2016-05-10 01:33:12 +08:00
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< li class = "toctree-l1" > < a class = "reference internal" href = "Section_intro.html" > 1. Introduction< / a > < / li >
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< li > fix ipi command< / li >
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< a href = "Section_commands.html#comm" > Commands< / a >
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< div class = "section" id = "fix-ipi-command" >
< span id = "index-0" > < / span > < h1 > fix ipi command< / h1 >
< div class = "section" id = "syntax" >
< h2 > Syntax< / h2 >
< div class = "highlight-default" > < div class = "highlight" > < pre > < span > < / span > < span class = "n" > fix< / span > < span class = "n" > ID< / span > < span class = "n" > group< / span > < span class = "o" > -< / span > < span class = "n" > ID< / span > < span class = "n" > ipi< / span > < span class = "n" > address< / span > < span class = "n" > port< / span > < span class = "p" > [< / span > < span class = "n" > unix< / span > < span class = "p" > ]< / span >
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< li > ID, group-ID are documented in < a class = "reference internal" href = "fix.html" > < span class = "doc" > fix< / span > < / a > command< / li >
< li > ipi = style name of this fix command< / li >
< li > address = internet address (FQDN or IP), or UNIX socket name< / li >
< li > port = port number (ignored for UNIX sockets)< / li >
< li > optional keyword = < em > unix< / em > , if present uses a unix socket< / li >
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< div class = "section" id = "examples" >
< h2 > Examples< / h2 >
< p > fix 1 all ipi my.server.com 12345
fix 1 all ipi mysocket 666 unix< / p >
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< div class = "section" id = "description" >
< h2 > Description< / h2 >
< p > This fix enables LAMMPS to be run as a client for the i-PI Python
wrapper < a class = "reference internal" href = "#ipi" > < span class = "std std-ref" > (IPI)< / span > < / a > for performing a path integral molecular dynamics
(PIMD) simulation. The philosophy behind i-PI is described in the
following publication < a class = "reference internal" href = "#ipicpc" > < span class = "std std-ref" > (IPI-CPC)< / span > < / a > .< / p >
< p > A version of the i-PI package, containing only files needed for use
with LAMMPS, is provided in the tools/i-pi directory. See the
tools/i-pi/manual.pdf for an introduction to i-PI. The
examples/USER/i-pi directory contains example scripts for using i-PI
with LAMMPS.< / p >
< p > In brief, the path integral molecular dynamics is performed by the
Python wrapper, while the client (LAMMPS in this case) simply computes
forces and energy for each configuration. The communication between
the two components takes place using sockets, and is reduced to the
bare minimum. All the parameters of the dynamics are specified in the
input of i-PI, and all the parameters of the force field must be
specified as LAMMPS inputs, preceding the < em > fix ipi< / em > command.< / p >
< p > The server address must be specified by the < em > address< / em > argument, and
can be either the IP address, the fully-qualified name of the server,
or the name of a UNIX socket for local, faster communication. In the
case of internet sockets, the < em > port< / em > argument specifies the port
number on which i-PI is listening, while the < em > unix< / em > optional switch
specifies that the socket is a UNIX socket.< / p >
< p > Note that there is no check of data integrity, or that the atomic
configurations make sense. It is assumed that the species in the i-PI
input are listed in the same order as in the data file of LAMMPS. The
initial configuration is ignored, as it will be substituted with the
coordinates received from i-PI before forces are ever evaluated.< / p >
< / div >
< div class = "section" id = "restart-fix-modify-output-run-start-stop-minimize-info" >
< h2 > Restart, fix_modify, output, run start/stop, minimize info< / h2 >
< p > There is no restart information associated with this fix, since all
the dynamical parameters are dealt with by i-PI.< / p >
< / div >
< div class = "section" id = "restrictions" >
< h2 > Restrictions< / h2 >
< p > Using this fix on anything other than all atoms requires particular
care, since i-PI will know nothing on atoms that are not those whose
coordinates are transferred. However, one could use this strategy to
define an external potential acting on the atoms that are moved by
i-PI.< / p >
< p > This fix is part of the USER-MISC package. It is only enabled if
LAMMPS was built with that package. See the < a class = "reference internal" href = "Section_start.html#start-3" > < span class = "std std-ref" > Making LAMMPS< / span > < / a > section for more info. Because of
the use of UNIX domain sockets, this fix will only work in a UNIX
environment.< / p >
< / div >
< div class = "section" id = "related-commands" >
< h2 > Related commands< / h2 >
2016-05-10 03:49:32 +08:00
< p > < a class = "reference internal" href = "fix_nve.html" > < span class = "doc" > fix nve< / span > < / a > < / p >
2016-05-10 01:33:12 +08:00
< hr class = "docutils" / >
< p id = "ipicpc" > < strong > (IPI-CPC)< / strong > Ceriotti, More and Manolopoulos, Comp Phys Comm, 185,
1019-1026 (2014).< / p >
< p id = "ipi" > < strong > (IPI)< / strong >
< a class = "reference external" href = "http://epfl-cosmo.github.io/gle4md/index.html?page=ipi" > http://epfl-cosmo.github.io/gle4md/index.html?page=ipi< / a > < / p >
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