Bug in pymatgen.core.lattice.py?

[mbkumar]

When trying to initialize Structure in core/structure.py, I am getting an error message.
Input to initializer:

1. lattice of type "pymatgen.core.lattice.Lattice"
2. species of type "List of strings"
3. coords of type "List of numpy arrays of size 3"
4. coords_are_cartesian=True
5. site_properties=dict{"property_name":List of numbers}

Error Message:
File "voronoi_node_symmetry.py", line 34, in
voronoi_struct = Structure(voronoi_lattice, s, c, coords_are_cartesian=True, site_properties={"voronoi_data":p})
File "/Library/Python/2.7/site-packages/pymatgen/core/structure.py", line 297, in init
properties=prop))
File "/Library/Python/2.7/site-packages/pymatgen/core/sites.py", line 312, in init
self._fcoords = self._lattice.get_fractional_coords(coords)
File "/Library/Python/2.7/site-packages/pymatgen/core/lattice.py", line 104, in get_fractional_coords
return dot(cart_coords, self.inv_matrix)
ValueError: data type must provide an itemsize

[shyuep]

Hi there,

I can't reproduce the error. You cannot just specify voronoi_data as site properties because there are only some properties allowed. But otherwise, I can't reproduce the error. Can you give me the exact forms of the variables voronoi_lattice, s and c? For example, the following works just fine:

Structure(Lattice.cubic(3), ["Fe"], [[0,0,0]], coords_are_cartesian=True)

[mbkumar]

May be what I am doing is wrong. In that case, let me know where I am wrong.
I am attaching the python script and the input data files.

Thanks,
Bharat

On 5/16/13 4:29 PM, Shyue Ping Ong wrote:

Hi there,

I can't reproduce the error. You cannot just specify voronoi_data as
site properties because there are only some properties allowed. But
otherwise, I can't reproduce the error. Can you give me the exact
forms of the variables voronoi_lattice, s and c? For example, the
following works just fine:

Structure(Lattice.cubic(3), ["Fe"], [[0,0,0]], coords_are_cartesian=True)

—
Reply to this email directly or view it on GitHub
#24 (comment).

4.2120 4.2120 4.2120
90.00 90.00 90.00 SPGR = 1 P 1 OPT = 1
8 0
0 Mg4 O4
1 Mg 0.0000 0.0000 0.0000 0 0 0 0 0 0 0 0 0.00
2 Mg 0.5000 0.5000 0.0000 0 0 0 0 0 0 0 0 0.00
3 Mg 0.5000 0.0000 0.5000 0 0 0 0 0 0 0 0 0.00
4 Mg 0.0000 0.5000 0.5000 0 0 0 0 0 0 0 0 0.00
5 O 0.5000 0.0000 0.0000 0 0 0 0 0 0 0 0 0.00
6 O 0.0000 0.5000 0.0000 0 0 0 0 0 0 0 0 0.00
7 O 0.0000 0.0000 0.5000 0 0 0 0 0 0 0 0 0.00
8 O 0.5000 0.5000 0.5000 0 0 0 0 0 0 0 0 0.00

[shyuep]

Hi Bharat,

I don't see an input file. Maybe you can email them directly to me at shyuep@gmail.com?

Regards,
Shyue Ping

On Thursday, May 16, 2013 at 7:45 PM, mbkumar wrote:

May be what I am doing is wrong. In that case, let me know where I am wrong.
I am attaching the python script and the input data files.

Thanks,
Bharat

On 5/16/13 4:29 PM, Shyue Ping Ong wrote:

Hi there,

I can't reproduce the error. You cannot just specify voronoi_data as
site properties because there are only some properties allowed. But
otherwise, I can't reproduce the error. Can you give me the exact
forms of the variables voronoi_lattice, s and c? For example, the
following works just fine:

Structure(Lattice.cubic(3), ["Fe"], [[0,0,0]], coords_are_cartesian=True)

—
Reply to this email directly or view it on GitHub
#24 (comment).

4.2120 4.2120 4.2120
90.00 90.00 90.00 SPGR = 1 P 1 OPT = 1
8 0
0 Mg4 O4
1 Mg 0.0000 0.0000 0.0000 0 0 0 0 0 0 0 0 0.00
2 Mg 0.5000 0.5000 0.0000 0 0 0 0 0 0 0 0 0.00
3 Mg 0.5000 0.0000 0.5000 0 0 0 0 0 0 0 0 0.00
4 Mg 0.0000 0.5000 0.5000 0 0 0 0 0 0 0 0 0.00
5 O 0.5000 0.0000 0.0000 0 0 0 0 0 0 0 0 0.00
6 O 0.0000 0.5000 0.0000 0 0 0 0 0 0 0 0 0.00
7 O 0.0000 0.0000 0.5000 0 0 0 0 0 0 0 0 0.00
8 O 0.5000 0.5000 0.5000 0 0 0 0 0 0 0 0 0.00

—
Reply to this email directly or view it on GitHub (#24 (comment)).

[mbkumar]

I'll send them tomorrow morning.

Bharat

On Thu, 16 May 2013 18:56:18 -0500, Shyue Ping Ong
notifications@github.com wrote:

Hi Bharat,

I don't see an input file. Maybe you can email them directly to me at
shyuep@gmail.com?

Regards,
Shyue Ping

On Thursday, May 16, 2013 at 7:45 PM, mbkumar wrote:

May be what I am doing is wrong. In that case, let me know where I am
wrong.
I am attaching the python script and the input data files.

Thanks,
Bharat

On 5/16/13 4:29 PM, Shyue Ping Ong wrote:

Hi there,

I can't reproduce the error. You cannot just specify voronoi_data as
site properties because there are only some properties allowed. But
otherwise, I can't reproduce the error. Can you give me the exact
forms of the variables voronoi_lattice, s and c? For example, the
following works just fine:

Structure(Lattice.cubic(3), ["Fe"], [[0,0,0]],
coords_are_cartesian=True)

—
Reply to this email directly or view it on GitHub

#24 (comment).

4.2120 4.2120 4.2120
90.00 90.00 90.00 SPGR = 1 P 1 OPT = 1
8 0
0 Mg4 O4
1 Mg 0.0000 0.0000 0.0000 0 0 0 0 0 0 0 0 0.00
2 Mg 0.5000 0.5000 0.0000 0 0 0 0 0 0 0 0 0.00
3 Mg 0.5000 0.0000 0.5000 0 0 0 0 0 0 0 0 0.00
4 Mg 0.0000 0.5000 0.5000 0 0 0 0 0 0 0 0 0.00
5 O 0.5000 0.0000 0.0000 0 0 0 0 0 0 0 0 0.00
6 O 0.0000 0.5000 0.0000 0 0 0 0 0 0 0 0 0.00
7 O 0.0000 0.0000 0.5000 0 0 0 0 0 0 0 0 0.00
8 O 0.5000 0.5000 0.5000 0 0 0 0 0 0 0 0 0.00

—
Reply to this email directly or view it on GitHub
(#24 (comment)).

---

Reply to this email directly or view it on GitHub:
#24 (comment)