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>.
|
||||
<TR><TD >nemd</TD><TD > non-equilibrium MD of 2d sheared system</TD></TR>
|
||||
<TR><TD >obstacle</TD><TD > flow around two voids in a 2d channel</TD></TR>
|
||||
<TR><TD >peptide</TD><TD > dynamics of a small solvated peptide chain (5-mer)</TD></TR>
|
||||
<TR><TD >peri</TD><TD > Peridynamics example of cylinder hit by projectile</TD></TR>
|
||||
<TR><TD >pour</TD><TD > pouring of granular particles into a 3d box, then chute flow</TD></TR>
|
||||
<TR><TD >rigid</TD><TD > rigid bodies modeled as independent or coupled</TD></TR>
|
||||
<TR><TD >shear</TD><TD > sideways shear applied to 2d solid, with and without a void
|
||||
|
||||
@ -41,6 +41,7 @@ min: energy minimization of 2d LJ melt
|
||||
nemd: non-equilibrium MD of 2d sheared system
|
||||
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
|
||||
rigid: rigid bodies modeled as independent or coupled
|
||||
shear: sideways shear applied to 2d solid, with and without a void :tb(s=:)
|
||||
|
||||
@ -32,7 +32,6 @@ are being worked on; some haven't been implemented because of lack of
|
||||
time or interest; others are just a lot of work!
|
||||
</P>
|
||||
<UL><LI>NPT with changing box shape (Parinello-Rahman)
|
||||
<LI>bond creation potentials
|
||||
<LI>long-range point dipole solver
|
||||
<LI>torsional shear boundary conditions and temperature calculation
|
||||
<LI>charge equilibration
|
||||
|
||||
@ -29,7 +29,6 @@ are being worked on; some haven't been implemented because of lack of
|
||||
time or interest; others are just a lot of work!
|
||||
|
||||
NPT with changing box shape (Parinello-Rahman)
|
||||
bond creation potentials
|
||||
long-range point dipole solver
|
||||
torsional shear boundary conditions and temperature calculation
|
||||
charge equilibration
|
||||
|
||||
@ -98,6 +98,21 @@ favorite interatomic potential, boundary condition, or atom type, see
|
||||
<A HREF = "Section_modify.html">this section</A>, which describes how you can add it to
|
||||
LAMMPS.
|
||||
</P>
|
||||
<P>General features: h4
|
||||
</P>
|
||||
<UL><LI> runs on a single processor or in parallel
|
||||
<LI> distributed-memory message-passing parallelism (MPI)
|
||||
<LI> spatial-decomposition of simulation domain for parallelism
|
||||
<LI> open-source distribution
|
||||
<LI> highly portable C++
|
||||
<LI> optional libraries needed: MPI and single-processor FFT
|
||||
<LI> easy to extend with new features and functionality
|
||||
<LI> in parallel, run one or multiple simulations simultaneously
|
||||
<LI> runs from an input script
|
||||
<LI> syntax for defining and using variables and formulas
|
||||
<LI> syntax for looping over runs and breaking out of loops
|
||||
<LI> run a series of simluations from one script
|
||||
</UL>
|
||||
<H4>Kinds of systems LAMMPS can simulate:
|
||||
</H4>
|
||||
<P>(<A HREF = "atom_style.html">atom style</A> command)
|
||||
@ -111,7 +126,7 @@ LAMMPS.
|
||||
<LI> coarse-grained mesoscale models
|
||||
<LI> ellipsoidal particles
|
||||
<LI> point dipolar particles
|
||||
<LI> hybrid systems
|
||||
<LI> hybrid combinations of these
|
||||
</UL>
|
||||
<H4>Force fields:
|
||||
</H4>
|
||||
@ -123,7 +138,8 @@ commands)
|
||||
<UL><LI> pairwise potentials: Lennard-Jones, Buckingham, Morse, Yukawa, soft, class 2 (COMPASS), tabulated
|
||||
<LI> charged pairwise potentials: Coulombic, point-dipole
|
||||
<LI> manybody potentials: EAM, Finnis/Sinclair EAM, modified EAM (MEAM), Stillinger-Weber, Tersoff, AI-REBO
|
||||
<LI> coarse-grain potentials: granular, DPD, GayBerne, REsquared, colloidal
|
||||
<LI> coarse-grain potentials: DPD, GayBerne, REsquared, colloidal
|
||||
<LI> mesoscopic potentials: granular, Peridynamics
|
||||
<LI> bond potentials: harmonic, FENE, Morse, nonlinear, class 2, quartic (breakable)
|
||||
<LI> angle potentials: harmonic, CHARMM, cosine, cosine/squared, class 2 (COMPASS)
|
||||
<LI> dihedral potentials: harmonic, CHARMM, multi-harmonic, helix, class 2 (COMPASS), OPLS
|
||||
@ -160,6 +176,7 @@ commands)
|
||||
<LI> harmonic (umbrella) constraint forces
|
||||
<LI> independent or coupled rigid body integration
|
||||
<LI> SHAKE bond and angle constraints
|
||||
<LI> bond breaking, formation, swapping
|
||||
<LI> walls of various kinds
|
||||
<LI> targeted molecular dynamics (TMD) and steered molecule dynamics (SMD) constraints
|
||||
<LI> non-equilibrium molecular dynamics (NEMD)
|
||||
@ -171,10 +188,9 @@ commands)
|
||||
</P>
|
||||
<UL><LI> velocity-Verlet integrator
|
||||
<LI> Brownian dynamics
|
||||
<LI> energy minimization via conjugate gradient relaxation
|
||||
<LI> energy minimization via conjugate gradient or steepest descent relaxation
|
||||
<LI> rRESPA hierarchical timestepping
|
||||
<LI> parallel tempering (replica exchange)
|
||||
<LI> run multiple independent simulations simultaneously
|
||||
</UL>
|
||||
<H4>Output:
|
||||
</H4>
|
||||
@ -455,6 +471,8 @@ the list.
|
||||
|
||||
|
||||
<DIV ALIGN=center><TABLE BORDER=1 >
|
||||
<TR><TD >Tersoff/ZBL potential </TD><TD > Dave Farrell (Northwestern U)</TD></TR>
|
||||
<TR><TD >peridynamics </TD><TD > Mike Parks (Sandia)</TD></TR>
|
||||
<TR><TD >fix smd for steered MD </TD><TD > Axel Kohlmeyer (U Penn)</TD></TR>
|
||||
<TR><TD >GROMACS pair potentials </TD><TD > Mark Stevens (Sandia)</TD></TR>
|
||||
<TR><TD >lmp2vmd tool </TD><TD > Axel Kohlmeyer (U Penn)</TD></TR>
|
||||
|
||||
@ -95,6 +95,21 @@ favorite interatomic potential, boundary condition, or atom type, see
|
||||
"this section"_Section_modify.html, which describes how you can add it to
|
||||
LAMMPS.
|
||||
|
||||
General features: h4
|
||||
|
||||
runs on a single processor or in parallel
|
||||
distributed-memory message-passing parallelism (MPI)
|
||||
spatial-decomposition of simulation domain for parallelism
|
||||
open-source distribution
|
||||
highly portable C++
|
||||
optional libraries needed: 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
|
||||
|
||||
Kinds of systems LAMMPS can simulate: :h4
|
||||
("atom style"_atom_style.html command)
|
||||
|
||||
@ -107,7 +122,7 @@ Kinds of systems LAMMPS can simulate: :h4
|
||||
coarse-grained mesoscale models
|
||||
ellipsoidal particles
|
||||
point dipolar particles
|
||||
hybrid systems :ul
|
||||
hybrid combinations of these :ul
|
||||
|
||||
Force fields: :h4
|
||||
("pair style"_pair_style.html, "bond style"_bond_style.html,
|
||||
@ -120,7 +135,8 @@ commands)
|
||||
charged pairwise potentials: Coulombic, point-dipole
|
||||
manybody potentials: EAM, Finnis/Sinclair EAM, modified EAM (MEAM), \
|
||||
Stillinger-Weber, Tersoff, AI-REBO
|
||||
coarse-grain potentials: granular, DPD, GayBerne, REsquared, colloidal
|
||||
coarse-grain potentials: DPD, GayBerne, REsquared, colloidal
|
||||
mesoscopic potentials: granular, Peridynamics
|
||||
bond potentials: harmonic, FENE, Morse, nonlinear, class 2, \
|
||||
quartic (breakable)
|
||||
angle potentials: harmonic, CHARMM, cosine, cosine/squared, \
|
||||
@ -160,6 +176,7 @@ Ensembles, constraints, and boundary conditions: :h4
|
||||
harmonic (umbrella) constraint forces
|
||||
independent or coupled rigid body integration
|
||||
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)
|
||||
@ -170,10 +187,9 @@ Integrators: :h4
|
||||
|
||||
velocity-Verlet integrator
|
||||
Brownian dynamics
|
||||
energy minimization via conjugate gradient relaxation
|
||||
energy minimization via conjugate gradient or steepest descent relaxation
|
||||
rRESPA hierarchical timestepping
|
||||
parallel tempering (replica exchange)
|
||||
run multiple independent simulations simultaneously :ul
|
||||
parallel tempering (replica exchange) :ul
|
||||
|
||||
Output: :h4
|
||||
("dump"_dump.html, "restart"_restart.html commands)
|
||||
@ -441,6 +457,8 @@ the list.
|
||||
|
||||
:link(sjp,http://www.cs.sandia.gov/~sjplimp)
|
||||
|
||||
Tersoff/ZBL potential : Dave Farrell (Northwestern U)
|
||||
peridynamics : Mike Parks (Sandia)
|
||||
fix smd for steered MD : Axel Kohlmeyer (U Penn)
|
||||
GROMACS pair potentials : Mark Stevens (Sandia)
|
||||
lmp2vmd tool : Axel Kohlmeyer (U Penn)
|
||||
|
||||
@ -297,6 +297,7 @@ typing "make package".
|
||||
<TR><TD >meam </TD><TD > modified embedded atom method (MEAM) potential</TD></TR>
|
||||
<TR><TD >molecule </TD><TD > force fields for molecular systems</TD></TR>
|
||||
<TR><TD >opt </TD><TD > optimized versions of a few pair potentials</TD></TR>
|
||||
<TR><TD >peri </TD><TD > Peridynamics model and potential</TD></TR>
|
||||
<TR><TD >poems </TD><TD > coupled rigid body motion</TD></TR>
|
||||
<TR><TD >xtc </TD><TD > dump atom snapshots in XTC format
|
||||
</TD></TR></TABLE></DIV>
|
||||
|
||||
@ -291,6 +291,7 @@ manybody : metal, 3-body, bond-order potentials
|
||||
meam : modified embedded atom method (MEAM) potential
|
||||
molecule : force fields for molecular systems
|
||||
opt : optimized versions of a few pair potentials
|
||||
peri : Peridynamics model and potential
|
||||
poems : coupled rigid body motion
|
||||
xtc : dump atom snapshots in XTC format :tb(s=:)
|
||||
|
||||
|
||||
@ -127,7 +127,6 @@ available in LAMMPS:
|
||||
<LI><A HREF = "compute_temp_asphere.html">temp/asphere</A> - temperature of aspherical particles
|
||||
<LI><A HREF = "compute_temp_com.html">temp/com</A> - temperature after subtracting center-of-mass velocity
|
||||
<LI><A HREF = "compute_temp_deform.html">temp/deform</A> - temperature excluding box deformation velocity
|
||||
<LI><A HREF = "compute_temp_dipole.html">temp/dipole</A> - temperature of point dipolar particles
|
||||
<LI><A HREF = "compute_temp_partial.html">temp/partial</A> - temperature excluding one or more dimensions of velocity
|
||||
<LI><A HREF = "compute_temp_ramp.html">temp/ramp</A> - temperature excluding ramped velocity component
|
||||
<LI><A HREF = "compute_temp_region.html">temp/region</A> - temperature of a region of atoms
|
||||
|
||||
@ -124,7 +124,6 @@ available in LAMMPS:
|
||||
"temp/asphere"_compute_temp_asphere.html - temperature of aspherical particles
|
||||
"temp/com"_compute_temp_com.html - temperature after subtracting center-of-mass velocity
|
||||
"temp/deform"_compute_temp_deform.html - temperature excluding box deformation velocity
|
||||
"temp/dipole"_compute_temp_dipole.html - temperature of point dipolar particles
|
||||
"temp/partial"_compute_temp_partial.html - temperature excluding one or more dimensions of velocity
|
||||
"temp/ramp"_compute_temp_ramp.html - temperature excluding ramped velocity component
|
||||
"temp/region"_compute_temp_region.html - temperature of a region of atoms
|
||||
|
||||
@ -35,11 +35,12 @@
|
||||
|
||||
<LI>args = list of arguments for a particular style
|
||||
|
||||
<LI> <I>xplane</I> or <I>yplane</I> or <I>zplane</I> args = lo hi
|
||||
<PRE> <I>xplane</I> or <I>yplane</I> or <I>zplane</I> args = lo hi
|
||||
lo,hi = position of lower and upper plane (distance units), either can be NULL)
|
||||
<I>zcylinder</I> args = radius
|
||||
radius = cylinder radius (distance units)
|
||||
zero or more keyword/value pairs may be appended to args
|
||||
</PRE>
|
||||
<LI>zero or more keyword/value pairs may be appended to args
|
||||
|
||||
<LI>keyword = <I>wiggle</I> or <I>shear</I>
|
||||
|
||||
|
||||
@ -25,7 +25,7 @@ args = list of arguments for a particular style :l
|
||||
{xplane} or {yplane} or {zplane} args = lo hi
|
||||
lo,hi = position of lower and upper plane (distance units), either can be NULL)
|
||||
{zcylinder} args = radius
|
||||
radius = cylinder radius (distance units)
|
||||
radius = cylinder radius (distance units) :pre
|
||||
zero or more keyword/value pairs may be appended to args :l
|
||||
keyword = {wiggle} or {shear} :l
|
||||
{wiggle} values = dim amplitude period
|
||||
|
||||
@ -105,9 +105,9 @@ the pair_style command, and coefficients specified by the associated
|
||||
<LI><A HREF = "pair_eam.html">pair_style eam/fs</A> - Finnis-Sinclair EAM
|
||||
<LI><A HREF = "pair_eam.html">pair_style eam/fs/opt</A> - optimized version of Finnis-Sinclair EAM
|
||||
<LI><A HREF = "pair_gayberne.html">pair_style gayberne</A> - Gay-Berne ellipsoidal potential
|
||||
<LI><A HREF = "pair_gran.html">pair_style gran/hertzian</A> - granular potential with Hertzian interactions
|
||||
<LI><A HREF = "pair_gran.html">pair_style gran/history</A> - granular potential with history effects
|
||||
<LI><A HREF = "pair_gran.html">pair_style gran/no_history</A> - granular potential without history effects
|
||||
<LI><A HREF = "pair_gran.html">pair_style gran/hertz/history</A> - granular potential with Hertzian interactions
|
||||
<LI><A HREF = "pair_gran.html">pair_style gran/hooke</A> - granular potential with history effects
|
||||
<LI><A HREF = "pair_gran.html">pair_style gran/hooke/history</A> - granular potential without history effects
|
||||
<LI><A HREF = "pair_charmm.html">pair_style lj/charmm/coul/charmm</A> - CHARMM potential with cutoff Coulomb
|
||||
<LI><A HREF = "pair_charmm.html">pair_style lj/charmm/coul/charmm/implicit</A> - CHARMM for implicit solvent
|
||||
<LI><A HREF = "pair_charmm.html">pair_style lj/charmm/coul/long</A> - CHARMM with long-range Coulomb
|
||||
|
||||
@ -101,9 +101,9 @@ the pair_style command, and coefficients specified by the associated
|
||||
"pair_style eam/fs"_pair_eam.html - Finnis-Sinclair EAM
|
||||
"pair_style eam/fs/opt"_pair_eam.html - optimized version of Finnis-Sinclair EAM
|
||||
"pair_style gayberne"_pair_gayberne.html - Gay-Berne ellipsoidal potential
|
||||
"pair_style gran/hertzian"_pair_gran.html - granular potential with Hertzian interactions
|
||||
"pair_style gran/history"_pair_gran.html - granular potential with history effects
|
||||
"pair_style gran/no_history"_pair_gran.html - granular potential without history effects
|
||||
"pair_style gran/hertz/history"_pair_gran.html - granular potential with Hertzian interactions
|
||||
"pair_style gran/hooke"_pair_gran.html - granular potential with history effects
|
||||
"pair_style gran/hooke/history"_pair_gran.html - granular potential without history effects
|
||||
"pair_style lj/charmm/coul/charmm"_pair_charmm.html - CHARMM potential with cutoff Coulomb
|
||||
"pair_style lj/charmm/coul/charmm/implicit"_pair_charmm.html - CHARMM for implicit solvent
|
||||
"pair_style lj/charmm/coul/long"_pair_charmm.html - CHARMM with long-range Coulomb
|
||||
|
||||
@ -107,9 +107,9 @@ the pair_style command, and coefficients specified by the associated
|
||||
<LI><A HREF = "pair_eam.html">pair_style eam/fs</A> - Finnis-Sinclair EAM
|
||||
<LI><A HREF = "pair_eam.html">pair_style eam/fs/opt</A> - optimized version of Finnis-Sinclair EAM
|
||||
<LI><A HREF = "pair_gayberne.html">pair_style gayberne</A> - Gay-Berne ellipsoidal potential
|
||||
<LI><A HREF = "pair_gran.html">pair_style gran/hertzian</A> - granular potential with Hertzian interactions
|
||||
<LI><A HREF = "pair_gran.html">pair_style gran/history</A> - granular potential with history effects
|
||||
<LI><A HREF = "pair_gran.html">pair_style gran/no_history</A> - granular potential without history effects
|
||||
<LI><A HREF = "pair_gran.html">pair_style gran/hertz/history</A> - granular potential with Hertzian interactions
|
||||
<LI><A HREF = "pair_gran.html">pair_style gran/hooke</A> - granular potential with history effects
|
||||
<LI><A HREF = "pair_gran.html">pair_style gran/hooke/history</A> - granular potential without history effects
|
||||
<LI><A HREF = "pair_charmm.html">pair_style lj/charmm/coul/charmm</A> - CHARMM potential with cutoff Coulomb
|
||||
<LI><A HREF = "pair_charmm.html">pair_style lj/charmm/coul/charmm/implicit</A> - CHARMM for implicit solvent
|
||||
<LI><A HREF = "pair_charmm.html">pair_style lj/charmm/coul/long</A> - CHARMM with long-range Coulomb
|
||||
|
||||
@ -103,9 +103,9 @@ the pair_style command, and coefficients specified by the associated
|
||||
"pair_style eam/fs"_pair_eam.html - Finnis-Sinclair EAM
|
||||
"pair_style eam/fs/opt"_pair_eam.html - optimized version of Finnis-Sinclair EAM
|
||||
"pair_style gayberne"_pair_gayberne.html - Gay-Berne ellipsoidal potential
|
||||
"pair_style gran/hertzian"_pair_gran.html - granular potential with Hertzian interactions
|
||||
"pair_style gran/history"_pair_gran.html - granular potential with history effects
|
||||
"pair_style gran/no_history"_pair_gran.html - granular potential without history effects
|
||||
"pair_style gran/hertz/history"_pair_gran.html - granular potential with Hertzian interactions
|
||||
"pair_style gran/hooke"_pair_gran.html - granular potential with history effects
|
||||
"pair_style gran/hooke/history"_pair_gran.html - granular potential without history effects
|
||||
"pair_style lj/charmm/coul/charmm"_pair_charmm.html - CHARMM potential with cutoff Coulomb
|
||||
"pair_style lj/charmm/coul/charmm/implicit"_pair_charmm.html - CHARMM for implicit solvent
|
||||
"pair_style lj/charmm/coul/long"_pair_charmm.html - CHARMM with long-range Coulomb
|
||||
|
||||
Reference in New Issue
Block a user