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ABACUS-ORBGEN: v3.0 (alpha)

Welcome to the new version of ABACUS Numerical Atomic Orbital Generation code development repository. We are still working on optimizing the quality of orbital by trying new formulation, new optimization algorithm and strategy. Our goal is to publish orbitals that can be used for not only ground-state involved cases but also for some excitation calculation. Once meet problem, bug in orbital generation, we suggest submit issue on ABACUS Github repository: https://github.com/deepmodeling/abacus-develop.

Configuration

Shortcut: for Bohrium(R) users

We have published a configured Bohrium images for users want to save their time as much as possible. You can register in Bohrium Platform, set-up one new container and use Bohrium image registry.dp.tech/dptech/prod-16047/abacus-orbgen-workshop:20240814. Then conda activate orbgen.

General: Virtual environment

WE STRONGLY RECOMMEND TO SET UP A NEW CONDA ENVIRONMENT/VIRTUAL ENVIRONMENT FOR ABACUS-ORBITALS BECAUSE IT CAN AUTOMATICALLY LINK YOUR Pytorch to MKL. OTHERWISE, YOU SHOULD ALWAYS ENSURE THE LINKAGE TO GET THE BEST PERFORMANCE.

git clone git clone https://github.com/kirk0830/ABACUS-ORBGEN.git
cd ABACUS-ORBGEN

Option1 (the most recommended): If you prefer to use conda, then run the following commands to create a new conda environment and activate it.

conda create -n orbgen python=3.10
conda activate orbgen

Option2: If you prefer to use virtual environment, then run the following commands to create a new virtual environment and activate it.

python3 -m venv orbgen
source orbgen/bin/activate

Installations

PERFORMANCE NOTE: WE RECOMMEND USE CONDA TO INSTALL pytorch PACKAGE BY conda install pytorch FIRST AND INSTALL ALL OTHERS BY FOLLOWING INSTRUCTION BELOW BE AWARE IF Intel-mkl IS SUCCESSFULLY LINKED TO pytorch
Once the virtual environment is activated (and mkl is ready), run the following commands to install ABACUS-orbitals.

pip install .

Keywords

Since ABACUS-ORBGEN v3.0, the plaintext input format has been deprecated thoroughly. Up to now, please use JSON format input file. An example of JSON format input file is shown below.

Note: the following document cannot be directly use after copy&paste, because the comments in JSON file is not supported.

{
    // PROGRAM CONFIGURATION
    // *********************
    "environment": "", // you can add `module load *` commands here
    "mpi_command": "mpirun -np 8", // the number of processors used in the calculation
    "abacus_command": "abacus", // path to your ABACUS executable

    // GENERAL
    // *******
    "pseudo_dir": "/path/to/your/pp", // path to your pseudopotential file
    "element": "Si", // the element symbol
    "bessel_nao_rcut": [10],

    // ELECTRONIC STRUCTURE CALCULATION
    // ********************************
    // besides the ecutwfc, all keywords supported by ABACUS can be
    // defined here. For example, smearing_sigma will help for hard
    // -converging systems.
    "ecutwfc": 60,

    // REFERENCE GEOMETRIES
    // ********************
    // orbitals are generated based on wavefunction of specific geometry
    // calculated. One specific geometry is defined via a structral proto 
    // plus a perturbation, specified by its kind and magnitude.
    // NOTE1:
    // the number of bands (nbands), spin channels (nspin) and 
    // lmaxmax (maximal angular momentum of wavefunction) MUST be defined.
    // NOTE2:
    // ABACUS parameters can also be defined here, will overwrite those
    // defined in the general section.
    "geoms": [
        {
            "proto": "dimer",
            "pertkind": "stretch",
            "pertmags": [1.62, 1.82, 2.22, 2.72, 3.22], // unit: Angstrom
            "nbands": 20,
            "nspin": 1,
            "lmaxmax": 2
        }
    ],

    // ORBITAL DEFINITION
    // ******************
    // define the orbital by its number of zeta functions for each angular 
    // momentum.
    "orbitals": [
        {
            "nzeta": [1, 1, 0],
            "geoms": [0],
            "nbands": ["occ", "occ", "occ", "occ", "occ"],
            "checkpoint": null // this is the first orbital to generate
        },
        {
            "nzeta": [1, 1, 1],
            "geoms": [0],
            "nbands": [4, 4, 4, 4, 4],
            "checkpoint": 0 // restart from the first orbital generated
        }
    ],

    // SPILLAGE DEFINITION AND OPTIMIZATION
    // ************************************
    "fit_basis": "jy",
    "primitive_type": "reduced",
    "optimizer": "torch.swats",
    "torch.lr": 0.001,
    "max_steps": 3000,
    "spill_guess": "atomic" // always use `atomic`
}

PROGRAM CONFIGURATION

In this section, user should define the executable files and the number of processors used in the calculation. The executable file of ABACUS is abacus. The executable file of MPI is mpirun. The number of processors used in the calculation is defined by mpi_command. For example, if the number of processors is 4, then mpi_command should be mpirun -np 4.

  • environment: the environment configuration load commands, should be organized in one line. Conventional example is like module load intel/2019.5.281 openmpi/3.1.4 intel-mkl/2019.5.281 intel-mpi/2019.5.281. If the environment configuration load commands are not needed, then environment should be #environment.
  • mpi_command: the executable file of MPI. If the executable file of MPI is in the PATH, then mpi_command should be mpirun. If the executable file of MPI is not in the PATH, then mpi_command should be the absolute path of the executable file of MPI. User may also need to specify the number of processors used in the calculation. For example, if the number of processors is 4, then mpi_command should be mpirun -np 4. Presently ABACUS does not support other parallelization modes.
  • abacus_command: the executable file of ABACUS. If the executable file of ABACUS is in the PATH, then abacus_command should be abacus. If the executable file of ABACUS is not in the PATH, then abacus_command should be the absolute path of the executable file of ABACUS.

GENERAL

  • pseudo_dir: the directory of the pseudopotential file. If the pseudopotential file is in the current directory, then pseudo_dir should be ./. THIS PARAMETER IS REQUIRED.
  • bessel_nao_rcut: the realspace cutoff of numerical atomic orbitals to generate, any number of cutoffs can be defined. The unit is Bohr, e.g. 6, 6 7 8 9 10. THIS PARAMETER IS REQUIRED.
  • element: the element symbol. THIS PARAMETER IS REQUIRED.

ELECTRONIC STRUCTURE CALCULATION

In this section, user should define the parameters used in the electronic structure calculation. As long as the parameters are available in ABACUS, they can be defined in this section. Some necessary and useful parameters are listed below:

  • ecutwfc: the energy cutoff of the plane wave basis set in Ry, e.g. 100 Ry. To get a good description of the system, the energy cutoff should be large enough. THIS PARAMETER IS REQUIRED.

For more available keywords, please refer to ABACUS online manual: Full List of INPUT Keywords

REFERENCE GEOMETRIES

In this section, user should define the reference gemometries. Reference geometries' wavefunctions are training set of numerical atomic orbitals, therefore the quailities of numerical atomic orbitals are determined by the specifications of reference systems and learning configurations. The parameters are listed below:

  • proto: the prototype of the reference system. The shape should be dimer, trimer, tetramer, but usually singly a dimer is enough, trimer is less necessary, and tetramer seems always not necessary. THIS PARAMETER IS REQUIRED.
  • pertkind: the kind of perturbation. Presently only stretch is supported. THIS PARAMETER IS REQUIRED.
  • pertmags: magnitude of perturbation, always should be specified as a list: [1.62, 1.82, 2.22, 2.72, 3.22]. For stretch pertkind, it is the interatomic distance in unit Angstrom. If specified as auto, will use default value built-in ABACUS-ORBGEN code. THIS PARAMETER IS REQUIRED.
  • nbands: the number of bands to calculate for the reference system. THIS PARAMETER IS REQUIRED.
  • nspin: the number of spin channels of the reference system. The number of spin channels should be the same as the number of spin channels of the system to calculate. It is always to be 1 but sometimes 2. THIS PARAMETER IS REQUIRED.
  • lmaxmax: the maximal angular momentum over all atomtypes in present set of geometries. THIS PARAMETER IS REQUIRED.

NOTE: user can define any number of sets of geometries.

ORBITAL DEFINITION

  • nzeta: number of zeta functions for each angular momentum, should be provided in a list like [1, 1, 0], which means 1s1p. WARNING: the length of list should not be larger than the lmaxmax THIS PARAMETER IS REQUIRED.
  • geoms: the indexes of sets of geometries whose wavefunctions will be used to calculate spillage function. Should specify as a list of int. THIS PARAMETER IS REQUIRED.
  • nbands: the number of bands to refer for geometry. Always it is specifed as a list of int, but can also be list of str, in which the str can be occ, occ+N, all, all-N, etc., are "all occupied bands", "occupied bands plus N virtual bands", "all bands calculated in dft procedure", "all bands except N highest bands", respectively. THIS PARAMETER IS REQUIRED.
  • checkpoint: for hierarchically generating orbitals. Each orbital is generated based on the previous orbital. If null is defined, all contraction coefficients will be optimized. If specified as an integer index, will restart orbital generation (spillage optimization) based on checkpoint results. THIS PARAMETER IS REQUIRED.

SPILLAGE DEFINITION AND OPTIMIZATION

In this section, user should define the spillage function and its optimization. The parameters are listed below:

  • fit_basis: the reference basis set, can be pw or jy. THIS PARAMETER IS REQUIRED.
  • primitive_type: the type of primitive jy basis used to contract to numerical atomic orbitals. Options are reduced and normalized. If there is no special reason, reduced is the only one recommended. THIS PARAMETER IS REQUIRED.
  • optimizer: the optimizer to use, can be scipy.bfgs, torch.swats, torch.yogi, torch.adamw, ..., etc.
  • spill_guess: the initial guess of Spillage, can be random or atomic. For atomic, an additional ABACUS calculation will run to calculate reference wavefunction of isolated atom. THIS PARAMETER IS OPTIONAL.
  • max_steps: the maximum optimization on Spillage function to perform. For optimizer as torch.*, a large number is always suggested, for bfgs, optimization will stop if convergence or max_steps is reached. THIS PARAMETER IS REQUIRED.

There are other optimizer-specific parameters, such as learning rate of torch optimizer, ..., can be set manually by keywords in the following:

  • torch.lr: learning rate of torch optimizer. It can be understood as the stepsize. If too large value is specified, the optimization may oscilate or fail. The default value is 1e-3.
  • torch.eps: a small parameter that add to dominator to avoid numerical instability, always being kept as default value.

Run

Common use

orbgen -i jy-v3.0.json

But we do not restrict user to name the input script as jy-v3.0.json. Once the job is done, you will get orbitals (*.orb) files that can be directly used in ABACUS. PNG-format orbital plots are also generated for quick check on orbital quality.