* Bug Fix

commit 5a375c9f846d4423e9bc3c6c3c012126a090b561
Author: Yuta Kawai <ykawai@gfd-dennou.org>
Date:   Sun Dec 1 17:14:39 2013 +0900

    * Fix bug that unallocated variables are deallocate in some setup modules.

commit aa8d1a97fd0c921c82804a4f73d64e6e2e5774b8
Author: Yuta Kawai <ykawai@gfd-dennou.org>
Date:   Sun Dec 1 17:09:57 2013 +0900

    * Fix bug that SpmlUtil_mod is not initialized in the serial execution.
* Add a tool to calculate some diagnostic variables from ogcm output variables.

commit 3b8a01bcfbf4aa7cf6ff7d748031431475f05d75
Author: Yuta Kawai <ykawai@gfd-dennou.org>
Date:   Wed Dec 4 23:12:41 2013 +0900

    * Finish implementing the minimum specifications necessary to
      the numerical experiment for wind-drivern circulation.

commit 530047968dd29c3c3ab7e5f6571c9b05811dbf93
Author: Yuta Kawai <ykawai@gfd-dennou.org>
Date:   Wed Dec 4 00:28:56 2013 +0900

    * Implemnet prototype source code to calculate and output diagnose variables
      using ogcm output.

commit 45542d1dccdc9b03b1f5f2f3056b4972ccaf9570
Author: Yuta Kawai <ykawai@gfd-dennou.org>
Date:   Sun Dec 1 16:53:48 2013 +0900

    * Create a main file of a program to diagnose output prognostic variables.
* Add a variable that ogcm can output.

commit 7bc43bd15bca6a4204adbe866ff280562a04606c
Author: Yuta Kawai <ykawai@gfd-dennou.org>
Date:   Wed Dec 4 13:57:23 2013 +0900

    * Finish implementing a function to output baroclinic pressure.

commit 425d7afeabdd536250bed5fe0822021b357c5139
Author: Yuta Kawai <ykawai@gfd-dennou.org>
Date:   Wed Dec 4 01:04:45 2013 +0900

    * Add a module to calculate some diagnostic variables.

commit afef6f0266762b6ed76384f8ce399a9381d0c4f4
Author: Yuta Kawai <ykawai@gfd-dennou.org>
Date:   Wed Dec 4 00:33:53 2013 +0900

    * Add some code to output baroclinic pressure.
Add a module for diagnosing some variable which was forgot to commit.
* Implement a module which provides the interfaces for various types of EOS.

commit 66e067bb71fae26b482fe113533bca1126a9bee2
Author: Yuta Kawai <ykawai@gfd-dennou.org>
Date:   Fri Dec 6 11:28:32 2013 +0900

    * Replace the hard-code for a linear EOS with the code in which calls each EOS  routine via EOS driver.

commit 5633241eb1133b346732565747addeedc61e19d1
Author: Yuta Kawai <ykawai@gfd-dennou.org>
Date:   Thu Dec 5 23:54:15 2013 +0900

    Recommit to add a EOS driver module which was forgot in the previous commit.

commit 223f665f7c8e528e4531437148a898614b144c6b
Author: Yuta Kawai <ykawai@gfd-dennou.org>
Date:   Thu Dec 5 23:46:29 2013 +0900

    Implement a driver module for each EOS module and add some physical constants.

commit ce8e34f4eea869c89c089fc2a1ff805291012293
Author: Yuta Kawai <ykawai@gfd-dennou.org>
Date:   Thu Dec 5 17:07:49 2013 +0900

    * Add a module for a linear EOS.

commit 7ceff9f777472283df250db3fc445198a1d84fa2
Author: Yuta Kawai <ykawai@gfd-dennou.org>
Date:   Sun Dec 1 16:51:39 2013 +0900

    * Create a driver module for EOS.
* Add a unit test for JM95 EOS and a page containing some figures of densify calculated by JM95.

commit c92b8f7e345874722b756e617a618b92095be500
Author: Yuta Kawai <ykawai@gfd-dennou.org>
Date:   Tue Dec 24 12:38:30 2013 +0900

    * Create a page which contains some figures of density calculated EOS of JM95.

commit 16b62d38e07f5cbc4b184d3d37a26ada574329c4
Author: Yuta Kawai <ykawai@gfd-dennou.org>
Date:   Tue Dec 24 03:23:50 2013 +0900

    * Add a unit test for EOS of JM95.
* merge numexp branch

commit 5f9076616c3f7dfe8adfcf0ab6e664979d4121de
Author: Yuta Kawai <ykawai@gfd-dennou.org>
Date:   Tue Dec 24 13:47:06 2013 +0900

    * Modify the header of some org files.

commit d01b33c363079f0f4c5ab64f604c4daad84d4f96
Author: Yuta Kawai <ykawai@gfd-dennou.org>
Date:   Tue Dec 24 00:42:18 2013 +0900

    * Add some org files written about the summary of numerical experiments.

commit caf6ed24540c3e87f081bfdbadb5c4b832f0c8c1
Author: Yuta Kawai <ykawai@gfd-dennou.org>
Date:   Wed Dec 11 13:05:55 2013 +0900

    * Move some EOS parameters in Variable_mod to Constant_mod and
      modify some modules in dynamics to deal with the change.

commit a7c2d6880ef610a561e269ce143e6ef3b797c4eb
Author: Yuta Kawai <ykawai@gfd-dennou.org>
Date:   Tue Dec 10 21:02:06 2013 +0900

    * Modify some codes associated with a barotropic Rossby wave experiment to deal with the recent change of master brach.

commit e90ad1542592324d520d72186674e31fe30785ed
Author: Yuta Kawai <ykawai@gfd-dennou.org>
Date:   Tue Dec 10 21:00:54 2013 +0900

    * Use a new subroutine in SpmlUtil_mod to set vertical boundary conditions.

commit 57637cc79a35ff4e448a364a81579bae10c8661e
Author: Yuta Kawai <ykawai@gfd-dennou.org>
Date:   Tue Dec 10 20:56:07 2013 +0900

    * Modify a utility module for spmodel to set vertical boundary conditions easily.
* Modify the figures for density calculated by JM95 EOS and commit a CSS file.
* Compile the results of numerical experiment 1 and 2.

commit ded08f3933eea263ef5c6685280f26132c2e7b6f
Author: Yuta Kawai <ykawai@gfd-dennou.org>
Date:   Mon Jan 13 19:51:56 2014 +0900

    * Finish compiling the results of numerical experiment 1 and 2.

commit c0f63d0494a0a23e32f6685bb32c9c4994209023
Author: KAWAI YUTA <ykawai@dennou-k.kugi-mete>
Date:   Mon Jan 13 14:00:35 2014 +0900

    * Modify collectImg.rb for a numerical experiment of barotropic Rossby wave.

commit 3c2d92bdd8db3700b175b1fa060509d2dcc0a754
Author: Yuta Kawai <ykawai@gfd-dennou.org>
Date:   Sat Jan 11 20:01:50 2014 +0900

    * Update a numerical experiment of barotropic Rossby wave.

commit cca2bed07887bded4a8548669f900e9c6d4b022a
Author: Yuta Kawai <ykawai@gfd-dennou.org>
Date:   Sat Jan 11 20:00:10 2014 +0900

    * Delete some routines in SpmlUtil_mod unused reccently.

commit 8a84779e03810d35e0e847ede4ffbd3fabfa0280
Author: Yuta Kawai <ykawai@gfd-dennou.org>
Date:   Sat Jan 11 19:57:15 2014 +0900

    * Add some namelists for each case of numerical experiment.

commit fff061f89d8f091da6691c4b256a6ddc0632e18b
Author: Yuta Kawai <ykawai@gfd-dennou.org>
Date:   Sat Jan 11 19:50:09 2014 +0900

    * Add some ruby scripts to create the figures automatically.
      Move a directory for numerical expermient and create the figures of the results.

commit 044a928223a5993e441b61f75f88c8cb8c95c297
Author: ykawai <ykawai@gfd-dennou.org>
Date:   Sun Jan 5 13:12:23 2014 +0900

    * Finish writing the org files containig the explanation for the numerical experiment of barotropic Rossby/internal gravity wave.

commit d07b93695ef587f9c31746ea9e3c5b7386c0ed8a
Author: Yuta Kawai <ykawai@gfd-dennou.org>
Date:   Sun Jan 5 01:54:19 2014 +0900

    * Change how to set the parameters in the internal gravity wave test.

commit 152ea0017afc999fc48f855ee0c73eca7add7840
Author: Yuta Kawai <ykawai@gfd-dennou.org>
Date:   Sun Jan 5 01:51:46 2014 +0900

    * Change a interface of subroutine to set a initial condition for each numerical experiment.

commit ebc5b64ca0c5813d52af383e5edb8ea6b10eec43
Author: Yuta Kawai <ykawai@gfd-dennou.org>
Date:   Sun Jan 5 01:38:22 2014 +0900

    * Modify a module which provides a linear EOS to add the pressure dependency.
      A EOS driver module and a module managing physical constants are updated to
      reflect the modification.

commit 2a1a057c33dd915a85198a6479a21b2cb3e3105c
Author: Yuta Kawai <ykawai@gfd-dennou.org>
Date:   Mon Dec 30 13:32:03 2013 +0900

    * Modify the explanation for numerical experiment.
* Standardize the OGCM variables.
* Add some functions of a tool to caluculate diagnose variables.
* Update a numerical experiment of wind driven circulation.

commit 2507748fbb7f8f5bb1548e4fb57305ea06289745
Author: Yuta Kawai <ykawai@gfd-dennou.org>
Date:   Sat Jan 25 19:26:48 2014 +0900

    * Use the subroutines of DiagnoseUtil_mod in dynamic core and update a numerical experiment of wind driven circulation.

commit 4bdf0ecdfcdb9b13dd41088e9dda989659a716cb
Author: Yuta Kawai <ykawai@gfd-dennou.org>
Date:   Sat Jan 25 19:00:24 2014 +0900

    * Add new functions and adopt the standardization of variables using Dennou-OGCM.

commit a5315de2fff8bb437da7d96c90b1f74af71f4fd0
Author: Yuta Kawai <ykawai@gfd-dennou.org>
Date:   Sat Jan 25 18:50:57 2014 +0900

    * Standardize the treatment of variables and modify some modules.
* Parallelize some subroutines with OpenMP.
  * The parallized subroutines contain the do loops for vertical axis or
    they are associated with ChebyShev polynominal spectral method.
* Output basic state and fix some bugs in DiagVar.
* Start writing the description for the limit of chebychev expansion in a numerical experiment of wind-driven circulation.