MDANSE issueshttps://code.ill.fr/scientific-software/mdanse/-/issues2020-03-28T14:03:20+01:00https://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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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