246 lines
11 KiB
ReStructuredText
246 lines
11 KiB
ReStructuredText
LAMMPS features
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---------------
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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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1. :ref:`General features <general>`
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2. :ref:`Particle and model types <particle>`
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3. :ref:`Interatomic potentials (force fields) <ff>`
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4. :ref:`Atom creation <create>`
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5. :ref:`Ensembles, constraints, and boundary conditions <ensemble>`
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6. :ref:`Integrators <integrate>`
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7. :ref:`Diagnostics <diag>`
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8. :ref:`Output <output>`
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9. :ref:`Multi-replica models <replica1>`
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10. :ref:`Pre- and post-processing <prepost>`
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11. :ref:`Specialized features (beyond MD itself) <special>`
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----------
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.. _general:
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General features
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^^^^^^^^^^^^^^^^
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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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* shared memory multi-threading parallelism (OpenMP)
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* spatial decomposition of simulation domain for MPI parallelism
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* particle decomposition inside spatial decomposition for OpenMP and GPU parallelism
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* GPLv2 licensed open-source distribution
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* highly portable C++-11
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* modular code with most functionality in optional packages
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* only depends on MPI library for basic parallel functionality, MPI stub for serial compilation
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* other libraries are optional and only required for specific packages
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* GPU (CUDA, OpenCL, HIP, SYCL), 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 (from C, C++, Fortran) or provided Python wrapper or SWIG based wrappers
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* couple with other codes: LAMMPS calls other code, other code calls LAMMPS, umbrella code calls both, MDI coupling interface
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* call out to Python for computing forces, time integration, or other tasks
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* plugin interface for loading external features at runtime
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* large integrated collection of tests
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.. _particle:
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Particle and model types
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^^^^^^^^^^^^^^^^^^^^^^^^
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(See :doc:`atom style <atom_style>` 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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* metal oxides
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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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* finite-size rounded polygons (2d) and polyhedra (3d) particles
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* point dipole particles
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* particles with magnetic spin
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* rigid collections of n particles
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* hybrid combinations of these
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.. _ff:
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Interatomic potentials (force fields)
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^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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(See :doc:`pair style <pair_style>`, :doc:`bond style <bond_style>`,
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:doc:`angle style <angle_style>`, :doc:`dihedral style <dihedral_style>`,
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:doc:`improper style <improper_style>`, :doc:`kspace style <kspace_style>`
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commands)
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* pairwise potentials: Lennard-Jones, Buckingham, Morse, Born-Mayer-Huggins, Yukawa, soft, Class II (COMPASS), hydrogen bond, harmonic, gaussian, tabulated, scripted
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* charged pairwise potentials: Coulombic, point-dipole
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* many-body potentials: EAM, Finnis/Sinclair, MEAM, MEAM+SW, EIM, EDIP, ADP, Stillinger-Weber, Tersoff, REBO, AIREBO, ReaxFF, COMB, Streitz-Mintmire, 3-body polymorphic, BOP, Vashishta
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* machine learning potentials: ACE, AGNI, GAP, Behler-Parrinello (N2P2), POD, RANN
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* interfaces to ML potentials distributed by external groups: ANI, ChIMES, DeepPot, HIPNN, MTP
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* long-range interactions for charge, point-dipoles, and LJ dispersion: Ewald, Wolf, PPPM (similar to particle-mesh Ewald), MSM, ScaFaCoS
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* polarization models: :doc:`QEq <fix_qeq>`, :doc:`core/shell model <Howto_coreshell>`, :doc:`Drude dipole model <Howto_drude>`
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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, oxDNA / oxRNA, SPICA
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* mesoscopic potentials: granular, Peridynamics, SPH, mesoscopic tubular potential (MESONT)
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* semi-empirical potentials: multi-ion generalized pseudopotential theory (MGPT), second moment tight binding + QEq (SMTB-Q), density functional tight-binding (LATTE)
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* electron force field (eFF, AWPMD)
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* bond potentials: harmonic, FENE, Morse, nonlinear, Class II (COMPASS), quartic (breakable), tabulated, scripted
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* angle potentials: harmonic, CHARMM, cosine, cosine/squared, cosine/periodic, Class II (COMPASS), tabulated, scripted
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* dihedral potentials: harmonic, CHARMM, multi-harmonic, helix, Class II (COMPASS), OPLS, tabulated, scripted
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* improper potentials: harmonic, cvff, umbrella, Class II (COMPASS), tabulated
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* polymer potentials: all-atom, united-atom, bead-spring, breakable
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* water potentials: TIP3P, TIP4P, SPC, SPC/E and variants
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* interlayer potentials for graphene and analogues, hetero-junctions
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* metal-organic framework potentials (QuickFF, MO-FF)
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* implicit solvent potentials: hydrodynamic lubrication, Debye
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* force-field compatibility with CHARMM, AMBER, DREIDING, OPLS, GROMACS, Class II (COMPASS), UFF, ClayFF, DREIDING, AMOEBA, INTERFACE
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* access to the `OpenKIM Repository <https://openkim.org>`_ of potentials via the :doc:`kim command <kim_commands>`
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* hybrid potentials: multiple pair, bond, angle, dihedral, improper potentials can be used in one simulation
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* overlaid potentials: superposition of multiple pair potentials (including many-body) with optional scale factor
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.. _create:
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Atom creation
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^^^^^^^^^^^^^
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(See :doc:`read_data <read_data>`, :doc:`lattice <lattice>`,
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:doc:`create_atoms <create_atoms>`, :doc:`delete_atoms <delete_atoms>`,
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:doc:`displace_atoms <displace_atoms>`, :doc:`replicate <replicate>` commands)
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* read in atom coordinates 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
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.. _ensemble:
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Ensembles, constraints, and boundary conditions
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^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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(See :doc:`fix <fix>` 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 / RATTLE bond and angle constraints
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* motion constraints to manifold surfaces
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* Monte Carlo bond breaking, formation, swapping, template based reaction modeling
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* atom/molecule insertion and deletion
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* walls of various kinds, static and moving
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* non-equilibrium molecular dynamics (NEMD)
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* variety of additional boundary conditions and constraints
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.. _integrate:
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Integrators
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^^^^^^^^^^^
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(See :doc:`run <run>`, :doc:`run_style <run_style>`, :doc:`minimize <minimize>` 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, steepest descent relaxation, or damped dynamics (FIRE, Quickmin)
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* rRESPA hierarchical timestepping
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* fixed or adaptive time step
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* rerun command for post-processing of dump files
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.. _diag:
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Diagnostics
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^^^^^^^^^^^
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* see various flavors of the :doc:`fix <fix>` and :doc:`compute <compute>` commands
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* introspection command for system, simulation, and compile time settings and configurations
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.. _output:
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Output
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^^^^^^
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(:doc:`dump <dump>`, :doc:`restart <restart>` commands)
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* log file of thermodynamic info
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* text dump files of atom coordinates, velocities, other per-atom quantities
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* dump output on fixed and variable intervals, based timestep or simulated time
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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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* custom partitioning (chunks) for binning, and static or dynamic grouping of atoms for analysis
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* spatial, time, and per-chunk averaging of per-atom quantities
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* time averaging and histogramming of system-wide quantities
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* atom snapshots in native, XYZ, XTC, DCD, CFG, NetCDF, HDF5, ADIOS2, YAML formats
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* on-the-fly compression of output and decompression of read in files
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.. _replica1:
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Multi-replica models
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^^^^^^^^^^^^^^^^^^^^
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* :doc:`nudged elastic band <neb>`
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* :doc:`hyperdynamics <hyper>`
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* :doc:`parallel replica dynamics <prd>`
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* :doc:`temperature accelerated dynamics <tad>`
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* :doc:`parallel tempering <temper>`
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* path-integral MD: `first variant <fix_pimd>`, `second variant <fix_ipi>`
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* multi-walker collective variables with :doc:`Colvars <fix_colvars>` and :doc:`Plumed <fix_plumed>`
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.. _prepost:
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Pre- and post-processing
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^^^^^^^^^^^^^^^^^^^^^^^^
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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 :doc:`Tools <Tools>` page.
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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 Pizza.py WWW site <pizza_>`_.
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.. _pizza: https://lammps.github.io/pizza
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.. _python: https://www.python.org
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.. _special:
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Specialized features
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^^^^^^^^^^^^^^^^^^^^
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LAMMPS can be built with optional packages which implement a variety of
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additional capabilities. See the :doc:`Optional Packages <Packages>`
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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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* :doc:`static <balance>` and :doc:`dynamic load-balancing <fix_balance>`, optional with recursive bisectioning decomposition
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* :doc:`generalized aspherical particles <Howto_body>`
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* :doc:`stochastic rotation dynamics (SRD) <fix_srd>`
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* :doc:`real-time visualization and interactive MD <fix_imd>`, :doc:`built-in renderer for images and movies <dump_image>`
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* calculate :doc:`virtual diffraction patterns <compute_xrd>`
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* calculate :doc:`finite temperature phonon dispersion <fix_phonon>` and the :doc:`dynamical matrix of minimized structures <dynamical_matrix>`
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* :doc:`atom-to-continuum coupling <fix_atc>` with finite elements
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* coupled rigid body integration via the :doc:`POEMS <fix_poems>` library
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* :doc:`QM/MM coupling <fix_qmmm>`
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* Monte Carlo via :doc:`GCMC <fix_gcmc>` and :doc:`tfMC <fix_tfmc>` and :doc:`atom swapping <fix_atom_swap>`
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* :doc:`path-integral molecular dynamics (PIMD) <fix_ipi>` and :doc:`this as well <fix_pimd>`
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* :doc:`Direct Simulation Monte Carlo <pair_dsmc>` for low-density fluids
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* :doc:`Peridynamics modeling <pair_peri>`
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* :doc:`Lattice Boltzmann fluid <fix_lb_fluid>`
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* :doc:`targeted <fix_tmd>` and :doc:`steered <fix_smd>` molecular dynamics
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* :doc:`two-temperature electron model <fix_ttm>`
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