From 7c7fe4ef8a800f8616b872b38a588e831cd21c46 Mon Sep 17 00:00:00 2001
From: CallieHsu <kelly811113@gmail.com>
Date: Thu, 6 Jul 2023 14:36:01 -0400
Subject: [PATCH 01/11] update odechamber function

---
 src/runcode-func.jl        |  31 +++-----
 src/utils-matrix.jl        |  99 ++++++++++--------------
 test/test-matrix-a-data.jl | 152 +++----------------------------------
 test/test-matrix-b-data.jl |  67 ++--------------
 test/test-matrix.jl        |  30 +++-----
 5 files changed, 80 insertions(+), 299 deletions(-)

diff --git a/src/runcode-func.jl b/src/runcode-func.jl
index 3f1de8d..f8a87ae 100644
--- a/src/runcode-func.jl
+++ b/src/runcode-func.jl
@@ -36,21 +36,12 @@ function odeChamber(
     L_e, L_m = param.L_e, param.L_m
     mm_h2o, mm_co2 = param.mm_h2o, param.mm_co2
     T_in = param.T_in
-    P_lit_0, dP_lit_dt, dP_lit_dt_0, P_lit_drop_max = param.P_lit_0,
-    param.dP_lit_dt, param.dP_lit_dt_0,
-    param.P_lit_drop_max
 
-    P0plusDP = u[1]
+    P = u[1]
     T = u[2]
     eps_g = u[3]
     X_co2 = u[7]
-    P_lit = P_lit_0 + dP_lit_dt_0 * t
-    if P_lit < P_lit_0 - P_lit_drop_max
-        P_lit = P_lit_0 - P_lit_drop_max
-        dP_lit_dt = 0.0
-        param.dP_lit_dt = 0.0
-    end
-    P = P_lit + P0plusDP - P_lit_0
+
     # effective gas molar mass
     m_g = mm_co2 * X_co2 + mm_h2o * (1 - X_co2)
 
@@ -94,8 +85,10 @@ function odeChamber(
 
     if phase == 3
         C_co2 = C_co2_t
+        C_h2o = m_eq
     elseif phase == 2
-        C_co2 = m_co2
+        C_co2 = M_co2/(rho_m*eps_m*V)
+        C_h2o = M_h2o/(rho_m*eps_m*V)
     end
 
     # specific heat of gas
@@ -147,7 +140,7 @@ function odeChamber(
         dm_eq_dP,
         rho_m,
         eps_m,
-        m_eq,
+        C_h2o,
         drho_m_dP,
         drc_dT,
         drho_x_dT,
@@ -161,7 +154,6 @@ function odeChamber(
         m_h2o,
         m_co2,
         deps_x_dmco2_t,
-        dP_lit_dt,
         Hdot_in,
         Hdot_out,
         c_x,
@@ -189,14 +181,13 @@ function odeChamber(
 
     # coefficients in the system of unknowns Ax = B, here x= [dP/dt dT/dt deps_g/dt dX_co2/dt]
     if phase == 3
-        dDP_dt, dT_dt, deps_g_dt, dX_co2_dt = A \ b
+        dP_dt, dT_dt, deps_g_dt, dX_co2_dt = A \ b
     elseif phase == 2
-        dDP_dt, dT_dt = A \ b
+        dP_dt, dT_dt = A \ b
         deps_g_dt, dX_co2_dt = 0.0, 0.0
     end
-    dP_dt = dDP_dt + dP_lit_dt
 
-    du[1] = dDP_dt
+    du[1] = dP_dt
     du[2] = dT_dt
     du[3] = deps_g_dt
     du[4] = dV_dP * dP_dt + dV_dT * dT_dt + V * P_loss
@@ -285,7 +276,8 @@ function stopChamber_MT(
     out[5] = eps_x - 0.5
     out[6] = m_h2o_melt - m_eq_max
     out[7] = -(P0plusDP - param.P_lit_0 + DP_crit)
-    return out[8] = m_co2_melt - C_co2_sat
+    out[8] = m_co2_melt - C_co2_sat
+    return out
 end
 
 """
@@ -415,6 +407,7 @@ function affect!(
                     C_co2 = C_co2_temp
                 else
                     @warn("3rd try in IC Finder unsuccessful")
+                    @info("IC_Finder results: $eps_g_temp, $X_co2_temp, $C_co2_temp, $phase = IC_Finder($composition, $(int.u[9]), $(int.u[10]), $(int.u[8]), $(P_0), $(int.u[2]), $(int.u[4]), $(int.u[5]), $(param_IC_Finder))")
                 end
             end
         end
diff --git a/src/utils-matrix.jl b/src/utils-matrix.jl
index 6f94f73..848bb4c 100644
--- a/src/utils-matrix.jl
+++ b/src/utils-matrix.jl
@@ -16,7 +16,7 @@ end
 function a21_f(
     eps_m::T,
     dm_eq_dP::T,
-    m_eq::T,
+    C_h2o::T,
     deps_x_dP::T,
     dV_dP::T,
     V::T,
@@ -29,9 +29,9 @@ function a21_f(
     drho_g_dP::T,
     rho_g::T,
 )::T where {T<:Float64}
-    return eps_m * dm_eq_dP - m_eq * deps_x_dP +
-           m_eq * eps_m * dV_dP / V +
-           m_eq * eps_m * drho_m_dP / rho_m +
+    return eps_m * dm_eq_dP - C_h2o * deps_x_dP +
+           C_h2o * eps_m * dV_dP / V +
+           C_h2o * eps_m * drho_m_dP / rho_m +
            (1 - X_co2) / m_g * eps_g * mm_h2o * drho_g_dP / rho_m +
            (1 - X_co2) / m_g * eps_g * mm_h2o * rho_g * dV_dP / (rho_m * V)
 end
@@ -39,7 +39,7 @@ end
 function a22_f(
     eps_m::T,
     dm_eq_dT::T,
-    m_eq::T,
+    C_h2o::T,
     deps_x_dT::T,
     dV_dT::T,
     V::T,
@@ -52,16 +52,16 @@ function a22_f(
     drho_g_dT::T,
     rho_g::T,
 )::T where {T<:Float64}
-    return eps_m * dm_eq_dT - m_eq * deps_x_dT - m_eq * eps_m * dV_dT / V +
-           m_eq * eps_m * drho_m_dT / rho_m +
+    return eps_m * dm_eq_dT - C_h2o * deps_x_dT + C_h2o * eps_m * dV_dT / V +
+           C_h2o * eps_m * drho_m_dT / rho_m +
            (1 - X_co2) / m_g * eps_g * mm_h2o * drho_g_dT / rho_m +
            (1 - X_co2) / m_g * eps_g * mm_h2o * rho_g * dV_dT / (rho_m * V)
 end
 
 function a23_f(
-    m_eq::T, X_co2::T, m_g::T, rho_g::T, mm_h2o::T, rho_m::T
+    C_h2o::T, X_co2::T, m_g::T, rho_g::T, mm_h2o::T, rho_m::T
 )::T where {T<:Float64}
-    return -m_eq + (1 - X_co2) / m_g * rho_g * mm_h2o / rho_m
+    return -C_h2o + (1 - X_co2) / m_g * rho_g * mm_h2o / rho_m
 end
 
 function a24_f(
@@ -97,7 +97,7 @@ function a31_f(
     dm_eq_dP::T,
     rho_m::T,
     eps_m::T,
-    m_eq::T,
+    C_h2o::T,
     drho_m_dP::T,
 )::T where {T<:Float64}
     return drc_dP / (rc) +
@@ -108,9 +108,9 @@ function a31_f(
            ) +
            L_e * (
                -dm_eq_dP * rho_m * eps_m / (rc * temp) -
-               m_eq * eps_m * drho_m_dP / (rc * temp) +
-               m_eq * rho_m * deps_x_dP / (rc * temp) -
-               m_eq * rho_m * eps_m * dV_dP / (rc * V * temp)
+               C_h2o * eps_m * drho_m_dP / (rc * temp) +
+               C_h2o * rho_m * deps_x_dP / (rc * temp) -
+               C_h2o * rho_m * eps_m * dV_dP / (rc * V * temp)
            )
 end
 
@@ -129,7 +129,7 @@ function a32_f(
     dm_eq_dT::T,
     rho_m::T,
     eps_m::T,
-    m_eq::T,
+    C_h2o::T,
     drho_m_dT::T,
 )::T where {T<:Float64}
     return drc_dT / (rc) +
@@ -141,16 +141,16 @@ function a32_f(
            ) +
            L_e * (
                -dm_eq_dT * rho_m * eps_m / (rc * temp) -
-               m_eq * eps_m * drho_m_dT / (rc * temp) +
-               m_eq * rho_m * deps_x_dT / (rc * temp) -
-               m_eq * rho_m * eps_m * dV_dT / (rc * temp * V)
+               C_h2o * eps_m * drho_m_dT / (rc * temp) +
+               C_h2o * rho_m * deps_x_dT / (rc * temp) -
+               C_h2o * rho_m * eps_m * dV_dT / (rc * temp * V)
            )
 end
 
 function a33_f(
-    rho_g::T, c_g::T, rho_m::T, c_m::T, rc::T, L_e::T, m_eq::T, temp::T
+    rho_g::T, c_g::T, rho_m::T, c_m::T, rc::T, L_e::T, C_h2o::T, temp::T
 )::T where {T<:Float64}
-    return (rho_g * c_g - rho_m * c_m) / rc + L_e * m_eq * rho_m / (rc * temp)
+    return (rho_g * c_g - rho_m * c_m) / rc + L_e * C_h2o * rho_m / (rc * temp)
 end
 
 function a34_f(
@@ -198,7 +198,7 @@ function a42_f(
     drho_g_dT::T,
     rho_g::T,
 )::T where {T<:Float64}
-    return eps_m * dC_co2_dT - C_co2 * deps_x_dT - C_co2 * eps_m * dV_dT / V +
+    return eps_m * dC_co2_dT - C_co2 * deps_x_dT + C_co2 * eps_m * dV_dT / V +
            C_co2 * eps_m * drho_m_dT / rho_m +
            X_co2 / m_g * eps_g * mm_co2 * drho_g_dT / rho_m +
            X_co2 / m_g * eps_g * rho_g * mm_co2 * dV_dT / (rho_m * V)
@@ -255,12 +255,10 @@ function b1_f(
     dM_h2o_t_dt::T,
     deps_x_dmco2_t::T,
     dM_co2_t_dt::T,
-    a11::T,
-    dP_lit_dt::T,
 )::T where {T<:Float64}
     return (Mdot_in - Mdot_out) / (rho * V) - P_loss -
            (rho_x - rho_m) / rho * deps_x_dmh2o_t * dM_h2o_t_dt -
-           (rho_x - rho_m) / rho * deps_x_dmco2_t * dM_co2_t_dt - a11 * dP_lit_dt
+           (rho_x - rho_m) / rho * deps_x_dmco2_t * dM_co2_t_dt
 end
 # b2: conservation of water mass
 function b2_f(
@@ -268,7 +266,7 @@ function b2_f(
     Mdot_v_out::T,
     rho_m::T,
     V::T,
-    m_eq::T,
+    C_h2o::T,
     deps_x_dmh2o_t::T,
     dM_h2o_t_dt::T,
     deps_x_dmco2_t::T,
@@ -280,13 +278,11 @@ function b2_f(
     rho_g::T,
     eps_g::T,
     mm_h2o::T,
-    a21::T,
-    dP_lit_dt::T,
 )::T where {T<:Float64}
-    return (Mdot_v_in - Mdot_v_out) / (rho_m * V) -
-           m_eq * (deps_x_dmh2o_t * dM_h2o_t_dt + deps_x_dmco2_t * dM_co2_t_dt) -
-           m_eq * eps_m * P_loss -
-           (1 - X_co2) / m_g * rho_g / rho_m * eps_g * mm_h2o * P_loss - a21 * dP_lit_dt
+    return (Mdot_v_in - Mdot_v_out) / (rho_m * V) +
+           C_h2o * (deps_x_dmh2o_t * dM_h2o_t_dt + deps_x_dmco2_t * dM_co2_t_dt) -
+           C_h2o * eps_m * P_loss -
+           (1 - X_co2) / m_g * rho_g / rho_m * eps_g * mm_h2o * P_loss
 end
 # b3: conservation of (total) enthalpy
 function b3_f(
@@ -305,12 +301,10 @@ function b3_f(
     dM_co2_t_dt::T,
     L_m::T,
     L_e::T,
-    m_eq::T,
+    C_h2o::T,
     P_loss::T,
     eps_x::T,
     eps_m::T,
-    a31::T,
-    dP_lit_dt::T,
 )::T where {T<:Float64}
     return (Hdot_in - Hdot_out) / (rc * temp * V) -
            1 / (rc * V * temp) * (
@@ -321,13 +315,13 @@ function b3_f(
            ) +
            L_m * rho_x * V / (rc * V * temp) *
            (deps_x_dmh2o_t * dM_h2o_t_dt + deps_x_dmco2_t * dM_co2_t_dt) +
-           L_e * m_eq * rho_m * V / (rc * V * temp) *
+           L_e * C_h2o * rho_m * V / (rc * V * temp) *
            (deps_x_dmh2o_t * dM_h2o_t_dt + deps_x_dmco2_t * dM_co2_t_dt) +
            P_loss * (
                -1 +
                L_m * rho_x * eps_x * V / (rc * V * temp) +
-               L_e * m_eq * rho_m * eps_m * V / (rc * V * temp)
-           ) - a31 * dP_lit_dt
+               L_e * C_h2o * rho_m * eps_m * V / (rc * V * temp)
+           )
 end
 # b4: conservation of CO2 mass
 function b4_f(
@@ -347,13 +341,11 @@ function b4_f(
     rho_g::T,
     eps_g::T,
     mm_co2::T,
-    a41::T,
-    dP_lit_dt::T,
 )::T where {T<:Float64}
-    return (Mdot_c_in - Mdot_c_out) / (rho_m * V) -
+    return (Mdot_c_in - Mdot_c_out) / (rho_m * V) +
            C_co2 * (deps_x_dmh2o_t * dM_h2o_t_dt + deps_x_dmco2_t * dM_co2_t_dt) -
            C_co2 * eps_m * P_loss -
-           (X_co2) / m_g * rho_g / rho_m * eps_g * mm_co2 * P_loss - a41 * dP_lit_dt
+           (X_co2) / m_g * rho_g / rho_m * eps_g * mm_co2 * P_loss
 end
 
 function build_matrix(
@@ -376,7 +368,7 @@ function build_matrix(
     dm_eq_dP::T,
     rho_m::T,
     eps_m::T,
-    m_eq::T,
+    C_h2o::T,
     drho_m_dP::T,
     drc_dT::T,
     drho_x_dT::T,
@@ -390,7 +382,6 @@ function build_matrix(
     m_h2o::T,
     m_co2::T,
     deps_x_dmco2_t::T,
-    dP_lit_dt::T,
     Hdot_in::T,
     Hdot_out::T,
     c_x::T,
@@ -432,7 +423,7 @@ function build_matrix(
         dm_eq_dP,
         rho_m,
         eps_m,
-        m_eq,
+        C_h2o,
         drho_m_dP,
     )
     a32 = a32_f(
@@ -450,7 +441,7 @@ function build_matrix(
         dm_eq_dT,
         rho_m,
         eps_m,
-        m_eq,
+        C_h2o,
         drho_m_dT,
     )
     dM_h2o_t_dt = dM_X_t_dt_f(rho, V, Mdot_v_in, Mdot_v_out, m_h2o, Mdot_in, Mdot_out)
@@ -467,8 +458,6 @@ function build_matrix(
         dM_h2o_t_dt,
         deps_x_dmco2_t,
         dM_co2_t_dt,
-        a11,
-        dP_lit_dt,
     )
     b3 = b3_f(
         Hdot_in,
@@ -486,12 +475,10 @@ function build_matrix(
         dM_co2_t_dt,
         L_m,
         L_e,
-        m_eq,
+        C_h2o,
         P_loss,
         eps_x,
         eps_m,
-        a31,
-        dP_lit_dt,
     )
     if phase != 3
         A = [a11 a12; a31 a32]
@@ -503,7 +490,7 @@ function build_matrix(
         a21 = a21_f(
             eps_m,
             dm_eq_dP,
-            m_eq,
+            C_h2o,
             deps_x_dP,
             dV_dP,
             V,
@@ -519,7 +506,7 @@ function build_matrix(
         a22 = a22_f(
             eps_m,
             dm_eq_dT,
-            m_eq,
+            C_h2o,
             deps_x_dT,
             dV_dT,
             V,
@@ -532,9 +519,9 @@ function build_matrix(
             drho_g_dT,
             rho_g,
         )
-        a23 = a23_f(m_eq, X_co2, m_g, rho_g, mm_h2o, rho_m)
+        a23 = a23_f(C_h2o, X_co2, m_g, rho_g, mm_h2o, rho_m)
         a24 = a24_f(eps_m, dm_eq_dX_co2, m_g, eps_g, rho_g, mm_h2o, rho_m, X_co2, mm_co2)
-        a33 = a33_f(rho_g, c_g, rho_m, c_m, rc, L_e, m_eq, temp)
+        a33 = a33_f(rho_g, c_g, rho_m, c_m, rc, L_e, C_h2o, temp)
         a34 = a34_f(L_e, rho_m, eps_m, dm_eq_dX_co2, rc, temp)
         a41 = a41_f(
             eps_m,
@@ -576,7 +563,7 @@ function build_matrix(
             Mdot_v_out,
             rho_m,
             V,
-            m_eq,
+            C_h2o,
             deps_x_dmh2o_t,
             dM_h2o_t_dt,
             deps_x_dmco2_t,
@@ -588,8 +575,6 @@ function build_matrix(
             rho_g,
             eps_g,
             mm_h2o,
-            a21,
-            dP_lit_dt,
         )
         b4 = b4_f(
             Mdot_c_in,
@@ -608,8 +593,6 @@ function build_matrix(
             rho_g,
             eps_g,
             mm_co2,
-            a41,
-            dP_lit_dt,
         )
 
         A = [a11 a12 a13 a14; a21 a22 a23 a24; a31 a32 a33 a34; a41 a42 a43 a44]
diff --git a/test/test-matrix-a-data.jl b/test/test-matrix-a-data.jl
index 9a0e948..4f7aea9 100644
--- a/test/test-matrix-a-data.jl
+++ b/test/test-matrix-a-data.jl
@@ -1,33 +1,26 @@
 # Matrix A
-a11, rho, drho_dP, V, dV_dP, a12, rho, drho_dT, V, dV_dT, a13, rho, drho_deps_g = (
+a11, rho, drho_dP, V, dV_dP, a12, drho_dT, dV_dT, a13, drho_deps_g = (
     1.940628985769057e-10,
     2418.587526302549,
     2.2749935318596593e-7,
     1.5848931924611135e9,
     0.15848931924611134,
     -0.0005521837206239375,
-    2418.587526302549,
     -1.3113187836653613,
-    1.5848931924611135e9,
     -15848.931924611135,
     -0.7964435246802597,
-    2418.587526302549,
     -1926.2683741961123,
 )
 a14 = 0
 
-a21, eps_m, dm_eq_dP, m_eq, deps_x_dP, m_eq, eps_m, dV_dP, V, m_eq, eps_m, drho_m_dP, rho_m, X_co2, m_g, eps_g, mm_h2o, drho_g_dP, rho_m, X_co2, m_g, eps_g, rho_g, mm_h2o, dV_dP, rho_m, V = (
+a21, eps_m, dm_eq_dP, C_h2o, deps_x_dP, dV_dP, V, drho_m_dP, rho_m, X_co2, m_g, eps_g, mm_h2o, drho_g_dP, rho_g= (
     1.0685041327468264e-10,
     0.8477225834910936,
     1.0893798285870895e-10,
     0.047334682467260976,
     -1.0742086782624915e-10,
-    0.047334682467260976,
-    0.8477225834910936,
     0.15848931924611134,
     1.5848931924611135e9,
-    0.047334682467260976,
-    0.8477225834910936,
     2.4e-7,
     2400.0,
     0.34604267590128396,
@@ -35,29 +28,17 @@ a21, eps_m, dm_eq_dP, m_eq, deps_x_dP, m_eq, eps_m, dV_dP, V, m_eq, eps_m, drho_
     0.005581589390717943,
     0.01802,
     1.323850814771934e-6,
-    2400.0,
-    0.34604267590128396,
-    0.027013649146674368,
-    0.005581589390717943,
     473.7316258038877,
-    0.01802,
-    0.15848931924611134,
-    2400.0,
-    1.5848931924611135e9,
 )
 
-a22, eps_m, dm_eq_dT, m_eq, deps_x_dT, m_eq, eps_m, V, dV_dT, m_eq, eps_m, drho_m_dT, rho_m, X_co2, m_g, eps_g, mm_h2o, drho_g_dT, rho_m, X_co2, m_g, eps_g, rho_g, mm_h2o, dV_dT, rho_m, V = (
+a22, eps_m, dm_eq_dT, C_h2o, deps_x_dT, V, dV_dT, drho_m_dT, rho_m, X_co2, m_g, eps_g, mm_h2o, drho_g_dT, rho_g = (
     0.000279875309539216,
     0.8477225834910936,
     -2.758667546233306e-5,
     0.047334682467260976,
     -0.006419421188193712,
-    0.047334682467260976,
-    0.8477225834910936,
     1.5848931924611135e9,
     -15848.931924611135,
-    0.047334682467260976,
-    0.8477225834910936,
     -0.024,
     2400.0,
     0.34604267590128396,
@@ -65,18 +46,10 @@ a22, eps_m, dm_eq_dT, m_eq, deps_x_dT, m_eq, eps_m, V, dV_dT, m_eq, eps_m, drho_
     0.005581589390717943,
     0.01802,
     -0.586770593194506,
-    2400.0,
-    0.34604267590128396,
-    0.027013649146674368,
-    0.005581589390717943,
     473.7316258038877,
-    0.01802,
-    -15848.931924611135,
-    2400.0,
-    1.5848931924611135e9,
 )
 
-a23, m_eq, X_co2, m_g, rho_g, mm_h2o, rho_m, a24, eps_m, dm_eq_dX_co2, m_g, eps_g, rho_g, mm_h2o, rho_m, X_co2, eps_g, rho_g, mm_h2o, mm_co2, mm_h2o, m_g, rho_m = (
+a23, C_h2o, X_co2, m_g, rho_g, mm_h2o, rho_m, a24, eps_m, dm_eq_dX_co2, eps_g, mm_co2 = (
     0.038773034927519844,
     0.047334682467260976,
     0.34604267590128396,
@@ -87,22 +60,11 @@ a23, m_eq, X_co2, m_g, rho_g, mm_h2o, rho_m, a24, eps_m, dm_eq_dX_co2, m_g, eps_
     -0.04065533023891952,
     0.8477225834910936,
     -0.04654587216001619,
-    0.027013649146674368,
-    0.005581589390717943,
-    473.7316258038877,
-    0.01802,
-    2400.0,
-    0.34604267590128396,
     0.005581589390717943,
-    473.7316258038877,
-    0.01802,
     0.04401,
-    0.01802,
-    0.027013649146674368,
-    2400.0,
 )
 
-a31, drc_dP, rc, dV_dP, V, L_m, eps_x, drho_x_dP, rc, T, rho_x, deps_x_dP, rc, T, rho_x, eps_x, dV_dP, rc, V, T, L_e, dm_eq_dP, rho_m, eps_m, rc, T, m_eq, eps_m, drho_m_dP, rc, T, m_eq, rho_m, deps_x_dP, rc, T, m_eq, rho_m, eps_m, dV_dP, rc, V, T = (
+a31, drc_dP, rc, dV_dP, V, L_m, eps_x, drho_x_dP, T, rho_x, deps_x_dP, L_e, dm_eq_dP, rho_m, eps_m, C_h2o, drho_m_dP = (
     1.65527030442498e-10,
     0.0002816380088198022,
     2.9053963660365245e6,
@@ -111,44 +73,18 @@ a31, drc_dP, rc, dV_dP, V, L_m, eps_x, drho_x_dP, rc, T, rho_x, deps_x_dP, rc, T
     290000.0,
     0.14669582711818843,
     2.6e-7,
-    2.9053963660365245e6,
     1046.7118332590333,
     2600.0,
     -1.0742086782624915e-10,
-    2.9053963660365245e6,
-    1046.7118332590333,
-    2600.0,
-    0.14669582711818843,
-    0.15848931924611134,
-    2.9053963660365245e6,
-    1.5848931924611135e9,
-    1046.7118332590333,
     610000.0,
     1.0893798285870895e-10,
     2400.0,
     0.8477225834910936,
-    2.9053963660365245e6,
-    1046.7118332590333,
     0.047334682467260976,
-    0.8477225834910936,
     2.4e-7,
-    2.9053963660365245e6,
-    1046.7118332590333,
-    0.047334682467260976,
-    2400.0,
-    -1.0742086782624915e-10,
-    2.9053963660365245e6,
-    1046.7118332590333,
-    0.047334682467260976,
-    2400.0,
-    0.8477225834910936,
-    0.15848931924611134,
-    2.9053963660365245e6,
-    1.5848931924611135e9,
-    1046.7118332590333,
 )
 
-a32, drc_dT, rc, T, dV_dT, V, L_m, eps_x, drho_x_dT, rc, T, rho_x, deps_x_dT, rc, T, rho_x, eps_x, dV_dT, rc, T, V, L_e, dm_eq_dT, rho_m, eps_m, rc, T, m_eq, eps_m, drho_m_dT, rc, T, m_eq, rho_m, deps_x_dT, rc, T, m_eq, rho_m, eps_m, dV_dT, rc, T, V = (
+a32, drc_dT, rc, T, dV_dT, V, L_m, eps_x, drho_x_dT, rho_x, deps_x_dT, L_e, dm_eq_dT, rho_m, eps_m, C_h2o, drho_m_dT = (
     0.0018601429959354673,
     -1577.411510355168,
     2.9053963660365245e6,
@@ -158,44 +94,17 @@ a32, drc_dT, rc, T, dV_dT, V, L_m, eps_x, drho_x_dT, rc, T, rho_x, deps_x_dT, rc
     290000.0,
     0.14669582711818843,
     -0.026000000000000002,
-    2.9053963660365245e6,
-    1046.7118332590333,
     2600.0,
     -0.006419421188193712,
-    2.9053963660365245e6,
-    1046.7118332590333,
-    2600.0,
-    0.14669582711818843,
-    -15848.931924611135,
-    2.9053963660365245e6,
-    1046.7118332590333,
-    1.5848931924611135e9,
     610000.0,
     -2.758667546233306e-5,
     2400.0,
     0.8477225834910936,
-    2.9053963660365245e6,
-    1046.7118332590333,
     0.047334682467260976,
-    0.8477225834910936,
     -0.024,
-    2.9053963660365245e6,
-    1046.7118332590333,
-    0.047334682467260976,
-    2400.0,
-    -0.006419421188193712,
-    2.9053963660365245e6,
-    1046.7118332590333,
-    0.047334682467260976,
-    2400.0,
-    0.8477225834910936,
-    -15848.931924611135,
-    2.9053963660365245e6,
-    1046.7118332590333,
-    1.5848931924611135e9,
 )
 
-a33, rho_g, c_g, rho_m, c_m, rc, L_e, m_eq, rho_m, rc, T, a34, L_e, rho_m, eps_m, dm_eq_dX_co2, rc, T = (
+a33, rho_g, c_g, rho_m, c_m, rc, L_e, C_h2o, T, a34, eps_m, dm_eq_dX_co2 = (
     -0.5821828067858482,
     473.7316258038877,
     2369.110965187085,
@@ -204,30 +113,20 @@ a33, rho_g, c_g, rho_m, c_m, rc, L_e, m_eq, rho_m, rc, T, a34, L_e, rho_m, eps_m
     2.9053963660365245e6,
     610000.0,
     0.047334682467260976,
-    2400.0,
-    2.9053963660365245e6,
     1046.7118332590333,
     0.018995182878197563,
-    610000.0,
-    2400.0,
     0.8477225834910936,
     -0.04654587216001619,
-    2.9053963660365245e6,
-    1046.7118332590333,
 )
 
-a41, eps_m, dC_co2_dP, C_co2, deps_x_dP, C_co2, eps_m, dV_dP, V, C_co2, eps_m, drho_m_dP, rho_m, X_co2, m_g, eps_g, mm_co2, drho_g_dP, rho_m, X_co2, m_g, eps_g, rho_g, mm_co2, dV_dP, rho_m, V = (
+a41, eps_m, dC_co2_dP, C_co2, deps_x_dP, dV_dP, V, drho_m_dP, rho_m, X_co2, m_g, eps_g, mm_co2, drho_g_dP, rho_g = (
     3.755479809937989e-12,
     0.8477225834910936,
     2.1580595452959046e-12,
     0.00046286158276856356,
     -1.0742086782624915e-10,
-    0.00046286158276856356,
-    0.8477225834910936,
     0.15848931924611134,
     1.5848931924611135e9,
-    0.00046286158276856356,
-    0.8477225834910936,
     2.4e-7,
     2400.0,
     0.34604267590128396,
@@ -235,29 +134,17 @@ a41, eps_m, dC_co2_dP, C_co2, deps_x_dP, C_co2, eps_m, dV_dP, V, C_co2, eps_m, d
     0.005581589390717943,
     0.04401,
     1.323850814771934e-6,
-    2400.0,
-    0.34604267590128396,
-    0.027013649146674368,
-    0.005581589390717943,
     473.7316258038877,
-    0.04401,
-    0.15848931924611134,
-    2400.0,
-    1.5848931924611135e9,
 )
 
-a42, eps_m, dC_co2_dT, C_co2, deps_x_dT, C_co2, eps_m, V, dV_dT, C_co2, eps_m, drho_m_dT, rho_m, X_co2, m_g, eps_g, mm_co2, drho_g_dT, rho_m, X_co2, m_g, eps_g, rho_g, mm_co2, dV_dT, rho_m, V = (
+a42, eps_m, dC_co2_dT, C_co2, deps_x_dT, V, dV_dT, drho_m_dT, rho_m, X_co2, m_g, eps_g, mm_co2, drho_g_dT, rho_g = (
     2.324870748635543e-6,
     0.8477225834910936,
     1.5230062068165274e-7,
     0.00046286158276856356,
     -0.006419421188193712,
-    0.00046286158276856356,
-    0.8477225834910936,
     1.5848931924611135e9,
     -15848.931924611135,
-    0.00046286158276856356,
-    0.8477225834910936,
     -0.024,
     2400.0,
     0.34604267590128396,
@@ -265,17 +152,9 @@ a42, eps_m, dC_co2_dT, C_co2, deps_x_dT, C_co2, eps_m, V, dV_dT, C_co2, eps_m, d
     0.005581589390717943,
     0.04401,
     -0.586770593194506,
-    2400.0,
-    0.34604267590128396,
-    0.027013649146674368,
-    0.005581589390717943,
     473.7316258038877,
-    0.04401,
-    -15848.931924611135,
-    2400.0,
-    1.5848931924611135e9,
 )
-a43, C_co2, X_co2, m_g, rho_g, mm_co2, rho_m, a44, eps_m, dC_co2_dX_co2, m_g, eps_g, rho_g, mm_co2, rho_m, X_co2, eps_g, rho_g, mm_co2, mm_co2, mm_h2o, m_g, rho_m = (
+a43, C_co2, X_co2, m_g, rho_g, mm_co2, rho_m, a44, eps_m, dC_co2_dX_co2, eps_g, mm_h2o = (
     0.11081759844073719,
     0.00046286158276856356,
     0.34604267590128396,
@@ -286,17 +165,6 @@ a43, C_co2, X_co2, m_g, rho_g, mm_co2, rho_m, a44, eps_m, dC_co2_dX_co2, m_g, ep
     0.0023274971026304033,
     0.8477225834910936,
     0.001333164745230419,
-    0.027013649146674368,
-    0.005581589390717943,
-    473.7316258038877,
-    0.04401,
-    2400.0,
-    0.34604267590128396,
     0.005581589390717943,
-    473.7316258038877,
-    0.04401,
-    0.04401,
     0.01802,
-    0.027013649146674368,
-    2400.0,
 )
diff --git a/test/test-matrix-b-data.jl b/test/test-matrix-b-data.jl
index 4dad85a..662fa98 100644
--- a/test/test-matrix-b-data.jl
+++ b/test/test-matrix-b-data.jl
@@ -1,5 +1,5 @@
 # Matrix B
-dM_h2o_t_dt, rho, V, Mdot_v_in, Mdot_v_out, m_h2o, Mdot_in, Mdot_out, dM_co2_t_dt, rho, V, Mdot_c_in, Mdot_c_out, m_co2, Mdot_in, Mdot_out = (
+dM_h2o_t_dt, rho, V, Mdot_v_in, Mdot_v_out, m_h2o, Mdot_in, Mdot_out, dM_co2_t_dt, Mdot_c_in, Mdot_c_out, m_co2 = (
     0.0,
     2418.587526302549,
     1.5848931924611135e9,
@@ -9,16 +9,12 @@ dM_h2o_t_dt, rho, V, Mdot_v_in, Mdot_v_out, m_h2o, Mdot_in, Mdot_out, dM_co2_t_d
     38.14210301577417,
     0.0,
     0.0,
-    2418.587526302549,
-    1.5848931924611135e9,
     0.038311627977535435,
     0.0,
     0.0010044445625269052,
-    38.14210301577417,
-    0.0,
 )
 
-b1, Mdot_in, Mdot_out, rho, V, P_loss, rho_x, rho_m, rho, deps_x_dmh2o_t, dM_h2o_t_dt, rho_x, rho_m, rho, deps_x_dmco2_t, dM_co2_t_dt, a11, dP_lit_dt = (
+b1, Mdot_in, Mdot_out, rho, V, P_loss, rho_x, rho_m, deps_x_dmh2o_t, dM_h2o_t_dt, deps_x_dmco2_t, dM_co2_t_dt = (
     9.950452390083293e-12,
     38.14210301577417,
     0.0,
@@ -27,18 +23,12 @@ b1, Mdot_in, Mdot_out, rho, V, P_loss, rho_x, rho_m, rho, deps_x_dmh2o_t, dM_h2o
     0.0,
     2600.0,
     2400.0,
-    2418.587526302549,
     -13.504456962894583,
     0.0,
-    2600.0,
-    2400.0,
-    2418.587526302549,
     17.951766506724482,
     0.0,
-    1.940628985769057e-10,
-    0.0,
 )
-b2, Mdot_v_in, Mdot_v_out, rho_m, V, m_eq, deps_x_dmh2o_t, dM_h2o_t_dt, deps_x_dmco2_t, dM_co2_t_dt, m_eq, eps_m, P_loss, X_co2, m_g, rho_g, rho_m, eps_g, mm_h2o, P_loss, a21, dP_lit_dt = (
+b2, Mdot_v_in, Mdot_v_out, rho_m, V, C_h2o, deps_x_dmh2o_t, dM_h2o_t_dt, deps_x_dmco2_t, dM_co2_t_dt, eps_m, P_loss, X_co2, m_g, rho_g, eps_g, mm_h2o, P_loss = (
     4.02883384190314e-13,
     1.5324651191014176,
     0.0,
@@ -49,80 +39,40 @@ b2, Mdot_v_in, Mdot_v_out, rho_m, V, m_eq, deps_x_dmh2o_t, dM_h2o_t_dt, deps_x_d
     0.0,
     17.951766506724482,
     0.0,
-    0.047334682467260976,
     0.8477225834910936,
     0.0,
     0.34604267590128396,
     0.027013649146674368,
     473.7316258038877,
-    2400.0,
     0.005581589390717943,
     0.01802,
     0.0,
     1.0685041327468264e-10,
     0.0,
 )
-b3, Hdot_in, Hdot_out, rc, T, V, rc, V, T, rho_x, c_x, rho_m, c_m, T, V, deps_x_dmh2o_t, dM_h2o_t_dt, deps_x_dmco2_t, dM_co2_t_dt, L_m, rho_x, V, rc, V, T, deps_x_dmh2o_t, dM_h2o_t_dt, deps_x_dmco2_t, dM_co2_t_dt, L_e, m_eq, rho_m, V, rc, V, T, deps_x_dmh2o_t, dM_h2o_t_dt, deps_x_dmco2_t, dM_co2_t_dt, P_loss, L_m, rho_x, eps_x, V, rc, V, T, L_e, m_eq, rho_m, eps_m, V, rc, V, T, a31, dP_lit_dt = (
+b3, Hdot_in, Hdot_out, rc, T, V, rho_x, c_x, rho_m, c_m, deps_x_dmh2o_t, dM_h2o_t_dt, deps_x_dmco2_t, dM_co2_t_dt, L_m, L_e, C_h2o, P_loss, eps_x, eps_m = (
     7.072846887312917e-12,
     5.0197074867341496e7,
     1.6107092267207935e7,
     2.9053963660365245e6,
     1046.7118332590333,
     1.5848931924611135e9,
-    2.9053963660365245e6,
-    1.5848931924611135e9,
-    1046.7118332590333,
     2600.0,
     1200.0,
     2400.0,
     1200.0,
-    1046.7118332590333,
-    1.5848931924611135e9,
     -13.504456962894583,
     0.0,
     17.951766506724482,
     0.0,
     290000.0,
-    2600.0,
-    1.5848931924611135e9,
-    2.9053963660365245e6,
-    1.5848931924611135e9,
-    1046.7118332590333,
-    -13.504456962894583,
-    0.0,
-    17.951766506724482,
-    0.0,
     610000.0,
     0.047334682467260976,
-    2400.0,
-    1.5848931924611135e9,
-    2.9053963660365245e6,
-    1.5848931924611135e9,
-    1046.7118332590333,
-    -13.504456962894583,
-    0.0,
-    17.951766506724482,
-    0.0,
     0.0,
-    290000.0,
-    2600.0,
     0.14669582711818843,
-    1.5848931924611135e9,
-    2.9053963660365245e6,
-    1.5848931924611135e9,
-    1046.7118332590333,
-    610000.0,
-    0.047334682467260976,
-    2400.0,
     0.8477225834910936,
-    1.5848931924611135e9,
-    2.9053963660365245e6,
-    1.5848931924611135e9,
-    1046.7118332590333,
-    1.65527030442498e-10,
-    0.0,
 )
-b4, Mdot_c_in, Mdot_c_out, rho_m, V, C_co2, deps_x_dmh2o_t, dM_h2o_t_dt, deps_x_dmco2_t, dM_co2_t_dt, C_co2, eps_m, P_loss, X_co2, m_g, rho_g, rho_m, eps_g, mm_co2, P_loss, a41, dP_lit_dt = (
+b4, Mdot_c_in, Mdot_c_out, rho_m, V, C_co2, deps_x_dmh2o_t, dM_h2o_t_dt, deps_x_dmco2_t, dM_co2_t_dt, eps_m, P_loss, X_co2, m_g, rho_g, eps_g, mm_co2 = (
     1.0072084604757847e-14,
     0.038311627977535435,
     0.0,
@@ -133,18 +83,13 @@ b4, Mdot_c_in, Mdot_c_out, rho_m, V, C_co2, deps_x_dmh2o_t, dM_h2o_t_dt, deps_x_
     0.0,
     17.951766506724482,
     0.0,
-    0.00046286158276856356,
     0.8477225834910936,
     0.0,
     0.34604267590128396,
     0.027013649146674368,
     473.7316258038877,
-    2400.0,
     0.005581589390717943,
     0.04401,
-    0.0,
-    3.755479809937989e-12,
-    0.0,
 )
 
 dDP_dt, dT_dt, deps_g_dt, dX_co2_dt, dP_dt, dV_dt, drho_m_dt, drho_x_dt = 0.0368391435777092,
@@ -155,3 +100,5 @@ dDP_dt, dT_dt, deps_g_dt, dX_co2_dt, dP_dt, dV_dt, drho_m_dt, drho_x_dt = 0.0368
 0.005856309011598884,
 8.868194837793256e-9,
 9.607211074276029e-9
+
+dP_lit_dt = 0
diff --git a/test/test-matrix.jl b/test/test-matrix.jl
index 6081ec0..5a9082f 100644
--- a/test/test-matrix.jl
+++ b/test/test-matrix.jl
@@ -7,7 +7,7 @@ include("test-matrix-a-data.jl")
     @test a21 == a21_f(
         eps_m,
         dm_eq_dP,
-        m_eq,
+        C_h2o,
         deps_x_dP,
         dV_dP,
         V,
@@ -23,7 +23,7 @@ include("test-matrix-a-data.jl")
     @test a22 == a22_f(
         eps_m,
         dm_eq_dT,
-        m_eq,
+        C_h2o,
         deps_x_dT,
         dV_dT,
         V,
@@ -36,7 +36,7 @@ include("test-matrix-a-data.jl")
         drho_g_dT,
         rho_g,
     )
-    @test a23 == a23_f(m_eq, X_co2, m_g, rho_g, mm_h2o, rho_m)
+    @test a23 == a23_f(C_h2o, X_co2, m_g, rho_g, mm_h2o, rho_m)
     @test a24 == a24_f(eps_m, dm_eq_dX_co2, m_g, eps_g, rho_g, mm_h2o, rho_m, X_co2, mm_co2)
 
     @test a31 == a31_f(
@@ -54,7 +54,7 @@ include("test-matrix-a-data.jl")
         dm_eq_dP,
         rho_m,
         eps_m,
-        m_eq,
+        C_h2o,
         drho_m_dP,
     )
     @test a32 == a32_f(
@@ -72,10 +72,10 @@ include("test-matrix-a-data.jl")
         dm_eq_dT,
         rho_m,
         eps_m,
-        m_eq,
+        C_h2o,
         drho_m_dT,
     )
-    @test a33 == a33_f(rho_g, c_g, rho_m, c_m, rc, L_e, m_eq, T)
+    @test a33 == a33_f(rho_g, c_g, rho_m, c_m, rc, L_e, C_h2o, T)
     @test a34 == a34_f(L_e, rho_m, eps_m, dm_eq_dX_co2, rc, T)
 
     @test a41 == a41_f(
@@ -129,15 +129,13 @@ include("test-matrix-b-data.jl")
         dM_h2o_t_dt,
         deps_x_dmco2_t,
         dM_co2_t_dt,
-        a11,
-        dP_lit_dt,
     )
     @test b2 == b2_f(
         Mdot_v_in,
         Mdot_v_out,
         rho_m,
         V,
-        m_eq,
+        C_h2o,
         deps_x_dmh2o_t,
         dM_h2o_t_dt,
         deps_x_dmco2_t,
@@ -149,8 +147,6 @@ include("test-matrix-b-data.jl")
         rho_g,
         eps_g,
         mm_h2o,
-        a21,
-        dP_lit_dt,
     )
     @test b3 == b3_f(
         Hdot_in,
@@ -168,12 +164,10 @@ include("test-matrix-b-data.jl")
         dM_co2_t_dt,
         L_m,
         L_e,
-        m_eq,
+        C_h2o,
         P_loss,
         eps_x,
         eps_m,
-        a31,
-        dP_lit_dt,
     )
     @test b4 == b4_f(
         Mdot_c_in,
@@ -192,8 +186,6 @@ include("test-matrix-b-data.jl")
         rho_g,
         eps_g,
         mm_co2,
-        a41,
-        dP_lit_dt,
     )
 end
 
@@ -218,7 +210,7 @@ A, b = build_matrix(
     dm_eq_dP,
     rho_m,
     eps_m,
-    m_eq,
+    C_h2o,
     drho_m_dP,
     drc_dT,
     drho_x_dT,
@@ -232,7 +224,6 @@ A, b = build_matrix(
     m_h2o,
     m_co2,
     deps_x_dmco2_t,
-    dP_lit_dt,
     Hdot_in,
     Hdot_out,
     c_x,
@@ -284,7 +275,7 @@ A, b = build_matrix(
     dm_eq_dP,
     rho_m,
     eps_m,
-    m_eq,
+    C_h2o,
     drho_m_dP,
     drc_dT,
     drho_x_dT,
@@ -298,7 +289,6 @@ A, b = build_matrix(
     m_h2o,
     m_co2,
     deps_x_dmco2_t,
-    dP_lit_dt,
     Hdot_in,
     Hdot_out,
     c_x,

From 6fadb4b43f5d4379b3c282caf28608b0f60a4dd7 Mon Sep 17 00:00:00 2001
From: CallieHsu <kelly811113@gmail.com>
Date: Thu, 6 Jul 2023 14:56:21 -0400
Subject: [PATCH 02/11] update test data

---
 test/test-matrix-a-data.jl |  4 ++--
 test/test-matrix-b-data.jl | 17 +++++++----------
 test/test-matrix.jl        |  9 ++++-----
 3 files changed, 13 insertions(+), 17 deletions(-)

diff --git a/test/test-matrix-a-data.jl b/test/test-matrix-a-data.jl
index 4f7aea9..d015406 100644
--- a/test/test-matrix-a-data.jl
+++ b/test/test-matrix-a-data.jl
@@ -32,7 +32,7 @@ a21, eps_m, dm_eq_dP, C_h2o, deps_x_dP, dV_dP, V, drho_m_dP, rho_m, X_co2, m_g,
 )
 
 a22, eps_m, dm_eq_dT, C_h2o, deps_x_dT, V, dV_dT, drho_m_dT, rho_m, X_co2, m_g, eps_g, mm_h2o, drho_g_dT, rho_g = (
-    0.000279875309539216,
+    0.0002790727759530185,
     0.8477225834910936,
     -2.758667546233306e-5,
     0.047334682467260976,
@@ -138,7 +138,7 @@ a41, eps_m, dC_co2_dP, C_co2, deps_x_dP, dV_dP, V, drho_m_dP, rho_m, X_co2, m_g,
 )
 
 a42, eps_m, dC_co2_dT, C_co2, deps_x_dT, V, dV_dT, drho_m_dT, rho_m, X_co2, m_g, eps_g, mm_co2, drho_g_dT, rho_g = (
-    2.324870748635543e-6,
+    2.3170231843006758e-6,
     0.8477225834910936,
     1.5230062068165274e-7,
     0.00046286158276856356,
diff --git a/test/test-matrix-b-data.jl b/test/test-matrix-b-data.jl
index 662fa98..d7c7989 100644
--- a/test/test-matrix-b-data.jl
+++ b/test/test-matrix-b-data.jl
@@ -92,13 +92,10 @@ b4, Mdot_c_in, Mdot_c_out, rho_m, V, C_co2, deps_x_dmh2o_t, dM_h2o_t_dt, deps_x_
     0.04401,
 )
 
-dDP_dt, dT_dt, deps_g_dt, dX_co2_dt, dP_dt, dV_dt, drho_m_dt, drho_x_dt = 0.0368391435777092,
--1.1166824642937388e-9,
--2.7431041382251222e-12,
-7.660751961816077e-11,
-0.0368391435777092,
-0.005856309011598884,
-8.868194837793256e-9,
-9.607211074276029e-9
-
-dP_lit_dt = 0
+dP_dt, dT_dt, deps_g_dt, dX_co2_dt, dV_dt, drho_m_dt, drho_x_dt = 0.036837350152411005,
+-1.1167995334788846e-9,
+-2.743459962090521e-12,
+7.662370641952041e-11,
+0.0058560266282658,
+8.867767225382134e-9,
+9.606747827497314e-9
diff --git a/test/test-matrix.jl b/test/test-matrix.jl
index 5a9082f..03d5bc5 100644
--- a/test/test-matrix.jl
+++ b/test/test-matrix.jl
@@ -317,11 +317,10 @@ x = A \ b
 @testset "Build Matrix phase=3" begin
     @test A == [a11 a12 a13 a14; a21 a22 a23 a24; a31 a32 a33 a34; a41 a42 a43 a44]
     @test b == [b1, b2, b3, b4]
-    @test x[1] == dDP_dt
-    @test round(x[2]; digits=24) == round(dT_dt; digits=24)
-    @test round(x[3]; digits=27) == round(deps_g_dt; digits=27)
-    @test round(x[4]; digits=25) == round(dX_co2_dt; digits=25)
-    @test dDP_dt + dP_lit_dt == dP_dt
+    @test x[1] == dP_dt
+    @test x[2] == dT_dt
+    @test x[3] == deps_g_dt
+    @test x[4] == dX_co2_dt
     @test dV_dP * dP_dt + dV_dT * dT_dt + V * P_loss == dV_dt
     @test drho_m_dP * dP_dt + drho_m_dT * dT_dt == drho_m_dt
     @test drho_x_dP * dP_dt + drho_x_dT * dT_dt == drho_x_dt

From 1ea2bf879836999cf5415fc0da3f3c6c8ad3e13e Mon Sep 17 00:00:00 2001
From: CallieHsu <kelly811113@gmail.com>
Date: Fri, 7 Jul 2023 17:00:28 -0400
Subject: [PATCH 03/11] add ic_phase_conversion function & format code

---
 src/runcode-func.jl        | 78 ++++++--------------------------------
 src/utils-matrix.jl        |  9 +++--
 src/utils.jl               | 67 +++++++++++++++++++++++++++++++-
 test/test-ic_finder.jl     |  9 ++++-
 test/test-matrix-a-data.jl |  2 +-
 5 files changed, 91 insertions(+), 74 deletions(-)

diff --git a/src/runcode-func.jl b/src/runcode-func.jl
index f8a87ae..66a777a 100644
--- a/src/runcode-func.jl
+++ b/src/runcode-func.jl
@@ -87,8 +87,8 @@ function odeChamber(
         C_co2 = C_co2_t
         C_h2o = m_eq
     elseif phase == 2
-        C_co2 = M_co2/(rho_m*eps_m*V)
-        C_h2o = M_h2o/(rho_m*eps_m*V)
+        C_co2 = M_co2 / (rho_m * eps_m * V)
+        C_h2o = M_h2o / (rho_m * eps_m * V)
     end
 
     # specific heat of gas
@@ -304,7 +304,6 @@ function affect!(
     param_IC_Finder::ParamICFinder{Float64},
     erupt_saved::EruptSaved{Float64},
 )
-    @info("*event idx: ", idx)
     composition = param.composition
     storeTime = param_saved_var.storeTime
     storeTemp = param_saved_var.storeTemp
@@ -332,17 +331,20 @@ function affect!(
         sw.eruption = 1
         rho_g0 = eos_g_rho_g(P_0, int.u[2])
         record_erupt_start(int.t, int.u[3], eps_x0, int.u[5], int.u[6], rho_g0, erupt_saved)
-        @info("time: $(int.t), Reached critical pressure and need to start an eruption")
+        @info(
+            "*event idx: $idx\n  time: $(int.t), Reached critical pressure and need to start an eruption"
+        )
     elseif idx == 4
         sw.eruption = 0
         record_erupt_end(int.t, erupt_saved, param)
-        @info("time: $(int.t), Finished an eruption...")
+        @info("*event idx: $idx\n  time: $(int.t), Finished an eruption...")
     elseif idx == 6 || idx == 8
         phase_here = param_saved_var.phase
         @info(
-            "time: $(int.t), starting ic finder for conversion of phase, phase_here: $phase_here",
+            "*event idx: $idx\n  time: $(int.t), starting ic finder for conversion of phase, phase_here: $phase_here",
         )
-        eps_g_temp, X_co2_temp, C_co2_temp, phase = IC_Finder(
+        eps_g_temp, X_co2_temp, C_co2_temp, phase = ic_phase_conversion(
+            phase_here,
             composition,
             int.u[9],
             int.u[10],
@@ -353,66 +355,10 @@ function affect!(
             int.u[5],
             param_IC_Finder,
         )
-
         param_saved_var.phase = phase
-        if phase_here != phase
-            @info("1st try in IC Finder successful")
-            int.u[3] = eps_g_temp
-            int.u[7] = X_co2_temp
-            C_co2 = C_co2_temp
-        else
-            @info("1st try in IC Finder unsuccessful, trying new IC parameters...")
-            param_IC_Finder.max_count = 150
-            eps_g_temp, X_co2_temp, C_co2_temp, phase = IC_Finder(
-                composition,
-                int.u[9],
-                int.u[10],
-                int.u[8],
-                P_0,
-                int.u[2],
-                int.u[4],
-                int.u[5],
-                param_IC_Finder,
-            )
-            param_saved_var.phase = phase
-            ## change back to initial max_count
-            param_IC_Finder.max_count = 100
-            if phase_here != phase
-                @info("2nd try in IC Finder successful")
-                int.u[3] = eps_g_temp
-                int.u[7] = X_co2_temp
-                C_co2 = C_co2_temp
-            else
-                @info("2nd try in IC Finder unsuccessful, trying new IC parameters...")
-                param_IC_Finder.max_count = 100
-                param_IC_Finder.Tol = param_IC_Finder.Tol * 0.1
-                eps_g_temp, X_co2_temp, C_co2_temp, phase = IC_Finder(
-                    composition,
-                    int.u[9],
-                    int.u[10],
-                    int.u[8],
-                    P_0,
-                    int.u[2],
-                    int.u[4],
-                    int.u[5],
-                    param_IC_Finder,
-                )
-                param_saved_var.phase = phase
-                ## change back to initial Tol
-                param_IC_Finder.Tol = param_IC_Finder.Tol * 10
-                if phase_here != phase
-                    @info("3rd try in IC Finder successful")
-                    int.u[3] = eps_g_temp
-                    int.u[7] = X_co2_temp
-                    C_co2 = C_co2_temp
-                else
-                    @warn("3rd try in IC Finder unsuccessful")
-                    @info("IC_Finder results: $eps_g_temp, $X_co2_temp, $C_co2_temp, $phase = IC_Finder($composition, $(int.u[9]), $(int.u[10]), $(int.u[8]), $(P_0), $(int.u[2]), $(int.u[4]), $(int.u[5]), $(param_IC_Finder))")
-                end
-            end
-        end
-        @info("phase_here: $phase_here, new_phase: $phase")
-
+        int.u[3] = eps_g_temp
+        int.u[7] = X_co2_temp
+        C_co2 = C_co2_temp
     elseif idx == 1 || idx == 2 || idx == 5 || idx == 7 || idx === nothing
         if idx == 1
             @info("eps_x became 0.")
diff --git a/src/utils-matrix.jl b/src/utils-matrix.jl
index 848bb4c..c09096f 100644
--- a/src/utils-matrix.jl
+++ b/src/utils-matrix.jl
@@ -52,7 +52,8 @@ function a22_f(
     drho_g_dT::T,
     rho_g::T,
 )::T where {T<:Float64}
-    return eps_m * dm_eq_dT - C_h2o * deps_x_dT + C_h2o * eps_m * dV_dT / V +
+    return eps_m * dm_eq_dT - C_h2o * deps_x_dT +
+           C_h2o * eps_m * dV_dT / V +
            C_h2o * eps_m * drho_m_dT / rho_m +
            (1 - X_co2) / m_g * eps_g * mm_h2o * drho_g_dT / rho_m +
            (1 - X_co2) / m_g * eps_g * mm_h2o * rho_g * dV_dT / (rho_m * V)
@@ -198,7 +199,8 @@ function a42_f(
     drho_g_dT::T,
     rho_g::T,
 )::T where {T<:Float64}
-    return eps_m * dC_co2_dT - C_co2 * deps_x_dT + C_co2 * eps_m * dV_dT / V +
+    return eps_m * dC_co2_dT - C_co2 * deps_x_dT +
+           C_co2 * eps_m * dV_dT / V +
            C_co2 * eps_m * drho_m_dT / rho_m +
            X_co2 / m_g * eps_g * mm_co2 * drho_g_dT / rho_m +
            X_co2 / m_g * eps_g * rho_g * mm_co2 * dV_dT / (rho_m * V)
@@ -344,8 +346,7 @@ function b4_f(
 )::T where {T<:Float64}
     return (Mdot_c_in - Mdot_c_out) / (rho_m * V) +
            C_co2 * (deps_x_dmh2o_t * dM_h2o_t_dt + deps_x_dmco2_t * dM_co2_t_dt) -
-           C_co2 * eps_m * P_loss -
-           (X_co2) / m_g * rho_g / rho_m * eps_g * mm_co2 * P_loss
+           C_co2 * eps_m * P_loss - (X_co2) / m_g * rho_g / rho_m * eps_g * mm_co2 * P_loss
 end
 
 function build_matrix(
diff --git a/src/utils.jl b/src/utils.jl
index e813217..8f0dd27 100644
--- a/src/utils.jl
+++ b/src/utils.jl
@@ -25,7 +25,6 @@ end
     mm_h2o::T = 18.02e-3     # molecular mass of H2O
 end
 
-
 """
 Rheology of the crust
 """
@@ -400,3 +399,69 @@ function record_erupt_end(
     push!(erupt_saved.volume, volume)
     return nothing
 end
+
+"""
+    ic_phase_conversion(phase_here::T, composition::Union{Silicic,Mafic}, M_h2o::T, M_co2::T, M_tot::T, P::T, Temp::T, V::T, rho_m::T, param_IC::ParamICFinder{T})::NamedTuple{(:eps_g_temp, :X_co2_temp, :C_co2_temp, :phase),NTuple{4,T}} where {T<:Float64}
+
+This function is used to handle phase conversion by iteratively modifying the `max_count` or `Tol` parameters of function `IC_Finder` until the correct phase is obtained.
+- This function is used within the `affect!` function.
+"""
+function ic_phase_conversion(
+    phase_here::T,
+    composition::Union{Silicic,Mafic},
+    M_h2o::T,
+    M_co2::T,
+    M_tot::T,
+    P::T,
+    Temp::T,
+    V::T,
+    rho_m::T,
+    param_IC::ParamICFinder{T},
+)::NamedTuple{
+    (:eps_g_temp, :X_co2_temp, :C_co2_temp, :phase),NTuple{4,T}
+} where {T<:Float64}
+    eps_g_temp, X_co2_temp, C_co2_temp, phase = IC_Finder(
+        composition, M_h2o, M_co2, M_tot, P, Temp, V, rho_m, param_IC
+    )
+    @info(
+        "1st attempt in IC Finder $(phase_here != phase ? "successful\n  phase_here: $phase_here, new_phase: $phase" : "unsuccessful")"
+    )
+    if phase_here != phase
+        return (; eps_g_temp, X_co2_temp, C_co2_temp, phase)
+    else
+        param_IC.max_count = 150
+        eps_g_temp, X_co2_temp, C_co2_temp, phase = IC_Finder(
+            composition, M_h2o, M_co2, M_tot, P, Temp, V, rho_m, param_IC
+        )
+        param_IC.max_count = 100
+        @info(
+            "2nd attempt in IC Finder $(phase_here != phase ? "successful\n  phase_here: $phase_here, new_phase: $phase" : "unsuccessful")"
+        )
+        if phase_here != phase
+            return (; eps_g_temp, X_co2_temp, C_co2_temp, phase)
+        else
+            i = 3
+            i_max = 6   # max iteration of IC_Finder
+            while phase_here == phase && i <= i_max
+                param_IC.Tol = param_IC.Tol * 0.1
+                eps_g_temp, X_co2_temp, C_co2_temp, phase = IC_Finder(
+                    composition, M_h2o, M_co2, M_tot, P, Temp, V, rho_m, param_IC
+                )
+                @info(
+                    "$i$(i == 3 ? "rd" : "th") attempt in IC Finder $(phase_here != phase ? "successful\n  phase_here: $phase_here, new_phase: $phase" : "unsuccessful")"
+                )
+                if phase_here != phase
+                    param_IC.Tol = param_IC.Tol * 10^(i - 2)
+                    break
+                elseif i == i_max
+                    param_IC.Tol = param_IC.Tol * 10^(i - 2)
+                    @warn(
+                        "phase conversion unsuccessful, IC_Finder results:\n  $eps_g_temp, $X_co2_temp, $C_co2_temp, $phase = IC_Finder($composition, $M_h2o, $M_co2, $M_tot, $P, $Temp, $V, $rho_m, $param_IC"
+                    )
+                end
+                i += 1
+            end
+            return (; eps_g_temp, X_co2_temp, C_co2_temp, phase)
+        end
+    end
+end
diff --git a/test/test-ic_finder.jl b/test/test-ic_finder.jl
index a01668f..764cceb 100644
--- a/test/test-ic_finder.jl
+++ b/test/test-ic_finder.jl
@@ -18,7 +18,9 @@ include("ic_finder-silicic-data.jl")
     eps_g, X_co2, mco2_diss, phase = IC_Finder(
         composition, M_h2o_3, M_co2_3, M_tot_3, P_3, T_3, V_3, rho_m_3, param_IC
     )
-    @test all((eps_g0_3, X_co20_3, mco2_diss0_3, phase0_3) .≈ (eps_g, X_co2, mco2_diss, phase))
+    @test all(
+        (eps_g0_3, X_co20_3, mco2_diss0_3, phase0_3) .≈ (eps_g, X_co2, mco2_diss, phase)
+    )
     param_IC.max_count = 100
 end
 
@@ -40,7 +42,10 @@ include("ic_finder-mafic-data.jl")
     eps_g, X_co2, mco2_diss, phase = IC_Finder(
         composition, M_h2o_3, M_co2_3, M_tot_3, P_3, T_3, V_3, rho_m_3, param_IC
     )
-    @test all([isapprox(a, b, atol=1e-12) for (a,b) in zip((eps_g0_3, X_co20_3, mco2_diss0_3, phase0_3), (eps_g, X_co2, mco2_diss, phase))])
+    @test all([
+        isapprox(a, b; atol=1e-12) for (a, b) in
+        zip((eps_g0_3, X_co20_3, mco2_diss0_3, phase0_3), (eps_g, X_co2, mco2_diss, phase))
+    ])
 
     # Case 4
     param_IC.max_count = 150
diff --git a/test/test-matrix-a-data.jl b/test/test-matrix-a-data.jl
index d015406..ed73631 100644
--- a/test/test-matrix-a-data.jl
+++ b/test/test-matrix-a-data.jl
@@ -13,7 +13,7 @@ a11, rho, drho_dP, V, dV_dP, a12, drho_dT, dV_dT, a13, drho_deps_g = (
 )
 a14 = 0
 
-a21, eps_m, dm_eq_dP, C_h2o, deps_x_dP, dV_dP, V, drho_m_dP, rho_m, X_co2, m_g, eps_g, mm_h2o, drho_g_dP, rho_g= (
+a21, eps_m, dm_eq_dP, C_h2o, deps_x_dP, dV_dP, V, drho_m_dP, rho_m, X_co2, m_g, eps_g, mm_h2o, drho_g_dP, rho_g = (
     1.0685041327468264e-10,
     0.8477225834910936,
     1.0893798285870895e-10,

From 3612fd5c941539bb3cc44c4db6e58717a76b4a28 Mon Sep 17 00:00:00 2001
From: CallieHsu <kelly811113@gmail.com>
Date: Thu, 13 Jul 2023 11:16:26 -0400
Subject: [PATCH 04/11] update test-matrix

---
 test/test-matrix.jl | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/test/test-matrix.jl b/test/test-matrix.jl
index 03d5bc5..7e78b70 100644
--- a/test/test-matrix.jl
+++ b/test/test-matrix.jl
@@ -318,9 +318,9 @@ x = A \ b
     @test A == [a11 a12 a13 a14; a21 a22 a23 a24; a31 a32 a33 a34; a41 a42 a43 a44]
     @test b == [b1, b2, b3, b4]
     @test x[1] == dP_dt
-    @test x[2] == dT_dt
-    @test x[3] == deps_g_dt
-    @test x[4] == dX_co2_dt
+    @test round(x[2]; digits=24) == round(dT_dt; digits=24)
+    @test round(x[3]; digits=26) == round(deps_g_dt; digits=26)
+    @test round(x[4]; digits=25) == round(dX_co2_dt; digits=25)
     @test dV_dP * dP_dt + dV_dT * dT_dt + V * P_loss == dV_dt
     @test drho_m_dP * dP_dt + drho_m_dT * dT_dt == drho_m_dt
     @test drho_x_dP * dP_dt + drho_x_dT * dT_dt == drho_x_dt

From 5653055ce9104e4a686da8cbae0551b537a6f284 Mon Sep 17 00:00:00 2001
From: CallieHsu <62089495+CallieHsu@users.noreply.github.com>
Date: Mon, 17 Jul 2023 12:58:22 -0400
Subject: [PATCH 05/11] Apply suggestions from code review

update code from Chris
---
 src/utils-matrix.jl | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/utils-matrix.jl b/src/utils-matrix.jl
index c09096f..8f363df 100644
--- a/src/utils-matrix.jl
+++ b/src/utils-matrix.jl
@@ -314,9 +314,9 @@ function b3_f(
                temp *
                V *
                (deps_x_dmh2o_t * dM_h2o_t_dt + deps_x_dmco2_t * dM_co2_t_dt)
-           ) +
+           ) -
            L_m * rho_x * V / (rc * V * temp) *
-           (deps_x_dmh2o_t * dM_h2o_t_dt + deps_x_dmco2_t * dM_co2_t_dt) +
+           (deps_x_dmh2o_t * dM_h2o_t_dt + deps_x_dmco2_t * dM_co2_t_dt) -
            L_e * C_h2o * rho_m * V / (rc * V * temp) *
            (deps_x_dmh2o_t * dM_h2o_t_dt + deps_x_dmco2_t * dM_co2_t_dt) +
            P_loss * (

From 918759370943432c811a39138083a9572b089357 Mon Sep 17 00:00:00 2001
From: CallieHsu <kelly811113@gmail.com>
Date: Mon, 17 Jul 2023 14:17:13 -0400
Subject: [PATCH 06/11] update test for chamber solution

---
 test/out.csv     | 280 +++++++++++++++++++++++------------------------
 test/runtests.jl |   2 +-
 2 files changed, 141 insertions(+), 141 deletions(-)

diff --git a/test/out.csv b/test/out.csv
index e926d5c..cfc3fbf 100644
--- a/test/out.csv
+++ b/test/out.csv
@@ -1,141 +1,141 @@
-timestamp,P+dP,T,eps_g,V,rho_m,rho_x,X_CO2,total_mass,total_mass_H2O,total_mass_CO2
+time,P+dP,T,eps_g,V,rho_m,rho_x,X_CO2,total_mass,total_mass_H2O,total_mass_CO2
 0.0,2.1582e8,1046.7118332590333,0.00558158923326805,1.5848931924611135e9,2400.0,2600.0,0.3460426759339731,3.8339430595912314e12,1.540393303504544e11,3.8509832587613597e9
-100000.0,2.1582368390507305e8,1046.7117215985018,0.0055813149413729835,1.5848937781121202e9,2400.000886817398,2600.0009607188476,0.3460503363690931,3.833946873801533e12,1.540394835969663e11,3.850987089924157e9
-762058.3711747054,2.1584807310013232e8,1046.7109826799758,0.005579499779821167,1.5848976563448932e9,2400.0067579747893,2600.0073211393546,0.3461010390442524,3.833972126100129e12,1.540404981783268e11,3.85101245445817e9
-2.8301548228142364e6,2.1592425586677435e8,1046.7086766993898,0.0055738349610975,1.5849097766538632e9,2400.02509732738,2600.0271887713284,0.3462593305977878,3.8340510076480337e12,1.540436674640015e11,3.851091686600037e9
-4.898251274453768e6,2.1600043503101456e8,1046.7063736591053,0.005568177159694788,1.5849219045944843e9,2400.0434358693738,2600.0470555251554,0.34641750174055347,3.8341298891959385e12,1.5404683674967618e11,3.8511709187419043e9
-6.966347726093299e6,2.1607661024428245e8,1046.7040738021217,0.0055625269496759845,1.584934040794788e9,2400.061773521641,2600.066921315112,0.3465755424077759,3.8342087707438433e12,1.5405000603535086e11,3.8512501508837714e9
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+8.511019448456123e8,2.2671909502707008e8,1045.7851741989514,0.004938699972662514,1.587055656102299e9,2402.639472935188,2602.8594290131145,0.36310967350686035,3.8471047665123857e12,1.5456813854840872e11,3.864203463710241e9
+8.611019448456123e8,2.2708136947742248e8,1045.7762281372486,0.0049158937481599396,1.5871197536422908e9,2402.7267309506665,2602.953958529882,0.3637845707645132,3.8474861875425435e12,1.545834631995978e11,3.8645865799899683e9
+8.711019448456123e8,2.2744340610097668e8,1045.767358045992,0.004893232518033381,1.5871840259534385e9,2402.81393316436,2603.048427594717,0.3644564237892739,3.847867608572701e12,1.545987878507869e11,3.8649696962696958e9
+8.811019448456123e8,2.278052006340217e8,1045.7585637616785,0.004870715071727065,1.5872484722434723e9,2402.901078549365,2603.142835095139,0.36512523835162003,3.848249029602859e12,1.5461411250197598e11,3.865352812549423e9
+8.911019448456123e8,2.2816674887094048e8,1045.7498451151725,0.00484834021002652,1.587313091726989e9,2402.988166092728,2603.237179933783,0.36579102038948,3.8486304506330166e12,1.5462943715316507e11,3.8657359288291507e9
+9.011019448456123e8,2.285280466638311e8,1045.741201931911,0.004826106744950777,1.5873778836254241e9,2403.075194795354,2603.3314610282946,0.3664537760047845,3.8490118716631743e12,1.5464476180435416e11,3.866119045108878e9
+9.111019448456123e8,2.288890899221145e8,1045.7326340320985,0.004804013499646906,1.5874428471670218e9,2403.1621636719096,2603.4256773112297,0.36711351145998866,3.849393292693332e12,1.5466008645554324e11,3.8665021613886056e9
+9.211019448456123e8,2.292498746121282e8,1045.724141230892,0.004782059308286825,1.587507981586801e9,2403.249071750724,2603.519827729945,0.36777023317456614,3.8497747137234897e12,1.5467541110673233e11,3.866885277668333e9
+9.311019448456123e8,2.296103967567076e8,1045.7157233385778,0.004760243015966301,1.5875732861265218e9,2403.3359180736866,2603.6139112464875,0.368423947721479,3.8501561347536475e12,1.5469073575792142e11,3.8672683939480605e9
+9.411019448456123e8,2.2997065243475443e8,1045.707380160739,0.004738563478605992,1.5876387600346475e9,2403.4227016961427,2603.7079268374814,0.36907466182362725,3.850537555783805e12,1.547060604091105e11,3.867651510227788e9
+9.511019448456123e8,2.3033063778079376e8,1045.6991114984125,0.004717019562854403,1.5877044025663054e9,2403.509421686784,2603.80187349401,0.3697223823502833,3.850918976813963e12,1.547213850602996e11,3.8680346265075154e9
+9.611019448456123e8,2.3069034898452008e8,1045.6909171482416,0.004695610145992615,1.5877702129832466e9,2403.5960771275422,2603.895750221498,0.37036711631351715,3.8513003978441206e12,1.5473670971148868e11,3.868417742787243e9
+9.711019448456123e8,2.3104978229033402e8,1045.6827969026187,0.004674334115840625,1.587836190553802e9,2403.6826671134727,2603.9895560395894,0.37100887086461687,3.8516818188742783e12,1.5475203436267776e11,3.8688008590669703e9
+9.811019448456123e8,2.3140893399686965e8,1045.6747505498204,0.004653190370665174,1.5879023345528388e9,2403.7691907526428,2604.083289982024,0.3716476532905117,3.852063239904436e12,1.5476735901386685e11,3.869183975346698e9
+9.911019448456123e8,2.317678004565145e8,1045.6667778741373,0.004632177819088902,1.5879686442617137e9,2403.855647166015,2604.1769510965105,0.3722834710102016,3.8524446609345938e12,1.5478268366505594e11,3.8695670916264253e9
+1.0e9,2.3208687912240884e8,1045.6597455277583,0.004613590158236053,1.5880277857528248e9,2403.9325193478444,2604.2602292934926,0.3728467387790435,3.8527840514709326e12,1.5479631962420618e11,3.869907990605181e9
diff --git a/test/runtests.jl b/test/runtests.jl
index 5d5758f..cd11bfc 100644
--- a/test/runtests.jl
+++ b/test/runtests.jl
@@ -43,5 +43,5 @@ include("matrix-a-data.jl")
     include("test-initial.jl")
     include("test-exsolve.jl")
     include("test-ic_finder.jl")
-    # include("test-sol.jl")
+    include("test-sol.jl")
 end

From 325b5ff402daf6b1a6133383eb24dfa275c6cb9c Mon Sep 17 00:00:00 2001
From: CallieHsu <kelly811113@gmail.com>
Date: Mon, 17 Jul 2023 14:59:58 -0400
Subject: [PATCH 07/11] update .gitignore

---
 .gitignore | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.gitignore b/.gitignore
index 1f343b1..1d1360b 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,4 +1,5 @@
 /.vscode
 202*
 sysimage_chamber*.so
-docs/build/
\ No newline at end of file
+docs/build/
+src/pplot.jl

From b1d356dbe39c09bb9f505686290234882a95e6a1 Mon Sep 17 00:00:00 2001
From: CallieHsu <kelly811113@gmail.com>
Date: Mon, 17 Jul 2023 15:57:08 -0400
Subject: [PATCH 08/11] runtest test-sol debug

---
 test/test-sol.jl | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/test/test-sol.jl b/test/test-sol.jl
index 9f19c41..5639086 100644
--- a/test/test-sol.jl
+++ b/test/test-sol.jl
@@ -3,6 +3,9 @@ using DelimitedFiles, DataFrames
 solve_exp = Float64.(readdlm("out.csv", ',')[2:end, :])
 df = chamber(Silicic(), 1e9, 0.2, 0.04, 0.001, -3.3, 8e3)
 
+println(solve_exp)
+println(Matrix(df))
+println(solve_exp .- Matrix(df))
 @testset "solve_ode" begin
-    @test all(abs.(solve_exp .- Matrix(df)) .< 0.00005)
+    @test all(abs.(solve_exp .- Matrix(df)) .< 1)
 end

From 4d99965dbce6727fc12df75cf07c6aaf49ec4217 Mon Sep 17 00:00:00 2001
From: CallieHsu <kelly811113@gmail.com>
Date: Mon, 17 Jul 2023 16:42:51 -0400
Subject: [PATCH 09/11] runtest test-sol debug

---
 test/test-sol.jl | 23 ++++++++++++++++++++---
 1 file changed, 20 insertions(+), 3 deletions(-)

diff --git a/test/test-sol.jl b/test/test-sol.jl
index 5639086..e8ae829 100644
--- a/test/test-sol.jl
+++ b/test/test-sol.jl
@@ -3,9 +3,26 @@ using DelimitedFiles, DataFrames
 solve_exp = Float64.(readdlm("out.csv", ',')[2:end, :])
 df = chamber(Silicic(), 1e9, 0.2, 0.04, 0.001, -3.3, 8e3)
 
-println(solve_exp)
-println(Matrix(df))
-println(solve_exp .- Matrix(df))
+println("1: ", solve_exp[:, 1] .- Matrix(df)[:, 1])
+println("2: ", solve_exp[:, 2] .- Matrix(df)[:, 2])
+println("3: ", solve_exp[:, 3] .- Matrix(df)[:, 3])
+println("4: ", solve_exp[:, 4] .- Matrix(df)[:, 4])
+println("5: ", solve_exp[:, 5] .- Matrix(df)[:, 5])
+println("6: ", solve_exp[:, 6] .- Matrix(df)[:, 6])
+println("7: ", solve_exp[:, 7] .- Matrix(df)[:, 7])
+println("8: ", solve_exp[:, 8] .- Matrix(df)[:, 8])
+println("9: ", solve_exp[:, 9] .- Matrix(df)[:, 9])
+println("10: ", solve_exp[:, 10] .- Matrix(df)[:, 10])
 @testset "solve_ode" begin
     @test all(abs.(solve_exp .- Matrix(df)) .< 1)
+    @test all(abs.(solve_exp[:, 1] .- Matrix(df)[:, 1]) .< 100.0)
+    @test all(abs.(solve_exp[:, 2] .- Matrix(df)[:, 2]) .< abs(solve_exp[end, 2]*1e-5))
+    @test all(abs.(solve_exp[:, 3] .- Matrix(df)[:, 3]) .< abs(solve_exp[end, 3]*1e-5))
+    @test all(abs.(solve_exp[:, 4] .- Matrix(df)[:, 4]) .< abs(solve_exp[end, 4]*1e-5))
+    @test all(abs.(solve_exp[:, 5] .- Matrix(df)[:, 5]) .< abs(solve_exp[end, 5]*1e-5))
+    @test all(abs.(solve_exp[:, 6] .- Matrix(df)[:, 6]) .< abs(solve_exp[end, 6]*1e-5))
+    @test all(abs.(solve_exp[:, 7] .- Matrix(df)[:, 7]) .< abs(solve_exp[end, 7]*1e-5))
+    @test all(abs.(solve_exp[:, 8] .- Matrix(df)[:, 8]) .< abs(solve_exp[end, 8]*1e-5))
+    @test all(abs.(solve_exp[:, 9] .- Matrix(df)[:, 9]) .< abs(solve_exp[end, 9]*1e-5))
+    @test all(abs.(solve_exp[:, 10] .- Matrix(df)[:, 10]) .< abs(solve_exp[end, 10]*1e-5))
 end

From 1c598aca9771df06d4e1ffa0def874830efc034b Mon Sep 17 00:00:00 2001
From: CallieHsu <kelly811113@gmail.com>
Date: Mon, 17 Jul 2023 17:38:56 -0400
Subject: [PATCH 10/11] runtest test-sol debug

---
 test/test-sol.jl | 25 ++++---------------------
 1 file changed, 4 insertions(+), 21 deletions(-)

diff --git a/test/test-sol.jl b/test/test-sol.jl
index e8ae829..1e9d500 100644
--- a/test/test-sol.jl
+++ b/test/test-sol.jl
@@ -3,26 +3,9 @@ using DelimitedFiles, DataFrames
 solve_exp = Float64.(readdlm("out.csv", ',')[2:end, :])
 df = chamber(Silicic(), 1e9, 0.2, 0.04, 0.001, -3.3, 8e3)
 
-println("1: ", solve_exp[:, 1] .- Matrix(df)[:, 1])
-println("2: ", solve_exp[:, 2] .- Matrix(df)[:, 2])
-println("3: ", solve_exp[:, 3] .- Matrix(df)[:, 3])
-println("4: ", solve_exp[:, 4] .- Matrix(df)[:, 4])
-println("5: ", solve_exp[:, 5] .- Matrix(df)[:, 5])
-println("6: ", solve_exp[:, 6] .- Matrix(df)[:, 6])
-println("7: ", solve_exp[:, 7] .- Matrix(df)[:, 7])
-println("8: ", solve_exp[:, 8] .- Matrix(df)[:, 8])
-println("9: ", solve_exp[:, 9] .- Matrix(df)[:, 9])
-println("10: ", solve_exp[:, 10] .- Matrix(df)[:, 10])
 @testset "solve_ode" begin
-    @test all(abs.(solve_exp .- Matrix(df)) .< 1)
-    @test all(abs.(solve_exp[:, 1] .- Matrix(df)[:, 1]) .< 100.0)
-    @test all(abs.(solve_exp[:, 2] .- Matrix(df)[:, 2]) .< abs(solve_exp[end, 2]*1e-5))
-    @test all(abs.(solve_exp[:, 3] .- Matrix(df)[:, 3]) .< abs(solve_exp[end, 3]*1e-5))
-    @test all(abs.(solve_exp[:, 4] .- Matrix(df)[:, 4]) .< abs(solve_exp[end, 4]*1e-5))
-    @test all(abs.(solve_exp[:, 5] .- Matrix(df)[:, 5]) .< abs(solve_exp[end, 5]*1e-5))
-    @test all(abs.(solve_exp[:, 6] .- Matrix(df)[:, 6]) .< abs(solve_exp[end, 6]*1e-5))
-    @test all(abs.(solve_exp[:, 7] .- Matrix(df)[:, 7]) .< abs(solve_exp[end, 7]*1e-5))
-    @test all(abs.(solve_exp[:, 8] .- Matrix(df)[:, 8]) .< abs(solve_exp[end, 8]*1e-5))
-    @test all(abs.(solve_exp[:, 9] .- Matrix(df)[:, 9]) .< abs(solve_exp[end, 9]*1e-5))
-    @test all(abs.(solve_exp[:, 10] .- Matrix(df)[:, 10]) .< abs(solve_exp[end, 10]*1e-5))
+    for i in 1:10
+        println("$i: ", maximum!([1.0], abs.(solve_exp[:, i] .- Matrix(df)[:, i])))
+        @test all(abs.(solve_exp[:, i] .- Matrix(df)[:, i]) .< abs(solve_exp[end, i]*1e-9))
+    end
 end

From 94a582e2cd0158323ca01d067c9c492dac2f925d Mon Sep 17 00:00:00 2001
From: CallieHsu <kelly811113@gmail.com>
Date: Mon, 17 Jul 2023 17:59:24 -0400
Subject: [PATCH 11/11] runtest test-sol debug

---
 test/test-sol.jl | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/test/test-sol.jl b/test/test-sol.jl
index 1e9d500..757c163 100644
--- a/test/test-sol.jl
+++ b/test/test-sol.jl
@@ -4,8 +4,8 @@ solve_exp = Float64.(readdlm("out.csv", ',')[2:end, :])
 df = chamber(Silicic(), 1e9, 0.2, 0.04, 0.001, -3.3, 8e3)
 
 @testset "solve_ode" begin
-    for i in 1:10
-        println("$i: ", maximum!([1.0], abs.(solve_exp[:, i] .- Matrix(df)[:, i])))
+    for i in 1:11
+        println("col$i maximum diff: ", maximum!([1.0], abs.(solve_exp[:, i] .- Matrix(df)[:, i])))
         @test all(abs.(solve_exp[:, i] .- Matrix(df)[:, i]) .< abs(solve_exp[end, i]*1e-9))
     end
 end