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''' (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.
== Overview ==


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.  This makes it very useful for computing future or past dates in scripts and computer programs.
* 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


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:
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.


# compute the Astronomical Juliay Day for 2008/01/01
== Table of Contents ==
# add 1000
# convert back to a calendar date


We'll return to this example in the next section.
=== GAMAP web pages ===


'''''TIP: In order to avoid confusing Julian Day with Astronomical Julian Day, we recommend that you refer to the number of days in a year as "Day of Year". This will remove all ambiguity.'''''
* [https://geoschem.github.io/gamap-manual/ GAMAP main page]
* [https://geoschem.github.io/gamap-manual/doc/index.html GAMAP Online User's Guide]


=== Astronomical Julian Day routines in IDL ===
=== GAMAP tips and tricks ===


IDL has two Astronomical Julian Day functions
* [[General GAMAP usage]]
* [[File I/O with GAMAP]]
* [[Color and graphics with GAMAP]]
* [[Regridding with GAMAP]]
* [[Date and time computations with GAMAP]]
* [[Text manipulation with GAMAP]]
* [[Removing extraneous lines from map plots]]
* [[TVMAP cheat sheet]]
* [[Reading binary files in IDL]]


* JULDAY -- converts a year, month, day (, hour, min, sec) to Astronomical Julian Date
--[[User:Bmy|Bob Y.]] 09:48, 11 March 2011 (EST)
* CALDAT -- converts an Astronomical Julian Day back to year, month, day (, hour, min, sec)
 
NOTE: The year, month, day are mandatory but you may omit the hour, min, sec.  If you omit hour, min, sec, then JULDAY will return an integer value.  If you include hour, min, sec, JULDAY wil return a double precision value.
 
JULDAY and CALDAT are used as follows:
 
; Compute the Astronomical Julian Day for 2008/01/10
; Note: the day is required, the hours, mins, seconds are optional
IDL> print, julday( 1, 10, 2008, 0, 0, 0 )
        2454475.5
; Convert the Astronomical Julian Day back to a calendar date
IDL> caldat, 2454475.5, y, m, d, h, mi, s
IDL> print, y, m, d, h, mi, s
            1          10        2008          0          0      0.0000000
 
To compute the date 1000 days after 2008/01/01 (from the example in the preceding section), you would do the following:
 
IDL> jd = julday( 1, 1, 2008 )
IDL> jd = jd + 1000
IDL> caldat, jd, y, m, d
IDL> print, y, m, d
          9          27        2010
 
We find that gives us the date 2010/09/27.  NOTE: This has also accounted for the leap-year-day on Feb 29, 2008.
 
For your convenience, GAMAP has a function called ADD_DATE which will do this for you in one fell swoop:
 
IDL> print, add_date( 20080101, 1000 )
    20100927
 
You can also use ADD_DATE to compute days prior to a given date.  Let's compute what the calendar date was 1000 days prior to Jan 1, 2008:
 
IDL> print, add_date( 20080101, -1000 )
    20050406
 
--[[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.
 
NOTE: Starting in GAMAP v2-12 (not released yet), you will be able to specify a single YYYYMMDD argument instead of the month, day, year arguments:
 
; Convert month/day/year to day of year
IDL> doy = day_of_year( 20080110 )
 
--[[User:Bmy|Bob Yantosca]] 15:40, 3 April 2008 (EDT)
 
== 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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