Use Mdapy Efficiently

The key point is re-using the neighborlist information.

import mdapy as mp
mp.__version__

'1.0.5a2'

Build a Copper system with 4,000,000 atoms.

system = mp.build_crystal('Cu', 'fcc', 3.615, nx=100, ny=100, nz=100)

Check the system information.

system

Atom Number: 4000000
Box information:
[[361.5   0.    0. ]
 [  0.  361.5   0. ]
 [  0.    0.  361.5]]
Origin: [0. 0. 0.]
Triclinic: False
Boundary: [1 1 1]
Particle Information:
shape: (4_000_000, 4)
┌──────────┬──────────┬──────────┬─────────┐
│ x        ┆ y        ┆ z        ┆ element │
│ ---      ┆ ---      ┆ ---      ┆ ---     │
│ f64      ┆ f64      ┆ f64      ┆ str     │
╞══════════╪══════════╪══════════╪═════════╡
│ 0.0      ┆ 0.0      ┆ 0.0      ┆ Cu      │
│ 1.8075   ┆ 1.8075   ┆ 0.0      ┆ Cu      │
│ 0.0      ┆ 1.8075   ┆ 1.8075   ┆ Cu      │
│ 1.8075   ┆ 0.0      ┆ 1.8075   ┆ Cu      │
│ 0.0      ┆ 0.0      ┆ 3.615    ┆ Cu      │
│ …        ┆ …        ┆ …        ┆ …       │
│ 359.6925 ┆ 357.885  ┆ 356.0775 ┆ Cu      │
│ 357.885  ┆ 357.885  ┆ 357.885  ┆ Cu      │
│ 359.6925 ┆ 359.6925 ┆ 357.885  ┆ Cu      │
│ 357.885  ┆ 359.6925 ┆ 359.6925 ┆ Cu      │
│ 359.6925 ┆ 357.885  ┆ 359.6925 ┆ Cu      │
└──────────┴──────────┴──────────┴─────────┘

Direct calculation.

%%time
system.cal_centro_symmetry_parameter(12)
system.cal_ackland_jones_analysis()
system.cal_structure_entropy(rc=5.0, sigma=0.2)

CPU times: user 1min 36s, sys: 9.58 s, total: 1min 45s
Wall time: 8.72 s

system.data.head()

shape: (5, 7)

x	y	z	element	csp	aja	entropy
f64	f64	f64	str	f64	i32	f64
0.0	0.0	0.0	"Cu"	3.2952e-26	1	-8.645166
1.8075	1.8075	0.0	"Cu"	1.0984e-26	1	-8.645166
0.0	1.8075	1.8075	"Cu"	1.0984e-26	1	-8.645166
1.8075	0.0	1.8075	"Cu"	1.0984e-26	1	-8.645166
0.0	0.0	3.615	"Cu"	2.1968e-26	1	-8.645166

Re-use neighborlist information.

%%time
system.build_neighbor(rc=5.0, max_neigh=50) # Obtain the neighbor first, the following calculation can use it.
system.cal_structure_entropy(rc=5.0, sigma=0.2)
system.cal_ackland_jones_analysis()
system.cal_centro_symmetry_parameter(12)

CPU times: user 1min 17s, sys: 891 ms, total: 1min 18s
Wall time: 6.39 s

system.data.head()

shape: (5, 7)

x	y	z	element	csp	aja	entropy
f64	f64	f64	str	f64	i32	f64
0.0	0.0	0.0	"Cu"	3.2952e-26	1	-8.645166
1.8075	1.8075	0.0	"Cu"	1.0984e-26	1	-8.645166
0.0	1.8075	1.8075	"Cu"	1.0984e-26	1	-8.645166
1.8075	0.0	1.8075	"Cu"	1.0984e-26	1	-8.645166
0.0	0.0	3.615	"Cu"	2.1968e-26	1	-8.645166