# basket cell test, Frank Postma
days=14;
events_append_seconds=0;
randomseed=0;
dt=100;
populationsizepyramidal=0;
populationsizeinterneuron=20;
shape=regions;
regions=pyrlayr;
pyrlayr.shape=box;
pyrlayr.neurons=1000;
pyrlayr.populationsizepyramidal=0;
pyrlayr.populationsizeinterneuron=20;
pyrlayr.minneuronseparation=300;
pyrlayr.centerX=0;
pyrlayr.centerY=0;
pyrlayr.centerZ=0;
pyrlayr.shape.height=3000;
pyrlayr.shape.width=3000;
pyrlayr.shape.depth=3000;
Agrowth_L0_min=9;		
Agrowth_L0_max=11;		
Dgrowth_L0_min=0;		
Dgrowth_L0_max=0;
growthfunction=vanPelt;		
Afibreswithturns=true;		
Dfibreswithturns=true;			
F_competes_with=same_arbor;

all_interneuron_axons.L0=0,0;	


# DENDRITE PARAMETER DEFINITIONS (from final4.txt)
interneuron.min_basal=5;
interneuron.max_basal=7;

all_dendrites.arbor_elongation_model=van_Pelt; 
all_dendrites.elongation_rate_initialization_model=nonnorm_BESTL_length_distribution; 
all_dendrites.growth_F=0; 
all_dendrites.growth_nu0=0.00011152; 
all_dendrites.F_competes_with=same_arbor; 
all_dendrites.eri.PDF=normal; 
all_dendrites.eri.PDF.mean=0.000066976; 
all_dendrites.eri.PDF.std= 0.0001109; 

// BAM
all_dendrites.branch_angle_model=Balanced_Forces;
all_dendrites.bam.PDF=normal;
all_dendrites.bam.PDF.mean=0;
all_dendrites.bam.PDF.std=0.4;


all_dendrites.TSTM=linear_rate;
all_dendrites.turn_separation=0.7;
all_dendrites.turn_rate=2;

all_dendrites.direction_model=segment_history_tension;
all_dendrites.dirhistory_selection=none;
dirhistory_selection=none;
all_dendrites.veeranglemin=0.1;
all_dendrites.veeranglemax=0.9;
all_dendrites.history_power=1.2;

all_dendrites.dm_label=dendritedm;
all_dendrites.dendritedm.direction_model=segment_history_tension;
all_dendrites.dendritedm.dm_weight=1;



all_dendrites.dm_weight=1;

all_dendrites.aem.PDF=delta; 
all_dendrites.aem.PDF.value=0; 

// lengte direct na branching event toegewezen 
all_dendrites.terminal_segment_elongation_model=nonnorm_BESTL; 
//all_dendrites.tsem.branch.PDF=delta; 
all_dendrites.tsem.branch.PDF=normal; 
all_dendrites.tsem.branch.PDF.mean=6; 
all_dendrites.tsem.branch.PDF.std=5; 
//all_dendrites.tsem.branch.PDF.value=6; 

// should be 0 so as not to use tsem but depend on eri 
all_dendrites.tsem.PDF=delta; 
all_dendrites.tsem.PDF.value=0; 

all_dendrites.branching_model=van_Pelt; 
all_dendrites.B_inf=2.6475; 
all_dendrites.tau=406570; 
all_dendrites.E_competes_with=same_arbor; 
all_dendrites.E=0.594; 
all_dendrites.TSBM=van_Pelt; 
all_dendrites.S=-0.259;  

// SPECIFICATION OF AXONS

all_axons.arbor_elongation_model=van_Pelt; 
all_axons.elongation_rate_initialization_model=nonnorm_BESTL_length_distribution; 
all_axons.growth_F=0; 
all_axons.growth_nu0=0.00000011152; 
all_axons.F_competes_with=same_arbor; 
all_axons.eri.PDF=normal; 
all_axons.eri.PDF.mean=0.03e-4; 
all_axons.eri.PDF.std=0.03e-4; 

all_axons.aem.PDF=delta; 
all_axons.aem.PDF.value=0; 

// lengte direct na branching event toegewezen 
all_axons.terminal_segment_elongation_model=nonnorm_BESTL; 
//all_axons.tsem.branch.PDF=delta; 
all_axons.tsem.branch.PDF=normal; 
all_axons.tsem.branch.PDF.mean=6; 
all_axons.tsem.branch.PDF.std=5; 
//all_axons.tsem.branch.PDF.value=6; 

// should be 0 so as not to use tsem but depend on eri 
all_axons.tsem.PDF=delta; 
all_axons.tsem.PDF.value=0; 

all_axons.branching_model=van_Pelt; 
all_axons.B_inf=0.1; 
all_axons.tau=831792; 
all_axons.E_competes_with=same_arbor; 
all_axons.E=0.65; 
all_axons.TSBM=van_Pelt; 
all_axons.S=-0.44; 


fibrediameter=true;
neurite_diameter_model=rall;
outattr_make_full_Txt=true;
outattr_Txt_sequence=false;		
outattr_Txt_separate_files=true;		
electrodes=false;		
branchatinitlength=false;		
Abranchesatturns=false;		
Dbranchesatturns=false;		
candidate_synapses=false;
outattr_track_nodegenesis=true;		
statsattr_collect_statistics=false;	
statsattr_store_raw_data=false;
outattr_show_progress=true;		
figattr_make_full_Fig=false;	
figattr_make_zoom_Fig=false;		
figattr_use_color=true;		
figattr_presynaptic=true;		
figattr_postsynaptic=true;		
figattr_synapses=false;		
figattr_partitions=false;		
figattr_progress=none;		
figattr_fibres_nobox=true;		
sample_dt=5000000;