From a6086c279b2f1286ef1f942bbe58b7f71851e298 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 9 Mar 2020 09:48:49 -0400 Subject: [PATCH] rename USER-MESO package to USER-MESODPD and update related files and folders --- cmake/CMakeLists.txt | 2 +- doc/src/Commands_pair.rst | 8 ++++---- doc/src/Packages_details.rst | 20 +++++++++---------- doc/src/Packages_user.rst | 2 +- doc/src/atom_style.rst | 2 +- doc/src/compute_edpd_temp_atom.rst | 4 ++-- doc/src/compute_tdpd_cc_atom.rst | 4 ++-- doc/src/fix_dpd_source.rst | 8 ++++---- doc/src/fix_mvv_dpd.rst | 12 +++++------ doc/src/{pair_meso.rst => pair_mesodpd.rst} | 2 +- doc/src/pair_style.rst | 8 ++++---- doc/src/set.rst | 4 ++-- examples/USER/{meso => mesodpd}/README | 0 examples/USER/{meso => mesodpd}/edpd/in.edpd | 0 .../edpd/log.16Aug17.edpd.g++.1 | 0 .../edpd/log.16Aug17.edpd.g++.4 | 0 .../edpd/temp.profile.16Aug17.edpd.g++.1 | 0 .../edpd/temp.profile.16Aug17.edpd.g++.4 | 0 examples/USER/{meso => mesodpd}/mdpd/in.mdpd | 0 .../mdpd/log.16Aug17.mdpd.g++.1 | 0 .../mdpd/log.16Aug17.mdpd.g++.4 | 0 .../tdpd/cc.profile.16Aug17.tdpd.g++.1 | 0 .../tdpd/cc.profile.16Aug17.tdpd.g++.4 | 0 examples/USER/{meso => mesodpd}/tdpd/in.tdpd | 0 .../tdpd/log.16Aug17.tdpd.g++.1 | 0 .../tdpd/log.16Aug17.tdpd.g++.4 | 0 src/Makefile | 2 +- src/{USER-MESO => USER-MESODPD}/README | 0 .../atom_vec_edpd.cpp | 0 .../atom_vec_edpd.h | 0 .../atom_vec_mdpd.cpp | 0 .../atom_vec_mdpd.h | 0 .../atom_vec_tdpd.cpp | 0 .../atom_vec_tdpd.h | 0 .../compute_edpd_temp_atom.cpp | 0 .../compute_edpd_temp_atom.h | 0 .../compute_tdpd_cc_atom.cpp | 0 .../compute_tdpd_cc_atom.h | 0 .../fix_edpd_source.cpp | 0 .../fix_edpd_source.h | 0 .../fix_mvv_dpd.cpp | 0 src/{USER-MESO => USER-MESODPD}/fix_mvv_dpd.h | 0 .../fix_mvv_edpd.cpp | 0 .../fix_mvv_edpd.h | 0 .../fix_mvv_tdpd.cpp | 0 .../fix_mvv_tdpd.h | 0 .../fix_tdpd_source.cpp | 0 .../fix_tdpd_source.h | 0 src/{USER-MESO => USER-MESODPD}/pair_edpd.cpp | 0 src/{USER-MESO => USER-MESODPD}/pair_edpd.h | 0 src/{USER-MESO => USER-MESODPD}/pair_mdpd.cpp | 0 src/{USER-MESO => USER-MESODPD}/pair_mdpd.h | 0 .../pair_mdpd_rhosum.cpp | 0 .../pair_mdpd_rhosum.h | 0 src/{USER-MESO => USER-MESODPD}/pair_tdpd.cpp | 0 src/{USER-MESO => USER-MESODPD}/pair_tdpd.h | 0 56 files changed, 39 insertions(+), 39 deletions(-) rename doc/src/{pair_meso.rst => pair_mesodpd.rst} (99%) rename examples/USER/{meso => mesodpd}/README (100%) rename examples/USER/{meso => mesodpd}/edpd/in.edpd (100%) rename examples/USER/{meso => mesodpd}/edpd/log.16Aug17.edpd.g++.1 (100%) rename examples/USER/{meso => mesodpd}/edpd/log.16Aug17.edpd.g++.4 (100%) rename examples/USER/{meso => mesodpd}/edpd/temp.profile.16Aug17.edpd.g++.1 (100%) rename examples/USER/{meso => mesodpd}/edpd/temp.profile.16Aug17.edpd.g++.4 (100%) rename examples/USER/{meso => mesodpd}/mdpd/in.mdpd (100%) rename examples/USER/{meso => mesodpd}/mdpd/log.16Aug17.mdpd.g++.1 (100%) rename examples/USER/{meso => mesodpd}/mdpd/log.16Aug17.mdpd.g++.4 (100%) rename examples/USER/{meso => mesodpd}/tdpd/cc.profile.16Aug17.tdpd.g++.1 (100%) rename examples/USER/{meso => mesodpd}/tdpd/cc.profile.16Aug17.tdpd.g++.4 (100%) rename examples/USER/{meso => mesodpd}/tdpd/in.tdpd (100%) rename examples/USER/{meso => mesodpd}/tdpd/log.16Aug17.tdpd.g++.1 (100%) rename examples/USER/{meso => mesodpd}/tdpd/log.16Aug17.tdpd.g++.4 (100%) rename src/{USER-MESO => USER-MESODPD}/README (100%) rename src/{USER-MESO => USER-MESODPD}/atom_vec_edpd.cpp (100%) rename src/{USER-MESO => USER-MESODPD}/atom_vec_edpd.h (100%) rename src/{USER-MESO => USER-MESODPD}/atom_vec_mdpd.cpp (100%) rename src/{USER-MESO => USER-MESODPD}/atom_vec_mdpd.h (100%) rename src/{USER-MESO => USER-MESODPD}/atom_vec_tdpd.cpp (100%) rename src/{USER-MESO => USER-MESODPD}/atom_vec_tdpd.h (100%) rename src/{USER-MESO => USER-MESODPD}/compute_edpd_temp_atom.cpp (100%) rename src/{USER-MESO => USER-MESODPD}/compute_edpd_temp_atom.h (100%) rename src/{USER-MESO => USER-MESODPD}/compute_tdpd_cc_atom.cpp (100%) rename src/{USER-MESO => USER-MESODPD}/compute_tdpd_cc_atom.h (100%) rename src/{USER-MESO => USER-MESODPD}/fix_edpd_source.cpp (100%) rename src/{USER-MESO => USER-MESODPD}/fix_edpd_source.h (100%) rename src/{USER-MESO => USER-MESODPD}/fix_mvv_dpd.cpp (100%) rename src/{USER-MESO => USER-MESODPD}/fix_mvv_dpd.h (100%) rename src/{USER-MESO => USER-MESODPD}/fix_mvv_edpd.cpp (100%) rename src/{USER-MESO => USER-MESODPD}/fix_mvv_edpd.h (100%) rename src/{USER-MESO => USER-MESODPD}/fix_mvv_tdpd.cpp (100%) rename src/{USER-MESO => USER-MESODPD}/fix_mvv_tdpd.h (100%) rename src/{USER-MESO => USER-MESODPD}/fix_tdpd_source.cpp (100%) rename src/{USER-MESO => USER-MESODPD}/fix_tdpd_source.h (100%) rename src/{USER-MESO => USER-MESODPD}/pair_edpd.cpp (100%) rename src/{USER-MESO => USER-MESODPD}/pair_edpd.h (100%) rename src/{USER-MESO => USER-MESODPD}/pair_mdpd.cpp (100%) rename src/{USER-MESO => USER-MESODPD}/pair_mdpd.h (100%) rename src/{USER-MESO => USER-MESODPD}/pair_mdpd_rhosum.cpp (100%) rename src/{USER-MESO => USER-MESODPD}/pair_mdpd_rhosum.h (100%) rename src/{USER-MESO => USER-MESODPD}/pair_tdpd.cpp (100%) rename src/{USER-MESO => USER-MESODPD}/pair_tdpd.h (100%) diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index faba3a5ce0..c2357fa059 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -131,7 +131,7 @@ set(LAMMPS_API_DEFINES) set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GRANULAR KSPACE LATTE MANYBODY MC MESSAGE MISC MOLECULE PERI POEMS QEQ REPLICA RIGID SHOCK SPIN SNAP SRD KIM PYTHON MSCG MPIIO VORONOI - USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-MESO USER-CGSDK USER-COLVARS + USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-MESODPD USER-CGSDK USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD USER-LB USER-MANIFOLD USER-MEAMC USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-PHONON USER-PLUMED USER-PTM USER-QTB USER-REACTION diff --git a/doc/src/Commands_pair.rst b/doc/src/Commands_pair.rst index 10873f1203..8624b555bc 100644 --- a/doc/src/Commands_pair.rst +++ b/doc/src/Commands_pair.rst @@ -95,7 +95,7 @@ OPT. * :doc:`eam/fs (gikot) ` * :doc:`edip (o) ` * :doc:`edip/multi ` - * :doc:`edpd ` + * :doc:`edpd ` * :doc:`eff/cut ` * :doc:`eim (o) ` * :doc:`exp6/rx (k) ` @@ -171,8 +171,8 @@ OPT. * :doc:`lubricate/poly (o) ` * :doc:`lubricateU ` * :doc:`lubricateU/poly ` - * :doc:`mdpd ` - * :doc:`mdpd/rhosum ` + * :doc:`mdpd ` + * :doc:`mdpd/rhosum ` * :doc:`meam/c ` * :doc:`meam/spline (o) ` * :doc:`meam/sw/spline ` @@ -242,7 +242,7 @@ OPT. * :doc:`sw (giko) ` * :doc:`table (gko) ` * :doc:`table/rx (k) ` - * :doc:`tdpd ` + * :doc:`tdpd ` * :doc:`tersoff (giko) ` * :doc:`tersoff/mod (gko) ` * :doc:`tersoff/mod/c (o) ` diff --git a/doc/src/Packages_details.rst b/doc/src/Packages_details.rst index 26b9026fb0..00103088a7 100644 --- a/doc/src/Packages_details.rst +++ b/doc/src/Packages_details.rst @@ -81,7 +81,7 @@ page gives those details. * :ref:`USER-LB ` * :ref:`USER-MANIFOLD ` * :ref:`USER-MEAMC ` - * :ref:`USER-MESO ` + * :ref:`USER-MESODPD ` * :ref:`USER-MGPT ` * :ref:`USER-MISC ` * :ref:`USER-MOFFF ` @@ -1793,10 +1793,10 @@ Sandia. ---------- -.. _PKG-USER-MESO: +.. _PKG-USER-MESODPD: -USER-MESO package ------------------ +USER-MESODPD package +-------------------- **Contents:** @@ -1812,14 +1812,14 @@ algorithm. **Supporting info:** -* src/USER-MESO: filenames -> commands -* src/USER-MESO/README +* src/USER-MESODPD: filenames -> commands +* src/USER-MESODPD/README * :doc:`atom_style edpd ` -* :doc:`pair_style edpd ` -* :doc:`pair_style mdpd ` -* :doc:`pair_style tdpd ` +* :doc:`pair_style edpd ` +* :doc:`pair_style mdpd ` +* :doc:`pair_style tdpd ` * :doc:`fix mvv/dpd ` -* examples/USER/meso +* examples/USER/mesodpd * http://lammps.sandia.gov/movies.html#mesodpd diff --git a/doc/src/Packages_user.rst b/doc/src/Packages_user.rst index 0e3a5e3f33..3c489564d7 100644 --- a/doc/src/Packages_user.rst +++ b/doc/src/Packages_user.rst @@ -65,7 +65,7 @@ package: +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ | :ref:`USER-MEAMC ` | modified EAM potential (C++) | :doc:`pair_style meam/c ` | meamc | no | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-MESO ` | mesoscale DPD models | :doc:`pair_style edpd ` | USER/meso | no | +| :ref:`USER-MESODPD ` | mesoscale DPD models | :doc:`pair_style edpd ` | USER/mesodpd | no | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ | :ref:`USER-MGPT ` | fast MGPT multi-ion potentials | :doc:`pair_style mgpt ` | USER/mgpt | no | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ diff --git a/doc/src/atom_style.rst b/doc/src/atom_style.rst index d0707559d7..7ae152851f 100644 --- a/doc/src/atom_style.rst +++ b/doc/src/atom_style.rst @@ -338,7 +338,7 @@ The *electron* style is part of the USER-EFF package for :doc:`electronic force The *dpd* style is part of the USER-DPD package for dissipative particle dynamics (DPD). -The *edpd*\ , *mdpd*\ , and *tdpd* styles are part of the USER-MESO package +The *edpd*\ , *mdpd*\ , and *tdpd* styles are part of the USER-MESODPD package for energy-conserving dissipative particle dynamics (eDPD), many-body dissipative particle dynamics (mDPD), and transport dissipative particle dynamics (tDPD), respectively. diff --git a/doc/src/compute_edpd_temp_atom.rst b/doc/src/compute_edpd_temp_atom.rst index e51e70e7f6..f71e04a2c2 100644 --- a/doc/src/compute_edpd_temp_atom.rst +++ b/doc/src/compute_edpd_temp_atom.rst @@ -46,13 +46,13 @@ Restrictions """""""""""" -This compute is part of the USER-MESO package. It is only enabled if +This compute is part of the USER-MESODPD package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. Related commands """""""""""""""" -:doc:`pair_style edpd ` +:doc:`pair_style edpd ` **Default:** none diff --git a/doc/src/compute_tdpd_cc_atom.rst b/doc/src/compute_tdpd_cc_atom.rst index bd3c5df074..ba1a9d5d0f 100644 --- a/doc/src/compute_tdpd_cc_atom.rst +++ b/doc/src/compute_tdpd_cc_atom.rst @@ -48,13 +48,13 @@ Restrictions """""""""""" -This compute is part of the USER-MESO package. It is only enabled if +This compute is part of the USER-MESODPD package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. Related commands """""""""""""""" -:doc:`pair_style tdpd ` +:doc:`pair_style tdpd ` **Default:** none diff --git a/doc/src/fix_dpd_source.rst b/doc/src/fix_dpd_source.rst index 368971b1c7..a9ae641a41 100644 --- a/doc/src/fix_dpd_source.rst +++ b/doc/src/fix_dpd_source.rst @@ -82,16 +82,16 @@ Restrictions """""""""""" -This fix is part of the USER-MESO package. It is only enabled if +This fix is part of the USER-MESODPD package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. -Fix *edpd/source* must be used with the :doc:`pair_style edpd ` command. Fix *tdpd/source* must be used with the -:doc:`pair_style tdpd ` command. +Fix *edpd/source* must be used with the :doc:`pair_style edpd ` command. Fix *tdpd/source* must be used with the +:doc:`pair_style tdpd ` command. Related commands """""""""""""""" -:doc:`pair_style edpd `, :doc:`pair_style tdpd `, +:doc:`pair_style edpd `, :doc:`pair_style tdpd `, :doc:`compute edpd/temp/atom `, :doc:`compute tdpd/cc/atom ` **Default:** none diff --git a/doc/src/fix_mvv_dpd.rst b/doc/src/fix_mvv_dpd.rst index 211642e7ec..dbe4231616 100644 --- a/doc/src/fix_mvv_dpd.rst +++ b/doc/src/fix_mvv_dpd.rst @@ -66,15 +66,15 @@ standard velocity-Verlet (VV) scheme. For more details, see :ref:`Groot `. Fix *mvv/dpd* updates the position and velocity of each atom. It can -be used with the :doc:`pair_style mdpd ` command or other +be used with the :doc:`pair_style mdpd ` command or other pair styles such as :doc:`pair dpd `. Fix *mvv/edpd* updates the per-atom temperature, in addition to -position and velocity, and must be used with the :doc:`pair_style edpd ` command. +position and velocity, and must be used with the :doc:`pair_style edpd ` command. Fix *mvv/tdpd* updates the per-atom chemical concentration, in addition to position and velocity, and must be used with the -:doc:`pair_style tdpd ` command. +:doc:`pair_style tdpd ` command. ---------- @@ -92,14 +92,14 @@ Restrictions """""""""""" -This fix is part of the USER-MESO package. It is only enabled if +This fix is part of the USER-MESODPD package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. Related commands """""""""""""""" -:doc:`pair_style mdpd `, :doc:`pair_style edpd `, -:doc:`pair_style tdpd ` +:doc:`pair_style mdpd `, :doc:`pair_style edpd `, +:doc:`pair_style tdpd ` Default """"""" diff --git a/doc/src/pair_meso.rst b/doc/src/pair_mesodpd.rst similarity index 99% rename from doc/src/pair_meso.rst rename to doc/src/pair_mesodpd.rst index a40ae3db10..f51b1b4a2c 100644 --- a/doc/src/pair_meso.rst +++ b/doc/src/pair_mesodpd.rst @@ -297,7 +297,7 @@ Restrictions """""""""""" The pair styles *edpd*\ , *mdpd*\ , *mdpd/rhosum* and *tdpd* are part of -the USER-MESO package. It is only enabled if LAMMPS was built with +the USER-MESODPD package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. diff --git a/doc/src/pair_style.rst b/doc/src/pair_style.rst index 96d8eb1d04..f2c1ed7c97 100644 --- a/doc/src/pair_style.rst +++ b/doc/src/pair_style.rst @@ -162,7 +162,7 @@ accelerated styles exist. * :doc:`eam/fs ` - Finnis-Sinclair EAM * :doc:`edip ` - three-body EDIP potential * :doc:`edip/multi ` - multi-element EDIP potential -* :doc:`edpd ` - eDPD particle interactions +* :doc:`edpd ` - eDPD particle interactions * :doc:`eff/cut ` - electron force field with a cutoff * :doc:`eim ` - embedded ion method (EIM) * :doc:`exp6/rx ` - reactive DPD potential @@ -239,8 +239,8 @@ accelerated styles exist. * :doc:`lubricate/poly ` - hydrodynamic lubrication forces with polydispersity * :doc:`lubricateU ` - hydrodynamic lubrication forces for Fast Lubrication Dynamics * :doc:`lubricateU/poly ` - hydrodynamic lubrication forces for Fast Lubrication with polydispersity -* :doc:`mdpd ` - mDPD particle interactions -* :doc:`mdpd/rhosum ` - mDPD particle interactions for mass density +* :doc:`mdpd ` - mDPD particle interactions +* :doc:`mdpd/rhosum ` - mDPD particle interactions for mass density * :doc:`meam/c ` - modified embedded atom method (MEAM) in C * :doc:`meam/spline ` - splined version of MEAM * :doc:`meam/sw/spline ` - splined version of MEAM with a Stillinger-Weber term @@ -309,7 +309,7 @@ accelerated styles exist. * :doc:`sw ` - Stillinger-Weber 3-body potential * :doc:`table ` - tabulated pair potential * :doc:`table/rx ` - -* :doc:`tdpd ` - tDPD particle interactions +* :doc:`tdpd ` - tDPD particle interactions * :doc:`tersoff ` - Tersoff 3-body potential * :doc:`tersoff/mod ` - modified Tersoff 3-body potential * :doc:`tersoff/mod/c ` - diff --git a/doc/src/set.rst b/doc/src/set.rst index c633587b25..e7f3620b0f 100644 --- a/doc/src/set.rst +++ b/doc/src/set.rst @@ -462,13 +462,13 @@ value >= 0.0, the internal temperature is set to that value. If it is temperature is set to that value. Keywords *edpd/temp* and *edpd/cv* set the temperature and volumetric -heat capacity of an eDPD particle as defined by the USER-MESO package. +heat capacity of an eDPD particle as defined by the USER-MESODPD package. Currently, only :doc:`atom_style edpd ` defines particles with these attributes. The values for the temperature and heat capacity must be positive. Keyword *cc* sets the chemical concentration of a tDPD particle for a -specified species as defined by the USER-MESO package. Currently, only +specified species as defined by the USER-MESODPD package. Currently, only :doc:`atom_style tdpd ` defines particles with this attribute. An integer for "index" selects a chemical species (1 to Nspecies) where Nspecies is set by the atom\_style command. The value diff --git a/examples/USER/meso/README b/examples/USER/mesodpd/README similarity index 100% rename from examples/USER/meso/README rename to examples/USER/mesodpd/README diff --git a/examples/USER/meso/edpd/in.edpd b/examples/USER/mesodpd/edpd/in.edpd similarity index 100% rename from examples/USER/meso/edpd/in.edpd rename to examples/USER/mesodpd/edpd/in.edpd diff --git a/examples/USER/meso/edpd/log.16Aug17.edpd.g++.1 b/examples/USER/mesodpd/edpd/log.16Aug17.edpd.g++.1 similarity index 100% rename from examples/USER/meso/edpd/log.16Aug17.edpd.g++.1 rename to examples/USER/mesodpd/edpd/log.16Aug17.edpd.g++.1 diff --git a/examples/USER/meso/edpd/log.16Aug17.edpd.g++.4 b/examples/USER/mesodpd/edpd/log.16Aug17.edpd.g++.4 similarity index 100% rename from examples/USER/meso/edpd/log.16Aug17.edpd.g++.4 rename to examples/USER/mesodpd/edpd/log.16Aug17.edpd.g++.4 diff --git a/examples/USER/meso/edpd/temp.profile.16Aug17.edpd.g++.1 b/examples/USER/mesodpd/edpd/temp.profile.16Aug17.edpd.g++.1 similarity index 100% rename from examples/USER/meso/edpd/temp.profile.16Aug17.edpd.g++.1 rename to examples/USER/mesodpd/edpd/temp.profile.16Aug17.edpd.g++.1 diff --git a/examples/USER/meso/edpd/temp.profile.16Aug17.edpd.g++.4 b/examples/USER/mesodpd/edpd/temp.profile.16Aug17.edpd.g++.4 similarity index 100% rename from examples/USER/meso/edpd/temp.profile.16Aug17.edpd.g++.4 rename to examples/USER/mesodpd/edpd/temp.profile.16Aug17.edpd.g++.4 diff --git a/examples/USER/meso/mdpd/in.mdpd b/examples/USER/mesodpd/mdpd/in.mdpd similarity index 100% rename from examples/USER/meso/mdpd/in.mdpd rename to examples/USER/mesodpd/mdpd/in.mdpd diff --git a/examples/USER/meso/mdpd/log.16Aug17.mdpd.g++.1 b/examples/USER/mesodpd/mdpd/log.16Aug17.mdpd.g++.1 similarity index 100% rename from examples/USER/meso/mdpd/log.16Aug17.mdpd.g++.1 rename to examples/USER/mesodpd/mdpd/log.16Aug17.mdpd.g++.1 diff --git a/examples/USER/meso/mdpd/log.16Aug17.mdpd.g++.4 b/examples/USER/mesodpd/mdpd/log.16Aug17.mdpd.g++.4 similarity index 100% rename from examples/USER/meso/mdpd/log.16Aug17.mdpd.g++.4 rename to examples/USER/mesodpd/mdpd/log.16Aug17.mdpd.g++.4 diff --git a/examples/USER/meso/tdpd/cc.profile.16Aug17.tdpd.g++.1 b/examples/USER/mesodpd/tdpd/cc.profile.16Aug17.tdpd.g++.1 similarity index 100% rename from examples/USER/meso/tdpd/cc.profile.16Aug17.tdpd.g++.1 rename to examples/USER/mesodpd/tdpd/cc.profile.16Aug17.tdpd.g++.1 diff --git a/examples/USER/meso/tdpd/cc.profile.16Aug17.tdpd.g++.4 b/examples/USER/mesodpd/tdpd/cc.profile.16Aug17.tdpd.g++.4 similarity index 100% rename from examples/USER/meso/tdpd/cc.profile.16Aug17.tdpd.g++.4 rename to examples/USER/mesodpd/tdpd/cc.profile.16Aug17.tdpd.g++.4 diff --git a/examples/USER/meso/tdpd/in.tdpd b/examples/USER/mesodpd/tdpd/in.tdpd similarity index 100% rename from examples/USER/meso/tdpd/in.tdpd rename to examples/USER/mesodpd/tdpd/in.tdpd diff --git a/examples/USER/meso/tdpd/log.16Aug17.tdpd.g++.1 b/examples/USER/mesodpd/tdpd/log.16Aug17.tdpd.g++.1 similarity index 100% rename from examples/USER/meso/tdpd/log.16Aug17.tdpd.g++.1 rename to examples/USER/mesodpd/tdpd/log.16Aug17.tdpd.g++.1 diff --git a/examples/USER/meso/tdpd/log.16Aug17.tdpd.g++.4 b/examples/USER/mesodpd/tdpd/log.16Aug17.tdpd.g++.4 similarity index 100% rename from examples/USER/meso/tdpd/log.16Aug17.tdpd.g++.4 rename to examples/USER/mesodpd/tdpd/log.16Aug17.tdpd.g++.4 diff --git a/src/Makefile b/src/Makefile index baeeda9716..bce5089500 100644 --- a/src/Makefile +++ b/src/Makefile @@ -60,7 +60,7 @@ PACKAGE = asphere body class2 colloid compress coreshell dipole gpu \ PACKUSER = user-adios user-atc user-awpmd user-bocs user-cgdna user-cgsdk user-colvars \ user-diffraction user-dpd user-drude user-eff user-fep user-h5md \ - user-intel user-lb user-manifold user-meamc user-meso \ + user-intel user-lb user-manifold user-meamc user-mesodpd \ user-mgpt user-misc user-mofff user-molfile \ user-netcdf user-omp user-phonon user-plumed user-ptm user-qmmm \ user-qtb user-quip user-reaction user-reaxc user-scafacos user-smd user-smtbq \ diff --git a/src/USER-MESO/README b/src/USER-MESODPD/README similarity index 100% rename from src/USER-MESO/README rename to src/USER-MESODPD/README diff --git a/src/USER-MESO/atom_vec_edpd.cpp b/src/USER-MESODPD/atom_vec_edpd.cpp similarity index 100% rename from src/USER-MESO/atom_vec_edpd.cpp rename to src/USER-MESODPD/atom_vec_edpd.cpp diff --git a/src/USER-MESO/atom_vec_edpd.h b/src/USER-MESODPD/atom_vec_edpd.h similarity index 100% rename from src/USER-MESO/atom_vec_edpd.h rename to src/USER-MESODPD/atom_vec_edpd.h diff --git a/src/USER-MESO/atom_vec_mdpd.cpp b/src/USER-MESODPD/atom_vec_mdpd.cpp similarity index 100% rename from src/USER-MESO/atom_vec_mdpd.cpp rename to src/USER-MESODPD/atom_vec_mdpd.cpp diff --git a/src/USER-MESO/atom_vec_mdpd.h b/src/USER-MESODPD/atom_vec_mdpd.h similarity index 100% rename from src/USER-MESO/atom_vec_mdpd.h rename to src/USER-MESODPD/atom_vec_mdpd.h diff --git a/src/USER-MESO/atom_vec_tdpd.cpp b/src/USER-MESODPD/atom_vec_tdpd.cpp similarity index 100% rename from src/USER-MESO/atom_vec_tdpd.cpp rename to src/USER-MESODPD/atom_vec_tdpd.cpp diff --git a/src/USER-MESO/atom_vec_tdpd.h b/src/USER-MESODPD/atom_vec_tdpd.h similarity index 100% rename from src/USER-MESO/atom_vec_tdpd.h rename to src/USER-MESODPD/atom_vec_tdpd.h diff --git a/src/USER-MESO/compute_edpd_temp_atom.cpp b/src/USER-MESODPD/compute_edpd_temp_atom.cpp similarity index 100% rename from src/USER-MESO/compute_edpd_temp_atom.cpp rename to src/USER-MESODPD/compute_edpd_temp_atom.cpp diff --git a/src/USER-MESO/compute_edpd_temp_atom.h b/src/USER-MESODPD/compute_edpd_temp_atom.h similarity index 100% rename from src/USER-MESO/compute_edpd_temp_atom.h rename to src/USER-MESODPD/compute_edpd_temp_atom.h diff --git a/src/USER-MESO/compute_tdpd_cc_atom.cpp b/src/USER-MESODPD/compute_tdpd_cc_atom.cpp similarity index 100% rename from src/USER-MESO/compute_tdpd_cc_atom.cpp rename to src/USER-MESODPD/compute_tdpd_cc_atom.cpp diff --git a/src/USER-MESO/compute_tdpd_cc_atom.h b/src/USER-MESODPD/compute_tdpd_cc_atom.h similarity index 100% rename from src/USER-MESO/compute_tdpd_cc_atom.h rename to src/USER-MESODPD/compute_tdpd_cc_atom.h diff --git a/src/USER-MESO/fix_edpd_source.cpp b/src/USER-MESODPD/fix_edpd_source.cpp similarity index 100% rename from src/USER-MESO/fix_edpd_source.cpp rename to src/USER-MESODPD/fix_edpd_source.cpp diff --git a/src/USER-MESO/fix_edpd_source.h b/src/USER-MESODPD/fix_edpd_source.h similarity index 100% rename from src/USER-MESO/fix_edpd_source.h rename to src/USER-MESODPD/fix_edpd_source.h diff --git a/src/USER-MESO/fix_mvv_dpd.cpp b/src/USER-MESODPD/fix_mvv_dpd.cpp similarity index 100% rename from src/USER-MESO/fix_mvv_dpd.cpp rename to src/USER-MESODPD/fix_mvv_dpd.cpp diff --git a/src/USER-MESO/fix_mvv_dpd.h b/src/USER-MESODPD/fix_mvv_dpd.h similarity index 100% rename from src/USER-MESO/fix_mvv_dpd.h rename to src/USER-MESODPD/fix_mvv_dpd.h diff --git a/src/USER-MESO/fix_mvv_edpd.cpp b/src/USER-MESODPD/fix_mvv_edpd.cpp similarity index 100% rename from src/USER-MESO/fix_mvv_edpd.cpp rename to src/USER-MESODPD/fix_mvv_edpd.cpp diff --git a/src/USER-MESO/fix_mvv_edpd.h b/src/USER-MESODPD/fix_mvv_edpd.h similarity index 100% rename from src/USER-MESO/fix_mvv_edpd.h rename to src/USER-MESODPD/fix_mvv_edpd.h diff --git a/src/USER-MESO/fix_mvv_tdpd.cpp b/src/USER-MESODPD/fix_mvv_tdpd.cpp similarity index 100% rename from src/USER-MESO/fix_mvv_tdpd.cpp rename to src/USER-MESODPD/fix_mvv_tdpd.cpp diff --git a/src/USER-MESO/fix_mvv_tdpd.h b/src/USER-MESODPD/fix_mvv_tdpd.h similarity index 100% rename from src/USER-MESO/fix_mvv_tdpd.h rename to src/USER-MESODPD/fix_mvv_tdpd.h diff --git a/src/USER-MESO/fix_tdpd_source.cpp b/src/USER-MESODPD/fix_tdpd_source.cpp similarity index 100% rename from src/USER-MESO/fix_tdpd_source.cpp rename to src/USER-MESODPD/fix_tdpd_source.cpp diff --git a/src/USER-MESO/fix_tdpd_source.h b/src/USER-MESODPD/fix_tdpd_source.h similarity index 100% rename from src/USER-MESO/fix_tdpd_source.h rename to src/USER-MESODPD/fix_tdpd_source.h diff --git a/src/USER-MESO/pair_edpd.cpp b/src/USER-MESODPD/pair_edpd.cpp similarity index 100% rename from src/USER-MESO/pair_edpd.cpp rename to src/USER-MESODPD/pair_edpd.cpp diff --git a/src/USER-MESO/pair_edpd.h b/src/USER-MESODPD/pair_edpd.h similarity index 100% rename from src/USER-MESO/pair_edpd.h rename to src/USER-MESODPD/pair_edpd.h diff --git a/src/USER-MESO/pair_mdpd.cpp b/src/USER-MESODPD/pair_mdpd.cpp similarity index 100% rename from src/USER-MESO/pair_mdpd.cpp rename to src/USER-MESODPD/pair_mdpd.cpp diff --git a/src/USER-MESO/pair_mdpd.h b/src/USER-MESODPD/pair_mdpd.h similarity index 100% rename from src/USER-MESO/pair_mdpd.h rename to src/USER-MESODPD/pair_mdpd.h diff --git a/src/USER-MESO/pair_mdpd_rhosum.cpp b/src/USER-MESODPD/pair_mdpd_rhosum.cpp similarity index 100% rename from src/USER-MESO/pair_mdpd_rhosum.cpp rename to src/USER-MESODPD/pair_mdpd_rhosum.cpp diff --git a/src/USER-MESO/pair_mdpd_rhosum.h b/src/USER-MESODPD/pair_mdpd_rhosum.h similarity index 100% rename from src/USER-MESO/pair_mdpd_rhosum.h rename to src/USER-MESODPD/pair_mdpd_rhosum.h diff --git a/src/USER-MESO/pair_tdpd.cpp b/src/USER-MESODPD/pair_tdpd.cpp similarity index 100% rename from src/USER-MESO/pair_tdpd.cpp rename to src/USER-MESODPD/pair_tdpd.cpp diff --git a/src/USER-MESO/pair_tdpd.h b/src/USER-MESODPD/pair_tdpd.h similarity index 100% rename from src/USER-MESO/pair_tdpd.h rename to src/USER-MESODPD/pair_tdpd.h