def __init__(self):
WeightedMultiTerm.__init__(self)
self.add_term(Electrostatics(), 0.1146)
self.add_term(NewHydrogenBonding(), 0.1852) #.0656*2.82292 = 0.1851836
self.add_term(NewVanDerWaalsHybridWeights(),
1.0) #varying weights in scorer
self.add_term(NewDesolvation(), 1.0) #.1711*0.10188 = 0.0174317
def __init__(self):
self.prop = 'ad4_energy'
WeightedMultiTerm.__init__(self)
AutoDockTermWeights4.__init__(self)
self.add_term(Electrostatics(), self.estat_weight)
self.add_term(NewHydrogenBonding(), self.hbond_weight)
self.add_term(NewVanDerWaals(), self.vdw_weight) #.1485*1.002
self.add_term(NewDesolvation(), self.dsolv_weight)
def __init__(self):
self.prop = 'ad305_energy'
WeightedMultiTerm.__init__(self)
AutoDockTermWeights305.__init__(self)
self.add_term(Electrostatics(), self.estat_weight)
self.add_term(HydrogenBonding(), self.hbond_weight)
self.add_term(VanDerWaals(), self.vdw_weight)
self.add_term(Desolvation(), self.dsolv_weight)
def setup_scorer(self):
# construct atom_map scorer...
self.atom_map_scorer = AutoGrid305Scorer()
self.atom_map_scorer.set_molecular_system(self.ms)
# ... and electrostatics scorer
self.estat_map_scorer = WeightedMultiTerm()
self.estat_map_scorer.add_term(Electrostatics(),
AutoDockTermWeights305().estat_weight)
self.estat_map_scorer.set_molecular_system(self.ms)
def __init__(self, exclude_torsFreeEnergy=False, verbose=False):
self.verbose = verbose
if verbose:
print "initialized exclude_torsFreeEnergy=", exclude_torsFreeEnergy
self.prop = 'ad41_energy'
self.exclude_torsFreeEnergy = exclude_torsFreeEnergy
WeightedMultiTerm.__init__(self)
AutoDockTermWeights41.__init__(self)
self.add_term(Electrostatics(), self.estat_weight)
self.add_term(NewHydrogenBonding(), self.hbond_weight)
self.add_term(NewVanDerWaals(), self.vdw_weight)
self.add_term(NewDesolvation(), self.dsolv_weight)
self.supported_types = self.get_supported_types()
def __init__(self,calc):
self.es = Electrostatics(calc,
charge_density = calc.get('charge_density'),
solver = calc.get('coulomb_solver'))
self.solver=Solver(calc)
self.calc=proxy(calc)
self.nat=len(calc.el)
self.norb=calc.el.get_nr_orbitals()
self.prev_dq=[None,None]
self.count=0
self.first_solve = True
self.SCC=calc.get('SCC')
self.rho=None
self.rhoe0=None
self.nk=None
def setup_scorer(self):
# construct atom_map scorer...
#lenB is required for newHydrogenBonding term
npts = self.grid_map.npts
self.ms.lenB = npts[0] * npts[1] * npts[2]
self.atom_map_scorer = AutoGrid4Scorer()
self.atom_map_scorer.set_molecular_system(self.ms)
# ... and newdesolvationdesolvmap scorer
self.desolv_map_scorer = WeightedMultiTerm()
self.desolv_map_scorer.add_term(NewDesolvationDesolvMap(),
AutoDockTermWeights4().dsolv_weight)
self.desolv_map_scorer.set_molecular_system(self.ms)
# ... and electrostatics scorer
self.estat_map_scorer = WeightedMultiTerm()
self.estat_map_scorer.add_term(Electrostatics(),
AutoDockTermWeights4().estat_weight)
self.estat_map_scorer.set_molecular_system(self.ms)
class States:
def __init__(self,calc):
self.es = Electrostatics(calc,
charge_density = calc.get('charge_density'),
solver = calc.get('coulomb_solver'))
self.solver=Solver(calc)
self.calc=proxy(calc)
self.nat=len(calc.el)
self.norb=calc.el.get_nr_orbitals()
self.prev_dq=[None,None]
self.count=0
self.first_solve = True
self.SCC=calc.get('SCC')
self.rho=None
self.rhoe0=None
self.nk=None
def setup_k_sampling(self,kpts,physical=True,rs='kappa'):
'''
Setup the k-point sampling and their weights.
@param kpts: 3-tuple: number of k-points in different directions
list of 3-tuples: k-points given explicitly
@param physical: No meaning for infinite periodicities. For physically
periodic systems only certain number of k-points are allowed.
(like wedge of angle 2*pi/N, only number of k-points that
divides N, is physically allowed). If physical=False,
allow interpolation of this k-sampling.
rs: use 'kappa'- or 'k'-point sampling
'''
if (len(kpts)==1 or isinstance(kpts,tuple) and kpts!=(1,1,1)) and self.calc.get('width')<1E-10:
raise AssertionError('With k-point sampling width must be>0!')
M = self.calc.el.get_number_of_transformations()
if isinstance(kpts,tuple):
table = self.calc.el.atoms.container.get_table()
# set up equal-weighted and spaced k-point mesh
if 0 in kpts:
raise AssertionError('Each direction must have at least one k-point! (Gamma-point)')
kl=[]
for i in range(3):
if M[i]==np.Inf:
# arbitrary sampling is allowed
spacing = 2*pi/kpts[i]
kl.append( np.linspace(-pi+spacing/2,pi-spacing/2,kpts[i]) )
else:
# TODO: choose the closest number of k-points if
# sampling should be physical
# first calculate possible numer of k-points, then
# select the ones closest to the desired one
# nks = M/divisors(M)
# nk1 = nks[abs(nks-nk).argmin()]
# discrete, well-defined sampling; any k-point is not allowed
if kpts[i] not in mix.divisors(M[i]) and physical:
print 'Allowed k-points for direction',i,'are',mix.divisors(M[i])
raise Warning('Non-physical k-point sampling! ')
else:
kl.append( np.linspace(0,2*pi-2*pi/kpts[i],kpts[i]) )
k=[]
wk=[]
kpt_indices = []
nk0 = np.prod(kpts)
for a in range(kpts[0]):
for b in range(kpts[1]):
for c in range(kpts[2]):
newk = np.array([kl[0][a], kl[1][b], kl[2][c]])
newind = (a,b,c)
one_equivalent = False
for i in range(3):
if 'equivalent' in table[i]:
if one_equivalent:
raise NotImplementedError('Surprising type of new symmetry; reconsider implementation.')
one_equivalent = True
n = table[i]['equivalent'] # symmetry op i is equivalent to tuple n
assert n[i]==0
newk[i] = newk[i] + 1.0*np.dot(n,newk)/M[i]
inv_exists = False
# if newk's inverse exists, increase its weight by default
for ik, oldk in enumerate(k):
if np.linalg.norm(oldk+newk)<1E-10:
inv_exists = True
wk[ik]+=1.0/nk0
# newk's inverse does not exist; make new k-point
if not inv_exists:
k.append( newk )
wk.append( 1.0/nk0 )
kpt_indices.append( newind )
nk=len(k)
k=np.array(k)
wk=np.array(wk)
else:
# work with a given set of k-points
nk=len(kpts)
if rs=='k':
k = k_to_kappa_points(kpts,self.calc.el.atoms)
else:
k=np.array(kpts)
wk=np.ones(nk)/nk
kl=None
kpt_indices=[]
# now sampling is set up. Check consistency.
pbc = self.calc.el.get_pbc()
self.kpt_indices = np.array(kpt_indices)
for i in range(3):
for kp in k:
if kp[i]>1E-10 and not pbc[i]:
raise AssertionError('Do not set (non-zero) k-points in non-periodic direction!')
return nk, k, kl, wk
def guess_dq(self):
n=len(self.calc.el)
if not self.SCC:
return np.zeros((n,))
if self.count==0:
return np.zeros((n,)) - float(self.calc.get('charge'))/n
elif self.count==1: # use previous charges
return self.prev_dq[0]
else: # linear extrapolation
return self.prev_dq[0] + (self.prev_dq[0]-self.prev_dq[1])
def solve(self):
if self.nk==None:
physical = self.calc.get('physical_k')
self.nk, self.k, self.kl, self.wk = self.setup_k_sampling( self.calc.get('kpts'),physical=physical,rs=self.calc.get('rs') )
width=self.calc.get('width')
self.occu = Occupations(self.calc.el.get_number_of_electrons(),width,self.wk)
self.calc.start_timing('solve')
# TODO: enable fixed dq-calculations in SCC (for band-structures)
dq=self.guess_dq()
if self.first_solve:
self.calc.memory_estimate()
self.first_solve = False
self.H0, self.S, self.dH0, self.dS = self.calc.ia.get_matrices()
if self.SCC:
self.es.construct_Gamma_matrix(self.calc.el.atoms)
self.e, self.wf = self.solver.get_states(self.calc,dq,self.H0,self.S)
self.check_mulliken_charges()
self.large_update()
self.count+=1
self.calc.stop_timing('solve')
def check_mulliken_charges(self):
""" Check that the Mulliken populations are physically
reasonable. """
dQ = self.mulliken()
if self.calc.verbose_SCC:
print>> self.calc.get_output(), "Mulliken populations: min=%0.3f, max=%0.3f" % (np.min(dQ),np.max(dQ))
Z = self.calc.el.get_atomic_numbers()
for dq, z in zip(dQ, Z):
if dq < -z or dq > z:
for dq, z in zip(dQ, Z):
print >> self.calc.get_output(), "Z=%i dq=%0.3f excess charge=%0.3f" % (z, dq, -dq)
raise Exception("The Mulliken charges are insane!")
def update(self,e,wf):
""" Update all essential stuff from given wave functions. """
self.calc.start_timing('update')
self.e=e
self.wf=wf
self.f=self.occu.occupy(e)
self.calc.start_timing('rho')
self.rho = compute_rho(self.wf,self.f)
self.calc.stop_timing('rho')
if self.SCC:
self.dq = self.mulliken()
self.es.set_dq(self.dq)
self.calc.stop_timing('update')
def large_update(self):
""" Update stuff from eigenstates needed later for forces etc. """
self.calc.start_timing('final update')
self.Swf = None
self.dH = np.zeros_like(self.dH0)
if self.SCC:
self.prev_dq=[self.dq, self.prev_dq[0]]
# TODO: do k-sum with numpy
for ik in range(self.nk):
for a in range(3):
self.dH[ik,:,:,a] = self.dH0[ik,:,:,a] + self.es.get_h1()*self.dS[ik,:,:,a]
else:
self.dH = self.dH0
# density matrix weighted by eigenenergies
self.rhoe = compute_rhoe(self.wf,self.f,self.e)
self.calc.stop_timing('final update')
def get_dq(self):
return self.dq.copy()
def get_eigenvalues(self):
return self.e.copy()
def get_band_energies(self, kpts, h1=False):
"""
Return the eigenvalue spectrum for a set of explicitly given k-points.
"""
H0, S, dH0, dS = self.calc.ia.get_matrices(kpts)
H1 = None
if h1:
H1 = self.es.get_h1()
e, wf = self.solver.get_eigenvalues_and_wavefunctions(H0, S, H1=H1)
return e
def get_occupations(self):
return self.f.copy()
def get_homo(self,occu=0.99):
""" Return highest *largely* occupied orbital (>occu)
0<=occu<=2. Recommended use only for molecules.
"""
for i in range(self.norb)[::-1]:
if np.any( self.f[:,i]>occu ): return i
def get_lumo(self,occu=1.01):
""" Return lowest *largely* unuccopied orbital (<occu)
0<=occu<=2. Recommended use only for molecules.
"""
for i in range(self.norb):
if np.any( self.f[:,i]<occu ): return i
def mulliken(self):
'''
Return excess Mulliken populations dq = dq(total)-dq0
dq_I = sum_k w_k Trace_I Re[ rho(k)*S(k) ]
= sum_(i in I) Re [ sum_k w_k sum_j rho(k)_ij*S(k)_ji ]
= sum_(i in I) Re [ sum_k w_k sum_j rho(k)_ij*S(k)^T_ij ]
= sum_(i in I) [ sum_k w_k diag(k)_i ],
= sum_(i in I) diag_i
where diag(k)_i = Re [sum_j rho(k)_ij * S(k)^T_ij]
and diag_i = sum_k w_k diag(k)_i
'''
diag = np.zeros((self.norb))
for ik in xrange(self.nk):
diag_k = ( self.rho[ik]*self.S[ik].transpose() ).sum(axis=1).real
diag = diag + self.wk[ik] * diag_k
q=[]
for o1, no in self.calc.el.get_property_lists(['o1','no']):
q.append( diag[o1:o1+no].sum() )
dq = np.array(q)-self.calc.el.get_valences()
q,c = sum(-dq),self.calc.get('charge')
if np.abs(q-c) > self.calc.get('tol_mulliken'):
raise RuntimeError('Mulliken charges (%.4f) do not add up to total charge (%.4f)!' %(q,c))
return dq
def get_band_structure_energy(self):
'''
Return band structure energy.
ebs = sum_k w_k ( sum_ij rho_ij * H0_ji )
= sum_k w_k ( sum_i [sum_j rho_ij * H0^T_ij] )
'''
self.calc.start_timing('e_bs')
ebs = 0.0
for ik in xrange(self.nk):
diagonal = ( self.rho[ik]*self.H0[ik].transpose() ).sum(axis=1)
ebs += self.wk[ik] * diagonal.sum()
assert ebs.imag<self.calc.get('tol_imaginary_e')
self.calc.stop_timing('e_bs')
return ebs.real
def get_band_structure_forces(self):
'''
Return band structure forces.
F_I = - sum_k w_k Trace_I [ dH(k)*rho(k) - dS(k)*rhoe(k) + c.c ]
= - sum_k w_k sum_(i in I) diag_i(k) + c.c.,
where diag_i(k) = [dH(k)*rho(k) - dS(k)*rhoe(k)]_ii
= sum_j [dH(k)_ij*rho(k)_ji - dS(k)_ij*rhoe(k)_ji]
= sum_j [dH(k)_ij*rho(k)^T_ij - dS(k)_ij*rhoe(k)^T_ij]
'''
self.calc.start_timing('f_bs')
diag = np.zeros((self.norb,3),complex)
for a in range(3):
for ik in range(self.nk):
diag_k = ( self.dH[ik,:,:,a]*self.rho[ik].transpose() \
- self.dS[ik,:,:,a]*self.rhoe[ik].transpose() ).sum(axis=1)
diag[:,a] = diag[:,a] - self.wk[ik] * diag_k
f=[]
for o1, no in self.calc.el.get_property_lists(['o1','no']):
f.append( 2*diag[o1:o1+no,:].sum(axis=0).real )
self.calc.stop_timing('f_bs')
return f
def __init__(self):
WeightedMultiTerm.__init__(self)
self.add_term(Electrostatics(), self.estat_weight)
self.add_term(NewHydrogenBonding(), self.hbond_weight)
self.add_term(NewVanDerWaals(), self.vdw_weight) #.1485*1.002
self.add_term(NewDesolvationLigOnly(), self.dsolv_weight)
