diff --git a/basalt_buff_tunespin_bisec_v2.py b/basalt_buff_tunespin_bisec_v2.py
index b018698..f8a7219 100644
--- a/basalt_buff_tunespin_bisec_v2.py
+++ b/basalt_buff_tunespin_bisec_v2.py
@@ -26,7 +26,7 @@
 phnorm_pw = False
 
 use_local_storage = True
-# use_local_storage = False
+use_local_storage = False
 
 cec=float(sys.argv[3])
 # targetpH = 6.0
@@ -38,12 +38,12 @@
 dep_sample = 0.15
 
 added_sp = 'gbas'
-added_sp = 'cc'
+# added_sp = 'cc'
 
 # mxing style
 
 imix = 2 # homogeneous
-# imix = 3 # tilling
+imix = 3 # tilling
 
     
 ztot_lab = 0.5
@@ -54,7 +54,7 @@
 
 water_frac = 5.
 water_frac = 1.
-water_frac = 2.5
+# water_frac = 2.5
 
 catlist = ['ca','mg','k','na']
 
@@ -90,10 +90,9 @@
 runname_lab     = expid+'_'+added_sp+'_lab_tpH'+sys.argv[1].replace('.','p')+'_tau'+sys.argv[2].replace('.','p')
 # runname = 'chk_iter_incl2nd_basalt_tpH'+sys.argv[1].replace('.','p')+'_tau'+sys.argv[2].replace('.','p')
 
-# outdir='/storage/scratch1/0/ykanzaki3/scepter_output/'
-outdir = '/storage/coda1/p-creinhard3/0/ykanzaki3/scepter_output/'
+outdir = '../scepter_output/'
 if use_local_storage:  
-    outdir_src = '/storage/coda1/p-creinhard3/0/ykanzaki3/scepter_output/'
+    outdir_src = '../scepter_output/'
     outdir = os.environ['TMPDIR'] + '/scepter_output/'
     for runname in [spinup_field,spinup_lab]:
 
@@ -131,7 +130,8 @@
     # fdust = 10000
 
 exename = 'scepter'
-exename_src = 'scepter_test'
+# exename_src = 'scepter_test'
+exename_src = 'scepter'
 to = ' '
 where = '/'
 
@@ -148,8 +148,8 @@
 with open(dst, 'w') as file:
     file.writelines(data)
 
-if added_sp == 'gbas': dustsrc = 'dust_gbasalt.in'
-if added_sp == 'cc': dustsrc = 'dust_lime.in'
+if added_sp == 'gbas': dustsrc = './data/dust_gbasalt.in'
+if added_sp == 'cc': dustsrc = './data/dust_lime.in'
 dustdst = 'dust.in'
 
 os.system('cp ' + dustsrc + to + outdir + runname_field + where + dustdst) 
@@ -229,7 +229,7 @@
     file.writelines(data)
     
 filename = '2ndslds.in'
-srcfile = '/storage/coda1/p-creinhard3/0/ykanzaki3/PyWeath/data/2ndslds_def.in'
+srcfile = './data/2ndslds_def.in'
 make_inputs.get_input_sld_properties(
     outdir=outdir
     ,runname=runname_field
@@ -245,11 +245,11 @@
     
 # compile 
 # os.system('make')
-os.system('make --file=makefile_test')
-for runname in [runname_field,runname_lab]:
-    if not os.path.exists( outdir + runname) : os.system('mkdir -p ' + outdir + runname)
-    # os.system('cp ' + exename + to + outdir + runname)
-    os.system('cp ' + exename_src + to + outdir + runname + where + exename)
+# os.system('make --file=makefile_test')
+# for runname in [runname_field,runname_lab]:
+    # if not os.path.exists( outdir + runname) : 
+        # os.system('mkdir -p ' + outdir + runname)
+        # os.system('cp ' + exename_src + to + outdir + runname + where + exename)
 
 maxiter = 50
 
diff --git a/get_inputs.py b/get_inputs.py
new file mode 100644
index 0000000..8bbbc52
--- /dev/null
+++ b/get_inputs.py
@@ -0,0 +1,216 @@
+import os
+import numpy as np
+from shutil import copyfile
+import time
+
+def get_input_frame(outdir,runname):
+    infile = outdir + runname + '/frame.in'
+    
+    with open(infile) as f:
+        lines = [line for line in f]
+    
+    ztot = float(lines[1].split()[0])
+    nz = int(lines[2].split()[0])
+    ttot = float(lines[3].split()[0])
+    temp = float(lines[4].split()[0])
+    fdust = float(lines[5].split()[0])
+    fdust2 = float(lines[6].split()[0])
+    taudust = float(lines[7].split()[0])
+    omrain = float(lines[8].split()[0])
+    zom = float(lines[9].split()[0])
+    poro = float(lines[10].split()[0])
+    moistsrf = float(lines[11].split()[0])
+    zwater = float(lines[12].split()[0])
+    zdust = float(lines[13].split()[0])
+    w = float(lines[14].split()[0])
+    q = float(lines[15].split()[0])
+    p = float(lines[16].split()[0])
+    nstep = int(lines[17].split()[0])
+    rstrt = (lines[18].split()[0])
+    runid = (lines[20].split()[0])
+    
+    return ztot,nz,ttot,temp,fdust,fdust2,taudust,omrain,zom,poro,moistsrf,zwater,zdust,w,q,p,nstep,rstrt,runid
+
+def get_input_switches(outdir,runname):    
+    infile = outdir + runname + '/switches.in'
+    
+    with open(infile) as f:
+        lines = [line for line in f]
+    
+    w_scheme = int(lines[1].split()[0])
+    mix_scheme = int(lines[2].split()[0])
+    poro_iter = (lines[3].split()[0])
+    sldmin_lim = (lines[4].split()[0])
+    display = (lines[5].split()[0])
+    disp_lim = (lines[6].split()[0])
+    restart = (lines[7].split()[0])
+    rough = (lines[8].split()[0])
+    act_ON = (lines[9].split()[0])
+    dt_fix = (lines[10].split()[0])
+    cec_on = (lines[11].split()[0])
+    dz_fix = (lines[12].split()[0])
+    close_aq = (lines[13].split()[0])
+    poro_evol = (lines[14].split()[0])
+    sa_evol_1 = (lines[15].split()[0])
+    sa_evol_2 = (lines[16].split()[0])
+    psd_bulk = (lines[17].split()[0])
+    psd_full = (lines[18].split()[0])
+    season = (lines[19].split()[0])
+    
+    return w_scheme,mix_scheme,poro_iter,sldmin_lim,display,disp_lim,restart,rough,act_ON,dt_fix \
+        ,cec_on,dz_fix,close_aq,poro_evol,sa_evol_1,sa_evol_2,psd_bulk,psd_full,season
+
+def get_input_tracers(outdir,runname):
+    
+    sld_list = np.genfromtxt(outdir + runname + '/slds.in',dtype='str',skip_header=1)
+    aq_list = np.genfromtxt(outdir + runname + '/solutes.in',dtype='str',skip_header=1)
+    gas_list = np.genfromtxt(outdir + runname + '/gases.in',dtype='str',skip_header=1)
+    exrxn_list = np.genfromtxt(outdir + runname + '/extrxns.in',dtype='str',skip_header=1)
+    
+    try:
+        sld_list = list(sld_list)
+    except:
+        sld_list = [str(sld_list)]
+    try:
+        aq_list = list(aq_list)
+    except:
+        aq_list = [aq_list[0]]
+    try:
+        gas_list = list(gas_list)
+    except:
+        print(gas_list.shape)
+        gas_list = [str(gas_list)]
+    try:
+        exrxn_list = list(exrxn_list)
+    except:
+        exrxn_list = [exrxn_list[0]]
+    
+    return sld_list,aq_list,gas_list,exrxn_list
+
+def get_input_tracer_bounds(**kwargs):
+    outdir      = kwargs.get('outdir',      '../scepter_output/')
+    runname     = kwargs.get('runname',     'test_input')
+    pr_list     = kwargs.get('pr_list',     [])
+    rain_list   = kwargs.get('rain_list',   []) 
+    atm_list    = kwargs.get('atm_list',    [('pco2',3.16e-4),('po2',0.21),('pnh3',1e-50),('pn2o',1e-50)]) 
+    
+    notes = [
+        '** parent rock wt fraction (e.g., "ab      0.2" in one line and "ka     0.001" in the next) (if not specified assumed 1e-20)'
+        ,'** solute concs. of rain in mol/L (if not specified assumed 1e-20)'
+        ,'** atmospheric composition in atm (if not specified assumed 1 PAL)'
+        ]
+    
+    pr_list.insert(0,'')
+    rain_list.insert(0,'')
+    atm_list.insert(0,'')
+        
+    values_lists = [
+        pr_list
+        ,rain_list
+        ,atm_list
+        ]
+        
+    filenames = [
+        'parentrock.in'
+        ,'rain.in'
+        ,'atm.in'
+        ]
+    
+    nn = 3
+    
+    if not os.path.exists(outdir + runname): os.makedirs(outdir + runname)
+    
+    for k in range(nn):
+        values = values_lists[k]
+        filename = filenames[k]
+        n = len(values)
+        input_text = ''
+        for i in range(n):
+            if i==0:
+                input_text += notes[k] + '\n'
+            else:
+                try:
+                    input_text += values[i][0] + '\t' + str(values[i][1]) + '\n'
+                except:
+                    print(n,i,values)
+                    time.sleep(100)
+        
+        input_file = outdir + runname + '/' + filename
+        
+        with open(input_file, 'w') as file:
+            file.write(input_text)
+        
+        print(input_text)
+    
+    
+    del pr_list[0]
+    del rain_list[0]
+    del atm_list[0]
+
+def get_input_sld_properties(outdir,runname,filename):
+
+    
+    infile = outdir + runname + '/' + filename
+    
+    sld_data_list = []
+    
+    
+    with open(infile) as f:
+        cnt2 = 0
+        for line in f:
+            if cnt2 ==0: 
+                cnt2 += 1
+                continue 
+            else:
+                cnt2 += 1
+            a = line.split()
+            tmplist = []
+            cnt = 0
+            for item in a:
+                if cnt ==0:  tmplist.append(item)
+                else: tmplist.append(float(item))
+                cnt += 1
+            
+            sld_data_list.append(tmplist)
+    
+    return sld_data_list
+    
+def main():
+
+    outdir = '../scepter_output/'
+    # runname = 'US_cropland_311_sph_N_spintuneup_field'
+    runname = 'test_Pot7'
+    
+    ztot,nz,ttot,temp,fdust,fdust2,taudust,omrain,zom,poro,moistsrf,zwater,zdust,w,q,p,nstep,rstrt,runid = get_input_frame(outdir,runname)
+    print(
+        ztot,nz,ttot,temp,fdust,fdust2,taudust,omrain,zom,poro,moistsrf,zwater,zdust,w,q,p,nstep,rstrt,runid
+        )
+        
+    w_scheme,mix_scheme,poro_iter,sldmin_lim,display,disp_lim,restart,rough,act_ON,dt_fix \
+        ,cec_on,dz_fix,close_aq,poro_evol,sa_evol_1,sa_evol_2,psd_bulk,psd_full,season = get_input_switches(outdir,runname)
+    print(
+        w_scheme,mix_scheme,poro_iter,sldmin_lim,display,disp_lim,restart,rough,act_ON,dt_fix 
+        ,cec_on,dz_fix,close_aq,poro_evol,sa_evol_1,sa_evol_2,psd_bulk,psd_full,season 
+        )
+        
+    sld_list,aq_list,gas_list,exrxn_list = get_input_tracers(outdir,runname)
+    print(
+        sld_list,aq_list,gas_list,exrxn_list
+        )
+    
+    filename = 'cec.in'
+    sld_data_list = get_input_sld_properties(outdir,runname,filename)
+    print(
+        sld_data_list,
+        sld_data_list[0][1]
+        )
+    
+    sld_data_list = get_input_sld_properties('./','data','dust_gbasalt.in')
+    print(
+        sld_data_list
+        )
+   
+if __name__ == '__main__':
+    main()
+    
+    
\ No newline at end of file
diff --git a/get_int_prof.py b/get_int_prof.py
index 42f7911..00bdb26 100644
--- a/get_int_prof.py
+++ b/get_int_prof.py
@@ -1042,7 +1042,7 @@ def get_dis_frac(outdir,runname,sp):
 
 
 def main():
-    outdir = '/storage/coda1/p-creinhard3/0/ykanzaki3/scepter_output/'
+    outdir = '../scepter_output/'
     runname = 'US_cropland_251_pph_N_cacl2_2p5_homo2_mgo_field_tpH7p0_tau10'
     dep_sample = 0.15
     get_intph_int_site(outdir,runname,dep_sample)
diff --git a/get_int_prof_time.py b/get_int_prof_time.py
index 5ae961e..2124edd 100644
--- a/get_int_prof_time.py
+++ b/get_int_prof_time.py
@@ -26,11 +26,6 @@ def linave(dep,phdep,ztot):
     return a
 
 def get_ph_int_site(outdir,runname,dep_sample,i):
-    # outdir = '../pyweath_output/'
-    # runname = ''
-    # runname = 'Sheldon_A_fick_noiter_test_psdfullpbe_w1_fit_r2000_sig0p2_loop_q0p2_chkall'
-
-    # dep_sample = float(sys.argv[1])
 
     infile = outdir+runname+'/prof/prof_aq-{:03d}.txt'.format(i)
     data = np.loadtxt(infile,skiprows=1)
@@ -49,11 +44,6 @@ def get_ph_int_site(outdir,runname,dep_sample,i):
     return phintval
 
 def get_ac_int_site(outdir,runname,dep_sample):
-    # outdir = '../pyweath_output/'
-    # runname = ''
-    # runname = 'Sheldon_A_fick_noiter_test_psdfullpbe_w1_fit_r2000_sig0p2_loop_q0p2_chkall'
-
-    # dep_sample = float(sys.argv[1])
 
     infile = outdir+runname+'/prof/prof_aq(ads%cec)-020.txt'
     data = np.loadtxt(infile,skiprows=1)
diff --git a/get_int_prof_time_dep.py b/get_int_prof_time_dep.py
index 8d0208d..ef5cbc5 100644
--- a/get_int_prof_time_dep.py
+++ b/get_int_prof_time_dep.py
@@ -26,11 +26,6 @@ def linave(dep,phdep,ztot):
     return a
 
 def get_ph_int_site(outdir,runname,idep,i):
-    # outdir = '../pyweath_output/'
-    # runname = ''
-    # runname = 'Sheldon_A_fick_noiter_test_psdfullpbe_w1_fit_r2000_sig0p2_loop_q0p2_chkall'
-
-    # dep_sample = float(sys.argv[1])
 
     infile = outdir+runname+'/prof/prof_aq-{:03d}.txt'.format(i)
     data = np.loadtxt(infile,skiprows=1)
@@ -42,11 +37,6 @@ def get_ph_int_site(outdir,runname,idep,i):
     return pH_dep
 
 def get_ac_int_site(outdir,runname,dep_sample):
-    # outdir = '../pyweath_output/'
-    # runname = ''
-    # runname = 'Sheldon_A_fick_noiter_test_psdfullpbe_w1_fit_r2000_sig0p2_loop_q0p2_chkall'
-
-    # dep_sample = float(sys.argv[1])
 
     infile = outdir+runname+'/prof/prof_aq(ads%cec)-020.txt'
     data = np.loadtxt(infile,skiprows=1)
diff --git a/get_soilpH_time.py b/get_soilpH_time.py
index de45c09..9ddce9c 100644
--- a/get_soilpH_time.py
+++ b/get_soilpH_time.py
@@ -62,8 +62,7 @@ def calc_soilpH(outdir, runname_field, dep_sample, itime, **kwargs):
     temp_lab=25
 
 
-    # outdir = '/storage/scratch1/0/ykanzaki3/scepter_output/'
-    # outdir = '/storage/coda1/p-creinhard3/0/ykanzaki3/scepter_output/'
+    # outdir = '../scepter_output/'
 
     exename = 'scepter'
     to = ' '
@@ -485,7 +484,7 @@ def calc_soilpH(outdir, runname_field, dep_sample, itime, **kwargs):
 
 def timeseries_soilpH():
     
-    outdir = '/storage/coda1/p-creinhard3/0/ykanzaki3/scepter_output/'
+    outdir = '../scepter_output/'
     runname_field   = 'US_cropland_297_sph_N_DIC_v2_spintuneup_field'
     runname_field   = 'US_cropland_311_sph_N_DIC_v2_spintuneup_field'
     runname_field   = 'US_cropland_311_sph_N_DIC_cacl2_2p5_all_spintuneup_field'
@@ -526,7 +525,7 @@ def CECseries_bufferpH(act_ON,database_name):
     cec_list = list(range(21))
     cec_list = list(range(13))
     
-    outdir = '/storage/coda1/p-creinhard3/0/ykanzaki3/scepter_output/'
+    outdir = '../scepter_output/'
     
     res_list = []
     
@@ -575,7 +574,7 @@ def S2006_bufferpH(
     use_local_storage,
     ):
     
-    # outdir = '/storage/coda1/p-creinhard3/0/ykanzaki3/scepter_output/'
+    # outdir = '../scepter_output/'
     # runname_field   = 'US_cropland_297_sph_N_DIC_v2_spintuneup_field'
     # runname_field   = 'US_cropland_311_sph_N_DIC_v2_spintuneup_field'
     # runname_field   = 'US_cropland_297_sph_N_DIC_act_all_spintuneup_field'
@@ -643,7 +642,7 @@ def MK2010_series_soilpH(
     use_local_storage,
     ):
     
-    # outdir = '/storage/coda1/p-creinhard3/0/ykanzaki3/scepter_output/'
+    # outdir = '../scepter_output/'
     # runname_field   = 'US_cropland_297_sph_N_DIC_v2_spintuneup_field'
     # runname_field   = 'US_cropland_311_sph_N_DIC_v2_spintuneup_field'
     # runname_field   = 'US_cropland_297_sph_N_DIC_act_all_spintuneup_field'
@@ -752,7 +751,7 @@ def MK2010_series_soilpH_2(
     use_local_storage,
     ):
     
-    # outdir = '/storage/coda1/p-creinhard3/0/ykanzaki3/scepter_output/'
+    # outdir = '../scepter_output/'
     # runname_field   = 'US_cropland_297_sph_N_DIC_v2_spintuneup_field'
     # runname_field   = 'US_cropland_311_sph_N_DIC_v2_spintuneup_field'
     # runname_field   = 'US_cropland_297_sph_N_DIC_act_all_spintuneup_field'
@@ -844,12 +843,11 @@ def main():
 
 
     # timeseries_soilpH()
+    # exit("end run")
     
     
-    # act_ON = False
     # act_ON = True
     # database_name = 'Sikora'
-    # database_name = 'Goldberg'
     # CECseries_bufferpH(act_ON,database_name)
     # exit("end run")
     
@@ -857,10 +855,10 @@ def main():
     
     
     
-    i_parallel = int(sys.argv[1])
-    n_parallel = int(sys.argv[2])
+    # i_parallel = int(sys.argv[1])
+    # n_parallel = int(sys.argv[2])
     
-    name_base  = sys.argv[3]
+    # name_base  = sys.argv[3]
     # name_base  = 'test_Pot7_25C_v2_alpha'
     name_base  = 'test_Pot7_25C_v2_poro0p4_alpha'
     name_base  = 'test_Pot7_25C_v2_densqrtz_alpha'
@@ -885,8 +883,9 @@ def main():
     
     name_base  = 'test_Pot7_25C_v2_act_2CEC{:.1f}-{:.1f}_pH{:.1f}_alpha'.format(cec_1,cec_2,ph_pw).replace('.','p')
     name_base  = 'chk_Pot7_25C_v2_act_2CEC{:.1f}-{:.1f}_pH{:.1f}_alpha'.format(cec_1,cec_2,ph_pw).replace('.','p')
+    name_base  = 'chk2_Pot7_25C_v2_act_2CEC{:.1f}-{:.1f}_pH{:.1f}_alpha'.format(cec_1,cec_2,ph_pw).replace('.','p')
     
-    outdir  = '/storage/coda1/p-creinhard3/0/ykanzaki3/scepter_output/'
+    outdir  = '../scepter_output/'
     
     alpha_list = list(np.linspace(0.1,5.5,19))
     alpha_list = [3.4]
@@ -897,7 +896,7 @@ def main():
     alpha_list = [1.1]
     alpha_list = [1.2]
     alpha_list = [1.3]
-    alpha_list = [1.4]
+    # alpha_list = [1.4]
     # alpha_list = [1.7]
     # alpha_list = [5.5]
     # alpha_list = [(0, 6)]
@@ -990,122 +989,6 @@ def main():
     
     
     
-    
-    outdir  = '/storage/coda1/p-creinhard3/0/ykanzaki3/scepter_output/'
-    runname_field_list = ['US_cropland_{:d}_sph_N_DIC_act_DA_1p1_spintuneup_field'.format(i) for i in [296,297,311,371]]
-    dep_sample = 0.15
-    include_N = True
-    include_Cl  = False
-    include_Al  = False
-    use_local_storage  = True
-    
-    cnt = 0
-    for runname_field in runname_field_list:
-        for include_DIC in [False,True]:                
-            if cnt%n_parallel!=i_parallel: 
-                cnt += 1
-                continue
-            else:
-                cnt += 1
-                
-            MK2010_series_soilpH_2(
-                outdir,
-                runname_field,
-                dep_sample,
-                include_N,
-                include_Cl,
-                include_Al,
-                include_DIC,
-                use_local_storage,
-                )
-                
-    
-    exit("end run")
-    
-    i_parallel = int(sys.argv[1])
-    n_parallel = int(sys.argv[2])
-    
-    name_base  = sys.argv[3]
-    
-    outdir  = '/storage/coda1/p-creinhard3/0/ykanzaki3/scepter_output/'
-    omrain_list = [100,300,600,900]
-    # ca_list = [1e-5,1e-4,1e-3,1e-2]
-    ca_list = [1e-6,1e-5,1e-4,1e-3]
-    cec_list = [5,10,20,30]
-    # cec_list = [0.01,0.1,1]
-    logkh_list = [5,6,7]
-    nacl_list = [1e-4,1e-3,1e-2,1e-1]
-    nacl_list = [1e-3,1e-2,1e-1,1e0]  # 0.01 0.1 1 10 kg/ha -->  1e-3, 1e-2, 1e-1, 1e0  g/m2
-    q_list = [1e-6,1e-4,1e-2,1e-1,1e0]
-    cnt = 0
-    for omrain in omrain_list:
-        for ca in ca_list:
-            for cec in cec_list:
-                # for logkh in logkh_list:
-                # for nacl in nacl_list:
-                for q in q_list:
-                
-                    if cnt%n_parallel!=i_parallel: 
-                        cnt += 1
-                        continue
-                    else:
-                        cnt += 1
-                        
-                    # runname_field = 'test_inrt-g2-nacl-pco2_{:d}resp_{:d}lognacl_{:d}cec_{:d}logkh'.format(  
-                    # runname_field = 'test_inrt-g2-ca-pco2_{:d}resp_{:d}logca_{:d}cec_{:d}logkh'.format(   
-                        # int(omrain),
-                        # int(-np.log10(ca)),
-                        # int(cec),
-                        # int(logkh),
-                        # )
-                    
-                    # if cec == int(cec):
-                        # runname_field = 'test_inrt-g2-ca-pco2_{:d}resp_{:d}logca_{:d}cec_{:d}logkh'.format(  
-                            # int(omrain),
-                            # int(-np.log10(ca)),
-                            # int(cec),
-                            # int(logkh),
-                            # )  
-                    # else :
-                        # runname_field = 'test_inrt-g2-ca-pco2_{:d}resp_{:d}logca_{}cec_{:d}logkh'.format(  
-                            # int(omrain),
-                            # int(-np.log10(ca)),
-                            # str(cec).replace('.','p'),
-                            # int(logkh),
-                            # )
-                        
-                    # runname_field = name_base + '_{:d}resp_{:d}logca_{:d}lognacl_{:d}cec'.format( 
-                        # int(omrain),
-                        # int(-np.log10(ca)),
-                        # int(-np.log10(nacl)),
-                        # int(cec),
-                        # )
-                        
-                    runname_field = name_base + '_{:d}resp_{:d}logca_{:d}logq_{:d}cec'.format( 
-                        int(omrain),
-                        int(-np.log10(ca)),
-                        int(-np.log10(q)),
-                        int(cec),
-                        )
-                        
-                    dep_sample = 0.15
-                    include_N = False
-                    include_Cl  = True
-                    include_Al  = False
-                    use_local_storage  = True
-                    for include_DIC in [False,True]:
-                        MK2010_series_soilpH(
-                            outdir,
-                            runname_field,
-                            dep_sample,
-                            include_N,
-                            include_Cl,
-                            include_Al,
-                            include_DIC,
-                            use_local_storage,
-                            )
-    
-    
                 
     
 if __name__ == '__main__':
diff --git a/get_soilpH_time_dep.py b/get_soilpH_time_dep.py
index 474b933..6f1fd0e 100644
--- a/get_soilpH_time_dep.py
+++ b/get_soilpH_time_dep.py
@@ -38,8 +38,7 @@ def calc_soilpH(inputlist):
     temp_lab=25
 
 
-    # outdir = '/storage/scratch1/0/ykanzaki3/scepter_output/'
-    outdir = '/storage/coda1/p-creinhard3/0/ykanzaki3/scepter_output/'
+    outdir = '../scepter_output/'
 
     exename = 'scepter'
     to = ' '
@@ -297,7 +296,7 @@ def main():
     
     field_dir = sys.argv[1]
     
-    outdir = '/storage/coda1/p-creinhard3/0/ykanzaki3/scepter_output/'
+    outdir = '../scepter_output/'
     
     for itime in range(n_time):
         file = outdir + field_dir + '/prof/soil_ph_{:03d}.txt'.format(itime+1)
diff --git a/make_inputs.py b/make_inputs.py
index 08190fb..f96a886 100644
--- a/make_inputs.py
+++ b/make_inputs.py
@@ -4,7 +4,7 @@
 import time
 
 def get_input_frame(**kwargs):
-    outdir      = kwargs.get('outdir',  '/storage/scratch1/0/ykanzaki3/scepter_output/')
+    outdir      = kwargs.get('outdir',  '../scepter_output/')
     runname     = kwargs.get('runname', 'test_input')
     ztot        = kwargs.get('ztot',    0.5)
     nz          = kwargs.get('nz',      30) 
@@ -99,7 +99,7 @@ def get_input_frame(**kwargs):
     print(input_text)
 
 def get_input_switches(**kwargs):
-    outdir      = kwargs.get('outdir',      '/storage/scratch1/0/ykanzaki3/scepter_output/')
+    outdir      = kwargs.get('outdir',      '../scepter_output/')
     runname     = kwargs.get('runname',     'test_input')
     w_scheme    = kwargs.get('w_scheme',    1)
     mix_scheme  = kwargs.get('mix_scheme',  1) 
@@ -189,7 +189,7 @@ def get_input_switches(**kwargs):
     print(input_text)
 
 def get_input_tracers(**kwargs):
-    outdir      = kwargs.get('outdir',      '/storage/scratch1/0/ykanzaki3/scepter_output/')
+    outdir      = kwargs.get('outdir',      '../scepter_output/')
     runname     = kwargs.get('runname',     'test_input')
     sld_list    = kwargs.get('sld_list',    [])
     aq_list     = kwargs.get('aq_list',     []) 
@@ -250,7 +250,7 @@ def get_input_tracers(**kwargs):
     del exrxn_list[0]
 
 def get_input_tracer_bounds(**kwargs):
-    outdir      = kwargs.get('outdir',      '/storage/scratch1/0/ykanzaki3/scepter_output/')
+    outdir      = kwargs.get('outdir',      '../scepter_output/')
     runname     = kwargs.get('runname',     'test_input')
     pr_list     = kwargs.get('pr_list',     [])
     rain_list   = kwargs.get('rain_list',   []) 
@@ -310,7 +310,7 @@ def get_input_tracer_bounds(**kwargs):
     del atm_list[0]
 
 def get_input_sld_properties(**kwargs):
-    outdir      = kwargs.get('outdir',      '/storage/scratch1/0/ykanzaki3/scepter_output/')
+    outdir      = kwargs.get('outdir',      '../scepter_output/')
     runname     = kwargs.get('runname',     'test_input')
     sld_varlist = kwargs.get('sld_varlist', [])
     filename    = kwargs.get('filename',    'kinspc.in')
@@ -448,8 +448,7 @@ def get_input_climate_temp(**kwargs):
         
 def main():
 
-    # outdir = '/storage/scratch1/0/ykanzaki3/scepter_output/'
-    outdir = '/storage/coda1/p-creinhard3/0/ykanzaki3/scepter_output/'
+    outdir = '../scepter_output/'
     runname = 'test_input'
     
     ztot=0.5
@@ -563,7 +562,7 @@ def main():
         ,atm_list=atm_list
         )
     filename = 'dust.in'
-    srcfile = '/storage/coda1/p-creinhard3/0/ykanzaki3/PyWeath/data/dust_gbasalt.in'
+    srcfile = './data/dust_gbasalt.in'
     sld_varlist =[]
     get_input_sld_properties(
         outdir=outdir
@@ -589,8 +588,8 @@ def main():
         ,sld_varlist=sld_varlist
         )
     filename = '2ndslds.in'
-    srcfile = '/storage/coda1/p-creinhard3/0/ykanzaki3/PyWeath/data/2ndslds_def.in'
-    srcfile = '/storage/coda1/p-creinhard3/0/ykanzaki3/PyWeath/data/2ndslds_rm_al2o3.in'
+    srcfile = './data/2ndslds_def.in'
+    srcfile = './data/2ndslds_rm_al2o3.in'
     sld_varlist =[]
     get_input_sld_properties(
         outdir=outdir
diff --git a/readme.txt b/readme.txt
index e4b8350..503bed0 100644
--- a/readme.txt
+++ b/readme.txt
@@ -1,16 +1,68 @@
 scepter
 
-scepter.f90                         - source code  
-makefile                            - compile (data dir needs to be specified)
+scepter.f90             - source code  
+makefile                - compile (data dir in L50 needs to be specified)
 
 
 scripts:
-get_int_prof.py                     - contain functions to get output data 
-make_inputs.py                      - contain functions to make input data
-tunespin_3_newton_inert_buff.py     - run 3 variable iterations (output dir needs to be specified)
-tunespin_3_newton_inert_buff_v2.py  - same as above but with an option to use soil pH with CaCl2
-water_amb.py                        - sample porewater and leave it in the beaker in lab (output dir needs to be specified; no use for pipeline?)
-basalt_buff_tunespin_bisec.py       - run basalt application for a target pH etc. (output dir needs to be specified)
-basalt_buff_tunespin_bisec_v2.py    - same as above but with an option to use soil pH with CaCl2
-sub_jobs.py                         - submit multiple jobs (for spinup and basalt exp)
-run_a_shell.sbatch                  - submit a single job (for GT cluster)
\ No newline at end of file
+get_int_prof.py         - contain functions to get output data 
+get_int_prof_time.py    - same above but with specifing the model time  
+get_int_prof_time_dep.py
+                        - same above but with specifing the model depth 
+get_soilpH_time.py      - contain functions to calculate soil pH 
+get_soilpH_time_dep.py  - same above but with specifing the model depth
+get_inputs.py           - contain functions to retrieve input data
+make_inputs.py          - contain functions to make input data
+tunespin_3_newton_inert_buff_v2_clean.py  
+                        - conduct 3 variable field-run iterations 
+                            (output dir needs to be specified)
+basalt_buff_tunespin_bisec_v2.py    
+                        - conduct field-run iteration to get to a target soil/pw pH 
+                            (output dir needs to be specified)
+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.
+
+
+
+$$ running example simulations in GMD paper $$
+
+1. test for Sikora buffer used in in Section 3
+1.1. in-silico field samples 
+    a. modify outdir in L20 of spinup_inert.py 
+    b. type: python3 spinup_inert.py
+1.1. buffer pH for field samples in silico
+    a. modify outdir in L528 and 
+        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
+    a. modify outdir in L159 of spinup_inrt2.py 
+    b. type: python3 spinup_inrt2.py
+
+2.2. 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 
+    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 
+        8.222189843654622 0.282726679550165 0.35136107875550837 0.0010131311683626316 
+        1.005952418781816
+    [ 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 
+    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
+    a. modify outdir in L49, L299 of get_soilpH_time_dep.py
+    b. type: get_soilpH_time_dep.py basalt_run_name
\ No newline at end of file
diff --git a/spinup.py b/spinup.py
index 3a026a7..54d7cf6 100644
--- a/spinup.py
+++ b/spinup.py
@@ -78,11 +78,12 @@ def run_a_scepter_run(
     
     # compile 
     exename = 'scepter'
-    exename_src = 'scepter_test'
+    exename_src = 'scepter'
+    # exename_src = 'scepter_test'
     to = ' '
     where = '/'
-    # os.system('make')
-    os.system('make --file=makefile_test')
+    os.system('make')
+    # os.system('make --file=makefile_test')
     if not os.path.exists( outdir + runname) : os.system('mkdir -p ' + outdir + runname)
     os.system('cp ' + exename_src + to + outdir + runname + where + exename)
 
@@ -208,7 +209,7 @@ def run_a_scepter_run(
         
 def main():
 
-    outdir_src = '/storage/coda1/p-creinhard3/0/ykanzaki3/scepter_output/'
+    outdir_src = '../scepter_output/'
     runname = 'test'
     
     #  >>>> input variables of interests 
diff --git a/spinup_inert.py b/spinup_inert.py
index b0032d6..8f29b26 100644
--- a/spinup_inert.py
+++ b/spinup_inert.py
@@ -5,7 +5,7 @@
 def run_closed_inert_cec(cec,act_ON_IN,data):
 
     use_local_storage = True
-    # use_local_storage = False
+    use_local_storage = False
     
     # cec = 0
     
@@ -17,7 +17,7 @@ def run_closed_inert_cec(cec,act_ON_IN,data):
     
     alpha = 3.4
     
-    outdir = '/storage/coda1/p-creinhard3/0/ykanzaki3/scepter_output/'
+    outdir = '../scepter_output/'
     if use_local_storage:  outdir = os.environ['TMPDIR'] + '/scepter_output/'
     # runname = 'test_inert_spinup_cec_{:d}'.format(cec) 
     if act_ON_IN: runname = 'test_inert_spinup_act_cec_{:d}'.format(cec) + '_'+ data
@@ -25,11 +25,12 @@ def run_closed_inert_cec(cec,act_ON_IN,data):
 
     # compile 
     exename = 'scepter'
-    exename_src = 'scepter_test'
+    exename_src = 'scepter'
+    # exename_src = 'scepter_test'
     to = ' '
     where = '/'
-    # os.system('make')
-    os.system('make --file=makefile_test')
+    os.system('make')
+    # os.system('make --file=makefile_test')
     if not os.path.exists( outdir + runname) : os.system('mkdir -p ' + outdir + runname)
     os.system('cp ' + exename_src + to + outdir + runname + where + exename)
     
@@ -154,7 +155,7 @@ def run_closed_inert_cec(cec,act_ON_IN,data):
         )
         
     filename = 'dust.in'
-    srcfile = '/storage/coda1/p-creinhard3/0/ykanzaki3/PyWeath/data/dust_gbasalt.in'
+    srcfile = './data/dust_gbasalt.in'
     sld_varlist =[]
     make_inputs.get_input_sld_properties(
         outdir=outdir
@@ -188,7 +189,7 @@ def run_closed_inert_cec(cec,act_ON_IN,data):
         
     if use_local_storage:
         src = outdir + runname 
-        dst = '/storage/coda1/p-creinhard3/0/ykanzaki3/scepter_output/' + runname 
+        dst = '../scepter_output/' + runname 
         
         if not os.path.exists(dst): 
             shutil.copytree(src, dst)
@@ -198,13 +199,11 @@ def run_closed_inert_cec(cec,act_ON_IN,data):
    
 def main():
     
-    # cec_list = [0,1,2,4,8,16,32,64]
     cec_list = list(range(21))
     act_ON_IN = False
     act_ON_IN = True
     
     data = 'Sikora'
-    # data = 'Goldberg'
     
     for cec in cec_list:
         run_closed_inert_cec(cec,act_ON_IN,data)
diff --git a/spinup_inrt2.py b/spinup_inrt2.py
index 145dcad..a882143 100644
--- a/spinup_inrt2.py
+++ b/spinup_inrt2.py
@@ -15,7 +15,6 @@ def spin_inert(outdir_src,runname,
     act_ON,
     ):
 
-    # outdir_src = '/storage/coda1/p-creinhard3/0/ykanzaki3/scepter_output/'
     # runname = 'test'
     
     # cec     = 10.0
@@ -157,7 +156,7 @@ def spin_inert(outdir_src,runname,
         
         
 def main():
-    outdir_src = '/storage/coda1/p-creinhard3/0/ykanzaki3/scepter_output/'
+    outdir_src = '../scepter_output/'
     
     runname = 'test_Pot7_25C_alpha0p0'
     runname = 'test_Pot7_25C_alpha3p1'
@@ -188,7 +187,7 @@ def main():
     cl_tmp = 2.9e-4  # double CEC OM - 120, pwpH=6.1, alpha = 1.1 
     cl_tmp = 2.8e-4  # double CEC OM - 120, pwpH=6.1, alpha = 1.2 
     cl_tmp = 2.68e-4  # double CEC OM - 120, pwpH=6.1, alpha = 1.3 
-    cl_tmp = 2.55e-4  # double CEC OM - 120, pwpH=6.1, alpha = 1.4 
+    # cl_tmp = 2.55e-4  # double CEC OM - 120, pwpH=6.1, alpha = 1.4 
     
     ph_pw = 6.68
     ph_pw = 6.3
@@ -269,16 +268,17 @@ def main():
     if cec_1<0: exit("cec_1<0")
     
     
-    i_parallel = int(sys.argv[1])
-    n_parallel = int(sys.argv[2])
+    # i_parallel = int(sys.argv[1])
+    # n_parallel = int(sys.argv[2])
     
-    name_base  = sys.argv[3]
+    # name_base  = sys.argv[3]
     # name_base  = 'test_Pot7_25C_v2_CEC10p0'
     name_base  = 'test_Pot7_25C_v2_noact_alpha'
     name_base  = 'test_Pot7_25C_v2_act_alpha'
     name_base  = 'test_Pot7_25C_v2_act_2alpha'
     name_base  = 'test_Pot7_25C_v2_act_2CEC{:.1f}-{:.1f}_pH{:.1f}_alpha'.format(cec_1,cec_2,ph_pw).replace('.','p')
     name_base  = 'chk_Pot7_25C_v2_act_2CEC{:.1f}-{:.1f}_pH{:.1f}_alpha'.format(cec_1,cec_2,ph_pw).replace('.','p')
+    name_base  = 'chk2_Pot7_25C_v2_act_2CEC{:.1f}-{:.1f}_pH{:.1f}_alpha'.format(cec_1,cec_2,ph_pw).replace('.','p')
     # name_base  = 'test_Pot7_25C_v3_noact_alpha'
     
     act_ON = 'true'
@@ -291,7 +291,7 @@ def main():
     alpha_list = [(1.1, 1.1)]
     alpha_list = [(1.2, 1.2)]
     alpha_list = [(1.3, 1.3)]
-    alpha_list = [(1.4, 1.4)]
+    # alpha_list = [(1.4, 1.4)]
     
     for i in range(len(alpha_list)):
                    
diff --git a/sub_jobs.py b/sub_jobs.py
deleted file mode 100644
index 999b008..0000000
--- a/sub_jobs.py
+++ /dev/null
@@ -1,177 +0,0 @@
-import os
-import numpy as np
-import time 
-
-input_dir = './data/'
-# input_dir = './'
-input_file = 'friendship.txt'
-input_file = 'GAdata.txt'
-input_file = 'SL004810.txt'
-skip_file = 'GA_fail.txt'
-skip_file = 'SL004810_sph_fail.txt'
-skip_file = 'SL004810_FAIL_sph_N_spintuneup_field.txt'
-
-data = np.loadtxt(input_dir+input_file,skiprows=1)
-skipdata = np.loadtxt(input_dir+skip_file)
-skipdata = [int(i) for i in skipdata]
-
-n_sample = data.shape[0]
-
-runs_chosen = [
-    # 2,6,7
-    # 7
-    ]
-
-runtype = 'spinup'
-runtype = 'basalt'
-
-for i in range(n_sample):
-
-
-    runtime = '12:20:00'
-    soft    = 'python3'
-    
-    if 'friendship' in input_file:
-
-        runid   = data[i,0]
-        soilpH  = data[i,1]
-        om      = data[i,2]
-        cec     = data[i,3]
-        acid    = data[i,4]
-        buffpH  = data[i,5]
-    
-        if acid ==0:acid = 0.1 
-        if soilpH  ==5.6: soilpH  = 5.7 
-    
-    elif 'GAdata' in input_file:
-        runid   = data[i,0]
-        soilpH  = data[i,8]
-        om      = 5  # no data given
-        cec     = data[i,1]
-        acid    = data[i,6]
-        buffpH  = 7  # no data given
-    
-    elif 'SL004810' in input_file:
-
-        runid   = data[i,0]
-        soilpH  = data[i,1]
-        om      = data[i,2]
-        cec     = data[i,3]
-        acid    = data[i,4]
-        buffpH  = 7  # no data given
-    
-    
-    if len(runs_chosen)!=0 and runid not in runs_chosen: continue
-    
-    if runtype == 'spinup':
-        
-        code    = 'tunespin_3_newton_inert_buff.py'
-        code    = 'tunespin_3_newton_inert_buff_v2.py'
-        # code    = 'tunespin_3b_newton_inert_buff.py'
-        
-        if code == 'tunespin_3b_newton_inert_buff.py' and np.isnan(buffpH): continue
-    
-        # runname = 'potato_'+str(int(runid))
-        # runname = 'potato_pw_'+str(int(runid))
-        # runname = 'potato_fert_'+str(int(runid))
-        # runname = 'potato_fert_pw_'+str(int(runid))
-        runname = 'potato_buff_'+str(int(runid))
-        runname = 'GA_OM5_sph_'+str(int(runid))
-        runname = input_file.replace('.txt','')+'_'+str(int(runid))
-        
-        # runname += '_sph'
-        runname += '_sph_N'
-
-        jobname = runname
-
-        inputs = [
-            runname
-            ,str(cec)
-            ,str(soilpH)
-            ,str(acid)
-            ,str(om)
-            ]
-        
-        if code == 'tunespin_3b_newton_inert_buff.py':
-            inputs = [
-                runname
-                ,str(cec)
-                ,str(soilpH)
-                ,str(buffpH)
-                ,str(om)
-                ]
-        
-        input_runtime = ' '.join(inputs)
-
-        command = 'sbatch  --output='+jobname+'.out --job-name='+jobname+' --time='+runtime + ' run_a_shell.sbatch ' + soft + ' ' + code  \
-            + ' ' + input_runtime
-            
-        print(command)
-        os.system(command)
-        
-        time.sleep(5)
-    
-    elif runtype == 'basalt':
-    
-        if acid <= 0.1 : continue
-        
-        # if 'GAdata' in input_file and int(runid) in skipdata: continue
-        if 'SL004810' in input_file and int(runid) in skipdata: continue
-    
-        code    = 'basalt_buff_tunespin_bisec.py'
-        code    = 'basalt_buff_tunespin_bisec_v2.py'
-    
-        # runname = 'potato_bas_'+str(int(runid))
-        # runname = 'potato_bas_pw_'+str(int(runid))
-        # runname = 'potato_bas_fert_50u_'+str(int(runid))
-        # runname = 'potato_bas_50u_'+str(int(runid))
-        # runname = 'potato_bas_50u_'+str(int(runid))
-        # runname = 'GA_OM5_sph_bas_10u_'+str(int(runid))
-        runname = input_file.replace('.txt','')+'_'+str(int(runid))
-        
-        # spinname = 'potato_'+str(int(runid))
-        # spinname = 'potato_pw_'+str(int(runid))
-        # spinname = 'potato_fert_'+str(int(runid))
-        spinname = 'GA_OM5_sph_'+str(int(runid))
-        spinname = input_file.replace('.txt','')+'_'+str(int(runid))
-        
-        # spinname += '_N'
-        # runname  += '_N_10u_bas'
-        # spinname += '_h'
-        # runname  += '_10u_bas'
-        # spinname += '_sph'
-        # runname  += '_sph_10u_bas'
-        spinname += '_sph_N'
-        runname  += '_sph_N_10u_bas'
-        
-        targetpHs = [6.5, 6.8]
-        targetpHs = [5.4, 5.6, 5.8]
-        targettaus = [1]
-        
-        for targetpH in targetpHs:
-            
-            if soilpH >=targetpH: continue
-            
-            for targettau in targettaus:
-        
-                jobname = runname+'_'+'_'.join([str(targetpH),str(targettau)]).replace('.','p')
-                
-                
-                inputs = [
-                    str(targetpH)
-                    ,str(targettau)
-                    ,str(cec)
-                    ,runname
-                    ,spinname
-                    ]
-
-                input_runtime = ' '.join(inputs)
-
-                command = 'sbatch  --output='+jobname+'.out --job-name='+jobname+' --time='+runtime + ' run_a_shell.sbatch ' + soft + ' ' + code  \
-                    + ' ' + input_runtime
-                    
-                print(command)
-                os.system(command)
-                
-                time.sleep(5)
-    # break
\ No newline at end of file
diff --git a/tunespin_3_newton_inert_buff_v2_clean.py b/tunespin_3_newton_inert_buff_v2_clean.py
index 6415523..01478a6 100644
--- a/tunespin_3_newton_inert_buff_v2_clean.py
+++ b/tunespin_3_newton_inert_buff_v2_clean.py
@@ -25,7 +25,7 @@
 alphase = 'amal'
 
 use_CaCl2 = False
-use_CaCl2 = True
+# use_CaCl2 = True
 
 phnorm_pw = True
 phnorm_pw = False
@@ -37,10 +37,10 @@
 use_local_storage = False
 
 make_initial_geuss = True
-# make_initial_geuss = False
+make_initial_geuss = False
 
 liming = True
-# liming = False
+liming = False
 
 limesp = 'cao'
 limemwt = 56.079
@@ -50,7 +50,7 @@
 
 water_frac = 5.
 water_frac = 1.
-water_frac = 2.5
+# water_frac = 2.5
 
 iter_max = 120
 iter_max = 3000
@@ -83,7 +83,7 @@
     make_initial_geuss = True
 
 if make_initial_geuss:
-    outdir_guess = '/storage/coda1/p-creinhard3/0/ykanzaki3/scepter_output/'
+    outdir_guess = '../scepter_output/'
     
     try:
         # filename = '/iteration_tmp.res'
@@ -145,8 +145,6 @@
 # dep_sample = 0.25
 
 
-outdir = '/storage/scratch1/0/ykanzaki3/scepter_output/'
-outdir = '/storage/coda1/p-creinhard3/0/ykanzaki3/scepter_output/'
 outdir = '../scepter_output/'
 if use_local_storage:  outdir = os.environ['TMPDIR'] + '/scepter_output/'
 simid = sys.argv[1]
@@ -155,11 +153,12 @@
 
 # compile 
 exename = 'scepter'
-exename_src = 'scepter_test'
+exename_src = 'scepter'
+# exename_src = 'scepter_test'
 to = ' '
 where = '/'
-# os.system('make')
-os.system('make --file=makefile_test')
+os.system('make')
+# os.system('make --file=makefile_test')
 prev_iter_exist = False
 if not os.path.exists( outdir + runname_field) : 
     os.system('mkdir -p ' + outdir + runname_field)
@@ -383,10 +382,13 @@
     
 filename = 'psdrain.in'
 srcfile = './data/psdrain_320um.in'
+sld_varlist = [ (5e-6,0.2,1), (5e-6,0.2,1), (5e-6,0.2,1), (5e-6,0.2,1), ] 
+# sld_varlist = [ (1e-6,0.2,1), (2e-6,0.2,1), (5e-6,0.2,1), (20e-6,0.2,1), ] 
 make_inputs.get_input_sld_properties(
     outdir=outdir
     ,runname=runname_field
     ,filename = filename
+    # ,sld_varlist=sld_varlist
     ,srcfile = srcfile
     )
     
@@ -551,6 +553,7 @@
 error = 1e4
 tol = 1e-4
 tol = 1e-3
+# tol = 1e-2
 
 cnt = 1
 res_list = []
@@ -1081,7 +1084,7 @@ def run_a_single_set(ca,logkh,omrain_field):
 if use_local_storage:
     for runname in [runname_field,runname_lab]:
         src = outdir + runname 
-        dst = '/storage/coda1/p-creinhard3/0/ykanzaki3/scepter_output/' + runname 
+        dst = '../scepter_output/' + runname 
         
         if not os.path.exists(dst): 
             shutil.copytree(src, dst)