Lots more restructuring, cleaning, refactoring, etc. Rearranged netcd…

…f stuff to make it a bit cleaner

src/CMakeLists.txt

@@ -24,6 +24,7 @@ SET(STRICT_MATH_FILES
 SET(FAST_MATH_FILES
             ${SRC}/globals/globals_module.f90
             ${SRC}/base/base_module.f90
+            ${SRC}/netcdf_io/netcdf_io_module.f90
             ${SRC}/misc/lambda_function_module.f90
             ${SRC}/misc/io_progress_bar_module.f90
             ${SRC}/encounter/encounter_module.f90
@@ -36,16 +37,6 @@ SET(FAST_MATH_FILES
             ${SRC}/rmvs/rmvs_module.f90
             ${SRC}/helio/helio_module.f90
             ${SRC}/symba/symba_module.f90
-            ${SRC}/swiftest/swiftest_discard.f90  
-            ${SRC}/swiftest/swiftest_io.f90         
-            ${SRC}/swiftest/swiftest_obl.f90    
-            ${SRC}/swiftest/swiftest_util.f90
-            ${SRC}/swiftest/swiftest_drift.f90    
-            ${SRC}/swiftest/swiftest_io_netcdf.f90  
-            ${SRC}/swiftest/swiftest_orbel.f90
-            ${SRC}/swiftest/swiftest_gr.f90       
-            ${SRC}/swiftest/swiftest_kick.f90       
-            ${SRC}/swiftest/swiftest_setup.f90
             ${SRC}/collision/collision_check.f90  
             ${SRC}/collision/collision_regime.f90   
             ${SRC}/collision/collision_setup.f90
@@ -67,6 +58,7 @@ SET(FAST_MATH_FILES
             ${SRC}/helio/helio_setup.f90
             ${SRC}/helio/helio_step.f90
             ${SRC}/helio/helio_util.f90
+            ${SRC}/netcdf_io/netcdf_io_implementations.f90  
             ${SRC}/operator/operator_cross.f90
             ${SRC}/operator/operator_mag.f90
             ${SRC}/operator/operator_unit.f90
@@ -75,6 +67,15 @@ SET(FAST_MATH_FILES
             ${SRC}/rmvs/rmvs_setup.f90
             ${SRC}/rmvs/rmvs_step.f90
             ${SRC}/rmvs/rmvs_util.f90
+            ${SRC}/swiftest/swiftest_discard.f90  
+            ${SRC}/swiftest/swiftest_io.f90         
+            ${SRC}/swiftest/swiftest_obl.f90    
+            ${SRC}/swiftest/swiftest_util.f90
+            ${SRC}/swiftest/swiftest_drift.f90    
+            ${SRC}/swiftest/swiftest_orbel.f90
+            ${SRC}/swiftest/swiftest_gr.f90       
+            ${SRC}/swiftest/swiftest_kick.f90       
+            ${SRC}/swiftest/swiftest_setup.f90 
             ${SRC}/symba/symba_discard.f90
             ${SRC}/symba/symba_drift.f90
             ${SRC}/symba/symba_encounter_check.f90

src/collision/collision_module.f90

@@ -137,7 +137,7 @@ module collision
 
 
    !! NetCDF dimension and variable names for the enounter save object
-   type, extends(encounter_io_parameters) :: collision_io_parameters
+   type, extends(encounter_netcdf_parameters) :: collision_netcdf_parameters
       integer(I4B)       :: stage_dimid                                    !! ID for the stage dimension
       integer(I4B)       :: stage_varid                                    !! ID for the stage variable  
       character(NAMELEN) :: stage_dimname            = "stage"             !! name of the stage dimension (before/after)
@@ -154,7 +154,7 @@ module collision
       integer(I4B)       :: regime_varid               !! ID for the collision regime variable
    contains
       procedure :: initialize => collision_io_initialize_output !! Initialize a set of parameters used to identify a NetCDF output object
-   end type collision_io_parameters
+   end type collision_netcdf_parameters
 
 
    type, extends(encounter_snapshot)  :: collision_snapshot
@@ -205,7 +205,7 @@ end subroutine collision_io_dump
 
       module subroutine collision_io_initialize_output(self, param)
          implicit none
-         class(collision_io_parameters), intent(inout) :: self  !! Parameters used to identify a particular NetCDF dataset
+         class(collision_netcdf_parameters), intent(inout) :: self  !! Parameters used to identify a particular NetCDF dataset
          class(base_parameters),   intent(in)    :: param !! Current run configuration parameters  
       end subroutine collision_io_initialize_output
 

src/encounter/encounter_check.f90

@@ -43,7 +43,7 @@ module subroutine encounter_check_all_plpl(param, npl, x, v, renc, dt, nenc, ind
       !          lfirst = .false.
       !          itimer%step_counter = INTERACTION_TIMER_CADENCE
       !       else 
-      !          if (itimer%io_netcdf_check(param, nplpl)) call itimer%time_this_loop(param, nplpl)
+      !          if (itimer%netcdf_io_check(param, nplpl)) call itimer%time_this_loop(param, nplpl)
       !       end if
       !    else
       !       param%lencounter_sas_plpl = .false.
@@ -117,7 +117,7 @@ module subroutine encounter_check_all_plplm(param, nplm, nplt, xplm, vplm, xplt,
       !          lfirst = .false.
       !          itimer%step_counter = INTERACTION_TIMER_CADENCE
       !       else 
-      !          if (itimer%io_netcdf_check(param, nplplm)) call itimer%time_this_loop(param, nplplm)
+      !          if (itimer%netcdf_io_check(param, nplplm)) call itimer%time_this_loop(param, nplplm)
       !       end if
       !    else
       !       param%lencounter_sas_plpl = .false.
@@ -214,7 +214,7 @@ module subroutine encounter_check_all_pltp(param, npl, ntp, xpl, vpl, xtp, vtp,
       !          if (lsecond) then ! This ensures that the encounter check methods are run at least once prior to timing. Sort and sweep improves on the second pass due to the bounding box extents needing to be nearly sorted 
       !             call itimer%time_this_loop(param, npltp)
       !             lsecond = .false.
-      !          else if (itimer%io_netcdf_check(param, npltp)) then
+      !          else if (itimer%netcdf_io_check(param, npltp)) then
       !             lsecond = .true.
       !             itimer%is_on = .false.
       !          end if