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multiscale
lammps
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61e7595a
Commit
61e7595a
authored
7 years ago
by
Axel Kohlmeyer
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remove references to xmovie, streamline dump and viz descriptions
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da909675
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doc/src/Section_howto.txt
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-30
6 additions, 30 deletions
doc/src/Section_howto.txt
doc/src/Section_intro.txt
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3 additions, 5 deletions
doc/src/Section_intro.txt
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35 deletions
doc/src/Section_howto.txt
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61e7595a
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@@ -759,23 +759,14 @@ LAMMPS itself does not do visualization, but snapshots from LAMMPS
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@@ -759,23 +759,14 @@ LAMMPS itself does not do visualization, but snapshots from LAMMPS
simulations can be visualized (and analyzed) in a variety of ways.
simulations can be visualized (and analyzed) in a variety of ways.
LAMMPS snapshots are created by the "dump"_dump.html command which can
LAMMPS snapshots are created by the "dump"_dump.html command which can
create files in several formats.
The native LAMMPS dump format is a
create files in several formats. The native LAMMPS dump format is a
text file (see "dump atom" or "dump custom") which can be visualized
text file (see "dump atom" or "dump custom") which can be visualized
by the "xmovie"_Section_tools.html#xmovie program, included with the
by several popular visualization tools. The "dump image"_dump_image.html
LAMMPS package. This produces simple, fast 2d projections of 3d
and "dump movie"_dump_image.html styles can output internally rendered
systems, and can be useful for rapid debugging of simulation geometry
images and convert a sequence of them to a movie during the MD run.
and atom trajectories.
Several programs included with LAMMPS as auxiliary tools can convert
Several programs included with LAMMPS as auxiliary tools can convert
native LAMMPS dump files to other formats. See the
between LAMMPS format files and other formats.
"Section 9"_Section_tools.html doc page for details. The first is
See the "Section 9"_Section_tools.html doc page for details.
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' Insight MD program files.
The third 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
A Python-based toolkit distributed by our group can read native LAMMPS
dump files, including custom dump files with additional columns of
dump files, including custom dump files with additional columns of
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@@ -788,22 +779,7 @@ RasMol visualization programs. Pizza.py has tools that do interactive
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@@ -788,22 +779,7 @@ RasMol visualization programs. Pizza.py has tools that do interactive
3d OpenGL visualization and one that creates SVG images of dump file
3d OpenGL visualization and one that creates SVG images of dump file
snapshots.
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.sandia.gov/~sjplimp/pizza.html)
:link(pizza,http://www.sandia.gov/~sjplimp/pizza.html)
:link(vmd,http://www.ks.uiuc.edu/Research/vmd)
:link(ensight,http://www.ensight.com)
:link(ensight,http://www.ensight.com)
:link(atomeye,http://mt.seas.upenn.edu/Archive/Graphics/A)
:link(atomeye,http://mt.seas.upenn.edu/Archive/Graphics/A)
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doc/src/Section_intro.txt
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@@ -338,15 +338,13 @@ dynamics timestepping, particularly if the computations are not
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@@ -338,15 +338,13 @@ dynamics timestepping, particularly if the computations are not
parallel, so it is often better to leave such analysis to
parallel, so it is often better to leave such analysis to
post-processing codes.
post-processing codes.
A very simple (yet fast) visualizer is provided with the LAMMPS
For high-quality visualization we recommend the
package - see the "xmovie"_Section_tools.html#xmovie tool in "this
section"_Section_tools.html. It creates xyz projection views of
atomic coordinates and animates them. We find it very useful for
debugging purposes. For high-quality visualization we recommend the
following packages:
following packages:
"VMD"_http://www.ks.uiuc.edu/Research/vmd
"VMD"_http://www.ks.uiuc.edu/Research/vmd
"AtomEye"_http://mt.seas.upenn.edu/Archive/Graphics/A
"AtomEye"_http://mt.seas.upenn.edu/Archive/Graphics/A
"OVITO"_http://www.ovito.org/
"ParaView"_http://www.paraview.org/
"PyMol"_http://www.pymol.org
"PyMol"_http://www.pymol.org
"Raster3d"_http://www.bmsc.washington.edu/raster3d/raster3d.html
"Raster3d"_http://www.bmsc.washington.edu/raster3d/raster3d.html
"RasMol"_http://www.openrasmol.org :ul
"RasMol"_http://www.openrasmol.org :ul
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