Protocol reaction

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

Input structure

The protocol requires following blocks in the input:

Keywords used

Keywords specific for this protocol:

Other keywords used by this protocol:

Examples

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