Library for generating highlyefficient generalized MonkhorstPack kpoint grids.
Project description
kplib
KpLib is a C++ library for finding the optimal Generalized MonkhorstPack kpoints grid. It can be imported into electronicstructure packages as a generator of efficient generalized kpoint grids, or be integrated into user scripts through the python interface.
For questions of kpLib and underlying algorithms, you are welcomed to check our paper at here or send emails to kpoints@jhu.edu.
Usage
Route I: Integrate kpLib as a C++ library
Compile kpLib
We use cmake
to detect native build environment and generate native build files. For Unixlike operating systems, users can build the project by:
$ git clone https://gitlab.com/muellergroup/kplib.git
$ cd kplib
$ mkdir build
$ cd build
$ cmake ..
$ make
Then you can find a static library libkpoints.a
and a dynamic library libkpoints.so
in the ./build
directory.
Use kpLib in your code
There are basically two steps:

copy the header file
src/kPointLatticeGenerator.h
to yourinclude
folder, and add the following line to your source code#include "kPointLatticeGenerator.h"

link the library at the linking stage.
For example, to link the static library and compile the object
myapp.o
to the final executablemyapp
, you can$ g++ myapp.o L /path/to/lib libkpoints.a o myapp
If you want to use the dynamic library, you can
$ export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/path/to/lib $ g++ myapp.o L /path/to/lib lkpoints o myapp
The first line tells the loader,
ld
, where to find the shared library at runtime, since the dynamic linkage only puts a reference of the library in the executable.
Then you are ready to go!
Route II: Integrate KpLib through Python Interface
Installation
The source code is downloaded at https://gitlab.com/muellergroup/kplib .
$ git clone https://gitlab.com/muellergroup/kplib.git
In order to install this package use pip:
$ pip install "kplib"
Commandline interface kpgen
You can use the command line interface to generate Generalized MonkhorstPack kpoints grid by calling kpGen
in terminal.
kpGen
reads the input file by using pymatgen
, so it in principle support all kinds
of structure format supported by pymatgen
. By default, it reads POSCAR as input file.
Currently, the output file which contain the kpoints is writen as VASP's KPOINTS file.
Users can check and see the details of the arguments and options by kpGen help
.
Python API reference and examples
For users who wants to use kplib
in their python packages, the recommended method is to use the get_kpoints
function. It returns a dict, the keys of which are:
min_periodic_distance
: The minimum distance between lattice points on the realspace superlattice.num_distinct_kpts
: The number of distinct kpoints reduced by lattice symmetry.num_total_kpts
: The number of total kpoints.coords
: The coordinates of kpoints, represented in refraction coordinate.weights
: The weights of corresponding kpoints.
import numpy as np from kplib import get_kpoints struc = ... kpts = get_kpoints(struc, minDistance=24.9, include_gamma=include_gamma)
How to cite
If you use the kplib in generating generalized kpoint grids, please cite the following article:
Wang, Y., Wisesa, P., Balasubramanian, A., Dwaraknath, S. & Mueller, T. Rapid generation of optimal generalized MonkhorstPack grids. Comp Mater Sci, 110100, doi:https://doi.org/10.1016/j.commatsci.2020.110100 (2020).
Documentation
C++ API
Class: kPointLatticeGenerator
template <typename T>
using Tensor = std::vector<std::vector<T>>;
/**
* Constructor.
*
* To see how the variables are defined, check the "Conventions" section below)
*
* @param primVectorsArray primitive lattice vectors in rows.
* @param conventionalVectorsArray conventional lattice vectors in rows.
* @param latticePointOperatorsArray point operators of the Laue Class
of the input structure, expressed
in the basis of primitive lattice vectors
* @param numOperators number of point operators in above array
* @param isConventionalHexaognal whether the conventional lattice is
hexagonal
*/
KPointLatticeGenerator(const double primVectorsArray[3][3],
const double conventionalVectorsArray[3][3],
const int latticePointOperatorsArray[][3][3],
const int numOperators,
const bool isConventionalHexagonal);
/*
* Specify whether to generate a gammacentered grid or a shifted grid.
* The available shifts are:
* {{0.0, 0.0, 0.5}, {0.0, 0.5, 0.0}, {0.5, 0.0, 0.0}, {0.5, 0.5, 0.0},
* {0.5, 0.0, 0.5}, {0.0, 0.5, 0.5}, {0.5, 0.5, 0.5}}
* Basiclly, side centers, face centers and the body center.
*
* @param includeGamma TRUE: gammacentered grid
* FALSE: grid with one of the above shift
* AUTO: search both shifted and gammacentered grid
* and return the best one.
*/
enum INCLUDE_GAMMA { TRUE, FALSE, AUTO };
void includeGamma(INCLUDE_GAMMA includeGamma);
/*
* @param minDistance The returned grid should have a corresponding
* realspace superlattice whose "minimum periodic distance"
* is no smaller than this value.
* @param minSize Minimum number of total kpoints of grids returned.
*/
KPointLattice getKPointLattice(const double minDistance,
const int minSize);
Class: KPointLattice
It's meant to hold the found kpoint grid and provide query functions.
The main query routines of this type:
double getMinPeriodicDistance();
int getNumDistinctKPoints();
int numTotalKPoints();
/*
* @return Tensor<double> 2D arrays of coordinates. It's basically a wrapper
* of "double coords[][3]".
*/
Tensor<double> getKPointCoordinates();
/*
* @return vector<int> 1D array of kpoints weights.
*/
std::vector<int> getKPointWeights();
Conventions
This section specifies the conventions we use for the variables used in kPointLatticeGenerator
constructor:
i.e. primVectors
, conventionalVectors
, latticePointOperators
and isConventionalHexagonal
.
Lattice Vectors
Lattice vectors are expressed as row vectors of the lattice matrix:
double primtiveVectors[3][3] = {{a_x, a_y, a_z},
{b_x, b_y, b_z},
{c_a, c_z, c_y}}
Point Operators
Each operation is a 3x3 integral matrix, representing how a fractional coordinate in the primitive lattice basis is transformed under this operation.
int latticePointOperations[][3][3];
Because of the lattice vectors are expressed as rows, each symmetry operation is done through "x' = x^{T} . R", i.e. vector times matrix.
Conventional Lattice Vectors
Becuase of the algorithm we use to efficiently iterate symmetrypreserving superlattice, the conventional lattice vectors should follow the below requirements:

For all lattice systems, except for triclinic, the cvector should be along the axis of the highest order rotational operation, i.e the 4fold, 6fold, 3fold, 4fold, any 2fold, and 2fold rotation for cubic, hexagonal, trigonal, tetragonal, orthorhombic, and monoclinic lattices, respectively. This direction is commonly referred as the "primary symmetry direction" in crystallography textbooks.

For trigonal lattices, the conventional lattices should be primitive hexagonal lattices, i.e. the trigonalcentered hexagonal.
The algorithm doesn't put constraints on triclinic system, or on the centering type of lattices in the 2/m and the mmm Laue class.
(Note: User could get the primary directions from the point symmetry opeartions.)
Example of using kplib  demo_kplib
To demonstrate the usage of the kpbib, we implement a simple C++ application to find Generalised MonkhorstPack kpoint grids. It use spglib
to determine symmetries (Togo and Tanaka, 2010) and output the kpoint grid in the format of VASP KPOINTS file.
It's under the folder demo_kplib
. To build this application, user should build spglib
and replace the library file libsymspg.a
in ./lib
. Then the executable demo_kplib
can be built by
$ cd demo_kplib
$ mkdir build
$ cd build
$ cmake ..
$ make
The binary is placed at ./build/demo_kplib
. To call it, use:
$ demo_kplib /path/to/POSCAR /path/to/PRECALC > KPOINTS
The POSCAR is one of the standard VASP input file. The PRECALC file is the input file of demo_kplib
and users can find its specifications on our website. Since it's for demonstration purposes, only the parameters MINDISTANCE
, MINTOTALKPOINTS
, and INCLUDEGAMMA
are valid.
There are some examples of using this application in demo_kplib/examples
.
For a more complete application, check our Kpoint Grid Generator and Kpoint Server.
Code snippet of demo_kpib
Below are excerpts from the application to show how to use the kplib API.
main.cpp
:
#include "kPointLatticeGenerator.h"
#include "utils.h"
#include "precalc.h"
#include "poscar.h"
#include <iostream>
int main(int argc, char **argv) {
if (argc < 3) {
std::cerr << "Usage: ./main /path/to/POSCAR /path/to/PRECALC"
<< std::endl;
return 1;
}
// Parse POSCAR and PRECALC.
Poscar poscar;
poscar.readFromPoscar(std::string(argv[1]));
Precalc precalc(argv[2]);
// Execute the main routines.
KPointLatticeGenerator generator = initializeKPointLatticeGeneratorObject(
poscar.primitiveLattice, poscar.coordinates, poscar.atomTypes);
if (precalc.getIncludeGamma() == "TRUE") {
generator.includeGamma(TRUE);
} else if (precalc.getIncludeGamma() == "FALSE") {
generator.includeGamma(FALSE);
} else if (precalc.getIncludeGamma() == "AUTO") {
generator.includeGamma(AUTO);
}
KPointLattice latticeGamma = generator.getKPointLattice(
precalc.getMinDistance(), precalc.getMinTotalKpoints());
outputLattice(latticeGamma);
}
utils.cpp
:
#include "utils.h"
#include "spglib.h"
... // other includes and functions
// Wrapper of the kPointLatticeGenerator constructor.
KPointLatticeGenerator initializeKPointLatticeGeneratorObject(
Tensor<double> primitiveLattice,
Tensor<double> coordinates,
std::vector<int> atomTypes) {
double primLatticeArray[3][3] = {0};
double conventionalLatticeArray[3][3] = {0};
int rotation[192][3][3] = {0};
int size = 0;
bool isConventionalHexagonal = false;
// use spglib to get necessary parameters for the consturctor
// of kPointLatticeGenerator.
...
KPointLatticeGenerator generator = KPointLatticeGenerator(primLatticeArray,
conventionalLatticeArray, rotation, size, isConventionalHexagonal);
return generator;
}
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