Commits November 2010

commits@lists.einsteintoolkit.org

9 participants
258 discussions

[svn:einsteintoolkit] tools/trunk/bibtex/ (Rev. 21)
by knarf＠cct.lsu.edu 15 Nov '10

15 Nov '10

User: knarf Date: 2010/11/15 04:55 PM Modified: /trunk/bibtex/ parse_bibtex.pl Log: update script File Changes: Directory: /trunk/bibtex/ ========================= File [modified]: parse_bibtex.pl Delta lines: +38 -18 =================================================================== --- trunk/bibtex/parse_bibtex.pl 2010-11-15 18:28:39 UTC (rev 20) +++ trunk/bibtex/parse_bibtex.pl 2010-11-15 22:55:56 UTC (rev 21) @@ -4,6 +4,7 @@ use Date::Manip; use Pod::Usage; use Getopt::Long; +use Data::Dumper; =head1 NAME @@ -13,10 +14,11 @@ # parse command line options my $inputfilename = undef; -my $status_s = undef; my $keys_s = undef; my $sort = undef; my $short = undef; +my $showkey = undef; +my $filter_s = undef; my $rsort = undef; my $help = undef; @@ -28,10 +30,6 @@ Specify input file name -=item B<--status=<list>> - -Filters for given 'status' fields - =item B<--keys=<list>> Filters for keys in given list @@ -44,6 +42,14 @@ Only prints keys +=item B<--filter=<list>> + +Filter entries with define keys in list + +=item B<--showkey=<key>> + +Only print entry key and given key value + =item B<--help> Prints this help message and exits @@ -51,22 +57,21 @@ =cut GetOptions('input=s' => \$inputfilename, - 'status=s' => \$status_s, 'keys=s' => \$keys_s, 'sort' => \$sort, 'short' => \$short, + 'filter=s' => \$filter_s, + 'showkey=s' => \$showkey, 'reversesort' => \$rsort, 'help' => \$help, ) or pod2usage(-verbose=>2); -if (defined($help)) { +if (defined($help) or !defined($inputfilename)) { pod2usage(1); } if (defined($sort) and defined($rsort)) { die("The two options --sort and --reversesort cannot be used together."); } -if (!defined($inputfilename)) { $inputfilename = "references.bib"; } -print "-> $inputfilename\n"; my $infile = new Text::BibTeX::File $inputfilename; my @entries = (); @@ -78,14 +83,27 @@ push(@entries, $entry); } # filter @entries -if (defined($status_s)) { - my %status; - if ($status_s =~ /,/) { - %status = map {$_=>1} split(",", $status_s); +if (defined($filter_s)) { + my %filter; + my @new_entries = (); + if ($filter_s =~ /,/) { + %filter = map {$_=~/([^=]*)=*(.*)/; $1=>$2} split(",", $filter_s); } else { - %status = map {$_=>1} split(" ", $status_s); + %filter = map {$_=~/([^=]*)=*(.*)/; $1=>$2} split(" ", $filter_s); } - @entries = grep {$status{$_->get('status')}} @entries; + #@entries = grep {$filter{$_->get('status')}} @entries; + # go through each specified filter key + foreach my $one_filter (keys(%filter)) { + # check if the key needs to be present or also have a certain value + if ($filter{$one_filter}) { + # only include entries with the key present and the value identical + @new_entries = (@new_entries, grep {$_->get($one_filter)eq$filter{$one_filter}} @entries); + } else { + # include entries which have the specified filter key present + @new_entries = (@new_entries, grep {$_->get($one_filter)} @entries); + } + } + @entries = @new_entries; } if (defined($keys_s)) { my %keys; @@ -105,10 +123,12 @@ } # generate output foreach my $entry (@entries) { - if (!defined($short)) { + if (defined($short)) { + $out .= $entry->key()."\n"; + } elsif (defined($showkey)) { + $out .= $entry->key()." ".$entry->get($showkey)."\n"; + } else { $out .= $entry->print_s(); - } else { - $out .= $entry->key()."\n"; } } print $out;

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[svn:einsteintoolkit] www/global/ (Rev. 407)
by bcmsma＠astro.rit.edu 15 Nov '10

15 Nov '10

User: bmundim Date: 2010/11/15 03:05 PM Modified: /global/ navigation.php Log: Reorder navigation menu and add citation link there. File Changes: Directory: /global/ =================== File [modified]: navigation.php Delta lines: +9 -8 =================================================================== --- global/navigation.php 2010-11-15 21:03:09 UTC (rev 406) +++ global/navigation.php 2010-11-15 21:05:46 UTC (rev 407) @@ -10,6 +10,15 @@ <li><a href="/about/governance/">Governance</a></li> </ul></li> +<li><a href="/toolkit/">Einstein Toolkit</a> +<ul class="subnav"> + <li><a href="/toolkit/releases">Releases</a></li> + <li><a href="/toolkit/capabilities/">Capabilities</a></li> + <li><a href="/toolkit/community/">Mail Lists</a></li> + <li><a href="/info/contribute/">Contribute</a></li> + <li><a href="/info/citing/">Cite</a></li> +</ul></li> + <li><a href="/info/">Using the Toolkit</a> <ul class="subnav"> <li><a href="/info/documentation/">Documentation</a></li> @@ -18,14 +27,6 @@ <li><a href="/info/tools/">Tools</a></li> </ul></li> -<li><a href="/toolkit/">Einstein Toolkit</a> -<ul class="subnav"> - <li><a href="/toolkit/releases">Releases</a></li> - <li><a href="/toolkit/capabilities/">Capabilities</a></li> - <li><a href="/toolkit/community/">Mail Lists</a></li> - <li><a href="/info/contribute/">Contribute</a></li> -</ul></li> - <!--<li><a href="/science/">Science Outputs</a> <ul class="subnav"> <li><a href="/science/grants/">Grants</a></li>

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[svn:einsteintoolkit] www/info/ (Rev. 406)
by bcmsma＠astro.rit.edu 15 Nov '10

15 Nov '10

User: bmundim Date: 2010/11/15 03:03 PM Added: /info/citing/ index.php Removed: /info/ citation.php Modified: /info/ index.php Log: Create www/info/citing, mv info/citation.php info/citing/index.php and fix linking to the new page location. File Changes: Directory: /info/citing/ ======================== File [added]: index.php Delta lines: +50 -0 =================================================================== --- info/citing/index.php (rev 0) +++ info/citing/index.php 2010-11-15 21:03:09 UTC (rev 406) @@ -0,0 +1,50 @@ +<?php $title='Citation Guidelines'; +include_once($_SERVER['DOCUMENT_ROOT'].'/global/header.php');?> + +The development of production level scientific software, such +as the components of the Einstein Toolkit, represents the academic +output of researchers who bring together skills in formulations, +algorithms and software engineering as well as substantial domain +knowledge. The scientific contributions of such researchers should be +acknowledged and respected on a par with those whose expertise lie solely in +theory or experiment. Further, most contributions to the Einstein +Toolkit have been provided by early stage researchers --- graduate +students, postdocs and young assistant professors, where proper +and appropriate citation of their contributions is crucial for +furthering academic careers. + +The current guidelines for citation of the Einstein Toolkit are: + +<ol> +<li> Authors are requested to cite the Einstein Toolkit web page (http://www.einsteintoolkit.org) in publications using results or software obtained from the +toolkit. + +<li> Authors are requested to individually cite publications for +identified key software components from the toolkit that are used to +obtain published results. These publications include, for example, details +of the equations, algorithms, and verification of components. +A list of components for which this applies is provided below. + +<li> Authors should consult the full publication page for the + Einstein Toolkit (not yet in place) to determine if in their judgement it would be +appropriate to provide citations for additional components than +described in 1) and 2). + +</ol> + + +<h2>Citations for Key Toolkit Components</h2> + +Authors whose published work is derived from results obtained using the Einstein Toolkit are requested to individually cite publications for +identified key software components used to obtain those results. These publications, that are listed below, include details of e.g. the equations, algorithm, + and verification of components. Obviously, citations should only be given for components that were actually used. + + +<?php +exec('../../bibtex/bib2xhtml -u -s unsortlist ../../manifest/einsteintoolkit.bib | perl -e \'my $a=join("",<stdin>); $a=~s/.*().*/$1/s; print $a;\'', $output); +foreach ($output as $line) { + echo $line."\n"; +} +?> + +<?php include_once($_SERVER['DOCUMENT_ROOT'].'/global/footer.php');?> Directory: /info/ ================= File [removed]: citation.php Delta lines: +0 -50 =================================================================== --- info/citation.php 2010-11-15 18:24:45 UTC (rev 405) +++ info/citation.php 2010-11-15 21:03:09 UTC (rev 406) @@ -1,50 +0,0 @@ -<?php $title='Citation Guidelines'; -include_once($_SERVER['DOCUMENT_ROOT'].'/global/header.php');?> - -The development of production level scientific software, such -as the components of the Einstein Toolkit, represents the academic -output of researchers who bring together skills in formulations, -algorithms and software engineering as well as substantial domain -knowledge. The scientific contributions of such researchers should be -acknowledged and respected on a par with those whose expertise lie solely in -theory or experiment. Further, most contributions to the Einstein -Toolkit have been provided by early stage researchers --- graduate -students, postdocs and young assistant professors, where proper -and appropriate citation of their contributions is crucial for -furthering academic careers. - -The current guidelines for citation of the Einstein Toolkit are: - -<ol> -<li> Authors are requested to cite the Einstein Toolkit web page (http://www.einsteintoolkit.org) in publications using results or software obtained from the -toolkit. - -<li> Authors are requested to individually cite publications for -identified key software components from the toolkit that are used to -obtain published results. These publications include, for example, details -of the equations, algorithms, and verification of components. -A list of components for which this applies is provided below. - -<li> Authors should consult the full publication page for the - Einstein Toolkit (not yet in place) to determine if in their judgement it would be -appropriate to provide citations for additional components than -described in 1) and 2). - -</ol> - - -<h2>Citations for Key Toolkit Components</h2> - -Authors whose published work is derived from results obtained using the Einstein Toolkit are requested to individually cite publications for -identified key software components used to obtain those results. These publications, that are listed below, include details of e.g. the equations, algorithm, - and verification of components. Obviously, citations should only be given for components that were actually used. - - -<?php -exec('../bibtex/bib2xhtml -u -s unsortlist ../manifest/einsteintoolkit.bib | perl -e \'my $a=join("",<stdin>); $a=~s/.*().*/$1/s; print $a;\'', $output); -foreach ($output as $line) { - echo $line."\n"; -} -?> - -<?php include_once($_SERVER['DOCUMENT_ROOT'].'/global/footer.php');?> File [modified]: index.php Delta lines: +1 -1 =================================================================== --- info/index.php 2010-11-15 18:24:45 UTC (rev 405) +++ info/index.php 2010-11-15 21:03:09 UTC (rev 406) @@ -34,7 +34,7 @@ -- "documentation" folder; I think it is easier to find there --> Cite the tools you use: the scientific contributions of the work represented in the toolkit - should be cited in a similar way to regular publications, please respect this request and <a href="citation.php">cite + should be cited in a similar way to regular publications, please respect this request and <a href="citing/index.php">cite appropriately following the Consortium's guidelines.</a>

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[svn:einsteintoolkit] Multipole/trunk/test/ (Rev. 69)
by ian.hinder＠aei.mpg.de 15 Nov '10

15 Nov '10

User: hinder Date: 2010/11/15 02:44 PM Modified: /trunk/test/ test_22.par, test_31.par, test_44.par, test_rads.par, test_simpson.par, test_vars.par Log: Use 3 ghost zones instead of 2 in the test suites, as required by Hermite interpolator Tests should now pass on >= 16 processes where they failed before. File Changes: Directory: /trunk/test/ ======================= File [modified]: test_22.par Delta lines: +1 -1 =================================================================== --- trunk/test/test_22.par 2010-11-15 20:42:48 UTC (rev 68) +++ trunk/test/test_22.par 2010-11-15 20:44:17 UTC (rev 69) @@ -36,7 +36,7 @@ # Carpet ############################################################# -Carpet::ghost_size = 2 +Carpet::ghost_size = 3 Carpet::domain_from_coordbase = "yes" Carpet::poison_new_timelevels = "yes" Carpet::check_for_poison = "no" File [modified]: test_31.par Delta lines: +1 -1 =================================================================== --- trunk/test/test_31.par 2010-11-15 20:42:48 UTC (rev 68) +++ trunk/test/test_31.par 2010-11-15 20:44:17 UTC (rev 69) @@ -36,7 +36,7 @@ # Carpet ############################################################# -Carpet::ghost_size = 2 +Carpet::ghost_size = 3 Carpet::domain_from_coordbase = "yes" Carpet::poison_new_timelevels = "yes" Carpet::check_for_poison = "no" File [modified]: test_44.par Delta lines: +1 -1 =================================================================== --- trunk/test/test_44.par 2010-11-15 20:42:48 UTC (rev 68) +++ trunk/test/test_44.par 2010-11-15 20:44:17 UTC (rev 69) @@ -36,7 +36,7 @@ # Carpet ############################################################# -Carpet::ghost_size = 2 +Carpet::ghost_size = 3 Carpet::domain_from_coordbase = "yes" Carpet::poison_new_timelevels = "yes" Carpet::check_for_poison = "no" File [modified]: test_rads.par Delta lines: +1 -1 =================================================================== --- trunk/test/test_rads.par 2010-11-15 20:42:48 UTC (rev 68) +++ trunk/test/test_rads.par 2010-11-15 20:44:17 UTC (rev 69) @@ -36,7 +36,7 @@ # Carpet ############################################################# -Carpet::ghost_size = 2 +Carpet::ghost_size = 3 Carpet::domain_from_coordbase = "yes" Carpet::poison_new_timelevels = "yes" Carpet::check_for_poison = "no" File [modified]: test_simpson.par Delta lines: +1 -1 =================================================================== --- trunk/test/test_simpson.par 2010-11-15 20:42:48 UTC (rev 68) +++ trunk/test/test_simpson.par 2010-11-15 20:44:17 UTC (rev 69) @@ -36,7 +36,7 @@ # Carpet ############################################################# -Carpet::ghost_size = 2 +Carpet::ghost_size = 3 Carpet::domain_from_coordbase = "yes" Carpet::poison_new_timelevels = "yes" Carpet::check_for_poison = "no" File [modified]: test_vars.par Delta lines: +1 -1 =================================================================== --- trunk/test/test_vars.par 2010-11-15 20:42:48 UTC (rev 68) +++ trunk/test/test_vars.par 2010-11-15 20:44:17 UTC (rev 69) @@ -36,7 +36,7 @@ # Carpet ############################################################# -Carpet::ghost_size = 2 +Carpet::ghost_size = 3 Carpet::domain_from_coordbase = "yes" Carpet::poison_new_timelevels = "yes" Carpet::check_for_poison = "no"

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[svn:einsteintoolkit] Multipole/trunk/ (Rev. 68)
by ian.hinder＠aei.mpg.de 15 Nov '10

15 Nov '10

User: hinder Date: 2010/11/15 02:42 PM Modified: /trunk/ param.ccl Log: Change default interpolator parameters to disable off-centering of stencil AEILocalInterp by default will off-centre the interpolation stencil if there are insufficient points to perform the interpolation. In a parallel setting, this could happen due to there being insufficient ghost points for the interpolator chosen. The off-centering leads to an interpolation error which is of the correct order but larger than for a centered stencil. More importantly, it leads to different results on different numbers of processes. With this commit, Multipole will (by default) disable off-centering in the interpolator. File Changes: Directory: /trunk/ ================== File [modified]: param.ccl Delta lines: +7 -1 =================================================================== --- trunk/param.ccl 2010-11-04 16:42:55 UTC (rev 67) +++ trunk/param.ccl 2010-11-15 20:42:48 UTC (rev 68) @@ -10,8 +10,14 @@ CCTK_STRING interpolator_pars "Parameters for the interpolator" { ".*" :: "Any string that Util_TableSetFromString() will take" -} "order=3" +} "order=3 boundary_off_centering_tolerance={0.0 0.0 0.0 0.0 0.0 0.0} boundary_extrapolation_tolerance={0.0 0.0 0.0 0.0 0.0 0.0}" +# The above makes sure that the interpolator doesn't off-centre the +# interpolation stencil if there are insufficient points to +# interpolate, which can happen if there are insufficient ghost-zones +# for the interpolation method used, and can lead to processor-number +# dependent results. + CCTK_STRING coord_system "What is the coord system?" { ".*" :: "Any smart string will do"

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[svn:einsteintoolkit] manifest/trunk/ (Rev. 46)
by knarf＠cct.lsu.edu 15 Nov '10

15 Nov '10

User: knarf Date: 2010/11/15 12:31 PM Modified: /trunk/ einsteintoolkit.bib Log: fix umlaut File Changes: Directory: /trunk/ ================== File [modified]: einsteintoolkit.bib Delta lines: +1 -1 =================================================================== --- trunk/einsteintoolkit.bib 2010-11-15 17:49:27 UTC (rev 45) +++ trunk/einsteintoolkit.bib 2010-11-15 18:31:34 UTC (rev 46) @@ -209,7 +209,7 @@ @Article{Hawke:2005zw, suggested-for ="EinsteinEvolve/GRHydro", - author = "Hawke, Ian and Loffler, Frank and Nerozzi, Andrea", + author = "Hawke, Ian and L{\"o}ffler, Frank and Nerozzi, Andrea", title = "{Excision methods for high resolution shock capturing schemes applied to general relativistic hydrodynamics}",

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[svn:einsteintoolkit] tools/trunk/bibtex/bib2xhtml-2.31/ (Rev. 20)
by knarf＠cct.lsu.edu 15 Nov '10

15 Nov '10

User: knarf Date: 2010/11/15 12:28 PM Added: /trunk/bibtex/bib2xhtml-2.31/ COPYING, ChangeLog, Makefile, README, bib2xhtml, bib2xhtml.html, bib2xhtml.man, bib2xhtml.pdf, bib2xhtml.txt, bibsearch, ex-alpha-c-u.html, ex-alpha-c.html, ex-alpha-cr-u.html, ex-alpha-cr.html, ex-alpha-k.html, ex-alpha-r-u.html, ex-alpha-r.html, ex-alpha-u-k.html, ex-alpha-u.html, ex-alpha.html, ex-empty-c-u.html, ex-empty-c.html, ex-empty-cr-u.html, ex-empty-cr.html, ex-empty-r-u.html, ex-empty-r.html, ex-empty-u.html, ex-empty.html, ex-named-c-u.html, ex-named-c.html, ex-named-cr-u.html, ex-named-cr.html, ex-named-k.html, ex-named-r-u.html, ex-named-r.html, ex-named-u-k.html, ex-named-u.html, ex-named.html, ex-paragraph-c-u.html, ex-paragraph-c.html, ex-paragraph-cr-u.html, ex-paragraph-cr.html, ex-paragraph-k.html, ex-paragraph-r-u.html, ex-paragraph-r.html, ex-paragraph-u-k.html, ex-paragraph-u.html, ex-paragraph.html, ex-plain-c-u.html, ex-plain-c.html, ex-plain-cr-u.html, ex-plain-cr.html, ex-plain-k.html, ex-plain-r-u.html, ex-plain-r.html, ex-plain-u-k.html, ex-plain-u.html, ex-plain.html, ex-unsort-k.html, ex-unsort-u-k.html, ex-unsort-u.html, ex-unsort.html, ex-unsortlist-u.html, ex-unsortlist.html, example.bib, gen-bst, html-a.bst, html-aa.bst, html-ac.bst, html-aca.bst, html-acr.bst, html-acra.bst, html-ar.bst, html-ara.bst, html-btxbst.doc, html-n.bst, html-na.bst, html-nc.bst, html-nca.bst, html-ncr.bst, html-ncra.bst, html-nr.bst, html-nra.bst, html-u.bst, html-ua.bst, index.html Log: include all files File Changes: Directory: /trunk/bibtex/bib2xhtml-2.31/ ======================================== File [added]: COPYING Delta lines: <Unavailable> File [added]: ChangeLog Delta lines: <Unavailable> File [added]: Makefile Delta lines: <Unavailable> File [added]: README Delta lines: <Unavailable> File [added]: bib2xhtml Delta lines: <Unavailable> File [added]: bib2xhtml.html Delta lines: <Unavailable> File [added]: bib2xhtml.man Delta lines: <Unavailable> File 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[svn:einsteintoolkit] tools/trunk/bibtex/ (Rev. 19)
by knarf＠cct.lsu.edu 15 Nov '10

15 Nov '10

User: knarf Date: 2010/11/15 12:28 PM Added: /trunk/bibtex/ bib2xhtml Removed: /trunk/bibtex/ bib2xhtml Log: include all files File Changes: Directory: /trunk/bibtex/ ========================= File [removed]: bib2xhtml Delta lines: <Unavailable> File [added]: bib2xhtml Delta lines: <Unavailable>

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[svn:einsteintoolkit] www/info/ (Rev. 405)
by knarf＠cct.lsu.edu 15 Nov '10

15 Nov '10

User: knarf Date: 2010/11/15 12:24 PM Modified: /info/ citation.php Log: correct php File Changes: Directory: /info/ ================= File [modified]: citation.php Delta lines: +2 -5 =================================================================== --- info/citation.php 2010-11-15 18:19:54 UTC (rev 404) +++ info/citation.php 2010-11-15 18:24:45 UTC (rev 405) @@ -40,11 +40,8 @@ and verification of components. Obviously, citations should only be given for components that were actually used. -<?php> -exec('../bibtex/bib2xhtml -u -s unsortlist ../manifest/einsteintoolkit.bib | ' - 'perl -e \'my $a=join("",<stdin>); $a=~s/.*().*/$1/s; print $a;\'', - $output); +<?php +exec('../bibtex/bib2xhtml -u -s unsortlist ../manifest/einsteintoolkit.bib | perl -e \'my $a=join("",<stdin>); $a=~s/.*().*/$1/s; print $a;\'', $output); foreach ($output as $line) { echo $line."\n"; }

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[svn:einsteintoolkit] www/ (Rev. 404)
by knarf＠cct.lsu.edu 15 Nov '10

15 Nov '10

User: knarf Date: 2010/11/15 12:19 PM Modified: / /info/ citation.php Log: first try on automatic html citations Directory Changes: Directory: / ============ Property changes on: ___________________________________________________________________ Directory: /svn:externals/ ========================== + bibtex https://svn.einsteintoolkit.org/tools/trunk/bibtex manifest https://svn.einsteintoolkit.org/manifest/trunk File Changes: Directory: /info/ ================= File [modified]: citation.php Delta lines: +9 -1 =================================================================== --- info/citation.php 2010-11-15 04:22:41 UTC (rev 403) +++ info/citation.php 2010-11-15 18:19:54 UTC (rev 404) @@ -40,6 +40,14 @@ and verification of components. Obviously, citations should only be given for components that were actually used. -LIST TO BE PROVIDED +<?php> +exec('../bibtex/bib2xhtml -u -s unsortlist ../manifest/einsteintoolkit.bib | ' + 'perl -e \'my $a=join("",<stdin>); $a=~s/.*().*/$1/s; print $a;\'', + $output); +foreach ($output as $line) { + echo $line."\n"; +} +?> <?php include_once($_SERVER['DOCUMENT_ROOT'].'/global/footer.php');?>

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Commits November 2010