Merge pull request #116 from cindytsai/dim

Support Dim 2/1 and Fix Bug

Author: cindytsai

.github/workflows/unit-test.yml

@@ -105,10 +105,10 @@ jobs:
           - "-DSERIAL_MODE=ON -DINTERACTIVE_MODE=ON -DLIBYT_RUN_TEST=ON -DUSE_PYBIND11=ON"
           - "-DSERIAL_MODE=ON -DINTERACTIVE_MODE=ON -DLIBYT_RUN_TEST=ON -DUSE_PYBIND11=OFF"
         include:
-          - os: ubuntu-20.04
+          - os: ubuntu-22.04
             python_version: '3.7'
             build_options: "-DSERIAL_MODE=ON -DINTERACTIVE_MODE=ON -DLIBYT_RUN_TEST=ON -DUSE_PYBIND11=ON"
-          - os: ubuntu-20.04
+          - os: ubuntu-22.04
             python_version: '3.7'
             build_options: "-DSERIAL_MODE=ON -DINTERACTIVE_MODE=ON -DLIBYT_RUN_TEST=ON -DUSE_PYBIND11=OFF"
 

CMakeLists.txt

@@ -3,7 +3,7 @@ cmake_minimum_required(VERSION 3.15)
 # cmake-format: off
 ###### PROJECT Info #####################################################################
 project(LIBYT_PROJECT
-        VERSION 0.2.0
+        VERSION 0.3.0
         DESCRIPTION "In situ Python analysis tool using yt and Python"
 )
 

doc/Doxyfile

@@ -48,7 +48,7 @@ PROJECT_NAME           = "libyt"
 # could be handy for archiving the generated documentation or if some version
 # control system is used.
 
-PROJECT_NUMBER         = 0.2.0
+PROJECT_NUMBER         = 0.3.0
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer a

doc/conf.py

@@ -12,8 +12,8 @@
 copyright = '2024, Shin-Rong Tsai, Hsi-Yu Schive, Matthew Turk'
 author = 'Shin-Rong Tsai, Hsi-Yu Schive, Matthew Turk'
 
-version = "0.2.0"
-release = "0.2.0"
+version = "0.3.0"
+release = "0.3.0"
 
 # -- General configuration ---------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration

doc/in-situ-python-analysis/libyt-python-module.md

@@ -6,7 +6,9 @@
 import libyt
 ```
 
-> {octicon}`info;1em;sd-text-info;` `libyt` Python module is only importable during simulation runtime.
+```{note}
+`libyt` Python module is only importable during simulation runtime.
+```
 
 ## Dictionaries
 
@@ -131,7 +133,9 @@ get_field_remote(fname_list : list,
 ```
 - Usage: Return a dictionary that contains requested field data. The data is scattered in different processes. It is a collective operation.
 
-> {octicon}`alert;1em;sd-text-danger;` This is a collective operation, and it requires every MPI process to participate.
+```{attention}
+This is a collective operation, and it requires every MPI process to participate.
+```
 
 ### `get_particle_remote`
 ```python
@@ -145,6 +149,8 @@ get_particle_remote(par_dict : dict,
 ```
 - Usage: Return a dictionary that contains requested particle data. The data is scattered in different processes. It is a collective operation.
 
-> {octicon}`alert;1em;sd-text-danger;` This is a collective operation, and it requires every MPI process to participate.
+```{attention}
+This is a collective operation, and it requires every MPI process to participate.
+```
 
 > {octicon}`calendar;1em;sd-text-secondary;` [`get_field_remote`](#get_field_remote) and [`get_particle_remote`](#get_particle_remote) may be hard to use in general case, since we have to prepare those list by ourselves. We will improve this and make it general in the future.

doc/index.md

@@ -3,7 +3,7 @@ hide-toc: true
 ---
 
 # libyt Documents
-{bdg-primary}`version 0.2.0`
+{bdg-primary}`version 0.3.0`
 
 `libyt` is an open source C library for simulation. 
 It is an in situ analysis tool that allows researchers to analyze and visualize data using [`yt`](https://yt-project.org/) or other Python packages in parallel during simulation runtime.

doc/libyt-api/yt_get_gridsptr.md

@@ -12,7 +12,7 @@ One `yt_grid` contains the hierarchy of the grid, particle counts, and field dat
 
 ### Hierarchy
 - `double left_edge[3], right_edge[3]` (Default=`DBL_UNDEFINED`)
-  - Usage: Grid left and right edge in code units.
+  - Usage: Grid left and right edge in code units. If it's a 2D/1D-simulation, fill the extra dimension with `0.0` and `1.0` for left and right edge respectively.
 - `long id` (Default=`LNG_UNDEFINED`)
   - Usage: Grid global id.
   - Valid Value: It should be contiguous starting from [`index_offset`](./yt_set_parameters.md#yt_param_yt).
@@ -22,7 +22,7 @@ One `yt_grid` contains the hierarchy of the grid, particle counts, and field dat
     - Should be in between `0` and `num_grids - 1`.
     - If the grid does not have parent grid, set to `-1`.
 - `int grid_dimensions[3]` (Default=`INT_UNDEFINED`)
-  - Usage: Number of cells along each direction in [x][y][z] <--> [0][1][2] order excluding ghost cells.
+  - Usage: Number of cells along each direction in [x][y][z] <--> [0][1][2] order excluding ghost cells. If it's a 2D/1D-simulation, fill the extra dimension with `1`.
 - `int level` (Default=`INT_UNDEFINED`)
   - Usage: AMR level of the grid.
   - Valid Value:
@@ -43,7 +43,7 @@ One `yt_grid` contains the hierarchy of the grid, particle counts, and field dat
   - Usage: a struct used for wrapping existing data pointers.
   - Data member:
     - `void* data_ptr`: Data pointer.
-    - `int data_dimensions[3]`: Dimension of `data_ptr`, which is the actual dimension of this pointer. If `data_ptr` is a 1-dim array, set the last two elements to 0. (This only happens in particle data, and we aren't rely on this value to wrap the data.)
+    - `int data_dimensions[3]`: Dimension of `data_ptr`, which is the actual dimension of this pointer. If `data_ptr` is a 2/1-dim array, the extra dimension is not in use. (This happens in particle data and 2/1-dimensional simulation, and we aren't rely on this value to wrap the data.)
     - `yt_dtype data_dtype`: Data type of `data_ptr`. We only need to set `data_dtype` when this grid's data type is different from the one set in fields'.
       - Valid Value: [`yt_dtype`](./data-type.md#yt_dtype)
 

doc/libyt-api/yt_getgridinfo.md

@@ -9,21 +9,21 @@
 ```cpp
 int yt_getGridInfo_Dimensions( const long gid, int (*dimensions)[3] );
 ```
-- Usage: Get dimension of grid `gid`. `dimensions[0]` corresponds to dimension in x-axis, `dimensions[1]` corresponds to dimension in y-axis, and `dimensions[2]` corresponds to dimension in z-axis, excluding ghost cells.
+- Usage: Get dimension of grid `gid`. `dimensions[0]` corresponds to dimension in x-axis, `dimensions[1]` corresponds to dimension in y-axis, and `dimensions[2]` corresponds to dimension in z-axis, excluding ghost cells. This also works with 2/1-dimensional simulation. The extra dimension will be filled with `1`.
 - Return: `YT_SUCCESS` or `YT_FAIL`
 
 ## `yt_getGridInfo_LeftEdge`
 ```cpp
 int yt_getGridInfo_LeftEdge(const long gid, double (*left_edge)[3]);
 ```
-- Usage: Get left edge of grid `gid`. `left_edge[0]` is left edge of the grid in x-axis in code length, `left_edge[1]` for y-axis, and `left_edge[2]` for z-axis.
+- Usage: Get left edge of grid `gid`. `left_edge[0]` is left edge of the grid in x-axis in code length, `left_edge[1]` for y-axis, and `left_edge[2]` for z-axis. This also works with 2/1-dimensional simulation. The extra dimension will be filled with `0.0`.
 - Return: `YT_SUCCESS` or `YT_FAIL`
 
 ## `yt_getGridInfo_RightEdge`
 ```cpp
 int yt_getGridInfo_RightEdge(const long gid, double (*right_edge)[3]);
 ```
-- Usage: Get right edge of grid `gid`. `right_edge[0]` is right edge of the grid in x-axis in code length, `right_edge[1]` for y-axis, and `right_edge[2]` for z-axis.
+- Usage: Get right edge of grid `gid`. `right_edge[0]` is right edge of the grid in x-axis in code length, `right_edge[1]` for y-axis, and `right_edge[2]` for z-axis. This also works with 2/1-dimensional simulation. The extra dimension will be filled with `1.0`.
 - Return: `YT_SUCCESS` or `YT_FAIL`
 
 ## `yt_getGridInfo_ParentId`
@@ -63,7 +63,7 @@ int yt_getGridInfo_FieldData(const long gid, const char *field_name, yt_data *fi
 - Return: `YT_SUCCESS` or `YT_FAIL` if it cannot get data.
 - `yt_data`
     - `data_ptr`: Data pointer.
-    - `data_dimensions[3]`: Dimension of the `data_ptr` array, in the point of view of itself.
+    - `data_dimensions[3]`: Dimension of the `data_ptr` array, in the point of view of itself. If it's a 2/1-dim array, the extra dimension will be `1`.
     - `data_dtype`: Data type of the array.
 
 > {octicon}`info;1em;sd-text-info;` Field name `field_name` should be same as what you passed in [`yt_get_FieldsPtr`](./field/yt_get_fieldsptr.md#yt_get_fieldsptr).

doc/libyt-api/yt_set_parameters.md

@@ -16,7 +16,7 @@ int yt_set_Parameters( yt_param_yt *param_yt )
 - `const char* fig_basename` (Default=`"Fig"`)
   - Usage: Base name of the output figures. Figure name will also be followed by counter number and `yt` functionality name.
 - `double domain_left_edge[3], domain_right_edge[3]` (Default=`DBL_UNDEFINED`)
-  - Usage: Simulation left and right edge in code units.
+  - Usage: Simulation left and right edge in code units. If it's a 2D/1D-simulation, fill the extra dimension with `0.0` and `1.0` for left and right edge respectively.
 - `double current_time` (Default=`DBL_UNDEFINED`)
   - Usage: Simulation time in code units.
 - `double current_redshift` (Default=`DBL_UNDEFINED`)
@@ -48,10 +48,9 @@ int yt_set_Parameters( yt_param_yt *param_yt )
     - `0`: No
     - `1`: Yes
 - `int dimensionality` (Default=`INT_UNDEFINED`)
-  - Usage: Dimensionality of the simulation. 
-  > {octicon}`alert;1em;sd-text-danger;` `libyt` only support 3 for now.
+  - Usage: Dimensionality of the simulation. Support 1/2/3-dimensional simulation.
 - `int domain_dimensions[3]` (Default=`INT_UNDEFINED`)
-  - Usage: Number of cells along each dimension on the root AMR level.
+  - Usage: Number of cells along each dimension on the root AMR level. If it's a 2D/1D-simulation, fill the extra dimension with `1`.
 - `int refine_by` (Default=`INT_UNDEFINED`)
   - Usage: Refinement factor between a grid and its subgrid.
 - `int index_offset` (Default=`0`)
@@ -81,7 +80,7 @@ param_yt.mass_unit = 1.9885e33;                                      // mass uni
 param_yt.time_unit = 3.1557e13;                                      // time unit (sec)
 param_yt.velocity_unit = param_yt.length_unit / param_yt.time_unit;  // velocity unit (cm/s)
 param_yt.current_time = time;                                        // simulation time in code units
-param_yt.dimensionality = 3;                                         // dimensionality, support 3 only
+param_yt.dimensionality = 3;                                         // dimensionality
 param_yt.refine_by = REFINE_BY;                                      // refinement factor between a grid and its subgrid
 param_yt.num_grids = num_grids;                                      // number of grids
 param_yt.num_grids_local = num_grids_local;                          // number of local grids

example/amr-example/example.cpp

@@ -176,7 +176,7 @@ int main(int argc, char* argv[]) {
     param_yt.velocity_unit =
         param_yt.length_unit / param_yt.time_unit;  // velocity unit (cm/s)
     param_yt.current_time = time;                   // simulation time in code units
-    param_yt.dimensionality = 3;                    // dimensionality, support 3 only
+    param_yt.dimensionality = 3;                    // dimensionality
     param_yt.refine_by = REFINE_BY;  // refinement factor between a grid and its subgrid
     param_yt.index_offset = 1;       // grid id starts at 1. (default is 0-indexed)
     param_yt.num_grids = num_grids;  // number of grids