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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1007 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp 2007-10-10 23:47:26 +00:00
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8 changed files with 116 additions and 66 deletions
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32
doc/Section_howto.html
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@ -838,7 +838,9 @@ indenter's interaction with the simulation atoms. These values are
accessed via the same format as a compute's values, as f_ID or
f_ID[N]. See the doc pages for individual fix commands to see which
ones generate global values that can be output with thermodynamic
info.
info. The <A HREF = "fix_ave_time.html">fix ave/time</A> command generates
time-averaged global quantities which can be accessed for
thermodynamic output.
</P>
<P>Input script variables of various kinds are defined by the
<A HREF = "variable.html">variable</A> command. All kinds except the atom-style
@ -874,20 +876,28 @@ accessed by the dump custom command, this is a general way to define
some quantity you want calculated and output in a dump file.
</P>
<P><A HREF = "fix.html">Fixes</A> can also generate per-atom values to output to dump
files. For example, the <A HREF = "fix_ave_atom.html">fix ave/atom</A> command does
time-averaging of atom quantities, such as velocity or energy or
stress which can then be output in a dump file. These values are
accessed as f_myKE for a scalar per-atom quantity or as
f_myStress[2] for a component of a vector per-atom quantity.
files. For example, the <A HREF = "fix_ave_atom.html">fix ave/atom</A> command
calculates time-averages of compute quantities. As indicated in the
preceeding paragraph, a <A HREF = "compute.html">compute quantity</A> can be a
calculated value such as <A HREF = "compute_epair_atom.html">energy</A> or
<A HREF = "compute_stress_atom.html">stress</A> or it can be a value calculated by
an atom-style <A HREF = "variable.html">variable</A>, or it can be an <A HREF = "compute_attribute_atom.html">atom
attribute</A> such as velocity or force.
These per-atom fix values are accessed by the <A HREF = "dump.html">dump custom</A>
command as f_myKE for a scalar per-atom quantity or as f_myStress[2]
for a component of a vector per-atom quantity.
</P>
<P>Two other fixes are of particular note for output. Neither produces
values for thermodynamic or dump output. Instead they output their
results directly to a file.
<P>Two other fixes are of particular note for output: <A HREF = "fix_ave_time.html">fix
ave/time</A> and <A HREF = "fix_ave_spatial.html">fix
ave/spatial</A>.
</P>
<P>The <A HREF = "fix_ave_time.html">fix ave/time</A> command enables time-averaging of
global quantities like temperature or pressure. The global quantities
are calculated by a <A HREF = "compute.html">compute</A> or a <A HREF = "fix.html">fix</A>. The
compute or fix must generate global scalar or vector quantities.
compute or fix must generate global scalar or vector quantities. The
time-averaged values generated by <A HREF = "fix_ave_time.html">fix ave/time</A> can
be written directly to a file and/or accessed by the <A HREF = "thermo_style.html">thermo_style
custom</A> command.
</P>
<P>The <A HREF = "fix_ave_spatial.html">fix ave/spatial</A> command enables
spatial-averaging of per-atom quantities like per-atom energy or
@ -897,6 +907,8 @@ compute or fix must generate per-atom scalar or vector quantities.
Note that if you use the <A HREF = "fix_ave_atom.html">fix ave/atom</A> command with
fix ave/spatial, it means you are effectively calculating a time
average of a spatial average of a time-averaged per-atom quantity.
The time-averaged values generated by <A HREF = "fix_ave_spatial.html">fix
ave/spatial</A> are written directly to a file.
</P>
<HR>

32
doc/Section_howto.txt
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@ -831,7 +831,9 @@ indenter's interaction with the simulation atoms. These values are
accessed via the same format as a compute's values, as f_ID or
f_ID\[N\]. See the doc pages for individual fix commands to see which
ones generate global values that can be output with thermodynamic
info.
info. The "fix ave/time"_fix_ave_time.html command generates
time-averaged global quantities which can be accessed for
thermodynamic output.
Input script variables of various kinds are defined by the
"variable"_variable.html command. All kinds except the atom-style
@ -867,20 +869,28 @@ accessed by the dump custom command, this is a general way to define
some quantity you want calculated and output in a dump file.
"Fixes"_fix.html can also generate per-atom values to output to dump
files. For example, the "fix ave/atom"_fix_ave_atom.html command does
time-averaging of atom quantities, such as velocity or energy or
stress which can then be output in a dump file. These values are
accessed as f_myKE for a scalar per-atom quantity or as
f_myStress\[2\] for a component of a vector per-atom quantity.
files. For example, the "fix ave/atom"_fix_ave_atom.html command
calculates time-averages of compute quantities. As indicated in the
preceeding paragraph, a "compute quantity"_compute.html can be a
calculated value such as "energy"_compute_epair_atom.html or
"stress"_compute_stress_atom.html or it can be a value calculated by
an atom-style "variable"_variable.html, or it can be an "atom
attribute"_compute_attribute_atom.html such as velocity or force.
These per-atom fix values are accessed by the "dump custom"_dump.html
command as f_myKE for a scalar per-atom quantity or as f_myStress\[2\]
for a component of a vector per-atom quantity.
Two other fixes are of particular note for output. Neither produces
values for thermodynamic or dump output. Instead they output their
results directly to a file.
Two other fixes are of particular note for output: "fix
ave/time"_fix_ave_time.html and "fix
ave/spatial"_fix_ave_spatial.html.
The "fix ave/time"_fix_ave_time.html command enables time-averaging of
global quantities like temperature or pressure. The global quantities
are calculated by a "compute"_compute.html or a "fix"_fix.html. The
compute or fix must generate global scalar or vector quantities.
compute or fix must generate global scalar or vector quantities. The
time-averaged values generated by "fix ave/time"_fix_ave_time.html can
be written directly to a file and/or accessed by the "thermo_style
custom"_thermo_style.html command.
The "fix ave/spatial"_fix_ave_spatial.html command enables
spatial-averaging of per-atom quantities like per-atom energy or
@ -890,6 +900,8 @@ compute or fix must generate per-atom scalar or vector quantities.
Note that if you use the "fix ave/atom"_fix_ave_atom.html command with
fix ave/spatial, it means you are effectively calculating a time
average of a spatial average of a time-averaged per-atom quantity.
The time-averaged values generated by "fix
ave/spatial"_fix_ave_spatial.html are written directly to a file.
:line

16
doc/fix_ave_time.html
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@ -23,7 +23,7 @@
<LI>style = <I>compute</I> or <I>fix</I>
<LI>ID = ID of compute or fix that performs the calculation
<LI>flag = 0 for scalar quantity, 1 for vector quantity, 2 for both
<LI>file = filename to write results to
<LI>file = filename to write results to (NULL = no file)
</UL>
<P><B>Examples:</B>
</P>
@ -33,12 +33,16 @@ fix 1 all ave/time 1 100 1000 fix indenter 0 temp.indent
<P><B>Description:</B>
</P>
<P>Calculate one or more instantaneous quantities every few timesteps,
average them over a longer timescale, and print the results to a file.
This can be used to time-average a <A HREF = "compute.html">compute</A> which
and average them over a longer timescale. The resulting averages can
be written to a file and/or used by other <A HREF = "Section_howto.html#4_15">output
commands</A> such as <A HREF = "thermo_style.html">thermo_style
custom</A>.
</P>
<P>This fix can be used to time-average a <A HREF = "compute.html">compute</A> which
calculates a global quantity such as a temperature or pressure or a
<A HREF = "fix.html">fix</A> which calculates such a global quantity. Note that
per-atom computes cannot be used with this fix; their values can be
averaged by the <A HREF = "fix_ave_spatial.html">fix ave/spatial</A> or <A HREF = "fix_ave_atom.html">fix
<A HREF = "fix.html">fix</A> which calculates a global quantity. Note that per-atom
computes cannot be used with this fix; their values can be averaged by
the <A HREF = "fix_ave_spatial.html">fix ave/spatial</A> or <A HREF = "fix_ave_atom.html">fix
ave/atom</A> commands.
</P>
<P>For style <I>compute</I> the <I>ID</I> specifies a <A HREF = "compute.html">compute</A> which

16
doc/fix_ave_time.txt
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@ -20,7 +20,7 @@ Nfreq = timestep frequency at which the average value is written to file
style = {compute} or {fix}
ID = ID of compute or fix that performs the calculation
flag = 0 for scalar quantity, 1 for vector quantity, 2 for both
file = filename to write results to :ul
file = filename to write results to (NULL = no file) :ul
[Examples:]
@ -30,12 +30,16 @@ fix 1 all ave/time 1 100 1000 fix indenter 0 temp.indent :pre
[Description:]
Calculate one or more instantaneous quantities every few timesteps,
average them over a longer timescale, and print the results to a file.
This can be used to time-average a "compute"_compute.html which
and average them over a longer timescale. The resulting averages can
be written to a file and/or used by other "output
commands"_Section_howto.html#4_15 such as "thermo_style
custom"_thermo_style.html.
This fix can be used to time-average a "compute"_compute.html which
calculates a global quantity such as a temperature or pressure or a
"fix"_fix.html which calculates such a global quantity. Note that
per-atom computes cannot be used with this fix; their values can be
averaged by the "fix ave/spatial"_fix_ave_spatial.html or "fix
"fix"_fix.html which calculates a global quantity. Note that per-atom
computes cannot be used with this fix; their values can be averaged by
the "fix ave/spatial"_fix_ave_spatial.html or "fix
ave/atom"_fix_ave_atom.html commands.
For style {compute} the {ID} specifies a "compute"_compute.html which

40
doc/thermo_style.html
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@ -207,14 +207,16 @@ been defined elsewhere in the input script. See the
<A HREF = "compute.html">compute</A> command for details. Note that only global
scalar or vector quantites calculated by a compute can be output as
thermodynamic data; per-atom quantities calcalated by a compute are
output by the <A HREF = "dump.html">dump custom</A> command. Note that some
computes calculate "intensive" global quantities like temperature;
others calculate "extensive" global quantities like kinetic energy
that are summed over all atoms in the compute group. Intensive
quantities are printed directly by thermo_style custom. Extensive
quantites may be normalized by the total number of atoms in the
simulation (NOT the number of atoms in the compute group) depending on
the <A HREF = "thermo_modify.html">thermo_modify norm</A> option being used.
output by the <A HREF = "dump.html">dump custom</A> command.
</P>
<P>Note that some computes calculate "intensive" global quantities like
temperature; others calculate "extensive" global quantities like
kinetic energy that are summed over all atoms in the compute group.
Intensive quantities are printed directly by thermo_style custom.
Extensive quantites may be normalized by the total number of atoms in
the simulation (NOT the number of atoms in the compute group)
depending on the <A HREF = "thermo_modify.html">thermo_modify norm</A> option being
used.
</P>
<P>If <I>c_ID</I> is used as a keyword, then the scalar quantity calculated by
the compute is printed. If <I>c_ID[N]</I> is used, then the compute must
@ -226,14 +228,20 @@ are.
<P>The <I>f_ID</I> and <I>f_ID[N]</I> keywords allow global scalar or vector
quantities calculated by a fix to be output. The ID in the keyword
should be replaced by the actual ID of the fix that has been defined
elsewhere in the input script. Note that some fixes calculate
"intensive" global quantities like timestep size; others calculate
"extensive" global quantities like energy that are summed over all
atoms in the fix group. Intensive quantities are printed directly by
thermo_style custom. Extensive quantites may be normalized by the
total number of atoms in the simulation (NOT the number of atoms in
the compute group) depending on the <A HREF = "thermo_modify.html">thermo_modify
norm</A> option being used.
elsewhere in the input script. See the doc pages for individual <A HREF = "fix.html">fix
commands</A> for details of which fixes generate global values.
One particularly useful fix to use in this context is the <A HREF = "fix_ave_time.html">fix
ave/time</A> command, which calculates time-averages of
global scalar and vector quantities calculated by other
<A HREF = "compute.html">computes</A> and <A HREF = "fix.html">fixes</A>.
</P>
<P>Note that some fixes calculate "intensive" global quantities like
timestep size; others calculate "extensive" global quantities like
energy that are summed over all atoms in the fix group. Intensive
quantities are printed directly by thermo_style custom. Extensive
quantites may be normalized by the total number of atoms in the
simulation (NOT the number of atoms in the fix group) depending on the
<A HREF = "thermo_modify.html">thermo_modify norm</A> option being used.
</P>
<P>If <I>f_ID</I> is used as a keyword, then the scalar quantity calculated by
the fix is printed. If <I>f_ID[N]</I> is used, then the fix must

40
doc/thermo_style.txt
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@ -201,14 +201,16 @@ been defined elsewhere in the input script. See the
"compute"_compute.html command for details. Note that only global
scalar or vector quantites calculated by a compute can be output as
thermodynamic data; per-atom quantities calcalated by a compute are
output by the "dump custom"_dump.html command. Note that some
computes calculate "intensive" global quantities like temperature;
others calculate "extensive" global quantities like kinetic energy
that are summed over all atoms in the compute group. Intensive
quantities are printed directly by thermo_style custom. Extensive
quantites may be normalized by the total number of atoms in the
simulation (NOT the number of atoms in the compute group) depending on
the "thermo_modify norm"_thermo_modify.html option being used.
output by the "dump custom"_dump.html command.
Note that some computes calculate "intensive" global quantities like
temperature; others calculate "extensive" global quantities like
kinetic energy that are summed over all atoms in the compute group.
Intensive quantities are printed directly by thermo_style custom.
Extensive quantites may be normalized by the total number of atoms in
the simulation (NOT the number of atoms in the compute group)
depending on the "thermo_modify norm"_thermo_modify.html option being
used.
If {c_ID} is used as a keyword, then the scalar quantity calculated by
the compute is printed. If {c_ID\[N\]} is used, then the compute must
@ -220,14 +222,20 @@ are.
The {f_ID} and {f_ID\[N\]} keywords allow global scalar or vector
quantities calculated by a fix to be output. The ID in the keyword
should be replaced by the actual ID of the fix that has been defined
elsewhere in the input script. Note that some fixes calculate
"intensive" global quantities like timestep size; others calculate
"extensive" global quantities like energy that are summed over all
atoms in the fix group. Intensive quantities are printed directly by
thermo_style custom. Extensive quantites may be normalized by the
total number of atoms in the simulation (NOT the number of atoms in
the compute group) depending on the "thermo_modify
norm"_thermo_modify.html option being used.
elsewhere in the input script. See the doc pages for individual "fix
commands"_fix.html for details of which fixes generate global values.
One particularly useful fix to use in this context is the "fix
ave/time"_fix_ave_time.html command, which calculates time-averages of
global scalar and vector quantities calculated by other
"computes"_compute.html and "fixes"_fix.html.
Note that some fixes calculate "intensive" global quantities like
timestep size; others calculate "extensive" global quantities like
energy that are summed over all atoms in the fix group. Intensive
quantities are printed directly by thermo_style custom. Extensive
quantites may be normalized by the total number of atoms in the
simulation (NOT the number of atoms in the fix group) depending on the
"thermo_modify norm"_thermo_modify.html option being used.
If {f_ID} is used as a keyword, then the scalar quantity calculated by
the fix is printed. If {f_ID\[N\]} is used, then the fix must

3
doc/timestep.html
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@ -36,7 +36,8 @@ the outer loop (largest) timestep.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "run.html">run</A>, <A HREF = "run_style.html">run_style</A> respa, <A HREF = "units.html">units</A>
<P><A HREF = "fix_dt_reset.html">fix dt/reset</A>, <A HREF = "run.html">run</A>,
<A HREF = "run_style.html">run_style</A> respa, <A HREF = "units.html">units</A>
</P>
<P><B>Default:</B>
</P>

3
doc/timestep.txt
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@ -33,7 +33,8 @@ the outer loop (largest) timestep.
[Related commands:]
"run"_run.html, "run_style"_run_style.html respa, "units"_units.html
"fix dt/reset"_fix_dt_reset.html, "run"_run.html,
"run_style"_run_style.html respa, "units"_units.html
[Default:]