def test_pyscf():
"""
Take ASE Diamond structure, input into PySCF and run
"""
ase_atom=Diamond(symbol='C', latticeconstant=3.5668)
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 = 'gth-szv'
cell.pseudo = 'gth-pade'
#cell.gs=np.array([10,10,10])
cell.gs=np.array([20,20,20])
cell.verbose=7
cell.build(None,None)
print cell._atom
print "Cell nimgs =", cell.nimgs
print "Cell _basis =", cell._basis
print "Cell _pseudo =", cell._pseudo
print "Cell nelectron =", cell.nelectron
mf=pbcdft.RKS(cell)
mf.xc='lda,vwn'
mf.analytic_int=False
print mf.scf() # [10,10,10]: -44.8811199336
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_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 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_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()
def test_calculator():
"""
Take ASE structure, PySCF object,
and run through ASE calculator interface.
This allows other ASE methods to be used with PySCF;
here we try to compute an equation of state.
"""
ase_atom=Diamond(symbol='C', latticeconstant=3.5668)
# Set up a cell; everything except atom; the ASE calculator will
# set the atom variable
cell = pbcgto.Cell()
cell.h=ase_atom.cell
cell.basis = 'gth-szv'
cell.pseudo = 'gth-pade'
cell.gs=np.array([8,8,8])
cell.verbose = 0
# Set up the kind of calculation to be done
# Additional variables for mf_class are passed through mf_dict
mf_class=pbcdft.RKS
mf_dict = { 'xc' : 'lda,vwn' }
# Once this is setup, ASE is used for everything from this point on
ase_atom.set_calculator(pyscf_ase.PySCF(molcell=cell, mf_class=mf_class, mf_dict=mf_dict))
print "ASE energy", ase_atom.get_potential_energy()
print "ASE energy (should avoid re-evaluation)", ase_atom.get_potential_energy()
# Compute equation of state
ase_cell=ase_atom.cell
volumes = []
energies = []
for x in np.linspace(0.95, 1.2, 5):
ase_atom.set_cell(ase_cell * x, scale_atoms = True)
print "[x: %f, E: %f]" % (x, ase_atom.get_potential_energy())
volumes.append(ase_atom.get_volume())
energies.append(ase_atom.get_potential_energy())
eos = EquationOfState(volumes, energies)
v0, e0, B = eos.fit()
print(B / kJ * 1.0e24, 'GPa')
eos.plot('eos.png')
""" 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
# Set up the kind of calculation to be done
# Additional variables for mf_class are passed through mf_dict
# E.g. gamma-point SCF calculation can be set to
mf_class = pbcdft.RKS
# SCF with k-point sampling can be set to
mf_class = lambda cell: pbcdft.KRKS(cell, kpts=cell.make_kpts([2, 2, 2]))
mf_dict = {'xc': 'lda,vwn'}
# Once this is setup, ASE is used for everything from this point on
ase_atom.set_calculator(
pyscf_ase.PySCF(molcell=cell, mf_class=mf_class, mf_dict=mf_dict))
print("ASE energy", ase_atom.get_potential_energy())
print("ASE energy (should avoid re-evaluation)",
ase_atom.get_potential_energy())
# Compute equation of state
ase_cell = ase_atom.cell
volumes = []
energies = []
for x in np.linspace(0.95, 1.2, 5):
ase_atom.set_cell(ase_cell * x, scale_atoms=True)
print "[x: %f, E: %f]" % (x, ase_atom.get_potential_energy())
volumes.append(ase_atom.get_volume())
energies.append(ase_atom.get_potential_energy())
eos = EquationOfState(volumes, energies)
v0, e0, B = eos.fit()
print(B / kJ * 1.0e24, 'GPa')
eos.plot('eos.png')
cell.verbose = 0
# Set up the kind of calculation to be done
# Additional variables for mf_class are passed through mf_dict
# E.g. gamma-point SCF calculation can be set to
mf_class = pbcdft.RKS
# SCF with k-point sampling can be set to
mf_class = lambda cell: pbcdft.KRKS(cell, kpts=cell.make_kpts([2,2,2]))
mf_dict = { 'xc' : 'lda,vwn' }
# Once this is setup, ASE is used for everything from this point on
ase_atom.set_calculator(pyscf_ase.PySCF(molcell=cell, mf_class=mf_class, mf_dict=mf_dict))
print("ASE energy", ase_atom.get_potential_energy())
print("ASE energy (should avoid re-evaluation)", ase_atom.get_potential_energy())
# Compute equation of state
ase_cell=ase_atom.cell
volumes = []
energies = []
for x in np.linspace(0.95, 1.2, 5):
ase_atom.set_cell(ase_cell * x, scale_atoms = True)
print "[x: %f, E: %f]" % (x, ase_atom.get_potential_energy())
volumes.append(ase_atom.get_volume())
energies.append(ase_atom.get_potential_energy())
eos = EquationOfState(volumes, energies)
v0, e0, B = eos.fit()
print(B / kJ * 1.0e24, 'GPa')
eos.plot('eos.png')
""" 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
