bartolsthoorn/seekpath_run.py

## seekpath_run.py
from pymatgen import Structure
from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
import seekpath
import json

structure = Structure.from_file('diamond.cif')

# spglib primitive cell
sga = SpacegroupAnalyzer(structure)
structure = sga.find_primitive()

#print(seekpath.getpaths.get_explicit_k_path(sga._cell))
#print(seekpath.getpaths.get_path(sga._cell))

# from seekpath_web_module.py
def get_json_for_visualizer(cell, relcoords, atomic_numbers):
    from seekpath import hpkot
    from seekpath.brillouinzone.brillouinzone import get_BZ
    import numpy as np
    #hpkot = seekpath_module.hpkot
    #brillouinzone = seekpath_module.brillouinzone

    system = (np.array(cell), np.array(relcoords), np.array(atomic_numbers))
    res = hpkot.get_path(system, with_time_reversal=False)

    real_lattice = res['primitive_lattice']
    #rec_lattice = np.linalg.inv(real_lattice).T # Missing 2pi!
    rec_lattice = np.array(hpkot.tools.get_reciprocal_cell_rows(real_lattice))
    b1, b2, b3 = rec_lattice

    #print(brillouinzone)
    faces_data = get_BZ(b1=b1, b2=b2, b3=b3)

    response = {}
    response['faces_data'] = faces_data
    response['b1'] = b1.tolist()
    response['b2'] = b2.tolist()
    response['b3'] = b3.tolist()
    ## Convert to absolute
    response['kpoints'] = {
        k: (v[0] * b1 + v[1] * b2 + v[2] * b3).tolist()
        for k, v in res['point_coords'].items()
    }
    response['kpoints_rel'] = {
        k: [v[0], v[1], v[2]] for k, v in res['point_coords'].items()
    }
    response['path'] = res['path']

    # It should use the same logic, so give the same cell as above
    res_explicit = seekpath.get_explicit_k_path(
        system, with_time_reversal=False)
    for k in res_explicit:
        if k == 'segments' or k.startswith('explicit_'):
            if isinstance(res_explicit[k], np.ndarray):
                response[k] = res_explicit[k].tolist()
            else:
                response[k] = res_explicit[k]

    if np.sum(
            np.abs(
                np.array(res_explicit['reciprocal_primitive_lattice']) -
                np.array(res['reciprocal_primitive_lattice']))) > 1.e-7:
        raise AssertionError("Got different reciprocal cells...")

    # Response for JS, and path_results
    return response, res


def tuple_from_pymatgen(pmgstructure):
    """
    Given a pymatgen structure, return a structure tuple as expected from seekpath

    :param pmgstructure: a pymatgen Structure object

    :return: a structure tuple (cell, positions, numbers) as accepted
        by seekpath.
    """
    frac_coords = [site.frac_coords.tolist() for site in pmgstructure.sites]
    structure_tuple = (pmgstructure.lattice.matrix.tolist(), frac_coords,
                       pmgstructure.atomic_numbers)
    return structure_tuple


jsondata = get_json_for_visualizer(*tuple_from_pymatgen(structure))[0]

print("""<!DOCTYPE html>
<html>
<head>
<meta charset="utf-8">
<link rel="stylesheet" type="text/css" href="http://127.0.0.1:5000/static/css/visualizer.min.css"/>
<link rel="stylesheet" type="text/css" href="http://127.0.0.1:5000/static/css/visualizer_base.min.css"/>
<script src="http://127.0.0.1:5000/static/js/three.min.js"></script>
<script src="http://127.0.0.1:5000/static/js/OrbitControls.min.js"></script>
<script src="http://127.0.0.1:5000/static/js/jquery-3.1.0.min.js"></script>
<script src="http://127.0.0.1:5000/static/js/BZVisualizer.min.js"></script>
<script>
var jsondata = """+ json.dumps(jsondata) +""";
var mainBZVisualizer = new BZVisualizer();
$( document ).ready(function() {
    mainBZVisualizer.loadBZ(canvasID='canvas3d',infoID='info',jsondata=jsondata);
    //canvas3d.dispatchEvent(new Event("dblclick"));
});
</script>
</head>
<body>
    <div id='canvas3dcontainer'>
        <div id='canvas3d'></div><div id='info'></div>
    </div>
</body>
</html>
""")
	from pymatgen import Structure
	from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
	import seekpath
	import json

	structure = Structure.from_file('diamond.cif')

	# spglib primitive cell
	sga = SpacegroupAnalyzer(structure)
	structure = sga.find_primitive()

	#print(seekpath.getpaths.get_explicit_k_path(sga._cell))
	#print(seekpath.getpaths.get_path(sga._cell))

	# from seekpath_web_module.py
	def get_json_for_visualizer(cell, relcoords, atomic_numbers):
	from seekpath import hpkot
	from seekpath.brillouinzone.brillouinzone import get_BZ
	import numpy as np
	#hpkot = seekpath_module.hpkot
	#brillouinzone = seekpath_module.brillouinzone

	system = (np.array(cell), np.array(relcoords), np.array(atomic_numbers))
	res = hpkot.get_path(system, with_time_reversal=False)

	real_lattice = res['primitive_lattice']
	#rec_lattice = np.linalg.inv(real_lattice).T # Missing 2pi!
	rec_lattice = np.array(hpkot.tools.get_reciprocal_cell_rows(real_lattice))
	b1, b2, b3 = rec_lattice

	#print(brillouinzone)
	faces_data = get_BZ(b1=b1, b2=b2, b3=b3)

	response = {}
	response['faces_data'] = faces_data
	response['b1'] = b1.tolist()
	response['b2'] = b2.tolist()
	response['b3'] = b3.tolist()
	## Convert to absolute
	response['kpoints'] = {
	k: (v[0] * b1 + v[1] * b2 + v[2] * b3).tolist()
	for k, v in res['point_coords'].items()
	}
	response['kpoints_rel'] = {
	k: [v[0], v[1], v[2]] for k, v in res['point_coords'].items()
	}
	response['path'] = res['path']

	# It should use the same logic, so give the same cell as above
	res_explicit = seekpath.get_explicit_k_path(
	system, with_time_reversal=False)
	for k in res_explicit:
	if k == 'segments' or k.startswith('explicit_'):
	if isinstance(res_explicit[k], np.ndarray):
	response[k] = res_explicit[k].tolist()
	else:
	response[k] = res_explicit[k]

	if np.sum(
	np.abs(
	np.array(res_explicit['reciprocal_primitive_lattice']) -
	np.array(res['reciprocal_primitive_lattice']))) > 1.e-7:
	raise AssertionError("Got different reciprocal cells...")

	# Response for JS, and path_results
	return response, res


	def tuple_from_pymatgen(pmgstructure):
	"""
	Given a pymatgen structure, return a structure tuple as expected from seekpath

	:param pmgstructure: a pymatgen Structure object

	:return: a structure tuple (cell, positions, numbers) as accepted
	by seekpath.
	"""
	frac_coords = [site.frac_coords.tolist() for site in pmgstructure.sites]
	structure_tuple = (pmgstructure.lattice.matrix.tolist(), frac_coords,
	pmgstructure.atomic_numbers)
	return structure_tuple


	jsondata = get_json_for_visualizer(*tuple_from_pymatgen(structure))[0]

	print("""<!DOCTYPE html>
	<html>
	<head>
	<meta charset="utf-8">
	<link rel="stylesheet" type="text/css" href="http://127.0.0.1:5000/static/css/visualizer.min.css"/>
	<link rel="stylesheet" type="text/css" href="http://127.0.0.1:5000/static/css/visualizer_base.min.css"/>
	<script src="http://127.0.0.1:5000/static/js/three.min.js"></script>
	<script src="http://127.0.0.1:5000/static/js/OrbitControls.min.js"></script>
	<script src="http://127.0.0.1:5000/static/js/jquery-3.1.0.min.js"></script>
	<script src="http://127.0.0.1:5000/static/js/BZVisualizer.min.js"></script>
	<script>
	var jsondata = """+ json.dumps(jsondata) +""";
	var mainBZVisualizer = new BZVisualizer();
	$( document ).ready(function() {
	mainBZVisualizer.loadBZ(canvasID='canvas3d',infoID='info',jsondata=jsondata);
	//canvas3d.dispatchEvent(new Event("dblclick"));
	});
	</script>
	</head>
	<body>
	<div id='canvas3dcontainer'>
	<div id='canvas3d'></div><div id='info'></div>
	</div>
	</body>
	</html>
	""")