def showZMat(self,s,sel):
view=self.treeview
s=Structure(s)
s.setCarthesian()
view.set_model(ZMatTreeModel(s,sel))
for x in self.treeview.get_columns():
view.remove_column(x)
renderer = gtk.CellRendererText()
column = gtk.TreeViewColumn("#", renderer, markup=0)
view.append_column(column)
renderer = gtk.CellRendererText()
column = gtk.TreeViewColumn("distance", renderer, markup=1)
view.append_column(column)
renderer = gtk.CellRendererText()
column = gtk.TreeViewColumn("angle", renderer, markup=2)
view.append_column(column)
renderer = gtk.CellRendererText()
column = gtk.TreeViewColumn("dihedral", renderer, markup=3)
view.append_column(column)
view.show()
def showDistances(self,s,sel):
view=self.treeview
s=Structure(s)
s.setCarthesian()
view.set_model(DistanceTreeModel(s,sel))
for x in self.treeview.get_columns():
view.remove_column(x)
renderer = gtk.CellRendererText()
column = gtk.TreeViewColumn("#", renderer, markup=0)
view.append_column(column)
renderer = gtk.CellRendererText()
for i in range(len(sel)):
n,nx,ny,nz=sel[i]
column = gtk.TreeViewColumn("%d (%d %d %d)"%(n+1,nx,ny,nz), renderer, markup=i+1)
view.append_column(column)
view.show()
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
from p4vasp.Structure import *
from p4vasp.sellang import *
#from p4vasp.SystemPM import *
#s=XMLSystemPM('vasprun.xml')
#p=s.INITIAL_STRUCTURE
p=Structure("CONTCAR")
p.setCarthesian()
l1=decode("-160",p)
l2=decode("161-",p)
print "Group 1 has %3d elements."%len(l1)
print "Group 2 has %3d elements."%len(l2)
d=[]
for i in l1:
for j in l2:
if i==j:
print "Substructures have a common atom %d."%(i+1)
else:
d.append((p.mindistCartVectors(p[i],p[j]),i,j))
m,i,j=min(d)
print "Minimal distance:",m
#!/usr/bin/python2
# p4vasp is a GUI-program and a library for processing outputs of the
# Vienna Ab-inition Simulation Package (VASP)
# (see http://cms.mpi.univie.ac.at/vasp/Welcome.html)
#
# Copyright (C) 2003 Orest Dubay <*****@*****.**>
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
from p4vasp.Structure import *
from sys import *
s = Structure("POSCAR")
s.setCarthesian()
for i in range(len(s)):
s[i][1] *= -1
s.toUnitCell()
s.write("POSCAR.Y-mirror")
# Vienna Ab-inition Simulation Package (VASP)
# (see http://cms.mpi.univie.ac.at/vasp/Welcome.html)
#
# Copyright (C) 2003 Orest Dubay <*****@*****.**>
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
from p4vasp.Structure import *
from sys import *
s=Structure("POSCAR")
s.setCarthesian()
for i in range(len(s)):
s[i][1]*=-1
s.toUnitCell()
s.write("POSCAR.Y-mirror")