Density cylinder tutorial#
To follow this tutorial, the data test files cntwater of MAICoS are needed. You can obtain it by cloning MAICoS repository:
git clone git@gitlab.com:maicos-devel/maicos.git
The airwater data files are located in tests/data/airwater/. First, let us ignore unnecessary warnings:
[1]:
import warnings
warnings.filterwarnings("ignore")
First, import MAICoS, NumPy, MDAnalysis, and PyPlot:
[2]:
import maicos
import numpy as np
import MDAnalysis as mda
import matplotlib.pyplot as plt
from matplotlib.ticker import AutoMinorLocator
---------------------------------------------------------------------------
ImportError Traceback (most recent call last)
Cell In [2], line 1
----> 1 import maicos
2 import numpy as np
3 import MDAnalysis as mda
File ~/checkouts/readthedocs.org/user_builds/maicos/envs/v0.5/lib/python3.10/site-packages/maicos/__init__.py:36
29 from .modules.density import DensityPlanar, DensityCylinder
30 from .modules.epsilon import (
31 EpsilonBulk,
32 EpsilonPlanar,
33 EpsilonCylinder,
34 DielectricSpectrum
35 )
---> 36 from .modules.structure import Saxs, Debye, Diporder
37 from .modules.timeseries import DipoleAngle, KineticEnergy
38 from .modules.transport import Velocity
File ~/checkouts/readthedocs.org/user_builds/maicos/envs/v0.5/lib/python3.10/site-packages/maicos/modules/structure.py:24
18 from .. import tables
19 from ..decorators import (
20 make_whole,
21 set_planar_class_doc,
22 set_verbose_doc,
23 )
---> 24 from ..lib import sfactor
25 from ..utils import check_compound, savetxt
27 logger = logging.getLogger(__name__)
ImportError: dynamic module does not define module export function (PyInit_sfactor)
and set a few parameters for plotting purpose:
[3]:
fontsize = 25
font = {'family': 'sans', 'color': 'black',
'weight': 'normal', 'size': fontsize}
my_color_1 = np.array([0.090, 0.247, 0.560])
my_color_2 = np.array([0.235, 0.682, 0.639])
my_color_3 = np.array([1.000, 0.509, 0.333])
my_color_4 = np.array([0.588, 0.588, 0.588])
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
Cell In [3], line 4
1 fontsize = 25
2 font = {'family': 'sans', 'color': 'black',
3 'weight': 'normal', 'size': fontsize}
----> 4 my_color_1 = np.array([0.090, 0.247, 0.560])
5 my_color_2 = np.array([0.235, 0.682, 0.639])
6 my_color_3 = np.array([1.000, 0.509, 0.333])
NameError: name 'np' is not defined
Define the path to the airwater data folder of MAICoS:
[4]:
datapath = "../../../../tests/data/cntwater/"
The cntwater system consists of a carbon nanotube (CNT) with axis in the \(z\) direction, a radius of about 2 nm, a length of 2.2 nm. The CNT is filled with 810 water molecules.
Create a universe using MDAnalysis and define a group containing the oxygen and the hydrogen atoms of the water molecules, as well as a group containing only the oxygen atoms, and a group containing only the hydrogen atoms:
[5]:
u = mda.Universe(datapath + 'lammps.data',
datapath + 'traj.xtc')
group_H2O = u.select_atoms('type 1 or type 2')
group_CNT = u.select_atoms('type 3')
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
Cell In [5], line 1
----> 1 u = mda.Universe(datapath + 'lammps.data',
2 datapath + 'traj.xtc')
3 group_H2O = u.select_atoms('type 1 or type 2')
4 group_CNT = u.select_atoms('type 3')
NameError: name 'mda' is not defined
Let us print a few information about the trajectory file:
[6]:
print(f"The number of water molecules is {np.int32(group_H2O.n_atoms/3)}")
print(f"The number of carbon atoms is {np.int32(group_CNT.n_atoms)}")
print(f"The CNT length is {np.round(u.dimensions[2]/10,2)} nm")
timestep = np.round(u.trajectory.dt,2)
print(f"The time intervl between the frames is {timestep} ps")
total_time = np.round(u.trajectory.totaltime,2)
print(f"The total simulation time is {total_time} ps")
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
Cell In [6], line 1
----> 1 print(f"The number of water molecules is {np.int32(group_H2O.n_atoms/3)}")
2 print(f"The number of carbon atoms is {np.int32(group_CNT.n_atoms)}")
3 print(f"The CNT length is {np.round(u.dimensions[2]/10,2)} nm")
NameError: name 'np' is not defined
Call the DensityCylinder module for the two groups at once:
[7]:
dcyl = maicos.DensityCylinder([group_H2O, group_CNT], center='all', binwidth = 0.01)
dcyl.run()
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
Cell In [7], line 1
----> 1 dcyl = maicos.DensityCylinder([group_H2O, group_CNT], center='all', binwidth = 0.01)
2 dcyl.run()
NameError: name 'maicos' is not defined
With the keyword center=‘all’, the center of mass of all the atoms of the group is used as the center of the density profile. If not specified, the center of the box is used.
Finally, extract the coordinates and the density profiles:
[8]:
rcoor = dcyl.results['r']
dens_H2O = dcyl.results['dens_mean'].T[0]
dens_CNT = dcyl.results['dens_mean'].T[1]
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
Cell In [8], line 1
----> 1 rcoor = dcyl.results['r']
2 dens_H2O = dcyl.results['dens_mean'].T[0]
3 dens_CNT = dcyl.results['dens_mean'].T[1]
NameError: name 'dcyl' is not defined
By default the binwidth is 0.1 nanometers, the units are kg/m\(^3\), and the axis is \(z\). Plot the density profile using :
[9]:
fig = plt.figure(figsize=(13,6.5))
ax1 = plt.subplot(1, 1, 1)
plt.xlabel(r"$r$ coordinate (nm)", fontdict=font)
plt.ylabel(r"density (kg/m$^3$]", fontdict=font)
plt.xticks(fontsize=fontsize)
plt.yticks(fontsize=fontsize)
ax1.plot(rcoor, dens_H2O, color=my_color_1, linewidth=4)
ax1.plot(rcoor, dens_CNT, color=my_color_2, linewidth=4)
ax1.yaxis.offsetText.set_fontsize(20)
ax1.minorticks_on()
ax1.tick_params('both', length=10, width=2, which='major', direction='in')
ax1.tick_params('both', length=6, width=1.4, which='minor', direction='in')
ax1.xaxis.set_ticks_position('both')
ax1.yaxis.set_ticks_position('both')
ax1.spines["top"].set_linewidth(2)
ax1.spines["bottom"].set_linewidth(2)
ax1.spines["left"].set_linewidth(2)
ax1.spines["right"].set_linewidth(2)
ax1.yaxis.offsetText.set_fontsize(30)
minor_locator_y = AutoMinorLocator(2)
ax1.yaxis.set_minor_locator(minor_locator_y)
minor_locator_x = AutoMinorLocator(2)
ax1.xaxis.set_minor_locator(minor_locator_x)
ax1.tick_params(axis='x', pad=10)
plt.show()
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
Cell In [9], line 1
----> 1 fig = plt.figure(figsize=(13,6.5))
2 ax1 = plt.subplot(1, 1, 1)
3 plt.xlabel(r"$r$ coordinate (nm)", fontdict=font)
NameError: name 'plt' is not defined