Difference between revisions of "Supercell"

	Included in psico; This command or function is available from psico, which is a PyMOL extension.
Module	psico.xtal

Latest revision as of 04:24, 1 July 2020

Example with 2 unit cells in c-direction, created with: supercell 1,1,2,2x19

supercell can display multiple copies of the unit cell. Can also fill the unit cell (and its copies) with symmetry mates.

See thread on pymol-users mailing list.

Requires numpy.

Example

# import psico.xtal, or run the standalone script:
run https://raw.githubusercontent.com/speleo3/pymol-psico/master/psico/xtal.py

fetch 2x19, async=0
supercell 2,1,1, 2x19, green
supercell 1,1,2, 2x19, orange, name=super2

Difference between revisions of "Supercell"

Latest revision as of 04:24, 1 July 2020

Example

See Also

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@@ Line 1: / Line 1: @@
-= Overview =
+{{Infobox psico
+|module    =  psico.xtal
+}}
-Can display multiple copies of the unit cell.
+[[File:SupercellExample.png|200px|thumb|right|Example with 2 unit cells in c-direction, created with: supercell 1,1,2,2x19]]
+'''supercell''' can display multiple copies of the unit cell.
 Can also fill the unit cell (and its copies) with symmetry mates.
 See [http://sourceforge.net/mailarchive/forum.php?thread_name=l2vdcf611bd1004140816zeca28714mf76b9f72008099ab%40mail.gmail.com&forum_name=pymol-users thread on pymol-users mailing list].
-= Example =
+Requires [http://numpy.scipy.org numpy].
+== Example ==
 <source lang="python">
-run supercell.py
+# import psico.xtal, or run the standalone script:
+run https://raw.githubusercontent.com/speleo3/pymol-psico/master/psico/xtal.py
 fetch 2x19, async=0
 supercell 2,1,1, 2x19, green
 supercell 1,1,2, 2x19, orange, name=super2
-supercell 1,1,2, 2x19, orange, name=super2, withmates=1
 </source>
-= The Code =
+== See Also ==
-<source lang="python">
-'''
-(c) 2010 Thomas Holder
-PyMOL python script (load with `run supercell.py`)
-Usage: See "help supercell" and "help symexpcell"
-'''
-from pymol import cmd, cgo, xray
-from math import cos, sin, radians, sqrt
-import numpy
-def cellbasis(angles, edges):
-	'''
-	For the unit cell with given angles and edge lengths calculate the basis
-	transformation (vectors) as a 4x4 numpy.array
-	'''
-	rad = [radians(i) for i in angles]
-	basis = numpy.identity(4)
-	basis[0][1] = cos(rad[2])
-	basis[1][1] = sin(rad[2])
-	basis[0][2] = cos(rad[1])
-	basis[1][2] = (cos(rad[0]) - basis[0][1]*basis[0][2])/basis[1][1]
-	basis[2][2] = sqrt(1 - basis[0][2]**2 - basis[1][2]**2)
-	edges.append(1.0)
-	return basis * edges # numpy.array multiplication!
-def supercell(a=1, b=1, c=1, object=None, color='blue', name='supercell', withmates=0):
-	'''
-DESCRIPTION
-    Draw a supercell, as requested by Nicolas Bock on the pymol-users
-    mailing list (Subject: [PyMOL] feature request: supercell construction
-    Date: 04/12/2010 10:12:17 PM (Mon, 12 Apr 2010 14:12:17 -0600))
-USAGE
-    supercell a, b, c [, object [, color [, name [, withmates]]]]
-ARGUMENTS
-    a, b, c = integer: repeat cell in x,y,z direction a,b,c times
-    {default: 1,1,1}
-    object = string: name of object to take cell definition from
-    color = string: color of cell {default: blue}
-    name = string: name of the cgo object to create {default: supercell}
-    withmates = bool: also create symmetry mates in displayed cells
-    {default: 0}
-SEE ALSO
-    show cell
-	'''
-	if object is None:
-		object = cmd.get_object_list()[0]
-	withmates = int(withmates)
-	sym = cmd.get_symmetry(object)
-	cell_edges = sym[0:3]
-	cell_angles = sym[3:6]
-	basis = cellbasis(cell_angles, cell_edges)
+* [[SuperSym]]
-	assert isinstance(basis, numpy.ndarray)
+* [[symexp]]
-	ts = list()
-	for i in range(int(a)):
-		for j in range(int(b)):
-			for k in range(int(c)):
-				ts.append([i,j,k])
-	obj = [
-		cgo.BEGIN,
-		cgo.LINES,
-		cgo.COLOR,
-	]
-	obj.extend(cmd.get_color_tuple(color))
-	for t in ts:
-		shift = basis[0:3,0:3] * t
-		shift = shift[:,0] + shift[:,1] + shift[:,2]
-		for i in range(3):
-			vi = basis[0:3,i]
-			vj = [
-				numpy.array([0.,0.,0.]),
-				basis[0:3,(i+1)%3],
-				basis[0:3,(i+2)%3],
-				basis[0:3,(i+1)%3] + basis[0:3,(i+2)%3]
-			]
-			for j in range(4):
-				obj.append(cgo.VERTEX)
-				obj.extend((shift + vj[j]).tolist())
-				obj.append(cgo.VERTEX)
-				obj.extend((shift + vj[j] + vi).tolist())
-		if withmates:
-			symexpcell('m%d%d%d_' % tuple(t), object, *t)
-	obj.append(cgo.END)
-	cmd.delete(name)
-	cmd.load_cgo(obj, name)
-def symexpcell(prefix='mate', object=None, a=0, b=0, c=0):
-	'''
-DESCRIPTION
-    Creates all symmetry-related objects for the specified object that
-    occur with their bounding box center within the unit cell.
-USAGE
-    symexpcell prefix, object, [a, b, c]
-ARGUMENTS
-    prefix = string: prefix of new objects
-    object = string: object for which to create symmetry mates
-    a, b, c = integer: create neighboring cell {default: 0,0,0}
-SEE ALSO
-    symexp
-	'''
-	if object is None:
-		object = cmd.get_object_list()[0]
-	sym = cmd.get_symmetry(object)
-	cell_edges = sym[0:3]
-	cell_angles = sym[3:6]
-	spacegroup = sym[6]
-	basis = cellbasis(cell_angles, cell_edges)
-	basis = numpy.matrix(basis)
-	extent = cmd.get_extent(object)
-	center = sum(numpy.array(extent)) * 0.5
-	center = numpy.matrix(center.tolist() + [1.0]).T
-	center_cell = basis.I * center
-	extra_shift = [[float(i)] for i in (a,b,c)]
-	i = 0
-	matrices = xray.sg_sym_to_mat_list(spacegroup)
-	for mat in matrices:
-		i += 1
-		mat = numpy.matrix(mat)
-		shift = numpy.floor(mat * center_cell)
-		mat[0:3,3] -= shift[0:3,0]
-		mat[0:3,3] += extra_shift
-		mat = basis * mat * basis.I
-		mat_list = list(mat.flat)
-		name = '%s%d' % (prefix, i)
-		cmd.create(name, object)
-		cmd.transform_object(name, mat_list)
-		cmd.color(i+1, name)
-cmd.extend('symexpcell', symexpcell)
-cmd.extend('supercell', supercell)
-</source>
 [[Category:Script_Library]]
 [[Category:Math_Scripts]]

Included in psico This command or function is available from psico, which is a PyMOL extension.
Module	psico.xtal