flos

• Index

Contents

• Requirements
• Installation
• Basic usage
• Usage in SIESTA

Manual

• README

Modules

• error
• Linear
• Tables

Classes

• MDStep
• Array
• Shape
• Optimizer
• CG
• FIRE
• LBFGS
• Line
• NEB

Examples

• add_force.lua
• conv_meshcutoff.lua
• force_constant.lua
• neb_simple.lua
• relax_cell.lua
• relax_cell_geometry.lua
• relax_geometry_cg.lua
• relax_geometry_fire.lua
• relax_geometry_lbfgs.lua

flos

This library enables optimization schemes created in Lua to be used together with SIESTA via the flook library, hence the same flo + SIESTA = flos.

This enables scripting level languages to inter-act and develop new MD schemes, such as new geometry constraints, geometry relaxations, etc.

The API documentation may be found here.

Requirements

The only requirement is the Lua language.

The require Lua version is 5.3. However, if you are stuck with Lua 5.2 you can apply this patch:

patch -p1 < lua_52.patch

Installation

This Lua library may be used out of the box. To enable the use of this library you only require the LUA_PATH to contain the path to the library.
Importantly this library requires an explicit <path>/?/init.lua definition.

As an example the following bash commands enables the library:

cd $HOME
git clone https://github.com/siesta-project/flos.git
cd flos
git submodule init
git submodule update
export LUA_PATH="$HOME/flos/?.lua;$HOME/flos/?/init.lua;$LUA_PATH;;"

and that is it. Now you can use the flos library.

Basic usage

To enable this library you should add this to your Lua script:

local flos = require "flos"

which enables you to interact with all implemented flos implemented algorithms.

Usage in SIESTA

In principle flos is not relying on the SIESTA routines and may be used as a regular Lua library, although it has been developed with SIESTA in mind.

In the examples/ folder there are several examples which may be directly used in any SIESTA run for relaxation (they are generalized for any structure).

In order to use any of these schemes you simply need to follow these steps:

1. Compile flook, see this page: flook
2. Compile SIESTA with flook support. If you have followed the procedure outlined here you should add this to the SIESTA arch.make:

FLOOK_PATH  = /path/to/flook/parent
FLOOK_LIBS  = -L$(FLOOK_PATH) -lflookall -ldl
FLOOK_INC   = -I$(FLOOK_PATH)
INCFLAGS += $(FLOOK_INC)
LIBS += $(FLOOK_LIBS)
FPPFLAGS += -DSIESTA__FLOOK

3. Then you have, for good (contrary to the constr routine in SIESTA), enabled the Lua hook and you may exchange Lua scripts with other users and use scripts as you please.
To enable Lua in SIESTA simply set these fdf-flags:

MD.TypeOfRun lua
LUA.Script <script-name>

For instance to use the flos L-BFGS relaxation method:

cp flos/examples/relax_geometry_lbfgs.lua <path-to-siesta-run>/relax.lua

and set the following fdf-flag:

MD.TypeOfRun LUA
LUA.Script relax.lua

Now run SIESTA.