def find_basis_evaluate(mfchk, hdf_opt, hdf_vmc, hdf_final):
"""Given a wave function in hdf_opt, compute the 1-RDM (stored in hdf_vmc) , generate a minimal atomic basis and compute the energy/OBDM/TBDM and store in hdf_final """
from pyqmc.obdm import OBDMAccumulator
from pyqmc.tbdm import TBDMAccumulator
from pyqmc import EnergyAccumulator
sys = pyqmc_from_hdf(mfchk)
mol = sys["mol"]
a = lo.orth_ao(mol, "lowdin")
obdm_up = OBDMAccumulator(mol=mol, orb_coeff=a, spin=0)
obdm_down = OBDMAccumulator(mol=mol, orb_coeff=a, spin=1)
with h5py.File(hdf_opt, "r") as hdf_in:
if f"wf" in hdf_in.keys():
print("reading in wave function")
grp = hdf_in[f"wf"]
for k in grp.keys():
sys["wf"].parameters[k] = np.array(grp[k])
configs = pyqmc.initial_guess(sys["mol"], 1000)
pyqmc.vmc(
sys["wf"],
configs,
nsteps=500,
hdf_file=hdf_vmc,
accumulators={
"obdm_up": obdm_up,
"obdm_down": obdm_down
},
)
with h5py.File(hdf_vmc, "r") as vmc_hdf:
obdm_up = np.mean(np.array(vmc_hdf["obdm_upvalue"]), axis=0)
obdm_down = np.mean(np.array(vmc_hdf["obdm_downvalue"]), axis=0)
basis_up = gen_basis(mol, sys["mf"], obdm_up)
basis_down = gen_basis(mol, sys["mf"], obdm_down)
obdm_up_acc = OBDMAccumulator(mol=mol, orb_coeff=basis_up, spin=0)
obdm_down_acc = OBDMAccumulator(mol=mol, orb_coeff=basis_down, spin=1)
tbdm = TBDMAccumulator(mol, np.array([basis_up, basis_down]), spin=(0, 1))
acc = {
"energy": EnergyAccumulator(mol),
"obdm_up": obdm_up_acc,
"obdm_down": obdm_down_acc,
"tbdm": tbdm,
}
configs = pyqmc.initial_guess(sys["mol"], 1000)
pyqmc.vmc(sys["wf"],
configs,
nsteps=500,
hdf_file=hdf_final,
accumulators=acc)
def dmc(self, nconfig=1000, **kwargs):
configs = pyqmc.initial_guess(self.mol, nconfig)
if self.client is None:
pyqmc.vmc(self.wf, configs, nsteps=10)
pyqmc.rundmc(
self.wf,
configs,
accumulators={"energy": pyqmc.EnergyAccumulator(self.mol)},
**kwargs,
)
else:
pyqmc.dasktools.distvmc(
self.wf,
configs,
nsteps=10,
client=self.client,
npartitions=self.npartitions,
)
pyqmc.rundmc(
self.wf,
configs,
accumulators={"energy": pyqmc.EnergyAccumulator(self.mol)},
propagate=pyqmc.dasktools.distdmc_propagate,
**kwargs,
client=self.client,
npartitions=self.npartitions,
)
def optimize_excited(mc_anchors, mc_calc, nconfig = 1000, **kwargs):
acc = pyqmc.gradient_generator(mc_calc['mol'], mc_calc['wf'], to_opt=mc_calc['to_opt'])
wfs = [x['wf'] for x in mc_anchors]
wfs.append(mc_calc['wf'])
configs = pyqmc.initial_guess(mc_calc['mol'], nconfig)
pyqmc.optimize_orthogonal.optimize_orthogonal(wfs,configs, acc, **kwargs)
def test_transform():
""" Just prints things out;
TODO: figure out a thing to test.
"""
from pyscf import gto, scf
import pyqmc
r = 1.54 / .529177
mol = gto.M(atom='H 0. 0. 0.; H 0. 0. %g' % r,
ecp='bfd',
basis='bfd_vtz',
unit='bohr',
verbose=1)
mf = scf.RHF(mol).run()
wf = pyqmc.slater_jastrow(mol, mf)
enacc = pyqmc.EnergyAccumulator(mol)
print(list(wf.parameters.keys()))
transform = LinearTransform(wf.parameters)
x = transform.serialize_parameters(wf.parameters)
nconfig = 10
configs = pyqmc.initial_guess(mol, nconfig)
wf.recompute(configs)
pgrad = wf.pgradient()
gradtrans = transform.serialize_gradients(pgrad)
assert gradtrans.shape[1] == len(x)
assert gradtrans.shape[0] == nconfig
def test_transform():
""" Just prints things out;
TODO: figure out a thing to test.
"""
from pyscf import gto, scf
r = 1.54 / 0.529177
mol = gto.M(
atom="H 0. 0. 0.; H 0. 0. %g" % r,
ecp="bfd",
basis="bfd_vtz",
unit="bohr",
verbose=1,
)
mf = scf.RHF(mol).run()
wf, to_opt = pyqmc.default_sj(mol, mf)
enacc = pyqmc.EnergyAccumulator(mol)
print(list(wf.parameters.keys()))
transform = LinearTransform(wf.parameters)
x = transform.serialize_parameters(wf.parameters)
nconfig = 10
configs = pyqmc.initial_guess(mol, nconfig)
wf.recompute(configs)
pgrad = wf.pgradient()
gradtrans = transform.serialize_gradients(pgrad)
assert gradtrans.shape[1] == len(x)
assert gradtrans.shape[0] == nconfig
def test_pbc_wfs():
"""
Ensure that the wave function objects are consistent in several situations.
"""
from pyscf.pbc import lib, gto, scf
from pyqmc.supercell import get_supercell
from pyqmc.slater import Slater
from pyqmc.multiplywf import MultiplyWF
from pyqmc import default_jastrow
import pyqmc
mol = gto.M(
atom="H 0. 0. 0.; H 1. 1. 1.",
basis="sto-3g",
unit="bohr",
a=(np.ones((3, 3)) - np.eye(3)) * 4,
)
mf = scf.KRKS(mol, mol.make_kpts((2, 2, 2))).run()
# mf_rohf = scf.KROKS(mol).run()
# mf_uhf = scf.KUKS(mol).run()
epsilon = 1e-5
nconf = 10
supercell = get_supercell(mol, S=(np.ones((3, 3)) - 2 * np.eye(3)))
epos = pyqmc.initial_guess(supercell, nconf)
# For multislaterpbc
# kinds = 0, 3, 5, 6 # G, X, Y, Z
# d1 = {kind: [0] for kind in kinds}
# d2 = d1.copy()
# d2.update({0: [], 3: [0, 1]})
# detwt = [2 ** 0.5, 2 ** 0.5]
# occup = [[d1, d2], [d1]]
# map_dets = [[0, 1], [0, 0]]
for wf in [
MultiplyWF(Slater(supercell, mf), default_jastrow(supercell)[0]),
Slater(supercell, mf),
]:
for k in wf.parameters:
if "mo_coeff" not in k and k != "det_coeff":
wf.parameters[k] = np.random.rand(*wf.parameters[k].shape)
_, epos = pyqmc.vmc(wf, epos, nblocks=1, nsteps=2, tstep=1) # move off node
for fname, func in zip(
["gradient", "laplacian", "pgradient"],
[
testwf.test_wf_gradient,
testwf.test_wf_laplacian,
testwf.test_wf_pgradient,
],
):
err = []
for delta in [1e-4, 1e-5, 1e-6, 1e-7, 1e-8]:
err.append(func(wf, epos, delta))
print(type(wf), fname, min(err))
assert min(err) < epsilon
for k, item in testwf.test_updateinternals(wf, epos).items():
print(k, item)
assert item < epsilon
def OPTIMIZE(
dft_checkfile,
output,
nconfig=1000,
start_from=None,
S=None,
client=None,
npartitions=None,
jastrow_kws=None,
slater_kws=None,
linemin_kws=None,
):
if linemin_kws is None:
linemin_kws = {}
mol, mf = pyqmc.recover_pyscf(dft_checkfile)
if S is not None:
mol = pyqmc.get_supercell(mol, np.asarray(S))
wf, to_opt = pyqmc.generate_wf(mol,
mf,
jastrow_kws=jastrow_kws,
slater_kws=slater_kws)
if start_from is not None:
pyqmc.read_wf(wf, start_from)
configs = pyqmc.initial_guess(mol, nconfig)
acc = pyqmc.gradient_generator(mol, wf, to_opt)
pyqmc.line_minimization(wf,
configs,
acc,
verbose=True,
hdf_file=output,
client=client,
npartitions=npartitions,
**linemin_kws)
def DMC(dft_checkfile,
output,
nconfig=1000,
start_from=None,
S=None,
client=None,
npartitions=None,
jastrow_kws=None,
slater_kws=None,
dmc_kws=None,
accumulators=None):
if dmc_kws is None:
dmc_kws = {}
mol, mf = pyqmc.recover_pyscf(dft_checkfile)
if S is not None:
mol = pyqmc.get_supercell(mol, np.asarray(S))
wf, _ = pyqmc.generate_wf(mol,
mf,
jastrow_kws=jastrow_kws,
slater_kws=slater_kws)
if start_from is not None:
pyqmc.read_wf(wf, start_from)
configs = pyqmc.initial_guess(mol, nconfig)
pyqmc.rundmc(wf,
configs,
accumulators=generate_accumulators(mol, mf, **accumulators),
verbose=True,
hdf_file=output,
client=client,
npartitions=npartitions,
**dmc_kws)
def OPTIMIZE(
dft_checkfile,
output,
anchors=None,
nconfig=1000,
ci_checkfile=None,
start_from=None,
S=None,
client=None,
npartitions=None,
jastrow_kws=None,
slater_kws=None,
linemin_kws=None,
):
if linemin_kws is None:
linemin_kws = {}
target_root = 0
if ci_checkfile is None:
mol, mf = pyqmc.recover_pyscf(dft_checkfile)
mc = None
else:
mol, mf, mc = pyqmc.recover_pyscf(dft_checkfile,
ci_checkfile=ci_checkfile)
mc.ci = mc.ci[target_root]
if S is not None:
mol = pyqmc.get_supercell(mol, np.asarray(S))
wf, to_opt = pyqmc.generate_wf(mol,
mf,
mc=mc,
jastrow_kws=jastrow_kws,
slater_kws=slater_kws)
if start_from is not None:
pyqmc.read_wf(wf, start_from)
configs = pyqmc.initial_guess(mol, nconfig)
acc = pyqmc.gradient_generator(mol, wf, to_opt)
if anchors is None:
pyqmc.line_minimization(wf,
configs,
acc,
verbose=True,
hdf_file=output,
client=client,
npartitions=npartitions,
**linemin_kws)
else:
wfs = [pyqmc.read_wf(copy.deepcopy(wf), a) for a in anchors]
wfs.append(wf)
pyqmc.optimize_orthogonal(
wfs,
configs,
acc,
# verbose=True,
hdf_file=output,
client=client,
npartitions=npartitions,
**linemin_kws)
def test():
from pyscf.pbc import gto, scf
import pyqmc
import pandas as pd
L = 4
mol = gto.M(
atom="""H {0} {0} {0}""".format(0.0),
basis="sto-3g",
a=np.eye(3) * L,
spin=1,
unit="bohr",
)
mf = scf.UKS(mol)
mf.xc = "pbe"
mf = mf.density_fit().run()
wf = pyqmc.PySCFSlaterUHF(mol, mf)
#####################################
## evaluate KE in PySCF
#####################################
ke_mat = mol.pbc_intor("int1e_kin", hermi=1, kpts=np.array([0, 0, 0]))
dm = mf.make_rdm1()
pyscfke = np.einsum("ij,ji", ke_mat, dm[0])
print("PySCF kinetic energy: {0}".format(pyscfke))
#####################################
## evaluate KE integral on grid
#####################################
X = np.linspace(0, 1, 20, endpoint=False)
XYZ = np.meshgrid(X, X, X, indexing="ij")
pts = [np.outer(p.ravel(), mol.a[i]) for i, p in enumerate(XYZ)]
coords = np.sum(pts, axis=0).reshape((-1, 1, 3))
phase, logdet = wf.recompute(coords)
psi = phase * np.exp(logdet)
lap = wf.laplacian(0, coords.reshape((-1, 3)))
gridke = np.sum(-0.5 * lap * psi ** 2) / np.sum(psi ** 2)
print("grid kinetic energy: {0}".format(gridke))
#####################################
## evaluate KE integral with VMC
#####################################
coords = pyqmc.initial_guess(mol, 600, 0.7)
coords = PeriodicConfigs(coords, mol.a)
warmup = 10
df, coords = pyqmc.vmc(
wf,
coords,
nsteps=128 + warmup,
tstep=L * 0.6,
accumulators={"energy": pyqmc.accumulators.EnergyAccumulator(mol)},
)
df = pd.DataFrame(df)
reblocked = pyqmc.reblock.optimally_reblocked(df["energyke"][warmup:])
print(
"VMC kinetic energy: {0} $\pm$ {1}".format(
reblocked["mean"], reblocked["standard error"]
)
)
def setup(self):
self.mol = pyscf.gto.M(atom="O 0 0 0; H 0 -2.757 2.587; H 0 2.757 2.587", basis=f'ccecpccpvdz', ecp='ccecp')
self.mf = pyscf.scf.RHF(self.mol).run()
self.configs = pyqmc.initial_guess(self.mol, 500)
self.slater, self.slater_to_opt = pyqmc.default_slater(self.mol, self.mf, optimize_orbitals=True)
self.jastrow, self.jastrow_to_opt = pyqmc.default_jastrow(self.mol)
self.pgrad_acc = pyqmc.gradient_generator(self.mol, self.slater, self.slater_to_opt)
self.slater.recompute(self.configs)
self.jastrow.recompute(self.configs)
def runtest(mol, mf, kind=0, do_mc=False):
if do_mc:
from pyscf import mcscf
mc = mcscf.CASCI(mf, ncas=4, nelecas=(1, 1))
mc.kernel()
wf = pyqmc.default_msj(mol, mf, mc)[0]
kpt = mf.kpt
dm = mc.make_rdm1()
if len(dm.shape) == 4:
dm = np.sum(dm, axis=0)
else:
kpt = mf.kpts[kind]
wf = pyqmc.Slater(mol, mf)
dm = mf.make_rdm1()
print("original dm shape", dm.shape)
if len(dm.shape) == 4:
dm = np.sum(dm, axis=0)
dm = dm[kind]
#####################################
## evaluate KE in PySCF
#####################################
ke_mat = mol.pbc_intor("int1e_kin", hermi=1, kpts=np.array(kpt))
print("ke_mat", ke_mat.shape)
print("dm", dm.shape)
pyscfke = np.real(np.einsum("ij,ji->", ke_mat, dm))
print("PySCF kinetic energy: {0}".format(pyscfke))
#####################################
## evaluate KE integral with VMC
#####################################
coords = pyqmc.initial_guess(mol, 1200, 0.7)
warmup = 10
start = time.time()
df, coords = pyqmc.vmc(
wf,
coords,
nsteps=100 + warmup,
tstep=1,
accumulators={"energy": pyqmc.accumulators.EnergyAccumulator(mol)},
verbose=False,
hdf_file=str(uuid.uuid4()),
)
print("VMC time", time.time() - start)
df = pd.DataFrame(df)
dfke = reblock(df["energyke"][warmup:], 10)
dfke /= mol.scale
vmcke, err = dfke.mean(), dfke.sem()
print("VMC kinetic energy: {0} +- {1}".format(vmcke, err))
assert (
np.abs(vmcke - pyscfke) < 5 * err
), "energy diff not within 5 sigma ({0:.6f}): energies \n{1} \n{2}".format(
5 * err, vmcke, pyscfke)
def generate_test_inputs():
import pyqmc
from pyqmc.coord import PeriodicConfigs
from pyscf.pbc import gto, scf
from pyscf.pbc.dft.multigrid import multigrid
from pyscf.pbc import tools
from pyscf import lib
from_chkfile = True
if from_chkfile:
def loadchkfile(chkfile):
cell = gto.cell.loads(lib.chkfile.load(chkfile, "mol"))
kpts = cell.make_kpts([1, 1, 1])
mf = scf.KRKS(cell, kpts)
mf.__dict__.update(lib.chkfile.load(chkfile, "scf"))
return cell, mf
cell1, mf1 = loadchkfile("mf1.chkfile")
cell2, mf2 = loadchkfile("mf2.chkfile")
else:
L = 4
cell2 = gto.M(
atom="""H {0} {0} {0}
H {1} {1} {1}""".format(0.0, L * 0.25),
basis="sto-3g",
a=np.eye(3) * L,
spin=0,
unit="bohr",
)
print("Primitive cell")
kpts = cell2.make_kpts((2, 2, 2))
mf2 = scf.KRKS(cell2, kpts)
mf2.xc = "pbe"
mf2.chkfile = "mf2.chkfile"
mf2 = mf2.run()
print("Supercell")
cell1 = tools.super_cell(cell2, [2, 2, 2])
kpts = [[0, 0, 0]]
mf1 = scf.KRKS(cell1, kpts)
mf1.xc = "pbe"
mf1.chkfile = "mf1.chkfile"
mf1 = mf1.run()
# wf1 = pyqmc.PySCFSlaterUHF(cell1, mf1)
wf1 = PySCFSlaterPBC(cell1, mf1, supercell=1 * np.eye(3))
wf2 = PySCFSlaterPBC(cell2, mf2, supercell=2 * np.eye(3))
configs = pyqmc.initial_guess(cell1, 10, 0.1)
return wf1, wf2, configs
def test_wfs():
"""
Ensure that the wave function objects are consistent in several situations.
"""
from pyscf import lib, gto, scf
from pyqmc.slater import PySCFSlater
from pyqmc.jastrowspin import JastrowSpin
from pyqmc.multiplywf import MultiplyWF
from pyqmc.manybody_jastrow import J3
import pyqmc
mol = gto.M(atom="Li 0. 0. 0.; H 0. 0. 1.5", basis="sto-3g", unit="bohr")
mf = scf.RHF(mol).run()
mf_rohf = scf.ROHF(mol).run()
mf_uhf = scf.UHF(mol).run()
epsilon = 1e-5
nconf = 10
epos = pyqmc.initial_guess(mol, nconf)
for wf in [
JastrowSpin(mol),
J3(mol),
MultiplyWF(PySCFSlater(mol, mf), JastrowSpin(mol)),
MultiplyWF(PySCFSlater(mol, mf), JastrowSpin(mol), J3(mol)),
PySCFSlater(mol, mf_uhf),
PySCFSlater(mol, mf),
PySCFSlater(mol, mf_rohf),
]:
for k in wf.parameters:
if k != "mo_coeff":
wf.parameters[k] = np.random.rand(*wf.parameters[k].shape)
for k, item in testwf.test_updateinternals(wf, epos).items():
print(k, item)
assert item < epsilon
testwf.test_mask(wf, 0, epos)
_, epos = pyqmc.vmc(wf, epos, nblocks=1, nsteps=2,
tstep=1) # move off node
for fname, func in zip(
["gradient", "laplacian", "pgradient"],
[
testwf.test_wf_gradient,
testwf.test_wf_laplacian,
testwf.test_wf_pgradient,
],
):
err = []
for delta in [1e-4, 1e-5, 1e-6, 1e-7, 1e-8]:
err.append(func(wf, epos, delta)[0])
print(type(wf), fname, min(err))
assert min(err) < epsilon, "epsilon {0}".format(epsilon)
def VMC(
dft_checkfile,
output,
nconfig=1000,
ci_checkfile=None,
start_from=None,
S=None,
client=None,
npartitions=None,
jastrow_kws=None,
slater_kws=None,
vmc_kws=None,
accumulators=None,
):
if vmc_kws is None:
vmc_kws = {}
target_root = 0
if ci_checkfile is None:
mol, mf = pyqmc.recover_pyscf(dft_checkfile)
mc = None
else:
mol, mf, mc = pyqmc.recover_pyscf(dft_checkfile,
ci_checkfile=ci_checkfile)
mc.ci = mc.ci[target_root]
if S is not None:
print("S", S)
mol = pyqmc.get_supercell(mol, np.asarray(S))
if accumulators is None:
accumulators = {}
wf, _ = pyqmc.generate_wf(mol,
mf,
mc=mc,
jastrow_kws=jastrow_kws,
slater_kws=slater_kws)
if start_from is not None:
pyqmc.read_wf(wf, start_from)
configs = pyqmc.initial_guess(mol, nconfig)
pyqmc.vmc(wf,
configs,
accumulators=generate_accumulators(mol, mf, **accumulators),
verbose=True,
hdf_file=output,
client=client,
npartitions=npartitions,
**vmc_kws)
def info_functions(mol, wf, accumulators):
accumulators["energy"] = accumulators["pgrad"].enacc
configs = pyqmc.initial_guess(mol, 100)
wf.recompute(configs)
for k, acc in accumulators.items():
shapes = acc.shapes()
keys = acc.keys()
assert shapes.keys() == keys, "keys: {0}\nshapes: {1}".format(
keys, shapes)
avg = acc.avg(configs, wf)
assert avg.keys() == keys, (k, avg.keys(), keys)
for ka in keys:
assert shapes[ka] == avg[ka].shape, "{0} {1}".format(
ka, avg[ka].shape)
def evaluate_big1rdm(mc_calc, output, nconfig =1000, **kwargs):
mol = mc_calc['mol']
a = pyscf.lo.orth_ao(mol, 'lowdin')
obdm_up = pyqmc.obdm.OBDMAccumulator(mol=mol, orb_coeff=a, spin=0)
obdm_down = pyqmc.obdm.OBDMAccumulator(mol=mol, orb_coeff=a, spin=1)
configs = pyqmc.initial_guess(mol, 1000)
pyqmc.vmc(mc_calc['wf'], configs, hdf_file=output,
accumulators = {
'obdm_up':obdm_up,
'obdm_down':obdm_down
},
**kwargs
)
def test_pbc_wfs():
"""
Ensure that the wave function objects are consistent in several situations.
"""
from pyscf.pbc import lib, gto, scf
from pyqmc.slaterpbc import PySCFSlaterPBC, get_supercell
from pyqmc.jastrowspin import JastrowSpin
from pyqmc.multiplywf import MultiplyWF
from pyqmc.coord import OpenConfigs
import pyqmc
mol = gto.M(atom="H 0. 0. 0.; H 1. 1. 1.",
basis="sto-3g",
unit="bohr",
a=np.eye(3) * 4)
mf = scf.KRKS(mol).run()
# mf_rohf = scf.KROKS(mol).run()
# mf_uhf = scf.KUKS(mol).run()
epsilon = 1e-5
nconf = 10
supercell = get_supercell(mol, S=np.eye(3))
epos = pyqmc.initial_guess(supercell, nconf)
for wf in [
MultiplyWF(PySCFSlaterPBC(supercell, mf), JastrowSpin(mol)),
PySCFSlaterPBC(supercell, mf),
# PySCFSlaterPBC(supercell, mf_uhf),
# PySCFSlaterPBC(supercell, mf_rohf),
]:
for k in wf.parameters:
if k != "mo_coeff":
wf.parameters[k] = np.random.rand(*wf.parameters[k].shape)
for fname, func in zip(
["gradient", "laplacian", "pgradient"],
[
testwf.test_wf_gradient,
testwf.test_wf_laplacian,
testwf.test_wf_pgradient,
],
):
err = []
for delta in [1e-4, 1e-5, 1e-6, 1e-7, 1e-8]:
err.append(func(wf, epos, delta)[0])
print(fname, min(err))
assert min(err) < epsilon
for k, item in testwf.test_updateinternals(wf, epos).items():
print(k, item)
assert item < epsilon
def evaluate_smallbasis(mc_calc, smallbasis_hdf, nconfig=1000, **kwargs):
with h5py.File(smallbasis_hdf,'r') as f:
basis_up = f['basis_up'][...]
basis_down = f['basis_down'][...]
mol = mc_calc['mol']
obdm_up_acc = pyqmc.obdm.OBDMAccumulator(mol=mol, orb_coeff=basis_up, spin=0)
obdm_down_acc = pyqmc.obdm.OBDMAccumulator(mol=mol, orb_coeff=basis_down, spin=1)
tbdm = pyqmc.tbdm.TBDMAccumulator(mol, np.array([basis_up,basis_down]), spin=(0,1))
acc = {'energy': pyqmc.EnergyAccumulator(mol),
'obdm_up':obdm_up_acc,
'obdm_down':obdm_down_acc,
'tbdm': tbdm }
configs = pyqmc.initial_guess(mc_calc['mol'], nconfig)
pyqmc.vmc(mc_calc['wf'], configs, accumulators = acc, **kwargs)
def test():
""" Optimize a Helium atom's wave function and check that it's
better than Hartree-Fock"""
mol = gto.M(atom="He 0. 0. 0.", basis="bfd_vdz", ecp="bfd", unit="bohr")
mf = scf.RHF(mol).run()
wf = slater_jastrow(mol, mf)
nconf = 500
wf, dfgrad, dfline = line_minimization(wf, initial_guess(mol, nconf),
gradient_generator(mol, wf))
dfgrad = pd.DataFrame(dfgrad)
mfen = mf.energy_tot()
enfinal = dfgrad["en"].values[-1]
enfinal_err = dfgrad["en_err"].values[-1]
assert mfen > enfinal
def genconfigs(n):
"""
Generate configurations and weights corresponding
to the highest determinant in MD expansion
"""
import os
os.system('mkdir -p vmc/')
mol, mf, mc, wf, to_opt, freeze = wavefunction(return_mf=True)
#Sample from the wave function which we're taking pderiv relative to
mf.mo_coeff = mc.mo_coeff
mf.mo_occ *= 0
mf.mo_occ[wf.wf1._det_occup[0][-1]] = 2
wfp = PySCFSlaterUHF(mol, mf)
#Lots of configurations
coords = pyqmc.initial_guess(mol, 100000)
eacc = EnergyAccumulator(mol)
transform = LinearTransform(wf.parameters, to_opt, freeze)
pgrad_bare = PGradTransform(eacc, transform, 0)
#Lots of steps
warmup = 10
for i in range(n + warmup + 1):
df, coords = vmc(wfp, coords, nsteps=1)
print(i)
if (i > warmup):
coords.configs.dump('vmc/coords' + str(i - warmup) + '.pickle')
val = wf.recompute(coords)
valp = wfp.value()
d = pgrad_bare(coords, wf)
data = {
'dpH': np.array(d['dpH'])[:, -1],
'dppsi': np.array(d['dppsi'])[:, -1],
'en': np.array(d['total']),
"wfval": val[1],
"wfpval": valp[1]
}
pd.DataFrame(data).to_json('vmc/evals' + str(i - warmup) + '.json')
return -1
def test_wfs():
"""
Ensure that the wave function objects are consistent in several situations.
"""
from pyscf import lib, gto, scf
from pyqmc.slateruhf import PySCFSlaterUHF
from pyqmc.jastrowspin import JastrowSpin
from pyqmc.multiplywf import MultiplyWF
from pyqmc.coord import OpenConfigs
import pyqmc
mol = gto.M(atom="Li 0. 0. 0.; H 0. 0. 1.5", basis="cc-pvtz", unit="bohr")
mf = scf.RHF(mol).run()
mf_rohf = scf.ROHF(mol).run()
mf_uhf = scf.UHF(mol).run()
epsilon = 1e-5
nconf = 10
epos = pyqmc.initial_guess(mol, nconf)
for wf in [
JastrowSpin(mol),
MultiplyWF(PySCFSlaterUHF(mol, mf), JastrowSpin(mol)),
PySCFSlaterUHF(mol, mf_uhf),
PySCFSlaterUHF(mol, mf),
PySCFSlaterUHF(mol, mf_rohf),
]:
for k in wf.parameters:
if k != "mo_coeff":
wf.parameters[k] = np.random.rand(*wf.parameters[k].shape)
for fname, func in zip(
["gradient", "laplacian", "pgradient"],
[
testwf.test_wf_gradient,
testwf.test_wf_laplacian,
testwf.test_wf_pgradient,
],
):
err = []
for delta in [1e-4, 1e-5, 1e-6, 1e-7, 1e-8]:
err.append(func(wf, epos, delta)[0])
print(fname, min(err))
assert min(err) < epsilon
for k, item in testwf.test_updateinternals(wf, epos).items():
print(k, item)
assert item < epsilon
def test():
print("running scf", flush=True)
mol = gto.M(atom="H 0. 0. 0.; H 0. 0. 1.6", basis="ccpvdz", unit="bohr")
mf = scf.UHF(mol).run()
mf.stdout = None
print("setting up wfs", flush=True)
wf0 = pyqmc.Slater(mol, mf)
mf.mo_coeff[0][:, 0] = np.mean(mf.mo_coeff[0][:, :2], axis=1)
wf1, to_opt = pyqmc.default_slater(mol, mf, optimize_orbitals=True)
pgrad = pyqmc.gradient_generator(mol, wf1, to_opt)
configs = pyqmc.initial_guess(mol, 2000)
wf0.recompute(configs)
wf1.recompute(configs)
wfs = [wf0, wf1]
print("warming up", flush=True)
block_avg, configs = oo.sample_overlap_worker(wfs,
configs,
pgrad,
20,
tstep=1.5)
print("computing gradients and normalization", flush=True)
data = get_data(wfs, configs, pgrad)
parameters = pgrad.transform.serialize_parameters(wfs[-1].parameters)
N = compute_normalization(wfs, [parameters], pgrad.transform, configs)
print(np.stack([data["N"], N]))
print("computing numerical gradients", flush=True)
error = {"N": [], "S": []}
deltas = [1e-4, 1e-5, 1e-6]
numgrad = numerical_gradient(wfs, configs, pgrad, deltas)
for k, ng in numgrad.items():
pgerr = data[k + "_derivative"].T[:, np.newaxis] - ng
error[k] = pgerr
print("computing errors", flush=True)
for k, er in error.items():
error[k] = np.amin(er, axis=1)
print(k)
print(error[k])
def optimize(self, nconfig=1000, **kwargs):
configs = pyqmc.initial_guess(self.mol, nconfig)
acc = pyqmc.gradient_generator(self.mol, self.wf, to_opt=self.to_opt)
if self.client is None:
pyqmc.line_minimization(self.wf, configs, acc, **kwargs)
else:
pyqmc.dasktools.line_minimization(
self.wf,
configs,
acc,
**kwargs,
client=self.client,
lmoptions={"npartitions": self.npartitions},
vmcoptions={
"npartitions": self.npartitions,
'nblocks': 5,
'nsteps_per_block': 20
},
)
def setup(self):
self.cell = pyscf.pbc.gto.Cell()
self.cell.atom = '''C 0. 0. 0.
C 0.8917 0.8917 0.8917
C 1.7834 1.7834 0.
C 2.6751 2.6751 0.8917
C 1.7834 0. 1.7834
C 2.6751 0.8917 2.6751
C 0. 1.7834 1.7834
C 0.8917 2.6751 2.6751'''
self.cell.basis = f'ccecpccpvdz'
self.cell.pseudo = 'ccecp'
self.cell.a = np.eye(3)*3.5668
self.cell.exp_to_discard=0.2
self.cell.build()
self.configs = pyqmc.initial_guess(self.cell, 500)
self.jastrow, self.jastrow_to_opt = pyqmc.default_jastrow(self.cell)
self.jastrow.recompute(self.configs)
def sweepelectron():
"""
Sweep an electron across the molecule
to find a guess for the nodal position
"""
import copy
from pyqmc.accumulators import EnergyAccumulator, LinearTransform, PGradTransform
#Generate wave function and bare parameter gradient objects
mol, wf, to_opt, freeze = wavefunction()
eacc = EnergyAccumulator(mol)
transform = LinearTransform(wf.parameters, to_opt, freeze)
pgrad = PGradTransform(eacc, transform, 1e-20)
#Initial coords
configs = pyqmc.initial_guess(mol, 1).configs[:,:,:]
#Sweep electron 0
full_df = None
e = 3 #electron
dim = 1 #Coordinate to vary
for i in np.linspace(0, 20, 200):
new_configs = copy.deepcopy(configs)
new_configs[:,e,dim] += i
shifted_configs = OpenConfigs(new_configs)
wfval = wf.recompute(shifted_configs)
d = pgrad(shifted_configs, wf)
small_df = pd.DataFrame({
'ke':[d['ke'][0]],
'total':[d['total'][0]],
'dppsi':[d['dppsi'][0][0]],
'dpH' :[d['dpH'][0][0]],
'wfval':[wfval[0][0]*np.exp(wfval[1][0])],
'ycoord': i,
'configs':[copy.deepcopy(new_configs)],
})
if(full_df is None): full_df = small_df
else: full_df = pd.concat((full_df, small_df), axis=0)
return full_df.reset_index()
def test():
chkfile = "h2.hdf5"
optfile = "linemin.hdf5"
run_scf(chkfile)
mol, mf = pyqmc.recover_pyscf(chkfile)
noise = (np.random.random(mf.mo_coeff.shape) - 0.5) * 0.2
mf.mo_coeff = mf.mo_coeff * 1j + noise
slater_kws = {"optimize_orbitals": True}
wf, to_opt = pyqmc.generate_wf(mol, mf, slater_kws=slater_kws)
configs = pyqmc.initial_guess(mol, 100)
acc = pyqmc.gradient_generator(mol, wf, to_opt)
pyqmc.line_minimization(wf,
configs,
acc,
verbose=True,
hdf_file=optfile,
max_iterations=5)
assert os.path.isfile(optfile)
os.remove(chkfile)
os.remove(optfile)
def runtest(mol, mf, kind):
kpt = mf.kpts[kind]
wf = pyqmc.PySCFSlaterUHF(mol, mf, twist=np.dot(kpt, mol.a.T / np.pi))
#####################################
## evaluate KE in PySCF
#####################################
ke_mat = mol.pbc_intor('int1e_kin', hermi=1, kpts=np.array(kpt))
dm = mf.make_rdm1()
if len(dm.shape) == 4:
dm = np.sum(dm, axis=0)
pyscfke = np.real(np.einsum('ij,ji->', ke_mat, dm[kind]))
print('PySCF kinetic energy: {0}'.format(pyscfke))
#####################################
## evaluate KE integral with VMC
#####################################
coords = pyqmc.initial_guess(mol, 1200, .7)
warmup = 10
start = time.time()
df, coords = pyqmc.vmc(
wf,
coords,
nsteps=32 + warmup,
tstep=1,
accumulators={"energy": pyqmc.accumulators.EnergyAccumulator(mol)},
verbose=False,
)
print("VMC time", time.time() - start)
df = pd.DataFrame(df)
dfke = reblock(df["energyke"][warmup:], 8)
vmcke, err = dfke.mean(), dfke.sem()
print('VMC kinetic energy: {0} +- {1}'.format(vmcke, err))
assert np.abs(vmcke-pyscfke) < 5 * err, \
"energy diff not within 5 sigma ({0:.6f}): energies \n{1} \n{2}".format(5 * err, vmcke, pyscfke)
def test_shci_wf():
mol = pyscf.gto.M(
atom="O 0. 0. 0.; H 0. 0. 2.0",
basis="ccecpccpvtz",
ecp="ccecp",
unit="bohr",
charge=-1,
)
mf = pyscf.scf.RHF(mol)
mf.kernel()
e_hf = mf.energy_tot()
cisolver = pyscf.hci.SCI(mol)
cisolver.select_cutoff = 0.1
nmo = mf.mo_coeff.shape[1]
nelec = mol.nelec
h1 = mf.mo_coeff.T.dot(mf.get_hcore()).dot(mf.mo_coeff)
h2 = pyscf.ao2mo.full(mol, mf.mo_coeff)
e, civec = cisolver.kernel(h1, h2, nmo, nelec, verbose=4)
cisolver.ci = civec[0]
ci_energy = mf.energy_nuc() + e
tol = 0.0
configs = pyqmc.initial_guess(mol, 1000)
wf = pyqmc.Slater(mol, mf, cisolver, tol=tol)
data, configs = pyqmc.vmc(
wf,
configs,
nblocks=40,
verbose=True,
accumulators={"energy": pyqmc.EnergyAccumulator(mol)},
)
en, err = avg(data["energytotal"][1:])
nsigma = 4
assert len(wf.parameters["det_coeff"]) == len(cisolver.ci)
assert en - nsigma * err < e_hf
assert en + nsigma * err > ci_energy
import pyqmc
import pyqmc.dasktools
from pyqmc.dasktools import distvmc as vmc
from pyqmc.dasktools import line_minimization
from pyqmc.cvmc import optimize
from dask.distributed import Client, LocalCluster
r = 1.1
ncore = 2
sys = setuph2(r)
cluster = LocalCluster(n_workers=ncore, threads_per_worker=1)
client = Client(cluster)
# Set up calculation
nconf = 800
configs = pyqmc.initial_guess(sys["mol"], nconf)
wf, dfgrad, dfline = line_minimization(
sys["wf"],
configs,
pyqmc.gradient_generator(sys["mol"], sys["wf"]),
client=client,
maxiters=5,
)
forcing = {}
obj = {}
for k in sys["descriptors"]:
forcing[k] = 0.0
obj[k] = 0.0