Install SHTOOLS - Revision history

Yfwang09: /* Visualization of spherical harmonic modes using scipy */

2019-02-19T19:11:31Z

Visualization of spherical harmonic modes using scipy

← Older revision		Revision as of 19:11, 19 February 2019
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	See the page [https://shtools.oca.eu/shtools/www/man/python/pyshexpanddh.html SHExpandDH] for the detailed description of the expanding function and the page [https://shtools.oca.eu/shtools/www/conventions.html Real Spherical Harmonics] for mathematical definition.		See the page [https://shtools.oca.eu/shtools/www/man/python/pyshexpanddh.html SHExpandDH] for the detailed description of the expanding function and the page [https://shtools.oca.eu/shtools/www/conventions.html Real Spherical Harmonics] for mathematical definition.

	== ~~Visualization of~~ spherical harmonic modes using scipy ==		== Visualize spherical harmonic modes using scipy ==

	We first import the necessary packages:		We first import the necessary packages:

2018-01-13T01:27:25Z

Install python + scipy + SHTOOLS on local directory

← Older revision		Revision as of 01:27, 13 January 2018
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	export PATH=${HOME}/.localpython/bin:$PATH		export PATH=${HOME}/.localpython/bin:$PATH
	export PYTHONPATH=${HOME}/.localpython/bin		export PYTHONPATH=${HOME}/.localpython/bin
			export LIBRARY_PATH=$LIBRARY_PATH:${HOME}/.localpython/lib
			export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:${HOME}/.localpython/lib

	if python version < 2.7.9, install pip by:		if python version < 2.7.9, install pip by:

2018-01-12T22:58:58Z

Install python + scipy + SHTOOLS on local directory

← Older revision		Revision as of 22:58, 12 January 2018
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	make		make
	make install		make install

		⚫	Add the following lines to ~/.bashrc:

		⚫	export PATH=${HOME}/.localpython/bin:$PATH
			export PYTHONPATH=${HOME}/.localpython/bin

	if python version < 2.7.9, install pip by:		if python version < 2.7.9, install pip by:
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	wget https://bootstrap.pypa.io/get-pip.py		wget https://bootstrap.pypa.io/get-pip.py
	python get-pip.py		python get-pip.py
			export PATH=${HOME}/.local/bin:$PATH

	Install SciPy Stack using pip on user's directory:		Install SciPy Stack using pip on user's directory:

	pip(pip3) install --user numpy scipy matplotlib ipython jupyter pandas sympy nose		pip(pip3) install --user numpy scipy matplotlib ipython jupyter pandas sympy nose

⚫	Add the following ~~command~~ to ~/.bashrc:

⚫	export PATH=~~"$PATH:~~${HOME}/.localpython/bin"

	Install pyshtools using pip:		Install pyshtools using pip:

2018-01-12T22:51:21Z

Install python + scipy + SHTOOLS on local directory

← Older revision		Revision as of 22:51, 12 January 2018
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	pip(pip3) install --user numpy scipy matplotlib ipython jupyter pandas sympy nose		pip(pip3) install --user numpy scipy matplotlib ipython jupyter pandas sympy nose

⚫	export PATH="$PATH:${HOME}/.~~local~~/bin"
			Add the following command to ~/.bashrc:

		⚫	export PATH="$PATH:${HOME}/.localpython/bin"

	Install pyshtools using pip:		Install pyshtools using pip:

2017-07-28T07:03:46Z

Visualization of spherical harmonic modes using scipy

← Older revision		Revision as of 07:03, 28 July 2017
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	plt.show()		plt.show()

	For example, the ~~picture~~ for (l, m) = (2, 0), (3, 2), and (1, 1) are:		For example, the figures for (l, m) = (2, 0), (3, 2), and (1, 1) are shown as below:
	<gallery caption="Fig.1 Visualization of Spherical Harmonics" widths="200px" heights="200px" perrow="3">		<gallery caption="Fig.1 Visualization of Spherical Harmonics" widths="200px" heights="200px" perrow="3">
	Image:sph_harm_Y20.png\|(a) <math> Y_{20}(\theta,\phi) </math>		Image:sph_harm_Y20.png\|(a) <math> Y_{20}(\theta,\phi) </math>

2017-07-28T07:03:17Z

Visualization of spherical harmonic modes using scipy

← Older revision		Revision as of 07:03, 28 July 2017
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	For example, the picture for (l, m) = (2, 0), (3, 2), and (1, 1) are:		For example, the picture for (l, m) = (2, 0), (3, 2), and (1, 1) are:
	<gallery caption="Fig.1 Visualization of ~~FCC~~ ~~structure~~" widths="200px" heights="200px" perrow="3">		<gallery caption="Fig.1 Visualization of Spherical Harmonics" widths="200px" heights="200px" perrow="3">
	Image:sph_harm_Y20.png\|(a) <math> Y_{20}(\theta,\phi) </math>		Image:sph_harm_Y20.png\|(a) <math> Y_{20}(\theta,\phi) </math>
	Image:sph_harm_Y32.png\|(b) <math> Y_{32}(\theta,\phi) </math>		Image:sph_harm_Y32.png\|(b) <math> Y_{32}(\theta,\phi) </math>

2017-07-28T07:02:17Z

How to Install SHTOOLS on mc2

@@ Line 35: / Line 35: @@
  ~/usr/lib/libfftw3.so
-And also, run:
+And also, run the command:
  ls /usr/lib64
@@ Line 50: / Line 50: @@
  ...
-Also before you proceed, make sure to load the python module (we use python 2 as an example):
+Before we proceed, we need to make sure to have python installed.
  module load python/2.7.8 (Whichever is available)

2017-05-18T08:15:04Z

Visualization of spherical harmonic modes using scipy

← Older revision		Revision as of 08:15, 18 May 2017
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	For example, the picture for (l, m) = (2, 0), (3, 2), and (1, 1) are:		For example, the picture for (l, m) = (2, 0), (3, 2), and (1, 1) are:
	<gallery caption="Fig.1 Visualization of FCC structure" widths="200px" heights="200px" perrow="3">		<gallery caption="Fig.1 Visualization of FCC structure" widths="200px" heights="200px" perrow="3">
	Image:sph_harm_Y20.~~jpg~~\|(a) <math> Y_{20}(\theta,\phi) </math>		Image:sph_harm_Y20.png\|(a) <math> Y_{20}(\theta,\phi) </math>
	Image:sph_harm_Y32.~~jpg~~\|(b) <math> Y_{32}(\theta,\phi) </math>		Image:sph_harm_Y32.png\|(b) <math> Y_{32}(\theta,\phi) </math>
	Image:sph_harm_Y11.~~jpg~~\|(c) <math> Y_{11}(\theta,\phi) </math>		Image:sph_harm_Y11.png\|(c) <math> Y_{11}(\theta,\phi) </math>
	</gallery>		</gallery>

2017-05-18T08:13:30Z

Visualization of spherical harmonic modes using scipy

← Older revision		Revision as of 08:13, 18 May 2017
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	For example, the picture for (l, m) = (2, 0), (3, 2), and (1, 1) are:		For example, the picture for (l, m) = (2, 0), (3, 2), and (1, 1) are:
			<gallery caption="Fig.1 Visualization of FCC structure" widths="200px" heights="200px" perrow="3">
			Image:sph_harm_Y20.jpg\|(a) <math> Y_{20}(\theta,\phi) </math>
			Image:sph_harm_Y32.jpg\|(b) <math> Y_{32}(\theta,\phi) </math>
			Image:sph_harm_Y11.jpg\|(c) <math> Y_{11}(\theta,\phi) </math>
			</gallery>

2017-02-11T01:23:02Z

Visualization of spherical harmonic modes using scipy

← Older revision		Revision as of 01:23, 11 February 2017
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	For a certain pair of parameters (m, l), we can plot the corresponding spherical harmonic mode Y(l, m) on the surface of a unit sphere using scipy and matplotlib packages. Here we use the meshgrid THETA, PHI, X, Y, and Z we generated in the previous section:		For a certain pair of parameters (m, l), we can plot the corresponding spherical harmonic mode Y(l, m) on the surface of a unit sphere using scipy and matplotlib packages. Here we use the meshgrid THETA, PHI, X, Y, and Z we generated in the previous section:

	fvalues = sph_harm(m, l, THETA, PHI).real # Get the values of spherical ~~har~~		fvalues = sph_harm(m, l, THETA, PHI).real # Get the values of spherical harmonic functions
	fmax, fmin = fvalues.max(), fvalues.min()		fmax, fmin = fvalues.max(), fvalues.min()
	fcolors = (fvalues - fmin)/(fmax - fmin) # normalize the values into range [0, 1]		fcolors = (fvalues - fmin)/(fmax - fmin) # normalize the values into range [0, 1]