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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1564 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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2008-03-01 01:13:20 +00:00
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doc/Section_howto.html
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@ -556,17 +556,17 @@ functions:
<PRE>void lammps_open(int, char **, MPI_Comm, void **);
void lammps_close(void *);
void lammps_file(void *, char *);
char *lammps_command(doivd *, char *);
char *lammps_command(void *, char *);
</PRE>
<P>The functions contain C++ code you could write in a C++ application
that was invoking LAMMPS directly. Note that LAMMPS classes are
defined wihin a LAMMPS namespace (LAMMPS_NS) if you use them
defined within a LAMMPS namespace (LAMMPS_NS) if you use them
from another C++ application.
</P>
<P>Two of the routines in library.cpp are of particular note. The
lammps_open() function initiates LAMMPS and takes an MPI communicator
as an argument. It returns a pointer to a LAMMPS "object". As with
C++, the lammps_open() function can be called mutliple times, to
C++, the lammps_open() function can be called multiple times, to
create multiple instances of LAMMPS.
</P>
<P>LAMMPS will run on the set of processors in the communicator. This
@ -604,7 +604,7 @@ create files in several formats. The native LAMMPS dump format is a
text file (see "dump atom" or "dump custom") which can be visualized
by the <A HREF = "Section_tools.html#xmovie">xmovie</A> program, included with the
LAMMPS package. This produces simple, fast 2d projections of 3d
systems, and can be useful for rapid debugging of simulation geoemtry
systems, and can be useful for rapid debugging of simulation geometry
and atom trajectories.
</P>
<P>Several programs included with LAMMPS as auxiliary tools can convert
@ -613,7 +613,7 @@ native LAMMPS dump files to other formats. See the
the <A HREF = "Section_tools.html#charmm">ch2lmp tool</A>, which contains a
lammps2pdb Perl script which converts LAMMPS dump files into PDB
files. The second is the <A HREF = "Section_tools.html#arc">lmp2arc tool</A> which
converts LAMMPS dump files into Accelrys's Insight MD program files.
converts LAMMPS dump files into Accelrys' Insight MD program files.
The third is the <A HREF = "Section_tools.html#cfg">lmp2cfg tool</A> which converts
LAMMPS dump files into CFG files which can be read into the
<A HREF = "http://164.107.79.177/Archive/Graphics/A">AtomEye</A> visualizer.
@ -723,9 +723,9 @@ the xy, xz, and yz tilt factors as a simulation runs.
<P>Non-equilibrium molecular dynamics or NEMD simulations are typically
used to measure a fluid's rheological properties such as viscosity.
In LAMMPS, such simulations can be performed by first setting up a
non-orthogonal simulation box (see the preceeding Howto section).
non-orthogonal simulation box (see the preceding Howto section).
</P>
<P>A shear strain can be applied to the simuaation box at a desired
<P>A shear strain can be applied to the simulation box at a desired
strain rate by using the <A HREF = "fix_deform.html">fix deform</A> command. The
<A HREF = "fix_nvt_sllod.html">fix nvt/sllod</A> command can be used to thermostat
the sheared fluid and integrate the SLLOD equations of motion for the
@ -765,7 +765,7 @@ The <A HREF = "pair_gayberne.html">pair_style gayberne</A> command can be used t
define a Gay-Berne (GB) potential for how ellipsoidal particles
interact with each other and with spherical particles. The GB
potential is like a Lennard-Jones (LJ) potential, generalized for
orientiation-dependent interactions.
orientation-dependent interactions.
</P>
<P>The orientation of ellipsoidal particles is stored as a quaternion.
See the <A HREF = "set.html">set</A> command for a brief explanation of quaternions
@ -821,9 +821,9 @@ generate values that can be output with these commands.
<P>The frequency and format of thermodynamic output is set by the
<A HREF = "thermo.html">thermo</A>, <A HREF = "thermo_style.html">thermo_style</A>, and
<A HREF = "thermo_modify.html">thermo_modify</A> commands. The
<A HREF = "themo_style.html">thermo_style</A> command also specifies what values are
<A HREF = "thermo_style.html">thermo_style</A> command also specifies what values are
calculated and written out. Pre-defined keywords can be specified
(e.g. press, etotal, etc). Three addtional kinds of keywords can also
(e.g. press, etotal, etc). Three additional kinds of keywords can also
be specified (c_ID, f_ID, v_name), where a <A HREF = "compute.html">compute</A> or
<A HREF = "fix.html">fix</A> or <A HREF = "variable.html">variable</A> provides the value to be
output. Each of these are described in turn.
@ -948,7 +948,7 @@ options for how it performs time averaging. The per-layer values it
produces can be used in two ways. First, they can be written directly
to a file. Note that the averaging parameters can be specified in
such a way that time averaging is not done, in which case this is a
convenient means of simply outputting desired quanitities (summed over
convenient means of simply outputting desired quantities (summed over
atoms within a 1d layer) directly to a separate file. Like other
fixes that produce global quantities, the results of this fix can also
be used as input by any command that accesses global quantities,