;; Reference: Cerebellar cortex oscillatory robustness from Golgi cell gap jncs (Simoes de Souza and De Schutter 2011)

(nemo-model Granule

  (
   (input v celsius)

   (component (type defaults) 
      (const V_t = -35)
      (const celsius = 30)
      (output celsius V_t)
      )

   (component (type membrane-capacitance)
	 (const C_m  = (1))
	 (output C_m  ))


   (component (type geometry) (name soma)
         (const L = 11.8)
         (const diam = 11.8)
	 (output L diam ))


   (component (type decaying-pool) (name ca)

      (input
       (cai from ion-pools)
       (ica from ion-currents))

      (const  F       = 96485.3)
      (const  d       = .2)
      (const  cao     = 2.)
      (const  cai0    = 1e-4)
      (const  beta    = 1.5)
      
      (d (ca) =  ((neg (ica) / (2 * F * d)) * 1e4 -
		  (beta * ((if (ca < cai0) then cai0 else ca) - cai0)))
	 (initial cai0))
      
      (output ca cao)
      )

   
   (component (type ionic-current) (name CaHVA )
	      
      (input 
       (cai from ion-pools)
       (cao from ion-pools))
	      
      (component (type gate)

		 ;; rate constants
		 
		 (Q10 = (pow (3 ((celsius - 20) / 10))))
		 
		 (const Aalpha_s  = 0.04944)
		 (const Kalpha_s  =  15.87301587302)
		 (const V0alpha_s = -29.06)
		 
		 (const Abeta_s  = 0.08298)
		 (const Kbeta_s  =  -25.641)
		 (const V0beta_s = -18.66)
		 
		 (const Aalpha_u  = 0.0013)
		 (const Kalpha_u  =  -18.183)
		 (const V0alpha_u = -48)
			 
		 (const Abeta_u = 0.0013)
		 (const Kbeta_u = 83.33)
		 (const V0beta_u = -48)
		 
		 ;; rate functions
		 
		 (defun alpha_s (v Q10)
		   (Q10 * Aalpha_s * exp((v - V0alpha_s) / Kalpha_s)))
		 
		 (defun beta_s (v Q10)
		   (Q10 * Abeta_s * exp((v - V0beta_s) / Kbeta_s)))
		 
		 (defun alpha_u (v Q10)
		   (Q10 * Aalpha_u * exp((v - V0alpha_u) / Kalpha_u)))
		 
		 (defun beta_u (v Q10) 
		   (Q10 * Abeta_u * exp((v - V0beta_u) / Kbeta_u)))

		 (s_inf = ((alpha_s (v Q10))/(alpha_s (v Q10) + beta_s (v Q10))))
		 (tau_s = (1 / (alpha_s (v Q10) + beta_s (v Q10)) ))

		 (u_inf = ((alpha_u (v Q10))/(alpha_u (v Q10) + beta_u (v Q10)) ))
		 (tau_u = (1 / (alpha_u (v Q10) + beta_u (v Q10)) ))

		 (hh-ionic-gate 
		  (CaHVA  ;; ion name: exported variables will be of the form {ion}_{id}
		   (initial-m  s_inf)
		   (initial-h  u_inf)
		   (m-power    2)
		   (h-power    1)
		   (m-inf      s_inf)
		   (m-tau      tau_s)
		   (h-inf      u_inf)
		   (h-tau      tau_u)
		   ))
		 )
      
      (component (type pore)
		 (const  gbar  = 0.00046)
		 (output gbar ))
      
      (component (type permeating-ion) (name ca)
		 (const F = 96485.3)
		 (const R = 8.31342)
		 (e = ((1e3) * (R * (celsius + 273.15)) / (2 * F) * ln (cao / cai)))
		 (output e)
		 )
      
      ) ;; end CaHVA current

   (component (type voltage-clamp) (name CaHVA)
	      
	      (const vchold   = -71)
	      (const vcbase   = -69)
	      (const vcinc    = 10)
	      (const vcsteps  = 8)
	      (const vchdur   = 30)
	      (const vcbdur   = 100)

	      (const cnhold   = 1e-4)
	      (const cnbase   = 1e-4)
	      (const cninc    = 0)
	      (const cnsteps  = 1)
	      (const cnout    = 2)
	      
	      (output vchold vcbase vcinc vcsteps vchdur vcbdur 
                      cnhold cnbase cninc cnsteps cnout)
	      )



   (component (type ionic-current) (name KA )

	      (defun sigm (x y) (1 / (exp (x / y) + 1)))
	      
	      (component (type gate)

			 ;; rate constants

			 (Q10 = (pow (3 ((celsius - 25.5) / 10))))

			 (const Aalpha_a  = 0.8147)
			 (const Kalpha_a  = -23.32708)
			 (const V0alpha_a = -9.17203)
			 (const Abeta_a   = 0.1655)
			 (const Kbeta_a   = 19.47175)
			 (const V0beta_a  = -18.27914)

			 (const Aalpha_b  = 0.0368)
			 (const Kalpha_b  = 12.8433)
			 (const V0alpha_b = -111.33209)
			 (const Abeta_b   = 0.0345)
			 (const Kbeta_b   = -8.90123)
			 (const V0beta_b  = -49.9537)

			 (const V0_ainf = -38)
			 (const  K_ainf = -17)

			 (const V0_binf   = -78.8)
			 (const K_binf    = 8.4)

			 
			 ;; rate functions

			 (defun alpha_a (v Q10)
			   (Q10 * Aalpha_a * sigm((v - V0alpha_a) Kalpha_a)))

			 (defun beta_a (v Q10)
			   (Q10 * (Abeta_a / exp((v - V0beta_a) / Kbeta_a))))

			 (defun alpha_b (v Q10)
			   (Q10 * Aalpha_b * sigm((v - V0alpha_b) Kalpha_b)))

			 (defun beta_b (v Q10)
			   (Q10 * Abeta_b * sigm((v - V0beta_b) Kbeta_b)))

			 (a_inf = (1 / (1 + exp ((v - V0_ainf) / K_ainf)))) 
			 (tau_a = (1 / (alpha_a (v Q10) + beta_a (v Q10)) ))
			 (b_inf = (1 / (1 + exp ((v - V0_binf) / K_binf))))
			 (tau_b = (1 / (alpha_b (v Q10) + beta_b (v Q10)) ))

			 (hh-ionic-gate 
			  (KA  ;; ion name: exported variables will be of the form {ion}_{id}
			   (initial-m  (1 / (1 + exp ((v - V0_ainf) / K_ainf))) )
			   (initial-h  (1 / (1 + exp ((v - V0_binf) / K_binf))) )
			   (m-power    3)
			   (h-power    1)
			   (m-inf      a_inf)
			   (m-tau      tau_a)
			   (h-inf      b_inf)
			   (h-tau      tau_b)
			   ))

			 )

	      	      
	      (component (type pore)
			 (const  gbar  = 0.0032)
			 (output gbar ))

	      
	      (component (type permeating-ion) (name k)
			 (const e = -84.69)
			 (output e ))
	      
	      ) ;; end KA current
	      

	      (component (type voltage-clamp) (name KA)
           
			 (const vchold   = -71)
			 (const vcbase   = -69)
			 (const vcinc    = 10)
			 (const vcsteps  = 8)
			 (const vchdur   = 30)
			 (const vcbdur   = 100)
           
			 (output vchold vcbase vcinc vcsteps vchdur vcbdur)
			 )
   

   (component (type ionic-current) (name KCa )


      (input
       (cai from ion-pools))

	      
      (component (type gate)
		 
		 ;; rate constants
		 (Q10 = (pow (3 ((celsius - 30) / 10))))
		 
		 (const Aalpha_c = 2.5)
		 (const Balpha_c = 1.5e-3)
		 
		 (const Kalpha_c =  -11.765)
		 
		 (const Abeta_c = 1.5)
		 (const Bbeta_c = 0.15e-3)

		 (const Kbeta_c = -11.765)

		 (cai1 = (if (cai < 1e-4) then 1e-4 else cai))

		 ;; rate functions
		 (defun alpha_c (v cai Q10)
		   (Q10 * Aalpha_c / (1 + (Balpha_c * exp(v / Kalpha_c) / cai ))))
		 
		 (defun beta_c (v cai Q10)
		   (Q10 * Abeta_c / (1 + (cai / (Bbeta_c * exp (v / Kbeta_c))) )))

                 (c_inf = ((alpha_c (v cai Q10)) / (alpha_c (v cai Q10) + beta_c (v cai Q10)) ))
                 (tau_c = (1 / (alpha_c (v cai Q10) + beta_c (v cai Q10)) ))

		 (hh-ionic-gate 
		  (KCa  ;; ion name: exported variables will be of the form {ion}_{id}
		   (initial-m  c_inf)
		   (m-power    1)
		   (h-power    0)
                   (m-inf      c_inf) 
                   (m-tau      tau_c)
		   ))
		 
		 )
      
      (component (type pore)
		 (const  gbar  = 0.04)
		 (output gbar ))
      
      
      (component (type permeating-ion) (name k)
		 (const e = -84.69)
		 (output e ))
      
      (component (type modulating-ion) (name ca)
		 )
	      
      ) ;; end KCa current

   (component (type voltage-clamp) (name KCa)
	      
	      (const vchold   = -71)
	      (const vcbase   = -69)
	      (const vcinc    = 10)
	      (const vcsteps  = 8)
	      (const vchdur   = 30)
	      (const vcbdur   = 100)

	      (const cnhold   = 1e-4)
	      (const cnbase   = 1e-4)
	      (const cninc    = 1e3)
	      (const cnsteps  = 1)
	      (const cnout    = 2)
	      
	      (output vchold vcbase vcinc vcsteps vchdur vcbdur 
                      cnhold cnbase cninc cnsteps cnout)
	      )



   (component (type ionic-current) (name Kir )
	      
	      (component (type gate)

			 ;; rate constants
			 (Q10 = (pow (3 ((celsius - 20) / 10))))

			 (const Aalpha_d = 0.13289)
			 (const Kalpha_d = -24.3902)

			 (const V0alpha_d = -83.94)
			 (const Abeta_d   = 0.16994)

			 (const Kbeta_d = 35.714)
			 (const V0beta_d = -83.94)
   
			 ;; rate functions
			 (defun alpha_d (v Q10)
			   (Q10 * Aalpha_d * exp((v - V0alpha_d) / Kalpha_d)))
			 
			 (defun beta_d (v Q10)
			   (Q10 * Abeta_d * exp((v - V0beta_d) / Kbeta_d) ))

			 (d_inf = ((alpha_d (v Q10)) / (alpha_d (v Q10) + beta_d (v Q10)) ))
			 (tau_d = (1 / (alpha_d (v Q10) + beta_d (v Q10)) ))

			 (hh-ionic-gate 
			  (Kir  ;; ion name: exported variables will be of the form {ion}_{id}
			   (initial-m  d_inf)
			   (m-power    1)
			   (h-power    0)
			   (m-inf      (d_inf))
			   (m-tau      (tau_d))
			   ))
			 
			 )


	      (component (type pore)
			 (const  gbar  = 0.0009)
			 (output gbar ))

	      
	      (component (type permeating-ion) (name k)
			 (const e = -84.69)
			 (output e ))
	      
	      ) ;; end Kir current

	      	      

   (component (type voltage-clamp) (name Kir)
	      
	      (const vchold   = -71)
	      (const vcbase   = -69)
	      (const vcinc    = 10)
	      (const vcsteps  = 8)
	      (const vchdur   = 30)
	      (const vcbdur   = 100)
	      
	      (output vchold vcbase vcinc vcsteps vchdur vcbdur)
	      )


   (component (type ionic-current) (name KM )
	      
	      (component (type gate)

			 ;; rate constants
			 (const Aalpha_n = 0.0033)

			 (const Kalpha_n  = 40)
			 (const V0alpha_n = -30)
			 (const Abeta_n   = 0.0033)

			 (const Kbeta_n  = -20)
			 (const V0beta_n = -30)
			 (const V0_ninf  = -35)
			 (const   B_ninf = 6)
			 
			 (Q10 = (pow (3 ((celsius - 22) / 10))))
			 
			 ;; rate equations
			 (defun alpha_n (v Q10)
			   (Q10 * Aalpha_n * exp((v - V0alpha_n) / Kalpha_n) ))

			 (defun beta_n (v Q10)
			   (Q10 * Abeta_n * exp((v - V0beta_n) / Kbeta_n) ))

			 (hh-ionic-gate 
			  (KM  ;; ion name: exported variables will be of the form {ion}_{id}
			   (initial-m  (1 / (1 + exp((neg (v - V0_ninf)) / B_ninf))))
			   (m-power    1)
			   (h-power    0)
			   (m-tau      (1 / (alpha_n(v Q10) + beta_n (v Q10)) ))
			   (m-inf      (1 / (1 + exp((neg (v - V0_ninf)) / B_ninf))))
			   ))
			 )
	      
	      (component (type pore)
			 (const  gbar  = 0.00025)
			 (output gbar ))
	      
	      (component (type permeating-ion) (name k)
			 (const e = -84.69)
			 (output e ))
	      
	      ) ;; end KM current


   (component (type voltage-clamp) (name KM)
	      
	      (const vchold   = -71)
	      (const vcbase   = -69)
	      (const vcinc    = 10)
	      (const vcsteps  = 8)
	      (const vchdur   = 30)
	      (const vcbdur   = 100)
	      
	      (output vchold vcbase vcinc vcsteps vchdur vcbdur)
	      )

   (component (type ionic-current) (name KV )

	      (defun linoid (x y) 
		(if ((abs (x / y)) < 1e-6) 
		    then (y * (1 - ((x / y) / 2)))
		    else (x / (exp (x / y) - 1))
		    ))
	      
	      (component (type gate)

			 ;; rate constants
			 (Q10 = (pow (3 ((celsius - 6.3) / 10))))

			 (const Aalpha_n = -0.01)
			 (const Kalpha_n = -10)
			 (const V0alpha_n = -25)
			 (const Abeta_n = 0.125)
	
			 (const Kbeta_n = -80)
			 (const V0beta_n = -35)

			 ;; rate functions
			 (defun alpha_n (v Q10) 
			   (Q10 * Aalpha_n * linoid ((v - V0alpha_n) Kalpha_n)))

			 (defun beta_n (v Q10) 
			   (Q10 * Abeta_n * exp((v - V0beta_n) / Kbeta_n) ))


                         (n_inf = ((alpha_n (v Q10)) / (alpha_n (v Q10) + beta_n (v Q10)) ))
                         (tau_n = (1 / (alpha_n (v Q10) + beta_n (v Q10)) ))

			 (hh-ionic-gate 
			  (KV  ;; ion name: exported variables will be of the form {ion}_{id}
			   (initial-m  n_inf)
			   (m-power    4)
			   (h-power    0)
			   (m-inf     (n_inf))
			   (m-tau     (tau_n))
			   ))
			 )


	      (component (type pore)
			 (const  gbar  = 0.003)
			 (output gbar ))
	      
	      (component (type permeating-ion) (name k)
			 (const e = -84.69)
			 (output e ))
	      
	      ) ;; end KV current
	      

   (component (type voltage-clamp) (name KV)
	      
	      (const vchold   = -71)
	      (const vcbase   = -69)
	      (const vcinc    = 10)
	      (const vcsteps  = 8)
	      (const vchdur   = 30)
	      (const vcbdur   = 100)
	      
	      (output vchold vcbase vcinc vcsteps vchdur vcbdur)
	      )
	      
   
   (component (type ionic-current) (name Lkg1)
	      
	      (component (type pore)
			 (const  gbar  = (5.68e-5))
			 (output gbar))
	      
	      (component (type permeating-ion) (name non-specific)
			 (const e = -16.5)
			 (output e ))
	      
	      ) ;; end leak current


   (component (type ionic-current) (name Lkg2)
	      
	      (component (type pore)
			 (const  ggaba  = (3e-5))
			 (output ggaba))
	      
	      (component (type permeating-ion) (name non-specific)
			 (const egaba = -65)
			 (output egaba ))
	      
	      ) ;; end leak current


   (component (type ionic-current) (name Na )
	      
	      (component (type gate)

			 ;; rate constants
			 (Q10 = (pow (3 ((celsius - 20) / 10))))

			 (const Aalfa = 353.91)
			 (const Valfa = 13.99)
			 (const Abeta = 1.272)
			 (const Vbeta = 13.99)
			 (const Agamma = 150)
			 (const Adelta = 40)
			 (const Aepsilon = 1.75)
			 (const Ateta = 0.0201)
			 (const Vteta = 25)
			 (const ACon = 0.005)
			 (const ACoff = 0.5)
			 (const	AOon = 0.75)
			 (const	AOoff = 0.005)
			 (const n1 = 5.422)
			 (const n2 = 3.279)
			 (const n3 = 1.83)
			 (const n4 = 0.738)
	
			 (gamma = (Q10 * Agamma))
			 (delta = (Q10 * Adelta))
			 (epsilon = (Q10 * Aepsilon))
			 (Con = (Q10 * ACon))
			 (Coff = (Q10 * ACoff))
			 (Oon = (Q10 * AOon))
			 (Ooff = (Q10 * AOoff))
			 (a = (pow ((Oon / Con) (1.0 / 4.0))))
			 (b = (pow ((Ooff / Coff) (1.0 / 4.0))))

			 ;; rate functions
			 (defun alfa (v Q10)	
			   (Q10 * Aalfa * exp (v / Valfa)))

			 (defun beta (v Q10)
			   (Q10 * Abeta * exp (neg (v) / Vbeta)))

			 (defun teta (v Q10)
			   (Q10 * Ateta * exp (neg (v) / Vteta)))
				

			 (reaction
			  (Na_z
			   (transitions
			    (<-> C1 C2 (n1 * alfa (v Q10)) (n4 * beta (v Q10)))
			    (<-> C2 C3 (n2 * alfa (v Q10)) (n3 * beta (v Q10)))
			    (<-> C3 C4 (n3 * alfa (v Q10)) (n2 * beta (v Q10)))
			    (<-> C4 C5 (n4 * alfa (v Q10)) (n1 * beta (v Q10)))
			    (<-> C5 O  gamma delta)
			    (<-> O  B  epsilon (teta (v Q10)))

			    (<-> I1 I2 (n1 * alfa (v Q10) * a) (n4 * beta (v Q10) * b))
			    (<-> I2 I3 (n2 * alfa (v Q10) * a) (n3 * beta (v Q10) * b))
			    (<-> I3 I4 (n3 * alfa (v Q10) * a) (n2 * beta (v Q10) * b))
			    (<-> I4 I5 (n4 * alfa (v Q10) * a) (n1 * beta (v Q10) * b))
			    (<-> I5 I6 gamma delta)

			    (<-> C1 I1 Con Coff)
			    (<-> C2 I2 (Con * a) (Coff * b))
			    (<-> C3 I3 (Con * pow (a 2)) (Coff * pow (b 2)))
			    (<-> C4 I4 (Con * pow (a 3)) (Coff * pow (b 3)))
			    (<-> C5 I5 (Con * pow (a 4)) (Coff * pow (b 4)))

			    (O <-> I6 Oon Ooff))
			   
			   (conserve ((1 = (C1 + C2 + C3 + C4 + C5 + O + B + I1 + I2 + I3 + I4 + I5 + I6))))
		     
			   (open O)   (power 1)))

			 (output Na_z )  

			 )
	      
	      (component (type pore)
			 (const  gbar  = 0.013)
			 (output gbar ))

	      
	      (component (type permeating-ion) (name na)
			 (const e = 87.39)
			 (output e ))
	      
	      ) ;; end Na current

   (component (type voltage-clamp) (name Na)

	      (const vchold   = -71)
	      (const vcbase   = -60)
	      (const vcinc    = 10)
	      (const vcsteps  = 9)
	      (const vchdur   = 30)
	      (const vcbdur   = 100)
           
	      (output vchold vcbase vcinc vcsteps vchdur vcbdur))

      )

;; Following are templates for various driver scripts used to run this model
   (
    (".hoc" ()  
#<<EOF

create soma
access soma

insert {{model_name}}

soma {
        nseg = 1 

{% with diam = default(diam, 11.8), L = default(L, 11.8) %}
        diam = {{diam}}
        L = {{L}} 
{% endwith %}

        cm = 1

        Ra = 100
    }
EOF
)

    ("template.hoc" ()  
#<<EOF


create soma

soma {
     
    nseg=1

{% with diam = default(diam, 11.8), L = default(L, 11.8) %}
    diam = {{diam}}
    L = {{L}} 
{% endwith %}

    Ra=100
    cm=1
    celsius = 30

    insert {{model_name}}_CaHVA
    insert {{model_name}}_ca
    insert {{model_name}}_KA
    insert {{model_name}}_KCa
    insert {{model_name}}_Kir    
    insert {{model_name}}_KM
    insert {{model_name}}_KV 
    insert {{model_name}}_Lkg1 
    insert {{model_name}}_Lkg2
    insert {{model_name}}_Na
}

EOF
)
    ("neuron_run.hoc" ()  

#<<EOF

load_file( "{{model_name}}_template.hoc" )

v_init = -70

celsius = 30 

{% with tstop = default(tstop, 1000) %}
tstop = {{tstop}} // for IClamp
{% endwith %}

dt = 0.025


access soma
psection()

printf("ena: %f", ena)
printf("ek: %f", ek)
printf("eca: %f", eca)
printf("celsius: %f", celsius)

stim_amp=0.01875

objectvar stim
soma stim = new IClamp(0.5)
stim.del = 1000
stim.dur = 1850
stim.amp = stim_amp
 
objref rec_v
rec_v = new Vector()
rec_v.record (&soma.v(0.5))

objref rec_t
rec_t = new Vector()
rec_t.record (&t)

dt = 0.025
tstop = 3000
run()

objref output_file
output_file = new File()
output_file.wopen("Granule.dat")

for (i=0; i < rec_v.size(); i=i+1) {
  output_file.printf("%g %g\n", rec_t.x[i], rec_v.x[i])
}
output_file.close()
quit()
	

EOF
)

    ("octave_odepkg_run.m" ()  

#<<EOF

## {{model_name}} model driver for Octave/odepkg

{{model_name}}_defs = "{{model_name}}.m";

autoload ("{{model_name}}", {{model_name}}_defs );
autoload ("{{model_name}}_init", {{model_name}}_defs );

{{model_name}}_init; 

global celsius cai 


{% with cai = default(cai, 1e-4), celsius = default(celsius, 30) %}
cai = {{cai}} ;
celsius = {{celsius}} ;
{% endwith %}

y0 = {{model_name}}_init(-70)

{% with tstop = default(tstop, 300) %}
tstop = {{tstop}} ;
{% endwith %}

t0 = 0.0;
t1 = tstop;

dt = 1e-3;

reltol=1e-2;
abstol=1e-2;

function y = step (x, k)
  y = 1 ./ (1 + exp(-2 * k * x));
end

function y = stepp (x, k)
  y = 2 ./ (1 + exp(2 * k * x));
end

function i = ifn(t,k,hc,cc,t1,t2)
  i = hc + (cc - hc) .* step(t - t1,k) .* step(t2 - t,k);
endfunction

function [dy] = my{{model_name}}(t, y)

  [dy] = {{model_name}}(t, y);

  i_stim = ifn(t,3,0,0.01875,10,290);
  
  dy(1) = dy(1) + i_stim;

endfunction


P = odeset ('RelTol', reltol, 'AbsTol', abstol, 'MaxStep', 1e-1, 'InitialStep', dt,
	   "OutputFcn", @odeplot);
sol = ode2r (@my{{model_name}}, [t0 t1], y0, P);

ys = [sol.x sol.y];

N = size(ys)(1);
{{model_name}}_v = [ys(:,1) ys(:,2)];
save -ascii "{{model_name}}_v.dat" {{model_name}}_v;

EOF
) 


    ("nestmodule_bootstrap.sh" ()  
#<<EOF
#!/bin/sh

echo "Bootstrapping Granule module..."

if test -d autom4te.cache ; then
# we must remove this cache, because it
# may screw up things if configure is run for
# different platforms. 
  echo "  -> Removing old automake cache ..."
  rm -rf autom4te.cache
fi

echo "  -> Running aclocal ..."
aclocal

echo "  -> Running libtoolize ..."
if [ `uname -s` = Darwin ] ; then
# libtoolize is glibtoolize on OSX
  LIBTOOLIZE=glibtoolize
else  
  LIBTOOLIZE=libtoolize
fi

libtool_major=`$LIBTOOLIZE --version | head -n1 | cut -d\) -f2 | cut -d\. -f1`
$LIBTOOLIZE --force --copy --ltdl

echo "  -> Re-running aclocal ..."
if test $libtool_major -le 2; then
  aclocal --force
else
  aclocal --force -I $(pwd)/libltdl/m4
fi

echo "  -> Running autoconf ..."
autoconf

# autoheader must run before automake 
echo "  -> Running autoheader ..."
autoheader

echo "  -> Running automake ..."
automake --foreign --add-missing --force-missing --copy

echo "Done."

EOF
)

    ("nestmodule_configure.ac" ()  
#<<EOF
AC_PREREQ(2.52)

AC_INIT(granulemodule, 1.0, raikov@oist.jp)

# These variables are exported to include/config.h
GRANULEMODULE_MAJOR=1
GRANULEMODULE_MINOR=0
GRANULEMODULE_PATCHLEVEL=0

# Exporting source and build directories requires full path names.
# Thus we have to expand.
# Here, we are in top build dir, since source dir must exist, we can just
# move there and call pwd
if test "x$srcdir" = x ; then
  PKGSRCDIR=`pwd`
else
  PKGSRCDIR=`cd $srcdir && pwd`
fi
PKGBUILDDIR=`pwd`

# If this is not called, install-sh will be put into .. by bootstrap.sh
# moritz, 06-26-06
AC_CONFIG_AUX_DIR(.)

AM_INIT_AUTOMAKE(nest, $GRANULEMODULE_VERSION)

# obtain host system type; HEP 2004-12-20
AC_CANONICAL_HOST

# ------------------------------------------------------------------------
# Handle options
#
# NOTE: No programs/compilations must be run in this section;
#       otherwise CFLAGS and CXXFLAGS may take on funny default
#       values.
#       HEP 2004-12-20
# ------------------------------------------------------------------------

# nest-config
NEST_CONFIG=`which nest-config`
AC_ARG_WITH(nest,[  --with-nest=script	nest-config script including path],
[
  if test "$withval" != yes; then
    NEST_CONFIG=$withval
  else
    AC_MSG_ERROR([--with-nest-config expects the nest-config script as argument. See README for details.])
  fi
])

# -------------------------------------------
# END Handle options
# -------------------------------------------

# sundials-config
SUNDIALS_CONFIG=`which sundials-config`
AC_ARG_WITH(sundials,[  --with-sundials=script	sundials-config script including path],
[
  if test "$withval" != yes; then
    SUNDIALS_CONFIG=$withval
#  else
#    AC_MSG_ERROR([--with-sundials-config expects the sundials-config script as argument. See README for details.])
  fi
])


# does nest-config work
AC_MSG_CHECKING([for nest-config ])
AC_CHECK_FILE($NEST_CONFIG, HAVE_NEST=yes, 
              AC_MSG_ERROR([No usable nest-config was found. You may want to use --with-nest-config.]))
AC_MSG_RESULT(found)

AC_MSG_CHECKING([for sundials-config ])
AC_CHECK_FILE($SUNDIALS_CONFIG, HAVE_SUNDIALS=yes, 
              AC_MSG_ERROR([No usable sundials-config was found. You may want to use --with-sundials-config.]))
AC_MSG_RESULT(found)

# the following will crash if nest-config does not run
# careful, lines below must not break
AC_MSG_CHECKING([for NEST directory information ])
NEST_PREFIX=`$NEST_CONFIG --prefix`
NEST_CPPFLAGS=`$NEST_CONFIG --cflags`
NEST_COMPILER=`$NEST_CONFIG --compiler`
if test $prefix = NONE; then prefix=`$NEST_CONFIG --prefix`; fi
AC_MSG_RESULT($NEST_CPPFLAGS)


AC_MSG_CHECKING([for SUNDIALS preprocessor flags ])
SUNDIALS_CPPFLAGS="`$SUNDIALS_CONFIG -m cvode -t s -l c -s cppflags`"
AC_MSG_RESULT($SUNDIALS_CPPFLAGS)

AC_MSG_CHECKING([for SUNDIALS linker options ])
SUNDIALS_LDFLAGS="`$SUNDIALS_CONFIG -m cvode -t s -l c -s libs` -lblas -llapack"
AC_MSG_RESULT($SUNDIALS_LDFLAGS)

# Set the platform-dependent compiler flags based on the canonical
# host string.  These flags are placed in AM_{C,CXX}FLAGS.  If
# {C,CXX}FLAGS are given as environment variables, then they are
# appended to the set of automatically chosen flags.  After
# {C,CXX}FLAGS have been read out, they must be cleared, since
# system-dependent defaults will otherwise be placed into the
# Makefiles.  HEP 2004-12-20.

# Before we can determine the proper compiler flags, we must know
# which compiler we are using.  Since the pertaining AC macros run the
# compiler and set CFLAGS, CXXFLAGS to system-dependent values, we
# need to save command line/enviroment settings of these variables
# first. AC_AIX must run before the compiler is run, so we must run it
# here.
# HEP 2004-12-21

GRANULEMODULE_SAVE_CXXFLAGS=$CXXFLAGS

# Must first check if we are on AIX
AC_AIX

# Check for C++ compiler, looking for the same compiler
# used with NEST
AC_PROG_CXX([ $NEST_COMPILER ])

# the following is makeshift, should have the macro set proper
# GRANULEMODULE_SET_CXXFLAGS
AM_CXXFLAGS=$GRANULEMODULE_SAVE_CXXFLAGS
CXXFLAGS=

## Configure C environment

AC_PROG_LD
AC_PROG_INSTALL

AC_LIBLTDL_CONVENIENCE	   ## put libltdl into a convenience library
AC_PROG_LIBTOOL		   ## use libtool
AC_CONFIG_SUBDIRS(libltdl) ## also configure subdir containing libltdl

#-- Set the language to C++
AC_LANG_CPLUSPLUS

#-- Look for programs needed in the Makefile
AC_PROG_CXXCPP
AM_PROG_LIBTOOL
AC_PATH_PROGS([MAKE],[gmake make],[make])

# ---------------------------------------------------------------
# Configure directories to be built
# ---------------------------------------------------------------

PKGDATADIR=$datadir/$PACKAGE
PKGDOCDIR=$datadir/doc/$PACKAGE

# set up directories from which to build help
# second line replaces space with colon as separator
HELPDIRS="$PKGSRCDIR $PKGSRCDIR/sli"
HELPDIRS=`echo $HELPDIRS | tr " " ":"`

#-- Replace these variables in *.in
AC_SUBST(HAVE_NEST)
AC_SUBST(NEST_CONFIG)
AC_SUBST(NEST_CPPFLAGS)
AC_SUBST(NEST_COMPILER)
AC_SUBST(NEST_PREFIX)
AC_SUBST(HELPDIRS)
AC_SUBST(PKGSRCDIR)
AC_SUBST(PKGBUILDDIR)
AC_SUBST(PKGDATADIR)
AC_SUBST(PKGDOCDIR)
AC_SUBST(KERNEL)
AC_SUBST(HOST)
AC_SUBST(SED)
AC_SUBST(LD)
AC_SUBST(host_os)
AC_SUBST(host_cpu)
AC_SUBST(host_vendor)
AC_SUBST(AS)
AC_SUBST(CXX)
AC_SUBST(AR)
AC_SUBST(ARFLAGS)
AC_SUBST(CXX_AR)
AC_SUBST(AM_CXXFLAGS)
AC_SUBST(AM_CFLAGS)
AC_SUBST(MAKE)
AC_SUBST(MAKE_FLAGS)
AC_SUBST(INCLTDL)
AC_SUBST(LIBLTDL)
AC_SUBST(SUNDIALS_CONFIG)
AC_SUBST(SUNDIALS_CPPFLAGS)
AC_SUBST(SUNDIALS_LDFLAGS)

AM_CONFIG_HEADER(granulemodule_config.h:granulemodule_config.h.in)
AC_CONFIG_FILES(Makefile)

# -----------------------------------------------
# Create output
# -----------------------------------------------
AC_OUTPUT


# -----------------------------------------------
# Report, after output at end of configure run
# Must come after AC_OUTPUT, so that it is 
# displayed after libltdl has been configured
# -----------------------------------------------

echo
echo "-------------------------------------------------------"
echo "Granule module Configuration Summary"
echo "-------------------------------------------------------"
echo
echo "C++ compiler        : $CXX"
echo "C++ compiler flags  : $AM_CXXFLAGS"
echo "NEST compiler flags : $NEST_CPPFLAGS"
echo "SUNDIALS compiler flags : $SUNDIALS_CPPFLAGS"
echo "SUNDIALS linker flags : $SUNDIALS_LDFLAGS"

# these variables will still contain '${prefix}'
# we want to have the versions where this is resolved, too:
eval eval eval  PKGDOCDIR_AS_CONFIGURED=$PKGDOCDIR
eval eval eval  PKGDATADIR_AS_CONFIGURED=$PKGDATADIR

echo
echo "-------------------------------------------------------"
echo
echo "You can build and install Granule module now, using"
echo "  make"
echo "  make install"
echo
echo "Granule module will be installed to:"
echo -n "  "; eval eval echo "$libdir"
echo

EOF
)

    ("nestmodule_makefile.am" ()  
#<<EOF

# Automake file for external dynamic modules for NEST
#
# Hans Ekkehard Plesser, April 2008
# Automake file for the Developer Module
# 
# libgranulemodule is built as a normal, installable library.
# It will be installed to $prefix/lib by make install.
# 
# Headers from this directory are not to be installed upon
# make install. They are therefore included in _SOURCES.


libdir= @libdir@/nest

lib_LTLIBRARIES=      granulemodule.la libgranulemodule.la

granulemodule_la_CXXFLAGS= @AM_CXXFLAGS@
granulemodule_la_SOURCES=  granulemodule.cpp      granulemodule.h      \
                      Granule.cpp Granule.h \
                      drop_odd_spike_connection.h
granulemodule_la_LDFLAGS=  -module

libgranulemodule_la_CXXFLAGS= $(granulemodule_la_CXXFLAGS) -DLINKED_MODULE
libgranulemodule_la_SOURCES=  $(granulemodule_la_SOURCES)

MAKEFLAGS= @MAKE_FLAGS@

AM_CPPFLAGS= @NEST_CPPFLAGS@ \
	     @SUNDIALS_CPPFLAGS@ \
             @INCLTDL@      

AM_LDFLAGS = @SUNDIALS_LDFLAGS@

.PHONY: install-slidoc

nobase_pkgdata_DATA=\
	granulemodule.sli

install-slidoc:
	NESTRCFILENAME=/dev/null $(DESTDIR)$(NEST_PREFIX)/bin/sli --userargs="@HELPDIRS@" $(NEST_PREFIX)/share/nest/sli/install-help.sli

install-data-hook: install-exec install-slidoc

EXTRA_DIST= sli

EOF
)

    ("nestmodule.cpp" ()  
#<<EOF
/*
 *  granulemodule.cpp
 *  This file is part of NEST.
 *
 *  Copyright (C) 2008 by
 *  The NEST Initiative
 *
 *  See the file AUTHORS for details.
 *
 *  Permission is granted to compile and modify
 *  this file for non-commercial use.
 *  See the file LICENSE for details.
 *
 */

// include necessary NEST headers
//#include "config.h"
#include "network.h"
#include "model.h"
#include "dynamicloader.h"
#include "genericmodel.h"
#include "generic_connector.h"
#include "booldatum.h"
#include "integerdatum.h"
#include "tokenarray.h"
#include "exceptions.h"
#include "sliexceptions.h"
#include "nestmodule.h"

// include headers with your own stuff
#include "granulemodule.h"
#include "Granule.h"
#include "drop_odd_spike_connection.h"

// -- Interface to dynamic module loader ---------------------------------------

/*
 * The dynamic module loader must be able to find your module. 
 * You make the module known to the loader by defining an instance of your 
 * module class in global scope. This instance must have the name
 *
 * <modulename>_LTX_mod
 *
 * The dynamicloader can then load modulename and search for symbol "mod" in it.
 */
 
granulenest::GranuleModule granulemodule_LTX_mod;

// -- DynModule functions ------------------------------------------------------

granulenest::GranuleModule::GranuleModule()
  { 
#ifdef LINKED_MODULE
     // register this module at the dynamic loader
     // this is needed to allow for linking in this module at compile time
     // all registered modules will be initialized by the main app's dynamic loader
     nest::DynamicLoaderModule::registerLinkedModule(this);
#endif     
   }

granulenest::GranuleModule::~GranuleModule()
   {
   }

   const std::string granulenest::GranuleModule::name(void) const
   {
     return std::string("Granule Module"); // Return name of the module
   }

   const std::string granulenest::GranuleModule::commandstring(void) const
   {
     /* 1. Tell interpreter that we provide the C++ part of GranuleModule with the
           current revision number. 
        2. Instruct the interpreter to check that granulemodule-init.sli exists, 
           provides at least version 1.0 of the SLI interface to GranuleModule, and
           to load it.
      */
     return std::string(
       "/granulemodule /C++ ($Revision: 8512 $) provide-component "
       "/granulemodule /SLI (7165) require-component"
       );
   }

   /* BeginDocumentation
      Name: StepPatternConnect - Connect sources and targets with a stepping pattern
      
      Synopsis:
      [sources] source_step [targets] target_step synmod StepPatternConnect -> n_connections
      
      Parameters:
      [sources]     - Array containing GIDs of potential source neurons
      source_step   - Make connection from every source_step'th neuron
      [targets]     - Array containing GIDs of potential target neurons
      target_step   - Make connection to every target_step'th neuron
      synmod        - The synapse model to use (literal, must be key in synapsedict)
      n_connections - Number of connections made
      
      Description:
      This function subsamples the source and target arrays given with steps
      source_step and target_step, beginning with the first element in each array,
      and connects the selected nodes.
      
      Example:
      /first_src 0 /network_size get def
      /last_src /iaf_neuron 20 Create def  % nodes  1 .. 20
      /src [first_src last_src] Range def
      /last_tgt /iaf_neuron 10 Create def  % nodes 21 .. 30
      /tgt [last_src 1 add last_tgt] Range def
      
      src 6 tgt 4 /drop_odd_spike StepPatternConnect 
  
      This connects nodes [1, 7, 13, 19] as sources to nodes [21, 25,
      29] as targets using synapses of type drop_odd_spike, and
      returning 12 as the number of connections.  The following
      command will print the connections (you must paste the SLI
      command as one long line):

      src { /s Set << /source s /synapse_type /static_synapse >> FindConnections { GetStatus /target get } Map dup length 0 gt { cout s <- ( -> ) <- exch <-- endl } if ; } forall
      1 -> [21 25 29]
      7 -> [21 25 29]
      13 -> [21 25 29]
      19 -> [21 25 29]
      
      Remark:
      This function is only provided as an example for how to write your own 
      interface function. 
      
      Author:
      Hans Ekkehard Plesser
      
      SeeAlso:
      Connect, ConvergentConnect, DivergentConnect
   */
   void granulenest::GranuleModule::StepPatternConnect_Vi_i_Vi_i_lFunction::execute(SLIInterpreter *i) const
   {
     // Check if we have (at least) five arguments on the stack.
     i->assert_stack_load(5);

     // Retrieve source, source step, target, target step from the stack
     const TokenArray sources = getValue<TokenArray> (i->OStack.pick(4)); // bottom
     const long src_step      = getValue<long>       (i->OStack.pick(3));
     const TokenArray targets = getValue<TokenArray> (i->OStack.pick(2));
     const long tgt_step      = getValue<long>       (i->OStack.pick(1));  
     const Name synmodel_name = getValue<std::string>(i->OStack.pick(0)); // top
     
     // Obtain synapse model index
     const Token synmodel 
       = nest::NestModule::get_network().get_synapsedict().lookup(synmodel_name);
     if ( synmodel.empty() )
       throw nest::UnknownSynapseType(synmodel_name.toString());
     const nest::index synmodel_id = static_cast<nest::index>(synmodel);

     // Build a list of targets with the given step
     TokenArray selected_targets;
     for ( size_t t = 0 ; t < targets.size() ; t += tgt_step )
       selected_targets.push_back(targets[t]);
     
     // Now connect all appropriate sources to this list of targets
     size_t Nconn = 0;  // counts connections
     for ( size_t s = 0 ; s < sources.size() ; s += src_step )
     {
       // We must first obtain the GID of the source as integer
       const nest::long_t sgid = getValue<nest::long_t>(sources[s]);

       // nest::network::divergent_connect() requires weight and delay arrays. We want to use
       // default values from the synapse model, so we pass empty arrays.
       nest::NestModule::get_network().divergent_connect(sgid, selected_targets, 
							 TokenArray(), TokenArray(),
							 synmodel_id);
       Nconn += selected_targets.size();
     }

     // We get here only if none of the operations above throws and exception.
     // Now we can safely remove the arguments from the stack and push Nconn
     // as our result. 
     i->OStack.pop(5);
     i->OStack.push(Nconn);
     
     // Finally, we pop the call to this functions from the execution stack.
     i->EStack.pop();
   }

  //-------------------------------------------------------------------------------------

  void granulenest::GranuleModule::init(SLIInterpreter *i, nest::Network*)
  {
    /* Register a neuron or device model.
       Give node type as template argument and the name as second argument.
       The first argument is always a reference to the network.
       Return value is a handle for later unregistration.
    */
    //printf ("before register model\n");
       nest::register_model<nest::Granule>(nest::NestModule::get_network(), 
					    "Granule");
       // printf ("after register model\n");

    /* Register a synapse type.
       Give synapse type as template argument and the name as second argument.
       The first argument is always a reference to the network.
    */
    nest::register_prototype_connection<DropOddSpikeConnection>(nest::NestModule::get_network(), 
                                                       "drop_odd_synapse");

    /* Register a SLI function.
       The first argument is the function name for SLI, the second a pointer to
       the function object. If you do not want to overload the function in SLI,
       you do not need to give the mangled name. If you give a mangled name, you
       should define a type trie in the granulemodule-init.sli file.
    */
    i->createcommand("StepPatternConnect_Vi_i_Vi_i_l", 
                     &stepPatternConnect_Vi_i_Vi_i_lFunction);

  }  // GranuleModule::init()

 

EOF
)

    ("nestmodule.h" ()  
#<<EOF
/*
 *  granulemodule.h
 *
 *  This file is part of NEST.
 *
 *  Copyright (C) 2008 by
 *  The NEST Initiative
 *
 *  See the file AUTHORS for details.
 *
 *  Permission is granted to compile and modify
 *  this file for non-commercial use.
 *  See the file LICENSE for details.
 *
 */

#ifndef GRANULEMODULE_H
#define GranuleMODULE_H

#include "dynmodule.h"
#include "slifunction.h"

namespace nest
{
  class Network;
}

// Put your stuff into your own namespace.
namespace granulenest {
  
/**
 * Class defining your model.
 * @note For each model, you must define one such class, with a unique name.
 */
class GranuleModule : public DynModule
{
public:

  // Interface functions ------------------------------------------
  
  /**
   * @note The constructor registers the module with the dynamic loader. 
   *       Initialization proper is performed by the init() method.
   */
  GranuleModule();
  
  /**
   * @note The destructor does not do much in modules. Proper "downrigging"
   *       is the responsibility of the unregister() method.
   */
  ~GranuleModule();

  /**
   * Initialize module by registering models with the network.
   * @param SLIInterpreter* SLI interpreter
   * @param nest::Network*  Network with which to register models
   * @note  Parameter Network is needed for historical compatibility
   *        only.
   */
  void init(SLIInterpreter*, nest::Network*);

  /**
   * Return the name of your model.
   */
  const std::string name(void) const;
  
  /**
   * Return the name of a sli file to execute when granulemodule is loaded.
   * This mechanism can be used to define SLI commands associated with your
   * module, in particular, set up type tries for functions you have defined.
   */
  const std::string commandstring(void) const;
     
public:
  
  // Classes implementing your functions -----------------------------
  
  /**
   * Implement a function for a step-pattern-based connection.
   * @note What this function does is described in the SLI documentation
   *       in the cpp file.
   * @note The mangled name indicates this function expects the following
   *       arguments on the stack (bottom first): vector of int, int, 
   *       vector of int, int. 
   * @note You must define a member object in your module class
   *       of the function class. execute() is later invoked on this
   *       member.
   */
  class StepPatternConnect_Vi_i_Vi_i_lFunction: public SLIFunction
     {
     public:
       void execute(SLIInterpreter *) const;
     };

     StepPatternConnect_Vi_i_Vi_i_lFunction stepPatternConnect_Vi_i_Vi_i_lFunction;
  };
} // namespace granulenest

#endif

EOF
)

    ("drop_odd_spike_connection.h" ()  
#<<EOF
#ifndef DROP_ODD_SPIKE_CONNECTION_H
#define DROP_ODD_SPIKE_CONNECTION_H

/*
 *  drop_odd_spike_connection.h
 *
 *  This file is part of NEST
 *
 *  Copyright (C) 2008 by
 *  The NEST Initiative
 *
 *  See the file AUTHORS for details.
 *
 *  Permission is granted to compile and modify
 *  this file for non-commercial use.
 *  See the file LICENSE for details.
 *
 */

#include "connection_het_wd.h"

/* BeginDocumentation
  Name: drop_odd_spike - Synapse dropping spikes with odd time stamps.

  Description:
  This synapse will not deliver any spikes with odd time stamps, while spikes with even
  time stamps go through unchanged.

  Transmits: SpikeEvent
  
  Remarks:
  This synapse type is provided only for illustration purposes in GranuleModule.

  SeeAlso: synapsedict
*/

namespace granulenest {

/**
 * Connection class for illustration purposes.
 */
class DropOddSpikeConnection : public nest::ConnectionHetWD
{
 public:

  /**
   * Default Constructor.
   * Sets default values for all parameters. Needed by GenericConnectorModel.
   */
  DropOddSpikeConnection() : ConnectionHetWD() {}

  /**
   * Default Destructor.
   */
  ~DropOddSpikeConnection() {}

  /**
   * Send an event to the receiver of this connection.
   * @param e The event to send
   * @param t_lastspike Point in time of last spike sent.
   * @param cp Common properties to all synapses (empty).
   */
  void send(nest::Event& e, nest::double_t t_lastspike, 
            const nest::CommonSynapseProperties &cp);

  //! Defining this as empty means we can handle spike events
  using Connection::check_event;  // see http://www.gotw.ca/gotw/005.htm
  void check_event(nest::SpikeEvent&) {}

};


inline
void DropOddSpikeConnection::send(nest::Event& e, nest::double_t last, 
                                  const nest::CommonSynapseProperties &props)
{
  if ( e.get_stamp().get_steps() % 2 ) // stamp is odd, drop it
    return;
    
  // Even time stamp, we send the spike using the normal sending mechnism  
  // send the spike to the target
  nest::ConnectionHetWD::send(e, last, props);
}
 
} // namespace

#endif // drop_odd_spike_connection.h

EOF
)
    ("granulemodule.sli" ()  
#<<EOF
/* 
 * Initialization file for GranuleModule.
 * Run automatically when GranuleModule is loaded.
 */

M_DEBUG (granulemodule.sli) (Initializing SLI support for GranuleModule.) message

/granulemodule /SLI ($Revision: 7918 $) provide-component
/granulemodule /C++ (7165) require-component

/StepPatternConnect [ /arraytype /integertype /arraytype /integertype /literaltype ]
{ 
  StepPatternConnect_Vi_i_Vi_i_l
} def

EOF
)
    ("testrun.sli" ()  
#<<EOF
/dt 0.025 def
(granulemodule) Install

ResetKernel
0
 << 
   /resolution  dt 
   /tics_per_ms  1e4
 >> SetStatus

/neuron /Granule Create def
/stepinput /step_current_generator Create def
/vlog /voltmeter Create def
/vlog_parameters << /interval dt /to_file true /to_memory false >> def
vlog vlog_parameters SetStatus

stepinput neuron Connect
vlog neuron Connect

/step_current_parameters << /amplitude_times [0.0 1000.0 2850.0] /amplitude_values [0.0 0.01875 0.0 ] >> def
stepinput step_current_parameters SetStatus

3000.0 Simulate

EOF
)


) ;; end template declarations
      
)