Add _rt.R file to repo

.gitignore

@@ -155,6 +155,7 @@ include/
 # But keep these specific files
 !bin/plot/
 !bin/dolo_fgcs_3.qs2
+!bin/dolo_fgcs_3_rt.R
 !bin/dolo_fgcs_3.R
 !bin/dolo_fgcs_3.pqi
 !bin/phreeqc_kin.dat

bin/dolo_fgcs_3_rt.R

@@ -0,0 +1,25 @@
+iterations <- 10000
+dt <- 200
+chkpt_interval <- 100
+ctrl_interval <- 100
+mape_threshold <- rep(0.0035, 13)
+mape_threshold[5] <- 1 #Charge
+zero_abs <- 1e-13
+rb_limit <- 3
+rb_interval_limit <- 100
+ctrl_cell_ids <- seq(0, (400*400)/2 - 1, by = 401)
+#out_save <- seq(500, iterations, by = 500)
+out_save = c(seq(1, 10), seq(10, 100, by= 10), seq(200, iterations, by=100))
+
+
+list(
+    timesteps = rep(dt, iterations),
+    store_result = TRUE,
+    out_save = out_save,
+    chkpt_interval = chkpt_interval,
+    ctrl_interval = ctrl_interval,
+    mape_threshold = mape_threshold,
+    zero_abs = zero_abs,
+    rb_limit = rb_limit,
+    rb_interval_limit = rb_interval_limit
+)

bin/run_poet.sh

@@ -1,7 +1,7 @@
 #!/bin/bash
-#SBATCH --job-name=p2_eps01_no_skip
-#SBATCH --output=p2_eps01_no_skip_%j.out
-#SBATCH --error=p2_eps01_no_skip_%j.err
+#SBATCH --job-name=p2_eps0035_v3
+#SBATCH --output=p2_eps0035_v3_%j.out
+#SBATCH --error=p2_eps0035_v3_%j.err
 #SBATCH --partition=long
 #SBATCH --nodes=6                                                    
 #SBATCH --ntasks-per-node=24 
@@ -15,5 +15,5 @@ module purge
 module load cmake gcc openmpi
 
 #mpirun -n 144 ./poet dolo_fgcs_3.R dolo_fgcs_3.qs2 dolo_only_pqc
-mpirun -n 144 ./poet --interp --rds dolo_fgcs_3_rt.R dolo_fgcs_3.qs2 p2_eps01_no_skip
+mpirun -n 144 ./poet --interp --rds dolo_fgcs_3_rt.R dolo_fgcs_3.qs2 p2_eps0035_v3
 #mpirun -n 144 ./poet --interp  barite_fgcs_4_new/barite_fgcs_4_new_rt.R barite_fgcs_4_new/barite_fgcs_4_new.qs2 barite