LATTE package doc update and some small code changes
This commit is contained in:
Steve Plimpton
@ -96,6 +96,7 @@ Package, Description, Doc page, Example, Library
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"KIM"_#KIM, OpenKIM wrapper, "pair_style kim"_pair_kim.html, kim, ext
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"KOKKOS"_#KOKKOS, Kokkos-enabled styles, "Section 5.3.3"_accelerate_kokkos.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, -
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"KSPACE"_#KSPACE, long-range Coulombic solvers, "kspace_style"_kspace_style.html, peptide, -
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"LATTE"_#LATTE, quantum DFTB forces via LATTE, "fix latte"_fix_latte.html, latte, ext
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"MANYBODY"_#MANYBODY, many-body potentials, "pair_style tersoff"_pair_tersoff.html, shear, -
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"MC"_#MC, Monte Carlo options, "fix gcmc"_fix_gcmc.html, -, -
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"MEAM"_#MEAM, modified EAM potential, "pair_style meam"_pair_meam.html, meam, int
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@ -695,6 +696,65 @@ bench/in.rhodo :ul
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:line
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LATTE package :link(LATTE),h4
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[Contents:]
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A fix command which wraps the LATTE DFTB code, so that molecular
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dynamics can be run with LAMMPS using density-functional tight-binding
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quantum forces calculated by LATTE.
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More information on LATTE can be found at this web site:
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"https://github.com/lanl/LATTE"_#latte_home. A brief technical
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description is given with the "fix latte"_fix_latte.html command.
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:link(latte_home,https://github.com/lanl/LATTE)
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[Authors:] Christian Negre (LANL) and Steve Plimpton (Sandia). LATTE
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itself is developed at Los Alamos National Laboratory by Marc
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Cawkwell, Anders Niklasson, and Christian Negre.
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[Install or un-install:]
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Before building LAMMPS with this package, you must first download and
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build the LATTE library. You can do this manually if you prefer;
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follow the instructions in lib/latte/README. You can also do it in
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one step from the lammps/src dir, using a command like these, which
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simply invokes the lib/latte/Install.py script with the specified
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args:
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make lib-latte # print help message
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make lib-latte args="-b" # download and build in lib/latte/LATTE-master
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make lib-latte args="-p $HOME/latte" # use existing LATTE installation in $HOME/latte
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make lib-latte args="-b -m gfortran" # download and build in lib/latte and
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# copy Makefile.lammps.gfortran to Makefile.lammps
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Note that 3 symbolic (soft) links, "includelink" and "liblink" and
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"filelink", are created in lib/latte to point into the LATTE home dir.
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When LAMMPS builds in src it will use these links. You should
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also check that the Makefile.lammps file you create is apporpriate
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for the compiler you use on your system to build LATTE.
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You can then install/un-install the package and build LAMMPS in the
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usual manner:
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make yes-latte
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make machine :pre
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make no-latte
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make machine :pre
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[Supporting info:]
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src/LATTE: filenames -> commands
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src/LATTE/README
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lib/latte/README
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"fix latte"_fix_latte.html
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examples/latte
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"LAMMPS-LATTE tutorial"_https://github.com/lanl/LATTE/wiki/Using-LATTE-through-LAMMPS :ul
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:line
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MANYBODY package :link(MANYBODY),h4
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[Contents:]
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200
doc/src/fix_latte.txt
Normal file
200
doc/src/fix_latte.txt
Normal file
@ -0,0 +1,200 @@
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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Section_commands.html#comm)
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:line
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fix latte command :h3
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[Syntax:]
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fix ID group-ID latte peID :pre
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ID, group-ID are documented in "fix"_fix.html command
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latte = style name of this fix command
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peID = NULL or ID of compute used to calculate per-atom energy :ul
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[Examples:]
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fix dftb all latte NULL :pre
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[Description:]
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This fix style is a wrapper on the self-consistent charge transfer
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density functional based tight binding (DFTB) code LATTE. If you
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download and build LATTE, it can be called as a library by LAMMPS via
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this fix to run dynamics or perform energy minimization using DFTB
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forces and energies computed by LATTE.
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LATTE is principally developed and supported by Marc Cawkwell and
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co-workers at Los Alamos National Laboratory (LANL). See the full
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list of contributors in the src/LATTE/README file.
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To use this fix, the LATTE program needs to be compiled as a library
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and linked with LAMMPS. LATTE can be downloaded (or cloned) from
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"https://github.com/lanl/LATTE"_https://github.com/lanl/LATTE.
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Instructions on how to download and build LATTE on your system can be
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found in the lib/latte/README. Note that you can also use the "make
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lib-latte" command from the LAMMPS src directory to automate this
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process.
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Once LAMMPS is built with the LATTE package, you can run the example
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input scripts for molecular dynamics or energy minimization that are
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found in examples/latte.
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A step-by-step tutorial can be follwed at: "LAMMPS-LATTE
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tutorial"_https://github.com/lanl/LATTE/wiki/Using-LATTE-through-LAMMPS
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The {peID} argument is not yet supported by fix latte, so it must be
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specified as NULL. Eventually it will be used to enable LAMMPS to
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calculate a Coulomb potential as an alternative to LATTE performing
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the calculation.
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:line
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LATTE is a code for performing self-consistent charge transfer
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tight-binding (SC-TB) calculations of total energies and the forces
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acting on atoms in molecules and solids. This tight-binding method is
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becoming more and more popular and widely used in chemistry,
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biochemistry, material science, etc.
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The SC-TB formalism is derived from an expansion of the Kohn-Sham
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density functional to second order in charge fluctuations about a
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reference charge of overlapping atom-centered densities and bond
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integrals are parameterized using a Slater-Koster tight-binding
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approach. This procedure, which usually is referred to as the DFTB
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method has been described in detail by ("Elstner"_#Elstner) and
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("Finnis"_#Finnis) and coworkers.
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The work of the LATTE developers follows that of Elstner closely with
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respect to the physical model. However, the development of LATTE is
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geared principally toward large-scale, long duration, microcanonical
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quantum-based Born-Oppenheimer molecular dynamics (QMD) simulations.
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One of the main bottlenecks of an electronic structure calculation is
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the solution of the generalized eigenvalue problem which scales with
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the cube of the system size O(N^3).
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The Theoretical and Computer sciences divisions at Los Alamos National
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Laboratory have accumulated large experience addressing this issue by
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calculating the density matrix directly instead of using
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diagonalization. We typically use a recursive sparse Fermi-operator
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expansion using second-order spectral projection functions
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(SP2-algorithm), which was introduced by Niklasson in 2002
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("Niklasson2002"_#Niklasson2002), ("Rubensson"_#Rubensson),
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("Mniszewski"_#Mniszewski). When the matrices involved in the
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recursive expansion are sufficiently sparse, the calculation of the
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density matrix scales linearly as a function of the system size O(N).
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Another important feature is the extended Lagrangian framework for
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Born-Oppenheimer molecular dynamics (XL-BOMD)
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("Niklasson2008"_#Niklasson2008) ("Niklasson2014"_#Niklasson2014),
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("Niklasson2017"_#Niklasson2017) that allows for a drastic reduction
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or even a complete removal of the iterative self-consistent field
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optimization. Often only a single density matrix calculation per
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molecular dynamics time step is required, yet total energy stability
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is well maintained. The SP2 and XL-BOMD techniques enables stable
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linear scaling MD simulations with a very small computational
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overhead. This opens a number of opportunities in many different
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areas of chemistry and materials science, as we now can simulate
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larger system sizes and longer time scales
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("Cawkwell2012"_#Cawkwell2012), ("Negre2016"_#Negre2016).
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:line
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[Restart, fix_modify, output, run start/stop, minimize info:]
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No information about this fix is written to "binary restart
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files"_restart.html.
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The "fix_modify"_fix_modify.html {energy} option is supported by this
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fix to add the potential energy computed by LATTE to the system's
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potential energy as part of "thermodynamic output"_thermo_style.html.
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This fix computes a global scalar which can be accessed by various
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"output commands"_Section_howto.html#howto_15. The scalar is the
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potential energy discussed above. The scalar value calculated by this
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fix is "extensive".
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No parameter of this fix can be used with the {start/stop} keywords of
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the "run"_run.html command.
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The DFTB forces computed by LATTE via this fix are imposed during an
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energy minimization, invoked by the "minimize"_minimize.html command.
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NOTE: If you want the potential energy associated with the DFTB
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forces to be included in the total potential energy of the system (the
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quantity being minimized), you MUST enable the
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"fix_modify"_fix_modify.html {energy} option for this fix.
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[Restrictions:]
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This fix is part of the LATTE package. It is only enabled if LAMMPS
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was built with that package. See the "Making
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LAMMPS"_Section_start.html#start_3 section for more info.
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You must use metal units, as set by the "units"_units command to use
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this fix.
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Currently, LAMMPS must be run in serial or as a single MPI task, to
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use this fix. This is typically not a bottleneck, since LATTE will be
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doing 99% or more of the work to compute quantum-accurate forces.
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NOTE: NEB calculations can be done using this fix using multiple
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replicas and running LAMMPS in parallel. However, each replica must
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be run on a single MPI task. For details, see the "neb"_neb.html
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command and -partition command-line explained in "Section
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2.6"_Section_start.html#start_6 of the manual.
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[Related commands:] none
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[Default:] none
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:line
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:link(Elstner)
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[(Elstner)] M. Elstner, D. Poresag, G. Jungnickel, J. Elsner,
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M. Haugk, T. Frauenheim, S. Suhai, and G. Seifert, Phys. Rev. B, 58,
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7260 (1998).
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:link(Elstner1)
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[(Elstner)] M. Elstner, D. Poresag, G. Jungnickel, J. Elsner,
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M. Haugk, T. Frauenheim, S. Suhai, and G. Seifert, Phys. Rev. B, 58,
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7260 (1998).
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:link(Finnis)
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[(Finnis)] M. W. Finnis, A. T. Paxton, M. Methfessel, and M. van
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Schilfgarde, Phys. Rev. Lett., 81, 5149 (1998).
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:link(Mniszewski)
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[(Mniszewski)] S. M. Mniszewski, M. J. Cawkwell, M. E. Wall,
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J. Mohd-Yusof, N. Bock, T. C. Germann, and A. M. N. Niklasson,
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J. Chem. Theory Comput., 11, 4644 (2015).
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:link(Niklasson2002)
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[(Niklasson2002)] A. M. N. Niklasson, Phys. Rev. B, 66, 155115 (2002).
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:link(Rubensson)
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[(Rubensson)] E. H. Rubensson, A. M. N. Niklasson, SIAM
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J. Sci. Comput. 36 (2), 147-170, (2014).
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:link(Niklasson2008)
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[(Niklasson2008)] A. M. N. Niklasson, Phys. Rev. Lett., 100, 123004
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(2008).
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:link(Niklasson2014)
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[(Niklasson2014)] A. M. N. Niklasson and M. Cawkwell, J. Chem. Phys.,
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141, 164123, (2014).
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:link(Niklasson2014)
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[(Niklasson2017)] A. M. N. Niklasson, J. Chem. Phys., 147, 054103 (2017).
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:link(Niklasson2012)
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[(Niklasson2017)] A. M. N. Niklasson, M. J. Cawkwell, Phys. Rev. B, 86
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(17), 174308 (2012).
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:link(Negre2016)
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[(Negre2016)] C. F. A. Negre, S. M. Mniszewski, M. J. Cawkwell,
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N. Bock, M. E. Wall, and A. M. N. Niklasson, J. Chem. Theory Comp.,
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12, 3063 (2016).
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