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fix a bunch more broken links

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This commit is contained in:
Axel Kohlmeyer
2023-02-19 20:45:08 -05:00
parent 7149143df8
commit 9220ea5695
35 changed files with 67 additions and 63 deletions
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2
doc/src/Developer_comm_ops.rst
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@ -77,7 +77,7 @@ buffer, and they will be communicated together to minimize
communication overhead. The communication buffers are defined vectors
containing ``double`` values. To correctly store integers that may be
64-bit (bigint, tagint, imageint) in the buffer, you need to use the
`ubuf union <Communication buffer coding with *ubuf*>`_ construct.
:ref:`ubuf union <communication_buffer_coding_with_ubuf>` construct.
The *Fix*, *Compute*, and *Dump* classes can also invoke the same kind
of forward and reverse communication operations using the same *Comm*

2
doc/src/Developer_utils.rst
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@ -643,6 +643,8 @@ Tohoku University (under MIT license)
---------------------------
.. _communication_buffer_coding_with_ubuf:
Communication buffer coding with *ubuf*
---------------------------------------

14
doc/src/Howto_wsl.rst
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@ -11,12 +11,14 @@ LAMMPS in workshop settings, we had to redirect Windows users to
Linux Virtual Machines such as VirtualBox or Unix-like compilation with
Cygwin.
With the latest updates in Windows 10 (Version 2004, Build 19041 or higher),
Microsoft has added a new way to work on Linux-based code. The Windows
Subsystem for Linux (WSL). With WSL Version 2, you now get a Linux Virtual
Machine that transparently integrates into Windows. All you need is to ensure
you have the latest Windows updates installed and enable this new feature.
Linux VMs are then easily installed using the Microsoft Store.
With the latest updates in Windows 10 (Version 2004, Build 19041 or
higher), Microsoft has added a new way to work on Linux-based code. The
`Windows Subsystem for Linux (WSL)
<https://learn.microsoft.com/en-us/windows/wsl/>`_. With WSL Version 2,
you now get a Linux Virtual Machine that transparently integrates into
Windows. All you need is to ensure you have the latest Windows updates
installed and enable this new feature. Linux VMs are then easily
installed using the Microsoft Store.
In this tutorial, I'll show you how to set up and compile LAMMPS for both serial
and MPI usage in WSL2.

50
doc/src/Packages_details.rst
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@ -228,8 +228,9 @@ conversion of atomic information to continuum fields.
**Install:**
This package has :ref:`specific installation instructions <atc>` on the :doc:`Build extras <Build_extras>` page.
The ATC package requires that also the `MANYBODY <PKG-MANYBODY>`_ package is installed.
This package has :ref:`specific installation instructions <atc>` on the
:doc:`Build extras <Build_extras>` page. The ATC package requires that
also the :ref:`MANYBODY <PKG-MANYBODY>` package is installed.
**Supporting info:**
@ -391,8 +392,8 @@ rigid-body integrators with improved stability.
**Install:**
The CG-DNA package requires that also the `MOLECULE <PKG-MOLECULE>`_ and
`ASPHERE <PKG-ASPHERE>`_ packages are installed.
The CG-DNA package requires that also the :ref:`MOLECULE <PKG-MOLECULE>`
and :ref:`ASPHERE <PKG-ASPHERE>` packages are installed.
**Supporting info:**
@ -1114,15 +1115,15 @@ INTEL package
**Contents:**
Dozens of pair, fix, bond, angle, dihedral, improper, and kspace
styles which are optimized for Intel CPUs and KNLs (Knights Landing).
All of them have an "intel" in their style name. The
:doc:`INTEL package <Speed_intel>` page gives details of what hardware and
compilers are required on your system, and how to build and use this
package. Its styles can be invoked at run time via the "-sf intel" or
"-suffix intel" :doc:`command-line switches <Run_options>`. Also see
the :ref:`KOKKOS <PKG-KOKKOS>`, :ref:`OPT <PKG-OPT>`, and :ref:`OPENMP <PKG-OPENMP>` packages,
which have styles optimized for CPUs and KNLs.
Dozens of pair, fix, bond, angle, dihedral, improper, and kspace styles
which are optimized for Intel CPUs and KNLs (Knights Landing). All of
them have an "intel" in their style name. The :doc:`INTEL package
<Speed_intel>` page gives details of what hardware and compilers are
required on your system, and how to build and use this package. Its
styles can be invoked at run time via the "-sf intel" or "-suffix intel"
:doc:`command-line switches <Run_options>`. Also see the :ref:`KOKKOS
<PKG-KOKKOS>`, :ref:`OPT <PKG-OPT>`, and :ref:`OPENMP <PKG-OPENMP>`
packages, which have styles optimized for CPUs and KNLs.
You need to have an Intel compiler, version 14 or higher to take full
advantage of this package. While compilation with GNU compilers is
@ -1249,12 +1250,13 @@ Dozens of atom, pair, bond, angle, dihedral, improper, fix, compute
styles adapted to compile using the Kokkos library which can convert
them to OpenMP or CUDA code so that they run efficiently on multicore
CPUs, KNLs, or GPUs. All the styles have a "kk" as a suffix in their
style name. The :doc:`KOKKOS package <Speed_kokkos>` page gives
details of 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" :doc:`command-line switches <Run_options>`. Also see the :ref:`GPU <PKG-GPU>`, :ref:`OPT <PKG-OPT>`,
:ref:`INTEL <PKG-INTEL>`, and :ref:`OPENMP <PKG-OPENMP>` packages, which
have styles optimized for CPUs, KNLs, and GPUs.
style name. The :doc:`KOKKOS package <Speed_kokkos>` page gives details
of 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" :doc:`command-line switches <Run_options>`.
Also see the :ref:`GPU <PKG-GPU>`, :ref:`OPT <PKG-OPT>`, :ref:`INTEL
<PKG-INTEL>`, and :ref:`OPENMP <PKG-OPENMP>` packages, which have styles
optimized for CPUs, KNLs, and GPUs.
You must have a C++14 compatible compiler to use this package.
KOKKOS makes extensive use of advanced C++ features, which can
@ -2328,7 +2330,7 @@ and third order tensor from finite differences.
**Install:**
The PHONON package requires that also the `KSPACE <PKG-KSPACE>`_
The PHONON package requires that also the :ref:`KSPACE <PKG-KSPACE>`
package is installed.
@ -2929,11 +2931,9 @@ VORONOI package
**Contents:**
A compute command which calculates the Voronoi tesselation of a
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.
.. _voro-home: https://math.lbl.gov/voro++
collection of atoms by wrapping the `Voro++ library
<https://math.lbl.gov/voro++/>`_. This can be used to calculate the
local volume or each atoms or its near neighbors.
To use this package you must have the Voro++ library available on your
system.

2
doc/src/compute_smd_contact_radius.rst
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@ -29,7 +29,7 @@ contact radius is used only to prevent particles belonging to
different physical bodies from penetrating each other. It is used by
the contact pair styles, e.g., smd/hertz and smd/tri_surface.
See `this PDF guide <PDF/SMD_LAMMPS_userguide.pdf>`_ to using Smooth
See `this PDF guide <PDF/MACHDYN_LAMMPS_userguide.pdf>`_ to using Smooth
Mach Dynamics in LAMMPS.
The value of the contact radius will be 0.0 for particles not in the

2
doc/src/compute_smd_damage.rst
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@ -26,7 +26,7 @@ Description
Define a computation that calculates the damage status of SPH particles
according to the damage model which is defined via the SMD SPH pair styles, e.g., the maximum plastic strain failure criterion.
See `this PDF guide <PDF/SMD_LAMMPS_userguide.pdf>`_ to use Smooth Mach Dynamics in LAMMPS.
See `this PDF guide <PDF/MACHDYN_LAMMPS_userguide.pdf>`_ to use Smooth Mach Dynamics in LAMMPS.
**Output Info:**

2
doc/src/compute_smd_hourglass_error.rst
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@ -34,7 +34,7 @@ configuration. This compute is only really useful for debugging the
hourglass control mechanism which is part of the Total-Lagrangian SPH
pair style.
See `this PDF guide <PDF/SMD_LAMMPS_userguide.pdf>`_ to use Smooth
See `this PDF guide <PDF/MACHDYN_LAMMPS_userguide.pdf>`_ to use Smooth
Mach Dynamics in LAMMPS.
**Output Info:**

2
doc/src/compute_smd_internal_energy.rst
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@ -26,7 +26,7 @@ Description
Define a computation which outputs the per-particle enthalpy, i.e.,
the sum of potential energy and heat.
See `this PDF guide <PDF/SMD_LAMMPS_userguide.pdf>`_ to use Smooth
See `this PDF guide <PDF/MACHDYN_LAMMPS_userguide.pdf>`_ to use Smooth
Mach Dynamics in LAMMPS.
Output Info

2
doc/src/compute_smd_plastic_strain.rst
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@ -27,7 +27,7 @@ Define a computation that outputs the equivalent plastic strain per
particle. This command is only meaningful if a material model with
plasticity is defined.
See `this PDF guide <PDF/SMD_LAMMPS_userguide.pdf>`_ to use Smooth
See `this PDF guide <PDF/MACHDYN_LAMMPS_userguide.pdf>`_ to use Smooth
Mach Dynamics in LAMMPS.
**Output Info:**

2
doc/src/compute_smd_plastic_strain_rate.rst
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@ -27,7 +27,7 @@ Define a computation that outputs the time rate of the equivalent
plastic strain. This command is only meaningful if a material model
with plasticity is defined.
See `this PDF guide <PDF/SMD_LAMMPS_userguide.pdf>`_ to use Smooth
See `this PDF guide <PDF/MACHDYN_LAMMPS_userguide.pdf>`_ to use Smooth
Mach Dynamics in LAMMPS.
**Output Info:**

2
doc/src/compute_smd_rho.rst
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@ -28,7 +28,7 @@ The mass density is the mass of a particle which is constant during
the course of a simulation, divided by its volume, which can change
due to mechanical deformation.
See `this PDF guide <PDF/SMD_LAMMPS_userguide.pdf>`_ to use Smooth
See `this PDF guide <PDF/MACHDYN_LAMMPS_userguide.pdf>`_ to use Smooth
Mach Dynamics in LAMMPS.
Output info

2
doc/src/compute_smd_tlsph_defgrad.rst
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@ -27,7 +27,7 @@ Define a computation that calculates the deformation gradient. It is
only meaningful for particles which interact according to the
Total-Lagrangian SPH pair style.
See `this PDF guide <PDF/SMD_LAMMPS_userguide.pdf>`_ to use Smooth
See `this PDF guide <PDF/MACHDYN_LAMMPS_userguide.pdf>`_ to use Smooth
Mach Dynamics in LAMMPS.
Output info

2
doc/src/compute_smd_tlsph_dt.rst
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@ -32,7 +32,7 @@ time step. This calculation is performed automatically in the
relevant SPH pair styles and this compute only serves to make the
stable time increment accessible for output purposes.
See `this PDF guide <PDF/SMD_LAMMPS_userguide.pdf>`_ to using Smooth
See `this PDF guide <PDF/MACHDYN_LAMMPS_userguide.pdf>`_ to using Smooth
Mach Dynamics in LAMMPS.
Output info

2
doc/src/compute_smd_tlsph_num_neighs.rst
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@ -27,7 +27,7 @@ Define a computation that calculates the number of particles inside of
the smoothing kernel radius for particles interacting via the
Total-Lagrangian SPH pair style.
See `this PDF guide <PDF/SMD_LAMMPS_userguide.pdf>`_ to using Smooth
See `this PDF guide <PDF/MACHDYN_LAMMPS_userguide.pdf>`_ to using Smooth
Mach Dynamics in LAMMPS.
Output info

2
doc/src/compute_smd_tlsph_shape.rst
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@ -28,7 +28,7 @@ associated with a particle as a rotated ellipsoid. It is only
meaningful for particles which interact according to the
Total-Lagrangian SPH pair style.
See `this PDF guide <PDF/SMD_LAMMPS_userguide.pdf>`_ to use Smooth
See `this PDF guide <PDF/MACHDYN_LAMMPS_userguide.pdf>`_ to use Smooth
Mach Dynamics in LAMMPS.
Output info

2
doc/src/compute_smd_tlsph_strain.rst
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@ -26,7 +26,7 @@ Description
Define a computation that calculates the Green-Lagrange strain tensor
for particles interacting via the Total-Lagrangian SPH pair style.
See `this PDF guide <PDF/SMD_LAMMPS_userguide.pdf>`_ to using Smooth
See `this PDF guide <PDF/MACHDYN_LAMMPS_userguide.pdf>`_ to using Smooth
Mach Dynamics in LAMMPS.
Output info

2
doc/src/compute_smd_tlsph_strain_rate.rst
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@ -26,7 +26,7 @@ Description
Define a computation that calculates the rate of the strain tensor for
particles interacting via the Total-Lagrangian SPH pair style.
See `this PDF guide <PDF/SMD_LAMMPS_userguide.pdf>`_ to using Smooth
See `this PDF guide <PDF/MACHDYN_LAMMPS_userguide.pdf>`_ to using Smooth
Mach Dynamics in LAMMPS.
Output info

2
doc/src/compute_smd_tlsph_stress.rst
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@ -26,7 +26,7 @@ Description
Define a computation that outputs the Cauchy stress tensor for
particles interacting via the Total-Lagrangian SPH pair style.
See `this PDF guide <PDF/SMD_LAMMPS_userguide.pdf>`_ to using Smooth
See `this PDF guide <PDF/MACHDYN_LAMMPS_userguide.pdf>`_ to using Smooth
Mach Dynamics in LAMMPS.
Output info

2
doc/src/compute_smd_triangle_vertices.rst
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@ -26,7 +26,7 @@ Description
Define a computation that returns the coordinates of the vertices
corresponding to the triangle-elements of a mesh created by the :doc:`fix smd/wall_surface <fix_smd_wall_surface>`.
See `this PDF guide <PDF/SMD_LAMMPS_userguide.pdf>`_ to using Smooth
See `this PDF guide <PDF/MACHDYN_LAMMPS_userguide.pdf>`_ to using Smooth
Mach Dynamics in LAMMPS.
Output info

2
doc/src/compute_smd_ulsph_effm.rst
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@ -26,7 +26,7 @@ Description
Define a computation that outputs the effective shear modulus for
particles interacting via the updated Lagrangian SPH pair style.
See `this PDF guide <PDF/SMD_LAMMPS_userguide.pdf>`_ to using Smooth
See `this PDF guide <PDF/MACHDYN_LAMMPS_userguide.pdf>`_ to using Smooth
Mach Dynamics in LAMMPS.
Output info

2
doc/src/compute_smd_ulsph_num_neighs.rst
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@ -27,7 +27,7 @@ Define a computation that returns the number of neighbor particles
inside of the smoothing kernel radius for particles interacting via
the updated Lagrangian SPH pair style.
See `this PDF guide <PDF/SMD_LAMMPS_userguide.pdf>`_ to using Smooth
See `this PDF guide <PDF/MACHDYN_LAMMPS_userguide.pdf>`_ to using Smooth
Mach Dynamics in LAMMPS.
Output info

2
doc/src/compute_smd_ulsph_strain.rst
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@ -26,7 +26,7 @@ Description
Define a computation that outputs the logarithmic strain tensor. for
particles interacting via the updated Lagrangian SPH pair style.
See `this PDF guide <PDF/SMD_LAMMPS_userguide.pdf>`_ to using Smooth
See `this PDF guide <PDF/MACHDYN_LAMMPS_userguide.pdf>`_ to using Smooth
Mach Dynamics in LAMMPS.
Output info

2
doc/src/compute_smd_ulsph_strain_rate.rst
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@ -27,7 +27,7 @@ Define a computation that outputs the rate of the logarithmic strain
tensor for particles interacting via the updated Lagrangian SPH pair
style.
See `this PDF guide <PDF/SMD_LAMMPS_userguide.pdf>`_ to using Smooth
See `this PDF guide <PDF/MACHDYN_LAMMPS_userguide.pdf>`_ to using Smooth
Mach Dynamics in LAMMPS.
Output info

2
doc/src/compute_smd_ulsph_stress.rst
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@ -25,7 +25,7 @@ Description
Define a computation that outputs the Cauchy stress tensor.
See `this PDF guide <PDF/SMD_LAMMPS_userguide.pdf>`_ to using Smooth
See `this PDF guide <PDF/MACHDYN_LAMMPS_userguide.pdf>`_ to using Smooth
Mach Dynamics in LAMMPS.
Output info

2
doc/src/compute_smd_vol.rst
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@ -26,7 +26,7 @@ Description
Define a computation that provides the per-particle volume and the sum
of the per-particle volumes of the group for which the fix is defined.
See `this PDF guide <PDF/SMD_LAMMPS_userguide.pdf>`_ to using Smooth
See `this PDF guide <PDF/MACHDYN_LAMMPS_userguide.pdf>`_ to using Smooth
Mach Dynamics in LAMMPS.
Output info

2
doc/src/fix_ave_spatial.rst
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@ -2,7 +2,7 @@ Fix ave/spatial command
=======================
.. meta::
:http-equiv=Refresh: 5; url='https://docs.lammps.org/Commands_removed.html#fix-ave-spatial-and-fix-ave-spatial-sphere'
:http-equiv=Refresh: 5; url=Commands_removed.html#fix-ave-spatial-and-fix-ave-spatial-sphere
.. deprecated:: 11Dec2015

2
doc/src/fix_ave_spatial_sphere.rst
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@ -2,7 +2,7 @@ Fix ave/spatial command
=======================
.. meta::
:http-equiv=Refresh: 5; url='https://docs.lammps.org/Commands_removed.html#fix-ave-spatial-and-fix-ave-spatial-sphere'
:http-equiv=Refresh: 5; url=https://docs.lammps.org/Commands_removed.html#fix-ave-spatial-and-fix-ave-spatial-sphere
.. deprecated:: 11Dec2015

2
doc/src/fix_smd_adjust_dt.rst
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@ -43,7 +43,7 @@ This fix inquires the minimum stable time increment across all
particles contained in the group for which this fix is defined. An
additional safety factor *s_fact* is applied to the time increment.
See `this PDF guide <PDF/SMD_LAMMPS_userguide.pdf>`_ to use Smooth Mach
See `this PDF guide <PDF/MACHDYN_LAMMPS_userguide.pdf>`_ to use Smooth Mach
Dynamics in LAMMPS.
Restart, fix_modify, output, run start/stop, minimize info

2
doc/src/fix_smd_integrate_tlsph.rst
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@ -34,7 +34,7 @@ Description
The fix performs explicit time integration for particles which
interact according with the Total-Lagrangian SPH pair style.
See `this PDF guide <PDF/SMD_LAMMPS_userguide.pdf>`_ to using Smooth Mach
See `this PDF guide <PDF/MACHDYN_LAMMPS_userguide.pdf>`_ to using Smooth Mach
Dynamics in LAMMPS.
The *limit_velocity* keyword will control the velocity, scaling the

2
doc/src/fix_smd_integrate_ulsph.rst
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@ -36,7 +36,7 @@ Description
The fix performs explicit time integration for particles which
interact with the updated Lagrangian SPH pair style.
See `this PDF guide <PDF/SMD_LAMMPS_userguide.pdf>`_ to using Smooth Mach
See `this PDF guide <PDF/MACHDYN_LAMMPS_userguide.pdf>`_ to using Smooth Mach
Dynamics in LAMMPS.
The *adjust_radius* keyword activates dynamic adjustment of the

2
doc/src/fix_smd_move_triangulated_surface.rst
View File

@ -60,7 +60,7 @@ particle to (omega cross Rperp) where omega is its angular velocity
around the rotation axis and Rperp is a perpendicular vector from the
rotation axis to the particle.
See `this PDF guide <PDF/SMD_LAMMPS_userguide.pdf>`_ to using Smooth Mach
See `this PDF guide <PDF/MACHDYN_LAMMPS_userguide.pdf>`_ to using Smooth Mach
Dynamics in LAMMPS.
Restart, fix_modify, output, run start/stop, minimize info

2
doc/src/fix_smd_wall_surface.rst
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@ -47,7 +47,7 @@ be run for 0 timesteps in order to properly register the new particles
in the system. See the "funnel_flow" example in the MACHDYN examples
directory.
See `this PDF guide <PDF/SMD_LAMMPS_userguide.pdf>`_ to use Smooth Mach
See `this PDF guide <PDF/MACHDYN_LAMMPS_userguide.pdf>`_ to use Smooth Mach
Dynamics in LAMMPS.
Restart, fix_modify, output, run start/stop, minimize info

2
doc/src/pair_smd_tlsph.rst
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@ -48,7 +48,7 @@ and a material model to compute shear stresses (the off-diagonal
components of the stress tensor). Damage and failure models can also
be added.
Please see the `SMD user guide <PDF/SMD_LAMMPS_userguide.pdf>`_ for a
Please see the `SMD user guide <PDF/MACHDYN_LAMMPS_userguide.pdf>`_ for a
complete listing of the possible keywords and material models.
----------

2
doc/src/pair_smd_ulsph.rst
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@ -59,7 +59,7 @@ Note that the use of \*GRADIENT_CORRECTION can lead to severe numerical
instabilities. For a general fluid simulation, \*NO_GRADIENT_CORRECTION
is recommended.
Please see the `SMD user guide <PDF/SMD_LAMMPS_userguide.pdf>`_ for a
Please see the `SMD user guide <PDF/MACHDYN_LAMMPS_userguide.pdf>`_ for a
complete listing of the possible keywords and material models.
----------

2
src/library.cpp
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@ -5302,7 +5302,7 @@ int lammps_config_has_jpeg_support() {
\verbatim embed:rst
The LAMMPS :doc:`dump style movie <dump_image>` supports generating movies
from images on-the-fly via creating a pipe to the
`ffmpeg <https://ffmpeg.org/ffmpeg/>`_ program.
`ffmpeg <https://ffmpeg.org/>`_ program.
This function checks whether this feature was :ref:`enabled at compile time <graphics>`.
It does **not** check whether the ``ffmpeg`` itself is installed and usable.
\endverbatim