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 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 = list(range(
stn.natom - 2, stn.natom)) #list of atoms which were added
else:
calc.build.listadded.extend(
list(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 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 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 = list(range(
stn.natom - 2, stn.natom)) #list of atoms which were added
else:
calc.build.listadded.extend(
list(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],
end=' ') #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], end=' '
) # 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, end=' ')
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