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Richard Berger
2020-11-29 12:26:30 -05:00
parent 62f5f3a3b8 a5858e350c
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2
doc/src/Commands_bond.rst
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@ -35,6 +35,7 @@ OPT.
* :doc:`class2 (ko) <bond_class2>`
* :doc:`fene (iko) <bond_fene>`
* :doc:`fene/expand (o) <bond_fene_expand>`
* :doc:`gaussian <bond_gaussian>`
* :doc:`gromos (o) <bond_gromos>`
* :doc:`harmonic (iko) <bond_harmonic>`
* :doc:`harmonic/shift (o) <bond_harmonic_shift>`
@ -84,6 +85,7 @@ OPT.
* :doc:`dipole (o) <angle_dipole>`
* :doc:`fourier (o) <angle_fourier>`
* :doc:`fourier/simple (o) <angle_fourier_simple>`
* :doc:`gaussian <angle_gaussian>` - multicentered Gaussian-based angle potential
* :doc:`harmonic (iko) <angle_harmonic>`
* :doc:`mm3 <angle_mm3>`
* :doc:`quartic (o) <angle_quartic>`

1
doc/src/Commands_fix.rst
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@ -62,6 +62,7 @@ OPT.
* :doc:`efield <fix_efield>`
* :doc:`ehex <fix_ehex>`
* :doc:`electron/stopping <fix_electron_stopping>`
* :doc:`electron/stopping/fit <fix_electron_stopping>`
* :doc:`enforce2d (k) <fix_enforce2d>`
* :doc:`eos/cv <fix_eos_cv>`
* :doc:`eos/table <fix_eos_table>`

69
doc/src/angle_gaussian.rst Normal file
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@ -0,0 +1,69 @@
.. index:: angle_style gaussian
angle_style gaussian command
================================
Syntax
""""""
.. code-block:: LAMMPS
angle_style gaussian
Examples
""""""""
.. code-block:: LAMMPS
angle_style gaussian
angle_coeff 1 300.0 2 0.0128 0.375 80.0 0.0730 0.148 123.0
Description
"""""""""""
The *gaussian* angle style uses the potential:
.. math::
E = -k_B T ln\left(\sum_{i=1}^{n} \frac{A_i}{w_i \sqrt{\pi/2}} exp\left( \frac{-(\theta-\theta_{i})^2}{w_i^2})\right) \right)
This analytical form is a suitable potential for obtaining
mesoscale effective force fields which can reproduce target atomistic distributions :ref:`(Milano) <Milano1>`
The following coefficients must be defined for each angle type via the
:doc:`angle_coeff <angle_coeff>` command as in the example above, or in
the data file or restart files read by the :doc:`read_data <read_data>`
or :doc:`read_restart <read_restart>` commands:
* T temperature at which the potential was derived
* :math:`n` (integer >=1)
* :math:`A_1` (-)
* :math:`w_1` (-)
* :math:`\theta_1` (degrees)
* ...
* :math:`A_n` (-)
* :math:`w_n` (-)
* :math:`\theta_n` (degrees)
Restrictions
""""""""""""
This angle style can only be used if LAMMPS was built with the
USER-MISC package. See the :doc:`Build package <Build_package>` doc
page for more info.
Related commands
""""""""""""""""
:doc:`angle_coeff <angle_coeff>`
Default
"""""""
none
----------
.. _Milano1:
**(Milano)** G. Milano, S. Goudeau, F. Mueller-Plathe, J. Polym. Sci. B Polym. Phys. 43, 871 (2005).

1
doc/src/angle_style.rst
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@ -87,6 +87,7 @@ of (g,i,k,o,t) to indicate which accelerated styles exist.
* :doc:`dipole <angle_dipole>` - angle that controls orientation of a point dipole
* :doc:`fourier <angle_fourier>` - angle with multiple cosine terms
* :doc:`fourier/simple <angle_fourier_simple>` - angle with a single cosine term
* :doc:`gaussian <angle_gaussian>` - multicentered Gaussian-based angle potential
* :doc:`harmonic <angle_harmonic>` - harmonic angle
* :doc:`mm3 <angle_mm3>` - anharmonic angle
* :doc:`quartic <angle_quartic>` - angle with cubic and quartic terms

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doc/src/bond_gaussian.rst Normal file
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@ -0,0 +1,70 @@
.. index:: bond_style gaussian
bond_style gaussian command
================================
Syntax
""""""
.. code-block:: LAMMPS
bond_style gaussian
Examples
""""""""
.. code-block:: LAMMPS
bond_style gaussian
bond_coeff 1 300.0 2 0.0128 0.375 3.37 0.0730 0.148 3.63
Description
"""""""""""
The *gaussian* bond style uses the potential:
.. math::
E = -k_B T ln\left(\sum_{i=1}^{n} \frac{A_i}{w_i \sqrt{\pi/2}} exp\left( \frac{-(r-r_{i})^2}{w_i^2})\right) \right)
This analytical form is a suitable potential for obtaining
mesoscale effective force fields which can reproduce target atomistic distributions :ref:`(Milano) <Milano0>`
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:
* T temperature at which the potential was derived
* :math:`n` (integer >=1)
* :math:`A_1` (-)
* :math:`w_1` (-)
* :math:`r_1` (length)
* ...
* :math:`A_n` (-)
* :math:`w_n` (-)
* :math:`r_n` (length)
Restrictions
""""""""""""
This bond style can only be used if LAMMPS was built with the
USER-MISC package. See the :doc:`Build package <Build_package>` doc
page for more info.
Related commands
""""""""""""""""
:doc:`bond_coeff <bond_coeff>`
Default
"""""""
none
----------
.. _Milano0:
**(Milano)** G. Milano, S. Goudeau, F. Mueller-Plathe, J. Polym. Sci. B Polym. Phys. 43, 871 (2005).

1
doc/src/bond_style.rst
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@ -87,6 +87,7 @@ accelerated styles exist.
* :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
* :doc:`gaussian <bond_gaussian>` - multicentered Gaussian-based bond potential
* :doc:`gromos <bond_gromos>` - GROMOS force field bond
* :doc:`harmonic <bond_harmonic>` - harmonic bond
* :doc:`harmonic/shift <bond_harmonic_shift>` - shifted harmonic bond

1
doc/src/fix.rst
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@ -205,6 +205,7 @@ accelerated styles exist.
* :doc:`efield <fix_efield>` - impose electric field on system
* :doc:`ehex <fix_ehex>` - enhanced heat exchange algorithm
* :doc:`electron/stopping <fix_electron_stopping>` - electronic stopping power as a friction force
* :doc:`electron/stopping/fit <fix_electron_stopping>` - electronic stopping power as a friction force
* :doc:`enforce2d <fix_enforce2d>` - zero out z-dimension velocity and force
* :doc:`eos/cv <fix_eos_cv>` -
* :doc:`eos/table <fix_eos_table>` -

52
doc/src/fix_electron_stopping.rst
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@ -1,28 +1,41 @@
.. index:: fix electron/stopping
.. index:: fix electron/stopping/fit
fix electron/stopping command
=============================
fix electron/stopping/fit command
=================================
Syntax
""""""
.. parsed-literal::
fix ID group-ID electron/stopping Ecut file keyword value ...
fix ID group-ID style args
* ID, group-ID are documented in :doc:`fix <fix>` command
* electron/stopping = style name of this fix command
* Ecut = minimum kinetic energy for electronic stopping (energy units)
* file = name of the file containing the electronic stopping power table
* zero or more keyword/value pairs may be appended to args
* keyword = *region* or *minneigh*
* style = *electron/stopping* or *electron/stopping/fit*
.. parsed-literal::
*electron/stopping* args = Ecut file keyword value ...
Ecut = minimum kinetic energy for electronic stopping (energy units)
file = name of the file containing the electronic stopping power table
*electron/stopping/fit* args = Ecut c1 c2 ...
Ecut = minimum kinetic energy for electronic stopping (energy units)
c1 c2 = linear and quadratic coefficients for the fitted quadratic polynomial
* zero or more keyword/value pairs may be appended to args for style = *electron/stopping*
.. parsed-literal::
keyword = *region* or *minneigh*
*region* value = region-ID
region-ID = region, whose atoms will be affected by this fix
region-ID = region whose atoms will be affected by this fix
*minneigh* value = minneigh
minneigh = minimum number of neighbors an atom to have stopping applied
minneigh = minimum number of neighbors an atom to have stopping applied
Examples
""""""""
@ -32,6 +45,8 @@ Examples
fix el all electron/stopping 10.0 elstop-table.txt
fix el all electron/stopping 10.0 elstop-table.txt minneigh 3
fix el mygroup electron/stopping 1.0 elstop-table.txt region bulk
fix 1 all electron/stopping/fit 4.63 3.3e-3 4.0e-8
fix 1 all electron/stopping/fit 3.49 1.8e-3 9.0e-8 7.57 4.2e-3 5.0e-8
Description
"""""""""""
@ -129,6 +144,19 @@ scientific publications, experimental databases or by using
of the impact parameter of the ion; these results can be used
to derive the stopping power.
----------
Style *electron/stopping/fit* calculates the electronic stopping power
and cumulative energy lost to the electron gas via a quadratic functional
and applies a drag force to the classical equations-of-motion for all
atoms moving above some minimum cutoff velocity (i.e., kinetic energy).
These coefficients can be determined by fitting a quadratic polynomial to
electronic stopping data predicted by, for example, SRIM or TD-DFT. Multiple
'Ecut c1 c2' values can be provided for multi-species simulations in the order
of the atom types. There is an examples/USER/misc/electron_stopping/ directory,
which illustrates uses of this command. Details of this implementation are
further described in :ref:`Stewart2018 <Stewart2018>` and :ref:`Lee2020 <Lee2020>`.
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
@ -181,3 +209,11 @@ The default is no limitation by region, and minneigh = 1.
.. _PASS:
**(PASS)** PASS webpage: https://www.sdu.dk/en/DPASS
.. _Stewart2018:
**(Stewart2018)** J.A. Stewart, et al. (2018) Journal of Applied Physics, 123(16), 165902.
.. _Lee2020:
**(Lee2020)** C.W. Lee, et al. (2020) Physical Review B, 102(2), 024107.

3
doc/src/package.rst
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@ -448,8 +448,7 @@ does not require atomic operations in the calculation of pair forces. For
that reason, *full* is the default setting for GPUs. However, when
running on CPUs, a *half* neighbor list is the default because it are
often faster, just as it is for non-accelerated pair styles. Similarly,
the *neigh/qeq* keyword determines how neighbor lists are built for :doc:`fix qeq/reax/kk <fix_qeq_reax>`. If not explicitly set, the value of
*neigh/qeq* will match *neigh*\ .
the *neigh/qeq* keyword determines how neighbor lists are built for :doc:`fix qeq/reax/kk <fix_qeq_reax>`.
If the *neigh/thread* keyword is set to *off*\ , then the KOKKOS package
threads only over atoms. However, for small systems, this may not expose