AtomEye 3: atomistic configuration viewer

Commands Download

Features

In addition to AtomEye 2;

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
parametersvalue(s)description
n->bgcolorr g b background
n->anchori -1: n->hook[] as anchor, >=0: certain atom
n->hooks0 s1 s2 real space coordinates
n->deltadelta rate of change (gear-box)
n->mgs_radiusd magic sphere for pointer rotation
n->atom_r_ratiod compared to ATOM_RADIUS
n->color_modei NORMAL(1), COORD(2), AUXILIARY(3) or SCRATCH(4)
n->wireframe_modei draw H-box
n->bond_model draw bonds
n->bond_radiusd in Angstrom
n->shell_viewer_model xv and ghostview
n->xtal_model
n->xtal_origins0 s1 s2 shifted xtal origin
n->auxiliary_idxi
n->auxiliary_cmapi which colormap should we use
n->auxiliary_threshold[0..33]d0 d1 lower/upper value
n->auxiliary_thresholds_saturationl 0: invisible if outside thresholds
n->auxiliary_thresholds_rigidl 0: floating thresholds
n->parallel_projectionl parallel / perspective projections
n->glob_advancei how fast the file list advances
n->fp[0..15].wireframe_modei
n->fp[0..15].s0s0 s1 s2
n->fp[0..15].dx_inputd0 d1 d2 d3
n->fp[0..15].dx_cached0 d1 d2 d3
AX_3D->xs0 s1 s2 coordinates of the viewpoint
AX_3D->kd 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->zcutd (0,zcut] of the view frustum
AX_3D->wxd viewpoint coordinates in window frame (pixels)
AX_3D->wyd
AX_3D->fp[i].d0d
AX_3D->fp[i].dxs0 s1 s2
CC[0..24]r g b atom coordination color
commands and default keybindings
commanddefault keybinding
advance delta
advance_decPage_Up+M
advance_incPage_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_coloringh+M
change_atom_r_ratio delta
change_atom_r_ratio_decPage_Down
change_atom_r_ratio_incPage_Up
change_aux_colormap n
change_aux_colormap_prevminus+M
change_aux_colormap_nextequal+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 bd
change_bond_color r g b R
change_bond_radius delta
change_bond_radius_decEnd
change_bond_radius_incHome
change_central_symm_neighbormaxh+S
change_coordination_color N r g b
change_cutting_plane_wireframe_modei+S
change_normal_color Z r g b R
change_shear_strain_subtract_meang+S
change_view_angle_amplification delta
change_view_angle_amplification_decEnd+S
change_view_angle_amplification_incHome+S
change_wireframe_modei
clonec
close / close_windowq
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 nf
flip_cutting_planep+S
free_scratchF2+C
isoatomic_reference_imprintEsc
key keysym
load_atom_color filenameF12
load_aux filenameF11
load_config filenameF9
load_config_firstInsert+C
load_config_backwardInsert
load_config_forwardDelete
load_config_lastDelete+C
load_script filenamel+M
look_at_the_anchora
newn
normal_coloringl
observer_gotog
original_normal_coloringo
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_patchr
finish_rcut_patchReturn
rcut_patch_dec, rcut_patch_inc End+C, Home+C
redraw
reload_configF10
reset_anchorw
reset_aux_property_thresholdsr+C
reset_scratchF2
reset_timer [reset] [label]
resize width height
rotate axis theta
rotate_0_dec, rotate_0_incUp, Down
rotate_1_dec, rotate_1_incRight, Left
rotate_2_dec, rotate_2_incDown+S, Up+S
save filename [key|both]
save_atom_indices; :
scratch_coloringF3
script_animate [filename]y
select_gear_[0-9][0-9]
set name value
shear_strain_coloringg+M
shift_cutting_plane delta
shift_cutting_plane_decLeft+S
shift_cutting_plane_incRight+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_rigidt+C
toggle_aux_property_thresholds_saturationa+C
toggle_bond_modeb
toggle_coordination_coloringk
toggle_parallel_projectionTab
toggle_rcut_patch_moder
toggle_shell_viewer_modev
toggle_xtal_modex
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_uprightu
xtal_origin_goto s0 s1 s2t
xtal_origin_zeroz

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
optiondescription
-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;

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)


Email: shimizu.futoshi@jaea.go.jp, liju@mit.edu,
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