Commit 5d1351b6 authored by sjplimp's avatar sjplimp
Browse files 

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@3546 f3b2605a-c512-4ea7-a41b-209d697bcdaa
parent 5a1047d3

doc/Section_commands.html

+3 −2
Original line number Diff line number Diff line
@@ -349,8 +349,9 @@ each style or click on the style itself for a full description: 
<TR ALIGN="center"><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_coord_atom.html">coord/atom</A></TD><TD ><A HREF = "compute_damage_atom.html">damage/atom</A></TD><TD ><A HREF = "compute_displace_atom.html">displace/atom</A></TD></TR>

<TR ALIGN="center"><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><TD ><A HREF = "compute_group_group.html">group/group</A></TD><TD ><A HREF = "compute_gyration.html">gyration</A></TD><TD ><A HREF = "compute_heat_flux.html">heat/flux</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_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_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><TD ><A HREF = "compute_temp_com.html">temp/com</A></TD></TR>

<TR ALIGN="center"><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><TD ><A HREF = "compute_temp_sphere.html">temp/sphere</A> 

<TR ALIGN="center"><TD ><A HREF = "compute_property_atom.html">property/atom</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> 

</TD></TR></TABLE></DIV>



<P>These are compute styles contributed by users, which can be used if

doc/Section_commands.txt

+1 −0
Original line number Diff line number Diff line
@@ -481,6 +481,7 @@ each style or click on the style itself for a full description: 
"pe"_compute_pe.html,

"pe/atom"_compute_pe_atom.html,

"pressure"_compute_pressure.html,

"property/atom"_compute_property_atom.html,

"reduce"_compute_reduce.html,

"reduce/region"_compute_reduce.html,

"stress/atom"_compute_stress_atom.html,

doc/Section_howto.html

+14 −6
Original line number Diff line number Diff line
@@ -1055,12 +1055,12 @@ command. 
<A HREF = "dump_modify.html">dump_modify</A> commands.  There are several

pre-defined formats (dump atom, dump xtc, etc).  There is also a <A HREF = "dump.html">dump

custom</A> format where the user specifies what values are

output with each atom.  Pre-defined keywords can be specified (id, x,

fx, etc).  Three additional kinds of keywords can also be specified

(c_ID, f_ID, v_name), where a <A HREF = "compute.html">compute</A> or <A HREF = "fix.html">fix</A>

or <A HREF = "variable.html">variable</A> provides the values to be output.  In each

case, the compute, fix, or variable must generate per-atom values for

input to the <A HREF = "dump.html">dump custom</A> command.

output with each atom.  Pre-defined atom attributes can be specified

(id, x, fx, etc).  Three additional kinds of keywords can also be

specified (c_ID, f_ID, v_name), where a <A HREF = "compute.html">compute</A> or

<A HREF = "fix.html">fix</A> or <A HREF = "variable.html">variable</A> provides the values to be

output.  In each case, the compute, fix, or variable must generate

per-atom values for input to the <A HREF = "dump.html">dump custom</A> command.

</P>

<H5><A NAME = "fixoutput"></A>Fixes that write output files 

</H5>
@@ -1117,6 +1117,13 @@ quantities as inputs and "reduce" them (sum, min, max, ave) to scalar 
quantities.  These are produced as output values which can be used as

input to other output commands.

</P>

<P>The <A HREF = "compute_property_atom.html">compute property/atom</A> command takes a

list of one or more pre-defined atom attributes (id, x, fx, etc) and

stores the values in a per-atom vector or array.  These are produced

as output values which can be used as input to other output commands.

The list of atom attributes is the same as for the <A HREF = "dump.html">dump

custom</A> command.

</P>

<H5><A NAME = "fixoutput"></A>Fixes that process output quantities 

</H5>

<P>The <A HREF = "fix_ave_atom.html">fix ave/atom</A> command performs time-averaging
@@ -1180,6 +1187,7 @@ vector input could be a column of an array. 
<TR><TD ><A HREF = "fix.html">fixes</A></TD><TD > N/A</TD><TD > global/per-atom/local scalar/vector/array</TD><TD ></TD></TR>

<TR><TD ><A HREF = "variable.html">variables</A></TD><TD > global scalars, per-atom vectors</TD><TD > global scalar, per-atom vector</TD><TD ></TD></TR>

<TR><TD ><A HREF = "compute_reduce.html">compute reduce</A></TD><TD > global/per-atom/local vectors</TD><TD > global scalar/vector</TD><TD ></TD></TR>

<TR><TD ><A HREF = "compute_property_atom.html">compute property/atom</A></TD><TD > per-atom vectors</TD><TD > per-atom vector/array</TD><TD ></TD></TR>

<TR><TD ><A HREF = "fix_ave_atom.html">fix ave/atom</A></TD><TD > per-atom vectors</TD><TD > per-atom vector/array</TD><TD ></TD></TR>

<TR><TD ><A HREF = "fix_ave_time.html">fix ave/time</A></TD><TD > global scalars/vectors</TD><TD > global scalar/vector/array, file</TD><TD ></TD></TR>

<TR><TD ><A HREF = "fix_ave_spatial.html">fix ave/spatial</A></TD><TD > per-atom vectors</TD><TD > global array, file</TD><TD ></TD></TR>

doc/Section_howto.txt

+14 −6
Original line number Diff line number Diff line
@@ -1046,12 +1046,12 @@ Dump file output is specified by the "dump"_dump.html and 
"dump_modify"_dump_modify.html commands.  There are several

pre-defined formats (dump atom, dump xtc, etc).  There is also a "dump

custom"_dump.html format where the user specifies what values are

output with each atom.  Pre-defined keywords can be specified (id, x,

fx, etc).  Three additional kinds of keywords can also be specified

(c_ID, f_ID, v_name), where a "compute"_compute.html or "fix"_fix.html

or "variable"_variable.html provides the values to be output.  In each

case, the compute, fix, or variable must generate per-atom values for

input to the "dump custom"_dump.html command.

output with each atom.  Pre-defined atom attributes can be specified

(id, x, fx, etc).  Three additional kinds of keywords can also be

specified (c_ID, f_ID, v_name), where a "compute"_compute.html or

"fix"_fix.html or "variable"_variable.html provides the values to be

output.  In each case, the compute, fix, or variable must generate

per-atom values for input to the "dump custom"_dump.html command.



Fixes that write output files :h5,link(fixoutput)
@@ -1108,6 +1108,13 @@ quantities as inputs and "reduce" them (sum, min, max, ave) to scalar 
quantities.  These are produced as output values which can be used as

input to other output commands.



The "compute property/atom"_compute_property_atom.html command takes a

list of one or more pre-defined atom attributes (id, x, fx, etc) and

stores the values in a per-atom vector or array.  These are produced

as output values which can be used as input to other output commands.

The list of atom attributes is the same as for the "dump

custom"_dump.html command.



Fixes that process output quantities :h5,link(fixoutput)



The "fix ave/atom"_fix_ave_atom.html command performs time-averaging
@@ -1170,6 +1177,7 @@ Command: Input: Output: 
"fixes"_fix.html: N/A: global/per-atom/local scalar/vector/array:

"variables"_variable.html: global scalars, per-atom vectors: global scalar, per-atom vector:

"compute reduce"_compute_reduce.html: global/per-atom/local vectors: global scalar/vector:

"compute property/atom"_compute_property_atom.html: per-atom vectors: per-atom vector/array:

"fix ave/atom"_fix_ave_atom.html: per-atom vectors: per-atom vector/array:

"fix ave/time"_fix_ave_time.html: global scalars/vectors: global scalar/vector/array, file:

"fix ave/spatial"_fix_ave_spatial.html: per-atom vectors: global array, file:

doc/compute_property_atom.html

0 → 100644
+96 −0
Original line number Diff line number Diff line 
<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 property/atom command 

</H3>

<P><B>Syntax:</B>

</P>

<PRE>compute ID group-ID property/atom input1 input2 ... 

</PRE>

<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command 



<LI>property/atom = style name of this compute command 



<LI>input = one or more atom attributes 



<PRE>  possible attributes = id, mol, type, mass,

 	                x, y, z, xs, ys, zs, xu, yu, zu, ix, iy, iz,

		        vx, vy, vz, fx, fy, fz,

                        q, mux, muy, muz,

                        radius, omegax, omegay, omegaz,

                        angmomx, angmomy, angmomz,

		        quatw, quati, quatj, quatk, tqx, tqy, tqz

      id = atom ID

      mol = molecule ID

      type = atom type

      mass = atom mass

      x,y,z = unscaled atom coordinates

      xs,ys,zs = scaled atom coordinates

      xu,yu,zu = unwrapped atom coordinates

      ix,iy,iz = box image that the atom is in

      vx,vy,vz = atom velocities

      fx,fy,fz = forces on atoms

      q = atom charge

      mux,muy,muz = orientation of dipolar atom

      radius = radius of extended spherical particle

      omegax,omegay,omegaz = angular velocity of extended particle

      angmomx,angmomy,angmomz = angular momentum of extended particle

      quatw,quati,quatj,quatk = quaternion components for aspherical particles

      tqx,tqy,tqz = torque on extended particles 

</PRE>



</UL>

<P><B>Examples:</B>

</P>

<PRE>compute 1 all property/atom xs vx fx mux 

compute 2 all property/atom type

compute 1 all property/atom ix iy iz 

</PRE>

<P><B>Description:</B>

</P>

<P>Define a computation that simply stores atom attributes for each atom

in the group.  This is useful so that the values can be used by other

<A HREF = "Section_howto.html#4_15">output commands</A> that take computes as

inputs.  See for example, the <A HREF = "compute_reduce.html">compute reduce</A>,

<A HREF = "fix_ave_atom.html">fix ave/atom</A>, <A HREF = "fix_ave_histo.html">fix ave/histo</A>,

<A HREF = "fix_ave_spatial.html">fix ave/spatial</A>, and <A HREF = "variable.html">atom-style

variable</A> commands.

</P>

<P>The list of possible attributes is the same as that used by the <A HREF = "dump.html">dump

custom</A> command, which describes their meaning.  Basically,

this list gives your input script access to any per-atom quantity

stored by LAMMPS.

</P>

<P>The values are stored in a per-atom vector or array as

discussed below.  Zeroes are stored for atoms not in the specified

group.

</P>

<P><B>Output info:</B>

</P>

<P>This compute calculates a per-atom vector or per-atom array depending

on the number of input values.  If a single input is specified, a

per-atom vector is produced.  If two or more inputs are specified, a

per-atom array is produced where the number of columns = the number of

inputs.  The vector or array can be accessed by any command that uses

per-atom 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><B>Restrictions:</B> none

</P>

<P><B>Related commands:</B>

</P>

<P><A HREF = "dump.html">dump custom</A>, <A HREF = "compute_reduce.html">compute reduce</A>, <A HREF = "fix_ave_atom.html">fix

ave/atom</A>, <A HREF = "fix_ave_spatial.html">fix ave/spatial</A>

</P>

<P><B>Default:</B> none

</P>

</HTML>

CRA Git | Maintained and supported by SUSTech CRA and CCSE