def run_on_server(command, addr):
printlog('Running', command, 'on server ...')
command = command.replace('\\', '/') # make sure is POSIX
# sys.exit()
if header.ssh_object:
# printlog('Using paramiko ...', imp = 'y')
out = header.ssh_object.run(command)
elif header.sshpass:
com = 'sshpass -f /home/aksenov/.ssh/p ssh ' + addr + ' "' + command + '"'
# sys.exit()
out = runBash(com)
# sys.exit()
else:
bash_comm = 'ssh ' + addr + ' "' + command + '"'
# print(bash_comm)
out = runBash(bash_comm)
out = out.split('#')[-1].strip()
printlog(out)
# sys.exit()
return out
def calculate_voronoi(self, state = 'end'):
# By default two quantities per atom are calculated by this compute.
# The first is the volume of the Voronoi cell around each atom.
# Any point in an atom's Voronoi cell is closer to that atom than any other.
# The second is the number of faces of the Voronoi cell, which
# is also the number of nearest neighbors of the atom in the middle of the cell.
# state - init or end; if init then saved in self.init.vorovol; if end than saved in self.vorovol
write_lammps(self, state, filepath = 'voronoi_analysis/structure.lammps') #write structure for lammps
runBash("rm voronoi_analysis/dump.voro; /home/aksenov/installed/lammps-1Feb14/src/lmp_serial < voronoi_analysis/voronoi.in > voronoi_analysis/log")
if state == 'end':
self.vorovol = []
self.vorofaces = []
vorovol = self.vorovol
vorofaces = self.vorofaces
elif state == 'init':
self.init.vorovol = []
self.init.vorofaces = []
vorovol = self.init.vorovol
vorofaces = self.init.vorofaces
vsum=0
wlist = []
with open('voronoi_analysis/dump.voro','r') as volfile: #analyze dump.voro
for line in volfile:
if 'ITEM: ATOMS ' in line:
break
for line in volfile:
ll = line.split()
if int(ll[1]) > 1:
wlist.append( [ll[0], ll[5], ll[6], ll[2]] )
# print 'Volume of atom ',ll[0],'is', ll[5]
vsum= vsum+float(ll[5])
print_and_log( 'Check total volume ', vsum, self.end.vol)
wlist.sort(key = itemgetter(0)) #sort according to the position of atoms
print_and_log( "atom #, voronoi vol, voronoi faces, x coordinate: ", )
print_and_log( wlist)
for w in wlist:
vorovol.append(float(w[1]))
vorofaces.append(int(w[2]))
# print 'Voro vol ',self.end.vorovol
# print 'Voro faces',self.end.vorofaces
# print len(wlist)
if hasattr(self, 'vorovol'):
voro = ''
if len(vorovol) == 2: #C and O
voro = " {0:5.2f} & {1:2d} & {2:5.2f} & {3:2d} ".format(vorovol[0], vorofaces[0], vorovol[1], vorofaces[1] ).center(25)
else:
voro = " {0:5.2f} & {1:2d} ".format(vorovol[0], vorofaces[0] ).center(25)
voro+='&'
else:
voro = ""
print_and_log( "Voronoi volume = ", voro, imp = 'y')
return voro
def run_on_server(command, addr):
command = command.replace('\\', '/') # make sure is POSIX
if header.ssh_object:
out = header.ssh_object.run(command)
else:
out = runBash('ssh '+addr+' "'+command+'"')
return out
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 = 'file not found'
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
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 = 'file not found'
else:
out = runBash('rsync -uaz '+addr+':'+file+ ' '+to_file)
if out:
res = out
else:
res = 'OK'
printlog('Download result is ', res)
return out
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 ))
printlog('push_to_server(): uploading files ', files, 'to', addr, to)
command = ' mkdir -p {:}'.format( to )
run_on_server(command, addr)
if header.ssh_object:
for file in files:
# print(file, to)
header.ssh_object.put(file, to+'/'+os.path.basename(file) )
out = ''
else:
out = runBash('rsync -uaz '+files_str+ ' '+addr+':'+to)
printlog(out)
return out
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:
# 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
# print(com)
# sys.exit()
out = runBash(com)
else:
out = runBash('rsync -uaz ' + files_str + ' ' + addr + ':' + to)
printlog(out)
return out
def cal_diff(ver):
"""1. Calculate differences Aksenov"""
# diffscript = '/home/aksenov/programs/vasp/vtstscripts/chgdiff.pl'
# dendiff = 'den/'+ver+'/'+ver+'.diff.CHG'
u =''
proj = '/home/aksenov/scientific_projects/cathode/'
# den1 = 'LiFePO4/neb///FePO4.pnma2v1.n7i1e2Lims.1ur30/1.CHG'
# den1 = 'LiFePO4/neb///LiFePO4.nebLi1v1.1u/CHG' #influence of U end point
# den2 = 'LiFePO4/neb///LiFePO4.nebLi1v1.if.0m/CHG'
# den1 = 'LiFePO4/neb///LiFePO4.nebLi1v1.1u/02/CHG' #influence of U saddle point
# den2 = 'LiFePO4/neb///LiFePO4.nebLi1v1.if.0m/4.CHG'
# den1 = 'LiFePO4//LiFePO4.1u/1.CHG' #influence of Li removal
# den2 = 'LiFePO4//LiFePO4.nebLi1v1.ifi.0u/1.CHG'
dendiff = 'den/CHG'
# u = 'U00'
if 1:
if 0:
den1 = 'Li2FePO4F/scaled//super//scaled///Li2FePO4F.ir.su.s10.su.if.0ur/100.U00.CHGCAR' #low energy without u-ramp
den2 = 'Li2FePO4F/scaled//super//scaled///Li2FePO4F.ir.su.s10.su.if.0ur/100.U40.CHGCAR' #low energy without u-ramp
dendiff = 'den/low/CHG'
else:
den1 = 'Li2FePO4F/scaled//super//scaled///Li2FePO4F.ir.su.s10.su.ifn.if.0ur/100.U00.CHGCAR' #high energy with u-ramp
den2 = 'Li2FePO4F/scaled//super//scaled///Li2FePO4F.ir.su.s10.su.ifn.if.0ur/100.U40.CHGCAR' #high energy with u-ramp
dendiff = 'den/high/CHG'
# print 'vasputil_chgarith.py '+den2+' - '+den1
# if not os.path.exists(dendiff):
runBash('./vasputil_chgarith.py -o '+dendiff+" "+proj+den1+' - '+proj+den2)
# print './vasputil_chgarith.py -o '+dendiff+" "+proj+den1+' - '+proj+den2
print 'chgarith.py OK'
return dendiff
def generate_latex_report(text, filename):
#
from header import runBash
fn = filename + '.tex'
makedir(fn)
head = r"""
\documentclass{article}
% General document formatting
\usepackage[margin=0.7in]{geometry}
\usepackage[parfill]{parskip}
\usepackage[utf8]{inputenc}
% Related to math
\usepackage{amsmath,amssymb,amsfonts,amsthm}
\begin{document}"""
with open(fn, 'w') as f:
f.write(head + '\n')
f.write(text + '\n')
f.write(r'\end{document}')
runBash('pdflatex ' + os.path.basename(fn), cwd=os.path.dirname(fn))
def file_exists_on_server(file, addr):
file = file.replace('\\', '/') # make sure is POSIX
printlog('Checking existence of file', file, 'on server', addr)
if header.ssh_object:
exist = header.ssh_object.fexists(file)
else:
exist = runBash('ssh ' + addr + ' ls ' + file)
if exist:
res = True
else:
res = False
printlog('File exist? ', res)
return res
def file_exists_on_server(file, addr):
file = file.replace('\\', '/') # make sure is POSIX
printlog('Checking existence of file', file, 'on server', addr )
if header.ssh_object:
exist = header.ssh_object.fexists(file)
else:
exist = runBash('ssh '+addr+' ls '+file)
if exist:
res = True
else:
res = False
printlog('File exist? ', res)
return res
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 add_impurity(it_new,
impurity_type=None,
addtype='central',
calc=[],
r_pore=0.5,
it_to='',
ise_to='',
verlist_to=[],
copy_geo_from="",
find_close_to=(),
add_to_version=0,
write_geo=True,
only_version=None,
fine=4,
put_exactly_to=None,
check_pore_vol=0,
replace_atom=None,
override=False):
"""
Add impurities in pores.
Input:
it_new - name of new structure with impurity
impurity_type - name of impurity from Mendeley table, for example 'C'
addtype - type of adding: ['central',]; 'central' means that impurity
will be placed as close to the geometrical center of cell as possible.
it_to , ise_to , verlist_to - completed calculations in which impurity
will be added
if 'verlist_to' is empty, function will try to find geometry files in 'geo_folder + struct_des[it_to].sfolder' folder;
even if 'it_to' is empty it will try to find files in 'geo_folder + struct_des[it_new].sfolder+'/from' ' folder.
'ise_to' also can be empty
if 'copy_geo_from' is not empty, then programm copy all files from folder 'copy_geo_from' to
folder 'geo_folder + struct_des[it_to].sfolder+"/"+it_to' or 'geo_folder + struct_des[it_new].sfolder+"/from" '
'find_close_to' is tuple of three reduced coordinates of point close to which you want to find impurity. If empty - ignored;
'add_to_version' is integer number added to each 'verlist_to' number to produce ver_new.
'only_version' - if == [v,], then instertion will be provided only for v. If None insertion will be made in all found versions
If you want to add impurity to relaxed structure ...
'fine' - integer number; allows to reduce number of small steps for defining center
Possible addtype's:
'central' - add one atom to the pore which is most close to the center of the cell but with reduced coordinates less than 0.5 0.5 0.5
'all_pore' - add atoms in every found pore
'all_local' - add atoms to every local point which allows to visualise topology of pores.
'gb' - uses self.gbpos and places atom close to this value assuming that it will be at gb
'grain_vol' - uses self.gbpos and assuming that cell contains two gb and two equal grains, places atom close to the centre of grain; y and z can be arbiratry
put_exactly_to - will add impurity to this point
find_close_to - will try to find closest void and insert pore here.
check_pore_vol - allows to estimate volume of pores; has problems for big cells
replace_atom - if not None, than the specified atom is substituted
Side effects: creates new geometry folder with input structures;
"""
struct_des = header.struct_des
def test_adding_of_impurities(added, init, v):
"""
Can be used only inside add_impurity()
Replicates the structure and find again pores
"""
global natoms_v1
if added == None: return
if v == 1: #TEST
natoms_v1 = len(added.init.xcart) # for test
st_rep_after = added.init.replic((1, 2, 1))
rep = copy.deepcopy(init)
rep.init = rep.init.replic((1, 2, 1))
#print rep
rep = add(znucl, "", rep, write_geo=False)
#print rep
#print "xcart of replic after adding ", st_rep_after.xcart
#print "xcart of adding to replic ", rep.init.xcart
if len(st_rep_after.xcart) != len(rep.init.xcart):
raise RuntimeError
p = 0
#for x2 in st_rep_after.xcart:
# print x2
for x in rep.init.xcart:
a = any((np.around(x2, p) == np.around(x, p)).all()
for x2 in st_rep_after.xcart)
#b = any( ( np.ceil(x2, p) == np.ceil(x, p) ).all() for x2 in st_rep_after.xcart )
#c = any( ( np.floor(x2, p) == np.floor(x, p) ).all() for x2 in st_rep_after.xcart )
#print a, b, c
#np.concatenate(a, b, c):
if not a:
print_and_log("Error! Can't find ", np.around(x, 3),
"in replic ")
raise RuntimeError
#assert all([ all( np.around(v1, 8) == np.around(v2, 8) ) for (v1, v2) in zip(st_rep_after.xcart, rep.init.xcart) ])
print_and_log("add_impurity: test succesfully done")
if natoms_v1 != len(added.init.xcart):
print_and_log(
"You have different number of pores in different versions\n")
raise RuntimeError
return
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
"""0.Begin----------------------------------------------------------------------------"""
znucl = element_name_inv(impurity_type)
if impurity_type != 'octa' and impurity_type not in it_new:
print_and_log("add_impurity: Your name 'it_new' is incorrect!\n\n")
raise RuntimeError
#del header.history[-2]
#
#hstring = ("add_impurity('%s', '%s', '%s', calc, %.3f, '%s', '%s', %s, '%s') #at %s" %
# (it_new, impurity_type, addtype, r_pore,
# it_to, ise_to, verlist_to, copy_geo_from,
# datetime.date.today() ) )
hstring = ("%s #on %s" %
(traceback.extract_stack(None, 2)[0][3], datetime.date.today()))
if hstring != header.history[-1]: header.history.append(hstring)
#geo_exists =
"""1. The case of insertion to existing calculations--------------------------------------------------"""
if verlist_to:
for v in verlist_to:
if only_version and v not in only_version:
continue # only_version = None works for all versions
id = (it_to, ise_to, v)
new = copy.deepcopy(calc[id])
new.init = new.end #replace init structure by the end structure
new.version = v + add_to_version
new.name = it_new #+'.'+id[1]+'.'+str(id[2])
new.des = 'Obtained from ' + str(
id) + ' by adding ' + impurity_type + ' impurity '
path_new_geo = struct_des[
it_new].sfolder + "/" + it_new + "/" + it_new + '.imp.' + addtype + '.' + str(
new.version) + '.' + 'geo'
new.init.name = it_new + ".init." + str(new.version)
xyzpath = struct_des[it_new].sfolder + "/" + it_new
new.path["input_geo"] = geo_folder + path_new_geo
print_and_log("File '" + new.path["input_geo"] +
"' with impurity will be created\n")
#new.init.name = 'test_before_add_impurity'
new = add(znucl,
xyzpath,
new,
write_geo,
put_exactly_to=put_exactly_to)
"""2. The case of insertion to geo files------------------------------------------------------------"""
else:
""" Please rewrite using new functions """
print_and_log(
"You does not set 'id' of relaxed calculation. I try to find geometry files in "
+ it_new + " folder\n")
if it_to:
geo_path = geo_folder + struct_des[it_to].sfolder + "/" + it_to
else:
geo_path = geo_folder + struct_des[
it_new].sfolder + "/" + it_new + '/from'
if copy_geo_from:
print_and_log("You asked to copy geo files from " + copy_geo_from +
" to " + geo_path + " folder\n")
#if not os.path.exists(os.path.dirname(geo_path)):
runBash("mkdir -p " + geo_path)
runBash("cp " + copy_geo_from + "/* " + geo_path)
if os.path.exists(geo_path):
print_and_log("Folder '" + geo_path +
"' was found. Trying to add impurity\n")
else:
print_and_log("Error! Folder " + geo_path + " does not exist\n")
raise RuntimeError
#geofilelist = glob.glob(geo_path+'/*.geo*') #Find input_geofile
#geofilelist = runBash('find '+geo_path+' -name "*grainA*.geo*" ').splitlines()
#geofilelist = runBash('find '+geo_path+' -name "*.geo*" ').splitlines()
geofilelist = glob.glob(geo_path + '/*.geo*')
print_and_log("There are several files here already: ",
geofilelist,
imp='y')
#print 'find '+geo_path+' -name "*.geo*" ',geofilelist
#return
for input_geofile in geofilelist:
v = int(runBash("grep version " + str(input_geofile)).split()[1])
if only_version and v not in only_version:
continue # only_version = None works for all versions
new = CalculationVasp()
new.version = v
new.name = input_geofile
new.read_geometry(input_geofile)
init = copy.deepcopy(new)
igl = input_geofile.split("/")
#new.name = igl[-3]+'/'+igl[-3] #+input_geofile
new.name = struct_des[it_new].sfolder + "/" + it_new + "/" + it_new
print_and_log("New path and part of name of file is ",
new.name,
imp='Y')
#return
new.des = 'Obtained from ' + input_geofile + ' by adding ' + impurity_type + ' impurity '
#new.init.xred = new.xred
#new.init.rprimd = new.rprimd
#print new.rprimd
new.init.name = new.name + '.imp.' + addtype + '.' + str(
new.version)
#new.path["input_geo"] = geo_folder+it_new+"/"+new.end.name+'.'+'geo'
new.path[
"input_geo"] = geo_folder + "/" + new.init.name + '.' + 'geo'
#new.init.name = 'test_before_add_impurity'
new = add(znucl, "", new, write_geo, put_exactly_to=put_exactly_to)
return new.path["input_geo"] #return for last version
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.xcart = xred2xcart(mat.init.xred, mat.init.rprimd) #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 add_impurity(it_new, impurity_type = None, addtype = 'central', calc = [], r_pore = 0.5,
it_to = '', ise_to = '', verlist_to = [], copy_geo_from = "", find_close_to = (),add_to_version = 0,
write_geo = True, only_version = None, fine = 4, put_exactly_to = None, check_pore_vol = 0, replace_atom = None, override = False):
"""
Add impurities in pores.
Input:
it_new - name of new structure with impurity
impurity_type - name of impurity from Mendeley table, for example 'C'
addtype - type of adding: ['central',]; 'central' means that impurity
will be placed as close to the geometrical center of cell as possible.
it_to , ise_to , verlist_to - completed calculations in which impurity
will be added
if 'verlist_to' is empty, function will try to find geometry files in 'geo_folder + struct_des[it_to].sfolder' folder;
even if 'it_to' is empty it will try to find files in 'geo_folder + struct_des[it_new].sfolder+'/from' ' folder.
'ise_to' also can be empty
if 'copy_geo_from' is not empty, then programm copy all files from folder 'copy_geo_from' to
folder 'geo_folder + struct_des[it_to].sfolder+"/"+it_to' or 'geo_folder + struct_des[it_new].sfolder+"/from" '
'find_close_to' is tuple of three reduced coordinates of point close to which you want to find impurity. If empty - ignored;
'add_to_version' is integer number added to each 'verlist_to' number to produce ver_new.
'only_version' - if == [v,], then instertion will be provided only for v. If None insertion will be made in all found versions
If you want to add impurity to relaxed structure ...
'fine' - integer number; allows to reduce number of small steps for defining center
Possible addtype's:
'central' - add one atom to the pore which is most close to the center of the cell but with reduced coordinates less than 0.5 0.5 0.5
'all_pore' - add atoms in every found pore
'all_local' - add atoms to every local point which allows to visualise topology of pores.
'gb' - uses self.gbpos and places atom close to this value assuming that it will be at gb
'grain_vol' - uses self.gbpos and assuming that cell contains two gb and two equal grains, places atom close to the centre of grain; y and z can be arbiratry
put_exactly_to - will add impurity to this point
find_close_to - will try to find closest void and insert pore here.
check_pore_vol - allows to estimate volume of pores; has problems for big cells
replace_atom - if not None, than the specified atom is substituted
Side effects: creates new geometry folder with input structures;
"""
struct_des = header.struct_des
def test_adding_of_impurities(added, init, v):
"""
Can be used only inside add_impurity()
Replicates the structure and find again pores
"""
global natoms_v1
if added == None: return
if v == 1: #TEST
natoms_v1 = len(added.init.xcart) # for test
st_rep_after = replic( added.init, (1,2,1) )
rep = copy.deepcopy(init)
rep.init = replic( rep.init, (1,2,1) );
#print rep
rep = add(znucl, "", rep, write_geo = False)
#print rep
#print "xcart of replic after adding ", st_rep_after.xcart
#print "xcart of adding to replic ", rep.init.xcart
if len(st_rep_after.xcart) != len(rep.init.xcart): raise RuntimeError
p = 0
#for x2 in st_rep_after.xcart:
# print x2
for x in rep.init.xcart:
a = any( ( np.around(x2, p) == np.around(x, p) ).all() for x2 in st_rep_after.xcart )
#b = any( ( np.ceil(x2, p) == np.ceil(x, p) ).all() for x2 in st_rep_after.xcart )
#c = any( ( np.floor(x2, p) == np.floor(x, p) ).all() for x2 in st_rep_after.xcart )
#print a, b, c
#np.concatenate(a, b, c):
if not a:
print_and_log( "Error! Can't find ", np.around(x,3), "in replic ")
raise RuntimeError
#assert all([ all( np.around(v1, 8) == np.around(v2, 8) ) for (v1, v2) in zip(st_rep_after.xcart, rep.init.xcart) ])
print_and_log( "add_impurity: test succesfully done")
if natoms_v1 != len(added.init.xcart): print_and_log("You have different number of pores in different versions\n"); raise RuntimeError
return
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.xcart = xred2xcart(st.xred, st.rprimd)
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
"""0.Begin----------------------------------------------------------------------------"""
znucl = element_name_inv(impurity_type)
if impurity_type != 'octa' and impurity_type not in it_new:
print_and_log("add_impurity: Your name 'it_new' is incorrect!\n\n")
raise RuntimeError
#del header.history[-2]
#
#hstring = ("add_impurity('%s', '%s', '%s', calc, %.3f, '%s', '%s', %s, '%s') #at %s" %
# (it_new, impurity_type, addtype, r_pore,
# it_to, ise_to, verlist_to, copy_geo_from,
# datetime.date.today() ) )
hstring = ("%s #on %s"% (traceback.extract_stack(None, 2)[0][3], datetime.date.today() ) )
if hstring != header.history[-1]: header.history.append( hstring )
#geo_exists =
"""1. The case of insertion to existing calculations--------------------------------------------------"""
if verlist_to:
for v in verlist_to:
if only_version and v not in only_version: continue # only_version = None works for all versions
id = (it_to, ise_to, v)
new = copy.deepcopy(calc[id])
new.init = new.end #replace init structure by the end structure
new.version = v+add_to_version
new.name = it_new#+'.'+id[1]+'.'+str(id[2])
new.des = 'Obtained from '+str(id)+' by adding '+impurity_type+' impurity '
path_new_geo = struct_des[it_new].sfolder+"/"+it_new+"/"+it_new+'.imp.'+addtype+'.'+str(new.version)+'.'+'geo'
new.init.name = it_new+".init."+str(new.version)
xyzpath = struct_des[it_new].sfolder+"/"+it_new
new.path["input_geo"] = geo_folder+path_new_geo
print_and_log("File '"+new.path["input_geo"] +"' with impurity will be created\n");
#new.init.name = 'test_before_add_impurity'
new = add(znucl, xyzpath, new, write_geo, put_exactly_to = put_exactly_to)
"""2. The case of insertion to geo files------------------------------------------------------------"""
else:
print_and_log("You does not set 'id' of relaxed calculation. I try to find geometry files in "+it_new+" folder\n")
if it_to: geo_path = geo_folder + struct_des[it_to].sfolder + "/" + it_to
else: geo_path = geo_folder + struct_des[it_new].sfolder + "/" + it_new+'/from'
if copy_geo_from:
print_and_log("You asked to copy geo files from "+copy_geo_from+" to " +geo_path+ " folder\n")
#if not os.path.exists(os.path.dirname(geo_path)):
runBash( "mkdir -p "+geo_path )
runBash( "cp "+copy_geo_from+"/* "+geo_path )
if os.path.exists(geo_path):
print_and_log("Folder '"+geo_path +"' was found. Trying to add impurity\n");
else:
print_and_log("Error! Folder "+geo_path+" does not exist\n"); raise RuntimeError
#geofilelist = glob.glob(geo_path+'/*.geo*') #Find input_geofile
#geofilelist = runBash('find '+geo_path+' -name "*grainA*.geo*" ').splitlines()
#geofilelist = runBash('find '+geo_path+' -name "*.geo*" ').splitlines()
geofilelist = glob.glob(geo_path+'/*.geo*')
print_and_log( "There are several files here already: ", geofilelist, imp = 'y' )
#print 'find '+geo_path+' -name "*.geo*" ',geofilelist
#return
for input_geofile in geofilelist:
v = int( runBash("grep version "+str(input_geofile) ).split()[1] )
if only_version and v not in only_version: continue # only_version = None works for all versions
new = CalculationVasp()
new.version = v
new.name = input_geofile
new.read_geometry(input_geofile)
init = copy.deepcopy(new)
igl = input_geofile.split("/")
#new.name = igl[-3]+'/'+igl[-3] #+input_geofile
new.name = struct_des[it_new].sfolder+"/"+it_new+"/"+it_new
print_and_log( "New path and part of name of file is ", new.name, imp = 'Y')
#return
new.des = 'Obtained from '+input_geofile+' by adding '+impurity_type+' impurity '
#new.init.xred = new.xred
#new.init.rprimd = new.rprimd
#print new.rprimd
new.init.name = new.name+'.imp.'+addtype+'.'+str(new.version)
#new.path["input_geo"] = geo_folder+it_new+"/"+new.end.name+'.'+'geo'
new.path["input_geo"] = geo_folder+"/"+new.init.name+'.'+'geo'
#new.init.name = 'test_before_add_impurity'
new = add(znucl, "", new, write_geo, put_exactly_to = put_exactly_to)
return new.path["input_geo"] #return for last version
def write_jmol(xyzfile, pngfile, scriptfile = None, atomselection = None, topview = False, orientation = None,
axis = False, bonds = True, rprimd = None, shift = None, rotate = None,
label = None, high_contrast = None, specialcommand = None,
boundbox = 2):
"""
atomselection - string in gmol format with number of atoms to be nrotateSelected
topview - additional top view, requires two models in xyz
orientation - additional rotation
axis - add axes
rotate - rotation of all atoms around view axis in degrees
"""
if not scriptfile:
scriptfile = os.getcwd()+'/'+'temporary_jmol_script'
with open(scriptfile,'w') as f:
f.write('set frank off\n') #no jmol label
if bonds:
f.write('set autobond on\n')
else:
f.write('set autobond off\n set bonds off\n')
f.write('load "'+xyzfile+'"\n')
f.write('select all \ncpk 250 \nwireframe 0.3\n') #250
f.write('background white \nselect Ti* \ncolor [20,120,250] \nselect C* \ncolor [80,80,80]\n cpk 100\n')
f.write('set perspectivedepth off\n')
if boundbox:
f.write('set boundbox ' +str(boundbox)+ ' \n')
# f.write('set specular 85\n set specpower 85\n set diffuse 85\n')
if high_contrast: #allows to make better view for black and white printing
f.write('set ambient 10 \nset specular 95\n set specpower 95\n set diffuse 95\n')
if axis:
f.write('set axes 10 \naxes scale 2.5 \n')
f.write('axes labels "X" "Y" "Z" "" \n')
f.write('color axes red \n')
f.write('font axes 26 \n')
if orientation:
f.write(orientation+'\n')
if atomselection:
f.write('select '+atomselection+'\n')
f.write('color purple \n')
if topview:
f.write('select * /2 \ntranslateSelected 0 '+str(-rprimd[1][1]*shift)+' 0\nrotateSelected X 90\n')
f.write('wireframe 0.1\ncpk 150\nmodel 0\n#zoom 60\n')
if label:
j = 1
name_old = ''
for i, el in enumerate(label):
name = el[0]+el[1]
if name != name_old: j = 1
label = str(j)+el[1]
# print "label",label
f.write('select '+el[0]+str(i+1)+'\ncpk 200\nset labeloffset 0 0\nset labelfront\ncolor label black\nlabel '+label+'\n font label 24 bold \n')
j+=1
name_old = name
if rotate:
f.write('rotate z '+str(rotate)+'\n')
if specialcommand:
f.write(specialcommand)
# f.write('write image 2800 2800 png "'+pngfile+'"')
f.write('write image 1800 1800 png "'+pngfile+'"')
print_and_log( runBash(header.path_to_jmol+' -ions '+scriptfile) )
# print runBash('convert '+pngfile+' -shave 0x5% -trim '+pngfile) #cut by 5% from up and down (shave) and that trim left background
print_and_log( pngfile )
print_and_log( runBash('convert '+pngfile+' -trim '+pngfile) ) # trim background
return
def calculate_voronoi(self, state='end'):
# By default two quantities per atom are calculated by this compute.
# The first is the volume of the Voronoi cell around each atom.
# Any point in an atom's Voronoi cell is closer to that atom than any other.
# The second is the number of faces of the Voronoi cell, which
# is also the number of nearest neighbors of the atom in the middle of the cell.
# state - init or end; if init then saved in self.init.vorovol; if end than saved in self.vorovol
write_lammps(self, state, filepath='voronoi_analysis/structure.lammps'
) #write structure for lammps
runBash(
"rm voronoi_analysis/dump.voro; /home/aksenov/installed/lammps-1Feb14/src/lmp_serial < voronoi_analysis/voronoi.in > voronoi_analysis/log"
)
if state == 'end':
self.vorovol = []
self.vorofaces = []
vorovol = self.vorovol
vorofaces = self.vorofaces
elif state == 'init':
self.init.vorovol = []
self.init.vorofaces = []
vorovol = self.init.vorovol
vorofaces = self.init.vorofaces
vsum = 0
wlist = []
with open('voronoi_analysis/dump.voro',
'r') as volfile: #analyze dump.voro
for line in volfile:
if 'ITEM: ATOMS ' in line:
break
for line in volfile:
ll = line.split()
if int(ll[1]) > 1:
wlist.append([ll[0], ll[5], ll[6], ll[2]])
# print 'Volume of atom ',ll[0],'is', ll[5]
vsum = vsum + float(ll[5])
print_and_log('Check total volume ', vsum, self.end.vol)
wlist.sort(key=itemgetter(0)) #sort according to the position of atoms
print_and_log("atom #, voronoi vol, voronoi faces, x coordinate: ", )
print_and_log(wlist)
for w in wlist:
vorovol.append(float(w[1]))
vorofaces.append(int(w[2]))
# print 'Voro vol ',self.end.vorovol
# print 'Voro faces',self.end.vorofaces
# print len(wlist)
if hasattr(self, 'vorovol'):
voro = ''
if len(vorovol) == 2: #C and O
voro = " {0:5.2f} & {1:2d} & {2:5.2f} & {3:2d} ".format(
vorovol[0], vorofaces[0], vorovol[1], vorofaces[1]).center(25)
else:
voro = " {0:5.2f} & {1:2d} ".format(vorovol[0],
vorofaces[0]).center(25)
voro += '&'
else:
voro = ""
print_and_log("Voronoi volume = ", voro, imp='y')
return voro
def write_lammps(st, filename = '', charges = None):
"""Writes structure in lammps format
charges (list of float) - list of charges for each atom type
"""
rprimd = st.rprimd
xcart = st.xcart
xred = st.xred
typat = st.typat
ntypat = st.ntypat
znucl = st.znucl
name = st.name
natom = st.natom
if natom != len(xred) != len(xcart) != len(typat) or len(znucl) != max(typat):
print_and_log( "Error! write_xyz: check your structure" )
if name == '':
name = 'noname'
if xcart == [] or len(xcart) != len(xred):
print_and_log( "Warining! write_xyz: len(xcart) != len(xred) making xcart from xred.\n", imp = 'y')
xcart = xred2xcart(xred, rprimd)
#print xcart[1]
if not filename:
filename = 'lammps/'+name
filename+='.inp'
makedir(filename)
"""Write lammps structure file; """
if 1:
""" My version; valid only for octahedral cells"""
printlog( "Warining! write_lammps(): this func supports only orthogonal cells", imp = 'Y')
with open(filename+'','w') as f:
f.write("Lammps format "+name+'\n')
f.write(str(natom)+" atoms\n")
f.write(str(ntypat)+" atom types\n")
f.write("{:10.8f} {:10.8f} xlo xhi\n".format(0, rprimd[0][0]))
f.write("{:10.8f} {:10.8f} ylo yhi\n".format(0, rprimd[1][1]))
f.write("{:10.8f} {:10.8f} zlo zhi\n".format(0, rprimd[2][2]))
f.write("0.00000000 0.00000000 0.00000000 xy xz yz\n")
f.write("\nAtoms\n\n")
for i, x in enumerate(xcart):
f.write("{0:8d} {1:2d}".format(i+1, typat[i]))
if charges:
f.write(" {:6.3f}".format(charges[typat[i]-1] ) )
f.write(" {:12.6f} {:12.6f} {:12.6f}\n".format(x[0], x[1], x[2] ))
f.write("\n")
printlog('File', filename, 'was written', imp = 'y')
else:
"""Write poscar and convert from poscar to lammps using external script; Valid for arbitary cells"""
cl.write_structure('POSCAR', 'dir', path = 'voronoi_analysis/', state = state)
runBash("voronoi_analysis/VASP-poscar2lammps.awk voronoi_analysis/POSCAR > "+filepath)
if 0:
"""Write lammps.in file """
with open('voronoi_analysis/voronoi.in','w') as f:
f.write("""units metal
atom_style atomic
boundary p p p\n""")
f.write("read_data /home/aksenov/programs/Simulation_wrapper/siman1/voronoi_analysis/structure.lammps\n")
# f.write('lattice custom 1 ')
# for i, a in enumerate(rprimd):
# f.write(' a'+str(i+1))
# for x in a:
# f.write(' '+str(x))
# f.write(' &\n')
# for x in xred:
# f.write(' basis {0:f} {1:f} {2:f}&\n '.format(x[0], x[1], x[2]) )
# f.write("""\n
# region 1 prism 0 1 0 1 0 1 1 0 0
# create_box 1 prism
# create_atoms 1 prism""")
for i in range(ntypat):
f.write('\nmass '+str(i+1)+' '+str(int(znucl[i]))+'\n')
f.write('pair_style lj/cut 2.0\n')
for i in range(ntypat):
for j in range(i, ntypat):
f.write('pair_coeff '+str(i+1)+' '+str(j+1)+' 0.0 1.0\n')
f.write("""compute v1 all voronoi/atom
dump d1 all custom 1 /home/aksenov/programs/Simulation_wrapper/siman1/voronoi_analysis/dump.voro id type x y z c_v1[1] c_v1[2]
run 0
uncompute v1\n""")
return
def write_lammps(st, filename='', charges=None):
"""Writes structure in lammps format
charges (list of float) - list of charges for each atom type
"""
rprimd = st.rprimd
xcart = st.xcart
xred = st.xred
typat = st.typat
ntypat = st.ntypat
znucl = st.znucl
name = st.name
natom = st.natom
if natom != len(xred) != len(xcart) != len(typat) or len(znucl) != max(
typat):
printlog("Error! write_xyz: check your structure")
if name == '':
name = 'noname'
if xcart == [] or len(xcart) != len(xred):
printlog(
"Warining! write_xyz: len(xcart) != len(xred) making xcart from xred.\n",
imp='y')
xcart = xred2xcart(xred, rprimd)
#print xcart[1]
if not filename:
filename = 'lammps/' + name
filename += '.inp'
makedir(filename)
"""Write lammps structure file; """
if 1:
""" My version; valid only for octahedral cells"""
printlog(
"Warining! write_lammps(): this func supports only orthogonal cells",
imp='Y')
with open(filename + '', 'w') as f:
f.write("Lammps format " + name + '\n')
f.write(str(natom) + " atoms\n")
f.write(str(ntypat) + " atom types\n")
f.write("{:10.8f} {:10.8f} xlo xhi\n".format(0, rprimd[0][0]))
f.write("{:10.8f} {:10.8f} ylo yhi\n".format(0, rprimd[1][1]))
f.write("{:10.8f} {:10.8f} zlo zhi\n".format(0, rprimd[2][2]))
f.write("0.00000000 0.00000000 0.00000000 xy xz yz\n")
f.write("\nAtoms\n\n")
for i, x in enumerate(xcart):
f.write("{0:8d} {1:2d}".format(i + 1, typat[i]))
if charges:
f.write(" {:6.3f}".format(charges[typat[i] - 1]))
f.write(" {:12.6f} {:12.6f} {:12.6f}\n".format(
x[0], x[1], x[2]))
f.write("\n")
printlog('File', filename, 'was written', imp='y')
else:
"""Write poscar and convert from poscar to lammps using external script; Valid for arbitary cells"""
cl.write_structure('POSCAR',
'dir',
path='voronoi_analysis/',
state=state)
runBash(
"voronoi_analysis/VASP-poscar2lammps.awk voronoi_analysis/POSCAR > "
+ filepath)
if 0:
"""Write lammps.in file """
with open('voronoi_analysis/voronoi.in', 'w') as f:
f.write("""units metal
atom_style atomic
boundary p p p\n""")
f.write(
"read_data /home/aksenov/programs/Simulation_wrapper/siman1/voronoi_analysis/structure.lammps\n"
)
# f.write('lattice custom 1 ')
# for i, a in enumerate(rprimd):
# f.write(' a'+str(i+1))
# for x in a:
# f.write(' '+str(x))
# f.write(' &\n')
# for x in xred:
# f.write(' basis {0:f} {1:f} {2:f}&\n '.format(x[0], x[1], x[2]) )
# f.write("""\n
# region 1 prism 0 1 0 1 0 1 1 0 0
# create_box 1 prism
# create_atoms 1 prism""")
for i in range(ntypat):
f.write('\nmass ' + str(i + 1) + ' ' + str(int(znucl[i])) +
'\n')
f.write('pair_style lj/cut 2.0\n')
for i in range(ntypat):
for j in range(i, ntypat):
f.write('pair_coeff ' + str(i + 1) + ' ' +
str(j + 1) + ' 0.0 1.0\n')
f.write("""compute v1 all voronoi/atom
dump d1 all custom 1 /home/aksenov/programs/Simulation_wrapper/siman1/voronoi_analysis/dump.voro id type x y z c_v1[1] c_v1[2]
run 0
uncompute v1\n""")
return
def write_jmol(xyzfile,
pngfile,
scriptfile=None,
atomselection=None,
topview=1,
orientation=None,
axis=False,
bonds=True,
rprimd=None,
shift=None,
rotate=None,
label=None,
high_contrast=None,
specialcommand=None,
boundbox=2,
atom_labels=None):
"""
atomselection - string in gmol format with number of atoms to be nrotateSelected
topview - additional top view, requires two models in xyz
orientation - additional rotation
axis - add axes
rotate - rotation of all atoms around view axis in degrees
label (tuple ()) - used for impurities, please decribe
atom_labels (bool) - turn on atom labels
"""
if not scriptfile:
scriptfile = os.getcwd() + '/' + 'temporary_jmol_script'
with open(scriptfile, 'w') as f:
f.write('set frank off\n') #no jmol label
if bonds:
f.write('set autobond on\n')
else:
f.write('set autobond off\n set bonds off\n')
f.write('load "' + xyzfile + '"\n')
f.write('select all \n') #250
if 0:
f.write('cpk 250 \nwireframe 0.3\n')
f.write('background white \n')
# f.write('select Ti* \ncolor [20,120,250] \nselect C* \ncolor [80,80,80]\n cpk 100\n')
f.write('set perspectivedepth off\n')
if boundbox:
f.write('set boundbox ' + str(boundbox) + ' \n')
# f.write('set specular 85\n set specpower 85\n set diffuse 85\n')
if high_contrast: #allows to make better view for black and white printing
f.write(
'set ambient 10 \nset specular 95\n set specpower 95\n set diffuse 95\n'
)
if axis:
f.write('set axes 10 \naxes scale 2.5 \n')
f.write('axes labels "X" "Y" "Z" "" \n')
f.write('color axes red \n')
f.write('font axes 26 \n')
if orientation:
f.write(orientation + '\n')
if atomselection:
f.write('select ' + atomselection + '\n')
f.write('color purple \n')
if topview:
f.write('select * /2 \ntranslateSelected 0 ' +
str(-rprimd[1][1] * shift) + ' 0\nrotateSelected X 90\n')
f.write('wireframe 0.1\ncpk 150\nmodel 0\n#zoom 60\n')
if label:
j = 1
name_old = ''
for i, el in enumerate(label):
name = el[0] + el[1]
if name != name_old: j = 1
label = str(j) + el[1]
# print "label",label
f.write(
'select ' + el[0] + str(i + 1) +
'\ncpk 200\nset labeloffset 0 0\nset labelfront\ncolor label black\nlabel '
+ label + '\n font label 24 bold \n')
j += 1
name_old = name
if atom_labels:
f.write(
'select all\nset label "%e"\nset labeloffset 0 0\nset labelfront off\ncolor label black\nfont label 18 bold \n'
)
if rotate:
f.write('rotate z ' + str(rotate) + '\n')
if specialcommand:
f.write(specialcommand + '\n')
# f.write('write image 2800 2800 png "'+pngfile+'"')
f.write('write image 1800 1800 png "' + pngfile + '"')
printlog(runBash(header.PATH2JMOL + ' -ions ' + scriptfile))
# print runBash('convert '+pngfile+' -shave 0x5% -trim '+pngfile) #cut by 5% from up and down (shave) and that trim left background
printlog(pngfile)
printlog(runBash('convert ' + pngfile + ' -trim ' +
pngfile)) # trim background
printlog('png file by Jmol', pngfile, 'was written', imp='y')
return
