Installation

There are two ways to install NAMD-LMI, downloading the pre-built binaries or building from scratch.

Download the binary from Github Release

We provide the pre-built binaries at Github Release.

There are several platforms we support with pre-built binaries, in which we can identify them by their file names parts:

• namd_lmi-: the version of NAMD-LMI;
• linux/macos/windows: which operating system it runs on;
• x86_64/aarch64: which CPU architecture it runs on;
• mkl-system/mkl-static/openblas-system/openblas-static: which BLAS implementation and which link scheme, where xxx-system requires you install corresponding BLAS implementation on system, while xxx-static statically link against to BLAS (which means you needn't install anything else) but come with larger binary sizes.
• .tar.gz/zip: which compressor format it uses. You need to decompress the binary first.

Example:

• namd_lmi-1.0.0-linux-x86_64-mkl-system.tar.gz should run on an x86 machine with 64-bit Linux installed, where the Intel-MKL should be installed.
• namd_lmi-1.0.0-macos-x86_64-mkl-system.tar.gz should run on macOS with Intel chip.
• namd_lmi-1.0.0-macos-aarch64-mkl-system.tar.gz should run on macOS with Apple Silicon.
• namd_lmi-1.0.0-windows-x86_64-mkl-static.zip should run on Windows 7 or upper with Intel/AMD or other x86 chips.

Build from scratch

The build requires Internet accessibility and Rust toolchain, Intel-MKL libraries.

• If you haven't installed Rust toolchain, run curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh and follow the instructions to configure it. When you finished the toolchain installation, you should be able to run cargo in command-line. Detailed instructions can be found here.
• If you have installed Rust toolchain and Intel-MKL already, just run cargo install --git https://github.com/Ionizing/NAMD-LMI. Several minutes later, the namd_lmi binary should be installed to ~/.cargo/bin, no need to modify the $PATH (or %PATH% on Windows).

There are four features to link BLAS implementations:

• intel-mkl-system: dynamically link against pre-installed Intel-MKL library. You need to install Intel-MKL first.
• intel-mkl-static: statically link against Intel-MKL library. If no pre-installed MKL is found, it will download Intel-MKL 2020 from web by itself.
• openblas-system: dynamically link against pre-installed OpenBLAS. You need to install OpenBLAS first.
• openblas-static: statically link against OpenBLAS library. If no pre-installed OpenBLAS is found, it will download OpenBLAS source code and build it from scratch.

Test the installation

Once you obtain the namd_lmi binary, just put it in your PATH, and then you should be able to run it with the output like

$ namd_lmi
+----------------------------------------------------------------------+
|                                                                      |
|    _   _            __  __  _____           _       __  __  _____    |
|   | \ | |    /\    |  \/  ||  __ \         | |     |  \/  ||_   _|   |
|   |  \| |   /  \   | \  / || |  | | ______ | |     | \  / |  | |     |
|   | . ` |  / /\ \  | |\/| || |  | ||______|| |     | |\/| |  | |     |
|   | |\  | / ____ \ | |  | || |__| |        | |____ | |  | | _| |_    |
|   |_| \_|/_/    \_\|_|  |_||_____/         |______||_|  |_||_____|   |
|                                                                      |
+----------------------------------------------------------------------+

Welcome to use namd!
    current version:    0.1.0
    git hash:           d659586
    author(s):          Ionizing
    host:               x86_64-unknown-linux-gnu
    built time:         2024-11-19 15:34:05 +08:00


Usage: namd_lmi <COMMAND>

Commands:
  nac      Calculate non-adiabatic coupling (NAC) including `<j| d/dt |k>` and momentum matrix `<i| p |j>`
  hamil    Generate the Hamiltonian from NAC according to config file
  surfhop  Perform the surface-hopping process with given Hamiltonian file and config file
  help     Print this message or the help of the given subcommand(s)

Options:
  -h, --help     Print help (see more with '--help')
  -V, --version  Print version