run_name = 'p1d1w2f5s1to6r1_20170107_spindling_comparison';
%{
# Run Simulation file
- Project 1:
    - Propofol PAC investigation
- Direction 1:
    - Thalamus-only propofol PAC modeling
- Writing item 2:
    - Journal article on results of p1d1
- Figure 5:
    - Explanations of propofol GABA-A sustained alpha mechanisms, using
    comparisons of baseline-silent depolarization & highdose-alpha, and
    baseline-spindling & highdose-alpha. Includes extreme Tau_T and propofol
    multiplier (spm) comparisons.
- Subfigures 1-6:
    - Just the baseline-spindling and highdose-alpha cases for comparison. Using
    slightly depolarized state 0.1, higher gh 0.0032
- Run 1:
    - There should probably only be a single run! Using slightly depolarized
    state 0.1, higher gh 0.0032
- Date Created:
    - 20170107
- Inherits from:
    - 'p1d1q41c4i5_20160905_cOFF_propomech_f5_spindling.m'
%}

% Define equations of cell model (same for all populations)
eqns={
  'dV/dt=Iapp+@current';
};

time_end = 8000; % in milliseconds
numcells = 50;

g_PYsyn = 0.05;

% Create DynaSim specification structure
s=[];
s.populations(1).name='TC';
s.populations(1).size=numcells;
s.populations(1).equations=eqns;
% this is where the magic happens
s.populations(1).mechanism_list={'iNaChing2010TC','iKChing2010TC',...
                                 'iLeakChing2010TC','iKLeakChing2010TC',...
                                 'CaBufferChing2010TC','iTChing2010TC',...
                                 'iHChing2010TCSwapped'};
s.populations(1).parameters={'Iapp',0};
s.populations(2).name='RE';
s.populations(2).size=numcells;
s.populations(2).equations=eqns;
s.populations(2).mechanism_list={'iNaChing2010RE','iKChing2010RE',...
                                 'iTChing2010RE','iLeakChing2010RE'};
s.populations(2).parameters={'Iapp',0};

s.connections(1).direction='TC->RE';
s.connections(1).mechanism_list={'iAMPAChing2010'};
s.connections(1).parameters={'gAMPA',0.08};

s.connections(2).direction='RE->TC';
s.connections(2).mechanism_list={'iGABAAChing2010','iGABABChing2010'};
s.connections(2).parameters={'gGABAA_base',0.069,'spm',1,'tauGABAA_base',5,...
                             'gGABAB',0.001};
% s.connections(3).direction='TC->TC';
% s.connections(3).mechanism_list={'iPoissonSpiketrainUncorr'};
% s.connections(3).parameters={'g_esyn',g_PYsyn,'rate',12,'T',time_end,...
%                              'tau_i',10,'prob_cxn',0.5,'jitter_stddev',500};
s.connections(3).direction='RE->RE';
s.connections(3).mechanism_list={'iGABAAChing2010'};
s.connections(3).parameters={'gGABAA_base',0.069,'spm',1,'tauGABAA_base',5};
% s.connections(4).direction='RE->RE';
% s.connections(4).mechanism_list={'iPoissonSpiketrainUncorr','iGABAAChing2010'};
% s.connections(4).parameters={'g_esyn',g_PYsyn,'rate',12,'T',time_end,...
%                              'tau_i',10,'prob_cxn',0.5,'jitter_stddev',500,...
%                              'gGABAA_base',0.069,'spm',1,'tauGABAA_base',5};

vary={
  'TC',                'gH',       [0.0032];
  '(TC,RE)',           'Iapp',     [0.1];
  '(RE->RE,RE->TC)',   'spm',      [1,3];
};

% % Example with reliable spikes/oscs
% vary={
%   'TC',                'gH',       [0.002, 0.004];
%   '(TC,RE)',           'Iapp',     [0.0,0.1]
%   '(RE->RE,RE->TC)',   'spm',      [3];
% };

%% Set simulation parameters

% How much RAM, options: 8G?, 24, 48, 96, 128
% are segfaults from too long of a sim?
% memlimit = '8G';
% memlimit = '16G';
% memlimit = '48G';
% memlimit = '96G';
memlimit = '254G';

% Save data/results to this directory. If just a single name, will
%   save to that directory name in the current directory from which it's run.
%   Will create directory if it does not exist.
data_dir = strcat('/projectnb/crc-nak/asoplata/dynasim_data/',...
                  run_name);

% Flags
cluster_flag = 1;
overwrite_flag = 1;
save_data_flag = 1;
% Even if `save_data_flag` is 0, if running on cluster this must be off too in
%   order to not save data?
save_results_flag = 1;
verbose_flag = 1;
compile_flag = 0;
disk_flag = 0;
downsample_factor = 6;

% local run of the simulation,
%   i.e. in the interactive session you're running this same script in
SimulateModel(s,'save_data_flag',save_data_flag,'study_dir',data_dir,...
              'cluster_flag',cluster_flag,'verbose_flag',verbose_flag,...
              'overwrite_flag',overwrite_flag,'tspan',[0 time_end],...
              'save_results_flag',save_results_flag,'solver','euler',...
              'memlimit',memlimit,'compile_flag',compile_flag,...
              'disk_flag',disk_flag,'downsample_factor',downsample_factor,...
              'vary',vary,...
              'plot_functions',{@PlotData,@PlotData},...
              'plot_options',{{'plot_type','waveform','format','png'},...
                              {'plot_type','power','format','png',...
                               'xlim',[0 40]}});
exit