def get_vectors(self, atoms):
if self.movemode == 2:
deloc = Delocalizer(atoms, periodic=True, dense=True)
coords = PC(deloc.x_ref.flatten(),
deloc.masses,
atoms=deloc.atoms,
ic=deloc.ic,
Li=deloc.u)
else:
deloc = Delocalizer(atoms)
tu = deloc.u
if self.constr:
e = deloc.constrainStretches()
deloc.constrain(e)
tu = deloc.u2
if not self.ads:
coords = DC(deloc.x_ref.flatten(),
deloc.masses,
atoms=deloc.atoms,
ic=deloc.ic,
u=tu)
else:
cell = self.atoms.get_cell() * self.cell_scale
coords = CDC(deloc.x_ref.flatten(),
deloc.masses,
unit=1.0,
atoms=deloc.atoms,
ic=deloc.ic,
u=tu,
cell=cell)
return coords.get_vectors()
def initialize(self):
#initialize curvilinear coordinates
d = Delocalizer(self.atoms,periodic=self.is_periodic,dense=True, weighted=False)
if self.is_periodic:
#NOT IMPLEMENTED YET
pass
else:
self.coords = DC(d.x_ref.flatten(), d.masses, internal=True,
atoms=d.atoms, ic=d.ic, L=None, Li=None, u=d.get_U(),
biArgs={'RIIS': 4, 'RIIS_maxLength': 6, 'maxStep':0.5,})
#setup model Hessian
self.init_hessian()
from ase.io import read
from winak.globaloptimization.delocalizer import *
from winak.curvilinear.Coordinates import DelocalizedCoordinates as DC
m = read('../testsystems/rea.xyz')
e = Delocalizer(m, dense=True)
d = []
n = 17
#c_vec = e.constrainStretches()
#e.constrain(c_vec)
coords=DC(e.x_ref.flatten(), e.masses, internal=True, atoms=e.atoms, \
#ic=e.ic, L=None, Li=None,u=e.get_constrained_U(),
ic=e.ic, L=None, Li=None,u=e.get_U(),
biArgs={'maxiter':100,'RIIS': True,
#'col_constraints':e.constraints_cart,
#'row_constraints':e.constraints_int,
})
coords.write_jmol('cdol') #constrained delocalizing out loud
"""
The next loop prints the C-C distance after displacing along a delocalized internal.
It varies by about 10%.
"""
#tmp=read('../testsystems/clethen.xyz')
#for i in coords.get_vectors():
#tmp.set_positions(e.x_ref+i)
##view(m)
#print np.linalg.norm(tmp[1].get_position()-tmp[0].get_position())
from winak.globaloptimization.delocalizer import *
m = read('../testsystems/clethen.xyz')
#TEST ICLIST
iclist = [
1, 1, 2, 1, 1, 3, 1, 1, 4, 1, 2, 5, 1, 2, 6, 2, 1, 5, 2, 2, 2, 4, 1, 2, 3,
4, 1, 2, 5, 6, 2, 2, 2, 3, 1, 2, 1, 6, 2, 3, 3, 1, 2, 5, 3, 3, 1, 2, 6, 3,
4, 1, 2, 6, 3, 4, 1, 2, 5, 4, 2, 3, 4, 1, 4, 6, 1, 5, 2, 0
]
#DENSE
d = Delocalizer(m, icList=iclist, periodic=False, dense=True,
weighted=True) #, weighted=True)
coords=DC(d.x_ref.flatten(), d.masses, internal=True, atoms=d.atoms, \
ic=d.ic, L=None, Li=None,u=d.get_U())#, biArgs={'iclambda' :0.0001})
coords.write_jmol('dol') #delocalizing out loud
coords.s[:] = 2.000
coords.s2x()
X1 = coords.x
print coords.getS(X1)
print X1
#SPARSE
d = Delocalizer(m, icList=iclist, periodic=False, dense=False,
weighted=False) #, weighted=True)
coords=DC(d.x_ref.flatten(), d.masses, internal=True, atoms=d.atoms, \
ic=d.ic, L=None, Li=None,u=d.get_U(), biArgs={'iclambda':0.000001})
coords.write_jmol('dol2') #delocalizing out loud
unit=1.0,
atoms=d.atoms,
ic=d.ic,
u=d.u,
cell=cell)
coords_s1.write_jmol('s1.jmol')
#subsystem2 Surface
subsystem2 = system[2:]
d = Delocalizer(subsystem2)
cell = subsystem1.get_cell() #*[1.0,1.0,1.0]
coords_s2 = DC(d.x_ref.flatten(),
d.masses,
unit=1.0,
atoms=d.atoms,
ic=d.ic,
u=d.u)
#atoms=d.atoms,ic=d.ic,u=d.u,cell=cell)
coords_s2.write_jmol('s2.jmol')
#put together
coords = Set_of_CDCs([coords_s1, coords_s2])
print coords.masses
print len(coords.masses)
print coords.x0.reshape(-1, 3)
s = coords.getS(coords.x0)
print s
from ase.all import *
from winak.globaloptimization.delocalizer import *
from winak.curvilinear.Coordinates import DelocalizedCoordinates as DC
m = read('../testsystems/clethen.xyz')
e = Delocalizer(m)
d = []
n = 17
e.constrainStretches()
coords=DC(e.x_ref.flatten(), e.masses, internal=True, atoms=e.atoms, \
ic=e.ic, L=None, Li=None,u=e.get_U())
coords.write_jmol('cdol') #constrained delocalizing out loud
"""
The next loop prints the C-C distance after displacing along a delocalized internal.
It varies by about 10%.
"""
tmp = read('../testsystems/clethen.xyz')
for i in coords.get_vectors():
tmp.set_positions(e.x_ref + i)
#view(m)
print np.linalg.norm(tmp[1].get('position') - tmp[0].get('position'))
dyn.run(0.001)
print 'Cartesian optimization finished...'
#TEST ICLIST
iclist = [1, 1, 2, 1, 1, 3, 1, 1, 4, 1, 2, 5, 1, 2, 6, 2, 1, 5, 2,
2, 2, 4, 1, 2, 3, 4, 1, 2, 5, 6, 2, 2, 2, 3, 1, 2, 1,
6, 2, 3, 3, 1, 2, 5, 3, 3, 1, 2, 6, 3, 4, 1, 2, 6, 3,
4, 1, 2, 5, 4, 2, 3, 4, 1, 4, 6, 1, 5, 2, 0]
#DENSE
d=Delocalizer(m, icList=iclist, periodic=False, dense=True, weighted=True)#, weighted=True)
coords=DC(d.x_ref.flatten(), d.masses, internal=True, atoms=d.atoms, \
ic=d.ic, L=None, Li=None,u=d.get_U(), #)#, biArgs={'iclambda' :0.0001})
biArgs={'RIIS': True, 'maxiter': 900, 'eps': 1e-6, 'maxEps':1e-7,
# 'iclambda' : 1e-6,
'RIIS_dim': 4, 'RIIS_maxLength':6, 'maxStep':0.5,})
coords.write_jmol('dol') #delocalizing out loud
print 'constructed DI coordinates'
# view(m)
mlist = [m.copy()]
for ss in np.linspace(0,100,10):
#transform from DCs to CC displacements
coords.s[:] = 0.0