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hctorreshctorres
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Added utility to write plotflile to hdf5. Added script to plot hdf5 file using matplotlib. Added run script to automate converting all the plotfiles in a directory and plotting them.
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‎swm_AMReX/plotting_utils/GNUmakefile

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# AMREX_HOME defines the directory in which we will find all the AMReX code.
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AMREX_HOME ?= PROVIDE_YOUR_OWN_PATH_TO_AMREX_HERE
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HDF5_HOME ?= PROVIDE_YOUR_OWN_PATH_TO_HDF5_HERE
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DEBUG = FALSE
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USE_MPI = TRUE # Dont really nedd MPI for the program but I am using an hdf5 that needs MPI
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USE_OMP = FALSE
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COMP = gnu
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DIM = 2
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USE_HDF5 = TRUE
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include $(AMREX_HOME)/Tools/GNUMake/Make.defs
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include ./Make.package
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## Set the target name explicitly
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#TARGET = plotfile2hdf5
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## Set the target name explicitly
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#EXEC = plotfile2hdf5
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#
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#executable = plotfile2hdf5.exe
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include $(AMREX_HOME)/Src/Base/Make.package
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vpath %.c : . $(vpathdir)
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vpath %.h : . $(vpathdir)
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vpath %.cpp : . $(vpathdir)
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vpath %.H : . $(vpathdir)
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vpath %.F : . $(vpathdir)
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vpath %.f : . $(vpathdir)
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vpath %.f90 : . $(vpathdir)
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include $(AMREX_HOME)/Tools/GNUMake/Make.rules

‎swm_AMReX/plotting_utils/Make.package

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#CEXE_sources += plotfile2hdf5.cpp
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CEXE_sources += main.cpp
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# Executable name
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#EXE = plotfile2hdf5

‎swm_AMReX/plotting_utils/convert_to_hdf5_and_plot.sh

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#!/bin/bash
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# This script is used to convert all AMReX plotfiles in a specified directory to HDF5 format
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# and then plot the hdf5 files using matplotlib.
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###############################################################################
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# User Input
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###############################################################################
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plotfile2hdf5_exe="$SWM_AMREX_ROOT"/plotting_utils/main2d.gnu.MPI.ex
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# Input directory argument must be provided
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if [ -z "$1" ]; then
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echo "Usage: $0 <directory with amrex plotfiles of the form plt_*>"
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exit 1
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fi
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# Set the directory to the provided argument
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input_directory="$1"
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# Remove trailing slash from input_directory if it exists... so the pattern in the for loop below works
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input_directory="${input_directory%/}"
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###############################################################################
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set -u
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set -e
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# Convenience function to print 80 character wide banners with centered text
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print_banner() {
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local message="$1"
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local border_char="#"
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local width=80
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local padding=$(( (width - ${#message} - 2) / 2 ))
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local border=$(printf "%-${width}s" | tr ' ' "$border_char")
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echo -e "\n$border"
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printf "%*s %s %*s\n" $padding "" "$message" $padding ""
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echo -e "$border\n"
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}
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# Loop over all files that start with plt_ followed by a series of numbers in the specified directory
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for infile in "$input_directory"/plt[0-9]*; do
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# Skip files that contain .old or .h5
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if [[ "$infile" == *".old"* || "$infile" == *".h5"* ]]; then
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continue
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fi
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print_banner "Converting $infile to HDF5 and Plotting"
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# Plotfiles are actually directories. Check that infile is a directory
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if [[ -d "$infile" ]]; then
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# Set the outfile name to the same as infile but with .h5 extension
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hdf5_file="${infile}.h5"
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# Run the program with the infile and outfile arguments
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"$plotfile2hdf5_exe" infile="$infile" outfile="$hdf5_file"
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fi
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python "$SWM_AMREX_ROOT"/plotting_utils/plot_hdf5.py "$hdf5_file" --output_dir "$input_directory"
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done

‎swm_AMReX/plotting_utils/main.cpp

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#include <string>
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#include <AMReX.H>
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#include <AMReX_ParmParse.H>
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#include <AMReX_PlotFileUtil.H>
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#include <AMReX_MultiFab.H>
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#include <hdf5.h>
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void WriteMultiFabToHDF5(const std::string& plotfile, const std::string& hdf5file) {
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amrex::PlotFileData plotfile_data(plotfile);
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amrex::Vector<std::string> varnames = plotfile_data.varNames();
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double time = plotfile_data.time();
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int time_step = plotfile_data.levelStep(0);
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amrex::MultiFab mf;
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amrex::VisMF::Read(mf, plotfile+"/Level_0/Cell");
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amrex::BoxArray ba = mf.boxArray();
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// Expecting a cell centered box with low and high index bounds {0,0} to {nx-1,ny-1}
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amrex::Box minimal_box = ba.minimalBox();
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AMREX_ASSERT(minimal_box.smallEnd(0) == 0);
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AMREX_ASSERT(minimal_box.smallEnd(1) == 0);
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hid_t file_id = H5Fcreate(hdf5file.c_str(), H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
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{
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hid_t attr_space_id = H5Screate(H5S_SCALAR);
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hid_t attr_id = H5Acreate(file_id, "time", H5T_NATIVE_DOUBLE, attr_space_id, H5P_DEFAULT, H5P_DEFAULT);
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H5Awrite(attr_id, H5T_NATIVE_DOUBLE, &time);
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H5Aclose(attr_id);
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H5Sclose(attr_space_id);
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}
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{
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hid_t attr_space_id = H5Screate(H5S_SCALAR);
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hid_t attr_id = H5Acreate(file_id, "time_step", H5T_NATIVE_INT, attr_space_id, H5P_DEFAULT, H5P_DEFAULT);
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H5Awrite(attr_id, H5T_NATIVE_INT, &time_step);
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H5Aclose(attr_id);
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H5Sclose(attr_space_id);
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}
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// Get the dimensions of the MultiFab
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hsize_t dims[2] = {static_cast<hsize_t>(minimal_box.length(0)), static_cast<hsize_t>(minimal_box.length(1))};
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// Iterate over the components of the MultiFab
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for (int component_idx = 0; component_idx < mf.nComp(); ++component_idx) {
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// Create a dataset for this component
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hid_t dataspace_id = H5Screate_simple(2, dims, NULL);
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hid_t dataset_id = H5Dcreate(file_id, varnames[component_idx].c_str(), H5T_NATIVE_DOUBLE, dataspace_id, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
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// Write the data to the dataset
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for (amrex::MFIter mfi(mf); mfi.isValid(); ++mfi) {
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const amrex::Box& bx = mfi.validbox();
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const amrex::Array4<const amrex::Real> &fab = mf.array(mfi);
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std::vector<double> data(bx.numPts());
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int idx = 0;
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for (int j = bx.smallEnd(1); j <= bx.bigEnd(1); ++j) {
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for (int i = bx.smallEnd(0); i <= bx.bigEnd(0); ++i) {
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data[idx++] = fab(i, j, 0, component_idx);
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}
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}
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H5Dwrite(dataset_id, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, data.data());
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}
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H5Dclose(dataset_id);
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H5Sclose(dataspace_id);
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}
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H5Fclose(file_id);
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}
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int main(int argc, char* argv[]) {
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amrex::Initialize(argc, argv);
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// Read in parameters from inputs file
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amrex::ParmParse pp;
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// Read in plotfile name
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std::string plotfile;
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pp.query("infile", plotfile);
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if (plotfile.empty()) {
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amrex::Abort("You must specify `infile'");
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}
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// Read in optional output hdf5 file name
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// Output hdf5 file (default to input plotfile name with .h5 extension)
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std::string hdf5file = plotfile + ".h5";
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pp.query("outfile", hdf5file);
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amrex::Print() << "Input Plotfile: " << plotfile << std::endl;
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WriteMultiFabToHDF5(plotfile, hdf5file);
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amrex::Print() << "Output HDF5 file: " << hdf5file << std::endl;
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amrex::Finalize();
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return 0;
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}

‎swm_AMReX/plotting_utils/plot_hdf5.py

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import argparse
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import os
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import h5py
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import numpy as np
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import matplotlib.pyplot as plt
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if __name__ == "__main__":
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parser = argparse.ArgumentParser(description='Read datasets from an HDF5 file. Save a plot of each dataset as a PNG file.')
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parser.add_argument('hdf5file', type=str, help='Path to the HDF5 file to read.')
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parser.add_argument('--output_dir', type=str, default=os.getcwd(), help='Directory to save the output PNG files to.')
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args = parser.parse_args()
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title_fontsize = 18
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label_fontsize = 12
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with h5py.File(args.hdf5file, 'r') as f:
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# Read the time attribute
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time_step = f.attrs['time_step']
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time = f.attrs['time']
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# Iterate over all datasets in the file
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for dataset_name in f:
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dataset = f[dataset_name]
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data = dataset[:]
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data_2d = np.array(data).reshape(dataset.shape)
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plt.figure()
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plt.imshow(data_2d, aspect='auto', cmap='viridis')
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plt.colorbar()
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plt.title(f"${dataset_name}$", fontsize=title_fontsize)
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plt.xlabel('$x$', fontsize=label_fontsize)
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plt.ylabel('$y$', fontsize=label_fontsize)
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# Print time step in the top left corner
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plt.gcf().text(0, 1.01,
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f"Time Step: {time_step}",
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transform=plt.gca().transAxes,
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fontsize=label_fontsize,
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verticalalignment='bottom',
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horizontalalignment='left')
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# Print time in the top right corner
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plt.gcf().text(1.00, 1.01,
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f"Time: {time}",
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transform=plt.gca().transAxes,
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fontsize=label_fontsize,
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verticalalignment='bottom',
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horizontalalignment='right')
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output_file = os.path.join(args.output_dir, f"{dataset_name}_{time_step:05d}.png")
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plt.savefig(output_file)
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print(f"Saved plot to {output_file}")

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