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()
def updateCreation(self): s = getCurrentSystemPM() self.creation = SetupPM(s) name = self.nameentry.get_text() self.creation.INCAR["SYSTEM"] = name if self.import_button.get_active(): self.creation = SetupPM(s) name = self.nameentry.get_text() self.creation.INCAR["SYSTEM"] = name self.updateImportDescription() # print "updateCreation",self.creation.NAME se = strip(self.step_entry.get_text()) buff = self.description_textview.get_buffer() start = buff.get_start_iter() end = buff.get_end_iter() self.creation.DESCRIPTION = str(buff.get_text(start, end)) try: n = int(se) try: struct = s.STRUCTURE_SEQUENCE_L[n] if n is not None: self.creation.INITIAL_STRUCTURE.setStructure(struct) except: msg().exception() self.creation.INITIAL_STRUCTURE = Structure() except: if len(se): if upper(se[0]) == "I": if s.INITIAL_STRUCTURE is not None: self.creation.INITIAL_STRUCTURE.setStructure( s.INITIAL_STRUCTURE) else: self.creation.INITIAL_STRUCTURE = Structure() elif upper(se[0]) == "F": if s.FINAL_STRUCTURE is not None: self.creation.INITIAL_STRUCTURE.setStructure( s.FINAL_STRUCTURE) else: self.creation.INITIAL_STRUCTURE = Structure() else: self.creation = SetupPM() name = self.nameentry.get_text() self.creation.INCAR["SYSTEM"] = name
def textview2struct(self): # print "before tv2s",len(self.getCurrentStructure()) try: b = self.textview.get_buffer() t = b.get_text(b.get_start_iter(), b.get_end_iter(), True) s = Structure() s.parse(t) self.getCurrentStructure().setStructure(s) self.no_coord_upd = 1 if s.isCarthesian(): self.carthesian_button.set_active(True) else: self.direct_button.set_active(True) # systemlist().notifySystemChanged() except ParseException: msg().error(str(sys.exc_info()[1])) except: msg().exception() else: msg().status("OK") self.no_coord_upd = 0
def makeZigzag(nn,aCC=1.419398,r=None,x_shift=0.0,y_shift=0.0,z_shift=0.0): s=Structure() s.setCartesian() s.comment="zigzag (%d,0), aCC=%f"%(nn,aCC) shift = 0.0 fi = 2*pi/nn if r is None: r = aCC*sqrt(3.0)/4/sin(fi/4) for i in range(0,nn): ffi=fi*i s.appendAtom(0,Vector(x_shift+r*cos(ffi),y_shift+r*sin(ffi),z_shift+shift)) shift = shift + aCC/2 for i in range(0,nn): ffi=fi*(i+0.5) s.appendAtom(0,Vector(x_shift+r*cos(ffi),y_shift+r*sin(ffi),z_shift+shift)) shift = shift + aCC for i in range(0,nn): ffi=fi*(i+0.5) s.appendAtom(0,Vector(x_shift+r*cos(ffi),y_shift+r*sin(ffi),z_shift+shift)) shift = shift + aCC/2 for i in range(0,nn): ffi=fi*(i) s.appendAtom(0,Vector(x_shift+r*cos(ffi),y_shift+r*sin(ffi),z_shift+shift)) s.basis[0][0] = 2*r+7 s.basis[1][1] = 2*r+7 s.basis[2][2] = shift s.R = r return s
def makeZigzag(nn, aCC=1.419398, r=None, x_shift=0.0, y_shift=0.0, z_shift=0.0): s = Structure() s.setCartesian() s.comment = "zigzag (%d,0), aCC=%f" % (nn, aCC) shift = 0.0 fi = 2 * pi / nn if r is None: r = aCC * sqrt(3.0) / 4 / sin(fi / 4) for i in range(0, nn): ffi = fi * i s.appendAtom( 0, Vector(x_shift + r * cos(ffi), y_shift + r * sin(ffi), z_shift + shift)) shift = shift + aCC / 2 for i in range(0, nn): ffi = fi * (i + 0.5) s.appendAtom( 0, Vector(x_shift + r * cos(ffi), y_shift + r * sin(ffi), z_shift + shift)) shift = shift + aCC for i in range(0, nn): ffi = fi * (i + 0.5) s.appendAtom( 0, Vector(x_shift + r * cos(ffi), y_shift + r * sin(ffi), z_shift + shift)) shift = shift + aCC / 2 for i in range(0, nn): ffi = fi * (i) s.appendAtom( 0, Vector(x_shift + r * cos(ffi), y_shift + r * sin(ffi), z_shift + shift)) s.basis[0][0] = 2 * r + 7 s.basis[1][1] = 2 * r + 7 s.basis[2][2] = shift s.R = r return s
###################################################################### # 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.
#!/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)
# (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.
#!/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 cartesian coords to stdout" sys.exit(1) space = re.compile(r'\s+') file = sys.argv[1] p=Structure(file) p.setCarthesian() p.write(sys.stdout)
# 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.
def clone(self): return Structure(pointer=_cp4vasp.Structure_clone(self.this))
# 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 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)
#!/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")
def __init__(self, a): '''constructor for the model.''' gtk.GenericTreeModel.__init__(self) self.a = a self.struct = Structure()
#!/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")
# 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))
import sys import re from p4vasp.Structure import * if len(sys.argv) < 7: print "Usage: "+sys.argv[0]+" <poscar file> <n> <m> <x> <y> <z>" print " <poscar file> is the input POSCAR" print " <n> <m> species the range of atoms to move (by index)" print " <x> <y> <z> is the translation vector to add to those atoms (cartesian)." print " The new POSCAR is output to stdout." sys.exit(1) space = re.compile(r'\s+') file = sys.argv[1] p=Structure(file) p.setCarthesian() n = int(sys.argv[2]) m = int(sys.argv[3]) x = float(sys.argv[4]) y = float(sys.argv[5]) z = float(sys.argv[6]) # do the move p.translate(Vector(x,y,z),range(n,m)) # convert back to direct p.setDirect() # write it out.
def makeArmchair(nn, aCC=1.419398, r=None, x_shift=0.0, y_shift=0.0, z_shift=0.0): s = Structure() s.setCartesian() s.comment = "armchair (%d,%d), aCC=%f" % (nn, nn, aCC) shift = 0.0 fi = 2 * pi / nn al = 2 * atan(2 * sin(fi / 4) / (1 + 2 * cos(fi / 4))) be = fi / 2 - al if r is None: r = aCC / 2 / sin(al / 2) for i in range(0, nn): ffi = fi * i s.appendAtom( 0, Vector(x_shift + r * cos(ffi), y_shift + r * sin(ffi), z_shift + shift)) for i in range(0, nn): ffi = al + fi * i s.appendAtom( 0, Vector(x_shift + r * cos(ffi), y_shift + r * sin(ffi), z_shift + shift)) shift = shift + aCC * sqrt(3.0) / 2 for i in range(0, nn): ffi = al + be + fi * (i) s.appendAtom( 0, Vector(x_shift + r * cos(ffi), y_shift + r * sin(ffi), z_shift + shift)) for i in range(0, nn): ffi = 2 * al + be + fi * (i) s.appendAtom( 0, Vector(x_shift + r * cos(ffi), y_shift + r * sin(ffi), z_shift + shift)) shift = shift + aCC * sqrt(3.0) / 2 s.basis[0][0] = 2 * r + 7 s.basis[1][1] = 2 * r + 7 s.basis[2][2] = shift s.R = r return s
# 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.
def makeArmchair(nn,aCC=1.419398,r=None,x_shift=0.0,y_shift=0.0,z_shift=0.0): s=Structure() s.setCartesian() s.comment="armchair (%d,%d), aCC=%f"%(nn,nn,aCC) shift = 0.0 fi = 2*pi/nn al = 2*atan(2*sin(fi/4)/(1+2*cos(fi/4))) be = fi/2-al if r is None: r = aCC/2/sin(al/2) for i in range(0,nn): ffi=fi*i s.appendAtom(0,Vector(x_shift+r*cos(ffi),y_shift+r*sin(ffi),z_shift+shift)) for i in range(0,nn): ffi=al+fi*i s.appendAtom(0,Vector(x_shift+r*cos(ffi),y_shift+r*sin(ffi),z_shift+shift)) shift = shift + aCC*sqrt(3.0)/2 for i in range(0,nn): ffi=al+be+fi*(i) s.appendAtom(0,Vector(x_shift+r*cos(ffi),y_shift+r*sin(ffi),z_shift+shift)) for i in range(0,nn): ffi=2*al+be+fi*(i) s.appendAtom(0,Vector(x_shift+r*cos(ffi),y_shift+r*sin(ffi),z_shift+shift)) shift = shift + aCC*sqrt(3.0)/2 s.basis[0][0] = 2*r+7 s.basis[1][1] = 2*r+7 s.basis[2][2] = shift s.R = r return s