https://github.com/briling/v
A simple X11 molecular viewer
https://github.com/briling/v
computational-chemistry molecular-visualization quantum-chemistry x11
Last synced: 3 months ago
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A simple X11 molecular viewer
- Host: GitHub
- URL: https://github.com/briling/v
- Owner: briling
- License: mit
- Created: 2019-02-17T21:15:49.000Z (over 7 years ago)
- Default Branch: master
- Last Pushed: 2026-03-08T14:32:01.000Z (3 months ago)
- Last Synced: 2026-03-08T14:46:20.056Z (3 months ago)
- Topics: computational-chemistry, molecular-visualization, quantum-chemistry, x11
- Language: C
- Homepage:
- Size: 26.8 MB
- Stars: 22
- Watchers: 3
- Forks: 2
- Open Issues: 12
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# v
A simple X11 molecular viewer.
## Contents
* [Supported formats](#formats-)
* [Download](#download-)
* [Build](#build-)
* [Usage](#usage-)
* [Examples](#examples-)
---
## Supported formats [↑](#download)
- [Priroda](http://rad.chem.msu.ru/~laikov) input and output files
- [`.xyz`](https://en.wikipedia.org/wiki/XYZ_file_format) files
- [extended `.xyz`](https://github.com/libAtoms/extxyz) files (currently the extra columns are ignored)
## Python package (wrapper / API) available
See python package page
[here.](python/README.md)
Provides wrapper scripts with a simple installation and
allows to open unsupported file formats with `cclib`.
## Download [↑](#download)
```
wget https://github.com/briling/v/releases/download/v2.0/v.2.0 -O v
chmod +x ./v
```
## Build [↑](#contents)
```
make v
```
### Requirements:
* `GNU/Linux` or `Cygwin`
* `X11`
* `gcc >= 4.7`
* `libX11-devel libXpm-devel xproto-devel` (`libx11-dev libxpm-dev x11proto-dev` on Ubuntu)
* `make`
## Usage [↑](#contents)
```
./v file [file2 ... fileN] [options]
```
A filename `-` stands for the standard input.
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) |
| `frame:%d` | frame to start with (default 1) |
| `font:%s` | font ([xlfd](https://en.wikipedia.org/wiki/X_logical_font_description)) |
| `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 |
| `center:%d` | origin is geometric center (`1`, default) / center of mass (`2`) / as is (`0`) |
| `inertia:%d` | if rotate molecules wrt axis of inertia (`1`) or not (`0`, default) |
| `gui:%d` | normal (default `1`) / headless (`0`) mode |
| `com:%s` | command sequence for `gui:0` |
| `exitcom:%s` | command sequence to run on exit (same as for `gui:0`) |
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`](https://en.wikipedia.org/wiki/X_PixMap) format)
| `f` | save all frames (vibration mode: save all frames to animate the selected normal mode)
| |
| `j` | jump to a frame (will be prompted): `enter` to confirm, `esc` to cancel
| |
| `q` / `esc` | 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 the standard input are processed
as if the corresponding keys were pressed in the normal mode.
Right now, only `p`, `x`, `z`, and `.` are available.
Command-line option `com:%s` overrides the standard input.
These examples are equivalent:
```
> echo . | ./v mol/mol0001.xyz gui:0
D*h
> ./v mol/mol0001.xyz gui:0 com:.
D*h
> cat mol/mol0001.xyz | ./v - gui:0 com:.
D*h
```
## Examples [↑](#contents)
* `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
```
---
