git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14950 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
355
doc/html/_sources/pair_eff.txt
Normal file
355
doc/html/_sources/pair_eff.txt
Normal file
@ -0,0 +1,355 @@
|
||||
.. index:: pair_style eff/cut
|
||||
|
||||
pair_style eff/cut command
|
||||
==========================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
pair_style eff/cut cutoff keyword args ...
|
||||
|
||||
* cutoff = global cutoff for Coulombic interactions
|
||||
* zero or more keyword/value pairs may be appended
|
||||
.. parsed-literal::
|
||||
|
||||
keyword = *limit/eradius* or *pressure/evirials* or *ecp*
|
||||
*limit/eradius* args = none
|
||||
*pressure/evirials* args = none
|
||||
*ecp* args = type element type element ...
|
||||
type = LAMMPS atom type (1 to Ntypes)
|
||||
element = element symbol (e.g. H, Si)
|
||||
|
||||
|
||||
|
||||
Examples
|
||||
""""""""
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
pair_style eff/cut 39.7
|
||||
pair_style eff/cut 40.0 limit/eradius
|
||||
pair_style eff/cut 40.0 limit/eradius pressure/evirials
|
||||
pair_style eff/cut 40.0 ecp 1 Si 3 C
|
||||
pair_coeff * *
|
||||
pair_coeff 2 2 20.0
|
||||
pair_coeff 1 s 0.320852 2.283269 0.814857
|
||||
pair_coeff 3 p 22.721015 0.728733 1.103199 17.695345 6.693621
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
This pair style contains a LAMMPS implementation of the electron Force
|
||||
Field (eFF) potential currently under development at Caltech, as
|
||||
described in :ref:`(Jaramillo-Botero) <Jaramillo-Botero>`. The eFF for Z<6
|
||||
was first introduced by :ref:`(Su) <Su>` in 2007. It has been extended to
|
||||
higher Zs by using effective core potentials (ECPs) that now cover up
|
||||
to 2nd and 3rd row p-block elements of the periodic table.
|
||||
|
||||
eFF can be viewed as an approximation to QM wave packet dynamics and
|
||||
Fermionic molecular dynamics, combining the ability of electronic
|
||||
structure methods to describe atomic structure, bonding, and chemistry
|
||||
in materials, and of plasma methods to describe nonequilibrium
|
||||
dynamics of large systems with a large number of highly excited
|
||||
electrons. Yet, eFF relies on a simplification of the electronic
|
||||
wavefunction in which electrons are described as floating Gaussian
|
||||
wave packets whose position and size respond to the various dynamic
|
||||
forces between interacting classical nuclear particles and spherical
|
||||
Gaussian electron wavepackets. The wavefunction is taken to be a
|
||||
Hartree product of the wave packets. To compensate for the lack of
|
||||
explicit antisymmetry in the resulting wavefunction, a spin-dependent
|
||||
Pauli potential is included in the Hamiltonian. Substituting this
|
||||
wavefunction into the time-dependent Schrodinger equation produces
|
||||
equations of motion that correspond - to second order - to classical
|
||||
Hamiltonian relations between electron position and size, and their
|
||||
conjugate momenta. The N-electron wavefunction is described as a
|
||||
product of one-electron Gaussian functions, whose size is a dynamical
|
||||
variable and whose position is not constrained to a nuclear
|
||||
center. This form allows for straightforward propagation of the
|
||||
wavefunction, with time, using a simple formulation from which the
|
||||
equations of motion are then integrated with conventional MD
|
||||
algorithms. In addition to this spin-dependent Pauli repulsion
|
||||
potential term between Gaussians, eFF includes the electron kinetic
|
||||
energy from the Gaussians. These two terms are based on
|
||||
first-principles quantum mechanics. On the other hand, nuclei are
|
||||
described as point charges, which interact with other nuclei and
|
||||
electrons through standard electrostatic potential forms.
|
||||
|
||||
The full Hamiltonian (shown below), contains then a standard
|
||||
description for electrostatic interactions between a set of
|
||||
delocalized point and Gaussian charges which include, nuclei-nuclei
|
||||
(NN), electron-electron (ee), and nuclei-electron (Ne). Thus, eFF is a
|
||||
mixed QM-classical mechanics method rather than a conventional force
|
||||
field method (in which electron motions are averaged out into ground
|
||||
state nuclear motions, i.e a single electronic state, and particle
|
||||
interactions are described via empirically parameterized interatomic
|
||||
potential functions). This makes eFF uniquely suited to simulate
|
||||
materials over a wide range of temperatures and pressures where
|
||||
electronically excited and ionized states of matter can occur and
|
||||
coexist. Furthermore, the interactions between particles -nuclei and
|
||||
electrons- reduce to the sum of a set of effective pairwise potentials
|
||||
in the eFF formulation. The *eff/cut* style computes the pairwise
|
||||
Coulomb interactions between nuclei and electrons (E_NN,E_Ne,E_ee),
|
||||
and the quantum-derived Pauli (E_PR) and Kinetic energy interactions
|
||||
potentials between electrons (E_KE) for a total energy expression
|
||||
given as,
|
||||
|
||||
.. image:: Eqs/eff_energy_expression.jpg
|
||||
:align: center
|
||||
|
||||
The individual terms are defined as follows:
|
||||
|
||||
.. image:: Eqs/eff_KE.jpg
|
||||
:align: center
|
||||
|
||||
.. image:: Eqs/eff_NN.jpg
|
||||
:align: center
|
||||
|
||||
.. image:: Eqs/eff_Ne.jpg
|
||||
:align: center
|
||||
|
||||
.. image:: Eqs/eff_ee.jpg
|
||||
:align: center
|
||||
|
||||
.. image:: Eqs/eff_Pauli.jpg
|
||||
:align: center
|
||||
|
||||
where, s_i correspond to the electron sizes, the sigmas i's to the
|
||||
fixed spins of the electrons, Z_i to the charges on the nuclei, R_ij
|
||||
to the distances between the nuclei or the nuclei and electrons, and
|
||||
r_ij to the distances between electrons. For additional details see
|
||||
:ref:`(Jaramillo-Botero) <Jaramillo-Botero>`.
|
||||
|
||||
The overall electrostatics energy is given in Hartree units of energy
|
||||
by default and can be modified by an energy-conversion constant,
|
||||
according to the units chosen (see :doc:`electron_units <units>`). The
|
||||
cutoff Rc, given in Bohrs (by default), truncates the interaction
|
||||
distance. The recommended cutoff for this pair style should follow
|
||||
the minimum image criterion, i.e. half of the minimum unit cell
|
||||
length.
|
||||
|
||||
Style *eff/long* (not yet available) computes the same interactions as
|
||||
style *eff/cut* except that an additional damping factor is applied so
|
||||
it can be used in conjunction with the
|
||||
:doc:`kspace_style <kspace_style>` command and its *ewald* or *pppm*
|
||||
option. The Coulombic cutoff specified for this style means that
|
||||
pairwise interactions within this distance are computed directly;
|
||||
interactions outside that distance are computed in reciprocal space.
|
||||
|
||||
This potential is designed to be used with :doc:`atom_style electron <atom_style>` definitions, in order to handle the
|
||||
description of systems with interacting nuclei and explicit electrons.
|
||||
|
||||
The following coefficients must be defined for each pair of atoms
|
||||
types via the :doc:`pair_coeff <pair_coeff>` command as in the examples
|
||||
above, or in the data file or restart files read by the
|
||||
:doc:`read_data <read_data>` or :doc:`read_restart <read_restart>`
|
||||
commands, or by mixing as described below:
|
||||
|
||||
* cutoff (distance units)
|
||||
|
||||
For *eff/cut*\ , the cutoff coefficient is optional. If it is not used
|
||||
(as in some of the examples above), the default global value specified
|
||||
in the pair_style command is used.
|
||||
|
||||
For *eff/long* (not yet available) no cutoff will be specified for an
|
||||
individual I,J type pair via the :doc:`pair_coeff <pair_coeff>` command.
|
||||
All type pairs use the same global cutoff specified in the pair_style
|
||||
command.
|
||||
|
||||
|
||||
----------
|
||||
|
||||
|
||||
The *limit/eradius* and *pressure/evirials* keywrods are optional.
|
||||
Neither or both must be specified. If not specified they are unset.
|
||||
|
||||
The *limit/eradius* keyword is used to restrain electron size from
|
||||
becoming excessively diffuse at very high temperatures were the
|
||||
Gaussian wave packet representation breaks down, and from expanding as
|
||||
free particles to infinite size. If unset, electron radius is free to
|
||||
increase without bounds. If set, a restraining harmonic potential of
|
||||
the form E = 1/2k_ss^2 for s > L_box/2, where k_s = 1 Hartrees/Bohr^2,
|
||||
is applied on the electron radius.
|
||||
|
||||
The *pressure/evirials* keyword is used to control between two types
|
||||
of pressure computation: if unset, the computed pressure does not
|
||||
include the electronic radial virials contributions to the total
|
||||
pressure (scalar or tensor). If set, the computed pressure will
|
||||
include the electronic radial virial contributions to the total
|
||||
pressure (scalar and tensor).
|
||||
|
||||
The *ecp* keyword is used to associate an ECP representation for a
|
||||
particular atom type. The ECP captures the orbital overlap between a
|
||||
core pseudo particle and valence electrons within the Pauli repulsion.
|
||||
A list of type:element-symbol pairs may be provided for all ECP
|
||||
representations, after the "ecp" keyword.
|
||||
|
||||
.. note::
|
||||
|
||||
Default ECP parameters are provided for C, N, O, Al, and Si.
|
||||
Users can modify these using the pair_coeff command as exemplified
|
||||
above. For this, the User must distinguish between two different
|
||||
functional forms supported, one that captures the orbital overlap
|
||||
assuming the s-type core interacts with an s-like valence electron
|
||||
(s-s) and another that assumes the interaction is s-p. For systems
|
||||
that exhibit significant p-character (e.g. C, N, O) the s-p form is
|
||||
recommended. The "s" ECP form requires 3 parameters and the "p" 5
|
||||
parameters.
|
||||
|
||||
.. note::
|
||||
|
||||
there are two different pressures that can be reported for eFF
|
||||
when defining this pair_style, one (default) that considers electrons
|
||||
do not contribute radial virial components (i.e. electrons treated as
|
||||
incompressible 'rigid' spheres) and one that does. The radial
|
||||
electronic contributions to the virials are only tallied if the
|
||||
flexible pressure option is set, and this will affect both global and
|
||||
per-atom quantities. In principle, the true pressure of a system is
|
||||
somewhere in between the rigid and the flexible eFF pressures, but,
|
||||
for most cases, the difference between these two pressures will not be
|
||||
significant over long-term averaged runs (i.e. even though the energy
|
||||
partitioning changes, the total energy remains similar).
|
||||
|
||||
|
||||
----------
|
||||
|
||||
|
||||
.. note::
|
||||
|
||||
This implemention of eFF gives a reasonably accurate description
|
||||
for systems containing nuclei from Z = 1-6 in "all electron"
|
||||
representations. For systems with increasingly non-spherical
|
||||
electrons, Users should use the ECP representations. ECPs are now
|
||||
supported and validated for most of the 2nd and 3rd row elements of
|
||||
the p-block. Predefined parameters are provided for C, N, O, Al, and
|
||||
Si. The ECP captures the orbital overlap between the core and valence
|
||||
electrons (i.e. Pauli repulsion) with one of the functional forms:
|
||||
|
||||
.. image:: Eqs/eff_ECP1.jpg
|
||||
:align: center
|
||||
|
||||
.. image:: Eqs/eff_ECP2.jpg
|
||||
:align: center
|
||||
|
||||
Where the 1st form correspond to core interactions with s-type valence
|
||||
electrons and the 2nd to core interactions with p-type valence
|
||||
electrons.
|
||||
|
||||
The current version adds full support for models with fixed-core and
|
||||
ECP definitions. to enable larger timesteps (i.e. by avoiding the
|
||||
high frequency vibrational modes -translational and radial- of the 2 s
|
||||
electrons), and in the ECP case to reduce the increased orbital
|
||||
complexity in higher Z elements (up to Z<18). A fixed-core should be
|
||||
defined with a mass that includes the corresponding nuclear mass plus
|
||||
the 2 s electrons in atomic mass units (2x5.4857990943e-4), and a
|
||||
radius equivalent to that of minimized 1s electrons (see examples
|
||||
under /examples/USER/eff/fixed-core). An pseudo-core should be
|
||||
described with a mass that includes the corresponding nuclear mass,
|
||||
plus all the core electrons (i.e no outer shell electrons), and a
|
||||
radius equivalent to that of a corresponding minimized full-electron
|
||||
system. The charge for a pseudo-core atom should be given by the
|
||||
number of outer shell electrons.
|
||||
|
||||
In general, eFF excels at computing the properties of materials in
|
||||
extreme conditions and tracing the system dynamics over multi-picosend
|
||||
timescales; this is particularly relevant where electron excitations
|
||||
can change significantly the nature of bonding in the system. It can
|
||||
capture with surprising accuracy the behavior of such systems because
|
||||
it describes consistently and in an unbiased manner many different
|
||||
kinds of bonds, including covalent, ionic, multicenter, ionic, and
|
||||
plasma, and how they interconvert and/or change when they become
|
||||
excited. eFF also excels in computing the relative thermochemistry of
|
||||
isodemic reactions and conformational changes, where the bonds of the
|
||||
reactants are of the same type as the bonds of the products. eFF
|
||||
assumes that kinetic energy differences dominate the overall exchange
|
||||
energy, which is true when the electrons present are nearly spherical
|
||||
and nodeless and valid for covalent compounds such as dense hydrogen,
|
||||
hydrocarbons, and diamond; alkali metals (e.g. lithium), alkali earth
|
||||
metals (e.g. beryllium) and semimetals such as boron; and various
|
||||
compounds containing ionic and/or multicenter bonds, such as boron
|
||||
dihydride.
|
||||
|
||||
|
||||
----------
|
||||
|
||||
|
||||
**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
|
||||
|
||||
For atom type pairs I,J and I != J, the cutoff distance for the
|
||||
*eff/cut* style can be mixed. The default mix value is *geometric*\ .
|
||||
See the "pair_modify" command for details.
|
||||
|
||||
The :doc:`pair_modify <pair_modify>` shift option is not relevant for
|
||||
these pair styles.
|
||||
|
||||
The *eff/long* (not yet available) style supports the
|
||||
:doc:`pair_modify <pair_modify>` table option for tabulation of the
|
||||
short-range portion of the long-range Coulombic interaction.
|
||||
|
||||
These pair styles do not support the :doc:`pair_modify <pair_modify>`
|
||||
tail option for adding long-range tail corrections to energy and
|
||||
pressure.
|
||||
|
||||
These pair styles write their information to :doc:`binary restart files <restart>`, so pair_style and pair_coeff commands do not need
|
||||
to be specified in an input script that reads a restart file.
|
||||
|
||||
These pair styles can only be used via the *pair* keyword of the
|
||||
:doc:`run_style respa <run_style>` command. They do not support the
|
||||
*inner*\ , *middle*\ , *outer* keywords.
|
||||
|
||||
|
||||
----------
|
||||
|
||||
|
||||
Restrictions
|
||||
""""""""""""
|
||||
|
||||
|
||||
These pair styles will only be enabled if LAMMPS is built with the
|
||||
USER-EFF package. It will only be enabled if LAMMPS was built with
|
||||
that package. See the :ref:`Making LAMMPS <start_3>`
|
||||
section for more info.
|
||||
|
||||
These pair styles require that particles store electron attributes
|
||||
such as radius, radial velocity, and radital force, as defined by the
|
||||
:doc:`atom_style <atom_style>`. The *electron* atom style does all of
|
||||
this.
|
||||
|
||||
Thes pair styles require you to use the :doc:`comm_modify vel yes <comm_modify>` command so that velocites are stored by ghost
|
||||
atoms.
|
||||
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
:doc:`pair_coeff <pair_coeff>`
|
||||
|
||||
Default
|
||||
"""""""
|
||||
|
||||
If not specified, limit_eradius = 0 and pressure_with_evirials = 0.
|
||||
|
||||
|
||||
----------
|
||||
|
||||
|
||||
.. _Su:
|
||||
|
||||
|
||||
|
||||
**(Su)** Su and Goddard, Excited Electron Dynamics Modeling of Warm
|
||||
Dense Matter, Phys Rev Lett, 99:185003 (2007).
|
||||
|
||||
.. _Jaramillo-Botero:
|
||||
|
||||
|
||||
|
||||
**(Jaramillo-Botero)** Jaramillo-Botero, Su, Qi, Goddard, Large-scale,
|
||||
Long-term Non-adiabatic Electron Molecular Dynamics for Describing
|
||||
Material Properties and Phenomena in Extreme Environments, J Comp
|
||||
Chem, 32, 497-512 (2011).
|
||||
|
||||
|
||||
.. _lws: http://lammps.sandia.gov
|
||||
.. _ld: Manual.html
|
||||
.. _lc: Section_commands.html#comm
|
||||
Reference in New Issue
Block a user