forked from lijiext/lammps
Merge pull request #1062 from lammps/doc-reformat
change format of Howto and Tools doc pages
This commit is contained in:
Steve Plimpton
GitHub
commit
2c19079707
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@ -8,27 +8,44 @@ Section"_Examples.html :c
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:line
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How to discussions :h2
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Howto discussions :h2
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These doc pages describe how to perform various tasks with LAMMPS,
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both for users and developers. The
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"glossary"_http://lammps.sandia.gov website page also lists MD
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terminology with links to corresponding LAMMPS manual pages.
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The example input scripts included in the examples dir of the LAMMPS
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terminology with links to corresponding LAMMPS manual pages. The
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example input scripts included in the examples dir of the LAMMPS
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distribution and highlighted on the "Examples"_Examples.html doc page
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also show how to setup and run various kinds of simulations.
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Tutorials howto :h3
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<!-- RST
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.. toctree::
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:name: tutorials
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:maxdepth: 1
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Howto_github
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Howto_pylammps
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Howto_bash
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END_RST -->
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<!-- HTML_ONLY -->
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"Using GitHub with LAMMPS"_Howto_github.html
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"PyLAMMPS interface to LAMMPS"_Howto_pylammps.html
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"Using LAMMPS with bash on Windows"_Howto_bash.html :all(b)
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<!-- END_HTML_ONLY -->
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General howto :h3
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<!-- RST
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.. toctree::
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:name: general
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:maxdepth: 1
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Howto_restart
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@ -38,35 +55,86 @@ also show how to setup and run various kinds of simulations.
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Howto_library
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Howto_couple
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.. toctree::
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:maxdepth: 1
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END_RST -->
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Howto_output
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Howto_chunk
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<!-- HTML_ONLY -->
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"Restart a simulation"_Howto_restart.html
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"Visualize LAMMPS snapshots"_Howto_viz.html
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"Run multiple simulations from one input script"_Howto_multiple.html
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"Multi-replica simulations"_Howto_replica.html
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"Library interface to LAMMPS"_Howto_library.html
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"Couple LAMMPS to other codes"_Howto_couple.html :all(b)
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<!-- END_HTML_ONLY -->
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Settings howto :h3
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<!-- RST
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.. toctree::
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:name: settings
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:maxdepth: 1
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Howto_2d
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Howto_triclinic
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Howto_walls
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Howto_nemd
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Howto_granular
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Howto_spherical
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Howto_dispersion
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.. toctree::
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:maxdepth: 1
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Howto_temperature
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Howto_thermostat
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Howto_barostat
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Howto_walls
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Howto_nemd
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Howto_dispersion
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END_RST -->
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<!-- HTML_ONLY -->
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"2d simulations"_Howto_2d.html
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"Triclinic (non-orthogonal) simulation boxes"_Howto_triclinic.html
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"Thermostats"_Howto_thermostat.html
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"Barostats"_Howto_barostat.html
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"Walls"_Howto_walls.html
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"NEMD simulations"_Howto_nemd.html
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"Long-range dispersion settings"_Howto_dispersion.html :all(b)
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<!-- END_HTML_ONLY -->
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Analysis howto :h3
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<!-- RST
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.. toctree::
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:name: analysis
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:maxdepth: 1
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Howto_output
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Howto_chunk
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Howto_temperature
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Howto_elastic
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Howto_kappa
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Howto_viscosity
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Howto_diffusion
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END_RST -->
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<!-- HTML_ONLY -->
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"Output from LAMMPS (thermo, dumps, computes, fixes, variables)"_Howto_output.html
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"Use chunks to calculate system properties"_Howto_chunk.html :all(b)
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"Calculate temperature"_Howto_temperature.html
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"Calculate elastic constants"_Howto_elastic.html
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"Calculate thermal conductivity"_Howto_kappa.html
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"Calculate viscosity"_Howto_viscosity.html
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"Calculate a diffusion coefficient"_Howto_diffusion.html :all(b)
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<!-- END_HTML_ONLY -->
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Force fields howto :h3
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<!-- RST
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.. toctree::
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:name: force
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:maxdepth: 1
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Howto_bioFF
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@ -74,9 +142,27 @@ also show how to setup and run various kinds of simulations.
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Howto_tip4p
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Howto_spc
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END_RST -->
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<!-- HTML_ONLY -->
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"CHARMM, AMBER, and DREIDING force fields"_Howto_bioFF.html
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"TIP3P water model"_Howto_tip3p.html
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"TIP4P water model"_Howto_tip4p.html
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"SPC water model"_Howto_spc.html :all(b)
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<!-- END_HTML_ONLY -->
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Packages howto :h3
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<!-- RST
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.. toctree::
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:name: packages
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:maxdepth: 1
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Howto_spherical
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Howto_granular
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Howto_body
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Howto_polarizable
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Howto_coreshell
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@ -87,43 +173,11 @@ also show how to setup and run various kinds of simulations.
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END_RST -->
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<!-- HTML_ONLY -->
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"Using GitHub with LAMMPS"_Howto_github.html
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"PyLAMMPS interface to LAMMPS"_Howto_pylammps.html
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"Using LAMMPS with bash on Windows"_Howto_bash.html :all(b)
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"Restart a simulation"_Howto_restart.html
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"Visualize LAMMPS snapshots"_Howto_viz.html
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"Run multiple simulations from one input script"_Howto_multiple.html
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"Multi-replica simulations"_Howto_replica.html
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"Library interface to LAMMPS"_Howto_library.html
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"Couple LAMMPS to other codes"_Howto_couple.html :all(b)
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"Output from LAMMPS (thermo, dumps, computes, fixes, variables)"_Howto_output.html
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"Use chunks to calculate system properties"_Howto_chunk.html :all(b)
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"2d simulations"_Howto_2d.html
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"Triclinic (non-orthogonal) simulation boxes"_Howto_triclinic.html
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"Walls"_Howto_walls.html
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"NEMD simulations"_Howto_nemd.html
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"Granular models"_Howto_granular.html
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"Finite-size spherical and aspherical particles"_Howto_spherical.html
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"Long-range dispersion settings"_Howto_dispersion.html :all(b)
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"Calculate temperature"_Howto_temperature.html
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"Thermostats"_Howto_thermostat.html
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"Barostats"_Howto_barostat.html
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"Calculate elastic constants"_Howto_elastic.html
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"Calculate thermal conductivity"_Howto_kappa.html
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"Calculate viscosity"_Howto_viscosity.html
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"Calculate a diffusion coefficient"_Howto_diffusion.html :all(b)
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"CHARMM, AMBER, and DREIDING force fields"_Howto_bioFF.html
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"TIP3P water model"_Howto_tip3p.html
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"TIP4P water model"_Howto_tip4p.html
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"SPC water model"_Howto_spc.html :all(b)
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"Granular models"_Howto_granular.html
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"Body style particles"_Howto_body.html
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"Polarizable models"_Howto_polarizable.html
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"Adiabatic core/shell model"_Howto_coreshell.html
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@ -66,7 +66,7 @@ every LAMMPS command.
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.. toctree::
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:maxdepth: 2
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:numbered:
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:numbered: 3
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:caption: User Documentation
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:name: userdoc
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:includehidden:
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@ -43,40 +43,55 @@ to edit for your platform) which will build several of the tools which
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reside in that directory. Most of them are larger packages in their
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own sub-directories with their own Makefiles and/or README files.
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"amber2lmp"_#amber
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"binary2txt"_#binary
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"ch2lmp"_#charmm
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"chain"_#chain
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"colvars"_#colvars
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"createatoms"_#createatoms
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"doxygen"_#doxygen
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"drude"_#drude
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"eam database"_#eamdb
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"eam generate"_#eamgn
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"eff"_#eff
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"emacs"_#emacs
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"fep"_#fep
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"i-pi"_#ipi
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"ipp"_#ipp
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"kate"_#kate
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"lmp2arc"_#arc
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"lmp2cfg"_#cfg
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"matlab"_#matlab
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"micelle2d"_#micelle
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"moltemplate"_#moltemplate
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"msi2lmp"_#msi
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"phonon"_#phonon
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"polybond"_#polybond
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"pymol_asphere"_#pymol
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"python"_#pythontools
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"reax"_#reax_tool
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"smd"_#smd
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"vim"_#vim
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"xmgrace"_#xmgrace :ul
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:line
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Pre-processing tools :h3
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"amber2lmp"_#amber,
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"ch2lmp"_#charmm,
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"chain"_#chain,
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"createatoms"_#createatoms,
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"drude"_#drude,
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"eam database"_#eamdb,
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"eam generate"_#eamgn,
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"eff"_#eff,
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"ipp"_#ipp,
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"micelle2d"_#micelle,
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"moltemplate"_#moltemplate,
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"msi2lmp"_#msi,
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"polybond"_#polybond :tb(c=6,ea=c,a=l)
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Post-processing tools :h3
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"amber2lmp"_#amber,
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"binary2txt"_#binary,
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"ch2lmp"_#charmm,
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"colvars"_#colvars,
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"eff"_#eff,
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"fep"_#fep,
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"lmp2arc"_#arc,
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"lmp2cfg"_#cfg,
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"matlab"_#matlab,
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"phonon"_#phonon,
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"pymol_asphere"_#pymol,
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"python"_#pythontools,
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"reax"_#reax_tool,
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"smd"_#smd,
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"xmgrace"_#xmgrace :tb(c=6,ea=c,a=l)
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Miscellaneous tools :h3
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"doxygen"_#doxygen,
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"emacs"_#emacs,
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"i-pi"_#ipi,
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"kate"_#kate,
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"vim"_#vim :tb(c=5,ea=c,a=l)
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:line
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amber2lmp tool :h3,link(amber)
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Tool descriptions :h3
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amber2lmp tool :h4,link(amber)
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The amber2lmp sub-directory contains two Python scripts for converting
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files back-and-forth between the AMBER MD code and LAMMPS. See the
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@ -91,7 +106,7 @@ necessary modifications yourself.
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:line
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binary2txt tool :h3,link(binary)
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binary2txt tool :h4,link(binary)
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The file binary2txt.cpp converts one or more binary LAMMPS dump file
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into ASCII text files. The syntax for running the tool is
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@ -104,7 +119,7 @@ since binary files are not compatible across all platforms.
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:line
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ch2lmp tool :h3,link(charmm)
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ch2lmp tool :h4,link(charmm)
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The ch2lmp sub-directory contains tools for converting files
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back-and-forth between the CHARMM MD code and LAMMPS.
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@ -129,7 +144,7 @@ Chris Lorenz (chris.lorenz at kcl.ac.uk), King's College London.
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:line
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chain tool :h3,link(chain)
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chain tool :h4,link(chain)
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The file chain.f creates a LAMMPS data file containing bead-spring
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polymer chains and/or monomer solvent atoms. It uses a text file
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@ -146,7 +161,7 @@ for the "chain benchmark"_Speed_bench.html.
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:line
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colvars tools :h3,link(colvars)
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colvars tools :h4,link(colvars)
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The colvars directory contains a collection of tools for postprocessing
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data produced by the colvars collective variable library.
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@ -168,7 +183,7 @@ gmail.com) at ICTP, Italy.
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:line
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createatoms tool :h3,link(createatoms)
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createatoms tool :h4,link(createatoms)
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The tools/createatoms directory contains a Fortran program called
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createAtoms.f which can generate a variety of interesting crystal
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@ -181,7 +196,7 @@ The tool is authored by Xiaowang Zhou (Sandia), xzhou at sandia.gov.
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:line
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doxygen tool :h3,link(doxygen)
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doxygen tool :h4,link(doxygen)
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The tools/doxygen directory contains a shell script called
|
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doxygen.sh which can generate a call graph and API lists using
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@ -193,7 +208,7 @@ The tool is authored by Nandor Tamaskovics, numericalfreedom at googlemail.com.
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:line
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drude tool :h3,link(drude)
|
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drude tool :h4,link(drude)
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|
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The tools/drude directory contains a Python script called
|
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polarizer.py which can add Drude oscillators to a LAMMPS
|
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|
|
@ -206,7 +221,7 @@ at univ-bpclermont.fr, alain.dequidt at univ-bpclermont.fr
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:line
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eam database tool :h3,link(eamdb)
|
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eam database tool :h4,link(eamdb)
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The tools/eam_database directory contains a Fortran program that will
|
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generate EAM alloy setfl potential files for any combination of 16
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@ -222,7 +237,7 @@ X. W. Zhou, R. A. Johnson, and H. N. G. Wadley, Phys. Rev. B, 69,
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:line
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|
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eam generate tool :h3,link(eamgn)
|
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eam generate tool :h4,link(eamgn)
|
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|
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The tools/eam_generate directory contains several one-file C programs
|
||||
that convert an analytic formula into a tabulated "embedded atom
|
||||
|
|
@ -235,7 +250,7 @@ The source files and potentials were provided by Gerolf Ziegenhain
|
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|
||||
:line
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||||
|
||||
eff tool :h3,link(eff)
|
||||
eff tool :h4,link(eff)
|
||||
|
||||
The tools/eff directory contains various scripts for generating
|
||||
structures and post-processing output for simulations using the
|
||||
|
|
@ -246,7 +261,7 @@ These tools were provided by Andres Jaramillo-Botero at CalTech
|
|||
|
||||
:line
|
||||
|
||||
emacs tool :h3,link(emacs)
|
||||
emacs tool :h4,link(emacs)
|
||||
|
||||
The tools/emacs directory contains an Emacs Lisp add-on file for GNU Emacs
|
||||
that enables a lammps-mode for editing input scripts when using GNU Emacs,
|
||||
|
|
@ -257,7 +272,7 @@ These tools were provided by Aidan Thompson at Sandia
|
|||
|
||||
:line
|
||||
|
||||
fep tool :h3,link(fep)
|
||||
fep tool :h4,link(fep)
|
||||
|
||||
The tools/fep directory contains Python scripts useful for
|
||||
post-processing results from performing free-energy perturbation
|
||||
|
|
@ -270,7 +285,7 @@ See README file in the tools/fep directory.
|
|||
|
||||
:line
|
||||
|
||||
i-pi tool :h3,link(ipi)
|
||||
i-pi tool :h4,link(ipi)
|
||||
|
||||
The tools/i-pi directory contains a version of the i-PI package, with
|
||||
all the LAMMPS-unrelated files removed. It is provided so that it can
|
||||
|
|
@ -287,7 +302,7 @@ calculations with LAMMPS.
|
|||
|
||||
:line
|
||||
|
||||
ipp tool :h3,link(ipp)
|
||||
ipp tool :h4,link(ipp)
|
||||
|
||||
The tools/ipp directory contains a Perl script ipp which can be used
|
||||
to facilitate the creation of a complicated file (say, a lammps input
|
||||
|
|
@ -301,7 +316,7 @@ tools/createatoms tool's input file.
|
|||
|
||||
:line
|
||||
|
||||
kate tool :h3,link(kate)
|
||||
kate tool :h4,link(kate)
|
||||
|
||||
The file in the tools/kate directory is an add-on to the Kate editor
|
||||
in the KDE suite that allow syntax highlighting of LAMMPS input
|
||||
|
|
@ -312,7 +327,7 @@ The file was provided by Alessandro Luigi Sellerio
|
|||
|
||||
:line
|
||||
|
||||
lmp2arc tool :h3,link(arc)
|
||||
lmp2arc tool :h4,link(arc)
|
||||
|
||||
The lmp2arc sub-directory contains a tool for converting LAMMPS output
|
||||
files to the format for Accelrys' Insight MD code (formerly
|
||||
|
|
@ -328,7 +343,7 @@ Greathouse at Sandia (jagreat at sandia.gov).
|
|||
|
||||
:line
|
||||
|
||||
lmp2cfg tool :h3,link(cfg)
|
||||
lmp2cfg tool :h4,link(cfg)
|
||||
|
||||
The lmp2cfg sub-directory contains a tool for converting LAMMPS output
|
||||
files into a series of *.cfg files which can be read into the
|
||||
|
|
@ -339,7 +354,7 @@ This tool was written by Ara Kooser at Sandia (askoose at sandia.gov).
|
|||
|
||||
:line
|
||||
|
||||
matlab tool :h3,link(matlab)
|
||||
matlab tool :h4,link(matlab)
|
||||
|
||||
The matlab sub-directory contains several "MATLAB"_matlabhome scripts for
|
||||
post-processing LAMMPS output. The scripts include readers for log
|
||||
|
|
@ -357,7 +372,7 @@ These scripts were written by Arun Subramaniyan at Purdue Univ
|
|||
|
||||
:line
|
||||
|
||||
micelle2d tool :h3,link(micelle)
|
||||
micelle2d tool :h4,link(micelle)
|
||||
|
||||
The file micelle2d.f creates a LAMMPS data file containing short lipid
|
||||
chains in a monomer solution. It uses a text file containing lipid
|
||||
|
|
@ -374,7 +389,7 @@ definition file. This tool was used to create the system for the
|
|||
|
||||
:line
|
||||
|
||||
moltemplate tool :h3,link(moltemplate)
|
||||
moltemplate tool :h4,link(moltemplate)
|
||||
|
||||
The moltemplate sub-directory contains a Python-based tool for
|
||||
building molecular systems based on a text-file description, and
|
||||
|
|
@ -388,7 +403,7 @@ supports it. It has its own WWW page at
|
|||
|
||||
:line
|
||||
|
||||
msi2lmp tool :h3,link(msi)
|
||||
msi2lmp tool :h4,link(msi)
|
||||
|
||||
The msi2lmp sub-directory contains a tool for creating LAMMPS template
|
||||
input and data files from BIOVIA's Materias Studio files (formerly Accelrys'
|
||||
|
|
@ -405,7 +420,7 @@ See the README file in the tools/msi2lmp folder for more information.
|
|||
|
||||
:line
|
||||
|
||||
phonon tool :h3,link(phonon)
|
||||
phonon tool :h4,link(phonon)
|
||||
|
||||
The phonon sub-directory contains a post-processing tool useful for
|
||||
analyzing the output of the "fix phonon"_fix_phonon.html command in
|
||||
|
|
@ -420,7 +435,7 @@ University.
|
|||
|
||||
:line
|
||||
|
||||
polybond tool :h3,link(polybond)
|
||||
polybond tool :h4,link(polybond)
|
||||
|
||||
The polybond sub-directory contains a Python-based tool useful for
|
||||
performing "programmable polymer bonding". The Python file
|
||||
|
|
@ -434,7 +449,7 @@ This tool was written by Zachary Kraus at Georgia Tech.
|
|||
|
||||
:line
|
||||
|
||||
pymol_asphere tool :h3,link(pymol)
|
||||
pymol_asphere tool :h4,link(pymol)
|
||||
|
||||
The pymol_asphere sub-directory contains a tool for converting a
|
||||
LAMMPS dump file that contains orientation info for ellipsoidal
|
||||
|
|
@ -452,7 +467,7 @@ This tool was written by Mike Brown at Sandia.
|
|||
|
||||
:line
|
||||
|
||||
python tool :h3,link(pythontools)
|
||||
python tool :h4,link(pythontools)
|
||||
|
||||
The python sub-directory contains several Python scripts
|
||||
that perform common LAMMPS post-processing tasks, such as:
|
||||
|
|
@ -468,7 +483,7 @@ README for more info on Pizza.py and how to use these scripts.
|
|||
|
||||
:line
|
||||
|
||||
reax tool :h3,link(reax_tool)
|
||||
reax tool :h4,link(reax_tool)
|
||||
|
||||
The reax sub-directory contains stand-alond codes that can
|
||||
post-process the output of the "fix reax/bonds"_fix_reax_bonds.html
|
||||
|
|
@ -479,7 +494,7 @@ These tools were written by Aidan Thompson at Sandia.
|
|||
|
||||
:line
|
||||
|
||||
smd tool :h3,link(smd)
|
||||
smd tool :h4,link(smd)
|
||||
|
||||
The smd sub-directory contains a C++ file dump2vtk_tris.cpp and
|
||||
Makefile which can be compiled and used to convert triangle output
|
||||
|
|
@ -495,7 +510,7 @@ Ernst Mach Institute in Germany (georg.ganzenmueller at emi.fhg.de).
|
|||
|
||||
:line
|
||||
|
||||
vim tool :h3,link(vim)
|
||||
vim tool :h4,link(vim)
|
||||
|
||||
The files in the tools/vim directory are add-ons to the VIM editor
|
||||
that allow easier editing of LAMMPS input scripts. See the README.txt
|
||||
|
|
@ -506,7 +521,7 @@ ziegenhain.com)
|
|||
|
||||
:line
|
||||
|
||||
xmgrace tool :h3,link(xmgrace)
|
||||
xmgrace tool :h4,link(xmgrace)
|
||||
|
||||
The files in the tools/xmgrace directory can be used to plot the
|
||||
thermodynamic data in LAMMPS log files via the xmgrace plotting
|
||||
|
|
|
|||
Loading…
Reference in New Issue