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Plugin only reads timeindependent species dataset, mass dataset, charge dataset #24

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jonaslandsgesell opened this issue Dec 19, 2016 · 2 comments
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@jonaslandsgesell
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timedependent datasets are ignored so far.

@jonaslandsgesell
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Since VMD itself has the limitation of not being able to deal with timedependent properties this is a won't fix issue:

Hi!

In principle, VMD is not really able to handle the case of time-dependent
properties of the atoms.

Since when? What about the user defined coloring, with which you can set a
value per atom per timestep.

what olaf means is that VMD currently has no mechanism to read per
timestep per atom data other than positions and velocities through molfile
plugins.
to make use of the user field, you need to feed the data into VMD through
some other means, e.g. by aliasing it into vx, vy, or vz and then copying
those fields to a user field with a script (as possible with the LAMMPS
plugin) or parse the trajectory file a second time from a tcl script and
then copy the data directly into the user field, or write the time
dependent data to a separate file and read that file from a tcl script and
assign the data to one of the 4 user fields.
olaf's plugin supports the second option by hooking part of the vtf molfile
plugin into the Tcl interpreter, so you don't have to write a Tcl parser.
axel.
https://www-s.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/23259.html

@jonaslandsgesell
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In some simulation packages the datasets are written timedependent (although not needed). In such cases it would be a solution to issue a warning that these datasets were timedependent but only the first timestep was used to display those properties.

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