forked from lijiext/lammps
198 lines
12 KiB
Plaintext
198 lines
12 KiB
Plaintext
Example problems
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================
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The LAMMPS distribution includes an examples sub-directory with many
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sample problems. Many are 2d models that run quickly are are
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straightforward to visualize, requiring at most a couple of minutes to
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run on a desktop machine. Each problem has an input script (in.*) and
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produces a log file (log.*) when it runs. Some use a data file
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(data.*) of initial coordinates as additional input. A few sample log
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file run on different machines and different numbers of processors are
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included in the directories to compare your answers to. E.g. a log
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file like log.date.crack.foo.P means the "crack" example was run on P
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processors of machine "foo" on that date (i.e. with that version of
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LAMMPS).
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Many of the input files have commented-out lines for creating dump
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files and image files.
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If you uncomment the :doc:`dump <dump>` command in the input script, a
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text dump file will be produced, which can be animated by various
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`visualization programs <http://lammps.sandia.gov/viz.html>`_. It can
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also be animated using the xmovie tool described in the :doc:`Additional Tools <Section_tools>` section of the LAMMPS documentation.
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If you uncomment the :doc:`dump image <dump>` command in the input
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script, and assuming you have built LAMMPS with a JPG library, JPG
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snapshot images will be produced when the simulation runs. They can
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be quickly post-processed into a movie using commands described on the
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:doc:`dump image <dump_image>` doc page.
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Animations of many of the examples can be viewed on the Movies section
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of the `LAMMPS web site <lws_>`_.
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There are two kinds of sub-directories in the examples dir. Lowercase
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dirs contain one or a few simple, quick-to-run problems. Uppercase
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dirs contain up to several complex scripts that illustrate a
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particular kind of simulation method or model. Some of these run for
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longer times, e.g. to measure a particular quantity.
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Lists of both kinds of directories are given below.
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----------
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Lowercase directories
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---------------------
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+-------------+------------------------------------------------------------------+
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| accelerate | run with various acceleration options (OpenMP, GPU, Phi) |
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+-------------+------------------------------------------------------------------+
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| balance | dynamic load balancing, 2d system |
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+-------------+------------------------------------------------------------------+
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| body | body particles, 2d system |
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+-------------+------------------------------------------------------------------+
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| colloid | big colloid particles in a small particle solvent, 2d system |
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+-------------+------------------------------------------------------------------+
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| comb | models using the COMB potential |
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+-------------+------------------------------------------------------------------+
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| coreshell | core/shell model using CORESHELL package |
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+-------------+------------------------------------------------------------------+
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| crack | crack propagation in a 2d solid |
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+-------------+------------------------------------------------------------------+
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| deposit | deposit atoms and molecules on a surface |
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+-------------+------------------------------------------------------------------+
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| dipole | point dipolar particles, 2d system |
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+-------------+------------------------------------------------------------------+
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| dreiding | methanol via Dreiding FF |
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+-------------+------------------------------------------------------------------+
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| eim | NaCl using the EIM potential |
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+-------------+------------------------------------------------------------------+
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| ellipse | ellipsoidal particles in spherical solvent, 2d system |
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+-------------+------------------------------------------------------------------+
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| flow | Couette and Poiseuille flow in a 2d channel |
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+-------------+------------------------------------------------------------------+
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| friction | frictional contact of spherical asperities between 2d surfaces |
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+-------------+------------------------------------------------------------------+
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| hugoniostat | Hugoniostat shock dynamics |
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+-------------+------------------------------------------------------------------+
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| indent | spherical indenter into a 2d solid |
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+-------------+------------------------------------------------------------------+
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| kim | use of potentials in Knowledge Base for Interatomic Models (KIM) |
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+-------------+------------------------------------------------------------------+
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| meam | MEAM test for SiC and shear (same as shear examples) |
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+-------------+------------------------------------------------------------------+
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| melt | rapid melt of 3d LJ system |
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+-------------+------------------------------------------------------------------+
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| micelle | self-assembly of small lipid-like molecules into 2d bilayers |
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+-------------+------------------------------------------------------------------+
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| min | energy minimization of 2d LJ melt |
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+-------------+------------------------------------------------------------------+
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| msst | MSST shock dynamics |
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+-------------+------------------------------------------------------------------+
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| nb3b | use of nonbonded 3-body harmonic pair style |
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+-------------+------------------------------------------------------------------+
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| neb | nudged elastic band (NEB) calculation for barrier finding |
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+-------------+------------------------------------------------------------------+
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| nemd | non-equilibrium MD of 2d sheared system |
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+-------------+------------------------------------------------------------------+
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| obstacle | flow around two voids in a 2d channel |
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+-------------+------------------------------------------------------------------+
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| peptide | dynamics of a small solvated peptide chain (5-mer) |
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+-------------+------------------------------------------------------------------+
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| peri | Peridynamic model of cylinder impacted by indenter |
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+-------------+------------------------------------------------------------------+
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| pour | pouring of granular particles into a 3d box, then chute flow |
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+-------------+------------------------------------------------------------------+
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| prd | parallel replica dynamics of vacancy diffusion in bulk Si |
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+-------------+------------------------------------------------------------------+
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| python | using embedded Python in a LAMMPS input script |
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+-------------+------------------------------------------------------------------+
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| qeq | use of the QEQ package for charge equilibration |
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+-------------+------------------------------------------------------------------+
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| reax | RDX and TATB models using the ReaxFF |
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+-------------+------------------------------------------------------------------+
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| rigid | rigid bodies modeled as independent or coupled |
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+-------------+------------------------------------------------------------------+
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| shear | sideways shear applied to 2d solid, with and without a void |
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+-------------+------------------------------------------------------------------+
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| snap | NVE dynamics for BCC tantalum crystal using SNAP potential |
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+-------------+------------------------------------------------------------------+
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| srd | stochastic rotation dynamics (SRD) particles as solvent |
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+-------------+------------------------------------------------------------------+
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| streitz | use of Streitz/Mintmire potential with charge equilibration |
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+-------------+------------------------------------------------------------------+
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| tad | temperature-accelerated dynamics of vacancy diffusion in bulk Si |
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+-------------+------------------------------------------------------------------+
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| vashishta | use of the Vashishta potential |
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+-------------+------------------------------------------------------------------+
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Here is how you can run and visualize one of the sample problems:
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.. parsed-literal::
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cd indent
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cp ../../src/lmp_linux . # copy LAMMPS executable to this dir
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lmp_linux -in in.indent # run the problem
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Running the simulation produces the files *dump.indent* and
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*log.lammps*\ . You can visualize the dump file of snapshots with a
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variety of 3rd-party tools highlighted on the
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`Visualization <http://lammps.sandia.gov/viz.html>`_ page of the LAMMPS
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web site.
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If you uncomment the :doc:`dump image <dump_image>` line(s) in the input
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script a series of JPG images will be produced by the run (assuming
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you built LAMMPS with JPG support; see :doc:`Section start 2.2 <Section_start>` for details). These can be viewed
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individually or turned into a movie or animated by tools like
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ImageMagick or QuickTime or various Windows-based tools. See the
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:doc:`dump image <dump_image>` doc page for more details. E.g. this
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Imagemagick command would create a GIF file suitable for viewing in a
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browser.
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.. parsed-literal::
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% convert -loop 1 *.jpg foo.gif
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----------
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Uppercase directories
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---------------------
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+-----------+--------------------------------------------------------------------------------------------------+
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| ASPHERE | various aspherical particle models, using ellipsoids, rigid bodies, line/triangle particles, etc |
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+-----------+--------------------------------------------------------------------------------------------------+
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| COUPLE | examples of how to use LAMMPS as a library |
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+-----------+--------------------------------------------------------------------------------------------------+
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| DIFFUSE | compute diffusion coefficients via several methods |
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+-----------+--------------------------------------------------------------------------------------------------+
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| ELASTIC | compute elastic constants at zero temperature |
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+-----------+--------------------------------------------------------------------------------------------------+
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| ELASTIC_T | compute elastic constants at finite temperature |
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+-----------+--------------------------------------------------------------------------------------------------+
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| KAPPA | compute thermal conductivity via several methods |
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+-----------+--------------------------------------------------------------------------------------------------+
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| MC | using LAMMPS in a Monte Carlo mode to relax the energy of a system |
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+-----------+--------------------------------------------------------------------------------------------------+
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| USER | examples for USER packages and USER-contributed commands |
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+-----------+--------------------------------------------------------------------------------------------------+
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| VISCOSITY | compute viscosity via several methods |
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+-----------+--------------------------------------------------------------------------------------------------+
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Nearly all of these directories have README files which give more
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details on how to understand and use their contents.
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The USER directory has a large number of sub-directories which
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correspond by name to a USER package. They contain scripts that
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illustrate how to use the command(s) provided in that package. Many
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of the sub-directories have their own README files which give further
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instructions. See the :doc:`Section packages <Section_packages>` doc
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page for more info on specific USER packages.
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.. _lws: http://lammps.sandia.gov
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.. _ld: Manual.html
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.. _lc: Section_commands.html#comm
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