TABLE OF CONTENTS

32-calcmol

DESCRIPTION

This example shows how to conveniently calculate a molecule and its molecular-orbital densities from the symbolic molecular SMILES specification.

For SMILES, see: https://en.wikipedia.org/wiki/Simplified_molecular-input_line-entry_system

::pwtk::calcmol requires the OpenBabel program (http://openbabel.org).

EXAMPLE SOURCE FILE

calcmol.pwtk

SOURCE

# 'outdir' & 'pseudo_dir' can also be set with ::pwtk::outdir & ::pwtk::pseudo_dir
outdir ./calcmol
pseudo_dir ./pseudo

# ::pwtk::calcmol only requires pseudopotentials & ecutwfc; other
# input data are set automatically

SYSTEM {
    ecutwfc = 20.0
    ecutrho = 200.0
}
ATOMIC_SPECIES {
    C  1.0  C.pbe-rrkjus.UPF
    H  1.0  H.pbe-rrkjus.UPF
}

# ::pwtk::calcmol syntax is:
#
#    calcmol ?OPTIONS? moleculeName SMILES
#
# where SMILES stands for "Simplified molecular-input line-entry system",
# https://en.wikipedia.org/wiki/Simplified_molecular-input_line-entry_system
#
# SMILES for benzene = "c1ccccc1"

calcmol -relax -vacuum 6 -center -mo benzene c1ccccc1