def vis_data(request):
global custom_data
data = {
"crystal_data": """Cr Te O
1.0
7.016000 0.000000 0.000000
0.000000 7.545000 0.000000
-1.637391 0.000000 9.589209
Cr O Te
4 22 8
direct
0.319200 0.501900 0.384200
0.680800 0.001900 0.115800
0.680800 0.498100 0.615800
0.319200 0.998100 0.884200
0.205000 0.644000 0.212100
0.795000 0.144000 0.287900
0.795000 0.356000 0.787900
0.205000 0.856000 0.712100
0.500000 0.000000 0.500000
0.500000 0.500000 0.000000
0.127000 0.314000 0.342900
0.873000 0.814000 0.157100
0.873000 0.686000 0.657100
0.127000 0.186000 0.842900
0.468000 0.375000 0.262300
0.532000 0.875000 0.237700
0.532000 0.625000 0.737700
0.468000 0.125000 0.762300
0.563000 0.641000 0.451700
0.437000 0.141000 0.048300
0.437000 0.359000 0.548300
0.563000 0.859000 0.951700
0.158000 0.649000 0.486600
0.842000 0.149000 0.013400
0.842000 0.351000 0.513400
0.158000 0.851000 0.986600
0.139700 0.859900 0.176200
0.860300 0.359900 0.323800
0.860300 0.140100 0.823800
0.139700 0.640100 0.676200
0.672300 0.861800 0.415800
0.327700 0.361800 0.084200
0.327700 0.138200 0.584200
0.672300 0.638200 0.915800"""
}
p = request.POST
if request.method == "POST":
custom_data = p.get("crystal_data", "")
data["crystal_data"] = custom_data
f = StringIO()
f.write(custom_data)
s = read(f)
s.symmetrize()
data["structure"] = s
data.update(csrf(request))
custom_data = data["crystal_data"]
return render(request, "analysis/view_data.html", context=get_globals(data))
from qmpy import DOS, io
from numpy import mean
strc = io.read("../files/relaxation/POSCAR")
dos = DOS.read("../files/relaxation/DOSCAR")
# Get the total DOS
print("Getting total DOS...")
total_dos = dos.dos
my_dos = dos.get_projected_dos(strc, "Mg", debug=True)
my_dos = my_dos * 2 * (dos.energy[1] - dos.energy[0])
error = mean([abs(x) for x in (total_dos - my_dos)])
print("\tMean difference between total DOS and projected: ", error)
# Get only d orbitals
print("Getting d orbital DOS...")
dos.get_projected_dos(strc, "Mg", orbital="d", debug=True)
def create(source, keywords=[], projects=[], **kwargs):
"""
Attempts to create an Entry object from a provided input file.
Processed in the following way:
#. If an Entry exists at the specified path, returns that Entry.
#. Create an Entry, and assign all fundamental attributes. (natoms,
ntypes, input, path, elements, keywords, projects).
#. If the input file is a CIF, and because CIF files have additional
composition and reference information, if that file format is
found, an additional test is performed to check that the reported
composition matches the composition of the resulting structure. The
reference for the work is also created and assigned to the entry.
#. Attempt to identify another entry that this is either exactly
equivalent to, or a defect cell of.
Keywords:
keywords: list of keywords to associate with the entry.
projects: list of project names to associate with the entry.
"""
source_file = os.path.abspath(source)
path = os.path.dirname(source_file)
# Step 1
if Entry.objects.filter(path=path).exists():
return Entry.objects.get(path=path)
# Step 2
entry = Entry(**kwargs)
structure = io.read(source_file)
structure.make_primitive()
entry.source_file = source_file
entry.path = os.path.dirname(source_file)
entry.input = structure
entry.ntypes = structure.ntypes
entry.natoms = len(structure.sites)
entry.elements = entry.comp.keys()
entry.composition = Composition.get(structure.comp)
for kw in keywords:
entry.add_keyword(kw)
entry.projects = projects
# Step 3
c1 = structure.composition
if 'cif' in source_file:
c2 = structure.reported_composition
if not c1.compare(c2, 5e-2):
entry.add_hold("composition mismatch in cif")
entry.composition = c2
entry.reference = io.cif.read_reference(source_file)
# check for perfect crystals
if not any([ s.partial for s in structure.sites ]):
dup = Entry.get(structure)
if not dup is None:
entry.duplicate_of = dup
entry.add_hold('duplicate')
return entry
# detect solid solution
if all([ s.occupancy > 0.99 for s in structure.sites ]):
if any([ len(s) > 1 for s in structure.sites ]):
entry.add_keyword('solid solution')
if any([ s.partial for s in structure.sites ]):
entry.add_hold('partial occupancy')
return entry
from qmpy import DOS, io
from numpy import mean
strc = io.read('../files/relaxation/POSCAR')
dos = DOS.read('../files/relaxation/DOSCAR')
# Get the total DOS
print "Getting total DOS..."
total_dos = dos.dos
my_dos = dos.get_projected_dos(strc, 'Mg', debug=True)
my_dos = my_dos * 2 * (dos.energy[1] - dos.energy[0])
error = mean([ abs(x) for x in (total_dos - my_dos)])
print "\tMean difference between total DOS and projected: ", error
# Get only d orbitals
print "Getting d orbital DOS..."
dos.get_projected_dos(strc, 'Mg', orbital='d', debug=True)
from qmpy import DOS, io
from numpy import mean
strc = io.read('../files/relaxation/POSCAR')
dos = DOS.read('../files/relaxation/DOSCAR')
# Get the total DOS
print "Getting total DOS..."
total_dos = dos.dos
my_dos = dos.get_projected_dos(strc, 'Mg', debug=True)
my_dos = my_dos * 2 * (dos.energy[1] - dos.energy[0])
error = mean([abs(x) for x in (total_dos - my_dos)])
print "\tMean difference between total DOS and projected: ", error
# Get only d orbitals
print "Getting d orbital DOS..."
dos.get_projected_dos(strc, 'Mg', orbital='d', debug=True)