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 from_dict(dct):
flare_calc_dict = json.load(open(dct["flare_calc"]))
# Build FLARE_Calculator from dict
if flare_calc_dict["class"] == "FLARE_Calculator":
flare_calc = FLARE_Calculator.from_file(dct["flare_calc"])
_kernels = None
# Build SGP_Calculator from dict
# TODO: we still have the issue that the c++ kernel needs to be
# in the current space, otherwise there is Seg Fault
# That's why there is the _kernels
elif flare_calc_dict["class"] == "SGP_Calculator":
from flare_pp.sparse_gp_calculator import SGP_Calculator
flare_calc, _kernels = SGP_Calculator.from_file(dct["flare_calc"])
else:
raise TypeError(
f"The calculator from {dct['flare_calc']} is not recognized."
)
flare_calc.reset()
dct["atoms"] = read(dct["atoms"])
dct["calculator"] = flare_calc
dct.pop("gp")
with open(dct["dft_loc"], "rb") as f:
dct["dft_calc"] = pickle.load(f)
for key in ["dt", "dft_loc"]:
dct.pop(key)
new_otf = ASE_OTF(**dct)
new_otf._kernels = _kernels
new_otf.dft_count = dct["dft_count"]
new_otf.curr_step = dct["curr_step"]
new_otf.std_tolerance = dct["std_tolerance"]
if new_otf.md_engine == "NPT":
if not new_otf.md.initialized:
new_otf.md.initialize()
return new_otf
def from_dict(dct):
flare_calc = FLARE_Calculator.from_file(dct["flare_calc"])
flare_calc.reset()
dct["atoms"] = read(dct["atoms"])
dct["atoms"].calc = flare_calc
dct.pop("gp")
with open(dct["dft_loc"], "rb") as f:
dct["dft_calc"] = pickle.load(f)
for key in ["dt", "dft_loc"]:
dct.pop(key)
new_otf = ASE_OTF(**dct)
new_otf.dft_count = dct["dft_count"]
new_otf.curr_step = dct["curr_step"]
if new_otf.md_engine == "NPT":
if not new_otf.md.initialized:
new_otf.md.initialize()
return new_otf
def from_dict(dct):
flare_calc = FLARE_Calculator.from_file(dct["flare_calc"])
# https://github.com/mir-group/flare/commit/88efe67e28f2b6a9cb5c6662675aad0209af134d
flare_calc.reset()
dct["atoms"] = read(dct["atoms"])
dct["atoms"].calc = flare_calc
dct.pop("gp")
with open(dct["dft_loc"], "rb") as f:
dct["dft_calc"] = pickle.load(f)
for key in ["dt", "dft_loc"]:
dct.pop(key)
new_otf = ASE_OTF(**dct)
new_otf.dft_count = dct["dft_count"]
new_otf.curr_step = dct["curr_step"]
new_otf.std_tolerance = dct["std_tolerance"]
if new_otf.md_engine == "NPT":
if not new_otf.md.initialized:
new_otf.md.initialize()
return new_otf
