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main_KirschBoskovRymer1994_OuterLoop.m
executable file
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main_KirschBoskovRymer1994_OuterLoop.m
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%%
% SPDX-FileCopyrightText: 2023 Matthew Millard <millard.matthew@gmail.com>
%
% SPDX-License-Identifier: MIT
%
% If you use this code in your work please cite the pre-print of this paper
% or the most recent peer-reviewed version of this paper:
%
% Matthew Millard, David W. Franklin, Walter Herzog.
% A three filament mechanistic model of musculotendon force and impedance.
% bioRxiv 2023.03.27.534347; doi: https://doi.org/10.1101/2023.03.27.534347
%
%%
%This flag allows us to avoid the memory clearing functions so that
%this can be timed using tic and tock from within main_OuterLoop
flag_OuterOuterLoopMode =1;
if(flag_OuterOuterLoopMode ==0)
clc;
close all;
clear all;
end
disp('----------------------------------------');
disp(' running main_KirschBoskovRymer1994_OuterLoop');
disp('----------------------------------------');
disp(' :run-time: 3h 45min (226 min) ');
disp(' :Why so long? Nearly 400 simulations are performed');
disp(' *Intel i7-3630QM @ 2.40 GHz, Ubuntu 22');
disp ' 8 GB ram, SSD harddrive');
disp('----------------------------------------');
rootDir = getRootProjectDirectory();
projectFolders = getProjectFolders(rootDir);
%%
%Run all of the simulations
%%
flag_runSimulations = 1;
flag_frequencyAnalysis = 1;
flag_generatePlots = 1;
%Parameters that are tuned
%updSlidingTimeConstant = 0.0005;
%updForceVelocityCalibrationFactor = 0.95;
flag_useCalibratedVexatCurves= 1;
flag_useTwoSidedTitinCurves = 0;
if(flag_runSimulations == 1)
%Hill and the proposed model
%Elastic tendon
flag_simulateHillModel = 1;
flag_simulateVexatModel = 1;
flag_fitToFig3KirchBoskovRymer1994 = 0;
flag_useElasticTendon = 1;
flag_useFiberDamping = 1;
flag_frequencyAnalysisMuscleModels = 0;
flag_plotAccelerationEquationFactors = 0;
flag_pubPlotFrequencyResponseKBR1994Fig3 = 0;
flag_pubPlotStiffnessDampingKBR1994Fig9Fig10 = 0;
flag_pubPlotStiffnessDampingKBR1994Fig12 = 0;
flag_pubTabulateStiffnessDampingVariation = 0;
flag_generateRandomInput = 1;
flag_processInputFunctions = 1;
main_KirschBoskovRymer1994;
close all;
%Hill and the proposed model
%Rigid tendon
flag_simulateHillModel = 1;
flag_simulateVexatModel = 1;
flag_fitToFig3KirchBoskovRymer1994 = 0;
flag_useElasticTendon = 0;
flag_useFiberDamping = 1;
flag_frequencyAnalysisMuscleModels = 0;
flag_plotAccelerationEquationFactors = 0;
flag_pubPlotFrequencyResponseKBR1994Fig3 = 0;
flag_pubPlotStiffnessDampingKBR1994Fig9Fig10 = 0;
flag_pubPlotStiffnessDampingKBR1994Fig12 = 0;
flag_pubTabulateStiffnessDampingVariation = 0;
flag_generateRandomInput = 0;
flag_processInputFunctions = 0;
main_KirschBoskovRymer1994;
close all;
%Proposed model only
%Elastic tendon
flag_simulateHillModel = 1;
flag_simulateVexatModel = 1;
flag_fitToFig3KirchBoskovRymer1994 = 1;
flag_useElasticTendon = 1;
flag_useFiberDamping = 1;
flag_frequencyAnalysisMuscleModels = 0;
flag_plotAccelerationEquationFactors = 0;
flag_pubPlotFrequencyResponseKBR1994Fig3 = 0;
flag_pubPlotStiffnessDampingKBR1994Fig9Fig10 = 0;
flag_pubPlotStiffnessDampingKBR1994Fig12 = 0;
flag_pubTabulateStiffnessDampingVariation = 0;
flag_generateRandomInput = 0;
flag_processInputFunctions = 0;
main_KirschBoskovRymer1994;
close all;
%Proposed model only
%Rigid tendon
flag_simulateHillModel = 1;
flag_simulateVexatModel = 1;
flag_fitToFig3KirchBoskovRymer1994 = 1;
flag_useElasticTendon = 0;
flag_useFiberDamping = 1;
flag_frequencyAnalysisMuscleModels = 0;
flag_plotAccelerationEquationFactors = 0;
flag_pubPlotFrequencyResponseKBR1994Fig3 = 0;
flag_pubPlotStiffnessDampingKBR1994Fig9Fig10 = 0;
flag_pubPlotStiffnessDampingKBR1994Fig12 = 0;
flag_pubTabulateStiffnessDampingVariation = 0;
flag_generateRandomInput = 0;
flag_processInputFunctions = 0;
main_KirschBoskovRymer1994;
close all;
end
%%
%Frequency Analysis
%%
if(flag_frequencyAnalysis==1)
flag_generateRandomInput = 0;
flag_processInputFunctions = 0;
%Rigid tendon - do not fit Kx and betaX to Kirsch et al. Fig 3
flag_simulateHillModel = 0;
flag_simulateVexatModel = 0;
flag_fitToFig3KirchBoskovRymer1994 = 0;
flag_useElasticTendon = 0;
flag_useFiberDamping = 1;
flag_frequencyAnalysisMuscleModels = 1;
flag_plotAccelerationEquationFactors = 0;
flag_pubPlotFrequencyResponseKBR1994Fig3 = 0;
flag_pubPlotStiffnessDampingKBR1994Fig9Fig10 = 0;
flag_pubPlotStiffnessDampingKBR1994Fig12 = 0;
flag_pubTabulateStiffnessDampingVariation = 0;
main_KirschBoskovRymer1994;
close all;
%Elastic tendon - do not fit Kx and betaX to Kirsch et al. Fig 3
flag_simulateHillModel = 0;
flag_simulateVexatModel = 0;
flag_fitToFig3KirchBoskovRymer1994 = 0;
flag_useElasticTendon = 1;
flag_useFiberDamping = 1;
flag_frequencyAnalysisMuscleModels = 1;
flag_plotAccelerationEquationFactors = 0;
flag_pubPlotFrequencyResponseKBR1994Fig3 = 0;
flag_pubPlotStiffnessDampingKBR1994Fig9Fig10 = 0;
flag_pubPlotStiffnessDampingKBR1994Fig12 = 0;
flag_pubTabulateStiffnessDampingVariation = 0;
main_KirschBoskovRymer1994;
close all;
%Rigid tendon - fit Kx and betaX to Kirsch et al. Fig 3
flag_simulateHillModel = 0;
flag_simulateVexatModel = 0;
flag_fitToFig3KirchBoskovRymer1994 = 1;
flag_useElasticTendon = 0;
flag_useFiberDamping = 1;
flag_frequencyAnalysisMuscleModels = 1;
flag_plotAccelerationEquationFactors = 0;
flag_pubPlotFrequencyResponseKBR1994Fig3 = 0;
flag_pubPlotStiffnessDampingKBR1994Fig9Fig10 = 0;
flag_pubPlotStiffnessDampingKBR1994Fig12 = 0;
flag_pubTabulateStiffnessDampingVariation = 0;
main_KirschBoskovRymer1994;
close all;
% Elastic tendon - fit Kx and betaX to Kirsch et al. Fig 3
flag_simulateHillModel = 0;
flag_simulateVexatModel = 0;
flag_fitToFig3KirchBoskovRymer1994 = 1;
flag_useElasticTendon = 1;
flag_useFiberDamping = 1;
flag_frequencyAnalysisMuscleModels = 1;
flag_plotAccelerationEquationFactors = 0;
flag_pubPlotFrequencyResponseKBR1994Fig3 = 0;
flag_pubPlotStiffnessDampingKBR1994Fig9Fig10 = 0;
flag_pubPlotStiffnessDampingKBR1994Fig12 = 0;
flag_pubTabulateStiffnessDampingVariation = 0;
main_KirschBoskovRymer1994;
close all;
end
%%
%Plots
%%
if(flag_generatePlots==1)
flag_generateRandomInput = 0;
flag_processInputFunctions = 0;
%Elastic tendon
flag_simulateHillModel = 0;
flag_simulateVexatModel = 0;
flag_fitToFig3KirchBoskovRymer1994 = 0;
flag_useElasticTendon = 1;
flag_useFiberDamping = 1;
flag_frequencyAnalysisMuscleModels = 0;
flag_plotAccelerationEquationFactors = 1;
flag_pubPlotFrequencyResponseKBR1994Fig3 = 0;
flag_pubPlotStiffnessDampingKBR1994Fig9Fig10 = 1;
flag_pubPlotStiffnessDampingKBR1994Fig12 = 1;
flag_pubTabulateStiffnessDampingVariation = 1;
main_KirschBoskovRymer1994;
%Rigid tendon
flag_simulateHillModel = 0;
flag_simulateVexatModel = 0;
flag_fitToFig3KirchBoskovRymer1994 = 0;
flag_useElasticTendon = 0;
flag_useFiberDamping = 1;
flag_frequencyAnalysisMuscleModels = 0;
flag_plotAccelerationEquationFactors = 1;
flag_pubPlotFrequencyResponseKBR1994Fig3 = 0;
flag_pubPlotStiffnessDampingKBR1994Fig9Fig10 = 1;
flag_pubPlotStiffnessDampingKBR1994Fig12 = 1;
flag_pubTabulateStiffnessDampingVariation = 1;
main_KirschBoskovRymer1994;
close all;
flag_simulateHillModel = 0;
flag_simulateVexatModel = 0;
flag_fitToFig3KirchBoskovRymer1994 = 0;
flag_useElasticTendon = 0;
flag_useFiberDamping = 1;
flag_frequencyAnalysisMuscleModels = 0;
flag_plotAccelerationEquationFactors = 1;
flag_pubPlotFrequencyResponseKBR1994Fig3 = 1;
flag_pubPlotStiffnessDampingKBR1994Fig9Fig10 = 0;
flag_pubPlotStiffnessDampingKBR1994Fig12 = 0;
flag_pubTabulateStiffnessDampingVariation = 0;
main_KirschBoskovRymer1994;
close all;
% %Rigid tendon - generate publication version of Kirsch et al. Fig 3
% flag_simulateHillModel = 0;
% flag_simulateVexatModel = 0;
% flag_fitToFig3KirchBoskovRymer1994 = 0;
% flag_useElasticTendon = 1;
% flag_useFiberDamping = 1;
% flag_frequencyAnalysisMuscleModels = 0;
% flag_plotAccelerationEquationFactors = 1;
% flag_pubPlotFrequencyResponseKBR1994Fig3 = 1;
% flag_pubPlotStiffnessDampingKBR1994Fig9Fig10 = 0;
% flag_pubPlotStiffnessDampingKBR1994Fig12 = 0;
% flag_pubTabulateStiffnessDampingVariation = 0;
%
% main_KirschBoskovRymer1994;
%
% close all;
end