# 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
######################################################################
# DESCRIPTION: #
######################################################################
# Removes the selective dynamics from the inputfile #
######################################################################
from p4vasp.Structure import *
from p4vasp.sellang import *
from p4vasp.SystemPM import *
from sys import *
# Read the structure.
p=Structure(argv[1])
p.setSelective(0) # Selective mode.
p.write("%s.notselective"%argv[1]) # Write the output.
# 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.setSelective(0)
nx = int(argv[1])
ny = int(argv[2])
nz = int(argv[3])
s.replicateCell(nx, ny, nz)
s.write("POSCAR_%d-%d-%d" % (nx, ny, nz))
######################################################################
# This is a selection script example. #
# The purpose of this script is to select (in the sense of the #
# "Selective dynamics") certain atom group. #
# #
# It is very simple and it is easier to modify this source #
# to do what you want, than to write a sophisticated user interface. #
# (see the comments) #
######################################################################
from p4vasp.Structure import *
from p4vasp.sellang import *
from p4vasp.SystemPM import *
# Read the structure.
p=Structure("POSCAR")
# Alternative:
#p=XMLSystemPM("vasprun.xml").FINAL_STRUCTURE
l=decode("#4",p) # Select the 4th specie
p.setSelective() # Selective mode.
for i in range(len(p)):
if i in l:
p.selective[i]=(1,1,1)
else:
p.selective[i]=(0,0,0)
p.write("POSCAR.selected") # Write the output.
# along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
######################################################################
# DESCRIPTION: #
######################################################################
# This is a removes all but selected atoms. #
# Selection is given by selection language at the #
# line with decode("..."). #
# #
# It is very simple and it is easier to modify this source #
# to do what you want, than to write a sophisticated user interface. #
# (see the comments) #
######################################################################
from p4vasp.Structure import *
from p4vasp.sellang import *
from p4vasp.SystemPM import *
# Read the structure.
p=Structure("POSCAR")
# Alternative:
#p=XMLSystemPM("vasprun.xml").FINAL_STRUCTURE
#del p[59]
#Now remove specie 2
p.remove("#2")
#Finally write the output.
p.write("POSCAR.removed") # Write the output.
#!/usr/bin/env python
import os
import time
import sys
import re
from p4vasp.Structure import *
if len(sys.argv) < 2:
print "Usage: "+sys.argv[0]+" <poscar file>"
print " outputs the direct coords to stdout"
sys.exit(1)
space = re.compile(r'\s+')
file = sys.argv[1]
p=Structure(file)
p.setDirect()
p.write(sys.stdout)
#!/usr/bin/python
from p4vasp.Structure import *
from sys import argv
p = Structure(argv[1])
#p.setSelective(0)
for i in range(p.types):
f = p.info.firstAtomIndexForSpecie(i)
l = []
if p.isSelective():
for j in range(p.atomspertype[i]):
l.append((p[j][2], p[j], p.selective[j]))
l.sort()
for j in range(p.atomspertype[i]):
p[j] = l[j][1]
p.selective[j] = l[j][2]
else:
for j in range(p.atomspertype[i]):
l.append((p[j][2], p[j]))
l.sort()
for j in range(p.atomspertype[i]):
p[j] = l[j][1]
p.write(argv[1] + ".sorted")
#!/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")
# (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.setSelective(0)
nx=int(argv[1])
ny=int(argv[2])
nz=int(argv[3])
s.replicateCell(nx,ny,nz)
s.write("POSCAR_%d-%d-%d"%(nx,ny,nz))
######################################################################
# This is a selection script example. #
# The purpose of this script is to select (in the sense of the #
# "Selective dynamics") certain atom group. #
# #
# It is very simple and it is easier to modify this source #
# to do what you want, than to write a sophisticated user interface. #
# (see the comments) #
######################################################################
from p4vasp.Structure import *
from p4vasp.sellang import *
from p4vasp.SystemPM import *
# Read the structure.
p=Structure("POSCAR")
# Alternative:
#p=XMLSystemPM("vasprun.xml").FINAL_STRUCTURE
l=decode("#4",p) # Select the 4th specie
p.setSelective() # Selective mode.
for i in range(len(p)):
if i in l:
p.selective[i]=(1,1,1)
else:
p.selective[i]=(0,0,0)
p.write("POSCAR.selected") # Write the output.
# 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")
# along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
######################################################################
# DESCRIPTION: #
######################################################################
# This is a removes all but selected atoms. #
# Selection is given by selection language at the #
# line with decode("..."). #
# #
# It is very simple and it is easier to modify this source #
# to do what you want, than to write a sophisticated user interface. #
# (see the comments) #
######################################################################
from p4vasp.Structure import *
from p4vasp.sellang import *
from p4vasp.SystemPM import *
# Read the structure.
p=Structure("POSCAR")
# Alternative:
#p=XMLSystemPM("vasprun.xml").FINAL_STRUCTURE
#del p[59]
#Now remove specie 2
p.remove("#2")
#Finally write the output.
p.write("POSCAR.removed") # Write the output.
# 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
######################################################################
# DESCRIPTION: #
######################################################################
# Removes the selective dynamics from the inputfile #
######################################################################
from p4vasp.Structure import *
from p4vasp.sellang import *
from p4vasp.SystemPM import *
from sys import *
# Read the structure.
p=Structure(argv[1])
p.setSelective(0) # Selective mode.
p.write("%s.notselective"%argv[1]) # Write the output.