jianmu
/
lammps
forked from lijiext/lammps
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@3526 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2009-12-11 21:41:25 +00:00
parent d654bb622e
commit 113ca39027
6 changed files with 361 additions and 192 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

9
doc/Section_howto.html
View File

@ -1068,14 +1068,17 @@ files: <A HREF = "fix_ave_time.html">fix ave/time</A>, <A HREF = "fix_ave_spatia
ave/spatial</A>, and <A HREF = "fix_print.html">fix print</A>.
</P>
<P>The <A HREF = "fix_ave_time.html">fix ave/time</A> command enables direct output to
a file and/or time-averaging of any global quantity. The user
a file and/or time-averaging of global scalars or vectors. The user
specifies one or more quantities as input. These can be global
<A HREF = "compute.html">compute</A> values, global <A HREF = "fix.html">fix</A> values, or
<A HREF = "variable.html">variables</A> of any style except the atom style which
produces per-atom values. Since a variable can refer to keywords used
by the <A HREF = "thermo_style.html">thermo_style custom</A> command (like temp or
press) and individual per-atom values, a wide variety of quantities
can be time averaged and/or output in this way. The time-averaged
can be time averaged and/or output in this way. If the inputs are one
or more scalar values, then the fix generate a global scalar or vector
of output. If the inputs are one or more vector values, then the fix
generates a global vector or array of output. The time-averaged
output of this fix can also be used as input to other output commands.
</P>
<P>The <A HREF = "fix_ave_spatial.html">fix ave/spatial</A> command enables direct
@ -1161,7 +1164,7 @@ 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 = "fix_ave_time.html">fix ave/time</A></TD><TD > global scalars</TD><TD > global scalar/vector, file</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>
<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 >

9
doc/Section_howto.txt
View File

@ -1059,14 +1059,17 @@ files: "fix ave/time"_fix_ave_time.html, "fix
ave/spatial"_fix_ave_spatial.html, and "fix print"_fix_print.html.
The "fix ave/time"_fix_ave_time.html command enables direct output to
a file and/or time-averaging of any global quantity. The user
a file and/or time-averaging of global scalars or vectors. The user
specifies one or more quantities as input. These can be global
"compute"_compute.html values, global "fix"_fix.html values, or
"variables"_variable.html of any style except the atom style which
produces per-atom values. Since a variable can refer to keywords used
by the "thermo_style custom"_thermo_style.html command (like temp or
press) and individual per-atom values, a wide variety of quantities
can be time averaged and/or output in this way. The time-averaged
can be time averaged and/or output in this way. If the inputs are one
or more scalar values, then the fix generate a global scalar or vector
of output. If the inputs are one or more vector values, then the fix
generates a global vector or array of output. The time-averaged
output of this fix can also be used as input to other output commands.
The "fix ave/spatial"_fix_ave_spatial.html command enables direct
@ -1151,7 +1154,7 @@ 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:
"fix ave/time"_fix_ave_time.html: global scalars: global scalar/vector, file:
"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:
"fix ave/atom"_fix_ave_atom.html: per-atom vectors: per-atom vector/array:
:tb(s=:)

54
doc/fix_ave_spatial.html
View File

@ -60,7 +60,7 @@
<I>title2</I> arg = string
string = text to print as 2nd line of output file = timestep, # of layers
<I>title3</I> arg = string
string = text to print as 3rd line of output file = values
string = text to print as 3rd line of output file = column headings for values
</PRE>
</UL>
@ -224,19 +224,6 @@ computed, i.e. Sample-quantity / Sample-count. The printed value for
the layer is the average of the <I>Nrepeat</I> "average sample values", In
other words it is an average of an average.
</P>
<P>The <I>file</I> keyword allows a filename to be specified. Every <I>Nfreq</I>
timesteps, layer info will be written to a text file 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 values in
each line corresponds to the number of values specified in the fix
ave/spatial command. 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>The <I>ave</I> keyword determines how the layer values produced every
<I>Nfreq</I> steps are averaged with layer values produced on previous
steps that were multiples of <I>Nfreq</I>, before they are accessed by
@ -263,23 +250,34 @@ then the output on step 10000 will be the average of the individual
layer values on steps 8000,9000,10000. Outputs on early steps will
average over less than M values if they are not available.
</P>
<P>The <I>file</I> keyword allows a filename to be specified. Every <I>Nfreq</I>
timesteps, a section of layer info will be written to a text file 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
values in each line corresponds to the number of values specified in
the fix ave/spatial command. 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>The <I>title1</I> and <I>title2</I> and <I>title3</I> keywords allow specification of
the strings that will be printed as the first 3 lines of the output
file, assuming the <I>file</I> keyword was used. LAMMPS uses default
values for each of these, so they do not need to be specified. By
default, theses lines are as follows:
values for each of these, so they do not need to be specified.
</P>
<P>By default, these header lines are as follows:
</P>
<PRE># Spatial-averaged data for fix ID and group name
# Timestep Number-of-layers
# Layer Coord Ncount value1 value2 ...
</PRE>
<P>In the first line, ID and name are replaced with the fix-ID and group
name. In the last line the values are replaced with the appropriate
fields from the fix ave/spatial command. Note the first line is
essentially a title for the file. The second line describes the
header line that appears at the first of each section of output. The
third line describes the columns of each layer line within a section
of output.
name. The second line describes the two values that are printed at
the first of each section of output. In the third line the values are
replaced with the appropriate fields from the fix ave/spatial command.
</P>
<HR>
@ -292,12 +290,12 @@ are relevant to this fix.
<P>This fix computes a global array of values which can be accessed by
various <A HREF = "Section_howto.html#4_15">output commands</A>. The values can
only be accessed on timesteps that are multiples of <I>Nfreq</I> since that
is when averaging is performed. The global array has Nlayers rows and
Nvalues+2 columns. The first column has the layer coordinate, the 2nd
column has the count of atoms in that layer, and the remaining columns
are the Nvalue quantities. When the array is accessed with an I that
exceeds the current number of layers, than a 0.0 is returned by the
fix instead of an error, since the number of layers can vary as a
is when averaging is performed. The global array has rows = Nlayers
and columns = Nvalues+2. The first column has the layer coordinate,
the 2nd column has the count of atoms in that layer, and the remaining
columns are the Nvalue quantities. When the array is accessed with an
I that exceeds the current number of layers, than a 0.0 is returned by
the fix instead of an error, since the number of layers can vary as a
simulation runs, depending on the simulation box size. The array
values calculated by this fix are "intensive", meaning they are
independent of the number of atoms in the simulation, since they are

55
doc/fix_ave_spatial.txt
View File

@ -45,7 +45,7 @@ keyword = {norm} or {units} or {file} or {ave} or {title1} or {title2} or {title
{title2} arg = string
string = text to print as 2nd line of output file = timestep, # of layers
{title3} arg = string
string = text to print as 3rd line of output file = values :pre
string = text to print as 3rd line of output file = column headings for values :pre
:ule
[Examples:]
@ -208,19 +208,6 @@ computed, i.e. Sample-quantity / Sample-count. The printed value for
the layer is the average of the {Nrepeat} "average sample values", In
other words it is an average of an average.
The {file} keyword allows a filename to be specified. Every {Nfreq}
timesteps, layer info will be written to a text file 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 values in
each line corresponds to the number of values specified in the fix
ave/spatial command. 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).
The {ave} keyword determines how the layer values produced every
{Nfreq} steps are averaged with layer values produced on previous
steps that were multiples of {Nfreq}, before they are accessed by
@ -247,23 +234,34 @@ then the output on step 10000 will be the average of the individual
layer values on steps 8000,9000,10000. Outputs on early steps will
average over less than M values if they are not available.
The {file} keyword allows a filename to be specified. Every {Nfreq}
timesteps, a section of layer info will be written to a text file 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
values in each line corresponds to the number of values specified in
the fix ave/spatial command. 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).
The {title1} and {title2} and {title3} keywords allow specification of
the strings that will be printed as the first 3 lines of the output
file, assuming the {file} keyword was used. LAMMPS uses default
values for each of these, so they do not need to be specified. By
default, theses lines are as follows:
values for each of these, so they do not need to be specified.
By default, these header lines are as follows:
# Spatial-averaged data for fix ID and group name
# Timestep Number-of-layers
# Layer Coord Ncount value1 value2 ... :pre
In the first line, ID and name are replaced with the fix-ID and group
name. In the last line the values are replaced with the appropriate
fields from the fix ave/spatial command. Note the first line is
essentially a title for the file. The second line describes the
header line that appears at the first of each section of output. The
third line describes the columns of each layer line within a section
of output.
name. The second line describes the two values that are printed at
the first of each section of output. In the third line the values are
replaced with the appropriate fields from the fix ave/spatial command.
:line
@ -276,12 +274,12 @@ are relevant to this fix.
This fix computes a global array of values which can be accessed by
various "output commands"_Section_howto.html#4_15. The values can
only be accessed on timesteps that are multiples of {Nfreq} since that
is when averaging is performed. The global array has Nlayers rows and
Nvalues+2 columns. The first column has the layer coordinate, the 2nd
column has the count of atoms in that layer, and the remaining columns
are the Nvalue quantities. When the array is accessed with an I that
exceeds the current number of layers, than a 0.0 is returned by the
fix instead of an error, since the number of layers can vary as a
is when averaging is performed. The global array has rows = Nlayers
and columns = Nvalues+2. The first column has the layer coordinate,
the 2nd column has the count of atoms in that layer, and the remaining
columns are the Nvalue quantities. When the array is accessed with an
I that exceeds the current number of layers, than a 0.0 is returned by
the fix instead of an error, since the number of layers can vary as a
simulation runs, depending on the simulation box size. The array
values calculated by this fix are "intensive", meaning they are
independent of the number of atoms in the simulation, since they are
@ -307,4 +305,3 @@ simulation box size doesn't change or if the {units} keyword is set to
The option defaults are units = lattice, norm = all, no file output,
and ave = one, title 1,2,3 = strings as described above.

214
doc/fix_ave_time.html
View File

@ -29,32 +29,44 @@
<LI>value = c_ID, c_ID[N], f_ID, f_ID[N], v_name
<PRE> c_ID = global scalar value calculated by a compute with ID
c_ID[N] = Nth component of global vector calculated by a compute with ID
f_ID = global scalar value calculated by a fix with ID
f_ID[N] = Nth component of global vector calculated by a fix with ID
<PRE> c_ID = global scalar or vector calculated by a compute with ID
c_ID[I] = Ith component of global vector or Ith column of global array calculated by a compute with ID
f_ID = global scalar or vector calculated by a fix with ID
f_ID[I] = Ith component of global vector or Ith column of global array calculated by a fix with ID
v_name = global value calculated by an equal-style variable with name
</PRE>
<LI>zero or more keyword/arg pairs may be appended
<LI>keyword = <I>file</I> or <I>ave</I> or <I>start</I>
<LI>keyword = <I>mode</I> or <I>file</I> or <I>ave</I> or <I>start</I> or <I>off</I> or <I>title1</I> or <I>title2</I> or <I>title3</I>
<PRE> <I>file</I> arg = filename
<PRE> <I>mode</I> arg = <I>scalar</I> or <I>vector</I>
scalar = all input values are global scalars
vector = all input values are global vectors
<I>file</I> arg = filename
filename = name of file to output time averages to
<I>ave</I> args = <I>one</I> or <I>running</I> or <I>window M</I>
one = output a new average value every Nfreq steps
running = output cumulative average of all previous Nfreq steps
window M = output average of M most recent Nfreq steps
<I>start</I> args = Nstart
Nstart = start averaging on this timestep
Nstart = start averaging on this timestep
<I>off</I> arg = M = do not average this value
M = value # from 1 to Nvalues
<I>title1</I> arg = string
string = text to print as 1st line of output file = title
<I>title2</I> arg = string
string = text to print as 2nd line of output file
<I>title3</I> arg = string
string = text to print as 3rd line of output file, only for vector mode
</PRE>
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix 1 all ave/time 100 5 1000 c_myTemp c_thermo_temp file temp.profile
fix 1 all ave/time 100 5 1000 c_thermo_press[2] ave window 20
fix 1 all ave/time 1 100 1000 f_indent f_indent[1] file temp.indent
fix 1 all ave/time 100 5 1000 c_thermo_press[2] ave window 20 &
title1 "My output values"
fix 1 all ave/time 1 100 1000 f_indent f_indent[1] file temp.indent off 1
</PRE>
<P><B>Description:</B>
</P>
@ -62,14 +74,13 @@ fix 1 all ave/time 1 100 1000 f_indent f_indent[1] file temp.indent
timesteps, and average them over longer timescales. The resulting
averages can be used by other <A HREF = "Section_howto.html#4_15">output
commands</A> such as <A HREF = "thermo_style.html">thermo_style
custom</A>, and can also be written to a file. If no
averaging is done, this command is a convenient way to simply write
one or more desired quantities to a separate file.
custom</A>, and can also be written to a file. Note
that if no time averaging is done, this command can simply be used as
a convenient way to output one or more desired quantities to a
separate file.
</P>
<P>Each listed value is averaged independently. If written to a file,
then over time, one column of numbers is produced for each value. The
group specified with the command is ignored, since calculations are
performed by computes and fixes which store their own "group"
<P>The group specified with this command is ignored, since calculations
are performed by computes and fixes which store their own "group"
definition,
</P>
<P>Each listed value can be the result of a <A HREF = "compute.html">compute</A> or
@ -90,6 +101,15 @@ individual fixes for info on which ones produce such values.
be used with this fix. Variables of style <I>atom</I> cannot be used,
since they produce per-atom values.
</P>
<P>The listed values must either be all global scalars or all global
vectors, depending on the setting of the <I>mode</I> option. In both
cases, the averaging is performed independently on every input
quantity. I.e. each input value and the elements of each input value
(if it is a vector) are averaged independently.
</P>
<P>If <I>mode</I> = vector, then all the input values must be vectors of the
same length.
</P>
<HR>
<P>The <I>Nevery</I>, <I>Nrepeat</I>, and <I>Nfreq</I> arguments specify on what
@ -111,49 +131,56 @@ averaging is done; values are simply generated on timesteps
<HR>
<P>If a value begins with "c_", a compute ID must follow which has been
previously defined in the input script. If no bracketed term is
appended, the global scalar calculated by the compute is used. If a
bracketed term is appended, the Nth vector value calculated by the
compute is used. Note that there is a <A HREF = "compute_reduce.html">compute
reduce</A> command which can sum per-atom quantities
into a global scalar or vector which can thus be accessed by fix
ave/time. Or it can be a compute defined not in your input script,
but by <A HREF = "thermo_style.html">thermodynamic output</A> or other fixes such as
<A HREF = "fix_nvt.html">fix nvt</A> or <A HREF = "fix_temp_rescale.html">fix temp/rescale</A>.
See the doc pages for these commands which give the IDs of these
computes. Users can also write code for their own compute styles and
<A HREF = "Section_modify.html">add them to LAMMPS</A>.
previously defined in the input script. If <I>mode</I> = scalar, then if
no bracketed term is appended, the global scalar calculated by the
compute is used. If a bracketed term is appended, the Ith element of
the global vector calculated by the compute is used. If <I>mode</I> =
vector, then if no bracketed term is appended, the global vector
calculated by the compute is used. If a bracketed term is appended,
the Ith column of the global array calculated by the compute is used.
</P>
<P>Note that there is a <A HREF = "compute_reduce.html">compute reduce</A> command
which can sum per-atom quantities into a global scalar or vector which
can thus be accessed by fix ave/time. Or it can be a compute defined
not in your input script, but by <A HREF = "thermo_style.html">thermodynamic
output</A> or other fixes such as <A HREF = "fix_nvt.html">fix
nvt</A> or <A HREF = "fix_temp_rescale.html">fix temp/rescale</A>. See
the doc pages for these commands which give the IDs of these computes.
Users can also write code for their own compute styles and <A HREF = "Section_modify.html">add them
to LAMMPS</A>.
</P>
<P>If a value begins with "f_", a fix ID must follow which has been
previously defined in the input script. If no bracketed term is
appended, the global scalar calculated by the fix is used. If a
bracketed term is appended, the Nth vector value calculated by the fix
is used. Note that some fixes only produce their values on certain
timesteps, which must be compatible with <I>Nevery</I>, else an error will
result. Users can also write code for their own fix styles and <A HREF = "Section_modify.html">add
them to LAMMPS</A>.
previously defined in the input script. If <I>mode</I> = scalar, then if
no bracketed term is appended, the global scalar calculated by the fix
is used. If a bracketed term is appended, the Ith element of the
global vector calculated by the fix is used. If <I>mode</I> = vector, then
if no bracketed term is appended, the global vector calculated by the
fix is used. If a bracketed term is appended, the Ith column of the
global array calculated by the fix is used.
</P>
<P>Note that some fixes only produce their values on certain timesteps,
which must be compatible with <I>Nevery</I>, else an error will result.
Users can also write code for their own fix styles and <A HREF = "Section_modify.html">add them to
LAMMPS</A>.
</P>
<P>If a value begins with "v_", a variable name must follow which has
been previously defined in the input script. Only equal-style
variables can be referenced. See the <A HREF = "variable.html">variable</A> command
for details. Variables of style <I>equal</I> define a formula which can
been previously defined in the input script. Variables can only be
used as input for <I>mode</I> = scalar. Only equal-style variables can be
referenced. See the <A HREF = "variable.html">variable</A> command for details.
Note that variables of style <I>equal</I> define a formula which can
reference individual atom properties or thermodynamic keywords, or
they can invoke other computes, fixes, or variables when they are
evaluated, so this is a very general means of generating quantities to
evaluated, so this is a very general means of specifying quantities to
time average.
</P>
<HR>
<P>Additional optional keywords also affect the operation of this fix.
</P>
<P>The <I>file</I> keyword allows a filename to be specified. Each timestamp,
one quantity is written to the file for each value specified in the
fix ave/time command. The file is in a self-explanatory text format.
</P>
<P>The <I>ave</I> keyword determines how the scalar and/or vector values
produced every <I>Nfreq</I> steps are averaged with values produced on
previous steps that were multiples of <I>Nfreq</I>, before they are
accessed by another output command or written to a file.
<P>The <I>ave</I> keyword determines how the values produced every <I>Nfreq</I>
steps are averaged with values produced on previous steps that were
multiples of <I>Nfreq</I>, before they are accessed by another output
command or written to a file.
</P>
<P>If the <I>ave</I> setting is <I>one</I>, then the values produced on timesteps
that are multiples of <I>Nfreq</I> are independent of each other; they are
@ -176,9 +203,54 @@ on step 10000 will be the average of the individual values on steps
values if they are not available.
</P>
<P>The <I>start</I> keyword specifies what timestep averaging will begin on.
The default is step 0. Often this value is 0.0, so setting <I>start</I> to
a larger value can avoid including a 0.0 in a running or windowed
average.
The default is step 0. Often input values can be 0.0 at time 0, so
setting <I>start</I> to a larger value can avoid including a 0.0 in a
running or windowed average.
</P>
<P>The <I>off</I> keyword can be used to flag any of the input values. If a
value is flagged, it will not be time averaged. Instead the most
recent input value will always be stored and output. This is useful
if one of more of the inputs produced by a compute or fix or variable
are effectively constant or are simply current values. E.g. they are
being written to a file with other time-averaged values for purposes
of creating well-formatted output.
</P>
<P>The <I>file</I> keyword allows a filename to be specified. Every <I>Nfreq</I>
steps, one quantity or vector of quantities is written to the file for
each input value specified in the fix ave/time command. For <I>mode</I> =
scalar, this means a single line is written each time output is
performed. Thus the file ends up to be a series of lines, i.e. one
column of numbers for each input value. For <I>mode</I> = vector, an array
of numbers is written each time output is performed. The number of
rows is the length of the input vectors, and the number of columns is
the number of values. Thus the file ends up to be a series of these
array sections.
</P>
<P>The <I>title1</I> and <I>title2</I> and <I>title3</I> keywords allow specification of
the strings that will be printed as the first 2 or 3 lines of the
output file, assuming the <I>file</I> keyword was used. LAMMPS uses
default values for each of these, so they do not need to be specified.
</P>
<P>By default, these header lines are as follows for <I>mode</I> = scalar:
</P>
<PRE># Time-averaged data for fix ID
# TimeStep value1 value2 ...
</PRE>
<P>In the first line, ID is replaced with the fix-ID. In the second line
the values are replaced with the appropriate fields from the fix
ave/time command. There is no third line in the header of the file,
so the <I>title3</I> setting is ignored when <I>mode</I> = scalar.
</P>
<P>By default, these header lines are as follows for <I>mode</I> = vector:
</P>
<PRE># Time-averaged data for fix ID
# TimeStep Number-of-rows
# Row value1 value2 ...
</PRE>
<P>In the first line, ID is replaced with the fix-ID. The second line
describes the two values that are printed at the first of each section
of output. In the third line the values are replaced with the
appropriate fields from the fix ave/time command.
</P>
<HR>
@ -188,20 +260,30 @@ average.
files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
are relevant to this fix.
</P>
<P>This fix produces a global scalar or vector which can be accessed by
various <A HREF = "Section_howto.html#4_15">output commands</A>. A scalar is
produced if only a single quantity is averaged by this fix. If two or
more quantities are averaged, then a vector of values is produced.
The global values can only be accessed on timesteps that are multiples
of <I>Nfreq</I> since that is when averaging is performed. Each value
(scalar or vector component) calculated by this fix may be either
"intensive" or "extensive". Intensive means the value is independent
of the number of atoms in the simulation. Extensive means the value
scales with the number of atoms in the simulation. If a compute or
fix provides the value being time averaged, then the compute or fix
determines whether the value is intensive or extensive; see the doc
page for that compute or fix for further info. Values produced by a
variable are whatever the variable calculates.
<P>This fix produces a global scalar or vector or array which can be
accessed by various <A HREF = "Section_howto.html#4_15">output commands</A>. The
values can only be accessed on timesteps that are multiples of <I>Nfreq</I>
since that is when averaging is performed.
</P>
<P>A scalar is produced if only a single input value is averaged and
<I>mode</I> = scalar. A vector is produced if multiple input values are
averaged for <I>mode</I> = scalar, or a single input value for <I>mode</I> =
vector. In the first case, the length of the vector is the number of
inputs. In the second case, the length of the vector is the same as
the length of the input vector. An array is produced if multiple
input values are averaged and <I>mode</I> = vector. The global array has
rows = length of the input vectors and columns = number of inputs.
</P>
<P>If the fix prouduces a scalar or vector, then the scalar and each
element of the vector may be either "intensive" or "extensive". If
the fix produces an array, then all elements in the array will be
either "intensive" or "extensive". Intensive means the value is
independent of the number of atoms in the simulation. Extensive means
the value scales with the number of atoms in the simulation. If a
compute or fix provides the value being time averaged, then the
compute or fix determines whether the value is intensive or extensive;
see the doc page for that compute or fix for further info. Values
produced by a variable are whatever the variable calculates.
</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
@ -217,6 +299,8 @@ ave/atom</A>
</P>
<P><B>Default:</B> none
</P>
<P>The option defaults no file output, ave = one, and start = 0.
<P>The option defaults are mode = scalar, ave = one, start = 0, no file
output, title 1,2,3 = strings as described above, and no off settings
for any input values.
</P>
</HTML>

212
doc/fix_ave_time.txt
View File

@ -19,14 +19,17 @@ Nrepeat = # of times to repeat the Nevery calculation before averaging :l
Nfreq = timestep frequency at which averages are computed :l
one or more values can be listed :l
value = c_ID, c_ID\[N\], f_ID, f_ID\[N\], v_name :l
c_ID = global scalar value calculated by a compute with ID
c_ID\[N\] = Nth component of global vector calculated by a compute with ID
f_ID = global scalar value calculated by a fix with ID
f_ID\[N\] = Nth component of global vector calculated by a fix with ID
c_ID = global scalar or vector calculated by a compute with ID
c_ID\[I\] = Ith component of global vector or Ith column of global array calculated by a compute with ID
f_ID = global scalar or vector calculated by a fix with ID
f_ID\[I\] = Ith component of global vector or Ith column of global array calculated by a fix with ID
v_name = global value calculated by an equal-style variable with name :pre
zero or more keyword/arg pairs may be appended :l
keyword = {file} or {ave} or {start} :l
keyword = {mode} or {file} or {ave} or {start} or {off} or {title1} or {title2} or {title3} :l
{mode} arg = {scalar} or {vector}
scalar = all input values are global scalars
vector = all input values are global vectors
{file} arg = filename
filename = name of file to output time averages to
{ave} args = {one} or {running} or {window M}
@ -34,14 +37,23 @@ keyword = {file} or {ave} or {start} :l
running = output cumulative average of all previous Nfreq steps
window M = output average of M most recent Nfreq steps
{start} args = Nstart
Nstart = start averaging on this timestep :pre
Nstart = start averaging on this timestep
{off} arg = M = do not average this value
M = value # from 1 to Nvalues
{title1} arg = string
string = text to print as 1st line of output file = title
{title2} arg = string
string = text to print as 2nd line of output file
{title3} arg = string
string = text to print as 3rd line of output file, only for vector mode :pre
:ule
[Examples:]
fix 1 all ave/time 100 5 1000 c_myTemp c_thermo_temp file temp.profile
fix 1 all ave/time 100 5 1000 c_thermo_press\[2\] ave window 20
fix 1 all ave/time 1 100 1000 f_indent f_indent\[1\] file temp.indent :pre
fix 1 all ave/time 100 5 1000 c_thermo_press\[2\] ave window 20 &
title1 "My output values"
fix 1 all ave/time 1 100 1000 f_indent f_indent\[1\] file temp.indent off 1 :pre
[Description:]
@ -49,14 +61,13 @@ Calculate one or more instantaneous global quantities every few
timesteps, and average them over longer timescales. The resulting
averages can be used by other "output
commands"_Section_howto.html#4_15 such as "thermo_style
custom"_thermo_style.html, and can also be written to a file. If no
averaging is done, this command is a convenient way to simply write
one or more desired quantities to a separate file.
custom"_thermo_style.html, and can also be written to a file. Note
that if no time averaging is done, this command can simply be used as
a convenient way to output one or more desired quantities to a
separate file.
Each listed value is averaged independently. If written to a file,
then over time, one column of numbers is produced for each value. The
group specified with the command is ignored, since calculations are
performed by computes and fixes which store their own "group"
The group specified with this command is ignored, since calculations
are performed by computes and fixes which store their own "group"
definition,
Each listed value can be the result of a "compute"_compute.html or
@ -77,6 +88,15 @@ individual fixes for info on which ones produce such values.
be used with this fix. Variables of style {atom} cannot be used,
since they produce per-atom values.
The listed values must either be all global scalars or all global
vectors, depending on the setting of the {mode} option. In both
cases, the averaging is performed independently on every input
quantity. I.e. each input value and the elements of each input value
(if it is a vector) are averaged independently.
If {mode} = vector, then all the input values must be vectors of the
same length.
:line
The {Nevery}, {Nrepeat}, and {Nfreq} arguments specify on what
@ -98,49 +118,56 @@ averaging is done; values are simply generated on timesteps
:line
If a value begins with "c_", a compute ID must follow which has been
previously defined in the input script. If no bracketed term is
appended, the global scalar calculated by the compute is used. If a
bracketed term is appended, the Nth vector value calculated by the
compute is used. Note that there is a "compute
reduce"_compute_reduce.html command which can sum per-atom quantities
into a global scalar or vector which can thus be accessed by fix
ave/time. Or it can be a compute defined not in your input script,
but by "thermodynamic output"_thermo_style.html or other fixes such as
"fix nvt"_fix_nvt.html or "fix temp/rescale"_fix_temp_rescale.html.
See the doc pages for these commands which give the IDs of these
computes. Users can also write code for their own compute styles and
"add them to LAMMPS"_Section_modify.html.
previously defined in the input script. If {mode} = scalar, then if
no bracketed term is appended, the global scalar calculated by the
compute is used. If a bracketed term is appended, the Ith element of
the global vector calculated by the compute is used. If {mode} =
vector, then if no bracketed term is appended, the global vector
calculated by the compute is used. If a bracketed term is appended,
the Ith column of the global array calculated by the compute is used.
Note that there is a "compute reduce"_compute_reduce.html command
which can sum per-atom quantities into a global scalar or vector which
can thus be accessed by fix ave/time. Or it can be a compute defined
not in your input script, but by "thermodynamic
output"_thermo_style.html or other fixes such as "fix
nvt"_fix_nvt.html or "fix temp/rescale"_fix_temp_rescale.html. See
the doc pages for these commands which give the IDs of these computes.
Users can also write code for their own compute styles and "add them
to LAMMPS"_Section_modify.html.
If a value begins with "f_", a fix ID must follow which has been
previously defined in the input script. If no bracketed term is
appended, the global scalar calculated by the fix is used. If a
bracketed term is appended, the Nth vector value calculated by the fix
is used. Note that some fixes only produce their values on certain
timesteps, which must be compatible with {Nevery}, else an error will
result. Users can also write code for their own fix styles and "add
them to LAMMPS"_Section_modify.html.
previously defined in the input script. If {mode} = scalar, then if
no bracketed term is appended, the global scalar calculated by the fix
is used. If a bracketed term is appended, the Ith element of the
global vector calculated by the fix is used. If {mode} = vector, then
if no bracketed term is appended, the global vector calculated by the
fix is used. If a bracketed term is appended, the Ith column of the
global array calculated by the fix is used.
Note that some fixes only produce their values on certain timesteps,
which must be compatible with {Nevery}, else an error will result.
Users can also write code for their own fix styles and "add them to
LAMMPS"_Section_modify.html.
If a value begins with "v_", a variable name must follow which has
been previously defined in the input script. Only equal-style
variables can be referenced. See the "variable"_variable.html command
for details. Variables of style {equal} define a formula which can
been previously defined in the input script. Variables can only be
used as input for {mode} = scalar. Only equal-style variables can be
referenced. See the "variable"_variable.html command for details.
Note that variables of style {equal} define a formula which can
reference individual atom properties or thermodynamic keywords, or
they can invoke other computes, fixes, or variables when they are
evaluated, so this is a very general means of generating quantities to
evaluated, so this is a very general means of specifying quantities to
time average.
:line
Additional optional keywords also affect the operation of this fix.
The {file} keyword allows a filename to be specified. Each timestamp,
one quantity is written to the file for each value specified in the
fix ave/time command. The file is in a self-explanatory text format.
The {ave} keyword determines how the scalar and/or vector values
produced every {Nfreq} steps are averaged with values produced on
previous steps that were multiples of {Nfreq}, before they are
accessed by another output command or written to a file.
The {ave} keyword determines how the values produced every {Nfreq}
steps are averaged with values produced on previous steps that were
multiples of {Nfreq}, before they are accessed by another output
command or written to a file.
If the {ave} setting is {one}, then the values produced on timesteps
that are multiples of {Nfreq} are independent of each other; they are
@ -163,9 +190,54 @@ on step 10000 will be the average of the individual values on steps
values if they are not available.
The {start} keyword specifies what timestep averaging will begin on.
The default is step 0. Often this value is 0.0, so setting {start} to
a larger value can avoid including a 0.0 in a running or windowed
average.
The default is step 0. Often input values can be 0.0 at time 0, so
setting {start} to a larger value can avoid including a 0.0 in a
running or windowed average.
The {off} keyword can be used to flag any of the input values. If a
value is flagged, it will not be time averaged. Instead the most
recent input value will always be stored and output. This is useful
if one of more of the inputs produced by a compute or fix or variable
are effectively constant or are simply current values. E.g. they are
being written to a file with other time-averaged values for purposes
of creating well-formatted output.
The {file} keyword allows a filename to be specified. Every {Nfreq}
steps, one quantity or vector of quantities is written to the file for
each input value specified in the fix ave/time command. For {mode} =
scalar, this means a single line is written each time output is
performed. Thus the file ends up to be a series of lines, i.e. one
column of numbers for each input value. For {mode} = vector, an array
of numbers is written each time output is performed. The number of
rows is the length of the input vectors, and the number of columns is
the number of values. Thus the file ends up to be a series of these
array sections.
The {title1} and {title2} and {title3} keywords allow specification of
the strings that will be printed as the first 2 or 3 lines of the
output file, assuming the {file} keyword was used. LAMMPS uses
default values for each of these, so they do not need to be specified.
By default, these header lines are as follows for {mode} = scalar:
# Time-averaged data for fix ID
# TimeStep value1 value2 ... :pre
In the first line, ID is replaced with the fix-ID. In the second line
the values are replaced with the appropriate fields from the fix
ave/time command. There is no third line in the header of the file,
so the {title3} setting is ignored when {mode} = scalar.
By default, these header lines are as follows for {mode} = vector:
# Time-averaged data for fix ID
# TimeStep Number-of-rows
# Row value1 value2 ... :pre
In the first line, ID is replaced with the fix-ID. The second line
describes the two values that are printed at the first of each section
of output. In the third line the values are replaced with the
appropriate fields from the fix ave/time command.
:line
@ -175,20 +247,30 @@ 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.
This fix produces a global scalar or vector which can be accessed by
various "output commands"_Section_howto.html#4_15. A scalar is
produced if only a single quantity is averaged by this fix. If two or
more quantities are averaged, then a vector of values is produced.
The global values can only be accessed on timesteps that are multiples
of {Nfreq} since that is when averaging is performed. Each value
(scalar or vector component) calculated by this fix may be either
"intensive" or "extensive". Intensive means the value is independent
of the number of atoms in the simulation. Extensive means the value
scales with the number of atoms in the simulation. If a compute or
fix provides the value being time averaged, then the compute or fix
determines whether the value is intensive or extensive; see the doc
page for that compute or fix for further info. Values produced by a
variable are whatever the variable calculates.
This fix produces a global scalar or vector or array which can be
accessed by various "output commands"_Section_howto.html#4_15. The
values can only be accessed on timesteps that are multiples of {Nfreq}
since that is when averaging is performed.
A scalar is produced if only a single input value is averaged and
{mode} = scalar. A vector is produced if multiple input values are
averaged for {mode} = scalar, or a single input value for {mode} =
vector. In the first case, the length of the vector is the number of
inputs. In the second case, the length of the vector is the same as
the length of the input vector. An array is produced if multiple
input values are averaged and {mode} = vector. The global array has
rows = length of the input vectors and columns = number of inputs.
If the fix prouduces a scalar or vector, then the scalar and each
element of the vector may be either "intensive" or "extensive". If
the fix produces an array, then all elements in the array will be
either "intensive" or "extensive". Intensive means the value is
independent of the number of atoms in the simulation. Extensive means
the value scales with the number of atoms in the simulation. If a
compute or fix provides the value being time averaged, then the
compute or fix determines whether the value is intensive or extensive;
see the doc page for that compute or fix for further info. Values
produced by a variable are whatever the variable calculates.
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
@ -204,4 +286,6 @@ ave/atom"_fix_ave_atom.html
[Default:] none
The option defaults no file output, ave = one, and start = 0.
The option defaults are mode = scalar, ave = one, start = 0, no file
output, title 1,2,3 = strings as described above, and no off settings
for any input values.