Wavecar.hpp

Introduction

This package implements a C++11 header-only library for reading WAVECAR files in the VASP5 format.

It is written as a literate program ^{LiteratePrograKnuth1984}, so we will try to keep the documentation and the code in the same place.

As a convenience you can find the header file in the include directory.

Header

We will only need libraries available in the standard library:

#include <iostream>
#include <fstream>
#include <map>
#include <array>
#include <assert.h>
#include <string>
#include <numeric>
#include <algorithm>
#include <vector>
#include <math.h>
#include <complex>

Main types

We define the main structure for the WAVECAR header,

using CellVector = std::array<double, 3>;

struct Cell {
  std::array<CellVector, 3> basis;
  double volume;
};

struct WavecarHeader {
  size_t recordLength;
  size_t nSpin;
  size_t version;
  size_t nKpoints;
  size_t nBands;
  size_t encut;
  double eFermi;
  size_t nPlaneWaves;
  Cell real, reciprocal;
};

using KPoint = CellVector;
using OrbitalCoefficients = std::vector<std::complex<double>>;
struct HorizontalBand {
  std::vector<double> realEnergies;
  std::vector<double> imagEnergies;
  std::vector<double> occupancies;
  std::vector<OrbitalCoefficients> coefficients;
};
using KBand = std::pair<KPoint, HorizontalBand>;

struct WaveDescriptor {
  std::vector<KBand> bands;
  inline size_t nKpoints() { return bands.size(); }
};

struct Wavecar {
  WavecarHeader header;
  std::vector<WaveDescriptor> descriptors;
};

`WAVECAR` parsing

Understanding the code

It can be quite challenging sometimes to understand binary formats coming from Fortran, or binary formats in general. It is quite instructive to peek into the binary structure of the files and try to backwards engineer the main structure of the file.

Here is an excerpt of a hexdump of a typical VASP5 format WAVECAR file:

                  BYTES      
 ADDRESS  1 2  3 4  4 6  7 8  | Comments
==============================|=========
00000000: 0000 0000 0018 d940 | Fortran record length
00000008: 0000 0000 0000 f03f | number of spin channels
00000010: 0000 0000 8006 ea40 | format version (RTAG)
00000018: 0000 0000 0000 0000 |
*                               (zero padding)
00006460: 0000 0000 0000 f03f | Number of k-points
00006468: 0000 0000 0020 b940 | Number of bands
00006470: 0000 0000 00e0 8540 | ENCUT
00006478: ba49 0c02 2b07 1140 | a[1,1] (lattice vectors)
00006480: ba49 0c02 2b07 1140 | a[1,2]
00006488: 0000 0000 0000 0000 | a[1,3]
00006490: 0000 0000 0000 0000 | a[2,1]
00006498: ba49 0c02 2b07 1140 | a[2,2]
000064a0: ba49 0c02 2b07 1140 | a[2,3]
000064a8: ba49 0c02 2b07 1140 | a[3,1]
000064b0: 0000 0000 0000 0000 | a[3,2]
000064b8: ba49 0c02 2b07 1140 | a[3,3]
000064c0: 1a6f 1d53 35e9 0540 | fermi energy
000064c8: 0000 0000 0000 0000 |
*                               (zero padding)
0000c8c0: 0000 0000 0018 a940 | number of plane waves
0000c8c8: 0000 0000 0000 0000 | kpoint[0]  \
0000c8d0: 0000 0000 0000 0000 | kpoint[1]   > Gamma point
0000c8d8: 0000 0000 0000 0000 | kpoint[2]  /
0000c8e0: f1e1 932b 1cee 56c0 | energy-real     x
0000c8e8: 0000 0000 0000 0000 | energy-complex  0
0000c8f0: 0000 0000 0000 f03f | occupation      1

Here there are a couple of things we should remark,

VASP5 format writes out everything using floating point numbers, even quantities that ought to be integers, this is done so that the binary format is compatible throughout machines (and most programming languages) since they follow IEEE standards.
Fortran can use an offset to read different parts of a file separated in records. The first quantity we get in the WAVECAR is this record length. In this particular case it is equal to 25696 or 0x6460 in hexadecimal notation. Notice that this is equal the address where the WAVECAR header begins by providing the number of ( k )-points.
The second time this record length arises, is when the first chunk of data for the wavefunction arises, i.e. 2*25696 = 0xc8c0, where we obtain for the first spin channel and first ( k )-point
- the number of plane-waves
- the real part of the eigenenergies
- the complex part of the eigenenergies
- the occupation numbers
- the plane-wave coefficients.

Wave descriptor

KBand
readWaveWaveDescriptor( const std::string &fileName
                      , const WavecarHeader &header
                      , const size_t &spinIndex
                      ) {

  std::vector<double> realEnergies(header.nBands)
    , imagEnergies(header.nBands)
    , occupancies(header.nBands)
    ;

  double buffer;
  std::fstream file(fileName, std::ios::binary | std::ios::in);
  size_t numberPlaneWaves;
  CellVector kpoint;
  std::vector<OrbitalCoefficients> coefficients;

  file.seekg((spinIndex + 2) * header.recordLength);

  // read numberPlaneWaves
  file.read((char*)&buffer, sizeof(double));
  numberPlaneWaves = size_t(buffer);

  //C.resize(header.nBands * numberPlaneWaves);

  file.read((char*)&kpoint, 3*sizeof(double));

  for (size_t n=0; n < header.nBands; n++) {
    file.read((char*)(realEnergies.data() + n), sizeof(double));
    file.read((char*)(imagEnergies.data() + n), sizeof(double));
    file.read((char*)(occupancies.data() + n), sizeof(double));
  }

  for (size_t n=0; n < header.nBands; n++) {
    OrbitalCoefficients C;
    C.resize(numberPlaneWaves);
    coefficients.push_back(C);
    file.read((char*)C.data(), numberPlaneWaves * 2 * sizeof(double));
  }

  return { kpoint
         , {realEnergies, imagEnergies, occupancies, coefficients}
         };

}

Header

WavecarHeader readWavecarHeader(const std::string &fileName) {
  WavecarHeader header;
  std::fstream file(fileName, std::ios::binary | std::ios::in);
  double buffer;
  std::vector<double> vvbuffer;

  assert(sizeof(double) == 8);
  assert(sizeof(header.real.basis) == 72);
  assert(sizeof(CellVector) == 3 * sizeof(double));

  file.read((char*)&buffer, sizeof(double));
  header.recordLength = size_t(buffer);
  file.read((char*)&buffer, sizeof(double));
  header.nSpin = size_t(buffer);
  file.read((char*)&buffer, sizeof(double));
  header.version = size_t(buffer);

  if (header.version != 53300)
    throw "This program only supports VASP5 format (RTAG: 53300)";

  file.seekg(header.recordLength);

  file.read((char*)&buffer, sizeof(double));
  header.nKpoints = size_t(buffer);
  file.read((char*)&buffer, sizeof(double));
  header.nBands = size_t(buffer);
  file.read((char*)&buffer, sizeof(double));
  header.encut = size_t(buffer);

  // Setup real cell
  file.read((char*)&header.real.basis, sizeof(header.real.basis));
  header.real.volume = cellVolume(header.real);

  file.read((char*)&buffer, sizeof(double));
  header.eFermi = buffer;

  // Setup Reciprocal cell
  header.reciprocal = reciprocalCell(header.real);



  return header;
}

The whole `WAVECAR`

Wavecar readWavecar(const std::string &fileName) {
  auto header(readWavecarHeader(fileName));
  std::vector<WaveDescriptor> descriptors;

  for (size_t i=0; i < header.nSpin; i++) {
    WaveDescriptor descriptor;
    for (size_t k=0; k < header.nKpoints; k++) {
      auto kBand(readWaveWaveDescriptor(fileName, header, i));
      descriptor.bands.push_back(kBand);
    }
    descriptors.push_back(descriptor);
  }
  return {header, descriptors};

}

`WAVECAR` writing

Our writer writes WAVECAR files in the VASP5 version.

`CellVector`

void writeToWavecar(std::ofstream &f, const CellVector &v) {
  f.write((char*)v.data(), sizeof(CellVector));
}

`Cell`

In the case of a cell we only write the basis elements in order,

void writeToWavecar(std::ofstream &f, const Cell &c) {
  for (const auto& v: c.basis) writeToWavecar(f, v);
}

`WavecarHeader`

In the case of the WavecarHeader we have to make sure the order is the correct one that VASP is expecting.

void writeToWavecar(std::ofstream &f, const WavecarHeader &h) {
  const auto writeInt
    = [&f](const size_t &i) {
        const double j(i);
        f.write((char*)&j, sizeof(double));
    };
  writeInt(h.recordLength);
  writeInt(h.nSpin);
  writeInt(h.version);

  f.seekp(h.recordLength);

  writeInt(h.nKpoints);
  writeInt(h.nBands);
  writeInt(h.encut);

  writeToWavecar(f, h.real);
  f.write((char*)&h.eFermi, sizeof(double));
}

`WaveDescriptor`

void writeToWavecar(std::ofstream &f, const WaveDescriptor &d) {
  for (auto const& kband: d.bands)  { // spin loop
    const auto& kVector(kband.first);
    const auto& vband(kband.second);
    const double numberPlaneWaves(vband.coefficients[0].size());

    f.write((char*)&numberPlaneWaves, sizeof(double));
    writeToWavecar(f, kVector);

    for (size_t n(0); n < vband.realEnergies.size(); n++) {
      f.write((char*)&vband.realEnergies[n], sizeof(double));
      f.write((char*)&vband.imagEnergies[n], sizeof(double));
      f.write((char*)&vband.occupancies[n], sizeof(double));
    }

    for (size_t n(0); n < vband.realEnergies.size(); n++) {
      f.write((char*)vband.coefficients[n].data(),
              numberPlaneWaves * 2 * sizeof(double));
    }

  }
}

`Wavecar`

Writing a WAVECAR consists in writing first the header and then the wave descriptor.

void writeToWavecar(std::ofstream &f, const Wavecar &w) {
  writeToWavecar(f, w.header);

  for (size_t ispin(0); ispin < w.descriptors.size(); ispin++) {
    f.seekp((ispin + 2) * w.header.recordLength);
    writeToWavecar(f, w.descriptors[ispin]);
  }

}

G grid

Types

using GGrid = std::pair<KPoint, std::vector<CellVector>>;
using HorizontalGrid = std::vector<GGrid>;
constexpr double hbarConst = 0.26246582250210965422;

Creating a grid from a wavecar

std::vector<HorizontalGrid>
mkGrid(const Wavecar &wavecar) {
  std::vector<HorizontalGrid> result;

  for (const auto& descriptor: wavecar.descriptors) {

    HorizontalGrid hGrid;

    for (const auto& kBand: descriptor.bands) {


    size_t count(0);
    const double actualNumberOfPlaneWaves = kBand.second.coefficients[0].size();

    const auto& K(kBand.first);
    std::vector<CellVector> gs(actualNumberOfPlaneWaves);

    const int numberOfPlaneWaves
      = 3 * std::ceil(std::pow(actualNumberOfPlaneWaves, 1.0/3));

    for (int z(0); z < 2 * numberOfPlaneWaves; z++) {
    for (int y(0); y < 2 * numberOfPlaneWaves; y++) {
    for (int x(0); x < 2 * numberOfPlaneWaves; x++) {

      const auto& cell(wavecar.header.reciprocal);
      const int G_i[]
        = { x > numberOfPlaneWaves ? x - 2 * numberOfPlaneWaves : x
          , y > numberOfPlaneWaves ? y - 2 * numberOfPlaneWaves : y
          , z > numberOfPlaneWaves ? z - 2 * numberOfPlaneWaves : z
          };

      double energy(0);
      CellVector g;
      for (size_t i(0); i < 3; i++) {
        double component
          = cell.basis[0][i] * ((double)G_i[0])
          + cell.basis[1][i] * ((double)G_i[1])
          + cell.basis[2][i] * ((double)G_i[2])
          ;
        component += K[i];

        g[i] = component;
        energy += component * component / hbarConst;
      }

      if (energy < wavecar.header.encut) {
        count++;
        gs[count] = g;
      }

    } // z
    } // y
    } // x

    if (count != actualNumberOfPlaneWaves)
      throw "Count and actualNumberOfPlaneWaves are different";

    hGrid.push_back({K, gs});

  } // kBand

    result.push_back(hGrid);

  } // descriptor

  return result;

}

Mathematical functions

Products

CellVector crossProduct(const CellVector &a, const CellVector &b) {
  return
    { a[1] * b[2] - a[2] * b[1]
    , a[2] * b[0] - a[0] * b[2]
    , a[0] * b[1] - a[1] * b[0]
    };
}

double dotProduct(const CellVector &a, const CellVector &b) {
  return std::inner_product(a.begin(), a.end(), b.begin(), 0.0);
}

Cell volume

We can use the products to calculate the cell volume given by a basis

double cellVolume(const Cell &c) {
  return
    dotProduct( c.basis[0]
              , crossProduct( c.basis[1]
                            , c.basis[2]
                            )
              );
}

Reciprocal cell

Here we calculate the reciprocal cell of a given cell

Cell reciprocalCell(const Cell &c) {
  Cell r;
  for (size_t i=0; i<3; i++) {
    auto itB(r.basis[i].begin());
    r.basis[i] = crossProduct( c.basis[(i+1) % 3]
                             , c.basis[(i+2) % 3]);
    std::transform( itB, itB + 3, itB
                  , [&c](double i){ return i*2*M_PI/c.volume; });
  }
  r.volume = cellVolume(r);
  return r;
}

Putting all together

Therefore this simple header-only library looks like this

#ifndef _WAVECAR_HPP_DEFINED
#define _WAVECAR_HPP_DEFINED

<<wavecar.hpp-header>>

<<wavecar.hpp-types>>

<<wavecar.hpp-mathfunctions>>

<<wavecar.hpp-parsing>>
<<wavecar.hpp-writing>>
<<wavecar.hpp-grid>>

#endif

Tests

The script `wavecar-show`

#include <Wavecar.hpp>

int main (int argc, char **argv) {

  std::cout << ">>> Parsing WAVECAR" << std::endl;
  auto wavecar(readWavecar("WAVECAR"));
  auto& header(wavecar.header);

  std::cout << "recordLength: " << header.recordLength << "\n"
            << "nSpin: " << header.nSpin << "\n"
            << "version: " << header.version << "\n"
            << "nKpoints: " << header.nKpoints << "\n"
            << "nBands: " << header.nBands << "\n"
            << "encut: " << header.encut << "\n"
            << "eFermi: " << header.eFermi << "\n"
            << "volume: " << header.real.volume << "\n"
            << "\n";

  std::cout << ">>> Creating grids" << std::endl;
  auto grids(mkGrid(wavecar));
  std::cout << grids.size() << " grids created" << std::endl;

  std::cout << "Lattice vectors: \n";
  for (const auto &b: header.real.basis)
    printf("  %f %f %f\n", b[0], b[1], b[2]);

  std::cout << "Reciprocal vectors: \n";
  for (const auto &b: header.reciprocal.basis)
    printf("  %f %f %f\n", b[0], b[1], b[2]);

  auto wavecar2(std::ofstream("WAVECAR-2", std::ios::binary));
  std::cout << "Writing WAVECAR-2" << std::endl;
  writeToWavecar(wavecar2, wavecar);

}

Bibliography

[LiteratePrograKnuth1984] Knuth, Literate Programming, The Computer Journal, 27, 97-111 (1984). link. doi. ↩

#+begin: papis-bibtex-refs :tangle /home/gallo/software/wavecar.hpp/README.bib

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Table of Contents

Wavecar.hpp

Introduction

Header

Main types

`WAVECAR` parsing

Understanding the code

Wave descriptor

Header

The whole `WAVECAR`

`WAVECAR` writing

`CellVector`

`Cell`

`WavecarHeader`

`WaveDescriptor`

`Wavecar`

G grid

Types

Creating a grid from a wavecar

Mathematical functions

Products

Cell volume

Reciprocal cell

Putting all together

Tests

The script `wavecar-show`

Bibliography

About

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alejandrogallo/wavecar.hpp

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Table of Contents

Wavecar.hpp

Introduction

Header

Main types

WAVECAR parsing

Understanding the code

Wave descriptor

Header

The whole WAVECAR

WAVECAR writing

CellVector

Cell

WavecarHeader

WaveDescriptor

Wavecar

G grid

Types

Creating a grid from a wavecar

Mathematical functions

Products

Cell volume

Reciprocal cell

Putting all together

Tests

The script wavecar-show

Bibliography

About

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`WAVECAR` parsing

The whole `WAVECAR`

`WAVECAR` writing

`CellVector`

`Cell`

`WavecarHeader`

`WaveDescriptor`

`Wavecar`

The script `wavecar-show`

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