def get_constraints(self, step, geom):
"""
There are three types of constraints:
1. fix a coordinate to the current value
2. change a coordinate and fix is to the new value
3. release a coordinate (only for gaussian)
"""
fix = []
change = []
release = []
if step < self.max_step:
#fix all the bond lengths
for i in range(self.species.natom - 1):
for j in range(i + 1, self.species.natom):
if self.species.bond[i][j] > 0:
fix.append([i + 1, j + 1])
if step < 12:
new_dihs = geometry.new_ring_dihedrals(self.species, self.instance,
step, 12)
for dih in range(len(self.instance) - 3):
constraint = []
for i in range(4):
constraint.append(self.instance[dih + i] + 1)
constraint.append(new_dihs[dih])
change.append(constraint)
elif step < 22:
for dih in range(len(self.instance) - 3):
constraint = []
for i in range(4):
constraint.append(self.instance[dih + i] + 1)
release.append(constraint)
fval = 1.35
val = geometry.new_bond_length(self.species, self.instance[0],
self.instance[-1], step - 11, 10,
fval, geom)
constraint = [self.instance[0] + 1, self.instance[-1] + 1, val]
change.append(constraint)
val = geometry.new_bond_length(self.species, self.instance[-2],
self.instance[-1], step - 11, 10,
fval, geom)
constraint = [self.instance[-2] + 1, self.instance[-1] + 1, val]
change.append(constraint)
#remove the bonds from the fix if they are in another constaint
for c in change:
if len(c) == 3:
index = -1
for i, fi in enumerate(fix):
if len(fi) == 2:
if sorted(fi) == sorted(c[:2]):
index = i
if index > -1:
del fix[index]
return step, fix, change, release
def get_constraints(self, step, geom):
"""
There are three types of constraints:
1. fix a coordinate to the current value
2. change a coordinate and fix is to the new value
3. release a coordinate (only for gaussian)
"""
fix = []
change = []
release = []
if step < self.max_step:
#fix all the bond lengths
for i in range(self.species.natom - 1):
for j in range(i + 1, self.species.natom):
if self.species.bond[i][j] > 0:
fix.append([i + 1, j + 1])
if step < 12:
new_dihs = geometry.new_ring_dihedrals(self.species, self.instance,
step, 12)
for dih in range(len(self.instance) - 3):
constraint = []
for i in range(4):
constraint.append(self.instance[dih + i] + 1)
constraint.append(new_dihs[dih])
change.append(constraint)
if step == 0 and len(self.instance) > 6:
for angle in range(len(self.instance) - 2):
constraint = []
for i in range(3):
constraint.append(self.instance[angle + i] + 1)
constraint.append(180. * (len(self.instance) - 2.) /
len(self.instance))
change.append(constraint)
else:
for angle in range(len(self.instance) - 2):
constraint = []
for i in range(3):
constraint.append(self.instance[angle + i] + 1)
fix.append(constraint)
elif step == 12:
if len(self.instance) > 3:
for dih in range(len(self.instance) - 3):
f = []
for i in range(4):
f.append(self.instance[dih + i] + 1)
fix.append(f)
for angle in range(len(self.instance) - 2):
constraint = []
for i in range(3):
constraint.append(self.instance[angle + i] + 1)
constraint.append(180. * (len(self.instance) - 2.) /
len(self.instance))
change.append(constraint)
else:
#val = 60.0
#constraint = [self.instance[-2] + 1,self.instance[-1] + 1,self.instance[0] + 1,val]
#change.append(constraint)
fval = 1.35
if self.species.atom[self.instance[0]] == 'O': fval = 1.2
constraint = [
self.instance[0] + 1, self.instance[-1] + 1, fval
]
change.append(constraint)
fval = 1.35
if self.species.atom[self.instance[-2]] == 'O': fval = 1.2
constraint = [
self.instance[-2] + 1, self.instance[-1] + 1, fval
]
change.append(constraint)
step = 13
elif step == 13:
for angle in range(len(self.instance) - 2):
constraint = []
for i in range(3):
constraint.append(self.instance[angle + i] + 1)
release.append(constraint)
for dih in range(len(self.instance) - 3):
constraint = []
for i in range(4):
constraint.append(self.instance[dih + i] + 1)
release.append(constraint)
fval = 1.35
if self.species.atom[self.instance[0]] == 'O': fval = 1.2
constraint = [self.instance[0] + 1, self.instance[-1] + 1, fval]
change.append(constraint)
#if len(self.instance) > 3 and np.sum(species.rad) == 0:
# fval = 1.35
# constraint = [self.instance[1] + 1,self.instance[-1] + 1,fval]
# change.append(constraint)
fval = 1.0
constraint = [self.instance[1] + 1, self.instance[-1] + 1, fval]
change.append(constraint)
fval = 1.35
if self.species.atom[self.instance[-2]] == 'O': fval = 1.2
constraint = [self.instance[-2] + 1, self.instance[-1] + 1, fval]
change.append(constraint)
#remove the bonds from the fix if they are in another constaint
for c in change:
if len(c) == 3:
index = -1
for i, fi in enumerate(fix):
if len(fi) == 2:
if sorted(fi) == sorted(c[:2]):
index = i
if index > -1:
del fix[index]
return step, fix, change, release
def get_constraints(self, step, geom):
"""
There are three types of constraints:
1. fix a coordinate to the current value
2. change a coordinate and fix is to the new value
3. release a coordinate (only for gaussian)
"""
fix = []
change = []
release = []
if step < self.max_step:
#fix all the bond lengths
for i in range(self.species.natom - 1):
for j in range(i + 1, self.species.natom):
if self.species.bond[i][j] > 0:
fix.append([i + 1, j + 1])
if step < 12:
new_dihs = geometry.new_ring_dihedrals(self.species, self.instance,
step, 12, geom)
for dih in range(len(self.instance) -
4): # do not include last atom
constraint = []
for i in range(4):
constraint.append(self.instance[dih + i] + 1)
constraint.append(new_dihs[dih])
change.append(constraint)
ldih = [
] # constraint for the last dihedral, which needs to be 180 degrees
for i in range(4):
ldih.append(self.instance[len(self.instance) - 4 + i] + 1)
dih = geometry.calc_dihedral(geom[ldih[0] - 1], geom[ldih[1] - 1],
geom[ldih[2] - 1],
geom[ldih[3] - 1])[0]
frac = 1. / (12. - step)
if dih < 0:
new_dih = dih - frac * (180. + dih)
ldih.append(new_dih)
else:
new_dih = dih + frac * (180. - dih)
ldih.append(new_dih)
change.append(ldih)
elif step < 22:
for dih in range(len(self.instance) - 3):
constraint = []
for i in range(4):
constraint.append(self.instance[dih + i] + 1)
release.append(constraint)
fdist1 = constants.st_bond[''.join(
sorted(self.species.atom[self.instance[0]] +
self.species.atom[self.instance[-2]]))] * 1.0
if ''.join(
sorted(self.species.atom[self.instance[0]] +
self.species.atom[self.instance[-2]])) == 'CO':
fdist1 = 1.68
ndist1 = geometry.new_bond_length(self.species, self.instance[0],
self.instance[-2], step - 11, 10,
fdist1, geom)
constraint = [self.instance[0] + 1, self.instance[-2] + 1, ndist1]
change.append(constraint)
fdist2 = constants.st_bond[''.join(
sorted(self.species.atom[self.instance[-1]] +
self.species.atom[self.instance[-2]]))] * 1.0
if ''.join(
sorted(self.species.atom[self.instance[-1]] +
self.species.atom[self.instance[-2]])) == 'CO':
fdist2 = 1.68
ndist2 = geometry.new_bond_length(self.species, self.instance[-1],
self.instance[-2], step - 11, 10,
fdist2, geom)
constraint = [self.instance[-1] + 1, self.instance[-2] + 1, ndist2]
change.append(constraint)
#remove the bonds from the fix if they are in another constaint
for c in change:
if len(c) == 3:
index = -1
for i, fi in enumerate(fix):
if len(fi) == 2:
if sorted(fi) == sorted(c[:2]):
index = i
if index > -1:
del fix[index]
return step, fix, change, release
def __init__(self,species,qc,par,instance,instance_name):
#st_pt of the reactant
self.species = species
#st_pt of the ts
self.ts = None
#st_pt of the product(s)
self.products = []
#bond matrix of the products
self.product_bonds = []
#optimization objects
self.ts_opt = None
self.prod_opt = []
self.qc = qc
self.par = par
#indices of the reactive atoms
self.instance = instance
#name of the reaction
self.instance_name = instance_name
#maximum number of steps for this reaction family
self.max_step = 22
#do a scan?
self.scan = 0
#skip the first 12 steps in case the instance has a length of 3?
self.skip = 0
def get_constraints(self,step, geom):
"""
There are three types of constraints:
1. fix a coordinate to the current value
2. change a coordinate and fix is to the new value
3. release a coordinate (only for gaussian)
"""
fix = []
change = []
release = []
if step < self.max_step:
#fix all the bond lengths
for i in range(self.species.natom - 1):
for j in range(i+1, self.species.natom):
if self.species.bond[i][j] > 0:
fix.append([i+1,j+1])
if step < 12:
new_dihs = geometry.new_ring_dihedrals(self.species, self.instance, step, 12)
for dih in range(len(self.instance)-3):
constraint = []
for i in range(4):
constraint.append(self.instance[dih+i] + 1)
constraint.append(new_dihs[dih])
change.append(constraint)
elif step < 22:
for dih in range(len(self.instance)-3):
constraint = []
for i in range(4):
constraint.append(self.instance[dih+i] + 1)
release.append(constraint)
fval = 1.35
val = geometry.new_bond_length(self.species,self.instance[0],self.instance[-1],step-11,10,fval,geom)
constraint = [self.instance[0] + 1,self.instance[-1] + 1,val]
change.append(constraint)
val = geometry.new_bond_length(self.species,self.instance[-2],self.instance[-1],step-11,10,fval,geom)
constraint = [self.instance[-2] + 1,self.instance[-1] + 1,val]
change.append(constraint)
#remove the bonds from the fix if they are in another constaint
for c in change:
if len(c) == 3:
index = -1
for i,fi in enumerate(fix):
if len(fi) == 2:
if sorted(fi) == sorted(c[:2]):
index = i
if index > -1:
del fix[index]
return step, fix, change, release