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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@3603 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2009-12-21 23:01:36 +00:00
parent 9c481bc49b
commit 13a3a1d174
6 changed files with 40 additions and 15 deletions
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8
doc/Section_commands.html
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@ -349,10 +349,10 @@ each style or click on the style itself for a full description:
<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_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><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_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><TD ><A HREF = "compute_event_displace.html">event/displace</A></TD></TR>
<TR ALIGN="center"><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><TD ><A HREF = "compute_ke.html">ke</A></TD></TR>
<TR ALIGN="center"><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_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></TR>
<TR ALIGN="center"><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><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></TR>
<TR ALIGN="center"><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><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></TR>
<TR ALIGN="center"><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><TD ><A HREF = "compute_temp_sphere.html">temp/sphere</A>
<TR ALIGN="center"><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_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></TR>
<TR ALIGN="center"><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><TD ><A HREF = "compute_rdf.html">rdf</A></TD><TD ><A HREF = "compute_reduce.html">reduce</A></TD></TR>
<TR ALIGN="center"><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><TD ><A HREF = "compute_temp_com.html">temp/com</A></TD><TD ><A HREF = "compute_temp_deform.html">temp/deform</A></TD></TR>
<TR ALIGN="center"><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><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

1
doc/Section_commands.txt
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@ -480,6 +480,7 @@ each style or click on the style itself for a full description:
"ke/atom"_compute_ke_atom.html,
"msd"_compute_msd.html,
"msd/molecule"_compute_msd_molecule.html,
"pair/local"_compute_pair_local.html,
"pe"_compute_pe.html,
"pe/atom"_compute_pe_atom.html,
"pressure"_compute_pressure.html,

1
doc/compute.html
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@ -188,6 +188,7 @@ available in LAMMPS:
<LI><A HREF = "compute_ke_atom.html">ke/atom</A> - kinetic energy for each atom
<LI><A HREF = "compute_msd.html">msd</A> - mean-squared displacement of group of atoms
<LI><A HREF = "compute_msd_molecule.html">msd/molecule</A> - mean-squared displacement for each molecule
<LI><A HREF = "compute_pair_local.html">pair/local</A> - distance/energy/force of each pairwise interaction
<LI><A HREF = "compute_pe.html">pe</A> - potential energy
<LI><A HREF = "compute_pe_atom.html">pe/atom</A> - potential energy for each atom
<LI><A HREF = "compute_pressure.html">pressure</A> - total pressure and pressure tensor

1
doc/compute.txt
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@ -183,6 +183,7 @@ available in LAMMPS:
"ke/atom"_compute_ke_atom.html - kinetic energy for each atom
"msd"_compute_msd.html - mean-squared displacement of group of atoms
"msd/molecule"_compute_msd_molecule.html - mean-squared displacement for each molecule
"pair/local"_compute_pair_local.html - distance/energy/force of each pairwise interaction
"pe"_compute_pe.html - potential energy
"pe/atom"_compute_pe_atom.html - potential energy for each atom
"pressure"_compute_pressure.html - total pressure and pressure tensor

23
doc/compute_property_local.html
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@ -21,12 +21,14 @@
<LI>input = one or more attributes
<PRE> possible attributes = batom1 batom2 btype
<PRE> possible attributes = patom1 patom2
batom1 batom2 btype
aatom1 aatom2 aatom3 atype
datom1 datom2 datom3 dtype
iatom1 iatom2 iatom3 itype
</PRE>
<PRE> batom1, batom2 = IDs of 2 atoms in each bond
<PRE> patom1, patom2 = IDs of 2 atoms in each pair
batom1, batom2 = IDs of 2 atoms in each bond
btype = bond type of each bond
aatom1, aatom2, aatom3 = IDs of 3 atoms in each angle
atype = angle type of each angle
@ -49,6 +51,7 @@ data so it can be accessed by other <A HREF = "Section_howto.html#4_15">output
commands</A>. If the input attributes refer to
bond information, then the number of datums generated, aggregated
across all processors, equals the number of bonds in the system.
Ditto for pairs, angles, etc.
</P>
<P>If multiple input attributes are specified then they must all generate
the same amount of information, so that the resulting local array has
@ -62,6 +65,14 @@ processor and extracting bond, angle, etc info. For bonds, info about
an individual bond will only be included if both atoms in the bond are
in the specified compute group. Likewise for angles, dihedrals, etc.
</P>
<P>In the case of pairs, the local data is generated by looping over the
pairwise neighbor list. Info about an individual pairwise interaction
will only be included if both atoms in the pair are in the specified
compute group, and if the current pairwise distance is less than the
force cutoff distance for that interaction, as defined by the
<A HREF = "pair_style.html">pair_style</A> and <A HREF = "pair_coeff.html">pair_coeff</A>
commands.
</P>
<P>Note that as atoms migrate from processor to processor, there will be
no consistent ordering of the entries within the local vector or array
from one timestep to the next. The only consistency that is
@ -72,10 +83,10 @@ bond/local</A> command can be combined with bond
atom indices from this command and output by the <A HREF = "dump.html">dump
local</A> command in a consistent way.
</P>
<P>The <I>batom1</I> and <I>batom2</I> attributes refer the atom IDs of the 2 atoms
in each <A HREF = "bond_style.html">bond</A>. The <I>btype</I> attribute refers to the
type of the bond, from 1 to Nbtypes = # of bond types. The number of
bond types is defined in the data file read by the
<P>The <I>batom1</I> and <I>batom2</I> attributes refer to the atom IDs of the 2
atoms in each <A HREF = "bond_style.html">bond</A>. The <I>btype</I> attribute refers to
the type of the bond, from 1 to Nbtypes = # of bond types. The number
of bond types is defined in the data file read by the
<A HREF = "read_data.html">read_data</A> command. The attributes that start with
"a", "d", "i", refer to similar values for <A HREF = "angle_style.html">angles</A>,
<A HREF = "dihedral_style.html">dihedrals</A>, and <A HREF = "improper_style.html">impropers</A>.

21
doc/compute_property_local.txt
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@ -15,11 +15,13 @@ compute ID group-ID property/local input1 input2 ... :pre
ID, group-ID are documented in "compute"_compute.html command :ulb,l
property/local = style name of this compute command :l
input = one or more attributes :l
possible attributes = batom1 batom2 btype
possible attributes = patom1 patom2
batom1 batom2 btype
aatom1 aatom2 aatom3 atype
datom1 datom2 datom3 dtype
iatom1 iatom2 iatom3 itype :pre
patom1, patom2 = IDs of 2 atoms in each pair
batom1, batom2 = IDs of 2 atoms in each bond
btype = bond type of each bond
aatom1, aatom2, aatom3 = IDs of 3 atoms in each angle
@ -42,6 +44,7 @@ data so it can be accessed by other "output
commands"_Section_howto.html#4_15. If the input attributes refer to
bond information, then the number of datums generated, aggregated
across all processors, equals the number of bonds in the system.
Ditto for pairs, angles, etc.
If multiple input attributes are specified then they must all generate
the same amount of information, so that the resulting local array has
@ -55,6 +58,14 @@ processor and extracting bond, angle, etc info. For bonds, info about
an individual bond will only be included if both atoms in the bond are
in the specified compute group. Likewise for angles, dihedrals, etc.
In the case of pairs, the local data is generated by looping over the
pairwise neighbor list. Info about an individual pairwise interaction
will only be included if both atoms in the pair are in the specified
compute group, and if the current pairwise distance is less than the
force cutoff distance for that interaction, as defined by the
"pair_style"_pair_style.html and "pair_coeff"_pair_coeff.html
commands.
Note that as atoms migrate from processor to processor, there will be
no consistent ordering of the entries within the local vector or array
from one timestep to the next. The only consistency that is
@ -65,10 +76,10 @@ bond/local"_compute_bond_local.html command can be combined with bond
atom indices from this command and output by the "dump
local"_dump.html command in a consistent way.
The {batom1} and {batom2} attributes refer the atom IDs of the 2 atoms
in each "bond"_bond_style.html. The {btype} attribute refers to the
type of the bond, from 1 to Nbtypes = # of bond types. The number of
bond types is defined in the data file read by the
The {batom1} and {batom2} attributes refer to the atom IDs of the 2
atoms in each "bond"_bond_style.html. The {btype} attribute refers to
the type of the bond, from 1 to Nbtypes = # of bond types. The number
of bond types is defined in the data file read by the
"read_data"_read_data.html command. The attributes that start with
"a", "d", "i", refer to similar values for "angles"_angle_style.html,
"dihedrals"_dihedral_style.html, and "impropers"_improper_style.html.