def Calculate(self):
"""Calculate everything."""
atoms = self.GetListOfAtoms()
self.energy, self.stress, self.forces = Sserver.get_forces(self,atoms)
self.cell = atoms.GetUnitCell()
self.positions = atoms.GetCartesianPositions()
self.numbers = atoms.GetAtomicNumbers()
self.bc = atoms.GetBoundaryConditions()
def Initialize(self):
atoms = self.GetListOfAtoms()
Sserver.run(self,atoms)
# Ready for action!
self.ready = True
def __init__(self,executable=None):
Sserver.__init__(self,executable)
self.ready = False
print "using executable: ", executable
#
# Standard bond length (units: Angstrom)
#
d0 = math.sqrt(0.757**2 + 0.586**2)
# Range of bond lengths around the presumed minimum
bonds = num.arange(0.8*d0,1.3*d0,0.1)
energy = 0.0*bonds
theta=0.5*(180.-105.0)*math.pi/180. # Angle with the x axis, in radians
print bonds
a = Siesta(executable="siesta") # Initialize object
##a.SetOption("DM.UseSaveDM","T")
# 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")
# First instance to launch
atoms = Structure([
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=executable)
a.launch(atoms)
energy, forces, stress = a.get_forces(atoms)
print "The energy is: ", energy
print forces
print stress
a.stop()
os.chdir(orig_dir)
# create a work subdirectory
orig_dir = os.getcwd()
dir = "client_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_test.psf")
urllib.urlretrieve(URLbase + "H.psf", "H.psf")
urllib.urlretrieve(URLbase + "O.psf", "O.psf")
a = Siesta(executable="/Users/ag/bin/siesta-xlf")
a.run(atoms,out="OUT")
blist = [ 0.4, 0.50, 0.60, 0.70, 0.80, 0.90]
energies = []
forces = []
energies = []
for d in blist:
atoms = Crystal([Atom('H', (d,0.586,0.),label="H_test"),
Atom('H', (-d,0.586,0.),magmom=1),
Atom('O', (0, 0, 0),magmom=1)],
cell=(6.0, 6.0, 6.0), periodic=1)
e, stress, fs = a.get_forces(atoms)
energies.append(e)
forces.append(fs)
