def plot_dos(cl1, cl2 = None, dostype = None, iatom = 0, orbitals = ('s'), up = None, neighbors = 6, show = 1, path = 'dos', xlim = (None, None), ylim = (None,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
up - 'up2' allows to download the file once again
iatom (int) - number of atom starting from 1 to plot DOS by default it is assumed that the last atom is used
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
xlim, ylim (tuple)- limits for plot
#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.
"""
iatom -= 1
"""1. Read dos"""
printlog("------Start plot_dos()-----", imp = 'Y')
dos = []
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', update = up);
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
"""2. Plot dos for different cases"""
if dostype == 'total':
fit_and_plot(show = show, image_name = os.path.join(path, cl1.name+'.dosTotal'), xlabel = "Energy (eV)", ylabel = "DOS (states/eV)",
xlim = xlim, ylim = ylim,
Total = (dos[0].energy, smoother(dos[0].dos, 10), 'b-'))
elif dostype == 'diff_total':
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)",
xlim = xlim, ylim = ylim,
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
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)
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)
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] # first atom is impurity if exist
printlog("Numbers of local atoms:", [n+1 for n in numbers] )
printlog("List of distances", [round(d,2) for d in local_atoms[3]] )
iX = numbers[0]
for j in range(len(dos)):
dos[j].p = [] #central and and surrounding
dos[j].d = [] #central atom and surrounding atoms
dos[j].d6 = 0 #sum by six atoms
for i in numbers: #Now for surrounding atoms in numbers list:
plist = [dos[j].site_dos(i, l) for l in (1,2,3) ]
dos[j].p.append( [ sum(x) for x in zip(*plist) ] )
dlist = [dos[j].site_dos(i, l) for l in (4,5,6,7,8) ] # For total d T96C
dsum = [ sum(x) for x in zip(*dlist) ]
dos[j].d.append( dsum )
dos[j].p6 = [ sum(pi) for pi in zip(*dos[j].p) ] #sum over neighbouring atoms
dos[j].d6 = [ sum(di) for di in zip(*dos[j].d) ] #sum over neighbouring atoms
# t2g = [dos[0].site_dos(iTi, l) for l in 4,5,7] # Now only for first Ti atom
# dos[0].t2g = [ sum(x) for x in zip(*t2g) ]
# eg = [dos[0].site_dos(iTi, l) for l in 8, 6] # Now only for first Ti atom
# dos[0].eg = [ sum(x) for x in zip(*eg) ]
"""Plotting"""
nsmooth = 15 # smooth of dos
d1 = dos[0]
energy1 = dos[0].energy
args = {}
i_orb = {'s':0, 'py':1, 'pz':2, 'px':3, 'dxy':4, 'dyz':5, 'dz2':6, 'dxz':7, 'dx2':8}
color = {'s':'k-', 'p':'g-', 'd':'b-', 'py':'r-', 'pz':'b-', 'px':'c-', 'dxy':'m-', 'dyz':'c-', 'dz2':'m-', 'dxz':'r-', 'dx2':'g-'}
for orb in orbitals:
if orb == 'p':
args[orb] = (d1.energy, smoother(d1.p[0], nsmooth), color[orb])
elif orb == 'd':
args[orb] = (d1.energy, smoother(d1.d[0], nsmooth), color[orb])
else:
args[orb] = (d1.energy, smoother(d1.site_dos(iX, i_orb[orb]), nsmooth), color[orb])
image_name = os.path.join(path, cl1.name+'.'+''.join(orbitals)+'.'+el+str(iX))
fit_and_plot(show = show, image_name = image_name, figsize = (4,6), xlabel = "Energy (eV)", ylabel = "DOS (states/eV)",
# title = cl1.name.split('.')[0]+'; V='+str(round(cl1.vol) )+' $\AA^3$; Impurity: '+el,
xlim = xlim, ylim = ylim, legend = 2,
**args
)
# printlog("Writing file", image_name, imp = 'Y')
"""Additional dos analysis; to be refined"""
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}
def pairs(in_calc, xcart_pores, central_atoms, prec=2, max_dist=20, max_dist_from_gb=4, pairtyp="gvol"):
"""
Searhing for pairs and make list of distances and numbers of atoms
prec - precision, allows to control which distances can be related to the same configurations
max_dist - maximum distance between atoms in pair
max_dist_from_gb -
pairtyp - 'gvol' assumes that central_atoms are in the grain volume, 'gb' assumes that central_atoms are in the grain boundary region
"""
st = in_calc.init
st_replic = replic(st, (2, 2, 2))
st_replic = replic(st_replic, (2, 2, 2), -1) # replic in negative direction also
r1x = in_calc.rprimd[0][0]
r3z = in_calc.rprimd[2][2]
print "Half length of r1x is", r1x / 2
if segtyp in ["segreg", "coseg", "grainvol"]:
gbpos2 = in_calc.gbpos
gbpos1 = gbpos2 - r1x / 2.0
print "\n\nPositions of boundaries gb1 and gb2", gbpos1, gbpos2
print "Maximum possible distance between boundary and impurity", r1x / 4
else:
gbpos2 = 0
gbpos1 = 0
dlist = []
d1list = []
d2list = []
dgb2list = []
n_neighbours = 8 # number of atoms to calculate sums
sumrulist = [] # list of sums (sumr1 or sumr2) of unique pores
unique_pores = [] # the same list but also with coordinates of pores
sumrlist = [] # list of sumr1+sumr2
k = 1
d2diff = 0
d1diff = 0
# z1 = 6 #charge of added impurity
# z2 = 8
diffprec = 0.02
# print xcart_pores
for i, x1 in enumerate(xcart_pores):
if i not in central_atoms:
continue
# iz = z1
for j, x2 in enumerate(xcart_pores):
if all(x1 == x2):
continue
d = abs(x2[0] - in_calc.gbpos)
if pairtyp == "gb" and d > max_dist_from_gb:
continue # second atom is too far from grain boundary
d1, d2 = image_distance(x1, x2, st.rprimd, 2) # the minimum distance and the next minimum dist
if d1 > max_dist:
continue
if (d1, d2) != image_distance(x1, x2, st.rprimd, 3):
raise RuntimeError # test, searching in father images
# d1 = round(d1,prec)
# d2 = round(d2,prec)
dgb1 = round(x2[0] - gbpos1, prec)
dgb2 = round(gbpos2 - x2[0], prec)
sumr1 = local_surrounding(x1, st_replic, n_neighbours) # sum of distances to surrounding atoms
sumr2 = local_surrounding(x2, st_replic, n_neighbours)
sumr = sumr2 + sumr1
if sumr1 not in sumrulist:
sumrulist.append(sumr1)
unique_pores.append((sumr1, x1)) # determine unique pores
if sumr2 not in sumrulist:
sumrulist.append(sumr2)
unique_pores.append((sumr2, x2)) # determine unique pores
# if d1 in d1list: continue
if sumr in sumrlist: # new condition based on sumr
ind = sumrlist.index(sumr)
i_min, smaller = min_diff(d1, d1list, diffprec)
if smaller:
continue
# if 0:#d1list:
# i_min, smaller = min_diff(d1, d1list, diffprec)# d1 has the smallest difference with di
# #print "exist"
# d2diff = abs(d2list[i_min]-d2)
# #print abs(d2list[i_min]-d2)
# #print central_atoms
# if smaller and abs(d2list[i_min]-d2) < diffprec*2 : continue #and abs(dgb2list[i_min]-dgb2) < diffprec
# i_min, smaller = min_diff(d2, d2list, diffprec)# d1 has the smallest difference with di
# d1diff = abs(d1list[i_min]-d1)
# if smaller and abs(d1list[i_min]-d1) < diffprec*2 : continue
# print "skiped"
# di, smaller = min_diff(d2, d2list, diffprec)
# if di != None and smaller: continue
# if min_diff(d2, d2list, diffprec): continue # be carefull here. this condition can pass some unique configrations; should make additional check like below
# if d2 in d2list and dgb2list[d2list.index(d2)] == dgb2: continue
# jz = z2
sumrlist.append(sumr)
d1list.append(d1)
# d2list.append(d2)
# dgb2list.append(dgb2)
sym = ""
if 0: # mannualy switched off
if abs(x1[1] - x2[1]) < diffprec: # Find symmetry
if abs(x1[2] - x2[2]) < diffprec:
sym = "ms" # if y and z are the same, than mirror symmetry
elif abs(x1[2] - x2[2]) - r3z < diffprec:
sym = "is" # inverse symmtry
elif (
abs(x1[2] + x2[2]) - 0.5 * r3z < diffprec
): # only for t111g; should be extended for general case of existing periods along y or z
sym = "is"
dlist.append(
[round(d1, prec), round(d2, prec), sym, sumr1, sumr2, dgb1, dgb2, x1, x2, sumr1, sumr2]
) # the first sumr1, sumr2 below replaced by their types
k += 1
dlist.sort(key=itemgetter(0))
unique_pores.sort(key=itemgetter(0))
sumrulist.sort()
print "Number of unique pores is", len(unique_pores)
print "Pores have the following sums: ", unique_pores
print "Searching for similar pairs but with different distances ..."
print "number, d1, d2, name, sumr1, sumr2, dgb1, dgb2; parallel pair with larger distances"
bname = element_name_inv(target_znucl[1]) + element_name_inv(target_znucl[2])
for i, el1 in enumerate(dlist):
typ1 = sumrulist.index(el1[3]) + 1 # typ of pore of the first atom
typ2 = sumrulist.index(el1[4]) + 1
el1[3] = typ1
el1[4] = typ2
if pairtyp == "gb":
dlist[i][2] = bname + "i" + str(i + 1) + "." + str(el1[3]) + "-" + str(el1[4]) + dlist[i][2]
elif pairtyp == "gvol":
dlist[i][2] = bname + ".v" + str(i + 1) + dlist[i][2]
print i + 1, el1[:3], el1[-2:], el1[-6], el1[-5], # number, d1, d2, name, sumr1, sumr2, dgb1, dgb2
for (
el2
) in (
dlist
): # this loop looks for pairs which are parallel to the same direction as el1 but have larger interdistances
if el1 == el2:
continue
mod = el2[0] / el1[0] % 1
if (mod < 0.005 or mod > 0.995) and abs(el1[0] - el2[0]) > dlist[0][
0
]: # only multiple distances and if difference is larger than smallest distance
# if round(el1[2],prec-1) != round(el2[2],prec-1): continue #In either case the sum the distances should be the same for the same direction
if el1[0] == el2[1]:
continue
print el2[0] / el1[0], # el2, this pair of atoms is analogus to el1 but have larger interdistance
print
print "Total number of structures is", len(dlist)
if 0:
print "\n\nSearching for pairs with equal distances by periodic boundary conditions:"
for el1 in dlist:
if el1[0] == el1[1]:
print el1
print "\nSearching for pairs with not equal distances by periodic boundary conditions:"
for el1 in dlist:
if el1[0] != el1[1]:
print el1
print "\nSearching for pairs with d2/d1>2:"
for el1 in dlist:
if el1[1] / el1[0] > 2:
print el1
dlist[0].append(unique_pores) # last element of dlist[0] is sum and coordinates of unique pores
return dlist
def pairs(in_calc,
xcart_pores,
central_atoms,
prec=2,
max_dist=20,
max_dist_from_gb=4,
pairtyp='gvol'):
"""
Searhing for pairs and make list of distances and numbers of atoms
prec - precision, allows to control which distances can be related to the same configurations
max_dist - maximum distance between atoms in pair
max_dist_from_gb -
pairtyp - 'gvol' assumes that central_atoms are in the grain volume, 'gb' assumes that central_atoms are in the grain boundary region
"""
st = in_calc.init
st_replic = replic(st, (2, 2, 2))
st_replic = replic(st_replic, (2, 2, 2),
-1) #replic in negative direction also
r1x = in_calc.rprimd[0][0]
r3z = in_calc.rprimd[2][2]
print "Half length of r1x is", r1x / 2
if segtyp in ['segreg', 'coseg', 'grainvol']:
gbpos2 = in_calc.gbpos
gbpos1 = gbpos2 - r1x / 2.
print "\n\nPositions of boundaries gb1 and gb2", gbpos1, gbpos2
print "Maximum possible distance between boundary and impurity", r1x / 4
else:
gbpos2 = 0
gbpos1 = 0
dlist = []
d1list = []
d2list = []
dgb2list = []
n_neighbours = 8 # number of atoms to calculate sums
sumrulist = [] #list of sums (sumr1 or sumr2) of unique pores
unique_pores = [] #the same list but also with coordinates of pores
sumrlist = [] #list of sumr1+sumr2
k = 1
d2diff = 0
d1diff = 0
#z1 = 6 #charge of added impurity
#z2 = 8
diffprec = 0.02
# print xcart_pores
for i, x1 in enumerate(xcart_pores):
if i not in central_atoms: continue
#iz = z1
for j, x2 in enumerate(xcart_pores):
if all(x1 == x2): continue
d = abs(x2[0] - in_calc.gbpos)
if pairtyp == 'gb' and d > max_dist_from_gb:
continue #second atom is too far from grain boundary
d1, d2 = image_distance(
x1, x2, st.rprimd,
2) # the minimum distance and the next minimum dist
if d1 > max_dist: continue
if (d1, d2) != image_distance(x1, x2, st.rprimd, 3):
raise RuntimeError #test, searching in father images
#d1 = round(d1,prec)
#d2 = round(d2,prec)
dgb1 = round(x2[0] - gbpos1, prec)
dgb2 = round(gbpos2 - x2[0], prec)
sumr1 = local_surrounding(
x1, st_replic,
n_neighbours) # sum of distances to surrounding atoms
sumr2 = local_surrounding(x2, st_replic, n_neighbours)
sumr = sumr2 + sumr1
if sumr1 not in sumrulist:
sumrulist.append(sumr1)
unique_pores.append((sumr1, x1)) #determine unique pores
if sumr2 not in sumrulist:
sumrulist.append(sumr2)
unique_pores.append((sumr2, x2)) #determine unique pores
#if d1 in d1list: continue
if sumr in sumrlist: # new condition based on sumr
ind = sumrlist.index(sumr)
i_min, smaller = min_diff(d1, d1list, diffprec)
if smaller: continue
# if 0:#d1list:
# i_min, smaller = min_diff(d1, d1list, diffprec)# d1 has the smallest difference with di
# #print "exist"
# d2diff = abs(d2list[i_min]-d2)
# #print abs(d2list[i_min]-d2)
# #print central_atoms
# if smaller and abs(d2list[i_min]-d2) < diffprec*2 : continue #and abs(dgb2list[i_min]-dgb2) < diffprec
# i_min, smaller = min_diff(d2, d2list, diffprec)# d1 has the smallest difference with di
# d1diff = abs(d1list[i_min]-d1)
# if smaller and abs(d1list[i_min]-d1) < diffprec*2 : continue
#print "skiped"
#di, smaller = min_diff(d2, d2list, diffprec)
#if di != None and smaller: continue
#if min_diff(d2, d2list, diffprec): continue # be carefull here. this condition can pass some unique configrations; should make additional check like below
#if d2 in d2list and dgb2list[d2list.index(d2)] == dgb2: continue
#jz = z2
sumrlist.append(sumr)
d1list.append(d1)
# d2list.append(d2)
# dgb2list.append(dgb2)
sym = ''
if 0: #mannualy switched off
if abs(x1[1] - x2[1]) < diffprec: #Find symmetry
if abs(x1[2] - x2[2]) < diffprec:
sym = 'ms' # if y and z are the same, than mirror symmetry
elif abs(x1[2] - x2[2]) - r3z < diffprec:
sym = 'is' # inverse symmtry
elif abs(
x1[2] + x2[2]
) - 0.5 * r3z < diffprec: # only for t111g; should be extended for general case of existing periods along y or z
sym = 'is'
dlist.append([
round(d1, prec),
round(d2, prec), sym, sumr1, sumr2, dgb1, dgb2, x1, x2,
sumr1, sumr2
]) #the first sumr1, sumr2 below replaced by their types
k += 1
dlist.sort(key=itemgetter(0))
unique_pores.sort(key=itemgetter(0))
sumrulist.sort()
print 'Number of unique pores is', len(unique_pores)
print 'Pores have the following sums: ', unique_pores
print "Searching for similar pairs but with different distances ..."
print "number, d1, d2, name, sumr1, sumr2, dgb1, dgb2; parallel pair with larger distances"
bname = element_name_inv(target_znucl[1]) + element_name_inv(
target_znucl[2])
for i, el1 in enumerate(dlist):
typ1 = sumrulist.index(el1[3]) + 1 #typ of pore of the first atom
typ2 = sumrulist.index(el1[4]) + 1
el1[3] = typ1
el1[4] = typ2
if pairtyp == 'gb':
dlist[i][2] = bname + 'i' + str(i + 1) + '.' + str(
el1[3]) + '-' + str(el1[4]) + dlist[i][2]
elif pairtyp == 'gvol':
dlist[i][2] = bname + '.v' + str(i + 1) + dlist[i][2]
print i + 1, el1[:3], el1[-2:], el1[-6], el1[
-5], #number, d1, d2, name, sumr1, sumr2, dgb1, dgb2
for el2 in dlist: #this loop looks for pairs which are parallel to the same direction as el1 but have larger interdistances
if el1 == el2: continue
mod = el2[0] / el1[0] % 1
if (mod < 0.005 or mod > 0.995
) and abs(el1[0] - el2[0]) > dlist[0][
0]: #only multiple distances and if difference is larger than smallest distance
#if round(el1[2],prec-1) != round(el2[2],prec-1): continue #In either case the sum the distances should be the same for the same direction
if el1[0] == el2[1]: continue
print el2[0] / el1[
0], # el2, this pair of atoms is analogus to el1 but have larger interdistance
print
print 'Total number of structures is', len(dlist)
if 0:
print "\n\nSearching for pairs with equal distances by periodic boundary conditions:"
for el1 in dlist:
if el1[0] == el1[1]:
print el1
print "\nSearching for pairs with not equal distances by periodic boundary conditions:"
for el1 in dlist:
if el1[0] != el1[1]:
print el1
print "\nSearching for pairs with d2/d1>2:"
for el1 in dlist:
if el1[1] / el1[0] > 2:
print el1
dlist[0].append(
unique_pores
) # last element of dlist[0] is sum and coordinates of unique pores
return dlist