/usr/share/xcrysden/Tcl/wnDensity.tcl is in xcrysden-data 1.5.53-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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# Author: #
# ------ #
# Anton Kokalj Email: Tone.Kokalj@ijs.si #
# Department of Physical and Organic Chemistry Phone: x 386 1 477 3523 #
# Jozef Stefan Institute Fax: x 386 1 477 3811 #
# Jamova 39, SI-1000 Ljubljana #
# SLOVENIA #
# #
# Source: $XCRYSDEN_TOPDIR/Tcl/wnDensity.tcl
# ------ #
# Copyright (c) 1996-2003 by Anton Kokalj #
#############################################################################
proc wnDensity dir {
global system geng
set filehead [file tail $dir]
if { ! [file isdirectory $dir] } {
# $dir is not a directory; ERROR
ErrorDialog "couldn't find directory \"$dir\" while trying to render wnDensity"
return 0
}
#cd $system(SCRDIR)
#exec cp $dir/$filehead.struct $filehead.struct
#if [catch {exec $system(FORDIR)/str2xcr $filehead}] {
# tk_dialog [WidgetName] ERROR \
# "ERROR while executing \"str2xcr\" program" \
# error 0 OK
# return
#}
#
#set geng(M3_ARGUMENT) [GetGengM3Arg BOHR 95]
##set xcMisc(titlefile) $filehead
#xcCatchExecReturn $system(FORDIR)/gengeom $geng(M1_PRIM) $geng(M2_CELL) \
# $geng(M3_ARGUMENT) 1 1 1 1 \
# $system(SCRDIR)/xc_struc.$system(PID) \
# $system(SCRDIR)/$filehead.xcr
#
# *.output5 & *.rho file must exists!!!
#
foreach file [list $dir/$filehead.output5 $dir/$filehead.rho] {
if { ! [file exists $file] } {
# $dir is not a directory; ERROR
ErrorDialog "couldn't find file \"$file\" while trying to render wnDensity"
return 0
}
}
#xcCatchExecReturn $system(awk) -f $system(AWKDIR)/getOV.awk $dir/$filehead.output5
if { [catch {set vec [exec $system(awk) -f $system(AWKDIR)/getOV.awk \
$dir/$filehead.output5]}] } {
ErrorDialog "error while executing \"getOV.awk\" program"
return
}
#
# since wnOpenSFile routine was called before wnDensity, the struct file
# already converted to $system(SCRDIR)/xc_struc.$system(PID)
set geom [ReadFile $system(SCRDIR)/xc_struc.$system(PID)]
update
set fID [open $dir/$filehead.rho r]
set outID [open $system(SCRDIR)/xc_struc.$system(PID) w]
################################
# make XCRYSDEN STRUCTURE FILE #
################################
puts $outID $geom
puts $outID "BEGIN_BLOCK_DATAGRID2D"
puts $outID "Density_by_WIEN____FILE_generated_by_XCrySDen"
puts $outID "DATAGRID_2D_Total_Density"
#
# WARNING: WIEN is writing grid as (den(i,j),j=1,ny),i=1,nx, BUT
# XCrySDen is reading it as (den(i,j),i=1,nx),j=1,ny
# FIXING: interchange vec-X with vec-Y and interchange nx with ny
#
set i 0
foreach line [split [read -nonewline $fID] \n] {
if { $i == 0 } {
puts $outID [concat [lindex $line 1] [lindex $line 0]]
puts $outID $vec
} else {
# read the rest of the file and write to datagrid
puts $outID $line
}
incr i
}
puts $outID "END_DATAGRID_2D"
puts $outID "END_BLOCK_DATAGRID2D"
flush $outID
close $outID
close $fID
#
# now execute xc_updatestr and ...
#
UpdateStruct .mesa $system(SCRDIR)/xc_struc.$system(PID)
Get_sInfoArray
xc_isodatagrid info
xc_isodatagrid 0 0 1.0
DataGrid2Isosurf
IsoControl2D
}
proc wnDensity2D_or_3D dir {
global prop wn
set wn(filehead) [file tail $dir]
if { ! [file isdirectory $dir] } {
# $dir is not a directory; ERROR
ErrorDialog "couldn't find directory \"$dir\" while trying to render wnDensity"
exit_pr
}
set wn(dir) $dir
# check if *.clmval[up|dn] exists
#if { [glob -nocomplain -- $dir/$filehead.clm*] == {} } {
# tk_dialog [WidgetName] ERROR \
# "ERROR: no \"$filehead.clm*\" files were found !!!" error 0 OK
# exit_pr
# return 0
#}
set wn(lapw5) {x lapw5}
if { $wn(complex) } { set wn(lapw5) {x lapw5 -c} }
#
# this is to prevent inconveniences; otherwise prop is used for CRYSTALXX
#
set prop(type_of_run) RHF
set wn(done) 0
SetIsoSurfArray
#
# ask user what to do: 2D/3D
#
set t [xcToplevel [WidgetName] "wnDensity: 2D/3D plot" \
"wnDensity" . 25 50 1]
grab $t
set f [frame $t.f -relief raised -bd 2 -class StressText]
pack $f -fill both -expand 1
label $f.l -text "Choose 2D/3D Density Plot" -relief groove -bd 2
set d2 [button $f.d2 -text "2D Density Plot" \
-command {global wn; set wn(plot_dim) 2D}]
set d3 [button $f.d3 -text "3D Density Plot" \
-command {global wn; set wn(plot_dim) 3D}]
pack $f.l $d2 $d3 -side top -padx 20 -pady 10 -ipadx 10 -ipady 10
tkwait variable wn(plot_dim)
grab release $t
destroy $t
SetIsoGridSpace \
"wnDensity $wn(plot_dim) Map - Grid Specification" "Grid" \
{WIEN} $wn(plot_dim)
tkwait variable wn(done)
}
proc wnMakeIn5_2D3D {pov {dim 2D}} {
global wn isosurf system
# 2D ... pov stands for points
# 3D ... pov stands for origin & vectors a,b,c
set t [WidgetName]
wnDensityFlags $t
tkwait window $t
set in5_file $wn(filehead).in5
if $wn(complex) {
set in5_file ${in5_file}c
}
if { $dim == "2D" } {
# point 1 will be taken for origin
# point 2 as X-end of plot
# point 3 as Y-end of plot
#
# 0--3 Y/0
# | | |
# 1--2 O/1--X/2
#
# points are in angstroms!!!
# X-vector
set v(0,0) [expr [lindex $pov 6] - [lindex $pov 3]]
set v(0,1) [expr [lindex $pov 7] - [lindex $pov 4]]
set v(0,2) [expr [lindex $pov 8] - [lindex $pov 5]]
# Y-vector
set v(1,0) [expr [lindex $pov 0] - [lindex $pov 3]]
set v(1,1) [expr [lindex $pov 1] - [lindex $pov 4]]
set v(1,2) [expr [lindex $pov 2] - [lindex $pov 5]]
} elseif { $dim == "3D" } {
# pov == origin
# vec1
# vec2
# vec3
set o(0) [lindex $pov 0]
set o(1) [lindex $pov 1]
set o(2) [lindex $pov 2]
xcDebug -debug "Pov:: $pov"
xcDebug -debug "Origin:: $o(0) $o(1) $o(2)"
for {set i 0} {$i < 3} {incr i} {
for {set j 0} {$j <3} {incr j} {
set index [expr 3 + $i*3 + $j]
set v($i,$j) [lindex $pov $index]
}
xcDebug -debug "Vector:: $v($i,0) $v($i,1) $v($i,2)"
}
} else {
xcDebug -stderr "************\nunknown dim $dim, must be 2D or 3D\n************"
return
}
set distX [expr sqrt($v(0,0)*$v(0,0) + $v(0,1)*$v(0,1) + $v(0,2)*$v(0,2))]
set distY [expr sqrt($v(1,0)*$v(1,0) + $v(1,1)*$v(1,1) + $v(1,2)*$v(1,2))]
if { $isosurf(res_type) == "points" } {
# let this be number of points in X-dir
set wn(nx) $isosurf(resol_poi)
set res [expr $distX / $wn(nx)]
} else {
if { $isosurf(mb_angs/bohr) == "Angstroms" } {
set res [expr double($isosurf(resol_ang))]
} else {
set res [Bohr2Angs $isosurf(resol_ang)]
}
set wn(nx) [expr round( $distX / $res )]
}
set wn(ny) [expr round( $distY / $res )]
if { $dim == "3D" } {
set distZ [expr sqrt($v(2,0)*$v(2,0) + $v(2,1)*$v(2,1) + $v(2,2)*$v(2,2))]
set wn(nz) [expr round( $distZ / $res )]
}
# find out the crystal lattice type from *.struct file??? This is save !!!
# WIENXX convention:
# P -> primitive
# F,B,C -> conventional
# H -> hexagonal primitive
# R -> hexagonal primitive (that is conventional for R)
switch -glob -- $wn(lattice_type) {
P* { set vtype prim }
F* { set vtype conv }
B* { set vtype conv }
CXY* { set vtype conv }
CYZ* { set vtype conv }
CXZ* { set vtype conv }
R* { set vtype prim }
H* { set vtype prim }
}
if { $dim == "2D" } {
set frpoi [xc_isospacesel .mesa fractcoor -vtype $vtype]
set m 1.0e7
set im [expr round($m)]
for {set i 0} {$i < 3} {incr i} {
set y($i) [expr round([lindex $frpoi [expr 0 + $i]] * $m)]
set o($i) [expr round([lindex $frpoi [expr 3 + $i]] * $m)]
set x($i) [expr round([lindex $frpoi [expr 6 + $i]] * $m)]
}
append in5 "[format %12d%12d%12d%14d $o(0) $o(1) $o(2) $im]\n"
append in5 "[format %12d%12d%12d%14d $x(0) $x(1) $x(2) $im]\n"
append in5 "[format %12d%12d%12d%14d $y(0) $y(1) $y(2) $im]\n"
append in5 "$wn(xnsh) $wn(ynsh) $wn(znsh)\n"
append in5 "$wn(nx) $wn(ny)\n"
append in5 [format "%-4s%-4s\n" $wn(den_flag) $wn(spin_flag)]
append in5 [format "%-4s%-4s%-4s\n" \
$wn(unit_flag) $wn(norm_flag) $wn(debu_flag)]
append in5 "NONORTHO\n"
#########################################################
# now give user the opportunity to check the *.in5 file #
#########################################################
set t [xcToplevel $t "wnDensity: check the $in5_file file" \
"wnDensity" . 25 50 1]
set f1 [frame $t.1 -relief raised -bd 2]
set f2 [frame $t.2 -relief raised -bd 2]
pack $f1 -side top -expand 1 -fill both
pack $f2 -side top -expand 1 -fill x
set text [DispText $f1.f $in5 60 15]
set ok [DefaultButton $f2.ok -text OK \
-command [list wnMakeIn5_2D_OK $t $text $in5_file]]
pack $ok -padx 5 -pady 10 -expand 1
} elseif { $dim == "3D" } {
# convert from Cartesian to Fractional
set orig [xc_fractcoor -ctype $vtype -coor [list $o(0) $o(1) $o(2)]]
set ori(0) [lindex $orig 0]
set ori(1) [lindex $orig 1]
set ori(2) [lindex $orig 2]
for {set i 0} {$i < 3} {incr i} {
set lvec [xc_fractcoor -ctype $vtype -coor [list $v($i,0) $v($i,1) $v($i,2)]]
for {set j 0} {$j < 3} {incr j} {
set vec($i,$j) [lindex $lvec $j]
}
}
set t [xcToplevel [WidgetName] "Calculating 3D grid of points" \
"Calculating" . 100 250 1]
set f [frame $t.f -relief raised -bd 2 -width 400]
pack $f -expand 1
set wn(calc_slice_text) "\
\n\
*** WIEN is calculating 3D grid of points ***\n\
\n\
Number of 2D slices to calculate: $wn(nz)\n\
Progress: 0 / $wn(nz)\n"
set m [label $f.m \
-textvariable wn(calc_slice_text) \
-justify left \
-relief groove -bd 2]
set ff [frame $f.f]
pack $m $ff -side top -expand 1 -ipadx 10 -ipady 10 -padx 10 -pady 10
set w [expr round(300 / $wn(nz))]
for {set i 1} {$i <= $wn(nz)} {incr i} {
frame $ff.$i -width $w -height 8m -relief raised -bd 2
grid $ff.$i -row 0 -column $i
}
file delete $system(SCRDIR)/xc_rho.$system(PID)
#############################
# vec(-1,$) is DUMMY & must be (0.0, 0.0, 0.0)!!!!!!!!
set vec(-1,0) 0.0
set vec(-1,1) 0.0
set vec(-1,2) 0.0
for {set i 0} {$i < $wn(nz)} {incr i} {
############################
# calculate $wn(nz) slices #
############################
if { $wn(nz) > 1 } {
set f [expr $i / [expr $wn(nz) - 1.0]]
} else {
set f 1.0
}
for {set j -1} {$j < 2} {incr j} {
set jj [expr $j + 1]
set v($i,$jj,0) \
[expr $ori(0) + $vec($j,0) + $f * $vec(2,0)]
set v($i,$jj,1) \
[expr $ori(1) + $vec($j,1) + $f * $vec(2,1)]
set v($i,$jj,2) \
[expr $ori(2) + $vec($j,2) + $f * $vec(2,2)]
xcDebug "Factor:: $f\nEndPoints:: $v($i,$jj,0) $v($i,$jj,1) $v($i,$jj,2)\n"
}
set m 1.0e7
set im [expr round($m)]
for {set j 0} {$j < 3} {incr j} {
set io($j) [expr round( $v($i,0,$j) * $m)]
set ix($j) [expr round( $v($i,1,$j) * $m)]
set iy($j) [expr round( $v($i,2,$j) * $m)]
}
set in5 {}
append in5 "[format %12d%12d%12d%14d $io(0) $io(1) $io(2) $im]\n"
append in5 "[format %12d%12d%12d%14d $ix(0) $ix(1) $ix(2) $im]\n"
append in5 "[format %12d%12d%12d%14d $iy(0) $iy(1) $iy(2) $im]\n"
append in5 "$wn(xnsh) $wn(ynsh) $wn(znsh)\n"
append in5 "$wn(nx) $wn(ny)\n"
append in5 [format "%-4s%-4s\n" $wn(den_flag) $wn(spin_flag)]
append in5 [format "%-4s%-4s%-4s\n" \
$wn(unit_flag) $wn(norm_flag) $wn(debu_flag)]
append in5 "NONORTHO\n"
xcDebug "****************************"
xcDebug "Calculating slice::::\n$in5"
xcDebug "****************************"
if { $i > 0 } {
file copy -force $in5_file ${in5_file}.$i
}
WriteFile $wn(dir)/$in5_file $in5 w
#
# now run WIEN2k
#
if { ![wnRunWIEN $wn(exe_flag) {WIEN program is calculating the grid of points now. It can take some time, so PLEASE WAIT!!!} \
$wn(dir)/$wn(filehead).output5] } {
# exit, since an error occured
destroy $t
exit_pr
return
}
# now append the *.rho file to $system(SCRDIR)/xc_rho.$$
wnAppendRhoFile
# update "progress" window
set ii [expr $i + 1]
set wn(calc_slice_text) "\
\n\
*** WIEN is calculating 3D grid of points ***\n\
\n\
Number of 2D slices to calculate: $wn(nz)\n\
Progress: $ii / $wn(nz)\n"
$ff.$ii config -bg "#5f5"
update
}
# destro progress widget
destroy $t
################################
# make XCRYSDEN STRUCTURE FILE #
################################
# since wnOpenSFile routine was called before wnDensity,
# the struct file already converted to
# $system(SCRDIR)/xc_struc.$system(PID)
set geom [ReadFile $system(SCRDIR)/xc_struc.$system(PID)]
update
set fID [open $system(SCRDIR)/xc_rho.$system(PID) r]
set outID [open $system(SCRDIR)/xc_struc.$system(PID) w]
#
# WARNING: WIEN is writing grid as (den(i,j),j=1,ny),i=1,nx, BUT
# XCrySDen is reading it as (den(i,j),i=1,nx),j=1,ny
# FIXING: interchange vec-X with vec-Y and interchange nx with ny
#
puts $outID $geom
puts $outID "BEGIN_BLOCK_DATAGRID3D"
puts $outID "Density_by_WIEN____FILE_generated_by_XCrySDen"
puts $outID "DATAGRID_3D_Total_Density"
puts $outID "$wn(ny) $wn(nx) $wn(nz)"
puts $outID "$o(0) $o(1) $o(2)"
puts $outID "$v(1,0) $v(1,1) $v(1,2)"
puts $outID "$v(0,0) $v(0,1) $v(0,2)"
puts $outID "$v(2,0) $v(2,1) $v(2,2)"
foreach line [split [read -nonewline $fID] \n] {
# read the rho file and write to struct file
puts $outID $line
}
puts $outID "END_DATAGRID_3D"
puts $outID "END_BLOCK_DATAGRID3D"
flush $outID
close $outID
close $fID
# rho file is no more needed, delete it
file delete $system(SCRDIR)/xc_rho.$system(PID)
#
# now execute xc_updatestr and render isosurface
#
UpdateStruct .mesa $system(SCRDIR)/xc_struc.$system(PID)
Get_sInfoArray
xc_isodatagrid info
xc_isodatagrid 0 0 1.0
DataGrid2Isosurf
IsoControl
}
}
proc wnAppendRhoFile {} {
global wn system
set out [ReadFile -nonewline $wn(dir)/$wn(filehead).rho]
set il 0
foreach line [split $out \n] {
if { $il > 0 } {
append output "$line\n"
}
incr il
}
#if { ! [file exists $system(SCRDIR)/xc_rho.$system(PID)] } {
# #exec touch $system(SCRDIR)/xc_rho.$system(PID)
# WriteFile $system(SCRDIR)/xc_rho.$system(PID) {}
#}
WriteFile $system(SCRDIR)/xc_rho.$system(PID) $output a
}
proc wnMakeIn5_2D_OK {t textw in5_file} {
global wn
# t ... toplevel
# textw ... text widget
set text [$textw get 1.0 end]
xcDebug "${in5_file}::\n$text"
WriteFile $wn(dir)/$in5_file $text w
CancelProc $t
#
# now run WIEN2k
#
if ![wnRunWIEN $wn(exe_flag) {WIEN program is calculating the grid of points now. It can take some time, so PLEASE WAIT!!!} \
$wn(dir)/$wn(filehead).output5] {
# exit, since an error occured
exit_pr
return
}
wnDensity $wn(dir)
}
proc wnDensityFlags t {
global wn
# some parameters must be queried
xcToplevel $t "wnDensity - Specify Flags" "wnDensity" . 25 50 1
set f1 [frame $t.f1 -relief raised -bd 2]
set f2 [frame $t.f2 -relief raised -bd 2]
pack $f1 $f2 -side top -expand 1 -fill both
set wn(exe_flag) $wn(lapw5)
if { $wn(spin_polarized) == 1 } {
set wn(exe_flag) [concat $wn(lapw5) -up]
}
set wn(xnsh) 3
set wn(ynsh) 2
set wn(znsh) 3
set wn(den_flag) RHO
set wn(spin_flag) ADD
set wn(unit_flag) ATU
set wn(norm_flag) VAL
set wn(debu_flag) NODEBUG
frame $f1.f
FillEntries $f1.f {"# of X shells:" "# of Y shells:" "# of Z shells:"} \
{wn(xnsh) wn(ynsh) wn(znsh)} 14 10
xcDebug -debug "wn(spin_polarized) = $wn(spin_polarized)"
if $wn(spin_polarized) {
set mt1 [concat $wn(lapw5) -up]
set mt2 [concat $wn(lapw5) -dn]
set mb_exeflag [xcMenuButton $f1 -labeltext "Execution Flag:" \
-labelwidth 14 \
-textvariable wn(exe_flag) \
-menu [list \
$mt1 {set wn(exe_flag) [concat $wn(lapw5) -up]} \
$mt2 {set wn(exe_flag) [concat $wn(lapw5) -dn]}]]
}
set mb_den [xcMenuButton $f1 -labeltext "Density Flag:" -labelwidth 14 \
-textvariable wn(den_flag) \
-menu {
"SCF Density (RHO)" {set wn(den_flag) RHO}
"Difference Density (DIFF)" {set wn(den_flag) DIFF}
"Superposition of Atomic Density (OVER)" {set wn(den_flag) OVER}
}]
set mb_spin [xcMenuButton $f1 -labeltext "Spin Flag:" -labelwidth 14 \
-textvariable wn(spin_flag) \
-menu {
"Total Density (ADD)" {set wn(spin_flag) ADD}
"Spin Density (SUB)" {set wn(spin_flag) SUB}
}]
if !$wn(spin_polarized) {
xcDisableAll $mb_spin
}
set mb_unit [xcMenuButton $f1 -labeltext "Unit Flag:" -labelwidth 14 \
-textvariable wn(unit_flag) \
-menu {
"e / a.u.^3 (ATU)" {set wn(unit_flag) ATU}
"e / A^3 (ANG)" {set wn(unit_flag) ANG}
}]
set mb_norm [xcMenuButton $f1 -labeltext "Norm. Flag:" -labelwidth 14 \
-textvariable wn(norm_flag) \
-menu {
"Valence Density (VAL)" {set wn(norm_flag) VAL}
"Total Density (TOT)" {set wn(norm_flag) TOT}
}]
set mb_debu [xcMenuButton $f1 -labeltext "Debug Flag:" -labelwidth 14 \
-textvariable wn(debu_flag) \
-menu {
"No Debugging (NODEBUG)" {set wn(debu_flag) NODEBUG}
"Debugging (DEBUG)" {set wn(debu_flag) DEBUG}
}]
grid $f1.f -column 0 -row 0 -sticky w -padx 10 -pady 5
if $wn(spin_polarized) {
grid $mb_exeflag -column 0 -row 1 -sticky w -padx 10 -pady 5
}
grid $mb_den -column 0 -row 2 -sticky w -padx 10 -pady 5
grid $mb_spin -column 0 -row 3 -sticky w -padx 10 -pady 5
grid $mb_unit -column 0 -row 4 -sticky w -padx 10 -pady 5
grid $mb_norm -column 0 -row 5 -sticky w -padx 10 -pady 5
grid $mb_debu -column 0 -row 6 -sticky w -padx 10 -pady 5
# let the user determine also execution type
set ok [DefaultButton $f2.ok -text OK \
-command [list wnDensityFlagsOK $t]]
set can [button $f2.can -text Cancel -command exit_pr]
pack $can $ok -side left -padx 5 -pady 10 -expand 1
}
proc wnDensityFlagsOK t {
global wn
#
# so far user will have to choose correct flags,
# no checking will be performed
#
CancelProc $t
set wn(done1) 1; #this is not needed !!!
}
# tmp proc::
#proc PrintDecIdv list {
#
# set idv [lindex $list 3]
#
# set i0 [expr double([lindex $list 0]) / double($idv)]
# set i1 [expr double([lindex $list 1]) / double($idv)]
# set i2 [expr double([lindex $list 2]) / double($idv)]
# xcDebug "$i0 $i1 $i2"
#}
#lappend auto_path "/home/tone/prog/XCrys/XCrySDen0.1"
#button .b -text TONE
#entry .e -text TONE
#set xcFonts(normal) [lindex [.b configure -font] end]
#set xcFonts(normal_entry) [lindex [.e configure -font] end]
#set xcFonts(small) [ModifyFontSize .b 10 \
# {-family helvetica -slant r -weight bold}]
#set xcFonts(small_entry) [ModifyFontSize .e 10 \
# {-family helvetica -slant r -weight normal}]
#destroy .b .e
#
#wnDensityFlags [WidgetName]
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