com value = yes or no +com value = yes or no + average value = yes or noExamples:
compute 1 all msd -compute 1 upper msd com yes +compute 1 upper msd com yes average yesDescription:
@@ -49,13 +50,34 @@ averaged over atoms in the group.The slope of the mean-squared displacement (MSD) versus time is proportional to the diffusion coefficient of the diffusing atoms.
-The displacement of an atom is from its original position at the time -the compute command was issued. The value of the displacement will be +
The displacement of an atom is from its reference position. This is +normally the original position at the time +the compute command was issued, unless the average keyword is set to yes. +The value of the displacement will be 0.0 for atoms not in the specified compute group.
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 xhe -displacment of each atom is calcluated. +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.
IMPORTANT NOTE: Initial coordinates are stored in "unwrapped" form, by using the image flags associated with each atom. See the dump @@ -70,7 +92,13 @@ to be continuous when running from a restart file< 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-atom quantities will also have the same ID, and thus be initialized -correctly with time=0 atom coordinates from the restart file. +correctly with atom reference positions from the restart file. +When average is set to yes, then the atom reference positions +are restored correctly, but not the number of samples used +obtain them. As a result, the reference positions from the restart +file are combined with subsequent positions as if they were from a +single sample, instead of many, which will change the values of msd +somewhat.
Output info:
@@ -94,6 +122,6 @@ msd/chunkDefault:
-The option default is com = no. +
The option default are com = no, average = no.