Rename compute to entropy/atom

doc/src/Section_commands.txt

@@ -851,6 +851,7 @@ package"_Section_start.html#start_3.
 "dpd"_compute_dpd.html,
 "dpd/atom"_compute_dpd_atom.html,
 "edpd/temp/atom"_compute_edpd_temp_atom.html,
+"entropy/atom"_compute_entropy_atom.html,
 "fep"_compute_fep.html,
 "force/tally"_compute_tally.html,
 "heat/flux/tally"_compute_tally.html,
@@ -861,7 +862,6 @@ package"_Section_start.html#start_3.
 "meso/t/atom"_compute_meso_t_atom.html,
 "pe/tally"_compute_tally.html,
 "pe/mol/tally"_compute_tally.html,
-"pentropy/atom"_compute_pentropy_atom.html,
 "pressure/uef"_compute_pressure_uef.html,
 "saed"_compute_saed.html,
 "smd/contact/radius"_compute_smd_contact_radius.html,

doc/src/compute_entropy_atom.txt

@@ -6,14 +6,14 @@
 
 :line
 
-compute pentropy/atom command :h3
+compute entropy/atom command :h3
 
 [Syntax:]
 
-compute ID group-ID pentropy/atom sigma cutoff keyword value ... :pre
+compute ID group-ID entropy/atom sigma cutoff keyword value ... :pre
 
 ID, group-ID are documented in "compute"_compute.html command :l
-pentropy/atom = style name of this compute command :l
+entropy/atom = style name of this compute command :l
 sigma = width of gaussians used in the g(r) smoothening :l
 cutoff = cutoff for the g(r) calculation :l
 one or more keyword/value pairs may be appended :l
@@ -27,9 +27,9 @@ keyword = {avg} or {local}
 
 [Examples:]
 
-compute 1 all pentropy/atom 0.25 5.
+compute 1 all entropy/atom 0.25 5.
-compute 1 all pentropy/atom 0.25 5. avg yes 5.
+compute 1 all entropy/atom 0.25 5. avg yes 5.
-compute 1 all pentropy/atom 0.125 7.3 avg yes 5.1 local yes :pre
+compute 1 all entropy/atom 0.125 7.3 avg yes 5.1 local yes :pre
 
 [Description:]
 
@@ -87,11 +87,11 @@ inhomogeneus systems such as those that have surfaces.
 Here are typical input parameters for fcc aluminum (lattice 
 constant 4.05 Angstroms),
 
-compute 1 all pentropy/atom 0.25 5.7 avg yes 3.7 :pre
+compute 1 all entropy/atom 0.25 5.7 avg yes 3.7 :pre
 
 and for bcc sodium (lattice constant 4.23 Angstroms),
 
-compute 1 all pentropy/atom 0.25 7.3 avg yes 5.1 :pre
+compute 1 all entropy/atom 0.25 7.3 avg yes 5.1 :pre
 
 
 [Output info:]
@@ -106,7 +106,11 @@ The pair entropy values have units of the Boltzmann constant. They are
 always negative, and lower values (lower entropy) correspond to more
 ordered environments.
 
-[Restrictions:] none
+[Restrictions:]
+
+This compute is part of the USER-MISC package.  It is only enabled if
+LAMMPS was built with that package.  See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info.
 
 [Related commands:]
 

doc/src/computes.txt

@@ -31,6 +31,7 @@ Computes :h1
    compute_dpd
    compute_dpd_atom
    compute_edpd_temp_atom
+   compute_entropy_atom
    compute_erotate_asphere
    compute_erotate_rigid
    compute_erotate_sphere
@@ -63,7 +64,6 @@ Computes :h1
    compute_pair_local
    compute_pe
    compute_pe_atom
-   compute_pentropy_atom
    compute_plasticity_atom
    compute_pressure
    compute_pressure_uef

doc/src/lammps.book

@@ -315,6 +315,7 @@ compute_displace_atom.html
 compute_dpd.html
 compute_dpd_atom.html
 compute_edpd_temp_atom.html
+compute_entropy_atom.html
 compute_erotate_asphere.html
 compute_erotate_rigid.html
 compute_erotate_sphere.html
@@ -347,7 +348,6 @@ compute_pair.html
 compute_pair_local.html
 compute_pe.html
 compute_pe_atom.html
-compute_pentropy_atom.html
 compute_plasticity_atom.html
 compute_pressure.html
 compute_pressure_uef.html

examples/USER/misc/entropy/in.entropy

@@ -16,13 +16,13 @@ neighbor 	4. bin
 
 # Define computes
 # Global density, no average
-compute         1 all pentropy/atom 0.25 7.75
+compute         1 all entropy/atom 0.25 7.75
 # Local density, no average
-compute         2 all pentropy/atom 0.25 7.75 local yes
+compute         2 all entropy/atom 0.25 7.75 local yes
 # Global density, average over neighbors
-compute         3 all pentropy/atom 0.25 7.75 avg yes 5.
+compute         3 all entropy/atom 0.25 7.75 avg yes 5.
 # Local density, average over neighbors
-compute         4 all pentropy/atom 0.25 7.75 avg yes 5. local yes
+compute         4 all entropy/atom 0.25 7.75 avg yes 5. local yes
 
 dump            myDump all custom 500 dump.interface id type x y z c_1 c_2 c_3 c_4
 

examples/USER/misc/entropy/log.entropy

@@ -28,13 +28,13 @@ neighbor 	4. bin
 
 # Define computes
 # Global density, no average
-compute         1 all pentropy/atom 0.25 7.75
+compute         1 all entropy/atom 0.25 7.75
 # Local density, no average
-compute         2 all pentropy/atom 0.25 7.75 local yes
+compute         2 all entropy/atom 0.25 7.75 local yes
 # Global density, average over neighbors
-compute         3 all pentropy/atom 0.25 7.75 avg yes 5.
+compute         3 all entropy/atom 0.25 7.75 avg yes 5.
 # Local density, average over neighbors
-compute         4 all pentropy/atom 0.25 7.75 avg yes 5. local yes
+compute         4 all entropy/atom 0.25 7.75 avg yes 5. local yes
 
 dump            myDump all custom 500 dump.interface id type x y z c_1 c_2 c_3 c_4
 
@@ -43,10 +43,10 @@ fix             1 all nph x 1. 1. 10.
 fix             2 all temp/csvr 350. 350. 0.1 64582
 
 run             100000
-WARNING: More than one compute pentropy/atom (../compute_pentropy_atom.cpp:138)
+WARNING: More than one compute entropy/atom (../compute_entropy_atom.cpp:138)
-WARNING: More than one compute pentropy/atom (../compute_pentropy_atom.cpp:138)
+WARNING: More than one compute entropy/atom (../compute_entropy_atom.cpp:138)
-WARNING: More than one compute pentropy/atom (../compute_pentropy_atom.cpp:138)
+WARNING: More than one compute entropy/atom (../compute_entropy_atom.cpp:138)
-WARNING: More than one compute pentropy/atom (../compute_pentropy_atom.cpp:138)
+WARNING: More than one compute entropy/atom (../compute_entropy_atom.cpp:138)
 Neighbor list info ...
   update every 1 steps, delay 10 steps, check yes
   max neighbors/atom: 2000, page size: 100000
@@ -59,22 +59,22 @@ Neighbor list info ...
       pair build: half/bin/newton/tri
       stencil: half/bin/3d/newton/tri
       bin: standard
-  (2) compute pentropy/atom, perpetual
+  (2) compute entropy/atom, perpetual
       attributes: full, newton on, ghost
       pair build: full/bin/ghost
       stencil: full/ghost/bin/3d
       bin: standard
-  (3) compute pentropy/atom, perpetual, copy from (2)
+  (3) compute entropy/atom, perpetual, copy from (2)
       attributes: full, newton on, ghost
       pair build: copy
       stencil: none
       bin: none
-  (4) compute pentropy/atom, perpetual, copy from (2)
+  (4) compute entropy/atom, perpetual, copy from (2)
       attributes: full, newton on, ghost
       pair build: copy
       stencil: none
       bin: none
-  (5) compute pentropy/atom, perpetual, copy from (2)
+  (5) compute entropy/atom, perpetual, copy from (2)
       attributes: full, newton on, ghost
       pair build: copy
       stencil: none

src/USER-MISC/README

@@ -29,7 +29,7 @@ bond_style harmonic/shift/cut, Carsten Svaneborg, science at zqex.dk, 8 Aug 11
 compute ackland/atom, Gerolf Ziegenhain, gerolf at ziegenhain.com, 4 Oct 2007
 compute basal/atom, Christopher Barrett, cdb333 at cavs.msstate.edu, 3 Mar 2013
 compute cnp/atom, Paulo Branicio (USC), branicio at usc.edu, 31 May 2017
-compute pentropy/atom, Pablo M. Piaggi (EPFL), , 15 June 2018
+compute entropy/atom, Pablo Piaggi (EPFL), pablo.piaggi at epfl.ch, 15 June 2018
 compute temp/rotate, Laurent Joly (U Lyon), ljoly.ulyon at gmail.com, 8 Aug 11
 compute PRESSURE/GREM, David Stelter, dstelter@bu.edu, 22 Nov 16
 dihedral_style cosine/shift/exp, Carsten Svaneborg, science at zqex.dk, 8 Aug 11

src/USER-MISC/compute_entropy_atom.cpp

@@ -18,7 +18,7 @@
 #include <cmath>
 #include <cstring>
 #include <cstdlib>
-#include "compute_pentropy_atom.h"
+#include "compute_entropy_atom.h"
 #include "atom.h"
 #include "update.h"
 #include "modify.h"
@@ -40,13 +40,13 @@ using namespace MathConst;
 
 /* ---------------------------------------------------------------------- */
 
-ComputePairEntropyAtom::
+ComputeEntropyAtom::
-ComputePairEntropyAtom(LAMMPS *lmp, int narg, char **arg) :
+ComputeEntropyAtom(LAMMPS *lmp, int narg, char **arg) :
   Compute(lmp, narg, arg),
   pair_entropy(NULL), pair_entropy_avg(NULL)
 {
   if (narg < 5 || narg > 10)
-    error->all(FLERR,"Illegal compute pentropy/atom command; wrong number"
+    error->all(FLERR,"Illegal compute entropy/atom command; wrong number"
                " of arguments");
 
   // Arguments are: sigma cutoff avg yes/no cutoff2 local yes/no
@@ -59,10 +59,10 @@ ComputePairEntropyAtom(LAMMPS *lmp, int narg, char **arg) :
   //     the g(r)
 
   sigma = force->numeric(FLERR,arg[3]);
-  if (sigma < 0.0) error->all(FLERR,"Illegal compute pentropy/atom"
+  if (sigma < 0.0) error->all(FLERR,"Illegal compute entropy/atom"
                               " command; negative sigma");
   cutoff = force->numeric(FLERR,arg[4]);
-  if (cutoff < 0.0) error->all(FLERR,"Illegal compute pentropy/atom"
+  if (cutoff < 0.0) error->all(FLERR,"Illegal compute entropy/atom"
                                " command; negative cutoff");
 
   avg_flag = 0;
@@ -73,24 +73,24 @@ ComputePairEntropyAtom(LAMMPS *lmp, int narg, char **arg) :
   while (iarg < narg) {
     if (strcmp(arg[iarg],"avg") == 0) {
       if (iarg+2 > narg)
-        error->all(FLERR,"Illegal compute pentropy/atom;"
+        error->all(FLERR,"Illegal compute entropy/atom;"
                    " missing arguments after avg");
       if (strcmp(arg[iarg+1],"yes") == 0) avg_flag = 1;
       else if (strcmp(arg[iarg+1],"no") == 0) avg_flag = 0;
-      else error->all(FLERR,"Illegal compute pentropy/atom;"
+      else error->all(FLERR,"Illegal compute entropy/atom;"
                       " argument after avg should be yes or no");
       cutoff2 = force->numeric(FLERR,arg[iarg+2]);
-      if (cutoff2 < 0.0) error->all(FLERR,"Illegal compute pentropy/atom"
+      if (cutoff2 < 0.0) error->all(FLERR,"Illegal compute entropy/atom"
                                     " command; negative cutoff2");
       cutsq2 = cutoff2*cutoff2;
       iarg += 3;
     } else if (strcmp(arg[iarg],"local") == 0) {
       if (strcmp(arg[iarg+1],"yes") == 0) local_flag = 1;
       else if (strcmp(arg[iarg+1],"no") == 0) local_flag = 0;
-      else error->all(FLERR,"Illegal compute pentropy/atom;"
+      else error->all(FLERR,"Illegal compute entropy/atom;"
                       " argument after local should be yes or no");
       iarg += 2;
-    } else error->all(FLERR,"Illegal compute pentropy/atom; argument after"
+    } else error->all(FLERR,"Illegal compute entropy/atom; argument after"
                       " sigma and cutoff should be avg or local");
   }
 
@@ -110,7 +110,7 @@ ComputePairEntropyAtom(LAMMPS *lmp, int narg, char **arg) :
 
 /* ---------------------------------------------------------------------- */
 
-ComputePairEntropyAtom::~ComputePairEntropyAtom()
+ComputeEntropyAtom::~ComputeEntropyAtom()
 {
   memory->destroy(pair_entropy);
   if (avg_flag) memory->destroy(pair_entropy_avg);
@@ -118,7 +118,7 @@ ComputePairEntropyAtom::~ComputePairEntropyAtom()
 
 /* ---------------------------------------------------------------------- */
 
-void ComputePairEntropyAtom::init()
+void ComputeEntropyAtom::init()
 {
   if (force->pair == NULL)
     error->all(FLERR,"Compute centro/atom requires a pair style be"
@@ -126,16 +126,16 @@ void ComputePairEntropyAtom::init()
 
   if ( (cutoff+cutoff2) > (force->pair->cutforce  + neighbor->skin) )
     {
-        error->all(FLERR,"Compute pentropy/atom cutoff is longer than the"
+        error->all(FLERR,"Compute entropy/atom cutoff is longer than the"
                    " pairwise cutoff. Increase the neighbor list skin"
                    " distance.");
     }
 
   int count = 0;
   for (int i = 0; i < modify->ncompute; i++)
-    if (strcmp(modify->compute[i]->style,"pentropy/atom") == 0) count++;
+    if (strcmp(modify->compute[i]->style,"entropy/atom") == 0) count++;
   if (count > 1 && comm->me == 0)
-    error->warning(FLERR,"More than one compute pentropy/atom");
+    error->warning(FLERR,"More than one compute entropy/atom");
 
   // need a full neighbor list with neighbors of the ghost atoms
 
@@ -151,14 +151,14 @@ void ComputePairEntropyAtom::init()
 
 /* ---------------------------------------------------------------------- */
 
-void ComputePairEntropyAtom::init_list(int id, NeighList *ptr)
+void ComputeEntropyAtom::init_list(int id, NeighList *ptr)
 {
   list = ptr;
 }
 
 /* ---------------------------------------------------------------------- */
 
-void ComputePairEntropyAtom::compute_peratom()
+void ComputeEntropyAtom::compute_peratom()
 {
   int i,j,ii,jj,inum,jnum;
   double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
@@ -179,15 +179,15 @@ void ComputePairEntropyAtom::compute_peratom()
     if (!avg_flag) {
       memory->destroy(pair_entropy);
       nmax = atom->nmax;
-      memory->create(pair_entropy,nmax,"pentropy/atom:pair_entropy");
+      memory->create(pair_entropy,nmax,"entropy/atom:pair_entropy");
       vector_atom = pair_entropy;
     } else {
       memory->destroy(pair_entropy);
       memory->destroy(pair_entropy_avg);
       nmax = atom->nmax;
-      memory->create(pair_entropy,nmax,"pentropy/atom:pair_entropy");
+      memory->create(pair_entropy,nmax,"entropy/atom:pair_entropy");
       memory->create(pair_entropy_avg,nmax,
-                     "pentropy/atom:pair_entropy_avg");
+                     "entropy/atom:pair_entropy_avg");
       vector_atom = pair_entropy_avg;
     }
   }
@@ -328,7 +328,7 @@ void ComputePairEntropyAtom::compute_peratom()
    memory usage of local atom-based array
 ------------------------------------------------------------------------- */
 
-double ComputePairEntropyAtom::memory_usage()
+double ComputeEntropyAtom::memory_usage()
 {
   double bytes;
   if (!avg_flag) {

src/USER-MISC/compute_entropy_atom.h

@@ -13,21 +13,21 @@
 
 #ifdef COMPUTE_CLASS
 
-ComputeStyle(pentropy/atom,ComputePairEntropyAtom)
+ComputeStyle(entropy/atom,ComputeEntropyAtom)
 
 #else
 
-#ifndef COMPUTE_PAIR_ENTROPY_ATOM_H
+#ifndef COMPUTE_ENTROPY_ATOM_H
-#define COMPUTE_PAIR_ENTROPY_ATOM_H
+#define COMPUTE_ENTROPY_ATOM_H
 
 #include "compute.h"
 
 namespace LAMMPS_NS {
 
-class ComputePairEntropyAtom : public Compute {
+class ComputeEntropyAtom : public Compute {
  public:
-  ComputePairEntropyAtom(class LAMMPS *, int, char **);
+  ComputeEntropyAtom(class LAMMPS *, int, char **);
-  ~ComputePairEntropyAtom();
+  ~ComputeEntropyAtom();
   void init();
   void init_list(int, class NeighList *);
   void compute_peratom();
@@ -59,13 +59,13 @@ Self-explanatory.  Check the input script syntax and compare to the
 documentation for the command.  You can use -echo screen as a
 command-line option when running LAMMPS to see the offending line.
 
-E: Compute pentropy/atom requires a pair style be defined
+E: Compute entropy/atom requires a pair style be defined
 
 This is because the computation of the pair entropy values
 uses a pairwise neighbor list.
 
-W: More than one compute pentropy/atom
+W: More than one compute entropy/atom
 
-It is not efficient to use compute pentropy/atom more than once.
+It is not efficient to use compute entropy/atom more than once.
 
 */