def move(self, ro, bests):
"""Move atoms by a random step."""
atoms = self.atoms
velocity = copy.deepcopy(self.velocity)
best_to_use = bests[-1]
best_dist = 1e32
for i in bests:
d = i.get_bcm() - self.get_bcm()
di = np.sqrt(np.vdot(d,d))
if(di<best_dist):
best_to_use = i
best_dist = di
print "using best: ", best_to_use.get_bcm()
# PSO heuristic
for i in range(len(ro)):
for j in range(3):
velocity[i][j] = self.inertia_weight*velocity[i][j] + random.uniform(0,2)*(self.rmin[i][j]-ro[i][j]) + random.uniform(0,2)*(best_to_use.positions[i][j]-ro[i][j])
rn = ro + velocity
rn = self.push_apart(rn)
atoms.set_positions(rn)
En = self.get_energy(rn)
cm = atoms.get_center_of_mass()
atoms.translate(self.cm - cm)
rn = atoms.get_positions()
world.broadcast(rn, 0)
atoms.set_positions(rn)
return En,atoms.get_positions(),velocity
def _startup(self):
"""Initiates a run, and determines if running from previous data or
a fresh run."""
status = np.array(-1.)
exists = self._read_minima()
if world.rank == 0:
if not exists:
# Fresh run with new minima file.
status = np.array(0.)
elif not os.path.exists(self._logfile):
# Fresh run with existing or shared minima file.
status = np.array(1.)
else:
# Must be resuming from within a working directory.
status = np.array(2.)
world.barrier()
world.broadcast(status, 0)
if status == 2.:
self._resume()
else:
self._counter = 0
self._log('init')
self._log('msg', 'Performing initial optimization.')
if status == 1.:
self._log(
'msg', 'Using existing minima file with %i prior '
'minima: %s' % (len(self._minima), self._minima_traj))
self._optimize()
self._check_results()
self._counter += 1
def _startup(self):
"""Initiates a run, and determines if running from previous data or
a fresh run."""
status = np.array(-1.)
exists = self._read_minima()
if rank == 0:
if not exists:
# Fresh run with new minima file.
status = np.array(0.)
elif not os.path.exists(self._logfile):
# Fresh run with existing or shared minima file.
status = np.array(1.)
else:
# Must be resuming from within a working directory.
status = np.array(2.)
world.barrier()
world.broadcast(status, 0)
if status == 2.:
self._resume()
else:
self._counter = 0
self._log('init')
self._log('msg', 'Performing initial optimization.')
if status == 1.:
self._log('msg', 'Using existing minima file with %i prior '
'minima: %s' % (len(self._minima),
self._minima_traj))
self._optimize()
self._check_results()
self._counter += 1
def move(self, step, ro, distribution):
"""Move atoms by a random step or MD"""
# random move (BH move)
if distribution != 'molecular_dynamics':
if distribution == 'uniform':
disp = np.random.uniform(-self.dr, self.dr,
(len(self.atoms), 3))
elif distribution == 'gaussian':
disp = np.random.normal(0, self.dr, size=(len(self.atoms), 3))
elif distribution == 'linear':
distgeo = self.get_dist_geo_center()
disp = np.zeros(np.shape(self.atoms.get_positions()))
for i in range(len(disp)):
maxdist = self.dr * distgeo[i]
disp[i] = np.random.uniform(-maxdist, maxdist, 3)
elif distribution == 'quadratic':
distgeo = self.get_dist_geo_center()
disp = np.zeros(np.shape(self.atoms.get_positions()))
for i in range(len(disp)):
maxdist = self.dr * distgeo[i] * distgeo[i]
disp[i] = np.random.uniform(-maxdist, maxdist, 3)
# there is a typo in distribution or jump distribution
else:
print 'distribution flag has typo'
sys.exit()
disp = np.random.uniform(-1 * self.dr, self.dr,
(len(self.atoms), 3))
# update atoms positions by the random move
rn = ro + disp
rn = self.push_apart(rn)
self.atoms.set_positions(rn)
# refix the center of mass after random move
if self.cm is not None:
cm = self.atoms.get_center_of_mass()
self.atoms.translate(self.cm - cm)
# MD move (MH move)
else:
N = None
# use the dimer method to create an initial velocity vector for MD
if self.dimer_method:
dimer = ModifiedDimer()
N = dimer(self.atoms, self.dimer_a, self.dimer_d,
self.dimer_steps)
self._molecular_dynamics(step, N)
rn = self.atoms.get_positions()
world.broadcast(rn, 0)
return rn
def calculate_energies_and_forces(self, all=False):
"""Calculate and store the forces and energies for the band."""
images = self.images
if all:
self.forces['real'][0] = images[0].get_forces()
self.forces['real'][-1] = images[-1].get_forces()
if not self.integrate_forces:
self.energies[0] = images[0].get_potential_energy()
self.energies[-1] = images[-1].get_potential_energy()
if not self.parallel:
# Do all images - one at a time:
for i in range(1, self.nimages - 1):
self.calculate_image_forces(i)
for i in range(1, self.nimages - 1):
self.calculate_image_energies(i)
else:
# Parallelize over images: first the forces ...
i = rank * (self.nimages - 2) // size + 1
try:
self.calculate_image_forces(i)
except:
# Make sure other images also fail:
error = world.sum(1.0)
raise
else:
error = world.sum(0.0)
if error:
raise RuntimeError('Parallel NEB failed')
for i in range(1, self.nimages - 1):
root = (i - 1) * size // (self.nimages - 2)
world.broadcast(self.forces['real'][i], root)
# ... and now the energies
try:
self.calculate_image_energies(i)
except:
# Make sure other images also fail:
error = world.sum(1.0)
raise
else:
error = world.sum(0.0)
if error:
raise RuntimeError('Parallel NEB failed')
for i in range(1, self.nimages - 1):
root = (i - 1) * size // (self.nimages - 2)
world.broadcast(self.energies[i : i + 1], root)
if all and self.integrate_forces:
# fill in the first and last energies by force integration
self.energies[0] = 0.
self.calculate_image_energies(len(self.images)-1)
def move(self, ro):
"""Move atoms by a random step."""
atoms = self.atoms
disp = np.zeros(np.shape(atoms.get_positions()))
while np.alltrue(disp == np.zeros(np.shape(atoms.get_positions()))):
if self.distribution == 'uniform':
disp = np.random.uniform(-self.dr, self.dr, (len(atoms), 3))
elif self.distribution == 'gaussian':
disp = np.random.normal(0, self.dr, size=(len(atoms), 3))
elif self.distribution == 'linear':
distgeo = self.get_dist_geo_center()
disp = np.zeros(np.shape(atoms.get_positions()))
for i in range(len(disp)):
maxdist = self.dr * distgeo[i]
# disp[i] = np.random.normal(0,maxdist,3)
disp[i] = np.random.uniform(-maxdist, maxdist, 3)
elif self.distribution == 'quadratic':
distgeo = self.get_dist_geo_center()
disp = np.zeros(np.shape(atoms.get_positions()))
for i in range(len(disp)):
maxdist = self.dr * distgeo[i] * distgeo[i]
# disp[i] = np.random.normal(0,maxdist,3)
disp[i] = np.random.uniform(-maxdist, maxdist, 3)
else:
disp = np.random.uniform(-1 * self.dr, self.dr,
(len(atoms), 3))
#Lei: set all other disp to zero except those selected to move
# the number of atoms that can be moved is defined by int(active_ratio * len(atoms))
if self.active_ratio is not None:
fix_space = len(atoms) - int(self.active_ratio * len(atoms))
fix_atoms = random.sample(range(len(atoms)), fix_space)
for i in range(len(fix_atoms)):
disp[fix_atoms[i]] = (0.0, 0.0, 0.0)
#Lei: suppose to only update 'ro' with local minimum when accept == true
# if self.significant_structure == True:
# rn = self.local_min_pos + disp
# if self.significant_structure2 == True:
# ro,reng = self.get_minimum()
# rn = ro + disp
# else:
rn = ro + disp
rn = self.push_apart(rn)
atoms.set_positions(rn)
if self.cm is not None:
cm = atoms.get_center_of_mass()
atoms.translate(self.cm - cm)
rn = atoms.get_positions()
world.broadcast(rn, 0)
atoms.set_positions(rn)
return atoms.get_positions()
def move(self, ro):
"""Move atoms by a random step."""
atoms = self.atoms
# displace coordinates
disp = np.random.uniform(-1., 1., (len(atoms), 3))
rn = ro + self.dr * disp
atoms.set_positions(rn)
if self.cm is not None:
cm = atoms.get_center_of_mass()
atoms.translate(self.cm - cm)
rn = atoms.get_positions()
world.broadcast(rn, 0)
atoms.set_positions(rn)
return atoms.get_positions()
def move(self, ro):
"""Move atoms by a random step."""
atoms = self.atoms
# displace coordinates
disp = np.random.uniform(-1., 1., (len(atoms), 3))
rn = ro + self.dr * disp
atoms.set_positions(rn)
if self.cm is not None:
cm = atoms.get_center_of_mass()
atoms.translate(self.cm - cm)
rn = atoms.get_positions()
world.broadcast(rn, 0)
atoms.set_positions(rn)
return atoms.get_positions()
def get_forces(self):
images = self.images
forces = np.empty(((self.nimages - 2), self.natoms, 3))
energies = np.empty(self.nimages - 2)
if not self.parallel:
# Do all images - one at a time:
for i in range(1, self.nimages - 1):
energies[i - 1] = images[i].get_potential_energy()
forces[i - 1] = images[i].get_forces()
else:
# Parallelize over images:
i = rank * (self.nimages - 2) // size + 1
energies[i - 1] = images[i].get_potential_energy()
forces[i - 1] = images[i].get_forces()
for i in range(1, self.nimages - 1):
root = (i - 1) * size // (self.nimages - 2)
world.broadcast(energies[i - 1:i], root)
world.broadcast(forces[i - 1], root)
imax = 1 + np.argsort(energies)[-1]
self.emax = energies[imax - 1]
tangent1 = images[1].get_positions() - images[0].get_positions()
for i in range(1, self.nimages - 1):
tangent2 = (images[i + 1].get_positions() -
images[i].get_positions())
if i < imax:
tangent = tangent2
elif i > imax:
tangent = tangent1
else:
tangent = tangent1 + tangent2
tt = np.vdot(tangent, tangent)
f = forces[i - 1]
ft = np.vdot(f, tangent)
if i == imax and self.climb:
f -= 2 * ft / tt * tangent
else:
f -= ft / tt * tangent
f -= (np.vdot(tangent1 - tangent2, tangent) *
self.k / tt * tangent)
tangent1 = tangent2
return forces.reshape((-1, 3))
def move(self, ro):
"""Move atoms by a random step."""
atoms = self.atoms
if self.distribution == 'uniform':
disp = np.random.uniform(-self.dr, self.dr, (len(atoms), 3))
elif self.distribution == 'gaussian':
disp = np.random.normal(0,self.dr,size=(len(atoms), 3))
elif self.distribution == 'linear':
distgeo = self.get_dist_geo_center()
disp = np.zeros(np.shape(atoms.get_positions()))
for i in range(len(disp)):
maxdist = self.dr*distgeo[i]
# disp[i] = np.random.normal(0,maxdist,3)
disp[i] = np.random.uniform(-maxdist,maxdist,3)
elif self.distribution == 'quadratic':
distgeo = self.get_dist_geo_center()
disp = np.zeros(np.shape(atoms.get_positions()))
for i in range(len(disp)):
maxdist = self.dr*distgeo[i]*distgeo[i]
# disp[i] = np.random.normal(0,maxdist,3)
disp[i] = np.random.uniform(-maxdist,maxdist,3)
### EDIT CODE FOR PROBLEM 5 HERE ###########################################
elif self.distribution == 'your_move':
## an example of distribution to pick is as follows: a fixed size move
arr = np.random.rand(len(atoms), 3)
for y in range(len(atoms)):
for x in range(3):
arr[y][x] = self.my_distribution(arr[y][x])
disp = self.dr * arr
############################################################################
else:
disp = np.random.uniform(-1*self.dr, self.dr, (len(atoms), 3))
if self.significant_structure == True:
ro,reng = self.get_minimum()
rn = ro +disp
else:
rn = ro + disp
rn = self.push_apart(rn)
atoms.set_positions(rn)
if self.cm is not None:
cm = atoms.get_center_of_mass()
atoms.translate(self.cm - cm)
rn = atoms.get_positions()
world.broadcast(rn, 0)
atoms.set_positions(rn)
return atoms.get_positions()
def move_del(self, ro, vectors):
"""Displace atoms by randomly selected delocalized 'normal mode' """
atoms = self.atoms[self.adsorbate[0]:self.adsorbate[1]]
atms = self.atoms
numvec = len(vectors)
numcomb = self.numdelmodes
while True:
disp = np.zeros((len(ro), 3))
start = 0 #find way for start to be number of stretches
if self.constr:
mm = atoms.get_masses()
x0 = atoms.get_positions().flatten()
vv = VCG(atoms.get_chemical_symbols(), masses=mm)
start = len(
icSystem(vv(x0), len(atoms), masses=mm,
xyz=x0).getStretchBendTorsOop()[0][0])
if numcomb > len(range(start, numvec)):
numcomb = len(range(start, numvec))
w = np.random.choice(range(start, numvec),
size=numcomb,
replace=False)
for i in w:
disp[self.adsorbate[0]:(
self.adsorbate[1]), :3] += vectors[i] * np.random.uniform(
-1., 1.) #this is important if there is an adsorbate.
disp /= np.max(np.abs(disp))
#from here on, everything is JUST COPIED from self.move(); should be sane
rn = ro + self.dr * disp
atms.set_positions(rn)
if self.cm is not None:
cm = atms.get_center_of_mass()
atms.translate(self.cm - cm)
rn = atms.get_positions()
world.broadcast(rn, 0)
atms.set_positions(rn)
if self.check_distances(atoms):
break
else:
print 'HIIIIGHWAY TO THE DANGERZONE!'
atoms.write('Maverick.xyz')
return atms.get_positions()
def get_forces(self):
"""Evaluate and return the forces."""
if self.parallel and self.images[1].minmode_init:
propagate_initial_values = True
else:
propagate_initial_values = False
# Update the clean forces and energies
self.calculate_energies_and_forces()
if self.parallel and propagate_initial_values:
for i in range(1, self.nimages - 1):
if self.images[i].eigenmodes is None:
self.images[i].eigenmodes = [np.zeros(self.images[i].get_positions().shape)]
self.images[i].minmode_init = False
self.images[i].rotation_required = True
self.images[i].check_atoms = self.images[i].atoms.copy()
root = (i - 1) * size // (self.nimages - 2)
world.broadcast(self.images[i].eigenmodes[0], root)
# Update the highest energy image
self.imax = 1 + np.argsort(self.energies[1:-1])[-1]
self.emax = self.energies[self.imax]
# BUG: self.imax can be an endimage.
# Calculate the tangents of all the images
self.update_tangents()
# IDEA: If f_c_perp is small force dimer rotation?
# Calculate the modes
self.calculate_eigenmodes()
# Prjoect the forces for each image
self.invert_eigenmode_forces()
self.project_forces(sort = 'dimer')
if self.plot_devplot:
self.plot_pseudo_3d_pes()
self.control.increment_counter('optcount')
return self.forces['neb'][1:self.nimages-1].reshape((-1, 3))
def move(self, ro):
"""Move atoms by a random step."""
atoms = self.atoms
# displace coordinates
disp = np.random.uniform(-1., 1., (len(atoms), 3))
rn = ro + self.dr * disp
# exchange two atoms
from numpy.random import randint
ind = randint(0,12, size=2)
postemp = rn[ind[0]].copy()
rn[ind[0]] = rn[ind[1]]
rn[ind[1]] = postemp
#
atoms.set_positions(rn)
if self.cm is not None:
cm = atoms.get_center_of_mass()
atoms.translate(self.cm - cm)
rn = atoms.get_positions()
world.broadcast(rn, 0)
atoms.set_positions(rn)
return atoms.get_positions()
def move(self, ro, bests):
"""Move atoms by a random step."""
atoms = self.atoms
velocity = copy.deepcopy(self.velocity)
# PSO heuristic
for i in range(len(ro)):
for j in range(3):
velocity[i][j] = self.inertia_weight*velocity[i][j] + random.uniform(0,2)*(self.rmin[i][j]-ro[i][j]) + random.uniform(0,2)*(bests[-1].positions[i][j]-ro[i][j])
rn = ro + velocity
rn = self.push_apart(rn)
atoms.set_positions(rn)
En = self.get_energy(rn)
cm = atoms.get_center_of_mass()
atoms.translate(self.cm - cm)
rn = atoms.get_positions()
world.broadcast(rn, 0)
atoms.set_positions(rn)
return En,atoms.get_positions(),velocity
def calculate_eigenmodes(self):
if self.parallel:
i = rank * (self.nimages - 2) // size + 1
try:
self.calculate_image_eigenmode(i)
except:
# Make sure other images also fail:
error = world.sum(1.0)
raise
else:
error = world.sum(0.0)
if error:
raise RuntimeError('Parallel ERM failed during eigenmode calculations.')
for i in range(1, self.nimages - 1):
if self.images[i].eigenmodes is None:
self.images[i].eigenmodes = [np.zeros(self.images[i].get_positions().shape)]
root = (i - 1) * size // (self.nimages - 2)
world.broadcast(self.images[i].eigenmodes[0], root)
# world.broadcast(self.images[i : i + 1].curvatures, root)
else:
for i in range(1, self.nimages - 1):
self.calculate_image_eigenmode(i)
def move(self, ro):
"""Move atoms by a random step."""
atoms = self.atoms
# displace coordinates
#disp = np.random.uniform(-1., 1., (len(atoms), 3))
disp = np.random.uniform(-1.0, 1.0, (int(len(atoms) / 3), 3))
final_dis = []
for i in range(int(len(atoms) / 3)):
d = disp[i].tolist()
for i in range(3):
final_dis.append(d)
disp = np.array(final_dis)
rn = ro + self.dr * disp
atoms.set_positions(rn)
if self.cm is not None:
cm = atoms.get_center_of_mass()
atoms.translate(self.cm - cm)
print('ajusted')
rn = atoms.get_positions()
world.broadcast(rn, 0)
atoms.set_positions(rn)
return atoms.get_positions()
def calculate_energies_and_forces(self):
images = self.images
if not self.parallel:
# Do all images - one at a time:
for i in range(1, self.nimages - 1):
self.calculate_image_energies_and_forces(i)
else:
# Parallelize over images:
i = rank * (self.nimages - 2) // size + 1
try:
self.calculate_image_energies_and_forces(i)
except:
# Make sure other images also fail:
error = world.sum(1.0)
raise
else:
error = world.sum(0.0)
if error:
raise RuntimeError('Parallel NEB failed')
for i in range(1, self.nimages - 1):
root = (i - 1) * size // (self.nimages - 2)
world.broadcast(self.energies[i : i + 1], root)
world.broadcast(self.forces['real'][i], root)
def test_attach_randomly():
"""Attach two molecules in random orientation."""
m1 = molecule('C6H6')
m2 = molecule('CF4')
distance = 2.5
if world.size > 1:
"Check that the coordinates are correctly distributed from master."
rng = np.random.RandomState(world.rank) # ensure different seed
atoms = attach_randomly_and_broadcast(m1, m2, distance, rng)
p0 = 1. * atoms[-1].position
world.broadcast(p0, 0)
for i in range(1, world.size):
pi = 1. * atoms[-1].position
world.broadcast(pi, i)
assert pi == pytest.approx(p0, 1e-8)
"Check that every core has its own structure"
rng = np.random.RandomState(world.rank) # ensure different seed
atoms = attach_randomly(m1, m2, distance, rng)
p0 = 1. * atoms[-1].position
world.broadcast(p0, 0)
for i in range(1, world.size):
pi = 1. * atoms[-1].position
world.broadcast(pi, i)
assert pi != pytest.approx(p0, 1e-8)
rng = np.random.RandomState(42) # ensure the same seed
pos2_ac = np.zeros((5, 3))
N = 25
for i in range(N):
atoms = attach_randomly(m1, m2, distance, rng=rng)
pos2_ac += atoms.get_positions()[12:, :]
# the average position should be "zero" approximately
assert (np.abs(pos2_ac / N) <= 1).all()
def move(self, ro, bests):
"""Move atoms by a random step."""
atoms = self.atoms
velocity = copy.deepcopy(self.velocity)
do_pso = True
if self.method == 'firefly':
do_pso = False
elif self.method == 'PSO_split':
best_to_use = bests[-1]
best_dist = 1e32
for i in bests:
d = i.get_bcm() - self.get_bcm()
di = np.sqrt(np.vdot(d,d))
if(di<best_dist):
best_to_use = i
best_dist = di
do_pso = True
else:
do_pso = True
best_to_use = bests[-1]
# PSO heuristic
if (not do_pso):
r_arr = [None] * len(bests)
r_sum = 0
pe_sum = 0
for i in range(len(bests)):
d = self.get_bcm() - bests[i].get_bcm()
r_arr[i] = np.sqrt(np.vdot(d,d))
r_sum += r_arr[i]
pe_sum += bests[i].get_energy()
r_mean = r_sum / len(bests)
pe_mean = abs(pe_sum / len(bests))
denom = math.sqrt(r_mean*pe_mean)
attract_arr = [None] * len(bests)
for i in range(len(bests)):
numer = bests[i].get_energy() * r_arr[i]
numer *= numer
attract_arr[i] = math.e**(-1*numer/denom)
sort_attract = sorted(attract_arr)
velocity = self.inertia_weight*velocity
E = np.random.normal(1,.01*min(15,sort_attract[-2]/max(0.0001,sort_attract[-1])), size=(len(atoms),3))
for i in range(len(bests)):
velocity += attract_arr[i]*(bests[i].positions-ro)*E/sort_attract[-1]
else:
print "using best: ", best_to_use.get_bcm()
for i in range(len(ro)):
for j in range(3):
velocity[i][j] = self.inertia_weight*velocity[i][j] + random.uniform(0,2)*(self.rmin[i][j]-ro[i][j]) + random.uniform(0,2)*(best_to_use.positions[i][j]-ro[i][j])
rn = ro + velocity
rn = self.push_apart(rn)
atoms.set_positions(rn)
En = self.get_energy(rn)
cm = atoms.get_center_of_mass()
atoms.translate(self.cm - cm)
rn = atoms.get_positions()
world.broadcast(rn, 0)
atoms.set_positions(rn)
return En,atoms.get_positions(),velocity