Cif export

[bnmajor]

No description provided.

[psavery]

Code looks good to me. Can you review, @saransh13?

[psavery]

This was rebased on master

[saransh13]

I think there is some formatting issue with the atom coordinates. The square brackets need to be removed:

_atom_site_label [Ti0]
_atom_site_type_symbol [Ti]
_atom_site_fract_x [0.33333334]
_atom_site_fract_y [0.66666669]
_atom_site_fract_z [0.25000000]
_atom_site_occupancy [1.00000000]

If there are multiple atoms present, then we need to loop over those and write the atom coordinates separately. Example cif file with multiple atoms below

loop_
_atom_site_label
_atom_site_type_symbol
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_occupancy
_atom_site_symmetry_multiplicity
_atom_site_Wyckoff_symbol
_atom_site_attached_hydrogens
_atom_site_calc_flag
_atom_site_thermal_displace_type
_atom_site_u_iso_or_equiv
C1 C -0.4668  0.1651  0.2568 ? 2 i ? d ? ?
C2 C -0.6267  0.0026  0.2487 ? 2 i ? d ? ?
C3 C -0.7850  0.0073  0.2487 ? 2 i ? d ? ?
C4 C -0.7856  0.1667  0.2511 ? 2 i ? d ? ?
C5 C -0.6240  0.3218  0.2442 ? 2 i ? d ? ?
C6 C -0.4621  0.3268  0.2520 ? 2 i ? d ? ?
H1 H -0.5330 -0.1430  0.2380 ? 2 i ? d ? ?
H2 H -0.7200 -0.2320  0.2600 ? 2 i ? d ? ?
H3 H -1.0170  0.0910  0.2540 ? 2 i ? d ? ?
H4 H -0.9290  0.2880  0.2540 ? 2 i ? d ? ?
H5 H -0.3180  0.5640  0.2440 ? 2 i ? d ? ?
H6 H -0.2210  0.4540  0.2240 ? 2 i ? d ? ?
N1 N -0.3079  0.1683  0.2695 ? 2 i ? d ? ?
N2 N -0.6307 -0.1466  0.2389 ? 2 i ? d ? ?
N3 N -0.9435 -0.1493  0.2467 ? 2 i ? d ? ?
N4 N -0.9290  0.1722  0.2578 ? 2 i ? d ? ?
N5 N -0.6253  0.4763  0.2350 ? 2 i ? d ? ?
N6 N -0.3158  0.4709  0.2517 ? 2 i ? d ? ?
O1 O -0.1665  0.3069  0.2820 ? 2 i ? d ? ?
O2 O -0.3073  0.0297  0.2641 ? 2 i ? d ? ?
O3 O -0.9488 -0.2919  0.2377 ? 2 i ? d ? ?
O4 O -1.0811 -0.1499  0.2525 ? 2 i ? d ? ?
O5 O -0.7620  0.4789  0.2304 ? 2 i ? d ? ?
O6 O -0.4869  0.6175  0.2357 ? 2 i ? d ? ?

[saransh13]

The other thing that should be fixed is that the apple export menu says open instead of save.

[bnmajor]

The other thing that should be fixed is that the apple export menu says open instead of save.

@saransh13 Would you prefer to get the "save file as" prompt when a single material is exported? For multiple selections we would keep the current approach of just having them select the directory to write out to.

[saransh13]

Ok, yes. That seems like a reasonable solution.

[bnmajor]

I think there is some formatting issue with the atom coordinates. The square brackets need to be removed:[...]

If there are multiple atoms present, then we need to loop over those and write the atom coordinates separately. Example cif file with multiple atoms below [...]

These formatting fixes are in HEXRD/hexrd#874

[saransh13]

@bnmajor There is one change and one enhancement in this PR. The enhancement can be a separate PR.
For the change, there is still All blocks output. printed to the terminal and in the message box. Can you suppress that. I will approve and you can merge after this change.

For the enhancement (future PR), we can

• get rid of the indent here:

• include the _atom_site_U_iso or _atom_site_U_aniso key in the loop. This will write the mean-squared atom displacement or the Debye-Waller factor.

[bnmajor]

@bnmajor There is one change and one enhancement in this PR. The enhancement can be a separate PR. For the change, there is still All blocks output. printed to the terminal and in the message box. Can you suppress that. I will approve and you can merge after this change.

This seems to come from the CifFile library I'll see if I can suppress it.

For the enhancement (future PR), we can

• get rid of the indent here:

* include the `_atom_site_U_iso` or `_atom_site_U_aniso` key in the loop. This will write the mean-squared atom displacement or the Debye-Waller factor.

I'm going to break this out into a new issue so we can discuss further. I'll need clarification on a few things.

[bnmajor]

There is one change and one enhancement in this PR. The enhancement can be a separate PR. For the change, there is still All blocks output. printed to the terminal and in the message box. Can you suppress that. I will approve and you can merge after this change.

@saransh13 This is suppressed in HEXRD/hexrd@41e8046