def ReadStruct(filename,species_map):
"""Return "Crystal" object read from Siesta STRUCT-file.
species_map is a dictionary mapping the species index to
atomic symbols. For example:
species_map = { "1" : "Mg",
"2" : "C" ,
"3" : "O" }
In a forthcoming version this information could be obtained
directly from the atomic number in the .STRUCT_{IN,OUT} file.
"""
f = open(filename)
#
# First read unit cell
#
cell = []
for i in range(3):
vector = f.readline()
x, y, z = vector.split()
cell.append([ float(x), float(y), float(z) ])
#
# Now the atoms
#
# Robust code to allow for broken lines.
# Accumulate all the data in a big list...
natoms = int(f.readline())
strings = []
while 1:
line = f.readline()
if not line: break
strings = strings + line.split()
# ... and extract the information for each atom in turn
#
crystal = Crystal([])
pos = 0
for a in range(natoms):
sublist = strings[pos:pos+5]
spindex, z , x, y, z = sublist
symbol = species_map[spindex]
crystal.append(Atom(symbol, [float(x), float(y), float(z)]))
pos = pos + 5
crystal.SetUnitCell(cell)
return crystal
def ReadStruct(filename, species_map):
"""Return "Crystal" object read from Siesta STRUCT-file.
species_map is a dictionary mapping the species index to
atomic symbols. For example:
species_map = { "1" : "Mg",
"2" : "C" ,
"3" : "O" }
In a forthcoming version this information could be obtained
directly from the atomic number in the .STRUCT_{IN,OUT} file.
"""
f = open(filename)
#
# First read unit cell
#
cell = []
for i in range(3):
vector = f.readline()
x, y, z = vector.split()
cell.append([float(x), float(y), float(z)])
#
# Now the atoms
#
# Robust code to allow for broken lines.
# Accumulate all the data in a big list...
natoms = int(f.readline())
strings = []
while 1:
line = f.readline()
if not line: break
strings = strings + line.split()
# ... and extract the information for each atom in turn
#
crystal = Crystal([])
pos = 0
for a in range(natoms):
sublist = strings[pos:pos + 5]
spindex, z, x, y, z = sublist
symbol = species_map[spindex]
crystal.append(Atom(symbol, [float(x), float(y), float(z)]))
pos = pos + 5
crystal.SetUnitCell(cell)
return crystal
#!/usr/bin/env python
from Siesta.Interface import Atom, Crystal
from Siesta.calculator import SiestaCalculator
from ASE.Dynamics.MDMin import MDMin
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=(6.0, 6.0, 6.0), periodic=1)
# create a work subdirectory
orig_dir = os.getcwd()
dir = "ase_relax_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")
b = SiestaCalculator(executable="/Users/ag/bin/siesta-xlf")
b.SetOption("DM.Tolerance","0.001")
atoms.SetCalculator(b)
#!/usr/bin/env python
from Siesta.Interface import Atom, Crystal
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
#!/usr/bin/env python
from Siesta.Interface import Atom, Crystal
from Siesta.calculator import SiestaCalculator
from ASE.Dynamics.VelocityVerlet import VelocityVerlet
from RandomArray import *
import urllib
import os, shutil
URLbase = "http://fisica.ehu.es/ag/siesta-psffiles/"
atoms = Crystal([Atom('H', (0.757,0.586,0.),label="H_sz"),
Atom('H', (-0.757,0.586,0.),magmom=1),
Atom('O', (0, 0, 0),magmom=1)],
cell=(6.0, 6.0, 6.0), periodic=1)
# create a work subdirectory
orig_dir = os.getcwd()
dir = "ase_verlet_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 + "O.psf", "O.psf")
b = SiestaCalculator(executable="/Users/ag/bin/siesta-xlf")
b.SetOption("DM.Tolerance","0.001")
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)