def energy(lamb):
#############################################################
# He created from H2 and external potential #
#############################################################
d = 0.74
a = 6.0
atoms_external = Atoms('H2',
positions=[(0, 0, 0), (0, 0, d)],
cell=(a, a, a))
atoms_external.center()
pc = PointChargePotential([lamb, -lamb],
[[3.0, 3.0, 2.63], [3.0, 3.0, 3.37]])
output = 'output/result' + str(lamb).replace('.', '_') + '.txt'
calc = GPAW(xc='PBE', txt=output, external=pc)
atoms_external.set_calculator(calc)
pot_en = atoms_external.get_potential_energy()
density = calc.get_all_electron_density(gridrefinement=4)
write('output/density_' + str(lamb).replace('.', '_') + '.cube',
atoms_external,
data=density)
return (pot_en)
atom_conf.set_calculator(calc)
pot_en = atom_conf.get_potential_energy()
#density = calc.get_all_electron_density(gridrefinement=4)
#return( pot_en, density )
return(pot_en)
d = 0.74
a = 6.0
rc_list=[-1, -0.1, -1e-2, 1e-2, 1e-1, 1]
for rc_item in rc_list:
output_He_expot_H2 = 'output/par_pc/'+'rc_'+str(rc_item).replace('.','_')+'.txt'
atom_conf_He_expot_H2=Atoms('H2', positions=[(0, 0, 0),(0, 0, d)], cell=(a,a,a) )
atom_conf_He_expot_H2.center()
pos=atom_conf_He_expot_H2.get_positions()
print('Position H2 = ' + str(pos))
pc_He_expot_H2 = PointChargePotential( [1.0, -1.0], [ pos[0], pos[1] ], rc=rc_item )
calc = GPAW(xc='PBE', txt=output_He_expot_H2, external=pc_He_expot_H2)
atom_conf_He_expot_H2.set_calculator(calc)
energy_He_expot_H2 = atom_conf_He_expot_H2.get_potential_energy()
#energy_He_expot_H2 = energy_calc_with_expot(atom_conf_He_expot_H2, output_He_expot_H2, pc_He_expot_H2)
print('Energy He calculated from H2 + external potential = ' + str(energy_He_expot_H2) )
density = calc.get_all_electron_density(gridrefinement=4)
write('output/par_pc/'+'dens_rc_'+str(rc_item).replace('.','_')+'.cube', atom_conf_He_expot_H2, data=density)
#print('Energy CO = ' + str(energy_N2) )
d = 0.74
a = 6
gs = 0.04
atom_conf_He_expot_H2 = Atoms('H2',
positions=[(0, 0, 0), (0, 0, d)],
cell=(a, a, a))
atom_conf_He_expot_H2.center()
pos = atom_conf_He_expot_H2.get_positions()
print('Position=' + str(pos))
output_He_expot_H2 = '/home/misa/APDFT/prototyping/gpaw/h2_he/output/alch_vs_normal/He_expot_H2.txt'
pc_H = PointChargePotential([1.0, -1.0], [pos[0], pos[1]], rc=1e-3, width=20)
calc = GPAW(xc='PBE', txt=output_He_expot_H2, external=pc_H, h=gs)
atom_conf_He_expot_H2.set_calculator(calc)
energy_He_expot_H2 = atom_conf_He_expot_H2.get_potential_energy()
#energy_He = energy_calc_with_expot(atom_conf_He, output_He, pc_He)
print('Energy He_expot_H2 = ' + str(energy_He_expot_H2))
#density = calc.get_all_electron_density(gridrefinement=4)
#write('output/density_He_expot_H2.cube', atom_conf_He_expot_H2, data=density)
atom_conf_He = Atoms('He', positions=[(0, 0, d)], cell=(a, a, a))
atom_conf_He.center()
output_He = 'output/alch_vs_normal/He.txt'
R_pv[0, v] += eps
ep = f(rc)
R_pv[0, v] -= 2 * eps
em = f(rc)
R_pv[0, v] += eps
F = -(ep - em) / (2 * eps) * h**3
equal(F, -F_pv[0, v], 1e-9)
# High-level test:
lih = Atoms('LiH')
lih[1].y += 1.64
lih.center(vacuum=3)
pos = lih.cell.sum(axis=0)
print(pos)
pc = PointChargePotential([-1.0], [pos])
lih.calc = GPAW(external=pc, txt='lih-pc.txt')
f1 = lih.get_forces()
fpc1 = pc.get_forces(lih.calc)
print(fpc1)
print(fpc1 + f1.sum(0))
f2 = [[numeric_force(lih, a, v) for v in range(3)] for a in range(2)]
print(f1)
print(f1 - f2)
assert abs(f1 - f2).max() < 2e-3
x = 0.0001
for v in range(3):
pos[v] += x
pc.set_positions([pos])
def embed(self, q_p, rc=0.2, rc2=np.inf, width=1.0):
"""Embed QM region in point-charges."""
pc = PointChargePotential(q_p, rc=rc, rc2=rc2, width=width)
self.set(external=pc)
return pc
"""
import numpy as np
from ase import Atoms
from ase.units import Bohr, Hartree
from gpaw import GPAW
from gpaw.external import PointChargePotential
a = 4.5
H = Atoms('H', [(a / 2, a / 2, a / 2)], pbc=0, cell=(a, a, a))
calc = GPAW(nbands=1, h=0.2, charge=1, txt='H.txt')
H.set_calculator(calc)
e0 = H.get_potential_energy()
assert abs(e0 + calc.get_reference_energy()) < 0.014
# Test the point charge potential with a smooth cutoff:
pcp = PointChargePotential([-1], rc2=5.5, width=1.5)
calc.set(external=pcp)
E = []
F = []
D = np.linspace(2, 6, 30)
for d in D:
pcp.set_positions([[a / 2, a / 2, a / 2 + d]])
e = H.get_potential_energy() - e0
f1 = H.get_forces()
f2 = pcp.get_forces(calc)
eref = -1 / d * Bohr * Hartree
print(d, e, eref, abs(f1 + f2).max())
if d < 4.0:
error = e + 1 / d * Bohr * Hartree
assert abs(error) < 0.01, error
assert abs(f1 + f2).max() < 0.01