[Pw_forum] monoclinic cell definition question

[Jonas Baltrusaitis]

Thanks Xenia I'll try pwgui maybe it automatically recognizes those. Maybe by that time we'll get answer from forum gurus, or better yet some hands on example (the one in tutorials and manuals doesn't count)

Jonas


--- On Tue, 5/12/09, Xenia Filip <xenia at itim-cj.ro> wrote:

> From: Xenia Filip <xenia at itim-cj.ro>
> Subject: Re: [Pw_forum] monoclinic cell definition question
> To: jasius_1 at yahoo.com, "PWSCF Forum" <pw_forum at pwscf.org>
> Date: Tuesday, May 12, 2009, 1:36 AM
> I have the same problem recently and due to a monoclinic
> cell I realize
> that I introduce in a wrong manner the coordinates of atoms
> and cell
> parameters in the input file. I admit that I didn't
> read carefully the
> INPUT_PW.txt file. Due to the discrepancy you talk I think
> that is not
> correct to take (x,y,z), (a,b,c) and (alpha, beta, gamma)
> from a *.cif
> file and put them on the same order in *scf.in file. I talk
> about the
> convention used in *.cif files with somebody which is doing
> X Ray
> Crystalography and if he has right the "b" axis
> in *.cif I think it
> correspond to "c" axis in *.scf.in. That means
> that it needs to permute
> (a,b,c) in (c,a,b), (x,y,z) in (z,x,y), (alpha, beta,
> gamma) in (gamma,
> alpha, beta). I am not expert in doing such calculation, I
> am interest
> just in chemical shift calculations (I'm doing NMR),
> and unfortunatelly I
> didn't succed yet to verify this. I am running now some
> test but it take
> some time (I do not have strong computers).
> I'm not sure if my ideea is correct but you can think
> at this posibility too.
> 
> Dr. Xenia Filip
> National Institute for R&D of
> Isotopic and Molecular Technologies
> Cluj 400293, Romania
> Tel: 0040 724 321420
> Fax: 0040 264 420042
> >
> > I found discrepancies in how monoclinic cell is
> defined in the manual and
> > how it's defined in experimental crystalography
> files:
> >
> > Namely,
> >
> > For P lattices: the special axis (c) is the z-axis,
> one basal-plane
> > vector (a) is along x, the other basal-plane vector
> (b) is at angle
> > gamma for monoclinic. While it is not clear angle to
> which axis, later on
> > gamma is defined as an angle between a and b. the
> problem is that ab is 90
> > degree angle, not a unique angle, if I visualize the
> structure with cell
> > axes.
> >
> > Furthermore, when I open any crystalography file in
> Mercury, I get for
> > monoclinic cell
> >
> > alpha 90.00 betta 115.6670(10) gamma 90.00 so gamma is
> again not a unique
> > angle but rather 90 degree angle. I assume this is not
> what needs to be
> > entered for monoclinic lattice in celldm(4), but
> rather a unique angle
> > which in both cases is between a and c, so it has
> nothing to do with b as
> > defined above
> >
> > Could anybody help out?
> >
> > Jonas Baltrusaitis
> > University of Iowa
> >
> >
> >
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