def test_weights(self):
cb = CalcBox(name="testbox",
pos=(0., 0., 0.),
cutoff=2.0,
dim=(100.0, 100.0, 100.0),
inner_dim=(50.0, 50.0, 50.0))
# test all three axis
test_positions = np.column_stack(
(np.linspace(-55.0, 55.0, 100), np.zeros(100), np.zeros(100)))
test_positions = np.append(test_positions,
np.column_stack(
(np.zeros(100),
np.linspace(-55.0, 55.0,
100), np.zeros(100))),
axis=0)
test_positions = np.append(test_positions,
np.column_stack(
(np.zeros(100), np.zeros(100),
np.linspace(-55.0, 55.0, 100))),
axis=0)
# and all 8 corners too
a = 37.5
test_positions = np.append(test_positions,
np.array(
((-a, -a, -a), (-a, -a, a), (-a, a, -a),
(-a, a, -a), (a, -a, -a), (a, -a, a),
(a, a, -a), (a, a, a))),
axis=0)
correct_weights = np.loadtxt("weight_test.csv", delimiter=",")
for i in range(len(test_positions)):
w = cb.get_weight(test_positions[i])
self.assertEqual(correct_weights[i], w)
def test_weights(self):
cb = CalcBox(name="testbox", pos=(0., 0., 0.),
cutoff=2.0,
dim=(100.0, 100.0, 100.0),
inner_dim=(50.0, 50.0, 50.0))
# test all three axis
test_positions = np.column_stack((np.linspace(-55.0, 55.0, 100),
np.zeros(100),
np.zeros(100)))
test_positions = np.append(test_positions, np.column_stack(
(np.zeros(100),
np.linspace(-55.0, 55.0, 100),
np.zeros(100))), axis=0)
test_positions = np.append(test_positions, np.column_stack(
(np.zeros(100),
np.zeros(100),
np.linspace(-55.0, 55.0, 100))),
axis=0)
# and all 8 corners too
a = 37.5
test_positions = np.append(test_positions, np.array((
(-a, -a, -a),
(-a, -a, a),
(-a, a, -a),
(-a, a, -a),
(a, -a, -a),
(a, -a, a),
(a, a, -a),
(a, a, a))),
axis=0)
correct_weights = np.loadtxt("weight_test.csv", delimiter=",")
for i in range(len(test_positions)):
w = cb.get_weight(test_positions[i])
self.assertEqual(correct_weights[i], w)
def test_calcbox_all(self):
cb = CalcBox(name="testbox",
pos=(0., 0., 0.),
dim=(self._edge + 5, self._edge + 5, self._edge + 5))
sa, srmap, sw = cb.select_atoms(self._atoms)
ra = self._atoms
self.assertEqual(ra, sa)
def test_calcbox_subset(self):
cb = CalcBox(name="testbox", pos=(0., 0., 0.),
cutoff=0.0,
dim=(50.0, 50.0, 50.0))
sa, srmap, sw = cb.select_atoms(self._atoms)
correct_ids = set([307, 215, 405, 280, 281, 410, 155, 156, 285, 286,
415, 160, 289, 290, 419, 165, 294, 455, 430, 432, 305, 306, 435,
180, 414, 310, 439, 312, 185, 186, 315, 188, 190, 181, 193, 343,
161, 457, 330, 311, 332, 205, 462, 335, 337, 210, 340, 213, 313,
218, 314, 465, 444, 338, 437, 440, 318, 319, 460])
self.assertEqual(set(Mixer.get_atom_ids(sa)), correct_ids)
def test_calcbox_subset(self):
cb = CalcBox(name="testbox",
pos=(0., 0., 0.),
cutoff=0.0,
dim=(50.0, 50.0, 50.0))
sa, srmap, sw = cb.select_atoms(self._atoms)
correct_ids = set([
307, 215, 405, 280, 281, 410, 155, 156, 285, 286, 415, 160, 289,
290, 419, 165, 294, 455, 430, 432, 305, 306, 435, 180, 414, 310,
439, 312, 185, 186, 315, 188, 190, 181, 193, 343, 161, 457, 330,
311, 332, 205, 462, 335, 337, 210, 340, 213, 313, 218, 314, 465,
444, 338, 437, 440, 318, 319, 460
])
self.assertEqual(set(Mixer.get_atom_ids(sa)), correct_ids)
def test_calcbox_moving_ch4(self):
cb = CalcBox(name="testbox",
pos=(0., 0., 0.),
cutoff=2.0,
dim=(55.0, 55.0, 55.0),
debug=0)
ch4 = [0, 1, 2, 3] # these are atoms indexes and ids
z = np.linspace(-self._edge / 2.0 - 25, self._edge / 2.0 + 25, 100)
x = np.zeros_like(z)
y = np.zeros_like(z)
pos = np.column_stack((x, y, z))
for i in range(len(pos)):
self._set_molecule_pos(self._atoms, ch4, pos[i])
sa, srmap, sw = cb.select_atoms(self._atoms)
s_ids = set(Mixer.get_atom_ids(sa))
all_ids = set(Mixer.get_atom_ids(self._atoms))
inside_ids = s_ids.intersection(set(ch4))
if not (len(inside_ids) == 0 or len(inside_ids) == 4):
print("CH4 pos: %s" % pos[i])
print("CH4 in selection: %s" % inside_ids)
def test_calcbox_moving_ch4(self):
cb = CalcBox(name="testbox", pos=(0., 0., 0.),
cutoff=2.0,
dim=(55.0, 55.0, 55.0),
debug=0)
ch4 = [0, 1, 2, 3] # these are atoms indexes and ids
z = np.linspace(-self._edge/2.0 - 25, self._edge/2.0 + 25, 100)
x = np.zeros_like(z)
y = np.zeros_like(z)
pos = np.column_stack((x, y, z))
for i in range(len(pos)):
self._set_molecule_pos(self._atoms,
ch4,
pos[i])
sa, srmap, sw = cb.select_atoms(self._atoms)
s_ids = set(Mixer.get_atom_ids(sa))
all_ids = set(Mixer.get_atom_ids(self._atoms))
inside_ids = s_ids.intersection(set(ch4))
if not (len(inside_ids) == 0 or len(inside_ids) == 4):
print("CH4 pos: %s" % pos[i])
print("CH4 in selection: %s" % inside_ids)
def test_calcbox_all(self):
cb = CalcBox(name="testbox", pos=(0., 0., 0.),
dim=(self._edge + 5, self._edge + 5, self._edge + 5))
sa, srmap, sw = cb.select_atoms(self._atoms)
ra = self._atoms
self.assertEqual(ra, sa)
Mixer.set_atom_ids(atoms) # this one is important!
calc_gpaw = GPAW(nbands=bands, txt="mixer_box_gpaw.log")
calc_reaxff_full = ReaxFF(ff_file_path=get_datafile("ffield.reax.new"),
implementation="C")
calc_reaxff_qbox = ReaxFF(ff_file_path=get_datafile("ffield.reax.new"),
implementation="C")
# debug disabled for non-master nodes, this is so on purpose!
debug = 0
if rank == 0:
debug = set_debug
filter_full_sys = CalcBox(name="full_sys",
pos=(0, 0, 0),
dim=cell,
cutoff=cutoff,
pbc=(1, 1, 1),
debug=debug)
filter_qbox = CalcBox(name="qbox",
pos=qbox_pos,
dim=q_cell,
cutoff=cutoff,
inner_dim=(q_cell[0] - transition_buffer * 2.0,
q_cell[1] - transition_buffer * 2.0,
q_cell[2] - transition_buffer * 2.0),
debug=debug)
# full system classical is taken as positive
forces_full_system = ForceCalculation("force_full",
selector=filter_full_sys,
calculator=calc_reaxff_full,
