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generic tools module

tools's Introduction

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'
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>
cmake --build builddir --target install

Using this code via docker

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

More detailed information:

You find the VOTCA-CTP repository here

License:

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.

tools's People

Contributors

Stargazers

Watchers

Forkers

junghans jkrajniak tomspur jdmoore2004 codacy-badger fossabot

tools's Issues

Cmake MKL_ThreadingLibrary

Recent building attempt on our cluster failed upon linking because

MKL_ThreadingLibrary_LINK_LIBRARY:FILEPATH

is not found. Cmake does not throw an error. Workaround only possible by adding the correct filename of libiomp5.so manually.

more votca_help2man warning

After most recent changes, we have the following new warnings:

/home/junghans/votca/build/sphinx/csg/csg_call.rst:31: WARNING: Unexpected indentation.
/home/junghans/votca/build/sphinx/csg/csg_call.rst:45: WARNING: Block quote ends without a blank line; unexpected unindent.
../../sphinx/csg/csg_boltzmann.rst:25: WARNING: Literal block expected; none found.
../../sphinx/csg/csg_boltzmann.rst:43: WARNING: Option list ends without a blank line; unexpected unindent.
../../sphinx/csg/csg_boltzmann.rst:45: WARNING: Definition list ends without a blank line; unexpected unindent.
../../sphinx/csg/csg_call.rst:31: WARNING: Unexpected indentation.
../../sphinx/csg/csg_call.rst:45: WARNING: Block quote ends without a blank line; unexpected unindent.
../../sphinx/csg/csg_density.rst:24: WARNING: Literal block expected; none found.
../../sphinx/csg/csg_density.rst:34: WARNING: Unexpected indentation.
../../sphinx/csg/csg_density.rst:35: WARNING: Block quote ends without a blank line; unexpected unindent.
../../sphinx/csg/csg_density.rst:44: WARNING: Unexpected indentation.
../../sphinx/csg/csg_density.rst:45: WARNING: Block quote ends without a blank line; unexpected unindent.
../../sphinx/csg/csg_density.rst:48: WARNING: Option list ends without a blank line; unexpected unindent.
../../sphinx/csg/csg_density.rst:55: WARNING: Option list ends without a blank line; unexpected unindent.
../../sphinx/csg/csg_density.rst:57: WARNING: Definition list ends without a blank line; unexpected unindent.
/home/junghans/votca/build/sphinx/csg/reference.rst:25: WARNING: Literal block expected; none found.
../../sphinx/csg/csg_dump.rst:24: WARNING: Literal block expected; none found.
../../sphinx/csg/csg_dump.rst:34: WARNING: Unexpected indentation.
../../sphinx/csg/csg_dump.rst:35: WARNING: Block quote ends without a blank line; unexpected unindent.
../../sphinx/csg/csg_fmatch.rst:24: WARNING: Literal block expected; none found.
../../sphinx/csg/csg_fmatch.rst:32: WARNING: Unexpected indentation.
../../sphinx/csg/csg_fmatch.rst:42: WARNING: Option list ends without a blank line; unexpected unindent.
../../sphinx/csg/csg_fmatch.rst:44: WARNING: Definition list ends without a blank line; unexpected unindent.
../../sphinx/csg/csg_gmxtopol.rst:25: WARNING: Literal block expected; none found.
../../sphinx/csg/csg_gmxtopol.rst:32: WARNING: Unexpected indentation.
../../sphinx/csg/csg_imc_solve.rst:24: WARNING: Literal block expected; none found.
../../sphinx/csg/csg_inverse.rst:31: WARNING: Unexpected indentation.
../../sphinx/csg/csg_reupdate.rst:24: WARNING: Literal block expected; none found.
../../sphinx/csg/csg_reupdate.rst:30: WARNING: Unexpected indentation.
../../sphinx/csg/csg_reupdate.rst:34: WARNING: Option list ends without a blank line; unexpected unindent.
../../sphinx/csg/csg_reupdate.rst:36: WARNING: Definition list ends without a blank line; unexpected unindent.
../../sphinx/csg/csg_reupdate.rst:38: WARNING: Unexpected indentation.
../../sphinx/csg/csg_reupdate.rst:39: WARNING: Option list ends without a blank line; unexpected unindent.
../../sphinx/csg/csg_reupdate.rst:43: WARNING: Unexpected indentation.
../../sphinx/csg/csg_reupdate.rst:50: WARNING: Option list ends without a blank line; unexpected unindent.
../../sphinx/csg/csg_reupdate.rst:52: WARNING: Definition list ends without a blank line; unexpected unindent.
../../sphinx/csg/csg_stat.rst:27: WARNING: Literal block expected; none found.
../../sphinx/csg/csg_stat.rst:37: WARNING: Unexpected indentation.
../../sphinx/csg/csg_stat.rst:38: WARNING: Block quote ends without a blank line; unexpected unindent.
../../sphinx/csg/csg_stat.rst:47: WARNING: Option list ends without a blank line; unexpected unindent.
../../sphinx/csg/csg_stat.rst:54: WARNING: Option list ends without a blank line; unexpected unindent.
../../sphinx/csg/csg_stat.rst:56: WARNING: Definition list ends without a blank line; unexpected unindent.
../../sphinx/csg/csg_fluctuations.rst:24: WARNING: Literal block expected; none found.
../../sphinx/csg/csg_fluctuations.rst:38: WARNING: Unexpected indentation.
../../sphinx/csg/csg_fluctuations.rst:39: WARNING: Block quote ends without a blank line; unexpected unindent.
../../sphinx/csg/csg_fluctuations.rst:51: WARNING: Option list ends without a blank line; unexpected unindent.
../../sphinx/csg/csg_fluctuations.rst:53: WARNING: Definition list ends without a blank line; unexpected unindent.
../../sphinx/csg/csg_orientcorr.rst:17: WARNING: Definition list ends without a blank line; unexpected unindent.
../../sphinx/csg/csg_orientcorr.rst:27: WARNING: Literal block ends without a blank line; unexpected unindent.
../../sphinx/csg/csg_orientcorr.rst:47: WARNING: Option list ends without a blank line; unexpected unindent.
../../sphinx/csg/csg_orientcorr.rst:49: WARNING: Definition list ends without a blank line; unexpected unindent.
../../sphinx/csg/csg_partial_rdf.rst:24: WARNING: Literal block expected; none found.
../../sphinx/csg/csg_partial_rdf.rst:34: WARNING: Unexpected indentation.
../../sphinx/csg/csg_partial_rdf.rst:35: WARNING: Block quote ends without a blank line; unexpected unindent.
../../sphinx/csg/csg_partial_rdf.rst:54: WARNING: Option list ends without a blank line; unexpected unindent.
../../sphinx/csg/csg_partial_rdf.rst:56: WARNING: Definition list ends without a blank line; unexpected unindent.
../../sphinx/csg/csg_radii.rst:24: WARNING: Literal block expected; none found.
../../sphinx/csg/csg_radii.rst:33: WARNING: Option list ends without a blank line; unexpected unindent.
../../sphinx/csg/csg_radii.rst:37: WARNING: Option list ends without a blank line; unexpected unindent.
../../sphinx/csg/csg_radii.rst:39: WARNING: Definition list ends without a blank line; unexpected unindent.
../../sphinx/csg/csg_sphericalorder.rst:27: WARNING: Literal block expected; none found.
../../sphinx/csg/csg_sphericalorder.rst:35: WARNING: Unexpected indentation.
../../sphinx/csg/csg_sphericalorder.rst:36: WARNING: Block quote ends without a blank line; unexpected unindent.
../../sphinx/csg/csg_sphericalorder.rst:38: WARNING: Definition list ends without a blank line; unexpected unindent.
../../sphinx/csg/csg_sphericalorder.rst:39: WARNING: Option list ends without a blank line; unexpected unindent.
../../sphinx/csg/csg_sphericalorder.rst:49: WARNING: Option list ends without a blank line; unexpected unindent.
../../sphinx/csg/csg_sphericalorder.rst:51: WARNING: Definition list ends without a blank line; unexpected unindent.
../../sphinx/csg/csg_traj_force.rst:24: WARNING: Literal block expected; none found.
../../sphinx/csg/csg_traj_force.rst:32: WARNING: Unexpected indentation.
../../sphinx/csg/csg_traj_force.rst:33: WARNING: Block quote ends without a blank line; unexpected unindent.
../../sphinx/csg/csg_traj_force.rst:37: WARNING: Option list ends without a blank line; unexpected unindent.
../../sphinx/csg/csg_traj_force.rst:39: WARNING: Definition list ends without a blank line; unexpected unindent.

drop tcsh support?

Can we drop support for tcsh? OSX switched to bash a decade ago.

Replace gsl in linalg with LAPACK calls

Property data structure does not really portray xml structure

The property class has a problem with multiple elements with the same name e.g.

<jobs>
<job></job>
<job></job>
</jobs>

Property will store all job children but, the get("job") will only return the last job. This can be problematic in many cases.

The reasons behind is that get() relies on a std::map<string,index_of_last_element> so whenever the key exists already in the map, the index ist just overwritten.

Possible solutions:

Do not allow multiple elements with the same tag. Would break many parts of votca like all mapping files etc...
Modify property so that it does not return the last array but a vector containing pointers to all job objects.
Rename get() , set(), etc... to getLast(), setLast() etc... to make the behaviour explicit.
We could also have a second map std::mapstd::string,int which returns the number of elements with the same tag

Make clearer error when attribute not found

https://groups.google.com/forum/#!topic/votca/Lt_Sor5w0p0

votca_help2doc warnings

After the lastest update (#345), here are the maining warnings:

/home/junghans/votca/build/sphinx/csg/csg_boltzmann.rst:26: WARNING: Explicit markup ends without a blank line; unexpected unindent.
/home/junghans/votca/build/sphinx/csg/csg_call.rst:30: WARNING: Explicit markup ends without a blank line; unexpected unindent.
/home/junghans/votca/build/sphinx/csg/csg_density.rst:25: WARNING: Explicit markup ends without a blank line; unexpected unindent.
/home/junghans/votca/build/sphinx/csg/csg_dlptopol.rst:33: WARNING: Explicit markup ends without a blank line; unexpected unindent.
/home/junghans/votca/build/sphinx/csg/csg_dump.rst:25: WARNING: Explicit markup ends without a blank line; unexpected unindent.
/home/junghans/votca/build/sphinx/csg/csg_fluctuations.rst:25: WARNING: Explicit markup ends without a blank line; unexpected unindent.
/home/junghans/votca/build/sphinx/csg/csg_fmatch.rst:25: WARNING: Explicit markup ends without a blank line; unexpected unindent.
/home/junghans/votca/build/sphinx/csg/csg_gmxtopol.rst:26: WARNING: Explicit markup ends without a blank line; unexpected unindent.
/home/junghans/votca/build/sphinx/csg/csg_imc_solve.rst:25: WARNING: Explicit markup ends without a blank line; unexpected unindent.
/home/junghans/votca/build/sphinx/csg/csg_inverse.rst:29: WARNING: Explicit markup ends without a blank line; unexpected unindent.
/home/junghans/votca/build/sphinx/csg/csg_map.rst:34: WARNING: Explicit markup ends without a blank line; unexpected unindent.
/home/junghans/votca/build/sphinx/csg/csg_orientcorr.rst:17: WARNING: Definition list ends without a blank line; unexpected unindent.
/home/junghans/votca/build/sphinx/csg/csg_orientcorr.rst:31: WARNING: Explicit markup ends without a blank line; unexpected unindent.
/home/junghans/votca/build/sphinx/csg/csg_part_dist.rst:26: WARNING: Explicit markup ends without a blank line; unexpected unindent.
/home/junghans/votca/build/sphinx/csg/csg_partial_rdf.rst:25: WARNING: Explicit markup ends without a blank line; unexpected unindent.
/home/junghans/votca/build/sphinx/csg/csg_property.rst:24: WARNING: Explicit markup ends without a blank line; unexpected unindent.
/home/junghans/votca/build/sphinx/csg/csg_radii.rst:25: WARNING: Explicit markup ends without a blank line; unexpected unindent.
/home/junghans/votca/build/sphinx/csg/csg_resample.rst:27: WARNING: Explicit markup ends without a blank line; unexpected unindent.
/home/junghans/votca/build/sphinx/csg/csg_reupdate.rst:25: WARNING: Explicit markup ends without a blank line; unexpected unindent.
../../sphinx/csg/scripts/calc_kbint.sh.rst:23: WARNING: Explicit markup ends without a blank line; unexpected unindent.
../../sphinx/csg/scripts/cma_processor.py.rst:24: WARNING: Explicit markup ends without a blank line; unexpected unindent.
../../sphinx/csg/scripts/dist_adjust.pl.rst:26: WARNING: Explicit markup ends without a blank line; unexpected unindent.
../../sphinx/csg/scripts/dist_boltzmann_invert.pl.rst:31: WARNING: Explicit markup ends without a blank line; unexpected unindent.
../../sphinx/csg/scripts/inverse.sh.rst:29: WARNING: Explicit markup ends without a blank line; unexpected unindent.
../../sphinx/csg/scripts/kbibi_ramp_correction.pl.rst:29: WARNING: Explicit markup ends without a blank line; unexpected unindent.
../../sphinx/csg/scripts/merge_tables.pl.rst:26: WARNING: Explicit markup ends without a blank line; unexpected unindent.
../../sphinx/csg/scripts/potential_extrapolate.sh.rst:24: WARNING: Explicit markup ends without a blank line; unexpected unindent.
../../sphinx/csg/scripts/potential_shift.pl.rst:28: WARNING: Explicit markup ends without a blank line; unexpected unindent.
../../sphinx/csg/scripts/potential_to_gromacs.sh.rst:24: WARNING: Explicit markup ends without a blank line; unexpected unindent.
../../sphinx/csg/scripts/potential_to_lammps.sh.rst:24: WARNING: Explicit markup ends without a blank line; unexpected unindent.
../../sphinx/csg/scripts/table_average.sh.rst:26: WARNING: Explicit markup ends without a blank line; unexpected unindent.
../../sphinx/csg/scripts/table_combine.pl.rst:24: WARNING: Explicit markup ends without a blank line; unexpected unindent.
../../sphinx/csg/scripts/table_dummy.sh.rst:23: WARNING: Explicit markup ends without a blank line; unexpected unindent.
../../sphinx/csg/scripts/table_extrapolate.pl.rst:24: WARNING: Explicit markup ends without a blank line; unexpected unindent.
../../sphinx/csg/scripts/table_functional.sh.rst:26: WARNING: Explicit markup ends without a blank line; unexpected unindent.
../../sphinx/csg/scripts/table_get_value.pl.rst:24: WARNING: Explicit markup ends without a blank line; unexpected unindent.
../../sphinx/csg/scripts/table_integrate.pl.rst:26: WARNING: Explicit markup ends without a blank line; unexpected unindent.
../../sphinx/csg/scripts/table_linearop.pl.rst:26: WARNING: Explicit markup ends without a blank line; unexpected unindent.
../../sphinx/csg/scripts/table_to_tab.pl.rst:29: WARNING: Explicit markup ends without a blank line; unexpected unindent.
../../sphinx/csg/scripts/table_to_xvg.pl.rst:28: WARNING: Explicit markup ends without a blank line; unexpected unindent.
/home/junghans/votca/build/sphinx/csg/csg_sphericalorder.rst:28: WARNING: Explicit markup ends without a blank line; unexpected unindent.
/home/junghans/votca/build/sphinx/csg/csg_stat.rst:28: WARNING: Explicit markup ends without a blank line; unexpected unindent.
/home/junghans/votca/build/sphinx/csg/csg_traj_force.rst:25: WARNING: Explicit markup ends without a blank line; unexpected unindent.
../../sphinx/csg/csg_boltzmann.rst:26: WARNING: Explicit markup ends without a blank line; unexpected unindent.
../../sphinx/csg/csg_call.rst:30: WARNING: Explicit markup ends without a blank line; unexpected unindent.
../../sphinx/csg/csg_density.rst:25: WARNING: Explicit markup ends without a blank line; unexpected unindent.
../../sphinx/csg/csg_dlptopol.rst:33: WARNING: Explicit markup ends without a blank line; unexpected unindent.
../../sphinx/csg/csg_dump.rst:25: WARNING: Explicit markup ends without a blank line; unexpected unindent.
../../sphinx/csg/csg_fmatch.rst:25: WARNING: Explicit markup ends without a blank line; unexpected unindent.
../../sphinx/csg/csg_gmxtopol.rst:26: WARNING: Explicit markup ends without a blank line; unexpected unindent.
../../sphinx/csg/csg_imc_solve.rst:25: WARNING: Explicit markup ends without a blank line; unexpected unindent.
../../sphinx/csg/csg_inverse.rst:29: WARNING: Explicit markup ends without a blank line; unexpected unindent.
../../sphinx/csg/csg_map.rst:34: WARNING: Explicit markup ends without a blank line; unexpected unindent.
../../sphinx/csg/csg_property.rst:24: WARNING: Explicit markup ends without a blank line; unexpected unindent.
../../sphinx/csg/csg_resample.rst:27: WARNING: Explicit markup ends without a blank line; unexpected unindent.
../../sphinx/csg/csg_reupdate.rst:25: WARNING: Explicit markup ends without a blank line; unexpected unindent.
../../sphinx/csg/csg_stat.rst:28: WARNING: Explicit markup ends without a blank line; unexpected unindent.
../../sphinx/csg/scripts/calc_kbint.sh.rst:23: WARNING: Explicit markup ends without a blank line; unexpected unindent.
../../sphinx/csg/scripts/cma_processor.py.rst:24: WARNING: Explicit markup ends without a blank line; unexpected unindent.
../../sphinx/csg/scripts/dist_adjust.pl.rst:26: WARNING: Explicit markup ends without a blank line; unexpected unindent.
../../sphinx/csg/scripts/dist_boltzmann_invert.pl.rst:31: WARNING: Explicit markup ends without a blank line; unexpected unindent.
../../sphinx/csg/scripts/inverse.sh.rst:29: WARNING: Explicit markup ends without a blank line; unexpected unindent.
../../sphinx/csg/scripts/kbibi_ramp_correction.pl.rst:29: WARNING: Explicit markup ends without a blank line; unexpected unindent.
../../sphinx/csg/scripts/merge_tables.pl.rst:26: WARNING: Explicit markup ends without a blank line; unexpected unindent.
../../sphinx/csg/scripts/potential_extrapolate.sh.rst:24: WARNING: Explicit markup ends without a blank line; unexpected unindent.
../../sphinx/csg/scripts/potential_shift.pl.rst:28: WARNING: Explicit markup ends without a blank line; unexpected unindent.
../../sphinx/csg/scripts/potential_to_gromacs.sh.rst:24: WARNING: Explicit markup ends without a blank line; unexpected unindent.
../../sphinx/csg/scripts/potential_to_lammps.sh.rst:24: WARNING: Explicit markup ends without a blank line; unexpected unindent.
../../sphinx/csg/scripts/table_average.sh.rst:26: WARNING: Explicit markup ends without a blank line; unexpected unindent.
../../sphinx/csg/scripts/table_combine.pl.rst:24: WARNING: Explicit markup ends without a blank line; unexpected unindent.
../../sphinx/csg/scripts/table_dummy.sh.rst:23: WARNING: Explicit markup ends without a blank line; unexpected unindent.
../../sphinx/csg/scripts/table_extrapolate.pl.rst:24: WARNING: Explicit markup ends without a blank line; unexpected unindent.
../../sphinx/csg/scripts/table_functional.sh.rst:26: WARNING: Explicit markup ends without a blank line; unexpected unindent.
../../sphinx/csg/scripts/table_get_value.pl.rst:24: WARNING: Explicit markup ends without a blank line; unexpected unindent.
../../sphinx/csg/scripts/table_integrate.pl.rst:26: WARNING: Explicit markup ends without a blank line; unexpected unindent.
../../sphinx/csg/scripts/table_linearop.pl.rst:26: WARNING: Explicit markup ends without a blank line; unexpected unindent.
../../sphinx/csg/scripts/table_to_tab.pl.rst:29: WARNING: Explicit markup ends without a blank line; unexpected unindent.
../../sphinx/csg/scripts/table_to_xvg.pl.rst:28: WARNING: Explicit markup ends without a blank line; unexpected unindent.
../../sphinx/csg/csg_fluctuations.rst:25: WARNING: Explicit markup ends without a blank line; unexpected unindent.
../../sphinx/csg/csg_orientcorr.rst:17: WARNING: Definition list ends without a blank line; unexpected unindent.
../../sphinx/csg/csg_orientcorr.rst:31: WARNING: Explicit markup ends without a blank line; unexpected unindent.
../../sphinx/csg/csg_part_dist.rst:26: WARNING: Explicit markup ends without a blank line; unexpected unindent.
../../sphinx/csg/csg_partial_rdf.rst:25: WARNING: Explicit markup ends without a blank line; unexpected unindent.
../../sphinx/csg/csg_radii.rst:25: WARNING: Explicit markup ends without a blank line; unexpected unindent.
../../sphinx/csg/csg_sphericalorder.rst:28: WARNING: Explicit markup ends without a blank line; unexpected unindent.
../../sphinx/csg/csg_traj_force.rst:25: WARNING: Explicit markup ends without a blank line; unexpected unindent.
/home/junghans/votca/build/sphinx/csg/scripts/calc_kbint.sh.rst:23: WARNING: Explicit markup ends without a blank line; unexpected unindent.
/home/junghans/votca/build/sphinx/csg/scripts/cma_processor.py.rst:24: WARNING: Explicit markup ends without a blank line; unexpected unindent.
/home/junghans/votca/build/sphinx/csg/scripts/dist_adjust.pl.rst:26: WARNING: Explicit markup ends without a blank line; unexpected unindent.
/home/junghans/votca/build/sphinx/csg/scripts/dist_boltzmann_invert.pl.rst:31: WARNING: Explicit markup ends without a blank line; unexpected unindent.
/home/junghans/votca/build/sphinx/csg/scripts/inverse.sh.rst:29: WARNING: Explicit markup ends without a blank line; unexpected unindent.
/home/junghans/votca/build/sphinx/csg/scripts/kbibi_ramp_correction.pl.rst:29: WARNING: Explicit markup ends without a blank line; unexpected unindent.
/home/junghans/votca/build/sphinx/csg/scripts/merge_tables.pl.rst:26: WARNING: Explicit markup ends without a blank line; unexpected unindent.
/home/junghans/votca/build/sphinx/csg/scripts/potential_extrapolate.sh.rst:24: WARNING: Explicit markup ends without a blank line; unexpected unindent.
/home/junghans/votca/build/sphinx/csg/scripts/potential_shift.pl.rst:28: WARNING: Explicit markup ends without a blank line; unexpected unindent.
/home/junghans/votca/build/sphinx/csg/scripts/potential_to_gromacs.sh.rst:24: WARNING: Explicit markup ends without a blank line; unexpected unindent.
/home/junghans/votca/build/sphinx/csg/scripts/potential_to_lammps.sh.rst:24: WARNING: Explicit markup ends without a blank line; unexpected unindent.
/home/junghans/votca/build/sphinx/csg/scripts/table_average.sh.rst:26: WARNING: Explicit markup ends without a blank line; unexpected unindent.
/home/junghans/votca/build/sphinx/csg/scripts/table_combine.pl.rst:24: WARNING: Explicit markup ends without a blank line; unexpected unindent.
/home/junghans/votca/build/sphinx/csg/scripts/table_dummy.sh.rst:23: WARNING: Explicit markup ends without a blank line; unexpected unindent.
/home/junghans/votca/build/sphinx/csg/scripts/table_extrapolate.pl.rst:24: WARNING: Explicit markup ends without a blank line; unexpected unindent.
/home/junghans/votca/build/sphinx/csg/scripts/table_functional.sh.rst:26: WARNING: Explicit markup ends without a blank line; unexpected unindent.
/home/junghans/votca/build/sphinx/csg/scripts/table_get_value.pl.rst:24: WARNING: Explicit markup ends without a blank line; unexpected unindent.
/home/junghans/votca/build/sphinx/csg/scripts/table_integrate.pl.rst:26: WARNING: Explicit markup ends without a blank line; unexpected unindent.
/home/junghans/votca/build/sphinx/csg/scripts/table_linearop.pl.rst:26: WARNING: Explicit markup ends without a blank line; unexpected unindent.
/home/junghans/votca/build/sphinx/csg/scripts/table_to_tab.pl.rst:29: WARNING: Explicit markup ends without a blank line; unexpected unindent.
/home/junghans/votca/build/sphinx/csg/scripts/table_to_xvg.pl.rst:28: WARNING: Explicit markup ends without a blank line; unexpected unindent.
../../sphinx/tools/votca_compare.rst:24: WARNING: Explicit markup ends without a blank line; unexpected unindent.
../../sphinx/tools/votca_help2doc.rst:24: WARNING: Explicit markup ends without a blank line; unexpected unindent.
../../sphinx/tools/votca_property.rst:25: WARNING: Explicit markup ends without a blank line; unexpected unindent.
/home/junghans/votca/build/sphinx/tools/votca_compare.rst:24: WARNING: Explicit markup ends without a blank line; unexpected unindent.
/home/junghans/votca/build/sphinx/tools/votca_help2doc.rst:24: WARNING: Explicit markup ends without a blank line; unexpected unindent.
/home/junghans/votca/build/sphinx/tools/votca_property.rst:25: WARNING: Explicit markup ends without a blank line; unexpected unindent.
../../sphinx/xtp/xtp_autogen_mapping.rst:24: WARNING: Explicit markup ends without a blank line; unexpected unindent.
../../sphinx/xtp/xtp_basisset.rst:24: WARNING: Explicit markup ends without a blank line; unexpected unindent.
../../sphinx/xtp/xtp_parallel.rst:26: WARNING: Explicit markup ends without a blank line; unexpected unindent.
../../sphinx/xtp/xtp_update_mapfile.rst:24: WARNING: Explicit markup ends without a blank line; unexpected unindent.
../../sphinx/xtp/xtp_qmmm2qm.rst:25: WARNING: Explicit markup ends without a blank line; unexpected unindent.
/home/junghans/votca/build/sphinx/xtp/xtp_autogen_mapping.rst:24: WARNING: Explicit markup ends without a blank line; unexpected unindent.
/home/junghans/votca/build/sphinx/xtp/xtp_basisset.rst:24: WARNING: Explicit markup ends without a blank line; unexpected unindent.
/home/junghans/votca/build/sphinx/xtp/xtp_map.rst:26: WARNING: Explicit markup ends without a blank line; unexpected unindent.
../../sphinx/xtp/xtp_map.rst:26: WARNING: Explicit markup ends without a blank line; unexpected unindent.
/home/junghans/votca/build/sphinx/xtp/xtp_parallel.rst:26: WARNING: Explicit markup ends without a blank line; unexpected unindent.
../../sphinx/xtp/xtp_parallel.rst:26: WARNING: Explicit markup ends without a blank line; unexpected unindent.
/home/junghans/votca/build/sphinx/xtp/xtp_qmmm2qm.rst:25: WARNING: Explicit markup ends without a blank line; unexpected unindent.
/home/junghans/votca/build/sphinx/xtp/xtp_run.rst:26: WARNING: Explicit markup ends without a blank line; unexpected unindent.
../../sphinx/xtp/xtp_run.rst:26: WARNING: Explicit markup ends without a blank line; unexpected unindent.
/home/junghans/votca/build/sphinx/xtp/xtp_tools.rst:26: WARNING: Explicit markup ends without a blank line; unexpected unindent.
../../sphinx/xtp/xtp_tools.rst:26: WARNING: Explicit markup ends without a blank line; unexpected unindent.
/home/junghans/votca/build/sphinx/xtp/xtp_update_mapfile.rst:24: WARNING: Explicit markup ends without a blank line; unexpected unindent.

votca_help2doc: more formatting

We are getting close, but https://www.votca.org/csg/reference.html#functions-common-sh still looks at bit strange.

cubicspline.cc fails to compile with eigen-3.3.6 in Debug mode on Fedora 29

[  2%] Building CXX object tools/src/libtools/CMakeFiles/votca_tools.dir/cubicspline.cc.o
In file included from /usr/include/eigen3/Eigen/Core:491,
                 from /usr/include/eigen3/Eigen/Dense:1,
                 from /votca/tools/include/votca/tools/eigen.h:49,
                 from /votca/tools/include/votca/tools/spline.h:21,
                 from /votca/tools/include/votca/tools/cubicspline.h:21,
                 from /votca/tools/src/libtools/cubicspline.cc:18:
/usr/include/eigen3/Eigen/src/Core/products/GeneralBlockPanelKernel.h: In member function ‘void Eigen::internal::gebp_kernel<LhsScalar, RhsScalar, Index, DataMapper, mr, nr, ConjugateLhs, ConjugateRhs>::operator()(const DataMapper&, const LhsScalar*, const RhsScalar*, Index, Index, Index, Eigen::internal::gebp_kernel<LhsScalar, RhsScalar, Index, DataMapper, mr, nr, ConjugateLhs, ConjugateRhs>::ResScalar, Index, Index, Index, Index) [with LhsScalar = double; RhsScalar = double; Index = long int; DataMapper = Eigen::internal::blas_data_mapper<double, long int, 0, 0>; int mr = 4; int nr = 4; bool ConjugateLhs = false; bool ConjugateRhs = false]’:
/usr/include/eigen3/Eigen/src/Core/products/GeneralBlockPanelKernel.h:1203:104: error: inconsistent operand constraints in an ‘asm’
             #define EIGEN_GEBP_2PX4_SPILLING_WORKAROUND __asm__  ("" : [a0] "+rm" (A0),[a1] "+rm" (A1));
                                                                                                        ^

it can be reproduced with the following dockerfile:

FROM fedora:29
RUN dnf install -y git cmake gcc-c++ expat-devel fftw-devel boost-devel txt2tags sqlite-devel hdf5-devel eigen3-devel gromacs-devel gromacs
RUN git clone --recursive https://github.com/votca/votca
WORKDIR votca/
RUN mkdir build
WORKDIR build/
RUN cmake -DCMAKE_BUILD_TYPE=Debug ..
RUN make

unit_test_graphalgorithm fails witn gcc-4.8.5 and boost-1.58.0

10/21 Test #10: unit_test_graphalgorithm ............***Failed    0.01 sec
Running 3 test cases...
unknown location(0): fatal error in "decoupleIsolatedSubGraphs_algorithm_test": memory access violation at address: 0x00000010: no mapping at fault address
/home/travis/votca/src/tools/src/tests/test_graphalgorithm.cc(133): last checkpoint

*** 1 failure detected in test suite "graphalgorithm_test"

details see here: https://api.travis-ci.org/v3/job/414739327/log.txt

Remove unused tex / groff generation code for application class

After #316 we can remove all the code to generate the tex and groff output from the application class.

Drop tf test case in travis

See votca/csg#172 for details

Create Rotation Matrix

Common requirement is to rotate the positional coordinates of a vec defined in vec.h. It would be convenient to create a rotation matrix based on matrix.h that does just this.

Replace fftw interface with Eigen fftw

would allow us to use eigen internal implementation without fftw library
and otherwise we could use fftw or MKL as a backend.

https://eigen.tuxfamily.org/dox/unsupported/group__FFT__Module.html

https://gitlab.math.ethz.ch/NumCSE/NumCSE/blob/43c3152296a97f4a927cd82fe3c19ac0c64537e4/CMake/Macros/set_eigen_fft_backend.cmake

Cleanup header namespace

Remove using from header files.

@JensWehner I'll see if I can get this done at least partly.

clang-9 warning: implicit conversion loses integer precision

/wrkdirs/usr/ports/science/votca/work/votca-1.6.1/tools/include/votca/tools/random.h:32:46: warning: implicit conversion loses integer precision: 'votca::Index' (aka 'long') to 'std::__1::mersenne_twister_engine<unsigned int, 32, 624, 397, 31, 2567483615, 11, 4294967295, 7, 2636928640, 15, 4022730752, 18, 1812433253>::result_type' (aka 'unsigned int') [-Wshorten-64-to-32]
  void init(Index seed) { _mt = std::mt19937(seed); }
                                ~~~          ^~~~
1 warning generated.

votca_help2doc: example section in groff out displayed correctly

The csg_map manpage generates with votca_help2doc looks like this:

CSG_MAP(1)                                            General Commands Manual                                            CSG_MAP(1)

NAME
       csg_map - Part of the VOTCA package

SYNOPSIS
       csg_map [OPTIONS]

       csg_map [--help]

DESCRIPTION
       Convert a reference atomistic trajectory or configuration into a coarse-grained one based on a mapping xml-file. The mapping
       can be applied to either an entire trajectory or a selected set of frames only (see options).  Examples: * csg_map --top FA-
       topol.tpr --trj FA-traj.trr --out CG-traj.xtc --cg cg-map.xml * csg_map --top FA-topol.tpr --trj FA-conf.gro --out CG-
       conf.gro --cg cg-map.xml * csg_map --top FA-topol.tpr --trj FA-traj.xtc --out FA-history.dlph --no-map * csg_map --top FA-
       field.dlpf --trj FA-history.dlph --out CG-history.dlph --cg cg-map.xml * csg_map --top .dlpf --trj .dlph --out .dlph --cg
       cg-map.xml  convert HISTORY to HISTORY_CGV

OPTIONS
       Allowed options:
           -h [ --help ]             display this help and exit
           --verbose                 be loud and noisy
           --verbose1                be very loud and noisy

The examples are parts of the DESCRIPTION and the formatting is broken.

Clang-10: warnings

../tools/src/libtools/edgecontainer.cc:60:34: error: loop variable 'neighbor_and_count' has type 'const pair<votca::Index, votca::Index> &' (aka 'const pair<long, long> &') but is initialized with type 'const std::pair<const long, long>' resulting in a copy [-Werror,-Wrange-loop-construct]
  for (const pair<Index, Index>& neighbor_and_count : adj_list_.at(vertex)) {
                                 ^
../tools/src/libtools/edgecontainer.cc:60:8: note: use non-reference type 'pair<votca::Index, votca::Index>' (aka 'pair<long, long>') to keep the copy or type 'const std::pair<const long, long> &' to prevent copying
  for (const pair<Index, Index>& neighbor_and_count : adj_list_.at(vertex)) {
       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../tools/src/libtools/edgecontainer.cc:148:36: error: loop variable 'neigh_and_count' has type 'const pair<votca::Index, votca::Index> &' (aka 'const pair<long, long> &') but is initialized with type 'const std::pair<const long, long>' resulting in a copy [-Werror,-Wrange-loop-construct]
    for (const pair<Index, Index>& neigh_and_count : adj_list_.at(vertex)) {
                                   ^
../tools/src/libtools/edgecontainer.cc:148:10: note: use non-reference type 'pair<votca::Index, votca::Index>' (aka 'pair<long, long>') to keep the copy or type 'const std::pair<const long, long> &' to prevent copying
    for (const pair<Index, Index>& neigh_and_count : adj_list_.at(vertex)) {
         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../tools/src/libtools/edgecontainer.cc:158:36: error: loop variable 'neigh_and_count' has type 'const pair<votca::Index, votca::Index> &' (aka 'const pair<long, long> &') but is initialized with type 'const std::pair<const long, long>' resulting in a copy [-Werror,-Wrange-loop-construct]
    for (const pair<Index, Index>& neigh_and_count : adj_list_.at(vertex)) {
                                   ^
../tools/src/libtools/edgecontainer.cc:158:10: note: use non-reference type 'pair<votca::Index, votca::Index>' (aka 'pair<long, long>') to keep the copy or type 'const std::pair<const long, long> &' to prevent copying
    for (const pair<Index, Index>& neigh_and_count : adj_list_.at(vertex)) {
         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../tools/src/libtools/edgecontainer.cc:171:36: error: loop variable 'neigh_and_count' has type 'const pair<votca::Index, votca::Index> &' (aka 'const pair<long, long> &') but is initialized with type 'const std::pair<const long, long>' resulting in a copy [-Werror,-Wrange-loop-construct]
    for (const pair<Index, Index>& neigh_and_count :
                                   ^
../tools/src/libtools/edgecontainer.cc:171:10: note: use non-reference type 'pair<votca::Index, votca::Index>' (aka 'pair<long, long>') to keep the copy or type 'const std::pair<const long, long> &' to prevent copying
    for (const pair<Index, Index>& neigh_and_count :
         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
4 errors generated.

slack/git slack/mailing list webhook

Limit notifications to PRs only.
Add slack/mailing list webhook and channel.

votca_help2doc: parse script help

I need a wait parse the help of the csg scripts.

E.g. one can call csg_call initstep ibi --help to get the help a the initstep script for ibi.

Could we add an option to votca_help to give extra arguments to the program specified by --name in votca_help2doc?

New table class doesn't read fortan style tables

$ cat x
  5.000000000000000E-002  0.000000000000000E+000
  0.150000000000000       0.000000000000000E+000
  0.250000000000000       0.000000000000000E+000
$ csg_resample --in x --out y --grid 0.05:0.1:0.25 --type linear
an error occurred:
invaid type: file x, line 1

as a workaround one can do:

awk '{print $1+0,$2+0}' x  > x.fixed

and

 csg_resample --in x.fixed --out y --grid 0.05:0.1:0.25 --type linear

will work

generate rst page from help

The --man option outputs a manpage, could we add something similar to print out an rst page to include in the website?

mkl download has a race condition

When running in parallel (make -j12) mkl build fails!

Details here:
https://groups.google.com/d/msg/votca/zxKFRbW7c_w/RujfffbPAgAJ

votca_help2doc: remove author and copyright section in rst pages

Looking at: https://www.votca.org/tools/reference.html, I think we don't need to include the copyright and author section in the rst pages.

unit_test_elements fails on i686

From: https://build.opensuse.org/package/live_build_log/openSUSE:Factory/votca-tools/standard/i586

[  151s]  6/23 Test  #6: unit_test_elements ..................***Failed    0.01 sec
[  151s] Running 2 test cases...
[  151s] /home/abuild/rpmbuild/BUILD/tools-1.5/src/tests/test_elements.cc(54): [1;31;49merror: in "elements_test/accessors_test": check round_(ele.getCovRad("Cl","ang"),3) == 1.02 has failed [1.02 != 1.02][0;39;49m
[  151s] /home/abuild/rpmbuild/BUILD/tools-1.5/src/tests/test_elements.cc(55): [1;31;49merror: in "elements_test/accessors_test": check round_(ele.getCovRad("Cl","nm"),3) == 0.102 has failed [0.10199999999999999 != 0.10199999999999999][0;39;49m
[  151s] 
[  151s] [1;31;49m*** 2 failures are detected in the test module "elements_test"
[  151s] [0;39;49m
[  151s]

Error when merging calculator defaults with User input

The Calculator's method UpdateWithUserOption, when merging the user_options with the defaults for a given calculator, assumes that the defaults options always contains the same or more information than the user_options, but there are options without a reasonable default that must be passed by the user.
This case has not been taken into account when merging.

MKL always links sequentially instead of the parallel versions

It has to do with 719d511

I do not really know what is happening, because we set the threading layer here

https://github.com/votca/tools/blob/master/CMakeLists.txt

tests fail to build: fatal error: 'ext/alloc_traits.h' file not found

AILED: tools/src/tests/CMakeFiles/unit_test_graphalgorithm.dir/test_graphalgorithm.cc.o 
/usr/bin/c++ -DBOOST_TEST_DYN_LINK -DTOOLS_TEST_DATA_FOLDER=\"/usr/ports/science/votca/work/votca-2021-rc.1-228-g1754257/tools/src/tests/DataFiles\" -I/usr/ports/science/votca/work/votca-2021-rc.1-228-g1754257/tools/include -Itools/include -Itools/include/votca/tools -isystem /usr/local/include -isystem /usr/local/include/eigen3 -O2 -pipe -fno-omit-frame-pointer -fstack-protector-strong -fno-strict-aliasing -fno-omit-frame-pointer -Wall -Wextra -Wpedantic -Wshadow -Wconversion -Wno-sign-conversion -O2 -pipe -fno-omit-frame-pointer -fstack-protector-strong -fno-strict-aliasing -fno-omit-frame-pointer -std=c++14 -MD -MT tools/src/tests/CMakeFiles/unit_test_graphalgorithm.dir/test_graphalgorithm.cc.o -MF tools/src/tests/CMakeFiles/unit_test_graphalgorithm.dir/test_graphalgorithm.cc.o.d -o tools/src/tests/CMakeFiles/unit_test_graphalgorithm.dir/test_graphalgorithm.cc.o -c /usr/ports/science/votca/work/votca-2021-rc.1-228-g1754257/tools/src/tests/test_graphalgorithm.cc
/usr/ports/science/votca/work/votca-2021-rc.1-228-g1754257/tools/src/tests/test_graphalgorithm.cc:36:10: fatal error: 'ext/alloc_traits.h' file not found
#include <ext/alloc_traits.h>
         ^~~~~~~~~~~~~~~~~~~~
1 error generated.

Revision: 2021-rc.1-228-g1754257
FreeBSD 12.2
clang-10

Implement davidson solver for symmetric and non symmetric matrices

for matrices and general operator-test vector product

Edge Class hash update

Update edge hash implementation as it does not conform to the standard as is.

Trim values in property class

Should we trim values, i.e should

<tag>A </tag> and
<tag>A
</tag>

be equivalent to <tag>A</tag>
We do that to string values already but it could violate the XML specs.

Unsafe public facing matrix api

The setters and getters in the matrix class do not check the scope of the indices against the size of the matrix. This is dangerous as a wrong index could easily be missed and could be potentially hard to debug as it might lead to random errors.

Check that the calculator input option has a valid input

Motivation

Unify all the defaults inside the xml files.
Reduce the amount of check performs by each Calculator.Initialize method.

Proposed changes

Read a new choices attribute for each option in the XML Calculators file.
Check that the value of each option after merging with the user input has valid input.
Introduced 5 new choices for continuous values: [bool,float, float+, int, int+] to represent reals, positive reals, integers, and positive integers, respectively.

Example

suppose there is a calculator with the following defaults:

<options>
  <calculator>
       <opt1 help="first option" default="foo" choices="foo,bar">foo</opt1>
       <opt2 help="second option" default="3.1415" choices="float+">3.1415</opt2> 
 </calculator>
</options>

The user can change both opt1 and opt2 but the changes must be valid values as declared by choices

Note

The options without a choices attribute is skip.

Replace random2 with std::random implementation

unit_test_table: fails on s390x

27/33 Test #27: unit_test_table .....................***Failed    0.01 sec
Running 10 test cases...
result value
1.50946 1.70621 1.91563 2.14274 2.39083 2.66271 2.96119 3.28637 3.62686
ref value
1.50946 1.70621 1.91527 2.14055 2.38962 2.65963 2.95959 3.28268 3.62686
/builddir/build/BUILD/tools-1.6_rc1/src/tests/test_table.cc(158): �[1;31;49merror: in "table_test/smoothing_test": check equal == true has failed [false != true]�[0;39;49m
�[1;31;49m*** 1 failure is detected in the test module "table_test"
�[0;39;49m

Details here

votca_help2doc queries

Could we change the syntax of the Usage: line, e.g. https://www.votca.org/csg/reference.html#id31, so that is looks the same as the other two line, i.e. bold face the first word and remove Usage: as the beginning.

Replace property tree object with boost property tree

Boost already supports a property tree object that can handle xml reading,there is no need to have our own.