pandoc/test/command/biblatex-kastenholz.md
John MacFarlane e0984a43a9 Add built-in citation support using new citeproc library.
This deprecates the use of the external pandoc-citeproc
filter; citation processing is now built in to pandoc.

* Add dependency on citeproc library.
* Add Text.Pandoc.Citeproc module (and some associated unexported
  modules under Text.Pandoc.Citeproc).  Exports `processCitations`.
  [API change]
* Add data files needed for Text.Pandoc.Citeproc:  default.csl
  in the data directory, and a citeproc directory that is just
  used at compile-time.  Note that we've added file-embed as a mandatory
  rather than a conditional depedency, because of the biblatex
  localization files. We might eventually want to use readDataFile
  for this, but it would take some code reorganization.
* Text.Pandoc.Loging: Add `CiteprocWarning` to `LogMessage` and use it
  in `processCitations`. [API change]
* Add tests from the pandoc-citeproc package as command tests (including
  some tests pandoc-citeproc did not pass).
* Remove instructions for building pandoc-citeproc from CI and
  release binary build instructions.  We will no longer distribute
  pandoc-citeproc.
* Markdown reader: tweak abbreviation support.  Don't insert a
  nonbreaking space after a potential abbreviation if it comes right before
  a note or citation.  This messes up several things, including citeproc's
  moving of note citations.
* Add `csljson` as and input and output format. This allows pandoc
  to convert between `csljson` and other bibliography formats,
  and to generate formatted versions of CSL JSON bibliographies.
* Add module Text.Pandoc.Writers.CslJson, exporting `writeCslJson`. [API
  change]
* Add module Text.Pandoc.Readers.CslJson, exporting `readCslJson`. [API
  change]
* Added `bibtex`, `biblatex` as input formats.  This allows pandoc
  to convert between BibLaTeX and BibTeX and other bibliography formats,
  and to generated formatted versions of BibTeX/BibLaTeX bibliographies.
* Add module Text.Pandoc.Readers.BibTeX, exporting `readBibTeX` and
  `readBibLaTeX`. [API change]
* Make "standalone" implicit if output format is a bibliography format.
  This is needed because pandoc readers for bibliography formats put
  the bibliographic information in the `references` field of metadata;
  and unless standalone is specified, metadata gets ignored.
  (TODO: This needs improvement. We should trigger standalone for the
  reader when the input format is bibliographic, and for the writer
  when the output format is markdown.)
* Carry over `citationNoteNum` to `citationNoteNumber`.  This was just
  ignored in pandoc-citeproc.
* Text.Pandoc.Filter: Add `CiteprocFilter` constructor to Filter.
  [API change] This runs the processCitations transformation.
  We need to treat it like a filter so it can be placed
  in the sequence of filter runs (after some, before others).
  In FromYAML, this is parsed from `citeproc` or `{type: citeproc}`,
  so this special filter may be specified either way in a defaults file
  (or by `citeproc: true`, though this gives no control of positioning
  relative to other filters).  TODO: we need to add something to the
  manual section on defaults files for this.
* Add deprecation warning if `upandoc-citeproc` filter is used.
* Add `--citeproc/-C` option to trigger citation processing.
  This behaves like a filter and will be positioned
  relative to filters as they appear on the command line.
* Rewrote the manual on citatations, adding a dedicated Citations
  section which also includes some information formerly found in
  the pandoc-citeproc man page.
* Look for CSL styles in the `csl` subdirectory of the pandoc user data
  directory.  This changes the old pandoc-citeproc behavior, which looked
  in `~/.csl`.  Users can simply symlink `~/.csl` to the `csl`
  subdirectory of their pandoc user data directory if they want
  the old behavior.
* Add support for CSL bibliography entry formatting to LaTeX, HTML,
  Ms writers.  Added CSL-related CSS to styles.html.
2020-09-21 10:15:50 -07:00

5.4 KiB

% pandoc -f biblatex -t markdown -s
@comment{

Adapted from biblatex-example.bib


Formatted with pandoc and chicago-author-date.csl, 2013-10-23:

(Kastenholz and Hünenberger 2006)

Kastenholz, M. A., and Philippe H. Hünenberger. 2006. “Computation of
Methodologyindependent Ionic Solvation Free Energies from Molecular
Simulations: I. the Electrostatic Potential in Molecular Liquids.”
*J. Chem. Phys.* 124.
doi:[10.1063/1.2172593](https://doi.org/10.1063/1.2172593 "10.1063/1.2172593").


Formatted with pandoc and apa.csl, 2013-10-23:

(Kastenholz & Hünenberger, 2006)

Kastenholz, M. A., & Hünenberger, P. H. (2006). Computation of
methodologyindependent ionic solvation free energies from molecular
simulations: I. the electrostatic potential in molecular liquids.
*J. Chem. Phys.*, *124*.
doi:[10.1063/1.2172593](https://doi.org/10.1063/1.2172593 "10.1063/1.2172593")


NOTES:

- biblio2xaml
	- fix conversion of "\hyphen”
	- the string "doi:" should not appear as part of the content of the "doi" field 

}

@string{ jchph   = {J.~Chem. Phys.} }

@Article{kastenholz,
  author       = {Kastenholz, M. A. and H{\"u}nenberger, Philippe H.},
  title        = {Computation of methodology\hyphen independent ionic solvation
                  free energies from molecular simulations},
  journaltitle = jchph,
  date         = 2006,
  subtitle     = {I. {The} electrostatic potential in molecular liquids},
  volume       = 124,
  eid          = 124106,
  doi          = {10.1063/1.2172593},
  hyphenation  = {american},
  indextitle   = {Computation of ionic solvation free energies},
  annotation   = {An article entry with an eid and a
                  doi field. Note that the \textsc{doi} is transformed
                  into a clickable link if hyperref support has been
                  enabled},
  abstract     = {The computation of ionic solvation free energies from
                  atomistic simulations is a surprisingly difficult problem that
                  has found no satisfactory solution for more than 15 years. The
                  reason is that the charging free energies evaluated from such
                  simulations are affected by very large errors. One of these is
                  related to the choice of a specific convention for summing up
                  the contributions of solvent charges to the electrostatic
                  potential in the ionic cavity, namely, on the basis of point
                  charges within entire solvent molecules (M scheme) or on the
                  basis of individual point charges (P scheme). The use of an
                  inappropriate convention may lead to a charge-independent
                  offset in the calculated potential, which depends on the
                  details of the summation scheme, on the quadrupole-moment
                  trace of the solvent molecule, and on the approximate form
                  used to represent electrostatic interactions in the
                  system. However, whether the M or P scheme (if any) represents
                  the appropriate convention is still a matter of on-going
                  debate. The goal of the present article is to settle this
                  long-standing controversy by carefully analyzing (both
                  analytically and numerically) the properties of the
                  electrostatic potential in molecular liquids (and inside
                  cavities within them).},
}

^D
---
nocite: '[@*]'
references:
- abstract: 'The computation of ionic solvation free energies from
    atomistic simulations is a surprisingly difficult problem that has
    found no satisfactory solution for more than 15 years. The reason is
    that the charging free energies evaluated from such simulations are
    affected by very large errors. One of these is related to the choice
    of a specific convention for summing up the contributions of solvent
    charges to the electrostatic potential in the ionic cavity, namely,
    on the basis of point charges within entire solvent molecules (M
    scheme) or on the basis of individual point charges (P scheme). The
    use of an inappropriate convention may lead to a charge-independent
    offset in the calculated potential, which depends on the details of
    the summation scheme, on the quadrupole-moment trace of the solvent
    molecule, and on the approximate form used to represent
    electrostatic interactions in the system. However, whether the M or
    P scheme (if any) represents the appropriate convention is still a
    matter of on-going debate. The goal of the present article is to
    settle this long-standing controversy by carefully analyzing (both
    analytically and numerically) the properties of the electrostatic
    potential in molecular liquids (and inside cavities within them).'
  annote: 'An article entry with an eid and a doi field. Note that the
    [doi]{.smallcaps} is transformed into a clickable link if hyperref
    support has been enabled'
  author:
  - family: Kastenholz
    given: M. A.
  - family: Hünenberger
    given: Philippe H.
  container-title: J. Chem. Phys.
  doi: 10.1063/1.2172593
  id: kastenholz
  issued: 2006
  language: 'en-US'
  title: 'Computation of methodology-independent ionic solvation free
    energies from molecular simulations: I. The electrostatic potential
    in molecular liquids'
  title-short: 'Computation of methodology-independent ionic solvation
    free energies from molecular simulations'
  type: 'article-journal'
  volume: 124
---