def test_get_dft_results_at_gcut_socorrofail():
"""
Reads energies and forces correctly frm socorro diaryf
files for every run at corrent gcut
"""
with tools_for_tests.TemporaryDirectory() as tmp_dir:
# set up two mock dft runs
main_pp_path_list = []
main_argvf_template_path = ''
main_crystal_template_path = ''
pos = []
gcut = -1
run1 = eval_pp.DftRun(main_pp_path_list, main_argvf_template_path, main_crystal_template_path, pos, gcut)
mock_run_dir_1 = 'dir_1'
os.mkdir(mock_run_dir_1)
run1.run_dir = mock_run_dir_1
run2 = eval_pp.DftRun(main_pp_path_list, main_argvf_template_path, main_crystal_template_path, pos, gcut)
mock_run_dir_2 = 'dir_2'
os.mkdir(mock_run_dir_2)
run2.run_dir = mock_run_dir_2
# move mock diaryf files to run dirs
shutil.copy(os.path.join(test_inputs_dir, 'diaryf.test_get_dft_results_1'),
os.path.join(mock_run_dir_1, 'diaryf'))
shutil.copy(os.path.join(test_inputs_dir, 'diaryf.test_get_dft_results_none'),
os.path.join(mock_run_dir_2, 'diaryf'))
with pytest.raises(eval_pp.SocorroFail):
_,_ = eval_pp.get_dft_results_at_gcut([run1, run2])
def test_run_socorro():
"""
Set up socorro input files, run socorro, check force/energy results
note: this might fail if socorro versions change because different
versions could give different reults even with the same input,
especially since total E is relative. Could I mock socorro instead?
Alternatively, I could run socorro twice, the second time with pre-
setup input files, and compare results
"""
inputs = test_inputs_dir + '/SiGe_single_run'
with tools_for_tests.TemporaryDirectory() as tmp_dir:
# create object to test
pp_path_list = [inputs + '/PAW.Si', inputs + '/PAW.Ge']
argvf_template_path = inputs + '/argvf.template'
crystal_template_path = inputs + '/crystal.template'
pos = [[0.0, 0, '0.1'], [0.24, 0.25, 0.26]]
testrun = eval_pp.DftRun(pp_path_list, argvf_template_path,
crystal_template_path, pos, 10.)
testrun.setup_files()
with open('socorro.log', 'w') as fout:
p = testrun.run_socorro(fout)
p.wait()
#assert force and energy reults
correct_energy = -312.593586340
correct_forces = np.array(
[0.246519, 0.247743, 0.243064, -0.246519, -0.247743, -0.243064])
assert np.isclose(testrun.read_energy(), correct_energy)
assert np.isclose(testrun.read_forces(), correct_forces,
atol=1.e-5).all()
def test_setup_files():
"""
test: setup_dir method makes files for socorro run
Expected behavior: calling setup_dir method will create correctly
preprocessed argvf file in current directory, directory named data/
and correctly preprocessed data/crystal file.
"""
correct_argvf = test_inputs_dir+'/argvf.example1'
correct_crystal = test_inputs_dir+'/crystal.example1'
correct_Si = test_inputs_dir+'/PAW.Si'
correct_Ge = test_inputs_dir+'/PAW.Ge'
with tools_for_tests.TemporaryDirectory() as tmp_dir:
# create object to test
pp_path_list = [test_inputs_dir+'/PAW.Si',
test_inputs_dir+'/PAW.Ge']
argvf_template_path = test_inputs_dir+'/argvf.template.example1'
crystal_template_path = test_inputs_dir+'/crystal.template.example1'
pos = [[0.0, 0, '0.1'], [0.5, 0.6, 0.7]]
testrun = eval_pp.DftRun(pp_path_list, argvf_template_path,
crystal_template_path, pos, 30.)
testrun.setup_files()
# compare preprocessed files with correct file examples
with open('argvf') as f1, open(correct_argvf) as f2:
assert f1.read() == f2.read()
with open('data/crystal') as f1, open(correct_crystal) as f2:
assert map(str.split, f1.readlines()) == map(str.split, f2.readlines())
with open('data/PAW.Si') as f1, open(correct_Si) as f2:
assert f1.read() == f2.read()
with open('data/PAW.Ge') as f1, open(correct_Ge) as f2:
assert f1.read() == f2.read()
def test_symlink_pseudopotentials():
"""
symlinks pseudopotentials into data/ directory and compares to
original pseudopotential files. Obviously they'll be the same
but this makes sure the file operations work
"""
with tools_for_tests.TemporaryDirectory() as tmp_dir:
# create object to test
pp_path_list = [test_inputs_dir+'/PAW.Si',
test_inputs_dir+'/PAW.Ge']
argvf_template_path = ''
crystal_template_path = ''
correct_argvf = ''
correct_crystal = ''
pos = []
gcut = -1
testrun = eval_pp.DftRun(pp_path_list, argvf_template_path,
crystal_template_path, pos, gcut)
# call _symlink_pseudopotentials method
os.mkdir('data')
testrun._symlink_pseudopotentials()
# check pseudopotential files have been copied to data/
with open('data/PAW.Si') as f1, open(pp_path_list[0]) as f2:
assert f1.read() == f2.read()
with open('data/PAW.Ge') as f1, open(pp_path_list[1]) as f2:
assert f1.read() == f2.read()
def test_preproc_argvf():
""" make sure {gcut} and {4gcut} are replaced in text correctly """
gcut = 40.
example_template = 'tests/test_inputs/argvf.template.example1'
testrun = eval_pp.DftRun([], example_template, '', [], gcut)
with open(example_template) as fin:
tmplt_txt = fin.readlines()
assert testrun._preproc_argvf(tmplt_txt) == ['asdfsd\n',
'asdf 40.0\n', 'asdfas 160.0\n', '\n', '\n', 'lkjlj\n']
def test_get_dft_results_at_gcut():
"""
Reads energies and forces correctly frm socorro diaryf
files for every run at corrent gcut
"""
with tools_for_tests.TemporaryDirectory() as tmp_dir:
# set up two mock dft runs
main_pp_path_list = []
main_argvf_template_path = ''
main_crystal_template_path = ''
pos = []
gcut = -1
run1 = eval_pp.DftRun(main_pp_path_list, main_argvf_template_path, main_crystal_template_path, pos, gcut)
mock_run_dir_1 = 'dir_1'
os.mkdir(mock_run_dir_1)
run1.run_dir = mock_run_dir_1
run2 = eval_pp.DftRun(main_pp_path_list, main_argvf_template_path, main_crystal_template_path, pos, gcut)
mock_run_dir_2 = 'dir_2'
os.mkdir(mock_run_dir_2)
run2.run_dir = mock_run_dir_2
# move mock diaryf files to run dirs
shutil.copy(os.path.join(test_inputs_dir, 'diaryf.test_get_dft_results_1'),
os.path.join(mock_run_dir_1, 'diaryf'))
shutil.copy(os.path.join(test_inputs_dir, 'diaryf.test_get_dft_results_2'),
os.path.join(mock_run_dir_2, 'diaryf'))
dft_results = eval_pp.get_dft_results_at_gcut([run1, run2])
correct_energy_list = [-20000., -738.821147137]
correct_forces_1 = np.array([0.1, -20.0, -0.08, -1000., 0.3, 0.9])
correct_forces_2 = np.array([0.007170, -0.015092, -0.069756, -0.007170, 0.015092, 0.069756])
assert np.isclose(dft_results['energies'], correct_energy_list).all()
assert np.isclose(dft_results['forces'][0], correct_forces_1).all()
assert np.isclose(dft_results['forces'][1], correct_forces_2).all()
def test_get_energy_none():
"""
should return None because no cell energy found in socorro output
"""
with tools_for_tests.TemporaryDirectory() as tmp_dir:
# set up fake dft_run
pp_path_list = []
argvf_template_path = ''
crystal_template_path = ''
pos = []
gcut = -1
testrun = eval_pp.DftRun(pp_path_list, argvf_template_path,
crystal_template_path, pos, gcut)
energy_in = testrun.read_energy(test_inputs_dir+'/diaryf.test_get_energy_none')
assert energy_in is None
def test_get_forces_none():
"""
Read forces from example socorro ouput and check value is correct.
Run inside temporary directory.
"""
with tools_for_tests.TemporaryDirectory() as tmp_dir:
# set up fake dft_run
pp_path_list = []
argvf_template_path = ''
crystal_template_path = ''
pos = []
gcut = -1
testrun = eval_pp.DftRun(pp_path_list, argvf_template_path,
crystal_template_path, pos, gcut)
forces_in = testrun.read_forces(test_inputs_dir+'/diaryf.test_get_forces_none')
assert forces_in is None
def test_get_energy():
"""
Read energy from example socorro ouput and check value is correct.
Run inside temporary directory.
"""
with tools_for_tests.TemporaryDirectory() as tmp_dir:
# set up fake dft_run
pp_path_list = []
argvf_template_path = ''
crystal_template_path = ''
pos = []
gcut = -1
testrun = eval_pp.DftRun(pp_path_list, argvf_template_path,
crystal_template_path, pos, gcut)
energy_in = testrun.read_energy(test_inputs_dir+'/diaryf.test_get_energy')
assert isclose(energy_in, -738.821147137)
def test_get_forces():
"""
Read forces from example socorro ouput and check value is correct.
Run inside temporary directory.
"""
with tools_for_tests.TemporaryDirectory() as tmp_dir:
# set up fake dft_run
pp_path_list = []
argvf_template_path = ''
crystal_template_path = ''
pos = []
gcut = -1
testrun = eval_pp.DftRun(pp_path_list, argvf_template_path,
crystal_template_path, pos, gcut)
forces_in = testrun.read_forces(test_inputs_dir+'/diaryf.test_get_forces')
correct_forces = np.array([0.007170, -0.015092, -0.069756, -0.007170, 0.015092, 0.069756])
assert np.isclose(forces_in, correct_forces, rtol=1e-9, atol=0.0).all()
def test_position_sweep():
"""
Four instances of socorro run in parallel, results correct
Sets up four DftRun instances with different atomic coordinates.
The socorro runs should run simulataneously in different threads.
note: this might fail if socorro versions change because different
versions could give different reults even with the same input,
especially since total E is relative. Could I mock socorro instead?
Alternatively, I could run socorro twice, the second time with pre-
setup input files, and compare results
"""
inputs = test_inputs_dir + '/SiGe_single_run'
with tools_for_tests.TemporaryDirectory() as tmp_dir:
positions = [[[0.0, 0.0, 0.1], [0.24, 0.25, 0.26]],
[[0.0, 0.0, 0.0], [0.50, 0.50, 0.50]],
[[0.0, 0.0, 0.0], [0.25, 0.25, 0.25]],
[[0.1, 0.0, 0.0], [0.49, 0.50, 0.51]]]
# create objects to test
pp_path_list = [inputs + '/PAW.Si', inputs + '/PAW.Ge']
argvf_template_path = inputs + '/argvf.template'
crystal_template_path = inputs + '/crystal.template'
testruns = []
for pos in positions:
testruns.append(
eval_pp.DftRun(pp_path_list, argvf_template_path,
crystal_template_path, pos, 10.))
# run position_sweep
eval_pp.position_sweep(testruns)
# get results from socorro runs
energies = []
forces = []
for run in testruns:
# get results and append to results array
os.chdir(run.run_dir)
energies.append(run.read_energy())
forces.append(run.read_forces())
os.chdir(tmp_dir)
print energies
print forces
# correct results
correct_en = [
-315.52682125, -314.613501131, -315.33638574, -314.797573776
]
correct_forces = [
np.array([
0.337666, 0.218549, 0.321221, -0.337666, -0.218549, -0.321221
]),
np.array([0., -0., -0., -0., 0., 0.]),
np.array([-0., 0., -0., 0., 0., 0.]),
np.array(
[0.29504, 0.341381, 0.008144, -0.29504, -0.341381, -0.008144])
]
assert np.isclose(energies, correct_en).all()
assert np.isclose(forces, correct_forces, atol=1.e-5).all()
def test_run_socorro_no_files():
"""
test: run_socorro prints warning if files not created
"""
testrun = eval_pp.DftRun([], [], [], [], 0)
assert testrun.run_socorro('') is False
