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list some more features

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This commit is contained in:
Axel Kohlmeyer
2021-08-25 22:02:02 -04:00
parent a2d77593bb
commit c3083785b7
1 changed files with 17 additions and 10 deletions
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doc/src/Intro_features.rst
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@ -58,9 +58,10 @@ Particle and model types
* coarse-grained mesoscale models
* finite-size spherical and ellipsoidal particles
* finite-size line segment (2d) and triangle (3d) particles
* finite-size rounded polygons (2d) and polyhedra (3d) particles
* point dipole particles
* particles with magnetic spin
* rigid collections of particles
* rigid collections of n particles
* hybrid combinations of these
.. _ff:
@ -81,15 +82,17 @@ commands)
* polarization models: :doc:`QEq <fix_qeq>`, :doc:`core/shell model <Howto_coreshell>`, :doc:`Drude dipole model <Howto_drude>`
* charge equilibration (QEq via dynamic, point, shielded, Slater methods)
* coarse-grained potentials: DPD, GayBerne, REsquared, colloidal, DLVO
* mesoscopic potentials: granular, Peridynamics, SPH
* mesoscopic potentials: granular, Peridynamics, SPH, mesoscopic tubular potential (MESONT)
* semi-empirical potentials: multi-ion generalized pseudopotential theory (MGPT), second moment tight binding + QEq (SMTB-Q), density functional tight-binding (LATTE)
* electron force field (eFF, AWPMD)
* bond potentials: harmonic, FENE, Morse, nonlinear, class 2, quartic (breakable), tabulated
* angle potentials: harmonic, CHARMM, cosine, cosine/squared, cosine/periodic, class 2 (COMPASS), tabulated
* dihedral potentials: harmonic, CHARMM, multi-harmonic, helix, class 2 (COMPASS), OPLS, tabulated
* improper potentials: harmonic, cvff, umbrella, class 2 (COMPASS), tabulated
* polymer potentials: all-atom, united-atom, bead-spring, breakable
* water potentials: TIP3P, TIP4P, SPC
* water potentials: TIP3P, TIP4P, SPC, SPC/E and variants
* interlayer potentials for graphene and analogues
* metal-organic framework potentials (QuickFF, MO-FF)
* implicit solvent potentials: hydrodynamic lubrication, Debye
* force-field compatibility with common CHARMM, AMBER, DREIDING, OPLS, GROMACS, COMPASS options
* access to the `OpenKIM Repository <http://openkim.org>`_ of potentials via :doc:`kim command <kim_commands>`
@ -127,9 +130,10 @@ Ensembles, constraints, and boundary conditions
* harmonic (umbrella) constraint forces
* rigid body constraints
* SHAKE bond and angle constraints
* Monte Carlo bond breaking, formation, swapping
* motion constraints to manifold surfaces
* Monte Carlo bond breaking, formation, swapping, template based reaction modeling
* atom/molecule insertion and deletion
* walls of various kinds
* walls of various kinds, static and moving
* non-equilibrium molecular dynamics (NEMD)
* variety of additional boundary conditions and constraints
@ -153,6 +157,7 @@ Diagnostics
^^^^^^^^^^^
* see various flavors of the :doc:`fix <fix>` and :doc:`compute <compute>` commands
* introspection command for system, simulation, and compile time settings and configurations
.. _output:
@ -167,8 +172,9 @@ Output
* parallel I/O of dump and restart files
* per-atom quantities (energy, stress, centro-symmetry parameter, CNA, etc)
* user-defined system-wide (log file) or per-atom (dump file) calculations
* spatial and time averaging of per-atom quantities
* time averaging of system-wide quantities
* custom partitioning (chunks) for binning, and static or dynamic grouping of atoms for analysis
* spatial, time, and per-chunk averaging of per-atom quantities
* time averaging and histogramming of system-wide quantities
* atom snapshots in native, XYZ, XTC, DCD, CFG formats
.. _replica1:
@ -181,7 +187,7 @@ Multi-replica models
* :doc:`parallel replica dynamics <prd>`
* :doc:`temperature accelerated dynamics <tad>`
* :doc:`parallel tempering <temper>`
* :doc:`path-integral MD <fix_pimd>`
* path-integral MD: `first variant <fix_pimd>`, `second variant <fix_ipi>`
* multi-walker collective variables with :doc:`Colvars <fix_colvars>` and :doc:`Plumed <fix_plumed>`
.. _prepost:
@ -213,11 +219,12 @@ page for details.
These are LAMMPS capabilities which you may not think of as typical
classical MD options:
* :doc:`static <balance>` and :doc:`dynamic load-balancing <fix_balance>`
* :doc:`static <balance>` and :doc:`dynamic load-balancing <fix_balance>`, optional with recursive bisectioning decomposition
* :doc:`generalized aspherical particles <Howto_body>`
* :doc:`stochastic rotation dynamics (SRD) <fix_srd>`
* :doc:`real-time visualization and interactive MD <fix_imd>`
* :doc:`real-time visualization and interactive MD <fix_imd>`, :doc:`built-in renderer for images and movies <dump_image>`
* calculate :doc:`virtual diffraction patterns <compute_xrd>`
* calculate :doc:`finite temperature phonon dispersion <fix_phonon>` and the :doc:`dynamical matrix of minimized structures <dynamical_matrix>`
* :doc:`atom-to-continuum coupling <fix_atc>` with finite elements
* coupled rigid body integration via the :doc:`POEMS <fix_poems>` library
* :doc:`QM/MM coupling <fix_qmmm>`