git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10180 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
@ -493,9 +493,9 @@ package</A>.
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<TR ALIGN="center"><TD ><A HREF = "pair_awpmd.html">awpmd/cut</A></TD><TD ><A HREF = "pair_coul_diel.html">coul/diel</A></TD><TD ><A HREF = "pair_eam.html">eam/cd</A></TD><TD ><A HREF = "pair_edip.html">edip</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_eff.html">eff/cut</A></TD><TD ><A HREF = "pair_gauss.html">gauss/cut</A></TD><TD ><A HREF = "pair_list.html">list</A></TD><TD ><A HREF = "pair_dipole.html">lj/cut/dipole/sf</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_sdk.html">lj/sdk</A></TD><TD ><A HREF = "pair_sdk.html">lj/sdk/coul/long</A></TD><TD ><A HREF = "pair_sdk.html">lj/sdk/coul/msm</A></TD><TD ><A HREF = "pair_lj_sf.html">lj/sf</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_meam_spline.html">meam/spline</A></TD><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></TR>
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<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>
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<TR ALIGN="center"><TD ><A HREF = "pair_sph_taitwater_morris.html">sph/taitwater/morris</A></TD><TD ><A HREF = "pair_tersoff.html">tersoff/table</A>
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<TR ALIGN="center"><TD ><A HREF = "pair_meam_spline.html">meam/spline</A></TD><TD ><A HREF = "pair_meam_sw_spline.html">meam/sw/spline</A></TD><TD ><A HREF = "pair_nb3b_harmonic.html">nb3b/harmonic</A></TD><TD ><A HREF = "pair_reax_c.html">reax/c</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_sph_heatconduction.html">sph/heatconduction</A></TD><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></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_sph_taitwater.html">sph/taitwater</A></TD><TD ><A HREF = "pair_sph_taitwater_morris.html">sph/taitwater/morris</A></TD><TD ><A HREF = "pair_tersoff.html">tersoff/table</A>
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</TD></TR></TABLE></DIV>
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<P>These are accelerated pair styles, which can be used if LAMMPS is
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@ -801,6 +801,7 @@ package"_Section_start.html#start_3.
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"lj/sf"_pair_lj_sf.html,
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"meam/spline"_pair_meam_spline.html,
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"meam/sw/spline"_pair_meam_sw_spline.html,
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"nb3b/harmonic"_pair_nb3b_harmonic.html,
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"reax/c"_pair_reax_c.html,
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"sph/heatconduction"_pair_sph_heatconduction.html,
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"sph/idealgas"_pair_sph_idealgas.html,
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104
doc/pair_nb3b_harmonic.html
Normal file
104
doc/pair_nb3b_harmonic.html
Normal file
@ -0,0 +1,104 @@
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<HTML>
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<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>
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</CENTER>
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<HR>
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<H3>pair_style nb3b/harmonic command
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</H3>
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<P><B>Syntax:</B>
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</P>
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<PRE>pair_style nb3b/harmonic
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</PRE>
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<P><B>Examples:</B>
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</P>
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<PRE>pair_style nb3b/harmonic
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pair_coeff * * MgOH.nb3bharmonic Mg O H
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</PRE>
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<P><B>Description:</B>
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</P>
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<P>This pair style computes a nonbonded 3-body harmonic potential for the
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energy E of a system of atoms as
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</P>
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<CENTER><IMG SRC = "Eqs/pair_3bnbharm.jpg">
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</CENTER>
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<P>where <I>theta_0</I> is the equilibrium value of the angle and <I>K</I> is a
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prefactor. Note that the usual 1/2 factor is included in <I>K</I>. The form
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of the potential is identical to that used in angle_style <I>harmonic</I>,
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but in this case, the atoms do not need to be explicitly bonded.
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</P>
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<P>Only a single pair_coeff command is used with this style which
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specifies a potential file with parameters for specified elements.
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These are mapped to LAMMPS atom types by specifying N additional
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arguments after the filename in the pair_coeff command, where N is the
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number of LAMMPS atom types:
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</P>
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<UL><LI>filename
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<LI>N element names = mapping of elements to atom types
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</UL>
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<P>See the <A HREF = "pair_coeff.html">pair_coeff</A> doc page for alternate ways
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to specify the path for the potential file.
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</P>
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<P>As an example, imagine a file SiC.nb3bharmonic has potential values
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for Si and C. If your LAMMPS simulation has 4 atoms types and you
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want the 1st 3 to be Si, and the 4th to be C, you would use the
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following pair_coeff command:
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</P>
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<PRE>pair_coeff * * SiC.nb3bharmonic Si Si Si C
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</PRE>
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<P>The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
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The first three Si arguments map LAMMPS atom types 1,2,3 to the Si
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element in the potential file. The final C argument maps LAMMPS atom
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type 4 to the C element in the potential file. If a mapping value is
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specified as NULL, the mapping is not performed. This can be used
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when the potential is used as part of the <I>hybrid</I> pair style. The
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NULL values are placeholders for atom types that will be used with
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other potentials. An example of a pair_coeff command for use with the
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<I>hybrid</I> pair style is:
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</P>
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<P>pair_coeff * * 3bnbharm MgOH.3bnbharm Mg O H
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</P>
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<P>Three-body nonbonded harmonic files in the <I>potentials</I> directory of
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the LAMMPS distribution have a ".nb3bharmonic" suffix. Lines that are
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not blank or comments (starting with #) define parameters for a
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triplet of elements.
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</P>
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<P>Each entry has six arguments. The first three are atom types as
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referenced in the LAMMPS input file. The first argument specifies the
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central atom. The fourth argument indicates the <I>K</I> parameter. The
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fifth argument indicates <I>theta_0</I>. The sixth argument indicates a
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separation cutoff in Angstroms.
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</P>
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<P>For a given entry, if the second and third arguments are identical,
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then the entry is for a cutoff for the distance between types 1 and 2
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(values for <I>K</I> and <I>theta_0</I> are irrelevant in this case).
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</P>
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<P>For a given entry, if the first three arguments are all different,
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then the entry is for the <I>K</I> and <I>theta_0</I> parameters (the cutoff in
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this case is irrelevant).
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</P>
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<P>It is <I>not</I> required that the potential file contain entries for all
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of the elements listed in the pair_coeff command. It can also contain
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entries for additional elements not being used in a particular
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simulation; LAMMPS ignores those entries.
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</P>
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<HR>
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<P><B>Restrictions:</B>
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</P>
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<P>This pair style can only be used if LAMMPS was built with the
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USER_MISC package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
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section for more info on packages.
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</P>
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<P><B>Related commands:</B>
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</P>
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<P><A HREF = "pair_coeff.html">pair_coeff</A>
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</P>
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<P><B>Default:</B> none
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</P>
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</HTML>
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99
doc/pair_nb3b_harmonic.txt
Normal file
99
doc/pair_nb3b_harmonic.txt
Normal file
@ -0,0 +1,99 @@
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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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pair_style nb3b/harmonic command :h3
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[Syntax:]
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pair_style nb3b/harmonic :pre
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[Examples:]
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pair_style nb3b/harmonic
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pair_coeff * * MgOH.nb3bharmonic Mg O H :pre
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[Description:]
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This pair style computes a nonbonded 3-body harmonic potential for the
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energy E of a system of atoms as
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:c,image(Eqs/pair_3bnbharm.jpg)
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where {theta_0} is the equilibrium value of the angle and {K} is a
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prefactor. Note that the usual 1/2 factor is included in {K}. The form
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of the potential is identical to that used in angle_style {harmonic},
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but in this case, the atoms do not need to be explicitly bonded.
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Only a single pair_coeff command is used with this style which
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specifies a potential file with parameters for specified elements.
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These are mapped to LAMMPS atom types by specifying N additional
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arguments after the filename in the pair_coeff command, where N is the
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number of LAMMPS atom types:
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filename
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N element names = mapping of elements to atom types :ul
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See the "pair_coeff"_pair_coeff.html doc page for alternate ways
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to specify the path for the potential file.
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As an example, imagine a file SiC.nb3bharmonic has potential values
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for Si and C. If your LAMMPS simulation has 4 atoms types and you
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want the 1st 3 to be Si, and the 4th to be C, you would use the
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following pair_coeff command:
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pair_coeff * * SiC.nb3bharmonic Si Si Si C :pre
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The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
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The first three Si arguments map LAMMPS atom types 1,2,3 to the Si
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element in the potential file. The final C argument maps LAMMPS atom
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type 4 to the C element in the potential file. If a mapping value is
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specified as NULL, the mapping is not performed. This can be used
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when the potential is used as part of the {hybrid} pair style. The
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NULL values are placeholders for atom types that will be used with
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other potentials. An example of a pair_coeff command for use with the
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{hybrid} pair style is:
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pair_coeff * * 3bnbharm MgOH.3bnbharm Mg O H
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Three-body nonbonded harmonic files in the {potentials} directory of
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the LAMMPS distribution have a ".nb3bharmonic" suffix. Lines that are
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not blank or comments (starting with #) define parameters for a
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triplet of elements.
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Each entry has six arguments. The first three are atom types as
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referenced in the LAMMPS input file. The first argument specifies the
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central atom. The fourth argument indicates the {K} parameter. The
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fifth argument indicates {theta_0}. The sixth argument indicates a
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separation cutoff in Angstroms.
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For a given entry, if the second and third arguments are identical,
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then the entry is for a cutoff for the distance between types 1 and 2
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(values for {K} and {theta_0} are irrelevant in this case).
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For a given entry, if the first three arguments are all different,
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then the entry is for the {K} and {theta_0} parameters (the cutoff in
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this case is irrelevant).
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It is {not} required that the potential file contain entries for all
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of the elements listed in the pair_coeff command. It can also contain
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entries for additional elements not being used in a particular
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simulation; LAMMPS ignores those entries.
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:line
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[Restrictions:]
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This pair style can only be used if LAMMPS was built with the
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USER_MISC package. See the "Making LAMMPS"_Section_start.html#start_3
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section for more info on packages.
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[Related commands:]
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"pair_coeff"_pair_coeff.html
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[Default:] none
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