ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

''

Browse Source 
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14239 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
2015-11-06 15:51:31 +00:00
parent f71eee1d4d
commit 9cd043e682
5 changed files with 131 additions and 11 deletions
Download Patch File Download Diff File Expand all files Collapse all files

4
doc/doc2/Manual.html.html
View File

@ -3,7 +3,7 @@
<!-- HTML_ONLY -->
<HEAD>
<TITLE>LAMMPS Users Manual</TITLE>
<META NAME="docnumber" CONTENT="26 Oct 2015 version">
<META NAME="docnumber" CONTENT="31 Oct 2015 version">
<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
</HEAD>
@ -21,7 +21,7 @@
<P><CENTER><H3>LAMMPS Documentation
</H3></CENTER>
<CENTER><H4>26 Oct 2015 version
<CENTER><H4>31 Oct 2015 version
</H4></CENTER>
<H4>Version info:
</H4>

15
doc/doc2/Section_commands.html
View File

@ -460,13 +460,14 @@ KOKKOS, o = USER-OMP, t = OPT.
<TR ALIGN="center"><TD ><A HREF = "compute_cluster_atom.html">cluster/atom</A></TD><TD ><A HREF = "compute_cna_atom.html">cna/atom</A></TD><TD ><A HREF = "compute_com.html">com</A></TD><TD ><A HREF = "compute_com_chunk.html">com/chunk</A></TD><TD ><A HREF = "compute_contact_atom.html">contact/atom</A></TD><TD ><A HREF = "compute_coord_atom.html">coord/atom</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_damage_atom.html">damage/atom</A></TD><TD ><A HREF = "compute_dihedral_local.html">dihedral/local</A></TD><TD ><A HREF = "compute_dilatation_atom.html">dilatation/atom</A></TD><TD ><A HREF = "compute_displace_atom.html">displace/atom</A></TD><TD ><A HREF = "compute_erotate_asphere.html">erotate/asphere</A></TD><TD ><A HREF = "compute_erotate_rigid.html">erotate/rigid</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_erotate_sphere.html">erotate/sphere</A></TD><TD ><A HREF = "compute_erotate_sphere_atom.html">erotate/sphere/atom</A></TD><TD ><A HREF = "compute_event_displace.html">event/displace</A></TD><TD ><A HREF = "compute_group_group.html">group/group</A></TD><TD ><A HREF = "compute_gyration.html">gyration</A></TD><TD ><A HREF = "compute_gyration_chunk.html">gyration/chunk</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_heat_flux.html">heat/flux</A></TD><TD ><A HREF = "compute_improper_local.html">improper/local</A></TD><TD ><A HREF = "compute_inertia_chunk.html">inertia/chunk</A></TD><TD ><A HREF = "compute_ke.html">ke</A></TD><TD ><A HREF = "compute_ke_atom.html">ke/atom</A></TD><TD ><A HREF = "compute_ke_rigid.html">ke/rigid</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_msd.html">msd</A></TD><TD ><A HREF = "compute_msd_chunk.html">msd/chunk</A></TD><TD ><A HREF = "compute_msd_nongauss.html">msd/nongauss</A></TD><TD ><A HREF = "compute_omega_chunk.html">omega/chunk</A></TD><TD ><A HREF = "compute_pair.html">pair</A></TD><TD ><A HREF = "compute_pair_local.html">pair/local</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_pe.html">pe (c)</A></TD><TD ><A HREF = "compute_pe_atom.html">pe/atom</A></TD><TD ><A HREF = "compute_plasticity_atom.html">plasticity/atom</A></TD><TD ><A HREF = "compute_pressure.html">pressure (c)</A></TD><TD ><A HREF = "compute_property_atom.html">property/atom</A></TD><TD ><A HREF = "compute_property_local.html">property/local</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_property_chunk.html">property/chunk</A></TD><TD ><A HREF = "compute_rdf.html">rdf</A></TD><TD ><A HREF = "compute_reduce.html">reduce</A></TD><TD ><A HREF = "compute_reduce.html">reduce/region</A></TD><TD ><A HREF = "compute_slice.html">slice</A></TD><TD ><A HREF = "compute_sna_atom.html">sna/atom</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_sna_atom.html">snad/atom</A></TD><TD ><A HREF = "compute_sna_atom.html">snav/atom</A></TD><TD ><A HREF = "compute_stress_atom.html">stress/atom</A></TD><TD ><A HREF = "compute_temp.html">temp (ck)</A></TD><TD ><A HREF = "compute_temp_asphere.html">temp/asphere</A></TD><TD ><A HREF = "compute_temp_com.html">temp/com</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_temp_chunk.html">temp/chunk</A></TD><TD ><A HREF = "compute_temp_deform.html">temp/deform</A></TD><TD ><A HREF = "compute_temp_partial.html">temp/partial (c)</A></TD><TD ><A HREF = "compute_temp_profile.html">temp/profile</A></TD><TD ><A HREF = "compute_temp_ramp.html">temp/ramp</A></TD><TD ><A HREF = "compute_temp_region.html">temp/region</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_temp_sphere.html">temp/sphere</A></TD><TD ><A HREF = "compute_ti.html">ti</A></TD><TD ><A HREF = "compute_torque_chunk.html">torque/chunk</A></TD><TD ><A HREF = "compute_vacf.html">vacf</A></TD><TD ><A HREF = "compute_vcm_chunk.html">vcm/chunk</A></TD><TD ><A HREF = "compute_voronoi_atom.html">voronoi/atom</A>
<TR ALIGN="center"><TD ><A HREF = "compute_heat_flux.html">heat/flux</A></TD><TD ><A HREF = "compute_hexorder_atom.html">hexorder/atom</A></TD><TD ><A HREF = "compute_improper_local.html">improper/local</A></TD><TD ><A HREF = "compute_inertia_chunk.html">inertia/chunk</A></TD><TD ><A HREF = "compute_ke.html">ke</A></TD><TD ><A HREF = "compute_ke_atom.html">ke/atom</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_ke_rigid.html">ke/rigid</A></TD><TD ><A HREF = "compute_msd.html">msd</A></TD><TD ><A HREF = "compute_msd_chunk.html">msd/chunk</A></TD><TD ><A HREF = "compute_msd_nongauss.html">msd/nongauss</A></TD><TD ><A HREF = "compute_omega_chunk.html">omega/chunk</A></TD><TD ><A HREF = "compute_pair.html">pair</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_pair_local.html">pair/local</A></TD><TD ><A HREF = "compute_pe.html">pe (c)</A></TD><TD ><A HREF = "compute_pe_atom.html">pe/atom</A></TD><TD ><A HREF = "compute_plasticity_atom.html">plasticity/atom</A></TD><TD ><A HREF = "compute_pressure.html">pressure (c)</A></TD><TD ><A HREF = "compute_property_atom.html">property/atom</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_property_local.html">property/local</A></TD><TD ><A HREF = "compute_property_chunk.html">property/chunk</A></TD><TD ><A HREF = "compute_rdf.html">rdf</A></TD><TD ><A HREF = "compute_reduce.html">reduce</A></TD><TD ><A HREF = "compute_reduce.html">reduce/region</A></TD><TD ><A HREF = "compute_slice.html">slice</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_sna_atom.html">sna/atom</A></TD><TD ><A HREF = "compute_sna_atom.html">snad/atom</A></TD><TD ><A HREF = "compute_sna_atom.html">snav/atom</A></TD><TD ><A HREF = "compute_stress_atom.html">stress/atom</A></TD><TD ><A HREF = "compute_temp.html">temp (ck)</A></TD><TD ><A HREF = "compute_temp_asphere.html">temp/asphere</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_temp_com.html">temp/com</A></TD><TD ><A HREF = "compute_temp_chunk.html">temp/chunk</A></TD><TD ><A HREF = "compute_temp_deform.html">temp/deform</A></TD><TD ><A HREF = "compute_temp_partial.html">temp/partial (c)</A></TD><TD ><A HREF = "compute_temp_profile.html">temp/profile</A></TD><TD ><A HREF = "compute_temp_ramp.html">temp/ramp</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_temp_region.html">temp/region</A></TD><TD ><A HREF = "compute_temp_sphere.html">temp/sphere</A></TD><TD ><A HREF = "compute_ti.html">ti</A></TD><TD ><A HREF = "compute_torque_chunk.html">torque/chunk</A></TD><TD ><A HREF = "compute_vacf.html">vacf</A></TD><TD ><A HREF = "compute_vcm_chunk.html">vcm/chunk</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_voronoi_atom.html">voronoi/atom</A>
</TD></TR></TABLE></DIV>
<P>These are additional compute styles in USER packages, which can be

1
doc/doc2/compute.html
View File

@ -202,6 +202,7 @@ page</A>.
<LI><A HREF = "compute_gyration.html">gyration</A> - radius of gyration of group of atoms
<LI><A HREF = "compute_gyration_chunk.html">gyration/chunk</A> - radius of gyration for each chunk
<LI><A HREF = "compute_heat_flux.html">heat/flux</A> - heat flux through a group of atoms
<LI><A HREF = "compute_hexorder_atom.html">hexorder/atom</A> - bond orientational order parameter q6
<LI><A HREF = "compute_improper_local.html">improper/local</A> - angle of each improper
<LI><A HREF = "compute_inertia_chunk.html">inertia/chunk</A> - inertia tensor for each chunk
<LI><A HREF = "compute_ke.html">ke</A> - translational kinetic energy

115
doc/doc2/compute_hexorder_atom.html Normal file
View File

@ -0,0 +1,115 @@
<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>compute hexorder/atom command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID hexorder/atom keyword values ...
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>hexorder/atom = style name of this compute command
<LI>zero or more keyword/value pairs may be appended
<LI>keyword = <I>degree</I>
<PRE> <I>n</I> value = degree of order parameter
</PRE>
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute 1 all hexorder/atom
compute 1 all hexorder/atom n 4
</PRE>
<P><B>Description:</B>
</P>
<P>Define a computation that calculates <I>qn</I> the bond-orientational
order parameter for each atom in a group. The hexatic (<I>n</I> = 6) order
parameter was introduced by <A HREF = "#Nelson">Nelson and Halperin</A> as a way to detect
hexagonal symmetry in two-dimensional systems. For each atom, <I>qn</I>
is a complex number (stored as two real numbers) defined as follows:
</P>
<CENTER><IMG SRC = "Eqs/hexorder.jpg">
</CENTER>
<P>where the sum is over the <I>n</I> nearest neighbors
of the central atom. The angle theta
is formed by the bond vector rij and the <I>x</I> axis. theta is calculated
only using the <I>x</I> and <I>y</I> components, whereas the distance from the
central atom is calculated using all three
<I>x</I>, <I>y</I>, and <I>z</I> components of the bond vector.
Neighbor atoms not in the group
are included in the order parameter of atoms in the group.
</P>
<P>The optional keyword <I>n</I> sets the degree of the order parameter.
The default value is 6. For a perfect hexagonal lattice,
<I>q</I>6 = exp(6 i phi) for all atoms, where the constant 0 < phi < pi/3
depends only on the orientation of the lattice relative to the x axis.
In an isotropic liquid, local neighborhoods may still exhibit
weak hexagonal symmetry, but because the orientational correlation
decays quickly with distance, the value of phi will be different for
different atoms, and |<<I>q</I>6>| << 1.
</P>
<P>The value of <I>qn</I> will be zero for atoms not in the
specified compute group. If the atom has less than <I>n</I> neighbors (within
the potential cutoff), then <I>qn</I> is set to zero.
</P>
<P>The neighbor list needed to compute this quantity is constructed each
time the calculation is performed (i.e. each time a snapshot of atoms
is dumped). Thus it can be inefficient to compute/dump this quantity
too frequently.
</P>
<P>IMPORTANT NOTE: If you have a bonded system, then the settings of
<A HREF = "special_bonds.html">special_bonds</A> command can remove pairwise
interactions between atoms in the same bond, angle, or dihedral. This
is the default setting for the <A HREF = "special_bonds.html">special_bonds</A>
command, and means those pairwise interactions do not appear in the
neighbor list. Because this fix uses the neighbor list, it also means
those pairs will not be included in the order parameter. One way
to get around this, is to write a dump file, and use the
<A HREF = "rerun.html">rerun</A> command to compute the order parameter for snapshots
in the dump file. The rerun script can use a
<A HREF = "special_bonds.html">special_bonds</A> command that includes all pairs in
the neighbor list.
</P>
<P><B>Output info:</B>
</P>
<P>This compute calculates a per-atom array with 2 columns, giving the
real and imaginary parts of <I>qn</I>, respectively.
</P>
<P>These values can be accessed by any command that uses
per-atom values from a compute as input. See <A HREF = "Section_howto.html#howto_15">Section_howto
15</A> for an overview of LAMMPS output
options.
</P>
<P>The per-atom array contain pairs of numbers representing the
real and imaginary parts of <I>qn</I>, a complex number subject to the
constraint |<I>qn</I>| <= 1.
</P>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "compute_coord_atom.html">compute coord/atom</A>, <A HREF = "compute_centro_atom.html">compute centro/atom</A>
</P>
<P><B>Default:</B>
</P>
<P>The option default is <I>n</I> = 6.
</P>
<HR>
<A NAME = "Nelson"></A>
<P><B>(Nelson)</B> Nelson, Halperin, Phys Rev B, 19, 2457 (1979).
</P>
</HTML>

7
doc/doc2/compute_rdf.html
View File

@ -139,13 +139,16 @@ also numbers >= 0.0.
since processors (in parallel) don't know about atom coordinates for
atoms further away than that distance. If you want an RDF for larger
distances, you can use the <A HREF = "rerun.html">rerun</A> command to post-process
a dump file. The definition of g(r) used by LAMMPS is only appropriate
a dump file and set the cutoff for the potential to be longer in the
rerun script. Note that in the rerun context, the force cutoff is
arbitrary, since you aren't running dynamics and thus are not changing
your model. The definition of g(r) used by LAMMPS is only appropriate
for characterizing atoms that are uniformly distributed throughout the
simulation cell. In such cases, the coordination number is still
correct and meaningful. As an example, if a large simulation cell
contains only one atom of type <I>itypeN</I> and one of <I>jtypeN</I>, then g(r)
will register an arbitrarily large spike at whatever distance they
happen to be at, and zero everywhere else. coord(r) will show a step
happen to be at, and zero everywhere else. Coord(r) will show a step
change from zero to one at the location of the spike in g(r).
</P>
<P><B>Related commands:</B>