From f0809e2428104aac21940a789317419a63323ca2 Mon Sep 17 00:00:00 2001
From: Joy Zhang <joycheung1994@gmail.com>
Date: Tue, 13 Aug 2024 16:05:12 -0700
Subject: [PATCH] minor bug fix

---
 qsdsan/sanunits/_junction.py                    | 4 ++--
 qsdsan/sanunits/_suspended_growth_bioreactor.py | 5 +----
 tests/test_exposan.py                           | 2 +-
 3 files changed, 4 insertions(+), 7 deletions(-)

diff --git a/qsdsan/sanunits/_junction.py b/qsdsan/sanunits/_junction.py
index 8151d17d..85fc14ac 100644
--- a/qsdsan/sanunits/_junction.py
+++ b/qsdsan/sanunits/_junction.py
@@ -893,7 +893,7 @@ def _compile_reactions(self):
         atol = self.atol
 
         cmps_asm = ins.components
-        S_NO_i_COD = cmps_asm.S_NO.i_COD
+        S_NO_i_COD = -40/14
         X_BH_i_N = cmps_asm.X_BH.i_N
         X_BA_i_N = cmps_asm.X_BA.i_N
         asm_X_I_i_N = cmps_asm.X_I.i_N
@@ -1054,7 +1054,7 @@ def asm2adm(asm_vals):
             S_IN = adm_vals[adm_ions_idx[0]]
             S_IC = (asm_charge_tot -  S_IN*alpha_IN)/alpha_IC
             net_Scat = asm_charge_tot + proton_charge
-            if net_Scat > 0:  
+            if net_Scat > 0:
                 S_cat = net_Scat
                 S_an = 0
             else:
diff --git a/qsdsan/sanunits/_suspended_growth_bioreactor.py b/qsdsan/sanunits/_suspended_growth_bioreactor.py
index 0b46da8a..5c305a59 100644
--- a/qsdsan/sanunits/_suspended_growth_bioreactor.py
+++ b/qsdsan/sanunits/_suspended_growth_bioreactor.py
@@ -293,7 +293,7 @@ def _init_state(self):
 
     def _update_state(self):
         arr = self._state
-        arr[arr < 2.2e-16] = 0.
+        arr[arr < 1e-16] = 0.
         arr[-1] = sum(ws.state[-1] for ws in self.ins)
         if self.split is None: self._outs[0].state = arr
         else:
@@ -364,7 +364,6 @@ def _compile_ODE(self):
             i = self.components.index(self._DO_ID)
             fixed_DO = self._aeration
             def dy_dt(t, QC_ins, QC, dQC_ins):
-                # QC[QC < 2.2e-16] = 0.
                 QC[i] = fixed_DO
                 dydt_cstr(QC_ins, QC, V, _dstate)
                 if hasexo: QC = np.append(QC, f_exovars(t))
@@ -376,7 +375,6 @@ def dy_dt(t, QC_ins, QC, dQC_ins):
             aer_stoi = aer._stoichiometry
             aer_frho = aer.rate_function
             def dy_dt(t, QC_ins, QC, dQC_ins):
-                # QC[QC < 2.2e-16] = 0.
                 dydt_cstr(QC_ins, QC, V, _dstate)
                 if hasexo: QC = np.append(QC, f_exovars(t))
                 _dstate[:-1] += r(QC) + aer_stoi * aer_frho(QC)
@@ -384,7 +382,6 @@ def dy_dt(t, QC_ins, QC, dQC_ins):
                 _update_dstate()
         else:
             def dy_dt(t, QC_ins, QC, dQC_ins):
-                # QC[QC < 2.2e-16] = 0.
                 dydt_cstr(QC_ins, QC, V, _dstate)
                 if hasexo: QC = np.append(QC, f_exovars(t))
                 _dstate[:-1] += r(QC)
diff --git a/tests/test_exposan.py b/tests/test_exposan.py
index 5be8c89d..5f645ba3 100644
--- a/tests/test_exposan.py
+++ b/tests/test_exposan.py
@@ -35,7 +35,7 @@ def test_exposan():
     from exposan.bsm1 import create_system as create_bsm1_system, biomass_IDs
     bsm1_sys = create_bsm1_system()
     bsm1_sys.simulate(t_span=(0,10), method='BDF')
-    print(get_SRT(bsm1_sys, biomass_IDs=biomass_IDs)) # to test the `get_SRT` function
+    print(get_SRT(bsm1_sys, biomass_IDs=biomass_IDs['asm1'])) # to test the `get_SRT` function
 
     #!!! Will use bsm2 to test the junction models
     # from exposan.interface import create_system as create_inter_system