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License: Apache License 2.0
The source of the votca-csg and xtp packages
License: Apache License 2.0
Useful to auto-detect libdir (lib
or lib64
) and to allow users to configure data location and stuff.
Gromacs units are hard-codes for the Boltzmann inversion of potentials.
Original issue reported on code.google.com by [email protected]
on 21 Jan 2014 at 4:20
-will be needed for analysis within espresso++
-useful to write quickly little analysis tools
Original issue reported on code.google.com by [email protected]
on 13 Dec 2010 at 5:51
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 [email protected]
on 4 Dec 2013 at 2:34
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 [email protected]
on 11 Dec 2010 at 3:07
csg_dump settings file generation
(something like: generate option --setting)
Original issue reported on code.google.com by [email protected]
on 11 Jan 2011 at 10:27
Something like:
git clone --recursive [email protected]:votca/votca
mv ~/${TRAVIS_REPO_SLUG} votca
(from trac)
-open a pipe to gnuplot
-allow plotting of table and distributions
Original issue reported on code.google.com by [email protected]
on 18 Oct 2010 at 5:38
(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 [email protected]
on 18 Oct 2010 at 5:31
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 [email protected]
on 5 Jan 2011 at 1:17
To see what comes next in 2016
Force matching of a large trajectory can take several hours.
Using threads would be very useful.
Original issue reported on code.google.com by [email protected]
on 10 Mar 2011 at 1:40
Using a tpr file from gromacs-2016 and running in the propane/atomistic
folder of csg-tutorials:
$ ~/votca/src/csg/src/tools/csg_map --no-map --top topol.tpr --trj conf.gro --out conf2.gro
The residue number differs in conf.gro
and conf2.gro
.
It seems atoms->nres
is 1even though there should be multiple copies of it.
Back when votca/csg#162 was fixed (f986dc5), it seemed to have worked!
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 [email protected]
on 13 Aug 2013 at 12:27
With lammps hitting fedora (lammps/lammps#400), we should enable the lammps tutorial for testing as well.
For that we need:
lammps
in votca/buildenv (votca/buildenv#3)CSG_MDRUN_STEPS
in run_genericsim.sh
in votca/csg (votca/csg#227)The last point is the difficult one.
I'm not sure if this is a LAMMPS issue or a VOTCA issue, but it appears in LAMMPS when doing interpolation between the ends of the table, LAMMPS is finding a discontinuity with it's tabulated dihedral. Issue propagates creating unphysical bond lengths, but when changing to an analytical fit of the dihedral, the issue goes away and I can take at least an order of magnitude larger timestep with a Langevin thermostat. Need to figure out how to best construct the table to interface with LAMMPS.
- number density
- improved atom selection capabilities
Original issue reported on code.google.com by [email protected]
on 28 Apr 2011 at 3:41
Looking at https://github.com/shirtsgroup/InterMol, it seems like a good place to add support to h5md and xmltogology.
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 [email protected]
on 23 Oct 2010 at 12:56
-add a section to the manual
-naming scheme
Original issue reported on code.google.com by [email protected]
on 16 Jun 2011 at 9:34
catastrophic error: cannot open source file "mkl_boost_ublas_matrix_prod.hpp"
#include "mkl_boost_ublas_matrix_prod.hpp"
It is a problem with both in and out of source build
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 [email protected]
on 6 Apr 2014 at 1:36
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 [email protected]
on 11 Oct 2014 at 10:09
Many member variables are not initialized, e.g. Bead userdata
Original issue reported on code.google.com by [email protected]
on 20 Jun 2011 at 8:33
Make a branch, which pulls all the "master" version of all the submodules:
if [[ ${TRAVIS_BRANCH} = future ]]; then
git submodule forearch git checkout master
git submodule forearch git pull
fi
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 [email protected]
on 30 Mar 2012 at 10:02
Add a build, which installs in user space, e.g. $HOME.
Needed for #6.
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 [email protected]
on 25 Nov 2010 at 8:11
Gromacs does it as well
http://redmine.gromacs.org/issues/685
Original issue reported on code.google.com by [email protected]
on 3 Feb 2011 at 4:16
Make a build without fftw, gsl, gmx and friends.
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 [email protected]
on 12 Nov 2013 at 7:12
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 [email protected]
on 3 May 2011 at 4:07
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 [email protected]
on 14 Dec 2010 at 11:36
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