MDANSE issueshttps://code.ill.fr/scientific-software/mdanse/-/issues2018-06-01T14:27:48+02:00https://code.ill.fr/scientific-software/mdanse/-/issues/1App frozen after opening Preferences dialog2018-06-01T14:27:48+02:00Jamie Hallhall@ill.euApp frozen after opening Preferences dialogThe application froze when the preferences dialog is opened. Tested on macos.The application froze when the preferences dialog is opened. Tested on macos.eric pellegrinieric pellegrinihttps://code.ill.fr/scientific-software/mdanse/-/issues/2Remove examples data from dmg file2018-06-04T12:10:15+02:00Jamie Hallhall@ill.euRemove examples data from dmg fileeric pellegrinieric pellegrinihttps://code.ill.fr/scientific-software/mdanse/-/issues/3macos dmg corrupted2017-04-23T17:28:08+02:00eric pellegrinimacos dmg corruptedThe macos dmg can not be opned due to a regression introduced when adding pkg_resources support in MDANSEThe macos dmg can not be opned due to a regression introduced when adding pkg_resources support in MDANSEeric pellegrinieric pellegrinihttps://code.ill.fr/scientific-software/mdanse/-/issues/4adding git commit id2017-04-23T17:28:08+02:00eric pellegriniadding git commit idAdding the git commit id of the version of MDANSE in use may be intersting (e.g. bug report)Adding the git commit id of the version of MDANSE in use may be intersting (e.g. bug report)eric pellegrinieric pellegrinihttps://code.ill.fr/scientific-software/mdanse/-/issues/7Error message when viewing a RBT trajectory2018-06-04T14:55:08+02:00Stephane RolsError message when viewing a RBT trajectoryAfter loading a RBT trajectory -> Viewer-> double click on Molecular Viewer generates an error window (see attached file) NOT SYSTEMATIC... came after several manipulations: trying to generate a RBT trajectory from a traj containg only a...After loading a RBT trajectory -> Viewer-> double click on Molecular Viewer generates an error window (see attached file) NOT SYSTEMATIC... came after several manipulations: trying to generate a RBT trajectory from a traj containg only atoms...
![Capture_errormdanse](/uploads/f71e2c40223a7931f5988a8da44ee601/Capture_errormdanse.PNG)https://code.ill.fr/scientific-software/mdanse/-/issues/9MDANSE crashed on some MacOS systems2018-06-04T12:09:50+02:00Remi PerenonMDANSE crashed on some MacOS systemsOn some MacOS systems, MDANSE crashes when launched.On some MacOS systems, MDANSE crashes when launched.https://code.ill.fr/scientific-software/mdanse/-/issues/10Implement Gromacs trajectory converter2018-07-03T15:31:45+02:00eric pellegriniImplement Gromacs trajectory convertereric pellegrinieric pellegrinihttps://code.ill.fr/scientific-software/mdanse/-/issues/11Get MDANSE compliant with 16.04 and 18.04 ubuntu systems2018-06-04T12:07:30+02:00Remi PerenonGet MDANSE compliant with 16.04 and 18.04 ubuntu systemshttps://code.ill.fr/scientific-software/mdanse/-/issues/12MDANSE should have 3 different phases (release, release-candidate, beta)2018-06-04T12:07:50+02:00Remi PerenonMDANSE should have 3 different phases (release, release-candidate, beta)https://code.ill.fr/scientific-software/mdanse/-/issues/13The changelog is not updated in the windows installer2018-06-14T15:33:36+02:00Remi PerenonThe changelog is not updated in the windows installer![Changelog1](/uploads/8b5e245489a9cf812bf68a46760c420c/Changelog1.png)
![Changelog2](/uploads/f291e3b0ff3199ce8106da5c914e2628/Changelog2.png)![Changelog1](/uploads/8b5e245489a9cf812bf68a46760c420c/Changelog1.png)
![Changelog2](/uploads/f291e3b0ff3199ce8106da5c914e2628/Changelog2.png)https://code.ill.fr/scientific-software/mdanse/-/issues/14Package name is not valid for debian package in 1.1.0 version2018-06-14T17:05:38+02:00Remi PerenonPackage name is not valid for debian package in 1.1.0 versionPackages are named "beta" and platform is systematically "Xenial"Packages are named "beta" and platform is systematically "Xenial"https://code.ill.fr/scientific-software/mdanse/-/issues/15The data format selector in GUI Data Loader does not appear on macOS, so ever...2018-06-20T16:51:20+02:00Remi PerenonThe data format selector in GUI Data Loader does not appear on macOS, so every data is loaded as mvihttps://code.ill.fr/scientific-software/mdanse/-/issues/16The data format selector in GUI Data Loader does not appear on macOS,2018-07-26T14:46:07+02:00Remi PerenonThe data format selector in GUI Data Loader does not appear on macOS,This problem was described in issue #15. It was partially solved by adding an automatic loader, but the GUI behavior is still a problem since the user cannot choose manually the data format on macOSThis problem was described in issue #15. It was partially solved by adding an automatic loader, but the GUI behavior is still a problem since the user cannot choose manually the data format on macOShttps://code.ill.fr/scientific-software/mdanse/-/issues/17Plotter is broken "no attribute axisbg"2018-06-28T09:32:05+02:00Remi PerenonPlotter is broken "no attribute axisbg"Error message "no attribute axisbg" appears when users tries to plot "in a new window"Error message "no attribute axisbg" appears when users tries to plot "in a new window"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 windowshttps://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/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/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/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/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 Gonzalez