From 269f3194a144f39dcf81bf5be4015a7308fec587 Mon Sep 17 00:00:00 2001 From: Daniel <46388253+dbkchu@users.noreply.github.com> Date: Fri, 7 Jun 2024 19:39:45 -0400 Subject: [PATCH 1/3] Default to short geometry name --- molSimplify/Scripts/inparse.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/molSimplify/Scripts/inparse.py b/molSimplify/Scripts/inparse.py index f354b24e..2e4a9c1c 100644 --- a/molSimplify/Scripts/inparse.py +++ b/molSimplify/Scripts/inparse.py @@ -140,7 +140,7 @@ def checkinput(args, calctype="base"): if args.coord and (not args.geometry or (args.geometry not in geomnames and args.geometry not in geomshorts)): print(('WARNING: No or unknown coordination geometry specified. Defining coordination geometry based on found coordination number: ' + globs.defaultgeometry[int(args.coord)][1])) - args.geometry = globs.defaultgeometry[int(args.coord)][0] + args.geometry = globs.defaultgeometry[int(args.coord)][1] if args.geometry and not args.coord: if args.geometry not in geomnames and args.geometry not in geomshorts: print( From 6e5bb9c2adc8545c975926fc3b2d20319e247383 Mon Sep 17 00:00:00 2001 From: dbkchu Date: Fri, 7 Jun 2024 19:42:42 -0400 Subject: [PATCH 2/3] Revert "Default to short geometry name" This reverts commit 269f3194a144f39dcf81bf5be4015a7308fec587. --- molSimplify/Scripts/inparse.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/molSimplify/Scripts/inparse.py b/molSimplify/Scripts/inparse.py index 2e4a9c1c..f354b24e 100644 --- a/molSimplify/Scripts/inparse.py +++ b/molSimplify/Scripts/inparse.py @@ -140,7 +140,7 @@ def checkinput(args, calctype="base"): if args.coord and (not args.geometry or (args.geometry not in geomnames and args.geometry not in geomshorts)): print(('WARNING: No or unknown coordination geometry specified. Defining coordination geometry based on found coordination number: ' + globs.defaultgeometry[int(args.coord)][1])) - args.geometry = globs.defaultgeometry[int(args.coord)][1] + args.geometry = globs.defaultgeometry[int(args.coord)][0] if args.geometry and not args.coord: if args.geometry not in geomnames and args.geometry not in geomshorts: print( From dee1d0cbd62cbbe0f6d74336da2d28375edf7b0f Mon Sep 17 00:00:00 2001 From: dbkchu Date: Fri, 7 Jun 2024 19:44:46 -0400 Subject: [PATCH 3/3] fix ordering of shortnames and names --- molSimplify/Classes/globalvars.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/molSimplify/Classes/globalvars.py b/molSimplify/Classes/globalvars.py index 8f72cbf5..b2620a24 100644 --- a/molSimplify/Classes/globalvars.py +++ b/molSimplify/Classes/globalvars.py @@ -600,7 +600,7 @@ def __init__(self): # Default geometries for each coordination number if none specified self.defaultgeometry = {8: ('sqap', 'square_antiprismatic'), 7: ('pbp', 'pentagonal_bipyramidal'), 6: ('oct', 'octahedral'), 5: ('tbp', 'trigonal bipyramidal'), 4: ('thd', 'tetrahedral'), - 3: ('trigonal planar', 'tpl'), 2: ('linear', 'li'), 1: ('one', 'one')} + 3: ('tpl', 'trigonal planar'), 2: ('li', 'linear'), 1: ('one', 'one')} # Default oxidation states for elements self.defaultoxstate = { 'au': 'I', 'gold': 'I', 'scandium': 'III', 'sc': 'III', 'ti': 'IV', 'titanium': 'IV'}