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Merge pull request #111 from lammps/master

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rebase
This commit is contained in:
Jacob Gissinger
2020-11-19 15:29:08 -05:00
committed by GitHub
parent dba84be75a d1af1aa12d
commit 9306f8a905
110 changed files with 8290 additions and 4474 deletions
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6
doc/src/Build_development.rst
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@ -111,8 +111,10 @@ error margin). The status of this automated testing can be viewed on
The unit testing facility is integrated into the CMake build process
of the LAMMPS source code distribution itself. It can be enabled by
setting ``-D ENABLE_TESTING=on`` during the CMake configuration step.
It requires the `PyYAML <http://pyyaml.org/>`_ library and development
headers to compile and will download and compile a recent version of the
It requires the `YAML <http://pyyaml.org/>`_ library and development
headers (if not found locally a recent version will be downloaded
and compiled transparently) to compile and will download and compile
a specific recent version of the
`Googletest <https://github.com/google/googletest/>`_ C++ test framework
for implementing the tests.

2
doc/src/Commands_fix.rst
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@ -195,7 +195,7 @@ OPT.
* :doc:`saed/vtk <fix_saed_vtk>`
* :doc:`setforce (k) <fix_setforce>`
* :doc:`setforce/spin <fix_setforce>`
* :doc:`shake <fix_shake>`
* :doc:`shake (k) <fix_shake>`
* :doc:`shardlow (k) <fix_shardlow>`
* :doc:`smd <fix_smd>`
* :doc:`smd/adjust_dt <fix_smd_adjust_dt>`

1
doc/src/Commands_pair.rst
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@ -241,6 +241,7 @@ OPT.
* :doc:`spin/dipole/long <pair_spin_dipole>`
* :doc:`spin/dmi <pair_spin_dmi>`
* :doc:`spin/exchange <pair_spin_exchange>`
* :doc:`spin/exchange/biquadratic <pair_spin_exchange>`
* :doc:`spin/magelec <pair_spin_magelec>`
* :doc:`spin/neel <pair_spin_neel>`
* :doc:`srp <pair_srp>`

1
doc/src/Errors_warnings.rst
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@ -119,7 +119,6 @@ Doc page with :doc:`ERROR messages <Errors_messages>`
:doc:`pair style zero <pair_zero>` with a suitable cutoff or use :doc:`comm_modify cutoff <comm_modify>`.
*Communication cutoff is shorter than a bond length based estimate. This may lead to errors.*
Since LAMMPS stores topology data with individual atoms, all atoms
comprising a bond, angle, dihedral or improper must be present on any
sub-domain that "owns" the atom with the information, either as a

4
doc/src/Howto_github.rst
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@ -72,7 +72,7 @@ explained in more detail here: `feature branch workflow <https://www.atlassian.c
**Feature branches**
First of all, create a clone of your version on github on your local
First of all, create a clone of your version on GitHub on your local
machine via HTTPS:
.. code-block:: bash
@ -155,7 +155,7 @@ useful message that explains the change.
.. code-block:: bash
$ git commit -m 'Finally updated the github tutorial'
$ git commit -m 'Finally updated the GitHub tutorial'
After the commit, the changes can be pushed to the same branch on GitHub:

2
doc/src/Howto_walls.rst
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@ -67,5 +67,5 @@ rotate.
The only frictional idealized walls currently in LAMMPS are flat or
curved surfaces specified by the :doc:`fix wall/gran <fix_wall_gran>`
command. At some point we plan to allow regoin surfaces to be used as
command. At some point we plan to allow region surfaces to be used as
frictional walls, as well as triangulated surfaces.

12
doc/src/Intro_citing.rst
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@ -24,13 +24,15 @@ DOI for the LAMMPS code
LAMMPS developers use the `Zenodo service at CERN
<https://zenodo.org/>`_ to create digital object identifies (DOI) for
stable releases of the LAMMPS code. There are two types of DOIs for the
LAMMPS source code: 1) the canonical DOI for **all** versions of LAMMPS,
which will always point to the latest stable release version is:
LAMMPS source code: the canonical DOI for **all** versions of LAMMPS,
which will always point to the **latest** stable release version is:
`DOI: 10.5281/zenodo.3726416 <https://dx.doi/org/10.5281/zenodo.3726416>`_
- DOI: `10.5281/zenodo.3726416 <https://dx.doi.org/10.5281/zenodo.3726416>`_
In addition there are DOIs for individual stable releases starting with
the `3 March 2020 version, DOI:10.5281/zenodo.3726417 <https://dx.doi/org/10.5281/zenodo.3726416>`_
In addition there are DOIs for individual stable releases. Currently there are:
- 3 March 2020 version: `DOI:10.5281/zenodo.3726417 <https://dx.doi.org/10.5281/zenodo.3726417>`_
- 29 October 2020 version: `DOI:10.5281/zenodo.4157471 <https://dx.doi.org/10.5281/zenodo.4157471>`_
Home page

2
doc/src/Packages_details.rst
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@ -1036,9 +1036,11 @@ the usual manner via MD. Various pair, fix, and compute styles.
* :doc:`pair_style spin/dipole/long <pair_spin_dipole>`
* :doc:`pair_style spin/dmi <pair_spin_dmi>`
* :doc:`pair_style spin/exchange <pair_spin_exchange>`
* :doc:`pair_style spin/exchange/biquadratic <pair_spin_exchange>`
* :doc:`pair_style spin/magelec <pair_spin_magelec>`
* :doc:`pair_style spin/neel <pair_spin_neel>`
* :doc:`fix nve/spin <fix_nve_spin>`
* :doc:`fix langevin/spin <fix_langevin_spin>`
* :doc:`fix precession/spin <fix_precession_spin>`
* :doc:`compute spin <compute_spin>`
* :doc:`neb/spin <neb_spin>`

2
doc/src/atc_output.rst
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@ -14,7 +14,7 @@ Syntax
* AtC fixID = ID of :doc:`fix atc <fix_atc>` instance
* *output* or *output index* = name of the AtC sub-command
* filename_prefix = prefix for data files (for *output*)
* frequency = frequency of output in time-steps (for *output*)
* frequency = frequency of output in timesteps (for *output*)
* optional keywords for *output*:
- text = creates text output of index, step and nodal variable values for unique nodes

2
doc/src/fix_filter_corotate.rst
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@ -56,7 +56,7 @@ is slightly modified only for the computation of long-range forces. A
good cluster decomposition constitutes in building clusters which
contain the fastest covalent bonds inside clusters.
If the clusters are chosen suitably, the :doc:`run_style respa <run_style>` is stable for outer time-steps of at least 8fs.
If the clusters are chosen suitably, the :doc:`run_style respa <run_style>` is stable for outer timesteps of at least 8fs.
----------

2
doc/src/fix_precession_spin.rst
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@ -62,7 +62,7 @@ with:
The field value in Tesla is multiplied by the gyromagnetic
ratio, :math:`g \cdot \mu_B/\hbar`, converting it into a precession frequency in
rad.THz (in metal units and with :math:`\mu_B = 5.788 eV/T`).
rad.THz (in metal units and with :math:`\mu_B = 5.788\cdot 10^{-5}` eV/T).
As a comparison, the figure below displays the simulation of a
single spin (of norm :math:`\mu_i = 1.0`) submitted to an external

4
doc/src/fix_rx.rst
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@ -90,10 +90,10 @@ accepted, *h* is increased by a proportional amount, and the next ODE step is be
Otherwise, *h* is shrunk and the ODE step is repeated.
Run-time diagnostics are available for the rkf45 ODE solver. The frequency
(in time-steps) that diagnostics are reported is controlled by the last (optional)
(in timesteps) that diagnostics are reported is controlled by the last (optional)
12th argument. A negative frequency means that diagnostics are reported once at the
end of each run. A positive value N means that the diagnostics are reported once
per N time-steps.
per N timesteps.
The diagnostics report the average # of integrator steps and RHS function evaluations
and run-time per ODE as well as the average/RMS/min/max per process. If the

3
doc/src/fix_shake.rst
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@ -1,9 +1,12 @@
.. index:: fix shake
.. index:: fix shake/kk
.. index:: fix rattle
fix shake command
=================
Accelerator Variants: *shake/kk*
fix rattle command
==================

11
doc/src/molecule.rst
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@ -201,11 +201,12 @@ bonds between nuclear cores and Drude electrons in a different manner.
Each section is listed below in alphabetic order. The format of each
section is described including the number of lines it must contain and
rules (if any) for whether it can appear in the data file. In each
case the ID is ignored; it is simply included for readability, and
should be a number from 1 to Nlines for the section, indicating which
atom (or bond, etc) the entry applies to. The lines are assumed to be
listed in order from 1 to Nlines, but LAMMPS does not check for this.
rules (if any) for whether it can appear in the data file. For per-
atom sections, entries should be numbered from 1 to Natoms (where
Natoms is the number of atoms in the template), indicating which atom
(or bond, etc) the entry applies to. Per-atom sections need to
include a setting for every atom, but the atoms can be listed in any
order.
----------

2
doc/src/pair_atm.rst
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@ -143,7 +143,7 @@ combinations, else an error will result.
Mixing, shift, table, tail correction, restart, rRESPA info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
This pair styles do not support the :doc:`pair_modify <pair_modify>`
This pair style do not support the :doc:`pair_modify <pair_modify>`
mix, shift, table, and tail options.
This pair style writes its information to :doc:`binary restart files

2
doc/src/pair_buck_long.rst
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@ -117,7 +117,7 @@ global Coulombic cutoff is allowed.
Mixing, shift, table, tail correction, restart, rRESPA info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
This pair styles does not support mixing. Thus, coefficients for all
This pair style does not support mixing. Thus, coefficients for all
I,J pairs must be specified explicitly.
This pair style supports the :doc:`pair_modify <pair_modify>` shift

2
doc/src/pair_gayberne.rst
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@ -160,7 +160,7 @@ For atom type pairs I,J and I != J, the epsilon and sigma coefficients
and cutoff distance for this pair style can be mixed. The default mix
value is *geometric*\ . See the "pair_modify" command for details.
This pair styles supports the :doc:`pair_modify <pair_modify>` shift
This pair style supports the :doc:`pair_modify <pair_modify>` shift
option for the energy of the Lennard-Jones portion of the pair
interaction, but only for sphere-sphere interactions. There is no
shifting performed for ellipsoidal interactions due to the anisotropic

9
doc/src/pair_lcbop.rst
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@ -75,14 +75,15 @@ This pair style can only be used via the *pair* keyword of the
Restrictions
""""""""""""
This pair styles is part of the MANYBODY package. It is only enabled
if LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
This pair style is part of the MANYBODY package. It is only enabled
if LAMMPS was built with that package.
See the :doc:`Build package <Build_package>` doc page for more info.
This pair potential requires the :doc:`newton <newton>` setting to be
"on" for pair interactions.
The C.lcbop potential file provided with LAMMPS (see the potentials
directory) is parameterized for metal :doc:`units <units>`. You can use
The ``C.lcbop`` potential file provided with LAMMPS (see the potentials
directory) is parameterized for :doc:`metal units <units>`. You can use
the LCBOP potential with any LAMMPS units, but you would need to
create your own LCBOP potential file with coefficients listed in the
appropriate units if your simulation does not use "metal" units.

2
doc/src/pair_polymorphic.rst
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@ -298,7 +298,7 @@ described above. For each of the F functions, nx values are listed.
Mixing, shift, table, tail correction, restart, rRESPA info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
This pair styles does not support the :doc:`pair_modify <pair_modify>`
This pair style does not support the :doc:`pair_modify <pair_modify>`
shift, table, and tail options.
This pair style does not write their information to :doc:`binary restart

2
doc/src/pair_resquared.rst
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@ -173,7 +173,7 @@ equation for the Hamaker constant presented here. Mixing of sigma and
epsilon followed by calculation of the energy prefactors using the
equations above is recommended.
This pair styles supports the :doc:`pair_modify <pair_modify>` shift
This pair style supports the :doc:`pair_modify <pair_modify>` shift
option for the energy of the Lennard-Jones portion of the pair
interaction, but only for sphere-sphere interactions. There is no
shifting performed for ellipsoidal interactions due to the anisotropic

161
doc/src/pair_spin_exchange.rst
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@ -1,14 +1,19 @@
.. index:: pair_style spin/exchange
.. index:: pair_style spin/exchange/biquadratic
pair_style spin/exchange command
================================
pair_style spin/exchange/biquadratic command
============================================
Syntax
""""""
.. code-block:: LAMMPS
pair_style spin/exchange cutoff
pair_style spin/exchange/biquadratic cutoff
* cutoff = global cutoff pair (distance in metal units)
@ -19,7 +24,11 @@ Examples
pair_style spin/exchange 4.0
pair_coeff * * exchange 4.0 0.0446928 0.003496 1.4885
pair_coeff 1 2 exchange 6.0 -0.01575 0.0 1.965
pair_coeff 1 2 exchange 6.0 -0.01575 0.0 1.965 offset yes
pair_style spin/exchange/biquadratic 4.0
pair_coeff * * biquadratic 4.0 0.05 0.03 1.48 0.05 0.03 1.48 offset no
pair_coeff 1 2 biquadratic 6.0 -0.01 0.0 1.9 0.0 0.1 19
Description
"""""""""""
@ -31,69 +40,163 @@ pairs of magnetic spins:
H_{ex} = -\sum_{i,j}^N J_{ij} (r_{ij}) \,\vec{s}_i \cdot \vec{s}_j
where :math:`\vec{s}_i` and :math:`\vec{s}_j` are two neighboring magnetic spins of two particles,
:math:`r_{ij} = \vert \vec{r}_i - \vec{r}_j \vert` is the inter-atomic distance between the two
particles. The summation is over pairs of nearest neighbors.
:math:`J(r_{ij})` is a function defining the intensity and the sign of the exchange
interaction for different neighboring shells. This function is defined as:
where :math:`\vec{s}_i` and :math:`\vec{s}_j` are two unit vectors representing
the magnetic spins of two particles (usually atoms), and
:math:`r_{ij} = \vert \vec{r}_i - \vec{r}_j \vert` is the inter-atomic distance
between those two particles. The summation is over pairs of nearest neighbors.
:math:`J(r_{ij})` is a function defining the intensity and the sign of the
exchange interaction for different neighboring shells.
Style *spin/exchange/biquadratic* computes a biquadratic exchange interaction
between pairs of magnetic spins:
.. math::
{J}\left( r_{ij} \right) = 4 a \left( \frac{r_{ij}}{d} \right)^2 \left( 1 - b \left( \frac{r_{ij}}{d} \right)^2 \right) e^{-\left( \frac{r_{ij}}{d} \right)^2 }\Theta (R_c - r_{ij})
H_{bi} = -\sum_{i, j}^{N} {J}_{ij} \left(r_{ij} \right)\,
\vec{s}_{i}\cdot \vec{s}_{j}
-\sum_{i, j}^{N} {K}_{ij} \left(r_{ij} \right)\,
\left(\vec{s}_{i}\cdot
\vec{s}_{j}\right)^2
where :math:`a`, :math:`b` and :math:`d` are the three constant coefficients defined in the associated
"pair_coeff" command, and :math:`R_c` is the radius cutoff associated to
the pair interaction (see below for more explanations).
where :math:`\vec{s}_i`, :math:`\vec{s}_j`, :math:`r_{ij}` and
:math:`J(r_{ij})` have the same definitions as above, and :math:`K(r_{ij})` is
a second function, defining the intensity and the sign of the biquadratic term.
The coefficients :math:`a`, :math:`b`, and :math:`d` need to be fitted so that the function above matches with
the value of the exchange interaction for the :math:`N` neighbor shells taken into account.
Examples and more explanations about this function and its parameterization are reported
in :ref:`(Tranchida) <Tranchida3>`.
The interatomic dependence of :math:`J(r_{ij})` and :math:`K(r_{ij})` in both
interactions above is defined by the following function:
.. math::
{f}\left( r_{ij} \right) = 4 a \left( \frac{r_{ij}}{d} \right)^2
\left( 1 - b \left( \frac{r_{ij}}{d} \right)^2 \right)
e^{-\left( \frac{r_{ij}}{d} \right)^2 }\Theta (R_c - r_{ij})
where :math:`a`, :math:`b` and :math:`d` are the three constant coefficients
defined in the associated "pair_coeff" command, and :math:`R_c` is the radius
cutoff associated to the pair interaction (see below for more explanations).
The coefficients :math:`a`, :math:`b`, and :math:`d` need to be fitted so that
the function above matches with the value of the exchange interaction for the
:math:`N` neighbor shells taken into account.
Examples and more explanations about this function and its parameterization
are reported in :ref:`(Tranchida) <Tranchida3>`.
When a *spin/exchange/biquadratic* pair style is defined, six coefficients
(three for :math:`J(r_{ij})`, and three for :math:`K(r_{ij})`) have to be
fitted.
From this exchange interaction, each spin :math:`i` will be submitted
to a magnetic torque :math:`\vec{\omega}`, and its associated atom can be submitted to a
force :math:`\vec{F}` for spin-lattice calculations (see :doc:`fix nve/spin <fix_nve_spin>`),
such as:
to a magnetic torque :math:`\vec{\omega}_{i}`, and its associated atom can be
submitted to a force :math:`\vec{F}_{i}` for spin-lattice calculations (see
:doc:`fix nve/spin <fix_nve_spin>`), such as:
.. math::
\vec{\omega}_{i} = \frac{1}{\hbar} \sum_{j}^{Neighb} {J}
\left(r_{ij} \right)\,\vec{s}_{j}
~~{\rm and}~~
\vec{F}_{i} = \sum_{j}^{Neighb} \frac{\partial {J} \left(r_{ij} \right)}{ \partial r_{ij}} \left( \vec{s}_{i}\cdot \vec{s}_{j} \right) \vec{e}_{ij}
\vec{F}_{i} = \sum_{j}^{Neighb} \frac{\partial {J} \left(r_{ij} \right)}{
\partial r_{ij}} \left( \vec{s}_{i}\cdot \vec{s}_{j} \right) \vec{e}_{ij}
with :math:`\hbar` the Planck constant (in metal units), and :math:`\vec{e}_{ij} = \frac{\vec{r}_i - \vec{r}_j}{\vert \vec{r}_i-\vec{r}_j \vert}` the unit
with :math:`\hbar` the Planck constant (in metal units), and :math:`\vec{e}_{ij}
= \frac{\vec{r}_i - \vec{r}_j}{\vert \vec{r}_i-\vec{r}_j \vert}` the unit
vector between sites :math:`i` and :math:`j`.
Equivalent forces and magnetic torques are generated for the biquadratic term
when a *spin/exchange/biquadratic* pair style is defined.
More details about the derivation of these torques/forces are reported in
:ref:`(Tranchida) <Tranchida3>`.
For the *spin/exchange* pair style, the following coefficients must be defined
for each pair of atoms types via the :doc:`pair_coeff <pair_coeff>` command as in
the examples above, or in the data file or restart files read by the
:doc:`read_data <read_data>` or :doc:`read_restart <read_restart>` commands, and
set in the following order:
For the *spin/exchange* and *spin/exchange/biquadratic* pair styles, the
following coefficients must be defined for each pair of atoms types via the
:doc:`pair_coeff <pair_coeff>` command as in the examples above, or in the data
file or restart files read by the :doc:`read_data <read_data>` or
:doc:`read_restart <read_restart>` commands, and set in the following order:
* :math:`R_c` (distance units)
* :math:`a` (energy units)
* :math:`b` (adim parameter)
* :math:`d` (distance units)
Note that :math:`R_c` is the radius cutoff of the considered exchange interaction,
and :math:`a`, :math:`b` and :math:`d` are the three coefficients performing the parameterization
of the function :math:`J(r_{ij})` defined above.
for the *spin/exchange* pair style, and:
* :math:`R_c` (distance units)
* :math:`a_j` (energy units)
* :math:`b_j` (adim parameter)
* :math:`d_j` (distance units)
* :math:`a_k` (energy units)
* :math:`b_k` (adim parameter)
* :math:`d_k` (distance units)
for the *spin/exchange/biquadratic* pair style.
Note that :math:`R_c` is the radius cutoff of the considered exchange
interaction, and :math:`a`, :math:`b` and :math:`d` are the three coefficients
performing the parameterization of the function :math:`J(r_{ij})` defined
above (in the *biquadratic* style, :math:`a_j`, :math:`b_j`, :math:`d_j` and
:math:`a_k`, :math:`b_k`, :math:`d_k` are the coefficients of :math:`J(r_{ij})`
and :math:`K(r_{ij})` respectively).
None of those coefficients is optional. If not specified, the
*spin/exchange* pair style cannot be used.
----------
**Offsetting magnetic forces and energies**\ :
For spin-lattice simulation, it can be useful to offset the
mechanical forces and energies generated by the exchange
interaction.
The *offset* keyword allows to apply this offset.
By setting *offset* to *yes*, the energy definitions above are
replaced by:
.. math::
H_{ex} = -\sum_{i,j}^N J_{ij} (r_{ij}) \,[ \vec{s}_i \cdot \vec{s}_j-1 ]
for the *spin/exchange* pair style, and:
.. math::
H_{bi} = -\sum_{i, j}^{N} {J}_{ij} \left(r_{ij} \right)\,
[ \vec{s}_{i}\cdot \vec{s}_{j} -1 ]
-\sum_{i, j}^{N} {K}_{ij} \left(r_{ij} \right)\,
[ \left(\vec{s}_{i}\cdot
\vec{s}_{j}\right)^2 -1]
for the *spin/exchange/biquadratic* pair style.
Note that this offset only affects the calculation of the energy
and mechanical forces. It does not modify the calculation of the
precession vectors (and thus does no impact the purely magnetic
properties).
This ensures that when all spins are aligned, the magnetic energy
and the associated mechanical forces (and thus the pressure
generated by the magnetic potential) are null.
.. note::
This offset term can be very important when calculations such as
equations of state (energy vs volume, or energy vs pressure) are
being performed. Indeed, setting the *offset* term ensures that
at the ground state of the crystal and at the equilibrium magnetic
configuration (typically ferromagnetic), the pressure is null,
as expected.
Otherwise, magnetic forces could generate a residual pressure.
When the *offset* option is set to *no*, no offset is applied
(also corresponding to the default option).
----------
Restrictions
""""""""""""
All the *pair/spin* styles are part of the SPIN package. These styles
are only enabled if LAMMPS was built with this package, and if the
atom_style "spin" was declared. See the :doc:`Build package <Build_package>` doc page for more info.
atom_style "spin" was declared.
See the :doc:`Build package <Build_package>` doc page for more info.
Related commands
""""""""""""""""
@ -105,7 +208,7 @@ Default
"""""""
none
The default *offset* keyword value is *no*.
----------

2
doc/src/pair_srp.rst
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@ -124,7 +124,7 @@ at the cutoff distance :math:`r_c`.
Mixing, shift, table, tail correction, restart, rRESPA info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
This pair styles does not support mixing.
This pair style does not support mixing.
This pair style does not support the :doc:`pair_modify <pair_modify>`
shift option for the energy of the pair interaction. Note that as

1
doc/src/pair_style.rst
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@ -305,6 +305,7 @@ accelerated styles exist.
* :doc:`spin/dipole/long <pair_spin_dipole>` -
* :doc:`spin/dmi <pair_spin_dmi>` -
* :doc:`spin/exchange <pair_spin_exchange>` -
* :doc:`spin/exchange/biquadratic <pair_spin_exchange>` -
* :doc:`spin/magelec <pair_spin_magelec>` -
* :doc:`spin/neel <pair_spin_neel>` -
* :doc:`srp <pair_srp>` -

2
doc/src/read_dump.rst
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@ -370,6 +370,8 @@ needed to generate absolute, unscaled coordinates.
Restrictions
""""""""""""
The *native* dump file reader does not support binary .bin dump files.
To read gzipped dump files, you must compile LAMMPS with the
-DLAMMPS_GZIP option. See the :doc:`Build settings <Build_settings>`
doc page for details.

29
doc/src/rerun.rst
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@ -99,14 +99,15 @@ files do not match the specified output frequency.
----------
If more than one dump file is specified, the dump files are read one
after the other. It is assumed that snapshot timesteps will be in
ascending order. If a snapshot is encountered that is not in
ascending order, it will skip the snapshot until it reads one that is.
after the other in the order specified. It is assumed that snapshot
timesteps will be in ascending order. If a snapshot is encountered that
is not in ascending order, it will skip the snapshot until it reads one
that is.
This allows skipping of a duplicate snapshot (same timestep),
e.g. that appeared at the end of one file and beginning of the next.
However if you specify a series of dump files in an incorrect order
(with respect to the timesteps they contain), you may skip large
numbers of snapshots
numbers of snapshots.
Note that the dump files specified as part of the *dump* keyword can be
parallel files, i.e. written as multiple files either per processor
@ -118,17 +119,24 @@ and write parallel dump files.
The *first*\ , *last*\ , *every*\ , *skip* keywords determine which
snapshots are read from the dump file(s). Snapshots are skipped until
they have a timestamp >= *Nfirst*\ . When a snapshot with a timestamp >
*Nlast* is encountered, the rerun command finishes. Note below that
they have a timestep >= *Nfirst*\ . When a snapshot with a timestep >
*Nlast* is encountered, the rerun command finishes. Note that
the defaults for *first* and *last* are to read all snapshots. If the
*every* keyword is set to a value > 0, then only snapshots with
timestamps that are a multiple of *Nevery* are read (the first
timesteps that are a multiple of *Nevery* are read (the first
snapshot is always read). If *Nevery* = 0, then this criterion is
ignored, i.e. every snapshot is read that meets the other criteria.
If the *skip* keyword is used, then after the first snapshot is read,
every Nth snapshot is read, where N = *Nskip*\ . E.g. if *Nskip* = 3,
then only 1 out of every 3 snapshots is read, assuming the snapshot
timestamp is also consistent with the other criteria.
timestep is also consistent with the other criteria.
.. note::
Not all dump formats contain the timestep and not all dump readers
support reading it. In that case individual snapshots are assigned
consecutive timestep numbers starting at 1.
The *start* and *stop* keywords do not affect which snapshots are read
from the dump file(s). Rather, they have the same meaning that they
@ -205,9 +213,8 @@ thermodynamic output or new dump file output.
Restrictions
""""""""""""
To read gzipped dump files, you must compile LAMMPS with the
-DLAMMPS_GZIP option. See the :doc:`Build settings <Build_settings>`
doc page for details.
The *rerun* command is subject to all restrictions of
the :doc:`read_dump <read_dump>` command.
Related commands
""""""""""""""""