def afunc(var,data=None):
rcs, rcp = var[0], var[1]
f=open("base.fdf","w")
f.write("%block PAO.Basis\n Ga 2\n")
f.write(" 0 1\n")
f.write("%10.5f\n1.0\n" % (rcs,) )
f.write("1 1\n")
f.write("%10.5f\n1.0\n" % (rcp,) )
f.write("%endblock PAO.Basis\n")
f.close()
atoms = ListOfAtoms([Atom('Ga', (0.0,0.0,0.0),magmom=0),
Atom('Ga', (2.0,0.0,0.0),magmom=0)])
a = Siesta(executable="/Users/ag/bin/siesta-xlf")
a.SetOption("%include","base.fdf")
energy = a.run(atoms)
print rcs, rcp, energy
return -energy
def afunc(var, data=None):
rcs, rcp = var[0], var[1]
f = open("base.fdf", "w")
f.write("%block PAO.Basis\n Ga 2\n")
f.write(" 0 1\n")
f.write("%10.5f\n1.0\n" % (rcs, ))
f.write("1 1\n")
f.write("%10.5f\n1.0\n" % (rcp, ))
f.write("%endblock PAO.Basis\n")
f.close()
atoms = ListOfAtoms([
Atom('Ga', (0.0, 0.0, 0.0), magmom=0),
Atom('Ga', (2.0, 0.0, 0.0), magmom=0)
])
a = Siesta(executable="/Users/ag/bin/siesta-xlf")
a.SetOption("%include", "base.fdf")
energy = a.run(atoms)
print rcs, rcp, energy
return -energy
from Siesta.siesta import Siesta
import urllib
import os, shutil
URLbase = "http://fisica.ehu.es/ag/siesta-psffiles/"
atoms = Crystal([Atom('H', (0.757,0.586,0.),label="H_test"),
Atom('H', (-0.757,0.586,0.),magmom=1),
Atom('O', (0, 0, 0),magmom=1)])
# cell=(4, 4, 4), periodic=1)
# create a work subdirectory
orig_dir = os.getcwd()
dir = "h2o_work"
if os.path.isdir(dir): # does dir exist?
shutil.rmtree(dir) # yes, remove old directory
os.mkdir(dir) # make dir directory
os.chdir(dir) # move to dir
urllib.urlretrieve(URLbase + "H.psf", "H.psf")
urllib.urlretrieve(URLbase + "H.psf", "H_test.psf")
urllib.urlretrieve(URLbase + "O.psf", "O.psf")
a = Siesta(executable="$HOME/bin/siesta-2.4-optim")
energy = a.run(atoms,out="OUT")
print "The energy is: ", energy
os.chdir(orig_dir)
# create a work subdirectory
orig_dir = os.getcwd()
dir = "bond_work"
if os.path.isdir(dir): # does dir exist?
shutil.rmtree(dir) # yes, remove old directory
os.mkdir(dir) # make dir directory
os.chdir(dir) # move to dir
URLbase = "http://fisica.ehu.es/ag/siesta-psffiles/"
urllib.urlretrieve(URLbase + "H.psf", "H.psf")
urllib.urlretrieve(URLbase + "O.psf", "O.psf")
for i in range(len(bonds)):
d = bonds[i]
print i, d
atoms = ListOfAtoms(
[Atom('H', (d*math.cos(theta),d*math.sin(theta),0.0),magmom=1),
Atom('H', (-d*math.cos(theta),d*math.sin(theta),0.0),magmom=1),
Atom('O', (0, 0, 0),magmom=1)
])
# cell=(4, 4, 4), periodic=1)
energy[i] = a.run(atoms) # Run Siesta and get the (free)energy
#
# Plot
#
p.add(biggles.Curve(bonds[:],energy[:]))
p.show()
os.chdir(orig_dir)
# create a work subdirectory
orig_dir = os.getcwd()
dir = "bond_work"
if os.path.isdir(dir): # does dir exist?
shutil.rmtree(dir) # yes, remove old directory
os.mkdir(dir) # make dir directory
os.chdir(dir) # move to dir
URLbase = "http://fisica.ehu.es/ag/siesta-psffiles/"
urllib.urlretrieve(URLbase + "H.psf", "H.psf")
urllib.urlretrieve(URLbase + "O.psf", "O.psf")
for i in range(len(bonds)):
d = bonds[i]
print i, d
atoms = ListOfAtoms([
Atom('H', (d * math.cos(theta), d * math.sin(theta), 0.0), magmom=1),
Atom('H', (-d * math.cos(theta), d * math.sin(theta), 0.0), magmom=1),
Atom('O', (0, 0, 0), magmom=1)
])
# cell=(4, 4, 4), periodic=1)
energy[i] = a.run(atoms) # Run Siesta and get the (free)energy
#
# Plot
#
p.add(biggles.Curve(bonds[:], energy[:]))
p.show()
os.chdir(orig_dir)
