# pyramidal test, Frank Postma
days=14;
events_append_seconds=0;
randomseed=0;
dt=100;
populationsizepyramidal=6;
populationsizeinterneuron=0;
shape=regions;
regions=pyrlayr;
pyrlayr.shape=box;
pyrlayr.neurons=1000;
pyrlayr.populationsizepyramidal=6;
pyrlayr.populationsizeinterneuron=0;
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;	


# APICAL DENDRITE PARAMETER DEFINITIONS

substitute=APD:all_apical_pyramidal_dendrites;

// A. trunk branching
APD.branching_model=van_Pelt;
APD.B_inf=0.1;
APD.tau=400000;
APD.E=0;
APD.E_competes_with=same_arbor;

// 
APD.direction_model=segment_history_tension;
APD.dirhistory_selection=none;
APD.veeranglemin=0.0;
APD.veeranglemax=0.1;
APD.history_power=1.2;

// B. trunk elongation
APD.arbor_elongation_model=van_Pelt;
APD.growth_F=0;
APD.growth_nu0=0.005208333;
// APD.growth_nu0=0.00005208333; no difference??
APD.F_competes_with=same_arbor;

//   B.1 arbor
APD.aem.PDF=delta;
APD.aem.PDF.value=0;

//   B.2 terminal segments
APD.terminal_segment_elongation_model=pyrAD_BESTLNN;
APD.tsem.trunklength.PDF=normal;
APD.tsem.trunklength.PDF.mean=180;
APD.tsem.trunklength.PDF.std=2;
//APD.tsem.trunklength.PDF.trunc=60;

APD.tsem.prefix=pyr1;

//     B.2.2 obliques parameters
APD.tsem.obliques.PDF=normal;
APD.tsem.obliques.PDF.mean=5;
APD.tsem.obliques.PDF.std=1;
APD.tsem.obliqueangle.PDF=normal;
APD.tsem.obliqueangle.PDF.mean=0;
APD.tsem.obliqueangle.PDF.std=1;

//     B.2.1 regular parameters
APD.tsem.branch.PDF=normal;
APD.tsem.branch.PDF.mean=6;
APD.tsem.branch.PDF.std=1;
APD.tsem.PDF=delta;
APD.tsem.PDF.value=0;
APD.elongation_rate_initialization_model=nonnorm_BESTL_length_distribution;
APD.eri.PDF=normal;
APD.eri.PDF.mean=0.0010208333;
APD.eri.PDF.std=0.0000256;

// C. tuft elongation and branching (***add direction?)
pyr1.tuft.terminal_segment_elongation_model=nonnorm_BESTL;
pyr1.tuft.tsem.branch.PDF=normal;
pyr1.tuft.tsem.branch.PDF.mean=6;
pyr1.tuft.tsem.branch.PDF.std=1;
pyr1.tuft.tsem.PDF=delta;
pyr1.tuft.tsem.PDF.value=0;
pyr1.tuft.elongation_rate_initialization_model=nonnorm_BESTL_length_distribution;
pyr1.tuft.eri.PDF=normal;
pyr1.tuft.eri.PDF.mean=0.000165;
pyr1.tuft.eri.PDF.std=0.000004;

//   C.1 tuft terminal segment branching model that uses a separate arbor branching model
pyr1.tuft.TSBM=van_Pelt_specBM;
pyr1.tuft.S=1;
pyr1.tuft.branching_model=van_Pelt;
//pyr1.tuft.B_inf=10;
pyr1.tuft.B_inf=25;

pyr1.tuft.tau=400000;
pyr1.tuft.E=0.3;
pyr1.tuft.E_competes_with=same_arbor;

pyr1.tuft.branch_angle_model=Balanced_Forces;
pyr1.tuft.bam.PDF=normal;
pyr1.tuft.bam.PDF.mean=-0.95;
pyr1.tuft.bam.PDF.std=0.01;
pyr1.tuft.direction_model=segment_history_tension;
pyr1.tuft.dirhistory_selection=none;
pyr1.tuft.veeranglemin=0.1;
pyr1.tuft.veeranglemax=0.9;
pyr1.tuft.history_power=1.2;



// D. oblique elongation and branching (***add direction?)
pyr1.oblique.terminal_segment_elongation_model=nonnorm_BESTL;
pyr1.oblique.tsem.branch.PDF=normal;
pyr1.oblique.tsem.branch.PDF.mean=6;
pyr1.oblique.tsem.branch.PDF.std=1;
pyr1.oblique.tsem.PDF=delta;
pyr1.oblique.tsem.PDF.value=0;
pyr1.oblique.elongation_rate_initialization_model=nonnorm_BESTL_length_distribution;
pyr1.oblique.eri.PDF=normal;
pyr1.oblique.eri.PDF.mean=0.00004;
pyr1.oblique.eri.PDF.std=0.000001;

//   D.1 oblique terminal segment branching model that uses a separate arbor branching model
pyr1.oblique.TSBM=van_Pelt_specBM;
pyr1.oblique.S=1;
pyr1.oblique.branching_model=van_Pelt;
pyr1.oblique.B_inf=1.5;
pyr1.oblique.tau=500000;
pyr1.oblique.E=0.3;
pyr1.oblique.E_competes_with=same_arbor;

// C. trunk direction
APD.direction_model=segment_history_tension;
APD.veeranglemin=0.0;
APD.veeranglemax=0.1;


# DENDRITE PARAMETER DEFINITIONS (from final4.txt)

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=0.0000914464; 
all_dendrites.eri.PDF.std=0.0000365786; 

// BAM
all_dendrites.branch_angle_model=Balanced_Forces;
all_dendrites.bam.PDF=normal;
all_dendrites.bam.PDF.mean=-0.7;
all_dendrites.bam.PDF.std=0.01;


//all_dendrites.bam_label=dendritebm;
//all_dendrites.bam_weight=0.1;
//all_dendrites.dendritebm.branch_angle_model=Balanced_Forces;
//all_dendrites.dendritebm.bam_weight=0.2;
//all_dendrites.dendritebm.bm_weight=0.2;
//all_dendrites.bm_weight=0.2;
//pyr1.tuft.bam.PDF.trunc=0.1;



all_dendrites.TSTM=linear_rate;
all_dendrites.turn_separation=0.7;
all_dendrites.turn_rate=5.4;

all_dendrites.direction_model=segment_history_tension;
all_dendrites.dirhistory_selection=none;
dirhistory_selection=none;
all_dendrites.veeranglemin=0.25;
all_dendrites.veeranglemax=1.0;
all_dendrites.history_power=0.4;

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=2.52; 
all_dendrites.tau=259680; 
all_dendrites.E_competes_with=same_arbor; 
all_dendrites.E=0.73; 
all_dendrites.TSBM=van_Pelt; 
all_dendrites.S=0.5;  

// 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;