Important units problem

grhawk commented 7 years ago

We just found an important bug: after the merge with fastxyz the units conversion in input will be applied based on the keyword in the file containing the positions file AND on the keywork in the initialize node of the input xml. For example: if the comment in the file contains position{angstrom} and the xml contains

<file units='angstrom'> namefile </file>

i-PI will convert the position of the atoms twice. The output is not guaranteed to be right!

mahrossi commented 7 years ago

Ugh! :( Good catch.

grhawk commented 7 years ago

@mahrossi well... I should have seen it before the merge... so it is not a so good catch... :(

grhawk commented 7 years ago

In the branch fix_iounit the input is working now with the following rules:

reading the units directly from xyz (pdb) file when is present something like position{angstrom} and cell{angstrom} in the comment (title) line.
if the attribute units is specified in the <file> node, then it will be applied anyway (this could still result in applying the conversion factor twice but otherwise, we would loose retro-compatibility.) but a warning is printed.
if the cell is specified in both, the xyz (pdb) file and in the xml: the last one is used (with the relative warning of overwriting the other property).
about the output: xyz is working fine. pdb now is working fine: there was an error in the pdb format

grhawk commented 7 years ago

Still todo:

[x] Check the warning messages they could probably be shorter...
[x] Update the documentation #150
[x] Update the examples #150
[ ] Move the output units conversion machinery into the io module

lab-cosmo / i-pi-dev_archive

Important units problem #147

Still todo: