diff --git a/README.md b/README.md index fffdda9..4d6a6f7 100644 --- a/README.md +++ b/README.md @@ -10,13 +10,11 @@ A simple X11 molecular viewer. - [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) -- various quantum-chemical outputs with [`cclib`](https://github.com/cclib/cclib), see the Python wrapper [page](python/README.md). - +- various quantum-chemical outputs with [cclib](https://github.com/cclib/cclib), see the Python wrapper [page](python/README.md). ## Python package (wrapper / API) available -See python package page -[here.](python/README.md) +See python package page [here](python/README.md). Provides wrapper scripts with a simple installation and allows to open unsupported file formats with `cclib`. @@ -43,7 +41,7 @@ See build [instructions](BUILD.md). ``` ./v file [file2 ... fileN] [options] ``` -A filename `-` stands for the standard input (xyz files only). +A filename '-' stands for the standard input (xyz files only). Show the reference: ``` @@ -75,8 +73,8 @@ Show the reference: | `cell:0` | disable PBC from the extended xyz file header | | `cell:b%%lf[,%%lf,%%lf[,%%lf,%%lf,%%lf,%%lf,%%lf,%%lf]]` | cubic / orthogonal / non-orhogonal cell parameters in a.u. | | `cell:%%lf[,%%lf,%%lf[,%%lf,%%lf,%%lf,%%lf,%%lf,%%lf]]` | cubic / orthogonal / non-orhogonal cell parameters in Å | -| `shell:b%%lf[,%%lf] | sphere(s) radii in a.u. | -| `shell:%%lf[,%%lf] | sphere(s) radii in Å | +| `shell:b%%lf[,%%lf]` | sphere(s) radii in a.u. | +| `shell:%%lf[,%%lf]` | sphere(s) 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` | gui (default `1`) / headless (`0`) mode | @@ -84,7 +82,6 @@ Show the reference: | `exitcom:%s` | command sequence to run on exit (same as for `gui:0`) | | `startcom:%s` | command sequence to run on startup | - ### Keyboard @@ -152,6 +149,9 @@ D*h ``` #### GUI mode +> [!WARNING] +> Currently this option is unstable. Please let me know if you encounter any problems. +> In the GUI mode, the symbols from the CLI option `exitcom:` are executed immediately before closing. For example, ``` @@ -171,10 +171,8 @@ moves the molecule to the left, and opens the file, computes the point group, save a picture to `mol/mol0001.xyz_1.xpm` and closes the window. For other examples, see [fig/regenerate.bash](fig/regenerate.bash) for the commands used to generate the figures on this page. -
Click to see currently available commands - | CLI regime symbol | GUI keyboard command | | GUI (`exitcom:`/`startcom:`) | headless (`com`) | | ------------------ | --------------------- | ----------------- | ---------------------------- | ---------------- | | `w`/`a`/`s`/`d` | `w`/`a`/`s`/`d` | move | + | + (PBC) | @@ -189,16 +187,11 @@ For other examples, see [fig/regenerate.bash](fig/regenerate.bash) for the comma | `.` | `.` | point group | + | + | | `x`,`z`,`p`,`u` | `x`,`z`,`p`,`u` | printing | + | + | -
- > [!NOTE] > The size depends on my screen and window layout, you might need to adjust the number of move/zoom in commands or the window size. -> [!WARNING] -> Currently this option is unstable. Please let me know if you encounter any problems. - ### Boundary conditions Two types of boundary conditions are recognized: * PBC (3D) @@ -246,7 +239,6 @@ Spherical confinement can be specified from the command-line by the following: - ## Examples * `mol/C3H6~mCPBA_01x11.qm.out` — geometries + vibrations ```