diff --git a/rmgpy/chemkin.pyx b/rmgpy/chemkin.pyx index 864c7f9dc68..d28ee47ce08 100644 --- a/rmgpy/chemkin.pyx +++ b/rmgpy/chemkin.pyx @@ -951,7 +951,7 @@ def load_transport_file(path, species_dict, skip_missing_species=False): continue species = species_dict[label] species.transport_data = TransportData( - shapeIndex=int(data[0]), + shapeIndex=int(float(data[0])), sigma=(float(data[2]), 'angstrom'), epsilon=(float(data[1]), 'K'), dipoleMoment=(float(data[3]), 'De'), @@ -1035,15 +1035,16 @@ def load_chemkin_file(path, dictionary_path=None, transport_path=None, read_comm # Read in the thermo data from the thermo file if thermo_path: with open(thermo_path, 'r') as f: - line0 = f.readline() + line0 = None while line0 != '': - line = remove_comment_from_line(line0)[0] - line = line.strip() + previous_line = f.tell() + line0 = f.readline() + line = remove_comment_from_line(line0)[0].strip() if 'THERM' in line.upper(): - f.seek(-len(line0), 1) + f.seek(previous_line) read_thermo_block(f, species_dict) break - line0 = f.readline() + # Index the reactions now to have identical numbering as in Chemkin index = 0 for reaction in reaction_list: diff --git a/rmgpy/data/test_data/thermo/groups/adsorptionPt111.py b/rmgpy/data/test_data/thermo/groups/adsorptionPt111.py deleted file mode 100755 index afa1d6893df..00000000000 --- a/rmgpy/data/test_data/thermo/groups/adsorptionPt111.py +++ /dev/null @@ -1,2263 +0,0 @@ -#!/usr/bin/env python -# encoding: utf-8 - -name = "Surface Adsorption Corrections" -shortDesc = "" -longDesc = """ -Changes due to adsorbing on a surface. -Here, Pt(111) -Note: "-h" means "horizontal". -""" - -entry( - index = 1, - label = "R*", - group= -""" -1 R u0 -2 X u0 -""", - thermo=None, - shortDesc="""Anything adsorbed anyhow.""", - longDesc=""" - R - x -*********** -This node should be empty, ensuring that one of the nodes below is used. -""", - metal="Pt", - facet="111", -) - -entry( - index = 1, - label = "R-*", - group = -""" -1 X u0 p0 c0 {2,S} -2 R u0 p0 c0 {1,S} -""", - thermo=ThermoData( - Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([-3.01, -1.78, -0.96, -0.41, 0.23, 0.56, 0.91], 'cal/(mol*K)'), - H298=(-86.29, 'kcal/mol'), - S298=(-26.39, 'cal/(mol*K)'), - ), - shortDesc="""Came from H single-bonded on Pt(111)""", - longDesc="""Calculated by Katrin Blondal at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). Based on DFT calculations by Jelena Jelic at KIT. - - R - | -*********** -""", - metal="Pt", - facet="111", -) - -entry( - index = 2, - label = "(R2)*", - group = -""" -1 X u0 p0 c0 -2 R u0 p0 c0 {3,S} -3 R u0 p0 c0 {2,S} -""", - thermo=ThermoData( - Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([1.13, 1.17, 1.19, 1.2, 1.21, 1.21, 1.22], 'cal/(mol*K)'), - H298=(-1.22, 'kcal/mol'), - S298=(-7.73, 'cal/(mol*K)'), - ), - shortDesc="""Came from H2 vdW-bonded on Pt(111)""", - longDesc="""Calculated by Katrin Blondal at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). Based on DFT calculations by Jelena Jelic at KIT. - - R-R - : -*********** -""", - metal="Pt", - facet="111", -) - -entry( - index = 3, - label = "(OR2)*", - group = -""" -1 X u0 p0 c0 -2 O u0 p2 c0 {3,S} {4,S} -3 R u0 p0 c0 {2,S} -4 R u0 p0 c0 {2,S} -""", - thermo=ThermoData( - Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([0.88, 1.49, 1.82, 2.02, 2.22, 2.33, 2.43], 'cal/(mol*K)'), - H298=(-4.85, 'kcal/mol'), - S298=(-22.53, 'cal/(mol*K)'), - ), - shortDesc="""Came from H2O vdW-bonded on Pt(111)""", - longDesc="""Calculated by Katrin Blondal at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). Based on DFT calculations by Jelena Jelic at KIT. - - RO-R - : -*********** -""", - metal="Pt", - facet="111", -) - -entry( - index = 4, - label = "O-*R", - group = -""" -1 X u0 p0 c0 {2,S} -2 O u0 p2 c0 {1,S} {3,S} -3 R u0 p0 c0 {2,S} -""", - thermo=ThermoData( - Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([1.34, 2.23, 2.7, 2.97, 3.25, 3.38, 3.5], 'cal/(mol*K)'), - H298=(-46.18, 'kcal/mol'), - S298=(-33.89, 'cal/(mol*K)'), - ), - shortDesc="""Came from OH single-bonded on Pt(111)""", - longDesc="""Calculated by Katrin Blondal at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). Based on DFT calculations by Jelena Jelic at KIT. - - R - | - O - | -*********** -""", - metal="Pt", - facet="111", -) - -entry( - index = 5, - label = "(OROR)*", - group = -""" -1 X u0 p0 c0 -2 O u0 p2 c0 {3,S} {4,S} -3 O u0 p2 c0 {2,S} {5,S} -4 R u0 p0 c0 {2,S} -5 R u0 p0 c0 {3,S} -""", - thermo=ThermoData( - Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([1.85, 2.13, 2.27, 2.35, 2.45, 2.51, 2.57], 'cal/(mol*K)'), - H298=(-6.72, 'kcal/mol'), - S298=(-26.31, 'cal/(mol*K)'), - ), - shortDesc="""Came from HO-OH vdW-bonded on Pt(111)""", - longDesc="""Calculated by Katrin Blondal at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). Based on DFT calculations by Jelena Jelic at KIT. - - RO-OR - : -*********** -""", - metal="Pt", - facet="111", -) - -entry( - index = 6, - label = "O-*O-*", - group = -""" -1 X u0 p0 c0 {2,S} {3,S} -2 X u0 p0 c0 {1,S} {4,S} -3 O u0 p2 c0 {1,S} {4,S} -4 O u0 p2 c0 {2,S} {3,S} -""", - thermo=ThermoData( - Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([2.43, 3.46, 3.9, 4.05, 4.07, 4.0, 3.85], 'cal/(mol*K)'), - H298=(-8.59, 'kcal/mol'), - S298=(-40.49, 'cal/(mol*K)'), - ), - shortDesc="""Came from O2 bidentate, twice single-bonded on Pt(111)""", - longDesc="""Calculated by Katrin Blondal at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). Based on DFT calculations by Jelena Jelic at KIT. - - O--O - | | -*********** -""", - metal="Pt", - facet="111", -) - -entry( - index = 7, - label = "O-*OR", - group = -""" -1 X u0 p0 c0 {2,S} -2 O u0 p2 c0 {1,S} {3,S} -3 O u0 p2 c0 {2,S} {4,S} -4 R u0 p0 c0 {3,S} -""", - thermo=ThermoData( - Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([2.69, 3.13, 3.18, 3.12, 2.92, 2.76, 2.56], 'cal/(mol*K)'), - H298=(-17.47, 'kcal/mol'), - S298=(-31.56, 'cal/(mol*K)'), - ), - shortDesc="""Came from OOH single-bonded on Pt(111)""", - longDesc="""Calculated by Katrin Blondal at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). Based on DFT calculations by Jelena Jelic at KIT. - - OR - | - O - | -*********** -""", - metal="Pt", - facet="111", -) - -entry( - index = 8, - label = "O=*", - group = -""" -1 X u0 p0 c0 {2,D} -2 O u0 p2 c0 {1,D} -""", - thermo=ThermoData( - Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([-0.39, 0.26, 0.58, 0.77, 0.96, 1.05, 1.14], 'cal/(mol*K)'), - H298=(-99.97, 'kcal/mol'), - S298=(-30.95, 'cal/(mol*K)'), - ), - shortDesc="""Came from O double-bonded on Pt(111)""", - longDesc="""Calculated by Katrin Blondal at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). Based on DFT calculations by Jelena Jelic at KIT. - - O - || -*********** -""", - metal="Pt", - facet="111", -) - -entry( - index = 9, - label = "O-*NR2", - group = -""" -1 X u0 p0 c0 {3,S} -2 N u0 p1 c0 {3,S} {4,S} {5,S} -3 O u0 p2 c0 {1,S} {2,S} -4 R u0 p0 c0 {2,S} -5 R u0 p0 c0 {2,S} -""", - thermo=ThermoData( - Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([0.33, 1.18, 1.65, 1.93, 2.2, 2.32, 2.41], 'cal/(mol*K)'), - H298=(-16.75, 'kcal/mol'), - S298=(-33.37, 'cal/(mol*K)'), - ), - shortDesc="""Came from O-NH2 single-bonded on Pt(111)""", - longDesc="""Calculated by Katrin Blondal at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). Based on DFT calculations by Jelena Jelic at KIT. - - NR2 - | - O - | -*********** -""", - metal="Pt", - facet="111", -) - -entry( - index = 10, - label = "O-*CR3", - group = -""" -1 X u0 p0 c0 {3,S} -2 C u0 p0 c0 {3,S} {4,S} {5,S} {6,S} -3 O u0 p2 c0 {1,S} {2,S} -4 R u0 p0 c0 {2,S} -5 R u0 p0 c0 {2,S} -6 R u0 p0 c0 {2,S} -""", - thermo=ThermoData( - Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([0.28, 0.58, 0.85, 1.08, 1.4, 1.61, 1.93], 'cal/(mol*K)'), - H298=(-32.28, 'kcal/mol'), - S298=(-34.6, 'cal/(mol*K)'), - ), - shortDesc="""Came from O-CH3 single-bonded on Pt(111)""", - longDesc="""Calculated by Katrin Blondal at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). Based on DFT calculations by Jelena Jelic at KIT. - - CR3 - | - O - | -*********** -""", - metal="Pt", - facet="111", -) - -entry( - index = 11, - label = "(NR3)*", - group = -""" -1 X u0 p0 c0 -2 N u0 p1 c0 {3,S} {4,S} {5,S} -3 R u0 p0 c0 {2,S} -4 R u0 p0 c0 {2,S} -5 R u0 p0 c0 {2,S} -""", - thermo=ThermoData( - Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([1.23, 2.36, 3.08, 3.56, 4.11, 4.4, 4.69], 'cal/(mol*K)'), - H298=(-16.11, 'kcal/mol'), - S298=(-32.0, 'cal/(mol*K)'), - ), - shortDesc="""Came from NH3 vdW-bonded on Pt(111)""", - longDesc="""Calculated by Katrin Blondal at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). Based on DFT calculations by Jelena Jelic at KIT. - - R2N-R - : -*********** -""", - metal="Pt", - facet="111", -) - -entry( - index = 12, - label = "N-*R2", - group = -""" -1 X u0 p0 c0 {2,S} -2 N u0 p1 c0 {1,S} {3,S} {4,S} -3 R u0 p0 c0 {2,S} -4 R u0 p0 c0 {2,S} -""", - thermo=ThermoData( - Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([-1.05, 0.88, 2.07, 2.81, 3.6, 3.99, 4.4], 'cal/(mol*K)'), - H298=(-48.33, 'kcal/mol'), - S298=(-47.88, 'cal/(mol*K)'), - ), - shortDesc="""Came from NH2 single-bonded on Pt(111)""", - longDesc="""Calculated by Katrin Blondal at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). Based on DFT calculations by Jelena Jelic at KIT. - - NR2 - | -*********** -""", - metal="Pt", - facet="111", -) - -entry( - index = 13, - label = "N=*R", - group = -""" -1 X u0 p0 c0 {2,D} -2 N u0 p1 c0 {1,D} {3,S} -3 R u0 p0 c0 {2,S} -""", - thermo=ThermoData( - Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([-2.14, -0.29, 0.86, 1.58, 2.37, 2.76, 3.18], 'cal/(mol*K)'), - H298=(-80.92, 'kcal/mol'), - S298=(-40.72, 'cal/(mol*K)'), - ), - shortDesc="""Came from NH double-bonded on Pt(111)""", - longDesc="""Calculated by Katrin Blondal at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). Based on DFT calculations by Jelena Jelic at KIT. -*********** -""", - metal="Pt", - facet="111", -) - -entry( - index = 14, - label = "N#*", - group = -""" -1 X u0 p0 c0 {2,T} -2 N u0 p1 c0 {1,T} -""", - thermo=ThermoData( - Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([-1.14, -0.25, 0.24, 0.52, 0.81, 0.96, 1.1], 'cal/(mol*K)'), - H298=(-147.51, 'kcal/mol'), - S298=(-32.92, 'cal/(mol*K)'), - ), - shortDesc="""Came from N triple-bonded on Pt(111)""", - longDesc="""Calculated by Katrin Blondal at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). Based on DFT calculations by Jelena Jelic at KIT. - - N - ||| -*********** -""", - metal="Pt", - facet="111", -) - -entry( - index = 15, - label = "(NR2OR)*", - group = -""" -1 X u0 p0 c0 -2 N u0 p1 c0 {3,S} {4,S} {5,S} -3 O u0 p2 c0 {2,S} {6,S} -4 R u0 p0 c0 {2,S} -5 R u0 p0 c0 {2,S} -6 R u0 p0 c0 {3,S} -""", - thermo=ThermoData( - Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([-0.44, 0.2, 0.73, 1.14, 1.69, 2.01, 2.35], 'cal/(mol*K)'), - H298=(-15.69, 'kcal/mol'), - S298=(-32.2, 'cal/(mol*K)'), - ), - shortDesc="""Came from H2N-OH vdW-bonded on Pt(111)""", - longDesc="""Calculated by Katrin Blondal at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). Based on DFT calculations by Jelena Jelic at KIT. - - R2N-OR - : -*********** -""", - metal="Pt", - facet="111", -) - -entry( - index = 16, - label = "(NRO)*", - group = -""" -1 X u0 p0 c0 -2 N u0 p1 c0 {3,D} {4,S} -3 O u0 p2 c0 {2,D} -4 R u0 p0 c0 {2,S} -""", - thermo=ThermoData( - Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([-0.27, 0.8, 1.4, 1.72, 1.98, 2.06, 2.17], 'cal/(mol*K)'), - H298=(-30.08, 'kcal/mol'), - S298=(-32.78, 'cal/(mol*K)'), - ), - shortDesc="""Came from HN-O vdW-bonded on Pt(111)""", - longDesc="""Calculated by Katrin Blondal at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). Based on DFT calculations by Jelena Jelic at KIT. - - RN=O - : -*********** -""", - metal="Pt", - facet="111", -) - -entry( - index = 17, - label = "N-*ROR", - group = -""" -1 X u0 p0 c0 {2,S} -2 N u0 p1 c0 {1,S} {3,S} {4,S} -3 O u0 p2 c0 {2,S} {5,S} -4 R u0 p0 c0 {2,S} -5 R u0 p0 c0 {3,S} -""", - thermo=ThermoData( - Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([2.24, 3.32, 3.89, 4.22, 4.56, 4.73, 4.88], 'cal/(mol*K)'), - H298=(-32.32, 'kcal/mol'), - S298=(-45.51, 'cal/(mol*K)'), - ), - shortDesc="""Came from HN-OH single-bonded on Pt(111)""", - longDesc="""Calculated by Katrin Blondal at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). Based on DFT calculations by Jelena Jelic at KIT. - - R-N-OR - | -*********** -""", - metal="Pt", - facet="111", -) - -entry( - index = 18, - label = "N-*O", - group = -""" -1 X u0 p0 c0 {2,S} -2 N u0 p1 c0 {1,S} {3,D} -3 O u0 p2 c0 {2,D} -""", - thermo=ThermoData( - Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([1.81, 2.7, 3.19, 3.47, 3.71, 3.77, 3.75], 'cal/(mol*K)'), - H298=(-37.18, 'kcal/mol'), - S298=(-40.63, 'cal/(mol*K)'), - ), - shortDesc="""Came from NO single-bonded on Pt(111)""", - longDesc="""Calculated by Katrin Blondal at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). Based on DFT calculations by Jelena Jelic at KIT. - - O - || - N - | -*********** -""", - metal="Pt", - facet="111", -) - -entry( - index = 19, - label = "N=*O-*", - group = -""" -1 X u0 p0 c0 {2,S} {3,D} -2 X u0 p0 c0 {1,S} {4,S} -3 N u0 p1 c0 {1,D} {4,S} -4 O u0 p2 c0 {2,S} {3,S} -""", - thermo=ThermoData( - Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([0.05, 0.57, 0.86, 1.04, 1.2, 1.25, 1.26], 'cal/(mol*K)'), - H298=(-32.66, 'kcal/mol'), - S298=(-29.32, 'cal/(mol*K)'), - ), - shortDesc="""Came from NO-h bidentate, double- and single-bonded on Pt(111)""", - longDesc="""Calculated by Katrin Blondal at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). Based on DFT calculations by Jelena Jelic at KIT. - - N--O - || | -*********** -""", - metal="Pt", - facet="111", -) - -entry( - index = 20, - label = "N=*OR", - group = -""" -1 X u0 p0 c0 {2,D} -2 N u0 p1 c0 {1,D} {3,S} -3 O u0 p2 c0 {2,S} {4,S} -4 R u0 p0 c0 {3,S} -""", - thermo=ThermoData( - Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([2.65, 3.78, 4.29, 4.49, 4.55, 4.5, 4.48], 'cal/(mol*K)'), - H298=(-75.72, 'kcal/mol'), - S298=(-44.7, 'cal/(mol*K)'), - ), - shortDesc="""Came from NOH double-bonded on Pt(111)""", - longDesc="""Calculated by Katrin Blondal at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). Based on DFT calculations by Jelena Jelic at KIT. - - OR - | - N - || -*********** -""", - metal="Pt", - facet="111", -) - -entry( - index = 21, - label = "(NR2NR2)*", - group = -""" -1 X u0 p0 c0 -2 N u0 p1 c0 {3,S} {4,S} {5,S} -3 N u0 p1 c0 {2,S} {6,S} {7,S} -4 R u0 p0 c0 {2,S} -5 R u0 p0 c0 {2,S} -6 R u0 p0 c0 {3,S} -7 R u0 p0 c0 {3,S} -""", - thermo=ThermoData( - Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([0.13, 0.74, 1.16, 1.46, 1.84, 2.06, 2.3], 'cal/(mol*K)'), - H298=(-23.19, 'kcal/mol'), - S298=(-31.95, 'cal/(mol*K)'), - ), - shortDesc="""Came from H2N-NH2 vdW-bonded on Pt(111)""", - longDesc="""Calculated by Katrin Blondal at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). Based on DFT calculations by Jelena Jelic at KIT. - - R2N-NR2 - : -*********** -""", - metal="Pt", - facet="111", -) - -entry( - index = 22, - label = "(NRNR)*", - group = -""" -1 X u0 p0 c0 -2 N u0 p1 c0 {3,D} {4,S} -3 N u0 p1 c0 {2,D} {5,S} -4 R u0 p0 c0 {2,S} -5 R u0 p0 c0 {3,S} -""", - thermo=ThermoData( - Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([3.21, 4.62, 5.24, 5.46, 5.43, 5.28, 5.02], 'cal/(mol*K)'), - H298=(-20.58, 'kcal/mol'), - S298=(-42.07, 'cal/(mol*K)'), - ), - shortDesc="""Came from HN-NH vdW-bonded on Pt(111)""", - longDesc="""Calculated by Katrin Blondal at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). Based on DFT calculations by Jelena Jelic at KIT. - - RN=NR - : -*********** -""", - metal="Pt", - facet="111", -) - -entry( - index = 23, - label = "N-*N-*", - group = -""" -1 X u0 p0 c0 {2,S} {3,S} -2 X u0 p0 c0 {1,S} {4,S} -3 N u0 p1 c0 {1,S} {4,D} -4 N u0 p1 c0 {2,S} {3,D} -""", - thermo=ThermoData( - Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([1.2, 1.21, 1.21, 1.21, 1.22, 1.22, 1.22], 'cal/(mol*K)'), - H298=(-2.39, 'kcal/mol'), - S298=(-13.89, 'cal/(mol*K)'), - ), - shortDesc="""Came from NN bidentate, twice single-bonded on Pt(111)""", - longDesc="""Calculated by Katrin Blondal at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). Based on DFT calculations by Jelena Jelic at KIT. - - N==N - | | -*********** -""", - metal="Pt", - facet="111", -) - -entry( - index = 24, - label = "N-*RNR2", - group = -""" -1 X u0 p0 c0 {2,S} -2 N u0 p1 c0 {1,S} {3,S} {4,S} -3 N u0 p1 c0 {2,S} {5,S} {6,S} -4 R u0 p0 c0 {2,S} -5 R u0 p0 c0 {3,S} -6 R u0 p0 c0 {3,S} -""", - thermo=ThermoData( - Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([1.92, 2.91, 3.52, 3.91, 4.35, 4.57, 4.79], 'cal/(mol*K)'), - H298=(-29.97, 'kcal/mol'), - S298=(-45.43, 'cal/(mol*K)'), - ), - shortDesc="""Came from HN-NH2 single-bonded on Pt(111)""", - longDesc="""Calculated by Katrin Blondal at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). Based on DFT calculations by Jelena Jelic at KIT. - - R-N-NR2 - | -*********** -""", - metal="Pt", - facet="111", -) - -entry( - index = 25, - label = "N-*NR", - group = -""" -1 X u0 p0 c0 {2,S} -2 N u0 p1 c0 {1,S} {3,D} -3 N u0 p1 c0 {2,D} {4,S} -4 R u0 p0 c0 {3,S} -""", - thermo=ThermoData( - Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([1.74, 2.91, 3.56, 3.93, 4.25, 4.37, 4.52], 'cal/(mol*K)'), - H298=(-25.14, 'kcal/mol'), - S298=(-43.45, 'cal/(mol*K)'), - ), - shortDesc="""Came from N-NH single-bonded on Pt(111)""", - longDesc="""Calculated by Katrin Blondal at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). Based on DFT calculations by Jelena Jelic at KIT. - - NR - || - N - | -*********** -""", - metal="Pt", - facet="111", -) - -entry( - index = 26, - label = "N=*NR2", - group = -""" -1 X u0 p0 c0 {2,D} -2 N u0 p1 c0 {1,D} {3,S} -3 N u0 p1 c0 {2,S} {4,S} {5,S} -4 R u0 p0 c0 {3,S} -5 R u0 p0 c0 {3,S} -""", - thermo=ThermoData( - Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([3.32, 4.56, 5.07, 5.2, 5.03, 4.79, 4.55], 'cal/(mol*K)'), - H298=(-47.66, 'kcal/mol'), - S298=(-43.17, 'cal/(mol*K)'), - ), - shortDesc="""Came from N-NH2 double-bonded on Pt(111)""", - longDesc="""Calculated by Katrin Blondal at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). Based on DFT calculations by Jelena Jelic at KIT. - - NR2 - | - N - || -*********** -""", - metal="Pt", - facet="111", -) - -entry( - index = 27, - label = "N-*RN-*R", - group = -""" -1 X u0 p0 c0 {2,S} {3,S} -2 X u0 p0 c0 {1,S} {4,S} -3 N u0 p1 c0 {1,S} {4,S} {5,S} -4 N u0 p1 c0 {2,S} {3,S} {6,S} -5 R u0 p0 c0 {3,S} -6 R u0 p0 c0 {4,S} -""", - thermo=ThermoData( - Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([2.53, 4.03, 4.78, 5.11, 5.24, 5.17, 5.0], 'cal/(mol*K)'), - H298=(-23.37, 'kcal/mol'), - S298=(-43.91, 'cal/(mol*K)'), - ), - shortDesc="""Came from HN-NH-h bidentate, twice single-bonded on Pt(111)""", - longDesc="""Calculated by Katrin Blondal at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). Based on DFT calculations by Jelena Jelic at KIT. - - RN--NR - | | -*********** -""", - metal="Pt", - facet="111", -) - -entry( - index = 28, - label = "N-*RCR3", - group = -""" -1 X u0 p0 c0 {3,S} -2 C u0 p0 c0 {3,S} {4,S} {5,S} {6,S} -3 N u0 p1 c0 {1,S} {2,S} {7,S} -4 R u0 p0 c0 {2,S} -5 R u0 p0 c0 {2,S} -6 R u0 p0 c0 {2,S} -7 R u0 p0 c0 {3,S} -""", - thermo=ThermoData( - Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([1.18, 2.22, 2.89, 3.33, 3.85, 4.12, 4.45], 'cal/(mol*K)'), - H298=(-43.5, 'kcal/mol'), - S298=(-46.63, 'cal/(mol*K)'), - ), - shortDesc="""Came from HN-CH3 single-bonded on Pt(111)""", - longDesc="""Calculated by Katrin Blondal at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). Based on DFT calculations by Jelena Jelic at KIT. - - R-N-CR3 - | -*********** -""", - metal="Pt", - facet="111", -) - -entry( - index = 29, - label = "N-*CR2", - group = -""" -1 X u0 p0 c0 {3,S} -2 C u0 p0 c0 {3,D} {4,S} {5,S} -3 N u0 p1 c0 {1,S} {2,D} -4 R u0 p0 c0 {2,S} -5 R u0 p0 c0 {2,S} -""", - thermo=ThermoData( - Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([1.99, 2.96, 3.5, 3.83, 4.17, 4.33, 4.54], 'cal/(mol*K)'), - H298=(-39.07, 'kcal/mol'), - S298=(-44.16, 'cal/(mol*K)'), - ), - shortDesc="""Came from N-CH2 single-bonded on Pt(111)""", - longDesc="""Calculated by Katrin Blondal at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). Based on DFT calculations by Jelena Jelic at KIT. - - CR2 - || - N - | -*********** -""", - metal="Pt", - facet="111", -) - -entry( - index = 30, - label = "N=*CR3", - group = -""" -1 X u0 p0 c0 {3,D} -2 C u0 p0 c0 {3,S} {4,S} {5,S} {6,S} -3 N u0 p1 c0 {1,D} {2,S} -4 R u0 p0 c0 {2,S} -5 R u0 p0 c0 {2,S} -6 R u0 p0 c0 {2,S} -""", - thermo=ThermoData( - Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([1.12, 1.89, 2.43, 2.81, 3.29, 3.59, 4.07], 'cal/(mol*K)'), - H298=(-71.1, 'kcal/mol'), - S298=(-47.17, 'cal/(mol*K)'), - ), - shortDesc="""Came from N-CH3 double-bonded on Pt(111)""", - longDesc="""Calculated by Katrin Blondal at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). Based on DFT calculations by Jelena Jelic at KIT. - - CR3 - | - N - || -*********** -""", - metal="Pt", - facet="111", -) - -entry( - index = 31, - label = "N-*O2", - group = -""" -1 X u0 p0 c0 {2,S} -2 N u0 p0 c+1 {1,S} {3,S} {4,D} -3 O u0 p2 c-1 {2,S} -4 O u0 p2 c0 {2,D} -""", - thermo=ThermoData( - Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([2.35, 2.6, 2.67, 2.66, 2.61, 2.57, 2.5], 'cal/(mol*K)'), - H298=(-16.1, 'kcal/mol'), - S298=(-33.93, 'cal/(mol*K)'), - ), - shortDesc="""Came from ON-O single-bonded on Pt(111)""", - longDesc="""Calculated by Katrin Blondal at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). Based on DFT calculations by Jelena Jelic at KIT. - - O-N=O - | -*********** -""", - metal="Pt", - facet="111", -) - -entry( - index = 32, - label = "Cq*", - group = -""" -1 X u0 p0 c0 {2,Q} -2 C u0 p0 c0 {1,Q} -""", - thermo=ThermoData( - Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([-2.0, -0.88, -0.22, 0.18, 0.61, 0.82, 1.04], 'cal/(mol*K)'), - H298=(-156.9, 'kcal/mol'), - S298=(-31.82, 'cal/(mol*K)'), - ), - shortDesc="""Came from C quadruple-bonded on Pt(111)""", - longDesc="""Calculated by Katrin Blondal at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). Based on DFT calculations by Jelena Jelic at KIT. - - C - |||| -*********** -""", - metal="Pt", - facet="111", -) - -entry( - index = 33, - label = "C-*C-*", - group = -""" -1 X u0 p0 c0 {2,S} {3,D} -2 X u0 p0 c0 {1,S} {4,D} -3 C u0 p0 c0 {1,D} {4,D} -4 C u0 p0 c0 {2,D} {3,D} -""", - thermo=ThermoData( - Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([0.98, 2.17, 2.79, 3.13, 3.44, 3.55, 3.63], 'cal/(mol*K)'), - H298=(-137.31, 'kcal/mol'), - S298=(-41.99, 'cal/(mol*K)'), - ), - shortDesc="""Came from C-C bidentate, twice double-bonded on Pt(111)""", - longDesc="""Calculated by Katrin Blondal at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). Based on DFT calculations by Jelena Jelic at KIT. - - C--C - | | -*********** -""", - metal="Pt", - facet="111", -) - -entry( - index = 34, - label = "C=*CR2", - group = -""" -1 X u0 p0 c0 {2,D} -2 C u0 p0 c0 {1,D} {3,D} -3 C u0 p0 c0 {2,D} {4,S} {5,S} -4 R u0 p0 c0 {3,S} -5 R u0 p0 c0 {3,S} -""", - thermo=ThermoData( - Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([-1.2, 0.67, 1.9, 2.71, 3.62, 4.07, 4.52], 'cal/(mol*K)'), - H298=(-93.15, 'kcal/mol'), - S298=(-48.06, 'cal/(mol*K)'), - ), - shortDesc="""Came from C-CH2 double-bonded on Pt(111)""", - longDesc="""Calculated by Katrin Blondal at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). Based on DFT calculations by Jelena Jelic at KIT. - - CR2 - || - C - || -*********** -""", - metal="Pt", - facet="111", -) - -entry( - index = 35, - label = "C#*CR3", - group = -""" -1 X u0 p0 c0 {3,T} -2 C u0 p0 c0 {3,S} {4,S} {5,S} {6,S} -3 C u0 p0 c0 {1,T} {2,S} -4 R u0 p0 c0 {2,S} -5 R u0 p0 c0 {2,S} -6 R u0 p0 c0 {2,S} -""", - thermo=ThermoData( - Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([0.98, 1.94, 2.58, 3.04, 3.6, 3.92, 4.33], 'cal/(mol*K)'), - H298=(-129.74, 'kcal/mol'), - S298=(-45.92, 'cal/(mol*K)'), - ), - shortDesc="""Came from C-CH3 triple-bonded on Pt(111)""", - longDesc="""Calculated by Katrin Blondal at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). Based on DFT calculations by Jelena Jelic at KIT. - - CR3 - | - C - ||| -*********** -""", - metal="Pt", - facet="111", -) - -entry( - index = 36, - label = "C#*R", - group = -""" -1 X u0 p0 c0 {2,T} -2 C u0 p0 c0 {1,T} {3,S} -3 R u0 p0 c0 {2,S} -""", - thermo=ThermoData( - Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([-2.35, -0.42, 0.76, 1.49, 2.29, 2.68, 3.14], 'cal/(mol*K)'), - H298=(-145.5, 'kcal/mol'), - S298=(-40.0, 'cal/(mol*K)'), - ), - shortDesc="""Came from CH triple-bonded on Pt(111)""", - longDesc="""Calculated by Katrin Blondal at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). Based on DFT calculations by Jelena Jelic at KIT. - - R - | - C - ||| -*********** -""", - metal="Pt", - facet="111", -) - -entry( - index = 37, - label = "C=*RC=*R", - group = -""" -1 X u0 p0 c0 {2,S} {3,D} -2 X u0 p0 c0 {1,S} {4,D} -3 C u0 p0 c0 {1,D} {4,S} {5,S} -4 C u0 p0 c0 {2,D} {3,S} {6,S} -5 R u0 p0 c0 {3,S} -6 R u0 p0 c0 {4,S} -""", - thermo=ThermoData( - Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([0.05, 1.59, 2.7, 3.47, 4.37, 4.8, 5.11], 'cal/(mol*K)'), - H298=(-47.33, 'kcal/mol'), - S298=(-31.36, 'cal/(mol*K)'), - ), - shortDesc="""Came from CH-CH bidentate, twice double-bonded on Pt(111)""", - longDesc="""Calculated by Katrin Blondal at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). Based on DFT calculations by Jelena Jelic at KIT. - - R-C--C-R - || || -*********** -""", - metal="Pt", - facet="111", -) - -entry( - index = 38, - label = "C=*R2", - group = -""" -1 X u0 p0 c0 {2,D} -2 C u0 p0 c0 {1,D} {3,S} {4,S} -3 R u0 p0 c0 {2,S} -4 R u0 p0 c0 {2,S} -""", - thermo=ThermoData( - Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([-1.54, 0.48, 1.74, 2.53, 3.38, 3.8, 4.29], 'cal/(mol*K)'), - H298=(-85.5, 'kcal/mol'), - S298=(-42.7, 'cal/(mol*K)'), - ), - shortDesc="""Came from CH2 double-bonded on Pt(111)""", - longDesc="""Calculated by Katrin Blondal at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). Based on DFT calculations by Jelena Jelic at KIT. - - R-C-R - || -*********** -""", - metal="Pt", - facet="111", -) - -entry( - index = 39, - label = "C-*R2C-*R2", - group = -""" -1 X u0 p0 c0 {2,S} {3,S} -2 X u0 p0 c0 {1,S} {4,S} -3 C u0 p0 c0 {1,S} {4,S} {5,S} {6,S} -4 C u0 p0 c0 {2,S} {3,S} {7,S} {8,S} -5 R u0 p0 c0 {3,S} -6 R u0 p0 c0 {3,S} -7 R u0 p0 c0 {4,S} -8 R u0 p0 c0 {4,S} -""", - thermo=ThermoData( - Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([1.94, 3.35, 4.13, 4.56, 4.94, 5.08, 5.11], 'cal/(mol*K)'), - H298=(-22.63, 'kcal/mol'), - S298=(-41.46, 'cal/(mol*K)'), - ), - shortDesc="""Came from CH2-CH2 bidentate, twice single-bonded on Pt(111)""", - longDesc="""Calculated by Katrin Blondal at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). Based on DFT calculations by Jelena Jelic at KIT. - - R2C--CR2 - | | -*********** -""", - metal="Pt", - facet="111", -) - -entry( - index = 40, - label = "C-*R3", - group = -""" -1 X u0 p0 c0 {2,S} -2 C u0 p0 c0 {1,S} {3,S} {4,S} {5,S} -3 R u0 p0 c0 {2,S} -4 R u0 p0 c0 {2,S} -5 R u0 p0 c0 {2,S} -""", - thermo=ThermoData( - Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([-0.56, 0.74, 1.74, 2.48, 3.45, 4.0, 4.58], 'cal/(mol*K)'), - H298=(-41.63, 'kcal/mol'), - S298=(-32.73, 'cal/(mol*K)'), - ), - shortDesc="""Came from CH3 single-bonded on Pt(111)""", - longDesc="""Calculated by Katrin Blondal at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). Based on DFT calculations by Jelena Jelic at KIT. - - CR3 - | -*********** -""", - metal="Pt", - facet="111", -) - -entry( - index = 41, - label = "(CR3CR3)*", - group = -""" -1 X u0 p0 c0 -2 C u0 p0 c0 {3,S} {4,S} {5,S} {6,S} -3 C u0 p0 c0 {2,S} {7,S} {8,S} {9,S} -4 R u0 p0 c0 {2,S} -5 R u0 p0 c0 {2,S} -6 R u0 p0 c0 {2,S} -7 R u0 p0 c0 {3,S} -8 R u0 p0 c0 {3,S} -9 R u0 p0 c0 {3,S} -""", - thermo=ThermoData( - Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([2.46, 2.5, 2.52, 2.53, 2.53, 2.53, 2.51], 'cal/(mol*K)'), - H298=(-4.64, 'kcal/mol'), - S298=(-15.11, 'cal/(mol*K)'), - ), - shortDesc="""Came from CH3-CH3 vdW-bonded on Pt(111)""", - longDesc="""Calculated by Katrin Blondal at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). Based on DFT calculations by Jelena Jelic at KIT. - - R3C-CR3 - : -*********** -""", - metal="Pt", - facet="111", -) - -entry( - index = 42, - label = "(CR4)*", - group = -""" -1 X u0 p0 c0 -2 C u0 p0 c0 {3,S} {4,S} {5,S} {6,S} -3 R u0 p0 c0 {2,S} -4 R u0 p0 c0 {2,S} -5 R u0 p0 c0 {2,S} -6 R u0 p0 c0 {2,S} -""", - thermo=ThermoData( - Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([2.42, 2.45, 2.46, 2.47, 2.48, 2.48, 2.47], 'cal/(mol*K)'), - H298=(-2.4, 'kcal/mol'), - S298=(-6.92, 'cal/(mol*K)'), - ), - shortDesc="""Came from CH4 vdW-bonded on Pt(111)""", - longDesc="""Calculated by Katrin Blondal at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). Based on DFT calculations by Jelena Jelic at KIT. - - R3C-R - : -*********** -""", - metal="Pt", - facet="111", -) - -entry( - index = 43, - label = "C=*N-*", - group = -""" -1 X u0 p0 c0 {2,S} {3,D} -2 X u0 p0 c0 {1,S} {4,S} -3 C u0 p0 c0 {1,D} {4,D} -4 N u0 p1 c0 {2,S} {3,D} -""", - thermo=ThermoData( - Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([2.99, 3.32, 3.51, 3.63, 3.74, 3.76, 3.74], 'cal/(mol*K)'), - H298=(-77.01, 'kcal/mol'), - S298=(-34.98, 'cal/(mol*K)'), - ), - shortDesc="""Came from CN bidentate, double- and single-bonded on Pt(111)""", - longDesc="""Calculated by Katrin Blondal at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). Based on DFT calculations by Jelena Jelic at KIT. - - C==N - || | -*********** -""", - metal="Pt", - facet="111", -) - -entry( - index = 44, - label = "C=*NR", - group = -""" -1 X u0 p0 c0 {2,D} -2 C u0 p0 c0 {1,D} {3,D} -3 N u0 p1 c0 {2,D} {4,S} -4 R u0 p0 c0 {3,S} -""", - thermo=ThermoData( - Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([2.64, 3.53, 4.09, 4.44, 4.81, 4.96, 5.04], 'cal/(mol*K)'), - H298=(-40.56, 'kcal/mol'), - S298=(-30.68, 'cal/(mol*K)'), - ), - shortDesc="""Came from CNH double-bonded on Pt(111)""", - longDesc="""Calculated by Katrin Blondal at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). Based on DFT calculations by Jelena Jelic at KIT. - - NR - || - C - || -*********** -""", - metal="Pt", - facet="111", -) - -entry( - index = 45, - label = "C#*NR2", - group = -""" -1 X u0 p0 c0 {2,T} -2 C u0 p0 c0 {1,T} {3,S} -3 N u0 p1 c0 {2,S} {4,S} {5,S} -4 R u0 p0 c0 {3,S} -5 R u0 p0 c0 {3,S} -""", - thermo=ThermoData( - Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([3.38, 4.13, 4.45, 4.59, 4.65, 4.62, 4.6], 'cal/(mol*K)'), - H298=(-94.24, 'kcal/mol'), - S298=(-49.82, 'cal/(mol*K)'), - ), - shortDesc="""Came from CNH2 triple-bonded on Pt(111)""", - longDesc="""Calculated by Katrin Blondal at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). Based on DFT calculations by Jelena Jelic at KIT. - - NR2 - | - C - ||| -*********** -""", - metal="Pt", - facet="111", -) - -entry( - index = 46, - label = "C=*O", - group = -""" -1 X u0 p0 c0 {2,D} -2 C u0 p0 c0 {1,D} {3,D} -3 O u0 p2 c0 {2,D} -""", - thermo=ThermoData( - Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([2.21, 2.9, 3.29, 3.53, 3.74, 3.8, 3.78], 'cal/(mol*K)'), - H298=(-34.7, 'kcal/mol'), - S298=(-38.09, 'cal/(mol*K)'), - ), - shortDesc="""Came from CO-f double-bonded on Pt(111)""", - longDesc="""Calculated by Katrin Blondal at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). Based on DFT calculations by Jelena Jelic at KIT. - - O - || - C - || -*********** -""", - metal="Pt", - facet="111", -) - -entry( - index = 47, - label = "C#*OR", - group = -""" -1 X u0 p0 c0 {2,T} -2 C u0 p0 c0 {1,T} {3,S} -3 O u0 p2 c0 {2,S} {4,S} -4 R u0 p0 c0 {3,S} -""", - thermo=ThermoData( - Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([2.23, 3.29, 3.83, 4.12, 4.34, 4.41, 4.5], 'cal/(mol*K)'), - H298=(-99.0, 'kcal/mol'), - S298=(-43.75, 'cal/(mol*K)'), - ), - shortDesc="""Came from COH triple-bonded on Pt(111)""", - longDesc="""Calculated by Katrin Blondal at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). Based on DFT calculations by Jelena Jelic at KIT. - - OR - | - C - ||| -*********** -""", - metal="Pt", - facet="111", -) - -entry( - index = 48, - label = "C-*R2C=*R", - group = -""" -1 X u0 p0 c0 {2,S} {3,S} -2 X u0 p0 c0 {1,S} {4,D} -3 C u0 p0 c0 {1,S} {4,S} {5,S} {6,S} -4 C u0 p0 c0 {2,D} {3,S} {7,S} -5 R u0 p0 c0 {3,S} -6 R u0 p0 c0 {3,S} -7 R u0 p0 c0 {4,S} -""", - thermo=ThermoData( - Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([-1.55, 0.65, 2.05, 2.94, 3.91, 4.38, 4.78], 'cal/(mol*K)'), - H298=(-65.6, 'kcal/mol'), - S298=(-53.04, 'cal/(mol*K)'), - ), - shortDesc="""Came from H2C-CH bidentate, single- and double-bonded on Pt(111)""", - longDesc="""Calculated by Katrin Blondal at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). Based on DFT calculations by Jelena Jelic at KIT. - - R2C--CR - | || -*********** -""", - metal="Pt", - facet="111", -) - -entry( - index = 49, - label = "C-*R2CR3", - group = -""" -1 X u0 p0 c0 {2,S} -2 C u0 p0 c0 {1,S} {3,S} {4,S} {5,S} -3 C u0 p0 c0 {2,S} {6,S} {7,S} {8,S} -4 R u0 p0 c0 {2,S} -5 R u0 p0 c0 {2,S} -6 R u0 p0 c0 {3,S} -7 R u0 p0 c0 {3,S} -8 R u0 p0 c0 {3,S} -""", - thermo=ThermoData( - Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([-1.67, -0.64, 0.12, 0.68, 1.38, 1.78, 2.19], 'cal/(mol*K)'), - H298=(-41.42, 'kcal/mol'), - S298=(-38.35, 'cal/(mol*K)'), - ), - shortDesc="""Came from H2C-CH3 single-bonded on Pt(111)""", - longDesc="""Calculated by Katrin Blondal at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). Based on DFT calculations by Jelena Jelic at KIT. - - R - | - R-C-CR3 - | -*********** -""", - metal="Pt", - facet="111", -) - -entry( - index = 50, - label = "(CR2NR)*", - group = -""" -1 X u0 p0 c0 -2 C u0 p0 c0 {3,D} {4,S} {5,S} -3 N u0 p1 c0 {2,D} {6,S} -4 R u0 p0 c0 {2,S} -5 R u0 p0 c0 {2,S} -6 R u0 p0 c0 {3,S} -""", - thermo=ThermoData( - Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([0.62, 1.68, 2.22, 2.47, 2.62, 2.62, 2.54], 'cal/(mol*K)'), - H298=(-5.98, 'kcal/mol'), - S298=(-33.14, 'cal/(mol*K)'), - ), - shortDesc="""Came from H2C-NH vdW-bonded on Pt(111)""", - longDesc="""Calculated by Katrin Blondal at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). Based on DFT calculations by Jelena Jelic at KIT. - - R2C=NR - : -*********** -""", - metal="Pt", - facet="111", -) - -entry( - index = 51, - label = "C-*R2NR2", - group = -""" -1 X u0 p0 c0 {2,S} -2 C u0 p0 c0 {1,S} {3,S} {4,S} {5,S} -3 N u0 p1 c0 {2,S} {6,S} {7,S} -4 R u0 p0 c0 {2,S} -5 R u0 p0 c0 {2,S} -6 R u0 p0 c0 {3,S} -7 R u0 p0 c0 {3,S} -""", - thermo=ThermoData( - Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([-1.06, -0.27, 0.37, 0.85, 1.47, 1.83, 2.21], 'cal/(mol*K)'), - H298=(-46.51, 'kcal/mol'), - S298=(-35.43, 'cal/(mol*K)'), - ), - shortDesc="""Came from H2C-NH2 single-bonded on Pt(111)""", - longDesc="""Calculated by Katrin Blondal at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). Based on DFT calculations by Jelena Jelic at KIT. - - R - | - R-C-NR2 - | -*********** -""", - metal="Pt", - facet="111", -) - -entry( - index = 52, - label = "(CR2O)*", - group = -""" -1 X u0 p0 c0 -2 C u0 p0 c0 {3,D} {4,S} {5,S} -3 O u0 p2 c0 {2,D} -4 R u0 p0 c0 {2,S} -5 R u0 p0 c0 {2,S} -""", - thermo=ThermoData( - Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([0.12, 1.56, 2.29, 2.63, 2.79, 2.75, 2.6], 'cal/(mol*K)'), - H298=(-5.18, 'kcal/mol'), - S298=(-34.64, 'cal/(mol*K)'), - ), - shortDesc="""Came from H2C-O vdW-bonded on Pt(111)""", - longDesc="""Calculated by Katrin Blondal at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). Based on DFT calculations by Jelena Jelic at KIT. - - R2C=O - : -*********** -""", - metal="Pt", - facet="111", -) - -entry( - index = 53, - label = "C-*R2OR", - group = -""" -1 X u0 p0 c0 {2,S} -2 C u0 p0 c0 {1,S} {3,S} {4,S} {5,S} -3 O u0 p2 c0 {2,S} {6,S} -4 R u0 p0 c0 {2,S} -5 R u0 p0 c0 {2,S} -6 R u0 p0 c0 {3,S} -""", - thermo=ThermoData( - Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([-1.37, -0.44, 0.27, 0.8, 1.48, 1.87, 2.27], 'cal/(mol*K)'), - H298=(-44.42, 'kcal/mol'), - S298=(-35.7, 'cal/(mol*K)'), - ), - shortDesc="""Came from H2C-OH single-bonded on Pt(111)""", - longDesc="""Calculated by Katrin Blondal at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). Based on DFT calculations by Jelena Jelic at KIT. - - R - | - R-C-OR - | -*********** -""", - metal="Pt", - facet="111", -) - -entry( - index = 54, - label = "(CR3NR2)*", - group = -""" -1 X u0 p0 c0 -2 C u0 p0 c0 {3,S} {4,S} {5,S} {6,S} -3 N u0 p1 c0 {2,S} {7,S} {8,S} -4 R u0 p0 c0 {2,S} -5 R u0 p0 c0 {2,S} -6 R u0 p0 c0 {2,S} -7 R u0 p0 c0 {3,S} -8 R u0 p0 c0 {3,S} -""", - thermo=ThermoData( - Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([0.09, 0.79, 1.24, 1.54, 1.88, 2.06, 2.26], 'cal/(mol*K)'), - H298=(-20.93, 'kcal/mol'), - S298=(-33.73, 'cal/(mol*K)'), - ), - shortDesc="""Came from H3C-NH2 vdW-bonded on Pt(111)""", - longDesc="""Calculated by Katrin Blondal at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). Based on DFT calculations by Jelena Jelic at KIT. - - R3C-NR2 - : -*********** -""", - metal="Pt", - facet="111", -) - -entry( - index = 55, - label = "(CR3OR)*", - group = -""" -1 X u0 p0 c0 -2 C u0 p0 c0 {3,S} {4,S} {5,S} {6,S} -3 O u0 p2 c0 {2,S} {7,S} -4 R u0 p0 c0 {2,S} -5 R u0 p0 c0 {2,S} -6 R u0 p0 c0 {2,S} -7 R u0 p0 c0 {3,S} -""", - thermo=ThermoData( - Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([1.69, 2.05, 2.23, 2.33, 2.4, 2.43, 2.45], 'cal/(mol*K)'), - H298=(-7.47, 'kcal/mol'), - S298=(-28.83, 'cal/(mol*K)'), - ), - shortDesc="""Came from H3C-OH vdW-bonded on Pt(111)""", - longDesc="""Calculated by Katrin Blondal at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). Based on DFT calculations by Jelena Jelic at KIT. - - R3C-OR - : -*********** -""", - metal="Pt", - facet="111", -) - -entry( - index = 56, - label = "C-*RC=*", - group = -""" -1 X u0 p0 c0 {2,S} {3,S} -2 X u0 p0 c0 {1,S} {4,D} -3 C u0 p0 c0 {1,S} {4,D} {5,S} -4 C u0 p0 c0 {2,D} {3,D} -5 R u0 p0 c0 {3,S} -""", - thermo=ThermoData( - Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([0.85, 2.25, 3.11, 3.66, 4.25, 4.53, 4.78], 'cal/(mol*K)'), - H298=(-95.45, 'kcal/mol'), - S298=(-42.29, 'cal/(mol*K)'), - ), - shortDesc="""Came from HC-C bidentate, single- and double-bonded on Pt(111)""", - longDesc="""Calculated by Katrin Blondal at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). Based on DFT calculations by Jelena Jelic at KIT. - - RC--C - | || -*********** -""", - metal="Pt", - facet="111", -) - -entry( - index = 57, - label = "C-*RCR2", - group = -""" -1 X u0 p0 c0 {2,S} -2 C u0 p0 c0 {1,S} {3,D} {4,S} -3 C u0 p0 c0 {2,D} {5,S} {6,S} -4 R u0 p0 c0 {2,S} -5 R u0 p0 c0 {3,S} -6 R u0 p0 c0 {3,S} -""", - thermo=ThermoData( - Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([0.22, 1.96, 3.02, 3.67, 4.35, 4.65, 4.89], 'cal/(mol*K)'), - H298=(-65.44, 'kcal/mol'), - S298=(-48.91, 'cal/(mol*K)'), - ), - shortDesc="""Came from HC-CH2 single-bonded on Pt(111)""", - longDesc="""Calculated by Katrin Blondal at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). Based on DFT calculations by Jelena Jelic at KIT. - - CR2 - || - C-R - | -*********** -""", - metal="Pt", - facet="111", -) - -entry( - index = 58, - label = "C=*RCR3", - group = -""" -1 X u0 p0 c0 {3,D} -2 C u0 p0 c0 {3,S} {4,S} {5,S} {6,S} -3 C u0 p0 c0 {1,D} {2,S} {7,S} -4 R u0 p0 c0 {2,S} -5 R u0 p0 c0 {2,S} -6 R u0 p0 c0 {2,S} -7 R u0 p0 c0 {3,S} -""", - thermo=ThermoData( - Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([1.11, 2.09, 2.75, 3.2, 3.72, 4.0, 4.37], 'cal/(mol*K)'), - H298=(-83.24, 'kcal/mol'), - S298=(-44.11, 'cal/(mol*K)'), - ), - shortDesc="""Came from HC-CH3 double-bonded on Pt(111)""", - longDesc="""Calculated by Katrin Blondal at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). Based on DFT calculations by Jelena Jelic at KIT. - - CR3 - | - C-R - || -*********** -""", - metal="Pt", - facet="111", -) - -entry( - index = 59, - label = "(CRN)*", - group = -""" -1 X u0 p0 c0 -2 C u0 p0 c0 {3,T} {4,S} -3 N u0 p1 c0 {2,T} -4 R u0 p0 c0 {2,S} -""", - thermo=ThermoData( - Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([-0.03, 0.84, 1.41, 1.79, 2.22, 2.4, 2.53], 'cal/(mol*K)'), - H298=(-0.94, 'kcal/mol'), - S298=(-22.92, 'cal/(mol*K)'), - ), - shortDesc="""Came from HCN vdW-bonded on Pt(111)""", - longDesc="""Calculated by Katrin Blondal at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). Based on DFT calculations by Jelena Jelic at KIT. - - RC#N - : -*********** -""", - metal="Pt", - facet="111", -) - -entry( - index = 60, - label = "C=*RN=*", - group = -""" -1 X u0 p0 c0 {2,S} {3,D} -2 X u0 p0 c0 {1,S} {4,D} -3 C u0 p0 c0 {1,D} {4,S} {5,S} -4 N u0 p1 c0 {2,D} {3,S} -5 R u0 p0 c0 {3,S} -""", - thermo=ThermoData( - Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([0.72, 2.17, 3.13, 3.78, 4.5, 4.82, 5.03], 'cal/(mol*K)'), - H298=(-15.96, 'kcal/mol'), - S298=(-35.76, 'cal/(mol*K)'), - ), - shortDesc="""Came from HCN-h bidentate, twice double-bonded on Pt(111)""", - longDesc="""Calculated by Katrin Blondal at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). Based on DFT calculations by Jelena Jelic at KIT. - - R - | - C--N - || || -*********** -""", - metal="Pt", - facet="111", -) - -entry( - index = 61, - label = "C-*RNR", - group = -""" -1 X u0 p0 c0 {2,S} -2 C u0 p0 c0 {1,S} {3,D} {4,S} -3 N u0 p1 c0 {2,D} {5,S} -4 R u0 p0 c0 {2,S} -5 R u0 p0 c0 {3,S} -""", - thermo=ThermoData( - Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([-0.28, 0.62, 1.17, 1.52, 1.89, 2.07, 2.25], 'cal/(mol*K)'), - H298=(-51.9, 'kcal/mol'), - S298=(-33.8, 'cal/(mol*K)'), - ), - shortDesc="""Came from HCNH single-bonded on Pt(111)""", - longDesc="""Calculated by Katrin Blondal at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). Based on DFT calculations by Jelena Jelic at KIT. - - NR - || - C-R - | -*********** -""", - metal="Pt", - facet="111", -) - -entry( - index = 62, - label = "C=*RN-*R", - group = -""" -1 X u0 p0 c0 {2,S} {3,D} -2 X u0 p0 c0 {1,S} {4,S} -3 C u0 p0 c0 {1,D} {4,S} {5,S} -4 N u0 p1 c0 {2,S} {3,S} {6,S} -5 R u0 p0 c0 {3,S} -6 R u0 p0 c0 {4,S} -""", - thermo=ThermoData( - Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([1.09, 2.47, 3.27, 3.76, 4.25, 4.47, 4.67], 'cal/(mol*K)'), - H298=(-58.44, 'kcal/mol'), - S298=(-46.17, 'cal/(mol*K)'), - ), - shortDesc="""Came from HCNH-h bidentate, double- and single-bonded on Pt(111)""", - longDesc="""Calculated by Katrin Blondal at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). Based on DFT calculations by Jelena Jelic at KIT. - - RC--NR - || | -*********** -""", - metal="Pt", - facet="111", -) - -entry( - index = 63, - label = "C=*RNR2", - group = -""" -1 X u0 p0 c0 {2,D} -2 C u0 p0 c0 {1,D} {3,S} {4,S} -3 N u0 p1 c0 {2,S} {5,S} {6,S} -4 R u0 p0 c0 {2,S} -5 R u0 p0 c0 {3,S} -6 R u0 p0 c0 {3,S} -""", - thermo=ThermoData( - Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([0.47, 1.4, 1.85, 2.07, 2.21, 2.24, 2.27], 'cal/(mol*K)'), - H298=(-62.35, 'kcal/mol'), - S298=(-33.34, 'cal/(mol*K)'), - ), - shortDesc="""Came from HCNH2 double-bonded on Pt(111)""", - longDesc="""Calculated by Katrin Blondal at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). Based on DFT calculations by Jelena Jelic at KIT. - - NR2 - | - C-R - || -*********** -""", - metal="Pt", - facet="111", -) - -entry( - index = 64, - label = "C-*RO", - group = -""" -1 X u0 p0 c0 {2,S} -2 C u0 p0 c0 {1,S} {3,D} {4,S} -3 O u0 p2 c0 {2,D} -4 R u0 p0 c0 {2,S} -""", - thermo=ThermoData( - Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([-0.71, 0.27, 0.89, 1.28, 1.69, 1.9, 2.14], 'cal/(mol*K)'), - H298=(-51.82, 'kcal/mol'), - S298=(-33.46, 'cal/(mol*K)'), - ), - shortDesc="""Came from HCO single-bonded on Pt(111)""", - longDesc="""Calculated by Katrin Blondal at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). Based on DFT calculations by Jelena Jelic at KIT. - - R - | - C=O - | -*********** -""", - metal="Pt", - facet="111", -) - -entry( - index = 65, - label = "C=*RO-*", - group = -""" -1 X u0 p0 c0 {2,S} {3,D} -2 X u0 p0 c0 {1,S} {4,S} -3 C u0 p0 c0 {1,D} {4,S} {5,S} -4 O u0 p2 c0 {2,S} {3,S} -5 R u0 p0 c0 {3,S} -""", - thermo=ThermoData( - Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([1.21, 2.72, 3.6, 4.09, 4.5, 4.63, 4.73], 'cal/(mol*K)'), - H298=(-44.71, 'kcal/mol'), - S298=(-45.92, 'cal/(mol*K)'), - ), - shortDesc="""Came from HCO-h bidentate, double- and single-bonded on Pt(111)""", - longDesc="""Calculated by Katrin Blondal at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). Based on DFT calculations by Jelena Jelic at KIT. - - R - | - C--O - || | -*********** -""", - metal="Pt", - facet="111", -) - -entry( - index = 66, - label = "C=*ROR", - group = -""" -1 X u0 p0 c0 {2,D} -2 C u0 p0 c0 {1,D} {3,S} {4,S} -3 O u0 p2 c0 {2,S} {5,S} -4 R u0 p0 c0 {2,S} -5 R u0 p0 c0 {3,S} -""", - thermo=ThermoData( - Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([-0.51, 0.59, 1.21, 1.58, 1.97, 2.17, 2.38], 'cal/(mol*K)'), - H298=(-69.06, 'kcal/mol'), - S298=(-33.81, 'cal/(mol*K)'), - ), - shortDesc="""Came from HCOH double-bonded on Pt(111)""", - longDesc="""Calculated by Katrin Blondal at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). Based on DFT calculations by Jelena Jelic at KIT. - - OR - | - C-R - || -*********** -""", - metal="Pt", - facet="111", -) - -entry( - index = 67, - label = "C*", - group = -""" -1 X u0 {2,[S,D,T,Q]} -2 C u0 {1,[S,D,T,Q]} -""", - thermo='C-*R3', -) - -entry( - index = 68, - label = "N*", - group = -""" -1 X u0 {2,[S,D,T,Q]} -2 N u0 {1,[S,D,T,Q]} -""", - thermo='N-*R2', -) - -entry( - index = 69, - label = "O*", - group = -""" -1 X u0 {2,[S,D,T,Q]} -2 O u0 {1,[S,D,T,Q]} -""", - thermo='O-*R', -) - -entry( - index = 70, - label = "R*single_chemisorbed", - group = -""" -1 X u0 {2,[S,D,T,Q]} -2 R u0 {1,[S,D,T,Q]} -""", - thermo=ThermoData( - Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([-0.09, 1.28, 2.17, 2.75, 3.43, 3.79, 4.16], 'cal/(mol*K)'), - H298=(-45.38, 'kcal/mol'), - S298=(-38.17, 'cal/(mol*K)'), - ), - shortDesc="""Average of C-*R3, N-*R2 and O-*R thermo. """, - metal="Pt", - facet="111", -) - -entry( - index = 71, - label = "C*C*", - group = -""" -1 X u0 -2 X u0 -3 C u0 -4 C u0 -""", - thermo='C-*R2C-*R2', -) - -entry( - index = 72, - label = "C*N*", - group = -""" -1 X u0 -2 X u0 -3 C u0 -4 N u0 -""", - thermo='C=*RN-*R', -) - -entry( - index = 73, - label = "C*O*", - group = -""" -1 X u0 -2 X u0 -3 C u0 -4 O u0 -""", - thermo='C=*RO-*R', -) - -entry( - index = 74, - label = "N*N*", - group = -""" -1 X u0 -2 X u0 -3 N u0 -4 N u0 -""", - thermo='N-*RN-*R', -) - -entry( - index = 75, - label = "R*bidentate", - group = -""" -1 X u0 -2 X u0 -3 R u0 -4 R u0 -""", - thermo=ThermoData( - Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([1.69, 3.14, 3.95, 4.38, 4.73, 4.84, 4,88], 'cal/(mol*K)'), - H298=(-37.29, 'kcal/mol'), - S298=(-44.37, 'cal/(mol*K)'), - ), - shortDesc="""Average of C-*R2C-*R2, C=*RN-*R, C=*RO-* and N-*RN-*R thermo. """, - metal="Pt", - facet="111", -) - -entry( - index = 76, - label = "R*vdW", - group = -""" -1 X u0 -2 R u0 -""", - thermo=ThermoData( - Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([1.51, 2.1, 2.45, 2.68, 2.94, 3.07, 3.2], 'cal/(mol*K)'), - H298=(-7.79, 'kcal/mol'), - S298=(-20.48, 'cal/(mol*K)'), - ), - shortDesc="""Average of (CR4)*, (NR3)* and (OR2)* thermo. """, - metal="Pt", - facet="111", -) - -entry( - index = 77, - label = "N*O*", - group = -""" -1 X u0 p0 c0 {2,S} {3,[S,D]} -2 X u0 p0 c0 {1,S} {4,[S,D]} -3 N u0 p1 c0 {1,[S,D]} {4,[S,D]} -4 O u0 p2 c0 {2,[S,D]} {3,[S,D]} -""", - thermo='N=*O-*', - longDesc="""Is there really any way to do N*O* besides N=*O-* ?""", - metal="Pt", - facet="111", -) - -entry( - index = 78, - label = "O*O*", - group = -""" -1 X u0 p0 c0 {2,S} {3,S} -2 X u0 p0 c0 {1,S} {4,S} -3 O u0 p2 c0 {1,S} {4,S} -4 O u0 p2 c0 {2,S} {3,S} -""", - thermo='O-*O-*', - longDesc="""Is there really any way to do O*O* besides O-*O-* ?""", - metal="Pt", - facet="111", -) - -entry( - index = 79, - label = "N#*R", - group = -""" -1 X u0 {2,T} -2 N u0 {1,T} {3,[S,D]} -3 R u0 {2,[S,D]} -""", - thermo='N*' -) - -entry( - index = 80, - label = "(CR3)*", - group = -""" -1 X u0 -2 C u0 {3,D} {4,S} {5,S} -3 R u0 {2,D} -4 R u0 {2,S} -5 R u0 {2,S} -""", - thermo='(CR2NR)*', - longDesc="""Perhaps should be an average?""", - metal="Pt", - facet="111", -) - -entry( - index = 81, - label = "(CR2)*", - group = -""" -1 X u0 -2 C u0 {3,[S,D,T]} {4,[S,D,T]} -3 R u0 {2,[S,D,T]} -4 R u0 {2,[S,D,T]} -""", - thermo='(CRN)*' -) - -entry( - index = 82, - label = "(NR2CR3)*", - group = -""" -1 X u0 p0 c0 -2 N u0 p1 c0 {3,S} {4,S} {5,S} -3 Cs u0 p0 c0 {2,S} -4 R u0 p0 c0 {2,S} -5 R u0 p0 c0 {2,S} -""", - thermo='(NR3)*', - longDesc="""Do we have data for this?""", - metal="Pt", - facet="111", -) - -entry( - index = 83, - label = "(NR2)*", - group = -""" -1 X u0 -2 N u0 {3,D} {4,S} -3 R u0 {2,D} -4 R u0 {2,S} -""", - thermo='(NRO)*', - longDesc="""Parent of (RN=O)* and (RN=NR)*. Should it be an average?""", - metal="Pt", - facet="111", -) - -tree( -""" -L1: R* - L2: R*bidentate - L3: C*C* - L4: C-*C-* - L4: C=*RC=*R - L4: C-*R2C-*R2 - L4: C-*R2C=*R - L4: C-*RC=* - L3: C*N* - L4: C=*N-* - L4: C=*RN=* - L4: C=*RN-*R - L3: C*O* - L4: C=*RO-* - L3: N*N* - L4: N-*N-* - L4: N-*RN-*R - L3: N*O* - L4: N=*O-* - L3: O*O* - L4: O-*O-* - L2: R*single_chemisorbed - L3: C* - L4: Cq* - L4: C#*R - L5: C#*CR3 - L5: C#*NR2 - L5: C#*OR - L4: C=*R2 - L5: C=*RCR3 - L5: C=*RNR2 - L5: C=*ROR - L5: C=*CR2 - L5: C=*NR - L4: C-*R3 - L5: C-*R2CR3 - L5: C-*R2NR2 - L5: C-*R2OR - L5: C-*RCR2 - L5: C-*RNR - L5: C-*RO - L3: N* - L4: N#*R - L4: N=*R - L5: N=*CR3 - L5: N=*NR2 - L5: N=*OR - L4: N-*R2 - L5: N-*RCR3 - L5: N-*RNR2 - L5: N-*ROR - L5: N-*CR2 - L5: N-*NR - L3: O* - L4: O=* - L4: O-*R - L5: O-*CR3 - L5: O-*NR2 - L5: O-*OR - L2: R*vdW - L3: (CR4)* - L4: (CR3CR3)* - L4: (CR3NR2)* - L4: (CR3OR)* - L3: (CR3)* - L4: (CR2NR)* - L4: (CR2O)* - L3: (CR2)* - L4: (CRN)* - L3: (NR3)* - L4: (NR2CR3)* - L4: (NR2NR2)* - L4: (NR2OR)* - L3: (NR2)* - L4: (NRO)* - L4: (NRNR)* - L3: (OR2)* - L4: (OROR)* - -""" -) diff --git a/rmgpy/data/test_data/thermo/groups/group.py b/rmgpy/data/test_data/thermo/groups/group.py deleted file mode 100644 index 13f409b70c3..00000000000 --- a/rmgpy/data/test_data/thermo/groups/group.py +++ /dev/null @@ -1,7 +0,0 @@ -#!/usr/bin/env python -# encoding: utf-8 - -name = "Functional Group Additivity Values" -shortDesc = "" -longDesc = """ -""" diff --git a/rmgpy/data/test_data/thermo/groups/longDistanceInteraction_cyclic.py b/rmgpy/data/test_data/thermo/groups/longDistanceInteraction_cyclic.py deleted file mode 100644 index 94a3e646cc8..00000000000 --- a/rmgpy/data/test_data/thermo/groups/longDistanceInteraction_cyclic.py +++ /dev/null @@ -1,8 +0,0 @@ -#!/usr/bin/env python -# encoding: utf-8 - -name = "Correction for interaction distance 1" -shortDesc = "" -longDesc = """ -""" - diff --git a/rmgpy/data/test_data/thermo/groups/longDistanceInteraction_noncyclic.py b/rmgpy/data/test_data/thermo/groups/longDistanceInteraction_noncyclic.py deleted file mode 100644 index 94a3e646cc8..00000000000 --- a/rmgpy/data/test_data/thermo/groups/longDistanceInteraction_noncyclic.py +++ /dev/null @@ -1,8 +0,0 @@ -#!/usr/bin/env python -# encoding: utf-8 - -name = "Correction for interaction distance 1" -shortDesc = "" -longDesc = """ -""" - diff --git a/rmgpy/data/test_data/thermo/groups/other.py b/rmgpy/data/test_data/thermo/groups/other.py deleted file mode 100644 index 15baad47403..00000000000 --- a/rmgpy/data/test_data/thermo/groups/other.py +++ /dev/null @@ -1,9 +0,0 @@ -#!/usr/bin/env python -# encoding: utf-8 - -name = "Other Corrections" -shortDesc = "" -longDesc = """ -""" - - diff --git a/rmgpy/data/test_data/thermo/groups/polycyclic.py b/rmgpy/data/test_data/thermo/groups/polycyclic.py deleted file mode 100644 index 8b591c1fbc7..00000000000 --- a/rmgpy/data/test_data/thermo/groups/polycyclic.py +++ /dev/null @@ -1,8 +0,0 @@ -#!/usr/bin/env python -# encoding: utf-8 - -name = "Polycyclic Ring Corrections" -shortDesc = "" -longDesc = """ -""" - diff --git a/rmgpy/data/test_data/thermo/groups/radical.py b/rmgpy/data/test_data/thermo/groups/radical.py deleted file mode 100644 index d4fa67b0491..00000000000 --- a/rmgpy/data/test_data/thermo/groups/radical.py +++ /dev/null @@ -1,112 +0,0 @@ -#!/usr/bin/env python -# encoding: utf-8 - -name = "Radical Corrections" -shortDesc = "" -longDesc = """ - -""" -entry( - index = 0, - label = "Radical", - group = "OR{RJ, RJ2_singlet}", - thermo = 'RJ', - shortDesc = """""", - longDesc = -""" - -""", -) - -entry( - index = 1, - label = "RJ", - group = -""" -1 * R u1 -""", - thermo = 'CJ', - shortDesc = """""", - longDesc = -""" - -""", -) - -entry( - index = 2, - label = "CJ", - group = -""" -1 * C u1 -""", - thermo = 'CsJ', - shortDesc = """""", - longDesc = -""" - -""", -) - -entry( - index = 3, - label = "CsJ", - group = -""" -1 * Cs u1 -""", - thermo = ThermoData( - Tdata = ([300,400,500,600,800,1000,1500],'K'), - Cpdata = ([0.71,0.34,-0.33,-1.07,-2.43,-3.54,-5.43],'cal/(mol*K)'), - H298 = (104.81,'kcal/mol','+|-',0.1), - S298 = (0.52,'cal/(mol*K)'), - ), - shortDesc = """""", - longDesc = -""" - -""", -) - -entry( - index = 94, - label = "OJ", - group = -""" -1 * O u1 -""", - thermo = 'RJ', - shortDesc = """""", - longDesc = -""" - -""", -) - - -entry( - index = 106, - label = "RJ2_triplet", - group = -""" -1 * R u2 -""", - thermo = 'CsJ', - shortDesc = """""", - longDesc = -""" - -""", -) -tree( -""" -L1: Radical - L2: RJ - L3: CJ - L4: CsJ - L3: OJ - L2: RJ2_triplet - -""" -) - diff --git a/rmgpy/data/test_data/thermo/groups/ring.py b/rmgpy/data/test_data/thermo/groups/ring.py deleted file mode 100644 index 657296db28d..00000000000 --- a/rmgpy/data/test_data/thermo/groups/ring.py +++ /dev/null @@ -1,8 +0,0 @@ -#!/usr/bin/env python -# encoding: utf-8 - -name = "Ring Corrections" -shortDesc = "" -longDesc = """ -""" - diff --git a/rmgpy/data/thermo.py b/rmgpy/data/thermo.py index 751088147da..7816d7ed2f2 100644 --- a/rmgpy/data/thermo.py +++ b/rmgpy/data/thermo.py @@ -813,7 +813,10 @@ def remove_group(self, group_to_remove): groups we also, need to re-point any unicode thermo_data that may have pointed to the entry. - Returns the removed group + This is not (as of 2024/03) used within RMG-Py, but could be useful for + people making ancillary scripts to manipulate or edit the database. + + Returns the removed group. """ # First call base class method diff --git a/test/rmgpy/data/thermoTest.py b/test/rmgpy/data/thermoTest.py index 7360b6f21ea..7d5db15a616 100644 --- a/test/rmgpy/data/thermoTest.py +++ b/test/rmgpy/data/thermoTest.py @@ -1208,6 +1208,65 @@ def test_adsorbate_thermo_generation_bidentate_nonadjacent(self): assert "radical" in thermo.comment, "Expected to need radical correctinos to find CH2j-CH2-CH2j" assert "Adsorption correction" in thermo.comment, "Adsorption correction not added to thermo." + def test_remove_group(self): + """ + Test removing groups, using nodes near the root of radical.py + """ + # load up test data designed for this test + database2 = ThermoDatabase() + path = os.path.join(os.path.dirname(__file__),"..","test_data","testing_database","thermo") + database2.load(path, depository=False) + + # load up the thermo radical database as a test + rad_group = database2.groups["radical"] + + # use root as removed groups parent, which should be an LogicOr node + root = rad_group.top[0] + # use group to remove as + group_to_remove = rad_group.entries["RJ"] + children = group_to_remove.children + + # set up for testing below + rad_group.entries["OJ"].data = "RJ" + + # remove the group + rad_group.remove_group(group_to_remove) + + # afterwards group_to_remove should not be in the database or root's children + assert group_to_remove not in list(rad_group.entries.values()) + assert group_to_remove not in root.children + + for child in children: + # group_to_remove children should all be in roots item.component and children attribuetes + assert child.label in root.item.components + assert child in root.children + # the children should all have root a their parent now + assert child.parent is root + + # Specific to ThermoDatabase, (above test apply to all base class Database) + # we check that unicode entry.data pointers are correctly reassigned + + # if group_to_remove is a pointer and another node pointed to it, we copy + # group_to_remove pointer + # OJ pointed to RJ and RJ pointed to CJ so if you remove RJ then OJ should point to CJ + assert rad_group.entries["OJ"].data is group_to_remove.data + + # Remove an entry with a ThermoData object + group_to_remove2 = rad_group.entries["Cs_P"] + rad_group.remove_group(group_to_remove2) + # If group_to_remove was a data object, we point toward parent instead + # CsCsJ pointed to Cs_P, which had data. + # After we remove Cs_P, CsCsJ points to the parent, which was CsJ + assert rad_group.entries["CsCsJ"].data == group_to_remove2.parent.label + # If the parent pointed toward group_to_remove, we need should have copied data object + # CsJ (the parent) used to just point at Cs_P. + # After we remove Cs_P, CsJ should contain the data copied from Cs_P + Tlist = [300, 400, 500, 600, 800, 1000, 1500] + assert not isinstance(group_to_remove2.parent.data, str) + assert group_to_remove2.parent.data.get_enthalpy(298) == group_to_remove2.data.get_enthalpy(298) + assert group_to_remove2.parent.data.get_entropy(298) == group_to_remove2.data.get_entropy(298) + assert all([group_to_remove2.parent.data.get_heat_capacity(x) == group_to_remove2.data.get_heat_capacity(x) for x in Tlist]) + class TestThermoAccuracy: """ @@ -1626,57 +1685,6 @@ def test_get_ring_groups_from_comments(self): self.database.get_ring_groups_from_comments(spc.thermo) - def test_remove_group(self): - """ - Test that removing groups using nodes near the root of radical.py - """ - # load up test data designed for this test - database2 = ThermoDatabase() - path = os.path.join(os.path.dirname(rmgpy.__file__), "data/test_data/") - database2.load(os.path.join(path, "thermo"), depository=False) - - # load up the thermo radical database as a test - rad_group = database2.groups["radical"] - - # use root as removed groups parent, which should be an LogicOr node - root = rad_group.top[0] - # use group to remove as - group_to_remove = rad_group.entries["RJ"] - children = group_to_remove.children - - # remove the group - rad_group.remove_group(group_to_remove) - - # afterwards group_to_remove should not be in the database or root's children - assert group_to_remove not in list(rad_group.entries.values()) - assert group_to_remove not in root.children - - for child in children: - # group_to_remove children should all be in roots item.component and children attribuetes - assert child.label in root.item.components - assert child in root.children - # the children should all have root a their parent now - assert child.parent is root - - # Specific to ThermoDatabase, (above test apply to all base class Database) - # we check that unicode entry.data pointers are correctly reassigned - - # if group_to_remove is a pointer and another node pointed to it, we copy - # group_to_remove pointer - assert rad_group.entries["OJ"].data is group_to_remove.data - - # Remove an entry with a ThermoData object - group_to_remove2 = rad_group.entries["CsJ"] - rad_group.remove_group(group_to_remove2) - # If group_to_remove was a data object, we point toward parent instead - assert rad_group.entries["RJ2_triplet"].data == group_to_remove2.parent.label - # If the parent pointed toward group_to_remove, we need should have copied data object - Tlist = [300, 400, 500, 600, 800, 1000, 1500] - assert not isinstance(group_to_remove2.parent.data, str) - assert group_to_remove2.parent.data.get_enthalpy(298) == group_to_remove2.data.get_enthalpy(298) - assert group_to_remove2.parent.data.get_entropy(298) == group_to_remove2.data.get_entropy(298) - assert all([group_to_remove2.parent.data.get_heat_capacity(x) == group_to_remove2.data.get_heat_capacity(x) for x in Tlist]) - def test_is_ring_partial_matched(self): # create testing molecule smiles = "C1CC2CCCC3CCCC(C1)C23"