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July 22, 2015 22:36
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gedit Syntax Highlighting for LAMMPS Molecular Dynamics Simulator (to use $sudo cp lammps.lang /usr/share/gtksourceview-3.0/language-specs)
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<?xml version="1.0" encoding="UTF-8"?> | |
<language id="lammps" _name="Lammps" version="2.0" _section="Scientific"> | |
<metadata> | |
<property name="mimetypes">text/lammps</property> | |
<property name="globs">*.in;*.lammps</property> | |
</metadata> | |
<styles> | |
<style id="comment" _name="Comment" map-to="def:comment"/> | |
<style id="keyword" _name="Keyword" map-to="def:keyword"/> | |
<style id="constant" _name="Sub-keyword" map-to="def:constant"/> | |
</styles> | |
<definitions> | |
<context id="lammps" class="no-spell-check"> | |
<include> | |
<context ref="def:decimal"/> | |
<context ref="def:float"/> | |
<context ref="def:string"/> | |
<context id="comment" style-ref="comment" end-at-line-end="true"> | |
<start>#</start> | |
<end>$</end> | |
</context> | |
<context id="keywords" style-ref="keyword"> | |
<keyword>angle_coeff</keyword> | |
<keyword>angle_style</keyword> | |
<keyword>atom_modify</keyword> | |
<keyword>atom_style</keyword> | |
<keyword>balance</keyword> | |
<keyword>bond_coeff</keyword> | |
<keyword>bond_style</keyword> | |
<keyword>boundary</keyword> | |
<keyword>side</keyword> | |
<keyword>change_box</keyword> | |
<keyword>clear comm_modify</keyword> | |
<keyword>comm_style</keyword> | |
<keyword>compute</keyword> | |
<keyword>compute_modify</keyword> | |
<keyword>create_atoms</keyword> | |
<keyword>create_bonds</keyword> | |
<keyword>create_box</keyword> | |
<keyword>delete_atoms</keyword> | |
<keyword>delete_bonds</keyword> | |
<keyword>dielectric</keyword> | |
<keyword>dihedral_coeff</keyword> | |
<keyword>dihedral_style</keyword> | |
<keyword>dimension</keyword> | |
<keyword>displace_atoms</keyword> | |
<keyword>dump</keyword> | |
<keyword>dump_modify</keyword> | |
<keyword>echo</keyword> | |
<keyword>fix</keyword> | |
<keyword>fix_modify</keyword> | |
<keyword>group</keyword> | |
<keyword>if</keyword> | |
<keyword>improper_coeff</keyword> | |
<keyword>improper_style</keyword> | |
<keyword>include</keyword> | |
<keyword>jump</keyword> | |
<keyword>kspace_modify</keyword> | |
<keyword>kspace_style</keyword> | |
<keyword>label</keyword> | |
<keyword>lattice</keyword> | |
<keyword>log</keyword> | |
<keyword>mass</keyword> | |
<keyword>minimize</keyword> | |
<keyword>min_modify</keyword> | |
<keyword>min_style</keyword> | |
<keyword>molecule</keyword> | |
<keyword>neb</keyword> | |
<keyword>neigh_modify</keyword> | |
<keyword>neighbor</keyword> | |
<keyword>newton</keyword> | |
<keyword>next</keyword> | |
<keyword>package</keyword> | |
<keyword>pair_coeff</keyword> | |
<keyword>pair_modify</keyword> | |
<keyword>pair_style</keyword> | |
<keyword>pair_write</keyword> | |
<keyword>partition</keyword> | |
<keyword>prd</keyword> | |
<keyword>print</keyword> | |
<keyword>processors</keyword> | |
<keyword>python</keyword> | |
<keyword>quit</keyword> | |
<keyword>read_data</keyword> | |
<keyword>read_dump</keyword> | |
<keyword>read_restart</keyword> | |
<keyword>region</keyword> | |
<keyword>replicate</keyword> | |
<keyword>reset_timestep</keyword> | |
<keyword>restart</keyword> | |
<keyword>run</keyword> | |
<keyword>run_style</keyword> | |
<keyword>set</keyword> | |
<keyword>shell</keyword> | |
<keyword>special_bonds</keyword> | |
<keyword>suffix</keyword> | |
<keyword>tad</keyword> | |
<keyword>temper</keyword> | |
<keyword>thermo</keyword> | |
<keyword>thermo_modify</keyword> | |
<keyword>thermo_style</keyword> | |
<keyword>timestep</keyword> | |
<keyword>uncompute</keyword> | |
<keyword>undump</keyword> | |
<keyword>unfix</keyword> | |
<keyword>units</keyword> | |
<keyword>variable</keyword> | |
<keyword>velocity</keyword> | |
<keyword>write_data</keyword> | |
<keyword>write_dump</keyword> | |
<keyword>write_restart</keyword> | |
<keyword>nvt</keyword> | |
<keyword>wall.*</keyword> | |
<keyword>ave.*</keyword> | |
</context> | |
<context id="constant" style-ref="constant"> | |
<keyword>adapt</keyword> | |
<keyword>deform</keyword> | |
<keyword>freeze</keyword> | |
<keyword>momentum</keyword> | |
<keyword>npt</keyword> | |
<keyword>nve/line</keyword> | |
<keyword>oneway</keyword> | |
<keyword>qeq/comb</keyword> | |
<keyword>rigid</keyword> | |
<keyword>rigid/small/nve</keyword> | |
<keyword>store/force</keyword> | |
<keyword>tmd</keyword> | |
<keyword>addforce</keyword> | |
<keyword>deposit</keyword> | |
<keyword>gcmc</keyword> | |
<keyword>move</keyword> | |
<keyword>npt/asphere</keyword> | |
<keyword>nve/noforce</keyword> | |
<keyword>orient/fcc</keyword> | |
<keyword>qeq/dynamic</keyword> | |
<keyword>rigid/nph</keyword> | |
<keyword>rigid/small/nvt</keyword> | |
<keyword>store/state</keyword> | |
<keyword>ttm</keyword> | |
<keyword>append/atoms</keyword> | |
<keyword>drag</keyword> | |
<keyword>gld</keyword> | |
<keyword>msst</keyword> | |
<keyword>npt/sphere</keyword> | |
<keyword>nve/sphere</keyword> | |
<keyword>planeforce</keyword> | |
<keyword>qeq/point</keyword> | |
<keyword>rigid/npt</keyword> | |
<keyword>setforce</keyword> | |
<keyword>temp/berendsen</keyword> | |
<keyword>tune/kspace</keyword> | |
<keyword>atom/swap</keyword> | |
<keyword>balance</keyword> | |
<keyword>dt/reset</keyword> | |
<keyword>gravity</keyword> | |
<keyword>neb</keyword> | |
<keyword>nve</keyword> | |
<keyword>nve/tri</keyword> | |
<keyword>poems</keyword> | |
<keyword>qeq/shielded</keyword> | |
<keyword>rigid/nve</keyword> | |
<keyword>shake</keyword> | |
<keyword>temp/csld</keyword> | |
<keyword>vector</keyword> | |
<keyword>bond/break</keyword> | |
<keyword>efield</keyword> | |
<keyword>heat</keyword> | |
<keyword>nph</keyword> | |
<keyword>nve/asphere</keyword> | |
<keyword>pour</keyword> | |
<keyword>qeq/slater</keyword> | |
<keyword>rigid/nvt</keyword> | |
<keyword>spring</keyword> | |
<keyword>temp/csvr</keyword> | |
<keyword>viscosity</keyword> | |
<keyword>bond/create</keyword> | |
<keyword>enforce2d</keyword> | |
<keyword>indent</keyword> | |
<keyword>nphug</keyword> | |
<keyword>nve/asphere/noforce</keyword> | |
<keyword>nvt/asphere</keyword> | |
<keyword>press/berendsen</keyword> | |
<keyword>reax/bonds</keyword> | |
<keyword>rigid/small</keyword> | |
<keyword>spring/rg</keyword> | |
<keyword>temp/rescale</keyword> | |
<keyword>viscous</keyword> | |
<keyword>bond/swap</keyword> | |
<keyword>evaporate</keyword> | |
<keyword>langevin</keyword> | |
<keyword>nph/asphere</keyword> | |
<keyword>nve/body</keyword> | |
<keyword>nvt/sllod</keyword> | |
<keyword>print</keyword> | |
<keyword>recenter</keyword> | |
<keyword>rigid/small/nph</keyword> | |
<keyword>spring/self</keyword> | |
<keyword>tfmc</keyword> | |
<keyword>box/relax</keyword> | |
<keyword>external</keyword> | |
<keyword>lineforce</keyword> | |
<keyword>nph/sphere</keyword> | |
<keyword>nve/limit</keyword> | |
<keyword>nvt/sphere</keyword> | |
<keyword>property/atom</keyword> | |
<keyword>restrain</keyword> | |
<keyword>rigid/small/npt</keyword> | |
<keyword>srd</keyword> | |
<keyword>thermal/conductivity</keyword> | |
<keyword>angle/local</keyword> | |
<keyword>cluster/atom</keyword> | |
<keyword>damage/atom</keyword> | |
<keyword>erotate/sphere</keyword> | |
<keyword>heat/flux</keyword> | |
<keyword>msd</keyword> | |
<keyword>pe</keyword> | |
<keyword>property/chunk</keyword> | |
<keyword>snad/atom</keyword> | |
<keyword>temp/chunk</keyword> | |
<keyword>temp/sphere</keyword> | |
<keyword>angmom/chunk</keyword> | |
<keyword>cna/atom</keyword> | |
<keyword>dihedral/local</keyword> | |
<keyword>erotate/sphere/atom</keyword> | |
<keyword>improper/local</keyword> | |
<keyword>msd/chunk</keyword> | |
<keyword>pe/atom</keyword> | |
<keyword>rdf</keyword> | |
<keyword>snav/atom</keyword> | |
<keyword>temp/deform</keyword> | |
<keyword>ti</keyword> | |
<keyword>body/local</keyword> | |
<keyword>com</keyword> | |
<keyword>dilatation/atom</keyword> | |
<keyword>event/displace</keyword> | |
<keyword>inertia/chunk</keyword> | |
<keyword>msd/nongauss</keyword> | |
<keyword>plasticity/atom</keyword> | |
<keyword>reduce</keyword> | |
<keyword>stress/atom</keyword> | |
<keyword>temp/partial</keyword> | |
<keyword>torque/chunk</keyword> | |
<keyword>bond/local</keyword> | |
<keyword>com/chunk</keyword> | |
<keyword>displace/atom</keyword> | |
<keyword>group/group</keyword> | |
<keyword>ke</keyword> | |
<keyword>omega/chunk</keyword> | |
<keyword>pressure</keyword> | |
<keyword>reduce/region</keyword> | |
<keyword>temp</keyword> | |
<keyword>temp/profile</keyword> | |
<keyword>vacf</keyword> | |
<keyword>centro/atom</keyword> | |
<keyword>contact/atom</keyword> | |
<keyword>erotate/asphere</keyword> | |
<keyword>gyration</keyword> | |
<keyword>ke/atom</keyword> | |
<keyword>pair</keyword> | |
<keyword>property/atom</keyword> | |
<keyword>slice</keyword> | |
<keyword>temp/asphere</keyword> | |
<keyword>temp/ramp</keyword> | |
<keyword>vcm/chunk</keyword> | |
<keyword>chunk/atom</keyword> | |
<keyword>coord/atom</keyword> | |
<keyword>erotate/rigid</keyword> | |
<keyword>gyration/chunk</keyword> | |
<keyword>ke/rigid</keyword> | |
<keyword>pair/local</keyword> | |
<keyword>property/local</keyword> | |
<keyword>sna/atom</keyword> | |
<keyword>temp/com</keyword> | |
<keyword>temp/region</keyword> | |
<keyword>voronoi/atom</keyword> | |
<keyword>none</keyword> | |
<keyword>airebo</keyword> | |
<keyword>born</keyword> | |
<keyword>brownian</keyword> | |
<keyword>buck/coul/long</keyword> | |
<keyword>comb</keyword> | |
<keyword>coul/dsf</keyword> | |
<keyword>coul/wolf</keyword> | |
<keyword>eam</keyword> | |
<keyword>gauss</keyword> | |
<keyword>gran/hooke/history</keyword> | |
<keyword>lcbop</keyword> | |
<keyword>lj/charmm/coul/long</keyword> | |
<keyword>lj/class2/coul/long</keyword> | |
<keyword>lj/cut/coul/dsf</keyword> | |
<keyword>lj/cut/dipole/long</keyword> | |
<keyword>lj/gromacs</keyword> | |
<keyword>lj/long/tip4p/long</keyword> | |
<keyword>lubricate</keyword> | |
<keyword>meam</keyword> | |
<keyword>nm/cut</keyword> | |
<keyword>peri/lps</keyword> | |
<keyword>rebo</keyword> | |
<keyword>sw</keyword> | |
<keyword>tersoff/zbl</keyword> | |
<keyword>yukawa</keyword> | |
<keyword>hybrid</keyword> | |
<keyword>beck</keyword> | |
<keyword>born/coul/long</keyword> | |
<keyword>brownian/poly</keyword> | |
<keyword>buck/coul/msm</keyword> | |
<keyword>comb3</keyword> | |
<keyword>coul/long</keyword> | |
<keyword>dpd</keyword> | |
<keyword>eam/alloy</keyword> | |
<keyword>gayberne</keyword> | |
<keyword>hbond/dreiding/lj</keyword> | |
<keyword>line/lj</keyword> | |
<keyword>lj/charmm/coul/msm</keyword> | |
<keyword>lj/cut</keyword> | |
<keyword>lj/cut/coul/long</keyword> | |
<keyword>lj/cut/tip4p/cut</keyword> | |
<keyword>lj/gromacs/coul/gromacs</keyword> | |
<keyword>lj/smooth</keyword> | |
<keyword>lubricate/poly</keyword> | |
<keyword>mie/cut</keyword> | |
<keyword>nm/cut/coul/cut</keyword> | |
<keyword>peri/pmb</keyword> | |
<keyword>resquared</keyword> | |
<keyword>table</keyword> | |
<keyword>tip4p/cut</keyword> | |
<keyword>yukawa/colloid</keyword> | |
<keyword>hybrid/overlay</keyword> | |
<keyword>body</keyword> | |
<keyword>born/coul/msm</keyword> | |
<keyword>buck</keyword> | |
<keyword>buck/long/coul/long</keyword> | |
<keyword>coul/cut</keyword> | |
<keyword>coul/msm</keyword> | |
<keyword>dpd/tstat</keyword> | |
<keyword>eam/fs</keyword> | |
<keyword>gran/hertz/history</keyword> | |
<keyword>hbond/dreiding/morse</keyword> | |
<keyword>lj/charmm/coul/charmm</keyword> | |
<keyword>lj/class2</keyword> | |
<keyword>lj/cut/coul/cut</keyword> | |
<keyword>lj/cut/coul/msm</keyword> | |
<keyword>lj/cut/tip4p/long</keyword> | |
<keyword>lj/long/coul/long</keyword> | |
<keyword>lj/smooth/linear</keyword> | |
<keyword>lubricateU</keyword> | |
<keyword>morse</keyword> | |
<keyword>nm/cut/coul/long</keyword> | |
<keyword>peri/ves</keyword> | |
<keyword>snap</keyword> | |
<keyword>tersoff</keyword> | |
<keyword>tip4p/long</keyword> | |
<keyword>zbl</keyword> | |
<keyword>adp</keyword> | |
<keyword>bop</keyword> | |
<keyword>born/coul/wolf</keyword> | |
<keyword>buck/coul/cut</keyword> | |
<keyword>colloid</keyword> | |
<keyword>coul/debye</keyword> | |
<keyword>coul/streitz</keyword> | |
<keyword>dsmc</keyword> | |
<keyword>eim</keyword> | |
<keyword>gran/hooke</keyword> | |
<keyword>kim</keyword> | |
<keyword>lj/charmm/coul/charmm/implicit</keyword> | |
<keyword>lj/class2/coul/cut</keyword> | |
<keyword>lj/cut/coul/debye</keyword> | |
<keyword>lj/cut/dipole/cut</keyword> | |
<keyword>lj/expand</keyword> | |
<keyword>lj/long/dipole/long</keyword> | |
<keyword>lj96/cut</keyword> | |
<keyword>lubricateU/poly</keyword> | |
<keyword>nb3b/harmonic</keyword> | |
<keyword>peri/eps</keyword> | |
<keyword>reax</keyword> | |
<keyword>soft</keyword> | |
<keyword>tersoff/mod</keyword> | |
<keyword>tri/lj</keyword> | |
<keyword>all</keyword> | |
<keyword>creat</keyword> | |
<keyword>mom</keyword> | |
<keyword>rot</keyword> | |
<keyword>dist</keyword> | |
<keyword>dcd</keyword> | |
<keyword>atomic</keyword> | |
<keyword>sphere</keyword> | |
<keyword>box</keyword> | |
<keyword>in</keyword> | |
<keyword>unwrap</keyword> | |
<keyword>multi</keyword> | |
<keyword>delta</keyword> | |
<keyword>equal</keyword> | |
<keyword>sum</keyword> | |
<keyword>custom</keyword> | |
<keyword>lj.*</keyword> | |
</context> | |
</include> | |
</context> | |
</definitions> | |
</language> |
batsari
commented
Jan 11, 2021
via email
Thank you very much for sharing your experience with me. I am now able to
smoothly run the examples and view output files.
Thank You once again.
…On Mon, 11 Jan 2021 4:38 AM Nanosmasher, ***@***.***> wrote:
***@***.**** commented on this gist.
------------------------------
Hi, I am learning how to use with LAMMPS package. I run some examples
given in the package, but it's difficult for me to identify the output
files. Please I need your help.
Thank you.
Yusuf Tajuddeen Batsari
Hey, I'm a bit late but:
From when I was using it, there's a couple of log files, and most of the
other output files come from assigning them in the script with
fix/dump/restart commands. For visualization I used OVITO, and Matab for
other data. Sorry I can't help you more but I would look at those commands
and see what output files they are spitting out.
—
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