203 lines
8.3 KiB
Plaintext
203 lines
8.3 KiB
Plaintext
"Higher level section"_Intro.html - "LAMMPS WWW Site"_lws - "LAMMPS
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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,Commands_all.html)
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:line
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LAMMPS features :h3
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LAMMPS is a classical molecular dynamics (MD) code with these general
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classes of functionality:
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"General features"_#general
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"Particle and model types"_#particle
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"Interatomic potentials (force fields)"_#ff
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"Atom creation"_#create
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"Ensembles, constraints, and boundary conditions"_#ensemble
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"Integrators"_#integrate
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"Diagnostics"_#diag
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"Output"_#output
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"Multi-replica models"_#replica1
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"Pre- and post-processing"_#prepost
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"Specialized features (beyond MD itself)"_#special :ul
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:line
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General features :h4,link(general)
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runs on a single processor or in parallel
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distributed-memory message-passing parallelism (MPI)
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spatial-decomposition of simulation domain for parallelism
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open-source distribution
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highly portable C++
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optional libraries used: MPI and single-processor FFT
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GPU (CUDA and OpenCL), Intel Xeon Phi, and OpenMP support for many code features
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easy to extend with new features and functionality
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runs from an input script
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syntax for defining and using variables and formulas
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syntax for looping over runs and breaking out of loops
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run one or multiple simulations simultaneously (in parallel) from one script
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build as library, invoke LAMMPS through library interface or provided Python wrapper
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couple with other codes: LAMMPS calls other code, other code calls LAMMPS, umbrella code calls both :ul
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Particle and model types :h4,link(particle)
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("atom style"_atom_style.html command)
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atoms
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coarse-grained particles (e.g. bead-spring polymers)
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united-atom polymers or organic molecules
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all-atom polymers, organic molecules, proteins, DNA
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metals
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granular materials
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coarse-grained mesoscale models
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finite-size spherical and ellipsoidal particles
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finite-size line segment (2d) and triangle (3d) particles
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point dipole particles
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rigid collections of particles
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hybrid combinations of these :ul
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Interatomic potentials (force fields) :h4,link(ff)
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("pair style"_pair_style.html, "bond style"_bond_style.html,
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"angle style"_angle_style.html, "dihedral style"_dihedral_style.html,
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"improper style"_improper_style.html, "kspace style"_kspace_style.html
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commands)
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pairwise potentials: Lennard-Jones, Buckingham, Morse, Born-Mayer-Huggins, \
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Yukawa, soft, class 2 (COMPASS), hydrogen bond, tabulated
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charged pairwise potentials: Coulombic, point-dipole
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many-body potentials: EAM, Finnis/Sinclair EAM, modified EAM (MEAM), \
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embedded ion method (EIM), EDIP, ADP, Stillinger-Weber, Tersoff, \
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REBO, AIREBO, ReaxFF, COMB, SNAP, Streitz-Mintmire, 3-body polymorphic
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long-range interactions for charge, point-dipoles, and LJ dispersion: \
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Ewald, Wolf, PPPM (similar to particle-mesh Ewald)
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polarization models: "QEq"_fix_qeq.html, \
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"core/shell model"_Howto_coreshell.html, \
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"Drude dipole model"_Howto_drude.html
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charge equilibration (QEq via dynamic, point, shielded, Slater methods)
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coarse-grained potentials: DPD, GayBerne, REsquared, colloidal, DLVO
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mesoscopic potentials: granular, Peridynamics, SPH
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electron force field (eFF, AWPMD)
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bond potentials: harmonic, FENE, Morse, nonlinear, class 2, \
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quartic (breakable)
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angle potentials: harmonic, CHARMM, cosine, cosine/squared, cosine/periodic, \
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class 2 (COMPASS)
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dihedral potentials: harmonic, CHARMM, multi-harmonic, helix, \
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class 2 (COMPASS), OPLS
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improper potentials: harmonic, cvff, umbrella, class 2 (COMPASS)
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polymer potentials: all-atom, united-atom, bead-spring, breakable
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water potentials: TIP3P, TIP4P, SPC
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implicit solvent potentials: hydrodynamic lubrication, Debye
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force-field compatibility with common CHARMM, AMBER, DREIDING, \
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OPLS, GROMACS, COMPASS options
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access to the "OpenKIM Repository"_http://openkim.org of potentials via \
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"kim_init, kim_interactions, and kim_query"_kim_commands.html commands
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hybrid potentials: multiple pair, bond, angle, dihedral, improper \
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potentials can be used in one simulation
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overlaid potentials: superposition of multiple pair potentials :ul
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Atom creation :h4,link(create)
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("read_data"_read_data.html, "lattice"_lattice.html,
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"create_atoms"_create_atoms.html, "delete_atoms"_delete_atoms.html,
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"displace_atoms"_displace_atoms.html, "replicate"_replicate.html commands)
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read in atom coords from files
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create atoms on one or more lattices (e.g. grain boundaries)
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delete geometric or logical groups of atoms (e.g. voids)
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replicate existing atoms multiple times
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displace atoms :ul
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Ensembles, constraints, and boundary conditions :h4,link(ensemble)
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("fix"_fix.html command)
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2d or 3d systems
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orthogonal or non-orthogonal (triclinic symmetry) simulation domains
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constant NVE, NVT, NPT, NPH, Parrinello/Rahman integrators
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thermostatting options for groups and geometric regions of atoms
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pressure control via Nose/Hoover or Berendsen barostatting in 1 to 3 dimensions
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simulation box deformation (tensile and shear)
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harmonic (umbrella) constraint forces
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rigid body constraints
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SHAKE bond and angle constraints
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Monte Carlo bond breaking, formation, swapping
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atom/molecule insertion and deletion
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walls of various kinds
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non-equilibrium molecular dynamics (NEMD)
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variety of additional boundary conditions and constraints :ul
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Integrators :h4,link(integrate)
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("run"_run.html, "run_style"_run_style.html, "minimize"_minimize.html commands)
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velocity-Verlet integrator
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Brownian dynamics
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rigid body integration
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energy minimization via conjugate gradient or steepest descent relaxation
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rRESPA hierarchical timestepping
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rerun command for post-processing of dump files :ul
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Diagnostics :h4,link(diag)
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see various flavors of the "fix"_fix.html and "compute"_compute.html commands :ul
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Output :h4,link(output)
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("dump"_dump.html, "restart"_restart.html commands)
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log file of thermodynamic info
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text dump files of atom coords, velocities, other per-atom quantities
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binary restart files
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parallel I/O of dump and restart files
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per-atom quantities (energy, stress, centro-symmetry parameter, CNA, etc)
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user-defined system-wide (log file) or per-atom (dump file) calculations
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spatial and time averaging of per-atom quantities
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time averaging of system-wide quantities
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atom snapshots in native, XYZ, XTC, DCD, CFG formats :ul
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Multi-replica models :h4,link(replica1)
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"nudged elastic band"_neb.html
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"parallel replica dynamics"_prd.html
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"temperature accelerated dynamics"_tad.html
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"parallel tempering"_temper.html :ul
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Pre- and post-processing :h4,link(prepost)
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A handful of pre- and post-processing tools are packaged with LAMMPS,
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some of which can convert input and output files to/from formats used
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by other codes; see the "Toos"_Tools.html doc page. :ulb,l
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Our group has also written and released a separate toolkit called
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"Pizza.py"_pizza which provides tools for doing setup, analysis,
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plotting, and visualization for LAMMPS simulations. Pizza.py is
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written in "Python"_python and is available for download from "the
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Pizza.py WWW site"_pizza. :l,ule
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:link(pizza,http://www.sandia.gov/~sjplimp/pizza.html)
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:link(python,http://www.python.org)
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Specialized features :h4,link(special)
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LAMMPS can be built with optional packages which implement a variety
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of additional capabilities. See the "Packages"_Packages.html doc
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page for details.
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These are LAMMPS capabilities which you may not think of as typical
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classical MD options:
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"static"_balance.html and "dynamic load-balancing"_fix_balance.html
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"generalized aspherical particles"_Howto_body.html
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"stochastic rotation dynamics (SRD)"_fix_srd.html
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"real-time visualization and interactive MD"_fix_imd.html
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calculate "virtual diffraction patterns"_compute_xrd.html
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"atom-to-continuum coupling"_fix_atc.html with finite elements
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coupled rigid body integration via the "POEMS"_fix_poems.html library
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"QM/MM coupling"_fix_qmmm.html
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Monte Carlo via "GCMC"_fix_gcmc.html and "tfMC"_fix_tfmc.html and "atom swapping"_fix_atom_swap.html
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"path-integral molecular dynamics (PIMD)"_fix_ipi.html and "this as well"_fix_pimd.html
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"Direct Simulation Monte Carlo"_pair_dsmc.html for low-density fluids
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"Peridynamics mesoscale modeling"_pair_peri.html
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"Lattice Boltzmann fluid"_fix_lb_fluid.html
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"targeted"_fix_tmd.html and "steered"_fix_smd.html molecular dynamics
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"two-temperature electron model"_fix_ttm.html :ul
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