Merge pull request #140 from duvivier/gh-pages

Updated HTML for PR #139

_sources/developer_guide/dg_about.rst.txt

@@ -20,14 +20,12 @@ are primarily from **icedrv\_step\_mod.F90** but there are others (search the dr
 for ``intfc``).
 
 Guiding principles for the creation of Icepack include the following: 
-CHECK THAT THESE ARE TRUE
-
-- The column physics modules shall be independent of all sea ice model infrastructural
-  elements that may vary from model to model.  Examples include input/output, timers,
-  references to CPUs or computational tasks, initialization other than that necessary for
-  strictly physical reasons, and anything related to a horizontal grid.
-- The column physics modules shall not call or reference any routines or code that 
-  reside outside of the **columnphysics/** directory.
-- Any capabilities required by a host sea ice model (e.g. calendar variables, tracer 
-  flags, diagnostics) shall be implemented in the driver and passed into or out of the 
-  column physics modules via array arguments.
+  - The column physics modules shall be independent of all sea ice model infrastructural
+    elements that may vary from model to model.  Examples include input/output, timers,
+    references to CPUs or computational tasks, initialization other than that necessary for
+    strictly physical reasons, and anything related to a horizontal grid.
+  - The column physics modules shall not call or reference any routines or code that 
+    reside outside of the **columnphysics/** directory.
+  - Any capabilities required by a host sea ice model (e.g. calendar variables, tracer 
+    flags, diagnostics) shall be implemented in the driver and passed into or out of the 
+    column physics modules via array arguments.

_sources/developer_guide/dg_col_phys.rst.txt

@@ -16,7 +16,6 @@ The column physics source code contains the following files
 |    **icepack_algae.F90**         biogeochemistry
 |    **icepack_atmo.F90**          stability-based parameterization for calculation of turbulent ice–atmosphere fluxes
 |    **icepack_brine.F90**         evolves the brine height tracer
-|    **icepack_constants.F90**     physical and numerical constants required for column package
 |    **icepack_firstyear.F90**     handles most work associated with the first-year ice area tracer
 |    **icepack_flux.F90**          fluxes needed/produced by the model
 |    **icepack_intfc.F90**         interface routines for linking Icepack with a host sea ice model
@@ -29,7 +28,7 @@ The column physics source code contains the following files
 |    **icepack_mushy_physics.F90** physics routines for mushy thermodynamics
 |    **icepack_ocean.F90**         mixed layer ocean model
 |    **icepack_orbital.F90**       orbital parameters for Delta-Eddington shortwave parameterization
-|    **icepack_parameters.F90**    basic model parameters
+|    **icepack_parameters.F90**    basic model parameters including physical and numerical constants requried for column package
 |    **icepack_shortwave.F90**     shortwave and albedo parameterizations
 |    **icepack_therm_0layer.F90**  zero-layer thermodynamics of :cite:`Semtner76`
 |    **icepack_therm_bl99.F90**    multilayer thermodynamics of :cite:`BL99`
@@ -56,7 +55,7 @@ that is running on multiple pes with a decomposed grid.
 
 The column physics does not have a time manager.  Calendaring is expected to be
 dealt with by the host model.  The column physics does not read any forcing data,
-that is passed into the column physics thru interfaces.  In fact, 
+that is passed into the column physics though interfaces.  In fact, 
 there are no direct IO capabilities in the column physics.  That is to say, the
 column physics does not open files to read or write.  The column physics is able to write 
 data via several different routines that specifically have a fortran unit number as an input
@@ -67,11 +66,11 @@ The warning package also provides access to an abort flag that the host model ca
 query after each call to check for successful completion of the column physics package.
 
 All column physics public interfaces and public data are defined in the **icepack_intfc.F90**
-file.  Internal column physics settings should all be accessible thru interfaces.
+file.  Internal column physics settings should all be accessible through interfaces.
 The internal constants, parameters, and tracer settings have init (set), query (get), and
 write interfaces that provides access to internal column physics settings.  The host model
 should not have to use "use" statements to access any of the column physics data outside
-of what is provided thru the icepack_intfc module.  
+of what is provided through the icepack_intfc module.  
 The public column physics interfaces use optional arguments where it makes sense and
 there is an ongoing effort to make more of the interfaces support keyword=value arguments
 for clarity and backwards compatibility.
@@ -88,7 +87,7 @@ how to use them will be described.
 Interfaces
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-Column physics data and subroutines are made public thru the **icepack_intfc.F90**
+Column physics data and subroutines are made public through the **icepack_intfc.F90**
 file.  That file contains the entire list of data and subroutines needed to
 initialize, setup, and run the column physics package.  That file points
 to other modules within the column physics where the interfaces are located.
@@ -104,7 +103,7 @@ icepack_kinds module::
       use icepack_kinds, only: icepack_dbl_kind  => dbl_kind
       use icepack_kinds, only: icepack_r16_kind  => r16_kind
 
-icepack_tracers defines a handful of parameters constants that provide information
+icepack_tracers defines a handful of parameters that provide information
 about maximum array sizes for static dimensioning::
 
       use icepack_tracers,   only: icepack_max_nbtrcr => max_nbtrcr
@@ -116,28 +115,16 @@ about maximum array sizes for static dimensioning::
       use icepack_tracers,   only: icepack_max_aero   => max_aero
       use icepack_tracers,   only: icepack_nmodal1    => nmodal1
       use icepack_tracers,   only: icepack_nmodal2    => nmodal2
-      use icepack_constants, only: icepack_nspint     => nspint
+      use icepack_parameters, only: icepack_nspint     => nspint
 
-icepack_constants provides a list of static parameter constants::
-
-      use icepack_constants, only: c0 => c0
-
-icepack_constants provides init, query, write, and recompute methods to
-define constant values.  These constants have defaults that the caller
-can query or reset::
-
-      use icepack_constants, only: icepack_init_constants
-      use icepack_constants, only: icepack_query_constants
-      use icepack_constants, only: icepack_write_constants
-      use icepack_constants, only: icepack_recompute_constants
-
-icepack_parameters provides init, query, and write methods to
-define model parameters.  These parameters have defaults that the caller
-can query or reset::
+icepack_parameters provides init, query, write, and recompute methods to
+define constant values and model parameters.  These constants have defaults 
+that the caller can query or reset::
 
       use icepack_parameters, only: icepack_init_parameters
       use icepack_parameters, only: icepack_query_parameters
       use icepack_parameters, only: icepack_write_parameters
+      use icepack_parameters, only: icepack_recompute_constants
 
 icepack_tracers provides init, query, and write methods to
 define various tracer sizes, flags, indices, and numbers.  The
@@ -248,7 +235,6 @@ start driver
 
 initialize driver and read in driver namelist
 
-* call *icepack_init_constants*
 * call *icepack_init_parameters*
 * call *icepack_init_tracers_*
 * call *icepack_init_trcr*
@@ -283,7 +269,7 @@ The Warning Package
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 Icepack has no IO capabilities.  It does not have direct knowledge of
-any input or output files.  However, it can write output thru specific
+any input or output files.  However, it can write output through specific
 interfaces that pass in a fortran file unit number.  There are several 
 methods in icepack that support writing data to a file this way including
 the various *icepack_write_* interfaces.
@@ -306,4 +292,4 @@ Alternatively, *icepack_warnings_getall* provides the saved icepack messages to
 the driver via an array of strings in the argument list.  This allows the driver
 to reformat that output as needed.  *icepack_warnings_print*
 writes out the messages but does not clear them, and *icepack_warnings_clear* zeros
-out the icepack warning messages.
+out the icepack warning messages.

_sources/developer_guide/dg_driver.rst.txt

@@ -29,7 +29,7 @@ The icepack driver consists of the following files
 |        **icedrv_init.F90**        general initialization routines
 |        **icedrv_init_column.F90** initialization routines specific to the column physics
 |        **icedrv_restart.F90**     driver for reading/writing restart files
-|        **icedrv_restart_column.F90**  (CHECK: RENAME bgc) restart routines specific to the column physics
+|        **icedrv_restart_column.F90**  restart routines specific to the column physics
 |        **icedrv_restart_shared.F90**  code shared by all restart options
 |        **icedrv_state.F90**       essential arrays to describe the state of the ice
 |        **icedrv_step.F90**        routines for time stepping the major code components
@@ -43,4 +43,4 @@ to run 4 different gridcells on one processor with the same forcing used for all
 There is no MPI and no threading built into the icepack driver.  There is limited IO capabilities,
 no history files, and no netcdf restart files.  The model generally runs very quickly.
 
-There are a few different forcings available.
+Forcing data and details on these data are available in :ref:`force`.

_sources/developer_guide/dg_scripts.rst.txt

@@ -26,7 +26,7 @@ The directory structure under configure/scripts is as follows.
 |        **icepack_in**            namelist input data
 |        **machines/**             machine specific files to set env and Macros
 |        **makdep.c**              determines module dependencies
-|        **options/**              other namelist configurations available from the icepack.create.case command line
+|        **options/**              other namelist configurations available from the icepack.setup command line
 |        **parse_namelist.sh**     replaces namelist with command-line configuration
 |        **parse_namelist_from_settings.sh**   replaces namelist with values from icepack.settings
 |        **parse_settings.sh**     replaces settings with command-line configuration
@@ -38,11 +38,11 @@ Strategy
 -----------
 
 The icepack scripts are implemented such that everything is resolved after
-**icepack.create.case** is called.  This is done by both copying specific files
-into the case directory and running scripts as part of the **icepack.create.case**
+**icepack.setup** is called.  This is done by both copying specific files
+into the case directory and running scripts as part of the **icepack.setup**
 command line to setup various files.
 
-**icepack.create.case** drives the case setup.  It is written in csh.  All supporting
+**icepack.setup** drives the case setup.  It is written in csh.  All supporting
 scripts are relatively simple csh or sh scripts.
 
 The file **icepack.settings** specifies a set of env defaults for the case.  The file
@@ -54,16 +54,16 @@ Preset Case Options
 ---------------------
 
 
-``icepack.create.case -s`` option allows the user to choose some predetermined icepack
+``icepack.setup -s`` option allows the user to choose some predetermined icepack
 settings and namelist.  Those options are defined in **configurations/scripts/options/**
-and the files are prefixed by either set_env, set_nml, or test_nml.  When **icepack.create.case**
+and the files are prefixed by either set_env, set_nml, or test_nml.  When **icepack.setup**
 is executed, the appropriate files are read from **configurations/scripts/options/**
 and the **icepack.settings** and/or **icepack_in** files are updated in the case directory
 based on the values in those files.
 
 The filename suffix determines the name of the -s option.  So, for instance, 
 
-  ``icepack.create.case -s diag1,debug,bgcISPOL``
+  ``icepack.setup -s diag1,debug,bgcISPOL``
 
 will search for option files with suffixes of diag1, debug, and bgcISPOL and then
 apply those settings.