https://github.com/odarbelaeze/neighbors

A cpp program that allows computing neighbor interactions using a k-dimensional tree (3D in this case)
https://github.com/odarbelaeze/neighbors

Last synced: 23 days ago
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A cpp program that allows computing neighbor interactions using a k-dimensional tree (3D in this case)

• Host: GitHub
• URL: https://github.com/odarbelaeze/neighbors
• Owner: odarbelaeze
• License: mit
• Created: 2015-01-26T23:38:13.000Z (almost 10 years ago)
• Default Branch: master
• Last Pushed: 2017-06-13T20:13:12.000Z (over 7 years ago)
• Last Synced: 2024-11-06T20:50:08.683Z (2 months ago)
• Language: C++
• Size: 69.3 KB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE.txt

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README

        
# neighbors

**neighbors** is a program that allows you to compute pair-wise

interactions, given different cut-off radiuses, in systems with large

amounts of atoms. The problem trying to be addressed here is that

computing pair wise interactions in a naïve way requires computations

of **O(n^2)** complexity. Using a _kdtree_ to wrap the input data would

reduce that complexity to **O(R N log(N))** where **R** is the average

number of interactions of each site.

## Getting started

### Installing

This program requires at least _gcc-4.9_ to compile, the installation

process may vary according to your operating system, but for Ubuntu

14.04 you need to pull in the toolchain testing repository, update and

install the g++-4.9 package as well as cmake that will be needed later

on,

    sudo add-apt-repository ppa:ubuntu-toolchain-r/test

    sudo apt-get update

    sudo apt-get install g++-4.9

Then you need to recursively clone the **neighbors** repository and

cd into the directory

    git clone --recursive https://github.com/odarbelaeze/neighbors.git

    cd neighbors

Finally you'll need to build the program, for this you'll need cmake,

    mkdir build

    cd build

    cmake ..

    make

Once you do this you'll have the neighbors program ready to go, you

could do `sudo make install` in order to install the program system

wide, but that's ill advised due to the early stage of development of

this program.

### Building the documentation

Documentation is a big part of the neighbors program, the code

documentation is written into the header files, you can build the

documentation using just by running doxygen in the projects, folder,

    # sudo apt-get install doxygen doxygen-latex

    doxygen

    cd docs

    make latex      # or latexpdf or html

The de documentation will be generated in the `docs/build` directory.

### Building the test suite

In order to build the test suite you just need to install

the [gtest](https://github.com/odarbelaeze/neighbors.git)

framework and make it findable by cmake, you can get instructions

[here](http://www.cmake.org/cmake/help/v3.0/module/FindGTest.html)

    # Install gtest and make it findable

    cd build

    cmake ..

    make

    ./tests

## Running the program

### Specifying interactions

In order to run the program you'll need a `neighbors.json` file this

specifies the kind of interactions that the program will deal with, an

example of the file is given next:

    {

        "doc": {

            "0": "Sites type 0 are this and that...",

            "1": "Sites type 1 are this and that...",

            "0-0": "This interaction is due to something and..."

        },

        "unitcell": {

            "scale": 1.0,

            "parameters": [1.0, 1.0, 1.0],

            "unit_vectors": {

                "uvx": [1.0, 0.0, 0.0],

                "uvy": [0.0, 1.0, 0.0],

                "uvz": [0.0, 0.0, 1.0]

            }

        },

        "periodicity": {

            "x": false,

            "y": false,

            "z": false

        },

        "interactions": {

            "0-0": {

                "cut": 1.0,

                "exchange": 0.5

            },

            "0-1": {

                "cut": 1.0,

                "exchange": 0.5

            },

            "1-0": {

                "cut": 1.0,

                "exchange": 0.5

            },

            "1-1": {

                "cut": 1.0,

                "exchange": 0.5

            }

        }

    }

The *doc* block specifies any documentation that you'll need to

understand the input file in the future, those are notes for the future

you. The *unitcell* block specifies the form of your system is useful

for repeating your system and defining interactions with periodic

boundary conditions. The *periodicity* object specifies if the cell

is periodic or free in each of the directions. Finally the *interactios*

object specify the different interactions between types of atoms.

### Representing the sites

**neighbors** expect a CSV representation of the sites to work with the

format is as follows,

       

The *type_id* should be a string without dashes ("-"), because the

interaction markers are made of two type ids separated with a dash.

### Interpreting the output

**neighbors** will output the information relevant to the interactions

in the system, the CSV format will be,

       [  ] 

*  * are toggled by leaving out the plain flag in the

program's invocation.