Commit 274bb164 authored by Marco Govoni's avatar Marco Govoni
Browse files

Updated Makefile. Added tutorial

parent dcf822cf
# Makefile for Sphinx documentation
# Minimal makefile for Sphinx documentation
#
# You can set these variables from the command line.
SPHINXOPTS =
SPHINXBUILD = sphinx-build
PAPER =
SPHINXPROJ = westpy
SOURCEDIR = ./
BUILDDIR = _build
# User-friendly check for sphinx-build
ifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $$?), 1)
$(error The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don't have Sphinx installed, grab it from http://sphinx-doc.org/)
endif
# Internal variables.
PAPEROPT_a4 = -D latex_paper_size=a4
PAPEROPT_letter = -D latex_paper_size=letter
ALLSPHINXOPTS = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
# the i18n builder cannot share the environment and doctrees with the others
I18NSPHINXOPTS = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest coverage gettext
# Put it first so that "make" without argument is like "make help".
help:
@echo "Please use \`make <target>' where <target> is one of"
@echo " html to make standalone HTML files"
@echo " dirhtml to make HTML files named index.html in directories"
@echo " singlehtml to make a single large HTML file"
@echo " pickle to make pickle files"
@echo " json to make JSON files"
@echo " htmlhelp to make HTML files and a HTML help project"
@echo " qthelp to make HTML files and a qthelp project"
@echo " applehelp to make an Apple Help Book"
@echo " devhelp to make HTML files and a Devhelp project"
@echo " epub to make an epub"
@echo " latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter"
@echo " latexpdf to make LaTeX files and run them through pdflatex"
@echo " latexpdfja to make LaTeX files and run them through platex/dvipdfmx"
@echo " text to make text files"
@echo " man to make manual pages"
@echo " texinfo to make Texinfo files"
@echo " info to make Texinfo files and run them through makeinfo"
@echo " gettext to make PO message catalogs"
@echo " changes to make an overview of all changed/added/deprecated items"
@echo " xml to make Docutils-native XML files"
@echo " pseudoxml to make pseudoxml-XML files for display purposes"
@echo " linkcheck to check all external links for integrity"
@echo " doctest to run all doctests embedded in the documentation (if enabled)"
@echo " coverage to run coverage check of the documentation (if enabled)"
clean:
rm -rf $(BUILDDIR)
html:
$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
@echo
@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
dirhtml:
$(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
@echo
@echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
singlehtml:
$(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml
@echo
@echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml."
pickle:
$(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
@echo
@echo "Build finished; now you can process the pickle files."
json:
$(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json
@echo
@echo "Build finished; now you can process the JSON files."
htmlhelp:
$(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp
@echo
@echo "Build finished; now you can run HTML Help Workshop with the" \
".hhp project file in $(BUILDDIR)/htmlhelp."
qthelp:
$(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp
@echo
@echo "Build finished; now you can run "qcollectiongenerator" with the" \
".qhcp project file in $(BUILDDIR)/qthelp, like this:"
@echo "# qcollectiongenerator $(BUILDDIR)/qthelp/signac.qhcp"
@echo "To view the help file:"
@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/signac.qhc"
applehelp:
$(SPHINXBUILD) -b applehelp $(ALLSPHINXOPTS) $(BUILDDIR)/applehelp
@echo
@echo "Build finished. The help book is in $(BUILDDIR)/applehelp."
@echo "N.B. You won't be able to view it unless you put it in" \
"~/Library/Documentation/Help or install it in your application" \
"bundle."
devhelp:
$(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
@echo
@echo "Build finished."
@echo "To view the help file:"
@echo "# mkdir -p $$HOME/.local/share/devhelp/signac"
@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/signac"
@echo "# devhelp"
epub:
$(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub
@echo
@echo "Build finished. The epub file is in $(BUILDDIR)/epub."
latex:
$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
@echo
@echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex."
@echo "Run \`make' in that directory to run these through (pdf)latex" \
"(use \`make latexpdf' here to do that automatically)."
latexpdf:
$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
@echo "Running LaTeX files through pdflatex..."
$(MAKE) -C $(BUILDDIR)/latex all-pdf
@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
latexpdfja:
$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
@echo "Running LaTeX files through platex and dvipdfmx..."
$(MAKE) -C $(BUILDDIR)/latex all-pdf-ja
@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
text:
$(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text
@echo
@echo "Build finished. The text files are in $(BUILDDIR)/text."
man:
$(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man
@echo
@echo "Build finished. The manual pages are in $(BUILDDIR)/man."
texinfo:
$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
@echo
@echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo."
@echo "Run \`make' in that directory to run these through makeinfo" \
"(use \`make info' here to do that automatically)."
info:
$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
@echo "Running Texinfo files through makeinfo..."
make -C $(BUILDDIR)/texinfo info
@echo "makeinfo finished; the Info files are in $(BUILDDIR)/texinfo."
gettext:
$(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale
@echo
@echo "Build finished. The message catalogs are in $(BUILDDIR)/locale."
changes:
$(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes
@echo
@echo "The overview file is in $(BUILDDIR)/changes."
linkcheck:
$(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck
@echo
@echo "Link check complete; look for any errors in the above output " \
"or in $(BUILDDIR)/linkcheck/output.txt."
doctest:
$(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
@echo "Testing of doctests in the sources finished, look at the " \
"results in $(BUILDDIR)/doctest/output.txt."
coverage:
$(SPHINXBUILD) -b coverage $(ALLSPHINXOPTS) $(BUILDDIR)/coverage
@echo "Testing of coverage in the sources finished, look at the " \
"results in $(BUILDDIR)/coverage/python.txt."
@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
xml:
$(SPHINXBUILD) -b xml $(ALLSPHINXOPTS) $(BUILDDIR)/xml
@echo
@echo "Build finished. The XML files are in $(BUILDDIR)/xml."
.PHONY: help Makefile
pseudoxml:
$(SPHINXBUILD) -b pseudoxml $(ALLSPHINXOPTS) $(BUILDDIR)/pseudoxml
@echo
@echo "Build finished. The pseudo-XML files are in $(BUILDDIR)/pseudoxml."
# Catch-all target: route all unknown targets to Sphinx using the new
# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS).
%: Makefile
@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
......@@ -11,4 +11,5 @@ Contents:
:maxdepth: 1
westpy_100.ipynb
westpy_101.ipynb
westpy_200.ipynb
%% Cell type:markdown id: tags:
This tutorial can be downloaded [link](http://greatfire.uchicago.edu/west-public/westpy/raw/master/doc/westpy_100.ipynb).
%% Cell type:markdown id: tags:
# 1.0 Getting Started: Ground State
%% Cell type:markdown id: tags:
We are going to generate an input file for the [QuantumEspresso](https://www.quantum-espresso.org/) code or [Qbox](http://qboxcode.org/). Each code will compute the ground state electronic stucture for the methane molecule using Density Functional Theory.
%% Cell type:markdown id: tags:
## Step 1: Load westpy
%% Cell type:code id: tags:
``` python
from westpy import *
```
%%%% Output: stream
_ _ _____ _____ _____
| | | | ___/ ___|_ _|
| | | | |__ \ `--. | |_ __ _ _
| |/\| | __| `--. \ | | '_ \| | | |
\ /\ / |___/\__/ / | | |_) | |_| |
\/ \/\____/\____/ \_/ .__/ \__, |
| | __/ |
|_| |___/
WEST version : 3.1.0
Today : 2018-06-25 07:01:41.214544
Today : 2018-06-25 18:12:53.140481
%% Cell type:markdown id: tags:
## Step 2: Geometry
%% Cell type:code id: tags:
``` python
geom = Geometry()
```
%% Cell type:markdown id: tags:
Let's define a cubic cell of edge 25 Bohr.
%% Cell type:code id: tags:
``` python
geom.setCell((25,0,0),(0,25,0),(0,0,25))
```
%% Cell type:markdown id: tags:
We load the atomic positions from a XYZ file, available online.
%% Cell type:code id: tags:
``` python
geom.addAtomsFromOnlineXYZ( "http://www.west-code.org/database/gw100/xyz/CH4.xyz" )
geom.addAtomsFromOnlineXYZ( "http://www.west-code.org/doc/training/CH4.xyz" )
```
%% Cell type:markdown id: tags:
We associate pseudopotential files to each species.
%% Cell type:code id: tags:
``` python
geom.addSpecies( "C", "http://www.quantum-simulation.org/potentials/sg15_oncv/upf/C_ONCV_PBE-1.0.upf")
geom.addSpecies( "H", "http://www.quantum-simulation.org/potentials/sg15_oncv/upf/H_ONCV_PBE-1.0.upf")
```
%% Cell type:markdown id: tags:
## Step 3.1: Ground State
%% Cell type:markdown id: tags:
The ground state calculation is defined by the geometry, a choice of the exchange-correlation functional, and by setting an energy cutoff for the wavefunctions.
%% Cell type:code id: tags:
``` python
gs = GroundState(geom,xc="PBE",ecut=40.0)
```
%% Cell type:markdown id: tags:
We are now able to generate the input file for QuantumEspresso.
%% Cell type:code id: tags:
``` python
gs.generateInputPW()
```
%%%% Output: stream
Generated file: pw.in
%% Cell type:markdown id: tags:
We can inspect the file pw.in
%% Cell type:code id: tags:
``` python
with open("pw.in","r") as file :
data = file.read()
print(data)
```
%%%% Output: stream
&CONTROL
calculation = 'scf'
restart_mode = 'from_scratch'
pseudo_dir = './'
outdir = './'
prefix = 'calc'
wf_collect = .TRUE.
/
&SYSTEM
ibrav = 0
nat = 5
ntyp = 2
ecutwfc = 40.0
nbnd = 8
input_dft = 'PBE'
nosym = .TRUE.
noinv = .TRUE.
/
&ELECTRONS
diago_full_acc = .TRUE.
conv_tol = 1.d-8
/
ATOMIC_SPECIES
C 12.011 C_ONCV_PBE-1.0.upf
H 1.008 H_ONCV_PBE-1.0.upf
ATOMIC_POSITIONS {bohr}
C 0.0 0.0 0.0
H 1.185992116575257 -1.185803143962673 1.185992116575257
H -1.185992116575257 1.185992116575257 1.185992116575257
H -1.185992116575257 -1.185992116575257 -1.185992116575257
H 1.185992116575257 1.185992116575257 -1.185992116575257
K_POINTS {gamma}
CELL_PARAMETERS {bohr}
25.0 0.0 0.0
0.0 25.0 0.0
0.0 0.0 25.0
%% Cell type:markdown id: tags:
We can optionally also download the pseudopotentials files.
%% Cell type:code id: tags:
``` python
gs.downloadPseudopotentials()
```
%%%% Output: stream
Downloaded file: C_ONCV_PBE-1.0.upf , from url: http://www.quantum-simulation.org/potentials/sg15_oncv/upf/C_ONCV_PBE-1.0.upf
Downloaded file: H_ONCV_PBE-1.0.upf , from url: http://www.quantum-simulation.org/potentials/sg15_oncv/upf/H_ONCV_PBE-1.0.upf
%% Cell type:markdown id: tags:
## Step 3.2: Ground State with Qbox
%% Cell type:markdown id: tags:
To generate the input for Qbox we can simply update Species to use the xml formats.
%% Cell type:code id: tags:
``` python
gs.updateSpecies("C", "http://www.quantum-simulation.org/potentials/sg15_oncv/xml/C_ONCV_PBE-1.0.xml")
gs.updateSpecies("H", "http://www.quantum-simulation.org/potentials/sg15_oncv/xml/H_ONCV_PBE-1.0.xml")
```
%% Cell type:markdown id: tags:
We are now able to generate the input file for QuantumEspresso.
%% Cell type:code id: tags:
``` python
gs.generateInputQbox()
```
%%%% Output: stream
Generated file: qbox.in
%% Cell type:markdown id: tags:
We can inspect the file qbox.in
%% Cell type:code id: tags:
``` python
with open("qbox.in","r") as file :
data = file.read()
print(data)
```
%%%% Output: stream
set cell 25.0 0.0 0.0 0.0 25.0 0.0 0.0 0.0 25.0
species Carbon C_ONCV_PBE-1.0.xml
species Hydrogen H_ONCV_PBE-1.0.xml
atom C1 Carbon 0.0 0.0 0.0
atom H2 Hydrogen 1.185992116575257 -1.185803143962673 1.185992116575257
atom H3 Hydrogen -1.185992116575257 1.185992116575257 1.185992116575257
atom H4 Hydrogen -1.185992116575257 -1.185992116575257 -1.185992116575257
atom H5 Hydrogen 1.185992116575257 1.185992116575257 -1.185992116575257
set ecut 40.0
set wf_dyn JD
set xc PBE
set scf_tol 1.e-8
randomize_wf
run -atomic_density 0 100 5
save gs.xml
%% Cell type:markdown id: tags:
We can optionally also download the pseudopotentials files.
%% Cell type:code id: tags:
``` python
gs.downloadPseudopotentials()
```
%%%% Output: stream
Downloaded file: C_ONCV_PBE-1.0.xml , from url: http://www.quantum-simulation.org/potentials/sg15_oncv/xml/C_ONCV_PBE-1.0.xml
Downloaded file: H_ONCV_PBE-1.0.xml , from url: http://www.quantum-simulation.org/potentials/sg15_oncv/xml/H_ONCV_PBE-1.0.xml
%% Cell type:code id: tags:
``` python
```
......
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