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Add example script for structural plasticity #753

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Add example script for structural plasticity #753

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b86af43
Add example script for structural plasticity
jakobj Jun 14, 2017
2c75797
Add some comments and remove experimental knobs
jakobj Jun 14, 2017
b9b85c6
Some renaming
jakobj Jun 20, 2017
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395 changes: 395 additions & 0 deletions examples/nest/structural_plasticity_benchmark.sli
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/*
* structural_plasticity_benchmark.sli
*
* This file is part of NEST.
*
* Copyright (C) 2004 The NEST Initiative
*
* NEST is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 2 of the License, or
* (at your option) any later version.
*
* NEST is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with NEST. If not, see <http://www.gnu.org/licenses/>.
*
*/

/*
This script simulates a network with two populations, 80% Excitatory, 20% Inhibitory,
initially without connections and relies on structuraly plasticity to generate
the connectivity. It uses Gaussian growth curves with different parameters for excitatory
and inhibitory synaptic elements.

Authors: Jakob Jordan, original implementation by Sandra Diaz in PyNEST
*/

%%% PARAMETER SECTION %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

% define all relevant parameters: changes should be made here
% all data is placed in the userdict dictionary

/overwrite_files true def
/seed 123 def

/nvp 2 def % total number of virtual processes
/n_neurons 6000 def % total number of neurons
/gamma 0.8 def % relative size of excitatory population

/psp_e 1.0 def % PSP of synapses created between neurons in the network (mV)
/g -1.0 def % IPSP amplitude relative to EPSP amplitude
/psp_ext 0.0106 def % mean EPSP amplitude for external input (mV)
/bg_rate 10000.0 def % rate of background Poisson input at each external input synapse (spikes/s)
/delay 1. def % delay of all connections (ms)

/simtime 12600. def % total simulation time (ms)
/presimtime 50. ms def % simulation time until reaching equilibrium (ms)
/dt 0.1 ms def % simulation step size (ms)
/record_spikes true def % switch to record spikes of excitatory neurons to file
/path_name (.) def % path where all files will have to be written
/log_file (log) def % naming scheme for the log files

% structural plasticity parameters

/sp_update_interval 100 def % update interval of structural plasticity in simulation steps
/sp_record_interval 1000 def % recording of structural plasticity status (Ca, #Axons) (ms)

% Growth curves for synaptic elements of excitatory neurons
% Excitatory synaptic elements
/growth_curve_e_e <<
/growth_curve /gaussian
/growth_rate 0.0001
/continuous false
/eta 0.0
/eps 0.05
>> def

% Inhibitory synaptic elements
/growth_curve_e_i <<
/growth_curve /gaussian
/growth_rate 0.0001
/continuous false
/eta 0.0
/eps growth_curve_e_e /eps get
>> def

% Growth curves for synaptic elements of inhibitory neurons
% Excitatory synaptic elements
/growth_curve_i_e <<
/growth_curve /gaussian
/growth_rate 0.0004
/continuous false
/eta 0.0
/eps 0.2
>> def

% Inhibitory synaptic elements
/growth_curve_i_i <<
/growth_curve /gaussian
/growth_rate 0.0001
/continuous false
/eta 0.0
/eps growth_curve_i_e /eps get
>> def

% neuron model parameters

/model_params <<
/tau_m 10.0 % membrane time constant (ms)
/tau_syn_ex 0.5 % excitatory synaptic time constant (ms)
/tau_syn_in 0.5 % inhibitory synaptic time constant (ms)
/t_ref 2.0 % absolute refractory period (ms)
/E_L -65.0 % resting membrane potential (mV)
/V_th -50.0 % spike threshold (mV)
/C_m 250.0 % membrane capacitance (pF)
/V_reset -65.0 % reset potential (mV)
>> def

%%% FUNCTION SECTION %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

% ------------------------------------------------------------------------------------

/*
This function defines a logger class used to properly log memory and timing
information from network simulations. It is used by hpc_benchmark.sli to
store the information to the log files.
*/

/logger
<<
/max_rank_cout 5 % copy output to cout for ranks 0..max_rank_cout-1
/max_rank_log 30 % write to log files for ranks 0..max_rank_log-1
/line_counter 0

% constructor
% expects file name on stack
/init
{
Rank max_rank_log lt {

(_) join

% convert rank to string, prepend 0 if necessary to make
% numbers equally wide for all ranks
Rank cvs
dup length max_rank_log cvs length exch sub
{
48 prepend % 48 is ASCII code for 0
}
repeat
join
(.dat) join

/f exch (w) ofsopen
{
def
}
{
/Logger_init /CannotOpenFile raiseerror
}
ifelse

} if
}

% logging function
% expects one operand on stack to write to file
/log
{
/value Set
Rank max_rank_log lt {
f line_counter <- ( ) <- Rank <- ( ) <- value <- (\n) <- pop
/line_counter line_counter 1 add def
} if
Rank max_rank_cout lt {
cout Rank <- ( ) <- value <- endl flush pop
cerr Rank <- ( ) <- value <- endl flush pop
} if
}

% closes file
/done
{
Rank max_rank_log lt {
f close
} if
}

>> def

% calculates the psc amplitude from the psp amplitude for alpha synapses
/derive_psc_parameters
{
model_params using

% factors for transforming PSP amplitude to PSC amplitude
/re tau_m tau_syn_ex div def
/de tau_syn_ex tau_m sub def
/ri tau_m tau_syn_in div def
/di tau_syn_in tau_m sub def

/psc_e_over_psp_e 1. 1. C_m div tau_m mul tau_syn_ex mul de div re tau_m de div pow re tau_syn_ex de div pow sub mul div def
/psc_i_over_psp_i 1. 1. C_m div tau_m mul tau_syn_in mul de div ri tau_m di div pow ri tau_syn_in di div pow sub mul div def

/psc_e psc_e_over_psp_e psp_e mul def
/psc_i psc_e_over_psp_e psp_e g mul mul def
/psc_ext psc_e_over_psp_e psp_ext mul def

endusing

} def

/derive_network_parameters
{
/n_neurons_e n_neurons gamma mul cvi def
/n_neurons_i n_neurons n_neurons_e sub def
} def

% sets kernel configuration and structural plasticity settings
/prepare_kernel
{
% open log file
log_file logger /init call

ResetKernel
M_ERROR setverbosity

0 <<
/resolution dt
/total_num_virtual_procs nvp
/overwrite_files overwrite_files
/rng_seeds [0 nvp 1 sub] Range seed add
/grng_seed seed nvp add
>> SetStatus

EnableStructuralPlasticity

/static_synapse /synapse_ex CopyModel
/synapse_ex << /weight psc_e /delay delay >> SetDefaults
/static_synapse /synapse_in CopyModel
/synapse_in << /weight psc_i /delay delay >> SetDefaults

<<
/structural_plasticity_update_interval sp_update_interval
/structural_plasticity_synapses <<
/synapse_ex <<
/model /synapse_ex
/post_synaptic_element /den_ex
/pre_synaptic_element /axon_ex
>>
/synapse_in <<
/model /synapse_in
/post_synaptic_element /den_in
/pre_synaptic_element /axon_in
>>
>>
>> SetStructuralPlasticityStatus

} def

% create neurons
/create_nodes
{
/min_gid_neurons_e 1 def
/iaf_psc_alpha n_neurons_e <<
/synaptic_elements <<
/den_ex growth_curve_e_e
/den_in growth_curve_e_i
/axon_ex growth_curve_e_e
>>
>> Create /max_gid_neurons_e Set
/nodes_e min_gid_neurons_e max_gid_neurons_e cvgidcollection def

/min_gid_neurons_i max_gid_neurons_e 1 add def
/iaf_psc_alpha n_neurons_i <<
/synaptic_elements <<
/den_ex growth_curve_i_e
/den_in growth_curve_i_i
/axon_in growth_curve_i_i
>>
>> Create /max_gid_neurons_i Set
/nodes_i min_gid_neurons_i max_gid_neurons_i cvgidcollection def
} def

% connects simulation and recording devices
/connect_stim_and_recording
{
/poisson_generator 1 << /rate bg_rate >> Create dup cvgidcollection /noise Set
noise nodes_e << /rule /all_to_all >> << /weight psc_ext /delay delay >> Connect
noise nodes_i << /rule /all_to_all >> << /weight psc_ext /delay delay >> Connect

record_spikes {
/spike_detector 1 << /to_file true >> Create dup cvgidcollection /spike_detector Set
nodes_e spike_detector Connect
nodes_i spike_detector Connect
} if
} def

% records the current Ca concentration for excitatory and inhibitory neurons
/record_local_ca_concentration
{
/t Set
% get Ca concentration for all local excitatory neurons
/ca_e 0. def
0 GetLocalNodes {
/gid Set
gid min_gid_neurons_e gt gid max_gid_neurons_e lt and
{
ca_e gid GetStatus /Ca get add
/ca_e Set
} if
} forall

% get Ca concentration for all local inhibitory neurons
/ca_i 0. def
0 GetLocalNodes {
/gid Set
gid min_gid_neurons_i gt gid max_gid_neurons_i lt and
{
ca_i gid GetStatus /Ca get add
/ca_i Set
} if
} forall

t cvs ( ) join ca_e cvs join ( # Ca concentration ex) join logger /log call
t cvs ( ) join ca_i cvs join ( # Ca concentration in) join logger /log call
} def

% records the current number of axonal synaptic elements for excitatory and inhibitory neurons
/record_local_number_of_axons
{
/t Set
% get synaptic elements from all local excitatory neurons
/syn_e 0 def
0 GetLocalNodes {
/gid Set
gid min_gid_neurons_e gt gid max_gid_neurons_e lt and
{
gid GetStatus /synaptic_elements get /axon_ex get /z_connected get syn_e add
/syn_e Set
} if
} forall

% get synaptic elements from all local inhibitory neurons
/syn_i 0 def
0 GetLocalNodes {
/gid Set
gid min_gid_neurons_i gt gid max_gid_neurons_i lt and
{
gid GetStatus /synaptic_elements get /axon_in get /z_connected get syn_i add
/syn_i Set
} if
} forall

t cvs ( ) join syn_e cvs join ( # axon count ex) join logger /log call
t cvs ( ) join syn_i cvs join ( # axon count in) join logger /log call
} def

% records the total number of spikes generated locally
/record_local_number_of_spikes
{
/t Set
t cvs ( ) join 0 GetStatus /local_spike_counter get cvs join ( # local spike count) join logger /log call
} def

%%% SIMULATION SECTION %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

derive_psc_parameters
derive_network_parameters

prepare_kernel
create_nodes
connect_stim_and_recording

/runtime 0. def % keeps track of simulation time

% simulate for a short time to separate initial transients
tic
presimtime Simulate
toc /presim_duration Set
runtime presimtime add /runtime Set
runtime cvs ( ) join presim_duration cvs join ( # presim_time) join logger /log call

% simulate in multiple steps to allow for recording of network status at particular intervals
/sim_duration 0. def % keeps track of wallclock time
{
tic
sp_record_interval Simulate
toc sim_duration add /sim_duration Set
runtime sp_record_interval add /runtime Set
runtime cvs ( ) join sim_duration cvs join ( # sim_time) join logger /log call

runtime record_local_ca_concentration
runtime record_local_number_of_axons
runtime record_local_number_of_spikes

runtime sp_record_interval add simtime gt
{
exit
} if
} loop