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Instructions.md

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Instructions

Step-1: Set-up

  • Open terminal
  • Run conda activate chemstarx

Step-2: Reactant optimization

  • Open Avogadro
  • Build Methyliodide molecule
  • Go to Build > Cartesian Editor > Sort by > Element
  • Generate input for geometry optimization using Avogadro NWCHem template Extensions > NWChem
  • Add required blocks of Basis sets, Iodine basis and XYZ output from "utilites" file
  • Run mpirun -np 4 nwchem CH3I_GS.nw > CH3I_GS.nwo in terminal

Step-3: Product optimization

  • Open Avogadro
  • Build Methylchloride molecule
  • Go to Build > Cartesian Editor > Sort by > Element
  • Generate input for geometry optimization using Avogadro NWCHem template Extensions > NWChem
  • Add required blocks of Basis sets and XYZ output from "utilites" file
  • Run mpirun -np 4 nwchem CH3Cl_GS.nw > CH3Cl_GS.nwo in terminal

Step-4: PES preliminary

  • Open Avogadro

  • Build CH3I + Cl- molecule

  • Go to Build > Cartersian Editor > Sort by > Element

  • Generate input for geometry optimization using Avogadro NWCHem template

  • Set C-Cl distance to 3.000 angstroms

  • Add required blocks of Basis sets, Iodine basis, XYZ output and geometric constraints from "utilites" file

  • Run mpirun -np 4 nwchem CH3I_Cl.nw > CH3I_Cl.nwo in terminal

  • Open Avogadro

  • Build CH3Cl + I- molecule

  • Go to Build > Cartersian Editor > Sort by > Element

  • Generate input for geometry optimization using Avogadro NWCHem template

  • Set C-I distance to 3.000 angstroms

  • Add required blocks of Basis sets, Iodine basis, XYZ output and geometric constraints from "utilites" file

  • Run mpirun -np 4 nwchem CH3I_Cl.nw > CH3I_Cl.nwo in terminal

Step-5: LIIC Calculation

  • Open the latest XYZ file for CH3I_Cl

  • Build Menu > Cartesian Editor > Sort bt "Element"

  • Copy Python block for LIIC from "utilities"

  • Fill in appropirate values for x0, y0, xmax, xmin and npts

  • mpirun -np 4 nwchem CH3I_Cl_PES1.nw > CH3I_Cl_PES1.nwo

  • Open the latest XYZ file for CH3Cl_I

  • Build Menu > Cartesian Editor > Sort bt "Element"

  • Copy Python block for LIIC from "utilities"

  • Fill in appropirate values for x0, y0, xmax, xmin and npts

  • mpirun -np 4 nwchem CH3Cl_I_PES1.nw > CH3Cl_I_PES1.nwo

Step-6: 2D PES Calculation

  • Open the latest XYZ file for CH3I_Cl

  • Build Menu > Cartesian Editor > Sort bt "Element"

  • Copy Python block for 2D PES from "utilities"

  • Fill in appropirate values for x0, y0, xmax, xmin and npts

  • mpirun -np 4 nwchem CH3I_Cl_PES2.nw > CH3I_Cl_PES2.nwo

  • Open the latest XYZ file for CH3Cl_I

  • Build Menu > Cartesian Editor > Sort bt "Element"

  • Copy Python block for 2D PES from "utilities"

  • Fill in appropirate values for x0, y0, xmax, xmin and npts

  • mpirun -np 4 nwchem CH3Cl_I_PES2.nw > CH3Cl_I_PES2.nwo