def chgsum(cll, el, site, silent = 1):
"""
calculate sum of Bader charges for particular atoms
"""
for cl in cll:
# print(cl.id, end = ' ')
try:
cl.chgsum[(el, site)] = 0
except:
pass
if not hasattr(cl, 'charges') or len(cl.charges) == 0:
cl.get_bader_ACF()
# determine_symmetry_positions(cl.end, el, silent = 0)
# print('')
try:
pos = determine_symmetry_positions(cll[0].end, el, silent = 1)
except:
printlog('chgsum() Warning!', cll[0].id, 'is broken!')
return 0
for p in pos[site]:
''
for cl in cll:
if not hasattr(cl, 'chgsum'):
cl.chgsum = {}
cl.chgsum[(el, site)] = 0
cl.chgsum[(el, site)] += cl.charges[p]
# print('{:5.3f}'.format(cl.charges[p]), end = ' ')
# print('')
if not silent:
print('Sum of charges for ', el+str(site+1), ':')
el_ind = cl.init.znucl.index(invert(el)) # index of element in znucl and zval and nznucl
zval = cl.init.zval[el_ind] # number of electrons in chosen potential
for cl in cll:
cl.chgsum[(el, site)]/=len(pos[site])
chgsum = zval - cl.chgsum[(el, site)]
if cl == cll[0]:
chgsum_ref = chgsum
if not silent:
print('{:5.2f}({:4.2f})'.format(chgsum, chgsum_ref-chgsum), end = ' ')
if not silent:
print('\n')
# print(cl.charges)
return chgsum
def form_en(sources, products, norm_el = None):
"""
Calculate formation energy of reaction
sources, products - list of tuples (x, cl), where x is multiplier and cl is calculation
norm_el - which element to use for normalization
'all' - normalize by total number of atoms
"""
El = []
Nzl = []
for ls in [sources, products]:
E = 0
Nz = {}
for x, cl in ls:
E += x*cl.e0
for i, z in enumerate(cl.end.znucl):
if z not in Nz:
Nz[z] = 0
Nz[z] += x*cl.end.nznucl[i]
El.append(E)
Nzl.append(Nz)
for z in Nzl[0]:
if abs(Nzl[0][z] - Nzl[1][z]) > 1e-5:
printlog('Error! Number of', invert(z), 'atoms in source and product are different!')
# norm = 1
if 'all' == norm_el:
norm = sum(Nzl[0].values())
elif type(norm_el) == str:
norm = Nzl[0][invert(norm_el)]
elif norm_el != None:
norm = norm_el
else:
norm = 1
# print('Normalizing by ', norm_el, norm, 'atoms')
print('dE = {:4.2f} eV'.format((El[1]-El[0])/norm))
def set_potential(self,znucl, arg = ''):
# print arg
if not arg:
arg = header.PATH2POTENTIALS+'/'+invert(znucl)
printlog('Attention!, Default potentials is chosen from ',header.PATH2POTENTIALS, 'for',invert(znucl) , imp ='Y')
if type(arg) not in (str,):
# sys.exit("\nset_potential error\n")
raise RuntimeError
if znucl in self.potdir:
if arg == self.potdir[znucl]:
print_and_log( "Warning! You already have the same potential for "+str(znucl)+" element\n" )
# print type(self.potdir)
self.potdir[znucl] = arg
self.history += "Potential for "+str(znucl)+" was changed to "+arg+"\n"
print_and_log( "Potential for "+str(znucl)+" was changed to "+arg+"\n" )
# self.update()
return
else:
cases = case_raw.keys()
if vectors == 'Binary':
# Take log base 2 to figure out how many bits we need for each
human_size = int(ceil(log(len(human), 2))) # 2
dec_size = int(ceil(log(len(declensions), 2))) # 3
gen_size = int(ceil(log(len(genders), 2))) # 2
case_size = int(ceil(log(len(cases), 2))) # 3
if casenum_sep == True:
num_size = int(ceil(log(len(numbers), 2))) # 1
# Now make two way dictionary with bit vectors
human_dict = functions.binaryDict(human)
dec_dict = functions.binaryDict(declensions)
dec_dict.update(functions.invert(dec_dict))
gen_dict = functions.binaryDict(genders)
gen_dict.update(functions.invert(gen_dict))
case_dict = functions.binaryDict(cases)
case_dict.update(functions.invert(case_dict))
if casenum_sep == True:
num_dict = functions.binaryDict(numbers)
num_dict.update(functions.invert(num_dict))
# Identity vectors
else:
human_size = len(human)
dec_size = len(declensions)
gen_size = len(genders)
case_size = len(cases)
if casenum_sep == True:
num_size = len(numbers)
else:
cases = case_raw.keys()
if vectors == 'Binary':
# Take log base 2 to figure out how many bits we need for each
human_size = int(ceil(log(len(human), 2))) # 2
dec_size = int(ceil(log(len(declensions), 2))) # 3
gen_size = int(ceil(log(len(genders), 2))) # 2
case_size = int(ceil(log(len(cases), 2))) # 3
if casenum_sep == True:
num_size = int(ceil(log(len(numbers), 2))) # 1
# Now make two way dictionary with bit vectors
human_dict = functions.binaryDict(human)
dec_dict = functions.binaryDict(declensions)
dec_dict.update(functions.invert(dec_dict))
gen_dict = functions.binaryDict(genders)
gen_dict.update(functions.invert(gen_dict))
case_dict = functions.binaryDict(cases)
case_dict.update(functions.invert(case_dict))
if casenum_sep == True:
num_dict = functions.binaryDict(numbers)
num_dict.update(functions.invert(num_dict))
# Identity vectors
else:
human_size = len(human)
dec_size = len(declensions)
gen_size = len(genders)
case_size = len(cases)
if casenum_sep == True:
num_size = len(numbers)
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
########
# Read in corpus
(corpus, suffixes) = objects.readCorpus(constants.corpus_file)
# Determine corpus size from this
corpus_size = len(corpus)
# Create suffix dictionary
if constants.vectors == 'binary':
suffix_size = int(ceil(log(len(suffixes), 2))) # 6
suffix_dict = functions.binaryDict(suffixes)
else:
suffix_size = len(suffixes)
suffix_dict = dict(zip(suffixes, map(tuple, identity(suffix_size))))
suf_to_tup = functions.invert(suffix_dict)
suffix_dict.update(functions.invert(suffix_dict))
##########
# OUTPUT #
##########
# Output layer will be list of potential suffixes, gathered from corpus
output_nodes = suffix_size
# Print information
print '''Training on %d Epochs
Number of Input Nodes: %d
Number of Hidden Nodes: %d
Number of Output Nodes: %d
Token Frequency taken into account: %s\n''' % (
# Determine corpus size from this
corpus_size = len(corpus)
root_size = int(ceil(log(corpus_size, 2)))
# Create suffix dictionary
suf_dict = {}
for suffix in suffixes:
phon_suf = functions.reworkSuffix(suffix)
feat_suf = ()
for phoneme in ''.join(phon_suf):
feat_suf += constants.phon_to_feat[phoneme]
suf_dict[suffix] = feat_suf
inv_suf = functions.invert(suf_dict)
# TOTAL input bits
# If binary and casenum separate: 9 + 2 + 3 + 2 + 3 + 1 = 20
# If binary and casenum together: 9 + 2 + 3 + 2 + 4 = 20
# If identity and casenum separate: 9 + 3 + 5 + 3 + 5 + 2 = 27
# If identity and casenum together: 9 + 3 + 5 + 3 + 10 = 30
input_nodes = sum([root_size, constants.human_size, constants.dec_size, constants.gen_size, constants.case_size])
if constants.casenum_sep == True:
input_nodes += constants.num_size
##########
# OUTPUT #
##########
# # Output layer will be list of potential suffixes, gathered from corpus
########
# Read in corpus
(corpus, suffixes) = objects.readCorpus(constants.corpus_file)
# Determine corpus size from this
corpus_size = len(corpus)
# Create suffix dictionary
if constants.vectors == 'binary':
suffix_size = int(ceil(log(len(suffixes), 2))) # 6
suffix_dict = functions.binaryDict(suffixes)
else:
suffix_size = len(suffixes)
suffix_dict = dict(zip(suffixes, map(tuple, identity(suffix_size))))
suf_to_tup = functions.invert(suffix_dict)
suffix_dict.update(functions.invert(suffix_dict))
##########
# OUTPUT #
##########
# Output layer will be list of potential suffixes, gathered from corpus
output_nodes = suffix_size
# Print information
print '''Training on %d Epochs
Number of Input Nodes: %d
Number of Hidden Nodes: %d
Number of Output Nodes: %d
Token Frequency taken into account: %s\n''' % (
# Determine corpus size from this
corpus_size = len(corpus)
root_size = int(ceil(log(corpus_size, 2)))
# Create suffix dictionary
suf_dict = {}
for suffix in suffixes:
phon_suf = functions.reworkSuffix(suffix)
feat_suf = ()
for phoneme in ''.join(phon_suf):
feat_suf += constants.phon_to_feat[phoneme]
suf_dict[suffix] = feat_suf
inv_suf = functions.invert(suf_dict)
# TOTAL input bits
# If binary and casenum separate: 9 + 2 + 3 + 2 + 3 + 1 = 20
# If binary and casenum together: 9 + 2 + 3 + 2 + 4 = 20
# If identity and casenum separate: 9 + 3 + 5 + 3 + 5 + 2 = 27
# If identity and casenum together: 9 + 3 + 5 + 3 + 10 = 30
input_nodes = sum([
root_size, constants.human_size, constants.dec_size, constants.gen_size,
constants.case_size
])
if constants.casenum_sep == True:
input_nodes += constants.num_size
##########
# OUTPUT #
def find_polaron(st, i_alk_ion, out_prec = 1):
"""
#using magmom, find the transition atoms that have different magnetic moments
#i_alk_ion - number of ion from 0 to calculate distances to transition metals
out_prec (int) - precision of magmom output
# maglist = cli.end.get_maglist()
# magm = np.array(cli.end.magmom)
# n_tm = len(magm[maglist])
# # print(len(maglist))
# numb, dist, chosen_ion = around_alkali(cli.end, n_tm, atom_num)
# # print(magm[numb][1:])
# mtm = magm[numb][1:] # the first is alkali
# m_av = sum(mtm)/len(mtm)
# print(mtm-m_av)
"""
def zscore(s):
# print(np.std(s))
return (s - np.mean(s)) / np.std(s)
magmom = np.array(st.magmom)
if len(magmom) == 0 :
printlog('Error! magmom is empty')
_, mag_numbers = st.get_maglist()
pol = {}
# for z in mag_numbers:
# pos = determine_symmetry_positions(st, invert(z))
# sys.exit()
magmom_tm = None
for key in mag_numbers:
printlog('Looking at polarons on transition atoms: ',invert(key) )
numbs = np.array(mag_numbers[key])
# print(numbs)
# print(magmom)
magmom_tm = magmom[numbs]
dev = np.absolute( zscore(magmom_tm) )
# print(magmom_tm)
# print(list(zip(magmom_tm, dev.round(1))))
# p = np.where(dev>2)[0] # 2 standard deviations
# print(dev>2)
# print (type(numbs))
nstd = 1.5
# nstd = 4
i_pols = numbs[dev>nstd]
if len(i_pols) > 0:
x1 = st.xcart[i_alk_ion]
d_to_pols = []
for j in i_pols:
x2 = st.xcart[j]
d, _ = st.image_distance(x1, x2, st.rprimd)
d_to_pols.append(d)
print('polarons are detected on atoms', [i+1 for i in i_pols], 'with magnetic moments:', magmom[i_pols], 'and distances: '+', '.join('{:2.2f}'.format(d) for d in d_to_pols), 'A' )
print('mag moments on trans. atoms:', magmom_tm.round(out_prec))
pol[key] = i_pols
else:
print('no polarons is detected with nstd', nstd)
print('mag moments on trans. atoms:', magmom_tm.round(out_prec))
# print(' deviations :', dev.round(1))
pol[key] = None
return pol, magmom_tm
def add_to_archive_database(cl, subgroup):
"""
cl is Calculation which should be added to database
subgroup (str) - subgroup folder
"""
from pymatgen.core.composition import Composition
from pymatgen.io.cif import CifWriter
from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
join = os.path.join
basename = os.path.basename
dirname = os.path.dirname
save_format = 'azh'
dbpath = header.PATH2DATABASE
it = cl.id[0]
# print(cl.path)
sub_folder = cl.path['output'].split('/')[
0] # usually basic chemical formula
# sub_folder = header.struct_des[it].sfolder.split('/')[0] # usually basic chemical formula
print('Processing ', cl.id)
cl.read_results()
if '4' not in cl.state:
return
st = cl.end
# print(cl.end.typat)
# sys.exit()
if 1:
#determine x
#universal method, supports several alkali elements
#requires cl.base_formula in 'Na2FePO4F' format
#requires pymatgen, would be nice to remove dependency
cmb = Composition(cl.base_formula)
cm = st.get_pm_composition()
rc = cl.end.get_reduced_composition().as_dict(
) #reduced composition dict
rcb = cmb.reduced_composition.as_dict()
# print(rc, rcb)
alk = list(set(st.get_specific_elements(
header.ALKALI_ION_ELEMENTS))) # list of unique alkali elements
tra = list(set(st.get_specific_elements(header.TRANSITION_ELEMENTS)))
# print(alk, tra)
el_for_norm = tra[0] #first element used for normalization
nnb = rcb[el_for_norm] #number of norm elements in base
nn = rc[el_for_norm] #number of norm elements in interesting structure
# print(nb, n)
mul = nn / nnb # multiplier that garanties normalization
# print(rcb)
nab = sum([
rcb[invert(z)] for z in header.ALKALI_ION_ELEMENTS
if invert(z) in rcb
])
na = sum([rc[el] for el in alk])
x = na / mul / nab
# determine formula
# cm = st.get_pm_composition() #get pymatgen composition class
# print( (cm/4).formula)
# print('Material detected:', formula, 'sub_folder:', sub_folder)
#obtain base without alk
formula = (cm.reduced_composition / mul).formula
# formula = formula.replace('1 ', '').replace(' ', '')
# print(formula)
cl.formula = formula
# print(Composition('Na0.75'))
print('Material detected:', formula, 'sub_folder:', sub_folder)
# sys.exit()
if 0:
#Old method, not robust at all!
#determine x for alkali ion from structure name
parsed = re.findall(r'([A-Z][a-z]*)(\d*)', formula)
parsed = [(el, x if x else '1') for (el, x) in parsed]
print(parsed)
print('detected element is ', parsed[0][0])
if parsed[0][0] in [invert(z) for z in header.ALKALI_ION_ELEMENTS]:
x = parsed[0][0]
if hasattr(cl, 'max_alk_ion_content'):
x = float(x) / cl.max_alk_ion_content
else:
x = '1'
else:
x = '0'
sfolder = os.path.join(dbpath, sub_folder)
name = []
if 'azh' in save_format:
#1. Single point calculation of total energy
# print(sfolder)
makedir(join(sfolder, 'dummy'))
if x < 1:
x = int(round(100 * x, 0))
else:
x = int(round(x, 0))
print('Concentration x:', x)
name.append('x' + str(x))
# sys.exit()
# if formula in ['LiCoO2', 'LiTiO2', 'LiFePO4', 'NaFePO4', 'LiMnPO4',
# 'LiNiO2', 'LiTiS2', 'LiMn2O4', 'LiVP2O7', 'LiVPO4F',
# 'NaMnAsO4', 'Na2FePO4F', 'Na2FeVF7', 'KFeSO4F', 'NaLiCoPO4F', 'KVPO4F' ]:
sfolder = join(sfolder, subgroup)
makedir(join(sfolder, 'dummy'))
cl.set.update()
# print(cl.potcar_lines)
potcar1_m = cl.potcar_lines[0][0]
if '_' in potcar1_m:
(pot, _) = potcar1_m.split('_')
else:
pot = potcar1_m
xc = cl.xc_inc
if '-' in xc:
xc = cl.xc_pot
if xc == 'PE':
func = 'PBE'
elif xc == 'CA':
func = 'LDA'
elif xc == 'PS':
func = 'PBEsol'
else:
print('uknown xc type:', xc)
sys.exit()
if cl.set.spin_polarized:
func = 'U' + func #unrestricted
u_ramping_flag = False
if hasattr(cl.set, 'u_ramping_nstep') and cl.set.u_ramping_nstep:
func += '-UR'
u_ramping_flag = True
elif cl.set.dftu:
func += '-U'
else:
func += '-'
func += pot.lower()
ecut = str(round(cl.set.ecut))
func += ecut
# print(func)
name.append(func)
name.extend([it.replace('.', '_')] + [cl.id[1]] + [str(cl.id[2])])
name_str = '_'.join(name)
# print('_'.join(name) )
# sys.exit()
outcar_name = name_str + '.out'
shutil.copyfile(cl.path["output"], join(sfolder, outcar_name))
if u_ramping_flag:
print(cl.associated_outcars)
for i, u_outcar in enumerate(
cl.associated_outcars[:-1]
): # except the last one, which was copied above
u = u_outcar.split('.')[1]
# print(u)
path_to_outcar = join(dirname(cl.path["output"]), u_outcar)
cl.read_results(load='o', choose_outcar=i + 1, only_load=1)
shutil.copyfile(path_to_outcar,
join(sfolder, name_str + '_' + u + '.out'))
# sys.exit()
cl.end.write_xyz(path=sfolder, filename=name_str)
pickle_file = cl.serialize(os.path.join(sfolder, 'bin', name_str))
# cl
#write input, problem with fitted version 100, which does not have input geometry, since they are created on cluster
# makedir(sfolder+'input/dummy')
# shutil.copyfile(cl.path["input_geo"], sfolder+'input/'+name_str+'.geo')
st_mp = cl.end.convert2pymatgen()
sg_before = st_mp.get_space_group_info()
# from pymatgen.symmetry.finder import SymmetryFinder
# sf = SymmetryFinder(st_mp_prim)
symprec = 0.1
sf = SpacegroupAnalyzer(st_mp, symprec=symprec)
st_mp_prim = sf.find_primitive()
# st_mp_prim = sf.get_primitive_standard_structure()
# st_mp_prim = sf.get_conventional_standard_structure()
# st_mp_conv = sf.get_conventional_standard_structure()
# print(st_mp_conv)
# print(st_mp_conv.lattice.matrix)
# print(st_mp_prim)
# print(st_mp_prim.lattice)
sg_after = st_mp_prim.get_space_group_info()
if sg_before[0] != sg_after[0]:
printlog(
'Attention! the space group was changed after primitive cell searching',
sg_before, sg_after)
printlog('I will save supercell in cif and reduce symprec to 0.01')
st_mp_prim = st_mp
symprec = 0.01
if st_mp_prim:
cif = CifWriter(st_mp_prim, symprec=symprec)
cif_name = name_str + '.cif'
cif.write_file(join(sfolder, cif_name))
printlog('Writing cif', cif_name)
if 0:
#get multiplication matrix which allows to obtain the supercell from primitive cell.
#however this matrix is not integer which is not convinient.
print(st_mp.lattice.matrix.round(2))
print(st_mp_prim.lattice.matrix.round(2))
mul_matrix = np.dot(st_mp.lattice.matrix,
np.linalg.inv(st_mp_prim.lattice.matrix))
print(mul_matrix.round(1))
rprimd = np.dot(mul_matrix, st_mp_prim.lattice.matrix)
print(rprimd.round(2))
#write chg
if 1:
path_to_chg = cl.get_chg_file('CHGCAR')
if path_to_chg:
makedir(join(sfolder, 'bin', 'dummy'))
printlog('path to chgcar', path_to_chg)
gz = '.gz'
if gz not in path_to_chg:
gz = ''
shutil.copyfile(path_to_chg,
join(sfolder, 'bin', name_str + '.chg' + gz))
#write dos
if subgroup in ['dos', 'DOS']:
DOSCAR = cl.get_file('DOSCAR', nametype='asoutcar')
if DOSCAR:
printlog('path to DOSCAR', DOSCAR)
gz = '.gz'
if gz not in path_to_chg:
gz = ''
shutil.copyfile(DOSCAR,
join(sfolder, 'bin', name_str + '.dos' + gz))
if subgroup in ['BAD']: #bader
cl.get_bader_ACF()
acf = cl.get_file(basename(cl.path['acf']))
# print(acf)
# sys.exit()
if acf:
shutil.copyfile(acf, join(sfolder, 'bin', name_str + '.acf'))
if subgroup in ['ph', 'PH']: #bader
# cl.get_bader_ACF()
xml = cl.get_file('vasprun.xml', nametype='asoutcar')
# print(acf)
# sys.exit()
if xml:
shutil.copyfile(xml, join(sfolder, 'bin', name_str + '.xml'))
#make dat
#incars
makedir(join(sfolder, 'dat', 'dummy'))
incars = glob.glob(join(cl.dir, '*INCAR*'))
# print(incars)
for inc in incars:
dest = join(sfolder, 'dat')
# inc_name =
if not os.path.exists(join(dest, basename(inc))):
shutil.copy(inc, dest)
#kpoints
if it in header.struct_des:
with open(join(sfolder, 'dat', 'kpoints_for_kspacings.json'),
'w',
newline='') as fp:
json.dump(
header.struct_des[it].ngkpt_dict_for_kspacings,
fp,
)
else:
printlog('Warning!, it not in struct_des:', it)
# print(cl.set.toJSON())
#prepare for neb
# makedir(sfolder+'neb_'+name_str+'/dummy')
return