devel (#12)

• work in progress: automatic supporting information (SI) generation (with bib entries)
• new printout showing the number of conformers within an energy window
• symmetry number correction (for part1) because of (DFT) unoptimized geometries
• the configuration file location information is saved and automatically reloaded on restart
• printing command line argument call at program startup
• experimental “read only” feature to fill the enso.json information by only reading the output of previous calculations (the program input arguments have to be exactly the same!)
• fixed NMR shielding constant calculations and MORead
• NMR new printout of min and max calculated shielding constants per investigated nuclei
• OR new printout of min and max OR value and corresponding conformers
• fixed balance option and wrong xtb call
• improved restarting of optical rotation calculations
• tutorial option has details on solvents and naming within CENSO, and information on functionals for OR is updated
• improved optimization routine

censo_qm/adf_job.py

@@ -1,3 +1,3 @@
 # adf_job.py
 
-# for J and S calculation only
+# for J and S calculation only

censo_qm/censo.py

@@ -62,7 +62,7 @@ def main(argv=None):
             sys.exit(1)
         toc = perf_counter()
         ensembledata.part_info["part0"] = toc - tic
-        ensembledata.previous_part_info["part0"] +=  ensembledata.part_info["part0"]
+        ensembledata.previous_part_info["part0"] += ensembledata.part_info["part0"]
         print(f"Ran part0 in {ensembledata.part_info['part0']:0.4f} seconds")
 
     # RUNNING PART1
@@ -87,7 +87,9 @@ def main(argv=None):
         toc = perf_counter()
         ensembledata.part_info["part1"] = toc - tic
         ensembledata.previous_part_info["part1"] += ensembledata.part_info["part1"]
-        ensembledata.previous_part_info["part1_firstsort"] += ensembledata.part_info["part1_firstsort"]
+        ensembledata.previous_part_info["part1_firstsort"] += ensembledata.part_info[
+            "part1_firstsort"
+        ]
         print(f"Ran part1 in {ensembledata.part_info['part1']:0.4f} seconds")
 
     # RUNNING PART2
@@ -112,7 +114,9 @@ def main(argv=None):
         toc = perf_counter()
         ensembledata.part_info["part2"] = toc - tic
         ensembledata.previous_part_info["part2"] += ensembledata.part_info["part2"]
-        ensembledata.previous_part_info["part2_opt"] += ensembledata.part_info["part2_opt"]
+        ensembledata.previous_part_info["part2_opt"] += ensembledata.part_info[
+            "part2_opt"
+        ]
         print(f"Ran part2 in {ensembledata.part_info['part2']:0.4f} seconds")
 
     # RUNNING PART3
@@ -196,6 +200,9 @@ def main(argv=None):
         config.provide_runinfo(),
     )
 
+    if args.create_si:
+        config.create_SI(ensembledata)
+
     # END of CENSO
     timings = 0.0
     prev_timings = 0.0
@@ -208,44 +215,47 @@ def main(argv=None):
         tmp = []
         tmp_prev = []
         if config.part0:
-            tmp.append(ensembledata.part_info['part0'])
-            tmp_prev.append(ensembledata.previous_part_info['part0'])
+            tmp.append(ensembledata.part_info["part0"])
+            tmp_prev.append(ensembledata.previous_part_info["part0"])
         if config.part1:
-            tmp.append(ensembledata.part_info['part1'])
-            tmp_prev.append(ensembledata.previous_part_info['part1'])
-            tmp_prev.append(ensembledata.previous_part_info['part1_firstsort'])
+            tmp.append(ensembledata.part_info["part1"])
+            tmp_prev.append(ensembledata.previous_part_info["part1"])
+            tmp_prev.append(ensembledata.previous_part_info["part1_firstsort"])
         if config.part2:
-            tmp.append(ensembledata.part_info['part2'])
-            tmp_prev.append(ensembledata.previous_part_info['part2'])
-            tmp.append(ensembledata.part_info['part2_opt'])
-            tmp_prev.append(ensembledata.previous_part_info['part2_opt'])
+            tmp.append(ensembledata.part_info["part2"])
+            tmp_prev.append(ensembledata.previous_part_info["part2"])
+            tmp.append(ensembledata.part_info["part2_opt"])
+            tmp_prev.append(ensembledata.previous_part_info["part2_opt"])
         if config.part3:
-            tmp.append(ensembledata.part_info['part3'])
-            tmp_prev.append(ensembledata.previous_part_info['part3'])
+            tmp.append(ensembledata.part_info["part3"])
+            tmp_prev.append(ensembledata.previous_part_info["part3"])
         if config.part4:
-            tmp.append(ensembledata.part_info['part4'])
-            tmp_prev.append(ensembledata.previous_part_info['part4'])
+            tmp.append(ensembledata.part_info["part4"])
+            tmp_prev.append(ensembledata.previous_part_info["part4"])
         if config.optical_rotation:
-            tmp.append(ensembledata.part_info['part5'])             
-            tmp_prev.append(ensembledata.previous_part_info['part5'])
-        timelen = max([len(f"{float(value):.2f}") for value in tmp]) +2
-        prev_timelen = max([len(f"{float(value):.2f}") for value in tmp_prev]) +2
+            tmp.append(ensembledata.part_info["part5"])
+            tmp_prev.append(ensembledata.previous_part_info["part5"])
+        timelen = max([len(f"{float(value):.2f}") for value in tmp]) + 2
+        prev_timelen = max([len(f"{float(value):.2f}") for value in tmp_prev]) + 2
         if timelen < 7:
             timelen = 7
     except Exception:
         timelen = 20
         prev_timelen = 20
 
-
-    print(f"\n\n{'Part':20}: {'#conf':>{conflength}}    {'time': >{timelen}}      time (including restarts)")
-    print("".ljust(int(PLENGTH/1.4), "-"))
-    print(f"{'Input':20}: {ensembledata.nconfs_per_part['starting']:{conflength}}    {'-':^{timelen+2}}    {'-':^{timelen+2}}")
+    print(
+        f"\n\n{'Part':20}: {'#conf':>{conflength}}    {'time': >{timelen}}      time (including restarts)"
+    )
+    print("".ljust(int(PLENGTH / 1.4), "-"))
+    print(
+        f"{'Input':20}: {ensembledata.nconfs_per_part['starting']:{conflength}}    {'-':^{timelen+2}}    {'-':^{timelen+2}}"
+    )
     if config.part0:
         print(
             f"{'Part0_all':20}: {ensembledata.nconfs_per_part['part0']:{conflength}}    {ensembledata.part_info['part0']:{timelen}.2f} s  {ensembledata.previous_part_info['part0']:>{prev_timelen}.2f} s"
         )
         timings += ensembledata.part_info["part0"]
-        prev_timings += ensembledata.previous_part_info['part0']
+        prev_timings += ensembledata.previous_part_info["part0"]
     if config.part1:
         print(
             f"{'Part1_initial_sort':20}: {ensembledata.nconfs_per_part['part1_firstsort']:{conflength}}    {ensembledata.part_info['part1_firstsort']:{timelen}.2f} s  {ensembledata.previous_part_info['part1_firstsort']:>{prev_timelen}.2f} s"
@@ -254,7 +264,7 @@ def main(argv=None):
             f"{'Part1_all':20}: {ensembledata.nconfs_per_part['part1_firstsort']:{conflength}}    {ensembledata.part_info['part1']:{timelen}.2f} s  {ensembledata.previous_part_info['part1']:>{prev_timelen}.2f} s"
         )
         timings += ensembledata.part_info["part1"]
-        prev_timings += ensembledata.previous_part_info['part1']
+        prev_timings += ensembledata.previous_part_info["part1"]
     if config.part2:
         print(
             f"{'Part2_opt':20}: {ensembledata.nconfs_per_part['part2_opt']:{conflength}}    {ensembledata.part_info['part2_opt']:{timelen}.2f} s  {ensembledata.previous_part_info['part2_opt']:>{prev_timelen}.2f} s"
@@ -263,26 +273,28 @@ def main(argv=None):
             f"{'Part2_all':20}: {ensembledata.nconfs_per_part['part2']:{conflength}}    {ensembledata.part_info['part2']:{timelen}.2f} s  {ensembledata.previous_part_info['part2']:>{prev_timelen}.2f} s"
         )
         timings += ensembledata.part_info["part2"]
-        prev_timings += ensembledata.previous_part_info['part2']
+        prev_timings += ensembledata.previous_part_info["part2"]
     if config.part3:
         print(
             f"{'Part3_all':20}: {ensembledata.nconfs_per_part['part3']:{conflength}}    {ensembledata.part_info['part3']:{timelen}.2f} s  {ensembledata.previous_part_info['part3']:>{prev_timelen}.2f} s"
         )
         timings += ensembledata.part_info["part3"]
-        prev_timings += ensembledata.previous_part_info['part3']
+        prev_timings += ensembledata.previous_part_info["part3"]
     if config.part4:
         print(
             f"{'Part4':20}: {'':{conflength}}    {ensembledata.part_info['part4']:{timelen}.2f} s  {ensembledata.previous_part_info['part4']:>{prev_timelen}.2f} s"
         )
         timings += ensembledata.part_info["part4"]
-        prev_timings += ensembledata.previous_part_info['part4']
+        prev_timings += ensembledata.previous_part_info["part4"]
     if config.optical_rotation:
         print(
             f"{'Part5':20}: {'':{conflength}}    {ensembledata.part_info['part5']:{timelen}.2f} s  {ensembledata.previous_part_info['part5']:>{prev_timelen}.2f} s"
         )
         timings += ensembledata.part_info["part5"]
-        prev_timings += ensembledata.previous_part_info['part5']
+        prev_timings += ensembledata.previous_part_info["part5"]
     print("".ljust(int(PLENGTH / 1.4), "-"))
-    print(f"{'All parts':20}: {'-':>{conflength}}    {timings:{timelen}.2f} s  {prev_timings:{prev_timelen}.2f} s")
+    print(
+        f"{'All parts':20}: {'-':>{conflength}}    {timings:{timelen}.2f} s  {prev_timings:{prev_timelen}.2f} s"
+    )
     print("\nCENSO all done!")
     return 0