[Yt-svn] yt: 3 new changesets
hg at spacepope.org
hg at spacepope.org
Tue Aug 10 13:44:12 PDT 2010
hg Repository: yt
details: yt/rev/361f4a811fbb
changeset: 1928:361f4a811fbb
user: Matthew Turk <matthewturk at gmail.com>
date:
Tue Aug 10 13:41:51 2010 -0700
description:
Adding Oliver Hahn's RamsesRead++ header files.
hg Repository: yt
details: yt/rev/6a37e518cb80
changeset: 1929:6a37e518cb80
user: Matthew Turk <matthewturk at gmail.com>
date:
Tue Aug 10 13:42:41 2010 -0700
description:
Merging in the (still incomplete) Ramses and Gadget readers from me and Chris
Moody, respectively. This includes Oliver Hahn's RamsesRead++ library, as
noted in the appropriate README file.
hg Repository: yt
details: yt/rev/3b7f2528e9b8
changeset: 1930:3b7f2528e9b8
user: Matthew Turk <matthewturk at gmail.com>
date:
Tue Aug 10 13:44:09 2010 -0700
description:
Updating CREDITS file
diffstat:
CREDITS | 7 +-
yt/ramses_headers/FortranUnformatted_IO.hh | 291 ++++++++++
yt/ramses_headers/RAMSES_amr_data.hh | 970 ++++++++++++++++++++++++++++++++++
yt/ramses_headers/RAMSES_hydro_data.hh | 666 +++++++++++++++++++++++
yt/ramses_headers/RAMSES_info.hh | 334 +++++++++++
yt/ramses_headers/RAMSES_particle_data.hh | 650 +++++++++++++++++++++++
yt/ramses_headers/RAMSES_poisson_data.hh | 249 ++++++++
yt/ramses_headers/RAMSES_typedefs.h | 21 +
yt/ramses_headers/README | 9 +
yt/ramses_headers/data_iterators.hh | 74 ++
yt/setup.py | 8 +-
11 files changed, 3273 insertions(+), 6 deletions(-)
diffs (truncated from 3338 to 300 lines):
diff -r f5cadbe92674 -r 3b7f2528e9b8 CREDITS
--- a/CREDITS Tue Aug 10 12:28:51 2010 -0700
+++ b/CREDITS Tue Aug 10 13:44:09 2010 -0700
@@ -8,10 +8,15 @@
Devin Silvia (devin.silvia at gmail.com)
John Wise (jwise at astro.princeton.edu)
David Collins (dcollins at physics.ucsd.edu)
+ Christopher Moody (cemoody at ucsc.edu)
+ Oliver Hahn (ohahn at stanford.edu)
+ John ZuHone (jzuhone at cfa.harvard.edu)
We also include the Delaunay Triangulation module written by Robert Kern of
Enthought, the cmdln.py module by Trent Mick, and the progressbar module by
Nilton Volpato. The PasteBin interface code (as well as the PasteBin itself)
-was written by the Pocoo collective (pocoo.org).
+was written by the Pocoo collective (pocoo.org). The RamsesRead++ library was
+developed by Oliver Hahn. Large parts of this code were guided by discussions
+with Tom Abel, Ralf Kaehler, Mike Norman and Greg Bryan.
Thanks to everyone for all your contributions!
diff -r f5cadbe92674 -r 3b7f2528e9b8 yt/ramses_headers/FortranUnformatted_IO.hh
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/yt/ramses_headers/FortranUnformatted_IO.hh Tue Aug 10 13:44:09 2010 -0700
@@ -0,0 +1,291 @@
+/*
+ FortranUnformatted_IO.hh
+ This file contains a C++ class for access to FORTRAN unformatted files
+
+ Copyright (C) 2008 Oliver Hahn, ojha at gmx.de
+
+ It is free software: you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ Foobar is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with Foobar. If not, see <http://www.gnu.org/licenses/>.
+*/
+
+#ifndef __FORTRAN_UNFORMATTED_HH
+#define __FORTRAN_UNFORMATTED_HH
+
+#include <fstream>
+#include <iostream>
+#include <iomanip>
+#include <vector>
+#include <stdexcept>
+#include <iterator>
+
+#define DEFAULT_ADDLEN 4
+
+//! A class to perform IO on FORTRAN unformatted files
+/*! FortranUnformatted provides sequential read access to FORTRAN
+ unformatted files.
+ */
+class FortranUnformatted{
+
+protected:
+ std::string m_filename; //!< the file name
+ std::fstream m_ifs; //!< STL ifstream object
+ int m_addlen; //!< number of bytes in pre-/suffix data of FORTRAN unformatted data
+
+public:
+
+ //! constructor for FortranUnformatted
+ /*! simple constructor for FortranUnformatted
+ * @param filename the name of the FORTRAN unformatted file to be opened for IO
+ * @param mode a combination of std::ios_base::openmode determining the mode in which the files are openend
+ * @param addlen the number of bytes which are pre- & postpended to unformatted arrays giving their size (default=4)
+ */
+ explicit FortranUnformatted( std::string filename, std::ios_base::openmode mode = std::ios_base::in, int addlen=DEFAULT_ADDLEN )
+ : m_filename( filename ),
+ m_ifs( m_filename.c_str(), mode|std::ios::binary ),
+ m_addlen( addlen )
+ {
+ if(!m_ifs.good() || !m_ifs.is_open() )
+ throw std::runtime_error("FortranUnformatted : unable to open file \'"
+ +m_filename+"\'for read access");
+ m_ifs.exceptions ( std::fstream::eofbit | std::fstream::failbit
+ | std::fstream::badbit );
+ }
+
+ //! read data from FORTRAN unformatted file
+ /*! read a scalar from FORTRAN unformatted file. If the data is not scalar
+ (i.e. an array) or the function is called with a template parameter of
+ a different size than the stored data, a std::runtime_error is thrown.
+ \param r reference to the return value
+ */
+ template< typename T > void read( T& r )
+ {
+ unsigned n1,n2;
+
+ try{
+ m_ifs.read( (char*)&n1, m_addlen );
+ m_ifs.read( (char*)&r, sizeof(T) );
+ m_ifs.read( (char*)&n2, m_addlen );
+ }catch(...){
+ throw;
+ }
+
+ if( n1 != sizeof(T) || n1 != n2 ){
+ throw std::runtime_error("FortranUnformatted::read : invalid type"\
+ " conversion when reading FORTRAN unformatted.");
+ }
+ }
+
+ //! write a single variable, arbitrary type to the Fortran unformatted file
+ /*!
+ * @param w the variable, arbitrary type
+ */
+ template< typename T > void write( T& w )
+ {
+ unsigned n1 = sizeof(T);
+
+ try{
+ m_ifs.write( (char*)&n1, m_addlen );
+ m_ifs.write( (char*)&w, n1 );
+ m_ifs.write( (char*)&n1, m_addlen );
+ }catch(...){
+ throw;
+ }
+ }
+
+
+ //! write a range of a container data object given by iterators
+ /*!
+ * @param begin iterator pointing to the beginning of the range
+ * @param end iterator pointing to the end of the range
+ */
+ template< typename _InputIterator >
+ void write( _InputIterator begin, _InputIterator end )
+ {
+ _InputIterator it(begin);
+ unsigned nelem = std::distance(begin,end);
+ unsigned sz = sizeof(*begin);
+ unsigned totsz = sz*nelem;
+
+ try{
+ m_ifs.write( (char*)&totsz, m_addlen );
+ while( it!=end ){
+ m_ifs.write( (char*)&(*it), sz );
+ ++it;
+ }
+ m_ifs.write( (char*)&totsz, m_addlen );
+ }catch(...){
+ throw;
+ }
+ }
+
+ //! read masked data
+ /*! this function reads data but discards all those for which the iterator
+ * mask is not set to a 'true' bit. It is necessary that the mask iterator
+ * can be increased the same number of times as there is data to be read.
+ * @param mask an iterator which is increased for each element read from the file and determines rejection or not
+ * @param data an output iterator to which the data is written
+ */
+ template< typename basetype, typename _InputIterator, typename _OutputIterator >
+ _InputIterator read( _InputIterator mask, _OutputIterator data )
+ {
+ _InputIterator oldmask = mask;
+ std::vector<basetype> temp;
+ typename std::vector<basetype>::iterator temp_it;
+
+ unsigned n1,n2;
+ try{
+ m_ifs.read( (char*)&n1, m_addlen );
+ temp.resize(n1/sizeof(basetype));
+ m_ifs.read( (char*)&temp[0], n1 );
+
+ for( temp_it = temp.begin(); temp_it!=temp.end(); ++temp_it ){
+ //... copy data if masked - this also performs a type conversion if needed ...//
+ if( *mask )
+ *data = *temp_it;
+ oldmask = mask++;
+ if( mask == oldmask ) break;
+ }
+ //std::copy(temp.begin(),temp.end(), data);
+
+ m_ifs.read( (char*)&n2, m_addlen );
+
+ }catch(...){
+ throw std::runtime_error("FortranUnformatted::read : error reading FORTRAN unformatted.");
+ }
+ if( n1!=n2 )
+ throw std::runtime_error("FortranUnformatted::read : invalid type conversion when"\
+ " reading FORTRAN unformatted.");
+
+ return mask;
+ }
+
+
+ //! read data
+ /*! this function reads data from a Fortran unformatted file and writes it to
+ * an output iterator.
+ * @param data an output iterator to which the data is written
+ */
+ template< typename basetype, typename _OutputIterator >
+ _OutputIterator read( _OutputIterator data )
+ {
+ std::vector<basetype> temp;
+ typename std::vector<basetype> temp_it;
+
+ unsigned n1,n2;
+ try{
+ m_ifs.read( (char*)&n1, m_addlen );
+ temp.resize(n1/sizeof(basetype));
+ m_ifs.read( (char*)&temp[0], n1 );
+ //... copy data - this also performs a type conversion if needed ...//
+ std::copy(temp.begin(),temp.end(), data);
+ m_ifs.read( (char*)&n2, m_addlen );
+
+ }catch(...){
+ throw std::runtime_error("FortranUnformatted::read : error reading FORTRAN unformatted.");
+ }
+ if( n1!=n2 )
+ throw std::runtime_error("FortranUnformatted::read : invalid type conversion when"\
+ " reading FORTRAN unformatted.");
+
+
+ return data;
+ }
+
+ //! check if beyond end-of-file
+ bool eof( void )
+ {
+ bool bcheck;
+ try{
+ bcheck = (m_ifs.peek()==EOF);
+ }catch(...){
+ m_ifs.clear();
+ return true;
+ }
+ return bcheck;
+ }
+
+ //! skip ahead in FORTRAN unformatted file
+ /*! skips n datasets ahead in FORTRAN unformatted file. Equivalent to
+ * n READ(X) without argument in FORTRAN
+ * @param n number of entries to skip ahead (scalar or arrays)
+ */
+ void skip_n( unsigned n )
+ {
+ unsigned ndone = 0;
+ while( ndone < n ){
+ int n1, n2;
+ try{
+ m_ifs.read( (char*)&n1, m_addlen );
+ m_ifs.seekg( n1, std::ios::cur );
+ m_ifs.read( (char*)&n2, m_addlen );
+ }catch(...){
+ throw std::runtime_error("FortranUnformatted::skip_n : error seeking in FORTRAN unformatted file.");
+ }
+ ++ndone;
+ }
+ }
+
+ //! just a std::streampos
+ typedef std::streampos streampos;
+
+ //! wrapper for the std::ifstream::tellg() function
+ streampos tellg( void )
+ { return m_ifs.tellg(); }
+
+ //! wrapper for the std::ifstream::seekg() function
+ void seekg( streampos pos )
+ { m_ifs.seekg( pos ); /*, std::ios::beg );*/ }
+
+
+ //! jump to dataset in FORTRAN unformatted files
+ /*! moves past the nth WRITE(X) operation from the beginning in a FORTRAN
+ * unformatted file
+ * @param n number of entries to skip (scalar or arrays)
+ * @sa skip_n()
+ */
+ void skip_n_from_start( unsigned n )
+ {
+ m_ifs.seekg(0,std::ios::beg);
+ skip_n( n );
+ }
+
+ //! skip ahead in FORTRAN unformatted file
+ /*! skips to next dataset in FORTRAN unformatted file. Equivalent to a
+ * READ(X) without argument in FORTRAN
+ * @sa skip_n
+ */
+ void skip( void )
+ {
+ skip_n(1);
+ }
+
+ //! rewind file
+ /*! rewinds the file to the beginning
+ */
+ void rewind( void )
+ {
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