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fix broken links in manual

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This commit is contained in:
Axel Kohlmeyer
2018-10-21 18:39:25 -04:00
parent c0dd187802
commit 8649081904
8 changed files with 24 additions and 20 deletions
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8
doc/src/Build_extras.txt
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@ -563,9 +563,9 @@ file.
VORONOI package :h4,link(voronoi)
To build with this package, you must download and build the "Voro++
library"_voro_home.
library"_voro-home.
:link(voro_home,http://math.lbl.gov/voro++)
:link(voro-home,http://math.lbl.gov/voro++)
[CMake build]:
@ -932,9 +932,9 @@ successfully build on your system.
USER-SCAFACOS package :h4,link(user-scafacos)
To build with this package, you must download and build the "ScaFaCoS
Coulomb solver library"_scafacos_home
Coulomb solver library"_scafacos-home
:link(scafacos_home,http://www.scafacos.de)
:link(scafacos-home,http://www.scafacos.de)
[CMake build]:

3
doc/src/Install_mac.txt
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@ -49,7 +49,8 @@ Lennard-Jones benchmark file:
% brew test lammps -v :pre
If you have problems with the installation you can post issues to
"this link"_https://github.com/Homebrew/homebrew-science/issues.
"this link"_homebrew.
Thanks to Derek Thomas (derekt at cello.t.u-tokyo.ac.jp) for setting
up the Homebrew capability.
:link(homebrew,https://github.com/Homebrew/homebrew-science/issues)

20
doc/src/Packages_details.txt
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@ -462,10 +462,10 @@ dynamics can be run with LAMMPS using density-functional tight-binding
quantum forces calculated by LATTE.
More information on LATTE can be found at this web site:
"https://github.com/lanl/LATTE"_latte_home. A brief technical
"https://github.com/lanl/LATTE"_latte-home. A brief technical
description is given with the "fix latte"_fix_latte.html command.
:link(latte_home,https://github.com/lanl/LATTE)
:link(latte-home,https://github.com/lanl/LATTE)
[Authors:] Christian Negre (LANL) and Steve Plimpton (Sandia). LATTE
itself is developed at Los Alamos National Laboratory by Marc
@ -668,9 +668,9 @@ MSCG package :link(PKG-mscg),h4
A "fix mscg"_fix_mscg.html command which can parameterize a
Multi-Scale Coarse-Graining (MSCG) model using the open-source "MS-CG
library"_mscg_home.
library"_mscg-home.
:link(mscg_home,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.
@ -1008,11 +1008,11 @@ VORONOI package :link(PKG-VORONOI),h4
[Contents:]
A compute command which calculates the Voronoi tesselation of a
collection of atoms by wrapping the "Voro++ library"_voro_home. 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(voro_home,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.
@ -1520,7 +1520,7 @@ USER-MEAMC package :link(PKG-USER-MEAMC),h4
[Contents:]
A pair style for the modified embedded atom (MEAM) potential
translated from the Fortran version in the "MEAM"_MEAM package
translated from the Fortran version in the "MEAM"_#PKG-MEAM package
to plain C++. In contrast to the MEAM package, no library
needs to be compiled and the pair style can be instantiated
multiple times.
@ -1601,7 +1601,7 @@ USER-MOLFILE package :link(PKG-USER-MOLFILE),h4
[Contents:]
A "dump molfile"_dump_molfile.html command which uses molfile plugins
that are bundled with the "VMD"_vmd_home
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.
@ -1653,11 +1653,11 @@ 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_home
"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)
:link(vmd_home,https://www.ks.uiuc.edu/Research/vmd/)
:link(vmd-home,https://www.ks.uiuc.edu/Research/vmd/)
:link(atomeye,http://www.libatoms.org)
[Author:] Lars Pastewka (Karlsruhe Institute of Technology).

1
doc/src/Packages_user.txt
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@ -74,3 +74,4 @@ Package, Description, Doc page, Example, Library
"USER-TALLY"_Packages_details.html#PKG-USER-TALLY, pairwise tally computes,"compute XXX/tally"_compute_tally.html, USER/tally, no
"USER-UEF"_Packages_details.html#PKG-USER-UEF, extensional flow,"fix nvt/uef"_fix_nh_uef.html, USER/uef, no
"USER-VTK"_Packages_details.html#PKG-USER-VTK, dump output via VTK, "compute vtk"_dump_vtk.html, n/a, ext :tb(ea=c,ca1=l)
:link(MOFplus,https://www.mofplus.org/content/show/MOF-FF)

1
doc/src/balance.txt
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@ -516,3 +516,4 @@ appear in {dimstr} for the {shift} style.
"fix balance"_fix_balance.html
[Default:] none
:link(pizza,http://pizza.sandia.gov)

6
doc/src/dump_h5md.txt
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@ -50,7 +50,7 @@ dump h5md1 all h5md 100 dump_h5md.h5 velocity author "John Doe" :pre
[Description:]
Dump a snapshot of atom coordinates every N timesteps in the
"HDF5"_HDF5_ws based "H5MD"_h5md file format "(de Buyl)"_#h5md_cpc.
"HDF5"_HDF5-ws based "H5MD"_h5md file format "(de Buyl)"_#h5md_cpc.
HDF5 files are binary, portable and self-describing. This dump style
will write only one file, on the root node.
@ -102,11 +102,11 @@ enabled if LAMMPS was built with that package. See the "Build
package"_Build_package.html doc page for more info. It also requires
(i) building the ch5md library provided with LAMMPS (See the "Build
package"_Build_package.html doc page for more info.) and (ii) having
the "HDF5"_HDF5_ws library installed (C bindings are sufficient) on
the "HDF5"_HDF5-ws library installed (C bindings are sufficient) on
your system. The library ch5md is compiled with the h5cc wrapper
provided by the HDF5 library.
:link(HDF5_ws,http://www.hdfgroup.org/HDF5/)
:link(HDF5-ws,http://www.hdfgroup.org/HDF5/)
:line

1
doc/src/fix_balance.txt
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@ -376,3 +376,4 @@ appear in {dimstr} for the {shift} style.
"group"_group.html, "processors"_processors.html, "balance"_balance.html
[Default:] none
:link(pizza,http://pizza.sandia.gov)

4
doc/src/message.txt
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@ -137,8 +137,8 @@ If LAMMPS is the server code, it will begin receiving messages when
the "server"_server.html command is invoked.
A fix client command will terminate its messaging with the server when
LAMMPS ends, or the fix is deleted via the "unfix"_unfix command. The
server command will terminate its messaging with the client when the
LAMMPS ends, or the fix is deleted via the "unfix"_unfix.html command.
The server command will terminate its messaging with the client when the
client signals it. Then the remainder of the LAMMPS input script will
be processed.