Hi David, Albert,
> The current reduceToPrimitive function is here:
>
> http://github.com/dlonie/avogadro/blob/master/libavogadro/src/extensions/crystallography/avospglib.cpp#L226
>
> What it does is:
>
> (1) Determine the spacegroup of the cell with spg_get_international
> (2) Clean up the structure with spg_refine_cell
> (3) Reduce the cell to it's primitive representation with spg_find_primitive
> (4) Update the molecule with the new cell matrix and coordinates
>
> The coordinates, lattice matrix, etc are kept in the same arrays
> throughout the process, so if refine_cell is changing the orientation,
> it should not matter since the reoriented matrix and refined
> coordinates are passed to the find_primitive function. I cannot see
> how calling the refine_cell function before the reduction would break
> the behavior, but I may be missing something.
I had a look at reduceToPrimitive and I also couldn't find something wrong.
So now I doubt spglib. There may be bug in spg_refine_cell in the
previous versions. I wrote the followng test code in C and confirmed
that the latest spglib works correctly. I've not tested but if this C
code also works for the spglib in the Avogadro, the problem might be
somewhere out of reduceToPrimitive.
#include "spglib.h"
#include <stdio.h>
int main()
{
double lattice[3][3] = { {3, 0, 0}, {0, 3, 0}, {0, 0, 3} };
double positions[32][3];
double pos_orig[][3] = {
{0, 0, 0},
{0.0, 0.5, 0.5},
{0.5, 0.5, 0.0},
{0.5, 0.0, 0.5},
{0.75, 0.25, 0.75},
{0.25, 0.25, 0.25},
{0.25, 0.75, 0.75},
{0.75, 0.75, 0.25}
};
int types[32];
int i, num_atom = 8, num_atom_prim, num_atom_bravais;
double symprec = 1e-5;
for (i = 0; i < num_atom; i++) {
positions[i][0] = pos_orig[i][0];
positions[i][1] = pos_orig[i][1];
positions[i][2] = pos_orig[i][2];
types[i] = 1;
}
num_atom_bravais = spg_refine_cell(lattice,
positions,
types,
num_atom,
symprec);
for (i = 0; i < 3; i++) {
printf("%f %f %f\n", lattice[i][0], lattice[i][1], lattice[i][2]);
}
for (i = 0; i < num_atom_bravais; i++) {
printf("%d: %f %f %f\n", i, positions[i][0], positions[i][1],
positions[i][2]);
}
num_atom_prim = spg_find_primitive(lattice, positions, types,
num_atom_bravais, symprec);
for (i = 0; i < 3; i++) {
printf("%f %f %f\n", lattice[i][0], lattice[i][1], lattice[i][2]);
}
for (i = 0; i < num_atom_prim; i++) {
printf("%d: %f %f %f\n", i, positions[i][0], positions[i][1],
positions[i][2]);
}
}
Togo
>
> As a side note, I've recently started using your phonopy software
> after giving up a fight with PHON (it wouldn't recognize the symmetry,
> and doesn't seem to have an adjustable tolerance...). Phonopy is a
> wonderful tool, and I'm especially impressed by the matplotlib
> integration. I've been recommending it to my coworkers -- keep up the
> good work! :-)
>
> Dave
--
Atsushi Togo
http://atztogo.users.sourceforge.net/
[email protected]
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