Source code for httk.iface.gulp_if

# 
#    The high-throughput toolkit (httk)
#    Copyright (C) 2012-2015 Rickard Armiento
#
#    This program is free software: you can redistribute it and/or modify
#    it under the terms of the GNU Affero General Public License as
#    published by the Free Software Foundation, either version 3 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 Affero General Public License for more details.
#
#    You should have received a copy of the GNU Affero General Public License
#    along with this program.  If not, see <http://www.gnu.org/licenses/>.

import tempfile, os, shutil

from httk.atomistic.data import periodictable
from math import sqrt
import httk

[docs]def generate_fake_potentials(species): potentials = "" potentials += "atomab\n" for s1 in species: ss1 = periodictable.atomic_symbol(s1) ns1 = periodictable.atomic_number(s1) potentials += "%s core %.4f %.4f 0 0\n" % (ss1,sqrt(0.5*ns1),pow(0.75*ns1,3.0/2.0)) #potentials = "lennard combine 12 6\n" potentials += "lennard 12 6 combine all\n" potentials += "0.0 20.0\n" #for s1 in species: # ss1 = periodictable.atomic_symbol(s1) # for s2 in species: # ss2 = periodictable.atomic_symbol(s2) # potentials += "%s core %s core %.4f %.4f\n" % (ss1, ss2,0.0,10.0) return potentials
[docs]def generate_fake_potentials_try2(species): potentials = "" potentials += "epsilon\n" for s1 in species: ss1 = periodictable.atomic_symbol(s1) ns1 = periodictable.atomic_number(s1) #potentials += "%s core %.4f %.4f 0 0\n" % (ss1,sqrt(0.5*ns1),pow(0.75*ns1,3.0/2.0)) # potentials += "%s core %.4f %.4f 0 0\n" % (ss1,pow(ns1,0.9783276738),pow(ns1,1.124243243)) potentials += "%s core %.4f %.4f 0 0\n" % (ss1,0.1*ns1,0.1*ns1) potentials += "lennard zero epsilon combine all\n" potentials += "0.0 12.0\n" return potentials
[docs]def structure_to_gulp(iof,struct,runspec="single conp",postcards=[],potentials=None): """ Writes a file on gulp input format. """ iof = httk.IoAdapterFileWriter.use(iof) f = iof.file f.write(str(runspec)+"\n") f.write("cell\n") f.write(" "+str(struct.a)+" "+str(struct.b)+" "+str(struct.c)+" ") f.write(str(struct.alpha)+" "+str(struct.beta)+" "+str(struct.gamma)+"\n") f.write("fractional\n") for i in range(struct.N): species = periodictable.atomic_symbol(struct.p1occupancies[i]) f.write(species+" ") f.write(" ".join([str(float(x)) for x in struct.p1coords[i]])+"\n") #print "X",species+str(idx)+" "+" ".join([str(float(x)) for x in struct.coords[i]])+"\n" for card in postcards: f.write(card+"\n") if potentials == None: f.write(generate_fake_potentials(set(struct.p1assignments))) f.write("\n") iof.close()