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.
2020-09-07 01:25:16 +02:00
|
|
|
|
```
|
|
|
|
|
% 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)
|
|
|
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|
|
|
|
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|
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)
|
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|
|
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|
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")
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
NOTES:
|
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|
|
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|
- 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
|
|
|
|
|
---
|
2020-10-08 08:03:14 +02:00
|
|
|
|
nocite: "[@*]"
|
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.
2020-09-07 01:25:16 +02:00
|
|
|
|
references:
|
2020-10-08 19:54:16 +02:00
|
|
|
|
- abstract: The computation of ionic solvation free energies from
|
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.
2020-09-07 01:25:16 +02:00
|
|
|
|
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
|
2020-10-08 19:54:16 +02:00
|
|
|
|
potential in molecular liquids (and inside cavities within them).
|
|
|
|
|
annote: An article entry with an eid and a doi field. Note that the
|
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.
2020-09-07 01:25:16 +02:00
|
|
|
|
[doi]{.smallcaps} is transformed into a clickable link if hyperref
|
2020-10-08 19:54:16 +02:00
|
|
|
|
support has been enabled
|
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.
2020-09-07 01:25:16 +02:00
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author:
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- family: Kastenholz
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given: M. A.
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- family: Hünenberger
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given: Philippe H.
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container-title: J. Chem. Phys.
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doi: 10.1063/1.2172593
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id: kastenholz
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issued: 2006
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2020-10-08 19:54:16 +02:00
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language: en-US
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2020-10-08 08:03:14 +02:00
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title: "Computation of methodology-independent ionic solvation free
|
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.
2020-09-07 01:25:16 +02:00
|
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|
energies from molecular simulations: I. The electrostatic potential
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2020-10-08 08:03:14 +02:00
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in molecular liquids"
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2020-10-08 19:54:16 +02:00
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title-short: Computation of methodology-independent ionic solvation
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free energies from molecular simulations
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|
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type: article-journal
|
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.
2020-09-07 01:25:16 +02:00
|
|
|
|
volume: 124
|
|
|
|
|
---
|
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|
|
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|
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|
|
|
|
|
```
|