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Axel Kohlmeyer
2021-07-21 10:23:04 -04:00
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51
doc/src/Build_extras.rst
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@ -31,36 +31,36 @@ This is the list of packages that may require additional steps.
.. table_from_list::
:columns: 6
* :ref:`COMPRESS <compress>`
* :ref:`GPU <gpu>`
* :ref:`KIM <kim>`
* :ref:`KOKKOS <kokkos>`
* :ref:`LATTE <latte>`
* :ref:`MESSAGE <message>`
* :ref:`ML-IAP <mliap>`
* :ref:`MSCG <mscg>`
* :ref:`OPT <opt>`
* :ref:`POEMS <poems>`
* :ref:`PYTHON <python>`
* :ref:`VORONOI <voronoi>`
* :ref:`ADIOS <adios>`
* :ref:`ATC <atc>`
* :ref:`AWPMD <awpmd>`
* :ref:`COLVARS <colvars>`
* :ref:`COMPRESS <compress>`
* :ref:`GPU <gpu>`
* :ref:`H5MD <h5md>`
* :ref:`ML-HDNNP <ml-hdnnp>`
* :ref:`INTEL <intel>`
* :ref:`KIM <kim>`
* :ref:`KOKKOS <kokkos>`
* :ref:`LATTE <latte>`
* :ref:`MACHDYN <machdyn>`
* :ref:`MDI <mdi>`
* :ref:`MESONT <mesont>`
* :ref:`MOLFILE <molfile>`
* :ref:`NETCDF <netcdf>`
* :ref:`MESSAGE <message>`
* :ref:`ML-HDNNP <ml-hdnnp>`
* :ref:`ML-IAP <mliap>`
* :ref:`ML-PACE <ml-pace>`
* :ref:`PLUMED <plumed>`
* :ref:`OPENMP <openmp>`
* :ref:`QMMM <qmmm>`
* :ref:`ML-QUIP <ml-quip>`
* :ref:`MOLFILE <molfile>`
* :ref:`MSCG <mscg>`
* :ref:`NETCDF <netcdf>`
* :ref:`OPENMP <openmp>`
* :ref:`OPT <opt>`
* :ref:`PLUMED <plumed>`
* :ref:`POEMS <poems>`
* :ref:`PYTHON <python>`
* :ref:`QMMM <qmmm>`
* :ref:`SCAFACOS <scafacos>`
* :ref:`MACHDYN <machdyn>`
* :ref:`VORONOI <voronoi>`
* :ref:`VTK <vtk>`
----------
@ -1857,8 +1857,8 @@ ML-QUIP package
To build with this package, you must download and build the QUIP
library. It can be obtained from GitHub. For support of GAP
potentials, additional files with specific licensing conditions need
to be downloaded and configured. See step 1 and step 1.1 in the
``lib/quip/README`` file for details on how to do this.
to be downloaded and configured. The automatic download will from
within CMake will download the non-commercial use version.
.. tabs::
@ -1866,11 +1866,14 @@ to be downloaded and configured. See step 1 and step 1.1 in the
.. code-block:: bash
-D DOWNLOAD_QUIP=value # download OpenKIM API v2 for build, value = no (default) or yes
-D QUIP_LIBRARY=path # path to libquip.a (only needed if a custom location)
CMake will **not** download and build the QUIP library. But once you have
done that, a CMake build of LAMMPS with ``-D PKG_ML-QUIP=yes`` should
work. Set the ``QUIP_LIBRARY`` variable if CMake cannot find the QUIP library.
CMake will try to download and build the QUIP library from GitHub, if it is not
found on the local machine. This requires to have git installed. It will use the same compilers
and flags as used for compiling LAMMPS. Currently this is only supported for the GNU and the
Intel compilers. Set the ``QUIP_LIBRARY`` variable if you want to use a previously compiled
and installed QUIP library and CMake cannot find it.
.. tab:: Traditional make

1
doc/src/Commands_compute.rst
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@ -72,6 +72,7 @@ KOKKOS, o = OPENMP, t = OPT.
* :doc:`gyration/shape/chunk <compute_gyration_shape_chunk>`
* :doc:`heat/flux <compute_heat_flux>`
* :doc:`heat/flux/tally <compute_tally>`
* :doc:`heat/flux/virial/tally <compute_tally>`
* :doc:`hexorder/atom <compute_hexorder_atom>`
* :doc:`hma <compute_hma>`
* :doc:`improper <compute_improper>`

1
doc/src/Commands_fix.rst
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@ -157,6 +157,7 @@ OPT.
* :doc:`orient/fcc <fix_orient>`
* :doc:`orient/eco <fix_orient_eco>`
* :doc:`pafi <fix_pafi>`
* :doc:`pair/tracker <fix_pair_tracker>`
* :doc:`phonon <fix_phonon>`
* :doc:`pimd <fix_pimd>`
* :doc:`planeforce <fix_planeforce>`

1
doc/src/Commands_pair.rst
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@ -273,6 +273,7 @@ OPT.
* :doc:`tip4p/cut (o) <pair_coul>`
* :doc:`tip4p/long (o) <pair_coul>`
* :doc:`tip4p/long/soft (o) <pair_fep_soft>`
* :doc:`tracker <pair_tracker>`
* :doc:`tri/lj <pair_tri_lj>`
* :doc:`ufm (got) <pair_ufm>`
* :doc:`vashishta (gko) <pair_vashishta>`

2
doc/src/Examples.rst
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@ -150,6 +150,8 @@ Lowercase directories
+-------------+------------------------------------------------------------------+
| threebody | regression test input for a variety of manybody potentials |
+-------------+------------------------------------------------------------------+
| tracker | track interactions in LJ melt |
+-------------+------------------------------------------------------------------+
| vashishta | use of the Vashishta potential |
+-------------+------------------------------------------------------------------+
| voronoi | Voronoi tesselation via compute voronoi/atom command |

7
doc/src/bond_oxdna.rst
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@ -84,6 +84,13 @@ commands:
the bond topology in the data file. The first (second) atom in a bond definition
is understood to point towards the 3'-end (5'-end) of the strand.
.. warning::
If data files are produced with :doc:`write_data <write_data>`, then the
:doc:`newton <newton>` command should be set to *newton on* or *newton off on*.
Otherwise the data files will not have the same 3'-to-5' polarity as the
initial data file. This limitation does not apply to binary restart files
produced with :doc:`write_restart <write_restart>`.
Example input and data files for DNA and RNA duplexes can be found in
examples/PACKAGES/cgdna/examples/oxDNA/ , /oxDNA2/ and /oxRNA2/. A simple python

11
doc/src/compute.rst
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@ -208,7 +208,7 @@ The individual style names on the :doc:`Commands compute <Commands_compute>` doc
* :doc:`event/displace <compute_event_displace>` - detect event on atom displacement
* :doc:`fabric <compute_fabric>` - calculates fabric tensors from pair interactions
* :doc:`fep <compute_fep>` -
* :doc:`force/tally <compute_tally>` -
* :doc:`force/tally <compute_tally>` - force between two groups of atoms via the tally callback mechanism
* :doc:`fragment/atom <compute_cluster_atom>` - fragment ID for each atom
* :doc:`global/atom <compute_global_atom>` -
* :doc:`group/group <compute_group_group>` - energy/force between two groups of atoms
@ -217,7 +217,8 @@ The individual style names on the :doc:`Commands compute <Commands_compute>` doc
* :doc:`gyration/shape <compute_gyration_shape>` - shape parameters from gyration tensor
* :doc:`gyration/shape/chunk <compute_gyration_shape_chunk>` - shape parameters from gyration tensor for each chunk
* :doc:`heat/flux <compute_heat_flux>` - heat flux through a group of atoms
* :doc:`heat/flux/tally <compute_tally>` -
* :doc:`heat/flux/tally <compute_tally>` - heat flux through a group of atoms via the tally callback mechanism
* :doc:`heat/flux/virial/tally <compute_tally>` - virial heat flux between two groups via the tally callback mechanism
* :doc:`hexorder/atom <compute_hexorder_atom>` - bond orientational order parameter q6
* :doc:`hma <compute_hma>` - harmonically mapped averaging for atomic crystals
* :doc:`improper <compute_improper>` - energy of each improper sub-style
@ -240,8 +241,8 @@ The individual style names on the :doc:`Commands compute <Commands_compute>` doc
* :doc:`pe <compute_pe>` - potential energy
* :doc:`pe/atom <compute_pe_atom>` - potential energy for each atom
* :doc:`mesont <compute_mesont>` - Nanotube bending,stretching, and intertube energies
* :doc:`pe/mol/tally <compute_tally>` -
* :doc:`pe/tally <compute_tally>` -
* :doc:`pe/mol/tally <compute_tally>` - potential energy between two groups of atoms separated into intermolecular and intramolecular components via the tally callback mechanism
* :doc:`pe/tally <compute_tally>` - potential energy between two groups of atoms via the tally callback mechanism
* :doc:`plasticity/atom <compute_plasticity_atom>` - Peridynamic plasticity for each atom
* :doc:`pressure <compute_pressure>` - total pressure and pressure tensor
* :doc:`pressure/cylinder <compute_pressure_cylinder>` - pressure tensor in cylindrical coordinates
@ -289,7 +290,7 @@ The individual style names on the :doc:`Commands compute <Commands_compute>` doc
* :doc:`stress/atom <compute_stress_atom>` - stress tensor for each atom
* :doc:`stress/mop <compute_stress_mop>` - normal components of the local stress tensor using the method of planes
* :doc:`stress/mop/profile <compute_stress_mop>` - profile of the normal components of the local stress tensor using the method of planes
* :doc:`stress/tally <compute_tally>` -
* :doc:`stress/tally <compute_tally>` - stress between two groups of atoms via the tally callback mechanism
* :doc:`tdpd/cc/atom <compute_tdpd_cc_atom>` - per-atom chemical concentration of a specified species for each tDPD particle
* :doc:`temp <compute_temp>` - temperature of group of atoms
* :doc:`temp/asphere <compute_temp_asphere>` - temperature of aspherical particles

96
doc/src/compute_tally.rst
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@ -1,5 +1,6 @@
.. index:: compute force/tally
.. index:: compute heat/flux/tally
.. index:: compute heat/flux/virial/tally
.. index:: compute pe/tally
.. index:: compute pe/mol/tally
.. index:: compute stress/tally
@ -10,6 +11,9 @@ compute force/tally command
compute heat/flux/tally command
===============================
compute heat/flux/virial/tally command
======================================
compute pe/tally command
========================
@ -27,7 +31,7 @@ Syntax
compute ID group-ID style group2-ID
* ID, group-ID are documented in :doc:`compute <compute>` command
* style = *force/tally* or *pe/tally* or *pe/mol/tally* or *stress/tally*
* style = *force/tally* or *heat/flux/tally* or *heat/flux/virial/tally* or * or *pe/tally* or *pe/mol/tally* or *stress/tally*
* group2-ID = group ID of second (or same) group
Examples
@ -38,13 +42,17 @@ Examples
compute 1 lower force/tally upper
compute 1 left pe/tally right
compute 1 lower stress/tally lower
compute 1 subregion heat/flux/tally all
compute 1 liquid heat/flux/virial/tally solid
Description
"""""""""""
Define a computation that calculates properties between two groups of
atoms by accumulating them from pairwise non-bonded computations. The
two groups can be the same. This is similar to :doc:`compute group/group <compute_group_group>` only that the data is
atoms by accumulating them from pairwise non-bonded computations.
Except for *heat/flux/virial/tally*, the two groups can be the same.
This is similar to :doc:`compute group/group <compute_group_group>`
only that the data is
accumulated directly during the non-bonded force computation. The
computes *force/tally*\ , *pe/tally*\ , *stress/tally*\ , and
*heat/flux/tally* are primarily provided as example how to program
@ -57,6 +65,76 @@ the based classes of LAMMPS.
----------
Compute *heat/flux/tally* obtains the heat flux
(strictly speaking, heat flow) inside the first group,
which is the sum of the convective contribution
due to atoms in the first group and the virial contribution
due to interaction between the first and second groups:
.. math::
\mathbf{Q}= \sum_{i \in \text{group 1}} e_i \mathbf{v}_i + \frac{1}{2} \sum_{i \in \text{group 1}} \sum_{\substack{j \in \text{group 2} \\ j \neq i } } \left( \mathbf{F}_{ij} \cdot \mathbf{v}_j \right) \mathbf{r}_{ij}
When the second group in *heat/flux/tally* is set to "all",
the resulting values will be identical
to that obtained by :doc:`compute heat/flux <compute_heat_flux>`,
provided only pairwise interactions exist.
Compute *heat/flux/virial/tally* obtains the total virial heat flux
(strictly speaking, heat flow) into the first group due to interaction
with the second group, and is defined as:
.. math::
Q = \frac{1}{2} \sum_{i \in \text{group 1}} \sum_{j \in \text{group 2}} \mathbf{F}_{ij} \cdot \left(\mathbf{v}_i + \mathbf{v}_j \right)
Although, the *heat/flux/virial/tally* compute
does not include the convective term,
it can be used to obtain the total heat flux over control surfaces,
when there are no particles crossing over,
such as is often in solid-solid and solid-liquid interfaces.
This would be identical to the method of planes method.
Note that the *heat/flux/virial/tally* compute is distinctly different
from the *heat/flux* and *heat/flux/tally* computes,
that are essentially volume averaging methods.
The following example demonstrates the difference:
.. code-block:: LAMMPS
# System with only pairwise interactions.
# Non-periodic boundaries in the x direction.
# Has LeftLiquid and RightWall groups along x direction.
# Heat flux over the solid-liquid interface
compute hflow_hfvt LeftLiquid heat/flux/virial/tally RightWall
variable hflux_hfvt equal c_hflow_hfvt/(ly*lz)
# x component of approximate heat flux vector inside the liquid region,
# two approaches.
#
compute myKE all ke/atom
compute myPE all pe/atom
compute myStress all stress/atom NULL virial
compute hflow_hf LeftLiquid heat/flux myKE myPE myStress
variable hflux_hf equal c_hflow_hf[1]/${volLiq}
#
compute hflow_hft LeftLiquid heat/flux/tally all
variable hflux_hft equal c_hflow_hft[1]/${volLiq}
# Pressure over the solid-liquid interface, three approaches.
#
compute force_gg RightWall group/group LeftLiquid
variable press_gg equal c_force_gg[1]/(ly*lz)
#
compute force_ft RightWall force/tally LeftLiquid
compute rforce_ft RightWall reduce sum c_force_ft[1]
variable press_ft equal c_rforce_ft/(ly*lz)
#
compute rforce_hfvt all reduce sum c_hflow_hfvt[1]
variable press_hfvt equal -c_rforce_hfvt/(ly*lz)
----------
The pairwise contributions are computing via a callback that the
compute registers with the non-bonded pairwise force computation.
This limits the use to systems that have no bonds, no Kspace, and no
@ -83,7 +161,17 @@ magnitude) and a per atom 3-element vector (force contribution from
each atom). Compute *stress/tally* calculates a global scalar
(average of the diagonal elements of the stress tensor) and a per atom
vector (the 6 elements of stress tensor contributions from the
individual atom).
individual atom). As in :doc:`compute heat/flux <compute_heat_flux>`,
compute *heat/flux/tally* calculates a global vector of length 6,
where the first 3 components are the :math:`x`, :math:`y`, :math:`z`
components of the full heat flow vector,
and the next 3 components are the corresponding components
of just the convective portion of the flow, i.e. the
first term in the equation for :math:`\mathbf{Q}`.
Compute *heat/flux/virial/tally* calculates a global scalar (heat flow)
and a per atom 3-element vector
(contribution to the force acting over atoms in the first group
from individual atoms in both groups).
Both the scalar and vector values calculated by this compute are
"extensive".

12
doc/src/dump_modify.rst
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@ -66,7 +66,7 @@ Syntax
*unwrap* arg = *yes* or *no*
* these keywords apply only to the *image* and *movie* :doc:`styles <dump_image>`
* keyword = *acolor* or *adiam* or *amap* or *backcolor* or *bcolor* or *bdiam* or *boxcolor* or *color* or *bitrate* or *framerate*
* keyword = *acolor* or *adiam* or *amap* or *backcolor* or *bcolor* or *bdiam* or *boxcolor* or *color* or *bitrate* or *framerate* or *header*
.. parsed-literal::
@ -113,6 +113,9 @@ Syntax
rate = target bitrate for movie in kbps
*framerate* arg = fps
fps = frames per second for movie
*header* arg = *yes* or *no*
*yes* to write the header
*no* to not write the header
* these keywords apply only to the */gz* and */zstd* dump styles
* keyword = *compression_level*
@ -977,6 +980,13 @@ images less frequently.
----------
The *header* keyword toggles whether the dump file will include a header.
Excluding a header will reduce the size of the dump file for fixes such as
:doc:`fix pair/tracker <fix_pair_tracker>` which do not require the information
typically written to the header.
----------
The COMPRESS package offers both GZ and Zstd compression variants of styles
atom, custom, local, cfg, and xyz. When using these styles the compression
level can be controlled by the :code:`compression_level` parameter. File names

3
doc/src/dump_netcdf.rst
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@ -73,6 +73,9 @@ NETCDF package. They are only enabled if LAMMPS was built with
that package. See the :doc:`Build package <Build_package>` doc page for
more info.
The *netcdf* and *netcdf/mpiio* dump styles currently cannot dump
string properties or properties from variables.
----------
Related commands

1
doc/src/fix.rst
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@ -300,6 +300,7 @@ accelerated styles exist.
* :doc:`orient/fcc <fix_orient>` - add grain boundary migration force for FCC
* :doc:`orient/eco <fix_orient_eco>` - add generalized grain boundary migration force
* :doc:`pafi <fix_pafi>` - constrained force averages on hyper-planes to compute free energies (PAFI)
* :doc:`pair/tracker <fix_pair_tracker>` - track properties of pairwise interactions
* :doc:`phonon <fix_phonon>` - calculate dynamical matrix from MD simulations
* :doc:`pimd <fix_pimd>` - Feynman path integral molecular dynamics
* :doc:`planeforce <fix_planeforce>` - constrain atoms to move in a plane

4
doc/src/fix_oneway.rst
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@ -50,7 +50,9 @@ the :doc:`run <run>` command. This fix is not invoked during :doc:`energy minim
Restrictions
""""""""""""
none
This fix is part of the MISC package. It is only enabled if LAMMPS
was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
Related commands
""""""""""""""""

124
doc/src/fix_pair_tracker.rst Normal file
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@ -0,0 +1,124 @@
.. index:: fix pair/tracker
fix pair/tracker command
========================
Syntax
""""""
.. parsed-literal::
fix ID group-ID pair/tracker N attribute1 attribute2 ... keyword values ...
* ID, group-ID are documented in :doc:`fix <fix>` command
* pair/tracker = style name of this fix command
* N = prepare data for output every this many timesteps
* one or more attributes may be appended
.. parsed-literal::
possible attributes = id1 id2 time/created time/broken time/total
rmin rave x y z
.. parsed-literal::
id1, id2 = IDs of the 2 atoms in each pair interaction
time/created = the time that the 2 atoms began interacting
time/broken = the time that the 2 atoms stopped interacting
time/total = the total time the 2 atoms interacted
r/min = the minimum radial distance between the 2 atoms during the interaction
r/ave = the average radial distance between the 2 atoms during the interaction
x, y, z = the center of mass position of the 2 atoms when they stopped interacting
* zero or more keyword/value pairs may be appended
* keyword = *time/min* or *type/include*
.. parsed-literal::
*time/min* value = T
T = minimum interaction time
*type/include* value = arg1 arg2
arg = separate lists of types (see below)
Examples
""""""""
.. code-block:: LAMMPS
fix 1 all pair/tracker 1000 id1 id2 time/min 100
fix 1 all pair/tracker 1000 time/created time/broken type/include 1 * type/include 2 3,4
Description
"""""""""""
Tracks properties of pairwise interactions between two atoms and records data
whenever the atoms move beyond the interaction cutoff.
Must be used in conjunction with :doc:`pair tracker <pair_tracker>`.
Data is accumulated over a span of *N* timesteps before being deleted.
The number of datums generated, aggregated across all processors, equals
the number of broken interactions. Interactions are only included if both
atoms are included in the specified fix group. Additional filters can be
applied using the *time/min* or *type/include* keywords described below.
.. note::
For extremely long-lived interactions, the calculation of *r/ave* may not be
correct due to double overflow.
The *time/min* keyword sets a minimum amount of time that an interaction must
persist to be included. This setting can be used to censor short-lived interactions.
The *type/include* keyword filters interactions based on the types of the two atoms.
Data is only saved for interactions between atoms with types in the two lists.
Each list consists of a series of type
ranges separated by commas. The range can be specified as a
single numeric value, or a wildcard asterisk can be used to specify a range
of values. This takes the form "\*" or "\*n" or "n\*" or "m\*n". For
example, if M = the number of atom types, then an asterisk with no numeric
values means all types from 1 to M. A leading asterisk means all types
from 1 to n (inclusive). A trailing asterisk means all types from n to M
(inclusive). A middle asterisk means all types from m to n (inclusive).
Multiple *type/include* keywords may be added.
----------
Restart, fix_modify, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
No information about this fix is written to :doc:`binary restart files <restart>`.
None of the :doc:`fix_modify <fix_modify>` options are
relevant to this fix.
No parameter of this fix can be used with the *start/stop* keywords of
the :doc:`run <run>` command.
Output info
"""""""""""
This compute calculates a local vector or local array depending on the
number of input values. The length of the vector or number of rows in
the array is the number of recorded, lost interactions. If a single input is
specified, a local vector is produced. If two or more inputs are
specified, a local array is produced where the number of columns = the
number of inputs. The vector or array can be accessed by any command
that uses local values from a compute as input. See the :doc:`Howto output <Howto_output>` doc page for an overview of LAMMPS output
options.
The vector or array values will be doubles that correspond to the
specified attribute.
Restrictions
""""""""""""
Must be used in conjunction with :doc:`pair style tracker <pair_tracker>`.
This fix is part of the MISC package. It is only enabled if LAMMPS
was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
Related commands
""""""""""""""""
:doc:`pair tracker <pair_tracker>`
Default
"""""""
none

6
doc/src/fix_plumed.rst
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@ -41,7 +41,7 @@ and when PLUMED is used as a stand alone code for analysis. The full
`documentation for PLUMED <plumeddocs_>`_ is available online and included
in the PLUMED source code. The PLUMED library development is hosted at
`https://github.com/plumed/plumed2 <https://github.com/plumed/plumed2>`_
A detailed discussion of the code can be found in :ref:`(PLUMED) <PLUMED>`.
A detailed discussion of the code can be found in :ref:`(Tribello) <Tribello>`.
There is an example input for using this package with LAMMPS in the
examples/PACKAGES/plumed directory.
@ -132,9 +132,9 @@ The default options are plumedfile = NULL and outfile = NULL
----------
.. _PLUMED:
.. _Tribello:
**(PLUMED)** G.A. Tribello, M. Bonomi, D. Branduardi, C. Camilloni and G. Bussi, Comp. Phys. Comm 185, 604 (2014)
**(Tribello)** G.A. Tribello, M. Bonomi, D. Branduardi, C. Camilloni and G. Bussi, Comp. Phys. Comm 185, 604 (2014)
.. _plumeddocs: https://www.plumed.org/doc.html

6
doc/src/pair_granular.rst
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@ -665,12 +665,6 @@ then LAMMPS will use that cutoff for the specified atom type
combination, and automatically set pairwise cutoffs for the remaining
atom types.
If two particles are moving away from each other while in contact, there
is a possibility that the particles could experience an effective attractive
force due to damping. If the *limit_damping* keyword is used, this option
will zero out the normal component of the force if there is an effective
attractive force. This keyword cannot be used with the JKR or DMT models.
----------
.. include:: accel_styles.rst

1
doc/src/pair_style.rst
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@ -338,6 +338,7 @@ accelerated styles exist.
* :doc:`tip4p/cut <pair_coul>` - Coulomb for TIP4P water w/out LJ
* :doc:`tip4p/long <pair_coul>` - long-range Coulomb for TIP4P water w/out LJ
* :doc:`tip4p/long/soft <pair_fep_soft>` -
* :doc:`tracker <pair_tracker>` - monitor information about pairwise interactions
* :doc:`tri/lj <pair_tri_lj>` - LJ potential between triangles
* :doc:`ufm <pair_ufm>` -
* :doc:`vashishta <pair_vashishta>` - Vashishta 2-body and 3-body potential

97
doc/src/pair_tracker.rst Normal file
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@ -0,0 +1,97 @@
.. index:: pair_style tracker
pair_style tracker command
==========================
Syntax
""""""
.. code-block:: LAMMPS
pair_style tracker keyword
* zero or more keyword/arg pairs may be appended
* keyword = *finite*
.. parsed-literal::
*finite* value = none
pair style uses atomic diameters to identify contacts
Examples
""""""""
.. code-block:: LAMMPS
pair_style hybrid/overlay tracker ...
pair_coeff 1 1 tracker 2.0
pair_style hybrid/overlay tracker finite ...
pair_coeff * * tracker
fix 1 all pair/tracker 1000 time/created time/broken
dump 1 all local 1000 dump.local f_1[1] f_1[2]
dump_modify 1 write_header no
Description
"""""""""""
Style *tracker* monitors information about pairwise interactions.
It does not calculate any forces on atoms.
:doc:`Pair hybrid/overlay <pair_hybrid>` can be used to combine this pair
style with another pair style. Style *tracker* must be used in conjunction
with about :doc:`fix pair_tracker <fix_pair_tracker>` which contains
information on what data can be output.
If the *finite* keyword is not defined, the following coefficients must be
defined for each pair of atom types via the :doc:`pair_coeff <pair_coeff>`
command as in the examples above, or in the data file or restart files
read by the :doc:`read_data <read_data>` or :doc:`read_restart <read_restart>`
commands, or by mixing as described below:
* cutoff (distance units)
If the *finite* keyword is defined, no coefficients may be defined.
Interaction cutoffs are alternatively calculated based on the
diameter of finite particles.
Mixing, shift, table, tail correction, restart, rRESPA info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
For atom type pairs I,J and I != J, the cutoff coefficient and cutoff
distance for this pair style can be mixed. The cutoff is always mixed via a
*geometric* rule. The cutoff is mixed according to the pair_modify
mix value. The default mix value is *geometric*\ . See the
"pair_modify" command for details.
This pair style writes its information to :doc:`binary restart files <restart>`, so
pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file.
The :doc:`pair_modify <pair_modify>` shift, table, and tail options
are not relevant for this pair style.
----------
Restrictions
""""""""""""
A corresponding :doc:`fix pair_tracker <fix_pair_tracker>` must be defined
to use this pair style.
This pair style is currently incompatible with granular pair styles that extend
beyond the contact (e.g. JKR and DMT).
This fix is part of the MISC package. It is only enabled if LAMMPS
was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
Related commands
""""""""""""""""
:doc:`fix pair_tracker <fix_pair_tracker>`
Default
"""""""
none