diff --git a/doc/src/Build_extras.rst b/doc/src/Build_extras.rst index fe974278eb..0cc90fdeba 100644 --- 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 ` * :ref:`USER-H5MD ` * :ref:`USER-INTEL ` + * :ref:`USER-MESONT ` * :ref:`USER-MOLFILE ` * :ref:`USER-NETCDF ` * :ref:`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 diff --git a/doc/src/Packages_details.rst b/doc/src/Packages_details.rst index 372df3e98b..0ed15a0799 100644 --- 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 +` is a (minimal) C++ implementation, and :doc:`pair_style +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 ` * :doc:`pair_style mesont/tpm ` * :doc:`compute mesont ` +* :doc:`pair_style mesocnt ` * examples/USER/mesont * tools/mesont diff --git a/doc/src/Packages_user.rst b/doc/src/Packages_user.rst index 563e0cf211..1d07539022 100644 --- a/doc/src/Packages_user.rst +++ b/doc/src/Packages_user.rst @@ -67,7 +67,7 @@ package: +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ | :ref:`USER-MESODPD ` | mesoscale DPD models | :doc:`pair_style edpd ` | USER/mesodpd | no | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-MESONT ` | mesoscopic tubular potential model for nanotubes | :doc:`pair_style mesont/tpm ` | USER/mesont | int | +| :ref:`USER-MESONT ` | mesoscopic tubular potential model for nanotubes | pair style :doc:`mesont/tpm `, :doc:`mesocnt ` | USER/mesont | int | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ | :ref:`USER-MGPT ` | fast MGPT multi-ion potentials | :doc:`pair_style mgpt ` | USER/mgpt | no | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt index addc74f618..d6804f1b3b 100644 --- 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 diff --git a/src/USER-MISC/README b/src/USER-MISC/README index 950ef3845d..e10d4c7904 100644 --- 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