Closed GoogleCodeExporter closed 8 years ago
Ok, have you tested your changes for the other two boundary conditions?
(Triclinic, Open)
And what does the newest version of csg_dump says, which boundary condition it
has found?
Original comment by christop...@gmail.com
on 4 Dec 2013 at 7:25
I tried with, rectangular, cubic, dodecahedron, octahedron and open box types:
The mapped configurations of rectangular and cubic box types give the same box
vectors as those of the atomistic configurations both before fix and after fix.
(expected as the diagonal elements of the matrix do not change)
However, the box vectors of the mapped configurations for dodecahedron and
octahedron box types match to their atomistic counterparts, after fix but fail
to match before fix.
Also, the lines match with the open box (where all the box vectors equal zero).
The latest csg_dump yields for all the box types above and for both cases of
before fix and after fix (except the open box, where I don't know how to
compile a box with zero vectors with grompp and generate a tpr file):
Boundary Condition: open
That shouldn't be right, I guess.
However, when I use csg_map to map the atomistic configuration, the correct box
types (orthorhombic, triclinic etc) seem to be assigned. (I uncommented the
cout lines in topology.cc (Topology::autoDetectBoxType, line 313).
So anything else, I should check?
Original comment by cahit.dalgicdir
on 5 Dec 2013 at 11:07
Sounds good to me, thanks for testing! Do you want to commit it yourself or do
you want to send me a patch?
Original comment by christop...@gmail.com
on 5 Dec 2013 at 6:34
OK, I did the commit. Thanks.
Original comment by cahit.dalgicdir
on 6 Dec 2013 at 3:25
Thanks!
Btw, please add the following block to your ~/.hgrc
[ui]
username = Steve Losh <steve@stevelosh.com>
Original comment by christop...@gmail.com
on 6 Dec 2013 at 4:41
With your name and email of course...
Original comment by christop...@gmail.com
on 6 Dec 2013 at 7:02
:) Sorry, fixed it now. Actually the block was there, but the name was not
typed correctly.
Original comment by cahit.dalgicdir
on 6 Dec 2013 at 8:00
this is a quite critical fix, so I reopened this issue for an additional check.
Could you please verify if csg_stat still produces the exact same rdf as g_rdf.
The following reason: The distance function relies on the fact that the box
matrix is upper triangular (or lower, don't remember which way), otherwise the
distances are wrong. I thought the distances were correct for a triclinic box,
but now the matrix is transposed. So it could be also that the writer is wrong
instead of the reader...
See also issue #125
Victor
Original comment by victor.r...@gmail.com
on 8 Dec 2013 at 10:53
sorry, I was not reading properly, i thought you were changing the reader.
closed again
Original comment by victor.r...@gmail.com
on 8 Dec 2013 at 10:56
I back-ported this fix to the 1.2 branch!
Original comment by christop...@gmail.com
on 13 Jul 2015 at 2:34
Original issue reported on code.google.com by
cahit.dalgicdir
on 4 Dec 2013 at 9:50Attachments: