2003-08-15 Mattias Ekström * arts-1-1-649 * arts/src/sensor.cc: Changed antenna_transfer_matrix so that calls to sensor_integration_vector is only done for changing antenna diagram. For spectrometer_transfer_matrix changes are made to incorporate the changes in sensor_responseBackend. Removed obsolete functions at end of file. * arts/src/m_sensor.cc: Added some extra input tests to sensor_responseBackend and also the possibility to use one channel reponse for all channels or individual ones, in analogy with sensor_responseAntenna1D. 2003-08-15 Oliver Lemke * arts-1-1-648 * src/math_funcs.{cc,h}: Added function fac to calculate factorials. * src/legendre.{cc,h}: Rename legendre_polynomial to legendre_poly. Added function legendre_poly_norm to calculate normalized associated legendre polynomials. * src/test_legendre.cc: Updated. * src/Makefile.am: Added math_funcs.{cc,h} and dependencies to test_legendre target. 2003-08-13 Mattias Ekström * arts-1-1-647 * src/sensor.{cc,h}: Altered the scale_antenna_diagram function, now it does not return any object. Also made changes to antenna_transfer_matrix so that it make use of the new insert_row for Sparse and to fit the new handle of antenna diagrams. * src/m_sensor.cc: Added a way to handle different antenna diagram input methods and an extra test that the antenna diagram does not expand outside the zenith angle measurement block. This function has not yet been tested. 2003-08-14 Oliver Lemke * arts-1-1-646 * src/legendre.cc: Declare variables inside the blocks where they are used, not at the top of the function. Minor optimizations. * src/legendre.h: Cosmetics. * src/test_legendre.cc: Added CPU time measurement over loop of 1000000 calculations. 2003-08-14 Oliver Lemke * arts-1-1-645 * src/legendre.{cc,h}: Added. Function calculates associated Legendre polynomials. The code is based on the Numerical recipes. Results were compared to the Legendre calculations from the GNU Scientific library and found to be identical. * src/poly_roots.cc: Added reference to the GNU Scientific library in doxygen header. * src/Makefile.am: Added legendre.{cc,h} and test_legendre. * src/test_legendre.cc: Added. * src/.cvsignore: Added test_legendre. 2003-08-13 Mattias Ekström * arts-1-1-644 * src/test_sparse.cc: Added test function for insert_row. 2003-08-13 Mattias Ekström * arts-1-1-643 * src/matpackII.{cc,h} (insert_row): Added function to insert a whole row at a time. * doc/uguide/main.tex: Added myself as contributor. 2003-08-13 Cory Davis * arts-1-1-642 * src/optproperties.cc (pha_mat_labCalc):changed za_inc_rad == PI etc to za_inc_rad > PI-ANGTOL etc. This seems to have fixed the problem of nans in 1D scattering calculations for stokes_dim==2. ANGTOL = 1e-6. 2003-08-13 Oliver Lemke * arts-1-1-641 * src/main.cc: Fixed bug reported by Christian. Option -b was not working (implementation was missing!?). 2003-08-12 Stefan Buehler * arts-1-1-640 * src/matpackII.cc (operator=): I had forgotten to delete previous content of the target in the assignment operator, introducing a memory leak. Fixed this. * src/test_sparse.cc: Extended copying test to confirm memory leak. * src/m_hdf.cc (binfile_write_vector): Fixed mismatched delete operator bug. (binfile_write_matrix): Fixed mismatched delete operator bug. * src/mystring.h (operator=): Correction in doxygen header. * doc/uguide/matrix_vector.tex: Fixed typo. Rephrased the part about transpose for sparse slightly. 2003-08-08 Stefan Buehler * arts-1-1-639 * src/matpackI.cc: Replaced delete by delete[] in destructors, to fix bug reported by valgrind. * src/matpackIII.cc: Replaced delete by delete[] in destructor, to fix bug reported by valgrind. * src/matpackIV.cc: Replaced delete by delete[] in destructor, to fix bug reported by valgrind. * src/matpackV.cc: Replaced delete by delete[] in destructor, to fix bug reported by valgrind. * src/matpackVI.cc: Replaced delete by delete[] in destructor, to fix bug reported by valgrind. * src/matpackVII.cc: Replaced delete by delete[] in destructor, to fix bug reported by valgrind. 2003-08-09 Mattias Ekström * arts-1-1-638 * src/matpackII.cc: Inserted again, I need it for compilation. * doc/uguide/matrix_vector.tex: Added section about Sparse. 2003-08-08 Stefan Buehler * arts-1-1-637 * src/matpackII.cc: Moved inclusion of here from matpackII.h. (operator=): Added this assignment operator for Sparse to fix a bug found by Mattias. It was a familiar problem (though it was still hard to find, because I had forgotten about it): If no assignment operator is defined explicitly, the compiler will automatically generate one, which does not do the right thing. * src/matpackII.h: Removed some unnecessary #includes. Added assignment operator. * src/test_sparse.cc: Added a test for sparse copying. 2003-08-07 Oliver Lemke * arts-1-1-636 * doc/doxygen/Makefile.am: Prevent doxygen from overwriting our own Makefile in latex/. * doc/doxygen/latex/Makefile.am: Added targets from doxygen Makefile. Define targets only in maintainer mode. If you want to get a ps or pdf version of the doxygen documentation, go to the latex directory and run: make refman.ps or make refman.pdf But note that the document is really large (resulting postscript file has >1800 pages and is nearly 30 MB in size). It might not even work with all doxygen versions. PS creation tested with doxygen v1.3.3. Pdf version does not build. 2003-08-07 Oliver Lemke * arts-1-1-635 * src/matpackII.cc (mult): Removed FIXME. Nothing to fix. :-) 2003-08-07 Oliver Lemke * arts-1-1-634 * src/matpackII.cc (transpose): Cast loop variable c of type size_t explicitly to Index in find function. c can never be >MAX(Index) because mrowind and mcolptr are themselves of type Index, so downcasting is ok here. 2003-08-06 Mattias Ekström * arts-1-1-633 * src/matpackII.cc (transpose, mult): Implemented changes proposed by Stefan. 2003-08-07 Oliver Lemke * arts-1-1-632 * doc/doxygen/latex/Makefile.am: Unset thisdoc_DATA to avoid automatic build of postscript file. 2003-08-06 Stefan Buehler * arts-1-1-631 * src/matpackII.cc (mult): Put in some comments, marked by FIXME. (transpose): Made one modification and put in some comments, all marked by FIXME. * src/test_sparse.cc: Test transpose. 2003-08-06 Mattias Ekström * arts-1-1-630 * src/matpackII.cc: Remade the sparse-sparse mulitplication method and the transpose method for the new simplified sparse matrix. Removed old functions. * src/matpackII.h: Removed old functions and added inclution of and needed by transpose and mult. * src/test_sparse.cc: Added two test function for testing transpose and multiplication. 2003-07-31 Oliver Lemke * arts-1-1-629 * src/m_montecarlo.cc (ScatteringMonteCarlo): Use ios::out. ios_base is undefined in gcc 2.x. * src/montecarlo.cc: l.562 Multiline string literals are not allowed in ANSI-C++. Leads to compiler error in gcc >= 3.3. 2003-07-31 Oliver Lemke * arts-1-1-628 * src/m_general.cc: Include unistd.h. Otherwise function sysconf is unknown on gcc2 systems. 2003-07-31 Oliver Lemke * arts-1-1-627 * src/methods.cc, src/m_general.cc: Added dummy Print method for group Timer. Added methods timerStart and timerStop. * src/m_general.h: Added dummy Print method for group Timer. Fixed filename in doxygen header. * src/workspace.cc: Added WSV timer. * src/groups.cc: Added group Timer. * src/make_auto_wsv_groups_h.cc: Include m_general.h in auto_wsv_groups.h. * src/make_auto_wsv_h.cc: Include m_general.h in auto_wsv.h. * src/Makefile.am: make_auto_wsv_h and make_auto_wsv_group_h must depend on m_general.h. * src/xml_io_basic_types.{h,cc}, src/xml_io_instantiation.h: Added dummy read/write functions for group Timer. * doc/doxygen/html/Makefile.am: Added graph_legend.dot and formula.repository to MAINTAINERCLEANFILES. * doc/doxygen/Makefile.am: Use CLEANFILES instead of target clean. Otherwise 'doxyfied' is not removed with make maintainer-clean. Readded latex to subdirs. * doc/doxygen/latex/.cvsignore: Added refman.out. * doc/doxygen/latex/Makefile.am: Define empty 'all' target as we don't won't to build ps/dvi by default but the user should be able to do so if she likes. Undef EXTRA_DIST. * doc/doxygen/Doxyfile.in: Disabled creation of man pages and rtf. If we want to support this, we should also create man and rtf directories with appropriate Makefiles in the repository. * configure.in: Readded doc/doxygen/latex/Makefile to AC_OUTPUT. We don't build latex doxygen documentation by default, but it should be possible to do it manually. For this case we need the Makefile. * src/gas_abs_lookup.cc: Put empty doxygen header in front of output operator to prevent doxygen confusion. * doc/doc++/{.,html,tex}/.cvsignore: Removed to make directories empty and pruned on checkout/update. * ChangeLog: Wrapped paragraphs with lines > 80 chars. Cory, your emacs sucks ;-) 2003-07-30 Cory Davis * arts-1-1-626 * src/methods.cc, src/m_montecarlo.cc (ScatteringMonteCarlo): Added control parameter los_sampling_method. * src/montecarlo.cc, src/montecarlo.h (Sample_los): added a new probability density function from which to sample the line of sight, there are now 2: g = 0.5sin(1-cos), and g = 0.5sin. The new argument los_sampling_method chooses between the two. 2003-07-30 Cory Davis * arts-1-1-625 * src/methods.cc, src/m_montecarlo.cc (ScatteringMonteCarlo): Added control parameters record_histdata and histdata_filename. These enable the output of each 'photon' contribution, which can then be analysed in MATLAB to investigate error reduction. Fixed bug in line of sight sampling. * src/montecarlo.cc, src/montecarlo.cc (Sample_los): Tidied Sample_los function. 2003-07-29 Sreerekha T.R. * arts-1-1-624 * src/m_cloudbox.cc (ybatchMetProfiles): Modified the method so that the lower cloudbox limit is the lowest pressure level. This makes it possible to set the ground emissivity other than 1. Improved documentation also. * src/m_scatrte.cc, src/scatrte.cc: Removed unnecesary couts which I used to test the ground emissivity part. 2003-07-29 Cory Davis * arts-1-1-623 * src/rng.cc: Sorry, I had forgotten to #include "arts.h" 2003-07-28 Cory Davis * arts-1-1-622 * src/rng.cc (rng::seed): temporarily enabled output of random number generator seed for use in debugging 2003-07-28 Cory Davis * arts-1-1-621 * src/methods.cc: added control parameter "silent" to ScatteringMonteCarlo WSM. This disables/enables iterative output. * src/m_montecarlo.cc (ScatteringMonteCarlo): added "silent control parameter" and added code to output estimated execution time. 2003-07-28 Oliver Lemke * arts-1-1-620 * src/test_matpack.cc: Added testcase for cory. 2003-07-25 Cory Davis * arts-1-1-619 * src/m_montecarlo.cc (ScatteringMonteCarlo): I have been testing the code for more optically thick cases. This has led to two modifications. 1. Introduced a cut off value for Q[0,0] below which higher scattering orders are neglected. 2. There were problems with inconsistency of the returned exit radiance and the estimated error. It seemed like a problem with rounding or type conversion. The problem seems to have gone away by including the following explicit cast (L631) I/=(Numeric) maxiter; //For some reason this cast seems to help? I is a Vector (the exit stokes vector) and maxiter is an Index. I don't really know why this helps - I would have thought the type conversion worked automatically. Any ideas? 2003-07-24 Patrick Eriksson * arts-1-1-618 * src/methods.cc: Revised the description of "my" methods. Renamed methods as follows: CloudboxOff -> cloudboxOff CloudboxSetManually -> cloudboxSetManually GroundNoScatteringSingleEmissivity -> groundNoScatteringSingleEmissivity GroundTreatAsBlackbody -> groundTreatAsBlackbody RefrIndexFieldAndGradients -> refr_indexFieldAndGradients 2003-07-24 Oliver Lemke * arts-1-1-617 * src/test_sparse.cc: Define joker to fix compilation with gcc 2.95.3. 2003-07-24 Oliver Lemke * arts-1-1-616 * src/Makefile.am: Added m_general.h. * src/m_general.h: Added template function implementation for general supergeneric workspace method Print and explicit prototypes for ArrayOfIndex, ArrayOfString and Ppath Print method. * src/m_general.cc: Removed *Print functions. Added explicit implementation of Print for ArrayOfIndex, ArrayOfString, Ppath. * src/make_auto_md_cc.cc: Include m_general.h in auto_md.cc. * src/m_ppath.cc: Removed PpathPrint. Now covered by general Print method. Include m_general.h * src/optproperties.{cc,h}: Added dummy output operator for ArrayOf/SingleScatteringData. * src/gas_abs_lookup.{cc,h}: Changed GasAbsLookup from struct to class. Added dummy output operator for GasAbsLookup. * src/m_scatrte.cc: Use new Print instead of PpathPrint. * src/methods.cc: Added supergeneric Print method. Removed all other *Print methods. * src/describe.cc: Do not include sstream. * src/montecarlo.{cc,h}: Include sstream in cc instead of h and put appropriate ifndef around. * src/m_montecarlo.cc: Do not include sstream. 2003-07-24 Oliver Lemke * arts-1-1-615 * src/agendas.cc: Added missing _ after scalar_gas_absorption_agenda in rte_agenda. 2003-07-23 Patrick Eriksson * arts-1-1-614 * src/xxx: Changed name of variables like a_pos, a_los and a_gp_p to start with rte_ throughout the code. * src/workspace.cc: Revised description of "my" variables. * src/agendas.cc: Revised description of "my" agendas. 2003-07-23 Patrick Eriksson * arts-1-1-613 * src/rte.cc (get_radiative_background): Fixed the bug reported by Sreerekha. The problem was that ground reflections gave clearly wrong results. There was a clear bug, connected with a confusion of a local version of ppath and the WSV ppath. As rte_agenda always uses the WSVs, I did not help to send a local variable to rte_calc. Now the orignal data are copied, the downwelling radiation is calculated, and the ppath data is put back into ppath. The results now looks OK, but no heavy checks. This is a general comment about the ground reflections. The code runs but I have not made any detailed checks of the correctness of the results. So, please take care. And try to check the results if you run cases with ground reflections. 2003-07-22 Oliver Lemke * arts-1-1-612 * src/methods.cc: GINPUT/GOUTPUT is called generic, not global. Corrected descriptions. 2003-07-22 Sreerekha T.R. * arts-1-1-611 * ChangeLog : Edited the ChangeLog message of the previous version as Stefan pointed out a wrong statement there. I had written that the clear-sky part and cloudbox part agree when the particle number density is zero. But there is a difference for low emissivity values. 2003-07-21 Sreerekha T.R. * arts-1-1-610 * src/scatrte.cc (cloud_ppath_update1D): Implemented the ground reflection part when cloudbox is set on. In the same way as clear-sky part we can use the method *GroundNoScatteringSingleEmissivity* to give different surface emissivity values keeping in mind that the cloudbox has to be extended to the ground. The results are compared with the clear-sky values when the particle number density is zero.This shows good agreement for higher emissivity values. For emissivity =0, there is a difference of about 1 K. Also Included some variables related to ground reflection in the parameter of this function. * src/scatrte.h: Added ground reflection parameters according to the function cloud_ppath_update1D. * src/m_scatrte.cc: Added ground reflection parameters for the method *i_fieldUpdateSeq1D*. * src/methods.cc: Adapted *i_fieldUpdateSeq1D* to the above changes. 2003-07-21 Oliver Lemke * arts-1-1-609 * src/version.cc: Replaced reconf with autogen.sh. 2003-07-21 Oliver Lemke * arts-1-1-608 * doc/uguide/development.tex: Replaced reconf with autogen.sh. 2003-07-21 Oliver Lemke * arts-1-1-607 * configure.in: Added check for arts-xml-data. Updated list of examples. * autogen.sh: Look for arts data packages in /usr/share on smiles PCs. * doc/examples/Makefile.am: Updated list of examples. * doc/examples/{cloud_rad_field1D_example.arts.in, i_field_example.arts.in}: Replaced path to arts xml data with @ac_arts_xml_data@. 2003-07-17 Cory Davis * arts-1-1-606 * src/workspace.cc: Removed ppathLOS * src/montecarlo.cc (Cloudbox_ppathCalc): made silent. (Cloudbox_ppath_rteCalc): disabled error checking in calls to rte_calc . This made an enormous improvement in performance. Depending on optical thickness I can now do 10^5 photons in 90 seconds with debugging disabled. Previously this took about 2 hours:) 2003-07-16 Stefan Buehler * arts-1-1-605 * src/matpackII.cc: Cleaned up the sparse matrix implementation. Everything related to views and ranges has been kicked out. WARNING: the function transpose and sparse-sparse multiplication are currently commented out. ARTS sensor model code will not work properly! * src/matpackII.h: Ditto for the header file. * doc/uguide/matrix_vector.tex: Added template section about sparse matrices. * src/test_sparse.cc: Added this file for sparse matrix tests. * src/test_matpack.cc: Moved sparse testing routines to test_sparse.cc. * src/Makefile.am: Added test_sparse. * src/.cvsignore: Added test_sparse. * src/xml_io_basic_types.cc: Small adaptations to cleaned up sparse matrices. * src/sensor.h: Small adaptations to cleaned up sparse matrices. * src/sensor.cc: Small adaptations to cleaned up sparse matrices. * src/matpackI.h: Small adaptations to cleaned up sparse matrices. * src/m_sensor.cc: Small adaptations to cleaned up sparse matrices. (sensorOff): Fixed typo in error message that lead to compiler warning. 2003-07-16 Cory Davis (rsh) * arts-1-1-604 * src/m_montecarlo.cc, src/methods.cc: removed TArrayCalc. * src/montecarlo.cc, src/montecarlo.h: added TArrayCalc and fixed bug. * src/workspace.cc: removed TArray, ext_matArray, abs_vecArray, and t_ppath. Removed I - output of ScatteringMonteCarlo now goes in i_rte. Changed Ierror to i_montecarlo_error 2003-07-14 Patrick Eriksson * arts-1-1-603 * src/m_sensor.cc (sensorOff): Fixed a bug reported by Sreerekha (who also found how to solve it). The mblock_za_grid was wrongly set to 1, instead of 0 (I was probably thinking about the length). 2003-07-13 Patrick Eriksson * arts-1-1-602 * src/workspace.cc: Removed y_rte as it is needed with new scheme for polarisation. Removed mblock_index as it can not be used as I thought. Added WSVs sensor_pol, sensor_rot, sensor_response_f, sensor_response_za and sensor_response_aa. * src/methods.cc: Removed yNoPolarisation and RteTest. * src/rte.cc (rte_calc): Added sensor_pol and sensor_rot as input arguments. Changed y_rte to y. The vector *y* is now only filled if *apply_sensor* = true. This means if the function is called to obtain monochromatic pencil beam values this has to be done for one line-of-sight at the time, and the result is returned by *i_rte*. This is the way the function is already used from CloudboxGetIncoming and ScatteringMonteCarlo. Implemented polarisation, beside the rotation part. * src/rte.cc (get_radiative_background): Removed antenna_dim as input. Changed call of rte_calc following changes given above. * src/m_cloudbox.cc (CloudboxGetIncoming): Adapted to changes in rte_calc. Made y a local variable. Removed y_rte as input. * src/montecarlo.cc (Cloudbox_ppath_rteCalc): Adapted to changes in rte_calc. Made y a local variable. Removed y_rte as input. * src/m_montecarlo.cc (ScatteringMonteCarlo): Removed y_rte as input. * src/m_sensor.cc (sensor_responseInit): Added sensor_pol, stokes_dim and atmosphere_dim as input. The function now considers the number of polarisations provided by the sensor. Added sensor_response_f, sensor_response_za and sensor_response_aa as output. Moved AntennaSet1D/2D to this file from m_general.cc. Added WSM sensorOff. * src/m_basic_types.cc (VectorSetElement): Removed this WSM as it took a vector index as argument. We have decided that WSM shall not take index as input, to avoid problems with 0 and 1 based indexing. (I was the one that had created the method) * src/m_physics.cc (VectorToTbByRJ): Modified the method to take sensor_response_f, sensor_response_za, sensor_response_aa and sensor_pol as input. Did the same for VectorToTbByPlanck, MatrixToTbByRJ and MatrixToTbByPlanck. * src/check_input.cc (chk_y_with_sensor): Added this function. 2003-07-08 Patrick Eriksson * arts-1-1-601 * Commit of changes made during the Bredbeck workshop. * src/ppath.cc (ppath_calc): Included flag to seperate standard path calculations from path calculations inside the cloudbox (for e.g. Montye Carlo calculations). * src/rte.cc (rte_calc): Included input argument to control agenda verbosity. Agendas are set to be quiet when called from scattering calculations. 2003-07-08 Oliver Lemke * arts-1-1-600 * Commit of changes made during the Bredbeck workshop. * src/Makefile.am: Added missing zeemanproperties.h to source file lists. * src/rte.cc (rte_calc): Removed dummy vector passed to chk_if_increasing to avoid copying of z_field. * src/matpackII.{h,cc}: FIXMEs added by Stefan. * doc/uguide/scattering.tex: Fixed typo. 2003-07-04 Oliver Lemke * arts-1-1-599 * src/test_mpi.cc: Implemented broadcasting and sending routines for Matrix. Only a first test version for performance testing. * src/matpackI.h (Matrix): Added get_raw_data function return the mdata pointer. Needed for mpi transfer routines to get direct access to the data. 2003-07-03 Claudia Emde * arts-1-1-598 * doc/uguide/scattering.tex: Updated parts of the text and took out the parts which are not up to date. Unfortunately there is still a lot of documentation missing for the new functions. * doc/uguide/integration.tex: Removed a reference to a section which no longer exists. * doc/uguide/references.bib: Included Mishchenkho's new book. 2003-07-02 Oliver Lemke * arts-1-1-597 * src/Makefile.am: Added test_mpi target. * src/test_mpi.cc: Added. * src/.cvsignore: Added test_mpi. 2003-07-02 Claudia Emde * arts-1-1-596 * m_scatrte.cc (cloud_ppath_update1D): Fixed bug reported by Sreerekha (stokes_dim = i_field.ncols()). 2003-07-01 Oliver Lemke * arts-1-1-595 * src/arts.h: Updated doxygen main page. * doc/doxygen/Makefile.am: Copy arts splash to html dir. * doc/arts-splash.gif: Added. Changed version in splash to pre2.0. 2003-06-30 Oliver Lemke * arts-1-1-594 * src/matpackI.h (Range): Added selectors for start, extent and range to avoid unnecessary need for friend declarations. Removed friend declaration of Sparse output operator, transpose and mult. * src/matpackII.{cc,h} (operator<<, mult, transpose): Use selector functions instead of direct member access. This has a little impact on speed when compiling without optimizations and is not noticeable with -O2 and higher. The operator() is for read-only access. To write elements the rw() modifier has to be used. Otherwise, e.g cout << sparse(1,1); will create the element instead of just outputting it. * src/m_sensor.cc (sensor_responseInit): Use rw() instead of operater(). * src/xml_io_basic_types.cc (xml_write_to_stream): Use selector functions instead of direct access for the Sparse range member attributes. 2003-06-30 Cory Davis * arts-1-1-593 * src/ppath.cc (ppath_start_3D) small change suggested by Patrick - use existing RTOL instead of new constant. * src/m_cloudbox.cc (CloudboxGetIncoming) Fixed bug that gave spurious assertion failure when checking that the current grid position is on the cloudbox boundary. Made function compatible with the small version of scat_i_p, scat_i_lat, scat_i_lon. (This means some work will be needed on Scat_iPut for the 3D case!) * src/methods.cc added WSM scat_iPutMonteCarlo. * src/m_montecarlo.cc added WSM scat_iPutMonteCarlo. This is a fairly ugly way of making the output of ScatteringMonteCarlo consistent with RteCalc for the final stage of the calculation - cloudbox->sensor. scat_i_p, scat_i_lat, and scat_i_lon are simply filled with many copies of the single cloudbox exit stokes vector I. 2003-06-27 Claudia Emde * arts-1-1-592 * src/m_scatrte.cc (i_fieldUpdateSeq1D): Included a special case for limb looking. Without this I missed some points while doing the sequential update. This modification has no effect on the nadir simulations. * src/optproperties.cc (pha_mat_labCalc): Fixed a bug in the formula for the transformation of the phase matrix. The formula I fixed is only used for polarized calculations, so the intensity simulations (stokes_dim = 1) we have already done are still correct. 2003-06-27 Mattias Ekström * arts-1-1-591 * src/matpackI.h: Added Sparse transpose- and multiplication function as friends in Range. Also added declaration of class bofstream. * src/matpackII.cc: Fixed bug in transpose- and multiplication function by changing to apparent row and column indices. * src/xml_io_basic_types.cc: Added corrections in xml_write_to_stream for Sparse to write the apparent row indices. The corrections are not yet implemented, since there is a problem with Range and private members. 2003-06-26 Cory Davis * arts-1-1-590 * src/m_montecarlo.cc: used new random number generator class Rng in functions Sample_los and Sample_pathlength, added rng_seed control parameter to ScatteringMonteCarlo. This means that you can choose a seed for random number generation, or have the seed derived from system time. The latter is acheivedt the first two components are required, in some cases, depending on the by setting rng_seed to a negative integer. * src/montecarlo.{cc-h}: used new random number generator class Rng in functions Sample_los and Sample_pathlength. * src/methods.cc: added rng_seed control parameter to ScatteringMonteCarlo. * src/Makefile.am: added rng.cc and rng.h * src/rng.cc and rng.h: Added. These files define Rng, a new random number generator class based on GNU Scientific Library gsl_rng_mt19937. 2003-06-25 Oliver Lemke * arts-1-1-589 * src/xml_io_array_types.cc: Fixed tag attribute in read function for SpeciesData. * src/xml_io_compound_types.cc: Fixed check for end tag in reading function for IsotopeRecord. * src/test_xml.cc: Updated. 2003-06-24 Oliver Lemke * arts-1-1-588 * ChangeLog: Removed conflict markers. * src/xml_io_array_types.cc: Corrected docs. 2003-06-24 Cory Davis * arts-1-1-587 * src/Makefile.am: Added m_montecarlo.cc, montecarlo.cc, and montecarlo.h. * src/methods.cc: Added Cloudbox_ppathCalc - an equivalent of ppathCalc for within the cloudbox, ScatteringMonteCarlo - 3D scattering calculation, shift_a_pos - shifts a_pos and a_los to the end of ppath, TArrayCalc - calculates arrays of several useful quantities along a propagation path within the cloud box. * src/workspace.cc: Added I - the stokes vector exiting the cloudbox in the direction of the sensor, Ierror - the estimated error in I. abs_vecArray - an array of absorbtion coefficient vectors along a cloudbox propagation path. ext_matArray - an array of extinction matrices along a cloudbox propagation path, TArray - an array of transmittance matrices along a cloudbox propagation path, t_ppath - a vector of temperatures along a cloudbox propagation path, ppathLOS - the propagation path for the initial line of sight. I realise that 'I' might be redundant, since i_rte is already available. This is something I will sort out once I have addressed radiative transfer from the cloudbox exit to the sensor. * src/m_montecarlo.cc: Added. This file includes WSM ScatteringMonteCarlo, which performs a 3D scattering calculation. A control file using this method is available on request. There are several issues that need to be addressed in this code, including efficiency issues, random number generation, and radiative transfer from the cloud box to the sensor. However, in it's current state it should be ready for comparison with the existing scattering code. * src/montecarlo.cc: Added. Helper functions for ScatteringMonteCarlo. * src/ppath.cc: fixed bug in ppath_start_3d() - removed double == double lines 03267-03268 2003-06-24 Oliver Lemke * arts-1-1-586 * src/xml_io_instantiation.h, src/xml_io_array_types.{cc,h}: Added Array reading/writing routines. * src/xml_io_instantiation.h, src/xml_io_compound_types.{cc,h}: Added IsotopeRecord reading/writing routines. Completed SpeciesRecord routines. * src/make_array.h: Added constructor to convert normal array to MakeArray. * src/test_xml.cc: Updated to test writing of species_data. 2003-06-24 Nikolay Koulev * arts-1-1-585 * src/test_zeemanproperties.cc: Major changes - added documentatation, replaced my frequency grid function by the ARTS Vector f_grid, threw away the output files producing part and replaced it by a short string function block. * src/test_zeemanproperties.cc: Minor changes - changed units to SI. 2003-06-23 Oliver Lemke * arts-1-1-584 * Huge doxygen cleanup: The cleaning involves removal of no longer existent, but still documented parameters, making the order of parameters in the documentation the same as in the function call, documentation of non-documented parameters. NOTE: For all parameters I did not know how to comment on, I've put a 'FIXME: Add documentation.' into the source code. Please look at your code and replace it with the appropriate documentation. You can also do a grep 'FIXME: Add documentation.' *.{cc,h} to get an overview of missing documentation. And for the future please remember to adapt the documentation immediately after changing a function's parameters. Otherwise, it is surely forgotten. Please have a look a the output of doxygen from time to time and try to fix the warnings if any. (cd doc/doxygen && make) * src/agenda_record.cc, src/describe.cc, src/file.cc, src/interpolation.cc, src/logic.h, src/m_abs.cc, src/m_absorption.cc, src/m_cloudbox.cc, src/m_optproperties.cc, src/m_scatrte, src/m_physics, src/check_input.cc, src/continua.cc, src/m_ignore.h, src/main.cc, src/messages.cc, src/refraction.cc, src/scatproperties.cc, src/ppath.cc, src/sensor.cc, src/special_interp.cc, src/species_data.cc, src/test_integration.cc, src/methods.h, src/xml_compound_types.cc src/agenda_class.cc, src/matpack{I,III,IV,V,VI,VII}.cc, src/absorption.h: Updated documentation. * doc/doxygen/Doxyfile.in: Exclude old_absorption.cc. 2003-06-23 Mattias Ekström * arts-1-1-583 * src/m_sensor.cc: Commented away lines with couts and xml_write_to_file. Those shouldn't have been commited last time, sorry for that. * src/matpackII.cc: Same as for m_sensor.cc. 2003-06-22 Oliver Lemke * arts-1-1-582 * doc/uguide/Makefile.am (uguide.pdf): Added one more pdflatex run to get cross-references right. * doc/doxygen/latex/Makefile.am (refman.ps): Pass -o to dvips. (refman.pdf): Added target for pdf creation. I did not make this the default target because the conversion from ps to pdf takes a very long time. * doc/doxygen/latex/.cvsignore: Added refman.pdf. * doc/doxygen/Doxyfile.in: Put pdf hyperlinks into dvi file. * src/xml_io_*_types.cc (xml_write_to_stream): Added documentation for name parameter. * src/xml_io*.cc: Cleanup of docs. * src/test_zeemanproperties.cc: Corrected filename in doxygen comment. 2003-06-20 Claudia Emde * arts-1-1-581 * src/m_scatrte.cc (i_fieldUpdate1D): Modified sequential update. Should be a bit more efficient and the code is better readable. * src/scatrte.cc (cloud_ppath_update1D): Fixed a bug. The intensity field was not interpolated on the correct zenith angles. This caused bad results in limb direction. * src/m_rte.cc (RteEmissionStd): Averaged temperature and pressure instead of absorption coefficients in the radiative transfer calculation. This has been an inconsistency between clearsky radiative transfer and RT in the cloudbox. 2003-06-19 Oliver Lemke * arts-1-1-580 * src/matpackII.h (SparseView), src/gas_abs_lookup.h (GasAbsLookup): Adapt prototyping for xml_write_to_stream. * src/xml_io_*_types.{cc,h}: Added an optional parameter to all xml_write_to_stream functions. A descriptive name could be supplied which is added as an attribute to the tag like Only used internally at the moment to document the structure members. * src/xml_io_compound_types.cc: Added descriptive names to members of GasAbsLookup, GriddedField3, GridPos and Ppath. 2003-06-19 Oliver Lemke * arts-1-1-579 * ChangeLog: Reformatted oversized lines. @mattias: Please limit your lines to 78 chars :-) * doc/doxygen/Doxyfile.in: Exclude getopt*.{c,h}. * src/gridded_fields.h: Added type GriddedField3. * src/xml_io_instantiation.h, src/xml_io_compound_types.{h,cc}: Added routines for GriddedField3. * src/matpackII.cc: Temporarely added include iostream. Should be removed along with the couts after testing. 2003-06-18 Claas Teichmann * arts-1-1-578 * src/math_funcs.cc: Modified comments 2003-06-18 Mattias Ekström * arts-1-1-577 * src/methods.cc: Added sensor_response to input list of RteCalc. * src/m_rte.{cc,h}: Added variables sensor_response and apply_sensor. NB: This means that the WSM sensor_responseInit has to be added to the controlfiles, before running RteCalc. * src/rte.{cc,h}: Implemented the sensor_response and apply_sensor variables in method rte_calc and changed call for RteCalc to rte_calc in method get_radiative_background. * src/m_cloudbox.cc: Added sensor_reponse as dummy variable and set apply_sensor to false for the rte_calc calls. * src/xml_io_basic_types.cc: Fixed bug in Sparse xml_write_to_stream function. * src/m_sensor.cc: Minor changes to runtime error output. * src/sensor.{cc,h}: Removed antenna_diagram_gaussian, which has been replaced by WSM GaussianResponse. * src/test_sensor.cc: Moved antenna_diagram_gaussian from sensor.cc here. 2003-06-18 Oliver Lemke * arts-1-1-576 * src/xml_io_basic_types.cc: Updated sparse reading/writing functions. nnz is now stored along with the SparseData, RowIndex and ColIndex vector. This is somehow redundant but matches the concept of xml that attributes should be stored with their object. Also, it is necessary for the atmlab xml routines. 2003-06-17 Oliver Lemke * arts-1-1-575 * src/xml_io_basictypes.cc: Extended sparse reading and writing routines. * src/test_xml.cc: Adapted for testing of sparse reading writing. 2003-06-16 Mattias Ekström * arts-1-1-574 * src/m_general.cc: Added SparsePrint. * src/methods.cc: Added SparsePrint. * src/matpackII.cc: Fixed bug in transpose and mult function. * src/xml_io_basictypes.cc: Wrote simple xml_write_to_stream and xml_read_from_stream functions for Sparse matrices. * src/workspace.cc: Added general WSV sparse_1. 2003-06-11 Mattias Ekström * arts-1-1-573 * src/m_refraction.cc: Removed compilation warning from Oliver's list. * src/m_sensor.cc: Added WSM sensor_responseMixer and made changes to sensor_responseBackend. * src/methods.cc: Changed input to GaussianResponse and added sensor_responseMixer. * src/sensor.{cc,h}: Added calculating methods for the mixer and backend response WSM. * src/workspace.cc: Added f_mixer and f_backend as WSV groups and removed previously added f_sensor. * src/matpackII.cc: Added resize function for sparse matrices. * src/test_sensor.cc: Added various test functions. * src/Makefile.am: Added constants, matpacks and interpolation to the test_sensor compilation group(?). * src/zeemanproperties.cc: Fixed compilation error (missing ;) 2003-06-11 Oliver Lemke * arts-1-1-572 * Cleaned-up/restructured XML sources. * src/Makefile.am: Added xml_io_basic_types.{cc,h}, xml_io_compound_types.{cc,h}, xml_io_array_types.{cc,h}, and xml_io_instantiation.h. Link test_linalg against constants.o for joker. * src/xml_io_basic_types.{cc,h}: Added. Contains the reading/writing routines for basic types like Index, Numeric and all matpack types. * src/xml_io_compound_types.{cc,h}: Added. Contains the reading/writing routines for compound types like structures. Compound types consist of basic types. * src/xml_io_array_types.{cc,h}: Added. Contains the reading/writing routines for array types. Arrays can contain basic or compound types or other arrays. * src/xml_io_instantiation.h: Added. Contains explicit template instantiations for xml_{read_from,write_to}_file functions. * src/xml_io.cc, src/xml_io_private.h: Removed functions which have moved to xml_io_*_types.{h,cc}. 2003-06-11 Nikolay Koulev * arts-1-1-571 * src/zeemanproperties.cc: changed extinction matrix and absorption vector to be calculated fully in a left-circular-right-circular polarization basis. 2003-06-11 Claudia Emde * arts-1-1-570 * src/m_scatrte.cc (i_fieldUpdataSeq3D): Small modifications. * src/scatrte{.cc,.h} (cloud_fieldsCalc): Fixed a bug here. I used VectorView instead of Vector& for a workspace variable which is initialized inside the function. This changes the address of the workspace variable. (cloud_ppath_update3D): Only a small modification. * src/optproperties{.cc, .h}: Fixed a bug in (ext_matTransform) The 3D calculations are working now with the new database and the sequential update. But it is still very slow as the transformation of the phase matrix from the scattering frame to the laboratory frame has to be done for each point and each angle combination. This part takes most of the time. (1 iteration for 2 stokes dimensions on my PC takes 2:50 h!, more than 2 hours for the calculation of the scattering integral!) 2003-06-06 Oliver Lemke * arts-1-1-569 * src/.cvsignore: Added gmon.out. * src/agenda_record.h (AgRecord::operator=), src/m_absorption.cc (gas_abs_lookupInit): Commented out parameter name to avoid warning. * src/xml_io.cc: Cosmetics. * src/test_integration.cc (main): Avoid segfault. @claas: ;-) 2003-06-11 Sreerekha T.R. * arts-1-1-568 * src/m_cloudbox.cc (ybatchMetProfilesClear): A distinction was made when the clear-sky calculations are performed with the met-office profiles. The difference with the *ybatchMetProfiles* method is that, here the pnd_field file is not read and the cloudbox is not set. * src/methods.cc: Added the method *ybatchMetProfilesClear*. 2003-06-10 Claas Teichmann * arts-1-1-567 * src/m_scatrte.cc (scat_fieldCalc): bug fixed. AngIntegrate_trapezoid_opti readded. 2003-06-10 Axel von_Engeln * arts-1-1-566 * aux/part_fct/: updated with new JPL partition functions and added some file output for Carmens work on a comparison between JPL and HITRAN part. fct. Fit for JPL is done now between 150K and 300K, as Carmens matlab fit. 2003-06-05 Claudia Emde * arts-1-1-565 * src/m_scatrte.cc (i_fieldUpdataSeq3D): Added this method. It updates the radiation field sequentially for a 3D cloudbox. Should be much faster than (i_fieldUpdata3D),but I have not yet tested the method. * src/scatrte{.cc,.h} (cloud_fieldsCalc): Fixed a bug. Included three new functions: (cloud_ppath_update3D): Used in the 3D sequential update. All interpolations on the intersection points and the RT step calculation are done in this function. (ppath_step_in_cloudbox): Sets up a ppath structure for a given point and calculates the intersection point with the next grid cell boundary. (is_inside_cloudbox): Checks, whether the intersection point of the propagation path with the next gridcell is inside or outside the cloudbox. * src/methods.cc: Included (i_fieldUpdateSeq3D). 2003-06-05 Oliver Lemke * arts-1-1-564 * src/agenda_record.h (operator=), src/methods.h (operator=): Return empty AgRecord/MdRecord. Code is never reached because arts_exit is called before but circumvents a gcc warning message. * src/absorption.h (SpeciesRecord): xml_read_from_stream is our friend. Include bifstream. * src/xml_io.cc, src/xml_io_private.h: Started read/write functions for species_data (Array) and SpeciesRecord. * .cvsignore: Added *.swp. 2003-06-05 Claas Teichmann * arts-1-1-563 * src/check_input{.cc,.h} (chk_atm_field): changed parameter: "const Tensor3&" to "ConstTensor3View" and "const Tensor4&" to "ConstTensor4View" to save computation time. The function created a new Tensor object, when it was called with a TensorView. * test_integration.cc: Modified. 2003-06-04 Claudia Emde * arts-1-1-562 * src/scatrte{.cc,.h}: Added. This file contains functions related to radiative transfer calculations in the cloudbox. * src/scatrte.cc (cloud_ppath_update1D): Included this function. It is used in the sequential update of the radiation field. Before this function was part of (i_fieldUpdate1D). (cloud_fieldsCalc): Added this function to calculate optical properties fields (absorption vector, extinction matrix) for all points in the cloudbox. Has also been part of (i_fieldUpdate1D) and (i_fieldUpdate3D). * src/m_scatrte (i_fieldUpdate1D) and (i_fieldUpdate3D): Separated the function into subfunctions defined in scvatrte.cc to make the code clearer. * src/Makefile.am: Included new files. 2003-06-04 Claas Teichmann * arts-1-1-561 * src/math_funcs.cc: Changed: Integration method in scat_fieldCalc is now AngIntegration_trapezoid_opti slightly faster if the grid_stepsize is constant * src/math_funcs.h: Added: AngIntegration_trapezoid_opti faster integration if the grid_stepsize is constant * src/methods.cc: Modified: definition of scat_fieldCalc * src/m_scatrte.cc: Modified: scat_fieldCalc and scat_fieldCalcFromAmpMat are using now AngIntegration_trapezoid_opti * src/test_integration.cc: Added: test of AngIntegration_trapezoid_opti * src/Makefile.am: Modified: removed non existing constants.h in definition 2003-06-02 Claudia Emde * arts-1-1-560 * src/optproperties.cc: Included special cases, which were missing before. Now the database is working for all Stokes dimensions. * src/lin_alg.cc: Modified the code according to suggestions in the programming seminar. 2003-06-02 Claas Teichmann * arts-1-1-559 * src/math_funcs.cc: Added: new integration method: AngIntegrate_trapezoid_opti: In addition to the "old fashined" integration method "AngIntegrate_trapezoid", it checks whether the stepsize is constant. If it is, it uses a faster method, if not, it uses the old one. * src/m_scatrte.cc: Changed: declaration of scat_fieldCalc: added *grid_stepsize* in function declaration * src/methods.cc: Changed: declaration of scat_fieldCalc: added *grid_stepsize* in function declaration * src/test_integration.cc: Modified. 2003-05-28 Claudia Emde * arts-1-1-558 * src/gas_abs_lookup.cc (GasAbsLookup::Extract): Fixed a bug here. For the monochromatic calculations (inside the cloudbox) only the first frequency in the frequency grid was calculated. * src/m_cloudbox.cc: Removed debugging output. * src/m_optproperties.cc: Only minor modification. 2003-05-27 Claas Teichmann * arts-1-1-557 * src/test_integration.cc: Added. File for testing purposes of the AngIntegrate_trapezoid function from math_funcs.cc * src/Makefile.am: Added dependencies of test_integration.cc * .cvsignore: Added the executable test_integration 2003-05-27 Claas Teichmann * arts-1-1-556 * src/methods.cc: Added *grid_stepsizeSet*. It calculates the stepsize of *scat_za_grid* and *scat_aa_grid* and stores the result in *grid_stepsize* * src/workspace.cc: Added Vector *grid_stepsize*. Here the gridstepsize of *scat_za_grid* and *scat_aa_grid* are stored. If the stepsize varies, -1 is stored. * src/m_scatrte.cc: Added *grid_stepsizeSet*. The implementation. 2003-05-27 Sreerekha T.R. * arts-1-1-555 * src/m_cloudbox.cc (ybatchMetProfiles): Modifed the function to take into account the orographic height corresponding to each profiles. The path to pnd_field_raw data is also modified. * src/methods.cc: Added *z_ground* in the output of *ybatchMetProfiles*. 2003-05-26 Oliver Lemke * arts-1-1-554 * src/Makefile.am: Added matpackII.{cc,h} to sources of most targets. * src/matpackII.{cc,h}: Added dummy resize function to Sparse. Move implementation of rw and ro to operator(). Make rw, ro wrappers calling operator(). * src/m_sensor.cc (sensor_responseBackend, sensor_responseAntenna1D): Changed type of sensor_response_tmp and ws output to Sparse. * src/workspace.cc: Changed group of sensor_response to Sparse. * src/test_matpack.cc: Include matpackII.h instead of matpackII.cc. Never include cc files!!! -> duplicate defined symbols. 2003-05-26 Claas Teichmann * arts-1-1-553 * src/math_funcs.cc: fixed integration routine 2003-05-26 Mattias Ekström * arts-1-1-552 * src/groups.cc: Added new WSV group Sparse. The group has not yet been fully implemented, the code compiles as long as no WSV beolngs to the group. This has to be fixed. * src/make_auto_wsv_h.cc: Include matpackII.h in auto_wsv.h * src/methods.cc: Added three new WSM; sensor_responseAntenna1D, sensor_responseBackend and sensor_responseInit. * src/m_sensor.cc: Implementation of the sensor_responseAntenna1D, sensor_responseBackend and sensor_responseInit which sets up the sensor_response matrix or modifies it with the antenna/backend response. * src/workspace.cc: Added two new WSV; sensor_response and f_sensor that are used in sensor modelling. The sensor_response is a matrix that describes the whole sensor block response and f_sensor is a vector that describes the sensor channel frequencies. * src/xml_io.cc: Dummy functions for xml I/O for Sparse. * src/xml_io_private.h: Declarations for the above I/O functions. 2003-05-22 Claudia Emde * arts-1-1-551 * src/methods.cc: Included documentation for recently added methods related to the new database format. * src/m_optproperties.cc: Documented and claened up the code. * src/optproperties.{cc,h}: Fixed inconcistencies. Now the data in the database has to be stored in SI units (m^2 for the optical properties). Before it was (um^2). Note: The new database works for stokes_dim = 1. There is still a problem for higher Stokes dimensions. I think that I do not handle some special cases correctly in the transformation from the scattering frame to the laboratory frame. For stokes_dim = 1 the transformation is very easy, but for higher Stokes dimensions the transformation formulas become rather complicated. 2003-05-15 Oliver Lemke * arts-1-1-550 * doc/doxygen/html/.cvsignore: Added graph_legend.dot. * src/m_sensor (GaussianResponse): Cast ceil return value to Index before assigning to nrows avoids warning message. Use log(2.) instead of log(2) because log is not overloaded for int and gcc cannot decide whether to cast to float or double. 2003-05-21 Mattias Ekström * arts-1-1-549 * src/m_sensor.cc: Added WSM GaussianResponse to set up a sensor response matrix with gaussian distribution. 2003-05-20 Mattias Ekström * arts-1-1-548 * src/m_ppath.cc: Added WSM VectorZtanToZaRefr that calculates zenith angles from a given set of true tangential altitude. It uses the refr_index_agenda to calculate the refractive index at tangential point. 2003-05-19 Oliver Lemke * arts-1-1-547 * src/m_cloudbox.cc: Final fix for ios::showpoint and ios::fixed. 2003-05-19 Mattias Ekström * arts-1-1-546 * src/sensor.{cc,h}: Added spectrometer_transfer_matrix that models the backend response for spectrometers. Also made fixed bugs in sensor_integration_vector. * src/refraction.{cc,h}: Added function refr_index_ir that calculates refraction index in the IR region, using formula from Michael Höpfner, Forchungszentrum Karlsruhe. * src/m_refraction.cc: Added refr_indexIR to interface with refr_index_ir. * src/methods.cc: Added refr_indexIR entry. 2003-05-19 Oliver Lemke * arts-1-1-545 * src/m_cloudbox.cc: Added include cmath for proper use of abs. Use showpoint and fixed from namespace ios. 2003-05-16 Sreerekha T.R. * arts-1-1-544 * src/m_cloudbox.cc (ybatchMetProfiles): Modified the method. The input to this method is now the AMSU datafile which has information about latitude, longitude, satellite zenith angle. The corresponding workspace variable is *met_amsu_data* which is a matrix. The method reads the profiles corresponding to the lat-lon. It now uses the correct *sensor_los* from the satellite zenith angle. It also sets the cloudbox from the profiles. The workspace variable *met_profile_basenames* is removed. * src/m_scatrte.cc : Modifications in the method *i_fieldUpdate1D_PlaneParallel* . * src/methods.cc: Modified the interface to the method *ybatchMetProfiles*. * src/workspace.cc : Added the new workspace variables *met_amsu_data* and *met_profile_path*. 2003-05-16 Oliver Lemke * arts-1-1-543 * src/Makefile.am: Fixed bug reported by Mattias. arts.cc was missing in some targets which caused undefined symbol arts_exit while linking. * src/absorption.cc: Include arts.h * src/agenda_class.cc: Include arts.h * src/xml_io.cc: Include arts.h 2003-05-14 Oliver Lemke * arts-1-1-542 * src/xml_io.cc: Added function xml_data_parse_error. Call xml_data_parse_error in all xml_read_from_stream functions when there is a problem while parsing the data of a tag. x_d_p_e outputs the tag name, the attribute list and additional information to help the user finding out where the error occured. * src/xml_io_private.h: Added function xml_data_parse_error. * src/main.cc (main): Use a separate report file for each process. First report file is CONTROLFILE.rep, report files of the child processes are called CONTROLFILE.1.rep, CONTROLFILE.2.rep... * src/arts_mpi.cc (MpiManager::startup): Set rank and nprocs. * src/Makefile.am: Removed dependency on arts_mpi.{cc,h} from make_auto_* files to avoid unnecessary recompilation. Maybe these have to be added again later when mpi is more and more integrated into arts. (xml_io.o): Must depend on xml_io.c. 2003-05-14 Oliver Lemke * arts-1-1-541 * src/main.cc (main): Use the mpi_manager. * src/arts.cc (arts_exit): Removed call to mpi_shutdown. Now handled by the destructor of the MpiManager. * src/arts_mpi.{cc,h}: Created MpiManager class. Takes care of initialization and finalization of MPI. Furthermore, provides access to MPI runtime information. * doc/doxygen/Makefile.am (doxyfied): Must depend on Doxyfile. * doc/doxygen/Doxyfile.in: Pass HAVE_MPI to preprocessor to enable MPI documentation. 2003-05-13 Claas Teichmann * arts-1-1-540 * src/math_funcs.cc (AngIntegrate_trapezoid): added function with integration over azimuth angle already calculated: gives a 2*PI 2003-05-13 Claudia Emde * arts-1-1-539 * src/optproperties.{cc,h} (pha_matTransform): Modified. Created new functions (interpolate_scat_angle) and (pha_mat_labCalc) to improve readability of the code. 2003-05-13 Oliver Lemke * arts-1-1-538 * src/main.cc (main): Replaced all return statements with arts_exit to avoid missing call to mpi finalize. 2003-05-07 Claas Teichmann * arts-1-1-537 * doc/uguide/scattering.tex: Fixed typos. 2003-05-07 Oliver Lemke * arts-1-1-536 * src/Makefile.am: Added arts_mpi.h. * src/arts_mpi.h: Added. * src/arts_mpi.cc: Added. Implemented basic mpi_startup and mpi_shutdown functions. * src/main.cc: Call mpi_startup at the beginning. Instead of return, call arts_exit at the end of main to cleany finalize mpi. * src/xml_io.cc: Replaced another exit. * src/arts.cc: Use MPI_ONLY macro. 2003-05-07 Oliver Lemke * arts-1-1-535 * src/methods.h, src/agenda_record.h, src/absorption.cc, src/agenda_class.cc, src/file.cc, src/main.cc, src/m_general.cc, src/m_scatrte.cc, src/old_absorption.cc, src/parameters.cc, src/parser.cc, src/token.cc: Replaced all calls to libc exit function with our own arts_exit function. Whenever you want to quit arts at some point, please use from now on arts_exit instead of exit. Currently there is nothing done in arts_exit, but in the near future we have to do some cleanup on exit (e.g. for MPI). * src/main.cc: Added MPI to output of arts -v. * src/arts.cc: Added. Added function arts_exit. * src/Makefile.am: Added arts.cc. 2003-05-02 Claudia Emde * arts-1-1-534 * src/agendas.cc: Added *scat_rte_agenda* and *scat_field_agenda*. These agendas are useful, because we have now many methods for calculating the 'cloudy' RT (sequential update, plane parallel or the 'normal' old method). For the scattering integral we have two methods which have to be chosen according to the database format (amp_mat or SingleScatteringData. It is now possible to do the scattering calculations with both data- base formats. The amplitude-matrix format will be removed later, but now we should keep it to eb able to compare the results. * src/m_scatrte.cc(i_fieldIterate): Modified. Execxute agendas above instead of functions. (ScatteringInitAmpMat): New method. Used for initializing scattering variables if amp_mat is used as data-format. (scat_fieldCalc): The standart function for calculating the scattering integral. Uses Single ScatteringData structure. (scat_fieldCalcFromAmpMat): Scattering integral calculation from amplitude matrix. * src/m_optproperties(pha_mat_sptCalc), (opt_prop_sptCalc): Bugs fixed. * src/optproperties(pha_matTransform): Included different cases which have to be considered for the coordinate transform. There still seems to be a problem if the zenith angle of the direction of the scattered radiation is 0. * src/methods.cc: Included new methods changes described above. * src/workspace.cc: Removed *part_types*. Redundant now. * src/m_cloudbox.cc(ybatchMetProfiles): Removed *part_types* and included *scat_raw_data* instead to get the information about the number of particle types. * src/rte.cc (rte_step): Modified unpoarized part. The scattering term has been missing there. 2003-04-30 Oliver Lemke * arts-1-1-533 * configure.in: Added option --with-mpi to support MPI. 2003-04-25 Stefan Buehler * arts-1-1-532 * General: Now I have removed CloneSize, as I promised a long time ago, but never did. * src/m_clonesize.cc: Removed. * src/methods.cc: Removed CloneSize. * src/Makefile.am: Removed CloneSize. * src/.cvsignore: Added test_sensor. 2003-04-25 Claudia Emde * arts-1-1-531 * src/m_cloudbox.cc: Changed names of reading routines for amplitude matrix data. These are now called *ParticleTypeInitAmpl* and *ParticleTypeAddAmpl*. The old names *ParticleTypeInit* and *ParticleTypeAdd* are now used for new methods which read the single scattering data from the new database format. * src/m_optproperties.cc: Completed *pha_mat_sptFromData* and *opt_prop_sptFromData*. The functions are ready but not tested yet. * src/optproperties.h: Typedef for ArrayOfSingleScatteringData. * src/groups.cc: Added ArrayOfSingleScatteringData. * src/workspace.cc: Added *scat_data_raw* : Variable of type ArrayOfSingleScatteringData which contains the scattering properties of all considered hydro-meteor species. * src/methods.cc: Included *ParticleTypeInitAmpl* and *ParticleTypeAddAmpl*. Modified *ParticleTypeInit* and *ParticleTypeAdd*. * src/xml_io.cc: Included reading and writing routines for *ArrayOfSingleScatteringData*. * src/xml_io_private.h: Included *ArrayOfSingleScatteringData*. * src/m_clonesize.cc: Included *ArrayOfSingleScatteringData*. 2003-04-25 Mattias Ekström * arts-1-1-530 * src/sensor.cc: Added normalisation to sensor_integration_vector. 2003-04-24 Claudia Emde * arts-1-1-529 * src/m_optproperties.cc: Added new methods to calculate the single particle properties from the new database format: *pha_mat_sptFromData* and *opt_prop_sptFromData* * src/optproperties.{cc,h}: Included transformations from the coordinate system used in the database to the laboratory coordinate system. So far only for the case of randomly oriented particles. Modified the structure *SingleScatteringData*: Included additional field for temperature. * src/xml_io.cc: Modified reading and writing routines for *SingleScatteringData*. * src/methods.cc: Included the methods above. * src/workspace.cc: Modified WSV *part_types*. It is now an ArrayOfString containing the filenames of the different particles which shall be included in the calculation. 2003-04-23 Nikolay Koulev * arts-1-1-528 * src/zeemanproperties.{cc,h}: Added the N- case of a Zeeman transition. Added more comments for lucidity reasons. * src/test_zeemanproperties.{cc}: Changed accordingly. 2003-04-23 Sreerekha T.R. * arts-1-1-527 * src/m_cloudbox.cc (ybatchMetProfiles): The method ybatchMetProfiles is modified in such a way that now the *p_grid* is set inside the function. This is done in such a way that the first element of the p_grid is taken from the profile data itself. The number of elements in the p_grid is now given as a keyword. Another modification is to define a variable which can store the path of the data. * src/workspace.cc : The workspace variable *met_profile_path* of type String is added. * src/methods.cc : Modified the interface of the method *ybatchMetProfiles*. 2003-04-22 Sreerekha T.R. * arts-1-1-526 * src/m_atmosphere.cc (pnd_fieldCalc): Implemented this method which intepolates the *pnd_field_raw* on to the grids, *p_grid*, *lat_grid*, and *lon_grid* for calculation. This method is similar to the method *AtmFieldsCalc* which does the interpolation for temperature, altitude and vmr. * src/methods.cc : Added the method pnd_fieldCalc. 2003-04-17 Sreerekha T.R. * arts-1-1-525 * src/workspace.cc : Added the variable *ybatch* and *met_profile_calc_agenda* * src/agendas.cc : Set up the agenda *met_profile_calc_agenda* * src/methods.cc : Added the method *ybatchMetProfiles* * src/m_cloudbox.cc (ybatchMetProfiles): This method is used for calculating spectra for the profiles from metoffice. The method does a loop around the profile basenames and executes the agenda *met_profile-calc_agenda* for absorption as well as radiative transfer calculations. It gives ybatch as the output. * src/test_sensor.cc: included iostream. 2003-04-15 Stefan Buehler * arts-1-1-524 * src/workspace.cc (define_wsv_data): Moved els_f_grid to the reight place in the alphabetical list. (define_wsv_data): Moved output_file_format to the reight place in the alphabetical list. (define_wsv_data): Added WSV met_profile_basenames. 2003-04-11 Mattias Ekström * arts-1-1-523 * src/Makefile.am: Added a test_sensor sources group. * src/test_sensor.cc: Added this for testing sensor modelling functions. * src/sensor.{cc,h} (antenna_transfer_matrix): Changed to sparse matrix representation. 2003-04-10 Oliver Lemke * arts-1-1-522 * src/matpackII.cc (transpose): Replaced Index* by std::vector::iterator to fix compilation error. 2003-04-09 Mattias Ekström * arts-1-1-521 * src/matpackII.{h,cc}: Added functions for sparse matrix operations; transposing, muliplication with full matrix and multiplication with sparse matrix. * src/test_matpack.cc: Added function for testing sparse matrix multiplication. 2003-04-06 Patrick Eriksson * arts-1-1-520 * src/m_rte.cc (RteEmissionTest): Made a quick hack to test an integration assuming B to be linear in optiocal thickness, following Equation 9.16 in Rodgers' book (though I think the expression is wrong). A first test showed no improvement at all!? I have to check the details. * src/rte.cc (rte_step): For scalar case, introduced a variable for transmission to save some time and make the code clearer. 2003-04-02 Nikolay Koulev * arts-1-1-519 * src/zeemanproperties.cc: Put a new line shape in the complex refractivity, giving at least provisionary meaningful results for the Zeeman absorption. Full implementation to the level of testing the routines through control files is pending. * src/zeemanproperties.h: Updated accordingly. * src/test_zeemanproperties.cc: Updated accordingly. 2003-04-02 Claudia Emde * arts-1-1-518 * src/m_scatrte.cc (i_fieldUpdateSeq1D): Added this method. It updates the radiation field sequentially. The function is at the moment hardwired in *i_fieldIterate* but later on I will make an agenda out of it so that you still have the possibilty to use *i_fieldUpdate1D*. I have made a test calculation, which indicates that the convergence behavior is much better. For most directions only three iterations are needed. Only in close to limb directions we still need 11 iterations (probably the multiple scattering effect). The number of iterations does not depend on the number of pressure levels !!! I took 12 pressure levels and 104 pressure levels and needed exactly the same number of iterations for both cases. * src/methods.cc: Added *i_fieldUpdateSeq1D*. 2003-04-02 Patrick Eriksson * arts-1-1-517 * doc/uguide/main.tex: Put Stefan and me as editors and created a table of authors. Take a look at the table and change if I got something wrong. I would have preferred to have this table on the first page, but the list of authors can eventually be long and I don't think that the table fit on the first page. This solution was a suggestion from Stefan to avoid the problem in how to order the author list. The author table is in alphabetical order. Please, keep the table updated and give comments if you don't like it. Feel free to give the table a nicer appearance. * src/methods.cc: Changed doc for ppath_stepGeometric to make clear that lmax=0 is the same as lmax<0. * doc/uguide/fm_definitions.tex: Added a sub-section to discuss the role of atmospheric grids and the path step length. I was not very inspired and there is nothing that it is not discussed in my emails. 2003-04-02 Oliver Lemke * arts-1-1-516 * src/xml_io.cc: Fixed bug reported by Nikolay. Precision was not set on output which caused Vector to be written with unsufficient decimals. 2003-04-01 Sreerekha T.R. * arts-1-1-515 * src/m_scatrte.cc (convergence_flagAbs_BT): Implemented a separate method for convergence test in brightness temperature units. The old method convergence_flagAbs is not modified. The convergence criteria keyword epsilon can be set in BT units. I used the function invrayjean to convert difference between radiance fields to brightness temperature. This is because Planck is non-linear for small radiances 2003-03-31 Sreerekha T.R. * arts-1-1-514 * src/m_scatrte.cc (convergence_flagAbs): The convergence criteria keyword epsilon can be now set in brightness temperature units. I used the function invplanck to convert radiance to brightness temperature. I had to add *f_grid* and *f_index* as input to this method. * src/methods.cc: Added f_grid and f_index as inputs to convergence_flagAbs. 2003-03-31 Patrick Eriksson * src/ppath.cc (raytrace_3d_linear_euler): For zenith and nadir paths along the end faces, the refraction can turn the path out of the grid in a way not captured by do_gridcell_3d. Additional checks to handle this included. * src/ppath.cc (raytrace_2d_linear_euler): Same change as above (but only for latitude). 2003-03-28 Mattias Ekström * arts-1-1-512 * src/matpackII.cc: Added file to repository 2003-03-28 Mattias Ekström * arts-1-1-511 * src/Makefile.am: Re-commit of changes in arts-1-1-509. * src/matpackI.h: Re-commit of changes in arts-1-1-509. * src/matpackII.{h,cc}: Re-commit of changes in arts-1-1-509. * src/test_matpack.cc: Re-commit of changes in arts-1-1-509. * src/binio.cc: Re-commit of changes in arts-1-1-509. 2003-03-28 Stefan Buehler * arts-1-1-510 * doc/uguide/uguide.tex: Added \FIXME command. Usage: \FIXME{Put your remark here.} This will typeset the remark in bold and add FIXME: in front of it. * doc/uguide/absorption.tex: Documentation for abs_scalar_gas_FieldCalc extended after comment from Sreerekha. 2003-03-27 Mattias Ekström * arts-1-1-509 * src/Makefile.am: Added matpackII.cc everywhere that matpackII.h was listed. I am not sure how to do this correctly (if both files should be listed at more places, for example in test_linalg etc). * src/matpackI.h: Changed SparseMatrixView to SparseView and added SparseView and Sparse as friends for VectorView and Range. * src/matpackII.{h,cc}: Divided matpackII.h into to files and add fixed some bugs and added a function for multiplication with vectors. * src/test_matpack.cc: Uncommented and altered test3 to fit the new sparse- matrix representation and functions. * src/binio.cc: Commented away the declarations of destructors. The compiler would otherwise complain about "redefinition of ..." 2003-03-26 Oliver Lemke * arts-1-1-508 * autogen.sh: Don't redirect output of rm command. Prevents autogen.sh from running properly with plain bourne shell. 2003-03-25 Oliver Lemke * arts-1-1-507 * src/binio.{cc,h}: Moved destructors for bin[io]stream from cc to header file to fix problem with gcc 3.0. 2003-03-25 Oliver Lemke * arts-1-1-506 * doc/uguide/Makefile.am: Bugfix :-) 2003-03-25 Oliver Lemke * arts-1-1-505 * doc/uguide/Makefile.am: arts_groups_to_latex.sh and arts_methods_to_latex.sh where missing in distribution (make dist). Added to EXTRA_DIST. 2003-03-21 Oliver Lemke * arts-1-1-504 * configure.in: Added check for dot tool from the graphviz package. * doc/doxygen/Doxyfile.in: Generate dependency graphs if dot tool is available. 2003-03-20 Claudia Emde * arts-1-1-503 * src/m_scatrte.cc (i_fieldUpdate3D, i_fieldUpdate1D): Small bug fix. *l_step* was taken to be constant inside one ppath step. 2003-03-19 Claudia Emde * arts-1-1-502 * src/m_scatrte.cc (i_fieldUpdate3D): Same modification as for the 1D function. I have tested the new *i_fieldUpdate1D* and the result is improved significantly in Limb direction. 2003-03-18 Claudia Emde * arts-1-1-501 * src/m_scatrte.cc (i_fieldUpdate1D): Modified gaseous absorption coefficients calculation. In the first version I calculated the coefficients for all grid points and interpolated the values inside the RT calculation. Now gaseous absorption is calculated inside the RT part using interpolated pressure, temperature and VMR. This reduces interpolation errors significantly. Attention: Extinction matrix and absorption vector have to be initialized also in *opt_prop_part_agenda* (You should put ext_matInit and abs_vecInit in this agenda, otherwise you will get an error message). This modification will be implemented in 3D later. 2003-03-18 Oliver Lemke * arts-1-1-500 * src/matpack{III,IV,V,VI,VII}.h: Removed inline keyword from copy function declarations. Because they are implemented in the cc file, they could not be inlined which leads to linker errors with -O3 and higher. * src/bofstream.cc: Removed output operator template. * src/refraction.cc: Added cmath include. 2003-03-17 Oliver Lemke * arts-1-1-499 * src/bifstream.h, src/bofstream.h: Implemented putRaw/getRaw. * src/binio.{cc,h}: Added pure virtual functions putRaw to binostream and getRaw to binistream. Modified writeFloat/readFloat to use putRaw/getRaw. Raw reading/writing is used instead of the byte-wise conversion-enabled routines when the data type size and endianness of the host machine matches the data file. Increases speed on pcs by 3.5. 2003-03-17 Mattias Ekström * arts-1-1-498 * src/sensor.cc: Added antenna_diagram_gaussian that sets up an gaussian antenna diagram for a certain frequency. Also added scale_antenna_diagram that scales the diagram to match another frequency. 2003-03-13 Oliver Lemke * arts-1-1-497 * src/binio.{h,cc}: Added. Contains classes for writing binary files including float/double, little-endian/big-endian and ieee-float/non-ieee-float conversions. * src/bifstream.{h,cc}, src/bofstream.{h,cc}: Make use of binio. bof/bifstream now use multiple inheritance. They inherit the file handling abilities from fstream and the architecture independent reading/writing features from binistream/binostream. Binio is quite dumb when no conversion for saving in the desired format is needed. This leads to drawbacks concerning speed. They will be extirpated in the next version. Note on current binary format: All float values are stored as IEEE-754 double precision. Integers are saved as 8 byte values. Byte order is always little endian (PC). * src/Makefile.am: Added binio.{h,cc}. * doc/index.html.in: Removed out-dated example files list. Instead added a link to the examples directory. 2003-03-10 Oliver Lemke * arts-1-1-496 * doc/doxygen/html/Makefile.am: Include png images. 2003-03-10 Patrick Eriksson * arts-1-1-495 * doc/uguide/main.tex: Changed the author list, to only include persons that have contributed to the present version of AUG. As Claudia took the step and broke the alphabetical order, I also moved the names around with the idea that the author list shall reflect the contribution to the user guide. As a pure coincidence my name ended up first! * doc/uguide/ppath.tex: Included control file examples. Fixed some smaller things that I discovered when working on the progress report. Commented out figure on spherical/ellipsiodal geoid. The figure is not correct. 2003-03-10 Stefan Buehler * arts-1-1-494 * doc/uguide/absorption.tex: Added Section about the absorption lookup table. * doc/uguide/symbol_defs: Renamed to symbol_defs.tex. * doc/uguide/symbol_defs.tex: What used to be symbol_defs. * doc/uguide/uguide.tex: Fixed the "destination with the same identifier has been already used" warning. (At least mostly.) The warning comes from incompatibilities of hyperref with other packages. Remaining problem: Algorithm and hyperref do not seem to agree very well. But I managed to remover all warnings except two. * doc/uguide/main.tex: Fixed the "destination with the same identifier has been already used" warning. All package includes are now in uguide.tex! 2003-03-10 Oliver Lemke * arts-1-1-493 * doc/index.html.in: Removed link to ps uguide. 2003-03-10 Claudia Emde * arts-1-1-492 * doc/uguide/main.tex: Updated author list. 2003-03-10 Oliver Lemke * arts-1-1-491 * src/xml_io.cc: Cleanup. Added check for matching frequency dimensions in f_grid and pha_mat_data. * src/xml_io_private.h: Cleanup. 2003-03-08 Patrick Eriksson * arts-1-1-490 * doc/uguide/ppath.tex: Completed description of Euler scheme for refraction. Added 3 new figures, showing properties of the refractive index. * src/ppath.cc (raytrace_2d_linear_euler): The bugs mentioned in last commit, were no bugs. It was late and I forgot that the scaling is performed as part of the functions returning the gradients of the refractive index. The idea is that the gradient in all directions shall have the same unit (the change of refractive index over 1 m). 2003-03-07 Patrick Eriksson * arts-1-1-489 * doc/uguide/ppath.tex: Continued writing on refrcation. 1D and 2D finished. Must check expressions for 3D. I have missed some scaling terms. Added a figure: euler.pdf * src/ppath.cc (raytrace_3d_linear_euler): There was an inconsistency regarding the values used to adjust LOS angles. Radius, lat and lon were taken from the start of the ray tracing step, while za and aa were taken from the end point. There are similar mistakes as for 2D mentioned below, and for the moment there will be an error if you attempt to use this function. (raytrace_2d_linear_euler): The division with the radius was missing for the term including the latitude gradient of the refractive index. 2003-03-07 Claudia Emde * arts-1-1-488 * src/m_scatrte.cc (i_fieldUpdate3D): Same bug fix as for (i_fieldUpdate1D). 2003-03-07 Claudia Emde * arts-1-1-487 * src/m_scatrte.cc (i_fieldUpdate1D): Fixed a bug. The function did not work when *ppath_step_agenda* putted extra points inside one layer (this can happen when you specify *lmax* or when you cross the tangent point). Now the radiative transfer calculation is done by going from one point to the next inside one layer. * src/workspace.cc: Included variable *single_scattering_data*. 2003-03-06 Oliver Lemke * arts-1-1-486 * src/xml_io.cc: Implemented reading/writing routines for SingleScatteringData. * src/test_xml.cc, src/test_binaryio.cc: Fixed warnings. 2003-03-07 Sreerekha T.R. * arts-1-1-485 * src/m_cloudbox.cc (CloudboxGetOutgoing): Fixed bug in this function. 2003-03-07 Claudia Emde * arts-1-1-484 * src/optproperties.h: Modified structure *SingleScatteringData* (see email to arts-dev mailing list). 2003-03-07 Patrick Eriksson * arts-1-1-483 * doc/uguide/ppath.tex: Started writing on refraction. * doc/uguide/symbol_defs: Added symbol for partil deravitive (\PartD) 2003-03-06 Patrick Eriksson * arts-1-1-482 * src/rte.cc (ground_specular_los): Removed an if-statement by instead using sign to seperate the cases of positive and negative zenith angles for 2D. * doc/uguide/introduction.tex: Removed some points in the the to do list :-) , but there are still many things to fix :-( * doc/uguide/Figs/ppath/mkfigs_ppath.m: Created this file to generate figures to visualize the calculation of propagation paths. Copied figures (with sligh editing) from ARTS-1 for Snells' law for a spherical symmetry. * doc/uguide/ppath.tex: Included the figures mentioned above and polished the old text. Started to write about refraction. * doc/uguide/Figs/fm_definitions/mkfigs_ppath_cases.m: Recreated old figure for ground reflections. * doc/uguide/fm_definitions.tex: Improved text for ground reflections. 2003-03-06 Mattias Ekström * arts-1-1-481 * src/m_sensor.cc Remove the old test WSM SensorIntegrationVector and add a new AntennaTransferMatrix. * src/sensor.{cc,h} Added function antenna_transfer_matrix that uses sensor_integration_vector to build up a matrix that covers both frequency and mblocks. Both antenna_transfer_matrix and sensor_integration_vector has been tested for a simple linear case. 2003-03-06 Oliver Lemke * arts-1-1-480 * src/matpackI.cc: Another unused joker eliminated. 2003-03-06 Oliver Lemke * arts-1-1-479 * src/m_clonesize.cc: Added function for SingleScatteringData. Fixed unused parameter warnings. * src/m_hdf.cc: Fixed unused parameter warnings. * src/matpackI.cc: Fixed joker warning. * src/Makefile.am: Added optproperties.{cc,h} in some places. * src/xml_io.cc: Added dummy read/write functions for SingleScatteringData. * src/xml_io_private.h: Added read/write functions for SingleScatteringData. * doc/examples/xml.arts: Updated. 2003-03-06 Claudia Emde * arts-1-1-478 * src/optproperties.{cc,h}: Created these files. Defined the new structure *SingleScatteringData* in optproperties.h. The functions concerning the transformation from the data to the relevant workspace variables will be put in optproperties.cc. * src/groups.cc: Added *SingleScatteringData*. * src/make_auto_wsv_h.cc: Included *SingleScatteringData*. * src/make_auto_wsv_groups_h.cc: Included *SingleScatteringData*. * src/Makefile.am (arts_SOURCES): Included optproperties.h, optproperties.cc. 2003-03-06 Oliver Lemke * arts-1-1-477 * src/make_auto_wsv_h.cc: Removed touch member function from WorkSpace. * src/agenda_class.h: Removed touch member function from MRecord. * src/m_ignore.h: Fixed unused parameter warning. * src/make_auto_md_cc.cc: If parameter ws or mr is unused then omit name in function definition to avoid compiler warning. * src/xml_io.cc: Fixed unused parameter warnings. 2003-03-06 Oliver Lemke * arts-1-1-476 * configure.in: Added doc/uguide/Figs/concept and doc/uguide/Figs/rte_theory to AC_OUTPUT. * doc/uguide/Figs/Makefile.am: Added rte_theory to SUBDIRS. 2003-03-06 Stefan Buehler * arts-1-1-475 * src/m_ignore.h (Ignore): Managed to suppress the unused parameter warning for parameter *in* with a somewhat nasty hack. But it works, and I made sure that there are some explantory comments why this is done. Oliver, I believe the same trick could be used to make a template function "touch" that works for any type. What do you think? 2003-03-05 Patrick Eriksson * arts-1-1-474 * doc/uguide/los1d.tex: Removed this file. * doc/uguide/fm_definitions.tex: Polished the text, and put in some details about ground reflections. * doc/uguide/rte_theory.tex: Created this chapter by copying text from a compendium I have written (originally from a old report). * doc/uguide/sensor.tex: Commented out all old text. * doc/uguide/main.tex: Activated sensor chapter, and added chapter on radiative transfer theory. 2003-03-05 Patrick Eriksson * arts-1-1-473 * doc/uguide/fm_definitions.tex: Improved and updated text. Added two figures (ppath_badcases.pdf and atm_dim_3dcross.pdf). Check out the figures of the chapter (except from last page). I think they are nice (of course). 2003-03-05 Patrick Eriksson * arts-1-1-472 * doc/uguide/fm_definitions.tex: Included figure for 3D atmosphere and modified figure text for 1D and 2D atmospheres. * src/XXXX: Fixed warnings about unused variables in "my" parts. * src/m_refraction.cc (refr_indexUnit): Removed input arguments not used. The function must now be combined by Ignore calls. 2003-03-05 Stefan Buehler * arts-1-1-471 * src/m_ignore.h (Ignore): Issue a level 2 message which WSV is ignored. This avoids the unused parameter warning for *inname*. However, there still is one for *in*. Don't know how to fix this right now. * src/m_copy.h (Copy): Removed call of CloneSize. 2003-03-05 Stefan Buehler * arts-1-1-470 * src/m_clonesize.cc: Added some level 2 and 3 output messages to surpress most unused parameter warnings. * src/methods.h (MdRecord operator=(const MdRecord& m)): Added output of m to suppress unused parameter warning. 2003-03-05 Oliver Lemke * arts-1-1-469 * configure.in: Don't use -Wno-unused (gcc2) and -Wno-unused-parameter (gcc3) any longer. Removed check for gcc version. * src/agenda_class.h: Added dummy method touch to MRecord. * src/make_auto_wsv_h.cc: Added dummy method touch to WorkSpace. * src/make_auto_md_cc.cc: If WorkSpace is not used in method call ws.touch to avoid unused parameter warning. Same for MRecord. 2003-03-04 Patrick Eriksson * arts-1-1-468 * doc/uguide/Figs/fm_definitions/mkfigs_atm_dims.m: Added 3D figure. 2003-03-04 Patrick Eriksson * arts-1-1-467 * doc/uguide/Figs/fm_definitions/mkfigs_atm_dims.m: Modified this function. It now uses atmlab/arts/arts_plot_atmgrids.m. * src/ppath.cc: Removed input argument t_field as it was no longer used. * src/m_ppath.cc (ZaSatOccultation): As above. 2003-03-03 Patrick Eriksson * arts-1-1-466 * src/m_ppath.cc (DoGridcell2D/3D): Removed these WSM. (ppathCalcTest): Removed also this WSM. * doc/uguide/Figs: Created the folder concept and moved two figures to that folder. Removed all remaining figures in the folder /Figs (as decided some time ago). If you want to use some of the removed figures, copy it from arts-1. The decision is that all figures shall be placed in sub-folders, one fore each chapter, where the folder name shall match the name of the Latex file. 2003-02-28 Stefan Buehler * arts-1-1-465 * src/gas_abs_lookup.cc (Extract): Calculate number density with the physics_funcs function number_density. (Extract): Fixed bug reported by Patrick: VMR scaling for the case with temperature variations was missing. (Extract): Fixed bug related to pressure interpolation for the variable T case. 2003-02-28 Mattias Ekström * arts-1-1-464 * src/sensor.cc (sensor_integration_vector): Added file and created function that calculates the (row) vector that multiplied with an unknown (column) vector approximates the integral of products between two functions, where the two vectors are the quantizied representation of the functions. See ARTS 1 User Guide, chapter 7 Sensor modelling for an in-depths explanation. * src/sensor.h: Added the file. * src/describe.h: Added line; #include "mystring.h". We need it for the compilation. 2003-02-27 Patrick Eriksson * arts-1-1-463 * src/rte.cc (get_radiative_background): Fixed a bug for cases with ground reflection. Bug reported by Sreerekha. The bug had no effect for a blackbody ground. The solution with agendas makes some things difficult. My solution for ground reflections involve a recursive call of RteCalc. The output from get_radiative_background is the WSV i_rte. When calling RteCalc recursively, I did this with a local variable, but RteCalc calls rte_agenda which will change the value of i_rte. The problem was that i_rte already contained interesting values. So I got a side effect from the agenda that I missed. I hope that there are now no such side effects left in this part. But changes for the agendas can easily affect this part, so we ahve to be careful when changing things for the agendas. 2003-02-27 Stefan Buehler * arts-1-1-462 * src/gas_abs_lookup.cc: I'm still working on the gas absorption lookup table. Beware! This is not yet the final version. I want to do some tests tomorrow, in order to see if temperature interpolation works. The case without temperature variations is tested and is believed to work correctly. IMPORTANT: We are now storing absorption cross-sections, rather than absorption coefficients in the table. Old tables will not work anymore, unfortunately. However, this is worth the inconvenience since it decreases interpolation error by two orders of magnitude! (See my email to arts-dev.) * src/gas_abs_lookup.h: Updated. * src/m_absorption.cc (abs_scalar_gas_fieldCalc): This method now takes f_index as input. Depending on f_index, the field will be calculated for all frequencies, or just for one frequency. * src/methods.cc: Updated record for abs_scalar_gas_fieldCalc. * src/agendas.cc (define_agenda_data): Added f_index in the input list of scalar_gas_absorption_agenda. * src/xml_io.cc (xml_read_from_stream): Read .xml instead of .abs. (xml_write_to_stream): Write .xml instead of .abs. * src/describe.cc: Added. This file contains a set of helper functions called \c describe, which you can use to output the dimensions of a tensor. This is just for testing purposes. * src/describe.h: Added. Header file for describe.cc. * src/test_matpack.cc: Modified some tests. * src/matpackIII.cc: Only linebreak changes. * src/matpackI.h: Only whitespace removed. * src/matpackI.cc: Only indentation changes. * src/m_scatrte.cc: Updated copyright notice. * src/m_cloudbox.cc: Updated copyright notice. * src/Makefile.am (test_matpack_SOURCES): Added describe. 2003-02-26 Claudia Emde * arts-1-1-461 * src/m_scatrte.cc (convergence_flagAbs): Modified the function. It has been a very special function for the radiation field. Now it is a general method which can be used for any Tensor6's. * src/m_scatrte.cc (i_fieldUpdate1D), (i_fieldUpdate3D): Structured the interface variables such that it is easier to see why they are needed in the function. Also removed some variables: There was a diskussion about *stokes_dim* and *atmosphere_dim* some time ago. I removed this variables now and extracted the dimensions from other variables. Furthermore I could remove some variables which had been used for executing *scat_rte_agenda* which is not there anymore. We decided to "hardwire" the RT method to be used. * src/m_scatrte (i_fieldIterate): Structured interface variables. * src/m_scatrte (ScatteringInit): Created this function to initialize the variables used in agendas for scattering calculations. Previously the initialization was done in *i_fieldIterate*. The structure becomes clearer when we have this additional function. * src/m_scatrte.cc (iteration_counterIncrease): Icluded this small function to be able to separate the iteration counter from the other methods (for modularity reasons). * src/methods.cc: Adjusted entries according to changes above. * src/agendas.cc: Modified input/output for *opt_prop_part_agenda* and *convergence_test_agenda*. * doc/examples/cloud_rad_field1D_example.arts.in: Added more desciption into the controfile to make clear, where which agenda is used. 2003-02-25 Patrick Eriksson * arts-1-1-460 * doc/uguide/ppath.tex: Added some missing terms in some equations. Some small polishing of the text. 2003-02-25 Mattias Ekström * arts-1-1-459 * src/m_basic_types.cc: Added VSM Tensor3Scale, Tensor4Scale, Tensor5Scale, Tensor6Scale and Tensor7Scale. * src/m_sensor.cc: Added this file for sensor modelling. 2003-02-24 Patrick Eriksson * arts-1-1-458 * src/m_rte.cc (RteEmissionStd): Removed a variable not used (with apossible size of up to 10 Mb!) and moved some lines to outside a for loop (to maybe save some time). 2003-02-23 Patrick Eriksson * arts-1-1-457 * doc/uguide/ppath.tex: Further work on documentation of the path calculations. Geometrical paths are close to be finished. Some details are missing. I plan also to create some figures. * doc/uguide/fm_definitions.tex: Added definition of the azimuth angle at the poles. 2003-02-17 Claudia Emde * arts-1-1-456 * src/main.cc: Set default reporting level for report file to 0. My ARTS jobs crash because the report file becaomes too large when I use report level 3. 2003-02-14 Patrick Eriksson * arts-1-1-455 * doc/uguide/ppath.tex: Text added to describe the calculation of propagation paths. Not ready, more to write. 2003-02-11 Patrick Eriksson * arts-1-1-454 * doc/uguide/ppath.tex: Modified existing text as a first step to finish this chapter in AUG. 2003-02-11 Mattias Ekström * arts-1-1-453 * src/m_ppath.cc (ZaSatOccultation): Created WSM for calculating zenith angles during satellite occultations. * src/ppath.h (geompath_lat_at_za): Added method to header file. 2003-02-07 Patrick Eriksson * arts-1-1-452 * src/m_cloudbox.cc (CloudboxSetManually): The function now behaves as expected for limits identical to grid values. * src/ppath.cc (do_gridcell_3d): Improvement in 1-1-451 for west-east cases was incorrect. In the hurry, the type for abs( aa_start ) was set to bool (instead of double). This turned the fix off, and there was a crash for Numeric=float. It appears that this fix is not needed for double, but I leave it, just in case. 2003-02-07 Patrick Eriksson * arts-1-1-451 * src/ppath.cc (ppath_start_stepping): Upward observations along the upper latitude limit is not allowed for 2D. That is, start position inside the atmosphere, za=0, and lat=last(lat_grid). (do_gridcell_3d): Test for finding strictly west-east observations was wrong. Strange that it has not crashed. All old 3D results are definitely wrong. 2003-02-06 Patrick Eriksson * arts-1-1-450 * src/ppath.cc (geompath_from_r1_to_r2): Using r2 instead of r[n] when calculating za[n], as r2 is always double. The conversion from double top float can result in a shift of 0.1 m, which can end up below ppc. Successful tests with refraction and Numeric=float for 1D and 2D. So, refraction for 1D and 2D is now hopefully working (3D with refrcation is NOT worling yet). 2003-02-06 Patrick Eriksson * arts-1-1-449 * src/ppath.cc (do_gridcell_3d): Introduced an allowed tolerance for latitudes and longitudes (LATLONTOL). This turned out to be necessary when using very fine pressure grids (the test was performed with a vertical step size of about 15 m). This problem was reported by Claudia. 2003-02-04 Nikolay Koulev * arts-1-1-448 * src/zeemanproperties.cc: Fixed another bug in the calculation of the relative intensities of individual Zeeman components. 2003-02-04 Patrick Eriksson * arts-1-1-447 * src/ppath.cc (do_gridcell_3d): I discovered that calculations from CloudboxGetIncoming with azimuth angles of exactly 90 degrees caused problems (at least for Numeric=float). Some special checks are now introduced for this case to avoid that the positions are shifted incorrectly to south or north for short step lengths (<1m). * src/m_cloudbox.cc (CloudboxGetIncoming): Removed some crap output to the screen. 2003-02-04 Nikolay Koulev * arts-1-1-446 * src/zeemanproperties.cc: Fixed a bug in the calculation of the relative intensities of individual Zeeman components. Added two more output variables in order to save the frequencies and the corresponding relative intensities of the components as matrixes in xml format. * src/zeemanproperties.h: Modified the file according the changes in the zeemanproperties.cc. * src/test_zeemanproperties.cc: Modified the file according the changes in the zeemanproperties.cc. 2003-02-04 Oliver Lemke * arts-1-1-445 * src/Makefile.am: Added m_xml.cc to arts_SOURCES. * src/test_binaryio.cc: Updated. * src/m_xml.h: Rename FType to FileType and FTYPE_{ASCII,BINARY} to FILE_TYPE_{ASCII,BINARY}. WriteXML gets file_format as input. Added output_file_formatSet{Ascii,Binary}. * src/m_xml.cc: Added. * src/xml_io.cc: Renamed FType to FileType and FTYPE_{ASCII,BINARY} to FILE_TYPE_{ASCII,BINARY}. (xml_read_header_from_stream): Read endian type and numeric type from input file. * src/xml_io.h, src/xml_io_private.h: Rename FType to FileType. * src/methods.cc: Added output_file_formatSet{Ascii,Binary}. WriteXML gets output_file_format as input. * src/workspace.cc: Added variable output_file_format. * src/.cvsignore: Added *.swp to ignore vim temporary files. 2003-02-04 Patrick Eriksson * arts-1-1-444 * src/ppath.cc (do_gridrange_1d and do_gridcell_2d): Same correction as for 3D in last commit. * src/ppath.cc (psurface_crossing_2d): Some upward cases were handled incorrectly. Fixed bug for c=0. * src/ppath.cc (ppath_start_stepping): The entrance point for negative zenith angles and the sensor outisde the atmosphere was calculated wrongly. 2003-02-03 Claudia Emde * arts-1-1-443 * m_scatrte.cc (i_fieldUpdate1D): Modified. The distinction between uplooking and downlooking cases is now done using the grid positions returned by the ppath_step_agenda instead of viewing directions (like in i_fieldUpdata3D). Now, also viewing directions close to 90° can be handled. Interpolation in altitude is done logarithmically (was linear before). * m_cloudbox.cc (CloudboxGetIncoming): Fixed 1D part. Didn't work after some modifications for the 3D part. 2003-02-03 Patrick Eriksson * arts-1-1-442 * src/ppath.cc (do_gridcell_3d): Had to introduce a correction in radius to handle Numeric=float as points can end up slightly outside the grid cell (up to 1 m for float). * src/ppath.cc (psurface_crossing_3d): This function handles now only surfaces with slope. Moved code from gridcell_crossing_3d to this function and removed gridcell_crossing_3d. 2003-02-03 Patrick Eriksson * arts-1-1-441 * src/ppath.cc: Started to remove code not used. Introduced the file-common variables DEV0AND180 and POLELAT to make the accuracy tuning more transperant. 2003-02-03 Claudia Emde * arts-1-1-440 * src/m_scatrte.cc (i_fieldUpdate3D): Included *scat_lat_index* and *scat_lon_index* required for optical properties calculation. Before the optical properties were only calculated for *scat_lat_index* and *scat_lon_index* equal 0. * src/methods.cc(i_fieldUpdate3D): Modified according to correction. 2003-02-03 Patrick Eriksson * arts-1-1-439 * src/ppath.cc: I found more new numerical problems with Numeric=float. This time for calculations with refrcation. It turned out that step lengths of e.g. 1 km could not be used. Decided then to test to hard-code double as far as possible in the function. Everything compiles without warnings. Not yet checked if things work better for Numeric=float. * src/math_funcs.h: Removed declaration of non-existing return version of function of type linspace. * src/m_basic_types.cc (VectorNLogSpace): Not using removed return version of nlogspace. * src/math_funcs.cc (nlinspace): The last value is now set to be stop exactly (not start + i*strep). Removed old return version of nlogspace. 2003-02-02 Patrick Eriksson * arts-1-1-438 * src/ppath.cc (psurface_slope_3d): Applied bigger disturbance for float. (do_gridcell_2d): Upper pressure surface is now checked even if start point is on top of that surface. This is needed for tilted surfaces. (psurface_crossing_2d): Included a threshold for r0=rp. * src/ppath.cc: Smaller fixes here and there. 2003-01-28 Patrick Eriksson * arts-1-1-437 * src/ppath.cc (do_gridcell_3d_try): Added ground intersections and some checks to handle paths along lon grid value. 2003-01-28 Patrick Eriksson * arts-1-1-436 * src/ppath.cc (do_gridcell_3d_try): I have worked on another scheme for this function. The new scheme is based on testing different step lengths, in a hopefully intelegent way, and simply test if the end point is inside or outside the grid cell. This scheme is slower than using a pure analytical solution, but it allows to compensate for numerical problems with float, and works for tilted pressure surfaces, So, if this is a success, both my present problems are solved. I am now trying to stress the new scheme to make it 100% safe. You will not use this new scheme when you compile. 2003-01-28 Nikolay Koulev * arts-1-1-435 * src/zeemanproperties.cc: Fixed several bugs. 2003-01-28 Claudia Emde * arts-1-1-434 * src/m_scatrte.cc (ScatteringMain): Removed clearsky field calculation on boundary (CloudboxGetIncoming) from this function. Now it is possible to read a pre-calculated clearsky field. This makes sense as we are interested to test clouds with different particle types. For those cases the clearsky field on the cloudbox boundary is always the same and it saves a lot of time not recalculating the clearsky field for each case. To do a convergence test it is now also possible to take an unrealistic field on the cloudbox boundary. * src/m_scatrte.cc (i_fieldUpdate3D): Fixed a small bug. * src/m_cloudbox.cc (i_fieldSetConst): Modified. This function is tested now and works correctly. * src/methods.cc (ScatteringMain): Modified interface variables. Note: I have made a 3D convergence test (in analogy to the 1D convergence test). It works, so we can be quite sure, that the 3D scattering implementation is correct! 2003-01-28 Mattias Ekström * arts-1-1-433 * src/m_basic_types.cc: added the WSM Matrix1ColFromVector Matrix2ColFromVectors Matrix3ColFromVectors Matrix1RowFromVector Matrix2RowFromVectors Matrix3RowFromVectors VectorZtanToZa removed the WSM MatrixFillWithVector MatrixSetElement 2003-01-28 Nikolay Koulev * arts-1-1-432 * src/test_zeemanproperties.cc: Fixed bug in the Zeeman test file. 2003-01-27 Oliver Lemke * arts-1-1-431 * Nearly completed binary file support. Missing features: - Integration into arts workspace. - Storing of Numeric/Index type in xml file. -> Currently binary files must be read with the same Numeric/Index type as they where written. * src/Makefile.am: Added test_binaryio target. Added b(i|o)fstream.{cc,h} where needed. * src/test_binaryio.cc: Added for testing binary io routines. * src/xml_io.{h,cc}, src/xml_io_private.h: xml_write_to_file functions take now three parameters. Third arg is the type of file to write (FTYPE_ASCII or FTYPE_BINARY). Default is ASCII. Changed parameters for xml_{write_to,read_from}_stream functions: Removed parameters is_data and os_data. Instead, a pointer to bifstream / bofstream is passed to the function. If the pointer is NULL the data is written to/read from the xml file, otherwise the binary stream is used. * src/bifstream.h: Removed ios::trunc from default openmode. * src/b(i|o)stream.{h,cc}: Added operator template instanciations for types int and long. * src/.cvsignore: Added test_binaryio. 2003-01-27 Nikolay Koulev * arts-1-1-430 * src/zeemanproperties.cc: Made notation of the extinction matrix and absorption vector with Zeeman effect compliant to the this of scattering. * src/zeemanproperties.h: The same for this file. * src/test_zeemanproperties.cc: The same for this file. 2003-01-24 Claudia Emde * arts-1-1-429 * src/m_cloudbox.cc (i_fieldSetClearsky): Bug fixed in 3D part. The limits of some loops were wrong. * src/m_scatrte.cc (scat_fieldCalc): Fixed 3D part: Included (pha_mat_sptCalc), this function was missing, so that the value of the scattering integral was always 0. Included also some dubugging outputs which will be removed later. * src/special_interp.cc: Reincluded iostream. 2003-01-24 Patrick Eriksson * arts-1-1-428 * Removed inclusion of iostream from some files. 2003-01-24 Patrick Eriksson * arts-1-1-427 * src/ppath.cc: Further work on 3D and float. Unfortunately (or maybe it could have been foreseen) it turned out that the spatial precision for 3D and float is as bad as 10 m. The smallest rounding error when going going to cartesian coordinates and back to spherical, shifts the position with about 1 m and some accumaled errors rise the error up to 10m. This high uncertainty makes the present solution in do_gridcell_3d impossible, it is very likely to end up in a situation that cannot be resolved. For double the spatial precison is about 1e-6 m, and the risk to end up in problems is very very small. I have to think about what to do. For the moment, use double. 2003-01-24 Oliver Lemke * arts-1-1-426 * Sorry for the exceeding commit rate, but I have to test the changes on different computers... * src/continua.cc: More pow fixes. Overloading of pow for both pow(float,double) and pow(double,float) breaks float compilation with gcc2. Added f to the numeric literals. * src/math_funcs.{cc,h}: Removed pow (float,double). Confuses gcc2 in many cases and we don't need it currently. 2003-01-24 Oliver Lemke * arts-1-1-425 * src/continua.cc: Fixed pow(Numeric n, int i) calls. For simple cases with i = 2 replaced by n*n. For other cases using 2. instead of 2 2003-01-23 Oliver Lemke * arts-1-1-424 * src/math_funcs.{cc,h}: Added functions pow(float, double) and pow(double, float). * src/continua.cc: Include math_funcs.h for additional pow functions. * src/ppath.cc: Changed constant from int to double as second argument to pow in some places. 2003-01-23 Oliver Lemke * arts-1-1-423 * src/complex.{h,cc}: Added operator+ and operator* with params complex, double and complex, float. * src/Makefile.am (arts_SOURCES) (test_zeemanproperties): Added complex.{h,cc}. * src/xml_io.h: Removed prototypes for xml_open_output_file and xml_open_input_file. * src/xml_io_private.h: Added prototypes for xml_open_output_file and xml_open_input_file. 2003-01-23 Patrick Eriksson * arts-1-1-422 * src/ppath.cc: Compiles now without any warnings with Numeric=float. 2003-01-23 Oliver Lemke * arts-1-1-421 * src/complex.{cc,h}: Added operator+ and operator* for arithmetic expressions where one argument is float and the other complex (or double and complex). The STL only contains functions for operands of same type such as float * complex. 2003-01-23 Patrick Eriksson * arts-1-1-420 * src/ppath.cc: Continued the work to hard-code double in the most critical functions. Don't compile without warnings with Numeric=float, but other parts don't compile at all with that option. 2003-01-23 Claudia Emde * arts-1-1-419 * doc/uguide/main.tex: Included index command to make an index for workspace agendas (\wsaindex). It works as \wsmindex. * doc/uguide/scattering.tex: Rewritten documentation for (i_fieldUpdateXX). * src/math_funcs.cc (AngIntegrate_trapezoid): Modified doxygen header. 2003-01-23 Oliver Lemke * arts-1-1-418 * src/bifstream.h src/bifstream.cc: Added class for binary input. * src/bofstream.cc: Removed matpackI include. * src/bofstream.h: Removed destructor. * src/Makefile.am (arts_SOURCES): Added bifstream.{h,cc}. 2003-01-22 Oliver Lemke * arts-1-1-417 * src/.cvsignore: Added test_zeemanproperties. 2003-01-22 Oliver Lemke * arts-1-1-416 * src/methods.h: Include iosfwd instead of iostream. (MdRecord::operator=): Replaced cout by out0. * src/xml_io.h: Include iosfwd instead of iostream. * src/gridded_fields.cc: Removed duplicate iostream include. * src/lin_alg.cc src/math_funcs.cc src/m_cloudbox.cc src/m_refraction.cc src/scatproperties.cc: Removed unnecessary iostream include. Note about iostream: Wherever possible, including iostream should be avoided because it has quite alot of overhead. If you use cout temporarely for debugging, don't forget to remove the iostream include together with the debug code afterwards. For header files containing function/class declarations which need only references to iostream classes, it is highly recommended to include iosfwd instead of iostream. iosfwd contains only forwarded class declarations which significantly affects compilation speed. 2003-01-22 Nikolay Koulev * arts-1-1-415 * src/zeemanproperties.cc: Added this file, containing the basic routines for calculating the extinction matrix and the absorption vector by the Zeeman effect.. * src/zeemanproperties.h: Header file for the zeemanproperties.cc. * src/test_zeemanproperties.cc: Test file for the Zeeman routines. * src/zeeman_intensity_coeff.xml: XML table of the intensity coefficients for the different transitions of the O2 Zeeman effect, used in zeemanproperties.cc. 2003-01-22 Patrick Eriksson * arts-1-1-414 * src/ppath.cc: Started the work to make things work for Numeric=float, but got time for just a few changes. 2003-01-22 Claudia Emde * arts-1-1-413 * doc/uguide/integration.tex: Included mathematical description of the used integration method. 2003-01-21 Patrick Eriksson * arts-1-1-412 * src/ppath.cc: Wrote some comments and made all function argument lists (in the headers) complete. * src/ppath.cc (raytrace_2d_linear_euler): Added check that zenith angle does not go outside +-180. 2003-01-21 Oliver Lemke * arts-1-1-411 * src/bofstream.{h,cc}: Added. Contains class for writing binary data by using output operators <<. * src/Makefile.am (arts_SOURCES): Added bofstream.{h,cc}. 2003-01-21 Claudia Emde * arts-1-1-410 * src/m_cloudbox.cc (i_fieldSetClearsky): Pressure interpolation changed from linear to logarithmic. * src/m_atmosphere.cc (AtmFieldsCalc): Also changed the pressure interpolation to logarithmic. * src/workspace.cc: Changed documentation of *tensor6_1*, it is a dummy variable to be used when you need a tensor6 somewhere. * doc/uguide/scattering.tex: Started updating this chapter. 2003-01-21 Patrick Eriksson * arts-1-1-409 * src/ppath.cc (raytrace_3d_linear_euler): Put in some fixes to improve the accuracy for zenith and azimuth angles. Included also checks that those angles do not go outside allowed ranges. * src/refraction.cc (refr_index_thayer_1974): Finally changed old parameter values (from Boudouris) to the ones from Thayer. 2003-01-20 Patrick Eriksson * arts-1-1-408 * src/refraction.cc (refr_gradients_1d): Created this function. * src/m_refraction.cc (RefrIndexFieldAndGradients): Finished this function. * src/refraction.cc: * src/ppath.cc: Changes to get a nice verbosity for refr_index_agenda. 2003-01-20 Oliver Lemke * arts-1-1-407 * src/xml_io.cc: Updated doxygen comments. 2003-01-20 Oliver Lemke * arts-1-1-406 * src/xml_io.cc, src/xml_io_private.h: Changed signatures of xml_read_from_stream/xml_write_to_stream functions. First step for binary file support. The read/write functions are now getting two streams as parameters. One is the file stream for the xml file and one the file stream where the data is written to. For ascii files both are the same, for binary the xml_data stream is a reference to the binary stream. This will make it possible to use the same reading/writing routines for both ascii and binary files. 2003-01-20 Patrick Eriksson * arts-1-1-405 * src/refraction.cc (refr_gradients_2d/3d): Changed the definition of the lat and lon gradients. The returned values are now the change of the refractive index over 1m, not 1 radian. * src/ppath.cc (raytrace_2d/3d_linear_euler): Adapted to change above. * src/special_interp.cc (p2gridpos): Created this function. This function SHALL be used when interpolating in pressure. See email to arts-dev. * src/m_refraction.cc (RefrIndexFieldAndGradients): Function basically finished, but there is not yet any function for 1D giving the radial gradient (which is not needed to calculate the paths, but can be interesting to plot). 2003-01-20 Patrick Eriksson * arts-1-1-404 * src/refraction.cc: Changes in most functions to change vertical input coordinate from geometric altitude to radius, which is needed to get lat and lon gradients correct. * src/m_refraction.cc (RefrIndexFieldAndGradients): Started on this WSM. * src/workspace.cc (define_wsv_data): Introduced tensor3_1 and tensor4_1. * src/ppath.cc (do_gridcell_2d): Introduced a more correct setting of the latitude of the end point, for positions between lat1 and lat3. * src/refraction.cc: Included input arguments to control the verbosity when calling *refr_index_agenda*, but there is now no way to use this argument as *refr_index_agenda* is called as part of *ppath_step_agenda* and no such argument can be passed from one agenda to next. * src/ppath.cc (ppath_start_stepping): Improved the accuracy for sensor positions outside the atmosphere and zenith angles of 180 and/or azimuth angles of 0 or 180 degrees. * src/refraction.cc (refr_gradients_3d): The variable dndlon was not set (dndlat was set twice). 2003-01-19 Patrick Eriksson * arts-1-1-403 * src/ppath.cc (raytrace_3d_linear_euler): Put in code for 3D with refraction. The stuff runs, but I have to check the used expressions and results more carefully. * src/m_refraction.cc (refr_indexUnit): Created this WSM. * src/refraction.cc (get_refr_index_3d): Found a bug. Latitude grid position was set twice, and longitude grid position not at all. * src/ppath.cc (do_gridcell_2d): Fixed two bugs connected to the tangent point for limb sounding with negative zenith angles. 2003-01-18 Patrick Eriksson * arts-1-1-402 * src/rte.cc (rte_calc): Forgot to mention that I introdoced this function. It does what RteCalc did, but has the option that input checks can be skipped. This saves some time in CloudboxGetIncoming. 2003-01-18 Patrick Eriksson * arts-1-1-401 * src/ppath.cc (gridcell_crossing_3d): Found a bug that affected the calculated length to a crossing of a given latitude. The original code was correct, but I later removed the calculation of (dx^2+dy^2+dz^2) as this term is always 1. I was then too quick and made a mistake. This bug fix solves the problem discussed for version 1-1-393. Great! 2003-01-18 Patrick Eriksson * arts-1-1-400 * src/m_cloudbox.cc (CloudboxGetIncoming): Some temporary messages that will be removed later (to check speed issues). * src/ppath.cc (gridcell_crossing_3d): Fixed a bug when both solutions for the length >= 0, and of them is 0. The length criterion for solutions close to zero is now applied consistently. (do_gridcell_3d): Allowed some marginals for the lat and lon asserts in the middle of the function. The values are later corrected as far as possible. * src/refraction.cc (get_refr_index_3d): Created this function. (refr_gradients_3d): Created this function. 2003-01-17 Claudia Emde * arts-1-1-399 * src/rte.cc (rte_step): Change condition for unpolarized case (extinction matrix diagonal). The problem is, that if you do a calculation for 2 Stokes dimensions, the extinction matrix can be diagonal although the radiation is polarised. Now the unpolarised calculation is performed if the extinction matrix is diagonal AND all components except the first of the absorption vector are zero. * src/m_cloudbox.cc (CloudboxGetIncoming): Changed the size of the interface variables scat_i_XXX. So far they were defined on the full atmospheric grids which is not necessary. Now they are only defined inside the cloudbox boundaries. Loop indices had to be adapted according to this change. * src/scat_rte.cc (ScatteringMain): Commented CloudboxGetIncoming. For testing constant values for the boundary variables are used. (i_fieldUpdate3D): Fixed bugs in the radiative transfer part. The function runs without crashes but I have to do some tests before I can assure that it works. 2003-01-17 Oliver Lemke * arts-1-1-398 * src/xml_io.cc: Detailed output goes now to out3. Only filenames of input/output files are reported to out2. 2003-01-16 Patrick Eriksson * arts-1-1-397 * Paths with refraction for 1D and 2D have been tested and everything appears to work. * src/refraction.cc (get_refr_index_2d): Wrong dimension was read to determine the number of species. * src/ppath.cc: Included more asserts in the key functions for 3D to catch problems as early as possible. (psurface_crossing_3d): Started on a new version of this function. For the moment it is only allowed to use pressure surfaces with constant radius. That is, the geoid must be spherical and the atmosphere spherically symmetric. * src/m_cloudbox.cc (CloudboxGetIncoming): Found some problematic points, reported to Claudia. 2003-01-15 Patrick Eriksson * arts-1-1-396 * src/refraction.cc (refr_gradients_2d): Created this function. 2D paths with refraction are now completed, but no tests have been performed. * src/ppath.cc (do_gridcell_3d): Added more asserts that should give an earlier and clear indication on that something has gone wrong. (psurface_crossing_2d): Removed some checks that had no impact (for the approximative solution, dlat = 0 was acceped if r0!=rp, but that can never happen as za=0 and za=180 are handled seperately). (raytrace_1d_linear_euler): Cleaned up the code and removed some variables that were not really needed. (raytrace_2d_linear_euler): As above and added call of refr_gradients_2d. 2003-01-15 Claudia Emde * arts-1-1-395 * src/m_cloudbox.cc (i_fieldSetClearsky). Fixed some bugs here. Limits of the loops were wrong. Tested now for 3D. * src/m_scatrte.cc (scat_fieldCalc). Fixed similar bug here. Now the 3D function works. (i_fieldUpdate3D) Also wrong limits at some places. A problem in the interpolation on the intersection point still has to be fixed. 2003-01-15 Patrick Eriksson * arts-1-1-394 * src/ppath.cc: I don't think that I have made any real changes, but a commit just in case if there is something I have missed. Still problems with a non-spherical geoid. A test to calculate the ingoing field to the cloud box for 3D and a spherical geoid was succesful. Claudia, you better make an update to make sure we use exactly the same version. 2003-01-15 Patrick Eriksson * arts-1-1-393 * src/ppath.cc (gridcell_crossing_3d): I discovered that there is an inconsistency between the tangent point position obtained by doing repeated path steps, and a direct calculation with geompath_tanpos_3d. The error, as a vertical displacement, is about 1.5 km. I have spent some time on trying to understand this, and my guess is that the problems appear in this function, but I have no final confirmation, and I don't know right now what to do about it. * src/ppath.cc (do_gridcell_1/2/3d): The tangent point is now not flagged as as an end face. A new flag especially for the tangent point has been introduced. No real imrpovement, but more logically as the tangent point is not an end face. * src/ppath.cc (do_gridcell_3d): Cases when a path step both starts and ends at the top surface, without having a tangent point inside the cell is now handled. 2003-01-14 Patrick Eriksson * arts-1-1-392 * src/ppath.cc: Just a commit to transfer last changes to laptop. 2003-01-14 Patrick Eriksson * arts-1-1-391 * src/m_cloudbox.cc (CloudboxGetIncoming): Fixed a bug. The longitude index was not set following the cloud box limits. * src/ppath.cc (psurface_crossing_3d): A slight improvement that should lower the chance for failures. However, another algorithm will be tested. 2003-01-14 Patrick Eriksson * arts-1-1-390 * src/ppath.cc: Work on 3D paths to handle all possible problems due to numerical inaccuracy. More work to be done (despite I have spent most of the day on this!), at least for cases with highly distorted grid cells. Can maybe work for nicer cases. * src/rte.cc (get_radiative_background): RteCalc is now not called if the ground is set to be a blackbody. Everything worked, but this saves some time. 2003-01-14 Claudia Emde * arts-1-1-389 * src/m_cloudbox.cc: Included 3D parts for (scat_iPut) and (CloudboxGetOutgoing). Now, all 3D functions for the scattering part are ready to be tested! * src/m_atmosphere.cc: Included checks and error messages. * src/m_scatrte.cc: Only small modifications. Mainly documentation. 2003-01-14 Patrick Eriksson * arts-1-1-388 * src/m_refraction.cc (refr_indexThayer): Finished this function and moved some code to refr_index_thayer_1974. * src/refraction.h: Created this file. * src/refraction.cc: Added this file and moved get_refr_index_1d to to this file. Made new version of get_refr_index_2d. Created the function refr_index_thayer_1974. * src/ppath.cc: Added input arguments to some function as a preperation for 2D with refrcation. 2003-01-13 Patrick Eriksson * arts-1-1-387 * src/ppath.cc: I had two parallel ways to number the corner points of 3D grid cells. Fixed. Also more stringent naming between 2D and 3D. (psurface_crossing_3d): Fixed a bug that appeared when the radius of pressure surfaces is not constant. I had been sloppy in checking such cases. (ppath_calc): Fixed a bug (hopefully) reported by Oliver (that went through my compiler). 2003-01-13 Patrick Eriksson * arts-1-1-386 * src/ppath.cc (do_gridcell_3d): Some smaller improvements for special zenith and azimuth angles. 2003-01-13 Stefan Buehler * arts-1-1-385 * src/absorption.cc (find_first_species_tg): Added. Finds first occurrence of species in tag groups. The species to look for must be specified by its species index, not by the name! (species_index_from_species_name): Added. Returns species index for given species name. You can use both functions together to find the first water vapor tag: Index firstH2O = find_first_species_tg(species_index_from_species_name("H2O")) If there is no water vapor in the tag list the result will be -1. * src/absorption.h: Added declarations for the two new functions. 2003-01-13 Oliver Lemke * arts-1-1-384 * doc/uguide/Makefile.am: Removed uguide.ps. * doc/uguide/Figs/{*.eps,*/*.eps}: Removed all eps files. * doc/uguide/Figs/{Makefile.am,*/Makefile.am}: Removed *eps from file list. 2003-01-13 Claudia Emde * arts-1-1-383 * src/m_cloudbox.cc (i_fieldSetConst): Included the 3D part. The function is used to set the radiation field to a constant value inside the cloudbox. The convergence test (same solution for different initial fields) should also be done for the 3D calculations. * doc/examples/cloud_rad_field1D_example.arts.in: Fixed some typos in documentation. 2003-01-12 Patrick Eriksson * arts-1-1-382 * src/ppath.cc (do_gridcell_3d): Added some code to try to catch a problem due to numerical problems with path start points on top of a pressure surface. Problem reported by Claudia. 2003-01-12 Oliver Lemke * arts-1-1-381 * configure.in: Applied patch provided by Randall Skelton : configure can now be told where it should look for the HDF library. Added LDFLAGS to the configuration summary. 2003-01-10 Claudia Emde * arts-1-1-380 * src/agendas.cc: Fixed bug in *refr_index_agenda* entry. * src/m_atmosphere.cc: Checks for raw data commented because they gave wrong error messages. They will be modified later. 2003-01-10 Oliver Lemke * arts-1-1-379 * src/m_cloudbox.cc, src/m_scatrte.cc: Replaced stdlib.h by cstdlib. We should always include the c++ versions of the header files. * src/m_refraction.cc: Replaced iostream.h by iostream. * src/old_absorption.cc: Replaced math.h by cmath. 2003-01-10 Claudia Emde * arts-1-1-378 Check-in failed for version arts-1-1-376. This is the next try. * src/m_cloudbox.cc (CloudboxGetIncoming): Some bug fixes. * src/m_refraction.cc: Included iostream.h. 2003-01-10 Patrick Eriksson * arts-1-1-377 * src/ppath.cc (varoius functions): Continued to change input and output arguments to send the variables needed for refr_index_agenda all the way down through all levels of functions. 2003-01-10 Claudia Emde * arts-1-1-376 * src/m_cloudbox.cc (CloudboxGetIncoming): Some bug fixes. * src/m_refraction.cc: Included iostream.h. 2003-01-10 Patrick Eriksson * arts-1-1-375 * src/m_refraction.cc (refr_indexThayer): Renamed refr_indexBoudouris. Add now added this file to the CVS repository. Sorry for the miss. 2003-01-09 Patrick Eriksson * arts-1-1-374 * src/agendas.cc: Added the agenda refr_index_agenda. * src/workspace.cc: Added the WSV refr_index. * src/m_refraction.cc (refr_indexBoudouris): Added this file and this function. * src/m_ppath.cc (ppath_stepRefractionEuler): Added new input arguments. 2003-01-09 Claudia Emde * arts-1-1-373 * src/m_atmosphere.cc (AtmFieldsCalc): Added checks for the consistency of input variables. * src/m_cloudbox.cc (CloudboxGetIncoming): Fixed a bug in the 3D part of the function. The sensor azimuth angle grid goes from -180° to + 180° whereas the scattering azimuth angle grid is defined from 0° to 360°. This caused a problem when calling RteCalc for all directions. * src/m_scatrte.cc (i_fieldUpdate3D): Minor modification. * doc/examples/cloud_rad_field1D_example.arts.in: Added this example control file for a 1D scattering calculation. The radiation field inside the cloudbox is calculated and all iterations are written into files. * doc/examples/Makefile.am: Included example above. 2003-01-09 Patrick Eriksson * arts-1-1-372 * src/m_rte.cc, rte.cc, ppath.cc, m_ppath.cc: Replaced Range(joker) with joker. 2003-01-09 Stefan Buehler * arts-1-1-371 * doc/uguide/matrix_vector.tex: Added documentation for using naked jokers in matrices and tensors. * src/test_matpack.cc: Added test for using naked joker in Vector. 2003-01-09 Patrick Eriksson * arts-1-1-370 * Clear sky spectra has now been produced with real absorption for 1D, 2D and 3D. AND IT WORKS!!!! Time to celebrate. Spectra were calculated for cases that should be identical for 1D, 2D and 3D. If lmax in ppath_stepGeometric is set to -1, some difference is noted between 1D and 2D/3D, as the crossings of the latitude grid in 2D/3D results in some extra points of the path which requieres an interpolation in pressure, not performed for 1D. If lmax is set to e.g. 1e3, the difference is very small (probably only rounding errors), which should be expected. So the consistency between 1D, 2D and 3D seems to be OK. At least for geometric paths. * src/m_atmosphere.cc (AtmFieldsCalcExpand1D): Created this function to make "2D or 3D view" of a 1D atmsophere. * src/m_rte.cc (RteEmissionStd): The order of some lines were wrong. Fixed that bug for 2D and 3D, and cleaned the code slightly. 2003-01-09 Oliver Lemke * arts-1-1-369 * src/xml_io.cc: Moved xml class declarations to xml_io_private.h. Reimplemented String and SpeciesTag reading routines to improve error and whitespace handling. * src/xml_io_private.h: Moved xml class declarations here. 2003-01-09 Claudia Emde * arts-1-1-368 * src/m_scatrte.cc (i_fieldUpdate3D): Added this function to calculte 3D radiative transfer inside the cloudbox. To test this function and also the 3D ppath functions I have to create 3D test scenarions. (i_fieldIterate): Included 3D case. * src/methods.cc: Added (i_fieldUpdate3D). 2003-01-09 Oliver Lemke * arts-1-1-367 * src/xml_io.cc: Improved parsing of String and SpeciesTag. IMPORTANT: Strings in ARTS XML file !!!MUST!!! be put inside quotes "". I think nobody wrote strings to xml files before but if so, you have to edit your xml files and add the quotes manually. 2003-01-08 Patrick Eriksson * arts-1-1-366 * src/m_ppath.cc (ppathCalc): This is now only a getaway function to ppath_calc, with agenda_verb = 0. For internal functions ppath_calc shall be called instead of this function. * src/m_rte.cc (RteCalc): Introduced a variable to get a more nice verbosity of the different agendas called. * src/ppath.cc (ppath_calc): Copied everything from old ppathCalc to this function and added a new input argument to control verbosity of ppath_step_agenda. 2003-01-08 Oliver Lemke * arts-1-1-365 * src/xml_io.cc, src/xml_io_private.h: Added reading/writing routines for Ppath, GridPos and ArrayOfGridPos. 2003-01-07 Patrick Eriksson * arts-1-1-364 * src/special_interp.h: Fixed typo. * src/m_rte.cc (RteEmissionStd): Modified the code added by Claudia to be a bit more efficient and to make use of some special interpolation functions. PLEASE NOTE: As it is the log of the pressure that is assumed vary linearly with altitude, the ordinary interpolation functions can't be used directly. The function *itw2p* is a special function for interpolating pressure, but this should be done in very few places. Untabified the file. 2003-01-07 Claudia Emde * arts-1-1-363 * src/m_optproperties.cc (ext_matInit), (abs_vecInit): Modified these functions. The scattering calculations are monochromatic. So the frequency dimension of these two variables has to be 1. *f_index* can be used for determine, whether the initialisaition is done in a clearsky calculation or in a cloudbox calculation. If f_index > 0 it is done in a cloudbox calculation. * src/m_rte.cc (RteEmissionStd): Rewritten this function. Now absorption is calculated for all ppath points using *scalar_gas_abs_agenda*. * src/m_scatrte.cc (i_fieldUpdate1D): Executing the finished *scalar_gas_absorption_agenda* required some modifications and additional variables. * src/methods.cc: Modified interfaces of (RteEmissionStd), (i_fieldUpdate1D), (ext_matInit) and (abs_vecInit). * src/rte.cc (rte_clearsky_with_emission): Removed. The general RT function (rte_step) can handle this special case and is used everywhere, now. * src/test_linalg.cc: Removed unused variables. 2003-01-07 Patrick Eriksson * arts-1-1-362 * src/ppath.cc (do_gridcell_3d): A start point, with a radius equal to the ground radius, could result in an intersection with the ground even if the zenith angle is upwards. Fixed (hopefully). * src/m_ppath.cc (sensor_posAddGeoidWGS84): Changed the code for 2D and 3D as the old version did not work when the latitudes are not sorted. * src/m_basic_types.cc (VectorSetElement): Created this WSM. (MatrixSetElement): Created this WSM. (MatrixSetTakingSizeFromMatrix): Created this WSM. 2003-01-07 Oliver Lemke * arts-1-1-361 * src/matpackI.{h,cc}: Commented out assignment operators for Vector with parameter type Array. If we want to split matpack from arts it should not depend on Array which belongs to arts, not to matpack. * src/parser.cc (parse_numvector): Use loop to copy Array to Vector because assignment operator is not longer present. * src/test_matpack.cc: Commented out test16 (Test for Array -> Vector assignment). 2003-01-07 Stefan Buehler * arts-1-1-360 * doc/index.html.in: Fixed link to pdf version of Uguide. * doc/uguide/development.tex: Updated documentation about using assertions with gdb. * src/arts.h: Updated GNU license information. 2003-01-06 Patrick Eriksson * arts-1-1-359 * It should now be possible to produce clear sky 3D spectra. However, no practical tests performed. * src/rte.cc (ground_specular_los): 3D activated, but ground tilt is not yet included. I wrote some codeto consider the ground tilt but I will look for a better and general solution, and the code is not active. * src/m_rte.cc (RteCalc): Included check that the atmosphere is 3D when a 2D antenna is selected. 2003-01-06 Oliver Lemke * arts-1-1-358 * src/array.h: Define all Arrays and ArraysOfArray here. NOTE: Only the typedefs are located here. If you want to use e.g. ArrayOfTensor3, it is not enough to include array.h, you also have to include matpackIII.h. * src/matpack*.h: Removed typedefs for Arrays. * src/arts.h: Removed typedefs for ArrayOfIndex and ArrayOfNumeric. 2003-01-05 Patrick Eriksson * arts-1-1-357 * src/ppath.cc: Several things fixed to make path along the end longitudes to work. Longitudes can now be in the range [-360,360], as described in AUG. I have tested a number of waht should be nasty cases and everything worked. It seems that 3D geometrical paths are now working. 2003-01-03 Patrick Eriksson * arts-1-1-356 * Paths above the pole are now basically working, except along lon +-180 degrees. Numerical inaccuracy is especially tricky around the poles (with the equations I have derived at least) and I don't think I will manage to solve all problems. Right now I consider to take back my decision to restrict lon_grid to [-180,180], which would be better for the usage and paths exectly at the border of the atmosphere could be avoided. But I want to document the present solution. * src/ppath.cc: Fixes in several functions to make things work for paths passing the poles. The fixes are needed as the longitude is undefined at the poles and as the azimuth angle is defined in other way at the poles. * src/m_ppath.cc (ppathCalc): Some fixes for the same reasons as above. 2003-01-01 Patrick Eriksson * arts-1-1-355 * 3D geometrical paths are not finished, but it is not too far away. Path passing exactly above the poles are not OK, but no other known bugs. Path passing longitude +-180 are working. Definition of accepted longitudes is changed. Longitudes must now be inside [-180,180]. To cover the whole globe, lowest and highest longitude must be -180 and 180, respectively. (AUG not updated on this point). I have done quite some cleaning, both for 2D and 3D. So 2D must be checked carefully later. My plan now is to finish all dimensions, with and without refraction, and make a careful, parallell check of all cases later. * src/ppath.cc: Fixed uncountable bugs, such as dividing with a trigonometric function becoming 0, lat index for longituide grids and pure logical mistakes. And ... * src/interpolation.h: Added declaration of functions for "red interpolation". The functions existed in interpolation.cc, but where not visible to the outside world. (Stefan, any reason for this that I have missed? I hope not, because I use now the red interpolation in many places.) * src/interpolation.cc (gridpos): Created a second version where a GridPos is created, instead of ArrayOfGridPos. 2002-12-30 Patrick Eriksson * arts-1-1-354 * src/ppath.cc: Code for 3D geometrical path steps compiles but so far no tests, beside for do_gridcell_3d and sub-functions. A number of new functions: poslos2cart cart2poslos gridcell_crossing_3d rsurf_at_latlon psurface_slope_3d psurface_crossing_3d ppath_start_3d ppath_end_3d 2002-12-25 Patrick Eriksson * arts-1-1-353 * src/ppath.cc (do_gridcell_3d): Started on this function. So far empty. (sph2cart): Created. * src/methods.cc: Created WSM DoGridCell3D. * src/ppath.cc (psurface_slope_2d): Created a second version of this function, not taking vectors as input. * src/rte.cc (ground_specular_los): Changed call of do_gridcell_2d. * src/m_ppath.cc (DoGridcell2D): Changed call of do_gridcell_2d. * src/ppath.cc (ppath_start_2d) - (do_gridcell_2d): Removed c2 and c4 as output of ppath_start_2d, and the transfer of these variables down to do_gridcell_2d, where the variables now are calculated internally. 2002-12-21 Patrick Eriksson * arts-1-1-352 * src/m_ppath.cc (DoGridcell2D): Added this WSM. This WSM should normally not be used. It is intended for test of the function do_gridcell_2d, and to make figures for AUG. This function can be called from Atmlab. 2002-12-21 Oliver Lemke * arts-1-1-351 * ami: Removed. * configure.in: Removed ami Makefiles. * Makefile.am: Removed ami directory. * src/m_optproperties.cc: Include cmath instead of math.h. 2002-12-20 Patrick Eriksson * arts-1-1-350 * src/m_optproperties.cc: Added #include because acos was not found. * src/ppath.cc (geompath_from_r1_to_r2): Improved a comment 2002-12-20 Stefan Buehler * arts-1-1-349 Two big changes in this version: 1. A first version of the gas absorption lookup table is ready and tested. I implemented a field variable for gas absorption, and a method to calculate absorption for all points in the field, in order to be able to do some testing. It is as yet unclear whether this could be useful also in other places. 2. Changed copy semantics for Array, Vector, and Tensors. Now the output argument is resized automatically. This was necessary to ensure that structures containing these objects are copied correctly. User code in ARTS is not affected, you should continue to use these data types exactly as you have done so far. In particular, views still have to match exactly, of course. Detailed changes: * src/gas_abs_lookup.cc: Some bug fixes and some cosmetic changes. * src/workspace.cc (define_wsv_data): Added abs_scalar_gas_field. It contains the scalar gas absorption for all species as a function of f_grid, p_grid, lat_grid, and lon_grid. This is mainly for testing and plotting gas absorption. For RT calculations, gas absorption is calculated or extracted locally, therefore there is no need to store a global field. But this variable is handy for easy plotting of absorption vs. pressure, for example. * src/m_absorption.cc (abs_scalar_gas_fieldCalc): Added. Calculates scalar gas absorption for all points in the atmosphere. An agenda is used to obtain absorption for one point at a time. * src/methods.cc (define_md_data_raw): Added abs_scalar_gas_fieldCalc. * src/agendas.cc (define_agenda_data): Added input parameters and documentation to scalar_gas_absorption_agenda. * src/check_input.cc (chk_atm_field): Added a version of this function for vmr_field (which is a Tensor4, not a Tensor3 like the other fields). * src/check_input.h: Updated. * src/array.h: Changed copy semantics. Operator= now adjusts dimension of target automatically. * src/matpackI.cc: Changed copy semantics for Vector and Matrix (not for VectorView and MatrixView!). Operator= now adjusts dimension of target automatically. * src/matpackIII.cc: Dito for Tensor3. * src/matpackIV.cc: Dito for Tensor4. * src/matpackV.cc: Dito for Tensor5. * src/matpackVI.cc: Dito for Tensor6. * src/matpackVII.cc: Dito for Tensor7. * src/matpackI.h: Only changes in comments. * src/test_matpack.cc (test35): A test for the new copy semantics. Only tested for Vector! Hope it works also for the higher order tensors... * doc/uguide/matrix_vector.tex: Updated text about copy semantics. 2002-12-19 Nikolay Koulev * arts-1-1-348 * src/test_complex.cc: Minor changes. 2002-12-20 Oliver Lemke * arts-1-1-347 * src/Makefile.am: Removed explicit definition of arts_DEPENDENCIES and redefinition of target arts. Seems to work exactly the same way if the definitions are omitted. 2002-12-19 Claudia Emde * arts-1-1-346 * src/agendas.cc (opt_prop_gas_agenda): Removed *f_index* from input variables list. * src/m_cloudbox.cc (CloudboxGetIncoming): Added the 3D version. * src/m_ppath.cc (ppathCalc): Inserted an assertion for number of points in ppath. * src/ppath.cc: Bug fixed according to Patrick's suggestion. Assure that 'n = Index( ceil( fabs( l2 - l1 ) / lmax ) )' does not become 0. * src/m_scatrte.cc: Minor modifications and included output messages. * src/methods.cc: Removed *abs_vec* from input list to function *abs_vecInit*. 2002-12-19 Oliver Lemke * arts-1-1-345 * src/complex.{h,cc}: Removed Complex class implementation and replaced it with a typedef complex Complex. If there is any need to implement functionality for complex numbers not covered by the STL class, add them here. * src/test_complex.cc: Adapted for new complex class. 2002-12-19 Sreerekha T.R. * arts-1-1-344 * src/m_optproperties.cc: The method *amp_matCalc* is modified to include the case of macroscopically symmetric and isotropic particles. Removed the argument *stokes_dim* from the methods calculating scattering properties. Modified accordingly when they are called in m_scatrte.cc. Also did some cosmetic changes so that they look better in doxygen. * src/methods.cc: Removed the input stokes_dim from the methods calculating scattering properties. * src/scattproperties.cc: Cosmetic changes so that they look better in doxygen. 2002-12-19 Oliver Lemke * arts-1-1-343 * src/xml_io.cc: Bug fix in reading of SpeciesTag. Did not work when opening tag was not followed by whitespace. 2002-12-19 Stefan Buehler * src/absorption.cc (SpeciesTag): Added white space removal to constructor from string for SpeciesTag. * src/m_absorption.cc (gas_speciesSet): Moved white space removal to SpeciesTag constuctor. * src/xml_io.cc: Work in progress (together with Oliver). 2002-12-18 Oliver Lemke * arts-1-1-342 * src/xml_io.cc: Added GasAbsLookup.gal.nonlinear_species to reading and writing routine for GasAbsLookup table. * src/Makefile.am: Added partition_function_data.cc to test_xml_SOURCES. 2002-12-18 Oliver Lemke * arts-1-1-341 * src/xml_io.cc: Implemented reading/writing of SpeciesTag. * src/Makefile.am: Added absorption.* and species_data.cc to test_xml_SOURCES. 2002-12-17 Nikolay Koulev * arts-1-1-340 * src/complex.h: Added functions for absolute value and phase of complex numbers. * src/test_complex.cc: Minor changes. 2002-12-17 Oliver Lemke * arts-1-1-339 * src/Makefile.am: Merged changes from arts-1-0 branch. Reintroduced BUILT_SOURCES to fix bug discovered by Christian, removed special targets and explicit dependencies for make_auto*. * src/logic.cc: Include algorithm for max function. Include cmath instead of math.h 2002-12-17 Stefan Buehler * arts-1-1-338 * src/complex.h: Untabified. (I was the bad guy.) * src/complex.cc: Untabified. (I was the bad guy.) 2002-12-16 Nikolay Koulev * arts-1-1-337 * src/complex.h: Implemented basic arithmetic operations with complex numbers. But absolute value and phase still to be added. * src/test_complex.cc: Added some new test examples on complex numbers. 2002-12-16 Mattias Ekström * arts-1-1-336 * configure.in: Just a demonstration commit to show Mattias how CVS works. 2002-12-16 Stefan Buehler * arts-1-1-335 * src/complex.h: Complex numbers for ARTS. This is a quick implementation of complex numbers. I think most of the basic features are there. The operators += and + are already implemented as examples for the other operators. Have I forgotten anything important? Documentation for AUG must still be written! * src/complex.cc: Source file for complex numbers. At the moment only the output operator is here, all member function implementations are in the class declaration in complex.h. * src/test_complex.cc: Test complex numbers. * src/Makefile.am: Added new target test_complex. 2002-12-12 Stefan Buehler * arts-1-1-334 * src/gas_abs_lookup.cc (Extract): Cosmetic changes to Doxygen header. 2002-12-12 Stefan Buehler * arts-1-1-333 * I think all methods for using gas lookup tables are there now, although not all cases are implemented inside the methods. NOTHING IS TESTED YET, THOUGH. * src/workspace.cc (define_wsv_data): Updated documentation of: abs_scalar_gas, Added WSV gas_abs_lookup_is_adapted, a flag indicating that the lookup table has been adapted to the current calculation. * src/methods.cc (define_md_data_raw): Added the new methods: abs_scalar_gasExtractFromLookup, gas_abs_lookupAdapt. Updated the methods: ext_matInit, ext_matAddGas, abs_vecInit, abs_vecAddGas. Removed unnecessary arguments and cleaned up the documentation. * src/m_scatrte.cc: The variable abs_scalar_gas is a Matrix, not a Vector. The dimensions are [f_grid,gas_species]. We are not taking the sum of the gas absorption for the different species here, the sum is taken inside ext_matAddGas and abs_vecAddGas. The helper variable scalar_gas_array, which is used in some places, is now also a matrix, because it has to store the absorption for the different gas species separately. * src/m_optproperties.cc: Removed unnecessary #includes. (ext_matInit): Added. (ext_matAddGas): Rewritten. (abs_vecInit): Added. (abs_vecAddGas): Rewritten. Note that in all these methods there is no need for a distinction between the cases inside and outside the scattering box. Only the leading dimensions of the arguments are different. The methods are now quite simple. * src/m_absorption.cc (gas_abs_lookupAdapt): Added. (abs_scalar_gasExtractFromLookup): Added. * src/gas_abs_lookup.h: Updated. * src/gas_abs_lookup.cc: Mostly cosmetic changes here. 2002-12-11 Stefan Buehler * arts-1-1-332 * src/interpolation.cc: Allow a little bit of extrapolation. To be precise, we require that the new grid is no more than half a grid spacing away on either side of the old grid. Extrapolation to such a short distance should be safe. The main reason for this modification is that it solves the numerical problems that used to occur if the new grid was practically the same as the old grid. (In these cases the edge values of the new grid numerically sometimes happened to fall just outside the old grid.) This has the important consequence, that fractional distances can be <0 and >1 for points outside the original grid range. The new condition is that -.5 <= fd <= 1.5. The sum of all weights still is one, of course. (All functions:) Modified the assertion that compared the sum of all weights to 1 to use the new "fuzzy" comparison function (see below). This was necessary because numerical noise led to spurious failures of the original sharp assertion statement. * src/logic.cc (is_same_within_epsilon): Added. This function implements comparison of two numbers as recommended by Oliver. Both the two numbers and the comparison epsilon have to be specified. I recommend to always use this function for this task in future, so that we have some consistency. It is applicable in cases where there is no physical justification to require a certain absolute agreement. Instead, it checks that the two numbers agree to a certain number of digits. * src/logic.h: Updated. * src/test_interpolation.cc (test06): Added this test for the new extrapolation feature. * src/Makefile.am: Added make_vector to sources for test_interpolation. 2002-12-10 Claudia Emde * arts-1-1-331 * src/m_atmosphere.cc (AtmFieldsCalc): Small modifications. This method is now tested and is working. * src/m_io.cc (AtmFieldsFromAscii2Xml): Included this method. It converts atmospheric data from ascii to xml and writes the atmospheric fields (temperature, altitude, vmr) as gridded fields, which can be read using (AtmRawRead). * src/methods.cc: Included (AtmFieldsFromAscii2Xml). 2002-12-06 Stefan Buehler * arts-1-1-330 * src/methods.cc (define_md_data_raw): Fixed typo bug in documentation of ppath_stepGeometric (removed backslash). (define_md_data_raw): Added method gas_speciesSet. This is basically the same method that used to be called tgsDefine in ARTS-1-0, except for the new feature of specifying "nl" instead of the isotope. * src/workspace.cc (define_wsv_data): Fixed documentation of gas_species. * src/old_absorption.cc: Moved define_species_map to absorption.cc. * src/absorption.cc (define_species_map): Moved over this function from old_absorption.cc * src/absorption.h: Updated. * src/m_abs.cc: Removed tgsDefine. * src/m_absorption.cc (gas_speciesSet): Added (from old tgsDefine). * src/main.cc: Initialize species_data and species_map. * doc/examples/absorption_lookup_example.arts.in: Added gas_speciesSet. * src/mystring.h: Added a find function. But then I thought better of it and decided that for string we should continue to use string.find(). So, the new function is commented out. 2002-12-06 Stefan Buehler * arts-1-1-329 *.cc, *.c, *.h: Untabified everything. 2002-12-03 Patrick Eriksson * arts-1-1-328 * src/ppath.cc: There are now fewer WSM, only ppath_stepGeometric and ppath_stepRefractionEuler. The different options are now selected by keywords. I found this easier than having a lot of WSMs. Especially as I decided to add another option for the refraction method. There is now an option for how the refractive index shall be determined, always calculated from scratch or interpolated from grid cell boundaries. See the on-line help for info. The special 1D option is not active for the moment. I have done this now in several ways and the results is always the same. If the tangent point is forced to be (very) exact, then the results do not converge when decreasing the ray tracing length. On the other hand, if the ray tracing is free to find its own tangent altitude, the results converge (and a very close to perfect tangent altitude is found). It must be the case that rounding errors balance each other in the second case. 2002-12-02 Stefan Buehler * arts-1-1-327 * Fixed bug reported by Patrick. It took a while to find this. The problem was that agendas were not copied correctly. Tracked the problem down to the copying of MRecords, which are a part of Agenda. The problem is that STRUCTURES CONTAINING ARRAYS ALWAYS MUST DEFINE THE ASSIGNMENT OPERATOR. Otherwise copying the structure will trigger an assertion unless all arrays have the same size in original and target structure. That is of course not what we want, normally. * src/agenda_class.cc: (MRecord::operator=): Added. This is the bug fix. Also added output operator for MRecord and Agenda for debugging purposes. The implementation resides in .print() member functions for both classes. (Agenda::print): Added. (MRecord::print): Added. Output operators and print functions are not tested! * src/agenda_class.h: Updated. * src/token.cc (operator<<): Fixed output format to look like the tokens are given in the controlfile. (Not tested, needed only for debugging.) * src/continua.cc (MPM93_N2_continuum): Commented out one line to remove unused variable warning. (PWR98H2OAbsModel): Commented out one line to remove unused variable warning. 2002-12-02 Patrick Eriksson * arts-1-1-326 * src/ppath.cc: Things have been moved around a bit. A pure Euler approach has been implemented for 1D (used in Euler/EulerWithLmax). The 1D and 2D versions give basically identical results. The results converge when making the step lengtn smaller. The special 1D version that gives a symmetric path around tangent points is moved to be part of a new WSM ppath_stepRefraction1D. The results for this version do not converge when making the ray tracing step length shorter (and I can't find out why this is the case). * src/m_atmosphere.cc (r_geoidSpherical): New WSM. 2002-12-02 Oliver Lemke * arts-1-1-325 * src/array.h (find_all): pos has to be a reference. * src/absorption.cc (SpeciesTag::SpeciesTag): Use Stefan's find_first instead of the STL version. * src/xml_io.cc (xml_read_header_from_stream): Slighty improved error message for invalid xml header. 2002-12-01 Patrick Eriksson * arts-1-1-324 * src/ppath.cc (ppath_step_refr_2d): Appears to be ready. In contrast to the 1D function, the results converge when making the ray tracing step length smaller. However, the algorithms differ slightly and I will copy the 2D algorithm to 1D to get 1D versions. Fixed several bugs in the functions of the file. 2002-11-29 Stefan Buehler * arts-1-1-323 * src/agenda_class.cc Untabified. (execute): Implemented reporting level 4 to override silent agenda execution. * src/main.cc Untabified. (set_reporting_level): Implemented reporting level 4 to override silent agenda execution. * src/check_input.h: Untabified. (chk_size): Added. (chk_contains): Added. Checks if an array contains a certain value. Has to be here in the .h file, because it is a template function that works for any kind of array. * src/check_input.cc: Untabified. (chk_size): Added these functions for Vector up to Tensor7. They are similar to the is_size functions, but throw runtime errors with appropriate messages if the size does not match. Could be convenient for others as well, please use. * src/workspace.cc: Untabified. (define_wsv_data): Moved variable abs_scalar_gas to the right place and added documentation. * src/methods.cc: Untabified. (define_md_data_raw): Put in stub for gas_abs_lookupAdapt method (still commented out). * src/parser.cc: Untabified. Removed unused variables. (Detected thanks to the great new warnings of Oliver.) * src/old_absorption.cc: Moved some stuff to absorption.cc. * src/absorption.cc: Untabified. Added some Functions for SpeciesTag. (Moved over from old_absorption.cc and updated.) * src/absorption.h: Ditto. * src/gas_abs_lookup.h: Updated. * src/gas_abs_lookup.cc (find_new_grid_in_old_grid): Added. (Adapt): Worked mainly on this function. It is now more or less complete, but not tested. * src/array.h: Untabified. (find_first): Added. (find_all): Added. 2002-11-29 Claudia Emde * arts-1-1-322 * src/m_atmosphere.cc: (AtmRawRead): Added this method to read atmospheric scenarios. (AtmFieldsCalc): Added. Interpolates atmospheric fields on the atmospheric grids for the RT calculation. * src/methods.cc: Added methods above. * src/workspace.cc: Included WSVs for methods above: t_field_raw, z_field_raw, vmr_field_raw, vmr_field * src/m_cloudbox.cc: Removed some unused variables. 2002-11-29 Patrick Eriksson * arts-1-1-321 * src/ppath.cc (ppath_step_refr_2d): Finished this function. * src/ppath.cc (raytrace_2d_linear_euler): Created this function. Basically works but there are bugs to be removed. * src/ppath.cc (psurface_crossing_2d): Fixed a bug for cases with presssure surfaces without any slope. 2002-11-28 Patrick Eriksson * arts-1-1-320 * src/ppath.cc (ppath_step_geom_2d): Moved parts of this function to seperate functions, to be used by the corresponding functions for refraction. 2002-11-28 Oliver Lemke * arts-1-1-319 * ami/xml/xmlReadTensor*.m: Bug fix in indexing. The indexing is now the same as in arts. Example: t = xmlLoad('tensor5.xml'); % Read tensor5 t(1,1,1,1,:) % Print first row of tensor t(:,1,1,1,1) % Print first element of each shelf Array are treat as cells: a = xmlLoad('arrmatrix.xml'); % Read array of matrix a{1}(1,1) % Print first element of first matrix a{2}{1,:) % Print first row of second matrix a{2} % Print second matrix * ami/xml/xmlReadTag.m: Added. Splitted tag parsing routine from xmlLoad. * ami/xml/xmlLoad.m: Moved parsing of tags to xmlReadTag.m. * ami/xml/xmlReadArray.m: Simplified by using xmlReadTag. * ami/xml/xmlReadGasAbsLookup.m: Added. 2002-11-28 Oliver Lemke * arts-1-1-318 * configure.in: Added -Wconversion flag to warnings. Don't use -Wno-unused but -Wno-unused-parameter instead. Because we don't want to be harassed with unused function parameters but with unused variable we do. (gcc3 only) Changed the behaviour for the warning flags: By default -W -Wall -Wconversion are active. All warnings produced with this settings SHOULD BE FIXED!!! In certain cases it could be useful to turn on even more warnings by using --enable-more-warnings. But be warned, with this setting gcc becomes really rebellious. :-) Pass --enable-more-warnings to autogen.sh or configure. You may get a lot of false alarms depending on your compiler version. -enable-more-warnings activates -Wshadow -Wunreachable-code (and more to come) * src/ppath.cc (ppath_start_stepping): np was defined twice as local variable. Second declaration shadows first one. Number of pressure levels does not change -> removed second variable. * src/parser.cc (read_integer) and (read_numeric): Ony dummy variable shadows another. Renamed second dummy variable to chtmp to make the code easier to understand. (parse_method): Same with iterator i. * src/mystring.h (my_basic_string): Renamed parameter npos to numpos to avoid shadowing of member attribute of same name. * src/make_wsv_pointers_cc.cc (main): Renamed parameter wsv_pointers in function define_wsv_pointers to ref_wsv_pointers to avoid shadowing of global wsv_pointers variable. * src/m_physics.cc (MatrixToTbByRJ): Removed unnecessary re-definition of irep, ii and icol from else block. * src/matpackI.h,cc (Range::Range): Renamed joker param in constructors to j to avoid shadowing of global joker object. * src/agenda_class.{h,cc} (Agenda::set_name): Renamed parameter name to nname to avoid shadowing of member function Agenda::name(). 2002-11-28 Claudia Emde * arts-1-1-317 * src/logic.{cc,h} (is_singular), (is_diagonal): Implemented these functions to check whether a matrix is singular or diagonal. * src/agendas.cc (scat_mono_agenda): Modified input and documentation. The method *amp_matCalc* has to be part of the agenda as *amp_mat* stores the amplitude matrix for one frequency. Before we calculated amp_mat outside the agenda but this can not work for more frequencies. * src/rte.cc (rte_step): Used is_diagonal. * src/scatrte.cc (ScatteringMain): Included a switch: If the frequency grid holds only 2 frequencys the radiation field inside the cloudbox is only calculated for the first frequency. (i_fieldUpdate1D): Used is_singular. Executing all agendas silently now. * src/m_ppath.cc (ppathCalc): Ppath_step angenda is here executed silently now (exept when it is called for the first time). * src/m_cloudbox.cc: Removed some "couts" which were only used for debugging. * src/m_optproperties.cc (ext_matAddGas), (abs_vecAddGas): Minor modifications. 2002-11-28 Sreerekha T.R. * arts-1-1-316 * src/m_scatrte.cc (i_fieldUpdate1D_PlaneParallel): This method is added. The method is similar to i_fieldUpdate1D except that it takes that inside the cloudbox the atmosphere is planeparallel. * src/methods.cc : Added the above method. 2002-11-27 Patrick Eriksson * arts-1-1-315 * src/ppath.cc: No functionality changed, despite some small steps forward for 2D refraction, but the code has been restructured to make the code more compact and simplify the implementation of other ray tracing schemes. 2002-11-27 Claudia Emde * arts-1-1-314 * src/lin_alg.cc (norm_inf): Fixed a bug due to missing initialization. * src/m_cloudbox.cc (scat_iPut): Bug fixed. * src/m_scatrte.cc (i_fieldUpdate1D): Minor changes. 2002-11-27 Oliver Lemke * arts-1-1-313 * src/make_auto_wsv_groups_h.cc (main): Don't put comma at end of enumerator list in auto_wsv_groups.h. * src/methods.cc: Commented out UpdatePlaneParallel. @rekha: Please have a look. 2002-11-26 Sreerekha T.R. * arts-1-1-312 * src/scatproperties.cc: Fixed the warnings due to uninitialised varibles. 2002-11-26 Patrick Eriksson * arts-1-1-311 * src/ppath.cc: A short report on quite a lot of work. I have been working on a basic function for 1D ppath steps with refraction. I was not happy with the result for the first algorith so I tried several improvements. Now I understand that there are inherent problems and I finally selected an algorithm that can be extended to 2D and 3D. This would help to check the implementation for the different dimensions. The WSM is now called ppath_stepRefractionEuler as the method used is basically an Euler solution of the differential problem. I will write this down sometime in AUG, but I take it shortly here. Unfortunately, the path calculations do not converge to some result when making the ray tracing steps smaller. It seems to converge when going down to step length of maybe 100 m, but then the results start to move away again. I can't find any bugs in my calculations (the result when setting the refractive index to 1 is perfect). It must be the case that when making the ray tracing step very small, rounding errors start to be noticed, making the final result to slide away. Several improvements are possible, but I will take that later. I will now implement the same approach for 2D, as a reference case for later, more elaborated, schemes. 2002-11-26 Claudia Emde * arts-1-1-310 * src/methods.cc (i_fieldUpdate1D) and (i_fieldIterate): Included *abs_scalar_gas* in interface. * src/rte.cc (rte_step): Bug fixed. Assertion in check, if matrix is diagonal had to be outside the loop. * src/m_scatrte.cc (i_fieldUpdate1D): Modified. * src/agendas.cc (scalar_gas_absorption_agenda): Removed f_index from input list for testing purposes. * src/m_optproperties.cc (abs_vecAddGas): Bug fixed. Now scattering calculations can be performed again for an example absorption, which can be defined in the control file by setting the variable *abs_scalar_gas* in scalar_gas_absorption_agenda. 2002-11-26 Oliver Lemke * arts-1-1-309 * src/getopt.c: Moved comment after include to separate line. * src/Makefile.am: Added constants.cc to test_interpolation_SOURCES. * configure.in: Use a more sophisticated way to determine whether we are using a GNU compiler. 2002-11-25 Oliver Lemke * arts-1-1-308 * src/gas_abs_lookup.h (class GasAbsLookup): Don't use qualified names in member function definition. * src/matpack*.{cc,h}: Reverted to version 1-1-303. "using" statement in class definition is not supported in gcc < 3.x. :-( Moved back iterator stuff into header after reverting. Moved all operators returning Numeric elements also to header files for performance reasons. * configure.in: Add "-ansi -pedantic" to compiler flags when gcc is in charge. 2002-11-25 Claudia Emde * arts-1-1-307 * src/m_scatrte.cc (i_fieldUpdate1D): Included arguments to agendas to suppress output. * src/agendas.cc (opt_prop_gas_agenda) and (opt_prop_part_agenda): Corrected input and output of these agendas again. * src/linalg.cc (ludcmp): Bug fix to avoid possible use of uninitialized index. 2002-11-25 Oliver Lemke * arts-1-1-306 * src/matpackI.h (class VectorView): Don't use qualified names in member function definition. * configure.in: Moved -DNDEBUG from compiler flags to preprocessor flags. 2002-11-25 Stefan Buehler * arts-1-1-305 * src/agenda_class.h: Changed declaration of Agenda. * src/agenda_class.cc: Implemented an optional argument for Agenda::execute. If the argument is true, the agenda is executed silently, i.e., all output, except level 0 (error messages) is suppressed. If you call Agenda::execute() in a loop, you should call it without argument for the first time, then call it with argument true for the remaining iterations. * src/arts.h: Removed the line about NDEBUG. This is set by configure --enable-debug or --disable-debug. Hence, it must not be set explicitly in the code. Moved include for cassert to another position. * src/m_hdf.cc: Removed inclusion of config.h. (This is included by arts.h.) * src/methods.cc: Removed inclusion of config.h. (This is included by arts.h.) * src/main.cc: Removed inclusion of config.h. (This is included by arts.h.) 2002-11-25 Oliver Lemke * arts-1-1-304 * src/matpack*.{h,cc}: Moved implementation of iterator stuff into class definitions to get them inlined because we need maximum performance here. Removed reimplementation of 'operater() const' from the view classes and replaced them with a single 'using ConstXXXView::operator()'. This forces the compiler to call the correct const function for the non-const View classes. All in all, 254 function implementations removed from matpack. * src/matpackI.h: Fixed copy/paste error in last version. * src/xml_io.cc: Bug fixes to avoid possible use of uninitialized variables in try-catch-blocks. 2002-11-25 Claudia Emde * arts-1-1-303 * src/m_optproperties.cc: Renamed (m_scatproperties.cc) as this file now contains all workspace methods for calculating optical properties, not only the scattering properties. * src/agendas.cc (opt_prop_gas_agenda): Corrected input and output of this agenda. 2002-11-22 Claudia Emde * arts-1-1-302 * src/rte.cc/.h (rte_step): Created the general radiative transfer step function. The diagonal case I have taken from Patricks function (rte_step_clearsky_with_emission). Shifted (stokes_vecGeneral) from scat_rte.cc to this file. * src/scat_rte.cc/.h: Removed these files. All radiative transfer functions are now in rte.cc. * src/Makefile.am: Removed files above. * src/m_scatrte.cc: Modified (i_fieldUpdate1D), it uses the general RT function, now. 2002-11-22 Oliver Lemke * arts-1-1-301 * configure.in: Fixed messed up CFLAGS/CXXFLAGS. Introduced new variable DEBUG_FLAGS. 2002-11-22 Oliver Lemke * arts-1-1-300 * src/matpack*.{h,cc}, src/Makefile.am: Added cc files for matpack and moved implementation part. Otherwise, a compiler ignoring the inline keyword gets multiple defined symbols. NOTE: At the moment compilation is twice as fast as before. BUT there are some drawbacks in calculation speed because some frequently called functions (iterator stuff) have to be moved back to the header file to be inlined again. * configure.in: Increased template depth to 40 to get non-debug compiles working. Use CFLAGS/CXXFLAGS from environment variable also in debug mode. For basic optimizations set CFLAGS and CXXFLAGS to something like: export CFLAGS="-O2 -march=i686" export CXXFLAGS="$CFLAGS" Rerun autogen.sh afterwards. For maximum performance try something like: export CFLAGS=" -O2 -march=i686 -fforce-addr -funroll-loops -frerun-cse-after-loop -frerun-loop-opt -falign-functions=4 -fomit-frame-pointer -fexpensive-optimizations" export CXXFLAGS="$CFLAGS" * ChangeLog: Removed arts-0-x-x history. * ChangeLog-0.x: Added. Moved pre-1.0 changelog entries here. 2002-11-22 Stefan Buehler * arts-1-1-299 * src/workspace.cc (define_wsv_data): Added the variables a_pressure, a_temperature, and a_vmr_list, which can hold the local pressure, temperature, and list of VMRs, respectively. They are intended for communication with agendas and methods calculating absorption coefficients. Also replaced gas_tgs by gas_species. 2002-11-21 Claudia Emde * arts-1-1-298 * src/workspace.cc: Removed *scat_rte_agenda*. * src/agendas.cc: Removed *scat_rte_agenda*. * src/m_scatrte.cc: Modified functions which uses scat_rte_agenda - (i_fieldIterate) and (i_fieldUpdate1D). Included more checks and initialized all variables for the scattering calculations in the beginning of (i_fieldIterate), where they appear first. * src/methods.cc: Changed interface of methods above. * src/m_cloudbox.cc: Included more checks. 2002-11-21 Claudia Emde * arts-1-1-297 * src/workspace.cc: Included variable for scalar gas absorption *abs_scalar_gas* and frequency index *f_index*. Modified WSVs *ext_mat* and *abs_vec*. Removed *ext_mat_gas*, *ext_mat_part*, *abs_vec_gas*, abs_vec_part*. Removed also *scat_f_index*. This variable is replaced by *f_index*. Included and removed entries for agendas (see agenda.cc). * src/methods.cc: Added: - ext_matAddGas - ext_matAddPart - abs_vecAddGas - abs_vecAddPart Removed: - ext_mat_partCalc - abs_vec_partCalc - ext_mat_gasCalc - abs_vec_gasCalc - ext_mat_partScat - ext_mat_gasExample // Commented out the examples, may be we - abs_vec_gasExample // can use them again. * src/agendas.cc: Added: - scalar_gas_absorption_agenda - opt_prop_gas_agenda - opt_prop_part_agenda Removed: - ext_mat_agenda - abs_vec_agenda * src/m_scatrte.cc: Modified the (i_fieldIterate) and (i_fieldUpdate1D) according to the new variable definitions and new agenda definitions. Moved (stokes_vecGeneral) and (stokes_vecScalar) to the new file scat.rte.cc. These methods are ordinary functions now. *scat_rte_agenda* which can use only these functions, will be removed. Replaced *scat_f_index* by *f_index*. * src/m_cloudbox.cc: Replaced *scat_f_index* by f_index*. * src/m_scatproperties.cc: Added: - ext_matAddGas - abs_vecAddGas These methods are only dummy functions, as the method scalar_gas_absExtractFromLookup is not yet implemented. - ext_matAddPart - abs_vecAddPart These are only slightly modified versions of the former methods *ext_mat_partCalc* and *abs_vec_partCalc*. Removed: - ext_mat_partCalc - abs_vec_partCalc - ext_mat_gasCalc - abs_vec_gasCalc These methods are replaced by the new method. - ext_mat_partScat This method was only used for the convergence test. I think we do not need it anymore. It does not work with the modified variables, so I commented it out. - ext_mat_gasExample - abs_vec_gasExample Commented out the Examples. They also have to be modified if they should work with the new variables. * src/scat_rte.cc/h: This file contains now the functions for a radiative step calculation with scattering integral term. * src/Makefile.am: Included scat_rte.cc/h. * src/rte.cc: Included "scat_rte.h". 2002-11-20 Oliver Lemke * arts-1-1-296 * src/Makefile.am: Fixed typos gridded_field.h -> gridded_fields.h Removed no longer existent los.h. * doc/uguide/Figs/Makefile.am: Added fm_definitions, interpolation, polarization, ppath and scattering to SUBDIRS. * doc/uguide/Figs/{polarization,interpolation,scattering}/Makefile.am: Added missing Makefiles needed to build dist. * doc/uguide/Figs/{polarization,interpolation,scattering}/.cvsignore: Added. * configure.in: WARNING_FLAGS and -ftemplate-depth- are gcc specific. Therefore, they are now only set if gcc/g++ is in use, otherwise we break compilation with non-gnu compilers (e.g. HP/NEC). Added missing Makefiles needed to build dist. 2002-11-20 Stefan Buehler * arts-1-1-295 * src/gas_abs_lookup.cc: Continued work on the lookup table. I have now a first implementation for the simple case without temperature interpolation. The next step is to test this. * src/gas_abs_lookup.h: Updated. * src/m_absorption.cc: Added. This should hold workspace methods related to the general calculation of absorption coefficients. * src/workspace.cc (define_wsv_data): Added gas_abs_lookup. * src/methods.cc (define_md_data_raw): Added gas_abs_lookupInit. * src/make_auto_wsv_h.cc: Updated. * src/make_auto_wsv_groups_h.cc: Updated. * src/m_clonesize.cc: Updated. * src/groups.cc (define_wsv_group_names): Added group GasAbsLookup. * doc/examples/absorption_lookup_example.arts.in: Added. * configure.in: Added new example file. * src/Makefile.am: Updated. 2002-11-19 Patrick Eriksson * arts-1-1-294 * src/special_interp.cc (z_at_lat_2d): Created this function. * src/ppath.cc (ppath_step_refr_std_2d): Started on this function. (get_refr_index_2d): Created this function. 2002-11-18 Patrick Eriksson * arts-1-1-293 * src/ppath.cc (refraction_gradient_2d): Created this function. (ppath_step_refr_std_1d): Some improved comments. (ppath_start_2d): Moved some code from ppath_geom_2d and created this function as this code will be common with functions for refraction. 2002-11-17 Oliver Lemke * arts-1-1-292 * src/test_scatproperties.cc: Include cmath. Required on some systems (like marvin). * src/special_interp.cc: Include iostream for cout (GCC3). * doc/uguide/arts_methods_to_latex.sh: Workaround to get it working on marvin. * doc/doxygen/Makefile.am: File 'doxyfied' is now removed with make clean in maintainer-mode. ---------- Fixes for upcoming release 1.3 of doxygen. We have to care more about the format and tags we use in our comments because it contains now a validating parser instead of a lexical scanner. * src/parser.cc (eat_whitespace): @exceptions no longer exists, it is now called @exception. * src/old_absorption.cc (get_tagindex_for_Strings): Use 

	instead of verbatim environment.

	* src/partition_function_data.cc (spec): Use 
.
	Inserted missing end tags.

	* src/species_data.cc: Inserted missing end tags.

2002-11-15  Patrick Eriksson  

	* arts-1-1-291

	* src/special_interp.cc/h: Created these files and moved atmospheric
	interpolation functions to these files from interpolation.cc/h.

	* src/ppath.cc (ppath_step_refr_std_1d): It seems that this function
	now works. So 1D with refaction should be finished. 
	This function is better than the corresponding function in arts-1.
	The tangent altitude is found with a better accuracy. The accuracy
	can be controled by a variable inside the function, which is now set
	to 0.1 m. The determination of the tangent altitude is not determined
	by the ray tracing step. 
	The maximum length of the ray tracing steps is now set by giving a 
	length. Small lengths can be used. I have tested steps down to 100m
	and it is very fast (as long as the calculation of refractive index is
	fast). However, some simple tests showed that step lengths below 1 km
	should not be needed (changing the ray tracing steps from 1 km to
	100m moved the tangent point about 250 m horisontally (for a tangent
	altitude close to ground), which should be compared to a total path
	length of many hundreds of km).

	(get_refr_index_1d): A temporary solution to get refractive index.
	The core function is taken from arts-1.

2002-11-15  Stefan Buehler  

	* arts-1-1-290

	* src/gas_abs_lookup.h: Continued to work on the structure of the table.

	* src/gas_abs_lookup.cc: Continued to work on the extraction function.

	* src/xml_io.cc: Adaptations to changed lookup table structure.

2002-11-15  Claudia Emde  

	* arts-1-1-289

	* src/m_scatrte.cc (convergence_flagAbs): Modified iteration counter.
	After the scattering calculation for the first frequency has converged 
	it is set to 100. This number indicates then that the iterations 
	should no longer be printed in (Tensor6WriteIteration).

	* src/m_cloudbox.cc (i_fieldSetClearsky): Initialization of i_field was
	missing.

	* src/m_scatproperties.cc

	I removed or commented the "cout"s, which we had included for 
	debugging.

2002-11-14  Patrick Eriksson  

	* arts-1-1-288

	* src/interpolation.cc (itw2p): Created this function to convert
	altitudes to pressures.
	
	(interp_atmsurface_XXXX and interp_atmfield_XXXX): Changed the name
	of the special functions to interpolate atmospheric fields and 
	surfaces, and changed the strategy somewhat. The following functions
	exist now (use them!):

           void interp_atm_field_gp2itw
           void interp_atmfield_by_itw
           void interp_atmfield_by_gp
           Numeric interp_atmfield_by_gp
           void interp_atmsurface_gp2itw
           void interp_atmsurface_by_itw
           void interp_atmsurface_by_gp
           Numeric interp_atmsurface_by_gp

	* src/m_ppath.cc (ppath_stepRefractionStd): The WSM to be used in the
	future for path calculations with refraction, using a basic/standard
	calculation approach.

	* src/ppath.cc (ppath_step_refr_std_1d): Started on this core function 
	for 1D path calculations with refraction.

2002-11-14  Oliver Lemke  

	* arts-1-1-287

	* ami/xml/xmlReadVector.m: Attribute is called nelem not nrows.

2002-11-14  Oliver Lemke  

	* arts-1-1-286

	* ami/xml/xmlReadVector.m: Added.

2002-11-14  Oliver Lemke  

	* arts-1-1-285

	* ami/xml/xmlReadTensor6.xml: Quick hack for Sreerekha. Exchanged
	order of col/rows.

2002-11-13  Claudia Emde  

	* arts-1-1-284

	* src/m_scatproperties.cc (pha_matCalc): Bug fixed in this function. 
	The off-diagonal elements were calculated wrongly, now the whole phase 
	matrix is calculated correctly.

	* src/m_scatrte.cc: Only documentation.

2002-11-11  Oliver Lemke  

	* arts-1-1-283

	* doc/doc++/Makefile.am, doc/doc++/html/Makefile.am,
	doc/doc++/tex/Makefile.am, doc/doc++/tex/docxx.sty: Removed.

	* doc/uguide/Makefile.am: Remove uguide.ind after generating dvi/pdf
	to avoid conflict between latex and pdflatex.

2002-11-11  Oliver Lemke  

	* arts-1-1-282

	* doc/uguide/uguide.tex: Use ifthen package to determine whether
	we are using pdflatex or vanilla latex. So, we don't need any
	longer the separate uguide_pdf.tex file.

	* doc/uguide/uguide_pdf.tex: Removed after merging into uguide.tex.

	* doc/uguide/Makefile.am: Adapted to create both ps and pdf file 
	from uguide.tex.

	Moved several files from MAINTAINERCLEANFILES to CLEANFILES.
	Everything except uguide.{ps,pdf,dvi} and automatically
	generated tex files can be removed.

	Remove uguide.toc after creation of ps/pdf file because latex and
	pdflatex use different formats for this file.

	Use -o option for dvips instead of output redirection.

	* doc/uguide/.cvsignore: Cleanup.

	* src/Makefile.am: $(EXEEXT) was still missing in some places.

2002-11-10  Oliver Lemke  

	* arts-1-1-281

	* configure.in: Version number correction.

2002-11-08  Claudia Emde  

	* arts-1-1-280

	* doc/uguide/scattering.tex: Restructured this chapter. Also 
	included some functions which have not been documented so far.

	* src/m_cloudbox.cc: Documentation.

	* src/m_scatrte.cc: Documentation.

2002-11-08  Oliver Lemke  

	* arts-1-1-279

	* src/Makefile.am: Append $(EXEEXT) to overridden targets. This
	prevents automake 1.5/1.6 from outputting errors but leads to
	warnings emitted by automake 1.4. But hey, a warning is better than
	an error, right? ;-) And it has the advantage that 'make' stops on
	errors but continues on warnings. automake 1.7 also just works fine.

2002-11-08  Oliver Lemke  

	* arts-1-1-278

	* configure.in: Use AM_MAINTAINER_MODE macro from automake instead
	of our homemade stuff. If --enable-maintainer-mode is used,
	additional dependencies are included in the generated Makefiles.
	E.g. when configure.in or any Makefile.am are changed the
	Makefiles are rebuild automatically with the next make. This
	is not necessary for end-users. --enable-maintainer-mode is
	passed by default to configure when you call autogen.sh.

	IMPORTANT NOTE: Dependency check on configure.in is only performed
	in top level directory. This means: After an update or modifying
	configure.in you *MUST* run make in the top level directory.

	Debugging is activated in maintainer-mode by default and disabled
	in end-user mode. This could be overridden by passing --enable-debug
	or --disable-debug to configure.

	Removed setting of arts-data path on smiles pcs to lookup2. Moved to
	autogen.sh because configure should not contain such special
	treatments.

	Cleanup. Removed some unused macros.

	* autogen.sh: Inserted hostname check and pass
	--with-arts-data=/pool/lookup2/arts-data to configure if we
	are on a smiles pc.

	* doc/uguide/Makefile.am, doc/doxygen/Makefile.am: Use
	MAINTAINER_MODE in conditional.

	* .cvsignore: Added autom4te.cache. Sorted.

2002-11-07  Oliver Lemke  

	* arts-1-1-277

	* src/xml_io.cc (ArtsXMLTag::read_from_stream): Skip
	 blocks. Comments are only allowed to be put
	directly after the  tag or in front of the  tag.

2002-11-06  Oliver Lemke  

	* arts-1-1-276

	* src/xml_io.cc: Added io routines for SpeciesTag, ArrayOfSpeciesTag,
	ArrayOfArrayOfSpeciesTag.
	Reading/writing of SpeciesTag writes only the empty tags because the
	implementation part of SpeciesTag is not yet done.
	Moved function declarations and template instantations to
	xml_io_private.h.

	* src/absorption.h: Added type ArrayOfSpeciesTag. At the moment, this
	type is only used to define ArrayOfArrayOfSpeciesType to keep
	consistency with the way ArraysOfArrays are defined in arts.

	* src/xml_io_private.h: Added. Separated function declarations and
	template instantiations from implementation part.

	* src/Makefile.am: Added xml_io_private.h in several places.

2002-11-05  Oliver Lemke  

	* arts-1-1-275

	* autogen.sh: Cleanup. Added --gnu option to automake.

	* configure.in: Added AM_MAINTAINER_MODE.

	* absorption.h, m_abs.cc, old_absorption.cc, workspace.cc, xml_io.cc:
	Renamed OneTag to SpeciesTag.

	* absorption.h, gas_abs_lookup.h, groups.cc, m_abs.cc,
	m_clonesize.cc, old_absorption.cc, workspace.cc, xml_io.cc:
	Renamed TagGroups to ArrayOfArrayOfSpeciesTag.

	* src/m_xml.h, src/xml_io.h: Cleanup.

	* src/xml_io.cc: Started to add io routines for GasAbsLookup.

2002-11-05  Claudia Emde  

	* arts-1-1-274

	* doc/uguide/scattering.tex: Updated the description of the iterative
	method.

	* doc/uguide/sybol_defs: New sybols for the fields (radiation field and
	scattered field).

	* doc/uguide/references.bib: Added a new reference (Sreerekhas paper).

	* doc/uguide/Figs/scattering: Added this directory. Included also 
	figures for scattering part here.

2002-10-31  Patrick Eriksson  

	* arts-1-1-273

	* doc/uguide/fm_definitions.tex: Wrote some new text for RT and ground
	reflections. 

	* doc/uguide/ppath.tex: Revised old text and wrote new text, especially
	a section on finding path crossings of pressure surfaces.

	* src/ppath.cc (psurface_crossing_2d): Modified this function to also
	handle a quadratic slope term.

2002-10-31  Sreerekha T.R.  
	
	* arts-1-1-272
	
	* src/scatproperties.cc (amp2abs): Fixed a bug here for
	calculating the absorption vector for 2nd,3rd and 4th components.
	
2002-10-22  Nikolay Koulev  

	* arts-1-1-271

	* src/m_lineshapes.cc (elsVoigt_Kuntz6, elsVoigt_Drayson): Added
	these new lineshapes, the Voigt-Kuntz approximation with relative
	accuracy better than 2*10^-6 and the Voigt-Drayson one.

	* src/methods.cc: Added the respective descriptions for these 
	lineshapes.
	
2002-10-22  Patrick Eriksson  

	* arts-1-1-270

	* src/ppath.cc (ppath_step_geom_1d): Added a call of
	gridpos_force_end_fd for path steps ending on a pressure surface.
	The function was not working without this call.

	* src/interpolation.cc: Reverted to version before version 1-1-264.

2002-10-19  Oliver Lemke  

	* arts-1-1-269

	* ami/xml/xmlReadTensor[56].m: Bug fixed. Where to put books without
	shelves? :-)

	* src/main.c: Beautified output of arts -v.

2002-10-21  Claudia Emde  

	* arts-1-1-268

	* src/lin_alg.cc: Fixed a bug in (norm_inf). This function is used in 
	the matrix exponential function. 

	* src/m_cloudbox.cc: Small bug fix.

2002-10-18  Christian Melsheimer  

	* arts-1-1-267

	* doc/uguide/scattering.tex: some small corrections.

	* doc/uguide/polarization.tex: some small corrections.

2002-10-18  Oliver Lemke  

	* arts-1-1-266

	* ami/xml/xmlLoad.m: Removed debug output.

	* ami/xml/xmlReadArray: Bug fixes.

	* ami/xml/xmlReadTensor[3-5]: Added.

	* ami/xml/xmlCheckSize: Added. Checks whether the number of read data
	item corresponds to the intended number.

	* ami/xml/xmlReadTensor6, ami/xml/xmlReadMatrix: Corrected permutation
	of input vector.

	NOTE: The function name which is called for reading a data type from
	an XML file is put together in xmlLoad.m. So, for every new data type
	only a file called xmlRead.m has to be put into the
	directory.  Array and ArrayOfArray are working automatically
	(hopefully).
	
	WARNING: All implemented reading routines work as long as the input
	file is correct. There is currently nearly no error checking. All
	kinds of strange things may happen.

2002-10-17  Sreerekha T.R.  

	* arts-1-1-265
	
	* src/m_cloudbox.cc (scat_iPut): The size of scat_i_p was resized
	to the 1D case.  

2002-10-17  Claudia Emde  

	* arts-1-1-264
	
	* src/interpolation.cc (is_gridpos_at_index_i) and (gridpos2gridrange):
	Fixed bugs here. Interpolation weights which are Numeric were 
	compared to Index which caused serious errors in the ppath_step 
	calculations. Patrick, I have included comments were I made 
	modifications.

	* src/m_cloudbox.cc (CloudboxGetIncoming): Some modifictions. This
	method seems to work now!!!!

	* src/m_scatrte.cc (ScatteringMain): Modified according to the change
	in (CloudboxGetIncoming).

2002-10-16  Claudia Emde  

	* arts-1-1-263
	
	* src/m_cloudbox.cc (CloudboxGetIncoming): Modified. The function 
	calculates the initial field at the whole cloudbox boundary. Before 
	it only doing one boundary at a time.

	* src/m_scatrte.cc (ScatteringMain): Modfied according to the change
	in (CloudboxGetIncoming).
	
	* src/methods.cc: Modified the inputs and outputs to the above
	mentioned methods.
	
2002-10-15  Patrick Eriksson  

	* arts-1-1-262

	* doc/uguide/fm_definitions.tex: Just removed a small out-dated 
	comment.

2002-10-14  Oliver Lemke  

	* arts-1-1-261
	
	* configure.in: Call init with autogen.sh instead of reconf.

	* Makefile.am (EXTRA_DIST): Include autogen.sh instead of reconf.

	* reconf: Purged.

2002-10-14  Sreerekha T.R.  
        
	* arts-1-1-260
	
	* src/m_cloudbox.cc: The method CloudboxGetIncoming is modified
	for using the method RteCalc.  The inputs and outputs of this
	method has to be changed quite lot.
        
	* src/m_scatrte.cc: The method ScatteringMain also had to be
	modified as it calls CloudboxGetIncoming.

	* src/methods.cc: Modified the inputs and outputs to the above
	mentioned methods.
	
2002-10-14  Oliver Lemke  

	* arts-1-1-259
	
	* doc/uguide/arts_methods_to_latex.sh: Use typewriter font instead
	of verbatim environment to allow automatic linebreaks.

	* doc/uguide/Makefile.am (uguide_pdf.pdf): Added dependency from
	autotexfiles.
	Don't redirect output to /dev/null.

2002-10-14  Oliver Lemke  

	* arts-1-1-258
	
	* doc/uguide/arts_methods_to_latex.sh: Added missing backslash in
	front of levelb.

2002-10-14  Oliver Lemke  

	* arts-1-1-257
	
	* autogen.sh: Renamed reconf for GNU compliance.

2002-10-10  Christian Melsheimer  

	* arts-1-1-256

	* doc/uguide/references.bib: added a reference (chandrasekhar:60)
	
	* doc/uguide/polarization.tex: Some minor corrections, and added
	the correct proof for the inequality I^2 >= Q^2 + U^2 + V^2. It is
	quite lengthy and maybe not really interesting for the uguide, but
	I wanted to write it down somewhere. 

	* doc/uguide/Figs/polarization: created this directory, moved
	figures for polarization.tex here

2002-10-10  Claudia Emde  

	* arts-1-1-255

	* src/agendas.cc: Included scat_mono_agenda.

	* src/m_scatrte.cc: Renamed (scat_mainCalc) Now it is called 
	(ScatteringMain). Included scat_mono_agenda in this method.

	* src/methods.cc: Modified entry for the method above.
		
	* src/workspace.cc: Included scat_mono_agenda.
	
2002-10-09  Sreerekha T.R.  
	
	* arts-1-1-254
	
	* src/m_cloudbox.cc: The method CloudboxGetIncoming is
	implemented. Only the 1D case is implemented
	
	* src/m_scatrte.cc: Added the method scat_mainCalc which
	gives the interface variables and the frequency inded.
	Both these methods are to be tested to fix bugs.

	* src/methods.cc : Added these two methods.
	
2002-10-08  Patrick Eriksson  

	* arts-1-1-253

	* doc/uguide/ppath.tex: Included a new figure.

	* doc/uguide/fm_definitions.tex: Revised some text and wrote some
	new text on RT. Included a new figure. More work to be done.

	* doc/uguide/introduction.tex: Removed some old text. Added a to do
	list.

2002-10-08  Christian Melsheimer  

	* arts-1-1-252

	* doc/uguide/polarization.tex: extended the subsection on partial
	polarization, some minor additions to the rest
	

2002-10-01  Christian Melsheimer  

	* arts-1-1-251

	* doc/uguide/polarization.tex: some small corrections

2002-09-26  Patrick Eriksson  

	* arts-1-1-250

	* doc/uguide/fm_definitions.tex: Revised this chapter to the start of
	Section 3.5. Main changes connected to that blackbody_ground is
	removed.

2002-09-25  Oliver Lemke  

	* arts-1-1-249
	
	* ami/xml/xmlGetAttrValue.m, ami/xml/xmlReadArray.m,
	ami/xml/xmlReadMatrix.m, ami/xml/xmlLoad.m,
	ami/xml/xmlReadAttributes.m, ami/xml/xmlReadTensor6.m:
	Added. Intermediate commit. Parsing of tags and attributes
	basically working. Parsing of data TBD.

	* configure.in: Added ami/xml/Makefile.

	* ami/xml/.cvsignore: Added.
	
	* ami/xml/Makefile.am: Added.

	* ami/xml: Created.

2002-09-25  Sreerekha T.R.  
	
	* arts-1-1-248
	
	* src/workspace.cc : Removed the variable name i_field_Tb and
	introduced tensor6_1. 
	
2002-09-25  Oliver Lemke  

	* arts-1-1-247
	
	* configure.in: Removed ami subdirs.

	* ami/: Purged.
	
	* ami/Makefile.am: Removed subdirs.

	* ami/init.m: Removed subdirs.

2002-09-22  Patrick Eriksson  

	* arts-1-1-246

	* src/interpolation.cc (interp_atmsurface): Created this function in
	two versions.

	(interp_atmsurface): Created a version of this function for a single
	position.

	* src/ppath.cc: Removed two functions to calculate the specular angle
	for ground reflections.

	* src/rte.cc (ground_specular_los): Created this function, partly
	based on code from ppath.cc.

	* src/m_atmosphere.cc (GroundNoScatteringSingleEmissivity): Created
	this function. 

	(GroundTreatAsBlackbody): Smaller changes in this function due to
	new interpolation functions.

	* src/workspace.cc: Wrote text, or extended text, for several 
	variables.

	* src/agendas.cc: Wrote text for ground_refl_agenda. Added r_geoid
	and z_ground as input to the agenda.

2002-09-20  Stefan Buehler  

	* arts-1-1-245

	* src/matpackI.h: Added Constructors to make a ConstVectorView and
	VectorView of a scalar. The conversion of a Vector to a 1-column
	matrix was already implemented.

	* src/matpackIII.h: Added Constructors to make a Tensor3View from
	a MatrixView. (Also constant versions.)

	* src/matpackIV.h: Added Constructors to make a Tensor4View from
	a Tensor3View. (Also constant versions.)

	* src/matpackV.h: Added Constructors to make a Tensor5View from
	a Tensor4View. (Also constant versions.)

	* src/matpackVI.h: Added Constructors to make a Tensor6View from
	a Tensor5View. (Also constant versions.)

	* src/matpackVII.h: Added Constructors to make a Tensor7View from
	a Tensor6View. (Also constant versions.)

	* doc/uguide/matrix_vector.tex: Put in documentation for the new
	matpack feature to make things appear of larger dimension than they
	are.

	* src/test_matpack.cc (test33): Added this test for the new
	capability to make things look bigger than they are.

	* src/gas_abs_lookup.cc (Extract): Continued to work on this
	function.  

	* src/gas_abs_lookup.h: Changed argument type of extract to allow
	vectors of pressure and temperature.

2002-09-19  Stefan Buehler  

	* arts-1-1-244

	* src/Makefile.am (arts_SOURCES): Added gas_abs_lookup.h
	and gas_abs_lookup.cc.

	* src/gas_abs_lookup.h: Started this file. It contains the
	declaration of the gas absorption lookup table.

	* src/gas_abs_lookup.cc: Started this file. It contains the
	implementation of gas absorption lookup member functions.

	* src/old_absorption.cc: Old stuff, should be removed eventually.

	* doc/uguide/old_absorption.tex: Old stuff, should be removed
	eventually. 

	* doc/examples/old_absorption_example.arts.in: Old stuff, should
	be removed eventually. 

	* src/agenda_record.cc: Corrected file name in doxygen header.

	* ami/path/.cvsignore: Created this file. Added Makefile and
	Makefile.in. 

2002-09-17  Patrick Eriksson  

	* arts-1-1-243

	* There have been rather big changes for the clear sky RTE part.
	Some comments are given below. However, as I am the only one working
	with this part I am saving the energy to later to describe the RTE
	part in a good way in AUG and the online documentation.

	The problems I encountered for the ground reflections made me think
	in somewhat new ways, and voila, I found a new and better structure
	for the calculations. So right now I am happy.

	The RTE part is now rather complete, but I have only done practical
	tests for a few simple cases. So much bug checking is to be done.
	
	* src/m_rte.cc (RteEmissionStd) and (RteCalc): The functions are to a
	large extent restructured. Several tasks have been lifted from 
	rte_agenda functions (where RteEmissionStd is the only existing one so
	far) which is an advantage. The task of rte_agenda methods is now much
	clearer. 
	The restructuring made it possible to call RteCalc in a recursive way.
	This was needed to handle ground reflections following the new
	approach. In fact, the appraoch for ground reflections could be 
	followed to make scattering calculations in another way (which however
	would require changes to the ppath calculations). It is my hope
	that this approach will allow calculation of weighting functions 
	without to much problems (the first task will be to fix WFs with
	a scattering ground).

	* src/rte.cc (get_radiative_background): The old function 
	set_to_radiative_background has been renamed and to large parts been
	rewritten. All cases execpt when the path starts inside the cloud box
	are now handled (but not tested).
	
	(rte_step_clearsky_with_emission): This function was created before
	last commit but I forgot to mention it. This function makes an 
	automatic switch to the best way to calculate the matrix exponential.
	Shall a simialr function be made for the cloud box?
	That is, there is no agenda for this for the clear sky part.

	* src/m_atmosphere.cc (GroundTreatAsBlackbody): Created this function.
	This is the first function implemented for ground_refl_agenda.

	* src/interpolation.cc (gridpos_copy): Created this function to copy
	a GridPos.

	* src/m_cloudbox.cc (CloudboxOff): The function now also sets 
	scat_i_p, scat_i_lat, scat_i_lon, scat_za_grid and scat_aa_grid to be
	empty. This is needed as the variables must be input to RteCalc.

	(CloudboxGetOutgoing): Added to cloudbox_on is input to check that the
	cloud box is actually turned on. Added also a check that scat_za_grid
	not is empty, which would be the case if CloudboxOff is called and
	later cloudbox_on is set to 1 but no cloud box calculations have been
	performed. 
	
	Claudia, should some more safety checks be added? The header of the
	file is not updated since the re-naming of the function.

2002-09-16  Patrick Eriksson  

	* arts-1-1-242

	* src/***: The WSV blackbody_ground is removed. It caused many and
	problematic dependencies between WSVs. Ground reflections will also
	be handled in a different way and there is no longer a big need for
	blackbody_ground.
	This means that there is no constrain now for placing the cloud box.
	It is up to the user to decide if it is OK to have a gap between the
	ground and the cloud box.

	* src/m_ppath and ppath: The fields ground, i_ground, symmetry and 
	i_symmetry are removed from the Ppath structure. 
	The calculation of a propagation path now stops at all intersections
	with the ground. 
	
	* src/workspace.cc: Removed the WSV t_ground and e_ground, and the
	corresponding agendas.
	Introduced new variables for handling ground reflections: 
	ground_refl_agenda, ground_emission, ground_los and ground_refl_coeffs.

	* src/m_rte and rte: Removed old ground variables and started to
	incorporate the new ones. 

2002-09-16  Claudia Emde  

	* arts-1-1-241

	* src/methods.cc: Included stokes_vec also as input to the methods
	(stokes_vecScalar) and (stokes_vecGeneral).

	* src/m_scatrte.cc: (stokes_vecScalar) and (stokes_vecGeneral): 
	Assertion for stokes_vec added.

2002-09-16  Claudia Emde  

	* arts-1-1-240

	* src/m_cloudbox.cc (CloudboxGetOutgoing): Changed the name of the 
	method. Earlier it was (y_scatCalc). Changed the interface of the
	function. *cloudbox_los* and *cloudbox_los* are removed, instead of
	these variables there are the gridpositions *a_gp_p*, *a_gp_lat*,
	*a_gp_lon* and *a_los* for the direction. The 3D part is still 
	missing.

	* src/workspace.cc: Removed WSVs *y_scat*, *cloudbox_pos* and 
	*cloudbox_los*. Added WSVs *a_gp_p*, *a_gp_lat* and *a_gp_lon*.

	* src/methods.cc: Changed (y_scatCalc) to (CloudboxGetOutgoing).

	* src/groups.cc: Included GridPos as a new group.

	* src/xml.io.cc: Added IO function dummies for GridPos.

	* src/m_clonesize.cc: Added clonesize dummy for GridPos.

2002-09-13  Stefan Buehler  

	* arts-1-1-239

	* src/xml_io.cc: Added IO function dummies for TagGroups.

	* src/workspace.cc (define_wsv_data): Added WSV gas_tgs.

	* src/groups.cc (define_wsv_group_names): Added group TagGroups.

2002-09-10  Claudia Emde  

	* arts-1-1-238

	* src/m_cloudbox.cc (y_scatCalc): Created this function (for 1D). It 
	returns the spectrum after a scattering calculation on the cloudbox
	boundary for given position and direction.
	(i_fieldSetConst): Generalized this method. Now you can specify 
	differnt values for each Stokes component of i_field inside 
	the cloudbox.

	* src/workspace.cc: Included the variables *y_scat*, *cloudbox_pos*
	and *cloudbox_los* for the method *y_scatCalc*.

	* src/methods.cc: Added *y_scatCalc*.

2002-09-10  Oliver Lemke  

	* arts-1-1-237
	
	* src/xml_io.cc: Output the element that failed while reading for
	all ArrayOf and ArrayOfArray data types.
	
2002-09-10  Sreerekha T.R.  
	
	* arts-1-1-236
	
	* src/m_scatrte.cc (scat_fieldCalc): Sorry that the last version
	didn't compile. I have fixed it now.   
	
2002-09-10  Oliver Lemke  

	* arts-1-1-235
	
	* src/xml_io.cc: Improved error output if reading fails. Added
	output of column, row, page... of the erroneous element.
	
2002-09-10  Sreerekha T.R.  
	
	* arts-1-1-234
	
	* src/m_scatproperties.cc : Included stokes_dim as input to
	methods calculating scattering properties.  Earlier stokes_dim was
	taken from inputs themselves. Now more checks are also included.  

	* src/methods.cc : Adapted all the methods calculating scattering
	properties to include stokes_dima as input.   

	* src/agendas.cc : Changed the online documentation for
	ext_mat_agenda and abs_vec_agenda.  Earlier there was a
	misunderstanding because they were not looking like examples.
	Patrick had pointed out this some time back.

2002-09-09  Claudia Emde  

	* arts-1-1-233

	* src/m_scatrte.cc (i_fieldUpdate1D): Changed the calculation of the 
	planck function for one layer. Now the mean of the temperature is
	calculated first and afterwards the planck function.

	* src/m_cloudbox.cc (scat_iPut): Included this method. It puts the 
	scattered radiation field into the interface variables between 
	cloudbox and clearsky calculations.
	(i_fieldSetClearsky), (i_fieldSetConst): Shifted these methods here, 
	because they have nothing to do with scattering properties.

	* src/m_scatproperties.cc: Shifted the two methods above.

	* src/methods.cc: Included entry for scat_iPut.

2002-09-06  Claudia Emde  

	* arts-1-1-232

	* src/m_scatrte.cc (scat_fieldCalc): Bug fixed. The scattering
	intergral was only calculated for 180° zenith angle, because 
	because *pha_mat_spt* was not calculated in this function.
	(i_fieldUpdate1D): Fixed another bug here. Insted of I_0 on the 
	gridpoints layer mean values were taken.

	* src/methods.cc: Modified interface for (scat_fieldCalc).

2002-09-06  Christian Melsheimer  

	* arts-1-1-231

	* doc/uguide/Figs/pol_ellipse_arbitrary.fig
	* doc/uguide/Figs/pol_ellipse_arbitrary.eps
	* doc/uguide/Figs/pol_ellipse_arbitrary.pdf: corrected, now zeta
	has the correct sign...

2002-09-05  Christian Melsheimer  

	* arts-1-1-230

	* doc/uguide/polarization.tex: inserted one more figure

	* doc/uguide/Figs/pol_e45.fig  
	* doc/uguide/Figs/pol_e45.eps
	* doc/uguide/Figs/pol_e45.pdf: added these files.

2002-09-03  Christian Melsheimer  

	* arts-1-1-229

	* doc/uguide/Figs/pol_ellipse_aligned.fig
	* doc/uguide/Figs/pol_ellipse_aligned.eps
	* doc/uguide/Figs/pol_ellipse_aligned.pdf
	* doc/uguide/Figs/pol_ellipse_aligned.fig
	* doc/uguide/Figs/pol_ellipse_arbitrary.eps
	* doc/uguide/Figs/pol_ellipse_arbitrary.pdf: added these files.
	* doc/uguide/polarization.tex: Small corrections, and inserted 2
	figures
	

2002-09-03  Claudia Emde  

	* arts-1-1-228	
		
	* agendas.cc (spt_calc_agenda): MAde this agenda for calculating 
	the properties for single particle types. Using this agenda it is 
/	easy to do the convergence test, which seems to be very important to 
	make sure, that the model delivers correct results.

	* workspace.cc: Icluded spt_calc_agenda.
	
	* m_scatproperties.cc (ext_mat_sptScat) (ext_mat_partScat): Created
	these methods to calculate the particle extinction due to scattering 
	(without absorption). These methods can be used for doing a
	convergence test.

	* methods.cc: Included the methods above.

	* m_scat_rte: Use *spt_calc_agenda* in (i_fieldUpdate1D).

2002-08-30  Nikolay Koulev  

	* arts-1-1-227

	* /: Increased ChangeLog number.
	
2002-08-30  Nikolay Koulev  

	* arts-1-1-226

	* src/methods.cc: Added the Doppler line-shape entry.
	
2002-08-29  Claudia Emde  

	* arts-1-1-225

	* src/m_scatproperties.cc: Removed *psh_mat_conv_sptCalc*. This was 
	only needed for testing.

2002-08-29  Sreerekha T.R.  

	* arts-1-1-224
	
	* doc/examples/clearsky_field.xml : This is modified and
	corresponds to midlatitude summer case.  

	* src/m_scatproperties.cc : Modified the method
	abs_vec_gasExample.  The example absorption now corresponds to
	midlatitude summer case.

2002-08-29  Oliver Lemke  

	* arts-1-1-223
	
	* configure.in: Removed ami/path from AC_OUTPUT.

	* ami/Makefile.am (SUBDIRS): Removed path.
	
2002-08-29  Oliver Lemke  

	* arts-1-1-222
	
	* ami/path: Started to remove old ami files. Tried this one to see
	if cvs handles removing of empty directory.

2002-08-28  Claudia Emde  

	* arts-1-1-221

	* src/m_scatrte.cc (i_fieldUpdate1D): Bug Fixed. The absorption 
	vector was only calculated for one direction. Before 
	abs_vec_sptCalc we have to call pha_mat_sptCalc in the same loop. 
	So I also had to modify the interface of the function, pha_mat_spt
	must not be declared as constant.

	* src/m_scatrte.cc (Tensor6WriteIteration), (convergence_flagAbs): 
	Moved the iteration counter to convergence_flagAbs. Now it should 
	be posible to print out scat_field and i_field at the same time.

	* src/methods.cc: Modified entry for i_fieldUpdate1D.
	

2002-08-28  Sreerekha T.R.  
	
	* arts-1-1-220
	
	* src/m_scatrte.cc (scat_fieldCalc): The method is modified so
	that it can handle 3D cases also more efficiently than before.  
	
2002-08-26  Claudia Emde  

	* arts-1-1-219

	* doc/example/i_field_arts.in: Included the new methods into the 
	example.

2002-08-26  Claudia Emde  

	* arts-1-1-218

	* src/m_scatproperties.cc (i_fieldSetConst): Created this function
	to define a constant initial field inside the cloudbox.
	Renamed *i_fieldSet*. Now this method is called *i_fieldSetClearsky*.

	* src/m_scatrte.cc (Tensor6WriteIteration): This function counts the
	number of iterations and prints the iterated fields to files. 

	* src/methods.cc: Included the methods above.

	* src/workspace.cc: Added the variable *iteration_counter* which holds 
	the actual number of iterations. 

	
2002-08-26  Oliver Lemke  

	* arts-1-1-217
	
	* src/physics_funcs.cc (invrayjean): Merged bug fix from arts-1-0.

2002-08-26  Sreerekha T.R.  
	
	* arts-1-1-216
	
	* src/m_scatrte.cc (scat_fieldCalc): Fixed a bug in this
	method. Earlier it was giving same field for all viewing angles of
	a particular pressure level.  
	
2002-08-23  Sreerekha T.R.  

	* arts-1-1-215
	
	* doc/uguide/integration.tex: Added this documentation for
	integration. 

	* doc/uguide/main.tex, doc/uguide/Makefile.am : Added
	integration.tex.

	* doc/uguide/scattering.tex : Improved the documentation for the
	method i_fieldSet.

2002-08-22  Oliver Lemke  

	* arts-1-1-214
	
	* src/m_scatrte.cc: Use ostringstream instead of sprintf.

2002-08-22  Claudia Emde  

	* arts-1-1-213

	* src/m_scatrte.cc (i_fieldUpdate1D): Modified this function to get
	boundary conditions right. Some loops are rearranged so that the 
	function is more efficient. The values of the zenith angles are taken 
	as criterion for upward or downward propagation.
	The special case (zenith angle a bit higher than 90°) is still not 
	included. Here the first intersection point is at the same altitude
	as the initial point.
	
2002-08-22  Oliver Lemke  

	* arts-1-1-212

	* src/Makefile.am (test_interpolation_SOURCES): Copy list of
	sources from arts_SOURCES (Without main.cc on second try :-))
	because we nearly need everything here.

	* src/test_interpolation.cc (test01): Don't define joker class.

2002-08-21  Patrick Eriksson  

	* arts-1-1-211

	* src/m_scatrte.cc: Added #include  to nmake sprintf known.

	* src/m_physics.cc: Added this file and moved methods for conversion
	to Tb to this file.

	* src/check_input.cc (chk_not_empty): Added this function to give
	an error if an agenda is empty (that should never be alowed, or?).
	This function is now called in "my parts" before an agenda is used.

	The inclusion of agendas in check_input has made that 
	test_interpolation cannot now be linked. I started to add files to
	the sources for test_interpolation, but I just needed to add more.

	What to do? Can test interpolation be removed?

	* src/rte.cc: Added header to the functions in the file. Note 
	especially the function ground_reflection_with_emission that is
	intended as a general function to call to consider ground reflections
	with emission.

	* src/m_rte.cc (RteEmissionStd): The function now uses *t_field*
	to determine the temperature along the propagation path.

	* src/m_rte.cc (RteCalc): The function has been slightly modified as
	a preperation to include Hb. 

	* doc/uguide/fm_definitions.tex: The existing text, beside part on
	ground reflections, has been revised and adapted to changes in the
	source code.

2002-08-20  Sreerekha T.R.  
	
	* arts-1-1-210
	
	* src/m_scatrte.cc: Added the method *Tensor6ToTbByPlanck* and
	removed the method i_fieldtoTb.  This
	is a Generic method following yesterday's discussion.  But the
	frequency grid is taken as specific input.  This is because,
	inside cloudbox we have only one frequency which is specified by
	the variable scat_f_index.  And mostly intensity fields inside the
	cloudbox only are Tensor6. 

	* src/methods.cc : Added the method Tensor6ToTbByPlanck and
	removed the method i_fieldtoTb.

	* doc/examples/i_field_example.i_field_Tb.xml : Removed this
	output file following ARTS convention of not including the output
	files. 

	* doc//examples/i_field_example.arts.in : Usage of Generic method
	Tensor6ToTbByPlanck instead of i_fieldtoTb.

2002-08-20  Claudia Emde  

	* arts-1-1-209

	* src/scat_rte.cc (convergence_flagAbs): Included a counter for the 
	number of iterations. Each iteration field is written to a file. This
	modification is only made for testing the convergence behaviour and 
	will be removed later.

2002-08-19  Claudia Emde  

	* arts-1-1-208

	* src/scat_rte.cc (i_fieldUpdate1D): Fixed some bugs related to the
	boundary conditions. 

2002-08-19  Sreerekha T.R.  

	* arts-1-1-207
	
	* src/m_scatrte.cc (i_fieldtoTb): This method converts the i_field
	in radiance units to Planck brightness temperature.  This uses the
	function *invplanck* in physics_funcs.cc 

	* src/methods.cc : Added the method i_fieldtoTb.

	* src/workspace.cc : Added the workspace variable i_field_Tb.

	* doc/examples/clearskyfield.xml : This is an example file added
	to give realistic input to the interface at cloudbox boundaries.
	This is created from ARTS.1.0.  The boundaries in pressure
	altitudes are 360 hPa and 280 hPa.

	* doc/examples/i_field_example.arts.in : The cloudbox boundary is
	changed to 360 hPa and 280 hPa. The example can now read the
	interface field from the above file.  The pnd_field is changed
	from 1 to a more realistic value 1297m^(-3).  The example file was
	giving a decent output until the last update.  After the last
	update the i_field is giving 0 and nan at some places because of
	which I cannot run this example.  But for having a look at the
	initial result I have a copy of the result in my smiles_local
	which I can add to the repositary which can be removed later.  

	* doc/examples/i_field_example.i_field_Tb.xml : This is the
	i_field in brightness temperature unit for 4 pressure grids(2 at
	cloudbox boundary and 2 inside the cloud box) inside
	the cloudbox. 

2002-08-19  Claudia Emde  

	* arts-1-1-206	
		
	* src/m_scatrte.cc (i_fieldUpdate1D): Included cloudbox boundary 
		conditions. Radiation travelling out of the cloudbox is 
		defined to be 0 as it is not needed for the iterations.
		
	* src/m_scatrte.cc (stokes_vecGeneral): Bug fixed.

	* src/test_linalg.cc (test_lusolve1D): Added this function to see
		if the LU decomposition also works for scalar equations.
	
2002-08-16  Sreerekha T.R.  

	* arts-1-1-205		
		
	* configure.in: While checking in last time, I edited  cd .. in
	this file by mistake.  

	* doc/examples/i_field_example.arts.in : Forgot to add this file to
	the repository.

	* doc/examples/Makefile.am : Forgot to add this in the list
	arts_examples 

2002-08-15  Sreerekha T.R.  

	* arts-1-1-204

	* src/m_scatproperties.cc (abs_vec_gasExample): Added this
	method.  This method is implemented for test purposes.  It is
	necessary to have some realistic values of absorption coefficents
	for radiative transfer calculations. The absorption coefficients
	calculated using ARTS.1.0 are used in this method and they are
	interpolated onto the pressure grid used for RT calculations.

	* src/m_scatproperties.cc (ext_mat_gasExample): This method is
	also for facilitating test calculations.  This gives extinction
	matrix for gaseous species.  The diagonal elements are the
	absorption coefficients calculated from abs_vec_gasExample and the
	off-diagonal elements are zero.  

	* src/methods.cc : Added the above two methods with minimum
	documentations. 
	
	* doc/examples/i_field_example.arts : This is an example control
	file which can be used to test the scattering RT calculation.
	
2002-08-14  Patrick Eriksson  

	* arts-1-1-203

	* src/m_rte.cc (RteEmissionStd): Pieces of this function have been 
	lifted out to be functions in rte.cc. This to make it easier to make
	other verions of methods for rte_agenda.

	* src/workspace.cc: The variable *e_ground* is now a matrix to allow
	more elaborated treatments of ground reflections later.

	* To summerize. The ground is now included in the RTE part. Spectra
	can be produced, but only for dummy atmospheric temperature and 
	absorption. No connection with the cloud box yet.

2002-08-11  Patrick Eriksson  

	* arts-1-1-202

	* src/workspace.cc: New WSV is mblock_index. The usage of a_pos and 
	a_los has been extended.

	* src/agendas.cc: New agenda is i_space_agenda.

	* src/methods.cc: New WSM are VectorToTbByRJ, VectorToTbByPlanck,
	MatrixToTbByRJ and MatrixToTbByPlanck.

	* src/m_rte.cc (RteEmissionStd): Adopted to i_space_agenda.

	* src/math_funcs.cc (integer_div): New function.

	* src/logic.cc (is_multiple): New function.

2002-08-09  Sreerekha T.R.  

	* arts-1-1-201
	
	* src/m_scatrte.cc (i_fieldUpdate1D): The changes made here are
	mainly with reference to the size of i_field and scat_field.  This
	comes in all methods which use these variables.  For example, In
	the previous version the size of i_field was 
	i_field( N_p, N_lat, N_lon, N_za, N_aa, N_i ) whereas now it is
	changed to i_field( cloudbox_limits[1] - cloudbox_limits[0]) +1,
       		        ( cloudbox_limits[3] - cloudbox_limits[2]) +1,
       			( cloudbox_limits[5] - cloudbox_limits[4]) +1,
       			 N_za, N_aa, N_i ).
	The code doesn't look very clean now because i have commented some
	parts of the code for Claudia to have a look at the changes i have
	made because she has written them.

	I had quite lot of problem at cloudbox boundaries while taking the
	average of *i_field* and *scat_field*.  That part has to be for
	sure rewritten.  But at present I retain them and comments on it
	will be really helpful.  

	* src/m_scatrte.cc (i_fieldIterate):There is some change in the
	input to *i_fieldIterate* which I forgot to enter in the Changelog
	file earlier.  The new input added to this method is scat_aa_grid.

	* src/m_scatrte.cc (scat_fieldCalc): Some bugs are fixed, as usual.

	* src/methods.cc : Changed inputs to i_fieldIterate.

	* src/workspace.cc : Changed the dimensions of i_field,
	i_field_old and scat_field.  Change the usage of amp_mat as output
	from amp_matCalc

2002-08-09  Patrick Eriksson  

	* arts-1-1-200

	* src/m_rte.cc (RteCalc): This function should now be ready. 

	* src/m_rte.cc (RteEmissionStd): The first attempt to create a
	method for rte_agenda.
	
	* src/m_rte.cc (VectorToTbByRJ): Started on this function. Not yet 
	ready.

	* src/m_rte.cc (yNoPolarisation): Created this function.

	* Polished on descriptions for included agendas, variables and methods.

	* The rather frequent commits depend on that I work both on the desktop
	and the laptop.

2002-08-08  Patrick Eriksson  

	* arts-1-1-199

	* src/m_rte.cc (RteCalc): Introduced some new variables and agendas
	around this function. Everything very preliminary so far.

2002-08-08  Oliver Lemke  

	* arts-1-1-198
	
	* src/check_input.cc: Bug fix.

2002-08-05  Nikolay Koulev   

	* arts-1-1-197
	
	* src/m_lineshapes.cc (elsDoppler): Added the Doppler line shape .
	
2002-08-08  Patrick Eriksson  

	* arts-1-1-196

	* src/m_rte.cc (RteCalc): Modified the input arguments and moved check
	of input to this function from ppathCalc. A first step to finish this
	function.

2002-08-05  Oliver Lemke  

	* arts-1-1-195
	
	* src/parser.cc (is_whitespace, eat_whitespace): Added backslash r
        as whitespace. Fixes bug which crashed arts when reading dos style
        control files under unix.
	
2002-08-01  Sreerekha T.R.  

	* arts-1-1-194

	* src/math_funcs.cc (AngIntegrate_trapezoid): Fixed bugs in this
	routine. 

	* scatproperties.cc : Again, fixed some bugs, mainly related to
	units of amplitude matrix, phase matrix and cross-sections. Tested
	the routines by reading in real values from the data base and it
	seems now that the calculation of scattering properties is
	correct.  I verified it with our old calculations when stokes_dim
	is equal to 1.  

2002-07-26  Sreerekha T.R.  
	
	* arts-1-1-193
	
	* src/m_scatproperties.cc (i_fieldSet): This methods interpolates
	the radiation field on all grid points inside the cloud box from
	the clear sky field.    This is the first guess for the iterative
	solution method.  The method is successfully tested for a 1-D case
	and hope that it works for 3-D too. 
	
	* src/methods.cc : Included the method i_fieldSet.
	
	* src/workspace.cc : Some minor corrections in the description of 
	scat_i_p and scat_i_lon.  
	
	* doc/examples : In the control file i_field.arts, added the path
	name for amplitude matrix data file.  But this data file cannot be
	used, as it has only one frequency and interpolation cannot be
	done if the old grid has only one point.  I made a new data file
	with more than one frequency and I am presently working with it
	for testing the scattering routines.  That data file is not at
	present in the package arts-data.  
	
2002-07-18  Patrick Eriksson  

	* arts-1-1-192

	* src/ppath.cc (ppath_step_geom_1d): Made a new version of this 
	function, using the same approach as in the same function for 2D. The
	code of the function is now much shorter and easier to understand.
	
	* src/ppath.cc (ppath_step_geom_2d): Fixed one bug. 

	* The 1D and 2D functions give the same result, for cases when this 
	shall be the case. The both functions are now hopefully finished.

2002-07-18  Claudia Emde  

	* arts-1-1-191

	* src/interpolation.cc: Included iostream.

2002-07-17  Claudia Emde  

	* arts-1-1-190

	* doc/uguide/scattering.tex: Some corrections according to
	suggestions by Sreerekha. 

2002-07-17  Patrick Eriksson  

	* arts-1-1-189

	* src/ppath.cc (ppath_step_geom_2d): 2D geometrical propagation path
	steps seem now to work, but no heavy bug checks (mainly a backup
	commit).

2002-07-15  Claudia Emde  

	* arts-1-1-188

	* doc/uguide/scattering.tex: Rewritten the explanation of the
	iteration scheme. More detailed now.

	* doc/uguide/main.tex: Renamed part III. Now it is "Mathematical
	functions" instead of "Linear algebra functions". 
	Added a new part "Theoretical background". Included chapter about
	polarization there. 

2002-07-05  Patrick Eriksson  

	* arts-1-1-187

	* src/ppath.cc: The story continues. Things work much better now. A 
	number of problems fixed. There is code for all parts, but there are 
	still some wormholes for more rare cases that must be fixed.

2002-07-04  Patrick Eriksson  

	* arts-1-1-186

	* src/ppath.cc: More work on 2D geom paths. A number of bugs fixed.
	Not all cases yet tested. Getting there slowly.
	(Mainly a commit to transfer changes to the laptop).

2002-07-04  Oliver Lemke  

	* arts-1-1-185
	
	* src/matpackVI.h (Tensor6), src/matpackVII (Tensor7): Replaced
	',' in member element initialization list in constructors by
	'*'. This was the reason for random segfaults while copying
	Tensor6 and Tensor7.

2002-07-04  Patrick Eriksson  

	* arts-1-1-184

	* src/ppath.cc: More work on 2D geoemtrical propagation paths. 
	A first version ready, but all bugs must be fixed and probelms with
	numerical inaccuracies must be handled (tricky, tricky).
	New functions:
	   geompath_from_r1_to_r2
	   za_geom2other_point
	   psurface_r_at_lat_2d
	   ppath_copy
	   ppath_append
	   ppath_fill_2d
	
2002-07-03  Patrick Eriksson  

	* arts-1-1-183

	* src/ppath.cc: Work to get 2D geometrical propagation paths to work.
	Not yet ready. This is mainly a backup commit.

	* src/m_ppath.cc: As above, but the work in this is hopefully ready.

	* src/interpolation.cc (ArrayOfGridPosPrint): Created this function.

	* src/math_funcs.cc (sign): Created this function.

2002-07-03  Christian Melsheimer  

	* arts-1-1-182

	* doc/uguide/Makefile.am (texfiles): Added entries
	polarization.tex and scattering.tex 

2002-07-03  Sreerekha T.R.  
	
	* arts-1-1-181
		
	* doc/uguide/scattering.tex: Added documentation for the method
	*amp_matCalc*

2002-07-02  Claudia Emde  

	* arts-1-1-180

	* doc/uguide/scattering.tex: Added description for the scattering 
	database and the reading routines. Furthermore the documentation
	for the convergence test.

	* doc/uguide/references.bib: Added references for Mishchenko code.

	* src/workspace.cc: Fixed documentation for *amp_mat_raw*.

2002-07-02  Sreerekha T.R.  
	
	* arts-1-1-179
	
	* src/m_scatproperties.cc (amp_matCalc): Added the method
	amp_matCalc which calculates the workspace variable
	amp_mat from amp_mat_raw.  amp_mat_raw is in this
	method an ArrayOfArrayOfTensor6.

	* src/methods.cc : Added this method.

	* src/m_scatrte.cc : Fixed some bugs in the method 
	scat_fieldCalc.

2002-07-02  Christian Melsheimer  

	* arts-1-1-178

	* doc/uguide/polarization.tex: Added more details, especially on
	how to measure the Stokes parameters.

2002-07-01  Claudia Emde  

	* arts-1-1-177

	* src/m_cloudbox.cc (ParticleTypeAdd), (ParticleTypeInit): Modified
	the methods. Now, it is avoided to copy tensors so that the
	methods are more efficient.

	* src/workspace.cc: Modified entries for the methods above.
		
	* src/groups.cc, m_clonesize.cc, matpackIII.h, matpackVI.h,
	xml_io.cc,groups.cc: Included ArrayOfArrayOfTensor3 and
	ArrayOfArrayOfTensor6 everywhere. These datatypes are needed to be
	able to use the gridded fields efficiently.

2002-06-29  Stefan Buehler  

	* arts-1-1-176

	* src/m_abs.cc (xsec_per_tgAddLines): Suppressed output of all
	transitions to do to out3. This takes longer than the calculation
	itself, if you calculate with the entire HITRAN database!

2002-06-28  Stefan Buehler  

	* arts-1-1-175

	* src/interpolation.cc (interpweights): Added "red" interpweights
	functions for dimensions 1 to 6.
	(interp): Added "red" interp functions for dimensions 1 to 6.
	Red interpolation means interpolation to a scalar. This is not yet
	tested at all.

2002-06-28  Oliver Lemke  

	* arts-1-1-174
	
	* src/m_cloudbox.cc (ParticleTypeAdd): Bugfix - endl not working
	in out2, replaced by newline.
	
2002-06-28  Oliver Lemke  

	* arts-1-1-173
	
	* src/gridded_fields.cc: Include iostream.
	
	* src/scatproperties.h: Removed non-used headers from includes.
	
	* src/scatproperties.cc: Moved include logic.h from header file.

	* src/test_tensor.cc, src/ppath.cc, src/poly_roots.cc,
	src/physics_funcs.cc, src/m_scatrte.cc, src/m_scatproperties.cc,
	src/m_ppath.cc, src/m_io.cc, src/m_hdf.cc, src/m_atmosphere.cc,
	src/math_funcs.cc, src/m_abs.cc, src/lineshapes.cc,
	src/lin_alg.cc, src/interpolation.cc, src/file.cc,
	src/continua.cc, src/cloudbox.cc: Include c++ header cmath instead
	of math.h.

	* src/arts.h: Removed commented list of non-included standard
	headers.

	* src/main.cc (main): Output precision with -v.

	* src/test_matpack.cc: Include cmath to compile properly on HP-UX.

2002-06-27  Claudia Emde  

	* arts-1-1-172
		
	* src/workspace.cc: Modified the documentation for *amp_mat_raw*
	and *pnd_field_raw*. We decided that these variables are gridded 
	fields.

	* src/gridded_fields.cc: Included error messages, runtime errors 
	instead of 'cout'.
	
2002-06-19  Stefan Buehler  

	* arts-1-1-171

	* doc/uguide/app_groups.tex: Replaced "WSV" by "workspace variable".

2002-06-27  Claudia Emde  

	* arts-1-1-170

	* src/gridded_fields.cc/h: Added. Reading routines for gridded
	fields which use Olivers gridded tensor validation routines.

	* src/Makefile.am: Added gridded_fields.cc/h.

	* src/m_cloudbox.cc: Added new methods (ParticleTypeInit) and
	(ParticleTypeAdd) to read from the scattering database and construct
	*amp_mat_raw*. 

	* src/methods.cc: Included the methods above.
		
	* src/m_scatrte.cc: Modified (i_fieldIterate), the scattering
	integral function is now included. 
		
2002-06-26  Oliver Lemke  

	* arts-1-1-169

	* src/test_griddedtensorcheck.cc: Added. Optimized gridded tensor
	validation routines. Temporarily added for testing, could be
	removed in the near future when everything works as expected.

	* src/Makefile.am: Added target test_griddedtensorcheck.

	* src/xml_io.cc (xml_read_from_stream): Added better error output
	when data reading fails (Only for tensor6 at the moment).

2002-06-26  Christian Melsheimer  

	* arts-1-1-168

	* doc/uguide/main.tex (paragraph{#1}}): Added \include{polarization}.

	* doc/uguide/scattering.tex: Moved section "Polarization and
	Stokes Parameters" to new file and chapter.

	* doc/uguide/polarization.tex: Created new file and moved the
	section "Polarization and Stokes Parameters" (was in
	scattering.tex, see arts-1-1-166) here, it is now a chapter.

2002-06-26  Oliver Lemke  

	* arts-1-1-167
	
	* doc/uguide/arts_groups_to_latex.sh: Replaced remaining echos
	with cat.

2002-06-26  Christian Melsheimer  

	* arts-1-1-166

	* doc/uguide/scattering.tex: Recommitted changes (see
	arts-1-1-164), probably I forgot to save before committing
	1-1-164·...

2002-06-25  Sreerekha T.R.  

	* arts-1-1-165

	* doc/uguide/scattering.tex : Some modifications in the part
	regarding the calculation of scattering properties.  Added the
	section about calculating the scattering integral.
	
	* src/m_scatproperties.cc, m_scatrte.cc, workspace.cc, methods.cc:
	Renamed workspace variable pha_mat_part to pha_mat.

	* src/m_scatproperties.cc, m_scatrte.cc, workspace.cc, methods.cc:
	Renamed workspace method pha_mat_partCalc to pha_matCalc.

	* src/m_scatrte.cc, methods.cc: Renamed workspace method 
	scat_integralCalc to scat_fieldCalc to be consistent with the
	naming scheme in ARTS.
	
2002-06-25  Christian Melsheimer  

	* arts-1-1-164

	* doc/uguide/fm_definitions.tex: Americanized spelling

	* doc/uguide/symbol_defs: Redefined \Re and \Im (real and imaginary
	part (now: non-italic "Re" and "Im", like function names)

	* doc/uguide/ppath.tex: Americanized spelling.

	* doc/uguide/scattering.tex: Added section "Polarization and
	Stokes Parameters", did spell check and americanized spelling.

2002-06-25  Oliver Lemke  

	* arts-1-1-163
	
	* src/xml_io.cc (read_from_stream): Fixed bug when more data is
	available inside tag than expected.

	* doc/uguide/arts_groups_to_latex.sh: Use cat instead of echo to
	avoid misinterpretation of escape chars.

	* doc/uguide/arts_methods_to_latex.sh: Rewritten. Use case instead
	of if/grep combinations -> speedup by factor 10.
	
	Use cat instead of echo to avoid misenterpretation of escape chars.

	* doc/uguide/app_methods.tex: Modified text.

2002-06-25  Sreerekha T.R.  
	
	* arts-1-1-162
	
	* doc/examples/scatproperties_example.arts.in: I
	forgot to add this file while checking in last time.
		
2002-06-25  Sreerekha T.R.  
	
	* arts-1-1-161
	
	* src/m_scatrte.cc: The method scat_integralCalc is 
	extended for 3-d case.  

	* src/m_scatproperties.cc : Added more comments and 
	checks.

	* doc/examples/scatproperties_example.arts.in : I used 
	this control file to check the methods used for 
	calculating single scattering properties.

2002-06-24  Sreerekha T.R.  

	* arts-1-1-160

	* src/m_scatrte.cc (scat_integralCalc): Added the workspace
	variables pha_mat_spt and pnd_field as input to this method.
	Earlier pha_mat_part was directly given as input, but now we
	calculate pha_mat_part inside the method from pha_mat_spt 
	and pnd_field.  

	* src/methods.cc: The inputs are changed here also. The 
	documentation is also modified.
		
2002-06-21  Claudia Emde  
	
	* arts-1-1-159

	* m/scatrte.cc (i_fieldUpdate1D) and (i_fieldIterate): Some
	modifications to include the scattering integral. 
	Calculation of optical properties modified.

	* src/methods.cc: Changed interfaces for the methods above.
	
2002-06-21  Sreerekha T.R.  

	* arts-1-1-158
	
	* src/m_scatrte.cc : Added the method scat_integralCalc which
	computes the scattering integral.

	* src/methods.cc : Added the method scat_integralCalc.
	
2002-06-21  Sreerekha T.R.  

	* arts-1-1-157
	
	* src/m_scatproperties.cc (abs_vec_partCalc): Changed the inputs
	to methods abs_vec_partCalc, ext_mat_partCalc, pha_mat_partCalc.

	* src/methods.cc : Changed the inputs for the above methods.

2002-06-20  Claudia Emde  

	* arts-1-1-156

	* src/m_rtescat.cc (i_fieldUpdate1D) and (i_fieldIterate):
	Included the functions and agendas for calculating the optical
	properties. Modified the interfaces of the functions.
	(convergence_flagAbs): Limiting values for the convergence test
	are now keywords, which can be specified in the control file.
	
	* src/methods.cc: Adapted interfaces according to the changes
	above.

	* doc/i_field.arts: Added agenda definitions for the calculations
	of optical properties.

2002-06-20  Claudia Emde  

	* arts-1-1-155
		
	* src/m_scatproperties.cc: Fixed and marked some bugs.

	* src/workspace.cc: Added variables *scat_p_index*, 
	*scat_lat_index*, *scat_lon_index*.

2002-06-19  Claudia Emde  

	* arts-1-1-154
		
	* src/workspace.cc: Added variables *amp_mat_raw* and
	*pnd_field_raw*.
		
	* src/groups.cc: Included ArrayOfTensor3 and ArrayOfTensor6 to be
	able to include the variables above.

	* src/xml_io.cc: Added reading and writing routines for
	ArrayOfTensor3 and ArrayOfTensor6.

	* src/m_clonesize.cc: Included ArrayOfTensor3 and ArrayOfTensor6.

	* src/m_scatrte.cc: Included this file. It should contain all
	functions concerning the radiative transfer inside the scattering
	box. 
	Worked on (i_fieldUpdate1D). Tried to put in Sreerekhas functions.
	This is not finished yet.

	* src/methods.cc: Modifications of the interfaces of
	(i_fieldUpdate1D) and (i_fieldIterate).
	
	* src/Makefile.am: Included m_scatrte.cc.

	* src/m_cloudbox.cc: Shifted a lot of functions to m_scatrte.cc.

	* src/agendas.cc: Only small modifications in the documentation.

2002-06-19  Sreerekha T.R.  

	* arts-1-1-153

	* src/agendas.cc: Added the agendas ext_mat_agenda
	and abs_vec_agenda.

	* src/m_scatproperties.cc : The dimension of pnd field
	is changed from pnd_field ( p_grid, lat_grid, long_grid, 
	part_types) to  pnd_field ( part_types, p_grid, lat_grid,
	long_grid)
	
2002-06-18  Stefan Buehler  

	* arts-1-1-152

	* src/methods.cc: Added supergeneric ReadXML and WriteXML
	methods. Removed other XML IO methods.

	* src/m_xml.h: Added. Contains the template functions for
	supergeneric XML IO. This is the original template function from
	Oliver Lemke, I've just moved it here.

	* src/m_xml.cc: Removed.

	* src/xml_io.cc: Added dummy functions for groups for XML IO is
	not yet implemented.

	* src/make_auto_md_cc.cc: Added #include for m_xml.h.

	* doc/examples/absorption_example.arts.in: Example now uses
	supergeneric WriteXML.

	* src/groups.cc: Commented out groups TagGroups,
	ArrayOfLineRecord, and ArrayOfArrayOfLineRecord.

2002-06-18  Sreerekha T.R.  

	* arts-1-1-151
	
	* src/m_scatproperties.cc (abs_vecCalc): The methods
	abs_vecCalc and ext_matCalc are implemented. The method
	abs_vecCalc sums up the particle absorption vector and 
	gaseous absorption vector (abs_vec_part + abs_vec_gas) 
	and the method ext_matCalc sums up the particle extinction
	matrix and gaseous extinction matrix (ext_mat_part + ext_mat_gas).

	* src/math_funcs.cc : moved the integration routine 
	AngIntegrate_trapezoid from scatproperties.cc to here. 

	* src/methods.cc : added the methods abs_vecCalc and 
	ext_matCalc

	* src/workspace.cc : added the variables ext_mat_gas 
	and abs_vec_gas.  The documentation for this is at present
	bit clumsy.

2002-06-18  Stefan Buehler  

	* arts-1-1-150

	* src/parser.cc: Fixed handling of supergeneric methods. 

	* src/methods_aux.cc: Fixed handling of supergeneric methods. 

	* src/methods.h: Fixed handling of supergeneric methods. 

	* src/make_auto_md_h.cc: Fixed handling of supergeneric methods. 

	* src/make_auto_md_cc.cc: Fixed handling of supergeneric methods. 

	* src/methods.h: Added field mactual_group and function
	ActualGroup to MdRecord.

	* src/m_clonesize.cc: Name no longer contains group.

	* src/methods.cc: Added Ignore.

	* src/m_ignore.h: Added. Implementation of supergeneric Ignore
	method. 

	* src/m_copy.cc: Removed.

	* src/m_copy.h: Added. Implementation of supergeneric Copy method
	is now a template function here.

	* src/Makefile.am: Added m_copy.h, m_ignore.h, remove m_copy.cc.

	* doc/examples/absorption_example.arts.in: Example uses now
	CloneSize and Ignore.

2002-06-18  Oliver Lemke  

	* arts-1-1-149
	
	* doc/uguide/app_methods.tex: Added.

	* doc/uguide/main.tex: Include app_methods.tex.

	* doc/uguide/.cvsignore: Added auto_methods.tex.

	* doc/uguide/Makefile.am: Added auto_methods.

	* doc/uguide/arts_methods_to_latex.sh: Added. Converts online
	documentation to latex.

	* src/methods.cc: Removed "backslash a"-typo from descriptions.

2002-06-18  Sreerekha T.R.  

	* arts-1-1-148

	* src/m_scatproperties.cc (pha_mat_partCalc): Added this method
	which calculates the phase matrix.  

	* src/workspace.cc : added variables pha_mat_part

	* src/methods.cc : added the method pha_mat_partCalc.

2002-06-18  Oliver Lemke  

	* arts-1-1-147

	* src/methods_aux.cc: Removed default argument which is already
	given in declaration.
	
2002-06-18  Oliver Lemke  

	* arts-1-1-146

	* src/methods.cc: Changed all md_data. to md_data_raw.

2002-06-17  Sreerekha T.R.  

	* arts-1-1-145

	* src/m_scatproperties.cc (abs_vec_partCalc): Added the methods
	abs_vec_partCalc and ext_mat_partCalc.  These methods sums up 
	the absorption as well as extinction matrices for single particle
	types weighted with the particle number density.

	* src/workspace.cc : added variables ext_mat_part, abs_vec_part
	and pnd_field.

	* src/methods.cc : added the method abs_vec_partCalc and 
	ext_mat_partCalc.

2002-06-17  Stefan Buehler  

	* arts-1-1-144

	* General: First implementation of supergeneric methods. Not quite
	finished yet, there are some things I want to modify in the next
	version. But basically it works.

	* src/supergeneric.h: Added.

	* src/m_copy.cc: Added.

	* src/m_clonesize.cc: Added.

	* src/groups.cc: Added group Any_.

	* src/methods.cc: Added supergeneric methods CloneSize and Copy.

	* src/parser.h: Put in supergeneric methods.

	* src/parser.cc: Put in supergeneric methods.

	* src/methods_aux.cc: Put in supergeneric methods.

	* src/methods.h: Put in supergeneric methods.

	* src/make_auto_wsv_groups_h.cc: Put in supergeneric methods.

	* src/make_auto_md_h.cc: Put in supergeneric methods.

	* src/make_auto_md_cc.cc: Put in supergeneric methods.

	* src/main.cc: Put in supergeneric methods.

	* src/globals_2.cc: Put in supergeneric methods.

	* src/Makefile.am: Added new source files.

	* src/matpackI.h (Matrix& Matrix::operator=(const Matrix& m)): 
	Added comment to doxygen header about deprecated resizing for
	empty target.
	(Vector& Vector::operator=(const Vector& v)): Implemented resizing for
	empty target, to allow ArrayOfVector (should we ever need
	this). Added comment to doxygen header about deprecated use of
	this feature in user code.

2002-06-17  Claudia Emde  

	* arts-1-1-143

	* src/m_cloudbox.cc (convergence_flagAbs): Added this function. It
	performs a convergence test checking the maximal absolute
	difference for all components of the radiation field.

	* src/workspace.cc: Added variables *convergence_flag* and
	*i_field_dim* (for a 1D atmosphere the radiation field can be 2D
	or 3D!)
		
	* src/methods.cc: Added method *convergence_flagAbs*.

	* src/agendas.cc (convergence_test_agenda): Added the agenda for
	the convergence test.

2002-06-17  Oliver Lemke  

	* arts-1-1-142
	
	* doc/uguide/arts_groups_to_latex.sh: Fixed doc header to use
	$ARTS and only use the first line from arts -v output.

2002-06-15  Sreerekha T.R.  
	
	* arts-1-1-141
	
	* src/m_scatproperties.cc (abs_vec_sptCalc): modified this method.
	Added *scat_za_grid* and *scat_aa_grid* as inputs to this method
	since this is required for integration of the phase matrix.  

	* src/methods.cc : added  *scat_za_grid* and *scat_aa_grid* as 
		input to the method abs_vec_sptCalc.
	
2002-06-14  Sreerekha T.R.  

	* arts-1-1-140
	
	* src/scatproperties.cc,
	  m_scatproperties.cc : a quick modification on the 
		coding style following Oliver's suggestions.
	
2002-06-14  Oliver Lemke  

	* arts-1-1-139
	
	Merged changes from ARTS-1-0 branch.
	
	* src/main.cc (main): Output os info with -v.
	
	* src/getopt.h: Use getopt_long prototyping for GNU C, HP-UX and
	SunOS.

	* configure.in: Determine operating system name and version. Name
	is defined in OS_NAME, version in OS_VERSION.

2002-06-14  Claudia Emde  

	* arts-1-1-138
		
	* doc/uguide/scattering.tex: Modified documentation according to
	the methods in (scatproperties.cc) and (m_cloudbox.cc). 

2002-06-14  Sreerekha T.R.  

	* arts-1-1-137
	
	* src/scatproperties.cc : completed the functions amp2ext,
	amp2pha,amp2abs called by ext_mat_sptCalc, pha_mat_sptCalc
	and abs_vec_sptCalc respectively.  Added more documentation
	in the comment.  Also the new routine for solid angle integration
	of Matrix is included here. I think it is better to shift this
	function to math_funcs.cc or so.   

2002-06-14  Claudia Emde  

	* arts-1-1-136

	* src/methods.cc: Included methods for RT with scattering:
	(stokes_vecGeneral) General computaion of the RTE, works for all 
	Stokes dimensions.
	(stokes_vecScalar) Special function which is more efficient for 
	computing the scalar RTE.

	* src/agendas.cc (scat_rte_agenda): Agenda to compute the RT inside
	the cloudbox.

	* src/workspace.cc: Included workspace variables for the methods
	above:
	- stokes_vec
	- l_step
	- planck_function
	- ext_mat
	- abs_vec
	- sca_vec

	* src/m_cloudbox.cc: (stokes_vecGeneral) and (stokes_vecScalar)
	added. (i_fieldIterate) and (i_fieldUpdate1D) modified so that
	(scat_rte_agenda) can be executed.

	* doc/examples/i_field.arts: This example executes now
	*ppath_step_agenda* and *scat_rte_agenda*).

	* src/cloudbox.cc/h: No functions are left here at the moment.

	* src/Makefile.am: Removed cloudbox.cc/h from arts_SOURCES.
	
2002-06-13  Stefan Buehler  

	* arts-1-1-135

	* doc/uguide/agendas.tex: Continued.

	* doc/uguide/concept.tex: Started to work on this again.

	* doc/uguide/main.tex: Changed "on" to "of" in \startsymbols.

	* doc/uguide/scattering.tex: Removed some TeX warnings, together
	with Claudia.

2002-06-12  Stefan Buehler  

	* arts-1-1-134
	
	* configure.in: Updated copyright notice.

	* doc/uguide/agendas.tex: Put in Section about WSVs. Started
	Section about WSMs. Agenda WSMs and Section on Agendas still
	missing. 

	* src/workspace.cc: Only cosmetic changes.

	* src/methods.cc: Only cosmetic changes in elsLorentz.

2002-06-12  Claudia Emde  

	* arts-1-1-133

	* src/cloudbox.cc,
	 src/cloudbox.h,
	 src/lin_alg.cc,
	 src/lin_alg.h,
	 src/m_cloudbox.cc,
	 src/test_linalg.cc: Formatted the files according to Olivers
	 remarks on coding style.

2002-06-12  Oliver Lemke  

	* arts-1-1-132
	
	* configure.in: Corrected definition of ac_arts_data.

	* src/scatproperties.cc,
	src/agenda_record.h,
	src/agenda_record.cc,
        src/m_cloudbox.cc: Include iostream for cout.

2002-06-11  Stefan Buehler  

	* arts-1-1-131

	* General: Implemented automatic Input/Output checking for
	agendas. That means, you no longer have to check in the calling
	function that the agenda does what it is supposed to do. There is
	now a special lookup table for agendas in file agendas.cc. Data
	records for new agendas have to be added in both workspace.cc and
	agendas.cc, however, the DESCRIPTION in workspace.cc should just
	be a reference to agendas.cc. Only the DESCRIPTION in agendas.cc
	is used by arts -d etc..
	
	* src/agendas.cc: Added. This contains the lookup data for
	agendas. You have to edit this everytime you add an agenda. But
	nevertheless, you also have to add an entry in
	workspace.cc. Documentation for the agenda must be in agendas.cc,
	not in workspace.cc.

	* src/agenda_record.h: Added.

	* src/agenda_record.cc: Added.

	* src/agenda_class.h: Added.

	* src/agenda_class.cc: Added.

	* src/agenda.h: Moved to agenda_class.h.

	* src/agenda.cc: Moved to agenda_class.cc.

	* src/Makefile.am: Added the new source files.

	* src/workspace_aux.cc: Moved output operator of WsvRecord to
	agenda_record.cc for technical reasons.

	* src/workspace.cc: Moved agenda DESCRIPTIONS to agendas.cc for
	all agendas that have been defined so far.

	* src/parser.h: Changed name of agenda header file to agenda_class.h.

	* src/methods.cc: Updated copyright notice, updated documentation
	for AgendaSet.

	* src/make_auto_wsv_h.cc: Changed name of agenda header file to agenda_class.h.

	* src/main.cc: Made command line switches work for agendas.

	* src/m_agenda.cc: Made AgendaSet check the input and output parameters.

	* src/globals_2.cc: Added AgendaMap.

2002-06-11  Claudia Emde  

	* arts-1-1-130

	* src/m_cloudboc.cc (i_fieldUpdate1D): Extended the function such
	that it adapts automatically to the scalar case if *stokes_dim* is
	set to 1.

	* src/cloudbox.cc (sto_vec1DCalc): Added this function to do the
	scalar radiative transfer calculation.

	* doc/uguide/scattering.tex: Included the scalar RTE as a special
	case. 
	
2002-06-10  Claudia Emde  

	* arts-1-1-129

	* doc/uguide/scattering.tex: Rewritten the part for radiative
	transfer inside the cloudbox to document the already existing
	functions. 

	* doc/uguide/lin_alg.tex: Replaced \verb by \artsstyle.

2002-06-10  Sreerekha T.R.  

	* arts-1-1-128

	* src/m_scatproperties.cc: Added this file.  This has so far the
	workspace methods ext_mat_sptCalc,pha_mat_sptCalc and 
	abs_vec_sptCalc.  Some changes are for sure expected in these
	methods.  

	* src/methods.cc: Added the methods ext_mat_sptCalc,
	pha_mat_sptCalc and abs_vec_sptCalc. 

	* src/Makefile.am : included in the source file list
	m_scatproperties.cc,scatproperties.cc and scatproperties.h
	
2002-06-10  Sreerekha T.R.  

	* arts-1-1-127

	* src/workspace.cc : Added the workspace variables scat_za_index
	and scat_aa_index necessary for the methods used for calculating
	scattering properties of particles.

2002-06-08  Stefan Buehler  

	* arts-1-1-126

	* src/workspace.cc: Added some #defines (NAME, DESCRIPTION,
	GROUP), so that this file is now formated similar to methods.cc. The
	main reason why I did this is because I wanted to add fields
	OUTPUT and INPUT to list output and input WSVs for
	agendas. However, it turns out that this problem cannot be solved
	so easily. The problem is this: The enum type for the different
	WSVs (ls_, f_grid_, etc.) is defined in auto_wsv.h, which is
	generated from workspace.cc. So, using the enum inside
	workspace.cc would generate a circular dependency. I played around
	with some tricks to solve this, but they all made things very
	complicated. So, my preferred solution at the moment is to add an
	extra file agendas.cc, which will contain agenda lookup
	data. Agendas will then have to be registered in two files, both
	workspace.cc and agendas.cc.

	* src/methods.h: Moved the #defines for OUTPUT, etc., to methods.cc.

	* src/methods.cc: Moved the #defines for OUTPUT, etc., here from
	methods.h. 

2002-06-08  Patrick Eriksson  

	* arts-1-1-125

	* src/ppath.cc (psurface_crossing_2d): Adapted the Matlab function
	psurface_crossing in AMI to create this function. I had to handle
	the case c=0 especially due to a limitation of poly_root_solve
	compared to the Matlab function roots. 
	Tests performed of the function and it looked OK.

2002-06-07  Stefan Buehler  

	* arts-1-1-124

	* doc/uguide/main.tex: Changed header for \typeindex from "data
	structures" to "data types". Added \include for app_groups.tex.

	* doc/uguide/matrix_vector.tex: Replaced \verb by \artsstyle. Added
	some index commands.

	* doc/uguide/development.tex: Replaced \verb by \artsstyle. Added
	some index commands.

	* doc/uguide/app_groups.tex: Added this file. It lists all WSV
	groups. 

	* doc/uguide/arts_groups_to_latex.sh: Added this script (written
	by Oliver), which puts the output of arts -g into LaTeX commands.

	* doc/uguide/Makefile.am: Added target auto_groups.tex, which is
	generated by the arts_groups_to_latex.sh script. Added variable
	$(autotexfiles), which now holds only auto_groups.tex.
	NOTE: If you try to build in doc/uguide with a pristine ARTS
	package (after make maintainer-clean at toplevel), you will now
	get an error message, because the arts executable is needed to
	generate auto_groups.tex. If you say make at toplevel, src is
	built first, so there is no problem.

	* doc/uguide/.cvsignore: Added auto_groups.tex.

	* src/main.cc (main): Changed output stream for --help and
	--version options from cerr to cout. Also, removed "This is" from
	--version output.

	* src/.cvsignore: Added test_scatproperties.

2002-06-07  Claudia Emde  

	* arts-1-1-123

	* src/methods.cc (i_fieldUpdate1D): Included this method to update
	the intensity field during the iteration. Performs RT calculation 
	with fixed scattered field.

	* src/m_cloudbox.cc (i_fieldUpdate1D): This function was in
	cloudbox.cc before. Now it uses the *ppath_step_agenda*, for this
	reason it is a workspace method now. 

	* src/cloudbox.cc (i_field_update1D): Removed this function.

	* src/workspace.cc: Included WSV *scat_field* and *i_field_old*.

	* doc/examples/i_field_arts: Example to test the cloudbox functions.
	
2002-06-07  Patrick Eriksson  

	* arts-1-1-122

	* src/ppath.cc (ppath_start_stepping): Some more work in getting 2D to
	work. Some results are now printed on the screen.

	* src/m_ppath.cc (ppathCalc): Sensor position and LOS printed as out2.

2002-06-06  Sreerekha T.R.  

	* arts-1-1-121	

	* src/test_scatproperties.cc: Renamed
	src/test_opt_properties.cc to test_scatproperties.cc to be 
	consistent.

	* src/workspace.cc: corrected the dimension of pha_mat_spt.

2002-06-06  Claudia Emde  

	* arts-1-1-120

	* src/workspace.cc: Included workspace variable amp_mat_raw.
		
	* src/physics_funcs.cc: Modified functions again, so that they 
	return numeric values. 

	* src/m_rte.cc and cloudbox.cc: Adjusted to the new Planck
	function.

2002-06-06  Sreerekha T.R.  

	* arts-1-1-119

	* src/scatproperties.cc : Added this file.  This contains some
	auxiliary functions like amp2ext,amp2pha,amp2abs which is called 
	by the workspace methods like ext_mat_sptCalc,pha_mat_sptCalc and
	abs_vec_sptCalc( Adding these methods is my immediate task.)

	* src/scatproperties.h : Added this file
	
	* src/test_opt_properties.cc (main): I added this file mainly 
	to test the scattering routines in scatproperties.cc

2002-06-05  Stefan Buehler  

	* arts-1-1-118

	* doc/uguide/agendas.tex: Continued to work on this.

	* doc/uguide/development.tex: Added references to the WSV, WSM,
	and agendas chapter in howtos.

	* src/agenda.h: Added set_name() and name() member functions to
	class Agenda, also added private member mname.

	* src/agenda.cc: Added implementation of set_name() and name().

	* src/main.cc: Set name for Main agenda.

	* src/parser.cc (parse_method): Removed duplicate level 3
	output. Cleaned up agenda output.

	* src/workspace.cc (define_wsv_data): Replace "function" by "method".

	* src/m_method_list.cc: Removed.

	* src/method_list.h: Removed.

2002-06-05  Sreerekha T.R.  
	
	* arts-1-1-117
	
	* src/workspace.cc: Added workspace variables, ext_mat_spt,
	pha_mat_spt, and abs_vec_spt.  

2002-06-05  Stefan Buehler  

	* arts-1-1-116

	* doc/uguide/agendas.tex: Started this file. It contains
	documentations about WSVs, WSMs, and particularly agendas. By
	doing this I noticed that WSM are sometimes called "workspace
	methods" and sometimes "workspace functions". But names should be
	consistent within AUG. Method is the older and more established
	term (that's for example why WSM files are called
	m_something.cc). So, I tried to enforce "method"
	everywhere. Please use the name "method" in future.

	* doc/uguide/main.tex: Renamed \structindex to \typeindex, as
	suggested by Sreerekha/Patrick. Replaced "workspace functions" by
	"workspace methods". Replaced \wsfindex by \wsmindex.

	* doc/uguide/scattering.tex: Replaced \wsfindex by \wsmindex.
	Replaced \wsmindex by \wsvindex for agendas, since agendas are
	WSVs, not WSMs. Replaced \wsmindex by \funcindex for matrix_exp,
	since this is a normal function, not a WSM. I suspect there are
	more functions marked by \wsmindex that really should be marked by
	\funcindex.

	* doc/uguide/lin_alg.tex: Replaced \wsfindex by \wsmindex.

	* doc/uguide/fm_definitions.tex: Replaced "workspace functions" by
	"workspace methods". Replaced \wsfindex by \wsmindex.

	* doc/uguide/concept.tex: Replaced "functions" by "methods".

	* doc/uguide/ppath.tex: Renamed \structindex to \typeindex, as
	suggested by Sreerekha/Patrick. Replaced "workspace functions" by
	"workspace methods". Replaced \wsfindex by \wsmindex.

	* doc/uguide/interpolation.tex: Renamed \structindex to \typeindex, as
	suggested by Sreerekha/Patrick.

2002-06-04  Patrick Eriksson  

	* arts-1-1-115

	* src/ppath.cc: Just some small steps forward for 2D. Status basically
	as for last commit from me.

	* doc/uguide/fm_definitions.tex: Polished the text. I happen to do this
	on the same time as Christian did his changes below and this caused
	a number of conflicts when updating. I hope that I managed to keep your
	changes Christian. 

	* doc/uguide/ppath.tex: Polished the text. Conflicts as above.

2002-06-04  Christian Melsheimer  

	* arts-1-1-114

	* doc/uguide/ppath.tex:  Fixed minor spelling/grammar errors.

	* doc/uguide/formalism.tex: Fixed minor spelling/grammar errors.

	* doc/uguide/fm_definitions.tex: Fixed minor spelling/grammar errors.

	* doc/uguide/introduction.tex: Fixed minor spelling/grammar error.

2002-06-04  Stefan Buehler  

	* arts-1-1-113

	* doc/examples/absorption_example.arts.in: The first agenda
	example works! Method lsWithCutoffAdd uses agenda els_agenda to
	compute the elementary lineshape.

	* src/methods.cc: Modified IO parameters of elsLorentz and
	lsWithCutoffAdd. 

	* src/workspace.cc (define_wsv_data): Introduced els, the WSV to
	hold the output of the els_agenda.

	* src/m_lineshapes.cc: Finished lsWithCutoffAdd.

	* src/interpolation.cc (interp): Added to all interp functions an
	assert that makes sure that the sum of all weights for the first
	interpolated value is 1. This condition should be fulfilled for
	all the weights, of course, but we check only the first set of
	weights.

2002-06-04 Claudia Emde  

	* arts-1-1-112

	* src/m_cloudbox.cc (i_field_itCalc): The method can be compiled and 
	tested using dummy variables for the scattering coefficients. But so
	far it only performs the update of the i_field for the 
	1D case.

	* src/workspace.cc: Changed amp_mat from Tensor7 to Tensor6. The 
	frequency dimension is taken out.
	
	* src/methods.cc: Changed amp_mat as input variable for  
	(i_field_itCalc).
	
	* src/physics_funcs.cc (planck): Fixed a bug here.

	* doc/uguide/scattering.tex: Started to write about 1D scattering 
	calculations.

2002-06-03  Patrick Eriksson  

	* arts-1-1-111

	* src/ppath.cc (ppath_start_stepping): Worked on this function for 2D.
	Finished for sensor positions inside the model atmosphere. More
	to do for other starting points.
	New internal functions:
	   psurface_slope_2D
	   psurface_tilt_2D
	   is_los_downwards_2D
	   angle_after_ground_2D

	* src/m_ppath.cc: Two now WSF:
	   a_posAddRgeoid
	   sensor_posAddRgeoid

2002-05-31  Stefan Buehler  

	* arts-1-1-110

	* Uff. I had some trouble resolving conflicts in workspace.cc. I
	seems that resorting this file (and methods.cc) was not such a
	great idea, since it leads to a lot of conflicts.
	
	* Started to work out agenda examples for lineshapes. Ran into a
	lot of problems (not so much related to the agendas, more to the
	lineshapes themselves). Nothing's working yet.

	* src/m_lineshapes.cc: Added.

	* src/workspace.cc: Added some lineshape variables.

	* src/methods.cc: Added some lineshape related methods. 
	(define_md_data): Removed abs_ from RteCalc input, following
	advice by Patrick. 
	(define_md_data): Replace "Global" by "Generic" everywhere.

	* src/groups.cc (define_wsv_group_names): Removed ArrayOfLineshapeSpec.

	* src/absorption.h: Removed all lineshape stuff.

	* src/absorption.cc: Removed all contents to old_absorption.cc.

	* src/Makefile.am: Added new source files.

	* doc/examples/absorption_example.arts.in: My playing field for
	agenda based absorption routines.

	* src/m_rte.cc (RteCalc): Removed abs input, following advice by
	Patrick. 

2002-05-31  Patrick Eriksson  

	* arts-1-1-109

	* src/methods.cc: Two new functions, a_posSet and a_losSet.

	* src/ppath.cc (ppath_start_stepping): Started to include 2D cases.

	* doc/uguide/ppath.tex: Polished old text and wrote some pages of new 
	text. The chapter is now up to date with what has been implemented. 

	* doc/uguide: Made new versions of figures created by Latex commands.
	The new figures are made in xfig. So there should now not be any errors
	due to this when making uguide_pdf.

2002-05-31  Sreerekha T.R.  

	* arts-1-1-108
	
	* doc/uguide/interpolation.tex: introduced the index commands which
	make reference at the indexpage of the AUG. Changed  all \verb
	commands to \artsstyle.

2002-05-31 Claudia Emde  

	* arts-1-1-107

	* src/methods.cc: Added TensorXSet methods for all dimensions (Tensor3
	to Tensor7). Added workspace function (i_field_itCalc).
		
	* src/m_basic_types.cc: Added TensorXSet functions for all dimensions.

	* src/m_cloudbox.cc (i_field_itCalc): Added this function which 
	will calculate the radiative transfer in the cloudbox with scattering
	using the iterative method.
	
	* src/workspace.cc: Modified description for *amp_mat*.

2002-05-30 Claudia Emde  

	* arts-1-1-106

	* src/workspace.cc: Added more workspace variables for scattering.

	* src/linalg.cc (ludcp): Modified documentation of the function. 

2002-05-30  Oliver Lemke  

	* arts-1-1-105

	* src/workspace.cc (define_wsv_data): Added workspace variable
	xml_output_type. Type is Index: 0 means Ascii, 1 binary output.

	* src/m_ppath.cc: Include iostream.

	* src/test_xml.cc (main): Added exception handler.

2002-05-30  Patrick Eriksson  

	* arts-1-1-104

	* Things fixed for this commit, or in 1-1-99:
	
	* Some workspace functions have been renamed. 
	  - The PrintXxx functions now ends with Pring, e.g. NumericPrint.
	  - The functions to set the atmospheric dimensionality are now called
	    AtmosphereSet1D etc.
	This to follow our naming scheme better.
	
	* New workspace functions:
	   FlagOn
	   FlagOff
	   i_spaceCBR
	   e_groundSet
	   AntennaSet1D
	   AntennaSet2D

	* Improved the out-messages from some functions, especially in 
	m_basic_types, but there is more to do here.

	* Started on the RTE part, but found it hard before the agendas are
	ready. So I leave this for the moment.

2002-05-30 Claudia Emde  

	* arts-1-1-103

	* src/cloudbox.cc/.h: Added these files for internal calculations 
	concerning scattering.
	(i_field_update1D): Added. Updates i_field on all points inside 
	the cloudbox.
	(rte_scat_vecCalc): Added. Performs 1D radiative 
 	transfer calculation with fixed scattering vector.	

	* src/linalg.cc/.h: (id_mat) Changed name of the function which 
	returns the identity matrix, as there was a conflict with another
	internal function named identity.

2002-05-29  Stefan Buehler  

	* arts-1-1-102

	* src/agenda.cc
	(nelem): Added.
	(is_input): Added.
	(is_output): Added.
	
	* src/agenda.h: Added declarations for new Agenda member functions.

	* src/m_agenda.cc (AgendaSet): Renamed from
	AgendaDefine. Implemented function body.

	* src/methods.cc (define_md_data): Renamed AgendaDefine to
	AgendaSet. Fixed documentation string. Moved to the right place in
	the alphabetical order. Also moved Main to the right place.

2002-05-29  Stefan Buehler  

	* arts-1-1-101

	* doc/uguide/interpolation.tex: Tried to make interpolation tensor
	clearer, following comment by Claudia.

2002-05-28 Claudia Emde  

	* arts-1-1-100 

	* src/workspace.cc: Introduced workspace variables for the scattering
	calculations.

	* doc/uguide/scattering.tex: Adjusted the text according to the 
	decision that there will be no special grids inside the cloudbox.

	* doc/uguide/symboldefs: Removed symbols for scattering grids.
	
2002-05-29  Patrick Eriksson  

	* arts-1-1-99

	* Sorry, but there will be no description right now. I must rush and
	want to make a commit to get a back-up of my work (if anything will
	happen). I will write a	description ASAP.

2002-05-28  Stefan Buehler  

	* arts-1-1-98

	* doc/uguide/myepstopdf: Added. Use this script to convert eps
	files to pdf.

	* doc/uguide/interpolation.tex: Finished first version of
	documentation for interpolation functions.

	* doc/uguide/Figs/interpolation/: Added interpolation chapter
	figures here.

	* doc/uguide/main.tex: Added include for interpolation.

	* src/interpolation.cc: Added \author and \date tags to my functions.

	* src/.cvsignore: Added test_xml and string.xml.

2002-05-28 Claudia Emde  

	* arts-1-1-97 

	* src/physics_funcs.cc/h: Changed the interfaces of the functions. 
	Input and Output variables are now for all physical functions 
	(Planck function, number density, ...) of type Numeric.

	* doc/uguide/lin_alg.tex: Fixed some undefined references.
	
2002-05-28  Patrick Eriksson  

	* arts-1-1-96

	* doc/uguide/fm_definitions.tex: Updated the text to follow some 
	changes regarding definitions and the name of variables. The parts
	on sensor variables and RTE calculations not yet ready.

	* src/m_ppath.cc and src/methods.cc: Added the functions:
	   ppath_stepGeometric
	   ppath_stepGeometricWithLmax

	* src/workspace.cc: The variable ppath_partial is re-named to 
	ppath_step.

2002-05-27  Patrick Eriksson  

	* arts-1-1-95

	* src/m_ppath.cc and src/ppath.cc: One 1D geometrical propagation paths
	now work. 

	* src/workspace.cc: Polished the text for some variables. 

	* src/m_atmosphere.cc (SetBlackbodyGround): Added this function.

	* doc/uguide/fm_definitions.tex: Started top revise this chapter
	after some changes of definitions.

2002-05-23  Patrick Eriksson  

	* arts-1-1-94

	* 1D geometrical propagation path calculations seem to work (but
	cloud box is not yet tested).
	
	* src/ppath.h: Added the fileds refraction, method and constant to
	the Ppath structure.

	* src/ppath.cc (ppath_step_1d_geom): Fixed several bugs. Adapted to
	new Ppath fields.

	* src/m_ppath.cc (ppathCalc): Fixed several bugs. Adapted to
	new Ppath fields. 

2002-05-22  Oliver Lemke  

	* arts-1-1-93
	
	* src/mystring.h (class my_basic_string): Make size_t of type
	Index.

	* src/xml_io.cc: Added documentation.
	(read_from_stream): Casting of String::npos no longer needed.

2002-05-22  Patrick Eriksson  

	* arts-1-1-92

	* Further work on propagation path calculations. Fixed numerous bugs.
	A simple upward 1D case works now at least. But more bugs to find.

	The biggest problem was to catch when the limited numerical precsion
	causes the fractional distance to be just below 0 or just above 1.

2002-05-21  Patrick Eriksson  

	* arts-1-1-91
	
	* Worked on doxygen headers and comments in the following files:
	   check_input.cc
	   check_input.h
	   m_atmosphere.cc
	   m_basic_types.cc
	   m_cloudbox.cc
	   m_general.cc
	   m_ppath.cc
	   m_rte.cc
	   math_funcs.cc
	   math_funcs.h
	   physics_funcs.cc
	   physics_funcs.h
	   ppath.cc
	   ppath.h 

2002-05-21  Oliver Lemke  

	* arts-1-1-90
	
	* src/xml_io.cc (xml_read_header_from_stream): Improved
	verification of xml header.

	Replaced most of endls with '\n' to avoid unnecessary flushings of
	output stream.
	
	* .cvsignore: Added depcomp, autom4te-2.5x.cache and stamp-h1
	generated by automake >= 1.6.

2002-05-21  Patrick Eriksson  

	* arts-1-1-89

	* Calculation of 1D geometrical path coded, but all bugs must be found.
	
	* src/ppath.cc: Added the functions:
	   geompath_l_at_r
	   geompath_r_at_l
	Changed also some of the geompath functions to take the tangent radius
	as input.
	
	* src/ppath.cc (ppath_step_1d_geom): This function is coded, but no
	test runs yet. There are bugs, for sure.

	* src/m_ppath.cc (ppathCalc): Put in a call to the function discussed
	above.

2002-05-20  Patrick Eriksson  

	* arts-1-1-88

	* src/m_ppath.cc (ppathCalc): The function should now be ready, but
	no bigger test runs yet. Tests for 2D cannot be made before a
	*ppath_step* function covering 2D exists.

	* src/ppath.cc (ppath_step_1d_geom): Started on this function.

2002-05-19  Patrick Eriksson  

	* arts-1-1-87

	* src/m_ppath.cc: Further work on the function. The structure of the
	function is now there, but many details are missing.

	* src/ppath.cc: Created the functions:
	   geometrical_tangent_radius
	   geompath_za_at_r
	   geompath_lat_at_za
	   angle_after_ground_1D
	   ppath_init_structure
	   ppath_set_background
	   ppath_what_background
	   ppath_start_stepping
	
	* src/Makefile.am (arts_SOURCES): Added interpolation.{h,cc}.

	* src/m_general.cc: Added the WSFs:
	   PrintArrayOfIndex
	   PrintArrayOfString
	   PrintIndex
	   PrintNumeric
	   PrintString

	* src/workspace.cc: Improved the text for some variables.

2002-05-16  Stefan Buehler  

	* arts-1-1-86

	* src/interpolation.cc: Finished interpweights and interp
	functions for Tensor 3 to 6. That means, all interpolation
	functions are ready!

	* src/interpolation.h: Added headers for new functions.

	* doc/uguide/interpolation.tex: Added this file. Nothing there yet.

	* doc/uguide/matrix_vector.tex: Added tensors.

	* src/main.cc (main): Added error handler for the case that the
	given controlfile name does not have extension ".arts", or no
	extension at all. (So far the program just crashed in this
	case.)

2002-05-16  Claudia Emde  

	* arts-1-1-85

	* doc/uguide/scattering.tex: Updated the text. 

2002-05-16  Patrick Eriksson  

	* arts-1-1-84

	* src/workspace.cc: Added the WSV:
	   azimuth_angle_1d
	   latitude_1d
	   sensor_pos  (not finsihed)

	* src/m_atmosphere.cc: Created this file to hold functions to
	set up the model atmosphere. Added the WSF:
	   r_geoidWGS84 

	* src/m_ppath.cc: Added the WSFs:
	   a_posAddGeoidWGS84 
	   sensor_posAddGeoidWGS84 

	* src/m_general.cc: Added the WSFs:
	   SetAtmosphere1D
	   SetAtmosphere2D
	   SetAtmosphere3D
	   PrintMatrix
	   PrintVector
	The function series PrintXxx is not ready. I will make more functions 
	later, but only for basic types (up to Tensor3?).
	
2002-05-15  Oliver Lemke  

	* arts-1-1-83
	
	*** ASCII XML reading/writing ready for bug hunting :-) ***
	
	* src/groups.cc (define_wsv_group_names): Added Tensor4-7.

	* src/methods.cc (define_md_data): Added reading/writing methods
	for Tensor3-7.

	* src/xml_io.{h,cc}: Moved all xml_read_from_stream function
	prototypes to cc file because there are not needed externally.

	Send debug output to out2 instead of cout.

	ArrayOfIndex, ArrayOfMatrix, ArrayOfString, ArrayOfVector, Index,
	Numeric, Matrix, String, Tensor3-7, Vector reading and writing
	works now.

	* src/m_xml.cc: Removed dummy output from remaining functions.

	Added read/write functions for Tensor3 - Tensor7.

	* src/Makefile.am: Added target test_xml.

	* src/test_xml.cc: Added.

2002-05-15  Oliver Lemke  

	* arts-1-1-82
	
	* doc/examples/xml.arts: Small conversion example.

	* src/xml_io.{h,cc}: Header/footer functions renamed.
	
	(class ArtsXMLTag): Renamed member functions to match ARTS style.

	Implemented Vector, Matrix, ArrayOfMatrix writing functions.

	* src/m_xml.cc: Use generic read/write functions for all data
	types.
	
	Removed dummy from Vector, Matrix, ArrayOfMatrix functions.

	*** Still under development *** Reading only works for Numeric and
	Index at the moment. *** Documentation still missing in most
	parts.

2002-05-15  Oliver Lemke  

	* arts-1-1-81
	
	* src/xml_io.{h,cc}: Implemented XML parser.

	To read the XML header I implemented a template function. Which
	reduces the number of needed read_from_file functions from n
	(n = Number of data types) to 1. From there the overloaded
	function read_from_stream is called to do the data type specific
	part.

	Currently there's only Index and Numeric ASCII read support. ASCII
	write support will follow, binary later.

	* src/methods.cc (define_md_data): Corrected indentation of XML
	functions.

	* src/m_xml.cc: Throw runtime error when unimplemented function is
	called.

	Implemented IndexReadXML and NumericReadXML.

	* src/file.cc (open_input_file): Documentation changed.

2002-05-15  Claudia Emde  

	* arts-1-1-80

	* src/test_linalg.cc (test_matrix_exp3D): Added this
	function. Restructured the other tests.

	* src/test_linalg.cc (norm_inf): Added some comments.
	
	* doc/uguide/scattering.tex: Added the symboltable.

2002-05-15  Patrick Eriksson  

	* arts-1-1-79

	* I had by mistake put a & after ConstVectorView in some places.
	Now fixed.

	* src/workspace.cc: Added two general vector variables vector1 and
	vector2.

	* src/m_basic_types.cc: Added the WSF MatrixFillWithVector and 
	Tensor3FillWithVector. Note that the vector can be put in along any
	dimension (in contrast to the old MatrixFillWithVector).

	* src/m_ppath.cc (ppathCalc): Added input checks for sensor position
	and los.

2002-05-14  Claudia Emde  

	* arts-1-1-78
		
	* src/lin_alg.cc/.h Modified function norm_inf and changed
	interface of exp_matrix.

	* doc/uguide/scattering.tex: Added this file to document the
	scattering part.

	* doc/uguide/references.bib: Added some references for the linear
	algebra part. 

2002-05-14  Patrick Eriksson  

	* arts-1-1-77
	
	* src/check_input.cc (chk_cloudbox): Added this function.

	* src/m_ppath.cc (ppathCalc): Worked a bit on this function.

	* src/m_general.cc (SetAtmosphericDimensionality): Added this WSF.

	* src/m_cloudbox.cc (NoCloudbox): Added this WSF.

	* src/m_rte.cc: Added this file.

2002-05-13  Oliver Lemke  

	* arts-1-1-76
	
	* src/methods.cc (define_md_data): Moved XML functions into
	alphabetical order.

2002-05-13  Oliver Lemke  

	* arts-1-1-75
	
	* src/mystring.h: Include system sstream if available otherwise use our
	own.
	
	* src/arts.h: Include sstream moved to mystring.h.

	* configure.in: Added check for sstream header file. If it is not
	found, we use our own sstream.h.

	* src/make_auto_wsv_groups_h.cc (main): Include iostream in
	auto_wsv_groups.h.

	* src/make_auto_wsv_h.cc: Include iostream.

2002-05-13  Oliver Lemke  

	* arts-1-1-74
	
	* src/test_linalg.cc: Include iostream.

	* src/file.cc (open_input_file): Only set badbit for input stream
	otherwise eof throws exception as well and that is not what we
	want.

	* src/methods.cc (define_md_data): Added xml workspace methods.

	* src/m_xml.cc: New file. XML io workspace methods. Only dummys at
	the moment.
	
	* src/xml_io.{h,cc}: New files. XML io functions. Only dummys at
	the moment.

	* src/Makefile.am (arts_SOURCES): Added xml_io.h, xml_io.cc and
	m_xml.cc.

2002-05-13  Patrick Eriksson  

	* arts-1-1-73

	* Cleaned up a bit regarding included .h files in ppath, check_input,
	math_funcs and ???.
	
	* src/interpolation.cc: Had to include some more .h files (which, don't
	remember now).

	* src/m_ppath.cc (ppathCalc): Started on this function.

	* src/check_input.cc: Changed alpha_grid and beta_grid to lat_grid and
	lon_grid. Removed all assert functions.

2002-05-12  Patrick Eriksson  

	* arts-1-1-72

	* I could not compile this version, but this could be due to local 
	settings.

	* src/atm_funcs.cc/h: These files do not exist any more. Moved some 
	functions to physics_func and deleted others.

	* src/physics_funcs.cc/h: Added these files.
	
2002-05-10  Claudia Emde  

	* arts-1-1-71

	* src/lin_alg.cc/h: Removed function lu_solve and added some
	assertions. Added some new functions:
		- exp_mat: Computing the exponential of a matrix.
		- norm_inf: Norm infinity of a matrix.
		- identity: Returns the identity matrix.

	* src/test_linalg.cc: Adapted the tests to the changes.


	* doc/uguide/lin_alg.tex: Added documentation for linear algebra
		functions.

	* doc/uguide/main.tex: Included lin_alg.tex. 

2002-05-09  Oliver Lemke  

	* arts-1-1-70
	
	* doc/doxygen/html/.cvsignore: Added *.png.

2002-05-09  Oliver Lemke  
	
	* arts-1-1-69

	* Lots of fixes to compile arts with gcc-3.1.
	
	* src/interpolation.cc (LOOPIT): Removed overflues ## in macro
	definition before '.'  Otherwise it does not expand into a valid
	preprocessor token.

	* src/arts.h: Added 'using namespace std' to fix compile errors
	with newer, more ansi-compliant gccs (3.1).

	Include sstream instead of sstream.h for the same reason.

	* src/matpackI.h (Range): Default arguments for parameters are
	only allowed to be declared once. Removed from implementation
	part.

	* src/methods_aux.cc (PrintTemplate): Removed default for second
	parameter from implementation part.
	
	* src/mystring.h: Include climits.

	* src/main.cc,
	src/m_abs.cc,
	src/absorption.cc: Include algorithm.

	* src/test_interpolation.cc,
	src/test_linalg.cc,
	src/test_tensor.cc,
	src/test_poly.cc,
	src/test_matpack.cc,
	src/methods.h,
	src/poly_roots.cc,
	src/parameters.cc,
	src/make_auto_wsv_groups_h.cc,
	src/messages.h: Include iostream, otherwise cerr and cout are
	undeclared.

	* src/exceptions.h (ParseError): Added dummy virtual destructor
	including missing throw().

	* src/messages.cc: Rename global variable basename to out_basename
	to avoid a conflict with the basename function from the new string
	standard include file.

	* src/m_hdf.cc (filename_bin),
	src/main.cc (main),
	src/m_abs.cc (linesWriteAscii),
	src/m_abs.cc (lines_per_tgWriteAsci),
	src/file.cc (filename_ascii): Renamed basename to out_basename.

	* src/mystring.h (my_basic_string),
	src/array.h: Added keyword typename to several definitions
	(e.g. typename Array::const_iterator xi;)

2002-05-08  Stefan Buehler  

	* arts-1-1-68

	* src/interpolation.cc: 2D Green interpolation works.

	* src/interpolation.h: Added headers for new functions.

	* src/test_interpolation.cc: Test case for this.

	* src/logic.cc: Added is_size functions for tensors up to rank 7.

	* src/logic.h: Added headers for new functions.

2002-05-08  Patrick Eriksson  

	* arts-1-1-67

	* src/m_basic_types.cc: Created this file and moved the relevant 
	functions from m_io.cc. The revision of the functions is not 
	finished. Several functions are already removed. 

	* src/m_general.cc: Created this file and moved Exit and Test to the 
	file.

	* src/m_cloudbox.cc: Created this file. No functions in the file yet.
	
	* src/m_ppath.cc: Created this file. No functions in the file yet.


2002-05-08  Stefan Buehler  

	* arts-1-1-66

	* doc/uguide/development.tex: Fixed typo that lead to LaTeX fail.

	* src/methods.cc (define_md_data): Small change in comment block.

2002-05-08  Patrick Eriksson  

	* arts-1-1-65

	* src/workspace.cc: Started to sort the variables in alphebetical 
	order. See note in the file. Placed all old functions below a line 
	with the idea to revise the functions before they are moved back.

	Introduced and wrote about: 
	  - atmosphere_dim
	  - a_los
	  - a_pos
	  - blackbody_ground
	  - cloudbox_on
	  - cloudbox_limits
	  - e_ground
	  - lat_grid
	  - lon_grid
	  - p_grid
	  - ppath
	  - ppath_partial
	  - ppath_step
	  - r_geoid
	  - t_field
	  - t_ground
	  - z_field
	  - z_ground

	Removed a lot of old WSV.
	
	* src/methods.cc: Started to sort the methods in alphebetical order.
	See note in the file. Placed all old functions below a line with the
	idea to revise the functions before they are moved back.

	Removed WSF hseXxxx, refrXxx

2002-05-07  Stefan Buehler  

	* arts-1-1-64

	* src/interpolation.cc: Finished all blue interpolation functions
	(interpweights and interp functions).

	* src/interpolation.h: Added headers for the new functions.

	* src/test_interpolation.cc: Some testing for the blue
	interpolation functions. They are fast! Turning assertions off
	gives a significant further speed increase, so the default for
	"real" calculations should be -O2 optimization and disabled
	assertions. (The speed impact of assertions is mainly due to the
	assertions inside the index operators, which are called a lot if
	tensor dimensions are looped.)

	* absorption.cc,
	atm_funcs.cc,
	continua.cc,
	file.cc,
	lineshapes.cc,
	m_abs.cc,
	m_hdf.cc,
	math_funcs.cc,
	matpackI.h,
	matpackIII.h,
	matpackIV.h,
	matpackV.h,
	matpackVI.h,
	matpackVII.h,
	ppath.cc: Changed "\retval x" to "\param x Output:". The use of
	retval for output parameters was a misunderstanding on my side and
	lead to spurious doxygen warning messages. Output parameters
	should be documented like this:
	\param A Output: Describe A here.

	* doc/uguide/development.tex: Updated instructions for Doxygen
	headers. 

2002-05-06  Stefan Buehler  

	* arts-1-1-63

	* src/interpolation.cc: Finished gridpos. Implemented 1D
	interpweights and 2D blue interpweights. If fd and 1-fd are stored
	in an array, one can use nested for loops to compute the
	weights. Great! 

	* src/test_matpack.cc (test32): Test case for mult.

	* src/matpackI.h: Made documentation of mult functions more clear:
	The input and output matrix must not be the same!

	* src/logic.cc: Made Index input arguments const Index&.

2002-05-06  Patrick Eriksson  

	* arts-1-1-62

	* src/species_data.cc: Included  JPL tags for HOBr.

2002-05-06  Claudia Emde  

	* arts-1-1-61
		
	* src/lin_alg.cc/h: Modified interfaces for LU- functions and
        added routine for the matrix exponential function.

	* src/test_linalg.cc: Test adapted to the new functions.

2002-05-06  Oliver Lemke  

	* arts-1-1-60
	
	* src/lin_alg.cc: Include math.h for gcc>=2.96.

	* src/test_tensor.cc: Include math.h for gcc>=2.96.

2002-05-05  Patrick Eriksson  

	* arts-1-1-59

	* src/workspace.cc: Started to introduce new workspace variables.

	* src/los.cc/h: Removed these files. Made corresponding changes
	throughout the files, e.g:

	* src/Makefile.am: Removed los.cc and los.h. 

	* src/groups.cc: Removed Los, added Ppath and Tensor3.

2002-05-03  Stefan Buehler  

	* arts-1-1-58

	* src/logic.cc: Added Matrix version of is_size.

	* src/logic.h: Added header for Matrix version of is_size.

	* doc/Makefile.am (SUBDIRS): Removed emacs directory.

2002-05-03  Stefan Buehler  

	* arts-1-1-57

	* src/logic.cc: New file. Contains all logical functions, i.e.,
	function called is_something that return bool. 
	These functions are intended to be used either inside "if"
	statements or inside "assert" statements.
	The condition should have a simple and intuitive meaning!

	* src/logic.h: New file, headers for logic.cc.

	* src/check_input.cc: Now includes logic.h.

	* src/ppath.cc: Now includes logic.h.

	* src/math_funcs.h: Removed is_something function headers.

	* src/math_funcs.cc: Moved is_something functions to logic.cc.

	* src/interpolation.cc: New file: Interpolation routines. 
	(grid_pos): I just started with this, it is not yet complete. Will
	probably continue tomorrow.

	* src/interpolation.h: New file: Header file for interpolation.cc.

	* src/test_interpolation.cc: Test program for interpolation
	functions. 

	* src/Makefile.am: Added test_interpolation.

	* doc/index.html.in: Removed the paragraph about the old Emacs
	doxygen macros, since they are no longer there.

	* configure.in: Removed output target doc/emacs/Makefile.

2002-05-02  Claudia Emde  

	* arts-1-1-56

	* src/lin_alg.cc/h: Created this file for the linear algebra
	functions we need for the radiative transfer
	calculations. Implemented functions to solve linear equation
	systems using the LU decomposition method.

	* src/test_linalg.cc: test the functions in lin_alg.cc

2002-04-25  Stefan Buehler  

	* arts-1-1-55

	* doc/uguide/development.tex: Updated this file. Some small
	changes. Most significant are the new recommendations for
	documentation headers.

	* doc/uguide/main.tex: Put development.tex back in.

	* src/workspace.cc (define_wsv_data): Added template for
	documentation strings.

	* doc/emacs/: Removed everything in this directory. There is now a
	better Doxygen package for Emacs:
	Doxymacs (http://doxymacs.sourceforge.net/). 

	* doc/examples/fantasy2.arts: Added this file, which contains more
	thinking about agendas.

2002-04-17  Patrick Eriksson  

	* arts-1-1-54

	* src/m_los.cc,m_wfs.cc,m_batch.cc: Removed these files as everything
	will be rewritten anyhow. I think it is a good idea to remove as much 
	as possible. It is no big danger to remove things as they still exist
	in arts-1 and can be copied back. So, PLEASE DO SOME CLEANING.
	
	* src/atm_funcs.cc: Removed obselete functions.

	* src/ppath.cc: Works now for 1D and no refraction. As soon as it is
	clear how refraction will be calculated (there should be an agenda
	as for absorption), it should be a rather quick thing to put in 1D
	with refraction.

2002-04-16  Patrick Eriksson  

	* arts-1-1-53

	* src/check_input.cc/h: Started this file. The intention of this file
	is to hold functions that help us to check the input to functions.
	By doing general functions, more careful checks can be done and better
	error messages can be given. If you have to type everything for each
	function, you tend to become sloppy. There are two series of functions:
	assert_xxx and chk_xx. Have a look in the file and you will understand.

	SO USE THESE FUNCTIONS, and ADD NEW ONES WHEN NEEDED.

	* src/math_funcs.cc: Started to revise this file. The existing 
	functions are moved down and my idea is that when we found that a 
	function really is needed, it can be moved up, and then be polished.
	I think there is some old junk in the file.

	* src/ppath.cc: Added this file. The file will include functions to
	determine propagation paths. Started to move things from los.cc
	(ppath.cc replaces los.cc). Changes are needed as the definition of
	the Ppath structure is changed. Quite some work, but nothing works
	yet.

	* src/ppath.h: Added this file to hold the declaration of the Ppath 
	structure and functions in ppath.cc.
	
2002-04-14  Stefan Buehler  

	* arts-1-1-52

	* doc/examples/fantasy.arts: Added this file to play around
	in. I'm not happy with the absorption part. Everything is so
	complicated and not user-friendly. But how to make it both modular
	and user friendly?

2002-04-12  Patrick Eriksson  

	* arts-1-1-51

	* doc/uguide/ppath.tex: Finished text for general 1D and 2D geometrical
	expressions. 

2002-04-12  Patrick Eriksson  

	* arts-1-1-50

	* doc/uguide/ppath.tex: Started some writing but not got time to finish
	it. I will continue at home.

2002-04-11  Patrick Eriksson  

	* arts-1-1-49

	* doc/uguide/main.tex: Added the commands \artsstyle, \textindex,
	\wsfindex, \wsvindex, \fileindex, \funcindex and \structindex.
	The command replaces the old \qindex. 

	ARTS workspace methods, variables etc. are no longer written using the
	\verb environment. Use now the \artsstyle command. This command will
	write the text with style \texttt. I made the change as verbatim
	cannot be used inside commands, figure text etc., which has been a 
	problem for me several times. The drawback of using \texttt is that
	underscores must be proceeded with a backslash (e.g. \_).

	The other commands, ending with "index", writes the text and makes
	on the same time a index mark. The commands beside \textindex are 
	releated to ARTS and writes the text by using \artsstyle and puts
	the reference as a subentry to an appropiate text string. For example,
	\wsvindex is the command to use when defining a ARTS workspace 
	variable. See the index page for the result.

	I hope that these indexes will help us to link AUG and ARTS better.
	The old AUG did very few direct references to ARTS. I am trying now
	to improve this by stating which function that does a special
	calculation etc. This can work the other way around, when writing the
	header of a function it should now be easier to make a reference to
	AUG if the function is indexed in AUG. Before you did not know in
	what section a description ended up (the section could be moved 
	around). We can now refer to the index page to find where a function
	is discussed.

	* doc/uguide: Included the new commands in the files that are presently
	included. You have to adapt the other files when they are included.

2002-04-11  Patrick Eriksson  

	* arts-1-1-48

	* doc/uguide/ppath.tex: Description of the propagation path structure,
	Ppath. Started on general geometric expressions for calculating the
	path.

2002-04-08  Oliver Lemke  

	* arts-1-1-47

	* configure.in: Added doc/uguide/Figs/ppath/Makefile.am

2002-04-05  Patrick Eriksson  

	* arts-1-1-46

	* doc/uguide/ppath.tex: Completed the part about geodetic issues.

2002-04-04  Patrick Eriksson  

	* arts-1-1-45

	* doc/uguide/ppath.tex: Some text about geoid ellipsoids etc. Made some
	figures.

	* doc/uguide/Figs/ppath: Added this folder and some figure files.

2002-04-04  Oliver Lemke  

	* arts-1-1-44

	* doc/uguide/Makefile.am: Added makeindex commands.

2002-04-02  Oliver Lemke  

	* arts-1-1-43

	* aii/Makefile.am, ami/arts/Makefile.am, ami/file/Makefile.am,
        ami/general/Makefile.am, ami/hmatrix/Makefile.am,
	ami/math/Makefile.am, ami/path/Makefile.am, ami/physics/Makefile.am,
        ami/plot/Makefile.am, ami/retrieval/Makefile.am,
	doc/uguide/Figs/Makefile.am: Use wildcards for EXTRA_DIST so we
	don't have to add each new file to Makefile.am.

2002-04-01  Patrick Eriksson  

	* arts-1-1-42

	* Please read, comment and/or correct what I have written in
	Chapter 2 of AUG.

	* doc/uguide/main.tex: Included the epic and eepic packages for drawing
	figures inside LaTex. Are these the best packages for this? These seem
	at least to be standard packages. But do you have any better sugestion?

	* doc/uguide/fm_definitions.tex: New figure for LOS angles and
	some new text. Corrected and polished existing text slightly. I am
	now ready with what I will write in this chapter this time. So,
	please read it.  I am sure that there are many language
	errors. Please fix what you find.

	* doc/uguide/ppath.tex: Added section headings and made a figure for
	geocentric and geodetic latitudes.

2002-03-28  Patrick Eriksson  

	* arts-1-1-41

	* AUG: Note that figures now shall be placed in sub-folders to
	Figs/ (as suggested by Stefan).  When the revision of AUG is
	ready, all figures in Figs/ will be removed. This has been done
	for fm_definitions (see below).
	
	* doc/uguide: Added style files for the algorithm and algorithmic
	packages. See fm_definitions for example on how to use these
	packages. I have a manaul (ps-file) that I can send you if you are
	interested.
	
	* doc/uguide/fm_definitions.tex: More writing. Mainly on the clear sky
	RTE part. Added two figures. Added an algorith over the RTE part.

	* doc/uguide/Figs/fm_definitions: Created this folder and moved
	the figures (and associated Matlab scripts) to this folder.
	
	* doc/uguide/Figs/fm_definitions/mkfigs_ppath_cases.m: Created this
	function to illustrate propagation paths.

2002-03-27  Patrick Eriksson  

	* arts-1-1-40

	* doc/uguide/fm_definitions.tex: Writing on the sensor section and
	started on the clear sky RTE section. 

2002-03-26  Stefan Buehler  

	* arts-1-1-39

	* src/test_tensor.cc (test8): Added a cute little test that checks
	all 128 const index functions.
	(test9): And another cute tests that checks the non-const index
	functions. 
	Result: Everything seems to work fine!

2002-03-25  Patrick Eriksson  

	* arts-1-1-38

	* When including the bug fixes from arts1 for temperature WFs, I missed
	a change in methods.cc so the program did not compile. Sorry, for that.
	
	* doc/uguide/fm_definitions.tex: Fixed some problems in the existing
	text. Did dome more writing on the compulsory sensor variables and
	changed text to follow the definition of the cloud box.
	Stefan, there are some comments for you inside the file at the end.

	* doc/uguide/Figs/mkfigs_atm_dims.m: The figures are now converted to
	PDF with epstopdf. Adapted to new cloud box definition.

2002-03-22  Stefan Buehler  

	* arts-1-1-37

	* src/matpackVII.h: First implementation of Tensor7 finished. This
	seems to push my present concept to the limit, since I had to
	manually edit the 128 different index functions. Higher order
	tensors are only feasible with some kind of automatic code
	generation system. 

        * src/matpackI.h, src/matpackIII.h, src/matpackIV.h,
	src/matpackV.h, src/matpackVI.h: Adjusted for Tensor7. (Mainly
	added friend declarations.)

	* src/test_tensor.cc: Added simple test for Tensor7. There should
	be some more thorough and systematic testing...

2002-03-22  Patrick Eriksson  

	* arts-1-1-36

	* Included changes made for arts1:

	* src/m_wfs.cc (k_temp_nohydro): Code changed according to the bug
	in the equation discussed below. Temperature WFs without HSE seems now
	to be OK. Checks have ben performed with text_Kt.m.

	To summerize, all temperature WFs have been looked at and everything
	seem to be OK. There were bugs for all three versions before. Sorry
	for that.

	* doc/uguide/wfuns_atm.tex: A mistake in the equation giving the
	temperature derivative of the Planck function found.

2002-03-20  Stefan Buehler  

	* arts-1-1-35

	* src/matpackVI.h: Added. Implementation of Tensor6. A first
	version of this is complete. 

	* src/matpackVII.h: Added. Implementation of Tensor7. This is
	still under construction.

	* src/Makefile.am: Added matpackVI and VII to test_tensor sources.

	* src/test_tensor.cc: Added some tests for Tensor6.

	* doc/uguide/references.bib: Added Mishchenko book.

	* doc/uguide/fm_definitions.tex: Started to write on the clear sky
	RT section.

2002-03-20  Oliver Lemke  

	* arts-1-1-34

	* src/matpackI.h: Changed order of parameters for poly_root_solve.

2002-03-20  Oliver Lemke  

	* arts-1-1-33

	* src/poly_roots.{h,cc}: Changed order of parameter.

2002-03-20  Oliver Lemke  

	* arts-1-1-32

	* src/poly_roots.{h,cc}: Changed interface of poly_root_solve to make
	it arts-compliant. The solution matrix is passed by reference to the
	function and must have the correct size.

	* src/poly_roots.cc: Use the pointer to coeffs.mdata and roots.mdate
	instead of copying all elements (if Numeric is not double we still
	have to copy them).

	* src/matpack1.h: Made poly_root_solve a friend function of
	ConstVectorView and ConstMatrixView to access mdata.

2002-03-18  Oliver Lemke  

	* arts-1-1-31

	* reconf: Removed --enable-more-warnings. This is now part of
	configure.in.

	* configure.in: Enable warnings in maintainer mode by default. Could
	still be turned off with ./reconf --disable-more-warnings.

2002-03-19  Patrick Eriksson  

	* arts-1-1-30

	* doc/uguide/fm_definitions.tex: Fixed and changed according to
	comments and discission input from Stefan.

	The main thing is that we decided that the most basic variable is
	put in as the outermost index in matrices and tensors. That is,
	reversed order compared to before.

2002-03-18  Stefan Buehler  

	* arts-1-1-29

	* doc/examples/*.arts.in: The outermost method must now simply be
	called Main. To use DefineAgenda was unlogical, since defining an
	agenda and executing an agenda are quite different things.

	* src/parser.cc: Adapted to new controlfile structure. Cleaned up
	output to out3.

	* src/array.h: Changed output operator for ConstVectorView to
	put all elements in one row.

	* src/matpackI.h: Changed output operator for ConstVectorView to
	put all elements in one row.

	* reconf: Added --enable-more-warnings switch to configure call. 

2002-03-18  Stefan Buehler  

	* arts-1-1-28

	* doc/uguide/fm_definitions.tex: Fixed some typos. Added some
	comments, marked by SAB.

	* doc/uguide/.cvsignore: Added uguide_pdf.idx.

2002-03-18  Patrick Eriksson  

	* arts-1-1-27

	* doc/uguide/fm_definitions.tex: More text written. Started on sensor 
	description.

	* doc/uguide/ppath.tex: Added this file to hold description of
	propagation paths.

2002-03-15  Stefan Buehler  

	* arts-1-1-26

	* configure.in: Added a switch to enable-more-warnings that turns
	off the checking of unused parameters. This, because dummy
	parameters are used as a trick to select functions, for example
	the joker in the matpack functions. Also the getaway functions for
	the engine have sometimes unused parameters. We don't want to
	issue a warning for that.

	* src/matpackV.h: Bug fix: Added missing return statements for
	const index functions. I discoverd this bug because of the enabled
	warnings, so warnings are clearly useful!

	* src/m_agenda.cc: Added this file, containing workspace methods
	for Agenda.

	* src/: Modified the parser and the overall control structure to
	accept agendas.

	* doc/examples: Removed old example files starting with auto_.
	Adapted all examples to work with the new controlfile
	syntax. (Added a surrounding AgendaDefine(main_agenda).)

2002-03-15  Patrick Eriksson  

	* arts-1-1-25

	* doc/uguide/main.tex: I have introduced index into AUG. The idea
	is not to make a complete index register, that is to ambitious.  I
	think it is sufficient, and a good help for the readers, just to
	make a reference to the page where a term is defined or
	introduced.  Is this a good idea? I have put in some test indexes
	in fm_definitions.  Note the macro \qindex, defined in main.tex,
	that makes it easier to put in an index. I don't think we shall
	have index of several levels, if the term consists of several words
	(normally not more than 2), refer to the words as one unit to make
	things simple.

	If anybody knows how to change the title for the index page from
	"Index" to "Definition of terms", please go ahead.

	To update the index list, you have to run "makeindex uguide"
	
	* doc/uguide/fm_definitions.tex: Started to write in this chapter.
	Please read the introduction part (present Chapter 1-2) and give
	comments, both on layout and content.

	* doc/uguide/symbol_defs: Moved symbol macros to this file. An idea
	with this is that it should be possible to use this macro file for
	other documents. The old macro names are changed and changes will
	be needed when re-introducing the chapters. Sorry for this, but as
	the old macro names were just a mess, I made this change. If it is a
	comfort, I will be the one that will have to most of the changes.
	I have tried to come up with a consistent naming scheme so it should
	be possible to remember, or figure out, the name of the macros.
	Note especially the aXxx macros which are handy and would help us
	to have a uniform style without making a macro for each subscript
	to a variable.

2002-03-14  Stefan Buehler  

	* arts-1-1-24

	* General: Started to work on agendas (what we used to call method
	lists).

	* src/agenda.h: Added.
	An agenda is a list of workspace methods (including keyword data) to
  	be executed. There are workspace variables of class agenda that can
  	contain a list of methods to execute for a particular purpose, for
  	example to compute the lineshape in an absorption calculation. The
  	controlfile contains a list of agenda definitions, including the
  	agenda `main', which is then executed. Overall, this concept is in
  	analogy to a C program that consists of various functions and one
  	function main.

	* src/agenda.cc: Added. Contains functions for Agenda.

	* src/main.cc: Removed executor and give_up. Instead, there is now
	a member function execute of Agenda.

	* src/make_auto_wsv_h.cc: Made the occupation list (which WSVs are
	occupied) a part of the WorkSpace. Added member functions to check
	and modify occupation.

	* src/wsv_aux.cc: Added. Contains implementation of member
	functions of WorkSpace.

	* src/parser.h: Adapted to use of Agenda. 

	* src/parser.cc: Adapted to use of Agenda. 
	
	* src/Makefile.am: Added the new files.

	* doc/doxygen/Makefile.am: Added generation of tags for
	doxymacs. The tags are stored in file arts.tag.

2002-03-12  Wolfram Haas  

	* arts-1-1-23

	* src/matpackV.h: Added three index functions with 2 Range and 3 Index.

2002-03-11  Patrick Eriksson  

	* arts-1-1-22

	* doc/uguide: Restart of the user guide for the new version.
	First of all, I have commented out most of the chapters (done in 
	main.tex). The idea is to enforce that the user guide only contains 
	stuff that is consistent with the new version. So before a chapter is 
	re-introduced, all its content shall be checked and the text shall be 
	changed where needed. Please, remember to also check the figure folder
	and to remove figures not used any longer. 

	Two new introduction chapters added. See notes in introduction.tex.
	Some text written and two figures included.

2002-03-11  Stefan Buehler  

	* arts-1-1-21

	* src/test_tensor.cc: Added Wolfram to copyright notice.

	* src/matpackIV.h: Changed author to Wolfram.

	* src/matpackV.h: Changed author to Wolfram.

2002-03-08  Wolfram Haas  

	* arts-1-1-20

	* src/matpackV.h: Added new file for tensor 5.

	* src/matpackIV.h: Added four friend class declarations.

	* src/matpackIII.h: Added two friend class declarations.

	* src/matpackI.h: Added nine friend class declarations.

	* src/test_tensor.cc: Added some tests for tensor 4 and tensor 5.

	* doc/uguide/utilities.tex: Corrected explanation for error message
	"There is some garbage at the end of the file." of the IDL reading
	routine 'read_datafile.pro'.
	
2002-03-08  Oliver Lemke  

	* arts-1-1-19

	* src/poly_roots.cc: Changed order of coefficients. Removed debug
	output.

	* src/test_poly.cc: Tweaked the example a little bit.

2002-03-07  Oliver Lemke  

	* arts-1-1-18

	* src/poly_roots.{h,cc}: Added functions to determine roots of
	polynomials. Taken from gsl and still some porting to be done.

	* src/test_poly.cc: Small prog to test poly_roots.

	* src/Makefile.am: Added poly_roots.{c,hh} to arts_SOURCES. Added
	target to create test_poly.

2002-03-05  Patrick Eriksson  

	* arts-1-1-17

	* src/los.cc: Cloud box - 1D paths ready. The sensor must now be above
	the ground and cannot be on the ground.

2002-03-03  Patrick Eriksson  

	* arts-1-1-16

	* src/los.cc: Started to include a cloud box in the propagation path
	calculations. In fact it is there, but no test runs have been 
	performed.

2002-02-28  Patrick Eriksson  

	* arts-1-1-15

	* Just some minor changes in los.cc to be backed up.

2002-02-24  Patrick Eriksson  

	* arts-1-1-14

	* src/los.cc: Further work on the propagation path calculations. No
	comments here, it will be described in AUG. 

	* Started on 2D but that code exists only so far as matlab functions 
	not included here.

2002-02-22  Stefan Buehler  

	* arts-1-1-13

	* src/matpackIV.h Iterator4D Tensor4View::begin(): Bug fix,
	removed const at end of line.
	Iterator4D Tensor4View::end(): Same.
	Recursive ConstTensor4View constructor: Bug fix, fixed typing
	error. 

	* src/matpackIII.h: Added some friend declarations.

	* src/matpackI.h: Added some friend declarations.

	* src/test_tensor.cc: Added definition of joker object. Added a
	test for selecting a book and a test for selecting the first
	letter of every page of every book.

2002-02-21  Wolfram Haas  

	* arts-1-1-12

	* src/matpackIV.h: Draft of an implementation of tensors of rank 4.

	* src/matpackIII.h: Made "friend class" entries in classes
	ConstTensor3View and Tensor3View.
	
	* src/matpackI.h: Made "friend class" entries in classes
	Range, ConstVectorView, VectorView, ConstMatrixView and MatrixView.

	* src/test_tensor.cc: Started first test for tensors of rank 4.
	
2002-02-18  Nikolay Koulev  

	* arts-1-1-11

	* src/absorption.h: Changes on the comments concerning the 
	different line intensity units in the catalogs.
	
2002-02-18  Nikolay Koulev  

	* arts-1-1-10

	* src/absorption.h: Fixed the wrong line intensity units
	from m^2/Hz to m^2*Hz.
	
2002-02-18  Nikolay Koulev  

	* arts-1-1-9

	* doc/uguide/absorption.tex: One more fix.
	
2002-02-18  Nikolay Koulev  

	* arts-1-1-8

	* doc/uguide/absorption.tex: Fixed the wrong line intensity units
	from m^2/Hz to m^2*Hz.	
	
2002-02-08  Patrick Eriksson  

	* arts-1-1-7

	* src/los.cc: 1D interpolation of an absorption Tensor3
	fixed. Note that is a temporary solution until we have more general
	ways to obtain the absorption at an arbitrary point.
	
	* src/los.cc: Wrote an outline describing my present ideas about how
	to fix the interpolations.
	
2002-02-08  Patrick Eriksson  

	* arts-1-1-6

	* src/los.cc: Started to work on interpolation and assert functions. 
	We should make set of functions for making asserts and size checks 
	simpler (as started by the check_xx functions ion arts1).

2002-02-07  Oliver Lemke  

	* arts-1-1-5
	
	* src/Makefile.am (test_tensor_SOURCES): Added target for
	test_tensor.

	* src/test_tensor.cc: Test program for matpackIV. Copied from
	test_matpack.cc.

	* src/matpackIV.h: Added empty file for tensor 4.

2002-02-05  Patrick Eriksson  

	* arts-1-1-4

	* SOME INFORMATION: I will not give any deatils here about my work
	to save time. The plan is to finish LOS/RTE calculations for 1D
	and 2D without refraction (i.e. including interpolation of
	absorption etc. and evaluation of the radiative transfer equation
	along the LOS) and then describe the approach taken in AUG.

	However, I should mention that I want to replace existing math
	functions and to remove the ones not used. For this reason, I put
	new math functions (or copies of existing ones, renamed by adding
	the number 2) in los.cc. This includes a new set of interpolation
	routines taking index positions as input. For example, the index
	position 6.5 means that a position is exactly between the points
	with index 6 and 7, index position 5 is exactly at the point with
	index 5 etc. As these index positions easily can be calculated
	when determining the LOS, this should save a lot of time for the
	interpolation. In addition, as the LOS points now mainly are placed
	at grid boundaries, for most points an interpolation is not needed and
	the index positions can be used to avoid unnecessary interpolation.
	
	* src/los.cc: Finished the LOS calculations for 1D and no refraction.
	As usual it is downwards observations from inside the atmosphere that
	makes everything complicated. 

2002-02-05  Patrick Eriksson  

	* arts-1-1-3

	* src/los.cc: Added this file for starting on the new implementation
	of the LOS calculations. Started on a function for 1D and no 
	refraction.

2002-01-25  Stefan Buehler  

	* arts-1-1-2
	
	* src/m_batch.cc (ybatchFromRadiosondeGlobal): Added message which
	profile is being processed.

	* src/m_batch.cc (ybatchFromRadiosonde): Added message which
	profile is being processed.

2002-01-22  Oliver Lemke  

	* arts-1-1-1
	
	* src/m_batch.cc: Moved #ifdef HDF_SUPPORT / #endif block to
	support radiosonde functions even without HDF compiled in.

2002-01-18  Oliver Lemke  

	* arts-1-1-0

	* This is the new development version of ARTS after the release
	All new features should go in here.

2002-01-18  Oliver Lemke  

	* arts-1-0-0
	
	* No problems occured in rc1 so we go for the release.
	
2002-01-18  Oliver Lemke  

	* arts-1-0-0-rc1

	* OK, this is release candidate 1. Just tagged this as a final
	version for testing. Hope next version will be the final release.

2002-01-18  Patrick Eriksson  

	* arts-1-0-0-pre10

	* src/m_wfs.cc: Improved check of input frequency limits for kContabs.
	There was in fact several bugs.
	Added length unit (m and km) for kContabs.

2002-01-17  Nikolay Koulev 

	* arts-1-0-0-pre9

	* doc/uguide/absorption.tex: Erased the strange artefacts after
	committing the pre8 version.
	
2002-01-17  Nikolay Koulev 

	* arts-1-0-0-pre8

	* doc/uguide/absorption.tex: Erased the strange artefacts after
	committing the pre7 version.
	
2002-01-17  Nikolay Koulev  

	* arts-1-0-0-pre7

	* doc/uguide/main.tex: Increased caption size for long tables.

	* doc/uguide/references.bib: Added two entries.

	* doc/uguide/wfuns_sensor.tex: Replaced main by uguide for xemacs.

2002-01-17  Nikolay Koulev 

	* arts-1-0-0-pre6

	* doc/examples/fullmodels.arts.in: Merged in changes from Thomas.

2002-01-17  Nikolay Koulev 

	* arts-1-0-0-pre5

	* doc/uguide/absorption.tex: Final edition and the species
	related tables now in. Resolving the referencies and warnings.
	
2002-01-16  Patrick Eriksson  

	* arts-1-0-0-pre4

	* uguide: Removed a reference to the sensor WFs section that is 
	commented out. There is almost nothing in this section and the little
	content is not in sync with ARTS, so no idea to include it.

2002-01-16  Patrick Eriksson  

	* arts-1-0-0-pre3

	* ami: Improved the README file slightly (I had forgotten that there 
	was one). Updated the Makefile.am files. Removed rand_test, that 
	existed in two folders.

2002-01-15  Patrick Eriksson  

	* arts-1-0-0-pre2

	* Sorry Oliver, but I have stuff that must be commited now.

	* ami/arts/tag2mo.m: The function now works for tag string with more
	than one part, e.g. "H2O-PWR98,H2O". 

	* ami/file/read_linefile.m: The reading can now be limited to a 
	frequency range.

	* ami/file/combine_lines.m: Created this function to lower the number
	of transitions in the linefile when several transitions are basically
	identical, which is the case for some species, such as HNO3. The
	intensities of such transitions are added to create a pseudo-line that
	gives the same contribution as the individual transitions.
	
2002-01-15  Oliver Lemke  

	* arts-1-0-0-pre1

	* Just tagged the current version as pre1. From now on only bug
	fixes for the 1.0 release should be checked in. All new stuff
	should go into arts2 which should be started at the end of this
	week. If you have to make any checkins the next version number
	should be arts-1-0-0-pre2.