httk quickstart

Install

Clone the master branch of the source code repository:

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.. code:: bash

     git clone https://github.com/httk/httk

Then, every time you want to use httk, initialize the environtment with:

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.. code:: bash

     source /path/to/httk/init.shell

Structures

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.

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.. code:: python

  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

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.. code:: python

  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)

Databases

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

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.. code:: python

  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

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.. code:: python

  #!/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)