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

doc/Manual.txt

@@ -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)

doc/Section_howto.html

@@ -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>

doc/Section_howto.txt

@@ -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)

doc/dump.html

@@ -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
+program).  We are told VMD will also read LAMMPS <I>atom</I> style dump
-someone added a LAMMPS plug-in to VMD.  I am told it requires an
+files since someone has added a LAMMPS format plug-in to VMD.  It may
-initial snapshot from an XYZ formatted file to get started.
+require an initial snapshot from an XYZ formatted file to get started.
 </P>
 <HR>
 

doc/dump.txt

@@ -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
+program).  We are told VMD will also read LAMMPS {atom} style dump
-someone added a LAMMPS plug-in to VMD.  I am told it requires an
+files since someone has added a LAMMPS format plug-in to VMD.  It may
-initial snapshot from an XYZ formatted file to get started.
+require an initial snapshot from an XYZ formatted file to get started.
 
 :line
 

doc/pair_dpd.html

@@ -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>

doc/pair_dpd.txt

@@ -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

doc/pair_eam.html

@@ -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>

doc/pair_eam.txt

@@ -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