forked from lijiext/lammps
added fix_latte.txt
This commit is contained in:
parent
60faca2896
commit
39daf3c6f6
|
@ -0,0 +1,171 @@
|
|||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
|
||||
:line
|
||||
|
||||
fix latte command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
fix ID group-ID latte peID :pre
|
||||
|
||||
ID, group-ID are documented in "fix"_fix.html command
|
||||
latte = style name of this fix command
|
||||
peID = NULL or ID of compute used to calculate per-atom energy :ul
|
||||
|
||||
[Examples:]
|
||||
|
||||
fix dftb all latte NULL :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
This fix style is a wrapper on the self-consistent charge transfer density functional
|
||||
based tight binding (DFTB) code LATTE. If you download and build LATTE, it can be called
|
||||
as a library by LAMMPS via this fix to run dynamics or perform energy
|
||||
minimization using DFTB forces and energies computed by LATTE.
|
||||
|
||||
LATTE is principally developed and supported by M.J. Cawkwell
|
||||
and co-workers at Los Alamos National Laboratories (LANL).
|
||||
See the full list of contributors in the /LATTE/README.md file.
|
||||
|
||||
The LATTE program needs to be compiled as a library and linked with LAMMPS.
|
||||
LATTE can be downloaded at
|
||||
"https://github.com/lanl/LATTE"_https://github.com/lanl/LATTE.
|
||||
and instructions on how to build LATTE on your system and be found
|
||||
in the lib/latte/README file.
|
||||
|
||||
Once LAMMPS is build with the LATTE package, you can run the example input
|
||||
scripts for molecular dynamics or geometry optimization that are found in examples/latte.
|
||||
|
||||
NOTE: LATTE is a code for performing self-consistent charge transfer
|
||||
tight-binding (SC-TB) calculations of total energies and the forces acting
|
||||
on atoms in molecules and solids. This tight-binding method is becoming more
|
||||
and more popular and widely used in chemistry, biochemistry, material science,
|
||||
etc. The SC-TB formalism is derived from an expansion of the Kohn-Sham
|
||||
density functional to second order in charge fluctuations about a reference charge of
|
||||
overlapping atom-centered densities and bond integrals are parameterized using
|
||||
a Slater-Koster tight-binding approach. This procedure, which usually is referred
|
||||
to as the DFTB method has been described in detail by ("Elstner"_#Elstner) and ("Finnis"_#Finnis)
|
||||
and coworkers. Our work follows
|
||||
that of Elstner closely with respect to the physical model. However, the development of
|
||||
LATTE is geared principally toward large-scale, long duration, microcanonical quantum-based
|
||||
Born-Oppenheimer molecular dynamics (QMD) simulations.
|
||||
One of the main bottlenecks of an electronic structure calculation is the solution
|
||||
of the generalized eigenvalue problem which scales with the cube of the
|
||||
system size O(N^3). The Theoretical and Computer sciences divisions at
|
||||
Los Alamos National Laboratory have accumulated a large experience
|
||||
addressing this issue by calculating the density matrix directly instead
|
||||
of using diagonalization. We typically use a recursive sparse Fermi-operator expansion
|
||||
using second-order spectral projection functions (SP2-algorithm), which was introduced
|
||||
by Niklasson in 2002 ("Niklasson2002"_#Niklasson2002), ("Rubensson"_#Rubensson),
|
||||
("Mniszewski"_#Mniszewski).
|
||||
When the matrices involved in the recursive expansion are
|
||||
sufficiently sparse, the calculation of the density matrix scales linearly as a function of the
|
||||
system size O(N). Another important feature is the extended Lagrangian framework
|
||||
for Born-Oppenheimer molecular dynamics (XL-BOMD) ("Niklasson2008"_#Niklasson2008)
|
||||
("Niklasson2014"_#Niklasson2014), ("Niklasson2017"_#Niklasson2017)
|
||||
that allows for a drastic reduction or even a complete removal of the
|
||||
iterative self-consistent field optimization. Often only a single density matrix
|
||||
calculation per molecular dynamics time step is required, yet total energy stability is well maintained.
|
||||
The SP2 and XL-BOMD techniques enables stable linear scaling MD simulations with a very
|
||||
small computational overhead. This opens a number of opportunities in many different
|
||||
areas of chemistry and materials science, as we now can simulate larger system
|
||||
sizes and longer time scales ("Cawkwell2012"_#Cawkwell2012), ("Negre2016"_#Negre2016).
|
||||
|
||||
The {peID} argument is not yet supported by fix latte, so it must be
|
||||
specified as NULL. Eventually it will be used to enable LAMMPS to
|
||||
calculate a Coulomb potential as an alternative to LATTE performing
|
||||
the calculation.
|
||||
|
||||
A step-by-step tutorial can be follwed at: "LAMMPS-LATTE tutorial"_https://github.com/lanl/LATTE/wiki/Using-LATTE-through-LAMMPS
|
||||
|
||||
|
||||
:line
|
||||
|
||||
[Restart, fix_modify, output, run start/stop, minimize info:]
|
||||
|
||||
No information about this fix is written to "binary restart
|
||||
files"_restart.html.
|
||||
|
||||
The "fix_modify"_fix_modify.html {energy} option is supported by this
|
||||
fix to add the potential energy computed by LATTE to the system's
|
||||
potential energy as part of "thermodynamic output"_thermo_style.html.
|
||||
|
||||
This fix computes a global scalar which can be accessed by various
|
||||
"output commands"_Section_howto.html#howto_15. The scalar is the
|
||||
potential energy discussed above. The scalar value calculated by this
|
||||
fix is "extensive".
|
||||
|
||||
No parameter of this fix can be used with the {start/stop} keywords of
|
||||
the "run"_run.html command.
|
||||
|
||||
The DFTB forces computed by LATTE via this fix are imposed during an
|
||||
energy minimization, invoked by the "minimize"_minimize.html command.
|
||||
|
||||
NOTE: If you want the potential energy associated with the DFTB
|
||||
forces to be included in the total potential energy of the system (the
|
||||
quantity being minimized), you MUST enable the
|
||||
"fix_modify"_fix_modify.html {energy} option for this fix.
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
This fix is part of the LATTE package. It is only enabled if LAMMPS
|
||||
was built with that package. See the "Making
|
||||
LAMMPS"_Section_start.html#start_3 section for more info.
|
||||
|
||||
Currently, LAMMPS must be run in serial or as a single MPI task, to use
|
||||
this fix. This is typically not a bottleneck, since LATTE will be
|
||||
doing 99% or more of the work to compute quantum-accurate forces.
|
||||
|
||||
NOTE: NEB calculations can be done using this fix. To do this LATTE will
|
||||
still be compiled serial but LAMMPS will be compiled with mpi.
|
||||
|
||||
You must use metal units, as set by the "units"_units command to use
|
||||
this fix.
|
||||
|
||||
[Related commands:] none
|
||||
|
||||
[Default:] none
|
||||
|
||||
:line
|
||||
|
||||
:link(Elstner)
|
||||
[(Elstner)] M. Elstner, D. Poresag, G. Jungnickel, J. Elsner, M. Haugk, T. Frauenheim,
|
||||
S. Suhai, and G. Seifert, Phys. Rev. B, 58, 7260 (1998).
|
||||
|
||||
:link(Elstner1)
|
||||
[(Elstner)] M. Elstner, D. Poresag, G. Jungnickel, J. Elsner, M. Haugk, T. Frauenheim,
|
||||
S. Suhai, and G. Seifert, Phys. Rev. B, 58, 7260 (1998).
|
||||
|
||||
:link(Finnis)
|
||||
[(Finnis)] M. W. Finnis, A. T. Paxton, M. Methfessel, and M. van Schilfgarde,
|
||||
Phys. Rev. Lett., 81, 5149 (1998).
|
||||
|
||||
:link(Mniszewski)
|
||||
[(Mniszewski)] S. M. Mniszewski, M. J. Cawkwell, M. E. Wall, J. Mohd-Yusof, N. Bock, T. C.
|
||||
Germann, and A. M. N. Niklasson, J. Chem. Theory Comput., 11, 4644 (2015).
|
||||
|
||||
:link(Niklasson2002)
|
||||
[(Niklasson2002)] A. M. N. Niklasson, Phys. Rev. B, 66, 155115 (2002).
|
||||
|
||||
:link(Rubensson)
|
||||
[(Rubensson)] E. H. Rubensson, A. M. N. Niklasson, SIAM J. Sci. Comput. 36 (2), 147-170, (2014).
|
||||
|
||||
:link(Niklasson2008)
|
||||
[(Niklasson2008)] A. M. N. Niklasson, Phys. Rev. Lett., 100, 123004 (2008).
|
||||
|
||||
:link(Niklasson2014)
|
||||
[(Niklasson2014)] A. M. N. Niklasson and M. Cawkwell, J. Chem. Phys., 141, 164123, (2014).
|
||||
|
||||
:link(Niklasson2014)
|
||||
[(Niklasson2017)] A. M. N. Niklasson, J. Chem. Phys., 147, 054103 (2017).
|
||||
|
||||
:link(Niklasson2012)
|
||||
[(Niklasson2017)] A. M. N. Niklasson, M. J. Cawkwell, Phys. Rev. B, 86 (17), 174308 (2012).
|
||||
|
||||
:link(Negre2016)
|
||||
[(Negre2016)] C. F. A. Negre, S. M. Mniszewski, M. J. Cawkwell, N. Bock, M. E. Wall,
|
||||
and A. M. N. Niklasson, J. Chem. Theory Comp., 12, 3063 (2016).
|
Loading…
Reference in New Issue