def test_cubic_diamond_C():
"""
Take ASE Diamond structure, input into PySCF and run
"""
ase_atom = Diamond(symbol='C', latticeconstant=3.5668)
print "Cell volume =", ase_atom.get_volume()
cell = pbcgto.Cell()
cell.atom = pyscf_ase.ase_atoms_to_pyscf(ase_atom)
cell.a = ase_atom.cell
cell.basis = "gth-szv"
cell.pseudo = "gth-pade"
cell.gs = np.array([10, 10, 10])
# cell.verbose = 7
cell.build(None, None)
mf = pbcdft.RKS(cell)
mf.analytic_int = False
mf.xc = 'lda,vwn'
print mf.scf()
# Gamma point gs: 10x10x10: -11.220279983393
# gs: 14x14x14: -11.220122248175
# K pt calc
scaled_kpts = ase.dft.kpoints.monkhorst_pack((2, 2, 2))
abs_kpts = cell.get_abs_kpts(scaled_kpts)
kmf = pyscf.pbc.scf.kscf.KRKS(cell, abs_kpts)
kmf.analytic_int = False
kmf.xc = 'lda,vwn'
kmf.verbose = 7
print kmf.scf()
def test_coulG(self):
numpy.random.seed(19)
kpt = numpy.random.random(3)
ase_atom = bulk('C', 'diamond', a=3.5668)
cell = pbcgto.Cell()
cell.unit = 'A'
cell.atom = pyscf_ase.ase_atoms_to_pyscf(ase_atom)
cell.a = ase_atom.cell + numpy.random.random((3,3)).T
cell.basis = 'gth-szv'
cell.pseudo = 'gth-pade'
cell.gs = [5,4,3]
cell.verbose = 5
cell.output = '/dev/null'
cell.build()
coulG = tools.get_coulG(cell, kpt)
self.assertAlmostEqual(finger(coulG), 62.75448804333378, 9)
cell.a = numpy.eye(3)
cell.unit = 'B'
coulG = tools.get_coulG(cell, numpy.array([0, numpy.pi, 0]))
self.assertAlmostEqual(finger(coulG), 4.6737453679713905, 9)
coulG = tools.get_coulG(cell, numpy.array([0, numpy.pi, 0]),
wrap_around=False)
self.assertAlmostEqual(finger(coulG), 4.5757877990664744, 9)
coulG = tools.get_coulG(cell, exx='ewald')
self.assertAlmostEqual(finger(coulG), 4.888843468914021, 9)
def get_cell(lc_bohr, atom, unit_cell, basis, mesh, pseudo, supercell=None):
cell = pbcgto.Cell()
boxlen = lc_bohr
ase_atom = ase.build.bulk(atom, unit_cell, a=boxlen)
cell.a = ase_atom.cell
cell.atom = pyscf_ase.ase_atoms_to_pyscf(ase_atom)
cell.basis = basis
cell.charge = 0
cell.dimension = 3
cell.incore_anyway = False
cell.max_memory = 8000
cell.mesh = numpy.array([mesh, mesh, mesh])
cell.pseudo = pseudo
cell.spin = 0
cell.unit = 'B'
cell.verbose = 10
print "*****BUILDING CELL!*****"
cell.build()
if supercell is not None:
print "*****BUILDING SUPERCELL!*****"
cell._built = False
cell = pbctools.super_cell(cell, supercell)
return cell
def run_lda(ase_atom, ngs, nmp=1):
cell = pbcgto.Cell()
cell.unit = 'A'
cell.atom = pyscf_ase.ase_atoms_to_pyscf(ase_atom)
cell.h = ase_atom.cell
cell.basis = 'gth-szv'
cell.pseudo = 'gth-pade'
cell.gs = np.array([ngs,ngs,ngs])
#cell.verbose = 4
cell.build()
print "-- The Gamma point calculation -----------"
mf = pbcdft.RKS(cell)
mf.xc = 'lda,vwn'
#mf.verbose = 7
print mf.scf()
print "-- The k-point sampling calculation ------"
scaled_kpts = ase.dft.kpoints.monkhorst_pack((nmp,nmp,nmp))
abs_kpts = cell.get_abs_kpts(scaled_kpts)
kmf = pbcdft.KRKS(cell, abs_kpts)
kmf.analytic_int = False
kmf.xc = 'lda,vwn'
#kmf.verbose = 7
print kmf.scf()
def test_coulG(self):
numpy.random.seed(19)
kpt = numpy.random.random(3)
ase_atom = bulk('C', 'diamond', a=3.5668)
cell = pbcgto.Cell()
cell.unit = 'A'
cell.atom = pyscf_ase.ase_atoms_to_pyscf(ase_atom)
cell.a = ase_atom.cell + numpy.random.random((3, 3)).T
cell.basis = 'gth-szv'
cell.pseudo = 'gth-pade'
cell.gs = [5, 4, 3]
cell.verbose = 5
cell.output = '/dev/null'
cell.build()
coulG = tools.get_coulG(cell, kpt)
self.assertAlmostEqual(finger(coulG), 62.75448804333378, 9)
cell.a = numpy.eye(3)
cell.unit = 'B'
coulG = tools.get_coulG(cell, numpy.array([0, numpy.pi, 0]))
self.assertAlmostEqual(finger(coulG), 4.6737453679713905, 9)
coulG = tools.get_coulG(cell,
numpy.array([0, numpy.pi, 0]),
wrap_around=False)
self.assertAlmostEqual(finger(coulG), 4.5757877990664744, 9)
coulG = tools.get_coulG(cell, exx='ewald')
self.assertAlmostEqual(finger(coulG), 4.888843468914021, 9)
def test_cubic_diamond_C():
"""
Take ASE Diamond structure, input into PySCF and run
"""
ase_atom = Diamond(symbol='C', latticeconstant=3.5668)
print "Cell volume =", ase_atom.get_volume()
cell = pbcgto.Cell()
cell.atom = pyscf_ase.ase_atoms_to_pyscf(ase_atom)
cell.h = ase_atom.cell
cell.basis = "gth-szv"
cell.pseudo = "gth-pade"
cell.gs = np.array([10,10,10])
# cell.verbose = 7
cell.build(None, None)
mf = pbcdft.RKS(cell)
mf.analytic_int = False
mf.xc = 'lda,vwn'
print mf.scf()
# Gamma point gs: 10x10x10: -11.220279983393
# gs: 14x14x14: -11.220122248175
# K pt calc
scaled_kpts = ase.dft.kpoints.monkhorst_pack((2,2,2))
abs_kpts = cell.get_abs_kpts(scaled_kpts)
kmf = pyscf.pbc.scf.kscf.KRKS(cell, abs_kpts)
kmf.analytic_int = False
kmf.xc = 'lda,vwn'
kmf.verbose = 7
print kmf.scf()
def build_cell(ase_atom,
unit='B',
ke=20.0,
gsmax=None,
basis='gth-szv',
pseudo='gth-pade',
dimension=3,
incore_anyway=False):
cell = pbcgto.Cell()
cell.unit = unit
cell.atom = pyscf_ase.ase_atoms_to_pyscf(ase_atom)
cell.a = ase_atom.cell
cell.basis = basis
cell.pseudo = pseudo
cell.dimension = dimension
cell.incore_anyway = incore_anyway
if gsmax is not None:
cell.gs = np.array([gsmax, gsmax, gsmax])
else:
cell.ke_cutoff = ke
cell.build()
return cell
def test_band_ase_kpts():
from ase.lattice import bulk
from ase.dft.kpoints import ibz_points, get_bandpath
c = bulk('C', 'diamond', a=3.5668)
print c.get_volume()
points = ibz_points['fcc']
G = points['Gamma']
X = points['X']
W = points['W']
K = points['K']
L = points['L']
band_kpts, x, X = get_bandpath([L, G, X, W, K, G], c.cell, npoints=30)
cell = pbcgto.Cell()
cell.atom=pyscf_ase.ase_atoms_to_pyscf(c)
cell.a=c.cell
cell.basis = 'gth-szv'
cell.pseudo = 'gth-pade'
cell.gs=np.array([5,5,5])
cell.verbose=7
cell.build(None,None)
scaled_kpts=ase.dft.kpoints.monkhorst_pack((1,1,1))
abs_kpts=cell.get_abs_kpts(scaled_kpts)
kmf = pbckscf.KRKS(cell, abs_kpts)
kmf.analytic_int=False
kmf.xc = 'lda,vwn'
print kmf.scf()
e_kn = []
for kpt in band_kpts:
fb, sb=kmf.get_band_fock_ovlp(kmf.get_hcore()+kmf.get_veff(),
kmf.get_ovlp(), kpt)
e, c=hf.eig(fb, sb)
print kpt, e
e_kn.append(e)
emin = -1
emax = 2
plt.figure(figsize=(5, 6))
nbands = cell.nao_nr()
for n in range(nbands):
plt.plot(x, [e_kn[i][n] for i in range(len(x))])
for p in X:
plt.plot([p, p], [emin, emax], 'k-')
plt.plot([0, X[-1]], [0, 0], 'k-')
plt.xticks(X, ['$%s$' % n for n in ['L', 'G', 'X', 'W', 'K', r'\Gamma']])
plt.axis(xmin=0, xmax=X[-1], ymin=emin, ymax=emax)
plt.xlabel('k-vector')
plt.show()
def test_band_ase_kpts():
from ase.lattice import bulk
from ase.dft.kpoints import ibz_points, get_bandpath
c = bulk('C', 'diamond', a=3.5668)
print c.get_volume()
points = ibz_points['fcc']
G = points['Gamma']
X = points['X']
W = points['W']
K = points['K']
L = points['L']
band_kpts, x, X = get_bandpath([L, G, X, W, K, G], c.cell, npoints=30)
cell = pbcgto.Cell()
cell.atom = pyscf_ase.ase_atoms_to_pyscf(c)
cell.h = c.cell.T
cell.basis = 'gth-szv'
cell.pseudo = 'gth-pade'
cell.gs = np.array([5, 5, 5])
cell.verbose = 7
cell.build(None, None)
scaled_kpts = ase.dft.kpoints.monkhorst_pack((1, 1, 1))
abs_kpts = cell.get_abs_kpts(scaled_kpts)
kmf = pbckscf.KRKS(cell, abs_kpts)
kmf.analytic_int = False
kmf.xc = 'lda,vwn'
print kmf.scf()
e_kn = []
for kpt in band_kpts:
fb, sb = kmf.get_band_fock_ovlp(kmf.get_hcore() + kmf.get_veff(),
kmf.get_ovlp(), kpt)
e, c = hf.eig(fb, sb)
print kpt, e
e_kn.append(e)
emin = -1
emax = 2
plt.figure(figsize=(5, 6))
nbands = cell.nao_nr()
for n in range(nbands):
plt.plot(x, [e_kn[i][n] for i in range(len(x))])
for p in X:
plt.plot([p, p], [emin, emax], 'k-')
plt.plot([0, X[-1]], [0, 0], 'k-')
plt.xticks(X, ['$%s$' % n for n in ['L', 'G', 'X', 'W', 'K', r'\Gamma']])
plt.axis(xmin=0, xmax=X[-1], ymin=emin, ymax=emax)
plt.xlabel('k-vector')
plt.show()
def build_cell(ase_atom, ngs):
cell = pbcgto.Cell()
cell.unit = 'A'
cell.a = ase_atom.cell
cell.gs = np.array([ngs,ngs,ngs])
cell.atom = pyscf_ase.ase_atoms_to_pyscf(ase_atom)
cell.basis = 'gth-szv'
cell.pseudo = 'gth-pade'
cell.verbose = 0
cell.build()
return cell
def build_cell(ase_atom, ngs):
cell = pbcgto.Cell()
cell.unit = 'A'
cell.h = ase_atom.cell.T
cell.gs = np.array([ngs, ngs, ngs])
cell.atom = pyscf_ase.ase_atoms_to_pyscf(ase_atom)
cell.basis = 'gth-szv'
cell.pseudo = 'gth-pade'
cell.verbose = 0
cell.build()
return cell
def from_ase(self, ase_atom):
'''Update cell based on given ase atom object
Examples:
>>> from ase.lattice import bulk
>>> cell.from_ase(bulk('C', 'diamond', a=LATTICE_CONST))
'''
from pyscf.pbc.tools import pyscf_ase
self.h = ase_atom.cell
self.atom = pyscf_ase.ase_atoms_to_pyscf(ase_atom)
return self
def from_ase(self, ase_atom):
'''Update cell based on given ase atom object
Examples:
>>> from ase.lattice import bulk
>>> cell.from_ase(bulk('C', 'diamond', a=LATTICE_CONST))
'''
from pyscf.pbc.tools import pyscf_ase
self.a = ase_atom.cell
self.atom = pyscf_ase.ase_atoms_to_pyscf(ase_atom)
return self
def test_diamond_C():
from ase.lattice import bulk
from ase.dft.kpoints import ibz_points, get_bandpath
C = bulk('C', 'diamond', a=3.5668)
cell = pbcgto.Cell()
cell.atom = pyscf_ase.ase_atoms_to_pyscf(C)
cell.a = C.cell
# cell.basis = 'gth-tzvp'
cell.basis = 'gth-szv'
# cell.basis = {'C': [[0, (4.3362376436, 0.1490797872), (1.2881838513, -0.0292640031), (0.4037767149, -0.688204051), (0.1187877657, -0.3964426906)], [1, (4.3362376436, -0.0878123619), (1.2881838513, -0.27755603), (0.4037767149, -0.4712295093), (0.1187877657, -0.4058039291)]]}
# Easier basis for quick testing
#cell.basis = {'C': [[0, (1.2881838513, -0.0292640031), (0.4037767149, -0.688204051)], [1, (1.2881838513, -0.27755603), (0.4037767149, -0.4712295093) ]]}
# Cell used for K-points
cell.pseudo = 'gth-pade'
cell.gs = np.array([8, 8, 8])
cell.verbose = 7
cell.build(None, None)
# Replicate cell NxNxN for comparison
# repcell = pyscf.pbc.tools.replicate_cell(cell, (2,2,2))
# repcell.gs = np.array([12,12,12]) # for 3 replicated cells, then
# # # ngs must be of the form [3gs0 + 1, gs1, gs2]
# repcell.build()
# # # Replicated MF calc
# mf = pbcdft.RKS(repcell)
# # mf.analytic_int = True
# mf.xc = 'lda,vwn'
# mf.init_guess = '1e'
# mf.diis = True
# mf.scf()
# K-pt calc
scaled_kpts = ase.dft.kpoints.monkhorst_pack((2, 2, 2))
# shift if 2x2x2 includes Gamma point
# shift = np.array([1./4., 1./4., 1./4.])
# scaled_kpts += shift
abs_kpts = cell.get_abs_kpts(scaled_kpts)
kmf = pyscf.pbc.scf.kscf.KRKS(cell, abs_kpts)
kmf.analytic_int = False
kmf.diis = True
kmf.init_guess = '1e'
kmf.xc = 'lda,vwn'
print "N imgs", cell.nimgs
print "Cutoff for 400 eV", pyscf.pbc.tools.cutoff_to_gs(
cell.lattice_vectors(), 400 / 27.2)
#kmf.max_cycle = 3
kmf.scf()
def test_diamond_C():
from ase.lattice import bulk
from ase.dft.kpoints import ibz_points, get_bandpath
C = bulk('C', 'diamond', a=3.5668)
cell = pbcgto.Cell()
cell.atom = pyscf_ase.ase_atoms_to_pyscf(C)
cell.h = C.cell
# cell.basis = 'gth-tzvp'
cell.basis = 'gth-szv'
# cell.basis = {'C': [[0, (4.3362376436, 0.1490797872), (1.2881838513, -0.0292640031), (0.4037767149, -0.688204051), (0.1187877657, -0.3964426906)], [1, (4.3362376436, -0.0878123619), (1.2881838513, -0.27755603), (0.4037767149, -0.4712295093), (0.1187877657, -0.4058039291)]]}
# Easier basis for quick testing
#cell.basis = {'C': [[0, (1.2881838513, -0.0292640031), (0.4037767149, -0.688204051)], [1, (1.2881838513, -0.27755603), (0.4037767149, -0.4712295093) ]]}
# Cell used for K-points
cell.pseudo = 'gth-pade'
cell.gs = np.array([8,8,8])
cell.verbose = 7
cell.build(None,None)
# Replicate cell NxNxN for comparison
# repcell = pyscf.pbc.tools.replicate_cell(cell, (2,2,2))
# repcell.gs = np.array([12,12,12]) # for 3 replicated cells, then
# # # ngs must be of the form [3gs0 + 1, gs1, gs2]
# repcell.build()
# # # Replicated MF calc
# mf = pbcdft.RKS(repcell)
# # mf.analytic_int = True
# mf.xc = 'lda,vwn'
# mf.init_guess = '1e'
# mf.diis = True
# mf.scf()
# K-pt calc
scaled_kpts = ase.dft.kpoints.monkhorst_pack((2,2,2))
# shift if 2x2x2 includes Gamma point
# shift = np.array([1./4., 1./4., 1./4.])
# scaled_kpts += shift
abs_kpts = cell.get_abs_kpts(scaled_kpts)
kmf = pyscf.pbc.scf.kscf.KRKS(cell, abs_kpts)
kmf.analytic_int = False
kmf.diis = True
kmf.init_guess = '1e'
kmf.xc = 'lda,vwn'
print "N imgs", cell.nimgs
print "Cutoff for 400 eV", pyscf.pbc.tools.cutoff_to_gs(cell.lattice_vectors(), 400/27.2)
#kmf.max_cycle = 3
kmf.scf()
def test_coulG(self):
numpy.random.seed(19)
kpt = numpy.random.random(3)
ase_atom = bulk('C', 'diamond', a=3.5668)
cell = pbcgto.Cell()
cell.unit = 'A'
cell.atom = pyscf_ase.ase_atoms_to_pyscf(ase_atom)
cell.h = ase_atom.cell + numpy.random.random((3, 3))
cell.basis = 'gth-szv'
cell.pseudo = 'gth-pade'
cell.gs = [5, 4, 3]
cell.verbose = 5
cell.output = '/dev/null'
cell.build()
coulG = tools.get_coulG(cell, kpt)
self.assertAlmostEqual(finger(coulG), 62.75448804333378, 9)
def make_primitive_cell(ngs):
ase_atom = bulk('C', 'diamond', a=3.5668)
cell = pbcgto.Cell()
cell.unit = 'A'
cell.atom = pyscf_ase.ase_atoms_to_pyscf(ase_atom)
cell.h = ase_atom.cell
cell.basis = 'gth-szv'
cell.pseudo = 'gth-pade'
cell.gs = np.array([ngs, ngs, ngs])
#cell.nimgs = np.array([7,7,7])
cell.verbose = 0
cell.build()
return cell
def test_coulG_ws(self):
ase_atom = bulk('C', 'diamond', a=3.5668)
cell = pbcgto.Cell()
cell.unit = 'A'
cell.atom = pyscf_ase.ase_atoms_to_pyscf(ase_atom)
cell.a = ase_atom.cell
cell.basis = 'gth-szv'
cell.pseudo = 'gth-pade'
cell.gs = [5] * 3
cell.verbose = 5
cell.output = '/dev/null'
cell.build()
mf = khf.KRHF(cell, exxdiv='vcut_ws')
mf.kpts = cell.make_kpts([2, 2, 2])
coulG = tools.get_coulG(cell, mf.kpts[2], True, mf)
self.assertAlmostEqual(finger(coulG), 1.3245117871351604, 9)
def GetMP():
ase_atom = ase.build.bulk(atomtype, unittype, a=lc)
cell = pbcgto.Cell()
cell.atom = pyscf_ase.ase_atoms_to_pyscf(ase_atom)
cell.a = ase_atom.cell #lattice vectors
cell.ke_cutoff = ecut #kinetic energy cutoff
cell.precision = 1.e-8
cell.dimension = 3 #3D PBC
cell.unit = 'B' #Bohr
cell.build()
k = cell.make_kpts(kpts, wrap_around=True) #get k-points from PySCF
a = cell.a #real lattice vectors
h = cell.reciprocal_vectors() #reciprocal lattice vectors
omega = np.linalg.det(a) #cell volume
return k, a, h, omega, cell
def make_primitive_cell(ngs):
ase_atom = bulk('C', 'diamond', a=3.5668)
cell = pbcgto.Cell()
cell.unit = 'A'
cell.atom = pyscf_ase.ase_atoms_to_pyscf(ase_atom)
cell.h = ase_atom.cell
cell.basis = 'gth-szv'
cell.pseudo = 'gth-pade'
cell.gs = np.array([ngs,ngs,ngs])
#cell.nimgs = np.array([7,7,7])
cell.verbose = 0
cell.build()
return cell
def test_coulG_ws(self):
ase_atom = bulk('C', 'diamond', a=3.5668)
cell = pbcgto.Cell()
cell.unit = 'A'
cell.atom = pyscf_ase.ase_atoms_to_pyscf(ase_atom)
cell.a = ase_atom.cell
cell.basis = 'gth-szv'
cell.pseudo = 'gth-pade'
cell.gs = [5]*3
cell.verbose = 5
cell.output = '/dev/null'
cell.build()
mf = khf.KRHF(cell, exxdiv='vcut_ws')
mf.kpts = cell.make_kpts([2,2,2])
coulG = tools.get_coulG(cell, mf.kpts[2], True, mf)
self.assertAlmostEqual(finger(coulG), 1.3245117871351604, 9)
def make_primitive_cell(ngs):
from ase.lattice import bulk
ase_atom = ase.build.bulk('C', 'diamond', a=3.5668)
cell = pbcgto.Cell()
cell.unit = 'A'
cell.atom = pyscf_ase.ase_atoms_to_pyscf(ase_atom)
cell.a = ase_atom.cell
cell.basis = 'gth-szv'
cell.pseudo = 'gth-pade'
cell.gs = np.array([ngs, ngs, ngs])
cell.verbose = 5
cell.output = '/dev/null'
cell.build()
return cell
def make_primitive_cell(ngs):
from ase.lattice import bulk
ase_atom = bulk("C", "diamond", a=3.5668)
cell = pbcgto.Cell()
cell.unit = "A"
cell.atom = pyscf_ase.ase_atoms_to_pyscf(ase_atom)
cell.h = ase_atom.cell
cell.basis = "gth-szv"
cell.pseudo = "gth-pade"
cell.gs = np.array([ngs, ngs, ngs])
# cell.verbose = 4
cell.build()
return cell
def test():
ANALYTIC=False
ase_atom=bulk('C', 'diamond', a=3.5668)
cell = pbcgto.Cell()
cell.atom=pyscf_ase.ase_atoms_to_pyscf(ase_atom)
cell.h=ase_atom.cell
cell.verbose = 7
# gth-szv for C
cell.basis = 'gth-szv'
cell.pseudo = 'gth-pade'
cell.gs = np.array([4,1,1])
cell.build(None, None)
print "N images: ", cell.nimgs
cell.nimgs = [10,1,1]
repcell = pyscf.pbc.tools.replicate_cell(cell, (3,1,1))
print "REPCELL", repcell.pseudo
mf = pbcdft.RKS(repcell)
mf.verbose = 5
mf.diis = False
mf.analytic_int=ANALYTIC
mf.xc = 'lda,vwn'
mf.max_cycle = 1
mf.init_guess = '1e'
mf.scf()
scaled_kpts=np.array(ase.dft.kpoints.monkhorst_pack((3,1,1)))
abs_kpts=cell.get_abs_kpts(scaled_kpts)
cell.gs = np.array([1,1,1])
cell.nimgs = [14,1,1]
cell.build(None, None)
kmf = pyscf.pbc.scf.kscf.KRKS(cell, abs_kpts)
kmf.analytic_int=ANALYTIC
kmf.diis = False
kmf.verbose = 5
kmf.xc = 'lda,vwn'
kmf.max_cycle = 1
kmf.init_guess = '1e'
kmf.scf()
def make_primitive_cell(ngs):
from ase.lattice import bulk
ase_atom = bulk('C', 'diamond', a=3.5668)
cell = pbcgto.Cell()
cell.unit = 'A'
cell.atom = pyscf_ase.ase_atoms_to_pyscf(ase_atom)
cell.a = ase_atom.cell
cell.basis = 'gth-szv'
cell.pseudo = 'gth-pade'
cell.gs = np.array([ngs,ngs,ngs])
cell.verbose = 5
cell.output = '/dev/null'
cell.build()
return cell
def run_hf(ase_atom, ngs):
cell = pbcgto.Cell()
cell.unit = 'A'
cell.atom = pyscf_ase.ase_atoms_to_pyscf(ase_atom)
cell.h = ase_atom.cell
cell.basis = 'gth-szv'
#cell.basis = 'gth-dzvp'
cell.pseudo = 'gth-pade'
cell.gs = np.array([ngs,ngs,ngs])
#cell.verbose = 4
cell.build()
print "-- The Gamma point calculation -----------"
mf = pbchf.RHF(cell)
mf.verbose = 7
print mf.scf()
print mf.mo_energy
def test_klda8_cubic_kpt_222(self):
ase_atom = Diamond(symbol='C', latticeconstant=LATTICE_CONST)
cell = pbcgto.Cell()
cell.unit = 'A'
cell.h = ase_atom.cell
cell.gs = np.array([8]*3)
cell.atom = pyscf_ase.ase_atoms_to_pyscf(ase_atom)
cell.basis = 'gth-szv'
cell.pseudo = 'gth-pade'
cell.verbose = 5
cell.output = '/dev/null'
cell.build()
kpts = cell.make_kpts((2,2,2))
mf = pbcdft.KUKS(cell, kpts)
mf.xc = 'lda,vwn'
e1 = mf.scf()
self.assertAlmostEqual(e1, -45.42583489512954, 8)
self.assertAlmostEqual(mf._ecoul, 3.2519161200384685, 8)
self.assertAlmostEqual(mf._exc, -13.937886385300949, 8)
def build_cell(ase_atom, unit='B', ke=20.0, gsmax=None, basis='gth-szv',
pseudo='gth-pade', dimension=3, incore_anyway=False):
cell = pbcgto.Cell()
cell.unit = unit
cell.atom = pyscf_ase.ase_atoms_to_pyscf(ase_atom)
cell.a = ase_atom.cell
cell.basis = basis
cell.pseudo = pseudo
cell.dimension = dimension
cell.incore_anyway = incore_anyway
if gsmax is not None:
cell.gs = np.array([gsmax,gsmax,gsmax])
else:
cell.ke_cutoff = ke
cell.build()
return cell
def test_klda8_cubic_kpt_222(self):
ase_atom = Diamond(symbol="C", latticeconstant=LATTICE_CONST)
cell = pbcgto.Cell()
cell.unit = "A"
cell.h = ase_atom.cell
cell.gs = np.array([8] * 3)
cell.atom = pyscf_ase.ase_atoms_to_pyscf(ase_atom)
cell.basis = "gth-szv"
cell.pseudo = "gth-pade"
cell.verbose = 5
cell.output = "/dev/null"
cell.build()
kpts = cell.make_kpts((2, 2, 2))
mf = pbcdft.KUKS(cell, kpts)
mf.xc = "lda,vwn"
e1 = mf.scf()
self.assertAlmostEqual(e1, -45.42583489512954, 8)
self.assertAlmostEqual(mf._ecoul, 3.2519161200384685, 8)
self.assertAlmostEqual(mf._exc, -13.937886385300949, 8)
def test_cell_n3(ngs):
import ase
import pyscf.pbc.tools.pyscf_ase as pyscf_ase
import ase.lattice
from ase.lattice import bulk
"""
Take ASE Diamond structure, input into PySCF and run
"""
ase_atom = bulk('C', 'diamond', a=3.5668)
cell = pbcgto.Cell()
cell.unit = 'A'
cell.atom = pyscf_ase.ase_atoms_to_pyscf(ase_atom)
cell.a = ase_atom.cell
#cell.basis = "gth-dzvp"
cell.basis = "gth-szv"
cell.pseudo = "gth-pade"
cell.gs = np.array([ngs, ngs, ngs])
cell.build()
return cell
def test_cell_n3( ngs ):
import ase
import pyscf.pbc.tools.pyscf_ase as pyscf_ase
import ase.lattice
from ase.lattice import bulk
"""
Take ASE Diamond structure, input into PySCF and run
"""
ase_atom = bulk('C', 'diamond', a=3.5668)
cell = pbcgto.Cell()
cell.unit = 'A'
cell.atom = pyscf_ase.ase_atoms_to_pyscf(ase_atom)
cell.h = ase_atom.cell
#cell.basis = "gth-dzvp"
cell.basis = "gth-szv"
cell.pseudo = "gth-pade"
cell.gs = np.array([ngs,ngs,ngs])
cell.build()
return cell
def test_cubic_diamond_He():
"""
Take ASE Diamond structure, input into PySCF and run
"""
ase_atom=Diamond(symbol='He', latticeconstant=3.5)
print ase_atom.get_volume()
cell = pbcgto.Cell()
cell.atom=pyscf_ase.ase_atoms_to_pyscf(ase_atom)
cell.h=ase_atom.cell.T
cell.basis = {"He" : [[0, (1.0, 1.0)], [0, (0.8, 1.0)]] }
cell.gs = np.array([15,15,15])
# cell.verbose = 7
cell.build(None, None)
mf = pbcdft.RKS(cell)
mf.analytic_int=False
mf.xc = 'lda,vwn'
print mf.scf()
# Diamond cubic: -18.2278622592408
mf = pbcdft.RKS(cell)
mf.analytic_int=True
mf.xc = 'lda,vwn'
print mf.scf()
# Diamond cubic (analytic): -18.2278622592283
# = -4.556965564807075 / cell
# K pt calc
scaled_kpts=ase.dft.kpoints.monkhorst_pack((2,2,2))
abs_kpts=cell.get_abs_kpts(scaled_kpts)
kmf = pyscf.pbc.scf.kscf.KRKS(cell, abs_kpts)
kmf.analytic_int=False
kmf.xc = 'lda,vwn'
print kmf.scf()
def test_diamond_He():
from ase.lattice import bulk
from ase.dft.kpoints import ibz_points, get_bandpath
He = bulk('He', 'diamond', a=3.5)
cell = pbcgto.Cell()
cell.atom=pyscf_ase.ase_atoms_to_pyscf(He)
cell.h=He.cell.T
cell.basis = {"He" : [[0, (1.0, 1.0)], [0, (0.8, 1.0)]] }
# cell.pseudo = 'gth-pade'
cell.gs=np.array([15,15,15])
cell.verbose=7
cell.build(None,None)
# replicate cell NxNxN
repcell = pyscf.pbc.tools.replicate_cell(cell, (2,2,2))
mf = pbcdft.RKS(repcell)
mf.analytic_int=False
mf.xc = 'lda,vwn'
# 1x1x1 Gamma -4.59565988176
# 2x2x2 Gamma [10x10x10 grid] -36.4239485658445
# = -4.552993570730562 / cell
# [20x20x20 grid] -4.55312928715 / cell
#
# 3x3x3 Gamma [15x15x15 grid] -4.553523556740741 / cell
# Diamond cubic: -4.56518345190625
scaled_kpts=ase.dft.kpoints.monkhorst_pack((3,3,3))
abs_kpts=cell.get_abs_kpts(scaled_kpts)
kmf = pyscf.pbc.scf.kscf.KRKS(cell, abs_kpts)
kmf.analytic_int=False
kmf.xc = 'lda,vwn'
kmf.scf()
def test_diamond_He():
from ase.lattice import bulk
from ase.dft.kpoints import ibz_points, get_bandpath
He = bulk('He', 'diamond', a=3.5)
cell = pbcgto.Cell()
cell.atom=pyscf_ase.ase_atoms_to_pyscf(He)
cell.h=He.cell
cell.basis = {"He" : [[0, (1.0, 1.0)], [0, (0.8, 1.0)]] }
# cell.pseudo = 'gth-pade'
cell.gs=np.array([15,15,15])
cell.verbose=7
cell.build(None,None)
# replicate cell NxNxN
repcell = pyscf.pbc.tools.replicate_cell(cell, (2,2,2))
mf = pbcdft.RKS(repcell)
mf.analytic_int=False
mf.xc = 'lda,vwn'
# 1x1x1 Gamma -4.59565988176
# 2x2x2 Gamma [10x10x10 grid] -36.4239485658445
# = -4.552993570730562 / cell
# [20x20x20 grid] -4.55312928715 / cell
#
# 3x3x3 Gamma [15x15x15 grid] -4.553523556740741 / cell
# Diamond cubic: -4.56518345190625
scaled_kpts=ase.dft.kpoints.monkhorst_pack((3,3,3))
abs_kpts=cell.get_abs_kpts(scaled_kpts)
kmf = pyscf.pbc.scf.kscf.KRKS(cell, abs_kpts)
kmf.analytic_int=False
kmf.xc = 'lda,vwn'
kmf.scf()
def test_cubic_diamond_He():
"""
Take ASE Diamond structure, input into PySCF and run
"""
ase_atom=Diamond(symbol='He', latticeconstant=3.5)
print ase_atom.get_volume()
cell = pbcgto.Cell()
cell.atom=pyscf_ase.ase_atoms_to_pyscf(ase_atom)
cell.h=ase_atom.cell
cell.basis = {"He" : [[0, (1.0, 1.0)], [0, (0.8, 1.0)]] }
cell.gs = np.array([15,15,15])
# cell.verbose = 7
cell.build(None, None)
mf = pbcdft.RKS(cell)
mf.analytic_int=False
mf.xc = 'lda,vwn'
print mf.scf()
# Diamond cubic: -18.2278622592408
mf = pbcdft.RKS(cell)
mf.analytic_int=True
mf.xc = 'lda,vwn'
print mf.scf()
# Diamond cubic (analytic): -18.2278622592283
# = -4.556965564807075 / cell
# K pt calc
scaled_kpts=ase.dft.kpoints.monkhorst_pack((2,2,2))
abs_kpts=cell.get_abs_kpts(scaled_kpts)
kmf = pyscf.pbc.scf.kscf.KRKS(cell, abs_kpts)
kmf.analytic_int=False
kmf.xc = 'lda,vwn'
print kmf.scf()
import pyscf.pbc.tools.pyscf_ase as pyscf_ase
import pyscf.pbc.gto as pbcgto
import pyscf.pbc.dft as pbcdft
import matplotlib.pyplot as plt
from ase.lattice import bulk
from ase.dft.kpoints import special_points, get_bandpath
c = bulk('C', 'diamond', a=3.5668)
print(c.get_volume())
cell = pbcgto.Cell()
cell.atom = pyscf_ase.ase_atoms_to_pyscf(c)
cell.a = c.cell
cell.basis = 'gth-szv'
cell.pseudo = 'gth-pade'
cell.verbose = 5
cell.build(None,None)
points = special_points['fcc']
G = points['G']
X = points['X']
W = points['W']
K = points['K']
L = points['L']
band_kpts, kpath, sp_points = get_bandpath([L, G, X, W, K, G], c.cell, npoints=50)
band_kpts = cell.get_abs_kpts(band_kpts)
#
def plot_bands(scftype, basis, ngs, nmp=None):
# Set-up the unit cell
from ase.lattice import bulk
from ase.dft.kpoints import ibz_points, kpoint_convert, get_bandpath
ase_atom = bulk('C', 'diamond', a=3.5668*ANG2BOHR)
print "Cell volume =", ase_atom.get_volume(), "Bohr^3"
# Set-up the band-path via special points
points = ibz_points['fcc']
G = points['Gamma']
X = points['X']
W = points['W']
K = points['K']
L = points['L']
band_kpts, x, X = get_bandpath([L, G, X, W, K, G], ase_atom.cell, npoints=30)
abs_kpts = kpoint_convert(ase_atom.cell, skpts_kc=band_kpts)
# Build the cell
cell = pbcgto.Cell()
cell.unit = 'B'
cell.atom = pyscf_ase.ase_atoms_to_pyscf(ase_atom)
cell.h = ase_atom.cell
cell.basis = 'gth-%s'%(basis)
#cell.basis = 'gth-szv'
#cell.basis = 'gth-dzvp'
cell.pseudo = 'gth-pade'
cell.gs = np.array([ngs,ngs,ngs])
cell.verbose = 7
cell.build(None,None)
# Perform the gamma-point SCF
if scftype == 'dft':
mf = pbcdft.RKS(cell)
mf.xc = 'lda,vwn'
elif scftype == 'hf':
mf = pbchf.RHF(cell, exxdiv=None)
else:
scaled_mp_kpts = ase.dft.kpoints.monkhorst_pack((nmp,nmp,nmp))
abs_mp_kpts = cell.get_abs_kpts(scaled_mp_kpts)
if scftype == 'kdft':
mf = pbcdft.KRKS(cell, abs_mp_kpts)
mf.xc = 'lda,vwn'
else:
mf = pbchf.KRHF(cell, abs_mp_kpts, exxdiv='vcut_sph')
mf.analytic_int = False
mf.scf()
print "SCF evals =", mf.mo_energy
# Proceed along k-point band-path
e_kn = []
efermi = -99
for kpt in abs_kpts:
e, c = mf.get_bands(kpt)
print kpt, e
e_kn.append(e)
if e[4-1] > efermi:
efermi = e[4-1]
for k, ek in enumerate(e_kn):
e_kn[k] = ek-efermi
# Write the bands to stdout
f = open('bands_%s_%s_%d_%d.dat'%(scftype,basis,ngs,nmp),'w')
f.write("# Special points:\n")
for point, label in zip(X,['L', 'G', 'X', 'W', 'K', 'G']):
f.write("# %0.6f %s\n"%(point,label))
for kk, ek in zip(x, e_kn):
f.write("%0.6f "%(kk))
for ekn in ek:
f.write("%0.6f "%(ekn))
f.write("\n")
f.close()
# Plot the band structure via matplotlib
emin = -1.0
emax = 1.0
plt.figure(figsize=(8, 4))
nbands = cell.nao_nr()
for n in range(nbands):
plt.plot(x, [e_kn[i][n] for i in range(len(x))])
for p in X:
plt.plot([p, p], [emin, emax], 'k-')
plt.plot([0, X[-1]], [0, 0], 'k-')
plt.xticks(X, ['$%s$' % n for n in ['L', r'\Gamma', 'X', 'W', 'K', r'\Gamma']])
plt.axis(xmin=0, xmax=X[-1], ymin=emin, ymax=emax)
plt.xlabel('k-vector')
plt.ylabel('Energy [au]')
#plt.show()
if nmp is None:
plt.savefig('bands_%s_%s_%d.png'%(scftype,basis,ngs))
else:
plt.savefig('bands_%s_%s_%d_%d.png'%(scftype,basis,ngs,nmp))
""" Take ASE Diamond structure, input into PySCF and run """ import numpy as np import pyscf.pbc.gto as pbcgto import pyscf.pbc.dft as pbcdft from pyscf.pbc.tools import pyscf_ase import ase import ase.lattice from ase.lattice.cubic import Diamond ase_atom = Diamond(symbol='C', latticeconstant=3.5668) print(ase_atom.get_volume()) cell = pbcgto.Cell() cell.verbose = 5 cell.atom = pyscf_ase.ase_atoms_to_pyscf(ase_atom) cell.a = ase_atom.cell cell.basis = 'gth-szv' cell.pseudo = 'gth-pade' cell.build() mf = pbcdft.RKS(cell) mf.xc = 'lda,vwn' print(mf.kernel()) # [10,10,10]: -44.8811199336
#!/usr/bin/env python
'''
CCSD with K-point sampling
'''
from pyscf.pbc import gto, scf, cc
from pyscf.pbc.tools import pyscf_ase
from ase.lattice import bulk
ase_atom = bulk('C', 'diamond', a=3.5668)
cell = gto.M(
h = ase_atom.cell,
atom = pyscf_ase.ase_atoms_to_pyscf(ase_atom),
basis = 'gth-szv'
pseudo = 'gth-pade'
gs = [10]*3,
verbose = 4,
)
nk = [2,2,2]
kpts = cell.make_kpts(nk)
#
# Running HF
#
kmf = scf.KRHF(cell, kpts, exxdiv=None)
ehf = kmf.kernel()
#