forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@3686 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
parent
4663686781
commit
f620c6449f
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@ -47,6 +47,7 @@ Site</A>.
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<TR><TD >peptide</TD><TD > dynamics of a small solvated peptide chain (5-mer)</TD></TR>
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<TR><TD >peri</TD><TD > Peridynamics example of cylinder hit by projectile</TD></TR>
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<TR><TD >pour</TD><TD > pouring of granular particles into a 3d box, then chute flow</TD></TR>
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<TR><TD >prd</TD><TD > parallel replica dynamics of a vacancy diffusion in bulk Si</TD></TR>
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<TR><TD >reax</TD><TD > simple example for ReaxFF force field</TD></TR>
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<TR><TD >rigid</TD><TD > rigid bodies modeled as independent or coupled</TD></TR>
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<TR><TD >shear</TD><TD > sideways shear applied to 2d solid, with and without a void
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@ -43,6 +43,7 @@ obstacle: flow around two voids in a 2d channel
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peptide: dynamics of a small solvated peptide chain (5-mer)
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peri: Peridynamics example of cylinder hit by projectile
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pour: pouring of granular particles into a 3d box, then chute flow
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prd: parallel replica dynamics of a vacancy diffusion in bulk Si
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reax: simple example for ReaxFF force field
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rigid: rigid bodies modeled as independent or coupled
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shear: sideways shear applied to 2d solid, with and without a void :tb(s=:)
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@ -29,15 +29,24 @@ GranFlow for granular materials.
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</P>
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<P>These are new features we'd like to eventually add to LAMMPS. Some
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are being worked on; some haven't been implemented because of lack of
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time or interest; others are just a lot of work!
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time or interest; others are just a lot of work! See <A HREF = "http://lammps.sandia.gov/future.html">this
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page</A> on the LAMMPS WWW site for more details.
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</P>
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<UL><LI>coupling to finite elements
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<LI>new ReaxFF implementation (in addition to existing one)
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<LI>stochastic rotation dynamics
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<UL><LI>Coupling to finite elements for streess-strain
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<LI>New ReaxFF implementation
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<LI>Nudged elastic band
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<LI>Temperature accelerated dynamics
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<LI>Triangulated particles
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<LI>Stochastic rotation dynamics
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<LI>Stokesian dynamics via fast lubrication dynamics
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<LI>NPT with changing box shape (Parinello-Rahman)
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<LI>long-range point-dipole solver
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<LI>torsional shear boundary conditions and temperature calculation
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<LI>Long-range point-dipole solver
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<LI>Per-atom energy and stress for long-range Coulombics
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<LI>Long-range Coulombics via Ewald and PPPM for triclinic boxes
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<LI>Metadynamics
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<LI>Direct Simulation Monte Carlo - DSMC
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</UL>
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<HR>
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|
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@ -26,15 +26,24 @@ GranFlow for granular materials.
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These are new features we'd like to eventually add to LAMMPS. Some
|
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are being worked on; some haven't been implemented because of lack of
|
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time or interest; others are just a lot of work!
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time or interest; others are just a lot of work! See "this
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page"_lwsfuture on the LAMMPS WWW site for more details.
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coupling to finite elements
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new ReaxFF implementation (in addition to existing one)
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stochastic rotation dynamics
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:link(lwsfuture,http://lammps.sandia.gov/future.html)
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Coupling to finite elements for streess-strain
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New ReaxFF implementation
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Nudged elastic band
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Temperature accelerated dynamics
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Triangulated particles
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Stochastic rotation dynamics
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Stokesian dynamics via fast lubrication dynamics
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NPT with changing box shape (Parinello-Rahman)
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long-range point-dipole solver
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torsional shear boundary conditions and temperature calculation :ul
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Long-range point-dipole solver
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Per-atom energy and stress for long-range Coulombics
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Long-range Coulombics via Ewald and PPPM for triclinic boxes
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Metadynamics
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Direct Simulation Monte Carlo - DSMC :ul
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:line
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|
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@ -105,27 +105,27 @@ LAMMPS.
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<LI> spatial-decomposition of simulation domain for parallelism
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<LI> open-source distribution
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<LI> highly portable C++
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<LI> optional libraries needed: MPI and single-processor FFT
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<LI> optional libraries used: MPI and single-processor FFT
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<LI> easy to extend with new features and functionality
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<LI> in parallel, run one or multiple simulations simultaneously
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<LI> runs from an input script
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<LI> syntax for defining and using variables and formulas
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<LI> syntax for looping over runs and breaking out of loops
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<LI> run a series of simluations from one script
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<LI> run one or multiple simulations simultaneously (in parallel) from one script
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</UL>
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<H4>Kinds of systems LAMMPS can simulate
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<H4>Particle and model types
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</H4>
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<P>(<A HREF = "atom_style.html">atom style</A> command)
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</P>
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<UL><LI> atomic (e.g. box of Lennard-Jonesium)
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<LI> bead-spring polymers
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<UL><LI> atoms
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<LI> coarse-grained particles (e.g. bead-spring polymers)
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<LI> united-atom polymers or organic molecules
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<LI> all-atom polymers, organic molecules, proteins, DNA
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<LI> metals
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<LI> granular materials
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<LI> coarse-grained mesoscale models
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<LI> ellipsoidal particles
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<LI> extended spherical and ellipsoidal particles
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<LI> point dipolar particles
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<LI> rigid collections of particles
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<LI> hybrid combinations of these
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</UL>
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<H4>Force fields
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@ -138,29 +138,32 @@ commands)
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<UL><LI> pairwise potentials: Lennard-Jones, Buckingham, Morse, Yukawa, soft, class 2 (COMPASS), tabulated
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<LI> charged pairwise potentials: Coulombic, point-dipole
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<LI> manybody potentials: EAM, Finnis/Sinclair EAM, modified EAM (MEAM), Stillinger-Weber, Tersoff, AI-REBO, ReaxFF
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<LI> coarse-grain potentials: DPD, GayBerne, REsquared, colloidal
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<LI> coarse-grained potentials: DPD, GayBerne, REsquared, colloidal, DLVO
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<LI> mesoscopic potentials: granular, Peridynamics
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<LI> bond potentials: harmonic, FENE, Morse, nonlinear, class 2, quartic (breakable)
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<LI> angle potentials: harmonic, CHARMM, cosine, cosine/squared, class 2 (COMPASS)
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<LI> dihedral potentials: harmonic, CHARMM, multi-harmonic, helix, class 2 (COMPASS), OPLS
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<LI> improper potentials: harmonic, cvff, class 2 (COMPASS)
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<LI> hybrid potentials: multiple pair, bond, angle, dihedral, improper potentials can be used in one simulation
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<LI> overlaid potentials: superposition of multiple pair potentials
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<LI> polymer potentials: all-atom, united-atom, bead-spring, breakable
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<LI> water potentials: TIP3P, TIP4P, SPC
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<LI> implicit solvent potentials: hydrodynamic lubrication, Debye
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<LI> long-range Coulombics and dispersion: Ewald, PPPM (similar to particle-mesh Ewald), Ewald/N for long-range Lennard-Jones
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<LI> force-field compatibility with common CHARMM, AMBER, OPLS, GROMACS options
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<LI> force-field compatibility with common CHARMM, AMBER, OPLS, GROMACS options
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<LI> handful of GPU-enabled pair styles
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</UL>
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<H4>Creation of atoms
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<P> 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
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</P>
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<H4>Atom creation
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</H4>
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<P>(<A HREF = "read_data.html">read_data</A>, <A HREF = "lattice.html">lattice</A>,
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<A HREF = "create_atoms.html">create_atoms</A>, <A HREF = "delete_atoms.html">delete_atoms</A>,
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<A HREF = "displace_atoms.html">displace_atoms</A> commands)
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<A HREF = "displace_atoms.html">displace_atoms</A>, <A HREF = "replicate.html">replicate</A> commands)
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</P>
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<UL><LI> read in atom coords from files
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<LI> create atoms on one or more lattices (e.g. grain boundaries)
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<LI> delete geometric or logical groups of atoms (e.g. voids)
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<LI> replicate existing atoms multiple times
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<LI> displace atoms
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</UL>
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<H4>Ensembles, constraints, and boundary conditions
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@ -174,29 +177,26 @@ commands)
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<LI> pressure control via Nose/Hoover or Berendsen barostatting in 1 to 3 dimensions
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<LI> simulation box deformation (tensile and shear)
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<LI> harmonic (umbrella) constraint forces
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<LI> independent or coupled rigid body integration
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<LI> rigid body constraints
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<LI> SHAKE bond and angle constraints
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<LI> bond breaking, formation, swapping
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<LI> walls of various kinds
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<LI> targeted molecular dynamics (TMD) and steered molecule dynamics (SMD) constraints
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<LI> non-equilibrium molecular dynamics (NEMD)
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<LI> variety of additional boundary conditions and constraints
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</UL>
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<H4>Integrators
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</H4>
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<P>(<A HREF = "run.html">run</A>, <A HREF = "run_style.html">run_style</A>, <A HREF = "temper.html">temper</A> commands)
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<P>(<A HREF = "run.html">run</A>, <A HREF = "run_style.html">run_style</A>, <A HREF = "minimize.html">minimize</A> commands)
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</P>
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<UL><LI> velocity-Verlet integrator
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<LI> Brownian dynamics
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<LI> rigid body integration
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<LI> energy minimization via conjugate gradient or steepest descent relaxation
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<LI> rRESPA hierarchical timestepping
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<LI> parallel tempering (replica exchange)
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<LI> rRESPA hierarchical timestepping
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</UL>
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<H4>Diagnostics
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</H4>
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<P>(<A HREF = "fix.html">fix</A> command, <A HREF = "compute.html">compute</A> command)
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</P>
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<UL><LI> see the various flavors of the fix and compute commands
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<UL><LI> see the various flavors of the <A HREF = "fix.html">fix</A> and <A HREF = "compute.html">compute</A> commands
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</UL>
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<H4>Output
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</H4>
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@ -209,20 +209,38 @@ commands)
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<LI> user-defined system-wide (log file) or per-atom (dump file) calculations
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<LI> spatial and time averaging of per-atom quantities
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<LI> time averaging of system-wide quantities
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<LI> atom snapshots in native, XYZ, XTC, DCD formats
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<LI> atom snapshots in native, XYZ, XTC, DCD, CFG formats
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</UL>
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<H4>Pre- and post-processing
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</H4>
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<P>Our group has also written and released a separate toolkit called
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<UL><LI>Various pre- and post-processing serial tools are packaged
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with LAMMPS; see these <A HREF = "Section_tools.html">doc pages</A>.
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<LI>Our group has also written and released a separate toolkit called
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<A HREF = "http://www.sandia.gov/~sjplimp/pizza.html">Pizza.py</A> 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 <A HREF = "http://www.python.org">Python</A> and is available for download from <A HREF = "http://www.sandia.gov/~sjplimp/pizza.html">the
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Pizza.py WWW site</A>.
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Pizza.py WWW site</A>.
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</UL>
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<H4>Specialized features
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</H4>
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<P>These are LAMMPS capabilities which you may not think of as typical
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molecular dynamics options:
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</P>
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<UL><LI><A HREF = "fix_imd.html">real-time visualization and interactive MD</A>
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<LI><A HREF = "fix_atc.html">atom-to-continuum coupling</A> with finite elements
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<LI>coupled rigid body integration via the <A HREF = "fix_poems.html">POEMS</A> library
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<LI><A HREF = "temper.html">parallel tempering</A>
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<LI><A HREF = "prd.html">parallel replica dynamics</A>
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<LI><A HREF = "pair_dsmc.html">Direct Simulation Monte Carlo</A> for low-density fluids
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<LI><A HREF = "pair_peri.html">Peridynamics mesoscale modeling</A>
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<LI><A HREF = "fix_tmd.html">targeted</A> and <A HREF = "fix_smd.html">steered</A> molecular dynamics
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<LI><A HREF = "fix_ttm.html">two-temperature electron model</A>
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</UL>
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<HR>
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<A NAME = "1_3"></A><H4>1.3 LAMMPS non-features
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|
@ -477,6 +495,19 @@ the list.
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<DIV ALIGN=center><TABLE BORDER=1 >
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<TR><TD >pair yukawa/colloid </TD><TD > Randy Schunk (Sandia)</TD></TR>
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<TR><TD >fix wall/colloid </TD><TD > Jeremy Lechman (Sandia)</TD></TR>
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<TR><TD >pair_style dsmc for Direct Simulation Monte Carlo (DSMC) modeling </TD><TD > Paul Crozier (Sandia)</TD></TR>
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<TR><TD >fix imd for real-time viz and interactive MD </TD><TD > Axel Kohlmeyer (Temple Univ)</TD></TR>
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<TR><TD >concentration-dependent EAM potential </TD><TD > Alexander Stukowski (Technical University of Darmstadt)</TD></TR>
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<TR><TD >parallel replica dymamics (PRD) </TD><TD > Mike Brown (Sandia)</TD></TR>
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<TR><TD >min_style hftn </TD><TD > Todd Plantenga (Sandia)</TD></TR>
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<TR><TD >fix atc </TD><TD > Reese Jones, Jon Zimmerman, Jeremy Templeton (Sandia)</TD></TR>
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<TR><TD >dump cfg </TD><TD > Liang Wan (Chinese Academy of Sciences)</TD></TR>
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<TR><TD >fix nvt with Nose/Hoover chains </TD><TD > Andy Ballard (U Maryland)</TD></TR>
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<TR><TD >pair_style lj/cut/gpu, pair_style gayberne/gpu </TD><TD > Mike Brown (Sandia)</TD></TR>
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<TR><TD >pair_style lj96/cut, bond_style table, angle_style table </TD><TD > Chuanfu Luo</TD></TR>
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<TR><TD >fix langevin tally </TD><TD > Carolyn Phillips (U Michigan)</TD></TR>
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<TR><TD >compute heat/flux for Green-Kubo </TD><TD > Reese Jones (Sandia), Philip Howell (Siemens), Vikas Varsney (AFRL)</TD></TR>
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<TR><TD >region cone </TD><TD > Pim Schravendijk</TD></TR>
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<TR><TD >fix reax/bonds </TD><TD > Aidan Thompson (Sandia)</TD></TR>
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|
|
|
@ -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
|
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|
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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)
|
||||
|
|
Loading…
Reference in New Issue