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https://github.com/TREX-CoE/trexio.git
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391 lines
14 KiB
Python
391 lines
14 KiB
Python
#!/usr/bin/env python3
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import numpy as np
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import pytest
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import trexio
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from benzene_data import *
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def clean(back_end, filename):
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"""Remove test files."""
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if back_end == trexio.TREXIO_HDF5:
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import os
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try:
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os.remove(filename)
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os.remove('unsafe_' + filename)
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except FileNotFoundError:
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pass
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else:
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import shutil
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try:
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shutil.rmtree(filename)
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shutil.rmtree('unsafe_' + filename)
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except FileNotFoundError:
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pass
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def test_info():
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"""Print the output of the trexio.info function."""
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trexio.info()
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def test_void():
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"""Check raise of an error upon I/O on non-existing file."""
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with pytest.raises(trexio.Error):
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_ = trexio.File('void.file', 'r', trexio.TREXIO_TEXT)
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def test_orbital_list():
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"""Convert one determinant into a list of orbitals."""
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orb_list_up, orb_list_dn = trexio.to_orbital_list_up_dn(int64_num, det_test)
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assert orb_list_up[0] == 0
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assert orb_list_dn[0] == 1
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def test_bitfield_list():
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"""Convert lists of occupied up- and down-spin orbitals into determinants."""
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# convert det_test list into a numpy array for .all() assertion to work
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det_test_np = np.array(det_test, dtype=np.int64)
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det_list_up = trexio.to_bitfield_list(int64_num, orb_up_test)
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assert (det_list_up == det_test_np[:int64_num]).all()
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det_list_dn = trexio.to_bitfield_list(int64_num, orb_dn_test)
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assert (det_list_dn == det_test_np[int64_num:]).all()
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class TestIO:
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"""Unit tests for writing/reading different blocks of the TREXIO file."""
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@pytest.fixture(autouse=True)
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def setup(self, backend):
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self.mode = 'w'
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self.test_file = None
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if backend == 'hdf5':
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self.back_end = trexio.TREXIO_HDF5
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self.filename = 'test_file_py.h5'
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elif backend == 'text':
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self.back_end = trexio.TREXIO_TEXT
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self.filename = 'test_file_py.dir'
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else:
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raise ValueError("Wrong TREXIO back-end supplied to pytest.")
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def test_clean(self):
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"""Clean existing files."""
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clean(self.back_end, self.filename)
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#def __del__(self):
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# """Class destructor."""
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# if self.test_file:
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# if self.test_file.isOpen:
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# self.test_file.close()
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def open(self, filename=None, mode=None, back_end=None):
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"""Create a TREXIO file and open it for writing."""
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if not filename:
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filename = self.filename
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else:
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self.filename = filename
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if not mode:
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mode = self.mode
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else:
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self.mode = mode
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if not back_end:
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back_end = self.back_end
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else:
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self.back_end = back_end
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self.test_file = trexio.File(filename, mode, back_end)
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assert self.test_file.exists
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def test_close(self):
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"""Close the file."""
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self.open()
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if self.test_file.isOpen:
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self.test_file.close()
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assert not self.test_file.isOpen
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def test_errors(self):
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"""Test some exceptions based on trexio.Error class."""
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self.open(filename='unsafe_' + self.filename, mode='w', back_end=self.back_end)
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# try to write a negative number (should raise an error)
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with pytest.raises(trexio.Error):
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trexio.write_nucleus_num(self.test_file, -100)
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trexio.write_nucleus_num(self.test_file, nucleus_num)
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# try to overwrite a number (should raise an error)
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with pytest.raises(trexio.Error):
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trexio.write_nucleus_num(self.test_file, nucleus_num * 2)
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if self.test_file.isOpen:
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self.test_file.close()
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def test_num(self):
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"""Write a number."""
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self.open()
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trexio.write_nucleus_num(self.test_file, nucleus_num)
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assert trexio.has_nucleus_num(self.test_file)
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if self.test_file.isOpen:
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self.test_file.close()
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def test_str(self):
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"""Write a string."""
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self.open()
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trexio.write_nucleus_point_group(self.test_file, point_group)
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assert trexio.has_nucleus_point_group(self.test_file)
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if self.test_file.isOpen:
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self.test_file.close()
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def test_array_str(self):
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"""Write an array of strings."""
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self.open()
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if not trexio.has_nucleus_num(self.test_file):
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self.test_num()
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trexio.write_nucleus_label(self.test_file, nucleus_label)
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assert trexio.has_nucleus_label(self.test_file)
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if self.test_file.isOpen:
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self.test_file.close()
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def test_array_1D(self):
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"""Write array of charges."""
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self.open()
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if not trexio.has_nucleus_num(self.test_file):
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self.test_num()
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trexio.write_nucleus_charge(self.test_file, nucleus_charge)
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assert trexio.has_nucleus_charge(self.test_file)
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if self.test_file.isOpen:
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self.test_file.close()
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def test_array_2D(self):
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"""Write array of coordinates."""
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self.open()
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if not trexio.has_nucleus_num(self.test_file):
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self.test_num()
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trexio.write_nucleus_coord(self.test_file, nucleus_coord)
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assert trexio.has_nucleus_coord(self.test_file)
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if self.test_file.isOpen:
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self.test_file.close()
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def test_indices(self):
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"""Write array of indices."""
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self.open()
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# type cast is important here because by default numpy transforms a list of integers into int64 array
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indices_np = np.array(nucleus_index, dtype=np.int64)
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# first write basis_shell_num because it is needed to check dimensions of basis_nucleus_index
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trexio.write_basis_shell_num(self.test_file, basis_shell_num)
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# now write the indices
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trexio.write_basis_nucleus_index(self.test_file, indices_np)
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assert trexio.has_basis_nucleus_index(self.test_file)
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if self.test_file.isOpen:
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self.test_file.close()
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def test_sparse(self):
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"""Write a sparse array."""
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self.open()
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# write ao_num (needed later to write sparse ao_2e_int_eri integrals)
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trexio.write_ao_num(self.test_file, ao_num)
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# one complete write (no chunking)
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offset = 0
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trexio.write_ao_2e_int_eri(self.test_file, offset, num_integrals, indices, values)
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assert trexio.has_ao_2e_int_eri(self.test_file)
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if self.test_file.isOpen:
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self.test_file.close()
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def test_determinant(self):
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"""Write CI determinants and coefficients."""
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self.open()
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# write mo_num (needed later to write determinants)
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trexio.write_mo_num(self.test_file, mo_num)
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# get the number of bit-strings per spin component
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int_num = trexio.get_int64_num(self.test_file)
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assert int_num == int64_num
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# write the data for the ground state
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offset = 0
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trexio.write_state_id(self.test_file, 0)
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trexio.write_determinant_list(self.test_file, offset, det_num, dets)
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assert trexio.has_determinant_list(self.test_file)
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trexio.write_determinant_coefficient(self.test_file, offset, det_num, coeffs)
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assert trexio.has_determinant_coefficient(self.test_file)
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# manually check the consistency between coefficient_size and number of determinants
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assert trexio.read_determinant_coefficient_size(self.test_file) == trexio.read_determinant_num(self.test_file)
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if self.test_file.isOpen:
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self.test_file.close()
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def test_delete_group(self):
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"""Delete a group."""
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self.open(filename='unsafe_' + self.filename, mode='u', back_end=self.back_end)
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trexio.write_nucleus_num(self.test_file, nucleus_num)
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trexio.write_nucleus_charge(self.test_file, nucleus_charge)
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trexio.flush(self.test_file)
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assert trexio.has_nucleus_num(self.test_file)
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assert trexio.has_nucleus_charge(self.test_file)
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assert trexio.has_nucleus(self.test_file)
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trexio.delete_nucleus(self.test_file)
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assert not trexio.has_nucleus_num(self.test_file)
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assert not trexio.has_nucleus_charge(self.test_file)
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assert not trexio.has_nucleus(self.test_file)
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if self.test_file.isOpen:
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self.test_file.close()
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def test_has_group(self):
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"""Check existense of a group."""
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self.open()
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assert trexio.has_nucleus(self.test_file)
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assert not trexio.has_rdm(self.test_file)
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if self.test_file.isOpen:
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self.test_file.close()
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def test_context_manager(self):
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"""Test the with ... as ... context handling."""
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with trexio.File(filename=self.filename, mode='u', back_end=self.back_end) as tfile:
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trexio.write_metadata_description(tfile, 'Test file produced by the Python API')
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assert trexio.has_metadata_description(tfile)
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assert tfile.isOpen
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# the file handle can remain existing but the file itself is closed upon exit from the `with` block
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assert not tfile.isOpen
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def test_read_num(self):
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"""Read a number."""
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self.open(mode='r')
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num_r = trexio.read_nucleus_num(self.test_file)
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assert num_r == nucleus_num
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if self.test_file.isOpen:
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self.test_file.close()
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def test_read_array_1D(self):
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"""Read an array."""
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self.open(mode='r')
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charges_np_r = trexio.read_nucleus_charge(self.test_file)
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assert charges_np_r.dtype is np.dtype(np.float64)
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assert charges_np_r.size == nucleus_num
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np.testing.assert_array_almost_equal(charges_np_r, np.array(nucleus_charge), decimal=8)
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if self.test_file.isOpen:
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self.test_file.close()
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def test_read_array_2D(self):
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"""Read an array."""
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self.open(mode='r')
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# read nuclear coordinates without providing optional argument dim
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coords_np = trexio.read_nucleus_coord(self.test_file)
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assert coords_np.dtype is np.dtype(np.float64)
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assert coords_np.size == nucleus_num * 3
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np.testing.assert_array_almost_equal(coords_np, np.array(nucleus_coord).reshape(nucleus_num,3), decimal=8)
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if self.test_file.isOpen:
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self.test_file.close()
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def test_read_errors(self):
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"""Test some reading errors."""
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self.open(mode='r')
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# unsafe call to read_safe should fail with error message corresponding to TREXIO_UNSAFE_ARRAY_DIM
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with pytest.raises(trexio.Error):
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_ = trexio.read_nucleus_charge(self.test_file, dim=nucleus_num/2)
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if self.test_file.isOpen:
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self.test_file.close()
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def test_read_integers(self):
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"""Read some integer arrays."""
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self.open(mode='r')
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indices_np_16 = trexio.read_basis_nucleus_index(self.test_file, dtype=np.int16)
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assert indices_np_16.dtype is np.dtype(np.int16)
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assert (indices_np_16 == np.array(nucleus_index)).all()
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indices_np_32 = trexio.read_basis_nucleus_index(self.test_file, dtype=np.int32)
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assert indices_np_32.dtype is np.dtype(np.int32)
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assert (indices_np_32 == np.array(nucleus_index)).all()
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indices_np_64 = trexio.read_basis_nucleus_index(self.test_file)
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assert indices_np_64.dtype is np.dtype(np.int64)
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assert indices_np_64.size == basis_shell_num
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assert (indices_np_64 == np.array(nucleus_index)).all()
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if self.test_file.isOpen:
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self.test_file.close()
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def test_sparse_read(self):
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"""Read a sparse array."""
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self.open(mode='r')
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# read sparse arrays on ao_2e_int_eri integrals
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buf_size = 60
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offset_file = 0
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# read full buf_size (i.e. the one that does not reach EOF)
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indices_sparse_np, value_sparse_np, read_buf_size, eof = trexio.read_ao_2e_int_eri(self.test_file, offset_file, buf_size)
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#print(f'First complete sparse read size: {read_buf_size}')
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assert not eof
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assert read_buf_size == buf_size
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assert indices_sparse_np[0][0] == 0
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assert indices_sparse_np[read_buf_size-1][3] == read_buf_size * 4 - 1
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offset_file += buf_size
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# read incomplete buf_size (i.e. the one that does reach EOF)
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indices_sparse_np, value_sparse_np, read_buf_size, eof = trexio.read_ao_2e_int_eri(self.test_file, offset_file, buf_size)
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#print(f'Second incomplete sparse read size: {read_buf_size}')
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assert eof
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assert read_buf_size == (num_integrals - buf_size)
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assert indices_sparse_np[0][0] == offset_file * 4
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assert indices_sparse_np[read_buf_size-1][3] == (offset_file + read_buf_size) * 4 - 1
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if self.test_file.isOpen:
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self.test_file.close()
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def test_determinant_read(self):
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"""Read the CI determinants."""
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self.open(mode='r')
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# read determinants (list of ints and float coefficients)
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buf_size = 100
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offset_file = 0
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# read full buf_size (i.e. the one that does not reach EOF)
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dets_np, read_buf_size, eof = trexio.read_determinant_list(self.test_file, offset_file, buf_size)
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#print(f'First complete read of determinant list: {read_buf_size}')
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assert not eof
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assert read_buf_size == buf_size
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assert dets_np[0][0] == 0
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assert dets_np[read_buf_size-1][int64_num*2-1] == read_buf_size * int64_num * 2- 1
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coefficients_np, read_buf_size, eof = trexio.read_determinant_coefficient(self.test_file, offset_file, buf_size)
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#print(f'First complete read of determinant coefficients: {read_buf_size}')
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assert not eof
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assert read_buf_size == buf_size
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if self.test_file.isOpen:
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self.test_file.close()
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def test_array_str_read(self):
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"""Read an array of strings."""
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self.open(mode='r')
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labels_r = trexio.read_nucleus_label(self.test_file)
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assert len(labels_r) == nucleus_num
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assert labels_r == nucleus_label
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if self.test_file.isOpen:
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self.test_file.close()
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def test_str_read(self):
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"""Read a string."""
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self.open(mode='r')
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point_group_r = trexio.read_nucleus_point_group(self.test_file)
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assert point_group_r == point_group
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if self.test_file.isOpen:
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self.test_file.close()
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