diff --git a/doc/src/Section_commands.txt b/doc/src/Section_commands.txt index c71acfe06f..771e830841 100644 --- a/doc/src/Section_commands.txt +++ b/doc/src/Section_commands.txt @@ -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) diff --git a/doc/src/Section_packages.txt b/doc/src/Section_packages.txt index 2a0a8386e8..cc44c05906 100644 --- a/doc/src/Section_packages.txt +++ b/doc/src/Section_packages.txt @@ -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 diff --git a/doc/src/Section_start.txt b/doc/src/Section_start.txt index 0a7209765e..dcd320655f 100644 --- a/doc/src/Section_start.txt +++ b/doc/src/Section_start.txt @@ -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:] diff --git a/doc/src/accelerate_kokkos.txt b/doc/src/accelerate_kokkos.txt index 3bfd4bf379..602c3191f6 100644 --- a/doc/src/accelerate_kokkos.txt +++ b/doc/src/accelerate_kokkos.txt @@ -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 diff --git a/doc/src/commands.txt b/doc/src/commands.txt index 2fdb69ea4d..7889ea5e7a 100644 --- a/doc/src/commands.txt +++ b/doc/src/commands.txt @@ -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 diff --git a/doc/src/lammps.book b/doc/src/lammps.book index b2b42aa7e6..6b3ca8aa07 100644 --- a/doc/src/lammps.book +++ b/doc/src/lammps.book @@ -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 diff --git a/src/.gitignore b/src/.gitignore index 1327704e47..620c6965d0 100644 --- a/src/.gitignore +++ b/src/.gitignore @@ -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 diff --git a/src/Purge.list b/src/Purge.list index 6326dbadf0..3bdfed3ed0 100644 --- a/src/Purge.list +++ b/src/Purge.list @@ -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