MDANSE issueshttps://code.ill.fr/scientific-software/mdanse/-/issues2020-11-12T12:31:49+01:00https://code.ill.fr/scientific-software/mdanse/-/issues/59Smart association in LAMMPS converter2020-11-12T12:31:49+01:00Remi PerenonSmart association in LAMMPS converterWhen two or more masses are matching in a LAMMPS trajectory, we should select the nearest one.When two or more masses are matching in a LAMMPS trajectory, we should select the nearest one.Remi PerenonRemi Perenonhttps://code.ill.fr/scientific-software/mdanse/-/issues/58Compatibility issues with LAMMPS files2020-11-09T18:03:42+01:00Remi PerenonCompatibility issues with LAMMPS files- Real coordinates column name can be <x,y,z> or <x,y,z>u
- Unordered LAMMPS files are read in a totally wrong way- Real coordinates column name can be <x,y,z> or <x,y,z>u
- Unordered LAMMPS files are read in a totally wrong wayRemi PerenonRemi Perenonhttps://code.ill.fr/scientific-software/mdanse/-/issues/57On macOS, MDANSE does not use the embedded python2020-07-09T08:15:01+02:00Remi PerenonOn macOS, MDANSE does not use the embedded pythonIn version 1.4.x, MDANSE uses the system python version, instead of the one included in the bundleIn version 1.4.x, MDANSE uses the system python version, instead of the one included in the bundleRemi PerenonRemi Perenonhttps://code.ill.fr/scientific-software/mdanse/-/issues/55Plotter issues2020-04-06T11:44:06+02:00Remi PerenonPlotter issuesError message when editing lines `/usr/local/lib/python2.7/dist-packages/MDANSE/GUI/Plugins/PlotterSettings.py -- 600 -- set_lines -- r,g,b = matplotlib.colors.colorConverter.colors[self.parent.plots[k][0].get_color()] -- KeyError: '#1f7...Error message when editing lines `/usr/local/lib/python2.7/dist-packages/MDANSE/GUI/Plugins/PlotterSettings.py -- 600 -- set_lines -- r,g,b = matplotlib.colors.colorConverter.colors[self.parent.plots[k][0].get_color()] -- KeyError: '#1f77b4'`
When editing axis with unknown units, error on quit (even if units are unchanged) `UnitsSettingsError: u'the axis unit (XXX) is inconsistent with the current unit (XXX) '`
When editing the axis, cannot move to log-scale `ValueError: provided too many kwargs, can only pass {'basex', 'subsx', nonposx'} or {'basey', 'subsy', nonposy'}. You passed {'basex': 2}`
When closing plotter settings (image, lines, axis, general), the GUI freezes on macOSRemi PerenonRemi Perenonhttps://code.ill.fr/scientific-software/mdanse/-/issues/56Layout on Windows differs from macOS and Linux2020-04-04T11:39:20+02:00Remi PerenonLayout on Windows differs from macOS and LinuxOrder of "Data" and "Plugins" panels are switched on WindowsOrder of "Data" and "Plugins" panels are switched on WindowsRemi PerenonRemi Perenonhttps://code.ill.fr/scientific-software/mdanse/-/issues/54Some Gromacs trajectories cannot be opened2020-03-30T11:32:24+02:00Remi PerenonSome Gromacs trajectories cannot be openedConcerns "dummy" M atom
`IOError: Database entry Atoms/m not found`Concerns "dummy" M atom
`IOError: Database entry Atoms/m not found`Remi PerenonRemi Perenonhttps://code.ill.fr/scientific-software/mdanse/-/issues/53VASP NPT trajectories cannot be opened2020-03-28T22:44:58+01:00Remi PerenonVASP NPT trajectories cannot be openedFile format is different if trajectory is NPT
Error is
`The number of atoms (%d) does not match the size of a frame (%d)`
Moreover, error message is mis-formed, leading to an error.
`TypeError: %d format: a number is required, not list`File format is different if trajectory is NPT
Error is
`The number of atoms (%d) does not match the size of a frame (%d)`
Moreover, error message is mis-formed, leading to an error.
`TypeError: %d format: a number is required, not list`Remi PerenonRemi Perenonhttps://code.ill.fr/scientific-software/mdanse/-/issues/52QVector circular lattice generator creates an error2020-03-28T14:03:20+01:00Remi PerenonQVector circular lattice generator creates an error![Bug_QVect_circular](/uploads/c8e2175ada8e38f24658d0b7969d6d1e/Bug_QVect_circular.png)![Bug_QVect_circular](/uploads/c8e2175ada8e38f24658d0b7969d6d1e/Bug_QVect_circular.png)Remi PerenonRemi Perenonhttps://code.ill.fr/scientific-software/mdanse/-/issues/50Inconsistent results when using multiple atom selections2020-02-27T16:05:04+01:00Remi PerenonInconsistent results when using multiple atom selectionshttps://code.ill.fr/scientific-software/mdanse/-/issues/49Some LAMMPS files cannot be converted2020-02-27T15:45:56+01:00Remi PerenonSome LAMMPS files cannot be convertedA phd student, could not convert its LAMMPS trajectory
Error traceback:
> idx, mass = lines[i+j].strip().split()
ValueError: too many values to unpackA phd student, could not convert its LAMMPS trajectory
Error traceback:
> idx, mass = lines[i+j].strip().split()
ValueError: too many values to unpackRemi PerenonRemi Perenonhttps://code.ill.fr/scientific-software/mdanse/-/issues/51SFFSF job (Structure Factor From Scattering Function) is accessible on MMTK t...2020-02-27T15:18:17+01:00Remi PerenonSFFSF job (Structure Factor From Scattering Function) is accessible on MMTK trajectory and molecular viewerhttps://code.ill.fr/scientific-software/mdanse/-/issues/48Bug in NeutronDynamicTotalStructureFactor analysis2020-02-27T14:42:05+01:00Miguel Angel GonzalezBug in NeutronDynamicTotalStructureFactor analysisA factor of 2 is missing when summing the partial components (for i != j terms) to give the total F(Q,t)/S(Q,w). A possible solution is to use this code at the end of the coherent block in the finalize function:
if pair[0] =...A factor of 2 is missing when summing the partial components (for i != j terms) to give the total F(Q,t)/S(Q,w). A possible solution is to use this code at the end of the coherent block in the finalize function:
if pair[0] == pair[1]:
self._outputData["f(q,t)_coh_total"][:] += self._outputData["f(q,t)_coh_weighted_%s%s" % pair][:]
self._outputData["s(q,f)_coh_total"][:] += self._outputData["s(q,f)_coh_weighted_%s%s" % pair][:]
else:
self._outputData["f(q,t)_coh_total"][:] += 2*self._outputData["f(q,t)_coh_weighted_%s%s" % pair][:]
self._outputData["s(q,f)_coh_total"][:] += 2*self._outputData["s(q,f)_coh_weighted_%s%s" % pair][:]Remi PerenonRemi Perenonhttps://code.ill.fr/scientific-software/mdanse/-/issues/47GUI converters does not close2020-02-27T11:56:12+01:00Remi PerenonGUI converters does not closeWhen asking "Your analysis is performing. Do you want to close ?" in a converter GUI, if answer is "Yes", the plugin does not close.
This bug is the following of issue #46When asking "Your analysis is performing. Do you want to close ?" in a converter GUI, if answer is "Yes", the plugin does not close.
This bug is the following of issue #46https://code.ill.fr/scientific-software/mdanse/-/issues/46Error when closing converter GUI2019-05-21T11:31:26+02:00Remi PerenonError when closing converter GUIAn errors appears and the converter plugin does not close
![Screenshot_2019-03-21_09-45-51](/uploads/be00d3078960e1fc110e307424ab8a48/Screenshot_2019-03-21_09-45-51.png)An errors appears and the converter plugin does not close
![Screenshot_2019-03-21_09-45-51](/uploads/be00d3078960e1fc110e307424ab8a48/Screenshot_2019-03-21_09-45-51.png)https://code.ill.fr/scientific-software/mdanse/-/issues/38Interface is frozen when jobs are launched2019-02-07T20:34:54+01:00Remi PerenonInterface is frozen when jobs are launchedhttps://code.ill.fr/scientific-software/mdanse/-/issues/45MSD computing on non-orthorombic universe is wrong2019-02-07T15:38:58+01:00Remi PerenonMSD computing on non-orthorombic universe is wrongBut the computation is right if the box is expressed in a "trianguar shape"
For a,b,c vectors:
ax 0.0 0.0
bx by 0.0
cx cy czBut the computation is right if the box is expressed in a "trianguar shape"
For a,b,c vectors:
ax 0.0 0.0
bx by 0.0
cx cy czhttps://code.ill.fr/scientific-software/mdanse/-/issues/44Error message when display, close and reopen molecular viewer and animation2019-02-06T10:59:49+01:00Remi PerenonError message when display, close and reopen molecular viewer and animationThe problem occurs specifically under Windows OS.
Reproducible if you open a molecular viewer, animate the viewer, close the viewer and make the same operation on another viewer
![image](/uploads/6136229c5615fe58aef231c51b92accd/image....The problem occurs specifically under Windows OS.
Reproducible if you open a molecular viewer, animate the viewer, close the viewer and make the same operation on another viewer
![image](/uploads/6136229c5615fe58aef231c51b92accd/image.png)https://code.ill.fr/scientific-software/mdanse/-/issues/43Weights are normalized with absolute sum2019-01-30T17:00:20+01:00Remi PerenonWeights are normalized with absolute sumAnd they should be normalized with regulat sumAnd they should be normalized with regulat sumhttps://code.ill.fr/scientific-software/mdanse/-/issues/42Plotter units can be inconsistent2019-01-24T14:37:06+01:00Remi PerenonPlotter units can be inconsistentIf the user set a inconsistent unit, the unit is displayed anywayIf the user set a inconsistent unit, the unit is displayed anywayhttps://code.ill.fr/scientific-software/mdanse/-/issues/40MDANSE cannot be used on Ubuntu Bionic systems2019-01-22T17:14:56+01:00Remi PerenonMDANSE cannot be used on Ubuntu Bionic systemspython-vtk is named python-vtk6 (dependencies must be forced)python-vtk is named python-vtk6 (dependencies must be forced)