libmwfn 0.0.3

A flexible .mwfn format handler

libmwfn

A flexible .mwfn format handler

Overview

mwfn is a text file format for gaussian-based wavefunctions of molecules and solids (described here). This library, libmwfn, is a flexible handler of the mwfn format. With libmwfn, the users are able to manipulate gaussian-based wavefunctions on their demand. libmwfn is written in C++ and provides Python interface by pybind11.

The motive of this library is my need for a tool to deal with wavefunction files in my other two projects, Chinium and Orbaplaw, written in C++ and Python, respectively.

Installation

Prerequisites

• A C++ compiler that supports C++20 standard
• GNU make and Eigen3 for C++
• setuptools and pybind11 for Python

C++

• Obtain the source code via git cloneing the repository or wgeting the latest release.
• Specify the C++ compiler and the Eigen3 directory in makefile.
• Build the library with make -j[N] and you will find the newly created directories include/ and lib/.
• Tryout. (Reading in an existent file test.mwfn and exporting its information to another test_new.mwfn)

// test.cpp
#include <libmwfn.h>
int main(){
	Mwfn mwfn("test.mwfn");
	mwfn.Export("test_new.mwfn");
	return 0;
}
// end of test.cpp
$ gcc test.cpp -I$(LIBMWFN)/include/ -L$(LIBMWFN)/lib/ -lmwfn # or -l:libmwfn.a

Python

• Install via pip.

$ pip install libmwfn

• Tryout. (Reading in an existent file test.mwfn and exporting its information to another test_new.mwfn)

$ python
>>> import libmwfn as lm
>>> mwfn = lm.Mwfn("test.mwfn")
>>> mwfn.Export("test_new.mwfn")

Usage

Here is a typical procedure to deal with wavefunctions in libmwfn.

Ab initio quantum chemistry computation

A wavefunction file given by an ab initio calculation is needed. This can be done by a variety of computational chemistry packages. Here we use Gaussian 16 as an example.

! Gaussian input file
%nprocshared=40
%mem=60GB
%chk=job.chk
# b3lyp 6-31g(d) 5d 7f

Title Card Required

0 1
[Geometry]

Converting wavefunction file

The resultant wavefunction is stored in job.chk, an chk format file which is not supported by libmwfn. We need to transform job.chk to fchk with formchk and then to mwfn format with Multiwfn.

$ # Shell
$ formchk job.chk # Now we have job.fchk
$ Multiwfn job.fchk
100 # Other functions (Part 1)
2 # Export various files (mwfn/pdb/xyz/wfn/wfx/molden/fch/47/mkl...) or generate input file of quantum chemistry programs
32 # Output current wavefunction as .mwfn file
# Default name: job.mwfn
2 # Export wavefunction, density matrix and overlap matrix
0 # Return
q # Exit Multiwfn.

Now we have job.mwfn.

Wavefunction processing

• Loading the libmwfn module.

// C++
#include <libmwfn.h>

# Python
import libmwfn as lm

• Reading and exporting wavefunction information from job.mwfn to job_new.mwfn.

// C++
Mwfn job_mwfn("job.mwfn");
job_mwfn.Export("job_new.mwfn");

# Python
job_mwfn = lm.Mwfn("job.mwfn")
job_mwfn.Export("job_new.mwfn")

• Getting the numbers of electrons.

// C++
int spin = 0; // 0 - default spin (depending on wavefunction types and functions); 1 - alpha; 2 - beta.
double n = job_mwfn.getNumElec(spin); // spin is optional. Default is 0, the total number of electrons of two spin types.
double n_alpha = job_mwfn.getNumElec(1); // The number of alpha electrons.
double n_beta = job_mwfn.getNumElec(2); // The number of beta electrons.
double charge = job_mwfn.getCharge(); // Total nuclear charges minus the number of electrons.

# Python
n = job_mwfn.getNumElec() # or job_mwfn.getNumElec(0)
n_alpha = job_mwfn.getNumElec(1)
n_beta = job_mwfn.getNumElec(2)
charge = job_mwfn.getCharge()

Note that the returned values are all floating-point numbers for the general case of fractional occupation.

• Getting and setting the occupation numbers.

// C++
int homo = std::round(job_mwfn.getNumElec(0) / 2) - 1; // The indices of the HOMO and LUMO.
int lumo = std::round(job_mwfn.getNumElec(0) / 2);
Eigen::VectorXd N = job_mwfn.getOccupation(0); // 0 for spin-restricted, 1 and 2 for alpha and beta in spin-unrestricted.
N(homo) = 0;
N(lumo) = 2; // Swapping the occupation numbers of the HOMO and LUMO.
job_mwfn.setOccupation(N, 0);

• Getting and setting the orbital energies.

// C++
Eigen::VectorXd E = job_mwfn.getEnergy(0);
E.setZero();
job_mwfn.setEnergy(E, 0); // Setting the orbital energies to zeros.

• Getting and setting the coefficient matrix.

// C++
Eigen::MatrixXd C = job_mwfn.getCoefficientMatrix(0);
Eigen::VectorXd C_0 = C.col(0); // The coefficient vector of the first orbital.
Eigen::VectorXd C_1 = C.col(1); // The coefficient vector of the second orbital.
C.col(0) = (C_0 + C_1) / 1.414213562; // Mixing the first two orbitals.
C.col(1) = (C_0 - C_1) / 1.414213562;
job_mwfn.setCoefficientMatrix(C, 0);

• Make a (deep) copy of a Mwfn instance.

// C++
std::unique_ptr<Mwfn> another_mwfn = job_mwfn.Clone();
std::cout << another_mwfn->getNumElec() << std::endl; // The copy is a pointer.

# Python
another_mwfn = job_mwfn.Clone()
print(another_mwfn.getNumElec()) # No need to worry about the pointer thing.

• Check the header libmwfn.h for more functions.

Caution

• Ordering of basis functions. The ordering of basis functions of $l \ge 2$ in libmwfn is [d-2, d-1, d0, d+1, d+2] and [f-3, f-2, f-1, f0, f+1, f+2, f+3], etc., different from [d0, d+1, d-1, d+2, d-2] and [f0, f+1, f-1, f+2, f-2, f+3, f-3, f+4, f-4], etc., in the mwfn file format. Upon I/O of mwfn file, a matrix transformation is applied to accommodate this difference.