def around_alkali(st, nn, alkali_ion_number):
#return numbers and distances to
n_neighbours = nn
alkali_ions = []
dist = []
ifmaglist = st.get_maglist()
for i, typ, x in zip(range(st.natom), st.typat, st.xcart):
z = st.znucl[typ-1]
if z in header.ALKALI_ION_ELEMENTS:
alkali_ions.append([i, z, x])
if len(alkali_ions) > 0:
if alkali_ion_number:
kk = alkali_ion_number-1
chosen_ion = (kk, st.znucl[st.typat[kk]-1], st.xcart[kk])
else:
chosen_ion = alkali_ions[0] #just the first one is used
# alkali_ions[min(alkali_ions)]
sur = local_surrounding(chosen_ion[2], st, n_neighbours = n_neighbours, control = 'atoms',
periodic = True, only_elements = header.TRANSITION_ELEMENTS)
# print (sur)
dist = np.array(sur[3]).round(2)
numb = np.array(sur[2])
else:
numb = ifmaglist # if no alk ions show for all mag atoms
chosen_ion = None
return numb, dist, chosen_ion
def determine_unique_final(st_pores, sums, avds, x_m):
final_table = []
insert_positions = []
"""Please determine unique positions with similar distances taking into acc PBC!!!
below is incorrect
"""
# crude_prec = 1
# sums_crude = np.unique(sums.round(crude_prec))
# print_and_log('The unique voids based on the sums:',
# '\nwith 0.01 A prec:',np.unique(sums.round(2)),
# '\nwith 0.1 A prec:',sums_crude,
# imp ='y')
# print_and_log('Based on crude criteria only', len(sums_crude),'types of void are relevant', imp = 'y')
# xcart_unique = []
# avds_unique = []
# sums_unique = []
# for i, s in enumerate(sums_crude):
# index_of_first = np.where(sums.round(crude_prec)==s)[0][0]
# xcart_unique.append(st_pores.xcart[index_of_first])
# avds_unique.append(avds[index_of_first] )
# sums_unique.append(sums[index_of_first] )
# st_pores_unique = copy.deepcopy(st_pores)
# st_pores_unique.xcart = xcart_unique
# st_pores_unique.xcart2xred()
sur = local_surrounding(x_m,
st_pores,
n_neighbours=len(st_pores.xcart),
control='atoms',
periodic=True)
# print('neb.determine_unique_final(): sur', sur)
print_and_log('I can suggest you ' + str(len(sur[0])) + ' end positions.',
imp='y')
for i, (x, d, ind) in enumerate(zip(sur[0], sur[3], sur[2])):
# if i == 0:
# continue
final_table.append(
[i, np.array(x).round(2),
round(d, 2), avds[ind], sums[ind]])
print_and_log(tabulate(final_table,
headers=['void #', 'Cart.', 'Dist', 'Dev.', 'Sum'],
tablefmt='psql'),
imp='Y')
return sur
def plot_dos(
cl1,
cl2=None,
dostype=None,
iatom=None,
iatom2=None,
orbitals=('s'),
up=None,
neighbors=6,
show=1,
labels=None,
path='dos',
xlim=(None, None),
ylim=(None, None),
savefile=True,
plot_param={},
suf2='',
fontsize=8,
nsmooth=12,
lts2='--',
split_type='octa',
plot_spin_pol=1,
show_gravity=None,
):
"""
cl1 (CalculationVasp) - object created by add_loop()
dostype (str) - control which dos to plot:
'total' - plot total dos
'diff_total' - difference of total dos, use cl2 for second calculation
'partial' - partial dos
orbitals (list of str) -
any from 's, p, d, py, pz, px, dxy, dyz, dz2, dxz, dx2' where 'p' and 'd' are sums of projections
also to sum around neigbours use p6 and d6 and neighbors parameter
up - 'up2' allows to download the file once again
labels - two manual labels for cl1 and cl2 instead of auto
iatom (int) - number of atom starting from 1 to plot DOS;
iatom ([float]*3) - cartesian coordinates of point around which atoms will be found
show (bool) - whether to show the dos
path (str) - path to folder with images
neighbors - number of neighbours around iatom to plot dos on them using p6 or d6; only p6 is implemented to the moment in plot section
xlim, ylim (tuple)- limits for plot
plot_param - dict of parameters to fit_and_plot
dashes - control of dahsed lines
suf2 - additional suffix
# nsmooth = 15 # smooth of dos
lts2 - style of lines for cl2
split_type -
octa - the names are t2g and eg
tetra - the names are t2 and e
plot_spin_pol -
0 - spin-polarized components are summed up
show_gravity (list) - print gravity centers (i, type, range, ); i - 1 or 2 cl
type (str)
'p6' - for p orbitals of neighbors
'p'
#0 s 1 py 2 pz 3 px 4 dxy 5 dyz 6 dz2 7 dxz 8 dx2
#In all cases, the units of the l- and site projected DOS are states/atom/energy.
"""
if fontsize:
header.mpl.rcParams.update({'font.size': fontsize + 4})
header.mpl.rc('legend', fontsize=fontsize)
if dostype == 'partial':
eld1, eld2 = {}, {}
for i, el in enumerate(cl1.end.get_elements()):
eld1[i + 1] = el
if cl2:
for i, el in enumerate(cl2.end.get_elements()):
eld2[i + 1] = el
if not iatom:
printlog(
'Warning! Please choose atom number *iatom* from the following list:\n'
)
printlog(eld)
sys.exit()
else:
printlog('cl1: Atom',
iatom,
'of type',
eld1[iatom],
'is choosen',
imp='y')
printlog('cl1: Atom numbers:', eld1, imp='y')
printlog('cl1:',
determine_symmetry_positions(cl1.end, eld1[iatom]),
imp='y')
# print(cl2)
if cl2:
if not iatom2:
printlog('Error! provide iatom2!')
printlog('cl2: Atom',
iatom2,
'of type',
eld2[iatom2],
'is choosen',
imp='y')
printlog('cl2:',
determine_symmetry_positions(cl2.end, eld2[iatom2]),
imp='y')
iatom -= 1
if cl2:
if not iatom2:
printlog('Error!, provide *iatom2*!')
iatom2 -= 1
if 'figsize' not in plot_param:
plot_param['figsize'] = (4, 6)
if 'legend' not in plot_param:
plot_param['legend'] = 'best'
"""1. Read dos"""
printlog("------Start plot_dos()-----", imp='Y')
dos = [] # main list for cl1 and cl2
for cl in cl1, cl2:
if cl == None:
continue
if not hasattr(cl, "efermi"):
cl.read_results('o')
printlog(cl.name, 'e_fermi', cl.efermi, imp='Y')
DOSCAR = cl.get_file('DOSCAR', nametype='asoutcar')
printlog('DOSCAR file is ', DOSCAR)
dos.append(VaspDos(DOSCAR, cl.efermi))
#determine number of zero energy
i_efermi = int(
len(dos[0].energy) * -dos[0].energy[0] /
(dos[0].energy[-1] -
dos[0].energy[0])) # number of point with zero fermi energy
if cl2:
i_efermi_e = int(
len(dos[1].energy) * -dos[1].energy[0] /
(dos[1].energy[-1] -
dos[1].energy[0])) # number of point with zero fermi energy
if len(dos[0].dos) == 2:
spin_pol = True
else:
spin_pol = False
"""2. Plot dos for different cases"""
if dostype == 'total':
# print(dos[0].dos)
ylabel = "DOS (states/eV)"
if spin_pol:
dosplot = {
'Tot up': {
'x': dos[0].energy,
'y': smoother(dos[0].dos[0], 10),
'c': 'b',
'ls': '-'
},
'Tot down': {
'x': dos[0].energy,
'y': -smoother(dos[0].dos[1], 10),
'c': 'r',
'ls': '-'
}
}
else:
dosplot = {
'Total': {
'x': dos[0].energy,
'y': smoother(dos[0].dos, 10),
'c': 'b',
'ls': '-'
}
}
# args[nam_down] = {'x':d.energy, 'y':-smoother(d.site_dos(iat, i_orb_down[orb]), nsmooth), 'c':color[orb], 'ls':l, 'label':None}
# xlabel = "Energy (eV)", ylabel = "DOS (states/eV)"
# print(plot_param)
image_name = os.path.join(path, cl1.name + '.dosTotal')
fit_and_plot(show=show,
image_name=image_name,
hor=True,
**plot_param,
**dosplot)
elif dostype == 'diff_total': #no spin-polarized!!!!
ylabel = "DOS (states/eV)"
if len(dos) > 1:
#calculate dos diff
dosd = [(d0 - d1) * e
for d0, d1, e in zip(dos[0].dos, dos[1].dos, dos[0].energy)
] #calculate difference
area = trapz(dosd[:i_efermi], dx=1)
printlog("area under dos difference = ", -area, imp='Y')
fit_and_plot(show=show,
image_name=cl1.name + '--' + cl2.name +
'.dosTotal_Diff',
xlabel="Energy (eV)",
ylabel="DOS (states/eV)",
hor=True,
**plot_param,
Diff_Total=(dos[0].energy, smoother(dosd, 15), 'b-'))
else:
printlog(
'You provided only one calculation; could not use diff_total')
elif 'partial' in dostype:
#Partial dos
#1 p carbon, d Ti
#0 s 1 py 2 pz 3 px 4 dxy 5 dyz 6 dz2 7 dxz 8 dx2
ylabel = "PDOS (states/atom/eV)"
try:
dos[0].site_dos(0, 4)
except:
printlog(
'Error! No information about partial dxy dos in DOSCAR; use LORBIT 12 to calculate it'
)
"""Determine neighbouring atoms """
# printlog("Number of considered neighbors is ", neighbors, imp = 'y')
if type(
iatom
) == int: #for the cases when we need to build surrounding around specific atom in this calculation - just use number of atom
t = cl1.end.typat[iatom]
z = cl1.end.znucl[t - 1]
el = element_name_inv(z)
printlog('Typat of chosen imp atom in cl1 is ', el, imp='y')
surround_center = cl1.end.xcart[iatom]
else: #for the case when coordinates of arbitary point are provided.
surround_center = iatom
el = 'undef'
local_atoms = local_surrounding(surround_center,
cl1.end,
neighbors,
control='atoms',
periodic=True)
numbers = local_atoms[2]
els = cl1.end.get_elements()
el_sur = els[numbers[1]] # element of surrounding type
printlog("Numbers of local atoms:", [n + 1 for n in numbers], imp='Y')
printlog("Elements of local atoms:", [els[i] for i in numbers],
imp='Y')
printlog("List of distances", [round(d, 2) for d in local_atoms[3]],
imp='Y')
iX = numbers[0] # first atom is impurity if exist
# printlog
numbers_list = [numbers] # numbers_list is list of lists
calcs = [cl1]
if cl2:
numbers_list.append([iatom2]) # for cl2 only one atom is supported
calcs.append(cl2)
for cl, d, numbers in zip(calcs, dos, numbers_list):
d.p = [] #central and surrounding
d.d = []
d.p_up = []
d.p_down = []
d.p_down = [] #central and and surrounding
d.d_up = [] #central atom and surrounding atoms
d.d_down = [] #central atom and surrounding atoms
d.t2g_up = []
d.t2g_down = []
d.eg_up = []
d.eg_down = []
d.p_all = [] #sum over all atoms
d.d_all = [] #sum over all atoms
d.p_all_up = [] #sum over all atoms
d.d_all_up = [] #sum over all atoms
d.p_all_down = [] #sum over all atoms
d.d_all_down = [] #sum over all atoms
if 'p_all' in orbitals or 'd_all' in orbitals:
#sum over all atoms
p = []
p_up = []
p_down = []
dd = []
d_up = []
d_down = []
els = cl.end.get_elements()
for i in range(cl.end.natom):
# if 'O' not in els[i]:
# continue
if spin_pol:
plist_up = [d.site_dos(i, l) for l in (2, 4, 6)]
plist_down = [d.site_dos(i, l) for l in (3, 5, 7)]
plist = plist_up + plist_down
p_up.append([sum(x) for x in zip(*plist_up)])
p_down.append([sum(x) for x in zip(*plist_down)])
p.append([sum(x) for x in zip(*plist)])
else:
plist = [d.site_dos(i, l) for l in (1, 2, 3)]
p.append([sum(x) for x in zip(*plist)])
if spin_pol:
dlist_up = [
d.site_dos(i, l) for l in (8, 10, 12, 14, 16)
] #
dlist_down = [
d.site_dos(i, l) for l in (9, 11, 13, 15, 17)
] #
dlist = dlist_up + dlist_down
d_up.append([sum(x) for x in zip(*dlist_up)])
d_down.append([sum(x) for x in zip(*dlist_down)])
dd.append([sum(x) for x in zip(*dlist)])
else:
dlist = [d.site_dos(i, l) for l in (4, 5, 6, 7, 8)] #
dd.append([sum(x) for x in zip(*dlist)])
d.p_all = [sum(pi) for pi in zip(*p)] #sum over all atoms
d.d_all = [sum(di) for di in zip(*dd)]
if spin_pol:
d.p_all_up = [sum(pi) for pi in zip(*p_up)]
d.p_all_down = [sum(pi) for pi in zip(*p_down)]
d.d_all_up = [sum(pi) for pi in zip(*d_up)]
d.d_all_down = [sum(pi) for pi in zip(*d_down)]
#sum by surrounding atoms atoms
n_sur = len(numbers)
for i in numbers: #Now for surrounding atoms in numbers list:
if spin_pol:
plist_up = [d.site_dos(i, l) for l in (2, 4, 6)]
plist_down = [d.site_dos(i, l) for l in (3, 5, 7)]
d.p_up.append([sum(x) for x in zip(*plist_up)])
d.p_down.append([sum(x) for x in zip(*plist_down)])
plist = plist_up + plist_down
d.p.append([sum(x) for x in zip(*plist)])
else:
plist = [d.site_dos(i, l) for l in (1, 2, 3)]
d.p.append([sum(x) for x in zip(*plist)])
if spin_pol:
dlist_up = [d.site_dos(i, l)
for l in (8, 10, 12, 14, 16)] #
dlist_down = [
d.site_dos(i, l) for l in (9, 11, 13, 15, 17)
] #
dlist = dlist_up + dlist_down
d.d.append([sum(x) for x in zip(*dlist)])
d.d_up.append([sum(x) for x in zip(*dlist_up)])
d.d_down.append([sum(x) for x in zip(*dlist_down)])
t2g_down = [d.site_dos(i, l) for l in (9, 11, 15)]
eg_down = [d.site_dos(i, l) for l in (13, 17)]
t2g_up = [d.site_dos(i, l) for l in (8, 10, 14)]
eg_up = [d.site_dos(i, l) for l in (12, 16)]
d.t2g_down.append([sum(x) for x in zip(*t2g_down)])
d.eg_down.append([sum(x) for x in zip(*eg_down)])
d.t2g_up.append([sum(x) for x in zip(*t2g_up)])
d.eg_up.append([sum(x) for x in zip(*eg_up)])
else:
dlist = [d.site_dos(i, l) for l in (4, 5, 6, 7, 8)] #
d.d.append([sum(x) for x in zip(*dlist)])
d.p6 = [sum(pi) / n_sur for pi in zip(*d.p)
] #sum over neighbouring atoms now only for spin up
if spin_pol:
d.p6_up = [sum(pi) / n_sur for pi in zip(*d.p_up)
] #sum over neighbouring atoms now only for spin up
d.p6_down = [
sum(pi) / n_sur for pi in zip(*d.p_down)
] #sum over neighbouring atoms now only for spin up
d.d6 = [sum(di) for di in zip(*d.d)] #sum over neighbouring atoms
"""Plotting"""
# nsmooth = 15 # smooth of dos
d1 = dos[0]
ds = [d1]
names = []
names = [cl1.id[0] + '_at_' + eld1[iatom + 1] + str(iatom + 1)]
atoms = [iatom]
els = [eld1[iatom + 1]]
lts = [
'-',
] #linetypes
if cl2:
ds.append(dos[1])
d2 = dos[1]
# if labels:
# names.append(labels[1])
# else:
names.append(cl2.id[0] + '_at_' + eld2[iatom2 + 1] +
str(iatom2 + 1))
lts.append(lts2)
atoms.append(iatom2)
els.append(eld2[iatom2 + 1])
if not spin_pol:
plot_spin_pol = 0 # could not plot spin polarization for non-spin polarization plot
if 'dashes' in plot_param:
dashes = plot_param['dashes']
del plot_param['dashes']
else:
dashes = (5, 1)
energy1 = dos[0].energy
args = {}
if spin_pol:
i_orb = {
's': 0,
'py': 2,
'pz': 4,
'px': 6,
'dxy': 8,
'dyz': 10,
'dz2': 12,
'dxz': 14,
'dx2': 16
}
i_orb_down = {
's': 1,
'py': 3,
'pz': 5,
'px': 7,
'dxy': 9,
'dyz': 11,
'dz2': 13,
'dxz': 15,
'dx2': 17
}
else:
i_orb = {
's': 0,
'py': 1,
'pz': 2,
'px': 3,
'dxy': 4,
'dyz': 5,
'dz2': 6,
'dxz': 7,
'dx2': 8
}
# color = {'s':'k', 'p':'#F14343', 'd':'#289191', 'py':'g', 'pz':'b', 'px':'c', 'dxy':'m', 'dyz':'c', 'dz2':'k', 'dxz':'r', 'dx2':'g', 't2g':'b', 'eg':'g', 'p6':'k'}
color = {
's': 'k',
'p': '#FF0018',
'd': '#138BFF',
'py': 'g',
'pz': 'b',
'px': 'c',
'dxy': 'm',
'dyz': 'c',
'dz2': 'k',
'dxz': 'r',
'dx2': 'g',
't2g': '#138BFF',
'eg': '#8E12FF',
'p6': '#FF0018',
'p_all': 'r',
'd_all': 'b'
} #http://paletton.com/#uid=54-100kwi++bu++hX++++rd++kX
# color = {'s':'k', 'p':'r', 'd':'g', 'py':'g', 'pz':'b', 'px':'c', 'dxy':'m', 'dyz':'c', 'dz2':'m', 'dxz':'r', 'dx2':'g'}
for orb in orbitals:
i = 0
for n, l, iat, el, d in zip(names, lts, atoms, els, ds):
if el in ['Fe', 'Co', 'V', 'Mn'] and orb in ['p', 's']:
continue
if el == 'O' and orb in ('d', 't2g', 'eg', 'dxy', 'dyz', 'dxz',
'dz2', 'dx2'):
continue
nam = orb
nam_down = nam + '_down'
# print('name', n)
# print('lts', l)
if labels:
formula = labels[i]
else:
formula = latex_chem(n.split('.')[0])
i += 1
if spin_pol:
nam += ''
suf = '; ' + n
nam += suf
nam_down += suf
if orb == 'p':
if plot_spin_pol:
args[nam] = {
'x': d.energy,
'y': smoother(d.p_up[0], nsmooth),
'c': color[orb],
'ls': l,
'label': formula + ' ' + el + suf2 + ' ' + orb,
'dashes': dashes
}
args[nam_down] = {
'x': d.energy,
'y': -smoother(d.p_down[0], nsmooth),
'c': color[orb],
'ls': l,
'label': None,
'dashes': dashes
}
color[orb] = 'c'
else:
args[nam] = {
'x': d.energy,
'y': smoother(d.p[0], nsmooth),
'c': color[orb],
'ls': l,
'label': formula + ' ' + el + suf2 + ' ' + orb,
'dashes': dashes
}
elif orb == 'p6':
# now spin-polarized components could not be shown
if plot_spin_pol:
args[nam] = {
'x': d.energy,
'y': smoother(d.p6_up, nsmooth),
'c': color[orb],
'ls': l,
'label': formula + ' ' + el_sur + suf2 + ' p',
'dashes': dashes
}
args[nam_down] = {
'x': d.energy,
'y': -smoother(d.p6_down, nsmooth),
'c': color[orb],
'ls': l,
'label': None,
'dashes': dashes
}
else:
args[nam] = {
'x': d.energy,
'y': smoother(d.p6, nsmooth),
'c': color[orb],
'ls': l,
'label': formula + ' ' + el_sur + suf2 + ' p',
'dashes': dashes
}
elif orb == 'd':
if plot_spin_pol:
args[nam] = {
'x': d.energy,
'y': smoother(d.d_up[0], nsmooth),
'c': color[orb],
'ls': l,
'label': formula + ' ' + el + suf2 + ' ' + orb
}
args[nam_down] = {
'x': d.energy,
'y': -smoother(d.d_down[0], nsmooth),
'c': color[orb],
'ls': l,
'label': None
}
color[orb] = 'm'
else:
args[nam] = {
'x': d.energy,
'y': smoother(d.d[0], nsmooth),
'c': color[orb],
'ls': l,
'label': formula + ' ' + el + suf2 + ' ' + orb
}
elif orb == 't2g':
if split_type == 'octa':
orb_name = orb
elif split_type == 'tetra':
orb_name = 't2'
args[nam] = {
'x': d.energy,
'y': smoother(d.t2g_up[0], nsmooth),
'c': color[orb],
'ls': l,
'label': formula + ' ' + el + suf2 + ' ' + orb_name
}
if spin_pol:
args[nam_down] = {
'x': d.energy,
'y': -smoother(d.t2g_down[0], nsmooth),
'c': color[orb],
'ls': l,
'label': None
}
elif orb == 'eg':
if split_type == 'octa':
orb_name = orb
elif split_type == 'tetra':
orb_name = 'e'
args[nam] = {
'x': d.energy,
'y': smoother(d.eg_up[0], nsmooth),
'c': color[orb],
'ls': l,
'label': formula + ' ' + el + suf2 + ' ' + orb_name
}
if spin_pol:
args[nam_down] = {
'x': d.energy,
'y': -smoother(d.eg_down[0], nsmooth),
'c': color[orb],
'ls': l,
'label': None
}
elif orb == 'p_all':
if plot_spin_pol:
args[nam] = {
'x': d.energy,
'y': smoother(d.p_all_up, nsmooth),
'c': color[orb],
'ls': l,
'label': formula + ' ' + el + suf2 + ' ' + orb
}
args[nam_down] = {
'x': d.energy,
'y': -smoother(d.p_all_down, nsmooth),
'c': color[orb],
'ls': l,
'label': None
}
# color[orb] = 'm'
else:
args[nam] = {
'x': d.energy,
'y': smoother(d.p_all, nsmooth),
'c': color[orb],
'ls': l,
'label': formula + ' ' + el + suf2 + ' ' + orb
}
elif orb == 'd_all':
if plot_spin_pol:
args[nam] = {
'x': d.energy,
'y': smoother(d.d_all_up, nsmooth),
'c': color[orb],
'ls': l,
'label': formula + ' ' + el + suf2 + ' ' + orb
}
args[nam_down] = {
'x': d.energy,
'y': -smoother(d.d_all_down, nsmooth),
'c': color[orb],
'ls': l,
'label': None
}
# color[orb] = 'm'
else:
args[nam] = {
'x': d.energy,
'y': smoother(d.d_all, nsmooth),
'c': color[orb],
'ls': l,
'label': formula + ' ' + el + suf2 + ' ' + orb
}
else:
# args[nam] = (d.energy, smoother(d.site_dos(iat, i_orb[orb]), nsmooth), color[orb]+l)
args[nam] = {
'x': d.energy,
'y': smoother(d.site_dos(iat, i_orb[orb]), nsmooth),
'c': color[orb],
'ls': l,
'label': formula + ' ' + el + suf2 + ' ' + orb
}
if spin_pol:
args[nam_down] = {
'x':
d.energy,
'y':
-smoother(d.site_dos(iat, i_orb_down[orb]),
nsmooth),
'c':
color[orb],
'ls':
l,
'label':
None
}
# args[nam_down] = (d.energy, -smoother(d.site_dos(iat, i_orb_down[orb]), nsmooth), color[orb]+l)
"""Additional dos analysis; to be refined"""
if show_gravity:
if show_gravity[0] == 1:
d = d1
elif show_gravity[0] == 2:
d = d2
if show_gravity[2]:
erange = show_gravity[2]
else:
erange = (-100, 0)
if show_gravity[1] == 'p6':
gc = det_gravity2(d.energy, d.p6, erange)
printlog(
'Gravity center for cl1 for p6 for {:} is {:5.2f}'.format(
erange, gc),
imp='Y')
# gc = det_gravity2(d.energy, d.d[0], erange)
# printlog('Gravity center for cl1 for d for {:} is {:5.2f}'.format(erange, gc), imp = 'Y')
elif show_gravity[1] == 'p':
gc = det_gravity2(d.energy, d.p[0],
erange) # for first atom for cl2
elif show_gravity[1] == 'p_all':
gc = det_gravity2(d.energy, d.p_all,
erange) # for first atom for cl2
printlog('Gravity center for cl1 for p_all for {:} is {:5.2f}'.
format(erange, gc),
imp='Y')
plot_param['ver_lines'] = [{'x': gc, 'c': 'k', 'ls': '--'}]
"""Plot everything"""
image_name = os.path.join(
path, '_'.join(names) + '.' + ''.join(orbitals) + '.' + el +
str(iat + 1))
if 'xlabel' not in plot_param:
plot_param['xlabel'] = "Energy (eV)"
if 'ylabel' not in plot_param:
plot_param['ylabel'] = ylabel
fit_and_plot(
show=show,
image_name=image_name,
hor=True,
# title = cl1.name.split('.')[0]+'; V='+str(round(cl1.vol) )+' $\AA^3$; Impurity: '+el,
**plot_param,
**args)
# printlog("Writing file", image_name, imp = 'Y')
if 0:
"""Calculate d DOS at Fermi level"""
nn = 50 #number to integrate in both directions
x1 = dos[0].energy[i_efermi - nn:i_efermi + nn]
y1 = smoother(dos[0].d6, nsmooth)[i_efermi - nn:i_efermi + nn]
x2 = dos[1].energy[i_efermi_e - nn:i_efermi_e + nn]
y2 = smoother(dos[1].d6, nsmooth)[i_efermi_e - nn:i_efermi_e + nn]
f1 = interp1d(x1, y1, kind='cubic')
f2 = interp1d(x2, y2, kind='cubic')
# if debug: print '\n'
# if debug: print dos[0].d6[i_efermi] - dos[1].d6[i_efermi_e], " - by points; change of d Ti DOS at the Fermi level due to the carbon"
# if debug: print f2(0), f1(0)
e_at_Ef_shift = f1(0) - f2(0)
printlog(
"{:5.2f} reduction of d dos at Fermi level; smoothed and interpolated"
.format(e_at_Ef_shift),
imp='Y')
if 0:
"""Calculate second derivative of d at the Fermi level"""
# tck1 = interpolate.splrep(x1, y1, s=0)
# tck2 = interpolate.splrep(x2, y2, s=0)
# e_at_Ef_shift_spline = interpolate.splev(0, tck1, der=0) - interpolate.splev(0, tck2, der=0)
# if debug: print "{:5.2f} smoothed and interpolated from spline".format( e_at_Ef_shift_spline )
# # if debug: print type(interpolate.splev(0, tck1, der=2))
# if debug: print "{:5.2f} {:5.2f} gb and bulk second derivative at Fermi from spline".format( float(interpolate.splev(0, tck1, der=2)), float(interpolate.splev(0, tck2, der=2)) )
if 0:
"""Calculate shift of d orbitals after adding impurity"""
d_shift = det_gravity(dos[0], Erange=(-2.8, 0)) - det_gravity(
dos[1], Erange=(-2.8, 0)
) #negative means impurity shifts states to negative energies, which is favourable
printlog("{:5.2f} Shift of Ti d center of gravity".format(d_shift),
imp='Y')
# if debug: print det_gravity(dos[0], Erange = (-2.8, 0)), det_gravity(dos[1], Erange = (-2.8, 0))
"""Calculate correlation between imp p and matrix d"""
def rmsdiff(a, b):
# rms difference of vectors a and b:
#Root-mean-square deviation
rmsdiff = 0
for (x, y) in zip(a, b):
rmsdiff += (
x -
y)**2 # NOTE: overflow danger if the vectors are long!
return math.sqrt(rmsdiff / min(len(a), len(b)))
pd_drms = 1 / rmsdiff(
dos[0].p,
dos[0].d6) # the higher the number the higher hybridization
printlog("{:5.2f} p-d hybridization estimate".format(pd_drms),
imp='Y')
# if debug: print "sqeuclidean", sqeuclidean(dos[0].p, dos[0].d6)/len(dos[0].d6)
# if debug: print "pearsonr", pearsonr(dos[0].p, dos[0].d6) #Pearson correlation coefficient; only shape; the larger number means more similarity in shape
# def autocorr(x):
# result = np.correlate(x, x, mode='full')
# return result[result.size/2:]
printlog("------End plot_dos()-----\n\n")
return {'name': cl1.name, 'filename': image_name}
def add_neb(
starting_calc=None,
st=None,
st_end=None,
it_new=None,
ise_new=None,
i_atom_to_move=None,
up='up2',
search_type='vacancy_creation',
images=None,
r_impurity=None,
corenum=None,
calc_method=['neb'],
inherit_option=None,
mag_config=None,
i_void_start=None,
i_void_final=None,
atom_to_insert=None,
atom_to_move=None,
rep_moving_atom=None,
end_pos_types_z=None,
replicate=None,
it_new_folder=None,
inherit_magmom=False,
x_start=None,
xr_start=None,
x_final=None,
xr_final=None,
upload_vts=False,
run=False,
add_loop_dic=None,
old_behaviour=None,
):
"""
Prepare needed files for NEB
Provides several regimes controlled by *search_type* flag:
- existing_voids - search for voids around atom and use them as a final position
- vacancy_creation - search for neighbors of the same type and make a vacancy as a start position
- interstitial_insertion - search for two neighboring voids; use them as start and final positions
by inserting atom *atom_to_insert*
- None - just use st and st2 as initial and final
###INPUT:
- starting_calc (Calculation) - Calculation object with structure
- st (Structure) - structure, can be used instead of Calculation
- it_new (str) - name for calculation
- st_end (Structure) - final structure
- i_atom_to_move (int) - number of atom for moving starting from 0;
- *mag_config* (int ) - choose magnetic configuration - allows to obtain different localizations of electron
- *replicate* (tuple 3*int) - replicate cell along rprimd
- i_void_start, i_void_final (int) - position numbers of voids (or atoms) from the suggested lists
- atom_to_insert (str) - element name of atom to insert
- atom_to_move (str) - element name of atom to move
- it_new_folder (str) - section folder
- inherit_option (str) - passed only to add_loop
- inherit_magmom (bool) - if True than magmom from starting_calc is used, else from set
- end_pos_types_z (list of int) - list of Z - type of atoms, which could be considered as final positions in vacancy creation mode
- calc_method (list)
- 'neb'
- 'only_neb' - run only footer
- x_start, x_final (array) - explicit xcart coordinates of moving atom for starting and final positions, combined with atom_to_insert
- xr_start, xr_final (array) - explicit xred
- rep_moving_atom (str)- replace moving atom by needed atom - can be useful than completly different atom is needed.
- upload_vts (bool) - if True upload Vasp.pm and nebmake.pl to server
- run (bool) - run on server
###RETURN:
None
###DEPENDS:
###TODO
1. Take care of manually provided i_atom_to_move in case of replicate flag using init_numbers
2. For search_type == None x_m and x_del should be determined for magnetic searching and for saving their coordinates
to struct_des; now their just (0,0,0)
"""
if old_behaviour:
naming_conventions209 = False #
else:
naming_conventions209 = True # set False to reproduce old behavior before 2.09.2017
# print(atom_to_insert)
# sys.exit()
calc = header.calc
struct_des = header.struct_des
varset = header.varset
if not add_loop_dic:
add_loop_dic = {}
if not end_pos_types_z:
end_pos_types_z = []
if not hasattr(calc_method, '__iter__'):
calc_method = [calc_method]
if starting_calc and st:
printlog(
'Warning! both *starting_calc* and *st* are provided. I use *starting_calc*'
)
st = copy.deepcopy(starting_calc.end)
elif starting_calc:
st = copy.deepcopy(starting_calc.end)
printlog('I use *starting_calc*')
elif st:
''
printlog('I use *st*')
else:
printlog(
'Error! no input structure. Use either *starting_calc* or *st*')
if corenum == None:
if images == 3:
corenum = 15
elif images == 5:
corenum = 15
elif images == 7:
corenum = 14
else:
printlog('add_neb(): Error! number of images', images,
'is unknown to me; please provide corenum!')
# print(atom_to_insert)
# sys.exit()
if corenum:
# header.corenum = corenum
''
else:
corenum = header.CORENUM
if corenum % images > 0:
print_and_log(
'Error! Number of cores should be dividable by number of IMAGES',
images, corenum)
if not ise_new:
ise_new = starting_calc.id[1]
printlog('I use', ise_new, 'as ise_new', imp='y')
name_suffix = ''
st_pores = []
name_suffix += 'n' + str(images)
"""Replicate cell """
if replicate:
print_and_log('You have chosen to replicate the structure by',
replicate)
st = replic(st, mul=replicate)
name_suffix += str(replicate[0]) + str(replicate[1]) + str(
replicate[2])
printlog('Search type is ', search_type)
if search_type == None:
if st_end == None:
printlog(
'Error! You have provided search_type == None, st_end should be provided!'
)
st1 = st
st2 = st_end
x_m = (0, 0, 0)
x_del = (0, 0, 0)
else:
"""1. Choose atom (or insert) for moving """
if is_list_like(xr_start):
x_start = xred2xcart([xr_start], st.rprimd)[0]
st1, i_m = st.add_atoms([x_start], atom_to_insert, return_ins=1)
x_m = x_start
# i_m = st1.find_atom_num_by_xcart(x_start)
# print(st1.get_elements()[i_m])
# sys.exit()
if i_atom_to_move:
nn = str(i_atom_to_move + 1)
else:
nn = str(i_void_start)
name_suffix += atom_to_insert + nn
write_xyz(st1, file_name=st.name + '_manually_start')
printlog('Start position is created manually by adding xr_start',
xr_start, x_start)
type_atom_to_move = atom_to_insert
el_num_suffix = ''
else:
atoms_to_move = []
atoms_to_move_types = []
# print('d', i_atom_to_move)
# sys.exit()
if i_atom_to_move:
typ = st.get_elements()[i_atom_to_move]
printlog('add_neb(): atom', typ, 'will be moved', imp='y')
atoms_to_move.append(
[i_atom_to_move, typ, st.xcart[i_atom_to_move]])
atoms_to_move_types.append(typ)
if naming_conventions209:
name_suffix += typ + str(i_atom_to_move + 1)
else:
#try to find automatically among alkali - special case for batteries
for i, typ, x in zip(range(st.natom), st.get_elements(),
st.xcart):
if typ in ['Li', 'Na', 'K', 'Rb', 'Mg']:
atoms_to_move.append([i, typ, x])
if typ not in atoms_to_move_types:
atoms_to_move_types.append(typ)
if atoms_to_move:
# print(atom_to_move)
# sys.exit()
if not atom_to_move:
atom_to_move = atoms_to_move_types[
0] # taking first found element
if len(atoms_to_move_types) > 1:
printlog(
'Error! More than one type of atoms available for moving detected',
atoms_to_move_types,
'please specify needed atom with *atom_to_move*')
type_atom_to_move = atom_to_move #atoms_to_move[0][1]
# printlog('atom ', type_atom_to_move, 'will be moved', imp ='y')
if i_atom_to_move:
printlog('add_neb(): *i_atom_to_move* = ',
i_atom_to_move,
'is used',
imp='y')
numbers = [[i_atom_to_move]]
i_void_start = 1
else:
printlog('add_neb(): determine_symmetry_positions ...',
imp='y')
numbers = determine_symmetry_positions(st, atom_to_move)
# print(numbers)
# sys.exit()
if len(numbers) > 0:
printlog('Please choose position using *i_void_start* :',
[i + 1 for i in range(len(numbers))],
imp='y')
printlog('*i_void_start* = ', i_void_start)
i_m = numbers[i_void_start - 1][0]
printlog('Position',
i_void_start,
'chosen, atom:',
i_m + 1,
type_atom_to_move,
imp='y')
else:
i_m = numbers[0][0]
x_m = st.xcart[i_m]
el_num_suffix = type_atom_to_move + str(i_m + 1)
atom_to_insert = atom_to_move
st1 = st
# elif atom_to_replace:
# num = st.get_specific_elements(atom_to_replace)
# if len(n)>0:
# printlog('Please choose position using *i_void_start* :', [i+1 for i in range(len(num))],imp = 'y' )
# printlog('*i_void_start* = ', i_void_start)
# i_m = num[i_void_start-1]
# printlog('Position',i_void_start,'chosen, atom to replace:', i_m+1, atom_to_replace, imp = 'y' )
# sys.exit()
else:
print_and_log(
'No atoms to move found, you probably gave me deintercalated structure',
important='y')
st_pores, sums, avds = determine_voids(st,
r_impurity,
step_dec=0.1,
fine=2)
insert_positions = determine_unique_voids(st_pores, sums, avds)
print_and_log(
'Please use *i_void_start* to choose the void for atom insertion from the Table above:',
end='\n',
imp='Y')
if i_void_start == None:
sys.exit()
if atom_to_insert == None:
printlog('Error! atom_to_insert = None')
st = st.add_atoms([
insert_positions[i_void_start],
], atom_to_insert)
name_suffix += 'i' + str(i_void_start)
i_m = st.natom - 1
x_m = st.xcart[i_m]
search_type = 'existing_voids'
type_atom_to_move = atom_to_insert
el_num_suffix = ''
st1 = st
"""2. Choose final position"""
if is_list_like(xr_final):
x_final = xred2xcart([xr_final], st.rprimd)[0]
#old
#check if i_atom_to_move should be removed
# st2 = st1.del_atom(i_m)
# st2 = st2.add_atoms([x_final], atom_to_insert)
#new
st2 = st1.mov_atoms(i_m, x_final)
# st1.printme()
# st2.printme()
# sys.exit()
x_del = x_final
search_type = 'manual_insertion'
name_suffix += 'v' + str(i_void_final)
write_xyz(st2, file_name=st.name + '_manually_final')
printlog('Final position is created manually by adding xr_final',
xr_final, x_del)
elif search_type == 'existing_voids':
#Search for voids around choosen atoms
if not st_pores:
st_pores, sums, avds = determine_voids(st, r_impurity)
sur = determine_unique_final(st_pores, sums, avds, x_m)
print_and_log('Please choose *i_void_final* from the Table above:',
end='\n',
imp='Y')
if i_void_final == None:
sys.exit()
x_final = sur[0][i_void_final] #
printlog('You chose:',
np.array(x_final).round(2),
end='\n',
imp='Y')
x_del = x_final #please compare with vacancy creation mode
write_xyz(st.add_atoms([x_final], 'H'),
replications=(2, 2, 2),
file_name=st.name + '_possible_positions2_replicated')
print_and_log('Choosing the closest position as end',
important='n')
st1 = st
st2 = st.mov_atoms(i_m, x_final)
name_suffix += el_num_suffix + 'e' + str(
i_void_final) + atom_to_insert
st1 = return_atoms_to_cell(st1)
st2 = return_atoms_to_cell(st2)
write_xyz(st1, file_name=st1.name + name_suffix + '_start')
write_xyz(st2, file_name=st2.name + name_suffix + '_final')
elif search_type == 'vacancy_creation':
#Create vacancy by removing some neibouring atom of the same type
print_and_log(
'You have chosen vacancy_creation mode of add_neb tool',
imp='Y')
print_and_log('Type of atom to move = ',
type_atom_to_move,
imp='y')
# print 'List of left atoms = ', np.array(st.leave_only(type_atom_to_move).xcart)
sur = local_surrounding(x_m,
st,
n_neighbours=12,
control='atoms',
only_elements=[invert(type_atom_to_move)] +
end_pos_types_z,
periodic=True) #exclude the atom itself
# print(x_m)
# print(sur)
# st.nn()
print_and_log(
'I can suggest you ' + str(len(sur[0][1:])) +
' end positions. The distances to them are : ',
np.round(sur[3][1:], 2),
' A\n ',
'They are ',
type_atom_to_move, [invert(z) for z in end_pos_types_z],
'atoms, use *i_void_final* to choose required: 1, 2, 3 ..',
imp='y')
if not i_void_final:
i_void_final = 1 #since zero is itself
print_and_log('Choosing position ',
i_void_final,
'with distance',
round(sur[3][i_void_final], 2),
'A',
imp='y')
name_suffix += el_num_suffix + 'v' + str(i_void_final)
x_del = sur[0][i_void_final]
printlog('xcart of atom to delete', x_del)
i_del = st.find_atom_num_by_xcart(x_del)
# print(x_del)
# print(st.xcart)
# for x in st.xcart:
# if x[0] > 10:
# print(x)
print_and_log('number of atom to delete = ', i_del, imp='y')
if i_del == None:
printlog('add_neb(): Error! I could find atom to delete!')
# print st.magmom
# print st1.magmom
# try:
if is_list_like(xr_start):
st2 = st1.mov_atoms(
i_m, x_del) # i_m and sur[0][neb_config] should coincide
# i_del = st1.find_atom_num_by_xcart(x_del)
st1 = st1.del_atom(i_del)
else:
print_and_log(
'Making vacancy at end position for starting configuration',
imp='y')
st1 = st.del_atom(i_del)
print_and_log(
'Making vacancy at start position for final configuration',
important='n')
st2 = st.mov_atoms(
i_m, x_del) # i_m and sur[0][neb_config] should coincide
# except:
# st2 = st
st2 = st2.del_atom(i_del) # these two steps provide the same order
"""Checking correctness of path"""
#if start and final positions are used, collisions with existing atoms are possible
if is_list_like(xr_start) and is_list_like(xr_final):
printlog('Checking correctness')
st1, _, _ = st1.remove_close_lying()
stt = st1.add_atoms([
x_final,
], 'Pu')
stt, x, _ = stt.remove_close_lying(
rm_both=True
) # now the final position is empty for sure; however the order can be spoiled
# print(st._removed)
if stt._removed:
st1 = stt # only if overlapping was found we assign new structure
st2, _, _ = st2.remove_close_lying(rm_first=stt._removed)
stt = st2.add_atoms([
x_start,
], 'Pu')
stt, x, _ = stt.remove_close_lying(
rm_both=True) # now the start position is empty for sure
if stt._removed:
st2 = stt
print(st2.get_elements())
# sys.exit()
elif is_list_like(xr_final) and not is_list_like(xr_start) or is_list_like(
xr_start) and not is_list_like(xr_final):
printlog(
'Attention! only start of final position is provided, please check that everything is ok with start and final states!!!'
)
""" Determining magnetic moments """
vp = varset[ise_new].vasp_params
if search_type != None: #for None not implemented; x_m should be determined first for this
if 'ISPIN' in vp and vp['ISPIN'] == 2:
print_and_log(
'Magnetic calculation detected. Preparing spin modifications ...',
imp='y')
cl_test = CalculationVasp(varset[ise_new])
cl_test.init = st1
# print 'asdfsdfasdfsadfsadf', st1.magmom
if inherit_magmom and hasattr(st, 'magmom') and st.magmom and any(
st.magmom):
print_and_log(
'inherit_magmom=True: You have chosen MAGMOM from provided structure',
imp='y')
name_suffix += 'mp' #Magmom from Previous
else:
cl_test.init.magmom = None
print_and_log(
'inherit_magmom=False or no magmom in input structure : MAGMOM will be determined from set',
imp='y')
name_suffix += 'ms' #Magmom from Set
cl_test.actualize_set() #find magmom for current structure
st1.magmom = copy.deepcopy(cl_test.init.magmom)
st2.magmom = copy.deepcopy(cl_test.init.magmom)
# sys.exit()
# print_and_log('The magnetic moments from set:')
# print cl_test.init.magmom
#checking for closest atoms now only for Fe, Mn, Ni, Co
sur = local_surrounding(x_m,
st1,
n_neighbours=3,
control='atoms',
periodic=True,
only_elements=header.TRANSITION_ELEMENTS)
dist = np.array(sur[3]).round(2)
numb = np.array(sur[2])
a = zip(numb, dist)
# a= np.array(a)
# print a[1]
# a = np.apply_along_axis(np.unique, 1, a)
# print a
def unique_by_key(elements, key=None):
if key is None:
# no key: the whole element must be unique
key = lambda e: e
return list({key(el): el for el in elements}.values())
# print a
mag_atoms_dists = unique_by_key(a, key=itemgetter(1))
# print (mag_atoms_dists)
# a = unique_by_key(a, key=itemgetter(1))
print_and_log(
'I change spin for the following atoms:\ni atom dist\n',
np.round(mag_atoms_dists, 2),
imp='y')
# print 'I have found closest Fe atoms'
muls = [(1.2, 0.6), (0.6, 1.2)]
mag_moments_variants = []
for mm in muls:
mags = copy.deepcopy(cl_test.init.magmom)
# print mags
for a, m in zip(mag_atoms_dists, mm):
# print t[1]
mags[a[0]] = mags[a[0]] * m
mag_moments_variants.append(mags)
print_and_log('The list of possible mag_moments:', imp='y')
for i, mag in enumerate(mag_moments_variants):
print_and_log(i, mag)
print_and_log(
'Please use *mag_config* arg to choose desired config',
imp='y')
if mag_config != None:
st1.magmom = copy.deepcopy(mag_moments_variants[mag_config])
st2.magmom = copy.deepcopy(mag_moments_variants[mag_config])
name_suffix += 'm' + str(mag_config)
print_and_log('You have chosen mag configuration #',
mag_config,
imp='y')
else:
print_and_log('Non-magnetic calculation continue ...')
"""3. Add to struct_des, create geo files, check set, add_loop """
if starting_calc:
it = starting_calc.id[0]
it_new = it + 'v' + str(starting_calc.id[2]) + '.' + name_suffix
if not it_new_folder:
it_new_folder = struct_des[it].sfolder + '/neb/'
obtained_from = str(starting_calc.id)
if not ise_new:
print_and_log('I will run add_loop() using the same set',
important='Y')
ise_new = cl.id[1]
elif st:
if not it_new:
printlog(
'Error! please provide *it_new* - name for your calculation',
important='Y')
it = None
it_new += '.' + name_suffix
obtained_from = st.name
if not ise_new:
printlog('Error! please provide *ise_new*', important='Y')
if not it_new_folder:
printlog(
'Error! please provide *it_new_folder* - folder for your new calculation',
important='Y')
if rep_moving_atom:
it_new += 'r' + rep_moving_atom
if it_new not in struct_des:
add_des(struct_des, it_new, it_new_folder,
'Automatically created and added from ' + obtained_from)
print_and_log(
'Creating geo files for starting and final configurations (versions 1 and 2) ',
important='y')
# if starting_calc:
# cl = copy.deepcopy(starting_calc)
# else:
cl = CalculationVasp()
#write start position
struct_des[it_new].x_m_ion_start = x_m
struct_des[it_new].xr_m_ion_start = xcart2xred([x_m], st1.rprimd)[0]
# st1, _, _ = st1.remove_close_lying()
# st2, _, _ = st2.remove_close_lying()
i1 = st1.find_atom_num_by_xcart(x_m, prec=0.3)
i2 = st2.find_atom_num_by_xcart(x_del, prec=0.3)
if rep_moving_atom: #replace the moving atom by required
st1 = st1.replace_atoms([i1], rep_moving_atom)
st2 = st2.replace_atoms([i2], rep_moving_atom)
else:
#allows to make correct order for nebmake.pl
st1 = st1.replace_atoms([i1], type_atom_to_move)
st2 = st2.replace_atoms([i2], type_atom_to_move)
i1 = st1.find_atom_num_by_xcart(x_m,
prec=0.3) # the positions were changed
i2 = st2.find_atom_num_by_xcart(x_del, prec=0.3)
cl.end = st1
ver_new = 1
cl.version = ver_new
cl.path["input_geo"] = header.geo_folder + struct_des[it_new].sfolder + '/' + \
it_new+"/"+it_new+'.auto_created_starting_position_for_neb_'+str(search_type)+'.'+str(ver_new)+'.'+'geo'
cl.write_siman_geo(geotype='end',
description='Starting conf. for neb from ' +
obtained_from,
override=True)
#write final position
struct_des[it_new].x_m_ion_final = x_del
struct_des[it_new].xr_m_ion_final = xcart2xred([x_del], st2.rprimd)[0]
cl.end = st2
ver_new = 2
cl.version = ver_new
cl.path["input_geo"] = header.geo_folder + struct_des[it_new].sfolder + '/' + \
it_new+"/"+it_new+'.auto_created_final_position_for_neb_'+str(search_type)+'.'+str(ver_new)+'.'+'geo'
cl.write_siman_geo(geotype='end',
description='Final conf. for neb from ' + obtained_from,
override=True)
if not rep_moving_atom:
st1s = st1.replace_atoms([i1], 'Pu')
st2s = st2.replace_atoms([i2], 'Pu')
else:
st1s = copy.deepcopy(st1)
st2s = copy.deepcopy(st2)
vec = st1.center_on(i1)
st1s = st1s.shift_atoms(vec)
st2s = st2s.shift_atoms(vec)
write_xyz(st1s, file_name=it_new + '_start')
write_xyz(st2s, file_name=it_new + '_end')
st1s.write_poscar('xyz/POSCAR1')
st2s.write_poscar('xyz/POSCAR2')
# print(a)
# runBash('cd xyz; mkdir '+it_new+'_all;'+"""for i in {00..04}; do cp $i/POSCAR """+ it_new+'_all/POSCAR$i; done; rm -r 00 01 02 03 04')
with cd('xyz'):
a = runBash(header.PATH2NEBMAKE + ' POSCAR1 POSCAR2 3')
dst = it_new + '_all'
makedir(dst + '/any')
for f in ['00', '01', '02', '03', '04']:
shutil.move(f + '/POSCAR', dst + '/POSCAR' + f)
shutil.rmtree(f)
#prepare calculations
# sys.exit()
#Check if nebmake is avail
# if int(runBash('ssh '+cluster_address+' test -e '+project_path_cluster+'/tools/vts/nebmake.pl; echo $?') ):
# ''
# print_and_log('Please upload vtsttools to ',cluster_address, project_path_cluster+'/tools/vts/')
# raise RuntimeError
# copy_to_server(path_to_wrapper+'/vtstscripts/nebmake.pl', to = project_path_cluster+'/tools/', addr = cluster_address)
# if int(runBash('ssh '+cluster_address+' test -e '+project_path_cluster+'/tools/Vasp.pm; echo $?') ):
# copy_to_server(path_to_wrapper+'/vtstscripts/Vasp.pm', to = project_path_cluster+'/tools/', addr = cluster_address)
inherit_ngkpt(it_new, it, varset[ise_new])
add_loop(it_new,
ise_new,
verlist=[1, 2],
up=up,
calc_method=calc_method,
savefile='oc',
inherit_option=inherit_option,
n_neb_images=images,
corenum=corenum,
run=run,
**add_loop_dic)
if upload_vts:
siman_dir = os.path.dirname(__file__)
# print(upload_vts)
push_to_server([
siman_dir + '/cluster_tools/nebmake.pl',
siman_dir + '/cluster_tools/Vasp.pm'
],
to=header.cluster_home + '/tools/vts',
addr=header.cluster_address)
else:
print_and_log('Please be sure that vtsttools are at',
header.cluster_address,
header.cluster_home + '/tools/vts/',
imp='Y')
printlog('add_neb finished')
return it_new
def add_neb(starting_calc = None, st = None,
it_new = None, ise_new = None, i_atom_to_move = None,
up = 'up1',
search_type = 'vacancy_creation',
images = 3, r_impurity = None, corenum = 15,
calc_method = ['neb'],
inherit_option = None, mag_config = None, i_void_start = None, i_void_final = None,
atom_to_insert = None,
replicate = None,
it_new_folder = None,
inherit_magmom = False,
x_start = None, xr_start = None,
x_final = None, xr_final = None,
upload_vts = False,
run = False
):
"""
Prepare needed files for NEB
Provides several regimes controlled by *search_type* flag:
- existing_voids - search for voids around atom and use them as a final position
- vacancy_creation - search for neighbors of the same type and make a vacancy as a start position
- interstitial_insertion - search for two neighboring voids; use them as start and final positions
by inserting atom *atom_to_insert*
###INPUT:
- starting_calc (Calculation) - Calculation object with structure
- st (Structure) - structure, can be used instead of Calculation
- it_new (str) - name for calculation
- i_atom_to_move (int) - number of atom for moving;
- *mag_config* (int ) - choose magnetic configuration - allows to obtain different localizations of electron
- *replicate* (tuple 3*int) - replicate cell along rprimd
- i_void_start, i_void_final (int) - number of voids from the suggested lists
- atom_to_insert (str) - element name of atom to insert
- it_new_folder (str) - section folder
- inherit_option (str) - passed only to add_loop
- inherit_magmom (bool) - if True than magmom from starting_calc is used, else from set
- calc_method (list)
- 'neb'
- 'only_neb' - run only footer
- x_start, x_final (array) - explicit coordinates of moving atom for starting and final positions, combined with atom_to_insert
- upload_vts (bool) - if True upload Vasp.pm and nebmake.pl to server
- run (bool) - run on server
###RETURN:
None
###DEPENDS:
###TODO
please take care of manually provided i_atom_to_move in case of replicate flag using init_numbers
"""
calc = header.calc
struct_des = header.struct_des
varset = header.varset
if not hasattr(calc_method, '__iter__'):
calc_method = [calc_method]
if starting_calc and st:
printlog('Warning! both *starting_calc* and *st* are provided. I use *starting_calc*')
st = copy.deepcopy(starting_calc.end)
elif starting_calc:
st = copy.deepcopy(starting_calc.end)
printlog('I use *starting_calc*')
elif st:
''
printlog('I use *st*')
else:
printlog('Error! no input structure. Use either *starting_calc* or *st*')
if corenum:
# header.corenum = corenum
''
else:
corenum = header.CORENUM
if corenum % images > 0:
print_and_log('Error! Number of cores should be dividable by number of IMAGES')
name_suffix = ''
st_pores = []
name_suffix+='n'+str(images)
"""Replicate cell """
if replicate:
print_and_log('You have chosen to replicate the structure by', replicate)
st = replic(st, mul = replicate)
name_suffix += str(replicate[0])+str(replicate[1])+str(replicate[2])
"""1. Choose atom (or insert) for moving """
atoms_to_move = []
for i, typ, x in zip(range(st.natom), st.typat, st.xcart): #try to find automatically
if st.znucl[typ-1] == 3: #Li
atoms_to_move.append([i, 'Li', x])
if st.znucl[typ-1] == 11: #
atoms_to_move.append([i, 'Na', x])
if st.znucl[typ-1] == 19: #
atoms_to_move.append([i, 'K', x])
if is_list_like(xr_start):
x_start = xred2xcart([xr_start], st.rprimd)[0]
st1 = st.add_atoms([x_start], atom_to_insert)
x_m = x_start
name_suffix+='s'
write_xyz(st1, file_name = st.name+'_manually_start')
printlog('Start position is created manually by adding xr_start', xr_start, x_start)
elif not atoms_to_move:
print_and_log('No atoms to move found, you probably gave me intercalated structure', important = 'y')
print_and_log('Searching for voids', important = 'y')
st_pores = find_pores(st, r_matrix = 0.5, r_impurity = r_impurity, fine = 1, calctype = 'all_pores')
print_and_log('List of found voids:\n', np.array(st_pores.xcart) )
write_xyz(st.add_atoms(st_pores.xcart, 'H'), file_name = st.name+'_possible_positions')
write_xyz(st.add_atoms(st_pores.xcart, 'H'), replications = (2,2,2), file_name = st.name+'_possible_positions_replicated')
sums = []
avds = []
for x in st_pores.xcart:
summ = local_surrounding(x, st, n_neighbours = 6, control = 'sum', periodic = True)
avd = local_surrounding(x, st, n_neighbours = 6, control = 'av_dev', periodic = True)
# print sur,
sums.append(summ)
avds.append(avd[0])
# print
sums = np.array(sums)
avds = np.array(avds).round(0)
print_and_log('Sum of distances to 6 neighboring atoms for each void (A):\n', sums, imp ='y')
print_and_log('Distortion of voids (0 - is symmetrical):\n', avds, imp ='y')
crude_prec = 1
sums_crude = np.unique(sums.round(crude_prec))
print_and_log('The unique voids based on the sums:',
'\nwith 0.01 A prec:',np.unique(sums.round(2)),
'\nwith 0.1 A prec:',sums_crude,
imp ='y')
print_and_log('Based on crude criteria only', len(sums_crude),'types of void are relevant')
print_and_log('Please use *i_void_start* to choose the void for atom insertion from this Table:',
end = '\n', imp = 'Y')
insert_positions = []
start_table = []
for i, s in enumerate(sums_crude):
index_of_first = np.where(sums.round(crude_prec)==s)[0][0]
start_table.append([i, st_pores.xcart[index_of_first].round(2), index_of_first,
avds[index_of_first], sums[index_of_first] ])
insert_positions.append( st_pores.xcart[index_of_first] )
print_and_log( tabulate(start_table, headers = ['Start void #', 'Cart.', 'Index', 'Dev.', 'Sum'], tablefmt='psql'), imp = 'Y' )
if i_void_start == None:
sys.exit()
st = st.add_atoms([insert_positions[i_void_start],], atom_to_insert)
name_suffix+='i'+str(i_void_start)
i_m = st.natom-1
x_m = st.xcart[i_m]
search_type = 'existing_voids'
type_atom_to_move = atom_to_insert
el_num_suffix = ''
else:
print_and_log('I have found', len(atoms_to_move), ' anion atoms', important = 'n')
print_and_log( 'Sums of bond lengths around these atoms:',)
sums = []
for a in atoms_to_move:
summ = local_surrounding(a[2], st, n_neighbours = 6, control = 'sum', periodic = True)
sums.append(summ)
# print( summ, end = '')
print_and_log('\nAmong them only',len(set(sums)), 'unique' , important = 'n')
# if
print_and_log('Choosing the first' , important = 'n')
type_atom_to_move = atoms_to_move[0][1]
i_atom_to_move = atoms_to_move[0][0]+1
el_num_suffix = type_atom_to_move +str(i_atom_to_move)
i_m = i_atom_to_move-1
x_m = st.xcart[i_m]
#highlight the moving atom for user for double-check
# st_new = st.change_atom_z(i_m, new_z = 100)
# search_type = 'vacancy_creation'
"""2. Choose final position"""
if is_list_like(xr_final):
x_final = xred2xcart([xr_final], st.rprimd)[0]
st2 = st.add_atoms([x_final], atom_to_insert)
x_del = x_final
search_type = 'manual_insertion'
name_suffix+='f'+atom_to_insert
write_xyz(st2, file_name = st.name+'_manually_final')
printlog('Final position is created manually by adding xr_final', xr_final, x_del)
elif search_type == 'existing_voids':
#Search for voids around choosen atoms
if not st_pores:
st_pores = find_pores(st, r_matrix = 0.5, r_impurity = r_impurity, fine = 2, calctype = 'all_pores')
sur = local_surrounding(x_m, st_pores, n_neighbours = len(st_pores.xcart), control = 'atoms', periodic = True)
# print sur
print_and_log(
'I can suggest you '+str (len(sur[0])-1 )+' end positions.' )
# The distances to them are : '+str(np.round(sur[3], 2) )+' A\n ',
# 'Openning Jmol end positions are highlighted by inserting H ', important = 'y')
# print x_m
# print sur[0]
print_and_log('Please choose *i_void_final* from the following Table:', end = '\n', imp = 'Y')
final_table = []
for i, (x, d, ind) in enumerate( zip(sur[0], sur[3], sur[2])[1:] ):
final_table.append([i, np.array(x).round(2), round(d, 2), avds[ind], sums[ind] ] )
print_and_log( tabulate(final_table, headers = ['Final void #', 'Cart.', 'Dist', 'Dev.', 'Sum'], tablefmt='psql'), imp = 'Y' )
if i_void_final == None:
sys.exit()
x_final = sur[0][i_void_final+1] # +1 because first element is x_m atom itself
write_xyz(st.add_atoms([ x_final], 'H'), replications = (2,2,2), file_name = st.name+'_possible_positions2_replicated')
# sys.exit()
# write_xyz(st.add_atoms(sur[0][2:3], 'H'), analysis = 'imp_surrounding', show_around = 230,nnumber = 10, replications = (2,2,2), file_name = 'local230')
# # write_xyz(st.add_atoms(sur[0][0:1], 'H'), analysis = 'imp_surrounding', show_around = 226,nnumber = 10, replications = (2,2,2), file_name = 'local')
# run_jmol
print_and_log('Choosing the closest position as end', important = 'n')
# i_void_final = 0
st1 = st
# print st1.natom
# sys.exit()
st2 = st.mov_atoms(i_m, x_final)
name_suffix += el_num_suffix+'e'+str(i_void_final)+atom_to_insert
st1 = return_atoms_to_cell(st1)
st2 = return_atoms_to_cell(st2)
write_xyz(st1, file_name = st1.name+name_suffix +'_start')
write_xyz(st2, file_name = st2.name+name_suffix +'_final')
elif search_type == 'vacancy_creation':
#Create vacancy by removing some neibouring atom of the same type
print_and_log('You have chosen vacancy_creation mode of add_neb tool', important = 'Y')
print_and_log( 'Type of atom to move = ', type_atom_to_move, imp = 'y')
# print 'List of left atoms = ', np.array(st.leave_only(type_atom_to_move).xcart)
sur = local_surrounding(x_m, st.leave_only(type_atom_to_move) , n_neighbours = 4, control = 'atoms',
periodic = False)
# print 'xcart of moving atom', x_m
# print 'Local surround = ', sur
# print 'len', len(sur[0])
if len(sur[0]) < 3:
# print 'rprimd = \n',np.array(st.rprimd)
# print 'r lengths = \n',( [np.linalg.norm(r) for r in st.rprimd] )
# print 'xred = \n', np.array(st.xred)
# print 'xcart = \n', np.array(st.xcart)
print_and_log('The supercell is too small, I increase it 8 times!')
st = replic(st, mul = (2,2,2) )
sur = local_surrounding(x_m, st.leave_only(type_atom_to_move) , n_neighbours = 4, control = 'atoms',
periodic = False)
# print 'xcart of moving atom', x_m
write_xyz(st, file_name = st.name+'_replicated')#replications = (2,2,2))
# print 'Local surround = ', sur
# sys.exit()
print_and_log(
'I can suggest you '+str (len(sur[0]) )+' end positions. The distances to them are : '+str(np.round(sur[3], 2) )+' A\n ',
'They are all', type_atom_to_move, 'atoms', important = 'y')
print_and_log('Choosing the closest position as end', important = 'n')
neb_config = 1 #cause the first item in sur is moving atom itself
x_del = sur[0][neb_config]
i_del = st.find_atom_num_by_xcart(x_del)
print_and_log('Making vacancy at end position for starting configuration', important = 'n')
print_and_log( 'number of atom to delete = ', i_del)
# print st.magmom
st1 = st.del_atom(i_del)
# print st1.magmom
print_and_log('Making vacancy at start position for final configuration', important = 'n')
st2 = st.mov_atoms(i_m, x_del) # i_m and sur[0][neb_config] should coincide
st2 = st2.del_atom(i_del) # these two steps provide the same order
name_suffix += el_num_suffix+'v'+str(neb_config)
write_xyz(st1, file_name = st1.name+'_start')# replications = (2,2,2))
write_xyz(st2, file_name = st2.name+'_end')# replications = (2,2,2))
# sys.exit()
# sys.exit()
""" Determining magnetic moments """
if varset[ise_new].vasp_params['ISPIN'] == 2:
print_and_log('Magnetic calculation detected. Preparing spin modifications ...', imp = 'y')
cl_test = CalculationVasp(varset[ise_new])
cl_test.init = st1
# print 'asdfsdfasdfsadfsadf', st1.magmom
if inherit_magmom and hasattr(st, 'magmom') and st.magmom and any(st.magmom):
print_and_log('inherit_magmom=True: You have chosen MAGMOM from provided structure', imp = 'y')
name_suffix+='mp' #Magmom from Previous
else:
cl_test.init.magmom = None
print_and_log('inherit_magmom=False or no magmom in input structure : MAGMOM will be determined from set', imp = 'y')
name_suffix+='ms' #Magmom from Set
cl_test.actualize_set() #find magmom for current structure
st1.magmom = copy.deepcopy(cl_test.init.magmom)
st2.magmom = copy.deepcopy(cl_test.init.magmom)
# sys.exit()
# print_and_log('The magnetic moments from set:')
# print cl_test.init.magmom
#checking for closest atoms now only for Fe, Mn, Ni, Co
sur = local_surrounding(x_m, st1, n_neighbours = 3, control = 'atoms',
periodic = True, only_elements = header.TRANSITION_ELEMENTS)
dist = np.array(sur[3]).round(2)
numb = np.array(sur[2])
a = zip(numb, dist )
# a= np.array(a)
# print a[1]
# a = np.apply_along_axis(np.unique, 1, a)
# print a
def unique_by_key(elements, key=None):
if key is None:
# no key: the whole element must be unique
key = lambda e: e
return list ( {key(el): el for el in elements}.values() )
# print a
mag_atoms_dists = unique_by_key(a, key=itemgetter(1))
# print (mag_atoms_dists)
# a = unique_by_key(a, key=itemgetter(1))
print_and_log( 'I change spin for the following atoms:\ni atom dist\n', np.round(mag_atoms_dists, 2) , imp = 'y' )
# print 'I have found closest Fe atoms'
muls = [(1.2, 0.6), (0.6, 1.2)]
mag_moments_variants = []
for mm in muls:
mags = copy.deepcopy(cl_test.init.magmom)
# print mags
for a, m in zip(mag_atoms_dists, mm):
# print t[1]
mags[a[0]] = mags[a[0]]*m
mag_moments_variants.append(mags)
print_and_log( 'The list of possible mag_moments:', imp = 'y' )
for i, mag in enumerate(mag_moments_variants):
print_and_log( i, mag)
print_and_log( 'Please use *mag_config* arg to choose desired config' , imp = 'y' )
if mag_config != None:
st1.magmom = copy.deepcopy(mag_moments_variants[mag_config])
st2.magmom = copy.deepcopy(mag_moments_variants[mag_config])
name_suffix+='m'+str(mag_config)
print_and_log('You have chosen mag configuration #',mag_config,imp = 'y')
else:
print_and_log('Non-magnetic calculation continue ...')
"""3. Add to struct_des, create geo files, check set, add_loop """
if starting_calc:
it = starting_calc.id[0]
it_new = it+'v'+str(starting_calc.id[2])+'.'+name_suffix
if not it_new_folder:
it_new_folder = struct_des[it].sfolder+'/neb/'
obtained_from = str(starting_calc.id)
if not ise_new:
print_and_log('I will run add_loop() using the same set', important = 'Y')
ise_new = cl.id[1]
elif st:
if not it_new:
printlog('Error! please provide *it_new* - name for your calculation', important = 'Y')
it = None
it_new+='.'+name_suffix
obtained_from = st.name
if not ise_new:
printlog('Error! please provide *ise_new*', important = 'Y')
if not it_new_folder:
printlog('Error! please provide *it_new_folder* - folder for your new calculation', important = 'Y')
if it_new not in struct_des:
add_des(struct_des, it_new, it_new_folder, 'Automatically created and added from '+obtained_from )
print_and_log('Creating geo files for starting and final configurations (versions 1 and 2) ', important = 'y')
# if starting_calc:
# cl = copy.deepcopy(starting_calc)
# else:
cl = CalculationVasp()
#write start position
struct_des[it_new].x_m_ion_start = x_m
struct_des[it_new].xr_m_ion_start = xcart2xred([x_m], st1.rprimd)[0]
cl.end = st1
ver_new = 1
cl.version = ver_new
cl.path["input_geo"] = header.geo_folder + struct_des[it_new].sfolder + '/' + \
it_new+"/"+it_new+'.auto_created_starting_position_for_neb_'+search_type+'.'+str(ver_new)+'.'+'geo'
cl.write_siman_geo(geotype = 'end', description = 'Starting conf. for neb from '+obtained_from, override = True)
#write final position
struct_des[it_new].x_m_ion_final = x_del
struct_des[it_new].xr_m_ion_final = xcart2xred([x_del], st2.rprimd)[0]
cl.end = st2
ver_new = 2
cl.version = ver_new
cl.path["input_geo"] = header.geo_folder + struct_des[it_new].sfolder + '/' + \
it_new+"/"+it_new+'.auto_created_final_position_for_neb_'+search_type+'.'+str(ver_new)+'.'+'geo'
cl.write_siman_geo(geotype = 'end', description = 'Final conf. for neb from '+obtained_from, override = True)
#prepare calculations
#Check if nebmake is avail
# if int(runBash('ssh '+cluster_address+' test -e '+project_path_cluster+'/tools/vts/nebmake.pl; echo $?') ):
# ''
# print_and_log('Please upload vtsttools to ',cluster_address, project_path_cluster+'/tools/vts/')
# raise RuntimeError
# copy_to_server(path_to_wrapper+'/vtstscripts/nebmake.pl', to = project_path_cluster+'/tools/', addr = cluster_address)
# if int(runBash('ssh '+cluster_address+' test -e '+project_path_cluster+'/tools/Vasp.pm; echo $?') ):
# copy_to_server(path_to_wrapper+'/vtstscripts/Vasp.pm', to = project_path_cluster+'/tools/', addr = cluster_address)
inherit_ngkpt(it_new, it, varset[ise_new])
add_loop(it_new, ise_new, verlist = [1,2], up = up, calc_method = calc_method, savefile = 'ov', inherit_option = inherit_option, n_neb_images = images, corenum = corenum, run =run )
if upload_vts:
siman_dir = os.path.dirname(__file__)
# print(upload_vts)
push_to_server([siman_dir+'/cluster_tools/nebmake.pl', siman_dir+'/cluster_tools/Vasp.pm'], to = header.cluster_home+'/tools/vts', addr = header.cluster_address)
else:
print_and_log('Please be sure that vtsttools are at',header.cluster_address, header.cluster_home+'/tools/vts/', imp = 'Y')
return it_new
def write_xyz(st=None,
path=None,
filename=None,
file_name=None,
include_vectors=True,
repeat=1,
shift_2view=1.0,
replications=None,
full_cell=False,
analysis=None,
show_around=None,
show_around_x=None,
nnumber=6,
only_elements=None,
gbpos2=None,
gbwidth=1,
withgb=False,
include_boundary=2,
imp_positions=[],
imp_sub_positions=None,
jmol=None,
specialcommand=None,
jmol_args=None,
sts=None):
"""Writes st structure in xyz format in the folder xyz/path
if repeat == 2: produces jmol script
shift_2view - in rprimd[1][1] - shift of the second view
gbpos2 - position of grain boundary in A
gbwidth - atoms aroung gbpos2 will be colored differently
imp_positions - (x1,x2,x3, element, label)- xcart and element name coordinates additionally to be added to structure; to visulaze all impurity positions: for jmol, additional key 's', 'i' can be added after element
imp_sub_positions - list of atom numbers; the typat of these atoms is changed: not used now
analysis - additional processing, allows to show only specifice atoms,
'imp_surrounding' - shows Ti atoms only around impurity
nnumber - number of neighbours to show
show_around - choose atom number around which to show, from 1
show_around_x - show atoms around point, has higher priority
only_elements - see local_surrounding
replications - list of replications, (2,2,2)
full_cell - returns atoms to cell and replicate boundary atoms
include_vectors (bool) - write primitive vectors to xyz
jmol - 1,0 - use jmol to produce png picture
jmol_args - see write_jmol()
specialcommand - any command at the end of jmol script
sts - list of Structure - write several structures to xyz file - other options are not working in this regime
"""
if jmol_args == None:
jmol_args = {}
if st == None:
st = sts[0]
if replications:
st = replic(st, mul=replications, inv=1)
def update_var(st):
if st.natom != len(st.xred) != len(st.xcart) != len(st.typat) or len(
st.znucl) != max(st.typat):
printlog("Error! write_xyz: check your arrays.\n\n")
if st.xcart == [] or len(st.xcart) != len(st.xred):
printlog(
"Warining! write_xyz: len(xcart) != len(xred) making xcart from xred.\n"
)
st.xcart = xred2xcart(st.xred, st.rprimd)
#print xcart[1]
return st.rprimd, st.xcart, st.xred, st.typat, st.znucl, len(st.xred)
rprimd, xcart, xred, typat, znucl, natom = update_var(st)
if file_name:
name = file_name
elif filename:
name = filename
else:
name = st.name
if sts:
name += '_traj'
printlog("write_xyz(): Name is", name, important='n')
if name == '':
name = 'noname'
if path:
basepath = path
else:
basepath = 'xyz/'
suf = ''
"""Processing section"""
if analysis == 'imp_surrounding':
if show_around == 0:
printlog('Error! number of atom *show_around* should start from 1')
suf = '_loc' + str(show_around)
lxcart = []
ltypat = []
i = 0
if is_list_like(show_around_x):
x = show_around_x
x_t = local_surrounding(x,
st,
nnumber,
control='atoms',
periodic=True,
only_elements=only_elements)
# print('write_xyz: local_surround:', x_t)
lxcart += x_t[0]
ltypat += x_t[1]
else:
for t, x in zip(typat, xcart):
condition = False
# print show_around, 'show'
if show_around:
# print i, condition
condition = (i + 1 == show_around)
# print i, condition
else:
condition = (
t > 1
) # compat with prev behav, to show around any impurities (all atoms with typat more than one)
# print 'se', condition
if condition:
# lxcart.append(x)
# ltypat.append(t)
# print x, ' x'
x_t = local_surrounding(x,
st,
nnumber,
control='atoms',
periodic=True,
only_elements=only_elements)
# print x_t[1]
lxcart += x_t[0]
ltypat += x_t[1]
i += 1
xcart = lxcart
typat = ltypat
natom = len(typat)
# print natom, 'nat'
name += suf
xyzfile = os.path.join(basepath, name + ".xyz")
makedir(xyzfile)
"""Include atoms on the edge of cell"""
if full_cell:
# print xred
# print natom
# st = return_atoms_to_cell(st)
# print xred
st = replic(st,
mul=(1, 1, 2),
inv=0,
cut_one_cell=1,
include_boundary=include_boundary)
# print natom, st.natom
# print st.xred
rprimd, xcart, xred, typat, znucl, natom = update_var(st)
# asdegf
"""Writing section"""
# printlog("Writing xyz: "+xyzfile, imp = 'y')
#analyze imp_positions
if imp_sub_positions == None:
imp_sub_positions = []
nsub = 0
for pos in imp_positions:
# if len(pos) > 4:
# if 's' not in pos[4]: continue # skip interstitial positions
xs = np.asarray([pos[0], pos[1], pos[2]])
nsub += 1
# print xs
for i, x in enumerate(xcart):
# print np.linalg.norm( x-xs)
if np.linalg.norm(x - xs) < 1:
imp_sub_positions.append(i)
if imp_sub_positions:
printlog(imp_sub_positions, ': numbers of found atoms to be changed ')
# for i in sorted(indices, reverse=True):
# del somelist[i]
if include_vectors:
nvect = 3
else:
nvect = 0
def write(st):
rprimd, xcart, xred, typat, znucl, natom = update_var(st)
f.write(str(natom + len(imp_positions) - nsub + nvect) +
"\n") #+3 vectors
f.write(name + "\n")
if imp_positions:
for i, el in enumerate(imp_positions):
# if len(el) != 4: continue
f.write("%s %.5f %.5f %.5f \n" % (el[3], el[0], el[1], el[2]))
# print 'composite -pointsize 60 label:{0:d} -geometry +{1:d}+{2:d} 1.png 2.png'.format(i, el[0], el[1])
for i in range(natom):
typ = typat[i] - 1
z = int(znucl[typ])
if i in imp_sub_positions:
# f.write( "Be " )
continue
else:
el = element_name_inv(z)
f.write(el + " ")
f.write("%.5f %.5f %.5f \n" %
(xcart[i][0], xcart[i][1], xcart[i][2]))
if include_vectors:
for r in st.rprimd:
f.write('Tv {:.10f} {:.10f} {:.10f}\n'.format(*r))
with open(xyzfile, 'w') as f:
if sts:
for st in sts:
write(st)
else:
for i in range(repeat):
write(st)
# os._exit(1)
printlog('File', xyzfile, 'was written', imp='y')
pngfile = None
if jmol:
"""
script mode for jmol. Create script file as well for elobarate visualization
"""
"""Choose gb atoms to change their color"""
printlog('position of boundary 2', gbpos2)
atomselection = ''
#create consistent xcart_new list like it will be in Jmol
xcart_new = []
for i, x in enumerate(xcart):
if i in imp_sub_positions: continue
xcart_new.append(x)
if gbpos2:
gbpos1 = gbpos2 - rprimd[0][0] / 2.
gbatoms = []
for i, x in enumerate(xcart_new):
# print i
# if x[0] > gbpos1 - gbwidth/2. and x[0] < gbpos1 + gbwidth/2.:
if abs(x[0] - gbpos1) < gbwidth / 2.:
gbatoms.append(i)
# print i, x[0], abs(x[0] - gbpos1)
if abs(x[0] - gbpos2) < gbwidth / 2.:
# if x[0] > gbpos2 - gbwidth/2. and x[0] < gbpos2 + gbwidth/2.:
# print i, x[0], abs(x[0] - gbpos2)
gbatoms.append(i)
printlog('Atoms at GB:', gbatoms)
atomselection = ''
for i in gbatoms:
atomselection += 'Ti' + str(i + 1 + len(imp_positions)) + ','
atomselection = atomselection[:-1]
# elif withgb: # color half of cell
# else: # color half of cell
# # pass
# atomselection = 'atomno>'+str(0+len(imp_positions) )+' and atomno<'+str(( natom + len(imp_positions) )/2-1)
xyzfile = os.getcwd() + '/' + xyzfile
scriptfile = basepath + name + ".jmol"
bn = (basepath + name).replace('.', '_')
pngfile = os.getcwd() + '/' + bn + ".png"
printlog('imp_positions = ', imp_positions)
write_jmol(xyzfile,
pngfile,
scriptfile,
atomselection,
rprimd=rprimd,
shift=shift_2view,
label=[(pos[3], pos[4]) for pos in imp_positions],
specialcommand=specialcommand,
**jmol_args)
return xyzfile, pngfile