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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13615 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp 2015-07-16 21:53:47 +00:00
parent b96e60f567
commit e4e7165fd2
4 changed files with 48 additions and 36 deletions
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44
doc/Section_intro.html
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@ -101,8 +101,8 @@ favorite interatomic potential, boundary condition, or atom type, see
<A HREF = "Section_modify.html">Section_modify</A>, which describes how you can add
it to LAMMPS.
</P>
<H4>General features
</H4>
<H5>General features
</H5>
<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
@ -118,8 +118,8 @@ it to LAMMPS.
<LI> build as library, invoke LAMMPS thru library interface or provided Python wrapper
<LI> couple with other codes: LAMMPS calls other code, other code calls LAMMPS, umbrella code calls both
</UL>
<H4>Particle and model types
</H4>
<H5>Particle and model types
</H5>
<P>(<A HREF = "atom_style.html">atom style</A> command)
</P>
<UL><LI> atoms
@ -135,8 +135,8 @@ it to LAMMPS.
<LI> rigid collections of particles
<LI> hybrid combinations of these
</UL>
<H4>Force fields
</H4>
<H5>Force fields
</H5>
<P>(<A HREF = "pair_style.html">pair style</A>, <A HREF = "bond_style.html">bond style</A>,
<A HREF = "angle_style.html">angle style</A>, <A HREF = "dihedral_style.html">dihedral style</A>,
<A HREF = "improper_style.html">improper style</A>, <A HREF = "kspace_style.html">kspace style</A>
@ -163,8 +163,8 @@ commands)
<LI> hybrid potentials: multiple pair, bond, angle, dihedral, improper potentials can be used in one simulation
<LI> overlaid potentials: superposition of multiple pair potentials
</UL>
<H4>Atom creation
</H4>
<H5>Atom creation
</H5>
<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>, <A HREF = "replicate.html">replicate</A> commands)
@ -175,8 +175,8 @@ commands)
<LI> replicate existing atoms multiple times
<LI> displace atoms
</UL>
<H4>Ensembles, constraints, and boundary conditions
</H4>
<H5>Ensembles, constraints, and boundary conditions
</H5>
<P>(<A HREF = "fix.html">fix</A> command)
</P>
<UL><LI> 2d or 3d systems
@ -194,8 +194,8 @@ commands)
<LI> non-equilibrium molecular dynamics (NEMD)
<LI> variety of additional boundary conditions and constraints
</UL>
<H4>Integrators
</H4>
<H5>Integrators
</H5>
<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
@ -205,12 +205,12 @@ commands)
<LI> rRESPA hierarchical timestepping
<LI> rerun command for post-processing of dump files
</UL>
<H4>Diagnostics
</H4>
<H5>Diagnostics
</H5>
<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>
<H5>Output
</H5>
<P>(<A HREF = "dump.html">dump</A>, <A HREF = "restart.html">restart</A> commands)
</P>
<UL><LI> log file of thermodynamic info
@ -223,15 +223,15 @@ commands)
<LI> time averaging of system-wide quantities
<LI> atom snapshots in native, XYZ, XTC, DCD, CFG formats
</UL>
<H4>Multi-replica models
</H4>
<H5>Multi-replica models
</H5>
<P><A HREF = "neb.html">nudged elastic band</A>
<A HREF = "prd.html">parallel replica dynamics</A>
<A HREF = "tad.html">temperature accelerated dynamics</A>
<A HREF = "temper.html">parallel tempering</A>
</P>
<H4>Pre- and post-processing
</H4>
<H5>Pre- and post-processing
</H5>
<UL><LI>Various pre- and post-processing serial tools are packaged
with LAMMPS; see these <A HREF = "Section_tools.html">doc pages</A>.
@ -245,8 +245,8 @@ Pizza.py WWW site</A>.
<H4>Specialized features
</H4>
<H5>Specialized features
</H5>
<P>These are LAMMPS capabilities which you may not think of as typical
molecular dynamics options:
</P>

22
doc/Section_intro.txt
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@ -97,7 +97,7 @@ favorite interatomic potential, boundary condition, or atom type, see
"Section_modify"_Section_modify.html, which describes how you can add
it to LAMMPS.
General features :h4
General features :h5
runs on a single processor or in parallel
distributed-memory message-passing parallelism (MPI)
@ -114,7 +114,7 @@ General features :h4
build as library, invoke LAMMPS thru library interface or provided Python wrapper
couple with other codes: LAMMPS calls other code, other code calls LAMMPS, umbrella code calls both :ul
Particle and model types :h4
Particle and model types :h5
("atom style"_atom_style.html command)
atoms
@ -130,7 +130,7 @@ Particle and model types :h4
rigid collections of particles
hybrid combinations of these :ul
Force fields :h4
Force fields :h5
("pair style"_pair_style.html, "bond style"_bond_style.html,
"angle style"_angle_style.html, "dihedral style"_dihedral_style.html,
"improper style"_improper_style.html, "kspace style"_kspace_style.html
@ -166,7 +166,7 @@ commands)
potentials can be used in one simulation
overlaid potentials: superposition of multiple pair potentials :ul
Atom creation :h4
Atom creation :h5
("read_data"_read_data.html, "lattice"_lattice.html,
"create_atoms"_create_atoms.html, "delete_atoms"_delete_atoms.html,
"displace_atoms"_displace_atoms.html, "replicate"_replicate.html commands)
@ -177,7 +177,7 @@ Atom creation :h4
replicate existing atoms multiple times
displace atoms :ul
Ensembles, constraints, and boundary conditions :h4
Ensembles, constraints, and boundary conditions :h5
("fix"_fix.html command)
2d or 3d systems
@ -195,7 +195,7 @@ Ensembles, constraints, and boundary conditions :h4
non-equilibrium molecular dynamics (NEMD)
variety of additional boundary conditions and constraints :ul
Integrators :h4
Integrators :h5
("run"_run.html, "run_style"_run_style.html, "minimize"_minimize.html commands)
velocity-Verlet integrator
@ -205,11 +205,11 @@ Integrators :h4
rRESPA hierarchical timestepping
rerun command for post-processing of dump files :ul
Diagnostics :h4
Diagnostics :h5
see the various flavors of the "fix"_fix.html and "compute"_compute.html commands :ul
Output :h4
Output :h5
("dump"_dump.html, "restart"_restart.html commands)
log file of thermodynamic info
@ -222,14 +222,14 @@ Output :h4
time averaging of system-wide quantities
atom snapshots in native, XYZ, XTC, DCD, CFG formats :ul
Multi-replica models :h4
Multi-replica models :h5
"nudged elastic band"_neb.html
"parallel replica dynamics"_prd.html
"temperature accelerated dynamics"_tad.html
"parallel tempering"_temper.html
Pre- and post-processing :h4
Pre- and post-processing :h5
Various pre- and post-processing serial tools are packaged
with LAMMPS; see these "doc pages"_Section_tools.html. :ulb,l
@ -243,7 +243,7 @@ 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
Specialized features :h5
These are LAMMPS capabilities which you may not think of as typical
molecular dynamics options:

10
doc/write_data.html
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@ -19,9 +19,10 @@
<LI>zero or more keyword/value pairs may be appended
<LI>keyword = <I>pair</I>
<LI>keyword = <I>pair</I> or <I>nocoeff</I>
<PRE> <I>pair</I> value = <I>ii</I> or <I>ij</I>
<PRE> <I>nocoeff</I> = do not write out force field info
<I>pair</I> value = <I>ii</I> or <I>ij</I>
<I>ii</I> = write one line of pair coefficient info per atom type
<I>ij</I> = write one line of pair coefficient info per IJ atom type pair
</PRE>
@ -84,6 +85,11 @@ data file is read.
</P>
<HR>
<P>The <I>nocoeff</I> keyword requests that no force field parameters should
be written to the data file. This can be very helpful, if one wants
to make significant changes to the force field or if the parameters
are read in separately anyway, e.g. from an include file.
</P>
<P>The <I>pair</I> keyword lets you specify in what format the pair
coefficient information is written into the data file. If the value
is specified as <I>ii</I>, then one line per atom type is written, to

8
doc/write_data.txt
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@ -14,7 +14,8 @@ write_data file keyword value ... :pre
file = name of data file to write out :ulb,l
zero or more keyword/value pairs may be appended :l
keyword = {pair} :l
keyword = {pair} or {nocoeff} :l
{nocoeff} = do not write out force field info
{pair} value = {ii} or {ij}
{ii} = write one line of pair coefficient info per atom type
{ij} = write one line of pair coefficient info per IJ atom type pair :pre
@ -77,6 +78,11 @@ data file is read.
:line
The {nocoeff} keyword requests that no force field parameters should
be written to the data file. This can be very helpful, if one wants
to make significant changes to the force field or if the parameters
are read in separately anyway, e.g. from an include file.
The {pair} keyword lets you specify in what format the pair
coefficient information is written into the data file. If the value
is specified as {ii}, then one line per atom type is written, to