Create example Jupyter notebook

bobbypaton · Jul 1, 2022 · 28b20f2 · 28b20f2
1 parent d4a7183
commit 28b20f2
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Showing 74 changed files with 2,440 additions and 8 deletions.
diff --git a/.ipynb_checkpoints/jupyter_goodvibes_examples-checkpoint.ipynb b/.ipynb_checkpoints/jupyter_goodvibes_examples-checkpoint.ipynb
diff --git a/goodvibes/GoodVibes.py b/goodvibes/GoodVibes.py
@@ -97,7 +97,7 @@ def add_time(tm, cpu):
     return fulldate
 
 
-def calc_cpu(thermo_data, options, log):
+def calc_cpu(thermo_data, log):
     # Initialize the total CPU time
     add_days = 0
     cpu = datetime(100, 1, 1, 00, 00, 00, 00)
@@ -115,7 +115,7 @@ def calc_cpu(thermo_data, options, log):
                                cpu.minute, 'mins', cpu.second, 'secs'))
 
 
-def get_vib_scale_factor(files, level_of_theory, freq_scale_factor, mm_freq_scale_factor, log):
+def get_vib_scale_factor(files, level_of_theory, log, freq_scale_factor=False, mm_freq_scale_factor=False):
     ''' Attempt to automatically obtain frequency scale factor
     Application of freq scale factors requires all outputs to be same level of theory'''
 
@@ -148,7 +148,8 @@ def get_vib_scale_factor(files, level_of_theory, freq_scale_factor, mm_freq_scal
                 levels_l_o_t.append(i)
             filtered_calcs_l_o_t.append(files_l_o_t)
             filtered_calcs_l_o_t.append(levels_l_o_t)
-            io.print_check_fails(log, filtered_calcs_l_o_t[1], filtered_calcs_l_o_t[0], "levels of theory")
+            print(filtered_calcs_l_o_t)
+            #io.print_check_fails(log, filtered_calcs_l_o_t[1], filtered_calcs_l_o_t[0], "levels of theory")
 
     # Exit program if molecular mechanics scaling factor is given and all files are not ONIOM calculations
     if mm_freq_scale_factor is not False:
@@ -608,7 +609,7 @@ def main():
     bbe_vals = [[]] * len(file_list) # initialize a list that will be populated with thermochemical values
 
     # scaling vibrational Frequencies
-    options.freq_scale_factor, options.mm_freq_scale_factor =  get_vib_scale_factor(file_list, l_o_t, options.freq_scale_factor, options.mm_freq_scale_factor, log)
+    options.freq_scale_factor, options.mm_freq_scale_factor =  get_vib_scale_factor(file_list, l_o_t, log, options.freq_scale_factor, options.mm_freq_scale_factor)
 
     for i, file in enumerate(file_list):
         d3_term = 0.0 # computes D3 term if requested
@@ -644,7 +645,7 @@ def main():
     gv_summary = io.summary(thermo_data, options, log, boltz_facs, clusters)
 
     if options.cputime: # Print CPU usage if requested
-        cpu = calc_cpu(thermo_data, options, log)
+        cpu = calc_cpu(thermo_data, log)
 
     if options.ee is not False: # Compute selectivity
         [a_name, b_name], [a_files, b_files], ee, er, ratio, dd_free_energy, preference = get_selectivity(options.ee, file_list, boltz_facs, options.temperature, log)

diff --git a/goodvibes/examples/reaction_profile/PhPy.yaml b/goodvibes/examples/reaction_profile/PhPy.yaml
@@ -22,7 +22,6 @@
     gridlines: True
     show_conformers: True
     show_gconf: False
-    dpi : 400
     title: Potential Energy Surface
 
 
diff --git a/...eaction_selecivity/opt/DATS_13_endo_i.log → ...action_selectivity/opt/DATS_13_endo_i.log b/...eaction_selecivity/opt/DATS_13_endo_i.log → ...action_selectivity/opt/DATS_13_endo_i.log
diff --git a/...action_selecivity/opt/DATS_13_endo_ii.log → ...ction_selectivity/opt/DATS_13_endo_ii.log b/...action_selecivity/opt/DATS_13_endo_ii.log → ...ction_selectivity/opt/DATS_13_endo_ii.log
diff --git a/...ction_selecivity/opt/DATS_13_endo_iii.log → ...tion_selectivity/opt/DATS_13_endo_iii.log b/...ction_selecivity/opt/DATS_13_endo_iii.log → ...tion_selectivity/opt/DATS_13_endo_iii.log
diff --git a/...action_selecivity/opt/DATS_13_endo_iv.log → ...ction_selectivity/opt/DATS_13_endo_iv.log b/...action_selecivity/opt/DATS_13_endo_iv.log → ...ction_selectivity/opt/DATS_13_endo_iv.log
diff --git a/...reaction_selecivity/opt/DATS_13_exo_i.log → ...eaction_selectivity/opt/DATS_13_exo_i.log b/...reaction_selecivity/opt/DATS_13_exo_i.log → ...eaction_selectivity/opt/DATS_13_exo_i.log
diff --git a/...eaction_selecivity/opt/DATS_13_exo_ii.log → ...action_selectivity/opt/DATS_13_exo_ii.log b/...eaction_selecivity/opt/DATS_13_exo_ii.log → ...action_selectivity/opt/DATS_13_exo_ii.log
diff --git a/...action_selecivity/opt/DATS_13_exo_iii.log → ...ction_selectivity/opt/DATS_13_exo_iii.log b/...action_selecivity/opt/DATS_13_exo_iii.log → ...ction_selectivity/opt/DATS_13_exo_iii.log
diff --git a/...eaction_selecivity/opt/DATS_13_exo_iv.log → ...action_selectivity/opt/DATS_13_exo_iv.log b/...eaction_selecivity/opt/DATS_13_exo_iv.log → ...action_selectivity/opt/DATS_13_exo_iv.log
diff --git a/...eaction_selecivity/opt/DATS_14_endo_i.log → ...action_selectivity/opt/DATS_14_endo_i.log b/...eaction_selecivity/opt/DATS_14_endo_i.log → ...action_selectivity/opt/DATS_14_endo_i.log
diff --git a/...action_selecivity/opt/DATS_14_endo_ii.log → ...ction_selectivity/opt/DATS_14_endo_ii.log b/...action_selecivity/opt/DATS_14_endo_ii.log → ...ction_selectivity/opt/DATS_14_endo_ii.log
diff --git a/...ction_selecivity/opt/DATS_14_endo_iii.log → ...tion_selectivity/opt/DATS_14_endo_iii.log b/...ction_selecivity/opt/DATS_14_endo_iii.log → ...tion_selectivity/opt/DATS_14_endo_iii.log
diff --git a/...action_selecivity/opt/DATS_14_endo_iv.log → ...ction_selectivity/opt/DATS_14_endo_iv.log b/...action_selecivity/opt/DATS_14_endo_iv.log → ...ction_selectivity/opt/DATS_14_endo_iv.log
diff --git a/...reaction_selecivity/opt/DATS_14_exo_i.log → ...eaction_selectivity/opt/DATS_14_exo_i.log b/...reaction_selecivity/opt/DATS_14_exo_i.log → ...eaction_selectivity/opt/DATS_14_exo_i.log
diff --git a/...eaction_selecivity/opt/DATS_14_exo_ii.log → ...action_selectivity/opt/DATS_14_exo_ii.log b/...eaction_selecivity/opt/DATS_14_exo_ii.log → ...action_selectivity/opt/DATS_14_exo_ii.log
diff --git a/...action_selecivity/opt/DATS_14_exo_iii.log → ...ction_selectivity/opt/DATS_14_exo_iii.log b/...action_selecivity/opt/DATS_14_exo_iii.log → ...ction_selectivity/opt/DATS_14_exo_iii.log
diff --git a/...eaction_selecivity/opt/DATS_14_exo_iv.log → ...action_selectivity/opt/DATS_14_exo_iv.log b/...eaction_selecivity/opt/DATS_14_exo_iv.log → ...action_selectivity/opt/DATS_14_exo_iv.log
diff --git a/...reaction_selecivity/opt/DATS_14_exo_v.log → ...eaction_selectivity/opt/DATS_14_exo_v.log b/...reaction_selecivity/opt/DATS_14_exo_v.log → ...eaction_selectivity/opt/DATS_14_exo_v.log
diff --git a/...selecivity/spc_01/DATS_13_endo_i_TZVP.log → ...electivity/spc_01/DATS_13_endo_i_TZVP.log b/...selecivity/spc_01/DATS_13_endo_i_TZVP.log → ...electivity/spc_01/DATS_13_endo_i_TZVP.log
diff --git a/...elecivity/spc_01/DATS_13_endo_ii_TZVP.log → ...lectivity/spc_01/DATS_13_endo_ii_TZVP.log b/...elecivity/spc_01/DATS_13_endo_ii_TZVP.log → ...lectivity/spc_01/DATS_13_endo_ii_TZVP.log
diff --git a/...lecivity/spc_01/DATS_13_endo_iii_TZVP.log → ...ectivity/spc_01/DATS_13_endo_iii_TZVP.log b/...lecivity/spc_01/DATS_13_endo_iii_TZVP.log → ...ectivity/spc_01/DATS_13_endo_iii_TZVP.log
diff --git a/...elecivity/spc_01/DATS_13_endo_iv_TZVP.log → ...lectivity/spc_01/DATS_13_endo_iv_TZVP.log b/...elecivity/spc_01/DATS_13_endo_iv_TZVP.log → ...lectivity/spc_01/DATS_13_endo_iv_TZVP.log
diff --git a/..._selecivity/spc_01/DATS_13_exo_i_TZVP.log → ...selectivity/spc_01/DATS_13_exo_i_TZVP.log b/..._selecivity/spc_01/DATS_13_exo_i_TZVP.log → ...selectivity/spc_01/DATS_13_exo_i_TZVP.log
diff --git a/...selecivity/spc_01/DATS_13_exo_ii_TZVP.log → ...electivity/spc_01/DATS_13_exo_ii_TZVP.log b/...selecivity/spc_01/DATS_13_exo_ii_TZVP.log → ...electivity/spc_01/DATS_13_exo_ii_TZVP.log
diff --git a/...elecivity/spc_01/DATS_13_exo_iii_TZVP.log → ...lectivity/spc_01/DATS_13_exo_iii_TZVP.log b/...elecivity/spc_01/DATS_13_exo_iii_TZVP.log → ...lectivity/spc_01/DATS_13_exo_iii_TZVP.log
diff --git a/...selecivity/spc_01/DATS_13_exo_iv_TZVP.log → ...electivity/spc_01/DATS_13_exo_iv_TZVP.log b/...selecivity/spc_01/DATS_13_exo_iv_TZVP.log → ...electivity/spc_01/DATS_13_exo_iv_TZVP.log
diff --git a/...selecivity/spc_01/DATS_14_endo_i_TZVP.log → ...electivity/spc_01/DATS_14_endo_i_TZVP.log b/...selecivity/spc_01/DATS_14_endo_i_TZVP.log → ...electivity/spc_01/DATS_14_endo_i_TZVP.log
diff --git a/...elecivity/spc_01/DATS_14_endo_ii_TZVP.log → ...lectivity/spc_01/DATS_14_endo_ii_TZVP.log b/...elecivity/spc_01/DATS_14_endo_ii_TZVP.log → ...lectivity/spc_01/DATS_14_endo_ii_TZVP.log
diff --git a/...lecivity/spc_01/DATS_14_endo_iii_TZVP.log → ...ectivity/spc_01/DATS_14_endo_iii_TZVP.log b/...lecivity/spc_01/DATS_14_endo_iii_TZVP.log → ...ectivity/spc_01/DATS_14_endo_iii_TZVP.log
diff --git a/...elecivity/spc_01/DATS_14_endo_iv_TZVP.log → ...lectivity/spc_01/DATS_14_endo_iv_TZVP.log b/...elecivity/spc_01/DATS_14_endo_iv_TZVP.log → ...lectivity/spc_01/DATS_14_endo_iv_TZVP.log
diff --git a/..._selecivity/spc_01/DATS_14_exo_i_TZVP.log → ...selectivity/spc_01/DATS_14_exo_i_TZVP.log b/..._selecivity/spc_01/DATS_14_exo_i_TZVP.log → ...selectivity/spc_01/DATS_14_exo_i_TZVP.log
diff --git a/...selecivity/spc_01/DATS_14_exo_ii_TZVP.log → ...electivity/spc_01/DATS_14_exo_ii_TZVP.log b/...selecivity/spc_01/DATS_14_exo_ii_TZVP.log → ...electivity/spc_01/DATS_14_exo_ii_TZVP.log
diff --git a/...elecivity/spc_01/DATS_14_exo_iii_TZVP.log → ...lectivity/spc_01/DATS_14_exo_iii_TZVP.log b/...elecivity/spc_01/DATS_14_exo_iii_TZVP.log → ...lectivity/spc_01/DATS_14_exo_iii_TZVP.log
diff --git a/...selecivity/spc_01/DATS_14_exo_iv_TZVP.log → ...electivity/spc_01/DATS_14_exo_iv_TZVP.log b/...selecivity/spc_01/DATS_14_exo_iv_TZVP.log → ...electivity/spc_01/DATS_14_exo_iv_TZVP.log
diff --git a/..._selecivity/spc_01/DATS_14_exo_v_TZVP.log → ...selectivity/spc_01/DATS_14_exo_v_TZVP.log b/..._selecivity/spc_01/DATS_14_exo_v_TZVP.log → ...selectivity/spc_01/DATS_14_exo_v_TZVP.log
diff --git a/...selecivity/spc_02/DATS_13_endo_i_TZVP.out → ...electivity/spc_02/DATS_13_endo_i_TZVP.out b/...selecivity/spc_02/DATS_13_endo_i_TZVP.out → ...electivity/spc_02/DATS_13_endo_i_TZVP.out
diff --git a/...elecivity/spc_02/DATS_13_endo_ii_TZVP.out → ...lectivity/spc_02/DATS_13_endo_ii_TZVP.out b/...elecivity/spc_02/DATS_13_endo_ii_TZVP.out → ...lectivity/spc_02/DATS_13_endo_ii_TZVP.out
diff --git a/...lecivity/spc_02/DATS_13_endo_iii_TZVP.out → ...ectivity/spc_02/DATS_13_endo_iii_TZVP.out b/...lecivity/spc_02/DATS_13_endo_iii_TZVP.out → ...ectivity/spc_02/DATS_13_endo_iii_TZVP.out
diff --git a/...elecivity/spc_02/DATS_13_endo_iv_TZVP.out → ...lectivity/spc_02/DATS_13_endo_iv_TZVP.out b/...elecivity/spc_02/DATS_13_endo_iv_TZVP.out → ...lectivity/spc_02/DATS_13_endo_iv_TZVP.out
diff --git a/..._selecivity/spc_02/DATS_13_exo_i_TZVP.out → ...selectivity/spc_02/DATS_13_exo_i_TZVP.out b/..._selecivity/spc_02/DATS_13_exo_i_TZVP.out → ...selectivity/spc_02/DATS_13_exo_i_TZVP.out
diff --git a/...selecivity/spc_02/DATS_13_exo_ii_TZVP.out → ...electivity/spc_02/DATS_13_exo_ii_TZVP.out b/...selecivity/spc_02/DATS_13_exo_ii_TZVP.out → ...electivity/spc_02/DATS_13_exo_ii_TZVP.out
diff --git a/...elecivity/spc_02/DATS_13_exo_iii_TZVP.out → ...lectivity/spc_02/DATS_13_exo_iii_TZVP.out b/...elecivity/spc_02/DATS_13_exo_iii_TZVP.out → ...lectivity/spc_02/DATS_13_exo_iii_TZVP.out
diff --git a/...selecivity/spc_02/DATS_13_exo_iv_TZVP.out → ...electivity/spc_02/DATS_13_exo_iv_TZVP.out b/...selecivity/spc_02/DATS_13_exo_iv_TZVP.out → ...electivity/spc_02/DATS_13_exo_iv_TZVP.out
diff --git a/...selecivity/spc_02/DATS_14_endo_i_TZVP.out → ...electivity/spc_02/DATS_14_endo_i_TZVP.out b/...selecivity/spc_02/DATS_14_endo_i_TZVP.out → ...electivity/spc_02/DATS_14_endo_i_TZVP.out
diff --git a/...elecivity/spc_02/DATS_14_endo_ii_TZVP.out → ...lectivity/spc_02/DATS_14_endo_ii_TZVP.out b/...elecivity/spc_02/DATS_14_endo_ii_TZVP.out → ...lectivity/spc_02/DATS_14_endo_ii_TZVP.out
diff --git a/...lecivity/spc_02/DATS_14_endo_iii_TZVP.out → ...ectivity/spc_02/DATS_14_endo_iii_TZVP.out b/...lecivity/spc_02/DATS_14_endo_iii_TZVP.out → ...ectivity/spc_02/DATS_14_endo_iii_TZVP.out
diff --git a/...elecivity/spc_02/DATS_14_endo_iv_TZVP.out → ...lectivity/spc_02/DATS_14_endo_iv_TZVP.out b/...elecivity/spc_02/DATS_14_endo_iv_TZVP.out → ...lectivity/spc_02/DATS_14_endo_iv_TZVP.out
diff --git a/..._selecivity/spc_02/DATS_14_exo_i_TZVP.out → ...selectivity/spc_02/DATS_14_exo_i_TZVP.out b/..._selecivity/spc_02/DATS_14_exo_i_TZVP.out → ...selectivity/spc_02/DATS_14_exo_i_TZVP.out
diff --git a/...selecivity/spc_02/DATS_14_exo_ii_TZVP.out → ...electivity/spc_02/DATS_14_exo_ii_TZVP.out b/...selecivity/spc_02/DATS_14_exo_ii_TZVP.out → ...electivity/spc_02/DATS_14_exo_ii_TZVP.out
diff --git a/...elecivity/spc_02/DATS_14_exo_iii_TZVP.out → ...lectivity/spc_02/DATS_14_exo_iii_TZVP.out b/...elecivity/spc_02/DATS_14_exo_iii_TZVP.out → ...lectivity/spc_02/DATS_14_exo_iii_TZVP.out
diff --git a/...selecivity/spc_02/DATS_14_exo_iv_TZVP.out → ...electivity/spc_02/DATS_14_exo_iv_TZVP.out b/...selecivity/spc_02/DATS_14_exo_iv_TZVP.out → ...electivity/spc_02/DATS_14_exo_iv_TZVP.out
diff --git a/..._selecivity/spc_02/DATS_14_exo_v_TZVP.out → ...selectivity/spc_02/DATS_14_exo_v_TZVP.out b/..._selecivity/spc_02/DATS_14_exo_v_TZVP.out → ...selectivity/spc_02/DATS_14_exo_v_TZVP.out
diff --git a/...elecivity/spc_03/DATS_13_endo_i_DLPNO.out → ...lectivity/spc_03/DATS_13_endo_i_DLPNO.out b/...elecivity/spc_03/DATS_13_endo_i_DLPNO.out → ...lectivity/spc_03/DATS_13_endo_i_DLPNO.out
diff --git a/...lecivity/spc_03/DATS_13_endo_ii_DLPNO.out → ...ectivity/spc_03/DATS_13_endo_ii_DLPNO.out b/...lecivity/spc_03/DATS_13_endo_ii_DLPNO.out → ...ectivity/spc_03/DATS_13_endo_ii_DLPNO.out
diff --git a/...ecivity/spc_03/DATS_13_endo_iii_DLPNO.out → ...ctivity/spc_03/DATS_13_endo_iii_DLPNO.out b/...ecivity/spc_03/DATS_13_endo_iii_DLPNO.out → ...ctivity/spc_03/DATS_13_endo_iii_DLPNO.out
diff --git a/...lecivity/spc_03/DATS_13_endo_iv_DLPNO.out → ...ectivity/spc_03/DATS_13_endo_iv_DLPNO.out b/...lecivity/spc_03/DATS_13_endo_iv_DLPNO.out → ...ectivity/spc_03/DATS_13_endo_iv_DLPNO.out
diff --git a/...selecivity/spc_03/DATS_13_exo_i_DLPNO.out → ...electivity/spc_03/DATS_13_exo_i_DLPNO.out b/...selecivity/spc_03/DATS_13_exo_i_DLPNO.out → ...electivity/spc_03/DATS_13_exo_i_DLPNO.out
diff --git a/...elecivity/spc_03/DATS_13_exo_ii_DLPNO.out → ...lectivity/spc_03/DATS_13_exo_ii_DLPNO.out b/...elecivity/spc_03/DATS_13_exo_ii_DLPNO.out → ...lectivity/spc_03/DATS_13_exo_ii_DLPNO.out
diff --git a/...lecivity/spc_03/DATS_13_exo_iii_DLPNO.out → ...ectivity/spc_03/DATS_13_exo_iii_DLPNO.out b/...lecivity/spc_03/DATS_13_exo_iii_DLPNO.out → ...ectivity/spc_03/DATS_13_exo_iii_DLPNO.out
diff --git a/...elecivity/spc_03/DATS_13_exo_iv_DLPNO.out → ...lectivity/spc_03/DATS_13_exo_iv_DLPNO.out b/...elecivity/spc_03/DATS_13_exo_iv_DLPNO.out → ...lectivity/spc_03/DATS_13_exo_iv_DLPNO.out
diff --git a/...elecivity/spc_03/DATS_14_endo_i_DLPNO.out → ...lectivity/spc_03/DATS_14_endo_i_DLPNO.out b/...elecivity/spc_03/DATS_14_endo_i_DLPNO.out → ...lectivity/spc_03/DATS_14_endo_i_DLPNO.out
diff --git a/...lecivity/spc_03/DATS_14_endo_ii_DLPNO.out → ...ectivity/spc_03/DATS_14_endo_ii_DLPNO.out b/...lecivity/spc_03/DATS_14_endo_ii_DLPNO.out → ...ectivity/spc_03/DATS_14_endo_ii_DLPNO.out
diff --git a/...ecivity/spc_03/DATS_14_endo_iii_DLPNO.out → ...ctivity/spc_03/DATS_14_endo_iii_DLPNO.out b/...ecivity/spc_03/DATS_14_endo_iii_DLPNO.out → ...ctivity/spc_03/DATS_14_endo_iii_DLPNO.out
diff --git a/...lecivity/spc_03/DATS_14_endo_iv_DLPNO.out → ...ectivity/spc_03/DATS_14_endo_iv_DLPNO.out b/...lecivity/spc_03/DATS_14_endo_iv_DLPNO.out → ...ectivity/spc_03/DATS_14_endo_iv_DLPNO.out
diff --git a/...selecivity/spc_03/DATS_14_exo_i_DLPNO.out → ...electivity/spc_03/DATS_14_exo_i_DLPNO.out b/...selecivity/spc_03/DATS_14_exo_i_DLPNO.out → ...electivity/spc_03/DATS_14_exo_i_DLPNO.out
diff --git a/...elecivity/spc_03/DATS_14_exo_ii_DLPNO.out → ...lectivity/spc_03/DATS_14_exo_ii_DLPNO.out b/...elecivity/spc_03/DATS_14_exo_ii_DLPNO.out → ...lectivity/spc_03/DATS_14_exo_ii_DLPNO.out
diff --git a/...lecivity/spc_03/DATS_14_exo_iii_DLPNO.out → ...ectivity/spc_03/DATS_14_exo_iii_DLPNO.out b/...lecivity/spc_03/DATS_14_exo_iii_DLPNO.out → ...ectivity/spc_03/DATS_14_exo_iii_DLPNO.out
diff --git a/...elecivity/spc_03/DATS_14_exo_iv_DLPNO.out → ...lectivity/spc_03/DATS_14_exo_iv_DLPNO.out b/...elecivity/spc_03/DATS_14_exo_iv_DLPNO.out → ...lectivity/spc_03/DATS_14_exo_iv_DLPNO.out
diff --git a/...selecivity/spc_03/DATS_14_exo_v_DLPNO.out → ...electivity/spc_03/DATS_14_exo_v_DLPNO.out b/...selecivity/spc_03/DATS_14_exo_v_DLPNO.out → ...electivity/spc_03/DATS_14_exo_v_DLPNO.out
diff --git a/goodvibes/io.py b/goodvibes/io.py
@@ -66,7 +66,7 @@ class Logger:
         log (file object): file to write GV output to.
         thermodata (bool): decides if string passed to logger is thermochemical data, needing to be separated by commas
     """
-    def __init__(self, filein, append, csv):
+    def __init__(self, filein, append='output', csv=False):
         self.csv = csv
         if not self.csv:
             suffix = 'dat'

diff --git a/goodvibes/pes.py b/goodvibes/pes.py
@@ -48,7 +48,7 @@ class get_pes:
         g_species_qhgzero (list):quasi-harmonic Gibbs free energy "zero" values used for graphing.
         g_rel_val (list): relative Gibbs free energy values used for graphing.
     """
-    def __init__(self, file, thermo_data, log, temperature, gconf, QH, cosmo=None, cosmo_int=None):
+    def __init__(self, file, thermo_data, log, temperature, gconf=True, QH=False, cosmo=None, cosmo_int=None):
         # Default values
         self.dec, self.units, self.boltz = 2, 'kcal/mol', False