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@ -171,23 +171,21 @@ The value of the displacement will be
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the center-of-mass of the group of atoms is subtracted out before the
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displacment of each atom is calculated.</p>
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<p>If the <em>average</em> option is set to <em>yes</em> then the reference position of
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an atom is based on the average position of that atom,
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corrected for center-of-mass motion if requested.
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The average position
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is a running average over all previous calls to the compute, including the
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current call. So on the first call
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it is current position, on the second call it is the arithmetic average of the
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current position and the position on the first call, and so on.
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Note that when using this option, the precise value of the mean square
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displacement will depend on the number of times the compute is
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called. So, for example, changing the frequency of thermo output may
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change the computed displacement. Also, the precise values will be
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changed if a single simulation is broken up into two parts, using
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either multiple run commands or a restart file. It only makes
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sense to use this option if the atoms are not diffusing, so that
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their average positions relative to the center of mass of the system
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are stationary. The most common case is crystalline solids undergoing
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thermal motion.</p>
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an atom is based on the average position of that atom, corrected for
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center-of-mass motion if requested. The average position is a running
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average over all previous calls to the compute, including the current
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call. So on the first call it is current position, on the second call
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it is the arithmetic average of the current position and the position
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on the first call, and so on. Note that when using this option, the
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precise value of the mean square displacement will depend on the
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number of times the compute is called. So, for example, changing the
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frequency of thermo output may change the computed displacement. Also,
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the precise values will be changed if a single simulation is broken up
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into two parts, using either multiple run commands or a restart
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file. It only makes sense to use this option if the atoms are not
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diffusing, so that their average positions relative to the center of
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mass of the system are stationary. The most common case is crystalline
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solids undergoing thermal motion.</p>
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<div class="admonition note">
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<p class="first admonition-title">Note</p>
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<p class="last">Initial coordinates are stored in “unwrapped” 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
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the center-of-mass of the group of atoms is subtracted out before the
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displacment of each atom is calculated.
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If the {average} option is set to {yes} then the reference position of
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an atom is based on the average position of that atom,
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corrected for center-of-mass motion if requested.
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The average position
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is a running average over all previous calls to the compute, including the
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current call. So on the first call
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it is current position, on the second call it is the arithmetic average of the
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current position and the position on the first call, and so on.
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Note that when using this option, the precise value of the mean square
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displacement will depend on the number of times the compute is
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called. So, for example, changing the frequency of thermo output may
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change the computed displacement. Also, the precise values will be
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changed if a single simulation is broken up into two parts, using
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either multiple run commands or a restart file. It only makes
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sense to use this option if the atoms are not diffusing, so that
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their average positions relative to the center of mass of the system
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are stationary. The most common case is crystalline solids undergoing
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thermal motion.
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If the {average} option is set to {yes} then the reference position of
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an atom is based on the average position of that atom, corrected for
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center-of-mass motion if requested. The average position is a running
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average over all previous calls to the compute, including the current
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call. So on the first call it is current position, on the second call
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it is the arithmetic average of the current position and the position
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on the first call, and so on. Note that when using this option, the
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precise value of the mean square displacement will depend on the
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number of times the compute is called. So, for example, changing the
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frequency of thermo output may change the computed displacement. Also,
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the precise values will be changed if a single simulation is broken up
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into two parts, using either multiple run commands or a restart
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file. It only makes sense to use this option if the atoms are not
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diffusing, so that their average positions relative to the center of
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mass of the system are stationary. The most common case is crystalline
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solids undergoing thermal motion.
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NOTE: Initial coordinates are stored in "unwrapped" form, by using the
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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
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</div>
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<div class="admonition note">
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<p class="first admonition-title">Note</p>
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<p class="last">Unlike the <a class="reference internal" href="compute_msd.html"><em>compute msd</em></a> command, this compute
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does not store the initial center-of-mass coorindates of its molecules
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in a restart file. Thus you cannot continue the MSD per chunk
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calculation of this compute when running from a <a class="reference internal" href="read_restart.html"><em>restart file</em></a>.</p>
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<p class="last">If you want the quantities calculated by this compute to be
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continuous when running from a <a class="reference internal" href="read_restart.html"><em>restart file</em></a>, then
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you should use the same ID for this compute, as in the original run.
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This is so that the fix this compute creates to store per-chunk
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quantities will also have the same ID, and thus be initialized
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correctly with chunk reference positions from the restart file.</p>
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</div>
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<p>The simplest way to output the results of the compute com/msd
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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
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(e.g. to 0) before invoking this compute by using the "set
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image"_set.html command.
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NOTE: Unlike the "compute msd"_compute_msd.html command, this compute
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does not store the initial center-of-mass coorindates of its molecules
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in a restart file. Thus you cannot continue the MSD per chunk
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calculation of this compute when running from a "restart
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file"_read_restart.html.
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NOTE: If you want the quantities calculated by this compute to be
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continuous when running from a "restart file"_read_restart.html, then
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you should use the same ID for this compute, as in the original run.
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This is so that the fix this compute creates to store per-chunk
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quantities will also have the same ID, and thus be initialized
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correctly with chunk reference positions from the restart file.
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The simplest way to output the results of the compute com/msd
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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
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<a class="reference internal" href="read_restart.html"><em>read_restart</em></a> command for info on how to re-specify
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a fix in an input script that reads a restart file, so that the
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operation of the fix continues in an uninterrupted fashion.</p>
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<p>IMPORTANNT NOTE: Because the move positions are a function of the
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current timestep and the initial timestep, you cannot reset the
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timestep to a different value after reading a restart file, if you
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expect a fix move command to work in an uninterrupted fashion.</p>
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<div class="admonition note">
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<p class="first admonition-title">Note</p>
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<p class="last">Because the move positions are a function of the current
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timestep and the initial timestep, you cannot reset the timestep to a
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different value after reading a restart file, if you expect a fix move
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command to work in an uninterrupted fashion.</p>
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</div>
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<p>None of the <a class="reference internal" href="fix_modify.html"><em>fix_modify</em></a> options are relevant to this
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fix.</p>
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<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
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a fix in an input script that reads a restart file, so that the
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operation of the fix continues in an uninterrupted fashion.
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IMPORTANNT NOTE: Because the move positions are a function of the
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current timestep and the initial timestep, you cannot reset the
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timestep to a different value after reading a restart file, if you
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expect a fix move command to work in an uninterrupted fashion.
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NOTE: Because the move positions are a function of the current
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timestep and the initial timestep, you cannot reset the timestep to a
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different value after reading a restart file, if you expect a fix move
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command to work in an uninterrupted fashion.
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None of the "fix_modify"_fix_modify.html options are relevant to this
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fix.
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