From 66cb5bb4908cc54192aadaa901ac9092861c60f7 Mon Sep 17 00:00:00 2001
From: Adrian Sandu <sandu.g.adrian@gmail.com>
Date: Tue, 1 Sep 2026 14:56:21 -0400
Subject: [PATCH 1/4] Allen Cahn splitting added

---
 toolboxPackaging.prj | 58 ++++++++++++++++++++++++++++++++++++++++++--
 1 file changed, 56 insertions(+), 2 deletions(-)

diff --git a/toolboxPackaging.prj b/toolboxPackaging.prj
index c9ddefa4..b4dd6978 100644
--- a/toolboxPackaging.prj
+++ b/toolboxPackaging.prj
@@ -1,5 +1,5 @@
 <deployment-project plugin="plugin.toolbox" plugin-version="1.0">
-  <configuration name="ODE Test Problems" target="target.toolbox" target-name="Package Toolbox">
+  <configuration file="/Users/sandu/GIT/GitHub/ODE-Test-Problems/toolboxPackaging.prj" location="/Users/sandu/GIT/GitHub/ODE-Test-Problems" name="toolboxPackaging" target="target.toolbox" target-name="Package Toolbox">
     <param.appname>ODE Test Problems</param.appname>
     <param.authnamewatermark>Steven Roberts, Andrey A. Popov, Arash Sarshar, Adrian Sandu</param.authnamewatermark>
     <param.email />
@@ -14,7 +14,7 @@
     <param.products.version />
     <param.platforms />
     <param.guid>0970ed36-a788-484f-beca-105eecd2562a</param.guid>
-    <param.exclude.filters></param.exclude.filters>
+    <param.exclude.filters />
     <param.exclude.pcodedmfiles>true</param.exclude.pcodedmfiles>
     <param.examples />
     <param.demosxml />
@@ -85,5 +85,59 @@
     <fileset.depfun.included />
     <fileset.depfun.excluded />
     <fileset.package />
+    <build-deliverables>
+      <file location="${PROJECT_ROOT}" name="ODE Test Problems.mltbx" optional="false">/Users/sandu/GIT/GitHub/ODE-Test-Problems/ODE Test Problems.mltbx</file>
+    </build-deliverables>
+    <workflow />
+    <matlab>
+      <root>/Applications/MATLAB_R2024b.app</root>
+      <toolboxes>
+        <toolbox name="matlabcoder" />
+        <toolbox name="embeddedcoder" />
+        <toolbox name="fixedpoint" />
+        <toolbox name="matlabhdlcoder" />
+        <toolbox name="neuralnetwork" />
+      </toolboxes>
+      <toolbox>
+        <matlabcoder>
+          <enabled>true</enabled>
+        </matlabcoder>
+      </toolbox>
+      <toolbox>
+        <embeddedcoder>
+          <enabled>true</enabled>
+        </embeddedcoder>
+      </toolbox>
+      <toolbox>
+        <fixedpoint>
+          <enabled>true</enabled>
+        </fixedpoint>
+      </toolbox>
+      <toolbox>
+        <matlabhdlcoder>
+          <enabled>true</enabled>
+        </matlabhdlcoder>
+      </toolbox>
+      <toolbox>
+        <neuralnetwork>
+          <enabled>true</enabled>
+        </neuralnetwork>
+      </toolbox>
+    </matlab>
+    <platform>
+      <unix>true</unix>
+      <mac>true</mac>
+      <windows>false</windows>
+      <win2k>false</win2k>
+      <winxp>false</winxp>
+      <vista>false</vista>
+      <linux>false</linux>
+      <solaris>false</solaris>
+      <osver>15.5</osver>
+      <os32>true</os32>
+      <os64>false</os64>
+      <arch>maci64</arch>
+      <matlab>true</matlab>
+    </platform>
   </configuration>
 </deployment-project>
\ No newline at end of file

From 4b3de2c085abfe04fb92e9c6244f5776959af2dd Mon Sep 17 00:00:00 2001
From: Adrian Sandu <sandu.g.adrian@gmail.com>
Date: Tue, 1 Sep 2026 15:02:10 -0400
Subject: [PATCH 2/4] AS on AllenCahn

---
 toolbox/+otp/+allencahn/f_diffusion.m        | 5 +++++
 toolbox/+otp/+allencahn/f_reaction.m         | 5 +++++
 toolbox/+otp/+allencahn/jacobian_diffusion.m | 5 +++++
 toolbox/+otp/+allencahn/jacobian_reaction.m  | 5 +++++
 4 files changed, 20 insertions(+)
 create mode 100644 toolbox/+otp/+allencahn/f_diffusion.m
 create mode 100644 toolbox/+otp/+allencahn/f_reaction.m
 create mode 100644 toolbox/+otp/+allencahn/jacobian_diffusion.m
 create mode 100644 toolbox/+otp/+allencahn/jacobian_reaction.m

diff --git a/toolbox/+otp/+allencahn/f_diffusion.m b/toolbox/+otp/+allencahn/f_diffusion.m
new file mode 100644
index 00000000..7fe2f16f
--- /dev/null
+++ b/toolbox/+otp/+allencahn/f_diffusion.m
@@ -0,0 +1,5 @@
+function du = f_diffusion(~, u, L, alpha, ~, ~)
+
+du = alpha*L*u;
+
+end
diff --git a/toolbox/+otp/+allencahn/f_reaction.m b/toolbox/+otp/+allencahn/f_reaction.m
new file mode 100644
index 00000000..f9778662
--- /dev/null
+++ b/toolbox/+otp/+allencahn/f_reaction.m
@@ -0,0 +1,5 @@
+function du = f_reaction(t, u, ~, ~, beta, forcing)
+
+du = beta * (u - u.^3) + forcing(t);
+
+end
diff --git a/toolbox/+otp/+allencahn/jacobian_diffusion.m b/toolbox/+otp/+allencahn/jacobian_diffusion.m
new file mode 100644
index 00000000..de0deabd
--- /dev/null
+++ b/toolbox/+otp/+allencahn/jacobian_diffusion.m
@@ -0,0 +1,5 @@
+function j = jacobian_diffusion(~, ~, L, alpha, ~, ~)
+
+j = alpha*L;
+
+end
diff --git a/toolbox/+otp/+allencahn/jacobian_reaction.m b/toolbox/+otp/+allencahn/jacobian_reaction.m
new file mode 100644
index 00000000..22c54077
--- /dev/null
+++ b/toolbox/+otp/+allencahn/jacobian_reaction.m
@@ -0,0 +1,5 @@
+function j = jacobian_reaction(~, u, L, ~, beta, ~)
+
+j = spdiags(beta * (1 - 3*u.^2), 0, size(L, 1), size(L, 2));
+
+end

From ff2533ce7e6780a365bc3f0188c175b1a1668545 Mon Sep 17 00:00:00 2001
From: Adrian Sandu <sandu.g.adrian@gmail.com>
Date: Tue, 1 Sep 2026 15:38:12 -0400
Subject: [PATCH 3/4] Linear-nonlinear splitting of Allen-Cahn

---
 toolbox/+otp/+allencahn/f_linear.m    | 8 ++++++++
 toolbox/+otp/+allencahn/f_nonlinear.m | 8 ++++++++
 2 files changed, 16 insertions(+)
 create mode 100644 toolbox/+otp/+allencahn/f_linear.m
 create mode 100644 toolbox/+otp/+allencahn/f_nonlinear.m

diff --git a/toolbox/+otp/+allencahn/f_linear.m b/toolbox/+otp/+allencahn/f_linear.m
new file mode 100644
index 00000000..52498144
--- /dev/null
+++ b/toolbox/+otp/+allencahn/f_linear.m
@@ -0,0 +1,8 @@
+% Linear-nonlinear splitting: f = f_linear + f_nonlinear
+% f_linear(u) = Jac*u,  f_nonlinear(u) = f(u)-Jac*u
+
+function du = f_linear(~, u, L, alpha, beta, ~)
+
+du = alpha*L*u + beta * (u - 3*u.^3);
+
+end
diff --git a/toolbox/+otp/+allencahn/f_nonlinear.m b/toolbox/+otp/+allencahn/f_nonlinear.m
new file mode 100644
index 00000000..0df35223
--- /dev/null
+++ b/toolbox/+otp/+allencahn/f_nonlinear.m
@@ -0,0 +1,8 @@
+% Linear-nonlinear splitting: f = f_linear + f_nonlinear
+% f_linear(u) = Jac*u,  f_nonlinear(u) = f(u)-Jac*u
+
+function du = f_nonlinear(t, u, ~, ~, beta, forcing)
+
+du = beta * (u - u.^3) - beta * (u - 3*u.^3) + forcing(t);
+
+end

From 7f5567e5694dd8e699d22fb749f20e642b1ace80 Mon Sep 17 00:00:00 2001
From: Adrian Sandu <sandu.g.adrian@gmail.com>
Date: Tue, 1 Sep 2026 15:44:15 -0400
Subject: [PATCH 4/4] Split Allen-Cahn into diffusion and reaction parts

---
 toolbox/+otp/+allencahn/f_diffusion.m        | 4 ++++
 toolbox/+otp/+allencahn/f_reaction.m         | 4 ++++
 toolbox/+otp/+allencahn/jacobian_diffusion.m | 4 ++++
 toolbox/+otp/+allencahn/jacobian_reaction.m  | 4 ++++
 4 files changed, 16 insertions(+)

diff --git a/toolbox/+otp/+allencahn/f_diffusion.m b/toolbox/+otp/+allencahn/f_diffusion.m
index 7fe2f16f..bbbb7778 100644
--- a/toolbox/+otp/+allencahn/f_diffusion.m
+++ b/toolbox/+otp/+allencahn/f_diffusion.m
@@ -1,3 +1,7 @@
+% Process splitting: 
+%   f = f_diffusion + f_reaction
+%   Jacobian = Jacobian_diffusion + Jacobian_reaction
+% 
 function du = f_diffusion(~, u, L, alpha, ~, ~)
 
 du = alpha*L*u;
diff --git a/toolbox/+otp/+allencahn/f_reaction.m b/toolbox/+otp/+allencahn/f_reaction.m
index f9778662..774d5bbd 100644
--- a/toolbox/+otp/+allencahn/f_reaction.m
+++ b/toolbox/+otp/+allencahn/f_reaction.m
@@ -1,3 +1,7 @@
+% Process splitting: 
+%   f = f_diffusion + f_reaction
+%   Jacobian = Jacobian_diffusion + Jacobian_reaction
+% 
 function du = f_reaction(t, u, ~, ~, beta, forcing)
 
 du = beta * (u - u.^3) + forcing(t);
diff --git a/toolbox/+otp/+allencahn/jacobian_diffusion.m b/toolbox/+otp/+allencahn/jacobian_diffusion.m
index de0deabd..c6e84cb7 100644
--- a/toolbox/+otp/+allencahn/jacobian_diffusion.m
+++ b/toolbox/+otp/+allencahn/jacobian_diffusion.m
@@ -1,3 +1,7 @@
+% Process splitting: 
+%   f = f_diffusion + f_reaction
+%   Jacobian = Jacobian_diffusion + Jacobian_reaction
+%
 function j = jacobian_diffusion(~, ~, L, alpha, ~, ~)
 
 j = alpha*L;
diff --git a/toolbox/+otp/+allencahn/jacobian_reaction.m b/toolbox/+otp/+allencahn/jacobian_reaction.m
index 22c54077..206d3b96 100644
--- a/toolbox/+otp/+allencahn/jacobian_reaction.m
+++ b/toolbox/+otp/+allencahn/jacobian_reaction.m
@@ -1,3 +1,7 @@
+% Process splitting: 
+%   f = f_diffusion + f_reaction
+%   Jacobian = Jacobian_diffusion + Jacobian_reaction
+% 
 function j = jacobian_reaction(~, u, L, ~, beta, ~)
 
 j = spdiags(beta * (1 - 3*u.^2), 0, size(L, 1), size(L, 2));