def push_to_server(files = None, to = None, addr = None):
"""
if header.ssh_object then use paramiko
to (str) - path to remote folder !
"""
if not is_list_like(files):
files = [files]
to = to.replace('\\', '/') # make sure is POSIX
files_str = ' '.join(np.array(files ))
command = ' mkdir -p {:}'.format( to )
# print('asfsadfdsf', to)
printlog('push_to_server():', command, run_on_server(command, addr))
# sys.exit()
printlog('push_to_server(): uploading files ', files, 'to', addr, to)
if header.ssh_object:
for file in files:
# print(file, to)
header.ssh_object.put(file, to+'/'+os.path.basename(file) )
out = ''
elif header.sshpass and header.sshpass == 'proxy':
com = 'tar cf - '+ files_str + ' | ssh sdv "sshpass -f ~/.ssh/p ssh '+addr+' \\"cd '+header.cluster_home+' && tar xvf -\\"" '
# print(com)
# sys.exit()
out = runBash(com)
# print(out)
# sys.exit()
elif header.sshpass:
# if '@' not in addr:
# printlog('Error! Please provide address in the form user@address')
# l = addr.split('@')
# print(l)
# user = l[0]
# ad = l[1]
# com = 'rsync --rsh='+"'sshpass -f /home/aksenov/.ssh/p ssh' " +' -uaz '+files_str+ ' '+addr+':'+to
com = 'rsync --rsh='+"'sshpass -f "+header.path2pass+" ssh' " +' -uaz '+files_str+ ' '+addr+':'+to
# print(com)
# sys.exit()
out = runBash(com)
else:
out = runBash('rsync -uaz '+files_str+ ' '+addr+':'+to)
printlog(out)
return out
def set_ngkpt(self,arg):
if not is_list_like(arg):
printlog("Error! set_ngkpt type error")
old = copy.copy(self.ngkpt)
self.ngkpt = copy.copy(arg)
self.kpoints_file = True
self.vasp_params['KSPACING'] = None
if old == arg:
print_and_log( "Warning! You did not change one of your parameters in new set", imp = 'y')
return
self.history += "ngkpt was changed from "+str(old)+" to "+str(arg) + " and KPOINTS file was swithed on\n"
return
def write_xyz(st=None,
path=None,
filename=None,
file_name=None,
include_vectors=True,
repeat=1,
shift_2view=1.0,
replications=None,
full_cell=False,
analysis=None,
show_around=None,
show_around_x=None,
nnumber=6,
only_elements=None,
gbpos2=None,
gbwidth=1,
withgb=False,
include_boundary=2,
imp_positions=[],
imp_sub_positions=None,
jmol=None,
specialcommand=None,
jmol_args=None,
sts=None,
mcif=0,
suf=''):
"""Writes st structure in xyz format in the folder xyz/path
#void are visualized with Pu
if repeat == 2: produces jmol script
shift_2view - in rprimd[1][1] - shift of the second view
gbpos2 - position of grain boundary in A
gbwidth - atoms aroung gbpos2 will be colored differently
imp_positions - (x1,x2,x3, element, label)- xcart and element name coordinates additionally to be added to structure; to visulaze all impurity positions: for jmol, additional key 's', 'i' can be added after element
imp_sub_positions - list of atom numbers; the typat of these atoms is changed: not used now
analysis - additional processing, allows to show only specifice atoms,
'imp_surrounding' - shows Ti atoms only around impurity
nnumber - number of neighbours to show
show_around - choose atom number around which to show, from 1
show_around_x - show atoms around point, has higher priority
only_elements - see local_surrounding
replications - list of replications, (2,2,2)
full_cell - returns atoms to cell and replicate boundary atoms
include_vectors (bool) - write primitive vectors to xyz
jmol - 1,0 - use jmol to produce png picture
jmol_args - see write_jmol()
mcif - write magnetic cif for jmol
specialcommand - any command at the end of jmol script
suf - additional suffix for name
sts - list of Structure - write several structures to xyz file - other options are not working in this regime
"""
if jmol_args == None:
jmol_args = {}
if st == None:
st = sts[0]
if replications:
st = replic(st, mul=replications, inv=1)
def update_var(st):
if st.natom != len(st.xred) != len(st.xcart) != len(st.typat) or len(
st.znucl) != max(st.typat):
printlog("Error! write_xyz: check your arrays.\n\n")
if st.xcart == [] or len(st.xcart) != len(st.xred):
printlog(
"Warining! write_xyz: len(xcart) != len(xred) making xcart from xred.\n"
)
st.xcart = xred2xcart(st.xred, st.rprimd)
#print xcart[1]
return st.rprimd, st.xcart, st.xred, st.typat, st.znucl, len(st.xred)
st = st.copy()
rprimd, xcart, xred, typat, znucl, natom = update_var(st)
if file_name:
name = file_name
elif filename:
name = filename
else:
name = st.name + suf
if sts:
name += '_traj'
printlog("write_xyz(): Name is", name, important='n')
if name == '':
name = 'noname'
if path:
basepath = path
else:
basepath = 'xyz/'
suf = ''
"""Processing section"""
if analysis == 'imp_surrounding':
printlog('analysis = imp_surrounding', imp='y')
if show_around == 0:
printlog('Error! number of atom *show_around* should start from 1')
suf = '_loc' + str(show_around)
lxcart = []
ltypat = []
i = 0
if is_list_like(show_around_x):
x = show_around_x
x_t = local_surrounding(x,
st,
nnumber,
control='atoms',
periodic=True,
only_elements=only_elements)
# print('write_xyz: local_surround:', x_t)
lxcart += x_t[0]
ltypat += x_t[1]
else:
for t, x in zip(typat, xcart):
condition = False
# print show_around, 'show'
if show_around:
# print i, condition
condition = (i + 1 == show_around)
# print i, condition
else:
condition = (
t > 1
) # compat with prev behav, to show around any impurities (all atoms with typat more than one)
# print 'se', condition
if condition:
# print('Atom at', x, 'used as central')
# lxcart.append(x)
# ltypat.append(t)
# print x, ' x'
x_t = local_surrounding(x,
st,
nnumber,
control='atoms',
periodic=True,
only_elements=only_elements)
print(x_t)
lxcart += x_t[0]
ltypat += x_t[1]
i += 1
xcart = lxcart
typat = ltypat
natom = len(typat)
# print natom, 'nat'
# print('Number of neighbours', natom )
st.xcart = xcart
st.typat = typat
st.natom = natom
st.update_xred()
"""Include atoms on the edge of cell"""
if full_cell:
# print xred
# print natom
# st = return_atoms_to_cell(st)
# print xred
st = replic(st,
mul=(1, 1, 2),
inv=0,
cut_one_cell=1,
include_boundary=include_boundary)
# print natom, st.natom
# print st.xred
rprimd, xcart, xred, typat, znucl, natom = update_var(st)
# asdegf
# printlog("Writing xyz: "+xyzfile, imp = 'y')
#analyze imp_positions
if imp_sub_positions == None:
imp_sub_positions = []
nsub = 0
for pos in imp_positions:
# if len(pos) > 4:
# if 's' not in pos[4]: continue # skip interstitial positions
xs = np.asarray([pos[0], pos[1], pos[2]])
nsub += 1
# print xs
for i, x in enumerate(xcart):
# print np.linalg.norm( x-xs)
if np.linalg.norm(x - xs) < 1:
imp_sub_positions.append(i)
if imp_sub_positions:
printlog(imp_sub_positions, ': numbers of found atoms to be changed ')
# for i in sorted(indices, reverse=True):
# del somelist[i]
if include_vectors:
nvect = 3
else:
nvect = 0
"""Writing section"""
name += suf
xyzfile = os.path.join(basepath, name + ".xyz")
makedir(xyzfile)
def write(st):
rprimd, xcart, xred, typat, znucl, natom = update_var(st)
f.write(str(natom + len(imp_positions) - nsub + nvect) +
"\n") #+3 vectors
f.write(name + "\n")
if imp_positions:
for i, el in enumerate(imp_positions):
# if len(el) != 4: continue
f.write("%s %.5f %.5f %.5f \n" % (el[3], el[0], el[1], el[2]))
# print 'composite -pointsize 60 label:{0:d} -geometry +{1:d}+{2:d} 1.png 2.png'.format(i, el[0], el[1])
for i in range(natom):
typ = typat[i] - 1
z = int(znucl[typ])
if i in imp_sub_positions:
# f.write( "Be " )
continue
else:
el = element_name_inv(z)
if el == 'void':
el = 'Pu'
f.write(el + " ")
f.write("%.5f %.5f %.5f \n" %
(xcart[i][0], xcart[i][1], xcart[i][2]))
if include_vectors:
for r in st.rprimd:
f.write('Tv {:.10f} {:.10f} {:.10f}\n'.format(*r))
with open(xyzfile, 'w') as f:
if sts:
for st in sts:
write(st)
else:
for i in range(repeat):
write(st)
# os._exit(1)
printlog('File', xyzfile, 'was written', imp='y')
pngfile = None
if jmol:
"""
script mode for jmol. Create script file as well for elobarate visualization
"""
"""Choose gb atoms to change their color"""
printlog('position of boundary 2', gbpos2)
atomselection = ''
#create consistent xcart_new list like it will be in Jmol
xcart_new = []
for i, x in enumerate(xcart):
if i in imp_sub_positions: continue
xcart_new.append(x)
if gbpos2:
gbpos1 = gbpos2 - rprimd[0][0] / 2.
gbatoms = []
for i, x in enumerate(xcart_new):
# print i
# if x[0] > gbpos1 - gbwidth/2. and x[0] < gbpos1 + gbwidth/2.:
if abs(x[0] - gbpos1) < gbwidth / 2.:
gbatoms.append(i)
# print i, x[0], abs(x[0] - gbpos1)
if abs(x[0] - gbpos2) < gbwidth / 2.:
# if x[0] > gbpos2 - gbwidth/2. and x[0] < gbpos2 + gbwidth/2.:
# print i, x[0], abs(x[0] - gbpos2)
gbatoms.append(i)
printlog('Atoms at GB:', gbatoms)
atomselection = ''
for i in gbatoms:
atomselection += 'Ti' + str(i + 1 + len(imp_positions)) + ','
atomselection = atomselection[:-1]
# elif withgb: # color half of cell
# else: # color half of cell
# # pass
# atomselection = 'atomno>'+str(0+len(imp_positions) )+' and atomno<'+str(( natom + len(imp_positions) )/2-1)
# xyzfile = os.getcwd()+'/'+xyzfile
if mcif:
xyzfile = st.write_cif(mcif=1)
else:
xyzfile = st.write_poscar()
scriptfile = basepath + name + ".jmol"
bn = (basepath + name).replace('.', '_')
pngfile = os.getcwd() + '/' + bn + ".png"
printlog('imp_positions = ', imp_positions)
write_jmol(xyzfile,
pngfile,
scriptfile,
atomselection,
rprimd=rprimd,
shift=shift_2view,
label=[(pos[3], pos[4]) for pos in imp_positions],
specialcommand=specialcommand,
**jmol_args)
return xyzfile, pngfile
def read_xyz(st, filename, rprimd=None):
"""
Read xyz file into st
rprimd (list of lists) - if None or [None, ] then Tv are read; if Tv does not exist then create automatically
"""
with open(filename, 'r') as f:
nlines = int(f.readline())
st.name = f.readline().strip()
# try:
if 'SG' in st.name:
printlog(
'Error! Space group record detected in xyz, please finish code',
imp='Y')
# st.name.split('SG')
elements = []
st.xcart = []
st.rprimd = []
for i in range(nlines):
xc = f.readline().split()
if len(xc) == 0:
printlog('Warning! xyz file is broken, not enough lines')
break
if 'Tv' in xc[0]:
st.rprimd.append(np.asarray(xc[1:], dtype=float))
else:
elements.append(xc[0])
st.xcart.append(np.asarray(xc[1:], dtype=float))
st.natom = len(st.xcart)
st.znucl = [element_name_inv(el) for el in unique_elements(elements)]
elements_z = [element_name_inv(el) for el in elements]
st.typat = []
for z in elements_z:
st.typat.append(st.znucl.index(z) + 1)
st.ntypat = len(st.znucl)
# print(st.rprimd)
if rprimd == None or None in rprimd or 0 in rprimd or len(rprimd) != 3:
printlog('None detected in *rprimd*, I use vectors from xyz file')
if len(st.rprimd) != 3:
printlog('Only these primitive vectors were found in xyz :\n',
np.round(st.rprimd, 3),
'\nI take rest from *rprimd*',
imp='y')
if rprimd:
for r in rprimd:
if is_list_like(r):
st.rprimd.append(r)
else:
printlog('Error! Please provide vector in *rprimd*')
else:
printlog('I use vectors from *rprimd*')
st.rprimd = rprimd
if len(st.rprimd) != 3:
printlog('Error! Check *rprimd* or Tv in xyz')
if st.get_volume() < 0:
printlog(
'Warning! rprimd gives negative volume, I exchange vectors 2 and 3',
imp='y')
t = st.rprimd[1]
st.rprimd[1] = st.rprimd[2]
st.rprimd[2] = t
if st.get_volume() < 0:
printlog(
'Error! still negative volume, check your primitive vectors',
imp='y')
st.tmap = [1, 3]
else:
st.tmap = [1, 2]
printlog('Final rprimd = \n', np.round(st.rprimd, 3), imp='y')
st.nznucl = st.get_nznucl()
st.recip = st.get_recip()
st.update_xred()
st.reorder_for_vasp(inplace=True)
# print(st.perm)
return st
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
def get_from_server(files=None, to=None, to_file=None, addr=None, trygz=True):
"""
Download files using either paramiko (higher priority) or rsync;
For paramiko header.ssh_object should be defined
files (list of str) - files on cluster to download
to (str) - path to local folder !
to_file (str) - path to local file (if name should be changed); in this case len(files) should be 1
The gz file is also checked
RETURN
result of download
TODO:
now for each file new connection is opened,
copy them in one connection
"""
# print(addr)
def download(file, to_file):
if header.ssh_object:
exist = file_exists_on_server(file, addr)
# try:
if exist:
printlog('Using paramiko: ssh_object.get(): from to ', file,
to_file)
header.ssh_object.get(file, to_file)
out = ''
# except FileNotFoundError:
else:
out = 'error, file not found'
elif header.sshpass and header.sshpass == 'proxy':
# com = 'ssh sdv "sshpass -f ~/.ssh/p ssh ' + addr + ' \\"tar zcf - '+ file +'\\"" | tar zxf - '+to_file # does not work?
com = 'ssh sdv "sshpass -f ~/.ssh/p ssh ' + addr + ' \\"tar cf - ' + file + '\\"" > ' + to_file
# print(com)
# sys.exit()
out = runBash(com)
elif header.sshpass:
com = 'rsync --rsh=' + "'sshpass -f /home/aksenov/.ssh/p ssh' " + ' -uaz ' + addr + ':' + file + ' ' + to_file
out = runBash(com)
else:
# print(addr,file,to_file)
out = runBash('rsync -uaz ' + addr + ':' + file + ' ' + to_file)
if 'error' in out:
res = out
else:
res = 'OK'
out = ''
printlog('Download result is ', res)
return out
if '*' in files:
printlog('get_from_server(): get by template')
files = run_on_server('ls ' + files, addr).splitlines()
# print(files)
# sys.exit()
printlog('get_from_server(): I download', files)
elif not is_list_like(files):
files = [files]
files = [file.replace('\\', '/')
for file in files] #make sure the path is POSIX
files_str = ', '.join(np.array(files))
printlog('Trying to download', files_str, 'from server', imp='n')
for file in files:
if not to and not to_file: #use temporary file
with tempfile.NamedTemporaryFile() as f:
to_file_l = f.name #system independent filename
elif not to_file: #obtain filename
to_file_l = os.path.join(to, os.path.basename(file))
else:
to_file_l = to_file
makedir(to_file_l)
out = download(file, to_file_l)
if out and trygz:
printlog('File', file, 'does not exist, trying gz', imp='n')
file += '.gz'
to_file_l += '.gz'
out = download(file, to_file_l)
if out:
printlog(' No gz either!', imp='n')
else:
gunzip_file(to_file_l)
return out
def latex_table(table,
caption,
label,
header=None,
fullpage='',
filename=None,
writetype='w',
header0=None,
size=None,
replace=None,
float_format=None,
tab_type='tabular',
width=0.75):
"""
If header is not provided, table[0] is used as a header
header0 - additional header0 befor main header for complex tables
path_to_paper should be provided
replace - list of tuples for replacements
float_format - list of float numbers
tab_type (str) - see latex types of tables
available:
'tabular'
'tabularx'
width (float) - in units of textwidth
"""
table_string = ''
def myprint(string):
nonlocal table_string
if filename:
f.write(string + "\n")
print(string)
else:
print(string)
table_string += string + '\n'
if filename:
# path = path_to_paper+'/tab/'
path = ''
f = open(path + filename, writetype)
print_and_log("Saving table to " + path + filename + '\n')
for i in range(len(table)):
if float_format:
formatter = iter(float_format)
else:
formatter = (2 for i in range(100))
if is_list_like(table[i]):
tab = ''
for j, l in enumerate(table[i]):
# print(type(l))
if type(l) != str:
fmt = '{:3.' + str(next(formatter)) + 'f}'
# fmt = 'a'
# print(fmt)
pos = fmt.format(l)
#
# fmt
# print(pos)
# pos = str(l)
else:
pos = str(l)
tab += pos + " & "
# tab = ' & '.join([str(l) for l in table[i]])
table[i] = tab[0:-3]
n = len(table[0].split('&')) - 2
print('Number of columns = ', n + 2)
myprint('\\begin{table' + fullpage + '}')
myprint('\\center')
if size: myprint('\\' + size)
myprint('\\caption{' + caption + '}')
myprint('\\label{' + label + '}')
if tab_type == 'tabular':
# tabular =
myprint('\\begin{tabular}{l' + n * 'c' + 'r}')
elif tab_type == 'tabularx':
myprint('\\begin{tabularx}{' + str(width) + '\\textwidth}{X' +
n * 'X' + 'X}')
else:
printlog('Error! Unknown type of tabular env!')
myprint('\\hline')
if header0:
myprint(header0 + '\\\\')
myprint('\\hline')
if header:
myprint(header + '\\\\')
tabbeg = 0
else:
myprint(table[0] + ' \\\\')
tabbeg = 1
myprint('\\hline')
for r in table[tabbeg:]:
if '&-' in r:
r = r.replace('-', '--')
else:
r = r.replace(' -', '--') #to save beautiful columns
r += ' '
if '-- ' in r:
r = r.replace('-- ', ' - ')
if replace:
for rep in replace:
# if rep[0] in r:
r = r.replace(*rep)
if 'hline' in r:
myprint(r)
else:
myprint(r + '\\\\')
myprint('\\hline')
myprint('\\end{' + tab_type + '}')
myprint('\\end{table' + fullpage + '}')
if filename:
f.close()
return table_string
def plot_mep(atom_pos,
mep_energies,
image_name=None,
filename=None,
show=None,
plot=1,
fitplot_args=None,
style_dic=None):
"""
Used for NEB method
atom_pos (list) - xcart positions of diffusing atom along the path or just coordinates along one line (for polarons)
mep_energies (list) - full energies of the system corresponding to atom_pos
image_name - deprecated, use filename
style_dic - dictionary with styles
'p' - style of points
'l' - style of labels
'label' - label of points
plot - if plot or not
"""
from siman.analysis import determine_barrier
if filename is None:
filename = image_name
#Create
if not style_dic:
style_dic = {'p': 'ro', 'l': 'b-', 'label': None}
if not fitplot_args:
fitplot_args = {}
# print
if is_list_like(atom_pos[0]):
atom_pos = np.array(atom_pos)
data = atom_pos.T #
tck, u = interpolate.splprep(
data
) #now we get all the knots and info about the interpolated spline
path = interpolate.splev(
np.linspace(0, 1, 500), tck
) #increase the resolution by increasing the spacing, 500 in this example
path = np.array(path)
diffs = np.diff(path.T, axis=0)
path_length = np.linalg.norm(diffs, axis=1).sum()
mep_pos = np.array([p * path_length for p in u])
else:
mep_pos = atom_pos
path_length = atom_pos[-1]
if 0: #plot the path in 3d
fig = plt.figure()
ax = Axes3D(fig)
ax.plot(data[0],
data[1],
data[2],
label='originalpoints',
lw=2,
c='Dodgerblue')
ax.plot(path[0], path[1], path[2], label='fit', lw=2, c='red')
ax.legend()
plt.show()
# if '_mep' not in calc:
calc['_mep'] = [
atom_pos, mep_energies
] # just save in temp list to use the results in neb_wrapper
if hasattr(header,
'plot_mep_invert') and header.plot_mep_invert: # for vacancy
mep_energies = list(reversed(mep_energies))
mine = min(mep_energies)
eners = np.array(mep_energies) - mine
xnew = np.linspace(0, path_length, 1000)
# ynew = spline(mep_pos, eners, xnew )
# spl = CubicSpline(mep_pos, eners, bc_type = 'natural' ) # second-derivative zero
# spl = CubicSpline(mep_pos, eners,) #
# spl = CubicSpline(mep_pos, eners, bc_type = 'periodic')
# spl = CubicSpline(mep_pos, eners, bc_type = 'clamped' ) #first derivative zero
spl = scipy.interpolate.PchipInterpolator(mep_pos, eners)
ynew = spl(xnew)
diff_barrier = determine_barrier(mep_pos, eners)
print_and_log('plot_mep(): Diffusion barrier =',
round(diff_barrier, 2),
' eV',
imp='y')
# sys.exit()
# print()
if 'fig_format' not in fitplot_args:
fitplot_args['fig_format'] = 'eps'
if 'xlim' not in fitplot_args:
fitplot_args['xlim'] = (-0.05, None)
if 'xlabel' not in fitplot_args:
fitplot_args['xlabel'] = 'Reaction coordinate ($\AA$)'
if 'ylabel' not in fitplot_args:
fitplot_args['ylabel'] = 'Energy (eV)'
path2saved = None
if plot:
# print(image_name)
path2saved = fit_and_plot(orig={
'x': mep_pos,
'y': eners,
'fmt': style_dic['p'],
'label': style_dic['label'],
'color': style_dic.get('color')
},
spline={
'x': xnew,
'y': ynew,
'fmt': style_dic['l'],
'label': None,
'color': style_dic.get('color')
},
image_name=image_name,
filename=filename,
show=show,
**fitplot_args)
# print(image_name, filename)
if 0:
with open(filename + '.txt', 'w') as f:
f.write('DFT points:\n')
for m, e in zip(mep_pos, eners):
f.write('{:10.5f}, {:10.5f} \n'.format(m, e))
f.write('Spline:\n')
for m, e in zip(xnew, ynew):
f.write('{:10.5f}, {:10.5f} \n'.format(m, e))
return path2saved, diff_barrier
