Description of Model output
As a result of running the SLM model, 3 different types of files are generated, which the user can download in a packed output.zip file. The three different files are as follows based on their content:
- depout.dat: Deposition distributions in different regions of the lung for values of multiple_run option.
- geometry_**.dat: Lung geometry for the modeled lung generations. This file is generated separately for each value (_**) of parameter defined in multiple_run.
- output_**.dat: Average deposition fraction for all simulated lung generations. This file is also generated separately for each value (_**) defined in multiple_run.
Every generated resulting output file header contains the values of certain input parameters.
The following sections detail the contents of each file.
depout.dat
This file provides key insights into the distribution of inhaled particles across different lung regions.
Each row in the file corresponds to a different value of the parameter defined in the multiple_run and detailed in the corresponding input parameter box.
The columns represent the deposition ratios for the particles in various regions of the respiratory system:
- Column 1 (parameter selected from the multiple_run list): The values of the selected parameter, as specified in the input.
- Column 2 (avg_ET): The average deposition fraction of particles in the extrathoracic region of the lungs.
- Column 3 (avg_br): The average deposition fraction of particles in the bronchial region of the lungs.
- Column 4 (avg_ac): The average deposition fraction of particles in the acinar region of the lungs.
- Column 5 (avg_tot): The total average deposition fraction of particles across the entire lung.
Example of depout.dat file:
# Inhalation time : 2.5
# Breath hold time : 0
# Tidal volume : 750
#particle_diameter avg_ET avg_br avg_ac avg_tot
0.1 0.04583 0.09053 0.26568 0.40203
0.2 0.03618 0.05879 0.20226 0.29722
0.3 0.03767 0.04611 0.18300 0.26678
0.4 0.04445 0.03970 0.16696 0.25111
0.5 0.05507 0.03678 0.16347 0.25531
In this run, we selected the particle_diameter parameter in the multiple_run and performed the run for 5 different particle sizes. Thus, in each row, the average deposition fraction values for the different particle sizes (0.1, 0.2, 0.3, 0.4 and 0.5 µm) are provided for the 3 different lung regions (Extrathoracic, bronchial and acinar region) as well as their total (total).
geometry_**.dat
This file provides key insights into the generated geometry of lung generations across different lung regions. Based on the built-in lung parameter distributions the model determines a new diameter, length, gravitational angle, and branching angle for each particle path. The average of these parameters are then determined by averaging each by the number of particle paths (thus, number of simulations). These average values are summarized in this file.
It is important to note that when calculating the average size of the bronchial airways, only the bronchial airways are considered, and for the acinar airways, only the acinar airways are taken into account. 12th to 21st generations are mixed, which means that depending on the specific particle path, both bronchial and acinar airways may be present.
Each row in the file corresponds to a different generation number.
The columns represent the following parameters of geometry:
- Column 1 (gen): The generation number of the lung.
- Column 2 (avg_len): The average length of lung generation.
- Column 3 (avg_diam): The average diameter of lung generation.
- Column 4 (avg_bran_ang): The average branching of lung generation.
- Column 5 (avg_grav_ang): The average gravitational of lung generation.
- Column 6 (avg_bron_len): The average length of lung generation in bronchial region of the lungs.
- Column 7 (avg_bron_diam): The average diameter of lung generation in bronchial region of the lungs.
- Column 8 (avg_bron_bran_ang): The average branching of lung generation in bronchial region of the lungs.
- Column 9 (avg_bron_grav_ang): The average gravitational of lung generation in bronchial region of the lungs.
- Column 10 (avg_acin_len): The average length of lung generation in acinar region of the lungs.
- Column 11 (avg_acin_diam): The average diameter of lung generation in acinar region of the lungs.
- Column 12 (avg_acin_bran_ang): The average branching of lung generation in acinar region of the lungs.
- Column 13 (avg_acin_grav_ang): The average gravitational of lung generation in acinar region of the lungs.
Example of geometry_**.dat file:
#gen avg_len avg_diam avg_bran_ang avg_grav_ang avg_bron_len avg_bron_diam avg_bron_bran_ang avg_bron_grav_ang avg_acin_len avg_acin_diam avg_acin_bran_ang avg_acin_grav_ang
1 10.56054 1.74822 0.00000 0.00000 10.56054 1.74822 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
2 3.63224 1.35475 41.98550 0.50852 3.63224 1.35475 41.98550 0.50852 0.00000 0.00000 0.00000 0.00000
3 1.81409 1.07572 24.76750 0.43180 1.81409 1.07572 24.76750 0.43180 0.00000 0.00000 0.00000 0.00000
4 1.36685 0.89728 19.10195 0.44595 1.36685 0.89728 19.10195 0.44595 0.00000 0.00000 0.00000 0.00000
5 1.30518 0.75285 21.54130 0.42747 1.30518 0.75285 21.54130 0.42747 0.00000 0.00000 0.00000 0.00000
6 0.95747 0.65898 22.42838 0.42030 0.95747 0.65898 22.42838 0.42030 0.00000 0.00000 0.00000 0.00000
7 0.75804 0.54638 24.46454 0.43363 0.75804 0.54638 24.46454 0.43363 0.00000 0.00000 0.00000 0.00000
8 0.67340 0.47988 27.71756 0.48778 0.67340 0.47988 27.71756 0.48778 0.00000 0.00000 0.00000 0.00000
9 0.54493 0.38845 31.18474 0.56222 0.54493 0.38845 31.18474 0.56222 0.00000 0.00000 0.00000 0.00000
10 0.46824 0.30127 35.89431 0.66123 0.46824 0.30127 35.89431 0.66123 0.00000 0.00000 0.00000 0.00000
11 0.38719 0.22997 39.73886 0.76708 0.38719 0.22997 39.73886 0.76708 0.00000 0.00000 0.00000 0.00000
12 0.32092 0.17802 43.52692 0.86686 0.32092 0.17802 43.52692 0.86686 0.00000 0.00000 0.00000 0.00000
13 0.25837 0.14139 46.64262 0.96250 0.25427 0.13953 44.38940 0.90503 0.00410 0.00186 2.25319 0.05747
14 0.20842 0.11290 49.20440 1.05873 0.19511 0.10685 42.24406 0.87962 0.01331 0.00605 6.96035 0.17911
15 0.16878 0.09120 50.75885 1.14311 0.14066 0.07842 36.15655 0.76938 0.02813 0.01278 14.60227 0.37374
16 0.14687 0.07504 51.72076 1.21313 0.10165 0.05448 28.14170 0.60816 0.04522 0.02056 23.57898 0.60497
17 0.13129 0.06357 52.86244 1.27863 0.07187 0.03657 20.99091 0.44788 0.05942 0.02701 31.87162 0.83074
18 0.11716 0.05515 53.32086 1.31790 0.04674 0.02314 14.07483 0.30692 0.07042 0.03201 39.24610 1.01098
19 0.10501 0.04891 53.99731 1.34750 0.02666 0.01329 8.58634 0.18521 0.07835 0.03561 45.41105 1.16229
20 0.09547 0.04413 53.82188 1.36251 0.01453 0.00733 4.77370 0.10252 0.08094 0.03679 49.04815 1.25999
21 0.08740 0.04015 53.87224 1.37367 0.00775 0.00395 2.59410 0.05656 0.07964 0.03620 51.27810 1.31711
22 0.08121 0.03691 53.91568 1.36610 0.00000 0.00000 0.00000 0.00000 0.08121 0.03691 53.91568 1.36610
23 0.07355 0.03343 52.93583 1.35354 0.00000 0.00000 0.00000 0.00000 0.07355 0.03343 52.93583 1.35354
24 0.06504 0.02956 50.42516 1.28603 0.00000 0.00000 0.00000 0.00000 0.06504 0.02956 50.42516 1.28603
25 0.05555 0.02525 46.12493 1.20065 0.00000 0.00000 0.00000 0.00000 0.05555 0.02525 46.12493 1.20065
26 0.04546 0.02066 40.13730 1.02668 0.00000 0.00000 0.00000 0.00000 0.04546 0.02066 40.13730 1.02668
27 0.03544 0.01611 33.02090 0.84774 0.00000 0.00000 0.00000 0.00000 0.03544 0.01611 33.02090 0.84774
28 0.02592 0.01178 25.30087 0.65558 0.00000 0.00000 0.00000 0.00000 0.02592 0.01178 25.30087 0.65558
29 0.01760 0.00800 17.76749 0.45427 0.00000 0.00000 0.00000 0.00000 0.01760 0.00800 17.76749 0.45427
30 0.01123 0.00510 11.85168 0.30778 0.00000 0.00000 0.00000 0.00000 0.01123 0.00510 11.85168 0.30778
31 0.00662 0.00301 7.29902 0.18767 0.00000 0.00000 0.00000 0.00000 0.00662 0.00301 7.29902 0.18767
32 0.00341 0.00155 4.15552 0.10610 0.00000 0.00000 0.00000 0.00000 0.00341 0.00155 4.15552 0.10610
33 0.00153 0.00069 2.00421 0.05132 0.00000 0.00000 0.00000 0.00000 0.00153 0.00069 2.00421 0.05132
34 0.00046 0.00021 0.64400 0.01774 0.00000 0.00000 0.00000 0.00000 0.00046 0.00021 0.64400 0.01774
35 0.00007 0.00003 0.09582 0.00295 0.00000 0.00000 0.00000 0.00000 0.00007 0.00003 0.09582 0.00295
This file belongs to one of the specified values of the parameter selected in the multiple_run. In this sample file, the simulation was conducted up to a depth of 35 generations, with the geometric parameters characteristic of each generation shown row by row.
output_**.dat
This file provides key insights into the distribution of inhaled particles across the lung generations. Deposition is only calculated where the particle actually reaches, as particles only travel to a certain depth based on the defined inhalation time. When the inhalation time is over, they stop and start moving back.
Each row in the file corresponds to a different generation number.
The columns represent the deposition ratios for the particles in various generations of the lung:
- Column 1 (gen): The generation number of the lung.
- Column 2 (avg_bronchial): The average deposition fraction of particles in the bronchial region of the lungs.
- Column 3 (avg_acinar): The average deposition fraction of particles in the acinar region of the lungs.
- Column 4 (avg_combined): The average deposition fraction of particles in the acinar and bronchial region of the lungs.
Example of output_**.dat file:
# upper airways : 0.04583
# bronchial : 0.09053
# acinar : 0.26568
# total : 0.40203
#gen avg_bronchial avg_acinar avg_combined
1 0.0015126661 0.0000000000 0.0015126661
2 0.0010180636 0.0000000000 0.0010180636
3 0.0009316732 0.0000000000 0.0009316732
4 0.0012309129 0.0000000000 0.0012309129
5 0.0016169662 0.0000000000 0.0016169662
6 0.0019082665 0.0000000000 0.0019082665
7 0.0023554617 0.0000000000 0.0023554617
8 0.0030616389 0.0000000000 0.0030616389
9 0.0037692981 0.0000000000 0.0037692981
10 0.0047688670 0.0000000000 0.0047688670
11 0.0059432359 0.0000000000 0.0059432359
12 0.0074188416 0.0000000000 0.0074188416
13 0.0087379701 0.0003116676 0.0090496317
14 0.0096798874 0.0013260538 0.0110059474
15 0.0095916744 0.0035722076 0.0131639009
16 0.0087447707 0.0072422312 0.0159869697
17 0.0074194185 0.0114354305 0.0188548192
18 0.0054673450 0.0160659067 0.0215332378
19 0.0031919822 0.0207257271 0.0239177123
20 0.0015069855 0.0249644127 0.0264713839
21 0.0006501388 0.0293742195 0.0300243441
22 0.0000000000 0.0351686999 0.0351686999
23 0.0000000000 0.0359525420 0.0359525420
24 0.0000000000 0.0354913101 0.0354913101
25 0.0000000000 0.0238335989 0.0238335989
26 0.0000000000 0.0130136982 0.0130136982
27 0.0000000000 0.0053006900 0.0053006900
28 0.0000000000 0.0014524353 0.0014524353
29 0.0000000000 0.0004353340 0.0004353340
30 0.0000000000 0.0000075308 0.0000075308
31 0.0000000000 0.0000019182 0.0000019182
32 0.0000000000 0.0000000054 0.0000000054
This file belongs to one of the specified values of the parameter selected in the multiple_run. In this sample file, the simulation was conducted up to a depth of 31 generations, with the average deposition fraction characteristic of each generation shown row by row.
Visualization:
The following two diagrams can be downloaded from the website.
The first diagram uses bar groups to illustrate the particle deposition fractions associated with each multiple run element in different lung regions (extrathoracic – Et, bronchial – Br, acinar – Ac). This visualization helps to understand how inhaled particles distribute across various parts of the respiratory system under specific environmental or experimental conditions.
The second diagram represents deposition fractions in the three lung regions (extrathoracic, bronchial, acinar) as a function of particle size, along with the total deposition (avg_tot). This figure is only generated if the particle diameter parameter has been assigned multiple values during the multiple run, allowing for an analysis of the impact of size distribution.
