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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5063 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2010-10-18 17:42:05 +00:00
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16
doc/Section_commands.html
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@ -352,14 +352,14 @@ of each style or click on the style itself for a full description:
each style or click on the style itself for a full description:
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "compute_angle_local.html">angle/local</A></TD><TD ><A HREF = "compute_bond_local.html">bond/local</A></TD><TD ><A HREF = "compute_centro_atom.html">centro/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_molecule.html">com/molecule</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_coord_atom.html">coord/atom</A></TD><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_displace_atom.html">displace/atom</A></TD><TD ><A HREF = "compute_erotate_asphere.html">erotate/asphere</A></TD><TD ><A HREF = "compute_erotate_sphere.html">erotate/sphere</A></TD></TR>
<TR ALIGN="center"><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_molecule.html">gyration/molecule</A></TD><TD ><A HREF = "compute_heat_flux.html">heat/flux</A></TD><TD ><A HREF = "compute_improper_local.html">improper/local</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_ke.html">ke</A></TD><TD ><A HREF = "compute_ke_atom.html">ke/atom</A></TD><TD ><A HREF = "compute_msd.html">msd</A></TD><TD ><A HREF = "compute_msd_molecule.html">msd/molecule</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</A></TD><TD ><A HREF = "compute_pe_atom.html">pe/atom</A></TD><TD ><A HREF = "compute_pressure.html">pressure</A></TD><TD ><A HREF = "compute_property_atom.html">property/atom</A></TD><TD ><A HREF = "compute_property_local.html">property/local</A></TD><TD ><A HREF = "compute_property_molecule.html">property/molecule</A></TD></TR>
<TR ALIGN="center"><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_stress_atom.html">stress/atom</A></TD><TD ><A HREF = "compute_temp.html">temp</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_deform.html">temp/deform</A></TD><TD ><A HREF = "compute_temp_partial.html">temp/partial</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>
<TR ALIGN="center"><TD ><A HREF = "compute_angle_local.html">angle/local</A></TD><TD ><A HREF = "compute_atom_molecule.html">atom/molecule</A></TD><TD ><A HREF = "compute_bond_local.html">bond/local</A></TD><TD ><A HREF = "compute_centro_atom.html">centro/atom</A></TD><TD ><A HREF = "compute_cna_atom.html">cna/atom</A></TD><TD ><A HREF = "compute_com.html">com</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_com_molecule.html">com/molecule</A></TD><TD ><A HREF = "compute_coord_atom.html">coord/atom</A></TD><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_displace_atom.html">displace/atom</A></TD><TD ><A HREF = "compute_erotate_asphere.html">erotate/asphere</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_erotate_sphere.html">erotate/sphere</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_molecule.html">gyration/molecule</A></TD><TD ><A HREF = "compute_heat_flux.html">heat/flux</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_improper_local.html">improper/local</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_msd.html">msd</A></TD><TD ><A HREF = "compute_msd_molecule.html">msd/molecule</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</A></TD><TD ><A HREF = "compute_pe_atom.html">pe/atom</A></TD><TD ><A HREF = "compute_pressure.html">pressure</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_molecule.html">property/molecule</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_stress_atom.html">stress/atom</A></TD><TD ><A HREF = "compute_temp.html">temp</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_temp_asphere.html">temp/asphere</A></TD><TD ><A HREF = "compute_temp_com.html">temp/com</A></TD><TD ><A HREF = "compute_temp_deform.html">temp/deform</A></TD><TD ><A HREF = "compute_temp_partial.html">temp/partial</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></TR></TABLE></DIV>
<P>These are compute styles contributed by users, which can be used if

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doc/Section_commands.txt
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@ -486,6 +486,7 @@ See the "compute"_compute.html command for one-line descriptions of
each style or click on the style itself for a full description:
"angle/local"_compute_angle_local.html,
"atom/molecule"_compute_atom_molecule.html,
"bond/local"_compute_bond_local.html,
"centro/atom"_compute_centro_atom.html,
"cna/atom"_compute_cna_atom.html,

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doc/compute.html
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@ -168,6 +168,7 @@ and what it does. Here is an alphabetic list of compute styles
available in LAMMPS:
</P>
<UL><LI><A HREF = "compute_bond_local.html">angle/local</A> - theta and energy of each angle
<LI><A HREF = "compute_atom_molecule.html">atom/molecule</A> - sum per-atom properties for each molecule
<LI><A HREF = "compute_bond_local.html">bond/local</A> - distance and energy of each bond
<LI><A HREF = "compute_centro_atom.html">centro/atom</A> - centro-symmetry parameter for each atom
<LI><A HREF = "compute_cna_atom.html">cna/atom</A> - common neighbor analysis (CNA) for each atom

1
doc/compute.txt
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@ -163,6 +163,7 @@ and what it does. Here is an alphabetic list of compute styles
available in LAMMPS:
"angle/local"_compute_bond_local.html - theta and energy of each angle
"atom/molecule"_compute_atom_molecule.html - sum per-atom properties for each molecule
"bond/local"_compute_bond_local.html - distance and energy of each bond
"centro/atom"_compute_centro_atom.html - centro-symmetry parameter for each atom
"cna/atom"_compute_cna_atom.html - common neighbor analysis (CNA) for each atom

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@ -0,0 +1,69 @@
<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 pair command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID pair pstyle
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>pair = style name of this compute command
<LI>pstyle = style name of a pair style that calculates additional values
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute 1 all pair gauss
compute 1 all pair reax
</PRE>
<P><B>Description:</B>
</P>
<P>Define a computation that extracts additional values calculated by a
pair style, sums them across processors, and makes them accessible for
output or further processing by other commands. The group specified
for this command is ignored.
</P>
<P>The specified <I>pstyle</I> must be a pair style that produces additional
values. If a <A HREF = "pair_hybrid.html">hybrid pair style</A> is used, then
<I>pstyle</I> should be the name of a sub-style.
</P>
<P>All pair styles tally a potential energy, which is accessed by the
<A HREF = "compute_pe.html">compute pe</A> and <A HREF = "compute_pe_atom.html">compute
pe/atom</A> commands. Some pair styles tally one or
more additional values, such as a breakdown of the total pair
potential energy into sub-categories. See the doc page for
<A HREF = "pair_style.html">individual pair styles</A> for info on these values.
</P>
<P>The compute pair command lets you access this data as a global vector
of values and then use other <A HREF = "Section_howto.html#4_15">output options</A>
that work with <A HREF = "compute.html">compute commands</A> to see or use the
values.
</P>
<P><B>Output info:</B>
</P>
<P>This compute calculates a global vector of length >= 1, as determined
by the pair style. These values can be used by any command that uses
global vector values from a compute as input. See <A HREF = "Section_howto.html#4_15">this
section</A> for an overview of LAMMPS output
options.
</P>
<P>The vector values calculated by this compute are "extensive". They
are in whatever units the pair style produces.
</P>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "compute_pe.html">compute pe</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>

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doc/compute_pair.txt Normal file
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@ -0,0 +1,64 @@
"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
compute pair command :h3
[Syntax:]
compute ID group-ID pair pstyle :pre
ID, group-ID are documented in "compute"_compute.html command
pair = style name of this compute command
pstyle = style name of a pair style that calculates additional values :ul
[Examples:]
compute 1 all pair gauss
compute 1 all pair reax :pre
[Description:]
Define a computation that extracts additional values calculated by a
pair style, sums them across processors, and makes them accessible for
output or further processing by other commands. The group specified
for this command is ignored.
The specified {pstyle} must be a pair style that produces additional
values. If a "hybrid pair style"_pair_hybrid.html is used, then
{pstyle} should be the name of a sub-style.
All pair styles tally a potential energy, which is accessed by the
"compute pe"_compute_pe.html and "compute
pe/atom"_compute_pe_atom.html commands. Some pair styles tally one or
more additional values, such as a breakdown of the total pair
potential energy into sub-categories. See the doc page for
"individual pair styles"_pair_style.html for info on these values.
The compute pair command lets you access this data as a global vector
of values and then use other "output options"_Section_howto.html#4_15
that work with "compute commands"_compute.html to see or use the
values.
[Output info:]
This compute calculates a global vector of length >= 1, as determined
by the pair style. These values can be used by any command that uses
global vector values from a compute as input. See "this
section"_Section_howto.html#4_15 for an overview of LAMMPS output
options.
The vector values calculated by this compute are "extensive". They
are in whatever units the pair style produces.
[Restrictions:] none
[Related commands:]
"compute pe"_compute_pe.html
[Default:] none

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doc/compute_property_molecule.html
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@ -21,9 +21,9 @@
<LI>input = one or more attributes
<PRE> possible attributes = mol
</PRE>
<PRE> mol = molecule ID
<PRE> possible attributes = mol count
mol = molecule ID
count = # of atoms in molecule
</PRE>
</UL>
@ -48,6 +48,8 @@ per-molecule datums. Thus this attribute can be used to produce
molecule IDs as labels for those datums when they are output to a
file, e.g. by the <A HREF = "fix_ave_time.html">fix ave/time</A> command.
</P>
<P>The <I>count</I> attribute is the number of atoms in the molecule.
</P>
<P><B>Output info:</B>
</P>
<P>This compute calculates a global vector or global array depending on

7
doc/compute_property_molecule.txt
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@ -15,8 +15,9 @@ compute ID group-ID property/molecule input1 input2 ... :pre
ID, group-ID are documented in "compute"_compute.html command :ulb,l
property/molecule = style name of this compute command :l
input = one or more attributes :l
possible attributes = mol :pre
mol = molecule ID :pre
possible attributes = mol count
mol = molecule ID
count = # of atoms in molecule :pre
:ule
[Examples:]
@ -40,6 +41,8 @@ per-molecule datums. Thus this attribute can be used to produce
molecule IDs as labels for those datums when they are output to a
file, e.g. by the "fix ave/time"_fix_ave_time.html command.
The {count} attribute is the number of atoms in the molecule.
[Output info:]
This compute calculates a global vector or global array depending on