VMD-L Mailing List
From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Apr 28 2015 - 10:41:55 CDT
On Tue, Apr 28, 2015 at 11:06 AM, Ryan McGreevy
> Miguel, you can truncate the density around your structure by using the
> "volmap mask" command in VMD to create a binary mask, then multiply that
> mask by your density using "volutil -mult".
i don't think that that will reduce the file size and/or storage
requirements (on the contrary).
a long time ago i wrote a utility that can perform such grid cutting
operations on gaussian style cube files.
i am attaching the (C) source code. it can do some additional
processing and trimming as well.
of course, if your grids are in a different format, you will need to
change the parts related to reading the data.
> On Tue, Apr 28, 2015 at 4:23 AM Miguel Caro <miguel.caro_at_aalto.fi> wrote:
>> Dear all,
>> I am working with charge density isosurfaces and have observed that for
>> the cell size and grid spacing I'm dealing with these become memory
>> I use big cells in my DFT calculations to prevent interactions with
>> periodic replicas of my molecule. This means that the cell region where the
>> wave functions are significantly different from zero is much smaller than
>> the overall cell size. I was wondering if, in order to lower the amount of
>> memory needed, I can somehow truncate the region in space where the
>> volumetric data is represented to some region around my molecule, for
>> instance by defining a spherical cutoff around some position in space.
>> Many thanks,
>> Dr. Miguel Caro
>> Postdoctoral researcher
>> Department of Electrical Engineering and Automation,
>> and COMP Centre of Excellence in Computational Nanoscience
>> Aalto University, Finland
>> Personal email: mcaroba_at_gmail.com
>> Work: miguel.caro_at_aalto.fi
>> Website: http://mcaroba.dyndns.org
-- Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy.
- application/x-gzip attachment: trimcube.c.gz