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moved contents of USER-MOP package to USER-MISC as suggested by @sjplimp

This commit is contained in:
Axel Kohlmeyer 2018-09-05 10:56:12 -04:00
parent cb4ffaf95c
commit 0c92c22755
15 changed files with 6 additions and 64 deletions
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2
cmake/CMakeLists.txt
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@ -215,7 +215,7 @@ set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE GRANULAR
SRD KIM PYTHON MSCG MPIIO VORONOI POEMS LATTE USER-ATC USER-AWPMD USER-BOCS
USER-CGDNA USER-MESO 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-MOP USER-MOFFF USER-MOLFILE USER-NETCDF USER-PHONON USER-QTB USER-REAXC
USER-MOFFF USER-MOLFILE USER-NETCDF USER-PHONON USER-QTB USER-REAXC
USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM)
set(ACCEL_PACKAGES USER-OMP KOKKOS OPT USER-INTEL GPU)
set(OTHER_PACKAGES CORESHELL QEQ)

24
doc/src/Packages_details.txt
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@ -84,7 +84,6 @@ as contained in the file name.
"USER-MGPT"_#PKG-USER-MGPT,
"USER-MISC"_#PKG-USER-MISC,
"USER-MOFFF"_#PKG-USER-MOFFF,
"USER-MOP"_#PKG-USER-MOP,
"USER-MOLFILE"_#PKG-USER-MOLFILE,
"USER-NETCDF"_#PKG-USER-NETCDF,
"USER-OMP"_#PKG-USER-OMP,
@ -1573,29 +1572,6 @@ examples/USER/mofff :ul
:line
USER-MOP package :link(PKG-USER-MOP),h4
[Contents:]
This package contains two compute styles: compute stress/mop and compute stress/mop/profile.
compute stress/mop calculates components of the local stress tensor using the method of planes, applied on one plane.
compute stress/mop/profile calculates profiles of components of the local stress tensor using the method of planes, applied on an array of regularly spaced planes.
[Author:] Laurent Joly (University of Lyon 1)
Romain Vermorel at (University of Pau and Pays de l'Adour)
[Supporting info:]
src/USER-MOP: filenames -> commands
src/USER-MOP/README
"compute stress/mop"_compute_stress_mop.html
"compute stress/mop/profile"_compute_stress_mop.html
examples/USER/mop :ul
:line
USER-MOLFILE package :link(PKG-USER-MOLFILE),h4
[Contents:]

1
doc/src/Packages_user.txt
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@ -57,7 +57,6 @@ Package, Description, Doc page, Example, Library
"USER-MESO"_Packages_details.html#PKG-USER-MESO, mesoscale DPD models, "pair_style edpd"_pair_meso.html, USER/meso, no
"USER-MGPT"_Packages_details.html#PKG-USER-MGPT, fast MGPT multi-ion potentials, "pair_style mgpt"_pair_mgpt.html, USER/mgpt, no
"USER-MISC"_Packages_details.html#PKG-USER-MISC, single-file contributions, USER-MISC/README, USER/misc, no
"USER-MOP"_Packages_details.html#PKG-USER-MOP, compute stress via method-of-planes, "compute_style stress/mop"_compute_stress_mop.html, USER/mop, no
"USER-MOFFF"_Packages_details.html#PKG-USER-MOFFF, styles for "MOF-FF"_MOFplus force field, "pair_style buck6d/coul/gauss"_pair_buck6d_coul_gauss.html, USER/mofff, no
"USER-MOLFILE"_Packages_details.html#PKG-USER-MOLFILE, "VMD"_https://www.ks.uiuc.edu/Research/vmd/ molfile plug-ins,"dump molfile"_dump_molfile.html, n/a, ext
"USER-NETCDF"_Packages_details.html#PKG-USER-NETCDF, dump output via NetCDF,"dump netcdf"_dump_netcdf.html, n/a, ext

4
doc/src/compute_stress_mop.txt
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@ -86,8 +86,8 @@ The values produced by this compute can be accessed by various "output commands"
[Restrictions:]
This style is part of the USER-MOP package. It is only enabled if LAMMPS
is built with that package. See the "Build package"_Build_package.html
These styles are part of the USER-MISC package. They are only enabled if
LAMMPS is built with that package. See the "Build package"_Build_package.html
doc page on for more info.
The method is only implemented for 3d orthogonal simulation boxes whose

0
examples/USER/mop/in.compute_stress_mop → examples/USER/misc/mop/in.compute_stress_mop
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0
examples/USER/mop/moppz.time.reference → examples/USER/misc/mop/moppz.time.reference
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0
examples/USER/mop/mopz0.time.reference → examples/USER/misc/mop/mopz0.time.reference
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examples/USER/mop/profile.z.reference → examples/USER/misc/mop/profile.z.reference
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2
src/Makefile
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@ -60,7 +60,7 @@ PACKAGE = asphere body class2 colloid compress coreshell dipole gpu \
PACKUSER = 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-mgpt user-misc user-mop user-mofff user-molfile \
user-mgpt user-misc user-mofff user-molfile \
user-netcdf user-omp user-phonon user-qmmm user-qtb \
user-quip user-reaxc user-smd user-smtbq user-sph user-tally \
user-uef user-vtk

2
src/USER-MISC/README
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@ -30,6 +30,8 @@ compute ackland/atom, Gerolf Ziegenhain, gerolf at ziegenhain.com, 4 Oct 2007
compute basal/atom, Christopher Barrett, cdb333 at cavs.msstate.edu, 3 Mar 2013
compute cnp/atom, Paulo Branicio (USC), branicio at usc.edu, 31 May 2017
compute entropy/atom, Pablo Piaggi (EPFL), pablo.piaggi at epfl.ch, 15 June 2018
compute stress/mop, Romain Vermorel (U Pau) & Laurent Joly (U Lyon), romain.vermorel at univ-pau.fr & ljoly.ulyon at gmail.com, 5 Sep 18
compute stress/mop/profile, Romain Vermorel (U Pau) & Laurent Joly (U Lyon), romain.vermorel at univ-pau.fr & ljoly.ulyon at gmail.com, 5 Sep 18
compute temp/rotate, Laurent Joly (U Lyon), ljoly.ulyon at gmail.com, 8 Aug 11
compute PRESSURE/GREM, David Stelter, dstelter@bu.edu, 22 Nov 16
dihedral_style cosine/shift/exp, Carsten Svaneborg, science at zqex.dk, 8 Aug 11

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src/USER-MOP/compute_stress_mop.cpp → src/USER-MISC/compute_stress_mop.cpp
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src/USER-MOP/compute_stress_mop.h → src/USER-MISC/compute_stress_mop.h
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src/USER-MOP/compute_stress_mop_profile.cpp → src/USER-MISC/compute_stress_mop_profile.cpp
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src/USER-MOP/compute_stress_mop_profile.h → src/USER-MISC/compute_stress_mop_profile.h
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35
src/USER-MOP/README
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@ -1,35 +0,0 @@
USER-MOP
============
This package provides the stress/mop and stress/mop/profile compute styles.
See the doc page for compute stress/mop or compute stress/mop/profile command for how to use
them.
PACKAGE DESCRIPTION
-------------------
These are LAMMPS (http://lammps.sandia.gov/) compute styles that calculate
components of the local stress tensor using the method of planes as described in
the paper by Todd et al. (B. D. Todd, Denis J. Evans, and Peter J. Daivis: "Pressure
tensor for inhomogeneous fluids", Phys. Rev. E 52, 1627 (1995)).
This package contains the source files of two compute styles:
* compute stress/mop calculates components of the local stress tensor using the method of planes, applied on one plane.
* compute stress/mop/profile calculates profiles of components of the local stress tensor using the method of planes, applied on an array of regularly spaced planes.
The persons who created these files are Laurent Joly at University of Lyon 1 and Romain Vermorel at University of Pau and Pays de l'Adour.
Contact them directly if you have questions.
Laurent Joly
Institut Lumière Matière
Université Lyon 1 et CNRS
43 boulevard du 11 novembre 1918
69622 Villeurbanne Cedex
e-mail: laurent.joly@univ-lyon1.fr
Romain Vermorel
Laboratory of Complex Fluids and their Reservoirs (LFCR)
Université de Pau et des Pays de l'Adour
Avenue de l'Université
64012 Pau
e-mail: romain.vermorel@univ-pau.fr