The lastet ctp code can be found here.
votca / ctp Goto Github PK
View Code? Open in Web Editor NEWcharge transport module
Home Page: https://gitlab.mpcdf.mpg.de/votca/votca
charge transport module
Home Page: https://gitlab.mpcdf.mpg.de/votca/votca
The lastet ctp code can be found here.
currently a python script; rewrite in a similar way to Gaussian
Original issue reported on code.google.com by [email protected]
on 6 Aug 2013 at 7:58
Useful if a user wants to print some run-time/input information of a program or
a calculator.
Original issue reported on code.google.com by [email protected]
on 11 Oct 2011 at 11:59
Enumeration sometimes starts with 0 sometimes with 1. This needs to be unified.
The same applies for crgunit ids. Internal and external representation must
also be identical.
Original issue reported on code.google.com by [email protected]
on 17 Sep 2011 at 6:29
The problem is that sqlite is pulled in as dependency by tools, but the include
pathes are not set properly.
Is there any other way than explicitly checking for sqlite in moo, ctp as well.
What is the best way to fix this in cmake?
Original issue reported on code.google.com by [email protected]
on 7 Oct 2011 at 1:17
Needs a lot of clean up, example:
$ ctp_dipro 123 456
/home/christoph/votca/bin/ctp_dipro: line 189: do_external: command not found
- rename it to *.in for getting version in there
- make use of csg_call functions as ctp depends on csg anyway
- rm do_external calls or source function_common
Comments?
Original issue reported on code.google.com by [email protected]
on 5 Nov 2011 at 3:30
ctp_run --list
ctp_run --description calculator_name
Original issue reported on code.google.com by [email protected]
on 22 May 2013 at 3:07
Currently only a single frame can be stored in the database. The problem is
connected to id labelling not unique for molecules and rigid fragments
(qmbeads).
Original issue reported on code.google.com by [email protected]
on 23 Sep 2011 at 8:40
In ecoulomb.cc we have a loop over the Molecules
MoleculeContainer::iterator imol;
for (imol = atop->Molecules().begin(); imol != atop->Molecules().end(); imol++)
because the atomistic beads can only be accessed by
Bead *bi = mol->getBead(i);
The Center of mass etc is taken from the corresponding CrgUnit
mol->getUserData<CrgUnit > ()->GetCom()
This works only if the Molecule is the CrgUnit.
->Change the loop to work only with CrgUnits (aka conjugated segments)
Similar for eoutersphere.cc
Original issue reported on code.google.com by [email protected]
on 2 Dec 2011 at 11:41
1) copy & paste license headers from csg into each file. Don't forget to adjust
the names
2) copy LICENSE file
3) Add README file mentioning the citation. See csg as template.
4) NOTICE file for every file that has different licencing information
Original issue reported on code.google.com by [email protected]
on 23 Sep 2011 at 10:41
Bad atom type reported by ctp map if moo cannot process it
Original issue reported on code.google.com by [email protected]
on 4 Oct 2011 at 10:44
Input file should support multiple frames
Original issue reported on code.google.com by [email protected]
on 29 Mar 2012 at 8:31
Calculates energy and density profiles, the input should be restructured
<profiles>
<axis>
<direction>
<min>
<max>
<bin>
<particles>
<type>
<range>
<output>
<density>
<energy>
Or even output all in one file? See gromacs with xmgrace -nxy bla.agr
Original issue reported on code.google.com by [email protected]
on 26 May 2013 at 5:24
This can happen if e.g. a double value is nan, writing to the database fails,
but no error is thrown. This leads to a broken database without the user
realiying it.
Check how to notice the error in sqlite commands.
Original issue reported on code.google.com by [email protected]
on 22 Sep 2011 at 2:25
should not be the case. check QMtopology and JCalc
Original issue reported on code.google.com by [email protected]
on 23 Nov 2011 at 8:02
UPDATE ... WHERE ... = ? AND ... = ? takes too long.
Original issue reported on code.google.com by [email protected]
on 29 Mar 2012 at 8:33
Make sure nothing can go wrong with <map2md>0 (or 1)</map2md> switch: Rename to
<use_coords>qm (or md)</use_coords>.
Original issue reported on code.google.com by [email protected]
on 5 Jun 2012 at 2:52
Base class for beads in CSG and neighbourlist based on this base class
Original issue reported on code.google.com by [email protected]
on 13 Aug 2013 at 1:44
GDMA currently needs g03 (fixed by someone?)
Basis set provided by an intermediate object (e.g. orbitals)?
Not parallel. Worth parallelization?
Original issue reported on code.google.com by [email protected]
on 13 Aug 2013 at 1:42
useful to check moo against the projection methods
Original issue reported on code.google.com by [email protected]
on 16 Dec 2011 at 2:33
Currently it is not verz clear what the function does. This has already caused
one bug in site energy histogram
Change Crg1 to something more meaningfull like getPBCGhostCopy (there has to be
a better name)
Original issue reported on code.google.com by [email protected]
on 22 Sep 2011 at 2:28
Should be a wrapper to calculators (current one will be for one hopper)
Original issue reported on code.google.com by [email protected]
on 5 Nov 2011 at 10:13
Check that
1) the options match the number of fragments
2) all positions are set
3) all positions are set only once
This check has to be a combination of moo and ctp fixes.
Original issue reported on code.google.com by [email protected]
on 10 Oct 2011 at 2:00
ctp fits better to charge transport
Original issue reported on code.google.com by [email protected]
on 16 Sep 2011 at 9:00
1. Consistent Thole polarizabilities needed (AMOEBA <-> Thole)
2. Introduce constant scaling factors for charge states
Original issue reported on code.google.com by [email protected]
on 5 Jun 2012 at 2:48
Sasha: if first three atoms in segments.xml and map.xml do not match mapping is
not working properly even if symmetry=3.
Original issue reported on code.google.com by [email protected]
on 11 Nov 2011 at 3:12
1. Implement spheres method in eoutersphere calculator (so far only
time-consuming dielectric method implemented).
2. Implement constant method in eoutersphere calculator.
Original issue reported on code.google.com by [email protected]
on 5 Jun 2012 at 2:50
need to figure out how to filter xml tags using Property class
Original issue reported on code.google.com by [email protected]
on 2 Oct 2011 at 5:21
will give improved error message
Original issue reported on code.google.com by [email protected]
on 23 Sep 2011 at 12:52
Undocumented options
constant, generate_from, generate_unsafe
it is useful, make it a separate option
<load help="">
<file help=""></file>
<unsafe help=""></unsafe>
</load>
Adjust to use default values and extend the help xml file
Original issue reported on code.google.com by [email protected]
on 26 May 2013 at 5:57
Move all classes to namescpaces ctp, moo, kmc
Original issue reported on code.google.com by [email protected]
on 22 Sep 2011 at 2:21
Input files, state file, and commands have changed. Update the manual.
Original issue reported on code.google.com by [email protected]
on 29 Mar 2012 at 8:37
for atoms with residue names of 3 symbols and 2 digits as an atom number the
HETATM line is shifted in traj_cg.pdb
ATOM 12 PTR1 PBT 1 53.536 1.292 1.230 0.00 0.00
HETATM 12 PTR12 REU 1 53.393 1.958 1.9622 0.00 0.00
Original issue reported on code.google.com by [email protected]
on 11 Nov 2011 at 1:03
Add attributes to every option
help=""
default=""
unit=""
Original issue reported on code.google.com by [email protected]
on 22 May 2013 at 3:05
complains ERROR: Estatify first.
Original issue reported on code.google.com by [email protected]
on 14 Jun 2013 at 7:54
In mixtures we need a neighbor list based on cutoffs which depend on types of
molecules
Original issue reported on code.google.com by [email protected]
on 1 Nov 2011 at 9:13
Add enum(helpLong, helpShort)
Move PrintDescription() to QMApplication (out of the ctp_run)
Original issue reported on code.google.com by [email protected]
on 2 Aug 2013 at 5:35
the link to the code was revised; a bug in the rotation of rigid fragments was
fixed. New test is needed.
Original issue reported on code.google.com by [email protected]
on 29 Mar 2012 at 8:36
... should only appear for Jortner rates.
Original issue reported on code.google.com by [email protected]
on 5 Jun 2012 at 3:21
shall be changed to
list<string>::iterator findAttribute(string key)
type getAttribute<type>(pos)
At the moment two lookups are needed and it is not safe
Original issue reported on code.google.com by [email protected]
on 2 Aug 2013 at 5:31
derive Gaussian, Turbomole from QMWrapper and register them in a factory
adjust edft, idf to use QMWrapper
Original issue reported on code.google.com by [email protected]
on 2 Aug 2013 at 5:37
Move csg_property to tools (might be used by both ctp and csg parts)
Original issue reported on code.google.com by [email protected]
on 12 Oct 2011 at 10:25
What steps will reproduce the problem?
1.
2.
3.
What is the expected output? What do you see instead?
Please use labels and text to provide additional information.
Original issue reported on code.google.com by [email protected]
on 29 Mar 2012 at 8:34
e.g.
--options in csg vs --opt in ctp
Original issue reported on code.google.com by [email protected]
on 22 Sep 2011 at 2:24
Check if all object created via an objectfactory Create method are destroyed at
the end of the run (qmpackage, event)
Original issue reported on code.google.com by [email protected]
on 11 Aug 2013 at 7:21
adapt to the base class QMPackage (currently does not compile)
Original issue reported on code.google.com by [email protected]
on 6 Aug 2013 at 8:00
xml file format has been extended to better reference things in the latex
manual. ctp_run --list now reads in the brief description from the xml file.
Original issue reported on code.google.com by [email protected]
on 2 Oct 2011 at 5:38
Needed to restart KMC runs
Original issue reported on code.google.com by [email protected]
on 13 Aug 2013 at 1:47
similar to the EventFactory object for Carriers
Original issue reported on code.google.com by [email protected]
on 13 Aug 2013 at 1:46
the current version is correct only for 90deg angles
Original issue reported on code.google.com by [email protected]
on 29 Mar 2012 at 8:32
Program hangs for large atomic numbers - QmTopoloqy or Crgunit classes?
Original issue reported on code.google.com by [email protected]
on 5 Nov 2011 at 9:33
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