httk quickstart

Load a cif file or poscar

This is a very simple example of just loading a structure from a .cif file and writing out some information about it.

import httk

struct = httk.load("example.cif")

print("Formula:", struct.formula)
print("Volume:", float(struct.uc_volume))
print("Assignments:", struct.uc_formula_symbols)
print("Counts:", struct.uc_counts )
print("Coords:", struct.uc_reduced_coords)

Running this generates the output:

('Formula:', 'BO2Tl')
('Volume', 509.24213999999984)
('Assignments',['B', 'O', 'Tl'])
('Counts:', [8, 16, 8])
('Coords', FracVector(((1350,4550,4250) , ... , ,10000)))

Create structures in code

from httk.atomistic import Structure

cell = [[1.0, 0.0, 0.0] ,
        [0.0, 1.0, 0.0] ,
        [0.0, 0.0, 1.0]]
coordgroups = [[
                  [0.5, 0.5, 0.5]
               ],[
                  [0.0, 0.0, 0.0]
               ],[
                  [0.5, 0.0, 0.0], [0.0, 0.5, 0.0], [0.0, 0.0, 0.5]
               ]]

assignments = ['Pb' ,'Ti' ,'O']
volume =62.79
struct = Structure.create(uc_cell = cell,
             uc_reduced_coordgroups = coordgroups,
             assignments = assignments,
             uc_volume = volume)

Create database file, store a structure in it, and retrive it

import httk, httk.db
from httk.atomistic import Structure

backend = httk.db.backend.Sqlite('example.sqlite')
store = httk.db.store.SqlStore(backend)

tablesalt = httk.load('NaCl.cif')
store.save(tablesalt)

arsenic = httk.load('As.cif')
store.save(arsenic)

# Search for anything with Na
search = store.searcher()
search_struct = search.variable(Structure)
search.add(search_struct.formula_symbols.is_in('Na'))

search.output(search_struct, 'structure')

for match, header in list(search):
    struct = match[0]
    print "Found structure", struct.formula, [str(struct.get_tags()[x]) for x in struct.get_tags()]

Create database file and store your own data in it

#!/usr/bin/env python

import httk, httk.db
from httk.atomistic import Structure

class StructureIsEdible(httk.HttkObject):

    @httk.httk_typed_init({'structure': Structure, 'is_edible': bool})
    def __init__(self, structure, is_edible):
        self.structure = structure
        self.is_edible = is_edible

backend = httk.db.backend.Sqlite('example.sqlite')
store = httk.db.store.SqlStore(backend)

tablesalt = httk.load('NaCl.cif')
edible = StructureIsEdible(tablesalt, True)
store.save(edible)

arsenic = httk.load('As.cif')
edible = StructureIsEdible(arsenic, False)
store.save(edible)