From 86519ce213f3341313922efd41407e5751036386 Mon Sep 17 00:00:00 2001 From: PabloPiaggi Date: Sun, 24 Jun 2018 00:25:07 +0200 Subject: [PATCH] Rename compute to entropy/atom --- doc/src/Section_commands.txt | 2 +- ...ropy_atom.txt => compute_entropy_atom.txt} | 22 ++++++---- doc/src/computes.txt | 2 +- doc/src/lammps.book | 2 +- .../Na_MendelevM_2014.eam.fs | 0 .../{pair_entropy => entropy}/data.interface | 0 .../in.pairentropy => entropy/in.entropy} | 8 ++-- .../log.pairentropy => entropy/log.entropy} | 24 +++++----- src/USER-MISC/README | 2 +- ...ropy_atom.cpp => compute_entropy_atom.cpp} | 44 +++++++++---------- ...pentropy_atom.h => compute_entropy_atom.h} | 18 ++++---- 11 files changed, 64 insertions(+), 60 deletions(-) rename doc/src/{compute_pentropy_atom.txt => compute_entropy_atom.txt} (86%) rename examples/USER/misc/{pair_entropy => entropy}/Na_MendelevM_2014.eam.fs (100%) rename examples/USER/misc/{pair_entropy => entropy}/data.interface (100%) rename examples/USER/misc/{pair_entropy/in.pairentropy => entropy/in.entropy} (72%) rename examples/USER/misc/{pair_entropy/log.pairentropy => entropy/log.entropy} (96%) rename src/USER-MISC/{compute_pentropy_atom.cpp => compute_entropy_atom.cpp} (87%) rename src/USER-MISC/{compute_pentropy_atom.h => compute_entropy_atom.h} (77%) diff --git a/doc/src/Section_commands.txt b/doc/src/Section_commands.txt index 25e3b5ffbe..043d57670d 100644 --- a/doc/src/Section_commands.txt +++ b/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, diff --git a/doc/src/compute_pentropy_atom.txt b/doc/src/compute_entropy_atom.txt similarity index 86% rename from doc/src/compute_pentropy_atom.txt rename to doc/src/compute_entropy_atom.txt index 8877321760..f7e7b8a667 100644 --- a/doc/src/compute_pentropy_atom.txt +++ b/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 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:] diff --git a/doc/src/computes.txt b/doc/src/computes.txt index ec197cb433..7848d4db04 100644 --- a/doc/src/computes.txt +++ b/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 diff --git a/doc/src/lammps.book b/doc/src/lammps.book index bea6767993..b9f02e54f0 100644 --- a/doc/src/lammps.book +++ b/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 diff --git a/examples/USER/misc/pair_entropy/Na_MendelevM_2014.eam.fs b/examples/USER/misc/entropy/Na_MendelevM_2014.eam.fs similarity index 100% rename from examples/USER/misc/pair_entropy/Na_MendelevM_2014.eam.fs rename to examples/USER/misc/entropy/Na_MendelevM_2014.eam.fs diff --git a/examples/USER/misc/pair_entropy/data.interface b/examples/USER/misc/entropy/data.interface similarity index 100% rename from examples/USER/misc/pair_entropy/data.interface rename to examples/USER/misc/entropy/data.interface diff --git a/examples/USER/misc/pair_entropy/in.pairentropy b/examples/USER/misc/entropy/in.entropy similarity index 72% rename from examples/USER/misc/pair_entropy/in.pairentropy rename to examples/USER/misc/entropy/in.entropy index 8740b270cb..fcaffb68a1 100644 --- a/examples/USER/misc/pair_entropy/in.pairentropy +++ b/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 diff --git a/examples/USER/misc/pair_entropy/log.pairentropy b/examples/USER/misc/entropy/log.entropy similarity index 96% rename from examples/USER/misc/pair_entropy/log.pairentropy rename to examples/USER/misc/entropy/log.entropy index 21474639af..5f00e42273 100644 --- a/examples/USER/misc/pair_entropy/log.pairentropy +++ b/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 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 diff --git a/src/USER-MISC/README b/src/USER-MISC/README index 6fb2dd6010..3f3d006b23 100644 --- a/src/USER-MISC/README +++ b/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 diff --git a/src/USER-MISC/compute_pentropy_atom.cpp b/src/USER-MISC/compute_entropy_atom.cpp similarity index 87% rename from src/USER-MISC/compute_pentropy_atom.cpp rename to src/USER-MISC/compute_entropy_atom.cpp index 271648e3c5..fe2947ed61 100644 --- a/src/USER-MISC/compute_pentropy_atom.cpp +++ b/src/USER-MISC/compute_entropy_atom.cpp @@ -18,7 +18,7 @@ #include #include #include -#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) { diff --git a/src/USER-MISC/compute_pentropy_atom.h b/src/USER-MISC/compute_entropy_atom.h similarity index 77% rename from src/USER-MISC/compute_pentropy_atom.h rename to src/USER-MISC/compute_entropy_atom.h index 3333127418..c8ea19ae76 100644 --- a/src/USER-MISC/compute_pentropy_atom.h +++ b/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 -#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. */