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6
doc/Section_commands.html
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@ -514,9 +514,9 @@ package</A>.
<TR ALIGN="center"><TD ><A HREF = "pair_list.html">list</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/long/soft (o)</A></TD><TD ><A HREF = "pair_lj_soft.html">lj/cut/coul/cut/soft (o)</A></TD><TD ><A HREF = "pair_lj_soft.html">lj/cut/coul/long/soft (o)</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_dipole.html">lj/cut/dipole/sf (go)</A></TD><TD ><A HREF = "pair_lj_soft.html">lj/cut/soft (o)</A></TD><TD ><A HREF = "pair_lj_soft.html">lj/cut/tip4p/long/soft (o)</A></TD><TD ><A HREF = "pair_sdk.html">lj/sdk (go)</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_sdk.html">lj/sdk/coul/long (go)</A></TD><TD ><A HREF = "pair_sdk.html">lj/sdk/coul/msm (o)</A></TD><TD ><A HREF = "pair_lj_sf.html">lj/sf (o)</A></TD><TD ><A HREF = "pair_meam_spline.html">meam/spline</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_meam_sw_spline.html">meam/sw/spline</A></TD><TD ><A HREF = "pair_reax_c.html">reax/c</A></TD><TD ><A HREF = "pair_sph_heatconduction.html">sph/heatconduction</A></TD><TD ><A HREF = "pair_sph_idealgas.html">sph/idealgas</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_sph_lj.html">sph/lj</A></TD><TD ><A HREF = "pair_sph_rhosum.html">sph/rhosum</A></TD><TD ><A HREF = "pair_sph_taitwater.html">sph/taitwater</A></TD><TD ><A HREF = "pair_sph_taitwater_morris.html">sph/taitwater/morris</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_srp.html">srp</A></TD><TD ><A HREF = "pair_tersoff.html">tersoff/table (o)</A></TD><TD ><A HREF = "pair_lj_soft.html">tip4p/long/soft (o)</A>
<TR ALIGN="center"><TD ><A HREF = "pair_meam_sw_spline.html">meam/sw/spline</A></TD><TD ><A HREF = "pair_quip.html">quip</A></TD><TD ><A HREF = "pair_reax_c.html">reax/c</A></TD><TD ><A HREF = "pair_sph_heatconduction.html">sph/heatconduction</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_sph_idealgas.html">sph/idealgas</A></TD><TD ><A HREF = "pair_sph_lj.html">sph/lj</A></TD><TD ><A HREF = "pair_sph_rhosum.html">sph/rhosum</A></TD><TD ><A HREF = "pair_sph_taitwater.html">sph/taitwater</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_sph_taitwater_morris.html">sph/taitwater/morris</A></TD><TD ><A HREF = "pair_srp.html">srp</A></TD><TD ><A HREF = "pair_tersoff.html">tersoff/table (o)</A></TD><TD ><A HREF = "pair_lj_soft.html">tip4p/long/soft (o)</A>
</TD></TR></TABLE></DIV>
<HR>

1
doc/Section_commands.txt
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@ -850,6 +850,7 @@ package"_Section_start.html#start_3.
"lj/sf (o)"_pair_lj_sf.html,
"meam/spline"_pair_meam_spline.html,
"meam/sw/spline"_pair_meam_sw_spline.html,
"quip"_pair_quip.html,
"reax/c"_pair_reax_c.html,
"sph/heatconduction"_pair_sph_heatconduction.html,
"sph/idealgas"_pair_sph_idealgas.html,

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doc/pair_quip.html Normal file
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@ -0,0 +1,98 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>pair_style quip command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>pair_style quip
</PRE>
<P><B>Examples:</B>
</P>
<PRE>pair_style quip
pair_coeff * * gap_example.xml "Potential xml_label=GAP_2014_5_8_60_17_10_38_466" 14
pair_coeff * * sw_example.xml "IP SW" 14
</PRE>
<P><B>Description:</B>
</P>
<P>Style <I>quip</I> provides an interface for calling potential routines from
the QUIP package. QUIP is built separately, and then linked to
LAMMPS. The most recent version of the QUIP package can be downloaded
from GitHub:
<A HREF = "https://github.com/libAtoms/QUIP">https://github.com/libAtoms/QUIP</A>. The
interface is chiefly intended to be used to run Gaussian Approximation
Potentials (GAP), which are described in the following publications:
<A HREF = "#Bartok_2010">(Bartok et al)</A> and <A HREF = "#Bartok_PhD">(PhD thesis of
Bartok)</A>.
</P>
<P>Only a single pair_coeff command is used with the <I>quip</I> style that
specifies a QUIP potential file containing the parameters of the
potential for all needed elements in XML format. This is followed by a
QUIP initialization string. Finally, the QUIP elements are mapped to
LAMMPS atom types by specifying N atomic numbers, where N is the
number of LAMMPS atom types:
</P>
<UL><LI>QUIP filename
<LI>QUIP initialization string
<LI>N atomic numbers = mapping of QUIP elements to atom types
</UL>
<P>See the <A HREF = "pair_coeff.html">pair_coeff</A> doc page for alternate ways
to specify the path for the potential file.
</P>
<P>A QUIP potential is fully specified by the filename which contains the
parameters of the potential in XML format, the initialisation string,
and the map of atomic numbers.
</P>
<P>GAP potentials can be obtained from the Data repository section of
<A HREF = "http://www.libatoms.org">http://www.libatoms.org</A>, where the
appropriate initialisation strings are also advised. The list of
atomic numbers must be matched to the LAMMPS atom types specified in
the LAMMPS data file or elsewhere.
</P>
<P>Two examples input scripts are provided in the examples/USER/quip
directory.
</P>
<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
</P>
<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
mix, shift, table, and tail options.
</P>
<P>This pair style does not write its information to <A HREF = "restart.html">binary restart
files</A>, since it is stored in potential files. Thus, you
need to re-specify the pair_style and pair_coeff commands in an input
script that reads a restart file.
</P>
<P>This pair style can only be used via the <I>pair</I> keyword of the
<A HREF = "run_style.html">run_style respa</A> command. It does not support the
<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
</P>
<P><B>Restrictions:</B>
</P>
<P>QUIP potentials are parametrised in electron-volts and angstroms and
therefore should be used with LAMMPS metal <A HREF = "units.html">units</A>.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "pair_coeff.html">pair_coeff</A>
</P>
<HR>
<A NAME = "Bartok_2010"></A>
<P><B>(Bartok_2010)</B> AP Bartok, MC Payne, R Kondor, and G Csanyi, Physical
Review Letters 104, 136403 (2010).
</P>
<A NAME = "Bartok_PhD"></A>
<P><B>(Bartok_PhD)</B> A Bartok-Partay, PhD Thesis, University of Cambridge,
(2010).
</P>
</HTML>

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@ -0,0 +1,92 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
pair_style quip command :h3
[Syntax:]
pair_style quip :pre
[Examples:]
pair_style quip
pair_coeff * * gap_example.xml "Potential xml_label=GAP_2014_5_8_60_17_10_38_466" 14
pair_coeff * * sw_example.xml "IP SW" 14 :pre
[Description:]
Style {quip} provides an interface for calling potential routines from
the QUIP package. QUIP is built separately, and then linked to
LAMMPS. The most recent version of the QUIP package can be downloaded
from GitHub:
"https://github.com/libAtoms/QUIP"_https://github.com/libAtoms/QUIP. The
interface is chiefly intended to be used to run Gaussian Approximation
Potentials (GAP), which are described in the following publications:
"(Bartok et al)"_#Bartok_2010 and "(PhD thesis of
Bartok)"_#Bartok_PhD.
Only a single pair_coeff command is used with the {quip} style that
specifies a QUIP potential file containing the parameters of the
potential for all needed elements in XML format. This is followed by a
QUIP initialization string. Finally, the QUIP elements are mapped to
LAMMPS atom types by specifying N atomic numbers, where N is the
number of LAMMPS atom types:
QUIP filename
QUIP initialization string
N atomic numbers = mapping of QUIP elements to atom types :ul
See the "pair_coeff"_pair_coeff.html doc page for alternate ways
to specify the path for the potential file.
A QUIP potential is fully specified by the filename which contains the
parameters of the potential in XML format, the initialisation string,
and the map of atomic numbers.
GAP potentials can be obtained from the Data repository section of
"http://www.libatoms.org"_http://www.libatoms.org, where the
appropriate initialisation strings are also advised. The list of
atomic numbers must be matched to the LAMMPS atom types specified in
the LAMMPS data file or elsewhere.
Two examples input scripts are provided in the examples/USER/quip
directory.
[Mixing, shift, table, tail correction, restart, rRESPA info]:
This pair style does not support the "pair_modify"_pair_modify.html
mix, shift, table, and tail options.
This pair style does not write its information to "binary restart
files"_restart.html, since it is stored in potential files. Thus, you
need to re-specify the pair_style and pair_coeff commands in an input
script that reads a restart file.
This pair style can only be used via the {pair} keyword of the
"run_style respa"_run_style.html command. It does not support the
{inner}, {middle}, {outer} keywords.
[Restrictions:]
QUIP potentials are parametrised in electron-volts and angstroms and
therefore should be used with LAMMPS metal "units"_units.html.
[Related commands:]
"pair_coeff"_pair_coeff.html
:line
:link(Bartok_2010)
[(Bartok_2010)] AP Bartok, MC Payne, R Kondor, and G Csanyi, Physical
Review Letters 104, 136403 (2010).
:link(Bartok_PhD)
[(Bartok_PhD)] A Bartok-Partay, PhD Thesis, University of Cambridge,
(2010).