def react_dots(
params,
dot_size1,
dot_size2,
prior_run_name1,
prior_run_name2,
random_seed=1,
run_name_prefix="react_",
on_queue=True,
method="metadynamics",
):
random_s = str(random_seed)
random.seed(random_seed)
run_name = run_name_prefix + str(dot_size1) + "_" + str(dot_size2)
spoc = utils.Molecule("/fs/home/jms875/Documents/nanocrystals/pb_oleate_hydrate_morse/" + spoc_name + ".arc")
atoms1, bonds1, angles1, dihedrals1 = cPickle.load(open("lammps/" + prior_run_name1 + ".pickle", "rb"))
atoms1, bonds1, angles1, dihedrals1 = remove_unattached_ligands(atoms1, bonds1, angles1, dihedrals1, spoc)
atoms2, bonds2, angles2, dihedrals2 = cPickle.load(open("lammps/" + prior_run_name2 + ".pickle", "rb"))
atoms2, bonds2, angles2, dihedrals2 = remove_unattached_ligands(atoms2, bonds2, angles2, dihedrals2, spoc)
atoms1_xyz = filetypes.parse_xyz(prior_run_name1 + ".xyz")
atoms2_xyz = filetypes.parse_xyz(prior_run_name2 + ".xyz")
goal_atoms = filetypes.parse_xyz("dot" + str(dot_size1 + dot_size2) + ".xyz")
# set starting coordinates
for a, b in zip(atoms1, atoms1_xyz):
a.x = b.x
a.y = b.y
a.z = b.z
for a, b in zip(atoms2, atoms2_xyz):
a.x = b.x
a.y = b.y
a.z = b.z
atoms = atoms1 + atoms2
bonds = bonds1 + bonds2
angles = angles1 + angles2
dihedrals = dihedrals1 + dihedrals2
# make sure atom types are the same in atom1 and atom2
atom_types_by_type_index = dict([(t.type.index, t.type) for t in atoms])
for i, a in enumerate(atoms):
a.type = atom_types_by_type_index[a.type.index]
a.index = i + 1
if coul_on and a.type.index in params:
a.charge = params[a.type.index]
else:
a.charge = a.type.charge
atom_types = dict([(t.type, True) for t in atoms]).keys()
atom_types.sort(key=lambda t: -t.element - t.index * 0.00001)
offset = (
radius_of_gyration([a for a in atoms1 if (a.type.notes == "PbS Nanocrystal Pb" or a.element == "S")])
+ radius_of_gyration([a for a in atoms2 if (a.type.notes == "PbS Nanocrystal Pb" or a.element == "S")])
+ 10.0
)
offset_vector = utils.matvec(utils.rand_rotation(), [offset, offset, offset])
rot = utils.rand_rotation()
for a in atoms2: # offset by random orientation vector
a.x, a.y, a.z = utils.matvec(rot, [a.x, a.y, a.z])
a.x += offset_vector[0]
a.y += offset_vector[1]
a.z += offset_vector[2]
box_size = [
15.0 + max([a.x for a in atoms]) - min([a.x for a in atoms]),
15.0 + max([a.y for a in atoms]) - min([a.y for a in atoms]),
15.0 + max([a.z for a in atoms]) - min([a.z for a in atoms]),
]
# goal_atoms = cPickle.load( open('lammps/dot'+str(dot_size1+dot_size2)+'.pickle', 'rb') )[0]
# filetypes.write_xyz('out_meta', atoms)
# exit()
os.chdir("lammps")
save_to_file(atoms, bonds, angles, dihedrals, atom_types, run_name)
lammps.write_data_file_general(
atoms, bonds, angles, dihedrals, box_size, run_name, atom_types=atom_types, pair_coeffs_included=False
)
os.system("cp ../" + sys.argv[0] + " " + run_name + ".py")
starting_rxn_coord = radius_of_gyration(
[a for a in atoms if (a.type.notes == "PbS Nanocrystal Pb" or a.element == "S")]
)
print len([a for a in atoms if (a.type.notes == "PbS Nanocrystal Pb" or a.element == "S")])
goal_rxn_coord = radius_of_gyration(goal_atoms[0 : 2 * (dot_size1 + dot_size2)])
colvars_file = open(run_name + ".colvars", "w")
colvars_file.write(
"""
colvarsTrajFrequency 10000
colvarsRestartFrequency 100000
colvar {
name gyr
width 0.1 #size of bins, in Angstroms
upperBoundary """
+ str(starting_rxn_coord)
+ """ #two separate dots
lowerBoundary """
+ str(goal_rxn_coord)
+ """ #one unified dot
lowerwallconstant 10.0
upperwallconstant 10.0
gyration {
atoms {
atomNumbers """
+ (" ".join([str(a.index) for a in atoms if (a.type.notes == "PbS Nanocrystal Pb" or a.element == "S")]))
+ """
}
}
}
"""
)
if method.lower() == "abf":
colvars_file.write(
"""
abf {
colvars gyr
hideJacobian # when using distance-based colvar: makes pmf flat at infinity
fullSamples 1000
}
"""
)
elif method.lower() == "metadynamics":
colvars_file.write(
"""
metadynamics {
colvars gyr
hillWeight 0.1
newHillFrequency 1000
}
"""
)
else:
raise Exception('Invalid free energy method "%s"' % method)
colvars_file.close()
f = open(run_name + ".in", "w")
write_input_header(f, run_name, atom_types, read_restart=False)
f.write(
"""
dump 1 all xyz 10000 """
+ run_name
+ """.xyz
minimize 0.0 1.0e-8 10000 1000
neigh_modify check yes every 1 delay 0
thermo_style custom pe temp
thermo 10000
restart 100000 """
+ run_name
+ """.restart1 """
+ run_name
+ """.restart2
fix motion all nve
fix implicit_solvent all langevin 400.0 400.0 100.0 """
+ random_s
+ """ zero yes gjf yes
fix col all colvars """
+ run_name
+ """.colvars output """
+ run_name
+ """ seed """
+ random_s
+ """ tstat implicit_solvent
velocity all create 400.0 """
+ random_s
+ """ mom yes
timestep 2.0
thermo_style custom step temp etotal pe ke epair ebond f_col tpcpu
run """
+ str(int(1e7))
+ """
write_restart """
+ run_name
+ """.restart
"""
)
f.close()
# run_job(run_name, on_queue)
os.chdir("..")
def build_dot(N, spoc, monomer, atoms, bonds, angles, dihedrals, random_seed=1):
random.seed(random_seed)
pb_type = monomer.atoms[0].type
s_type = monomer.atoms[1].type
Q = 2.968
L = int(math.ceil((2 * N) ** 0.333))
center = utils.Struct(x=0.0, y=0.0, z=0.0)
core_atoms = []
if L * Q < 30: # octahedron
L += 6
for zi in range(L):
# L2 = int(( math.sqrt(3)*( L/2-abs(zi-L/2) ) ))
L2 = (L / 2 - abs(zi - L / 2)) * 2
for xi in range(L2):
for yi in range(L2):
x = (xi - L2 * 0.5 + 0.5) * Q
y = (yi - L2 * 0.5 + 0.5) * Q
z = (zi - L * 0.5 + 0.5) * Q
core_atoms.append(
utils.Struct(
x=x,
y=y,
z=z,
element="Pb" if (xi + yi + zi) % 2 else "S",
type=pb_type if (xi + yi + zi) % 2 else s_type,
)
)
else: # cube
L += 2
for xi in range(L):
for yi in range(L):
for zi in range(L):
x = (xi - L * 0.5 + 0.5) * Q
y = (yi - L * 0.5 + 0.5) * Q
z = (zi - L * 0.5 + 0.5) * Q
core_atoms.append(
utils.Struct(
x=x,
y=y,
z=z,
element="Pb" if (xi + yi + zi) % 2 else "S",
type=pb_type if (xi + yi + zi) % 2 else s_type,
)
)
# filetypes.write_xyz('out', core_atoms)
# sys.exit()
for a in core_atoms:
a.dist = dist = utils.dist(a, center)
a.neighbors = []
for b in core_atoms:
if a is not b and utils.dist_squared(a, b) < Q ** 2 + 0.1:
a.neighbors.append(b)
core_atoms.sort(key=lambda a: a.dist)
s_atoms = [a for a in core_atoms if a.element == "S"][:N]
pb_atoms = {}
for s in s_atoms:
for a in s.neighbors:
if a.type is pb_type:
pb_atoms[a] = True
pb_atoms = pb_atoms.keys()
pb_atoms.sort(key=lambda a: a.dist)
# excess_pb_atoms = pb_atoms[N:] #tends to pick all from one side
closest_dist_to_remove = pb_atoms[N].dist
core_pb_atoms = [a for a in pb_atoms if a.dist < closest_dist_to_remove - 0.01]
marginal_pb_atoms = [
a for a in pb_atoms if (abs(a.dist - closest_dist_to_remove) < 0.01 and a not in core_pb_atoms)
]
random.shuffle(marginal_pb_atoms)
core_pb_atoms = core_pb_atoms + marginal_pb_atoms[: N - len(core_pb_atoms)]
excess_pb_atoms = [a for a in pb_atoms if a not in core_pb_atoms]
for a in s_atoms + core_pb_atoms:
atoms.append(a)
import numpy
def add_spoc_at_pb(pb):
spoc.add_to(0.0, 0.0, 0.0, atoms, bonds, angles, dihedrals)
direction = [pb.x, pb.y, pb.z]
direction /= numpy.linalg.norm(direction)
dot = numpy.dot(direction, [1.0, 0.0, 0.0])
theta = math.acos(dot)
cross = numpy.cross(direction, [1.0, 0.0, 0.0])
cross /= -numpy.linalg.norm(cross)
w = numpy.array(cross)
for a in atoms[-len(spoc.atoms) :]:
v = numpy.array([a.x, a.y, a.z])
a.x, a.y, a.z = (
v * math.cos(theta) + numpy.cross(w, v) * math.sin(theta) + w * numpy.dot(w, v) * (1 - math.cos(theta))
) # Rodrigues' rotation formula
a.x += pb.x
a.y += pb.y
a.z += pb.z
for pb in excess_pb_atoms:
add_spoc_at_pb(pb)
# add more Pb complexes as needed
new_pb = 0
while new_pb < N + 3:
x, y, z = [Q * (3 + (2 * N) ** 0.333) / 2] * 3
M = utils.rand_rotation()
x, y, z = utils.matvec(M, [x, y, z])
pb = utils.Struct(x=x, y=y, z=z, element="Pb", type=pb_type)
too_close = False
for a in atoms:
if utils.dist_squared(a, pb) < (Q + 2) ** 2:
too_close = True
break
if not too_close:
add_spoc_at_pb(pb)
new_pb += 1