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Merge remote-tracking branch 'github/master' into Ncreate_atoms

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# Conflicts:
#	src/create_atoms.cpp
This commit is contained in:
Axel Kohlmeyer
2020-01-21 15:52:01 -05:00
parent 646dc83394 7728c5069f
commit a6f59a8607
25 changed files with 65 additions and 68 deletions
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12
doc/src/Commands_all.rst
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@ -132,10 +132,8 @@ An alphabetic list of all general LAMMPS commands.
* :doc:`units <units>`
* :doc:`variable <variable>`
* :doc:`velocity <velocity>`
* :doc:`write\_coeff <write_coeff>`
* :doc:`write\_data <write_data>`
* :doc:`write\_dump <write_dump>`
* :doc:`write\_restart <write_restart>`
*
*
*
* :doc:`write_coeff <write_coeff>`
* :doc:`write_data <write_data>`
* :doc:`write_dump <write_dump>`
* :doc:`write_restart <write_restart>`

5
doc/src/Commands_bond.rst
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@ -47,7 +47,6 @@ OPT.
* :doc:`oxrna2/fene <bond_oxdna>`
* :doc:`quartic (o) <bond_quartic>`
* :doc:`table (o) <bond_table>`
*
.. _angle:
@ -89,7 +88,6 @@ OPT.
* :doc:`quartic (o) <angle_quartic>`
* :doc:`sdk (o) <angle_sdk>`
* :doc:`table (o) <angle_table>`
*
.. _dihedral:
@ -127,8 +125,6 @@ OPT.
* :doc:`spherical <dihedral_spherical>`
* :doc:`table (o) <dihedral_table>`
* :doc:`table/cut <dihedral_table_cut>`
*
*
.. _improper:
@ -162,4 +158,3 @@ OPT.
* :doc:`ring (o) <improper_ring>`
* :doc:`sqdistharm <improper_sqdistharm>`
* :doc:`umbrella (o) <improper_umbrella>`
*

4
doc/src/Commands_compute.rst
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@ -163,6 +163,4 @@ KOKKOS, o = USER-OMP, t = OPT.
* :doc:`vcm/chunk <compute_vcm_chunk>`
* :doc:`voronoi/atom <compute_voronoi_atom>`
* :doc:`xrd <compute_xrd>`
*
*
*

4
doc/src/Commands_fix.rst
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@ -240,7 +240,3 @@ OPT.
* :doc:`wall/region <fix_wall_region>`
* :doc:`wall/region/ees <fix_wall_ees>`
* :doc:`wall/srd <fix_wall_srd>`
*
*
*
*

1
doc/src/Commands_kspace.rst
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@ -37,4 +37,3 @@ OPT.
* :doc:`pppm/stagger <kspace_style>`
* :doc:`pppm/tip4p (o) <kspace_style>`
* :doc:`scafacos <kspace_style>`
*

1
doc/src/Commands_pair.rst
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@ -257,4 +257,3 @@ OPT.
* :doc:`yukawa (gko) <pair_yukawa>`
* :doc:`yukawa/colloid (go) <pair_yukawa_colloid>`
* :doc:`zbl (gko) <pair_zbl>`
*

8
doc/src/_ext/table_from_list.py
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@ -1,6 +1,6 @@
from docutils import nodes
from sphinx.util.docutils import SphinxDirective
from docutils.nodes import Element, Node
from docutils.nodes import Element, Node, list_item
from typing import Any, Dict, List
from sphinx import addnodes
from sphinx.util import logging
@ -26,8 +26,12 @@ class TableFromList(SphinxDirective):
raise SphinxError('table_from_list content is not a list')
fulllist = node.children[0]
# fill list with empty items to have a number of entries
# that is divisible by ncolumns
if (len(fulllist) % ncolumns) != 0:
raise SphinxError('number of list elements not a multiple of column number')
missing = int(ncolumns - (len(fulllist) % ncolumns))
for i in range(0,missing):
fulllist += list_item()
table = nodes.table()
tgroup = nodes.tgroup(cols=ncolumns)

2
doc/src/pair_lj.rst
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@ -97,7 +97,7 @@ pair\_style lj/cut/tip4p/long command
=====================================
pair\_style lj/cut/tip4p/long/gpu command
========================================
=========================================
pair\_style lj/cut/tip4p/long/omp command
=========================================

2
doc/src/read_dump.rst
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@ -144,7 +144,7 @@ i.e. the current directory.
The *adios* format supports reading data that was written by the
:doc:`dump adios <dump_adios>` command. The
entire dump is read in parallel across all the processes, dividing
the atoms evenly amongs the processes. The number of writers that
the atoms evenly among the processes. The number of writers that
has written the dump file does not matter. Using the adios style for
dump and read_dump is a convenient way to dump all atoms from *N*
writers and read it back by *M* readers. If one is running two