Supercell - Revision history

Cchem: 1 revision

2020-07-20T16:19:42Z

1 revision

Speleo3: remove code

2020-07-01T08:24:46Z

remove code

Cchem: 1 revision

2016-06-27T02:04:49Z

1 revision

Speleo3: all states

2016-06-23T17:35:46Z

all states

Bell: 8 revisions

2014-03-28T03:56:02Z

8 revisions

Speleo3: Infobox psico

2012-07-31T07:56:26Z

Infobox psico

Speleo3: headers, withmates=1 as default, tab-completion, see also

2011-08-05T07:27:43Z

headers, withmates=1 as default, tab-completion, see also

Speleo3: example picture

2010-07-21T15:14:52Z

example picture

Speleo3: cgo.END

2010-04-19T12:17:18Z

cgo.END

Speleo3: symexpcell

2010-04-17T09:30:39Z

symexpcell

@@ Line 15: / Line 15: @@
 <source lang="python">
-run supercell.py
+# import psico.xtal, or run the standalone script:
 fetch 2x19, async=0
 supercell 2,1,1, 2x19, green
 supercell 1,1,2, 2x19, orange, name=super2
 </source>

@@ Line 187: / Line 187: @@
 		name = '%s%d' % (prefix, i)
 		cmd.create(name, object)
-		cmd.transform_object(name, mat_list)
+		cmd.transform_object(name, mat_list, 0)
 		cmd.color(i+1, name)

← Older revision		Revision as of 07:56, 31 July 2012
Line 1:		Line 1:
		+	{{Infobox psico
		+	\|module = psico.xtal
		+	}}
		+
	[[File:SupercellExample.png\|200px\|thumb\|right\|Example with 2 unit cells in c-direction, created with: supercell 1,1,2,2x19]]		[[File:SupercellExample.png\|200px\|thumb\|right\|Example with 2 unit cells in c-direction, created with: supercell 1,1,2,2x19]]

@@ Line 1: / Line 1: @@
-[[File:SupercellExample.png|200px|thumb|right|Example with 2 unit cells in c-direction, created with: supercell 1,1,2,2x19,withmates=1]]
+[[File:SupercellExample.png|200px|thumb|right|Example with 2 unit cells in c-direction, created with: supercell 1,1,2,2x19]]
-= Overview =
+'''supercell''' can display multiple copies of the unit cell.
 Can also fill the unit cell (and its copies) with symmetry mates.
@@ Line 10: / Line 8: @@
 Requires [http://numpy.scipy.org numpy].
-= Example =
+== Example ==
 <source lang="python">
@@ Line 17: / Line 15: @@
 supercell 2,1,1, 2x19, green
 supercell 1,1,2, 2x19, orange, name=super2
 </source>
-= The Code =
+== The Code ==
 <source lang="python">
@@ Line 49: / Line 46: @@
 	return basis * edges # numpy.array multiplication!
-def supercell(a=1, b=1, c=1, object=None, color='blue', name='supercell', withmates=0):
+def supercell(a=1, b=1, c=1, object=None, color='blue', name='supercell', withmates=1):
 	'''
 DESCRIPTION
@@ Line 73: / Line 70: @@
      withmates = bool: also create symmetry mates in displayed cells
-     {default: 0}
+     {default: 1}
 SEE ALSO
@@ Line 151: / Line 148: @@
 SEE ALSO
-     symexp
+     symexp, http://www.pymolwiki.org/index.php/SuperSym
 	'''
 	if object is None:
@@ Line 191: / Line 188: @@
 cmd.extend('symexpcell', symexpcell)
 cmd.extend('supercell', supercell)
 </source>
 [[Category:Script_Library]]
 [[Category:Math_Scripts]]

@@ Line 1: / Line 1: @@
 = Overview =
@@ Line 5: / Line 7: @@
 See [http://sourceforge.net/mailarchive/forum.php?thread_name=l2vdcf611bd1004140816zeca28714mf76b9f72008099ab%40mail.gmail.com&forum_name=pymol-users thread on pymol-users mailing list].
 = Example =

← Older revision	Revision as of 16:19, 20 July 2020
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← Older revision	Revision as of 02:04, 27 June 2016
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← Older revision	Revision as of 03:56, 28 March 2014
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@@ Line 120: / Line 120: @@
 		if withmates:
 			symexpcell('m%d%d%d_' % tuple(t), object, *t)
 	cmd.delete(name)

@@ Line 2: / Line 2: @@
 Can display multiple copies of the unit cell.
 See [http://sourceforge.net/mailarchive/forum.php?thread_name=l2vdcf611bd1004140816zeca28714mf76b9f72008099ab%40mail.gmail.com&forum_name=pymol-users thread on pymol-users mailing list].
@@ Line 12: / Line 13: @@
 supercell 2,1,1, 2x19, green
 supercell 1,1,2, 2x19, orange, name=super2
 </source>
@@ Line 21: / Line 23: @@
 PyMOL python script (load with `run supercell.py`)
-Usage: See "help supercell"
+Usage: See "help supercell" and "help symexpcell"
 '''
-from pymol import cmd, cgo
+from pymol import cmd, cgo, xray
 from math import cos, sin, radians, sqrt
 import numpy
@@ Line 43: / Line 45: @@
 	return basis * edges # numpy.array multiplication!
-def supercell(a=1, b=1, c=1, object=None, color='blue', name='supercell'):
+def supercell(a=1, b=1, c=1, object=None, color='blue', name='supercell', withmates=0):
 	'''
 DESCRIPTION
@@ Line 53: / Line 55: @@
 USAGE
-     supercell a, b, c [, object [, color [, name]]]
+     supercell a, b, c [, object [, color [, name [, withmates]]]]
 ARGUMENTS
@@ Line 65: / Line 67: @@
      name = string: name of the cgo object to create {default: supercell}
 SEE ALSO
@@ Line 73: / Line 78: @@
 	if object is None:
 		object = cmd.get_object_list()[0]
 	sym = cmd.get_symmetry(object)
@@ Line 111: / Line 117: @@
 				obj.append(cgo.VERTEX)
 				obj.extend((shift + vj[j] + vi).tolist())
 	cmd.delete(name)
 	cmd.load_cgo(obj, name)
 cmd.extend('supercell', supercell)
 </source>