def neb_analysis(cl,
show,
up=None,
push2archive=None,
old_behaviour=None,
results_dic=None,
fitplot_args=None,
style_dic=None,
params=None):
"""
Analyse traectories and polarons
params
mep_shift_vector
"""
def determing_rms_for_surrounding_atoms(sts):
# change of rms on each step compared to first structure
#here first and last structures should correspond to first and last images
st1 = sts[0]
st_interp = interpolate(sts[0], sts[-1], 1)[0]
rms_list = []
for st in sts:
rms = rms_pos_diff(st_interp, st)
rms_list.append(rms)
print('rms is {:.3f}'.format(rms))
print('d rms is {:.3f}'.format(abs(rms_list[3] - rms_list[0])))
rms_change = abs(min(rms_list) - max(rms_list))
return rms_change
def determing_born_barrier(sts):
#here first and last structures should correspond to first and last images
local_born_e = []
i = find_moving_atom(sts[0], sts[-1])
for st in sts:
local_born_e.append(site_repulsive_e(st, i))
# import matplotlib.pyplot as plt
# plt.plot(local_born_e)
# plt.show()
return abs(min(local_born_e) - max(local_born_e))
if params is None:
params = {}
if results_dic is None:
results_dic = {}
calc = header.calc
path2mep_s = cl.project_path_cluster + '/' + cl.dir + '/mep.eps'
itise = cl.id[0] + '.' + cl.id[1]
# print(cl.ldauu)
# sys.exit()
name_without_ext = 'mep.' + itise + '.U' + str(max(cl.ldauu))
path2mep_l = cl.dir + name_without_ext + '.eps'
# print(path2mep_l)
if not os.path.exists(path2mep_l) or '2' in up:
''
get_from_server(
files=path2mep_s,
to_file=path2mep_l,
addr=cl.cluster_address,
)
movie_to = cl.dir + '/movie.xyz'
get_from_server(
files=cl.project_path_cluster + '/' + cl.dir + '/movie.xyz',
to_file=movie_to,
addr=cl.cluster_address,
)
if os.path.exists(movie_to):
makedir('figs/' + name_without_ext + '.xyz')
shutil.copyfile(movie_to, 'figs/' + name_without_ext + '.xyz')
# trying to get one image closest to the saddle point
if old_behaviour and cl.version == 2: #old behaviour, now created automatically in add callc
im = cl.set.vasp_params['IMAGES']
# if im % 2 > 0: #odd
# i = im//2 + 1
# else:
# i = im/2
# if choose_image:
# i = choose_image
for i in range(im):
i += 1
cl_i = copy.deepcopy(cl)
cl_i.version += i
cl_i.id = (cl.id[0], cl.id[1], cl_i.version)
cl_i.name = str(cl_i.id[0]) + '.' + str(cl_i.id[1]) + '.' + str(
cl_i.id[2])
# print cl_i.name
cl_i.path["output"] = cl_i.dir + '0' + str(i) + "/OUTCAR"
# for i in range():
cl_i.associated_outcars = [
aso[2:] for aso in cl_i.associated_outcars
]
# print cl_i.path["output"]
cl_i.state = '2. Ready to read outcar'
# if not os.path.exists(cl_i.path["output"]):
# load = 'o'
outst2 = ("%s" % cl_i.name).ljust(name_field_length)
if readfiles:
print(outst2 + '|' + cl_i.read_results(
loadflag, show=show, choose_outcar=choose_outcar))
else:
print_and_log(outst2 + ' | File was not read')
if cl_i.id in calc: #move creation of calcs with images to add_neb
''
# print_and_log('Please test code below this message to save prev calcs')
# if cl_i != calc[cl_i.id]
# if hasattr(calc[cl_i.id], 'prev') and calc[cl_i.id].prev:
# prevlist = calc[cl_i.id].prev
# else:
# prevlist = [calc[cl_i.id]]
# cl_i.prev = prevlist
# calc[cl_i.id] = cl_i
else:
calc[cl_i.id] = cl_i
# print path2mep_l
if 0:
if os.path.exists(path2mep_l):
# get_from_server(file = path2mep_s, to = path2mep_l, addr = cluster_address)
runBash('evince ' + path2mep_l)
else:
a = glob.glob(cl.dir + '*mep*')
if a:
runBash('evince ' + a[0])
cl1 = calc[cl.id[0], cl.id[1], 1]
cl2 = calc[cl.id[0], cl.id[1], 2]
atom_num = find_moving_atom(cl1.end, cl2.end)
# cl1.poscar()
# cl2.poscar()
# print('atom_num',atom_num)
# sys.exit()
#prepare lists
ni = cl.set.vasp_params['IMAGES']
vlist = [1] + list(range(3, ni + 3)) + [2]
# print( vlist)
mep_energies = []
atom_pos = []
pols = []
sts = []
sts_loc = []
dAO2 = [] # A-(O,F) distance for each image
dAO4 = [] # A-(O,F) distance for each image
dAO6 = []
dAO6harm = []
dAO6dev = []
for v in vlist:
cli = calc[cl.id[0], cl.id[1], v]
# if v == 1:
# cli = db['NaVP2O7_a.su.s101015v100.n5Na1v1ms.ifn.1mls.1']
# print(cl.id[0], cl.id[1], v, cli.state)
if '4' not in cli.state and 'un' not in up:
printlog('Attention! res_loop(): analys_type == neb, Calc', cli.id,
'is not finished; return')
return {}, []
# print cli.id
# cli.end = return_to_cell(cli.end)
# mep_energies.append( min(cli.list_e_sigma0) ) #use minimum energy - not very good, sometimes unconverged energy could be lower!
e0 = cli.energy_sigma0
if params and params.get(
'neb_penult_e'
): # allows to take e from the previous relaxation step in case the calculation was aborted
e0 = cli.list_e_sigma0[-2]
mep_energies.append(e0) #use last energy
atom_pos.append(cli.end.xcart[atom_num])
# Find polaron positions
if 'polaron' in show: # if 1 cause error for nomag calc
pol, mag = find_polaron(cli.end, atom_num)
if pol:
for key in pol:
if np.any(pol[key]):
for n in pol[key]:
if n not in pols:
pols.append(n)
else:
''
# print('Mag_moments on trans,', mag.round(1))
if 0 or 'neb_geo' in show:
#visualization of path
# print(atom_num)
st = copy.deepcopy(cli.end)
# print('moving_atom', st.xcart[atom_num])
info = st.nn(atom_num, 15, from_one=False, silent=1)
st.moving_atom_i = atom_num
st_loc = info['st']
# print(st_loc.xcart)
# st_loc = st_loc.shift
if v == vlist[0]:
st1 = copy.deepcopy(st)
vec = st.center_on(atom_num)
# vec = np.asarray([0.,0.,0.])
if params is not None and 'mep_shift_vector' in params:
# vec += np.array([0.11,0.11,0]) # path4
# print(params['mep_shift_vector'])
vec += np.array(params['mep_shift_vector']) # path4
# print(vec)
st_loc = st_loc.shift_atoms(vec)
if 0:
st_loc.write_xyz()
# st.write_cif('xyz/'+st.name)
if 0:
st.shift_atoms(vec).write_xyz()
sts_loc.append(st_loc)
st1 = st1.add_atom(st.xred[atom_num], 'Rb')
sts.append(st.shift_atoms(vec))
if 0 or 'neb_geo2' in show:
printlog('\n\nVersion {:}:'.format(v), imp='y')
info1 = st.nn(atom_num,
2,
from_one=False,
silent=1,
more_info=1)
print('Av. dist A-2(O,F) {:.3f} A'.format(
info1['av(A-O,F)']))
# print('Av. squared dist A-2(O,F) {:.3f} A'.format(info1['avsq(A-O,F)']))
dAO2.append(info1['av(A-O,F)'])
info12 = st.nn(atom_num, 3, from_one=False, silent=1)
print('Average distance A-3(O,F) {:.2f} A'.format(
info12['av(A-O,F)']))
info2 = st.nn(atom_num, 4, from_one=False, silent=1)
print('Average distance A-4(O,F) {:.2f} A'.format(
info2['av(A-O,F)']))
dAO4.append(info2['av(A-O,F)'])
info3 = st.nn(atom_num,
6,
from_one=False,
silent=1,
more_info=1)
print('Average_distance A-6(O,F) {:.2f} A '.format(
info3['av(A-O,F)']))
print('Av. harm. dist A-6(O,F) {:.2f} A'.format(
info3['avharm(A-O,F)']))
print('Average_deviation A-6(O,F) {:.1f} mA'.format(
info3['avdev(A-O,F)']))
dAO6.append(info3['av(A-O,F)'])
dAO6dev.append(info3['avdev(A-O,F)'])
dAO6harm.append(info3['avharm(A-O,F)'])
if 'neb_rms' in show:
rms_change = determing_rms_for_surrounding_atoms(sts)
results_dic['rms_change'] = rms_change
if 'neb_born' in show:
results_dic['born_barrier'] = determing_born_barrier(sts)
print('Born barrier is {:.2f} eV '.format(results_dic['born_barrier']))
# print(results_dic['rms_change'])
# print('show is', show)
# sys.exit()
# print('flag ', 'neb_noxyz' not in show, show)
if 'neb_noxyz' not in show and sts:
write_xyz(sts=sts) # write traectory
write_xyz(sts=sts_loc) # write traectory
if 'jmol' in params:
write_xyz(sts=sts, jmol=1, jmol_args=params['jmol']) # write jmol
st1 = st1.shift_atoms(vec)
st1.name += '_all'
# st1.write_cif('xyz/'+st1.name)
st1.write_xyz()
if dAO2: # find maximum change of distance during migration
dAO2_change = abs(min(dAO2) - max(dAO2))
results_dic['dAO2_change'] = dAO2_change
if dAO4: # find maximum change of distance during migration
dAO4_change = abs(min(dAO4) - max(dAO4))
results_dic['dAO4_change'] = dAO4_change
if dAO6: #
dAO6_change = abs(min(dAO6) - max(dAO6))
results_dic['dAO6_change'] = dAO6_change
if dAO6harm: #
results_dic['dAO6harm_change'] = abs(min(dAO6harm) - max(dAO6harm))
if dAO6dev: #
results_dic['dAO6dev_change'] = abs(min(dAO6dev) - max(dAO6dev))
results_dic[
'sts_loc'] = sts_loc # list of local structures, each structure contains dlist - distances from central cation to anions, and ellist - types of elements
results_dic[
'sts'] = sts # list of mep structures, each structure contains moving_atom_i - number of moving atom
if len(pols) > 0:
print(
'During migration of alkali ions polarons are detected on atoms:',
pols)
elif len(pols) > 1:
printlog(
'Attention! polaron is moving during migration! Obtained barrier is ambiguous'
)
else:
printlog(
'Compare magnetic moments above! In principle should be the same!')
# print np.array(atom_pos)
#test if the distances between points are not spoiled by PBC
nbc = range(-1, 2)
jj = 0
for x in atom_pos:
x2 = atom_pos[jj + 1]
# x = np.array(x)
# x2 = np.array(x2)
r = cl.end.rprimd
d1, _ = image_distance(x, x2, r, order=1) #minimal distance
x2_gen = (x2 + (r[0] * i + r[1] * j + r[2] * k) for i in nbc
for j in nbc for k in nbc) #generator over PBC images
x2c = copy.deepcopy(x2)
ii = 0
while np.linalg.norm(x -
x2c) > d1: #find the closest PBC image position
if ii > 100:
break
ii += 1
x2c = next(x2_gen)
atom_pos[jj + 1] = x2c
jj += 1
if jj == len(
atom_pos
) - 1: # the last point is not needed, we could not use slice since we need to use changed atom_pos in place
break
# print np.linalg.norm(x - x2c), d1
_, diff_barrier = plot_mep(atom_pos,
mep_energies,
plot=0,
show=0,
fitplot_args=fitplot_args,
style_dic=style_dic)
results_dic['barrier'] = diff_barrier
middle_image = len(vlist) // 2
results_dic['dEm1'] = mep_energies[middle_image] - mep_energies[0]
cl1.barrier = diff_barrier
cl2.barrier = diff_barrier
results_dic['atom_pos'] = [list(pos) for pos in atom_pos]
results_dic['mep_energies'] = mep_energies
if 'mep' in show:
if 'mepp' in show:
show_flag = True
else:
show_flag = False
# sys.exit()
plot_mep(atom_pos,
mep_energies,
image_name='figs/' + name_without_ext + '_my.eps',
show=show_flag,
fitplot_args=fitplot_args,
style_dic=style_dic)
if push2archive:
path2saved, _ = plot_mep(atom_pos,
mep_energies,
image_name='figs/' + name_without_ext + '_my',
fitplot_args=fitplot_args,
style_dic=style_dic)
push_figure_to_archive(local_figure_path=path2saved,
caption=description_for_archive)
if 0: #copy files according to chosen outcar to run nebresults locally
wd = cl_i.dir
out_i = cl_i.associated_outcars[choose_outcar - 1]
out_1 = calc[cl.id[0], cl.id[1],
1].associated_outcars[choose_outcar - 1]
out_2 = calc[cl.id[0], cl.id[1],
2].associated_outcars[choose_outcar - 1]
# print out_1
# print out_2
shutil.copyfile(wd + out_1, wd + '00/OUTCAR')
shutil.copyfile(wd + out_2, wd + '04/OUTCAR')
for d in ['01/', '02/', '03/']:
shutil.copyfile(wd + d + out_i, wd + d + 'OUTCAR')
# print wd+d+out_i
return results_dic
def fit_a(conv, n, description_for_archive, analysis_type, show, push2archive):
"""Fit equation of state for bulk systems.
The following equation is used::
sjeos (default)
A third order inverse polynomial fit 10.1103/PhysRevB.67.026103
2 3 -1/3
E(V) = c + c t + c t + c t , t = V
0 1 2 3
taylor
A third order Taylor series expansion about the minimum volume
murnaghan
PRB 28, 5480 (1983)
birch
Intermetallic compounds: Principles and Practice,
Vol I: Principles. pages 195-210
birchmurnaghan
PRB 70, 224107
pouriertarantola
PRB 70, 224107
vinet
PRB 70, 224107
antonschmidt
Intermetallics 11, 23-32 (2003)
p3
A third order polynomial fit
Use::
eos = EquationOfState(volumes, energies, eos='sjeos')
v0, e0, B = eos.fit()
eos.plot()
"""
# e, v, emin, vmin = plot_conv( conv[n], calc, "fit_gb_volume2")
alist = []
vlist = []
etotlist = []
magn1 = []
magn2 = []
alphas = []
for id in conv[n]:
cl = db[id]
st = cl.end
alist.append(cl.end.rprimd[0][0])
etotlist.append(cl.energy_sigma0)
vlist.append(cl.end.vol)
magn1.append(cl.magn1)
magn2.append(cl.magn2)
alpha, beta, gamma = st.get_angles()
alphas.append(alpha)
print('alpha, energy: {:4.2f}, {:6.3f}'.format(alpha,
cl.energy_sigma0))
fit_and_plot(U1=(alphas, etotlist, 'o-r'),
image_name='figs/angle',
ylabel='Total energy, eV',
xlabel='Angle, deg',
xlim=(89, 92.6))
if ase_flag:
if 'angle' in analysis_type:
eos = EquationOfState(alphas, etotlist, eos='sjeos')
else:
eos = EquationOfState(vlist, etotlist, eos='sjeos')
# import inspect
# print (inspect.getfile(EquationOfState))
v0, e0, B = eos.fit()
#print "c = ", clist[2]
printlog('''
v0 = {0} A^3
a0 = {1} A
E0 = {2} eV
B = {3} eV/A^3'''.format(v0, v0**(1. / 3), e0, B),
imp='Y')
savedpath = 'figs/' + cl.name + '.png'
makedir(savedpath)
cl.B = B * 160.218
# plt.close()
# plt.clf()
# plt.close('all')
if 'fit' in show:
mpl.rcParams.update({'font.size': 14})
eos.plot(savedpath, show=True)
printlog('fit results are saved in ', savedpath, imp='y')
else:
printlog('To use fitting install ase: pip install ase')
# plt.clf()
if push2archive:
push_figure_to_archive(local_figure_path=savedpath,
caption=description_for_archive)
return