v

A simple viewer for Priroda outputs, .xyz files, and beyond.

Contents

• Download
• Build
• Usage
• Examples

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Download ↑

wget https://github.com/briling/v/releases/download/v2.0/v.2.0 -O v
chmod +x ./v

Build ↑

make v

Requirements:

• GNU/Linux or Cygwin
• X11
• gcc >= 4.7
• libX11-devel, libXpm-devel, xproto-devel
• make

Usage ↑

./v file [file2 ... fileN] [options]

Show the reference:

./v

Command-line options

vib:%d	force to show geometries (0) / vibrations (1)
bonds:0	disable bonds
bohr:1	assume input files are in Bohr (default is Å)
dt:%lf	delay between frames in seconds (default 0.02)
symtol:%lf	tolerance for symmetry determination in Å (default 0.001)
bmax:%lf	max. length of a bond to display
z:%d,%d,%d,%d,%d	show an internal coordinate (1,i,j,0,0 — distance i-j; 2,i,j,k,0 — angle i-j-k; 3,i,j,k,l — torsion i-j-k-l)
rot:%lf,%lf,%lf,%lf,%lf,%lf,%lf,%lf,%lf	rotation matrix to start with (default identity matrix)
font:%s	font (xlfd)
cell:b%lf,%lf,%lf	cuboid size in a.u. (for periodical boundary conditions)
cell:%lf,%lf,%lf	cuboid size in Å
cell:b%lf,%lf,%lf,%lf,%lf,%lf,%lf,%lf,%lf	cell parameters in a.u.
cell:%lf,%lf,%lf,%lf,%lf,%lf,%lf,%lf,%lf	cell parameters in Å
shell:b%lf,%lf	spheres radii in a.u.
shell:%lf,%lf	spheres radii in Å
gui:%d	normal (default 1) / headless (0) mode

Keyboard reference

←/↑/→/↓/pgup/pgdn	rotate (slower with ctrl or shift)
w/a/s/d or ↑/←/↓/→ on numpad	move (slower with ctrl or shift)
0	go to the first point
=	go to the last point
enter/backspace	next/previous point
ins	play forwards / stop (vibration mode: animate selected normal mode / stop)
del	play backwards / stop
home/end	zoom in/out
1/2	scale bond lengths
3/4	scale atom sizes
.	show point group
n	show/hide atom numbers
t	show/hide atom types
l	show/hide bond lengths
b	show/hide bonds
tab	read new points
r	reread file
x	print molecule (Priroda input + bonds)
z	print molecule (.xyz)
p	print molecule (input for an .svg generator)
u	print current rotation matrix
m	save the current frame (.xpm format)
f	save all frames (vibration mode: save all frames to animate the selected normal mode)
q	quit

Mouse (in development)

One can also use the mouse to rotate the molecule and zoom in/out.

Headless mode (in development)

If run in the headless mode with gui:0, the symbols from stdio are processed as if the corresponding keys were pressed in the normal mode. Right now, only p, x, z, and . are available. For example,

> echo . | ./v mol/mol0001.xyz gui:0
D*h

Examples ↑

• mol/C3H6~mCPBA_01x11.qm.out — geometries + vibrations

./v mol/C3H6~mCPBA_01x11.qm.out font:-*-*-medium-*-*--15-*-*-*-*-*-*-1

./v mol/C3H6~mCPBA_01x11.qm.out vib:0 z:1,23,24,0,0

• mol/S8.qm.out — geometries

./v mol/S8.qm.out z:1,1,2,0,0 font:-*-*-medium-*-*--15-*-*-*-*-*-*-1

• mol/C10H16.qm.out — vibrations

./v mol/C10H16.qm.out font:-*-*-medium-*-*--15-*-*-*-*-*-*-1

• mol/1372_D02.340_1.out — PBC simulation

./v mol/1372_D02.340_1.out bonds:0 cell:b10.7,10.7,1.07 font:-*-*-medium-*-*--15-*-*-*-*-*-*-1

• mol/mol0001.xyz, mol/mol0002.xyz — .xyz files with atomic numbers and atomic symbols

./v mol/mol0001.xyz mol/mol0002.xyz symtol:1e-2 font:-*-*-medium-*-*--15-*-*-*-*-*-*-1

• mol/MOL_3525.xyz — organic crystal with non-orthogonal cell

./v mol/MOL_3525.xyz cell:8.929542,0.0,0.0,4.197206,8.892922,0.0,0.480945,2.324788,10.016044 font:-*-*-medium-*-*--15-*-*-*-*-*-*-1

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