Merge pull request #91 from smolins/glenn-update-petsc-pflotran-versi…

…on-numbers

updated README to reflect version numbers for xSDK 1.0.0 release, and…

README.rst

@@ -8,7 +8,7 @@ Status
 Description
 -----------
 
-Alquimia provides a generic interface between flow and transport simulators (drivers) and biogeochemical reaction capabilities (engines). Alquimia consists of two parts: an application programming interface, API, and a wrapper library. The API describes in detail how information is exchanged between the driver and the engine. This includes the function call signatures and data structures required for implementing alquimia in a mixed language (C/C++/Fortran) programming environment. The library is an implementation of the documented API, providing an interface into the biogeochemistry routines supplied by other codes: Alquimia does not do any geochemical calculations. Version 1.0 provides interfaces to the open source codes (BSD) CrunchFlow/CrunchTope and (LGPL) PFLOTRAN. Version 1.0 meets the policies set forth by (and is part of) the Extreme-scale Scientific Software Development Kit, xSDK version 0.6.0.
+Alquimia provides a generic interface between flow and transport simulators (drivers) and biogeochemical reaction capabilities (engines). Alquimia consists of two parts: an application programming interface, API, and a wrapper library. The API describes in detail how information is exchanged between the driver and the engine. This includes the function call signatures and data structures required for implementing alquimia in a mixed language (C/C++/Fortran) programming environment. The library is an implementation of the documented API, providing an interface into the biogeochemistry routines supplied by other codes: Alquimia does not do any geochemical calculations. Version 1.x provides interfaces to the open source codes (BSD) CrunchFlow/CrunchTope and (LGPL) PFLOTRAN. Version 1.x meets the policies set forth by (and is part of) the Extreme-scale Scientific Software Development Kit, xSDK version 0.6.0.
 
 Originally developed as part of the DOE ASCEM project, it is now mantained and developed under the 
 U.S. Department of Energy's `IDEAS Watersheds <https://ideas-productivity.org/>`_ project
@@ -75,13 +75,13 @@ to ensure compatibility. Currently:
 +------------+------------+
 |            | Version    |
 +------------+------------+
-|xSDK        | 0.8.0      |
+|xSDK        | 1.0.0      |
 +------------+------------+
-|Alquimia    | 1.0.10     |
+|Alquimia    | 1.1.0      |
 +------------+------------+
-|PETSc       | 3.18       |
+|PETSc       | 3.20.0     |
 +------------+------------+
-|PFLOTRAN    | 4.0.1      |
+|PFLOTRAN    | 5.0.0      |
 +------------+------------+
 |CrunchFlow  | dev        |
 +------------+------------+

doc/api/APIv1_functions.rst

@@ -165,9 +165,11 @@ Take one reaction step in operator split mode with the specified delta t.
         input: delta_t <double>,
         input: properties <struct: Alquimia Properties>,
         in/out: state <struct: Alquimia State>,
-        in/out: aux_data <struct: Alquimia Auxiliary Data>
+        in/out: aux_data <struct: Alquimia Auxiliary Data>,
+	in: natural_id <int>,
         out: status <struct: Alquimia Status>)
 
+The variable natural_id comunicates to the engine an index that uniquely identifies the grid cell it is solving the problem for. (This is intended mostly for debugging purposes on the Alquimia/Engine side.)
 
 Alquimia: Get Auxiliary Output
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~