Loading doc/src/Section_packages.txt +60 −0 Original line number Original line Diff line number Diff line Loading @@ -96,6 +96,7 @@ Package, Description, Doc page, Example, Library "KIM"_#KIM, OpenKIM wrapper, "pair_style kim"_pair_kim.html, kim, ext "KIM"_#KIM, OpenKIM wrapper, "pair_style kim"_pair_kim.html, kim, ext "KOKKOS"_#KOKKOS, Kokkos-enabled styles, "Section 5.3.3"_accelerate_kokkos.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, - "KOKKOS"_#KOKKOS, Kokkos-enabled styles, "Section 5.3.3"_accelerate_kokkos.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, - "KSPACE"_#KSPACE, long-range Coulombic solvers, "kspace_style"_kspace_style.html, peptide, - "KSPACE"_#KSPACE, long-range Coulombic solvers, "kspace_style"_kspace_style.html, peptide, - "LATTE"_#LATTE, quantum DFTB forces via LATTE, "fix latte"_fix_latte.html, latte, ext "MANYBODY"_#MANYBODY, many-body potentials, "pair_style tersoff"_pair_tersoff.html, shear, - "MANYBODY"_#MANYBODY, many-body potentials, "pair_style tersoff"_pair_tersoff.html, shear, - "MC"_#MC, Monte Carlo options, "fix gcmc"_fix_gcmc.html, -, - "MC"_#MC, Monte Carlo options, "fix gcmc"_fix_gcmc.html, -, - "MEAM"_#MEAM, modified EAM potential, "pair_style meam"_pair_meam.html, meam, int "MEAM"_#MEAM, modified EAM potential, "pair_style meam"_pair_meam.html, meam, int Loading Loading @@ -695,6 +696,65 @@ bench/in.rhodo :ul :line :line LATTE package :link(LATTE),h4 [Contents:] A fix command which wraps the LATTE DFTB code, so that molecular dynamics can be run with LAMMPS using density-functional tight-binding quantum forces calculated by LATTE. More information on LATTE can be found at this web site: "https://github.com/lanl/LATTE"_#latte_home. A brief technical description is given with the "fix latte"_fix_latte.html command. :link(latte_home,https://github.com/lanl/LATTE) [Authors:] Christian Negre (LANL) and Steve Plimpton (Sandia). LATTE itself is developed at Los Alamos National Laboratory by Marc Cawkwell, Anders Niklasson, and Christian Negre. [Install or un-install:] Before building LAMMPS with this package, you must first download and build the LATTE library. You can do this manually if you prefer; follow the instructions in lib/latte/README. You can also do it in one step from the lammps/src dir, using a command like these, which simply invokes the lib/latte/Install.py script with the specified args: make lib-latte # print help message make lib-latte args="-b" # download and build in lib/latte/LATTE-master make lib-latte args="-p $HOME/latte" # use existing LATTE installation in $HOME/latte make lib-latte args="-b -m gfortran" # download and build in lib/latte and # copy Makefile.lammps.gfortran to Makefile.lammps Note that 3 symbolic (soft) links, "includelink" and "liblink" and "filelink", are created in lib/latte to point into the LATTE home dir. When LAMMPS builds in src it will use these links. You should also check that the Makefile.lammps file you create is apporpriate for the compiler you use on your system to build LATTE. You can then install/un-install the package and build LAMMPS in the usual manner: make yes-latte make machine :pre make no-latte make machine :pre [Supporting info:] src/LATTE: filenames -> commands src/LATTE/README lib/latte/README "fix latte"_fix_latte.html examples/latte "LAMMPS-LATTE tutorial"_https://github.com/lanl/LATTE/wiki/Using-LATTE-through-LAMMPS :ul :line MANYBODY package :link(MANYBODY),h4 MANYBODY package :link(MANYBODY),h4 [Contents:] [Contents:] Loading src/fix_latte.txt→doc/src/fix_latte.txt +200 −0 Original line number Original line Diff line number Diff line Loading @@ -22,66 +22,84 @@ fix dftb all latte NULL :pre [Description:] [Description:] This fix style is a wrapper on the self-consistent charge transfer density functional This fix style is a wrapper on the self-consistent charge transfer based tight binding (DFTB) code LATTE. If you download and build LATTE, it can be called density functional based tight binding (DFTB) code LATTE. If you as a library by LAMMPS via this fix to run dynamics or perform energy download and build LATTE, it can be called as a library by LAMMPS via minimization using DFTB forces and energies computed by LATTE. this fix to run dynamics or perform energy minimization using DFTB forces and energies computed by LATTE. LATTE is principally developed and supported by Marc Cawkwell and co-workers at Los Alamos National Laboratory (LANL). See the full list of contributors in the src/LATTE/README file. To use this fix, the LATTE program needs to be compiled as a library and linked with LAMMPS. LATTE can be downloaded (or cloned) from "https://github.com/lanl/LATTE"_https://github.com/lanl/LATTE. Instructions on how to download and build LATTE on your system can be found in the lib/latte/README. Note that you can also use the "make lib-latte" command from the LAMMPS src directory to automate this process. LATTE is principally developed and supported by M.J. Cawkwell Once LAMMPS is built with the LATTE package, you can run the example and co-workers at Los Alamos National Laboratories (LANL). input scripts for molecular dynamics or energy minimization that are See the full list of contributors in the /LATTE/README.md file. found in examples/latte. The LATTE program needs to be compiled as a library and linked with LAMMPS. A step-by-step tutorial can be follwed at: "LAMMPS-LATTE LATTE can be downloaded at tutorial"_https://github.com/lanl/LATTE/wiki/Using-LATTE-through-LAMMPS "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 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 specified as NULL. Eventually it will be used to enable LAMMPS to calculate a Coulomb potential as an alternative to LATTE performing calculate a Coulomb potential as an alternative to LATTE performing the calculation. 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 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. The work of the LATTE developers 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 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). :line :line Loading Loading @@ -116,16 +134,19 @@ This fix is part of the LATTE package. It is only enabled if LAMMPS was built with that package. See the "Making was built with that package. See the "Making LAMMPS"_Section_start.html#start_3 section for more info. 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 You must use metal units, as set by the "units"_units command to use this fix. this fix. 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 using multiple replicas and running LAMMPS in parallel. However, each replica must be run on a single MPI task. For details, see the "neb"_neb.html command and -partition command-line explained in "Section 2.6"_Section_start.html#start_6 of the manual. [Related commands:] none [Related commands:] none [Default:] none [Default:] none Loading @@ -133,39 +154,47 @@ this fix. :line :line :link(Elstner) :link(Elstner) [(Elstner)] M. Elstner, D. Poresag, G. Jungnickel, J. Elsner, M. Haugk, T. Frauenheim, [(Elstner)] M. Elstner, D. Poresag, G. Jungnickel, J. Elsner, S. Suhai, and G. Seifert, Phys. Rev. B, 58, 7260 (1998). M. Haugk, T. Frauenheim, S. Suhai, and G. Seifert, Phys. Rev. B, 58, 7260 (1998). :link(Elstner1) :link(Elstner1) [(Elstner)] M. Elstner, D. Poresag, G. Jungnickel, J. Elsner, M. Haugk, T. Frauenheim, [(Elstner)] M. Elstner, D. Poresag, G. Jungnickel, J. Elsner, S. Suhai, and G. Seifert, Phys. Rev. B, 58, 7260 (1998). M. Haugk, T. Frauenheim, S. Suhai, and G. Seifert, Phys. Rev. B, 58, 7260 (1998). :link(Finnis) :link(Finnis) [(Finnis)] M. W. Finnis, A. T. Paxton, M. Methfessel, and M. van Schilfgarde, [(Finnis)] M. W. Finnis, A. T. Paxton, M. Methfessel, and M. van Phys. Rev. Lett., 81, 5149 (1998). Schilfgarde, Phys. Rev. Lett., 81, 5149 (1998). :link(Mniszewski) :link(Mniszewski) [(Mniszewski)] S. M. Mniszewski, M. J. Cawkwell, M. E. Wall, J. Mohd-Yusof, N. Bock, T. C. [(Mniszewski)] S. M. Mniszewski, M. J. Cawkwell, M. E. Wall, Germann, and A. M. N. Niklasson, J. Chem. Theory Comput., 11, 4644 (2015). J. Mohd-Yusof, N. Bock, T. C. Germann, and A. M. N. Niklasson, J. Chem. Theory Comput., 11, 4644 (2015). :link(Niklasson2002) :link(Niklasson2002) [(Niklasson2002)] A. M. N. Niklasson, Phys. Rev. B, 66, 155115 (2002). [(Niklasson2002)] A. M. N. Niklasson, Phys. Rev. B, 66, 155115 (2002). :link(Rubensson) :link(Rubensson) [(Rubensson)] E. H. Rubensson, A. M. N. Niklasson, SIAM J. Sci. Comput. 36 (2), 147-170, (2014). [(Rubensson)] E. H. Rubensson, A. M. N. Niklasson, SIAM J. Sci. Comput. 36 (2), 147-170, (2014). :link(Niklasson2008) :link(Niklasson2008) [(Niklasson2008)] A. M. N. Niklasson, Phys. Rev. Lett., 100, 123004 (2008). [(Niklasson2008)] A. M. N. Niklasson, Phys. Rev. Lett., 100, 123004 (2008). :link(Niklasson2014) :link(Niklasson2014) [(Niklasson2014)] A. M. N. Niklasson and M. Cawkwell, J. Chem. Phys., 141, 164123, (2014). [(Niklasson2014)] A. M. N. Niklasson and M. Cawkwell, J. Chem. Phys., 141, 164123, (2014). :link(Niklasson2014) :link(Niklasson2014) [(Niklasson2017)] A. M. N. Niklasson, J. Chem. Phys., 147, 054103 (2017). [(Niklasson2017)] A. M. N. Niklasson, J. Chem. Phys., 147, 054103 (2017). :link(Niklasson2012) :link(Niklasson2012) [(Niklasson2017)] A. M. N. Niklasson, M. J. Cawkwell, Phys. Rev. B, 86 (17), 174308 (2012). [(Niklasson2017)] A. M. N. Niklasson, M. J. Cawkwell, Phys. Rev. B, 86 (17), 174308 (2012). :link(Negre2016) :link(Negre2016) [(Negre2016)] C. F. A. Negre, S. M. Mniszewski, M. J. Cawkwell, N. Bock, M. E. Wall, [(Negre2016)] C. F. A. Negre, S. M. Mniszewski, M. J. Cawkwell, and A. M. N. Niklasson, J. Chem. Theory Comp., 12, 3063 (2016). N. Bock, M. E. Wall, and A. M. N. Niklasson, J. Chem. Theory Comp., 12, 3063 (2016). examples/README +1 −0 Original line number Original line Diff line number Diff line Loading @@ -79,6 +79,7 @@ granregion: use of fix wall/region/gran as boundary on granular particles hugoniostat: Hugoniostat shock dynamics hugoniostat: Hugoniostat shock dynamics indent: spherical indenter into a 2d solid indent: spherical indenter into a 2d solid kim: use of potentials in Knowledge Base for Interatomic Models (KIM) kim: use of potentials in Knowledge Base for Interatomic Models (KIM) latte: use of LATTE density-functional tight-binding quantum code meam: MEAM test for SiC and shear (same as shear examples) meam: MEAM test for SiC and shear (same as shear examples) melt: rapid melt of 3d LJ system melt: rapid melt of 3d LJ system micelle: self-assembly of small lipid-like molecules into 2d bilayers micelle: self-assembly of small lipid-like molecules into 2d bilayers Loading examples/latte/data.sucrose_non_opt.lmpdeleted 100644 → 0 +0 −63 Original line number Original line Diff line number Diff line LAMMPS Description 45 atoms 3 atom types 0.0000000000000000 18.917000000000002 xlo xhi 0.0000000000000000 17.350999999999999 ylo yhi 0.0000000000000000 15.472000000000000 zlo zhi Masses 1 15.994915008544922 2 12.000000000000000 3 1.0078250169754028 Atoms 1 1 1 0.0 11.47359 7.39174 7.26456 2 1 2 0.0 12.66159 8.24474 7.53356 3 1 3 0.0 13.49759 7.72474 7.00656 4 1 2 0.0 12.92859 8.18374 9.02956 5 1 1 0.0 13.69659 9.10274 10.46556 6 1 2 0.0 12.83959 10.10474 6.64056 7 1 3 0.0 13.24359 10.33074 7.58456 8 1 1 0.0 13.17359 9.67874 5.60956 9 1 2 0.0 11.20559 10.26374 6.86456 10 1 3 0.0 11.22159 11.15674 6.18156 11 1 1 0.0 10.78559 10.69674 8.19156 12 1 2 0.0 10.23459 9.20474 6.34356 13 1 3 0.0 9.23359 9.62574 6.11656 14 1 1 0.0 10.73959 8.65074 5.08856 15 1 2 0.0 10.18759 8.08774 7.38056 16 1 3 0.0 10.03259 8.49174 8.42656 17 1 1 0.0 9.22959 7.03374 7.08156 18 1 2 0.0 7.79359 7.27874 7.34356 19 1 1 0.0 7.44259 8.64274 6.96956 20 1 2 0.0 7.01059 9.43674 8.13856 21 1 3 0.0 5.95059 9.74974 7.96256 22 1 2 0.0 7.08359 8.51474 9.35656 23 1 3 0.0 8.19359 8.08474 9.80956 24 1 1 0.0 5.86059 8.56174 10.14056 25 1 2 0.0 7.34259 7.10674 8.80356 26 1 3 0.0 6.37259 6.54074 8.80556 27 1 1 0.0 8.32159 6.38474 9.58156 28 1 2 0.0 7.89859 10.67174 8.17156 29 1 1 0.0 6.06859 12.11474 7.59256 30 1 2 0.0 7.47359 7.05174 5.99256 31 1 1 0.0 5.66359 6.54374 6.50656 32 1 3 0.0 12.00659 8.11374 9.61556 33 1 3 0.0 13.35859 7.21774 9.30856 34 1 3 0.0 13.67759 8.46774 11.22956 35 1 3 0.0 12.44459 9.34474 5.00556 36 1 3 0.0 11.54859 11.18274 8.59756 37 1 3 0.0 11.00959 7.71574 5.30056 38 1 3 0.0 5.09459 8.45474 9.52056 39 1 3 0.0 7.92859 6.23074 10.47756 40 1 3 0.0 8.53259 10.62974 7.23156 41 1 3 0.0 8.58159 10.63874 9.05856 42 1 3 0.0 6.42359 13.37374 7.86056 43 1 3 0.0 7.58559 6.90074 4.62256 44 1 3 0.0 7.35159 5.27974 6.61456 45 1 3 0.0 5.22759 6.18974 5.69256 examples/latte/in.latte.sucrose.min→examples/latte/in.latte.sucrose +4 −7 Original line number Original line Diff line number Diff line # simple water model with LATTE # simple sucrose model with LATTE units metal units metal atom_style full atom_style full Loading Loading @@ -34,10 +34,7 @@ fix_modify 2 energy yes thermo_style custom step temp pe etotal thermo_style custom step temp pe etotal # minimization # dynamics thermo 1 thermo 10 min_style cg run 100 min_modify dmax 0.1 min_modify line quadratic minimize 1.0e-6 1.0e-6 10000 10000 Loading
doc/src/Section_packages.txt +60 −0 Original line number Original line Diff line number Diff line Loading @@ -96,6 +96,7 @@ Package, Description, Doc page, Example, Library "KIM"_#KIM, OpenKIM wrapper, "pair_style kim"_pair_kim.html, kim, ext "KIM"_#KIM, OpenKIM wrapper, "pair_style kim"_pair_kim.html, kim, ext "KOKKOS"_#KOKKOS, Kokkos-enabled styles, "Section 5.3.3"_accelerate_kokkos.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, - "KOKKOS"_#KOKKOS, Kokkos-enabled styles, "Section 5.3.3"_accelerate_kokkos.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, - "KSPACE"_#KSPACE, long-range Coulombic solvers, "kspace_style"_kspace_style.html, peptide, - "KSPACE"_#KSPACE, long-range Coulombic solvers, "kspace_style"_kspace_style.html, peptide, - "LATTE"_#LATTE, quantum DFTB forces via LATTE, "fix latte"_fix_latte.html, latte, ext "MANYBODY"_#MANYBODY, many-body potentials, "pair_style tersoff"_pair_tersoff.html, shear, - "MANYBODY"_#MANYBODY, many-body potentials, "pair_style tersoff"_pair_tersoff.html, shear, - "MC"_#MC, Monte Carlo options, "fix gcmc"_fix_gcmc.html, -, - "MC"_#MC, Monte Carlo options, "fix gcmc"_fix_gcmc.html, -, - "MEAM"_#MEAM, modified EAM potential, "pair_style meam"_pair_meam.html, meam, int "MEAM"_#MEAM, modified EAM potential, "pair_style meam"_pair_meam.html, meam, int Loading Loading @@ -695,6 +696,65 @@ bench/in.rhodo :ul :line :line LATTE package :link(LATTE),h4 [Contents:] A fix command which wraps the LATTE DFTB code, so that molecular dynamics can be run with LAMMPS using density-functional tight-binding quantum forces calculated by LATTE. More information on LATTE can be found at this web site: "https://github.com/lanl/LATTE"_#latte_home. A brief technical description is given with the "fix latte"_fix_latte.html command. :link(latte_home,https://github.com/lanl/LATTE) [Authors:] Christian Negre (LANL) and Steve Plimpton (Sandia). LATTE itself is developed at Los Alamos National Laboratory by Marc Cawkwell, Anders Niklasson, and Christian Negre. [Install or un-install:] Before building LAMMPS with this package, you must first download and build the LATTE library. You can do this manually if you prefer; follow the instructions in lib/latte/README. You can also do it in one step from the lammps/src dir, using a command like these, which simply invokes the lib/latte/Install.py script with the specified args: make lib-latte # print help message make lib-latte args="-b" # download and build in lib/latte/LATTE-master make lib-latte args="-p $HOME/latte" # use existing LATTE installation in $HOME/latte make lib-latte args="-b -m gfortran" # download and build in lib/latte and # copy Makefile.lammps.gfortran to Makefile.lammps Note that 3 symbolic (soft) links, "includelink" and "liblink" and "filelink", are created in lib/latte to point into the LATTE home dir. When LAMMPS builds in src it will use these links. You should also check that the Makefile.lammps file you create is apporpriate for the compiler you use on your system to build LATTE. You can then install/un-install the package and build LAMMPS in the usual manner: make yes-latte make machine :pre make no-latte make machine :pre [Supporting info:] src/LATTE: filenames -> commands src/LATTE/README lib/latte/README "fix latte"_fix_latte.html examples/latte "LAMMPS-LATTE tutorial"_https://github.com/lanl/LATTE/wiki/Using-LATTE-through-LAMMPS :ul :line MANYBODY package :link(MANYBODY),h4 MANYBODY package :link(MANYBODY),h4 [Contents:] [Contents:] Loading
src/fix_latte.txt→doc/src/fix_latte.txt +200 −0 Original line number Original line Diff line number Diff line Loading @@ -22,66 +22,84 @@ fix dftb all latte NULL :pre [Description:] [Description:] This fix style is a wrapper on the self-consistent charge transfer density functional This fix style is a wrapper on the self-consistent charge transfer based tight binding (DFTB) code LATTE. If you download and build LATTE, it can be called density functional based tight binding (DFTB) code LATTE. If you as a library by LAMMPS via this fix to run dynamics or perform energy download and build LATTE, it can be called as a library by LAMMPS via minimization using DFTB forces and energies computed by LATTE. this fix to run dynamics or perform energy minimization using DFTB forces and energies computed by LATTE. LATTE is principally developed and supported by Marc Cawkwell and co-workers at Los Alamos National Laboratory (LANL). See the full list of contributors in the src/LATTE/README file. To use this fix, the LATTE program needs to be compiled as a library and linked with LAMMPS. LATTE can be downloaded (or cloned) from "https://github.com/lanl/LATTE"_https://github.com/lanl/LATTE. Instructions on how to download and build LATTE on your system can be found in the lib/latte/README. Note that you can also use the "make lib-latte" command from the LAMMPS src directory to automate this process. LATTE is principally developed and supported by M.J. Cawkwell Once LAMMPS is built with the LATTE package, you can run the example and co-workers at Los Alamos National Laboratories (LANL). input scripts for molecular dynamics or energy minimization that are See the full list of contributors in the /LATTE/README.md file. found in examples/latte. The LATTE program needs to be compiled as a library and linked with LAMMPS. A step-by-step tutorial can be follwed at: "LAMMPS-LATTE LATTE can be downloaded at tutorial"_https://github.com/lanl/LATTE/wiki/Using-LATTE-through-LAMMPS "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 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 specified as NULL. Eventually it will be used to enable LAMMPS to calculate a Coulomb potential as an alternative to LATTE performing calculate a Coulomb potential as an alternative to LATTE performing the calculation. 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 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. The work of the LATTE developers 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 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). :line :line Loading Loading @@ -116,16 +134,19 @@ This fix is part of the LATTE package. It is only enabled if LAMMPS was built with that package. See the "Making was built with that package. See the "Making LAMMPS"_Section_start.html#start_3 section for more info. 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 You must use metal units, as set by the "units"_units command to use this fix. this fix. 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 using multiple replicas and running LAMMPS in parallel. However, each replica must be run on a single MPI task. For details, see the "neb"_neb.html command and -partition command-line explained in "Section 2.6"_Section_start.html#start_6 of the manual. [Related commands:] none [Related commands:] none [Default:] none [Default:] none Loading @@ -133,39 +154,47 @@ this fix. :line :line :link(Elstner) :link(Elstner) [(Elstner)] M. Elstner, D. Poresag, G. Jungnickel, J. Elsner, M. Haugk, T. Frauenheim, [(Elstner)] M. Elstner, D. Poresag, G. Jungnickel, J. Elsner, S. Suhai, and G. Seifert, Phys. Rev. B, 58, 7260 (1998). M. Haugk, T. Frauenheim, S. Suhai, and G. Seifert, Phys. Rev. B, 58, 7260 (1998). :link(Elstner1) :link(Elstner1) [(Elstner)] M. Elstner, D. Poresag, G. Jungnickel, J. Elsner, M. Haugk, T. Frauenheim, [(Elstner)] M. Elstner, D. Poresag, G. Jungnickel, J. Elsner, S. Suhai, and G. Seifert, Phys. Rev. B, 58, 7260 (1998). M. Haugk, T. Frauenheim, S. Suhai, and G. Seifert, Phys. Rev. B, 58, 7260 (1998). :link(Finnis) :link(Finnis) [(Finnis)] M. W. Finnis, A. T. Paxton, M. Methfessel, and M. van Schilfgarde, [(Finnis)] M. W. Finnis, A. T. Paxton, M. Methfessel, and M. van Phys. Rev. Lett., 81, 5149 (1998). Schilfgarde, Phys. Rev. Lett., 81, 5149 (1998). :link(Mniszewski) :link(Mniszewski) [(Mniszewski)] S. M. Mniszewski, M. J. Cawkwell, M. E. Wall, J. Mohd-Yusof, N. Bock, T. C. [(Mniszewski)] S. M. Mniszewski, M. J. Cawkwell, M. E. Wall, Germann, and A. M. N. Niklasson, J. Chem. Theory Comput., 11, 4644 (2015). J. Mohd-Yusof, N. Bock, T. C. Germann, and A. M. N. Niklasson, J. Chem. Theory Comput., 11, 4644 (2015). :link(Niklasson2002) :link(Niklasson2002) [(Niklasson2002)] A. M. N. Niklasson, Phys. Rev. B, 66, 155115 (2002). [(Niklasson2002)] A. M. N. Niklasson, Phys. Rev. B, 66, 155115 (2002). :link(Rubensson) :link(Rubensson) [(Rubensson)] E. H. Rubensson, A. M. N. Niklasson, SIAM J. Sci. Comput. 36 (2), 147-170, (2014). [(Rubensson)] E. H. Rubensson, A. M. N. Niklasson, SIAM J. Sci. Comput. 36 (2), 147-170, (2014). :link(Niklasson2008) :link(Niklasson2008) [(Niklasson2008)] A. M. N. Niklasson, Phys. Rev. Lett., 100, 123004 (2008). [(Niklasson2008)] A. M. N. Niklasson, Phys. Rev. Lett., 100, 123004 (2008). :link(Niklasson2014) :link(Niklasson2014) [(Niklasson2014)] A. M. N. Niklasson and M. Cawkwell, J. Chem. Phys., 141, 164123, (2014). [(Niklasson2014)] A. M. N. Niklasson and M. Cawkwell, J. Chem. Phys., 141, 164123, (2014). :link(Niklasson2014) :link(Niklasson2014) [(Niklasson2017)] A. M. N. Niklasson, J. Chem. Phys., 147, 054103 (2017). [(Niklasson2017)] A. M. N. Niklasson, J. Chem. Phys., 147, 054103 (2017). :link(Niklasson2012) :link(Niklasson2012) [(Niklasson2017)] A. M. N. Niklasson, M. J. Cawkwell, Phys. Rev. B, 86 (17), 174308 (2012). [(Niklasson2017)] A. M. N. Niklasson, M. J. Cawkwell, Phys. Rev. B, 86 (17), 174308 (2012). :link(Negre2016) :link(Negre2016) [(Negre2016)] C. F. A. Negre, S. M. Mniszewski, M. J. Cawkwell, N. Bock, M. E. Wall, [(Negre2016)] C. F. A. Negre, S. M. Mniszewski, M. J. Cawkwell, and A. M. N. Niklasson, J. Chem. Theory Comp., 12, 3063 (2016). N. Bock, M. E. Wall, and A. M. N. Niklasson, J. Chem. Theory Comp., 12, 3063 (2016).
examples/README +1 −0 Original line number Original line Diff line number Diff line Loading @@ -79,6 +79,7 @@ granregion: use of fix wall/region/gran as boundary on granular particles hugoniostat: Hugoniostat shock dynamics hugoniostat: Hugoniostat shock dynamics indent: spherical indenter into a 2d solid indent: spherical indenter into a 2d solid kim: use of potentials in Knowledge Base for Interatomic Models (KIM) kim: use of potentials in Knowledge Base for Interatomic Models (KIM) latte: use of LATTE density-functional tight-binding quantum code meam: MEAM test for SiC and shear (same as shear examples) meam: MEAM test for SiC and shear (same as shear examples) melt: rapid melt of 3d LJ system melt: rapid melt of 3d LJ system micelle: self-assembly of small lipid-like molecules into 2d bilayers micelle: self-assembly of small lipid-like molecules into 2d bilayers Loading
examples/latte/data.sucrose_non_opt.lmpdeleted 100644 → 0 +0 −63 Original line number Original line Diff line number Diff line LAMMPS Description 45 atoms 3 atom types 0.0000000000000000 18.917000000000002 xlo xhi 0.0000000000000000 17.350999999999999 ylo yhi 0.0000000000000000 15.472000000000000 zlo zhi Masses 1 15.994915008544922 2 12.000000000000000 3 1.0078250169754028 Atoms 1 1 1 0.0 11.47359 7.39174 7.26456 2 1 2 0.0 12.66159 8.24474 7.53356 3 1 3 0.0 13.49759 7.72474 7.00656 4 1 2 0.0 12.92859 8.18374 9.02956 5 1 1 0.0 13.69659 9.10274 10.46556 6 1 2 0.0 12.83959 10.10474 6.64056 7 1 3 0.0 13.24359 10.33074 7.58456 8 1 1 0.0 13.17359 9.67874 5.60956 9 1 2 0.0 11.20559 10.26374 6.86456 10 1 3 0.0 11.22159 11.15674 6.18156 11 1 1 0.0 10.78559 10.69674 8.19156 12 1 2 0.0 10.23459 9.20474 6.34356 13 1 3 0.0 9.23359 9.62574 6.11656 14 1 1 0.0 10.73959 8.65074 5.08856 15 1 2 0.0 10.18759 8.08774 7.38056 16 1 3 0.0 10.03259 8.49174 8.42656 17 1 1 0.0 9.22959 7.03374 7.08156 18 1 2 0.0 7.79359 7.27874 7.34356 19 1 1 0.0 7.44259 8.64274 6.96956 20 1 2 0.0 7.01059 9.43674 8.13856 21 1 3 0.0 5.95059 9.74974 7.96256 22 1 2 0.0 7.08359 8.51474 9.35656 23 1 3 0.0 8.19359 8.08474 9.80956 24 1 1 0.0 5.86059 8.56174 10.14056 25 1 2 0.0 7.34259 7.10674 8.80356 26 1 3 0.0 6.37259 6.54074 8.80556 27 1 1 0.0 8.32159 6.38474 9.58156 28 1 2 0.0 7.89859 10.67174 8.17156 29 1 1 0.0 6.06859 12.11474 7.59256 30 1 2 0.0 7.47359 7.05174 5.99256 31 1 1 0.0 5.66359 6.54374 6.50656 32 1 3 0.0 12.00659 8.11374 9.61556 33 1 3 0.0 13.35859 7.21774 9.30856 34 1 3 0.0 13.67759 8.46774 11.22956 35 1 3 0.0 12.44459 9.34474 5.00556 36 1 3 0.0 11.54859 11.18274 8.59756 37 1 3 0.0 11.00959 7.71574 5.30056 38 1 3 0.0 5.09459 8.45474 9.52056 39 1 3 0.0 7.92859 6.23074 10.47756 40 1 3 0.0 8.53259 10.62974 7.23156 41 1 3 0.0 8.58159 10.63874 9.05856 42 1 3 0.0 6.42359 13.37374 7.86056 43 1 3 0.0 7.58559 6.90074 4.62256 44 1 3 0.0 7.35159 5.27974 6.61456 45 1 3 0.0 5.22759 6.18974 5.69256
examples/latte/in.latte.sucrose.min→examples/latte/in.latte.sucrose +4 −7 Original line number Original line Diff line number Diff line # simple water model with LATTE # simple sucrose model with LATTE units metal units metal atom_style full atom_style full Loading Loading @@ -34,10 +34,7 @@ fix_modify 2 energy yes thermo_style custom step temp pe etotal thermo_style custom step temp pe etotal # minimization # dynamics thermo 1 thermo 10 min_style cg run 100 min_modify dmax 0.1 min_modify line quadratic minimize 1.0e-6 1.0e-6 10000 10000
