Christoph Junghans

Interfacing with the ASI package

3

An interface with https://gitlab.com/pvst/asi could be nice. Also see: https://gitlab.com/pvst/asi/-/issues/3

Build with Intel's new `dpcpp` compiler fails: ``` [ 4%] Building CXX object tools/src/libtools/CMakeFiles/votca_tools.dir/calculator.cc.o cd /__w/votca/votca/builddir/tools/src/libtools && /opt/intel/oneapi/compiler/latest/linux/bin/dpcpp -Dvotca_tools_EXPORTS -I/__w/votca/votca/builddir/tools/src/libtools -I/__w/votca/votca/tools/include -I/__w/votca/votca/builddir/tools/include -I/__w/votca/votca/builddir/tools/include/votca/tools -isystem /usr/include/eigen3 -isystem /opt/intel/oneapi/mkl/latest/include -isystem /opt/intel/oneapi/mkl/latest/include/fftw -Wall...

Replacement for https://github.com/votca/csg-tutorials/pull/88

Replacement for https://github.com/votca/csg/pull/658

[csg] warning H5Tcopy(): not a datatype or dataset

11

Reported here https://groups.google.com/g/votca/c/FT_Xu85qmfA/m/NZiWJENfCQAJ ``` HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0: #000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset major: Invalid arguments to routine minor: Inappropriate...

[csg] parse xml options used by the scripts

4

Last things that is missing, to replace the old pdf manual, is to parse what options a script is using. For the old manual, we basically called `csg_call --cat tag1...

[csg] H5MD reader: reads the wrong unit

15

If I run: ``` csg_stat --nt 1 --options settings.xml --top topol.xml --trj traj.h5 --begin 0 --first-frame 0 ``` with these [inputs](https://github.com/votca/csg/files/4664174/input.zip), the output (`CG-CG.dist.new`) is all zeros, even though the...

``` Starting program: /home/christoph/votca/src/votca/build/csg/src/tools/csg_reupdate --options /home/christoph/votca/src/votca/csg/src/tools/references/spce/settings_re.xml --top /home/christoph/votca/src/votca/csg/src/tools/references/spce/topol_cg.xml --trj /home/christoph/votca/src/votca/csg/src/tools/references/spce/frame.dump [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". I have 216 beads in 216 molecules Reading frame, timestep...

[csg] csg_dump don't complain about non-existing map option

7

``` csg_dump --top topol.tpr --mapx hexane_cg.xml ``` give an error: ``` an error occurred: error parsing command line: unrecognised option '--mapx' ``` but: ``` csg_dump --top topol.tpr --map hexane_cg.xml ```...

[csg] Some mdrun options will be removed

1

https://github.com/gromacs/gromacs/commit/f5cb6c1302561aedaf5fdd97d13a5e6a071804a1 The options `-nsteps` (used for testing) and `-multi` (used in votca/csg#223) will be removed.