Branching airways 3min model-added constructCubeAlveoli function

covid_ba.config

@@ -99,7 +99,7 @@ max-block-dim =               10
 output =                      results
 
 ; *Directory containing files for lung model
-lung-model =                  /users/<Your-User-Name>/simcov
+lung-model =                  /users/arianav/simcov
 
 ; Show progress
 progress =                    true

create_config.py

@@ -0,0 +1,47 @@
+import argparse
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser()
+    parser.add_argument("--dim" , nargs='+', type=int, help="Dimensions: x y z", default=[15000, 15000, 1])
+    parser.add_argument("--whole-lung-dim" , nargs='+', type=int, help="Whole lung dimensions: x y z", default=[48000, 40000, 20000])
+    parser.add_argument("--timesteps" , type=int, help="Number of timesteps (assuming 1 min per timestep)", default=4000)
+    parser.add_argument("--infection-coords" , type=str, help="Location (distribution) of initial infections", default="uniform:1")
+    parser.add_argument("--initial-infection" , type=int, help="Number of virions at initial infection locations", default=1000)
+    parser.add_argument("--incubation-period" , type=int, help="Average number of time steps to expressing virions after cell is infected", default=480)
+    parser.add_argument("--apoptosis-period" , type=int, help="Average number of time steps to death after apoptosis is induced", default=180)
+    parser.add_argument("--expressing-period" , type=int, help="Average number of time steps to death after a cell starts expresssing", default=900)
+    parser.add_argument("--infectivity" , type=float, help="Factor multiplied by number of virions to determine probability of infection", default=0.001)
+    parser.add_argument("--infectivity-multiplier" , type=float, help="Multiplier reducing infectivity where inflammatory signal is present", default=1.0)
+    parser.add_argument("--virion-production" , type=float, help="Number of virions produced by expressing cell each time step", default=1.1)
+    parser.add_argument("--virion-production-multiplier" , type=float, help="Multiplier reducing virion production rate where inflammatory signal is present", default=1.0)
+    parser.add_argument("--virion-clearance" , type=float, help="Fraction by which virion count drops each time step", default=0.004)
+    parser.add_argument("--virion-diffusion" , type=float, help="Fraction of virions that diffuse into all neighbors each time step", default=0.15)
+    parser.add_argument("--virion-air-diffusion" , type=float, help="Fraction of chemokine concentration that diffuses into all neighbors through air each time step", default=0.0)
+    parser.add_argument("--chemokine-production" , type=float, help="Amount of chemokine produced by expressing cells each time step", default=1.0)
+    parser.add_argument("--chemokine-decay" , type=float, help="Amount by which chemokine concentration drops each time step", default=0.01)
+    parser.add_argument("--chemokine-diffusion" , type=float, help="Fraction of chemokine concentration that diffuses into all neighbors each time step", default=1.0)
+    parser.add_argument("--chemokine-air-diffusion" , type=float, help="Fraction of chemokine concentration that diffuses into all neighbors through air each time step", default=0.0)
+    parser.add_argument("--min-chemokine" , type=float, help="Minimum chemokine concentration that triggers a T cell", default=1e-6)
+    parser.add_argument("--antibody-factor" , type=int, help="Impact of antibodies; multiplier for virion decay (setting to 1 means this has no effect)", default=1)
+    parser.add_argument("--antibody-period" , type=int, help="Number of time steps before antibodies start to be produced", default=5760)
+    parser.add_argument("--tcell-generation-rate" , type=int, help="Number of tcells generated at each timestep for the whole lung", default=105000)
+    parser.add_argument("--tcell-initial-delay" , type=int, help="Number of time steps before T cells start to be produced", default=10080)
+    parser.add_argument("--tcell-vascular-period" , type=int, help="Average number of time steps to death for a T cell in the vasculature", default=5760)
+    parser.add_argument("--tcell-tissue-period" , type=int, help="Average number of time steps to death after a T cell extravasates", default=1440)
+    parser.add_argument("--tcell-binding-period" , type=int, help="Number of time steps a T cell is bound to an epithelial cell when inducing apoptosis", default=10)
+    parser.add_argument("--max-binding-prob" , type=int, help="Max probability of a T cell binding to an infected cell in one time step", default=1)
+    parser.add_argument("--tcells-follow-gradient" , type=str, help="T cells in tissue follow the chemokine gradient", default="false")
+    parser.add_argument("--seed" , type=int, help="Random seed", default=29)
+    parser.add_argument("--sample-period" , type=int, help="Number of timesteps between samples (set to 0 to disable sampling)", default=10080)
+    parser.add_argument("--sample-resolution" , type=int, help="Resolution for sampling", default=1)
+    parser.add_argument("--max-block-dim" , type=int, help="Max. block dimension - larger means more locality but worse load balance. Set to 0 for largest possible", default=10)
+    parser.add_argument("--output" , type=str, help="Output directory (automatically generated)", default="results")
+
+    args = vars(parser.parse_args())
+    for key in args:
+        print(key.replace("_", "-"), end='=')
+        if isinstance(args[key], list):
+            args[key] = list(map(str, args[key]))
+            print(' '.join(args[key]))
+        else:
+            print(args[key])

experiments/j-0.0007632_m-0.007632.config

@@ -0,0 +1,32 @@
+dim=15000 15000 1
+whole-lung-dim=48000 40000 20000
+timesteps=33120
+infection-coords=uniform:1
+initial-infection=1000
+incubation-period=480
+apoptosis-period=180
+expressing-period=900
+infectivity=0.001
+infectivity-multiplier=1.0
+virion-production=1.1
+virion-production-multiplier=1.0
+virion-clearance=0.004
+virion-diffusion=0.0007632
+chemokine-production=1.0
+chemokine-decay=0.01
+chemokine-diffusion=0.007632
+min-chemokine=1e-06
+antibody-factor=1
+antibody-period=5760
+tcell-generation-rate=105000
+tcell-initial-delay=10080
+tcell-vascular-period=5760
+tcell-tissue-period=1440
+tcell-binding-period=10
+max-binding-prob=1
+tcells-follow-gradient=false
+seed=29
+sample-period=0
+sample-resolution=1
+max-block-dim=10
+output=experiments/j-0.0007632_m-0.007632

experiments/j-0.0007632_m-0.007632/simcov.config

@@ -0,0 +1,98 @@
+; Dimensions: x y z
+  dim =                         15000 15000 1
+
+; Whole lung dimensions: x y z
+  whole-lung-dim =              48000 40000 20000
+
+; Number of timesteps
+  timesteps =                   33120
+
+; Location of multiple initial infections, of form "x1,y1,z1,t1 x2,y2,z2,t2..."
+; where x,y,z are grid coords and t is a timestep, or
+; "uniform:N" for N uniformly distributed points or
+; "random:N" for N randomly distributed points
+  infection-coords =            uniform:1
+
+; Number of virions at initial infection locations
+  initial-infection =           1000
+
+; Average number of time steps to expressing virions after cell is infected
+  incubation-period =           480
+
+; Average number of time steps to death after apoptosis is induced
+  apoptosis-period =            180
+
+; Average number of time steps to death after a cell starts expresssing
+  expressing-period =           900
+
+; Factor multiplied by number of virions to determine probability of infection
+  infectivity =                 0.001
+
+; Multiplier to reduce infectivity rate
+  infectivity-multiplier =      1.0
+
+; Number of virions produced by expressing cell each time step
+  virion-production =           1.1
+
+; Multiplier to reduce virion production rate
+  virion-production-multiplier = 1.0
+
+; Fraction by which virion count drops each time step
+  virion-clearance =            0.004
+
+; Fraction of virions that diffuse into all neighbors each time step
+  virion-diffusion =            0.0007632
+
+; Amount of chemokine produced by expressing cells each time step
+  chemokine-production =        1.0
+
+; Amount by which chemokine concentration drops each time step
+  chemokine-decay =             0.01
+
+; Fraction of chemokine concentration that diffuses into all neighbors each time step
+  chemokine-diffusion =         0.007632
+
+; Minimum chemokine concentration that triggers a T cell
+  min-chemokine =               1e-06
+
+; Impact of antibodies; multiplier for virion clearance
+  antibody-factor =             1
+
+; Number of time steps before antibodies start to be produced
+  antibody-period =             5760
+
+; Number of tcells generated at each timestep for the whole lung
+  tcell-generation-rate =       105000
+
+; Number of time steps before T cells start to be produced
+  tcell-initial-delay =         10080
+
+; Average number of time steps to death for a T cell in the vasculature
+  tcell-vascular-period =       5760
+
+; Average number of time steps to death after a T cell extravasates
+  tcell-tissue-period =         1440
+
+; Number of time steps a T cell is bound to an epithelial cell when inducing apoptosis
+  tcell-binding-period =        10
+
+; Max probability of a T cell binding to an infected cell in one time step
+  max-binding-prob =            1
+
+; T cells in tissue follow the chemokine gradient
+  tcells-follow-gradient =      false
+
+; Random seed
+  seed =                        29
+
+; Number of timesteps between samples (set to 0 to disable sampling)
+  sample-period =               0
+
+; Resolution for sampling
+  sample-resolution =           1
+
+; Max. block dimension - larger means more locality but worse load balance. Set to 0 for largest possible
+  max-block-dim =               10
+
+; Output directory
+  output =                      experiments/j-0.0007632_m-0.007632