def test_replicate_gp():
"""
Based on gp_test_al.out, ensures that given hyperparameters and DFT calls
a GP model can be reproduced and correctly re-predict forces and
uncertainties
:return:
"""
parsed = OtfAnalysis('test_files/VelocityVerlet.log')
positions = parsed.position_list
forces = parsed.force_list
gp_model = parsed.make_gp(kernel_name="two_plus_three_body_mc")
structures = parsed.output_md_structures()
assert np.isclose(structures[-1].positions, positions[-1]).all()
assert np.isclose(structures[-1].forces, forces[-1]).all()
final_structure = structures[-1]
pred_for, pred_stds = predict_on_structure(final_structure, gp_model)
assert np.isclose(final_structure.forces, pred_for, rtol=1e-3).all()
assert np.isclose(final_structure.stds, pred_stds, rtol=1e-3).all()
set_of_structures = structures[-3:-1]
for structure in set_of_structures:
pred_for, pred_stds = predict_on_structure(structure, gp_model)
assert np.isclose(structure.forces, pred_for, rtol=1e-3,
atol=1e-6).all()
assert np.isclose(structure.stds, pred_stds, rtol=1e-3,
atol=1e-6).all()
def test_replicate_gp():
"""
Based on gp_test_al.out, ensures that given hyperparameters and DFT calls
a GP model can be reproduced and correctly re-predict forces and
uncertainties
:return:
"""
os.system('cp test_files/sample_h2_otf.out .')
parsed = OtfAnalysis('sample_h2_otf.out')
positions = parsed.position_list
forces = parsed.force_list
gp_model = parsed.make_gp()
structures = parsed.output_md_structures()
assert np.isclose(structures[-1].positions, positions[-1]).all()
assert np.isclose(structures[-1].forces, forces[-1]).all()
final_structure = structures[-1]
pred_for, pred_stds = predict_on_structure(final_structure, gp_model)
assert np.isclose(final_structure.forces, pred_for).all()
assert np.isclose(final_structure.stds, pred_stds).all()
set_of_structures = structures[-3:-1]
for structure in set_of_structures:
pred_for, pred_stds = predict_on_structure(structure, gp_model)
assert np.isclose(structure.forces, pred_for, atol=1e-6).all()
assert np.isclose(structure.stds, pred_stds, atol=1e-6).all()
os.system('rm sample_slab_otf.out')
def test_update_L_alpha():
# set up gp model
kernel = mc_simple.two_plus_three_body_mc
kernel_grad = mc_simple.two_plus_three_body_mc_grad
cutoffs = [6.0, 5.0]
hyps = np.array([0.001770, 0.183868, -0.001415, 0.372588, 0.026315])
# get an otf traj from file for training data
old_otf = OtfAnalysis('test_files/AgI_snippet.out')
call_no = 1
cell = old_otf.header['cell']
gp_model = old_otf.make_gp(kernel=kernel,
kernel_grad=kernel_grad,
call_no=call_no,
cutoffs=cutoffs,
hyps=hyps)
# update database & use update_L_alpha to get ky_mat
for n in range(call_no, call_no + 1):
positions = old_otf.gp_position_list[n]
species = old_otf.gp_species_list[n]
atoms = old_otf.gp_atom_list[n]
forces = old_otf.gp_force_list[n]
struc_curr = Structure(cell, species, positions)
gp_model.update_db(struc_curr, forces, custom_range=atoms)
gp_model.update_L_alpha()
ky_mat_from_update = np.copy(gp_model.ky_mat)
# use set_L_alpha to get ky_mat
gp_model.set_L_alpha()
ky_mat_from_set = np.copy(gp_model.ky_mat)
assert (np.all(np.absolute(ky_mat_from_update - ky_mat_from_set)) < 1e-6)
def test_otf_parser_from_checkpt(software):
if not os.environ.get(cmd[software], False):
pytest.skip(f"{cmd[software]} not found in environment:"
" Please install the code "
f" and set the {cmd[software]} env. "
"variable to point to the executable.")
if software == "cp2k":
pytest.skip()
example = 1
casename = name_list[example]
log_name = f"{casename}_otf_{software}"
output_name = f"{log_name}.out"
otf_traj = OtfAnalysis(output_name)
try:
replicated_gp = otf_traj.make_gp()
except:
init_gp = GaussianProcess.from_file(log_name + "_gp.json")
replicated_gp = otf_traj.make_gp(init_gp=init_gp)
outdir = f"test_outputs_{software}"
if not os.path.isdir(outdir):
os.mkdir(outdir)
for f in os.listdir("./"):
if f"{casename}_otf_{software}" in f:
shutil.move(f, outdir)
cleanup(software, f"{casename}_otf_{software}")
def test_otf_parser(software):
if not os.environ.get(cmd[software], False):
pytest.skip(f"{cmd[software]} not found in environment:"
" Please install the code "
f" and set the {cmd[software]} env. "
"variable to point to the executable.")
example = 1
casename = name_list[example]
output_name = f"{casename}_otf_{software}.out"
otf_traj = OtfAnalysis(output_name)
replicated_gp = otf_traj.make_gp()
# TODO: debug cp2k
if software == "cp2k":
pytest.skip()
otf = pytest.my_otf
assert otf.dft_count == len(otf_traj.gp_position_list)
assert otf.curr_step == len(otf_traj.position_list) + 1
assert otf.dft_count == len(otf_traj.gp_thermostat["temperature"])
assert otf.curr_step == len(otf_traj.thermostat["temperature"]) + 1
if otf_traj.gp_cell_list:
assert otf.dft_count == len(otf_traj.gp_cell_list)
def test_otf2xyz():
xyz_file = "h2.xyz"
parsed = OtfAnalysis("test_files/sample_h2_otf.out", calculate_energy=True)
parsed.to_xyz(xyz_file)
xyz_trj = read(xyz_file, index=":")
assert np.allclose(xyz_trj[-1].positions[0, 0], 2.2794)
assert np.allclose(xyz_trj[-2].get_forces()[-1, 2], 0.0000)
os.system("rm h2.xyz")
def test_output_md_structures():
parsed = OtfAnalysis('test_files/VelocityVerlet.log')
positions = parsed.position_list
forces = parsed.force_list
structures = parsed.output_md_structures()
assert np.isclose(structures[-1].positions, positions[-1]).all()
assert np.isclose(structures[-1].forces, forces[-1]).all()
def test_output_md_structures():
os.system('cp test_files/sample_slab_otf.out .')
parsed = OtfAnalysis('sample_slab_otf.out')
positions = parsed.position_list
forces = parsed.force_list
structures = parsed.output_md_structures()
assert np.isclose(structures[-1].positions, positions[-1]).all()
assert np.isclose(structures[-1].forces, forces[-1]).all()
def test_otf_parser(md_engine):
output_name = f"{md_engine}.out"
otf_traj = OtfAnalysis(output_name)
try:
replicated_gp = otf_traj.make_gp()
except:
init_flare = FLARE_Calculator.from_file(md_engine + "_flare.json")
replicated_gp = otf_traj.make_gp(init_gp=init_flare.gp_model)
print("ase otf traj parsed")
for f in glob.glob(md_engine + "*"):
os.remove(f)
def test_otf_parser(md_engine):
output_name = f"{md_engine}.out"
otf_traj = OtfAnalysis(output_name)
try:
replicated_gp = otf_traj.make_gp()
except:
init_flare = FLARE_Calculator.from_file(md_engine + "_flare.json")
replicated_gp = otf_traj.make_gp(init_gp=init_flare.gp_model)
print("ase otf traj parsed")
# Check that the GP forces change.
comp1 = otf_traj.force_list[0][1, 0]
comp2 = otf_traj.force_list[-1][1, 0]
assert (comp1 != comp2)
for f in glob.glob(md_engine + "*"):
os.remove(f)
def test_otf_parser(md_engine, write_model):
output_name = f"{md_engine}_{write_model}"
otf_traj = OtfAnalysis(output_name + ".out")
try:
replicated_gp = otf_traj.make_gp()
except:
init_flare = FLARE_Calculator.from_file(output_name + "_flare.json")
replicated_gp = otf_traj.make_gp(init_gp=init_flare.gp_model)
print("ase otf traj parsed")
# Check that the GP forces change.
comp1 = otf_traj.force_list[-2][1, 0]
comp2 = otf_traj.force_list[-1][1, 0]
assert comp1 != comp2
for f in glob.glob(output_name + "*"):
os.remove(f)
for f in glob.glob("*_ckpt_*"):
shutil.rmtree(f, ignore_errors=True)
def test_md_parser():
"""
Test the capability of otf parser to read MD info
:return:
"""
os.system('cp test_files/sample_slab_otf.out .')
parsed = OtfAnalysis('sample_slab_otf.out')
pos1 = 10.09769665
assert(pos1 == parsed.position_list[0][0][2])
assert(len(parsed.position_list[0]) == 28)
def test_md_parser():
"""
Test the capability of otf parser to read MD info
:return:
"""
parsed = OtfAnalysis('test_files/VelocityVerlet.log')
pos1 = -0.172516
assert (pos1 == parsed.position_list[0][0][2])
assert (len(parsed.position_list[0]) == 4)
def test_md_parser():
"""
Test the capability of otf parser to read MD info
:return:
"""
os.system("cp test_files/sample_slab_otf.out .")
parsed = OtfAnalysis("sample_slab_otf.out")
pos1 = 10.09769665
assert pos1 == parsed.position_list[0][0][2]
assert len(parsed.position_list[0]) == 28
os.system("rm sample_slab_otf.out")
def test_parse_header():
header_dict = OtfAnalysis('test_files/VelocityVerlet.log').header
assert header_dict['frames'] == 0
assert header_dict['atoms'] == 4
assert header_dict['species_set'] == {'Ag', 'I'}
assert header_dict['dt'] == .001
assert header_dict['kernel_name'] == 'two_plus_three_body_mc'
assert header_dict['n_hyps'] == 5
assert header_dict['algo'] == 'BFGS'
assert np.equal(
header_dict['cell'],
np.array([[7.71, 0., 0.], [0., 3.855, 0.], [0., 0., 3.855]])).all()
def test_parse_header():
os.system('cp test_files/sample_slab_otf.out .')
header_dict = OtfAnalysis('sample_slab_otf.out').header
assert header_dict['frames'] == 5000
assert header_dict['atoms'] == 28
assert header_dict['species_set'] == {'Al'}
assert header_dict['dt'] == .001
assert header_dict['kernel'] == 'two_plus_three_body'
assert header_dict['n_hyps'] == 5
assert header_dict['algo'] == 'BFGS'
assert np.equal(header_dict['cell'],
np.array([[8.59135, 0., 0.],
[4.29567, 7.44033, 0.],
[0., 0., 26.67654]])).all()
def test_parse_header():
os.system("cp test_files/sample_slab_otf.out .")
header_dict = OtfAnalysis("sample_slab_otf.out").header
assert header_dict["frames"] == 5000
assert header_dict["atoms"] == 28
assert header_dict["species_set"] == {"Al"}
assert header_dict["dt"] == 0.001
assert header_dict["kernel_name"] == "two_plus_three_body"
assert header_dict["n_hyps"] == 5
assert header_dict["algo"] == "BFGS"
assert np.equal(
header_dict["cell"],
np.array([[8.59135, 0.0, 0.0], [4.29567, 7.44033, 0.0],
[0.0, 0.0, 26.67654]]),
).all()
os.system("rm sample_slab_otf.out")
def test_gp_parser():
"""
Test the capability of otf parser to read GP/DFT info
:return:
"""
parsed = OtfAnalysis('test_files/VelocityVerlet.log')
assert (parsed.gp_species_list == [['Ag', 'I'] * 2])
gp_positions = parsed.gp_position_list
assert len(gp_positions) == 1
pos1 = 1.819218
pos2 = -0.141231
assert (pos1 == gp_positions[0][-1][1])
assert (pos2 == gp_positions[-1][0][2])
force1 = -0.424080
force2 = 0.498037
assert (force1 == parsed.gp_force_list[0][-1][1])
assert (force2 == parsed.gp_force_list[-1][0][2])
def test_gp_parser():
"""
Test the capability of otf parser to read GP/DFT info
:return:
"""
os.system('cp test_files/sample_slab_otf.out .')
parsed = OtfAnalysis('sample_slab_otf.out')
assert (parsed.gp_species_list == [['Al']*28] * 4)
gp_positions = parsed.gp_position_list
assert len(gp_positions) == 4
pos1 = 1.50245891
pos2 = 10.06179079
assert(pos1 == gp_positions[0][-1][1])
assert(pos2 == gp_positions[-1][0][2])
force1 = 0.29430943
force2 = -0.02350709
assert(force1 == parsed.gp_force_list[0][-1][1])
assert(force2 == parsed.gp_force_list[-1][0][2])
def test_gp_parser():
"""
Test the capability of otf parser to read GP/DFT info
:return:
"""
os.system("cp test_files/sample_slab_otf.out .")
parsed = OtfAnalysis("sample_slab_otf.out")
assert parsed.gp_species_list == [["Al"] * 28] * 4
gp_positions = parsed.gp_position_list
assert len(gp_positions) == 4
pos1 = 1.50245891
pos2 = 10.06179079
assert pos1 == gp_positions[0][-1][1]
assert pos2 == gp_positions[-1][0][2]
force1 = 0.29430943
force2 = -0.02350709
assert force1 == parsed.gp_force_list[0][-1][1]
assert force2 == parsed.gp_force_list[-1][0][2]
os.system("rm sample_slab_otf.out")
def test_otf_md(md_engine, md_params, super_cell, flare_calc, qe_calc, write_model):
np.random.seed(12345)
flare_calculator = flare_calc[md_engine]
output_name = f"{md_engine}_{write_model}"
# set up OTF MD engine
otf_params = {
"init_atoms": [0, 1, 2, 3],
"output_name": output_name,
"std_tolerance_factor": 1.0,
"max_atoms_added": len(super_cell.positions),
"freeze_hyps": 10,
"write_model": write_model,
}
# 'use_mapping': flare_calculator.use_mapping}
md_kwargs = md_params[md_engine]
# intialize velocity
temperature = md_params["temperature"]
MaxwellBoltzmannDistribution(super_cell, temperature * units.kB)
Stationary(super_cell) # zero linear momentum
ZeroRotation(super_cell) # zero angular momentum
super_cell.calc = flare_calculator
test_otf = ASE_OTF(
super_cell,
timestep=1 * units.fs,
number_of_steps=number_of_steps,
dft_calc=qe_calc,
md_engine=md_engine,
md_kwargs=md_kwargs,
trajectory=f"{output_name}_otf.traj",
**otf_params,
)
# TODO: test if mgp matches gp
# TODO: see if there's difference between MD timestep & OTF timestep
test_otf.run()
# Check that the GP forces change.
otf_traj = OtfAnalysis(output_name + ".out")
comp1 = otf_traj.force_list[-2][1, 0]
comp2 = otf_traj.force_list[-1][1, 0]
assert comp1 != comp2
for f in glob.glob("scf*.pw*"):
os.remove(f)
for f in glob.glob("*.npy"):
os.remove(f)
for f in glob.glob("kv3*"):
shutil.rmtree(f)
for f in glob.glob("otf_data"):
shutil.rmtree(f, ignore_errors=True)
for f in glob.glob("out"):
shutil.rmtree(f, ignore_errors=True)
for f in os.listdir("./"):
if ".mgp" in f or ".var" in f:
os.remove(f)
if "slurm" in f:
os.remove(f)
def test_stress_with_lammps():
"""
Based on gp_test_al.out, ensures that given hyperparameters and DFT calls
a GP model can be reproduced and correctly re-predict forces and
uncertainties
:return:
"""
# build up GP from a previous trajectory
parsed = OtfAnalysis('test_files/VelocityVerlet.log')
positions = parsed.position_list
forces = parsed.force_list
gp_model = parsed.make_gp(kernel=two_plus_three_body_mc,
kernel_grad=two_plus_three_body_mc_grad)
# build up MGP from GP
struc_params = {
'species': [47, 53],
'cube_lat': np.eye(3) * 100,
'mass_dict': {
'0': 27,
'1': 16
}
}
# grid parameters
lower_cut = 2.5
grid_num_2 = 64
grid_num_3 = 32
two_cut = 5.0
three_cut = 5.0
grid_params = {
'bounds_2': [[lower_cut], [two_cut]],
'bounds_3': [[lower_cut, lower_cut, -1], [three_cut, three_cut, 1]],
'grid_num_2': grid_num_2,
'grid_num_3': [grid_num_3, grid_num_3, grid_num_3],
'svd_rank_2': 0,
'svd_rank_3': 0,
'bodies': [2, 3],
'load_grid': None,
'update': True
}
mgp_model = MappedGaussianProcess(gp_model.hyps,
gp_model.cutoffs,
grid_params,
struc_params,
mean_only=True,
container_only=False,
GP=gp_model,
lmp_file_name='lmp.mgp')
# ------------ create ASE's flare calculator -----------------------
flare_calc = FLARE_Calculator(gp_model,
mgp_model,
par=True,
use_mapping=True)
a = 3.855
alpha = 90
super_cell = crystal(
['Ag', 'I'], # Ag, I
basis=[(0, 0, 0), (0.5, 0.5, 0.5)],
size=(2, 1, 1),
cellpar=[a, a, a, alpha, alpha, alpha])
super_cell.positions = positions[-1]
super_cell.set_calculator(flare_calc)
super_cell.get_forces()
stresses = super_cell.calc.results['stresses']
# parse lammps stress
lmp_file = open('test_files/stress.lammps')
lines = lmp_file.readlines()[9:]
for ind, line in enumerate(lines):
line = line.split()
strs = np.array([float(l) for l in line[1:]]) / 1.60217662e6
assert np.isclose(stresses[ind], strs, rtol=1e-3).all()
os.system('rm -r __pycache__')
os.system('rm grid3*')
os.system('rm -r kv3')
os.system('rm lmp.mgp')