def test_chkfile_k_point(self):
cell = pbcgto.Cell()
cell.a = np.eye(3) * 6
cell.mesh = [21] * 3
cell.unit = 'B'
cell.atom = '''He 2. 2. 3.
He 3. 2. 3.'''
cell.basis = {'He': 'sto3g'}
cell.verbose = 0
cell.build()
mf1 = pbcdft.RKS(cell)
mf1.chkfile = tempfile.NamedTemporaryFile().name
mf1.max_cycle = 1
mf1.kernel()
cell = pbcgto.Cell()
cell.a = np.eye(3) * 6
cell.mesh = [41] * 3
cell.unit = 'B'
cell.atom = '''He 2. 2. 3.
He 3. 2. 3.'''
cell.basis = {'He': 'ccpvdz'}
cell.verbose = 5
cell.output = '/dev/null'
cell.nimgs = [2, 2, 2]
cell.build()
mf = pbcdft.RKS(cell)
np.random.seed(10)
mf.kpt = np.random.random(3)
mf.max_cycle = 1
dm = mf.from_chk(mf1.chkfile)
mf.conv_check = False
self.assertAlmostEqual(mf.scf(dm), -4.7090816314173365, 8)
def test_chkfile_k_point(self):
cell = pbcgto.Cell()
cell.h = np.eye(3) * 6
cell.gs = [10, 10, 10]
cell.unit = 'B'
cell.atom = '''He 2. 2. 3.
He 3. 2. 3.'''
cell.basis = {'He': 'sto3g'}
cell.verbose = 0
cell.build()
mf1 = pbcdft.RKS(cell)
mf1.max_cycle = 1
mf1.kernel()
cell = pbcgto.Cell()
cell.h = np.eye(3) * 6
cell.gs = [20, 20, 20]
cell.unit = 'B'
cell.atom = '''He 2. 2. 3.
He 3. 2. 3.'''
cell.basis = {'He': 'ccpvdz'}
cell.verbose = 5
cell.output = '/dev/null'
cell.nimgs = [2, 2, 2]
cell.build()
mf = pbcdft.RKS(cell)
np.random.seed(10)
mf.kpt = np.random.random(3)
mf.max_cycle = 1
dm = mf.from_chk(mf1.chkfile)
self.assertAlmostEqual(mf.scf(dm), -4.7088482555684914, 8)
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_kpt_vs_supercell(self):
ngs = 5
nk = (3, 1, 1)
# Comparison is only perfect for odd-numbered supercells and kpt sampling
assert all(np.array(nk) % 2 == np.array([1, 1, 1]))
cell = make_primitive_cell(ngs)
scaled_kpts = ase.dft.kpoints.monkhorst_pack(nk)
abs_kpts = cell.get_abs_kpts(scaled_kpts)
kmf = pbcdft.KRKS(cell, abs_kpts)
kmf.xc = 'lda,vwn'
#kmf.analytic_int = False
#kmf.verbose = 7
ekpt = kmf.scf()
supcell = pyscf.pbc.tools.super_cell(cell, nk)
supcell.gs = np.array([
nk[0] * ngs + (nk[0] - 1) // 2, nk[1] * ngs + (nk[1] - 1) // 2,
nk[2] * ngs + (nk[2] - 1) // 2
])
#supcell.verbose = 7
supcell.build()
mf = pbcdft.RKS(supcell)
mf.xc = 'lda,vwn'
#mf.verbose = 7
esup = mf.scf() / np.prod(nk)
#print("kpt sampling energy =", ekpt)
#print("supercell energy =", esup)
self.assertAlmostEqual(ekpt, esup, 5)
def xtest_gamma(self):
cell = make_primitive_cell(8)
mf = pbcdft.RKS(cell)
mf.xc = 'lda,vwn'
#mf.verbose = 7
e1 = mf.scf()
self.assertAlmostEqual(e1, -10.2214263103747, 8)
def run_dft(cell):
"""Run a gamma-point DFT (LDA) calculation."""
mf = pbcdft.RKS(cell)
mf.xc = 'lda,vwn'
mf.verbose = 7
print mf.scf()
return mf
def test_rsh_aft_high_cost(self):
from pyscf.pbc.df.aft import AFTDF
mf = pbcdft.RKS(cell)
mf.with_df = AFTDF(cell)
mf.xc = 'camb3lyp'
mf.kernel()
self.assertAlmostEqual(mf.e_tot, -2.4745140705800446, 7)
def test_nr_rks_lda(self):
mf = dft.RKS(cell)
mf.xc = 'lda,'
mf = scf.newton(mf)
mf.conv_tol_grad = 1e-4
mf.kernel()
self.assertAlmostEqual(mf.e_tot, -9.7670882971475663, 8)
def test_pp_RKS(self):
cell = pbcgto.Cell()
cell.unit = 'A'
cell.atom = '''
Si 0.000000000 0.000000000 0.000000000;
Si 0.000000000 2.715348700 2.715348700;
Si 2.715348700 2.715348700 0.000000000;
Si 2.715348700 0.000000000 2.715348700;
Si 4.073023100 1.357674400 4.073023100;
Si 1.357674400 1.357674400 1.357674400;
Si 1.357674400 4.073023100 4.073023100;
Si 4.073023100 4.073023100 1.357674400
'''
cell.basis = 'gth-szv'
cell.pseudo = 'gth-pade'
Lx = Ly = Lz = 5.430697500
cell.h = np.diag([Lx, Ly, Lz])
cell.gs = np.array([10, 10, 10])
cell.verbose = 5
cell.output = '/dev/null'
cell.build()
mf = pbcdft.RKS(cell)
mf.xc = 'lda,vwn'
self.assertAlmostEqual(mf.scf(), -31.081616722101646, 8)
def test_klda8_primitive_gamma(self):
cell = make_primitive_cell(8)
mf = pbcdft.RKS(cell)
mf.xc = 'lda,vwn'
#kmf.verbose = 7
e1 = mf.scf()
self.assertAlmostEqual(e1, -10.221426445656439, 8)
def test_nr_rks_gga(self):
mf = dft.RKS(cell)
mf.xc = 'b88,'
mf = scf.newton(mf)
mf.conv_tol_grad = 1e-4
mf.kernel()
self.assertAlmostEqual(mf.e_tot, -9.9355341416893559, 8)
def test_rsh_0d_ewald(self):
L = 4.
cell = pbcgto.Cell()
cell.verbose = 0
cell.a = np.eye(3) * L
cell.atom = [
['He', (L / 2 + 0., L / 2 + 0., L / 2 + 1.)],
]
cell.basis = {'He': [[0, (4.0, 1.0)], [0, (1.0, 1.0)]]}
cell.dimension = 0
cell.mesh = [60] * 3
cell.build()
mf = pbcdft.RKS(cell).density_fit()
mf.xc = 'camb3lyp'
mf.omega = '0.7'
mf.exxdiv = 'ewald'
mf.kernel()
self.assertAlmostEqual(mf.e_tot, -2.4836186361124617, 7)
mol = cell.to_mol()
mf1 = mol.RKS().density_fit()
mf1.xc = 'camb3lyp'
mf1.omega = '0.7'
mf1.kernel()
self.assertAlmostEqual(mf1.e_tot, mf.e_tot, 4)
def test_klda8_cubic_gamma(self):
cell = build_cell([17]*3)
mf = pbcdft.RKS(cell)
mf.xc = 'lda,vwn'
#kmf.verbose = 7
e1 = mf.scf()
self.assertAlmostEqual(e1, -44.892502703975893, 8)
def test_multigrid_rks(self):
mf = dft.RKS(cell_he)
mf.xc = 'lda,'
ref = mf.get_veff(cell_he, dm_he[0])
out = multigrid.multigrid(mf).get_veff(cell_he, dm_he[0])
self.assertAlmostEqual(float(abs(ref - out).max()), 0, 9)
self.assertAlmostEqual(abs(ref.exc - out.exc).max(), 0, 9)
self.assertAlmostEqual(abs(ref.ecoul - out.ecoul).max(), 0, 9)
def test_rsh_mdf(self):
mf = pbcdft.RKS(cell).mix_density_fit()
mf.xc = 'camb3lyp'
mf.kernel()
self.assertAlmostEqual(mf.e_tot, -2.4745138538438827, 7)
mf.omega = .15
mf.kernel()
self.assertAlmostEqual(mf.e_tot, -2.4766174820185456, 7)
def test_custom_rsh_df(self):
mf = pbcdft.RKS(cell).density_fit()
mf.xc = 'camb3lyp'
mf.kernel()
self.assertAlmostEqual(mf.e_tot, -2.474520122522153, 7)
mf.omega = .15
mf.kernel()
self.assertAlmostEqual(mf.e_tot, -2.4766238116030683, 7)
def test_rsh_fft(self):
mf = pbcdft.RKS(cell)
mf.xc = 'camb3lyp'
mf.kernel()
self.assertAlmostEqual(mf.e_tot, -2.4745140703871877, 7)
mf.omega = .15
mf.kernel()
self.assertAlmostEqual(mf.e_tot, -2.476617717375184, 7)
def test_rsh_fft(self):
mf = pbcdft.RKS(cell)
mf.xc = 'camb3lyp'
mf.kernel()
self.assertAlmostEqual(mf.e_tot, -2.3032261128220544, 7)
mf.omega = .15
mf.kernel()
self.assertAlmostEqual(mf.e_tot, -2.3987595548455523, 7)
def test_rsh_mdf(self):
mf = pbcdft.RKS(cell).mix_density_fit()
mf.xc = 'camb3lyp'
mf.kernel()
self.assertAlmostEqual(mf.e_tot, -2.303225896642264, 7)
mf.omega = .15
mf.kernel()
self.assertAlmostEqual(mf.e_tot, -2.398759319488945, 7)
def test_custom_rsh_df(self):
mf = pbcdft.RKS(cell).density_fit()
mf.xc = 'camb3lyp'
mf.kernel()
self.assertAlmostEqual(mf.e_tot, -2.303232164939132, 7)
mf.omega = .15
mf.kernel()
self.assertAlmostEqual(mf.e_tot, -2.3987656490734555, 7)
def test_gamma_vs_ks_high_cost(self):
mf = pdft.KRKS(cell)
mf.kpts = cell.make_kpts([1, 1, 3])
ek = mf.kernel()
scell = ptools.super_cell(cell, [1, 1, 3])
scell.mesh = [25, 25, 73]
mf = pdft.RKS(scell)
eg = mf.kernel()
self.assertAlmostEqual(ek, eg / 3, 5)
def test_gamma_vs_ks(self):
mf = pdft.KRKS(cell)
mf.kpts = cell.make_kpts([1, 1, 3])
ek = mf.kernel()
scell = ptools.super_cell(cell, [1, 1, 3])
scell.gs = [12, 12, 36]
mf = pdft.RKS(scell)
eg = mf.kernel()
self.assertAlmostEqual(ek, eg / 3, 5)
def test_klda8_primitive_gamma(self):
ase_atom = bulk('C', 'diamond', a=LATTICE_CONST)
cell = build_cell(ase_atom, 8)
mf = pbcdft.RKS(cell)
mf.xc = 'lda,vwn'
#kmf.verbose = 7
e1 = mf.scf()
#print "mf._ecoul =", mf._ecoul
#print "mf._exc =", mf._exc
self.assertAlmostEqual(e1, -10.221426938778345, 8)
def test_klda8_cubic_gamma(self):
ase_atom = Diamond(symbol='C', latticeconstant=LATTICE_CONST)
cell = build_cell(ase_atom, 8)
mf = pbcdft.RKS(cell)
mf.xc = 'lda,vwn'
#kmf.verbose = 7
e1 = mf.scf()
#print "mf._ecoul =", mf._ecoul
#print "mf._exc =", mf._exc
self.assertAlmostEqual(e1, -44.892502703975893, 8)
def test_density_fit(self):
L = 4.
cell = pbcgto.Cell()
cell.a = np.eye(3) * L
cell.atom = [['He', (L / 2 + 0., L / 2 + 0., L / 2 + 1.)],
['He', (L / 2 + 1., L / 2 + 0., L / 2 + 1.)]]
cell.basis = {'He': [[0, (4.0, 1.0)], [0, (1.0, 1.0)]]}
cell.build()
mf = pbcdft.RKS(cell).density_fit()
mf.kernel()
self.assertAlmostEqual(mf.e_tot, -4.717699891018736, 7)
def test_band_ase():
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)
mf = pbcdft.RKS(cell)
mf.analytic_int = False
mf.xc = 'lda,vwn'
print mf.scf()
e_kn = []
for kpt in band_kpts:
fb, sb = mf.get_band_fock_ovlp(mf.get_hcore() + mf.get_veff(),
mf.get_ovlp(), kpt)
# fb, sb=mf.get_band_fock_ovlp(mf.get_hcore(),
# mf.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_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():
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 test_ccsd_t_non_hf_frozen(self):
'''Tests ccsd and ccsd_t for non-Hartree-Fock references with frozen orbitals
using supercell vs k-point calculation.'''
n = 14
cell = make_test_cell.test_cell_n3([n] * 3)
#import sys
#cell.stdout = sys.stdout
#cell.verbose = 7
nk = [2, 1, 1]
kpts = cell.make_kpts(nk)
kpts -= kpts[0]
kks = pbcdft.KRKS(cell, kpts=kpts)
ekks = kks.kernel()
khf = pbcscf.KRHF(cell)
khf.__dict__.update(kks.__dict__)
mycc = pbcc.KRCCSD(khf, frozen=1)
eris = mycc.ao2mo()
ekcc, t1, t2 = mycc.kernel(eris=eris)
ekcc_t = mycc.ccsd_t(eris=eris)
# Run supercell
from pyscf.pbc.tools.pbc import super_cell
supcell = super_cell(cell, nk)
rks = pbcdft.RKS(supcell)
erks = rks.kernel()
rhf = pbcscf.RHF(supcell)
rhf.__dict__.update(rks.__dict__)
mycc = pbcc.RCCSD(rhf, frozen=2)
eris = mycc.ao2mo()
ercc, t1, t2 = mycc.kernel(eris=eris)
self.assertAlmostEqual(ercc / np.prod(nk), -0.11467718013872311, 6)
self.assertAlmostEqual(ercc / np.prod(nk), ekcc, 6)
ercc_t = mycc.ccsd_t(eris=eris)
self.assertAlmostEqual(ercc_t / np.prod(nk), -0.00066503872045200996,
6)
self.assertAlmostEqual(ercc_t / np.prod(nk), ekcc_t, 6)
def test_lda_grid30(self):
cell = pbcgto.Cell()
cell.unit = 'B'
L = 10
cell.a = np.diag([L]*3)
cell.gs = np.array([20]*3)
cell.atom = [['He', (L/2.,L/2.,L/2.)], ]
# these are some exponents which are not hard to integrate
cell.basis = { 'He': [[0, (0.8, 1.0)],
[0, (1.0, 1.0)],
[0, (1.2, 1.0)]] }
cell.verbose = 5
cell.output = '/dev/null'
cell.pseudo = None
cell.build()
mf = pbcdft.RKS(cell)
mf.xc = 'LDA,VWN_RPA'
mf.kpt = np.ones(3)
e1 = mf.scf()
self.assertAlmostEqual(e1, -2.6409616064015591, 8)