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This is VOTCA, which provides the two following subpackages:

  • VOTCA-CSG, a library which provides tools to develop coarse-grained potentials from atomistic simulation data
  • VOTCA-XTP, a library providing the DFT+GW-BSE method to calculate electronically excited states in single molecules, in molecular materials with quantum-classical embedding, as well as electron, hole, and exciton dynamics in atomistic MD-trajectories.

Basic installation

(see performance advice in Install Guide)

prefix=WHERE/TO/INSTALL/VOTCA
version=master # or 'v2024.1'
git clone -b ${version} https://github.com/votca/votca.git
cmake -B builddir -S votca -DBUILD_XTP=ON -DCMAKE_INSTALL_PREFIX=${prefix}
cmake --build builddir --parallel <number of cores>
ctest --test-dir builddir # to test build
cmake --build builddir --target install

Using this code via docker

docker pull votca/votca
docker run -it votca/votca /bin/bash

More detailed information:

  1. Installation
  2. Further Information
  3. Developers Guide
  4. VOTCA_LANGUAGE_GUIDE
  5. Code of Conduct

You find the VOTCA-CTP repository here

License:

Copyright 2009-2023 The VOTCA Development Team (http://www.votca.org)

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at

http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.

csg's People

Contributors

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csg's Issues

replace GNU gsl by lapack

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

review akima stuff

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

linear fit shows artifacts

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:

csg_resample: error

$ 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

csg_inverse: better logging

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

Code review request - thread documenation

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

Give warning if no box is read

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

Initial guess flag problem can lead to kink in dpot

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

Give a warning if version of libgmx has changed

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

threaded analysis engine

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

  • Blocking: #30

Better control on exclusions

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

Create binary packages

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

Shift potentials before converting to gromacs

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

csg_stat: change message

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

add readline support to csg_boltzmann

(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

  • Merged into: #9

csg_inverse: multiple simulation per step

-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

  • Blocking: #28

Fix gromacs dependance of testsuite results

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

Cleanup googlesites_upload.py

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

make scripts use threads

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

csg_call: clean up

-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

csg_stat: crash if no trj given

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_inverse: weaker die function

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

csg_inverse: user interactions

-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

  • Blocking: #11
  • Blocked on: #28

pbc for mapping

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

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