How to use the ccf.cal_ccf_d function in ccf
To help you get started, we’ve selected a few ccf examples, based on popular ways it is used in public projects.
Secure your code as it's written. Use Snyk Code to scan source code in minutes - no build needed - and fix issues immediately.
chuanxun / StructurePrototypeAnalysisPackage / SPAP.py View on Github 
structures[i].ccf = struc2ccf(
Atoms(cell=structures[i].cell * (volume / structures[i].get_volume()) ** (1.0 / 3.0),
scaled_positions=scaled_positions, numbers=structures[i].numbers, pbc=True), r_cut_off, r_vector)
# if i == 57:
# ccf_file = open('ccf.dat', 'wb')
# pickle.dump(structures[i].ccf,ccf_file)
# ccf_file.close()
# rvf=open('rvf.dat','wb')
# pickle.dump(r_vector,rvf)
# rvf.close()
# write('out.cif',Atoms(cell=structures[i].cell * (volume / structures[i].get_volume()) ** (1.0 / 3.0),
# scaled_positions=scaled_positions, numbers=structures[i].numbers,pbc=True))
# print(Atoms(cell=structures[i].cell * (volume / structures[i].get_volume()) ** (1.0 / 3.0),
# scaled_positions=scaled_positions, numbers=structures[i].numbers,pbc=True).get_volume())
for j in [prototype_id[-1 - j2] for j2 in range(len(prototype_id))]:
struc_d[i][1] = cal_ccf_d(structures[j].ccf, structures[i].ccf)
if struc_d[i][1] < threshold:
struc_d[i][0] = j
break
elif l_same_cell:
struc_d[i][1] = cal_ccf_d(
structures[j].ccf, struc2ccf(Atoms(cell=structures[j].cell, scaled_positions=scaled_positions,
numbers=structures[i].numbers, pbc=True), r_cut_off,
r_vector))
if struc_d[i][1] < threshold:
struc_d[i][0] = j
break
# Mark this structure as a new prototype.
if struc_d[i][0] == -1:
struc_d[i] = [-2, 0.0]
prototype_id.append(i)
pass# pickle.dump(structures[i].ccf,ccf_file)
# ccf_file.close()
# rvf=open('rvf.dat','wb')
# pickle.dump(r_vector,rvf)
# rvf.close()
# write('out.cif',Atoms(cell=structures[i].cell * (volume / structures[i].get_volume()) ** (1.0 / 3.0),
# scaled_positions=scaled_positions, numbers=structures[i].numbers,pbc=True))
# print(Atoms(cell=structures[i].cell * (volume / structures[i].get_volume()) ** (1.0 / 3.0),
# scaled_positions=scaled_positions, numbers=structures[i].numbers,pbc=True).get_volume())
for j in [prototype_id[-1 - j2] for j2 in range(len(prototype_id))]:
struc_d[i][1] = cal_ccf_d(structures[j].ccf, structures[i].ccf)
if struc_d[i][1] < threshold:
struc_d[i][0] = j
break
elif l_same_cell:
struc_d[i][1] = cal_ccf_d(
structures[j].ccf, struc2ccf(Atoms(cell=structures[j].cell, scaled_positions=scaled_positions,
numbers=structures[i].numbers, pbc=True), r_cut_off,
r_vector))
if struc_d[i][1] < threshold:
struc_d[i][0] = j
break
# Mark this structure as a new prototype.
if struc_d[i][0] == -1:
struc_d[i] = [-2, 0.0]
prototype_id.append(i)
pass# pickle.dump(structures[i].ccf,ccf_file)
# ccf_file.close()
# rvf=open('rvf.dat','wb')
# pickle.dump(r_vector,rvf)
# rvf.close()
# write('out.cif',Atoms(cell=structures[i].cell * (volume / structures[i].get_volume()) ** (1.0 / 3.0),
# scaled_positions=scaled_positions, numbers=structures[i].numbers,pbc=structures[0].pbc))
# print(Atoms(cell=structures[i].cell * (volume / structures[i].get_volume()) ** (1.0 / 3.0),
# scaled_positions=scaled_positions, numbers=structures[i].numbers,pbc=structures[0].pbc).get_volume())
for j in [prototype_id[-1 - j2] for j2 in range(len(prototype_id))]:
struc_d[i][1] = cal_ccf_d(structures[j].ccf, structures[i].ccf)
if struc_d[i][1] < threshold:
struc_d[i][0] = j
break
elif l_same_cell:
struc_d[i][1] = cal_ccf_d(
structures[j].ccf, struc2ccf(Atoms(
cell=structures[j].cell * (volume / structures[j].get_volume()) ** (1.0 / 3.0),
scaled_positions=scaled_positions, numbers=structures[i].numbers,
pbc=structures[0].pbc), r_cut_off, r_vector))
if struc_d[i][1] < threshold:
struc_d[i][0] = j
break
# Mark this structure as a new prototype.
if struc_d[i][0] == -1:
struc_d[i] = [-2, 0.0]
prototype_id.append(i)
passAtoms(cell=structures[i].cell * (volume / structures[i].get_volume()) ** (1.0 / 3.0),
scaled_positions=scaled_positions, numbers=structures[i].numbers, pbc=structures[0].pbc),
r_cut_off, r_vector)
# if i == 57:
# ccf_file = open('ccf.dat', 'wb')
# pickle.dump(structures[i].ccf,ccf_file)
# ccf_file.close()
# rvf=open('rvf.dat','wb')
# pickle.dump(r_vector,rvf)
# rvf.close()
# write('out.cif',Atoms(cell=structures[i].cell * (volume / structures[i].get_volume()) ** (1.0 / 3.0),
# scaled_positions=scaled_positions, numbers=structures[i].numbers,pbc=structures[0].pbc))
# print(Atoms(cell=structures[i].cell * (volume / structures[i].get_volume()) ** (1.0 / 3.0),
# scaled_positions=scaled_positions, numbers=structures[i].numbers,pbc=structures[0].pbc).get_volume())
for j in [prototype_id[-1 - j2] for j2 in range(len(prototype_id))]:
struc_d[i][1] = cal_ccf_d(structures[j].ccf, structures[i].ccf)
if struc_d[i][1] < threshold:
struc_d[i][0] = j
break
elif l_same_cell:
struc_d[i][1] = cal_ccf_d(
structures[j].ccf, struc2ccf(Atoms(
cell=structures[j].cell * (volume / structures[j].get_volume()) ** (1.0 / 3.0),
scaled_positions=scaled_positions, numbers=structures[i].numbers,
pbc=structures[0].pbc), r_cut_off, r_vector))
if struc_d[i][1] < threshold:
struc_d[i][0] = j
break
# Mark this structure as a new prototype.
if struc_d[i][0] == -1:
struc_d[i] = [-2, 0.0]
prototype_id.append(i)ccf
Set of tools and utilities for the Confidential Consortium Framework (CCF)
