git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5065 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
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doc/compute_atom_molecute.html
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doc/compute_atom_molecute.html
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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>compute atom/molecule command
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</H3>
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<P><B>Syntax:</B>
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</P>
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<PRE>compute ID group-ID atom/molecule input1 input2 ...
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</PRE>
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<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
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<LI>atom/molecule = style name of this compute command
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<LI>one or more inputs can be listed
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<LI>input = c_ID, c_ID[N], f_ID, f_ID[N], v_name
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<PRE> c_ID = per-atom vector calculated by a compute with ID
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c_ID[I] = Ith column of per-atom array calculated by a compute with ID
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f_ID = per-atom vector calculated by a fix with ID
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f_ID[I] = Ith column of per-atom array calculated by a fix with ID
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v_name = per-atom vector calculated by an atom-style variable with name
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</PRE>
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</UL>
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<P><B>Examples:</B>
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</P>
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<P>compute 1 all atom/molecule sum c_force
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compute 1 all reduce/region subbox sum c_force
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</P>
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<P><B>Description:</B>
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</P>
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<P>Define a calculation that "reduces" one or more vector inputs into
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scalar values, one per listed input. The inputs can be per-atom or
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local quantities; they cannot be global quantities. Atom attributes
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are per-atom quantities, <A HREF = "compute.html">computes</A> and <A HREF = "fix.html">fixes</A>
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may generate any of the three kinds of quantities, and <A HREF = "variable.html">atom-style
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variables</A> generate per-atom quantities. See the
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<A HREF = "variable">variable</A> command and its special functions which can
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perform the same operations as the compute reduce command on global
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vectors.
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</P>
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<P>The reduction operation is specified by the <I>mode</I> setting. The <I>sum</I>
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option adds the values in the vector into a global total. The <I>min</I>
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or <I>max</I> options find the minimum or maximum value across all vector
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values. The <I>ave</I> setting adds the vector values into a global total,
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then divides by the number of values in the vector.
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</P>
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<P>Each listed input is operated on independently. For per-atom inputs,
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the group specified with this command means only atoms within the
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group contribute to the result. For per-atom inputs, if the compute
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reduce/region command is used, the atoms must also currently be within
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the region. Note that an input that produces per-atom quantities may
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define its own group which affects the quantities it returns. For
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example, if a compute is used as an input which generates a per-atom
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vector, it will generate values of 0.0 for atoms that are not in the
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group specified for that compute.
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</P>
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<P>Each listed input can be an atom attribute (position, velocity, force
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component) or can be the result of a <A HREF = "compute.html">compute</A> or
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<A HREF = "fix.html">fix</A> or the evaluation of an atom-style
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<A HREF = "variable.html">variable</A>.
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</P>
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<P>The atom attribute values (x,y,z,vx,vy,vz,fx,fy,fz) are
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self-explanatory. Note that other atom attributes can be used as
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inputs to this fix by using the <A HREF = "compute_property_atom.html">compute
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property/atom</A> command and then specifying
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an input value from that compute.
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</P>
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<P>If a value begins with "c_", a compute ID must follow which has been
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previously defined in the input script. Computes can generate
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per-atom or local quantities. See the individual
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<A HREF = "compute.html">compute</A> doc page for details. If no bracketed integer
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is appended, the vector calculated by the compute is used. If a
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bracketed interger is appended, the Ith column of the array calculated
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by the compute is used. Users can also write code for their own
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compute styles and <A HREF = "Section_modify.html">add them to LAMMPS</A>.
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</P>
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<P>If a value begins with "f_", a fix ID must follow which has been
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previously defined in the input script. Fixes can generate per-atom
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or local quantities. See the individual <A HREF = "fix.html">fix</A> doc page for
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details. Note that some fixes only produce their values on certain
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timesteps, which must be compatible with when compute reduce
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references the values, else an error results. If no bracketed integer
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is appended, the vector calculated by the fix is used. If a bracketed
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integer is appended, the Ith column of the array calculated by the fix
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is used. Users can also write code for their own fix style and <A HREF = "Section_modify.html">add
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them to LAMMPS</A>.
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</P>
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<P>If a value begins with "v_", a variable name must follow which has
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been previously defined in the input script. It must be an
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<A HREF = "variable.html">atom-style variable</A>. Atom-style variables can
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reference thermodynamic keywords and various per-atom attributes, or
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invoke other computes, fixes, or variables when they are evaluated, so
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this is a very general means of generating per-atom quantities to
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reduce.
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</P>
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<HR>
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<P>If the <I>replace</I> keyword is used, two indices <I>vec1</I> and <I>vec2</I> are
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specified, where each index ranges from 1 to the # of input values.
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The replace keyword can only be used if the <I>mode</I> is <I>min</I> or <I>max</I>.
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It works as follows. A min/max is computed as usual on the <I>vec2</I>
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input vector. The index N of that value within <I>vec2</I> is also stored.
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Then, instead of performing a min/max on the <I>vec1</I> input vector, the
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stored index is used to select the Nth element of the <I>vec1</I> vector.
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</P>
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<P>Thus, for example, if you wish to use this compute to find the bond
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with maximum stretch, you can do it as follows:
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</P>
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<PRE>compute 1 all property/local batom1 batom2
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compute 2 all bond/local dist
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compute 3 all reduce max c_1[1] c_1[2] c_2 replace 1 3 replace 2 3
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thermo_style custom step temp c_3[1] c_3[2] c_3[3]
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</PRE>
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<P>The first two input values in the compute reduce command are vectors
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with the IDs of the 2 atoms in each bond, using the <A HREF = "compute_property_local.html">compute
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property/local</A> command. The last input
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value is bond distance, using the <A HREF = "compute_bond_local.html">compute
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bond/local</A> command. Instead of taking the
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max of the two atom ID vectors, which does not yield useful
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information in this context, the <I>replace</I> keywords will extract the
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atom IDs for the two atoms in the bond of maximum stretch. These atom
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IDs and the bond stretch will be printed with thermodynamic output.
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</P>
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<HR>
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<P>If a single input is specified this compute produces a global scalar
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value. If multiple inputs are specified, this compute produces a
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global vector of values, the length of which is equal to the number of
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inputs specified.
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</P>
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<P>As discussed below, for <I>sum</I> mode, the value(s) produced by this
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compute are all "extensive", meaning their value scales linearly with
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the number of atoms involved. If normalized values are desired, this
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compute can be accessed by the <A HREF = "thermo_style.html">thermo_style custom</A>
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command with <A HREF = "thermo_modify.html">thermo_modify norm yes</A> set as an
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option. Or it can be accessed by a <A HREF = "variable.html">variable</A> that
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divides by the appropriate atom count.
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</P>
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<HR>
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<P><B>Output info:</B>
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</P>
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<P>This compute calculates a global scalar if a single input value is
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specified or a global vector of length N where N is the number of
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inputs, and which can be accessed by indices 1 to N. These values can
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be used by any command that uses global scalar or vector values from a
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compute as input. See <A HREF = "Section_howto.html#4_15">this section</A> for an
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overview of LAMMPS output options.
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</P>
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<P>All the scalar or vector values calculated by this compute are
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"intensive", except when the <I>sum</I> mode is used on per-atom or local
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vectors, in which case the calculated values are "extensive".
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</P>
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<P>The scalar or vector values will be in whatever <A HREF = "units.html">units</A> the
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quantities being reduced are in.
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</P>
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<P><B>Restrictions:</B> none
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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 = "compute.html">compute</A>, <A HREF = "fix.html">fix</A>, <A HREF = "variable.html">variable</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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165
doc/compute_atom_molecute.txt
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165
doc/compute_atom_molecute.txt
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@ -0,0 +1,165 @@
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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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compute atom/molecule command :h3
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[Syntax:]
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compute ID group-ID atom/molecule input1 input2 ... :pre
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ID, group-ID are documented in "compute"_compute.html command :ulb,l
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atom/molecule = style name of this compute command :l
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one or more inputs can be listed :l
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input = c_ID, c_ID\[N\], f_ID, f_ID\[N\], v_name :l
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c_ID = per-atom vector calculated by a compute with ID
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c_ID\[I\] = Ith column of per-atom array calculated by a compute with ID
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f_ID = per-atom vector calculated by a fix with ID
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f_ID\[I\] = Ith column of per-atom array calculated by a fix with ID
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v_name = per-atom vector calculated by an atom-style variable with name :pre
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:ule
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[Examples:]
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compute 1 all atom/molecule sum c_force
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compute 1 all reduce/region subbox sum c_force
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[Description:]
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Define a calculation that "reduces" one or more vector inputs into
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scalar values, one per listed input. The inputs can be per-atom or
|
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local quantities; they cannot be global quantities. Atom attributes
|
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are per-atom quantities, "computes"_compute.html and "fixes"_fix.html
|
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may generate any of the three kinds of quantities, and "atom-style
|
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variables"_variable.html generate per-atom quantities. See the
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"variable"_variable command and its special functions which can
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perform the same operations as the compute reduce command on global
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vectors.
|
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|
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The reduction operation is specified by the {mode} setting. The {sum}
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option adds the values in the vector into a global total. The {min}
|
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or {max} options find the minimum or maximum value across all vector
|
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values. The {ave} setting adds the vector values into a global total,
|
||||
then divides by the number of values in the vector.
|
||||
|
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Each listed input is operated on independently. For per-atom inputs,
|
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the group specified with this command means only atoms within the
|
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group contribute to the result. For per-atom inputs, if the compute
|
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reduce/region command is used, the atoms must also currently be within
|
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the region. Note that an input that produces per-atom quantities may
|
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define its own group which affects the quantities it returns. For
|
||||
example, if a compute is used as an input which generates a per-atom
|
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vector, it will generate values of 0.0 for atoms that are not in the
|
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group specified for that compute.
|
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|
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Each listed input can be an atom attribute (position, velocity, force
|
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component) or can be the result of a "compute"_compute.html or
|
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"fix"_fix.html or the evaluation of an atom-style
|
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"variable"_variable.html.
|
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|
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The atom attribute values (x,y,z,vx,vy,vz,fx,fy,fz) are
|
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self-explanatory. Note that other atom attributes can be used as
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inputs to this fix by using the "compute
|
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property/atom"_compute_property_atom.html command and then specifying
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an input value from that compute.
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|
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If a value begins with "c_", a compute ID must follow which has been
|
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previously defined in the input script. Computes can generate
|
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per-atom or local quantities. See the individual
|
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"compute"_compute.html doc page for details. If no bracketed integer
|
||||
is appended, the vector calculated by the compute is used. If a
|
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bracketed interger is appended, the Ith column of the array calculated
|
||||
by the compute is used. Users can also write code for their own
|
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compute styles and "add them to LAMMPS"_Section_modify.html.
|
||||
|
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If a value begins with "f_", a fix ID must follow which has been
|
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previously defined in the input script. Fixes can generate per-atom
|
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or local quantities. See the individual "fix"_fix.html doc page for
|
||||
details. Note that some fixes only produce their values on certain
|
||||
timesteps, which must be compatible with when compute reduce
|
||||
references the values, else an error results. If no bracketed integer
|
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is appended, the vector calculated by the fix is used. If a bracketed
|
||||
integer is appended, the Ith column of the array calculated by the fix
|
||||
is used. Users can also write code for their own fix style and "add
|
||||
them to LAMMPS"_Section_modify.html.
|
||||
|
||||
If a value begins with "v_", a variable name must follow which has
|
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been previously defined in the input script. It must be an
|
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"atom-style variable"_variable.html. Atom-style variables can
|
||||
reference thermodynamic keywords and various per-atom attributes, or
|
||||
invoke other computes, fixes, or variables when they are evaluated, so
|
||||
this is a very general means of generating per-atom quantities to
|
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reduce.
|
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|
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:line
|
||||
|
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If the {replace} keyword is used, two indices {vec1} and {vec2} are
|
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specified, where each index ranges from 1 to the # of input values.
|
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The replace keyword can only be used if the {mode} is {min} or {max}.
|
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It works as follows. A min/max is computed as usual on the {vec2}
|
||||
input vector. The index N of that value within {vec2} is also stored.
|
||||
Then, instead of performing a min/max on the {vec1} input vector, the
|
||||
stored index is used to select the Nth element of the {vec1} vector.
|
||||
|
||||
Thus, for example, if you wish to use this compute to find the bond
|
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with maximum stretch, you can do it as follows:
|
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|
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compute 1 all property/local batom1 batom2
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compute 2 all bond/local dist
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compute 3 all reduce max c_1\[1\] c_1\[2\] c_2 replace 1 3 replace 2 3
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thermo_style custom step temp c_3\[1\] c_3\[2\] c_3\[3\] :pre
|
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|
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The first two input values in the compute reduce command are vectors
|
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with the IDs of the 2 atoms in each bond, using the "compute
|
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property/local"_compute_property_local.html command. The last input
|
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value is bond distance, using the "compute
|
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bond/local"_compute_bond_local.html command. Instead of taking the
|
||||
max of the two atom ID vectors, which does not yield useful
|
||||
information in this context, the {replace} keywords will extract the
|
||||
atom IDs for the two atoms in the bond of maximum stretch. These atom
|
||||
IDs and the bond stretch will be printed with thermodynamic output.
|
||||
|
||||
:line
|
||||
|
||||
If a single input is specified this compute produces a global scalar
|
||||
value. If multiple inputs are specified, this compute produces a
|
||||
global vector of values, the length of which is equal to the number of
|
||||
inputs specified.
|
||||
|
||||
As discussed below, for {sum} mode, the value(s) produced by this
|
||||
compute are all "extensive", meaning their value scales linearly with
|
||||
the number of atoms involved. If normalized values are desired, this
|
||||
compute can be accessed by the "thermo_style custom"_thermo_style.html
|
||||
command with "thermo_modify norm yes"_thermo_modify.html set as an
|
||||
option. Or it can be accessed by a "variable"_variable.html that
|
||||
divides by the appropriate atom count.
|
||||
|
||||
:line
|
||||
|
||||
[Output info:]
|
||||
|
||||
This compute calculates a global scalar if a single input value is
|
||||
specified or a global vector of length N where N is the number of
|
||||
inputs, and which can be accessed by indices 1 to N. These values can
|
||||
be used by any command that uses global scalar or vector values from a
|
||||
compute as input. See "this section"_Section_howto.html#4_15 for an
|
||||
overview of LAMMPS output options.
|
||||
|
||||
All the scalar or vector values calculated by this compute are
|
||||
"intensive", except when the {sum} mode is used on per-atom or local
|
||||
vectors, in which case the calculated values are "extensive".
|
||||
|
||||
The scalar or vector values will be in whatever "units"_units.html the
|
||||
quantities being reduced are in.
|
||||
|
||||
[Restrictions:] none
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"compute"_compute.html, "fix"_fix.html, "variable"_variable.html
|
||||
|
||||
[Default:] none
|
||||
@ -21,7 +21,7 @@
|
||||
|
||||
<LI>input = one or more attributes
|
||||
|
||||
<PRE> possible attributes = mol count
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||||
<PRE> possible attributes = mol cout
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||||
mol = molecule ID
|
||||
count = # of atoms in molecule
|
||||
</PRE>
|
||||
|
||||
@ -15,7 +15,7 @@ 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 count
|
||||
possible attributes = mol cout
|
||||
mol = molecule ID
|
||||
count = # of atoms in molecule :pre
|
||||
:ule
|
||||
|
||||
Reference in New Issue
Block a user