Merge branch 'master' into mc-fix-bond-create-angle
This commit is contained in:
Axel Kohlmeyer
@ -105,10 +105,10 @@ CMake build
|
||||
# generic (default) or intel (Intel CPU) or fermi, kepler, cypress (NVIDIA)
|
||||
-D GPU_ARCH=value # primary GPU hardware choice for GPU_API=cuda
|
||||
# value = sm_XX, see below
|
||||
# default is sm_30
|
||||
# default is sm_50
|
||||
-D HIP_ARCH=value # primary GPU hardware choice for GPU_API=hip
|
||||
# value depends on selected HIP_PLATFORM
|
||||
# default is 'gfx906' for HIP_PLATFORM=hcc and 'sm_30' for HIP_PLATFORM=nvcc
|
||||
# default is 'gfx906' for HIP_PLATFORM=hcc and 'sm_50' for HIP_PLATFORM=nvcc
|
||||
-D HIP_USE_DEVICE_SORT=value # enables GPU sorting
|
||||
# value = yes (default) or no
|
||||
-D CUDPP_OPT=value # optimization setting for GPU_API=cuda
|
||||
@ -1255,6 +1255,15 @@ also typically :ref:`install the USER-OMP package <user-omp>`, as it can be
|
||||
used in tandem with the USER-INTEL package to good effect, as explained
|
||||
on the :doc:`Speed intel <Speed_intel>` doc page.
|
||||
|
||||
When using Intel compilers version 16.0 or later is required. You can
|
||||
also use the GNU or Clang compilers and they will provide performance
|
||||
improvements over regular styles and USER-OMP styles, but less so than
|
||||
with the Intel compilers. Please also note, that some compilers have
|
||||
been found to apply memory alignment constraints incompletely or
|
||||
incorrectly and thus can cause segmentation faults in otherwise correct
|
||||
code when using features from the USER-INTEL package.
|
||||
|
||||
|
||||
CMake build
|
||||
^^^^^^^^^^^
|
||||
|
||||
|
||||
@ -46,13 +46,6 @@ An alphabetic list of all general LAMMPS commands.
|
||||
* :doc:`dimension <dimension>`
|
||||
* :doc:`displace_atoms <displace_atoms>`
|
||||
* :doc:`dump <dump>`
|
||||
* :doc:`dump atom/adios <dump_adios>`
|
||||
* :doc:`dump custom/adios <dump_adios>`
|
||||
* :doc:`dump image <dump_image>`
|
||||
* :doc:`dump movie <dump_image>`
|
||||
* :doc:`dump netcdf <dump_netcdf>`
|
||||
* :doc:`dump netcdf/mpiio <dump_netcdf>`
|
||||
* :doc:`dump vtk <dump_vtk>`
|
||||
* :doc:`dump_modify <dump_modify>`
|
||||
* :doc:`dynamical_matrix <dynamical_matrix>`
|
||||
* :doc:`echo <echo>`
|
||||
@ -108,7 +101,8 @@ An alphabetic list of all general LAMMPS commands.
|
||||
* :doc:`region <region>`
|
||||
* :doc:`replicate <replicate>`
|
||||
* :doc:`rerun <rerun>`
|
||||
* :doc:`reset_ids <reset_ids>`
|
||||
* :doc:`reset_atom_ids <reset_atom_ids>`
|
||||
* :doc:`reset_mol_ids <reset_mol_ids>`
|
||||
* :doc:`reset_timestep <reset_timestep>`
|
||||
* :doc:`restart <restart>`
|
||||
* :doc:`run <run>`
|
||||
|
||||
@ -80,6 +80,7 @@ KOKKOS, o = USER-OMP, t = OPT.
|
||||
* :doc:`ke/eff <compute_ke_eff>`
|
||||
* :doc:`ke/rigid <compute_ke_rigid>`
|
||||
* :doc:`mesont <compute_mesont>`
|
||||
* :doc:`mliap <compute_mliap>`
|
||||
* :doc:`momentum <compute_momentum>`
|
||||
* :doc:`msd <compute_msd>`
|
||||
* :doc:`msd/chunk <compute_msd_chunk>`
|
||||
@ -122,6 +123,7 @@ KOKKOS, o = USER-OMP, t = OPT.
|
||||
* :doc:`smd/tlsph/strain/rate <compute_smd_tlsph_strain_rate>`
|
||||
* :doc:`smd/tlsph/stress <compute_smd_tlsph_stress>`
|
||||
* :doc:`smd/triangle/vertices <compute_smd_triangle_vertices>`
|
||||
* :doc:`smd/ulsph/effm <compute_smd_ulsph_effm>`
|
||||
* :doc:`smd/ulsph/num/neighs <compute_smd_ulsph_num_neighs>`
|
||||
* :doc:`smd/ulsph/strain <compute_smd_ulsph_strain>`
|
||||
* :doc:`smd/ulsph/strain/rate <compute_smd_ulsph_strain_rate>`
|
||||
|
||||
@ -136,22 +136,22 @@ OPT.
|
||||
* :doc:`lj/class2/soft <pair_fep_soft>`
|
||||
* :doc:`lj/cubic (go) <pair_lj_cubic>`
|
||||
* :doc:`lj/cut (gikot) <pair_lj>`
|
||||
* :doc:`lj/cut/coul/cut (gko) <pair_lj>`
|
||||
* :doc:`lj/cut/coul/cut (gko) <pair_lj_cut_coul>`
|
||||
* :doc:`lj/cut/coul/cut/soft (o) <pair_fep_soft>`
|
||||
* :doc:`lj/cut/coul/debye (gko) <pair_lj>`
|
||||
* :doc:`lj/cut/coul/dsf (gko) <pair_lj>`
|
||||
* :doc:`lj/cut/coul/long (gikot) <pair_lj>`
|
||||
* :doc:`lj/cut/coul/debye (gko) <pair_lj_cut_coul>`
|
||||
* :doc:`lj/cut/coul/dsf (gko) <pair_lj_cut_coul>`
|
||||
* :doc:`lj/cut/coul/long (gikot) <pair_lj_cut_coul>`
|
||||
* :doc:`lj/cut/coul/long/cs <pair_cs>`
|
||||
* :doc:`lj/cut/coul/long/soft (o) <pair_fep_soft>`
|
||||
* :doc:`lj/cut/coul/msm (go) <pair_lj>`
|
||||
* :doc:`lj/cut/coul/wolf (o) <pair_lj>`
|
||||
* :doc:`lj/cut/coul/msm (go) <pair_lj_cut_coul>`
|
||||
* :doc:`lj/cut/coul/wolf (o) <pair_lj_cut_coul>`
|
||||
* :doc:`lj/cut/dipole/cut (go) <pair_dipole>`
|
||||
* :doc:`lj/cut/dipole/long (g) <pair_dipole>`
|
||||
* :doc:`lj/cut/dipole/sf (go) <pair_dipole>`
|
||||
* :doc:`lj/cut/soft (o) <pair_fep_soft>`
|
||||
* :doc:`lj/cut/thole/long (o) <pair_thole>`
|
||||
* :doc:`lj/cut/tip4p/cut (o) <pair_lj>`
|
||||
* :doc:`lj/cut/tip4p/long (got) <pair_lj>`
|
||||
* :doc:`lj/cut/tip4p/cut (o) <pair_lj_cut_tip4p>`
|
||||
* :doc:`lj/cut/tip4p/long (got) <pair_lj_cut_tip4p>`
|
||||
* :doc:`lj/cut/tip4p/long/soft (o) <pair_fep_soft>`
|
||||
* :doc:`lj/expand (gko) <pair_lj_expand>`
|
||||
* :doc:`lj/expand/coul/long (g) <pair_lj_expand>`
|
||||
|
||||
@ -102,8 +102,8 @@ documentation for the formula it computes.
|
||||
* :doc:`pair_style <pair_buck>` buck/coul/cut
|
||||
* :doc:`pair_style <pair_buck>` buck/coul/long
|
||||
* :doc:`pair_style <pair_lj>` lj/cut
|
||||
* :doc:`pair_style <pair_lj>` lj/cut/coul/cut
|
||||
* :doc:`pair_style <pair_lj>` lj/cut/coul/long
|
||||
* :doc:`pair_style <pair_lj_cut_coul>` lj/cut/coul/cut
|
||||
* :doc:`pair_style <pair_lj_cut_coul>` lj/cut/coul/long
|
||||
|
||||
* :doc:`pair_style <pair_hbond_dreiding>` hbond/dreiding/lj
|
||||
* :doc:`pair_style <pair_hbond_dreiding>` hbond/dreiding/morse
|
||||
|
||||
@ -3,13 +3,15 @@ Output from LAMMPS (thermo, dumps, computes, fixes, variables)
|
||||
|
||||
There are four basic kinds of LAMMPS output:
|
||||
|
||||
* :doc:`Thermodynamic output <thermo_style>`, which is a list
|
||||
of quantities printed every few timesteps to the screen and logfile.
|
||||
* :doc:`Thermodynamic output <thermo_style>`, which is a list of
|
||||
quantities printed every few timesteps to the screen and logfile.
|
||||
* :doc:`Dump files <dump>`, which contain snapshots of atoms and various
|
||||
per-atom values and are written at a specified frequency.
|
||||
* Certain fixes can output user-specified quantities to files: :doc:`fix ave/time <fix_ave_time>` for time averaging, :doc:`fix ave/chunk <fix_ave_chunk>` for spatial or other averaging, and :doc:`fix print <fix_print>` for single-line output of
|
||||
:doc:`variables <variable>`. Fix print can also output to the
|
||||
screen.
|
||||
* Certain fixes can output user-specified quantities to files:
|
||||
:doc:`fix ave/time <fix_ave_time>` for time averaging,
|
||||
:doc:`fix ave/chunk <fix_ave_chunk>` for spatial or other averaging, and
|
||||
:doc:`fix print <fix_print>` for single-line output of
|
||||
:doc:`variables <variable>`. Fix print can also output to the screen.
|
||||
* :doc:`Restart files <restart>`.
|
||||
|
||||
A simulation prints one set of thermodynamic output and (optionally)
|
||||
@ -41,7 +43,7 @@ to output and the kind of data they operate on and produce:
|
||||
.. _global:
|
||||
|
||||
Global/per-atom/local data
|
||||
---------------------------------------
|
||||
--------------------------
|
||||
|
||||
Various output-related commands work with three different styles of
|
||||
data: global, per-atom, or local. A global datum is one or more
|
||||
@ -54,7 +56,7 @@ bond distances.
|
||||
.. _scalar:
|
||||
|
||||
Scalar/vector/array data
|
||||
-------------------------------------
|
||||
------------------------
|
||||
|
||||
Global, per-atom, and local datums can each come in three kinds: a
|
||||
single scalar value, a vector of values, or a 2d array of values. The
|
||||
@ -81,10 +83,27 @@ the dimension twice (array -> scalar). Thus a command that uses
|
||||
scalar values as input can typically also process elements of a vector
|
||||
or array.
|
||||
|
||||
.. _disambiguation:
|
||||
|
||||
Disambiguation
|
||||
--------------
|
||||
|
||||
Some computes and fixes produce data in multiple styles, e.g. a global
|
||||
scalar and a per-atom vector. Usually the context in which the input
|
||||
script references the data determines which style is meant. Example: if
|
||||
a compute provides both a global scalar and a per-atom vector, the
|
||||
former will be accessed by using ``c_ID`` in an equal-style variable,
|
||||
while the latter will be accessed by using ``c_ID`` in an atom-style
|
||||
variable. Note that atom-style variable formulas can also access global
|
||||
scalars, but in this case it is not possible to do directly because of
|
||||
the ambiguity. Instead, an equal-style variable can be defined which
|
||||
accesses the global scalar, and that variable used in the atom-style
|
||||
variable formula in place of ``c_ID``.
|
||||
|
||||
.. _thermo:
|
||||
|
||||
Thermodynamic output
|
||||
---------------------------------
|
||||
--------------------
|
||||
|
||||
The frequency and format of thermodynamic output is set by the
|
||||
:doc:`thermo <thermo>`, :doc:`thermo_style <thermo_style>`, and
|
||||
@ -112,7 +131,7 @@ intensive result.
|
||||
.. _dump:
|
||||
|
||||
Dump file output
|
||||
---------------------------
|
||||
----------------
|
||||
|
||||
Dump file output is specified by the :doc:`dump <dump>` and
|
||||
:doc:`dump_modify <dump_modify>` commands. There are several
|
||||
@ -138,7 +157,7 @@ command.
|
||||
.. _fixoutput:
|
||||
|
||||
Fixes that write output files
|
||||
---------------------------------------------
|
||||
-----------------------------
|
||||
|
||||
Several fixes take various quantities as input and can write output
|
||||
files: :doc:`fix ave/time <fix_ave_time>`, :doc:`fix ave/chunk <fix_ave_chunk>`, :doc:`fix ave/histo <fix_ave_histo>`,
|
||||
@ -192,7 +211,7 @@ from normal thermodynamic or dump file output.
|
||||
.. _computeoutput:
|
||||
|
||||
Computes that process output quantities
|
||||
-----------------------------------------------------------
|
||||
---------------------------------------
|
||||
|
||||
The :doc:`compute reduce <compute_reduce>` and :doc:`compute reduce/region <compute_reduce>` commands take one or more per-atom
|
||||
or local vector quantities as inputs and "reduce" them (sum, min, max,
|
||||
@ -219,7 +238,7 @@ output commands.
|
||||
.. _fixprocoutput:
|
||||
|
||||
Fixes that process output quantities
|
||||
--------------------------------------------------------
|
||||
------------------------------------
|
||||
|
||||
The :doc:`fix vector <fix_vector>` command can create global vectors as
|
||||
output from global scalars as input, accumulating them one element at
|
||||
@ -244,7 +263,7 @@ The output of this fix can be used as input to other output commands.
|
||||
.. _compute:
|
||||
|
||||
Computes that generate values to output
|
||||
-----------------------------------------------------
|
||||
---------------------------------------
|
||||
|
||||
Every :doc:`compute <compute>` in LAMMPS produces either global or
|
||||
per-atom or local values. The values can be scalars or vectors or
|
||||
@ -257,7 +276,7 @@ without the word "atom" or "local" produce global values.
|
||||
.. _fix:
|
||||
|
||||
Fixes that generate values to output
|
||||
----------------------------------------------
|
||||
------------------------------------
|
||||
|
||||
Some :doc:`fixes <fix>` in LAMMPS produces either global or per-atom or
|
||||
local values which can be accessed by other commands. The values can
|
||||
@ -269,7 +288,7 @@ describes them.
|
||||
.. _variable:
|
||||
|
||||
Variables that generate values to output
|
||||
-------------------------------------------------------
|
||||
----------------------------------------
|
||||
|
||||
:doc:`Variables <variable>` defined in an input script can store one or
|
||||
more strings. But equal-style, vector-style, and atom-style or
|
||||
@ -284,7 +303,7 @@ commands described in this section.
|
||||
.. _table:
|
||||
|
||||
Summary table of output options and data flow between commands
|
||||
--------------------------------------------------------------------------
|
||||
--------------------------------------------------------------
|
||||
|
||||
This table summarizes the various commands that can be used for
|
||||
generating output from LAMMPS. Each command produces output data of
|
||||
|
||||
@ -11,11 +11,11 @@ angle style of *harmonic* or *charmm* should also be used.
|
||||
A TIP4P model is run with LAMMPS using either this command
|
||||
for a cutoff model:
|
||||
|
||||
* :doc:`pair_style lj/cut/tip4p/cut <pair_lj>`
|
||||
* :doc:`pair_style lj/cut/tip4p/cut <pair_lj_cut_tip4p>`
|
||||
|
||||
or these two commands for a long-range model:
|
||||
|
||||
* :doc:`pair_style lj/cut/tip4p/long <pair_lj>`
|
||||
* :doc:`pair_style lj/cut/tip4p/long <pair_lj_cut_tip4p>`
|
||||
* :doc:`kspace_style pppm/tip4p <kspace_style>`
|
||||
|
||||
For both models, the bond lengths and bond angles should be held fixed
|
||||
@ -95,7 +95,7 @@ typically best in an efficiency sense to use a LJ cutoff >= Coulomb
|
||||
cutoff + 2\*(OM distance), to shrink the size of the neighbor list.
|
||||
This leads to slightly larger cost for the long-range calculation, so
|
||||
you can test the trade-off for your model. The OM distance and the LJ
|
||||
and Coulombic cutoffs are set in the :doc:`pair_style lj/cut/tip4p/long <pair_lj>` command.
|
||||
and Coulombic cutoffs are set in the :doc:`pair_style lj/cut/tip4p/long <pair_lj_cut_tip4p>` command.
|
||||
|
||||
Wikipedia also has a nice article on `water models <http://en.wikipedia.org/wiki/Water_model>`_.
|
||||
|
||||
|
||||
@ -21,8 +21,14 @@ Pre-built Ubuntu Linux executables
|
||||
A pre-built LAMMPS executable suitable for running on the latest
|
||||
Ubuntu Linux versions, can be downloaded as a Debian package. This
|
||||
allows you to install LAMMPS with a single command, and stay
|
||||
up-to-date with the current version of LAMMPS by simply updating your
|
||||
operating system.
|
||||
up-to-date with the current stable version of LAMMPS by simply updating
|
||||
your operating system. Please note, that the repository below offers
|
||||
two LAMMPS packages, ``lammps-daily`` and ``lammps-stable``. The
|
||||
LAMMPS developers recommend to use the ``lammps-stable`` package for
|
||||
any production simulations. The ``lammps-daily`` package is built
|
||||
from the LAMMPS development sources, and those versions may have known
|
||||
issues and bugs when new features are added and the software has not
|
||||
undergone full release testing.
|
||||
|
||||
To install the appropriate personal-package archives (PPAs), do the
|
||||
following once:
|
||||
@ -37,16 +43,16 @@ To install LAMMPS do the following once:
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
$ sudo apt-get install lammps-daily
|
||||
$ sudo apt-get install lammps-stable
|
||||
|
||||
This downloads an executable named ``lmp_daily`` to your box, which
|
||||
This downloads an executable named ``lmp_stable`` to your box, which
|
||||
can then be used in the usual way to run input scripts:
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
$ lmp_daily -in in.lj
|
||||
$ lmp_stable -in in.lj
|
||||
|
||||
To update LAMMPS to the most current version, do the following:
|
||||
To update LAMMPS to the most current stable version, do the following:
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
@ -58,25 +64,25 @@ To get a copy of the current documentation and examples:
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
$ sudo apt-get install lammps-daily-doc
|
||||
$ sudo apt-get install lammps-stable-doc
|
||||
|
||||
which will download the doc files in
|
||||
``/usr/share/doc/lammps-daily-doc/doc`` and example problems in
|
||||
``/usr/share/doc/lammps-stable-doc/doc`` and example problems in
|
||||
``/usr/share/doc/lammps-doc/examples``.
|
||||
|
||||
To get a copy of the current potentials files:
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
$ sudo apt-get install lammps-daily-data
|
||||
$ sudo apt-get install lammps-stable-data
|
||||
|
||||
which will download the potentials files to
|
||||
``/usr/share/lammps-daily/potentials``. The ``lmp_daily`` binary is
|
||||
``/usr/share/lammps-stable/potentials``. The ``lmp_stable`` binary is
|
||||
hard-coded to look for potential files in this directory (it does not
|
||||
use the `LAMMPS_POTENTIALS` environment variable, as described
|
||||
in :doc:`pair_coeff <pair_coeff>` command).
|
||||
|
||||
The ``lmp_daily`` binary is built with the :ref:`KIM package <kim>` which
|
||||
The ``lmp_stable`` binary is built with the :ref:`KIM package <kim>` which
|
||||
results in the above command also installing the `kim-api` binaries when LAMMPS
|
||||
is installed. In order to use potentials from `openkim.org <openkim_>`_, you
|
||||
can install the `openkim-models` package
|
||||
@ -89,9 +95,9 @@ To un-install LAMMPS, do the following:
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
$ sudo apt-get remove lammps-daily
|
||||
$ sudo apt-get remove lammps-stable
|
||||
|
||||
Please use ``lmp_daily -help`` to see which compilation options, packages,
|
||||
Please use ``lmp_stable -help`` to see which compilation options, packages,
|
||||
and styles are included in the binary.
|
||||
|
||||
Thanks to Anton Gladky (gladky.anton at gmail.com) for setting up this
|
||||
|
||||
@ -306,7 +306,8 @@ gpu" or "-suffix gpu" :doc:`command-line switches <Run_options>`. See
|
||||
also the :ref:`KOKKOS <PKG-KOKKOS>` package, which has GPU-enabled styles.
|
||||
|
||||
**Authors:** Mike Brown (Intel) while at Sandia and ORNL and Trung Nguyen
|
||||
(Northwestern U) while at ORNL.
|
||||
(Northwestern U) while at ORNL and later. AMD HIP support by Evgeny
|
||||
Kuznetsov, Vladimir Stegailov, and Vsevolod Nikolskiy (HSE University).
|
||||
|
||||
**Install:**
|
||||
|
||||
|
||||
@ -50,6 +50,10 @@ but this can be overridden using the device option of the :doc:`package <package
|
||||
command. run lammps/lib/gpu/ocl_get_devices to get a list of available
|
||||
platforms and devices with a suitable ICD available.
|
||||
|
||||
To compute and use this package in HIP mode, you have to have the AMD ROCm
|
||||
software installed. Versions of ROCm older than 3.5 are currently deprecated
|
||||
by AMD.
|
||||
|
||||
**Building LAMMPS with the GPU package:**
|
||||
|
||||
See the :ref:`Build extras <gpu>` doc page for
|
||||
|
||||
@ -138,10 +138,10 @@ For Intel Xeon Phi co-processors (Offload):
|
||||
|
||||
**Required hardware/software:**
|
||||
|
||||
When using Intel compilers version 16.0 or later is required.
|
||||
|
||||
In order to use offload to co-processors, an Intel Xeon Phi
|
||||
co-processor and an Intel compiler are required. For this, the
|
||||
recommended version of the Intel compiler is 14.0.1.106 or
|
||||
versions 15.0.2.044 and higher.
|
||||
co-processor and an Intel compiler are required.
|
||||
|
||||
Although any compiler can be used with the USER-INTEL package,
|
||||
currently, vectorization directives are disabled by default when
|
||||
|
||||
@ -49,13 +49,14 @@ The following coefficients must be defined for each angle type via the
|
||||
the data file or restart files read by the :doc:`read_data <read_data>`
|
||||
or :doc:`read_restart <read_restart>` commands:
|
||||
|
||||
* :math:`K` (energy/radian\^2)
|
||||
* :math:`K` (energy)
|
||||
* :math:`\theta_0` (degrees)
|
||||
* :math:`K_{ub}` (energy/distance\^2)
|
||||
* :math:`r_{ub}` (distance)
|
||||
|
||||
:math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians
|
||||
internally; hence the units of :math:`K` are in energy/radian\^2.
|
||||
:math:`\theta_0` is specified in degrees, but LAMMPS converts it to
|
||||
radians internally; hence :math:`K` is effectively energy per
|
||||
radian\^2.
|
||||
|
||||
----------
|
||||
|
||||
|
||||
@ -41,27 +41,29 @@ The *class2* angle style uses the potential
|
||||
E_{bb} & = M (r_{ij} - r_1) (r_{jk} - r_2) \\
|
||||
E_{ba} & = N_1 (r_{ij} - r_1) (\theta - \theta_0) + N_2(r_{jk} - r_2)(\theta - \theta_0)
|
||||
|
||||
where :math:`E_a` is the angle term, :math:`E_{bb}` is a bond-bond term, and :math:`E_{ba}` is a
|
||||
bond-angle term. :math:`\theta_0` is the equilibrium angle and :math:`r_1` and :math:`r_2` are
|
||||
the equilibrium bond lengths.
|
||||
where :math:`E_a` is the angle term, :math:`E_{bb}` is a bond-bond
|
||||
term, and :math:`E_{ba}` is a bond-angle term. :math:`\theta_0` is
|
||||
the equilibrium angle and :math:`r_1` and :math:`r_2` are the
|
||||
equilibrium bond lengths.
|
||||
|
||||
See :ref:`(Sun) <angle-Sun>` for a description of the COMPASS class2 force field.
|
||||
|
||||
Coefficients for the :math:`E_a`, :math:`E_{bb}`, and :math:`E_{ba}` formulas must be defined for
|
||||
each angle type via the :doc:`angle_coeff <angle_coeff>` command as in
|
||||
the example above, or in the data file or restart files read by the
|
||||
:doc:`read_data <read_data>` or :doc:`read_restart <read_restart>`
|
||||
commands.
|
||||
Coefficients for the :math:`E_a`, :math:`E_{bb}`, and :math:`E_{ba}`
|
||||
formulas must be defined for each angle type via the :doc:`angle_coeff
|
||||
<angle_coeff>` command as in the example above, or in the data file or
|
||||
restart files read by the :doc:`read_data <read_data>` or
|
||||
:doc:`read_restart <read_restart>` commands.
|
||||
|
||||
These are the 4 coefficients for the :math:`E_a` formula:
|
||||
|
||||
* :math:`\theta_0` (degrees)
|
||||
* :math:`K_2` (energy/radian\^2)
|
||||
* :math:`K_3` (energy/radian\^3)
|
||||
* :math:`K_4` (energy/radian\^4)
|
||||
* :math:`K_2` (energy)
|
||||
* :math:`K_3` (energy)
|
||||
* :math:`K_4` (energy)
|
||||
|
||||
:math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians
|
||||
internally; hence the units of the various :math:`K` are in per-radian.
|
||||
:math:`\theta_0` is specified in degrees, but LAMMPS converts it to
|
||||
radians internally; hence the various :math:`K` are effectively energy
|
||||
per radian\^2 or radian\^3 or radian\^4.
|
||||
|
||||
For the :math:`E_{bb}` formula, each line in a :doc:`angle_coeff <angle_coeff>`
|
||||
command in the input script lists 4 coefficients, the first of which
|
||||
@ -122,11 +124,15 @@ The *class2/p6* angle style uses the *class2* potential expanded to sixth order:
|
||||
In this expanded term 6 coefficients for the :math:`E_a` formula need to be set:
|
||||
|
||||
* :math:`\theta_0` (degrees)
|
||||
* :math:`K_2` (energy/radian\^2)
|
||||
* :math:`K_3` (energy/radian\^3)
|
||||
* :math:`K_4` (energy/radian\^4)
|
||||
* :math:`K_5` (energy/radian\^5)
|
||||
* :math:`K_6` (energy/radian\^6)
|
||||
* :math:`K_2` (energy)
|
||||
* :math:`K_3` (energy)
|
||||
* :math:`K_4` (energy)
|
||||
* :math:`K_5` (energy)
|
||||
* :math:`K_6` (energy)
|
||||
|
||||
:math:`\theta_0` is specified in degrees, but LAMMPS converts it to
|
||||
radians internally; hence the various :math:`K` are effectively energy
|
||||
per radian\^2 or radian\^3 or radian\^4 or radian\^5 or radian\^6.
|
||||
|
||||
The bond-bond and bond-angle terms remain unchanged.
|
||||
|
||||
|
||||
@ -40,14 +40,15 @@ the data file or restart files read by the :doc:`read_data <read_data>`
|
||||
or :doc:`read_restart <read_restart>` commands:
|
||||
|
||||
* :math:`K_{SS}` (energy/distance\^2)
|
||||
* :math:`K_{BS0}` (energy/distance/rad)
|
||||
* :math:`K_{BS1}` (energy/distance/rad)
|
||||
* :math:`K_{BS0}` (energy/distance)
|
||||
* :math:`K_{BS1}` (energy/distance)
|
||||
* :math:`r_{12,0}` (distance)
|
||||
* :math:`r_{32,0}` (distance)
|
||||
* :math:`\theta_0` (degrees)
|
||||
|
||||
:math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians
|
||||
internally; hence the units of :math:`K_{BS0}` and :math:`K_{BS1}` are in energy/distance/radian.
|
||||
:math:`\theta_0` is specified in degrees, but LAMMPS converts it to
|
||||
radians internally; hence the :math:`K_{BS0}` and :math:`K_{BS1}` are
|
||||
effectively energy/distance per radian.
|
||||
|
||||
Restrictions
|
||||
""""""""""""
|
||||
|
||||
@ -44,11 +44,12 @@ The following coefficients must be defined for each angle type via the
|
||||
the data file or restart files read by the :doc:`read_data <read_data>`
|
||||
or :doc:`read_restart <read_restart>` commands:
|
||||
|
||||
* :math:`K` (energy/radian\^2)
|
||||
* :math:`K` (energy)
|
||||
* :math:`\theta_0` (degrees)
|
||||
|
||||
:math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians
|
||||
internally; hence the units of :math:`K` are in energy/radian\^2.
|
||||
:math:`\theta_0` is specified in degrees, but LAMMPS converts it to
|
||||
radians internally; hence :math:`K` is effectively energy per
|
||||
radian\^2.
|
||||
|
||||
----------
|
||||
|
||||
@ -61,11 +62,13 @@ produce the same results, except for round-off and precision issues.
|
||||
|
||||
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
|
||||
USER-OMP and OPT packages, respectively. They are only enabled if
|
||||
LAMMPS was built with those packages. See the :doc:`Build package <Build_package>` doc page for more info.
|
||||
LAMMPS was built with those packages. See the :doc:`Build package
|
||||
<Build_package>` doc page for more info.
|
||||
|
||||
You can specify the accelerated styles explicitly in your input script
|
||||
by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
|
||||
:doc:`suffix <suffix>` command in your input script.
|
||||
by including their suffix, or you can use the :doc:`-suffix
|
||||
command-line switch <Run_options>` when you invoke LAMMPS, or you can
|
||||
use the :doc:`suffix <suffix>` command in your input script.
|
||||
|
||||
See the :doc:`Speed packages <Speed_packages>` doc page for more
|
||||
instructions on how to use the accelerated styles effectively.
|
||||
|
||||
@ -28,20 +28,22 @@ as defined in :ref:`(Allinger) <mm3-allinger1989>`
|
||||
|
||||
E = K (\theta - \theta_0)^2 \left[ 1 - 0.014(\theta - \theta_0) + 5.6(10)^{-5} (\theta - \theta_0)^2 - 7.0(10)^{-7} (\theta - \theta_0)^3 + 9(10)^{-10} (\theta - \theta_0)^4 \right]
|
||||
|
||||
where :math:`\theta_0` is the equilibrium value of the angle, and :math:`K` is a
|
||||
prefactor. The anharmonic prefactors have units :math:`\deg^{-n}`, for example
|
||||
:math:`-0.014 \deg^{-1}`, :math:`5.6 \cdot 10^{-5} \deg^{-2}`, ...
|
||||
where :math:`\theta_0` is the equilibrium value of the angle, and
|
||||
:math:`K` is a prefactor. The anharmonic prefactors have units
|
||||
:math:`\deg^{-n}`, for example :math:`-0.014 \deg^{-1}`, :math:`5.6
|
||||
\cdot 10^{-5} \deg^{-2}`, ...
|
||||
|
||||
The following coefficients must be defined for each angle type via the
|
||||
:doc:`angle_coeff <angle_coeff>` command as in the example above, or in
|
||||
the data file or restart files read by the :doc:`read_data <read_data>`
|
||||
or :doc:`read_restart <read_restart>` commands:
|
||||
|
||||
* :math:`K` (energy/radian\^2)
|
||||
* :math:`K` (energy)
|
||||
* :math:`\theta_0` (degrees)
|
||||
|
||||
:math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians
|
||||
internally; hence the units of :math:`K` are in energy/radian\^2.
|
||||
:math:`\theta_0` is specified in degrees, but LAMMPS converts it to
|
||||
radians internally; hence :math:`K` is effectively energy per
|
||||
radian\^2.
|
||||
|
||||
Restrictions
|
||||
""""""""""""
|
||||
|
||||
@ -39,12 +39,13 @@ the data file or restart files read by the :doc:`read_data <read_data>`
|
||||
or :doc:`read_restart <read_restart>` commands:
|
||||
|
||||
* :math:`\theta_0` (degrees)
|
||||
* :math:`K_2` (energy/radian\^2)
|
||||
* :math:`K_3` (energy/radian\^3)
|
||||
* :math:`K_4` (energy/radian\^4)
|
||||
* :math:`K_2` (energy)
|
||||
* :math:`K_3` (energy)
|
||||
* :math:`K_4` (energy)
|
||||
|
||||
:math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians
|
||||
internally; hence the units of :math:`K` are in energy/radian\^2.
|
||||
:math:`\theta_0` is specified in degrees, but LAMMPS converts it to
|
||||
radians internally; hence the various :math:`K` are effectively energy
|
||||
per radian\^2 or radian\^3 or radian\^4.
|
||||
|
||||
----------
|
||||
|
||||
|
||||
@ -44,13 +44,15 @@ is included in :math:`K`.
|
||||
The following coefficients must be defined for each angle type via the
|
||||
:doc:`angle_coeff <angle_coeff>` command as in the example above:
|
||||
|
||||
* :math:`K` (energy/radian\^2)
|
||||
* :math:`K` (energy)
|
||||
* :math:`\theta_0` (degrees)
|
||||
|
||||
:math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians
|
||||
internally; hence the units of :math:`K` are in energy/radian\^2.
|
||||
The also required *lj/sdk* parameters will be extracted automatically
|
||||
from the pair_style.
|
||||
:math:`\theta_0` is specified in degrees, but LAMMPS converts it to
|
||||
radians internally; hence :math:`K` is effectively energy per
|
||||
radian\^2.
|
||||
|
||||
The required *lj/sdk* parameters are extracted automatically from the
|
||||
pair_style.
|
||||
|
||||
----------
|
||||
|
||||
@ -63,7 +65,8 @@ produce the same results, except for round-off and precision issues.
|
||||
|
||||
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
|
||||
USER-OMP and OPT packages, respectively. They are only enabled if
|
||||
LAMMPS was built with those packages. See the :doc:`Build package <Build_package>` doc page for more info.
|
||||
LAMMPS was built with those packages. See the :doc:`Build package
|
||||
<Build_package>` doc page for more info.
|
||||
|
||||
You can specify the accelerated styles explicitly in your input script
|
||||
by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
|
||||
|
||||
@ -88,7 +88,8 @@ Commands
|
||||
region
|
||||
replicate
|
||||
rerun
|
||||
reset_ids
|
||||
reset_atom_ids
|
||||
reset_mol_ids
|
||||
reset_timestep
|
||||
restart
|
||||
run
|
||||
|
||||
@ -225,6 +225,7 @@ 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:`mliap <compute_mliap>` - gradients of energy and forces w.r.t. model parameters and related quantities for training machine learning interatomic potentials
|
||||
* :doc:`momentum <compute_momentum>` - translational momentum
|
||||
* :doc:`msd <compute_msd>` - mean-squared displacement of group of atoms
|
||||
* :doc:`msd/chunk <compute_msd_chunk>` - mean-squared displacement for each chunk
|
||||
@ -268,12 +269,13 @@ The individual style names on the :doc:`Commands compute <Commands_compute>` doc
|
||||
* :doc:`smd/tlsph/strain/rate <compute_smd_tlsph_strain_rate>` -
|
||||
* :doc:`smd/tlsph/stress <compute_smd_tlsph_stress>` - per-particle Cauchy stress tensor for SPH particles
|
||||
* :doc:`smd/triangle/vertices <compute_smd_triangle_vertices>` -
|
||||
* :doc:`smd/ulsph/effm <compute_smd_ulsph_effm>` - per-particle effective shear modulus
|
||||
* :doc:`smd/ulsph/num/neighs <compute_smd_ulsph_num_neighs>` -
|
||||
* :doc:`smd/ulsph/strain <compute_smd_ulsph_strain>` -
|
||||
* :doc:`smd/ulsph/strain/rate <compute_smd_ulsph_strain_rate>` -
|
||||
* :doc:`smd/ulsph/stress <compute_smd_ulsph_stress>` - per-particle Cauchy stress tensor and von Mises equivalent stress in Smooth Mach Dynamics
|
||||
* :doc:`smd/vol <compute_smd_vol>` - per-particle volumes and their sum in Smooth Mach Dynamics
|
||||
* :doc:`snap <compute_sna_atom>` - bispectrum components and related quantities for a group of atoms
|
||||
* :doc:`snap <compute_sna_atom>` - gradients of SNAP energy and forces w.r.t. linear coefficients and related quantities for fitting SNAP potentials
|
||||
* :doc:`sna/atom <compute_sna_atom>` - bispectrum components for each atom
|
||||
* :doc:`snad/atom <compute_sna_atom>` - derivative of bispectrum components for each atom
|
||||
* :doc:`snav/atom <compute_sna_atom>` - virial contribution from bispectrum components for each atom
|
||||
|
||||
@ -622,14 +622,16 @@ cylinder, x for a y-axis cylinder, and x for a z-axis cylinder.
|
||||
|
||||
**Output info:**
|
||||
|
||||
This compute calculates a per-atom vector, which can be accessed by
|
||||
any command that uses per-atom values from a compute as input. See
|
||||
the :doc:`Howto output <Howto_output>` doc page for an overview of
|
||||
This compute calculates a per-atom vector (the chunk ID), which can
|
||||
be accessed by any command that uses per-atom values from a compute
|
||||
as input. It also calculates a global scalar (the number of chunks),
|
||||
which can be similarly accessed everywhere outside of a per-atom context.
|
||||
See the :doc:`Howto output <Howto_output>` doc page for an overview of
|
||||
LAMMPS output options.
|
||||
|
||||
The per-atom vector values are unitless chunk IDs, ranging from 1 to
|
||||
*Nchunk* (inclusive) for atoms assigned to chunks, and 0 for atoms not
|
||||
belonging to a chunk.
|
||||
belonging to a chunk. The scalar contains the value of *Nchunk*.
|
||||
|
||||
Restrictions
|
||||
""""""""""""
|
||||
|
||||
@ -15,12 +15,18 @@ Syntax
|
||||
.. parsed-literal::
|
||||
|
||||
compute ID group-ID cluster/atom cutoff
|
||||
compute ID group-ID fragment/atom
|
||||
compute ID group-ID fragment/atom keyword value ...
|
||||
compute ID group-ID aggregate/atom cutoff
|
||||
|
||||
* ID, group-ID are documented in :doc:`compute <compute>` command
|
||||
* *cluster/atom* or *fragment/atom* or *aggregate/atom* = style name of this compute command
|
||||
* cutoff = distance within which to label atoms as part of same cluster (distance units)
|
||||
* zero or more keyword/value pairs may be appended to *fragment/atom*
|
||||
* keyword = *single*
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
*single* value = *yes* or *no* to treat single atoms (no bonds) as fragments
|
||||
|
||||
Examples
|
||||
""""""""
|
||||
@ -29,27 +35,36 @@ Examples
|
||||
|
||||
compute 1 all cluster/atom 3.5
|
||||
compute 1 all fragment/atom
|
||||
|
||||
compute 1 all fragment/atom single no
|
||||
compute 1 all aggregate/atom 3.5
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
Define a computation that assigns each atom a cluster, fragment,
|
||||
or aggregate ID.
|
||||
Define a computation that assigns each atom a cluster, fragment, or
|
||||
aggregate ID. Only atoms in the compute group are clustered and
|
||||
assigned cluster IDs. Atoms not in the compute group are assigned an
|
||||
ID = 0.
|
||||
|
||||
A cluster is defined as a set of atoms, each of which is within the
|
||||
cutoff distance from one or more other atoms in the cluster. If an
|
||||
atom has no neighbors within the cutoff distance, then it is a 1-atom
|
||||
cluster.
|
||||
|
||||
A fragment is similarly defined as a set of atoms, each of
|
||||
which has an explicit bond (i.e. defined via a :doc:`data file <read_data>`,
|
||||
the :doc:`create_bonds <create_bonds>` command, or through fixes like
|
||||
:doc:`fix bond/create <fix_bond_create>`, :doc:`fix bond/swap <fix_bond_swap>`,
|
||||
or :doc:`fix bond/break <fix_bond_break>`). The cluster ID or fragment ID
|
||||
of every atom in the cluster will be set to the smallest atom ID of any atom
|
||||
in the cluster or fragment, respectively.
|
||||
A fragment is similarly defined as a set of atoms, each of which has a
|
||||
bond to another atom in the fragment. Bonds can be defined initially
|
||||
via the :doc:`data file <read_data>` or :doc:`create_bonds
|
||||
<create_bonds>` commands, or dynamically by fixes which create or
|
||||
break bonds like :doc:`fix bond/react <fix_bond_react>`, :doc:`fix
|
||||
bond/create <fix_bond_create>`, :doc:`fix bond/swap <fix_bond_swap>`,
|
||||
or :doc:`fix bond/break <fix_bond_break>`. The cluster ID or fragment
|
||||
ID of every atom in the cluster will be set to the smallest atom ID of
|
||||
any atom in the cluster or fragment, respectively.
|
||||
|
||||
For the *fragment/atom* style, the *single* keyword determines whether
|
||||
single atoms (not bonded to another atom) are treated as one-atom
|
||||
fragments or not, based on the *yes* or *no* setting. If the setting
|
||||
is *no* (the default), their fragment IDs are set to 0.
|
||||
|
||||
An aggregate is defined by combining the rules for clusters and
|
||||
fragments, i.e. a set of atoms, where each of it is within the cutoff
|
||||
@ -57,19 +72,11 @@ distance from one or more atoms within a fragment that is part of
|
||||
the same cluster. This measure can be used to track molecular assemblies
|
||||
like micelles.
|
||||
|
||||
Only atoms in the compute group are clustered and assigned cluster
|
||||
IDs. Atoms not in the compute group are assigned a cluster ID = 0.
|
||||
For fragments, only bonds where **both** atoms of the bond are included
|
||||
in the compute group are assigned to fragments, so that only fragments
|
||||
are detected where **all** atoms are in the compute group. Thus atoms
|
||||
may be included in the compute group, yes still have a fragment ID of 0.
|
||||
|
||||
For computes *cluster/atom* and *aggregate/atom* the neighbor list needed
|
||||
to compute this quantity is constructed each time the calculation is
|
||||
performed (i.e. each time a snapshot of atoms is dumped). Thus it can be
|
||||
inefficient to compute/dump this quantity too frequently or to have
|
||||
multiple compute/dump commands, each of a *cluster/atom* or
|
||||
*aggregate/atom* style.
|
||||
For computes *cluster/atom* and *aggregate/atom* a neighbor list
|
||||
needed to compute cluster IDs is constructed each time the compute is
|
||||
invoked. Thus it can be inefficient to compute/dump this quantity too
|
||||
frequently or to have multiple *cluster/atom* or *aggregate/atom*
|
||||
style computes.
|
||||
|
||||
.. note::
|
||||
|
||||
@ -89,6 +96,14 @@ multiple compute/dump commands, each of a *cluster/atom* or
|
||||
:doc:`special_bonds <special_bonds>` command that includes all pairs in
|
||||
the neighbor list.
|
||||
|
||||
.. note::
|
||||
|
||||
For the compute fragment/atom style, each fragment is identified
|
||||
using the current bond topology. This will not account for bonds
|
||||
broken by the :doc:`bond_style quartic <bond_quartic>` command
|
||||
because it does not perform a full update of the bond topology data
|
||||
structures within LAMMPS.
|
||||
|
||||
**Output info:**
|
||||
|
||||
This compute calculates a per-atom vector, which can be accessed by
|
||||
@ -107,4 +122,7 @@ Related commands
|
||||
|
||||
:doc:`compute coord/atom <compute_coord_atom>`
|
||||
|
||||
**Default:** none
|
||||
**Default:**
|
||||
|
||||
The default for fragment/atom is single no.
|
||||
|
||||
|
||||
@ -160,63 +160,63 @@ pair styles and parameters that can be used with this compute. See
|
||||
the doc pages for individual pair styles and their energy formulas for
|
||||
the meaning of these parameters:
|
||||
|
||||
+---------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`born <pair_born>` | a,b,c | type pairs |
|
||||
+---------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`buck <pair_buck>` | a,c | type pairs |
|
||||
+---------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`buck/mdf <pair_mdf>` | a,c | type pairs |
|
||||
+---------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`coul/cut <pair_coul>` | scale | type pairs |
|
||||
+---------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`coul/cut/soft <pair_fep_soft>` | lambda | type pairs |
|
||||
+---------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`coul/long, coul/msm <pair_coul>` | scale | type pairs |
|
||||
+---------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`coul/long/soft <pair_fep_soft>` | scale, lambda | type pairs |
|
||||
+---------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`eam <pair_eam>` | scale | type pairs |
|
||||
+---------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`gauss <pair_gauss>` | a | type pairs |
|
||||
+---------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`lennard/mdf <pair_mdf>` | a,b | type pairs |
|
||||
+---------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`lj/class2 <pair_class2>` | epsilon,sigma | type pairs |
|
||||
+---------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`lj/class2/coul/cut, lj/class2/coul/long <pair_class2>` | epsilon,sigma | type pairs |
|
||||
+---------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`lj/cut <pair_lj>` | epsilon,sigma | type pairs |
|
||||
+---------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`lj/cut/soft <pair_fep_soft>` | epsilon,sigma,lambda | type pairs |
|
||||
+---------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`lj/cut/coul/cut, lj/cut/coul/long, lj/cut/coul/msm <pair_lj>` | epsilon,sigma | type pairs |
|
||||
+---------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`lj/cut/coul/cut/soft, lj/cut/coul/long/soft <pair_fep_soft>` | epsilon,sigma,lambda | type pairs |
|
||||
+---------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`lj/cut/tip4p/cut, lj/cut/tip4p/long <pair_lj>` | epsilon,sigma | type pairs |
|
||||
+---------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`lj/cut/tip4p/long/soft <pair_fep_soft>` | epsilon,sigma,lambda | type pairs |
|
||||
+---------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`lj/expand <pair_lj_expand>` | epsilon,sigma,delta | type pairs |
|
||||
+---------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`lj/mdf <pair_mdf>` | epsilon,sigma | type pairs |
|
||||
+---------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`lj/sf/dipole/sf <pair_dipole>` | epsilon,sigma,scale | type pairs |
|
||||
+---------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`mie/cut <pair_mie>` | epsilon,sigma,gamR,gamA | type pairs |
|
||||
+---------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`morse, morse/smooth/linear <pair_morse>` | d0,r0,alpha | type pairs |
|
||||
+---------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`morse/soft <pair_morse>` | d0,r0,alpha,lambda | type pairs |
|
||||
+---------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`nm/cut <pair_nm>` | e0,r0,nn,mm | type pairs |
|
||||
+---------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`nm/cut/coul/cut, nm/cut/coul/long <pair_nm>` | e0,r0,nn,mm | type pairs |
|
||||
+---------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`ufm <pair_ufm>` | epsilon,sigma,scale | type pairs |
|
||||
+---------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`soft <pair_soft>` | a | type pairs |
|
||||
+---------------------------------------------------------------------+-------------------------+------------+
|
||||
+------------------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`born <pair_born>` | a,b,c | type pairs |
|
||||
+------------------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`buck <pair_buck>` | a,c | type pairs |
|
||||
+------------------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`buck/mdf <pair_mdf>` | a,c | type pairs |
|
||||
+------------------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`coul/cut <pair_coul>` | scale | type pairs |
|
||||
+------------------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`coul/cut/soft <pair_fep_soft>` | lambda | type pairs |
|
||||
+------------------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`coul/long, coul/msm <pair_coul>` | scale | type pairs |
|
||||
+------------------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`coul/long/soft <pair_fep_soft>` | scale, lambda | type pairs |
|
||||
+------------------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`eam <pair_eam>` | scale | type pairs |
|
||||
+------------------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`gauss <pair_gauss>` | a | type pairs |
|
||||
+------------------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`lennard/mdf <pair_mdf>` | a,b | type pairs |
|
||||
+------------------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`lj/class2 <pair_class2>` | epsilon,sigma | type pairs |
|
||||
+------------------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`lj/class2/coul/cut, lj/class2/coul/long <pair_class2>` | epsilon,sigma | type pairs |
|
||||
+------------------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`lj/cut <pair_lj>` | epsilon,sigma | type pairs |
|
||||
+------------------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`lj/cut/soft <pair_fep_soft>` | epsilon,sigma,lambda | type pairs |
|
||||
+------------------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`lj/cut/coul/cut, lj/cut/coul/long, lj/cut/coul/msm <pair_lj_cut_coul>` | epsilon,sigma | type pairs |
|
||||
+------------------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`lj/cut/coul/cut/soft, lj/cut/coul/long/soft <pair_fep_soft>` | epsilon,sigma,lambda | type pairs |
|
||||
+------------------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`lj/cut/tip4p/cut, lj/cut/tip4p/long <pair_lj_cut_tip4p>` | epsilon,sigma | type pairs |
|
||||
+------------------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`lj/cut/tip4p/long/soft <pair_fep_soft>` | epsilon,sigma,lambda | type pairs |
|
||||
+------------------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`lj/expand <pair_lj_expand>` | epsilon,sigma,delta | type pairs |
|
||||
+------------------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`lj/mdf <pair_mdf>` | epsilon,sigma | type pairs |
|
||||
+------------------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`lj/sf/dipole/sf <pair_dipole>` | epsilon,sigma,scale | type pairs |
|
||||
+------------------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`mie/cut <pair_mie>` | epsilon,sigma,gamR,gamA | type pairs |
|
||||
+------------------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`morse, morse/smooth/linear <pair_morse>` | d0,r0,alpha | type pairs |
|
||||
+------------------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`morse/soft <pair_morse>` | d0,r0,alpha,lambda | type pairs |
|
||||
+------------------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`nm/cut <pair_nm>` | e0,r0,nn,mm | type pairs |
|
||||
+------------------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`nm/cut/coul/cut, nm/cut/coul/long <pair_nm>` | e0,r0,nn,mm | type pairs |
|
||||
+------------------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`ufm <pair_ufm>` | epsilon,sigma,scale | type pairs |
|
||||
+------------------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`soft <pair_soft>` | a | type pairs |
|
||||
+------------------------------------------------------------------------------+-------------------------+------------+
|
||||
|
||||
Note that it is easy to add new potentials and their parameters to
|
||||
this list. All it typically takes is adding an extract() method to
|
||||
|
||||
170
doc/src/compute_mliap.rst
Normal file
170
doc/src/compute_mliap.rst
Normal file
@ -0,0 +1,170 @@
|
||||
.. index:: compute mliap
|
||||
|
||||
compute mliap command
|
||||
=====================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
compute ID group-ID mliap ... keyword values ...
|
||||
|
||||
* ID, group-ID are documented in :doc:`compute <compute>` command
|
||||
* mliap = style name of this compute command
|
||||
* two keyword/value pairs must be appended
|
||||
* keyword = *model* or *descriptor*
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
*model* values = style Nelems Nparams
|
||||
style = *linear* or *quadratic*
|
||||
Nelems = number of elements
|
||||
Nparams = number of parameters per element
|
||||
*descriptor* values = style filename
|
||||
style = *sna*
|
||||
filename = name of file containing descriptor definitions
|
||||
|
||||
Examples
|
||||
""""""""
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
compute mliap model linear 2 31 descriptor sna Ta06A.mliap.descriptor
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
Compute style *mliap* provides a general interface to the gradient
|
||||
of machine-learning interatomic potentials w.r.t. model parameters.
|
||||
It is used primarily for calculating the gradient of energy, force, and
|
||||
stress components w.r.t. model parameters, which is useful when training
|
||||
:doc:`mliap pair_style <pair_mliap>` models to match target data.
|
||||
It provides separate
|
||||
definitions of the interatomic potential functional form (*model*)
|
||||
and the geometric quantities that characterize the atomic positions
|
||||
(*descriptor*). By defining *model* and *descriptor* separately,
|
||||
it is possible to use many different models with a given descriptor,
|
||||
or many different descriptors with a given model. Currently, the
|
||||
compute supports just two models, *linear* and *quadratic*,
|
||||
and one descriptor, *sna*, the SNAP descriptor used by
|
||||
:doc:`pair_style snap <pair_snap>`, including the linear, quadratic,
|
||||
and chem variants. Work is currently underway to extend
|
||||
the interface to handle neural network energy models,
|
||||
and it is also straightforward to add new descriptor styles.
|
||||
|
||||
The compute *mliap* command must be followed by two keywords
|
||||
*model* and *descriptor* in either order.
|
||||
|
||||
The *model* keyword is followed by a model style, currently limited to
|
||||
either *linear* or *quadratic*. In both cases,
|
||||
this is followed by two arguments. *nelems* is the number of elements.
|
||||
It must be equal to the number of LAMMPS atom types. *nparams*
|
||||
is the number of parameters per element for this model i.e.
|
||||
the number of parameter gradients for each element. Note these definitions
|
||||
are identical to those of *nelems* and *nparams* in the
|
||||
:doc:`pair_style mliap <pair_mliap>` model file.
|
||||
|
||||
The *descriptor* keyword is followed by a descriptor style, and additional arguments.
|
||||
Currently the only descriptor style is *sna*, indicating the bispectrum component
|
||||
descriptors used by the Spectral Neighbor Analysis Potential (SNAP) potentials of
|
||||
:doc:`pair_style snap <pair_snap>`.
|
||||
The \'p\' in SNAP is dropped, because keywords that match pair_styles are silently stripped
|
||||
out by the LAMMPS command parser. A single additional argument specifies the descriptor filename
|
||||
containing the parameters and setting used by the SNAP descriptor.
|
||||
The descriptor filename usually ends in the *.mliap.descriptor* extension.
|
||||
The format of this file is identical to the descriptor file in the
|
||||
:doc:`pair_style mliap <pair_mliap>`, and is described in detail
|
||||
there.
|
||||
|
||||
.. note::
|
||||
|
||||
The number of LAMMPS atom types (and the value of *nelems* in the model)
|
||||
must match the value of *nelems* in the descriptor file.
|
||||
|
||||
Compute *mliap* calculates a global array containing gradient information.
|
||||
The number of columns in the array is :math:`nelems \times nparams + 1`.
|
||||
The first row of the array contain the derivative of potential energy w.r.t. to
|
||||
each parameter and each element. The last six rows
|
||||
of the array contain the corresponding derivatives of the
|
||||
virial stress tensor, listed in Voigt notation: *pxx*, *pyy*, *pzz*,
|
||||
*pyz*, *pxz*, *pxy*. In between the energy and stress rows are
|
||||
the 3\*\ *N* rows containing the derivatives of the force components.
|
||||
See section below on output for a detailed description of how
|
||||
rows and columns are ordered.
|
||||
|
||||
The element in the last column of each row contains
|
||||
the potential energy, force, or stress, according to the row.
|
||||
These quantities correspond to the user-specified reference potential
|
||||
that must be subtracted from the target data when training a model.
|
||||
The potential energy calculation uses the built in compute *thermo_pe*.
|
||||
The stress calculation uses a compute called *mliap_press* that is
|
||||
automatically created behind the scenes, according to the following
|
||||
command:
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
compute mliap_press all pressure NULL virial
|
||||
|
||||
See section below on output for a detailed explanation of the data
|
||||
layout in the global array.
|
||||
|
||||
Atoms not in the group do not contribute to this compute.
|
||||
Neighbor atoms not in the group do not contribute to this compute.
|
||||
The neighbor list needed to compute this quantity is constructed each
|
||||
time the calculation is performed (i.e. each time a snapshot of atoms
|
||||
is dumped). Thus it can be inefficient to compute/dump this quantity
|
||||
too frequently.
|
||||
|
||||
.. note::
|
||||
|
||||
If the user-specified reference potentials includes bonded and
|
||||
non-bonded pairwise interactions, then the settings of
|
||||
:doc:`special_bonds <special_bonds>` command can remove pairwise
|
||||
interactions between atoms in the same bond, angle, or dihedral. This
|
||||
is the default setting for the :doc:`special_bonds <special_bonds>`
|
||||
command, and means those pairwise interactions do not appear in the
|
||||
neighbor list. Because this fix uses the neighbor list, it also means
|
||||
those pairs will not be included in the calculation. The :doc:`rerun <rerun>`
|
||||
command is not an option here, since the reference potential is required
|
||||
for the last column of the global array. A work-around is to prevent
|
||||
pairwise interactions from being removed by explicitly adding a
|
||||
*tiny* positive value for every pairwise interaction that would otherwise be
|
||||
set to zero in the :doc:`special_bonds <special_bonds>` command.
|
||||
|
||||
----------
|
||||
|
||||
**Output info:**
|
||||
|
||||
Compute *mliap* evaluates a global array.
|
||||
The columns are arranged into
|
||||
*nelems* blocks, listed in order of element *I*\ . Each block
|
||||
contains one column for each of the *nparams* model parameters.
|
||||
A final column contains the corresponding energy, force component
|
||||
on an atom, or virial stress component. The rows of the array appear
|
||||
in the following order:
|
||||
|
||||
* 1 row: Derivatives of potential energy w.r.t. each parameter of each element.
|
||||
* 3\*\ *N* rows: Derivatives of force components. x, y, and z components of force on atom *i* appearing in consecutive rows. The atoms are sorted based on atom ID.
|
||||
* 6 rows: Derivatives of virial stress tensor w.r.t. each parameter of each element. The ordering of the rows follows Voigt notation: *pxx*, *pyy*, *pzz*, *pyz*, *pxz*, *pxy*.
|
||||
|
||||
These values can be accessed by any command that uses a global array
|
||||
from a compute as input. See the :doc:`Howto output <Howto_output>` doc
|
||||
page for an overview of LAMMPS output options. To see how this command
|
||||
can be used within a Python workflow to train machine-learning interatomic
|
||||
potentials, see the examples in `FitSNAP <https://github.com/FitSNAP/FitSNAP>`_.
|
||||
|
||||
Restrictions
|
||||
""""""""""""
|
||||
|
||||
This compute is part of the MLIAP package. It is only enabled if
|
||||
LAMMPS was built with that package. In addition, building LAMMPS with the MLIAP package
|
||||
requires building LAMMPS with the SNAP package.
|
||||
See the :doc:`Build package <Build_package>` doc page for more info.
|
||||
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
:doc:`pair_style mliap <pair_mliap>`
|
||||
|
||||
**Default:** none
|
||||
56
doc/src/compute_smd_ulsph_effm.rst
Normal file
56
doc/src/compute_smd_ulsph_effm.rst
Normal file
@ -0,0 +1,56 @@
|
||||
.. index:: compute smd/ulsph/effm
|
||||
|
||||
compute smd/ulsph/effm command
|
||||
================================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
compute ID group-ID smd/ulsph/effm
|
||||
|
||||
* ID, group-ID are documented in :doc:`compute <compute>` command
|
||||
* smd/ulsph/effm = style name of this compute command
|
||||
|
||||
Examples
|
||||
""""""""
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
compute 1 all smd/ulsph/effm
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
Define a computation that outputs the effective shear modulus for
|
||||
particles interacting via the updated Lagrangian SPH pair style.
|
||||
|
||||
See `this PDF guide <PDF/SMD_LAMMPS_userguide.pdf>`_ to using Smooth
|
||||
Mach Dynamics in LAMMPS.
|
||||
|
||||
**Output info:**
|
||||
|
||||
This compute calculates a per-particle vector, which can be accessed
|
||||
by any command that uses per-particle values from a compute as input.
|
||||
See the :doc:`Howto output <Howto_output>` doc page for an overview of
|
||||
LAMMPS output options.
|
||||
|
||||
The per-particle vector contains the current effective per atom shear
|
||||
modulus as computed by the :doc:`pair smd/ulsph <pair_smd_ulsph>` pair
|
||||
style.
|
||||
|
||||
Restrictions
|
||||
""""""""""""
|
||||
|
||||
This compute is part of the USER-SMD package. It is only enabled if
|
||||
LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info. This compute can
|
||||
only be used for particles which interact with the updated Lagrangian
|
||||
SPH pair style.
|
||||
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
:doc:`pair smd/ulsph <pair_smd_ulsph>`
|
||||
|
||||
**Default:** none
|
||||
@ -391,7 +391,9 @@ of :math:`K N_{elem}^3` columns.
|
||||
|
||||
These values can be accessed by any command that uses per-atom values
|
||||
from a compute as input. See the :doc:`Howto output <Howto_output>` doc
|
||||
page for an overview of LAMMPS output options.
|
||||
page for an overview of LAMMPS output options. To see how this command
|
||||
can be used within a Python workflow to train SNAP potentials,
|
||||
see the examples in `FitSNAP <https://github.com/FitSNAP/FitSNAP>`_.
|
||||
|
||||
Restrictions
|
||||
""""""""""""
|
||||
|
||||
@ -89,7 +89,7 @@ number of atoms in the system. Note that this is not done for
|
||||
molecular systems (see the :doc:`atom_style <atom_style>` command),
|
||||
regardless of the *compress* setting, since it would foul up the bond
|
||||
connectivity that has already been assigned. However, the
|
||||
:doc:`reset_ids <reset_ids>` command can be used after this command to
|
||||
:doc:`reset_atom_ids <reset_atom_ids>` command can be used after this command to
|
||||
accomplish the same thing.
|
||||
|
||||
Note that the re-assignment of IDs is not really a compression, where
|
||||
@ -157,7 +157,7 @@ using molecule template files via the :doc:`molecule <molecule>` and
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
:doc:`create_atoms <create_atoms>`, :doc:`reset_ids <reset_ids>`
|
||||
:doc:`create_atoms <create_atoms>`, :doc:`reset_atom_ids <reset_atom_ids>`
|
||||
|
||||
Default
|
||||
"""""""
|
||||
|
||||
@ -111,34 +111,34 @@ be listed under a *AngleTorsion Coeffs* heading and you must leave out
|
||||
the *at*, i.e. only list 8 coefficients after the dihedral type.
|
||||
|
||||
* *at*
|
||||
* :math:`D_1` (energy/radian)
|
||||
* :math:`D_2` (energy/radian)
|
||||
* :math:`D_3` (energy/radian)
|
||||
* :math:`E_1` (energy/radian)
|
||||
* :math:`E_2` (energy/radian)
|
||||
* :math:`E_3` (energy/radian)
|
||||
* :math:`D_1` (energy)
|
||||
* :math:`D_2` (energy)
|
||||
* :math:`D_3` (energy)
|
||||
* :math:`E_1` (energy)
|
||||
* :math:`E_2` (energy)
|
||||
* :math:`E_3` (energy)
|
||||
* :math:`\theta_1` (degrees)
|
||||
* :math:`\theta_2` (degrees)
|
||||
|
||||
:math:`\theta_1` and :math:`\theta_2` are specified in degrees, but LAMMPS converts
|
||||
them to radians internally; hence the units of :math:`D` and :math:`E` are in
|
||||
energy/radian.
|
||||
:math:`\theta_1` and :math:`\theta_2` are specified in degrees, but
|
||||
LAMMPS converts them to radians internally; hence the various
|
||||
:math:`D` and :math:`E` are effectively energy per radian.
|
||||
|
||||
For the :math:`E_{aat}` formula, each line in a
|
||||
:doc:`dihedral_coeff <dihedral_coeff>` command in the input script lists
|
||||
4 coefficients, the first of which is *aat* to indicate they are
|
||||
AngleAngleTorsion coefficients. In a data file, these coefficients
|
||||
should be listed under a *AngleAngleTorsion Coeffs* heading and you
|
||||
must leave out the *aat*, i.e. only list 3 coefficients after the
|
||||
dihedral type.
|
||||
For the :math:`E_{aat}` formula, each line in a :doc:`dihedral_coeff
|
||||
<dihedral_coeff>` command in the input script lists 4 coefficients,
|
||||
the first of which is *aat* to indicate they are AngleAngleTorsion
|
||||
coefficients. In a data file, these coefficients should be listed
|
||||
under a *AngleAngleTorsion Coeffs* heading and you must leave out the
|
||||
*aat*, i.e. only list 3 coefficients after the dihedral type.
|
||||
|
||||
* *aat*
|
||||
* :math:`M` (energy/radian\^2)
|
||||
* :math:`M` (energy)
|
||||
* :math:`\theta_1` (degrees)
|
||||
* :math:`\theta_2` (degrees)
|
||||
|
||||
:math:`\theta_1` and :math:`\theta_2` are specified in degrees, but LAMMPS converts
|
||||
them to radians internally; hence the units of M are in energy/radian\^2.
|
||||
:math:`\theta_1` and :math:`\theta_2` are specified in degrees, but
|
||||
LAMMPS converts them to radians internally; hence :math:`M` is
|
||||
effectively energy per radian\^2.
|
||||
|
||||
For the :math:`E_{bb13}` formula, each line in a
|
||||
:doc:`dihedral_coeff <dihedral_coeff>` command in the input script lists
|
||||
|
||||
@ -39,9 +39,13 @@ above, or in the data file or restart files read by the
|
||||
:doc:`read_data <read_data>` or :doc:`read_restart <read_restart>`
|
||||
commands:
|
||||
|
||||
* :math:`K` (energy/radian\^2)
|
||||
* :math:`K` (energy)
|
||||
* :math:`\phi_0` (degrees)
|
||||
|
||||
:math:`\phi_0` is specified in degrees, but LAMMPS converts it to
|
||||
radians internally; hence :math:`K` is effectively energy per
|
||||
radian\^2.
|
||||
|
||||
----------
|
||||
|
||||
Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
|
||||
|
||||
@ -123,87 +123,85 @@ current list of pair styles and parameters that can be varied by this
|
||||
fix. See the doc pages for individual pair styles and their energy
|
||||
formulas for the meaning of these parameters:
|
||||
|
||||
+---------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||
| :doc:`born <pair_born>` | a,b,c | type pairs |
|
||||
+---------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||
| :doc:`born/coul/long, born/coul/msm <pair_born>` | coulombic_cutoff | type global |
|
||||
+---------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||
| :doc:`buck <pair_buck>` | a,c | type pairs |
|
||||
+---------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||
| :doc:`buck/coul/long, buck/coul/msm <pair_buck>` | coulombic_cutoff | type global |
|
||||
+---------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||
| :doc:`buck/mdf <pair_mdf>` | a,c | type pairs |
|
||||
+---------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||
| :doc:`coul/cut <pair_coul>` | scale | type pairs |
|
||||
+---------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||
| :doc:`coul/cut/soft <pair_fep_soft>` | lambda | type pairs |
|
||||
+---------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||
| :doc:`coul/debye <pair_coul>` | scale | type pairs |
|
||||
+---------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||
| :doc:`coul/dsf <pair_coul>` | coulombic_cutoff | type global |
|
||||
+---------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||
| :doc:`coul/long, coul/msm <pair_coul>` | coulombic_cutoff, scale | type pairs |
|
||||
+---------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||
| :doc:`coul/long/soft <pair_fep_soft>` | scale, lambda, coulombic_cutoff | type pairs |
|
||||
+---------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||
| :doc:`eam, eam/alloy, eam/fs <pair_eam>` | scale | type pairs |
|
||||
+---------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||
| :doc:`gauss <pair_gauss>` | a | type pairs |
|
||||
+---------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||
| :doc:`lennard/mdf <pair_mdf>` | A,B | type pairs |
|
||||
+---------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||
| :doc:`lj/class2 <pair_class2>` | epsilon,sigma | type pairs |
|
||||
+---------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||
| :doc:`lj/class2/coul/cut, lj/class2/coul/long <pair_class2>` | epsilon,sigma,coulombic_cutoff | type pairs |
|
||||
+---------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||
| :doc:`lj/cut <pair_lj>` | epsilon,sigma | type pairs |
|
||||
+---------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||
| :doc:`lj/cut/coul/cut, lj/cut/coul/long, lj/cut/coul/msm <pair_lj>` | epsilon,sigma,coulombic_cutoff | type pairs |
|
||||
+---------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||
| :doc:`lj/cut/coul/cut/soft, lj/cut/coul/long/soft <pair_fep_soft>` | epsilon,sigma,lambda,coulombic_cutoff | type pairs |
|
||||
+---------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||
| :doc:`lj/cut/coul/dsf <pair_lj>` | cutoff | type global |
|
||||
+---------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||
| :doc:`lj/cut/tip4p/cut <pair_lj>` | epsilon,sigma,coulombic_cutoff | type pairs |
|
||||
+---------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||
| :doc:`lj/cut/soft <pair_fep_soft>` | epsilon,sigma,lambda | type pairs |
|
||||
+---------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||
| :doc:`lj/expand <pair_lj_expand>` | epsilon,sigma,delta | type pairs |
|
||||
+---------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||
| :doc:`lj/mdf <pair_mdf>` | epsilon,sigma | type pairs |
|
||||
+---------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||
| :doc:`lj/sf/dipole/sf <pair_dipole>` | epsilon,sigma,scale | type pairs |
|
||||
+---------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||
| :doc:`lubricate <pair_lubricate>` | mu | global |
|
||||
+---------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||
| :doc:`mie/cut <pair_mie>` | epsilon,sigma,gamma_repulsive,gamma_attractive | type pairs |
|
||||
+---------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||
| :doc:`morse, morse/smooth/linear <pair_morse>` | D0,R0,alpha | type pairs |
|
||||
+---------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||
| :doc:`morse/soft <pair_morse>` | D0,R0,alpha,lambda | type pairs |
|
||||
+---------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||
| :doc:`nm/cut <pair_nm>` | E0,R0,m,n | type pairs |
|
||||
+---------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||
| :doc:`nm/cut/coul/cut, nm/cut/coul/long <pair_nm>` | E0,R0,m,n,coulombic_cutoff | type pairs |
|
||||
+---------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||
| :doc:`reax/c <pair_reaxc>` | chi, eta, gamma | type global |
|
||||
+---------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||
| :doc:`spin/dmi <pair_spin_dmi>` | coulombic_cutoff | type global |
|
||||
+---------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||
| :doc:`spin/exchange <pair_spin_exchange>` | coulombic_cutoff | type global |
|
||||
+---------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||
| :doc:`spin/magelec <pair_spin_magelec>` | coulombic_cutoff | type global |
|
||||
+---------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||
| :doc:`spin/neel <pair_spin_neel>` | coulombic_cutoff | type global |
|
||||
+---------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||
| :doc:`table <pair_table>` | table_cutoff | type pairs |
|
||||
+---------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||
| :doc:`ufm <pair_ufm>` | epsilon,sigma | type pairs |
|
||||
+---------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||
| :doc:`soft <pair_soft>` | a | type pairs |
|
||||
+---------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||
| | | |
|
||||
+---------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||
| :doc:`born <pair_born>` | a,b,c | type pairs |
|
||||
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||
| :doc:`born/coul/long, born/coul/msm <pair_born>` | coulombic_cutoff | type global |
|
||||
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||
| :doc:`buck <pair_buck>` | a,c | type pairs |
|
||||
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||
| :doc:`buck/coul/long, buck/coul/msm <pair_buck>` | coulombic_cutoff | type global |
|
||||
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||
| :doc:`buck/mdf <pair_mdf>` | a,c | type pairs |
|
||||
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||
| :doc:`coul/cut <pair_coul>` | scale | type pairs |
|
||||
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||
| :doc:`coul/cut/soft <pair_fep_soft>` | lambda | type pairs |
|
||||
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||
| :doc:`coul/debye <pair_coul>` | scale | type pairs |
|
||||
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||
| :doc:`coul/dsf <pair_coul>` | coulombic_cutoff | type global |
|
||||
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||
| :doc:`coul/long, coul/msm <pair_coul>` | coulombic_cutoff, scale | type pairs |
|
||||
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||
| :doc:`coul/long/soft <pair_fep_soft>` | scale, lambda, coulombic_cutoff | type pairs |
|
||||
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||
| :doc:`eam, eam/alloy, eam/fs <pair_eam>` | scale | type pairs |
|
||||
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||
| :doc:`gauss <pair_gauss>` | a | type pairs |
|
||||
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||
| :doc:`lennard/mdf <pair_mdf>` | A,B | type pairs |
|
||||
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||
| :doc:`lj/class2 <pair_class2>` | epsilon,sigma | type pairs |
|
||||
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||
| :doc:`lj/class2/coul/cut, lj/class2/coul/long <pair_class2>` | epsilon,sigma,coulombic_cutoff | type pairs |
|
||||
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||
| :doc:`lj/cut <pair_lj>` | epsilon,sigma | type pairs |
|
||||
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||
| :doc:`lj/cut/coul/cut, lj/cut/coul/long, lj/cut/coul/msm <pair_lj_cut_coul>` | epsilon,sigma,coulombic_cutoff | type pairs |
|
||||
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||
| :doc:`lj/cut/coul/cut/soft, lj/cut/coul/long/soft <pair_fep_soft>` | epsilon,sigma,lambda,coulombic_cutoff | type pairs |
|
||||
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||
| :doc:`lj/cut/coul/dsf <pair_lj_cut_coul>` | cutoff | type global |
|
||||
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||
| :doc:`lj/cut/tip4p/cut <pair_lj_cut_tip4p>` | epsilon,sigma,coulombic_cutoff | type pairs |
|
||||
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||
| :doc:`lj/cut/soft <pair_fep_soft>` | epsilon,sigma,lambda | type pairs |
|
||||
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||
| :doc:`lj/expand <pair_lj_expand>` | epsilon,sigma,delta | type pairs |
|
||||
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||
| :doc:`lj/mdf <pair_mdf>` | epsilon,sigma | type pairs |
|
||||
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||
| :doc:`lj/sf/dipole/sf <pair_dipole>` | epsilon,sigma,scale | type pairs |
|
||||
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||
| :doc:`lubricate <pair_lubricate>` | mu | global |
|
||||
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||
| :doc:`mie/cut <pair_mie>` | epsilon,sigma,gamma_repulsive,gamma_attractive | type pairs |
|
||||
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||
| :doc:`morse, morse/smooth/linear <pair_morse>` | D0,R0,alpha | type pairs |
|
||||
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||
| :doc:`morse/soft <pair_morse>` | D0,R0,alpha,lambda | type pairs |
|
||||
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||
| :doc:`nm/cut <pair_nm>` | E0,R0,m,n | type pairs |
|
||||
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||
| :doc:`nm/cut/coul/cut, nm/cut/coul/long <pair_nm>` | E0,R0,m,n,coulombic_cutoff | type pairs |
|
||||
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||
| :doc:`reax/c <pair_reaxc>` | chi, eta, gamma | type global |
|
||||
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||
| :doc:`spin/dmi <pair_spin_dmi>` | coulombic_cutoff | type global |
|
||||
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||
| :doc:`spin/exchange <pair_spin_exchange>` | coulombic_cutoff | type global |
|
||||
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||
| :doc:`spin/magelec <pair_spin_magelec>` | coulombic_cutoff | type global |
|
||||
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||
| :doc:`spin/neel <pair_spin_neel>` | coulombic_cutoff | type global |
|
||||
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||
| :doc:`table <pair_table>` | table_cutoff | type pairs |
|
||||
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||
| :doc:`ufm <pair_ufm>` | epsilon,sigma | type pairs |
|
||||
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||
| :doc:`soft <pair_soft>` | a | type pairs |
|
||||
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||
|
||||
.. note::
|
||||
|
||||
|
||||
@ -117,63 +117,63 @@ change. This is the current list of pair styles and parameters that
|
||||
can be varied by this fix. See the doc pages for individual pair
|
||||
styles and their energy formulas for the meaning of these parameters:
|
||||
|
||||
+---------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`born <pair_born>` | a,b,c | type pairs |
|
||||
+---------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`buck <pair_buck>` | a,c | type pairs |
|
||||
+---------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`buck/mdf <pair_mdf>` | a,c | type pairs |
|
||||
+---------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`coul/cut <pair_coul>` | scale | type pairs |
|
||||
+---------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`coul/cut/soft <pair_fep_soft>` | lambda | type pairs |
|
||||
+---------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`coul/long, coul/msm <pair_coul>` | scale | type pairs |
|
||||
+---------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`coul/long/soft <pair_fep_soft>` | scale, lambda | type pairs |
|
||||
+---------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`eam <pair_eam>` | scale | type pairs |
|
||||
+---------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`gauss <pair_gauss>` | a | type pairs |
|
||||
+---------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`lennard/mdf <pair_mdf>` | a,b | type pairs |
|
||||
+---------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`lj/class2 <pair_class2>` | epsilon,sigma | type pairs |
|
||||
+---------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`lj/class2/coul/cut, lj/class2/coul/long <pair_class2>` | epsilon,sigma | type pairs |
|
||||
+---------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`lj/cut <pair_lj>` | epsilon,sigma | type pairs |
|
||||
+---------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`lj/cut/soft <pair_fep_soft>` | epsilon,sigma,lambda | type pairs |
|
||||
+---------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`lj/cut/coul/cut, lj/cut/coul/long, lj/cut/coul/msm <pair_lj>` | epsilon,sigma | type pairs |
|
||||
+---------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`lj/cut/coul/cut/soft, lj/cut/coul/long/soft <pair_fep_soft>` | epsilon,sigma,lambda | type pairs |
|
||||
+---------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`lj/cut/tip4p/cut, lj/cut/tip4p/long <pair_lj>` | epsilon,sigma | type pairs |
|
||||
+---------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`lj/cut/tip4p/long/soft <pair_fep_soft>` | epsilon,sigma,lambda | type pairs |
|
||||
+---------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`lj/expand <pair_lj_expand>` | epsilon,sigma,delta | type pairs |
|
||||
+---------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`lj/mdf <pair_mdf>` | epsilon,sigma | type pairs |
|
||||
+---------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`lj/sf/dipole/sf <pair_dipole>` | epsilon,sigma,scale | type pairs |
|
||||
+---------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`mie/cut <pair_mie>` | epsilon,sigma,gamR,gamA | type pairs |
|
||||
+---------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`morse, morse/smooth/linear <pair_morse>` | d0,r0,alpha | type pairs |
|
||||
+---------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`morse/soft <pair_morse>` | d0,r0,alpha,lambda | type pairs |
|
||||
+---------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`nm/cut <pair_nm>` | e0,r0,nn,mm | type pairs |
|
||||
+---------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`nm/cut/coul/cut, nm/cut/coul/long <pair_nm>` | e0,r0,nn,mm | type pairs |
|
||||
+---------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`ufm <pair_ufm>` | epsilon,sigma,scale | type pairs |
|
||||
+---------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`soft <pair_soft>` | a | type pairs |
|
||||
+---------------------------------------------------------------------+-------------------------+------------+
|
||||
+------------------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`born <pair_born>` | a,b,c | type pairs |
|
||||
+------------------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`buck <pair_buck>` | a,c | type pairs |
|
||||
+------------------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`buck/mdf <pair_mdf>` | a,c | type pairs |
|
||||
+------------------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`coul/cut <pair_coul>` | scale | type pairs |
|
||||
+------------------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`coul/cut/soft <pair_fep_soft>` | lambda | type pairs |
|
||||
+------------------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`coul/long, coul/msm <pair_coul>` | scale | type pairs |
|
||||
+------------------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`coul/long/soft <pair_fep_soft>` | scale, lambda | type pairs |
|
||||
+------------------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`eam <pair_eam>` | scale | type pairs |
|
||||
+------------------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`gauss <pair_gauss>` | a | type pairs |
|
||||
+------------------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`lennard/mdf <pair_mdf>` | a,b | type pairs |
|
||||
+------------------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`lj/class2 <pair_class2>` | epsilon,sigma | type pairs |
|
||||
+------------------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`lj/class2/coul/cut, lj/class2/coul/long <pair_class2>` | epsilon,sigma | type pairs |
|
||||
+------------------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`lj/cut <pair_lj>` | epsilon,sigma | type pairs |
|
||||
+------------------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`lj/cut/soft <pair_fep_soft>` | epsilon,sigma,lambda | type pairs |
|
||||
+------------------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`lj/cut/coul/cut, lj/cut/coul/long, lj/cut/coul/msm <pair_lj_cut_coul>` | epsilon,sigma | type pairs |
|
||||
+------------------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`lj/cut/coul/cut/soft, lj/cut/coul/long/soft <pair_fep_soft>` | epsilon,sigma,lambda | type pairs |
|
||||
+------------------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`lj/cut/tip4p/cut, lj/cut/tip4p/long <pair_lj_cut_tip4p>` | epsilon,sigma | type pairs |
|
||||
+------------------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`lj/cut/tip4p/long/soft <pair_fep_soft>` | epsilon,sigma,lambda | type pairs |
|
||||
+------------------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`lj/expand <pair_lj_expand>` | epsilon,sigma,delta | type pairs |
|
||||
+------------------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`lj/mdf <pair_mdf>` | epsilon,sigma | type pairs |
|
||||
+------------------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`lj/sf/dipole/sf <pair_dipole>` | epsilon,sigma,scale | type pairs |
|
||||
+------------------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`mie/cut <pair_mie>` | epsilon,sigma,gamR,gamA | type pairs |
|
||||
+------------------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`morse, morse/smooth/linear <pair_morse>` | d0,r0,alpha | type pairs |
|
||||
+------------------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`morse/soft <pair_morse>` | d0,r0,alpha,lambda | type pairs |
|
||||
+------------------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`nm/cut <pair_nm>` | e0,r0,nn,mm | type pairs |
|
||||
+------------------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`nm/cut/coul/cut, nm/cut/coul/long <pair_nm>` | e0,r0,nn,mm | type pairs |
|
||||
+------------------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`ufm <pair_ufm>` | epsilon,sigma,scale | type pairs |
|
||||
+------------------------------------------------------------------------------+-------------------------+------------+
|
||||
| :doc:`soft <pair_soft>` | a | type pairs |
|
||||
+------------------------------------------------------------------------------+-------------------------+------------+
|
||||
|
||||
.. note::
|
||||
|
||||
|
||||
@ -15,7 +15,7 @@ Syntax
|
||||
* dir = *x* or *y* or *z*
|
||||
* shockvel = shock velocity (strictly positive, velocity units)
|
||||
* zero or more keyword/value pairs may be appended
|
||||
* keyword = *q* or *mu* or *p0* or *v0* or *e0* or *tscale* or *damp* or *seed*\ or *f_max* or *N_f* or *eta* or *beta* or *T_init*
|
||||
* keyword = *q* or *mu* or *p0* or *v0* or *e0* or *tscale* or *damp* or *seed* or *f_max* or *N_f* or *eta* or *beta* or *T_init*
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
|
||||
@ -183,11 +183,13 @@ the restraint is
|
||||
|
||||
with the following coefficients:
|
||||
|
||||
* :math:`K` (energy/radian\^2)
|
||||
* :math:`K` (energy)
|
||||
* :math:`\theta_0` (degrees)
|
||||
|
||||
:math:`K` and :math:`\theta_0` are specified with the fix. Note that the usual 1/2
|
||||
factor is included in :math:`K`.
|
||||
:math:`K` and :math:`\theta_0` are specified with the fix.
|
||||
:math:`\theta_0` is specified in degrees, but LAMMPS converts it to
|
||||
radians internally; hence :math:`K` is effectively energy per
|
||||
radian\^2. Note that the usual 1/2 factor is included in :math:`K`.
|
||||
|
||||
----------
|
||||
|
||||
|
||||
@ -93,7 +93,7 @@ Related commands
|
||||
""""""""""""""""
|
||||
|
||||
:doc:`kspace_style <kspace_style>`, :doc:`boundary <boundary>`
|
||||
:doc:`kspace_modify <kspace_modify>`, :doc:`pair_style lj/cut/coul/long <pair_lj>`, :doc:`pair_style lj/charmm/coul/long <pair_charmm>`, :doc:`pair_style lj/long <pair_lj_long>`, :doc:`pair_style lj/long/coul/long <pair_lj_long>`,
|
||||
:doc:`kspace_modify <kspace_modify>`, :doc:`pair_style lj/cut/coul/long <pair_lj_cut_coul>`, :doc:`pair_style lj/charmm/coul/long <pair_charmm>`, :doc:`pair_style lj/long <pair_lj_long>`, :doc:`pair_style lj/long/coul/long <pair_lj_long>`,
|
||||
:doc:`pair_style buck/coul/long <pair_buck>`
|
||||
|
||||
Default
|
||||
|
||||
@ -74,29 +74,31 @@ commands.
|
||||
|
||||
These are the 2 coefficients for the :math:`E_i` formula:
|
||||
|
||||
* :math:`K` (energy/radian\^2)
|
||||
* :math:`K` (energy)
|
||||
* :math:`\chi_0` (degrees)
|
||||
|
||||
:math:`\chi_0` is specified in degrees, but LAMMPS converts it to radians
|
||||
internally; hence the units of K are in energy/radian\^2.
|
||||
:math:`\chi_0` is specified in degrees, but LAMMPS converts it to
|
||||
radians internally; hence :math:`K` is effectively energy per
|
||||
radian\^2.
|
||||
|
||||
For the :math:`E_{aa}` formula, each line in a
|
||||
:doc:`improper_coeff <improper_coeff>` command in the input script lists
|
||||
7 coefficients, the first of which is *aa* to indicate they are
|
||||
AngleAngle coefficients. In a data file, these coefficients should be
|
||||
listed under a *AngleAngle Coeffs* heading and you must leave out the
|
||||
*aa*, i.e. only list 6 coefficients after the improper type.
|
||||
For the :math:`E_{aa}` formula, each line in a :doc:`improper_coeff
|
||||
<improper_coeff>` command in the input script lists 7 coefficients,
|
||||
the first of which is *aa* to indicate they are AngleAngle
|
||||
coefficients. In a data file, these coefficients should be listed
|
||||
under a *AngleAngle Coeffs* heading and you must leave out the *aa*,
|
||||
i.e. only list 6 coefficients after the improper type.
|
||||
|
||||
* *aa*
|
||||
* :math:`M_1` (energy/distance)
|
||||
* :math:`M_2` (energy/distance)
|
||||
* :math:`M_3` (energy/distance)
|
||||
* :math:`M_1` (energy)
|
||||
* :math:`M_2` (energy)
|
||||
* :math:`M_3` (energy)
|
||||
* :math:`\theta_1` (degrees)
|
||||
* :math:`\theta_2` (degrees)
|
||||
* :math:`\theta_3` (degrees)
|
||||
|
||||
The theta values are specified in degrees, but LAMMPS converts them to
|
||||
radians internally; hence the units of M are in energy/radian\^2.
|
||||
The :math:`\theta` values are specified in degrees, but LAMMPS
|
||||
converts them to radians internally; hence the hence the various
|
||||
:math:`M` are effectively energy per radian\^2.
|
||||
|
||||
----------
|
||||
|
||||
@ -109,7 +111,8 @@ produce the same results, except for round-off and precision issues.
|
||||
|
||||
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
|
||||
USER-OMP and OPT packages, respectively. They are only enabled if
|
||||
LAMMPS was built with those packages. See the :doc:`Build package <Build_package>` doc page for more info.
|
||||
LAMMPS was built with those packages. See the :doc:`Build package
|
||||
<Build_package>` doc page for more info.
|
||||
|
||||
You can specify the accelerated styles explicitly in your input script
|
||||
by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
|
||||
|
||||
@ -59,11 +59,12 @@ above, or in the data file or restart files read by the
|
||||
:doc:`read_data <read_data>` or :doc:`read_restart <read_restart>`
|
||||
commands:
|
||||
|
||||
* :math:`K` (energy/radian\^2)
|
||||
* :math:`K` (energy)
|
||||
* :math:`\chi_0` (degrees)
|
||||
|
||||
:math:`\chi_0` is specified in degrees, but LAMMPS converts it to radians
|
||||
internally; hence the units of K are in energy/radian\^2.
|
||||
:math:`\chi_0` is specified in degrees, but LAMMPS converts it to
|
||||
radians internally; hence :math:`K` is effectively energy per
|
||||
radian\^2.
|
||||
|
||||
----------
|
||||
|
||||
@ -76,11 +77,13 @@ produce the same results, except for round-off and precision issues.
|
||||
|
||||
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
|
||||
USER-OMP and OPT packages, respectively. They are only enabled if
|
||||
LAMMPS was built with those packages. See the :doc:`Build package <Build_package>` doc page for more info.
|
||||
LAMMPS was built with those packages. See the :doc:`Build package
|
||||
<Build_package>` doc page for more info.
|
||||
|
||||
You can specify the accelerated styles explicitly in your input script
|
||||
by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
|
||||
:doc:`suffix <suffix>` command in your input script.
|
||||
by including their suffix, or you can use the :doc:`-suffix
|
||||
command-line switch <Run_options>` when you invoke LAMMPS, or you can
|
||||
use the :doc:`suffix <suffix>` command in your input script.
|
||||
|
||||
See the :doc:`Speed packages <Speed_packages>` doc page for more
|
||||
instructions on how to use the accelerated styles effectively.
|
||||
|
||||
@ -437,7 +437,7 @@ virial, so this contribution is not included.
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
:doc:`kspace_modify <kspace_modify>`, :doc:`pair_style lj/cut/coul/long <pair_lj>`, :doc:`pair_style lj/charmm/coul/long <pair_charmm>`, :doc:`pair_style lj/long/coul/long <pair_lj_long>`, :doc:`pair_style buck/coul/long <pair_buck>`
|
||||
:doc:`kspace_modify <kspace_modify>`, :doc:`pair_style lj/cut/coul/long <pair_lj_cut_coul>`, :doc:`pair_style lj/charmm/coul/long <pair_charmm>`, :doc:`pair_style lj/long/coul/long <pair_lj_long>`, :doc:`pair_style buck/coul/long <pair_buck>`
|
||||
|
||||
Default
|
||||
"""""""
|
||||
|
||||
@ -231,7 +231,7 @@ so that its energy is 0.0 at the cutoff via the
|
||||
:doc:`pair_modify <pair_modify>` command. See the doc pages for
|
||||
individual :doc:`pair styles <pair_style>` for details. Note that
|
||||
Coulombic potentials always have a cutoff, unless versions with a
|
||||
long-range component are used (e.g. :doc:`pair_style lj/cut/coul/long <pair_lj>`). The CHARMM potentials go to 0.0 at
|
||||
long-range component are used (e.g. :doc:`pair_style lj/cut/coul/long <pair_lj_cut_coul>`). The CHARMM potentials go to 0.0 at
|
||||
the cutoff (e.g. :doc:`pair_style lj/charmm/coul/charmm <pair_charmm>`),
|
||||
as do the GROMACS potentials (e.g. :doc:`pair_style lj/gromacs <pair_gromacs>`).
|
||||
|
||||
|
||||
@ -518,7 +518,7 @@ script are supported by the KOKKOS package. In this case data can stay
|
||||
on the GPU for many timesteps without being moved between the host and
|
||||
GPU, if you use the *device* value. If your script uses styles (e.g.
|
||||
fixes) which are not yet supported by the KOKKOS package, then data has
|
||||
to be move between the host and device anyway, so it is typically faster
|
||||
to be moved between the host and device anyway, so it is typically faster
|
||||
to let the host handle communication, by using the *host* value. Using
|
||||
*host* instead of *no* will enable use of multiple threads to
|
||||
pack/unpack communicated data. When running small systems on a GPU,
|
||||
|
||||
@ -120,7 +120,7 @@ the "/cs" in the name:
|
||||
* :doc:`pair_style buck/coul/long <pair_buck>`
|
||||
* :doc:`pair_style coul/long <pair_coul>`
|
||||
* :doc:`pair_style coul/wolf <pair_coul>`
|
||||
* :doc:`pair_style lj/cut/coul/long <pair_lj>`
|
||||
* :doc:`pair_style lj/cut/coul/long <pair_lj_cut_coul>`
|
||||
* :doc:`pair_style lj/class2/coul/long <pair_class2>`
|
||||
|
||||
except that they correctly treat the special case where the distance
|
||||
|
||||
@ -1,109 +1,15 @@
|
||||
.. index:: pair_style lj/cut
|
||||
.. index:: pair_style lj/cut/gpu
|
||||
.. index:: pair_style lj/cut/intel
|
||||
.. index:: pair_style lj/cut/kk
|
||||
.. index:: pair_style lj/cut/opt
|
||||
.. index:: pair_style lj/cut/omp
|
||||
|
||||
|
||||
pair_style lj/cut command
|
||||
=========================
|
||||
|
||||
pair_style lj/cut/gpu command
|
||||
=============================
|
||||
|
||||
pair_style lj/cut/intel command
|
||||
===============================
|
||||
|
||||
pair_style lj/cut/kk command
|
||||
============================
|
||||
|
||||
pair_style lj/cut/opt command
|
||||
=============================
|
||||
|
||||
pair_style lj/cut/omp command
|
||||
=============================
|
||||
|
||||
pair_style lj/cut/coul/cut command
|
||||
==================================
|
||||
|
||||
pair_style lj/cut/coul/cut/gpu command
|
||||
======================================
|
||||
|
||||
pair_style lj/cut/coul/cut/kk command
|
||||
=====================================
|
||||
|
||||
pair_style lj/cut/coul/cut/omp command
|
||||
======================================
|
||||
|
||||
pair_style lj/cut/coul/debye command
|
||||
====================================
|
||||
|
||||
pair_style lj/cut/coul/debye/gpu command
|
||||
========================================
|
||||
|
||||
pair_style lj/cut/coul/debye/kk command
|
||||
=======================================
|
||||
|
||||
pair_style lj/cut/coul/debye/omp command
|
||||
========================================
|
||||
|
||||
pair_style lj/cut/coul/dsf command
|
||||
==================================
|
||||
|
||||
pair_style lj/cut/coul/dsf/gpu command
|
||||
======================================
|
||||
|
||||
pair_style lj/cut/coul/dsf/kk command
|
||||
=====================================
|
||||
|
||||
pair_style lj/cut/coul/dsf/omp command
|
||||
======================================
|
||||
|
||||
pair_style lj/cut/coul/long command
|
||||
===================================
|
||||
|
||||
pair_style lj/cut/coul/long/gpu command
|
||||
=======================================
|
||||
|
||||
pair_style lj/cut/coul/long/kk command
|
||||
======================================
|
||||
|
||||
pair_style lj/cut/coul/long/intel command
|
||||
=========================================
|
||||
|
||||
pair_style lj/cut/coul/long/opt command
|
||||
=======================================
|
||||
|
||||
pair_style lj/cut/coul/long/omp command
|
||||
=======================================
|
||||
|
||||
pair_style lj/cut/coul/msm command
|
||||
==================================
|
||||
|
||||
pair_style lj/cut/coul/msm/gpu command
|
||||
======================================
|
||||
|
||||
pair_style lj/cut/coul/msm/omp command
|
||||
======================================
|
||||
|
||||
pair_style lj/cut/coul/wolf command
|
||||
===================================
|
||||
|
||||
pair_style lj/cut/coul/wolf/omp command
|
||||
=======================================
|
||||
|
||||
pair_style lj/cut/tip4p/cut command
|
||||
===================================
|
||||
|
||||
pair_style lj/cut/tip4p/cut/omp command
|
||||
=======================================
|
||||
|
||||
pair_style lj/cut/tip4p/long command
|
||||
====================================
|
||||
|
||||
pair_style lj/cut/tip4p/long/gpu command
|
||||
========================================
|
||||
|
||||
pair_style lj/cut/tip4p/long/omp command
|
||||
========================================
|
||||
|
||||
pair_style lj/cut/tip4p/long/opt command
|
||||
========================================
|
||||
Accelerator Variants: *lj/cut/gpu*, *lj/cut/intel*, *lj/cut/kk*, *lj/cut/opt*, *lj/cut/omp*
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
@ -112,46 +18,13 @@ Syntax
|
||||
|
||||
pair_style style args
|
||||
|
||||
* style = *lj/cut* or *lj/cut/coul/cut* or *lj/cut/coul/debye* or *lj/cut/coul/dsf* or *lj/cut/coul/long* *lj/cut/coul/msm* or *lj/cut/tip4p/long*
|
||||
* style = *lj/cut*
|
||||
* args = list of arguments for a particular style
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
*lj/cut* args = cutoff
|
||||
cutoff = global cutoff for Lennard Jones interactions (distance units)
|
||||
*lj/cut/coul/cut* args = cutoff (cutoff2)
|
||||
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
|
||||
cutoff2 = global cutoff for Coulombic (optional) (distance units)
|
||||
*lj/cut/coul/debye* args = kappa cutoff (cutoff2)
|
||||
kappa = inverse of the Debye length (inverse distance units)
|
||||
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
|
||||
cutoff2 = global cutoff for Coulombic (optional) (distance units)
|
||||
*lj/cut/coul/dsf* args = alpha cutoff (cutoff2)
|
||||
alpha = damping parameter (inverse distance units)
|
||||
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
|
||||
cutoff2 = global cutoff for Coulombic (distance units)
|
||||
*lj/cut/coul/long* args = cutoff (cutoff2)
|
||||
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
|
||||
cutoff2 = global cutoff for Coulombic (optional) (distance units)
|
||||
*lj/cut/coul/msm* args = cutoff (cutoff2)
|
||||
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
|
||||
cutoff2 = global cutoff for Coulombic (optional) (distance units)
|
||||
*lj/cut/coul/wolf* args = alpha cutoff (cutoff2)
|
||||
alpha = damping parameter (inverse distance units)
|
||||
cutoff = global cutoff for LJ (and Coulombic if only 2 arg) (distance units)
|
||||
cutoff2 = global cutoff for Coulombic (optional) (distance units)
|
||||
*lj/cut/tip4p/cut* args = otype htype btype atype qdist cutoff (cutoff2)
|
||||
otype,htype = atom types for TIP4P O and H
|
||||
btype,atype = bond and angle types for TIP4P waters
|
||||
qdist = distance from O atom to massless charge (distance units)
|
||||
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
|
||||
cutoff2 = global cutoff for Coulombic (optional) (distance units)
|
||||
*lj/cut/tip4p/long* args = otype htype btype atype qdist cutoff (cutoff2)
|
||||
otype,htype = atom types for TIP4P O and H
|
||||
btype,atype = bond and angle types for TIP4P waters
|
||||
qdist = distance from O atom to massless charge (distance units)
|
||||
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
|
||||
cutoff2 = global cutoff for Coulombic (optional) (distance units)
|
||||
|
||||
Examples
|
||||
""""""""
|
||||
@ -162,46 +35,6 @@ Examples
|
||||
pair_coeff * * 1 1
|
||||
pair_coeff 1 1 1 1.1 2.8
|
||||
|
||||
pair_style lj/cut/coul/cut 10.0
|
||||
pair_style lj/cut/coul/cut 10.0 8.0
|
||||
pair_coeff * * 100.0 3.0
|
||||
pair_coeff 1 1 100.0 3.5 9.0
|
||||
pair_coeff 1 1 100.0 3.5 9.0 9.0
|
||||
|
||||
pair_style lj/cut/coul/debye 1.5 3.0
|
||||
pair_style lj/cut/coul/debye 1.5 2.5 5.0
|
||||
pair_coeff * * 1.0 1.0
|
||||
pair_coeff 1 1 1.0 1.5 2.5
|
||||
pair_coeff 1 1 1.0 1.5 2.5 5.0
|
||||
|
||||
pair_style lj/cut/coul/dsf 0.05 2.5 10.0
|
||||
pair_coeff * * 1.0 1.0
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
pair_style lj/cut/coul/long 10.0
|
||||
pair_style lj/cut/coul/long 10.0 8.0
|
||||
pair_coeff * * 100.0 3.0
|
||||
pair_coeff 1 1 100.0 3.5 9.0
|
||||
|
||||
pair_style lj/cut/coul/msm 10.0
|
||||
pair_style lj/cut/coul/msm 10.0 8.0
|
||||
pair_coeff * * 100.0 3.0
|
||||
pair_coeff 1 1 100.0 3.5 9.0
|
||||
|
||||
pair_style lj/cut/tip4p/cut 1 2 7 8 0.15 12.0
|
||||
pair_style lj/cut/tip4p/cut 1 2 7 8 0.15 12.0 10.0
|
||||
pair_coeff * * 100.0 3.0
|
||||
pair_coeff 1 1 100.0 3.5 9.0
|
||||
|
||||
pair_style lj/cut/coul/wolf 0.2 5. 10.0
|
||||
pair_coeff * * 1.0 1.0
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
pair_style lj/cut/tip4p/long 1 2 7 8 0.15 12.0
|
||||
pair_style lj/cut/tip4p/long 1 2 7 8 0.15 12.0 10.0
|
||||
pair_coeff * * 100.0 3.0
|
||||
pair_coeff 1 1 100.0 3.5 9.0
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
@ -214,150 +47,36 @@ given by
|
||||
\left(\frac{\sigma}{r}\right)^6 \right]
|
||||
\qquad r < r_c
|
||||
|
||||
Rc is the cutoff.
|
||||
:math:`r_c` is the cutoff.
|
||||
|
||||
Style *lj/cut/coul/cut* adds a Coulombic pairwise interaction given by
|
||||
See the :doc:`lj/cut/coul <pair_lj_cut_coul>` styles to add a Coulombic
|
||||
pairwise interaction and the :doc:`lj/cut/tip4p <pair_lj_cut_tip4p>` styles to
|
||||
add the TIP4P water model.
|
||||
|
||||
.. math::
|
||||
Coefficients
|
||||
""""""""""""
|
||||
|
||||
E = \frac{C q_i q_j}{\epsilon r} \qquad r < r_c
|
||||
|
||||
where C is an energy-conversion constant, :math:`q_i` and :math:`q_j`
|
||||
are the charges on the 2 atoms, and :math:`\epsilon` is the dielectric
|
||||
constant which can be set by the :doc:`dielectric <dielectric>` command.
|
||||
If one cutoff is specified in the pair_style command, it is used for
|
||||
both the LJ and Coulombic terms. If two cutoffs are specified, they are
|
||||
used as cutoffs for the LJ and Coulombic terms respectively.
|
||||
|
||||
Style *lj/cut/coul/debye* adds an additional exp() damping factor
|
||||
to the Coulombic term, given by
|
||||
|
||||
.. math::
|
||||
|
||||
E = \frac{C q_i q_j}{\epsilon r} \exp(- \kappa r) \qquad r < r_c
|
||||
|
||||
where :math:`\kappa` is the inverse of the Debye length. This potential
|
||||
is another way to mimic the screening effect of a polar solvent.
|
||||
|
||||
Style *lj/cut/coul/dsf* computes the Coulombic term via the damped
|
||||
shifted force model described in :ref:`Fennell <Fennell2>`, given by:
|
||||
|
||||
.. math::
|
||||
|
||||
E =
|
||||
q_iq_j \left[ \frac{\mbox{erfc} (\alpha r)}{r} - \frac{\mbox{erfc} (\alpha r_c)}{r_c} +
|
||||
\left( \frac{\mbox{erfc} (\alpha r_c)}{r_c^2} + \frac{2\alpha}{\sqrt{\pi}}\frac{\exp (-\alpha^2 r^2_c)}{r_c} \right)(r-r_c) \right] \qquad r < r_c
|
||||
|
||||
where :math:`\alpha` is the damping parameter and erfc() is the complementary
|
||||
error-function. This potential is essentially a short-range,
|
||||
spherically-truncated, charge-neutralized, shifted, pairwise *1/r*
|
||||
summation. The potential is based on Wolf summation, proposed as an
|
||||
alternative to Ewald summation for condensed phase systems where
|
||||
charge screening causes electrostatic interactions to become
|
||||
effectively short-ranged. In order for the electrostatic sum to be
|
||||
absolutely convergent, charge neutralization within the cutoff radius
|
||||
is enforced by shifting the potential through placement of image
|
||||
charges on the cutoff sphere. Convergence can often be improved by
|
||||
setting :math:`\alpha` to a small non-zero value.
|
||||
|
||||
Styles *lj/cut/coul/long* and *lj/cut/coul/msm* compute the same
|
||||
Coulombic interactions as style *lj/cut/coul/cut* except that an
|
||||
additional damping factor is applied to the Coulombic term so it can
|
||||
be used in conjunction with the :doc:`kspace_style <kspace_style>`
|
||||
command and its *ewald* or *pppm* option. The Coulombic cutoff
|
||||
specified for this style means that pairwise interactions within this
|
||||
distance are computed directly; interactions outside that distance are
|
||||
computed in reciprocal space.
|
||||
|
||||
Style *coul/wolf* adds a Coulombic pairwise interaction via the Wolf
|
||||
summation method, described in :ref:`Wolf <Wolf1>`, given by:
|
||||
|
||||
.. math::
|
||||
|
||||
E_i = \frac{1}{2} \sum_{j \neq i}
|
||||
\frac{q_i q_j {\rm erfc}(\alpha r_{ij})}{r_{ij}} +
|
||||
\frac{1}{2} \sum_{j \neq i}
|
||||
\frac{q_i q_j {\rm erf}(\alpha r_{ij})}{r_{ij}} \qquad r < r_c
|
||||
|
||||
where :math:`\alpha` is the damping parameter, and erfc() is the
|
||||
complementary error-function terms. This potential is essentially a
|
||||
short-range, spherically-truncated, charge-neutralized, shifted,
|
||||
pairwise *1/r* summation. With a manipulation of adding and subtracting
|
||||
a self term (for i = j) to the first and second term on the
|
||||
right-hand-side, respectively, and a small enough :math:`\alpha` damping
|
||||
parameter, the second term shrinks and the potential becomes a
|
||||
rapidly-converging real-space summation. With a long enough cutoff and
|
||||
small enough :math:`\alpha` parameter, the energy and forces calculated by the
|
||||
Wolf summation method approach those of the Ewald sum. So it is a means
|
||||
of getting effective long-range interactions with a short-range
|
||||
potential.
|
||||
|
||||
Styles *lj/cut/tip4p/cut* and *lj/cut/tip4p/long* implement the TIP4P
|
||||
water model of :ref:`(Jorgensen) <Jorgensen2>`, which introduces a massless
|
||||
site located a short distance away from the oxygen atom along the
|
||||
bisector of the HOH angle. The atomic types of the oxygen and
|
||||
hydrogen atoms, the bond and angle types for OH and HOH interactions,
|
||||
and the distance to the massless charge site are specified as
|
||||
pair_style arguments. Style *lj/cut/tip4p/cut* uses a cutoff for
|
||||
Coulomb interactions; style *lj/cut/tip4p/long* is for use with a
|
||||
long-range Coulombic solver (Ewald or PPPM).
|
||||
|
||||
.. note::
|
||||
|
||||
For each TIP4P water molecule in your system, the atom IDs for
|
||||
the O and 2 H atoms must be consecutive, with the O atom first. This
|
||||
is to enable LAMMPS to "find" the 2 H atoms associated with each O
|
||||
atom. For example, if the atom ID of an O atom in a TIP4P water
|
||||
molecule is 500, then its 2 H atoms must have IDs 501 and 502.
|
||||
|
||||
See the :doc:`Howto tip4p <Howto_tip4p>` doc page for more information
|
||||
on how to use the TIP4P pair styles and lists of parameters to set.
|
||||
Note that the neighbor list cutoff for Coulomb interactions is
|
||||
effectively extended by a distance 2\*qdist when using the TIP4P pair
|
||||
style, to account for the offset distance of the fictitious charges on
|
||||
O atoms in water molecules. Thus it is typically best in an
|
||||
efficiency sense to use a LJ cutoff >= Coulombic cutoff + 2\*qdist, to
|
||||
shrink the size of the neighbor list. This leads to slightly larger
|
||||
cost for the long-range calculation, so you can test the trade-off for
|
||||
your model.
|
||||
|
||||
For all of the *lj/cut* pair styles, the following coefficients must
|
||||
be defined for each pair of atoms 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:
|
||||
The following coefficients must be defined for each pair of atoms 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:
|
||||
|
||||
* :math:`\epsilon` (energy units)
|
||||
* :math:`\sigma` (distance units)
|
||||
* cutoff1 (distance units)
|
||||
* cutoff2 (distance units)
|
||||
* LJ cutoff (distance units)
|
||||
|
||||
Note that :math:`\sigma` is defined in the LJ formula as the zero-crossing
|
||||
distance for the potential, not as the energy minimum at :math:`2^{\frac{1}{6}} \sigma`.
|
||||
|
||||
The latter 2 coefficients are optional. If not specified, the global
|
||||
LJ and Coulombic cutoffs specified in the pair_style command are used.
|
||||
If only one cutoff is specified, it is used as the cutoff for both LJ
|
||||
and Coulombic interactions for this type pair. If both coefficients
|
||||
are specified, they are used as the LJ and Coulombic cutoffs for this
|
||||
type pair. You cannot specify 2 cutoffs for style *lj/cut*\ , since it
|
||||
has no Coulombic terms.
|
||||
|
||||
For *lj/cut/coul/long* and *lj/cut/coul/msm* and *lj/cut/tip4p/cut*
|
||||
and *lj/cut/tip4p/long* only the LJ cutoff can be specified since a
|
||||
Coulombic cutoff cannot be specified for an individual I,J type pair.
|
||||
All type pairs use the same global Coulombic cutoff specified in the
|
||||
pair_style command.
|
||||
The last coefficient is optional. If not specified, the global
|
||||
LJ cutoff specified in the pair_style command are used.
|
||||
|
||||
----------
|
||||
|
||||
A version of these styles with a soft core, *lj/cut/soft*\ , suitable
|
||||
for use in free energy calculations, is part of the USER-FEP package and
|
||||
is documented with the :doc:`pair_style */soft <pair_fep_soft>`
|
||||
styles. The version with soft core is only available if LAMMPS was built
|
||||
with that package. See the :doc:`Build package <Build_package>` doc page
|
||||
for more info.
|
||||
styles.
|
||||
|
||||
----------
|
||||
|
||||
@ -381,21 +100,17 @@ instructions on how to use the accelerated styles effectively.
|
||||
|
||||
----------
|
||||
|
||||
**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
|
||||
**Mixing, shift, table, tail correction, restart, rRESPA info:**
|
||||
|
||||
For atom type pairs I,J and I != J, the epsilon and sigma coefficients
|
||||
and cutoff distance for all of the lj/cut pair styles can be mixed.
|
||||
The default mix value is *geometric*\ . See the "pair_modify" command
|
||||
The default mix value is *geometric*. See the "pair_modify" command
|
||||
for details.
|
||||
|
||||
All of the *lj/cut* pair styles support the
|
||||
:doc:`pair_modify <pair_modify>` shift option for the energy of the
|
||||
Lennard-Jones portion of the pair interaction.
|
||||
|
||||
The *lj/cut/coul/long* and *lj/cut/tip4p/long* pair styles support the
|
||||
:doc:`pair_modify <pair_modify>` table option since they can tabulate
|
||||
the short-range portion of the long-range Coulombic interaction.
|
||||
|
||||
All of the *lj/cut* pair styles support the
|
||||
:doc:`pair_modify <pair_modify>` tail option for adding a long-range
|
||||
tail correction to the energy and pressure for the Lennard-Jones
|
||||
@ -404,7 +119,7 @@ portion of the pair interaction.
|
||||
All of the *lj/cut* pair styles write their 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 *lj/cut* and *lj/cut/coul/long* pair styles support the use of the
|
||||
The *lj/cut* pair styles support the use of the
|
||||
*inner*\ , *middle*\ , and *outer* keywords of the :doc:`run_style respa <run_style>` command, meaning the pairwise forces can be
|
||||
partitioned by distance at different levels of the rRESPA hierarchy.
|
||||
The other styles only support the *pair* keyword of run_style respa.
|
||||
@ -412,30 +127,17 @@ See the :doc:`run_style <run_style>` command for details.
|
||||
|
||||
----------
|
||||
|
||||
Restrictions
|
||||
""""""""""""
|
||||
|
||||
The *lj/cut/coul/long* and *lj/cut/tip4p/long* styles are part of the
|
||||
KSPACE package. The *lj/cut/tip4p/cut* style is part of the MOLECULE
|
||||
package. These styles are only enabled if LAMMPS was built with those
|
||||
packages. See the :doc:`Build package <Build_package>` doc page for
|
||||
more info.
|
||||
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
:doc:`pair_coeff <pair_coeff>`
|
||||
* :doc:`pair_coeff <pair_coeff>`
|
||||
* :doc:`pair_style lj/cut/coul/cut <pair_lj_cut_coul>`
|
||||
* :doc:`pair_style lj/cut/coul/debye <pair_lj_cut_coul>`
|
||||
* :doc:`pair_style lj/cut/coul/dsf <pair_lj_cut_coul>`
|
||||
* :doc:`pair_style lj/cut/coul/long <pair_lj_cut_coul>`
|
||||
* :doc:`pair_style lj/cut/coul/msm <pair_lj_cut_coul>`
|
||||
* :doc:`pair_style lj/cut/coul/wolf <pair_lj_cut_coul>`
|
||||
* :doc:`pair_style lj/cut/tip4p/cut <pair_lj_cut_tip4p>`
|
||||
* :doc:`pair_style lj/cut/tip4p/long <pair_lj_cut_tip4p>`
|
||||
|
||||
**Default:** none
|
||||
|
||||
----------
|
||||
|
||||
.. _Jorgensen2:
|
||||
|
||||
**(Jorgensen)** Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem
|
||||
Phys, 79, 926 (1983).
|
||||
|
||||
.. _Fennell2:
|
||||
|
||||
**(Fennell)** C. J. Fennell, J. D. Gezelter, J Chem Phys, 124,
|
||||
234104 (2006).
|
||||
|
||||
328
doc/src/pair_lj_cut_coul.rst
Normal file
328
doc/src/pair_lj_cut_coul.rst
Normal file
@ -0,0 +1,328 @@
|
||||
.. index:: pair_style lj/cut/coul/cut
|
||||
.. index:: pair_style lj/cut/coul/cut/gpu
|
||||
.. index:: pair_style lj/cut/coul/cut/kk
|
||||
.. index:: pair_style lj/cut/coul/cut/omp
|
||||
.. index:: pair_style lj/cut/coul/debye
|
||||
.. index:: pair_style lj/cut/coul/debye/gpu
|
||||
.. index:: pair_style lj/cut/coul/debye/kk
|
||||
.. index:: pair_style lj/cut/coul/debye/omp
|
||||
.. index:: pair_style lj/cut/coul/dsf
|
||||
.. index:: pair_style lj/cut/coul/dsf/gpu
|
||||
.. index:: pair_style lj/cut/coul/dsf/kk
|
||||
.. index:: pair_style lj/cut/coul/dsf/omp
|
||||
.. index:: pair_style lj/cut/coul/long
|
||||
.. index:: pair_style lj/cut/coul/long/gpu
|
||||
.. index:: pair_style lj/cut/coul/long/kk
|
||||
.. index:: pair_style lj/cut/coul/long/intel
|
||||
.. index:: pair_style lj/cut/coul/long/opt
|
||||
.. index:: pair_style lj/cut/coul/long/omp
|
||||
.. index:: pair_style lj/cut/coul/msm
|
||||
.. index:: pair_style lj/cut/coul/msm/gpu
|
||||
.. index:: pair_style lj/cut/coul/msm/omp
|
||||
.. index:: pair_style lj/cut/coul/wolf
|
||||
.. index:: pair_style lj/cut/coul/wolf/omp
|
||||
|
||||
pair_style lj/cut/coul/cut command
|
||||
==================================
|
||||
|
||||
Accelerator Variants: *lj/cut/coul/cut/gpu*, *lj/cut/coul/cut/kk*, *lj/cut/coul/cut/omp*
|
||||
|
||||
pair_style lj/cut/coul/debye command
|
||||
====================================
|
||||
|
||||
Accelerator Variants: *lj/cut/coul/debye/gpu*, lj/cut/coul/debye/kk, *lj/cut/coul/debye/omp*
|
||||
|
||||
pair_style lj/cut/coul/dsf command
|
||||
==================================
|
||||
|
||||
Accelerator Variants: *lj/cut/coul/dsf/gpu*, *lj/cut/coul/dsf/kk*, *lj/cut/coul/dsf/omp*
|
||||
|
||||
pair_style lj/cut/coul/long command
|
||||
===================================
|
||||
|
||||
Accelerator Variants: *lj/cut/coul/long/gpu*, *lj/cut/coul/long/kk*, *lj/cut/coul/long/intel*, *lj/cut/coul/long/opt*, *lj/cut/coul/long/omp*
|
||||
|
||||
pair_style lj/cut/coul/msm command
|
||||
==================================
|
||||
|
||||
Accelerator Variants: *lj/cut/coul/msm/gpu*, *lj/cut/coul/msm/omp*
|
||||
|
||||
pair_style lj/cut/coul/wolf command
|
||||
===================================
|
||||
|
||||
Accelerator Variants: *lj/cut/coul/wolf/omp*
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
pair_style style args
|
||||
|
||||
* style = *lj/cut/coul/cut* or *lj/cut/coul/debye* or *lj/cut/coul/dsf* or *lj/cut/coul/long* *lj/cut/coul/msm* or *lj/cut/coul/wolf*
|
||||
* args = list of arguments for a particular style
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
*lj/cut/coul/cut* args = cutoff (cutoff2)
|
||||
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
|
||||
cutoff2 = global cutoff for Coulombic (optional) (distance units)
|
||||
*lj/cut/coul/debye* args = kappa cutoff (cutoff2)
|
||||
kappa = inverse of the Debye length (inverse distance units)
|
||||
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
|
||||
cutoff2 = global cutoff for Coulombic (optional) (distance units)
|
||||
*lj/cut/coul/dsf* args = alpha cutoff (cutoff2)
|
||||
alpha = damping parameter (inverse distance units)
|
||||
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
|
||||
cutoff2 = global cutoff for Coulombic (distance units)
|
||||
*lj/cut/coul/long* args = cutoff (cutoff2)
|
||||
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
|
||||
cutoff2 = global cutoff for Coulombic (optional) (distance units)
|
||||
*lj/cut/coul/msm* args = cutoff (cutoff2)
|
||||
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
|
||||
cutoff2 = global cutoff for Coulombic (optional) (distance units)
|
||||
*lj/cut/coul/wolf* args = alpha cutoff (cutoff2)
|
||||
alpha = damping parameter (inverse distance units)
|
||||
cutoff = global cutoff for LJ (and Coulombic if only 2 arg) (distance units)
|
||||
cutoff2 = global cutoff for Coulombic (optional) (distance units)
|
||||
|
||||
Examples
|
||||
""""""""
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
pair_style lj/cut/coul/cut 10.0
|
||||
pair_style lj/cut/coul/cut 10.0 8.0
|
||||
pair_coeff * * 100.0 3.0
|
||||
pair_coeff 1 1 100.0 3.5 9.0
|
||||
pair_coeff 1 1 100.0 3.5 9.0 9.0
|
||||
|
||||
pair_style lj/cut/coul/debye 1.5 3.0
|
||||
pair_style lj/cut/coul/debye 1.5 2.5 5.0
|
||||
pair_coeff * * 1.0 1.0
|
||||
pair_coeff 1 1 1.0 1.5 2.5
|
||||
pair_coeff 1 1 1.0 1.5 2.5 5.0
|
||||
|
||||
pair_style lj/cut/coul/dsf 0.05 2.5 10.0
|
||||
pair_coeff * * 1.0 1.0
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
pair_style lj/cut/coul/long 10.0
|
||||
pair_style lj/cut/coul/long 10.0 8.0
|
||||
pair_coeff * * 100.0 3.0
|
||||
pair_coeff 1 1 100.0 3.5 9.0
|
||||
|
||||
pair_style lj/cut/coul/msm 10.0
|
||||
pair_style lj/cut/coul/msm 10.0 8.0
|
||||
pair_coeff * * 100.0 3.0
|
||||
pair_coeff 1 1 100.0 3.5 9.0
|
||||
|
||||
pair_style lj/cut/coul/wolf 0.2 5. 10.0
|
||||
pair_coeff * * 1.0 1.0
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
The *lj/cut/coul* styles compute the standard 12/6 Lennard-Jones potential,
|
||||
given by
|
||||
|
||||
.. math::
|
||||
|
||||
E = 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} -
|
||||
\left(\frac{\sigma}{r}\right)^6 \right]
|
||||
\qquad r < r_c
|
||||
|
||||
:math:`r_c` is the cutoff.
|
||||
|
||||
Style *lj/cut/coul/cut* adds a Coulombic pairwise interaction given by
|
||||
|
||||
.. math::
|
||||
|
||||
E = \frac{C q_i q_j}{\epsilon r} \qquad r < r_c
|
||||
|
||||
where :math:`C` is an energy-conversion constant, :math:`q_i` and :math:`q_j`
|
||||
are the charges on the 2 atoms, and :math:`\epsilon` is the dielectric
|
||||
constant which can be set by the :doc:`dielectric <dielectric>` command.
|
||||
If one cutoff is specified in the pair_style command, it is used for
|
||||
both the LJ and Coulombic terms. If two cutoffs are specified, they are
|
||||
used as cutoffs for the LJ and Coulombic terms respectively.
|
||||
|
||||
Style *lj/cut/coul/debye* adds an additional exp() damping factor
|
||||
to the Coulombic term, given by
|
||||
|
||||
.. math::
|
||||
|
||||
E = \frac{C q_i q_j}{\epsilon r} \exp(- \kappa r) \qquad r < r_c
|
||||
|
||||
where :math:`\kappa` is the inverse of the Debye length. This potential
|
||||
is another way to mimic the screening effect of a polar solvent.
|
||||
|
||||
Style *lj/cut/coul/dsf* computes the Coulombic term via the damped
|
||||
shifted force model described in :ref:`Fennell <Fennell2>`, given by:
|
||||
|
||||
.. math::
|
||||
|
||||
E =
|
||||
q_iq_j \left[ \frac{\mbox{erfc} (\alpha r)}{r} - \frac{\mbox{erfc} (\alpha r_c)}{r_c} +
|
||||
\left( \frac{\mbox{erfc} (\alpha r_c)}{r_c^2} + \frac{2\alpha}{\sqrt{\pi}}\frac{\exp (-\alpha^2 r^2_c)}{r_c} \right)(r-r_c) \right] \qquad r < r_c
|
||||
|
||||
where :math:`\alpha` is the damping parameter and erfc() is the complementary
|
||||
error-function. This potential is essentially a short-range,
|
||||
spherically-truncated, charge-neutralized, shifted, pairwise *1/r*
|
||||
summation. The potential is based on Wolf summation, proposed as an
|
||||
alternative to Ewald summation for condensed phase systems where
|
||||
charge screening causes electrostatic interactions to become
|
||||
effectively short-ranged. In order for the electrostatic sum to be
|
||||
absolutely convergent, charge neutralization within the cutoff radius
|
||||
is enforced by shifting the potential through placement of image
|
||||
charges on the cutoff sphere. Convergence can often be improved by
|
||||
setting :math:`\alpha` to a small non-zero value.
|
||||
|
||||
Styles *lj/cut/coul/long* and *lj/cut/coul/msm* compute the same
|
||||
Coulombic interactions as style *lj/cut/coul/cut* except that an
|
||||
additional damping factor is applied to the Coulombic term so it can
|
||||
be used in conjunction with the :doc:`kspace_style <kspace_style>`
|
||||
command and its *ewald* or *pppm* option. The Coulombic cutoff
|
||||
specified for this style means that pairwise interactions within this
|
||||
distance are computed directly; interactions outside that distance are
|
||||
computed in reciprocal space.
|
||||
|
||||
Style *coul/wolf* adds a Coulombic pairwise interaction via the Wolf
|
||||
summation method, described in :ref:`Wolf <Wolf3>`, given by:
|
||||
|
||||
.. math::
|
||||
|
||||
E_i = \frac{1}{2} \sum_{j \neq i}
|
||||
\frac{q_i q_j {\rm erfc}(\alpha r_{ij})}{r_{ij}} +
|
||||
\frac{1}{2} \sum_{j \neq i}
|
||||
\frac{q_i q_j {\rm erf}(\alpha r_{ij})}{r_{ij}} \qquad r < r_c
|
||||
|
||||
where :math:`\alpha` is the damping parameter, and erfc() is the
|
||||
complementary error-function terms. This potential is essentially a
|
||||
short-range, spherically-truncated, charge-neutralized, shifted,
|
||||
pairwise *1/r* summation. With a manipulation of adding and subtracting
|
||||
a self term (for i = j) to the first and second term on the
|
||||
right-hand-side, respectively, and a small enough :math:`\alpha` damping
|
||||
parameter, the second term shrinks and the potential becomes a
|
||||
rapidly-converging real-space summation. With a long enough cutoff and
|
||||
small enough :math:`\alpha` parameter, the energy and forces calculated by the
|
||||
Wolf summation method approach those of the Ewald sum. So it is a means
|
||||
of getting effective long-range interactions with a short-range
|
||||
potential.
|
||||
|
||||
Coefficients
|
||||
""""""""""""
|
||||
|
||||
For all of the *lj/cut/coul* pair styles, the following coefficients must
|
||||
be defined for each pair of atoms 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:
|
||||
|
||||
* :math:`\epsilon` (energy units)
|
||||
* :math:`\sigma` (distance units)
|
||||
* cutoff1 (distance units)
|
||||
* cutoff2 (distance units)
|
||||
|
||||
Note that :math:`\sigma` is defined in the LJ formula as the zero-crossing
|
||||
distance for the potential, not as the energy minimum at :math:`2^{\frac{1}{6}} \sigma`.
|
||||
|
||||
The latter 2 coefficients are optional. If not specified, the global
|
||||
LJ and Coulombic cutoffs specified in the pair_style command are used.
|
||||
If only one cutoff is specified, it is used as the cutoff for both LJ
|
||||
and Coulombic interactions for this type pair. If both coefficients
|
||||
are specified, they are used as the LJ and Coulombic cutoffs for this
|
||||
type pair.
|
||||
|
||||
For *lj/cut/coul/long* and *lj/cut/coul/msm* only the LJ cutoff can be
|
||||
specified since a Coulombic cutoff cannot be specified for an individual I,J
|
||||
type pair. All type pairs use the same global Coulombic cutoff specified in
|
||||
the pair_style command.
|
||||
|
||||
----------
|
||||
|
||||
A version of these styles with a soft core, *lj/cut/coul/soft*\ and
|
||||
*lj/cut/coul/long/soft*\ , suitable for use in free energy calculations, is
|
||||
part of the USER-FEP package and is documented with the :doc:`pair_style */soft <pair_fep_soft>` styles.
|
||||
|
||||
----------
|
||||
|
||||
Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
|
||||
functionally the same as the corresponding style without the suffix.
|
||||
They have been optimized to run faster, depending on your available
|
||||
hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
|
||||
page. The accelerated styles take the same arguments and should
|
||||
produce the same results, except for round-off and precision issues.
|
||||
|
||||
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
|
||||
USER-OMP and OPT packages, respectively. They are only enabled if
|
||||
LAMMPS was built with those packages. See the :doc:`Build package <Build_package>` doc page for more info.
|
||||
|
||||
You can specify the accelerated styles explicitly in your input script
|
||||
by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
|
||||
:doc:`suffix <suffix>` command in your input script.
|
||||
|
||||
See the :doc:`Speed packages <Speed_packages>` doc page for more
|
||||
instructions on how to use the accelerated styles effectively.
|
||||
|
||||
----------
|
||||
|
||||
**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
|
||||
|
||||
For atom type pairs I,J and I != J, the epsilon and sigma coefficients
|
||||
and cutoff distance for all of the lj/cut pair styles can be mixed.
|
||||
The default mix value is *geometric*\ . See the "pair_modify" command
|
||||
for details.
|
||||
|
||||
All of the *lj/cut* pair styles support the
|
||||
:doc:`pair_modify <pair_modify>` shift option for the energy of the
|
||||
Lennard-Jones portion of the pair interaction.
|
||||
|
||||
The *lj/cut/coul/long* pair styles support the
|
||||
:doc:`pair_modify <pair_modify>` table option since they can tabulate
|
||||
the short-range portion of the long-range Coulombic interaction.
|
||||
|
||||
All of the *lj/cut* pair styles support the
|
||||
:doc:`pair_modify <pair_modify>` tail option for adding a long-range
|
||||
tail correction to the energy and pressure for the Lennard-Jones
|
||||
portion of the pair interaction.
|
||||
|
||||
All of the *lj/cut* pair styles write their 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 *lj/cut/coul/long* pair styles support the use of the
|
||||
*inner*\ , *middle*\ , and *outer* keywords of the :doc:`run_style respa <run_style>` command, meaning the pairwise forces can be
|
||||
partitioned by distance at different levels of the rRESPA hierarchy.
|
||||
The other styles only support the *pair* keyword of run_style respa.
|
||||
See the :doc:`run_style <run_style>` command for details.
|
||||
|
||||
----------
|
||||
|
||||
Restrictions
|
||||
""""""""""""
|
||||
|
||||
The *lj/cut/coul/long* styles are part of the KSPACE package.
|
||||
These styles are only enabled if LAMMPS was built with those
|
||||
packages. See the :doc:`Build package <Build_package>` doc page for
|
||||
more info.
|
||||
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
:doc:`pair_coeff <pair_coeff>`
|
||||
|
||||
**Default:** none
|
||||
|
||||
----------
|
||||
|
||||
.. _Wolf3:
|
||||
|
||||
**(Wolf)** D. Wolf, P. Keblinski, S. R. Phillpot, J. Eggebrecht, J Chem
|
||||
Phys, 110, 8254 (1999).
|
||||
|
||||
.. _Fennell2:
|
||||
|
||||
**(Fennell)** C. J. Fennell, J. D. Gezelter, J Chem Phys, 124,
|
||||
234104 (2006).
|
||||
230
doc/src/pair_lj_cut_tip4p.rst
Normal file
230
doc/src/pair_lj_cut_tip4p.rst
Normal file
@ -0,0 +1,230 @@
|
||||
.. index:: pair_style lj/cut/tip4p/cut
|
||||
.. index:: pair_style lj/cut/tip4p/cut/omp
|
||||
.. index:: pair_style lj/cut/tip4p/long
|
||||
.. index:: pair_style lj/cut/tip4p/long/gpu
|
||||
.. index:: pair_style lj/cut/tip4p/long/omp
|
||||
.. index:: pair_style lj/cut/tip4p/long/opt
|
||||
|
||||
|
||||
pair_style lj/cut/tip4p/cut command
|
||||
===================================
|
||||
|
||||
Accelerator Variants: *lj/cut/tip4p/cut/omp*
|
||||
|
||||
pair_style lj/cut/tip4p/long command
|
||||
====================================
|
||||
|
||||
Accelerator Variants: *lj/cut/tip4p/long/gpu*, *lj/cut/tip4p/long/omp*, *lj/cut/tip4p/long/opt*
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
pair_style style args
|
||||
|
||||
* style = *lj/cut/tip4p/cut* or *lj/cut/tip4p/long*
|
||||
* args = list of arguments for a particular style
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
*lj/cut/tip4p/cut* args = otype htype btype atype qdist cutoff (cutoff2)
|
||||
otype,htype = atom types for TIP4P O and H
|
||||
btype,atype = bond and angle types for TIP4P waters
|
||||
qdist = distance from O atom to massless charge (distance units)
|
||||
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
|
||||
cutoff2 = global cutoff for Coulombic (optional) (distance units)
|
||||
*lj/cut/tip4p/long* args = otype htype btype atype qdist cutoff (cutoff2)
|
||||
otype,htype = atom types for TIP4P O and H
|
||||
btype,atype = bond and angle types for TIP4P waters
|
||||
qdist = distance from O atom to massless charge (distance units)
|
||||
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
|
||||
cutoff2 = global cutoff for Coulombic (optional) (distance units)
|
||||
|
||||
Examples
|
||||
""""""""
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
pair_style lj/cut/tip4p/cut 1 2 7 8 0.15 12.0
|
||||
pair_style lj/cut/tip4p/cut 1 2 7 8 0.15 12.0 10.0
|
||||
pair_coeff * * 100.0 3.0
|
||||
pair_coeff 1 1 100.0 3.5 9.0
|
||||
|
||||
pair_style lj/cut/tip4p/long 1 2 7 8 0.15 12.0
|
||||
pair_style lj/cut/tip4p/long 1 2 7 8 0.15 12.0 10.0
|
||||
pair_coeff * * 100.0 3.0
|
||||
pair_coeff 1 1 100.0 3.5 9.0
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
The *lj/cut/tip4p* styles compute the standard 12/6 Lennard-Jones potential,
|
||||
given by
|
||||
|
||||
.. math::
|
||||
|
||||
E = 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} -
|
||||
\left(\frac{\sigma}{r}\right)^6 \right]
|
||||
\qquad r < r_c
|
||||
|
||||
:math:`r_c` is the cutoff.
|
||||
|
||||
They add Coulombic pairwise interactions given by
|
||||
|
||||
.. math::
|
||||
|
||||
E = \frac{C q_i q_j}{\epsilon r} \qquad r < r_c
|
||||
|
||||
where :math:`C` is an energy-conversion constant, :math:`q_i` and :math:`q_j`
|
||||
are the charges on the 2 atoms, and :math:`\epsilon` is the dielectric
|
||||
constant which can be set by the :doc:`dielectric <dielectric>` command.
|
||||
If one cutoff is specified in the pair_style command, it is used for
|
||||
both the LJ and Coulombic terms. If two cutoffs are specified, they are
|
||||
used as cutoffs for the LJ and Coulombic terms respectively.
|
||||
|
||||
Style *lj/cut/tip4p/long* compute the same
|
||||
Coulombic interactions as style *lj/cut/tip4p/cut* except that an
|
||||
additional damping factor is applied to the Coulombic term so it can
|
||||
be used in conjunction with the :doc:`kspace_style <kspace_style>`
|
||||
command and its *ewald* or *pppm* option. The Coulombic cutoff
|
||||
specified for this style means that pairwise interactions within this
|
||||
distance are computed directly; interactions outside that distance are
|
||||
computed in reciprocal space.
|
||||
|
||||
The *lj/cut/tip4p* styles implement the TIP4P
|
||||
water model of :ref:`(Jorgensen) <Jorgensen2>`, which introduces a massless
|
||||
site located a short distance away from the oxygen atom along the
|
||||
bisector of the HOH angle. The atomic types of the oxygen and
|
||||
hydrogen atoms, the bond and angle types for OH and HOH interactions,
|
||||
and the distance to the massless charge site are specified as
|
||||
pair_style arguments. Style *lj/cut/tip4p/cut* uses a cutoff for
|
||||
Coulomb interactions; style *lj/cut/tip4p/long* is for use with a
|
||||
long-range Coulombic solver (Ewald or PPPM).
|
||||
|
||||
.. note::
|
||||
|
||||
For each TIP4P water molecule in your system, the atom IDs for
|
||||
the O and 2 H atoms must be consecutive, with the O atom first. This
|
||||
is to enable LAMMPS to "find" the 2 H atoms associated with each O
|
||||
atom. For example, if the atom ID of an O atom in a TIP4P water
|
||||
molecule is 500, then its 2 H atoms must have IDs 501 and 502.
|
||||
|
||||
See the :doc:`Howto tip4p <Howto_tip4p>` doc page for more information
|
||||
on how to use the TIP4P pair styles and lists of parameters to set.
|
||||
Note that the neighbor list cutoff for Coulomb interactions is
|
||||
effectively extended by a distance 2\*qdist when using the TIP4P pair
|
||||
style, to account for the offset distance of the fictitious charges on
|
||||
O atoms in water molecules. Thus it is typically best in an
|
||||
efficiency sense to use a LJ cutoff >= Coulombic cutoff + 2\*qdist, to
|
||||
shrink the size of the neighbor list. This leads to slightly larger
|
||||
cost for the long-range calculation, so you can test the trade-off for
|
||||
your model.
|
||||
|
||||
Coefficients
|
||||
""""""""""""
|
||||
|
||||
For all of the *lj/cut* pair styles, the following coefficients must
|
||||
be defined for each pair of atoms 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:
|
||||
|
||||
* :math:`\epsilon` (energy units)
|
||||
* :math:`\sigma` (distance units)
|
||||
* LJ cutoff (distance units)
|
||||
|
||||
Note that :math:`\sigma` is defined in the LJ formula as the zero-crossing
|
||||
distance for the potential, not as the energy minimum at :math:`2^{\frac{1}{6}} \sigma`.
|
||||
|
||||
The last coefficient is optional. If not specified, the global
|
||||
LJ cutoff specified in the pair_style command is used.
|
||||
|
||||
For *lj/cut/tip4p/cut* and *lj/cut/tip4p/long* only the LJ cutoff can be
|
||||
specified since a Coulombic cutoff cannot be specified for an individual I,J
|
||||
type pair. All type pairs use the same global Coulombic cutoff specified in
|
||||
the pair_style command.
|
||||
|
||||
----------
|
||||
|
||||
A version of these styles with a soft core, *lj/cut/tip4p/long/soft*\ , suitable
|
||||
for use in free energy calculations, is part of the USER-FEP package and
|
||||
is documented with the :doc:`pair_style */soft <pair_fep_soft>`
|
||||
styles.
|
||||
|
||||
----------
|
||||
|
||||
Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
|
||||
functionally the same as the corresponding style without the suffix.
|
||||
They have been optimized to run faster, depending on your available
|
||||
hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
|
||||
page. The accelerated styles take the same arguments and should
|
||||
produce the same results, except for round-off and precision issues.
|
||||
|
||||
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
|
||||
USER-OMP and OPT packages, respectively. They are only enabled if
|
||||
LAMMPS was built with those packages. See the :doc:`Build package <Build_package>` doc page for more info.
|
||||
|
||||
You can specify the accelerated styles explicitly in your input script
|
||||
by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
|
||||
:doc:`suffix <suffix>` command in your input script.
|
||||
|
||||
See the :doc:`Speed packages <Speed_packages>` doc page for more
|
||||
instructions on how to use the accelerated styles effectively.
|
||||
|
||||
----------
|
||||
|
||||
**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
|
||||
|
||||
For atom type pairs I,J and I != J, the epsilon and sigma coefficients
|
||||
and cutoff distance for all of the lj/cut pair styles can be mixed.
|
||||
The default mix value is *geometric*\ . See the "pair_modify" command
|
||||
for details.
|
||||
|
||||
All of the *lj/cut* pair styles support the
|
||||
:doc:`pair_modify <pair_modify>` shift option for the energy of the
|
||||
Lennard-Jones portion of the pair interaction.
|
||||
|
||||
The *lj/cut/coul/long* and *lj/cut/tip4p/long* pair styles support the
|
||||
:doc:`pair_modify <pair_modify>` table option since they can tabulate
|
||||
the short-range portion of the long-range Coulombic interaction.
|
||||
|
||||
All of the *lj/cut* pair styles support the
|
||||
:doc:`pair_modify <pair_modify>` tail option for adding a long-range
|
||||
tail correction to the energy and pressure for the Lennard-Jones
|
||||
portion of the pair interaction.
|
||||
|
||||
All of the *lj/cut* pair styles write their 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 *lj/cut* and *lj/cut/coul/long* pair styles support the use of the
|
||||
*inner*\ , *middle*\ , and *outer* keywords of the :doc:`run_style respa <run_style>` command, meaning the pairwise forces can be
|
||||
partitioned by distance at different levels of the rRESPA hierarchy.
|
||||
The other styles only support the *pair* keyword of run_style respa.
|
||||
See the :doc:`run_style <run_style>` command for details.
|
||||
|
||||
----------
|
||||
|
||||
Restrictions
|
||||
""""""""""""
|
||||
|
||||
The *lj/cut/tip4p/long* styles are part of the
|
||||
KSPACE package. The *lj/cut/tip4p/cut* style is part of the MOLECULE
|
||||
package. These styles are only enabled if LAMMPS was built with those
|
||||
packages. See the :doc:`Build package <Build_package>` doc page for
|
||||
more info.
|
||||
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
:doc:`pair_coeff <pair_coeff>`
|
||||
|
||||
**Default:** none
|
||||
|
||||
----------
|
||||
|
||||
.. _Jorgensen2:
|
||||
|
||||
**(Jorgensen)** Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem
|
||||
Phys, 79, 926 (1983).
|
||||
@ -8,7 +8,19 @@ Syntax
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
pair_style mliap
|
||||
pair_style mliap ... keyword values ...
|
||||
|
||||
* two keyword/value pairs must be appended
|
||||
* keyword = *model* or *descriptor*
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
*model* values = style filename
|
||||
style = *linear* or *quadratic*
|
||||
filename = name of file containing model definitions
|
||||
*descriptor* values = style filename
|
||||
style = *sna*
|
||||
filename = name of file containing descriptor definitions
|
||||
|
||||
Examples
|
||||
""""""""
|
||||
@ -22,8 +34,8 @@ Examples
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
Pair style *mliap* provides a general interface to families of
|
||||
machine-learning interatomic potentials. It provides separate
|
||||
Pair style *mliap* provides a general interface to families of
|
||||
machine-learning interatomic potentials. It allows separate
|
||||
definitions of the interatomic potential functional form (*model*)
|
||||
and the geometric quantities that characterize the atomic positions
|
||||
(*descriptor*). By defining *model* and *descriptor* separately,
|
||||
@ -34,6 +46,9 @@ and one descriptor, *sna*, the SNAP descriptor used by :doc:`pair_style snap <pa
|
||||
and chem variants. Work is currently underway to extend
|
||||
the interface to handle neural network energy models,
|
||||
and it is also straightforward to add new descriptor styles.
|
||||
In order to train a model, it is useful to know the gradient or derivative
|
||||
of energy, force, and stress w.r.t. model parameters. This information
|
||||
can be accessed using the related :doc:`compute mliap <compute_mliap>` command.
|
||||
|
||||
The pair_style *mliap* command must be followed by two keywords
|
||||
*model* and *descriptor* in either order. A single
|
||||
@ -46,10 +61,10 @@ where N is the number of LAMMPS atom types.
|
||||
|
||||
The *model* keyword is followed by a model style, currently limited to
|
||||
either *linear* or *quadratic*. In both cases,
|
||||
this is followed by a single argument specifying the model filename containing the
|
||||
linear or quadratic coefficients for a set of elements.
|
||||
this is followed by a single argument specifying the model filename containing the
|
||||
parameters for a set of elements.
|
||||
The model filename usually ends in the *.mliap.model* extension.
|
||||
It may contain coefficients for many elements. The only requirement is that it
|
||||
It may contain parameters for many elements. The only requirement is that it
|
||||
contain at least those element names appearing in the
|
||||
*pair_coeff* command.
|
||||
|
||||
@ -58,10 +73,10 @@ but follows a strict format after that. The first non-blank non-comment
|
||||
line must contain two integers:
|
||||
|
||||
* nelems = Number of elements
|
||||
* ncoeff = Number of coefficients
|
||||
* nparams = Number of parameters
|
||||
|
||||
This is followed by one block for each of the *nelem* elements.
|
||||
Each block consists of *ncoeff* coefficients, one per line.
|
||||
Each block consists of *nparams* parameters, one per line.
|
||||
Note that this format is similar, but not identical to that used
|
||||
for the :doc:`pair_style snap <pair_snap>` coefficient file.
|
||||
Specifically, the line containing the element weight and radius is omitted,
|
||||
@ -131,6 +146,6 @@ See the :doc:`Build package <Build_package>` doc page for more info.
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
:doc:`pair_style snap <pair_snap>`,
|
||||
:doc:`pair_style snap <pair_snap>`, :doc:`compute mliap <compute_mliap>`
|
||||
|
||||
**Default:** none
|
||||
|
||||
@ -201,21 +201,21 @@ accelerated styles exist.
|
||||
* :doc:`lj/class2/soft <pair_fep_soft>` - COMPASS (class 2) force field with no Coulomb with a soft core
|
||||
* :doc:`lj/cubic <pair_lj_cubic>` - LJ with cubic after inflection point
|
||||
* :doc:`lj/cut <pair_lj>` - cutoff Lennard-Jones potential without Coulomb
|
||||
* :doc:`lj/cut/coul/cut <pair_lj>` - LJ with cutoff Coulomb
|
||||
* :doc:`lj/cut/coul/cut <pair_lj_cut_coul>` - LJ with cutoff Coulomb
|
||||
* :doc:`lj/cut/coul/cut/soft <pair_fep_soft>` - LJ with cutoff Coulomb with a soft core
|
||||
* :doc:`lj/cut/coul/debye <pair_lj>` - LJ with Debye screening added to Coulomb
|
||||
* :doc:`lj/cut/coul/dsf <pair_lj>` - LJ with Coulomb via damped shifted forces
|
||||
* :doc:`lj/cut/coul/long <pair_lj>` - LJ with long-range Coulomb
|
||||
* :doc:`lj/cut/coul/debye <pair_lj_cut_coul>` - LJ with Debye screening added to Coulomb
|
||||
* :doc:`lj/cut/coul/dsf <pair_lj_cut_coul>` - LJ with Coulomb via damped shifted forces
|
||||
* :doc:`lj/cut/coul/long <pair_lj_cut_coul>` - LJ with long-range Coulomb
|
||||
* :doc:`lj/cut/coul/long/cs <pair_cs>` - LJ with long-range Coulomb with core/shell adjustments
|
||||
* :doc:`lj/cut/coul/long/soft <pair_fep_soft>` - LJ with long-range Coulomb with a soft core
|
||||
* :doc:`lj/cut/coul/msm <pair_lj>` - LJ with long-range MSM Coulomb
|
||||
* :doc:`lj/cut/coul/wolf <pair_lj>` - LJ with Coulomb via Wolf potential
|
||||
* :doc:`lj/cut/coul/msm <pair_lj_cut_coul>` - LJ with long-range MSM Coulomb
|
||||
* :doc:`lj/cut/coul/wolf <pair_lj_cut_coul>` - LJ with Coulomb via Wolf potential
|
||||
* :doc:`lj/cut/dipole/cut <pair_dipole>` - point dipoles with cutoff
|
||||
* :doc:`lj/cut/dipole/long <pair_dipole>` - point dipoles with long-range Ewald
|
||||
* :doc:`lj/cut/soft <pair_fep_soft>` - LJ with a soft core
|
||||
* :doc:`lj/cut/thole/long <pair_thole>` - LJ with Coulomb with thole damping
|
||||
* :doc:`lj/cut/tip4p/cut <pair_lj>` - LJ with cutoff Coulomb for TIP4P water
|
||||
* :doc:`lj/cut/tip4p/long <pair_lj>` - LJ with long-range Coulomb for TIP4P water
|
||||
* :doc:`lj/cut/tip4p/cut <pair_lj_cut_tip4p>` - LJ with cutoff Coulomb for TIP4P water
|
||||
* :doc:`lj/cut/tip4p/long <pair_lj_cut_tip4p>` - LJ with long-range Coulomb for TIP4P water
|
||||
* :doc:`lj/cut/tip4p/long/soft <pair_fep_soft>` - LJ with cutoff Coulomb for TIP4P water with a soft core
|
||||
* :doc:`lj/expand <pair_lj_expand>` - Lennard-Jones for variable size particles
|
||||
* :doc:`lj/expand/coul/long <pair_lj_expand>` - Lennard-Jones for variable size particles with long-range Coulomb
|
||||
|
||||
@ -98,7 +98,7 @@ more of the optional keywords listed above for the pair_style command.
|
||||
These are *ewald* or *pppm* or *msm* or *dispersion* or *tip4p*\ . This
|
||||
is so LAMMPS can insure the short-range potential and long-range
|
||||
solver are compatible with each other, as it does for other
|
||||
short-range pair styles, such as :doc:`pair_style lj/cut/coul/long <pair_lj>`. Note that it is up to you to insure
|
||||
short-range pair styles, such as :doc:`pair_style lj/cut/coul/long <pair_lj_cut_coul>`. Note that it is up to you to insure
|
||||
the tabulated values for each pair of atom types has the correct
|
||||
functional form to be compatible with the matching long-range solver.
|
||||
|
||||
|
||||
@ -182,7 +182,7 @@ Related commands
|
||||
""""""""""""""""
|
||||
|
||||
:doc:`fix drude <fix_drude>`, :doc:`fix langevin/drude <fix_langevin_drude>`, :doc:`fix drude/transform <fix_drude_transform>`, :doc:`compute temp/drude <compute_temp_drude>`
|
||||
:doc:`pair_style lj/cut/coul/long <pair_lj>`
|
||||
:doc:`pair_style lj/cut/coul/long <pair_lj_cut_coul>`
|
||||
|
||||
**Default:** none
|
||||
|
||||
|
||||
@ -1,14 +1,14 @@
|
||||
.. index:: reset_ids
|
||||
.. index:: reset_atom_ids
|
||||
|
||||
reset_ids command
|
||||
=================
|
||||
reset_atom_ids command
|
||||
======================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
reset_ids keyword values ...
|
||||
reset_atom_ids keyword values ...
|
||||
|
||||
* zero or more keyword/value pairs may be appended
|
||||
* keyword = *sort*
|
||||
@ -22,8 +22,8 @@ Examples
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
reset_ids
|
||||
reset_ids sort yes
|
||||
reset_atom_ids
|
||||
reset_atom_ids sort yes
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
@ -77,7 +77,7 @@ processor have consecutive IDs, as the :doc:`create_atoms
|
||||
that are owned by other processors. The :doc:`comm_modify cutoff <comm_modify>` command can be used to correct this issue.
|
||||
Or you can define a pair style before using this command. If you do
|
||||
the former, you should unset the comm_modify cutoff after using
|
||||
reset_ids so that subsequent communication is not inefficient.
|
||||
reset_atom_ids so that subsequent communication is not inefficient.
|
||||
|
||||
Restrictions
|
||||
""""""""""""
|
||||
116
doc/src/reset_mol_ids.rst
Normal file
116
doc/src/reset_mol_ids.rst
Normal file
@ -0,0 +1,116 @@
|
||||
.. index:: reset_mol_ids
|
||||
|
||||
reset_mol_ids command
|
||||
=====================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
reset_mol_ids group-ID keyword value ...
|
||||
|
||||
* group-ID = ID of group of atoms whose molecule IDs will be reset
|
||||
* zero or more keyword/value pairs may be appended
|
||||
* keyword = *compress* or *offset* or *single*
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
*compress* value = *yes* or *no*
|
||||
*offset* value = *Noffset* >= -1
|
||||
*single* value = *yes* or *no* to treat single atoms (no bonds) as molecules
|
||||
|
||||
Examples
|
||||
""""""""
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
reset_mol_ids all
|
||||
reset_mol_ids all offset 10 single yes
|
||||
reset_mol_ids solvent compress yes offset 100
|
||||
reset_mol_ids solvent compress no
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
Reset molecule IDs for a group of atoms based on current bond
|
||||
connectivity. This will typically create a new set of molecule IDs
|
||||
for atoms in the group. Only molecule IDs for atoms in the specified
|
||||
group are reset; molecule IDs for atoms not in the group are not
|
||||
changed.
|
||||
|
||||
For purposes of this operation, molecules are identified by the current
|
||||
bond connectivity in the system, which may or may not be consistent with
|
||||
the current molecule IDs. A molecule in this context is a set of atoms
|
||||
connected to each other with explicit bonds. The specific algorithm
|
||||
used is the one of :doc:`compute fragment/atom <compute_cluster_atom>`
|
||||
Once the molecules are identified and a new molecule ID computed for
|
||||
each, this command will update the current molecule ID for all atoms in
|
||||
the group with the new molecule ID. Note that if the group excludes
|
||||
atoms within molecules, one (physical) molecule may become two or more
|
||||
(logical) molecules. For example if the group excludes atoms in the
|
||||
middle of a linear chain, then each end of the chain is considered an
|
||||
independent molecule and will be assigned a different molecule ID.
|
||||
|
||||
This can be a useful operation to perform after running reactive
|
||||
molecular dynamics run with :doc:`fix bond/react <fix_bond_react>`,
|
||||
:doc:`fix bond/create <fix_bond_create>`, or :doc:`fix bond/break
|
||||
<fix_bond_break>`, all of which can change molecule topologies. It can
|
||||
also be useful after molecules have been deleted with the
|
||||
:doc:`delete_atoms <delete_atoms>` command or after a simulation which
|
||||
has lost molecules, e.g. via the :doc:`fix evaporate <fix_evaporate>`
|
||||
command.
|
||||
|
||||
The *compress* keyword determines how new molecule IDs are computed. If
|
||||
the setting is *yes* (the default) and there are N molecules in the
|
||||
group, the new molecule IDs will be a set of N contiguous values. See
|
||||
the *offset* keyword for details on selecting the range of these values.
|
||||
If the setting is *no*, the molecule ID of every atom in the molecule
|
||||
will be set to the smallest atom ID of any atom in the molecule.
|
||||
|
||||
The *single* keyword determines whether single atoms (not bonded to
|
||||
another atom) are treated as one-atom molecules or not, based on the
|
||||
*yes* or *no* setting. If the setting is *no* (the default), their
|
||||
molecule IDs are set to 0. This setting can be important if the new
|
||||
molecule IDs will be used as input to other commands such as
|
||||
:doc:`compute chunk/atom molecule <compute_chunk_atom>` or :doc:`fix
|
||||
rigid molecule <fix_rigid>`.
|
||||
|
||||
The *offset* keyword is only used if the *compress* setting is *yes*.
|
||||
Its default value is *Noffset* = -1. In that case, if the specified
|
||||
group is *all*, then the new compressed molecule IDs will range from 1
|
||||
to N. If the specified group is not *all* and the largest molecule ID
|
||||
of atoms outside that group is M, then the new compressed molecule IDs will
|
||||
range from M+1 to M+N, to avoid collision with existing molecule
|
||||
IDs. If an *Noffset* >= 0 is specified, then the new compressed
|
||||
molecule IDs will range from *Noffset*\ +1 to *Noffset*\ +N. If the group
|
||||
is not *all* there may be collisions with the molecule IDs of other atoms.
|
||||
|
||||
.. note::
|
||||
|
||||
The same as explained for the :doc:`compute fragment/atom
|
||||
<compute_cluster_atom>` command, molecules are identified using the
|
||||
current bond topology. This will not account for bonds broken by
|
||||
the :doc:`bond_style quartic <bond_quartic>` command because it
|
||||
does not perform a full update of the bond topology data structures
|
||||
within LAMMPS.
|
||||
|
||||
Restrictions
|
||||
""""""""""""
|
||||
none
|
||||
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
:doc:`reset_atom_ids <reset_atom_ids>`, :doc:`fix bond/react <fix_bond_react>`,
|
||||
:doc:`fix bond/create <fix_bond_create>`,
|
||||
:doc:`fix bond/break <fix_bond_break>`,
|
||||
:doc:`fix evaporate <fix_evaporate>`,
|
||||
:doc:`delete_atoms <delete_atoms>`,
|
||||
:doc:`compute fragment/atom <compute_cluster_atom>`
|
||||
|
||||
Default
|
||||
"""""""
|
||||
|
||||
The default keyword settings are compress = yes, single = no, and
|
||||
offset = -1.
|
||||
Reference in New Issue
Block a user