From 6de4569483e2ea5dd8ee6a1db5d7ee0f7efd7745 Mon Sep 17 00:00:00 2001
From: PabloPiaggi <ppiaggi@gmail.com>
Date: Tue, 22 May 2018 17:29:51 +0200
Subject: [PATCH] Removed unused variables - corrected documentation
---
doc/src/compute_pair_entropy_atom.txt | 32 ++++++++++-----------
src/USER-MISC/compute_pair_entropy_atom.cpp | 5 ++--
2 files changed, 18 insertions(+), 19 deletions(-)
diff --git a/doc/src/compute_pair_entropy_atom.txt b/doc/src/compute_pair_entropy_atom.txt
index b9d63c8bc9..8877321760 100644
--- a/doc/src/compute_pair_entropy_atom.txt
+++ b/doc/src/compute_pair_entropy_atom.txt
@@ -37,19 +37,19 @@ Define a computation that calculates the pair entropy fingerprint for
each atom in the group. The fingerprint is useful to distinguish between
ordered and disordered environments, for instance liquid and solid-like
environments, or glassy and crystalline-like environments. Some
- applications could be the identification of grain boundaries, a
- melt-solid interface, or a solid cluster emerging from the melt.
+applications could be the identification of grain boundaries, a
+melt-solid interface, or a solid cluster emerging from the melt.
The advantage of this parameter over others is that no a priori
- information about the solid structure is required.
+information about the solid structure is required.
This parameter for atom i is computed using the following formula from
-"(Piaggi)"_#Piaggi and "(Nettleton)"_#Nettleton
+"(Piaggi)"_#Piaggi and "(Nettleton)"_#Nettleton ,
:c,image(Eqs/pair_entropy.jpg)
where r is a distance, g(r) is the radial distribution function of atom
- i and rho is the density of the system. The g(r) computed for each
- atom i can be noisy and therefore it is smoothened using:
+i and rho is the density of the system. The g(r) computed for each
+atom i can be noisy and therefore it is smoothened using:
:c,image(Eqs/pair_entropy2.jpg)
@@ -57,22 +57,22 @@ where the sum in j goes through the neighbors of atom i, and sigma is a
parameter to control the smoothening.
The input parameters are {sigma} the smoothening parameter, and the
- {cutoff} for the calculation of g(r).
+{cutoff} for the calculation of g(r).
If the keyword {avg} has the setting {yes}, then this compute also
- averages the parameter over the neighbors of atom i according to:
+averages the parameter over the neighbors of atom i according to:
:c,image(Eqs/pair_entropy3.jpg)
where the sum j goes over the neighbors of atom i and N is the number
- of neighbors. This procedure provides a sharper distinction between
+of neighbors. This procedure provides a sharper distinction between
order and disorder environments. In this case the input parameter
- {cutoff2} is the cutoff for the averaging over the neighbors and
- must also be specified.
+{cutoff2} is the cutoff for the averaging over the neighbors and
+must also be specified.
If the {avg yes} option is used, the effective cutoff of the neighbor
- list should be {cutoff}+{cutoff2} and therefore it might be necessary
- to increase the skin of the neighbor list with:
+list should be {cutoff}+{cutoff2} and therefore it might be necessary
+to increase the skin of the neighbor list with:
neighbor skin bin :pre
@@ -85,7 +85,7 @@ by the corresponding volume. This option can be useful when dealing with
inhomogeneus systems such as those that have surfaces.
Here are typical input parameters for fcc aluminum (lattice
- constant 4.05 Angstroms),
+constant 4.05 Angstroms),
compute 1 all pentropy/atom 0.25 5.7 avg yes 3.7 :pre
@@ -103,8 +103,8 @@ uses per-atom values from a compute as input. See "Section
options.
The pair entropy values have units of the Boltzmann constant. They are
- always negative, and lower values (lower entropy) correspond to more
- ordered environments.
+always negative, and lower values (lower entropy) correspond to more
+ordered environments.
[Restrictions:] none
diff --git a/src/USER-MISC/compute_pair_entropy_atom.cpp b/src/USER-MISC/compute_pair_entropy_atom.cpp
index 18c0b39fb0..b5da941f7f 100644
--- a/src/USER-MISC/compute_pair_entropy_atom.cpp
+++ b/src/USER-MISC/compute_pair_entropy_atom.cpp
@@ -160,8 +160,8 @@ void ComputePairEntropyAtom::init_list(int id, NeighList *ptr)
void ComputePairEntropyAtom::compute_peratom()
{
- int i,j,k,ii,jj,kk,n,inum,jnum;
- double xtmp,ytmp,ztmp,delx,dely,delz,rsq,value;
+ int i,j,ii,jj,inum,jnum;
+ double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
int *ilist,*jlist,*numneigh,**firstneigh;
double rbin[nbin], rbinsq[nbin];
@@ -198,7 +198,6 @@ void ComputePairEntropyAtom::compute_peratom()
firstneigh = list->firstneigh;
// Compute some constants
- double nlist_cutoff = force->pair->cutforce;
double sigmasq2=2*sigma*sigma;
double volume = domain->xprd * domain->yprd * domain->zprd;
double density = atom->natoms / volume;
--
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