A direction we want to go in is also atom manipulation in a robust manner. To this end we need a set of methods that can access atom and manipulate them.
import pyscal.crystal_structures as pcs
from pyscal.core import System
import matplotlib.pyplot as plt
import numpy as np
import warnings
atoms, box = pcs.make_crystal(structure="fcc", repetitions=(5,5,5))
atoms,box
({'positions': [[0.0, 0.0, 0.0], [0.5, 0.0, 0.5], [0.0, 0.5, 0.5], [0.5, 0.5, 0.0], [0.0, 0.0, 1.0], [0.5, 0.0, 1.5], [0.0, 0.5, 1.5], [0.5, 0.5, 1.0], [0.0, 0.0, 2.0], [0.5, 0.0, 2.5], [0.0, 0.5, 2.5], [0.5, 0.5, 2.0], [0.0, 0.0, 3.0], [0.5, 0.0, 3.5], [0.0, 0.5, 3.5], [0.5, 0.5, 3.0], [0.0, 0.0, 4.0], [0.5, 0.0, 4.5], [0.0, 0.5, 4.5], [0.5, 0.5, 4.0], [0.0, 1.0, 0.0], [0.5, 1.0, 0.5], [0.0, 1.5, 0.5], [0.5, 1.5, 0.0], [0.0, 1.0, 1.0], [0.5, 1.0, 1.5], [0.0, 1.5, 1.5], [0.5, 1.5, 1.0], [0.0, 1.0, 2.0], [0.5, 1.0, 2.5], [0.0, 1.5, 2.5], [0.5, 1.5, 2.0], [0.0, 1.0, 3.0], [0.5, 1.0, 3.5], [0.0, 1.5, 3.5], [0.5, 1.5, 3.0], [0.0, 1.0, 4.0], [0.5, 1.0, 4.5], [0.0, 1.5, 4.5], [0.5, 1.5, 4.0], [0.0, 2.0, 0.0], [0.5, 2.0, 0.5], [0.0, 2.5, 0.5], [0.5, 2.5, 0.0], [0.0, 2.0, 1.0], [0.5, 2.0, 1.5], [0.0, 2.5, 1.5], [0.5, 2.5, 1.0], [0.0, 2.0, 2.0], [0.5, 2.0, 2.5], [0.0, 2.5, 2.5], [0.5, 2.5, 2.0], [0.0, 2.0, 3.0], [0.5, 2.0, 3.5], [0.0, 2.5, 3.5], [0.5, 2.5, 3.0], [0.0, 2.0, 4.0], [0.5, 2.0, 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0, 5.0]])
Atoms are dicts. Thats fine. Atoms could be class inherited from dict, so we have extra methods that are useful. Lets try this approach. But first we do a simple calculation to benchmark the speed.
class Atoms(dict):
def __init__(self):
pass
@property
def positions(self):
return self["positions"]
rep = 5
atoms, box = pcs.make_crystal(structure="fcc", repetitions=(rep,rep,rep))
sys = System()
sys.box = box
sys.atoms = atoms
%%timeit
sys.find_neighbors(method="cutoff", cutoff=0)
373 ms ± 8.08 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)
at = Atoms()
for key, val in atoms.items():
at[key] = val
at.positions
[[0.0, 0.0, 0.0], [0.5, 0.0, 0.5], [0.0, 0.5, 0.5], [0.5, 0.5, 0.0], [0.0, 0.0, 1.0], [0.5, 0.0, 1.5], [0.0, 0.5, 1.5], [0.5, 0.5, 1.0], [0.0, 0.0, 2.0], [0.5, 0.0, 2.5], [0.0, 0.5, 2.5], [0.5, 0.5, 2.0], [0.0, 0.0, 3.0], [0.5, 0.0, 3.5], [0.0, 0.5, 3.5], [0.5, 0.5, 3.0], [0.0, 0.0, 4.0], [0.5, 0.0, 4.5], [0.0, 0.5, 4.5], [0.5, 0.5, 4.0], [0.0, 0.0, 5.0], [0.5, 0.0, 5.5], [0.0, 0.5, 5.5], [0.5, 0.5, 5.0], [0.0, 0.0, 6.0], [0.5, 0.0, 6.5], [0.0, 0.5, 6.5], [0.5, 0.5, 6.0], [0.0, 0.0, 7.0], [0.5, 0.0, 7.5], [0.0, 0.5, 7.5], [0.5, 0.5, 7.0], [0.0, 0.0, 8.0], [0.5, 0.0, 8.5], [0.0, 0.5, 8.5], [0.5, 0.5, 8.0], [0.0, 0.0, 9.0], [0.5, 0.0, 9.5], [0.0, 0.5, 9.5], [0.5, 0.5, 9.0], [0.0, 0.0, 10.0], [0.5, 0.0, 10.5], [0.0, 0.5, 10.5], [0.5, 0.5, 10.0], [0.0, 0.0, 11.0], [0.5, 0.0, 11.5], [0.0, 0.5, 11.5], [0.5, 0.5, 11.0], [0.0, 1.0, 0.0], [0.5, 1.0, 0.5], [0.0, 1.5, 0.5], [0.5, 1.5, 0.0], [0.0, 1.0, 1.0], [0.5, 1.0, 1.5], [0.0, 1.5, 1.5], [0.5, 1.5, 1.0], [0.0, 1.0, 2.0], [0.5, 1.0, 2.5], [0.0, 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10.5], [1.0, 4.5, 10.5], [1.5, 4.5, 10.0], [1.0, 4.0, 11.0], [1.5, 4.0, 11.5], [1.0, 4.5, 11.5], [1.5, 4.5, 11.0], [1.0, 5.0, 0.0], [1.5, 5.0, 0.5], [1.0, 5.5, 0.5], [1.5, 5.5, 0.0], [1.0, 5.0, 1.0], [1.5, 5.0, 1.5], [1.0, 5.5, 1.5], [1.5, 5.5, 1.0], [1.0, 5.0, 2.0], [1.5, 5.0, 2.5], [1.0, 5.5, 2.5], [1.5, 5.5, 2.0], [1.0, 5.0, 3.0], [1.5, 5.0, 3.5], [1.0, 5.5, 3.5], [1.5, 5.5, 3.0], [1.0, 5.0, 4.0], [1.5, 5.0, 4.5], [1.0, 5.5, 4.5], [1.5, 5.5, 4.0], [1.0, 5.0, 5.0], [1.5, 5.0, 5.5], [1.0, 5.5, 5.5], [1.5, 5.5, 5.0], [1.0, 5.0, 6.0], [1.5, 5.0, 6.5], [1.0, 5.5, 6.5], [1.5, 5.5, 6.0], [1.0, 5.0, 7.0], [1.5, 5.0, 7.5], [1.0, 5.5, 7.5], [1.5, 5.5, 7.0], [1.0, 5.0, 8.0], [1.5, 5.0, 8.5], [1.0, 5.5, 8.5], [1.5, 5.5, 8.0], [1.0, 5.0, 9.0], [1.5, 5.0, 9.5], [1.0, 5.5, 9.5], [1.5, 5.5, 9.0], [1.0, 5.0, 10.0], [1.5, 5.0, 10.5], [1.0, 5.5, 10.5], [1.5, 5.5, 10.0], [1.0, 5.0, 11.0], [1.5, 5.0, 11.5], [1.0, 5.5, 11.5], [1.5, 5.5, 11.0], [1.0, 6.0, 0.0], [1.5, 6.0, 0.5], [1.0, 6.5, 0.5], [1.5, 6.5, 0.0], [1.0, 6.0, 1.0], [1.5, 6.0, 1.5], [1.0, 6.5, 1.5], [1.5, 6.5, 1.0], [1.0, 6.0, 2.0], [1.5, 6.0, 2.5], [1.0, 6.5, 2.5], [1.5, 6.5, 2.0], [1.0, 6.0, 3.0], [1.5, 6.0, 3.5], [1.0, 6.5, 3.5], [1.5, 6.5, 3.0], [1.0, 6.0, 4.0], [1.5, 6.0, 4.5], [1.0, 6.5, 4.5], [1.5, 6.5, 4.0], [1.0, 6.0, 5.0], [1.5, 6.0, 5.5], [1.0, 6.5, 5.5], [1.5, 6.5, 5.0], [1.0, 6.0, 6.0], [1.5, 6.0, 6.5], [1.0, 6.5, 6.5], [1.5, 6.5, 6.0], [1.0, 6.0, 7.0], [1.5, 6.0, 7.5], [1.0, 6.5, 7.5], [1.5, 6.5, 7.0], [1.0, 6.0, 8.0], [1.5, 6.0, 8.5], [1.0, 6.5, 8.5], [1.5, 6.5, 8.0], [1.0, 6.0, 9.0], [1.5, 6.0, 9.5], [1.0, 6.5, 9.5], [1.5, 6.5, 9.0], [1.0, 6.0, 10.0], [1.5, 6.0, 10.5], [1.0, 6.5, 10.5], [1.5, 6.5, 10.0], [1.0, 6.0, 11.0], [1.5, 6.0, 11.5], [1.0, 6.5, 11.5], [1.5, 6.5, 11.0], [1.0, 7.0, 0.0], [1.5, 7.0, 0.5], [1.0, 7.5, 0.5], [1.5, 7.5, 0.0], [1.0, 7.0, 1.0], [1.5, 7.0, 1.5], [1.0, 7.5, 1.5], [1.5, 7.5, 1.0], [1.0, 7.0, 2.0], [1.5, 7.0, 2.5], [1.0, 7.5, 2.5], [1.5, 7.5, 2.0], [1.0, 7.0, 3.0], [1.5, 7.0, 3.5], [1.0, 7.5, 3.5], [1.5, 7.5, 3.0], [1.0, 7.0, 4.0], [1.5, 7.0, 4.5], [1.0, 7.5, 4.5], [1.5, 7.5, 4.0], [1.0, 7.0, 5.0], [1.5, 7.0, 5.5], [1.0, 7.5, 5.5], [1.5, 7.5, 5.0], [1.0, 7.0, 6.0], [1.5, 7.0, 6.5], [1.0, 7.5, 6.5], [1.5, 7.5, 6.0], [1.0, 7.0, 7.0], [1.5, 7.0, 7.5], [1.0, 7.5, 7.5], [1.5, 7.5, 7.0], [1.0, 7.0, 8.0], [1.5, 7.0, 8.5], [1.0, 7.5, 8.5], [1.5, 7.5, 8.0], [1.0, 7.0, 9.0], [1.5, 7.0, 9.5], [1.0, 7.5, 9.5], [1.5, 7.5, 9.0], [1.0, 7.0, 10.0], [1.5, 7.0, 10.5], [1.0, 7.5, 10.5], [1.5, 7.5, 10.0], [1.0, 7.0, 11.0], [1.5, 7.0, 11.5], [1.0, 7.5, 11.5], [1.5, 7.5, 11.0], [1.0, 8.0, 0.0], [1.5, 8.0, 0.5], [1.0, 8.5, 0.5], [1.5, 8.5, 0.0], [1.0, 8.0, 1.0], [1.5, 8.0, 1.5], [1.0, 8.5, 1.5], [1.5, 8.5, 1.0], [1.0, 8.0, 2.0], [1.5, 8.0, 2.5], [1.0, 8.5, 2.5], [1.5, 8.5, 2.0], [1.0, 8.0, 3.0], [1.5, 8.0, 3.5], [1.0, 8.5, 3.5], [1.5, 8.5, 3.0], [1.0, 8.0, 4.0], [1.5, 8.0, 4.5], [1.0, 8.5, 4.5], [1.5, 8.5, 4.0], [1.0, 8.0, 5.0], [1.5, 8.0, 5.5], [1.0, 8.5, 5.5], [1.5, 8.5, 5.0], [1.0, 8.0, 6.0], [1.5, 8.0, 6.5], [1.0, 8.5, 6.5], [1.5, 8.5, 6.0], [1.0, 8.0, 7.0], [1.5, 8.0, 7.5], [1.0, 8.5, 7.5], [1.5, 8.5, 7.0], [1.0, 8.0, 8.0], [1.5, 8.0, 8.5], [1.0, 8.5, 8.5], [1.5, 8.5, 8.0], [1.0, 8.0, 9.0], [1.5, 8.0, 9.5], [1.0, 8.5, 9.5], [1.5, 8.5, 9.0], ...]
sys2 = System()
sys2.box = box
sys2.atoms = at
%%timeit
sys2.find_neighbors(method="cutoff", cutoff=0)
406 ms ± 27.4 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)
at.head = sys2
at.mapdict = {"ghostx":"ghost"}
at.keys()
dict_keys(['positions', 'ids', 'types', 'ghost', 'mask_1', 'mask_2', 'condition', 'head', 'neighbors', 'neighbordist', 'temp_neighbors', 'temp_neighbordist', 'neighborweight', 'diff', 'r', 'theta', 'phi', 'cutoff'])
repetitions = [2, 5, 7, 10, 12]
at_dict = [68.9, 31.6, 68, 258, 449]
at_class = [73, 32.5, 70, 250, 441]
plt.plot(repetitions, at_dict, "-o");
plt.plot(repetitions, at_class, "-o");
This is quite nice and fine; the way therefore is to draft a new class with convenient properties aimed at the user.
class Atoms(dict):
def __init__(self, *args, **kwargs):
self.update(*args, **kwargs)
def __getitem__(self, key):
if isinstance(key, slice):
return self._get_atoms(key)
elif isinstance(key, int):
return self._get_atoms(key)
else:
val = dict.__getitem__(self, key)
return val
def __setitem__(self, key, val):
dict.__setitem__(self, key, val)
def __repr__(self):
dictrepr = dict.__repr__(self)
return '%s(%s)' % (type(self).__name__, dictrepr)
def update(self, *args, **kwargs):
for k, v in dict(*args, **kwargs).items():
self[k] = v
def _get_atoms(self, index):
atom_dict = {}
for key in self.keys():
atom_dict[key] = self[key][index]
return atom_dict
Speedtest this class
rep = 12
atoms, box = pcs.make_crystal(structure="fcc", repetitions=(rep,rep,rep))
at = Atoms()
for key, val in atoms.items():
at[key] = val
sys = System()
sys.box = box
sys.atoms = atoms
%%timeit
sys.find_neighbors(method="cutoff", cutoff=0)
473 ms ± 44.1 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)
at_class_v2 = [72, 32, 68, 260, 473]
plt.plot(repetitions, at_dict, "-o");
plt.plot(repetitions, at_class, "-o");
plt.plot(repetitions, at_class_v2, "-o");
It is not particularly more expensive, we go with this definition and extend it.
We have to use the very new type-converted class and see if it affects the speed
rep = 10
atoms, box = pcs.make_crystal(structure="bcc", lattice_constant=3.147, repetitions=(rep,rep,rep))
sys = System()
sys.box = box
sys.atoms = atoms
atoms.natoms
2000
sys.find_neighbors(method="cutoff", cutoff=0)
type(sys.atoms["positions"])
pyscal.attributes.MyList
at_class_v3 = [1.6, 6.21, 17.6]
plt.plot(repetitions, at_dict, "-o");
plt.plot(repetitions, at_class, "-o");
plt.plot(repetitions, at_class_v2, "-o");
plt.plot(repetitions, at_class_v3, "-o");