lijiext
/
lammps
mirror of https://github.com/lammps/lammps.git
1
0
Fork 1
Code Issues Packages Projects Releases Wiki Activity

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@337 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2007-02-22 16:52:24 +00:00
parent 90724304f5
commit c44928bd65
9 changed files with 166 additions and 13 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

4
doc/Manual.txt
View File

@ -69,7 +69,8 @@ we can improve the LAMMPS documentation.
4.7 "TIP3P water model"_4_7 :b
4.8 "TIP4P water model"_4_8 :b
4.9 "SPC water model"_4_9 :b
4.10 "Coupling LAMMPS to other codes"_4_10 :ule,b
4.10 "Coupling LAMMPS to other codes"_4_10
4.11 "Visualizing LAMMPS snapshots"_4_11 :ule,b
"Example problems"_Section_example.html :l
"Performance & scalability"_Section_perf.html :l
"Additional tools"_Section_tools.html :l
@ -114,6 +115,7 @@ we can improve the LAMMPS documentation.
:link(4_8,Section_howto.html#4_8)
:link(4_9,Section_howto.html#4_9)
:link(4_10,Section_howto.html#4_10)
:link(4_11,Section_howto.html#4_11)
:link(9_1,Section_errors.html#9_1)
:link(9_2,Section_errors.html#9_2)

62
doc/Section_howto.html
View File

@ -23,7 +23,8 @@ certain kinds of LAMMPS simulations.
4.7 <A HREF = "#4_7">TIP3P water model</A><BR>
4.8 <A HREF = "#4_8">TIP4P water model</A><BR>
4.9 <A HREF = "#4_9">SPC water model</A><BR>
4.10 <A HREF = "#4_10">Coupling LAMMPS to other codes</A> <BR>
4.10 <A HREF = "#4_10">Coupling LAMMPS to other codes</A><BR>
4.11 <A HREF = "#4_11">Visualizing LAMMPS snapshots</A> <BR>
<P>The example input scripts included in the LAMMPS distribution and
highlighted in <A HREF = "Section_example.html">this section</A> also show how to
@ -587,6 +588,65 @@ show how a stand-alone code can link LAMMPS as a library, run LAMMPS
on a subset of processors, grab data from LAMMPS, change it, and put
it back into LAMMPS.
</P>
<HR>
<A NAME = "4_11"></A><H4>4.11 Visualizing LAMMPS snapshots
</H4>
<P>LAMMPS itself does not do visualization, but snapshots from LAMMPS
simulations can be visualized (and analyzed) in a variety of ways.
</P>
<P>LAMMPS snapshots are created by the <A HREF = "dump.html">dump</A> command which can
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
and atom trajectories.
</P>
<P>Several programs included with LAMMPS as auxiliary tools can convert
native LAMMPS dump files to other formats. See the
<A HREF = "Section_tools.html">Section_tools</A> doc page for details. The first is
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.
The thrid 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.
</P>
<P>A Python-based toolkit distributed by our group can read native LAMMPS
dump files, including custom dump files with additional columns of
user-specified atom information, and convert them to various formats
or pipe them into visualization software directly. See the <A HREF = "http://www.cs.sandia.gov/~sjplimp/pizza.html">Pizza.py
WWW site</A> for details. Specifically, Pizza.py can convert
LAMMPS dump files into PDB, XYZ, <A HREF = "http://www.ensight.com">Ensight</A>, and VTK formats.
Pizza.py can pipe LAMMPS dump files directly into the Raster3d and
RasMol visualization programs. Pizza.py has tools that do interactive
3d OpenGL visualization and one that creates SVG images of dump file
snapshots.
</P>
<P>LAMMPS can create XYZ files directly (via "dump xyz") which is a
simple text-based file format used by many visualization programs
including <A HREF = "http://www.ks.uiuc.edu/Research/vmd">VMD</A>.
</P>
<P>LAMMPS can create DCD files directly (via "dump dcd") which can be
read by <A HREF = "http://www.ks.uiuc.edu/Research/vmd">VMD</A> in conjunction with a CHARMM PSF file. Using this
form of output avoids the need to convert LAMMPS snapshots to PDB
files. See the <A HREF = "dump.html">dump</A> command for more information on DCD
files.
</P>
<P>LAMMPS can create XTC files directly (via "dump xtc") which is GROMACS
file format which can also be read by <A HREF = "http://www.ks.uiuc.edu/Research/vmd">VMD</A> for visualization.
See the <A HREF = "dump.html">dump</A> command for more information on XTC files.
</P>
<HR>
<A NAME = "Cornell"></A>

59
doc/Section_howto.txt
View File

@ -20,7 +20,8 @@ certain kinds of LAMMPS simulations.
4.7 "TIP3P water model"_#4_7
4.8 "TIP4P water model"_#4_8
4.9 "SPC water model"_#4_9
4.10 "Coupling LAMMPS to other codes"_#4_10 :all(b)
4.10 "Coupling LAMMPS to other codes"_#4_10
4.11 "Visualizing LAMMPS snapshots"_#4_11 :all(b)
The example input scripts included in the LAMMPS distribution and
highlighted in "this section"_Section_example.html also show how to
@ -583,6 +584,62 @@ show how a stand-alone code can link LAMMPS as a library, run LAMMPS
on a subset of processors, grab data from LAMMPS, change it, and put
it back into LAMMPS.
:line
4.11 Visualizing LAMMPS snapshots :link(4_11),h4
LAMMPS itself does not do visualization, but snapshots from LAMMPS
simulations can be visualized (and analyzed) in a variety of ways.
LAMMPS snapshots are created by the "dump"_dump.html command which can
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 "xmovie"_Section_tools.html#xmovie 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
and atom trajectories.
Several programs included with LAMMPS as auxiliary tools can convert
native LAMMPS dump files to other formats. See the
"Section_tools"_Section_tools.html doc page for details. The first is
the "ch2lmp tool"_Section_tools.html#charmm, which contains a
lammps2pdb Perl script which converts LAMMPS dump files into PDB
files. The second is the "lmp2arc tool"_Section_tools.html#arc which
converts LAMMPS dump files into Accelrys's Insight MD program files.
The thrid is the "lmp2cfg tool"_Section_tools.html#cfg which converts
LAMMPS dump files into CFG files which can be read into the
"AtomEye"_atomeye visualizer.
A Python-based toolkit distributed by our group can read native LAMMPS
dump files, including custom dump files with additional columns of
user-specified atom information, and convert them to various formats
or pipe them into visualization software directly. See the "Pizza.py
WWW site"_pizza for details. Specifically, Pizza.py can convert
LAMMPS dump files into PDB, XYZ, "Ensight"_ensight, and VTK formats.
Pizza.py can pipe LAMMPS dump files directly into the Raster3d and
RasMol visualization programs. Pizza.py has tools that do interactive
3d OpenGL visualization and one that creates SVG images of dump file
snapshots.
LAMMPS can create XYZ files directly (via "dump xyz") which is a
simple text-based file format used by many visualization programs
including "VMD"_vmd.
LAMMPS can create DCD files directly (via "dump dcd") which can be
read by "VMD"_vmd in conjunction with a CHARMM PSF file. Using this
form of output avoids the need to convert LAMMPS snapshots to PDB
files. See the "dump"_dump.html command for more information on DCD
files.
LAMMPS can create XTC files directly (via "dump xtc") which is GROMACS
file format which can also be read by "VMD"_vmd for visualization.
See the "dump"_dump.html command for more information on XTC files.
:link(pizza,http://www.cs.sandia.gov/~sjplimp/pizza.html)
:link(vmd,http://www.ks.uiuc.edu/Research/vmd)
:link(ensight,http://www.ensight.com)
:link(atomeye,http://164.107.79.177/Archive/Graphics/A)
:line
:link(Cornell)

8
doc/dump.html
View File

@ -142,7 +142,7 @@ files are binary and thus may not be portable to different machines.
The dump group must be <I>all</I> for the <I>dcd</I> style.
</P>
<P>The <I>xtc</I> style writes XTC files, a compressed trajectory format used
by the Gromacs molecular dynamics package, and described
by the GROMACS molecular dynamics package, and described
<A HREF = "http://www.gromacs.org/documentation/reference_3.3/online/xtc.html">here</A>.
The precision used in XTC files can be specified; for example, a value
of 100 means that coordinates are stored to 1/100 nanometer accuracy.
@ -155,9 +155,9 @@ coordinate format that many codes can read.
</P>
<P>Note that DCD, XTC, and XYZ formatted files can be read directly by
<A HREF = "http://www.ks.uiuc.edu/Research/vmd">VMD</A> (a popular molecular viewing
program). VMD will also read LAMMPS <I>atom</I> style dump files since
someone added a LAMMPS plug-in to VMD. I am told it requires an
initial snapshot from an XYZ formatted file to get started.
program). We are told VMD will also read LAMMPS <I>atom</I> style dump
files since someone has added a LAMMPS format plug-in to VMD. It may
require an initial snapshot from an XYZ formatted file to get started.
</P>
<HR>

8
doc/dump.txt
View File

@ -132,7 +132,7 @@ files are binary and thus may not be portable to different machines.
The dump group must be {all} for the {dcd} style.
The {xtc} style writes XTC files, a compressed trajectory format used
by the Gromacs molecular dynamics package, and described
by the GROMACS molecular dynamics package, and described
"here"_http://www.gromacs.org/documentation/reference_3.3/online/xtc.html.
The precision used in XTC files can be specified; for example, a value
of 100 means that coordinates are stored to 1/100 nanometer accuracy.
@ -145,9 +145,9 @@ coordinate format that many codes can read.
Note that DCD, XTC, and XYZ formatted files can be read directly by
"VMD"_http://www.ks.uiuc.edu/Research/vmd (a popular molecular viewing
program). VMD will also read LAMMPS {atom} style dump files since
someone added a LAMMPS plug-in to VMD. I am told it requires an
initial snapshot from an XYZ formatted file to get started.
program). We are told VMD will also read LAMMPS {atom} style dump
files since someone has added a LAMMPS format plug-in to VMD. It may
require an initial snapshot from an XYZ formatted file to get started.
:line

8
doc/pair_dpd.html
View File

@ -66,6 +66,14 @@ LAMMPS</A> section for more info.
<A HREF = "pair_modify.hmtl">pair_modify</A> <I>mix</I> option. Coefficients for all i,j
pairs must be specified explicitly.
</P>
<P>The default frequency for rebuilding neighbor lists is every 10 steps
(see the <A HREF = "neigh_modify.html">neigh_modify</A> command). This may be too
infrequent for DPD simulations since particles move rapidly and can
overlap by large amounts. If this setting yields a non-zero number of
"dangerous" reneighborings (printed at the end of a simulation), you
should experiment with forcing reneighboring more often and see if
system energies/trajectories change.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "pair_coeff.html">pair_coeff</A>

8
doc/pair_dpd.txt
View File

@ -63,6 +63,14 @@ The {dpd} potential does not support the
"pair_modify"_pair_modify.hmtl {mix} option. Coefficients for all i,j
pairs must be specified explicitly.
The default frequency for rebuilding neighbor lists is every 10 steps
(see the "neigh_modify"_neigh_modify.html command). This may be too
infrequent for DPD simulations since particles move rapidly and can
overlap by large amounts. If this setting yields a non-zero number of
"dangerous" reneighborings (printed at the end of a simulation), you
should experiment with forcing reneighboring more often and see if
system energies/trajectories change.
[Related commands:]
"pair_coeff"_pair_coeff.html

11
doc/pair_eam.html
View File

@ -68,7 +68,7 @@ the <A HREF = "pair_coeff.html">pair_coeff</A> command. These are ASCII text fi
in a DYNAMO-style format which is described below. DYNAMO is a serial
MD code. Several DYNAMO potential files for different metals are
included in the "potentials" directory of the LAMMPS distribution.
All of these are parameterized in terms of LAMMPS <A HREF = "units.html">metal
All of these files are parameterized in terms of LAMMPS <A HREF = "units.html">metal
units</A>.
</P>
<P>IMPORTANT NOTE: The <I>eam</I> style reads single-element EAM potentials in
@ -332,6 +332,15 @@ LAMMPS</A> section for more info.
</P>
<P><A HREF = "pair_coeff.html">pair_coeff</A>
</P>
<P>Here are 2 WWW sites that discuss EAM potentials formulated in
alternate file formats:
</P>
<PRE>http://www.ims.uconn.edu/centers/simul/pot
http://cst-www.nrl.navy.mil/ccm6/ap
</PRE>
<P>In principle, these potentials could be converted to the DYNAMO file
format described above and used by LAMMPS.
</P>
<P><B>Default:</B> none
</P>
<HR>

11
doc/pair_eam.txt
View File

@ -60,7 +60,7 @@ the "pair_coeff"_pair_coeff.html command. These are ASCII text files
in a DYNAMO-style format which is described below. DYNAMO is a serial
MD code. Several DYNAMO potential files for different metals are
included in the "potentials" directory of the LAMMPS distribution.
All of these are parameterized in terms of LAMMPS "metal
All of these files are parameterized in terms of LAMMPS "metal
units"_units.html.
IMPORTANT NOTE: The {eam} style reads single-element EAM potentials in
@ -324,6 +324,15 @@ LAMMPS"_Section_start.html#2_3 section for more info.
"pair_coeff"_pair_coeff.html
Here are 2 WWW sites that discuss EAM potentials formulated in
alternate file formats:
http://www.ims.uconn.edu/centers/simul/pot
http://cst-www.nrl.navy.mil/ccm6/ap :pre
In principle, these potentials could be converted to the DYNAMO file
format described above and used by LAMMPS.
[Default:] none
:line