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():
# Default multi-Slater wave function
mol = gto.M(atom="Li 0. 0. 0.; H 0. 0. 1.5",
basis="cc-pvtz",
unit="bohr",
spin=0)
mf = scf.RHF(mol).run()
mc = mcscf.CASCI(mf, ncas=2, nelecas=(1, 1))
mc.kernel()
wf, to_opt = default_msj(mol, mf, mc)
old_parms = wf.parameters
lt = LinearTransform(wf.parameters, to_opt)
# Test serialize parameters
x0 = lt.serialize_parameters(wf.parameters)
x0 += np.random.normal(size=x0.shape)
wf.parameters = lt.deserialize(x0)
assert wf.parameters["wf1det_coeff"][0] == old_parms["wf1det_coeff"][0]
assert np.sum(wf.parameters["wf2bcoeff"][0] -
old_parms["wf2bcoeff"][0]) == 0
# Test serialize gradients
configs = OpenConfigs(np.random.randn(10, 4, 3))
wf.recompute(configs)
pgrad = wf.pgradient()
pgrad_serial = lt.serialize_gradients(pgrad)
assert np.sum(pgrad_serial[:, :3] - pgrad["wf1det_coeff"][:, 1:4]) == 0
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_constraints(H2_ccecp_casci_s0):
mol, mf, mc = H2_ccecp_casci_s0
wf, to_opt = pyq.generate_wf(mol, mf, mc=mc)
old_parms = copy.deepcopy(wf.parameters)
lt = LinearTransform(wf.parameters, to_opt)
# Test serialize parameters
x0 = lt.serialize_parameters(wf.parameters)
x0 += np.random.normal(size=x0.shape)
for k, it in lt.deserialize(wf, x0).items():
assert wf.parameters[k].shape == it.shape
wf.parameters[k] = it
# to_opt is supposed to be false for both of these.
assert wf.parameters["wf1det_coeff"][0] == old_parms["wf1det_coeff"][0]
assert np.sum(wf.parameters["wf2bcoeff"][0] -
old_parms["wf2bcoeff"][0]) == 0
# While this one is supposed to change.
assert np.sum(wf.parameters["wf2bcoeff"][1] -
old_parms["wf2bcoeff"][1]) != 0
# Test serialize gradients
configs = pyq.initial_guess(mol, 10)
wf.recompute(configs)
pgrad = wf.pgradient()
pgrad_serial = lt.serialize_gradients(pgrad)
# Pgrad should be walkers, configs
assert pgrad_serial.shape[1] == x0.shape[0]
def test_transform(LiH_sto3g_rhf):
"""Tests that the shapes are ok"""
mol, mf = LiH_sto3g_rhf
wf, to_opt = pyq.generate_wf(mol, mf)
transform = LinearTransform(wf.parameters)
x = transform.serialize_parameters(wf.parameters)
nconfig = 10
configs = pyq.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 eval_configs(data, cutoffs):
"""
Evaluate values using the
regularization we have constructed
"""
mol, wf, to_opt, freeze = wavefunction()
eacc = EnergyAccumulator(mol)
transform = LinearTransform(wf.parameters, to_opt, freeze)
print("data loaded")
r2 = data['distance_squared']
weight = data['weight_total']
d = {}
for cutoff in list(cutoffs):
node_cut = r2 < cutoff**2
print(cutoff, node_cut.sum())
c = 7. / (cutoff**6)
b = -15. / (cutoff**4)
a = 9. / (cutoff**2)
l2 = r2[node_cut]
dpH = np.copy(data['dpH'])
dpH[node_cut] *= a * l2 + b * l2**2 + c * l2**3
hist, bin_edges = np.histogram(np.log10(np.abs(dpH)[np.abs(dpH) > 0]),
bins=200,
density=True,
weights=weight[np.abs(dpH) > 0])
d['hist' + str(cutoff)] = list(np.log10(hist)) + [None]
d['bins' + str(cutoff)] = bin_edges
df = pd.DataFrame(d)
df.to_pickle('histogram.pickle')
def viznode(node_coords, node_grad, cutoffs, vizfile='viznode.pdf'):
from wavefunction import wavefunction
mol, wf, to_opt, freeze = wavefunction()
eacc = EnergyAccumulator(mol)
transform = LinearTransform(wf.parameters, to_opt, freeze)
#Generate the distances we want
x = np.arange(np.sqrt(1 / 0.01), 1001)
x = 1. / x**2
x = np.append(x, np.linspace(0.01, 0.12, 100))
x = np.append(x, np.array([0, 1e-15, 1e-12, 1e-8] + [-y for y in x]))
x = np.sort(x)
coord_path = np.einsum('ij,l->lij', node_grad[0], x) + node_coords[0]
coord_path = OpenConfigs(coord_path)
#Move across the node in this path
val = wf.recompute(coord_path)
fig, ax = plt.subplots(nrows=2, ncols=1, figsize=(3, 6), sharex=True)
for k, cutoff in enumerate([1e-8] + cutoffs):
pgrad = PGradTransform_new(eacc,
transform,
nodal_cutoff=np.array([cutoff]))
d = pgrad(coord_path, wf)
total = d['total']
dpH = np.array(d['dpH'])[:, 0, 0]
if (cutoff == 1e-8):
ax[0].plot(x,
dpH * (val[0] * np.exp(val[1]))**2,
'k-',
label=r'$10^{' + str(int(np.log10(cutoff))) + '}$')
ax[1].plot(x, np.log10(dpH**2 * (val[0] * np.exp(val[1]))**2),
'k-')
else:
ax[0].plot(x,
dpH * (val[0] * np.exp(val[1]))**2,
'-',
label=r'$10^{' + str(int(np.log10(cutoff))) + '}$')
ax[1].plot(x, np.log10(dpH**2 * (val[0] * np.exp(val[1]))**2), '-')
ax[0].set_ylabel(r'$E_L\frac{\partial_p \Psi}{\Psi} f_\epsilon |\Psi|^2$')
ax[1].set_ylabel(
r'log$_{10}((E_L\frac{\partial_p \Psi}{\Psi})^2 f_\epsilon^2|\Psi|^2)$'
)
ax[1].set_xlabel(r'$l$ (Bohr)')
ax[0].set_xlim((-max(x) - 0.02, max(x) + 0.02))
ax[1].set_xlim((-max(x) - 0.02, max(x) + 0.02))
ax[0].legend(loc='best', title=r'$\epsilon$ (Bohr)')
plt.savefig(vizfile, bbox_inches='tight')
plt.close()
def collectconfigs(n, dump_file):
"""
Collect all the configurations from genconfig
into a single place
"""
dpH_total = []
weight_total = []
logweight_total = []
distance_squared = []
mol, wf, to_opt, freeze = wavefunction()
eacc = EnergyAccumulator(mol)
transform = LinearTransform(wf.parameters, to_opt, freeze)
pgrad_bare = PGradTransform_new(eacc, transform, 1e-20)
for i in range(1, n + 1):
print(i)
coords = OpenConfigs(pd.read_pickle('vmc/coords' + str(i) + '.pickle'))
df = pd.read_json('vmc/evals' + str(i) + '.json')
wf.recompute(coords)
print("Recomputed")
node_cut, r2 = pgrad_bare._node_cut(coords, wf)
print("nodes cut")
dpH = df['dpH'].values
wfval = df['wfval'].values
wfpval = df['wfpval'].values
logweight = 2 * (wfval - wfpval)
weight = np.exp(logweight)
print(i, weight[weight == 0])
dpH_total += list(dpH)
weight_total += list(weight)
logweight_total += list(logweight)
distance_squared += list(r2)
print(i, np.array(weight_total)[np.array(weight_total) == 0])
df = pd.DataFrame({
'dpH': dpH_total,
'weight_total': weight_total,
'logweight_total': logweight_total,
'distance_squared': distance_squared
})
df.to_pickle(dump_file)
return df
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():
from pyscf import lib, gto, scf
from pyqmc.accumulators import EnergyAccumulator, PGradTransform, LinearTransform
from pyqmc.multiplywf import MultiplyWF
from pyqmc.jastrow import Jastrow2B
from pyqmc.func3d import GaussianFunction
from pyqmc.slater import PySCFSlaterRHF
from pyqmc.mc import initial_guess
mol = gto.M(atom='H 0. 0. 0.; H 0. 0. 1.5',
basis='cc-pvtz',
unit='bohr',
verbose=5)
mf = scf.RHF(mol).run()
nconf = 2500
nsteps = 70
warmup = 20
coords = initial_guess(mol, nconf)
basis = {
'wf2coeff':
[GaussianFunction(0.2),
GaussianFunction(0.4),
GaussianFunction(0.6)]
}
wf = MultiplyWF(PySCFSlaterRHF(mol, mf), Jastrow2B(mol, basis['wf2coeff']))
params0 = {'wf2coeff': np.array([-0.8, -0.2, 0.4])}
for k, p in wf.parameters.items():
if k in params0:
wf.parameters[k] = params0[k]
energy_acc = EnergyAccumulator(mol)
pgrad_acc = PGradTransform(energy_acc, LinearTransform(wf.parameters))
# Gradient descent
wf, data = gradient_descent(wf,
coords,
pgrad_acc,
vmcoptions={'nsteps': nsteps},
warmup=warmup,
step=0.5,
eps=0.1,
maxiters=50,
datafile='sropt.json')
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 gradient_generator(mol, wf, to_opt=None, **ewald_kwargs):
return PGradTransform(EnergyAccumulator(mol, **ewald_kwargs),
LinearTransform(wf.parameters, to_opt))
def setuph2(r, obdm_steps=5):
from pyscf import gto, scf, lo
from pyqmc.accumulators import LinearTransform, EnergyAccumulator
from pyqmc.obdm import OBDMAccumulator
from pyqmc.cvmc import DescriptorFromOBDM, PGradDescriptor
import itertools
# ccECP from A. Annaberdiyev et al. Journal of Chemical Physics 149, 134108 (2018)
basis = {
"H":
gto.basis.parse("""
H S
23.843185 0.00411490
10.212443 0.01046440
4.374164 0.02801110
1.873529 0.07588620
0.802465 0.18210620
0.343709 0.34852140
0.147217 0.37823130
0.063055 0.11642410
""")
}
"""
H S
0.040680 1.00000000
H S
0.139013 1.00000000
H P
0.166430 1.00000000
H P
0.740212 1.00000000
"""
ecp = {
"H":
gto.basis.parse_ecp("""
H nelec 0
H ul
1 21.24359508259891 1.00000000000000
3 21.24359508259891 21.24359508259891
2 21.77696655044365 -10.85192405303825
""")
}
mol = gto.M(atom=f"H 0. 0. 0.; H 0. 0. {r}",
unit="bohr",
basis=basis,
ecp=ecp,
verbose=5)
mf = scf.RHF(mol).run()
mo_occ = mf.mo_coeff[:, mf.mo_occ > 0]
a = lo.iao.iao(mol, mo_occ)
a = lo.vec_lowdin(a, mf.get_ovlp())
obdm_up = OBDMAccumulator(mol=mol, orb_coeff=a, nstep=obdm_steps, spin=0)
obdm_down = OBDMAccumulator(mol=mol, orb_coeff=a, nstep=obdm_steps, spin=1)
wf = pyqmc.slater_jastrow(mol, mf)
freeze = {}
for k in wf.parameters:
freeze[k] = np.zeros(wf.parameters[k].shape, dtype='bool')
print(freeze.keys())
print(wf.parameters['wf1mo_coeff_alpha'])
#this freezing allows us to easily go between bonding and
# AFM configurations.
freeze['wf1mo_coeff_alpha'][0, 0] = True
freeze['wf1mo_coeff_beta'][1, 0] = True
descriptors = {
"t": [[(1.0, (0, 1)), (1.0, (1, 0))], [(1.0, (0, 1)), (1.0, (1, 0))]],
"trace": [[(1.0, (0, 0)), (1.0, (1, 1))], [(1.0, (0, 0)),
(1.0, (1, 1))]],
}
for i in [0, 1]:
descriptors[f"nup{i}"] = [[(1.0, (i, i))], []]
descriptors[f"ndown{i}"] = [[], [(1.0, (i, i))]]
acc = PGradDescriptor(
EnergyAccumulator(mol),
LinearTransform(wf.parameters, freeze=freeze),
[obdm_up, obdm_down],
DescriptorFromOBDM(descriptors, norm=2.0),
)
return {
"wf": wf,
"acc": acc,
"mol": mol,
"mf": mf,
"descriptors": descriptors
}
from wavefunction import wavefunction
if __name__ == '__main__':
nconfig_per_core = 100
ncore = 20
nsteps = 2000000
cutoffs = list(np.logspace(-8, -1, 20)) + list([
0.05, 0.075, 0.11, 0.12, 0.13, 0.14, 0.15, 0.16, 0.17, 0.18, 0.19, 0.20
])
cutoffs = np.sort(cutoffs)
mol, mf, mc, wf, to_opt, freeze = wavefunction(return_mf=True)
wf.parameters['wf1det_coeff'] *= 0
wf.parameters['wf1det_coeff'][[0, 10]] = 1. / np.sqrt(2.)
eacc = EnergyAccumulator(mol)
transform = LinearTransform(wf.parameters, to_opt, freeze)
pgrad = PGradTransform_new(eacc, transform, np.array(cutoffs))
#Client
cluster = LocalCluster(n_workers=ncore, threads_per_worker=1)
client = Client(cluster)
distvmc(wf,
pyqmc.initial_guess(mol, nconfig_per_core * ncore),
client=client,
accumulators={"pgrad": pgrad},
nsteps_per=100,
nsteps=nsteps,
hdf_file='dedp_vmc_local.hdf5')
def gradient_generator(mol, wf, to_opt=None, freeze=None):
return PGradTransform(EnergyAccumulator(mol),
LinearTransform(wf.parameters, to_opt, freeze))
def integratenode(node_coords,
node_grad,
vizfile='integratenode.pdf',
integ_range=1e-1,
poly=1e-2,
max_cutoff=0.1):
from wavefunction import wavefunction
import scipy.integrate as integrate
from numpy.polynomial import polynomial
mol, wf, to_opt, freeze = wavefunction()
eacc = EnergyAccumulator(mol)
transform = LinearTransform(wf.parameters, to_opt, freeze)
pgrad_bare = PGradTransform(eacc, transform, 1e-15)
#Integrate biases and variances
biases = []
biases_err = []
variances = []
cutoffs = list(np.logspace(-6, -1, 20)) + [0.05, 0.075]
'''
normalization = integrate.quad(lambda x: psi2(x, node_coords, node_grad, wf), -integ_range, integ_range, epsabs = 1e-15, epsrel = 1e-15)
for cutoff in cutoffs:
print(cutoff)
pgrad = PGradTransform_new(eacc, transform, nodal_cutoff = np.array([cutoff]))
bias = integrate.quad(lambda x: dpH(x, pgrad, pgrad_bare, node_coords, node_grad, wf)/1e-40, -cutoff, cutoff, epsabs = 1e-15, epsrel = 1e-15, points=[0])
variance = integrate.quad(lambda x: dpH2(x, pgrad, node_coords, node_grad, wf), -cutoff, cutoff, epsabs = 1e-15, epsrel = 1e-15, points=[0])
variance += integrate.quad(lambda x: dpH2(x, pgrad, node_coords, node_grad, wf), -integ_range + cutoff, integ_range - cutoff, epsabs = 1e-15, epsrel = 1e-15)
biases.append(bias[0]*1e-40/normalization[0])
variances.append(variance[0]/normalization[0])
df = pd.DataFrame({'cutoff': cutoffs, 'bias': biases, 'variance': variances})
df.to_pickle('integratenode.pickle')
'''
df = pd.read_pickle('integratenode.pickle')
#Fit theory curves and visualize
ind = np.argsort(df['cutoff'])
ind = ind[df['cutoff'].iloc[ind] <= max_cutoff]
fig, ax = plt.subplots(nrows=2, ncols=1, figsize=(3, 6), sharex=True)
x = df['cutoff'].iloc[ind]
y = np.abs(df['bias']).iloc[ind]
y = y[2:]
x = x[2:]
p = polynomial.polyfit(x, y, [3])
print("Fit for bias ", p)
xfit = np.linspace(min(x), max(x[x < poly]), 1000)
fit = p[3] * (xfit)**3
ax[0].plot(np.log10(x), np.log10(y), 'o')
ax[0].plot(np.log10(xfit), np.log10(fit), '--')
ax[0].set_ylabel(r'log$_{10}$(Bias)')
x = df['cutoff'].iloc[ind]
y = df['variance'].iloc[ind]
y = y[2:]
x = x[2:]
x = np.log10(x)
y = np.log10(y)
poly = np.log10(poly)
p = polynomial.polyfit(x[x < poly], y[x < poly], [1, 0])
print("Fit for variance ", p)
xfit = np.logspace(min(x), max(x[x <= poly]), 1000)
fit = p[0] + p[1] * np.log10(xfit)
ax[1].plot(x, y, 'o')
ax[1].plot(np.log10(xfit), fit, '--')
ax[1].set_xlabel(r'$log_{10}(\epsilon/$Bohr$)$')
ax[1].set_ylabel(r'log$_{10}$(Variance)')
#ax[1].set_xlim((-3.2, 2.3))
#ax[1].set_xticks(np.arange(-3,3))
plt.savefig(vizfile, bbox_inches='tight')
plt.close()
def test():
import parsl
from pyscf import lib, gto, scf
import numpy as np
import pandas as pd
import logging
from parsl.config import Config
from parsl.providers import LocalProvider
from parsl.channels import LocalChannel
from parsl.launchers import SimpleLauncher
from parsl.executors import ExtremeScaleExecutor
ncore = 4
config = Config(
executors=[
ExtremeScaleExecutor(label="Extreme_Local",
worker_debug=True,
ranks_per_node=ncore,
provider=LocalProvider(
channel=LocalChannel(),
init_blocks=1,
max_blocks=1,
launcher=SimpleLauncher()))
],
strategy=None,
)
parsl.load(config)
mol = gto.M(atom='H 0. 0. 0.; H 0. 0. 2.0',
unit='bohr',
ecp='bfd',
basis='bfd_vtz')
mf = scf.RHF(mol).run()
mol.output = None
mol.stdout = None
mf.output = None
mf.stdout = None
mf.chkfile = None
from pyqmc import ExpCuspFunction, GaussianFunction, MultiplyWF, PySCFSlaterRHF, JastrowSpin, initial_guess, EnergyAccumulator
from pyqmc.accumulators import PGradTransform, LinearTransform
nconf = 1600
basis = [
ExpCuspFunction(2.0, 1.5),
GaussianFunction(0.5),
GaussianFunction(2.0),
GaussianFunction(.25),
GaussianFunction(1.0),
GaussianFunction(4.0),
GaussianFunction(8.0)
]
wf = MultiplyWF(PySCFSlaterRHF(mol, mf), JastrowSpin(mol, basis, basis))
coords = initial_guess(mol, nconf)
energy_acc = EnergyAccumulator(mol)
pgrad_acc = PGradTransform(
energy_acc, LinearTransform(wf.parameters, ['wf2acoeff', 'wf2bcoeff']))
from pyqmc.optsr import gradient_descent
gradient_descent(wf,
coords,
pgrad_acc,
vmc=distvmc,
vmcoptions={
'npartitions': ncore,
'nsteps': 100,
'nsteps_per': 100
})