plot_structure.sh

This bash script plot POSCAR and CONTCAR in folders ini and fin. If you have many structures to plot, this script can be efficient after necessary modification.

# get picture of ini&fin(POSCAR&CONTCAR)
for i in ini fin
do    for j in POSCAR CONTCAR
do pos2xyz.pl $i/$j
cat >xcrysden.script <<EOF
::scripting::open --xyz $i/$j.xyz
# ------------------------------------------------------------------------
# END: XSF structure data
# ------------------------------------------------------------------------
# ======================================================================== #
# #
# STATE-PART OF THE FILE #
# #
# ======================================================================== #
# ------------------------------------------------------------------------
# definition of xcMisc array
# ------------------------------------------------------------------------

array set xcMisc {ImageMagick.import /usr/bin/import reduce_to {} rescale_image_list {up down left right center rotXY rotXZ rotYZ rotAB rotAC rotBC wireframes_2d pointlines_2d pipeballs_2d ballsticks2_2d ballsticks1_2d spacefills_2d spacefills_3d ballsticks_3d pipeballs_3d sticks_3d dm_wire dm_solid dm_anaglyph dm_stereo dm_smooth dm_flat rep_unit rep_asym} resolution 1440x870 gif_encoder convert status_init_label {Building GUI ...} wm_rootYshift 0 movie_encoder ppmtompeg debug 0 ppmtompeg /usr/bin/ppmtompeg convert /usr/bin/convert titlefile /tmp/xc_20968/a.xsf xwd /usr/bin/xwd resolution_ratio1 1.0 resolutionX 1440 resolution_ratio2 1.0 wm_rootXshift 0 resolutionY 870 ImageMagick.convert /usr/bin/convert}

# ------------------------------------------------------------------------
# display "waiting" toplevel and watch-cursor
# ------------------------------------------------------------------------

set wait_window [DisplayUpdateWidget "Reconstructing" "Reconstructing the structure and display parameters. Please wait"]
SetWatchCursor
set xcCursor(dont_update) 1

# ------------------------------------------------------------------------
# size of the main window fonts
# ------------------------------------------------------------------------

wm geometry . 1440x851

# ------------------------------------------------------------------------
# BEGIN: create fonts
# ------------------------------------------------------------------------

saveState:fontCreate font10 -family helvetica -size 10 -weight normal -slant roman -underline 0 -overstrike 0
saveState:fontCreate font1 -family helvetica -size 10 -weight normal -slant roman -underline 0 -overstrike 0
saveState:fontCreate font11 -family helvetica -size 10 -weight normal -slant roman -underline 0 -overstrike 0
saveState:fontCreate font2 -family helvetica -size 8 -weight normal -slant roman -underline 0 -overstrike 0
saveState:fontCreate font12 -family helvetica -size 10 -weight normal -slant roman -underline 0 -overstrike 0
saveState:fontCreate font3 -family helvetica -size 12 -weight normal -slant roman -underline 0 -overstrike 0
saveState:fontCreate font13 -family helvetica -size 10 -weight normal -slant roman -underline 0 -overstrike 0
saveState:fontCreate font4 -family helvetica -size 10 -weight normal -slant roman -underline 0 -overstrike 0
saveState:fontCreate TkDefaultFont -family helvetica -size 10 -weight normal -slant roman -underline 0 -overstrike 0
saveState:fontCreate TkMenuFont -family helvetica -size 10 -weight normal -slant roman -underline 0 -overstrike 0
saveState:fontCreate font14 -family courier -size 10 -weight normal -slant roman -underline 0 -overstrike 0
saveState:fontCreate font5 -family helvetica -size 10 -weight normal -slant roman -underline 0 -overstrike 0
saveState:fontCreate font6 -family helvetica -size 8 -weight normal -slant roman -underline 0 -overstrike 0
saveState:fontCreate font7 -family helvetica -size 10 -weight normal -slant roman -underline 0 -overstrike 0
saveState:fontCreate TkHeadingFont -family helvetica -size 10 -weight bold -slant roman -underline 0 -overstrike 0
saveState:fontCreate font8 -family helvetica -size 10 -weight normal -slant roman -underline 0 -overstrike 0
saveState:fontCreate font9 -family helvetica -size 10 -weight normal -slant roman -underline 0 -overstrike 0
saveState:fontCreate TkTooltipFont -family helvetica -size 8 -weight normal -slant roman -underline 0 -overstrike 0
saveState:fontCreate TkTextFont -family helvetica -size 10 -weight normal -slant roman -underline 0 -overstrike 0
saveState:fontCreate TkCaptionFont -family helvetica -size 11 -weight bold -slant roman -underline 0 -overstrike 0
saveState:fontCreate TkSmallCaptionFont -family helvetica -size 8 -weight normal -slant roman -underline 0 -overstrike 0
saveState:fontCreate TkFixedFont -family courier -size 10 -weight normal -slant roman -underline 0 -overstrike 0
saveState:fontCreate TkIconFont -family helvetica -size 10 -weight normal -slant roman -underline 0 -overstrike 0

# ------------------------------------------------------------------------
# END: create fonts
# ------------------------------------------------------------------------



# ------------------------------------------------------------------------
# BEGIN: take care of display-mode
# ------------------------------------------------------------------------

set translationStep 0.05
set rotstep 10
set light On
Lighting On
array set mode2D {PL Off SF Off WF Off BS1 Off PB Off BS2 Off}
array set mode3D {space Off sticks On pipe Off balls On}
array set dispmode {mode3D_name BS mode3D Preset mode3D_f2_packinfo {-in .ctrl.c.f.fr3 -anchor center -expand 1 -fill x -ipadx 0 -ipady 0 -padx 0 -pady 0 -side top} style 3D mode3D_ModeFrame .ctrl.c.f.fr3.2.a0}
saveState:displayMode
set style3D(draw) solid; Style3D draw solid
set style3D(shade) smooth; Style3D shade smooth
set viewer(rot_zoom_button_mode) Discrete; Viewer:rotZoomButtonMode

# ------------------------------------------------------------------------
# END: take care of display-mode
# ------------------------------------------------------------------------



# ------------------------------------------------------------------------
# Number of Units Drawn
# ------------------------------------------------------------------------

set nxdir 1
set nydir 1
set nzdir 1

# ------------------------------------------------------------------------
# BEGIN: Atomic-Labels/Fonts
# ------------------------------------------------------------------------

array set atomLabel {atomFont {} globalFont {} atomFont.brightColor {1.0 1.0 1.0} globalFont.brightColor {1.0 1.0 1.0} atomFont.do_display 1 atomFont.label {} globalFont.do_display 1 atomFont.darkColor {0.0 0.0 0.0} atomFont.id {} globalFont.darkColor {0.0 0.0 0.0} fontBrowser {Simple Font Browser}}
set t [ModAtomLabels]
.mesa xc_setfont {} {1.0 1.0 1.0} {0.0 0.0 0.0}
ModAtomLabels:advancedCheckButton default
ModAtomLabels:advancedCheckButton custom
ModAtomLabels:advancedCloseUpdate dummy update
CancelProc \$t

# ------------------------------------------------------------------------
# END: Atomic-Labels/Fonts
# ------------------------------------------------------------------------



# ------------------------------------------------------------------------
# BEGIN: Various colors
# ------------------------------------------------------------------------

xc_newvalue .mesa 8 0 0.770000 1.000000 0.420000
xc_newvalue .mesa 8 1 0.000000 0.950000 0.950000
xc_newvalue .mesa 8 2 0.950000 0.950000 0.950000
xc_newvalue .mesa 8 3 0.950000 0.950000 0.950000
xc_newvalue .mesa 8 4 0.707900 0.707900 0.707900
xc_newvalue .mesa 8 5 0.707900 0.707900 0.707900
xc_newvalue .mesa 8 6 0.950000 0.950000 0.000000
xc_newvalue .mesa 8 7 0.644500 0.804700 0.856900
xc_newvalue .mesa 8 8 0.700000 0.000000 0.000000
xc_newvalue .mesa 8 9 0.834500 0.950000 0.950000
xc_newvalue .mesa 8 10 0.950000 0.950000 0.950000
xc_newvalue .mesa 8 11 0.000000 0.950000 0.950000
xc_newvalue .mesa 8 12 0.000000 0.950000 0.950000
xc_newvalue .mesa 8 13 0.950000 0.000000 0.950000
xc_newvalue .mesa 8 14 0.000000 0.950000 0.950000
xc_newvalue .mesa 8 15 0.950000 0.950000 0.000000
xc_newvalue .mesa 8 16 0.950000 0.950000 0.450000
xc_newvalue .mesa 8 17 0.710000 1.000000 0.000000
xc_newvalue .mesa 8 18 0.950000 0.950000 0.950000
xc_newvalue .mesa 8 19 0.000000 0.950000 0.950000
xc_newvalue .mesa 8 20 0.000000 0.950000 0.950000
xc_newvalue .mesa 8 21 0.000000 0.950000 0.950000
xc_newvalue .mesa 8 22 0.600000 0.600000 0.600000
xc_newvalue .mesa 8 23 0.644500 0.804700 0.856900
xc_newvalue .mesa 8 24 0.644500 0.804700 0.856900
xc_newvalue .mesa 8 25 0.644500 0.804700 0.856900
xc_newvalue .mesa 8 26 0.950000 0.000000 0.000000
xc_newvalue .mesa 8 27 0.644500 0.804700 0.856900
xc_newvalue .mesa 8 28 0.644500 0.804700 0.856900
xc_newvalue .mesa 8 29 0.820000 0.450000 0.140000
xc_newvalue .mesa 8 30 0.950000 0.000000 0.950000
xc_newvalue .mesa 8 31 0.950000 0.000000 0.950000
xc_newvalue .mesa 8 32 0.950000 0.000000 0.950000
xc_newvalue .mesa 8 33 0.950000 0.950000 0.000000
xc_newvalue .mesa 8 34 0.950000 0.950000 0.000000
xc_newvalue .mesa 8 35 0.950000 0.000000 0.000000
xc_newvalue .mesa 8 36 0.750000 0.750000 0.750000
xc_newvalue .mesa 8 37 0.000000 0.950000 0.950000
xc_newvalue .mesa 8 38 0.000000 0.950000 0.950000
xc_newvalue .mesa 8 39 0.750000 0.750000 0.750000
xc_newvalue .mesa 8 40 0.750000 0.750000 0.750000
xc_newvalue .mesa 8 41 0.750000 0.750000 0.750000
xc_newvalue .mesa 8 42 0.750000 0.750000 0.750000
xc_newvalue .mesa 8 43 0.750000 0.750000 0.750000
xc_newvalue .mesa 8 44 0.750000 0.750000 0.750000
xc_newvalue .mesa 8 45 0.750000 0.750000 0.750000
xc_newvalue .mesa 8 46 1.000000 1.000000 1.000000
xc_newvalue .mesa 8 47 1.000000 1.000000 1.000000
xc_newvalue .mesa 8 48 0.750000 0.750000 0.750000
xc_newvalue .mesa 8 49 0.750000 0.750000 0.750000
xc_newvalue .mesa 8 50 0.750000 0.750000 0.750000
xc_newvalue .mesa 8 51 0.750000 0.750000 0.750000
xc_newvalue .mesa 8 52 0.750000 0.750000 0.750000
xc_newvalue .mesa 8 53 0.750000 0.750000 0.750000
xc_newvalue .mesa 8 54 0.750000 0.750000 0.750000
xc_newvalue .mesa 8 55 0.000000 0.950000 0.950000
xc_newvalue .mesa 8 56 0.000000 0.950000 0.950000
xc_newvalue .mesa 8 57 0.750000 0.750000 0.750000
xc_newvalue .mesa 8 58 0.750000 0.750000 0.750000
xc_newvalue .mesa 8 59 0.750000 0.750000 0.750000
xc_newvalue .mesa 8 60 0.750000 0.750000 0.750000
xc_newvalue .mesa 8 61 0.750000 0.750000 0.750000
xc_newvalue .mesa 8 62 0.750000 0.750000 0.750000
xc_newvalue .mesa 8 63 0.750000 0.750000 0.750000
xc_newvalue .mesa 8 64 0.750000 0.750000 0.750000
xc_newvalue .mesa 8 65 0.750000 0.750000 0.750000
xc_newvalue .mesa 8 66 0.750000 0.750000 0.750000
xc_newvalue .mesa 8 67 0.750000 0.750000 0.750000
xc_newvalue .mesa 8 68 0.750000 0.750000 0.750000
xc_newvalue .mesa 8 69 0.750000 0.750000 0.750000
xc_newvalue .mesa 8 70 0.750000 0.750000 0.750000
xc_newvalue .mesa 8 71 0.750000 0.750000 0.750000
xc_newvalue .mesa 8 72 0.750000 0.750000 0.750000
xc_newvalue .mesa 8 73 0.750000 0.750000 0.750000
xc_newvalue .mesa 8 74 0.750000 0.750000 0.750000
xc_newvalue .mesa 8 75 0.750000 0.750000 0.750000
xc_newvalue .mesa 8 76 0.750000 0.750000 0.750000
xc_newvalue .mesa 8 77 0.750000 0.750000 0.750000
xc_newvalue .mesa 8 78 0.750000 0.750000 0.750000
xc_newvalue .mesa 8 79 1.000000 0.850000 0.000000
xc_newvalue .mesa 8 80 0.750000 0.750000 0.750000
xc_newvalue .mesa 8 81 0.750000 0.750000 0.750000
xc_newvalue .mesa 8 82 0.750000 0.750000 0.750000
xc_newvalue .mesa 8 83 0.750000 0.750000 0.750000
xc_newvalue .mesa 8 84 0.750000 0.750000 0.750000
xc_newvalue .mesa 8 85 0.750000 0.750000 0.750000
xc_newvalue .mesa 8 86 0.750000 0.750000 0.750000
xc_newvalue .mesa 8 87 0.750000 0.750000 0.750000
xc_newvalue .mesa 8 88 0.750000 0.750000 0.750000
xc_newvalue .mesa 8 89 0.750000 0.750000 0.750000
xc_newvalue .mesa 8 90 0.750000 0.750000 0.750000
xc_newvalue .mesa 8 91 0.750000 0.750000 0.750000
xc_newvalue .mesa 8 92 0.750000 0.750000 0.750000
xc_newvalue .mesa 8 93 0.750000 0.750000 0.750000
xc_newvalue .mesa 8 94 0.750000 0.750000 0.750000
xc_newvalue .mesa 8 95 0.750000 0.750000 0.750000
xc_newvalue .mesa 8 96 0.750000 0.750000 0.750000
xc_newvalue .mesa 8 97 0.750000 0.750000 0.750000
xc_newvalue .mesa 8 98 0.750000 0.750000 0.750000
xc_newvalue .mesa 8 99 0.931400 0.875500 0.801000
xc_newvalue .mesa 8 100 0.931400 0.875500 0.801000
xc_newvalue .mesa 26 1.000000 1.000000 1.000000 1.0
xc_newvalue .mesa 17 0.880000 1.000000 0.670000

# ------------------------------------------------------------------------
# END: Various colors
# ------------------------------------------------------------------------
xc_newvalue .mesa 0

# ------------------------------------------------------------------------
# BEGIN: Atomic radii
# ------------------------------------------------------------------------

xc_newvalue .mesa 4 0 0.532000
xc_newvalue .mesa 4 1 0.532000
xc_newvalue .mesa 4 2 0.532000
xc_newvalue .mesa 4 3 1.722000
xc_newvalue .mesa 4 4 1.246000
xc_newvalue .mesa 4 5 1.274000
xc_newvalue .mesa 4 6 1.078000
xc_newvalue .mesa 4 7 1.050000
xc_newvalue .mesa 4 8 1.022000
xc_newvalue .mesa 4 9 0.994000
xc_newvalue .mesa 4 10 0.994000
xc_newvalue .mesa 4 11 2.240000
xc_newvalue .mesa 4 12 1.960000
xc_newvalue .mesa 4 13 1.750000
xc_newvalue .mesa 4 14 1.554000
xc_newvalue .mesa 4 15 1.400000
xc_newvalue .mesa 4 16 1.456000
xc_newvalue .mesa 4 17 1.386000
xc_newvalue .mesa 4 18 1.372000
xc_newvalue .mesa 4 19 2.982000
xc_newvalue .mesa 4 20 2.436000
xc_newvalue .mesa 4 21 2.240000
xc_newvalue .mesa 4 22 1.960000
xc_newvalue .mesa 4 23 1.890000
xc_newvalue .mesa 4 24 1.960000
xc_newvalue .mesa 4 25 1.960000
xc_newvalue .mesa 4 26 1.960000
xc_newvalue .mesa 4 27 1.890000
xc_newvalue .mesa 4 28 1.890000
xc_newvalue .mesa 4 29 1.890000
xc_newvalue .mesa 4 30 1.890000
xc_newvalue .mesa 4 31 1.820000
xc_newvalue .mesa 4 32 1.750000
xc_newvalue .mesa 4 33 1.610000
xc_newvalue .mesa 4 34 1.610000
xc_newvalue .mesa 4 35 1.596000
xc_newvalue .mesa 4 36 1.568000
xc_newvalue .mesa 4 37 3.080000
xc_newvalue .mesa 4 38 2.800000
xc_newvalue .mesa 4 39 2.590000
xc_newvalue .mesa 4 40 2.170000
xc_newvalue .mesa 4 41 2.030000
xc_newvalue .mesa 4 42 2.030000
xc_newvalue .mesa 4 43 1.890000
xc_newvalue .mesa 4 44 1.820000
xc_newvalue .mesa 4 45 1.890000
xc_newvalue .mesa 4 46 1.960000
xc_newvalue .mesa 4 47 2.240000
xc_newvalue .mesa 4 48 2.170000
xc_newvalue .mesa 4 49 2.170000
xc_newvalue .mesa 4 50 1.974000
xc_newvalue .mesa 4 51 2.030000
xc_newvalue .mesa 4 52 1.960000
xc_newvalue .mesa 4 53 1.960000
xc_newvalue .mesa 4 54 1.834000
xc_newvalue .mesa 4 55 3.640000
xc_newvalue .mesa 4 56 2.800000
xc_newvalue .mesa 4 57 2.450000
xc_newvalue .mesa 4 58 2.170000
xc_newvalue .mesa 4 59 2.170000
xc_newvalue .mesa 4 60 2.170000
xc_newvalue .mesa 4 61 2.170000
xc_newvalue .mesa 4 62 2.170000
xc_newvalue .mesa 4 63 2.170000
xc_newvalue .mesa 4 64 2.170000
xc_newvalue .mesa 4 65 2.170000
xc_newvalue .mesa 4 66 2.170000
xc_newvalue .mesa 4 67 2.170000
xc_newvalue .mesa 4 68 2.170000
xc_newvalue .mesa 4 69 2.170000
xc_newvalue .mesa 4 70 2.170000
xc_newvalue .mesa 4 71 2.170000
xc_newvalue .mesa 4 72 2.170000
xc_newvalue .mesa 4 73 2.030000
xc_newvalue .mesa 4 74 1.890000
xc_newvalue .mesa 4 75 1.890000
xc_newvalue .mesa 4 76 1.820000
xc_newvalue .mesa 4 77 1.890000
xc_newvalue .mesa 4 78 1.890000
xc_newvalue .mesa 4 79 1.890000
xc_newvalue .mesa 4 80 2.100000
xc_newvalue .mesa 4 81 2.660000
xc_newvalue .mesa 4 82 2.520000
xc_newvalue .mesa 4 83 2.240000
xc_newvalue .mesa 4 84 2.170000
xc_newvalue .mesa 4 85 2.170000
xc_newvalue .mesa 4 86 2.170000
xc_newvalue .mesa 4 87 3.920000
xc_newvalue .mesa 4 88 2.016000
xc_newvalue .mesa 4 89 2.730000
xc_newvalue .mesa 4 90 2.170000
xc_newvalue .mesa 4 91 2.170000
xc_newvalue .mesa 4 92 2.170000
xc_newvalue .mesa 4 93 2.170000
xc_newvalue .mesa 4 94 2.170000
xc_newvalue .mesa 4 95 2.170000
xc_newvalue .mesa 4 96 2.170000
xc_newvalue .mesa 4 97 2.170000
xc_newvalue .mesa 4 98 2.170000
xc_newvalue .mesa 4 99 2.170000
xc_newvalue .mesa 4 100 2.170000
xc_newvalue .mesa 10004 0 0.000000
xc_newvalue .mesa 10004 1 0.399000
xc_newvalue .mesa 10004 2 0.399000
xc_newvalue .mesa 10004 3 1.291500
xc_newvalue .mesa 10004 4 0.934500
xc_newvalue .mesa 10004 5 0.955500
xc_newvalue .mesa 10004 6 0.808500
xc_newvalue .mesa 10004 7 0.787500
xc_newvalue .mesa 10004 8 0.766500
xc_newvalue .mesa 10004 9 0.745500
xc_newvalue .mesa 10004 10 0.745500
xc_newvalue .mesa 10004 11 1.680000
xc_newvalue .mesa 10004 12 1.470000
xc_newvalue .mesa 10004 13 1.312500
xc_newvalue .mesa 10004 14 1.165500
xc_newvalue .mesa 10004 15 1.050000
xc_newvalue .mesa 10004 16 1.092000
xc_newvalue .mesa 10004 17 1.039500
xc_newvalue .mesa 10004 18 1.029000
xc_newvalue .mesa 10004 19 2.236500
xc_newvalue .mesa 10004 20 1.827000
xc_newvalue .mesa 10004 21 1.680000
xc_newvalue .mesa 10004 22 1.470000
xc_newvalue .mesa 10004 23 1.417500
xc_newvalue .mesa 10004 24 1.470000
xc_newvalue .mesa 10004 25 1.470000
xc_newvalue .mesa 10004 26 1.470000
xc_newvalue .mesa 10004 27 1.417500
xc_newvalue .mesa 10004 28 1.417500
xc_newvalue .mesa 10004 29 1.417500
xc_newvalue .mesa 10004 30 1.417500
xc_newvalue .mesa 10004 31 1.365000
xc_newvalue .mesa 10004 32 1.312500
xc_newvalue .mesa 10004 33 1.207500
xc_newvalue .mesa 10004 34 1.207500
xc_newvalue .mesa 10004 35 1.197000
xc_newvalue .mesa 10004 36 1.176000
xc_newvalue .mesa 10004 37 2.310000
xc_newvalue .mesa 10004 38 2.100000
xc_newvalue .mesa 10004 39 1.942500
xc_newvalue .mesa 10004 40 1.627500
xc_newvalue .mesa 10004 41 1.522500
xc_newvalue .mesa 10004 42 1.522500
xc_newvalue .mesa 10004 43 1.417500
xc_newvalue .mesa 10004 44 1.365000
xc_newvalue .mesa 10004 45 1.417500
xc_newvalue .mesa 10004 46 1.470000
xc_newvalue .mesa 10004 47 1.680000
xc_newvalue .mesa 10004 48 1.627500
xc_newvalue .mesa 10004 49 1.627500
xc_newvalue .mesa 10004 50 1.480500
xc_newvalue .mesa 10004 51 1.522500
xc_newvalue .mesa 10004 52 1.470000
xc_newvalue .mesa 10004 53 1.470000
xc_newvalue .mesa 10004 54 1.375500
xc_newvalue .mesa 10004 55 2.730000
xc_newvalue .mesa 10004 56 2.100000
xc_newvalue .mesa 10004 57 1.837500
xc_newvalue .mesa 10004 58 1.627500
xc_newvalue .mesa 10004 59 1.627500
xc_newvalue .mesa 10004 60 1.627500
xc_newvalue .mesa 10004 61 1.627500
xc_newvalue .mesa 10004 62 1.627500
xc_newvalue .mesa 10004 63 1.627500
xc_newvalue .mesa 10004 64 1.627500
xc_newvalue .mesa 10004 65 1.627500
xc_newvalue .mesa 10004 66 1.627500
xc_newvalue .mesa 10004 67 1.627500
xc_newvalue .mesa 10004 68 1.627500
xc_newvalue .mesa 10004 69 1.627500
xc_newvalue .mesa 10004 70 1.627500
xc_newvalue .mesa 10004 71 1.627500
xc_newvalue .mesa 10004 72 1.627500
xc_newvalue .mesa 10004 73 1.522500
xc_newvalue .mesa 10004 74 1.417500
xc_newvalue .mesa 10004 75 1.417500
xc_newvalue .mesa 10004 76 1.365000
xc_newvalue .mesa 10004 77 1.417500
xc_newvalue .mesa 10004 78 1.417500
xc_newvalue .mesa 10004 79 1.417500
xc_newvalue .mesa 10004 80 1.575000
xc_newvalue .mesa 10004 81 1.995000
xc_newvalue .mesa 10004 82 1.890000
xc_newvalue .mesa 10004 83 1.680000
xc_newvalue .mesa 10004 84 1.627500
xc_newvalue .mesa 10004 85 1.627500
xc_newvalue .mesa 10004 86 1.627500
xc_newvalue .mesa 10004 87 2.940000
xc_newvalue .mesa 10004 88 1.512000
xc_newvalue .mesa 10004 89 2.047500
xc_newvalue .mesa 10004 90 1.627500
xc_newvalue .mesa 10004 91 1.627500
xc_newvalue .mesa 10004 92 1.627500
xc_newvalue .mesa 10004 93 1.627500
xc_newvalue .mesa 10004 94 1.627500
xc_newvalue .mesa 10004 95 1.627500
xc_newvalue .mesa 10004 96 1.627500
xc_newvalue .mesa 10004 97 1.627500
xc_newvalue .mesa 10004 98 1.627500
xc_newvalue .mesa 10004 99 1.627500
xc_newvalue .mesa 10004 100 1.627500

# ------------------------------------------------------------------------
# END: Atomic radii
# ------------------------------------------------------------------------



# ------------------------------------------------------------------------
# Various parameters
# ------------------------------------------------------------------------

xc_newvalue .mesa 13 1.050000000000000
xc_newvalue .mesa 6 0.400000000000000
xc_newvalue .mesa 7 0.600000000000000
xc_newvalue .mesa 9 1.000000000000000
xc_newvalue .mesa 10 1.000000000000000
xc_newvalue .mesa 18 1.000000000000000
xc_newvalue .mesa 10010 1.000000000000000
xc_newvalue .mesa 10009 1.000000000000000
xc_newvalue .mesa 11 6.000000000000000
xc_newvalue .mesa 19 0.100000000000000
xc_newvalue .mesa 24 15.000000000000000
xc_newvalue .mesa 28 3.000000000000000
xc_newvalue .mesa 29 2.500000000000000
xc_newvalue .mesa 10029 1.000000000000000
xc_newvalue .mesa 23 1.000000 1.000000 1.000000 1.000000

# ------------------------------------------------------------------------
# Various displays (i.e. checkbuttons of DISPLAY menu)
# ------------------------------------------------------------------------

array set check {pseudoDens 0 perspective 0 labels 0 depthcuing 0 crds 0 wigner 0 antialias 0 Hbonds 0 forces 0 frames 0 unibond 0 perpective 0}
CrdSist
AtomLabels
CrysFrames
Unibond
forceVectors .mesa
WignerSeitz
Perspective

# ------------------------------------------------------------------------
# Various displays (i.e. radiobuttons DISPLAY menu)
# ------------------------------------------------------------------------

array set radio {space {SpaceFill based on covalent radii} .mesa,bg #ffffff cellmode conv frames rods unitrep cell hexamode parapipedal ball {Balls based on covalent radii}}
xc_newvalue .mesa 2

# ------------------------------------------------------------------------
# load appropriate color-scheme
# ------------------------------------------------------------------------

array set colSh {slab_dir -z slabrange_min 0.00 slabrange_max 1.00 scheme atomic slab_colbas monocrome dist_r 1.0 dist_coltyp combined dist_alpha 0.65 dist_x 0.0 slab_fractional 1 slab_coltyp combined dist_y 0.0 dist_z 0.0 slab_alpha 0.65 dist_colbas monocrome}
ColorSchemeUpdate .mesa

# ------------------------------------------------------------------------
# BEGIN: Isosurface colors/transparency ...
# ------------------------------------------------------------------------

xc_setGLparam material -what isosurf pos front \
-shininess 0.000000 \
-specular {0.000000 0.000000 0.000000 0.000000} \
-ambient {0.000000 0.000000 0.000000 0.000000} \
-diffuse {0.000000 0.000000 0.000000 0.000000} \
-emission {0.000000 0.000000 0.000000 0.000000}
xc_setGLparam material -what isosurf pos back \
-shininess 0.000000 \
-specular {0.000000 0.000000 0.000000 0.000000} \
-ambient {0.000000 0.000000 0.000000 0.000000} \
-diffuse {0.000000 0.000000 0.000000 0.000000} \
-emission {0.000000 0.000000 0.000000 0.000000}
xc_setGLparam material -what isosurf neg front \
-shininess 0.000000 \
-specular {0.000000 0.000000 0.000000 0.000000} \
-ambient {0.000000 0.000000 0.000000 0.000000} \
-diffuse {0.000000 0.000000 0.000000 0.000000} \
-emission {0.000000 0.000000 0.000000 0.000000}
xc_setGLparam material -what isosurf neg back \
-shininess 0.000000 \
-specular {0.000000 0.000000 0.000000 0.000000} \
-ambient {0.000000 0.000000 0.000000 0.000000} \
-diffuse {0.000000 0.000000 0.000000 0.000000} \
-emission {0.000000 0.000000 0.000000 0.000000}
xc_setGLparam material -what isosurf one front \
-shininess 0.000000 \
-specular {0.000000 0.000000 0.000000 0.000000} \
-ambient {0.000000 0.000000 0.000000 0.000000} \
-diffuse {0.000000 0.000000 0.000000 0.000000} \
-emission {0.000000 0.000000 0.000000 0.000000}
xc_setGLparam material -what isosurf one back \
-shininess 0.000000 \
-specular {0.000000 0.000000 0.000000 0.000000} \
-ambient {0.000000 0.000000 0.000000 0.000000} \
-diffuse {0.000000 0.000000 0.000000 0.000000} \
-emission {0.000000 0.000000 0.000000 0.000000}
xc_setGLparam blendfunc -what isosurf -sfunc GL_SRC_ALPHA -dfunc GL_ONE_MINUS_SRC_ALPHA

# ------------------------------------------------------------------------
# END: Isosurface colors/transparency ...
# ------------------------------------------------------------------------



# ------------------------------------------------------------------------
# rotation matrix and zooming factor, and translation displacements
# ------------------------------------------------------------------------

xc_rotationmatrix set 1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 1.000000000000000e+00
xc_translparam set 0.000000000000000e+00 0.000000000000000e+00 2.038778501368373e+00

# this is used to force the update of display
.mesa cry_toglzoom 0.0

# ------------------------------------------------------------------------
# Anti-Aliasing & Depth-Cuing & PseudoDensity (these are time consuming)
# ------------------------------------------------------------------------

DepthCuing; PseudoDensity; AntiAlias

# ------------------------------------------------------------------------
# reset cursor
# ------------------------------------------------------------------------

set xcCursor(dont_update) 0
ResetCursor
destroy \$wait_window

# now print the MO
update
scripting::printToFile $i-$j.png
exit
EOF
# end of embedded xcrysden.script

# now we load the just created xcrysden.script into xcrysden
xcrysden -s xcrysden.script
done
done
rm xcrysden.script

mkdir ini-fin
mv conv-ini-fin.jpg ini-fin
mv *.png ini-fin
mv result.lipai ini-fin
mogrify -trim ini-fin/*.png
mogrify -trim ini-fin/*.jpg