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doc/Section_intro.txt
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@ -105,6 +105,8 @@ Kinds of systems LAMMPS can simulate: :h4
metals
granular materials
coarse-grained mesoscale models
ellipsoidal particles
point dipolar particles
hybrid systems :ul
Force fields: :h4
@ -113,18 +115,21 @@ Force fields: :h4
"improper style"_improper_style.html, "kspace style"_kspace_style.html
commands)
pairwise potentials: Lennard-Jones, Coulombic, Buckingham, Morse, \
Yukawa, frictional granular, Debye, soft, DPD, class 2 (COMPASS), \
tabulated, hybrid
manybody potentials: EAM, Finnis/Sinclair, modified EAM (MEAM), \
pairwise potentials: Lennard-Jones, Buckingham, Morse, \
Yukawa, Debye, soft, class 2 (COMPASS), tabulated
charged pairwise potentials: Coulombic, point-dipole
manybody potentials: EAM, Finnis/Sinclair EAM, modified EAM (MEAM), \
Stillinger-Weber, Tersoff
coarse-grain potentials: granular, DPD, GayBerne, colloidal
bond potentials: harmonic, FENE, Morse, nonlinear, class 2, \
quartic (breakable), hybrid
quartic (breakable)
angle potentials: harmonic, CHARMM, cosine, cosine/squared, \
class 2 (COMPASS), hybrid
class 2 (COMPASS)
dihedral potentials: harmonic, CHARMM, multi-harmonic, helix, \
class 2 (COMPASS), OPLS, hybrid
improper potentials: harmonic, cvff, class 2 (COMPASS), hybrid
class 2 (COMPASS), OPLS
improper potentials: harmonic, cvff, class 2 (COMPASS)
hybrid potentials: multiple pair, bond, angle, dihedral, improper \
potentials can be used
polymer potentials: all-atom, united-atom, bead-spring, breakable
water potentials: TIP3P, TIP4P, SPC
long-range Coulombics: Ewald, PPPM (similar to particle-mesh Ewald)
@ -143,18 +148,19 @@ Creation of atoms: :h4
Ensembles, constraints, and boundary conditions: :h4
("fix"_fix.html command)
2d or 3d systems
orthogonal or non-orthogonal (triclinic symmetry) simulation domains
constant NVE, NVT, NPT, NPH integrators
thermostatting options for groups and geometric regions of atoms
pressure control via Nose/Hoover barostatting in 1 to 3 dimensions
volume rescaling
altered motion via velocity and force constraints
simulation box deformation (tensile and shear)
harmonic (umbrella) constraint forces
dragging of atoms to new positions
independent or coupled rigid body integration
SHAKE bond and angle constraints
wall constraints of various kinds
walls of various kinds
targeted molecular dynamics (TMD) constraints
gravity :ul
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)
@ -164,15 +170,17 @@ Integrators: :h4
energy minimization via conjugate gradient relaxation
rRESPA hierarchical timestepping
parallel tempering (replica exchange)
multiple independent simulations simultaneously :ul
run multiple independent simulations simultaneously :ul
Output: :h4
("dump"_dump.html, "restart"_restart.html commands)
log file of thermodynanmic info
text dump files of atom coords, velocities, other per-atom quantities
binary restart files
text dump files of atom coords, velocities, other per-atom attributes
atom snapshots in native, XYZ, XTC, DCD formats
per-atom energy, stress, centro-symmetry parameter :ul
per-atom energy, stress, centro-symmetry parameter
user-defined system-wide (log file) or per-atom (dump file) calculations
atom snapshots in native, XYZ, XTC, DCD formats :ul
Pre- and post-processing: :h4
@ -226,14 +234,14 @@ to all atoms and bonds. LAMMPS will not build molecular systems and
assign force-field parameters for you.
For atomic systems LAMMPS provides a "create_atoms"_create_atoms.html
command which places atoms on solid-state lattices (fcc, bcc, etc).
Assigning small numbers of force field coefficients can be done via
the "pair coeff"_pair_coeff.html, "bond coeff"_bond_coeff.html, "angle
coeff"_angle_coeff.html, etc commands. For molecular systems or more
complicated simulation geometries, users typically use another code as
a builder and convert its output to LAMMPS input format, or write
their own code to generate atom coordinate and molecular topology for
LAMMPS to read in.
command which places atoms on solid-state lattices (fcc, bcc,
user-defined, etc). Assigning small numbers of force field
coefficients can be done via the "pair coeff"_pair_coeff.html, "bond
coeff"_bond_coeff.html, "angle coeff"_angle_coeff.html, etc commands.
For molecular systems or more complicated simulation geometries, users
typically use another code as a builder and convert its output to
LAMMPS input format, or write their own code to generate atom
coordinate and molecular topology for LAMMPS to read in.
For complicated molecular systems (e.g. a protein), a multitude of
topology information and hundreds of force-field coefficients must
@ -247,12 +255,13 @@ Similarly, LAMMPS creates output files in a simple format. Most users
post-process these files with their own analysis tools or re-format
them for input into other programs, including visualization packages.
If you are convinced you need to compute something on-the-fly as
LAMMPS runs, see "this section"_Section_modify.html for a discussion of how you
can use the "dump"_dump.html and "fix"_fix.html commands to print out
data of your choosing. Keep in mind that complicated computations can
slow down the molecular dynamics timestepping, particularly if the
computations are not parallel, so it is often better to leave such
analysis to post-processing codes.
LAMMPS runs, see "this section"_Section_modify.html for a discussion
of how you can use the "dump"_dump.html and "compute"_compute.html and
"fix"_fix.html commands to print out data of your choosing. Keep in
mind that complicated computations can slow down the molecular
dynamics timestepping, particularly if the computations are not
parallel, so it is often better to leave such analysis to
post-processing codes.
A very simple (yet fast) visualizer is provided with the LAMMPS
package - see the "xmovie"_Section_tools.html#xmovie tool in "this
@ -261,10 +270,11 @@ atomic coordinates and animates them. We find it very useful for
debugging purposes. For high-quality visualization we recommend the
following packages:
"Raster3d"_http://www.bmsc.washington.edu/raster3d/raster3d.html
"RasMol"_http://www.openrasmol.org
"VMD"_http://www.ks.uiuc.edu/Research/vmd
"AtomEye"_http://164.107.79.177/Archive/Graphics/A :ul
"AtomEye"_http://164.107.79.177/Archive/Graphics/A
"PyMol"_http://pymol.sourceforge.net
"Raster3d"_http://www.bmsc.washington.edu/raster3d/raster3d.html
"RasMol"_http://www.openrasmol.org :ul
Other features that LAMMPS does not yet (and may never) support are
discussed in "this section"_Section_history.html.
@ -479,7 +489,19 @@ region prism : Pieter in't Veld (Sandia)
Stillinger-Weber and Tersoff potentials : Aidan Thompson (Sandia)
fix wall/lj126 : Mark Stevens (Sandia)
optimized pair potentials for lj/cut, charmm/long, eam, morse : James Fischer (High Performance Tech), David Richie and Vincent Natol (Stone Ridge Technologies)
MEAM potential : Greg Wagner (Sandia) :tb(s=:)
MEAM potential : Greg Wagner (Sandia)
fix ave/time and fix ave/spatial : Pieter in 't Veld (Sandia)
thermo_extract tool: Vikas Varshney (Wright Patterson AFB)
triclinic (non-orthogonal) simulation domains : Pieter in 't Veld (Sandia)
MATLAB post-processing scripts : Arun Subramaniyan (Purdue)
neighbor multi and communicate multi : Pieter in 't Veld (Sandia)
fix heat : Paul Crozier and Ed Webb (Sandia)
colloid potentials : Pieter in 't Veld (Sandia)
ellipsoidal particles : Mike Brown (Sandia)
GayBerne potential : Mike Brown (Sandia)
tensile and shear box deformations :
NEMD SLLOD integration : Pieter in 't Veld (Sandia)
pymol_asphere viz tool : Mike Brown (Sandia) :tb(s=:)
Other CRADA partners involved in the design and testing of LAMMPS were