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gpkde

Fortran Code for Grid Projected Kernel Density Estimation of Discrete Particle Distributions Continuous Integration

Overview

The program performs Grid Projected Kernel Density Estimation (GPKDE) of a discrete dataset in one, two or three dimensional domains and is parallelized with the OpenMP library.

It works as a standalone program by reading an input simulation file, which configures the loading of a source file with data points and additional parameters for defining the reconstruction grid and the optimization for bandwidth selection.

Build

Get the code

Clone the repository

git clone https://github.com/upc-ghs/gpkde.git

Makefile

Repository includes two makefiles at the folder make:

  • Makefile: for the gfortran compiler, with compilation verified for gfortran>=8.4.0.
  • Makefile-ifort: for the ifort compiler, with compilation verified for ifort@2021.9.0.

Note: The preprocessor variable -DREAL32 can be added to the compiler flags in order to build with single precision floating point. Compilation via makefiles create the folder make/objtemp. It is recommended to remove this folder while developing source code or integrating program changes for a consistent compilation.

Meson

The project can also be built with the meson build system:

  • Setup the project configuration
    meson setup builddir -Ddebug=false --prefix=$(pwd) --libdir=bin
  • Compile
    meson install -C builddir
  • Basic tests
    meson test --verbose --no-rebuild -C builddir

Note: For building with single precision floating point, the option --Dreal32=true can be given to the setup instruction.

Visual Studio and Windows

The folder msvs contains the project and solution files verified for Visual Studio 2019 and 2022 on a Windows system. An executable file and complementary dll's providing the OpenMP library are available at the folder wbin/. Users can make easy use of these files at a system level by extending the PATH environment variable, adding their specific address to the wbin/ folder (as here or here).

The necessary dll's can also be installed from the Intel and Visual Studio redistributables (x64), respectively:

Note: The windows executable gpkdesp.exe is built with single precision floating point (/DREAL32) which requires less memory specially for large three dimensional problems. This option is enabled by default in the Visual Studio solution/project files and can be disabled by modifying the project properties, leaving empty the field Project>Properties>Fortran>Preprocessor>Preprocessor Definitions. The executable gpkde.exe is built with double precision floating point.

Command line interface

Some basic command line arguments have been implemented in order to control program execution. These can be requested as help with the instruction gpkde --help or gpkde -h, which displays the following message in console:

GPKDE version *.*.*               
Program compiled Apr 12 2023 19:44:24 with GFORTRAN compiler (ver. *.*.*)       

Fortran code for Grid Projected Kernel Density Estimation of discrete particle distributions

usage:

  gpkde [options] simfile

options:

  -h         --help                Show this message                             
  -l  <str>  --logname    <str>    Write program logs to <str>                   
  -nl        --nolog               Do not write log file                         
  -np <int>  --nprocs     <int>    Run with <int> processes                      
  -p         --parallel            Run in parallel                               
  -v         --version             Show program version                          

For bug reports and updates, follow:                                             
  https://github.com/upc-ghs/gpkde

Simulation file

For details about the configuration of input files please refer to the program Documentation.

Examples

A set of possible use cases of the reconstruction module are included as example files in this repository. The currently available simulations include:

License

MIT License

References

Pérez-Illanes R., Fernàndez-Garcia, D., 2024, A General Purpose Parallel Fortran Code for Grid Projected Concentration Reconstruction from Multidimensional Particle Distributions, Environmental Modelling & Software, doi: 10.1016/j.envsoft.2024.106008.

Resources