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correct malformed tables

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This commit is contained in:
Axel Kohlmeyer
2020-01-24 12:30:15 -05:00
parent c9cc13c2a6
commit 0302c0ba24
4 changed files with 23 additions and 29 deletions
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2
doc/src/Howto_output.rst
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@ -304,7 +304,7 @@ vector input could be a column of an array.
+--------------------------------------------------------+----------------------------------------------+-------------------------------------------+
| Command | Input | Output |
+--------------------------------------------------------+----------------------------------------------+-------------------------------------------+
| :doc:`thermo_style custom <thermo_style>` | global scalars | screen, log file |
| :doc:`thermo_style custom <thermo_style>` | global scalars | screen, log file |
+--------------------------------------------------------+----------------------------------------------+-------------------------------------------+
| :doc:`dump custom <dump>` | per-atom vectors | dump file |
+--------------------------------------------------------+----------------------------------------------+-------------------------------------------+

16
doc/src/Packages_standard.rst
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@ -29,29 +29,29 @@ package:
+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`BODY <PKG-BODY>` | body-style particles | :doc:`Howto body <Howto_body>` | body | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`CLASS2 <PKG-CLASS2>` | class 2 force fields | :doc:`pair_style lj/class2 <pair_class2>` | n/a | no |
| :ref:`CLASS2 <PKG-CLASS2>` | class 2 force fields | :doc:`pair_style lj/class2 <pair_class2>` | n/a | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`COLLOID <PKG-COLLOID>` | colloidal particles | :doc:`atom_style colloid <atom_style>` | colloid | no |
| :ref:`COLLOID <PKG-COLLOID>` | colloidal particles | :doc:`atom_style colloid <atom_style>` | colloid | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`COMPRESS <PKG-COMPRESS>` | I/O compression | :doc:`dump \*/gz <dump>` | n/a | sys |
+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`CORESHELL <PKG-CORESHELL>` | adiabatic core/shell model | :doc:`Howto coreshell <Howto_coreshell>` | coreshell | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`DIPOLE <PKG-DIPOLE>` | point dipole particles | :doc:`pair_style dipole/cut <pair_dipole>` | dipole | no |
| :ref:`DIPOLE <PKG-DIPOLE>` | point dipole particles | :doc:`pair_style dipole/cut <pair_dipole>` | dipole | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`GPU <PKG-GPU>` | GPU-enabled styles | :doc:`Section gpu <Speed_gpu>` | `Benchmarks <http://lammps.sandia.gov/bench.html>`_ | int |
+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`GRANULAR <PKG-GRANULAR>` | granular systems | :doc:`Howto granular <Howto_granular>` | pour | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`KIM <PKG-KIM>` | OpenKIM wrapper | :doc:`pair_style kim <pair_kim>` | kim | ext |
| :ref:`KIM <PKG-KIM>` | OpenKIM wrapper | :doc:`pair_style kim <pair_kim>` | kim | ext |
+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`KOKKOS <PKG-KOKKOS>` | Kokkos-enabled styles | :doc:`Speed kokkos <Speed_kokkos>` | `Benchmarks <http://lammps.sandia.gov/bench.html>`_ | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`KSPACE <PKG-KSPACE>` | long-range Coulombic solvers | :doc:`kspace_style <kspace_style>` | peptide | no |
| :ref:`KSPACE <PKG-KSPACE>` | long-range Coulombic solvers | :doc:`kspace_style <kspace_style>` | peptide | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`LATTE <PKG-LATTE>` | quantum DFTB forces via LATTE | :doc:`fix latte <fix_latte>` | latte | ext |
+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`MANYBODY <PKG-MANYBODY>` | many-body potentials | :doc:`pair_style tersoff <pair_tersoff>` | shear | no |
| :ref:`MANYBODY <PKG-MANYBODY>` | many-body potentials | :doc:`pair_style tersoff <pair_tersoff>` | shear | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`MC <PKG-MC>` | Monte Carlo options | :doc:`fix gcmc <fix_gcmc>` | n/a | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
@ -67,7 +67,7 @@ package:
+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`OPT <PKG-OPT>` | optimized pair styles | :doc:`Speed opt <Speed_opt>` | `Benchmarks <http://lammps.sandia.gov/bench.html>`_ | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`PERI <PKG-PERI>` | Peridynamics models | :doc:`pair_style peri <pair_peri>` | peri | no |
| :ref:`PERI <PKG-PERI>` | Peridynamics models | :doc:`pair_style peri <pair_peri>` | peri | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`POEMS <PKG-POEMS>` | coupled rigid body motion | :doc:`fix poems <fix_poems>` | rigid | int |
+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
@ -81,7 +81,7 @@ package:
+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`SHOCK <PKG-SHOCK>` | shock loading methods | :doc:`fix msst <fix_msst>` | n/a | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`SNAP <PKG-SNAP>` | quantum-fitted potential | :doc:`pair_style snap <pair_snap>` | snap | no |
| :ref:`SNAP <PKG-SNAP>` | quantum-fitted potential | :doc:`pair_style snap <pair_snap>` | snap | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`SPIN <PKG-SPIN>` | magnetic atomic spin dynamics | :doc:`Howto spins <Howto_spins>` | SPIN | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+

32
doc/src/Packages_user.rst
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@ -35,13 +35,13 @@ package:
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`USER-ATC <PKG-USER-ATC>` | Atom-to-Continuum coupling | :doc:`fix atc <fix_atc>` | USER/atc | int |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`USER-AWPMD <PKG-USER-AWPMD>` | wave packet MD | :doc:`pair_style awpmd/cut <pair_awpmd>` | USER/awpmd | int |
| :ref:`USER-AWPMD <PKG-USER-AWPMD>` | wave packet MD | :doc:`pair_style awpmd/cut <pair_awpmd>` | USER/awpmd | int |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`USER-BOCS <PKG-USER-BOCS>` | BOCS bottom up coarse graining | :doc:`fix bocs <fix_bocs>` | USER/bocs | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`USER-CGDNA <PKG-USER-CGDNA>` | coarse-grained DNA force fields | src/USER-CGDNA/README | USER/cgdna | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`USER-CGSDK <PKG-USER-CGSDK>` | SDK coarse-graining model | :doc:`pair_style lj/sdk <pair_sdk>` | USER/cgsdk | no |
| :ref:`USER-CGSDK <PKG-USER-CGSDK>` | SDK coarse-graining model | :doc:`pair_style lj/sdk <pair_sdk>` | USER/cgsdk | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`USER-COLVARS <PKG-USER-COLVARS>` | collective variables library | :doc:`fix colvars <fix_colvars>` | USER/colvars | int |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
@ -51,7 +51,7 @@ package:
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`USER-DRUDE <PKG-USER-DRUDE>` | Drude oscillators | :doc:`Howto drude <Howto_drude>` | USER/drude | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`USER-EFF <PKG-USER-EFF>` | electron force field | :doc:`pair_style eff/cut <pair_eff>` | USER/eff | no |
| :ref:`USER-EFF <PKG-USER-EFF>` | electron force field | :doc:`pair_style eff/cut <pair_eff>` | USER/eff | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`USER-FEP <PKG-USER-FEP>` | free energy perturbation | :doc:`compute fep <compute_fep>` | USER/fep | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
@ -63,15 +63,15 @@ package:
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`USER-MANIFOLD <PKG-USER-MANIFOLD>` | motion on 2d surfaces | :doc:`fix manifoldforce <fix_manifoldforce>` | USER/manifold | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`USER-MEAMC <PKG-USER-MEAMC>` | modified EAM potential (C++) | :doc:`pair_style meam/c <pair_meamc>` | meamc | no |
| :ref:`USER-MEAMC <PKG-USER-MEAMC>` | modified EAM potential (C++) | :doc:`pair_style meam/c <pair_meamc>` | meamc | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`USER-MESO <PKG-USER-MESO>` | mesoscale DPD models | :doc:`pair_style edpd <pair_meso>` | USER/meso | no |
| :ref:`USER-MESO <PKG-USER-MESO>` | mesoscale DPD models | :doc:`pair_style edpd <pair_meso>` | USER/meso | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`USER-MGPT <PKG-USER-MGPT>` | fast MGPT multi-ion potentials | :doc:`pair_style mgpt <pair_mgpt>` | USER/mgpt | no |
| :ref:`USER-MGPT <PKG-USER-MGPT>` | fast MGPT multi-ion potentials | :doc:`pair_style mgpt <pair_mgpt>` | USER/mgpt | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`USER-MISC <PKG-USER-MISC>` | single-file contributions | USER-MISC/README | USER/misc | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`USER-MOFFF <PKG-USER-MOFFF>` | styles for `MOF-FF <MOFplus_>`_ force field | :doc:`pair_style buck6d/coul/gauss <pair_buck6d_coul_gauss>` | USER/mofff | no |
| :ref:`USER-MOFFF <PKG-USER-MOFFF>` | styles for `MOF-FF <MOFplus_>`_ force field | :doc:`pair_style buck6d/coul/gauss <pair_buck6d_coul_gauss>` | USER/mofff | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`USER-MOLFILE <PKG-USER-MOLFILE>` | `VMD <https://www.ks.uiuc.edu/Research/vmd/>`_ molfile plug-ins | :doc:`dump molfile <dump_molfile>` | n/a | ext |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
@ -89,17 +89,17 @@ package:
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`USER-QTB <PKG-USER-QTB>` | quantum nuclear effects | :doc:`fix qtb <fix_qtb>` :doc:`fix qbmsst <fix_qbmsst>` | qtb | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`USER-QUIP <PKG-USER-QUIP>` | QUIP/libatoms interface | :doc:`pair_style quip <pair_quip>` | USER/quip | ext |
| :ref:`USER-QUIP <PKG-USER-QUIP>` | QUIP/libatoms interface | :doc:`pair_style quip <pair_quip>` | USER/quip | ext |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`USER-REAXC <PKG-USER-REAXC>` | ReaxFF potential (C/C++) | :doc:`pair_style reaxc <pair_reaxc>` | reax | no |
| :ref:`USER-REAXC <PKG-USER-REAXC>` | ReaxFF potential (C/C++) | :doc:`pair_style reaxc <pair_reaxc>` | reax | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`USER-SCAFACOS <PKG-USER-SCAFACOS>` | wrapper on ScaFaCoS solver | :doc:`kspace_style scafacos <kspace_style>` | USER/scafacos | ext |
| :ref:`USER-SCAFACOS <PKG-USER-SCAFACOS>` | wrapper on ScaFaCoS solver | :doc:`kspace_style scafacos <kspace_style>` | USER/scafacos | ext |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`USER-SDPD <PKG-USER-SDPD>` | smoothed dissipative particle dynamics | :doc:`pair_style sdpd/taitwater/isothermal <pair_sdpd_taitwater_isothermal>` | USER/sdpd | no |
| :ref:`USER-SDPD <PKG-USER-SDPD>` | smoothed dissipative particle dynamics | :doc:`pair_style sdpd/taitwater/isothermal <pair_sdpd_taitwater_isothermal>` | USER/sdpd | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`USER-SMD <PKG-USER-SMD>` | smoothed Mach dynamics | `SMD User Guide <PDF/SMD_LAMMPS_userguide.pdf>`_ | USER/smd | ext |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`USER-SMTBQ <PKG-USER-SMTBQ>` | second moment tight binding QEq potential | :doc:`pair_style smtbq <pair_smtbq>` | USER/smtbq | no |
| :ref:`USER-SMTBQ <PKG-USER-SMTBQ>` | second moment tight binding QEq potential | :doc:`pair_style smtbq <pair_smtbq>` | USER/smtbq | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`USER-SPH <PKG-USER-SPH>` | smoothed particle hydrodynamics | `SPH User Guide <PDF/SPH_LAMMPS_userguide.pdf>`_ | USER/sph | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
@ -109,18 +109,12 @@ package:
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`USER-VTK <PKG-USER-VTK>` | dump output via VTK | :doc:`compute vtk <dump_vtk>` | n/a | ext |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`USER-YAFF <PKG-USER-YAFF>` | additional styles implemented in YAFF | :doc:`angle_style cross <angle_cross>` | USER/yaff | no |
| :ref:`USER-YAFF <PKG-USER-YAFF>` | additional styles implemented in YAFF | :doc:`angle_style cross <angle_cross>` | USER/yaff | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
.. _MOFplus: https://www.mofplus.org/content/show/MOF-FF
.. _PLUMED: http://www.plumed.org
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

2
doc/src/Tools.rst
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@ -60,7 +60,7 @@ Post-processing tools
+--------------------------+----------------------------+------------------------+--------------------------+-------------------------------+-----------------------------+
| :ref:`amber2lmp <amber>` | :ref:`binary2txt <binary>` | :ref:`ch2lmp <charmm>` | :ref:`colvars <colvars>` | :ref:`eff <eff>` | :ref:`fep <fep>` |
+--------------------------+----------------------------+------------------------+--------------------------+-------------------------------+-----------------------------+
| :ref:`lmp2arc <arc>` | :ref:`lmp2cfg <cfg>` | :ref:`matlab <matlab>` | :ref:`phonon <phonon>` | :ref:`pymol_asphere <pymol>` | :ref:`python <pythontools>` |
| :ref:`lmp2arc <arc>` | :ref:`lmp2cfg <cfg>` | :ref:`matlab <matlab>` | :ref:`phonon <phonon>` | :ref:`pymol_asphere <pymol>` | :ref:`python <pythontools>` |
+--------------------------+----------------------------+------------------------+--------------------------+-------------------------------+-----------------------------+
| :ref:`reax <reax_tool>` | :ref:`replica <replica>` | :ref:`smd <smd>` | :ref:`spin <spin>` | :ref:`xmgrace <xmgrace>` | |
+--------------------------+----------------------------+------------------------+--------------------------+-------------------------------+-----------------------------+