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adahbingee/pais-mvs 44

Multi-view stereo image-based 3D reconstruction

abhinavguptas/tolerado-sfdc-wsc-apis 1

Automatically exported from code.google.com/p/tolerado-sfdc-wsc-apis

adelikat/yabause-rr 1

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06b/doctype-mirror 0

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0Knowledge/gflags 0

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0xbrock/intellectualponderingscode 0

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297chrisc/playn 0

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3agv2004/domoticaOS 0

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a1waysbeta/foo-wsh-panel-mod 0

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a29888778/android-smb-streaming 0

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issue openedvotca/votca

add nrexcl to mapping file.

Adding an nrexcl like option to the mapping file would be nice to avoid the 
need to create phantom bonds to model the same exclusions as gromacs.

Also see issue votca/csg#161 for details.

Original issue reported on code.google.com by christop...@gmail.com on 11 Oct 2014 at 10:09

created time in a month

issue openedvotca/votca

relative entropy: add reweighting based update of parameters

Currently short CG MD simulation is performed in each relative entropy update 
step to compute CG ensemble averages. Alternative approach is to reweight the 
initial (step 0) CG configurations to obtain CG ensemble averages (Eq. 54 
Chaimovich and Shell, J. Chem. Phys. 134, 094112, 2011). 
This eliminates the need to perform CG-MD in each RE update and hence, reduces 
the computation time.

Original issue reported on code.google.com by symasha...@gmail.com on 6 Apr 2014 at 1:36

created time in a month

issue openedvotca/votca

csg_boltzmann: has gromacs units hard-codes

Gromacs units are hard-codes for the Boltzmann inversion of potentials.

Original issue reported on code.google.com by christop...@gmail.com on 21 Jan 2014 at 4:20

created time in a month

issue openedvotca/votca

add support for dcd trajectories

DCD trajectory support is needed for native NAMD support. Unfortunately, DCD is 
a very complicated format.

I guess the easiest would be to copy vmd* from the gromacs sources and change 
the functions in vmdio.c to a VOTCA trajectory reader.

The VMD files are under BSD license so that should not be a problem.

As a bonus we get all other formats supported by VMD for free.

Original issue reported on code.google.com by christop...@gmail.com on 4 Dec 2013 at 2:34

created time in a month

issue openedvotca/votca

pressure correction with relative entropy

add pressure correction update scheme for relative entropy based 
coarse-graining similar to that in IBI. Model CG interactions as B-spline + 
A(1-r/rcut) and update B-Spline knots with RE and A from pressure correction 
update formula. Store both B-spline knots and A at each iteration.

Original issue reported on code.google.com by symasha...@gmail.com on 12 Nov 2013 at 7:12

created time in a month

issue openedvotca/votca

csg_stat: normalization of bonded interactions

It seems like bonded distributions are not normalized correctly for bonded 
interactions.

For IBI that doesn't matter too much, but we should at least normalize them 
with bin size and count.

Original issue reported on code.google.com by christop...@gmail.com on 13 Aug 2013 at 12:27

created time in a month

issue openedvotca/votca

Check validity of box matrix

All pbc algorithms have special conditions which are not checked currently. 
This should be done in setBox, make this function virutal which also allows to 
initialize other variables for the pbc algorithm which might be required in 
future.

Original issue reported on code.google.com by victor.r...@gmail.com on 30 Mar 2012 at 10:02

created time in a month

issue openedvotca/votca

Check initialization in constructor

Many member variables are not initialized, e.g. Bead userdata

Original issue reported on code.google.com by falk....@googlemail.com on 20 Jun 2011 at 8:33

  • Blocking: votca/csg#112

created time in a month

issue openedvotca/votca

scriptframwork introduction

-add a section to the manual
-naming scheme

Original issue reported on code.google.com by christop...@gmail.com on 16 Jun 2011 at 9:34

created time in a month

issue openedvotca/votca

improve documentation about potential.do

Dominik said potential.do and pressure.do are very unclear in the manual. We 
need to add an example and improve the doc (also in the xml file)

Original issue reported on code.google.com by christop...@gmail.com on 3 May 2011 at 4:07

created time in a month

issue openedvotca/votca

Improve csg_density

- number density
- improved atom selection capabilities

Original issue reported on code.google.com by victor.r...@gmail.com on 28 Apr 2011 at 3:41

created time in a month

issue openedvotca/votca

csg_fmatch: use threads

Force matching of a large trajectory can take several hours.
Using threads would be very useful.

Original issue reported on code.google.com by christop...@gmail.com on 10 Mar 2011 at 1:40

created time in a month

issue openedvotca/votca

csg: umbrella binary

Gromacs does it as well

http://redmine.gromacs.org/issues/685

Original issue reported on code.google.com by christop...@gmail.com on 3 Feb 2011 at 4:16

created time in a month

issue openedvotca/votca

make csg_dump generate a template settings file

csg_dump settings file generation
(something like: generate option --setting)

Original issue reported on code.google.com by gh...@students.uni-mainz.de on 11 Jan 2011 at 10:27

created time in a month

issue openedvotca/votca

csg_stat: allow different kind of types (index groups)

Now type1, type2 are glob matched (only ?*) against the type in topology.

Add advanced type selection by:
-name
-index group (reading of these file types is not implemented yet)
-advanced stuff by python functions

Original issue reported on code.google.com by christop...@gmail.com on 5 Jan 2011 at 1:17

  • Blocked on: votca/votca#775

created time in a month

issue openedvotca/votca

check table format in csg_boltzmann

table format should be:
x y ... flag
(flag in last column)

Check if csg_boltzmann used this format

Original issue reported on code.google.com by christop...@gmail.com on 14 Dec 2010 at 11:36

created time in a month

issue openedvotca/votca

python bindings

-will be needed for analysis within espresso++
-useful to write quickly little analysis tools

Original issue reported on code.google.com by christop...@gmail.com on 13 Dec 2010 at 5:51

  • Blocking: votca/csg#51, votca/csg#51

created time in a month

issue openedvotca/votca

TrajectoryReader, change FirstFrame and NextFrame to single function ReadFrame

The two functions FirstFrame and NextFrame in many casees is very unhandy to 
use in code. A single ReadFrame function would be more convenient.

Original issue reported on code.google.com by victor.r...@gmail.com on 11 Dec 2010 at 3:07

created time in a month

issue openedvotca/votca

Check pointer/index/id handling

Using index numbers, ids or pointers is not done consistently. Access by index 
should be avoided whenever possible since it can lead to serious problems when 
e.g. changing number of particles or reordering them.

Original issue reported on code.google.com by victor.r...@gmail.com on 25 Nov 2010 at 8:11

created time in a month

issue openedvotca/votca

Rework interaction concept

Bonded and non-bonded interactions have no uniform interface in c++. This would 
be good to have to allow for easier implementation of e.g. many body 
interactions and more, especially for force-matching.

A concept similar to espresso++ would be nice.

Original issue reported on code.google.com by victor.r...@gmail.com on 23 Oct 2010 at 12:56

created time in a month

issue openedvotca/votca

csg_boltzmann: better interactive usage

(from trac)

-open a pipe to gnuplot
-allow plotting of table and distributions

Original issue reported on code.google.com by christop...@gmail.com on 18 Oct 2010 at 5:38

created time in a month

issue openedvotca/votca

comment lines in output files

(from trac)

when writing out files for histograms, potential tables or value lists, it 
would be nice to have a comment line in the beginning, that describes, which 
data have been used actually.

For example in a value file:

votca/csg#1:BAB-angle:2 (containing beads B2 A3 B3), 1:ABAB-dihedral:2 (containing 
beads A2 B2 A3 B3)

Original issue reported on code.google.com by christop...@gmail.com on 18 Oct 2010 at 5:31

created time in a month

issue openedTWiStErRob/net.twisterrob.cinema

Ideas

What is the use case for the task at hand?
As a Developer I want to be able to create a useful application.

What is the expected output of the task?
Comments on this task about new ideas.

Are there any pointers which may help the implementation?
Use the following template:

Title: ...
Description: ...max few lines...
References:
 * ...

Original issue reported on code.google.com by papp.robert.s on 28 Aug 2012 at 11:10

created time in a month

issue openedTWiStErRob/net.twisterrob.cinema

Caching logic for filling the internal DB and reaching for data when needed

What is the use case for the task at hand?
As a User I want to be able to have as little bandwidth usage as possible with 
almost up-to-date data.

What is the expected output of the task?
 * Another Accessor-like implementation which wraps JSON and DB access

Are there any pointers which may help the implementation?
none.

Original issue reported on code.google.com by papp.robert.s on 28 Aug 2012 at 6:24

  • Blocked on: TWiStErRob/net.twisterrob.cinema#64

created time in a month

issue openedTWiStErRob/net.twisterrob.cinema

Database access layer

What is the use case for the task at hand?
As a Developer I want to be able to use the Database as the JSON API before.

What is the expected output of the task?
 * CineworldDBAccessor or alike
 * Having the same or mostly similar API as CineworldAccessor (extract interface)
 * Refactor CineworldAccessor to implement the same interface
 * Rename classes appropriately

Are there any pointers which may help the implementation?
com.twister.cineworld.model.json.CineworldAccessor

Original issue reported on code.google.com by papp.robert.s on 28 Aug 2012 at 6:20

  • Blocking: TWiStErRob/cineworld-extra#20
  • Blocked on: TWiStErRob/net.twisterrob.cinema#62, TWiStErRob/net.twisterrob.cinema#63

created time in a month

issue openedTWiStErRob/net.twisterrob.cinema

Initial SQL DDL schema definition

What is the use case for the task at hand?
As a User I want to be able to access data from phone-local DB.

What is the expected output of the task?
 * Usable schema for storing data retrieved from Cineworld
 * Few predictable metadata fields

Are there any pointers which may help the implementation?
https://www.cineworld.co.uk/developer/api

Original issue reported on code.google.com by papp.robert.s on 28 Aug 2012 at 6:17

  • Blocking: TWiStErRob/cineworld-extra#19

created time in a month

issue openedTWiStErRob/net.twisterrob.cinema

SQLite Database access layer

What is the use case for the task at hand?
As a Developer I want to be able to write DB schema in an SQL file.

What is the expected output of the task?
 * SQLiteOpenHelper implementation for the project
 * Easily accessible (preferably singleton) instance
 * Basic table creation script as an example

Are there any pointers which may help the implementation?
http://developer.android.com/reference/android/database/sqlite/SQLiteOpenHelper.
html

Original issue reported on code.google.com by papp.robert.s on 28 Aug 2012 at 6:12

  • Blocking: TWiStErRob/cineworld-extra#19

created time in a month

issue openedTWiStErRob/net.twisterrob.cinema

Set up JUnit test project

What is the use case for the task at hand?
As a Developer I want to be able to unit test my code.

What is the expected output of the task?
 * Possible extraction of general code to a library/jar (new project?)
 * A separate project with JUnit tests under version control
 * The JUnit project should run without phone on the developer machine

Are there any pointers which may help the implementation?
none.

Original issue reported on code.google.com by papp.robert.s on 28 Aug 2012 at 6:06

created time in a month

issue openedTWiStErRob/net.twisterrob.cinema

Tidy Eclipse formatter and Save actions a little

What is the use case for the task at hand?
As a Developer I want to read/write code with easy.

What is the expected output of the task?
 * Automatically put this in front of instance members (m_*)
 * Try to remove Class name in front of s_* and CONSTANTS if they're in the same class

Are there any pointers which may help the implementation?
Project properties > Java Code Style > Formatter
Project properties > Java Editor > Save Actions
and maybe Project properties > Java Code Style > Code Cleanup

Original issue reported on code.google.com by papp.robert.s on 28 Aug 2012 at 6:04

created time in a month

issue openedTWiStErRob/net.twisterrob.cinema

Handle exceptions gracefully on UI displaying a fancy message box

What is the use case for the task at hand?
As a User I want to see user-friendly error message.

What is the expected output of the task?
 * Message box displaying a user-friendly error message
 * Message box with a "More..."-like button for quick diagnostics
 * Message box with a "Report" button is out of scope for this task

Are there any pointers which may help the implementation?
none.

Original issue reported on code.google.com by papp.robert.s on 28 Aug 2012 at 6:00

created time in a month