I was thinking to use Jupyter notebook for quite a some time and finally I started using it. Here is a quick installation guide for Linux (Ubuntu).
If Python is already installed
pip3 install --upgrade pip pip3 install jupyter
Also you can install it with Anaconda. Details here
To run notebook
This will open up a webpage in your default browser and you can click on New and create a new notebook.
Gnuplot with Jupyter
I always wanted to have a gnuplot module integrated with Jupyter hence I installed the Gnuplot kernel with Jupyter notebook. The instructions are here
- System installation og Gnuplot in either Linux or Mac
- Installation of Jupyter notebook
Install Metakernel by following command
pip install metakernel --upgrade
Installation of Gnuplot kernel
pip install git+https://github.com/has2k1/gnuplot_kernel.git@master
Now when you will open jupyter notebook you will see Python 3 and Gnuplot option under New.
You can use bash within Jupyter notebook cell by starting with the following command
Matplotlib with Jupyter
Jupyter uses matplotlib as one of the default plotting programme. If you have a .dat file (space separated) you can use something like following and click Run to see the plot. Make sure you have numpy, pandas installed.
import pandas as pd import numpy as np
import numpy as np import matplotlib.pyplot as plt %matplotlib inline plt.style.use('ggplot') # read data NPT=pd.read_csv('data/NPT_time_vol_pres.dat',sep='\s+'); nDataPts = len(NPT.index); selFrames = np.arange(0,nDataPts,10); # compute running average def movingaverage(interval, window_size): window = np.ones(int(window_size))/float(window_size); return np.convolve(interval, window, 'same'); p_ma = movingaverage(NPT['PRESS'],1000); #plot plt.figure(figsize=(15,5)) plt.scatter(NPT["TIME(PS)"][selFrames], NPT["PRESS"][selFrames],alpha=0.3, edgecolors='none'); plt.plot(NPT['TIME(PS)'],p_ma); plt.xlabel('time (ps)'); plt.ylabel('pressure (bar)'); plt.title('pressure fluctuations during NPT simulation');
Table of contents in Jupyter
Often Jupyter notebook gets long enough by inclusion of plots and figures. In order to navigate easily within the notebook it needs a hyperlinked Table of Contents. All the jupyter extensions such as Table of Contents can be downloaded from here.
sudo pip install https://github.com/ipython-contrib/jupyter_contrib_nbextensions/tarball/master
jupyter contrib nbextension install --user
Now load the jupyter notebook. You can then open the
nbextensions tab on the tree (dashboard/file browser) notebook page to configure nbextensions. You will have access there to a dashboard where extensions can be enabled/disabled via checkboxes. Additionally a short documentation for each extension is displayed, and configuration options are presented.
Note: To be continued