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Rename compute to entropy/atom

This commit is contained in:
PabloPiaggi 2018-06-24 00:25:07 +02:00
parent b2e6863d93
commit 86519ce213
11 changed files with 64 additions and 60 deletions
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2
doc/src/Section_commands.txt
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@ -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,

22
doc/src/compute_pentropy_atom.txt → doc/src/compute_entropy_atom.txt
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@ -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 pentropy/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 0.25 5.
compute 1 all entropy/atom 0.25 5. avg yes 5.
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:]

2
doc/src/computes.txt
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@ -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

2
doc/src/lammps.book
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@ -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

0
examples/USER/misc/pair_entropy/Na_MendelevM_2014.eam.fs → examples/USER/misc/entropy/Na_MendelevM_2014.eam.fs
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0
examples/USER/misc/pair_entropy/data.interface → examples/USER/misc/entropy/data.interface
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8
examples/USER/misc/pair_entropy/in.pairentropy → examples/USER/misc/entropy/in.entropy
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@ -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

24
examples/USER/misc/pair_entropy/log.pairentropy → examples/USER/misc/entropy/log.entropy
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@ -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 pentropy/atom (../compute_pentropy_atom.cpp:138)
WARNING: More than one compute pentropy/atom (../compute_pentropy_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 entropy/atom (../compute_entropy_atom.cpp:138)
WARNING: More than one compute entropy/atom (../compute_entropy_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

2
src/USER-MISC/README
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@ -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

44
src/USER-MISC/compute_pentropy_atom.cpp → src/USER-MISC/compute_entropy_atom.cpp
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@ -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::
ComputePairEntropyAtom(LAMMPS *lmp, int narg, char **arg) :
ComputeEntropyAtom::
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) {

18
src/USER-MISC/compute_pentropy_atom.h → src/USER-MISC/compute_entropy_atom.h
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@ -13,21 +13,21 @@
#ifdef COMPUTE_CLASS
ComputeStyle(pentropy/atom,ComputePairEntropyAtom)
ComputeStyle(entropy/atom,ComputeEntropyAtom)
#else
#ifndef COMPUTE_PAIR_ENTROPY_ATOM_H
#define COMPUTE_PAIR_ENTROPY_ATOM_H
#ifndef COMPUTE_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 **);
~ComputePairEntropyAtom();
ComputeEntropyAtom(class LAMMPS *, int, char **);
~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.
*/