User News & Notices

Python framework for working with atomic configurations, potentials, and algorithms.

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ryeterrell
Posts: 23
Joined: Fri Jun 27, 2008 8:49 pm

User News & Notices

Post by ryeterrell » Thu Jul 17, 2008 11:31 pm

22 July 2008

* Added parallel tempering. Uses Rye's metropolis. -Matt
* Added simulated annealer with four sample schedule methods. Uses Rye's metropolis. -Matt

21 July 2008

* Added toy potential -Matt
* Massively rewrote atom picker (still no solution for ambiguous wx events) - Matt

18 July 2008

* Dyn now uses True/False instead of 1/0. This shouldn't break any code since bool(1)=True and bool(0)=False. -Matt

15 July 2008

* Significant changes to the organization of the io module have been made. Be certain to take a look at the documentation page to see how things work now. Also, the examples/min/min.py example, at least, works with the new organization. -Rye Terrell

8 July 2008

* data.point.elements has been removed in favor of the cleaner data.point.get_element(index) -Rye Terrell

1 July 2008

* Added a menu bar to vsr, complete with load, save, close, and help. -Matt
* Added a general purpose "debug" function that prints debug lines if current.debug is true. This can be found in the "printf.py" file. -Rye Terrell
* Added a general purpose "printf" function. Use this instead of "print" for all tsse code, along with the flags WRN and ERR and the current.verbosity flag to make tsse quiet or loud, accordingly. current.quiet will be phased out. -Rye Terrell
* Added local minimization function to vsr, currently bound to 'z'. Try moving atoms while holding 'z'. -Matt

25 June 2008

* Added pot.combo() to combine two potentials. -Matt

23 June 2008

* tsserc has been moved to .tsserc in the root tsse directory.
* Everything else has been migrated up to the root tsse directory. Please let me know if there are any problems. -Rye Terrell
* Example min was repaired. -Rye Terrell
* pot.simple was removed, along with the reference to the nonexistent polynomial potential. -Rye Terrell
* In accordance with the new minimal subdirectory paradigm, current.py and util.py have been moved to the root tsse directory, and their directories removed. It is not expected that changes of this kind will affect the typical tsse import. -Rye Terrell

16 June 2008

* vsr.show() has been fixed so that it now displays tsse.current.point by default, or some point structure passed to it as an option. -Rye Terrell
* Added "loadinto" to the standard alias list "loadinto a somefile" ==> a = io.load("somefile") -Rye Terrell

13 June 2008

* Happy Friday the Thirteenth. To kick things off, I've removed the multiple window capability from vsr. Nice as it was, it just wasn't feasible to keep in the face of platform incompatibilities and painful threading issues. Also removed is the ability to show() some point you have loaded. vsr.show() now only works for the tsse.current.point. This was done to address some of the threading issues. There are ways around this, and it will be restored in the future. Also, there's currently a bug that requires you to hide and show when you change tsse.current.point. It's on my to-fix list. -Rye Terrell

12 June 2008

* io.iscon() now allows for commented files, tcon-generated files are still broken. -Matt
* A bug fix was rolled back because it caused an error on macs. -Rye Terrell
* The generic, classless minimize function in tsse.min.min has been moved to tsse.minimize. The min class still exists as it did, but if you've been using the generic version since I put it in a while back, you'll now find the goods in tsse.minimize. If you from tsse import *, it'll be imported as simply minimize(). We will likely remove tsse.min at some point in the not-so-distant future, so it is recommended that you begin to port your code to use the classless tsse.minimize() function.-Rye Terrell
* A bug in vsr was fixed so that you wont receive an error from the atexit call if you never initialized vsr. -Rye Terrell
* The tsse shell now only reports errors from commands that do not succeed as system calls. This means that 'errs' will not return a long list of "name 'ls' is not defined" -Rye Terrell
* Optimized vsr to be more responsive with multiple windows open. -Rye Terrell
* After a 2 day (yes 2 days) struggle with vsr, an idiosyncrasy of wxPython was discovered and addressed, leaving us with a more stable exit from vsr. This is pre-mac testing, so you may be hearing more from me in a few hours... -Rye Terrell

11 June 2008

* All file loading methods should give points with attributes of the same type. -Matt
* Morse potential now works after atom deletion. All other potentials seem to be fine. -Matt

10 June 2008

* You can now delete atoms in vsr. Hold down 'd' and click on the spheres that displease you. -Matt
* The point class now has a deleteAtom() method, which takes as an argument the index of that atom. It should deal with all of the many fields of the point object appropriately. -Matt
* Made opt.*() actually call the constructor.

Code: Select all

 
o = opt.qm()
 o.init()
is no longer necessary. A thin wrapper was added so that scripts using this syntax will not break. -Matt

So, now you can initialize the constructor so:

Code: Select all

o = opt.qm()
or

Code: Select all

o = opt.qm(maxmove = 0.2)
etc... -Rye Terrell

* made the FIRE minimizer quiet when tsse.current.quiet is set -Matt
* examples/neb repaired. -Rye Terrell

9 June 2008

* Atom manipulation in the tsse shell is now operable. Here's a summary of the mouse/keyboard controls: Left/right mouse buttons will rotate the molecule. Holding down shift while left-clicking and dragging an atom will move an atom parallel to the view plane (up, down, left, and right). Holding down control while left clicking and dragging an atom will move an atom perpendicular to the view plane (in and out). -Rye Terrell

7 June 2008

* Some changes were made to vsr that will hopefully make it more stable on macs. -Rye Terrell
* Some fledgling atom manipulation is in place. The right mouse button has been mapped to move an atom in the x-y plane. These controls are temporary and for testing purposes only, but something similar will take its place in the near future. -Rye Terrell

6 June 2008

* ~ now substitutes for home directory in tab-completion. -Rye Terrell
* All of the io.load functions now load with filename first, and an optional point second. They all return a loaded point, now. -Rye Terrell
* Fixed alias bug. -Rye Terrell

5 June 2008

* Added a 'help' command that displays the new readme manual. No, it does not conflict with help(). -Rye Terrell
* Added a readme manual to the root tsse directory giving getting started hints. Yes, it needs work. -Rye Terrell

4 June 2008

* Command history for the tsse shell is now saved in ~/.tssehist, and loaded when tsse boots. -Rye Terrell
* Tab completion for the tsse shell is... complete. -Rye Terrell
* data.ParametricSplineND and data.Spline2D have been merged into data.spline. -Rye Terrell
* You may now alias and unalias from within the tsse shell with the commands alias and unalias, e.g. alias foo print "bar" and unalias foo. All changes are updated immediately in the user's .tsserc file. If a system tsserc alias is unaliased, it will be removed from memory, but not from the system tsserc file; it will return when tsse is restarted. -Rye Terrell
* The syntax of the system and user tsserc files has changed. Aliases are now prefixed with "alias", and the equals "=" sign is gone. You may now add initialization code to the tsserc file by prefixing each line of code with "run". -Rye Terrell
* Now right and left mouse buttons rotate molecules in the vsr window. -Rye Terrell
* current.quiet now working, but only affects min at the moment. -Rye Terrell
* The splash text shown when the tsse shell begins is configurable with the .splash text file in the root tsse directory, now. -Rye Terrell
* The tsse shell now searches for ~/.tsserc for a configuration file, and if it is not found, places an empty one there. -Rye Terrell
* The tsse executable and tssesh.py were merged and placed into tsse/bin. -Rye Terrell
* The molecules in the vsr window are now rotated with the left mouse button. The right mouse button does nothing at the moment. -Rye Terrell
* A new general-purpose load function was added, and can be located in io.load. -Rye Terrell

31 May 2008

* tsse.vsr was replaced with a newer tsse.vsr, based on wxpython instead of pygame. Hopefully it will work on more systems. -Rye Terrell

29 May 2008

* The syntax for tsse.io.loadcon has been modified slightly. -Rye Terrell
* tsse.current has been added. -Rye Terrell

28 May 2008

* A new 3D graphics package was added, tsse.vsr. This package requires pyopengl and pygame to be installed. -Rye Terrell
* All functions from tsse.math and tsse.func have been moved into the single module tsse.util. -Rye Terrell
* tsse is now lowercase. -Rye Terrell

ryeterrell
Posts: 23
Joined: Fri Jun 27, 2008 8:49 pm

Re: User News & Notices

Post by ryeterrell » Fri Jul 18, 2008 11:08 pm

vsr_2d has been added to the vsr directory. This can be used to visualize 2d potentials, along with drawing simple primitive shapes on top of them. Look at mc_metropolis.py and dimer.py for an example.

matt
Posts: 37
Joined: Thu Jul 17, 2008 10:51 pm

Re: User News & Notices

Post by matt » Thu Jul 24, 2008 4:42 pm

Add atom now works in vsr. Select an atom type via the Atom Picker, hold 'a' and click. The atom should appear at your mouse's x and y, and a reasonable z. Still needs a little polish.

Also, box can now be drawn via View>Show Box. Supports non-orthogonal boxes (not very useful, nothing else in tsse supports non-orthagonal boxes)

ryeterrell
Posts: 23
Joined: Fri Jun 27, 2008 8:49 pm

Re: User News & Notices

Post by ryeterrell » Sat Jul 26, 2008 3:41 am

I changed how vsr displays things a little bit. This is the maxz thing that was bugging me, Matt. You might want to make sure it didn't mess up your addatom supergizmo.

We should probably fix how cameraZ is initialized. One way is to check to see if an atom is available when the canvas is initialized, and then set the cameraZ to some constant times the maximum distance an atom is away from the middle of the molecule. Or add a constant to this distance.

ryeterrell
Posts: 23
Joined: Fri Jun 27, 2008 8:49 pm

Re: User News & Notices

Post by ryeterrell » Tue Aug 05, 2008 10:29 pm

tsse can now switch between perspective and orthogonal views with the 'p' key.

Matt, in order to do this, I added a "self.zoom_factor" to the vsr.canvas class. What do you think about initializing the zoom factor to something larger for darwin platforms? I'd do it myself, but I can't run macos in virtualbox, yet. ;)

-Rye

ryeterrell
Posts: 23
Joined: Fri Jun 27, 2008 8:49 pm

Re: User News & Notices

Post by ryeterrell » Tue Aug 05, 2008 10:30 pm

Tools->Distance will spit out in the console window the distance between the last two clicked atoms on the vsr screen.

-Rye

ryeterrell
Posts: 23
Joined: Fri Jun 27, 2008 8:49 pm

Re: User News & Notices

Post by ryeterrell » Tue Aug 12, 2008 12:06 am

The "p" key has been removed for perspective/orthogonal toggling, and replaced with a menu item under "View". -Rye

ryeterrell
Posts: 23
Joined: Fri Jun 27, 2008 8:49 pm

Re: User News & Notices

Post by ryeterrell » Tue Aug 12, 2008 6:45 pm

The glut of opengl stuff in the epydoc documentation (http://theory.cm.utexas.edu/henkelman/code/tssedoc/) has been removed -Rye

ryeterrell
Posts: 23
Joined: Fri Jun 27, 2008 8:49 pm

Re: User News & Notices

Post by ryeterrell » Tue Aug 12, 2008 10:32 pm

You can now adjust the radii of atoms shown in vsr (View->Radius->5,10,15, etc...). -Rye

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