forked from lijiext/lammps
262 lines
10 KiB
Plaintext
262 lines
10 KiB
Plaintext
<HEAD>
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<TITLE>LAMMPS Users Manual</TITLE>
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<META NAME="docnumber" CONTENT="14 Mar 2015 version">
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<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
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<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
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</HEAD>
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<BODY>
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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Section_commands.html#comm)
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:line
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<H1></H1>
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LAMMPS Documentation :c,h3
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14 Mar 2015 version :c,h4
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Version info: :h4
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The LAMMPS "version" is the date when it was released, such as 1 May
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2010. LAMMPS is updated continuously. Whenever we fix a bug or add a
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feature, we release it immediately, and post a notice on "this page of
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the WWW site"_bug. Each dated copy of LAMMPS contains all the
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features and bug-fixes up to and including that version date. The
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version date is printed to the screen and logfile every time you run
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LAMMPS. It is also in the file src/version.h and in the LAMMPS
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directory name created when you unpack a tarball, and at the top of
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the first page of the manual (this page).
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If you browse the HTML doc pages on the LAMMPS WWW site, they always
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describe the most current version of LAMMPS. :ulb,l
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If you browse the HTML doc pages included in your tarball, they
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describe the version you have. :l
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The "PDF file"_Manual.pdf on the WWW site or in the tarball is updated
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about once per month. This is because it is large, and we don't want
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it to be part of every patch. :l
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There is also a "Developer.pdf"_Developer.pdf file in the doc
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directory, which describes the internal structure and algorithms of
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LAMMPS. :ule,l
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LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel
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Simulator.
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LAMMPS is a classical molecular dynamics simulation code designed to
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run efficiently on parallel computers. It was developed at Sandia
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National Laboratories, a US Department of Energy facility, with
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funding from the DOE. It is an open-source code, distributed freely
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under the terms of the GNU Public License (GPL).
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The primary developers of LAMMPS are "Steve Plimpton"_sjp, Aidan
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Thompson, and Paul Crozier who can be contacted at
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sjplimp,athomps,pscrozi at sandia.gov. The "LAMMPS WWW Site"_lws at
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http://lammps.sandia.gov has more information about the code and its
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uses.
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:link(bug,http://lammps.sandia.gov/bug.html)
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:link(sjp,http://www.sandia.gov/~sjplimp)
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:line
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The LAMMPS documentation is organized into the following sections. If
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you find errors or omissions in this manual or have suggestions for
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useful information to add, please send an email to the developers so
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we can improve the LAMMPS documentation.
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Once you are familiar with LAMMPS, you may want to bookmark "this
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page"_Section_commands.html#comm at Section_commands.html#comm since
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it gives quick access to documentation for all LAMMPS commands.
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"PDF file"_Manual.pdf of the entire manual, generated by
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"htmldoc"_http://freecode.com/projects/htmldoc
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"Introduction"_Section_intro.html :olb,l
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1.1 "What is LAMMPS"_intro_1 :ulb,b
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1.2 "LAMMPS features"_intro_2 :b
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1.3 "LAMMPS non-features"_intro_3 :b
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1.4 "Open source distribution"_intro_4 :b
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1.5 "Acknowledgments and citations"_intro_5 :ule,b
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"Getting started"_Section_start.html :l
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2.1 "What's in the LAMMPS distribution"_start_1 :ulb,b
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2.2 "Making LAMMPS"_start_2 :b
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2.3 "Making LAMMPS with optional packages"_start_3 :b
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2.4 "Building LAMMPS via the Make.py script"_start_4 :b
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2.5 "Building LAMMPS as a library"_start_5 :b
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2.6 "Running LAMMPS"_start_6 :b
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2.7 "Command-line options"_start_7 :b
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2.8 "Screen output"_start_8 :b
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2.9 "Tips for users of previous versions"_start_9 :ule,b
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"Commands"_Section_commands.html :l
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3.1 "LAMMPS input script"_cmd_1 :ulb,b
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3.2 "Parsing rules"_cmd_2 :b
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3.3 "Input script structure"_cmd_3 :b
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3.4 "Commands listed by category"_cmd_4 :b
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3.5 "Commands listed alphabetically"_cmd_5 :ule,b
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"Packages"_Section_packages.html :l
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4.1 "Standard packages"_pkg_1 :ulb,b
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4.2 "User packages"_pkg_2 :ule,b
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"Accelerating LAMMPS performance"_Section_accelerate.html :l
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5.1 "Measuring performance"_acc_1 :ulb,b
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5.2 "Algorithms and code options to boost performace"_acc_2 :b
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5.3 "Accelerator packages with optimized styles"_acc_3 :b
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5.3.1 "USER-CUDA package"_accelerate_cuda.html :ulb,b
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5.3.2 "GPU package"_accelerate_gpu.html :b
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5.3.3 "USER-INTEL package"_accelerate_intel.html :b
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5.3.4 "KOKKOS package"_accelerate_kokkos.html :b
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5.3.5 "USER-OMP package"_accelerate_omp.html :b
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5.3.6 "OPT package"_accelerate_opt.html :ule,b
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5.4 "Comparison of various accelerator packages"_acc_4 :ule,b
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"How-to discussions"_Section_howto.html :l
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6.1 "Restarting a simulation"_howto_1 :ulb,b
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6.2 "2d simulations"_howto_2 :b
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6.3 "CHARMM and AMBER force fields"_howto_3 :b
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6.4 "Running multiple simulations from one input script"_howto_4 :b
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6.5 "Multi-replica simulations"_howto_5 :b
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6.6 "Granular models"_howto_6 :b
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6.7 "TIP3P water model"_howto_7 :b
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6.8 "TIP4P water model"_howto_8 :b
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6.9 "SPC water model"_howto_9 :b
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6.10 "Coupling LAMMPS to other codes"_howto_10 :b
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6.11 "Visualizing LAMMPS snapshots"_howto_11 :b
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6.12 "Triclinic (non-orthogonal) simulation boxes"_howto_12 :b
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6.13 "NEMD simulations"_howto_13 :b
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6.14 "Finite-size spherical and aspherical particles"_howto_14 :b
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6.15 "Output from LAMMPS (thermo, dumps, computes, fixes, variables)"_howto_15 :b
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6.16 "Thermostatting, barostatting, and compute temperature"_howto_16 :b
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6.17 "Walls"_howto_17 :b
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6.18 "Elastic constants"_howto_18 :b
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6.19 "Library interface to LAMMPS"_howto_19 :b
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6.20 "Calculating thermal conductivity"_howto_20 :b
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6.21 "Calculating viscosity"_howto_21 :b
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6.22 "Calculating a diffusion coefficient"_howto_22 :b
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6.23 "Using chunks to calculate system properties"_howto_23 :b
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6.24 "Setting parameters for pppm/disp"_howto_24 :ule,b
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"Example problems"_Section_example.html :l
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"Performance & scalability"_Section_perf.html :l
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"Additional tools"_Section_tools.html :l
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"Modifying & extending LAMMPS"_Section_modify.html :l
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10.1 "Atom styles"_mod_1 :ulb,b
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10.2 "Bond, angle, dihedral, improper potentials"_mod_2 :b
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10.3 "Compute styles"_mod_3 :b
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10.4 "Dump styles"_mod_4 :b
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10.5 "Dump custom output options"_mod_5 :b
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10.6 "Fix styles"_mod_6 :b
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10.7 "Input script commands"_mod_7 :b
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10.8 "Kspace computations"_mod_8 :b
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10.9 "Minimization styles"_mod_9 :b
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10.10 "Pairwise potentials"_mod_10 :b
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10.11 "Region styles"_mod_11 :b
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10.12 "Body styles"_mod_12 :b
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10.13 "Thermodynamic output options"_mod_13 :b
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10.14 "Variable options"_mod_14 :b
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10.15 "Submitting new features for inclusion in LAMMPS"_mod_15 :ule,b
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"Python interface"_Section_python.html :l
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11.1 "Overview of running LAMMPS from Python"_py_1 :ulb,b
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11.2 "Overview of using Python from a LAMMPS script"_py_2 :b
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11.3 "Building LAMMPS as a shared library"_py_3 :b
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11.4 "Installing the Python wrapper into Python"_py_4 :b
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11.5 "Extending Python with MPI to run in parallel"_py_5 :b
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11.6 "Testing the Python-LAMMPS interface"_py_6 :b
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11.7 "Using LAMMPS from Python"_py_7 :b
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11.8 "Example Python scripts that use LAMMPS"_py_8 :ule,b
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"Errors"_Section_errors.html :l
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12.1 "Common problems"_err_1 :ulb,b
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12.2 "Reporting bugs"_err_2 :b
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12.3 "Error & warning messages"_err_3 :ule,b
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"Future and history"_Section_history.html :l
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13.1 "Coming attractions"_hist_1 :ulb,b
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13.2 "Past versions"_hist_2 :ule,b
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:ole
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:link(intro_1,Section_intro.html#intro_1)
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:link(intro_2,Section_intro.html#intro_2)
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:link(intro_3,Section_intro.html#intro_3)
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:link(intro_4,Section_intro.html#intro_4)
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:link(intro_5,Section_intro.html#intro_5)
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:link(start_1,Section_start.html#start_1)
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:link(start_2,Section_start.html#start_2)
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:link(start_3,Section_start.html#start_3)
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:link(start_4,Section_start.html#start_4)
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:link(start_5,Section_start.html#start_5)
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:link(start_6,Section_start.html#start_6)
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:link(start_7,Section_start.html#start_7)
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:link(start_8,Section_start.html#start_8)
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:link(start_9,Section_start.html#start_9)
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:link(cmd_1,Section_commands.html#cmd_1)
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:link(cmd_2,Section_commands.html#cmd_2)
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:link(cmd_3,Section_commands.html#cmd_3)
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:link(cmd_4,Section_commands.html#cmd_4)
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:link(cmd_5,Section_commands.html#cmd_5)
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:link(pkg_1,Section_packages.html#pkg_1)
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:link(pkg_2,Section_packages.html#pkg_2)
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:link(acc_1,Section_accelerate.html#acc_1)
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:link(acc_2,Section_accelerate.html#acc_2)
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:link(acc_3,Section_accelerate.html#acc_3)
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:link(acc_4,Section_accelerate.html#acc_4)
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:link(howto_1,Section_howto.html#howto_1)
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:link(howto_2,Section_howto.html#howto_2)
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:link(howto_3,Section_howto.html#howto_3)
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:link(howto_4,Section_howto.html#howto_4)
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:link(howto_5,Section_howto.html#howto_5)
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:link(howto_6,Section_howto.html#howto_6)
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:link(howto_7,Section_howto.html#howto_7)
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:link(howto_8,Section_howto.html#howto_8)
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:link(howto_9,Section_howto.html#howto_9)
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:link(howto_10,Section_howto.html#howto_10)
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:link(howto_11,Section_howto.html#howto_11)
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:link(howto_12,Section_howto.html#howto_12)
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:link(howto_13,Section_howto.html#howto_13)
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:link(howto_14,Section_howto.html#howto_14)
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:link(howto_15,Section_howto.html#howto_15)
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:link(howto_16,Section_howto.html#howto_16)
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:link(howto_17,Section_howto.html#howto_17)
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:link(howto_18,Section_howto.html#howto_18)
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:link(howto_19,Section_howto.html#howto_19)
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:link(howto_20,Section_howto.html#howto_20)
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:link(howto_21,Section_howto.html#howto_21)
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:link(mod_1,Section_modify.html#mod_1)
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:link(mod_2,Section_modify.html#mod_2)
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:link(mod_3,Section_modify.html#mod_3)
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:link(mod_4,Section_modify.html#mod_4)
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:link(mod_5,Section_modify.html#mod_5)
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:link(mod_6,Section_modify.html#mod_6)
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:link(mod_7,Section_modify.html#mod_7)
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:link(mod_8,Section_modify.html#mod_8)
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:link(mod_9,Section_modify.html#mod_9)
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:link(mod_10,Section_modify.html#mod_10)
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:link(mod_11,Section_modify.html#mod_11)
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:link(mod_12,Section_modify.html#mod_12)
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:link(mod_13,Section_modify.html#mod_13)
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:link(mod_14,Section_modify.html#mod_14)
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:link(mod_15,Section_modify.html#mod_15)
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:link(py_1,Section_python.html#py_1)
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:link(py_2,Section_python.html#py_2)
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:link(py_3,Section_python.html#py_3)
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:link(py_4,Section_python.html#py_4)
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:link(py_5,Section_python.html#py_5)
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:link(py_6,Section_python.html#py_6)
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:link(err_1,Section_errors.html#err_1)
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:link(err_2,Section_errors.html#err_2)
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:link(err_3,Section_errors.html#err_3)
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:link(hist_1,Section_history.html#hist_1)
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:link(hist_2,Section_history.html#hist_2)
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</BODY>
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