def calculate(coords):
coord_count = 0
for s in NEB.states[1:-1]:
for a in s:
a.x, a.y, a.z = coords[coord_count], coords[coord_count+1], coords[coord_count+2]
coord_count += 3
#start DFT jobs
running_jobs = []
for i,state in enumerate(NEB.states[1:-1]):
guess = '' if NEB.step==0 else ' Guess=Read'
running_jobs.append( job('%s-%d-%d'%(NEB.name,NEB.step,i), NEB.theory+' Force'+guess, state, queue=queue, force=True, previous=('%s-%d-%d'%(NEB.name,NEB.step-1,i)) if NEB.step>0 else None, extra_section=extra_section) )
#wait for jobs to finish
for j in running_jobs: j.wait()
#get forces and energies from DFT calculations
energies = []
for i,state in enumerate(NEB.states[1:-1]):
try:
new_energy, new_atoms = parse_atoms('%s-%d-%d'%(NEB.name,NEB.step,i))
except:
print 'Job failed: %s-%d-%d'%(NEB.name,NEB.step,i); exit()
energies.append(new_energy)
for a,b in zip(state, new_atoms):
a.fx = b.fx; a.fy = b.fy; a.fz = b.fz
dft_energies = copy.deepcopy(energies)
#add spring forces to atoms
for i,state in enumerate(NEB.states[1:-1]):
for j,b in enumerate(state):
a,c = NEB.states[i-1][j], NEB.states[i+1][j]
if j in spring_atoms:
b.fx += NEB.k*(a.x-b.x) + NEB.k*(c.x-b.x)
b.fy += NEB.k*(a.y-b.y) + NEB.k*(c.y-b.y)
b.fz += NEB.k*(a.z-b.z) + NEB.k*(c.z-b.z)
energies[i] += 0.5*NEB.k*(utils.dist_squared(a,b) + utils.dist_squared(b,c))
#set error
NEB.error = sum(energies)
#set forces
NEB.forces = []
for state in NEB.states[1:-1]:
for a in state:
NEB.forces += [-a.fx, -a.fy, -a.fz] #derivative of the error
#increment step
NEB.step += 1
#write to xyz file
NEB.xyz = open(name+'.xyz', 'w')
for state in NEB.states:
files.write_xyz(state, NEB.xyz)
NEB.xyz.close()
#print data
print NEB.step, NEB.error, ('%10.7g '*len(dft_energies)) % tuple(dft_energies)
def remove_unattached_ligands(atoms, bonds, angles, dihedrals, spoc):
sulfurs = [a for a in atoms if a.element == "S"]
remove_count = 0
atoms_to_remove = {}
for i, a in enumerate(atoms):
if a.element == "Pb":
nearest_sulfur = min([utils.dist_squared(a, b) for b in sulfurs])
if nearest_sulfur > 5 ** 2:
# remove whole spoc, based on size of spoc and where pb is within it (always first?)
remove_count = len(spoc.atoms)
if remove_count > 0:
remove_count -= 1
atoms_to_remove[a] = True
atoms = [a for a in atoms if a not in atoms_to_remove]
bonds = [b for b in bonds if b.atoms[0] not in atoms_to_remove and b.atoms[1] not in atoms_to_remove]
angles = [
a
for a in angles
if a.atoms[0] not in atoms_to_remove and a.atoms[1] not in atoms_to_remove and a.atoms[2] not in atoms_to_remove
]
dihedrals = [
d
for d in dihedrals
if d.atoms[0] not in atoms_to_remove
and d.atoms[1] not in atoms_to_remove
and d.atoms[2] not in atoms_to_remove
and d.atoms[3] not in atoms_to_remove
]
return atoms, bonds, angles, dihedrals
def do_route(route, limit): # return new route if limit == 0: return route # don't change depot for i in range(0, len(route)-2): u_1 = route[i].pos u_2 = route[i+1].pos for j in range(i+1, len(route)-1): v_1 = route[j].pos v_2 = route[j+1].pos if ( dist_squared(u_1, u_2) + dist_squared(v_1, v_2) ) > \ ( dist_squared(u_1, v_1) + dist_squared(u_2, v_2) ): # is better, put v_1 after u_1, then in reverse order until u_2, then v_2 # TODO: do in place? route_prime = route[:i+1] + list(reversed(route[i+1:j+1])) + route[j+1:] return do_route(route_prime, limit-1) return route # nothing found
def get_bonds(atoms): bonds = [] for a in atoms: a.bonded = [] for i,a in enumerate(atoms): for b in atoms[i+1:]: d = utils.dist_squared(a,b)**0.5 if (a.element not in [1,'H'] and b.element not in [1,'H'] and d<2.) or (d < 1.2 and (a.element in [1,'H'])!=(b.element in [1,'H']) ): bonds.append( utils.Struct(atoms=(a,b), d=d, e=None) ) #offset from current, distance a.bonded.append(b) b.bonded.append(a) return bonds
def do_route(route, limit): # return new route
if limit == 0:
return route
# don't change depot
for i in range(0, len(route) - 2):
u_1 = route[i].pos
u_2 = route[i + 1].pos
for j in range(i + 1, len(route) - 1):
v_1 = route[j].pos
v_2 = route[j + 1].pos
if ( dist_squared(u_1, u_2) + dist_squared(v_1, v_2) ) > \
( dist_squared(u_1, v_1) + dist_squared(u_2, v_2) ):
# is better, put v_1 after u_1, then in reverse order until u_2, then v_2
# TODO: do in place?
route_prime = route[:i + 1] + list(
reversed(route[i + 1:j + 1])) + route[j + 1:]
return do_route(route_prime, limit - 1)
return route # nothing found
def _get_closest_depots(instance, genotype):
"""Returns the closest depots for the genotype values. Currently unrandomized."""
raise RuntimeError("don't use anymore")
closest_depots=[]
for vehicle_base in genotype:
#pprint.pprint(list( ( ( (vehicle_base[0]-d.pos[0])**2 + (vehicle_base[1]-d.pos[1])**2 ), d_id) for (d_id, d) in enumerate(instance.depots) ) )
# use squared dist
closest = min( (dist_squared(vehicle_base, d.pos), d_id) for (d_id, d) in enumerate(instance.depots) )
closest_depots.append( instance.depots[ closest[1] ] )
return closest_depots
def _get_closest_depots(instance, genotype):
"""Returns the closest depots for the genotype values. Currently unrandomized."""
raise RuntimeError("don't use anymore")
closest_depots = []
for vehicle_base in genotype:
#pprint.pprint(list( ( ( (vehicle_base[0]-d.pos[0])**2 + (vehicle_base[1]-d.pos[1])**2 ), d_id) for (d_id, d) in enumerate(instance.depots) ) )
# use squared dist
closest = min((dist_squared(vehicle_base, d.pos), d_id)
for (d_id, d) in enumerate(instance.depots))
closest_depots.append(instance.depots[closest[1]])
return closest_depots
def parse_tinker_arc(molecule_file, parameter_file=None):
if parameter_file:
elements, atom_types, bond_types, angle_types, dihedral_types = lammps.parse_opls_parameters(parameter_file)
atoms = []
for line in open(molecule_file):
columns = line.split()
if len(columns)>3:
atoms.append( utils.Struct(index=int(columns[0]), element=columns[1], x=float(columns[2]), y=float(columns[3]), z=float(columns[4]), bonded=[int(s) for s in columns[6:]], type=([t for t in atom_types if t.index==int(columns[5][-3:])][0] if parameter_file else None), charge=None) )
if len(columns[5])>3:
atom_types.append( copy.deepcopy(atoms[-1].type) )
atoms[-1].type.index = int(columns[5])
bond_set = {}
for a in atoms:
a.bonded = [atoms[i-1] for i in a.bonded]
for b in a.bonded:
if (b,a) not in bond_set:
bond_set[(a,b)] = True
bonds = [utils.Struct(atoms=b, d=utils.dist_squared(b[0],b[1])**0.5, e=None, type=None) for b in bond_set.keys()]
angles, dihedrals = get_angles_and_dihedrals(atoms, bonds)
return atoms, bonds, angles, dihedrals
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
def radius_of_gyration(atoms):
center = center_of_geometry(atoms)
return math.sqrt(1.0 / len(atoms) * sum([utils.dist_squared(a, center) for a in atoms]))
def calculate(coords):
coord_count = 0
for s in NEB.states[1:-1]:
for a in s:
a.x, a.y, a.z = coords[coord_count], coords[
coord_count + 1], coords[coord_count + 2]
coord_count += 3
#start DFT jobs
running_jobs = []
for i, state in enumerate(NEB.states[1:-1]):
guess = '' if NEB.step == 0 else ' Guess=Read'
running_jobs.append(
job('%s-%d-%d' % (NEB.name, NEB.step, i),
NEB.theory + ' Force' + guess,
state,
queue=queue,
force=True,
previous=('%s-%d-%d' % (NEB.name, NEB.step - 1, i))
if NEB.step > 0 else None,
extra_section=extra_section))
#wait for jobs to finish
for j in running_jobs:
j.wait()
#get forces and energies from DFT calculations
energies = []
for i, state in enumerate(NEB.states[1:-1]):
try:
new_energy, new_atoms = parse_atoms(
'%s-%d-%d' % (NEB.name, NEB.step, i))
except:
print 'Job failed: %s-%d-%d' % (NEB.name, NEB.step, i)
exit()
energies.append(new_energy)
for a, b in zip(state, new_atoms):
a.fx = b.fx
a.fy = b.fy
a.fz = b.fz
dft_energies = copy.deepcopy(energies)
#add spring forces to atoms
for i, state in enumerate(NEB.states[1:-1]):
for j, b in enumerate(state):
a, c = NEB.states[i - 1][j], NEB.states[i + 1][j]
if j in spring_atoms:
b.fx += NEB.k * (a.x - b.x) + NEB.k * (c.x - b.x)
b.fy += NEB.k * (a.y - b.y) + NEB.k * (c.y - b.y)
b.fz += NEB.k * (a.z - b.z) + NEB.k * (c.z - b.z)
energies[i] += 0.5 * NEB.k * (utils.dist_squared(
a, b) + utils.dist_squared(b, c))
#set error
NEB.error = sum(energies)
#set forces
NEB.forces = []
for state in NEB.states[1:-1]:
for a in state:
NEB.forces += [-a.fx, -a.fy,
-a.fz] #derivative of the error
#increment step
NEB.step += 1
#write to xyz file
NEB.xyz = open(name + '.xyz', 'w')
for state in NEB.states:
files.write_xyz(state, NEB.xyz)
NEB.xyz.close()
#print data
print NEB.step, NEB.error, (
'%10.7g ' * len(dft_energies)) % tuple(dft_energies)