git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1045 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2007-10-15 15:07:59 +00:00
parent 12371d39bd
commit 0e0c16c301
6 changed files with 128 additions and 84 deletions

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@ -805,7 +805,7 @@ at a specified frequency. A simulation prints one set of
thermodynamic output; it may generate zero, or one, or multiple dump
files. LAMMPS gives you a variety of ways to determine what
quantities are computed and printed when thermodynamic info or dump
files are output. There are also three fixes which do their own
files are output. There are also three fixes which can do their own
output of user-defined quantities: <A HREF = "fix_ave_time.html">fix ave/time</A>
for time averaging, <A HREF = "fix_ave_spatial.html">fix ave/spatial</A> for spatial
averaging, and <A HREF = "fix_print.html">fix print</A>. These are described below.
@ -895,7 +895,8 @@ 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. 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
be written directly to a file and/or accessed by any output command
that uses fixes as a source of input, e.g. 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
@ -907,7 +908,9 @@ Note that if you use the <A HREF = "fix_ave_atom.html">fix ave/atom</A> command
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.
ave/spatial</A> can be written directly to a file
and/or accessed by any output command that uses fixes as a source of
input, e.g. the <A HREF = "thermo_style.html">thermo_style custom</A> command.
</P>
<P>The <A HREF = "fix_print.html">fix print</A> command can generate a line of output
written to the screen and log file periodically during a running

View File

@ -798,7 +798,7 @@ at a specified frequency. A simulation prints one set of
thermodynamic output; it may generate zero, or one, or multiple dump
files. LAMMPS gives you a variety of ways to determine what
quantities are computed and printed when thermodynamic info or dump
files are output. There are also three fixes which do their own
files are output. There are also three fixes which can do their own
output of user-defined quantities: "fix ave/time"_fix_ave_time.html
for time averaging, "fix ave/spatial"_fix_ave_spatial.html for spatial
averaging, and "fix print"_fix_print.html. These are described below.
@ -888,7 +888,8 @@ 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. 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
be written directly to a file and/or accessed by any output command
that uses fixes as a source of input, e.g. the "thermo_style
custom"_thermo_style.html command.
The "fix ave/spatial"_fix_ave_spatial.html command enables
@ -900,7 +901,9 @@ 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.
ave/spatial"_fix_ave_spatial.html can be written directly to a file
and/or accessed by any output command that uses fixes as a source of
input, e.g. the "thermo_style custom"_thermo_style.html command.
The "fix print"_fix_print.html command can generate a line of output
written to the screen and log file periodically during a running

View File

@ -23,7 +23,7 @@
<LI>Nrepeat = # of times to repeat the Nevery calculation before averaging
<LI>Nfreq = timestep frequency at which the average value is written to file
<LI>Nfreq = timestep frequency at which the average value is computed
<LI>dim = <I>x</I> or <I>y</I> or <I>z</I>
@ -31,7 +31,7 @@
<LI>delta = thickness of spatial layers in dim (distance units)
<LI>file = filename to write results to
<LI>file = filename to write results to (NULL = no file)
<LI>style = <I>density</I> or <I>compute</I> or <I>fix</I>
@ -41,8 +41,6 @@
<I>compute</I> arg = compute-ID that stores or calculates per-atom quantities
<I>fix</I> arg = fix-ID that stores or calculates per-atom quantities
</PRE>
<PRE>
</PRE>
<LI>zero or more keyword/value pairs may be appended
<PRE>keyword = <I>norm</I> or <I>units</I>
@ -61,11 +59,15 @@ fix 1 flow ave/spatial 100 5 1000 y 0.0 2.5 dens.profile density mass
</P>
<P>Calculate one or more instantaneous per-atom quantities every few
timesteps, average them by layer in a chosen dimension and over a
longer timescale, and print the results to a file. This can be used
to spatially average per-atom properties (velocity, force) or per-atom
quantities calculated by a <A HREF = "compute.html">compute</A> (energy, stress) or
by another fix (see the <A HREF = "fix_ave_atom.html">fix ave/atom</A> command) or
by a variable via an equation you define (see the <A HREF = "compute_variable_atom.html">compute
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 spatially average per-atom properties
(velocity, force) or per-atom quantities calculated by a
<A HREF = "compute.html">compute</A> (energy, stress) or by another fix (see the
<A HREF = "fix_ave_atom.html">fix ave/atom</A> command) or by a variable via an
equation you define (see the <A HREF = "compute_variable_atom.html">compute
variable/atom</A> command).
</P>
<P>The <I>density</I> styles means to simply count the number of atoms in each
@ -153,8 +155,8 @@ computed every <I>Nfreq</I> timesteps. The average is over <I>Nrepeat</I>
values, computed in the preceeding portion of the simulation every
<I>Nevery</I> timesteps. Thus if Nevery=2, Nrepeat=6, and Nfreq=100, then
values on timesteps 90,92,94,96,98,100 will be used to compute the
final average written to the file on timestep 100. Similary for
timesteps 190,192,194,196,198,200 on timestep 200, etc.
final average on timestep 100. Similary for timesteps
190,192,194,196,198,200 on timestep 200, etc.
</P>
<P>The <I>norm</I> keyword also affects how time-averaging is done. For an
<I>all</I> setting, a layer quantity is summed over all atoms in all
@ -168,15 +170,15 @@ computed, i.e. Sample-quantity / Sample-count. The printed value for
the layer is the average of the M "average sample values", where M =
Nfreq/Nevery. In other words it is an average of an average.
</P>
<P>Each time info is written to the file, it is in the following format.
A line with the timestep and number of layers is written. Then one
line per layer is written, containing the layer ID (1-N), the
coordinate of the center of the layer, the number of atoms in the
layer, and one or more calculated values. The number of atoms and the
value(s) are average quantities. If the value of the <I>units</I> keyword
is <I>box</I> or <I>lattice</I>, the "coord" is printed in box units. If the
value of the <I>units</I> keyword is <I>reduced</I>, the "coord" is printed in
reduced units (0-1).
<P>If file output is specified, each time info is written to the file, it
is in the following format. A line with the timestep and number of
layers is written. Then one line per layer is written, containing the
layer ID (1-N), the coordinate of the center of the layer, the number
of atoms in the layer, and one or more calculated values. The number
of atoms and the value(s) are average quantities. If the value of the
<I>units</I> keyword is <I>box</I> or <I>lattice</I>, the "coord" is printed in box
units. If the value of the <I>units</I> keyword is <I>reduced</I>, the "coord"
is printed in reduced units (0-1).
</P>
<P>If the <I>density</I> keyword is used, or the <I>compute</I> or <I>fix</I> keyword
with a compute/fix that calculates a single quantity per atom, then a
@ -197,11 +199,22 @@ fix ave/spatial, it can slow down a simulation.
</P>
<P>No information about this fix is written to <A HREF = "restart.html">binary restart
files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
are relevant to this fix. No global scalar or vector or per-atom
quantities are stored by this fix for access by various <A HREF = "Section_howto.html#4_15">output
commands</A>. No parameter of this fix can be
used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A> command.
This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
are relevant to this fix.
</P>
<P>This fix computes a vector of quantities which can be accessed by
various <A HREF = "Section_howto.html#4_15">output commands</A>. The values should
only be accessed on timesteps that are multiples of <I>Nfreq</I> since that
is when averaging is complete. The vector is of length N =
nlayers*nvalues where nvalues is the number of per-atom quantities
produced by the compute or fix that fix ave/spatial accesses. Nvalues
= 1 if the style is <I>density</I>. If nvalues > 1 and vector value N is
accessed by another output command, then the average quantity for the
Ith layer and Jth value in that layer is accessed, where I = N /
nvalues + 1 and J = N % nvalues + 1.
</P>
<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
minimization</A>.
</P>
<P><B>Restrictions:</B> none
</P>

View File

@ -16,25 +16,21 @@ ID, group-ID are documented in "fix"_fix.html command :ulb,l
ave/spatial = style name of this fix command :l
Nevery = calculate property every this many timesteps :l
Nrepeat = # of times to repeat the Nevery calculation before averaging :l
Nfreq = timestep frequency at which the average value is written to file :l
Nfreq = timestep frequency at which the average value is computed :l
dim = {x} or {y} or {z} :l
origin = {lower} or {center} or {upper} or coordinate value (distance units) :l
delta = thickness of spatial layers in dim (distance units) :l
file = filename to write results to :l
file = filename to write results to (NULL = no file) :l
style = {density} or {compute} or {fix} :l
{density} arg = {mass} or {number}
{mass} = compute mass density
{number} = compute number density
{compute} arg = compute-ID that stores or calculates per-atom quantities
{fix} arg = fix-ID that stores or calculates per-atom quantities :pre
:pre
zero or more keyword/value pairs may be appended :l
keyword = {norm} or {units}
{norm} value = {all} or {sample}
{units} value = {box} or {lattice} or {reduced} :pre
:ule
[Examples:]
@ -47,11 +43,15 @@ fix 1 flow ave/spatial 100 5 1000 y 0.0 2.5 dens.profile density mass :pre
Calculate one or more instantaneous per-atom quantities every few
timesteps, average them by layer in a chosen dimension and over a
longer timescale, and print the results to a file. This can be used
to spatially average per-atom properties (velocity, force) or per-atom
quantities calculated by a "compute"_compute.html (energy, stress) or
by another fix (see the "fix ave/atom"_fix_ave_atom.html command) or
by a variable via an equation you define (see the "compute
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 spatially average per-atom properties
(velocity, force) or per-atom quantities calculated by a
"compute"_compute.html (energy, stress) or by another fix (see the
"fix ave/atom"_fix_ave_atom.html command) or by a variable via an
equation you define (see the "compute
variable/atom"_compute_variable_atom.html command).
The {density} styles means to simply count the number of atoms in each
@ -139,8 +139,8 @@ computed every {Nfreq} timesteps. The average is over {Nrepeat}
values, computed in the preceeding portion of the simulation every
{Nevery} timesteps. Thus if Nevery=2, Nrepeat=6, and Nfreq=100, then
values on timesteps 90,92,94,96,98,100 will be used to compute the
final average written to the file on timestep 100. Similary for
timesteps 190,192,194,196,198,200 on timestep 200, etc.
final average on timestep 100. Similary for timesteps
190,192,194,196,198,200 on timestep 200, etc.
The {norm} keyword also affects how time-averaging is done. For an
{all} setting, a layer quantity is summed over all atoms in all
@ -154,15 +154,15 @@ computed, i.e. Sample-quantity / Sample-count. The printed value for
the layer is the average of the M "average sample values", where M =
Nfreq/Nevery. In other words it is an average of an average.
Each time info is written to the file, it is in the following format.
A line with the timestep and number of layers is written. Then one
line per layer is written, containing the layer ID (1-N), the
coordinate of the center of the layer, the number of atoms in the
layer, and one or more calculated values. The number of atoms and the
value(s) are average quantities. If the value of the {units} keyword
is {box} or {lattice}, the "coord" is printed in box units. If the
value of the {units} keyword is {reduced}, the "coord" is printed in
reduced units (0-1).
If file output is specified, each time info is written to the file, it
is in the following format. A line with the timestep and number of
layers is written. Then one line per layer is written, containing the
layer ID (1-N), the coordinate of the center of the layer, the number
of atoms in the layer, and one or more calculated values. The number
of atoms and the value(s) are average quantities. If the value of the
{units} keyword is {box} or {lattice}, the "coord" is printed in box
units. If the value of the {units} keyword is {reduced}, the "coord"
is printed in reduced units (0-1).
If the {density} keyword is used, or the {compute} or {fix} keyword
with a compute/fix that calculates a single quantity per atom, then a
@ -183,11 +183,22 @@ fix ave/spatial, it can slow down a simulation.
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global scalar or vector or per-atom
quantities are stored by this fix for access by various "output
commands"_Section_howto.html#4_15. No parameter of this fix can be
used with the {start/stop} keywords of the "run"_run.html command.
This fix is not invoked during "energy minimization"_minimize.html.
are relevant to this fix.
This fix computes a vector of quantities which can be accessed by
various "output commands"_Section_howto.html#4_15. The values should
only be accessed on timesteps that are multiples of {Nfreq} since that
is when averaging is complete. The vector is of length N =
nlayers*nvalues where nvalues is the number of per-atom quantities
produced by the compute or fix that fix ave/spatial accesses. Nvalues
= 1 if the style is {density}. If nvalues > 1 and vector value N is
accessed by another output command, then the average quantity for the
Ith layer and Jth value in that layer is accessed, where I = N /
nvalues + 1 and J = N % nvalues + 1.
No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command. This fix is not invoked during "energy
minimization"_minimize.html.
[Restrictions:] none

View File

@ -13,16 +13,16 @@
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID ave/time Nevery Nrepeat Nfreq style ID flag file
<PRE>fix ID group-ID ave/time Nevery Nrepeat Nfreq style ID type file
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>ave/time = style name of this fix command
<LI>Nevery = calculate property every this many timesteps
<LI>Nrepeat = # of times to repeat the Nevery calculation before averaging
<LI>Nfreq = timestep frequency at which the average value is written to file
<LI>Nfreq = timestep frequency at which the average value is computed
<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>type = 0 for scalar quantity, 1 for vector quantity, 2 for both
<LI>file = filename to write results to (NULL = no file)
</UL>
<P><B>Examples:</B>
@ -68,15 +68,16 @@ computed every <I>Nfreq</I> timesteps. The average is over <I>Nrepeat</I>
values, computed in the preceeding portion of the simulation every
<I>Nevery</I> timesteps. Thus if Nevery=2, Nrepeat=6, and Nfreq=100, then
values on timesteps 90,92,94,96,98,100 will be used to compute the
final average written to the file on timestep 100. Similary for
timesteps 190,192,194,196,198,200 on timestep 200, etc.
final average on timestep 100. Similary for timesteps
190,192,194,196,198,200 on timestep 200, etc.
</P>
<P>The <I>flag</I> argument chooses whether the scalar and/or vector
<P>The <I>type</I> argument chooses whether the scalar and/or vector
calculation of the compute or fix is invoked. The former computes a
single global value. The latter computes N global values, where N is
defined by the compute or fix, e.g. 6 pressure tensor components. In
the vector case, each of the N values is averaged independently and N
values are written to the file at each output.
the vector case, each of the N values is averaged independently. If
file output is specified, all N values are written to the file at each
output.
</P>
<P>Since the calculation is performed by the compute or fix which stores
its own "group" definition, the group specified for with the fix
@ -94,11 +95,17 @@ calculating virial terms for the pressure every timestep.
</P>
<P>No information about this fix is written to <A HREF = "restart.html">binary restart
files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
are relevant to this fix. No global scalar or vector or per-atom
quantities are stored by this fix for access by various <A HREF = "Section_howto.html#4_15">output
commands</A>. No parameter of this fix can be
used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A> command.
This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
are relevant to this fix.
</P>
<P>Depending on the setting of the <I>type</I> parameter, this fix computes a
scalar and/or a vector of quantities which can be accessed by various
<A HREF = "Section_howto.html#4_15">output commands</A>. The values should only be
accessed on timesteps that are multiples of <I>Nfreq</I> since that is when
averaging is complete.
</P>
<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
minimization</A>.
</P>
<P><B>Restrictions:</B> none
</P>

View File

@ -10,16 +10,16 @@ fix ave/time command :h3
[Syntax:]
fix ID group-ID ave/time Nevery Nrepeat Nfreq style ID flag file :pre
fix ID group-ID ave/time Nevery Nrepeat Nfreq style ID type file :pre
ID, group-ID are documented in "fix"_fix.html command
ave/time = style name of this fix command
Nevery = calculate property every this many timesteps
Nrepeat = # of times to repeat the Nevery calculation before averaging
Nfreq = timestep frequency at which the average value is written to file
Nfreq = timestep frequency at which the average value is computed
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
type = 0 for scalar quantity, 1 for vector quantity, 2 for both
file = filename to write results to (NULL = no file) :ul
[Examples:]
@ -65,15 +65,16 @@ computed every {Nfreq} timesteps. The average is over {Nrepeat}
values, computed in the preceeding portion of the simulation every
{Nevery} timesteps. Thus if Nevery=2, Nrepeat=6, and Nfreq=100, then
values on timesteps 90,92,94,96,98,100 will be used to compute the
final average written to the file on timestep 100. Similary for
timesteps 190,192,194,196,198,200 on timestep 200, etc.
final average on timestep 100. Similary for timesteps
190,192,194,196,198,200 on timestep 200, etc.
The {flag} argument chooses whether the scalar and/or vector
The {type} argument chooses whether the scalar and/or vector
calculation of the compute or fix is invoked. The former computes a
single global value. The latter computes N global values, where N is
defined by the compute or fix, e.g. 6 pressure tensor components. In
the vector case, each of the N values is averaged independently and N
values are written to the file at each output.
the vector case, each of the N values is averaged independently. If
file output is specified, all N values are written to the file at each
output.
Since the calculation is performed by the compute or fix which stores
its own "group" definition, the group specified for with the fix
@ -91,11 +92,17 @@ calculating virial terms for the pressure every timestep.
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global scalar or vector or per-atom
quantities are stored by this fix for access by various "output
commands"_Section_howto.html#4_15. No parameter of this fix can be
used with the {start/stop} keywords of the "run"_run.html command.
This fix is not invoked during "energy minimization"_minimize.html.
are relevant to this fix.
Depending on the setting of the {type} parameter, this fix computes a
scalar and/or a vector of quantities which can be accessed by various
"output commands"_Section_howto.html#4_15. The values should only be
accessed on timesteps that are multiples of {Nfreq} since that is when
averaging is complete.
No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command. This fix is not invoked during "energy
minimization"_minimize.html.
[Restrictions:] none