Implemented script to evaluate initialization and simulation time for…

… 10 runs of the Potjans Diesmann 2014 model

python/Potjans_2014/script_eval_time.sh

@@ -0,0 +1,4 @@
+for i in $(seq 0 9); do
+    cat sim_params_norec.templ | sed "s/__seed__/1234$i/" > sim_params_norec.py
+    python3  eval_microcircuit_time.py | tee log$i.txt
+done

python/Potjans_2014/sim_params_norec.templ

@@ -0,0 +1,57 @@
+# -*- coding: utf-8 -*-
+#
+# sim_params.py
+#
+# 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/>.
+
+"""PyNEST Microcircuit: Simulation Parameters
+------------------------------------------------
+
+A dictionary with parameters defining the simulation.
+
+"""
+
+import os
+
+sim_dict = {
+    # The full simulation time is the sum of a presimulation time and the main
+    # simulation time.
+    # presimulation time (in ms)
+    't_presim': 0.1,
+    # simulation time (in ms)
+    't_sim': 10000.0,
+    # resolution of the simulation (in ms)
+    'sim_resolution': 0.1,
+    # list of recording devices, default is 'spike_detector'. A 'voltmeter' can
+    # be added to record membrane voltages of the neurons. Nothing will be
+    # recorded if an empty list is given.
+    'rec_dev': [],
+    # path to save the output data
+    'data_path': os.path.join(os.getcwd(), 'data/'),
+    # masterseed for NeuronGPU and NumPy
+    'master_seed': __seed__, #55,
+    # number of threads per MPI process
+    'local_num_threads': 1,
+    # recording interval of the membrane potential (in ms)
+    'rec_V_int': 1.0,
+    # if True, data will be overwritten,
+    # if False, a NESTError is raised if the files already exist
+    'overwrite_files': True,
+    # print the time progress. This should only be used when the simulation
+    # is run on a local machine.
+    'print_time': True}