def determine_voids(st, r_impurity, fine=1, step_dec=0.05):
if not r_impurity:
printlog('add_neb(): Error!, Please provide *r_impurity* (1.6 A?)')
sums = []
avds = []
printlog('Searching for voids', important='y')
st_pores = find_pores(st,
r_matrix=0.5,
r_impurity=r_impurity,
step_dec=step_dec,
fine=fine,
calctype='all_pores')
printlog('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')
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)
summ, avd = local_surrounding2(x,
st,
n_neighbours=6,
control='sum_av_dev',
periodic=True)
# print (summ, avd)
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')
return st_pores, sums, avds
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 insert(it_ins, ise_ins, mat_path, it_new, calc, type_of_insertion="xcart"):
"""For insertion of atoms to cells with changed lateral sizes
Input:
'type_of_insertion = xred' used to add xred coordinates
mat_path - path to geo files which are supposed to be changed
it_ins - already existed calculation; xred will be used from this calculation.
it_new - new folder in geo folder for obtained structure
This function finds version of calculation in folder mat_path and tries to use the same version of it_ins
"""
if not os.path.exists(mat_path):
print_and_log("Error! Path " + mat_path + " does not exist\n\n")
raise RuntimeError
if it_ins not in mat_path and it_ins not in it_new:
print_and_log('Cells are', it_ins, mat_path, it_new)
print_and_log(
"Error! you are trying to insert coordinates from cell with different name\n\n"
)
#raise RuntimeError
hstring = ("%s #on %s" %
(traceback.extract_stack(None, 2)[0][3], datetime.date.today()))
if hstring != header.history[-1]: header.history.append(hstring)
geofilelist = runBash('find ' + mat_path +
'/target -name "*.geo*" ').splitlines()
if geofilelist == []:
print_and_log(
"Warning! Target folder is empty. Trying to find in root folder ..."
)
geofilelist = runBash('find ' + mat_path +
'/ -name "*.geo*" ').splitlines()
ins = None
for mat_geofile in geofilelist:
mat = CalculationVasp()
mat.name = mat_geofile
mat.read_geometry(mat_geofile)
#step = 0.27
#r_pore = 0.56
#r_mat = mat.hex_a / 2 - step
#pores = find_pores(mat.init, r_mat, r_pore, step, 0.3, 'central') #octahedral
#mat.xcart.append ( pores.xcart[0] )
#mat.typat.append(1)
try:
ins_working = ins
ins = calc[(it_ins, ise_ins, mat.version)]
except KeyError:
print_and_log("No key", (it_ins, ise_ins, mat.version),
"I use previous working version !!!",
imp='y')
ins = ins_working
#return
#ins.end.znucl = ins.znucl
#ins.end.nznucl = ins.nznucl
#ins.end.ntypat = ins.ntypat
#ins.end.typat = ins.typat
#print ins.xcart[-1]
mat_geopath = geo_folder + struct_des[it_new].sfolder + '/'
if type_of_insertion == "xcart":
#Please update here!
mat_filename = '/' + it_new + "." + "inserted." + str(
mat.version) + '.' + 'geo'
v = np.zeros(3)
result = insert_cluster(ins.end, v, mat.init, v)
mat.end = result
mat.init = result
# mat.znucl = mat.end.znucl
# mat.nznucl = mat.end.nznucl
# mat.ntypat = mat.end.ntypat
# mat.typat = mat.end.typat
# mat.natom = len(mat.end.xred)
#mat.version = ins.version
des = ins.name + " was inserted to " + mat_geofile
elif type_of_insertion == "xred":
mat_filename = '/from/' + it_new + ".xred." + str(
mat.version) + '.' + 'geo'
#mat.end.rprimd = mat.rprimd
#mat.init.xred = copy.deepcopy(ins.end.xred)
#mat.init.typat = copy.deepcopy(ins.end.)
#print ins.end.xcart
rprimd = copy.deepcopy(mat.init.rprimd)
#build = mat.build
mat.init = copy.deepcopy(ins.end)
#mat.build = build
mat.init.rprimd = rprimd #return initial rprimd
mat.init.xred2xcart() #calculate xcart with new rprimd
des = "atoms with reduced coord. from " + ins.name + " was fully copied to " + mat_geofile
mat.init.name = 'test_insert_xred' + str(mat.version)
write_xyz(mat.init)
mat.path["input_geo"] = mat_geopath + it_new + mat_filename
if not mat.write_geometry("init", des): continue
print_and_log("Xred from " + it_ins + " was inserted in " +
mat_geofile + " and saved as " + mat_filename + " \n\n")
return
def insert_cluster(insertion, i_center, matrix, m_center):
"""
Take care of orientation; typat should be consistent
Input:
insertion - object of class Structure(), which is supposed to be inserted in matrix
in such a way that i_center will be combined with m_center.
matrix - object of class Structure().
i_center, m_center - numpy arrays (3).
"""
ins = copy.deepcopy(insertion)
mat = copy.deepcopy(matrix)
r = mat.rprimd
for i, z in enumerate(ins.znucl):
if z not in mat.znucl:
mat.znucl.append(z)
mat.ntypat += 1
mat.nznucl.append(ins.nznucl[i])
hproj = [(r[0][i] + r[1][i] + r[2][i]) * 0.5
for i in (0, 1, 2)] #projection of vectors on three axis
for i, x in enumerate(ins.xcart):
ins.xcart[i] = x - i_center
for i, x in enumerate(mat.xcart):
mat.xcart[i] = x - m_center
max_dis = 1
for i_x, ix in enumerate(ins.xcart):
dv_min = max_dis
print_and_log(
"Insertion atom ",
ix,
)
for j, mx in enumerate(mat.xcart):
dv = mx - ix
for i in 0, 1, 2:
if dv[i] > hproj[i]:
dv = dv - mat.rprimd[
i] #periodic boundary conditions - can be not correct (in the sense that closest image can lie not 100 % in the neighbourhood image cell ) for oblique cells and large absolute values of dv
if dv[i] < -hproj[i]: dv = dv + mat.rprimd[i]
len1 = np.linalg.norm(dv)
len2, second_len2 = mat.image_distance(mx, ix, r, 2) #check len1
#print "Lengths calculated with two methods ", len1, len2
len1 = len2 #just use second method
#assert np.around(len1,1) == np.around(len2,1)
if len1 < dv_min:
dv_min = len1
j_r = j # number of matrix atom to replace
if dv_min == max_dis:
print_and_log(" is more far away from any matrix atom than ",
dv_min, " A; I insert it")
mat.xcart.append(ix)
print_and_log('type of added atom is ', ins.typat[i_x])
mat.typat.append(ins.typat[i_x])
else:
print_and_log("will replace martix atom", mat.xcart[j_r])
mat.xcart[j_r] = ix.copy()
mat.rprimd = r
mat.xcart2xred()
mat.natom = len(mat.xcart)
mat.name = 'test_of_insert'
write_xyz(mat)
return mat
def add(znucl, xyzpath="", new=None, write_geo=True, put_exactly_to=None):
"if put_exactly_to is True, then atom just added and nothing are searched"
if write_geo and os.path.exists(
new.path["input_geo"]) and not override:
print_and_log("add: File '" + new.path["input_geo"] +
"' already exists; continue\n",
imp='Y')
return new
#new.init = return_atoms_to_cell(new.init)
if replace_atom:
#atom substitution
if znucl not in new.init.znucl:
new.init.znucl.append(znucl)
new.init.ntypat += 1
new.init.typat[replace_atom] = new.init.ntypat
else:
ind = new.init.znucl.index(znucl)
new.init.typat[replace_atom] = ind + 1
new.init.nznucl = []
for typ in range(1, new.init.ntypat + 1):
new.init.nznucl.append(new.init.typat.count(typ))
else:
new_before = copy.deepcopy(new)
# new.init.xcart[-2][0]-=0.9 #was made once manually for c1gCOi10.1
# new.init.xcart[-2][2]+=0.2
# new.init.xred = xcart2xred(new.init.xcart, new.init.rprimd)
write_xyz(new.init)
#step = 0.042
step = 0.06
#r_pore = 0.56
#fine = 0.3 # for visualisation of pores
#fine = 4 #controls small steps; the steps are smaller for larger numbers
#r_pore = 0.54
prec = 0.004 # precision of center Angs
if new.hex_a == None:
r_mat = 1.48 - step
else:
r_mat = new.hex_a / 2 - step
if put_exactly_to:
pores_xred = [
np.array(put_exactly_to),
]
print_and_log('Inmpurity just put in ', pores_xred, imp='Y')
else:
pores = find_pores(new.init, r_mat, r_pore, step, fine, prec,
addtype, new.gbpos, find_close_to,
check_pore_vol) #octahedral
pores_xred = pores.xred
npores = len(pores_xred)
st = new.init
#delete last oxygen; was made once manually for c1gCOi10.1
# st.natom-=1
# del st.xred[-1]
# del st.typat[-1]
st.natom += npores
st.xred.extend(pores_xred)
if znucl in st.znucl:
print_and_log("znucl of added impurity is already in cell")
ind = st.znucl.index(znucl)
typat = ind + 1
st.nznucl[ind] += npores
else:
st.ntypat += 1
typat = st.ntypat
st.znucl.append(znucl)
st.nznucl.append(npores)
for i in range(npores):
st.typat.append(typat)
st.xred2xcart()
new.init = st
#print "Add impurity: len(xred ", len(new.init.xred)
#print "natom", new.init.natom
#For automatisation of fit
try:
#new.build
if new.build.nadded == None: new.build.nadded = npores
else: new.build.nadded += npores
if new.build.listadded == [None]:
new.build.listadded = range(
new.natom - npores,
new.natom) #list of atoms which were added
else:
new.build.listadded.extend(
range(new.natom - npores, new.natom))
#print "Warning!!! Information about added impurities rewritten"
except AttributeError:
pass
#new.init.znucl = new.znucl
#new.init.typat = new.typat
#write_xyz(replic(new.init, (2,1,2)) , xyzpath)
#test_adding_of_impurities(new, new_before, v)
print_and_log("Impurity with Z=" + str(znucl) +
" has been added to the found pore in " + new.name +
"\n\n")
if write_geo:
write_xyz(new.init, xyzpath)
new.write_geometry("init", new.des, override=override)
print_and_log("\n")
return new
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
"""
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)
#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 = []
dAO = [] # A-(O,F) distance for each image
for v in vlist:
cli = calc[cl.id[0], cl.id[1], v]
# 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!
mep_energies.append( cli.energy_sigma0 ) #use last energy
atom_pos.append( cli.end.xcart[atom_num] )
# Find polaron positions
if 1 or 'polaron' in show:
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 1 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)
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:
info1 = st.nn(atom_num, 2, from_one = False, silent = 1)
print('Average_distance A-2(O,F)', info1['av(A-O,F)'], 'A')
dAO.append (info1['av(A-O,F)'])
if 0 or 'neb_geo' in show:
av = st.nn(atom_num, 2, from_one = False, silent = 1, more_info = 1)['avsq(A-O,F)']
print('Average squared distance A-2(O,F)', av, 'A')
info2 = st.nn(atom_num, 4, from_one = False, silent = 1)
print('Average_distance A-4(O,F)', info2['av(A-O,F)'], 'A')
print('Elements are ', info2['el'])
info3 = st.nn(atom_num, 6, from_one = False, silent = 1, more_info = 1)
print('Average_distance A-6(O,F)', info3['av(A-O,F)'], 'A')
print('Average_deviation A-6(O,F)', info3['avdev(A-O,F)'], 'mA')
print('Elements are ', info3['el'])
write_xyz(sts = sts) # write traectory
write_xyz(sts = sts_loc) # write traectory
st1 = st1.shift_atoms(vec)
st1.name +='_all'
# st1.write_cif('xyz/'+st1.name)
st1.write_xyz()
if dAO: # find maximum change of distance during migration
dAO_change = abs(min(dAO) - max(dAO))
results_dic['dAO_change'] = dAO_change
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]
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
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