def random_purturbation_index():
if is_pbc():
struct=readstructure(crystal=True,molecule=False)
natom=len(struct)
d=np.zeros(2,dtype=int)
while d[0]==d[1]:
d=np.random.randint(0,natom,2)
coord=struct.frac_coords
coord[[d[0], d[1]], :] = coord[[d[1], d[0]], :]
tmp_struct=Structure(struct.lattice,struct.species,coord)
fname='swap_'+str(d[0]+1)+'_'+str(d[1]+1)+'.vasp'
proc_str="Saving data to "+ fname +" File ..."
procs(proc_str,0,sp='-->>')
tmp_struct.to(filename=fname,fmt='poscar')
else:
struct=readstructure(crystal=False,molecule=True)
# print(struct)
coord=struct.cart_coords
natom=len(struct)
d=np.zeros(2,dtype=int)
while d[0]==d[1]:
d=np.random.randint(0,natom,2)
coord[[d[0], d[1]], :] = coord[[d[1], d[0]], :]
tmp_struct=Molecule(struct.species,coord)
fname='swap_'+str(d[0]+1)+'_'+str(d[1]+1)+'.xyz'
proc_str="Saving data to "+ fname +" File ..."
procs(proc_str,0,sp='-->>')
tmp_struct.to(filename=fname,fmt='xyz')
return
def structure_finger_print():
h_str = "# "
if is_pbc():
struct = readstructure(crystal=True, molecule=False, cano=True)
struct_ana = CrystalAnalysis(struct)
(rdf_x, rdf_species) = struct_ana.fp_oganov()
else:
struct = readstructure(crystal=False, molecule=True, cano=True)
struct_ana = MoleculeAnalysis(struct)
(rdf_x,
rdf_species) = struct_ana.discrete_radial_distribution_function()
data = np.zeros((len(rdf_x), len(rdf_species) + 1))
data[:, 0] = rdf_x
tmp1_str = "#%(key1)+12s"
tmp2_dic = {'key1': 'Distance/A'}
for i, key in enumerate(rdf_species.keys()):
data[:, i + 1] = rdf_species[key]
tmp1_str += "%(key" + str(i + 2) + ")+12s"
if (isinstance(struct, MStructure)):
tmp2_dic["key" + str(i + 2)] = str(key)
if (isinstance(struct, Molecule)):
tmp2_dic["key" + str(i + 2)] = str((key[0].number, key[1].number))
for el in struct.types_of_specie:
h_str += str(el) + ' |->' + str(el.number) + ' '
head_line = h_str + '\n' + tmp1_str % tmp2_dic
filename = "FingerPrint.dat"
proc_str = "Writting data to " + filename + " File ..."
procs(proc_str, 0, sp='-->>')
write_col_data(filename, data, head_line=head_line)
def structures_difference(distance_tolerance=0.1, rcut=30):
if is_pbc():
structs, fnames = readstructure(crystal=True,
molecule=False,
multi_files=True,
cano=True)
else:
structs, fnames = readstructure(crystal=False,
molecule=True,
multi_files=True,
cano=True)
for i in structs:
print(i)
for i in fnames:
print(i)
n_struct = len(structs)
proc_str = "Total Number of Files are : " + str(n_struct)
procs(proc_str, 0, sp='-->>')
dij = np.zeros((n_struct, n_struct))
for i, j in itertools.combinations(range(n_struct), 2):
struct_i = structs[i]
struct_j = structs[j]
if isinstance(struct_i, MStructure):
dij[i, j] = distance(struct_i, struct_j, rcut, pbc=True)
dij[j, i] = dij[i, j]
else:
dij[i, j] = distance(struct_i, struct_j, rcut, pbc=False)
dij[j, i] = dij[i, j]
filename = "StructureDistance.dat"
proc_str = "Writting data to " + filename + " File ..."
procs(proc_str, 0, sp='-->>')
write_col_data(filename, dij, head_line='')
data = ''
for i, st_name in enumerate(fnames):
data += "%(key1)+5s %(key2)+s" % {
'key1': str(i),
'key2': fnames[i]
} + '\n'
filename = "StructureList.dat"
proc_str = "Writting data to " + filename + " File ..."
procs(proc_str, 0, sp='-->>')
head_line = "#%(key1)+5s %(key2)+s" % {
'key1': 'index',
'key2': 'structure_name'
} + '\n'
data = head_line + data
write_col_data(filename, data, str_data=True)
def strain_operation():
struct = readstructure()
if isinstance(Structure, Molecule):
print("strain operation is only supported for periodic structure")
return
print('input the strain component like :')
print("0.01")
print("it means aplly a strain of 1% along all directions")
print("or")
print("0.01 0.0 0.0")
print("it means apply a strain of 1% along the x direction")
print("or")
print("0.01:0.03:5 0.0 0.0")
print("it means to devide strain range into 5 parts")
wait_sep()
strain_str = input()
tmp_list = strain_str.split(" ")
if len(tmp_list) == 1:
strain = [[float(tmp_list[0]), float(tmp_list[0]), float(tmp_list[0])]]
elif len(tmp_list) == 3 and not ":" in strain_str:
strain = [[float(x) for x in tmp_list]]
elif len(tmp_list) == 3 and strain_str.count(":") % 2 == 0:
tmp1 = [float(x) for x in tmp_list[0].split(":")]
tmp2 = [float(x) for x in tmp_list[1].split(":")]
tmp3 = [float(x) for x in tmp_list[2].split(":")]
strain = []
if len(tmp1) == 3:
x_range = np.linspace(tmp1[0], tmp1[1], int(tmp1[2]))
else:
x_range = tmp1
if len(tmp2) == 3:
y_range = np.linspace(tmp2[0], tmp2[1], int(tmp2[2]))
else:
y_range = tmp2
if len(tmp3) == 3:
z_range = np.linspace(tmp3[0], tmp3[1], int(tmp3[2]))
else:
z_range = tmp3
for ix in x_range:
for iy in y_range:
for iz in z_range:
strain.append([ix, iy, iz])
else:
print("unknow format")
i_count = 0
fis_name = 'index_strain.dat'
fis = open(fis_name, 'w')
for i_strain in strain:
outfile_name = 'strain_' + str(i_count) + '.vasp'
# print(outfile_name)
struct_cp = struct.copy()
struct_cp.apply_strain(i_strain)
# print(struct_cp)
fis.writelines("%3d %7.4f %7.4f %7.4f\n" %
(i_count, strain[i_count][0], strain[i_count][1],
strain[i_count][2]))
struct_cp.to(filename=outfile_name, fmt='poscar')
i_count += 1
fis.close()
def random_disturbing_lat():
struct=readstructure(crystal=True,molecule=False)
print("input the maximum displacement and with fix diagonal ")
print("or non-diagonal element like this: 0.01 T F")
print("it means maximum displacement is 0.01 ")
print("the diagonal element will be fixed,")
print("while random disturbing will be add to non-digaonal element")
wait_sep()
in_str=""
while in_str=="":
in_str=input().strip().split()
# print(in_str)
maxdelta=float(in_str[0])
diag=in_str[1].lower()=='t'
nondiag=in_str[2].lower()=='t'
# print(diag)
# print(nondiag)
stress_eps = np.random.random(6) * 2 * maxdelta - maxdelta
if diag:
stress_eps[:3] = 0
if nondiag:
stress_eps[-3:] = 0
new_lattice=deform_cell(struct,stress_eps)
tmp_struct=Structure(new_lattice,struct.species,struct.frac_coords)
fname='random.vasp'
proc_str="Saving data to "+ fname +" File ..."
procs(proc_str,0,sp='-->>')
tmp_struct.to(filename=fname,fmt='poscar')
return
def structure_symmetry():
if is_pbc():
struct = readstructure(crystal=True, molecule=False)
ast = analyzer.SpacegroupAnalyzer(struct)
print("{} : {}".format('Structure Type', 'periodicity'))
print("{} : {}".format('Lattice Type', ast.get_lattice_type()))
print("{} : {}".format('Space Group ID', ast.get_space_group_number()))
print("{} : {}".format('International Symbol',
ast.get_space_group_symbol()))
print("{} : {}".format('Hall Symbol', ast.get_hall()))
return
else:
struct = readstructure(crystal=False, molecule=True)
ast = analyzer.PointGroupAnalyzer(struct)
print("{} : {}".format('Structure Type', 'non-periodicity'))
print("{} : {}".format('International Symbol', ast.get_pointgroup()))
return
def random_disturbing_pos():
def random_move_one_atom(coords, mu=0.1, sigma=0.01):
index = random.randint(0, len(coords) - 1)
radius = np.abs(np.random.normal(mu, sigma))
theta_x = 2 * np.pi * np.random.random_sample()
theta_y = 2 * np.pi * np.random.random_sample()
theta_z = 2 * np.pi * np.random.random_sample()
vector = apply_rotation([1, 0, 0], theta_x, theta_y, theta_z)
coords[index] += vector*radius
return coords
print("input the maximum displacement(<0.25 in Angstrom)")
wait_sep()
in_str=""
while in_str=="":
in_str=input().strip()
epsilon=float(in_str)
assert epsilon < 0.3
if is_pbc():
struct=readstructure(crystal=True,molecule=False)
coords=struct.cart_coords
for iatom in range(len(struct)):
coords=random_move_one_atom(coords,mu=epsilon)
tmp_struct=Structure(struct.lattice,struct.species,coords,coords_are_cartesian=True)
fname='random.vasp'
proc_str="Saving data to "+ fname +" File ..."
procs(proc_str,0,sp='-->>')
tmp_struct.to(filename=fname,fmt='poscar')
else:
struct=readstructure(crystal=False,molecule=True)
coords=struct.cart_coords
for iatom in range(len(struct)):
coords=random_move_one_atom(coords,mu=epsilon)
tmp_struct=Molecule(struct.species,coords)
fname='random.xyz'
proc_str="Saving data to "+ fname +" File ..."
procs(proc_str,0,sp='-->>')
tmp_struct.to(filename=fname,fmt='xyz')
return
def get_conventional_cell():
struct = readstructure()
sepline(ch='conventional cell', sp='-')
ast = analyzer.SpacegroupAnalyzer(struct)
conv_st = ast.get_conventional_standard_structure()
print(conv_st)
sepline()
print('save to ' + NAME + '_convention.vasp')
conv_st.to(filename=NAME + '_conventional.vasp', fmt='poscar')
sepline()
return
def get_primitive_cell():
struct = readstructure()
sepline(ch='Primitive Cell', sp='-')
ast = analyzer.SpacegroupAnalyzer(struct)
prim_st = ast.find_primitive()
print(prim_st)
sepline()
print('save to ' + NAME + '_primitive.vasp')
prim_st.to(filename=NAME + '_primitive.vasp', fmt='poscar')
sepline()
return
def covert_operation():
print('your choice ?')
print('{} >>> {}'.format('1', 'crystal'))
print('{} >>> {}'.format('2', 'single molecule'))
wait_sep()
in_str = ""
while in_str == "":
in_str = input().strip()
choice = int(in_str)
assert choice in [1, 2]
if choice == 1:
structs, fnames = readstructure(crystal=True,
molecule=False,
multi_files=True)
print('input the target file format')
print("supported format: vasp xsf cif nc json yaml ")
else:
structs, fnames = readstructure(crystal=False,
molecule=True,
multi_files=True)
print('input the target file format')
print("supported format: xyz mol nc json yaml ")
#print(fnames)
wait_sep()
in_str = ""
while in_str == "":
in_str = input().strip()
fmt = in_str
for fname, struct in zip(fnames, structs):
if fmt == 'vasp':
struct.to(filename=fname.replace(fname.split('.')[-1], fmt),
fmt='poscar')
else:
struct.to(filename=fname.replace(fname.split('.')[-1], fmt),
fmt=fmt)
def get_xrd():
struct = readstructure()
xrd = XRDCalculator()
# xrd_data=xrd.get_xrd_pattern(struct)
xrd_data = xrd.get_pattern(struct)
jxrd_data = jsanitize(xrd_data.as_dict())
fname = 'XRD.json'
proc_str = "Saving data to " + fname + " File ..."
procs(proc_str, 1, sp='-->>')
json_store(jxrd_data, fname)
data = np.vstack((xrd_data.x, xrd_data.y)).T
margin = 10.
ds = xrd_data.x[0] - margin
de = xrd_data.x[-1] + margin
tmp_data = [ds] + xrd_data.x.tolist() + [de]
tmp_data1 = np.diff(tmp_data).tolist()
tmp_data2 = np.array([0] + np.cumsum(tmp_data1).tolist())
tmp_data3 = tmp_data2 / tmp_data2[-1]
x_data = np.linspace(ds, de, 10000)
y_data = np.zeros((len(x_data)))
for i in range(1, len(tmp_data3) - 1):
index = int(tmp_data3[i] * 10000)
y_data[index] = xrd_data.y[i - 1]
data = np.vstack((x_data, y_data))
data = (smear(data, sigma=0.1)).T
head_line = "#%(key1)+12s %(key2)+12s" % {
'key1': '2theta',
'key2': 'Intensity'
}
fname = 'XRD.dat'
proc_str = "Saving data to " + fname + " File ..."
procs(proc_str, 2, sp='-->>')
write_col_data(fname, data, head_line)
check_matplotlib()
fname = 'XRD.png'
proc_str = "Saving plot to " + fname + " File ..."
procs(proc_str, 3, sp='-->>')
plt = xrd.get_plot(struct)
plt.savefig(fname, format='png')
def select_function(choice):
# structure operation
if choice == "a1":
random_operation()
elif choice == "a2":
covert_operation()
elif choice == "a3":
build_operation()
elif choice == "a4":
cleave_operation()
elif choice == "a5":
strain_operation()
elif choice == 'a6':
twoD_operation()
# structure analysis
elif choice == "b1":
structure_symmetry()
elif choice == "b2":
structure_finger_print()
elif choice == "b3":
structures_difference()
elif choice == "b4":
get_primitive_cell()
elif choice == "b5":
get_conventional_cell()
elif choice == "b6":
get_xrd()
# vasp in/out tools
elif choice == "c1":
struct = readstructure(crystal=True,
molecule=False,
filename='POSCAR',
cano=False)
sepline(ch=' prepare intput files ', sp='-')
print('your choce ?')
print('{} >>> {}'.format('1', 'prepare all files automatically'))
print('{} >>> {}'.format('2', 'prepare INCAR file'))
print('{} >>> {}'.format('3', 'prepare KPOINTS file'))
print('{} >>> {}'.format('4', 'prepare POTCAR file'))
wait_sep()
in_str = ""
while in_str == "":
in_str = input().strip()
choice = int(in_str)
if choice == 1:
generate_all_input(struct)
elif choice == 2:
generate_incar(struct)
elif choice == 3:
generate_kpoint(struct)
elif choice == 4:
generate_potcar(struct)
else:
print("unknown choice")
elif choice == "cxx":
sepline(ch=' summary output files ', sp='=')
print('{} >>> {}'.format('1', 'describe OUCAR file'))
print('{} >>> {}'.format('2', 'describe OSICAR file'))
print('{} >>> {}'.format('3', 'describe vasprun.xml file'))
wait_sep()
in_str = ""
while in_str == "":
in_str = input().strip()
choice = int(in_str)
if choice == 1:
describe_outcar()
elif choice == 2:
describe_OSICAR()
elif choice == 3:
describe_vasprun()
else:
print("unknow choice")
elif choice == "c2":
sepline(ch=' vasp output analysis ', sp='-')
print('{} >>> {}'.format('1 ', 'total density of states'))
print('{} >>> {}'.format('2 ', 'projected density of states'))
print('{} >>> {}'.format('3 ', 'band structure'))
print('{} >>> {}'.format('4 ', 'projected band structure'))
print('{} >>> {}'.format('5 ', 'select one band structure'))
print('{} >>> {}'.format('6 ', 'charge density'))
print('{} >>> {}'.format('7 ', 'spin density'))
print('{} >>> {}'.format('8 ', 'charge density difference'))
print('{} >>> {}'.format('9 ', 'spin density component: up/down'))
print('{} >>> {}'.format('10', 'average charge density/potential'))
print('{} >>> {}'.format('11', 'optics analysis'))
print('{} >>> {}'.format('12', 'mechanical analysis'))
print('{} >>> {}'.format('13',
'ab initio molecular dynamics analysis'))
wait_sep()
in_str = ""
while in_str == "":
in_str = input().strip()
choice = int(in_str)
if choice == 1:
total_dos()
elif choice == 2:
projected_dos()
elif choice == 3:
band_structure()
elif choice == 4:
projected_band_structure()
elif choice == 5:
select_one_band_structure()
elif choice == 6:
charge_density()
elif choice == 7:
spin_density()
elif choice == 8:
charge_density_diff()
elif choice == 9:
spin_density_component()
elif choice == 10:
chg_locp_average()
elif choice == 11:
optics_analysis()
elif choice == 12:
elastic_analysis()
elif choice == 13:
aimd_analysis()
else:
print("unknow choice")
# online exctraction
elif choice == "e1":
online_get_banddos()
elif choice == "e2":
online_get_structure()
elif choice == "e3":
online_get_properties()
elif choice == "e4":
online_get_phase_graph()
elif choice == "88":
return
else:
print("unknow choice")
return
def build_operation():
print('your choice ?')
print('{} >>> {}'.format('1', 'build supercell'))
print('{} >>> {}'.format('2', 'build nanotube'))
print('{} >>> {}'.format('3', 'build absorption configuration'))
wait_sep()
in_str = ""
while in_str == "":
in_str = input().strip()
choice = int(in_str)
assert choice in [1, 2, 3]
if choice == 1:
struct = readstructure()
wait_sep()
tip = """
Several options are available:
a. A full 3x3 scaling matrix defining the linear combination
the old lattice vectors. E.g., 2 1 0 0 1 0 0 0 3
generates a new structure with lattice vectors a' =
2a + b, b' = 3b, c' = c where a, b, and c are the lattice
vectors of the original structure.
b. An sequence of three scaling factors. E.g., 2 1 1
specifies that the supercell should have dimensions 2a x b x
c.
c. A number, which simply scales all lattice vectors by the
same factor.
"""
print(tip)
wait_sep()
in_str = ""
while in_str == "":
in_str = input().strip()
choice = in_str
scaling_list = [int(x) for x in choice.split()]
print(scaling_list)
if len(scaling_list) == 1:
scales = scaling_list[0]
elif len(scaling_list) == 3:
scales = scaling_list
elif len(scaling_list) == 9:
scales = [scaling_list[0:3], scaling_list[3:6], scaling_list[6:9]]
print(scales)
struct_cp = struct.copy()
struct_cp.make_supercell(scales)
print(struct_cp)
struct_cp.to(filename='supercell.vasp', fmt='poscar')
# if struct_cp==struct and :
# print('unreasonable input')
# build_operation()
# else:
# return
elif choice == 2:
struct = readstructure()
wait_sep()
tip = """
unsupported now !
"""
print(tip)
return
else:
data = {
'max_index': 2,
'min_vacum': 20,
'min_slab': 8,
'repeat': [3, 3, 1]
}
def read_adsorb_config(filename):
with open(filename, 'r') as f:
datas = f.readlines()
list_data = []
for i in range(len(datas)):
list_data.append(
datas[i][0:datas[i].find('#')].strip().split('='))
defined_keys = [
'method', 'crystal', 'molecule', 'max_index', 'min_vacum',
'min_slab', 'repeat'
]
data_dict = {}
for key in defined_keys:
for li in list_data:
if key in li[0]:
data_dict[key] = li[1]
data_dict['method'] = int(data_dict.get('method').strip())
data_dict['crystal'] = data_dict.get('crystal').strip()
data_dict['molecule'] = data_dict.get('molecule').strip()
data_dict['max_index'] = int(
data_dict.get('max_index', '1').strip())
data_dict['min_vacum'] = int(
data_dict.get('min_vacum', '15').strip())
data_dict['min_slab'] = int(data_dict.get('min_slab', '5').strip())
data_dict['repeat'] = [
int(x)
for x in data_dict.get('repeat', '1 1 1').strip().split()
]
return data_dict
def proc_adsorb(cryst, mol, data):
if data['method'] == 1:
asf_slab = AdsorbateSiteFinder(cryst)
ads_sites = asf_slab.find_adsorption_sites()
ads_structs = asf_slab.generate_adsorption_structures(
mol, repeat=data['repeat'])
for i in range(len(ads_structs)):
ads_struct = ads_structs[i]
try:
miller_str = [str(j) for j in cryst.miller_index]
except:
miller_str = ['adsorb']
filename = '_'.join(miller_str) + '-' + str(i) + '.vasp'
ads_struct.to(filename=filename, fmt='POSCAR')
else:
slabs = generate_all_slabs(cryst,
max_index=data['max_index'],
min_slab_size=data['min_slab'],
min_vacuum_size=data['min_vacum'],
lll_reduce=True)
for slab in slabs:
asf_slab = AdsorbateSiteFinder(slab)
ads_sites = asf_slab.find_adsorption_sites()
ads_structs = asf_slab.generate_adsorption_structures(
mol, repeat=data['repeat'])
for i in range(len(ads_structs)):
ads_struct = ads_structs[i]
miller_str = [str(j) for j in slab.miller_index]
filename = 'adsorb' + '_'.join(miller_str) + '-' + str(
i) + '.vasp'
ads_struct.to(filename=filename, fmt='POSCAR')
filename = 'adsorb.cfg'
if os.path.exists(filename):
data = read_adsorb_config(filename)
assert data['method'] in [1, 2]
cryst = readstructure(filename=data['crystal'])
mol = readstructure(filename=data['molecule'])
proc_adsorb(cryst, mol, data)
else:
print('your choice ?')
print('{} >>> {}'.format('1', 'read slab from file'))
print('{} >>> {}'.format('2', 'build slab by bulk'))
wait_sep()
in_str = ""
while in_str == "":
in_str = input().strip()
choice = int(in_str)
assert choice in [1, 2]
data['method'] = choice
cryst = readstructure(crystal=True, molecule=False)
mol = readstructure(crystal=False, molecule=True)
proc_adsorb(cryst, mol, data)
def twoD_operation():
#sepline(ch='2D structure operation',sp='=')
print('your choice ?')
print('{} >>> {}'.format('1', 'build rippled structure'))
print('{} >>> {}'.format('2', 'build multi-layered structure'))
print('{} >>> {}'.format('3', 'split multi-layered structure'))
print('{} >>> {}'.format('4', 'resize vacuum layer'))
print('{} >>> {}'.format('5', 'center atomic-layer along z direction'))
print('{} >>> {}'.format('6', 'apply strain along different direction'))
print('{} >>> {}'.format('7', 'constrain atom in specific range'))
print('{} >>> {}'.format('8',
'get a substrate for 2D material (online!!!)'))
wait_sep()
in_str = ""
while in_str == "":
in_str = input().strip()
choice = int(in_str)
if choice == 1:
struct = readstructure()
margin_dist = 1.0 #
assert (struct.lattice.is_orthogonal)
print("input the supercell scaling factor")
print('for x direction can be: 10 1 1')
print('for y direction can be: 1 10 1')
wait_sep()
scale_str = input()
scaling = [int(x) for x in scale_str.split()]
if (len(scaling) != 3):
print('unknow format')
else:
if scaling[0] >= scaling[1]:
direction = 0 # for x direction
else:
direction = 1 # for y direction
print("input the strain range")
print("example: 0.02:0.1:10 ")
wait_sep()
strain_str = input()
tmp = [float(x) for x in strain_str.split(":")]
strain = []
if len(tmp) == 3:
strain_range = np.linspace(tmp[0], tmp[1], int(tmp[2]))
# print(strain_range)
else:
print("unknow format")
return
print("input the index of atom need to be fixed")
print("example: 1 10 11 20 ")
print("0 means fix the atom automatically")
wait_sep()
atom_index_str = input()
try:
atom_index = [int(x) for x in strain_str.split("")]
auto_fix = False
except:
atom_index = [int(atom_index_str)]
auto_fix = True
struct_sc = struct.copy()
struct_sc.make_supercell(scaling)
natom = struct_sc.num_sites
min_z = np.min(struct_sc.cart_coords[:, 2])
tmp_coords = np.ones((struct_sc.num_sites, 1)) * min_z
cart_coords = struct_sc.cart_coords
cart_coords[:, 2] = cart_coords[:, 2] - tmp_coords.T + 0.01
frac_coords_new = np.dot(cart_coords,
np.linalg.inv(struct_sc.lattice.matrix))
for i_strain in strain_range:
new_lat_matrix = struct_sc.lattice.matrix
new_lat_matrix[direction, direction] = struct_sc.lattice.matrix[
direction, direction] * (1 - i_strain)
fname = "%10.5f" % (
i_strain
) + '_wo.vasp' # structure only applied with in-plan strain
struct_wo_ripple = Structure(new_lat_matrix, struct_sc.species,
frac_coords_new)
struct_wo_ripple.to(filename=fname.strip(), fmt='poscar')
frac_coords_new_cp = struct_wo_ripple.frac_coords.copy()
cart_coords_new_cp = struct_wo_ripple.cart_coords.copy()
nz = 0
selective_dynamics = [[True for col in range(3)]
for row in range(natom)]
z_shift = np.zeros((natom, 3))
for i_atom in range(natom):
z_shift[i_atom,
2] = 40 * (2 * i_strain - 10 * i_strain**2) * np.sin(
cart_coords_new_cp[i_atom, direction] * np.pi /
new_lat_matrix[direction, direction])
if cart_coords_new_cp[i_atom,
direction] < nz or cart_coords_new_cp[
i_atom, direction] > new_lat_matrix[
direction, direction] - nz:
z_shift[i_atom, 2] = 0.0
if auto_fix:
if struct_wo_ripple[i_atom].coords[direction]<margin_dist or \
struct_wo_ripple[i_atom].coords[direction] > new_lat_matrix[direction,direction]-margin_dist:
selective_dynamics[i_atom] = [False, False, False]
else:
if i_atom in atom_index:
selective_dynamics[i_atom] = [False, False, False]
struct_w_ripple=Structure(new_lat_matrix,struct_sc.species,cart_coords_new_cp+z_shift,coords_are_cartesian=True,\
site_properties={'selective_dynamics':selective_dynamics})
fname = "%10.5f" % (
i_strain
) + '_w.vasp' # structure applied with in-plan strain and ripple
struct_w_ripple.to(filename=fname.strip(), fmt='poscar')
elif choice == 2:
struct = readstructure()
print("input the number of layers")
wait_sep()
in_str = ""
while in_str == "":
in_str = input().strip()
layer_number = int(in_str)
print("input the layer distance")
wait_sep()
species = []
in_str = ""
while in_str == "":
in_str = input().strip()
layer_distance = float(in_str)
new_struct = move_to_zcenter(struct)
struct_thickness = np.max(new_struct.cart_coords[:, 2]) - np.min(
new_struct.cart_coords[:, 2])
natom = new_struct.num_sites
new_cart_coords = np.zeros((natom * layer_number, 3))
for i in range(layer_number):
new_cart_coords[i * natom:(i + 1) * natom,
0:2] = new_struct.cart_coords[:, 0:2]
new_cart_coords[i * natom:(i + 1) * natom,
2] = new_struct.cart_coords[:, 2] + i * (
layer_distance + struct_thickness)
species.extend(new_struct.species)
new_lat = new_struct.lattice.matrix
new_lat[2, 2] = new_lat[2, 2] + layer_distance * layer_number
tmp_struct = Structure(new_lat,
species,
new_cart_coords,
coords_are_cartesian=True)
tmp1_struct = move_to_zcenter(tmp_struct)
tmp2_struct = tmp1_struct.get_sorted_structure()
tmp2_struct.to(filename='layer_' + str(layer_number) + '.vasp',
fmt='poscar')
elif choice == 3:
ProperDist = 3.5 # Ang
struct = readstructure()
(atom_index, in_str) = atom_selection(struct)
print("input the splitting distance, 10 Ang is enough!")
wait_sep()
in_str = ""
while in_str == "":
in_str = input().strip()
SplitDistance = float(in_str)
print("numbers of splitting site, 50 sites are enough!")
wait_sep()
in_str = ""
while in_str == "":
in_str = input().strip()
NumberSplitSite = int(in_str)
DensityN = int(NumberSplitSite * 0.75)
SparseN = NumberSplitSite - DensityN + 1
# print(DensityN,SparseN)
dist = ProperDist / (DensityN - 1)
SplitDistanceArray = np.zeros(NumberSplitSite + 1)
for Nsite in range(DensityN):
SplitDistanceArray[Nsite] = (Nsite) * dist
dist = (SplitDistance - ProperDist) / SparseN
for Nsite in range(SparseN):
SplitDistanceArray[Nsite +
DensityN] = ProperDist + (Nsite + 1) * dist
# print(SplitDistanceArray)
coords = struct.cart_coords
for Nsite in range(NumberSplitSite + 1):
coords = struct.cart_coords
for atom in atom_index:
coords[atom, 2] = coords[atom, 2] + SplitDistanceArray[Nsite]
tmp_struct = Structure(struct.lattice,
struct.species,
coords,
coords_are_cartesian=True)
fname = str(Nsite) + '.vasp'
tmp_struct.to(filename=fname, fmt='poscar')
data = np.zeros((NumberSplitSite + 1, 2))
for i, j in enumerate(SplitDistanceArray):
data[i][0] = i
data[i][1] = j
head_line = "#%(key1)+12s %(key2)+12s" % {
'key1': 'index',
'key2': 'distance/Ang'
}
fmt = "%12d %12.6f" + '\n'
write_col_data('split.dat', data, head_line, sp_fmt=fmt)
return
elif choice == 4:
struct = readstructure()
new_struct = move_to_zcenter(struct)
struct_thickness = np.max(new_struct.cart_coords[:, 2]) - np.min(
new_struct.cart_coords[:, 2])
vac_layer_thickness = new_struct.lattice.c - struct_thickness
print("current vacuum layer thickness is %6.3f Ang" %
(vac_layer_thickness))
print("input the new value of vacuum layer thickness")
wait_sep()
in_str = ""
while in_str == "":
in_str = input().strip()
nvac_layer_thickness = float(in_str)
assert (nvac_layer_thickness > struct_thickness)
new_lat = new_struct.lattice.matrix
new_lat[2, 2] = nvac_layer_thickness
tmp_struct = Structure(new_lat,
new_struct.species,
new_struct.cart_coords,
coords_are_cartesian=True)
center_struct = move_to_zcenter(tmp_struct)
center_struct.to(filename='new_vacuum.vasp', fmt='poscar')
return
elif choice == 5:
struct = readstructure()
new_struct = move_to_zcenter(struct)
new_struct.to(filename='z-center.vasp', fmt='poscar')
return
elif choice == 6:
struct = readstructure()
assert (struct.lattice.is_orthogonal)
try:
import sympy
except:
print("you must install sympy module")
return
new_struct = move_to_zcenter(struct)
print("input the elastic of material by order : C11 C12 C22 C66")
wait_sep()
in_str = ""
while in_str == "":
in_str = input().strip().split()
elastic_constant = [float(x) for x in in_str]
if len(elastic_constant) != 4:
print("you must input C11 C12 C22 C66")
return
C11 = elastic_constant[0]
C12 = elastic_constant[1]
C22 = elastic_constant[2]
C66 = elastic_constant[3]
print("input applied force: e.x. 1.0 GPa nm")
wait_sep()
in_str = ""
while in_str == "":
in_str = input().strip()
sigma = float(in_str)
orig_struct = new_struct.copy()
new_struct = new_struct.copy()
natom = orig_struct.num_sites
lat = orig_struct.lattice.matrix
pos = orig_struct.frac_coords
nps = 37
phi = np.linspace(0, 360, nps) * np.pi / 180
vzz = C12 / C22
temp_num = (C11 * C22 - C12**2) / (C22 * C66)
d1 = C11 / C22 + 1.0 - temp_num
d2 = -(2.0 * C12 / C22 - temp_num)
d3 = C11 / C22
F = sigma * C22 / (C11 * C22 - C12**2.0)
Poisson=(vzz*(np.cos(phi))**4.0-d1*(np.cos(phi))**2.0*(np.sin(phi))**2.0+vzz*(np.sin(phi))**4.0)/\
((np.cos(phi))**4.0+d2*(np.cos(phi))**2.0*(np.sin(phi))**2.0+d3*(np.sin(phi))**4.0)
eps_theta = F * ((np.cos(phi))**4 + d2 * (np.cos(phi))**2.0 *
(np.sin(phi))**2.0 + d3 * (np.sin(phi))**4.0)
t = sympy.Symbol('t', real=True)
e = sympy.Symbol('e', real=True)
v = sympy.Symbol('v', real=True)
eprim = sympy.Matrix([[e + 1, 0], [0, 1 - e * v]])
R = sympy.Matrix([[sympy.cos(t), -sympy.sin(t)],
[sympy.sin(t), sympy.cos(t)]])
eps_mat = R * eprim * R.adjugate()
for k in range(len(phi)):
cur__phi = phi[k] * 180 / np.pi
Rot = eps_mat.subs({e: eps_theta[k], v: Poisson[k], t: phi[k]})
fname = str(k) + '.vasp'
final_lat = np.matrix(np.eye(3))
final_lat[0, 0] = Rot[0, 0]
final_lat[0, 1] = Rot[0, 1]
final_lat[1, 0] = Rot[1, 0]
final_lat[1, 1] = Rot[1, 1]
lat_new = lat * final_lat
tmp_struct = Structure(lat_new, new_struct.species, pos)
tmp_struct.to(filename=fname, fmt='poscar')
return
elif choice == 7:
struct = readstructure()
natom = struct.num_sites
atom_index, in_str = atom_selection(struct)
selective_dynamics = [[True for col in range(3)]
for row in range(natom)]
for i in range(natom):
if i in atom_index:
selective_dynamics[i] = [False, False, False]
tmp_struct = Structure(
struct.lattice,
struct.species,
struct.frac_coords,
site_properties={'selective_dynamics': selective_dynamics})
poscar = Poscar(tmp_struct)
poscar.comment = poscar.comment + ' |--> ' + in_str
poscar.write_file('Fixed.vasp')
return
elif choice == 8:
print('your choice ?')
print('{} >>> {}'.format('1', 'input 2D structure from local disk'))
print('{} >>> {}'.format('2', 'get 2D structure online'))
wait_sep()
in_str = ""
while in_str == "":
in_str = input().strip()
choice = int(in_str)
if choice == 1:
mpid = None
struct = readstructure()
else:
print("input the mp-id for your structure")
wait_sep()
in_str = ""
while in_str == "":
in_str = input().strip()
mpid = in_str
struct = None
film, substrates = make_connect(mpid=mpid, struct=struct)
df = get_subs(film, substrates)
df.to_csv('substrate.csv', sep=',', header=True, index=True)
return
else:
print("unkonw choice")
return
def cleave_operation():
struct = readstructure()
if isinstance(Structure, Molecule):
print("cleave operation is only supported for periodic structure")
return
print('your choice ?')
print('{} >>> {}'.format('1', 'cleave surface'))
print('{} >>> {}'.format('2', 'cleave sphere cluster'))
print('{} >>> {}'.format('3', 'cleave shell structure'))
wait_sep()
in_str = ""
while in_str == "":
in_str = input().strip()
choice = int(in_str)
if choice == 1:
print(
" input the miller index, minimum size in angstroms of layers containing atomssupercell"
)
print(
" and Minimize size in angstroms of layers containing vacuum like this:"
)
print(' 1 0 0 | 5 | 5')
print(' it means miller index is [1,0,0]')
print(" min_slab_size is 5 Ang ")
print(" min_vacum_size is 5 Ang ")
print(" or like this : ")
print(' 2 | 5 | 5')
print(' it will generate all slab with miller index less than 2')
def generate_selected_slab(in_str):
tmp_list = in_str.split('|')
miller_index = [int(x) for x in tmp_list[0].strip().split()]
min_slab_size = float(tmp_list[1])
min_vac_size = float(tmp_list[2])
slab = SlabGenerator(struct,
miller_index,
min_slab_size=min_slab_size,
min_vacuum_size=min_vac_size,
lll_reduce=True)
slab_struct = slab.get_slab()
slab_struct.sort()
miller_str = [str(i) for i in miller_index]
filename = '_'.join(miller_str) + '.vasp'
slab_struct.to(filename=filename, fmt='POSCAR')
def generate_all_slab(in_str):
tmp_list = in_str.split('|')
max_index = int(tmp_list[0])
min_slab_size = float(tmp_list[1])
min_vac_size = float(tmp_list[2])
slabs = generate_all_slabs(struct,
max_index=max_index,
min_slab_size=min_slab_size,
min_vacuum_size=min_vac_size,
lll_reduce=True)
for slab_struct in slabs:
slab_struct.sort()
miller_str = [str(i) for i in slab_struct.miller_index]
filename = '_'.join(miller_str) + '.vasp'
slab_struct.to(filename=filename, fmt='POSCAR')
wait_sep()
in_str = ""
while in_str == "":
in_str = input().strip()
len_para = len(in_str.split('|')[0].split())
#if in_str.strip().startswith('a'):
if len_para == 3:
generate_selected_slab(in_str)
#elif in_str.strip().startswith('b'):
elif len_para == 1:
generate_all_slab(in_str)
else:
print("unknow format")
os._exit()
elif choice == 2:
print(
" input the center atom index, sphere radius and vacuum layer thickness"
)
print(' 1 3.5 15')
print(
' it means the sphere will be selected according to the 1st atom')
print(
" with the radius equals 5Ang, and vacuum layer thickness is 15 Ang"
)
wait_sep()
in_str = ""
while in_str == "":
in_str = input().strip()
para = in_str.split()
center_atom = int(para[0]) - 1
radius = float(para[1])
vacuum = float(para[2])
center_coord = struct[center_atom].coords
sites = struct.get_neighbors_in_shell(center_coord, 0, radius)
coords = [site[0].coords for site in sites]
species = [site[0].specie for site in sites]
mol = Molecule(coords=coords, species=species)
max_dist = np.max(mol.distance_matrix)
a = b = c = max_dist + vacuum
box_struct = mol.get_boxed_structure(a, b, c)
file_name = "sphere.vasp"
box_struct.to(filename=file_name, fmt='poscar')
elif choice == 3:
print(
" input the center atom index, start radius, shell thickness and")
print(" vacuum layer thickness")
print(' 1 5 10 15')
print(
' it means the ball shell will be selected according to the 1st atom'
)
print(" with the 5< r <15Ang, and vacuum layer thickness is 15 Ang")
wait_sep()
in_str = ""
while in_str == "":
in_str = input().strip()
para = in_str.split()
center_atom = int(para[0]) - 1
radius = float(para[1])
shell = float(para[2])
vacuum = float(para[3])
center_coord = struct[center_atom].coords
sites = struct.get_neighbors_in_shell(center_coord, radius, shell)
coords = [site[0].coords for site in sites]
species = [site[0].specie for site in sites]
mol = Molecule(coords=coords, species=species)
max_dist = np.max(mol.distance_matrix)
a = b = c = max_dist + vacuum
box_struct = mol.get_boxed_structure(a, b, c)
file_name = "shell.vasp"
box_struct.to(filename=file_name, fmt='poscar')
else:
print("unkown choice")
return
