Release 4.2.1 · CIFASIS/qss-solver@efbaa2e

Commit

Release 4.2.1

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        Release 4.2.0

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        [iss-227]
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        Date:   Wed Nov 2 11:25:53 2022 -0300

            Configure statement reinits.

        commit 9199f6b10aaa187a556869ad11fdce2cafef2289
        Author: joaquin.f.fernandez <joaquin.f.fernandez@gmail.com>
        Date:   Wed Nov 2 11:25:35 2022 -0300

            Set algorithm configuration in event printers.

        commit 6b324d00be0bbb2ee14fb525d279ada200454f83
        Author: joaquin.f.fernandez <joaquin.f.fernandez@gmail.com>
        Date:   Wed Nov 2 11:25:11 2022 -0300

            Added reinit and algorithm cheker methods to model config.

        commit 51437559b32dd48b9011289de5c6b8bedb78594e
        Author: j…

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joaquinffernandez committed Jun 28, 2023

1 parent d352a3f commit efbaa2e

.github/ISSUE_TEMPLATE/bug_report.md

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+Diff line change
@@ -0,0 +1,24 @@
+    ---
+    name: Bug report
+    about: Create a report to help us improve
+    title: ''
+    labels: ''
+    assignees: ''
+    ---
+    **Describe the bug**
+    A clear and concise description of what the bug is.
+    **To Reproduce**
+    Steps to reproduce the behavior:
+. Go to '...'
+. Click on '....'
+. Scroll down to '....'
+. See error
+    **Expected behavior**
+    A clear and concise description of what you expected to happen.
+    **Additional context**
+    Add any other context about the problem here.

.github/ISSUE_TEMPLATE/feature_request.md

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@@ -0,0 +1,15 @@
+    ---
+    name: Feature request
+    about: Suggest an idea for this project
+    title: ''
+    labels: ''
+    assignees: ''
+    ---
+    **Is your feature request related to a problem? Please describe.**
+    A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+    **Describe the solution you'd like**
+    A clear and concise description of what you want to happen.

CHANGELOG

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@@ -1,5 +1,13 @@
     ## Changelog
+    ## [4.2.1] - 28-06-2023
+    ### Added
+    - Added mLIQSS article models to distribution.
+    ### Changed
+    - Fix mLIQSS recompute next time to only update the Jacobian approximation when the influencer is a state variable.
     ## [4.2.0] - 01-06-2023
     ### Added
@@ Expand Down @@

README.md

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+Diff line change
@@ -1,4 +1,4 @@
-    ## QSS Solver 4.2.0
+    ## QSS Solver 4.2.1
     The QSS Solver is a modeling and simulation environment for
     continuous and hybrid systems and it's optimized for large scale model simulation.
@@ Expand Down Expand Up / @@ -219,6 +219,14 @@ The makefile script accepts the following targets: @@
     ## Changelog
+    ## [4.2.1] - 28-06-2023
+    ### Added
+    - Added mLIQSS article models to distribution.
+    ### Changed
+    - Fix mLIQSS recompute next time to only update the Jacobian approximation when the influencer is a state variable.
     ## [4.2.0] - 01-06-2023
     ### Added
@@ Expand All / @@ -231,18 +239,6 @@ The makefile script accepts the following targets: @@
     ### Changed
     - Fix terminate command code generation.
-    ## [4.0.1] - 03-11-2022
-    ### Added
-    - Compilation **Ubuntu 22.04** is now supported.
-    - Use State variables values instead of quantized approximation in handler reinit statements for QSS methods.
-    ### Changed
-    - The QSS methods event structure **SD_EventData** now contains a new matrix that defines the RHS state variables not used in LHS state assignments.
-    ### Removed
-    - Gtest lib compilation, the compiled libraries are distributed now.
     ## Licensing
     Please see the file called LICENSE.
@@ Expand Down @@

bin/build.sh

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@@ Expand Up / @@ -15,7 +15,7 @@ @@
     #         NOTES: ---
     #        AUTHOR: Joaquin Fernandez, joaquin.f.fernandez@gmail.com
     #       PROJECT: QSS Solver
-    #       VERSION: 4.2.0
+    #       VERSION: 4.2.1
     #===================================================================================
     FILE=$1
@@ Expand Down @@

bin/compile.sh

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@@ Expand Up / @@ -18,7 +18,7 @@ @@
     #         NOTES: ---
     #        AUTHOR: Joaquin Fernandez, joaquin.f.fernandez@gmail.com
     #       PROJECT: QSS Solver
-    #       VERSION: 4.2.0
+    #       VERSION: 4.2.1
     #===================================================================================
     FILE=$1
@@ Expand Down @@

bin/createLog.sh

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@@ Expand Up / @@ -14,7 +14,7 @@ @@
     #         NOTES: ---
     #        AUTHOR: Joaquin Fernandez, joaquin.f.fernandez@gmail.com
     #       PROJECT: QSS Solver
-    #       VERSION: 4.2.0
+    #       VERSION: 4.2.1
     #===================================================================================
     MODEL=$1
@@ Expand Down @@

bin/exportvars.sh

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@@ Expand Up / @@ -14,7 +14,7 @@ @@
     #         NOTES: ---
     #        AUTHOR: Joaquin Fernandez, joaquin.f.fernandez@gmail.com
     #       PROJECT: QSS Solver
-    #       VERSION: 4.2.0
+    #       VERSION: 4.2.1
     #===================================================================================
     cd ..
@@ Expand Down @@

bin/gnuplot.sh

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@@ Expand Up / @@ -13,7 +13,7 @@ @@
     #         NOTES: -persist is the default option used by the QSS Solver GUI.
     #        AUTHOR: Joaquin Fernandez, joaquin.f.fernandez@gmail.com
     #       PROJECT: QSS Solver
-    #       VERSION: 4.2.0
+    #       VERSION: 4.2.1
     #===================================================================================
     OPTIONS=$1
@@ Expand Down @@

bin/mmoc.sh

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@@ Expand Up / @@ -14,7 +14,7 @@ @@
     #         NOTES: ---
     #        AUTHOR: Joaquin Fernandez, joaquin.f.fernandez@gmail.com
     #       PROJECT: QSS Solver
-    #       VERSION: 4.2.0
+    #       VERSION: 4.2.1
     #===================================================================================
     OPTIONS=$1
@@ Expand Down @@

bin/registervars.sh

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@@ Expand Up / @@ -14,7 +14,7 @@ @@
     #         NOTES: ---
     #        AUTHOR: Joaquin Fernandez, joaquin.f.fernandez@gmail.com
     #       PROJECT: QSS Solver
-    #       VERSION: 4.2.0
+    #       VERSION: 4.2.1
     #===================================================================================
     cd ..
@@ Expand Down @@

bin/run.sh

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@@ Expand Up / @@ -17,7 +17,7 @@ @@
     #         NOTES: ---
     #        AUTHOR: Joaquin Fernandez, joaquin.f.fernandez@gmail.com
     #       PROJECT: QSS Solver
-    #       VERSION: 4.2.0
+    #       VERSION: 4.2.1
     #===================================================================================
@@ Expand Down @@

bin/runqss.sh

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@@ Expand Up / @@ -16,7 +16,7 @@ @@
     #         NOTES: ---
     #        AUTHOR: Joaquin Fernandez, joaquin.f.fernandez@gmail.com
     #       PROJECT: QSS Solver
-    #       VERSION: 4.2.0
+    #       VERSION: 4.2.1
     #===================================================================================
     FILE=$1
@@ Expand Down @@

bin/sbml.sh

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@@ Expand Up / @@ -16,7 +16,7 @@ @@
     #         NOTES: ---
     #        AUTHOR: Joaquin Fernandez, joaquin.f.fernandez@gmail.com
     #       PROJECT: QSS Solver
-    #       VERSION: 4.2.0
+    #       VERSION: 4.2.1
     #===================================================================================
     OPTIONS=$1
@@ Expand Down @@

bin/simulate.sh

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@@ Expand Up / @@ -20,7 +20,7 @@ @@
     #         NOTES: ---
     #        AUTHOR: Joaquin Fernandez, joaquin.f.fernandez@gmail.com
     #       PROJECT: QSS Solver
-    #       VERSION: 4.2.0
+    #       VERSION: 4.2.1
     #===================================================================================
     FILE=$1
@@ Expand Down @@

bin/sortDiscretes.sh

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@@ Expand Up / @@ -15,7 +15,7 @@ @@
     #         NOTES: ---
     #        AUTHOR: Joaquin Fernandez, joaquin.f.fernandez@gmail.com
     #       PROJECT: QSS Solver
-    #       VERSION: 4.2.0
+    #       VERSION: 4.2.1
     #===================================================================================
     if test -n "$(find . -maxdepth 1 -name '*-discrete-*.dat' -print -quit)"; then
@@ Expand Down @@

bin/uploadDoc.sh

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@@ Expand Up / @@ -13,7 +13,7 @@ @@
     #         NOTES: ---
     #        AUTHOR: Joaquin Fernandez, joaquin.f.fernandez@gmail.com
     #       PROJECT: QSS Solver
-    #       VERSION: 4.2.0
+    #       VERSION: 4.2.1
     #===================================================================================
     cd $MMOC_SRC/engine/usr/doc/html
@@ Expand Down @@

deploy/linux/build.sh

100644 → 100755

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@@ Expand Up / @@ -15,7 +15,7 @@ @@
     #         NOTES: ---
     #        AUTHOR: Joaquin Fernandez, joaquin.f.fernandez@gmail.com
     #       PROJECT: QSS Solver
-    #       VERSION: 4.2.0
+    #       VERSION: 4.2.1
     #===================================================================================
     rm -rf qss-solver-*.deb
@@ Expand Down @@

deploy/linux/deb/DEBIAN/control.amd64

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@@ Expand Up / @@ -2,6 +2,8 @@ Package: qss-solver @@
     Version:
     Architecture: amd64
     Maintainer: Joaquin Fernandez <fernandez@cifasis-conicet.gov.ar>
+    aintainer: Joaquin Fernandez <fernandez@cifasis-conicet.gov.ar>
+    Installed-Size: 372736
     Depends: gnuplot-x11, build-essential (>= 11.4), qt5-default, zenity, gfortran (>=4.6.3), libconfig-dev, libblas-dev, libgsl0-dev, libsuitesparse-dev, libcln6, libatlas-base-dev
     Section: science
     Priority: extra
@@ Expand Down @@

deploy/linux/deb/DEBIAN/control.amd64.u22

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@@ Expand Up / @@ -2,6 +2,7 @@ Package: qss-solver @@
     Version:
     Architecture: amd64
     Maintainer: Joaquin Fernandez <fernandez@cifasis-conicet.gov.ar>
+    Installed-Size: 372736
     Depends: gnuplot-x11, build-essential (>= 11.4), qtbase5-dev, qt5-qmake, zenity, gfortran (>=4.6.3), libconfig-dev, libblas-dev, libgsl0-dev, libsuitesparse-dev, libcln6, libatlas-base-dev
     Section: science
     Priority: extra
@@ Expand Down @@

deploy/linux/version

Original file line number	Diff line number	Diff line change
		@@ -1 +1 @@
		4.2.0
		4.2.1

models/mLIQSS/mliqss_TYSON.mo

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+    model mliqss_TYSON
+    	import math;
+    	// BioRica Constant k1
+    	parameter Real k1 = 0.015;
+    	// BioRica Constant k2
+    	parameter Real k2 = 0.0;
+    	// BioRica Constant k3
+    	parameter Real k3 = 200;
+    	// BioRica Constant k4
+    	parameter Real k4 = 180;
+    	// BioRica Constant k4prim
+    	parameter Real k4prim = 0.018;
+    	// BioRica Constant k5
+    	parameter Real k5 = 0.0;
+    	// BioRica Constant k6
+    	parameter Real k6 = 1.0;
+    	// BioRica Constant k7
+    	parameter Real k7 = 0.6;
+    	// BioRica Constant k8
+    	parameter Real k8 = 1000000.0;
+    	// BioRica Constant k9
+    	parameter Real k9 = 1000.0;
+    	Real CP(start = 0.75);
+    	Real yt;
+    	Real C2(start = 0.0);
+    	Real M(start = 0.0);
+    	Real pM(start = 0.25);
+    	Real CT;
+    	Real Y(start = 0.0);
+    	Real YT;
+    	Real F;
+    	Real yP(start = 0.0);
+    	equation
+    		// BioRica Formula CT instance:
+    		CT = C2+CP+pM+M;
+    		// BioRica Formula YT instance:
+    		YT = Y+yP+pM+M;
+    		// BioRica Formula F instance:
+    		F = k4prim+k4*pow((M*1.0/CT),2);
+    		yt = YT;
+    		der(C2) = k6*M-k8*C2+k9*CP;
+    		der(CP) = -k3*CP*Y+k8*C2-k9*CP;
+    		der(pM) = k3*CP*Y+-pM*F+k5*M;
+    		der(M) = pM*F-k5*M-k6*M;
+    		der(Y) = k1-k2*Y-k3*CP*Y;
+    		der(yP) = k6*M-k7*yP;
+    	annotation(
+    	experiment(
+    		MMO_Description="TYSON automatic model translation.",
+    		MMO_Solver=mLIQSS2,
+    		MMO_SymDiff=false,
+    		MMO_PartitionMethod=Metis,
+    		MMO_Output={C2,CP,pM,M,Y,yP},
+    		Jacobian=Dense,
+    		MMO_BDF_PDepth=1,
+    		MMO_BDF_Max_Step=0,
+    		StartTime=0.0,
+    		StopTime=100,
+    		Tolerance={1e-3},
+    		AbsTolerance={1e-6}
+    	));
+    end mliqss_TYSON;

models/mLIQSS/mliqss_adr.mo

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@@ -0,0 +1,37 @@
+    model mliqss_adr
+      constant Integer N = 1000;
+      parameter Real a=1;
+      parameter Real d=0.001;
+      parameter Real r=1000;
+      parameter Real dx=10/N;
+      Real u[N];
+      initial algorithm
+      for i in 1:N/5 loop
+        u[i]:=1;
+      end for;
+      equation
+      der(u[1])=-a*(u[1]-1)/dx + d*(u[2]-2*u[1] + 1)/(dx^2)+ r*(u[1]^2)*(1-u[1]);
+      der(u[N])=-a*(u[N]-u[N-1])/dx + d*(u[N-1]-2*u[N] + u[N-1])/(dx^2) + r*(u[N]^2)*(1-u[N]);
+      for i in 2:N-1 loop
+        der(u[i])=-a*(u[i]-u[i-1])/dx +d*(u[i + 1]-2*u[i] + u[i-1])/(dx^2) +r*(u[i]^2)*(1-u[i]);
+      end for;
+    	annotation(
+    	experiment(
+    		MMO_Description="Advection",
+    		MMO_Solver=mLIQSS2,
+    		MMO_PartitionMethod=Scotch,
+    		MMO_LPS=2,
+    		MMO_DT_Min=2,
+    		MMO_Output={u[1:100:N]},
+    		Jacobian=Dense,
+    		MMO_BDF_PDepth=1,
+    		MMO_BDF_Max_Step=0,
+    		StartTime=0.0,
+    		StopTime=10,
+    		Tolerance={1e-3},
+    		AbsTolerance={1e-3}
+    	));
+    end mliqss_adr;

models/mLIQSS/mliqss_cuk.mo

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+    model mliqss_cuk
+      constant Integer N = 4;
+      parameter Real R = 10, U = 24, T = 1e-4, DC = 0.25, ROn = 1e-5, ROff = 1e5;
+      parameter Real C1=1e-4,L1=1e-4, C2 = 1e-4, L2 = 1e-4;
+      discrete Real Rd(start=1e5), Rs(start=1e-5), nextT(start=T),lastT,diodeon;
+      Real uC1[N],iL1[N],uC2,iL2[N],iD[N],s[N];
+      equation
+    for i in 1:N loop
+        s[i]=diodeon*iD[i]+(1-diodeon)*iD[i]*Rd;
+        iD[i]=(Rs*(iL1[i]+iL2[i])-uC1[i])/(Rs+Rd);
+        der(iL1[i]) =  (U-uC1[i]-iD[i]*Rs)/L1;
+        der(iL2[i]) =  (-uC2-iD[i]*Rs)/L2;
+         der(uC1[i]) = (iD[i] - iL2[i])/C1;
+    end for;
+         der(uC2) = (sum(iL2) - uC2/R)/C2;
+    algorithm
+        when time > nextT then
+          lastT:=nextT;
+          nextT:=nextT+T;
+          Rs := ROn;
+        end when;
+        when time - lastT-DC*T>0 then
+          Rs := ROff;
+        end when;
+    for i in 1:N loop
+        when s[i]>0 then
+          Rd:=ROn;
+          diodeon:=1;
+        elsewhen s[i]<0 then
+          Rd := ROff;
+           diodeon:=0;
+        end when;
+    end for;
+    	annotation(
+    	experiment(
+    		MMO_Description="Cuk converter with non-solved stiffness.",
+    		MMO_Solver=mLIQSS2,
+    		MMO_PartitionMethod=Metis,
+    		MMO_Output={uC1,iL1,uC2,iL2},
+    		Jacobian=Dense,
+    		MMO_BDF_PDepth=1,
+    		MMO_BDF_Max_Step=0,
+    		StartTime=0,
+    		StopTime=0.02,
+    		Tolerance={ 1e-3},
+    		AbsTolerance={ 1e-3}
+    	));
+    end mliqss_cuk;

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