Direct radiative effects of airborne microplastics

Authors: Laura E. Revell¹, Peter Kuma^1,*, Eric C. Le Ru², Walter R. C. Somerville², Sally K. Gaw¹

¹School of Physical and Chemical Sciences, University of Canterbury, Christchurch 8140, New Zealand.
²The MacDiarmid Institute for Advanced Materials and Nanotechnology, School of Chemical and Physical Sciences, Victoria University of Wellington, Wellington 6140, New Zealand.
^*Now at: Department of Meteorology, Stockholm University, Stockholm SE-106 91, Sweden.

This repository contains programs and data accompanying the paper by Revell et al. (2021), "Direct radiative effects of airborne microplastics".

Requirements

The programs contained in this repository can be run on a Linux distribution. They have been tested on the Devuan GNU/Linux 3 (beowulf) Linux distribution with Python 3.7.3. The original versions of Python packages used to run the Python scripts are available from the Python Package Index (PyPI):

numpy 1.20.1
scipy 1.6.1
matplotlib 3.3.4
basemap 1.2.2
cartopy 0.18.0
aquarius-time 0.1.0
pst-format 1.1.1
ds-format 1.1.0

It is possible to install these packages inside a Python Virtual Environment (venv) with the command pip3 install -r requirements.txt. See Python documentation on how to set up a virtual environment.

Equivalent Linux distributions such as Ubuntu or Fedora may work equally well. On Windows, the Windows Subsystem for Linux (WSL) with the Ubuntu distribution (available from the Microsoft Store), is recommended for running the programs.

The run_cscatter and run_cscatter_average programs depend on the SOCRATES radiative transfer code, which is only available to the Unified Model (UM) Partnership members.

To calculate the optical properties of fibres, R is required (tested on 4.0.2), as well as MATLAB or octave. The R package provided in fibre_optical_property_scripts/Rpathlength_1.1.1.tar.gz should be installed.

CIRC cases

Continual Intercomparison of Radiation Codes (CIRC) cases are located in data/circ. Each case contains files extracted from the original input and output archives of the CIRC case. To process case data and run SOCRATES, use the following sequence of programs:

convert_circ_levels: Convert levels txt file to NetCDF.
prepare_socrates: Prepare SOCRATES profiles of MP mixing ratio and get MP aerosol blocks to be inserted into sp_sw_ga7 and sp_lw_ga7.
run_socrates: Run the single column model.
plot_profile_all: Plot the resulting flux and heating rate profiles.

See examples in each program documentation below on how to run it.

Programs (`bin`)

Below is a list of programs contained in this repository with a brief description of how to use them. The programs can be executed from the UNIX command line from the main directory as bin/<program> <arg>..., where <program> is the name of the program and <arg> are command-line arguments of the program, documented below.

calc_rad_eff

Calculate radiative effect.

Usage: calc_rad_eff <input1> <input2> <output> <plot>

Arguments:

input1: HadGEM output 1 (directory with NetCDF files).
input2: HadGEM output 2 (directory with NetCDF files).
output: Output file (NetCDF)
plot: Output plot file prefix.

confidence_intervals

Calculate and print confidence intervals from yearly HadGEM3 model output files.

Usage: confidence_intervals <input>

Arguments:

input: Input yearly files (NetCDF). The files should contain rsut_cs2, rlut_cs2, lat and lon variables.

convert_circ_levels

Convert CIRC level_input_case<i>.txt file to NetCDF.

Usage: convert_circ_levels <input> <output>

Arguments:

input: Input file (txt). This should be the level_input_case<n>.txt file.
output: Output file (NetCDF).

Examples:

Convert CIRC case levels to NetCDF.

for i in {1..7}; do bin/convert_circ_levels data/circ/case"$i"/level_input_case"$i".txt data/circ/case"$i"/level_input_case"$i".nc; done

convert_size_dist

Convert size distribution CSV file to NetCDF.

Usage: convert_size_dist <input> <output>

Arguments:

input: Input file (CSV).
output: Output file (NetCDF).

Examples:

Convert size distribution in allen2019_fibers.csv to allen2019_fibers.nc.

bin/convert_size_dist data/size_dist/allen2019_fibers.{csv,nc}

create_size_dist

Create theoretical size distribution.

Usage: create_size_dist <type> <p1> <p2> <output>

Arguments:

type: Distribution type ("gamma").
p1: Parameter 1 (shape).
p2: Parameter 2 (scale in um).
output: Output file (NetCDF).

Examples:

Create size distribution for fibers, films and fragments.

bin/create_size_dist gamma 2.5 250 plot/size_dist_theor/gamma_fibers.nc
bin/create_size_dist gamma 1.5 20 plot/size_dist_theor/gamma_films.nc
bin/create_size_dist gamma 2 15 plot/size_dist_theor/gamma_fragments.nc

gen_refractive_index

Generate theoretical refractive index for use with Cscatter.

Usage: gen_refractive_index <A> <B> <c0> ... <cn>

Arguments:

A, B: Coefficients of the real part.
c0, ..., cn: Coefficients of the imaginary part (n-th order polynomial).

Examples:

Generate refractive index with coefficients as in the paper.

bin/gen_refractive_index 1.41 1.06e-7 552.717 458.983 140.513 18.8141 0.926965 \
> data/cscatter/refract

plot_abs_sca [Figure 2]

Plot absorption and scattering of microplastics.

Usage: plot_abs_sca <input> <output>

Arguments:

input: Input directory with input files (txt).
output: Output plot (PDF).

Example:

Plot absorption and scattering based on txt files in data/opt_prop.

bin/plot_abs_sca data/opt_prop 'plot/Microplastics optical properties.pdf'

plot_color [Extended Data Figure 6]

Plot microplastics color.

Usage: plot_color <input>... <output>

Arguments:

input: Input file (CSV).
output: Output plot file (PDF).

Examples:

Plot microplastics color from source files in data/color.

bin/plot_color data/color/*.csv 'plot/Microplastics colour.pdf'

plot_composition [Extended Data Figure 1]

Plot microplastics composition.

Usage: plot_composition <input> <output> <title>

Arguments:

input: Input file (CSV).
output: Output plot file (PDF).
title: Plot title.

Examples:

Plot composition of fibers and fragments from source files in data/composition.

bin/plot_composition data/composition/fibers.csv 'plot/Microplastics composition fibers.pdf' fibers
bin/plot_composition data/composition/fragments.csv 'plot/Microplastics composition fragments.pdf' fragments

plot_concentration

Plot microplastics concentration.

Usage: plot_concentration <input> <output>

Arguments:

input: Input file (CSV).
output: Output plot file (PDF).

Examples:

Plot microplastics concentration from a source CSV file data/concentration/concentration.csv.

bin/plot_concentration data/concentration/concentration.csv \
'plot/Microplastics concentration.pdf'

plot_fibers [Extended Data Figure 7]

Plot fiber diameter-to-length ratio.

Usage: plot_fibers <input> <output>

Arguments:

input: Input file (CSV).
output: Output plot file (PDF).

Examples:

bin/plot_fibers data/fibers/bergmann2019.csv 'plot/Fibers aspect ratio.pdf'

plot_fibers_regime

Plot scattering regime of fibers.

Usage: plot_fiber_regime <output>

Arguments:

output: Output filename (PDF).

Examples:

Plot scattering regime of fibers.

bin/plot_fiber_regime 'plot/Scattering regime of fibers.pdf'

plot_map [Figure 1]

Plot MP concentration map.

Usage: plot_map <output>

Arguments:

output: Output plot (PDF).

Examples:

Plot MP concentration map in "plot/Microplastics concentration map.pdf".

bin/plot_map 'plot/Microplastics concentration map.pdf'

plot_morphotype [Extended Data Figure 4]

Plot microplastics shape distribution.

Usage: plot_morphotype <input> <output>

Arguments:

input: Input file (CSV).
output: Output plot file (PDF).

Examples:

Plot microplastics shape from a source CSV file data/morphotype/morphotype.csv.

bin/plot_morphotype data/morphotype/morphotype.csv 'plot/Microplastics morphotype.pdf'

plot_mp_rf [Figure 3]

Plot microplastics radiative forcing.

Usage: plot_mp_rf <output>

Arguments:

output: Output plot (PDF).

Examples:

bin/plot_mp_rf 'plot/Microplastics RF.pdf'

plot_opt_prop

Plot optical properties (absorption and scattering cross section) from Cscatter data.

Usage: plot_opt_prop <input> <output>

Arguments:

input: Input file (output of Cscatter).
output: Output plot (PDF).

Examples:

Plot optical properties of fragments.

bin/plot_opt_prop data/cscatter/opt_prop_fragments \
'plot/Optical properties fragments.pdf'

plot_profile_all

Plot flux profiles of multiple CIRC cases.

Usage: plot_profile_all <input>... <type> <output> <title>

Arguments:

input: Input directory.
type: Profile type.
output: Output plot file (PDF).
title: Plot title.

Examples:

Plot profiles of CIRC cases for fragments.

bin/plot_profile_all data/circ/case* fragments 'plot/CIRC fragments.pdf' 'Microplastic fragments: 100 MP m-3' > 'csv/CIRC fragments.csv'
bin/plot_profile_all data/circ/case* fibers 'plot/CIRC fibers.pdf' 'Microplastic fibers: 100 MP m-3' > 'csv/CIRC fibers.csv'
bin/plot_profile_all data/circ/case* fibers_and_fragments 'plot/CIRC fibers and fragments.pdf' 'Microplastics combined: 100 MP m-3' > 'csv/CIRC fibers and fragments.csv'
bin/plot_profile_all data/circ/case* fibers_and_fragments_2km 'plot/CIRC fibers and fragments (2 km).pdf' 'Microplastics boundary layer: 100 MP m-3' > 'csv/CIRC fibers and fragments (2 km).csv'

plot_refractive_index [Extended Data Figure 5]

Plot refractive index of polymers.

Usage: plot_refractive_index <input>... <output>

Arguments:

input: Input file (CSV).
output: Output plot file (PDF).

Examples:

bin/plot_refractive_index data/refractive_index/*.csv \
'plot/Refractive index.pdf'

plot_size_dist [Extended Data Figure 2 and 3]

Plot particle size distribution.

Usage: plot_size_dist <input>... <output> <title> <max_x>

Arguments:

input: Input file (NetCDF).
output: Output file (PDF).
title: Plot title.
max_x: Upper size limit (um).

Examples:

Plot size distribution of fibers and fragments from source files in data/size_dist.

bin/plot_size_dist data/size_dist/fibers/*.nc 'plot/Microplastics size distribution fibers.pdf' fibers 4000
bin/plot_size_dist data/size_dist/fragments/*.nc 'plot/Microplastics size distribution fragments.pdf' fragments 400

prepare_cscatter

Prepare input for Cscatter_average from a CSV file. The output is printed to the standard output.

Usage: prepare_cscatter <input>

Arguments:

input: Input file with absorption and scattering coefficients and asymmetry factor per wavelength (CSV). The CSV file should contain a header line and the following columns:
1. wavelength (m)
2. absorption coefficient (m^-1)
3. scattering coefficient (m^-1)
4. asymmetry factor (1)

Examples:

Prepare Cscatter_average input for fibers.

bin/prepare_cscatter data/opt_prop_fibers/fibers.csv > data/cscatter/opt_prop_fibers

prepare_ea

Prepare EasyAerosol input files (NetCDF). The files are saved in the current directory.

Usage: prepare_ea <orog> <opt>

Arguments:

orog: HadGEM orography file (NetCDF).
opt: Optical properties (py).

Examples:

Prepare EasyAerosol input files for fibers.

bin/prepare_ea data/orography/qrparm.orog.nc data/ea/fibers.py

Prepare EasyAerosol input files for fibers and fragments.

bin/prepare_ea data/orography/qrparm.orog.nc data/ea/fibers_and_fragments.py

Prepare EasyAerosol input files for fibers with peaks in refractive index.

bin/prepare_ea data/orography/qrparm.orog.nc data/ea/fibers_peak.py

Prepare EasyAerosol input files for fragments.

bin/prepare_ea data/orography/qrparm.orog.nc data/ea/fragments.py

prepare_socrates

Prepare SOCRATES aerosol file. Spectra blocks for shortwave and longwave and printed to the standard output.

Usage: prepare_socrates <opt> <levels> <output>

Arguments:

opt: Optical properties file (py).
levels: Atmosphere levels file (NetCDF). This file should contain variables zhalf, phalf and ta.
output: Output file - common for shortwave and longwave (NetCDF).

Examples:

Prepare SOCRATES profiles for CIRC cases. The standard output blocks should be inserted in the data/circ/common/sp_{sw,lw}_ga7_<type> spectral files. These should be otherwise the same as the original sp_{sw,lw}_ga7 files.

for i in {1..7}; do bin/prepare_socrates data/ea/fragments.py data/circ/case"$i"/level_input_case"$i".nc data/circ/case"$i"/case"$i".fragments.nc; done
for i in {1..7}; do bin/prepare_socrates data/ea/fibers.py data/circ/case"$i"/level_input_case"$i".nc data/circ/case"$i"/case"$i".fibers.nc; done
for i in {1..7}; do bin/prepare_socrates data/ea/fibers_and_fragments.py data/circ/case"$i"/level_input_case"$i".nc data/circ/case"$i"/case"$i".fibers_and_fragments.nc; done
for i in {1..7}; do bin/prepare_socrates data/ea/fibers_and_fragments_2km.py data/circ/case"$i"/level_input_case"$i".nc data/circ/case"$i"/case"$i".fibers_and_fragments_2km.nc; done

run_cscatter

Run Cscatter to calculate optical properties of a given constituent. The output is saved in data/cscatter/opt_prop_<type>.

Usage: run_cscatter <type>

Arguments:

type: Type of constituent (one of: "fragments", "fragments_fit")

Examples:

Calculate optical properties of fragments.

bin/run_cscatter fragments

Calculate optical properties of fragments (fit).

bin/run_cscatter fragments_fit

run_cscatter_average

Run Cscatter_average to calculate optical properties of a given constituent averaged on model spectral bands. The output is saved in data/cscatter/avg_sw_<type> and data/cscatter/avg_lw_<type>.

Usage: run_cscatter <type>

Arguments:

type: Type of constituent (one of: "fibers", "fragments", "fragments_fit").

Examples:

Calculate averaged optical properties of fibers.

bin/run_cscatter_average fibers

Calculate averaged optical properties of fragments.

bin/run_cscatter_average fragments

Calculate averaged optical properties of fragments (fit).

bin/run_cscatter_average fragments_fit

run_socrates

Run SOCRATES on CIRC case.

Usage: bin/run_socrates <dir> <n>

Arguments:

dir: Directory with the CIRC case.
n: Case number.

Examples:

Run SOCRATES for the 7 CIRC cases.

for i in {1..7}; do echo "$i"; bin/run_socrates data/circ/case"$i" "$i"; done

Data (`data`)

Below is a list of data files contained in the data directory with a brief description of their meaning.

circ: CIRC cases for running a single column model.
color: Microplastics color distributions sourced from past studies.
composition: Microplastics composition sourced from past studies.
morphotype: Microplastics morphotype sourced from past studies.
cscatter: SOCRATES Cscatter and Cscatter_average input and output files.
ea: EasyAerosol optical properties for use with prepare_ea.
fibers: Microplastic fibers length-diameter size distribution sourced from past studies.
opt_prop: Optical properties of fragments and fibers.
opt_prop_fibers: Optical properties of fibers.
orography: HadGEM3 orography.
refractive_index: Refractive index of polymers sourced from past studies.
size_dist: Microplastic size distributions sourced from past studies.

Plots (`plot`)

The directory plot contains plots generated with the programs contained in this repository. Plots which appear in the paper Revell et al. (2021) are not included in the directory for licensing reasons, but they can be generated with the programs described above (annotated with the figure number).

Fibre optical properties (`fibre_optical_property_scripts`)

As provided the scripts are configured for octave, fibre_optical_property_scripts/RunLSA.sh should have octave lines commented and matlab lines uncommented to use MATLAB. The script fibre_optical_property_scripts/RunLSA.sh will perform all of the necessary calculations. A brief outline of the files included follows.

calculate_single_wavelength_size_fibre.m: MATLAB/octave script that calculates the optical properties for a fibre in the large size approximation.
combine_csv.sh: Shell script to combine many output files into a single file.
create_input_parameters.m: MATLAB/octave script to write parameters of interest into a file.
create_lsa_script.r: R script that creates a MATLAB/octave script to run calculate_single_wavelength_size_fibre.m with appropriate parameters.
epsPETfit.m: Dielectric function of PET for calculations.
generate_values_for_interpolation.r: R script that runs ray tracing simulations to obtain values needed in fibre calculations. This script takes significant time to run.
interpolate_ray_tracing_quantities.m: MATLAB/octave script that interpolates output of generate_values_for_interpolation.r.
Rpathlength_1.1.1.tar.gz: R package for running ray tracing simulations.
RunLSA.sh: Shell script that runs all other scripts as needed, and outputs into LSA_all_results.csv.
save_lsa_script.r: R script that is used to save the output of create_lsa_script.r to a file, and print the filename.

License

The programs distributed in this repository are available under the terms of an MIT License.

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

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Direct radiative effects of airborne microplastics

Requirements

CIRC cases

Programs (`bin`)

calc_rad_eff

confidence_intervals

convert_circ_levels

convert_size_dist

create_size_dist

gen_refractive_index

plot_abs_sca [Figure 2]

plot_color [Extended Data Figure 6]

plot_composition [Extended Data Figure 1]

plot_concentration

plot_fibers [Extended Data Figure 7]

plot_fibers_regime

plot_map [Figure 1]

plot_morphotype [Extended Data Figure 4]

plot_mp_rf [Figure 3]

plot_opt_prop

plot_profile_all

plot_refractive_index [Extended Data Figure 5]

plot_size_dist [Extended Data Figure 2 and 3]

prepare_cscatter

prepare_ea

prepare_socrates

run_cscatter

run_cscatter_average

run_socrates

Data (`data`)

Plots (`plot`)

Fibre optical properties (`fibre_optical_property_scripts`)

License

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Name		Name	Last commit message	Last commit date
Latest commit History 1 Commit
bin		bin
csv		csv
data		data
fibre_optical_property_scripts		fibre_optical_property_scripts
plot		plot
.editorconfig		.editorconfig
README.md		README.md
requirements.txt		requirements.txt

peterkuma/microplastics2021

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Direct radiative effects of airborne microplastics

Requirements

CIRC cases

Programs (bin)

calc_rad_eff

confidence_intervals

convert_circ_levels

convert_size_dist

create_size_dist

gen_refractive_index

plot_abs_sca [Figure 2]

plot_color [Extended Data Figure 6]

plot_composition [Extended Data Figure 1]

plot_concentration

plot_fibers [Extended Data Figure 7]

plot_fibers_regime

plot_map [Figure 1]

plot_morphotype [Extended Data Figure 4]

plot_mp_rf [Figure 3]

plot_opt_prop

plot_profile_all

plot_refractive_index [Extended Data Figure 5]

plot_size_dist [Extended Data Figure 2 and 3]

prepare_cscatter

prepare_ea

prepare_socrates

run_cscatter

run_cscatter_average

run_socrates

Data (data)

Plots (plot)

Fibre optical properties (fibre_optical_property_scripts)

License

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Contributors 2

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Programs (`bin`)

Data (`data`)

Plots (`plot`)

Fibre optical properties (`fibre_optical_property_scripts`)