def test_random_distance():
system = System(box_size=[10, 10, 10])
methane = Molecule(os.path.join(here, 'data', 'methane.xyz'))
system.add_molecules(methane, n=4)
config = system.random(min_dist_threshold=1.5)
for coord in config.coordinates():
assert np.min(coord) > 0.0
assert np.max(coord) < 10 - 1.5
def test_perturbation():
system = System(box_size=[7, 7, 7])
system.add_molecules(h2o, n=5)
config = system.random(min_dist_threshold=1.5, sigma=0.1, max_length=0.2)
pcoords = config.coordinates()
# Adding a displacement to each atom should still afford a reasonably
# sensible structure (no short distances)
dist_matrix = distance_matrix(pcoords, pcoords)
dist_matrix += np.identity(len(pcoords))
assert np.min(dist_matrix) > 0.6
def test_density():
"""Test the density calculation with a few water boxes"""
req_density = 1.0
mw = 18.02 # Density of water
for n_waters in [1, 2, 3, 5, 7, 127]:
length = (((mw * n_waters / (6.022E23 * req_density)) / 1E6)**(1 / 3) *
1E10)
system = System(box_size=[length, length, length])
system.add_molecules(h2o, n=n_waters)
assert np.abs(system.density - req_density) < 1E-3
def test_autode_parallel_orca():
if 'GT_ORCA' not in os.environ or not os.environ['GT_ORCA'] == 'True':
return
# Check that orca runs work
water = System(box_size=[10, 10, 10])
water.add_molecules(h2o, n=2)
configs = Data()
for _ in range(3):
configs += water.random(with_intra=True)
configs.parallel_orca()
def test_autode_xtb():
if 'GT_XTB' not in os.environ or not os.environ['GT_XTB'] == 'True':
return
# Check that orca and xtb runs work
water = System(box_size=[10, 10, 10])
water.add_molecules(h2o, n=5)
config = water.random()
config.run_xtb()
assert config.energy is not None
assert config.forces is not None
def test_print_gro_file():
water_box = System(box_size=[10, 10, 10])
water_box.add_molecules(molecule=get_solvent('h2o'), n=10)
for molecule in water_box.molecules:
molecule.set_mm_atom_types()
config = Configuration(system=water_box)
config.wrap()
config.print_gro_file(system=water_box)
assert os.path.exists('input.gro')
os.remove('input.gro')
def test_n_mols():
system = System(box_size=[5, 5, 5])
system.add_molecules(methane, n=1)
system.add_molecules(h2o, n=1)
assert system.n_unique_molecules == 2
system.add_molecules(h2o, n=5)
assert system.n_unique_molecules == 2
def test_grid_positions():
n_molecules = 10
density = 0.786 # g cm-3
mw = 3 * 1.01 + 2 * 12.01 + 14.01
length = ((mw * n_molecules / (6.022E23 * density)) / 1E6)**(1 / 3) * 1E10
system = System(box_size=[length, length, length])
system.add_molecules(Molecule(os.path.join(here, 'data', 'mecn.xyz')),
n=n_molecules)
config = system.grid(min_dist_threshold=1.7)
config.save(filename='test_random.xyz')
assert os.path.exists('test_random.xyz')
os.remove('test_random.xyz')
def test_random_grid_positions():
system = System(box_size=[10, 12, 14])
methane = Molecule(os.path.join(here, 'data', 'methane.xyz'))
system.add_molecules(methane, n=5)
config = system.random(grid=True)
config.save(filename='test_random.xyz')
# Minimum pairwise distance should be ~ the C-H distance (1.109 Å)
atoms = xyz_file_to_atoms('test_random.xyz')
coords = np.array([atom.coord for atom in atoms])
dist_matrix = distance_matrix(coords, coords)
# Distance matrix has zeros along the diagonals so add the identity
assert np.min(dist_matrix + 9 * np.identity(len(coords))) > 1.1
os.remove('test_random.xyz')
def test_histogram():
water_dimer = System(box_size=[7, 7, 7])
water_dimer.add_molecules(h2o, n=2)
data = Data(name='test')
data += water_dimer.random()
# Can't histogram energies and forces with no energies
with pytest.raises(NoEnergy):
data.histogram(name='test')
data[0].energy = 1
data[0].forces = np.zeros(shape=(6, 3))
data.histogram(name='test')
assert os.path.exists('test.png')
os.remove('test.png')
def test_gap():
water_dimer = System(box_size=[7, 7, 7])
water_dimer.add_molecules(h2o, n=2)
data = Data(name='test')
for _ in range(2):
data += water_dimer.random()
assert len(data) == 2
coords1 = data[0].coordinates()
assert coords1.shape == (6, 3)
coords2 = data[1].coordinates()
# Coordinates should be somewhat different
assert np.min(distance_matrix(coords1, coords2)) > 1E-3
def test_dftb_plus():
water_box = System(box_size=[5, 5, 5])
config = water_box.configuration()
config.set_atoms(xyz_filename=os.path.join(here, 'data', 'h2o_10.xyz'))
if 'GT_DFTB' not in os.environ or not os.environ['GT_DFTB'] == 'True':
return
config.run_dftb()
assert config.energy is not None
forces = config.forces
assert type(forces) is np.ndarray
assert forces.shape == (30, 3)
# Should all be non-zero length force vectors in ev Å^-1
assert all(0 < np.linalg.norm(force) < 70 for force in forces)
def test_load():
xyz_path = os.path.join(here, 'data', 'configs.xyz')
configs = ConfigurationSet()
configs.load(xyz_path)
assert len(configs) == 2
# Should default to uncharged singlet
for config in configs:
assert config.box is not None
assert config.charge == 0
assert config.mult == 1
zn_aq = System(gt.Ion('Zn', charge=2), box_size=[12, 12, 12])
zn_aq.add_solvent('h2o', n=52)
configs = ConfigurationSet()
configs.load(xyz_path, system=zn_aq)
for config in configs:
assert config.box is not None
assert config.charge == 2
assert config.mult == 1
configs = ConfigurationSet()
configs.load(xyz_path, charge=2)
for config in configs:
assert config.box is not None
assert config.charge == 2
assert config.mult == 1
with open('tmp.xyz', 'w') as test_xyz:
print('1\n', file=test_xyz)
# Should fail to load with no atoms in the xyz file
configs = ConfigurationSet()
with pytest.raises(LoadingFailed):
configs.load(filename='tmp.xyz')
os.remove('tmp.xyz')
def test_with_charges():
# Slightly modified ASE calculator to be compatible with the latest DFTB+
calculator = DFTB()
assert isinstance(calculator, Dftb)
# Can't get the fermi level with no calculation run
with pytest.raises(TypeError):
calculator.read_fermi_levels()
if 'GT_DFTB' not in os.environ or not os.environ['GT_DFTB'] == 'True':
return
# Check that charges work
na_water = System(box_size=[10, 10, 10])
na_water.add_molecules(Ion('Na', charge=1), n=1)
na_water.add_molecules(h2o, n=5)
assert na_water.charge() == 1
config = na_water.random()
config.run_dftb()
def test_system():
system = System(box_size=[5, 5, 5])
# No molecules yet in the system
assert len(system) == 0
system += h2o
assert len(system) == 1
system.add_molecules(h2o, 10)
assert len(system) == 11
two_waters = [h2o, h2o]
system += two_waters
assert len(system) == 13
assert system.n_unique_molecules == 1
assert str(system) == 'H2O_13' or str(system) == 'OH2_13'
# Should be able to print an xyz file of the configuration
system.configuration().save(filename='test.xyz')
assert os.path.exists('test.xyz')
os.remove('test.xyz')
from gaptrain.loss import RMSE
from gaptrain.configurations import ConfigurationSet
from gaptrain.systems import System
import numpy as np
system = System(box_size=[10, 10, 10])
system.add_solvent('h2o', n=3)
def test_rmse():
configs = ConfigurationSet()
for _ in range(2):
configs += system.random()
configs[0].energy = 1
configs[1].energy = 2
true_configs = configs.copy()
true_configs[0].energy = 1.1
true_configs[1].energy = 1.8
rmse = RMSE(configs, true_configs)
expected = np.sqrt(((1 - 1.1)**2 + (2 - 1.8)**2) / 2.0)
assert np.abs(rmse.energy - expected) < 1E-6
from gaptrain.exceptions import LoadingFailed
from gaptrain.systems import System
from gaptrain.molecules import Molecule
from gaptrain.solvents import get_solvent
import gaptrain as gt
import numpy as np
import pytest
import ase
import os
here = os.path.abspath(os.path.dirname(__file__))
h2o = Molecule(os.path.join(here, 'data', 'h2o.xyz'))
side_length = 7.0
system = System(box_size=[side_length, side_length, side_length])
system.add_molecules(h2o, n=3)
def test_print_exyz():
configs = ConfigurationSet(name='test')
for _ in range(5):
configs += system.random()
configs.save()
assert os.path.exists('test.xyz')
os.remove('test.xyz')
# If the energy and forces are set for all the configurations an exyz
