Merge pull request #149 from AetherModel/restart_fix

Restart fix

Author: aaronjridley

doc/installation.md

@@ -111,4 +111,4 @@ cd run.test
 The output should LOOK LIKE THIS
 
 For more details about running Aether, see the documentation about creating and
-modifying input files HERE.
+modifying input files in the document running_aether.md.

include/output.h

@@ -133,7 +133,12 @@ class OutputContainer {
      \brief write a binary file with the information in the container
    **/
   bool write_container_binary();
-  
+
+  /**********************************************************************
+     \brief read a binary file with the information into a container
+   **/
+  bool read_container_binary();
+
   /**********************************************************************
      \brief write a netcdf file with the information in the container
    **/
@@ -142,7 +147,7 @@ class OutputContainer {
   /**********************************************************************
      \brief read from a file an load into the container
    **/
-  void read();
+  bool read();
 
   /**********************************************************************
      \brief display information contained in the container
@@ -152,7 +157,7 @@ class OutputContainer {
   /**********************************************************************
      \brief read a netcdf file - put the information in the container
    **/
-  int read_container_netcdf();
+  bool read_container_netcdf();
 
   /**********************************************************************
      \brief clears the vector of variables 

include/times.h

@@ -82,6 +82,11 @@ class Times {
    **/
   double get_current();
 
+  /**************************************************************
+     \brief Sets the start time at the start of the time loop
+   **/
+  void set_start_time_loop();
+
   /**************************************************************
      \brief Returns the end time in seconds since ref date
    **/
@@ -237,6 +242,9 @@ class Times {
   /// This is the system time at the start of the simulation
   time_t sys_time_start;
 
+  /// This is the system time at the start of time loop
+  time_t sys_time_start_time_loop;
+
   /// This is the current system time of the simulation
   time_t sys_time_current;
 

share/run/UA/inputs/defaults.json

@@ -114,8 +114,8 @@
 	"species" : ["O2", "O2+"]},
 
     "Outputs" : {
-	"type" : ["neutrals"],
-	"dt" : [900, 0.0]},
+	"type" : ["states", "grid"],
+	"dt" : [900, -1]},
 
     "Restart" : {
 	"do" : false,