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fix spelling, formatting, and cross-link/indexing issues

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This commit is contained in:
Axel Kohlmeyer
2022-04-08 18:34:45 -04:00
parent 2c509d96a6
commit 6849356d63
8 changed files with 27 additions and 31 deletions
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2
doc/src/Commands_all.rst
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@ -67,7 +67,7 @@ An alphabetic list of all general LAMMPS commands.
* :doc:`lattice <lattice>`
* :doc:`log <log>`
* :doc:`mass <mass>`
* :doc:`mdi <mdi_engine>`
* :doc:`mdi <mdi>`
* :doc:`message <message>`
* :doc:`minimize <minimize>`
* :doc:`min_modify <min_modify>`

5
doc/src/Howto_client_server.rst
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@ -1,11 +1,6 @@
Using LAMMPS in client/server mode
==================================
.. note::
As of March 2022, this Howto page will soon be deprecated in favor
of the :doc:`Howto mdi <Howto_mdi>` doc page.
Client/server coupling of two codes is where one code is the "client"
and sends request messages to a "server" code. The server responds to
each request with a reply message. This enables the two codes to work

11
doc/src/Howto_mdi.rst
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@ -1,11 +1,6 @@
Using LAMMPS with the MDI library for code coupling
===================================================
.. note::
As of April 2022, this Howto page will soon replace the :doc:`Howto
client/server <Howto_client_server>` doc page.
Client/server coupling of two (or more) codes is where one code is the
"client" and sends request messages (data) to one (or more) "server"
code(s). A server responds to each request with a reply message
@ -69,7 +64,7 @@ enables LAMMPS to operate as an MDI driver and load an MDI engine as a
plugin library.
The package also has a `fix mdi/aimd <fix_mdi_aimd>` command in which
LAMMPS operates as an MDI driver to peform *ab initio* MD simulations
LAMMPS operates as an MDI driver to perform *ab initio* MD simulations
in conjunction with a quantum mechanics code. Its post_force() method
illustrates how a driver issues MDI commands to another code. This
command can be used to couple to an MDI engine which is either a
@ -81,7 +76,7 @@ The examples/mdi directory contains Python scripts and LAMMPS input
script which use LAMMPS as either an MDI driver or engine or both.
Three example use cases are provided:
* Run ab intitio MD (AIMD) using 2 instances of LAMMPS, one as driver
* Run ab initio MD (AIMD) using 2 instances of LAMMPS, one as driver
and one as an engine. As an engine, LAMMPS is a surrogate for a
quantum code.
@ -115,7 +110,7 @@ itself. The list of QCEngine-supported and i-PI-supported quantum
codes is on the `MDI webpage
<https://molssi-mdi.github.io/MDI_Library/html/index.html>`_.
Here is how to build QE as a stand-alond ``pw.x`` file which can be
Here is how to build QE as a stand-alone ``pw.x`` file which can be
used in stand-alone mode:
.. code-block:: bash

2
doc/src/Packages_details.rst
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@ -1412,7 +1412,7 @@ This package has :ref:`specific installation instructions <message>` on the :doc
* src/MDI/README
* lib/mdi/README
* :doc:`Howto MDI <Howto_mdi>`
* :doc:`mdi/engine <mdi_engine>`
* :doc:`mdi <mdi>`
* :doc:`fix mdi/aimd <fix_mdi_aimd>`
* examples/PACKAGES/mdi

2
doc/src/commands_list.rst
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@ -59,7 +59,7 @@ Commands
lattice
log
mass
mdi_engine
mdi
message
min_modify
min_spin

8
doc/src/fix_mdi_aimd.rst
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@ -31,14 +31,14 @@ simulations.
More specifically, this command causes LAMMPS to begin using the `MDI
Library <https://molssi-mdi.github.io/MDI_Library/html/index.html>`_
to run as an MDI driver (client), whicn sends MDI commands to an
to run as an MDI driver (client), which sends MDI commands to an
external MDI engine code (server) which in the case of AIMD is a
quantum mechanics (QM) code, or could be LAMMPS itself, actings as a
quantum mechanics (QM) code, or could be LAMMPS itself, acting as a
surrogate for a QM code. See the :doc:`Howto mdi <Howto_mdi>` page
for more information about how LAMMPS can operate as either an MDI
driver or engine.
The examples/mdi directory contains input scripts perfoming AIMD in
The examples/mdi directory contains input scripts performing AIMD in
this manner with LAMMPS acting as both a driver and an engine
(surrogate for a QM code). The examples/mdi/README file explains how
to launch both driver and engine codes so that they communicate using
@ -70,7 +70,7 @@ input scripts. LAMMPS then begins its timestepping.
At the point in each timestep when LAMMPS needs the force on each
atom, it communicates with the engine code. It sends the current
simulation box size and shape (if they change dynamicaly, e.g. during
simulation box size and shape (if they change dynamically, e.g. during
an NPT simulation), and the current atom coordinates. The engine code
computes quantum forces on each atom and returns them to LAMMPS. If
LAMMPS also needs the system energy and/or virial, it requests those

23
doc/src/mdi.rst
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@ -14,14 +14,15 @@ Syntax
.. parsed-literal::
*engine* args = none
*plugin* args = name keyword value keyword value ...
name = name of plugin library, e.g. lammps means a liblammps.so library will be loaded
keywords = *mdi* or *infile* or *extra* or *command*
*mdi* value = args passed to MDI for driver to operate with plugins
*infile* value = filename the engine will read at start-up
*extra* value = aditional command-line args to pass to engine library when loaded
*command value = a LAMMPS input script command to execute
*engine* args = none
*plugin* args = name keyword value keyword value
name = name of plugin library, e.g. lammps means a liblammps.so library will be loaded
keywords = *mdi* or *infile* or *extra* or *command*
*mdi* value = args passed to MDI for driver to operate with plugins
*infile* value = filename the engine will read at start-up
*extra* value = aditional command-line args to pass to engine library when loaded
*command* value = a LAMMPS input script command to execute
Examples
""""""""
@ -110,9 +111,9 @@ commands, which are described further below.
* - <MASSES
- Request mass of each atom (N values)
* - MD
Perform an MD simulation for N timestpes (most recent >NSTEPS value)
- Perform an MD simulation for N timesteps (most recent >NSTEPS value)
* - OPTG
Perform an energy minimization to convergence (most recent >TOLERANCE values)
- Perform an energy minimization to convergence (most recent >TOLERANCE values)
* - >NATOMS or <NATOMS
- Sends/request number of atoms in the system (1 value)
* - >NSTEPS
@ -157,7 +158,7 @@ more info below.
The MD command performs a simulation using the most recent >NSTEPS
value. The OPTG command performs a minimization using the 4
convergence paremeters from the most recent >TOLERANCE command. The 4
convergence parameters from the most recent >TOLERANCE command. The 4
parameters sent are those used by the :doc:`minimize <minimize>`
command in LAMMPS: etol, ftol, maxiter, and maxeval.

5
doc/utils/sphinx-config/false_positives.txt
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@ -1414,6 +1414,7 @@ initializations
InitiatorIDs
initio
InP
inq
inregion
instantiation
Institut
@ -1735,6 +1736,7 @@ libdl
libfftw
libgcc
libgpu
libinqmdi
libjpeg
libkim
liblammps
@ -1749,6 +1751,7 @@ libplumed
libplumedKernel
libpng
libpoems
libqemdi
libqmmm
librar
libreax
@ -2202,6 +2205,7 @@ Nbondtypes
nBOt
nbrhood
Nbtypes
Nbytes
nc
Nc
nchunk
@ -3644,6 +3648,7 @@ Wittmaack
wn
Wolde
workflow
workflows
Worley
Wriggers
Wuppertal