Fix checkpoint value parsing

CHANGELOG.md

@@ -2,6 +2,8 @@
 
 ## Develop
 
+- Fixed checkpoint JSON parameter parsing and their documentation. The
+  `output_checkpoints` parameter no longer has a default value.
 - Added `vector_list_t` and `name` to `vector_t`.
 - Rework hash table iterators, significantly faster (O(tsize) => O(entries)
 - Remove redundant directory in `site-packages` when installing pyneko
@@ -14,10 +16,10 @@
 - Support for user-defined scalar schemes are now added.
 - Added source term for direct forcing from a field defined in the registry.
 - Add description of the `fld` file format to the documentation.
-- Added possibility to assign names to boundary conditions in the case file. The 
+- Added possibility to assign names to boundary conditions in the case file. The
   `bc_list_t` now supports item retrieval by name or zone_index.
-- Runtime statistics fields are now retrievable from the registry, for both 
-  fluid_stats and user_stats. The naming convention of the fields in the 
+- Runtime statistics fields are now retrievable from the registry, for both
+  fluid_stats and user_stats. The naming convention of the fields in the
   registry is `name_of_simcomp + "/mean_" + name_of_field`.
 - Updated field types with a wrapper and ensure lifetime management of field
   data in field lists and arrays.

doc/pages/user-guide/case-file.md

@@ -80,17 +80,46 @@ but also defines several parameters that pertain to the simulation as a whole.
 | `output_layout`       | Data layout for `adios2` files. (Choose `2` or `3` for ADIOS2 supported compressors BigWhoop or ZFP.) | Positive integer `1`, `2`, `3`                  | `1`           |
 | `load_balancing`      | Whether to apply load balancing.                                                                      | `true` or `false`                               | `false`       |
 | `output_partitions`   | Whether to write a `partitions.vtk` file with domain partitioning.                                    | `true` or `false`                               | `false`       |
-| `output_checkpoints`  | Whether to output checkpoints, i.e. restart files.                                                    | `true` or `false`                               | `false`       |
+| `output_checkpoints`  | Whether to output checkpoints, i.e. restart files.                                                    | `true` or `false`                               | -       |
 | `checkpoint_control`  | Defines the interpretation of `checkpoint_value` to define the frequency of writing checkpoint files. | `nsamples`, `simulationtime`, `tsteps`, `never` | -             |
 | `checkpoint_value`    | The frequency of sampling in terms of `checkpoint_control`.                                           | Positive real or integer                       | -             |
 | `checkpoint_filename` | The filename of written checkpoint.                                                                   | Strings such as `my_name`                       | `fluid`       |
 | `checkpoint_format`   | The file format of checkpoints                                                                        | `chkp` or `hdf5`                                | `chkp`        |
 | `restart_file`        | checkpoint to use for a restart from previous data                                                    | Strings ending with `.chkp`                     | -             |
 | `restart_mesh_file`   | If the restart file is on a different mesh, specify the .nmsh file used to generate it here           | Strings ending with `.nmsh`                     | -             |
 | `mesh2mesh_tolerance` | Tolerance for the restart when restarting from another mesh                                           | Positive reals                                  | 1e-6          |
-| `job_timelimit`       | The maximum wall clock duration of the simulation.                                                    | String formatted as HH:MM:SS                    | No limit      |
+| `job_timelimit`       | The maximum wall clock duration of the simulation.                                                   | String formatted as HH:MM:SS                    | No limit      |
 | `output_at_end`       | Whether to always write all enabled output at the end of the run.                                     | `true` or `false`                               | `true`        |
 
+Some additional practical comments are provided regarding the output triggered
+by `job_timelimit` and `output_at_end` keywords.
+
+If `output_at_end` is set to `true`, an additional write is performed after the
+execution of the simulation time-loop is finished. This triggers most outputs,
+like the fluid solvers, the checkpoint, etc. Note that if your case settings are
+such that a particular output is written at the last time step regardless of
+`output_at_end` (e.g. `end_time: 5`, `checkpoint_value: 5`,
+ `checkpoint_control: simulationtime` ) you will get two outputs with the same
+values: one from your ordinary write and one triggered by `output_at_end`.
+
+@note This has a rather detrimental effect on outputs from various
+statistics-related [simulation components](@ref simcomps). Since the collected
+statistics are reset on write, the data written by `output_at_end` will be just
+zeroes.
+
+The purpose of `job_timelimit` is to gracefully stop the simulation in a typical
+supercomputer environment, where your runtime is limited. When Neko detects that
+the time of the run exceeds the `job_timelimit`, it exits the time-loop. At this
+point, if one sets `output_at_end` to `true`, this will trigger a write as per
+usual. However, if `output_at_end` is `false`, Neko will still write a special
+checkpoint file, with the filename called `joblimit#####.chkp`. This is done so
+that the user is at least provided a restart file, and none of the computer time
+spent on the simulation is wasted. Generally, however, it is recommended to
+have `output_at_end` set to `true` in tandem with `job_timelimit`, so that what
+exactly gets written is controlled by the case file settings.
+
+
+
 ### Constants
 The `constants` array allows the user to define parameters that are global to
 the case file, and can be referred to when setting the values of other

examples/rayleigh_benard/rayleigh.case

@@ -4,6 +4,7 @@
         "mesh_file": "box.nmsh",
         "output_at_end": true,
         "output_boundary": true,
+        "output_checkpoints": false,
         "time": {
             "end_time": 100.0,
             "timestep": 0.01

src/case.f90

@@ -1,4 +1,4 @@
-! Copyright (c) 2020-2025, The Neko Authors
+! Copyright (c) 2020-2026, The Neko Authors
 ! All rights reserved.
 !
 ! Redistribution and use in source and binary forms, with or without
@@ -512,19 +512,19 @@ subroutine case_init_common(this)
             always_write_mesh = logical_val)
     end if
 
-    call json_get_or_default(this%params, 'case.fluid.output_control',&
-         string_val, 'org')
+    call json_get(this%params, 'case.fluid.output_control', string_val)
 
     if (trim(string_val) .eq. 'org') then
        ! yes, it should be real_val below for type compatibility
-       call json_get(this%params, 'case.nsamples', integer_val)
+       call json_get_or_lookup(this%params, 'case.nsamples', integer_val)
        real_val = real(integer_val, kind=rp)
        call this%output_controller%add(this%f_out, real_val, 'nsamples')
     else if (trim(string_val) .eq. 'never') then
        call this%output_controller%add(this%f_out, 0.0_rp, 'never')
     else if (trim(string_val) .eq. 'tsteps' .or. &
          trim(string_val) .eq. 'nsamples') then
-       call json_get(this%params, 'case.fluid.output_value', integer_val)
+       call json_get_or_lookup(this%params, 'case.fluid.output_value', &
+            integer_val)
        real_val = real(integer_val, kind=rp)
        call this%output_controller%add(this%f_out, real_val, string_val)
     else if (trim(string_val) .eq. 'simulationtime') then
@@ -538,19 +538,29 @@ subroutine case_init_common(this)
     !
     ! Save checkpoints (if nothing specified, default to saving at end of sim)
     !
-    call json_get_or_default(this%params, 'case.output_checkpoints',&
-         logical_val, .true.)
+    call json_get(this%params, 'case.output_checkpoints',&
+         logical_val)
     if (logical_val) then
        call json_get_or_default(this%params, 'case.checkpoint_filename', &
             name, "fluid")
        call json_get_or_default(this%params, 'case.checkpoint_format', &
             string_val, "chkp")
        call this%chkp_out%init(this%chkp, name = name,&
             path = this%output_directory, fmt = trim(string_val))
-       call json_get_or_default(this%params, 'case.checkpoint_control', &
-            string_val, "simulationtime")
-       call json_get_or_lookup_or_default(this%params, &
-            'case.checkpoint_value', real_val, 1e10_rp)
+       call json_get(this%params, 'case.checkpoint_control', &
+            string_val)
+       if (trim(string_val) .eq. 'tsteps' .or. &
+            trim(string_val) .eq. 'nsamples') then
+          call json_get_or_lookup(this%params, 'case.checkpoint_value', &
+               integer_val)
+          real_val = real(integer_val, kind=rp)
+       else if (trim(string_val) .eq. 'simulationtime') then
+          call json_get_or_lookup(this%params, 'case.checkpoint_value', &
+               real_val)
+       else if (trim(string_val) .eq. 'never') then
+          real_val = 0.0_rp
+       end if
+
        call this%output_controller%add(this%chkp_out, real_val, string_val, &
             NEKO_EPS)
     end if

tests/reframe/src/rayleigh.case.template

@@ -4,6 +4,7 @@
     "mesh_file": "box.nmsh",
     "output_at_end": true,
     "output_boundary": true,
+    "output_checkpoints": false,
     "time": {
         "end_time": 100,
         "timestep": 0.01