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Merge pull request #471 from akohlmey/fix-4may2017-issues 

Fix a bunch of remaining issues in the 4 may 2017 release
This commit is contained in:
sjplimp 2017-05-11 09:24:35 -06:00 committed by GitHub
parent deff6ffaac 9f7ce39f9f
commit 96d1de8575
8 changed files with 52 additions and 44 deletions
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6
doc/src/Section_commands.txt
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@ -527,9 +527,9 @@ These are additional commands in USER packages, which can be used if
"LAMMPS is built with the appropriate
package"_Section_start.html#start_3.
"dump custom/vtk"_dump_custom_vtk.html,
"dump nc"_dump_nc.html,
"dump nc/mpiio"_dump_nc.html,
"dump netcdf"_dump_netcdf.html,
"dump netcdf/mpiio"_dump_netcdf.html,
"dump vtk"_dump_vtk.html,
"group2ndx"_group2ndx.html,
"ndx2group"_group2ndx.html,
"temper/grem"_temper_grem.html :tb(c=3,ea=c)

37
doc/src/Section_packages.txt
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@ -123,7 +123,7 @@ Package, Description, Doc page, Example, Library
"USER-MANIFOLD"_#USER-MANIFOLD, motion on 2d surfaces,"fix manifoldforce"_fix_manifoldforce.html, USER/manifold, -
"USER-MGPT"_#USER-MGPT, fast MGPT multi-ion potentials, "pair_style mgpt"_pair_mgpt.html, USER/mgpt, -
"USER-MISC"_#USER-MISC, single-file contributions, USER-MISC/README, USER/misc, -
"USER-MOLFILE"_#USER-MOLFILE, "VMD"_VMD molfile plug-ins,"dump molfile"_dump_molfile.html, -, ext
"USER-MOLFILE"_#USER-MOLFILE, "VMD"_vmd_home molfile plug-ins,"dump molfile"_dump_molfile.html, -, ext
"USER-NETCDF"_#USER-NETCDF, dump output via NetCDF,"dump netcdf"_dump_netcdf.html, -, ext
"USER-OMP"_#USER-OMP, OpenMP-enabled styles,"Section 5.3.4"_accelerate_omp.html, WWW bench, -
"USER-PHONON"_#USER-PHONON, phonon dynamical matrix,"fix phonon"_fix_phonon.html, USER/phonon, -
@ -135,7 +135,7 @@ Package, Description, Doc page, Example, Library
"USER-SMTBQ"_#USER-SMTBQ, second moment tight binding QEq potential,"pair_style smtbq"_pair_smtbq.html, USER/smtbq, -
"USER-SPH"_#USER-SPH, smoothed particle hydrodynamics,"SPH User Guide"_PDF/SPH_LAMMPS_userguide.pdf, USER/sph, -
"USER-TALLY"_#USER-TALLY, pairwise tally computes,"compute XXX/tally"_compute_tally.html, USER/tally, -
"USER-VTK"_#USER-VTK, dump output via VTK, "compute custom/vtk"_dump_custom_vtk.html, -, ext
"USER-VTK"_#USER-VTK, dump output via VTK, "compute vtk"_dump_vtk.html, -, ext
:tb(ea=c,ca1=l)
:line
@ -529,7 +529,7 @@ what hardware and software is required on your system, and how to
build and use this package. Its styles can be invoked at run time via
the "-sf kk" or "-suffix kk" "command-line
switches"_Section_start.html#start_7. Also see the "GPU"_#GPU,
"OPT"_#OPT, "USER-INTEL"_#USER-INTEL, and "USER-OMP"_#USER_OMP
"OPT"_#OPT, "USER-INTEL"_#USER-INTEL, and "USER-OMP"_#USER-OMP
packages, which have styles optimized for CPUs, KNLs, and GPUs.
You must have a C++11 compatible compiler to use this package.
@ -856,15 +856,15 @@ src/MPIIO: filenames -> commands
:line
MSCG package :link(MSCG),h4
MSCG package :link(mscg),h4
[Contents:]
A "fix mscg"_fix_mscg.html command which can parameterize a
Mulit-Scale Coarse-Graining (MSCG) model using the open-source "MS-CG
library"_mscg.
library"_mscg_home.
:link(mscg,https://github.com/uchicago-voth/MSCG-release)
:link(mscg_home,https://github.com/uchicago-voth/MSCG-release)
To use this package you must have the MS-CG library available on your
system.
@ -1323,11 +1323,11 @@ VORONOI package :link(VORONOI),h4
[Contents:]
A compute command which calculates the Voronoi tesselation of a
collection of atoms by wrapping the "Voro++ library"_voronoi. This
collection of atoms by wrapping the "Voro++ library"_voro_home. This
can be used to calculate the local volume or each atoms or its near
neighbors.
:link(voronoi,http://math.lbl.gov/voro++)
:link(voro_home,http://math.lbl.gov/voro++)
To use this package you must have the Voro++ library available on your
system.
@ -1488,7 +1488,6 @@ make machine :pre
src/USER-AWPMD: filenames -> commands
src/USER-AWPMD/README
"pair awpmd/cut"_pair_awpmd.html
"fix nve/awpmd"_fix_nve_awpmd.html
examples/USER/awpmd :ul
:line
@ -1520,7 +1519,7 @@ src/USER-CGDNA: filenames -> commands
"pair_style oxdna/*"_pair_oxdna.html
"pair_style oxdna2/*"_pair_oxdna2.html
"bond_style oxdna/*"_bond_oxdna.html
"bond_style oxdna2/*"_bond_oxdna2.html
"bond_style oxdna2/*"_bond_oxdna.html
"fix nve/dotc/langevin"_fix_nve_dotc_langevin.html :ul
:line
@ -1748,8 +1747,8 @@ src/USER-EFF: filenames -> commands
src/USER-EFF/README
"atom_style electron"_atom_style.html
"fix nve/eff"_fix_nve_eff.html
"fix nvt/eff"_fix_nvt_eff.html
"fix npt/eff"_fix_npt_eff.html
"fix nvt/eff"_fix_nh_eff.html
"fix npt/eff"_fix_nh_eff.html
"fix langevin/eff"_fix_langevin_eff.html
"compute temp/eff"_compute_temp_eff.html
"pair eff/cut"_pair_eff.html
@ -2045,8 +2044,8 @@ src/USER-MANIFOLD: filenames -> commands
src/USER-MANIFOLD/README
"doc/manifolds"_manifolds.html
"fix manifoldforce"_fix_manifoldforce.html
"fix nve/manifold/rattle"_fix_nve_manifold/rattle.html
"fix nvt/manifold/rattle"_fix_nvt_manifold/rattle.html
"fix nve/manifold/rattle"_fix_nve_manifold_rattle.html
"fix nvt/manifold/rattle"_fix_nvt_manifold_rattle.html
examples/USER/manifold
http://lammps.sandia.gov/movies.html#manifold :ul
@ -2057,11 +2056,13 @@ USER-MOLFILE package :link(USER-MOLFILE),h4
[Contents:]
A "dump molfile"_dump_molfile.html command which uses molfile plugins
that are bundled with the "VMD"_http://www.ks.uiuc.edu/Research/vmd
that are bundled with the "VMD"_vmd_home
molecular visualization and analysis program, to enable LAMMPS to dump
snapshots in formats compatible with various molecular simulation
tools.
:link(vmd_home,http://www.ks.uiuc.edu/Research/vmd)
To use this package you must have the desired VMD plugins available on
your system.
@ -2118,7 +2119,7 @@ Note that NetCDF files can be directly visualized with the following
tools:
"Ovito"_ovito (Ovito supports the AMBER convention and the extensions mentioned above)
"VMD"_vmd
"VMD"_vmd_home
"AtomEye"_atomeye (the libAtoms version of AtomEye contains a NetCDF reader not present in the standard distribution) :ul
:link(ovito,http://www.ovito.org)
@ -2563,7 +2564,7 @@ USER-VTK package :link(USER-VTK),h4
[Contents:]
A "dump custom/vtk"_dump_custom_vtk.html command which outputs
A "dump vtk"_dump_vtk.html command which outputs
snapshot info in the "VTK format"_vtk, enabling visualization by
"Paraview"_paraview or other visuzlization packages.
@ -2598,4 +2599,4 @@ make machine :pre
src/USER-VTK: filenames -> commands
src/USER-VTK/README
lib/vtk/README
"dump custom/vtk"_dump_custom_vtk.html :ul
"dump vtk"_dump_vtk.html :ul

7
doc/src/Section_start.txt
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@ -655,8 +655,7 @@ This section has the following sub-sections:
2.3.1 "Package basics"_#start_3_1
2.3.2 "Including/excluding packages"_#start_3_2
2.3.3 "Packages that require extra libraries"_#start_3_3
2.3.4 "Packages that require Makefile.machine settings"_#start_3_4 :all(b)
2.3.3 "Packages that require extra libraries"_#start_3_3 :all(b)
:line
@ -828,13 +827,13 @@ Packages in the tables "Section 4"_Section_packages.html with an "ext"
in the last column link to exernal libraries whose source code is not
included with LAMMPS. You must first download and install the library
before building LAMMPS with that package installed. E.g. the voronoi
package links to the freely available "Voro++ library"_voronoi. You
package links to the freely available "Voro++ library"_voro_home2. You
can often do the download/build in one step by typing "make lib-name
args=..." from the src dir, with appropriate arguments. You can leave
off the args to see a help message. See "Section
4"_Section_packages.html for details for each package.
:link(voronoi,http://math.lbl.gov/voro++)
:link(voro_home2,http://math.lbl.gov/voro++)
[Possible errors:]

10
doc/src/accelerate_kokkos.txt
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@ -415,15 +415,15 @@ For binding threads with the KOKKOS OMP option, use thread affinity
environment variables to force binding. With OpenMP 3.1 (gcc 4.7 or
later, intel 12 or later) setting the environment variable
OMP_PROC_BIND=true should be sufficient. For binding threads with the
KOKKOS pthreads option, compile LAMMPS the KOKKOS HWLOC=yes option, as
discussed in "Section 2.3.4"_Sections_start.html#start_3_4 of the
manual.
KOKKOS pthreads option, compile LAMMPS the KOKKOS HWLOC=yes option
(see "this section"_Section_packages.html#KOKKOS of the manual for
details).
[Running on GPUs:]
Insure the -arch setting in the machine makefile you are using,
e.g. src/MAKE/Makefile.cuda, is correct for your GPU hardware/software
(see "this section"_Section_start.html#start_3_4 of the manual for
e.g. src/MAKE/Makefile.cuda, is correct for your GPU hardware/software.
(see "this section"_Section_packages.html#KOKKOS of the manual for
details).
The -np setting of the mpirun command should set the number of MPI

4
doc/src/commands.txt
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@ -32,12 +32,12 @@ Commands :h1
dimension
displace_atoms
dump
dump_custom_vtk
dump_h5md
dump_image
dump_modify
dump_molfile
dump_nc
dump_netcdf
dump_vtk
echo
fix
fix_modify

4
doc/src/lammps.book
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@ -55,12 +55,12 @@ dihedral_style.html
dimension.html
displace_atoms.html
dump.html
dump_custom_vtk.html
dump_h5md.html
dump_image.html
dump_modify.html
dump_molfile.html
dump_nc.html
dump_netcdf.html
dump_vtk.html
echo.html
fix.html
fix_modify.html

20
src/.gitignore vendored
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@ -281,14 +281,14 @@
/dump_custom_gz.h
/dump_custom_mpiio.cpp
/dump_custom_mpiio.h
/dump_custom_vtk.cpp
/dump_custom_vtk.h
/dump_h5md.cpp
/dump_h5md.h
/dump_nc.cpp
/dump_nc.h
/dump_nc_mpiio.cpp
/dump_nc_mpiio.h
/dump_netcdf.cpp
/dump_netcdf.h
/dump_netcdf_mpiio.cpp
/dump_netcdf_mpiio.h
/dump_vtk.cpp
/dump_vtk.h
/dump_xtc.cpp
/dump_xtc.h
/dump_xyz_mpiio.cpp
@ -461,8 +461,8 @@
/fix_qmmm.h
/fix_reax_bonds.cpp
/fix_reax_bonds.h
/fix_reax_c.cpp
/fix_reax_c.h
/fix_reaxc.cpp
/fix_reaxc.h
/fix_reaxc_bonds.cpp
/fix_reaxc_bonds.h
/fix_reaxc_species.cpp
@ -784,8 +784,8 @@
/pair_reax.cpp
/pair_reax.h
/pair_reax_fortran.h
/pair_reax_c.cpp
/pair_reax_c.h
/pair_reaxc.cpp
/pair_reaxc.h
/pair_rebo.cpp
/pair_rebo.h
/pair_resquared.cpp

8
src/Purge.list
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@ -17,8 +17,16 @@ style_neigh_bin.h
style_neigh_pair.h
style_neigh_stencil.h
# deleted on 4 May 2017
dump_custom_vtk.cpp
dump_custom_vtk.h
dump_nc.cpp
dump_nc.h
dump_nc_mpiio.cpp
dump_nc_mpiio.h
pair_reax_c.cpp
pair_reax_c.h
fix_reax_c.cpp
fix_reax_c.h
fix_reax_c_bonds.cpp
fix_reax_c_bonds.h
fix_reax_c_species.cpp