git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@907 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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@ -27,7 +27,8 @@ certain kinds of LAMMPS simulations.
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4.11 <A HREF = "#4_11">Visualizing LAMMPS snapshots</A><BR>
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4.12 <A HREF = "#4_12">Non-orthogonal simulation boxes</A><BR>
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4.13 <A HREF = "#4_13">NEMD simulations</A><BR>
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4.14 <A HREF = "#4_14">Aspherical particles</A> <BR>
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4.14 <A HREF = "#4_14">Aspherical particles</A><BR>
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4.15 <A HREF = "#4_15">Output from LAMMPS</A> <BR>
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<P>The example input scripts included in the LAMMPS distribution and
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highlighted in <A HREF = "Section_example.html">this section</A> also show how to
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@ -793,6 +794,105 @@ lj/cut</A>.
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</P>
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<HR>
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<A NAME = "4_15"></A><H4>4.15 Output from LAMMPS
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</H4>
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<P>There are two basic kinds of LAMMPS output. The first is
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thermodynamic output, which is a list of quantities printed every few
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timesteps to the screen and logfile. The second is dump files, which
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contain snapshots of atoms and various per-atom values and are written
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at a specified frequency. A simulation prints one set of
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thermodynamic output; it may generate zero, or one, or multiple dump
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files. LAMMPS gives you a variety of ways to determine what
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quantities are computed and printed when thermodynamic info or dump
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files are output. There are also two fixes which perform time and
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spatial averaging of user-defined quantities, fix ave/time and fix
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ave/spatial. These produce their own output files and are described
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below.
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</P>
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<P>The frequency and format of thermodynamic output is set by the
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<A HREF = "thermo.html">thermo</A>, <A HREF = "thermo_style.html">thermo_style</A>, and
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<A HREF = "thermo_modify.html">thermo_modify</A> commands. The
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<A HREF = "themo_style.html">thermo_style</A> command also specifies what values are
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calculated and written out. Pre-defined keywords can be specified
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(e.g. press, etotal, etc) which include time-averaged versions of
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temperature, pressure, and a few other variables (tave, pave, etc).
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Three addtional kinds of keywords can also be specified (c_ID, f_ID,
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v_name), where a <A HREF = "compute.html">compute</A> or <A HREF = "fix.html">fix</A> or
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<A HREF = "variable.html">variable</A> provides the value(s) to be output. Each of
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these are described in turn.
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</P>
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<P>In LAMMPS, a <A HREF = "compute.html">compute</A> comes in two flavors: ones that
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compute one or more global values (e.g. temperature, kinetic energy
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tensor) and ones that compute one or more per-atom values. Only the
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former can be used for thermodynamic output. The user-defined ID of
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the compute is used along with an optional subscript as part of the
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<A HREF = "thermo_style.html">thermo_style</A> command. E.g. c_myTemp outputs the
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single scalar value generated by the compute; c_myTemp[2] would
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output the 2nd vector value.
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</P>
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<P><A HREF = "fix.html">Fixes</A> can also generate values to output with thermodynamic
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output, e.g. the energy of an indenter's interaction with the
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simulation atoms. These values are accessed via the same format as
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compute's values, as f_ID or f_ID[N]. See the doc pages for
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individual fix commands to see which ones generate global values that
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can be output with thermodynamic info.
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</P>
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<P>Input script variables of various kinds are defined by the
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<A HREF = "variable.html">variable</A> command. All kinds except the atom-style
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variable can be used for thermodynamic output. A variable with name
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"abc" is referenced in a thermo_style command as v_abc.
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</P>
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<P>The variable formula defined in the input script can contain math
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functions (add, exp, etc), atom values (x[N], fx[N]), groups
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quantities (mass(), vcm(), etc), references to thermodynamic
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quantities (e.g. temp, volume, etc), or references to other variables
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or <A HREF = "compute.html">computes</A>. Thus a variable is the most general way
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to define some quantity you want calculated and output with
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thermodynamic info.
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</P>
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<P>Dump file output is specified by the <A HREF = "dump.html">dump</A> and
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<A HREF = "dump_modify.html">dump_modify</A> commands. There are several
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pre-defined formats (dump atom, dump xtc, etc). There is also a <A HREF = "dump.html">dump
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custom</A> format where you specify what values are output with
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each atom. Pre-defined keywords can be specified (e.g. tag, type, x,
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etc). Two additional kinds of keywords can also be specified (c_ID,
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f_ID), where a <A HREF = "compute.html">compute</A> or <A HREF = "fix.html">fix</A> provides the
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values to be output.
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</P>
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<P><A HREF = "compute.html">Computes</A> that generate per-atom values can be accessed
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by the dump custom command. These are computes that have the word
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"atom" in their style name, e.g. ke/atom, stress/atom, etc. The
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values are accessed as described above: c_myKE or c_myStress[2].
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The <A HREF = "compute_variable_atom.html">compute variable/atom</A> command takes a
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user-defined atom-style <A HREF = "variable.html">variable</A> as input and
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calculates its value for each atom. Since this compute can be
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accessed by the dump custom command, this is a general way to define
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some quantity you want calculated and output in a dump file.
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</P>
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<P><A HREF = "fix.html">Fixes</A> can also generate values to output to dump files.
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For example, the <A HREF = "fix_ave_atom.html">fix ave/atom</A> command does
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time-averaging of atom quantites, such as velocity or energy or stress
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which can then be output in a dump file. These values are accessed as
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describe above, as f_ID or f_ID[N].
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</P>
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<P>Two other fixes are of particular note for output. Neither produces
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values for thermodynamic or dump output, rather they output their
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results directly to a file.
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</P>
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<P>The <A HREF = "fix_ave_time.html">fix ave/time</A> command enables time-averaging of
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global quantities like temperature or pressure. The global quantities
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are calculated by a <A HREF = "compute.html">compute</A>.
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</P>
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<P>The <A HREF = "fix_ave_spatial.html">fix ave/spatial</A> command enables
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spatial-averaging of per-atom quantities like per-atom energy or
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stress. The per-atom quantities can be atom density (mass or number)
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or be calculated by a by a <A HREF = "compute.html">compute</A>. They can also be
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quantities calculated by <A HREF = "fix_ave_atom.html">fix ave/atom</A>, which means
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you are effectively calculating a time average of a spatial average of
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a time-averaged per-atom quantity.
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</P>
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<HR>
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<A NAME = "Cornell"></A>
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<P><B>(Cornell)</B> Cornell, Cieplak, Bayly, Gould, Merz, Ferguson,
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