Protocol automating calculation of reaction energies. It can parse a reaction formula in the SMILES notation and generate geometries of the molecules.

- calculation - Setup for the calculation

The following examples, along with all other files needed to run them, can be found in the directory cuby4/protocols/reaction/examples

```
#===============================================================================
# Reaction protocol example 1: simple reaction
#===============================================================================
# Automated calculation of reaction energetics
job: reaction
# The reaction is specified by a formula with defined stoichiometry and
# arbitrary names of the compounds
reaction_formula: 2 H2 + O2 -> 2 H2O
# For each compound, a geometry is provided
reaction_geometries:
H2: h2.xyz
O2: o2.xyz
H2O: h2o.xyz
# Calculation is defined only once
calculation:
job: energy
interface: dftb
method: scc-dftb
charge: 0
```

```
#===============================================================================
# Reaction protocol example 2: multi-step calculation
#===============================================================================
# This example features the same reaction as example 1 to for each compound,
# a multi-step calculation is applied
job: reaction
reaction_formula: 2 H2 + O2 -> 2 H2O
reaction_geometries:
H2: h2.xyz
O2: o2.xyz
H2O: h2o.xyz
calculation:
# Multi-step protocol is used
job: multistep
multistep_print: no
steps: opt, energy
# First step - geometry optimization
# Geometry is taken from parent block, it is the 'calculation' level
calculation_opt:
job: optimize
optimize_print: "" # Disable printing of optimization steps
interface: dftb
method: scc-dftb
charge: 0
geometry: parent_block
# Second step: energy calculation
# The geometry is taken from the previous step, it is after the optimization
calculation_energy:
job: energy
interface: dftb
method: scc-dftb
charge: 0
geometry: previous_step
```

```
#===============================================================================
# Reaction protocol example 3: SMILES notation
#===============================================================================
# This example demonstrates the use SMILES notation in the reaction formula
job: reaction
# The SMILES mode has to be switched on
reaction_smiles: yes
# Instead of just labels, the items are SMILES formulas directly
reaction_formula: 2 C=C -> C1CCC1
# Then, coordinates are generated from SMILES, no specification of geometries
# is needed
calculation:
job: multistep
multistep_print: no
steps: opt, energy
calculation_opt:
job: optimize
optimize_print: ""
interface: dftb
method: scc-dftb
charge: 0
geometry: parent_block
calculation_energy:
job: energy
interface: dftb
method: scc-dftb
charge: 0
geometry: previous_step
```