Commit 256432a5 authored by Tuomas Rossi's avatar Tuomas Rossi
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Use :doi: role for doi links

parent 661547a9
......@@ -19,7 +19,7 @@ In Explicit Interaction QMMM, the QM and MM regions
are explicitly coupled with an electrostatic interaction term.
This requires that the electrostatic potential from the classical charges of the
MM subsystem is fed into the QM calculator. This is built into GPAW_. More info
`In this paper <https://doi.org/10.1021/acs.jctc.7b00621>`__, which should be
:doi:`in this paper <10.1021/acs.jctc.7b00621>`, which should be
cited if the method is used.
Other ASE-calculators that currently support EIQMMM:
......@@ -88,9 +88,9 @@ Force-based QM/MM
This QM/MM calculator mixes forces from any pair of ASE calculators.
A finite buffer is added around the core QM region to ensure accurate forces; careful testing
of the required buffer size is required. See
`N. Bernstein, J. R. Kermode, and G. Csányi, Rep. Prog. Phys. 72, 026501 (2009) <https://doi.org/10.1088/0034-4885/72/2/026501>`__
:doi:`N. Bernstein, J. R. Kermode, and G. Csányi, Rep. Prog. Phys. 72, 026501 (2009) <10.1088/0034-4885/72/2/026501>`
for a review of force-based QM/MM approaches, which should be cited if this method is used,
and `T. D. Swinburne and J. R. Kermode, Phys. Rev. B 96, 144102 (2017). <https://journals.aps.org/prb/abstract/10.1103/PhysRevB.96.144102>`__
and :doi:`T. D. Swinburne and J. R. Kermode, Phys. Rev. B 96, 144102 (2017) <10.1103/PhysRevB.96.144102>`
for an application which used this implementation.
.. autoclass:: ForceQMMM
......
......@@ -11,7 +11,7 @@ algorithms in which ASE moves the atoms while the external code
calculates energies, forces, and stress. Note that ASE does not
require i-PI, but simply uses the same protocol.
The reference article for i-PI is `Ceriotti, More, Manolopoulos, Comp. Phys. Comm. 185, 1019-1026 (2014) <https://doi.org/10.1016/j.cpc.2013.10.027>`_.
The reference article for i-PI is :doi:`Ceriotti, More, Manolopoulos, Comp. Phys. Comm. 185, 1019-1026 (2014) <10.1016/j.cpc.2013.10.027>`.
Introduction
......
......@@ -53,14 +53,14 @@ Structures and data from:
"Error estimates for solid-state density-functional theory predictions:
an overview by means of the ground-state elemental crystals",
Crit. Rev. Solid State (2014).
https://doi.org/10.1080/10408436.2013.772503
:doi:`10.1080/10408436.2013.772503`
.. [Lejaeghere2016]
Kurt Lejaeghere *et al.*:
"Reproducibility in density functional theory calculations of solids",
Science 351 (6280), aad3000 (2016).
https://doi.org/10.1126/science.aad3000
:doi:`10.1126/science.aad3000`
This collection has WIEN2k and experimental data for:
......@@ -99,4 +99,4 @@ Molecules from [Curtiss1997]_.
"Assessment of Gaussian-2 and density functional theories for the
computation of enthalpies of formation",
J. Chem. Phys. 106, 1063 (1997).
https://doi.org/10.1063/1.473182
:doi:`10.1063/1.473182`
......@@ -73,17 +73,17 @@ radii are taken from [Alvarez13]_.
.. [Meija2016] *Atomic weights of the elements 2013
(IUPAC Technical Report).* Meija, J., Coplen, T., Berglund, M., et al.
(2016). Pure and Applied Chemistry, 88(3), pp. 265-291.
Retrieved 30 Nov. 2016, from doi:10.1515/pac-2015-0305
Retrieved 30 Nov. 2016, from :doi:`10.1515/pac-2015-0305`
.. [Cordeo08] *Covalent radii revisited*,
Beatriz Cordero, Verónica Gómez, Ana E. Platero-Prats, Marc Revés,
Jorge Echeverría, Eduard Cremades, Flavia Barragán and Santiago Alvarez,
Dalton Trans., 2008, 2832-2838 DOI:10.1039/B801115J
Dalton Trans., 2008, 2832-2838 :doi:`10.1039/B801115J`
.. [Alvarez13] *A cartography of the van der Waals territories*,
Alvarez, S.,
Dalton Trans., 2013, 42, 8617-8636,
DOI:10.1039/C3DT50599E
:doi:`10.1039/C3DT50599E`
.. _vdw.py: https://gitlab.com/ase/ase/blob/master/ase/data/vdw.py
......
......@@ -41,6 +41,7 @@ array([[-0.375, 0. , 0. ],
Hendrik J. Monkhorst and James D. Pack:
*Special points for Brillouin-zone integrations*,
Phys. Rev. B 13, 5188–5192 (1976)
:doi:`10.1103/PhysRevB.13.5188`
Special points in the Brillouin zone
......@@ -64,7 +65,7 @@ The below table lists the special points from [Setyawan-Curtarolo]_.
Computational Materials Science,
Volume 49, Issue 2, August 2010, Pages 299–312
https://doi.org/10.1016/j.commatsci.2010.05.010
:doi:`10.1016/j.commatsci.2010.05.010`
You can find the special points in the Brillouin zone:
......
......@@ -27,27 +27,21 @@ The method is described in detail in the following publications:
For **small clusters on/in support material** in:
| L. B. Vilhelmsen and B. Hammer
| `A genetic algorithm for first principles global structure optimization of supported nano structures`__
| :doi:`A genetic algorithm for first principles global structure optimization of supported nano structures <10.1063/1.4886337>`
| The Journal of chemical physics, Vol. 141 (2014), 044711
__ https://doi.org/10.1063/1.4886337
For **medium sized alloy clusters** in:
| S. Lysgaard, D. D. Landis, T. Bligaard and T. Vegge
| `Genetic Algorithm Procreation Operators for Alloy Nanoparticle Catalysts`__
| :doi:`Genetic Algorithm Procreation Operators for Alloy Nanoparticle Catalysts <10.1007/s11244-013-0160-9>`
| Topics in Catalysis, Vol **57**, No. 1-4, pp. 33-39, (2014)
__ https://doi.org/10.1007/s11244-013-0160-9
A search for **mixed metal ammines for ammonia storage** have been performed
using the GA in:
| P. B. Jensen, S. Lysgaard, U. J. Quaade and T. Vegge
| `Designing Mixed Metal Halide Ammines for Ammonia Storage Using Density Functional Theory and Genetic Algorithms`__
| :doi:`Designing Mixed Metal Halide Ammines for Ammonia Storage Using Density Functional Theory and Genetic Algorithms <10.1039/C4CP03133D>`
| Physical Chemistry Chemical Physics, Vol **16**, No. 36, pp. 19732-19740, (2014)
__ https://doi.org/10.1039/C4CP03133D
A simple tutorial explaining how to set up a database and perform a
similar search can be found here: :ref:`fcc_alloys_tutorial`
......@@ -189,11 +189,9 @@ to speed up BFGS local minimzations.
Read more about this algorithm here:
| Estefanía Garijo del Río, Jens Jørgen Mortensen, Karsten W. Jacobsen
| `Local Bayesian optimizer for atomic structures`__
| :doi:`Local Bayesian optimizer for atomic structures <10.1103/PhysRevB.100.104103>`
| Physical Review B, Vol. **100**, 104103 (2019)
__ https://link.aps.org/doi/10.1103/PhysRevB.100.104103
.. warning:: The memory of the optimizer scales as O(n²N²) where
N is the number of atoms and n the number of steps.
If the number of atoms is sufficiently high, this
......@@ -210,11 +208,9 @@ FIRE
Read about this algorithm here:
| Erik Bitzek, Pekka Koskinen, Franz Gähler, Michael Moseler, and Peter Gumbsch
| `Structural Relaxation Made Simple`__
| :doi:`Structural Relaxation Made Simple <10.1103/PhysRevLett.97.170201>`
| Physical Review Letters, Vol. **97**, 170201 (2006)
__ https://doi.org/10.1103/PhysRevLett.97.170201
MDMin
-----
......@@ -317,11 +313,9 @@ the :class:`ase.optimize.precon.lbfgs.PreconLBFGS` and
You can read more about the theory and implementation here:
| D. Packwood, J.R. Kermode; L. Mones, N. Bernstein, J. Woolley, N. Gould, C. Ortner and G. Csányi
| `A universal preconditioner for simulating condensed phase materials`__
| :doi:`A universal preconditioner for simulating condensed phase materials <10.1063/1.4947024>`
| J. Chem. Phys. *144*, 164109 (2016).
__ https://doi.org/10.1063/1.4947024
Tests with a variety of solid-state systems using both DFT and classical
interatomic potentials driven though ASE calculators show speedup factors of up
to an order of magnitude for preconditioned L-BFGS over standard L-BFGS, and the
......@@ -473,18 +467,15 @@ local optimization algorithm::
Read more about this algorithm here:
| David J. Wales and Jonathan P. K. Doye
| `Global Optimization by Basin-Hopping and the Lowest Energy Structures of Lennard-Jones Clusters Containing up to 110 Atoms`__
| :doi:`Global Optimization by Basin-Hopping and the Lowest Energy Structures of Lennard-Jones Clusters Containing up to 110 Atoms <10.1021/jp970984n>`
| J. Phys. Chem. A, Vol. **101**, 5111-5116 (1997)
__ https://doi.org/10.1021/jp970984n
and here:
| David J. Wales and Harold A. Scheraga
| `Global Optimization of Clusters, Crystals, and Biomolecules`__
| :doi:`Global Optimization of Clusters, Crystals, and Biomolecules <10.1126/science.285.5432.1368>`
| Science, Vol. **285**, 1368 (1999)
__ https://science.sciencemag.org/content/285/5432/1368.abstract
Minima hopping
--------------
......@@ -492,11 +483,9 @@ Minima hopping
The minima hopping algorithm was developed and described by Goedecker:
| Stefan Goedecker
| `Minima hopping: An efficient search method for the global minimum of the potential energy surface of complex molecular systems`__
| :doi:`Minima hopping: An efficient search method for the global minimum of the potential energy surface of complex molecular systems <10.1063/1.1724816>`
| J. Chem. Phys., Vol. **120**, 9911 (2004)
__ https://doi.org/10.1063/1.1724816
This algorithm utilizes a series of alternating steps of NVE molecular dynamics and local optimizations, and has two parameters that the code dynamically adjusts in response to the progress of the search. The first parameter is the initial temperature of the NVE simulation. Whenever a step finds a new minimum this temperature is decreased; if the step finds a previously found minimum the temperature is increased. The second dynamically adjusted parameter is `E_\mathrm{diff}`, which is an energy threshold for accepting a newly found minimum. If the new minimum is no more than `E_\mathrm{diff}` eV higher than the previous minimum, it is acccepted and `E_\mathrm{diff}` is decreased; if it is more than `E_\mathrm{diff}` eV higher it is rejected and `E_\mathrm{diff}` is increased. The method is used as::
from ase.optimize.minimahopping import MinimaHopping
......
......@@ -88,6 +88,6 @@ For an example of how to use the :mod:`ase.transport` module, see section 9.2
in the ASE-paper:
J. Phys. Condens. Matter:
`The Atomic Simulation Environment | A Python library for working with
atoms <https://doi.org/10.1088/1361-648X/aa680e>`__
:doi:`The Atomic Simulation Environment | A Python library for working with
atoms <10.1088/1361-648X/aa680e>`
(7 June 2017).
......@@ -24,9 +24,7 @@ This module contains utility functions and classes.
Symmetry equivalence checker
============================
This module compares two atomic structures to see if they are symmetrically equivalent. It is based on the recipe used in `XtalComp`__
__ https://doi.org/10.1016/j.cpc.2011.11.007
This module compares two atomic structures to see if they are symmetrically equivalent. It is based on the recipe used in :doi:`XtalComp <10.1016/j.cpc.2011.11.007>`
.. autoclass:: ase.utils.structure_comparator.SymmetryEquivalenceCheck
:members:
......
......@@ -113,5 +113,5 @@ References
==========
.. [Debye1915] P. Debye Ann. Phys. **351**, 809–823 (1915)
.. [Iwasa2007] T. Iwasa, K. Nobusada J. Phys. Chem. C, **111**, 45-49 (2007) https://doi.org/10.1021/jp063532w
.. [Iwasa2007] T. Iwasa, K. Nobusada J. Phys. Chem. C, **111**, 45-49 (2007) :doi:`10.1021/jp063532w`
.. [Waasmaier1995] D. Waasmaier, A. Kirfel Acta Cryst. **A51**, 416-431 (1995)
......@@ -10,10 +10,12 @@ extensions = ['ext',
'images',
'sphinx.ext.autodoc',
'sphinx.ext.doctest',
'sphinx.ext.extlinks',
'sphinx.ext.mathjax',
'sphinx.ext.viewcode',
'sphinx.ext.napoleon',
'sphinx.ext.intersphinx']
extlinks = {'doi': ('https://doi.org/%s', 'doi:')}
source_suffix = '.rst'
master_doc = 'index'
project = 'ASE'
......
......@@ -66,19 +66,15 @@ If you find ASE useful in your research please cite:
| Lars Pastewka, Andrew Peterson, Carsten Rostgaard, Jakob Schiøtz,
| Ole Schütt, Mikkel Strange, Kristian S. Thygesen, Tejs Vegge,
| Lasse Vilhelmsen, Michael Walter, Zhenhua Zeng, Karsten Wedel Jacobsen
| `The Atomic Simulation Environment—A Python library for working with atoms`__
| :doi:`The Atomic Simulation Environment—A Python library for working with atoms <10.1088/1361-648X/aa680e>`
| J. Phys.: Condens. Matter Vol. **29** 273002, 2017
__ https://doi.org/10.1088/1361-648X/aa680e
An older paper corresponding to an early version of ASE is:
| S. R. Bahn and K. W. Jacobsen
| `An object-oriented scripting interface to a legacy electronic structure code`__
| :doi:`An object-oriented scripting interface to a legacy electronic structure code <10.1109/5992.998641>`
| Comput. Sci. Eng., Vol. **4**, 56-66, 2002
__ https://doi.org/10.1109/5992.998641
BibTex (:git:`doc/ASE.bib`):
.. literalinclude:: ASE.bib
......@@ -98,8 +98,8 @@ News
* :ref:`Reference paper <cite>` in
J. Phys. Condens. Matter:
`The Atomic Simulation Environment | A Python library for working with
atoms <https://doi.org/10.1088/1361-648X/aa680e>`__
:doi:`The Atomic Simulation Environment | A Python library for working with
atoms <10.1088/1361-648X/aa680e>`
(7 June 2017).
* :ref:`ASE version 3.13.0 <releasenotes>` released (7 February 2017).
......
......@@ -248,4 +248,4 @@ follows::
.. [Erhart] P. Erhart, B. Sadigh, A. Schleife, and D. Åberg.
First-principles study of codoping in lanthanum bromide,
Phys. Rev. B, Vol **91**, 165206 (2012),
`doi: 10.1103/PhysRevB.91.165206 <https://doi.org/10.1103/PhysRevB.91.165206>`_; Appendix C
:doi:`10.1103/PhysRevB.91.165206`; Appendix C
......@@ -27,11 +27,9 @@ the example below demonstrates.
The method is described in the article:
| P.M. Larsen, M. Pandey, M. Strange, and K. W. Jacobsen
| `Definition of a scoring parameter to identify low-dimensional materials components`__
| :doi:`Definition of a scoring parameter to identify low-dimensional materials components <10.1103/PhysRevMaterials.3.034003>`
| Phys. Rev. Materials 3 034003, 2019
__ https://doi.org/10.1103/PhysRevMaterials.3.034003
A preprint is available `here <https://arxiv.org/pdf/1808.02114.pdf>`_.
.. seealso::
......
......@@ -9,11 +9,9 @@ Here we will use the GA to predict a crystal structure of a given chemical compo
The implementation is based on:
| M. Van den Bossche, H. Grönbeck, and B. Hammer
| `Tight-Binding Approximation-Enhanced Global Optimization`__
| :doi:`Tight-Binding Approximation-Enhanced Global Optimization <10.1021/acs.jctc.8b00039>`
| J. Chem. Theory Comput. 2018, 14, 2797−2807
__ https://doi.org/10.1021/acs.jctc.8b00039
and has much the same functionality as e.g. the USPEX program from the Oganov
group and the XtalOpt code by the Zurek group.
......
......@@ -12,11 +12,9 @@ to the recent search for mixed metal ammines with superior properties for
ammonia storage described here:
| P. B. Jensen, S. Lysgaard, U. J. Quaade and T. Vegge
| `Designing Mixed Metal Halide Ammines for Ammonia Storage Using Density Functional Theory and Genetic Algorithms`__
| :doi:`Designing Mixed Metal Halide Ammines for Ammonia Storage Using Density Functional Theory and Genetic Algorithms <10.1039/C4CP03133D>`
| Physical Chemistry Chemical Physics, Vol **16**, No. 36, pp. 19732-19740, (2014)
__ https://doi.org/10.1039/C4CP03133D
.. contents::
......
......@@ -17,7 +17,7 @@ is considerably reduced.
This assumption, of course, also needs to be checked --
at high pressures, for example, nitrogen is
`known to polymerize <https://doi.org/10.1038/nmat1146>`__ and so
:doi:`known to polymerize <10.1038/nmat1146>` and so
will no longer consist of individual :mol:`N_2` molecules!
The same approach can also be used e.g. for compounds with polyatomic ions
......
......@@ -11,19 +11,15 @@ optimization within ase. The optimizer consists of its own module
The method was first described in the supplemental material of
| L. B. Vilhelmsen and B. Hammer
| `Systematic Study of Au6 to Au12 Gold Clusters on MgO(100) F Centers Using Density-Functional Theory`__
| :doi:`Systematic Study of Au6 to Au12 Gold Clusters on MgO(100) F Centers Using Density-Functional Theory <10.1103/PhysRevLett.108.126101>`
| Physical Review Letters, Vol. 108 (Mar 2012), 126101
__ https://doi.org/10.1103/physrevlett.108.126101
and a full account of the method is given in
| L. B. Vilhelmsen and B. Hammer
| `A genetic algorithm for first principles global optimization of supported nano structures`__
| :doi:`A genetic algorithm for first principles global optimization of supported nano structures <10.1063/1.4886337>`
| Journal of Chemical Physics, Vol 141, 044711 (2014)
__ https://doi.org/10.1063/1.4886337
Any questions about how to use the GA can be asked at the mailing
list.
......
......@@ -25,8 +25,5 @@ This will make a summary figure, which should look something like the one below.
You can see examples of the implementation of this for real adsorbates as well as find suitable parameters for the Hookean constraints:
| Andrew Peterson
| `Global optimization of adsorbate–surface structures while preserving molecular identity`__
| :doi:`Global optimization of adsorbate–surface structures while preserving molecular identity <10.1021/jp063532w>`
| Top. Catal., Vol. **57**, 40 (2014)
__ https://doi.org/10.1007/s11244-013-0161-8
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