def thesis_presentation_pictures():
#Pictures for presentation
# write_xyz(calc[('hs332C.f','93', 1)].end, repeat = 2, analysis = 'imp_surrounding',nnumber = 6,topview = 0, boundbox = None,
# specialcommand = 'select all\nwireframe 0.1\nselect Ti*\ncpk 200\nselect C*\ncpk 230\ncolor red\n',
# orientation = 'moveto /* time, axisAngle */ 1.0 { 233 510 828 162.65} /* zoom, translation */ 75.61 0.0 0.0 /* center, rotationRadius */ {3.396805 2.94223 3.50884} 3.7937615 /* navigation center, translation, depth */ {0 0 0} 0 0 0 /* cameraDepth, cameraX, cameraY */ 3.0 0.0 0.0;' )
write_xyz(calc[('hs443C.f','93', 1)].init, repeat = 2, topview = 0 )
return
def seg_energy_vs_voronoi(calc, conv, varset, plot = 0):
"""
Was used to calculate all segregation energies vs voronoi volume to find some dependence
plot - if 1: than plot dependence
"""
aggregate_list = []
if 0:
"""1. Start processing of calculation specific information"""
#base = 't111gCOv2'
base = 't111gCvOvms'
coseg_list = ['t111gCOi1.4-3', 't111gOCi1.4-3', 't111gCOi2.2-1', 't111gOCi2.2-1', 't111gCOi3.4-1', 't111gOCi3.4-1', \
't111gCOi4.4-4is','t111gCOi5.2-2is', 't111gCOi6.1-1is', 't111gCOi7.3-3is','t111gCOi8.2-3','t111gOCi8.2-3', \
't111gCOi9.4-4ms','t111gCOi10.2-2ms','t111gCOi11.4-3', 't111gOCi11.4-3', \
't111gCOi12.1-3', 't111gOCi12.1-3', 't111gCOi13.4-2', 't111gOCi13.4-2', 't111gCOi14.2-1', 't111gOCi14.2-1', 't111gCOi15.4-4is','t111gCOi16.2-2is']
seg_list = ['t111gCi1Ov', 't111gCi2Ov','t111gCi3Ov','t111gCi4Ov','t111gOi1Cv','t111gOi2Cv','t111gOi3Cv','t111gOi4Cv',]
bulk_list = ['t111gCOv2', 't111gCOv5' ]
list = res_loop(base,'93kp9',range(2,3),calc,conv,varset, 'coseg', (base,) , voronoi = True )
aggregate_list.append(list)
# os._exit(0)
for key in seg_list:
# print key
# if 'Oi' in key: continue
list = res_loop(key,'93kp9',range(2,3),calc,conv,varset, 'coseg', (base,) , voronoi = True )
aggregate_list.append(list)
pass
# res_loop('t112gCOi6.1-1is','93kp9',range(1,5),calc,conv,varset, 'coseg', ('t112gCvOvms',) )
base = 'c1gCvOvms'
coseg_list = [
'c1gCOi1.2-1',
'c1gCOi2.2-1',
'c1gCOi3.1-2',
'c1gCOi4.2-1',
'c1gCOi5.2-1',
'c1gCOi6.1-2',
'c1gCOi7.1-1',
'c1gCOi8.2-2',
'c1gOCi1.2-1',
'c1gOCi2.2-1',
'c1gOCi3.1-2',
'c1gOCi4.2-1',
'c1gOCi5.2-1',
'c1gOCi6.1-2',
'c1gOCi7.1-1',
'c1gOCi8.2-2',
'c1gCOi10.1'
]
bulk_list = ['c1gCOv2',
'c1gCOv4',
'c1gCOv7',]
seg_list = ['c1gCi1Ov', 'c1gCi2Ov', 'c1gOi1Cv', 'c1gOi2Cv', ]
list = res_loop(base,'93kp7',range(2,3),calc,conv,varset, 'coseg', (base,), voronoi = True )
aggregate_list.append(list)
for key in seg_list:
# print key
# if 'Oi' in key: continue
list = res_loop(key,'93kp7',range(2,3),calc,conv,varset, 'coseg', (base,) , voronoi = True )
aggregate_list.append(list)
pass
base = 't111sgCvOvms'
seg_list = ['t111sgCi1Ov', 't111sgCi2Ov', 't111sgCi3Ov', 't111sgCi4Ov', 't111sgCi5Ov', 't111sgCi6Ov', 't111sgCi7Ov', 't111sgOi1Cv', 't111sgOi2Cv', 't111sgOi3Cv', 't111sgOi4Cv', 't111sgOi5Cv', 't111sgOi6Cv', 't111sgOi7Cv', ]
list = res_loop(base,'93kp9',range(2,3),calc,conv,varset, 'coseg', (base,) , voronoi = True )
aggregate_list.append(list)
for key in seg_list:
# print key
# if 'Oi' in key: continue
list = res_loop(key,'93kp9',range(2,3),calc,conv,varset, 'coseg', (base,) , voronoi = True )
aggregate_list.append(list)
pass
base = 't21gCvOvms'
seg_list = ['t21gCi1Ov', 't21gCi2Ov', 't21gCi3Ov', 't21gCi4Ov', 't21gOi1Cv', 't21gOi2Cv', 't21gOi3Cv', 't21gOi4Cv', ]
list = res_loop(base,'93',range(2,3),calc,conv,varset, 'coseg', (base,), voronoi = True )
aggregate_list.append(list)
for key in seg_list:
# print key
# if 'Oi' in key: continue
list = res_loop(key,'93',range(2,3),calc,conv,varset, 'coseg', (base,) , voronoi = True )
aggregate_list.append(list)
write_xyz( replic(calc[(key, '93', 1)].end, (1,2,2)), )
pass
base = 'csl71sgCvOvms'
seg_list = ['csl71sgCi1Ov', 'csl71sgCi2Ov', 'csl71sgCi3Ov', 'csl71sgCi4Ov', 'csl71sgCi5Ov', 'csl71sgCi6Ov', 'csl71sgOi1Cv', 'csl71sgOi2Cv', 'csl71sgOi3Cv', 'csl71sgOi4Cv', 'csl71sgOi5Cv', 'csl71sgOi6Cv', ]
list = res_loop(base,'93',range(2,3),calc,conv,varset, 'coseg', (base,) , voronoi = True )
aggregate_list.append(list)
for key in seg_list:
# print key
# if 'Oi' in key: continue
list = res_loop(key,'93',range(2,3),calc,conv,varset, 'coseg', (base,) , voronoi = True )
aggregate_list.append(list)
pass
calc['voronoi'] = aggregate_list
else:
aggregate_list = calc['voronoi']
pass
if 1:
# print res_loop('hs221C','83',101,calc,conv,varset, voronoi = True )
# # print res_loop('hs221.f','83',1,calc,conv,varset, voronoi = True )
# # print res_loop('csl71b_r','83kp8',1,calc,conv,varset, voronoi = True )
# print res_loop('hs221C.f','93',1,calc,conv,varset, voronoi = True ) #9.25 But the sum of Voronoi volume for hexagonal cell is wrong!!!
# print res_loop('hs332C.f','93',1,calc,conv,varset, voronoi = True ) #9.18 But volume for internal atoms seems to be OK,
# print res_loop('hs443C.f','93',1,calc,conv,varset, voronoi = True ) #9.13 But for edge atoms it is even zero.
# print res_loop('hs554C.f','93',1,calc,conv,varset, voronoi = True ) #9.14 It seems that Voronoi module does not recognize oblique cell geometry.
"""2. Analysis"""
esegC = [float(x[1]) for x in aggregate_list if 'Oi' not in x[0]] # C segregation including CvOvms
vorovolC = [float(x[2]) for x in aggregate_list if 'Oi' not in x[0]]
# print esegC,
esegO = [float(x[1]) for x in aggregate_list if 'Ci' not in x[0]] # O segregation including CvOvms
vorovolO = [float(x[4]) for x in aggregate_list if 'Ci' not in x[0]]
"""Plot dependence"""
name = 'Voronoi volume - segregation energy'
set = 'Eng'
fig, (ax1, ax2) = plt.subplots(nrows=2, ncols=1)
if set == 'Rus':
matplotlib.rcParams.update({'font.size': 16})
xlabel = u'Энергия сегрегации (мэВ)'
# print xlabel
ylabel = u'Объем Вороного ($\AA^3$)'
label1 = u'Рассчет'
label2 = u'Аппроксимация'
title1 = u'Углерод'
title2 = u'Кислород'
else:
xlabel = 'Segregation energy (meV)'
ylabel = 'Voronoi volume ($\AA^3$)'
label1 = 'Calculated'
label2 = 'Fitted'
title1 = 'Carbon'
title2 = 'Oxygen'
# plt.figure()
#plt.title(name)
ax1.plot(esegC, vorovolC, 'o',label = label1)
k, b = np.polyfit(esegC, vorovolC, 1)
ax1.plot(esegC, np.asarray(esegC) * k + b, '-r',label = label2)
ax1.set_title(title1)
# ax1.legend(loc =4)
# image_name = 'eseg_vorovol_C'
# plt.savefig('images/'+str(image_name)+'.png',format='png', dpi = 300)
# plt.cla()
#plt.title(name)
# plt.ylabel(ylabel)
# plt.xlabel(xlabel)
ax2.plot(esegO, vorovolO, 'o',label = label1)
k, b = np.polyfit(esegO, vorovolO, 1)
ax2.plot(esegO, np.asarray(esegO) * k + b, '-r',label = label2)
ax2.set_title(title2)
ax2.set_xlabel(xlabel)
# ax2.legend(loc =4)
# image_name = 'eseg_vorovol_O'
plt.figtext(0.03, 0.5, ylabel, ha='center', va='center', rotation='vertical')
# fig.set_ylabel(ylabel, va ='center')
# plt.yaxis.set_label_coords(0, 0.5)
# plt.xlabel(xlabel)
plt.tight_layout()
plt.subplots_adjust(left=0.15, bottom = 0.15)
image_name = 'eseg_vorovol_CandO'
plt.savefig('images/'+str(image_name)+'.png',format='png', dpi = 300)
return
def add_neb(starting_calc = None, st = None,
it_new = None, ise_new = None, i_atom_to_move = None,
up = 'up1',
search_type = 'vacancy_creation',
images = 3, r_impurity = None, corenum = 15,
calc_method = ['neb'],
inherit_option = None, mag_config = None, i_void_start = None, i_void_final = None,
atom_to_insert = 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
):
"""
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*
###INPUT:
- starting_calc (Calculation) - Calculation object with structure
- st (Structure) - structure, can be used instead of Calculation
- it_new (str) - name for calculation
- i_atom_to_move (int) - number of atom for moving;
- *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) - number of voids from the suggested lists
- atom_to_insert (str) - element name of atom to insert
- 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
- calc_method (list)
- 'neb'
- 'only_neb' - run only footer
- x_start, x_final (array) - explicit coordinates of moving atom for starting and final positions, combined with atom_to_insert
- upload_vts (bool) - if True upload Vasp.pm and nebmake.pl to server
- run (bool) - run on server
###RETURN:
None
###DEPENDS:
###TODO
please take care of manually provided i_atom_to_move in case of replicate flag using init_numbers
"""
calc = header.calc
struct_des = header.struct_des
varset = header.varset
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:
# 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')
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])
"""1. Choose atom (or insert) for moving """
atoms_to_move = []
for i, typ, x in zip(range(st.natom), st.typat, st.xcart): #try to find automatically
if st.znucl[typ-1] == 3: #Li
atoms_to_move.append([i, 'Li', x])
if st.znucl[typ-1] == 11: #
atoms_to_move.append([i, 'Na', x])
if st.znucl[typ-1] == 19: #
atoms_to_move.append([i, 'K', x])
if is_list_like(xr_start):
x_start = xred2xcart([xr_start], st.rprimd)[0]
st1 = st.add_atoms([x_start], atom_to_insert)
x_m = x_start
name_suffix+='s'
write_xyz(st1, file_name = st.name+'_manually_start')
printlog('Start position is created manually by adding xr_start', xr_start, x_start)
elif not atoms_to_move:
print_and_log('No atoms to move found, you probably gave me intercalated structure', important = 'y')
print_and_log('Searching for voids', important = 'y')
st_pores = find_pores(st, r_matrix = 0.5, r_impurity = r_impurity, fine = 1, calctype = 'all_pores')
print_and_log('List of found voids:\n', np.array(st_pores.xcart) )
write_xyz(st.add_atoms(st_pores.xcart, 'H'), file_name = st.name+'_possible_positions')
write_xyz(st.add_atoms(st_pores.xcart, 'H'), replications = (2,2,2), file_name = st.name+'_possible_positions_replicated')
sums = []
avds = []
for x in st_pores.xcart:
summ = local_surrounding(x, st, n_neighbours = 6, control = 'sum', periodic = True)
avd = local_surrounding(x, st, n_neighbours = 6, control = 'av_dev', periodic = True)
# print sur,
sums.append(summ)
avds.append(avd[0])
# print
sums = np.array(sums)
avds = np.array(avds).round(0)
print_and_log('Sum of distances to 6 neighboring atoms for each void (A):\n', sums, imp ='y')
print_and_log('Distortion of voids (0 - is symmetrical):\n', avds, imp ='y')
crude_prec = 1
sums_crude = np.unique(sums.round(crude_prec))
print_and_log('The unique voids based on the sums:',
'\nwith 0.01 A prec:',np.unique(sums.round(2)),
'\nwith 0.1 A prec:',sums_crude,
imp ='y')
print_and_log('Based on crude criteria only', len(sums_crude),'types of void are relevant')
print_and_log('Please use *i_void_start* to choose the void for atom insertion from this Table:',
end = '\n', imp = 'Y')
insert_positions = []
start_table = []
for i, s in enumerate(sums_crude):
index_of_first = np.where(sums.round(crude_prec)==s)[0][0]
start_table.append([i, st_pores.xcart[index_of_first].round(2), index_of_first,
avds[index_of_first], sums[index_of_first] ])
insert_positions.append( st_pores.xcart[index_of_first] )
print_and_log( tabulate(start_table, headers = ['Start void #', 'Cart.', 'Index', 'Dev.', 'Sum'], tablefmt='psql'), imp = 'Y' )
if i_void_start == None:
sys.exit()
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 = ''
else:
print_and_log('I have found', len(atoms_to_move), ' anion atoms', important = 'n')
print_and_log( 'Sums of bond lengths around these atoms:',)
sums = []
for a in atoms_to_move:
summ = local_surrounding(a[2], st, n_neighbours = 6, control = 'sum', periodic = True)
sums.append(summ)
# print( summ, end = '')
print_and_log('\nAmong them only',len(set(sums)), 'unique' , important = 'n')
# if
print_and_log('Choosing the first' , important = 'n')
type_atom_to_move = atoms_to_move[0][1]
i_atom_to_move = atoms_to_move[0][0]+1
el_num_suffix = type_atom_to_move +str(i_atom_to_move)
i_m = i_atom_to_move-1
x_m = st.xcart[i_m]
#highlight the moving atom for user for double-check
# st_new = st.change_atom_z(i_m, new_z = 100)
# search_type = 'vacancy_creation'
"""2. Choose final position"""
if is_list_like(xr_final):
x_final = xred2xcart([xr_final], st.rprimd)[0]
st2 = st.add_atoms([x_final], atom_to_insert)
x_del = x_final
search_type = 'manual_insertion'
name_suffix+='f'+atom_to_insert
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 = find_pores(st, r_matrix = 0.5, r_impurity = r_impurity, fine = 2, calctype = 'all_pores')
sur = local_surrounding(x_m, st_pores, n_neighbours = len(st_pores.xcart), control = 'atoms', periodic = True)
# print sur
print_and_log(
'I can suggest you '+str (len(sur[0])-1 )+' end positions.' )
# The distances to them are : '+str(np.round(sur[3], 2) )+' A\n ',
# 'Openning Jmol end positions are highlighted by inserting H ', important = 'y')
# print x_m
# print sur[0]
print_and_log('Please choose *i_void_final* from the following Table:', end = '\n', imp = 'Y')
final_table = []
for i, (x, d, ind) in enumerate( zip(sur[0], sur[3], sur[2])[1:] ):
final_table.append([i, np.array(x).round(2), round(d, 2), avds[ind], sums[ind] ] )
print_and_log( tabulate(final_table, headers = ['Final void #', 'Cart.', 'Dist', 'Dev.', 'Sum'], tablefmt='psql'), imp = 'Y' )
if i_void_final == None:
sys.exit()
x_final = sur[0][i_void_final+1] # +1 because first element is x_m atom itself
write_xyz(st.add_atoms([ x_final], 'H'), replications = (2,2,2), file_name = st.name+'_possible_positions2_replicated')
# sys.exit()
# write_xyz(st.add_atoms(sur[0][2:3], 'H'), analysis = 'imp_surrounding', show_around = 230,nnumber = 10, replications = (2,2,2), file_name = 'local230')
# # write_xyz(st.add_atoms(sur[0][0:1], 'H'), analysis = 'imp_surrounding', show_around = 226,nnumber = 10, replications = (2,2,2), file_name = 'local')
# run_jmol
print_and_log('Choosing the closest position as end', important = 'n')
# i_void_final = 0
st1 = st
# print st1.natom
# sys.exit()
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', important = '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.leave_only(type_atom_to_move) , n_neighbours = 4, control = 'atoms',
periodic = False)
# print 'xcart of moving atom', x_m
# print 'Local surround = ', sur
# print 'len', len(sur[0])
if len(sur[0]) < 3:
# print 'rprimd = \n',np.array(st.rprimd)
# print 'r lengths = \n',( [np.linalg.norm(r) for r in st.rprimd] )
# print 'xred = \n', np.array(st.xred)
# print 'xcart = \n', np.array(st.xcart)
print_and_log('The supercell is too small, I increase it 8 times!')
st = replic(st, mul = (2,2,2) )
sur = local_surrounding(x_m, st.leave_only(type_atom_to_move) , n_neighbours = 4, control = 'atoms',
periodic = False)
# print 'xcart of moving atom', x_m
write_xyz(st, file_name = st.name+'_replicated')#replications = (2,2,2))
# print 'Local surround = ', sur
# sys.exit()
print_and_log(
'I can suggest you '+str (len(sur[0]) )+' end positions. The distances to them are : '+str(np.round(sur[3], 2) )+' A\n ',
'They are all', type_atom_to_move, 'atoms', important = 'y')
print_and_log('Choosing the closest position as end', important = 'n')
neb_config = 1 #cause the first item in sur is moving atom itself
x_del = sur[0][neb_config]
i_del = st.find_atom_num_by_xcart(x_del)
print_and_log('Making vacancy at end position for starting configuration', important = 'n')
print_and_log( 'number of atom to delete = ', i_del)
# print st.magmom
st1 = st.del_atom(i_del)
# print st1.magmom
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
st2 = st2.del_atom(i_del) # these two steps provide the same order
name_suffix += el_num_suffix+'v'+str(neb_config)
write_xyz(st1, file_name = st1.name+'_start')# replications = (2,2,2))
write_xyz(st2, file_name = st2.name+'_end')# replications = (2,2,2))
# sys.exit()
# sys.exit()
""" Determining magnetic moments """
if varset[ise_new].vasp_params['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 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]
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_'+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_'+search_type+'.'+str(ver_new)+'.'+'geo'
cl.write_siman_geo(geotype = 'end', description = 'Final conf. for neb from '+obtained_from, override = True)
#prepare calculations
#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 = 'ov', inherit_option = inherit_option, n_neb_images = images, corenum = corenum, run =run )
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')
return it_new
def insert_cluster(insertion, i_center, matrix, m_center):
"""
Take care of orientation; typat should be consistent
Input:
insertion - object of class Structure(), which is supposed to be inserted in matrix
in such a way that i_center will be combined with m_center.
matrix - object of class Structure().
i_center, m_center - numpy arrays (3).
"""
ins = copy.deepcopy(insertion)
mat = copy.deepcopy(matrix)
r = mat.rprimd
for i, z in enumerate(ins.znucl):
if z not in mat.znucl:
mat.znucl.append(z)
mat.ntypat+=1
mat.nznucl.append( ins.nznucl[i] )
hproj = [ (r[0][i]+r[1][i]+r[2][i]) * 0.5 for i in 0,1,2 ] #projection of vectors on three axis
for i, x in enumerate(ins.xcart):
ins.xcart[i] = x - i_center
for i, x in enumerate(mat.xcart):
mat.xcart[i] = x - m_center
max_dis = 1
for i_x, ix in enumerate(ins.xcart):
dv_min = max_dis
print "Insertion atom ",ix,
for j, mx in enumerate(mat.xcart):
dv = mx - ix
for i in 0,1,2:
if dv[i] > hproj[i]: dv = dv - mat.rprimd[i] #periodic boundary conditions - can be not correct (in the sense that closest image can lie not 100 % in the neighbourhood image cell ) for oblique cells and large absolute values of dv
if dv[i] < -hproj[i]: dv = dv + mat.rprimd[i]
len1 = np.linalg.norm(dv)
len2, second_len2 = image_distance(mx, ix, r, 2) #check len1
#print "Lengths calculated with two methods ", len1, len2
len1 = len2 #just use second method
#assert np.around(len1,1) == np.around(len2,1)
if len1 < dv_min:
dv_min = len1;
j_r = j # number of matrix atom to replace
if dv_min == max_dis:
print " is more far away from any matrix atom than ",dv_min," A; I insert it"
mat.xcart.append( ix )
print 'type of added atom is ', ins.typat[i_x]
mat.typat.append( ins.typat[i_x] )
else:
print "will replace martix atom", mat.xcart[j_r]
mat.xcart[j_r] = ix.copy()
mat.xred = xcart2xred(mat.xcart, r)
mat.natom = len(mat.xcart)
mat.name = 'test_of_insert'
write_xyz(mat)
return mat
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 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 "No key", (it_ins, ise_ins, mat.version), "I use previous working version !!!"
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(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"]):
print_and_log("add: File '"+new.path["input_geo"]+"' already exists; continue\n");
return new
#new.init = return_atoms_to_cell(new.init)
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 'Inmpurity just put in ', pores_xred
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 "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)
print "\n"
return new
def write_geometry_files(
dlist,
in_calc,
xcart_pores,
segtyp,
take_final_rprimd_from=None,
add_name_before="",
tlist=[],
configver=False,
add_typat=None,
):
"""Creating files
dlist - list of pairs with distances and numbers
in_calc - base calculation without pores
tlist - list of additional atoms in the case of triples; list of structures
configver - if True each configuration saved as a new version
add_typat - manually determined; please automatize!
"""
print "Warning! add_typat", add_typat
if tlist == []: # convert dlist to tlist - to do earlier
for el in dlist:
config = Structure()
config.name = el[2]
config.length = el[0]
config.typat = add_typat
config.xcart = [el[7], el[8]]
tlist.append(config)
for i, el in enumerate(tlist): # by all found structures
print "el name is ", el.name
stn = copy.deepcopy(in_calc.init)
calc = copy.deepcopy(in_calc)
stn.typat.extend(el.typat)
stn.xcart.extend(el.xcart)
stn.xred = xcart2xred(stn.xcart, stn.rprimd)
xcart_check = xred2xcart(stn.xred, stn.rprimd)
assert len(xcart_check) == len(stn.xcart) # test
assert all(
[all(np.around(v1, 8) == np.around(v2, 8)) for (v1, v2) in zip(stn.xcart, xcart_check)]
) # check if xcart2xred(stn.xcart,r) and xred2xcart(stn.xred,r) are working correctly up to the eight digits after
stn.natom = len(stn.xcart)
"""Adapt new rprimd"""
print "take final rprimd is ", take_final_rprimd_from
if take_final_rprimd_from: # read final rprimd and version
print "Start to read rprimd and version from " + take_final_rprimd_from
in_calc_rprimd = CalculationVasp()
in_calc_rprimd.name = "temp"
in_calc_rprimd.read_geometry(take_final_rprimd_from)
stn.rprimd = in_calc_rprimd.init.rprimd
stn.xcart = xred2xcart(stn.xred, stn.rprimd)
calc.version = in_calc_rprimd.version
elif configver:
calc.version = i + 1
calc.init = stn
des = (
" was obtained by the insertion of C-O pair into "
+ in_calc_name
+ "; final vectors taken from corresponding ver"
)
calc.build.ipairlen = el.length # Initial length of pair
if not hasattr(calc.build, "nadded") or calc.build.nadded == None:
calc.build.nadded = 2
else:
calc.build.nadded += 2
if not hasattr(calc.build, "listadded") or calc.build.listadded == [None]:
calc.build.listadded = range(stn.natom - 2, stn.natom) # list of atoms which were added
else:
calc.build.listadded.extend(range(stn.natom - 2, stn.natom))
structure_name = calc.name + el.name.split(".")[0]
# calc.name = add_name_before+calc.name+ '.' +el[2]+'.'+str(calc.version)
print "Structure_name", structure_name
if structure_name in struct_des:
if configver:
fname = structure_name # calc.name+'C2O2'
calc.path["input_geo"] = (
geo_folder
+ struct_des[fname].sfolder
+ "/"
+ fname
+ "/"
+ structure_name
+ "."
+ segtyp
+ "."
+ str(calc.version)
+ ".geo"
)
else:
calc.path["input_geo"] = (
geo_folder
+ struct_des[structure_name].sfolder
+ "/"
+ structure_name
+ "/"
+ structure_name
+ "."
+ segtyp
+ "."
+ str(calc.version)
+ ".geo"
)
print "write geo to ", calc.path["input_geo"]
calc.write_geometry("init", des)
print "write_geometry_files(): name ", el.name
stn.name = add_name_before + calc.name + "" + str(el.name) + "." + str(calc.version)
# stn = replic(stn, (1,2,2))
write_xyz(stn)
print "__________________________\n\n\n"
return
def find_pairs(
base_name,
segtyp,
in_calc,
central_atoms=[],
xcart1imp=None,
input_dlist_coseg=None,
prec=2,
gvolume_config_num=None,
gbpos=None,
take_final_rprimd_from=None,
main_path=None,
based_on=None,
target_znucl=[22, 6, 8],
max_dist_between_atoms=4.8,
add_typat=[2, 3],
):
"""
Find uniq pairs of atoms and analyse them
Input:
segtyp -
three regimes for cells with grain boundaries:
'segreg' assumes that in_calc contains carbon atom in grain volume, and creates all cases;
'coseg' assumes pure cell and creates only coseg cases.
cosegregation cases of course should be the same for two regimes, however co-segregation configuations after 'coseg' is more easy to relax.
'grainvol' - searching for pairs in grain volume
two regimes for bulk cells:
'bulk_triple' - used for bulk cells without grain boundaries; first step is searching for pairs, second step for triples.
'bulk_pairs' - used for bulk cells without grain boundaries; searching for pairs.
new_name - name of created structures; at first should be added to struct_des[]
in_calc - Calculation() type or path to geo file
region - list of numbers which determine region
central_atoms - list of atoms for which pairs are constructed (Warinig! numbers in new array xcart_pores!);
- parameter to change mode;
xcart1imp - coordinates of first interstitial in the grain interior
input_dlist_coseg - list of configurations with cosegregation cases. Needed to construct corresponding segregation cases. the format is quiet tricky
prec - precision of lengths used to determine unique positions.
gvolume_config_num - number of configuration with two atoms in grain volume choosen by user (usually should be the most favourable)
gbpos - position of grain boundary
take_final_rprimd_from - path to geo file from which rprimd will be used
target_znucl - numbers of target atoms
max_dist_between_atoms - now at least used for 'bulk_pairs' and 'bulk_triple'; maximum length of found pairs.
add_typat - mannualy set please update
"""
def write_geometry_files(
dlist,
in_calc,
xcart_pores,
segtyp,
take_final_rprimd_from=None,
add_name_before="",
tlist=[],
configver=False,
add_typat=None,
):
"""Creating files
dlist - list of pairs with distances and numbers
in_calc - base calculation without pores
tlist - list of additional atoms in the case of triples; list of structures
configver - if True each configuration saved as a new version
add_typat - manually determined; please automatize!
"""
print "Warning! add_typat", add_typat
if tlist == []: # convert dlist to tlist - to do earlier
for el in dlist:
config = Structure()
config.name = el[2]
config.length = el[0]
config.typat = add_typat
config.xcart = [el[7], el[8]]
tlist.append(config)
for i, el in enumerate(tlist): # by all found structures
print "el name is ", el.name
stn = copy.deepcopy(in_calc.init)
calc = copy.deepcopy(in_calc)
stn.typat.extend(el.typat)
stn.xcart.extend(el.xcart)
stn.xred = xcart2xred(stn.xcart, stn.rprimd)
xcart_check = xred2xcart(stn.xred, stn.rprimd)
assert len(xcart_check) == len(stn.xcart) # test
assert all(
[all(np.around(v1, 8) == np.around(v2, 8)) for (v1, v2) in zip(stn.xcart, xcart_check)]
) # check if xcart2xred(stn.xcart,r) and xred2xcart(stn.xred,r) are working correctly up to the eight digits after
stn.natom = len(stn.xcart)
"""Adapt new rprimd"""
print "take final rprimd is ", take_final_rprimd_from
if take_final_rprimd_from: # read final rprimd and version
print "Start to read rprimd and version from " + take_final_rprimd_from
in_calc_rprimd = CalculationVasp()
in_calc_rprimd.name = "temp"
in_calc_rprimd.read_geometry(take_final_rprimd_from)
stn.rprimd = in_calc_rprimd.init.rprimd
stn.xcart = xred2xcart(stn.xred, stn.rprimd)
calc.version = in_calc_rprimd.version
elif configver:
calc.version = i + 1
calc.init = stn
des = (
" was obtained by the insertion of C-O pair into "
+ in_calc_name
+ "; final vectors taken from corresponding ver"
)
calc.build.ipairlen = el.length # Initial length of pair
if not hasattr(calc.build, "nadded") or calc.build.nadded == None:
calc.build.nadded = 2
else:
calc.build.nadded += 2
if not hasattr(calc.build, "listadded") or calc.build.listadded == [None]:
calc.build.listadded = range(stn.natom - 2, stn.natom) # list of atoms which were added
else:
calc.build.listadded.extend(range(stn.natom - 2, stn.natom))
structure_name = calc.name + el.name.split(".")[0]
# calc.name = add_name_before+calc.name+ '.' +el[2]+'.'+str(calc.version)
print "Structure_name", structure_name
if structure_name in struct_des:
if configver:
fname = structure_name # calc.name+'C2O2'
calc.path["input_geo"] = (
geo_folder
+ struct_des[fname].sfolder
+ "/"
+ fname
+ "/"
+ structure_name
+ "."
+ segtyp
+ "."
+ str(calc.version)
+ ".geo"
)
else:
calc.path["input_geo"] = (
geo_folder
+ struct_des[structure_name].sfolder
+ "/"
+ structure_name
+ "/"
+ structure_name
+ "."
+ segtyp
+ "."
+ str(calc.version)
+ ".geo"
)
print "write geo to ", calc.path["input_geo"]
calc.write_geometry("init", des)
print "write_geometry_files(): name ", el.name
stn.name = add_name_before + calc.name + "" + str(el.name) + "." + str(calc.version)
# stn = replic(stn, (1,2,2))
write_xyz(stn)
print "__________________________\n\n\n"
return
def min_diff(f, list, diffprec):
"""
calculates difference between one number and list of other numbers. return the index of number with smallest difference.
if difference is smaller than diffprec returns true as the second argument.
"""
# print list
if list == []:
return 0, False
mind = min([abs(f - l) for l in list])
with_i = np.asarray([abs(f - l) for l in list]).argmin()
return with_i, (mind < diffprec)
def pairs(in_calc, xcart_pores, central_atoms, prec=2, max_dist=20, max_dist_from_gb=4, pairtyp="gvol"):
"""
Searhing for pairs and make list of distances and numbers of atoms
prec - precision, allows to control which distances can be related to the same configurations
max_dist - maximum distance between atoms in pair
max_dist_from_gb -
pairtyp - 'gvol' assumes that central_atoms are in the grain volume, 'gb' assumes that central_atoms are in the grain boundary region
"""
st = in_calc.init
st_replic = replic(st, (2, 2, 2))
st_replic = replic(st_replic, (2, 2, 2), -1) # replic in negative direction also
r1x = in_calc.rprimd[0][0]
r3z = in_calc.rprimd[2][2]
print "Half length of r1x is", r1x / 2
if segtyp in ["segreg", "coseg", "grainvol"]:
gbpos2 = in_calc.gbpos
gbpos1 = gbpos2 - r1x / 2.0
print "\n\nPositions of boundaries gb1 and gb2", gbpos1, gbpos2
print "Maximum possible distance between boundary and impurity", r1x / 4
else:
gbpos2 = 0
gbpos1 = 0
dlist = []
d1list = []
d2list = []
dgb2list = []
n_neighbours = 8 # number of atoms to calculate sums
sumrulist = [] # list of sums (sumr1 or sumr2) of unique pores
unique_pores = [] # the same list but also with coordinates of pores
sumrlist = [] # list of sumr1+sumr2
k = 1
d2diff = 0
d1diff = 0
# z1 = 6 #charge of added impurity
# z2 = 8
diffprec = 0.02
# print xcart_pores
for i, x1 in enumerate(xcart_pores):
if i not in central_atoms:
continue
# iz = z1
for j, x2 in enumerate(xcart_pores):
if all(x1 == x2):
continue
d = abs(x2[0] - in_calc.gbpos)
if pairtyp == "gb" and d > max_dist_from_gb:
continue # second atom is too far from grain boundary
d1, d2 = image_distance(x1, x2, st.rprimd, 2) # the minimum distance and the next minimum dist
if d1 > max_dist:
continue
if (d1, d2) != image_distance(x1, x2, st.rprimd, 3):
raise RuntimeError # test, searching in father images
# d1 = round(d1,prec)
# d2 = round(d2,prec)
dgb1 = round(x2[0] - gbpos1, prec)
dgb2 = round(gbpos2 - x2[0], prec)
sumr1 = local_surrounding(x1, st_replic, n_neighbours) # sum of distances to surrounding atoms
sumr2 = local_surrounding(x2, st_replic, n_neighbours)
sumr = sumr2 + sumr1
if sumr1 not in sumrulist:
sumrulist.append(sumr1)
unique_pores.append((sumr1, x1)) # determine unique pores
if sumr2 not in sumrulist:
sumrulist.append(sumr2)
unique_pores.append((sumr2, x2)) # determine unique pores
# if d1 in d1list: continue
if sumr in sumrlist: # new condition based on sumr
ind = sumrlist.index(sumr)
i_min, smaller = min_diff(d1, d1list, diffprec)
if smaller:
continue
# if 0:#d1list:
# i_min, smaller = min_diff(d1, d1list, diffprec)# d1 has the smallest difference with di
# #print "exist"
# d2diff = abs(d2list[i_min]-d2)
# #print abs(d2list[i_min]-d2)
# #print central_atoms
# if smaller and abs(d2list[i_min]-d2) < diffprec*2 : continue #and abs(dgb2list[i_min]-dgb2) < diffprec
# i_min, smaller = min_diff(d2, d2list, diffprec)# d1 has the smallest difference with di
# d1diff = abs(d1list[i_min]-d1)
# if smaller and abs(d1list[i_min]-d1) < diffprec*2 : continue
# print "skiped"
# di, smaller = min_diff(d2, d2list, diffprec)
# if di != None and smaller: continue
# if min_diff(d2, d2list, diffprec): continue # be carefull here. this condition can pass some unique configrations; should make additional check like below
# if d2 in d2list and dgb2list[d2list.index(d2)] == dgb2: continue
# jz = z2
sumrlist.append(sumr)
d1list.append(d1)
# d2list.append(d2)
# dgb2list.append(dgb2)
sym = ""
if 0: # mannualy switched off
if abs(x1[1] - x2[1]) < diffprec: # Find symmetry
if abs(x1[2] - x2[2]) < diffprec:
sym = "ms" # if y and z are the same, than mirror symmetry
elif abs(x1[2] - x2[2]) - r3z < diffprec:
sym = "is" # inverse symmtry
elif (
abs(x1[2] + x2[2]) - 0.5 * r3z < diffprec
): # only for t111g; should be extended for general case of existing periods along y or z
sym = "is"
dlist.append(
[round(d1, prec), round(d2, prec), sym, sumr1, sumr2, dgb1, dgb2, x1, x2, sumr1, sumr2]
) # the first sumr1, sumr2 below replaced by their types
k += 1
dlist.sort(key=itemgetter(0))
unique_pores.sort(key=itemgetter(0))
sumrulist.sort()
print "Number of unique pores is", len(unique_pores)
print "Pores have the following sums: ", unique_pores
print "Searching for similar pairs but with different distances ..."
print "number, d1, d2, name, sumr1, sumr2, dgb1, dgb2; parallel pair with larger distances"
bname = element_name_inv(target_znucl[1]) + element_name_inv(target_znucl[2])
for i, el1 in enumerate(dlist):
typ1 = sumrulist.index(el1[3]) + 1 # typ of pore of the first atom
typ2 = sumrulist.index(el1[4]) + 1
el1[3] = typ1
el1[4] = typ2
if pairtyp == "gb":
dlist[i][2] = bname + "i" + str(i + 1) + "." + str(el1[3]) + "-" + str(el1[4]) + dlist[i][2]
elif pairtyp == "gvol":
dlist[i][2] = bname + ".v" + str(i + 1) + dlist[i][2]
print i + 1, el1[:3], el1[-2:], el1[-6], el1[-5], # number, d1, d2, name, sumr1, sumr2, dgb1, dgb2
for (
el2
) in (
dlist
): # this loop looks for pairs which are parallel to the same direction as el1 but have larger interdistances
if el1 == el2:
continue
mod = el2[0] / el1[0] % 1
if (mod < 0.005 or mod > 0.995) and abs(el1[0] - el2[0]) > dlist[0][
0
]: # only multiple distances and if difference is larger than smallest distance
# if round(el1[2],prec-1) != round(el2[2],prec-1): continue #In either case the sum the distances should be the same for the same direction
if el1[0] == el2[1]:
continue
print el2[0] / el1[0], # el2, this pair of atoms is analogus to el1 but have larger interdistance
print
print "Total number of structures is", len(dlist)
if 0:
print "\n\nSearching for pairs with equal distances by periodic boundary conditions:"
for el1 in dlist:
if el1[0] == el1[1]:
print el1
print "\nSearching for pairs with not equal distances by periodic boundary conditions:"
for el1 in dlist:
if el1[0] != el1[1]:
print el1
print "\nSearching for pairs with d2/d1>2:"
for el1 in dlist:
if el1[1] / el1[0] > 2:
print el1
dlist[0].append(unique_pores) # last element of dlist[0] is sum and coordinates of unique pores
return dlist
"""0. BEGIN-------------------------------------------------------------------------------"""
hstring = "%s #on %s" % (traceback.extract_stack(None, 2)[0][3], datetime.date.today())
if hstring != header.history[-1]:
header.history.append(hstring)
print_and_log("\n\n------Starting find_pairs()-----------...\n")
if type(central_atoms) == int: # not in [tuple, list]:
central_atoms = [central_atoms]
# transform to list
if type(in_calc) == str:
in_calc_name = in_calc
in_calc = CalculationVasp()
# in_calc.name = str(in_calc_name)
in_calc.name = base_name
print "in_calc name is ", in_calc.name
in_calc.read_geometry(in_calc_name)
if gbpos:
in_calc.gbpos = gbpos # rewrite gbpos
st = in_calc.init
else:
"""End relaxed structure is used!!!"""
st = copy.deepcopy(in_calc.end)
in_calc_name = str(in_calc.id)
"""1. Create separate list of pores and remove them from xcart--------------------------------------------------------"""
if "hcp_octa_xred":
in_calc.init.name = segtyp + "_all_pores"
rep = replic(in_calc.init, (2, 2, 2), -1)
write_xyz(rep) # just to check
"""Coordinates of octapores provided in xcart; znucl = 200;"""
xcart = st.xcart
typat = st.typat
st.typat = []
st.xcart = []
xcart_pores = []
# clean structure from pores with z == 200 and construct xcart_pores
for i, x in enumerate(xcart):
z = st.znucl[typat[i] - 1]
if z == 200:
xcart_pores.append(x)
# print "Found pore"
else:
st.xcart.append(x)
st.typat.append(typat[i])
st.natom = len(st.xcart)
print "Number of found pores with znucl = 200 is ", len(xcart_pores)
for n in central_atoms:
if n >= len(xcart_pores):
raise RuntimeError
"""2. Preprocess segreg and grainvol cases--------------------------------------------------------"""
# in_calc can be of two types: pure and with C in grain volume; using pure we construct co-segregation cases; using carbon in volume we can construct segregation cases
if segtyp in ("segreg", "grainvol"):
if 2 in st.typat: # impurity in grain volume; (now assume that Carbon)
iimp = st.typat.index(2)
xcart1imp = st.xcart[iimp] # save coordinates of carbon atom
del st.xcart[iimp]
del st.typat[iimp]
st.natom -= 1 # and remove it
# del st.xred[iimp]
st.ntypat -= 1
del st.znucl[1]
print "Impurity atom was removed from cell"
if xcart1imp: # for compatibility with previous cases; better not to use
imp1 = len(xcart_pores)
xcart_pores.append(xcart1imp)
xcart2imp = (
xcart1imp - 0.5 * st.rprimd[0]
) # determine coordinates of second impurity assuming that we have mirror symmetry
if xcart2imp[0] < 0:
xcart2imp = xcart1imp + 0.5 * st.rprimd[0]
imp2 = imp1 + 1
xcart_pores.append(xcart2imp)
else: # new version; both central pores are found in the pure cell!!!
# We have pure cell here; Find central pore in 1st grain and 2nd grain:
xcen1 = in_calc.gbpos - 0.25 * st.rprimd[0][0] # x center of the first grain
xcen2 = in_calc.gbpos - 0.75 * st.rprimd[0][0] # z center of the second grain
# print "xcen", xcen1, xcen2
d1l = []
d2l = []
rpxx05 = st.rprimd[0][0] * 0.5
for x in xcart_pores:
d1 = xcen1 - x[0]
d2 = xcen2 - x[0]
if d2 < -rpxx05:
d2 += st.rprimd[0][0] # assuming that periodic boundary conditions needed only here
d1l.append(abs(d1))
d2l.append(abs(d2))
# print d1,d2
imp1 = np.argmin(d1l) # needed numbers of pores
imp2 = np.argmin(d2l)
# print imp1, imp2
xcart1imp = xcart_pores[imp1]
xcart2imp = xcart_pores[imp2]
# print "xcartimp", xcart1imp, xcart2imp
"""3. Define central atoms for segregation and co-segregation cases--------------------------------------------------------"""
max_dist_from_gb = 100
if segtyp in ("segreg", "coseg"):
# central_atoms = []
max_dist_between_atoms = 4.8
max_dist_from_gb = 3 # main controls
for i, x in enumerate(xcart_pores): # generate central atoms
d = abs(x[0] - in_calc.gbpos)
if d < max_dist_from_gb:
central_atoms.append(i)
"""4. Assume that we always have target_znucl, but only three !!!--------------------------------------------------------"""
st.znucl = target_znucl # Please make this part more general
st.ntypat = len(set(st.znucl))
print "Warning! Found only ", st.ntypat, "of unique atoms in target_znucl"
st.xred = xcart2xred(st.xcart, st.rprimd)
"""5. Find segreg and co-segreg cases--------------------------------------------------------"""
in_calc.init = st
dlist_coseg = []
if segtyp == "coseg":
print "\nStart searching pairs in gb"
# main_path = 'T2/CO/' #! please make more general
dlist_coseg = pairs(
in_calc, xcart_pores, central_atoms, prec, max_dist_between_atoms, max_dist_from_gb, pairtyp="gb"
)
dlist_coseg_exc = []
for el in copy.deepcopy(dlist_coseg): # Exchange C and O only for unsymmetrical cases
if "s" in el[2]:
continue # not needed for symmetrical cases
el[2] = el[2].replace("C", "x")
el[2] = el[2].replace("O", "C")
el[2] = el[2].replace("x", "O")
el[7], el[8] = el[8], el[7]
el[3], el[4] = el[4], el[3]
dlist_coseg_exc.append(el)
for el in dlist_coseg + dlist_coseg_exc: # Helper
stname = base_name + el[2]
path = main_path + base_name + "_coseg"
print (
(
"struct_des['{0:s}'] = des('{1:s}', 'co-segregation configurations; made from " + based_on + "' )"
).format(stname, path)
)
for el in dlist_coseg + dlist_coseg_exc: # Helper
stname = base_name + el[2]
path = main_path + base_name + "_coseg"
print "add_loop('" + stname + "','" + based_on.split(".")[
1
] + "',range(1,5),calc,conv,varset, 'up1', inherit_option = 'inherit_xred')"
write_geometry_files(
dlist_coseg + dlist_coseg_exc, in_calc, xcart_pores, segtyp, take_final_rprimd_from, add_typat=add_typat
)
elif segtyp == "segreg":
"""Produce segregation cases only in the case of segreg"""
print "\nStart producing segragation cases"
dlist_segreg = []
# dlist_segreg1 = copy.deepcopy(input_dlist_coseg) #in this case we use input_dlist with co-segragation cases from pure cell.
# dlist_segreg2 = copy.deepcopy(input_dlist_coseg) #There is small error, because positions of pores at grain boundary
# #differs in pure cell and cell with impurity in grain volume
# for i, el in enumerate(input_dlist_coseg):
# sym = ''
# if 'is' in el[2]: sym = 'is'
# elif 'ms' in el[2]: sym = 'ms'
# dlist_segreg1[i][7] = xcart1imp
# dlist_segreg1[i][2] = 'CvOi'+str(i+1)+sym
# dlist_segreg2[i][8] = xcart1imp
# dlist_segreg2[i][2] = 'CiOv'+str(i+1)+sym
"""new determination based on input_dlist_coseg[0][-1]"""
el = copy.deepcopy(input_dlist_coseg[0])
unique = el[-1] # sums and coordinates of unique pores
print "unique", unique
for i, sx in enumerate(unique):
el[2] = "Ci" + str(i + 1) + "Ov"
el[7] = sx[1]
d1, dnext = image_distance(sx[1], xcart1imp, st.rprimd, 2)
d2, dnext = image_distance(sx[1], xcart2imp, st.rprimd, 2)
if d1 > d2:
el[8] = xcart1imp
else:
el[8] = xcart2imp # the farthest impurity in grain volume is used
dlist_segreg.append(copy.deepcopy(el))
# dlist_segreg = dlist_segreg1 + dlist_segreg2 #Segregation of the first impurity and of the second
dlist_segreg_exc = []
for el in copy.deepcopy(dlist_segreg): # Exchange C and O only for unsymmetrical cases
if "s" in el[2]:
continue # not needed for symmetrical cases
el[2] = el[2].replace("C", "x")
el[2] = el[2].replace("O", "C")
el[2] = el[2].replace("x", "O")
el[7], el[8] = el[8], el[7]
el[3], el[4] = el[4], el[3]
dlist_segreg_exc.append(el)
# helper
for el in dlist_segreg + dlist_segreg_exc:
stname = base_name + el[2]
path = main_path + base_name + "_segreg"
print (
(
"struct_des['{0:s}'] = des('{1:s}', 'co-segregation configurations; made from " + based_on + "' )"
).format(stname, path)
)
for el in dlist_segreg + dlist_segreg_exc:
stname = base_name + el[2]
path = main_path + base_name + "_segreg"
print "add_loop('" + stname + "','" + based_on.split(".")[
1
] + "',range(1,5),calc,conv,varset, 'up1', inherit_option = 'inherit_xred')"
write_geometry_files(
dlist_segreg + dlist_segreg_exc, in_calc, xcart_pores, segtyp, take_final_rprimd_from, add_typat=add_typat
)
"""6. Find volume cases--------------------------------------------------------"""
# this part for construction volume cases
if segtyp == "grainvol": # take care that you have only one carbon atom in the grain
print "\nStart searching pairs in the volume"
central_atoms = [imp1]
max_dist_between_atoms = 4.0
# gvolume_config_num = 0 #please choose manually
dlist = pairs(
in_calc, xcart_pores, central_atoms, prec, max_dist_between_atoms, max_dist_from_gb, pairtyp="gvol"
)
# dlist = [dlist[0], copy.deepcopy(dlist[gvolume_config_num-1]) ]
# dlist[0][4] = imp2 #no matter wht was dlist[0]; used for vv case
dlist.append(copy.deepcopy(dlist[0]))
dlist[-1][8] = xcart2imp # last element for both atoms in grain volumes
dlist[-1][2] = "CvOvms"
# helper
for el in dlist:
stname = base_name + el[2]
path = main_path + base_name + "_gvol" # grain volume
print "add_loop('" + stname + "','" + based_on.split(".")[
1
] + "',range(1,5),calc,conv,varset, 'up1', inherit_option = 'inherit_xred')"
for el in dlist:
stname = base_name + el[2]
path = main_path + base_name + "_gvol" # grain volume
print (
(
"struct_des['{0:s}'] = des('{1:s}', 'co-segregation configurations; made from " + based_on + "' )"
).format(stname, path)
)
write_geometry_files(dlist, in_calc, xcart_pores, segtyp, take_final_rprimd_from, add_typat=add_typat)
""". Triple cases--------------------------------------------------------"""
def triples(addatom=("O", 3), dlist=[], tlist=[], in_calc=None, xcart_pores=[], max_dist_to_next_atom=3):
"""
Add addatom to all configurations in tlist;
addatom[1] - type of atom in typat
dlist - list of configurations with two impurity atoms; Used if tlist == []; the format of dlist is quiet special
tlist - list of configurations with arbirtary number of atoms;
RETURN:
tlist - list of configurations with add atoms
"""
st = in_calc.init
if dlist and tlist == []:
for el in dlist:
par = el
print "pair 1", par,
x1 = par[7]
x2 = par[8]
print "x1 = ", x1
print "x2 = ", x2
config = Structure()
config.xcart = [x1, x2]
config.typat = [2, 3]
config.name = el[2]
tlist.append(config)
tlist_new = []
for config in tlist:
xcart = config.xcart
typat = config.typat
name = config.name
print "\n\n\nStart to adding atom to ", name
i = 1
dlistlist = []
diffprec = 0.001
[dlistlist.append([]) for x in xcart]
print len(dlistlist)
for xpor in xcart_pores:
skip = True
for j, x in enumerate(xcart): # list of 2 or 3 initial atoms to which additional atom will be added
if all(np.around(xpor, 5) == np.around(x, 5)):
skip = True
break
d1, d2 = image_distance(x, xpor, st.rprimd, 2) # the minimum distance and the next minimum dist
if d1 > max_dist_to_next_atom:
skip = True
break # if only one pore is larger from atom than limit, the pore is skiped
# suml = d11+d21+par[0]
# for dl in dlistlist:
# print 'j is ', j
i_min, smaller = min_diff(
d1, dlistlist[j], diffprec
) # old condition - bad - removes unique configurations
# if smaller: skip = True; continue # symmetrical pores deleted
dlistlist[j].append(d1)
skip = False # all conditions are fullfilled - this configuration is unique
# else:
# print 'List of distances to atoms'
if skip:
continue #
# print "Pore can be used", xpor #sum of distances for triple
new = Structure()
new.name = name + addatom[0] + str(i)
new.xcart = copy.deepcopy(xcart)
new.xcart.append(xpor)
new.typat = copy.deepcopy(typat)
new.typat.append(addatom[1])
# print 'new.typat =', new.typat
# calculate sum of lengths
new.length = 0
new.lengthCO = 0
new.lengthCC = 0
new.lengthOO = 0
new.xcartC = []
new.xcartO = []
for m, x1 in enumerate(new.xcart):
if new.typat[m] == 2:
new.xcartC.append(x1)
if new.typat[m] == 3:
new.xcartO.append(x1)
for x2 in new.xcart:
d1, d2 = image_distance(x1, x2, st.rprimd, 2)
new.length += d1
for xC in new.xcartC:
for xO in new.xcartO:
d1, d2 = image_distance(xC, xO, st.rprimd, 2)
new.lengthCO += d1
for xC1 in new.xcartC:
for xC2 in new.xcartC:
d1, d2 = image_distance(xC1, xC2, st.rprimd, 2)
new.lengthCC += d1
for xO1 in new.xcartO:
for xO2 in new.xcartO:
d1, d2 = image_distance(xO1, xO2, st.rprimd, 2)
new.lengthOO += d1
skip = False
n = len(new.xcart)
"""additional conditions to leave only unique configurations"""
for config in tlist_new:
if 1:
nr = 0
for (v1, t1) in zip(new.xcart, new.typat):
for (v2, t2) in zip(config.xcart, config.typat):
if all(np.around(v1, 8) == np.around(v2, 8)) and t1 == t2:
nr += 1
if nr == n:
print "The configurations", new.name, "and", config.name, "consist of the same atoms, continue"
skip = True
break
# print all([ all( np.around(v1, 8) == np.around(v2, 8) ) for (v1, v2) in zip(new.xcart, config.xcart) ])
# check identity using sum of distances
# i_min, smaller = min_diff(config.length, [new.length], diffprec)
# if smaller:
# print "Configuration ", new.name, "has the same sum of lengths as", config.name
i_min, smaller1 = min_diff(config.lengthCO, [new.lengthCO], diffprec)
i_min, smaller2 = min_diff(config.lengthCC, [new.lengthCC], diffprec)
i_min, smaller3 = min_diff(config.lengthOO, [new.lengthOO], diffprec)
# print 'Compare', new.name, config.name, smaller1, smaller2, smaller3
if smaller1 and smaller2 and smaller3:
print "\nConfiguration ", new.name, "has the same sum of C-O, C-C and O-O lengths as", config.name
print
skip = True
break
if skip:
continue
print "\nSum of CO lengths in :", new.name, new.lengthCC, new.lengthOO, new.lengthCO
tlist_new.append(new)
i += 1
return tlist_new
if segtyp == "bulk_triple" or segtyp == "bulk_pairs":
# max_dist_between_atoms = 4.8
print "\nSearching pairs ..."
dlist = pairs(in_calc, xcart_pores, central_atoms, prec, max_dist_between_atoms, pairtyp="gvol")
if segtyp == "bulk_pairs":
write_geometry_files(
dlist, in_calc, xcart_pores, segtyp, take_final_rprimd_from, configver=True, add_typat=add_typat
)
if segtyp == "bulk_triple":
max_dist_to_next_atom = 5.5
print "\nSearching triples ..." # , tlist
tlist = []
tlist = triples(("O", 3), dlist, tlist, in_calc, xcart_pores, max_dist_to_next_atom)
tlist = triples(("C", 2), dlist, tlist, in_calc, xcart_pores, max_dist_to_next_atom)
write_geometry_files(
dlist,
in_calc,
xcart_pores,
segtyp,
take_final_rprimd_from,
tlist=tlist,
configver=True,
add_typat=add_typat,
)
return dlist_coseg, xcart_pores
def write_geometry_files(dlist,
in_calc,
xcart_pores,
segtyp,
take_final_rprimd_from=None,
add_name_before='',
tlist=[],
configver=False,
add_typat=None):
"""Creating files
dlist - list of pairs with distances and numbers
in_calc - base calculation without pores
tlist - list of additional atoms in the case of triples; list of structures
configver - if True each configuration saved as a new version
add_typat - manually determined; please automatize!
"""
print "Warning! add_typat", add_typat
if tlist == []: #convert dlist to tlist - to do earlier
for el in dlist:
config = Structure()
config.name = el[2]
config.length = el[0]
config.typat = add_typat
config.xcart = [el[7], el[8]]
tlist.append(config)
for i, el in enumerate(tlist): #by all found structures
print "el name is ", el.name
stn = copy.deepcopy(in_calc.init)
calc = copy.deepcopy(in_calc)
stn.typat.extend(el.typat)
stn.xcart.extend(el.xcart)
stn.xred = xcart2xred(stn.xcart, stn.rprimd)
xcart_check = xred2xcart(stn.xred, stn.rprimd)
assert len(xcart_check) == len(stn.xcart) #test
assert all(
[
all(np.around(v1, 8) == np.around(v2, 8))
for (v1, v2) in zip(stn.xcart, xcart_check)
]
) #check if xcart2xred(stn.xcart,r) and xred2xcart(stn.xred,r) are working correctly up to the eight digits after
stn.natom = len(stn.xcart)
"""Adapt new rprimd"""
print "take final rprimd is ", take_final_rprimd_from
if take_final_rprimd_from: #read final rprimd and version
print "Start to read rprimd and version from " + take_final_rprimd_from
in_calc_rprimd = CalculationVasp()
in_calc_rprimd.name = 'temp'
in_calc_rprimd.read_geometry(take_final_rprimd_from)
stn.rprimd = in_calc_rprimd.init.rprimd
stn.xcart = xred2xcart(stn.xred, stn.rprimd)
calc.version = in_calc_rprimd.version
elif configver:
calc.version = i + 1
calc.init = stn
des = ' was obtained by the insertion of C-O pair into ' + in_calc_name + '; final vectors taken from corresponding ver'
calc.build.ipairlen = el.length # Initial length of pair
if not hasattr(calc.build, 'nadded') or calc.build.nadded == None:
calc.build.nadded = 2
else:
calc.build.nadded += 2
if not hasattr(calc.build,
'listadded') or calc.build.listadded == [None]:
calc.build.listadded = range(
stn.natom - 2, stn.natom) #list of atoms which were added
else:
calc.build.listadded.extend(range(stn.natom - 2, stn.natom))
structure_name = calc.name + el.name.split('.')[0]
#calc.name = add_name_before+calc.name+ '.' +el[2]+'.'+str(calc.version)
print 'Structure_name', structure_name
if structure_name in struct_des:
if configver:
fname = structure_name # calc.name+'C2O2'
calc.path["input_geo"] = geo_folder + struct_des[
fname].sfolder + '/' + fname + '/' + structure_name + '.' + segtyp + '.' + str(
calc.version) + '.geo'
else:
calc.path["input_geo"] = geo_folder + struct_des[
structure_name].sfolder + '/' + structure_name + '/' + structure_name + '.' + segtyp + '.' + str(
calc.version) + '.geo'
print "write geo to ", calc.path["input_geo"]
calc.write_geometry('init', des)
print "write_geometry_files(): name ", el.name
stn.name = add_name_before + calc.name + '' + str(
el.name) + '.' + str(calc.version)
#stn = replic(stn, (1,2,2))
write_xyz(stn)
print "__________________________\n\n\n"
return
def find_pairs(base_name,
segtyp,
in_calc,
central_atoms=[],
xcart1imp=None,
input_dlist_coseg=None,
prec=2,
gvolume_config_num=None,
gbpos=None,
take_final_rprimd_from=None,
main_path=None,
based_on=None,
target_znucl=[22, 6, 8],
max_dist_between_atoms=4.8,
add_typat=[2, 3]):
"""
Find uniq pairs of atoms and analyse them
Input:
segtyp -
three regimes for cells with grain boundaries:
'segreg' assumes that in_calc contains carbon atom in grain volume, and creates all cases;
'coseg' assumes pure cell and creates only coseg cases.
cosegregation cases of course should be the same for two regimes, however co-segregation configuations after 'coseg' is more easy to relax.
'grainvol' - searching for pairs in grain volume
two regimes for bulk cells:
'bulk_triple' - used for bulk cells without grain boundaries; first step is searching for pairs, second step for triples.
'bulk_pairs' - used for bulk cells without grain boundaries; searching for pairs.
new_name - name of created structures; at first should be added to struct_des[]
in_calc - Calculation() type or path to geo file
region - list of numbers which determine region
central_atoms - list of atoms for which pairs are constructed (Warinig! numbers in new array xcart_pores!);
- parameter to change mode;
xcart1imp - coordinates of first interstitial in the grain interior
input_dlist_coseg - list of configurations with cosegregation cases. Needed to construct corresponding segregation cases. the format is quiet tricky
prec - precision of lengths used to determine unique positions.
gvolume_config_num - number of configuration with two atoms in grain volume choosen by user (usually should be the most favourable)
gbpos - position of grain boundary
take_final_rprimd_from - path to geo file from which rprimd will be used
target_znucl - numbers of target atoms
max_dist_between_atoms - now at least used for 'bulk_pairs' and 'bulk_triple'; maximum length of found pairs.
add_typat - mannualy set please update
"""
def write_geometry_files(dlist,
in_calc,
xcart_pores,
segtyp,
take_final_rprimd_from=None,
add_name_before='',
tlist=[],
configver=False,
add_typat=None):
"""Creating files
dlist - list of pairs with distances and numbers
in_calc - base calculation without pores
tlist - list of additional atoms in the case of triples; list of structures
configver - if True each configuration saved as a new version
add_typat - manually determined; please automatize!
"""
print "Warning! add_typat", add_typat
if tlist == []: #convert dlist to tlist - to do earlier
for el in dlist:
config = Structure()
config.name = el[2]
config.length = el[0]
config.typat = add_typat
config.xcart = [el[7], el[8]]
tlist.append(config)
for i, el in enumerate(tlist): #by all found structures
print "el name is ", el.name
stn = copy.deepcopy(in_calc.init)
calc = copy.deepcopy(in_calc)
stn.typat.extend(el.typat)
stn.xcart.extend(el.xcart)
stn.xred = xcart2xred(stn.xcart, stn.rprimd)
xcart_check = xred2xcart(stn.xred, stn.rprimd)
assert len(xcart_check) == len(stn.xcart) #test
assert all(
[
all(np.around(v1, 8) == np.around(v2, 8))
for (v1, v2) in zip(stn.xcart, xcart_check)
]
) #check if xcart2xred(stn.xcart,r) and xred2xcart(stn.xred,r) are working correctly up to the eight digits after
stn.natom = len(stn.xcart)
"""Adapt new rprimd"""
print "take final rprimd is ", take_final_rprimd_from
if take_final_rprimd_from: #read final rprimd and version
print "Start to read rprimd and version from " + take_final_rprimd_from
in_calc_rprimd = CalculationVasp()
in_calc_rprimd.name = 'temp'
in_calc_rprimd.read_geometry(take_final_rprimd_from)
stn.rprimd = in_calc_rprimd.init.rprimd
stn.xcart = xred2xcart(stn.xred, stn.rprimd)
calc.version = in_calc_rprimd.version
elif configver:
calc.version = i + 1
calc.init = stn
des = ' was obtained by the insertion of C-O pair into ' + in_calc_name + '; final vectors taken from corresponding ver'
calc.build.ipairlen = el.length # Initial length of pair
if not hasattr(calc.build, 'nadded') or calc.build.nadded == None:
calc.build.nadded = 2
else:
calc.build.nadded += 2
if not hasattr(calc.build,
'listadded') or calc.build.listadded == [None]:
calc.build.listadded = range(
stn.natom - 2, stn.natom) #list of atoms which were added
else:
calc.build.listadded.extend(range(stn.natom - 2, stn.natom))
structure_name = calc.name + el.name.split('.')[0]
#calc.name = add_name_before+calc.name+ '.' +el[2]+'.'+str(calc.version)
print 'Structure_name', structure_name
if structure_name in struct_des:
if configver:
fname = structure_name # calc.name+'C2O2'
calc.path["input_geo"] = geo_folder + struct_des[
fname].sfolder + '/' + fname + '/' + structure_name + '.' + segtyp + '.' + str(
calc.version) + '.geo'
else:
calc.path["input_geo"] = geo_folder + struct_des[
structure_name].sfolder + '/' + structure_name + '/' + structure_name + '.' + segtyp + '.' + str(
calc.version) + '.geo'
print "write geo to ", calc.path["input_geo"]
calc.write_geometry('init', des)
print "write_geometry_files(): name ", el.name
stn.name = add_name_before + calc.name + '' + str(
el.name) + '.' + str(calc.version)
#stn = replic(stn, (1,2,2))
write_xyz(stn)
print "__________________________\n\n\n"
return
def min_diff(f, list, diffprec):
"""
calculates difference between one number and list of other numbers. return the index of number with smallest difference.
if difference is smaller than diffprec returns true as the second argument.
"""
#print list
if list == []: return 0, False
mind = min([abs(f - l) for l in list])
with_i = np.asarray([abs(f - l) for l in list]).argmin()
return with_i, (mind < diffprec)
def pairs(in_calc,
xcart_pores,
central_atoms,
prec=2,
max_dist=20,
max_dist_from_gb=4,
pairtyp='gvol'):
"""
Searhing for pairs and make list of distances and numbers of atoms
prec - precision, allows to control which distances can be related to the same configurations
max_dist - maximum distance between atoms in pair
max_dist_from_gb -
pairtyp - 'gvol' assumes that central_atoms are in the grain volume, 'gb' assumes that central_atoms are in the grain boundary region
"""
st = in_calc.init
st_replic = replic(st, (2, 2, 2))
st_replic = replic(st_replic, (2, 2, 2),
-1) #replic in negative direction also
r1x = in_calc.rprimd[0][0]
r3z = in_calc.rprimd[2][2]
print "Half length of r1x is", r1x / 2
if segtyp in ['segreg', 'coseg', 'grainvol']:
gbpos2 = in_calc.gbpos
gbpos1 = gbpos2 - r1x / 2.
print "\n\nPositions of boundaries gb1 and gb2", gbpos1, gbpos2
print "Maximum possible distance between boundary and impurity", r1x / 4
else:
gbpos2 = 0
gbpos1 = 0
dlist = []
d1list = []
d2list = []
dgb2list = []
n_neighbours = 8 # number of atoms to calculate sums
sumrulist = [] #list of sums (sumr1 or sumr2) of unique pores
unique_pores = [] #the same list but also with coordinates of pores
sumrlist = [] #list of sumr1+sumr2
k = 1
d2diff = 0
d1diff = 0
#z1 = 6 #charge of added impurity
#z2 = 8
diffprec = 0.02
# print xcart_pores
for i, x1 in enumerate(xcart_pores):
if i not in central_atoms: continue
#iz = z1
for j, x2 in enumerate(xcart_pores):
if all(x1 == x2): continue
d = abs(x2[0] - in_calc.gbpos)
if pairtyp == 'gb' and d > max_dist_from_gb:
continue #second atom is too far from grain boundary
d1, d2 = image_distance(
x1, x2, st.rprimd,
2) # the minimum distance and the next minimum dist
if d1 > max_dist: continue
if (d1, d2) != image_distance(x1, x2, st.rprimd, 3):
raise RuntimeError #test, searching in father images
#d1 = round(d1,prec)
#d2 = round(d2,prec)
dgb1 = round(x2[0] - gbpos1, prec)
dgb2 = round(gbpos2 - x2[0], prec)
sumr1 = local_surrounding(
x1, st_replic,
n_neighbours) # sum of distances to surrounding atoms
sumr2 = local_surrounding(x2, st_replic, n_neighbours)
sumr = sumr2 + sumr1
if sumr1 not in sumrulist:
sumrulist.append(sumr1)
unique_pores.append((sumr1, x1)) #determine unique pores
if sumr2 not in sumrulist:
sumrulist.append(sumr2)
unique_pores.append((sumr2, x2)) #determine unique pores
#if d1 in d1list: continue
if sumr in sumrlist: # new condition based on sumr
ind = sumrlist.index(sumr)
i_min, smaller = min_diff(d1, d1list, diffprec)
if smaller: continue
# if 0:#d1list:
# i_min, smaller = min_diff(d1, d1list, diffprec)# d1 has the smallest difference with di
# #print "exist"
# d2diff = abs(d2list[i_min]-d2)
# #print abs(d2list[i_min]-d2)
# #print central_atoms
# if smaller and abs(d2list[i_min]-d2) < diffprec*2 : continue #and abs(dgb2list[i_min]-dgb2) < diffprec
# i_min, smaller = min_diff(d2, d2list, diffprec)# d1 has the smallest difference with di
# d1diff = abs(d1list[i_min]-d1)
# if smaller and abs(d1list[i_min]-d1) < diffprec*2 : continue
#print "skiped"
#di, smaller = min_diff(d2, d2list, diffprec)
#if di != None and smaller: continue
#if min_diff(d2, d2list, diffprec): continue # be carefull here. this condition can pass some unique configrations; should make additional check like below
#if d2 in d2list and dgb2list[d2list.index(d2)] == dgb2: continue
#jz = z2
sumrlist.append(sumr)
d1list.append(d1)
# d2list.append(d2)
# dgb2list.append(dgb2)
sym = ''
if 0: #mannualy switched off
if abs(x1[1] - x2[1]) < diffprec: #Find symmetry
if abs(x1[2] - x2[2]) < diffprec:
sym = 'ms' # if y and z are the same, than mirror symmetry
elif abs(x1[2] - x2[2]) - r3z < diffprec:
sym = 'is' # inverse symmtry
elif abs(
x1[2] + x2[2]
) - 0.5 * r3z < diffprec: # only for t111g; should be extended for general case of existing periods along y or z
sym = 'is'
dlist.append([
round(d1, prec),
round(d2, prec), sym, sumr1, sumr2, dgb1, dgb2, x1, x2,
sumr1, sumr2
]) #the first sumr1, sumr2 below replaced by their types
k += 1
dlist.sort(key=itemgetter(0))
unique_pores.sort(key=itemgetter(0))
sumrulist.sort()
print 'Number of unique pores is', len(unique_pores)
print 'Pores have the following sums: ', unique_pores
print "Searching for similar pairs but with different distances ..."
print "number, d1, d2, name, sumr1, sumr2, dgb1, dgb2; parallel pair with larger distances"
bname = element_name_inv(target_znucl[1]) + element_name_inv(
target_znucl[2])
for i, el1 in enumerate(dlist):
typ1 = sumrulist.index(el1[3]) + 1 #typ of pore of the first atom
typ2 = sumrulist.index(el1[4]) + 1
el1[3] = typ1
el1[4] = typ2
if pairtyp == 'gb':
dlist[i][2] = bname + 'i' + str(i + 1) + '.' + str(
el1[3]) + '-' + str(el1[4]) + dlist[i][2]
elif pairtyp == 'gvol':
dlist[i][2] = bname + '.v' + str(i + 1) + dlist[i][2]
print i + 1, el1[:3], el1[-2:], el1[-6], el1[
-5], #number, d1, d2, name, sumr1, sumr2, dgb1, dgb2
for el2 in dlist: #this loop looks for pairs which are parallel to the same direction as el1 but have larger interdistances
if el1 == el2: continue
mod = el2[0] / el1[0] % 1
if (mod < 0.005 or mod > 0.995
) and abs(el1[0] - el2[0]) > dlist[0][
0]: #only multiple distances and if difference is larger than smallest distance
#if round(el1[2],prec-1) != round(el2[2],prec-1): continue #In either case the sum the distances should be the same for the same direction
if el1[0] == el2[1]: continue
print el2[0] / el1[
0], # el2, this pair of atoms is analogus to el1 but have larger interdistance
print
print 'Total number of structures is', len(dlist)
if 0:
print "\n\nSearching for pairs with equal distances by periodic boundary conditions:"
for el1 in dlist:
if el1[0] == el1[1]:
print el1
print "\nSearching for pairs with not equal distances by periodic boundary conditions:"
for el1 in dlist:
if el1[0] != el1[1]:
print el1
print "\nSearching for pairs with d2/d1>2:"
for el1 in dlist:
if el1[1] / el1[0] > 2:
print el1
dlist[0].append(
unique_pores
) # last element of dlist[0] is sum and coordinates of unique pores
return dlist
"""0. BEGIN-------------------------------------------------------------------------------"""
hstring = ("%s #on %s" %
(traceback.extract_stack(None, 2)[0][3], datetime.date.today()))
if hstring != header.history[-1]: header.history.append(hstring)
print_and_log("\n\n------Starting find_pairs()-----------...\n")
if type(central_atoms) == int: #not in [tuple, list]:
central_atoms = [central_atoms]
#transform to list
if type(in_calc) == str:
in_calc_name = in_calc
in_calc = CalculationVasp()
#in_calc.name = str(in_calc_name)
in_calc.name = base_name
print "in_calc name is ", in_calc.name
in_calc.read_geometry(in_calc_name)
if gbpos: in_calc.gbpos = gbpos #rewrite gbpos
st = in_calc.init
else:
"""End relaxed structure is used!!!"""
st = copy.deepcopy(in_calc.end)
in_calc_name = str(in_calc.id)
"""1. Create separate list of pores and remove them from xcart--------------------------------------------------------"""
if "hcp_octa_xred":
in_calc.init.name = segtyp + '_all_pores'
rep = replic(in_calc.init, (2, 2, 2), -1)
write_xyz(rep) #just to check
"""Coordinates of octapores provided in xcart; znucl = 200;"""
xcart = st.xcart
typat = st.typat
st.typat = []
st.xcart = []
xcart_pores = []
#clean structure from pores with z == 200 and construct xcart_pores
for i, x in enumerate(xcart):
z = st.znucl[typat[i] - 1]
if z == 200:
xcart_pores.append(x)
#print "Found pore"
else:
st.xcart.append(x)
st.typat.append(typat[i])
st.natom = len(st.xcart)
print 'Number of found pores with znucl = 200 is ', len(xcart_pores)
for n in central_atoms:
if n >= len(xcart_pores):
raise RuntimeError
"""2. Preprocess segreg and grainvol cases--------------------------------------------------------"""
# in_calc can be of two types: pure and with C in grain volume; using pure we construct co-segregation cases; using carbon in volume we can construct segregation cases
if segtyp in ('segreg', 'grainvol'):
if 2 in st.typat: # impurity in grain volume; (now assume that Carbon)
iimp = st.typat.index(2)
xcart1imp = st.xcart[iimp] #save coordinates of carbon atom
del st.xcart[iimp]
del st.typat[iimp]
st.natom -= 1 #and remove it
#del st.xred[iimp]
st.ntypat -= 1
del st.znucl[1]
print "Impurity atom was removed from cell"
if xcart1imp: #for compatibility with previous cases; better not to use
imp1 = len(xcart_pores)
xcart_pores.append(xcart1imp)
xcart2imp = xcart1imp - 0.5 * st.rprimd[
0] #determine coordinates of second impurity assuming that we have mirror symmetry
if xcart2imp[0] < 0: xcart2imp = xcart1imp + 0.5 * st.rprimd[0]
imp2 = imp1 + 1
xcart_pores.append(xcart2imp)
else: #new version; both central pores are found in the pure cell!!!
#We have pure cell here; Find central pore in 1st grain and 2nd grain:
xcen1 = in_calc.gbpos - 0.25 * st.rprimd[0][
0] #x center of the first grain
xcen2 = in_calc.gbpos - 0.75 * st.rprimd[0][
0] #z center of the second grain
# print "xcen", xcen1, xcen2
d1l = []
d2l = []
rpxx05 = st.rprimd[0][0] * 0.5
for x in xcart_pores:
d1 = xcen1 - x[0]
d2 = xcen2 - x[0]
if d2 < -rpxx05:
d2 += st.rprimd[0][
0] # assuming that periodic boundary conditions needed only here
d1l.append(abs(d1))
d2l.append(abs(d2))
# print d1,d2
imp1 = np.argmin(d1l) #needed numbers of pores
imp2 = np.argmin(d2l)
# print imp1, imp2
xcart1imp = xcart_pores[imp1]
xcart2imp = xcart_pores[imp2]
# print "xcartimp", xcart1imp, xcart2imp
"""3. Define central atoms for segregation and co-segregation cases--------------------------------------------------------"""
max_dist_from_gb = 100
if segtyp in ('segreg', 'coseg'):
# central_atoms = []
max_dist_between_atoms = 4.8
max_dist_from_gb = 3 #main controls
for i, x in enumerate(xcart_pores): #generate central atoms
d = abs(x[0] - in_calc.gbpos)
if d < max_dist_from_gb:
central_atoms.append(i)
"""4. Assume that we always have target_znucl, but only three !!!--------------------------------------------------------"""
st.znucl = target_znucl #Please make this part more general
st.ntypat = len(set(st.znucl))
print 'Warning! Found only ', st.ntypat, 'of unique atoms in target_znucl'
st.xred = xcart2xred(st.xcart, st.rprimd)
"""5. Find segreg and co-segreg cases--------------------------------------------------------"""
in_calc.init = st
dlist_coseg = []
if segtyp == 'coseg':
print "\nStart searching pairs in gb"
# main_path = 'T2/CO/' #! please make more general
dlist_coseg = pairs(in_calc,
xcart_pores,
central_atoms,
prec,
max_dist_between_atoms,
max_dist_from_gb,
pairtyp='gb')
dlist_coseg_exc = []
for el in copy.deepcopy(
dlist_coseg): #Exchange C and O only for unsymmetrical cases
if 's' in el[2]: continue # not needed for symmetrical cases
el[2] = el[2].replace('C', 'x')
el[2] = el[2].replace('O', 'C')
el[2] = el[2].replace('x', 'O')
el[7], el[8] = el[8], el[7]
el[3], el[4] = el[4], el[3]
dlist_coseg_exc.append(el)
for el in dlist_coseg + dlist_coseg_exc: # Helper
stname = base_name + el[2]
path = main_path + base_name + '_coseg'
print((
"struct_des['{0:s}'] = des('{1:s}', 'co-segregation configurations; made from "
+ based_on + "' )").format(stname, path))
for el in dlist_coseg + dlist_coseg_exc: # Helper
stname = base_name + el[2]
path = main_path + base_name + '_coseg'
print "add_loop('" + stname + "','" + based_on.split(
'.'
)[1] + "',range(1,5),calc,conv,varset, 'up1', inherit_option = 'inherit_xred')"
write_geometry_files(dlist_coseg + dlist_coseg_exc,
in_calc,
xcart_pores,
segtyp,
take_final_rprimd_from,
add_typat=add_typat)
elif segtyp == 'segreg':
"""Produce segregation cases only in the case of segreg"""
print "\nStart producing segragation cases"
dlist_segreg = []
# dlist_segreg1 = copy.deepcopy(input_dlist_coseg) #in this case we use input_dlist with co-segragation cases from pure cell.
# dlist_segreg2 = copy.deepcopy(input_dlist_coseg) #There is small error, because positions of pores at grain boundary
# #differs in pure cell and cell with impurity in grain volume
# for i, el in enumerate(input_dlist_coseg):
# sym = ''
# if 'is' in el[2]: sym = 'is'
# elif 'ms' in el[2]: sym = 'ms'
# dlist_segreg1[i][7] = xcart1imp
# dlist_segreg1[i][2] = 'CvOi'+str(i+1)+sym
# dlist_segreg2[i][8] = xcart1imp
# dlist_segreg2[i][2] = 'CiOv'+str(i+1)+sym
"""new determination based on input_dlist_coseg[0][-1]"""
el = copy.deepcopy(input_dlist_coseg[0])
unique = el[-1] #sums and coordinates of unique pores
print "unique", unique
for i, sx in enumerate(unique):
el[2] = 'Ci' + str(i + 1) + 'Ov'
el[7] = sx[1]
d1, dnext = image_distance(sx[1], xcart1imp, st.rprimd, 2)
d2, dnext = image_distance(sx[1], xcart2imp, st.rprimd, 2)
if d1 > d2:
el[8] = xcart1imp
else:
el[8] = xcart2imp # the farthest impurity in grain volume is used
dlist_segreg.append(copy.deepcopy(el))
#dlist_segreg = dlist_segreg1 + dlist_segreg2 #Segregation of the first impurity and of the second
dlist_segreg_exc = []
for el in copy.deepcopy(
dlist_segreg): #Exchange C and O only for unsymmetrical cases
if 's' in el[2]: continue # not needed for symmetrical cases
el[2] = el[2].replace('C', 'x')
el[2] = el[2].replace('O', 'C')
el[2] = el[2].replace('x', 'O')
el[7], el[8] = el[8], el[7]
el[3], el[4] = el[4], el[3]
dlist_segreg_exc.append(el)
#helper
for el in dlist_segreg + dlist_segreg_exc:
stname = base_name + el[2]
path = main_path + base_name + '_segreg'
print((
"struct_des['{0:s}'] = des('{1:s}', 'co-segregation configurations; made from "
+ based_on + "' )").format(stname, path))
for el in dlist_segreg + dlist_segreg_exc:
stname = base_name + el[2]
path = main_path + base_name + '_segreg'
print "add_loop('" + stname + "','" + based_on.split(
'.'
)[1] + "',range(1,5),calc,conv,varset, 'up1', inherit_option = 'inherit_xred')"
write_geometry_files(dlist_segreg + dlist_segreg_exc,
in_calc,
xcart_pores,
segtyp,
take_final_rprimd_from,
add_typat=add_typat)
"""6. Find volume cases--------------------------------------------------------"""
# this part for construction volume cases
if segtyp == "grainvol": #take care that you have only one carbon atom in the grain
print "\nStart searching pairs in the volume"
central_atoms = [imp1]
max_dist_between_atoms = 4.
#gvolume_config_num = 0 #please choose manually
dlist = pairs(in_calc,
xcart_pores,
central_atoms,
prec,
max_dist_between_atoms,
max_dist_from_gb,
pairtyp='gvol')
#dlist = [dlist[0], copy.deepcopy(dlist[gvolume_config_num-1]) ]
#dlist[0][4] = imp2 #no matter wht was dlist[0]; used for vv case
dlist.append(copy.deepcopy(dlist[0]))
dlist[-1][8] = xcart2imp #last element for both atoms in grain volumes
dlist[-1][2] = 'CvOvms'
#helper
for el in dlist:
stname = base_name + el[2]
path = main_path + base_name + '_gvol' #grain volume
print "add_loop('" + stname + "','" + based_on.split(
'.'
)[1] + "',range(1,5),calc,conv,varset, 'up1', inherit_option = 'inherit_xred')"
for el in dlist:
stname = base_name + el[2]
path = main_path + base_name + '_gvol' #grain volume
print((
"struct_des['{0:s}'] = des('{1:s}', 'co-segregation configurations; made from "
+ based_on + "' )").format(stname, path))
write_geometry_files(dlist,
in_calc,
xcart_pores,
segtyp,
take_final_rprimd_from,
add_typat=add_typat)
""". Triple cases--------------------------------------------------------"""
def triples(addatom=('O', 3),
dlist=[],
tlist=[],
in_calc=None,
xcart_pores=[],
max_dist_to_next_atom=3):
"""
Add addatom to all configurations in tlist;
addatom[1] - type of atom in typat
dlist - list of configurations with two impurity atoms; Used if tlist == []; the format of dlist is quiet special
tlist - list of configurations with arbirtary number of atoms;
RETURN:
tlist - list of configurations with add atoms
"""
st = in_calc.init
if dlist and tlist == []:
for el in dlist:
par = el
print 'pair 1', par,
x1 = par[7]
x2 = par[8]
print 'x1 = ', x1
print 'x2 = ', x2
config = Structure()
config.xcart = [x1, x2]
config.typat = [2, 3]
config.name = el[2]
tlist.append(config)
tlist_new = []
for config in tlist:
xcart = config.xcart
typat = config.typat
name = config.name
print '\n\n\nStart to adding atom to ', name
i = 1
dlistlist = []
diffprec = 0.001
[dlistlist.append([]) for x in xcart]
print len(dlistlist)
for xpor in xcart_pores:
skip = True
for j, x in enumerate(
xcart
): # list of 2 or 3 initial atoms to which additional atom will be added
if all(np.around(xpor, 5) == np.around(x, 5)):
skip = True
break
d1, d2 = image_distance(
x, xpor, st.rprimd,
2) # the minimum distance and the next minimum dist
if d1 > max_dist_to_next_atom:
skip = True
break #if only one pore is larger from atom than limit, the pore is skiped
# suml = d11+d21+par[0]
# for dl in dlistlist:
# print 'j is ', j
i_min, smaller = min_diff(
d1, dlistlist[j], diffprec
) #old condition - bad - removes unique configurations
#if smaller: skip = True; continue # symmetrical pores deleted
dlistlist[j].append(d1)
skip = False # all conditions are fullfilled - this configuration is unique
# else:
# print 'List of distances to atoms'
if skip: continue #
#print "Pore can be used", xpor #sum of distances for triple
new = Structure()
new.name = name + addatom[0] + str(i)
new.xcart = copy.deepcopy(xcart)
new.xcart.append(xpor)
new.typat = copy.deepcopy(typat)
new.typat.append(addatom[1])
# print 'new.typat =', new.typat
#calculate sum of lengths
new.length = 0
new.lengthCO = 0
new.lengthCC = 0
new.lengthOO = 0
new.xcartC = []
new.xcartO = []
for m, x1 in enumerate(new.xcart):
if new.typat[m] == 2: new.xcartC.append(x1)
if new.typat[m] == 3: new.xcartO.append(x1)
for x2 in new.xcart:
d1, d2 = image_distance(x1, x2, st.rprimd, 2)
new.length += d1
for xC in new.xcartC:
for xO in new.xcartO:
d1, d2 = image_distance(xC, xO, st.rprimd, 2)
new.lengthCO += d1
for xC1 in new.xcartC:
for xC2 in new.xcartC:
d1, d2 = image_distance(xC1, xC2, st.rprimd, 2)
new.lengthCC += d1
for xO1 in new.xcartO:
for xO2 in new.xcartO:
d1, d2 = image_distance(xO1, xO2, st.rprimd, 2)
new.lengthOO += d1
skip = False
n = len(new.xcart)
"""additional conditions to leave only unique configurations"""
for config in tlist_new:
if 1:
nr = 0
for (v1, t1) in zip(new.xcart, new.typat):
for (v2, t2) in zip(config.xcart, config.typat):
if all(np.around(v1, 8) == np.around(
v2, 8)) and t1 == t2:
nr += 1
if nr == n:
print "The configurations", new.name, 'and', config.name, 'consist of the same atoms, continue'
skip = True
break
# print all([ all( np.around(v1, 8) == np.around(v2, 8) ) for (v1, v2) in zip(new.xcart, config.xcart) ])
#check identity using sum of distances
# i_min, smaller = min_diff(config.length, [new.length], diffprec)
# if smaller:
# print "Configuration ", new.name, "has the same sum of lengths as", config.name
i_min, smaller1 = min_diff(config.lengthCO, [new.lengthCO],
diffprec)
i_min, smaller2 = min_diff(config.lengthCC, [new.lengthCC],
diffprec)
i_min, smaller3 = min_diff(config.lengthOO, [new.lengthOO],
diffprec)
# print 'Compare', new.name, config.name, smaller1, smaller2, smaller3
if smaller1 and smaller2 and smaller3:
print "\nConfiguration ", new.name, "has the same sum of C-O, C-C and O-O lengths as", config.name
print
skip = True
break
if skip: continue
print '\nSum of CO lengths in :', new.name, new.lengthCC, new.lengthOO, new.lengthCO
tlist_new.append(new)
i += 1
return tlist_new
if segtyp == "bulk_triple" or segtyp == "bulk_pairs":
# max_dist_between_atoms = 4.8
print "\nSearching pairs ..."
dlist = pairs(in_calc,
xcart_pores,
central_atoms,
prec,
max_dist_between_atoms,
pairtyp='gvol')
if segtyp == "bulk_pairs":
write_geometry_files(dlist,
in_calc,
xcart_pores,
segtyp,
take_final_rprimd_from,
configver=True,
add_typat=add_typat)
if segtyp == "bulk_triple":
max_dist_to_next_atom = 5.5
print "\nSearching triples ..." #, tlist
tlist = []
tlist = triples(('O', 3), dlist, tlist, in_calc, xcart_pores,
max_dist_to_next_atom)
tlist = triples(('C', 2), dlist, tlist, in_calc, xcart_pores,
max_dist_to_next_atom)
write_geometry_files(dlist,
in_calc,
xcart_pores,
segtyp,
take_final_rprimd_from,
tlist=tlist,
configver=True,
add_typat=add_typat)
return dlist_coseg, xcart_pores