TABLE OF CONTENTS
::pwtk::calcmol
SYNOPSIS
proc ::pwtk::calcmol {args} {
DESCRIPTION
Utility for making a fast molecule-in-a-box calculation. Orthorhombic "box" will be automatically constructed, based on the size of the molecule.
Beware that this routine requires obabel and xsf2_manipulator programs.
USAGE
calcmol [-relax|-scf] [-vacuum vacuum] [-center|-orig] [-mo] molecule SMILE
ARGUMENTS
- [options] -- see OPTIONS below
- molecule -- name of molecule
- SMILE -- SMILE specification of molecular structure (SMILE stands for "Simplified Molecular-Input Line-Entry")
Default options: -relax -center -vacuum 8.0
OPTIONS
List of options:
-relax|-scf make either a molecular structural relaxation (-relax)
or SCF calculation (-scf); Default = -relax
-vacuum <size> size of vacuum around the molecule; Default = 8 Angstroms
-center|-orig shift the molecule either to the center or to the
origin of the simulation BOX; Default = -center
-mo calculate signed molecular-orbital densities and write them to XSF files
-magn <nelec> total magnetization, i.e., number of unpaired electrons
-smear <value> smearing value for occupiations = 'smearing'
(e.g., use in case of convergency problems;
usable values are in range of, say, 1e-2 to 1e-3)
SOURCE
# check if obabel and xsf_manipulator exist if { [auto_execok obabel] == "" } { ::pwtk::error {"obabel" program does not exist} 1 } if { [auto_execok xsf2_manipulator] == "" } { ::pwtk::error {"xsf2_manipulator" program does not exist} 1 } # parse options set options { {relax "make a molecular structural relaxation"} {scf "make a single point SCF calculation"} {vacuum.arg 8.0 "size of vacuum around the molecule (the same in each direction)"} {center "shift the molecule to the center of the simulation BOX"} {orig "shift the molecule to the origin of the simulation BOX"} {mo "calculate signed molecular-orbital densities and write them to XSF file"} {magn.arg 0 "total magnetization, i.e., number of unpaired electrons"} {smear.arg -1 "smearing value for occupiations = 'smearing' (e.g., use in case of convergency problems; usable values are in range of, say, 1e-2 to 1e-3)"} } set usage " Usage: calcmol \[-relax|-scf] \[-vacuum value] \[-center|-orig] \[-mo] \[-magn value] \[-smear value] molecule SMILE where: molecule : name of molecule SMILE : SMILE specification of molecular structure (SMILE stands for \"Simplified Molecular-Input Line-Entry\") options are:" set args_copy $args array set opt [::cmdline::getoptions args $options $usage] # consistency-check if { $opt(relax) && $opt(scf) } { ::pwtk::error "incompatible -relax and -scf options specified; please specify only one of them" 1 } if { $opt(center) && $opt(orig) } { ::pwtk::error "incompatible -center and -orig options specified; please specify only one of them" 1 } # # SET-UP # set calc "relax" set origin "0.5 0.5 0.5" set shift center if { $opt(scf) } { set calc "scf" } if { $opt(orig) } { set origin "0.0 0.0 0.0"; set shift origin } set name [lindex $args 0] set smile [lindex $args 1] set prefix [regsub , $name .]; # get rid of "," printTitle CALCMOL "Building and calculating \"$name\" molecular structure" print "Specified command-line : $args_copy\n" if { $smile == {} || [llength $args] != 2 } { puts [::cmdline::usage $options $usage] exit 1 } # # GENERATE STRUCTURE from SMILE # catch { exec obabel -:$smile -oxyz -O /tmp/smile.xyz --gen3D --best } set xyz [::pwtk::skipEmptyLines [readFile /tmp/smile.xyz]] set xyzn [split $xyz \n] set nat [lindex $xyzn 0] set coor [join [lrange $xyzn 1 end] \n] if { $nat == 1 } { set calc scf } print " Structure name : $name" print " SMILE : $smile" print "Calculation type : [string toupper $calc]\n" print "Summary of generated molecular structure from SMILE" print "Number of atoms : $nat" #print "Atomic positions :\n" #puts $coor # put molecule in a box print " MOLECULE in a BOX SETTINGS: - requested vacuum size (in each direction): $opt(vacuum) Angstroms - molecule shifted to : box-$shift" set head "MOLECULE\nPRIMCOORD\n" append head $xyz\n append head "BOXIFY\n$opt(vacuum)\n$origin" writeFile /tmp/smile.xsf2 $head exec xsf2_manipulator /tmp/smile.xsf2 /tmp/smile.xsf2_angs # # CALCULATE # input_pushpop { # pw.x CONTROL " calculation = '$calc', prefix = '$prefix' " if { $calc == "relax" } { IONS "" } ::pwtk::pwi::CELL_PARAMETERS_and_ATOMIC_POSITIONS_fromXSF /tmp/smile.xsf2_angs print "Box unit-cell vectors:" print [::pwtk::pwi::CELL_PARAMETERS_math_parser [::pwtk::pwi::getPrimVec]] print "Box atomic positions:" print [::pwtk::pwi::ATOMIC_POSITIONS_math_parser [::pwtk::pwi::getAtmPos]] # smearing ? if { $opt(smear) > 0.0 } { set smearing [::pwtk::input::namelistGetVarValue SYSTEM smearing] if { $smearing == {} } { set smearing 'm-p' } set occ "occupations = 'smearing', smearing = $smearing, degauss = $opt(smear)" print "\nSmearing requested :" print "( $occ )\n" SYSTEM $occ } # set the spin/magnetization setup set nbnd [spinSetup $opt(magn) $opt(mo)] if { $calc == "scf" } { printTitle SCF "making an [string toupper $calc] calculation of \"$name\" via pw.x" } else { printTitle RELAX "making a [string toupper $calc] calculation of \"$name\" via pw.x" } runPW pw.$name.$calc # do we want to calculate also MO ? if { $opt(mo) } { INPUTPP " filplot = 'psi2.$prefix' plot_num = 7 kpoint = 1 kband(1) = 1 kband(2) = $nbnd lsign = .true. " PLOT { nfile = 1, weight(1) = 1.0, iflag = 3, fileout = '.xsf' output_format = 5, } printTitle ORBITALS "Calculating valence signed molecular-orbital densities (up to LUMO orbital)" runPP pp.$name.psi2 set last [format %03d $nbnd] print "Molecular orbital densities written to files : psi2.${prefix}_K001_B001.xsf, ..., psi2.${prefix}_K001_B$last.xsf\n" print "You can visualize signed molecular-obital densities as, e.g.: xcrysden --xsf psi2.${prefix}_K001_B001.xsf\n" # delete the PP files #print "(deleting temporary psi2.${prefix}_K001_B??? files)" foreach file [glob -nocomplain psi2.${prefix}_K001_B???] { file delete $file } } } }