def test_emt1(testdir):
a = 3.6
b = a / 2
cu = Atoms('Cu2Ag',
positions=[(0, 0, 0),
(b, b, 0),
(a, a, b)],
calculator=EMT())
e0 = cu.get_potential_energy()
print(e0)
d0 = cu.get_distance(0, 1)
cu.set_constraint(FixBondLength(0, 1))
def f():
print(cu.get_distance(0, 1))
qn = BFGS(cu)
with Trajectory('cu2ag.traj', 'w', cu) as t:
qn.attach(t.write)
qn.attach(f)
qn.run(fmax=0.001)
assert abs(cu.get_distance(0, 1) - d0) < 1e-14
def test_emt1():
from ase import Atoms
from ase.calculators.emt import EMT
from ase.constraints import FixBondLength
from ase.io import Trajectory
from ase.optimize import BFGS
a = 3.6
b = a / 2
cu = Atoms('Cu2Ag',
positions=[(0, 0, 0), (b, b, 0), (a, a, b)],
calculator=EMT())
e0 = cu.get_potential_energy()
print(e0)
d0 = cu.get_distance(0, 1)
cu.set_constraint(FixBondLength(0, 1))
t = Trajectory('cu2ag.traj', 'w', cu)
qn = BFGS(cu)
qn.attach(t.write)
def f():
print(cu.get_distance(0, 1))
qn.attach(f)
qn.run(fmax=0.001)
assert abs(cu.get_distance(0, 1) - d0) < 1e-14
def test_au111(wrap):
zpos = cos(134.3 / 2.0 * pi / 180.0) * 1.197
xpos = sin(134.3 / 2.0 * pi / 180.0) * 1.19
co2 = Atoms('COO',
positions=[(-xpos + 1.2, 0, -zpos), (-xpos + 1.2, -1.1, -zpos),
(-xpos + 1.2, 1.1, -zpos)])
slab = fcc111('Au', size=(2, 2, 4), vacuum=2 * 5, orthogonal=True)
slab.center()
add_adsorbate(slab, co2, 1.5, 'bridge')
slab.set_pbc((True, True, False))
d0 = co2.get_distance(-3, -2)
d1 = co2.get_distance(-3, -1)
d2 = co2.get_distance(-2, -1)
calc = EMT()
slab.set_calculator(calc)
if wrap:
# Remap into the cell so bond is actually wrapped:
slab.set_scaled_positions(slab.get_scaled_positions() % 1.0)
constraint = FixLinearTriatomic(triples=[(-2, -3, -1)])
slab.set_constraint(constraint)
dyn = BFGS(slab, trajectory='relax_%d.traj' % wrap)
dyn.run(fmax=0.05)
assert abs(slab.get_distance(-3, -2, mic=1) - d0) < 1e-9
assert abs(slab.get_distance(-3, -1, mic=1) - d1) < 1e-9
assert abs(slab.get_distance(-2, -1, mic=1) - d2) < 1e-9
def test_external_force():
"""Tests for class ExternalForce in ase/constraints.py"""
f_ext = 0.2
atom1 = 0
atom2 = 1
atom3 = 2
atoms = Atoms('H3', positions=[(0, 0, 0), (0.751, 0, 0), (0, 1., 0)])
atoms.calc = EMT()
# Without external force
optimize(atoms)
dist1 = atoms.get_distance(atom1, atom2)
# With external force
con1 = ExternalForce(atom1, atom2, f_ext)
atoms.set_constraint(con1)
optimize(atoms)
dist2 = atoms.get_distance(atom1, atom2)
# Distance should increase due to the external force
assert dist2 > dist1
# Combine ExternalForce with FixBondLength
# Fix the bond on which the force acts
con2 = FixBondLength(atom1, atom2)
# ExternalForce constraint at the beginning of the list!!!
atoms.set_constraint([con1, con2])
optimize(atoms)
f_con = con2.constraint_forces
# It was already optimized with this external force, therefore
# the constraint force should be almost zero
assert norm(f_con[0]) <= fmax
# To get the complete constraint force (with external force),
# use only the FixBondLength constraint, after the optimization with
# ExternalForce
atoms.set_constraint(con2)
optimize(atoms)
f_con = con2.constraint_forces[0]
assert round(norm(f_con), 2) == round(abs(f_ext), 2)
# Fix another bond and incrase the external force
f_ext *= 2
con1 = ExternalForce(atom1, atom2, f_ext)
d1 = atoms.get_distance(atom1, atom3)
con2 = FixBondLength(atom1, atom3)
# ExternalForce constraint at the beginning of the list!!!
atoms.set_constraint([con1, con2])
optimize(atoms)
d2 = atoms.get_distance(atom1, atom3)
# Fixed distance should not change
assert round(d1, 5) == round(d2, 5)
def test_CO2linear_Au111_langevin(testdir):
"""Test Langevin with constraints for rigid linear
triatomic molecules"""
rng = np.random.RandomState(0)
eref = 3.133526
zpos = cos(134.3 / 2.0 * pi / 180.0) * 1.197
xpos = sin(134.3 / 2.0 * pi / 180.0) * 1.19
co2 = Atoms('COO',
positions=[(-xpos + 1.2, 0, -zpos), (-xpos + 1.2, -1.1, -zpos),
(-xpos + 1.2, 1.1, -zpos)])
slab = fcc111('Au', size=(2, 2, 4), vacuum=2 * 5, orthogonal=True)
slab.center()
add_adsorbate(slab, co2, 1.5, 'bridge')
slab.set_pbc((True, True, False))
d0 = co2.get_distance(-3, -2)
d1 = co2.get_distance(-3, -1)
d2 = co2.get_distance(-2, -1)
calc = EMT()
slab.calc = calc
constraint = FixLinearTriatomic(triples=[(-2, -3, -1)])
slab.set_constraint(constraint)
fr = 0.1
dyn = Langevin(slab,
2.0 * units.fs,
temperature_K=300,
friction=fr,
trajectory='langevin_%.1f.traj' % fr,
logfile='langevin_%.1f.log' % fr,
loginterval=20,
rng=rng)
dyn.run(100)
# Check that the temperature is within a reasonable range
T = slab.get_temperature()
assert T > 100
assert T < 500
# Check that the constraints work
assert abs(slab.get_distance(-3, -2, mic=1) - d0) < 1e-9
assert abs(slab.get_distance(-3, -1, mic=1) - d1) < 1e-9
assert abs(slab.get_distance(-2, -1, mic=1) - d2) < 1e-9
# If the energy differs from the reference energy
# it is most probable that the redistribution of
# random forces in Langevin is not working properly
assert abs(slab.get_potential_energy() - eref) < 1e-4
def test_atom():
m = Atoms('H2')
a = m[0]
b = Atom('H')
for c in [a, b]:
assert c.x == 0
c.z = 24.0
assert c.position[2] == 24.0
assert c.symbol == 'H'
c.number = 92
assert c.symbol == 'U'
c.symbol = 'Fe'
assert c.number == 26
c.tag = 42
assert c.tag == 42
c.momentum = (1, 2, 3)
assert m[0].tag == 42
momenta = m.get_momenta()
assert abs(momenta).sum() > 0
m = Atoms('LiH')
for a in m:
print(a.symbol)
for a in m:
if a.symbol == 'H':
a.z = 0.75
assert m.get_distance(0, 1) == 0.75
a = m.pop()
m += a
del m[:1]
print(m)
def test_CO2_Au111(wrap, testdir):
zpos = cos(134.3 / 2.0 * pi / 180.0) * 1.197
xpos = sin(134.3 / 2.0 * pi / 180.0) * 1.19
co2 = Atoms('COO', positions=[(-xpos + 1.2, 0, -zpos),
(-xpos + 1.2, -1.1, -zpos),
(-xpos + 1.2, 1.1, -zpos)])
slab = fcc111('Au', size=(2, 2, 4), vacuum=2 * 5, orthogonal=True)
slab.center()
add_adsorbate(slab, co2, 1.5, 'bridge')
slab.set_pbc((True, True, False))
d0 = co2.get_distance(-3, -2)
d1 = co2.get_distance(-3, -1)
calc = EMT()
slab.calc = calc
if wrap:
# Remap into the cell so bond is actually wrapped:
slab.set_scaled_positions(slab.get_scaled_positions() % 1.0)
constraint = FixBondLengths([[-3, -2], [-3, -1]])
slab.set_constraint(constraint)
with BFGS(slab, trajectory='relax_%d.traj' % wrap) as dyn:
dyn.run(fmax=0.05)
assert abs(slab.get_distance(-3, -2, mic=1) - d0) < 1e-9
assert abs(slab.get_distance(-3, -1, mic=1) - d1) < 1e-9
def test_qmmm_acn():
import numpy as np
import ase.units as units
from ase import Atoms
from ase.calculators.acn import (ACN, m_me, r_cn, r_mec,
sigma_me, sigma_c, sigma_n,
epsilon_me, epsilon_c, epsilon_n)
from ase.calculators.qmmm import SimpleQMMM, LJInteractionsGeneral, EIQMMM
from ase.constraints import FixLinearTriatomic
from ase.optimize import BFGS
# From https://www.sciencedirect.com/science/article/pii/S0166128099002079
eref = 4.9 * units.kcal / units.mol
dref = 3.368
aref = 79.1
sigma = np.array([sigma_me, sigma_c, sigma_n])
epsilon = np.array([epsilon_me, epsilon_c, epsilon_n])
inter = LJInteractionsGeneral(sigma, epsilon, sigma, epsilon, 3)
for calc in [ACN(),
SimpleQMMM([0, 1, 2], ACN(), ACN(), ACN()),
SimpleQMMM([0, 1, 2], ACN(), ACN(), ACN(), vacuum=3.0),
EIQMMM([0, 1, 2], ACN(), ACN(), inter),
EIQMMM([0, 1, 2], ACN(), ACN(), inter, vacuum=3.0),
EIQMMM([3, 4, 5], ACN(), ACN(), inter, vacuum=3.0)]:
dimer = Atoms('CCNCCN',
[(-r_mec, 0, 0),
(0, 0, 0),
(r_cn, 0, 0),
(r_mec, 3.7, 0),
(0, 3.7, 0),
(-r_cn, 3.7, 0)])
masses = dimer.get_masses()
masses[::3] = m_me
dimer.set_masses(masses)
dimer.calc = calc
fixd = FixLinearTriatomic(triples=[(0, 1, 2), (3, 4, 5)])
dimer.set_constraint(fixd)
opt = BFGS(dimer, maxstep=0.04,
trajectory=calc.name + '.traj', logfile=calc.name + 'd.log')
opt.run(0.001, steps=1000)
e0 = dimer.get_potential_energy()
d0 = dimer.get_distance(1, 4)
a0 = dimer.get_angle(2, 1, 4)
fmt = '{0:>25}: {1:.3f} {2:.3f} {3:.1f}'
print(fmt.format(calc.name, -e0, d0, a0))
assert abs(e0 + eref) < 0.013
assert abs(d0 - dref) < 0.224
assert abs(a0 - aref) < 2.9
print(fmt.format('reference', eref, dref, aref))
def test_n2():
from ase import Atoms
from ase.calculators.emt import EMT
from ase.optimize import QuasiNewton
n2 = Atoms('N2', positions=[(0, 0, 0), (0, 0, 1.1)], calculator=EMT())
QuasiNewton(n2).run(0.01)
print(n2.get_distance(0, 1), n2.get_potential_energy())
class Polycrystal(OrthoBox):
def __init__(self, boxsize, numcrystallites, crystallitenames,
crystallitecenters):
super().__init__(boxsize)
self.numcrystallites = numcrystallites
self.crystaltype = crystallitenames
self.crystallitecenters = crystallitecenters
self.crystallites = [Atoms() for n in range(numcrystallites)]
self.crystalliteids = [[i] for i in range(numcrystallites)]
def setgraintypes(self, typemap):
self.graintypes = typemap
def embedatoms(self, maskcrystal, grainid, keepatoms, compress=True):
crystal = maskcrystal.copy()
slicecrystal = crystal[keepatoms]
natoms = slicecrystal.get_global_number_of_atoms()
self.crystalliteids[grainid] = [grainid for i in range(natoms)]
self.crystallites[grainid] = slicecrystal
def compress(self):
polycrystalbox = self.sidelens + self.angles
self.polycrystal = Atoms(cell=polycrystalbox, pbc=True)
for i, c in enumerate(self.crystallites):
cids = self.crystalliteids[i]
c.set_tags(cids)
self.polycrystal += c
self.natoms = self.polycrystal.get_global_number_of_atoms()
chemsym = set(self.polycrystal.get_chemical_symbols())
self.chemmap = {c: i + 1 for i, c in enumerate(chemsym)}
self.nspecies = len(chemsym)
def pruneoverlap(self, criteria=0.5, verbose=False):
''' TODO: remove atoms overlapping assume PBC conditions'''
print(
"NOTICE: The pruning routine does not accoutn for stoichiometry restrictions."
)
cutoff = neighborlist.natural_cutoffs(self.polycrystal)
neighbors = neighborlist.NeighborList(cutoff,
self_interaction=False,
bothways=False)
neighbors.update(self.polycrystal)
isremoved = []
for a in self.polycrystal:
ineigh = neighbors.get_neighbors(a.index)
for j in ineigh[0]:
r = self.polycrystal.get_distance(a.index, j, mic=True)
if r < criteria and j not in isremoved:
isremoved.append(j)
if verbose:
print("Atom ID %i removed due to overlap!" % (j))
del self.polycrystal[isremoved]
self.natoms = self.polycrystal.get_global_number_of_atoms()
def test_atoms_distance():
# Setup a chain of H,O,C
# H-O Dist = 2
# O-C Dist = 3
# C-H Dist = 5 with mic=False
# C-H Dist = 4 with mic=True
a = Atoms('HOC', positions=[(1, 1, 1), (3, 1, 1), (6, 1, 1)])
a.set_cell((9, 2, 2))
a.set_pbc((True, False, False))
# Calculate indiviually with mic=True
assert a.get_distance(0, 1, mic=True) == 2
assert a.get_distance(1, 2, mic=True) == 3
assert a.get_distance(0, 2, mic=True) == 4
# Calculate indiviually with mic=False
assert a.get_distance(0, 1, mic=False) == 2
assert a.get_distance(1, 2, mic=False) == 3
assert a.get_distance(0, 2, mic=False) == 5
# Calculate in groups with mic=True
assert (a.get_distances(0, [1, 2], mic=True) == [2, 4]).all()
# Calculate in groups with mic=False
assert (a.get_distances(0, [1, 2], mic=False) == [2, 5]).all()
# Calculate all with mic=True
assert (a.get_all_distances(mic=True) == [[0, 2, 4],
[2, 0, 3],
[4, 3, 0]]).all()
# Calculate all with mic=False
assert (a.get_all_distances(mic=False) == [[0, 2, 5],
[2, 0, 3],
[5, 3, 0]]).all()
# Scale Distance
old = a.get_distance(0, 1)
a.set_distance(0, 1, 0.9, add=True, factor=True)
new = a.get_distance(0, 1)
diff = new - 0.9 * old
assert abs(diff) < 10e-6
# Change Distance
old = a.get_distance(0, 1)
a.set_distance(0, 1, 0.9, add=True)
new = a.get_distance(0, 1)
diff = new - old - 0.9
assert abs(diff) < 10e-6
def iterate(atoms : Atoms):
delta = 0.01
global bond1
global bond2
force = atoms.get_forces()[i['DIFFATOM']]
bond1_dist = atoms.get_distance(i['DIFFATOM'], i['CONSATOM1'], vector=False)
bond1_vector = atoms.get_distance(i['DIFFATOM'], i['CONSATOM1'], vector=True )
bond1_unit = bond1_vector / bond1_dist
bond2_dist = atoms.get_distance(i['DIFFATOM'], i['CONSATOM2'], vector=False)
bond2_vector = atoms.get_distance(i['DIFFATOM'], i['CONSATOM2'], vector=True )
bond2_unit = bond2_vector / bond2_dist
bond1_projection = np.dot(force, bond1_unit)
bond2_projection = np.dot(force, bond2_unit)
if abs(bond1_projection) > bond2_projection:
if bond1_projection > 0:
print('Growing Bond 1')
bond1 += delta
bond2 -= delta / 4
else:
print('Shrinking Bond 1')
bond1 -= delta
bond2 += delta / 4
else:
if bond2_projection > 0:
print('Growing Bond 2')
bond2 += delta
bond1 -= delta / 4
else:
print('Shrinking Bond 2')
bond2 -= delta
bond1 += delta / 4
bonds = [
[ bond1, [ i['DIFFATOM'], i['CONSATOM1'] ] ],
[ bond2, [ i['DIFFATOM'], i['CONSATOM2'] ] ]
]
return FixInternals(bonds=bonds)
def get_fingerprint(Optimizer, indiv, binsize, cutoffdist):
"""Function to calculate the fingerprint of a structure
"""
rs = numpy.linspace(0.0, cutoffdist, cutoffdist / binsize)
indi = indiv[0]
Vuc = indi.get_volume()
if Optimizer.structure == 'Defect':
solid = Atoms()
solid.extend(indi)
solid.extend(indiv.bulki)
elif Optimizer.structure == 'Crystal':
solid = indi.repeat([3, 3, 3])
else:
solid = indi.copy()
syms = sorted(list(set([atm.symbol for atm in solid])))
fingerprints = []
for i in range(len(syms)):
for j in range(i, len(syms)):
indl = [atm for atm in indi if atm.symbol == syms[i]]
ind = Atoms()
for one in indl:
ind.append(one)
soll = [atm for atm in solid if atm.symbol == syms[j]]
sol = Atoms()
for one in soll:
sol.append(one)
soli = [atm for atm in solid if atm.symbol == syms[i]]
value = []
for R in rs:
value2 = []
for k in range(len(ind)):
value1 = []
for m in range(len(sol)):
if k != m:
rij = sol.get_distance(k, m, mic=True)
if rij == 0:
pass
#pdb.set_trace()
value1.append(
dirac(R, a=rij, sig=0.02) * 1 /
(4 * math.pi * rij**2 * binsize * len(soli) *
len(sol) / Vuc))
value2.append(sum(value1))
value.append(sum(value2))
fingerprints.append(value)
fpt = []
for one in fingerprints:
fpt.extend(one)
return fpt
def get_fingerprint(Optimizer, indiv, binsize, cutoffdist):
"""Function to calculate the fingerprint of a structure"""
rs = numpy.linspace(0.0, cutoffdist, cutoffdist/binsize)
indi = indiv[0]
Vuc = indi.get_volume()
if Optimizer.structure == 'Defect':
solid = Atoms()
solid.extend(indi)
solid.extend(indiv.bulki)
elif Optimizer.structure == 'Crystal':
solid = indi.repeat([3, 3, 3])
else:
solid = indi.copy()
syms = sorted(list(set([atm.symbol for atm in solid])))
fingerprints = []
for i in range(len(syms)):
for j in range(i, len(syms)):
indl = [atm for atm in indi if atm.symbol == syms[i]]
ind = Atoms()
for one in indl:
ind.append(one)
soll = [atm for atm in solid if atm.symbol == syms[j]]
sol = Atoms()
for one in soll:
sol.append(one)
soli = [atm for atm in solid if atm.symbol == syms[i]]
value = []
for R in rs:
value2 = []
for k in range(len(ind)):
value1 = []
for m in range(len(sol)):
if k != m:
rij = sol.get_distance(k, m, mic = True)
if rij == 0:
pass
#pdb.set_trace()
value1.append(dirac(R, a=rij, sig=0.02) * 1. / (4*math.pi * rij** 2*binsize * len(soli) * len(sol) / Vuc))
value2.append(sum(value1))
value.append(sum(value2))
fingerprints.append(value)
fpt = []
for one in fingerprints:
fpt.extend(one)
return fpt
def check_min_dist(totalsol, type='Defect', nat=None, min_len=0.7, STR=''):
if type == 'Defect' or type == 'Crystal' or type == 'Surface':
if nat == None:
nat = len(totalsol)
cutoffs = [2.0 for one in totalsol]
nl = NeighborList(cutoffs, bothways=True, self_interaction=False)
nl.update(totalsol)
for one in totalsol[0:nat]:
nbatoms = Atoms()
nbatoms.append(one)
indices, offsets = nl.get_neighbors(one.index)
for index, d in zip(indices, offsets):
index = int(index)
sym = totalsol[index].symbol
pos = totalsol[index].position + numpy.dot(
d, totalsol.get_cell())
at = Atom(symbol=sym, position=pos)
nbatoms.append(at)
while True:
dflag = False
for i in range(1, len(nbatoms)):
d = nbatoms.get_distance(0, i)
if d < min_len:
nbatoms.set_distance(0, i, min_len + .01, fix=0.5)
STR += '--- WARNING: Atoms too close (<0.7A) - Implement Move ---\n'
dflag = True
if dflag == False:
break
for i in range(len(indices)):
totalsol[indices[i]].position = nbatoms[i + 1].position
totalsol[one.index].position = nbatoms[0].position
nl.update(totalsol)
elif type == 'Cluster':
for i in range(len(totalsol)):
for j in range(len(totalsol)):
if i != j:
d = totalsol.get_distance(i, j)
if d < min_len:
totalsol.set_distance(i, j, min_len, fix=0.5)
STR += '--- WARNING: Atoms too close (<0.7A) - Implement Move ---\n'
else:
print 'WARNING: In Check_Min_Dist in EvalEnergy: Structure Type not recognized'
return totalsol, STR
def get_distances(indices, positions, rvecs=None):
"""Compute distances between particles"""
atoms = Atoms(positions=positions, )
if rvecs is not None:
cell = ase.geometry.Cell(rvecs)
atoms.set_cell(cell)
atoms.set_pbc(True)
mic = True
else:
cell = None
mic = False
ndist = indices.shape[0]
distances = np.zeros(ndist)
for i in range(ndist):
distances[i] = atoms.get_distance(indices[i, 0],
indices[i, 1],
mic=mic)
return distances
def check_min_dist(totalsol, type='Defect', nat=None, min_len=0.7, STR=''):
if type=='Defect' or type=='Crystal' or type=='Surface':
if nat==None:
nat=len(totalsol)
cutoffs=[2.0 for one in totalsol]
nl=NeighborList(cutoffs,bothways=True,self_interaction=False)
nl.update(totalsol)
for one in totalsol[0:nat]:
nbatoms=Atoms()
nbatoms.append(one)
indices, offsets=nl.get_neighbors(one.index)
for index, d in zip(indices,offsets):
index = int(index)
sym=totalsol[index].symbol
pos=totalsol[index].position + numpy.dot(d,totalsol.get_cell())
at=Atom(symbol=sym,position=pos)
nbatoms.append(at)
while True:
dflag=False
for i in range(1,len(nbatoms)):
d=nbatoms.get_distance(0,i)
if d < min_len:
nbatoms.set_distance(0,i,min_len+.01,fix=0.5)
STR+='--- WARNING: Atoms too close (<0.7A) - Implement Move ---\n'
dflag=True
if dflag==False:
break
for i in range(len(indices)):
totalsol[indices[i]].position=nbatoms[i+1].position
totalsol[one.index].position=nbatoms[0].position
nl.update(totalsol)
elif type=='Cluster':
for i in range(len(totalsol)):
for j in range(len(totalsol)):
if i != j:
d=totalsol.get_distance(i,j)
if d < min_len:
totalsol.set_distance(i,j,min_len,fix=0.5)
STR+='--- WARNING: Atoms too close (<0.7A) - Implement Move ---\n'
else:
print 'WARNING: In Check_Min_Dist in EvalEnergy: Structure Type not recognized'
return totalsol, STR
def main():
arg = sys.argv
inputfile = arg[1]
outputfile = arg[2]
atom1 = int(arg[3])
atom2 = int(arg[4])
f = open(inputfile)
output = open(outputfile, 'w')
atoms = None
atom_output = Trajectory('trajectory.traj', 'w', atoms)
iteration = 0
trajectories = []
a = 10.0
b = 10.0
c = 10.0
cell_atoms = np.array([[a, 0, 0], [0, b, 0], [0, 0, c]])
while True:
coordinates = []
type_atoms = []
line = f.readline()
if not line:
break
atom_numb = int(line.split()[0])
line = f.readline()
for i in range(0, atom_numb):
line = f.readline()
fields = line.split()
type_atoms.append(fields[0])
coordinates.append(
[float(fields[1]),
float(fields[2]),
float(fields[3])])
traj = Atoms(np.array(type_atoms),
positions=np.array(coordinates),
cell=cell_atoms,
pbc=True)
traj.wrap()
atom_output.write(traj)
output.write("%6d %8.4f\n" %
(iteration, traj.get_distance(atom1, atom2, mic=True)))
iteration += 1
def voids(atoms_in):
"""Find location and size of voids in a given structure.
Returns the voids as 'X' atoms. The atoms' charge is misused
to contain the voids' radius.
"""
trials = 6 # XXX do not hardwire
atoms = atoms_in.copy()
# append moving atom
atoms.append(Atom('X'))
atoms.set_calculator(RepulsivePotential())
voids_a = Atoms()
voids_a.set_cell(atoms.get_cell())
voids_a.set_pbc(atoms.get_pbc())
positions = atoms.get_positions()
for pos in positions[:-1]:
for c in range(trials):
positions[-1] = pos + 0.1 * np.random.uniform(-1, 1, size=3)
atoms.set_positions(positions)
# XXX do not hardwire
relax = FIRE(atoms,
logfile=None
)
# XXX do not hardwire
relax.run(fmax=0.001, steps=100)
# get minimal distance
Rmin = 100000
for b in range(len(atoms) - 1):
R = atoms.get_distance(b, -1, mic=True)
if R < Rmin:
Rmin = R
# check if new or better
voids_a.append(Atom('X',
atoms.get_positions()[-1],
charge=Rmin))
voids_a.set_positions(voids_a.get_positions(wrap=True))
remove = []
last = len(voids_a) - 1
for ia, a in enumerate(voids_a[:-1]):
d = voids_a.get_distance(ia, -1, mic=True)
if d < a.charge or d < Rmin:
if a.charge > Rmin:
remove.append(last)
else:
remove.append(ia)
remove.sort()
if last not in remove:
p = voids_a.get_positions()[-1]
print('found new void at [%g,%g,%g], R=%g' %
(p[0], p[1], p[2], Rmin))
for a in remove[::-1]:
if a != last:
p = voids_a.get_positions()[a]
print('removing void at [%g,%g,%g], R=%g' %
(p[0], p[1], p[2], voids_a[a].charge))
voids_a.pop(a)
return voids_a
def eval_energy(input):
"""Function to evaluate energy of an individual
Inputs:
input = [Optimizer class object with parameters, Individual class structure to be evaluated]
Outputs:
energy, bul, individ, signal
energy = energy of Individual evaluated
bul = bulk structure of Individual if simulation structure is Defect
individ = Individual class structure evaluated
signal = string of information about evaluation
"""
if input[0]==None:
energy=0
bul=0
individ=0
rank = MPI.COMM_WORLD.Get_rank()
signal='Evaluated none individual on '+repr(rank)+'\n'
else:
[Optimizer, individ]=input
if Optimizer.calc_method=='MAST':
energy = individ.energy
bul = individ.energy
signal = 'Recieved MAST structure\n'
else:
if Optimizer.parallel: rank = MPI.COMM_WORLD.Get_rank()
if not Optimizer.genealogy:
STR='----Individual ' + str(individ.index)+ ' Optimization----\n'
else:
STR='----Individual ' + str(individ.history_index)+ ' Optimization----\n'
indiv=individ[0]
if 'EE' in Optimizer.debug:
debug = True
else:
debug = False
if debug:
write_xyz(Optimizer.debugfile,indiv,'Recieved by eval_energy')
Optimizer.debugfile.flush()
if Optimizer.structure=='Defect':
indi=indiv.copy()
if Optimizer.alloy==True:
bulk=individ.bulki
else:
bulk=individ.bulko
nat=indi.get_number_of_atoms()
csize=bulk.get_cell()
totalsol=Atoms(cell=csize, pbc=True)
totalsol.extend(indi)
totalsol.extend(bulk)
for sym,c,m,u in Optimizer.atomlist:
nc=len([atm for atm in totalsol if atm.symbol==sym])
STR+='Defect configuration contains '+repr(nc)+' '+repr(sym)+' atoms\n'
elif Optimizer.structure=='Surface':
totalsol=Atoms()
totalsol.extend(indiv)
nat=indiv.get_number_of_atoms()
totalsol.extend(individ.bulki)
for sym,c,m,u in Optimizer.atomlist:
nc=len([atm for atm in totalsol if atm.symbol==sym])
STR+='Surface-Bulk configuration contains '+repr(nc)+' '+repr(sym)+' atoms\n'
cell=numpy.maximum.reduce(indiv.get_cell())
totalsol.set_cell([cell[0],cell[1],500])
totalsol.set_pbc([True,True,False])
if Optimizer.constrain_position:
ts = totalsol.copy()
indc,indb,vacant,swap,stro = find_defects(ts,Optimizer.solidbulk,0)
sbulk = Optimizer.solidbulk.copy()
bcom = sbulk.get_center_of_mass()
#totalsol.translate(-bulkcom)
#indc.translate(-bulkcom)
#totalsol.append(Atom(position=[0,0,0]))
# for one in indc:
# index = [atm.index for atm in totalsol if atm.position[0]==one.position[0] and atm.position[1]==one.position[1] and atm.position[2]==one.position[2]][0]
# if totalsol.get_distance(-1,index) > Optimizer.sf:
# r = random.random()
# totalsol.set_distance(-1,index,Optimizer.sf*r,fix=0)
# totalsol.pop()
# totalsol.translate(bulkcom)
com = indc.get_center_of_mass()
dist = (sum((bcom[i] - com[i])**2 for i in range(3)))**0.5
if dist > Optimizer.sf:
STR+='Shifting structure to within region\n'
r = random.random()*Optimizer.sf
comv = numpy.linalg.norm(com)
ncom = [one*r/comv for one in com]
trans = [ncom[i]-com[i] for i in range(3)]
indices = []
for one in indc:
id = [atm.index for atm in totalsol if atm.position[0]==one.position[0] and atm.position[1]==one.position[1] and atm.position[2]==one.position[2]][0]
totalsol[id].position += trans
# Check for atoms that are too close
min_len=0.7
#pdb.set_trace()
if not Optimizer.fixed_region:
if Optimizer.structure=='Defect' or Optimizer.structure=='Surface':
cutoffs=[2.0 for one in totalsol]
nl=NeighborList(cutoffs,bothways=True,self_interaction=False)
nl.update(totalsol)
for one in totalsol[0:nat]:
nbatoms=Atoms()
nbatoms.append(one)
indices, offsets=nl.get_neighbors(one.index)
for index, d in zip(indices,offsets):
index = int(index)
sym=totalsol[index].symbol
pos=totalsol[index].position + numpy.dot(d,totalsol.get_cell())
at=Atom(symbol=sym,position=pos)
nbatoms.append(at)
while True:
dflag=False
for i in range(1,len(nbatoms)):
d=nbatoms.get_distance(0,i)
if d < min_len:
nbatoms.set_distance(0,i,min_len+.01,fix=0.5)
STR+='--- WARNING: Atoms too close (<0.7A) - Implement Move ---\n'
dflag=True
if dflag==False:
break
for i in range(len(indices)):
totalsol[indices[i]].position=nbatoms[i+1].position
totalsol[one.index].position=nbatoms[0].position
nl.update(totalsol)
if debug:
write_xyz(Optimizer.debugfile,totalsol,'After minlength check')
Optimizer.debugfile.flush()
else:
for i in range(len(indiv)):
for j in range(len(indiv)):
if i != j:
d=indiv.get_distance(i,j)
if d < min_len:
indiv.set_distance(i,j,min_len,fix=0.5)
STR+='--- WARNING: Atoms too close (<0.7A) - Implement Move ---\n'
if debug:
write_xyz(Optimizer.debugfile,indiv,'After minlength check')
Optimizer.debugfile.flush()
# Set calculator to use to get forces/energies
if Optimizer.parallel:
calc = setup_calculator(Optimizer)
if Optimizer.fixed_region:
pms=copy.deepcopy(calc.parameters)
try:
pms['mass'][len(pms['mass'])-1] += '\ngroup RO id >= '+repr(nat)+'\nfix freeze RO setforce 0.0 0.0 0.0\n'
except KeyError:
pms['pair_coeff'][0] += '\ngroup RO id >= '+repr(nat)+'\nfix freeze RO setforce 0.0 0.0 0.0\n'
calc = LAMMPS(parameters=pms, files=calc.files, keep_tmp_files=calc.keep_tmp_files, tmp_dir=calc.tmp_dir)
lmin = copy.copy(Optimizer.lammps_min)
Optimizer.lammps_min = None
Optimizer.static_calc = setup_calculator(Optimizer)
Optimizer.lammps_min = lmin
else:
calc=Optimizer.calc
if Optimizer.structure=='Defect' or Optimizer.structure=='Surface':
totalsol.set_calculator(calc)
totalsol.set_pbc(True)
else:
indiv.set_calculator(calc)
indiv.set_pbc(True) #Current bug in ASE optimizer-Lammps prevents pbc=false
if Optimizer.structure=='Cluster':
indiv.set_cell([500,500,500])
indiv.translate([250,250,250])
cwd=os.getcwd()
# Perform Energy Minimization
if not Optimizer.parallel:
Optimizer.output.flush()
if Optimizer.ase_min == True:
try:
if Optimizer.structure=='Defect' or Optimizer.structure=='Surface':
dyn=BFGS(totalsol)
else:
dyn=BFGS(indiv)
dyn.run(fmax=Optimizer.ase_min_fmax, steps=Optimizer.ase_min_maxsteps)
except OverflowError:
STR+='--- Error: Infinite Energy Calculated - Implement Random ---\n'
box=Atoms()
indiv=gen_pop_box(Optimizer.natoms, Optimizer.atomlist, Optimizer.size)
indiv.set_calculator(calc)
dyn=BFGS(indiv)
dyn.run(fmax=fmax, steps=steps)
except numpy.linalg.linalg.LinAlgError:
STR+='--- Error: Singular Matrix - Implement Random ---\n'
indiv=gen_pop_box(Optimizer.natoms, Optimizer.atomlist, Optimizer.size)
indiv.set_calculator(calc)
dyn=BFGS(indiv)
dyn.run(fmax=fmax, steps=steps)
# Get Energy of Minimized Structure
if Optimizer.structure=='Defect' or Optimizer.structure=='Surface':
en=totalsol.get_potential_energy()
#force=numpy.maximum.reduce(abs(totalsol.get_forces()))
if Optimizer.fitness_scheme == 'enthalpyfit':
pressure=totalsol.get_isotropic_pressure(totalsol.get_stress())
cell_max=numpy.maximum.reduce(totalsol.get_positions())
cell_min=numpy.minimum.reduce(totalsol.get_positions())
cell=cell_max-cell_min
volume=cell[0]*cell[1]*cell[2]
else:
pressure=0
volume=0
na=totalsol.get_number_of_atoms()
ena=en/na
energy=en
individ[0]=totalsol[0:nat]
bul=totalsol[(nat):len(totalsol)]
STR+='Number of positions = '+repr(len(bul)+len(individ[0]))+'\n'
individ[0].set_cell(csize)
indiv=individ[0]
else:
en=indiv.get_potential_energy()
if Optimizer.fitness_scheme == 'enthalpyfit':
pressure=indiv.get_isotropic_pressure(indiv.get_stress())
cell_max=numpy.maximum.reduce(indiv.get_positions())
cell_min=numpy.minimum.reduce(indiv.get_positions())
cell=cell_max-cell_min
volume=cell[0]*cell[1]*cell[2]
else:
pressure=0
volume=0
na=indiv.get_number_of_atoms()
ena=en/na
energy=ena
individ[0]=indiv
bul=0
else:
if Optimizer.structure=='Defect' or Optimizer.structure=='Surface':
if Optimizer.calc_method=='VASP':
en=totalsol.get_potential_energy()
calcb=Vasp(restart=True)
totalsol=calcb.get_atoms()
stress=calcb.read_stress()
else:
try:
totcop=totalsol.copy()
if debug: write_xyz(Optimizer.debugfile,totcop,'Individual sent to lammps')
OUT=totalsol.calc.calculate(totalsol)
totalsol=OUT['atoms']
totalsol.set_pbc(True)
if Optimizer.fixed_region:
if debug:
print 'Energy of fixed region calc = ', OUT['thermo'][-1]['pe']
totalsol.set_calculator(Optimizer.static_calc)
OUT=totalsol.calc.calculate(totalsol)
totalsol=OUT['atoms']
totalsol.set_pbc(True)
if debug:
print 'Energy of static calc = ', OUT['thermo'][-1]['pe']
en=OUT['thermo'][-1]['pe']
stress=numpy.array([OUT['thermo'][-1][i] for i in ('pxx','pyy','pzz','pyz','pxz','pxy')])*(-1e-4*GPa)
#force=numpy.maximum.reduce(abs(totalsol.get_forces()))
if debug:
write_xyz(Optimizer.debugfile,totalsol,'After Lammps Minimization')
Optimizer.debugfile.flush()
except Exception, e:
os.chdir(cwd)
STR+='WARNING: Exception during energy eval:\n'+repr(e)+'\n'
f=open('problem-structures.xyz','a')
write_xyz(f,totcop,data='Starting structure hindex='+individ.history_index)
write_xyz(f,totalsol,data='Lammps Min structure')
en=10
stress=0
f.close()
if Optimizer.fitness_scheme == 'enthalpyfit':
pressure=totalsol.get_isotropic_pressure(stress)
cell_max=numpy.maximum.reduce(totalsol.get_positions())
cell_min=numpy.minimum.reduce(totalsol.get_positions())
cell=cell_max-cell_min
volume=cell[0]*cell[1]*cell[2]
else:
pressure=totalsol.get_isotropic_pressure(stress)
volume=0
na=totalsol.get_number_of_atoms()
ena=en/na
energy=en
if Optimizer.structure=='Defect':
if Optimizer.fixed_region==True or Optimizer.finddefects==False:
individ[0]=totalsol[0:nat]
bul=totalsol[(nat):len(totalsol)]
individ[0].set_cell(csize)
else:
if 'FI' in Optimizer.debug:
outt=find_defects(totalsol,Optimizer.solidbulk,Optimizer.sf,atomlistcheck=Optimizer.atomlist,trackvacs=Optimizer.trackvacs,trackswaps=Optimizer.trackswaps,debug=Optimizer.debugfile)
else:
outt=find_defects(totalsol,Optimizer.solidbulk,Optimizer.sf,atomlistcheck=Optimizer.atomlist,trackvacs=Optimizer.trackvacs,trackswaps=Optimizer.trackswaps,debug=False)
individ[0]=outt[0]
bul=outt[1]
individ.vacancies = outt[2]
individ.swaps = outt[3]
STR += outt[4]
indiv=individ[0]
else:
top,bul=find_top_layer(totalsol,Optimizer.surftopthick)
indiv=top.copy()
individ[0]=top.copy()
else:
# plt.plot(D, E)
F1 = np.polyval(np.polyder(np.polyfit(D, E, 7)), D)
F2 = F[:, :3, 0].sum(1)
error = abs(F1 - F2).max()
dimer.constraints = FixInternals(
bonds=[(r, (0, 2)), (r, (1, 2)),
(r, (3, 5)), (r, (4, 5))],
angles=[(a, (0, 2, 1)), (a, (3, 5, 4))])
opt = GPMin(dimer,
trajectory=calc.name + '.traj', logfile=calc.name + 'd.log')
opt.run(0.01)
e0 = dimer.get_potential_energy()
d0 = dimer.get_distance(2, 5)
R = dimer.positions
v1 = R[1] - R[5]
v2 = R[5] - (R[3] + R[4]) / 2
a0 = np.arccos(np.dot(v1, v2) /
(np.dot(v1, v1) * np.dot(v2, v2))**0.5) / np.pi * 180
fmt = '{0:>20}: {1:.3f} {2:.3f} {3:.3f} {4:.1f}'
print(fmt.format(calc.name, -min(E), -e0, d0, a0))
assert abs(e0 + eexp) < 0.002
assert abs(d0 - dexp) < 0.01
assert abs(a0 - aexp) < 4
print(fmt.format('reference', 9.999, eexp, dexp, aexp))
# plt.show()
def check_min_dist(Optimizer, totalsol, type='Defect', nat=None, min_len=0.7, STR=''):
if type=='Defect' or type=='Crystal' or type=='Surface':
if nat==None:
nat=len(totalsol)
cutoffs=[2.0 for one in totalsol]
nl=NeighborList(cutoffs,bothways=True,self_interaction=False)
nl.update(totalsol)
for one in totalsol[0:nat]:
nbatoms=Atoms()
nbatoms.append(one)
indices, offsets=nl.get_neighbors(one.index)
for index, d in zip(indices,offsets):
index = int(index)
sym=totalsol[index].symbol
pos=totalsol[index].position + numpy.dot(d,totalsol.get_cell())
at=Atom(symbol=sym,position=pos)
nbatoms.append(at)
while True:
dflag=False
for i in range(1,len(nbatoms)):
d=nbatoms.get_distance(0,i)
if d < min_len:
nbatoms.set_distance(0,i,min_len+.01,fix=0.5)
STR+='--- WARNING: Atoms too close (<0.7A) - Implement Move ---\n'
dflag=True
if dflag==False:
break
for i in range(len(indices)):
totalsol[indices[i]].position=nbatoms[i+1].position
totalsol[one.index].position=nbatoms[0].position
nl.update(totalsol)
elif type=='Cluster':
if not 'LAMMPS' in Optimizer.modules:
for i in range(len(totalsol)):
for j in range(len(totalsol)):
if i != j:
d=totalsol.get_distance(i,j)
if d < min_len:
totalsol.set_distance(i,j,min_len,fix=0.5)
STR+='--- WARNING: Atoms too close (<0.7A) - Implement Move ---\n'
else:
rank = MPI.COMM_WORLD.Get_rank()
#logger = logging.getLogger(Optimizer.loggername)
R = totalsol.arrays['positions']
tol = 0.01
epsilon = 0.05
fix = 0.5
closelist = numpy.arange(len(totalsol))
iter = 0
while len(closelist) > 0 and iter<2:
iter+=1
closelist = []
dist=spatial.distance.cdist(R,R)
numpy.fill_diagonal(dist,1.0)
smalldist = numpy.where(dist < min_len-tol)
for ind in range(len(smalldist[0])):
i = smalldist[0][ind]
j = smalldist[1][ind]
if i < j and dist[i][j] < min_len-tol:
closelist.append(i)
closelist.append(j)
if dist[i][j] > epsilon:
x = 1.0 - min_len / dist[i][j]
D = R[j]-R[i]
R[i] += (x * fix) * D
R[j] -= (x * (1.0 - fix)) * D
else:
R[i] += [0.2, 0.0, 0.0]
R[j] -= [0.2, 0.0, 0.0]
R2P = [R[i],R[j]]
dist2P=spatial.distance.cdist(R2P,R)
dist[i] = dist2P[0]
dist[j] = dist2P[1]
for k in range(len(R)):
dist[k][i] = dist[i][k]
dist[k][j] = dist[j][k]
closelist=list(set(closelist))
closelist.sort()
#if len(closelist) != 0:
# logger.info('M:iter {0}, closelist size {1}'.format(iter,len(closelist)))
else:
print 'WARNING: In Check_Min_Dist in EvalEnergy: Structure Type not recognized'
return totalsol, STR
from ase.lattice.surface import fcc111, add_adsorbate
from math import sqrt, cos, sin
for mic in [ False, True ]:
zpos = cos(134.3/2.0*pi/180.0)*1.197
xpos = sin(134.3/2.0*pi/180.0)*1.19
co2 = Atoms('COO', positions=[(-xpos+1.2,0,-zpos),
(-xpos+1.2,-1.1,-zpos),
(-xpos+1.2,1.1,-zpos)])
slab = fcc111('Au', size=(2, 2, 4), vacuum=2*5, orthogonal=True)
slab.center()
add_adsorbate(slab,co2,1.5,'bridge')
slab.set_pbc((True,True,False))
d0 = co2.get_distance(-3, -2)
d1 = co2.get_distance(-3, -1)
calc = EMT()
slab.set_calculator(calc)
if mic:
# Remap into the cell so bond is actually wrapped.
slab.set_scaled_positions(slab.get_scaled_positions()%1.0)
constraint = FixBondLengths([[-3,-2],[-3,-1]], mic=True, atoms=slab)
else:
constraint = FixBondLengths([[-3,-2],[-3,-1]])
slab.set_constraint(constraint)
dyn = BFGS(slab, trajectory='relax_%s.traj' % ('mic' if mic else 'no_mic'))
dyn.run(fmax=0.05)
assert abs(slab.get_distance(-3, -2, mic=mic) - d0) < 1e-9
assert abs(slab.get_distance(-3, -1, mic=mic) - d1) < 1e-9
f_ext = 0.2
atom1 = 0
atom2 = 1
atom3 = 2
fmax = 0.001
atoms = Atoms('H3', positions=[(0, 0, 0), (0.751, 0, 0), (0, 1., 0)])
atoms.set_calculator(EMT())
# Without external force
opt = FIRE(atoms)
opt.run(fmax=fmax)
dist1 = atoms.get_distance(atom1, atom2)
# With external force
con1 = ExternalForce(atom1, atom2, f_ext)
atoms.set_constraint(con1)
opt = FIRE(atoms)
opt.run(fmax=fmax)
dist2 = atoms.get_distance(atom1, atom2)
# Distance should increase due to the external force
assert dist2 > dist1
# Combine ExternalForce with FixBondLength
# Fix the bond on which the force acts
con2 = FixBondLength(atom1, atom2)
# ExternalForce constraint at the beginning of the list!!!
name = dire + 'Pt-bulk-fcc-%.0f-%.0f-%.4f' % (ecut, k, a)
filename = name + '.txt'
b = a / 2
c = 'a-Pt-%.0f-%.0f-%.4f' % (ecut, k, a)
bulk = Atoms('Pt',
cell=[[0, b, b], [b, 0, b], [b, b, 0]],
pbc=True)
#bulk = L1_0(symbol=('Co','Pt'),latticeconstant=(a,c), pbc=True)
if not os.path.exists(os.path.dirname(filename)):
try:
os.makedirs(os.path.dirname(filename))
except OSError as exc: # Guard against race condition
if exc.errno != errno.EEXIST:
raise
bulk *= [2, 2, 2]
distancebefore = bulk.get_distance(1, 2)
bulk.pop(4)
bulk.append(Atom('Co', [0.0, 1.96, 1.96]))
bulk.pop(6)
bulk.append(
Atom('Co', [
3.9199999999999999, 3.9199999999999999, 3.9199999999999999
]))
#bulk.set_initial_magnetic_moments([1,1,1,1])
calc = GPAW(
mode=PW(ecut), # cutoff
kpts=(k, k, k), # k-points
xc='PBE',
txt=filename) # output file
bulk.set_calculator(calc)
relax = QuasiNewton(bulk, logfile=c + '.log')
def test_turbomole_qmmm():
"""Test the Turbomole calculator in simple QMMM and
explicit interaction QMMM simulations."""
r = rOH
a = angleHOH * pi / 180
D = np.linspace(2.5, 3.5, 30)
interaction = LJInteractions({('O', 'O'): (epsilon0, sigma0)})
qm_par = {'esp fit': 'kollman', 'multiplicity': 1}
for calc in [
TIP3P(),
SimpleQMMM([0, 1, 2], Turbomole(**qm_par), TIP3P(), TIP3P()),
SimpleQMMM([0, 1, 2],
Turbomole(**qm_par),
TIP3P(),
TIP3P(),
vacuum=3.0),
EIQMMM([0, 1, 2], Turbomole(**qm_par), TIP3P(), interaction),
EIQMMM([3, 4, 5],
Turbomole(**qm_par),
TIP3P(),
interaction,
vacuum=3.0),
EIQMMM([0, 1, 2],
Turbomole(**qm_par),
TIP3P(),
interaction,
vacuum=3.0)
]:
dimer = Atoms('H2OH2O',
[(r * cos(a), 0, r * sin(a)), (r, 0, 0), (0, 0, 0),
(r * cos(a / 2), r * sin(a / 2), 0),
(r * cos(a / 2), -r * sin(a / 2), 0), (0, 0, 0)])
dimer.calc = calc
E = []
F = []
for d in D:
dimer.positions[3:, 0] += d - dimer.positions[5, 0]
E.append(dimer.get_potential_energy())
F.append(dimer.get_forces())
F = np.array(F)
F1 = np.polyval(np.polyder(np.polyfit(D, E, 7)), D)
F2 = F[:, :3, 0].sum(1)
error = abs(F1 - F2).max()
assert error < 0.9
dimer.set_constraint(
FixInternals(bonds=[(r, (0, 2)), (r, (1, 2)), (r, (3, 5)),
(r, (4, 5))],
angles_deg=[(angleHOH, (0, 2, 1)),
(angleHOH, (3, 5, 4))]))
opt = BFGS(dimer,
trajectory=calc.name + '.traj',
logfile=calc.name + 'd.log')
opt.run(0.01)
e0 = dimer.get_potential_energy()
d0 = dimer.get_distance(2, 5)
R = dimer.positions
v1 = R[1] - R[5]
v2 = R[5] - (R[3] + R[4]) / 2
a0 = np.arccos(
np.dot(v1, v2) /
(np.dot(v1, v1) * np.dot(v2, v2))**0.5) / np.pi * 180
fmt = '{0:>20}: {1:.3f} {2:.3f} {3:.3f} {4:.1f}'
print(fmt.format(calc.name, -min(E), -e0, d0, a0))
from ase import Atoms
from ase.calculators.emt import EMT
from ase.constraints import FixBondLength
from ase.io import Trajectory
from ase.optimize import BFGS
a = 3.6
b = a / 2
cu = Atoms('Cu2Ag',
positions=[(0, 0, 0),
(b, b, 0),
(a, a, b)],
calculator=EMT())
e0 = cu.get_potential_energy()
print(e0)
d0 = cu.get_distance(0, 1)
cu.set_constraint(FixBondLength(0, 1))
t = Trajectory('cu2ag.traj', 'w', cu)
qn = BFGS(cu)
qn.attach(t.write)
def f(): print(cu.get_distance(0,1))
qn.attach(f)
qn.run(fmax=0.01)
assert abs(cu.get_distance(0, 1) - d0) < 1e-14
# corresponding total energy, bond length and angle
for e_s in e_shifts:
starttime = time.time()
calc = Siesta('h2o',meshcutoff=200.0 * units.Ry, mix=0.5, pulay=4)
calc.set_fdf('PAO.EnergyShift', e_s * units.eV)
calc.set_fdf('PAO.SplitNorm', 0.15)
calc.set_fdf('PAO.BasisSize', 'SZ')
h2o.set_calculator(calc)
# Make a -traj file named h2o_current_shift.traj:
dyn = QuasiNewton(h2o, trajectory='h2o_%s.traj' % e_s)
dyn.run(fmax=0.02) # Perform the relaxation
E = h2o.get_potential_energy()
print # Make the output more readable
print "E_shift: %.2f" %e_s
print "----------------"
print "Total Energy: %.4f" % E # Print total energy
d = h2o.get_distance(0,2)
print "Bond length: %.4f" % d # Print bond length
p = h2o.positions
d1 = p[0] - p[2]
d2 = p[1] - p[2]
r = np.dot(d1, d2) / (np.linalg.norm(d1) * np.linalg.norm(d2))
angle = np.arccos(r) / pi * 180
print "Bond angle: %.4f" % angle # Print bond angle
endtime = time.time()
walltime = endtime - starttime
print 'Wall time: %.5f' % walltime
print # Make the output more readable
class Conformer():
"""
A class for generating and editing 3D conformers of molecules
"""
def __init__(self, smiles=None, rmg_molecule=None, index=0):
self.energy = None
self.index = index
if (smiles or rmg_molecule):
if smiles and rmg_molecule:
assert rmg_molecule.isIsomorphic(RMGMolecule(
SMILES=smiles)), "SMILES string did not match RMG Molecule object"
self.smiles = smiles
self.rmg_molecule = rmg_molecule
elif rmg_molecule:
self.rmg_molecule = rmg_molecule
self.smiles = rmg_molecule.toSMILES()
else:
self.smiles = smiles
self.rmg_molecule = RMGMolecule(SMILES=smiles)
self.rmg_molecule.updateMultiplicity()
self.get_molecules()
self.get_geometries()
self._symmetry_number = None
else:
self.smiles = None
self.rmg_molecule = None
self.rdkit_molecule = None
self.ase_molecule = None
self.bonds = []
self.angles = []
self.torsions = []
self.cistrans = []
self.chiral_centers = []
self._symmetry_number = None
def __repr__(self):
return '<Conformer "{}">'.format(self.smiles)
def copy(self):
copy_conf = Conformer()
copy_conf.smiles = self.smiles
copy_conf.rmg_molecule = self.rmg_molecule.copy()
copy_conf.rdkit_molecule = self.rdkit_molecule.__copy__()
copy_conf.ase_molecule = self.ase_molecule.copy()
copy_conf.get_geometries()
copy_conf.energy = self.energy
return copy_conf
@property
def symmetry_number(self):
if not self._symmetry_number:
self._symmetry_number = self.calculate_symmetry_number()
return self._symmetry_number
def get_rdkit_mol(self):
"""
A method for creating an rdkit geometry from an rmg mol
"""
assert self.rmg_molecule, "Cannot create an RDKit geometry without an RMG molecule object"
RDMol = self.rmg_molecule.toRDKitMol(removeHs=False)
rdkit.Chem.AllChem.EmbedMolecule(RDMol)
self.rdkit_molecule = RDMol
mol_list = AllChem.MolToMolBlock(self.rdkit_molecule).split('\n')
for i, atom in enumerate(self.rmg_molecule.atoms):
j = i + 4
coords = mol_list[j].split()[:3]
for k, coord in enumerate(coords):
coords[k] = float(coord)
atom.coords = np.array(coords)
return self.rdkit_molecule
def get_ase_mol(self):
"""
A method for creating an ase atoms object from an rdkit mol
"""
if not self.rdkit_molecule:
self.get_rdkit_mol()
mol_list = AllChem.MolToMolBlock(self.rdkit_molecule).split('\n')
ase_atoms = []
for i, line in enumerate(mol_list):
if i > 3:
try:
atom0, atom1, bond, rest = line
atom0 = int(atom0)
atom0 = int(atom1)
bond = float(bond)
except ValueError:
try:
x, y, z, symbol = line.split()[0:4]
x = float(x)
y = float(y)
z = float(z)
ase_atoms.append(
Atom(symbol=symbol, position=(x, y, z)))
except BaseException:
continue
self.ase_molecule = Atoms(ase_atoms)
return self.ase_molecule
def get_molecules(self):
if not self.rmg_molecule:
self.rmg_molecule = RMGMolecule(SMILES=self.smiles)
self.rdkit_molecule = self.get_rdkit_mol()
self.ase_molecule = self.get_ase_mol()
self.get_geometries()
return self.rdkit_molecule, self.ase_molecule
def view(self):
"""
A method designed to create a 3D figure of the AutoTST_Molecule with py3Dmol from the rdkit_molecule
"""
mb = Chem.MolToMolBlock(self.rdkit_molecule)
p = py3Dmol.view(width=600, height=600)
p.addModel(mb, "sdf")
p.setStyle({'stick': {}})
p.setBackgroundColor('0xeeeeee')
p.zoomTo()
return p.show()
def get_bonds(self):
"""
A method for identifying all of the bonds in a conformer
"""
bond_list = []
for bond in self.rdkit_molecule.GetBonds():
bond_list.append((bond.GetBeginAtomIdx(), bond.GetEndAtomIdx()))
bonds = []
for index, indices in enumerate(bond_list):
i, j = indices
length = self.ase_molecule.get_distance(i, j)
center = False
if ((self.rmg_molecule.atoms[i].label) and (
self.rmg_molecule.atoms[j].label)):
center = True
bond = Bond(index=index,
atom_indices=indices,
length=length,
reaction_center=center)
mask = self.get_mask(bond)
bond.mask = mask
bonds.append(bond)
self.bonds = bonds
return self.bonds
def get_angles(self):
"""
A method for identifying all of the angles in a conformer
"""
angle_list = []
for atom1 in self.rdkit_molecule.GetAtoms():
for atom2 in atom1.GetNeighbors():
for atom3 in atom2.GetNeighbors():
if atom1.GetIdx() == atom3.GetIdx():
continue
to_add = (atom1.GetIdx(), atom2.GetIdx(), atom3.GetIdx())
if (to_add in angle_list) or (
tuple(reversed(to_add)) in angle_list):
continue
angle_list.append(to_add)
angles = []
for index, indices in enumerate(angle_list):
i, j, k = indices
degree = self.ase_molecule.get_angle(i, j, k)
ang = Angle(index=index,
atom_indices=indices,
degree=degree,
mask=[])
mask = self.get_mask(ang)
reaction_center = False
angles.append(Angle(index=index,
atom_indices=indices,
degree=degree,
mask=mask,
reaction_center=reaction_center))
self.angles = angles
return self.angles
def get_torsions(self):
"""
A method for identifying all of the torsions in a conformer
"""
torsion_list = []
for bond1 in self.rdkit_molecule.GetBonds():
atom1 = bond1.GetBeginAtom()
atom2 = bond1.GetEndAtom()
if atom1.IsInRing() or atom2.IsInRing():
# Making sure that bond1 we're looking at are not in a ring
continue
bond_list1 = list(atom1.GetBonds())
bond_list2 = list(atom2.GetBonds())
if not len(bond_list1) > 1 and not len(bond_list2) > 1:
# Making sure that there are more than one bond attached to
# the atoms we're looking at
continue
# Getting the 0th and 3rd atom and insuring that atoms
# attached to the 1st and 2nd atom are not terminal hydrogens
# We also make sure that all of the atoms are properly bound
# together
# If the above are satisfied, we append a tuple of the torsion our
# torsion_list
got_atom0 = False
got_atom3 = False
for bond0 in bond_list1:
atomX = bond0.GetOtherAtom(atom1)
# if atomX.GetAtomicNum() == 1 and len(atomX.GetBonds()) == 1:
# This means that we have a terminal hydrogen, skip this
# NOTE: for H_abstraction TSs, a non teminal H should exist
# continue
if atomX.GetIdx() != atom2.GetIdx():
got_atom0 = True
atom0 = atomX
for bond2 in bond_list2:
atomY = bond2.GetOtherAtom(atom2)
# if atomY.GetAtomicNum() == 1 and len(atomY.GetBonds()) == 1:
# This means that we have a terminal hydrogen, skip this
# continue
if atomY.GetIdx() != atom1.GetIdx():
got_atom3 = True
atom3 = atomY
if not (got_atom0 and got_atom3):
# Making sure atom0 and atom3 were not found
continue
# Looking to make sure that all of the atoms are properly bonded to
# eached
if (
"SINGLE" in str(
self.rdkit_molecule.GetBondBetweenAtoms(
atom1.GetIdx(),
atom2.GetIdx()).GetBondType()) and self.rdkit_molecule.GetBondBetweenAtoms(
atom0.GetIdx(),
atom1.GetIdx()) and self.rdkit_molecule.GetBondBetweenAtoms(
atom1.GetIdx(),
atom2.GetIdx()) and self.rdkit_molecule.GetBondBetweenAtoms(
atom2.GetIdx(),
atom3.GetIdx())):
torsion_tup = (atom0.GetIdx(), atom1.GetIdx(),
atom2.GetIdx(), atom3.GetIdx())
already_in_list = False
for torsion_entry in torsion_list:
a, b, c, d = torsion_entry
e, f, g, h = torsion_tup
if (b, c) == (f, g) or (b, c) == (g, f):
already_in_list = True
if not already_in_list:
torsion_list.append(torsion_tup)
torsions = []
for index, indices in enumerate(torsion_list):
i, j, k, l = indices
dihedral = self.ase_molecule.get_dihedral(i, j, k, l)
tor = Torsion(index=index,
atom_indices=indices,
dihedral=dihedral,
mask=[])
mask = self.get_mask(tor)
reaction_center = False
torsions.append(Torsion(index=index,
atom_indices=indices,
dihedral=dihedral,
mask=mask,
reaction_center=reaction_center))
self.torsions = torsions
return self.torsions
def get_cistrans(self):
"""
A method for identifying all possible cistrans bonds in a molecule
"""
torsion_list = []
cistrans_list = []
for bond1 in self.rdkit_molecule.GetBonds():
atom1 = bond1.GetBeginAtom()
atom2 = bond1.GetEndAtom()
if atom1.IsInRing() or atom2.IsInRing():
# Making sure that bond1 we're looking at are not in a ring
continue
bond_list1 = list(atom1.GetBonds())
bond_list2 = list(atom2.GetBonds())
if not len(bond_list1) > 1 and not len(bond_list2) > 1:
# Making sure that there are more than one bond attached to
# the atoms we're looking at
continue
# Getting the 0th and 3rd atom and insuring that atoms
# attached to the 1st and 2nd atom are not terminal hydrogens
# We also make sure that all of the atoms are properly bound
# together
# If the above are satisfied, we append a tuple of the torsion our
# torsion_list
got_atom0 = False
got_atom3 = False
for bond0 in bond_list1:
atomX = bond0.GetOtherAtom(atom1)
# if atomX.GetAtomicNum() == 1 and len(atomX.GetBonds()) == 1:
# This means that we have a terminal hydrogen, skip this
# NOTE: for H_abstraction TSs, a non teminal H should exist
# continue
if atomX.GetIdx() != atom2.GetIdx():
got_atom0 = True
atom0 = atomX
for bond2 in bond_list2:
atomY = bond2.GetOtherAtom(atom2)
# if atomY.GetAtomicNum() == 1 and len(atomY.GetBonds()) == 1:
# This means that we have a terminal hydrogen, skip this
# continue
if atomY.GetIdx() != atom1.GetIdx():
got_atom3 = True
atom3 = atomY
if not (got_atom0 and got_atom3):
# Making sure atom0 and atom3 were not found
continue
# Looking to make sure that all of the atoms are properly bonded to
# eached
if (
"DOUBLE" in str(
self.rdkit_molecule.GetBondBetweenAtoms(
atom1.GetIdx(),
atom2.GetIdx()).GetBondType()) and self.rdkit_molecule.GetBondBetweenAtoms(
atom0.GetIdx(),
atom1.GetIdx()) and self.rdkit_molecule.GetBondBetweenAtoms(
atom1.GetIdx(),
atom2.GetIdx()) and self.rdkit_molecule.GetBondBetweenAtoms(
atom2.GetIdx(),
atom3.GetIdx())):
torsion_tup = (atom0.GetIdx(), atom1.GetIdx(),
atom2.GetIdx(), atom3.GetIdx())
already_in_list = False
for torsion_entry in torsion_list:
a, b, c, d = torsion_entry
e, f, g, h = torsion_tup
if (b, c) == (f, g) or (b, c) == (g, f):
already_in_list = True
if not already_in_list:
cistrans_list.append(torsion_tup)
cistrans = []
for ct_index, indices in enumerate(cistrans_list):
i, j, k, l = indices
b0 = self.rdkit_molecule.GetBondBetweenAtoms(i, j)
b1 = self.rdkit_molecule.GetBondBetweenAtoms(j, k)
b2 = self.rdkit_molecule.GetBondBetweenAtoms(k, l)
b0.SetBondDir(Chem.BondDir.ENDUPRIGHT)
b2.SetBondDir(Chem.BondDir.ENDDOWNRIGHT)
Chem.AssignStereochemistry(self.rdkit_molecule, force=True)
if "STEREOZ" in str(b1.GetStereo()):
if round(self.ase_molecule.get_dihedral(i, j, k, l), -1) == 0:
atom = self.rdkit_molecule.GetAtomWithIdx(k)
bonds = atom.GetBonds()
for bond in bonds:
indexes = [
bond.GetBeginAtomIdx(),
bond.GetEndAtomIdx()]
if not ((sorted([j, k]) == sorted(indexes)) or (
sorted([k, l]) == sorted(indexes))):
break
for index in indexes:
if not (index in indices):
l = index
break
indices = [i, j, k, l]
stero = "Z"
else:
if round(
self.ase_molecule.get_dihedral(
i, j, k, l), -1) == 180:
atom = self.rdkit_molecule.GetAtomWithIdx(k)
bonds = atom.GetBonds()
for bond in bonds:
indexes = [
bond.GetBeginAtomIdx(),
bond.GetEndAtomIdx()]
if not ((sorted([j, k]) == sorted(indexes)) or (
sorted([k, l]) == sorted(indexes))):
break
for index in indexes:
if not (index in indices):
l = index
break
indices = [i, j, k, l]
stero = "E"
dihedral = self.ase_molecule.get_dihedral(i, j, k, l)
tor = CisTrans(index=ct_index,
atom_indices=indices,
dihedral=dihedral,
mask=[],
stero=stero)
mask = self.get_mask(tor)
reaction_center = False
cistrans.append(CisTrans(index=ct_index,
atom_indices=indices,
dihedral=dihedral,
mask=mask,
stero=stero
)
)
self.cistrans = cistrans
return self.cistrans
def get_mask(self, geometry):
"""
Getting the right hand mask for a geometry object:
- self: an AutoTST Conformer object
- geometry: a Bond, Angle, Dihedral, or Torsion object
"""
rdkit_atoms = self.rdkit_molecule.GetAtoms()
if (isinstance(geometry, autotst.geometry.Torsion) or
isinstance(geometry, autotst.geometry.CisTrans)):
L1, L0, R0, R1 = geometry.atom_indices
# trying to get the left hand side of this torsion
LHS_atoms_index = [L0, L1]
RHS_atoms_index = [R0, R1]
elif isinstance(geometry, autotst.geometry.Angle):
a1, a2, a3 = geometry.atom_indices
LHS_atoms_index = [a2, a1]
RHS_atoms_index = [a2, a3]
elif isinstance(geometry, autotst.geometry.Bond):
a1, a2 = geometry.atom_indices
LHS_atoms_index = [a1]
RHS_atoms_index = [a2]
complete_RHS = False
i = 0
atom_index = RHS_atoms_index[0]
while complete_RHS is False:
try:
RHS_atom = rdkit_atoms[atom_index]
for neighbor in RHS_atom.GetNeighbors():
if (neighbor.GetIdx() in RHS_atoms_index) or (
neighbor.GetIdx() in LHS_atoms_index):
continue
else:
RHS_atoms_index.append(neighbor.GetIdx())
i += 1
atom_index = RHS_atoms_index[i]
except IndexError:
complete_RHS = True
mask = [index in RHS_atoms_index for index in range(
len(self.ase_molecule))]
return mask
def get_chiral_centers(self):
"""
A method to identify
"""
centers = rdkit.Chem.FindMolChiralCenters(
self.rdkit_molecule, includeUnassigned=True)
chiral_centers = []
for index, center in enumerate(centers):
atom_index, chirality = center
chiral_centers.append(
ChiralCenter(
index=index,
atom_index=atom_index,
chirality=chirality))
self.chiral_centers = chiral_centers
return self.chiral_centers
def get_geometries(self):
"""
A helper method to obtain all geometry things
"""
self.bonds = self.get_bonds()
self.angles = self.get_angles()
self.torsions = self.get_torsions()
self.cistrans = self.get_cistrans()
self.chiral_centers = self.get_chiral_centers()
return (
self.bonds,
self.angles,
self.torsions,
self.cistrans,
self.chiral_centers)
def update_coords(self):
"""
A function that creates distance matricies for the RMG, ASE, and RDKit molecules and finds which
(if any) are different. If one is different, this will update the coordinates of the other two
with the different one. If all three are different, nothing will happen. If all are the same,
nothing will happen.
"""
rdkit_dm = rdkit.Chem.rdmolops.Get3DDistanceMatrix(self.rdkit_molecule)
ase_dm = self.ase_molecule.get_all_distances()
l = len(self.rmg_molecule.atoms)
rmg_dm = np.zeros((l, l))
for i, atom_i in enumerate(self.rmg_molecule.atoms):
for j, atom_j in enumerate(self.rmg_molecule.atoms):
rmg_dm[i][j] = np.linalg.norm(atom_i.coords - atom_j.coords)
d1 = round(abs(rdkit_dm - ase_dm).max(), 3)
d2 = round(abs(rdkit_dm - rmg_dm).max(), 3)
d3 = round(abs(ase_dm - rmg_dm).max(), 3)
if np.all(np.array([d1, d2, d3]) > 0):
return False, None
if np.any(np.array([d1, d2, d3]) > 0):
if d1 == 0:
diff = "rmg"
self.update_coords_from("rmg")
elif d2 == 0:
diff = "ase"
self.update_coords_from("ase")
else:
diff = "rdkit"
self.update_coords_from("rdkit")
return True, diff
else:
return True, None
def update_coords_from(self, mol_type="ase"):
"""
A method to update the coordinates of the RMG, RDKit, and ASE objects with a chosen object.
"""
possible_mol_types = ["ase", "rmg", "rdkit"]
assert (mol_type.lower() in possible_mol_types), "Please specifiy a valid mol type. Valid types are {}".format(
possible_mol_types)
if mol_type.lower() == "rmg":
conf = self.rdkit_molecule.GetConformers()[0]
ase_atoms = []
for i, atom in enumerate(self.rmg_molecule.atoms):
x, y, z = atom.coords
symbol = atom.symbol
conf.SetAtomPosition(i, [x, y, z])
ase_atoms.append(Atom(symbol=symbol, position=(x, y, z)))
self.ase_molecule = Atoms(ase_atoms)
# self.calculate_symmetry_number()
elif mol_type.lower() == "ase":
conf = self.rdkit_molecule.GetConformers()[0]
for i, position in enumerate(self.ase_molecule.get_positions()):
self.rmg_molecule.atoms[i].coords = position
conf.SetAtomPosition(i, position)
# self.calculate_symmetry_number()
elif mol_type.lower() == "rdkit":
mol_list = AllChem.MolToMolBlock(self.rdkit_molecule).split('\n')
for i, atom in enumerate(self.rmg_molecule.atoms):
j = i + 4
coords = mol_list[j].split()[:3]
for k, coord in enumerate(coords):
coords[k] = float(coord)
atom.coords = np.array(coords)
self.get_ase_mol()
# self.calculate_symmetry_number()
def set_bond_length(self, bond_index, length):
"""
This is a method to set bond lengths
Variabels:
- bond_index (int): the index of the bond you want to edit
- length (float, int): the distance you want to set the bond (in angstroms)
"""
assert isinstance(length, (float, int))
matched = False
for bond in self.bonds:
if bond.index == bond_index:
matched = True
break
if not matched:
logging.info("Angle index provided is out of range. Nothing was changed.")
return self
i, j = bond.atom_indices
self.ase_molecule.set_distance(
a0=i,
a1=j,
distance=length,
mask=bond.mask,
fix=0
)
bond.length = length
self.update_coords_from(mol_type="ase")
return self
def set_angle(self, angle_index, angle):
"""
A method that will set the angle of an Angle object accordingly
"""
assert isinstance(
angle, (int, float)), "Plese provide a float or an int for the angle"
matched = False
for a in self.angles:
if a.index == angle_index:
matched = True
break
if not matched:
logging.info("Angle index provided is out of range. Nothing was changed.")
return self
i, j, k = a.atom_indices
self.ase_molecule.set_angle(
a1=i,
a2=j,
a3=k,
angle=angle,
mask=a.mask
)
a.degree = angle
self.update_coords_from(mol_type="ase")
return self
def set_torsion(self, torsion_index, dihedral):
"""
A method that will set the diehdral angle of a Torsion object accordingly.
"""
assert isinstance(
dihedral, (int, float)), "Plese provide a float or an int for the diehdral angle"
matched = False
for torsion in self.torsions:
if torsion.index == torsion_index:
matched = True
break
if not matched:
logging.info("Torsion index provided is out of range. Nothing was changed.")
return self
i, j, k, l = torsion.atom_indices
self.ase_molecule.set_dihedral(
a1=i,
a2=j,
a3=k,
a4=l,
angle=dihedral,
mask=torsion.mask
)
torsion.dihedral = dihedral
self.update_coords_from(mol_type="ase")
return self
def set_cistrans(self, cistrans_index, stero="E"):
"""
A module that will set a corresponding cistrans bond to the proper E/Z config
"""
assert stero.upper() in [
"E", "Z"], "Please specify a valid stero direction."
matched = False
for cistrans in self.cistrans:
if cistrans.index == cistrans_index:
matched = True
break
if not matched:
logging.info("CisTrans index provided is out of range. Nothing was changed.")
return self
if cistrans.stero == stero.upper():
self.update_coords_from("ase")
return self
else:
cistrans.stero = stero.upper()
i, j, k, l = cistrans.atom_indices
self.ase_molecule.rotate_dihedral(
a1=i,
a2=j,
a3=k,
a4=l,
angle=float(180),
mask=cistrans.mask
)
cistrans.stero = stero.upper()
self.update_coords_from(mol_type="ase")
return self
def set_chirality(self, chiral_center_index, stero="R"):
"""
A module that can set the orientation of a chiral center.
"""
assert stero.upper() in ["R", "S"], "Specify a valid stero orientation"
centers_dict = {
'R': Chem.rdchem.ChiralType.CHI_TETRAHEDRAL_CW,
'S': Chem.rdchem.ChiralType.CHI_TETRAHEDRAL_CCW
}
assert isinstance(chiral_center_index,
int), "Please provide an integer for the index"
rdmol = self.rdkit_molecule.__copy__()
match = False
for chiral_center in self.chiral_centers:
if chiral_center.index == chiral_center_index:
match = True
break
if not match:
logging.info("ChiralCenter index provided is out of range. Nothing was changed")
return self
rdmol.GetAtomWithIdx(chiral_center.atom_index).SetChiralTag(
centers_dict[stero.upper()])
rdkit.Chem.rdDistGeom.EmbedMolecule(rdmol)
old_torsions = self.torsions[:] + self.cistrans[:]
self.rdkit_molecule = rdmol
self.update_coords_from(mol_type="rdkit")
# Now resetting dihedral angles in case if they changed.
for torsion in old_torsions:
i, j, k, l = torsion.atom_indices
self.ase_molecule.set_dihedral(
a1=i,
a2=j,
a3=k,
a4=l,
mask=torsion.mask,
angle=torsion.dihedral,
)
self.update_coords_from(mol_type="ase")
return self
def calculate_symmetry_number(self):
from rmgpy.qm.symmetry import PointGroupCalculator
from rmgpy.qm.qmdata import QMData
atom_numbers = self.ase_molecule.get_atomic_numbers()
coordinates = self.ase_molecule.get_positions()
qmdata = QMData(
groundStateDegeneracy=1, # Only needed to check if valid QMData
numberOfAtoms=len(atom_numbers),
atomicNumbers=atom_numbers,
atomCoords=(coordinates, str('angstrom')),
energy=(0.0, str('kcal/mol')) # Only needed to avoid error
)
settings = type(str(''), (), dict(symmetryPath=str(
'symmetry'), scratchDirectory="."))() # Creates anonymous class
pgc = PointGroupCalculator(settings, self.smiles, qmdata)
pg = pgc.calculate()
#os.remove("{}.symm".format(self.smiles))
if pg is not None:
symmetry_number = pg.symmetryNumber
else:
symmetry_number = 1
return symmetry_number
import numpy as np
from ase import Atoms
from ase.optimize import BFGS
from gpaw import GPAW
from gpaw.wavefunctions.pw import PW
from gpaw.test import equal
from gpaw.mpi import world
a = 2.65
slab = Atoms('Li2',
[(0, 0, 0), (0, 0, a)],
cell=(a, a, 3 * a),
pbc=True)
k = 4
calc = GPAW(mode=PW(200),
eigensolver='rmm-diis',
parallel={'band': min(world.size, 4)},
idiotproof=0,
kpts=(k, k, 1))
slab.set_calculator(calc)
BFGS(slab).run(fmax=0.01)
assert abs(slab.get_distance(0, 1) - 2.4594) < 0.001, slab.get_distance(0, 1)
from ase.calculators.emt import EMT
from ase.constraints import FixBondLengths
from ase.optimize import BFGS
from ase.build import fcc111, add_adsorbate
for wrap in [False, True]:
zpos = cos(134.3 / 2.0 * pi / 180.0) * 1.197
xpos = sin(134.3 / 2.0 * pi / 180.0) * 1.19
co2 = Atoms('COO',
positions=[(-xpos + 1.2, 0, -zpos), (-xpos + 1.2, -1.1, -zpos),
(-xpos + 1.2, 1.1, -zpos)])
slab = fcc111('Au', size=(2, 2, 4), vacuum=2 * 5, orthogonal=True)
slab.center()
add_adsorbate(slab, co2, 1.5, 'bridge')
slab.set_pbc((True, True, False))
d0 = co2.get_distance(-3, -2)
d1 = co2.get_distance(-3, -1)
calc = EMT()
slab.set_calculator(calc)
if wrap:
# Remap into the cell so bond is actually wrapped:
slab.set_scaled_positions(slab.get_scaled_positions() % 1.0)
constraint = FixBondLengths([[-3, -2], [-3, -1]])
slab.set_constraint(constraint)
dyn = BFGS(slab, trajectory='relax_%d.traj' % wrap)
dyn.run(fmax=0.05)
assert abs(slab.get_distance(-3, -2, mic=1) - d0) < 1e-9
assert abs(slab.get_distance(-3, -1, mic=1) - d1) < 1e-9
from ase import Atom, Atoms
m = Atoms('H2')
a = m[0]
b = Atom('H')
for c in [a, b]:
assert c.x == 0
c.z = 24.0
assert c.position[2] == 24.0
assert c.symbol == 'H'
c.number = 92
assert c.symbol == 'U'
c.symbol = 'Fe'
assert c.number == 26
c.tag = 42
assert c.tag == 42
c.momentum = (1,2,3)
assert m[0].tag == 42
momenta = m.get_momenta()
m = Atoms('LiH')
for a in m:
print(a.symbol)
for a in m:
if a.symbol == 'H':
a.z = 0.75
assert m.get_distance(0, 1) == 0.75
a = m.pop()
m += a
del m[:1]
print(m)
def lattice_alteration_nn(indiv, Optimizer):
"""Move function to perform random move along random axis for nearest neighbor distance to random atoms
Inputs:
indiv = Individual class object to be altered
Optimizer = Optimizer class object with needed parameters
Outputs:
indiv = Altered Individual class object
"""
if 'MU' in Optimizer.debug:
debug = True
else:
debug = False
if Optimizer.structure == 'Defect':
if Optimizer.isolate_mutation:
indc, indb, vacant, swaps, stro = find_defects(
indiv[0], Optimizer.solidbulk, 0)
ind = indc.copy()
ind.extend(indb)
else:
ind = indiv[0].copy()
indc = indiv[0].copy()
else:
ind = indiv[0].copy()
indc = indiv[0].copy()
if len(indc) != 0:
ctoff1 = [1.0 for one in ind]
nl = NeighborList(ctoff1, bothways=True, self_interaction=False)
nl.update(ind)
try:
natomsmove = random.randint(1, len(indc) / 2)
except ValueError:
natomsmove = 1
passn = 0
for count in range(natomsmove):
try:
indexmv = random.choice([i for i in range(len(indc))])
indices, offsets = nl.get_neighbors(indexmv)
nns = Atoms()
nns.append(ind[indexmv])
for index, d in zip(indices, offsets):
index = int(index)
pos = ind[index].position + numpy.dot(d, ind.get_cell())
nns.append(Atom(symbol=ind[index].symbol, position=pos))
dist = [nns.get_distance(0, i) for i in range(1, len(nns))]
r = sum(dist) / len(dist)
dir = random.choice([[1, 0, 0], [-1, 0, 0], [0, 1, 0],
[0, -1, 0], [0, 0, 1], [0, 0, -1]])
ind[indexmv].position += [i * r for i in dir]
except:
passn += 1
indiv[0] = ind.copy()
else:
natomsmove = 0
passn = 0
Optimizer.output.write(
'Lattice Alteration NN Mutation performed on individual\n')
Optimizer.output.write('Index = ' + repr(indiv.index) + '\n')
natomsmove -= passn
Optimizer.output.write('Number of atoms moved = ' + repr(natomsmove) +
'\n')
Optimizer.output.write(repr(indiv[0]) + '\n')
muttype = 'LANN' + repr(natomsmove)
if indiv.energy == 0:
indiv.history_index = indiv.history_index + 'm' + muttype
else:
indiv.history_index = repr(indiv.index) + 'm' + muttype
return indiv
from ase import Atoms
from ase.calculators.emt import EMT
from ase.constraints import FixBondLengths
from ase.optimize import BFGS, QuasiNewton
from ase.neb import SingleCalculatorNEB
from ase.lattice.surface import fcc111, add_adsorbate
from math import sqrt, cos, sin
zpos = cos(134.3/2.0*pi/180.0)*1.197
xpos = sin(134.3/2.0*pi/180.0)*1.19
co2 = Atoms('COO', positions=[(-xpos+1.2,0,-zpos),
(-xpos+1.2,-1.1,-zpos),
(-xpos+1.2,1.1,-zpos)])
slab = fcc111('Au', size=(2, 2, 4), vacuum=2*5, orthogonal=True)
slab.center()
add_adsorbate(slab,co2,1.5,'bridge')
slab.set_pbc((True,True,False))
d0 = co2.get_distance(-3, -2)
d1 = co2.get_distance(-3, -1)
calc = EMT()
slab.set_calculator(calc)
constraint = FixBondLengths([[-3,-2],[-3,-1]])
slab.set_constraint(constraint)
dyn = BFGS(slab, trajectory='relax.traj')
dyn.run(fmax=0.05)
assert abs(co2.get_distance(-3, -2) - d0) < 1e-14
assert abs(co2.get_distance(-3, -1) - d1) < 1e-14
from math import sqrt, pi
from ase import Atoms
from ase.calculators.emt import EMT
from ase.constraints import FixBondLengths
from ase.optimize import BFGS, QuasiNewton
from ase.neb import SingleCalculatorNEB
from ase.lattice.surface import fcc111, add_adsorbate
from math import sqrt, cos, sin
zpos = cos(134.3 / 2.0 * pi / 180.0) * 1.197
xpos = sin(134.3 / 2.0 * pi / 180.0) * 1.19
co2 = Atoms('COO',
positions=[(-xpos + 1.2, 0, -zpos), (-xpos + 1.2, -1.1, -zpos),
(-xpos + 1.2, 1.1, -zpos)])
slab = fcc111('Au', size=(2, 2, 4), vacuum=2 * 5, orthogonal=True)
slab.center()
add_adsorbate(slab, co2, 1.5, 'bridge')
slab.set_pbc((True, True, False))
d0 = co2.get_distance(-3, -2)
d1 = co2.get_distance(-3, -1)
calc = EMT()
slab.set_calculator(calc)
constraint = FixBondLengths([[-3, -2], [-3, -1]])
slab.set_constraint(constraint)
dyn = BFGS(slab, trajectory='relax.traj')
dyn.run(fmax=0.05)
assert abs(co2.get_distance(-3, -2) - d0) < 1e-14
assert abs(co2.get_distance(-3, -1) - d1) < 1e-14
# plt.plot(D, E)
F1 = np.polyval(np.polyder(np.polyfit(D, E, 7)), D)
F2 = F[:, :3, 0].sum(1)
error = abs(F1 - F2).max()
dimer.constraints = FixInternals(
bonds=[(r, (0, 2)), (r, (1, 2)),
(r, (3, 5)), (r, (4, 5))],
angles=[(a, (0, 2, 1)), (a, (3, 5, 4))])
opt = BFGS(dimer,
trajectory=calc.name + '.traj', logfile=calc.name + 'd.log')
opt.run(0.01)
e0 = dimer.get_potential_energy()
d0 = dimer.get_distance(2, 5)
R = dimer.positions
v1 = R[1] - R[5]
v2 = R[5] - (R[3] + R[4]) / 2
a0 = np.arccos(np.dot(v1, v2) /
(np.dot(v1, v1) * np.dot(v2, v2))**0.5) / np.pi * 180
fmt = '{0:>20}: {1:.3f} {2:.3f} {3:.3f} {4:.1f}'
print(fmt.format(calc.name, -min(E), -e0, d0, a0))
assert abs(e0 + eexp) < 0.002
assert abs(d0 - dexp) < 0.006
assert abs(a0 - aexp) < 2
print(fmt.format('reference', 9.999, eexp, dexp, aexp))
# plt.show()
dimer.positions[3:, 0] += 2.8
dimer.constraints = FixBondLengths([
((selection[i] + 3) % 6, (selection[i - 1] + 3) % 6) for i in range(3)
])
dimer.calc = EIQMMM(selection,
GPAW(txt=name + '.txt', h=0.16),
TIP4P(),
interaction,
vacuum=4,
embedding=Embedding(rc=0.2, rc2=20, width=1),
output=name + '.out')
opt = LBFGS(dimer, trajectory=name + '.traj')
opt.run(0.02)
monomer = dimer[selection]
monomer.center(vacuum=4)
monomer.calc = GPAW(txt=name + 'M.txt', h=0.16)
opt = PreconLBFGS(monomer, precon=Exp(A=3), trajectory=name + 'M.traj')
opt.run(0.02)
e0 = monomer.get_potential_energy()
be = dimer.get_potential_energy() - e0
d = dimer.get_distance(0, 3)
print(name, be, d)
if name == '012':
assert abs(be - -0.288) < 0.002
assert abs(d - 2.76) < 0.02
else:
assert abs(be - -0.316) < 0.002
assert abs(d - 2.67) < 0.02
from ase import Atoms
from ase.calculators.emt import EMT
from ase.constraints import FixBondLength
from ase.io import PickleTrajectory
from ase.optimize import BFGS
a = 3.6
b = a / 2
cu = Atoms('Cu2Ag',
positions=[(0, 0, 0),
(b, b, 0),
(a, a, b)],
calculator=EMT())
e0 = cu.get_potential_energy()
print e0
d0 = cu.get_distance(0, 1)
cu.set_constraint(FixBondLength(0, 1))
t = PickleTrajectory('cu2ag.traj', 'w', cu)
qn = BFGS(cu)
qn.attach(t.write)
def f(): print cu.get_distance(0,1)
qn.attach(f)
qn.run(fmax=0.01)
assert abs(cu.get_distance(0, 1) - d0) < 1e-14
mode=PW(700),
kpts=kpts,
xc='PBE',
txt=myGpaw.symstr+'.out',
occupations=FermiDirac(width=0.05),
# nbands=-2,
convergence={'energy': 0.0005, # eV / electron
'density': 1.0e-4,
'eigenstates': 4.0e-8, # eV^2 / electron
'bands': 'CBM+2.0',
'forces': float('inf')}, # eV / Ang Max
)
atoms.calc = calc
e2 = atoms.get_potential_energy()
d0 = atoms.get_distance(0, 1)
calc.write(myGpaw.symstr+'.gpw')
fd = open('optimization.txt', 'w')
print('experimental bond length:', file=fd)
print('experimental energy: %5.2f eV' % e2, file=fd)
print('bondlength : %5.2f Ang' % d0, file=fd)
# # Find the theoretical bond length:
relax = QuasiNewton(atoms, logfile='qn.log', trajectory=myGpaw.symstr+'.emt.traj')
relax.run(fmax=0.05)
e2 = atoms.get_potential_energy()
d0 = atoms.get_distance(0, 1)
# calc.write(myGpaw.symstr+'relax.gpw')
from ase import Atoms
from ase.calculators.emt import EMT
from ase.optimize import QuasiNewton
n2 = Atoms('N2', positions=[(0, 0, 0), (0, 0, 1.1)],
calculator=EMT())
QuasiNewton(n2).run(0.01)
print(n2.get_distance(0, 1), n2.get_potential_energy())
def test_qmmm_tip4p():
from math import cos, sin, pi
import numpy as np
#import matplotlib.pyplot as plt
import ase.units as units
from ase import Atoms
from ase.calculators.tip4p import TIP4P, epsilon0, sigma0, rOH, angleHOH
from ase.calculators.qmmm import (SimpleQMMM, EIQMMM, LJInteractions,
LJInteractionsGeneral)
from ase.constraints import FixInternals
from ase.optimize import BFGS
r = rOH
a = angleHOH * pi / 180
# From https://doi.org/10.1063/1.445869
eexp = 6.24 * units.kcal / units.mol
dexp = 2.75
aexp = 46
D = np.linspace(2.5, 3.5, 30)
i = LJInteractions({('O', 'O'): (epsilon0, sigma0)})
# General LJ interaction object
sigma_mm = np.array([sigma0, 0, 0])
epsilon_mm = np.array([epsilon0, 0, 0])
sigma_qm = np.array([sigma0, 0, 0])
epsilon_qm = np.array([epsilon0, 0, 0])
ig = LJInteractionsGeneral(sigma_qm, epsilon_qm, sigma_mm, epsilon_mm, 3)
for calc in [
TIP4P(),
SimpleQMMM([0, 1, 2], TIP4P(), TIP4P(), TIP4P()),
SimpleQMMM([0, 1, 2], TIP4P(), TIP4P(), TIP4P(), vacuum=3.0),
EIQMMM([0, 1, 2], TIP4P(), TIP4P(), i),
EIQMMM([3, 4, 5], TIP4P(), TIP4P(), i, vacuum=3.0),
EIQMMM([0, 1, 2], TIP4P(), TIP4P(), i, vacuum=3.0),
EIQMMM([0, 1, 2], TIP4P(), TIP4P(), ig),
EIQMMM([3, 4, 5], TIP4P(), TIP4P(), ig, vacuum=3.0),
EIQMMM([0, 1, 2], TIP4P(), TIP4P(), ig, vacuum=3.0)
]:
dimer = Atoms('OH2OH2', [(0, 0, 0), (r * cos(a), 0, r * sin(a)),
(r, 0, 0), (0, 0, 0),
(r * cos(a / 2), r * sin(a / 2), 0),
(r * cos(a / 2), -r * sin(a / 2), 0)])
dimer.calc = calc
E = []
F = []
for d in D:
dimer.positions[3:, 0] += d - dimer.positions[3, 0]
E.append(dimer.get_potential_energy())
F.append(dimer.get_forces())
F = np.array(F)
#plt.plot(D, E)
F1 = np.polyval(np.polyder(np.polyfit(D, E, 7)), D)
F2 = F[:, :3, 0].sum(1)
error = abs(F1 - F2).max()
assert error < 0.01
dimer.constraints = FixInternals(bonds=[(r, (0, 1)), (r, (0, 2)),
(r, (3, 4)), (r, (3, 5))],
angles=[(a, (2, 0, 1)),
(a, (5, 3, 4))])
opt = BFGS(dimer,
maxstep=0.04,
trajectory=calc.name + '.traj',
logfile=calc.name + 'd.log')
opt.run(0.01)
e0 = dimer.get_potential_energy()
d0 = dimer.get_distance(0, 3)
R = dimer.positions
v1 = R[2] - R[3]
v2 = R[3] - (R[5] + R[4]) / 2
a0 = np.arccos(
np.dot(v1, v2) /
(np.dot(v1, v1) * np.dot(v2, v2))**0.5) / np.pi * 180
fmt = '{0:>23}: {1:.3f} {2:.3f} {3:.3f} {4:.1f}'
print(fmt.format(calc.name, -min(E), -e0, d0, a0))
assert abs(e0 + eexp) < 0.002
assert abs(d0 - dexp) < 0.006
assert abs(a0 - aexp) < 2.5
print(fmt.format('reference', 9.999, eexp, dexp, aexp))
F1 = np.polyval(np.polyder(np.polyfit(D, E, 7)), D)
F2 = F[:, :3, 0].sum(1)
error = abs(F1 - F2).max()
dimer.constraints = FixBondLengths([(3 * i + j, 3 * i + (j + 1) % 3)
for i in range(2)
for j in [0, 1, 2]])
opt = BFGS(dimer,
trajectory=calc.name + '.traj', logfile=calc.name + 'd.log')
opt.run(0.001)
if calc.name == 'tip4p': # save optimized geom for EIQMMM test
tip4pdimer = dimer.copy()
e0 = dimer.get_potential_energy()
d0 = dimer.get_distance(0, 3)
R = dimer.positions
v1 = R[2] - R[3]
v2 = R[3] - (R[4] + R[5]) / 2
a0 = np.arccos(np.dot(v1, v2) /
(np.dot(v1, v1) * np.dot(v2, v2))**0.5) / np.pi * 180
fmt = '{0:>25}: {1:.3f} {2:.3f} {3:.3f} {4:.1f}'
print(fmt.format(calc.name, -min(E), -e0, d0, a0))
assert abs(e0 + eexp) < 0.002
assert abs(d0 - dexp) < 0.006
assert abs(a0 - aexp) < 2.5
# plt.show()
print(fmt.format('reference', 9.999, eexp, dexp, aexp))
t.write(co)
del t
# append to a nonexisting file
if netcdftrajectory.have_nc == netcdftrajectory.NC_IS_NETCDF4:
fname = '2.nc'
if os.path.isfile(fname):
os.remove(fname)
t = NetCDFTrajectory(fname, 'a', co)
del t
fname = '3.nc'
t = NetCDFTrajectory(fname, 'w', co)
# File is not created before first write
co.set_pbc([True, False, False])
d = co.get_distance(0, 1)
t.write(co)
del t
# Check pbc
t = NetCDFTrajectory(fname)
a = t[-1]
assert a.pbc[0] and not a.pbc[1] and not a.pbc[2]
assert abs(a.get_distance(0, 1) - d) < 1e-6
del t
# Append something in Voigt notation
t = NetCDFTrajectory(fname, 'a')
for frame, a in enumerate(t):
test = np.random.random([len(a), 6])
a.set_array('test', test)
t.write_arrays(a, frame, ['test'])
del t
class AutoTST_Molecule():
"""
A class that allows for one to create RMG, RDKit and ASE
molecules from a single string with identical atom indicies
Inputs:
* smiles (str): a SMILES string that describes the molecule of interest
* rmg_molecule (RMG Molecule object): an rmg molecule that we can extract information from
"""
def __init__(self, smiles=None, rmg_molecule=None):
assert (
smiles or rmg_molecule
), "Please provide a SMILES string and / or an RMG Molecule object."
if smiles and rmg_molecule:
assert rmg_molecule.isIsomorphic(
Molecule(SMILES=smiles
)), "SMILES string did not match RMG Molecule object"
self.smiles = smiles
self.rmg_molecule = rmg_molecule
elif rmg_molecule:
self.rmg_molecule = rmg_molecule
self.smiles = rmg_molecule.toSMILES()
else:
self.smiles = smiles
self.rmg_molecule = Molecule(SMILES=smiles)
self.get_rdkit_molecule()
self.set_rmg_coords("RDKit")
self.get_ase_molecule()
self.get_torsions()
self.get_angles()
self.get_bonds()
def __repr__(self):
return '<AutoTST Molecule "{0}">'.format(self.smiles)
def get_rdkit_molecule(self):
"""
A method to create an RDKit Molecule from the rmg_molecule.
Indicies will be the same as in the RMG Molecule
"""
RDMol = self.rmg_molecule.toRDKitMol(removeHs=False)
rdkit.Chem.AllChem.EmbedMolecule(RDMol)
self.rdkit_molecule = RDMol
def get_ase_molecule(self):
"""
A method to create an ASE Molecule from the rdkit_molecule.
Indicies will be the same as in the RMG and RDKit Molecule.
"""
mol_list = AllChem.MolToMolBlock(self.rdkit_molecule).split('\n')
ase_atoms = []
for i, line in enumerate(mol_list):
if i > 3:
try:
atom0, atom1, bond, rest = line
atom0 = int(atom0)
atom0 = int(atom1)
bond = float(bond)
except ValueError:
try:
x, y, z, symbol = line.split()[0:4]
x = float(x)
y = float(y)
z = float(z)
ase_atoms.append(
Atom(symbol=symbol, position=(x, y, z)))
except:
continue
self.ase_molecule = Atoms(ase_atoms)
return self.ase_molecule
def view_mol(self):
"""
A method designed to create a 3D figure of the AutoTST_Molecule with py3Dmol from the rdkit_molecule
"""
mb = Chem.MolToMolBlock(self.rdkit_molecule)
p = py3Dmol.view(width=400, height=400)
p.addModel(mb, "sdf")
p.setStyle({'stick': {}})
p.setBackgroundColor('0xeeeeee')
p.zoomTo()
return p.show()
#############################################################################
def get_bonds(self):
rdmol_copy = self.rdkit_molecule
bond_list = []
for bond in rdmol_copy.GetBonds():
bond_list.append((bond.GetBeginAtomIdx(), bond.GetEndAtomIdx()))
bonds = []
for indices in bond_list:
i, j = indices
length = self.ase_molecule.get_distance(i, j)
reaction_center = "No"
bond = Bond(indices=indices,
length=length,
reaction_center=reaction_center)
bonds.append(bond)
self.bonds = bonds
return self.bonds
def get_angles(self):
rdmol_copy = self.rdkit_molecule
angle_list = []
for atom1 in rdmol_copy.GetAtoms():
for atom2 in atom1.GetNeighbors():
for atom3 in atom2.GetNeighbors():
if atom1.GetIdx() == atom3.GetIdx():
continue
to_add = (atom1.GetIdx(), atom2.GetIdx(), atom3.GetIdx())
if (to_add in angle_list) or (tuple(reversed(to_add))
in angle_list):
continue
angle_list.append(to_add)
angles = []
for indices in angle_list:
i, j, k = indices
degree = self.ase_molecule.get_angle(i, j, k)
ang = Angle(indices=indices,
degree=degree,
left_mask=[],
right_mask=[])
left_mask = self.get_left_mask(ang)
right_mask = self.get_right_mask(ang)
reaction_center = "No"
angles.append(
Angle(indices, degree, left_mask, right_mask, reaction_center))
self.angles = angles
return self.angles
def get_torsions(self):
rdmol_copy = self.rdkit_molecule
torsion_list = []
cistrans_list = []
for bond1 in rdmol_copy.GetBonds():
atom1 = bond1.GetBeginAtom()
atom2 = bond1.GetEndAtom()
if atom1.IsInRing() or atom2.IsInRing():
# Making sure that bond1 we're looking at are not in a ring
continue
bond_list1 = list(atom1.GetBonds())
bond_list2 = list(atom2.GetBonds())
if not len(bond_list1) > 1 and not len(bond_list2) > 1:
# Making sure that there are more than one bond attached to
# the atoms we're looking at
continue
# Getting the 0th and 3rd atom and insuring that atoms
# attached to the 1st and 2nd atom are not terminal hydrogens
# We also make sure that all of the atoms are properly bound together
# If the above are satisfied, we append a tuple of the torsion our torsion_list
got_atom0 = False
got_atom3 = False
for bond0 in bond_list1:
atomX = bond0.GetOtherAtom(atom1)
# if atomX.GetAtomicNum() == 1 and len(atomX.GetBonds()) == 1:
# This means that we have a terminal hydrogen, skip this
# NOTE: for H_abstraction TSs, a non teminal H should exist
# continue
if atomX.GetIdx() != atom2.GetIdx():
got_atom0 = True
atom0 = atomX
for bond2 in bond_list2:
atomY = bond2.GetOtherAtom(atom2)
# if atomY.GetAtomicNum() == 1 and len(atomY.GetBonds()) == 1:
# This means that we have a terminal hydrogen, skip this
# continue
if atomY.GetIdx() != atom1.GetIdx():
got_atom3 = True
atom3 = atomY
if not (got_atom0 and got_atom3):
# Making sure atom0 and atom3 were not found
continue
# Looking to make sure that all of the atoms are properly bonded to eached
if ("SINGLE" in str(
rdmol_copy.GetBondBetweenAtoms(
atom1.GetIdx(), atom2.GetIdx()).GetBondType())
and rdmol_copy.GetBondBetweenAtoms(atom0.GetIdx(),
atom1.GetIdx())
and rdmol_copy.GetBondBetweenAtoms(atom1.GetIdx(),
atom2.GetIdx())
and rdmol_copy.GetBondBetweenAtoms(atom2.GetIdx(),
atom3.GetIdx())):
torsion_tup = (atom0.GetIdx(), atom1.GetIdx(), atom2.GetIdx(),
atom3.GetIdx())
already_in_list = False
for torsion_entry in torsion_list:
a, b, c, d = torsion_entry
e, f, g, h = torsion_tup
if (b, c) == (f, g) or (b, c) == (g, f):
already_in_list = True
if not already_in_list:
torsion_list.append(torsion_tup)
if ("DOUBLE" in str(
rdmol_copy.GetBondBetweenAtoms(
atom1.GetIdx(), atom2.GetIdx()).GetBondType())
and rdmol_copy.GetBondBetweenAtoms(atom0.GetIdx(),
atom1.GetIdx())
and rdmol_copy.GetBondBetweenAtoms(atom1.GetIdx(),
atom2.GetIdx())
and rdmol_copy.GetBondBetweenAtoms(atom2.GetIdx(),
atom3.GetIdx())):
torsion_tup = (atom0.GetIdx(), atom1.GetIdx(), atom2.GetIdx(),
atom3.GetIdx())
already_in_list = False
for torsion_entry in torsion_list:
a, b, c, d = torsion_entry
e, f, g, h = torsion_tup
if (b, c) == (f, g) or (b, c) == (g, f):
already_in_list = True
if not already_in_list:
cistrans_list.append(torsion_tup)
torsions = []
cistrans = []
for indices in torsion_list:
i, j, k, l = indices
dihedral = self.ase_molecule.get_dihedral(i, j, k, l)
tor = Torsion(indices=indices,
dihedral=dihedral,
left_mask=[],
right_mask=[])
left_mask = self.get_left_mask(tor)
right_mask = self.get_right_mask(tor)
reaction_center = "No"
torsions.append(
Torsion(indices, dihedral, left_mask, right_mask,
reaction_center))
for indices in cistrans_list:
i, j, k, l = indices
dihedral = self.ase_molecule.get_dihedral(i, j, k, l)
tor = CisTrans(indices=indices,
dihedral=dihedral,
left_mask=[],
right_mask=[])
left_mask = self.get_left_mask(tor)
right_mask = self.get_right_mask(tor)
reaction_center = "No"
cistrans.append(
CisTrans(indices, dihedral, left_mask, right_mask,
reaction_center))
self.torsions = torsions
self.cistrans = cistrans
return self.torsions
def get_right_mask(self, torsion_or_angle):
rdmol_copy = self.rdkit_molecule
rdkit_atoms = rdmol_copy.GetAtoms()
if (isinstance(torsion_or_angle, autotst.geometry.Torsion)
or isinstance(torsion_or_angle, autotst.geometry.CisTrans)):
L1, L0, R0, R1 = torsion_or_angle.indices
# trying to get the left hand side of this torsion
LHS_atoms_index = [L0, L1]
RHS_atoms_index = [R0, R1]
elif isinstance(torsion_or_angle, autotst.geometry.Angle):
a1, a2, a3 = torsion_or_angle.indices
LHS_atoms_index = [a2, a1]
RHS_atoms_index = [a2, a3]
complete_RHS = False
i = 0
atom_index = RHS_atoms_index[0]
while complete_RHS is False:
try:
RHS_atom = rdkit_atoms[atom_index]
for neighbor in RHS_atom.GetNeighbors():
if (neighbor.GetIdx()
in RHS_atoms_index) or (neighbor.GetIdx()
in LHS_atoms_index):
continue
else:
RHS_atoms_index.append(neighbor.GetIdx())
i += 1
atom_index = RHS_atoms_index[i]
except IndexError:
complete_RHS = True
right_mask = [
index in RHS_atoms_index for index in range(len(self.ase_molecule))
]
return right_mask
def get_left_mask(self, torsion_or_angle):
rdmol_copy = self.rdkit_molecule
rdkit_atoms = rdmol_copy.GetAtoms()
if (isinstance(torsion_or_angle, autotst.geometry.Torsion)
or isinstance(torsion_or_angle, autotst.geometry.CisTrans)):
L1, L0, R0, R1 = torsion_or_angle.indices
# trying to get the left hand side of this torsion
LHS_atoms_index = [L0, L1]
RHS_atoms_index = [R0, R1]
elif isinstance(torsion_or_angle, autotst.geometry.Angle):
a1, a2, a3 = torsion_or_angle.indices
LHS_atoms_index = [a2, a1]
RHS_atoms_index = [a2, a3]
complete_LHS = False
i = 0
atom_index = LHS_atoms_index[0]
while complete_LHS is False:
try:
LHS_atom = rdkit_atoms[atom_index]
for neighbor in LHS_atom.GetNeighbors():
if (neighbor.GetIdx()
in LHS_atoms_index) or (neighbor.GetIdx()
in RHS_atoms_index):
continue
else:
LHS_atoms_index.append(neighbor.GetIdx())
i += 1
atom_index = LHS_atoms_index[i]
except IndexError:
complete_LHS = True
left_mask = [
index in LHS_atoms_index for index in range(len(self.ase_molecule))
]
return left_mask
def set_rmg_coords(self, molecule_base):
if molecule_base == "RDKit":
mol_list = AllChem.MolToMolBlock(self.rdkit_molecule).split('\n')
for i, atom in enumerate(self.rmg_molecule.atoms):
j = i + 4
coords = mol_list[j].split()[:3]
for k, coord in enumerate(coords):
coords[k] = float(coord)
atom.coords = np.array(coords)
elif molecule_base == "ASE":
for i, position in enumerate(self.ase_molecule.get_positions()):
self.rmg_molecule.atoms[i].coords = position
def update_from_rdkit_mol(self):
# In order to update the ase molecule you simply need to rerun the get_ase_molecule method
self.get_ase_molecule()
self.set_rmg_coords("RDKit")
# Getting the new torsion angles
self.get_torsions()
def update_from_ase_mol(self):
self.set_rmg_coords("ASE")
# setting the geometries of the rdkit molecule
positions = self.ase_molecule.get_positions()
conf = self.rdkit_molecule.GetConformers()[0]
for i, atom in enumerate(self.rdkit_molecule.GetAtoms()):
conf.SetAtomPosition(i, positions[i])
# Getting the new torsion angles
self.get_torsions()
def update_from_rmg_mol(self):
conf = self.rdkit_molecule.GetConformers()[0]
ase_atoms = []
for i, atom in enumerate(self.rmg_molecule.atoms):
x, y, z = atom.coords
symbol = atom.symbol
conf.SetAtomPosition(i, [x, y, z])
ase_atoms.append(Atom(symbol=symbol, position=(x, y, z)))
self.ase_molecule = Atoms(ase_atoms)
# Getting the new torsion angles
self.get_torsions()
def check_min_dist(Optimizer, totalsol, type='Defect', nat=None, min_len=0.7, STR=''):
if type=='Defect' or type=='Crystal' or type=='Surface':
if nat==None:
nat=len(totalsol)
cutoffs=[2.0 for one in totalsol]
nl=NeighborList(cutoffs,bothways=True,self_interaction=False)
nl.update(totalsol)
for one in totalsol[0:nat]:
nbatoms=Atoms()
nbatoms.append(one)
indices, offsets=nl.get_neighbors(one.index)
for index, d in zip(indices,offsets):
index = int(index)
sym=totalsol[index].symbol
pos=totalsol[index].position + numpy.dot(d,totalsol.get_cell())
at=Atom(symbol=sym,position=pos)
nbatoms.append(at)
while True:
dflag=False
for i in range(1,len(nbatoms)):
d=nbatoms.get_distance(0,i)
if d < min_len:
nbatoms.set_distance(0,i,min_len+.01,fix=0.5)
STR+='--- WARNING: Atoms too close (<0.7A) - Implement Move ---\n'
dflag=True
if dflag==False:
break
for i in range(len(indices)):
totalsol[indices[i]].position=nbatoms[i+1].position
totalsol[one.index].position=nbatoms[0].position
nl.update(totalsol)
elif type=='Cluster':
rank = MPI.COMM_WORLD.Get_rank()
logger = logging.getLogger(Optimizer.loggername)
R = totalsol.arrays['positions']
tol = 0.01
epsilon = 0.05
fix = 0.5
if Optimizer.forcing == 'EllipoidShape' or Optimizer.forcing == 'FreeNatom':
com = totalsol.get_center_of_mass()
cmax = numpy.maximum.reduce(R)
cmin = numpy.minimum.reduce(R)
rmax= (cmax-cmin)/2.0
if Optimizer.forcing == 'FreeNatom':
rcutoff = 44.0
cutoff = [44.0,44.0,20.0]
else:
rcutoff = 11.0
cutoff = [12.0,12.0,12.0]
rcutoff = 44.0
cutoff = [44.0,44.0,20.0]
#check if atoms are isolated outside of cluster
cutoffs=[3.0 for one in totalsol]
nl=NeighborList(cutoffs,bothways=True,self_interaction=False)
nl.update(totalsol)
for i in range(len(totalsol)):
indices, offsets=nl.get_neighbors(i)
D = R[i]-com
radius = (numpy.dot(D,D))**0.5 #numpy.linalg.norm(D)
if len(indices) < 12 or radius > rcutoff :
# logger.info('M:move atoms back when indice {0} or radius {1}'.format(len(indices),radius))
# R[i] = [com[j] + D[j]/radius*rcutoff for j in range(3)]
theta=math.radians(random.uniform(0,360))
phi=math.radians(random.uniform(0,180))
R[i][0] = com[0] + (rmax[0]+2.5)*math.sin(theta)*math.cos(phi) #allow atoms expend by 2.5 ang
R[i][1] = com[1] + (rmax[1]+2.5)*math.sin(theta)*math.sin(phi)
R[i][2] = com[2] + rmax[2]*math.cos(theta)
# logger.info('M:move atoms back new pos {0} {1} {2}'.format(rmax[0]*math.sin(theta)*math.cos(phi),rmax[1]*math.sin(theta)*math.sin(phi),rmax[2]*math.cos(theta)))
# check if atoms are within cluster region
for i in range(0,len(totalsol)):
# D = R[i]-com
for j in range(3):
if D[j] > cutoff[j] or D[j] < -cutoff[j]:
# logger.info('M:before move R {0} & com {1}'.format(R[i][j],com[j]))
#if rank==0:
# print "before:",j,R[i][j],com[j]
R[i][j] = com[j]+numpy.sign(D[j])*cutoff[j]*random.random()
# logger.info('M:after move R {0} '.format(R[i][j]))
#if rank==0:
# print "after:",R[i][j]
# STR+='--- WARNING: Atoms too far along x-y (>44A) - Implement Move ---\n'
D = R[i]-com
# radius = (numpy.dot(D,D))**0.5 #numpy.linalg.norm(D)
# STR+='--- WARNING: Atoms too far (>56A) - Implement Move ---\n'
closelist = numpy.arange(len(totalsol))
iter = 0
while len(closelist) > 0 and iter<2:
iter+=1
# checklist = numpy.copy(closelist)
closelist = []
dist=scipy.spatial.distance.cdist(R,R)
numpy.fill_diagonal(dist,1.0)
smalldist = numpy.where(dist < min_len-tol)
# for i in checklist:
# for j in range(i+1,len(totalsol)):
# if len(checklist) == len(totalsol):
# jstart = i+1
# else:
# jstart = 0
# for j in range(jstart,len(totalsol)):
# if i != j and dist[i][j] < min_len:
# d=totalsol.get_distance(i,j)
# if d < min_len:
# totalsol.set_distance(i,j,min_len,fix=0.5)
# d = (D[0]*D[0]+D[1]*D[1]+D[2]*D[2])**0.5
for ind in range(len(smalldist[0])):
i = smalldist[0][ind]
j = smalldist[1][ind]
if i < j and dist[i][j] < min_len-tol:
closelist.append(i)
closelist.append(j)
if dist[i][j] > epsilon:
x = 1.0 - min_len / dist[i][j]
D = R[j]-R[i]
# print "node:",rank,"x",x,R[i],R[j],D, dist[i][j]
R[i] += (x * fix) * D
R[j] -= (x * (1.0 - fix)) * D
else:
R[i] += [0.2, 0.0, 0.0]
R[j] -= [0.2, 0.0, 0.0]
R2P = [R[i],R[j]]
dist2P=scipy.spatial.distance.cdist(R2P,R)
dist[i] = dist2P[0]
dist[j] = dist2P[1]
for k in range(len(R)):
dist[k][i] = dist[i][k]
dist[k][j] = dist[j][k]
# STR+='--- WARNING: Atoms too close (<0.7A) - Implement Move ---\n'
closelist=list(set(closelist))
closelist.sort()
if len(closelist) != 0:
logger.info('M:iter {0}, closelist size {1}'.format(iter,len(closelist)))
# print "rank", rank, closelist
else:
print 'WARNING: In Check_Min_Dist in EvalEnergy: Structure Type not recognized'
return totalsol, STR
def lattice_alteration_nn(indiv, Optimizer):
"""Move function to perform random move along random axis for nearest neighbor distance to random atoms
Inputs:
indiv = Individual class object to be altered
Optimizer = Optimizer class object with needed parameters
Outputs:
indiv = Altered Individual class object
"""
if 'MU' in Optimizer.debug:
debug = True
else:
debug = False
if Optimizer.structure=='Defect':
if Optimizer.isolate_mutation:
indc,indb,vacant,swaps,stro = find_defects(indiv[0],Optimizer.solidbulk,0)
ind = indc.copy()
ind.extend(indb)
else:
ind=indiv[0].copy()
indc=indiv[0].copy()
else:
ind=indiv[0].copy()
indc=indiv[0].copy()
if len(indc) != 0:
ctoff1 = [1.0 for one in ind]
nl = NeighborList(ctoff1, bothways=True, self_interaction=False)
nl.update(ind)
try:
natomsmove=random.randint(1,len(indc)/2)
except ValueError:
natomsmove=1
passn=0
for count in range(natomsmove):
try:
indexmv = random.choice([i for i in range(len(indc))])
indices, offsets = nl.get_neighbors(indexmv)
nns = Atoms()
nns.append(ind[indexmv])
for index, d in zip(indices,offsets):
index = int(index)
pos = ind[index].position + numpy.dot(d,ind.get_cell())
nns.append(Atom(symbol=ind[index].symbol, position=pos))
dist = [nns.get_distance(0,i) for i in range(1, len(nns))]
r = sum(dist)/len(dist)
dir = random.choice([[1,0,0],[-1,0,0],[0,1,0],[0,-1,0],[0,0,1],[0,0,-1]])
ind[indexmv].position += [i*r for i in dir]
except:
passn+=1
indiv[0]=ind.copy()
else:
natomsmove=0
passn=0
Optimizer.output.write('Lattice Alteration NN Mutation performed on individual\n')
Optimizer.output.write('Index = '+repr(indiv.index)+'\n')
natomsmove-=passn
Optimizer.output.write('Number of atoms moved = '+repr(natomsmove)+'\n')
Optimizer.output.write(repr(indiv[0])+'\n')
muttype='LANN'+repr(natomsmove)
if indiv.energy==0:
indiv.history_index=indiv.history_index+'m'+muttype
else:
indiv.history_index=repr(indiv.index)+'m'+muttype
return indiv
from ase import Atoms
# Setup a chain of H,O,C
# H-O Dist = 2
# O-C Dist = 3
# C-H Dist = 5 with mic=False
# C-H Dist = 4 with mic=True
a = Atoms('HOC', positions=[(1, 1, 1), (3, 1, 1), (6, 1, 1)])
a.set_cell((9, 2, 2))
a.set_pbc((True, False, False))
# Calculate indiviually with mic=True
assert a.get_distance(0, 1, mic=True) == 2
assert a.get_distance(1, 2, mic=True) == 3
assert a.get_distance(0, 2, mic=True) == 4
# Calculate indiviually with mic=False
assert a.get_distance(0, 1, mic=False) == 2
assert a.get_distance(1, 2, mic=False) == 3
assert a.get_distance(0, 2, mic=False) == 5
# Calculate in groups with mic=True
assert (a.get_distances(0, [1, 2], mic=True) == [2, 4]).all()
# Calculate in groups with mic=False
assert (a.get_distances(0, [1, 2], mic=False) == [2, 5]).all()
# Calculate all with mic=True
assert (a.get_all_distances(mic=True) == [[0, 2, 4],
[2, 0, 3],
a = 10
d = 1.17103
CO2 = Atoms('CO2',
positions=[[a / 2, a / 2, a / 2], [a / 2 - d, a / 2, a / 2],
[a / 2 + d, a / 2, a / 2]],
cell=(a, a, a))
# Next, we need to create a calculator object
# The optimization calculation
# First we create the GPAW object
calc_PBE = GPAW(xc='PBE')
CO2.set_calculator(calc_PBE)
# By the way: by default, convergence of SCF is such that difference in energy is < 0.0005
# We can change this by adding the parameter: convergence={'energy': 0.0001}
# Next, we use a relaxation procedure
# Here, the atoms will be moved small steps in search for the optimal structure until the force on each atom is less that 0.05 eV/Ang
relax = QuasiNewton(CO2)
relax.run(fmax=0.05)
CO2.get_distance(0, 1)
# We started from the correct structure, that's why the optimization finished in only 1 step.
# Change d to 1 and see what happens. The optimization will finish in a number of iterations.
co.pbc = True
t.write(co)
del t
# append to a nonexisting file
fname = '2.nc'
if os.path.isfile(fname):
os.remove(fname)
t = NetCDFTrajectory(fname, 'a', co)
del t
fname = '3.nc'
t = NetCDFTrajectory(fname, 'w', co)
# File is not created before first write
co.set_pbc([True, False, False])
d = co.get_distance(0, 1)
with warnings.catch_warnings():
warnings.simplefilter('ignore', UserWarning)
t.write(co)
del t
# Check pbc
for c in [1, 1000]:
t = NetCDFTrajectory(fname, chunk_size=c)
a = t[-1]
assert a.pbc[0] and not a.pbc[1] and not a.pbc[2]
assert abs(a.get_distance(0, 1) - d) < 1e-6
del t
# Append something in Voigt notation
t = NetCDFTrajectory(fname, 'a')
for frame, a in enumerate(t):
test = np.random.random([len(a), 6])
def test_qmmm(testdir):
r = rOH
a = angleHOH * pi / 180
# From https://doi.org/10.1063/1.445869
eexp = 6.50 * units.kcal / units.mol
dexp = 2.74
aexp = 27
D = np.linspace(2.5, 3.5, 30)
i = LJInteractions({('O', 'O'): (epsilon0, sigma0)})
# General LJ interaction object
sigma_mm = np.array([0, 0, sigma0])
epsilon_mm = np.array([0, 0, epsilon0])
sigma_qm = np.array([0, 0, sigma0])
epsilon_qm = np.array([0, 0, epsilon0])
ig = LJInteractionsGeneral(sigma_qm, epsilon_qm, sigma_mm, epsilon_mm, 3)
for calc in [
TIP3P(),
SimpleQMMM([0, 1, 2], TIP3P(), TIP3P(), TIP3P()),
SimpleQMMM([0, 1, 2], TIP3P(), TIP3P(), TIP3P(), vacuum=3.0),
EIQMMM([0, 1, 2], TIP3P(), TIP3P(), i),
EIQMMM([3, 4, 5], TIP3P(), TIP3P(), i, vacuum=3.0),
EIQMMM([0, 1, 2], TIP3P(), TIP3P(), i, vacuum=3.0),
EIQMMM([0, 1, 2], TIP3P(), TIP3P(), ig),
EIQMMM([3, 4, 5], TIP3P(), TIP3P(), ig, vacuum=3.0),
EIQMMM([0, 1, 2], TIP3P(), TIP3P(), ig, vacuum=3.0)
]:
dimer = Atoms('H2OH2O',
[(r * cos(a), 0, r * sin(a)), (r, 0, 0), (0, 0, 0),
(r * cos(a / 2), r * sin(a / 2), 0),
(r * cos(a / 2), -r * sin(a / 2), 0), (0, 0, 0)])
dimer.calc = calc
E = []
F = []
for d in D:
dimer.positions[3:, 0] += d - dimer.positions[5, 0]
E.append(dimer.get_potential_energy())
F.append(dimer.get_forces())
F = np.array(F)
F1 = np.polyval(np.polyder(np.polyfit(D, E, 7)), D)
F2 = F[:, :3, 0].sum(1)
error = abs(F1 - F2).max()
assert error < 0.01
dimer.constraints = FixInternals(bonds=[(r, (0, 2)), (r, (1, 2)),
(r, (3, 5)), (r, (4, 5))],
angles_deg=[
(np.degrees(a), (0, 2, 1)),
(np.degrees(a), (3, 5, 4))
])
opt = GPMin(dimer,
trajectory=calc.name + '.traj',
logfile=calc.name + 'd.log')
opt.run(0.01)
e0 = dimer.get_potential_energy()
d0 = dimer.get_distance(2, 5)
R = dimer.positions
v1 = R[1] - R[5]
v2 = R[5] - (R[3] + R[4]) / 2
a0 = np.arccos(
np.dot(v1, v2) /
(np.dot(v1, v1) * np.dot(v2, v2))**0.5) / np.pi * 180
fmt = '{0:>20}: {1:.3f} {2:.3f} {3:.3f} {4:.1f}'
print(fmt.format(calc.name, -min(E), -e0, d0, a0))
assert abs(e0 + eexp) < 0.002
assert abs(d0 - dexp) < 0.01
assert abs(a0 - aexp) < 4
print(fmt.format('reference', 9.999, eexp, dexp, aexp))
