fully integrate and update USER-MESONT docs. Add notes about C++ pair style... (497e30af) · Commits · 郑智淋 / lammps

doc/src/Build_extras.rst

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		@@ -44,6 +44,7 @@ This is the list of packages that may require additional steps.
		* :ref:`USER-COLVARS <user-colvars>`
		* :ref:`USER-H5MD <user-h5md>`
		* :ref:`USER-INTEL <user-intel>`
		* :ref:`USER-MESONT <user-mesont>`
		* :ref:`USER-MOLFILE <user-molfile>`
		* :ref:`USER-NETCDF <user-netcdf>`
		* :ref:`USER-PLUMED <user-plumed>`
		@@ -1275,6 +1276,45 @@ For KNLs:

		----------

		.. _user-mesont:

		USER-MESONT package
		-------------------------

		This package includes a library written in Fortran 90 in the
		``lib/mesont`` folder, so a working Fortran 90 compiler is required to
		compile it. Also, the files with the force field data for running the
		bundled examples are not included in the source distribution. Instead
		they will be downloaded the first time this package is installed.

		CMake build\ :

		No additional settings are needed besides ``-D PKG_USER-MESONT=yes``

		Traditional make\ :

		Before building LAMMPS, you must build the mesont library in ``lib/mesont``\ .
		You can also do it in one step from the ``lammps/src`` dir, using a command like
		these, which simply invoke the ``lib/mesont/Install.py`` script with the specified
		args:

		.. code-block:: bash

		$ make lib-mesont # print help message
		$ make lib-mesont args="-m gfortran" # build with GNU g++ compiler (settings as with "make serial")
		$ make lib-mesont args="-m ifort" # build with Intel icc compiler

		The build should produce two files: ``lib/mesont/libmesont.a`` and
		``lib/mesont/Makefile.lammps``\ . The latter is copied from an existing
		``Makefile.lammps.\*`` and has settings needed to build LAMMPS with the
		mesont library (though typically the settings contain only the Fortran
		runtime library). If necessary, you can edit/create a new
		``lib/mesont/Makefile.machine`` file for your system, which should
		define an ``EXTRAMAKE`` variable to specify a corresponding
		``Makefile.lammps.machine`` file.

		----------

		.. _user-molfile:

		USER-MOLFILE package

doc/src/Packages_details.rst

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		@@ -1725,16 +1725,32 @@ USER-MESONT package

		Contents:

		USER-MESONT is a LAMMPS package for simulation of nanomechanics of carbon
		USER-MESONT is a LAMMPS package for simulation of nanomechanics of
		nanotubes (NTs). The model is based on a coarse-grained representation
		of CNTs as "flexible cylinders" consisting of a variable number of
		segments. Internal interactions within a CNT and the van der Waals
		interaction between the tubes are described by a mesoscopic force
		field designed and parameterized based on the results of atomic-level
		molecular dynamics simulations. The description of the force field
		is provided in the papers listed below.
		of NTs as "flexible cylinders" consisting of a variable number of
		segments. Internal interactions within a NT and the van der Waals
		interaction between the tubes are described by a mesoscopic force field
		designed and parameterized based on the results of atomic-level
		molecular dynamics simulations. The description of the force field is
		provided in the papers listed below. This package contains two
		independent implementations of this model: :doc:`pair_style mesocnt
		<pair_mesocnt>` is a (minimal) C++ implementation, and :doc:`pair_style
		mesont/tpm <pair_mesont_tpm>` is a more general and feature rich
		implementation based on a Fortran library in the ``lib/mesont`` folder.

		Author: Maxim V. Shugaev (University of Virginia), Alexey N. Volkov (University of Alabama), Leonid V. Zhigilei (University of Virginia)
		Download of potential files:

		The potential files for these pair styles are very large and thus
		are not included in the regular downloaded packages of LAMMPS or the
		git repositories. Instead, they will be automatically downloaded
		from a web server when the package is installed for the first time.

		*Authors of the mesont* styles:**

		Maxim V. Shugaev (University of Virginia), Alexey N. Volkov (University of Alabama), Leonid V. Zhigilei (University of Virginia)

		*Author of the mesocnt* pair style:**
		Philipp Kloza (U Cambridge)

		Supporting info:

		@@ -1743,6 +1759,7 @@ is provided in the papers listed below.
		* :doc:`atom_style mesont <atom_style>`
		* :doc:`pair_style mesont/tpm <pair_mesont_tpm>`
		* :doc:`compute mesont <compute_mesont>`
		* :doc:`pair_style mesocnt <pair_mesocnt>`
		* examples/USER/mesont
		* tools/mesont

doc/src/Packages_user.rst

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		@@ -67,7 +67,7 @@ package:
		+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
		\| :ref:`USER-MESODPD <PKG-USER-MESODPD>` \| mesoscale DPD models \| :doc:`pair_style edpd <pair_mesodpd>` \| USER/mesodpd \| no \|
		+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
		\| :ref:`USER-MESONT <PKG-USER-MESONT>` \| mesoscopic tubular potential model for nanotubes \| :doc:`pair_style mesont/tpm <pair_mesont_tpm>` \| USER/mesont \| int \|
		\| :ref:`USER-MESONT <PKG-USER-MESONT>` \| mesoscopic tubular potential model for nanotubes \| pair style :doc:`mesont/tpm <pair_mesont_tpm>`, :doc:`mesocnt <pair_mesocnt>` \| USER/mesont \| int \|
		+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
		\| :ref:`USER-MGPT <PKG-USER-MGPT>` \| fast MGPT multi-ion potentials \| :doc:`pair_style mgpt <pair_mgpt>` \| USER/mgpt \| no \|
		+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+

doc/utils/sphinx-config/false_positives.txt

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		@@ -1434,6 +1434,7 @@ kk
		Klahn
		Klapp
		Kloss
		Kloza
		kmax
		Kmax
		KMP
		@@ -2277,6 +2278,7 @@ Pettifor
		pfactor
		pgi
		ph
		Philipp
		Phillpot
		Philos
		phiphi

src/USER-MISC/README

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		@@ -97,7 +97,6 @@ pair_style kolmogorov/crespi/full, Wengen Ouyang (Tel Aviv University), w.g.ouya
		pair_style kolmogorov/crespi/z, Jaap Kroes (Radboud U), jaapkroes at gmail dot com, 28 Feb 17
		pair_style meam/spline, Alexander Stukowski (LLNL), alex at stukowski.com, 1 Feb 12
		pair_style meam/sw/spline, Robert Rudd (LLNL), robert.rudd at llnl.gov, 1 Oct 12
		pair_style mesocnt, Philipp Kloza (U Cambridge), pak37 at cam.ac.uk, 15 Jan 20
		pair_style morse/smooth/linear, Stefan Paquay (TU Eindhoven), stefanpaquay at gmail.com, 29 Feb 16
		pair_style srp, Tim Sirk, tim.sirk at us.army.mil, 21 Nov 14
		pair_style tersoff/table, Luca Ferraro, luca.ferraro@caspur.it, 1 Dec 11

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