The csg code is now part of votca.
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View Code? Open in Web Editor NEWCoarse-graining potentials from atomistic references made easy
Coarse-graining potentials from atomistic references made easy
The csg code is now part of votca.
No description was provided for this review request. See branch link for all
revisions related to this review.
Original issue reported on code.google.com by konstantin.koschke
on 8 Dec 2010 at 2:46
To allow for better treatment and speedup if complexity of triclinix box is not
needed.
Original issue reported on code.google.com by [email protected]
on 25 Nov 2010 at 8:09
This issue was created by revision a466e19f90.
Please read and improve
Original issue reported on code.google.com by junghans%[email protected]
on 15 Dec 2010 at 1:55
e.g. allow for solvent free mapping
Original issue reported on code.google.com by [email protected]
on 23 Oct 2010 at 1:02
Changeset 00a04ceed1a4 of csg repo
Original issue reported on code.google.com by [email protected]
on 10 Jan 2011 at 6:35
check mdp vs xml options
Original issue reported on code.google.com by [email protected]
on 10 Dec 2010 at 11:49
need to find what's going on, looks like some bogus pointer / buffer overflow
stuff.
Original issue reported on code.google.com by [email protected]
on 23 Oct 2010 at 1:00
The die function does 'kill 0', which will stop all process up to the master
process. This is problem in the testsuite.
On the other hand die should still sub-, subsub- and subsubsubshells.
Original issue reported on code.google.com by [email protected]
on 18 Oct 2010 at 5:29
Defaults are everywhere (script, csg_stat, ...)
Put all of them in one xml and install it in /usr/share
Original issue reported on code.google.com by [email protected]
on 5 Jan 2011 at 10:49
all=( $(for_all '$(csg_get_interaction_property name)') )
for i in all;
for j>i;
i = j & die "double name"
Original issue reported on code.google.com by [email protected]
on 12 Jan 2011 at 5:45
if setting xml file does not contain an interaction, trajectory is still
read-in and nothing is done.
Original issue reported on code.google.com by [email protected]
on 25 Nov 2010 at 9:16
forbid beads, which are bigger than l_box/2.
Correct treatment of pbc in mapping.
Original issue reported on code.google.com by [email protected]
on 8 Dec 2010 at 2:37
Box size can be read from pdb, but if no box is specified, open bc are used
(currently beeing implemented, not yet in default branch). In this case print
warning.
Original issue reported on code.google.com by [email protected]
on 22 Dec 2010 at 3:59
-allow conf.gro or confout.gro to be the initial condition.
-make an option in xml file
Original issue reported on code.google.com by [email protected]
on 8 Dec 2010 at 2:38
This would allow specifying some interactions using a different method and
apply force matching to the remaining ones.
Original issue reported on code.google.com by [email protected]
on 25 Nov 2010 at 8:16
-Set equi_time to 10000
-g_rdf will fail
-calc_rdf_gromacs will still continue
Original issue reported on code.google.com by [email protected]
on 12 Jan 2011 at 5:49
This issue was created by revision a51a5141a6.
Please read and improve
Original issue reported on code.google.com by junghans%[email protected]
on 15 Dec 2010 at 1:33
csg_stat always shows "begin to calculate inverse monte carlo parameters" even
if we calculate no imc stuff.
Original issue reported on code.google.com by [email protected]
on 29 Nov 2010 at 9:27
Changes to integrate.pl
-add an option --wtih-error
-read-in table with errors using readin_table_err (needs to be written first)
-use formula from pmf calculation
Original issue reported on code.google.com by [email protected]
on 28 Oct 2010 at 10:22
We have threads ready:
- csg_stat should be called by default instead of multi_g_rdf
- rename 'mpi' block to 'parallel' in setting file
- if number of tasks = 0 get it from $(grep -c processor /proc/cpuinfo)
Original issue reported on code.google.com by [email protected]
on 7 Dec 2010 at 5:59
This script is needed to automatically update google sites reference sections.
It should have options for:
- user/password (this is already implemented)
- which site to update
- specifying local file for site update
- update attachements/download files to publish manual
Ths script is in the admin repository scripts/googlesites_upload.py
Original issue reported on code.google.com by [email protected]
on 13 Jan 2011 at 10:00
Segfault, if the bead specified in bond or angle of mapping xml does not exist.
Original issue reported on code.google.com by [email protected]
on 2 Dec 2010 at 10:38
If the topology file is given, but the trajectory file not csg_stat will stop
with the following strange error message:
{{{
an error occurred:
boost::bad_any_cast: failed conversion using boost::any_cast
}}}
Can we improve this error message?
Original issue reported on code.google.com by [email protected]
on 2 Dec 2010 at 2:54
csg_resample currently uses cubic splines which are known to have some
problems. Akima splines might be better.
Original issue reported on code.google.com by [email protected]
on 2 Nov 2010 at 4:47
Need to implement threaded support for csg_stat. Should not be a big issue
Original issue reported on code.google.com by [email protected]
on 2 Dec 2010 at 7:43
Property not found is a not very helpful error message. Add more detailed error
messages to property class e.g. missing option in file xyz.xml.
Original issue reported on code.google.com by [email protected]
on 16 Oct 2010 at 6:53
The last flag in step_000/CG-CG.pot.new can be o (probably due to resampling of
initial guess / initial user potential). This can lead to kinks in the dpot
since last point is not updated.
Possible problems + fixes:
- Check whether csg_resamble writes flags correctly
- Improve the update script
Original issue reported on code.google.com by [email protected]
on 25 Nov 2010 at 8:07
-add bibliography function to create a bibtex file with used methods for papers
Original issue reported on code.google.com by [email protected]
on 18 Oct 2010 at 5:36
$ cat table
0 0
1.4 0
$csg_resample --type cubic --in table --out table2 --grid 0:0.01:1.4
works, but
$csg_resample --type akima --in table --out table2 --grid 0:0.01:1.4
Check failed in file /usr/include/boost/numeric/ublas/storage.hpp at line 195:
i < size_
terminate called after throwing an instance of
'boost::numeric::ublas::bad_index'
what(): bad index
Aborted
Original issue reported on code.google.com by [email protected]
on 12 Jan 2011 at 5:21
Currently, the nbsearch only and always excluded every intramolecular
contribution which belongs to a bonded interaction. This should be better
customizable to exclude e.g. all intra-molecular contributions, or to add
manual exclusion lists.
Original issue reported on code.google.com by [email protected]
on 11 Dec 2010 at 3:08
-already used (kind of) by Sebastian for TF
-we will need a clear definition of type1, type2 (and more) in settings file,
now can be a name from index file for ibi or pattern for atom names in the case
of imc.
Original issue reported on code.google.com by [email protected]
on 18 Oct 2010 at 5:12
No description was provided for this review request. See branch link for all
revisions related to this review.
Original issue reported on code.google.com by konstantin.koschke
on 24 Nov 2010 at 3:51
(from trac)
-make iterative process work for bonded
-extrapolation script are there
-What happens to undefined data points in the middle
Original issue reported on code.google.com by [email protected]
on 18 Oct 2010 at 5:47
-copy color code from build utils
-add a function to function inverse
-add --no-color option
Original issue reported on code.google.com by [email protected]
on 10 Dec 2010 at 4:38
Doxygen title page is empty, see:
http://doc.votca.org
Original issue reported on code.google.com by [email protected]
on 14 Dec 2010 at 10:43
We are just using qr solve, which also available via lapack.
And lapack is also available on HPC machines.
Original issue reported on code.google.com by [email protected]
on 7 Dec 2010 at 3:44
Ubuntu offers a Personal Package Archive:
https://help.launchpad.net/Packaging/PPA
we should create a binary package some when soon.
Original issue reported on code.google.com by [email protected]
on 18 Oct 2010 at 5:43
mdrun, g_energy, g_rdf and Espresso_bin are hardcoded in USES lines of some
scripts. Move the check
Original issue reported on code.google.com by junghans%[email protected]
on 13 Oct 2010 at 2:07
simplex seems to work, so we should start merging the basic functions.
Original issue reported on code.google.com by [email protected]
on 2 Dec 2010 at 2:27
There are unpredictable segfaults when the loaded version of libgmx differs
from the one compiled with (binary incompatibility).
CsgApplication should drop a warning at rumtime if the version differs.
Original issue reported on code.google.com by [email protected]
on 6 Jan 2011 at 9:58
No description was provided for this review request. See branch link for all
revisions related to this review.
Original issue reported on code.google.com by [email protected]
on 8 Dec 2010 at 11:42
Check this, does this issue still exist? Might be a good thing to do already on
.pot level. This issue is also connected to the procedure how to convert
potentials to the simulation program (e.g. when should be extrapolated, etc).
Original issue reported on code.google.com by [email protected]
on 2 Nov 2010 at 4:50
The testsuite calls gromacs to perform short runs which are then analyzed. The
result of the run depends on the gromacs version which should not be the case.
Best way might be to provide fixed trajectories, however this would increase
the size of the testsuite.
Original issue reported on code.google.com by [email protected]
on 6 Dec 2010 at 4:29
Now we have logging everywhere. We need to clean it up and use a special file
descriptor for output on screen.
Example:
$cat logtest.sh
#!/bin/bash
msg() { echo "$*" >&3; }
echo STOUT;echo STDERR >&2; msg "SCREEN"
$./logtest.sh 3>&1 &> logfile
SCREEN
$cat logfile
STOUT
STDERR
This makes it also much easier to write custom scripts.
Original issue reported on code.google.com by [email protected]
on 18 Oct 2010 at 5:19
e.g. allow for solvent free mapping
Original issue reported on code.google.com by [email protected]
on 23 Oct 2010 at 1:02
-Allow to run a minimization before the actual simulation
-Maybe group them to allow multiple simulations at the same time for simplex
and genetic algorithms
-Allow groups of GMX options
Original issue reported on code.google.com by [email protected]
on 18 Oct 2010 at 5:26
What steps will reproduce the problem?
1. csg_resample --in dens.SOL.xvg --out out.xvg --grid .55:0.01:2.65 --type
linear --fitgrid .55:0.1:2.65
(dens.SOL.xvg attached)
What is the expected output? What do you see instead?
linear fit does not go through data for low x values
Original issue reported on code.google.com by [email protected]
on 9 Dec 2010 at 10:09
Attachments:
If topol.tpr does not exist,
$csg_dump --top topol.tpr
Segmentation fault
Original issue reported on code.google.com by [email protected]
on 11 Jan 2011 at 8:28
-make it use source inverse_start.sh
-move csg_inverse specific functions to functions_inverse
-make csg_call do not use logfile (fd 3)
Original issue reported on code.google.com by [email protected]
on 21 Dec 2010 at 8:38
(from trac)
-readline support (history, up and down keys, etc.) would be nice in
csg_boltzmann
See this guide:
http://cc.byexamples.com/20080613/gnu-readline-how-to-keep-a-history-list-of-ent
ered-command-lines/
Original issue reported on code.google.com by [email protected]
on 18 Oct 2010 at 5:58
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