added CARLsim version

.gitignore

@@ -1,2 +1,4 @@
 *.class
-*.csv
+*.csv
+/CARLsim_version/iz_fp_eval/build_dir
+/CARLsim_version/iz_fp_eval/scripts/*.png

CARLsim_version/iz_fp_eval/CMakeLists.txt

@@ -0,0 +1,32 @@
+project(iz_fp_eval)
+
+# Targets  
+add_executable(iz_fp_eval
+    src/main_iz_fp_eval.cpp
+)
+
+# definitions     
+if(CARLSIM_NO_CUDA)
+    target_compile_definitions(iz_fp_eval PUBLIC
+        -D__NO_CUDA__ )
+endif()
+
+# Linking    
+target_link_libraries(iz_fp_eval PRIVATE
+    carlsim
+    carlsim-stopwatch
+)
+target_include_directories(iz_fp_eval PRIVATE
+    ../../tools/stopwatch
+)
+
+
+# Installation   
+install(TARGETS iz_fp_eval
+    EXPORT carlsim
+    RUNTIME 
+        DESTINATION $<$<CONFIG:Debug>:debug/>samples 
+        COMPONENT iz_fp_eval
+        )
+
+#install(FILES run_iz_fp_eval DESTINATION $<$<CONFIG:Debug>:debug/>samples)          

CARLsim_version/iz_fp_eval/rebuild_stellate.sh

@@ -0,0 +1 @@
+make clean && make && ./iz_fp_eval 118.000000 0.62 -58.53 -43.52 0.005 8.0 11.48 -49.52 8.5

CARLsim_version/iz_fp_eval/scripts/demoOAT.m

@@ -0,0 +1,37 @@
+% A simple demo of the NetworkMonitor functionality
+
+% add Offline Analysis Toolbox to path
+initOAT;
+
+% init NetworkMonitor
+NM = NetworkMonitor('../results/sim_hello world.dat');
+
+% plot network activity
+disp('NetworkMonitor.plot')
+disp('-------------------')
+disp('Press ''p'' to pause.')
+disp('Press ''q'' to quit.')
+disp(['Press ''s'' to enter stepping mode; then press the ' ...
+	'right arrow key to step'])
+disp('one frame forward, press the left arrow key to step one frame back.')
+disp('Press ''s'' again to leave stepping mode.')
+disp(' ')
+NM.plot;
+
+
+% init ConnectionMonitor
+CM = ConnectionMonitor('input','output','../results/');
+
+% visualize receptive fields (little 2D Gaussian kernels for each post-neuron)
+disp('ConnectionMonitor.plot(''receptivefield'')')
+disp('-------------------')
+disp('Press ''p'' to pause.')
+disp('Press ''q'' to quit.')
+disp(['Press ''s'' to enter stepping mode; then press the ' ...
+	'right arrow key to step'])
+disp('one frame forward, press the left arrow key to step one frame back.')
+disp('Press ''s'' again to leave stepping mode.')
+CM.plot('receptivefield')
+
+% analogously, the response field of each pre-neuron can be visualized:
+% CM.plot('responsefield')

CARLsim_version/iz_fp_eval/scripts/initOAT.m

@@ -0,0 +1,3 @@
+% add path to Offline Analysis Toolbox
+%addpath('../../../tools/offline_analysis_toolbox')
+addpath('/comp_neuro/Software/CARLsim4_dgx_hc_09_18_21/tools/offline_analysis_toolbox')

CARLsim_version/iz_fp_eval/scripts/plot_results.m

@@ -0,0 +1,18 @@
+% analyze voltage from a neuron using IZ 9-param model
+
+function []=plot_results(volt_file, output_desc)
+	initOAT;
+	save_plot=1;
+	neur_read = NeuronReader(volt_file);
+	voltages = neur_read.readValues();
+	t_start = 1; % start time
+	t_end = 1100; % end time
+	t_range = linspace(t_start,t_end,(t_end-t_start+1));
+	selected_volt = voltages.v(1,t_start:t_end);
+	% plot
+	plot(t_range, selected_volt,'Color','#80B3FF','LineWidth',1.5);
+	if save_plot
+	    output_filename = sprintf("voltage_%s.png",output_desc);
+	    exportgraphics(gcf,output_filename,'Resolution',300)
+	end
+end

CARLsim_version/iz_fp_eval/scripts/run_plot.m

@@ -0,0 +1 @@
+plot_results('../build_dir/results/n_neuron.dat', 'test');

CARLsim_version/iz_fp_eval/src/.readme

@@ -0,0 +1 @@
+# Put all source files (.cpp and .cu) here

CARLsim_version/iz_fp_eval/src/main_iz_fp_eval.cpp

@@ -0,0 +1,85 @@
+/* * Copyright (c) 2016 Regents of the University of California. All rights reserved.
+*
+* Redistribution and use in source and binary forms, with or without
+* modification, are permitted provided that the following conditions
+* are met:
+*
+* 1. Redistributions of source code must retain the above copyright
+*    notice, this list of conditions and the following disclaimer.
+*
+* 2. Redistributions in binary form must reproduce the above copyright
+*    notice, this list of conditions and the following disclaimer in the
+*    documentation and/or other materials provided with the distribution.
+*
+* 3. The names of its contributors may not be used to endorse or promote
+*    products derived from this software without specific prior written
+*    permission.
+*
+* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+* "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+* LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+* A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
+* CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+* EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+* PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+* PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+* LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+* NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+* SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+*
+* *********************************************************************************************** *
+* CARLsim
+* created by: (MDR) Micah Richert, (JN) Jayram M. Nageswaran
+* maintained by:
+* (MA) Mike Avery <[email protected]>
+* (MB) Michael Beyeler <[email protected]>,
+* (KDC) Kristofor Carlson <[email protected]>
+* (TSC) Ting-Shuo Chou <[email protected]>
+* (HK) Hirak J Kashyap <[email protected]>
+*
+* CARLsim v1.0: JM, MDR
+* CARLsim v2.0/v2.1/v2.2: JM, MDR, MA, MB, KDC
+* CARLsim3: MB, KDC, TSC
+* CARLsim4: TSC, HK
+* CARLsim5: HK, JX, KC
+* CARLsim6: LN, JX, KC, KW
+*
+* CARLsim available from http://socsci.uci.edu/~jkrichma/CARLsim/
+* Ver 12/31/2016
+*/
+
+// include CARLsim user interface
+#include <carlsim.h>
+
+int main(int argc, char *argv[]) {
+	if (argc != 10) {
+		printf("\nUsage: iz_fp_eval <9_IM_params>\n");
+		printf("%d arguments found.\n",argc);
+	}
+	else {
+		// ---------------- CONFIG STATE -------------------
+		CARLsim sim("hello world", GPU_MODE, USER, 1, 42);
+		int dummy = sim.createSpikeGeneratorGroup("dummy_connection", 1, EXCITATORY_NEURON, 0, GPU_CORES);
+		int neuron=sim.createGroup("neuron", 1, EXCITATORY_NEURON, ANY, GPU_CORES);
+		sim.setNeuronParameters(neuron, atof(argv[1]), 0.0f, atof(argv[2]), 
+	    0.0f, atof(argv[3]), 0.0f, atof(argv[4]), 0.0f, atof(argv[5]), 0.0f, 
+	    atof(argv[6]), 0.0f, atof(argv[7]), 0.0f, atof(argv[8]), 0.0f, 
+	    atof(argv[9]), 0.0f, 150);
+		sim.connect(dummy, neuron, "one-to-one", 0.0f, SYN_FIXED); // CARLsim seems to require at least one connection. This is a dummy connection with no signaling to the other neuron.
+		sim.setNeuronMonitor(neuron,"DEFAULT");
+		sim.setIntegrationMethod(RUNGE_KUTTA4, 1);//40);
+		// ---------------- SETUP STATE -------------------
+		sim.setupNetwork();
+		SpikeMonitor* spk_mon = sim.setSpikeMonitor(neuron, "DEFAULT");
+		// ---------------- RUN STATE -------------------
+		spk_mon->startRecording();
+		for (int i=0; i<100; i++) {
+			if (i==1) {sim.setExternalCurrent(neuron, 200.0f);}
+			if (i==10) {sim.setExternalCurrent(neuron, 0.0f);}
+			sim.runNetwork(0,100, false);
+		}
+		spk_mon->stopRecording();
+	}
+
+	return 0;
+}

CARLsim_version/iz_fp_eval/standalone/CMakeLists.txt

@@ -0,0 +1,58 @@
+project(carlsim-hello-world)
+cmake_minimum_required(VERSION 3.19.4)
+
+
+# Dependencies
+
+  find_package(carlsim REQUIRED)
+
+# Targets
+
+    add_executable(hello_world
+        src/main_hello_world.cpp
+    )
+
+    if(CARLSIM_NO_CUDA)
+        target_compile_definitions(hello_world 
+            PUBLIC
+                -D__NO_CUDA__
+            )
+    endif()
+
+# include 
+    target_include_directories(hello_world PRIVATE
+        ${CARLSIM_INCLUDE_DIR}
+        )
+
+# Linking
+
+    target_link_directories(hello_world PRIVATE        
+        ${CARLSIM_LIB_DIR}
+        )
+
+    if(NOT CARLSIM_NO_CUDA)
+        target_link_directories(hello_world PRIVATE
+        ${CARLSIM_CUDA_LIB_DIR}    
+        )
+    endif()
+
+    target_link_libraries(hello_world PRIVATE
+         carlsim$<$<CONFIG:Debug>:d>.lib
+         carlsim-stopwatch$<$<CONFIG:Debug>:d>.lib
+#        carlsim-interface
+#       carlsim-kernel
+#       carlsim-monitor
+#        carlsim-simple-weight-tuner
+#        carlsim-spike-generators
+#        carlsim-stopwatch
+#        carlsim-visual-stimulus
+    )
+
+    if(NOT CARLSIM_NO_CUDA)
+        target_link_libraries(hello_world PRIVATE
+            carlsim-kernel-cuda
+            cudart
+            curand
+        )
+    endif()
+