Nanoengineer-1 Software

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technologiclee

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Nov 9, 2009, 6:14:21 AM11/9/09
to Open Manufacturing

Nanoengineer-1 has been mentioned on this list before. Has anyone here
used it?

http://nanoengineer-1.com/content/

An account to download the software can be obtained by sending a
request to sup...@nanorex.com

There was a nice list of software in recent posts by Heath and Bryan.
Do any of those packages have the engineering CAD style available in
NE-1?

There was also a question about atomic positions. NE-1 uses .mmp
(molecular machine part) files. basically x,y,z data, atom type, and
bond information. NE-1 can also make a .pdb file.



Heath Matlock

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Nov 10, 2009, 12:29:26 AM11/10/09
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On Mon, Nov 9, 2009 at 11:14 AM, technologiclee
<technol...@gmail.com> wrote:
>
>
> Nanoengineer-1 has been mentioned on this list before. Has anyone here
> used it?
>
> http://nanoengineer-1.com/content/

Indeed, it does look nice. I think a few of us attempted to install
but never got it running due to its many external sources and lack of
time. Ben Lipkowitz says the instructions are decent, I can't recall.

> An account to download the software can be obtained by sending a
> request to sup...@nanorex.com

You just have to go register at http://nanoengineer-1.com and and then
click download, no need in taking the long way about things :-)

> There was a nice list of software in recent posts by Heath and Bryan.
> Do any of those packages have the engineering CAD style available in
> NE-1?

Having not used Nanoengineer, I'm not sure exactly what it's interface
is like. However, SKDB ( http://adl.serveftp.org/dokuwiki/skdb ) uses
Open CASCADE ( see http://en.wikipedia.org/wiki/Open_CASCADE and
http://adl.serveftp.org/dokuwiki/occ ) and PythonOCC ( see
http://pythonocc.org/ and http://adl.serveftp.org/dokuwiki/pythonocc
). I've actually been working on creating a .deb file for the program
this past week, ask me how far along I've come in a month.. And also
in SKDB is heeks_coords.py which extracts coordinates from HeeksCAD
files.

http://code.google.com/p/heekscad/
Debian packages for it: http://yamato.hyte.de/packages/heeks/

If you are on Windows and don't mind the .NET junk, NaroCAD looks
decent: http://narocad.com/

--
Heath Matlock
+1 256 274 4225

Eugen Leitl

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Nov 16, 2009, 11:37:41 AM11/16/09
to openmanu...@googlegroups.com
On Mon, Nov 09, 2009 at 03:14:21AM -0800, technologiclee wrote:
>
>
> Nanoengineer-1 has been mentioned on this list before. Has anyone here
> used it?

Yes, a few years ago. Still not open sourced, is it?



> http://nanoengineer-1.com/content/
>
> An account to download the software can be obtained by sending a
> request to sup...@nanorex.com
>
> There was a nice list of software in recent posts by Heath and Bryan.
> Do any of those packages have the engineering CAD style available in
> NE-1?
>
> There was also a question about atomic positions. NE-1 uses .mmp

Not a question, at least not about NE-1.

> (molecular machine part) files. basically x,y,z data, atom type, and
> bond information. NE-1 can also make a .pdb file.

The problem with this is that you typically have CAD, which is bulk,
and molecular editors, which are atomically accurate but don't scale
to even mesoscale. So you need a hybrid approach, where you can describe
parts at atomic detail, iterations of such (e.g. tilings a la crystal
lattice) and ways of using bulk, but with bond-precision attachement
tools. And you have to think about the facility which will make use
of such descriptions. This still hasn't been done yet.

--
Eugen* Leitl <a href="http://leitl.org">leitl</a> http://leitl.org
______________________________________________________________
ICBM: 48.07100, 11.36820 http://www.ativel.com http://postbiota.org
8B29F6BE: 099D 78BA 2FD3 B014 B08A 7779 75B0 2443 8B29 F6BE

Lee Nelson

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Nov 16, 2009, 1:14:56 PM11/16/09
to openmanu...@googlegroups.com

The problem with this is that you typically have CAD, which is bulk,
and molecular editors, which are atomically accurate but don't scale
to even mesoscale. So you need a hybrid approach, where you can describe
parts at atomic detail, iterations of such (e.g. tilings a la crystal
lattice) and ways of using bulk, but with bond-precision attachement
tools. And you have to think about the facility which will make use
of such descriptions. This still hasn't been done yet.


I noticed that and agree. NE-1 can handle a few thousand atoms on a dual core desktop 8Gb Ram 512mb Video Ram. This is not even enough for for most components, or subsystems let alone whole machines.

Could this software be integrated in a standard cad package as a module? Once a systems 'global properties' are determined, collections of systems could be used as parts. (I think this is what you just said, but in the way I have been thinking of it).


There is software for a NanoHive@home - which is like SETI@home and allows large simulations to be distributed across many computers. I signed up for the project, but when I asked how to start, received an email to the effect that it was not activated or some such.
http://www.nanohive-1.org/

I have installed NE-1 on Ubuntu repeatedly - it did take a while for a command line novice to get through the hoops, but now I can install it in fairly short order.

I have my request for help which is linked to my notes on installation here.
http://ubuntuforums.org/showthread.php?t=1080172

I had attempted to write a script to install NE-1 - It currently will get about half way through the process ( the last half is trivial it's just one hitch with PyQt). I shared this information with Ben L. when he had mentioned NE-1. For what it is worth, it is here - maybe someone could kick the field-goal.
http://docs.google.com/View?id=dc26889x_114gktkjhgx

My problem at this point is that the simulator does not work (in linux). The guy who wrote it says the new gcc may have broken it and lists some options. None of which my programming skills are up to (yet),
http://ngineers.ning.com/profiles/blogs/nanohive1-install

If anyone could take a look at this and at least give me a pointer, I would appreciate it. Note that it runs fine on Win XP (& Mac), the last time I had access to that system, I made these training videos. I have not been able to use it for simulations since.
http://www.youtube.com/user/technologicleenelson#p/a/u/1/wvcwY5pSXZs
http://www.youtube.com/user/technologicleenelson#p/a/u/0/nqfXzTrwI3c

Netbeans IDE has python support and I have run NE-1 from inside Netbeans - I found it a very useful way to look at the code.

NE-1 is released under GPL - I believe - does than make it open source so that anyone could fork and modify it?
It is listed at sourceforge but there are no packages to download there.
http://sourceforge.net/projects/nanoengineer-1/

I submitted an Ubuntu Launchpad 'bug report' asking for the software to be packaged and offered in the repository. It has been assigned the status of 'wish list' - so it could happen - especially if some programmers got behind it. I also looked into things like BitRock Install Builder Program that makes .rpm s . It looks simple to use, but I do not quite get it yet
https://bugs.launchpad.net/ubuntu/+bug/357053
http://bitrock.com/

It should be noted that the project seems to have gone dormant with no reasons given by the project owner. The paid developers are no longer employed on that project - and have not been replace that I know of. It is speculated that the software is to be made proprietary. I would have thought it would have sold by now and that the new release would be in someones hands. Even so, could we still use the versions up to 1.1.2 or 1.1.4 for Windows?

There was once a DNA origami feature - It seemed to work well - the new versions seem to have disabled or removed it. Does anyone have old copies of the software?

Whether NE-1 or another software; this is the best I have seen, much more complete and user friendly than SARSE or anything
from www.nanohub.org or any of the few packages I have tried from the Linux repositories, we need something along these lines.



Since biology is our current state of the art in nanofactories,
I downloaded caDNAno and Adobe Air. From the review, caDNAno only seems to offer a fraction of what NE-1 does. This is how to install Adobe Air on Ubuntu:
http://www.sizlopedia.com/2008/04/06/how-to-install-adobe-air-on-ubuntu/
http://cadnano.org/

I did not see a Readme.txt or installation instructions for caDNAno. I did not find anything from a quick google search either. I would appreciate anyone enlightening me on my oversight. Is it a $make, make install kind of thing?



technologiclee

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Dec 10, 2009, 5:29:08 PM12/10/09
to Open Manufacturing

> NE-1 is released under GPL - I believe - does than make it open source so
> that anyone could fork and modify it?
> It is listed at sourceforge but there are no packages to download there.http://sourceforge.net/projects/nanoengineer-1/
>
> I submitted an Ubuntu Launchpad 'bug report' asking for the software to be
> packaged and offered in the repository. It has been assigned the status of
> 'wish list' - so it could happen - especially if some programmers got behind
> it.


Fedora Review Request: NanoEngineer-1
http://www.spinics.net/lists/fedora-package-review/msg147071.html

This is what needs to be done:
http://www.spinics.net.nyud.net:8080/lists/fedora-package-review/msg147448.html

Lee Nelson

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Dec 13, 2009, 1:25:08 AM12/13/09
to openmanu...@googlegroups.com

My problem at this point is that the simulator does not work (in linux). The guy who wrote it says the new gcc may have broken it and lists some options. None of which my programming skills are up to (yet),
http://ngineers.ning.com/profiles/blogs/nanohive1-install

If anyone could take a look at this and at least give me a pointer, I would appreciate it. Note that it runs fine on Win XP (& Mac), the last time I had access to that system, I made these training videos. I have not been able to use it for simulations since.
http://www.youtube.com/user/technologicleenelson#p/a/u/1/wvcwY5pSXZs
http://www.youtube.com/user/technologicleenelson#p/a/u/0/nqfXzTrwI3c

Netbeans IDE has python support and I have run NE-1 from inside Netbeans - I found it a very useful way to look at the code.


This is the error from Netbeans when I try to run the simulator. Any suggestions?

error trying to import dylib sim: <type 'exceptions.ImportError'>: No module named sim
  [runSim.py:787]
sim parameters used by NE1 read from: [/home/lee/nesuite1.1.12./cad/plugins/NanoDynamics-1/sim-params.txt]
bug in simulator-calling code: <type 'exceptions.AttributeError'>: SimRunner instance has no attribute 'system_parameters_file'
  [runSim.py:372] [runSim.py:970] [runSim.py:1089]
exception opening trace file '/home/lee/Nanorex/Untitled.2009-12-13-00-18-10-trace.txt': <type 'exceptions.IOError'>: [Errno 2] No such file or directory: '/home/lee/Nanorex/Untitled.2009-12-13-00-18-10-trace.txt'
  [runSim.py:1936]


Screenshot-NanoEngineer-1 - [Untitled]*.png
Screenshot-nesuite2 - NetBeans IDE 6.5.png

technologiclee

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Dec 21, 2009, 4:18:41 AM12/21/09
to Open Manufacturing

It appears that a .RPM is now available for NE-1

https://bugzilla.redhat.com/show_bug.cgi?id=541765

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