MDANSE issueshttps://code.ill.fr/scientific-software/mdanse/-/issues2018-09-21T11:59:33+02:00https://code.ill.fr/scientific-software/mdanse/-/issues/39Time scale in Gromacs converter is incorrect2018-09-21T11:59:33+02:00Remi PerenonTime scale in Gromacs converter is incorrectA factor 1e-3 seems to be appliedA factor 1e-3 seems to be appliedhttps://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/36Jobs cannot be launched on windows machines2018-09-13T12:25:47+02:00Remi PerenonJobs cannot be launched on windows machines![Analysis_Error](/uploads/97eea17f63a032f5bfa32b0c6fdaeaa3/Analysis_Error.png)![Analysis_Error](/uploads/97eea17f63a032f5bfa32b0c6fdaeaa3/Analysis_Error.png)https://code.ill.fr/scientific-software/mdanse/-/issues/35Improper behavior of RBT job2018-08-10T14:55:18+02:00Remi PerenonImproper behavior of RBT jobhttps://code.ill.fr/scientific-software/mdanse/-/issues/34Renaming MDANSE to Src2018-08-07T19:49:08+02:00eric pellegriniRenaming MDANSE to SrcAfter building and installing MDANSE, it is annoying to always have to leave the `mdanse` directory to test the package. By renaming `MDANSE` to, say, `Src`, this problem will not occur anymore.After building and installing MDANSE, it is annoying to always have to leave the `mdanse` directory to test the package. By renaming `MDANSE` to, say, `Src`, this problem will not occur anymore.eric pellegrinieric pellegrinihttps://code.ill.fr/scientific-software/mdanse/-/issues/33Make macOS dmg lighter2018-08-07T16:43:01+02:00Remi PerenonMake macOS dmg lighterSome data are not necessary into the macOS dmg, so we suggest to remove themSome data are not necessary into the macOS dmg, so we suggest to remove themhttps://code.ill.fr/scientific-software/mdanse/-/issues/32Result of DCSF is incorrect2018-08-07T15:15:47+02:00Remi PerenonResult of DCSF is incorrecteric pellegrinieric pellegrinihttps://code.ill.fr/scientific-software/mdanse/-/issues/31Result of RMSD is incorrect (sqrt not performed)2018-08-07T15:15:47+02:00Remi PerenonResult of RMSD is incorrect (sqrt not performed)eric pellegrinieric pellegrinihttps://code.ill.fr/scientific-software/mdanse/-/issues/30Normalization of VACF total value is incorrect2018-08-01T16:11:09+02:00Remi PerenonNormalization of VACF total value is incorrectMiguel Angel GonzalezMiguel Angel Gonzalezhttps://code.ill.fr/scientific-software/mdanse/-/issues/29Improper behavior if first time label is not zero2018-08-01T16:11:02+02:00Remi PerenonImproper behavior if first time label is not zeroDifferent jobs (AC, CCF, DOS, DACF, DCSF, DISF, GACF, MSD, PACF, RMSD, VACF) are affectedDifferent jobs (AC, CCF, DOS, DACF, DCSF, DISF, GACF, MSD, PACF, RMSD, VACF) are affectedMiguel Angel GonzalezMiguel Angel Gonzalezhttps://code.ill.fr/scientific-software/mdanse/-/issues/28Time steps are sometimes incorrects when converting dcd file2018-07-27T16:01:19+02:00Remi PerenonTime steps are sometimes incorrects when converting dcd fileeric pellegrinieric pellegrinihttps://code.ill.fr/scientific-software/mdanse/-/issues/27Jobs error messages are not explicit enough in the GUI2018-07-26T12:53:10+02:00Remi PerenonJobs error messages are not explicit enough in the GUIhttps://code.ill.fr/scientific-software/mdanse/-/issues/26MDANSE error when deleting a opened data2018-07-26T16:52:38+02:00Remi PerenonMDANSE error when deleting a opened data![Bug_Suppr](/uploads/5e82ef59510338d8760716196a368989/Bug_Suppr.png)![Bug_Suppr](/uploads/5e82ef59510338d8760716196a368989/Bug_Suppr.png)https://code.ill.fr/scientific-software/mdanse/-/issues/25Plotter crashes on Ubuntu 16.042018-07-25T11:27:28+02:00eric pellegriniPlotter crashes on Ubuntu 16.04Opening a plot in a new window using matplotlib < 2.0.0 triggers the following error
![MDANSE__Molecular_Dynamics_Analysis_for_Neutron_Scattering_Experiments_053](/uploads/81de9771c7f0c15eb1f6ee8e61c283b3/MDANSE__Molecular_Dynamics_Anal...Opening a plot in a new window using matplotlib < 2.0.0 triggers the following error
![MDANSE__Molecular_Dynamics_Analysis_for_Neutron_Scattering_Experiments_053](/uploads/81de9771c7f0c15eb1f6ee8e61c283b3/MDANSE__Molecular_Dynamics_Analysis_for_Neutron_Scattering_Experiments_053.png)eric pellegrinieric pellegrinihttps://code.ill.fr/scientific-software/mdanse/-/issues/24Wrong Q vectors in CurrentCorrelationFunction2018-08-01T16:10:57+02:00Miguel Angel GonzalezWrong Q vectors in CurrentCorrelationFunctionThe Q vectors to use in the calculation of the current correlation function should be the real Q vectors, i.e. (2*pi/L)*(hkl) for a cubic box and not the normalized ones 2*pi*(hkl). This can be simply solved by removing the two lines tha...The Q vectors to use in the calculation of the current correlation function should be the real Q vectors, i.e. (2*pi/L)*(hkl) for a cubic box and not the normalized ones 2*pi*(hkl). This can be simply solved by removing the two lines that perform the conversion:
qVectors = traj.universe._boxToRealPointArray(qVectors.T)
qVectors = qVectors.T
Looking to this with Eric, we found that in the DynamicCoherentStructureFactor calculation, there is a double conversion: From real Q vectors to normalized vectors and from real atomic coordinates to fractional coordinates. This is correct, but unnecessary. One can remove both transformations and the result is the same (I checked this).
I will submit a pull request with the suggested changes for both files.Miguel Angel GonzalezMiguel Angel Gonzalezhttps://code.ill.fr/scientific-software/mdanse/-/issues/22Sphinx does not run on Windows2018-07-24T16:42:37+02:00eric pellegriniSphinx does not run on Windowshttps://code.ill.fr/scientific-software/mdanse/-/issues/21"Save a template for new analysis" button produces an error2018-07-03T15:01:42+02:00Remi Perenon"Save a template for new analysis" button produces an error![Screen_Shot_2018-07-03_at_14.06.11](/uploads/d3ff226c9be1b15d39ff17db462c2931/Screen_Shot_2018-07-03_at_14.06.11.png)![Screen_Shot_2018-07-03_at_14.06.11](/uploads/d3ff226c9be1b15d39ff17db462c2931/Screen_Shot_2018-07-03_at_14.06.11.png)https://code.ill.fr/scientific-software/mdanse/-/issues/20"Theoretical background" does not open on MacOS2018-07-24T17:22:40+02:00Remi Perenon"Theoretical background" does not open on MacOShttps://code.ill.fr/scientific-software/mdanse/-/issues/19Cannot display user definition qvectors "Cannot expand hidden root"2018-06-28T09:32:09+02:00Remi PerenonCannot display user definition qvectors "Cannot expand hidden root"![Screenshot_2018-06-27_12-31-11](/uploads/b321907e07c3a776c0c8ded7de5814e5/Screenshot_2018-06-27_12-31-11.png)![Screenshot_2018-06-27_12-31-11](/uploads/b321907e07c3a776c0c8ded7de5814e5/Screenshot_2018-06-27_12-31-11.png)https://code.ill.fr/scientific-software/mdanse/-/issues/18Output format ComboBox in jobs parameters cannot be clicked on macos or windows2018-08-01T15:09:40+02:00Remi PerenonOutput format ComboBox in jobs parameters cannot be clicked on macos or windows