Commit 63ea410b authored by Paul Erhart's avatar Paul Erhart

DOC: updated documentation, added "related software"

parent f3b47cdb
<div style="text-align: right;">
<a href="https://gitlab.com/materials-modeling/dynasor" target="_blank">gitlab/dynasor</a>
| <a href="https://materialsmodeling.org/software" target="_blank">materialsmodeling.org/software</a>
| <a href={{ pathto('genindex') }}>index</a>
</div>
<div class="rst-versions" data-toggle="rst-versions" role="note" aria-label="versions">
<span class="rst-current-version" data-toggle="rst-current-version">
<span class="fa fa-book">Related software</span>
<span class="fa fa-caret-down"></span>
</span>
<div class="rst-other-versions">
<dl>
{% for slug, url, desc in software %}
<dd><a href="{{ url }}">{{ slug }}<br>
<div style="text-indent:1em; font-size:small; color:gray">{{ desc }}</div>
</a></dd>
{% endfor %}
</dl>
</div>
</div>
......@@ -5,4 +5,4 @@ References
**********
.. bibliography:: references.bib
:all:
This diff is collapsed.
......@@ -3,9 +3,9 @@ Examples
The `examples` folder contains serveral simple examples that
demonstate how to use :program:`dynasor`. Specifically, these examples
illustrate the analysis of an elemental liquid (`molten Al
<example_liquid_aluminum>`), an elemental crystal (`fcc Al
<example_crystalline_aluminum>`), as well as a compound (`molten
illustrate the analysis of an elemental liquid (:ref:`molten Al
<example_liquid_aluminum>`), an elemental crystal (:ref:`fcc Al
<example_crystalline_aluminum>`), as well as a compound (:ref:`molten
sodium chloride <example_sodium_chloride>`).
In setting up these examples, suitable parameters were chosen for the
......@@ -13,14 +13,13 @@ MD simulations that provide physically sound (albeit not necessarily
highly converged) results. In practice, it is strongly recommended to
carefully test the effect of e.g., system size, sampling time, spacing
of snapshots, possibly potential/force field, and
:program:`dynasor`averaging parameters.
:program:`dynasor` averaging parameters.
The MD simulations that are analyzed here were carried out using the
(`lammps`)[http://lammps.sandia.gov/] code. The input files used to
generate the trajectroies are included for reference and can be found
in the `examples` directory.
.. rubric:: Contents
.. toctree::
......
......@@ -20,10 +20,9 @@ Quickstart
==========
:program:`dynasor` requires :program:`Python` 2.6/2.7 or higher,
:program:`numpy`, as well as a C99-complient C-compiler. On *nix
:program:systems, compilation is usually staightforward and merely
:program:requires executing` the following command on the command line
:program:::
:program:`numpy`, as well as a C99-complient C-compiler. On nix
systems, compilation is usually staightforward and merely requires
executing the following command on the command line::
./setup.py install --prefix=<build-path>
......
......@@ -88,7 +88,7 @@ example the command ::
dynasor ... --nt=500 --max-frames=2000
.. figure:: figs/window_sampling.png
.. figure:: _static/window_sampling.png
:scale: 30 %
:align: center
......
......@@ -66,7 +66,7 @@
@article{PetHeiTra91,
title = {Phonon dispersion of the bcc phase of group-{IV} metals. {I}. bcc titanium},
author = {Petry, W. and Heiming, A. and Trampenau, J. and Alba, M. and Herzig, C. and Schober, H. R. and Vogl, G.},
journal = {Phys. Rev. B},
journal = {Physical Review B},
volume = {43},
issue = {13},
pages = {10933--10947},
......@@ -77,9 +77,9 @@
}
@article{MeyEnt98,
title = {Martensite-austenite transition and phonon dispersion curves of ${\mathrm{Fe}}_{1-x}{\mathrm{Ni}}_{x}$ studied by molecular-dynamics simulations},
title = {Martensite-austenite transition and phonon dispersion curves of {Fe(1-x)Ni(x)} studied by molecular-dynamics simulations},
author = {Meyer, R. and Entel, P.},
journal = {Phys. Rev. B},
journal = {Physical Review B},
volume = {57},
issue = {9},
pages = {5140--5147},
......@@ -93,7 +93,7 @@
@article{TogChaTan15,
title = {Distributions of phonon lifetimes in {Brillouin} zones},
author = {Togo, Atsushi and Chaput, Laurent and Tanaka, Isao},
journal = {Phys. Rev. B},
journal = {Physical Review B},
volume = {91},
issue = {9},
pages = {094306},
......
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