diff --git a/doc/Section_example.html b/doc/Section_example.html index e683efc169..c52d848d18 100644 --- a/doc/Section_example.html +++ b/doc/Section_example.html @@ -47,6 +47,7 @@ Site. peptide dynamics of a small solvated peptide chain (5-mer) peri Peridynamics example of cylinder hit by projectile pour pouring of granular particles into a 3d box, then chute flow +prd parallel replica dynamics of a vacancy diffusion in bulk Si reax simple example for ReaxFF force field rigid rigid bodies modeled as independent or coupled shear sideways shear applied to 2d solid, with and without a void diff --git a/doc/Section_example.txt b/doc/Section_example.txt index 4db9e70784..f1698e17c9 100644 --- a/doc/Section_example.txt +++ b/doc/Section_example.txt @@ -43,6 +43,7 @@ obstacle: flow around two voids in a 2d channel peptide: dynamics of a small solvated peptide chain (5-mer) peri: Peridynamics example of cylinder hit by projectile pour: pouring of granular particles into a 3d box, then chute flow +prd: parallel replica dynamics of a vacancy diffusion in bulk Si reax: simple example for ReaxFF force field rigid: rigid bodies modeled as independent or coupled shear: sideways shear applied to 2d solid, with and without a void :tb(s=:) diff --git a/doc/Section_history.html b/doc/Section_history.html index ffcbaf90ba..dd0f264abc 100644 --- a/doc/Section_history.html +++ b/doc/Section_history.html @@ -29,15 +29,24 @@ GranFlow for granular materials.

These are new features we'd like to eventually add to LAMMPS. Some are being worked on; some haven't been implemented because of lack of -time or interest; others are just a lot of work! +time or interest; others are just a lot of work! See this +page on the LAMMPS WWW site for more details.

- -

Kinds of systems LAMMPS can simulate +

Particle and model types

(atom style command)

-

Integrators

-

(run, run_style, temper commands) +

(run, run_style, minimize commands)

Diagnostics

-

(fix command, compute command) -

-

Pre- and post-processing

-

Our group has also written and released a separate toolkit called +

+ + + + +

Specialized features +

+

These are LAMMPS capabilities which you may not think of as typical +molecular dynamics options:

- - - - +

1.3 LAMMPS non-features @@ -477,6 +495,19 @@ the list.
+ + + + + + + + + + + + + diff --git a/doc/Section_intro.txt b/doc/Section_intro.txt index a86c2cd2a7..af7ebae66b 100644 --- a/doc/Section_intro.txt +++ b/doc/Section_intro.txt @@ -102,26 +102,26 @@ General features :h4 spatial-decomposition of simulation domain for parallelism open-source distribution highly portable C++ - optional libraries needed: MPI and single-processor FFT + optional libraries used: MPI and single-processor FFT easy to extend with new features and functionality - in parallel, run one or multiple simulations simultaneously runs from an input script syntax for defining and using variables and formulas syntax for looping over runs and breaking out of loops - run a series of simluations from one script :ul + run one or multiple simulations simultaneously (in parallel) from one script :ul -Kinds of systems LAMMPS can simulate :h4 +Particle and model types :h4 ("atom style"_atom_style.html command) - atomic (e.g. box of Lennard-Jonesium) - bead-spring polymers + atoms + coarse-grained particles (e.g. bead-spring polymers) united-atom polymers or organic molecules all-atom polymers, organic molecules, proteins, DNA metals granular materials coarse-grained mesoscale models - ellipsoidal particles + extended spherical and ellipsoidal particles point dipolar particles + rigid collections of particles hybrid combinations of these :ul Force fields :h4 @@ -135,7 +135,7 @@ commands) charged pairwise potentials: Coulombic, point-dipole manybody potentials: EAM, Finnis/Sinclair EAM, modified EAM (MEAM), \ Stillinger-Weber, Tersoff, AI-REBO, ReaxFF - coarse-grain potentials: DPD, GayBerne, REsquared, colloidal + coarse-grained potentials: DPD, GayBerne, REsquared, colloidal, DLVO mesoscopic potentials: granular, Peridynamics bond potentials: harmonic, FENE, Morse, nonlinear, class 2, \ quartic (breakable) @@ -144,24 +144,26 @@ commands) dihedral potentials: harmonic, CHARMM, multi-harmonic, helix, \ class 2 (COMPASS), OPLS improper potentials: harmonic, cvff, class 2 (COMPASS) - hybrid potentials: multiple pair, bond, angle, dihedral, improper \ - potentials can be used in one simulation - overlaid potentials: superposition of multiple pair potentials polymer potentials: all-atom, united-atom, bead-spring, breakable water potentials: TIP3P, TIP4P, SPC implicit solvent potentials: hydrodynamic lubrication, Debye long-range Coulombics and dispersion: Ewald, \ PPPM (similar to particle-mesh Ewald), Ewald/N for long-range Lennard-Jones - force-field compatibility with common CHARMM, AMBER, OPLS, GROMACS options :ul + force-field compatibility with common CHARMM, AMBER, OPLS, GROMACS options + handful of GPU-enabled pair styles :ul + hybrid potentials: multiple pair, bond, angle, dihedral, improper \ + potentials can be used in one simulation + overlaid potentials: superposition of multiple pair potentials -Creation of atoms :h4 +Atom creation :h4 ("read_data"_read_data.html, "lattice"_lattice.html, "create_atoms"_create_atoms.html, "delete_atoms"_delete_atoms.html, -"displace_atoms"_displace_atoms.html commands) +"displace_atoms"_displace_atoms.html, "replicate"_replicate.html commands) read in atom coords from files create atoms on one or more lattices (e.g. grain boundaries) delete geometric or logical groups of atoms (e.g. voids) + replicate existing atoms multiple times displace atoms :ul Ensembles, constraints, and boundary conditions :h4 @@ -174,27 +176,25 @@ Ensembles, constraints, and boundary conditions :h4 pressure control via Nose/Hoover or Berendsen barostatting in 1 to 3 dimensions simulation box deformation (tensile and shear) harmonic (umbrella) constraint forces - independent or coupled rigid body integration + rigid body constraints SHAKE bond and angle constraints bond breaking, formation, swapping walls of various kinds - targeted molecular dynamics (TMD) and steered molecule dynamics (SMD) constraints non-equilibrium molecular dynamics (NEMD) variety of additional boundary conditions and constraints :ul Integrators :h4 -("run"_run.html, "run_style"_run_style.html, "temper"_temper.html commands) +("run"_run.html, "run_style"_run_style.html, "minimize"_minimize.html commands) velocity-Verlet integrator Brownian dynamics + rigid body integration energy minimization via conjugate gradient or steepest descent relaxation - rRESPA hierarchical timestepping - parallel tempering (replica exchange) :ul + rRESPA hierarchical timestepping :ul Diagnostics :h4 -("fix"_fix.html command, "compute"_compute.html command) - see the various flavors of the fix and compute commands :ul + see the various flavors of the "fix"_fix.html and "compute"_compute.html commands :ul Output :h4 ("dump"_dump.html, "restart"_restart.html commands) @@ -206,19 +206,37 @@ Output :h4 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 - atom snapshots in native, XYZ, XTC, DCD formats :ul + atom snapshots in native, XYZ, XTC, DCD, CFG formats :ul Pre- and post-processing :h4 +Various pre- and post-processing serial tools are packaged +with LAMMPS; see these "doc pages"_Section_tools.html. :ulb,l + Our group has also written and released a separate toolkit called "Pizza.py"_pizza which provides tools for doing setup, analysis, plotting, and visualization for LAMMPS simulations. Pizza.py is written in "Python"_python and is available for download from "the -Pizza.py WWW site"_pizza. +Pizza.py WWW site"_pizza. :l,ule :link(pizza,http://www.sandia.gov/~sjplimp/pizza.html) :link(python,http://www.python.org) +Specialized features :h4 + +These are LAMMPS capabilities which you may not think of as typical +molecular dynamics options: + +"real-time visualization and interactive MD"_fix_imd.html +"atom-to-continuum coupling"_fix_atc.html with finite elements +coupled rigid body integration via the "POEMS"_fix_poems.html library +"parallel tempering"_temper.html +"parallel replica dynamics"_prd.html +"Direct Simulation Monte Carlo"_pair_dsmc.html for low-density fluids +"Peridynamics mesoscale modeling"_pair_peri.html +"targeted"_fix_tmd.html and "steered"_fix_smd.html molecular dynamics +"two-temperature electron model"_fix_ttm.html :ul + :line 1.3 LAMMPS non-features :link(1_3),h4 @@ -462,6 +480,19 @@ the list. :link(sjp,http://www.cs.sandia.gov/~sjplimp) +pair yukawa/colloid : Randy Schunk (Sandia) +fix wall/colloid : Jeremy Lechman (Sandia) +pair_style dsmc for Direct Simulation Monte Carlo (DSMC) modeling : Paul Crozier (Sandia) +fix imd for real-time viz and interactive MD : Axel Kohlmeyer (Temple Univ) +concentration-dependent EAM potential : Alexander Stukowski (Technical University of Darmstadt) +parallel replica dymamics (PRD) : Mike Brown (Sandia) +min_style hftn : Todd Plantenga (Sandia) +fix atc : Reese Jones, Jon Zimmerman, Jeremy Templeton (Sandia) +dump cfg : Liang Wan (Chinese Academy of Sciences) +fix nvt with Nose/Hoover chains : Andy Ballard (U Maryland) +pair_style lj/cut/gpu, pair_style gayberne/gpu : Mike Brown (Sandia) +pair_style lj96/cut, bond_style table, angle_style table : Chuanfu Luo +fix langevin tally : Carolyn Phillips (U Michigan) compute heat/flux for Green-Kubo : Reese Jones (Sandia), Philip Howell (Siemens), Vikas Varsney (AFRL) region cone : Pim Schravendijk fix reax/bonds : Aidan Thompson (Sandia)
pair yukawa/colloid Randy Schunk (Sandia)
fix wall/colloid Jeremy Lechman (Sandia)
pair_style dsmc for Direct Simulation Monte Carlo (DSMC) modeling Paul Crozier (Sandia)
fix imd for real-time viz and interactive MD Axel Kohlmeyer (Temple Univ)
concentration-dependent EAM potential Alexander Stukowski (Technical University of Darmstadt)
parallel replica dymamics (PRD) Mike Brown (Sandia)
min_style hftn Todd Plantenga (Sandia)
fix atc Reese Jones, Jon Zimmerman, Jeremy Templeton (Sandia)
dump cfg Liang Wan (Chinese Academy of Sciences)
fix nvt with Nose/Hoover chains Andy Ballard (U Maryland)
pair_style lj/cut/gpu, pair_style gayberne/gpu Mike Brown (Sandia)
pair_style lj96/cut, bond_style table, angle_style table Chuanfu Luo
fix langevin tally Carolyn Phillips (U Michigan)
compute heat/flux for Green-Kubo Reese Jones (Sandia), Philip Howell (Siemens), Vikas Varsney (AFRL)
region cone Pim Schravendijk
fix reax/bonds Aidan Thompson (Sandia)