GAMAP tips and tricks: Difference between revisions

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== Date and time ==
----
<span style="color:red"><big><strong>[https://geoschem.github.io/gamap-manual/GAMAP GAMAP] is now obsolete.  We recommend using [https://gcpy.readthedocs.io GCPy] for analyzing output from recent GEOS-Chem versions.  But we will preserve the GAMAP wiki documentation for reference.</strong></big></span>
----


=== Julian Day vs. Astronomical Julian Day ===


The Julian Day (JD) is used to denote the number of days that have elapsed since the start of a year.  For example, the Julian Day number of 2008/01/10 is 10 (since it is the 10th day of 2008).   
On this page we list information about GAMAP, the Global Atmospheric Model Analysis Package.   


However, another term that is sometimes confused with the Julian Day is the Astronomical Julian Day
== Overview ==
(AJD).  This is the number of days that have elapsed since 12:00 GMT on January 1, 4713 BC.  The Astronomical Julian Day at 00:00 GMT on 2008/01/10 is 2454475.5.


The Astronomical Julian Day is mostly used in astrophysics and space sciences to compute long intervals of time that may span many years (e.g. the period of a variable star, etc.).  You can find algorithms for computing AJD in several textbooks, including ''Practical Astronomy with Your Calculator'' by Peter Duffett-Smith, Cambridge Univ. Press, 1992.
GAMAP


The chief advantage of using the Astronomical Julian Day is that its computation accounts for the end-of-month, end-of-year, end-of-century, and end-of-millenium transitions.  For example, if you want to compute what the date will be 1000 days from 2008/01/01, then all you have to do is:
* is a self-contained, consistent, and user-friendly software package for reading and visualizing output from chemical tracer models (CTM's)
* consists of a suite of routines written in IDL (Interactive Data Language)
* makes extensive use of IDL's powerful plotting features
* can produce line plots, 2D plots, 2D animations, or 3D isocontour surface plots
* can read 2D, 3D or 4D data blocks
* can read output from the GEOS–Chem, GISS and FSU model families
* can be easily customized to keep pace with ongoing model development
* can be installed on any platform that supports IDL, thus ensuring a high degree of portability
* can be coupled with the ION (IDL on the Net) interface to create interactive plots which can be served to a web page
* can read data from ASCII, binary, netCDF (including COARDS conventions!), and HDF–EOS file formats
* contains helper routines to read from / write to various file formats


# compute the Astronomical Juliay Day for 2008/01/01
The main GAMAP program contains a user-friendly, menu-driven interface; however, users may also call GAMAP subroutines independently of the main program. This makes it possible to embed GAMAP routines within existing IDL code.
# add 1000
# convert back to a calendar date


Doing this computation we find that 1000 days after 2008/01/01 is 2010/09/27.  NOTE: This also accounted for the leap-year-day on Feb 29, 2008.
== Table of Contents ==


IDL has two Astronomical Julian Day functions
=== GAMAP web pages ===


* JULDAY -- converts a year, month, day (, hour, min, sec) to Astronomical Julian Date
* [https://geoschem.github.io/gamap-manual/ GAMAP main page]
* CALDAT -- converts an Astronomical Julian Day back to year, month, day (, hour, min, sec)
* [https://geoschem.github.io/gamap-manual/doc/index.html GAMAP Online User's Guide]


and they are called as follows:
=== GAMAP tips and tricks ===


; Compute the Astronomical Julian Day for 2008/01/10
* [[General GAMAP usage]]
; Note: the day is required, the hours, mins, seconds are optional
* [[File I/O with GAMAP]]
IDL> print, julday( 1, 10, 2008, 0, 0, 0 )
* [[Color and graphics with GAMAP]]
        2454475.5
* [[Regridding with GAMAP]]
* [[Date and time computations with GAMAP]]
; Convert the Astronomical Julian Day back to a calendar date
* [[Text manipulation with GAMAP]]
IDL> caldat, 2454475.5, y, m, d, h, mi, s
* [[Removing extraneous lines from map plots]]
IDL> print, y, m, d, h, mi, s
* [[TVMAP cheat sheet]]
            1          10        2008          0          0      0.0000000
* [[Reading binary files in IDL]]


Therefore, in order to avoid confusion, we recommended to refer to the number of days in a year as "Day of Year" rather than Julian Day.
--[[User:Bmy|Bob Y.]] 09:48, 11 March 2011 (EST)
 
--[[User:Bmy|Bob Yantosca]] 15:40, 3 April 2008 (EDT)
 
=== Computing the day of year from a calendar date (and vice-versa) ===
 
A quick way to compute the day of the year is w/ IDL's JULDAY function:
 
Day_of_Year = JULDAY( Month, Day, Year ) - JULDAY( 1, 0, Year )
 
For example:
 
IDL> print, julday( 1, 10, 2008 ) - julday( 1, 0, 2008 )
      10
 
JULDAY( 1, 0, 2008 ) is essentially 12/31/2007. This is used so that you don't have to add one to the above difference.  (This is equivalent to JULDAY( 1, 10, 2008 ) - JULDAY( 1, 1, 2008 ) + 1.)
 
This is essentially done for you in the GAMAP function <tt>~/IDL/gamap2/date_time/day_of_year.pro</tt>.  You could replace the above code with:
 
IDL> print, day_of_year( 1, 10, 2008 )
      10
 
To compute the calendar date from the day of the year (the inverse operation), you can use IDL's CALDAT function.  However, you must also add the Astronomical Julian day for the first of the year, for example:
 
IDL> caldat, julday( 1, 0, 2008 )+10, y, m, d
IDL> print, y, m, d
        1          10        2008
 
You can also do this with the GAMAP functions DAY_OF_YEAR and ADD_DATE, as follows
 
    ; Convert month/day/year to day of year
    IDL> doy = day_of_year( 1, 10, 2008 )
    IDL> print, doy
          10
    ; convert day of year back to month/day/year
    IDL> print, add_date( 20080101, 10-1 )
        20080110
 
The only thing to remember is you have to subtract 1 from the day of year due to the way that  ADD_DATE is written.
 
== Combining output from timeseries files ==
 
'''''Ray Nassar (ray@io.as.harvard.edu) wrote:'''''
 
:I just have a quick question, is there any GAMAP routine that can average all hourly data blocks in a timeseries file to make a single daily average bpch file? 
 
:It appears like I could use the average option of ctm_sum.pro but I do not quite understand where the averaged data goes and afterwards would still have to write to bpch.
 
'''''Philippe Le Sager (plesager@seas.harvard.edu) replied:'''''
 
:Check the
 
    /gamap2/timeseries/gc_combine_nd49.pro
    /gamap2/timeseries/gc_combine_nd48.pro
 
:routines, which combines daily bpch files (nd48 & nd49 output, but also met field input files) into 4D data blocks. It has many options. You can extract a subset of data according to time and/or location, or process the data (moving average, daily max, shift to local time). You can either save the data into a new bpch file or just get an array of data in output.
 
:I wrote a tutorial that gives some pointers [http://www-as.harvard.edu/chemistry/trop/gamap/doc/timeseries_brief_tutorial.pdf here.]
 
:-Philippe
 
--[[User:Bmy|Bob Yantosca]] 09:43, 1 April 2008 (EDT)
 
== Memory management and CTM_MAKE_DATAINFO ==
 
When using CTM_MAKE_DATAINFO, you create few pointers and allocate memory to pointed data. Three scenarios to free that memory are possible.
 
(1) By default, GAMAP keeps track of the pointers in a global structure, and you can clean up the memory by calling CTM_CLEANUP (with or without the keyword /NO_GC):
 
    ctm_make_datainfo(data, ...)
    CTM_WriteBpch, DataInfo, FileInfo, FileName=file
    ctm_cleanup
 
(2) If you use the keyword /NO_GLOBAL when calling CTM_MAKE_DATAINFO, the story is a little bit more subtle. Now, GAMAP has no idea of the created pointers. If you use CTM_CLEANUP without the keyword /NO_GC, everything is clean up because there is a call to heap_gc. But you are also loosing **all other** pointers and objects.
 
    ctm_make_datainfo(data, ..., /No_global)
    CTM_WriteBpch, DataInfo, FileInfo, FileName=file
    ctm_cleanup
 
Note if you do not call ctm_cleanup or call it with /No_GC, then the memory allocated by CTM_MAKE_DATAINFO is still allocated and the pointers that refers to it are alive... until you exit the routine (unless they are passed back). Once you are out of the routine, this memory remains allocated but is useless since unaccessible, in other words you have memory leak.
 
(3) So, if you want to keep some objects and/or pointers alive in your code (i.e., you do not want to call heap_gc or ctm_cleanup,/no_gc), you need to free only the created pointers as follows:
 
    ctm_make_datainfo(data, datainfo, fileinfo, ..., /No_global)
    CTM_WriteBpch, DataInfo, FileInfo, FileName=file
    ptr_free, DataInfo.data
    ptr_free, fileinfo.gridinfo
 
To free only the heap memory created by multiple calls to CTM_MAKE_DATAINFO, the procedure is:
 
  for D=0L, NTracers-1L do begin
     
      Success = CTM_Make_DataInfo( Data[*,*,D], DataInfo, FileInfo, ..., /No_Global )
     
      ArrDataInfo = D eq 0l ? [ DataInfo ] : [ ArrDataInfo, DataInfo ]
     
      if D ne Ntracers-1l then ptr_free, Fileinfo.gridinfo
     
  endfor
     
  CTM_WriteBpch, ArrDataInfo, FileInfo, FileName=OutFileName
     
  for d=0, n_elements(ArrDataInfo)-1l do ptr_free, ArrDataInfo[d].data
  ptr_free, fileinfo.gridinfo
 
--[[User:Phs|Philippe Le Sager]] 10:28, 13 February 2008

Latest revision as of 19:02, 16 September 2022

GAMAP is now obsolete. We recommend using GCPy for analyzing output from recent GEOS-Chem versions. But we will preserve the GAMAP wiki documentation for reference.


On this page we list information about GAMAP, the Global Atmospheric Model Analysis Package.

Overview

GAMAP

  • is a self-contained, consistent, and user-friendly software package for reading and visualizing output from chemical tracer models (CTM's)
  • consists of a suite of routines written in IDL (Interactive Data Language)
  • makes extensive use of IDL's powerful plotting features
  • can produce line plots, 2D plots, 2D animations, or 3D isocontour surface plots
  • can read 2D, 3D or 4D data blocks
  • can read output from the GEOS–Chem, GISS and FSU model families
  • can be easily customized to keep pace with ongoing model development
  • can be installed on any platform that supports IDL, thus ensuring a high degree of portability
  • can be coupled with the ION (IDL on the Net) interface to create interactive plots which can be served to a web page
  • can read data from ASCII, binary, netCDF (including COARDS conventions!), and HDF–EOS file formats
  • contains helper routines to read from / write to various file formats

The main GAMAP program contains a user-friendly, menu-driven interface; however, users may also call GAMAP subroutines independently of the main program. This makes it possible to embed GAMAP routines within existing IDL code.

Table of Contents

GAMAP web pages

GAMAP tips and tricks

--Bob Y. 09:48, 11 March 2011 (EST)

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