;; Cerebellar Purkinje Cell: resurgent Na current and high frequency
;; firing (Khaliq et al 2003).

(nemo-model Khaliq03
 
 (
  (input v) 

  (const ena = 60)
  (const ek = -88)
  (const ca0 = 1e-4)

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

             (input (ica from ion-currents))

             (const  F = 96485.309)
             (const  ca_depth   = 0.1)
             (const  ca_beta    = 1.0)
             (const cao     = 2.4)

             (d (ca) =  ((neg (ica) / (2 * ca0 * F * ca_depth)) -
                          ((if (ca < ca0) then ca0 else ca) * ca_beta))
                (initial ca0))

             (cac = (if (ca < ca0) then ca0 else ca))

             (output cac cao))


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


   (component (type geometry) (name soma)
         (const L = 20)
         (const diam = 20)
	 (output L diam ))

  (component (type ionic-current) (name CaBK)
   ;: BK-type Purkinje calcium-activated potassium current

             (input 
              (cai from ion-pools)
              (cao from ion-pools))

             (component (type gate)

                        ;; constants
                        (const ztau = 1.0)

                        ;; rate functions

                        (CaBK_v = (v + 5))

                        (minf = (let ((vh -28.9)
			              (k  6.2))
                                  (1.0 / (1.0 + exp (neg ((CaBK_v - vh) / k))))))

                        (mtau = (let
                                    ((y0   0.000505)
                                     (vh1  -33.3)
                                     (k1   -10.0)
                                     (vh2  86.4)
                                     (k2   10.1))
	                          ((1e3) * (y0 + 1 / (exp ((CaBK_v + vh1) / k1) + 
                                                          exp ((CaBK_v + vh2) / k2))))))

                        (hinf = (let 
                                    ((y0  0.085)
                                     (vh  -32.0)
                                     (k   5.8))
	                          (y0 + (1 - y0) / (1 + exp ((CaBK_v - vh) / k)))))
                              

                        (htau = (let
                                    ((y0   0.0019)
                                     (vh1  -54.2)
                                     (k1   -12.9)
                                     (vh2   48.5)
                                     (k2    5.2))
	                          ((1e3) * (y0 + 1 / (exp ((CaBK_v + vh1) / k1) + exp ((CaBK_v + vh2) / k2))))))


                        (zinf = (let ((k 0.001))
	                          (1 / (1 + (k / cai)))))

                        (z_alpha = (zinf / ztau))
                        (z_beta  = ((1 - zinf) / ztau))

                        (reaction
			  (z
                           (transitions (<-> O C z_alpha z_beta))
                           (conserve  ((1 = (O + C))))
                           (initial   (let ((k 0.001)) 
                                        (1 / (1 + k / ca0))))
                           (open O)
                           (power 2)))
			 
                        (output z)
			 
                        (hh-ionic-gate 
                         (CaBK  ;; ion name: exported variables will be of the form {ion}_{id}
                          (initial-m  (minf))
                          (initial-h  (hinf))
                          (m-power    3)
                          (h-power    1)
                          (m-inf      (minf))
                          (m-tau      (mtau))
                          (h-inf      (hinf))
                          (h-tau      (htau))))

                        )
              
              (component (type pore)
			 (const  gbar_CaBK  = 0.007)
			 (output gbar_CaBK ))
              
              (component (type permeating-ion) (name k)
			 (const e_CaBK = ek)
			 (output e_CaBK))
              
              ;; end BK current
              )

   
  (component (type ionic-current) (name CaP)
              ;; HH P-type Calcium current

             (input 
              (cai from ion-pools)
              (cao from ion-pools))
              
             (component (type gate)

                        
                        ;; rate functions
                        (inf =  (let ((cv  -19)  (ck  5.5))
	                          (1.0 / (1.0 + exp (neg ((v - cv) / ck))))))

                        (tau = ((1e3) *
	                        (if (v > -50) 
                                    then (0.000191 + (0.00376 * exp (neg (((v + 41.9) / 27.8) ^ 2))))
                                    else (0.00026367 + (0.1278 * exp (0.10327 * v))))))


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

             (component (type permeability)

                        (fun ghk (v ci co)
                             (let ((F  9.6485e4)
                                   (R  8.3145)
                                   (T  (22 + 273.19))  
                                   (Z  2)
                                   (E  ((1e-3) * v)))
                               (let ((k0 ((Z * (F * E)) / (R * T))))
                                 (let ((k1 (exp (neg (k0))))
                                       (k2 (((Z ^ 2) * (E * (F ^ 2))) / (R * T))))
                                   (1e-6) * (if (abs (1 - k1) < 1e-6) 
                                                then (Z * F * (ci - (co * k1)) * (1 - k0))
                                                else (k2 * (ci - (co * k1)) / (1 - k1)))))))
			 
                        (const pcabar  = 0.00005)
                        (pca           = (pcabar * ghk (v cai cao)))

                        (output pca pcabar))
              
             (component (type permeating-ion) (name ca))

             ;; end CaP current
             )


  (component (type ionic-current) (name K1)
             
             ;; HH TEA-sensitive Purkinje potassium current

             (component (type gate)

			 ;; constants

			 ;; rate functions
                        
                        (K1_v = (v + 11)) ;; account for junction potential

                        (minf = (let ((mivh -24)
		                      (mik  15.4))
                                  (1 / (1 + exp (neg (K1_v - mivh) / mik)))))


                        (mtau = (let ((mty0   0.00012851)
	                              (mtvh1  100.7)
		                      (mtk1   12.9)
		                      (mtvh2  -56.0)
		                      (mtk2   -23.1))
                                  (1e3 * (if (K1_v < -35) 
                                             then (3.0 * (3.4225e-5 + 0.00498 * exp (neg (K1_v) / -28.29)))
                                             else (mty0 + 1.0 / (exp ((K1_v + mtvh1) / mtk1) + exp ((K1_v + mtvh2) / mtk2)))
                                             ))))

                        (hinf = (let ((hiy0  0.31)
		                      (hiA   0.78)
		                      (hivh  -5.802)
		                      (hik   11.2))
                                  (hiy0 + hiA / (1 + exp ((K1_v - hivh) / hik)))))


                        (htau =  (1e3 * (if ( K1_v > 0 ) 
                                            then (0.0012 + 0.0023 * exp (-0.141 * K1_v))
                                            else (1.2202e-05 + 0.012 * exp (neg (((K1_v - (-56.3)) / 49.6) ^ 2))))))

                        (hh-ionic-gate 
                         (K1  ;; ion name: exported variables will be of the form {ion}_{id}
                          (initial-m  (minf))
                          (initial-h  (hinf))
                          (m-power    3)
                          (h-power    1)
                          (m-inf      (minf))
                          (m-tau      (mtau))
                          (h-inf      (hinf))
                          (h-tau      (htau))))

                        )
              
             (component (type pore)
                        (const  gbar  = 0.004)
                        (output gbar))
              
             (component (type permeating-ion) (name k)
                        (const e = ek)
                        (output e))
             
             ;; end K1 current
             )


  (component (type ionic-current) (name K2)
             ;; HH Low TEA-sensitive Purkinje potassium current
             
             (component (type gate)
                        
                        ;; constants
                        
                        ;; rate functions
                        
                        (K2_v = (v + 11)) ;; account for junction potential

                        (minf = (let ((mivh -24)
		                      (mik  20.4))
                                  (1 / (1 + exp ((neg (K2_v - mivh)) / mik)))))


                        (mtau = ((1e3) * (if (K2_v < -20) 
                                             then (0.000688 + 1 / (exp ((K2_v + 64.2) / 6.5) + exp ((K2_v - 141.5) / -34.8)))
                                             else (0.00016 + 0.0008 * exp (-0.0267 * K2_v)))))
                              
			 
                        (hh-ionic-gate 
                         (K2  ;; ion name: exported variables will be of the form {ion}_{id}
                          (initial-m  (minf))
                          (m-power    4)
                          (h-power    0)
                          (m-inf      (minf))
                          (m-tau      (mtau))))
                        )
              
             (component (type pore)
                        (const  gbar  = 0.002)
                        (output gbar))
              
             (component (type permeating-ion) (name k)
                        (const e = ek)
                        (output e))
              
             ;; end K2 current
             )

	
  (component (type ionic-current) (name K3)
             ;; HH slow TEA-insensitive Purkinje potassium current
             
             (component (type gate)
                        
                        ;; constants

                        ;; rate functions

                        (K3_v = (v + 11)) ;; account for junction potential

                        (minf = (let ((mivh -16.5)
		                      (mik  18.4))
                                  (1 / (1 + exp ((neg (K3_v - mivh)) / mik)))))


                        (mtau = ((1e3) * (0.000796 + 1.0 / (exp ((K3_v + 73.2) / 11.7) + exp ((K3_v - 306.7) / -74.2)))))
			 
                        (hh-ionic-gate 
                         (K3  ;; ion name: exported variables will be of the form {ion}_{id}
                          (initial-m  (minf))
                          (m-power    4)
                          (h-power    0)
                          (m-inf      (minf))
                          (m-tau      (mtau))))
                        )

             
             (component (type pore)
                        (const  gbar  =  0.004)
                        (output gbar))
              
             (component (type permeating-ion) (name k)
                        (const e = ek)
                        (output e))
              ;; end K3 current

             )

  
  (component (type ionic-current) (name Narsg) 
             
             ;; constants
             
             (component (type gate)
				
                        (const Con   = 0.005)
                        (const Coff  = 0.5)
                        (const Oon   = 0.75)
                        (const Ooff  = 0.005)

                        (const alfac = (pow ((Oon / Con) (1.0 / 4.0))))
                        (const btfac = (pow ((Ooff / Coff) (1.0 / 4.0))))
                         
                        (const alpha = 150)
                        (const beta  = 3)
                        (const gamma = 150)
                        (const delta = 40)
                        (const epsilon = 1.75)
                        (const zeta = 0.03)
                        (const x1 = 20)
                        (const x2 = -20)
                        (const x3 = 1e12)
                        (const x4 = -1e12)
                        (const x5 = 1e12)
                        (const x6 = -25)
  
                         ;; rate functions
                         
                        (f01 = (4.0 * alpha * exp (v / x1)))
                         (f02 = (3.0 * alpha * exp (v / x1)))
                         (f03 = (2.0 * alpha * exp (v / x1)))
                         (f04 = (alpha * exp (v / x1)))
                         (f0O = (gamma * exp (v / x3)))
                         (fip = (epsilon * exp (v / x5)))
                         (f11 = (4.0 * alpha * alfac * exp (v / x1)))
                         (f12 = (3.0 * alpha * alfac * exp (v / x1)))
                         (f13 = (2.0 * alpha * alfac * exp (v / x1)))
                         (f14 = (alpha * alfac * exp (v / x1)))
                         (f1n = (gamma * exp (v / x3)))
                         
                         (fi1 = (Con))
                         (fi2 = (Con * alfac))
                         (fi3 = (Con * alfac * alfac))
                         (fi4 = (Con * alfac * alfac * alfac))
                         (fi5 = (Con * alfac * alfac * alfac * alfac))
                         (fin = (Oon))
		 
                         (b01 = (beta * exp (v / x2)))
                         (b02 = (2.0 * beta * exp (v / x2)))
                         (b03 = (3.0 * beta * exp (v / x2)))
                         (b04 = (4.0 * beta * exp (v / x2)))
                         (b0O = (delta * exp (v / x4)))
                         (bip = (zeta * exp (v / x6)))
                         
                         (b11 = (beta * btfac * exp (v / x2)))
                         (b12 = (2.0 * beta * btfac * exp (v / x2)))
                         (b13 = (3.0 * beta * btfac * exp (v / x2)))
                         (b14 = (4.0 * beta * btfac * exp (v / x2)))
                         (b1n = (delta * exp (v / x4)))
                         
                         (bi1 = (Coff))
                         (bi2 = (Coff * btfac))
                         (bi3 = (Coff * btfac * btfac))
                         (bi4 = (Coff * btfac * btfac * btfac))
                         (bi5 = (Coff * btfac * btfac * btfac * btfac))
                         (bin = (Ooff))

                         (reaction
                          (Narsg_z
                           (transitions
                            (<-> C1 C2 f01 b01)
                            (<-> C2 C3 f02 b02)
                            (<-> C3 C4 f03 b03)
                            (<-> C4 C5 f04 b04)
                            (<-> C5 O  f0O b0O)
                            (<-> O  B  fip bip)
                            (<-> O  I6 fin bin)
                            (<-> C1 I1 fi1 bi1)
                            (<-> C2 I2 fi2 bi2)
                            (<-> C3 I3 fi3 bi3)
                            (<-> C4 I4 fi4 bi4)
                            (<-> C5 I5 fi5 bi5)
                            (<-> I1 I2 f11 b11)
                            (<-> I2 I3 f12 b12)
                            (<-> I3 I4 f13 b13)
                            (<-> I4 I5 f14 b14)
                            (<-> I5 I6 f1n b1n)
                            )
                           (conserve ((1 = (I1 + I2 + I3 + I4 + I5 + I6 + C1 + C2 + C3 + C4 + C5 + O + B))))
                           (open O)
                           (power 1))
                           )
                   
                         (output Narsg_z)
                         )
             
             (component (type pore)
                        (const  gbar  = 0.015)
                        (output gbar))
		
             (component (type permeating-ion) (name na)
                        (const e = ena)
                        (output e))

             )
                         
  (component (type ionic-current) (name Ih)
              
             (component (type gate)
                         
                        ;; rate functions
                        
                        (inf = (1.0 / (1.0 + exp ((v + 90.1) / 9.9))))
			 
                        (tau = ((1e3) * (0.19 + 0.72 * exp (neg (((v - (-81.5)) / 11.9) ^ 2)))))

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

              (component (type pore)
			 (const  gbar  = 0.0001)
			 (output gbar))
              
              (component (type permeating-ion) (name non-specific)
                         (const e = -30)
                         (output e))
              
              ;; end Ih current
              )
	
  (component (type ionic-current) (name Leak)
              
             (component (type pore)
                        (const  gbar  = 5e-5)
                        (output gbar))
              
             (component (type permeating-ion) (name non-specific)
                        (const e = -60)
                        (output e))
              
             ;; end leak current
             )


  (component (type voltage-clamp) (name K1)
           
             (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 voltage-clamp) (name K2)
   
             (const vchold   = -71)
             (const vcbase   = -69)
             (const vcinc    = 10)
             (const vcsteps  = 9)
             (const vchdur   = 30)
             (const vcbdur   = 100)

           (output vchold vcbase vcinc vcsteps vchdur vcbdur)
           )


  (component (type voltage-clamp) (name K3)

             (const vchold   = -71)
             (const vcbase   = -61)
             (const vcinc    = 10)
             (const vcsteps  = 8)
             (const vchdur   = 30)
             (const vcbdur   = 100)

           (output vchold vcbase vcinc vcsteps vchdur vcbdur)
           )


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

             (const vchold   = -90)
             (const vcbase   = -40)
             (const vcinc    = 10)
             (const vcsteps  = 5)
             (const vchdur   = 5)
             (const vcbdur   = 20)

             (component (type default-concentration) (name ca)
                        (const cn       = 1e-4)
                        (const cnout    = 2)
                        (output cn cnout))
             
             (output vchold vcbase vcinc vcsteps vchdur vcbdur)
             )


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

             (const vchold   = -90)
             (const vcbase   = -90)
             (const vcinc    = 10)
             (const vcsteps  = 11)
             (const vchdur   = 5)
             (const vcbdur   = 10)

             (component (type default-concentration) (name ca)
                        (const cn       = 1e-4)
                        (const cnout    = 2)
                        (output cn cnout))
             
             (output vchold vcbase vcinc vcsteps vchdur vcbdur)
             )


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

             (const vchold   = -50)
             (const vcbase   = -60)
             (const vcinc    = -10)
             (const vcsteps  = 7)
             (const vchdur   = 100)
             (const vcbdur   = 200)

           (output vchold vcbase vcinc vcsteps vchdur vcbdur)
           )


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

             (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
	diam = 20
	L = 20
        cm = 1
    }

EOF
)

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

public soma

create soma

proc init() {

  soma {
	nseg = 1
	diam = 20
	L = 20
        cm = 1

        insert {{model_name}}_ca
        insert {{model_name}}_CaBK
        insert {{model_name}}_CaP
        insert {{model_name}}_K1
        insert {{model_name}}_K2
        insert {{model_name}}_K3
        insert {{model_name}}_Narsg
        insert {{model_name}}_Ih
        insert {{model_name}}_Leak

        ena = 60
        ek = -88
        cai = 1e-4
  }
}

endtemplate Purkinje
EOF
)


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

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

{% with tstop = default(tstop, 3000) %}
tstop = {{tstop}}
{% endwith %}

dt = 0.025

objref pc
pc = new Purkinje()

stim_amp=0.01875

objref stim
pc.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 (&pc.soma.v(0.5))

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

run()

objref output_file
output_file = new File()
output_file.wopen("Purkinje.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
)


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

echo "Bootstrapping {{model_name}} 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({{model_name}}module, 1.0, raikov@oist.jp)

# These variables are exported to include/config.h
{{model_name}}MODULE_MAJOR=1
{{model_name}}MODULE_MINOR=0
{{model_name}}MODULE_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, ${{model_name}}MODULE_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_WARN([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

{{model_name}}MODULE_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
# {{model_name}}MODULE_SET_CXXFLAGS
AM_CXXFLAGS=${{model_name}}MODULE_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({{model_name}}module_config.h:{{model_name}}module_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 "{{model_name}} 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 {{model_name}} module now, using"
echo "  make"
echo "  make install"
echo
echo "{{model_name}} 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
# 
# lib{{model_name}}module 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=      {{model_name}}module.la lib{{model_name}}module.la

{{model_name}}module_la_CXXFLAGS= @AM_CXXFLAGS@
{{model_name}}module_la_SOURCES=  {{model_name}}module.cpp      {{model_name}}module.h      \
                      {{model_name}}.cpp {{model_name}}.h 
{{model_name}}module_la_LDFLAGS=  -module

lib{{model_name}}module_la_CXXFLAGS= $({{model_name}}module_la_CXXFLAGS) -DLINKED_MODULE
lib{{model_name}}module_la_SOURCES=  $({{model_name}}module_la_SOURCES)

MAKEFLAGS= @MAKE_FLAGS@

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

AM_LDFLAGS = @SUNDIALS_LDFLAGS@

.PHONY: install-slidoc

nobase_pkgdata_DATA=\
	{{model_name}}module.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
/*
 *  {{model_name}}module.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 "{{model_name}}module.h"
#include "{{model_name}}.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.
 */
 
{{model_name}}nest::{{model_name}}Module {{model_name}}module_LTX_mod;

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

{{model_name}}nest::{{model_name}}Module::{{model_name}}Module()
  { 
#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     
   }

{{model_name}}nest::{{model_name}}Module::~{{model_name}}Module()
   {
   }

   const std::string {{model_name}}nest::{{model_name}}Module::name(void) const
   {
     return std::string("{{model_name}} Module"); // Return name of the module
   }

   const std::string {{model_name}}nest::{{model_name}}Module::commandstring(void) const
   {
     /* 1. Tell interpreter that we provide the C++ part of {{model_name}}Module with the
           current revision number. 
        2. Instruct the interpreter to check that {{model_name}}module-init.sli exists, 
           provides at least version 1.0 of the SLI interface to {{model_name}}Module, and
           to load it.
      */
     return std::string(
       "/{{model_name}}module /C++ ($Revision: 8512 $) provide-component "
       "/{{model_name}}module /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 {{model_name}}nest::{{model_name}}Module::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 {{model_name}}nest::{{model_name}}Module::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.
    */
       nest::register_model<nest::{{model_name}}>(nest::NestModule::get_network(), 
					    "{{model_name}}");


    /* 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 {{model_name}}module-init.sli file.
    */
    i->createcommand("StepPatternConnect_Vi_i_Vi_i_l", 
                     &stepPatternConnect_Vi_i_Vi_i_lFunction);

  }  // {{model_name}}Module::init()

 

EOF
)

    ("nestmodule.h" ()  
#<<EOF
/*
 *  {{model_name}}module.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 {{model_name}}MODULE_H
#define {{model_name}}MODULE_H

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

namespace nest
{
  class Network;
}

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

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

  /**
   * 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 {{model_name}}module 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 {{model_name}}nest

#endif

EOF
)

    ("module.sli" ()  
#<<EOF
/* 
 * Initialization file for {{model_name}}Module.
 * Run automatically when {{model_name}}Module is loaded.
 */

M_DEBUG ({{model_name}}module.sli) (Initializing SLI support for {{model_name}}Module.) message

/{{model_name}}module /SLI ($Revision: 7918 $) provide-component
/{{model_name}}module /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

ResetKernel
0
 << 
   /resolution  dt 
 >> SetStatus

({{model_name}}module) Install
/neuron /{{model_name}} Create def
/neuron_params << /V_m -65.0 >> def
neuron neuron_params SetStatus

/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. 18.75 0. ] >> def
stepinput step_current_parameters SetStatus

3000.0 Simulate

EOF
)


))