Read and Save file

mdapy can read/save file very efficiently. Including Dump, Data and Dump.gz formats.

The performance of mdapy is around 2-7 times higher than ovito.

[11]:

import mdapy as mp
from time import time
import matplotlib.pyplot as plt
mp.init()

[Taichi] Starting on arch=x64

[12]:

mp.__version__

[12]:

'0.9.9'

[13]:

import ovito
ovito.version

[13]:

(3, 9, 2)

Prepare a Data, Dump, Dump.gz files

[14]:

def prepare():
    FCC = mp.LatticeMaker(3.615, 'FCC', 100, 100, 100)
    FCC.compute()
    print(f'Atom number is {FCC.N}.')
    print('Saving to mdapy.data.')
    FCC.write_data(output_name='mdapy.data')
    print('Saving to mdapy.dump')
    FCC.write_dump(output_name='mdapy.dump')
    print('Saving to mdapy.dump.gz')
    FCC.write_dump(output_name='mdapy.dump.gz', compress=True)
    return FCC.N

[15]:

N = prepare()

Atom number is 4000000.
Saving to mdapy.data.
Saving to mdapy.dump
Saving to mdapy.dump.gz

Read a dump file in mdapy

[16]:

start = time()
for _ in range(3):
    _ = mp.System('mdapy.dump')
end = time()
mdapy_time = (end - start)/3
print(mdapy_time, 's')

0.22403152783711752 s

Read a dump file in OVITO

[17]:

start = time()
for _ in range(3):
    _ = ovito.io.import_file('mdapy.dump')
end = time()
ovito_time = (end - start)/3
print(ovito_time, 's')

1.1576457023620605 s

[18]:

fig, _ = mp.set_figure(figsize=(10, 6), use_pltset=True)
plt.bar([0, 1], [mdapy_time, ovito_time])
plt.xticks([0, 1], ['mdapy', 'ovito'])
plt.ylabel('Time (s)')
plt.title(f'Read dump with {N} atoms.')

[18]:

Text(0.5, 1.0, 'Read dump with 4000000 atoms.')

../_images/gettingstarted_reading_and_saving_file_12_1.png

Read a data file in mdapy

[19]:

start = time()
for _ in range(3):
    _ = mp.System('mdapy.data')
end = time()
mdapy_time = (end - start)/3
print(mdapy_time, 's')

0.6062424182891846 s

Read a data file in ovito

[20]:

start = time()
for _ in range(3):
    _ = ovito.io.import_file('mdapy.data')
end = time()
ovito_time = (end - start)/3
print(ovito_time, 's')

2.51231058438619 s

[21]:

fig, _ = mp.set_figure(figsize=(10, 6), use_pltset=True)
plt.bar([0, 1], [mdapy_time, ovito_time])
plt.xticks([0, 1], ['mdapy', 'ovito'])
plt.ylabel('Time (s)')
plt.title(f'Read data with {N} atoms.')

[21]:

Text(0.5, 1.0, 'Read data with 4000000 atoms.')

../_images/gettingstarted_reading_and_saving_file_17_1.png

Read a dump.gz file in mdapy

[22]:

start = time()
for _ in range(3):
    _ = mp.System('mdapy.dump.gz')
end = time()
mdapy_time = (end - start)/3
print(mdapy_time, 's')

0.6917309761047363 s

Read a dump.gz file in ovito

[23]:

start = time()
for _ in range(3):
    _ = ovito.io.import_file('mdapy.dump.gz')
end = time()
ovito_time = (end - start)/3
print(ovito_time, 's')

1.7169297536214192 s

[24]:

fig, _ = mp.set_figure(figsize=(10, 6), use_pltset=True)
plt.bar([0, 1], [mdapy_time, ovito_time])
plt.xticks([0, 1], ['mdapy', 'ovito'])
plt.ylabel('Time (s)')
plt.title(f'Read dump.gz with {N} atoms.')

[24]:

Text(0.5, 1.0, 'Read dump.gz with 4000000 atoms.')

../_images/gettingstarted_reading_and_saving_file_22_1.png

Save a dump file in mdapy

[25]:

system = mp.System('mdapy.dump')
start = time()
for _ in range(3):
    system.write_dump()
end = time()
mdapy_time = (end - start)/3
print(mdapy_time, 's')

0.6115530331929525 s

Save a dump file in OVITO

[26]:

pipeline = ovito.io.import_file('mdapy.dump')
start = time()
for _ in range(3):
    ovito.io.export_file(pipeline, 'ovito.dump', format='lammps/dump', columns=["Particle Identifier", "Particle Type", "Position.X", "Position.Y", "Position.Z"])
end = time()
ovito_time = (end - start)/3
print(ovito_time, 's')

4.530352512995402 s

[27]:

fig, _ = mp.set_figure(figsize=(10, 6), use_pltset=True)
plt.bar([0, 1], [mdapy_time, ovito_time])
plt.xticks([0, 1], ['mdapy', 'ovito'])
plt.ylabel('Time (s)')
plt.title(f'Save dump with {N} atoms.')

[27]:

Text(0.5, 1.0, 'Save dump with 4000000 atoms.')

../_images/gettingstarted_reading_and_saving_file_27_1.png

Save a data file in mdapy

[28]:

start = time()
for _ in range(3):
    system.write_data()
end = time()
mdapy_time = (end - start)/3
print(mdapy_time, 's')

0.5885759989420573 s

Save a data file in ovito

[29]:

start = time()
for _ in range(3):
    ovito.io.export_file(pipeline, 'ovito.data', format='lammps/data', atom_style='atomic')
end = time()
ovito_time = (end - start)/3
print(ovito_time, 's')

4.610602299372355 s

[30]:

fig, _ = mp.set_figure(figsize=(10, 6), use_pltset=True)
plt.bar([0, 1], [mdapy_time, ovito_time])
plt.xticks([0, 1], ['mdapy', 'ovito'])
plt.ylabel('Time (s)')
plt.title(f'Save data with {N} atoms.')

[30]:

Text(0.5, 1.0, 'Save data with 4000000 atoms.')

../_images/gettingstarted_reading_and_saving_file_32_1.png

Save a dump.gz file in mdapy

[31]:

start = time()
for _ in range(3):
    system.write_dump(compress=True)
end = time()
mdapy_time = (end - start)/3
print(mdapy_time, 's')

1.5111037890116374 s

Save a dump.gz file in ovito

[32]:

start = time()
for _ in range(3):
    ovito.io.export_file(pipeline, 'ovito.dump.gz', format='lammps/dump', columns=["Particle Identifier", "Particle Type", "Position.X", "Position.Y", "Position.Z"])
end = time()
ovito_time = (end - start)/3
print(ovito_time, 's')

10.900876919428507 s

[33]:

fig, _ = mp.set_figure(figsize=(10, 6), use_pltset=True)
plt.bar([0, 1], [mdapy_time, ovito_time])
plt.xticks([0, 1], ['mdapy', 'ovito'])
plt.ylabel('Time (s)')
plt.title(f'Save dump.gz with {N} atoms.')

[33]:

Text(0.5, 1.0, 'Save dump.gz with 4000000 atoms.')

../_images/gettingstarted_reading_and_saving_file_37_1.png

[34]:

# Clear the output
import os
from glob import glob
file_list = glob('*dump*') + glob("*.data")
for file in file_list:
    try:
        os.remove(file)
    except Exception:
        pass