git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@2357 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
@ -45,6 +45,7 @@ Site</A>.
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<TR><TD >nemd</TD><TD > non-equilibrium MD of 2d sheared system</TD></TR>
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<TR><TD >obstacle</TD><TD > flow around two voids in a 2d channel</TD></TR>
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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 >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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@ -41,6 +41,7 @@ min: energy minimization of 2d LJ melt
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nemd: non-equilibrium MD of 2d sheared system
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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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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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@ -32,7 +32,6 @@ 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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</P>
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<UL><LI>NPT with changing box shape (Parinello-Rahman)
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<LI>bond creation potentials
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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>charge equilibration
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@ -29,7 +29,6 @@ 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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NPT with changing box shape (Parinello-Rahman)
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bond creation potentials
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long-range point dipole solver
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torsional shear boundary conditions and temperature calculation
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charge equilibration
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@ -98,6 +98,21 @@ favorite interatomic potential, boundary condition, or atom type, see
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<A HREF = "Section_modify.html">this section</A>, which describes how you can add it to
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LAMMPS.
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</P>
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<P>General features: h4
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</P>
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<UL><LI> runs on a single processor or in parallel
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<LI> distributed-memory message-passing parallelism (MPI)
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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> 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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</UL>
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<H4>Kinds of systems LAMMPS can simulate:
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</H4>
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<P>(<A HREF = "atom_style.html">atom style</A> command)
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@ -111,7 +126,7 @@ LAMMPS.
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<LI> coarse-grained mesoscale models
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<LI> ellipsoidal particles
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<LI> point dipolar particles
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<LI> hybrid systems
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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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</H4>
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@ -123,7 +138,8 @@ 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
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<LI> coarse-grain potentials: granular, DPD, GayBerne, REsquared, colloidal
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<LI> coarse-grain potentials: DPD, GayBerne, REsquared, colloidal
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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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@ -160,6 +176,7 @@ commands)
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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> 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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@ -171,10 +188,9 @@ 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> energy minimization via conjugate gradient relaxation
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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> run multiple independent simulations simultaneously
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<LI> parallel tempering (replica exchange)
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</UL>
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<H4>Output:
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</H4>
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@ -455,6 +471,8 @@ the list.
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<DIV ALIGN=center><TABLE BORDER=1 >
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<TR><TD >Tersoff/ZBL potential </TD><TD > Dave Farrell (Northwestern U)</TD></TR>
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<TR><TD >peridynamics </TD><TD > Mike Parks (Sandia)</TD></TR>
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<TR><TD >fix smd for steered MD </TD><TD > Axel Kohlmeyer (U Penn)</TD></TR>
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<TR><TD >GROMACS pair potentials </TD><TD > Mark Stevens (Sandia)</TD></TR>
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<TR><TD >lmp2vmd tool </TD><TD > Axel Kohlmeyer (U Penn)</TD></TR>
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@ -95,6 +95,21 @@ favorite interatomic potential, boundary condition, or atom type, see
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"this section"_Section_modify.html, which describes how you can add it to
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LAMMPS.
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General features: h4
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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 needed: MPI and single-processor FFT
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easy to extend with new features and functionality
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in parallel, run one or multiple simulations simultaneously
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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 a series of simluations from one script :ul
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Kinds of systems LAMMPS can simulate: :h4
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("atom style"_atom_style.html command)
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@ -107,7 +122,7 @@ Kinds of systems LAMMPS can simulate: :h4
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coarse-grained mesoscale models
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ellipsoidal particles
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point dipolar particles
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hybrid systems :ul
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hybrid combinations of these :ul
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Force fields: :h4
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("pair style"_pair_style.html, "bond style"_bond_style.html,
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@ -120,7 +135,8 @@ commands)
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charged pairwise potentials: Coulombic, point-dipole
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manybody potentials: EAM, Finnis/Sinclair EAM, modified EAM (MEAM), \
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Stillinger-Weber, Tersoff, AI-REBO
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coarse-grain potentials: granular, DPD, GayBerne, REsquared, colloidal
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coarse-grain potentials: DPD, GayBerne, REsquared, colloidal
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mesoscopic potentials: granular, Peridynamics
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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, \
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@ -160,6 +176,7 @@ Ensembles, constraints, and boundary conditions: :h4
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harmonic (umbrella) constraint forces
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independent or coupled rigid body integration
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SHAKE bond and angle constraints
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bond breaking, formation, swapping
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walls of various kinds
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targeted molecular dynamics (TMD) and steered molecule dynamics (SMD) constraints
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non-equilibrium molecular dynamics (NEMD)
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@ -170,10 +187,9 @@ Integrators: :h4
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velocity-Verlet integrator
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Brownian dynamics
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energy minimization via conjugate gradient relaxation
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energy minimization via conjugate gradient or steepest descent relaxation
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rRESPA hierarchical timestepping
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parallel tempering (replica exchange)
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run multiple independent simulations simultaneously :ul
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parallel tempering (replica exchange) :ul
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Output: :h4
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("dump"_dump.html, "restart"_restart.html commands)
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@ -441,6 +457,8 @@ the list.
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:link(sjp,http://www.cs.sandia.gov/~sjplimp)
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Tersoff/ZBL potential : Dave Farrell (Northwestern U)
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peridynamics : Mike Parks (Sandia)
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fix smd for steered MD : Axel Kohlmeyer (U Penn)
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GROMACS pair potentials : Mark Stevens (Sandia)
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lmp2vmd tool : Axel Kohlmeyer (U Penn)
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@ -297,6 +297,7 @@ typing "make package".
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<TR><TD >meam </TD><TD > modified embedded atom method (MEAM) potential</TD></TR>
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<TR><TD >molecule </TD><TD > force fields for molecular systems</TD></TR>
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<TR><TD >opt </TD><TD > optimized versions of a few pair potentials</TD></TR>
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<TR><TD >peri </TD><TD > Peridynamics model and potential</TD></TR>
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<TR><TD >poems </TD><TD > coupled rigid body motion</TD></TR>
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<TR><TD >xtc </TD><TD > dump atom snapshots in XTC format
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</TD></TR></TABLE></DIV>
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@ -291,6 +291,7 @@ manybody : metal, 3-body, bond-order potentials
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meam : modified embedded atom method (MEAM) potential
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molecule : force fields for molecular systems
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opt : optimized versions of a few pair potentials
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peri : Peridynamics model and potential
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poems : coupled rigid body motion
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xtc : dump atom snapshots in XTC format :tb(s=:)
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@ -127,7 +127,6 @@ available in LAMMPS:
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<LI><A HREF = "compute_temp_asphere.html">temp/asphere</A> - temperature of aspherical particles
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<LI><A HREF = "compute_temp_com.html">temp/com</A> - temperature after subtracting center-of-mass velocity
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<LI><A HREF = "compute_temp_deform.html">temp/deform</A> - temperature excluding box deformation velocity
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<LI><A HREF = "compute_temp_dipole.html">temp/dipole</A> - temperature of point dipolar particles
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<LI><A HREF = "compute_temp_partial.html">temp/partial</A> - temperature excluding one or more dimensions of velocity
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<LI><A HREF = "compute_temp_ramp.html">temp/ramp</A> - temperature excluding ramped velocity component
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<LI><A HREF = "compute_temp_region.html">temp/region</A> - temperature of a region of atoms
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@ -124,7 +124,6 @@ available in LAMMPS:
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"temp/asphere"_compute_temp_asphere.html - temperature of aspherical particles
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"temp/com"_compute_temp_com.html - temperature after subtracting center-of-mass velocity
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"temp/deform"_compute_temp_deform.html - temperature excluding box deformation velocity
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"temp/dipole"_compute_temp_dipole.html - temperature of point dipolar particles
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"temp/partial"_compute_temp_partial.html - temperature excluding one or more dimensions of velocity
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"temp/ramp"_compute_temp_ramp.html - temperature excluding ramped velocity component
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"temp/region"_compute_temp_region.html - temperature of a region of atoms
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@ -35,11 +35,12 @@
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<LI>args = list of arguments for a particular style
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<LI> <I>xplane</I> or <I>yplane</I> or <I>zplane</I> args = lo hi
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<PRE> <I>xplane</I> or <I>yplane</I> or <I>zplane</I> args = lo hi
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lo,hi = position of lower and upper plane (distance units), either can be NULL)
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<I>zcylinder</I> args = radius
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radius = cylinder radius (distance units)
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zero or more keyword/value pairs may be appended to args
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radius = cylinder radius (distance units)
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</PRE>
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<LI>zero or more keyword/value pairs may be appended to args
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<LI>keyword = <I>wiggle</I> or <I>shear</I>
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@ -25,7 +25,7 @@ args = list of arguments for a particular style :l
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{xplane} or {yplane} or {zplane} args = lo hi
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lo,hi = position of lower and upper plane (distance units), either can be NULL)
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{zcylinder} args = radius
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radius = cylinder radius (distance units)
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radius = cylinder radius (distance units) :pre
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zero or more keyword/value pairs may be appended to args :l
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keyword = {wiggle} or {shear} :l
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{wiggle} values = dim amplitude period
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@ -105,9 +105,9 @@ the pair_style command, and coefficients specified by the associated
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<LI><A HREF = "pair_eam.html">pair_style eam/fs</A> - Finnis-Sinclair EAM
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<LI><A HREF = "pair_eam.html">pair_style eam/fs/opt</A> - optimized version of Finnis-Sinclair EAM
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<LI><A HREF = "pair_gayberne.html">pair_style gayberne</A> - Gay-Berne ellipsoidal potential
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<LI><A HREF = "pair_gran.html">pair_style gran/hertzian</A> - granular potential with Hertzian interactions
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<LI><A HREF = "pair_gran.html">pair_style gran/history</A> - granular potential with history effects
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<LI><A HREF = "pair_gran.html">pair_style gran/no_history</A> - granular potential without history effects
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<LI><A HREF = "pair_gran.html">pair_style gran/hertz/history</A> - granular potential with Hertzian interactions
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<LI><A HREF = "pair_gran.html">pair_style gran/hooke</A> - granular potential with history effects
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<LI><A HREF = "pair_gran.html">pair_style gran/hooke/history</A> - granular potential without history effects
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<LI><A HREF = "pair_charmm.html">pair_style lj/charmm/coul/charmm</A> - CHARMM potential with cutoff Coulomb
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<LI><A HREF = "pair_charmm.html">pair_style lj/charmm/coul/charmm/implicit</A> - CHARMM for implicit solvent
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<LI><A HREF = "pair_charmm.html">pair_style lj/charmm/coul/long</A> - CHARMM with long-range Coulomb
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@ -101,9 +101,9 @@ the pair_style command, and coefficients specified by the associated
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"pair_style eam/fs"_pair_eam.html - Finnis-Sinclair EAM
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"pair_style eam/fs/opt"_pair_eam.html - optimized version of Finnis-Sinclair EAM
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"pair_style gayberne"_pair_gayberne.html - Gay-Berne ellipsoidal potential
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"pair_style gran/hertzian"_pair_gran.html - granular potential with Hertzian interactions
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"pair_style gran/history"_pair_gran.html - granular potential with history effects
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"pair_style gran/no_history"_pair_gran.html - granular potential without history effects
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"pair_style gran/hertz/history"_pair_gran.html - granular potential with Hertzian interactions
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"pair_style gran/hooke"_pair_gran.html - granular potential with history effects
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"pair_style gran/hooke/history"_pair_gran.html - granular potential without history effects
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"pair_style lj/charmm/coul/charmm"_pair_charmm.html - CHARMM potential with cutoff Coulomb
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"pair_style lj/charmm/coul/charmm/implicit"_pair_charmm.html - CHARMM for implicit solvent
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"pair_style lj/charmm/coul/long"_pair_charmm.html - CHARMM with long-range Coulomb
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@ -107,9 +107,9 @@ the pair_style command, and coefficients specified by the associated
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<LI><A HREF = "pair_eam.html">pair_style eam/fs</A> - Finnis-Sinclair EAM
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<LI><A HREF = "pair_eam.html">pair_style eam/fs/opt</A> - optimized version of Finnis-Sinclair EAM
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<LI><A HREF = "pair_gayberne.html">pair_style gayberne</A> - Gay-Berne ellipsoidal potential
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<LI><A HREF = "pair_gran.html">pair_style gran/hertzian</A> - granular potential with Hertzian interactions
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<LI><A HREF = "pair_gran.html">pair_style gran/history</A> - granular potential with history effects
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<LI><A HREF = "pair_gran.html">pair_style gran/no_history</A> - granular potential without history effects
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<LI><A HREF = "pair_gran.html">pair_style gran/hertz/history</A> - granular potential with Hertzian interactions
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<LI><A HREF = "pair_gran.html">pair_style gran/hooke</A> - granular potential with history effects
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<LI><A HREF = "pair_gran.html">pair_style gran/hooke/history</A> - granular potential without history effects
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<LI><A HREF = "pair_charmm.html">pair_style lj/charmm/coul/charmm</A> - CHARMM potential with cutoff Coulomb
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<LI><A HREF = "pair_charmm.html">pair_style lj/charmm/coul/charmm/implicit</A> - CHARMM for implicit solvent
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<LI><A HREF = "pair_charmm.html">pair_style lj/charmm/coul/long</A> - CHARMM with long-range Coulomb
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@ -103,9 +103,9 @@ the pair_style command, and coefficients specified by the associated
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"pair_style eam/fs"_pair_eam.html - Finnis-Sinclair EAM
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"pair_style eam/fs/opt"_pair_eam.html - optimized version of Finnis-Sinclair EAM
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"pair_style gayberne"_pair_gayberne.html - Gay-Berne ellipsoidal potential
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"pair_style gran/hertzian"_pair_gran.html - granular potential with Hertzian interactions
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"pair_style gran/history"_pair_gran.html - granular potential with history effects
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"pair_style gran/no_history"_pair_gran.html - granular potential without history effects
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"pair_style gran/hertz/history"_pair_gran.html - granular potential with Hertzian interactions
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"pair_style gran/hooke"_pair_gran.html - granular potential with history effects
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"pair_style gran/hooke/history"_pair_gran.html - granular potential without history effects
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"pair_style lj/charmm/coul/charmm"_pair_charmm.html - CHARMM potential with cutoff Coulomb
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"pair_style lj/charmm/coul/charmm/implicit"_pair_charmm.html - CHARMM for implicit solvent
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"pair_style lj/charmm/coul/long"_pair_charmm.html - CHARMM with long-range Coulomb
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