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rename USER-MEAMC to MEAM and pair style meam/c to meam (keeping meam/c as an alias)

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This commit is contained in:
Axel Kohlmeyer
2021-06-29 16:59:05 -04:00
parent 995195606e
commit dc3efd17d2
41 changed files with 118 additions and 201 deletions
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2
.github/CODEOWNERS vendored
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@ -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

2
bench/POTENTIALS/in.meamc → bench/POTENTIALS/in.meam
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@ -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

6
bench/POTENTIALS/log.9Oct20.meamc.1 → bench/POTENTIALS/log.9Oct20.meam.1
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@ -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

6
bench/POTENTIALS/log.9Oct20.meamc.4 → bench/POTENTIALS/log.9Oct20.meam.4
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@ -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

2
cmake/CMakeLists.txt
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@ -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)

2
cmake/presets/all_off.cmake
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@ -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

2
cmake/presets/all_on.cmake
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@ -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

2
cmake/presets/mingw-cross.cmake
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@ -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

2
cmake/presets/most.cmake
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@ -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)

2
doc/src/Commands_pair.rst
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@ -190,7 +190,7 @@ OPT.
* :doc:`lubricateU/poly <pair_lubricateU>`
* :doc:`mdpd <pair_mesodpd>`
* :doc:`mdpd/rhosum <pair_mesodpd>`
* :doc:`meam/c <pair_meamc>`
* :doc:`meam <pair_meam>`
* :doc:`meam/spline (o) <pair_meam_spline>`
* :doc:`meam/sw/spline <pair_meam_sw_spline>`
* :doc:`mesocnt <pair_mesocnt>`

15
doc/src/Commands_removed.rst
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@ -25,15 +25,12 @@ The reset_ids command has been renamed to :doc:`reset_atom_ids <reset_atom_ids>`
MEAM package
------------
The MEAM package has been removed since it was superseded by the
:ref:`USER-MEAMC package <PKG-USER-MEAMC>`. 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 <pair_meamc>` 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 <PKG-MEAM>` 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 <pair_meam>` has the exact same syntax.
REAX package
------------

16
doc/src/Packages_details.rst
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@ -85,7 +85,7 @@ page gives those details.
* :ref:`USER-LB <PKG-USER-LB>`
* :ref:`USER-MANIFOLD <PKG-USER-MANIFOLD>`
* :ref:`USER-MDI <PKG-USER-MDI>`
* :ref:`USER-MEAMC <PKG-USER-MEAMC>`
* :ref:`MEAM <PKG-MEAM>`
* :ref:`USER-MESODPD <PKG-USER-MESODPD>`
* :ref:`USER-MESONT <PKG-USER-MESONT>`
* :ref:`USER-MGPT <PKG-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 <pair_meamc>`
* examples/meamc
* src/MEAM: filenames -> commands
* src/MEAM/README
* :doc:`pair_style meam <pair_meam>`
* examples/meam
----------

2
doc/src/Packages_user.rst
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@ -71,7 +71,7 @@ package:
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-MDI <PKG-USER-MDI>` | client-server coupling | :doc:`MDI Howto <Howto_mdi>` | USER/mdi | ext |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-MEAMC <PKG-USER-MEAMC>` | modified EAM potential (C++) | :doc:`pair_style meam/c <pair_meamc>` | meamc | no |
| :ref:`MEAM <PKG-MEAM>` | modified EAM potential (C++) | :doc:`pair_style meam <pair_meam>` | meam | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-MESODPD <PKG-USER-MESODPD>` | mesoscale DPD models | :doc:`pair_style edpd <pair_mesodpd>` | USER/mesodpd | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+

16
doc/src/pair_meamc.rst → doc/src/pair_meam.rst
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@ -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) <Baskes>`. Conceptually, it is an extension to the original
:doc:`EAM potentials <pair_eam>` 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 <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

2
doc/src/pair_meam_spline.rst
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@ -151,7 +151,7 @@ info.
Related commands
""""""""""""""""
:doc:`pair_coeff <pair_coeff>`, :doc:`pair_style meam/c <pair_meamc>`
:doc:`pair_coeff <pair_coeff>`, :doc:`pair_style meam <pair_meam>`
Default
"""""""

2
doc/src/pair_meam_sw_spline.rst
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@ -131,7 +131,7 @@ info.
Related commands
""""""""""""""""
:doc:`pair_coeff <pair_coeff>`, :doc:`pair_style meam/c <pair_meamc>`,
:doc:`pair_coeff <pair_coeff>`, :doc:`pair_style meam <pair_meam>`,
:doc:`pair_style meam/spline <pair_meam_spline>`
Default

2
doc/src/pair_style.rst
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@ -255,7 +255,7 @@ accelerated styles exist.
* :doc:`lubricateU/poly <pair_lubricateU>` - hydrodynamic lubrication forces for Fast Lubrication with polydispersity
* :doc:`mdpd <pair_mesodpd>` - mDPD particle interactions
* :doc:`mdpd/rhosum <pair_mesodpd>` - mDPD particle interactions for mass density
* :doc:`meam/c <pair_meamc>` - modified embedded atom method (MEAM) in C
* :doc:`meam <pair_meam>` - modified embedded atom method (MEAM) in C
* :doc:`meam/spline <pair_meam_spline>` - splined version of MEAM
* :doc:`meam/sw/spline <pair_meam_sw_spline>` - splined version of MEAM with a Stillinger-Weber term
* :doc:`mesocnt <pair_mesocnt>` - mesoscale model for (carbon) nanotubes

3
doc/utils/sphinx-config/false_positives.txt
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@ -1891,8 +1891,7 @@ mdi
mdpd
mDPD
meam
meamc
MEAMC
MEAM
meamf
meanDist
mech

2
examples/meam/in.meamc → examples/meam/in.meam
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@ -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

79
examples/meam/in.meamc.shear
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@ -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

6
examples/meam/log.27Nov18.meamc.g++.1 → examples/meam/log.27Nov18.meam.g++.1
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@ -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

6
examples/meam/log.27Nov18.meamc.g++.4 → examples/meam/log.27Nov18.meam.g++.4
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@ -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

6
examples/meam/log.27Nov18.meamc.shear.g++.1 → examples/meam/log.27Nov18.meam.shear.g++.1
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@ -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

6
examples/meam/log.27Nov18.meamc.shear.g++.4 → examples/meam/log.27Nov18.meam.shear.g++.4
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@ -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

4
src/.gitignore vendored
View File

@ -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

26
src/MEAM/README Normal file
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@ -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.

0
src/USER-MEAMC/meam.h → src/MEAM/meam.h
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0
src/USER-MEAMC/meam_dens_final.cpp → src/MEAM/meam_dens_final.cpp
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0
src/USER-MEAMC/meam_dens_init.cpp → src/MEAM/meam_dens_init.cpp
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0
src/USER-MEAMC/meam_force.cpp → src/MEAM/meam_force.cpp
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0
src/USER-MEAMC/meam_funcs.cpp → src/MEAM/meam_funcs.cpp
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0
src/USER-MEAMC/meam_impl.cpp → src/MEAM/meam_impl.cpp
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0
src/USER-MEAMC/meam_setup_done.cpp → src/MEAM/meam_setup_done.cpp
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0
src/USER-MEAMC/meam_setup_global.cpp → src/MEAM/meam_setup_global.cpp
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0
src/USER-MEAMC/meam_setup_param.cpp → src/MEAM/meam_setup_param.cpp
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44
src/USER-MEAMC/pair_meamc.cpp → src/MEAM/pair_meam.cpp
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@ -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<lattice_t> 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;

18
src/USER-MEAMC/pair_meamc.h → src/MEAM/pair_meam.h
View File

@ -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 **);
};

2
src/Makefile
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@ -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 \

26
src/USER-MEAMC/README
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@ -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.

4
unittest/force-styles/tests/atomic-pair-meam_c.yaml → unittest/force-styles/tests/atomic-pair-meam.yaml
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@ -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: ! |

4
unittest/force-styles/tests/manybody-pair-meam_c.yaml → unittest/force-styles/tests/manybody-pair-meam.yaml
View File

@ -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: ! |