fully integrate and update USER-MESONT docs. Add notes about C++ pair style and download of potential files

2020-06-12 09:02:56 -04:00
parent 92d54d2764
commit 497e30af82
5 changed files with 69 additions and 11 deletions
--- a/doc/src/Build_extras.rst
+++ b/doc/src/Build_extras.rst
@ -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
--- a/doc/src/Packages_details.rst
+++ b/doc/src/Packages_details.rst
@ -1725,16 +1725,32 @@ USER-MESONT package

 **Contents:**

-USER-MESONT is a LAMMPS package for simulation of nanomechanics of carbon 
-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.
+USER-MESONT is a LAMMPS package for simulation of nanomechanics of
+nanotubes (NTs). The model is based on a coarse-grained representation
+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

--- a/doc/src/Packages_user.rst
+++ b/doc/src/Packages_user.rst
@ -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      |
 +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
--- a/doc/utils/sphinx-config/false_positives.txt
+++ b/doc/utils/sphinx-config/false_positives.txt
@ -1434,6 +1434,7 @@ kk
 Klahn
 Klapp
 Kloss
+Kloza
 kmax
 Kmax
 KMP
@ -2277,6 +2278,7 @@ Pettifor
 pfactor
 pgi
 ph
+Philipp
 Phillpot
 Philos
 phiphi
--- a/src/USER-MISC/README
+++ b/src/USER-MISC/README
@ -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