def main(args):
param = InputParams()
for filename in [f for f in os.listdir() if f.endswith(".yaml")]:
try:
param = InputParams.from_file(filename)
break
except:
continue
pseudos = not (args.no_pseudos)
positions = [
Posinp.from_file(args.positions_dir + file)
for file in os.listdir(args.positions_dir) if file.endswith(".xyz")
]
# Create directories
os.makedirs("run_dir/", exist_ok=True)
os.makedirs("saved_results/", exist_ok=True)
os.chdir("run_dir/")
for i in range(args.n_structs):
j = int(np.random.choice(len(positions), 1))
posinp = generate_random_structure(positions[j])
run(posinp, i, args, param, pseudos)
def test_run_with_dry_run(self):
with Job(inputparams=self.inp, name="dry_run", run_dir="tests") as job:
# Run the calculation
job.clean()
assert not job.is_completed
job.run(dry_run=True, nmpi=2, nomp=4)
assert job.is_completed
# There must be input and output files afterwards
new_inp = InputParams.from_file(job.input_name)
assert new_inp == self.inp
new_pos = Posinp.from_file(job.posinp_name)
assert new_pos == self.pos
bigdft_tool_log = Logfile.from_file(job.logfile_name)
assert bigdft_tool_log.energy is None
def test_run_with_dry_run_with_posinp(self):
with Job(inputparams=self.inp,
posinp=self.pos,
name="dry_run",
run_dir="tests") as job:
job.clean()
assert not job.is_completed
job.run(dry_run=True, nmpi=2, nomp=4)
assert job.is_completed
# Make sure that input, posinp and output files are created
new_inp = InputParams.from_file(job.input_name)
assert new_inp == self.inp
new_pos = Posinp.from_file(job.posinp_name)
assert new_pos == self.pos
bigdft_tool_log = Logfile.from_file(job.logfile_name)
assert bigdft_tool_log.energy is None
def prepare_calculations(overwrite=False):
r"""
Determines which files are present and which need to be generated.
Parameters:
-------------
overwrite : bool
(default : False) if True, the present files are ignored
Returns:
base_inp : InputParams
base input parameters for the calculation
base_pos : Posinp
base atomic positions for the calculation
jobname : string
Name of the calculation if there is a pos file,
string "jobname" if no position file.
"""
files = [f for f in os.listdir() if f.endswith((".xyz", ".yaml"))]
posinp_is_present, jobname = verify_posinp(files)
if verify_input(files):
base_inp = InputParams.from_file("input.yaml")
else:
base_inp = InputParams()
if posinp_is_present:
base_pos = Posinp.from_file(jobname + ".xyz")
elif base_inp.posinp is not None:
base_pos = base_inp.posinp
jobname = "jobname"
base_pos.write(jobname + ".xyz")
else:
raise ValueError("No atomic positions are available.")
return base_inp, base_pos, jobname
def main(args):
initpos = generate_graphene_cell(args.xsize, args.zsize)
param = InputParams()
for filename in [f for f in os.listdir() if f.endswith(".yaml")]:
try:
param = InputParams.from_file(filename)
break
except:
continue
pseudos = not (args.no_pseudos)
# Create directories
os.makedirs("run_dir/", exist_ok=True)
os.makedirs("saved_results/", exist_ok=True)
os.chdir("run_dir/")
if args.n_defects == 0:
for i in range(1, args.n_structs + 1):
posinp = generate_random_structure(initpos)
run(posinp, i, args, param, pseudos)
elif args.n_defects == 1:
initpos, _ = place_first_nitrogen(initpos)
for i in range(1, args.n_structs + 1):
posinp = generate_random_structure(initpos)
run(posinp, i, args, param, pseudos)
elif args.n_defects == 2:
initpos, first_idx = place_first_nitrogen(initpos)
root = np.sqrt(args.n_structs)
if root % 1 == 0:
n_angle, n_radius = root, root
else:
n_angle, n_radius = np.ceil(root), np.floor(root)
max_radius = np.max(np.array(initpos.cell) / 2)
radiuses = np.linspace(1.0, max_radius, n_radius)
angles = np.linspace(0, 2 * np.pi, n_angle)
i = 0
# distances = np.zeros(int(n_angle * n_radius))
for theta in angles:
for r in radiuses:
i += 1
posinp, second_idx = place_second_nitrogen(
initpos, theta, r, first_idx)
# distances[i-1] = np.linalg.norm(posinp.positions[first_idx] - posinp.positions[second_idx])
run(posinp, i, args, param, pseudos)
# np.savetxt("distances.data", distances)
elif args.n_defects == 3:
root = np.sqrt(args.n_structs)
if root % 1 == 0:
n_angle, n_radius = root, root
else:
n_angle, n_radius = np.ceil(root), np.floor(root)
else:
raise NotImplementedError("No method for this number of defects.")
def test_from_file(self):
inp = InputParams.from_file(self.filename)
assert inp == {}
