Precautions

Here we discuss some precautions when using mdapy.

import mdapy as mp
import polars as pl
mp.init()

[Taichi] version 1.6.0, llvm 15.0.1, commit f1c6fbbd, win, python 3.8.0
[Taichi] Starting on arch=x64

mp.__version__

'0.9.9'

system = mp.System('../../../example/solidliquid.data')

print(system)

Filename: ../../../example/solidliquid.data
Atom Number: 8192
Simulation Box:
[[52.01907282  0.          0.        ]
 [ 0.         52.01907282  0.        ]
 [ 0.          0.         52.01907282]
 [-0.39698541 -0.39698541 -0.39698541]]
TimeStep: 0
Boundary: [1, 1, 1]
Particle Information:
shape: (5, 8)
┌──────┬──────┬───────────┬───────────┬───────────┬───────────┬──────────┬──────────┐
│ id   ┆ type ┆ x         ┆ y         ┆ z         ┆ vx        ┆ vy       ┆ vz       │
│ ---  ┆ ---  ┆ ---       ┆ ---       ┆ ---       ┆ ---       ┆ ---      ┆ ---      │
│ i64  ┆ i64  ┆ f64       ┆ f64       ┆ f64       ┆ f64       ┆ f64      ┆ f64      │
╞══════╪══════╪═══════════╪═══════════╪═══════════╪═══════════╪══════════╪══════════╡
│ 7913 ┆ 1    ┆ 2.64108   ┆ 3.2152    ┆ 1.74197   ┆ 2.90096   ┆ 1.72875  ┆ -1.77975 │
│ 4098 ┆ 1    ┆ -0.091857 ┆ 0.4658    ┆ 0.936675  ┆ -0.166803 ┆ 0.959803 ┆ 3.70312  │
│ 4414 ┆ 1    ┆ 51.3076   ┆ 2.93742   ┆ 2.12484   ┆ 4.50605   ┆ -1.06924 ┆ -1.41931 │
│ 4    ┆ 1    ┆ 3.57773   ┆ -0.024408 ┆ 2.31072   ┆ -6.04709  ┆ 5.23451  ┆ 9.18538  │
│ 37   ┆ 1    ┆ 45.219    ┆ 19.5654   ┆ -0.241386 ┆ -5.20306  ┆ 3.79694  ┆ -2.15249 │
└──────┴──────┴───────────┴───────────┴───────────┴───────────┴──────────┴──────────┘

Check the position information

system.pos[:5]

array([[ 2.64108e+00,  3.21520e+00,  1.74197e+00],
       [-9.18574e-02,  4.65800e-01,  9.36675e-01],
       [ 5.13076e+01,  2.93742e+00,  2.12484e+00],
       [ 3.57773e+00, -2.44078e-02,  2.31072e+00],
       [ 4.52190e+01,  1.95654e+01, -2.41386e-01]])

Generally speaking, we do not need to change the position. So the pos information is inmutable for users. If you try to change it, it will raise an error. This is for data safety.

system.pos[0, 0] = 1.

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
e:\MyPackage\mdapy\doc\source\gettingstarted\matters_need_attention.ipynb 单元格 10 line 1
----> <a href='vscode-notebook-cell:/e%3A/MyPackage/mdapy/doc/source/gettingstarted/matters_need_attention.ipynb#X12sZmlsZQ%3D%3D?line=0'>1</a> system.pos[0, 0] = 1.

ValueError: assignment destination is read-only

If you really need to change ths positions for system object, you can modify the system.data and update it mannually!!! Considering you want let atoms with z < 10 moves right 2 along x, you can do like below:

• The first way:

system.update_data(
    system.data.
    with_columns(
    pl.when(pl.col('z')<10).
    then(pl.col('x')+2).
    otherwise(pl.col('x')).
    alias('x')),
    update_pos=True)
# The first parameter is a new Dataframe, the second indicates mdapy will update the position information.

system.data.head() # x[0] from 2.64108 to 4.64108

shape: (5, 8)

id	type	x	y	z	vx	vy	vz
i64	i64	f64	f64	f64	f64	f64	f64
7913	1	4.64108	3.2152	1.74197	2.90096	1.72875	-1.77975
4098	1	1.9081426	0.4658	0.936675	-0.166803	0.959803	3.70312
4414	1	53.3076	2.93742	2.12484	4.50605	-1.06924	-1.41931
4	1	5.57773	-0.024408	2.31072	-6.04709	5.23451	9.18538
37	1	47.219	19.5654	-0.241386	-5.20306	3.79694	-2.15249

system.pos[:5] # updated correspondingly.

array([[ 4.6410800e+00,  3.2152000e+00,  1.7419700e+00],
       [ 1.9081426e+00,  4.6580000e-01,  9.3667500e-01],
       [ 5.3307600e+01,  2.9374200e+00,  2.1248400e+00],
       [ 5.5777300e+00, -2.4407800e-02,  2.3107200e+00],
       [ 4.7219000e+01,  1.9565400e+01, -2.4138600e-01]])

• The second way

system.data.replace(
    'y',
    system.data.select(
    pl.when(pl.col('z')<10).
    then(pl.col('y')+2).
    otherwise(pl.col('y'))
    ).to_series()
) # Replace the 'y' directly.
system.update_pos() # update the position mannully.

system.data.head() # y[0] from 3.2152 to 5.2152

shape: (5, 8)

id	type	x	y	z	vx	vy	vz
i64	i64	f64	f64	f64	f64	f64	f64
7913	1	4.64108	5.2152	1.74197	2.90096	1.72875	-1.77975
4098	1	1.9081426	2.4658	0.936675	-0.166803	0.959803	3.70312
4414	1	53.3076	4.93742	2.12484	4.50605	-1.06924	-1.41931
4	1	5.57773	1.9755922	2.31072	-6.04709	5.23451	9.18538
37	1	47.219	21.5654	-0.241386	-5.20306	3.79694	-2.15249

system.pos[:5] # updated correspondingly.

array([[ 4.64108  ,  5.2152   ,  1.74197  ],
       [ 1.9081426,  2.4658   ,  0.936675 ],
       [53.3076   ,  4.93742  ,  2.12484  ],
       [ 5.57773  ,  1.9755922,  2.31072  ],
       [47.219    , 21.5654   , -0.241386 ]])

velocity is all the same with position.

system.vel[:5]

array([[ 2.90096 ,  1.72875 , -1.77975 ],
       [-0.166803,  0.959803,  3.70312 ],
       [ 4.50605 , -1.06924 , -1.41931 ],
       [-6.04709 ,  5.23451 ,  9.18538 ],
       [-5.20306 ,  3.79694 , -2.15249 ]])

If you try to modify it directly, raise an error.

system.vel[0, 0] = 3.5

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
Cell In[14], line 1
----> 1 system.vel[0, 0] = 3.5

ValueError: assignment destination is read-only

You can change the data to modify the velocities.

system.data[0, 'vx'] = 3.5

system.update_vel() # Update the velocity mannually.

system.data.head()

system.data.head() # vx[0] from 2.90096 to 3.5

shape: (5, 8)

id	type	x	y	z	vx	vy	vz
i64	i64	f64	f64	f64	f64	f64	f64
7913	1	4.64108	5.2152	1.74197	3.5	1.72875	-1.77975
4098	1	1.9081426	2.4658	0.936675	-0.166803	0.959803	3.70312
4414	1	53.3076	4.93742	2.12484	4.50605	-1.06924	-1.41931
4	1	5.57773	1.9755922	2.31072	-6.04709	5.23451	9.18538
37	1	47.219	21.5654	-0.241386	-5.20306	3.79694	-2.15249

system.vel[:5] # updated correspondingly.

array([[ 3.5     ,  1.72875 , -1.77975 ],
       [-0.166803,  0.959803,  3.70312 ],
       [ 4.50605 , -1.06924 , -1.41931 ],
       [-6.04709 ,  5.23451 ,  9.18538 ],
       [-5.20306 ,  3.79694 , -2.15249 ]])