ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

fix code related issues

Browse Source
This commit is contained in:
iafoss
2020-03-20 14:21:24 -04:00
parent bdbbe00ec7
commit 53ccc4c607
98 changed files with 4210 additions and 3657 deletions
Download Patch File Download Diff File Expand all files Collapse all files

16
doc/src/Commands_compute.rst
View File

@ -20,7 +20,7 @@ additional letters in parenthesis: g = GPU, i = USER-INTEL, k =
KOKKOS, o = USER-OMP, t = OPT.
.. table_from_list::
:columns: 5
:columns: 6
* :doc:`ackland/atom <compute_ackland_atom>`
* :doc:`adf <compute_adf>`
@ -39,13 +39,6 @@ KOKKOS, o = USER-OMP, t = OPT.
* :doc:`cluster/atom <compute_cluster_atom>`
* :doc:`cna/atom <compute_cna_atom>`
* :doc:`cnp/atom <compute_cnp_atom>`
* :doc:`cnt/Es <compute_cnt>`
* :doc:`cnt/Eb <compute_cnt>`
* :doc:`cnt/Et <compute_cnt>`
* :doc:`cnt/B <compute_cnt>`
* :doc:`cnt/Es_tot <compute_cnt>`
* :doc:`cnt/Eb_tot <compute_cnt>`
* :doc:`cnt/Et_tot <compute_cnt>`
* :doc:`com <compute_com>`
* :doc:`com/chunk <compute_com_chunk>`
* :doc:`contact/atom <compute_contact_atom>`
@ -86,6 +79,13 @@ KOKKOS, o = USER-OMP, t = OPT.
* :doc:`ke/atom/eff <compute_ke_atom_eff>`
* :doc:`ke/eff <compute_ke_eff>`
* :doc:`ke/rigid <compute_ke_rigid>`
* :doc:`mesont/Es <compute_mesont>`
* :doc:`mesont/Eb <compute_mesont>`
* :doc:`mesont/Et <compute_mesont>`
* :doc:`mesont/B <compute_mesont>`
* :doc:`mesont/Es_tot <compute_mesont>`
* :doc:`mesont/Eb_tot <compute_mesont>`
* :doc:`mesont/Et_tot <compute_mesont>`
* :doc:`meso/e/atom <compute_meso_e_atom>`
* :doc:`meso/rho/atom <compute_meso_rho_atom>`
* :doc:`meso/t/atom <compute_meso_t_atom>`

8
doc/src/Commands_pair.rst
View File

@ -26,10 +26,6 @@ OPT.
* :doc:`zero <pair_zero>`
* :doc:`hybrid (k) <pair_hybrid>`
* :doc:`hybrid/overlay (k) <pair_hybrid>`
* :doc:`kim <pair_kim>`
* :doc:`list <pair_list>`
*
*
*
*
*
@ -64,7 +60,6 @@ OPT.
* :doc:`buck/mdf <pair_mdf>`
* :doc:`buck6d/coul/gauss/dsf <pair_buck6d_coul_gauss>`
* :doc:`buck6d/coul/gauss/long <pair_buck6d_coul_gauss>`
* :doc:`cnt/tpm <pair_cnt_tpm>`
* :doc:`colloid (go) <pair_colloid>`
* :doc:`comb (o) <pair_comb>`
* :doc:`comb3 <pair_comb>`
@ -113,12 +108,14 @@ OPT.
* :doc:`hbond/dreiding/lj (o) <pair_hbond_dreiding>`
* :doc:`hbond/dreiding/morse (o) <pair_hbond_dreiding>`
* :doc:`ilp/graphene/hbn <pair_ilp_graphene_hbn>`
* :doc:`kim <pair_kim>`
* :doc:`kolmogorov/crespi/full <pair_kolmogorov_crespi_full>`
* :doc:`kolmogorov/crespi/z <pair_kolmogorov_crespi_z>`
* :doc:`lcbop <pair_lcbop>`
* :doc:`lebedeva/z <pair_lebedeva_z>`
* :doc:`lennard/mdf <pair_mdf>`
* :doc:`line/lj <pair_line_lj>`
* :doc:`list <pair_list>`
* :doc:`lj/charmm/coul/charmm (iko) <pair_charmm>`
* :doc:`lj/charmm/coul/charmm/implicit (ko) <pair_charmm>`
* :doc:`lj/charmm/coul/long (gikot) <pair_charmm>`
@ -178,6 +175,7 @@ OPT.
* :doc:`meam/spline (o) <pair_meam_spline>`
* :doc:`meam/sw/spline <pair_meam_sw_spline>`
* :doc:`mesocnt <pair_mesocnt>`
* :doc:`mesont/tpm <pair_mesont_tpm>`
* :doc:`mgpt <pair_mgpt>`
* :doc:`mie/cut (g) <pair_mie>`
* :doc:`mm3/switch3/coulgauss/long <pair_mm3_switch3_coulgauss_long>`

39
doc/src/Packages_details.rst
View File

@ -82,6 +82,7 @@ page gives those details.
* :ref:`USER-MANIFOLD <PKG-USER-MANIFOLD>`
* :ref:`USER-MEAMC <PKG-USER-MEAMC>`
* :ref:`USER-MESO <PKG-USER-MESO>`
* :ref:`USER-MESONT <PKG-USER-MESONT>`
* :ref:`USER-MGPT <PKG-USER-MGPT>`
* :ref:`USER-MISC <PKG-USER-MISC>`
* :ref:`USER-MOFFF <PKG-USER-MOFFF>`
@ -1826,6 +1827,44 @@ algorithm.
----------
.. _PKG-USER-MESONT:
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.
**Author:** Maxim V. Shugaev (University of Virginia), Alexey N. Volkov (University of Alabama), Leonid V. Zhigilei (University of Virginia)
**Supporting info:**
* src/USER-MESONT: filenames -> commands
* src/USER-MESONT/README
* :doc:`atom_style mesont <atom_style>`
* :doc:`pair_style mesont/tpm <pair_mesont_tpm>`
* :doc:`mesont/Es <compute_mesont>`
* :doc:`mesont/Eb <compute_mesont>`
* :doc:`mesont/Et <compute_mesont>`
* :doc:`mesont/B <compute_mesont>`
* :doc:`mesont/Es_tot <compute_mesont>`
* :doc:`mesont/Eb_tot <compute_mesont>`
* :doc:`mesont/Et_tot <compute_mesont>`
* examples/USER/mesont
* tools/mesont
----------
.. _PKG-USER-MOFFF:
USER-MOFFF package

2
doc/src/Packages_user.rst
View File

@ -67,6 +67,8 @@ package:
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`USER-MESO <PKG-USER-MESO>` | mesoscale DPD models | :doc:`pair_style edpd <pair_meso>` | USER/meso | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`USER-MESONT <PKG-USER-MESONT>` | mesoscopic tubular potential model | :doc:`pair_style mesont/tpm <pair_mesont_tpm>` | USER/mesont | int |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`USER-MGPT <PKG-USER-MGPT>` | fast MGPT multi-ion potentials | :doc:`pair_style mgpt <pair_mgpt>` | USER/mgpt | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`USER-MISC <PKG-USER-MISC>` | single-file contributions | USER-MISC/README | USER/misc | no |

6
doc/src/atom_style.rst
View File

@ -88,7 +88,7 @@ quantities.
+--------------+-----------------------------------------------------+--------------------------------------+
| *charge* | charge | atomic system with charges |
+--------------+-----------------------------------------------------+--------------------------------------+
| *cnt* | mass, radius, length, buckling, connections, tube id| Carbon nanotubes |
| *mesont* | mass, radius, length, buckling, connections, tube id| Carbon nanotubes |
+--------------+-----------------------------------------------------+--------------------------------------+
| *dipole* | charge and dipole moment | system with dipolar particles |
+--------------+-----------------------------------------------------+--------------------------------------+
@ -223,7 +223,7 @@ For the *tri* style, the particles are planar triangles and each
stores a per-particle mass and size and orientation (i.e. the corner
points of the triangle).
For the *cnt* style, the particles represent nodes of Carbon Nanotube
For the *mesont* style, the particles represent nodes of Nanotube
segments, and each stores a per-particle mass, radius, segment
length, tube id, buckling flag, and connections with neighbor nodes.
@ -358,7 +358,7 @@ The *spin* style is part of the SPIN package.
The *wavepacket* style is part of the USER-AWPMD package for the
:doc:`antisymmetrized wave packet MD method <pair_awpmd>`.
The *cnt* style is part of the USER-CNT package.
The *mesont* style is part of the USER-MESONT package.
Related commands
""""""""""""""""

14
doc/src/compute.rst
View File

@ -197,13 +197,6 @@ The individual style names on the :doc:`Commands compute <Commands_compute>` doc
* :doc:`cluster/atom <compute_cluster_atom>` - cluster ID for each atom
* :doc:`cna/atom <compute_cna_atom>` - common neighbor analysis (CNA) for each atom
* :doc:`cnp/atom <compute_cnp_atom>` - common neighborhood parameter (CNP) for each atom
* :doc:`cnt/Es <compute_cnt>` - Carbon Nanotube (CNT) stretching per node energy
* :doc:`cnt/Eb <compute_cnt>` - CNT bending per node energy
* :doc:`cnt/Et <compute_cnt>` - CNT intertube per node energy
* :doc:`cnt/B <compute_cnt>` - CNT per node buckling flag
* :doc:`cnt/Es_tot <compute_cnt>` - CNT stretching energy
* :doc:`cnt/Eb_tot <compute_cnt>` - CNT bending energy
* :doc:`cnt/Et_tot <compute_cnt>` - CNT intertube energy
* :doc:`com <compute_com>` - center-of-mass of group of atoms
* :doc:`com/chunk <compute_com_chunk>` - center-of-mass for each chunk
* :doc:`contact/atom <compute_contact_atom>` - contact count for each spherical particle
@ -244,6 +237,13 @@ The individual style names on the :doc:`Commands compute <Commands_compute>` doc
* :doc:`ke/atom/eff <compute_ke_atom_eff>` - per-atom translational and radial kinetic energy in the electron force field model
* :doc:`ke/eff <compute_ke_eff>` - kinetic energy of a group of nuclei and electrons in the electron force field model
* :doc:`ke/rigid <compute_ke_rigid>` - translational kinetic energy of rigid bodies
* :doc:`mesont/Es <compute_mesont>` - Nanotube (NT) stretching per node energy
* :doc:`mesont/Eb <compute_mesont>` - NT bending per node energy
* :doc:`mesont/Et <compute_mesont>` - NT intertube per node energy
* :doc:`mesont/B <compute_mesont>` - NT per node buckling flag
* :doc:`mesont/Es_tot <compute_mesont>` - NT stretching energy
* :doc:`mesont/Eb_tot <compute_mesont>` - NT bending energy
* :doc:`mesont/Et_tot <compute_mesont>` - NT intertube energy
* :doc:`meso/e/atom <compute_meso_e_atom>` - per-atom internal energy of Smooth-Particle Hydrodynamics atoms
* :doc:`meso/rho/atom <compute_meso_rho_atom>` - per-atom mesoscopic density of Smooth-Particle Hydrodynamics atoms
* :doc:`meso/t/atom <compute_meso_t_atom>` - per-atom internal temperature of Smooth-Particle Hydrodynamics atoms

78
doc/src/compute_cnt.rst
View File

@ -1,78 +0,0 @@
.. index:: compute cnt
compute cnt/Es command
=======================
compute cnt/Eb command
=======================
compute cnt/Et command
=======================
compute cnt/B command
=======================
compute cnt/Es\_tot command
============================
compute cnt/Eb\_tot command
============================
compute cnt/Et\_tot command
============================
Syntax
""""""
.. parsed-literal::
compute ID group-ID cnt/Es
* ID, group-ID are documented in :doc:`compute <compute>` command
* cnt/Es = style name of the compute command
Examples
""""""""
.. parsed-literal::
compute 1 all cnt/Es
Description
"""""""""""
These computes define computations for the per-node stretching (cnt/Es),
bending (cnt/Eb), and intertube (cnt/Et) energies, buckling flag (cnt/B),
as well as the total stretching (cnt/Es\_tot), bending (cnt/Eb\_tot), and
intertube (cnt/Et\_tot) energies for each atom (node) in a group.
**Output info:**
These computes calculate per-node (per-atom) vectors (cnt/Es, cnt/Eb, cnt/Et, cnt/B),
which can be accessed by any command that uses per-atom values from a
compute as input, and global scalars (cnt/Es\_tot, cnt/Eb\_tot,
cnt/Et\_tot). See the :doc:`Howto output <Howto_output>` doc page for an
overview of LAMMPS output options.
The per-atom vector values will be in energy :doc:`units <units>`.
Restrictions
""""""""""""
These computes are part of the USER-CNT package. They are only enabled if
LAMMPS is built with that package. See the :doc:`Build package <Build_package>`
doc page for more info. In addition, :doc:`cnt pair_style <pair_style>`
must be used.
Related commands
""""""""""""""""
:doc:`dump custom <dump>`
**Default:** none
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

78
doc/src/compute_mesont.rst Normal file
View File

@ -0,0 +1,78 @@
.. index:: compute mesont
compute mesont/Es command
==========================
compute mesont/Eb command
==========================
compute mesont/Et command
==========================
compute mesont/B command
==========================
compute mesont/Es\_tot command
===============================
compute mesont/Eb\_tot command
===============================
compute mesont/Et\_tot command
===============================
Syntax
""""""
.. parsed-literal::
compute ID group-ID mesont/Es
* ID, group-ID are documented in :doc:`compute <compute>` command
* mesont/Es = style name of the compute command
Examples
""""""""
.. parsed-literal::
compute 1 all mesont/Es
Description
"""""""""""
These computes define computations for the per-node stretching (mesont/Es),
bending (mesont/Eb), and intertube (mesont/Et) energies, buckling flag (mesont/B),
as well as the total stretching (mesont/Es\_tot), bending (mesont/Eb\_tot), and
intertube (mesont/Et\_tot) energies for each atom (node) in a group.
**Output info:**
These computes calculate per-node (per-atom) vectors (mesont/Es, mesont/Eb, mesont/Et, mesont/B),
which can be accessed by any command that uses per-atom values from a
compute as input, and global scalars (mesont/Es\_tot, mesont/Eb\_tot,
mesont/Et\_tot). See the :doc:`Howto output <Howto_output>` doc page for an
overview of LAMMPS output options.
The per-atom vector values will be in energy :doc:`units <units>`.
Restrictions
""""""""""""
These computes are part of the USER-MESONT package. They are only enabled if
LAMMPS is built with that package. See the :doc:`Build package <Build_package>`
doc page for more info. In addition, :doc:`mesont pair_style <pair_style>`
must be used.
Related commands
""""""""""""""""
:doc:`dump custom <dump>`
**Default:** none
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

48
doc/src/pair_cnt_tpm.rst → doc/src/pair_mesont_tpm.rst
View File

@ -1,7 +1,7 @@
.. index:: pair\_style cnt/tpm
.. index:: pair\_style mesont/tpm
pair\_style cnt/tpm command
============================
pair\_style mesont/tpm command
==============================
Syntax
""""""
@ -9,7 +9,7 @@ Syntax
.. parsed-literal::
pair_style cnt/tpm cut table\_path BendingMode TPMType
pair_style mesont/tpm cut table\_path BendingMode TPMType
* cut = the cutoff distance
* table\_path = the path to the potential table, the default value is ./
@ -24,7 +24,7 @@ Examples
.. parsed-literal::
pair_style cnt/tpm 25.0 ./ 0 0
pair_style mesont/tpm 25.0 ./ 0 0
Description
"""""""""""
@ -43,17 +43,18 @@ The potential force field that controls the dynamic behavior of a system of
interacting nanotubes is given by the following equation defining the potential
energy of the system:
.. image:: Eqs/cnt_eq.jpg
:align: center
.. math::
where U\_str is the harmonic potential describing the stretching of CNTs
:ref:`[1] <Srivastava>`, U\_bnd is the potential for nanotube bending
U = U_{str} + U_{bnd} + U_{vdW}
where :math:`U_{str}` is the harmonic potential describing the stretching of nanotube
:ref:`[1] <Srivastava>`, :math:`U_{bnd}` is the potential for nanotube bending
:ref:`[1] <Srivastava>` and bending-buckling :ref:`[2] <Zhigilei1>`, and
U\_vdW is the potential describing van-der Waals interaction between nanotubes
:ref:`[3 <Zhigilei2>`, :ref:`4] <Zhigilei3>`. The stretching energy, U\_str,
:math:`U_{vdW}` is the potential describing van-der Waals interaction between nanotubes
:ref:`[3 <Zhigilei2>`, :ref:`4] <Zhigilei3>`. The stretching energy, :math:`U_{str}` ,
is given by the sum of stretching energies of individual nanotube segments.
The bending energy, U\_bnd, is given by the sum of bending energies in all
internal nanotube nodes. The tube-tube interaction energy, U\_vdW, is calculated
The bending energy, :math:`U_{bnd}` , is given by the sum of bending energies in all
internal nanotube nodes. The tube-tube interaction energy, :math:`U_{vdW}` , is calculated
based on the tubular potential method suggested in Ref. :ref:`[3] <Zhigilei2>`.
The tubular potential method is briefly described below.
@ -82,7 +83,7 @@ interaction can impede sliding of nanotubes with respect to each other and
affect the kinetics of structural rearrangements in a system of nanotubes at
moderate mesoscopic temperatures. In the second case, activated when parameter
TPMType is equal to 1, the inter-tube interaction term is calculated based on
the segment-chain approach. In this case, for each CNT segment, the list of its
the segment-chain approach. In this case, for each NT segment, the list of its
neighboring segments is divided into short continuous chains of segments
belonging to individual nanotubes. For each pair of a segment and a chain, the
curved chain is approximated by a straight equivalent nanotube based on the
@ -116,9 +117,9 @@ between nanotubes :ref:`[12] <Banna>` have also been developed but are not
included in this first release of the LAMMPS implementation of the force field.
Further details can be found in references provided below.
The CNT package also provides TMDGen code designed to generate initial samples
The MESONT package also provides TMDGen code designed to generate initial samples
composed of straight and dispersed nanotubes of given chirality and length at a
given material density, which is availible in tools directory. In the generated
given material density, which is available in tools directory. In the generated
samples, nanotubes are distributed with random positions and orientations. Both
periodic and free boundary conditions are available along each axis of the
system of coordinates. All parameters in the sample files generated with TMDGen
@ -128,22 +129,18 @@ Restrictions
""""""""""""
This pair style is a part of the USER-CNT package, and it is only enabled if
This pair style is a part of the USER-MSEONT package, and it is only enabled if
LAMMPS is built with that package. See the :doc:`Build package <Build_package>`
doc page for more information.
This pair potential requires use of :doc:`cnt atomic style <atom_style>`.
This pair potential requires use of :doc:`mesont atomic style <atom_style>`.
This pair potential requires the :doc:`newton <newton>` setting to be "on" for
pair interactions.
The cutoff distance should be set to be at least:
.. image:: Eqs/cnt_cut.jpg
:align: center
The cutoff distance should be set to be at least :math:`max\left[2L,\sqrt{L^2/2+(2R+T_{cut})^2}\right]` ,
where L is the maximum segment length, R is the maximum tube radius, and
T_cut = 10.2 A is the maximum distance between the surfaces of interacting
:math:`T_{cut}` = 10.2 A is the maximum distance between the surfaces of interacting
segments.
The TPMSSTP.xrs and TPMA.xrs potential files provided with LAMMPS (see the
@ -156,9 +153,6 @@ does not use "metal" units.
The chirality parameters set during system generation must match the values
specified during generation of the potential tables.
This pair style has not been developed to support :doc:`hybrid <pair_hybrid>`
pair style and has never been tested for this style.
Related commands
""""""""""""""""

14
doc/src/pair_style.rst
View File

@ -1,13 +1,13 @@
.. index:: pair_style
.. index:: pair\_style
pair_style command
==================
pair\_style command
===================
Syntax
""""""
.. code-block:: LAMMPS
.. parsed-literal::
pair_style style args
@ -18,7 +18,7 @@ Examples
""""""""
.. code-block:: LAMMPS
.. parsed-literal::
pair_style lj/cut 2.5
pair_style eam/alloy
@ -131,7 +131,7 @@ accelerated styles exist.
* :doc:`buck/mdf <pair_mdf>` - Buckingham with a taper function
* :doc:`buck6d/coul/gauss/dsf <pair_buck6d_coul_gauss>` - dispersion-damped Buckingham with damped-shift-force model
* :doc:`buck6d/coul/gauss/long <pair_buck6d_coul_gauss>` - dispersion-damped Buckingham with long-range Coulombics
* :doc:`cnt/tpm <pair_cnt_tpm>` - carbon nanotubes mesoscopic force field
* :doc:`mesont/tpm <pair_mesont_tpm>` - nanotubes mesoscopic force field
* :doc:`colloid <pair_colloid>` - integrated colloidal potential
* :doc:`comb <pair_comb>` - charge-optimized many-body (COMB) potential
* :doc:`comb3 <pair_comb>` - charge-optimized many-body (COMB3) potential
@ -355,7 +355,7 @@ Default
"""""""
.. code-block:: LAMMPS
.. parsed-literal::
pair_style none