settings.py

# -*- coding: utf-8 -*-
"""
User set variable input file for INCHEM-Py. 
A detailed description of this file can be found within the user manual.

Copyright (C) 2019-2021 
David Shaw : david.shaw@york.ac.uk
Nicola Carslaw : nicola.carslaw@york.ac.uk

All rights reserved.

This file is part of INCHEM-Py.

INCHEM-Py is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.

INCHEM-Py is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License
along with INCHEM-Py.  If not, see <https://www.gnu.org/licenses/>.

Version: 1.2.1
"""

filename = 'mcm_v331.fac' # facsimile format input filename

particles = True # Are we including particles. Boolean. Only accurate if INCHEM_additional also True

INCHEM_additional = True #Set to True if additional reactions from the INCHEM are being used
#that do not appear in the MCM download

custom = False # Custom reactions that are not in the MCM included?
# The default filename is custom_input.txt, this can be renamed to have multiple custom
# input files.
custom_filename = 'custom_input.txt'

# Temperatures are interpolated from values given here using either a linear method
# or a BSpline. Details of these methods are given in the user manual. 
# A constant temperature can also be set without interpolation.
spline = 293. # either 'BSpline', 'Linear' or a temperature in K for constant
temperatures = [[25200,288.15],[50400,294.15]] # not used if spline parameter is a numerical value
# [[time (s), temperature (K)],[time (s), temperature (K)], ...]
# Make sure the times are ascending

rel_humidity = 50.  # relative humidity
M = 2.51e+19        # number density of air (molecule cm^-3)

# place any species you wish to remain constant in the below dictionary. Follow the format
const_dict = { 
    'O2':0.2095*M,
    'N2':0.7809*M,
    'H2':550e-9*M,
    'saero':1.3e-2} #aerosol surface area concentration


"""
Outdoor indoor change rates
"""
# Dictionary of air change rates per second
# Needs to be in the format {time (s) from which ACRate should apply : ACRate}
ACRate =    {0        :   0.5/3600,
            3600 * 24:   1/3600,
            3600 * 48:   2/3600} 
diurnal = True    # diurnal outdoor concentrations. Boolean
city = "Bergen_urban" #source city of outdoor concentrations of O3, NO, NO2, and PM2.5
# options are "London_urban", "London_suburban" or "Bergen_urban"
# Changes to outdoor concentrations can be done in outdoor_concentrations.py
# See the INCHEM-Py manual for details of sources and fits


"""
Photolysis
"""
date = "21-06-2020"  # day of simulation in format "DD-MM-YYYY"
lat = 45         # Latitude of simulation location
light_type="Incand"  # Can be "Incand", "Halogen", "LED", "CFL", "UFT", "CFT", "FT", or "off"
#"off" sets all light attenuation factors to 0 and therefore no indoor lighting is present.
light_on_times=[[7,19],[31,43],[55,67],[79,91]] 
#[[light on time (hours), light off time (hours)],[light on time (hours),light_off_time (hours)],...]
glass="glass_C" # Can be "glass_C", "low_emissivity", "low_emissivity_film", or "no_sunlight".
#"no_sunlight" sets all window attenuation factors to 0 and therefore no light enters from outdoors.


"""
Surface deposition
"""
# The surface dictionary exists in surface_dictionary.py in the modules folder.
# To change any surface deposition rates of individual species, or to add species
# this file must be edited. Production rates can be added as normal reactions
# in the custom inputs file.

# Room volume (cm^3)
volume = 2.97e7

# Schemes for deposition of O3 and H2O2 are optionally provided. These schemes 
# provide calculated surface emissions proportional to O3 and H2O2 deposition
# to different surfaces. The schemes can be turned off or on below.
# Surface deposition of other species is calculates using the total of the surface 
# areas given divided by the volume. To avoid surface emissions from H2O2 and O3
# deposition then set H2O2_dep and O3_dep to False

surface_area = {          # (cm2)
    'SOFT' : 10.42e4,      # soft furnishings
    'PAINT' : 33.76e4,     # painted surfaces
    'WOOD' : 18.23e4,      # wood
    'METAL' : 7.46e4,      # metal
    'CONCRETE' : 0.391e4,  # concrete
    'PAPER' : 1.89e4,      # paper
    'LINO' : 0,            # linoleum
    'PLASTIC' : 14.18e4,   # plastic
    'GLASS' : 2.61e4,      # glass
    'HUMAN' : 0,           # humans, does not automatically include breath emissions
    'OTHER': 0}            # other surfaces, no emissions

H2O2_dep = True
O3_dep = True

'''
Breath emissions from humans
'''
adults = 0     #Number of adults in the room
children = 0   #Number of children in the room (10 years old)

"""
Initial concentrations in molecules/cm^3 saved in a text file
"""
initials_from_run = False
# initial gas concentrations can be taken from a previous run of the model. 
# Set initials_from_run to True if this is the case and move a previous out_data.pickle
# to the main folder and rename to in_data.pickle. The code will then take this
# file and extract the concentrations from the time point closest to t0 as 
# initial conditions.

# in_data.pickle must contain all of the species required, including particles if used.

# If initials_from_run is set to False then initial gas conditions must be available
# in the file specified by initial_conditions_gas, the inclusion of particles is optional.
initial_conditions_gas = 'initial_concentrations.txt'


"""
Timed concentrations
"""
timed_emissions = False # is there a species, or set of species that has a forced density change
# at a specific point in time during the integration? If so then this needs to be set to True
# and the dictionary called timed_inputs (below) needs to be populated

# When using timed emissions it's suggested that the start time and end times are divisible by dt
# and that (start time - end time) is larger then 2*dt to avoid the integrator skipping any 
# emissions over small periods of time.

# the dictionary should be populated as
# timed_inputs = {species1:[[start time (s), end time (s), rate of increase in (mol/cm^3)/s]],
#                 species2:[[start time (s), end time (s), rate of increase in (mol/cm^3)/s]]}
timed_inputs = {"LIMONENE":[[46800,47400,5e10],[107600,108000,5e8]],
                "BPINENE":[[46800,47400,5e10]]}


"""
Constrained inputs
"""
constrained_file = None
# Default value = None
# To use a constrained input = 'filename.csv'
# A csv file can be used to constrain concentrations of indoor and outdoor species, 
# J values and rates. The csv must have the first column as the time of day (s) and all
# subsequent columns must have the name of the species or variable to constrain in the
# first row with concentrations or values below in the appropriate units (molecule cm-3 for 
# species concentrations). 

# The use of this file will set the start and end of the simulation to be the start and end
# timed in the csv file. If you want to see decay from a constrained species then run one
# simulation using the constrained file and then another using the initials_from_run setting.

# example_constraints.csv gives an example of the required format of the file


"""
Integration
"""

dt = 60                        # Time between outputs (s), simulation may fail if this is too large
                                # also used as max_step for the scipy.integrate.ode integrator 
t0 = 0                          # time of day, in seconds from midnight, to start the simulation
seconds_to_integrate = 86400    # how long to run the model in seconds (86400*3 will run 3 days)


"""
Output
"""
# An output pickle file is automatically saved so that all data can be recovered
# at a later date for analysis. Applies to folder name and settings file copy name.
custom_name = "Bergen_urban"

# INCHEM-Py calculates the rate constant for each reaction at every time point
# Setting reactions_output to True saves all reactions and their assigned constant
# to reactions.pickle and adds all calculated reaction rates to the out_data.pickle
# file which will increase its size substantially. Surface deposition rates are also
# added to the out_data.pickle file for analysis.  
reactions_output = True

# This function purely outputs a graph to the 
# output folder of a list of selected species and a CSV of concentrations. 
# If the species do not exist in the run then a key error will cause it to fail
output_graph = True #Boolean
output_species = ['LIMONENE','BPINENE']


"""
Run the simulation
"""
if __name__ == "__main__":
    from modules.inchem_main import run_inchem
    run_inchem(filename, particles, INCHEM_additional, custom, rel_humidity,
               M, const_dict, ACRate, diurnal, city, date, lat, light_type, 
               light_on_times, glass, volume, initials_from_run,
               initial_conditions_gas, timed_emissions, timed_inputs, dt, t0,
               seconds_to_integrate, custom_name, output_graph, output_species,
               reactions_output, H2O2_dep, O3_dep, adults,
               children, surface_area, __file__, temperatures, spline, custom_filename,
               constrained_file)