/usr/share/xcrysden/Tcl/isoStuff.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/isoStuff.tcl
# ------ #
# Copyright (c) 1996-2003 by Anton Kokalj #
#############################################################################
proc SetXC_Iso {{dim 3D}} {
global isosurf dif_isosurf prop isosign isodata
if { ! [info exists dif_isosurf(dif_map)] } {
set dif_isosurf(dif_map) 0
}
######################
# ISOSIGN parameters #
######################
set isosign {}
append isosign "xc_isosign 3 0 +1; "
append isosign "xc_isosign 2 0 +1; "
append isosign "xc_isosign 1 all +1; "
if { $dif_isosurf(dif_map) == 1 } {
###################
# DIFFERENCE MAPS #
###################
append isosign "xc_isosign 3 1 -1; "
}
if { $prop(spin_case) } {
#############
# SPIN CASE #
#############
if { $isosurf(spin) == "ALPHA" } {
append isosign "xc_isosign 0 0 +1; "
append isosign "xc_isosign 0 1 +1; "
} elseif { $isosurf(spin) == "BETA" } {
append isosign "xc_isosign 0 0 +1; "
append isosign "xc_isosign 0 1 -1; "
} elseif { $isosurf(spin) == "ALPHA+BETA" } {
append isosign "xc_isosign 0 0 +1; "
append isosign "xc_isosign 0 1 0; "
} elseif { $isosurf(spin) == "ALPHA-BETA" } {
append isosign "xc_isosign 0 0 0; "
append isosign "xc_isosign 0 1 +1; "
}
} else {
#################
# NON-SPIN CASE #
#################
append isosign "xc_isosign 0 0 +1; "
}
######################
# ISODATA parameters #
######################
set NPZ_1 [expr $prop(NPZ) - 1]
set isodata {}
if { $dif_isosurf(dif_map) == 0 } {
if $prop(spin_case) {
if { $isosurf(spin) == "ALPHA+BETA" } {
if { $dim == "3D" } {
append isodata "xc_isodata 0 0 0-$NPZ_1 0; "
} elseif { $dim == "2D" } {
append isodata "xc_isodata 0 0 0 0; "
}
} elseif { $isosurf(spin) == "ALPHA-BETA" } {
if { $dim == "3D" } {
append isodata "xc_isodata 0 0 0-$NPZ_1 1; "
} elseif { $dim == "2D" } {
append isodata "xc_isodata 0 0 0 1; "
}
} elseif { $isosurf(spin) == "ALPHA" || \
$isosurf(spin) == "BETA" } {
MakeIsoData $NPZ_1 0 0
}
} else {
if { $dim == "3D" } {
append isodata "xc_isodata 0 0 0-$NPZ_1 0; "
} elseif { $dim == "2D" } {
append isodata "xc_isodata 0 0 0 0; "
}
}
} elseif { $dif_isosurf(dif_map) == 1 } {
###################
# DIFFERENCE MAPS #
###################
if $prop(spin_case) {
if { $isosurf(spin) == "ALPHA+BETA" } {
if { $dim == "3D" } {
append isodata "xc_isodata 0 0 0-$NPZ_1 0; "
append isodata "xc_isodata 1 0 0-$NPZ_1 0; "
} elseif { $dim == "2D" } {
append isodata "xc_isodata 0 0 0 0; "
append isodata "xc_isodata 1 0 0 0; "
}
} elseif { $isosurf(spin) == "ALPHA-BETA" } {
if { $dim == "3D" } {
append isodata "xc_isodata 0 0 0-$NPZ_1 1; "
append isodata "xc_isodata 1 0 0-$NPZ_1 1; "
} elseif { $dim == "2D" } {
append isodata "xc_isodata 0 0 0 1; "
append isodata "xc_isodata 1 0 0 1; "
}
} elseif { $isosurf(spin) == "ALPHA" || \
$isosurf(spin) == "BETA" } {
MakeIsoData $NPZ_1 0 0
MakeIsoData $NPZ_1 1 0
}
} else {
# RHF
if { $dim == "3D" } {
append isodata "xc_isodata 0 0 0-$NPZ_1 0; "
append isodata "xc_isodata 1 0 0-$NPZ_1 0; "
} elseif { $dim == "2D" } {
append isodata "xc_isodata 0 0 0 0; "
append isodata "xc_isodata 1 0 0 0; "
}
}
}
}
proc MakeIsoData {NPZ_1 stack3 stack2} {
global isodata
# because xc_isodata must be specified in sequential fashion
# care must be taken
xcDebug "MakeIsoData:: $NPZ_1"
for {set i 0} {$i <= $NPZ_1} {incr i} {
append isodata "xc_isodata $stack3 $stack2 $i 0; "
append isodata "xc_isodata $stack3 $stack2 $i 1; "
}
}
proc GetCrystalVec {which_vec nvec} {
global vec system
# which_vec.......either prim, conv; lately converted to PRIMVEC/CONVVEC
# nvec............number of vectors to read!!!!
if { $which_vec != "prim" && $which_vec != "conv" } {
tk_dialog [WidgetName] ERROR "ERROR: this is bug in program, please report to author !!!\nCode: GetCrystalVec {which_vec}" error 0 OK
return
}
# if { $which_vec == "prim" } { set which_vec "PRIMVEC" }
# if { $which_vec == "conv" } { set which_vec "CONVVEC" }
if { $which_vec == "prim" } {
set which_vec "PRIMVEC"
} else {
set which_vec "CONVVEC"
}
# xc_gengeom must automatically exists when In properties mode
# (c95_properties_render)
set fileID [open "$system(SCRDIR)/xc_gengeom.$system(PID)" r]
# initialise vec($,$)
for {set i 0} {$i < 3} {incr i} {
for {set j 0} {$j < 3} {incr j} {
set vec($i,$j) 0
}
}
set n 0
set output [split [read $fileID] \n]
foreach line $output {
xcDebug "line: $line"
if [string match " $which_vec*" $line] {
set n1 [expr $n + 1]
set n2 [expr $n + 2]
set n3 [expr $n + 3]
for {set j 0} {$j < $nvec} {incr j} {
set vec(0,$j) [Angs2Bohr [lindex [lindex $output $n1] $j]]
set vec(1,$j) [Angs2Bohr [lindex [lindex $output $n2] $j]]
set vec(2,$j) [Angs2Bohr [lindex [lindex $output $n3] $j]]
xcDebug "PRIMVEC: $vec(0,$j) $vec(1,$j) $vec(2,$j)\n"
}
break
}
incr n
}
close $fileID
}
# this is new routine (Mon May 3 13:02:04 CEST 1999), which is now used
# instead of GetCrystalVec, since xc_isospacesel is used now !!!
proc GetCageVecOrig pov {
global vec isosurf
# which_vec.......either prim, conv; lately converted to PRIMVEC/CONVVEC
# nvec............number of vectors to read!!!!
set isosurf(origin,0) [Angs2Bohr [lindex $pov 0]]
set isosurf(origin,1) [Angs2Bohr [lindex $pov 1]]
set isosurf(origin,2) [Angs2Bohr [lindex $pov 2]]
for {set i 0} {$i < 3} {incr i} {
for {set j 0} {$j <3} {incr j} {
set index [expr 3 + $i*3 + $j]
set vec($i,$j) [Angs2Bohr [lindex $pov $index]]
}
}
}
proc GetNPY {com} {
global vec prop isosurf
# vec.........crystal vectors in Bohrs
if { $isosurf(res_type) == "points" } {
set prop(NPY) $isosurf(resol_poi)
} else {
# ANGSTROMS OR BOHRS; convert to NPY
if { $com == "ECHD" } {
# take vec(1); look at "GetNumberOfPoints"
set distY [expr sqrt( \
$vec(1,0) * $vec(1,0) + \
$vec(1,1) * $vec(1,1) + \
$vec(1,2) * $vec(1,2))]
} else {
# for "ECHG and rest" take vec(0); look at "GetNumberOfPoints"
set distY [expr sqrt( \
$vec(0,0) * $vec(0,0) + \
$vec(0,1) * $vec(0,1) + \
$vec(0,2) * $vec(0,2))]
}
if { $isosurf(mb_angs/bohr) == "Angstroms" } {
set res [Angs2Bohr $isosurf(resol_ang)]
} else {
set res $isosurf(resol_ang)
}
set prop(NPY) [expr round( $distY / $res )]
}
}
proc GetNumberOfPoints {command dim} {
global prop vec
# dim.............dimension of map to render 2/3
if { $command == "ECHD" } {
#######################################################################
# the order of points submited must to "properties" program must be:
# ---------------------------------------------------------------------
# for ECHD:
# ( 1,NPY)
# ( 1, 1)
# (NPX, 1)
#
# so the order of points is:
# ECHD_order == point2, point0, point1
# and because point2 is inheriter of vec(1), it is vec(1) who is
# criteria for NPY
# ---------------------------------------------------------------------
set disY [expr sqrt( \
$vec(1,0) * $vec(1,0) + \
$vec(1,1) * $vec(1,1) + \
$vec(1,2) * $vec(1,2))]
set dY [expr $disY / [expr $prop(NPY) - 1.0]]
xcDebug "distY = $disY; dY = $dY"
if { $dim == 3} {
set disZ [expr sqrt(\
$vec(2,0) * $vec(2,0) + \
$vec(2,1) * $vec(2,1) + \
$vec(2,2) * $vec(2,2))]
set prop(NPZ) [expr round( $disZ / $dY ) + 1]
set dZ [expr $disZ / [expr $prop(NPZ) - 1.0]]
xcDebug "distZ = $disZ; NPZ = $prop(NPZ)";
xcDebug "NPZ = $prop(NPZ); dZ = $dZ"
}
} else {
#######################################################################
# for ECHG:
# ( 1, 1)
# (NPY, 1)
# (NPY,NPX)
#
# so the order of points is:
# ECHG_order == point0, point1, (point2 + vecA)
# and because point1 is inheriter of vec(0), it is vec(0) who is
# criteria for NPY
# ---------------------------------------------------------------------
set disY [expr sqrt( \
$vec(0,0) * $vec(0,0) + \
$vec(0,1) * $vec(0,1) + \
$vec(0,2) * $vec(0,2))]
set dY [expr $disY / [expr $prop(NPY) - 1.0]]
if { $dim == 3 } {
set disZ [expr sqrt(\
$vec(2,0) * $vec(2,0) + \
$vec(2,1) * $vec(2,1) + \
$vec(2,2) * $vec(2,2))]
set prop(NPZ) [expr round( $disZ / $dY ) + 1]
set dZ [expr $disZ / [expr $prop(NPZ) - 1.0]]
}
}
}
proc IsoCalc {n command {c95_output {}} {dir {}}} {
global system vec prop isosurf dif_isosurf
# n ........ this is used for diff. maps to know is it map A or
# map B
# c95_output ........ c95's output file
# dir ........ working directory for RunC95
#############################
# vec(-1,$) 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 < $prop(NPZ)} {incr i} {
if { $prop(NPZ) > 1 } {
set f [expr $i / [expr $prop(NPZ) - 1.0]]
} else {
set f 1.0
}
for {set j -1} {$j < 2} {incr j} {
set jj [expr $j + 1]
set v($i,$jj,0) [expr $isosurf(origin,0) + \
$vec($j,0) + $f * $vec(2,0)]
set v($i,$jj,1) [expr $isosurf(origin,1) + \
$vec($j,1) + $f * $vec(2,1)]
set v($i,$jj,2) [expr $isosurf(origin,2) + \
$vec($j,2) + $f * $vec(2,2)]
xcDebug "$f\n$v($i,$jj,0) $v($i,$jj,1) $v($i,$jj,2)\n"
}
}
##########################################################################
# the order of points submited to "properties" program must be:
#
# -------------------------------------------------------------------------
# for ECHD:
# ( 1,NPY)
# ( 1, 1)
# (NPX, 1)
#
# so the order of points is:
# ECHD_order == point2, point0, point1
# -------------------------------------------------------------------------
# for ECHG:
# ( 1, 1)
# (NPY, 1)
# (NPY,NPX)
#
# so the order of points is:
# ECHG_order == point0, point1, (point2 + vecA)
# -------------------------------------------------------------------------
###############################
# take care of density matrix #
###############################
if { $dif_isosurf(dif_map) == 1 } {
if { $n == 1 } {
if { $dif_isosurf(denmat_A) == "Density matrix as superposition of atomic densities" } {
if { $prop(PATO_newbasis_A) == 0 } {
set input "PATO\n"
append input "0 0\n"
} else {
###############################
# new basis set was specified #
###############################
# insert code here
}
}
} elseif { $n == 2 } {
if { $dif_isosurf(denmat_B) == "SCF density matrix" && \
$dif_isosurf(denmat_A) != "SCF density matrix" } {
set input "PSCF\n"
}
if { $dif_isosurf(denmat_B) == "Density matrix as superposition of atomic densities" } {
if { $prop(PATO_newbasis_B) == 0 } {
set input "PATO\n"
append input "0 0\n"
} else {
###############################
# new basis set was specified #
###############################
# insert code here
}
}
}
}
##########################################################################
# t.k. - this is temporal, just to se the gamma point 5-th band of Rh band
##########################################################################
#append input "NEWK\n0 0 0\n0 0\nPBAN\n1 0 1\n1 0 0 0\n10\n"
##########################################################################
append input "BOHR\n"
########################################
# prototype model for PBAN
# append input "NEWK\n0 0 0\n1 0\n"
# append input "PBAN\n2 0\n1 2\n"
########################################
if { $command == "POTM" } {
append input "POLI\n4 1\n0\n"
}
for {set i 0} {$i < $prop(NPZ)} {incr i} {
if { $command == "ECHD" } {
# ECHD
append input "ECHD\n$prop(NPY) 25 0 1\n"
append input "$v($i,2,0) $v($i,2,1) $v($i,2,2)\n"
append input "$v($i,0,0) $v($i,0,1) $v($i,0,2)\n"
append input "$v($i,1,0) $v($i,1,1) $v($i,1,2)\n"
} else {
# ECHG & REST
if { [string match ECHG* $command] } {
append input "$command\n$prop(NPY)\nCOORDINA\n"
}
if { $command == "POTM" } {
append input "POTM\n0 5\n$prop(NPY)\nCOORDINA\n"
}
set p1 [expr $v($i,2,0) + $vec(0,0)]
set p2 [expr $v($i,2,1) + $vec(0,1)]
set p3 [expr $v($i,2,2) + $vec(0,2)]
append input "$v($i,0,0) $v($i,0,1) $v($i,0,2)\n"
append input "$v($i,1,0) $v($i,1,1) $v($i,1,2)\n"
append input "$p1 $p2 $p3\n"
}
if { [string match ECHG* $command] || $command == "POTM" } {
append input "END\n"
}
}
append input "END\n"
xcDebug -stderr "CRYSTALxx INPUT:"
xcDebug -stderr "----------------"
xcDebug -stderr $input
#------------------------------------------------------------------------
# t.k.: here user can make some manuall editing of CRYSTAL d3 input !!!
#------------------------------------------------------------------------
if { $prop(editScript) == 1 } {
cd $system(SCRDIR)
set file CRYSTAL-map$n.d3
WriteFile $file $input w
update
xcEditFile $file -foreground
# can-not chack if editing was OK -> to long to wait -> take a risk !!!
#
# drop the comments from file
#
set input {}
foreach line [split [ReadFile -nonewline $file] \n] {
if { [string match *\#* $line] == 0 } {
if { $line != {} } {
append input [format "%s\n" $line]
}
}
}
}
###################################################################
# because calculating "Grid of Points" can take some time, it's needed to
# give some feed back to the user -> message mode of RunC95
if ![RunC95 $system(c95_properties) {message "The CRYSTAL program is calculating the grid of points now.\nIt can take some time, so PLEASE WAIT!!!"} \
$input $c95_output {} $dir] {
# error occure
# tk_dialog .err "ERROR" "ERROR: $err" error 0 OK
return 0
}
return 1
}
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