// GENESIS SETUP FILE
silent
int i
str tstr, hstr, readcompartment
//initialize parameters
include ../common/genesis_funcs_nws.g
include ../common/GP1_defaults_nws_syn.g
//include ../common/simdefaults.g
//include ../common/simdefaults_NaF_art.g
include ../common/simdefaults_synBack.g
/* COMMENT
ALL intrinsic model params have now been initialized and set.
They can be safely overwritten any time between now and the calling of
the make_GP_library file. Once the library has been created, parameter values
are set and cannot be changed except with explicit calls to setfield.
*/
int i
str tstr, hstr, readcompartment
//PARAMETERS:
float stimType = //set from parameter file
// 1, 2, 3, 4, or 5 for CIP, uniform EXC synaptic, uniform INH synaptic, weighted EXC synaptic, weighted INH synaptic
float stimMag = //set from parameter file
// in pA if CIP or pS if synaptic
float stimInterval = //set from parameter file
float stimDur = //set from parameter file
// unneccessary if stimType is synaptic
float stimComptsIdx = //set from parameter file
// a number reflecting a list of compartments receiving the stimulus
// (either soma, or a subset of dendritic compts)
//float modelType = {getarg {arglist {parrow}} -arg 6}
float modelType = 3
// 1 or 2 for nonspiking or spiking
float currentComptsIdx = //set from parameter file
// a number reflecting the grouping of compartment conductances to be saved
// 1 for FULL, 2 for THIRDS, 3 for SUB, etc.
float voltageComptsIdx = //set from parameter file
// a number reflecting the group of compartment voltages to be saved
float HVA_PRC_scalefac = //set from parameter file
float SK_PRC_scalefac = //set from parameter file
//float KV4F_PRC_scalefac = {getarg {arglist {parrow}} -arg 11}
float KV4F_PRC_scalefac = 1
//float KV4S_PRC_scalefac = {getarg {arglist {parrow}} -arg 12}
float KV4S_PRC_scalefac = 1
float store_mode = //set from parameter file
store_mode = 2
STN_rate = //set from parameter file
striatum_rate = //set from parameter file
// 0 is asynchronous and 1 is synchronous
//float synBack_synch = {getarg {arglist {parrow}} -arg 14}
float synBack_synch = 0
float spikeIdx = //set from parameter file
//spikeIdx = ({spikeIdx}+25)
float syngain = //set from parameter file
float NaF_base = //set from parameter file
float NaP_base = //set from parameter file
float KV2_base = //set from parameter file
//float KV3_base = {KV2_base}
float KV3_base = //set from parameter file
//KV3_base = ({KV2_base}*10)
float KV4_base = //set from parameter file
// Start with 75
float HVA_base = //set from parameter file
float SK_base = //set from parameter file
float KCNQ_base = //set from parameter file
float spiCurDist = //set from parameter file
//float spiCurDist = 11.11111
spiCurDist = ({spiCurDist}/100)
float dendSpiCurMult = //set from parameter file
float NaPdendmult = //set from parameter file
//float NaISMult = {getarg {arglist {parrow}} -arg 25}
float NaISMult = 57
//float KdrISMult = {getarg {arglist {parrow}} -arg 26}
float KdrISMult = 40
float SKsomaMult = //set from parameter file
float SKdendMult = //set from parameter file
//float NaF_dq10_m = {getarg {arglist {parrow}} -arg 22}
float NaF_dq10_m = .25
float dq10_NaF_m = {NaF_dq10_m}
//float NaF_dq10_h1 = {getarg {arglist {parrow}} -arg 23}
float NaF_dq10_h1 = .6667
float dq10_NaF_h1 = {NaF_dq10_h1}
//float NaF_dq10_h2 = {getarg {arglist {parrow}} -arg 24}
float NaF_dq10_h2 = 1
float dq10_NaF_h2 = {NaF_dq10_h2}
//float KV2_taunDiv = {getarg {arglist {parrow}} -arg 26}
float KV2_taunDiv = 1
//float KV3_taunDiv = {getarg {arglist {parrow}} -arg 27}
float KV3_taunDiv = 1
//float KV4_taunDiv = {getarg {arglist {parrow}} -arg 28}
float KV4_taunDiv = 1
//float Eshift = {getarg {arglist {parrow}} -arg 28}
//float Eshift = 0
float Eshift = {getarg {arglist {parrow}} -arg 28}
echo
echo Eshift is {Eshift} mV
echo
Eshift = {Eshift}/1000
//float constcurr_loc = {getarg {arglist {parrow}} -arg 28}
float constcurr_loc = 1
//float NaPdendmult = {getarg {arglist {parrow}} -arg 27}
E_AMPA = 0+{Eshift}
E_NMDA = 0+{Eshift}
E_GABA = -0.080+{Eshift}
float GsynMult = 0
float Esyn = -0.06
float Rmembr = {RM_sd}
float Gcomb = ({GsynMult}+1)*(1/{Rmembr})
float Ecomb = ({ELEAK_sd}+{GsynMult}*{Esyn})/({GsynMult}+1)
RM_sd = 1/{Gcomb}
//RM_ax = 1/{Gcomb}
ELEAK_sd = {Ecomb}
//ELEAK_ax = {Ecomb}
echo
echo spikeidx {spikeIdx}
echo syngain {syngain}
echo
include ../common/calc_syn_integ.g
float unitary_gSTN = {calc_syn_integ 250 .001 .003}
echo unitary_gSTN is {unitary_gSTN}
float unitary_gSTR = {calc_syn_integ 250 .0005 .00491}
echo unitary_gSTR is {unitary_gSTR}
//quit
float snapgate = 0
if ({snapgate}==1)
str out_dir = "/data/snapshots/simData_synGrid_alldata/"
str spktime_dest_dir = "/data/snapshots/spiketimes_synGrid_alldata/"
mkdir {spktime_dest_dir}
mkdir {out_dir}
else
str out_dir = "/data/simData_synGrid_alldata/"
str spktime_dest_dir = "/data/spiketimes_synGrid_alldata/"
mkdir {spktime_dest_dir}
mkdir {out_dir}
end
if ({store_mode}==1)
str strStoreMode = "currents_"
end
if ({store_mode}==2)
str strStoreMode = "conductances_"
end
// use conductance scalefacs from par file to set multipliers
include ../common/g_mult_PRC2
// Nonspiking or spiking model? Include appropriate passive or active parameters:
if ({modelType}==1)
include ../common/paspars.g
str strModel = "_nonspiking_"
end
if ({modelType}==2)
include ../common/actpars.g
str strModel = "_spiking_"
end
if ({modelType}==3)
// include ../common/varpars_newGP_dendNaP.g
include ../common/varpars_GPbase_synback.g
str strModel = "_GPbase_"
end
// stimComptsNum reflects the number of compartments receiving a stimulus
float stimComptsNum
if ({stimComptsIdx}==1)
include ../common/stimComptsIdxs1toTen
else
include ../common/stimComptsIdxs11toSeventeen
end
if ({stimType}==1)
str strStim = "_cipStim_"
end
if ({stimType}==2)
str strStim = "_EXCsynStim_"
end
if ({stimType}==3)
str strStim = "_INHsynStim_"
end
// include list of control spike times for calculation of stimTimes:
//include ../common/dendComptGroups/control_spikeTimes_PRC
//include ../common/dendComptGroups/control_spikeTimes_dendComptGroups
//include ../common/control_spikeTimes_GPbase_synback_oscillator
//include ../common/control_spikeTimes_GPbase_synback_Eshift
//include ../common/control_spikeTimes_synback_Eshift_CNS09_paper2
include ../common/control_spikeTimes_synback_synGrid
// if CIP stimulus:
if ({stimType}==1)
float cip = {stimMag}
cip = {cip}/{stimComptsNum}
float cipTime = {{spike1time}+{{({stimInterval}-1)}*{({spike2time}-{spike1time})}/72}}
echo
echo Stimulus time is {cipTime}
float cipDur = {stimDur}
echo The current injected into each compartment of {strStimLoc} is {cip} pA
echo
else
//if synaptic stimulation:
float Gmax_PRC = {stimMag}
Gmax_PRC = {Gmax_PRC}/((1e12)*{stimComptsNum})
float synTime = {spike1time} + {{({stimInterval}-1)}*{({spike2time}-{spike1time})}/72}
end
// Now that all params have been established, create library objects.
// Intrinsic params should be left alone from this point forward.
echo
echo cci is {currentComptsIdx}
echo
include ../common/make_GP_library_NaF_art.g
//filename based on variable parameters (don't include path!)
if ({stimType}==1)
if ({stimMag}==0)
str basefilename = {stimMag} @ "_pA_" @ {strStimLoc} @ {spikeIdx} @ "_spikeIdx_" @ {syngain} @ "_syngain_" @ {STN_rate} @ "_STNrate_" @ {striatum_rate} @ "_STRIATUMrate_" @ {spiCurDist} @ "_dist_" @ {Eshift} @ "_Eshift_" @ {dendSpiCurMult} @ "_dendIspikeMult_" @ {NaPdendmult} @ "_NaPdendmult_" @ {SKsomaMult} @ "_SKsomaX_" @ {SKdendMult} @ "_SKdendX_" @ {stimType} @ {strStim} @ "GPbase_baseModels_SynBackControl_"
else
str basefilename = {pad_num_gen {stimInterval} 3} @ "_stimInt_" @ {stimMag} @ "_pA_" @ {cipTime} @ "_msTime_" @ {cipDur} @ "_msDur" @ {strStimLoc} @ {spikeIdx} @ "_spikeIdx_" @ {syngain} @ "_syngain_" @ {STN_rate} @ "_STNrate_" @ {striatum_rate} @ "_STRIATUMrate_" @ {spiCurDist} @ "_dist_" @ {Eshift} @ "_Eshift_" @ {dendSpiCurMult} @ "_dendIspikeMult_" @ {NaPdendmult} @ "_NaPdendmult_" @ {SKsomaMult} @ "_SKsomaX_" @ {SKdendMult} @ "_SKdendX_" @ {stimType} @ {strStim} @ "GPbase_baseModels_SynBack_"
end
end
if (! ({stimType}==1))
if ({stimMag}==0)
str basefilename = {stimMag} @ "_pS_" @ {strStimLoc} @ {spikeIdx} @ "_spikeIdx_" @ {syngain} @ "_syngain_" @ {STN_rate} @ "_STNrate_" @ {striatum_rate} @ "_STRIATUMrate_" @ {spiCurDist} @ "_dist_" @ {Eshift} @ "_Eshift_" @ {dendSpiCurMult} @ "_dendIspikeMult_" @ {NaPdendmult} @ "_NaPdendmult_" @ {SKsomaMult} @ "_SKsomaX_" @ {SKdendMult} @ "_SKdendX_" @ {stimType} @ {strStim} @ "GPbase_baseModels_SynBackControl_"
else
str basefilename = {pad_num_gen {stimInterval} 3} @ "_stimInt_" @ {stimMag} @ "_pS_" @ {synTime} @ "_msTime_" @ {stimDur} @ "_msDur" @ {strStimLoc} @ {spikeIdx} @ "_spikeIdx_" @ {syngain} @ "_syngain_" @ {STN_rate} @ "_STNrate_" @ {striatum_rate} @ "_STRIATUMrate_" @ {spiCurDist} @ "_dist_" @ {Eshift} @ "_Eshift_" @ {dendSpiCurMult} @ "_dendIspikeMult_" @ {NaPdendmult} @ "_NaPdendmult_" @ {SKsomaMult} @ "_SKsomaX_" @ {SKdendMult} @ "_SKdendX_" @ {stimType} @ {strStim} @ "GPbase_baseModels_SynBack_"
end
end
if ({currentComptsIdx}==4)
str strCurrentsLoc = {currentComptsIdx} @ "_dend1" @ {strStoreMode}
str strCaLoc = {currentComptsIdx} @ "_dend1calcium_"
end
if ({currentComptsIdx}==5)
str strCurrentsLoc = {currentComptsIdx} @ "_dend2" @ {strStoreMode}
str strCaLoc = {currentComptsIdx} @ "_dend2calcium_"
end
if ({currentComptsIdx}==6)
str strCurrentsLoc = {currentComptsIdx} @ "_dend3" @ {strStoreMode}
str strCaLoc = {currentComptsIdx} @ "_dend3calcium_"
end
if ({voltageComptsIdx}==1)
str strVoltagesLoc = {voltageComptsIdx} @ "_somaVm_"
end
if ({voltageComptsIdx}==2)
str strVoltagesLoc = {voltageComptsIdx} @ "_stimlocVms_"
end
if ({voltageComptsIdx}==3)
str strVoltagesLoc = {voltageComptsIdx} @ "_dend1voltages_"
end
if ({voltageComptsIdx}==4)
str strVoltagesLoc = {voltageComptsIdx} @ "_dend2voltages_"
end
if ({voltageComptsIdx}==5)
str strVoltagesLoc = {voltageComptsIdx} @ "_dend3voltages_"
end
echo {basefilename}
str filename_v = {basefilename} @ {strVoltagesLoc} @ "v.bin"
str filename_gtot = {basefilename} @ {strCurrentsLoc} @ "itot.bin"
str filename_ca = {basefilename} @ {strCaLoc} @ "ca.bin"
str filename_gsyns = {basefilename} @ "_gsyns.bin"
str filename_mhhnn = {basefilename} @ "mhhnn.bin"
dt = 2e-5
if ({snapgate}==1)
dt = 1e-5
echo
echo This should not be happening except for snapshot simulations!!!!!!!
echo
end
//set up clocks
setclock 0 {dt} // simulation
//output set to 1e-4 under normal circumstances
setclock 1 {1e-4} // output
//rundur = 13.5 // simulation length
//rundur = {({spike6time}/1000)+(.05)}
rundur=1
if ({snapgate}==1)
rundur = 10
end
if (({snapgate}==0) & ({stimMag}==0))
rundur = 2
end
//load compartments with ion channels
//if ({currentComptsIdx}==1)
// readcell ../common/GP1/GP1_FULLdendsort.p {cellpath} -hsolve
//end
//if ({currentComptsIdx}==2)
// readcell ../common/GP1/GP1_THIRDSdendsort.p {cellpath} -hsolve
//end
//if ({currentComptsIdx}==3)
// readcell ../common/GP1/GP1_SUBdendsort.p {cellpath} -hsolve
//end
if (({currentComptsIdx}>=4) & ({currentComptsIdx}<=6))
readcell ../common/GP1_dendComptGroups.p {cellpath} -hsolve
end
//add synapses to appropriate compartments
include ../common/read_STN_nocluster_ratescaled_nws_Kopell
/*
if ({currentComptsIdx}==1)
include ../common/read_clusters_FULLdendsort
end
if ({currentComptsIdx}==2)
include ../common/read_clusters_THIRDSdendsort
end
if ({currentComptsIdx}==3)
include ../common/read_clusters_SUBdendsort
end
if (({currentComptsIdx}>=4) & ({currentComptsIdx}<=6))
include ../common/read_clusters_dendComptGroups
end
*/
include ../common/read_striatum_syns_ratescaled_nws_Kopell
include ../common/add_pallidum_syns
create pulsegen /constantcurrent
setfield /constantcurrent \
level1 {0e-12} \
width1 11 \
delay1 0 \
delay2 50 \
baselevel 0 \
trig_mode 0
str readcompartment
if ({constcurr_loc}==1)
str constcurr_filename = "../common/comptlists/constcurr_soma.txt"
end
if ({constcurr_loc}==2)
str constcurr_filename = "../common/comptlists/constcurr_axIS.txt"
end
openfile {constcurr_filename} r
readcompartment = {readfile {constcurr_filename}}
while (! {eof {constcurr_filename}})
addmsg /constantcurrent {cellpath}/{readcompartment} INJECT output
readcompartment = {readfile {constcurr_filename}}
end
closefile {constcurr_filename}
//set up current injection
if ({stimType}==1)
create pulsegen /pulse
setfield /pulse \
level1 {{cip}*1e-12} \
width1 {{cipDur}*1e-3} \
delay1 {{cipTime}*1e-3} \
delay2 50 \
baselevel 0 \
trig_mode 0
// NWS: add msg with while loop to distribute CIP
str readcompartment
if ({stimComptsIdx}==1)
str CIPfilename = "../common/comptlists/nws_soma_only.txt"
end
if ({stimComptsIdx}==2)
str CIPfilename = "../common/comptlists/nws_proximal_FULLdendcompts.txt"
end
if ({stimComptsIdx}==3)
str CIPfilename = "../common/comptlists/nws_mid_FULLdendcompts.txt"
end
if ({stimComptsIdx}==4)
str CIPfilename = "../common/comptlists/nws_distal_FULLdendcompts.txt"
end
if ({stimComptsIdx}==5)
str CIPfilename = "../common/comptlists/nws_proximal_THIRDSdendcompts.txt"
end
if ({stimComptsIdx}==6)
str CIPfilename = "../common/comptlists/nws_mid_THIRDSdendcompts.txt"
end
if ({stimComptsIdx}==7)
str CIPfilename = "../common/comptlists/nws_distal_THIRDSdendcompts.txt"
end
if ({stimComptsIdx}==8)
str CIPfilename = "../common/comptlists/nws_proximal_SUBdendcompts.txt"
end
if ({stimComptsIdx}==9)
str CIPfilename = "../common/comptlists/nws_mid_SUBdendcompts.txt"
end
if ({stimComptsIdx}==10)
str CIPfilename = "../common/comptlists/nws_distal_SUBdendcompts.txt"
end
if ({stimComptsIdx}==11)
str CIPfilename = "../common/comptlists/dend1_proximal25compts.txt"
end
if ({stimComptsIdx}==12)
str CIPfilename = "../common/comptlists/dend1_distal25compts.txt"
end
if ({stimComptsIdx}==13)
str CIPfilename = "../common/comptlists/dend2_proximal25compts.txt"
end
if ({stimComptsIdx}==14)
str CIPfilename = "../common/comptlists/dend2_distal25compts.txt"
end
if ({stimComptsIdx}==15)
str CIPfilename = "../common/comptlists/dend3_proximal25compts.txt"
end
if ({stimComptsIdx}==16)
str CIPfilename = "../common/comptlists/dend3_mid25compts.txt"
end
if ({stimComptsIdx}==17)
str CIPfilename = "../common/comptlists/dend3_distal25compts.txt"
end
openfile {CIPfilename} r
readcompartment = {readfile {CIPfilename}}
while (! {eof {CIPfilename}})
addmsg /pulse {cellpath}/{readcompartment} INJECT output
readcompartment = {readfile {CIPfilename}}
end
closefile {CIPfilename}
end
//default valence (not used with CIP)
if ({stimType}==1)
str valence = "AMPA"
end
if ({stimType}==2 || {stimType}==4)
str valence = "AMPA"
end
if ({stimType}==3 || {stimType}==5)
str valence = "GABA"
end
if ({stimType}==1)
include ../common/PRCsynDend_CIP
else
include ../common/PRCsynDend
end
silent -1
//set up hines solver
setfield {cellpath} \
path {cellpath}/##[][TYPE=compartment] \
comptmode 1 \
chanmode 4 \
calcmode 0 \
outclock 1 \
storemode {store_mode}
call {cellpath} SETUP
setmethod 11
//set up outputs
create disk_out /out_v
useclock /out_v 1
setfield /out_v filename {{out_dir} @ {filename_v}} flush 0 append 0 leave_open 1
create disk_out /out_gsyns
useclock /out_gsyns 1
setfield /out_gsyns filename {{out_dir} @ {filename_gsyns}} flush 0 append 0 leave_open 1
// NWS for simulations with tiny timestep when itot isn't needed, comment out:
create disk_out /out_gtot
useclock /out_gtot 1
setfield /out_gtot filename {{out_dir} @ {filename_gtot}} flush 0 append 0 leave_open 1
create disk_out /out_ca
useclock /out_ca 1
setfield /out_ca filename {{out_dir} @ {filename_ca}} flush 0 append 0 leave_open 1
/*
//save Vm of selected compartments to file: soma, axon, dends
int n
openfile {outputcompsfname} r
readcompartment = {readfile {outputcompsfname}}
while (! {eof {outputcompsfname}})
hstr={findsolvefield {cellpath} {cellpath}/{readcompartment} Vm}
addmsg {cellpath} /out_v SAVE {hstr}
readcompartment = {readfile {outputcompsfname}}
end
closefile {outputcompsfname}
*/
// Save Vm for a sample of compartments
if ({voltageComptsIdx}==1)
str voltageCompts = "../common/comptlists/nws_soma_only.txt"
str calciumCompts = "../common/comptlists/nws_soma_only.txt"
end
if ({voltageComptsIdx}==2)
str voltageCompts = "../common/comptlists/nws_stimloc_subset.txt"
str calciumCompts = "../common/comptlists/nws_noCaConc_in_ax.txt"
end
if ({voltageComptsIdx}==3)
str voltageCompts = "../common/comptlists/save_dend1voltageCompts.txt"
str calciumCompts = "../common/comptlists/save_dend1calciumCompts.txt"
end
if ({voltageComptsIdx}==4)
str voltageCompts = "../common/comptlists/save_dend2voltageCompts.txt"
str calciumCompts = "../common/comptlists/save_dend2calciumCompts.txt"
end
if ({voltageComptsIdx}==5)
str voltageCompts = "../common/comptlists/save_dend3voltageCompts.txt"
str calciumCompts = "../common/comptlists/save_dend3calciumCompts.txt"
end
openfile {voltageCompts} r
readcompartment = {readfile {voltageCompts}}
while(! {eof {voltageCompts}})
// Vm
hstr={findsolvefield {cellpath} {cellpath}/{readcompartment} Vm}
addmsg {cellpath} /out_v SAVE {hstr}
// Gsyn
//hstr={findsolvefield {cellpath} {cellpath}/{readcompartment}/AMPA Gk}
//addmsg {cellpath} /out_gsyns SAVE {hstr}
// Get next compt name
readcompartment = {readfile {voltageCompts}}
end
/*
USED THIS FOR POST-KOPELL WORKSHOP
create disk_out /out_mhhnn
useclock /out_mhhnn 1
setfield /out_mhhnn filename {{out_dir} @ {filename_mhhnn}} flush 0 append 0 leave_open 1
hstr = {findsolvefield {cellpath} {cellpath}/soma Vm}
addmsg {cellpath} /out_mhhnn SAVE {hstr}
//echo {showfield {cellpath}/soma *}
//echo {le {cellpath}/soma/ *}
//echo {showfield {cellpath}/soma/Na_fast_GP_somahill *}
hstr = {findsolvefield {cellpath} {cellpath}/soma/Na_fast_GP_somahill X}
addmsg {cellpath} /out_mhhnn SAVE {hstr}
hstr = {findsolvefield {cellpath} {cellpath}/soma/Na_fast_GP_somahill Y}
addmsg {cellpath} /out_mhhnn SAVE {hstr}
hstr = {findsolvefield {cellpath} {cellpath}/soma/Na_fast_GP_somahill Z}
addmsg {cellpath} /out_mhhnn SAVE {hstr}
hstr = {findsolvefield {cellpath} {cellpath}/soma/Kv3_GP_somahill X}
addmsg {cellpath} /out_mhhnn SAVE {hstr}
hstr = {findsolvefield {cellpath} {cellpath}/soma/Kv2_GP_somahill X}
addmsg {cellpath} /out_mhhnn SAVE {hstr}
*/
create neutral /PRCspiketimes
create spikegen /PRCspiketimes/soma_spikegen
setfield /PRCspiketimes/soma_spikegen \
output_amp 1 thresh 0 abs_refract .002
hstr={findsolvefield {cellpath} {cellpath}/soma Vm}
addmsg {cellpath} /PRCspiketimes/soma_spikegen INPUT {hstr}
create spikehistory /PRCspiketimes/soma_spikehistory
setfield /PRCspiketimes/soma_spikehistory \
filename {{spktime_dest_dir} @ {basefilename} @ "spikehistory.asci"} \
initialize 1 leave_open 1 flush 1 ident_toggle 1
addmsg /PRCspiketimes/soma_spikegen /PRCspiketimes/soma_spikehistory SPIKESAVE
call /PRCspiketimes/soma_spikehistory RESET
echo {showfield /PRCspiketimes/soma_spikehistory *}
//IF WE DO THE 'ENTRAINMENT TO PERIODIC STN INPUT EXPERIMENT', THIS WILL GET USED
// Save Gsyn AND Vm for every STN synapse to file
openfile {STNfilename} r
readcompartment = {readfile {STNfilename}}
while(! {eof {STNfilename}})
// Vm
hstr={findsolvefield {cellpath} {cellpath}/{readcompartment} Vm}
addmsg {cellpath} /out_v SAVE {hstr}
// Gsyn
hstr={findsolvefield {cellpath} {cellpath}/{readcompartment}/AMPA Gk}
addmsg {cellpath} /out_gsyns SAVE {hstr}
// Get next compt name
readcompartment = {readfile {STNfilename}}
end
// save the selected total conductances or currents into filename_g
// commented out when not saving itot
/*
if ({currentComptsIdx}==4)
// stimulus to dendrite 1
for(i=0; i<=0; i=i+1)
addmsg {cellpath} /out_gtot SAVE itotal[{i}]
end
for(i=71; i<=92; i=i+1)
addmsg {cellpath} /out_gtot SAVE itotal[{i}]
end
for(i=106; i<=117; i=i+1)
addmsg {cellpath} /out_gtot SAVE itotal[{i}]
end
end
if ({currentComptsIdx}==5)
//stimulus to dendrite 2
for(i=0; i<=0; i=i+1)
addmsg {cellpath} /out_gtot SAVE itotal[{i}]
end
for(i=49; i<=70; i=i+1)
addmsg {cellpath} /out_gtot SAVE itotal[{i}]
end
for(i=106; i<=117; i=i+1)
addmsg {cellpath} /out_gtot SAVE itotal[{i}]
end
end
if ({currentComptsIdx}==6)
// stimulus to dendrite 3
for(i=0; i<=0; i=i+1)
addmsg {cellpath} /out_gtot SAVE itotal[{i}]
end
for(i=14; i<=48; i=i+1)
addmsg {cellpath} /out_gtot SAVE itotal[{i}]
end
for(i=106; i<=117; i=i+1)
addmsg {cellpath} /out_gtot SAVE itotal[{i}]
end
end
*/
//for all currents (throughout dendrite) from dendComptGroups:
for(i=0; i<=117; i=i+1)
addmsg {cellpath} /out_gtot SAVE itotal[{i}]
end
/*
//This block of channels to save in itot works for dend3_distal (prior to dendComptGroups)
for(i=0; i<=0; i=i+1)
addmsg {cellpath} /out_gtot SAVE itotal[{i}]
end
for(i=14; i<=48; i=i+1)
addmsg {cellpath} /out_gtot SAVE itotal[{i}]
end
for(i=62; i<=73; i=i+1)
addmsg {cellpath} /out_gtot SAVE itotal[{i}]
end
*/
openfile {calciumCompts} r
readcompartment = {readfile {calciumCompts}}
while(! {eof {calciumCompts}})
// Ca++
hstr={findsolvefield {cellpath} {cellpath}/{readcompartment}/Ca_GP_conc Ca}
addmsg {cellpath} /out_ca SAVE {hstr}
// Get next compt name
readcompartment = {readfile {calciumCompts}}
end
if ({modelType}==1)
if ({currentComptsIdx}==1)
str snapshotname = "../common/snapshots/nonspiking_FULLdendsort_snapshot.save"
end
if ({currentComptsIdx}==2)
str snapshotname = "../common/snapshots/nonspiking_THIRDSdendsort_snapshot.save"
end
if ({currentComptsIdx}==3)
str snapshotname = "../common/snapshots/nonspiking_SUBdendsort_snapshot.save"
end
if (({currentComptsIdx}>=4) & ({currentComptsIdx}<=6))
str snapshotname = "../common/snapshots/dendComptGroups/synBack/Kopell/Kopell_nonspiking" @ {strStimLoc} @ {HVA_PRC_scalefac} @ "_xHVA_" @ {SK_PRC_scalefac} @ "_xSK_" @ {STN_rate} @ "_HzSTN_" @ {striatum_rate} @ "_HzSTR_" @ {synBack_synch} @ "_synch_snapshot.save"
end
end
if ({modelType}==2)
if ({currentComptsIdx}==1)
str snapshotname = "../common/snapshots/spiking_FULLdendsort_snapshot.save"
end
if ({currentComptsIdx}==2)
str snapshotname = "../common/snapshots/spiking_THIRDSdendsort_snapshot.save"
end
if ({currentComptsIdx}==3)
str snapshotname = "../common/snapshots/spiking_SUBdendsort_snapshot.save"
end
if (({currentComptsIdx}>=4) & ({currentComptsIdx}<=6))
str snapshotname = "../common/snapshots/dendComptGroups/synBack/spiking" @ {strStimLoc} @ {HVA_PRC_scalefac} @ "_xHVA_" @ {SK_PRC_scalefac} @ "_xSK_" @ {STN_rate} @ "_HzSTN_" @ {striatum_rate} @ "_HzSTR_" @ {synBack_synch} @ "_synch_" @ "snapshot.save"
end
end
if ({modelType}==3)
if (({currentComptsIdx}>=4) & ({currentComptsIdx}<=6))
str snapshotname = "../common/snapshots/GP" @ {strStimLoc} @ {syngain} @ "_syngain_" @ {STN_rate} @ "_STNrate_" @ {striatum_rate} @ "_STRIATUMrate_" @ {spiCurDist} @ "_dist_" @ {Eshift} @ "_Eshift_" @ {dendSpiCurMult} @ "_dendIspikeMult_" @ {NaPdendmult} @ "_NaPdendmult_" @ {SKsomaMult} @ "_SKsomaX_" @ {SKdendMult} @ "_SKdendX" @ {strStim} @ "synback_baseModels_snapshot.save"
end
end
echo
echo Snapshot to be made or used by this simulation is
echo {snapshotname}
echo
include ../common/snapshotGP_nws
/* for getting axial resistance of each compt:
str thiscompt
foreach thiscompt ({el {cellpath}/##[][OBJECT=compartment]})
echo {thiscompt} {getfield {thiscompt} Ra}
end
quit
*/
/* for getting surface areas of each compt:
str thiscompt
foreach thiscompt ({el {cellpath}/##[][OBJECT=compartment]})
echo {thiscompt} {({getfield {thiscompt} len})*({getfield {thiscompt} dia})*3.141592653589793}
end
quit
*/
include ../common/spiCurDist_echoDist.g
/*
echo somaNaFGbar {getfield /GP/soma/Na_fast_GP_somahill Gbar}
echo somaNaSGbar {getfield /GP/soma/Na_slow_GP_somahill Gbar}
echo somaKV3Gbar {getfield /GP/soma/Kv3_GP_somahill Gbar}
echo somaKV2Gbar {getfield /GP/soma/Kv2_GP_somahill Gbar}
echo somaRM {getfield /GP/soma Rm}
echo somaCM {getfield /GP/soma Cm}
*/
if ({snapgate}==1)
reset
step {rundur} -time
take_snapshot
//compress data files
// str filename_v_c = {compress_data_file {{out_dir} @ {filename_v}}}
// str filename_gtot_c = {compress_data_file {{out_dir} @ {filename_gtot}}}
// str filename_ca_c = {compress_data_file {{out_dir} @ {filename_ca}}}
// Copy file from temporary location (on nodes) to desired location (on /scratch)
// mv {filename_v_c} {dest_dir}
// mv {filename_gtot_c} {dest_dir}&
// mv {filename_ca_c} {dest_dir}&
quit
else
//run the simulation
reset
restore_snapshot
step {rundur} -time
//compress data files
// str filename_v_c = {compress_data_file {{out_dir} @ {filename_v}}}
// str filename_gtot_c = {compress_data_file {{out_dir} @ {filename_gtot}}}
// str filename_ca_c = {compress_data_file {{out_dir} @ {filename_ca}}}
// Copy file from temporary location (on nodes) to desired location (on /scratch)
// mv {filename_v_c} {dest_dir}
// mv {filename_gtot_c} {dest_dir}&
// mv {filename_ca_c} {dest_dir}&
quit
end
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