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GIST Entropy improvements #947

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Merged
drroe merged 16 commits into from
Feb 28, 2022
Merged

GIST Entropy improvements #947

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2bbf359
Speed up six-dimensional entropy calculation in GIST
fwaibl Jan 28, 2022
411887f
Increase cpptraj revision to 6.2.2
fwaibl Jan 31, 2022
01576c2
Implement exact volume equations for GIST nearest-neighbor entropy.
fwaibl Feb 2, 2022
c7d88b4
Implement generalized nearest neighbor (NN) search.
fwaibl Feb 16, 2022
49667a7
Bump version (revision) number to 6.2.3.
fwaibl Feb 16, 2022
fcac321
Merge branch 'master' of https://github.com/Amber-MD/cpptraj into Amb…
fwaibl Feb 16, 2022
a840937
Update cpptrajdepend (make depend) after GIST entropy changes
fwaibl Feb 17, 2022
7c930b6
Merge branch 'master' into master
drroe Feb 17, 2022
10723f6
Remove declaration of unused TransEntropy function
fwaibl Feb 22, 2022
76f962f
Fix command line parsing in GIST
fwaibl Feb 23, 2022
72a8937
In GIST, omit entropy for waters if no nearest neighbor is found.
fwaibl Feb 24, 2022
4d35647
Update GIST tests to new entropy calculation
fwaibl Feb 25, 2022
e56c6fa
Merge branch 'Amber-MD:master' into master
fwaibl Feb 25, 2022
92c22fd
Merge branch 'master' of github.com:fwaibl/cpptraj
fwaibl Feb 25, 2022
48f385f
GIST code cleanup and command line checking
fwaibl Feb 28, 2022
e7a139d
Merge branch 'Amber-MD:master' into master
fwaibl Feb 28, 2022
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255 changes: 98 additions & 157 deletions src/Action_GIST.cpp
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3 changes: 2 additions & 1 deletion src/Action_GIST.h
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Original file line number Diff line number Diff line change
Expand Up @@ -37,7 +37,6 @@ class Action_GIST : public Action {
typedef std::vector<Farray> Xarray;
typedef std::vector<double> Darray;

inline void TransEntropy(float,float,float,float,float,float,float,int,double&,double&) const;
static inline void Ecalc(double, double, double, NonbondType const&, double&, double&);
void NonbondEnergy_pme(Frame const&);
void NonbondEnergy(Frame const&, Topology const&);
Expand Down Expand Up @@ -192,10 +191,12 @@ class Action_GIST : public Action {
unsigned int nMolAtoms_; ///< Number of atoms in a water molecule.+
int NFRAME_; ///< Total # frames analyzed
int max_nwat_; ///< Max number of waters in any voxel
int nNnSearchLayers_; ///< Number of layers of voxels to search for nearest neighbors in the entropy search.
bool doOrder_; ///< If true do the order calc
bool doEij_; ///< If true do the i-j energy calc
bool skipE_; ///< If true skip the nonbond energy calc
bool includeIons_; ///< If true include ions in solute region.
bool skipS_; ///< If true does not calculate entropy
bool exactNnVolume_; ///< If true use the exact volume equation for the NN entropy
};
#endif
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