def get_next(self):
"""
Iterate the parameters and return them as a dictionary
"""
O = AbstractParticle.get_next(self)
O["particle_model"] = "atoms"
O["atomic_numbers"] = self.get_atomic_numbers()
O["atomic_positions"] = self.get_atomic_positions()
return O
def get_next(self):
"""
Iterate the parameters and return them as a dictionary
"""
O = AbstractParticle.get_next(self)
O["particle_model"] = "atoms"
O["atomic_numbers"] = self.get_atomic_numbers()
O["atomic_positions"] = self.get_atomic_positions()
return O
def get_conf(self):
"""
Get configuration in form of a dictionary. Another identically configured ParticleAtoms instance can be initialised by:
.. code-block:: python
conf = P0.get_conf() # P0: already existing ParticleAtoms instance
P1 = condor.ParticleAtoms(**conf) # P1: new ParticleMolcule instance with the same configuration as P0
"""
conf = {}
conf.update(AbstractParticle.get_conf())
conf["atomic_numbers"] = self.get_atomic_numbers()
conf["atomic_positions"] = self.get_atomic_positions()
return conf
def get_conf(self):
"""
Get configuration in form of a dictionary. Another identically configured ParticleAtoms instance can be initialised by:
.. code-block:: python
conf = P0.get_conf() # P0: already existing ParticleAtoms instance
P1 = condor.ParticleAtoms(**conf) # P1: new ParticleMolcule instance with the same configuration as P0
"""
conf = {}
conf.update(AbstractParticle.get_conf())
conf["atomic_numbers"] = self.get_atomic_numbers()
conf["atomic_positions"] = self.get_atomic_positions()
return conf
class ParticleAtoms(AbstractParticle):
"""
Class for a particle model
*Model:* Discrete atomic positions
Kwargs:
:pdb_filename (str): See :meth:`set_atoms_from_pdb_file` (default ``None``)
:pdb_id (str): See :meth:`set_atoms_from_pdb_id` (default ``None``)
:atomic_numbers (array): See :meth:`set_atoms_from_arrays` (default ``None``)
:atomic_positions (array): See :meth:`set_atoms_from_arrays` (default ``None``)
.. note:: The atomic positions have to be specified either by a ``pdb_filename`` or by ``atomic_numbers`` and ``atomic_positions``.
:rotation_values (array): See :meth:`condor.particle.particle_abstract.AbstractParticle.set_alignment` (default ``None``)
:rotation_formalism (str): See :meth:`condor.particle.particle_abstract.AbstractParticle.set_alignment` (default ``None``)
:rotation_mode (str): See :meth:`condor.particle.particle_abstract.AbstractParticle.set_alignment` (default ``None``)
:number (float): Expectation value for the number of particles in the interaction volume. (defaukt ``1.``)
:arrival (str): Arrival of particles at the interaction volume can be either ``'random'`` or ``'synchronised'``. If ``sync`` at every event the number of particles in the interaction volume equals the rounded value of ``number``. If ``'random'`` the number of particles is Poissonian and ``number`` is the expectation value. (default ``'synchronised'``)
:position (array): See :class:`condor.particle.particle_abstract.AbstractParticle` (default ``None``)
:position_variation (str): See :meth:`condor.particle.particle_abstract.AbstractParticle.set_position_variation` (default ``None``)
:position_spread (float): See :meth:`condor.particle.particle_abstract.AbstractParticle.set_position_variation` (default ``None``)
:position_variation_n (int): See :meth:`condor.particle.particle_abstract.AbstractParticle.set_position_variation` (default ``None``)
"""
def __init__(self,
pdb_filename=None,
pdb_id=None,
atomic_numbers=None,
atomic_positions=None,
rotation_values=None,
rotation_formalism=None,
rotation_mode="extrinsic",
number=1.,
arrival="synchronised",
position=None,
position_variation=None,
position_spread=None,
position_variation_n=None):
try:
import spsim
except Exception, e:
print str(e)
log_and_raise_error(
logger,
"Cannot import spsim module. This module is necessary to simulate diffraction for particle model of discrete atoms. Please install spsim from https://github.com/FilipeMaia/spsim and try again."
)
return
# Initialise base class
AbstractParticle.__init__(self,
rotation_values=rotation_values,
rotation_formalism=rotation_formalism,
rotation_mode=rotation_mode,
number=number,
arrival=arrival,
position=position,
position_variation=position_variation,
position_spread=position_spread,
position_variation_n=position_variation_n)
self._atomic_positions = None
self._atomic_numbers = None
self._pdb_filename = None
self._diameter_mean = None
if pdb_filename is not None:
log_debug(logger,
"Attempt reading atoms from PDB file %s." % pdb_filename)
if (pdb_id is not None or atomic_numbers is not None
or atomic_positions is not None):
log_and_raise_error(
logger,
"Atom configuration is ambiguous. pdb_filename is specified but also at least one of the following arguments: atomic_numbers, atomic_positions, pdb_id."
)
sys.exit(1)
elif not os.path.isfile(pdb_filename):
log_and_raise_error(
logger,
"Cannot initialize particle model. PDB file %s does not exist."
% pdb_filename)
sys.exit(1)
else:
self.set_atoms_from_pdb_file(pdb_filename)
elif pdb_id is not None:
log_debug(logger, "Attempt fetching PDB entry of ID=%s" % pdb_id)
if (atomic_numbers is not None or atomic_positions is not None):
log_and_raise_error(
logger,
"Atom configuration is ambiguous. pdb_id is specified but also at least one of the following arguments: atomic_numbers, atomic_positions."
)
sys.exit(1)
else:
self.set_atoms_from_pdb_id(pdb_id)
elif atomic_numbers is not None and atomic_positions is not None:
log_debug(logger, "Attempt reading atoms from lists/attays.")
self.set_atoms_from_arrays(atomic_numbers, atomic_positions)
else:
log_and_raise_error(
logger,
"Cannot initialise particle model. The atomic positions have to be specified either by a pdb_filename, pdb_id or by atomic_numbers and atomic_positions."
)