Surface support and other thoughts

Hi,

I just wanted to let you know that I have added the iso.h and iso.cpp
files to our repository from the Zhu3D project. I was actually going to
implement the exact same algorithm from the web page referenced in the
source files and then came across this where all the work had been done.
It looks pretty good already.

Hopefully it will not be long before I can get these files working with
our source but I wanted to let you see where I started. The class is
already thread safe and doesn’t seem to be too tied to the Zhu3D
application. The marching cubes algorithm as implemented here should
allow for the most flexibility as far as I understand the algorithm and
its implementation.

I think surfaces are the largest widely asked for feature we are
currently missing and so would love to get this in ASAP. I will be
traveling soon though and so can’t give time lines (and wouldn’t want to
where surface support is concerned).

Hope you all had a great holiday period and are ready to squash those
bugs, run KDE 4.0 and get the Avogadro API into a well tested state
before we make a 1.0 release and agree to be bound by our decisions
until 2.0!

Thanks,

Marcus

Hi,

How is the progress on the surface engine going? The reference in the
source seems to explain the method well. Did you allready do some work
that isn’t in SVN? This mail is not to check on you off course, I was
just curious because I really want surfaces :-).

If you have allready done some work and don’t have time to finnish
it, could you commit? Don’t want to waste my time if it is almost
finnished… Should I take a look at it? (in other words: do you have
time to work on it in the near future?)

Thanks in advance,
Tim

On Jan 12, 2008 6:01 AM, Marcus D. Hanwell mhanwell@gmail.com wrote:

Hi,

I just wanted to let you know that I have added the iso.h and iso.cpp
files to our repository from the Zhu3D project. I was actually going to
implement the exact same algorithm from the web page referenced in the
source files and then came across this where all the work had been done.
It looks pretty good already.

Hopefully it will not be long before I can get these files working with
our source but I wanted to let you see where I started. The class is
already thread safe and doesn’t seem to be too tied to the Zhu3D
application. The marching cubes algorithm as implemented here should
allow for the most flexibility as far as I understand the algorithm and
its implementation.

I think surfaces are the largest widely asked for feature we are
currently missing and so would love to get this in ASAP. I will be
traveling soon though and so can’t give time lines (and wouldn’t want to
where surface support is concerned).

Hope you all had a great holiday period and are ready to squash those
bugs, run KDE 4.0 and get the Avogadro API into a well tested state
before we make a 1.0 release and agree to be bound by our decisions
until 2.0!

Thanks,

Marcus


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On Feb 5, 2008, at 12:15 PM, Tim Vandermeersch wrote:

How is the progress on the surface engine going? The reference in the
source seems to explain the method well. Did you allready do some work
that isn’t in SVN? This mail is not to check on you off course, I was
just curious because I really want surfaces :-).

If you have allready done some work and don’t have time to finnish
it, could you commit? Don’t want to waste my time if it is almost
finnished… Should I take a look at it? (in other words: do you have
time to work on it in the near future?)

Hi,

I was away for a few weeks where I really didn’t get the chance to do
very much at all. I am now working on it again and should be able to
spend some more time on it today. It is currently my top priority
(although I did commit a few fixes and enhancements to the
ClickMeasureTool).

That isn’t to say you can’t look at it if you want to - that is why I
committed it so that people could see where I was planning to go and
where I started from. I don’t have a working surface engine just yet
but hopefully it will not take very much longer.

I always welcome help and pointers but I had actually been reading the
referenced site before I found this code. Sorry if I have been a
little silent on this. I will also hopefully be around on IRC too if
you need anything.

Thanks,

Marcus

Hi,

Just committed surfaceengine2., It is based on the previous
surfaceengine.cpp and the iso.
files. You can allready view the dots
which make up the surface. Much more needs to be done however. Making
it more thread-safe (doesn’t really use threads at the moment),
normals, colouring, saving the surface for later (e.g. calculate
surface when atoms ar added/deleted or their position changes), …

The code is still very messy, but I committed it to avoid doing some
work twice…

note: you need the latest openbabel SVN, there was a small bug in grid.cpp

Small demo movie: http://home.scarlet.be/~bb224761/surface.avi

Tim

On Feb 5, 2008 7:00 PM, Marcus D. Hanwell mhanwell@gmail.com wrote:

On Feb 5, 2008, at 12:15 PM, Tim Vandermeersch wrote:

How is the progress on the surface engine going? The reference in the
source seems to explain the method well. Did you allready do some work
that isn’t in SVN? This mail is not to check on you off course, I was
just curious because I really want surfaces :-).

If you have allready done some work and don’t have time to finnish
it, could you commit? Don’t want to waste my time if it is almost
finnished… Should I take a look at it? (in other words: do you have
time to work on it in the near future?)

Hi,

I was away for a few weeks where I really didn’t get the chance to do
very much at all. I am now working on it again and should be able to
spend some more time on it today. It is currently my top priority
(although I did commit a few fixes and enhancements to the
ClickMeasureTool).

That isn’t to say you can’t look at it if you want to - that is why I
committed it so that people could see where I was planning to go and
where I started from. I don’t have a working surface engine just yet
but hopefully it will not take very much longer.

I always welcome help and pointers but I had actually been reading the
referenced site before I found this code. Sorry if I have been a
little silent on this. I will also hopefully be around on IRC too if
you need anything.

Thanks,

Marcus