import time
# ======= setup
path = './'
decay = -1.0 # WARRNING ... with positive decay you get bullshit
# ======= Prepare inputs
eigEn, coefs, Ratin = RS.read_FIREBALL_all(name=path + 'phik_example_',
geom=path + 'crazy_mol.xyz',
fermi=None,
orbs='sp',
pbc=(0, 0),
cut_min=-1.0,
cut_max=+1.0,
cut_at=-1,
lower_atoms=[],
lower_coefs=[])
print("---------------")
print("Ratin ", Ratin)
print("---------------")
print("coefs ", coefs)
print("---------------")
print("eigEn.shape ", eigEn.shape)
print("coefs.shape ", coefs.shape)
print("Ratin.shape ", Ratin.shape)
atoms = ocl.xyzq2float4(
print(
"Importing positions of PP from the PP-AFM calculations. Path for the data:"
)
path_pos = "Q%1.2fK%1.2f/" % (Q, K)
print(path_pos)
tip_r, lvec, nDim = GU.load_vec_field(path_pos + 'PPpos',
data_format=data_format)
extent = (lvec[0, 0], lvec[0, 0] + lvec[1, 0], lvec[0, 1],
lvec[0, 1] + lvec[2, 1])
#print "DEBUG: extent", extent
print("PP postions imported")
dx = lvec[1, 0] / (nDim[2] - 1)
dy = lvec[2, 1] / (nDim[1] - 1)
dz = lvec[3, 2] / (nDim[0] - 1)
tip_r0 = RS.mkSpaceGrid(lvec[0, 0], lvec[0, 0] + lvec[1, 0], dx,
lvec[0, 1], lvec[0, 1] + lvec[2, 1], dy,
lvec[0, 2], lvec[0, 2] + lvec[3, 2], dz)
#print "DEBUG: dx, dy, dz", dx, dy, dz
#print "DEBUG: tip_r.shape, tip_r0.shape", tip_r.shape, tip_r0.shape
else:
print("Priparing the scan grid for fixed scan")
extent = (x[0], x[1], y[0], y[1])
tip_r = RS.mkSpaceGrid(x[0], x[1], x[2], y[0], y[1], y[2], z[0], z[1],
z[2])
lvec = np.array([[x[0], y[0], z[0]], [x[1] - x[0], 0., 0.],
[0., y[1] - y[0], 0.], [0., 0., z[1] - z[0]]])
#print "DEBUG: extent", extent
#print "DEBUG: lvec", lvec
tip_r0 = tip_r
print("scan grids prepared")
together = ''.join(map(str, args)) # avoid the arg is not str
#print together
return together
# --- Initial check --- #
assert( PNG or TXT ), "No output set to be True; I'm not going to do anything if there is no output. I'm too lazy like a Gartfield. "
# --- reading of the eigen-energies, the LCAO coefficients and geometry --- #
print("Reading electronic & geometry structure files")
cell=[[0,0],[0,0]];pbc=(0,0);lower_coefs=[];
if ((dft_code == 'fireball') or(dft_code == 'Fireball') or (dft_code == 'FIREBALL')):
eigEn, coefs, Ratin = RS.read_FIREBALL_all(name = files_path + 'phik_0001_', geom=files_path+geometry_file, lvs = cell, fermi=fermi, orbs = sample_orbs, pbc=pbc, cut_min=cut_min, cut_max=cut_max,cut_at=cut_atoms, lower_atoms=lower_atoms, lower_coefs=lower_coefs);
elif ((dft_code == 'gpaw') or(dft_code == 'GPAW')):
eigEn, coefs, Ratin = RS.read_GPAW_all( name = files_path + cp2k_name + '.gpw', fermi=fermi, orbs = sample_orbs, pbc=pbc, cut_min=cut_min, cut_max=cut_max, cut_at=cut_atoms, lower_atoms=lower_atoms, lower_coefs=lower_coefs);
elif ((dft_code == 'aims') or(dft_code == 'AIMS') or (dft_code == 'FHI-AIMS')):
if ((spin == None) or (spin == False)):
name = 'KS_eigenvectors.band_1.kpt_1.out'
elif ((spin == 'up')or(spin == 'alpha')or(spin == 'both')):
name = 'KS_eigenvectors_up.band_1.kpt_1.out'
elif ((spin == 'down')or(spin == 'beta')or(spin == 'dn')):
name = 'KS_eigenvectors_dn.band_1.kpt_1.out'
else :
print("unknown spin, I'm going to sleep. Good Night"); exit()
eigEn, coefs, Ratin = RS.read_AIMS_all(name = files_path + name , geom= files_path + geometry_file, fermi=fermi, orbs = sample_orbs, pbc=pbc, cut_min=cut_min, cut_max=cut_max, cut_at=cut_atoms, lower_atoms=lower_atoms, lower_coefs=lower_coefs);
if (spin == 'both'):
lvec2).all(), "lvec1 != lvec2 control your input files"
assert np.array(nDim2).all() == np.array(
nDim2).all(), "nDim1 != nDim2 control your input files"
print("STM for V:", namez[i], " imported")
#print "DEBUG: current1.shape", current1.shape
lvec = lvec1
nDim = nDim1
extent = (lvec[0,
0], lvec[0, 0] + lvec[1, 0], lvec[0,
1], lvec[0, 1] + lvec[2, 1])
#print "DEBUG: extent", extent
dx = lvec[1, 0] / (nDim[2] - 1)
dy = lvec[2, 1] / (nDim[1] - 1)
dz = lvec[3, 2] / (nDim[0] - 1)
tip_r0 = RS.mkSpaceGrid(lvec[0, 0], lvec[0, 0] + lvec[1, 0], dx, lvec[0, 1],
lvec[0, 1] + lvec[2, 1], dy, lvec[0, 2],
lvec[0, 2] + lvec[3, 2], dz)
#print "DEBUG: tip_r0", tip_r0
# --- main part --- #
if STM_b:
current = tip_orb1_amount * current1 + tip_orb2_amount * current2
if didv_b:
didv = tip_orb1_amount * didv1 + tip_orb2_amount * didv2
# =========== Utils for plotting atoms =========================
def plotAtoms(atoms, atomSize=0.1, edge=True, ec='k', color='w'):
plt.fig = plt.gcf()
eta = 0.1 # 0.1 - standart for semiconductors
# -- next two parameters will be specified in the main loop
#WF_decay=1.0 # for STM only - how fast the exponential decay fall, with the applied bias ( if 1 - 1:1 correspondence with bias; if 0, it doesn't change)
#nV = 9 # for STM only - number of STM integrational steps nV ~ V/eta
lower_atoms = [
] # No atoms has lowered hopping - be aware python numbering occurs here [0] - means lowering of the 1st atom
lower_coefs = [] # Lowering of the hoppings
# --- downloading and examples of downloading of the eigen-energies, the LCAO coefficients and geometry (this time for spin-unpolarized calculations):
eigEn, coefs, Ratin = RS.read_FIREBALL_all(name=path + 'phik_0001_',
geom=path + 'input.xyz',
fermi=fermi,
orbs=orbs,
pbc=pbc,
cut_min=cut_min,
cut_max=cut_max,
cut_at=cut_at,
lvs=lvs,
lower_atoms=lower_atoms,
lower_coefs=lower_coefs)
#eigEn, coefs, Ratin = RS.read_AIMS_all(name = 'KS_eigenvectors_up.band_1.kpt_1.out', geom='geometry.in',fermi=fermi, orbs = 'sp', pbc=pbc,
# imaginary = False, cut_min=cut_min, cut_max=cut_max, cut_at=cut_at,
# lower_atoms=lower_atoms, lower_coefs=lower_coefs)
#eigEn, coefs, Ratin = RS.read_GPAW_all(name = 'out_LCAO_LDA.gpw', fermi=fermi, orbs = orbs, pbc=pbc,
# cut_min=cut_min, cut_max=cut_max, cut_at=cut_at, lower_atoms=lower_atoms, lower_coefs=lower_coefs);
# --- the grid on which the STM signal is calculated; tip_r2 - uniform grid:
dz = 0.1
dx = dy = 0.25
eta = 0.01 # very low to pronounce single orbitals only
# --- these two not needed now (no STM in this script)
#WF_decay=1.0 # for STM only - how fast the exponential decay fall, with the applied bias ( if 1 - 1:1 correspondence with bias; if 0, it doesn't change)
#nV = 9 # for STM only - number of STM integrational steps nV ~ V/eta
lower_atoms=[22,23,24] # atoms 23-25 - oxygens will have lowered tunneling !!! python numbering of atoms !!!
lower_coefs=[0.75,0.75,0.75] # Lowering of the hoppings # NOTE: it seems, that for the CP2K input there is not suc a big need to lower down the contributions from
# oxygens (on a TOAT), then from the other codes - 0.5
# --- downloading and examples of downloading of the eigen-energies, the LCAO coefficients and geometry (this time for spin-unpolarized calculations):
#eigEn, coefs, Ratin = RS.read_FIREBALL_all(name = path+'phik_example_', geom=path+'crazy_mol.xyz', fermi=fermi, orbs = orbs, pbc=pbc,
# cut_min=cut_min, cut_max=cut_max,cut_at=cut_at, lower_atoms=lower_atoms, lower_coefs=lower_coefs);
#eigEn, coefs, Ratin = RS.read_AIMS_all(name = 'KS_exx_1_spin_up.out', geom='geometry.in',fermi=fermi, orbs = orbs, pbc=pbc,
# imaginary = False, cut_min=cut_min, cut_max=cut_max, cut_at=cut_at,
# lower_atoms=lower_atoms, lower_coefs=lower_coefs)
eigEn, coefs, Ratin = RS.read_CP2K_all(name = 'TOAT', fermi=fermi, orbs = orbs, pbc=pbc,
cut_min=cut_min, cut_max=cut_max, cut_at=cut_at, lower_atoms=lower_atoms, lower_coefs=lower_coefs);
#eigEn, coefs, Ratin = RS.read_GPAW_all(name = 'out_LCAO_LDA.gpw', fermi=fermi, orbs = orbs, pbc=pbc,
# cut_min=cut_min, cut_max=cut_max, cut_at=cut_at, lower_atoms=lower_atoms, lower_coefs=lower_coefs);
# --- the grid on which the STM signal is calculated; no tip_r1 - PP distored by the relaxation in the PPAFM code; only tip_r2 - uniform grid:
tip_r1, lvec, nDim = GU.load_vec_field( path_pos+'PPpos' ,data_format=data_format)
dz=0.1
dx=dy =0.1
xl = lvec[1,0]
yl = lvec[2,1]
zl = lvec[3,2]
extent = (lvec[0,0],lvec[0,0]+xl,lvec[0,1],lvec[0,1]+yl)
#eigEn, coefs, Ratin = RS.read_FIREBALL_all(name = path+'phik_example_', geom=path+'crazy_mol.xyz', fermi=fermi, orbs = orbs, pbc=pbc,
# cut_min=cut_min, cut_max=cut_max,cut_at=cut_at, lower_atoms=lower_atoms, lower_coefs=lower_coefs);
#eigEn1, coefs1, Ratin = RS.read_AIMS_all(name = 'KS_eigenvectors_up.band_1.kpt_1.out', geom='geometry.in',fermi=fermi, orbs = orbs, pbc=pbc,
# imaginary = False, cut_min=cut_min, cut_max=cut_max, cut_at=cut_at,
# lower_atoms=lower_atoms, lower_coefs=lower_coefs)
#eigEn2, coefs2, Ratin = RS.read_AIMS_all(name = 'KS_eigenvectors_dn.band_1.kpt_1.out', geom='geometry.in',fermi=fermi, orbs = orbs, pbc=pbc,
# imaginary = False, cut_min=cut_min, cut_max=cut_max, cut_at=cut_at,
# lower_atoms=lower_atoms, lower_coefs=lower_coefs)
#eigEn, coefs, Ratin = RS.read_GPAW_all(name = 'out_LCAO_LDA.gpw', fermi=fermi, orbs = orbs, pbc=pbc,
# cut_min=cut_min, cut_max=cut_max, cut_at=cut_at, lower_atoms=lower_atoms, lower_coefs=lower_coefs);
eigEn1, coefs1, Ratin = RS.read_CP2K_all(name='CuPc',
fermi=fermi,
orbs=orbs,
pbc=pbc,
cut_min=cut_min,
cut_max=cut_max,
cut_at=cut_at,
lower_atoms=lower_atoms,
lower_coefs=lower_coefs,
spin="alpha")
eigEn2, coefs2, Ratin = RS.read_CP2K_all(name='CuPc',
fermi=fermi,
orbs=orbs,
pbc=pbc,
cut_min=cut_min,
cut_max=cut_max,
cut_at=cut_at,
lower_atoms=lower_atoms,
lower_coefs=lower_coefs,
spin="beta")
#nV = 9 # for STM only - number of STM integrational steps nV ~ V/eta
lower_atoms = [
] # No atoms has lowered hopping - be aware python numbering occurs here [0] - means lowering of the 1st atom
lower_coefs = [] # Lowering of the hoppings
M = 16 # Effective mass of CO frustrated translation - only O - 16
# --- downloading and examples of downloading of the eigen-energies, the LCAO coefficients and geometry (this time for spin-unpolarized calculations):
#eigEn, coefs, Ratin = RS.read_FIREBALL_all(name = path+'phik_example_', geom=path+'crazy_mol.xyz', fermi=fermi, orbs = orbs, pbc=pbc,
# cut_min=cut_min, cut_max=cut_max,cut_at=cut_at, lower_atoms=lower_atoms, lower_coefs=lower_coefs);
eigEn1, coefs1, Ratin = RS.read_AIMS_all(name="eigen_up.out",
geom='geom-cube.in',
fermi=fermi,
orbs=orbs,
pbc=pbc,
imaginary=False,
cut_min=cut_min,
cut_max=cut_max,
cut_at=cut_at,
lower_atoms=lower_atoms,
lower_coefs=lower_coefs)
eigEn2, coefs2, Ratin = RS.read_AIMS_all(name="eigen_dn.out",
geom='geom-cube.in',
fermi=fermi,
orbs=orbs,
pbc=pbc,
imaginary=False,
cut_min=cut_min,
cut_max=cut_max,
cut_at=cut_at,
lower_atoms=lower_atoms,
#lvs = np.array([[15., 0.,0.],[0.,15.,0],[0.,0.,15.]]
WorkFunction = 5.0 #more or less standart.
fermi=None # the Fermi from phik ... .dat file; !!! All energies are relative to Fermi !!!! None - means: -5.04612664712 eV
orbs= 'sp' # 'sp' works now, 'spd' works for fireball as well
cut_min=-1.0 # H**O -0.88 bellow the Fermi Level, other orbitals cut
cut_max=+1.0 # LUMO -0.88 above the Fermi Level
cut_at=-1 # All atoms of the molecule
eta = 0.01 # very low, to pronounce the single orbitals only
WF_decay=1.0 # for STM only - how fast the exponential decay fall, with the applied bias ( if 1 - 1:1 correspondence with bias; if 0, it doesn't change)
nV = 9 # for STM only - number of STM integrational steps nV ~ V/eta
lower_atoms=[] # No atoms has lowered hopping - be aware python numbering occurs here [0] - means lowering of the 1st atom
lower_coefs=[] # Lowering of the hoppings
# --- downloading and examples of downloading of the eigen-energies, the LCAO coefficients and geometry (this time for spin-unpolarized calculations):
eigEn, coefs, Ratin = RS.read_FIREBALL_all(name = path+'phik_example_', geom=path+'crazy_mol.xyz', fermi=fermi, orbs = orbs, pbc=pbc,
cut_min=cut_min, cut_max=cut_max,cut_at=cut_at, lower_atoms=lower_atoms, lower_coefs=lower_coefs);
#eigEn, coefs, Ratin = RS.read_AIMS_all(name = 'KS_eigenvectors_up.band_1.kpt_1.out', geom='geometry.in',fermi=fermi, orbs = 'sp', pbc=pbc,
# imaginary = False, cut_min=cut_min, cut_max=cut_max, cut_at=cut_at,
# lower_atoms=lower_atoms, lower_coefs=lower_coefs)
#eigEn, coefs, Ratin = RS.read_GPAW_all(name = 'out_LCAO_LDA.gpw', fermi=fermi, orbs = orbs, pbc=pbc,
# cut_min=cut_min, cut_max=cut_max, cut_at=cut_at, lower_atoms=lower_atoms, lower_coefs=lower_coefs);
#eigEn, coefs, Ratin = RS.read_CP2K_all(name = 'crazy_mol', fermi=fermi, orbs = orbs, pbc=pbc,
# cut_min=cut_min, cut_max=cut_max, cut_at=cut_at, lower_atoms=lower_atoms, lower_coefs=lower_coefs);
# --- the grid on which the STM signal is calculated; tip_r1 - PP distored by the relaxation in the PPAFM code; tip_r2 - uniform grid:
tip_r1, lvec, nDim = GU.load_vec_field( path_pos+'PPpos' ,data_format=data_format)
dz=0.1
dx=dy =0.1
cut_at = 18 # All atoms of the highest layer
eta = 0.1 # very low, to pronounce the single orbitals only
# -- next two not needed for IETS
#WF_decay=1.0 # for STM only - how fast the exponential decay fall, with the applied bias ( if 1 - 1:1 correspondence with bias; if 0, it doesn't change)
#nV = 9 # for STM only - number of STM integrational steps nV ~ V/eta
lower_atoms = [
] # No atoms has lowered hopping - be aware python numbering occurs here [0] - means lowering of the 1st atom
lower_coefs = [] # Lowering of the hoppings
# --- downloading and examples of downloading of the eigen-energies, the LCAO coefficients and geometry (this time for spin-unpolarized calculations):
eigEn, coefs, Ratin = RS.read_FIREBALL_all(name='phik_0001_',
geom='input.xyz',
fermi=fermi,
orbs=orbs,
pbc=pbc,
cut_min=cut_min,
cut_max=cut_max,
cut_at=cut_at,
lower_atoms=lower_atoms,
lower_coefs=lower_coefs)
# --- on which energies you want to plot pseudo-projected density of states
energies = np.arange(-2.0, 2.0, 0.01)
# --- getting P-PDOS for different atoms and spherical functions
#PDOS0 = SU.pPDOS(eigEn, coefs, energies, eta=eta, atoms=[], orbs=orbs ,spherical='all') # all atoms = []
PDOS1 = SU.pPDOS(eigEn,
coefs,
energies,
