Navigating the source code bundle - Revision history

Yjzhang at 01:59, 23 December 2014

2014-12-23T01:59:00Z

Yjzhang at 01:50, 23 December 2014

2014-12-23T01:50:30Z

Yjzhang at 23:12, 22 December 2014

2014-12-22T23:12:30Z

Yjzhang at 23:10, 22 December 2014

2014-12-22T23:10:41Z

Yjzhang at 16:53, 18 December 2014

2014-12-18T16:53:00Z

Yjzhang at 12:22, 24 June 2013

2013-06-24T12:22:55Z

Yjzhang at 12:48, 6 June 2013

2013-06-06T12:48:31Z

Yjzhang at 12:47, 6 June 2013

2013-06-06T12:47:08Z

Yjzhang at 13:59, 12 April 2013

2013-04-12T13:59:16Z

Yjzhang at 13:55, 12 April 2013

2013-04-12T13:55:15Z

@@ Line 24: / Line 24: @@
 <UL>
    <LI> All modules: Core, Driver, Hydro, EcoSim, ICM, OilSpill-Jung, ParMetis-3.1.-Sep2010, Sediment, and WWMII
    <LI> GNU make files: Makefile
    <LI> cmake files: CMakeLists.txt
    <LI> beta_notes: this file details all the changes in input file format for each version
-   <LI> Utility: this dir contains a lot of useful utility code. The header of each program generally has info on its purpose and instructions on how to use it.
+   <LI> Utility: this dir contains a lot of useful utility scripts. The header of each program generally has info on its purpose and instructions on how to use it.
    <UL>
        <LI>ACE: source code and install notes for ACE tools; see [http://ccrm.vims.edu/w/index.php/ACE_tools] for more details.
        <LI>Combining_Scripts: FORTRAN and perl scripts used to gather outputs from SCHISM (e.g., outputs/?_0000_elev.61 etc) into one binary file (?_elev.61)
-       <LI>Grid_Scripts: FORTRAN codes to interpolate depths from DEM files in either structured grid (raster) or unstructured grid format. While xmgredit5 can do similar things, these scripts are mostly for interpolating from very large DEM files.
+       <LI>Grid_Scripts: FORTRAN codes to interpolate depths from DEM files in either structured grid (raster) or unstructured grid format. While ACE/xmgredit5 can do similar things, these scripts are mostly for interpolating from very large DEM files.
-       <LI>NCOM: scripts to read NCOM outputs and prepare hotstart.in and salt_nu.in, temp_nu.in, and Z0 components on the boundary in bctides.in.
+      <LI> Gen_Hotstart: scripts for preparing hotstart.in
-       <LI>OneWayNestScripts: scripts for 1-way nesting, by preparing *3D.th (elevation, horizontal velocity, salinity and temperature boundary condition) that can be used for the 'small-domain' run.
+       <LI> NCOM: scripts to read NCOM outputs and prepare hotstart.in and salt_nu.in, temp_nu.in, and Z0 components on the boundary in bctides.in.
        <LI>Particle_Tracking: particle tracking code that uses SCHISM's outputs for 3D tracking
-       <LI>Post-Processing-Fortran: FORTRAN codes for extracting time series at selected 3D points (including transects). You can easily modify these codes for your own purposes.
+       <LI>Post-Processing-Fortran/More: FORTRAN codes for extracting time series at selected 3D points (including transects). You can easily modify these codes for your own purposes.
        <LI>Sflux_nc: matlab scripts useful for preparing your own .nc files for sflux/. NARR_util/ has scripts to prepare .nc files from NCEP's NARR products.
        <LI>SMS: scripts to convert between .2dm of SMS and .gr3
-       <LI>Vis_Matlab: matlab scripts for viz. We suggest you use this for presentations/publications, and use ACE tools for daily research.
+       <LI>Vis_Matlab: matlab scripts for viz. We suggest you use this for presentations/publications, and use ACE tools or VisIT for daily research.
    </UL>
 </UL>

@@ Line 1: / Line 1: @@
-You can find a lot of useful information/files in the source code bundle. In general, each directory has a readme type file. Particularly useful is beta_notes in src/, which details all algorithmic and non-algorithmic changes. You can also find a number of sample  input files in src/.
+You can find a wealth of useful information/files in the source code bundle. In general, each directory has a readme type file. Particularly useful is beta_notes in src/, which details all algorithmic and non-algorithmic changes. You can also find a number of sample  input files in src/.
 We use v4.1 as an example to explain the structure inside.
@@ Line 18: / Line 18: @@
 ;test
-This dir has all the test cases used to benchmark each version of SCHISM
+This dir has some test cases used to benchmark each version of SCHISM
 ;src

← Older revision		Revision as of 23:12, 22 December 2014
Line 1:		Line 1:
−	You can find a lot of useful information/files in the source code bundle. In general, each directory has a readme type file.	+	You can find a lot of useful information/files in the source code bundle. In general, each directory has a readme type file. Particularly useful is beta_notes in src/, which details all algorithmic and non-algorithmic changes. You can also find a number of sample input files in src/.

	We use v4.1 as an example to explain the structure inside.		We use v4.1 as an example to explain the structure inside.

@@ Line 1: / Line 1: @@
 You can find a lot of useful information/files in the source code bundle. In general, each directory has a readme type file.
-We use v3.2.x as an example to explain the structure inside.
+We use v4.1 as an example to explain the structure inside.
 ;cmake

@@ Line 4: / Line 4: @@
 ;cmake
-The README inside explains how to use cmake (needs to be installed on your system) to build SELFE. See [http://ccrm.vims.edu/w/index.php/CMake_Build_System]for more details.
+The README inside explains how to use cmake (needs to be installed on your system) to build SCHISM. See [http://ccrm.vims.edu/w/index.php/CMake_Build_System]for more details.
 ;mk
@@ Line 18: / Line 18: @@
 ;test
-This dir has all the test cases used to benchmark each version of SELFE
+This dir has all the test cases used to benchmark each version of SCHISM
 ;src
@@ Line 30: / Line 30: @@
    <UL>
        <LI>ACE: source code and install notes for ACE tools; see [http://ccrm.vims.edu/w/index.php/ACE_tools] for more details.
-       <LI>ArcGIS: some scripts to massage SELFE grid and outputs into ArcGIS
+       <LI>ArcGIS: some scripts to massage SCHISM grid and outputs into ArcGIS
-       <LI>Combining_Scripts: FORTRAN and perl scripts used to gather outputs from SELFE (e.g., outputs/?_0000_elev.61 etc) into one binary file (?_elev.61)
+       <LI>Combining_Scripts: FORTRAN and perl scripts used to gather outputs from SCHISM (e.g., outputs/?_0000_elev.61 etc) into one binary file (?_elev.61)
        <LI>Grid_Scripts: FORTRAN codes to interpolate depths from DEM files in either structured grid (raster) or unstructured grid format. While xmgredit5 can do similar things, these scripts are mostly for interpolating from very large DEM files.
        <LI>NCOM: scripts to read NCOM outputs and prepare hotstart.in and salt_nu.in, temp_nu.in, and Z0 components on the boundary in bctides.in.
        <LI>OneWayNestScripts: scripts for 1-way nesting, by preparing *3D.th (elevation, horizontal velocity, salinity and temperature boundary condition) that can be used for the 'small-domain' run.
-       <LI>Particle_Tracking: particle tracking code that uses SELFE's outputs for 3D tracking
+       <LI>Particle_Tracking: particle tracking code that uses SCHISM's outputs for 3D tracking
        <LI>Post-Processing-Fortran: FORTRAN codes for extracting time series at selected 3D points (including transects). You can easily modify these codes for your own purposes.
        <LI>Sflux_nc: matlab scripts useful for preparing your own .nc files for sflux/. NARR_util/ has scripts to prepare .nc files from NCEP's NARR products.

@@ Line 12: / Line 12: @@
 (I'm using 'HZG' as an example here)
-If you cannot find your local environment here, you can use one of the files as a starting point and add your own env.
+If you cannot find your local environment here, you can use one of the files as a starting point and add your own env in Make.defs.local.
-Edit Make.defs.local to toggle on/off optional modules inside. Then cd ../src and make (to make sure you purge previous options, do make clean first).
+Edit Make.defs.local (which is invoked by ../src/Makefile) to toggle on/off optional modules inside. Then cd ../src and make (to make sure you purge previous options, do make clean first).
 ;test

@@ Line 7: / Line 7: @@
 ;mk
-The files in this dir are local configuration settings used by src/Makefile
+The files in this dir are local configuration settings used by src/Makefile. If your group happens to have a Make.defs.*, you can simply symlink it:
 ;test