From c44928bd65185b06e0dc04c2bc8ccdc676615d05 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Thu, 22 Feb 2007 16:52:24 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@337 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/Manual.txt | 4 ++- doc/Section_howto.html | 62 +++++++++++++++++++++++++++++++++++++++++- doc/Section_howto.txt | 59 +++++++++++++++++++++++++++++++++++++++- doc/dump.html | 8 +++--- doc/dump.txt | 8 +++--- doc/pair_dpd.html | 8 ++++++ doc/pair_dpd.txt | 8 ++++++ doc/pair_eam.html | 11 +++++++- doc/pair_eam.txt | 11 +++++++- 9 files changed, 166 insertions(+), 13 deletions(-) diff --git a/doc/Manual.txt b/doc/Manual.txt index 3f4abcaa6d..23ba766b03 100644 --- a/doc/Manual.txt +++ b/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) diff --git a/doc/Section_howto.html b/doc/Section_howto.html index 0f8ae2da8e..7e42cb57f9 100644 --- a/doc/Section_howto.html +++ b/doc/Section_howto.html @@ -23,7 +23,8 @@ certain kinds of LAMMPS simulations. 4.7 TIP3P water model
4.8 TIP4P water model
4.9 SPC water model
-4.10 Coupling LAMMPS to other codes
+4.10 Coupling LAMMPS to other codes
+4.11 Visualizing LAMMPS snapshots

The example input scripts included in the LAMMPS distribution and highlighted in this section 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.

+
+ +

4.11 Visualizing LAMMPS snapshots +

+

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 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 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 doc page for details. The first is +the ch2lmp tool, which contains a +lammps2pdb Perl script which converts LAMMPS dump files into PDB +files. The second is the lmp2arc tool which +converts LAMMPS dump files into Accelrys's Insight MD program files. +The thrid is the lmp2cfg tool which converts +LAMMPS dump files into CFG files which can be read into the +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 for details. Specifically, Pizza.py can convert +LAMMPS dump files into PDB, XYZ, 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. +

+

LAMMPS can create DCD files directly (via "dump dcd") which can be +read by 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 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 for visualization. +See the dump command for more information on XTC files. +

+ + + + + + + +
diff --git a/doc/Section_howto.txt b/doc/Section_howto.txt index 009593e1a6..3a1c742723 100644 --- a/doc/Section_howto.txt +++ b/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) diff --git a/doc/dump.html b/doc/dump.html index 5f0a707f60..1cdde36a8b 100644 --- a/doc/dump.html +++ b/doc/dump.html @@ -142,7 +142,7 @@ 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. 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.

Note that DCD, XTC, and XYZ formatted files can be read directly by 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.

diff --git a/doc/dump.txt b/doc/dump.txt index 03c1a29572..4fe9625d02 100644 --- a/doc/dump.txt +++ b/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 -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 diff --git a/doc/pair_dpd.html b/doc/pair_dpd.html index 851a8a0bd3..5c28e85428 100644 --- a/doc/pair_dpd.html +++ b/doc/pair_dpd.html @@ -66,6 +66,14 @@ LAMMPS section for more info. pair_modify 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 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 diff --git a/doc/pair_dpd.txt b/doc/pair_dpd.txt index a2fdb47ddc..cfd8c5f565 100644 --- a/doc/pair_dpd.txt +++ b/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 diff --git a/doc/pair_eam.html b/doc/pair_eam.html index 4fd322d386..9c38768b66 100644 --- a/doc/pair_eam.html +++ b/doc/pair_eam.html @@ -68,7 +68,7 @@ the pair_coeff 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 metal +All of these files are parameterized in terms of LAMMPS metal units.

IMPORTANT NOTE: The eam style reads single-element EAM potentials in @@ -332,6 +332,15 @@ LAMMPS section for more info.

pair_coeff

+

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 
+
+

In principle, these potentials could be converted to the DYNAMO file +format described above and used by LAMMPS. +

Default: none

diff --git a/doc/pair_eam.txt b/doc/pair_eam.txt index 84af287c40..0d069fea6a 100644 --- a/doc/pair_eam.txt +++ b/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