AtomEye 3: atomistic configuration viewer

Commands Download

Features

In addition to AtomEye 2;

scripting interface
reconfigurable keybinding
parallel computing

Manual

usage

command line

./A [options] [config_filename]

startup script file

When AtomEye3 is stared, it searches your home directory for a file named .A and executes the commands in the file.

options

option	description
`-v2`	behave as compatible with version 2
`-xterm[="xterm-command and options"]`	run in a new x-terminal (like as version 2)
`-f=script_filename`	load a script file
`-nofep`	disable front-end-processor (readline functions)
`-nowindow`	disable viewport window
`-display display`	specify the display to use
`-geometry WIDTH[xHEIGHT]`	define the initial window geometry (size only)
`-listen[=port]`	listen a port for socket communication
`-connect[=[host:]port]`	terminal mode (with front-end-processor)

socket communication

When AtomEye3 is stared with -listen option, it behave as a TCP/IP server. It can be accessed by "./A -connect[=[host:]port]" as well as "telnet host port". Default host name and port number are localhost and 21040, respectively.

scripting interface and keybinding

closing viewport window / quit: close
... close the current viewport window
quit
... terminate AtomEye3
disconnecting terminal / end of file: disconnect
end
loading commands from a file: load [filename]
... default filename is scr_cmds.
saving AtomEye's internal parameters to a file: save [filename]
save filename key
save filename both
... default filename is scr_cmds.
sending keybord command: key Down
... default keybinding for Down is rotate_0_inc.
changing keybindkings: set key->Down rotate_0_inc
set key->Down+S rotate_2_dec
set key->Down+CS translate_2_dec
... keyname is KeySym+(S:Shift, C:Ctrl, M:Meta/Lock)
changing AtomEye's state parameters and redrawing: set n->bgcolor 0.5 0.5 0.5
redraw

parameters value(s) description

n->bgcolor r g b background

n->anchor i -1: n->hook[] as anchor, >=0: certain atom

n->hook s0 s1 s2 real space coordinates

n->delta delta rate of change (gear-box)

n->mgs_radius d magic sphere for pointer rotation

n->atom_r_ratio d compared to ATOM_RADIUS

n->color_mode i NORMAL(1), COORD(2), AUXILIARY(3) or SCRATCH(4)

n->wireframe_mode i draw H-box

n->bond_mode l draw bonds

n->bond_radius d in Angstrom

n->shell_viewer_mode l xv and ghostview

n->xtal_mode l

n->xtal_origin s0 s1 s2 shifted xtal origin

n->auxiliary_idx i

n->auxiliary_cmap i which colormap should we use

n->auxiliary_threshold[0..33] d0 d1 lower/upper value

n->auxiliary_thresholds_saturation l 0: invisible if outside thresholds

n->auxiliary_thresholds_rigid l 0: floating thresholds

n->parallel_projection l parallel / perspective projections

n->glob_advance i how fast the file list advances

n->fp[0..15].wireframe_mode i

n->fp[0..15].s0 s0 s1 s2

n->fp[0..15].dx_input d0 d1 d2 d3

n->fp[0..15].dx_cache d0 d1 d2 d3

AX_3D->x s0 s1 s2 coordinates of the viewpoint

AX_3D->k d conversion factor from radian to window pixels

AX_3D->V[0..2] d0 d1 d2 AX_3D->V[i] is the normalized ith axis of viewport

AX_3D->zcut d (0,zcut] of the view frustum

AX_3D->wx d viewpoint coordinates in window frame (pixels)

AX_3D->wy d

AX_3D->fp[i].d0 d

AX_3D->fp[i].dx s0 s1 s2

CC[0..24] r g b atom coordination color
commands and default keybindings: command default keybinding

advance delta

advance_dec Page_Up+M

advance_inc Page_Down+M

aux_property_coloring n

aux_property_coloring_0..15 [0-9,a-f]+M

aux_property_coloring_16..19 [g-j]+C

aux_property_coloring_20..29 [0-9]+C

aux_property_coloring_30..31 [k-l]+C

capture png|jpg|eps [filename [resolution]]

capture_eps [filename [resolution]] e

capture_jpg [filename [resolution]] j

capture_png [filename [resolution]] p

central_symmetry_coloring h+M

change_atom_r_ratio delta

change_atom_r_ratio_dec Page_Down

change_atom_r_ratio_inc Page_Up

change_aux_colormap n

change_aux_colormap_prev minus+M

change_aux_colormap_next equal+M

change_aux_property_threshold lower|upper delta

change_aux_property_threshold_lower_dec Page_Down+C

change_aux_property_threshold_lower_inc Page_Up+C

change_aux_property_threshold_upper_dec Page_Down+S

change_aux_property_threshold_upper_inc Page_Up+S

change_bgcolor r g b d

change_bond_color r g b R

change_bond_radius delta

change_bond_radius_dec End

change_bond_radius_inc Home

change_central_symm_neighbormax h+S

change_coordination_color N r g b

change_cutting_plane_wireframe_mode i+S

change_normal_color Z r g b R

change_shear_strain_subtract_mean g+S

change_view_angle_amplification delta

change_view_angle_amplification_dec End+S

change_view_angle_amplification_inc Home+S

change_wireframe_mode i

clone c

close / close_window q

cutting_plane n [dx dy dz s0 s1 s2]

cutting_plane_[0-9,a-f] [dx dy dz s0 s1 s2] [0-9,a-f]+S

delete_cutting_plane_[0-9,a-f] [0-9,a-f]+MS

disconnect / end

find_atom n f

flip_cutting_plane p+S

free_scratch F2+C

isoatomic_reference_imprint Esc

key keysym

load_atom_color filename F12

load_aux filename F11

load_config filename F9

load_config_first Insert+C

load_config_backward Insert

load_config_forward Delete

load_config_last Delete+C

load_script filename l+M

look_at_the_anchor a

new n

normal_coloring l

observer_goto g

original_normal_coloring o

pause seconds

print_atom_info_pair ,

print_atom_info_quartet /

print_atom_info_triplet .

quit

rcut_patch start sym sym | finish | dec/inc [delta]

start_rcut_patch r

finish_rcut_patch Return

rcut_patch_dec, rcut_patch_inc End+C, Home+C

redraw

reload_config F10

reset_anchor w

reset_aux_property_thresholds r+C

reset_scratch F2

reset_timer [reset] [label]

resize width height

rotate axis theta

rotate_0_dec, rotate_0_inc Up, Down

rotate_1_dec, rotate_1_inc Right, Left

rotate_2_dec, rotate_2_inc Down+S, Up+S

save filename [key|both]

save_atom_indices ; :

scratch_coloring F3

script_animate [filename] y

select_gear_[0-9] [0-9]

set name value

shear_strain_coloring g+M

shift_cutting_plane delta

shift_cutting_plane_dec Left+S

shift_cutting_plane_inc Right+S

shift_cutting_plane_to_anchor_[0-9,a-f] [0-9,a-f]+CS

shift_xtal axis delta

shift_xtal_0_dec, shift_xtal_0_inc Right+M, Left+M

shift_xtal_1_dec, shift_xtal_1_inc Down+M, Up+M

shift_xtal_2_dec, shift_xtal_2_inc Down+MS, Up+MS

timer [label]

toggle_aux_property_thresholds_rigid t+C

toggle_aux_property_thresholds_saturation a+C

toggle_bond_mode b

toggle_coordination_coloring k

toggle_parallel_projection Tab

toggle_rcut_patch_mode r

toggle_shell_viewer_mode v

toggle_xtal_mode x

translate axis delta

translate_0_dec, translate_0_inc Left+C, Right+C

translate_1_dec, translate_1_inc Up+C, Down+C

translate_2_dec, translate_2_inc Down+CS, Up+CS

typein_auxiliary_threshold

viewframe_upright u

xtal_origin_goto s0 s1 s2 t

xtal_origin_zero z

parameters	value(s)	description
`n->bgcolor`	r g b	background
`n->anchor`	i	-1: `n->hook[]` as anchor, >=0: certain atom
`n->hook`	s0 s1 s2	real space coordinates
`n->delta`	delta	rate of change (gear-box)
`n->mgs_radius`	d	magic sphere for pointer rotation
`n->atom_r_ratio`	d	compared to `ATOM_RADIUS`
`n->color_mode`	i	`NORMAL`(1), `COORD`(2), `AUXILIARY`(3) or `SCRATCH`(4)
`n->wireframe_mode`	i	draw H-box
`n->bond_mode`	l	draw bonds
`n->bond_radius`	d	in Angstrom
`n->shell_viewer_mode`	l	xv and ghostview
`n->xtal_mode`	l
`n->xtal_origin`	s0 s1 s2	shifted xtal origin
`n->auxiliary_idx`	i
`n->auxiliary_cmap`	i	which colormap should we use
`n->auxiliary_threshold[0..33]`	d0 d1	lower/upper value
`n->auxiliary_thresholds_saturation`	l	0: invisible if outside thresholds
`n->auxiliary_thresholds_rigid`	l	0: floating thresholds
`n->parallel_projection`	l	parallel / perspective projections
`n->glob_advance`	i	how fast the file list advances
`n->fp[0..15].wireframe_mode`	i
`n->fp[0..15].s0`	s0 s1 s2
`n->fp[0..15].dx_input`	d0 d1 d2 d3
`n->fp[0..15].dx_cache`	d0 d1 d2 d3
`AX_3D->x`	s0 s1 s2	coordinates of the viewpoint
`AX_3D->k`	d	conversion factor from radian to window pixels
`AX_3D->V[0..2]`	d0 d1 d2	`AX_3D->V[i]` is the normalized ith axis of viewport
`AX_3D->zcut`	d	(0,zcut] of the view frustum
`AX_3D->wx`	d	viewpoint coordinates in window frame (pixels)
`AX_3D->wy`	d
`AX_3D->fp[i].d0`	d
`AX_3D->fp[i].dx`	s0 s1 s2
`CC[0..24]`	r g b	atom coordination color

command	default keybinding
advance delta
advance_dec	Page_Up+M
advance_inc	Page_Down+M
aux_property_coloring n
aux_property_coloring_0..15	[0-9,a-f]+M
aux_property_coloring_16..19	[g-j]+C
aux_property_coloring_20..29	[0-9]+C
aux_property_coloring_30..31	[k-l]+C
capture png\|jpg\|eps [filename [resolution]]
capture_eps [filename [resolution]]	e
capture_jpg [filename [resolution]]	j
capture_png [filename [resolution]]	p
central_symmetry_coloring	h+M
change_atom_r_ratio delta
change_atom_r_ratio_dec	Page_Down
change_atom_r_ratio_inc	Page_Up
change_aux_colormap n
change_aux_colormap_prev	minus+M
change_aux_colormap_next	equal+M
change_aux_property_threshold lower\|upper delta
change_aux_property_threshold_lower_dec	Page_Down+C
change_aux_property_threshold_lower_inc	Page_Up+C
change_aux_property_threshold_upper_dec	Page_Down+S
change_aux_property_threshold_upper_inc	Page_Up+S
change_bgcolor r g b	d
change_bond_color r g b R
change_bond_radius delta
change_bond_radius_dec	End
change_bond_radius_inc	Home
change_central_symm_neighbormax	h+S
change_coordination_color N r g b
change_cutting_plane_wireframe_mode	i+S
change_normal_color Z r g b R
change_shear_strain_subtract_mean	g+S
change_view_angle_amplification delta
change_view_angle_amplification_dec	End+S
change_view_angle_amplification_inc	Home+S
change_wireframe_mode	i
clone	c
close / close_window	q
cutting_plane n [dx dy dz s0 s1 s2]
cutting_plane_[0-9,a-f] [dx dy dz s0 s1 s2]	[0-9,a-f]+S
delete_cutting_plane_[0-9,a-f]	[0-9,a-f]+MS
disconnect / end
find_atom n	f
flip_cutting_plane	p+S
free_scratch	F2+C
isoatomic_reference_imprint	Esc
key keysym
load_atom_color filename	F12
load_aux filename	F11
load_config filename	F9
load_config_first	Insert+C
load_config_backward	Insert
load_config_forward	Delete
load_config_last	Delete+C
load_script filename	l+M
look_at_the_anchor	a
new	n
normal_coloring	l
observer_goto	g
original_normal_coloring	o
pause seconds
print_atom_info_pair	,
print_atom_info_quartet	/
print_atom_info_triplet	.
quit
rcut_patch start sym sym \| finish \| dec/inc [delta]
start_rcut_patch	r
finish_rcut_patch	Return
rcut_patch_dec, rcut_patch_inc	End+C, Home+C
redraw
reload_config	F10
reset_anchor	w
reset_aux_property_thresholds	r+C
reset_scratch	F2
reset_timer [reset] [label]
resize width height
rotate axis theta
rotate_0_dec, rotate_0_inc	Up, Down
rotate_1_dec, rotate_1_inc	Right, Left
rotate_2_dec, rotate_2_inc	Down+S, Up+S
save filename [key\|both]
save_atom_indices	; :
scratch_coloring	F3
script_animate [filename]	y
select_gear_[0-9]	[0-9]
set name value
shear_strain_coloring	g+M
shift_cutting_plane delta
shift_cutting_plane_dec	Left+S
shift_cutting_plane_inc	Right+S
shift_cutting_plane_to_anchor_[0-9,a-f]	[0-9,a-f]+CS
shift_xtal axis delta
shift_xtal_0_dec, shift_xtal_0_inc	Right+M, Left+M
shift_xtal_1_dec, shift_xtal_1_inc	Down+M, Up+M
shift_xtal_2_dec, shift_xtal_2_inc	Down+MS, Up+MS
timer [label]
toggle_aux_property_thresholds_rigid	t+C
toggle_aux_property_thresholds_saturation	a+C
toggle_bond_mode	b
toggle_coordination_coloring	k
toggle_parallel_projection	Tab
toggle_rcut_patch_mode	r
toggle_shell_viewer_mode	v
toggle_xtal_mode	x
translate axis delta
translate_0_dec, translate_0_inc	Left+C, Right+C
translate_1_dec, translate_1_inc	Up+C, Down+C
translate_2_dec, translate_2_inc	Down+CS, Up+CS
typein_auxiliary_threshold
viewframe_upright	u
xtal_origin_goto s0 s1 s2	t
xtal_origin_zero	z

Parallel Computing

Parallelization of AtomEye is based on spatial decomposition algorithm; the whole system cell is divided int sub-cells and each process is responsible for the calculation of atoms within the sub-cell. Executed with the option '-decomp=', The program runs in MPI mode in either case of that it is executed with the option '-decomp=' or that the name of executable file ends in the letter 'p'.

running MPI programs: mpiexec -n 4 ./Ap -decomp=[px[,py[,pz]]] [options] [config_filename]; ln -s ./A ./Ap; mpiexec -n 4 ./Ap [options] [config_filename]
MPI-related option: option description

-decomp=[px[,py[,pz]]] number of processes in a Cartesian grid
distributed file I/O: If '%' character appears in config_file name, each process will try to open the file which name is produced using printf(3) with its process number (MPI-rank); e.g.
ex_%d.cfg -> ex_0.cfg, ex_1.cfg, ... ex_10.cfg, ...
ex_%02d.cfg -> ex_00.cfg, ex_01.cfg, ... ex_10.cfg, ...
unimplemented functions: Functions listed blow are not implemented;
find_atom

load_atom_color

load_aux

new

scratch_coloring

isoatomic_reference_imprint

save_atom_indices

applying extra color patch

option	description
`-decomp=[px[,py[,pz]]]`	number of processes in a Cartesian grid

Download source code (2012) bzip2 -cd Src.tar.bz2 | tar xf - cd Src cp -r A A3 cd A3 patch < A3.patch executables (binary w/o MPI) x86_64 Linux (2012) i686 Linux (2006) ia64 Linux (2006) Mac OS X with X (2006) Windows with Cygwin/X11 (2006) Email: shimizu.futoshi@jaea.go.jp, liju@mit.edu, Site Counter