def set_vaspp(self, token, arg, des = "see manual"):
"""
Used for setting vasp parameters.
"""
if token in ("ISMEAR",):
if type(arg) not in [int, None, ]:
raise TypeError
if token in ("KSPACING",):
if type(arg) not in [float, None, ]:
raise TypeError
old = self.vasp_params[token]
self.vasp_params[token] = arg
if old == arg:
print_and_log("Warning! You did not change "+token+" in "+self.ise+" set\n")
else:
self.history += " "+token+" was changed from "+str(old)+" to "+str(arg) + "\n"
print_and_log(token+" was changed from "+str(old)+" to "+str(arg) +" - "+ des+" in set "+self.ise+" \n")
self.update()
return
def read_vectors(token, number_of_vectors, list_of_words):
"""Returns the list of numpy vectors for the last match"""
number_of_matches = list_of_words.count(token)
if number_of_matches == 0:
#print_and_log("Warning token '"+token+"' was not found! return empty\n")
return [None]
if number_of_matches > 1:
print_and_log("Warning token '" + token +
"' was found more than one times\n")
raise RuntimeError
index = list_of_words.index(token, number_of_matches -
1) #Return the index of the last match
#print list_of_words[index]
list_of_vectors = []
vector = np.zeros((3))
for i in range(number_of_vectors):
vector[0] = float(list_of_words[index + 1])
vector[1] = float(list_of_words[index + 2])
vector[2] = float(list_of_words[index + 3])
index += 3
list_of_vectors.append(vector.copy())
return list_of_vectors
def set_relaxation_type(self,type_of_relaxation):
name = "Type of relaxation ISIF"
if type(type_of_relaxation) not in [str, ]:
raise TypeError
old = self.vasp_params["ISIF"]
if "ions" == type_of_relaxation:
if int(self.ise[0]) != 9:
print_and_log("Warning! The name of set is uncostintent with relaxation type\n")
raise TypeError
self.vasp_params["ISIF"] = 2
# self.set_nmdsteps(200)
elif type_of_relaxation == "full":
if int(self.ise[0]) != 2:
print_and_log("Warning! The name of set is uncostintent with relaxation type\n")
raise TypeError
self.vasp_params["ISIF"] = 3
else:
print_and_log("Error! Uncorrect type of relaxation\n")
raise TypeError
arg = self.vasp_params["ISIF"]
if old == arg:
print_and_log("Warning! You did not change "+name+" in "+self.ise+" set\n")
return
self.history += " "+name+" was changed from "+str(old)+" to "+str(arg) + "\n"
print_and_log(name+" was changed from "+str(old)+" to "+str(arg) + " in set "+self.ise+" \n")
self.update()
#print self.history
return
def set_potential(self, znucl, arg=''):
# print arg
if not arg:
arg = header.PATH2POTENTIALS + '/' + invert(znucl)
printlog('Attention!, Default potentials is chosen from ',
header.PATH2POTENTIALS,
'for',
invert(znucl),
imp='Y')
if type(arg) not in (str, ):
# sys.exit("\nset_potential error\n")
raise RuntimeError
if znucl in self.potdir:
if arg == self.potdir[znucl]:
print_and_log(
"Warning! You already have the same potential for " +
str(znucl) + " element\n")
# print type(self.potdir)
self.potdir[znucl] = arg
self.history += "Potential for " + str(
znucl) + " was changed to " + arg + "\n"
print_and_log("Potential for " + str(znucl) + " was changed to " +
arg + "\n")
# self.update()
return
def load(self, param, inplace=False):
"""
Update parameters of set from dict param
"""
# print(param)
if inplace:
s = self
else:
s = copy.deepcopy(self)
for key in param:
if key in vasp_keys:
s.set_vaspp(key, param[key])
elif key == 'set_potential':
for key2 in param[key]:
# print key2, 'key2'
s.set_potential(key2, param[key][key2])
elif key == 'add_nbands':
# print param[key]
s.set_add_nbands(param[key])
elif key == 'ngkpt':
s.set_ngkpt(param[key])
elif key == 'bfolder':
print_and_log('New blockfolder', param[key])
elif key in siman_keys:
s.set_attrp(key, param[key])
elif key in aims_keys:
s.set_vaspp(key, param[key])
else:
print_and_log('Error! Uknown key: ' + key)
raise RuntimeError
if key == 'set_sequence':
sets = []
for se in s.set_sequence:
sets.append(copy.deepcopy(header.varset[se]))
s.set_sequence = sets #put objects instead of names
# if hasattr(s, 'set_sequence') and s.set_sequence:
# sets = []
# for se in s.set_sequence:
# if type(se) == str:
# sets.append(copy.deepcopy(varset[se]))
# else:
# sets.append(copy.deepcopy(se))
# s.set_sequence = sets #put objects instead of names
return s
def printme(self):
for key in self.vasp_params:
if self.vasp_params[key] == None: continue
print_and_log( "{:30s} = {:s} ".format("s.vasp_params['"+key+"']", str(self.vasp_params[key]) ), imp = 'Y', end = '\n' )
printlog('ngkpt:', self.ngkpt, imp = 'Y')
printlog('POTDIR:', self.potdir, imp = 'Y', end = '\n' )
def add_conv_kpoint(self, arg):
if type(arg) is not str:
sys.exit("\nadd_conv_kpoint error\n")
if arg in self.conv_kpoint:
print_and_log("Warning! You already have this name in list")
return
self.conv_kpoint.append(arg)
self.history += "Name " + arg + " was added to self.conv_kpoint\n"
self.update()
def determine_unique_final(st_pores, sums, avds, x_m):
final_table = []
insert_positions = []
"""Please determine unique positions with similar distances taking into acc PBC!!!
below is incorrect
"""
# 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', imp = 'y')
# xcart_unique = []
# avds_unique = []
# sums_unique = []
# for i, s in enumerate(sums_crude):
# index_of_first = np.where(sums.round(crude_prec)==s)[0][0]
# xcart_unique.append(st_pores.xcart[index_of_first])
# avds_unique.append(avds[index_of_first] )
# sums_unique.append(sums[index_of_first] )
# st_pores_unique = copy.deepcopy(st_pores)
# st_pores_unique.xcart = xcart_unique
# st_pores_unique.xcart2xred()
sur = local_surrounding(x_m,
st_pores,
n_neighbours=len(st_pores.xcart),
control='atoms',
periodic=True)
# print('neb.determine_unique_final(): sur', sur)
print_and_log('I can suggest you ' + str(len(sur[0])) + ' end positions.',
imp='y')
for i, (x, d, ind) in enumerate(zip(sur[0], sur[3], sur[2])):
# if i == 0:
# continue
final_table.append(
[i, np.array(x).round(2),
round(d, 2), avds[ind], sums[ind]])
print_and_log(tabulate(final_table,
headers=['void #', 'Cart.', 'Dist', 'Dev.', 'Sum'],
tablefmt='psql'),
imp='Y')
return sur
def set_ngkpt(self,arg):
if not is_list_like(arg):
printlog("Error! set_ngkpt type error")
old = copy.copy(self.ngkpt)
self.ngkpt = copy.copy(arg)
self.kpoints_file = True
self.vasp_params['KSPACING'] = None
if old == arg:
print_and_log( "Warning! You did not change one of your parameters in new set", imp = 'y')
return
self.history += "ngkpt was changed from "+str(old)+" to "+str(arg) + " and KPOINTS file was swithed on\n"
return
def add_conv_tsmear(self,arg):
if type(arg) is not str:
sys.exit("\nadd_conv_tsmear type error\n")
try:
self.conv_tsmear[0]
except AttributeError:
print_and_log( "Error! Set "+self.ise+" does not have conv_tsmear, I create new\n")
self.conv_tsmear = []
if arg in self.conv_tsmear:
print_and_log( "Warning! You already have this name in list", imp = 'y')
return
self.conv_tsmear.append(arg)
self.history += "Name "+arg+" was added to self.conv_tsmear\n"
self.update()
def add_conv(self, arg, type_of_conv):
if type(arg) is not str:
raise TypeError
if type_of_conv not in [
"kpoint_conv", "tsmear_conv", "ecut_conv", "nband_conv",
"npar_conv"
]:
raise TypeError
try:
self.conv[type_of_conv][0]
except AttributeError:
print_and_log("Warning! Set " + self.ise +
" does not have conv, I create new\n")
self.conv = {}
except KeyError:
print_and_log(
"Warning! Set " + self.ise +
" does not have list for this key in conv, I add new\n")
self.conv[type_of_conv] = []
except IndexError:
pass
if arg in self.conv[type_of_conv]:
print_and_log( "Warning! You already have name %s in list of conv %s. Nothing done.\n" % \
(str(arg), str(self.conv[type_of_conv]) ) )
return
self.conv[type_of_conv].append(arg)
self.history += "Name " + arg + " was added to self.conv[" + type_of_conv + "]\n"
print_and_log("Name " + arg + " was added to self.conv[" +
type_of_conv + "] of set " + self.ise + " \n")
self.update()
def gb_energy_volume(gb,bulk):
if (gb.end.rprimd[1] != bulk.end.rprimd[1]).any() or (gb.end.rprimd[2] != bulk.end.rprimd[2]).any():
print_and_log("Warning! You are trying to calculate gb_energy from cells with different lateral sizes:"+str(gb.end.rprimd)+" "+str(bulk.end.rprimd)+"\n")
#print bulk.vol
V_1at = bulk.vol / bulk.natom #* to_ang**3
E_1at = bulk.energy_sigma0 / bulk.natom
A = np.linalg.norm( np.cross(gb.end.rprimd[1], gb.end.rprimd[2]) ) #surface area of gb
#print A
gb.v_gb = ( gb.vol - V_1at * gb.natom) / A / 2. * 1000
gb.e_gb = ( gb.energy_sigma0 - E_1at * gb.natom) / A / 2. * eV_A_to_J_m * 1000
gb.e_gb_init = ( gb.list_e_sigma0[0] - E_1at * gb.natom) / A / 2. * eV_A_to_J_m * 1000
gb.bulk_extpress = bulk.extpress
#print "Calc %s; e_gb_init = %.3f J/m^2; e_gb = %.3f J/m; v_gb = %.3f angstrom "%(gb.name, gb.e_gb_init, gb.e_gb, gb.v_gb )
outst = "%15s&%7.0f&%7.0f"%(gb.name, gb.e_gb, gb.v_gb)
return outst
def calc_ac(a1, c1, a2, c2, a_b = 0.1, c_b = 0.1, type = "two_atoms"):
"""
Calculate values of hexagonal lattice parameters for cell with two different atoms.
The used assumption is:
1. Provided lattice constants are for large enougth cells, in which excess volume (dV) of impurity does not depend on the size of cell.
2. Two atoms do not interact with each other, which allows to use dV(CO) = dV(C) + dV(O)
Two regimes:
two_atoms - calculate cell sizes if additional atom was added
double_cell - if cell was doubled; only first cell and second_cell are needed
Input:
a1, c1 - lattice constants of cell with first impurity atom (first cell)
a2, c2 - lattice constants of cell with second impurity atom (second cell)
a_b, c_b - lattice constants of cell with pure hexagonal metall
Output:
a, c - lattice constants of cell with two atoms
"""
hstring = ("%s #on %s"% (traceback.extract_stack(None, 2)[0][3], datetime.date.today() ) )
if hstring != header.history[-1]: header.history.append( hstring )
A = (a1**2 * c1) + (a2**2 * c2) - (a_b**2 * c_b)
B = 0.5 * (c1/a1 + c2/a2)
C = ( (a1**2 * c1) + (a2**2 * c2) ) * 0.5 #sum of cell volumes divided by 2 since during the construction of new cell we will use multiplication by 2
# print "A,B=",A,B
a = (A/B)**(1./3)
c = a * B
a = round(a,5)
c = round(c,5)
print_and_log( "a, c, c/a for cell with pure hcp ", a_b, c_b, round(c_b/a_b,4), imp ='y' )
print_and_log( "a, c, c/a for cell with first atom ", a1, c1, round(c1/a1,4), imp ='y' )
print_and_log( "a, c, c/a for cell with second atom ", a2, c2, round(c2/a2,4), imp ='y' )
#for double cell
a3 = (C/B)**(1./3)
c3 = a3 * B
a3 = round(a3,5)
c3 = round(c3,5)
if type == "two_atoms":
print_and_log( "a, c, c/a for cell with two atoms ", a, c, round(c/a,4), "# the same cell but with two atoms\n", imp ='y')
elif type == "double_cell":
print_and_log( "a, c, c/a for new cell ", a3, c3, round(c3/a3,4), "# for cell with V = V(first_cell) + V(second cell), but only for the case if V(second cell) == V(first_cell)", imp ='y')
return a, c
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 read_vectors(token,
number_of_vectors,
list_of_words,
type_func=None,
lists=False):
"""Returns the list of numpy vectors for the last match"""
# lists - return list of lists instead list of vectors
if type_func is None:
type_func = lambda a: float(a)
number_of_matches = list_of_words.count(token)
if number_of_matches == 0:
#print_and_log("Warning token '"+token+"' was not found! return empty\n")
return [None]
if number_of_matches > 1:
print_and_log("Warning token '" + token +
"' was found more than one times\n")
raise RuntimeError
index = list_of_words.index(token, number_of_matches -
1) #Return the index of the last match
#print list_of_words[index]
list_of_vectors = []
list_of_lists = []
vector = np.zeros((3))
for i in range(number_of_vectors):
vector[0] = type_func(list_of_words[index + 1])
vector[1] = type_func(list_of_words[index + 2])
vector[2] = type_func(list_of_words[index + 3])
list3 = []
for j in 1, 2, 3:
list3.append(type_func(list_of_words[index + j]))
index += 3
list_of_vectors.append(vector.copy())
list_of_lists.append(list3)
if lists:
out = list_of_lists
else:
out = list_of_vectors
return out
def determine_voids(st, r_impurity, fine=1, step_dec=0.05):
if not r_impurity:
printlog('add_neb(): Error!, Please provide *r_impurity* (1.6 A?)')
sums = []
avds = []
printlog('Searching for voids', important='y')
st_pores = find_pores(st,
r_matrix=0.5,
r_impurity=r_impurity,
step_dec=step_dec,
fine=fine,
calctype='all_pores')
printlog('List of found voids:\n', np.array(st_pores.xcart))
write_xyz(st.add_atoms(st_pores.xcart, 'H'),
file_name=st.name + '_possible_positions')
write_xyz(st.add_atoms(st_pores.xcart, 'H'),
replications=(2, 2, 2),
file_name=st.name + '_possible_positions_replicated')
for x in st_pores.xcart:
# summ = local_surrounding(x, st, n_neighbours = 6, control = 'sum', periodic = True)
# avd = local_surrounding(x, st, n_neighbours = 6, control = 'av_dev', periodic = True)
summ, avd = local_surrounding2(x,
st,
n_neighbours=6,
control='sum_av_dev',
periodic=True)
# print (summ, avd)
sums.append(summ)
avds.append(avd[0])
# print
sums = np.array(sums)
avds = np.array(avds).round(0)
print_and_log(
'Sum of distances to 6 neighboring atoms for each void (A):\n',
sums,
imp='y')
print_and_log('Distortion of voids (0 - is symmetrical):\n', avds, imp='y')
return st_pores, sums, avds
def element_name_inv(el):
el_dict = header.el_dict
nu_dict = header.nu_dict
# print type(el), el, type(str('sdf') )
if is_string_like(el):
try:
elinv = el_dict[el]
except:
print_and_log("Error! Unknown element: " + str(el))
raise RuntimeError
else:
el = int(el)
try:
elinv = nu_dict[el]
except:
print_and_log("Error! Unknown element: " + str(el))
raise RuntimeError
return elinv # inversed notion of element
def set_add_nbands(self,arg):
name = "add_nbands"
# print(type(arg))
if type(arg) not in [float, int, type(None) ]:
raise TypeError
try:
self.add_nbands
except AttributeError:
self.add_nbands = None
old = self.add_nbands
self.add_nbands = arg
if old == arg:
print_and_log("Warning! You did not change "+name+" in "+self.ise+" set\n")
return
self.history += " "+name+" was changed from "+str(old)+" to "+str(arg) + "\n"
print_and_log(" "+name+" was changed from "+str(old)+" to "+str(arg) + " in set "+self.ise+" \n")
return
def determine_unique_voids(st_pores, sums, avds):
crude_prec = 1 # number of signs after 0
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',
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=['void #', 'Cart.', 'Index', 'Dev.', 'Sum'],
tablefmt='psql'),
imp='Y')
return insert_positions
def set_attrp(self, token, arg, des="see manual"):
"""
set any attribute.
"""
# print (token)
if hasattr(self, token):
old = getattr(self, token)
if old == arg:
print_and_log("Warning! You did not change " + token +
" in " + self.ise + " set\n")
else:
setattr(self, token, arg)
self.history += " " + token + " was changed from " + str(
old) + " to " + str(arg) + "\n"
print_and_log(token + " was changed from " + str(old) +
" to " + str(arg) + " - " + des + " in set " +
self.ise + " \n")
else:
setattr(self, token, arg)
print_and_log("New attribute " + token + " added to " +
self.ise + " set\n")
self.history += " " + token + " was added as a new attr with " + str(
arg) + " value \n"
return
def inherit_iset(ise_new,
ise_from,
varset,
override=False,
newblockfolder=None):
""" Create new set copying from existing and update some fields. If ise_from does not exist create new"""
ise_new = ise_new.strip()
ise_from = ise_from.strip()
if ise_from not in varset:
print_and_log("\nError! Set " + ise_from +
" does not exist. I return new empty set\n")
return InputSet(ise_new)
old = varset[ise_from]
for key in vasp_electronic_keys + vasp_ionic_keys + vasp_other_keys: #check if new keys was added
if key not in old.vasp_params:
old.vasp_params[key] = None
if override:
print_and_log("\nAttention! You have chosen to override set " +
ise_new + "\n")
elif ise_new in varset:
print_and_log(
"\nSet " + ise_new +
" already exists. I return it without changes. Be carefull not to spoil it\n"
)
return varset[ise_new]
new = copy.deepcopy(old)
new.ise = ise_new
new.compare_with = ise_from + " "
new.des = "no description for these set, see history"
new.conv = {}
print_and_log("New set " + ise_new + " was inherited from set " +
ise_from + "\n")
new.history = old.history + "\nSet " + ise_new + " was inherited from: " + ise_from + "\n"
if newblockfolder:
new.history += 'blockfolder changed from ' + new.blockfolder + ' to ' + newblockfolder + '\n'
new.blockfolder = newblockfolder
varset[ise_new] = new
return new
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 insert(it_ins, ise_ins, mat_path, it_new, calc, type_of_insertion="xcart"):
"""For insertion of atoms to cells with changed lateral sizes
Input:
'type_of_insertion = xred' used to add xred coordinates
mat_path - path to geo files which are supposed to be changed
it_ins - already existed calculation; xred will be used from this calculation.
it_new - new folder in geo folder for obtained structure
This function finds version of calculation in folder mat_path and tries to use the same version of it_ins
"""
if not os.path.exists(mat_path):
print_and_log("Error! Path " + mat_path + " does not exist\n\n")
raise RuntimeError
if it_ins not in mat_path and it_ins not in it_new:
print_and_log('Cells are', it_ins, mat_path, it_new)
print_and_log(
"Error! you are trying to insert coordinates from cell with different name\n\n"
)
#raise RuntimeError
hstring = ("%s #on %s" %
(traceback.extract_stack(None, 2)[0][3], datetime.date.today()))
if hstring != header.history[-1]: header.history.append(hstring)
geofilelist = runBash('find ' + mat_path +
'/target -name "*.geo*" ').splitlines()
if geofilelist == []:
print_and_log(
"Warning! Target folder is empty. Trying to find in root folder ..."
)
geofilelist = runBash('find ' + mat_path +
'/ -name "*.geo*" ').splitlines()
ins = None
for mat_geofile in geofilelist:
mat = CalculationVasp()
mat.name = mat_geofile
mat.read_geometry(mat_geofile)
#step = 0.27
#r_pore = 0.56
#r_mat = mat.hex_a / 2 - step
#pores = find_pores(mat.init, r_mat, r_pore, step, 0.3, 'central') #octahedral
#mat.xcart.append ( pores.xcart[0] )
#mat.typat.append(1)
try:
ins_working = ins
ins = calc[(it_ins, ise_ins, mat.version)]
except KeyError:
print_and_log("No key", (it_ins, ise_ins, mat.version),
"I use previous working version !!!",
imp='y')
ins = ins_working
#return
#ins.end.znucl = ins.znucl
#ins.end.nznucl = ins.nznucl
#ins.end.ntypat = ins.ntypat
#ins.end.typat = ins.typat
#print ins.xcart[-1]
mat_geopath = geo_folder + struct_des[it_new].sfolder + '/'
if type_of_insertion == "xcart":
#Please update here!
mat_filename = '/' + it_new + "." + "inserted." + str(
mat.version) + '.' + 'geo'
v = np.zeros(3)
result = insert_cluster(ins.end, v, mat.init, v)
mat.end = result
mat.init = result
# mat.znucl = mat.end.znucl
# mat.nznucl = mat.end.nznucl
# mat.ntypat = mat.end.ntypat
# mat.typat = mat.end.typat
# mat.natom = len(mat.end.xred)
#mat.version = ins.version
des = ins.name + " was inserted to " + mat_geofile
elif type_of_insertion == "xred":
mat_filename = '/from/' + it_new + ".xred." + str(
mat.version) + '.' + 'geo'
#mat.end.rprimd = mat.rprimd
#mat.init.xred = copy.deepcopy(ins.end.xred)
#mat.init.typat = copy.deepcopy(ins.end.)
#print ins.end.xcart
rprimd = copy.deepcopy(mat.init.rprimd)
#build = mat.build
mat.init = copy.deepcopy(ins.end)
#mat.build = build
mat.init.rprimd = rprimd #return initial rprimd
mat.init.xred2xcart() #calculate xcart with new rprimd
des = "atoms with reduced coord. from " + ins.name + " was fully copied to " + mat_geofile
mat.init.name = 'test_insert_xred' + str(mat.version)
write_xyz(mat.init)
mat.path["input_geo"] = mat_geopath + it_new + mat_filename
if not mat.write_geometry("init", des): continue
print_and_log("Xred from " + it_ins + " was inserted in " +
mat_geofile + " and saved as " + mat_filename + " \n\n")
return
def insert_cluster(insertion, i_center, matrix, m_center):
"""
Take care of orientation; typat should be consistent
Input:
insertion - object of class Structure(), which is supposed to be inserted in matrix
in such a way that i_center will be combined with m_center.
matrix - object of class Structure().
i_center, m_center - numpy arrays (3) cartesian coordinates
"""
ins = copy.deepcopy(insertion)
mat = copy.deepcopy(matrix)
r = mat.rprimd
hproj = [(r[0][i] + r[1][i] + r[2][i]) * 0.5
for i in (0, 1, 2)] #projection of vectors on three axis
if 1:
for i, x in enumerate(ins.xcart):
ins.xcart[i] = x - i_center
for i, x in enumerate(mat.xcart):
mat.xcart[i] = x - m_center
max_dis = 1
for i_x, ix in enumerate(ins.xcart):
dv_min = max_dis
print_and_log(
"Insertion atom ",
ix,
)
if 1:
for j, mx in enumerate(mat.xcart):
dv = mx - ix
for i in 0, 1, 2:
if dv[i] > hproj[i]:
dv = dv - mat.rprimd[
i] #periodic boundary conditions - can be not correct (in the sense that closest image can lie not 100 % in the neighbourhood image cell ) for oblique cells and large absolute values of dv
if dv[i] < -hproj[i]: dv = dv + mat.rprimd[i]
len1 = np.linalg.norm(dv)
len2, second_len2 = mat.image_distance(mx, ix, r,
1) #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 1:
#Modify to replace overlapping atoms
if dv_min == max_dis:
print_and_log(" is more far away from any matrix atom than ",
dv_min, " A; I insert it")
# mat.xcart.append( ix )
# print_and_log( 'type of added atom is ', ins.typat[i_x])
# mat.typat.append( ins.typat[i_x] )
mat = mat.add_atom(xc=ix, element=ins.get_elements()[i_x])
else:
print_and_log("will replace martix atom", mat.xcart[j_r])
mat.xcart[j_r] = ix.copy()
mat.rprimd = r
mat.xcart2xred()
mat.natom = len(mat.xcart)
mat.name = 'test_of_insert'
st = mat
# print(st.natom, len(st.xcart), len(st.typat), len(st.znucl), max(st.typat) )
# write_xyz(mat)
mat = mat.return_atoms_to_cell()
mat.write_poscar()
return mat
def add(znucl, xyzpath="", new=None, write_geo=True, put_exactly_to=None):
"if put_exactly_to is True, then atom just added and nothing are searched"
if write_geo and os.path.exists(
new.path["input_geo"]) and not override:
print_and_log("add: File '" + new.path["input_geo"] +
"' already exists; continue\n",
imp='Y')
return new
#new.init = return_atoms_to_cell(new.init)
if replace_atom:
#atom substitution
if znucl not in new.init.znucl:
new.init.znucl.append(znucl)
new.init.ntypat += 1
new.init.typat[replace_atom] = new.init.ntypat
else:
ind = new.init.znucl.index(znucl)
new.init.typat[replace_atom] = ind + 1
new.init.nznucl = []
for typ in range(1, new.init.ntypat + 1):
new.init.nznucl.append(new.init.typat.count(typ))
else:
new_before = copy.deepcopy(new)
# new.init.xcart[-2][0]-=0.9 #was made once manually for c1gCOi10.1
# new.init.xcart[-2][2]+=0.2
# new.init.xred = xcart2xred(new.init.xcart, new.init.rprimd)
write_xyz(new.init)
#step = 0.042
step = 0.06
#r_pore = 0.56
#fine = 0.3 # for visualisation of pores
#fine = 4 #controls small steps; the steps are smaller for larger numbers
#r_pore = 0.54
prec = 0.004 # precision of center Angs
if new.hex_a == None:
r_mat = 1.48 - step
else:
r_mat = new.hex_a / 2 - step
if put_exactly_to:
pores_xred = [
np.array(put_exactly_to),
]
print_and_log('Inmpurity just put in ', pores_xred, imp='Y')
else:
pores = find_pores(new.init, r_mat, r_pore, step, fine, prec,
addtype, new.gbpos, find_close_to,
check_pore_vol) #octahedral
pores_xred = pores.xred
npores = len(pores_xred)
st = new.init
#delete last oxygen; was made once manually for c1gCOi10.1
# st.natom-=1
# del st.xred[-1]
# del st.typat[-1]
st.natom += npores
st.xred.extend(pores_xred)
if znucl in st.znucl:
print_and_log("znucl of added impurity is already in cell")
ind = st.znucl.index(znucl)
typat = ind + 1
st.nznucl[ind] += npores
else:
st.ntypat += 1
typat = st.ntypat
st.znucl.append(znucl)
st.nznucl.append(npores)
for i in range(npores):
st.typat.append(typat)
st.xred2xcart()
new.init = st
#print "Add impurity: len(xred ", len(new.init.xred)
#print "natom", new.init.natom
#For automatisation of fit
try:
#new.build
if new.build.nadded == None: new.build.nadded = npores
else: new.build.nadded += npores
if new.build.listadded == [None]:
new.build.listadded = range(
new.natom - npores,
new.natom) #list of atoms which were added
else:
new.build.listadded.extend(
range(new.natom - npores, new.natom))
#print "Warning!!! Information about added impurities rewritten"
except AttributeError:
pass
#new.init.znucl = new.znucl
#new.init.typat = new.typat
#write_xyz(replic(new.init, (2,1,2)) , xyzpath)
#test_adding_of_impurities(new, new_before, v)
print_and_log("Impurity with Z=" + str(znucl) +
" has been added to the found pore in " + new.name +
"\n\n")
if write_geo:
write_xyz(new.init, xyzpath)
new.write_geometry("init", new.des, override=override)
print_and_log("\n")
return new
def find_pores(st_in,
r_matrix=1.4,
r_impurity=0.6,
step_dec=0.05,
fine=0.3,
prec=0.1,
calctype='central',
gbpos=0,
find_close_to=(),
check_pore_vol=0):
"""
st_in - input Structure() object
r_impurity (A)- all pores smaller than this radius will be found
r_matrix (A) - radius of matrix atoms disregarding to their type
step_dec - scanning step of the cell in Angstroms
fine - allows to change density of local points; local_step = step_dec/fine
prec - precicion of pore center determination
check_pore_vol - allows to estimate volume of pores; has problems for big cells
'find_close_to' - works in the cases of gb and grain_vol; allows to ignore all and find pore close to provided three reduced coordinates
return - instance of Structure() class with coordinates of pores. Number and type of included pores depend on the argument of 'calctype'.
"""
xred = st_in.xred
natom = len(xred)
rprimd = st_in.rprimd
name = st_in.name
#print xred
"""Additional values"""
# check_pore_vol = 1
#if calctype in ("pore_vol","gb","grain_vol","all_local" ): check_pore_vol = 1 #something wrong with this function, especially for big cells
"""----Conversions of types for C++"""
r1 = create_c_array(rprimd[0], float)
r2 = create_c_array(rprimd[1], float)
r3 = create_c_array(rprimd[2], float)
xred1 = (c_float * len(xred))(*[x[0] for x in xred])
xred2 = (c_float * len(xred))(*[x[1] for x in xred])
xred3 = (c_float * len(xred))(*[x[2] for x in xred])
max_npores = 10000
ntot = ctypes.c_int32()
npores = ctypes.c_int32()
l_pxred1 = (c_float * max_npores)(0) #make static arrays fol local points
l_pxred2 = (c_float * max_npores)(0)
l_pxred3 = (c_float * max_npores)(0)
l_npores = (ctypes.c_int32 * max_npores)(0)
pxred1 = (c_float * max_npores)(0) #make static arrays natoms + npore
pxred2 = (c_float * max_npores)(0)
pxred3 = (c_float * max_npores)(0)
"""----Run C++ function"""
print_and_log("Starting C++ function lib.findpores()...\n")
# print(r_matrix, r_impurity, step_dec, fine, prec)
lib.findpores ( check_pore_vol, \
max_npores, \
byref(ntot), l_pxred1, l_pxred2, l_pxred3, l_npores, \
byref(npores), pxred1, pxred2, pxred3, \
natom, xred1, xred2, xred3, \
c_float(r_matrix), c_float(r_impurity), c_float(step_dec), c_float(fine), c_float(prec), \
r1, r2, r3 )
print_and_log("ntot is ", ntot.value)
print_and_log("l_npores[0] is ", l_npores[0])
v = np.zeros((3))
l_pxred = []
shift1 = 0
shift2 = 0
for i_por in range(npores.value):
l_pxred.append([])
shift2 += l_npores[i_por]
for i in range(shift1, shift2):
v[0] = l_pxred1[i]
v[1] = l_pxred2[i]
v[2] = l_pxred3[i]
l_pxred[i_por].append(v.copy())
shift1 = shift2
if shift2 != ntot.value:
print_and_log("Error! final shift2 not equal to ntot")
#print l_pxred[0]
pxred = [] # only coordinates of pores
#print pxred1[natom]
for i in range(npores.value):
v[0] = pxred1[i + natom]
v[1] = pxred2[i + natom]
v[2] = pxred3[
i +
natom] #with shift, because first natom elements are coordinates of atoms
pxred.append(v.copy())
#print pxred
"""----End of C++; result is two lists: lpxred - local geometry of all pores, pxred - coordinates of all pores"""
""" Analyse of pores """
# st_result = Structure()
st_result = st_in.new()
st_result.rprimd = rprimd
targetp = np.array((0., 0., 0.))
if find_close_to:
targetp = np.asarray(find_close_to) #targer point
print_and_log("Target point is ", targetp)
a = step_dec / fine #the side of little cube formed by the mesh which is used to find spheres inside the pore.
aaa = a * a * a
#find most central pore
if calctype == 'central': #return coordinates of the most central pore
st_result.name = "central_pore_from " + name
center = np.array((0.5, 0.5, 0.5)) #center of cell
d_min = 100
for x in pxred:
d = np.linalg.norm(x - center)
#print x, x-center, d
if d < d_min and x[0] <= 0.5 and x[1] <= 0.5 and x[2] <= 0.5:
d_min = d
x_min = x
print_and_log("The closest pore to the center has coordinates", x_min)
st_result.xred.append(x_min)
elif calctype == 'gb': #add impurity at gb
st_result.name = "gb_pore_from " + name
d_min = 100
#d2_min = 100
dt_min = 100
i_min = 0
x_min = np.zeros((3))
for i, x in enumerate(pxred):
#print "l_npores ",l_npores[i]
d = abs(x[0] - gbpos / rprimd[0][0]) #
#print x[0], d
if find_close_to: closer = (np.linalg.norm(targetp - x) < dt_min)
else: closer = (d < d_min) # and x[1]>0.3 and x[2]>0.3:
if closer:
x_pre = x_min
i_pre = i_min
d_min = d
dt_min = np.linalg.norm(targetp - x)
x_min = x
i_min = i
#find and add impurity in bulk
#d2 = abs( x[0] - (gbpos/rprimd[0][0] - 0.25) )
#if d2 < d2_min:
# d2_min = d2
# x2_min = x
# i2_min = i
#print "rprimd[0][0]", rprimd[0][0]
print_and_log("Position of boundary is ", gbpos / rprimd[0][0])
#x_min[0] = gbpos/rprimd[0][0]
if find_close_to:
print_and_log(
"The closest pore to the target point is [ %.2f %.2f %.2f ]"
% (x_min[0], x_min[1], x_min[2]))
else:
print_and_log("The closest pore to the gb has coordinates", x_min)
st_result.xred.append(x_min)
#st_result.xred.append( x_pre )
#Calculate volume of the pore using local balls:
print_and_log("The number of pore is ", i_min, " ; It has ",
l_npores[i_min], "local balls")
print_and_log("Volume of pore is ", l_npores[i_min] * a * a * a,
" A^3")
#st_result.xred.extend( l_pxred[i_min] )
#st_result.xred.extend( l_pxred[i_pre] )
#print "The closest pore to the center of bulk has coordinates",x2_min
#st_result.xred.append( x2_min )
#Calculate volume of the pore using local balls:
#print "The number of bulk pore is ",i2_min," ; It has ",l_npores[i2_min], "local balls"
#print "Volume of pore is ", l_npores[i2_min] * a*a*a, " A^3";
#st_result.xred.extend( l_pxred[i2_min] )
elif calctype == 'grain_vol': #add impurity to volume of grain
st_result.name = "grain_volume_pore_from " + name
d2_min = 100
dt_min = 100
i_min = 0
x_min = np.zeros((3))
for i, x in enumerate(pxred):
#find and add impurity to the bulk
d2 = abs(x[0] - (gbpos / rprimd[0][0] - 0.25))
if find_close_to: closer = (np.linalg.norm(targetp - x) < dt_min)
else: closer = (d2 < d2_min) # and x[1]>0.3 and x[2]>0.3:
if closer:
dt_min = np.linalg.norm(targetp - x)
d2_min = d2
x2_min = x
i2_min = i
if find_close_to:
print_and_log(
"The closest pore to the target point is [ %.2f %.2f %.2f ]"
% (x2_min[0], x2_min[1], x2_min[2]))
else:
print_and_log(
"The closest pore to the center of bulk has coordinates",
x2_min)
st_result.xred.append(x2_min)
#Calculate volume of the pore using local balls:
print_and_log("The number of bulk pore is ", i2_min, " ; It has ",
l_npores[i2_min], "local balls")
print_and_log("Volume of pore is ", l_npores[i2_min] * a * a * a,
" A^3")
st_result.xred.extend(l_pxred[i2_min])
elif calctype == 'all_local':
st_result.name = "all_local_points_from " + name
v_max = 0
i_max = 0
for i in range(npores.value):
v_pore = l_npores[i] * aaa
print_and_log("Volume of pore is ", l_npores[i] * aaa, " A^3")
if v_pore > v_max:
v_max = v_pore
i_max = i
print_and_log("Pore number ", i_max, "has the largest volume ", v_max,
" A^3")
# st_result.xred = l_pxred[i_max] # here coordinates of all local points to show geometry of pore with largerst volume
st_result.xred = [x for group in l_pxred for x in group] # all pores
elif calctype == 'all_pores':
st_result.name = "all_local_pores_from " + name
st_result.xred = pxred
st_result.rprimd = rprimd
st_result.xred2xcart()
st_result.typat = [1 for x in st_result.xred]
st_result.ntypat = 1
st_result.natom = len(st_result.typat)
st_result.znucl = [200]
st_ntypat = 1
return st_result
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 determine_barrier(positions=None, energies=None):
"""
The sign of barrier determined by the curvuture at saddle point. Minimum at saddle point corresponds to negative barrier
The saddle point is determined as maximum deviation from energy in initial position
"""
import scipy
if positions is None:
positions = range(len(energies))
if energies is None:
printlog('Error! Please provide at least energies')
spl = scipy.interpolate.PchipInterpolator(positions, energies)
spl_der = spl.derivative()
spl_der2 = spl_der.derivative()
mi = min(positions)
ma = max(positions)
r = spl_der.roots()
# print(r)
r = r[np.logical_and(
mi < r, r < ma)] # only roots inside the interval are interesting
e_at_roots = spl(r)
if len(e_at_roots) > 0:
# diff_barrier = max( e_at_roots ) # the maximum value
printlog('roots are at ', r, e_at_roots)
#find r for saddle point. the energy at saddle point is most far away from the energy at initial position by definition
de_s = np.abs(e_at_roots - energies[0])
i_r_de_max = np.argmax(de_s)
# print(de_s)
# print(i_r_de_max)
r_de_max = r[i_r_de_max]
e = spl(r_de_max)
curvuture_at_saddle = spl_der2(r_de_max)
sign = -np.sign(curvuture_at_saddle)
if curvuture_at_saddle < 0:
critical_point_type = 'maximum'
elif curvuture_at_saddle > 0:
critical_point_type = 'minimum'
else:
critical_point_type = 'undefined'
# print(type(r_de_max), type(e), critical_point_type)
print('Saddle point at {:.2f} {:.2f} is a local {:}'.format(
r_de_max, float(e), critical_point_type))
else:
print_and_log('Warning! no roots')
# diff_barrier = 0
sign = 1
mine = min(energies)
maxe = max(energies)
de = abs(mine - maxe)
# if de > diff_barrier:
diff_barrier = de * sign
print('Migration barrier is {:.2f}'.format(diff_barrier))
# plt.plot(spl(np.linspace(0, ma, 1000)))
# plt.show()
return diff_barrier
def neb_analysis(cl,
show,
up=None,
push2archive=None,
old_behaviour=None,
results_dic=None,
fitplot_args=None,
style_dic=None,
params=None):
"""
Analyse traectories and polarons
params
mep_shift_vector
"""
def determing_rms_for_surrounding_atoms(sts):
# change of rms on each step compared to first structure
#here first and last structures should correspond to first and last images
st1 = sts[0]
st_interp = interpolate(sts[0], sts[-1], 1)[0]
rms_list = []
for st in sts:
rms = rms_pos_diff(st_interp, st)
rms_list.append(rms)
print('rms is {:.3f}'.format(rms))
print('d rms is {:.3f}'.format(abs(rms_list[3] - rms_list[0])))
rms_change = abs(min(rms_list) - max(rms_list))
return rms_change
def determing_born_barrier(sts):
#here first and last structures should correspond to first and last images
local_born_e = []
i = find_moving_atom(sts[0], sts[-1])
for st in sts:
local_born_e.append(site_repulsive_e(st, i))
# import matplotlib.pyplot as plt
# plt.plot(local_born_e)
# plt.show()
return abs(min(local_born_e) - max(local_born_e))
if params is None:
params = {}
if results_dic is None:
results_dic = {}
calc = header.calc
path2mep_s = cl.project_path_cluster + '/' + cl.dir + '/mep.eps'
itise = cl.id[0] + '.' + cl.id[1]
# print(cl.ldauu)
# sys.exit()
name_without_ext = 'mep.' + itise + '.U' + str(max(cl.ldauu))
path2mep_l = cl.dir + name_without_ext + '.eps'
# print(path2mep_l)
if not os.path.exists(path2mep_l) or '2' in up:
''
get_from_server(
files=path2mep_s,
to_file=path2mep_l,
addr=cl.cluster_address,
)
movie_to = cl.dir + '/movie.xyz'
get_from_server(
files=cl.project_path_cluster + '/' + cl.dir + '/movie.xyz',
to_file=movie_to,
addr=cl.cluster_address,
)
if os.path.exists(movie_to):
makedir('figs/' + name_without_ext + '.xyz')
shutil.copyfile(movie_to, 'figs/' + name_without_ext + '.xyz')
# trying to get one image closest to the saddle point
if old_behaviour and cl.version == 2: #old behaviour, now created automatically in add callc
im = cl.set.vasp_params['IMAGES']
# if im % 2 > 0: #odd
# i = im//2 + 1
# else:
# i = im/2
# if choose_image:
# i = choose_image
for i in range(im):
i += 1
cl_i = copy.deepcopy(cl)
cl_i.version += i
cl_i.id = (cl.id[0], cl.id[1], cl_i.version)
cl_i.name = str(cl_i.id[0]) + '.' + str(cl_i.id[1]) + '.' + str(
cl_i.id[2])
# print cl_i.name
cl_i.path["output"] = cl_i.dir + '0' + str(i) + "/OUTCAR"
# for i in range():
cl_i.associated_outcars = [
aso[2:] for aso in cl_i.associated_outcars
]
# print cl_i.path["output"]
cl_i.state = '2. Ready to read outcar'
# if not os.path.exists(cl_i.path["output"]):
# load = 'o'
outst2 = ("%s" % cl_i.name).ljust(name_field_length)
if readfiles:
print(outst2 + '|' + cl_i.read_results(
loadflag, show=show, choose_outcar=choose_outcar))
else:
print_and_log(outst2 + ' | File was not read')
if cl_i.id in calc: #move creation of calcs with images to add_neb
''
# print_and_log('Please test code below this message to save prev calcs')
# if cl_i != calc[cl_i.id]
# if hasattr(calc[cl_i.id], 'prev') and calc[cl_i.id].prev:
# prevlist = calc[cl_i.id].prev
# else:
# prevlist = [calc[cl_i.id]]
# cl_i.prev = prevlist
# calc[cl_i.id] = cl_i
else:
calc[cl_i.id] = cl_i
# print path2mep_l
if 0:
if os.path.exists(path2mep_l):
# get_from_server(file = path2mep_s, to = path2mep_l, addr = cluster_address)
runBash('evince ' + path2mep_l)
else:
a = glob.glob(cl.dir + '*mep*')
if a:
runBash('evince ' + a[0])
cl1 = calc[cl.id[0], cl.id[1], 1]
cl2 = calc[cl.id[0], cl.id[1], 2]
atom_num = find_moving_atom(cl1.end, cl2.end)
# cl1.poscar()
# cl2.poscar()
# print('atom_num',atom_num)
# sys.exit()
#prepare lists
ni = cl.set.vasp_params['IMAGES']
vlist = [1] + list(range(3, ni + 3)) + [2]
# print( vlist)
mep_energies = []
atom_pos = []
pols = []
sts = []
sts_loc = []
dAO2 = [] # A-(O,F) distance for each image
dAO4 = [] # A-(O,F) distance for each image
dAO6 = []
dAO6harm = []
dAO6dev = []
for v in vlist:
cli = calc[cl.id[0], cl.id[1], v]
# if v == 1:
# cli = db['NaVP2O7_a.su.s101015v100.n5Na1v1ms.ifn.1mls.1']
# print(cl.id[0], cl.id[1], v, cli.state)
if '4' not in cli.state and 'un' not in up:
printlog('Attention! res_loop(): analys_type == neb, Calc', cli.id,
'is not finished; return')
return {}, []
# print cli.id
# cli.end = return_to_cell(cli.end)
# mep_energies.append( min(cli.list_e_sigma0) ) #use minimum energy - not very good, sometimes unconverged energy could be lower!
e0 = cli.energy_sigma0
if params and params.get(
'neb_penult_e'
): # allows to take e from the previous relaxation step in case the calculation was aborted
e0 = cli.list_e_sigma0[-2]
mep_energies.append(e0) #use last energy
atom_pos.append(cli.end.xcart[atom_num])
# Find polaron positions
if 'polaron' in show: # if 1 cause error for nomag calc
pol, mag = find_polaron(cli.end, atom_num)
if pol:
for key in pol:
if np.any(pol[key]):
for n in pol[key]:
if n not in pols:
pols.append(n)
else:
''
# print('Mag_moments on trans,', mag.round(1))
if 0 or 'neb_geo' in show:
#visualization of path
# print(atom_num)
st = copy.deepcopy(cli.end)
# print('moving_atom', st.xcart[atom_num])
info = st.nn(atom_num, 15, from_one=False, silent=1)
st.moving_atom_i = atom_num
st_loc = info['st']
# print(st_loc.xcart)
# st_loc = st_loc.shift
if v == vlist[0]:
st1 = copy.deepcopy(st)
vec = st.center_on(atom_num)
# vec = np.asarray([0.,0.,0.])
if params is not None and 'mep_shift_vector' in params:
# vec += np.array([0.11,0.11,0]) # path4
# print(params['mep_shift_vector'])
vec += np.array(params['mep_shift_vector']) # path4
# print(vec)
st_loc = st_loc.shift_atoms(vec)
if 0:
st_loc.write_xyz()
# st.write_cif('xyz/'+st.name)
if 0:
st.shift_atoms(vec).write_xyz()
sts_loc.append(st_loc)
st1 = st1.add_atom(st.xred[atom_num], 'Rb')
sts.append(st.shift_atoms(vec))
if 0 or 'neb_geo2' in show:
printlog('\n\nVersion {:}:'.format(v), imp='y')
info1 = st.nn(atom_num,
2,
from_one=False,
silent=1,
more_info=1)
print('Av. dist A-2(O,F) {:.3f} A'.format(
info1['av(A-O,F)']))
# print('Av. squared dist A-2(O,F) {:.3f} A'.format(info1['avsq(A-O,F)']))
dAO2.append(info1['av(A-O,F)'])
info12 = st.nn(atom_num, 3, from_one=False, silent=1)
print('Average distance A-3(O,F) {:.2f} A'.format(
info12['av(A-O,F)']))
info2 = st.nn(atom_num, 4, from_one=False, silent=1)
print('Average distance A-4(O,F) {:.2f} A'.format(
info2['av(A-O,F)']))
dAO4.append(info2['av(A-O,F)'])
info3 = st.nn(atom_num,
6,
from_one=False,
silent=1,
more_info=1)
print('Average_distance A-6(O,F) {:.2f} A '.format(
info3['av(A-O,F)']))
print('Av. harm. dist A-6(O,F) {:.2f} A'.format(
info3['avharm(A-O,F)']))
print('Average_deviation A-6(O,F) {:.1f} mA'.format(
info3['avdev(A-O,F)']))
dAO6.append(info3['av(A-O,F)'])
dAO6dev.append(info3['avdev(A-O,F)'])
dAO6harm.append(info3['avharm(A-O,F)'])
if 'neb_rms' in show:
rms_change = determing_rms_for_surrounding_atoms(sts)
results_dic['rms_change'] = rms_change
if 'neb_born' in show:
results_dic['born_barrier'] = determing_born_barrier(sts)
print('Born barrier is {:.2f} eV '.format(results_dic['born_barrier']))
# print(results_dic['rms_change'])
# print('show is', show)
# sys.exit()
# print('flag ', 'neb_noxyz' not in show, show)
if 'neb_noxyz' not in show and sts:
write_xyz(sts=sts) # write traectory
write_xyz(sts=sts_loc) # write traectory
if 'jmol' in params:
write_xyz(sts=sts, jmol=1, jmol_args=params['jmol']) # write jmol
st1 = st1.shift_atoms(vec)
st1.name += '_all'
# st1.write_cif('xyz/'+st1.name)
st1.write_xyz()
if dAO2: # find maximum change of distance during migration
dAO2_change = abs(min(dAO2) - max(dAO2))
results_dic['dAO2_change'] = dAO2_change
if dAO4: # find maximum change of distance during migration
dAO4_change = abs(min(dAO4) - max(dAO4))
results_dic['dAO4_change'] = dAO4_change
if dAO6: #
dAO6_change = abs(min(dAO6) - max(dAO6))
results_dic['dAO6_change'] = dAO6_change
if dAO6harm: #
results_dic['dAO6harm_change'] = abs(min(dAO6harm) - max(dAO6harm))
if dAO6dev: #
results_dic['dAO6dev_change'] = abs(min(dAO6dev) - max(dAO6dev))
results_dic[
'sts_loc'] = sts_loc # list of local structures, each structure contains dlist - distances from central cation to anions, and ellist - types of elements
results_dic[
'sts'] = sts # list of mep structures, each structure contains moving_atom_i - number of moving atom
if len(pols) > 0:
print(
'During migration of alkali ions polarons are detected on atoms:',
pols)
elif len(pols) > 1:
printlog(
'Attention! polaron is moving during migration! Obtained barrier is ambiguous'
)
else:
printlog(
'Compare magnetic moments above! In principle should be the same!')
# print np.array(atom_pos)
#test if the distances between points are not spoiled by PBC
nbc = range(-1, 2)
jj = 0
for x in atom_pos:
x2 = atom_pos[jj + 1]
# x = np.array(x)
# x2 = np.array(x2)
r = cl.end.rprimd
d1, _ = image_distance(x, x2, r, order=1) #minimal distance
x2_gen = (x2 + (r[0] * i + r[1] * j + r[2] * k) for i in nbc
for j in nbc for k in nbc) #generator over PBC images
x2c = copy.deepcopy(x2)
ii = 0
while np.linalg.norm(x -
x2c) > d1: #find the closest PBC image position
if ii > 100:
break
ii += 1
x2c = next(x2_gen)
atom_pos[jj + 1] = x2c
jj += 1
if jj == len(
atom_pos
) - 1: # the last point is not needed, we could not use slice since we need to use changed atom_pos in place
break
# print np.linalg.norm(x - x2c), d1
_, diff_barrier = plot_mep(atom_pos,
mep_energies,
plot=0,
show=0,
fitplot_args=fitplot_args,
style_dic=style_dic)
results_dic['barrier'] = diff_barrier
middle_image = len(vlist) // 2
results_dic['dEm1'] = mep_energies[middle_image] - mep_energies[0]
cl1.barrier = diff_barrier
cl2.barrier = diff_barrier
results_dic['atom_pos'] = [list(pos) for pos in atom_pos]
results_dic['mep_energies'] = mep_energies
if 'mep' in show:
if 'mepp' in show:
show_flag = True
else:
show_flag = False
# sys.exit()
plot_mep(atom_pos,
mep_energies,
image_name='figs/' + name_without_ext + '_my.eps',
show=show_flag,
fitplot_args=fitplot_args,
style_dic=style_dic)
if push2archive:
path2saved, _ = plot_mep(atom_pos,
mep_energies,
image_name='figs/' + name_without_ext + '_my',
fitplot_args=fitplot_args,
style_dic=style_dic)
push_figure_to_archive(local_figure_path=path2saved,
caption=description_for_archive)
if 0: #copy files according to chosen outcar to run nebresults locally
wd = cl_i.dir
out_i = cl_i.associated_outcars[choose_outcar - 1]
out_1 = calc[cl.id[0], cl.id[1],
1].associated_outcars[choose_outcar - 1]
out_2 = calc[cl.id[0], cl.id[1],
2].associated_outcars[choose_outcar - 1]
# print out_1
# print out_2
shutil.copyfile(wd + out_1, wd + '00/OUTCAR')
shutil.copyfile(wd + out_2, wd + '04/OUTCAR')
for d in ['01/', '02/', '03/']:
shutil.copyfile(wd + d + out_i, wd + d + 'OUTCAR')
# print wd+d+out_i
return results_dic
def add_neb(starting_calc=None,
st=None,
st_end=None,
it_new=None,
ise_new=None,
i_atom_to_move=None,
up='up2',
search_type='vacancy_creation',
images=None,
r_impurity=None,
calc_method=['neb'],
inherit_option=None,
mag_config=None,
i_void_start=None,
i_void_final=None,
atom_to_insert=None,
atom_to_move=None,
rep_moving_atom=None,
end_pos_types_z=None,
replicate=None,
it_new_folder=None,
it_folder=None,
inherit_magmom=False,
x_start=None,
xr_start=None,
x_final=None,
xr_final=None,
upload_vts=False,
center_on_moving=True,
run=False,
add_loop_dic=None,
old_behaviour=None,
params=None):
"""
Prepare needed files for NEB
Provides several regimes controlled by *search_type* flag:
- existing_voids - search for voids around atom and use them as a final position
- vacancy_creation - search for neighbors of the same type and make a vacancy as a start position
- interstitial_insertion - search for two neighboring voids; use them as start and final positions
by inserting atom *atom_to_insert*
- None - just use st and st2 as initial and final
###INPUT:
- starting_calc (Calculation) - Calculation object with structure
- st (Structure) - structure, can be used instead of Calculation
- it_new (str) - name for calculation
- st_end (Structure) - final structure
- i_atom_to_move (int) - number of atom for moving starting from 0;
- *mag_config* (int ) - choose magnetic configuration - allows to obtain different localizations of electron
- *replicate* (tuple 3*int) - replicate cell along rprimd
- i_void_start, i_void_final (int) - position numbers of voids (or atoms) from the suggested lists
- atom_to_insert (str) - element name of atom to insert
- atom_to_move (str) - element name of atom to move
- it_new_folder or it_folder (str) - section folder
- inherit_option (str) - passed only to add_loop
- inherit_magmom (bool) - if True than magmom from starting_calc is used, else from set
- end_pos_types_z (list of int) - list of Z - type of atoms, which could be considered as final positions in vacancy creation mode
- calc_method (list)
- 'neb'
- 'only_neb' - run only footer
- x_start, x_final (array) - explicit xcart coordinates of moving atom for starting and final positions, combined with atom_to_insert
- xr_start, xr_final (array) - explicit xred
- rep_moving_atom (str)- replace moving atom by needed atom - can be useful than completly different atom is needed.
- upload_vts (bool) - if True upload Vasp.pm and nebmake.pl to server
- run (bool) - run on server
- old_behaviour (str) - choose naming behavior before some date in the past for compatibility with your projects
'020917'
'261018' - after this moment new namig convention applied if end_pos_types_z is used
- add_loop_dic - standart parameters of add()
- params (dic) - provide additional parameters to add() # should be removed
###RETURN:
None
###DEPENDS:
###TODO
1. Take care of manually provided i_atom_to_move in case of replicate flag using init_numbers
2. For search_type == None x_m and x_del should be determined for magnetic searching and for saving their coordinates
to struct_des; now their just (0,0,0)
"""
naming_conventions209 = True # set False to reproduce old behavior before 2.09.2017
if old_behaviour == '020917':
naming_conventions209 = False #
# print('atom_to_insert', atom_to_insert)
# sys.exit()
calc = header.calc
struct_des = header.struct_des
varset = header.varset
if not add_loop_dic:
add_loop_dic = {}
if not end_pos_types_z:
end_pos_types_z = []
end_pos_types_z = sorted(end_pos_types_z)
if not hasattr(calc_method, '__iter__'):
calc_method = [calc_method]
if starting_calc and st:
printlog(
'Warning! both *starting_calc* and *st* are provided. I use *starting_calc*'
)
st = copy.deepcopy(starting_calc.end)
elif starting_calc:
st = copy.deepcopy(starting_calc.end)
printlog('I use *starting_calc*')
elif st:
''
printlog('I use *st*')
else:
printlog(
'Error! no input structure. Use either *starting_calc* or *st*')
corenum = add_loop_dic.get('corenum')
# print(corenum)
# sys.exit()
if corenum == None:
if images == 3:
corenum = 15
elif images == 5:
corenum = 15
elif images == 7:
corenum = 14
else:
printlog('add_neb(): Error! number of images', images,
'is unknown to me; please provide corenum!')
# print(corenum)
# sys.exit()
# print(atom_to_insert)
# sys.exit()
if corenum:
# header.corenum = corenum
''
else:
corenum = header.CORENUM
if corenum % images > 0:
print_and_log(
'Error! Number of cores should be dividable by number of IMAGES',
images, corenum)
if not ise_new:
ise_new = starting_calc.id[1]
printlog('I use', ise_new, 'as ise_new', imp='y')
name_suffix = ''
st_pores = []
name_suffix += 'n' + str(images)
"""Replicate cell """
if replicate:
print_and_log('You have chosen to replicate the structure by',
replicate)
st = replic(st, mul=replicate)
name_suffix += str(replicate[0]) + str(replicate[1]) + str(
replicate[2])
printlog('Search type is ', search_type)
if search_type == None:
if st_end == None:
printlog(
'Error! You have provided search_type == None, st_end should be provided!'
)
st1 = st
st2 = st_end
x_m = (0, 0, 0)
x_del = (0, 0, 0)
else:
"""1. Choose atom (or insert) for moving """
if is_list_like(xr_start):
x_start = xred2xcart([xr_start], st.rprimd)[0]
# print('atom_to_insert', atom_to_insert)
# sys.exit()
st1, i_m = st.add_atoms([x_start], atom_to_insert, return_ins=1)
x_m = x_start
# i_m = st1.find_atom_num_by_xcart(x_start)
# print(st1.get_elements()[i_m])
# sys.exit()
if i_atom_to_move:
nn = str(i_atom_to_move + 1)
else:
nn = str(i_void_start)
name_suffix += atom_to_insert + nn
write_xyz(st1, file_name=st.name + '_manually_start')
printlog('Start position is created manually by adding xr_start',
xr_start, x_start)
type_atom_to_move = atom_to_insert
el_num_suffix = ''
else:
atoms_to_move = []
atoms_to_move_types = []
# print('d', i_atom_to_move)
# sys.exit()
if i_atom_to_move:
typ = st.get_elements()[i_atom_to_move]
printlog('add_neb(): atom', typ, 'will be moved', imp='y')
atoms_to_move.append(
[i_atom_to_move, typ, st.xcart[i_atom_to_move]])
atoms_to_move_types.append(typ)
if naming_conventions209:
name_suffix += typ + str(i_atom_to_move + 1)
else:
#try to find automatically among alkali - special case for batteries
for i, typ, x in zip(range(st.natom), st.get_elements(),
st.xcart):
if typ in ['Li', 'Na', 'K', 'Rb', 'Mg']:
atoms_to_move.append([i, typ, x])
if typ not in atoms_to_move_types:
atoms_to_move_types.append(typ)
if atoms_to_move:
# print(atom_to_move)
# sys.exit()
if not atom_to_move:
atom_to_move = atoms_to_move_types[
0] # taking first found element
if len(atoms_to_move_types) > 1:
printlog(
'Error! More than one type of atoms available for moving detected',
atoms_to_move_types,
'please specify needed atom with *atom_to_move*')
type_atom_to_move = atom_to_move #atoms_to_move[0][1]
# printlog('atom ', type_atom_to_move, 'will be moved', imp ='y')
if i_atom_to_move:
printlog('add_neb(): *i_atom_to_move* = ',
i_atom_to_move,
'is used',
imp='y')
numbers = [[i_atom_to_move]]
i_void_start = 1
else:
printlog('add_neb(): determine_symmetry_positions ...',
imp='y')
numbers = determine_symmetry_positions(st, atom_to_move)
# print(numbers)
# sys.exit()
if len(numbers) > 0:
printlog('Please choose position using *i_void_start* :',
[i + 1 for i in range(len(numbers))],
imp='y')
printlog('*i_void_start* = ', i_void_start)
i_m = numbers[i_void_start - 1][0]
printlog('Position',
i_void_start,
'chosen, atom:',
i_m + 1,
type_atom_to_move,
imp='y')
else:
i_m = numbers[0][0]
x_m = st.xcart[i_m]
el_num_suffix = type_atom_to_move + str(i_m + 1)
atom_to_insert = atom_to_move
st1 = st
# elif atom_to_replace:
# num = st.get_specific_elements(atom_to_replace)
# if len(n)>0:
# printlog('Please choose position using *i_void_start* :', [i+1 for i in range(len(num))],imp = 'y' )
# printlog('*i_void_start* = ', i_void_start)
# i_m = num[i_void_start-1]
# printlog('Position',i_void_start,'chosen, atom to replace:', i_m+1, atom_to_replace, imp = 'y' )
# sys.exit()
else:
print_and_log(
'No atoms to move found, you probably gave me deintercalated structure',
important='y')
st_pores, sums, avds = determine_voids(st,
r_impurity,
step_dec=0.1,
fine=2)
insert_positions = determine_unique_voids(st_pores, sums, avds)
print_and_log(
'Please use *i_void_start* to choose the void for atom insertion from the Table above:',
end='\n',
imp='Y')
if i_void_start == None:
sys.exit()
if atom_to_insert == None:
printlog('Error! atom_to_insert = None')
st = st.add_atoms([
insert_positions[i_void_start],
], atom_to_insert)
name_suffix += 'i' + str(i_void_start)
i_m = st.natom - 1
x_m = st.xcart[i_m]
search_type = 'existing_voids'
type_atom_to_move = atom_to_insert
el_num_suffix = ''
st1 = st
"""2. Choose final position"""
if is_list_like(xr_final):
x_final = xred2xcart([xr_final], st.rprimd)[0]
#old
#check if i_atom_to_move should be removed
# st2 = st1.del_atom(i_m)
# st2 = st2.add_atoms([x_final], atom_to_insert)
#new
st2 = st1.mov_atoms(i_m, x_final)
# st1.printme()
# st2.printme()
# sys.exit()
x_del = x_final
search_type = 'manual_insertion'
name_suffix += 'v' + str(i_void_final)
write_xyz(st2, file_name=st.name + '_manually_final')
printlog('Final position is created manually by adding xr_final',
xr_final, x_del)
elif search_type == 'existing_voids':
#Search for voids around choosen atoms
if not st_pores:
st_pores, sums, avds = determine_voids(st, r_impurity)
sur = determine_unique_final(st_pores, sums, avds, x_m)
print_and_log('Please choose *i_void_final* from the Table above:',
end='\n',
imp='Y')
if i_void_final == None:
sys.exit()
x_final = sur[0][i_void_final] #
printlog('You chose:',
np.array(x_final).round(2),
end='\n',
imp='Y')
x_del = x_final #please compare with vacancy creation mode
write_xyz(st.add_atoms([x_final], 'H'),
replications=(2, 2, 2),
file_name=st.name + '_possible_positions2_replicated')
print_and_log('Choosing the closest position as end',
important='n')
st1 = st
st2 = st.mov_atoms(i_m, x_final)
name_suffix += el_num_suffix + 'e' + str(
i_void_final) + atom_to_insert
st1 = return_atoms_to_cell(st1)
st2 = return_atoms_to_cell(st2)
write_xyz(st1, file_name=st1.name + name_suffix + '_start')
write_xyz(st2, file_name=st2.name + name_suffix + '_final')
elif search_type == 'vacancy_creation':
#Create vacancy by removing some neibouring atom of the same type
print_and_log(
'You have chosen vacancy_creation mode of add_neb tool',
imp='Y')
print_and_log('Type of atom to move = ',
type_atom_to_move,
imp='y')
# print 'List of left atoms = ', np.array(st.leave_only(type_atom_to_move).xcart)
final_pos_z = end_pos_types_z or [
invert(type_atom_to_move)
] # by default only moving atom is considered
end_pos_types_el = [invert(z) for z in end_pos_types_z]
sur = local_surrounding(x_m,
st,
n_neighbours=14,
control='atoms',
only_elements=final_pos_z,
periodic=True) #exclude the atom itself
# print(x_m)
# print(sur)
# st.nn()
end_pos_n = sur[2][1:]
print_and_log(
'I can suggest you ' + str(len(end_pos_n)) +
' end positions. The distances to them are : ',
np.round(sur[3][1:], 2),
' A\n ',
'They are ', [invert(z) for z in final_pos_z],
'atoms, use *i_void_final* to choose required: 1, 2, 3 ..',
imp='y')
i_sym_final_l = []
for j in end_pos_n:
for i, l in enumerate(numbers):
if j in l:
i_sym_final_l.append(i + 1)
printlog('Their symmetry positions are ', i_sym_final_l, imp='y')
# sys.exit()
if not i_void_final:
printlog('Changing i_void_final: None -> 1', imp='y')
i_void_final = 1 #since zero is itself
chosen_dist = sur[3][i_void_final]
print_and_log('Choosing position ',
i_void_final,
'with distance',
round(chosen_dist, 2),
'A',
imp='y')
# print(end_pos_n)
i_sym_final = 0
n_final = sur[2][i_void_final]
for i, l in enumerate(numbers):
if n_final in l:
i_sym_final = i + 1
printlog('It is symmetrically non-equiv position #',
i_sym_final,
imp='y')
# sys.exit()
header.temp_chosen_dist = chosen_dist
if old_behaviour == '261018':
name_suffix += el_num_suffix + 'v' + str(i_void_final)
else:
name_suffix += el_num_suffix + 'v' + str(
i_void_final) + list2string(end_pos_types_el, joiner='')
# print(name_suffix)
# sys.exit()
x_del = sur[0][i_void_final]
printlog('xcart of atom to delete', x_del)
i_del = st.find_atom_num_by_xcart(x_del)
# print(x_del)
# print(st.xcart)
# for x in st.xcart:
# if x[0] > 10:
# print(x)
print_and_log('number of atom to delete = ', i_del, imp='y')
if i_del == None:
printlog('add_neb(): Error! I could find atom to delete!')
# print st.magmom
# print st1.magmom
# try:
if is_list_like(xr_start):
st2 = st1.mov_atoms(
i_m, x_del) # i_m and sur[0][neb_config] should coincide
# i_del = st1.find_atom_num_by_xcart(x_del)
st1 = st1.del_atom(i_del)
else:
print_and_log(
'Making vacancy at end position for starting configuration',
imp='y')
st1 = st.del_atom(i_del)
print_and_log(
'Making vacancy at start position for final configuration',
important='n')
st2 = st.mov_atoms(
i_m, x_del) # i_m and sur[0][neb_config] should coincide
# except:
# st2 = st
st2 = st2.del_atom(i_del) # these two steps provide the same order
"""Checking correctness of path"""
#if start and final positions are used, collisions with existing atoms are possible
if is_list_like(xr_start) and is_list_like(xr_final):
printlog('Checking correctness')
st1, _, _ = st1.remove_close_lying()
stt = st1.add_atoms([
x_final,
], 'Pu')
stt, x, _ = stt.remove_close_lying(
rm_both=True
) # now the final position is empty for sure; however the order can be spoiled
# print(st._removed)
if stt._removed:
st1 = stt # only if overlapping was found we assign new structure
st2, _, _ = st2.remove_close_lying(rm_first=stt._removed)
stt = st2.add_atoms([
x_start,
], 'Pu')
stt, x, _ = stt.remove_close_lying(
rm_both=True) # now the start position is empty for sure
if stt._removed:
st2 = stt
print(st2.get_elements())
# sys.exit()
elif is_list_like(xr_final) and not is_list_like(xr_start) or is_list_like(
xr_start) and not is_list_like(xr_final):
printlog(
'Attention! only start or final position is provided, please check that everything is ok with start and final states!!!'
)
""" Determining magnetic moments """
vp = varset[ise_new].vasp_params
if 'ISPIN' in vp and vp['ISPIN'] == 2:
print_and_log(
'Magnetic calculation detected. Preparing spin modifications ...',
imp='y')
cl_test = CalculationVasp(varset[ise_new])
cl_test.init = st1
# print 'asdfsdfasdfsadfsadf', st1.magmom
if inherit_magmom and hasattr(st, 'magmom') and st.magmom and any(
st.magmom):
print_and_log(
'inherit_magmom=True: You have chosen MAGMOM from provided structure',
imp='y')
name_suffix += 'mp' #Magmom from Previous
else:
cl_test.init.magmom = None
print_and_log(
'inherit_magmom=False or no magmom in input structure : MAGMOM will be determined from set',
imp='y')
name_suffix += 'ms' #Magmom from Set
cl_test.actualize_set() #find magmom for current structure
st1.magmom = copy.deepcopy(cl_test.init.magmom)
st2.magmom = copy.deepcopy(cl_test.init.magmom)
# sys.exit()
# print_and_log('The magnetic moments from set:')
# print cl_test.init.magmom
if search_type != None: # for None not implemented; x_m should be determined first for this
#checking for closest atoms now only for Fe, Mn, Ni, Co
sur = local_surrounding(x_m,
st1,
n_neighbours=3,
control='atoms',
periodic=True,
only_elements=header.TRANSITION_ELEMENTS)
dist = np.array(sur[3]).round(2)
numb = np.array(sur[2])
a = zip(numb, dist)
# a= np.array(a)
# print a[1]
# a = np.apply_along_axis(np.unique, 1, a)
# print a
def unique_by_key(elements, key=None):
if key is None:
# no key: the whole element must be unique
key = lambda e: e
return list({key(el): el for el in elements}.values())
# print a
mag_atoms_dists = unique_by_key(a, key=itemgetter(1))
# print (mag_atoms_dists)
# a = unique_by_key(a, key=itemgetter(1))
print_and_log(
'I change spin for the following atoms:\ni atom dist\n',
np.round(mag_atoms_dists, 2),
imp='y')
# print 'I have found closest Fe atoms'
muls = [(1.2, 0.6), (0.6, 1.2)]
mag_moments_variants = []
for mm in muls:
mags = copy.deepcopy(cl_test.init.magmom)
# print mags
for a, m in zip(mag_atoms_dists, mm):
# print t[1]
mags[a[0]] = mags[a[0]] * m
mag_moments_variants.append(mags)
print_and_log('The list of possible mag_moments:', imp='y')
for i, mag in enumerate(mag_moments_variants):
print_and_log(i, mag)
print_and_log(
'Please use *mag_config* arg to choose desired config',
imp='y')
if mag_config != None:
st1.magmom = copy.deepcopy(mag_moments_variants[mag_config])
st2.magmom = copy.deepcopy(mag_moments_variants[mag_config])
name_suffix += 'm' + str(mag_config)
print_and_log('You have chosen mag configuration #',
mag_config,
imp='y')
else:
print_and_log('Non-magnetic calculation continue ...')
"""3. Add to struct_des, create geo files, check set, add_loop """
if starting_calc:
it = starting_calc.id[0]
it_new = it + 'v' + str(starting_calc.id[2]) + '.' + name_suffix
if not it_new_folder:
it_new_folder = struct_des[it].sfolder + '/neb/'
obtained_from = str(starting_calc.id)
if not ise_new:
print_and_log('I will run add_loop() using the same set',
important='Y')
ise_new = cl.id[1]
elif st:
if not it_new:
printlog(
'Error! please provide *it_new* - name for your calculation',
important='Y')
it = None
it_new += '.' + name_suffix
obtained_from = st.name
if not ise_new:
printlog('Error! please provide *ise_new*', important='Y')
if not it_new_folder and not it_folder:
printlog(
'Error! please provide *it_new_folder* - folder for your new calculation',
important='Y')
if it_folder:
it_new_folder = it_folder
if rep_moving_atom:
it_new += 'r' + rep_moving_atom
if it_new not in struct_des:
add_des(struct_des, it_new, it_new_folder,
'Automatically created and added from ' + obtained_from)
print_and_log(
'Creating geo files for starting and final configurations (versions 1 and 2) ',
important='y')
# if starting_calc:
# cl = copy.deepcopy(starting_calc)
# else:
cl = CalculationVasp()
#write start position
if search_type is not None:
struct_des[it_new].x_m_ion_start = x_m
struct_des[it_new].xr_m_ion_start = xcart2xred([x_m], st1.rprimd)[0]
# st1, _, _ = st1.remove_close_lying()
# st2, _, _ = st2.remove_close_lying()
print('Trying to find x_m', x_m)
i1 = st1.find_atom_num_by_xcart(
x_m,
prec=0.45,
)
# sys.exit()
print('Trying to find x_del', x_del)
i2 = st2.find_atom_num_by_xcart(
x_del,
prec=0.45,
)
if rep_moving_atom: #replace the moving atom by required
st1 = st1.replace_atoms([i1], rep_moving_atom)
st2 = st2.replace_atoms([i2], rep_moving_atom)
else:
#allows to make correct order for nebmake.pl
st1 = st1.replace_atoms([i1], type_atom_to_move)
st2 = st2.replace_atoms([i2], type_atom_to_move)
i1 = st1.find_atom_num_by_xcart(
x_m,
prec=0.45) # the positions were changed # check if this is correct
i2 = st2.find_atom_num_by_xcart(x_del, prec=0.45)
cl.end = st1
ver_new = 1
cl.version = ver_new
cl.path["input_geo"] = header.geo_folder + struct_des[it_new].sfolder + '/' + \
it_new+"/"+it_new+'.auto_created_starting_position_for_neb_'+str(search_type)+'.'+str(ver_new)+'.'+'geo'
cl.write_siman_geo(geotype='end',
description='Starting conf. for neb from ' +
obtained_from,
override=True)
#write final position
struct_des[it_new].x_m_ion_final = x_del
struct_des[it_new].xr_m_ion_final = xcart2xred([x_del], st2.rprimd)[0]
cl.end = st2
ver_new = 2
cl.version = ver_new
cl.path["input_geo"] = header.geo_folder + struct_des[it_new].sfolder + '/' + \
it_new+"/"+it_new+'.auto_created_final_position_for_neb_'+str(search_type)+'.'+str(ver_new)+'.'+'geo'
cl.write_siman_geo(geotype='end',
description='Final conf. for neb from ' + obtained_from,
override=True)
if not rep_moving_atom and search_type is not None:
st1s = st1.replace_atoms([i1], 'Pu')
st2s = st2.replace_atoms([i2], 'Pu')
else:
st1s = copy.deepcopy(st1)
st2s = copy.deepcopy(st2)
if center_on_moving and search_type is not None:
vec = st1.center_on(i1)
st1s = st1s.shift_atoms(vec)
st2s = st2s.shift_atoms(vec)
write_xyz(st1s, file_name=it_new + '_start')
write_xyz(st2s, file_name=it_new + '_end')
st1s.write_poscar('xyz/POSCAR1')
st2s.write_poscar('xyz/POSCAR2')
# print(a)
# runBash('cd xyz; mkdir '+it_new+'_all;'+"""for i in {00..04}; do cp $i/POSCAR """+ it_new+'_all/POSCAR$i; done; rm -r 00 01 02 03 04')
with cd('xyz'):
a = runBash(header.PATH2NEBMAKE + ' POSCAR1 POSCAR2 3')
print(a)
dst = it_new + '_all'
makedir(dst + '/any')
for f in ['00', '01', '02', '03', '04']:
shutil.move(f + '/POSCAR', dst + '/POSCAR' + f)
shutil.rmtree(f)
#prepare calculations
# sys.exit()
#Check if nebmake is avail
# if int(runBash('ssh '+cluster_address+' test -e '+project_path_cluster+'/tools/vts/nebmake.pl; echo $?') ):
# ''
# print_and_log('Please upload vtsttools to ',cluster_address, project_path_cluster+'/tools/vts/')
# raise RuntimeError
# copy_to_server(path_to_wrapper+'/vtstscripts/nebmake.pl', to = project_path_cluster+'/tools/', addr = cluster_address)
# if int(runBash('ssh '+cluster_address+' test -e '+project_path_cluster+'/tools/Vasp.pm; echo $?') ):
# copy_to_server(path_to_wrapper+'/vtstscripts/Vasp.pm', to = project_path_cluster+'/tools/', addr = cluster_address)
inherit_ngkpt(it_new, it, varset[ise_new])
if run:
add_loop_dic['run'] = run
add_loop_dic['corenum'] = corenum
# print(add_loop_dic)
add_loop(
it_new,
ise_new,
verlist=[1, 2],
up=up,
calc_method=calc_method,
savefile='oc',
inherit_option=inherit_option,
n_neb_images=images,
# params=params,
**add_loop_dic)
if upload_vts:
siman_dir = os.path.dirname(__file__)
# print(upload_vts)
push_to_server([
siman_dir + '/cluster_tools/nebmake.pl',
siman_dir + '/cluster_tools/Vasp.pm'
],
to=header.cluster_home + '/tools/vts',
addr=header.cluster_address)
else:
print_and_log('Please be sure that vtsttools are at',
header.cluster_address,
header.cluster_home + '/tools/vts/',
imp='Y')
printlog('add_neb finished')
return it_new