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
vasprun_command = params.get('vasp_run') or 'vasp'
nmcstep = params.get('mcsteps') or 2 # minimum two steps are done
thickness = params.get('thickness') or 6 # minimum layer
temperature = params.get('temp') or 1
printlog('\n\n\nStarting Monte-Carlo script!')
printlog('Command to run vasp', vasprun_command)
printlog('Total number of steps is', nmcstep)
printlog('Thickness is ', thickness)
printlog('Temperature is ', temperature, 'K')
"""1. Run initial calculation"""
if debug:
cl = CalculationVasp()
cl.read_poscar('1.POSCAR')
cl.end = cl.init
last_number = 0
else:
files_yes = glob.glob('*yes.pickle') #get list of calculated yes files
files_all = glob.glob('*.pickle') #get list of all calculated files
"""Find last yes pickle file"""
if files_yes:
yes_numbers = [int(file.split('-')[0]) for file in files_yes]
all_numbers = [int(file.split('-')[0]) for file in files_all]
last_yes_n = max(yes_numbers)
last_number = max(all_numbers)
last_yes_file = str(last_yes_n) + '-yes.pickle'
printlog('Last calculation file is ', last_yes_file, imp='y')
else:
def initial_run(xcart_voids, ):
"""1. Run initial calculation"""
if debug:
cl = CalculationVasp()
cl.read_poscar('1.POSCAR')
cl.end = cl.init
if xcart_voids: # read void coordinates
cl.end = cl.end.add_atoms(xcart_voids, 'void')
last_number = 0
else:
files_yes = glob.glob('*yes.pickle') #get list of calculated yes files
files_all = glob.glob('*.pickle') #get list of all calculated files
"""Find last yes pickle file"""
if files_yes:
yes_numbers = [int(file.split('-')[0]) for file in files_yes]
all_numbers = [int(file.split('-')[0]) for file in files_all]
last_yes_n = max(yes_numbers)
last_number = max(all_numbers)
last_yes_file = str(last_yes_n)+'-yes.pickle'
printlog('Last calculation file is ', last_yes_file, imp = 'y')
else:
last_number = 0
last_yes_file = None
"""Read last pickle file or run vasp """
if last_yes_file:
cl = CalculationVasp().deserialize(last_yes_file)
printlog('Successfully deserialized')
xcart_voids = cl.end.get_specific_elements([300], fmt = 'x') # extract voids form the last calculation
else:
cl = vasp_run(3, 'first run', vasprun_command = vasprun_command)
if xcart_voids: # read void coordinates
cl.end = cl.end.add_atoms(xcart_voids, 'void')
printlog('I found', len(xcart_voids), 'voids in config file. Added to structure.')
if check(cl) == 0:
cl.serialize('0-yes')
copyfile('OUTCAR', 'OUTCAR-0')
copyfile('OSZICAR', 'OSZICAR-0')
copyfile('CONTCAR', 'CONTCAR-0')
copyfile('OUTCAR', 'OUTCAR_last')
copyfile('CONTCAR', 'CONTCAR_last')
with open('ENERGIES', 'w') as f:
f.write('{:5d} {:.5f}\n'.format(0, cl.e0))
else:
printlog('Calculation is broken, no data was saved, exiting ...', imp = 'y')
sys.exit()
if debug2:
sys.exit()
return cl, last_number
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,
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,
it_folder=None,
inherit_magmom=False,
x_start=None,
xr_start=None,
x_final=None,
xr_final=None,
upload_vts=False,
center_on_moving=True,
run=False,
add_loop_dic=None,
old_behaviour=None,
params=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 or it_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
- old_behaviour (str) - choose naming behavior before some date in the past for compatibility with your projects
'020917'
'261018' - after this moment new namig convention applied if end_pos_types_z is used
- add_loop_dic - standart parameters of add()
- params (dic) - provide additional parameters to add() # should be removed
###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)
"""
naming_conventions209 = True # set False to reproduce old behavior before 2.09.2017
if old_behaviour == '020917':
naming_conventions209 = False #
# print('atom_to_insert', 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 = []
end_pos_types_z = sorted(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*')
corenum = add_loop_dic.get('corenum')
# print(corenum)
# sys.exit()
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(corenum)
# sys.exit()
# 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]
# print('atom_to_insert', atom_to_insert)
# sys.exit()
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)
final_pos_z = end_pos_types_z or [
invert(type_atom_to_move)
] # by default only moving atom is considered
end_pos_types_el = [invert(z) for z in end_pos_types_z]
sur = local_surrounding(x_m,
st,
n_neighbours=14,
control='atoms',
only_elements=final_pos_z,
periodic=True) #exclude the atom itself
# print(x_m)
# print(sur)
# st.nn()
end_pos_n = sur[2][1:]
print_and_log(
'I can suggest you ' + str(len(end_pos_n)) +
' end positions. The distances to them are : ',
np.round(sur[3][1:], 2),
' A\n ',
'They are ', [invert(z) for z in final_pos_z],
'atoms, use *i_void_final* to choose required: 1, 2, 3 ..',
imp='y')
i_sym_final_l = []
for j in end_pos_n:
for i, l in enumerate(numbers):
if j in l:
i_sym_final_l.append(i + 1)
printlog('Their symmetry positions are ', i_sym_final_l, imp='y')
# sys.exit()
if not i_void_final:
printlog('Changing i_void_final: None -> 1', imp='y')
i_void_final = 1 #since zero is itself
chosen_dist = sur[3][i_void_final]
print_and_log('Choosing position ',
i_void_final,
'with distance',
round(chosen_dist, 2),
'A',
imp='y')
# print(end_pos_n)
i_sym_final = 0
n_final = sur[2][i_void_final]
for i, l in enumerate(numbers):
if n_final in l:
i_sym_final = i + 1
printlog('It is symmetrically non-equiv position #',
i_sym_final,
imp='y')
# sys.exit()
header.temp_chosen_dist = chosen_dist
if old_behaviour == '261018':
name_suffix += el_num_suffix + 'v' + str(i_void_final)
else:
name_suffix += el_num_suffix + 'v' + str(
i_void_final) + list2string(end_pos_types_el, joiner='')
# print(name_suffix)
# sys.exit()
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 or 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 '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
if search_type != None: # for None not implemented; x_m should be determined first for this
#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 and not it_folder:
printlog(
'Error! please provide *it_new_folder* - folder for your new calculation',
important='Y')
if it_folder:
it_new_folder = it_folder
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
if search_type is not None:
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()
print('Trying to find x_m', x_m)
i1 = st1.find_atom_num_by_xcart(
x_m,
prec=0.45,
)
# sys.exit()
print('Trying to find x_del', x_del)
i2 = st2.find_atom_num_by_xcart(
x_del,
prec=0.45,
)
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=0.45) # the positions were changed # check if this is correct
i2 = st2.find_atom_num_by_xcart(x_del, prec=0.45)
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 and search_type is not None:
st1s = st1.replace_atoms([i1], 'Pu')
st2s = st2.replace_atoms([i2], 'Pu')
else:
st1s = copy.deepcopy(st1)
st2s = copy.deepcopy(st2)
if center_on_moving and search_type is not None:
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')
print(a)
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])
if run:
add_loop_dic['run'] = run
add_loop_dic['corenum'] = corenum
# print(add_loop_dic)
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,
# params=params,
**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
xcart_voids = st_new_init.get_specific_elements([300], fmt = 'x')
printlog('The following voids after changes were extracted from st:', xcart_voids)
if debug:
st_new_init.write_poscar('POSCAR-'+str(i_mcstep))
st_new_init = read_poscar(st_new_init, 'POSCAR-'+str(i_mcstep))
# print(xcart_voids)
# sys.exit()
if xcart_voids:
st_new_init = st_new_init.add_atoms(xcart_voids, 'void')
# xcart_voids = st_new_init.get_specific_elements([300], fmt = 'x')
# print('After writing and reading the voids are ', xcart_voids)
st = st_new_init
cl = CalculationVasp()
cl_new = CalculationVasp()
cl.end = st
cl_new.end = st_new_init
cl.e0 = random.random()
cl_new.e0 = random.random()
else:
"""4. Write new structure and calculate energy """
st_new_init.write_poscar('POSCAR') #here voids are lost
cl_new = vasp_run(3, 'mcstep '+str(i_mcstep), vasprun_command = vasprun_command)
if check(cl_new):
printlog('{:5d} is unlucky configuration, trying another ... '.format(i_mcstep), imp = 'y')
continue