467 |
|
|
//Most of the compilers will organize the memory of vector continuously |
468 |
gezelter |
490 |
setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl, |
469 |
gezelter |
1150 |
&nGlobalExcludes, globalExcludes, molMembershipArray, |
470 |
gezelter |
1217 |
&mfact[0], &ngroup, &FglobalGroupMembership[0], &isError); |
471 |
|
|
|
472 |
mmeineke |
377 |
if( isError ){ |
473 |
gezelter |
1150 |
|
474 |
mmeineke |
377 |
sprintf( painCave.errMsg, |
475 |
gezelter |
1150 |
"There was an error setting the simulation information in fortran.\n" ); |
476 |
mmeineke |
377 |
painCave.isFatal = 1; |
477 |
chrisfen |
1221 |
painCave.severity = OOPSE_ERROR; |
478 |
mmeineke |
377 |
simError(); |
479 |
|
|
} |
480 |
gezelter |
1150 |
|
481 |
mmeineke |
377 |
#ifdef IS_MPI |
482 |
|
|
sprintf( checkPointMsg, |
483 |
|
|
"succesfully sent the simulation information to fortran.\n"); |
484 |
|
|
MPIcheckPoint(); |
485 |
|
|
#endif // is_mpi |
486 |
gezelter |
1150 |
|
487 |
gezelter |
474 |
this->ndf = this->getNDF(); |
488 |
|
|
this->ndfRaw = this->getNDFraw(); |
489 |
tim |
767 |
this->ndfTrans = this->getNDFtranslational(); |
490 |
mmeineke |
377 |
} |
491 |
|
|
|
492 |
mmeineke |
841 |
void SimInfo::setDefaultRcut( double theRcut ){ |
493 |
gezelter |
1150 |
|
494 |
mmeineke |
859 |
haveRcut = 1; |
495 |
mmeineke |
841 |
rCut = theRcut; |
496 |
gezelter |
1154 |
rList = rCut + 1.0; |
497 |
gezelter |
1150 |
|
498 |
gezelter |
1154 |
notifyFortranCutOffs( &rCut, &rSw, &rList ); |
499 |
mmeineke |
841 |
} |
500 |
|
|
|
501 |
gezelter |
1154 |
void SimInfo::setDefaultRcut( double theRcut, double theRsw ){ |
502 |
mmeineke |
841 |
|
503 |
gezelter |
1154 |
rSw = theRsw; |
504 |
|
|
setDefaultRcut( theRcut ); |
505 |
mmeineke |
841 |
} |
506 |
|
|
|
507 |
mmeineke |
626 |
|
508 |
|
|
void SimInfo::checkCutOffs( void ){ |
509 |
gezelter |
770 |
|
510 |
mmeineke |
626 |
if( boxIsInit ){ |
511 |
|
|
|
512 |
|
|
//we need to check cutOffs against the box |
513 |
mmeineke |
859 |
|
514 |
|
|
if( rCut > maxCutoff ){ |
515 |
mmeineke |
626 |
sprintf( painCave.errMsg, |
516 |
chrisfen |
1221 |
"cutoffRadius is too large for the current periodic box.\n" |
517 |
gezelter |
1154 |
"\tCurrent Value of cutoffRadius = %G at time %G\n " |
518 |
gezelter |
1097 |
"\tThis is larger than half of at least one of the\n" |
519 |
|
|
"\tperiodic box vectors. Right now, the Box matrix is:\n" |
520 |
tim |
1131 |
"\n" |
521 |
gezelter |
965 |
"\t[ %G %G %G ]\n" |
522 |
|
|
"\t[ %G %G %G ]\n" |
523 |
|
|
"\t[ %G %G %G ]\n", |
524 |
tim |
1131 |
rCut, currentTime, |
525 |
mmeineke |
874 |
Hmat[0][0], Hmat[0][1], Hmat[0][2], |
526 |
|
|
Hmat[1][0], Hmat[1][1], Hmat[1][2], |
527 |
|
|
Hmat[2][0], Hmat[2][1], Hmat[2][2]); |
528 |
gezelter |
1218 |
painCave.severity = OOPSE_ERROR; |
529 |
mmeineke |
859 |
painCave.isFatal = 1; |
530 |
mmeineke |
626 |
simError(); |
531 |
gezelter |
1154 |
} |
532 |
tim |
767 |
} else { |
533 |
|
|
// initialize this stuff before using it, OK? |
534 |
gezelter |
770 |
sprintf( painCave.errMsg, |
535 |
chrisfen |
1221 |
"Trying to check cutoffs without a box.\n" |
536 |
gezelter |
965 |
"\tOOPSE should have better programmers than that.\n" ); |
537 |
gezelter |
1218 |
painCave.severity = OOPSE_ERROR; |
538 |
gezelter |
770 |
painCave.isFatal = 1; |
539 |
|
|
simError(); |
540 |
mmeineke |
626 |
} |
541 |
gezelter |
770 |
|
542 |
mmeineke |
626 |
} |
543 |
tim |
658 |
|
544 |
|
|
void SimInfo::addProperty(GenericData* prop){ |
545 |
|
|
|
546 |
|
|
map<string, GenericData*>::iterator result; |
547 |
|
|
result = properties.find(prop->getID()); |
548 |
|
|
|
549 |
|
|
//we can't simply use properties[prop->getID()] = prop, |
550 |
|
|
//it will cause memory leak if we already contain a propery which has the same name of prop |
551 |
|
|
|
552 |
|
|
if(result != properties.end()){ |
553 |
|
|
|
554 |
|
|
delete (*result).second; |
555 |
|
|
(*result).second = prop; |
556 |
|
|
|
557 |
|
|
} |
558 |
|
|
else{ |
559 |
|
|
|
560 |
|
|
properties[prop->getID()] = prop; |
561 |
|
|
|
562 |
|
|
} |
563 |
|
|
|
564 |
|
|
} |
565 |
|
|
|
566 |
|
|
GenericData* SimInfo::getProperty(const string& propName){ |
567 |
|
|
|
568 |
|
|
map<string, GenericData*>::iterator result; |
569 |
|
|
|
570 |
|
|
//string lowerCaseName = (); |
571 |
|
|
|
572 |
|
|
result = properties.find(propName); |
573 |
|
|
|
574 |
|
|
if(result != properties.end()) |
575 |
|
|
return (*result).second; |
576 |
|
|
else |
577 |
|
|
return NULL; |
578 |
|
|
} |
579 |
|
|
|
580 |
tim |
1144 |
|
581 |
gezelter |
1214 |
void SimInfo::getFortranGroupArrays(SimInfo* info, |
582 |
|
|
vector<int>& FglobalGroupMembership, |
583 |
|
|
vector<double>& mfact){ |
584 |
|
|
|
585 |
tim |
1157 |
Molecule* myMols; |
586 |
gezelter |
1150 |
Atom** myAtoms; |
587 |
tim |
1144 |
int numAtom; |
588 |
gezelter |
1150 |
double mtot; |
589 |
tim |
1157 |
int numMol; |
590 |
|
|
int numCutoffGroups; |
591 |
|
|
CutoffGroup* myCutoffGroup; |
592 |
|
|
vector<CutoffGroup*>::iterator iterCutoff; |
593 |
|
|
Atom* cutoffAtom; |
594 |
|
|
vector<Atom*>::iterator iterAtom; |
595 |
|
|
int atomIndex; |
596 |
tim |
1158 |
double totalMass; |
597 |
tim |
1157 |
|
598 |
tim |
1144 |
mfact.clear(); |
599 |
gezelter |
1214 |
FglobalGroupMembership.clear(); |
600 |
gezelter |
1150 |
|
601 |
tim |
1157 |
|
602 |
gezelter |
1214 |
// Fix the silly fortran indexing problem |
603 |
|
|
#ifdef IS_MPI |
604 |
|
|
numAtom = mpiSim->getNAtomsGlobal(); |
605 |
|
|
#else |
606 |
|
|
numAtom = n_atoms; |
607 |
|
|
#endif |
608 |
|
|
for (int i = 0; i < numAtom; i++) |
609 |
|
|
FglobalGroupMembership.push_back(globalGroupMembership[i] + 1); |
610 |
gezelter |
1217 |
|
611 |
gezelter |
1214 |
|
612 |
tim |
1157 |
myMols = info->molecules; |
613 |
|
|
numMol = info->n_mol; |
614 |
|
|
for(int i = 0; i < numMol; i++){ |
615 |
|
|
numCutoffGroups = myMols[i].getNCutoffGroups(); |
616 |
gezelter |
1214 |
for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff); |
617 |
|
|
myCutoffGroup != NULL; |
618 |
|
|
myCutoffGroup =myMols[i].nextCutoffGroup(iterCutoff)){ |
619 |
tim |
1158 |
|
620 |
|
|
totalMass = myCutoffGroup->getMass(); |
621 |
tim |
1157 |
|
622 |
gezelter |
1214 |
for(cutoffAtom = myCutoffGroup->beginAtom(iterAtom); |
623 |
|
|
cutoffAtom != NULL; |
624 |
|
|
cutoffAtom = myCutoffGroup->nextAtom(iterAtom)){ |
625 |
tim |
1158 |
mfact.push_back(cutoffAtom->getMass()/totalMass); |
626 |
tim |
1157 |
} |
627 |
gezelter |
1214 |
} |
628 |
|
|
} |
629 |
tim |
1157 |
|
630 |
tim |
1144 |
} |