git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1060 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
@ -13,43 +13,68 @@
|
||||
</H3>
|
||||
<P><B>Syntax:</B>
|
||||
</P>
|
||||
<PRE>fix ID group-ID ave/time Nevery Nrepeat Nfreq style ID type file
|
||||
<PRE>fix ID group-ID ave/time Nevery Nrepeat Nfreq style ID keyword args ...
|
||||
</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 computed
|
||||
<LI>style = <I>compute</I> or <I>fix</I>
|
||||
<LI>ID = ID of compute or fix that performs the calculation
|
||||
<LI>type = 0 for scalar quantity, 1 for vector quantity, 2 for both
|
||||
<LI>file = filename to write results to (NULL = no file)
|
||||
<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 computed
|
||||
|
||||
<LI>style = <I>compute</I> or <I>fix</I>
|
||||
|
||||
<LI>ID = ID of compute or fix that performs the calculation
|
||||
|
||||
<LI>zero or more keyword/arg pairs may be appended
|
||||
|
||||
<LI>keyword = <I>type</I> or <I>file</I> or <I>ave</I>
|
||||
|
||||
<PRE> <I>type</I> arg = <I>scalar</I> or <I>vector</I> or <I>both</I>
|
||||
scalar = single scalar value from fix or compute
|
||||
vector = vector of values from fix or compute
|
||||
both = both a single value and vector of values from fix or compute
|
||||
<I>file</I> arg = filename
|
||||
filename = file to write results to
|
||||
<I>ave</I> args = <I>one</I> or <I>running</I> or <I>window M</I>
|
||||
one = output new average value every Nfreq steps
|
||||
running = output cummulative average of all previous Nfreq steps
|
||||
window M = output average of M most recent Nfreq steps
|
||||
</PRE>
|
||||
|
||||
</UL>
|
||||
<P><B>Examples:</B>
|
||||
</P>
|
||||
<PRE>fix 1 all ave/time 100 5 1000 compute myTemp 0 temp.stats
|
||||
fix 1 all ave/time 1 100 1000 fix indenter 0 temp.indent
|
||||
<PRE>fix 1 all ave/time 100 5 1000 compute myTemp
|
||||
fix 1 all ave/time 100 5 1000 compute myTemp ave window 20
|
||||
fix 1 all ave/time 1 100 1000 fix indenter value both file temp.indent
|
||||
</PRE>
|
||||
<P><B>Description:</B>
|
||||
</P>
|
||||
<P>Calculate one or more instantaneous quantities every few timesteps,
|
||||
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>.
|
||||
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 also written to a file.
|
||||
</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 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
|
||||
quantities cannot be averaged 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>Since the calculation is performed by the compute or fix which stores
|
||||
its own "group" definition, the group specified as part of the fix
|
||||
ave/time command is ignored.
|
||||
</P>
|
||||
<P>For style <I>compute</I> the <I>ID</I> specifies a <A HREF = "compute.html">compute</A> which
|
||||
calculates the desired property. The compute must be a "global"
|
||||
compute that calculates one or more global properties rather than a
|
||||
"per-atom" compute. The fix must be previously defined in the input
|
||||
script. Or it can be a compute defined by <A HREF = "thermo_style.html">thermodynamic
|
||||
"per-atom" compute. The compute must be previously defined in the
|
||||
input script. Or it can be a compute defined 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>. Users
|
||||
can write code for their own compute styles and <A HREF = "Section_modify.html">add them to
|
||||
@ -62,35 +87,61 @@ individual fix commands for details. The fix must be previously
|
||||
defined in the input script. Users can write code for their own fix
|
||||
styles and <A HREF = "Section_modify.html">add them to LAMMPS</A>.
|
||||
</P>
|
||||
<P>The <I>Nevery</I>, <I>Nrepeat</I>, and <I>Nfreq</I> arguments specify how the
|
||||
property will be time-averaged. The final averaged value(s) are
|
||||
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 on timestep 100. Similary for timesteps
|
||||
190,192,194,196,198,200 on timestep 200, etc.
|
||||
<P>The <I>Nevery</I>, <I>Nrepeat</I>, and <I>Nfreq</I> arguments specify on what
|
||||
timesteps the property will be evaluated in order to contribute to the
|
||||
average. The final averaged value(s) are 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.
|
||||
<I>Nfreq</I> must be a multiple of <I>Nevery</I> and <I>Nevery</I> must be non-zero
|
||||
even if <I>Nrepeat</I> is 1.
|
||||
</P>
|
||||
<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. If
|
||||
file output is specified, all N values are written to the file at each
|
||||
output.
|
||||
<P>For example, 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
|
||||
on timestep 100. Similary for timesteps 190,192,194,196,198,200 on
|
||||
timestep 200, etc.
|
||||
</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
|
||||
ave/time command is ignored.
|
||||
<HR>
|
||||
|
||||
<P>Additional optional keywords also affect the averaging.
|
||||
</P>
|
||||
<P>If the style is <I>compute</I> and the compute calculates pressure, it will
|
||||
cause the force computations performed by LAMMPS (pair, bond, angle,
|
||||
etc) to calculate virial terms each Nevery timesteps. If this is more
|
||||
frequent than thermodynamic output, this adds extra cost to a
|
||||
simulation. However, if a constant pressure simulation is being run
|
||||
(<A HREF = "fix_npt.html">fix npt</A> or <A HREF = "fix_nph.html">fix nph</A>), LAMMPS is already
|
||||
calculating virial terms for the pressure every timestep.
|
||||
<P>The <I>type</I> keyword chooses whether the scalar and/or vector quantities
|
||||
produced by the compute or fix are used. For a setting of <I>scalar</I> a
|
||||
single global value is used. For a setting of <I>vector</I> N global
|
||||
values are used, where N is defined by the compute or fix, e.g. 6
|
||||
pressure tensor components. For a setting of <I>both</I>, both a scalar
|
||||
the vector values are used. When vectors are used, each of the N
|
||||
values is averaged independently.
|
||||
</P>
|
||||
<P>The <I>file</I> keyword allows a filename to be specified. The scalar
|
||||
and/or N vector quantities are written to the file 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 each other 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
|
||||
output as-is without further averaging.
|
||||
</P>
|
||||
<P>If the <I>ave</I> setting is <I>running</I>, then the values produced on
|
||||
timesteps that are multiples of <I>Nfreq</I> are summed and averaged in a
|
||||
cummulative sense before being output. Each output value is thus the
|
||||
average of the value on that timestep with all preceeding values.
|
||||
This running average begins when the fix is defined; it can only be
|
||||
restarted by deleting the fix via the <A HREF = "unfix.html">unfix</A> command, or
|
||||
re-defining the fix by re-specifying it.
|
||||
</P>
|
||||
<P>If the <I>ave</I> setting is <I>window</I>, then the values produced on
|
||||
timesteps that are multiples of <I>Nfreq</I> are summed and averaged within
|
||||
a moving "window" of time, so that the last M values are used to
|
||||
produce the output. E.g. if M = 3 and Nfreq = 1000, then the output
|
||||
on step 10000 will be the average of the individual values on steps
|
||||
8000,9000,10000. Outputs on early steps will average over less than M
|
||||
values if they are not available.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
|
||||
</P>
|
||||
<P>No information about this fix is written to <A HREF = "restart.html">binary restart
|
||||
@ -101,13 +152,22 @@ are relevant to this fix.
|
||||
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.
|
||||
averaging is performed.
|
||||
</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><B>Restrictions:</B>
|
||||
</P>
|
||||
<P>If the style is <I>compute</I> and the specified compute calculates
|
||||
pressure, it will cause the force computations performed by LAMMPS
|
||||
(pair, bond, angle, etc) to calculate virial terms each Nevery
|
||||
timesteps. If this is more frequent than thermodynamic output, this
|
||||
adds extra cost to a simulation. However, if a constant pressure
|
||||
simulation is being run (<A HREF = "fix_npt.html">fix npt</A> or <A HREF = "fix_nph.html">fix
|
||||
nph</A>), LAMMPS is already calculating virial terms for the
|
||||
pressure every timestep.
|
||||
</P>
|
||||
<P><B>Related commands:</B>
|
||||
</P>
|
||||
@ -116,4 +176,6 @@ ave/spatial</A>
|
||||
</P>
|
||||
<P><B>Default:</B> none
|
||||
</P>
|
||||
<P>The option defaults are style = scalar, no file output, and ave = one.
|
||||
</P>
|
||||
</HTML>
|
||||
|
||||
@ -10,43 +10,59 @@ fix ave/time command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
fix ID group-ID ave/time Nevery Nrepeat Nfreq style ID type file :pre
|
||||
fix ID group-ID ave/time Nevery Nrepeat Nfreq style ID keyword args ... :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 computed
|
||||
style = {compute} or {fix}
|
||||
ID = ID of compute or fix that performs the calculation
|
||||
type = 0 for scalar quantity, 1 for vector quantity, 2 for both
|
||||
file = filename to write results to (NULL = no file) :ul
|
||||
ID, group-ID are documented in "fix"_fix.html command :ulb,l
|
||||
ave/time = 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 computed :l
|
||||
style = {compute} or {fix} :l
|
||||
ID = ID of compute or fix that performs the calculation :l
|
||||
|
||||
zero or more keyword/arg pairs may be appended :l
|
||||
keyword = {type} or {file} or {ave} :l
|
||||
{type} arg = {scalar} or {vector} or {both}
|
||||
scalar = single scalar value from fix or compute
|
||||
vector = vector of values from fix or compute
|
||||
both = both a single value and vector of values from fix or compute
|
||||
{file} arg = filename
|
||||
filename = file to write results to
|
||||
{ave} args = {one} or {running} or {window M}
|
||||
one = output new average value every Nfreq steps
|
||||
running = output cummulative average of all previous Nfreq steps
|
||||
window M = output average of M most recent Nfreq steps :pre
|
||||
:ule
|
||||
|
||||
[Examples:]
|
||||
|
||||
fix 1 all ave/time 100 5 1000 compute myTemp 0 temp.stats
|
||||
fix 1 all ave/time 1 100 1000 fix indenter 0 temp.indent :pre
|
||||
fix 1 all ave/time 100 5 1000 compute myTemp
|
||||
fix 1 all ave/time 100 5 1000 compute myTemp ave window 20
|
||||
fix 1 all ave/time 1 100 1000 fix indenter value both file temp.indent :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Calculate one or more instantaneous quantities every few timesteps,
|
||||
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.
|
||||
be used by other "output commands"_Section_howto.html#4_15 such as
|
||||
"thermo_style custom"_thermo_style.html, and also written to a file.
|
||||
|
||||
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 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
|
||||
quantities cannot be averaged 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.
|
||||
|
||||
Since the calculation is performed by the compute or fix which stores
|
||||
its own "group" definition, the group specified as part of the fix
|
||||
ave/time command is ignored.
|
||||
|
||||
For style {compute} the {ID} specifies a "compute"_compute.html which
|
||||
calculates the desired property. The compute must be a "global"
|
||||
compute that calculates one or more global properties rather than a
|
||||
"per-atom" compute. The fix must be previously defined in the input
|
||||
script. Or it can be a compute defined by "thermodynamic
|
||||
"per-atom" compute. The compute must be previously defined in the
|
||||
input script. Or it can be a compute defined by "thermodynamic
|
||||
output"_thermo_style.html or other fixes such as "fix
|
||||
nvt"_fix_nvt.html or "fix temp/rescale"_fix_temp_rescale.html. Users
|
||||
can write code for their own compute styles and "add them to
|
||||
@ -59,34 +75,60 @@ individual fix commands for details. The fix must be previously
|
||||
defined in the input script. Users can write code for their own fix
|
||||
styles and "add them to LAMMPS"_Section_modify.html.
|
||||
|
||||
The {Nevery}, {Nrepeat}, and {Nfreq} arguments specify how the
|
||||
property will be time-averaged. The final averaged value(s) are
|
||||
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 on timestep 100. Similary for timesteps
|
||||
190,192,194,196,198,200 on timestep 200, etc.
|
||||
The {Nevery}, {Nrepeat}, and {Nfreq} arguments specify on what
|
||||
timesteps the property will be evaluated in order to contribute to the
|
||||
average. The final averaged value(s) are computed every {Nfreq}
|
||||
timesteps. The average is over {Nrepeat} values, computed in the
|
||||
preceeding portion of the simulation every {Nevery} timesteps.
|
||||
{Nfreq} must be a multiple of {Nevery} and {Nevery} must be non-zero
|
||||
even if {Nrepeat} is 1.
|
||||
|
||||
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. If
|
||||
file output is specified, all N values are written to the file at each
|
||||
output.
|
||||
For example, 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
|
||||
on timestep 100. Similary for timesteps 190,192,194,196,198,200 on
|
||||
timestep 200, etc.
|
||||
|
||||
Since the calculation is performed by the compute or fix which stores
|
||||
its own "group" definition, the group specified for with the fix
|
||||
ave/time command is ignored.
|
||||
:line
|
||||
|
||||
If the style is {compute} and the compute calculates pressure, it will
|
||||
cause the force computations performed by LAMMPS (pair, bond, angle,
|
||||
etc) to calculate virial terms each Nevery timesteps. If this is more
|
||||
frequent than thermodynamic output, this adds extra cost to a
|
||||
simulation. However, if a constant pressure simulation is being run
|
||||
("fix npt"_fix_npt.html or "fix nph"_fix_nph.html), LAMMPS is already
|
||||
calculating virial terms for the pressure every timestep.
|
||||
Additional optional keywords also affect the averaging.
|
||||
|
||||
The {type} keyword chooses whether the scalar and/or vector quantities
|
||||
produced by the compute or fix are used. For a setting of {scalar} a
|
||||
single global value is used. For a setting of {vector} N global
|
||||
values are used, where N is defined by the compute or fix, e.g. 6
|
||||
pressure tensor components. For a setting of {both}, both a scalar
|
||||
the vector values are used. When vectors are used, each of the N
|
||||
values is averaged independently.
|
||||
|
||||
The {file} keyword allows a filename to be specified. The scalar
|
||||
and/or N vector quantities are written to the file in a
|
||||
self-explanatory text format.
|
||||
|
||||
The {ave} keyword determines how the scalar and/or vector values
|
||||
produced every {Nfreq} steps are averaged with each other 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
|
||||
output as-is without further averaging.
|
||||
|
||||
If the {ave} setting is {running}, then the values produced on
|
||||
timesteps that are multiples of {Nfreq} are summed and averaged in a
|
||||
cummulative sense before being output. Each output value is thus the
|
||||
average of the value on that timestep with all preceeding values.
|
||||
This running average begins when the fix is defined; it can only be
|
||||
restarted by deleting the fix via the "unfix"_unfix.html command, or
|
||||
re-defining the fix by re-specifying it.
|
||||
|
||||
If the {ave} setting is {window}, then the values produced on
|
||||
timesteps that are multiples of {Nfreq} are summed and averaged within
|
||||
a moving "window" of time, so that the last M values are used to
|
||||
produce the output. E.g. if M = 3 and Nfreq = 1000, then the output
|
||||
on step 10000 will be the average of the individual values on steps
|
||||
8000,9000,10000. Outputs on early steps will average over less than M
|
||||
values if they are not available.
|
||||
|
||||
:line
|
||||
|
||||
[Restart, fix_modify, output, run start/stop, minimize info:]
|
||||
|
||||
@ -98,13 +140,22 @@ 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.
|
||||
averaging is performed.
|
||||
|
||||
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
|
||||
[Restrictions:]
|
||||
|
||||
If the style is {compute} and the specified compute calculates
|
||||
pressure, it will cause the force computations performed by LAMMPS
|
||||
(pair, bond, angle, etc) to calculate virial terms each Nevery
|
||||
timesteps. If this is more frequent than thermodynamic output, this
|
||||
adds extra cost to a simulation. However, if a constant pressure
|
||||
simulation is being run ("fix npt"_fix_npt.html or "fix
|
||||
nph"_fix_nph.html), LAMMPS is already calculating virial terms for the
|
||||
pressure every timestep.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
@ -112,3 +163,5 @@ minimization"_minimize.html.
|
||||
ave/spatial"_fix_ave_spatial.html
|
||||
|
||||
[Default:] none
|
||||
|
||||
The option defaults are style = scalar, no file output, and ave = one.
|
||||
|
||||
@ -65,6 +65,12 @@ the shear velocity profile is the viscosity of the fluid, in
|
||||
appopriate units. See the <A HREF = "#Muller-Plathe">Muller-Plathe paper</A> for
|
||||
details.
|
||||
</P>
|
||||
<P>IMPORTANT NOTE: After equilibration, if the velocity profile you
|
||||
observe is not linear, then you are likely swapping momentum too
|
||||
frequently and are not in a regime of linear response. In this case
|
||||
you cannot accurately infer a viscosity and should try increasing
|
||||
the Nevery parameter.
|
||||
</P>
|
||||
<P>An alternative method for calculating a viscosity is to run a NEMD
|
||||
simulation, as described in <A HREF = "Section_howto.html#4_13">this section</A> of
|
||||
the manual. NEMD simulations deform the simmulation box via the <A HREF = "fix_deform.html">fix
|
||||
|
||||
@ -62,6 +62,12 @@ the shear velocity profile is the viscosity of the fluid, in
|
||||
appopriate units. See the "Muller-Plathe paper"_#Muller-Plathe for
|
||||
details.
|
||||
|
||||
IMPORTANT NOTE: After equilibration, if the velocity profile you
|
||||
observe is not linear, then you are likely swapping momentum too
|
||||
frequently and are not in a regime of linear response. In this case
|
||||
you cannot accurately infer a viscosity and should try increasing
|
||||
the Nevery parameter.
|
||||
|
||||
An alternative method for calculating a viscosity is to run a NEMD
|
||||
simulation, as described in "this section"_Section_howto.html#4_13 of
|
||||
the manual. NEMD simulations deform the simmulation box via the "fix
|
||||
|
||||
@ -26,8 +26,6 @@
|
||||
<I>format</I> values = <I>int</I> string or <I>float</I> string or M string
|
||||
M = integer from 1 to N, where N = # of quantities being printed
|
||||
string = C-style format string
|
||||
<I>window</I> value = N
|
||||
N = number of previous print-outs to average over
|
||||
<I>temp</I> value = compute ID that calculates a temperature
|
||||
<I>press</I> value = compute ID that calculates a pressure
|
||||
<I>drot</I> value = compute ID that calculates rotational energy for dipolar atoms
|
||||
@ -84,10 +82,6 @@ printed in each output line, the 5th column of output in this case.
|
||||
If the format for a specific column has been set, it will take
|
||||
precedent over the <I>int</I> or <I>float</I> setting.
|
||||
</P>
|
||||
<P>The <I>window</I> keyword sets the number of previous thermodynamic screen
|
||||
outputs over which <A HREF = "thermo_style.html">thermo_style custom</A> <I>ave</I>
|
||||
quantities are averaged when printed.
|
||||
</P>
|
||||
<P>The <I>temp</I> keyword is used to determine how thermodynamic temperature
|
||||
is calculated, which is used by all thermo quantities that require a
|
||||
temperature ("temp", "press", "ke", "etotal", "enthalpy", "pxx etc",
|
||||
@ -136,8 +130,7 @@ default.
|
||||
</P>
|
||||
<P>The option defaults are lost = error, norm = yes for unit style of
|
||||
<I>lj</I>, norm = no for unit style of <I>real</I> and <I>metal</I>, flush = no,
|
||||
window = 10, temp/press/drot/grot = compute IDs defined by
|
||||
thermo_style.
|
||||
temp/press/drot/grot = compute IDs defined by thermo_style.
|
||||
</P>
|
||||
<P>The defaults for the line and format options depend on the thermo
|
||||
style. For styles "one", "granular", and "custom" the line and format
|
||||
|
||||
@ -21,8 +21,6 @@ keyword = {lost} or {norm} or {flush} or {line} or {format} or {temp} or {press}
|
||||
{format} values = {int} string or {float} string or M string
|
||||
M = integer from 1 to N, where N = # of quantities being printed
|
||||
string = C-style format string
|
||||
{window} value = N
|
||||
N = number of previous print-outs to average over
|
||||
{temp} value = compute ID that calculates a temperature
|
||||
{press} value = compute ID that calculates a pressure
|
||||
{drot} value = compute ID that calculates rotational energy for dipolar atoms
|
||||
@ -78,10 +76,6 @@ printed in each output line, the 5th column of output in this case.
|
||||
If the format for a specific column has been set, it will take
|
||||
precedent over the {int} or {float} setting.
|
||||
|
||||
The {window} keyword sets the number of previous thermodynamic screen
|
||||
outputs over which "thermo_style custom"_thermo_style.html {ave}
|
||||
quantities are averaged when printed.
|
||||
|
||||
The {temp} keyword is used to determine how thermodynamic temperature
|
||||
is calculated, which is used by all thermo quantities that require a
|
||||
temperature ("temp", "press", "ke", "etotal", "enthalpy", "pxx etc",
|
||||
@ -130,8 +124,7 @@ default.
|
||||
|
||||
The option defaults are lost = error, norm = yes for unit style of
|
||||
{lj}, norm = no for unit style of {real} and {metal}, flush = no,
|
||||
window = 10, temp/press/drot/grot = compute IDs defined by
|
||||
thermo_style.
|
||||
temp/press/drot/grot = compute IDs defined by thermo_style.
|
||||
|
||||
The defaults for the line and format options depend on the thermo
|
||||
style. For styles "one", "granular", and "custom" the line and format
|
||||
|
||||
@ -30,7 +30,6 @@
|
||||
vol, lx, ly, lz, xlo, xhi, ylo, yhi, zlo, zhi,
|
||||
pxx, pyy, pzz, pxy, pxz, pyz
|
||||
drot, grot,
|
||||
tave, pave, eave, peave,
|
||||
c_ID, c_ID[n], f_ID, f_ID[n], v_name
|
||||
step = timestep
|
||||
atoms = # of atoms
|
||||
@ -57,7 +56,6 @@
|
||||
pxx,pyy,pzz,pxy,pxz,pyz = 6 components of pressure tensor
|
||||
drot = rotational energy of dipolar atoms
|
||||
grot = rotational energy of granular atoms
|
||||
tave, pave, eave, peave = time-averaged temp, press, etotal, pe
|
||||
c_ID = scalar quantity calculated by a compute identified by its ID
|
||||
c_ID[N] = Nth vector quantity calculated by a compute identified by its ID
|
||||
f_ID = scalar quantity calculated by a fix identified by its ID
|
||||
@ -103,6 +101,12 @@ outputting essentially any desired quantity as a simulation proceeds.
|
||||
<P>All styles except <I>custom</I> have <I>vol</I> appended to their list of
|
||||
outputs if the simulation box volume changes during the simulation.
|
||||
</P>
|
||||
<P>The values printed by the various keywords are instantaneous values,
|
||||
calculated on the current timestep. Time-averaged quantities, which
|
||||
include values from previous timesteps, can be output by using the
|
||||
f_ID keyword and accessing a fix that does time-averaging such as the
|
||||
<A HREF = "fix_ave_time.html">fix ave/time</A> command.
|
||||
</P>
|
||||
<P>Options invoked by the <A HREF = "thermo_modify.html">thermo_modify</A> command can
|
||||
be used to set the one- or multi-line format of the print-out, the
|
||||
normalization of energy quantities (total or per-atom), and the
|
||||
@ -117,9 +121,9 @@ use the thermo_modify command after it.
|
||||
<HR>
|
||||
|
||||
<P>Several of the thermodynamic quantities require a temperature to be
|
||||
computed: "temp", "press", "ke", "etotal", "enthalpy", "pxx etc",
|
||||
"tave", "pave". By default this is done by using the "thermo_temp"
|
||||
compute which is created by LAMMPS as if this command had been issued:
|
||||
computed: "temp", "press", "ke", "etotal", "enthalpy", "pxx etc". By
|
||||
default this is done by using the "thermo_temp" compute which is
|
||||
created by LAMMPS as if this command had been issued:
|
||||
</P>
|
||||
<PRE>compute thermo_temp all temp
|
||||
</PRE>
|
||||
@ -193,11 +197,6 @@ is included in <I>evdwl</I>, <I>pe</I>, and <I>etotal</I>, and the corresponding
|
||||
correction to the pressure is included in <I>press</I> and <I>pxx</I>, <I>pyy</I>,
|
||||
etc.
|
||||
</P>
|
||||
<P>The time-averaged keywords <I>tave, pave, eave, peave</I> are averaged over
|
||||
the last N thermodynamic outputs to the screen (not the last N
|
||||
timesteps), where N is the value set by the <I>window</I> option of the
|
||||
<A HREF = "thermo_modify.html">thermo_modify</A> command (N = 10 by default).
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<P>The <I>c_ID</I> and <I>c_ID[N]</I> keywords allow global scalar or vector
|
||||
|
||||
@ -25,7 +25,6 @@ args = list of arguments for a particular style :l
|
||||
vol, lx, ly, lz, xlo, xhi, ylo, yhi, zlo, zhi,
|
||||
pxx, pyy, pzz, pxy, pxz, pyz
|
||||
drot, grot,
|
||||
tave, pave, eave, peave,
|
||||
c_ID, c_ID\[n\], f_ID, f_ID\[n\], v_name
|
||||
step = timestep
|
||||
atoms = # of atoms
|
||||
@ -52,7 +51,6 @@ args = list of arguments for a particular style :l
|
||||
pxx,pyy,pzz,pxy,pxz,pyz = 6 components of pressure tensor
|
||||
drot = rotational energy of dipolar atoms
|
||||
grot = rotational energy of granular atoms
|
||||
tave, pave, eave, peave = time-averaged temp, press, etotal, pe
|
||||
c_ID = scalar quantity calculated by a compute identified by its ID
|
||||
c_ID\[N\] = Nth vector quantity calculated by a compute identified by its ID
|
||||
f_ID = scalar quantity calculated by a fix identified by its ID
|
||||
@ -97,6 +95,12 @@ outputting essentially any desired quantity as a simulation proceeds.
|
||||
All styles except {custom} have {vol} appended to their list of
|
||||
outputs if the simulation box volume changes during the simulation.
|
||||
|
||||
The values printed by the various keywords are instantaneous values,
|
||||
calculated on the current timestep. Time-averaged quantities, which
|
||||
include values from previous timesteps, can be output by using the
|
||||
f_ID keyword and accessing a fix that does time-averaging such as the
|
||||
"fix ave/time"_fix_ave_time.html command.
|
||||
|
||||
Options invoked by the "thermo_modify"_thermo_modify.html command can
|
||||
be used to set the one- or multi-line format of the print-out, the
|
||||
normalization of energy quantities (total or per-atom), and the
|
||||
@ -111,9 +115,9 @@ use the thermo_modify command after it.
|
||||
:line
|
||||
|
||||
Several of the thermodynamic quantities require a temperature to be
|
||||
computed: "temp", "press", "ke", "etotal", "enthalpy", "pxx etc",
|
||||
"tave", "pave". By default this is done by using the "thermo_temp"
|
||||
compute which is created by LAMMPS as if this command had been issued:
|
||||
computed: "temp", "press", "ke", "etotal", "enthalpy", "pxx etc". By
|
||||
default this is done by using the "thermo_temp" compute which is
|
||||
created by LAMMPS as if this command had been issued:
|
||||
|
||||
compute thermo_temp all temp :pre
|
||||
|
||||
@ -187,11 +191,6 @@ is included in {evdwl}, {pe}, and {etotal}, and the corresponding tail
|
||||
correction to the pressure is included in {press} and {pxx}, {pyy},
|
||||
etc.
|
||||
|
||||
The time-averaged keywords {tave, pave, eave, peave} are averaged over
|
||||
the last N thermodynamic outputs to the screen (not the last N
|
||||
timesteps), where N is the value set by the {window} option of the
|
||||
"thermo_modify"_thermo_modify.html command (N = 10 by default).
|
||||
|
||||
:line
|
||||
|
||||
The {c_ID} and {c_ID\[N\]} keywords allow global scalar or vector
|
||||
|
||||
Reference in New Issue
Block a user