From daa10e2a68913ba1f215567217b88f4e0d48162e Mon Sep 17 00:00:00 2001 From: davidfarinajr Date: Mon, 26 Jul 2021 12:09:17 -0400 Subject: [PATCH] removed metal and facet from surface thermo group entries Since we now consider metal attrs when descending the tree, these need to be removed from thermo group entries --- input/thermo/groups/adsorptionNi111.py | 62 ++--- input/thermo/groups/adsorptionPt111.py | 298 +++++++------------------ 2 files changed, 92 insertions(+), 268 deletions(-) diff --git a/input/thermo/groups/adsorptionNi111.py b/input/thermo/groups/adsorptionNi111.py index aeda5f7874..2249c69685 100644 --- a/input/thermo/groups/adsorptionNi111.py +++ b/input/thermo/groups/adsorptionNi111.py @@ -2,6 +2,8 @@ # encoding: utf-8 name = "Surface Adsorption Corrections Ni(111)" +metal = 'Ni' +facet = '111' shortDesc = u"Surface adsorption Ni(111), Goldsmith 2016" longDesc = u""" Changes due to adsorbing on a surface. @@ -23,9 +25,7 @@ x *********** This node should be empty, ensuring that one of the nodes below is used. -""", - metal = "Ni", - facet = "111", +""" ) entry( @@ -48,9 +48,7 @@ x <--(single, double, triple, or quadruple bond) ******** Data made up. Do not use! -""", - metal = "Ni", - facet = "111", +""" ) entry( @@ -78,9 +76,7 @@ This binds too strongly and won't desorb until ~2500K, so we're trying -2 kcal/mol and -15 cal/mol/K -""", - metal = "Ni", - facet = "111", +""" ) @@ -99,9 +95,7 @@ C x *********** -""", - metal = "Ni", - facet = "111", +""" ) entry( @@ -118,9 +112,7 @@ O x *********** -""", - metal = "Ni", - facet = "111", +""" ) @@ -144,9 +136,7 @@ R-C ||| *********** -""", - metal = "Ni", - facet = "111", +""" ) entry( @@ -170,9 +160,7 @@ R-C-R || *********** -""", - metal = "Ni", - facet = "111", +""" ) entry( @@ -199,9 +187,7 @@ R-C-R | *********** -""", - metal = "Ni", - facet = "111", +""" ) entry( @@ -222,9 +208,7 @@ R2-C-R2 : *********** -""", - metal = "Ni", - facet = "111", +""" ) entry( @@ -243,9 +227,7 @@ R-O-R : *********** -""", - metal = "Ni", - facet = "111", +""" ) entry( @@ -269,9 +251,7 @@ R--C--R || | *********** -""", - metal = "Ni", - facet = "111", +""" ) entry( @@ -322,9 +302,7 @@ R2--C--R | | *********** -""", - metal = "Ni", - facet = "111", +""" ) entry( @@ -407,9 +385,7 @@ R-C-OR | *********** -""", - metal = "Ni", - facet = "111", +""" ) entry( @@ -433,9 +409,7 @@ O-R : *********** -""", - metal = "Ni", - facet = "111", +""" ) entry( @@ -461,9 +435,7 @@ RO--C--R || | *********** -""", - metal = "Ni", - facet = "111", +""" ) tree( diff --git a/input/thermo/groups/adsorptionPt111.py b/input/thermo/groups/adsorptionPt111.py index b43cbf25d0..9626acbab4 100755 --- a/input/thermo/groups/adsorptionPt111.py +++ b/input/thermo/groups/adsorptionPt111.py @@ -3,6 +3,8 @@ name = "Surface Adsorption Corrections Pt(111)" shortDesc = u"Surface adsorption Pt(111), Blondal 2018" +metal = 'Pt' +facet = '111' longDesc = u""" Changes due to adsorbing on a surface. Here, Pt(111) @@ -35,9 +37,7 @@ do not like that. It should be OK, because things would check the tree in order, and if there *was* a bond it would match either R*bidentate or R*single_chemisorbed and thus not R*vdW. -""", - metal = "Pt", - facet = "111", +""" ) #entry( @@ -123,9 +123,7 @@ RO-R : *********** -""", - metal = "Pt", - facet = "111", +""" ) entry( @@ -153,9 +151,7 @@ O | *********** -""", - metal = "Pt", - facet = "111", +""" ) entry( @@ -184,9 +180,7 @@ RO-OR : *********** -""", - metal = "Pt", - facet = "111", +""" ) entry( @@ -213,9 +207,7 @@ O--O | | ***** ***** -""", - metal = "Pt", - facet = "111", +""" ) entry( @@ -244,9 +236,7 @@ O | *********** -""", - metal = "Pt", - facet = "111", +""" ) entry( @@ -271,9 +261,7 @@ O || *********** -""", - metal = "Pt", - facet = "111", +""" ) entry( @@ -303,9 +291,7 @@ O | *********** -""", - metal = "Pt", - facet = "111", +""" ) entry( @@ -336,9 +322,7 @@ O | *********** -""", - metal = "Pt", - facet = "111", +""" ) entry( @@ -366,9 +350,7 @@ R2N-R : *********** -""", - metal = "Pt", - facet = "111", +""" ) entry( @@ -394,9 +376,7 @@ NR2 | *********** -""", - metal = "Pt", - facet = "111", +""" ) entry( @@ -422,9 +402,7 @@ NR || *********** -""", - metal = "Pt", - facet = "111", +""" ) entry( @@ -449,9 +427,7 @@ N ||| *********** -""", - metal = "Pt", - facet = "111", +""" ) entry( @@ -481,9 +457,7 @@ R2N-OR : *********** -""", - metal = "Pt", - facet = "111", +""" ) entry( @@ -510,9 +484,7 @@ RN=O : *********** -""", - metal = "Pt", - facet = "111", +""" ) entry( @@ -540,9 +512,7 @@ R-N-OR | *********** -""", - metal = "Pt", - facet = "111", +""" ) entry( @@ -570,9 +540,7 @@ N | *********** -""", - metal = "Pt", - facet = "111", +""" ) entry( @@ -599,9 +567,7 @@ N--O || | *********** -""", - metal = "Pt", - facet = "111", +""" ) entry( @@ -630,9 +596,7 @@ N || *********** -""", - metal = "Pt", - facet = "111", +""" ) entry( @@ -663,9 +627,7 @@ R2N-NR2 : *********** -""", - metal = "Pt", - facet = "111", +""" ) entry( @@ -693,9 +655,7 @@ RN=NR : *********** -""", - metal = "Pt", - facet = "111", +""" ) @@ -752,9 +712,7 @@ R-N-NR2 | *********** -""", - metal = "Pt", - facet = "111", +""" ) entry( @@ -783,9 +741,7 @@ N | *********** -""", - metal = "Pt", - facet = "111", +""" ) entry( @@ -815,9 +771,7 @@ N || *********** -""", - metal = "Pt", - facet = "111", +""" ) entry( @@ -846,9 +800,7 @@ RN--NR | | *********** -""", - metal = "Pt", - facet = "111", +""" ) entry( @@ -878,9 +830,7 @@ R-N-CR3 | *********** -""", - metal = "Pt", - facet = "111", +""" ) entry( @@ -910,9 +860,7 @@ N | *********** -""", - metal = "Pt", - facet = "111", +""" ) entry( @@ -943,9 +891,7 @@ N || *********** -""", - metal = "Pt", - facet = "111", +""" ) ### Leads to AtomTypeError: Unable to determine atom type for atom O-, which has 3 single bonds, 0 double bonds to C, 0 double bonds to O, 0 double bonds to S, 0 triple bonds, 0 benzene bonds, 0 lone pairs, and 2 charge. @@ -1001,9 +947,7 @@ C |||| *********** -""", - metal = "Pt", - facet = "111", +""" ) entry( @@ -1030,9 +974,7 @@ C--C | | *********** -""", - metal = "Pt", - facet = "111", +""" ) entry( @@ -1063,9 +1005,7 @@ Because the C atom bonded to the surface only has one ligand not two, it is not a child of the C=*R2 node -""", - metal = "Pt", - facet = "111", +""" ) entry( @@ -1096,9 +1036,7 @@ C ||| *********** -""", - metal = "Pt", - facet = "111", +""" ) entry( @@ -1126,9 +1064,7 @@ C ||| *********** -""", - metal = "Pt", - facet = "111", +""" ) entry( @@ -1157,9 +1093,7 @@ R-C--C-R || || *********** -""", - metal = "Pt", - facet = "111", +""" ) entry( @@ -1186,9 +1120,7 @@ R-C-R || *********** -""", - metal = "Pt", - facet = "111", +""" ) entry( @@ -1219,9 +1151,7 @@ R2C--CR2 | | *********** -""", - metal = "Pt", - facet = "111", +""" ) entry( @@ -1248,9 +1178,7 @@ CR3 | *********** -""", - metal = "Pt", - facet = "111", +""" ) entry( @@ -1283,9 +1211,7 @@ R3C-CR3 : *********** -""", - metal = "Pt", - facet = "111", +""" ) entry( @@ -1315,9 +1241,7 @@ R3C-R : *********** -""", - metal = "Pt", - facet = "111", +""" ) entry( @@ -1344,9 +1268,7 @@ C==N || | *********** -""", - metal = "Pt", - facet = "111", +""" ) entry( @@ -1375,9 +1297,7 @@ C || *********** -""", - metal = "Pt", - facet = "111", +""" ) entry( @@ -1407,9 +1327,7 @@ C ||| *********** -""", - metal = "Pt", - facet = "111", +""" ) @@ -1470,9 +1388,7 @@ C ||| *********** -""", - metal = "Pt", - facet = "111", +""" ) entry( @@ -1502,9 +1418,7 @@ R2C--CR | || *********** -""", - metal = "Pt", - facet = "111", +""" ) entry( @@ -1537,9 +1451,7 @@ R-C-CR3 | *********** -""", - metal = "Pt", - facet = "111", +""" ) entry( @@ -1569,9 +1481,7 @@ R2C=NR : *********** -""", - metal = "Pt", - facet = "111", +""" ) entry( @@ -1603,9 +1513,7 @@ R-C-NR2 | *********** -""", - metal = "Pt", - facet = "111", +""" ) entry( @@ -1633,9 +1541,7 @@ R2C=O : *********** -""", - metal = "Pt", - facet = "111", +""" ) entry( @@ -1666,9 +1572,7 @@ R-C-OR | *********** -""", - metal = "Pt", - facet = "111", +""" ) entry( @@ -1700,9 +1604,7 @@ R3C-NR2 : *********** -""", - metal = "Pt", - facet = "111", +""" ) entry( @@ -1733,9 +1635,7 @@ R3C-OR : *********** -""", - metal = "Pt", - facet = "111", +""" ) entry( @@ -1763,9 +1663,7 @@ RC--C | || *********** -""", - metal = "Pt", - facet = "111", +""" ) entry( @@ -1796,9 +1694,7 @@ C-R | *********** -""", - metal = "Pt", - facet = "111", +""" ) entry( @@ -1830,9 +1726,7 @@ C-R || *********** -""", - metal = "Pt", - facet = "111", +""" ) entry( @@ -1860,9 +1754,7 @@ RC#N : *********** -""", - metal = "Pt", - facet = "111", +""" ) entry( @@ -1892,9 +1784,7 @@ C--N || || *********** -""", - metal = "Pt", - facet = "111", +""" ) entry( @@ -1924,9 +1814,7 @@ C-R | *********** -""", - metal = "Pt", - facet = "111", +""" ) entry( @@ -1955,9 +1843,7 @@ RC--NR || | *********** -""", - metal = "Pt", - facet = "111", +""" ) entry( @@ -1988,9 +1874,7 @@ C-R || *********** -""", - metal = "Pt", - facet = "111", +""" ) entry( @@ -2019,9 +1903,7 @@ C=O | *********** -""", - metal = "Pt", - facet = "111", +""" ) entry( @@ -2051,9 +1933,7 @@ C--O || | *********** -""", - metal = "Pt", - facet = "111", +""" ) entry( @@ -2083,9 +1963,7 @@ C-R || *********** -""", - metal = "Pt", - facet = "111", +""" ) entry( @@ -2138,9 +2016,7 @@ H298=(-48.58, 'kcal/mol'), S298=(-38.17, 'cal/(mol*K)'), ), - shortDesc=u"""Average of C-*R3, N-*R2 and O-*R thermo. """, - metal = "Pt", - facet = "111", + shortDesc=u"""Average of C-*R3, N-*R2 and O-*R thermo. """ ) entry( @@ -2214,9 +2090,7 @@ H298=(-45.455, 'kcal/mol'), S298=(-43.39, 'cal/(mol*K)'), ), - shortDesc=u"""Average of C-*R2C-*R2, C=*RN-*R, C=*RO-* and N-*RN-*R thermo. """, - metal = "Pt", - facet = "111", + shortDesc=u"""Average of C-*R2C-*R2, C=*RN-*R, C=*RO-* and N-*RN-*R thermo. """ ) entry( @@ -2233,9 +2107,7 @@ H298=(-7.937, 'kcal/mol'), S298=(-20.48, 'cal/(mol*K)'), ), - shortDesc=u"""Average of (CR4)*, (NR3)* and (OR2)* thermo. """, - metal = "Pt", - facet = "111", + shortDesc=u"""Average of (CR4)*, (NR3)* and (OR2)* thermo. """ ) entry( @@ -2249,9 +2121,7 @@ 4 O u0 p2 c0 {2,[S,D]} {3,[S,D]} """, thermo=u'N=*O-*', - longDesc=u"""Is there really any way to do N*O* besides N=*O-* ?""", - metal = "Pt", - facet = "111", + longDesc=u"""Is there really any way to do N*O* besides N=*O-* ?""" ) #entry( @@ -2295,8 +2165,6 @@ 2 N u0 p1 {1,T} """, thermo=u'N*', - metal = "Pt", - facet = "111", ) entry( index = 80, @@ -2326,8 +2194,6 @@ 4 R u0 {2,S} """, thermo=u'(CRN)*', - metal = "Pt", - facet = "111", ) entry( @@ -2341,9 +2207,7 @@ 4 R u0 {2,S} """, thermo=u'(NRO)*', - longDesc=u"""Parent of (RN=O)* and (RN=NR)*. Should it be an average?""", - metal = "Pt", - facet = "111", + longDesc=u"""Parent of (RN=O)* and (RN=NR)*. Should it be an average?""" ) entry( @@ -2371,9 +2235,7 @@ RN--N | | *********** -""", - metal = "Pt", - facet = "111", +""" ) entry( @@ -2402,9 +2264,7 @@ RC#CR : *********** -""", - metal = "Pt", - facet = "111", +""" ) entry( @@ -2433,9 +2293,7 @@ R2C--N | || *********** -""", - metal = "Pt", - facet = "111", +""" ) entry( @@ -2465,9 +2323,7 @@ R2C--NR | | *********** -""", - metal = "Pt", - facet = "111", +""" ) entry( @@ -2498,9 +2354,7 @@ Because the C atom bonded to the surface only has one ligand not two, it is not a child of the C=*R2 node -""", - metal = "Pt", - facet = "111", +""" ) entry( @@ -2530,9 +2384,7 @@ R2C--O | | *********** -""", - metal = "Pt", - facet = "111", +""" ) entry(