Merge remote-tracking branch 'lammps/develop' into electrode
This commit is contained in:
Ludwig Ahrens
@ -486,14 +486,14 @@ The following options are available.
|
||||
make fix-whitespace # correct whitespace issues in files
|
||||
make check-homepage # search for files with old LAMMPS homepage URLs
|
||||
make fix-homepage # correct LAMMPS homepage URLs in files
|
||||
make check-errordocs # search for deprecated error docs in header files
|
||||
make fix-errordocs # remove error docs in header files
|
||||
make check-permissions # search for files with permissions issues
|
||||
make fix-permissions # correct permissions issues in files
|
||||
make check # run all check targets from above
|
||||
|
||||
These should help to replace all TAB characters with blanks and remove
|
||||
any trailing whitespace. Also all LAMMPS homepage URL references can be
|
||||
updated to the location change from Sandia to the lammps.org domain.
|
||||
And the permission check can remove executable permissions from non-executable
|
||||
files (like source code).
|
||||
These should help to make source and documentation files conforming
|
||||
to some the coding style preferences of the LAMMPS developers.
|
||||
|
||||
Clang-format support
|
||||
--------------------
|
||||
|
||||
@ -141,8 +141,6 @@ CMake build
|
||||
|
||||
:code:`GPU_ARCH` settings for different GPU hardware is as follows:
|
||||
|
||||
* sm_12 or sm_13 for GT200 (supported by CUDA 3.2 until CUDA 6.5)
|
||||
* sm_20 or sm_21 for Fermi (supported by CUDA 3.2 until CUDA 7.5)
|
||||
* sm_30 for Kepler (supported since CUDA 5 and until CUDA 10.x)
|
||||
* sm_35 or sm_37 for Kepler (supported since CUDA 5 and until CUDA 11.x)
|
||||
* sm_50 or sm_52 for Maxwell (supported since CUDA 6)
|
||||
@ -160,6 +158,12 @@ Thus the GPU_ARCH setting is merely an optimization, to have code for
|
||||
the preferred GPU architecture directly included rather than having to wait
|
||||
for the JIT compiler of the CUDA driver to translate it.
|
||||
|
||||
When compiling for CUDA or HIP with CUDA, version 8.0 or later of the CUDA toolkit
|
||||
is required and a GPU architecture of Kepler or later, which must *also* be
|
||||
supported by the CUDA toolkit in use **and** the CUDA driver in use.
|
||||
When compiling for OpenCL, OpenCL version 1.2 or later is required and the
|
||||
GPU must be supported by the GPU driver and OpenCL runtime bundled with the driver.
|
||||
|
||||
When building with CMake, you **must NOT** build the GPU library in ``lib/gpu``
|
||||
using the traditional build procedure. CMake will detect files generated by that
|
||||
process and will terminate with an error and a suggestion for how to remove them.
|
||||
|
||||
@ -78,11 +78,12 @@ folder. The following ``make`` commands are available:
|
||||
|
||||
make html # generate HTML in html dir using Sphinx
|
||||
make pdf # generate PDF as Manual.pdf using Sphinx and PDFLaTeX
|
||||
make fetch # fetch HTML pages and PDF files from LAMMPS website
|
||||
# and unpack into the html_www folder and Manual_www.pdf
|
||||
make epub # generate LAMMPS.epub in ePUB format using Sphinx
|
||||
make mobi # generate LAMMPS.mobi in MOBI format using ebook-convert
|
||||
|
||||
make fasthtml # generate approximate HTML in fasthtml dir using Sphinx
|
||||
# some Sphinx extensions do not work correctly with this
|
||||
|
||||
make clean # remove intermediate RST files created by HTML build
|
||||
make clean-all # remove entire build folder and any cached data
|
||||
|
||||
@ -193,8 +194,13 @@ folder need to be updated or new files added. These files are written in
|
||||
`reStructuredText <rst_>`_ markup for translation with the Sphinx tool.
|
||||
|
||||
Before contributing any documentation, please check that both the HTML
|
||||
and the PDF format documentation can translate without errors. Please also
|
||||
check the output to the console for any warnings or problems. There will
|
||||
and the PDF format documentation can translate without errors. During
|
||||
testing the html translation, you may use the ``make fasthtml`` command
|
||||
which does an approximate translation (i.e. not all Sphinx features and
|
||||
extensions will work), but runs very fast because it will only translate
|
||||
files that have been changed since the last ``make fasthtml`` command.
|
||||
|
||||
Please also check the output to the console for any warnings or problems. There will
|
||||
be multiple tests run automatically:
|
||||
|
||||
- A test for correctness of all anchor labels and their references
|
||||
|
||||
@ -32,6 +32,8 @@ OPT.
|
||||
*
|
||||
*
|
||||
*
|
||||
* :doc:`bpm/rotational <bond_bpm_rotational>`
|
||||
* :doc:`bpm/spring <bond_bpm_spring>`
|
||||
* :doc:`class2 (ko) <bond_class2>`
|
||||
* :doc:`fene (iko) <bond_fene>`
|
||||
* :doc:`fene/expand (o) <bond_fene_expand>`
|
||||
|
||||
@ -33,6 +33,7 @@ KOKKOS, o = OPENMP, t = OPT.
|
||||
* :doc:`body/local <compute_body_local>`
|
||||
* :doc:`bond <compute_bond>`
|
||||
* :doc:`bond/local <compute_bond_local>`
|
||||
* :doc:`born/matrix <compute_born_matrix>`
|
||||
* :doc:`centro/atom <compute_centro_atom>`
|
||||
* :doc:`centroid/stress/atom <compute_stress_atom>`
|
||||
* :doc:`chunk/atom <compute_chunk_atom>`
|
||||
@ -91,6 +92,7 @@ KOKKOS, o = OPENMP, t = OPT.
|
||||
* :doc:`msd <compute_msd>`
|
||||
* :doc:`msd/chunk <compute_msd_chunk>`
|
||||
* :doc:`msd/nongauss <compute_msd_nongauss>`
|
||||
* :doc:`nbond/atom <compute_nbond_atom>`
|
||||
* :doc:`omega/chunk <compute_omega_chunk>`
|
||||
* :doc:`orientorder/atom (k) <compute_orientorder_atom>`
|
||||
* :doc:`pair <compute_pair>`
|
||||
|
||||
@ -144,6 +144,7 @@ OPT.
|
||||
* :doc:`nve/manifold/rattle <fix_nve_manifold_rattle>`
|
||||
* :doc:`nve/noforce <fix_nve_noforce>`
|
||||
* :doc:`nve/sphere (ko) <fix_nve_sphere>`
|
||||
* :doc:`nve/bpm/sphere <fix_nve_bpm_sphere>`
|
||||
* :doc:`nve/spin <fix_nve_spin>`
|
||||
* :doc:`nve/tri <fix_nve_tri>`
|
||||
* :doc:`nvk <fix_nvk>`
|
||||
@ -161,7 +162,6 @@ OPT.
|
||||
* :doc:`orient/fcc <fix_orient>`
|
||||
* :doc:`orient/eco <fix_orient_eco>`
|
||||
* :doc:`pafi <fix_pafi>`
|
||||
* :doc:`pair/tracker <fix_pair_tracker>`
|
||||
* :doc:`phonon <fix_phonon>`
|
||||
* :doc:`pimd <fix_pimd>`
|
||||
* :doc:`planeforce <fix_planeforce>`
|
||||
|
||||
@ -53,6 +53,7 @@ OPT.
|
||||
* :doc:`born/coul/msm (o) <pair_born>`
|
||||
* :doc:`born/coul/wolf (go) <pair_born>`
|
||||
* :doc:`born/coul/wolf/cs (g) <pair_cs>`
|
||||
* :doc:`bpm/spring <pair_bpm_spring>`
|
||||
* :doc:`brownian (o) <pair_brownian>`
|
||||
* :doc:`brownian/poly (o) <pair_brownian>`
|
||||
* :doc:`buck (giko) <pair_buck>`
|
||||
@ -123,7 +124,7 @@ OPT.
|
||||
* :doc:`hbond/dreiding/lj (o) <pair_hbond_dreiding>`
|
||||
* :doc:`hbond/dreiding/morse (o) <pair_hbond_dreiding>`
|
||||
* :doc:`hdnnp <pair_hdnnp>`
|
||||
* :doc:`ilp/graphene/hbn <pair_ilp_graphene_hbn>`
|
||||
* :doc:`ilp/graphene/hbn (t) <pair_ilp_graphene_hbn>`
|
||||
* :doc:`ilp/tmd <pair_ilp_tmd>`
|
||||
* :doc:`kolmogorov/crespi/full <pair_kolmogorov_crespi_full>`
|
||||
* :doc:`kolmogorov/crespi/z <pair_kolmogorov_crespi_z>`
|
||||
@ -151,7 +152,7 @@ OPT.
|
||||
* :doc:`lj/cut/coul/cut/dielectric (o) <pair_dielectric>`
|
||||
* :doc:`lj/cut/coul/cut/soft (o) <pair_fep_soft>`
|
||||
* :doc:`lj/cut/coul/debye (gko) <pair_lj_cut_coul>`
|
||||
* :doc:`lj/cut/coul/debye/dielectric <pair_dielectric>`
|
||||
* :doc:`lj/cut/coul/debye/dielectric (o) <pair_dielectric>`
|
||||
* :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>`
|
||||
|
||||
@ -211,6 +211,12 @@ Convenience functions
|
||||
.. doxygenfunction:: logmesg(LAMMPS *lmp, const std::string &mesg)
|
||||
:project: progguide
|
||||
|
||||
.. doxygenfunction:: errorurl
|
||||
:project: progguide
|
||||
|
||||
.. doxygenfunction:: missing_cmd_args
|
||||
:project: progguide
|
||||
|
||||
.. doxygenfunction:: flush_buffers(LAMMPS *lmp)
|
||||
:project: progguide
|
||||
|
||||
|
||||
@ -11,6 +11,7 @@ them.
|
||||
:maxdepth: 1
|
||||
|
||||
Errors_common
|
||||
Errors_details
|
||||
Errors_bugs
|
||||
Errors_debug
|
||||
Errors_messages
|
||||
|
||||
27
doc/src/Errors_details.rst
Normal file
27
doc/src/Errors_details.rst
Normal file
@ -0,0 +1,27 @@
|
||||
Error and warning details
|
||||
=========================
|
||||
|
||||
Many errors or warnings are self-explanatory and thus straightforward to
|
||||
resolve. However, there are also cases, where there is no single cause
|
||||
and explanation, where LAMMPS can only detect symptoms of an error but
|
||||
not the exact cause, or where the explanation needs to be more detailed than
|
||||
what can be fit into a message printed by the program. The following are
|
||||
discussions of such cases.
|
||||
|
||||
.. _err0001:
|
||||
|
||||
Unknown identifier in data file
|
||||
-------------------------------
|
||||
|
||||
This error happens when LAMMPS encounters a line of text in an unexpected format
|
||||
while reading a data file. This is most commonly cause by inconsistent header and
|
||||
section data. The header section informs LAMMPS how many entries or lines are expected in the
|
||||
various sections (like Atoms, Masses, Pair Coeffs, *etc.*\ ) of the data file.
|
||||
If there is a mismatch, LAMMPS will either keep reading beyond the end of a section
|
||||
or stop reading before the section has ended.
|
||||
|
||||
Such a mismatch can happen unexpectedly when the first line of the data
|
||||
is *not* a comment as required by the format. That would result in
|
||||
LAMMPS expecting, for instance, 0 atoms because the "atoms" header line
|
||||
is treated as a comment.
|
||||
|
||||
@ -54,6 +54,8 @@ Lowercase directories
|
||||
+-------------+------------------------------------------------------------------+
|
||||
| body | body particles, 2d system |
|
||||
+-------------+------------------------------------------------------------------+
|
||||
| bpm | BPM simulations of pouring elastic grains and plate impact |
|
||||
+-------------+------------------------------------------------------------------+
|
||||
| cmap | CMAP 5-body contributions to CHARMM force field |
|
||||
+-------------+------------------------------------------------------------------+
|
||||
| colloid | big colloid particles in a small particle solvent, 2d system |
|
||||
|
||||
@ -23,6 +23,8 @@ General howto
|
||||
Howto_library
|
||||
Howto_couple
|
||||
Howto_mdi
|
||||
Howto_bpm
|
||||
Howto_broken_bonds
|
||||
|
||||
Settings howto
|
||||
==============
|
||||
|
||||
119
doc/src/Howto_bpm.rst
Normal file
119
doc/src/Howto_bpm.rst
Normal file
@ -0,0 +1,119 @@
|
||||
Bonded particle models
|
||||
======================
|
||||
|
||||
The BPM package implements bonded particle models which can be used to
|
||||
simulate mesoscale solids. Solids are constructed as a collection of
|
||||
particles which each represent a coarse-grained region of space much
|
||||
larger than the atomistic scale. Particles within a solid region are
|
||||
then connected by a network of bonds to provide solid elasticity.
|
||||
|
||||
Unlike traditional bonds in molecular dynamics, the equilibrium bond
|
||||
length can vary between bonds. Bonds store the reference state. This
|
||||
includes setting the equilibrium length equal to the initial distance
|
||||
between the two particles but can also include data on the bond
|
||||
orientation for rotational models. This produces a stress free initial
|
||||
state. Furthermore, bonds are allowed to break under large strains
|
||||
producing fracture. The examples/bpm directory has sample input scripts
|
||||
for simulations of the fragmentation of an impacted plate and the
|
||||
pouring of extended, elastic bodies.
|
||||
|
||||
----------
|
||||
|
||||
Bonds can be created using a :doc:`read data <read_data>` or
|
||||
:doc:`create bonds <create_bonds>` command. Alternatively, a
|
||||
:doc:`molecule <molecule>` template with bonds can be used with
|
||||
:doc:`fix deposit <fix_deposit>` or :doc:`fix pour <fix_pour>` to
|
||||
create solid grains.
|
||||
|
||||
In this implementation, bonds store their reference state when they are
|
||||
first computed in the setup of the first simulation run. Data is then
|
||||
preserved across run commands and is written to :doc:`binary restart
|
||||
files <restart>` such that restarting the system will not reset the
|
||||
reference state of a bond. Bonds that are created midway into a run,
|
||||
such as those created by pouring grains using :doc:`fix pour
|
||||
<fix_pour>`, are initialized on that timestep.
|
||||
|
||||
As bonds can be broken between neighbor list builds, the
|
||||
:doc:`special_bonds <special_bonds>` command works differently for BPM
|
||||
bond styles. There are two possible settings which determine how pair
|
||||
interactions work between bonded particles. First, one can turn off
|
||||
all pair interactions between bonded particles. Unlike :doc:`bond
|
||||
quartic <bond_quartic>`, this is not done by subtracting pair forces
|
||||
during the bond computation but rather by dynamically updating the
|
||||
special bond list. This is the default behavior of BPM bond styles and
|
||||
is done by updating the 1-2 special bond list as bonds break. To do
|
||||
this, LAMMPS requires :doc:`newton <newton>` bond off such that all
|
||||
processors containing an atom know when a bond breaks. Additionally,
|
||||
one must do either (A) or (B).
|
||||
|
||||
A) Use the following special bond settings
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
special_bonds lj 0 1 1 coul 1 1 1
|
||||
|
||||
These settings accomplish two goals. First, they turn off 1-3 and 1-4
|
||||
special bond lists, which are not currently supported for BPMs. As
|
||||
BPMs often have dense bond networks, generating 1-3 and 1-4 special
|
||||
bond lists is expensive. By setting the lj weight for 1-2 bonds to
|
||||
zero, this turns off pairwise interactions. Even though there are no
|
||||
charges in BPM models, setting a nonzero coul weight for 1-2 bonds
|
||||
ensures all bonded neighbors are still included in the neighbor list
|
||||
in case bonds break between neighbor list builds.
|
||||
|
||||
B) Alternatively, one can simply overlay pair interactions such that all
|
||||
bonded particles also feel pair interactions. This can be
|
||||
accomplished by using the *overlay/pair* keyword present in all bpm
|
||||
bond styles and by using the following special bond settings
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
special_bonds lj/coul 1 1 1
|
||||
|
||||
See the :doc:`Howto <Howto_broken_bonds>` page on broken bonds for
|
||||
more information.
|
||||
|
||||
----------
|
||||
|
||||
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 <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 :doc:`granular package
|
||||
<Howto_granular>`, :doc:`atom style sphere <atom_style>`. However,
|
||||
they must also track the current orientation of particles and store bonds
|
||||
and therefore use a :doc:`bpm/sphere atom style <atom_style>`.
|
||||
This also requires a unique integrator :doc:`fix nve/bpm/sphere
|
||||
<fix_nve_bpm_sphere>` which numerically integrates orientation similar
|
||||
to :doc:`fix nve/asphere <fix_nve_asphere>`.
|
||||
|
||||
To monitor the fracture of bonds in the system, all BPM bond styles
|
||||
have the ability to record instances of bond breakage to output using
|
||||
the :doc:`dump local <dump>` command. Additionally, one can use
|
||||
:doc:`compute nbond/atom <compute_nbond_atom>` to tally the current
|
||||
number of bonds per atom.
|
||||
|
||||
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.
|
||||
|
||||
----------
|
||||
|
||||
While LAMMPS has many utilities to create and delete bonds, *only*
|
||||
the following are currently compatible with BPM bond styles:
|
||||
|
||||
* :doc:`create_bonds <create_bonds>`
|
||||
* :doc:`delete_bonds <delete_bonds>`
|
||||
* :doc:`fix bond/create <fix_bond_create>`
|
||||
* :doc:`fix bond/break <fix_bond_break>`
|
||||
* :doc:`fix bond/swap <fix_bond_swap>`
|
||||
|
||||
Note :doc:`create_bonds <create_bonds>` requires certain special_bonds settings.
|
||||
To subtract pair interactions, one will need to switch between different
|
||||
special_bonds settings in the input script. An example is found in
|
||||
examples/bpm/impact.
|
||||
48
doc/src/Howto_broken_bonds.rst
Normal file
48
doc/src/Howto_broken_bonds.rst
Normal file
@ -0,0 +1,48 @@
|
||||
Broken Bonds
|
||||
============
|
||||
|
||||
Typically, bond interactions persist for the duration of a simulation
|
||||
in LAMMPS. However, there are some exceptions that allow for bonds to
|
||||
break including the :doc:`quartic bond style <bond_quartic>` and the
|
||||
bond styles in the :doc:`BPM package <Howto_bpm>` which contains the
|
||||
:doc:`bpm/spring <bond_bpm_spring>` and
|
||||
:doc:`bpm/rotational <bond_bpm_rotational>` bond styles. In these cases,
|
||||
a bond can be broken if it is stretched beyond a user-defined threshold.
|
||||
LAMMPS accomplishes this by setting the bond type to zero such that the
|
||||
bond force is no longer computed.
|
||||
|
||||
Users are normally able to weight the contribution of pair forces to atoms
|
||||
that are bonded using the :doc:`special_bonds command <special_bonds>`.
|
||||
When bonds break, this is not always the case. For the quartic bond style,
|
||||
pair forces are always turned off between bonded particles. LAMMPS does
|
||||
this via a computational sleight-of-hand. It subtracts the pairwise
|
||||
interaction as part of the bond computation. When the bond breaks, the
|
||||
subtraction stops. For this to work, the pairwise interaction must always
|
||||
be computed by the :doc:`pair_style <pair_style>` command, whether the bond
|
||||
is broken or not. This means that :doc:`special_bonds <special_bonds>` must
|
||||
be set to 1,1,1. After the bond breaks, the pairwise interaction between the
|
||||
two atoms is turned on, since they are no longer bonded.
|
||||
|
||||
In the BPM package, one can either turn off all pair interactions between
|
||||
bonded particles or leave them on, overlaying pair forces on top of bond
|
||||
forces. To remove pair forces, the special bond list is dynamically
|
||||
updated. More details can be found on the :doc:`Howto BPM <Howto_bpm>`
|
||||
page.
|
||||
|
||||
Bonds can also be broken by fixes which change bond topology, including
|
||||
:doc:`fix bond/break <fix_bond_break>` and
|
||||
:doc:`fix bond/react <fix_bond_react>`. These fixes will automatically
|
||||
trigger a rebuild of the neighbor list and update special bond data structures
|
||||
when bonds are broken.
|
||||
|
||||
Note that when bonds are dumped to a file via the :doc:`dump local <dump>` command, bonds with type 0 are not included. The
|
||||
:doc:`delete_bonds <delete_bonds>` command can also be used to query the
|
||||
status of broken bonds or permanently delete them, e.g.:
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
delete_bonds all stats
|
||||
delete_bonds all bond 0 remove
|
||||
|
||||
The compute :doc:`nbond/atom <compute_nbond_atom>` can also be used
|
||||
to tally the current number of bonds per atom, excluding broken bonds.
|
||||
@ -18,23 +18,52 @@ At zero temperature, it is easy to estimate these derivatives by
|
||||
deforming the simulation box in one of the six directions using the
|
||||
:doc:`change_box <change_box>` command and measuring the change in the
|
||||
stress tensor. A general-purpose script that does this is given in the
|
||||
examples/elastic directory described on the :doc:`Examples <Examples>`
|
||||
examples/ELASTIC directory described on the :doc:`Examples <Examples>`
|
||||
doc page.
|
||||
|
||||
Calculating elastic constants at finite temperature is more
|
||||
challenging, because it is necessary to run a simulation that performs
|
||||
time averages of differential properties. One way to do this is to
|
||||
measure the change in average stress tensor in an NVT simulations when
|
||||
time averages of differential properties. There are at least
|
||||
3 ways to do this in LAMMPS. The most reliable way to do this is
|
||||
by exploiting the relationship between elastic constants, stress
|
||||
fluctuations, and the Born matrix, the second derivatives of energy
|
||||
w.r.t. strain :ref:`(Ray) <Ray>`.
|
||||
The Born matrix calculation has been enabled by
|
||||
the :doc:`compute born/matrix <compute_born_matrix>` command,
|
||||
which works for any bonded or non-bonded potential in LAMMPS.
|
||||
The most expensive part of the calculation is the sampling of
|
||||
the stress fluctuations. Several examples of this method are
|
||||
provided in the examples/ELASTIC_T/BORN_MATRIX directory
|
||||
described on the :doc:`Examples <Examples>` doc page.
|
||||
|
||||
A second way is to measure
|
||||
the change in average stress tensor in an NVT simulations when
|
||||
the cell volume undergoes a finite deformation. In order to balance
|
||||
the systematic and statistical errors in this method, the magnitude of
|
||||
the deformation must be chosen judiciously, and care must be taken to
|
||||
fully equilibrate the deformed cell before sampling the stress
|
||||
tensor. Another approach is to sample the triclinic cell fluctuations
|
||||
tensor. An example of this method is provided in the
|
||||
examples/ELASTIC_T/DEFORMATION directory
|
||||
described on the :doc:`Examples <Examples>` doc page.
|
||||
|
||||
Another approach is to sample the triclinic cell fluctuations
|
||||
that occur in an NPT simulation. This method can also be slow to
|
||||
converge and requires careful post-processing :ref:`(Shinoda) <Shinoda1>`
|
||||
converge and requires careful post-processing :ref:`(Shinoda) <Shinoda1>`.
|
||||
We do not provide an example of this method.
|
||||
|
||||
A nice review of the advantages and disadvantages of all of these methods
|
||||
is provided in the paper by Clavier et al. :ref:`(Clavier) <Clavier>`.
|
||||
|
||||
----------
|
||||
|
||||
.. _Ray:
|
||||
|
||||
**(Ray)** J. R. Ray and A. Rahman, J Chem Phys, 80, 4423 (1984).
|
||||
|
||||
.. _Shinoda1:
|
||||
|
||||
**(Shinoda)** Shinoda, Shiga, and Mikami, Phys Rev B, 69, 134103 (2004).
|
||||
|
||||
.. _Clavier:
|
||||
|
||||
**(Clavier)** G. Clavier, N. Desbiens, E. Bourasseau, V. Lachet, N. Brusselle-Dupend and B. Rousseau, Mol Sim, 43, 1413 (2017).
|
||||
|
||||
@ -9,34 +9,34 @@ A new atom style can be created if one of the existing atom styles
|
||||
does not define all the attributes you need to store and communicate
|
||||
with atoms.
|
||||
|
||||
Atom_vec_atomic.cpp is the simplest example of an atom style.
|
||||
The file ``atom_vec_atomic.cpp`` is the simplest example of an atom style.
|
||||
Examining the code for others will make these instructions more clear.
|
||||
|
||||
Note that the :doc:`atom style hybrid <atom_style>` command can be
|
||||
used to define atoms or particles which have the union of properties
|
||||
of individual styles. Also the :doc:`fix property/atom <fix_property_atom>`
|
||||
command can be used to add a single property (e.g. charge
|
||||
or a molecule ID) to a style that does not have it. It can also be
|
||||
used to add custom properties to an atom, with options to communicate
|
||||
them with ghost atoms or read them from a data file. Other LAMMPS
|
||||
commands can access these custom properties, as can new pair, fix,
|
||||
compute styles that are written to work with these properties. For
|
||||
Note that the :doc:`atom style hybrid <atom_style>` command can be used
|
||||
to define atoms or particles which have the union of properties of
|
||||
individual styles. Also the :doc:`fix property/atom
|
||||
<fix_property_atom>` command can be used to add a single property
|
||||
(e.g. charge or a molecule ID) to a style that does not have it. It can
|
||||
also be used to add custom properties to an atom, with options to
|
||||
communicate them with ghost atoms or read them from a data file. Other
|
||||
LAMMPS commands can access these custom properties, as can new pair,
|
||||
fix, compute styles that are written to work with these properties. For
|
||||
example, the :doc:`set <set>` command can be used to set the values of
|
||||
custom per-atom properties from an input script. All of these methods
|
||||
are less work than writing code for a new atom style.
|
||||
are less work than writing and testing(!) code for a new atom style.
|
||||
|
||||
If you follow these directions your new style will automatically work
|
||||
in tandem with others via the :doc:`atom_style hybrid <atom_style>`
|
||||
command.
|
||||
|
||||
The first step is to define a set of strings in the constructor of the
|
||||
new derived class. Each string will have zero or more space-separated
|
||||
variable names which are identical to those used in the atom.h header
|
||||
file for per-atom properties. Note that some represent per-atom
|
||||
The first step is to define a set of string lists in the constructor of
|
||||
the new derived class. Each list will have zero or more comma-separated
|
||||
strings that correspond to the variable names used in the ``atom.h``
|
||||
header file for per-atom properties. Note that some represent per-atom
|
||||
vectors (q, molecule) while other are per-atom arrays (x,v). For all
|
||||
but the last 2 strings you do not need to specify any of
|
||||
but the last two lists you do not need to specify any of
|
||||
(id,type,x,v,f). Those are included automatically as needed in the
|
||||
other strings.
|
||||
other lists.
|
||||
|
||||
.. list-table::
|
||||
|
||||
@ -65,16 +65,16 @@ other strings.
|
||||
* - fields_data_vel
|
||||
- list of properties (in order) in the Velocities section of a data file, as read by :doc:`read_data <read_data>`
|
||||
|
||||
In these strings you can list variable names which LAMMPS already
|
||||
defines (in some other atom style), or you can create new variable
|
||||
names. You should not re-use a LAMMPS variable for something with
|
||||
different meaning in your atom style. If the meaning is related, but
|
||||
interpreted differently by your atom style, then using the same
|
||||
variable name means a user should not use your style and the other
|
||||
style together in a :doc:`atom_style hybrid <atom_style>` command.
|
||||
Because there will only be one value of the variable and different
|
||||
parts of LAMMPS will then likely use it differently. LAMMPS has
|
||||
no way of checking for this.
|
||||
In these lists you can list variable names which LAMMPS already defines
|
||||
(in some other atom style), or you can create new variable names. You
|
||||
should not re-use a LAMMPS variable in your atom style that is used for
|
||||
something with a different meaning in another atom style. If the
|
||||
meaning is related, but interpreted differently by your atom style, then
|
||||
using the same variable name means a user must not use your style and
|
||||
the other style together in a :doc:`atom_style hybrid <atom_style>`
|
||||
command. Because there will only be one value of the variable and
|
||||
different parts of LAMMPS will then likely use it differently. LAMMPS
|
||||
has no way of checking for this.
|
||||
|
||||
If you are defining new variable names then make them descriptive and
|
||||
unique to your new atom style. For example choosing "e" for energy is
|
||||
@ -85,32 +85,31 @@ If any of the variable names in your new atom style do not exist in
|
||||
LAMMPS, you need to add them to the src/atom.h and atom.cpp files.
|
||||
|
||||
Search for the word "customize" or "customization" in these 2 files to
|
||||
see where to add your variable. Adding a flag to the 2nd
|
||||
customization section in atom.h is only necessary if your code (e.g. a
|
||||
pair style) needs to check that a per-atom property is defined. These
|
||||
flags should also be set in the constructor of the atom style child
|
||||
class.
|
||||
see where to add your variable. Adding a flag to the 2nd customization
|
||||
section in ``atom.h`` is only necessary if your code (e.g. a pair style)
|
||||
needs to check that a per-atom property is defined. These flags should
|
||||
also be set in the constructor of the atom style child class.
|
||||
|
||||
In atom.cpp, aside from the constructor and destructor, there are 3
|
||||
In ``atom.cpp``, aside from the constructor and destructor, there are 3
|
||||
methods that a new variable name or flag needs to be added to.
|
||||
|
||||
In Atom::peratom_create() when using the add_peratom() method, a
|
||||
final length argument of 0 is for per-atom vectors, a length > 1 is
|
||||
for per-atom arrays. Note the use of an extra per-thread flag and the
|
||||
add_peratom_vary() method when last dimension of the array is
|
||||
In ``Atom::peratom_create()`` when using the ``Atom::add_peratom()``
|
||||
method, a cols argument of 0 is for per-atom vectors, a length >
|
||||
1 is for per-atom arrays. Note the use of the extra per-thread flag and
|
||||
the add_peratom_vary() method when last dimension of the array is
|
||||
variable-length.
|
||||
|
||||
Adding the variable name to Atom::extract() enable the per-atom data
|
||||
Adding the variable name to Atom::extract() enables the per-atom data
|
||||
to be accessed through the :doc:`LAMMPS library interface
|
||||
<Howto_library>` by a calling code, including from :doc:`Python
|
||||
<Python_head>`.
|
||||
|
||||
The constructor of the new atom style will also typically set a few
|
||||
flags which are defined at the top of atom_vec.h. If these are
|
||||
flags which are defined at the top of ``atom_vec.h``. If these are
|
||||
unclear, see how other atom styles use them.
|
||||
|
||||
The grow_pointers() method is also required to make
|
||||
a copy of peratom data pointers, as explained in the code.
|
||||
The grow_pointers() method is also required to make a copy of peratom
|
||||
data pointers, as explained in the code.
|
||||
|
||||
There are a number of other optional methods which your atom style can
|
||||
implement. These are only needed if you need to do something
|
||||
|
||||
@ -223,6 +223,13 @@ and readable by all and no executable permissions. Executable
|
||||
permissions (0755) should only be on shell scripts or python or similar
|
||||
scripts for interpreted script languages.
|
||||
|
||||
You can check for these issues with the python scripts in the
|
||||
:ref:`"tools/coding_standard" <coding_standard>` folder. When run
|
||||
normally with a source file or a source folder as argument, they will
|
||||
list all non-conforming lines. By adding the `-f` flag to the command
|
||||
line, they will modify the flagged files to try removing the detected
|
||||
issues.
|
||||
|
||||
Indentation and Placement of Braces (strongly preferred)
|
||||
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
||||
|
||||
@ -240,6 +247,53 @@ reformatting from clang-format yields undesirable output may be
|
||||
protected with placing a pair `// clang-format off` and `// clang-format
|
||||
on` comments around that block.
|
||||
|
||||
Error or warning messages and explanations (preferred)
|
||||
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
||||
|
||||
.. versionchanged:: 27Apr2022
|
||||
|
||||
Starting with LAMMPS version 27 April 2022 the LAMMPS developers have
|
||||
agreed on a new policy for error and warning messages.
|
||||
|
||||
Previously, all error and warning strings were supposed to be listed in
|
||||
the class header files with an explanation. Those would then be
|
||||
regularly "harvested" and transferred to alphabetically sorted lists in
|
||||
the manual. To avoid excessively long lists and to reduce effort, this
|
||||
came with a requirement to have rather generic error messages (e.g.
|
||||
"Illegal ... command"). To identify the specific cause, the name of the
|
||||
source file and the line number of the error location would be printed,
|
||||
so that one could look up the cause by reading the source code.
|
||||
|
||||
The new policy encourages more specific error messages that ideally
|
||||
indicate the cause directly and no further lookup would be needed.
|
||||
This is aided by using the `{fmt} library <https://fmt.dev>`_ to convert
|
||||
the Error class commands so that they take a variable number of arguments
|
||||
and error text will be treated like a {fmt} syntax format string.
|
||||
Error messages should still kept to a single line or two lines at the most.
|
||||
|
||||
For more complex explanations or errors that have multiple possible
|
||||
reasons, a paragraph should be added to the `Error_details` page with an
|
||||
error code reference (e.g. ``.. _err0001:``) then the utility function
|
||||
:cpp:func:`utils::errorurl() <LAMMPS_NS::utils::errorurl>` can be used
|
||||
to generate an URL that will directly lead to that paragraph. An error
|
||||
for missing arguments can be easily generated using the
|
||||
:cpp:func:`utils::missing_cmd_args()
|
||||
<LAMMPS_NS::utils::missing_cmd_args>` convenience function.
|
||||
|
||||
The transformation of existing LAMMPS code to this new scheme is ongoing
|
||||
and - given the size of the LAMMPS source code - will take a significant
|
||||
amount of time until completion. However, for new code following the
|
||||
new approach is strongly preferred. The expectation is that the new
|
||||
scheme will make it easier for LAMMPS users, developers, and
|
||||
maintainers.
|
||||
|
||||
An example for this approach would be the
|
||||
``src/read_data.cpp`` and ``src/atom.cpp`` files that implement the
|
||||
:doc:`read_data <read_data>` and :doc:`atom_modify <atom_modify>`
|
||||
commands and that may create :ref:`"Unknown identifier in data file" <err0001>`
|
||||
errors that seem difficult to debug for users because they may have
|
||||
one of multiple possible reasons, and thus require some additional explanations.
|
||||
|
||||
Programming language standards (required)
|
||||
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
||||
|
||||
|
||||
@ -32,6 +32,7 @@ page gives those details.
|
||||
* :ref:`AWPMD <PKG-AWPMD>`
|
||||
* :ref:`BOCS <PKG-BOCS>`
|
||||
* :ref:`BODY <PKG-BODY>`
|
||||
* :ref:`BPM <PKG-BPM>`
|
||||
* :ref:`BROWNIAN <PKG-BROWNIAN>`
|
||||
* :ref:`CG-DNA <PKG-CG-DNA>`
|
||||
* :ref:`CG-SDK <PKG-CG-SDK>`
|
||||
@ -284,6 +285,33 @@ overview.
|
||||
|
||||
----------
|
||||
|
||||
.. _PKG-BPM:
|
||||
|
||||
BPM package
|
||||
------------
|
||||
|
||||
**Contents:**
|
||||
|
||||
Pair styles, bond styles, fixes, and computes for bonded particle
|
||||
models for mesoscale simulations of solids and fracture. See the
|
||||
:doc:`Howto bpm <Howto_bpm>` page for an overview.
|
||||
|
||||
**Authors:** Joel T. Clemmer (Sandia National Labs)
|
||||
|
||||
**Supporting info:**
|
||||
|
||||
* src/BPM filenames -> commands
|
||||
* :doc:`Howto_bpm <Howto_bpm>`
|
||||
* :doc:`atom_style bpm/sphere <atom_style>`
|
||||
* :doc:`bond_style bpm/rotational <bond_bpm_rotational>`
|
||||
* :doc:`bond_style bpm/spring <bond_bpm_spring>`
|
||||
* :doc:`compute nbond/atom <compute_nbond_atom>`
|
||||
* :doc:`fix nve/bpm/sphere <fix_nve_bpm_sphere>`
|
||||
* :doc:`pair_style bpm/spring <pair_bpm_spring>`
|
||||
* examples/bpm
|
||||
|
||||
----------
|
||||
|
||||
.. _PKG-BROWNIAN:
|
||||
|
||||
BROWNIAN package
|
||||
@ -529,8 +557,20 @@ To use this package, also the :ref:`KSPACE <PKG-KSPACE>` and
|
||||
**Supporting info:**
|
||||
|
||||
* src/DIELECTRIC: filenames -> commands
|
||||
* :doc:`atom_style dielectric <atom_style>`
|
||||
* :doc:`pair_style coul/cut/dielectric <pair_dielectric>`
|
||||
* :doc:`pair_style coul/long/dielectric <pair_dielectric>`
|
||||
* :doc:`pair_style lj/cut/coul/cut/dielectric <pair_dielectric>`
|
||||
* :doc:`pair_style lj/cut/coul/debye/dielectric <pair_dielectric>`
|
||||
* :doc:`pair_style lj/cut/coul/long/dielectric <pair_dielectric>`
|
||||
* :doc:`pair_style lj/cut/coul/msm/dielectric <pair_dielectric>`
|
||||
* :doc:`pair_style pppm/dielectric <kspace_style>`
|
||||
* :doc:`pair_style pppm/disp/dielectric <kspace_style>`
|
||||
* :doc:`pair_style msm/dielectric <kspace_style>`
|
||||
* :doc:`fix_style polarize/bem/icc <fix_polarize>`
|
||||
* :doc:`fix_style polarize/bem/gmres <fix_polarize>`
|
||||
* :doc:`fix_style polarize/functional <fix_polarize>`
|
||||
* :doc:`compute efield/atom <compute_efield_atom>`
|
||||
* TODO: add all styles
|
||||
* examples/PACKAGES/dielectric
|
||||
|
||||
----------
|
||||
@ -1571,7 +1611,6 @@ listing, "ls src/MISC", to see the list of commands.
|
||||
* :doc:`pair_style list <pair_list>`
|
||||
* :doc:`pair_style srp <pair_srp>`
|
||||
* :doc:`pair_style tracker <pair_tracker>`
|
||||
* :doc:`fix pair/tracker <fix_pair_tracker>`
|
||||
|
||||
----------
|
||||
|
||||
|
||||
@ -58,6 +58,11 @@ whether an extra library is needed to build and use the package:
|
||||
- :doc:`Howto body <Howto_body>`
|
||||
- body
|
||||
- no
|
||||
* - :ref:`BPM <PKG-BPM>`
|
||||
- bonded particle models
|
||||
- :doc:`Howto bpm <Howto_bpm>`
|
||||
- bpm
|
||||
- no
|
||||
* - :ref:`BROWNIAN <PKG-BROWNIAN>`
|
||||
- Brownian dynamics, self-propelled particles
|
||||
- :doc:`fix brownian <fix_brownian>`, :doc:`fix propel/self <fix_propel_self>`
|
||||
|
||||
@ -87,7 +87,7 @@ Miscellaneous tools
|
||||
.. table_from_list::
|
||||
:columns: 6
|
||||
|
||||
* :ref:`CMake <cmake>`
|
||||
* :ref:`LAMMPS coding standards <coding_standard>`
|
||||
* :ref:`emacs <emacs>`
|
||||
* :ref:`i-pi <ipi>`
|
||||
* :ref:`kate <kate>`
|
||||
@ -189,27 +189,32 @@ for the :doc:`chain benchmark <Speed_bench>`.
|
||||
|
||||
----------
|
||||
|
||||
.. _cmake:
|
||||
.. _coding_standard:
|
||||
|
||||
CMake tools
|
||||
-----------
|
||||
LAMMPS coding standard
|
||||
----------------------
|
||||
|
||||
The ``cmbuild`` script is a wrapper around using ``cmake --build <dir>
|
||||
--target`` and allows compiling LAMMPS in a :ref:`CMake build folder
|
||||
<cmake_build>` with a make-like syntax regardless of the actual build
|
||||
tool and the specific name of the program used (e.g. ``ninja-v1.10`` or
|
||||
``gmake``) when using ``-D CMAKE_MAKE_PROGRAM=<name>``.
|
||||
The ``coding_standard`` folder contains multiple python scripts to
|
||||
check for and apply some LAMMPS coding conventions. The following
|
||||
scripts are available:
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
Usage: cmbuild [-v] [-h] [-C <dir>] [-j <num>] [<target>]
|
||||
permissions.py # detects if sources have executable permissions and scripts have not
|
||||
whitespace.py # detects TAB characters and trailing whitespace
|
||||
homepage.py # detects outdated LAMMPS homepage URLs (pointing to sandia.gov instead of lammps.org)
|
||||
errordocs.py # detects deprecated error docs in header files
|
||||
|
||||
Options:
|
||||
-h print this message
|
||||
-j <NUM> allow processing of NUM concurrent tasks
|
||||
-C DIRECTORY execute build in folder DIRECTORY
|
||||
-v produce verbose output
|
||||
The tools need to be given the main folder of the LAMMPS distribution
|
||||
or individual file names as argument and will by default check them
|
||||
and report any non-compliance. With the optional ``-f`` argument the
|
||||
corresponding script will try to change the non-compliant file(s) to
|
||||
match the conventions.
|
||||
|
||||
For convenience this scripts can also be invoked by the make file in
|
||||
the ``src`` folder with, `make check-whitespace` or `make fix-whitespace`
|
||||
to either detect or edit the files. Correspondingly for the other python
|
||||
scripts. `make check` will run all checks.
|
||||
|
||||
----------
|
||||
|
||||
|
||||
@ -10,7 +10,7 @@ Syntax
|
||||
|
||||
atom_style style args
|
||||
|
||||
* style = *angle* or *atomic* or *body* or *bond* or *charge* or *dipole* or *dpd* or *edpd* or *electron* or *ellipsoid* or *full* or *line* or *mdpd* or *molecular* or *oxdna* or *peri* or *smd* or *sph* or *sphere* or *spin* or *tdpd* or *tri* or *template* or *hybrid*
|
||||
* style = *angle* or *atomic* or *body* or *bond* or *charge* or *dipole* or *dpd* or *edpd* or *electron* or *ellipsoid* or *full* or *line* or *mdpd* or *molecular* or *oxdna* or *peri* or *smd* or *sph* or *sphere* or *bpm/sphere* or *spin* or *tdpd* or *tri* or *template* or *hybrid*
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
@ -21,6 +21,7 @@ Syntax
|
||||
see the :doc:`Howto body <Howto_body>` doc
|
||||
page for details
|
||||
*sphere* arg = 0/1 (optional) for static/dynamic particle radii
|
||||
*bpm/sphere* arg = 0/1 (optional) for static/dynamic particle radii
|
||||
*tdpd* arg = Nspecies
|
||||
Nspecies = # of chemical species
|
||||
*template* arg = template-ID
|
||||
@ -120,6 +121,8 @@ quantities.
|
||||
+--------------+-----------------------------------------------------+--------------------------------------+
|
||||
| *sphere* | diameter, mass, angular velocity | granular models |
|
||||
+--------------+-----------------------------------------------------+--------------------------------------+
|
||||
| *bpm/sphere* | diameter, mass, angular velocity, quaternion | granular bonded particle models (BPM)|
|
||||
+--------------+-----------------------------------------------------+--------------------------------------+
|
||||
| *spin* | magnetic moment | system with magnetic particles |
|
||||
+--------------+-----------------------------------------------------+--------------------------------------+
|
||||
| *tdpd* | chemical concentration | tDPD particles |
|
||||
@ -141,8 +144,9 @@ quantities.
|
||||
output the custom values.
|
||||
|
||||
All of the above styles define point particles, except the *sphere*,
|
||||
*ellipsoid*, *electron*, *peri*, *wavepacket*, *line*, *tri*, and
|
||||
*body* styles, which define finite-size particles. See the :doc:`Howto spherical <Howto_spherical>` page for an overview of using
|
||||
*bpm/sphere*, *ellipsoid*, *electron*, *peri*, *wavepacket*, *line*,
|
||||
*tri*, and *body* styles, which define finite-size particles. See the
|
||||
:doc:`Howto spherical <Howto_spherical>` page for an overview of using
|
||||
finite-size particle models with LAMMPS.
|
||||
|
||||
All of the point-particle styles assign mass to particles on a
|
||||
@ -150,15 +154,15 @@ per-type basis, using the :doc:`mass <mass>` command, The finite-size
|
||||
particle styles assign mass to individual particles on a per-particle
|
||||
basis.
|
||||
|
||||
For the *sphere* style, the particles are spheres and each stores a
|
||||
For the *sphere* and *bpm/sphere* styles, the particles are spheres and each stores a
|
||||
per-particle diameter and mass. If the diameter > 0.0, the particle
|
||||
is a finite-size sphere. If the diameter = 0.0, it is a point
|
||||
particle. Note that by use of the *disc* keyword with the :doc:`fix
|
||||
nve/sphere <fix_nve_sphere>`, :doc:`fix nvt/sphere <fix_nvt_sphere>`,
|
||||
:doc:`fix nph/sphere <fix_nph_sphere>`, :doc:`fix npt/sphere
|
||||
<fix_npt_sphere>` commands, spheres can be effectively treated as 2d
|
||||
<fix_npt_sphere>` commands for the *sphere* style, spheres can be effectively treated as 2d
|
||||
discs for a 2d simulation if desired. See also the :doc:`set
|
||||
density/disc <set>` command. The *sphere* style takes an optional 0
|
||||
density/disc <set>` command. The *sphere* and *bpm/sphere* styles take an optional 0
|
||||
or 1 argument. A value of 0 means the radius of each sphere is
|
||||
constant for the duration of the simulation. A value of 1 means the
|
||||
radii may vary dynamically during the simulation, e.g. due to use of
|
||||
@ -195,6 +199,8 @@ position, which is represented by the eradius = electron size.
|
||||
For the *peri* style, the particles are spherical and each stores a
|
||||
per-particle mass and volume.
|
||||
|
||||
The *bpm/sphere* style is part of the BPM package.
|
||||
|
||||
The *oxdna* style is for coarse-grained nucleotides and stores the
|
||||
3'-to-5' polarity of the nucleotide strand, which is set through
|
||||
the bond topology in the data file. The first (second) atom in a
|
||||
|
||||
258
doc/src/bond_bpm_rotational.rst
Normal file
258
doc/src/bond_bpm_rotational.rst
Normal file
@ -0,0 +1,258 @@
|
||||
.. index:: bond_style bpm/rotational
|
||||
|
||||
bond_style bpm/rotational command
|
||||
=================================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
bond_style bpm/rotational keyword value attribute1 attribute2 ...
|
||||
|
||||
* optional keyword = *overlay/pair* or *store/local* or *smooth*
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
*store/local* values = fix_ID N attributes ...
|
||||
* fix_ID = ID of associated internal fix to store data
|
||||
* N = prepare data for output every this many timesteps
|
||||
* attributes = zero or more of the below attributes may be appended
|
||||
|
||||
*id1, id2* = IDs of 2 atoms in the bond
|
||||
*time* = the timestep the bond broke
|
||||
*x, y, z* = the center of mass position of the 2 atoms when the bond broke (distance units)
|
||||
*x/ref, y/ref, z/ref* = the initial center of mass position of the 2 atoms (distance units)
|
||||
|
||||
*overlay/pair* value = none
|
||||
bonded particles will still interact with pair forces
|
||||
|
||||
*smooth* value = *yes* or *no*
|
||||
smooths bond forces near the breaking point
|
||||
|
||||
Examples
|
||||
""""""""
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
bond_style bpm/rotational
|
||||
bond_coeff 1 1.0 0.2 0.02 0.02 0.20 0.04 0.04 0.04 0.1 0.02 0.002 0.002
|
||||
|
||||
bond_style bpm/rotational myfix 1000 time id1 id2
|
||||
fix myfix all store/local 1000 3
|
||||
dump 1 all local 1000 dump.broken f_myfix[1] f_myfix[2] f_myfix[3]
|
||||
dump_modify 1 write_header no
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
The *bpm/rotational* bond style computes forces and torques based on
|
||||
deviations from the initial reference state of the two atoms. The
|
||||
reference state is stored by each bond when it is first computed in
|
||||
the setup of a run. Data is then preserved across run commands and is
|
||||
written to :doc:`binary restart files <restart>` such that restarting
|
||||
the system will not reset the reference state of a bond.
|
||||
|
||||
Forces include a normal and tangential component. The base normal force
|
||||
has a magnitude of
|
||||
|
||||
.. math::
|
||||
|
||||
f_r = k_r (r - r_0)
|
||||
|
||||
where :math:`k_r` is a stiffness and :math:`r` is the current distance and
|
||||
:math:`r_0` is the initial distance between the two particles.
|
||||
|
||||
A tangential force is applied perpendicular to the normal direction
|
||||
which is proportional to the tangential shear displacement with a
|
||||
stiffness of :math:`k_s`. This tangential force also induces a torque.
|
||||
In addition, bending and twisting torques are also applied to
|
||||
particles which are proportional to angular bending and twisting
|
||||
displacements with stiffnesses of :math`k_b` and :math:`k_t',
|
||||
respectively. Details on the calculations of shear displacements and
|
||||
angular displacements can be found in :ref:`(Wang) <Wang2009>` and
|
||||
:ref:`(Wang and Mora) <Wang2009b>`.
|
||||
|
||||
Bonds will break under sufficient stress. A breaking criteria is calculated
|
||||
|
||||
.. math::
|
||||
|
||||
B = \mathrm{max}\{0, \frac{f_r}{f_{r,c}} + \frac{|f_s|}{f_{s,c}} +
|
||||
\frac{|\tau_b|}{\tau_{b,c}} + \frac{|\tau_t|}{\tau_{t,c}} \}
|
||||
|
||||
where :math:`|f_s|` is the magnitude of the shear force and
|
||||
:math:`|\tau_b|` and :math:`|\tau_t|` are the magnitudes of the
|
||||
bending and twisting forces, respectively. The corresponding variables
|
||||
:math:`f_{r,c}` :math:`f_{s,c}`, :math:`\tau_{b,c}`, and
|
||||
:math:`\tau_{t,c}` are critical limits to each force or torque. If
|
||||
:math:`B` is ever equal to or exceeds one, the bond will break. This
|
||||
is done by setting by setting its type to 0 such that forces and
|
||||
torques are no longer computed.
|
||||
|
||||
After computing the base magnitudes of the forces and torques, they
|
||||
can be optionally multiplied by an extra factor :math:`w` to smoothly
|
||||
interpolate forces and torques to zero as the bond breaks. This term
|
||||
is calculated as :math:`w = (1.0 - B^4)`. This smoothing factor can be
|
||||
added or removed using the *smooth* keyword.
|
||||
|
||||
Finally, additional damping forces and torques are applied to the two
|
||||
particles. A force is applied proportional to the difference in the
|
||||
normal velocity of particles using a similar construction as
|
||||
dissipative particle dynamics (:ref:`(Groot) <Groot3>`):
|
||||
|
||||
.. math::
|
||||
|
||||
F_D = - \gamma_n w (\hat{r} \bullet \vec{v})
|
||||
|
||||
where :math:`\gamma_n` is the damping strength, :math:`\hat{r}` is the
|
||||
radial normal vector, and :math:`\vec{v}` is the velocity difference
|
||||
between the two particles. Similarly, tangential forces are applied to
|
||||
each atom proportional to the relative differences in sliding
|
||||
velocities with a constant prefactor :math:`\gamma_s` (:ref:`(Wang et
|
||||
al.) <Wang20152>`) along with their associated torques. The rolling and
|
||||
twisting components of the relative angular velocities of the two
|
||||
atoms are also damped by applying torques with prefactors of
|
||||
:math:`\gamma_r` and :math:`\gamma_t`, respectively.
|
||||
|
||||
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_r` (force/distance units)
|
||||
* :math:`k_s` (force/distance units)
|
||||
* :math:`k_t` (force*distance/radians units)
|
||||
* :math:`k_b` (force*distance/radians units)
|
||||
* :math:`f_{r,c}` (force units)
|
||||
* :math:`f_{s,c}` (force units)
|
||||
* :math:`\tau_{b,c}` (force*distance units)
|
||||
* :math:`\tau_{t,c}` (force*distance units)
|
||||
* :math:`\gamma_n` (force/velocity units)
|
||||
* :math:`\gamma_s` (force/velocity units)
|
||||
* :math:`\gamma_r` (force*distance/velocity units)
|
||||
* :math:`\gamma_t` (force*distance/velocity units)
|
||||
|
||||
By default, pair forces are not calculated between bonded particles.
|
||||
Pair forces can alternatively be overlaid on top of bond forces using
|
||||
the *overlay/pair* keyword. These settings require specific
|
||||
:doc:`special_bonds <special_bonds>` settings described in the
|
||||
restrictions. Further details can be found in the `:doc: how to
|
||||
<Howto_BPM>` page on BPMs.
|
||||
|
||||
If the *store/local* keyword is used, this 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
|
||||
local data to be accessed by other LAMMPS commands.
|
||||
Following any optional keyword/value arguments, a list of one or more
|
||||
attributes is specified. These include the IDs of the two atoms in
|
||||
the bond. The other attributes for the two atoms include the timestep
|
||||
during which the bond broke and the current/initial center of mass
|
||||
position of the two atoms.
|
||||
|
||||
Data is continuously accumulated over intervals of *N*
|
||||
timesteps. At the end of each interval, all of the saved accumulated
|
||||
data is deleted to make room for new data. Individual datum may
|
||||
therefore persist anywhere between *1* to *N* timesteps depending on
|
||||
when they are saved. This data can be accessed using the *fix_ID* and a
|
||||
:doc:`dump local <dump>` command. To ensure all data is output,
|
||||
the dump frequency should correspond to the same interval of *N*
|
||||
timesteps. A dump frequency of an integer multiple of *N* can be used
|
||||
to regularly output a sample of the accumulated data.
|
||||
|
||||
Note that when unbroken bonds are dumped to a file via the
|
||||
:doc:`dump local <dump>` command, bonds with type 0 (broken bonds)
|
||||
are not included.
|
||||
The :doc:`delete_bonds <delete_bonds>` command can also be used to
|
||||
query the status of broken bonds or permanently delete them, e.g.:
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
delete_bonds all stats
|
||||
delete_bonds all bond 0 remove
|
||||
|
||||
|
||||
----------
|
||||
|
||||
Restart and other info
|
||||
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
|
||||
|
||||
This bond style writes the reference state of each bond to
|
||||
:doc:`binary restart files <restart>`. Loading a restart file will
|
||||
properly resume bonds.
|
||||
|
||||
The single() function of these pair styles returns 0.0 for the energy
|
||||
of a pairwise interaction, since energy is not conserved in these
|
||||
dissipative potentials. It also returns only the normal component of
|
||||
the pairwise interaction force.
|
||||
|
||||
The accumulated data is not written to restart files and should be
|
||||
output before a restart file is written to avoid missing data.
|
||||
|
||||
The internal fix calculates a local vector or local array depending on the
|
||||
number of input values. The length of the vector or number of rows in
|
||||
the array is the number of recorded, lost interactions. If a single
|
||||
input is specified, a local vector is produced. If two or more inputs
|
||||
are specified, a local array is produced where the number of columns =
|
||||
the number of inputs. The vector or array can be accessed by any
|
||||
command that uses local values from a compute as input. See the
|
||||
:doc:`Howto output <Howto_output>` page for an overview of LAMMPS
|
||||
output options.
|
||||
|
||||
The vector or array will be floating point values that correspond to
|
||||
the specified attribute.
|
||||
|
||||
Restrictions
|
||||
""""""""""""
|
||||
|
||||
This bond style can only be used if LAMMPS was built with the BPM
|
||||
package. See the :doc:`Build package <Build_package>` doc page for
|
||||
more info.
|
||||
|
||||
By default if pair interactions are to be disabled, this bond style
|
||||
requires setting
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
special_bonds lj 0 1 1 coul 1 1 1
|
||||
|
||||
and :doc:`newton <newton>` must be set to bond off. If the
|
||||
*overlay/pair* option is used, this bond style alternatively requires
|
||||
setting
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
special_bonds lj/coul 1 1 1
|
||||
|
||||
The *bpm/rotational* style requires :doc:`atom style bpm/sphere <atom_style>`.
|
||||
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
:doc:`bond_coeff <bond_coeff>`, :doc:`fix nve/bpm/sphere <fix_nve_bpm_sphere>`
|
||||
|
||||
Default
|
||||
"""""""
|
||||
|
||||
The option defaults are *smooth* = *yes*
|
||||
|
||||
----------
|
||||
|
||||
.. _Wang2009:
|
||||
|
||||
**(Wang)** Wang, Acta Geotechnica, 4,
|
||||
p 117-127 (2009).
|
||||
|
||||
.. _Wang2009b:
|
||||
|
||||
**(Wang and Mora)** Wang, Mora, Advances in Geocomputing,
|
||||
119, p 183-228 (2009).
|
||||
|
||||
.. _Groot3:
|
||||
|
||||
**(Groot)** Groot and Warren, J Chem Phys, 107, 4423-35 (1997).
|
||||
|
||||
.. _Wang20152:
|
||||
|
||||
**(Wang et al, 2015)** Wang, Y., Alonso-Marroquin, F., & Guo,
|
||||
W. W. (2015). Rolling and sliding in 3-D discrete element
|
||||
models. Particuology, 23, 49-55.
|
||||
202
doc/src/bond_bpm_spring.rst
Normal file
202
doc/src/bond_bpm_spring.rst
Normal file
@ -0,0 +1,202 @@
|
||||
.. index:: bond_style bpm/spring
|
||||
|
||||
bond_style bpm/spring command
|
||||
=============================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
bond_style bpm/spring keyword value attribute1 attribute2 ...
|
||||
|
||||
* optional keyword = *overlay/pair* or *store/local* or *smooth*
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
*store/local* values = fix_ID N attributes ...
|
||||
* fix_ID = ID of associated internal fix to store data
|
||||
* N = prepare data for output every this many timesteps
|
||||
* attributes = zero or more of the below attributes may be appended
|
||||
|
||||
*id1, id2* = IDs of 2 atoms in the bond
|
||||
*time* = the timestep the bond broke
|
||||
*x, y, z* = the center of mass position of the 2 atoms when the bond broke (distance units)
|
||||
*x/ref, y/ref, z/ref* = the initial center of mass position of the 2 atoms (distance units)
|
||||
|
||||
*overlay/pair* value = none
|
||||
bonded particles will still interact with pair forces
|
||||
|
||||
*smooth* value = *yes* or *no*
|
||||
smooths bond forces near the breaking point
|
||||
|
||||
Examples
|
||||
""""""""
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
bond_style bpm/spring
|
||||
bond_coeff 1 1.0 0.05 0.1
|
||||
|
||||
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
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
The *bpm/spring* bond style computes forces and torques based on
|
||||
deviations from the initial reference state of the two atoms. The
|
||||
reference state is stored by each bond when it is first computed in
|
||||
the setup of a run. Data is then preserved across run commands and is
|
||||
written to :doc:`binary restart files <restart>` such that restarting
|
||||
the system will not reset the reference state of a bond.
|
||||
|
||||
This bond style only applies central-body forces which conserve the
|
||||
translational and rotational degrees of freedom of a bonded set of
|
||||
particles. The force has a magnitude of
|
||||
|
||||
.. math::
|
||||
|
||||
F = k (r - r_0) w
|
||||
|
||||
where :math:`k_r` is a stiffness, :math:`r` is the current distance
|
||||
and :math:`r_0` is the initial distance between the two particles, and
|
||||
:math:`w` is an optional smoothing factor discussed below. Bonds will
|
||||
break at a strain of :math:`\epsilon_c`. This is done by setting by
|
||||
setting its type to 0 such that forces are no longer computed.
|
||||
|
||||
An additional damping force is applied to the bonded
|
||||
particles. This forces is proportional to the difference in the
|
||||
normal velocity of particles using a similar construction as
|
||||
dissipative particle dynamics (:ref:`(Groot) <Groot4>`):
|
||||
|
||||
.. math::
|
||||
|
||||
F_D = - \gamma w (\hat{r} \bullet \vec{v})
|
||||
|
||||
where :math:`\gamma` is the damping strength, :math:`\hat{r}` is the
|
||||
radial normal vector, and :math:`\vec{v}` is the velocity difference
|
||||
between the two particles.
|
||||
|
||||
The smoothing factor :math:`w` can be added or removed using the
|
||||
*smooth* keyword. It is constructed such that forces smoothly go
|
||||
to zero, avoiding discontinuities, as bonds approach the critical strain
|
||||
|
||||
.. math::
|
||||
|
||||
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)
|
||||
|
||||
By default, pair forces are not calculated between bonded particles.
|
||||
Pair forces can alternatively be overlaid on top of bond forces using
|
||||
the *overlay/pair* keyword. These settings require specific
|
||||
:doc:`special_bonds <special_bonds>` settings described in the
|
||||
restrictions. Further details can be found in the `:doc: how to
|
||||
<Howto_BPM>` page on BPMs.
|
||||
|
||||
If the *store/local* keyword is used, this 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
|
||||
local data to be accessed by other LAMMPS commands.
|
||||
Following any optional keyword/value arguments, a list of one or more
|
||||
attributes is specified. These include the IDs of the two atoms in
|
||||
the bond. The other attributes for the two atoms include the timestep
|
||||
during which the bond broke and the current/initial center of mass
|
||||
position of the two atoms.
|
||||
|
||||
Data is continuously accumulated over intervals of *N*
|
||||
timesteps. At the end of each interval, all of the saved accumulated
|
||||
data is deleted to make room for new data. Individual datum may
|
||||
therefore persist anywhere between *1* to *N* timesteps depending on
|
||||
when they are saved. This data can be accessed using the *fix_ID* and a
|
||||
:doc:`dump local <dump>` command. To ensure all data is output,
|
||||
the dump frequency should correspond to the same interval of *N*
|
||||
timesteps. A dump frequency of an integer multiple of *N* can be used
|
||||
to regularly output a sample of the accumulated data.
|
||||
|
||||
Note that when unbroken bonds are dumped to a file via the
|
||||
:doc:`dump local <dump>` command, bonds with type 0 (broken bonds)
|
||||
are not included.
|
||||
The :doc:`delete_bonds <delete_bonds>` command can also be used to
|
||||
query the status of broken bonds or permanently delete them, e.g.:
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
delete_bonds all stats
|
||||
delete_bonds all bond 0 remove
|
||||
|
||||
----------
|
||||
|
||||
Restart and other info
|
||||
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
|
||||
|
||||
This bond style writes the reference state of each bond to
|
||||
:doc:`binary restart files <restart>`. Loading a restart
|
||||
file will properly resume bonds.
|
||||
|
||||
The single() function of these pair styles returns 0.0 for the energy
|
||||
of a pairwise interaction, since energy is not conserved in these
|
||||
dissipative potentials.
|
||||
|
||||
The accumulated data is not written to restart files and should be
|
||||
output before a restart file is written to avoid missing data.
|
||||
|
||||
The internal fix calculates a local vector or local array depending on the
|
||||
number of input values. The length of the vector or number of rows in
|
||||
the array is the number of recorded, lost interactions. If a single
|
||||
input is specified, a local vector is produced. If two or more inputs
|
||||
are specified, a local array is produced where the number of columns =
|
||||
the number of inputs. The vector or array can be accessed by any
|
||||
command that uses local values from a compute as input. See the
|
||||
:doc:`Howto output <Howto_output>` page for an overview of LAMMPS
|
||||
output options.
|
||||
|
||||
The vector or array will be floating point values that correspond to
|
||||
the specified attribute.
|
||||
|
||||
Restrictions
|
||||
""""""""""""
|
||||
|
||||
This bond style can only be used if LAMMPS was built with the BPM
|
||||
package. See the :doc:`Build package <Build_package>` doc page for
|
||||
more info.
|
||||
|
||||
By default if pair interactions are to be disabled, this bond style
|
||||
requires setting
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
special_bonds lj 0 1 1 coul 1 1 1
|
||||
|
||||
and :doc:`newton <newton>` must be set to bond off. If the
|
||||
*overlay/pair* option is used, this bond style alternatively requires
|
||||
setting
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
special_bonds lj/coul 1 1 1
|
||||
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
:doc:`bond_coeff <bond_coeff>`, :doc:`pair bpm/spring <pair_bpm_spring>`
|
||||
|
||||
Default
|
||||
"""""""
|
||||
|
||||
The option defaults are *smooth* = *yes*
|
||||
|
||||
----------
|
||||
|
||||
.. _Groot4:
|
||||
|
||||
**(Groot)** Groot and Warren, J Chem Phys, 107, 4423-35 (1997).
|
||||
@ -67,7 +67,8 @@ local maximum. If a bond length ever becomes :math:`> R_c`, LAMMPS "breaks"
|
||||
the bond, which means two things. First, the bond potential is turned
|
||||
off by setting its type to 0, and is no longer computed. Second, a
|
||||
pairwise interaction between the two atoms is turned on, since they
|
||||
are no longer bonded.
|
||||
are no longer bonded. See the :doc:`Howto <Howto_broken_bonds>` page
|
||||
on broken bonds for more information.
|
||||
|
||||
LAMMPS does the second task via a computational sleight-of-hand. It
|
||||
subtracts the pairwise interaction as part of the bond computation.
|
||||
|
||||
@ -84,6 +84,8 @@ accelerated styles exist.
|
||||
* :doc:`zero <bond_zero>` - topology but no interactions
|
||||
* :doc:`hybrid <bond_hybrid>` - define multiple styles of bond interactions
|
||||
|
||||
* :doc:`bpm/rotational <bond_bpm_rotational>` - breakable bond with forces and torques based on deviation from reference state
|
||||
* :doc:`bpm/spring <bond_bpm_spring>` - breakable bond with forces based on deviation from reference length
|
||||
* :doc:`class2 <bond_class2>` - COMPASS (class 2) bond
|
||||
* :doc:`fene <bond_fene>` - FENE (finite-extensible non-linear elastic) bond
|
||||
* :doc:`fene/expand <bond_fene_expand>` - FENE bonds with variable size particles
|
||||
|
||||
@ -179,6 +179,7 @@ The individual style names on the :doc:`Commands compute <Commands_compute>` pag
|
||||
* :doc:`body/local <compute_body_local>` - attributes of body sub-particles
|
||||
* :doc:`bond <compute_bond>` - energy of each bond sub-style
|
||||
* :doc:`bond/local <compute_bond_local>` - distance and energy of each bond
|
||||
* :doc:`born/matrix <compute_born_matrix>` - second derivative or potential with respect to strain
|
||||
* :doc:`centro/atom <compute_centro_atom>` - centro-symmetry parameter for each atom
|
||||
* :doc:`centroid/stress/atom <compute_stress_atom>` - centroid based stress tensor for each atom
|
||||
* :doc:`chunk/atom <compute_chunk_atom>` - assign chunk IDs to each atom
|
||||
@ -236,6 +237,7 @@ The individual style names on the :doc:`Commands compute <Commands_compute>` pag
|
||||
* :doc:`msd <compute_msd>` - mean-squared displacement of group of atoms
|
||||
* :doc:`msd/chunk <compute_msd_chunk>` - mean-squared displacement for each chunk
|
||||
* :doc:`msd/nongauss <compute_msd_nongauss>` - MSD and non-Gaussian parameter of group of atoms
|
||||
* :doc:`nbond/atom <compute_nbond_atom>` - calculates number of bonds per atom
|
||||
* :doc:`omega/chunk <compute_omega_chunk>` - angular velocity for each chunk
|
||||
* :doc:`orientorder/atom <compute_orientorder_atom>` - Steinhardt bond orientational order parameters Ql
|
||||
* :doc:`pair <compute_pair>` - values computed by a pair style
|
||||
|
||||
213
doc/src/compute_born_matrix.rst
Normal file
213
doc/src/compute_born_matrix.rst
Normal file
@ -0,0 +1,213 @@
|
||||
.. index:: compute born/matrix
|
||||
|
||||
compute born/matrix command
|
||||
===========================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
compute ID group-ID born/matrix keyword value ...
|
||||
|
||||
* ID, group-ID are documented in :doc:`compute <compute>` command
|
||||
* born/matrix = style name of this compute command
|
||||
* zero or more keyword/value pairs may be appended
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
keyword = *numdiff*
|
||||
*numdiff* values = delta virial-ID
|
||||
delta = magnitude of strain (dimensionless)
|
||||
virial-ID = ID of pressure compute for virial (string)
|
||||
|
||||
Examples
|
||||
""""""""
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
compute 1 all born/matrix
|
||||
compute 1 all born/matrix bond angle
|
||||
compute 1 all born/matrix numdiff 1.0e-4 myvirial
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
Define a compute that calculates
|
||||
:math:`\frac{\partial{}^2U}{\partial\varepsilon_{i}\partial\varepsilon_{j}}` the
|
||||
second derivatives of the potential energy :math:`U` w.r.t. strain
|
||||
tensor :math:`\varepsilon` elements. These values are related to:
|
||||
|
||||
.. math::
|
||||
|
||||
C^{B}_{i,j}=\frac{1}{V}\frac{\partial{}^2U}{\partial{}\varepsilon_{i}\partial\varepsilon_{j}}
|
||||
|
||||
also called the Born term of elastic constants in the stress-stress fluctuation
|
||||
formalism. This quantity can be used to compute the elastic constant tensor.
|
||||
Using the symmetric Voigt notation, the elastic constant tensor can be written
|
||||
as a 6x6 symmetric matrix:
|
||||
|
||||
.. math::
|
||||
|
||||
C_{i,j} = \langle{}C^{B}_{i,j}\rangle
|
||||
+ \frac{V}{k_{B}T}\left(\langle\sigma_{i}\sigma_{j}\rangle\right.
|
||||
\left.- \langle\sigma_{i}\rangle\langle\sigma_{j}\rangle\right)
|
||||
+ \frac{Nk_{B}T}{V}
|
||||
\left(\delta_{i,j}+(\delta_{1,i}+\delta_{2,i}+\delta_{3,i})\right.
|
||||
\left.*(\delta_{1,j}+\delta_{2,j}+\delta_{3,j})\right)
|
||||
|
||||
In the above expression, :math:`\sigma` stands for the virial stress
|
||||
tensor, :math:`\delta` is the Kronecker delta and the usual notation apply for
|
||||
the number of particle, the temperature and volume respectively :math:`N`,
|
||||
:math:`T` and :math:`V`. :math:`k_{B}` is the Boltzmann constant.
|
||||
|
||||
The Born term is a symmetric 6x6 matrix, as is the matrix of second derivatives
|
||||
of potential energy w.r.t strain,
|
||||
whose 21 independent elements are output in this order:
|
||||
|
||||
.. math::
|
||||
|
||||
\begin{matrix}
|
||||
C_{1} & C_{7} & C_{8} & C_{9} & C_{10} & C_{11} \\
|
||||
C_{7} & C_{2} & C_{12} & C_{13} & C_{14} & C_{15} \\
|
||||
\vdots & C_{12} & C_{3} & C_{16} & C_{17} & C_{18} \\
|
||||
\vdots & C_{13} & C_{16} & C_{4} & C_{19} & C_{20} \\
|
||||
\vdots & \vdots & \vdots & C_{19} & C_{5} & C_{21} \\
|
||||
\vdots & \vdots & \vdots & \vdots & C_{21} & C_{6}
|
||||
\end{matrix}
|
||||
|
||||
in this matrix the indices of :math:`C_{k}` value are the corresponding element
|
||||
:math:`k` in the global vector output by this compute. Each term comes from the sum
|
||||
of the derivatives of every contribution to the potential energy
|
||||
in the system as explained in :ref:`(VanWorkum)
|
||||
<VanWorkum>`.
|
||||
|
||||
The output can be accessed using usual Lammps routines:
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
compute 1 all born/matrix
|
||||
compute 2 all pressure NULL virial
|
||||
variable S1 equal -c_2[1]
|
||||
variable S2 equal -c_2[2]
|
||||
variable S3 equal -c_2[3]
|
||||
variable S4 equal -c_2[4]
|
||||
variable S5 equal -c_2[5]
|
||||
variable S6 equal -c_2[6]
|
||||
fix 1 all ave/time 1 1 1 v_S1 v_S2 v_S3 v_S4 v_S5 v_S6 c_1[*] file born.out
|
||||
|
||||
In this example, the file *born.out* will contain the information needed to
|
||||
compute the first and second terms of the elastic constant matrix in a post
|
||||
processing procedure. The other required quantities can be accessed using any
|
||||
other *LAMMPS* usual method. Several examples of this method are
|
||||
provided in the examples/ELASTIC_T/BORN_MATRIX directory
|
||||
described on the :doc:`Examples <Examples>` doc page.
|
||||
|
||||
NOTE: In the above :math:`C_{i,j}` computation, the fluctuation
|
||||
term involving the virial stress tensor :math:`\sigma` is the
|
||||
covariance between each elements. In a
|
||||
solid the stress fluctuations can vary rapidly, while average
|
||||
fluctuations can be slow to converge.
|
||||
A detailed analysis of the convergence rate of all the terms in
|
||||
the elastic tensor
|
||||
is provided in the paper by Clavier et al. :ref:`(Clavier) <Clavier2>`.
|
||||
|
||||
Two different computation methods for the Born matrix are implemented in this
|
||||
compute and are mutually exclusive.
|
||||
|
||||
The first one is a direct computation from the analytical formula from the
|
||||
different terms of the potential used for the simulations :ref:`(VanWorkum)
|
||||
<VanWorkum>`. However, the implementation of such derivations must be done
|
||||
for every potential form. This has not been done yet and can be very
|
||||
complicated for complex potentials. At the moment a warning message is
|
||||
displayed for every term that is not supporting the compute at the moment.
|
||||
This method is the default for now.
|
||||
|
||||
The second method uses finite differences of energy to numerically approximate
|
||||
the second derivatives :ref:`(Zhen) <Zhen>`. This is useful when using
|
||||
interaction styles for which the analytical second derivatives have not been
|
||||
implemented. In this cases, the compute applies linear strain fields of
|
||||
magnitude *delta* to all the atoms relative to a point at the center of the
|
||||
box. The strain fields are in six different directions, corresponding to the
|
||||
six Cartesian components of the stress tensor defined by LAMMPS. For each
|
||||
direction it applies the strain field in both the positive and negative senses,
|
||||
and the new stress virial tensor of the entire system is calculated after each.
|
||||
The difference in these two virials divided by two times *delta*, approximates
|
||||
the corresponding components of the second derivative, after applying a
|
||||
suitable unit conversion.
|
||||
|
||||
.. note::
|
||||
|
||||
It is important to choose a suitable value for delta, the magnitude of
|
||||
strains that are used to generate finite difference
|
||||
approximations to the exact virial stress. For typical systems, a value in
|
||||
the range of 1 part in 1e5 to 1e6 will be sufficient.
|
||||
However, the best value will depend on a multitude of factors
|
||||
including the stiffness of the interatomic potential, the thermodynamic
|
||||
state of the material being probed, and so on. The only way to be sure
|
||||
that you have made a good choice is to do a sensitivity study on a
|
||||
representative atomic configuration, sweeping over a wide range of
|
||||
values of delta. If delta is too small, the output values will vary
|
||||
erratically due to truncation effects. If delta is increased beyond a
|
||||
certain point, the output values will start to vary smoothly with
|
||||
delta, due to growing contributions from higher order derivatives. In
|
||||
between these two limits, the numerical virial values should be largely
|
||||
independent of delta.
|
||||
|
||||
The keyword requires the additional arguments *delta* and *virial-ID*.
|
||||
*delta* gives the size of the applied strains. *virial-ID* gives
|
||||
the ID string of the pressure compute that provides the virial stress tensor,
|
||||
requiring that it use the virial keyword e.g.
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
compute myvirial all pressure NULL virial
|
||||
compute 1 all born/matrix numdiff 1.0e-4 myvirial
|
||||
|
||||
**Output info:**
|
||||
|
||||
This compute calculates a global vector with 21 values that are
|
||||
the second derivatives of the potential energy w.r.t. strain.
|
||||
The values are in energy units.
|
||||
The values are ordered as explained above. These values can be used
|
||||
by any command that uses global values from a compute as input. See
|
||||
the :doc:`Howto output <Howto_output>` doc page for an overview of
|
||||
LAMMPS output options.
|
||||
|
||||
The array values calculated by this compute are all "extensive".
|
||||
|
||||
Restrictions
|
||||
""""""""""""
|
||||
|
||||
This compute is part of the EXTRA-COMPUTE package. It is only enabled if
|
||||
LAMMPS was built with that package. See the :doc:`Build package
|
||||
<Build_package>` page for more info. LAMMPS was built with that package. See
|
||||
the :doc:`Build package <Build_package>` page for more info.
|
||||
|
||||
The Born term can be decomposed as a product of two terms. The first one is a
|
||||
general term which depends on the configuration. The second one is specific to
|
||||
every interaction composing your force field (non-bonded, bonds, angle...).
|
||||
Currently not all LAMMPS interaction styles implement the *born_matrix* method
|
||||
giving first and second order derivatives and LAMMPS will exit with an error if
|
||||
this compute is used with such interactions unless the *numdiff* option is
|
||||
also used. The *numdiff* option cannot be used with any other keyword. In this
|
||||
situation, LAMMPS will also exit with an error.
|
||||
|
||||
Default
|
||||
"""""""
|
||||
|
||||
none
|
||||
|
||||
----------
|
||||
|
||||
.. _VanWorkum:
|
||||
|
||||
**(Van Workum)** K. Van Workum et al., J. Chem. Phys. 125 144506 (2006)
|
||||
|
||||
.. _Clavier2:
|
||||
|
||||
**(Clavier)** G. Clavier, N. Desbiens, E. Bourasseau, V. Lachet, N. Brusselle-Dupend and B. Rousseau, Mol Sim, 43, 1413 (2017).
|
||||
|
||||
.. _Zhen:
|
||||
|
||||
**(Zhen)** Y. Zhen, C. Chu, Computer Physics Communications 183(2012)261-265
|
||||
52
doc/src/compute_nbond_atom.rst
Normal file
52
doc/src/compute_nbond_atom.rst
Normal file
@ -0,0 +1,52 @@
|
||||
.. index:: compute nbond/atom
|
||||
|
||||
compute nbond/atom command
|
||||
==========================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
compute ID group-ID nbond/atom
|
||||
|
||||
* ID, group-ID are documented in :doc:`compute <compute>` command
|
||||
* nbond/atom = style name of this compute command
|
||||
|
||||
Examples
|
||||
""""""""
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
compute 1 all nbond/atom
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
Define a computation that computes the number of bonds each atom is
|
||||
part of. Bonds which are broken are not counted in the tally. See
|
||||
the :doc:`Howto broken bonds <Howto_bpm>` page for more information.
|
||||
The number of bonds will be zero for atoms not in the specified
|
||||
compute group. This compute does not depend on Newton bond settings.
|
||||
|
||||
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
|
||||
LAMMPS output options.
|
||||
|
||||
Restrictions
|
||||
""""""""""""
|
||||
|
||||
This fix can only be used if LAMMPS was built with the BPM package.
|
||||
See the :doc:`Build package <Build_package>` doc page for more info.
|
||||
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
Default
|
||||
"""""""
|
||||
|
||||
none
|
||||
@ -127,19 +127,16 @@ The *vx*, *vy*, *vz*, *fx*, *fy*, *fz* attributes are components of
|
||||
the COM velocity and force on the COM of the body.
|
||||
|
||||
The *omegax*, *omegay*, and *omegaz* attributes are the angular
|
||||
velocity components of the body around its COM.
|
||||
velocity components of the body in the system frame around its COM.
|
||||
|
||||
The *angmomx*, *angmomy*, and *angmomz* attributes are the angular
|
||||
momentum components of the body around its COM.
|
||||
momentum components of the body in the system frame around its COM.
|
||||
|
||||
The *quatw*, *quati*, *quatj*, and *quatk* attributes are the
|
||||
components of the 4-vector quaternion representing the orientation of
|
||||
the rigid body. See the :doc:`set <set>` command for an explanation of
|
||||
the quaternion vector.
|
||||
|
||||
The *angmomx*, *angmomy*, and *angmomz* attributes are the angular
|
||||
momentum components of the body around its COM.
|
||||
|
||||
The *tqx*, *tqy*, *tqz* attributes are components of the torque acting
|
||||
on the body around its COM.
|
||||
|
||||
|
||||
@ -76,21 +76,28 @@ velocity for each atom. Note that if there is only one atom in the
|
||||
bin, its thermal velocity will thus be 0.0.
|
||||
|
||||
After the spatially-averaged velocity field has been subtracted from
|
||||
each atom, the temperature is calculated by the formula KE = (dim\*N
|
||||
- dim\*Nx\*Ny\*Nz) k T/2, where KE = total kinetic energy of the group of
|
||||
atoms (sum of 1/2 m v\^2), dim = 2 or 3 = dimensionality of the
|
||||
simulation, N = number of atoms in the group, k = Boltzmann constant,
|
||||
and T = temperature. The dim\*Nx\*Ny\*Nz term are degrees of freedom
|
||||
subtracted to adjust for the removal of the center-of-mass velocity in
|
||||
each of Nx\*Ny\*Nz bins, as discussed in the :ref:`(Evans) <Evans1>` paper.
|
||||
each atom, the temperature is calculated by the formula
|
||||
*KE* = (*dim\*N* - *Ns\*Nx\*Ny\*Nz* - *extra* ) *k* *T*/2, where *KE* = total
|
||||
kinetic energy of the group of atoms (sum of 1/2 *m* *v*\^2), *dim* = 2
|
||||
or 3 = dimensionality of the simulation, *Ns* = 0, 1, 2 or 3 for
|
||||
streaming velocity subtracted in 0, 1, 2 or 3 dimensions, *extra* = extra
|
||||
degrees-of-freedom, *N* = number of atoms in the group, *k* = Boltzmann
|
||||
constant, and *T* = temperature. The *Ns\*Nx\*Ny\*Nz* term is degrees
|
||||
of freedom subtracted to adjust for the removal of the center-of-mass
|
||||
velocity in each direction of the *Nx\*Ny\*Nz* bins, as discussed in the
|
||||
:ref:`(Evans) <Evans1>` paper. The extra term defaults to (*dim* - *Ns*)
|
||||
and accounts for overall conservation of center-of-mass velocity across
|
||||
the group in directions where streaming velocity is *not* subtracted. This
|
||||
can be altered using the *extra* option of the
|
||||
:doc:`compute_modify <compute_modify>` command.
|
||||
|
||||
If the *out* keyword is used with a *tensor* value, which is the
|
||||
default, a kinetic energy tensor, stored as a 6-element vector, is
|
||||
also calculated by this compute for use in the computation of a
|
||||
pressure tensor. The formula for the components of the tensor is the
|
||||
same as the above formula, except that v\^2 is replaced by vx\*vy for
|
||||
the xy component, etc. The 6 components of the vector are ordered xx,
|
||||
yy, zz, xy, xz, yz.
|
||||
same as the above formula, except that *v*\^2 is replaced by *vx\*vy* for
|
||||
the xy component, etc. The 6 components of the vector are ordered *xx,
|
||||
yy, zz, xy, xz, yz.*
|
||||
|
||||
If the *out* keyword is used with a *bin* value, the count of atoms
|
||||
and computed temperature for each bin are stored for output, as an
|
||||
@ -123,10 +130,20 @@ needed, the subtracted degrees-of-freedom can be altered using the
|
||||
.. note::
|
||||
|
||||
When using the *out* keyword with a value of *bin*, the
|
||||
calculated temperature for each bin does not include the
|
||||
degrees-of-freedom adjustment described in the preceding paragraph,
|
||||
for fixes that constrain molecular motion. It does include the
|
||||
adjustment due to the *extra* option, which is applied to each bin.
|
||||
calculated temperature for each bin includes the degrees-of-freedom
|
||||
adjustment described in the preceding paragraph for fixes that
|
||||
constrain molecular motion, as well as the adjustment due to
|
||||
the *extra* option (which defaults to *dim* - *Ns* as described above),
|
||||
by fractionally applying them based on the fraction of atoms in each
|
||||
bin. As a result, the bin degrees-of-freedom summed over all bins exactly
|
||||
equals the degrees-of-freedom used in the scalar temperature calculation,
|
||||
:math:`\Sigma N_{DOF_i} = N_{DOF}` and the corresponding relation for temperature
|
||||
is also satisfied :math:`\Sigma N_{DOF_i} T_i = N_{DOF} T`.
|
||||
These relations will breakdown in cases where the adjustment
|
||||
exceeds the actual number of degrees-of-freedom in a bin. This could happen
|
||||
if a bin is empty or in situations where rigid molecules
|
||||
are non-uniformly distributed, in which case the reported
|
||||
temperature within a bin may not be accurate.
|
||||
|
||||
See the :doc:`Howto thermostat <Howto_thermostat>` page for a
|
||||
discussion of different ways to compute temperature and perform
|
||||
|
||||
@ -474,8 +474,9 @@ The *fileper* keyword is documented below with the *nfile* keyword.
|
||||
|
||||
The *header* keyword toggles whether the dump file will include a
|
||||
header. Excluding a header will reduce the size of the dump file for
|
||||
fixes such as :doc:`fix pair/tracker <fix_pair_tracker>` which do not
|
||||
require the information typically written to the header.
|
||||
data produced by :doc:`pair tracker <pair_tracker>` or
|
||||
:doc:`bpm bond styles <Howto_bpm>` which may not require the
|
||||
information typically written to the header.
|
||||
|
||||
----------
|
||||
|
||||
|
||||
@ -287,6 +287,7 @@ accelerated styles exist.
|
||||
* :doc:`nve/manifold/rattle <fix_nve_manifold_rattle>` -
|
||||
* :doc:`nve/noforce <fix_nve_noforce>` - NVE without forces (v only)
|
||||
* :doc:`nve/sphere <fix_nve_sphere>` - NVE for spherical particles
|
||||
* :doc:`nve/bpm/sphere <fix_nve_bpm_sphere>` - NVE for spherical particles used in the BPM package
|
||||
* :doc:`nve/spin <fix_nve_spin>` - NVE for a spin or spin-lattice system
|
||||
* :doc:`nve/tri <fix_nve_tri>` - NVE for triangles
|
||||
* :doc:`nvk <fix_nvk>` - constant kinetic energy time integration
|
||||
@ -304,7 +305,6 @@ accelerated styles exist.
|
||||
* :doc:`orient/fcc <fix_orient>` - add grain boundary migration force for FCC
|
||||
* :doc:`orient/eco <fix_orient_eco>` - add generalized grain boundary migration force
|
||||
* :doc:`pafi <fix_pafi>` - constrained force averages on hyper-planes to compute free energies (PAFI)
|
||||
* :doc:`pair/tracker <fix_pair_tracker>` - track properties of pairwise interactions
|
||||
* :doc:`phonon <fix_phonon>` - calculate dynamical matrix from MD simulations
|
||||
* :doc:`pimd <fix_pimd>` - Feynman path integral molecular dynamics
|
||||
* :doc:`planeforce <fix_planeforce>` - constrain atoms to move in a plane
|
||||
|
||||
@ -14,7 +14,7 @@ Syntax
|
||||
* adapt = style name of this fix command
|
||||
* N = adapt simulation settings every this many timesteps
|
||||
* one or more attribute/arg pairs may be appended
|
||||
* attribute = *pair* or *bond* or *kspace* or *atom*
|
||||
* attribute = *pair* or *bond* or *angle* or *kspace* or *atom*
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
@ -28,11 +28,16 @@ Syntax
|
||||
bparam = parameter to adapt over time
|
||||
I = type bond to set parameter for
|
||||
v_name = variable with name that calculates value of bparam
|
||||
*angle* args = astyle aparam I v_name
|
||||
astyle = angle style name, e.g. harmonic
|
||||
aparam = parameter to adapt over time
|
||||
I = type angle to set parameter for
|
||||
v_name = variable with name that calculates value of aparam
|
||||
*kspace* arg = v_name
|
||||
v_name = variable with name that calculates scale factor on K-space terms
|
||||
*atom* args = aparam v_name
|
||||
aparam = parameter to adapt over time
|
||||
v_name = variable with name that calculates value of aparam
|
||||
*atom* args = atomparam v_name
|
||||
atomparam = parameter to adapt over time
|
||||
v_name = variable with name that calculates value of atomparam
|
||||
|
||||
* zero or more keyword/value pairs may be appended
|
||||
* keyword = *scale* or *reset* or *mass*
|
||||
@ -283,30 +288,62 @@ operates. The only difference is that now a bond coefficient for a
|
||||
given bond type is adapted.
|
||||
|
||||
A wild-card asterisk can be used in place of or in conjunction with
|
||||
the bond type argument to set the coefficients for multiple bond types.
|
||||
This takes the form "\*" or "\*n" or "n\*" or "m\*n". If N = the number of
|
||||
atom types, then an asterisk with no numeric values means all types
|
||||
from 1 to N. A leading asterisk means all types from 1 to n (inclusive).
|
||||
A trailing asterisk means all types from n to N (inclusive). A middle
|
||||
asterisk means all types from m to n (inclusive).
|
||||
the bond type argument to set the coefficients for multiple bond
|
||||
types. This takes the form "\*" or "\*n" or "n\*" or "m\*n". If N =
|
||||
the number of bond types, then an asterisk with no numeric values
|
||||
means all types from 1 to N. A leading asterisk means all types from
|
||||
1 to n (inclusive). A trailing asterisk means all types from n to N
|
||||
(inclusive). A middle asterisk means all types from m to n
|
||||
(inclusive).
|
||||
|
||||
Currently *bond* does not support bond_style hybrid nor bond_style
|
||||
hybrid/overlay as bond styles. The only bonds that currently are
|
||||
working with fix_adapt are
|
||||
hybrid/overlay as bond styles. 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:`gromos <bond_gromos>` | k, r0 | type bonds |
|
||||
+------------------------------------+-------+------------+
|
||||
| :doc:`harmonic <bond_harmonic>` | k,r0 | type bonds |
|
||||
+------------------------------------+-------+------------+
|
||||
| :doc:`morse <bond_morse>` | r0 | type bonds |
|
||||
+------------------------------------+-------+------------+
|
||||
| :doc:`nonlinear <bond_nonlinear>` | r0 | type bonds |
|
||||
+------------------------------------+-------+------------+
|
||||
+------------------------------------+-------+-----------------+
|
||||
| :doc:`class2 <bond_class2>` | r0 | type bonds |
|
||||
+------------------------------------+-------+-----------------+
|
||||
| :doc:`fene <bond_fene>` | k,r0 | 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:`morse <bond_morse>` | r0 | type bonds |
|
||||
+------------------------------------+-------+-----------------+
|
||||
| :doc:`nonlinear <bond_nonlinear>` | epsilon,r0 | type bonds |
|
||||
+------------------------------------+-------+-----------------+
|
||||
|
||||
----------
|
||||
|
||||
The *angle* keyword uses the specified variable to change the value of
|
||||
an angle coefficient over time, very similar to how the *pair* keyword
|
||||
operates. The only difference is that now an angle coefficient for a
|
||||
given angle type is adapted.
|
||||
|
||||
A wild-card asterisk can be used in place of or in conjunction with
|
||||
the angle type argument to set the coefficients for multiple angle
|
||||
types. This takes the form "\*" or "\*n" or "n\*" or "m\*n". If N =
|
||||
the number of angle types, then an asterisk with no numeric values
|
||||
means all types from 1 to N. A leading asterisk means all types from
|
||||
1 to n (inclusive). A trailing asterisk means all types from n to N
|
||||
(inclusive). A middle asterisk means all types from m to n
|
||||
(inclusive).
|
||||
|
||||
Currently *angle* does not support angle_style hybrid nor angle_style
|
||||
hybrid/overlay as angle styles. The angle styles that currently work
|
||||
with fix_adapt are
|
||||
|
||||
+------------------------------------+-------+-----------------+
|
||||
| :doc:`harmonic <angle_harmonic>` | k,theta0 | type angles |
|
||||
+------------------------------------+-------+-----------------+
|
||||
| :doc:`cosine <angle_cosine>` | k | 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.
|
||||
|
||||
----------
|
||||
|
||||
|
||||
@ -113,6 +113,9 @@ You can dump out snapshots of the current bond topology via the :doc:`dump local
|
||||
may need to thermostat your system to compensate for energy changes
|
||||
resulting from broken bonds (and angles, dihedrals, impropers).
|
||||
|
||||
See the :doc:`Howto <Howto_broken_bonds>` page on broken bonds for more
|
||||
information on related features in LAMMPS.
|
||||
|
||||
----------
|
||||
|
||||
Restart, fix_modify, output, run start/stop, minimize info
|
||||
|
||||
@ -35,6 +35,10 @@ consistent with the microcanonical ensemble (NVE) provided there
|
||||
are (full) periodic boundary conditions and no other "manipulations"
|
||||
of the system (e.g. fixes that modify forces or velocities).
|
||||
|
||||
This fix invokes the velocity form of the
|
||||
Stoermer-Verlet time integration algorithm (velocity-Verlet). Other
|
||||
time integration options can be invoked using the :doc:`run_style <run_style>` command.
|
||||
|
||||
----------
|
||||
|
||||
.. include:: accel_styles.rst
|
||||
@ -57,7 +61,7 @@ Restrictions
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
:doc:`fix nvt <fix_nh>`, :doc:`fix npt <fix_nh>`
|
||||
:doc:`fix nvt <fix_nh>`, :doc:`fix npt <fix_nh>`, :doc:`run_style <run_style>`
|
||||
|
||||
Default
|
||||
"""""""
|
||||
|
||||
87
doc/src/fix_nve_bpm_sphere.rst
Normal file
87
doc/src/fix_nve_bpm_sphere.rst
Normal file
@ -0,0 +1,87 @@
|
||||
.. index:: fix nve/bpm/sphere
|
||||
|
||||
fix nve/bpm/sphere command
|
||||
==========================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
fix ID group-ID nve/bpm/sphere
|
||||
|
||||
* ID, group-ID are documented in :doc:`fix <fix>` command
|
||||
* nve/bpm/sphere = style name of this fix command
|
||||
* zero or more keyword/value pairs may be appended
|
||||
* keyword = *disc*
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
*disc* value = none = treat particles as 2d discs, not spheres
|
||||
|
||||
Examples
|
||||
""""""""
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
fix 1 all nve/bpm/sphere
|
||||
fix 1 all nve/bpm/sphere disc
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
Perform constant NVE integration to update position, velocity, angular
|
||||
velocity, and quaternion orientation for finite-size spherical
|
||||
particles in the group each timestep. V is volume; E is energy. This
|
||||
creates a system trajectory consistent with the microcanonical
|
||||
ensemble.
|
||||
|
||||
This fix differs from the :doc:`fix nve <fix_nve>` command, which
|
||||
assumes point particles and only updates their position and velocity.
|
||||
It also differs from the :doc:`fix nve/sphere <fix_nve_sphere>`
|
||||
command which assumes finite-size spheroid particles which do not
|
||||
store a quaternion. It thus does not update a particle's orientation
|
||||
or quaternion.
|
||||
|
||||
If the *disc* keyword is used, then each particle is treated as a 2d
|
||||
disc (circle) instead of as a sphere. This is only possible for 2d
|
||||
simulations, as defined by the :doc:`dimension <dimension>` keyword.
|
||||
The only difference between discs and spheres in this context is their
|
||||
moment of inertia, as used in the time integration.
|
||||
|
||||
----------
|
||||
|
||||
Restart, fix_modify, output, run start/stop, minimize info
|
||||
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
|
||||
|
||||
No information about this fix is written to :doc:`binary restart files
|
||||
<restart>`. None of the :doc:`fix_modify <fix_modify>` options are
|
||||
relevant to this fix. No global or per-atom quantities are stored by
|
||||
this fix for access by various :doc:`output commands <Howto_output>`.
|
||||
No parameter of this fix can be used with the *start/stop* keywords of
|
||||
the :doc:`run <run>` command. This fix is not invoked during
|
||||
:doc:`energy minimization <minimize>`.
|
||||
|
||||
Restrictions
|
||||
""""""""""""
|
||||
|
||||
This fix requires that atoms store torque, angular velocity (omega), a
|
||||
radius, and a quaternion as defined by the :doc:`atom_style bpm/sphere
|
||||
<atom_style>` command.
|
||||
|
||||
All particles in the group must be finite-size spheres with
|
||||
quaternions. They cannot be point particles.
|
||||
|
||||
Use of the *disc* keyword is only allowed for 2d simulations, as
|
||||
defined by the :doc:`dimension <dimension>` keyword.
|
||||
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
:doc:`fix nve <fix_nve>`, :doc:`fix nve/sphere <fix_nve_sphere>`
|
||||
|
||||
Default
|
||||
"""""""
|
||||
|
||||
none
|
||||
|
||||
@ -1,124 +0,0 @@
|
||||
.. index:: fix pair/tracker
|
||||
|
||||
fix pair/tracker command
|
||||
========================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
fix ID group-ID pair/tracker N attribute1 attribute2 ... keyword values ...
|
||||
|
||||
* ID, group-ID are documented in :doc:`fix <fix>` command
|
||||
* pair/tracker = style name of this fix command
|
||||
* N = prepare data for output every this many timesteps
|
||||
* one or more attributes may be appended
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
possible attributes = id1 id2 time/created time/broken time/total
|
||||
rmin rave x y z
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
id1, id2 = IDs of the 2 atoms in each pair interaction
|
||||
time/created = the time that the 2 atoms began interacting
|
||||
time/broken = the time that the 2 atoms stopped interacting
|
||||
time/total = the total time the 2 atoms interacted
|
||||
r/min = the minimum radial distance between the 2 atoms during the interaction
|
||||
r/ave = the average radial distance between the 2 atoms during the interaction
|
||||
x, y, z = the center of mass position of the 2 atoms when they stopped interacting
|
||||
|
||||
* zero or more keyword/value pairs may be appended
|
||||
* keyword = *time/min* or *type/include*
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
*time/min* value = T
|
||||
T = minimum interaction time
|
||||
*type/include* value = arg1 arg2
|
||||
arg = separate lists of types (see below)
|
||||
|
||||
Examples
|
||||
""""""""
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
fix 1 all pair/tracker 1000 id1 id2 time/min 100
|
||||
fix 1 all pair/tracker 1000 time/created time/broken type/include 1 * type/include 2 3,4
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
Tracks properties of pairwise interactions between two atoms and records data
|
||||
whenever the atoms move beyond the interaction cutoff.
|
||||
Must be used in conjunction with :doc:`pair tracker <pair_tracker>`.
|
||||
Data is accumulated over a span of *N* timesteps before being deleted.
|
||||
The number of datums generated, aggregated across all processors, equals
|
||||
the number of broken interactions. Interactions are only included if both
|
||||
atoms are included in the specified fix group. Additional filters can be
|
||||
applied using the *time/min* or *type/include* keywords described below.
|
||||
|
||||
.. note::
|
||||
|
||||
For extremely long-lived interactions, the calculation of *r/ave* may not be
|
||||
correct due to double overflow.
|
||||
|
||||
The *time/min* keyword sets a minimum amount of time that an interaction must
|
||||
persist to be included. This setting can be used to censor short-lived interactions.
|
||||
The *type/include* keyword filters interactions based on the types of the two atoms.
|
||||
Data is only saved for interactions between atoms with types in the two lists.
|
||||
Each list consists of a series of type
|
||||
ranges separated by commas. The range can be specified as a
|
||||
single numeric value, or a wildcard asterisk can be used to specify a range
|
||||
of values. This takes the form "\*" or "\*n" or "n\*" or "m\*n". For
|
||||
example, if M = the number of atom types, then an asterisk with no numeric
|
||||
values means all types from 1 to M. A leading asterisk means all types
|
||||
from 1 to n (inclusive). A trailing asterisk means all types from n to M
|
||||
(inclusive). A middle asterisk means all types from m to n (inclusive).
|
||||
Multiple *type/include* keywords may be added.
|
||||
|
||||
----------
|
||||
|
||||
Restart, fix_modify, run start/stop, minimize info
|
||||
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
|
||||
|
||||
No information about this fix is written to :doc:`binary restart files <restart>`.
|
||||
None of the :doc:`fix_modify <fix_modify>` options are
|
||||
relevant to this fix.
|
||||
No parameter of this fix can be used with the *start/stop* keywords of
|
||||
the :doc:`run <run>` command.
|
||||
|
||||
Output info
|
||||
"""""""""""
|
||||
|
||||
This compute calculates a local vector or local array depending on the
|
||||
number of input values. The length of the vector or number of rows in
|
||||
the array is the number of recorded, lost interactions. If a single input is
|
||||
specified, a local vector is produced. If two or more inputs are
|
||||
specified, a local array is produced where the number of columns = the
|
||||
number of inputs. The vector or array can be accessed by any command
|
||||
that uses local values from a compute as input. See the :doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
|
||||
options.
|
||||
|
||||
The vector or array values will be doubles that correspond to the
|
||||
specified attribute.
|
||||
|
||||
Restrictions
|
||||
""""""""""""
|
||||
|
||||
Must be used in conjunction with :doc:`pair style tracker <pair_tracker>`.
|
||||
|
||||
This fix is part of the MISC package. It is only enabled if LAMMPS
|
||||
was built with that package. See the :doc:`Build package <Build_package>` page for more info.
|
||||
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
:doc:`pair tracker <pair_tracker>`
|
||||
|
||||
Default
|
||||
"""""""
|
||||
|
||||
none
|
||||
@ -80,7 +80,7 @@ It is assumed that the particles cannot pass through the interface during the si
|
||||
so that its local dielectric constant value does not change.
|
||||
|
||||
There are some example scripts for using these fixes
|
||||
with LAMMPS in the ``examples/PACKAGES/dielectric directory``. The README file
|
||||
with LAMMPS in the ``examples/PACKAGES/dielectric`` directory. The README file
|
||||
therein contains specific details on the system setup. Note that the example data files
|
||||
show the additional fields (columns) needed for :doc:`atom_style dielectric <atom_style>`
|
||||
beyond the conventional fields *id*, *mol*, *type*, *q*, *x*, *y*, and *z*.
|
||||
@ -91,7 +91,7 @@ For fix *polarize/bem/gmres* and fix *polarize/bem/icc* the induced
|
||||
charges of the atoms in the specified group, which are the vertices on
|
||||
the interface, are computed using the equation:
|
||||
|
||||
..math::
|
||||
.. math::
|
||||
|
||||
\sigma_b(\mathbf{s}) = \dfrac{1 - \bar{\epsilon}}{\bar{\epsilon}}
|
||||
\sigma_f(\mathbf{s}) - \epsilon_0 \dfrac{\Delta \epsilon}{\bar{\epsilon}}
|
||||
@ -154,6 +154,9 @@ if LAMMPS was built with that package, which requires that also the
|
||||
KSPACE package is installed. See the :doc:`Build package
|
||||
<Build_package>` page for more info.
|
||||
|
||||
Note that the *polarize/bem/gmres* and *polarize/bem/icc* fixes only support
|
||||
:doc:`units <units>` *lj*, *real*, *metal*, *si* and *nano* at the moment.
|
||||
|
||||
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
@ -304,13 +304,15 @@ uninterrupted fashion.
|
||||
.. warning::
|
||||
|
||||
When reading data from a restart file, this fix command has to be
|
||||
specified **exactly** the same was in the input script that created
|
||||
the restart file. LAMMPS will only check whether a fix is of the
|
||||
same style and has the same fix ID and in case of a match will then
|
||||
try to initialize the fix with the data stored in the binary
|
||||
restart file. If the names and associated date types in the new
|
||||
fix property/atom command do not match the old one exactly, data
|
||||
can be corrupted or LAMMPS may crash.
|
||||
specified **after** the *read_restart* command and **exactly** the
|
||||
same was in the input script that created the restart file. LAMMPS
|
||||
will only check whether a fix is of the same style and has the same
|
||||
fix ID and in case of a match will then try to initialize the fix
|
||||
with the data stored in the binary restart file. If the names and
|
||||
associated date types in the new fix property/atom command do not
|
||||
match the old one exactly, data can be corrupted or LAMMPS may crash.
|
||||
If the fix is specified **before** the *read_restart* command its
|
||||
data will not be restored.
|
||||
|
||||
None of the :doc:`fix_modify <fix_modify>` options are relevant to
|
||||
this fix. No global or per-atom quantities are stored by this fix for
|
||||
|
||||
@ -214,10 +214,10 @@ generate an error. LAMMPS will check if a "UNITS:" tag is in the first
|
||||
line and stop with an error, if there is a mismatch with the current
|
||||
units used.
|
||||
|
||||
..note::
|
||||
.. note::
|
||||
|
||||
The electronic temperature at each grid point must be a non-zero
|
||||
positive value, both initially, and as the temperature evovles over
|
||||
positive value, both initially, and as the temperature evolves over
|
||||
time. Thus you must use either the *set* or *infile* keyword or be
|
||||
restarting a simulation that used this fix previously.
|
||||
|
||||
|
||||
@ -258,11 +258,17 @@ assignment is made at the beginning of the minimization, but not
|
||||
during the iterations of the minimizer.
|
||||
|
||||
The point in the timestep at which atoms are assigned to a dynamic
|
||||
group is after the initial stage of velocity Verlet time integration
|
||||
has been performed, and before neighbor lists or forces are computed.
|
||||
This is the point in the timestep where atom positions have just
|
||||
changed due to the time integration, so the region criterion should be
|
||||
accurate, if applied.
|
||||
group is after interatomic forces have been computed, but before any
|
||||
fixes which alter forces or otherwise update the system have been
|
||||
invoked. This means that atom positions have been updated, neighbor
|
||||
lists and ghost atoms are current, and both intermolecular and
|
||||
intramolecular forces have been calculated based on the new
|
||||
coordinates. Thus the region criterion, if applied, should be
|
||||
accurate. Also, any computes invoked by an atom-style variable should
|
||||
use updated information for that timestep, e.g. potential energy/atom
|
||||
or coordination number/atom. Similarly, fixes or computes which are
|
||||
invoked after that point in the timestep, should operate on the new
|
||||
group of atoms.
|
||||
|
||||
.. note::
|
||||
|
||||
|
||||
114
doc/src/pair_bpm_spring.rst
Normal file
114
doc/src/pair_bpm_spring.rst
Normal file
@ -0,0 +1,114 @@
|
||||
.. index:: pair_style bpm/spring
|
||||
|
||||
pair_style bpm/spring command
|
||||
=============================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
pair_style bpm/spring
|
||||
|
||||
Examples
|
||||
""""""""
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
pair_style bpm/spring
|
||||
pair_coeff * * 1.0 1.0 1.0
|
||||
pair_coeff 1 1 1.0 1.0 1.0
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
Style *bpm/spring* computes pairwise forces with the formula
|
||||
|
||||
.. math::
|
||||
|
||||
F = k (r - r_c)
|
||||
|
||||
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
|
||||
|
||||
.. math::
|
||||
|
||||
F_D = - \gamma w (\hat{r} \bullet \vec{v})
|
||||
|
||||
where :math:`\gamma` is the damping strength, :math:`\hat{r}` is the
|
||||
radial normal vector, :math:`\vec{v}` is the velocity difference
|
||||
between the two particles, and :math:`w` is a smoothing factor.
|
||||
This smoothing factor is constructed such that damping forces go to zero
|
||||
as particles come out of contact to avoid discontinuities. It is
|
||||
given by
|
||||
|
||||
.. math::
|
||||
|
||||
w = 1.0 - \left( \frac{r}{r_c} \right)^8 .
|
||||
|
||||
This pair style is designed for use in a spring-based bonded particle
|
||||
model. It mirrors the construction of the :doc:`bpm/spring
|
||||
<bond_bpm_spring>` bond style.
|
||||
|
||||
This pair interaction is always applied to pairs of non-bonded particles
|
||||
that are within the interaction distance. For pairs of bonded particles
|
||||
that are within the interaction distance, there is the option to either
|
||||
include this pair interaction and overlay the pair force over the bond
|
||||
force or to exclude this pair interaction such that the two particles
|
||||
only interact via the bond force. See discussion of the *overlay/pair*
|
||||
option for BPM bond styles and the :doc:`special_bonds <special_bonds>`
|
||||
command in the `:doc: how to <Howto_BPM>` page on BPMs for more details.
|
||||
|
||||
The following coefficients must be defined for each pair of atom types
|
||||
via the :doc:`pair_coeff <pair_coeff>` command as in the examples
|
||||
above, or in the data file or restart files read by the
|
||||
:doc:`read_data <read_data>` or :doc:`read_restart <read_restart>`
|
||||
commands, or by mixing as described below:
|
||||
|
||||
* :math:`k` (force/distance units)
|
||||
* :math:`r_c` (distance units)
|
||||
* :math:`\gamma` (force/velocity units)
|
||||
|
||||
|
||||
----------
|
||||
|
||||
Mixing, shift, table, tail correction, restart, rRESPA info
|
||||
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
|
||||
|
||||
For atom type pairs I,J and I != J, the A coefficient and cutoff
|
||||
distance for this pair style can be mixed. A is always mixed via a
|
||||
*geometric* rule. The cutoff is mixed according to the pair_modify
|
||||
mix value. The default mix value is *geometric*\ . See the
|
||||
"pair_modify" command for details.
|
||||
|
||||
This pair style does not support the :doc:`pair_modify <pair_modify>`
|
||||
shift option, since the pair interaction goes to 0.0 at the cutoff.
|
||||
|
||||
The :doc:`pair_modify <pair_modify>` table and tail options are not
|
||||
relevant for this pair style.
|
||||
|
||||
This pair style writes its information to :doc:`binary restart files
|
||||
<restart>`, so pair_style and pair_coeff commands do not need to be
|
||||
specified in an input script that reads a restart file.
|
||||
|
||||
This pair style can only be used via the *pair* keyword of the
|
||||
:doc:`run_style respa <run_style>` command. It does not support the
|
||||
*inner*, *middle*, *outer* keywords.
|
||||
|
||||
----------
|
||||
|
||||
Restrictions
|
||||
""""""""""""
|
||||
none
|
||||
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
:doc:`pair_coeff <pair_coeff>`, :doc:`bond bpm/spring <bond_bpm_spring>`
|
||||
|
||||
Default
|
||||
"""""""
|
||||
|
||||
none
|
||||
@ -3,6 +3,7 @@
|
||||
.. index:: pair_style lj/cut/coul/cut/dielectric
|
||||
.. index:: pair_style lj/cut/coul/cut/dielectric/omp
|
||||
.. index:: pair_style lj/cut/coul/debye/dielectric
|
||||
.. index:: pair_style lj/cut/coul/debye/dielectric/omp
|
||||
.. index:: pair_style lj/cut/coul/long/dielectric
|
||||
.. index:: pair_style lj/cut/coul/long/dielectric/omp
|
||||
.. index:: pair_style lj/cut/coul/msm/dielectric
|
||||
@ -22,6 +23,8 @@ Accelerator Variants: *lj/cut/coul/cut/dielectric/omp*
|
||||
pair_style lj/cut/coul/debye/dielectric command
|
||||
===============================================
|
||||
|
||||
Accelerator Variants: *lj/cut/coul/debye/dielectric/omp*
|
||||
|
||||
pair_style lj/cut/coul/long/dielectric command
|
||||
==============================================
|
||||
|
||||
|
||||
@ -1,8 +1,11 @@
|
||||
.. index:: pair_style ilp/graphene/hbn
|
||||
.. index:: pair_style ilp/graphene/hbn/opt
|
||||
|
||||
pair_style ilp/graphene/hbn command
|
||||
===================================
|
||||
|
||||
Accelerator Variant: *ilp/graphene/hbn/opt*
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
@ -125,6 +128,10 @@ headings) the following commands could be included in an input script:
|
||||
|
||||
----------
|
||||
|
||||
.. include:: accel_styles.rst
|
||||
|
||||
----------
|
||||
|
||||
Mixing, shift, table, tail correction, restart, rRESPA info
|
||||
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
|
||||
|
||||
|
||||
@ -238,7 +238,7 @@ none
|
||||
|
||||
.. _Veld2:
|
||||
|
||||
**(In 't Veld)** In 't Veld, Ismail, Grest, J Chem Phys (accepted) (2007).
|
||||
**(In 't Veld)** In 't Veld, Ismail, Grest, J Chem Phys, 127, 144711 (2007).
|
||||
|
||||
.. _Jorgensen4:
|
||||
|
||||
|
||||
@ -131,6 +131,7 @@ accelerated styles exist.
|
||||
* :doc:`born/coul/msm <pair_born>` - Born with long-range MSM Coulomb
|
||||
* :doc:`born/coul/wolf <pair_born>` - Born with Wolf potential for Coulomb
|
||||
* :doc:`born/coul/wolf/cs <pair_cs>` - Born with Wolf potential for Coulomb and core/shell model
|
||||
* :doc:`bpm/spring <pair_bpm_spring>` - repulsive harmonic force with damping
|
||||
* :doc:`brownian <pair_brownian>` - Brownian potential for Fast Lubrication Dynamics
|
||||
* :doc:`brownian/poly <pair_brownian>` - Brownian potential for Fast Lubrication Dynamics with polydispersity
|
||||
* :doc:`buck <pair_buck>` - Buckingham potential
|
||||
|
||||
@ -8,89 +8,182 @@ Syntax
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
pair_style tracker keyword
|
||||
pair_style tracker fix_ID N keyword values attribute1 attribute2 ...
|
||||
|
||||
* zero or more keyword/arg pairs may be appended
|
||||
* keyword = *finite*
|
||||
* fix_ID = ID of associated internal fix to store data
|
||||
* N = prepare data for output every this many timesteps
|
||||
* zero or more keywords may be appended
|
||||
* keyword = *finite* or *time/min* or *type/include*
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
*finite* value = none
|
||||
pair style uses atomic diameters to identify contacts
|
||||
*time/min* value = T
|
||||
T = minimum number of timesteps of interaction
|
||||
*type/include* value = list1 list2
|
||||
list1,list2 = separate lists of types (see below)
|
||||
|
||||
* one or more attributes may be appended
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
possible attributes = id1 id2 time/created time/broken time/total
|
||||
r/min r/ave x y z
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
id1, id2 = IDs of the 2 atoms in each pair interaction
|
||||
time/created = the timestep that the 2 atoms began interacting
|
||||
time/broken = the timestep that the 2 atoms stopped interacting
|
||||
time/total = the total number of timesteps the 2 atoms interacted
|
||||
r/min = the minimum radial distance between the 2 atoms during the interaction (distance units)
|
||||
r/ave = the average radial distance between the 2 atoms during the interaction (distance units)
|
||||
x, y, z = the center of mass position of the 2 atoms when they stopped interacting (distance units)
|
||||
|
||||
Examples
|
||||
""""""""
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
pair_style hybrid/overlay tracker ...
|
||||
pair_style hybrid/overlay tracker myfix 1000 id1 id2 type/include 1 * type/include 2 3,4 lj/cut 2.5
|
||||
pair_coeff 1 1 tracker 2.0
|
||||
|
||||
pair_style hybrid/overlay tracker finite ...
|
||||
pair_style hybrid/overlay tracker myfix 1000 finite x y z time/min 100 granular
|
||||
pair_coeff * * tracker
|
||||
|
||||
fix 1 all pair/tracker 1000 time/created time/broken
|
||||
dump 1 all local 1000 dump.local f_1[1] f_1[2]
|
||||
dump 1 all local 1000 dump.local f_myfix[1] f_myfix[2] f_myfix[3]
|
||||
dump_modify 1 write_header no
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
Style *tracker* monitors information about pairwise interactions.
|
||||
It does not calculate any forces on atoms.
|
||||
:doc:`Pair hybrid/overlay <pair_hybrid>` can be used to combine this pair
|
||||
style with another pair style. Style *tracker* must be used in conjunction
|
||||
with about :doc:`fix pair_tracker <fix_pair_tracker>` which contains
|
||||
information on what data can be output.
|
||||
Style *tracker* monitors information about pairwise interactions. It
|
||||
does not calculate any forces on atoms. :doc:`Pair hybrid/overlay
|
||||
<pair_hybrid>` can be used to combine this pair style with any other
|
||||
pair style, as shown in the examples above.
|
||||
|
||||
If the *finite* keyword is not defined, the following coefficients must be
|
||||
defined for each pair of atom types via the :doc:`pair_coeff <pair_coeff>`
|
||||
command as in the examples above, or in the data file or restart files
|
||||
read by the :doc:`read_data <read_data>` or :doc:`read_restart <read_restart>`
|
||||
commands, or by mixing as described below:
|
||||
At each timestep, if two neighboring atoms move beyond the interaction
|
||||
cutoff, pairwise data is processed and transferred to an internal fix
|
||||
labeled *fix_ID*. This allows the local data to be accessed by other
|
||||
LAMMPS commands. Additional
|
||||
filters can be applied using the *time/min* or *type/include* keywords
|
||||
described below. Note that this is the interaction cutoff defined by
|
||||
this pair style, not the short-range cutoff defined by the pair style
|
||||
that is calculating forces on atoms.
|
||||
|
||||
Following any optional keyword/value arguments, a list of one or more
|
||||
attributes is specified. These include the IDs of the two atoms in
|
||||
the pair. The other attributes for the pair of atoms are the
|
||||
duration of time they were "interacting" or at the point in time they
|
||||
started or stopped interacting. In this context, "interacting" means
|
||||
the time window during which the two atoms were closer than the
|
||||
interaction cutoff distance. The attributes for time/* refer to
|
||||
timesteps.
|
||||
|
||||
Data is continuously accumulated by the internal fix over intervals of *N*
|
||||
timesteps. At the end of each interval, all of the saved accumulated
|
||||
data is deleted to make room for new data. Individual datum may
|
||||
therefore persist anywhere between *1* to *N* timesteps depending on
|
||||
when they are saved. This data can be accessed using the *fix_ID* and a
|
||||
:doc:`dump local <dump>` command. To ensure all data is output,
|
||||
the dump frequency should correspond to the same interval of *N*
|
||||
timesteps. A dump frequency of an integer multiple of *N* can be used
|
||||
to regularly output a sample of the accumulated data.
|
||||
|
||||
----------
|
||||
|
||||
The following optional keywords may be used.
|
||||
|
||||
If the *finite* keyword is not used, the following coefficients must
|
||||
be defined for each pair of atom types via the :doc:`pair_coeff
|
||||
<pair_coeff>` command as in the examples above, or in the data file or
|
||||
restart files read by the :doc:`read_data <read_data>` or
|
||||
:doc:`read_restart <read_restart>` commands, or by mixing as described
|
||||
below:
|
||||
|
||||
* cutoff (distance units)
|
||||
|
||||
If the *finite* keyword is defined, no coefficients may be defined.
|
||||
Interaction cutoffs are alternatively calculated based on the
|
||||
diameter of finite particles.
|
||||
If the *finite* keyword is used, there are no additional coefficients
|
||||
to set for each pair of atom types via the
|
||||
:doc:`pair_coeff <pair_coeff>` command. Interaction cutoffs are
|
||||
instead calculated based on the diameter of finite particles. However
|
||||
you must still use the :doc:`pair_coeff <pair_coeff>` for all atom
|
||||
types. For example the command
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
pair_coeff * *
|
||||
|
||||
should be used.
|
||||
|
||||
The *time/min* keyword sets a minimum amount of time that an
|
||||
interaction must persist to be included. This setting can be used to
|
||||
censor short-lived interactions.
|
||||
|
||||
The *type/include* keyword filters interactions based on the types of
|
||||
the two atoms. Data is only saved for interactions between atoms
|
||||
whose two atom types appear in *list1* and *list2*. Atom type 1 must
|
||||
be in list1 and atom type 2 in list2. Or vice versa.
|
||||
|
||||
Each type list consists of a series of type ranges separated by
|
||||
commas. Each range can be specified as a single numeric value, or a
|
||||
wildcard asterisk can be used to specify a range of values. This
|
||||
takes the form "\*" or "\*n" or "n\*" or "m\*n". For example, if M =
|
||||
the number of atom types, then an asterisk with no numeric values
|
||||
means all types from 1 to M. A leading asterisk means all types from
|
||||
1 to n (inclusive). A trailing asterisk means all types from n to M
|
||||
(inclusive). A middle asterisk means all types from m to n
|
||||
(inclusive). Note that the *type/include* keyword can be specified
|
||||
multiple times.
|
||||
|
||||
Mixing, shift, table, tail correction, restart, rRESPA info
|
||||
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
|
||||
|
||||
For atom type pairs I,J and I != J, the cutoff coefficient and cutoff
|
||||
distance for this pair style can be mixed. The cutoff is always mixed via a
|
||||
*geometric* rule. The cutoff is mixed according to the pair_modify
|
||||
mix value. The default mix value is *geometric*\ . See the
|
||||
"pair_modify" command for details.
|
||||
distance for this pair style can be mixed. The cutoff is always mixed
|
||||
via a *geometric* rule. The cutoff is mixed according to the
|
||||
pair_modify mix value. The default mix value is *geometric*\ . See
|
||||
the "pair_modify" command for details.
|
||||
|
||||
This pair style writes its information to :doc:`binary restart files <restart>`, so
|
||||
pair_style and pair_coeff commands do not need
|
||||
to be specified in an input script that reads a restart file.
|
||||
This pair style writes its information to :doc:`binary restart files
|
||||
<restart>`, so pair_style and pair_coeff commands do not need to be
|
||||
specified in an input script that reads a restart file.
|
||||
|
||||
The :doc:`pair_modify <pair_modify>` shift, table, and tail options
|
||||
are not relevant for this pair style.
|
||||
|
||||
The accumulated data is not written to restart files and should be
|
||||
output before a restart file is written to avoid missing data.
|
||||
|
||||
The internal fix calculates a local vector or local array depending on the
|
||||
number of input values. The length of the vector or number of rows in
|
||||
the array is the number of recorded, lost interactions. If a single
|
||||
input is specified, a local vector is produced. If two or more inputs
|
||||
are specified, a local array is produced where the number of columns =
|
||||
the number of inputs. The vector or array can be accessed by any
|
||||
command that uses local values from a compute as input. See the
|
||||
:doc:`Howto output <Howto_output>` page for an overview of LAMMPS
|
||||
output options.
|
||||
|
||||
The vector or array will be floating point values that correspond to
|
||||
the specified attribute.
|
||||
|
||||
----------
|
||||
|
||||
Restrictions
|
||||
""""""""""""
|
||||
|
||||
A corresponding :doc:`fix pair_tracker <fix_pair_tracker>` must be defined
|
||||
to use this pair style.
|
||||
|
||||
This pair style is currently incompatible with granular pair styles that extend
|
||||
beyond the contact (e.g. JKR and DMT).
|
||||
|
||||
This fix is part of the MISC package. It is only enabled if LAMMPS
|
||||
was built with that package. See the :doc:`Build package <Build_package>` page for more info.
|
||||
was built with that package. See the :doc:`Build package
|
||||
<Build_package>` page for more info.
|
||||
|
||||
This pair style is currently incompatible with granular pair styles
|
||||
that extend beyond the contact (e.g. JKR and DMT).
|
||||
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
:doc:`fix pair_tracker <fix_pair_tracker>`
|
||||
|
||||
Default
|
||||
"""""""
|
||||
|
||||
|
||||
@ -650,6 +650,8 @@ of analysis.
|
||||
- atom-ID atom-type rho esph cv x y z
|
||||
* - sphere
|
||||
- atom-ID atom-type diameter density x y z
|
||||
* - bpm/sphere
|
||||
- atom-ID molecule-ID atom-type diameter density x y z
|
||||
* - spin
|
||||
- atom-ID atom-type x y z spx spy spz sp
|
||||
* - tdpd
|
||||
|
||||
@ -67,7 +67,8 @@ Description
|
||||
Choose the style of time integrator used for molecular dynamics
|
||||
simulations performed by LAMMPS.
|
||||
|
||||
The *verlet* style is a standard velocity-Verlet integrator.
|
||||
The *verlet* style is the velocity form of the
|
||||
Stoermer-Verlet time integration algorithm (velocity-Verlet)
|
||||
|
||||
----------
|
||||
|
||||
|
||||
161
doc/src/set.rst
161
doc/src/set.rst
@ -22,7 +22,7 @@ Syntax
|
||||
*volume* or *image* or *bond* or *angle* or *dihedral* or
|
||||
*improper* or *sph/e* or *sph/cv* or *sph/rho* or
|
||||
*smd/contact/radius* or *smd/mass/density* or *dpd/theta* or
|
||||
*edpd/temp* or *edpd/cv* or *cc* or
|
||||
*edpd/temp* or *edpd/cv* or *cc* or *epsilon* or
|
||||
*i_name* or *d_name* or *i2_name* or *d2_name*
|
||||
|
||||
.. parsed-literal::
|
||||
@ -124,6 +124,7 @@ Syntax
|
||||
*cc* values = index cc
|
||||
index = index of a chemical species (1 to Nspecies)
|
||||
cc = chemical concentration of tDPD particles for a species (mole/volume units)
|
||||
*epsilon* value = dielectric constant of the medium where the atoms reside
|
||||
*i_name* value = custom integer vector with name
|
||||
*d_name* value = custom floating-point vector with name
|
||||
*i2_name* value = column of a custom integer array with name
|
||||
@ -372,13 +373,13 @@ vector of the particles is set to the 3 specified components.
|
||||
|
||||
Keyword *omega* sets the angular velocity of selected atoms. The
|
||||
particles must be spheres as defined by the :doc:`atom_style sphere
|
||||
<atom_style>` command. The angular velocity vector of the particles
|
||||
is set to the 3 specified components.
|
||||
<atom_style>` command. The angular velocity vector of the particles is
|
||||
set to the 3 specified components.
|
||||
|
||||
Keyword *mass* sets the mass of all selected particles. The particles
|
||||
must have a per-atom mass attribute, as defined by the
|
||||
:doc:`atom_style <atom_style>` command. See the "mass" command for
|
||||
how to set mass values on a per-type basis.
|
||||
must have a per-atom mass attribute, as defined by the :doc:`atom_style
|
||||
<atom_style>` command. See the "mass" command for how to set mass
|
||||
values on a per-type basis.
|
||||
|
||||
Keyword *density* or *density/disc* also sets the mass of all selected
|
||||
particles, but in a different way. The particles must have a per-atom
|
||||
@ -387,22 +388,21 @@ command. If the atom has a radius attribute (see :doc:`atom_style
|
||||
sphere <atom_style>`) and its radius is non-zero, its mass is set from
|
||||
the density and particle volume for 3d systems (the input density is
|
||||
assumed to be in mass/distance\^3 units). For 2d, the default is for
|
||||
LAMMPS to model particles with a radius attribute as spheres.
|
||||
However, if the *density/disc* keyword is used, then they can be
|
||||
modeled as 2d discs (circles). Their mass is set from the density and
|
||||
particle area (the input density is assumed to be in mass/distance\^2
|
||||
units).
|
||||
LAMMPS to model particles with a radius attribute as spheres. However,
|
||||
if the *density/disc* keyword is used, then they can be modeled as 2d
|
||||
discs (circles). Their mass is set from the density and particle area
|
||||
(the input density is assumed to be in mass/distance\^2 units).
|
||||
|
||||
If the atom has a shape attribute (see :doc:`atom_style ellipsoid
|
||||
<atom_style>`) and its 3 shape parameters are non-zero, then its mass
|
||||
is set from the density and particle volume (the input density is
|
||||
assumed to be in mass/distance\^3 units). The *density/disc* keyword
|
||||
has no effect; it does not (yet) treat 3d ellipsoids as 2d ellipses.
|
||||
<atom_style>`) and its 3 shape parameters are non-zero, then its mass is
|
||||
set from the density and particle volume (the input density is assumed
|
||||
to be in mass/distance\^3 units). The *density/disc* keyword has no
|
||||
effect; it does not (yet) treat 3d ellipsoids as 2d ellipses.
|
||||
|
||||
If the atom has a length attribute (see :doc:`atom_style line
|
||||
<atom_style>`) and its length is non-zero, then its mass is set from
|
||||
the density and line segment length (the input density is assumed to
|
||||
be in mass/distance units). If the atom has an area attribute (see
|
||||
<atom_style>`) and its length is non-zero, then its mass is set from the
|
||||
density and line segment length (the input density is assumed to be in
|
||||
mass/distance units). If the atom has an area attribute (see
|
||||
:doc:`atom_style tri <atom_style>`) and its area is non-zero, then its
|
||||
mass is set from the density and triangle area (the input density is
|
||||
assumed to be in mass/distance\^2 units).
|
||||
@ -410,84 +410,91 @@ assumed to be in mass/distance\^2 units).
|
||||
If none of these cases are valid, then the mass is set to the density
|
||||
value directly (the input density is assumed to be in mass units).
|
||||
|
||||
Keyword *volume* sets the volume of all selected particles.
|
||||
Currently, only the :doc:`atom_style peri <atom_style>` command defines
|
||||
particles with a volume attribute. Note that this command does not
|
||||
adjust the particle mass.
|
||||
Keyword *volume* sets the volume of all selected particles. Currently,
|
||||
only the :doc:`atom_style peri <atom_style>` command defines particles
|
||||
with a volume attribute. Note that this command does not adjust the
|
||||
particle mass.
|
||||
|
||||
Keyword *image* sets which image of the simulation box the atom is
|
||||
considered to be in. An image of 0 means it is inside the box as
|
||||
defined. A value of 2 means add 2 box lengths to get the true value.
|
||||
A value of -1 means subtract 1 box length to get the true value.
|
||||
LAMMPS updates these flags as atoms cross periodic boundaries during
|
||||
the simulation. The flags can be output with atom snapshots via the
|
||||
:doc:`dump <dump>` command. If a value of NULL is specified for any
|
||||
of nx,ny,nz, then the current image value for that dimension is
|
||||
unchanged. For non-periodic dimensions only a value of 0 can be
|
||||
specified. This command can be useful after a system has been
|
||||
equilibrated and atoms have diffused one or more box lengths in
|
||||
various directions. This command can then reset the image values for
|
||||
atoms so that they are effectively inside the simulation box, e.g if a
|
||||
diffusion coefficient is about to be measured via the :doc:`compute
|
||||
msd <compute_msd>` command. Care should be taken not to reset the
|
||||
image flags of two atoms in a bond to the same value if the bond
|
||||
straddles a periodic boundary (rather they should be different by +/-
|
||||
1). This will not affect the dynamics of a simulation, but may mess
|
||||
up analysis of the trajectories if a LAMMPS diagnostic or your own
|
||||
analysis relies on the image flags to unwrap a molecule which
|
||||
straddles the periodic box.
|
||||
defined. A value of 2 means add 2 box lengths to get the true value. A
|
||||
value of -1 means subtract 1 box length to get the true value. LAMMPS
|
||||
updates these flags as atoms cross periodic boundaries during the
|
||||
simulation. The flags can be output with atom snapshots via the
|
||||
:doc:`dump <dump>` command. If a value of NULL is specified for any of
|
||||
nx,ny,nz, then the current image value for that dimension is unchanged.
|
||||
For non-periodic dimensions only a value of 0 can be specified. This
|
||||
command can be useful after a system has been equilibrated and atoms
|
||||
have diffused one or more box lengths in various directions. This
|
||||
command can then reset the image values for atoms so that they are
|
||||
effectively inside the simulation box, e.g if a diffusion coefficient is
|
||||
about to be measured via the :doc:`compute msd <compute_msd>` command.
|
||||
Care should be taken not to reset the image flags of two atoms in a bond
|
||||
to the same value if the bond straddles a periodic boundary (rather they
|
||||
should be different by +/- 1). This will not affect the dynamics of a
|
||||
simulation, but may mess up analysis of the trajectories if a LAMMPS
|
||||
diagnostic or your own analysis relies on the image flags to unwrap a
|
||||
molecule which straddles the periodic box.
|
||||
|
||||
Keywords *bond*, *angle*, *dihedral*, and *improper*, set the bond
|
||||
type (angle type, etc) of all bonds (angles, etc) of selected atoms to
|
||||
the specified value from 1 to nbondtypes (nangletypes, etc). All
|
||||
atoms in a particular bond (angle, etc) must be selected atoms in
|
||||
order for the change to be made. The value of nbondtype (nangletypes,
|
||||
etc) was set by the *bond types* (\ *angle types*, etc) field in the
|
||||
header of the data file read by the :doc:`read_data <read_data>`
|
||||
command. These keywords do not allow use of an atom-style variable.
|
||||
Keywords *bond*, *angle*, *dihedral*, and *improper*, set the bond type
|
||||
(angle type, etc) of all bonds (angles, etc) of selected atoms to the
|
||||
specified value from 1 to nbondtypes (nangletypes, etc). All atoms in a
|
||||
particular bond (angle, etc) must be selected atoms in order for the
|
||||
change to be made. The value of nbondtype (nangletypes, etc) was set by
|
||||
the *bond types* (\ *angle types*, etc) field in the header of the data
|
||||
file read by the :doc:`read_data <read_data>` command. These keywords
|
||||
do not allow use of an atom-style variable.
|
||||
|
||||
Keywords *sph/e*, *sph/cv*, and *sph/rho* set the energy, heat
|
||||
capacity, and density of smoothed particle hydrodynamics (SPH)
|
||||
particles. See `this PDF guide <PDF/SPH_LAMMPS_userguide.pdf>`_
|
||||
to using SPH in LAMMPS.
|
||||
Keywords *sph/e*, *sph/cv*, and *sph/rho* set the energy, heat capacity,
|
||||
and density of smoothed particle hydrodynamics (SPH) particles. See
|
||||
`this PDF guide <PDF/SPH_LAMMPS_userguide.pdf>`_ to using SPH in LAMMPS.
|
||||
|
||||
Keyword *smd/mass/density* sets the mass of all selected particles,
|
||||
but it is only applicable to the Smooth Mach Dynamics package
|
||||
MACHDYN. It assumes that the particle volume has already been
|
||||
correctly set and calculates particle mass from the provided mass
|
||||
density value.
|
||||
Keyword *smd/mass/density* sets the mass of all selected particles, but
|
||||
it is only applicable to the Smooth Mach Dynamics package MACHDYN. It
|
||||
assumes that the particle volume has already been correctly set and
|
||||
calculates particle mass from the provided mass density value.
|
||||
|
||||
Keyword *smd/contact/radius* only applies to simulations with the
|
||||
Smooth Mach Dynamics package MACHDYN. Itsets an interaction radius
|
||||
for computing short-range interactions, e.g. repulsive forces to
|
||||
prevent different individual physical bodies from penetrating each
|
||||
other. Note that the SPH smoothing kernel diameter used for computing
|
||||
long range, nonlocal interactions, is set using the *diameter*
|
||||
keyword.
|
||||
Keyword *smd/contact/radius* only applies to simulations with the Smooth
|
||||
Mach Dynamics package MACHDYN. Itsets an interaction radius for
|
||||
computing short-range interactions, e.g. repulsive forces to prevent
|
||||
different individual physical bodies from penetrating each other. Note
|
||||
that the SPH smoothing kernel diameter used for computing long range,
|
||||
nonlocal interactions, is set using the *diameter* keyword.
|
||||
|
||||
Keyword *dpd/theta* sets the internal temperature of a DPD particle as
|
||||
defined by the DPD-REACT package. If the specified value is a number
|
||||
it must be >= 0.0. If the specified value is NULL, then the kinetic
|
||||
temperature Tkin of each particle is computed as 3/2 k Tkin = KE = 1/2
|
||||
m v\^2 = 1/2 m (vx\*vx+vy\*vy+vz\*vz). Each particle's internal
|
||||
defined by the DPD-REACT package. If the specified value is a number it
|
||||
must be >= 0.0. If the specified value is NULL, then the kinetic
|
||||
temperature Tkin of each particle is computed as 3/2 k Tkin = KE = 1/2 m
|
||||
v\^2 = 1/2 m (vx\*vx+vy\*vy+vz\*vz). Each particle's internal
|
||||
temperature is set to Tkin. If the specified value is an atom-style
|
||||
variable, then the variable is evaluated for each particle. If a
|
||||
value >= 0.0, the internal temperature is set to that value. If it is
|
||||
< 0.0, the computation of Tkin is performed and the internal
|
||||
temperature is set to that value.
|
||||
variable, then the variable is evaluated for each particle. If a value
|
||||
>= 0.0, the internal temperature is set to that value. If it is < 0.0,
|
||||
the computation of Tkin is performed and the internal temperature is set
|
||||
to that value.
|
||||
|
||||
Keywords *edpd/temp* and *edpd/cv* set the temperature and volumetric
|
||||
heat capacity of an eDPD particle as defined by the DPD-MESO package.
|
||||
Currently, only :doc:`atom_style edpd <atom_style>` defines particles
|
||||
with these attributes. The values for the temperature and heat
|
||||
capacity must be positive.
|
||||
with these attributes. The values for the temperature and heat capacity
|
||||
must be positive.
|
||||
|
||||
Keyword *cc* sets the chemical concentration of a tDPD particle for a
|
||||
specified species as defined by the DPD-MESO package. Currently, only
|
||||
:doc:`atom_style tdpd <atom_style>` defines particles with this
|
||||
attribute. An integer for "index" selects a chemical species (1 to
|
||||
Nspecies) where Nspecies is set by the atom_style command. The value
|
||||
for the chemical concentration must be >= 0.0.
|
||||
Nspecies) where Nspecies is set by the atom_style command. The value for
|
||||
the chemical concentration must be >= 0.0.
|
||||
|
||||
Keyword *epsilon* sets the dielectric constant of a particle, precisely
|
||||
of the medium where the particle resides as defined by the DIELECTRIC
|
||||
package. Currently, only :doc:`atom_style dielectric <atom_style>`
|
||||
defines particles with this attribute. The value for the dielectric
|
||||
constant must be >= 0.0. Note that the set command with this keyword
|
||||
will rescale the particle charge accordingly so that the real charge
|
||||
(e.g., as read from a data file) stays intact. To change the real
|
||||
charges, one needs to use the set command with the *charge*
|
||||
keyword. Care must be taken to ensure that the real and scaled charges,
|
||||
and dielectric constants are consistent.
|
||||
|
||||
Keywords *i_name*, *d_name*, *i2_name*, *d2_name* refer to custom
|
||||
per-atom integer and floating-point vectors or arrays that have been
|
||||
|
||||
@ -252,6 +252,6 @@ flush = no, and temp/press = compute IDs defined by thermo_style.
|
||||
|
||||
The defaults for the line and format options depend on the thermo style.
|
||||
For styles "one" and "custom", the line and format defaults are "one",
|
||||
"%10d", and "%12.8g". For style "multi", the line and format defaults
|
||||
"%10d", and "%14.8g". For style "multi", the line and format defaults
|
||||
are "multi", "%14d", and "%14.4f". For style "yaml", the line and format
|
||||
defaults are "%d" and "%.15g".
|
||||
|
||||
@ -10,7 +10,7 @@ Syntax
|
||||
|
||||
thermo_style style args
|
||||
|
||||
* style = *one* or *multi* *yaml* or *custom*
|
||||
* style = *one* or *multi* or *yaml* or *custom*
|
||||
* args = list of arguments for a particular style
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
Reference in New Issue
Block a user