Removed unused variables - corrected documentation

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
 

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;