Merge branch 'develop' into rheo
This commit is contained in:
jtclemm
@ -178,6 +178,7 @@ OPT.
|
||||
* :doc:`python/move <fix_python_move>`
|
||||
* :doc:`qbmsst <fix_qbmsst>`
|
||||
* :doc:`qeq/comb (o) <fix_qeq_comb>`
|
||||
* :doc:`qeq/ctip <fix_qeq>`
|
||||
* :doc:`qeq/dynamic <fix_qeq>`
|
||||
* :doc:`qeq/fire <fix_qeq>`
|
||||
* :doc:`qeq/point <fix_qeq>`
|
||||
|
||||
@ -44,7 +44,7 @@ OPT.
|
||||
* :doc:`born/coul/wolf/cs (g) <pair_cs>`
|
||||
* :doc:`born/gauss <pair_born_gauss>`
|
||||
* :doc:`bpm/spring <pair_bpm_spring>`
|
||||
* :doc:`brownian (o) <pair_brownian>`
|
||||
* :doc:`brownian (ko) <pair_brownian>`
|
||||
* :doc:`brownian/poly (o) <pair_brownian>`
|
||||
* :doc:`buck (giko) <pair_buck>`
|
||||
* :doc:`buck/coul/cut (giko) <pair_buck>`
|
||||
@ -59,6 +59,7 @@ OPT.
|
||||
* :doc:`comb (o) <pair_comb>`
|
||||
* :doc:`comb3 <pair_comb>`
|
||||
* :doc:`cosine/squared <pair_cosine_squared>`
|
||||
* :doc:`coul/ctip <pair_coul>`
|
||||
* :doc:`coul/cut (gko) <pair_coul>`
|
||||
* :doc:`coul/cut/dielectric <pair_dielectric>`
|
||||
* :doc:`coul/cut/global (o) <pair_coul>`
|
||||
|
||||
@ -1,5 +1,5 @@
|
||||
CHARMM, AMBER, COMPASS, and DREIDING force fields
|
||||
=================================================
|
||||
CHARMM, AMBER, COMPASS, DREIDING, and OPLS force fields
|
||||
=======================================================
|
||||
|
||||
A compact summary of the concepts, definitions, and properties of
|
||||
force fields with explicit bonded interactions (like the ones discussed
|
||||
@ -236,6 +236,40 @@ documentation for the formula it computes.
|
||||
|
||||
* :doc:`special_bonds <special_bonds>` dreiding
|
||||
|
||||
OPLS
|
||||
----
|
||||
|
||||
OPLS (Optimized Potentials for Liquid Simulations) is a general force
|
||||
field for atomistic simulation of organic molecules in solvent. It was
|
||||
developed by the `Jorgensen group
|
||||
<https://traken.chem.yale.edu/oplsaam.html>`_ at Purdue University and
|
||||
later at Yale University. Multiple versions of the OPLS parameters
|
||||
exist for united atom representations (OPLS-UA) and for all-atom
|
||||
representations (OPLS-AA).
|
||||
|
||||
This force field is based on atom types mapped to specific functional
|
||||
groups in organic and biological molecules. Each atom includes a
|
||||
static, partial atomic charge reflecting the oxidation state of the
|
||||
element derived from its bonded neighbors :ref:`(Jorgensen)
|
||||
<howto-jorgensen>` and computed based on increments determined by the
|
||||
atom type of the atoms bond to it.
|
||||
|
||||
The interaction styles listed below compute force field formulas that
|
||||
are fully or in part consistent with the OPLS style force fields. See
|
||||
each command's documentation for the formula it computes. Some are only
|
||||
compatible with a subset of OPLS interactions.
|
||||
|
||||
* :doc:`bond_style <bond_harmonic>` harmonic
|
||||
* :doc:`angle_style <angle_harmonic>` harmonic
|
||||
* :doc:`dihedral_style <dihedral_opls>` opls
|
||||
* :doc:`improper_style <improper_cvff>` cvff
|
||||
* :doc:`improper_style <improper_fourier>` fourier
|
||||
* :doc:`improper_style <improper_harmonic>` harmonic
|
||||
* :doc:`pair_style <pair_lj_cut_coul>` lj/cut/coul/cut
|
||||
* :doc:`pair_style <pair_lj_cut_coul>` lj/cut/coul/long
|
||||
* :doc:`pair_modify <pair_modify>` geometric
|
||||
* :doc:`special_bonds <special_bonds>` lj/coul 0.0 0.0 0.5
|
||||
|
||||
----------
|
||||
|
||||
.. _Typelabel2:
|
||||
@ -266,3 +300,6 @@ documentation for the formula it computes.
|
||||
|
||||
**(Mayo)** Mayo, Olfason, Goddard III (1990). J Phys Chem, 94, 8897-8909. https://doi.org/10.1021/j100389a010
|
||||
|
||||
.. _howto-Jorgensen:
|
||||
|
||||
**(Jorgensen)** Jorgensen, Tirado-Rives (1988). J Am Chem Soc, 110, 1657-1666. https://doi.org/10.1021/ja00214a001
|
||||
|
||||
@ -42,7 +42,8 @@ Currently, there are two types of bonds included in the BPM package. The
|
||||
first bond style, :doc:`bond bpm/spring <bond_bpm_spring>`, only applies
|
||||
pairwise, central body forces. Point particles must have :doc:`bond atom
|
||||
style <atom_style>` and may be thought of as nodes in a spring
|
||||
network. Alternatively, the second bond style, :doc:`bond bpm/rotational
|
||||
network. An optional multibody term can be used to adjust the network's
|
||||
Poisson's ratio. Alternatively, the second bond style, :doc:`bond bpm/rotational
|
||||
<bond_bpm_rotational>`, resolves tangential forces and torques arising
|
||||
with the shearing, bending, and twisting of the bond due to rotation or
|
||||
displacement of particles. Particles are similar to those used in the
|
||||
@ -55,8 +56,9 @@ orientation similar to :doc:`fix nve/asphere <fix_nve_asphere>`.
|
||||
|
||||
In addition to bond styles, a new pair style :doc:`pair bpm/spring
|
||||
<pair_bpm_spring>` was added to accompany the bpm/spring bond
|
||||
style. This pair style is simply a hookean repulsion with similar
|
||||
velocity damping as its sister bond style.
|
||||
style. By default, this pair style is simply a hookean repulsion with
|
||||
similar velocity damping as its sister bond style, but optional
|
||||
arguments can be used to modify the force.
|
||||
|
||||
----------
|
||||
|
||||
|
||||
@ -58,28 +58,30 @@ chunk ID for an individual atom can also be static (e.g. a molecule
|
||||
ID), or dynamic (e.g. what spatial bin an atom is in as it moves).
|
||||
|
||||
Note that this compute allows the per-atom output of other
|
||||
:doc:`computes <compute>`, :doc:`fixes <fix>`, and
|
||||
:doc:`variables <variable>` to be used to define chunk IDs for each
|
||||
atom. This means you can write your own compute or fix to output a
|
||||
per-atom quantity to use as chunk ID. See the :doc:`Modify <Modify>`
|
||||
doc pages for info on how to do this. You can also define a :doc:`per-atom variable <variable>` in the input script that uses a formula to
|
||||
generate a chunk ID for each atom.
|
||||
:doc:`computes <compute>`, :doc:`fixes <fix>`, and :doc:`variables
|
||||
<variable>` to be used to define chunk IDs for each atom. This means
|
||||
you can write your own compute or fix to output a per-atom quantity to
|
||||
use as chunk ID. See the :doc:`Modify <Modify>` doc pages for info on
|
||||
how to do this. You can also define a :doc:`per-atom variable
|
||||
<variable>` in the input script that uses a formula to generate a chunk
|
||||
ID for each atom.
|
||||
|
||||
Fix ave/chunk command:
|
||||
----------------------
|
||||
|
||||
This fix takes the ID of a :doc:`compute chunk/atom <compute_chunk_atom>` command as input. For each chunk,
|
||||
it then sums one or more specified per-atom values over the atoms in
|
||||
each chunk. The per-atom values can be any atom property, such as
|
||||
velocity, force, charge, potential energy, kinetic energy, stress,
|
||||
etc. Additional keywords are defined for per-chunk properties like
|
||||
density and temperature. More generally any per-atom value generated
|
||||
by other :doc:`computes <compute>`, :doc:`fixes <fix>`, and :doc:`per-atom variables <variable>`, can be summed over atoms in each chunk.
|
||||
This fix takes the ID of a :doc:`compute chunk/atom
|
||||
<compute_chunk_atom>` command as input. For each chunk, it then sums
|
||||
one or more specified per-atom values over the atoms in each chunk. The
|
||||
per-atom values can be any atom property, such as velocity, force,
|
||||
charge, potential energy, kinetic energy, stress, etc. Additional
|
||||
keywords are defined for per-chunk properties like density and
|
||||
temperature. More generally any per-atom value generated by other
|
||||
:doc:`computes <compute>`, :doc:`fixes <fix>`, and :doc:`per-atom
|
||||
variables <variable>`, can be summed over atoms in each chunk.
|
||||
|
||||
Similar to other averaging fixes, this fix allows the summed per-chunk
|
||||
values to be time-averaged in various ways, and output to a file. The
|
||||
fix produces a global array as output with one row of values per
|
||||
chunk.
|
||||
fix produces a global array as output with one row of values per chunk.
|
||||
|
||||
Compute \*/chunk commands:
|
||||
--------------------------
|
||||
@ -97,17 +99,20 @@ category:
|
||||
* :doc:`compute torque/chunk <compute_vcm_chunk>`
|
||||
* :doc:`compute vcm/chunk <compute_vcm_chunk>`
|
||||
|
||||
They each take the ID of a :doc:`compute chunk/atom <compute_chunk_atom>` command as input. As their names
|
||||
indicate, they calculate the center-of-mass, radius of gyration,
|
||||
moments of inertia, mean-squared displacement, temperature, torque,
|
||||
and velocity of center-of-mass for each chunk of atoms. The :doc:`compute property/chunk <compute_property_chunk>` command can tally the
|
||||
count of atoms in each chunk and extract other per-chunk properties.
|
||||
They each take the ID of a :doc:`compute chunk/atom
|
||||
<compute_chunk_atom>` command as input. As their names indicate, they
|
||||
calculate the center-of-mass, radius of gyration, moments of inertia,
|
||||
mean-squared displacement, temperature, torque, and velocity of
|
||||
center-of-mass for each chunk of atoms. The :doc:`compute
|
||||
property/chunk <compute_property_chunk>` command can tally the count of
|
||||
atoms in each chunk and extract other per-chunk properties.
|
||||
|
||||
The reason these various calculations are not part of the :doc:`fix ave/chunk command <fix_ave_chunk>`, is that each requires a more
|
||||
The reason these various calculations are not part of the :doc:`fix
|
||||
ave/chunk command <fix_ave_chunk>`, is that each requires a more
|
||||
complicated operation than simply summing and averaging over per-atom
|
||||
values in each chunk. For example, many of them require calculation
|
||||
of a center of mass, which requires summing mass\*position over the
|
||||
atoms and then dividing by summed mass.
|
||||
values in each chunk. For example, many of them require calculation of
|
||||
a center of mass, which requires summing mass\*position over the atoms
|
||||
and then dividing by summed mass.
|
||||
|
||||
All of these computes produce a global vector or global array as
|
||||
output, with one or more values per chunk. The output can be used in
|
||||
@ -118,9 +123,10 @@ various ways:
|
||||
* As input to the :doc:`fix ave/histo <fix_ave_histo>` command to
|
||||
histogram values across chunks. E.g. a histogram of cluster sizes or
|
||||
molecule diffusion rates.
|
||||
* As input to special functions of :doc:`equal-style variables <variable>`, like sum() and max() and ave(). E.g. to
|
||||
find the largest cluster or fastest diffusing molecule or average
|
||||
radius-of-gyration of a set of molecules (chunks).
|
||||
* As input to special functions of :doc:`equal-style variables
|
||||
<variable>`, like sum() and max() and ave(). E.g. to find the largest
|
||||
cluster or fastest diffusing molecule or average radius-of-gyration of
|
||||
a set of molecules (chunks).
|
||||
|
||||
Other chunk commands:
|
||||
---------------------
|
||||
@ -138,9 +144,10 @@ spatially average per-chunk values calculated by a per-chunk compute.
|
||||
|
||||
The :doc:`compute reduce/chunk <compute_reduce_chunk>` command reduces a
|
||||
peratom value across the atoms in each chunk to produce a value per
|
||||
chunk. When used with the :doc:`compute chunk/spread/atom <compute_chunk_spread_atom>` command it can
|
||||
create peratom values that induce a new set of chunks with a second
|
||||
:doc:`compute chunk/atom <compute_chunk_atom>` command.
|
||||
chunk. When used with the :doc:`compute chunk/spread/atom
|
||||
<compute_chunk_spread_atom>` command it can create peratom values that
|
||||
induce a new set of chunks with a second :doc:`compute chunk/atom
|
||||
<compute_chunk_atom>` command.
|
||||
|
||||
Example calculations with chunks
|
||||
--------------------------------
|
||||
|
||||
@ -31,18 +31,19 @@ Operating systems
|
||||
^^^^^^^^^^^^^^^^^
|
||||
|
||||
The primary development platform for LAMMPS is Linux. Thus, the chances
|
||||
for LAMMPS to compile without problems on Linux machines are the best.
|
||||
for LAMMPS to compile without problems are the best on Linux machines.
|
||||
Also, compilation and correct execution on macOS and Windows (using
|
||||
Microsoft Visual C++) is checked automatically for largest part of the
|
||||
source code. Some (optional) features are not compatible with all
|
||||
Microsoft Visual C++) is checked automatically for the largest part of
|
||||
the source code. Some (optional) features are not compatible with all
|
||||
operating systems, either through limitations of the corresponding
|
||||
LAMMPS source code or through source code or build system
|
||||
incompatibilities of required libraries.
|
||||
LAMMPS source code or through incompatibilities of source code or
|
||||
build system of required external libraries or packages.
|
||||
|
||||
Executables for Windows may be created natively using either Cygwin or
|
||||
Visual Studio or with a Linux to Windows MinGW cross-compiler.
|
||||
|
||||
Additionally, FreeBSD and Solaris have been tested successfully.
|
||||
Additionally, FreeBSD and Solaris have been tested successfully to
|
||||
run LAMMPS and produce results consistent with those on Linux.
|
||||
|
||||
Compilers
|
||||
^^^^^^^^^
|
||||
|
||||
@ -880,7 +880,7 @@ groups of atoms that interact with the remaining atoms as electrolyte.
|
||||
|
||||
**Authors:** The ELECTRODE package is written and maintained by Ludwig
|
||||
Ahrens-Iwers (TUHH, Hamburg, Germany), Shern Tee (UQ, Brisbane, Australia) and
|
||||
Robert Meissner (TUHH, Hamburg, Germany).
|
||||
Robert Meissner (Helmholtz-Zentrum Hereon, Geesthacht and TUHH, Hamburg, Germany).
|
||||
|
||||
.. versionadded:: 4May2022
|
||||
|
||||
|
||||
@ -3,71 +3,70 @@ Running LAMMPS on Windows
|
||||
|
||||
To run a serial (non-MPI) executable, follow these steps:
|
||||
|
||||
* Get a command prompt by going to Start->Run... ,
|
||||
then typing "cmd".
|
||||
* Move to the directory where you have your input script,
|
||||
* Install a LAMMPS installer package from https://packages.lammps.org/windows.html
|
||||
* Open the "Command Prompt" or "Terminal" app.
|
||||
* Change to the directory where you have your input script,
|
||||
(e.g. by typing: cd "Documents").
|
||||
* At the command prompt, type "lmp -in in.file", where
|
||||
in.file is the name of your LAMMPS input script.
|
||||
* At the command prompt, type "lmp -in in.file.lmp", where
|
||||
``in.file.lmp`` is the name of your LAMMPS input script.
|
||||
|
||||
Note that the serial executable includes support for multi-threading
|
||||
parallelization from the styles in the OPENMP packages. To run with
|
||||
4 threads, you can type this:
|
||||
parallelization from the styles in the OPENMP and KOKKOS packages.
|
||||
To run with 4 threads, you can type this:
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
lmp -in in.lj -pk omp 4 -sf omp
|
||||
lmp -in in.lj.lmp -pk omp 4 -sf omp
|
||||
lmp -in in.lj.lmp -k on t 4 -sf kk
|
||||
|
||||
Alternately, you can also install a package with LAMMPS-GUI included and
|
||||
open the LAMMPS-GUI app (the package includes the command line version
|
||||
of LAMMPS as well) and open the input file in the GUI and run it from
|
||||
there. For details on LAMMPS-GUI, see :doc:`Howto_lammps_gui`.
|
||||
|
||||
----------
|
||||
|
||||
For the MPI executable, which allows you to run LAMMPS under Windows
|
||||
in parallel, follow these steps.
|
||||
For the MS-MPI executables, which allow you to run LAMMPS under Windows
|
||||
in parallel using MPI rather than multi-threading, follow these steps.
|
||||
|
||||
Download and install a compatible MPI library binary package:
|
||||
|
||||
* for 32-bit Windows: `mpich2-1.4.1p1-win-ia32.msi <https://download.lammps.org/thirdparty/mpich2-1.4.1p1-win-ia32.msi>`_
|
||||
* for 64-bit Windows: `mpich2-1.4.1p1-win-x86-64.msi <https://download.lammps.org/thirdparty/mpich2-1.4.1p1-win-x86-64.msi>`_
|
||||
|
||||
The LAMMPS Windows installer packages will automatically adjust your
|
||||
path for the default location of this MPI package. After the
|
||||
installation of the MPICH2 software, it needs to be integrated into
|
||||
the system. For this you need to start a Command Prompt in
|
||||
*Administrator Mode* (right click on the icon and select it). Change
|
||||
into the MPICH2 installation directory, then into the subdirectory
|
||||
**bin** and execute **smpd.exe -install**\ . Exit the command window.
|
||||
|
||||
* Get a new, regular command prompt by going to Start->Run... ,
|
||||
then typing "cmd".
|
||||
* Move to the directory where you have your input file
|
||||
(e.g. by typing: cd "Documents").
|
||||
Download and install the MS-MPI runtime package ``msmpisetup.exe`` from
|
||||
https://www.microsoft.com/en-us/download/details.aspx?id=105289 (Note
|
||||
that the ``msmpisdk.msi`` is **only** required for **compilation** of
|
||||
LAMMPS from source on Windows using Microsoft Visual Studio). After
|
||||
installation of MS-MPI perform a reboot.
|
||||
|
||||
Then you can run the executable in serial like in the example above
|
||||
or in parallel using MPI with one of the following commands:
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
mpiexec -localonly 4 lmp -in in.file
|
||||
mpiexec -np 4 lmp -in in.file
|
||||
mpiexec -localonly 4 lmp -in in.file.lmp
|
||||
mpiexec -np 4 lmp -in in.file.lmp
|
||||
|
||||
where in.file is the name of your LAMMPS input script. For the latter
|
||||
case, you may be prompted to enter the password that you set during
|
||||
installation of the MPI library software.
|
||||
where ``in.file.lmp`` is the name of your LAMMPS input script. For the
|
||||
latter case, you may be prompted to enter the password that you set
|
||||
during installation of the MPI library software.
|
||||
|
||||
In this mode, output may not immediately show up on the screen, so if
|
||||
your input script takes a long time to execute, you may need to be
|
||||
patient before the output shows up.
|
||||
|
||||
The parallel executable can also run on a single processor by typing
|
||||
something like this:
|
||||
Note that the parallel executable also includes OpenMP multi-threading
|
||||
through both the OPENMP and the KOKKOS package, which can be combined
|
||||
with MPI using something like:
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
lmp -in in.lj
|
||||
mpiexec -localonly 2 lmp -in in.lj.lmp -pk omp 2 -sf omp
|
||||
mpiexec -localonly 2 lmp -in in.lj.lmp -kokkos on t 2 -sf kk
|
||||
|
||||
Note that the parallel executable also includes OpenMP
|
||||
multi-threading, which can be combined with MPI using something like:
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
mpiexec -localonly 2 lmp -in in.lj -pk omp 2 -sf omp
|
||||
-------------
|
||||
|
||||
MPI parallelization will work for *all* functionality in LAMMPS and in
|
||||
many cases the MPI parallelization is more efficient than
|
||||
multi-threading since LAMMPS was designed from ground up for MPI
|
||||
parallelization using domain decomposition. Multi-threading is only
|
||||
available for selected styles and implemented on top of the MPI
|
||||
parallelization. Multi-threading is most useful for systems with large
|
||||
load imbalances when using domain decomposition and a smaller number
|
||||
of threads (<= 8).
|
||||
|
||||
@ -1,8 +0,0 @@
|
||||
Angle Styles
|
||||
############
|
||||
|
||||
.. toctree::
|
||||
:maxdepth: 1
|
||||
:glob:
|
||||
|
||||
angle_*
|
||||
@ -10,7 +10,7 @@ Syntax
|
||||
|
||||
bond_style bpm/spring keyword value attribute1 attribute2 ...
|
||||
|
||||
* optional keyword = *overlay/pair* or *store/local* or *smooth* or *break*
|
||||
* optional keyword = *overlay/pair* or *store/local* or *smooth* or *break* or *volume/factor*
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
@ -36,6 +36,9 @@ Syntax
|
||||
*break* value = *yes* or *no*
|
||||
indicates whether bonds break during a run
|
||||
|
||||
*volume/factor* value = *yes* or *no*
|
||||
indicates whether forces include the volumetric contribution
|
||||
|
||||
Examples
|
||||
""""""""
|
||||
|
||||
@ -44,6 +47,9 @@ Examples
|
||||
bond_style bpm/spring
|
||||
bond_coeff 1 1.0 0.05 0.1
|
||||
|
||||
bond_style bpm/spring volume/factor yes
|
||||
bond_coeff 1 1.0 0.05 0.1 0.5
|
||||
|
||||
bond_style bpm/spring myfix 1000 time id1 id2
|
||||
dump 1 all local 1000 dump.broken f_myfix[1] f_myfix[2] f_myfix[3]
|
||||
dump_modify 1 write_header no
|
||||
@ -97,15 +103,6 @@ approach the critical strain
|
||||
|
||||
w = 1.0 - \left( \frac{r - r_0}{r_0 \epsilon_c} \right)^8 .
|
||||
|
||||
The following coefficients must be defined for each bond type via the
|
||||
:doc:`bond_coeff <bond_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` (force/distance units)
|
||||
* :math:`\epsilon_c` (unit less)
|
||||
* :math:`\gamma` (force/velocity units)
|
||||
|
||||
If the *normalize* keyword is set to *yes*, the elastic bond force will be
|
||||
normalized by :math:`r_0` such that :math:`k` must be given in force units.
|
||||
|
||||
@ -123,6 +120,43 @@ during a simulation run. This will prevent some unnecessary calculation.
|
||||
However, if a bond reaches a strain greater than :math:`\epsilon_c`,
|
||||
it will trigger an error.
|
||||
|
||||
.. versionadded:: TBD
|
||||
|
||||
The *volume/factor* keyword toggles whether an additional multibody
|
||||
contribution is added to he force using the formulation in
|
||||
:ref:`(Clemmer2) <multibody-Clemmer>`,
|
||||
|
||||
.. math::
|
||||
|
||||
\alpha_v \left(\left[\frac{V_i + V_j}{V_{0,i} + V_{0,j}}\right]^{1/3} - \frac{r_{ij}}{r_{0,ij}}\right)
|
||||
|
||||
where :math:`\alpha_v` is a user specified coefficient and :math:`V_i`
|
||||
and :math:`V_{0,i}` are estimates of the current and local volume
|
||||
of atom :math:`i`. These volumes are calculated as the sum of current
|
||||
or initial bond lengths cubed. In 2D, the volume is replaced with an area
|
||||
calculated using bond lengths squared and the cube root in the above equation
|
||||
is accordingly replaced with a square root. This approximation assumes bonds
|
||||
are evenly distributed on a spherical surface and neglects constant prefactors
|
||||
which are irrelevant since only the ratio of volumes matters. This term may be
|
||||
used to adjust the Poisson's ratio.
|
||||
|
||||
If a bond is broken (or created), :math:`V_{0,i}` is updated by subtracting
|
||||
(or adding) that bond's contribution.
|
||||
|
||||
The following coefficients must be defined for each bond type via the
|
||||
:doc:`bond_coeff <bond_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` (force/distance units)
|
||||
* :math:`\epsilon_c` (unit less)
|
||||
* :math:`\gamma` (force/velocity units)
|
||||
|
||||
Additionally, if *volume/factor* is set to *yes*, a fourth coefficient
|
||||
must be provided:
|
||||
|
||||
* :math:`a_v` (force units)
|
||||
|
||||
If the *store/local* keyword is used, an internal fix will track bonds that
|
||||
break during the simulation. Whenever a bond breaks, data is processed
|
||||
and transferred to an internal fix labeled *fix_ID*. This allows the
|
||||
@ -213,7 +247,7 @@ Related commands
|
||||
Default
|
||||
"""""""
|
||||
|
||||
The option defaults are *overlay/pair* = *no*, *smooth* = *yes*, *normalize* = *no*, and *break* = *yes*
|
||||
The option defaults are *overlay/pair* = *no*, *smooth* = *yes*, *normalize* = *no*, *break* = *yes*, and *volume/factor* = *no*
|
||||
|
||||
----------
|
||||
|
||||
@ -224,3 +258,7 @@ The option defaults are *overlay/pair* = *no*, *smooth* = *yes*, *normalize* = *
|
||||
.. _Groot4:
|
||||
|
||||
**(Groot)** Groot and Warren, J Chem Phys, 107, 4423-35 (1997).
|
||||
|
||||
.. _multibody-Clemmer:
|
||||
|
||||
**(Clemmer2)** Clemmer, Monti, Lechman, Soft Matter, 20, 1702 (2024).
|
||||
|
||||
@ -1,8 +0,0 @@
|
||||
Bond Styles
|
||||
###########
|
||||
|
||||
.. toctree::
|
||||
:maxdepth: 1
|
||||
:glob:
|
||||
|
||||
bond_*
|
||||
@ -78,7 +78,7 @@ system and output the statistics in various ways:
|
||||
compute 2 all angle/local eng theta v_cos v_cossq set theta t
|
||||
dump 1 all local 100 tmp.dump c_1[*] c_2[*]
|
||||
|
||||
compute 3 all reduce ave c_2[*]
|
||||
compute 3 all reduce ave c_2[*] inputs local
|
||||
thermo_style custom step temp press c_3[*]
|
||||
|
||||
fix 10 all ave/histo 10 10 100 -1 1 20 c_2[3] mode vector file tmp.histo
|
||||
|
||||
@ -139,7 +139,7 @@ output the statistics in various ways:
|
||||
compute 2 all bond/local engpot dist v_dsq set dist d
|
||||
dump 1 all local 100 tmp.dump c_1[*] c_2[*]
|
||||
|
||||
compute 3 all reduce ave c_2[*]
|
||||
compute 3 all reduce ave c_2[*] inputs local
|
||||
thermo_style custom step temp press c_3[*]
|
||||
|
||||
fix 10 all ave/histo 10 10 100 0 6 20 c_2[3] mode vector file tmp.histo
|
||||
|
||||
@ -88,6 +88,10 @@ too frequently.
|
||||
|
||||
----------
|
||||
|
||||
.. include:: accel_styles.rst
|
||||
|
||||
----------
|
||||
|
||||
Output info
|
||||
"""""""""""
|
||||
|
||||
|
||||
@ -76,7 +76,7 @@ angle in the system and output the statistics in various ways:
|
||||
compute 2 all dihedral/local phi v_cos v_cossq set phi p
|
||||
dump 1 all local 100 tmp.dump c_1[*] c_2[*]
|
||||
|
||||
compute 3 all reduce ave c_2[*]
|
||||
compute 3 all reduce ave c_2[*] inputs local
|
||||
thermo_style custom step temp press c_3[*]
|
||||
|
||||
fix 10 all ave/histo 10 10 100 -1 1 20 c_2[2] mode vector file tmp.histo
|
||||
|
||||
@ -125,10 +125,6 @@ where thermo_temp is the ID of a similarly defined compute of style
|
||||
|
||||
----------
|
||||
|
||||
.. include:: accel_styles.rst
|
||||
|
||||
----------
|
||||
|
||||
Output info
|
||||
"""""""""""
|
||||
|
||||
|
||||
@ -206,11 +206,13 @@ IDs and the bond stretch will be printed with thermodynamic output.
|
||||
|
||||
The *inputs* keyword allows selection of whether all the inputs are
|
||||
per-atom or local quantities. As noted above, all the inputs must be
|
||||
the same kind (per-atom or local). Per-atom is the default setting.
|
||||
If a compute or fix is specified as an input, it must produce per-atom
|
||||
or local data to match this setting. If it produces both, e.g. for
|
||||
the same kind (per-atom or local). Per-atom is the default setting. If
|
||||
a compute or fix is specified as an input, it must produce per-atom or
|
||||
local data to match this setting. If it produces both, like for example
|
||||
the :doc:`compute voronoi/atom <compute_voronoi_atom>` command, then
|
||||
this keyword selects between them.
|
||||
this keyword selects between them. If a compute *only* produces local
|
||||
data, like for example the :doc:`compute bond/local command
|
||||
<compute_bond_local>`, the setting "inputs local" is *required*.
|
||||
|
||||
----------
|
||||
|
||||
|
||||
@ -37,55 +37,57 @@ Description
|
||||
|
||||
Define a calculation that reduces one or more per-atom vectors into
|
||||
per-chunk values. This can be useful for diagnostic output. Or when
|
||||
used in conjunction with the :doc:`compute chunk/spread/atom <compute_chunk_spread_atom>` command it can be
|
||||
used to create per-atom values that induce a new set of chunks with a
|
||||
second :doc:`compute chunk/atom <compute_chunk_atom>` command. An
|
||||
example is given below.
|
||||
used in conjunction with the :doc:`compute chunk/spread/atom
|
||||
<compute_chunk_spread_atom>` command it can be used to create per-atom
|
||||
values that induce a new set of chunks with a second :doc:`compute
|
||||
chunk/atom <compute_chunk_atom>` command. An example is given below.
|
||||
|
||||
In LAMMPS, chunks are collections of atoms defined by a :doc:`compute chunk/atom <compute_chunk_atom>` command, which assigns each atom
|
||||
to a single chunk (or no chunk). The ID for this command is specified
|
||||
as chunkID. For example, a single chunk could be the atoms in a
|
||||
molecule or atoms in a spatial bin. See the :doc:`compute chunk/atom <compute_chunk_atom>` and :doc:`Howto chunk <Howto_chunk>`
|
||||
doc pages for details of how chunks can be defined and examples of how
|
||||
they can be used to measure properties of a system.
|
||||
In LAMMPS, chunks are collections of atoms defined by a :doc:`compute
|
||||
chunk/atom <compute_chunk_atom>` command, which assigns each atom to a
|
||||
single chunk (or no chunk). The ID for this command is specified as
|
||||
chunkID. For example, a single chunk could be the atoms in a molecule
|
||||
or atoms in a spatial bin. See the :doc:`compute chunk/atom
|
||||
<compute_chunk_atom>` and :doc:`Howto chunk <Howto_chunk>` doc pages for
|
||||
details of how chunks can be defined and examples of how they can be
|
||||
used to measure properties of a system.
|
||||
|
||||
For each atom, this compute accesses its chunk ID from the specified
|
||||
*chunkID* compute. The per-atom value from an input contributes
|
||||
to a per-chunk value corresponding the the chunk ID.
|
||||
*chunkID* compute. The per-atom value from an input contributes to a
|
||||
per-chunk value corresponding the chunk ID.
|
||||
|
||||
The reduction operation is specified by the *mode* setting and is
|
||||
performed over all the per-atom values from the atoms in each chunk.
|
||||
The *sum* option adds the pre-atom values to a per-chunk total. The
|
||||
*min* or *max* options find the minimum or maximum value of the
|
||||
per-atom values for each chunk.
|
||||
The *sum* option adds the per-atom values to a per-chunk total. The
|
||||
*min* or *max* options find the minimum or maximum value of the per-atom
|
||||
values for each chunk.
|
||||
|
||||
Note that only atoms in the specified group contribute to the
|
||||
reduction operation. If the *chunkID* compute returns a 0 for the
|
||||
chunk ID of an atom (i.e., the atom is not in a chunk defined by the
|
||||
:doc:`compute chunk/atom <compute_chunk_atom>` command), that atom will
|
||||
also not contribute to the reduction operation. An input that is a
|
||||
compute or fix may define its own group which affects the quantities
|
||||
it returns. For example, a compute with return a zero value for atoms
|
||||
that are not in the group specified for that compute.
|
||||
Note that only atoms in the specified group contribute to the reduction
|
||||
operation. If the *chunkID* compute returns a 0 for the chunk ID of an
|
||||
atom (i.e., the atom is not in a chunk defined by the :doc:`compute
|
||||
chunk/atom <compute_chunk_atom>` command), that atom will also not
|
||||
contribute to the reduction operation. An input that is a compute or
|
||||
fix may define its own group which affects the quantities it returns.
|
||||
For example, a compute will return a zero value for atoms that are not
|
||||
in the group specified for that compute.
|
||||
|
||||
Each listed input is operated on independently. Each input can be the
|
||||
result of a :doc:`compute <compute>` or :doc:`fix <fix>` or the evaluation
|
||||
of an atom-style :doc:`variable <variable>`.
|
||||
result of a :doc:`compute <compute>` or :doc:`fix <fix>` or the
|
||||
evaluation of an atom-style :doc:`variable <variable>`.
|
||||
|
||||
Note that for values from a compute or fix, the bracketed index I can
|
||||
be specified using a wildcard asterisk with the index to effectively
|
||||
Note that for values from a compute or fix, the bracketed index I can be
|
||||
specified using a wildcard asterisk with the index to effectively
|
||||
specify multiple values. This takes the form "\*" or "\*n" or "m\*" or
|
||||
"m\*n". If :math:`N` is the size of the vector (for *mode* = scalar) or the
|
||||
number of columns in the array (for *mode* = vector), then an asterisk
|
||||
with no numeric values means all indices from 1 to :math:`N`. A leading
|
||||
asterisk means all indices from 1 to n (inclusive). A trailing
|
||||
asterisk means all indices from n to :math:`N` (inclusive). A middle asterisk
|
||||
means all indices from m to n (inclusive).
|
||||
"m\*n". If :math:`N` is the size of the vector (for *mode* = scalar) or
|
||||
the number of columns in the array (for *mode* = vector), then an
|
||||
asterisk with no numeric values means all indices from 1 to :math:`N`.
|
||||
A leading asterisk means all indices from 1 to n (inclusive). A
|
||||
trailing asterisk means all indices from n to :math:`N` (inclusive). A
|
||||
middle asterisk means all indices from m to n (inclusive).
|
||||
|
||||
Using a wildcard is the same as if the individual columns of the array
|
||||
had been listed one by one. For example, the following two compute reduce/chunk
|
||||
commands are equivalent, since the
|
||||
:doc:`compute property/chunk <compute_property_chunk>` command creates a per-atom
|
||||
had been listed one by one. For example, the following two compute
|
||||
reduce/chunk commands are equivalent, since the :doc:`compute
|
||||
property/chunk <compute_property_chunk>` command creates a per-atom
|
||||
array with 3 columns:
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
@ -164,13 +166,14 @@ Output info
|
||||
"""""""""""
|
||||
|
||||
This compute calculates a global vector if a single input value is
|
||||
specified, otherwise a global array is output. The number of columns
|
||||
in the array is the number of inputs provided. The length of the
|
||||
vector or the number of vector elements or array rows = the number of
|
||||
chunks *Nchunk* as calculated by the specified :doc:`compute chunk/atom <compute_chunk_atom>` command. The vector or array can
|
||||
be accessed by any command that uses global values from a compute as
|
||||
input. See the :doc:`Howto output <Howto_output>` page for an
|
||||
overview of LAMMPS output options.
|
||||
specified, otherwise a global array is output. The number of columns in
|
||||
the array is the number of inputs provided. The length of the vector or
|
||||
the number of vector elements or array rows = the number of chunks
|
||||
*Nchunk* as calculated by the specified :doc:`compute chunk/atom
|
||||
<compute_chunk_atom>` command. The vector or array can be accessed by
|
||||
any command that uses global values from a compute as input. See the
|
||||
:doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
|
||||
options.
|
||||
|
||||
The per-atom values for the vector or each column of the array will be
|
||||
in whatever :doc:`units <units>` the corresponding input value is in.
|
||||
@ -183,7 +186,9 @@ Restrictions
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
:doc:`compute chunk/atom <compute_chunk_atom>`, :doc:`compute reduce <compute_reduce>`, :doc:`compute chunk/spread/atom <compute_chunk_spread_atom>`
|
||||
:doc:`compute chunk/atom <compute_chunk_atom>`,
|
||||
:doc:`compute reduce <compute_reduce>`,
|
||||
:doc:`compute chunk/spread/atom <compute_chunk_spread_atom>`
|
||||
|
||||
Default
|
||||
"""""""
|
||||
|
||||
@ -81,7 +81,7 @@ includes *xx*, *xy*, *yx*, and *yy*. In 3D, this includes *xx*, *xy*, *xz*,
|
||||
Many properties require their respective fixes, listed below in related
|
||||
commands, be defined. For instance, the *viscosity* attribute is the
|
||||
viscosity of a particle calculated by
|
||||
:doc:`fix rheo/viscous <fix_rheo_viscosity>`. The meaning of less obvious
|
||||
:doc:`fix rheo/viscosity <fix_rheo_viscosity>`. The meaning of less obvious
|
||||
properties is described below.
|
||||
|
||||
The *phase* property indicates whether the particle is in a fluid state,
|
||||
|
||||
@ -129,6 +129,9 @@ package <Build_package>` doc page on for more info.
|
||||
The method is implemented for orthogonal simulation boxes whose
|
||||
size does not change in time, and axis-aligned planes.
|
||||
|
||||
Contributions from bonds, angles, and dihedrals are not compatible
|
||||
with MPI parallel runs.
|
||||
|
||||
The method only works with two-body pair interactions, because it
|
||||
requires the class method ``Pair::single()`` to be implemented, which is
|
||||
not possible for manybody potentials. In particular, compute
|
||||
|
||||
@ -128,6 +128,12 @@ See the :doc:`Howto thermostat <Howto_thermostat>` page for a
|
||||
discussion of different ways to compute temperature and perform
|
||||
thermostatting.
|
||||
|
||||
----------
|
||||
|
||||
.. include:: accel_styles.rst
|
||||
|
||||
----------
|
||||
|
||||
Output info
|
||||
"""""""""""
|
||||
|
||||
|
||||
@ -82,12 +82,6 @@ See the :doc:`Howto thermostat <Howto_thermostat>` page for a
|
||||
discussion of different ways to compute temperature and perform
|
||||
thermostatting.
|
||||
|
||||
----------
|
||||
|
||||
.. include:: accel_styles.rst
|
||||
|
||||
----------
|
||||
|
||||
Output info
|
||||
"""""""""""
|
||||
|
||||
|
||||
@ -1,8 +0,0 @@
|
||||
Computes
|
||||
########
|
||||
|
||||
.. toctree::
|
||||
:maxdepth: 1
|
||||
:glob:
|
||||
|
||||
compute_*
|
||||
@ -1,8 +0,0 @@
|
||||
Dihedral Styles
|
||||
###############
|
||||
|
||||
.. toctree::
|
||||
:maxdepth: 1
|
||||
:glob:
|
||||
|
||||
dihedral_*
|
||||
@ -357,6 +357,7 @@ accelerated styles exist.
|
||||
* :doc:`python/move <fix_python_move>` - move particles using a Python function during a simulation run
|
||||
* :doc:`qbmsst <fix_qbmsst>` - quantum bath multi-scale shock technique time integrator
|
||||
* :doc:`qeq/comb <fix_qeq_comb>` - charge equilibration for COMB potential
|
||||
* :doc:`qeq/ctip <fix_qeq>` - charge equilibration for CTIP potential
|
||||
* :doc:`qeq/dynamic <fix_qeq>` - charge equilibration via dynamic method
|
||||
* :doc:`qeq/fire <fix_qeq>` - charge equilibration via FIRE minimizer
|
||||
* :doc:`qeq/point <fix_qeq>` - charge equilibration via point method
|
||||
|
||||
@ -322,29 +322,33 @@ all types from 1 to :math:`N`. A leading asterisk means all types from
|
||||
If :doc:`bond_style hybrid <bond_hybrid>` is used, *bstyle* should be a
|
||||
sub-style name. The bond styles that currently work with fix adapt are:
|
||||
|
||||
+---------------------------------------------------+---------------------------+------------+
|
||||
| :doc:`class2 <bond_class2>` | r0 | type bonds |
|
||||
+---------------------------------------------------+---------------------------+------------+
|
||||
| :doc:`fene <bond_fene>` | k,r0 | type bonds |
|
||||
+---------------------------------------------------+---------------------------+------------+
|
||||
| :doc:`fene/expand <bond_fene_expand>` | k,r0,epsilon,sigma,shift | type bonds |
|
||||
+---------------------------------------------------+---------------------------+------------+
|
||||
| :doc:`fene/nm <bond_fene>` | k,r0 | type bonds |
|
||||
+---------------------------------------------------+---------------------------+------------+
|
||||
| :doc:`gromos <bond_gromos>` | k,r0 | type bonds |
|
||||
+---------------------------------------------------+---------------------------+------------+
|
||||
| :doc:`harmonic <bond_harmonic>` | k,r0 | type bonds |
|
||||
+---------------------------------------------------+---------------------------+------------+
|
||||
| :doc:`harmonic/shift <bond_harmonic_shift>` | k,r0,r1 | type bonds |
|
||||
+---------------------------------------------------+---------------------------+------------+
|
||||
| :doc:`harmonic/restrain <bond_harmonic_restrain>` | k | type bonds |
|
||||
+---------------------------------------------------+---------------------------+------------+
|
||||
| :doc:`mm3 <bond_mm3>` | k,r0 | type bonds |
|
||||
+---------------------------------------------------+---------------------------+------------+
|
||||
| :doc:`morse <bond_morse>` | r0 | type bonds |
|
||||
+---------------------------------------------------+---------------------------+------------+
|
||||
| :doc:`nonlinear <bond_nonlinear>` | epsilon,r0 | type bonds |
|
||||
+---------------------------------------------------+---------------------------+------------+
|
||||
+-----------------------------------------------------+---------------------------+------------+
|
||||
| :doc:`class2 <bond_class2>` | k2,k3,k4,r0 | type bonds |
|
||||
+-----------------------------------------------------+---------------------------+------------+
|
||||
| :doc:`fene <bond_fene>` | k,r0 | type bonds |
|
||||
+-----------------------------------------------------+---------------------------+------------+
|
||||
| :doc:`fene/expand <bond_fene_expand>` | k,r0,epsilon,sigma,shift | type bonds |
|
||||
+-----------------------------------------------------+---------------------------+------------+
|
||||
| :doc:`fene/nm <bond_fene>` | k,r0 | type bonds |
|
||||
+-----------------------------------------------------+---------------------------+------------+
|
||||
| :doc:`gaussian <bond_gaussian>` | alpha,width,r0 | type bonds |
|
||||
+-----------------------------------------------------+---------------------------+------------+
|
||||
| :doc:`gromos <bond_gromos>` | k,r0 | type bonds |
|
||||
+-----------------------------------------------------+---------------------------+------------+
|
||||
| :doc:`harmonic <bond_harmonic>` | k,r0 | type bonds |
|
||||
+-----------------------------------------------------+---------------------------+------------+
|
||||
| :doc:`harmonic/restrain <bond_harmonic_restrain>` | k | type bonds |
|
||||
+-----------------------------------------------------+---------------------------+------------+
|
||||
| :doc:`harmonic/shift <bond_harmonic_shift>` | k,r0,r1 | type bonds |
|
||||
+-----------------------------------------------------+---------------------------+------------+
|
||||
| :doc:`harmonic/shift/cut <bond_harmonic_shift_cut>` | k,r0,r1 | type bonds |
|
||||
+-----------------------------------------------------+---------------------------+------------+
|
||||
| :doc:`mm3 <bond_mm3>` | k,r0 | type bonds |
|
||||
+-----------------------------------------------------+---------------------------+------------+
|
||||
| :doc:`morse <bond_morse>` | d0,alpha,r0 | type bonds |
|
||||
+-----------------------------------------------------+---------------------------+------------+
|
||||
| :doc:`nonlinear <bond_nonlinear>` | lamda,epsilon,r0 | type bonds |
|
||||
+-----------------------------------------------------+---------------------------+------------+
|
||||
|
||||
----------
|
||||
|
||||
@ -367,31 +371,37 @@ all types from 1 to :math:`N`. A leading asterisk means all types from
|
||||
If :doc:`angle_style hybrid <angle_hybrid>` is used, *astyle* should be a
|
||||
sub-style name. The angle styles that currently work with fix adapt are:
|
||||
|
||||
+--------------------------------------------------------------------+-----------------+-------------+
|
||||
| :doc:`harmonic <angle_harmonic>` | k,theta0 | type angles |
|
||||
+--------------------------------------------------------------------+-----------------+-------------+
|
||||
| :doc:`charmm <angle_charmm>` | k,theta0 | type angles |
|
||||
+--------------------------------------------------------------------+-----------------+-------------+
|
||||
| :doc:`class2 <angle_class2>` | k2,k3,k4,theta0 | type angles |
|
||||
+--------------------------------------------------------------------+-----------------+-------------+
|
||||
| :doc:`cosine <angle_cosine>` | k | type angles |
|
||||
+--------------------------------------------------------------------+-----------------+-------------+
|
||||
| :doc:`cosine/periodic <angle_cosine_periodic>` | k,b,n | type angles |
|
||||
+--------------------------------------------------------------------+-----------------+-------------+
|
||||
| :doc:`cosine/squared/restricted <angle_cosine_squared_restricted>` | k,theta0 | type angles |
|
||||
+--------------------------------------------------------------------+-----------------+-------------+
|
||||
| :doc:`dipole <angle_dipole>` | k,gamma0 | type angles |
|
||||
+--------------------------------------------------------------------+-----------------+-------------+
|
||||
| :doc:`fourier <angle_fourier>` | k,c0,c1,c2 | type angles |
|
||||
+--------------------------------------------------------------------+-----------------+-------------+
|
||||
| :doc:`fourier/simple <angle_fourier_simple>` | k,c,n | type angles |
|
||||
+--------------------------------------------------------------------+-----------------+-------------+
|
||||
| :doc:`mm3 <angle_mm3>` | k,theta0 | type angles |
|
||||
+--------------------------------------------------------------------+-----------------+-------------+
|
||||
| :doc:`quartic <angle_quartic>` | k2,k3,k4,theta0 | type angles |
|
||||
+--------------------------------------------------------------------+-----------------+-------------+
|
||||
| :doc:`spica <angle_spica>` | k,theta0 | type angles |
|
||||
+--------------------------------------------------------------------+-----------------+-------------+
|
||||
+--------------------------------------------------------------------+--------------------+-------------+
|
||||
| :doc:`harmonic <angle_harmonic>` | k,theta0 | type angles |
|
||||
+--------------------------------------------------------------------+--------------------+-------------+
|
||||
| :doc:`charmm <angle_charmm>` | k,theta0 | type angles |
|
||||
+--------------------------------------------------------------------+--------------------+-------------+
|
||||
| :doc:`class2 <angle_class2>` | k2,k3,k4,theta0 | type angles |
|
||||
+--------------------------------------------------------------------+--------------------+-------------+
|
||||
| :doc:`cosine <angle_cosine>` | k | type angles |
|
||||
+--------------------------------------------------------------------+--------------------+-------------+
|
||||
| :doc:`cosine/delta <angle_cosine_delta>` | k | type angles |
|
||||
+--------------------------------------------------------------------+--------------------+-------------+
|
||||
| :doc:`cosine/periodic <angle_cosine_periodic>` | k,b,n | type angles |
|
||||
+--------------------------------------------------------------------+--------------------+-------------+
|
||||
| :doc:`cosine/squared <angle_cosine_squared>` | k,theta0 | type angles |
|
||||
+--------------------------------------------------------------------+--------------------+-------------+
|
||||
| :doc:`cosine/squared/restricted <angle_cosine_squared_restricted>` | k,theta0 | type angles |
|
||||
+--------------------------------------------------------------------+--------------------+-------------+
|
||||
| :doc:`dipole <angle_dipole>` | k,gamma0 | type angles |
|
||||
+--------------------------------------------------------------------+--------------------+-------------+
|
||||
| :doc:`fourier <angle_fourier>` | k,c0,c1,c2 | type angles |
|
||||
+--------------------------------------------------------------------+--------------------+-------------+
|
||||
| :doc:`fourier/simple <angle_fourier_simple>` | k,c,n | type angles |
|
||||
+--------------------------------------------------------------------+--------------------+-------------+
|
||||
| :doc:`gaussian <angle_gaussian>` | alpha,width,theta0 | type angles |
|
||||
+--------------------------------------------------------------------+--------------------+-------------+
|
||||
| :doc:`mm3 <angle_mm3>` | k,theta0 | type angles |
|
||||
+--------------------------------------------------------------------+--------------------+-------------+
|
||||
| :doc:`quartic <angle_quartic>` | k2,k3,k4,theta0 | type angles |
|
||||
+--------------------------------------------------------------------+--------------------+-------------+
|
||||
| :doc:`spica <angle_spica>` | k,theta0 | type angles |
|
||||
+--------------------------------------------------------------------+--------------------+-------------+
|
||||
|
||||
Note that internally, theta0 is stored in radians, so the variable
|
||||
this fix uses to reset theta0 needs to generate values in radians.
|
||||
|
||||
@ -115,10 +115,6 @@ correctly, the minimization will not converge properly.
|
||||
|
||||
----------
|
||||
|
||||
.. include:: accel_styles.rst
|
||||
|
||||
----------
|
||||
|
||||
Restart, fix_modify, output, run start/stop, minimize info
|
||||
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
|
||||
|
||||
|
||||
@ -119,15 +119,14 @@ groups of atoms that have different charges, these charges will not be
|
||||
changed when the atom types change.
|
||||
|
||||
Since this fix computes total potential energies before and after
|
||||
proposed swaps, so even complicated potential energy calculations are
|
||||
OK, including the following:
|
||||
proposed swaps, even complicated potential energy calculations are
|
||||
acceptable, including the following:
|
||||
|
||||
* long-range electrostatics (:math:`k`-space)
|
||||
* many body pair styles
|
||||
* hybrid pair styles
|
||||
* eam pair styles
|
||||
* hybrid pair styles (with restrictions)
|
||||
* EAM pair styles
|
||||
* triclinic systems
|
||||
* need to include potential energy contributions from other fixes
|
||||
|
||||
Some fixes have an associated potential energy. Examples of such fixes
|
||||
include: :doc:`efield <fix_efield>`, :doc:`gravity <fix_gravity>`,
|
||||
@ -181,6 +180,10 @@ This fix is part of the MC package. It is only enabled if LAMMPS was
|
||||
built with that package. See the :doc:`Build package <Build_package>`
|
||||
doc page for more info.
|
||||
|
||||
When this fix is used with a :doc:`hybrid pair style <pair_hybrid>`
|
||||
system, only swaps between atom types of the same sub-style (or
|
||||
combination of sub-styles) are permitted.
|
||||
|
||||
This fix cannot be used with systems that do not have per-type masses
|
||||
(e.g. atom style sphere) since the implemented algorithm pre-computes
|
||||
velocity rescaling factors from per-type masses and ignores any per-atom
|
||||
|
||||
@ -71,10 +71,6 @@ to it.
|
||||
|
||||
----------
|
||||
|
||||
.. include:: accel_styles.rst
|
||||
|
||||
----------
|
||||
|
||||
Restart, fix_modify, output, run start/stop, minimize info
|
||||
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
|
||||
|
||||
|
||||
@ -50,8 +50,8 @@ Syntax
|
||||
*intra_energy* value = intramolecular energy (energy units)
|
||||
*tfac_insert* value = scale up/down temperature of inserted atoms (unitless)
|
||||
*overlap_cutoff* value = maximum pair distance for overlap rejection (distance units)
|
||||
*max* value = Maximum number of molecules allowed in the system
|
||||
*min* value = Minimum number of molecules allowed in the system
|
||||
*max* value = Maximum number of atoms allowed in the fix group (and region)
|
||||
*min* value = Minimum number of atoms allowed in the fix group (and region)
|
||||
|
||||
Examples
|
||||
""""""""
|
||||
@ -380,10 +380,11 @@ an infinite positive energy to all new configurations that place any
|
||||
pair of atoms closer than the specified overlap cutoff distance.
|
||||
|
||||
The *max* and *min* keywords allow for the restriction of the number of
|
||||
atoms in the simulation. They automatically reject all insertion or
|
||||
deletion moves that would take the system beyond the set boundaries.
|
||||
Should the system already be beyond the boundary, only moves that bring
|
||||
the system closer to the bounds may be accepted.
|
||||
atoms in the fix group (and region in case the *region* keyword is
|
||||
used). They automatically reject all insertion or deletion moves that
|
||||
would take the system beyond the set boundaries. Should the system
|
||||
already be beyond the boundary, only moves that bring the system closer
|
||||
to the bounds may be accepted.
|
||||
|
||||
The *group* keyword adds all inserted atoms to the :doc:`group <group>`
|
||||
of the group-ID value. The *grouptype* keyword adds all inserted atoms
|
||||
|
||||
@ -101,7 +101,7 @@ hstyle = bondmax option.
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
compute bdist all bond/local dist
|
||||
compute bmax all reduce max c_bdist
|
||||
compute bmax all reduce max c_bdist inputs local
|
||||
variable bondmax equal c_bmax
|
||||
|
||||
Thus these two versions of a fix halt command will do the same thing:
|
||||
|
||||
@ -231,12 +231,6 @@ the particles. As described below, this energy can then be printed
|
||||
out or added to the potential energy of the system to monitor energy
|
||||
conservation.
|
||||
|
||||
.. note::
|
||||
|
||||
This accumulated energy does NOT include kinetic energy removed
|
||||
by the *zero* flag. LAMMPS will print a warning when both options are
|
||||
active.
|
||||
|
||||
The keyword *zero* can be used to eliminate drift due to the
|
||||
thermostat. Because the random forces on different atoms are
|
||||
independent, they do not sum exactly to zero. As a result, this fix
|
||||
|
||||
@ -102,7 +102,6 @@ zeroed. The *update* reference style implies the reference state will be updated
|
||||
*nstep* timesteps. The *offset* reference will update the reference state *nstep*
|
||||
timesteps before a multiple of *nevery* timesteps.
|
||||
|
||||
|
||||
----------
|
||||
|
||||
Restart, fix_modify, output, run start/stop, minimize info
|
||||
@ -129,6 +128,12 @@ This compute is part of the EXTRA-FIX package. It is only enabled if
|
||||
LAMMPS was built with that package. See the
|
||||
:doc:`Build package <Build_package>` page for more info.
|
||||
|
||||
As this fix depends on a run including specific reference timesteps, it
|
||||
currently does not update peratom values if used in conjunction with the
|
||||
:doc:`rerun command <rerun>` since it cannot ensure the necessary reference
|
||||
timesteps are included.
|
||||
|
||||
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
|
||||
@ -79,8 +79,6 @@ It also means that changing attributes of *thermo_temp* or
|
||||
|
||||
----------
|
||||
|
||||
.. include:: accel_styles.rst
|
||||
|
||||
Restart, fix_modify, output, run start/stop, minimize info
|
||||
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
|
||||
|
||||
|
||||
@ -103,8 +103,6 @@ remaining thermal degrees of freedom, and the bias is added back in.
|
||||
|
||||
----------
|
||||
|
||||
.. include:: accel_styles.rst
|
||||
|
||||
Restart, fix_modify, output, run start/stop, minimize info
|
||||
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
|
||||
|
||||
|
||||
@ -85,8 +85,6 @@ remaining thermal degrees of freedom, and the bias is added back in.
|
||||
|
||||
----------
|
||||
|
||||
.. include:: accel_styles.rst
|
||||
|
||||
Restart, fix_modify, output, run start/stop, minimize info
|
||||
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
|
||||
|
||||
|
||||
@ -155,6 +155,22 @@ many timesteps until the desired # of particles has been inserted.
|
||||
the :doc:`compute_modify dynamic/dof yes <compute_modify>` command
|
||||
for the temperature compute you are using.
|
||||
|
||||
.. admonition:: Implementation Notes
|
||||
:class: Hint
|
||||
|
||||
The exact insertion procedure depends on many factors (e.g. the range of
|
||||
diameters inserted or whether molecules are being inserted). However, in
|
||||
the simplest scenario of monodisperse atoms, the procedure works as
|
||||
follows. First, the number of timesteps between two insertion events is
|
||||
calculated as the time for a particle to fall through the insertion region,
|
||||
accounting for gravity and any region motion. Next, the target number of
|
||||
particles inserted per event (assuming no failed insertions due to overlaps)
|
||||
is calculated as the product of the volume fraction and the volume of the
|
||||
insertion region divided by the volume of a particle (or area in 2D).
|
||||
Events are repeated until all N particles have been inserted, where
|
||||
the final event is likely interrupted upon reaching N. Estimates of this
|
||||
process are printed to the log/screen at the start of a run.
|
||||
|
||||
----------
|
||||
|
||||
All other keywords are optional with defaults as shown below.
|
||||
|
||||
@ -1,6 +1,7 @@
|
||||
.. index:: fix qeq/point
|
||||
.. index:: fix qeq/shielded
|
||||
.. index:: fix qeq/slater
|
||||
.. index:: fix qeq/ctip
|
||||
.. index:: fix qeq/dynamic
|
||||
.. index:: fix qeq/fire
|
||||
|
||||
@ -13,6 +14,9 @@ fix qeq/shielded command
|
||||
fix qeq/slater command
|
||||
======================
|
||||
|
||||
fix qeq/ctip command
|
||||
====================
|
||||
|
||||
fix qeq/dynamic command
|
||||
=======================
|
||||
|
||||
@ -27,18 +31,20 @@ Syntax
|
||||
fix ID group-ID style Nevery cutoff tolerance maxiter qfile keyword ...
|
||||
|
||||
* ID, group-ID are documented in :doc:`fix <fix>` command
|
||||
* style = *qeq/point* or *qeq/shielded* or *qeq/slater* or *qeq/dynamic* or *qeq/fire*
|
||||
* style = *qeq/point* or *qeq/shielded* or *qeq/slater* or *qeq/ctip* or *qeq/dynamic* or *qeq/fire*
|
||||
* Nevery = perform charge equilibration every this many steps
|
||||
* cutoff = global cutoff for charge-charge interactions (distance unit)
|
||||
* tolerance = precision to which charges will be equilibrated
|
||||
* maxiter = maximum iterations to perform charge equilibration
|
||||
* qfile = a filename with QEq parameters or *coul/streitz* or *reaxff*
|
||||
* qfile = a filename with QEq parameters or *coul/streitz* or *coul/ctip* or *reaxff*
|
||||
* zero or more keyword/value pairs may be appended
|
||||
* keyword = *alpha* or *qdamp* or *qstep* or *warn*
|
||||
* keyword = *alpha* or *cdamp* or *maxrepeat* or *qdamp* or *qstep* or *warn*
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
*alpha* value = Slater type orbital exponent (qeq/slater only)
|
||||
*cdamp* value = damping parameter for Coulomb interactions (qeq/ctip only)
|
||||
*maxrepeat* value = number of equilibration cycles allowed to ensure no atoms cross charge bounds (qeq/ctip only)
|
||||
*qdamp* value = damping factor for damped dynamics charge solver (qeq/dynamic and qeq/fire only)
|
||||
*qstep* value = time step size for damped dynamics charge solver (qeq/dynamic and qeq/fire only)
|
||||
*warn* value = do (=yes) or do not (=no) print a warning when the maximum number of iterations is reached
|
||||
@ -51,6 +57,7 @@ Examples
|
||||
fix 1 all qeq/point 1 10 1.0e-6 200 param.qeq1
|
||||
fix 1 qeq qeq/shielded 1 8 1.0e-6 100 param.qeq2
|
||||
fix 1 all qeq/slater 5 10 1.0e-6 100 params alpha 0.2
|
||||
fix 1 all qeq/ctip 1 12 1.0e-8 100 coul/ctip cdamp 0.30 maxrepeat 10
|
||||
fix 1 qeq qeq/dynamic 1 12 1.0e-3 100 my_qeq
|
||||
fix 1 all qeq/fire 1 10 1.0e-3 100 my_qeq qdamp 0.2 qstep 0.1
|
||||
|
||||
@ -103,7 +110,7 @@ equalizes the derivative of energy with respect to charge of all the
|
||||
atoms) by adjusting the partial charge on individual atoms based on
|
||||
interactions with their neighbors within *cutoff*\ . It requires a few
|
||||
parameters in the appropriate units for each atom type which are read
|
||||
from a file specified by *qfile*\ . The file has the following format
|
||||
from a file specified by *qfile*\ . The file has the following format:
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
@ -112,20 +119,32 @@ from a file specified by *qfile*\ . The file has the following format
|
||||
...
|
||||
Ntype chi eta gamma zeta qcore
|
||||
|
||||
except for fix style *qeq/ctip* where the format is:
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
1 chi eta gamma zeta qcore qmin qmax omega
|
||||
2 chi eta gamma zeta qcore qmin qmax omega
|
||||
...
|
||||
Ntype chi eta gamma zeta qcore qmin qmax omega
|
||||
|
||||
There have to be parameters given for every atom type. Wildcard entries
|
||||
are possible using the same type range syntax as for "coeff" commands
|
||||
(i.e., n\*m, n\*, \*m, \*). Later entries will overwrite previous ones.
|
||||
Empty lines or any text following the pound sign (#) are ignored.
|
||||
Each line starts with the atom type followed by five parameters.
|
||||
Only a subset of the parameters is used by each QEq style as described
|
||||
below, thus the others can be set to 0.0 if desired, but all five
|
||||
entries per line are required.
|
||||
Empty lines or any text following the pound sign (#) are ignored. Each
|
||||
line starts with the atom type followed by eight parameters. Only a
|
||||
subset of the parameters is used by each QEq style as described below,
|
||||
thus the others can be set to 0.0 if desired, but all eight entries per
|
||||
line are required.
|
||||
|
||||
* *chi* = electronegativity in energy units
|
||||
* *eta* = self-Coulomb potential in energy units
|
||||
* *gamma* = shielded Coulomb constant defined by :ref:`ReaxFF force field <vanDuin>` in distance units
|
||||
* *zeta* = Slater type orbital exponent defined by the :ref:`Streitz-Mintmire <Streitz1>` potential in reverse distance units
|
||||
* *qcore* = charge of the nucleus defined by the :ref:`Streitz-Mintmire potential <Streitz1>` potential in charge units
|
||||
* *qmin* = lower bound on the allowed charge defined by the :ref:`CTIP <CTIP1>` potential in charge units
|
||||
* *qmax* = upper bound on the allowed charge defined by the :ref:`CTIP <CTIP1>` potential in charge units
|
||||
* *omega* = penalty parameter used to enforce charge bounds defined by the :ref:`CTIP <CTIP1>` potential in energy units
|
||||
|
||||
The fix qeq styles will print a warning if the charges are not
|
||||
equilibrated within *tolerance* by *maxiter* steps, unless the
|
||||
@ -171,6 +190,22 @@ on atoms via the matrix inversion method. A tolerance of 1.0e-6 is
|
||||
usually a good number. Keyword *alpha* can be used to change the Slater
|
||||
type orbital exponent.
|
||||
|
||||
.. versionadded:: TBD
|
||||
|
||||
The *qeq/ctip* style describes partial charges on atoms in the same way
|
||||
as style *qeq/shielded* but also enables the definition of charge
|
||||
bounds. Only the *chi*, *eta*, *gamma*, *qmin*, *qmax*, and *omega*
|
||||
parameters from the *qfile* file are used. When using the string
|
||||
*coul/ctip* as filename, these parameters are extracted directly from an
|
||||
active *coul/ctip* pair style. This style solves partial charges on
|
||||
atoms via the matrix inversion method. Keyword *cdamp* can be used to
|
||||
change the damping parameter used to calculate Coulomb interactions.
|
||||
Keyword *maxrepeat* can be used to adjust the number of equilibration
|
||||
cycles allowed to ensure no atoms have crossed the charge bounds. A
|
||||
value of 10 is usually a good choice. A tolerance between 1.0e-6 and
|
||||
1.0e-8 is usually a good choice but should be checked in conjunction
|
||||
with the timestep for adequate energy conservation during dynamic runs.
|
||||
|
||||
The *qeq/dynamic* style describes partial charges on atoms as point
|
||||
charges that interact through 1/r, but the extended Lagrangian method is
|
||||
used to solve partial charges on atoms. Only the *chi* and *eta*
|
||||
@ -186,7 +221,7 @@ minimization algorithm to solve for equilibrium charges. Keyword
|
||||
*qdamp* can be used to change the damping factor, while keyword *qstep*
|
||||
can be used to change the time step size.
|
||||
|
||||
Note that *qeq/point*, *qeq/shielded*, and *qeq/slater* describe
|
||||
Note that *qeq/point*, *qeq/shielded*, *qeq/slater*, and *qeq/ctip* describe
|
||||
different charge models, whereas the matrix inversion method and the
|
||||
extended Lagrangian method (\ *qeq/dynamic* and *qeq/fire*\ ) are
|
||||
different solvers.
|
||||
@ -266,6 +301,11 @@ Chemistry, 95, 3358-3363 (1991).
|
||||
**(Streitz-Mintmire)** F. H. Streitz, J. W. Mintmire, Physical Review B, 50,
|
||||
16, 11996 (1994)
|
||||
|
||||
.. _CTIP1:
|
||||
|
||||
**(CTIP)** G. Plummer, J. P. Tavenner, M. I. Mendelev, Z. Wu, J. W. Lawson,
|
||||
in preparation
|
||||
|
||||
.. _vanDuin:
|
||||
|
||||
**(ReaxFF)** A. C. T. van Duin, S. Dasgupta, F. Lorant, W. A. Goddard III, J
|
||||
|
||||
@ -16,8 +16,7 @@ Syntax
|
||||
* kstyle = *quintic* or *RK0* or *RK1* or *RK2*
|
||||
* zmin = minimal number of neighbors for reproducing kernels
|
||||
* zero or more keyword/value pairs may be appended to args
|
||||
* keyword = *thermal* or *interface/reconstruct* or *surface/detection* or
|
||||
*shift* or *rho/sum* or *density* or *self/mass* or *speed/sound*
|
||||
* keyword = *thermal* or *interface/reconstruct* or *surface/detection* or *shift* or *rho/sum* or *density* or *self/mass* or *speed/sound*
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
|
||||
@ -123,6 +123,12 @@ also be potentially mitigated by using more multiple walls.
|
||||
conservative as possible (every timestep if needed). Those are the
|
||||
default settings.
|
||||
|
||||
----------
|
||||
|
||||
.. include:: accel_styles.rst
|
||||
|
||||
----------
|
||||
|
||||
Restart, fix_modify, output, run start/stop, minimize info
|
||||
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
|
||||
|
||||
|
||||
@ -1,8 +0,0 @@
|
||||
Fixes
|
||||
#####
|
||||
|
||||
.. toctree::
|
||||
:maxdepth: 1
|
||||
:glob:
|
||||
|
||||
fix_*
|
||||
@ -162,7 +162,7 @@ potential energy is above the threshold value :math:`-3.0`.
|
||||
compute 1 all pe/atom
|
||||
compute 2 all reduce sum c_1
|
||||
thermo_style custom step temp pe c_2
|
||||
run 0
|
||||
run 0 post no
|
||||
|
||||
variable eatom atom "c_1 > -3.0"
|
||||
group hienergy variable eatom
|
||||
@ -173,7 +173,7 @@ Note that these lines
|
||||
|
||||
compute 2 all reduce sum c_1
|
||||
thermo_style custom step temp pe c_2
|
||||
run 0
|
||||
run 0 post no
|
||||
|
||||
are necessary to ensure that the "eatom" variable is current when the
|
||||
group command invokes it. Because the eatom variable computes the
|
||||
|
||||
@ -1,8 +0,0 @@
|
||||
Improper Styles
|
||||
###############
|
||||
|
||||
.. toctree::
|
||||
:maxdepth: 1
|
||||
:glob:
|
||||
|
||||
improper_*
|
||||
@ -3,6 +3,8 @@
|
||||
min_style cg command
|
||||
====================
|
||||
|
||||
Accelerator Variant: *cg/kk*
|
||||
|
||||
min_style hftn command
|
||||
======================
|
||||
|
||||
|
||||
@ -8,7 +8,14 @@ Syntax
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
pair_style bpm/spring
|
||||
pair_style bpm/spring keyword value ...
|
||||
|
||||
* optional keyword = *anharmonic*
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
*anharmonic* value = *yes* or *no*
|
||||
whether forces include the anharmonic term
|
||||
|
||||
Examples
|
||||
""""""""
|
||||
@ -17,7 +24,8 @@ Examples
|
||||
|
||||
pair_style bpm/spring
|
||||
pair_coeff * * 1.0 1.0 1.0
|
||||
pair_coeff 1 1 1.0 1.0 1.0
|
||||
pair_style bpm/spring anharmonic yes
|
||||
pair_coeff 1 1 1.0 1.0 1.0 50.0
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
@ -28,12 +36,16 @@ Style *bpm/spring* computes pairwise forces with the formula
|
||||
|
||||
.. math::
|
||||
|
||||
F = k (r - r_c)
|
||||
F = k (r - r_c) + k_a (r - r_c)^3
|
||||
|
||||
where :math:`k` is a stiffness and :math:`r_c` is the cutoff length.
|
||||
An additional damping force is also applied to interacting
|
||||
particles. The force is proportional to the difference in the
|
||||
normal velocity of particles
|
||||
where :math:`k` is a stiffness, :math:`r_c` is the cutoff
|
||||
length, and :math:`k_a` is an optional anharmonic cubic prefactor
|
||||
that can be enabled using the *anharmonic* keyword. The anharmonic
|
||||
term may be useful in scenarios that need to prevent large particle overlap.
|
||||
|
||||
An additional damping force is also applied to interacting particles.
|
||||
The force is proportional to the difference in the normal velocity of
|
||||
particles
|
||||
|
||||
.. math::
|
||||
|
||||
@ -73,6 +85,12 @@ commands, or by mixing as described below:
|
||||
* :math:`r_c` (distance units)
|
||||
* :math:`\gamma` (force/velocity units)
|
||||
|
||||
.. versionadded:: TBD
|
||||
|
||||
Additionally, if *anharmonic* is set to *yes*, a fourth coefficient
|
||||
must be provided:
|
||||
|
||||
* :math:`k_a` (force/distance\^3 units)
|
||||
|
||||
----------
|
||||
|
||||
@ -117,4 +135,5 @@ Related commands
|
||||
Default
|
||||
"""""""
|
||||
|
||||
none
|
||||
The option defaults are *anharmonic* = *no*
|
||||
|
||||
|
||||
@ -1,12 +1,13 @@
|
||||
.. index:: pair_style brownian
|
||||
.. index:: pair_style brownian/omp
|
||||
.. index:: pair_style brownian/kk
|
||||
.. index:: pair_style brownian/poly
|
||||
.. index:: pair_style brownian/poly/omp
|
||||
|
||||
pair_style brownian command
|
||||
===========================
|
||||
|
||||
Accelerator Variants: *brownian/omp*
|
||||
Accelerator Variants: *brownian/omp*, *brownian/kk*
|
||||
|
||||
pair_style brownian/poly command
|
||||
================================
|
||||
|
||||
@ -4,6 +4,7 @@
|
||||
.. index:: pair_style coul/cut/omp
|
||||
.. index:: pair_style coul/cut/global
|
||||
.. index:: pair_style coul/cut/global/omp
|
||||
.. index:: pair_style coul/ctip
|
||||
.. index:: pair_style coul/debye
|
||||
.. index:: pair_style coul/debye/gpu
|
||||
.. index:: pair_style coul/debye/kk
|
||||
@ -38,6 +39,9 @@ pair_style coul/cut/global command
|
||||
|
||||
Accelerator Variants: *coul/cut/omp*
|
||||
|
||||
pair_style coul/ctip command
|
||||
============================
|
||||
|
||||
pair_style coul/debye command
|
||||
=============================
|
||||
|
||||
@ -79,7 +83,6 @@ pair_style tip4p/long command
|
||||
|
||||
Accelerator Variants: *tip4p/long/omp*
|
||||
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
@ -87,6 +90,7 @@ Syntax
|
||||
|
||||
pair_style coul/cut cutoff
|
||||
pair_style coul/cut/global cutoff
|
||||
pair_style coul/ctip alpha cutoff
|
||||
pair_style coul/debye kappa cutoff
|
||||
pair_style coul/dsf alpha cutoff
|
||||
pair_style coul/exclude cutoff
|
||||
@ -116,6 +120,9 @@ Examples
|
||||
pair_coeff * *
|
||||
pair_coeff 2 2 3.5
|
||||
|
||||
pair_style coul/ctip 0.30 12.0
|
||||
pair_coeff * * NiO.ctip Ni O
|
||||
|
||||
pair_style coul/debye 1.4 3.0
|
||||
pair_coeff * *
|
||||
pair_coeff 2 2 3.5
|
||||
@ -173,6 +180,33 @@ coulomb styles in :doc:`hybrid pair styles <pair_hybrid>`.
|
||||
|
||||
----------
|
||||
|
||||
.. versionadded:: TBD
|
||||
|
||||
Style *coul/ctip* computes the Coulomb interactions as described in
|
||||
:ref:`Plummer <Plummer1>`. It uses the the damped shifted model as in
|
||||
style *coul/dsf* but is further extended to the second derivative of the
|
||||
potential and incorporates empirical charge shielding meant to
|
||||
approximate the more expensive Coulomb integrals used in style
|
||||
*coul/streitz*. More details can be found in the referenced paper. Like
|
||||
the style *coul/streitz*, style *coul/ctip* is a variable charge
|
||||
potential and must be hybridized with a short-range potential via the
|
||||
:doc:`pair_style hybrid/overlay <pair_hybrid>` command. Charge
|
||||
equilibration must be performed with the :doc:`fix qeq/ctip <fix_qeq>`
|
||||
command. For example:
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
pair_style hybrid/overlay eam/fs coul/ctip 0.30 12.0
|
||||
pair_coeff * * eam/fs NiO.eam.fs Ni O
|
||||
pair_coeff * * coul/ctip NiO.ctip Ni O
|
||||
fix 1 all qeq/ctip 1 12.0 1.0e-8 100 coul/ctip cdamp 0.30 maxrepeat 10
|
||||
|
||||
See the examples/ctip directory for an example input script using the
|
||||
CTIP potential. An Ni-O CTIP and EAM/FS parameterization are included
|
||||
for use with the example.
|
||||
|
||||
----------
|
||||
|
||||
Style *coul/debye* adds an additional exp() damping factor to the
|
||||
Coulombic term, given by
|
||||
|
||||
@ -399,16 +433,18 @@ Restrictions
|
||||
""""""""""""
|
||||
|
||||
The *coul/long*, *coul/msm*, *coul/streitz*, and *tip4p/long* styles are
|
||||
part of the KSPACE package. The *coul/cut/global*, *coul/exclude* styles are
|
||||
part of the EXTRA-PAIR package. The *tip4p/cut* style is part of the MOLECULE
|
||||
package. A pair style is only enabled if LAMMPS was built with its
|
||||
corresponding package. See the :doc:`Build package <Build_package>`
|
||||
doc page for more info.
|
||||
part of the KSPACE package. The *coul/cut/global*, *coul/exclude*, and
|
||||
*coul/ctip* styles are part of the EXTRA-PAIR package. The *tip4p/cut*
|
||||
style is part of the MOLECULE package. A pair style is only enabled if
|
||||
LAMMPS was built with its corresponding package. See the
|
||||
:doc:`Build package <Build_package>` page for more info.
|
||||
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
:doc:`pair_coeff <pair_coeff>`, :doc:`pair_style, hybrid/overlay <pair_hybrid>`, :doc:`kspace_style <kspace_style>`
|
||||
:doc:`pair_coeff <pair_coeff>`,
|
||||
:doc:`pair_style hybrid/overlay <pair_hybrid>`,
|
||||
:doc:`kspace_style <kspace_style>`
|
||||
|
||||
Default
|
||||
"""""""
|
||||
@ -432,6 +468,11 @@ Phys, 110, 8254 (1999).
|
||||
**(Streitz)** F. H. Streitz, J. W. Mintmire, Phys Rev B, 50, 11996-12003
|
||||
(1994).
|
||||
|
||||
.. _Plummer1:
|
||||
|
||||
**(Plummer)** G. Plummer, J. P. Tavenner, M. I. Mendelev, Z. Wu, J. W. Lawson,
|
||||
in preparation
|
||||
|
||||
.. _Jorgensen3:
|
||||
|
||||
**(Jorgensen)** Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem
|
||||
|
||||
@ -71,6 +71,10 @@ The global cutoff (:math:`r_c`) specified in the pair_style command is used.
|
||||
|
||||
----------
|
||||
|
||||
.. include:: accel_styles.rst
|
||||
|
||||
----------
|
||||
|
||||
Mixing, shift, table, tail correction, restart, rRESPA info
|
||||
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
|
||||
|
||||
|
||||
@ -77,6 +77,10 @@ The global decay length of the charge (:math:`\lambda`) specified in the pair_st
|
||||
|
||||
----------
|
||||
|
||||
.. include:: accel_styles.rst
|
||||
|
||||
----------
|
||||
|
||||
Mixing, shift, table, tail correction, restart, rRESPA info
|
||||
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
|
||||
|
||||
|
||||
@ -741,10 +741,6 @@ atom types.
|
||||
|
||||
----------
|
||||
|
||||
.. include:: accel_styles.rst
|
||||
|
||||
----------
|
||||
|
||||
Mixing, shift, table, tail correction, restart, rRESPA info
|
||||
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
|
||||
|
||||
|
||||
@ -287,6 +287,10 @@ concentration profiles of the two chemical species as
|
||||
|
||||
----------
|
||||
|
||||
.. include:: accel_styles.rst
|
||||
|
||||
----------
|
||||
|
||||
Mixing, shift, table, tail correction, restart, rRESPA info
|
||||
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
|
||||
|
||||
|
||||
@ -62,6 +62,10 @@ cutoff specified in the pair_style command is used.
|
||||
|
||||
----------
|
||||
|
||||
.. include:: accel_styles.rst
|
||||
|
||||
----------
|
||||
|
||||
Mixing, shift, table, tail correction, restart, rRESPA info
|
||||
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
|
||||
|
||||
|
||||
@ -39,6 +39,10 @@ above.
|
||||
|
||||
----------
|
||||
|
||||
.. include:: accel_styles.rst
|
||||
|
||||
----------
|
||||
|
||||
Mixing, shift, table, tail correction, restart, rRESPA info
|
||||
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
|
||||
|
||||
|
||||
@ -43,6 +43,10 @@ above.
|
||||
|
||||
----------
|
||||
|
||||
.. include:: accel_styles.rst
|
||||
|
||||
----------
|
||||
|
||||
Mixing, shift, table, tail correction, restart, rRESPA info
|
||||
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
|
||||
|
||||
|
||||
@ -52,6 +52,10 @@ above.
|
||||
|
||||
----------
|
||||
|
||||
.. include:: accel_styles.rst
|
||||
|
||||
----------
|
||||
|
||||
Mixing, shift, table, tail correction, restart, rRESPA info
|
||||
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
|
||||
|
||||
|
||||
@ -151,6 +151,7 @@ accelerated styles exist.
|
||||
* :doc:`comb <pair_comb>` - charge-optimized many-body (COMB) potential
|
||||
* :doc:`comb3 <pair_comb>` - charge-optimized many-body (COMB3) potential
|
||||
* :doc:`cosine/squared <pair_cosine_squared>` - Cooke-Kremer-Deserno membrane model potential
|
||||
* :doc:`coul/ctip <pair_coul>` - Charge Transfer Interatomic (Coulomb) Potential
|
||||
* :doc:`coul/cut <pair_coul>` - cutoff Coulomb potential
|
||||
* :doc:`coul/cut/dielectric <pair_dielectric>` -
|
||||
* :doc:`coul/cut/global <pair_coul>` - cutoff Coulomb potential
|
||||
|
||||
@ -1,8 +0,0 @@
|
||||
Pair Styles
|
||||
###########
|
||||
|
||||
.. toctree::
|
||||
:maxdepth: 1
|
||||
:glob:
|
||||
|
||||
pair_*
|
||||
@ -115,10 +115,11 @@ to tell LAMMPS how many parallel files exist, via its specified
|
||||
|
||||
The format of the dump file is selected through the *format* keyword.
|
||||
If specified, it must be the last keyword used, since all remaining
|
||||
arguments are passed on to the dump reader. The *native* format is
|
||||
for native LAMMPS dump files, written with a :doc:`dump atom <dump>`
|
||||
or :doc:`dump custom <dump>` command. The *xyz* format is for generic XYZ
|
||||
formatted dump files. These formats take no additional values.
|
||||
arguments are passed on to the dump reader. The *native* format is for
|
||||
native LAMMPS dump files, written with a :doc:`dump atom <dump>` or
|
||||
:doc:`dump custom <dump>` command. The *xyz* format is for generic XYZ
|
||||
formatted dump files (see details below). These formats take no
|
||||
additional values.
|
||||
|
||||
The *molfile* format supports reading data through using the `VMD <vmd_>`_
|
||||
molfile plugin interface. This dump reader format is only available,
|
||||
@ -230,23 +231,39 @@ will then have a label corresponding to the fix-ID rather than "x" or
|
||||
"xs". The *label* keyword can also be used to specify new column
|
||||
labels for fields *id* and *type*\ .
|
||||
|
||||
For dump files in *xyz* format, only the *x*, *y*, and *z* fields are
|
||||
supported. The dump file does not store atom IDs, so these are
|
||||
assigned consecutively to the atoms as they appear in the dump file,
|
||||
starting from 1. Thus you should ensure that order of atoms is
|
||||
consistent from snapshot to snapshot in the XYZ dump file. See
|
||||
the :doc:`dump_modify sort <dump_modify>` command if the XYZ dump file
|
||||
was written by LAMMPS.
|
||||
For dump files in *xyz* format, only the *type*, *x*, *y*, and *z*
|
||||
fields are supported. There are many variants of the XYZ file format.
|
||||
LAMMPS will read the number of atoms from the first line of each frame,
|
||||
ignore the second (title) line, and then read one line for each atom in the format:
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
<label> <x coordinate> <y coordinate> <z coordinate>
|
||||
|
||||
|
||||
If the atom label is a numeric integer (like with XYZ files created by
|
||||
created with default settings by :doc:`dump style <dump>` *xyz*), that
|
||||
number will be used as the atom type. If the atom label is a string,
|
||||
then a type map must be created using the :doc:`labelmap command
|
||||
<labelmap>`. This map needs to associate each (numeric) atom type with
|
||||
a string label. The numeric atom type is stored internally.
|
||||
|
||||
The xyz format dump file does not store atom IDs, so these are assigned
|
||||
consecutively to the atoms as they appear in the dump file, starting
|
||||
from 1. Thus you should ensure that the order of atoms is consistent
|
||||
from snapshot to snapshot in the XYZ dump file. See the
|
||||
:doc:`dump_modify sort <dump_modify>` command if the XYZ dump file was
|
||||
written by LAMMPS.
|
||||
|
||||
For dump files in *molfile* format, the *x*, *y*, *z*, *vx*, *vy*, and
|
||||
*vz* fields can be specified. However, not all molfile formats store
|
||||
velocities, or their respective plugins may not support reading of
|
||||
velocities. The molfile dump files do not store atom IDs, so these
|
||||
are assigned consecutively to the atoms as they appear in the dump
|
||||
file, starting from 1. Thus you should ensure that order of atoms are
|
||||
consistent from snapshot to snapshot in the molfile dump file.
|
||||
See the :doc:`dump_modify sort <dump_modify>` command if the dump file
|
||||
was written by LAMMPS.
|
||||
velocities. The molfile dump files do not store atom IDs, so these are
|
||||
assigned consecutively to the atoms as they appear in the dump file,
|
||||
starting from 1. Thus you should ensure that the order of atoms are
|
||||
consistent from snapshot to snapshot in the molfile dump file. See the
|
||||
:doc:`dump_modify sort <dump_modify>` command if the dump file was
|
||||
written by LAMMPS.
|
||||
|
||||
The *adios* format supports all fields that the *native* format supports
|
||||
except for the *q* charge field.
|
||||
|
||||
Reference in New Issue
Block a user