git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14429 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2016-01-12 16:27:19 +00:00
parent fbd03b390f
commit b9ab7a0cd5
7 changed files with 55 additions and 53 deletions

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@ -171,23 +171,21 @@ The value of the displacement will be
the center-of-mass of the group of atoms is subtracted out before the
displacment of each atom is calculated.</p>
<p>If the <em>average</em> option is set to <em>yes</em> then the reference position of
an atom is based on the average position of that atom,
corrected for center-of-mass motion if requested.
The average position
is a running average over all previous calls to the compute, including the
current call. So on the first call
it is current position, on the second call it is the arithmetic average of the
current position and the position on the first call, and so on.
Note that when using this option, the precise value of the mean square
displacement will depend on the number of times the compute is
called. So, for example, changing the frequency of thermo output may
change the computed displacement. Also, the precise values will be
changed if a single simulation is broken up into two parts, using
either multiple run commands or a restart file. It only makes
sense to use this option if the atoms are not diffusing, so that
their average positions relative to the center of mass of the system
are stationary. The most common case is crystalline solids undergoing
thermal motion.</p>
an atom is based on the average position of that atom, corrected for
center-of-mass motion if requested. The average position is a running
average over all previous calls to the compute, including the current
call. So on the first call it is current position, on the second call
it is the arithmetic average of the current position and the position
on the first call, and so on. Note that when using this option, the
precise value of the mean square displacement will depend on the
number of times the compute is called. So, for example, changing the
frequency of thermo output may change the computed displacement. Also,
the precise values will be changed if a single simulation is broken up
into two parts, using either multiple run commands or a restart
file. It only makes sense to use this option if the atoms are not
diffusing, so that their average positions relative to the center of
mass of the system are stationary. The most common case is crystalline
solids undergoing thermal motion.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">Initial coordinates are stored in &#8220;unwrapped&#8221; form, by using the

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@ -52,24 +52,22 @@ If the {com} option is set to {yes} then the effect of any drift in
the center-of-mass of the group of atoms is subtracted out before the
displacment of each atom is calculated.
If the {average} option is set to {yes} then the reference position of
an atom is based on the average position of that atom,
corrected for center-of-mass motion if requested.
The average position
is a running average over all previous calls to the compute, including the
current call. So on the first call
it is current position, on the second call it is the arithmetic average of the
current position and the position on the first call, and so on.
Note that when using this option, the precise value of the mean square
displacement will depend on the number of times the compute is
called. So, for example, changing the frequency of thermo output may
change the computed displacement. Also, the precise values will be
changed if a single simulation is broken up into two parts, using
either multiple run commands or a restart file. It only makes
sense to use this option if the atoms are not diffusing, so that
their average positions relative to the center of mass of the system
are stationary. The most common case is crystalline solids undergoing
thermal motion.
If the {average} option is set to {yes} then the reference position of
an atom is based on the average position of that atom, corrected for
center-of-mass motion if requested. The average position is a running
average over all previous calls to the compute, including the current
call. So on the first call it is current position, on the second call
it is the arithmetic average of the current position and the position
on the first call, and so on. Note that when using this option, the
precise value of the mean square displacement will depend on the
number of times the compute is called. So, for example, changing the
frequency of thermo output may change the computed displacement. Also,
the precise values will be changed if a single simulation is broken up
into two parts, using either multiple run commands or a restart
file. It only makes sense to use this option if the atoms are not
diffusing, so that their average positions relative to the center of
mass of the system are stationary. The most common case is crystalline
solids undergoing thermal motion.
NOTE: Initial coordinates are stored in "unwrapped" form, by using the
image flags associated with each atom. See the "dump

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@ -203,10 +203,12 @@ how they are set for each atom. You can reset the image flags
</div>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">Unlike the <a class="reference internal" href="compute_msd.html"><em>compute msd</em></a> command, this compute
does not store the initial center-of-mass coorindates of its molecules
in a restart file. Thus you cannot continue the MSD per chunk
calculation of this compute when running from a <a class="reference internal" href="read_restart.html"><em>restart file</em></a>.</p>
<p class="last">If you want the quantities calculated by this compute to be
continuous when running from a <a class="reference internal" href="read_restart.html"><em>restart file</em></a>, then
you should use the same ID for this compute, as in the original run.
This is so that the fix this compute creates to store per-chunk
quantities will also have the same ID, and thus be initialized
correctly with chunk reference positions from the restart file.</p>
</div>
<p>The simplest way to output the results of the compute com/msd
calculation to a file is to use the <a class="reference internal" href="fix_ave_time.html"><em>fix ave/time</em></a>

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@ -84,11 +84,12 @@ how they are set for each atom. You can reset the image flags
(e.g. to 0) before invoking this compute by using the "set
image"_set.html command.
NOTE: Unlike the "compute msd"_compute_msd.html command, this compute
does not store the initial center-of-mass coorindates of its molecules
in a restart file. Thus you cannot continue the MSD per chunk
calculation of this compute when running from a "restart
file"_read_restart.html.
NOTE: If you want the quantities calculated by this compute to be
continuous when running from a "restart file"_read_restart.html, then
you should use the same ID for this compute, as in the original run.
This is so that the fix this compute creates to store per-chunk
quantities will also have the same ID, and thus be initialized
correctly with chunk reference positions from the restart file.
The simplest way to output the results of the compute com/msd
calculation to a file is to use the "fix ave/time"_fix_ave_time.html

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@ -310,10 +310,13 @@ the motion can be continuous in a restarted simulation. See the
<a class="reference internal" href="read_restart.html"><em>read_restart</em></a> command for info on how to re-specify
a fix in an input script that reads a restart file, so that the
operation of the fix continues in an uninterrupted fashion.</p>
<p>IMPORTANNT NOTE: Because the move positions are a function of the
current timestep and the initial timestep, you cannot reset the
timestep to a different value after reading a restart file, if you
expect a fix move command to work in an uninterrupted fashion.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">Because the move positions are a function of the current
timestep and the initial timestep, you cannot reset the timestep to a
different value after reading a restart file, if you expect a fix move
command to work in an uninterrupted fashion.</p>
</div>
<p>None of the <a class="reference internal" href="fix_modify.html"><em>fix_modify</em></a> options are relevant to this
fix.</p>
<p>This fix produces a per-atom array which can be accessed by various

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@ -191,10 +191,10 @@ the motion can be continuous in a restarted simulation. See the
a fix in an input script that reads a restart file, so that the
operation of the fix continues in an uninterrupted fashion.
IMPORTANNT NOTE: Because the move positions are a function of the
current timestep and the initial timestep, you cannot reset the
timestep to a different value after reading a restart file, if you
expect a fix move command to work in an uninterrupted fashion.
NOTE: Because the move positions are a function of the current
timestep and the initial timestep, you cannot reset the timestep to a
different value after reading a restart file, if you expect a fix move
command to work in an uninterrupted fashion.
None of the "fix_modify"_fix_modify.html options are relevant to this
fix.

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