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Avoid errors with STATE variables without DERIVATE block #2

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merged 4 commits into from
May 30, 2022
Merged

Avoid errors with STATE variables without DERIVATE block #2

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67001b5
NEURON 9.0 compatibility.
olupton May 17, 2022
55ad03c
Avoid errors with STATE variables without DERIVATE block
pramodk May 23, 2022
ab7dc6e
Convert STATE variables to ASSIGN and revert previous change
pramodk May 24, 2022
4fa51ba
update readme
pramodk May 24, 2022
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12 changes: 12 additions & 0 deletions README.html
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Expand Up @@ -91,5 +91,17 @@
For any questions or further assistance please contact:
salvadordura at gmail.com


------------------------------------------------------------------------------------------------------
Changelog
-------------------------------------------------------------------------------------------------------

2022-05:
* Updated MOD files to compile with upcoming 9.0 neuron release
with migration to C++.
* izhi2007.mod is updated in order to compile with current neuron
releases where STATE variables without ODEs or SOLVE block gives an error.
See discussion in https://github.com/ModelDBRepository/194897/pull/2

</pre></html>

10 changes: 4 additions & 6 deletions izhi2007.mod
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Expand Up @@ -78,13 +78,12 @@ ASSIGNED {
:t0 : Previous time
factor : Voltage factor used for calculating the current
eventflag : For diagnostic information
}

: State variables without ODEs / SOLVE block and hence converted
: to ASSIGN. See https://github.com/ModelDBRepository/194897/pull/2

: State variables
STATE {
V (mV) : Membrane voltage
u (mV) : Slow current/recovery variable
V : Membrane voltage
u : Slow current/recovery variable
gAMPA : AMPA conductance
gNMDA : NMDA conductance
gGABAA : GABAA conductance
Expand Down Expand Up @@ -125,7 +124,6 @@ PROCEDURE useverbose() { : Create user-accessible function
}



: Define neuron dynamics
BREAKPOINT {
delta = t-t0 : Find time difference
Expand Down
7 changes: 6 additions & 1 deletion nsloc.mod
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Expand Up @@ -79,8 +79,13 @@ FUNCTION invl(mean (ms)) (ms) {
}
}
VERBATIM
#ifndef NRN_VERSION_GTEQ_8_2_0
double nrn_random_pick(void* r);
void* nrn_random_arg(int argpos);
#define RANDCAST
#else
#define RANDCAST (Rand*)
#endif
ENDVERBATIM

FUNCTION erand() {
Expand All @@ -91,7 +96,7 @@ VERBATIM
: each instance. However, the corresponding hoc Random
: distribution MUST be set to Random.negexp(1)
*/
_lerand = nrn_random_pick(_p_donotuse);
_lerand = nrn_random_pick(RANDCAST _p_donotuse);
}else{
/* only can be used in main thread */
if (_nt != nrn_threads) {
Expand Down
14 changes: 7 additions & 7 deletions vecevent.mod
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Expand Up @@ -32,8 +32,8 @@ NET_RECEIVE (w) {

DESTRUCTOR {
VERBATIM
void* vv = (void*)(_p_ptr);
if (vv) {
IvocVect* vv = (IvocVect*)(_p_ptr);
if (vv) {
hoc_obj_unref(*vector_pobj(vv));
}
ENDVERBATIM
Expand All @@ -46,8 +46,8 @@ VERBATIM
if (i >= 0) {
vv = (void*)(_p_ptr);
if (vv) {
size = vector_capacity(vv);
px = vector_vec(vv);
size = vector_capacity((IvocVect*)vv);
px = vector_vec((IvocVect*)vv);
if (i < size) {
etime = px[i];
index += 1.;
Expand All @@ -65,15 +65,15 @@ ENDVERBATIM
PROCEDURE play() {
VERBATIM
void** pv;
void* ptmp = NULL;
IvocVect* ptmp = NULL;
if (ifarg(1)) {
ptmp = vector_arg(1);
hoc_obj_ref(*vector_pobj(ptmp));
}
pv = (void**)(&_p_ptr);
if (*pv) {
hoc_obj_unref(*vector_pobj(*pv));
hoc_obj_unref(*vector_pobj((IvocVect*)*pv));
}
*pv = ptmp;
ENDVERBATIM
}
}