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correct broken links and references in documentation

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This commit is contained in:
Axel Kohlmeyer
2017-05-09 17:15:07 -04:00
parent 3f4aee1046
commit 29ae8d4ca3
6 changed files with 34 additions and 34 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 "LAMMPS is built with the appropriate
package"_Section_start.html#start_3. package"_Section_start.html#start_3.
"dump custom/vtk"_dump_custom_vtk.html, "dump netcdf"_dump_netcdf.html,
"dump nc"_dump_nc.html, "dump netcdf/mpiio"_dump_netcdf.html,
"dump nc/mpiio"_dump_nc.html, "dump vtk"_dump_vtk.html,
"group2ndx"_group2ndx.html, "group2ndx"_group2ndx.html,
"ndx2group"_group2ndx.html, "ndx2group"_group2ndx.html,
"temper/grem"_temper_grem.html :tb(c=3,ea=c) "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-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-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-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-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-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, - "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-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-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-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) :tb(ea=c,ca1=l)
:line :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 build and use this package. Its styles can be invoked at run time via
the "-sf kk" or "-suffix kk" "command-line the "-sf kk" or "-suffix kk" "command-line
switches"_Section_start.html#start_7. Also see the "GPU"_#GPU, 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. packages, which have styles optimized for CPUs, KNLs, and GPUs.
You must have a C++11 compatible compiler to use this package. You must have a C++11 compatible compiler to use this package.
@ -856,15 +856,15 @@ src/MPIIO: filenames -> commands
:line :line
MSCG package :link(MSCG),h4 MSCG package :link(mscg),h4
[Contents:] [Contents:]
A "fix mscg"_fix_mscg.html command which can parameterize a A "fix mscg"_fix_mscg.html command which can parameterize a
Mulit-Scale Coarse-Graining (MSCG) model using the open-source "MS-CG 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 To use this package you must have the MS-CG library available on your
system. system.
@ -1323,11 +1323,11 @@ VORONOI package :link(VORONOI),h4
[Contents:] [Contents:]
A compute command which calculates the Voronoi tesselation of a 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 can be used to calculate the local volume or each atoms or its near
neighbors. 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 To use this package you must have the Voro++ library available on your
system. system.
@ -1488,7 +1488,6 @@ make machine :pre
src/USER-AWPMD: filenames -> commands src/USER-AWPMD: filenames -> commands
src/USER-AWPMD/README src/USER-AWPMD/README
"pair awpmd/cut"_pair_awpmd.html "pair awpmd/cut"_pair_awpmd.html
"fix nve/awpmd"_fix_nve_awpmd.html
examples/USER/awpmd :ul examples/USER/awpmd :ul
:line :line
@ -1520,7 +1519,7 @@ src/USER-CGDNA: filenames -> commands
"pair_style oxdna/*"_pair_oxdna.html "pair_style oxdna/*"_pair_oxdna.html
"pair_style oxdna2/*"_pair_oxdna2.html "pair_style oxdna2/*"_pair_oxdna2.html
"bond_style oxdna/*"_bond_oxdna.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 "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html :ul
:line :line
@ -1748,8 +1747,8 @@ src/USER-EFF: filenames -> commands
src/USER-EFF/README src/USER-EFF/README
"atom_style electron"_atom_style.html "atom_style electron"_atom_style.html
"fix nve/eff"_fix_nve_eff.html "fix nve/eff"_fix_nve_eff.html
"fix nvt/eff"_fix_nvt_eff.html "fix nvt/eff"_fix_nh_eff.html
"fix npt/eff"_fix_npt_eff.html "fix npt/eff"_fix_nh_eff.html
"fix langevin/eff"_fix_langevin_eff.html "fix langevin/eff"_fix_langevin_eff.html
"compute temp/eff"_compute_temp_eff.html "compute temp/eff"_compute_temp_eff.html
"pair eff/cut"_pair_eff.html "pair eff/cut"_pair_eff.html
@ -2045,8 +2044,8 @@ src/USER-MANIFOLD: filenames -> commands
src/USER-MANIFOLD/README src/USER-MANIFOLD/README
"doc/manifolds"_manifolds.html "doc/manifolds"_manifolds.html
"fix manifoldforce"_fix_manifoldforce.html "fix manifoldforce"_fix_manifoldforce.html
"fix nve/manifold/rattle"_fix_nve_manifold/rattle.html "fix nve/manifold/rattle"_fix_nve_manifold_rattle.html
"fix nvt/manifold/rattle"_fix_nvt_manifold/rattle.html "fix nvt/manifold/rattle"_fix_nvt_manifold_rattle.html
examples/USER/manifold examples/USER/manifold
http://lammps.sandia.gov/movies.html#manifold :ul http://lammps.sandia.gov/movies.html#manifold :ul
@ -2057,11 +2056,13 @@ USER-MOLFILE package :link(USER-MOLFILE),h4
[Contents:] [Contents:]
A "dump molfile"_dump_molfile.html command which uses molfile plugins 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 molecular visualization and analysis program, to enable LAMMPS to dump
snapshots in formats compatible with various molecular simulation snapshots in formats compatible with various molecular simulation
tools. tools.
:link(vmd_home,http://www.ks.uiuc.edu/Research/vmd)
To use this package you must have the desired VMD plugins available on To use this package you must have the desired VMD plugins available on
your system. your system.
@ -2118,7 +2119,7 @@ Note that NetCDF files can be directly visualized with the following
tools: tools:
"Ovito"_ovito (Ovito supports the AMBER convention and the extensions mentioned above) "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 "AtomEye"_atomeye (the libAtoms version of AtomEye contains a NetCDF reader not present in the standard distribution) :ul
:link(ovito,http://www.ovito.org) :link(ovito,http://www.ovito.org)
@ -2563,7 +2564,7 @@ USER-VTK package :link(USER-VTK),h4
[Contents:] [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 snapshot info in the "VTK format"_vtk, enabling visualization by
"Paraview"_paraview or other visuzlization packages. "Paraview"_paraview or other visuzlization packages.
@ -2598,4 +2599,4 @@ make machine :pre
src/USER-VTK: filenames -> commands src/USER-VTK: filenames -> commands
src/USER-VTK/README src/USER-VTK/README
lib/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 2.3.1 "Package basics"_#start_3_1
2.3.2 "Including/excluding packages"_#start_3_2 2.3.2 "Including/excluding packages"_#start_3_2
2.3.3 "Packages that require extra libraries"_#start_3_3 2.3.3 "Packages that require extra libraries"_#start_3_3 :all(b)
2.3.4 "Packages that require Makefile.machine settings"_#start_3_4 :all(b)
:line :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 in the last column link to exernal libraries whose source code is not
included with LAMMPS. You must first download and install the library included with LAMMPS. You must first download and install the library
before building LAMMPS with that package installed. E.g. the voronoi 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 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 args=..." from the src dir, with appropriate arguments. You can leave
off the args to see a help message. See "Section off the args to see a help message. See "Section
4"_Section_packages.html for details for each package. 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:] [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 environment variables to force binding. With OpenMP 3.1 (gcc 4.7 or
later, intel 12 or later) setting the environment variable later, intel 12 or later) setting the environment variable
OMP_PROC_BIND=true should be sufficient. For binding threads with the OMP_PROC_BIND=true should be sufficient. For binding threads with the
KOKKOS pthreads option, compile LAMMPS the KOKKOS HWLOC=yes option, as KOKKOS pthreads option, compile LAMMPS the KOKKOS HWLOC=yes option
discussed in "Section 2.3.4"_Sections_start.html#start_3_4 of the (see "this section"_Section_packages.html#KOKKOS of the manual for
manual. details).
[Running on GPUs:] [Running on GPUs:]
Insure the -arch setting in the machine makefile you are using, Insure the -arch setting in the machine makefile you are using,
e.g. src/MAKE/Makefile.cuda, is correct for your GPU hardware/software 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 (see "this section"_Section_packages.html#KOKKOS of the manual for
details). details).
The -np setting of the mpirun command should set the number of MPI 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 dimension
displace_atoms displace_atoms
dump dump
dump_custom_vtk
dump_h5md dump_h5md
dump_image dump_image
dump_modify dump_modify
dump_molfile dump_molfile
dump_nc dump_netcdf
dump_vtk
echo echo
fix fix
fix_modify fix_modify

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