Development

.github/workflows/build.yml

@@ -10,7 +10,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        version: ['3.8', '3.10']
+        version: ['3.8']
 
     steps:
     - name: Cancel Previous Runs
@@ -27,23 +27,23 @@ jobs:
     - name: Install essential
       run: |
         sudo apt update
-        sudo apt install build-essential
+        sudo apt install build-essential pandoc
     - name: Install conda packages
       run: |
         conda install -c anaconda cmake
-        conda install mpi4py h5py pytorch==2.0.0 torchvision==0.15.0 cpuonly -c pytorch -c conda-forge
+        conda install rdkit mpi4py h5py pytorch==2.0.0 torchvision==0.15.0 cpuonly -c pytorch -c conda-forge
         conda install -c conda-forge libstdcxx-ng
         conda install -c anaconda gxx_linux-64
 
     - name: Install the package
-      run: python -m pip install .[test,hpc]
+      run: python -m pip install .[test,hpc,doc]
       env:
         CONDA_PREFIX: /usr/share/miniconda
 
-    - name: Test with multithreading
-      env:
-        CONDA_PREFIX: /usr/share/miniconda
-      run: mpirun -np 2 coverage run -m pytest tests_hvd
+    # - name: Test with multithreading
+    #   env:
+    #     CONDA_PREFIX: /usr/share/miniconda
+    #   run: mpirun -np 2 coverage run -m pytest tests_hvd
 
     - name: Test with single thread
       env:

.prospector.yml

@@ -26,4 +26,5 @@ pep257:
         D212,  # Multi-line docstring summary should start at the first line
         D213,  # Multi-line docstring summary should start at the second line
         D404,  # First word of the docstring should not be This
+        R0913, # too many arguments
     ]

CHANGELOG.rst

@@ -2,6 +2,32 @@
 Change Log
 ##########
 
+
+0.4.0 [Unreleased]
+******************
+
+Change
+---------
+
+* Change sugnature of Jastrow and Baclflow modules (#174)
+* Limit testing to Python 3.8 (#174)
+
+
+0.3.3 [Released]
+******************
+
+Change
+-----------
+
+* Fig bug in the AO norm (#172)
+
+0.3.2 [Released]
+******************
+
+Change
+----------
+* Fix a minor OSX bug regarding torch type cast to int
+
 0.3.1 [Released]
 *****************
 

README.md

@@ -8,6 +8,7 @@ Pytorch Implementation of Real Space Quantum Monte Carlo Simulations of Molecula
 [![Codacy Badge](https://app.codacy.com/project/badge/Grade/1c52407422a7428083968833341b5945)](https://app.codacy.com/gh/NLESC-JCER/QMCTorch/dashboard?utm_source=gh&utm_medium=referral&utm_content=&utm_campaign=Badge_grade)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3780094.svg)](https://doi.org/10.5281/zenodo.3780094)
 [![DOI](https://joss.theoj.org/papers/10.21105/joss.05472/status.svg)](https://doi.org/10.21105/joss.05472)
+[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
 
 ## Installation
 

bin/qmctorch_energy_plotter

@@ -0,0 +1,55 @@
+#!/usr/bin/env python
+import h5py
+import matplotlib.pyplot as plt
+import argparse
+
+
+def get_energy(mol):
+    with h5py.File(mol, 'r') as f5:
+        data = f5['wf_opt']['energy'][()]
+    return data
+
+
+def get_correlation_energy(e, e0, ehf):
+    return 1 - (e-e0)/(ehf-e0)
+
+
+def plot_percent_correlation_energy(args):
+
+    nepoch = args.num_epoch
+    energy = []
+    percent_correlation_energy = []
+    for mol in args.filename:
+        e = get_energy(mol)[:nepoch]
+        print(e[-1])
+        energy.append(e)
+        percent_correlation_energy.append(
+            get_correlation_energy(e, args.exact_energy, args.hf_energy))
+
+    plt_fn = plt.plot
+    if args.semi_logy:
+        plt_fn = plt.semilogy
+
+    for ec in percent_correlation_energy:
+        plt_fn(ec)
+    plt.show()
+
+
+if __name__ == "__main__":
+
+    parser = argparse.ArgumentParser()
+    parser.add_argument('filename', nargs='+',
+                        help='name of the files')
+    parser.add_argument('-l', '--labels', nargs='+',
+                        help='label of the data')
+    parser.add_argument('-ne', '--num_epoch', type=int,
+                        default=-1, help='Number of epcoh to plot')
+    parser.add_argument('-e0', '--exact_energy', type=float,
+                        default=None, help='True exact energy of thre system')
+    parser.add_argument('-ehf', '--hf_energy', type=float,
+                        default=None, help='Hartree Fock energy of thre system')
+    parser.add_argument('-log', '--semi_logy', action='store_true',
+                        help='plot on semilog y axis')
+    args = parser.parse_args()
+
+    plot_percent_correlation_energy(args)

docs/conf.py

@@ -262,4 +262,5 @@
 
 autoclass_content = 'init'
 autodoc_member_order = 'bysource'
-nbsphinx_allow_errors = True
+nbsphinx_allow_errors = True
+nbsphinx_execute = 'never'

docs/example/autocorrelation/h2.py

@@ -0,0 +1,53 @@
+import torch
+from torch import optim
+
+from qmctorch.sampler import Metropolis
+from qmctorch.scf import Molecule
+from qmctorch.solver import Solver
+from qmctorch.utils.plot_data import plot_correlation_coefficient, plot_integrated_autocorrelation_time
+from qmctorch.wavefunction.slater_jastrow import SlaterJastrow
+from qmctorch.wavefunction.jastrows.elec_elec import JastrowFactor, PadeJastrowKernel
+torch.manual_seed(0)
+
+# molecule
+mol = Molecule(
+    atom='H 0 0 -0.69; H 0 0 0.69',
+    unit='bohr',
+    calculator='pyscf',
+    basis='sto-3g')
+
+
+# jastrow
+jastrow = JastrowFactor(mol, PadeJastrowKernel)
+
+# wave funtion
+wf = SlaterJastrow(mol, kinetic='auto',
+                   jastrow=jastrow,
+                   configs='single(2,2)')
+
+# sampler
+sampler = Metropolis(
+    nwalkers=10,
+    nstep=1000,
+    ntherm=0,
+    ndecor=1,
+    step_size=0.5,
+    ndim=wf.ndim,
+    nelec=wf.nelec,
+    init=mol.domain('normal'),
+    move={
+        'type': 'all-elec',
+        'proba': 'normal'})
+
+opt = optim.Adam(wf.parameters(), lr=0.01)
+
+solver = Solver(wf=wf, sampler=sampler, optimizer=opt)
+
+pos = solver.sampler(wf.pdf)
+obs = solver.sampling_traj(pos)
+
+rho, tau = plot_correlation_coefficient(obs.local_energy)
+print(f'fit exp(-x/tau), tau={tau}')
+iat = plot_integrated_autocorrelation_time(
+    obs.local_energy, rho=rho, C=5)
+print(f"integrated autocorrelation time: {iat}")

docs/example/backflow/backflow.py

@@ -3,8 +3,13 @@
 from torch import nn
 
 from qmctorch.scf import Molecule
+
+from qmctorch.wavefunction.orbitals.backflow import BackFlowTransformation
 from qmctorch.wavefunction.orbitals.backflow.kernels import BackFlowKernelBase
-from qmctorch.wavefunction import SlaterJastrowBackFlow
+
+
+from qmctorch.wavefunction.slater_jastrow import SlaterJastrow
+from qmctorch.wavefunction.jastrows.elec_elec import JastrowFactor, PadeJastrowKernel
 
 
 class MyBackflow(BackFlowKernelBase):
@@ -25,11 +30,17 @@ def forward(self, x):
 mol = Molecule(atom='Li 0. 0. 0.; H 3.14 0. 0.', unit='angs',
                calculator='pyscf', basis='sto-3g', name='LiH')
 
+# jastrow
+jastrow = JastrowFactor(mol, PadeJastrowKernel)
+
+# backflow
+backflow = BackFlowTransformation(mol, MyBackflow, {'size': 64})
+
 # define the wave function
-wf = SlaterJastrowBackFlow(mol, kinetic='jacobi',
-                           backflow_kernel=MyBackflow,
-                           backflow_kernel_kwargs={'size': 64},
-                           configs='single_double(2,2)')
+wf = SlaterJastrow(mol, kinetic='jacobi',
+                   jastrow=jastrow,
+                   backflow=backflow,
+                   configs='single_double(2,2)')
 
 pos = torch.rand(10, wf.nelec*3)
 print(wf(pos))

docs/example/gpu/h2.py

@@ -1,6 +1,7 @@
 from torch import optim
 
 from qmctorch.scf import Molecule
+from qmctorch.wavefunction.jastrows.elec_elec import JastrowFactor, PadeJastrowKernel
 from qmctorch.wavefunction import SlaterJastrow
 from qmctorch.solver import Solver
 from qmctorch.sampler import Metropolis
@@ -20,9 +21,14 @@
                basis='dzp',
                unit='bohr')
 
+
+# jastrow
+jastrow = JastrowFactor(mol, PadeJastrowKernel)
+
 # define the wave function
 wf = SlaterJastrow(mol, kinetic='jacobi',
                    configs='cas(2,2)',
+                   jastrow=jastrow,
                    cuda=True)
 
 # sampler

docs/example/horovod/h2.py

@@ -22,9 +22,9 @@
 set_torch_double_precision()
 
 # define the molecule
-mol = Molecule(atom='H 0 0 -0.69; H 0 0 0.69',
+mol = Molecule(atom='H 0 0 -0.69; H 0 0 0.69', unit='bohr',
                calculator='pyscf', basis='sto-3g',
-               unit='bohr', rank=hvd.local_rank())
+               rank=hvd.local_rank(), mpi_size=hvd.local_size())
 
 
 # define the wave function

docs/example/optimization/h2.py

@@ -1,39 +1,47 @@
-
+import torch
+import numpy as np
 from torch import optim
 
 from qmctorch.scf import Molecule
-from qmctorch.wavefunction import SlaterJastrow
+
 from qmctorch.solver import Solver
-from qmctorch.sampler import Metropolis
+from qmctorch.sampler import Metropolis, Hamiltonian
 from qmctorch.utils import set_torch_double_precision
-from qmctorch.utils import (plot_energy, plot_data)
-
-from qmctorch.wavefunction.jastrows.elec_elec.kernels import PadeJastrowKernel
+from qmctorch.utils.plot_data import (plot_energy, plot_data)
+from qmctorch.wavefunction.slater_jastrow import SlaterJastrow
+from qmctorch.wavefunction.jastrows.elec_elec import JastrowFactor, PadeJastrowKernel
 
 # bond distance : 0.74 A -> 1.38 a
 # optimal H positions +0.69 and -0.69
 # ground state energy : -31.688 eV -> -1.16 hartree
 # bond dissociation energy 4.478 eV -> 0.16 hartree
 
 set_torch_double_precision()
+torch.random.manual_seed(0)
+np.random.seed(0)
 
 # define the molecule
 mol = Molecule(atom='H 0 0 -0.69; H 0 0 0.69',
                calculator='pyscf',
                basis='sto-3g',
                unit='bohr')
 
+# jastrow
+jastrow = JastrowFactor(mol, PadeJastrowKernel)
+
 # define the wave function
 wf = SlaterJastrow(mol, kinetic='jacobi',
                    configs='single_double(2,2)',
-                   jastrow_kernel=PadeJastrowKernel).gto2sto()
+                   jastrow=jastrow)
 
 # sampler
-sampler = Metropolis(nwalkers=5000,
-                     nstep=200, step_size=0.2,
-                     ntherm=-1, ndecor=100,
-                     nelec=wf.nelec, init=mol.domain('atomic'),
-                     move={'type': 'all-elec', 'proba': 'normal'})
+# sampler = Hamiltonian(nwalkers=100, nstep=100, nelec=wf.nelec,
+#                       step_size=0.1, L=30,
+#                       ntherm=-1, ndecor=10,
+#                       init=mol.domain('atomic'))
+
+sampler = Metropolis(nwalkers=10, nstep=200, nelec=wf.nelec, ntherm=100, ndecor=10,
+                     step_size=0.05, init=mol.domain('atomic'))
 
 # optimizer
 lr_dict = [{'params': wf.jastrow.parameters(), 'lr': 1E-2},
@@ -46,23 +54,24 @@
 scheduler = optim.lr_scheduler.StepLR(opt, step_size=10, gamma=0.90)
 
 # QMC solver
-solver = Solver(wf=wf, sampler=sampler,
-                             optimizer=opt, scheduler=None)
+solver = Solver(wf=wf, sampler=sampler, optimizer=opt, scheduler=None)
 
 # perform a single point calculation
-obs = solver.single_point()
+# obs = solver.single_point()
 
 # configure the solver
 solver.configure(track=['local_energy', 'parameters'], freeze=['ao'],
                  loss='energy', grad='manual',
                  ortho_mo=False, clip_loss=False,
                  resampling={'mode': 'update',
                              'resample_every': 1,
-                             'nstep_update': 25})
+                             'nstep_update': 150,
+                             'ntherm_update': 50}
+                 )
 
 # optimize the wave function
-obs = solver.run(50)
+obs = solver.run(5)  # , batchsize=10)
 
 # plot
-plot_energy(obs.local_energy, e0=-1.1645, show_variance=True)
-plot_data(solver.observable, obsname='jastrow.jastrow_kernel.weight')
+# plot_energy(obs.local_energy, e0=-1.1645, show_variance=True)
+# plot_data(solver.observable, obsname='jastrow.weight')

docs/example/scf/scf.py

@@ -2,9 +2,9 @@
 
 # Select the SCF calculator
 calc = ['pyscf',            # pyscf  
-        'adf',          # adf 2019 
-        'adf2019'               # adf 2020+
-    ][0]
+        'adf',              # adf 2020+ 
+        'adf2019'           # adf 2019
+    ][1]
 
 # select an appropriate basis
 basis = {
@@ -17,7 +17,8 @@
 mol = Molecule(atom='H 0 0 -0.69; H 0 0 0.69',
             calculator=calc,
             basis=basis,
-            unit='bohr')
+            unit='bohr',
+            redo_scf=True)