6.12615 5.62330
1.00000 1.00000
n=6 2 1 E 135.64896 4.82387
5.14075
1.00000
%EndBlock PAO.Basis
""")
URLbase = "http://fisica.ehu.es/ag/siesta-psffiles/"
urllib.urlretrieve(URLbase + "Pb.psf", "Pb.psf")
cell = Num.array([ [0.5,0.5,0.0], [0.5,0.0,0.5], [0.0,0.5,0.5]])
cell = 4.89*cell
atoms = ListOfAtoms([Atom('Pb', (0.0,0.0,0.0))], cell=cell, periodic=1)
for i in range(len(cutoffs)):
cutoff = cutoffs[i]
print i, cutoff
a = Siesta(executable="$HOME/bin/siesta-2.6.9") # Initialize object
### a.SetOption("FilterCutoff"," 100.0 Ry") # Optional Filtering
a.SetOption("Meshcutoff", str(cutoff)+" Ry")
a.SetOption("%include"," basis.fdf")
energy[i], dum, dum2 = a.run(atoms) # Run Siesta and get the (free)energy
#
# Plot
#
p.add(biggles.Curve(cutoffs[:],energy[:]))
p.show()
os.chdir(orig_dir)
output_file=os.path.abspath(label+".eggbox."+str(cutoff))
print "The output will be in file: ", output_file
# create a work subdirectory
orig_dir = os.getcwd()
import tempfile
workdir = tempfile.mkdtemp(prefix="eggbox.work.",dir=".")
print "Working directory: ", workdir
os.chdir(workdir) # move to dir
#
os.system("cp -p " + pseudo_file + " .")
os.system("cp -p " + basis_file + " .")
g=open(output_file,"w")
for i in range(len(disps)):
d = i*dx/(m-1)
# could generalize the displacement here (1,1,1), (1,0,1)...
atoms=Crystal([Atom(symbol=symbol,label=label,position=(0,0,d))])
atoms.SetUnitCell(cell,fix=True)
atoms.SetBoundaryConditions(periodic=True)
energy[i], force, stress = a.run(atoms) # Run Siesta - get the (free)energy
print i, d, energy[i]
fforce = [ float(j) for j in force[0]]
g.write(" %10.6f %20.6f %15.6f%15.6f%15.6f\n" % (float(d), float(energy[i]), fforce[0], fforce[1], fforce[2] ))
#
g.close()
os.chdir(orig_dir)