def test_with_cp2k(name: str, dir_name: str) -> None:
"""Test :class:`ARMC` and :class:`ARMCPT`."""
with open(f'tests/test_files/{name}', 'r') as f:
dct = yaml.load(f.read(), Loader=UniqueLoader)
dct["monte_carlo"]["keep_files"] = True
armc, job_kwargs = dict_to_armc(dct)
try:
run_armc(armc, restart=False, **job_kwargs)
except Exception as ex:
err_file = PATH / dir_name / 'md' / 'md.err'
out_file = PATH / dir_name / 'md' / 'md.out'
has_err_file = os.path.isfile(err_file)
has_out_file = os.path.isfile(out_file)
if not (has_err_file or has_out_file):
raise
msg = ""
if has_err_file:
with open(err_file, 'r', encoding='utf-8') as f:
msg += f"{err_file}:\n{f.read()}"
if out_file:
with open(out_file, 'r', encoding='utf-8') as f:
msg += f"{out_file}:\n{f.read()}"
raise AssertionError(msg) from ex
def test_armc(name: str) -> None:
"""Test :class:`ARMC` and :class:`ARMCPT`."""
file = PATH / name
with open(file, 'r') as f:
dct = yaml.load(f.read(), Loader=UniqueLoader)
armc, job_kwargs = dict_to_armc(dct)
if name == 'armc_ref.yaml':
REF = ARMC_REF
armc.package_manager.hook = iter(load_results(ARMC_REF, n=1))
else:
iterator = _get_phi_iter()
def swap_phi(*args: Any, **kwargs: Any) -> List[Tuple[int, int]]:
return next(iterator)
REF = ARMCPT_REF
armc.swap_phi = swap_phi
armc.package_manager.hook = iter(load_results(ARMCPT_REF, n=3))
hdf5_ref = REF / 'armc.hdf5'
hdf5 = PATH / job_kwargs['folder'] / 'armc.hdf5'
run_armc(armc, restart=False, **job_kwargs)
assertion.assert_(next, armc.package_manager.hook, exception=StopIteration)
with h5py.File(hdf5, 'r') as f1, h5py.File(hdf5_ref, 'r') as f2:
compare_hdf5(f1, f2, skip={'/param', '/aux_error_mod'})
assertion.shape_eq(f1['param'], f2['param'])
assertion.shape_eq(f1['aux_error_mod'], f2['aux_error_mod'])
assertion.eq(f1['param'].dtype, f2['param'].dtype)
assertion.eq(f1['aux_error_mod'].dtype, f2['aux_error_mod'].dtype)
# Validate that the non-charges are updated independently of each other
with h5py.File(hdf5, 'r') as f1:
_index = f1['param'].attrs['index'][0] != b"charge"
index = np.nonzero(_index)[0]
param = f1['param'][..., index]
grad = param[:, 1:] - param[:, :-1]
grad[grad < 1e-8] = 0
assertion.le(np.count_nonzero(grad, axis=-1), 2, post_process=np.all)
def test_armc_restart(name: str) -> None:
"""Test the restart functionality of :class:`ARMC` and :class:`ARMCPT`."""
file = PATH / name
with open(file, 'r') as f:
dct = yaml.load(f.read(), Loader=UniqueLoader)
sub_iter = 5
super_iter = 8
i = 2 + (super_iter * 10 + sub_iter)
armc, job_kwargs = dict_to_armc(dct)
if name == 'armc_ref.yaml':
REF = ARMC_REF
armc.package_manager.hook = iter(load_results(ARMC_REF, n=1)[i:])
else:
iterator = _get_phi_iter()
def swap_phi(*args: Any, **kwargs: Any) -> List[Tuple[int, int]]:
return next(iterator)
REF = ARMCPT_REF
armc.swap_phi = swap_phi
armc.package_manager.hook = iter(load_results(ARMCPT_REF, n=3)[i:])
_prepare_restart(REF, PATH / job_kwargs['folder'], super_iter, sub_iter)
hdf5_ref = REF / 'armc.hdf5'
hdf5 = PATH / job_kwargs['folder'] / 'armc.hdf5'
run_armc(armc, restart=True, **job_kwargs)
assertion.assert_(next, armc.package_manager.hook, exception=StopIteration)
with h5py.File(hdf5, 'r') as f1, h5py.File(hdf5_ref, 'r') as f2:
compare_hdf5(f1, f2, skip={'/param', '/aux_error_mod'})
assertion.shape_eq(f1['param'], f2['param'])
assertion.shape_eq(f1['aux_error_mod'], f2['aux_error_mod'])
assertion.eq(f1['param'].dtype, f2['param'].dtype)
assertion.eq(f1['aux_error_mod'].dtype, f2['aux_error_mod'].dtype)
from scm.plams import add_to_class, Cp2kJob
from FOX.armc import dict_to_armc, run_armc
@add_to_class(Cp2kJob)
def get_runscript(self):
inp, out = self._filename('inp'), self._filename('out')
return f'cp2k.ssmp -i {inp} -o {out}'
# Prepare the ARMC settings
file = 'armc_new.yaml'
with open(file, 'r') as f:
dct = yaml.load(f.read(), Loader=yaml.FullLoader)
try:
armc, job_kwargs = dict_to_armc(dct)
except Exception as ex:
exc = ex
raise ex
# Start ARMC
try:
workdir = os.path.join(job_kwargs['path'], job_kwargs['folder'])
shutil.rmtree(workdir)
except FileNotFoundError:
pass
run_armc(armc, restart=False, **job_kwargs)
"""A Recipe for MM-MD parameter optimizations with CP2K 3.1 or 6.1."""
import yaml
from FOX.armc import dict_to_armc, run_armc
# Prepare the ARMC settings
file = str(...)
with open(file, 'r') as f:
dct = yaml.load(f.read(), Loader=yaml.SafeLoader)
armc, kwargs = dict_to_armc(dct)
run_armc(armc, **kwargs)