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1
doc/Section_example.html
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@ -47,6 +47,7 @@ Site</A>.
<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 >prd</TD><TD > parallel replica dynamics of a vacancy diffusion in bulk Si</TD></TR>
<TR><TD >reax</TD><TD > simple example for ReaxFF force field</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

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doc/Section_example.txt
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@ -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=:)

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doc/Section_history.html
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@ -29,15 +29,24 @@ GranFlow for granular materials.
</P>
<P>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 <A HREF = "http://lammps.sandia.gov/future.html">this
page</A> on the LAMMPS WWW site for more details.
</P>
<UL><LI>coupling to finite elements
<LI>new ReaxFF implementation (in addition to existing one)
<LI>stochastic rotation dynamics
<UL><LI>Coupling to finite elements for streess-strain
<LI>New ReaxFF implementation
<LI>Nudged elastic band
<LI>Temperature accelerated dynamics
<LI>Triangulated particles
<LI>Stochastic rotation dynamics
<LI>Stokesian dynamics via fast lubrication dynamics
<LI>NPT with changing box shape (Parinello-Rahman)
<LI>long-range point-dipole solver
<LI>torsional shear boundary conditions and temperature calculation
<LI>Long-range point-dipole solver
<LI>Per-atom energy and stress for long-range Coulombics
<LI>Long-range Coulombics via Ewald and PPPM for triclinic boxes
<LI>Metadynamics
<LI>Direct Simulation Monte Carlo - DSMC
</UL>
<HR>

21
doc/Section_history.txt
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@ -26,15 +26,24 @@ 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"_lwsfuture on the LAMMPS WWW site for more details.
coupling to finite elements
new ReaxFF implementation (in addition to existing one)
stochastic rotation dynamics
:link(lwsfuture,http://lammps.sandia.gov/future.html)
Coupling to finite elements for streess-strain
New ReaxFF implementation
Nudged elastic band
Temperature accelerated dynamics
Triangulated particles
Stochastic rotation dynamics
Stokesian dynamics via fast lubrication dynamics
NPT with changing box shape (Parinello-Rahman)
long-range point-dipole solver
torsional shear boundary conditions and temperature calculation :ul
Long-range point-dipole solver
Per-atom energy and stress for long-range Coulombics
Long-range Coulombics via Ewald and PPPM for triclinic boxes
Metadynamics
Direct Simulation Monte Carlo - DSMC :ul
:line

87
doc/Section_intro.html
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@ -105,27 +105,27 @@ LAMMPS.
<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> optional libraries used: 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
<LI> run one or multiple simulations simultaneously (in parallel) from one script
</UL>
<H4>Kinds of systems LAMMPS can simulate
<H4>Particle and model types
</H4>
<P>(<A HREF = "atom_style.html">atom style</A> command)
</P>
<UL><LI> atomic (e.g. box of Lennard-Jonesium)
<LI> bead-spring polymers
<UL><LI> atoms
<LI> coarse-grained particles (e.g. bead-spring polymers)
<LI> united-atom polymers or organic molecules
<LI> all-atom polymers, organic molecules, proteins, DNA
<LI> metals
<LI> granular materials
<LI> coarse-grained mesoscale models
<LI> ellipsoidal particles
<LI> extended spherical and ellipsoidal particles
<LI> point dipolar particles
<LI> rigid collections of particles
<LI> hybrid combinations of these
</UL>
<H4>Force fields
@ -138,29 +138,32 @@ 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, ReaxFF
<LI> coarse-grain potentials: DPD, GayBerne, REsquared, colloidal
<LI> coarse-grained potentials: DPD, GayBerne, REsquared, colloidal, DLVO
<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
<LI> improper potentials: harmonic, cvff, class 2 (COMPASS)
<LI> hybrid potentials: multiple pair, bond, angle, dihedral, improper potentials can be used in one simulation
<LI> overlaid potentials: superposition of multiple pair potentials
<LI> polymer potentials: all-atom, united-atom, bead-spring, breakable
<LI> water potentials: TIP3P, TIP4P, SPC
<LI> implicit solvent potentials: hydrodynamic lubrication, Debye
<LI> long-range Coulombics and dispersion: Ewald, PPPM (similar to particle-mesh Ewald), Ewald/N for long-range Lennard-Jones
<LI> force-field compatibility with common CHARMM, AMBER, OPLS, GROMACS options
<LI> force-field compatibility with common CHARMM, AMBER, OPLS, GROMACS options
<LI> handful of GPU-enabled pair styles
</UL>
<H4>Creation of atoms
<P> hybrid potentials: multiple pair, bond, angle, dihedral, improper potentials can be used in one simulation
overlaid potentials: superposition of multiple pair potentials
</P>
<H4>Atom creation
</H4>
<P>(<A HREF = "read_data.html">read_data</A>, <A HREF = "lattice.html">lattice</A>,
<A HREF = "create_atoms.html">create_atoms</A>, <A HREF = "delete_atoms.html">delete_atoms</A>,
<A HREF = "displace_atoms.html">displace_atoms</A> commands)
<A HREF = "displace_atoms.html">displace_atoms</A>, <A HREF = "replicate.html">replicate</A> commands)
</P>
<UL><LI> read in atom coords from files
<LI> create atoms on one or more lattices (e.g. grain boundaries)
<LI> delete geometric or logical groups of atoms (e.g. voids)
<LI> replicate existing atoms multiple times
<LI> displace atoms
</UL>
<H4>Ensembles, constraints, and boundary conditions
@ -174,29 +177,26 @@ commands)
<LI> pressure control via Nose/Hoover or Berendsen barostatting in 1 to 3 dimensions
<LI> simulation box deformation (tensile and shear)
<LI> harmonic (umbrella) constraint forces
<LI> independent or coupled rigid body integration
<LI> rigid body constraints
<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)
<LI> variety of additional boundary conditions and constraints
</UL>
<H4>Integrators
</H4>
<P>(<A HREF = "run.html">run</A>, <A HREF = "run_style.html">run_style</A>, <A HREF = "temper.html">temper</A> commands)
<P>(<A HREF = "run.html">run</A>, <A HREF = "run_style.html">run_style</A>, <A HREF = "minimize.html">minimize</A> commands)
</P>
<UL><LI> velocity-Verlet integrator
<LI> Brownian dynamics
<LI> rigid body integration
<LI> energy minimization via conjugate gradient or steepest descent relaxation
<LI> rRESPA hierarchical timestepping
<LI> parallel tempering (replica exchange)
<LI> rRESPA hierarchical timestepping
</UL>
<H4>Diagnostics
</H4>
<P>(<A HREF = "fix.html">fix</A> command, <A HREF = "compute.html">compute</A> command)
</P>
<UL><LI> see the various flavors of the fix and compute commands
<UL><LI> see the various flavors of the <A HREF = "fix.html">fix</A> and <A HREF = "compute.html">compute</A> commands
</UL>
<H4>Output
</H4>
@ -209,20 +209,38 @@ commands)
<LI> user-defined system-wide (log file) or per-atom (dump file) calculations
<LI> spatial and time averaging of per-atom quantities
<LI> time averaging of system-wide quantities
<LI> atom snapshots in native, XYZ, XTC, DCD formats
<LI> atom snapshots in native, XYZ, XTC, DCD, CFG formats
</UL>
<H4>Pre- and post-processing
</H4>
<P>Our group has also written and released a separate toolkit called
<UL><LI>Various pre- and post-processing serial tools are packaged
with LAMMPS; see these <A HREF = "Section_tools.html">doc pages</A>.
<LI>Our group has also written and released a separate toolkit called
<A HREF = "http://www.sandia.gov/~sjplimp/pizza.html">Pizza.py</A> which provides tools for doing setup, analysis,
plotting, and visualization for LAMMPS simulations. Pizza.py is
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
Pizza.py WWW site</A>.
Pizza.py WWW site</A>.
</UL>
<H4>Specialized features
</H4>
<P>These are LAMMPS capabilities which you may not think of as typical
molecular dynamics options:
</P>
<UL><LI><A HREF = "fix_imd.html">real-time visualization and interactive MD</A>
<LI><A HREF = "fix_atc.html">atom-to-continuum coupling</A> with finite elements
<LI>coupled rigid body integration via the <A HREF = "fix_poems.html">POEMS</A> library
<LI><A HREF = "temper.html">parallel tempering</A>
<LI><A HREF = "prd.html">parallel replica dynamics</A>
<LI><A HREF = "pair_dsmc.html">Direct Simulation Monte Carlo</A> for low-density fluids
<LI><A HREF = "pair_peri.html">Peridynamics mesoscale modeling</A>
<LI><A HREF = "fix_tmd.html">targeted</A> and <A HREF = "fix_smd.html">steered</A> molecular dynamics
<LI><A HREF = "fix_ttm.html">two-temperature electron model</A>
</UL>
<HR>
<A NAME = "1_3"></A><H4>1.3 LAMMPS non-features
@ -477,6 +495,19 @@ the list.
<DIV ALIGN=center><TABLE BORDER=1 >
<TR><TD >pair yukawa/colloid </TD><TD > Randy Schunk (Sandia)</TD></TR>
<TR><TD >fix wall/colloid </TD><TD > Jeremy Lechman (Sandia)</TD></TR>
<TR><TD >pair_style dsmc for Direct Simulation Monte Carlo (DSMC) modeling </TD><TD > Paul Crozier (Sandia)</TD></TR>
<TR><TD >fix imd for real-time viz and interactive MD </TD><TD > Axel Kohlmeyer (Temple Univ)</TD></TR>
<TR><TD >concentration-dependent EAM potential </TD><TD > Alexander Stukowski (Technical University of Darmstadt)</TD></TR>
<TR><TD >parallel replica dymamics (PRD) </TD><TD > Mike Brown (Sandia)</TD></TR>
<TR><TD >min_style hftn </TD><TD > Todd Plantenga (Sandia)</TD></TR>
<TR><TD >fix atc </TD><TD > Reese Jones, Jon Zimmerman, Jeremy Templeton (Sandia)</TD></TR>
<TR><TD >dump cfg </TD><TD > Liang Wan (Chinese Academy of Sciences)</TD></TR>
<TR><TD >fix nvt with Nose/Hoover chains </TD><TD > Andy Ballard (U Maryland)</TD></TR>
<TR><TD >pair_style lj/cut/gpu, pair_style gayberne/gpu </TD><TD > Mike Brown (Sandia)</TD></TR>
<TR><TD >pair_style lj96/cut, bond_style table, angle_style table </TD><TD > Chuanfu Luo</TD></TR>
<TR><TD >fix langevin tally </TD><TD > Carolyn Phillips (U Michigan)</TD></TR>
<TR><TD >compute heat/flux for Green-Kubo </TD><TD > Reese Jones (Sandia), Philip Howell (Siemens), Vikas Varsney (AFRL)</TD></TR>
<TR><TD >region cone </TD><TD > Pim Schravendijk</TD></TR>
<TR><TD >fix reax/bonds </TD><TD > Aidan Thompson (Sandia)</TD></TR>

77
doc/Section_intro.txt
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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
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)