in which case the reference energy is defined. The choice of me:HfAT0, me:Hf298, arbitrary vs defined reference state is encapsulated by the notion of an energy convention. The location of PES features must be entered with either one or other of these conventions for the whole input file, otherwise the different reference states will lead to inconsistencies, so MESMER checks if the same convention is being used and will stop if a mixed specification is detected. Figure 3: Schematic PES illustrating the definitions of used in MESMER ΔH reactionList is composed of each individual that may occur in a ME reactionList reaction system. Effectively, the specifies which are connected via reactionList molecules which transition state. A may be one of a number of types listed in Table3. The reaction reaction type assigned for a given reaction is determined by the number of species and their species types (more detail below) involved in the reaction, and these are also listed in Table 3. If MESMER cannot assign a reaction to one these types it will stop. Each may include the following: reaction An attribute, is used to identify the reaction; id An attribute. If this is the reaction is ignored by MESMER. This active feature makes it possible to do calculations on only part of a complex reaction system. A can also have this attribute, but this does not affect the molecule calculation. Inactive reactions and molecules are shown either greyed or omitted (at the users choice) when the XML file is viewed in Firefox. Reactant 1 Reactant 2 Product 1 Product 2 Reaction type Absent Absent Isomerization modelled modelled deficientReactant excessReactant modelled Absent Association
me:HfAT0, me:Hf298, in which case the reference energy is defined. The choice of arbitrary vs defined reference state is encapsulated by the notion of an energy convention. The location of PES features must be entered with either one or other of these conventions for the whole input file, otherwise the different reference states will lead to inconsistencies, so MESMER checks if the same convention is being used and will stop if a mixed specification is detected. Figure 3: Schematic PES illustrating the definitions of ΔH used in MESMER reactionList reactionList is composed of each individual reaction that may occur in a ME system. Effectively, the reactionList specifies which molecules are connected via which transition state. A reaction may be one of a number of types listed in Table3. The reaction type assigned for a given reaction is determined by the number of species and their species types (more detail below) involved in the reaction, and these are also listed in Table 3. If MESMER cannot assign a reaction to one these types it will stop. Each reaction may include the following: An id attribute, is used to identify the reaction; An active attribute. If this is the reaction is ignored by MESMER. This feature makes it possible to do calculations on only part of a complex reaction system. A molecule can also have this attribute, but this does not affect the calculation. Inactive reactions and molecules are shown either greyed or omitted (at the users choice) when the XML file is viewed in Firefox. Reactant 1 Reactant 2 Product 1 Product 2 Reaction type modelled Absent modelled Absent Isomerization deficientReactant excessReactant modelled Absent Association
MESMER_manual.docx