diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index 190ef3b2e0389987f331f1e32ed6c416551dfb13..eecdc6d132636b3d4f5480c19928e6e86f3ad493 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -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) diff --git a/doc/src/Packages_details.txt b/doc/src/Packages_details.txt index 36071064c07f24e81c98c95bd853f47a0e10f370..381dc2e99589f5702dfd4ebf3f5ec615c2dd307b 100644 --- a/doc/src/Packages_details.txt +++ b/doc/src/Packages_details.txt @@ -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:] diff --git a/doc/src/Packages_user.txt b/doc/src/Packages_user.txt index 5b9b8734b34f05b3989da5b60bbbbff3fb073250..7db2fa895ceaa020552d6e05502b67bc174ca54b 100644 --- a/doc/src/Packages_user.txt +++ b/doc/src/Packages_user.txt @@ -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 diff --git a/doc/src/compute_stress_mop.txt b/doc/src/compute_stress_mop.txt index 8d95ef42e29bfb8233e532d6de6f9dce22a0eb2a..1006463179acf18cecff15105d4738c9f2bdc87a 100644 --- a/doc/src/compute_stress_mop.txt +++ b/doc/src/compute_stress_mop.txt @@ -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 diff --git a/examples/USER/mop/in.compute_stress_mop b/examples/USER/misc/mop/in.compute_stress_mop similarity index 100% rename from examples/USER/mop/in.compute_stress_mop rename to examples/USER/misc/mop/in.compute_stress_mop diff --git a/examples/USER/mop/moppz.time.reference b/examples/USER/misc/mop/moppz.time.reference similarity index 100% rename from examples/USER/mop/moppz.time.reference rename to examples/USER/misc/mop/moppz.time.reference diff --git a/examples/USER/mop/mopz0.time.reference b/examples/USER/misc/mop/mopz0.time.reference similarity index 100% rename from examples/USER/mop/mopz0.time.reference rename to examples/USER/misc/mop/mopz0.time.reference diff --git a/examples/USER/mop/profile.z.reference b/examples/USER/misc/mop/profile.z.reference similarity index 100% rename from examples/USER/mop/profile.z.reference rename to examples/USER/misc/mop/profile.z.reference diff --git a/src/Makefile b/src/Makefile index 6b1a2bdb98f54271c25ad81ee197d987da5e4009..948d203cfe078a51e70ca617375e0b90b44a3257 100644 --- a/src/Makefile +++ b/src/Makefile @@ -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 diff --git a/src/USER-MISC/README b/src/USER-MISC/README index 0f9e7bf383bf3e005b828672ad24b360d6f9b440..eb221c07db67bbd8569ac7d61f4594af29b76654 100644 --- a/src/USER-MISC/README +++ b/src/USER-MISC/README @@ -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 diff --git a/src/USER-MOP/compute_stress_mop.cpp b/src/USER-MISC/compute_stress_mop.cpp similarity index 100% rename from src/USER-MOP/compute_stress_mop.cpp rename to src/USER-MISC/compute_stress_mop.cpp diff --git a/src/USER-MOP/compute_stress_mop.h b/src/USER-MISC/compute_stress_mop.h similarity index 100% rename from src/USER-MOP/compute_stress_mop.h rename to src/USER-MISC/compute_stress_mop.h diff --git a/src/USER-MOP/compute_stress_mop_profile.cpp b/src/USER-MISC/compute_stress_mop_profile.cpp similarity index 100% rename from src/USER-MOP/compute_stress_mop_profile.cpp rename to src/USER-MISC/compute_stress_mop_profile.cpp diff --git a/src/USER-MOP/compute_stress_mop_profile.h b/src/USER-MISC/compute_stress_mop_profile.h similarity index 100% rename from src/USER-MOP/compute_stress_mop_profile.h rename to src/USER-MISC/compute_stress_mop_profile.h diff --git a/src/USER-MOP/README b/src/USER-MOP/README deleted file mode 100644 index 15fcb3701a9d7aedfe78f3ea9021aa764c06c10f..0000000000000000000000000000000000000000 --- a/src/USER-MOP/README +++ /dev/null @@ -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