updated readme

readme.txt

@@ -1,7 +1,7 @@
 scepter
 
 scepter.f90             - source code  
-makefile                - compile (data dir in L50 needs to be specified)
+makefile                - compile (data dir in L52 needs to be specified)
 
 
 scripts:
@@ -22,6 +22,14 @@ basalt_buff_tunespin_bisec_v2.py
 spinup.py               - run a spin-up run
 spinup_inert.py         - run series of run with bulk speces varying CECs
 spinup_inrt2.py         - run series of run with bulk and OM speces varying CECs etc.
+test_phreeqc_ex11.py	- run series of run with an exchanger bulk species 
+							initially equilibrated with porewater of 1 mM Na and 0.2 mM K and 1.2 mM NO3
+							and replaced by porewater with a different composition with 1.2 mM CaCl2
+							through advection and dispersion characterized with the Peclet number 40 
+							as in Appelo (1994)
+test_phreeqc_ex11_init.py
+						- run series of run with an exchanger bulk species 
+							with 1 mM Na and 0.2 mM K and 1-15 mM NO3
 
 
 
@@ -36,18 +44,32 @@ $$ running example simulations in GMD paper $$
         undo comments-out in L849-852 of get_soilpH_time.py
     b. type: python3 get_soilpH_time.py
 
-2. mesocosm experiment in Section 3 
-2.1. field simulation
+2. cation exchange experiment in Section 3 
+2.1. cation exchange equilibrium simulation
+    a. modify outdir in L176 of test_phreeqc_ex11_init.py
+    b. type: python3 test_phreeqc_ex11_init.py
+2.2. cation exchange + advection + dispersion simulation
+	2.2.1. spin-up
+		a. modify outdir in L176 of test_phreeqc_ex11.py
+		b. type: python3 test_phreeqc_ex11.py
+	2.1.2. dynamic simulation 
+		a. undo comment-out in L16,17 of makefile
+		b. type: make 
+		c. undo comment-out in L277-280 of test_phreeqc_ex11.py
+		d. type: python3 test_phreeqc_ex11.py
+
+3. mesocosm experiment in Section 3 
+3.1. field simulation
     a. modify outdir in L159 of spinup_inrt2.py 
     b. type: python3 spinup_inrt2.py
 
-2.2. laboratory simulation
+3.2. laboratory simulation
     a. modify outdir in L528, L888 of get_soilpH_time.py 
     b. type: python3 get_soilpH_time.py
 
-3. alkalinity requiremnt for ERW in Section 4 
-3.1. field + laboratory simulation
-3.1.1. spin/tune-up 
+4. alkalinity requiremnt for ERW in Section 4 
+4.1. field + laboratory simulation
+4.1.1. spin/tune-up 
     a. modify outdir in L148 of tunespin_3_newton_inert_buff_v2_clean.py 
     b. type: python3 tunespin_3_newton_inert_buff_v2_clean.py spinup_run_name 
         21.103289732688683 6.058006742238197 20.980309042371502 2.0516666666666667 
@@ -56,13 +78,13 @@ $$ running example simulations in GMD paper $$
     [ note that the runtime inputs are to specify: run ID, CEC (cmol/kg), target soil pH, 
         target exchange acidity (%CEC), target soil OM (wt%), temperature (oC),
         moisture, runoff (m/yr), erosion rate (m/yr), nitrification rate (gN/m2/yr) ]
-3.1.2. basalt application 
+4.1.2. basalt application 
     a. modify outdir in L93 of basalt_buff_tunespin_bisec_v2.py and
         option of using soil/porewater pH (phnorm_pw=False/True, L25-26)
     b. type: python3 basalt_buff_tunespin_bisec_v2.py 6.2 1 21.103289732688683 
         basalt_run_name spinup_run_name
     [ note that the runtime inputs are to specify: 
         target pH, duration of run, CEC (cmol/kg), basalt run name, spin/tune-up run name ]
-3.2. calculating soil pH prodiles
+4.2. calculating soil pH prodiles
     a. modify outdir in L49, L299 of get_soilpH_time_dep.py
     b. type: get_soilpH_time_dep.py basalt_run_name