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more precise tags, added problematic tag to tests

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This commit is contained in:
Guilhem Fauré 2023-05-09 14:37:30 +02:00
parent aa046aa45c
commit c5c04cc645
3 changed files with 22 additions and 11 deletions
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23
spip2md/spip.lark
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@ -37,8 +37,8 @@ _block_tag: pair_block_tag
pair_block_tag: _PAIR_TAG_ANGLE TAG_NAME ( _OPTION_SEP TAG_OPTION )* ">" start "</" _PURE_TEXT ">" -> tag pair_block_tag: _PAIR_TAG_ANGLE TAG_NAME ( _OPTION_SEP TAG_OPTION )* ">" start "</" _PURE_TEXT ">" -> tag
orphan_block_tag: _ORPHAN_TAG_ANGLE "/"? TAG_NAME ( _OPTION_SEP TAG_OPTION )* ">" -> orphan_tag orphan_block_tag: _ORPHAN_TAG_ANGLE "/"? TAG_NAME ( _OPTION_SEP TAG_OPTION )* ">" -> orphan_tag
_PAIR_TAG_ANGLE: /<(?=([0-9A-Za-z_:|,=\/\-\. ]+)>\r?\n[\s\S]+<\/\1>)/ _PAIR_TAG_ANGLE: /<(?=([0-9A-Za-z]+)[0-9A-Za-z_:|,="\/\-\. ]*>\r?\n[\s\S]+<\/\1>)/
_ORPHAN_TAG_ANGLE: /<(?=([0-9A-Za-z_:|,=\/\-\. ])+>\r?\n)(?![\s\S]+\<\/\1\>)/ _ORPHAN_TAG_ANGLE: /<(?=([0-9A-Za-z]+)[0-9A-Za-z_:|,="\/\-\. ]*>\r?\n)(?![\s\S]+\<\/\1\>)/
paragraph{begin, text}: _inline{begin} _N? ( _inline{text} _N? )* paragraph{begin, text}: _inline{begin} _N? ( _inline{text} _N? )*
@ -49,13 +49,16 @@ _inline{text}: _inline_tag
| text | text
_inline_tag: pair_inline_tag _inline_tag: pair_inline_tag
| short_inline_tag
| orphan_inline_tag | orphan_inline_tag
pair_inline_tag: _PAIR_INLINE_TAG_ANGLE TAG_NAME ( _OPTION_SEP TAG_OPTION )* ">" _N? paragraph{TEXT, TEXT} ( "</" _PURE_TEXT ">" | _N )? -> tag pair_inline_tag: _INLINE_TAG_ANGLE TAG_NAME ( _OPTION_SEP TAG_OPTION )* ">" _N? paragraph{TEXT, TEXT} "</" _PURE_TEXT ">" -> tag
orphan_inline_tag: _INLINE_TAG_ANGLE TAG_NAME ( _OPTION_SEP TAG_OPTION )* ">" -> orphan_tag short_inline_tag: _SHORT_INLINE_TAG_ANGLE TAG_NAME ( _OPTION_SEP TAG_OPTION )* ">" _N? paragraph{TEXT, TEXT} -> tag
orphan_inline_tag: _ORPHAN_INLINE_TAG_ANGLE TAG_NAME ( _OPTION_SEP TAG_OPTION )* ">" -> orphan_tag
_PAIR_INLINE_TAG_ANGLE: /<(?!\/|img|emb|doc)(?=[0-9A-Za-z_:,=\/\.\|\- ]*>)/i _INLINE_TAG_ANGLE: /<(?=([0-9A-Za-z]+)[0-9A-Za-z_:|,="\/\-\. ]*>[\s\S]+<\/\1>)/
_INLINE_TAG_ANGLE: /<\/?(?=(?:img|emb|doc)[0-9A-Za-z\|_:,=\/\.\|\- ]+>)/i _SHORT_INLINE_TAG_ANGLE: /<(?=([0-9A-Za-z]+)[0-9A-Za-z_:,="\/\.\|\- ]*>)(?!\/|img|emb|doc|[\s\S]+<\/\1>)/i
_ORPHAN_INLINE_TAG_ANGLE: /<(?=(img|emb|doc)[0-9A-Za-z\|_:,="\/\.\|\- ]*>)/i
_link: footnote _link: footnote
| wikilink | wikilink
@ -71,10 +74,10 @@ FOOTNOTE_CONTENT: /[0-9A-Za-z_:\/\-\.\ ]+/
HREF: _PURE_TEXT | _PLACEHOLDER HREF: _PURE_TEXT | _PLACEHOLDER
A_TEXT: /[^\r\n\{]+?(?=->)/ A_TEXT: /[^\r\n\{]+?(?=->)/
strong: _B ( _inline{MARKED_TEXT} )+ ( "}}" | _N ) strong: _STRONG ( _inline{MARKED_TEXT} )+ ( "}}" | _N )
emphasis: _I ( _inline{MARKED_TEXT} )+ ( "}" | _N ) emphasis: _EM ( _inline{MARKED_TEXT} )+ ( "}" | _N )
_B: /{{(?=[^\{])/ _STRONG: /{{(?=[^\{])/
_I: /{(?=[^\{])/ _EM: /{(?=[^\{])/
PARAGRAPH_TEXT: / [^\r\n|\-{<] PARAGRAPH_TEXT: / [^\r\n|\-{<]
(?:[^\r\n{<](?! (?:[^\r\n{<](?!

2
test/0.spip
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@ -56,7 +56,7 @@ Culpa proident adipisicing id {nulla} nisi laboris ex in Lorem sunt duis officia
{{{Un bout de {{poesie}}}}} {{{Un bout de {{poesie}}}}}
<poesie> <poesie>
Lorem ipsum dolor sit amet, officia excepteur ex fugiat reprehenderit enim labore culpa sint ad nisi Lorem pariatur mollit ex esse exercitation amet. Nisi anim cupidatat excepteur officia. Reprehenderit nostrud nostrud ipsum Lorem est aliquip amet voluptate voluptate dolor minim nulla est proident. Nostrud officia pariatur ut officia. Sit irure elit esse ea nulla sunt ex occaecat reprehenderit commodo officia dolor Lorem duis laboris cupidatat officia voluptate.<imageAuMilieuPoesie> Culpa proident adipisicing id nulla nisi laboris ex in Lorem sunt duis officia eiusmod. Aliqua reprehenderit commodo ex non excepteur duis sunt velit enim. Voluptate laboris sint cupidatat ullamco ut ea consectetur et est culpa et culpa duis. Lorem ipsum dolor sit amet, officia excepteur ex fugiat reprehenderit enim labore culpa sint ad nisi Lorem pariatur mollit ex esse exercitation amet. Nisi anim cupidatat excepteur officia. Reprehenderit nostrud nostrud ipsum Lorem est aliquip amet voluptate voluptate dolor minim nulla est proident. Nostrud officia pariatur ut officia. Sit irure elit esse ea nulla sunt ex occaecat reprehenderit commodo officia dolor Lorem duis laboris cupidatat officia voluptate.<img4523> Culpa proident adipisicing id nulla nisi laboris ex in Lorem sunt duis officia eiusmod. Aliqua reprehenderit commodo ex non excepteur duis sunt velit enim. Voluptate laboris sint cupidatat ullamco ut ea consectetur et est culpa et culpa duis.
</poesie> </poesie>
{{{Cadre de code}}} {{{Cadre de code}}}

8
test/1.spip
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@ -85,6 +85,14 @@ Other collaborations :
* {{Water clusters embedded in an argon matrix : a DFTB/Force Field Study}}. Finite-temperature infrared spectra of water clusters - described at the SCC-DFTB level - embedded in an argon 'super-cluster' - described with a force field ( FF)- are determined and compared with experimental data. * {{Water clusters embedded in an argon matrix : a DFTB/Force Field Study}}. Finite-temperature infrared spectra of water clusters - described at the SCC-DFTB level - embedded in an argon 'super-cluster' - described with a force field ( FF)- are determined and compared with experimental data.
----
{{{Un paragraphe justifié}}}
<p align="justify">Anthony Scemama, l'un des deux coordinateurs du CNRS pour le centre d'excellence européen H2020 [T.REX->https://trex-coe.eu/], répond aux questions de "CNRS Le Journal" sur la révolution exascale des supercalculateurs.</p>
[Lien vers l'article->https://lejournal.cnrs.fr/articles/revolution-en-vue-pour-percer-les-secrets-de-la-matiere]
from {{ A. Simon, C. Iftner, J. Mascetti, F. Spiegelman ’Water clusters in an argon matrix : infrared spectra from molecular dynamics simulations with a self-consistent charge density functional based tight binding/force field potential’ J. Phys. Chem. A 2015, 119, 2449-2467 (DOI : 10.1021/jp508533k)}} from {{ A. Simon, C. Iftner, J. Mascetti, F. Spiegelman ’Water clusters in an argon matrix : infrared spectra from molecular dynamics simulations with a self-consistent charge density functional based tight binding/force field potential’ J. Phys. Chem. A 2015, 119, 2449-2467 (DOI : 10.1021/jp508533k)}}
ABSTRACT: The present theoretical study aims at investigating the effects of an argon matrix on the structures, energetics, dynamics, and infrared (IR) spectra of small water clusters (H2O)n (n = 1−6). The potential energy surface is obtained from a hybrid selfconsistent charge density functional-based tight binding/force-field approach (SCCDFTB/FF) in which the water clusters are treated at the SCC-DFTB level and the matrix is modeled at the FF level by a cluster consisting of ∼340 Ar atoms with a face centered cubic (fcc) structure, namely (H2O)n/Ar. With respect to a pure FF scheme, this allows a quantum description of the molecular system embedded in the matrix, along with all-atom geometry optimization and molecular dynamics (MD) simulations of the (H2O)n/Ar system. Finite-temperature IR spectra are derived from the MD simulations. The SCC-DFTB/FF scheme is first benchmarked on (H2O)Arn clusters against correlated wave function results and DFT calculations performed in the present work, and against FF data available in the literature. Regarding (H2O)n/Ar systems, the geometries of the water clusters are found to adapt to the fcc environment, possibly leading to intermolecular distortion and matrix perturbation. Several energetical quantities are estimated to characterize the water clusters in the matrix. In the particular case of the water hexamer, substitution and insertion energies for the prism, bag, and cage are found to be lower than that for the 6-member ring isomer. Finite-temperature MD simulations show that the water monomer has a quasifree rotation motion at 13 K, in agreement with experimental data. In the case of the water dimer, the only large-amplitude motion is a distortion−rotation intermolecular motion, whereas only vibration motions around the nuclei equilibrium positions are observed for clusters with larger sizes. Regarding the IR spectra, we find that the matrix environment leads to redshifts of the stretching modes and almost no shift of the bending modes. This is in agreement with experimental data. Furthermore, in the case of the water monomer and dimer, the magnitudes of the computed shifts are in fair agreement with the experimental values. The complex case of the water hexamer, which presents several low-energy isomers, is discussed. ABSTRACT: The present theoretical study aims at investigating the effects of an argon matrix on the structures, energetics, dynamics, and infrared (IR) spectra of small water clusters (H2O)n (n = 1−6). The potential energy surface is obtained from a hybrid selfconsistent charge density functional-based tight binding/force-field approach (SCCDFTB/FF) in which the water clusters are treated at the SCC-DFTB level and the matrix is modeled at the FF level by a cluster consisting of ∼340 Ar atoms with a face centered cubic (fcc) structure, namely (H2O)n/Ar. With respect to a pure FF scheme, this allows a quantum description of the molecular system embedded in the matrix, along with all-atom geometry optimization and molecular dynamics (MD) simulations of the (H2O)n/Ar system. Finite-temperature IR spectra are derived from the MD simulations. The SCC-DFTB/FF scheme is first benchmarked on (H2O)Arn clusters against correlated wave function results and DFT calculations performed in the present work, and against FF data available in the literature. Regarding (H2O)n/Ar systems, the geometries of the water clusters are found to adapt to the fcc environment, possibly leading to intermolecular distortion and matrix perturbation. Several energetical quantities are estimated to characterize the water clusters in the matrix. In the particular case of the water hexamer, substitution and insertion energies for the prism, bag, and cage are found to be lower than that for the 6-member ring isomer. Finite-temperature MD simulations show that the water monomer has a quasifree rotation motion at 13 K, in agreement with experimental data. In the case of the water dimer, the only large-amplitude motion is a distortion−rotation intermolecular motion, whereas only vibration motions around the nuclei equilibrium positions are observed for clusters with larger sizes. Regarding the IR spectra, we find that the matrix environment leads to redshifts of the stretching modes and almost no shift of the bending modes. This is in agreement with experimental data. Furthermore, in the case of the water monomer and dimer, the magnitudes of the computed shifts are in fair agreement with the experimental values. The complex case of the water hexamer, which presents several low-energy isomers, is discussed.