def optimize(atoms, fmax=0.01):
atoms.center(vacuum=6)
atoms.rattle()
if atoms.get_calculator() == None:
atoms.set_calculator(Hotbit())
dyn = QuasiNewton(atoms, maxstep=0.01)
dyn.run(fmax=fmax)
def __init__(self, rf, pars):
from copy import copy
from hotbit import Hotbit
self.pars = pars
self.trajectories = []
self.calculators = []
for data in rf._get_trajs_for_fitting():
filename = data['filename']
del data['filename']
c = Hotbit()
for key, value in data.iteritems():
c.__dict__[key] = data[key]
self.trajectories.append(filename)
self.calculators.append(c)
self.points = []
self.ref_points = []
self.colors = ['cyan','red','orange','#8DEE1E','magenta','green','black']
def __init__(self, rf, pars):
from copy import copy
from hotbit import Hotbit
self.pars = pars
self.trajectories = []
self.calculators = []
for data in rf._get_trajs_for_fitting():
filename = data['filename']
del data['filename']
c = Hotbit()
for key, value in data.items():
c.__dict__[key] = data[key]
self.trajectories.append(filename)
self.calculators.append(c)
self.points = []
self.ref_points = []
self.colors = ['cyan','red','orange','#8DEE1E','magenta','green','black']
def get_isolated_energies(self, trajs, par):
"""
Return the energies of an isolated atoms.
"""
elements = []
energies = {}
for t in trajs:
traj = PickleTrajectory(t)
for atom in traj[0]:
if not atom.symbol in elements:
elements.append(atom.symbol)
el1, el2 = par.split("_")[0:2]
for el in elements:
ss = "%s%s" % (el, el)
if el1 == el2 and el1 == el:
tables = {ss:par, 'rest':'default'}
calc = Hotbit(SCC=True, tables=tables)
else:
calc = Hotbit(SCC=True)
atoms = Atoms(ss, ((0,0,0),(200,0,0)))
atoms.center(vacuum=100)
atoms.set_calculator(calc)
energies[el] = atoms.get_potential_energy() / 2
return energies
def check_db(db, params):
if debug:
print "%10s %10s %10s ( %10s )" \
% ( "bond", "value", "reference", "error" )
for mol, values in db.iteritems():
#if mol == 'H2O':
if 1:
if debug:
print mol
a = molecule(mol)
a.center(vacuum=10.0)
a.set_pbc(False)
#print a.get_chemical_symbols()
calc = Hotbit(
charge_density = 'Slater',
SCC = True,
width = 1e-6,
txt = 'mio.out',
**params)
a.set_calculator(calc)
#calc.ia.plot_table('H', 'H')
#calc.rep.get_repulsion('H', 'H').plot()
OPT(a, logfile='opt.log').run(fmax=FMAX)
#print a.get_charges()
for name, ( ( i1, i2 ), refvalue ) in values.iteritems():
value = a.get_distance(i1, i2)
if debug:
print '%10s %10.3f %10.3f ( %10.3f )' % \
( name, value, refvalue, abs(value-refvalue) )
assert abs(value-refvalue) < 0.01
from hotbit import Hotbit
from ase import *
from box import Atoms
from box.md import quench
from hotbit.test.misc import default_param
#import cgitb; cgitb.enable()
h2o = read('H2O.xyz')
h2o.center(vacuum=5)
calc = Hotbit(verbose=True,
SCC=True,
verbose_SCC=False,
txt='h2o.cal',
**default_param)
h2o.set_calculator(calc)
print h2o.get_potential_energy()
#print h2o.get_forces()
calc.timer.summary()
print calc.timer.get_timings()
except:
plot = False
import numpy as np
from box import mix
from ase.units import Hartree
Na3 = Atoms('Na3',
positions=[(1.69649997, 0, 0), (-1.69649997, 0, 0),
(0, 2.9384241, 0)],
cell=(50, 50, 50),
pbc=False)
tm = mix.Timer()
calc = Hotbit(charge=1, SCC=True, txt='test_lr.cal', **default_param)
Na3.set_calculator(calc)
calc.solve_ground_state(Na3)
lr = LinearResponse(calc)
omega, F = lr.get_linear_response()
e, f = mix.broaden(omega, F, width=0.1)
if plot:
pl.scatter(e2, f2)
pl.plot(e, f, label='python')
pl.legend()
pl.show()
calc = Hotbit(SCC=True, txt='test_lr.cal', **default_param)
C60 = Atoms(read('C60.xyz'))
C60.set_calculator(calc)
atoms.set_cell((4 * 2.45951, 1000, 3000)) atoms.center() # view(atoms) # assert False default_param["Anderson_memory"] = 0 default_param["convergence"] = 1e-2 default_param["mixing_constant"] = 0.1 default_param["width"] = 0.1 # calc0=Calculator0(verbose=True,SCC=True,gamma_cut=3,txt='sizef.cal',**default_param) # atoms.set_calculator(calc0) ##atoms.get_forces() # t() # calc0.finalize() calc = Hotbit(verbose=True, SCC=True, gamma_cut=3, verbose_SCC=True, txt="size.cal", **default_param) atoms.set_calculator(calc) atoms.get_forces() calc.__del__() # print calc.st.solver.get_iteration_info() t() # systems=['H2COH','AuC'] # default_param['convergence']=1E-5 # default_param['Anderson_memory']=3 # default_param['width']=0.01
import sys
from box.fd_forces import check_forces
systems = ['AuC', 'H2COH']
#default_param['convergence']=1E-5
#default_param['Anderson_memory']=3
default_param['width'] = 0.1
for charge_density in [None, 'Gaussian', 'Slater']:
for system in systems:
if charge_density is None:
print(' ... forces for %s, no SCC' % system)
calc = Hotbit(verbose=True,
SCC=False,
txt='forces.cal',
**default_param)
else:
print(' ... forces for %s, SCC, charge density = %s' % \
( system, charge_density ))
calc = Hotbit(verbose=True,
SCC=True,
charge_density=charge_density,
txt='forces.cal',
**default_param)
atoms = molecule(system)
#view(atoms)
atoms.center(vacuum=5)
atoms[0].x += 0.1
atoms = Atoms(atoms)
atoms.set_calculator(calc)
from ase import *
from hotbit import Hotbit
from hotbit.test.misc import default_param
calc = Hotbit(SCC=True, txt='test.cal', **default_param)
Au2 = Atoms('Au2',
positions=[(0, 0, 0), (1.6, 1.2, 0.2)],
cell=(10, 10, 10),
pbc=False)
Au2.center(vacuum=10)
Au2.set_calculator(calc)
print Au2.get_potential_energy()
# calculate Au dimer
from ase import *
from hotbit import Hotbit
calc = Hotbit(SCC=True, width=0.05, txt='test.cal')
Au2 = Atoms('Au2',
positions=[(0, 0, 0), (2.6, 0, 0)],
cell=(10, 10, 10),
pbc=False)
Au2.center(vacuum=10)
Au2.set_calculator(calc)
print Au2.get_potential_energy()
###
if debug:
for SCC in [ False, True ]:
if SCC:
print "--- SCC ---"
else:
print "--- no SCC ---"
calc = Hotbit(
charge_density = 'Slater',
SCC = SCC,
verbose = True,
verbose_SCC = True,
mixer = {
'name': 'anderson',
'convergence': 1e-6,
'mixing_constant': 0.01 },
maxiter = 1000,
txt = 'mio.out',
**params)
a = read('formamide.xyz')
a.center(vacuum=10.0)
a.set_pbc(False)
a.set_calculator(calc)
OPT(a, logfile='opt.log').run(fmax=FMAX)
iO = 0
iC = 1
from ase import *
from hotbit import Hotbit
from hotbit.analysis import LinearResponse
from ase.data.molecules import molecule
from hotbit.test.misc import default_param
atoms = Atoms('Na3', [(1.6964999745231999, 0, 0), (-1.6964999745231999, 0, 0),
(0, 2.9384240999630005, 0)])
atoms.center(vacuum=5)
default_param['width'] = 0.0136
calc = Hotbit(SCC=True, charge=1, txt='linear_response.cal', **default_param)
atoms.set_calculator()
calc.solve_ground_state(atoms)
lr = LinearResponse(calc, energy_cut=2000, txt='linear_response.txt')
lr.run()
lr.plot_spectrum('Na3+_lr.png', width=0.08)
el = [1.81951, 1.81951, 7.43599, 7.43599]
fl = [0.43036, 0.43036, 4.27744, 4.27744]
for i in range(4):
e, f = lr.get_excitation(i)
assert abs(e - el[i]) < 1E-4 and abs(f - fl[i]) < 1E-4
# calculate CO dimer
from ase import *
from hotbit import Hotbit
for SCC in [False,True]:
calc=Hotbit(SCC=SCC,width=0.05,txt='test.cal')
atoms=Atoms('CO',positions=[(0,0,0),(1.13,0,0)],cell=(10,10,10),pbc=False)
atoms.center(vacuum=10) #not necessary
atoms.set_calculator(calc)
print(atoms.get_potential_energy())
energies0 = [
-153.471502365, -232.206844117, -166.801950557, -19.356876265,
-313.487801685, -287.534640343
]
free = [
-113.81982575044, -191.66618644170001, -141.09652875422,
-12.680510375480001, -248.57609931692002, -214.95914112540004
]
energies = [e - ef for e, ef in zip(energies0, free)]
eps = 1E-3
for system, e in zip(systems, energies):
atoms = molecule(system)
atoms.center(vacuum=10)
atoms.set_pbc(False)
if e == 0:
calc = Calculator0(verbose=True,
SCC=False,
txt='standard.cal',
**default_param)
atoms.set_calculator(calc)
print('new system', system, atoms.get_potential_energy())
sys.exit(0)
calc = Hotbit(verbose=True, SCC=True, txt='standard.cal', **default_param)
atoms.set_calculator(calc)
e1 = atoms.get_potential_energy()
if abs(e1 - e) > eps:
raise AssertionError('Energy for %s is %.7f, while should be %.7f' %
(system, e1, e))
###
dir1 = '/Users/pas/Sourcen/hotbit/param/'
#dir2 = '/Users/pas/Sourcen/hotbit/param/'
dir2 = '/Users/pas/Sourcen/mdcore/data/slater_koster_tables/Frauenheim/download-2009-10-23/mio-0-1/'
###
a = ase.molecule('C6H6')
a.center(vacuum=6.0)
c = Hotbit(elements={
'H': dir2 + 'H-H.skf',
'C': dir2 + 'C-C.skf'
},
tables={
'HH': dir2 + 'H-H.skf',
'CH': dir2 + 'C-H.skf',
'CC': dir2 + 'C-C.skf'
},
SCC=False)
a.set_calculator(c)
ase.FIRE(a).run(fmax=0.01)
ase.write('C6H6.cfg', a)
###
for i in c.el.get_present():
el = c.el.get_element(i)
sym = el.get_symbol()
plot=True
try:
import pylab as pl
except:
plot=False
import numpy as np
from box import mix
from ase.units import Hartree
Na3=Atoms('Na3',positions=[(1.69649997,0,0),(-1.69649997,0,0),(0,2.9384241,0)],cell=(50,50,50),pbc=False)
tm=mix.Timer()
calc=Hotbit(charge=1,SCC=True,txt='test_lr.cal',**default_param)
Na3.set_calculator(calc)
calc.solve_ground_state(Na3)
lr=LinearResponse(calc)
omega,F=lr.get_linear_response()
e,f=mix.broaden(omega,F,width=0.1)
if plot:
pl.scatter(e2,f2)
pl.plot(e,f,label='python')
pl.legend()
pl.show()
calc=Hotbit(SCC=True,txt='test_lr.cal',**default_param)
C60=Atoms(read('C60.xyz'))
C60.set_calculator(calc)
import pylab as pl
from box import Atoms
for SCC in [True, False]:
timings = []
norbs = []
sccs = ['non-SCC', 'SCC'][SCC]
for nx in [1, 2, 3, 4, 5]:
for ny in [1, 2, 3, 4, 5]:
print('nx', nx, ny)
atoms = FaceCenteredCubic(directions=[[1,-1,0], [1,1,-2], [1,1,1]],\
size=(nx,ny,1), symbol='Au', pbc=(0,0,0))
calc = Hotbit(verbose=True,
SCC=SCC,
gamma_cut=3,
txt='size2.cal',
**default_param)
atoms.set_calculator(calc)
try:
atoms.get_forces()
except:
continue
calc.timer.summary()
timings.append(calc.timer.get_timings())
norbs.append(calc.el.get_nr_orbitals())
calc.__del__()
order = argsort(norbs)
norbs = sort(norbs)
timings2 = []
from ase import *
from hotbit import Hotbit
from hotbit.analysis import LinearResponse
from ase.data.molecules import molecule
from hotbit.test.misc import default_param
atoms=Atoms('Na3',[(1.6964999745231999,0,0),(-1.6964999745231999,0,0),(0,2.9384240999630005,0)])
atoms.center(vacuum=5)
default_param['width'] = 0.0136
calc=Hotbit(SCC=True,charge=1,txt='linear_response.cal',**default_param)
atoms.set_calculator()
calc.solve_ground_state(atoms)
lr=LinearResponse(calc,energy_cut=2000,txt='linear_response.txt')
lr.run()
lr.plot_spectrum('Na3+_lr.png',width=0.08)
el = [1.81951,1.81951,7.43599,7.43599]
fl = [0.43036,0.43036,4.27744,4.27744]
for i in range(4):
e,f = lr.get_excitation(i)
assert abs(e-el[i])<1E-4 and abs(f-fl[i])<1E-4
