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

doc/compute_msd.html

@@ -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

doc/compute_msd.txt

@@ -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

doc/compute_msd_chunk.html

@@ -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>

doc/compute_msd_chunk.txt

@@ -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

doc/fix_move.html

@@ -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

doc/fix_move.txt

@@ -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.