diff --git a/.github/CODEOWNERS b/.github/CODEOWNERS index 3e6f9eddcb..74d6c67355 100644 --- a/.github/CODEOWNERS +++ b/.github/CODEOWNERS @@ -32,7 +32,7 @@ src/ML-HDNNP/* @singraber src/USER-INTEL/* @wmbrownintel src/USER-MANIFOLD/* @Pakketeretet2 src/USER-MDI/* @taylor-a-barnes -src/USER-MEAMC/* @martok +src/MEAM/* @martok src/USER-MESONT/* @iafoss src/USER-MOFFF/* @hheenen src/USER-MOLFILE/* @akohlmey diff --git a/bench/POTENTIALS/in.meamc b/bench/POTENTIALS/in.meam similarity index 94% rename from bench/POTENTIALS/in.meamc rename to bench/POTENTIALS/in.meam index 0739b49411..9c6e06cd4d 100644 --- a/bench/POTENTIALS/in.meamc +++ b/bench/POTENTIALS/in.meam @@ -8,7 +8,7 @@ region box block 0 20 0 20 0 20 create_box 1 box create_atoms 1 box -pair_style meam/c +pair_style meam pair_coeff * * library.meam Ni4 Ni.meam Ni4 velocity all create 1600.0 376847 loop geom diff --git a/bench/POTENTIALS/log.9Oct20.meamc.1 b/bench/POTENTIALS/log.9Oct20.meam.1 similarity index 96% rename from bench/POTENTIALS/log.9Oct20.meamc.1 rename to bench/POTENTIALS/log.9Oct20.meam.1 index d6bebcd664..03e027674f 100644 --- a/bench/POTENTIALS/log.9Oct20.meamc.1 +++ b/bench/POTENTIALS/log.9Oct20.meam.1 @@ -15,7 +15,7 @@ create_atoms 1 box Created 32000 atoms create_atoms CPU = 0.002 seconds -pair_style meam/c +pair_style meam pair_coeff * * library.meam Ni4 Ni.meam Ni4 Reading potential file library.meam with DATE: 2012-06-29 Reading potential file Ni.meam with DATE: 2007-06-11 @@ -38,12 +38,12 @@ Neighbor list info ... ghost atom cutoff = 5 binsize = 2.5, bins = 29 29 29 2 neighbor lists, perpetual/occasional/extra = 2 0 0 - (1) pair meam/c, perpetual + (1) pair meam, perpetual attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard - (2) pair meam/c, perpetual, half/full from (1) + (2) pair meam, perpetual, half/full from (1) attributes: half, newton on pair build: halffull/newton stencil: none diff --git a/bench/POTENTIALS/log.9Oct20.meamc.4 b/bench/POTENTIALS/log.9Oct20.meam.4 similarity index 96% rename from bench/POTENTIALS/log.9Oct20.meamc.4 rename to bench/POTENTIALS/log.9Oct20.meam.4 index 4ccae5ddce..fa343e33b5 100644 --- a/bench/POTENTIALS/log.9Oct20.meamc.4 +++ b/bench/POTENTIALS/log.9Oct20.meam.4 @@ -15,7 +15,7 @@ create_atoms 1 box Created 32000 atoms create_atoms CPU = 0.001 seconds -pair_style meam/c +pair_style meam pair_coeff * * library.meam Ni4 Ni.meam Ni4 Reading potential file library.meam with DATE: 2012-06-29 Reading potential file Ni.meam with DATE: 2007-06-11 @@ -38,12 +38,12 @@ Neighbor list info ... ghost atom cutoff = 5 binsize = 2.5, bins = 29 29 29 2 neighbor lists, perpetual/occasional/extra = 2 0 0 - (1) pair meam/c, perpetual + (1) pair meam, perpetual attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard - (2) pair meam/c, perpetual, half/full from (1) + (2) pair meam, perpetual, half/full from (1) attributes: half, newton on pair build: halffull/newton stencil: none diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index 3381d88a02..fe5045fa15 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -143,7 +143,7 @@ set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE PLUGIN QEQ REPLICA RIGID SHOCK SPIN ML-SNAP SRD KIM PYTHON MSCG MPIIO VORONOI USER-ADIOS USER-ATC USER-AWPMD USER-BOCS CG-DNA USER-MESODPD CG-SDK USER-COLVARS USER-DIELECTRIC USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP - USER-H5MD ML-HDNNP USER-LB USER-MANIFOLD USER-MDI USER-MEAMC USER-MESONT USER-MGPT + USER-H5MD ML-HDNNP USER-LB USER-MANIFOLD USER-MDI MEAM USER-MESONT USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-PHONON USER-PLUMED USER-PTM USER-QTB ML-RANN USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-VTK ML-QUIP USER-QMMM USER-YAFF ML-PACE USER-BROWNIAN) diff --git a/cmake/presets/all_off.cmake b/cmake/presets/all_off.cmake index 7adb69dbfb..e5f5afcd67 100644 --- a/cmake/presets/all_off.cmake +++ b/cmake/presets/all_off.cmake @@ -7,7 +7,7 @@ set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU SRD VORONOI USER-ADIOS USER-ATC USER-AWPMD USER-BROWNIAN USER-BOCS CG-DNA CG-SDK USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD - ML-HDNNP USER-INTEL USER-LB USER-MANIFOLD USER-MDI USER-MEAMC USER-MESODPD + ML-HDNNP USER-INTEL USER-LB USER-MANIFOLD USER-MDI MEAM USER-MESODPD USER-MESONT USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP ML-PACE USER-PHONON USER-PLUMED USER-PTM USER-QMMM USER-QTB ML-QUIP ML-RANN USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH diff --git a/cmake/presets/all_on.cmake b/cmake/presets/all_on.cmake index f1287e63b6..575c2b1575 100644 --- a/cmake/presets/all_on.cmake +++ b/cmake/presets/all_on.cmake @@ -9,7 +9,7 @@ set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU SRD VORONOI USER-ADIOS USER-ATC USER-AWPMD USER-BROWNIAN USER-BOCS CG-DNA CG-SDK USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD - ML-HDNNP USER-INTEL USER-LB USER-MANIFOLD USER-MDI USER-MEAMC USER-MESODPD + ML-HDNNP USER-INTEL USER-LB USER-MANIFOLD USER-MDI MEAM USER-MESODPD USER-MESONT USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP ML-PACE USER-PHONON USER-PLUMED USER-PTM USER-QMMM USER-QTB ML-QUIP ML-RANN USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH diff --git a/cmake/presets/mingw-cross.cmake b/cmake/presets/mingw-cross.cmake index c046ebb327..284ab265de 100644 --- a/cmake/presets/mingw-cross.cmake +++ b/cmake/presets/mingw-cross.cmake @@ -3,7 +3,7 @@ set(WIN_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU PERI POEMS QEQ REPLICA RIGID SHOCK ML-SNAP SPIN SRD VORONOI USER-ATC USER-AWPMD USER-BOCS USER-BROWNIAN CG-DNA CG-SDK USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP - ML-HDNNP USER-INTEL USER-MANIFOLD USER-MDI USER-MEAMC USER-MESODPD + ML-HDNNP USER-INTEL USER-MANIFOLD USER-MDI MEAM USER-MESODPD USER-MESONT USER-MISC USER-MGPT USER-MOFFF USER-MOLFILE USER-OMP USER-PHONON USER-PTM USER-QTB USER-REACTION USER-REAXC USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF diff --git a/cmake/presets/most.cmake b/cmake/presets/most.cmake index 8abe396521..e6cc7b81b1 100644 --- a/cmake/presets/most.cmake +++ b/cmake/presets/most.cmake @@ -6,7 +6,7 @@ set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GRANULAR KSPACE MANYBODY MC MISC ML-IAP MOLECULE OPT PERI PLUGIN POEMS PYTHON QEQ REPLICA RIGID SHOCK ML-SNAP SPIN SRD VORONOI USER-BROWNIAN USER-BOCS CG-DNA CG-SDK USER-COLVARS - USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-MEAMC + USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP MEAM USER-MESODPD USER-MISC USER-MOFFF USER-OMP USER-PHONON USER-REACTION USER-REAXC USER-SDPD USER-SPH USER-SMD USER-UEF USER-YAFF USER-DIELECTRIC) diff --git a/doc/src/Commands_pair.rst b/doc/src/Commands_pair.rst index 192c40b27a..53233c7846 100644 --- a/doc/src/Commands_pair.rst +++ b/doc/src/Commands_pair.rst @@ -190,7 +190,7 @@ OPT. * :doc:`lubricateU/poly ` * :doc:`mdpd ` * :doc:`mdpd/rhosum ` - * :doc:`meam/c ` + * :doc:`meam ` * :doc:`meam/spline (o) ` * :doc:`meam/sw/spline ` * :doc:`mesocnt ` diff --git a/doc/src/Commands_removed.rst b/doc/src/Commands_removed.rst index 1f6da57945..4be3fd89a6 100644 --- a/doc/src/Commands_removed.rst +++ b/doc/src/Commands_removed.rst @@ -25,15 +25,12 @@ The reset_ids command has been renamed to :doc:`reset_atom_ids ` MEAM package ------------ -The MEAM package has been removed since it was superseded by the -:ref:`USER-MEAMC package `. The code in -the USER-MEAMC package is a translation of the Fortran code of MEAM into C++, -which removes several restrictions (e.g. there can be multiple instances -in hybrid pair styles) and allows for some optimizations leading -to better performance. The new pair style :doc:`meam/c ` has -the exact same syntax as the old "meam" pair style and thus pair style -meam is an alias to the new style and backward -compatibility of old inputs is preserved. +The MEAM package in Fortran has been replaced by a C++ implementation. +The code in the :ref:`MEAM package ` is a translation of the +Fortran code of MEAM into C++, which removes several restrictions +(e.g. there can be multiple instances in hybrid pair styles) and allows +for some optimizations leading to better performance. The pair style +:doc:`meam ` has the exact same syntax. REAX package ------------ diff --git a/doc/src/Packages_details.rst b/doc/src/Packages_details.rst index df88a17440..48766dacf7 100644 --- a/doc/src/Packages_details.rst +++ b/doc/src/Packages_details.rst @@ -85,7 +85,7 @@ page gives those details. * :ref:`USER-LB ` * :ref:`USER-MANIFOLD ` * :ref:`USER-MDI ` - * :ref:`USER-MEAMC ` + * :ref:`MEAM ` * :ref:`USER-MESODPD ` * :ref:`USER-MESONT ` * :ref:`USER-MGPT ` @@ -1803,16 +1803,16 @@ other atomic or molecular simulation codes via the `MolSSI Driver Interface ---------- -.. _PKG-USER-MEAMC: +.. _PKG-MEAM: -USER-MEAMC package +MEAM package ------------------ **Contents:** A pair style for the modified embedded atom (MEAM) potential translated from the Fortran version in the (obsolete) MEAM package -to plain C++. The USER-MEAMC fully replaces the MEAM package, which +to plain C++. The MEAM fully replaces the MEAM package, which has been removed from LAMMPS after the 12 December 2018 version. **Author:** Sebastian Huetter, (Otto-von-Guericke University Magdeburg) @@ -1821,10 +1821,10 @@ Sandia. **Supporting info:** -* src/USER-MEAMC: filenames -> commands -* src/USER-MEAMC/README -* :doc:`pair_style meam/c ` -* examples/meamc +* src/MEAM: filenames -> commands +* src/MEAM/README +* :doc:`pair_style meam ` +* examples/meam ---------- diff --git a/doc/src/Packages_user.rst b/doc/src/Packages_user.rst index 83c5064dc4..86b8eb1947 100644 --- a/doc/src/Packages_user.rst +++ b/doc/src/Packages_user.rst @@ -71,7 +71,7 @@ package: +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ | :ref:`USER-MDI ` | client-server coupling | :doc:`MDI Howto ` | USER/mdi | ext | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-MEAMC ` | modified EAM potential (C++) | :doc:`pair_style meam/c ` | meamc | no | +| :ref:`MEAM ` | modified EAM potential (C++) | :doc:`pair_style meam ` | meam | no | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ | :ref:`USER-MESODPD ` | mesoscale DPD models | :doc:`pair_style edpd ` | USER/mesodpd | no | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ diff --git a/doc/src/pair_meamc.rst b/doc/src/pair_meam.rst similarity index 98% rename from doc/src/pair_meamc.rst rename to doc/src/pair_meam.rst index 757c4c6712..c55967a756 100644 --- a/doc/src/pair_meamc.rst +++ b/doc/src/pair_meam.rst @@ -1,6 +1,6 @@ -.. index:: pair_style meam/c +.. index:: pair_style meam -pair_style meam/c command +pair_style meam command ========================= Syntax @@ -8,14 +8,14 @@ Syntax .. code-block:: LAMMPS - pair_style meam/c + pair_style meam Examples """""""" .. code-block:: LAMMPS - pair_style meam/c + pair_style meam pair_coeff * * ../potentials/library.meam Si ../potentials/si.meam Si pair_coeff * * ../potentials/library.meam Ni Al NULL Ni Al Ni Ni @@ -28,13 +28,13 @@ Description as of November 2010; see description below of the mixture_ref_t parameter -Style *meam/c* computes pairwise interactions for a variety of materials +Style *meam* computes pairwise interactions for a variety of materials using modified embedded-atom method (MEAM) potentials :ref:`(Baskes) `. Conceptually, it is an extension to the original :doc:`EAM potentials ` which adds angular forces. It is thus suitable for modeling metals and alloys with fcc, bcc, hcp and diamond cubic structures, as well as covalently bonded materials like -silicon and carbon. Style *meam/c* is a translation of the (now obsolete) +silicon and carbon. Style *meam* is a translation of the (now obsolete) *meam* code from Fortran to C++. It is functionally equivalent to *meam* but more efficient, and thus *meam* has been removed from LAMMPS after the 12 December 2018 release. @@ -383,7 +383,7 @@ This pair style can only be used via the *pair* keyword of the Restrictions """""""""""" -The *meam/c* style is provided in the USER-MEAMC package. It is +The *meam* style is provided in the MEAM package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. @@ -391,7 +391,7 @@ The maximum number of elements, that can be read from the MEAM library file, is determined at compile time. The default is 5. If you need support for more elements, you have to change the define for the constant 'maxelt' at the beginning of the file -src/USER-MEAMC/meam.h and update/recompile LAMMPS. There is no +src/MEAM/meam.h and update/recompile LAMMPS. There is no limit on the number of atoms types. Related commands diff --git a/doc/src/pair_meam_spline.rst b/doc/src/pair_meam_spline.rst index 6bedb9b4fb..a24b74bc7f 100644 --- a/doc/src/pair_meam_spline.rst +++ b/doc/src/pair_meam_spline.rst @@ -151,7 +151,7 @@ info. Related commands """""""""""""""" -:doc:`pair_coeff `, :doc:`pair_style meam/c ` +:doc:`pair_coeff `, :doc:`pair_style meam ` Default """"""" diff --git a/doc/src/pair_meam_sw_spline.rst b/doc/src/pair_meam_sw_spline.rst index 1f7ae2ff9f..f1bc9df582 100644 --- a/doc/src/pair_meam_sw_spline.rst +++ b/doc/src/pair_meam_sw_spline.rst @@ -131,7 +131,7 @@ info. Related commands """""""""""""""" -:doc:`pair_coeff `, :doc:`pair_style meam/c `, +:doc:`pair_coeff `, :doc:`pair_style meam `, :doc:`pair_style meam/spline ` Default diff --git a/doc/src/pair_style.rst b/doc/src/pair_style.rst index 1f023a7312..99ed142af6 100644 --- a/doc/src/pair_style.rst +++ b/doc/src/pair_style.rst @@ -255,7 +255,7 @@ accelerated styles exist. * :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:`meam/c ` - modified embedded atom method (MEAM) in C +* :doc:`meam ` - 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 * :doc:`mesocnt ` - mesoscale model for (carbon) nanotubes diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt index 5d9b3eb8c1..20231c4be5 100644 --- a/doc/utils/sphinx-config/false_positives.txt +++ b/doc/utils/sphinx-config/false_positives.txt @@ -1891,8 +1891,7 @@ mdi mdpd mDPD meam -meamc -MEAMC +MEAM meamf meanDist mech diff --git a/examples/meam/in.meamc b/examples/meam/in.meam similarity index 96% rename from examples/meam/in.meamc rename to examples/meam/in.meam index f6815cd7d4..b4463be365 100644 --- a/examples/meam/in.meamc +++ b/examples/meam/in.meam @@ -7,7 +7,7 @@ atom_style atomic read_data data.meam -pair_style meam/c +pair_style meam pair_coeff * * library.meam Si C SiC.meam Si C neighbor 0.3 bin diff --git a/examples/meam/in.meamc.shear b/examples/meam/in.meamc.shear deleted file mode 100644 index e4584d9744..0000000000 --- a/examples/meam/in.meamc.shear +++ /dev/null @@ -1,79 +0,0 @@ -# 3d metal shear simulation - -units metal -boundary s s p - -atom_style atomic -lattice fcc 3.52 -region box block 0 16.0 0 10.0 0 2.828427 -create_box 3 box - -lattice fcc 3.52 orient x 1 0 0 orient y 0 1 1 orient z 0 -1 1 & - origin 0.5 0 0 -create_atoms 1 box - -pair_style meam/c -pair_coeff * * library.meam Ni4 Ni.meam Ni4 Ni4 Ni4 - -neighbor 0.3 bin -neigh_modify delay 5 - -region lower block INF INF INF 0.9 INF INF -region upper block INF INF 6.1 INF INF INF -group lower region lower -group upper region upper -group boundary union lower upper -group mobile subtract all boundary - -set group lower type 2 -set group upper type 3 - -# void - -#region void cylinder z 8 5 2.5 INF INF -#delete_atoms region void - -# temp controllers - -compute new3d mobile temp -compute new2d mobile temp/partial 0 1 1 - -# equilibrate - -velocity mobile create 300.0 5812775 temp new3d -fix 1 all nve -fix 2 boundary setforce 0.0 0.0 0.0 - -fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0 -fix_modify 3 temp new3d - -thermo 25 -thermo_modify temp new3d - -timestep 0.001 -run 100 - -# shear - -velocity upper set 1.0 0 0 -velocity mobile ramp vx 0.0 1.0 y 1.4 8.6 sum yes - -unfix 3 -fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0 -fix_modify 3 temp new2d - -#dump 1 all atom 500 dump.meam.shear - -#dump 2 all image 100 image.*.jpg type type & -# axes yes 0.8 0.02 view 0 0 zoom 1.5 up 0 1 0 adiam 2.0 -#dump_modify 2 pad 4 - -#dump 3 all movie 100 movie.mpg type type & -# axes yes 0.8 0.02 view 0 0 zoom 1.5 up 0 1 0 adiam 2.0 -#dump_modify 3 pad 4 - -thermo 100 -thermo_modify temp new2d - -reset_timestep 0 -run 3000 diff --git a/examples/meam/log.27Nov18.meamc.g++.1 b/examples/meam/log.27Nov18.meam.g++.1 similarity index 97% rename from examples/meam/log.27Nov18.meamc.g++.1 rename to examples/meam/log.27Nov18.meam.g++.1 index 2fcd24077b..40f999c00a 100644 --- a/examples/meam/log.27Nov18.meamc.g++.1 +++ b/examples/meam/log.27Nov18.meam.g++.1 @@ -13,7 +13,7 @@ read_data data.meam reading atoms ... 128 atoms -pair_style meam/c +pair_style meam pair_coeff * * library.meam Si C SiC.meam Si C Reading potential file library.meam with DATE: 2012-06-29 Reading potential file SiC.meam with DATE: 2007-06-11 @@ -41,12 +41,12 @@ Neighbor list info ... ghost atom cutoff = 4.3 binsize = 2.15, bins = 6 6 6 2 neighbor lists, perpetual/occasional/extra = 2 0 0 - (1) pair meam/c, perpetual + (1) pair meam, perpetual attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard - (2) pair meam/c, perpetual, half/full from (1) + (2) pair meam, perpetual, half/full from (1) attributes: half, newton on pair build: halffull/newton stencil: none diff --git a/examples/meam/log.27Nov18.meamc.g++.4 b/examples/meam/log.27Nov18.meam.g++.4 similarity index 97% rename from examples/meam/log.27Nov18.meamc.g++.4 rename to examples/meam/log.27Nov18.meam.g++.4 index b97f18b25c..8a8070b28a 100644 --- a/examples/meam/log.27Nov18.meamc.g++.4 +++ b/examples/meam/log.27Nov18.meam.g++.4 @@ -13,7 +13,7 @@ read_data data.meam reading atoms ... 128 atoms -pair_style meam/c +pair_style meam pair_coeff * * library.meam Si C SiC.meam Si C Reading potential file library.meam with DATE: 2012-06-29 Reading potential file SiC.meam with DATE: 2007-06-11 @@ -41,12 +41,12 @@ Neighbor list info ... ghost atom cutoff = 4.3 binsize = 2.15, bins = 6 6 6 2 neighbor lists, perpetual/occasional/extra = 2 0 0 - (1) pair meam/c, perpetual + (1) pair meam, perpetual attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard - (2) pair meam/c, perpetual, half/full from (1) + (2) pair meam, perpetual, half/full from (1) attributes: half, newton on pair build: halffull/newton stencil: none diff --git a/examples/meam/log.27Nov18.meamc.shear.g++.1 b/examples/meam/log.27Nov18.meam.shear.g++.1 similarity index 98% rename from examples/meam/log.27Nov18.meamc.shear.g++.1 rename to examples/meam/log.27Nov18.meam.shear.g++.1 index 4aff7d2399..e183bc698a 100644 --- a/examples/meam/log.27Nov18.meamc.shear.g++.1 +++ b/examples/meam/log.27Nov18.meam.shear.g++.1 @@ -19,7 +19,7 @@ create_atoms 1 box Created 1912 atoms Time spent = 0.000667334 secs -pair_style meam/c +pair_style meam pair_coeff * * library.meam Ni4 Ni.meam Ni4 Ni4 Ni4 Reading potential file library.meam with DATE: 2012-06-29 Reading potential file Ni.meam with DATE: 2007-06-11 @@ -75,12 +75,12 @@ Neighbor list info ... ghost atom cutoff = 4.3 binsize = 2.15, bins = 27 17 5 2 neighbor lists, perpetual/occasional/extra = 2 0 0 - (1) pair meam/c, perpetual + (1) pair meam, perpetual attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard - (2) pair meam/c, perpetual, half/full from (1) + (2) pair meam, perpetual, half/full from (1) attributes: half, newton on pair build: halffull/newton stencil: none diff --git a/examples/meam/log.27Nov18.meamc.shear.g++.4 b/examples/meam/log.27Nov18.meam.shear.g++.4 similarity index 98% rename from examples/meam/log.27Nov18.meamc.shear.g++.4 rename to examples/meam/log.27Nov18.meam.shear.g++.4 index 702e13f554..63f6adf8a1 100644 --- a/examples/meam/log.27Nov18.meamc.shear.g++.4 +++ b/examples/meam/log.27Nov18.meam.shear.g++.4 @@ -19,7 +19,7 @@ create_atoms 1 box Created 1912 atoms Time spent = 0.000405788 secs -pair_style meam/c +pair_style meam pair_coeff * * library.meam Ni4 Ni.meam Ni4 Ni4 Ni4 Reading potential file library.meam with DATE: 2012-06-29 Reading potential file Ni.meam with DATE: 2007-06-11 @@ -75,12 +75,12 @@ Neighbor list info ... ghost atom cutoff = 4.3 binsize = 2.15, bins = 27 17 5 2 neighbor lists, perpetual/occasional/extra = 2 0 0 - (1) pair meam/c, perpetual + (1) pair meam, perpetual attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard - (2) pair meam/c, perpetual, half/full from (1) + (2) pair meam, perpetual, half/full from (1) attributes: half, newton on pair build: halffull/newton stencil: none diff --git a/src/.gitignore b/src/.gitignore index 37955b454d..8d73a5b295 100644 --- a/src/.gitignore +++ b/src/.gitignore @@ -70,8 +70,8 @@ /meam*.h /meam*.cpp -/pair_meamc.cpp -/pair_meamc.h +/pair_meam.cpp +/pair_meam.h /compute_mliap.cpp /compute_mliap.h diff --git a/src/MEAM/README b/src/MEAM/README new file mode 100644 index 0000000000..8015f6c699 --- /dev/null +++ b/src/MEAM/README @@ -0,0 +1,26 @@ +This package implements the MEAM potential as a LAMMPS pair style. + +============================================================================== + +This package is a translation and extension of the Fortran MEAM +package to native C++. + +Translation by + Sebastian Hütter, sebastian.huetter@ovgu.de + Institute of Materials and Joining Technology + Otto-von-Guericke University Magdeburg, Germany + +The original Fortran implementation was created by + Greg Wagner (while at Sandia, now at Northwestern U). + +============================================================================== + +Use "make yes-meam" to enable this package or use +-DPKG_MEAM=on when configuring building LAMMPS + + +In your LAMMPS input script, specify + pair_style meam +to enable the use of this implementation. parameters, input files and +outputs are compatible to those for the Fortran version of pair_style meam. + diff --git a/src/USER-MEAMC/meam.h b/src/MEAM/meam.h similarity index 100% rename from src/USER-MEAMC/meam.h rename to src/MEAM/meam.h diff --git a/src/USER-MEAMC/meam_dens_final.cpp b/src/MEAM/meam_dens_final.cpp similarity index 100% rename from src/USER-MEAMC/meam_dens_final.cpp rename to src/MEAM/meam_dens_final.cpp diff --git a/src/USER-MEAMC/meam_dens_init.cpp b/src/MEAM/meam_dens_init.cpp similarity index 100% rename from src/USER-MEAMC/meam_dens_init.cpp rename to src/MEAM/meam_dens_init.cpp diff --git a/src/USER-MEAMC/meam_force.cpp b/src/MEAM/meam_force.cpp similarity index 100% rename from src/USER-MEAMC/meam_force.cpp rename to src/MEAM/meam_force.cpp diff --git a/src/USER-MEAMC/meam_funcs.cpp b/src/MEAM/meam_funcs.cpp similarity index 100% rename from src/USER-MEAMC/meam_funcs.cpp rename to src/MEAM/meam_funcs.cpp diff --git a/src/USER-MEAMC/meam_impl.cpp b/src/MEAM/meam_impl.cpp similarity index 100% rename from src/USER-MEAMC/meam_impl.cpp rename to src/MEAM/meam_impl.cpp diff --git a/src/USER-MEAMC/meam_setup_done.cpp b/src/MEAM/meam_setup_done.cpp similarity index 100% rename from src/USER-MEAMC/meam_setup_done.cpp rename to src/MEAM/meam_setup_done.cpp diff --git a/src/USER-MEAMC/meam_setup_global.cpp b/src/MEAM/meam_setup_global.cpp similarity index 100% rename from src/USER-MEAMC/meam_setup_global.cpp rename to src/MEAM/meam_setup_global.cpp diff --git a/src/USER-MEAMC/meam_setup_param.cpp b/src/MEAM/meam_setup_param.cpp similarity index 100% rename from src/USER-MEAMC/meam_setup_param.cpp rename to src/MEAM/meam_setup_param.cpp diff --git a/src/USER-MEAMC/pair_meamc.cpp b/src/MEAM/pair_meam.cpp similarity index 95% rename from src/USER-MEAMC/pair_meamc.cpp rename to src/MEAM/pair_meam.cpp index a4ea3abdce..0d607b8fb2 100644 --- a/src/USER-MEAMC/pair_meamc.cpp +++ b/src/MEAM/pair_meam.cpp @@ -16,7 +16,7 @@ Contributing author: Greg Wagner (SNL) ------------------------------------------------------------------------- */ -#include "pair_meamc.h" +#include "pair_meam.h" #include "atom.h" #include "comm.h" @@ -47,7 +47,7 @@ static const char *keywords[] = { /* ---------------------------------------------------------------------- */ -PairMEAMC::PairMEAMC(LAMMPS *lmp) : Pair(lmp) +PairMEAM::PairMEAM(LAMMPS *lmp) : Pair(lmp) { single_enable = 0; restartinfo = 0; @@ -72,7 +72,7 @@ PairMEAMC::PairMEAMC(LAMMPS *lmp) : Pair(lmp) check if allocated, since class can be destructed when incomplete ------------------------------------------------------------------------- */ -PairMEAMC::~PairMEAMC() +PairMEAM::~PairMEAM() { delete meam_inst; @@ -85,7 +85,7 @@ PairMEAMC::~PairMEAMC() /* ---------------------------------------------------------------------- */ -void PairMEAMC::compute(int eflag, int vflag) +void PairMEAM::compute(int eflag, int vflag) { int i,ii,n,inum_half,errorflag; int *ilist_half,*numneigh_half,**firstneigh_half; @@ -173,7 +173,7 @@ void PairMEAMC::compute(int eflag, int vflag) /* ---------------------------------------------------------------------- */ -void PairMEAMC::allocate() +void PairMEAM::allocate() { allocated = 1; int n = atom->ntypes; @@ -189,7 +189,7 @@ void PairMEAMC::allocate() global settings ------------------------------------------------------------------------- */ -void PairMEAMC::settings(int narg, char ** /*arg*/) +void PairMEAM::settings(int narg, char ** /*arg*/) { if (narg != 0) error->all(FLERR,"Illegal pair_style command"); } @@ -198,7 +198,7 @@ void PairMEAMC::settings(int narg, char ** /*arg*/) set coeffs for one or more type pairs ------------------------------------------------------------------------- */ -void PairMEAMC::coeff(int narg, char **arg) +void PairMEAM::coeff(int narg, char **arg) { int m,n; @@ -309,7 +309,7 @@ void PairMEAMC::coeff(int narg, char **arg) init specific to this pair style ------------------------------------------------------------------------- */ -void PairMEAMC::init_style() +void PairMEAM::init_style() { if (force->newton_pair == 0) error->all(FLERR,"Pair style MEAM requires newton pair on"); @@ -329,7 +329,7 @@ void PairMEAMC::init_style() half or full ------------------------------------------------------------------------- */ -void PairMEAMC::init_list(int id, NeighList *ptr) +void PairMEAM::init_list(int id, NeighList *ptr) { if (id == 1) listfull = ptr; else if (id == 2) listhalf = ptr; @@ -339,7 +339,7 @@ void PairMEAMC::init_list(int id, NeighList *ptr) init for one type pair i,j and corresponding j,i ------------------------------------------------------------------------- */ -double PairMEAMC::init_one(int i, int j) +double PairMEAM::init_one(int i, int j) { if (setflag[i][j] == 0) scale[i][j] = 1.0; scale[j][i] = scale[i][j]; @@ -348,16 +348,16 @@ double PairMEAMC::init_one(int i, int j) /* ---------------------------------------------------------------------- */ -void PairMEAMC::read_files(const std::string &globalfile, +void PairMEAM::read_files(const std::string &globalfile, const std::string &userfile) { - read_global_meamc_file(globalfile); - read_user_meamc_file(userfile); + read_global_meam_file(globalfile); + read_user_meam_file(userfile); } /* ---------------------------------------------------------------------- */ -void PairMEAMC::read_global_meamc_file(const std::string &globalfile) +void PairMEAM::read_global_meam_file(const std::string &globalfile) { // allocate parameter arrays std::vector lat(nlibelements); @@ -498,7 +498,7 @@ void PairMEAMC::read_global_meamc_file(const std::string &globalfile) /* ---------------------------------------------------------------------- */ -void PairMEAMC::read_user_meamc_file(const std::string &userfile) +void PairMEAM::read_user_meam_file(const std::string &userfile) { // done if user param file is "NULL" @@ -577,7 +577,7 @@ void PairMEAMC::read_user_meamc_file(const std::string &userfile) /* ---------------------------------------------------------------------- */ -int PairMEAMC::pack_forward_comm(int n, int *list, double *buf, +int PairMEAM::pack_forward_comm(int n, int *list, double *buf, int /*pbc_flag*/, int * /*pbc*/) { int i,j,k,m; @@ -621,7 +621,7 @@ int PairMEAMC::pack_forward_comm(int n, int *list, double *buf, /* ---------------------------------------------------------------------- */ -void PairMEAMC::unpack_forward_comm(int n, int first, double *buf) +void PairMEAM::unpack_forward_comm(int n, int first, double *buf) { int i,k,m,last; @@ -662,7 +662,7 @@ void PairMEAMC::unpack_forward_comm(int n, int first, double *buf) /* ---------------------------------------------------------------------- */ -int PairMEAMC::pack_reverse_comm(int n, int first, double *buf) +int PairMEAM::pack_reverse_comm(int n, int first, double *buf) { int i,k,m,last; @@ -697,7 +697,7 @@ int PairMEAMC::pack_reverse_comm(int n, int first, double *buf) /* ---------------------------------------------------------------------- */ -void PairMEAMC::unpack_reverse_comm(int n, int *list, double *buf) +void PairMEAM::unpack_reverse_comm(int n, int *list, double *buf) { int i,j,k,m; @@ -732,7 +732,7 @@ void PairMEAMC::unpack_reverse_comm(int n, int *list, double *buf) memory usage of local atom-based arrays ------------------------------------------------------------------------- */ -double PairMEAMC::memory_usage() +double PairMEAM::memory_usage() { double bytes = 11 * meam_inst->nmax * sizeof(double); bytes += (double)(3 + 6 + 10 + 3 + 3 + 3) * meam_inst->nmax * sizeof(double); @@ -747,7 +747,7 @@ double PairMEAMC::memory_usage() done once per reneighbor so that neigh_f2c and neigh_c2f don't see them ------------------------------------------------------------------------- */ -void PairMEAMC::neigh_strip(int inum, int *ilist, +void PairMEAM::neigh_strip(int inum, int *ilist, int *numneigh, int **firstneigh) { int i,j,ii,jnum; @@ -763,7 +763,7 @@ void PairMEAMC::neigh_strip(int inum, int *ilist, /* ---------------------------------------------------------------------- */ -void *PairMEAMC::extract(const char *str, int &dim) +void *PairMEAM::extract(const char *str, int &dim) { dim = 2; if (strcmp(str,"scale") == 0) return (void *) scale; diff --git a/src/USER-MEAMC/pair_meamc.h b/src/MEAM/pair_meam.h similarity index 92% rename from src/USER-MEAMC/pair_meamc.h rename to src/MEAM/pair_meam.h index 08166c7bd7..06be670eb9 100644 --- a/src/USER-MEAMC/pair_meamc.h +++ b/src/MEAM/pair_meam.h @@ -13,13 +13,13 @@ #ifdef PAIR_CLASS // clang-format off -PairStyle(meam/c,PairMEAMC); -PairStyle(meam,PairMEAMC); +PairStyle(meam,PairMEAM); +PairStyle(meam/c,PairMEAM); // clang-format on #else -#ifndef LMP_PAIR_MEAMC_H -#define LMP_PAIR_MEAMC_H +#ifndef LMP_PAIR_MEAM_H +#define LMP_PAIR_MEAM_H #include "pair.h" @@ -27,10 +27,10 @@ PairStyle(meam,PairMEAMC); namespace LAMMPS_NS { -class PairMEAMC : public Pair { +class PairMEAM : public Pair { public: - PairMEAMC(class LAMMPS *); - ~PairMEAMC(); + PairMEAM(class LAMMPS *); + ~PairMEAM(); void compute(int, int); void settings(int, char **); void coeff(int, char **); @@ -56,8 +56,8 @@ class PairMEAMC : public Pair { void allocate(); void read_files(const std::string &, const std::string &); - void read_global_meamc_file(const std::string &); - void read_user_meamc_file(const std::string &); + void read_global_meam_file(const std::string &); + void read_user_meam_file(const std::string &); void neigh_strip(int, int *, int *, int **); }; diff --git a/src/Makefile b/src/Makefile index 5e3d1bba4d..a2a637126a 100644 --- a/src/Makefile +++ b/src/Makefile @@ -54,7 +54,7 @@ PACKAGE = asphere body class2 colloid compress coreshell dipole gpu \ PACKUSER = user-adios user-atc user-awpmd user-brownian user-bocs cg-dna \ cg-sdk user-colvars user-dielectric user-diffraction user-dpd user-drude \ user-eff user-fep user-h5md ml-hdnnp user-intel user-lb user-manifold \ - user-mdi user-meamc user-mesodpd user-mesont user-mgpt user-misc \ + user-mdi meam user-mesodpd user-mesont user-mgpt user-misc \ user-mofff user-molfile user-netcdf user-omp user-phonon \ ml-pace user-plumed user-ptm user-qmmm user-qtb ml-quip \ ml-rann user-reaction user-reaxc user-scafacos user-smd user-smtbq \ diff --git a/src/USER-MEAMC/README b/src/USER-MEAMC/README deleted file mode 100644 index dcb70d670c..0000000000 --- a/src/USER-MEAMC/README +++ /dev/null @@ -1,26 +0,0 @@ -This package implements the MEAM/C potential as a LAMMPS pair style. - -============================================================================== - -This package is a translation of the MEAM package to native C++. See -that package as well as the Fortran code distributed in lib/meam for -the original sources and information. - - -Translation by - Sebastian Hütter, sebastian.huetter@ovgu.de - Institute of Materials and Joining Technology - Otto-von-Guericke University Magdeburg, Germany - -The original Fortran implementation was created by - Greg Wagner (while at Sandia, now at Northwestern U). - -============================================================================== - -Use "make yes-user-meamc" to enable this package when building LAMMPS. - -In your LAMMPS input script, specify - pair_style meam/c -to enable the use of this implementation. All parameters, input files and -outputs are exactly identical to these used with pair_style meam. - diff --git a/unittest/force-styles/tests/atomic-pair-meam_c.yaml b/unittest/force-styles/tests/atomic-pair-meam.yaml similarity index 99% rename from unittest/force-styles/tests/atomic-pair-meam_c.yaml rename to unittest/force-styles/tests/atomic-pair-meam.yaml index 7d93a698e0..6f262c032a 100644 --- a/unittest/force-styles/tests/atomic-pair-meam_c.yaml +++ b/unittest/force-styles/tests/atomic-pair-meam.yaml @@ -3,13 +3,13 @@ lammps_version: 10 Feb 2021 date_generated: Fri Feb 26 23:09:03 2021 epsilon: 5e-13 prerequisites: ! | - pair meam/c + pair meam pre_commands: ! | variable newton_pair delete if "$(is_active(package,gpu)) > 0.0" then "variable newton_pair index off" else "variable newton_pair index on" post_commands: ! "" input_file: in.metal -pair_style: meam/c +pair_style: meam pair_coeff: ! | * * library.meam Al Si Mg Cu Fe AlSiMgCuFe.meam Mg Fe extract: ! | diff --git a/unittest/force-styles/tests/manybody-pair-meam_c.yaml b/unittest/force-styles/tests/manybody-pair-meam.yaml similarity index 99% rename from unittest/force-styles/tests/manybody-pair-meam_c.yaml rename to unittest/force-styles/tests/manybody-pair-meam.yaml index e2867c4dd6..4237f5ffc2 100644 --- a/unittest/force-styles/tests/manybody-pair-meam_c.yaml +++ b/unittest/force-styles/tests/manybody-pair-meam.yaml @@ -3,13 +3,13 @@ lammps_version: 10 Feb 2021 date_generated: Fri Feb 26 23:09:15 2021 epsilon: 7.5e-12 prerequisites: ! | - pair meam/c + pair meam pre_commands: ! | variable newton_pair delete if "$(is_active(package,gpu)) > 0.0" then "variable newton_pair index off" else "variable newton_pair index on" post_commands: ! "" input_file: in.manybody -pair_style: meam/c +pair_style: meam pair_coeff: ! | * * library.meam Si C SiC.meam C C C C Si Si Si Si extract: ! |