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@@ -21,30 +21,37 @@ Please refer to our [GitHub repository](https://github.com/deepmodeling/abacus-d
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-[Download and install](#download-and-install)
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-[Quickstart guide](#quickstart-guide)
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-[Input files](#input-files)
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-[Run ABACUS](#run-abacus)
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-[Output files](#output-files)
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-[Features](#features)
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-[Functionalities](#functionalities)
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-[Examples](#examples)
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-[For developers](#for-developers)
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-[Hands-on examples](#hands-on-examples)
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-[Citations](#citations)
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-[Development team](#development-team)
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-[Communicating and making contributions](#communicating-and-making-contributions)
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# Features
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ABACUS provides the following features and functionalities:
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1. Ground-state total energy calculations using Kohn-Sham (KS) density functional theory
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(DFT) with local-density, generalized gradient approximations (LDA/GGAs), and hybrid functionals
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(PBE0 and HSE06, only for LCAO).
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2. Brillouin zone sampling using the Monkhorst-Pack special k-points.
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3. Geometry relaxations with Conjugated Gradient (CG) and BFGS methods.
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1. Three types of supported basis sets: pw, LCAO, and LCAO-in-pw.
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2. Ground-state total energy calculations using Kohn-Sham (KS) density functional theory (DFT) with local-density, generalized gradient approximations (LDA/GGAs), Meta-GGA(requires LIBXC, only for PW), and hybrid functionals (PBE0 and HSE06, only for LCAO and currently under test).
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3. Geometry relaxations with Conjugated Gradient (CG), BFGS, and FIRE methods.
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4. Semi-empirical van der Waals energy correction using the Grimme DFT-D2/D3 scheme.
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5. NVT molecular dynamics simulation.
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5. NVT and NVE molecular dynamics simulation. AIMD, DP potential, LJ potential are supported.
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6. Stress calculations and cell relaxations.
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7. Electric polarization calculation using Berry Phase theory.
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8. Interface to the Wannier90 package.
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9. Real-time time dependent density functional theory (TDDFT).
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10. Electrostatic potential.
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11. Mulliken charge analysis.
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12. Projected density of states (PDOS).
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10. Print-out of the electrostatic potential.
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11. Mulliken charge analysis (only for LCAO).
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12. Projected density of states (PDOS) (only for LCAO).
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13. DFT+U calculation (only for LCAO).
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14. Solvation model method for solvation energy.
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15. Stochastic DFT (only for PW).
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16. DeePKS method (under development, only for LCAO).
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17. Electric field and dipole correction.
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18. Orbital-free DFT.
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19. (subsidiary tool)Plot_tools for plot PDOS and PBANDS.
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20. (subsidiary tool)Generator for second generation numerical orbital basis.
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[back to top](#readme-top)
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@@ -62,33 +69,47 @@ Please refer to the [installation guide](docs/install.md) for instruction on the
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The following files are the central input files for ABACUS. Before executing the program, please make sure these files are prepared and stored in the working directory.
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-The INPUT file
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-`INPUT`
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The file named INPUT contains the setting parameters used in the calculation, which informs the program “what to do and how to do it”. Most parameters are supplied with default values, but some important parameters must be explicitly set by the user. For a complete list of the input parameters, please consult this [instruction](docs/input-main.md).
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This is the main input file that contains the setting parameters used in the calculation. For a complete list of the input parameters, please consult this [instruction](docs/input-main.md).
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*Attention: Users cannot change the filename “INPUT” to other names.*
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- The structure file
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The default name for structure file is STRU.The name can however be changed to a different name by explicitly specifying the name in the INPUT file.
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-`STRU`
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The STRU file contains the structural information about the system, e.g., lattice constant, lattice vectors, and positions of the atoms within a unit cell. The positions can be given either in direct or Cartesian coordinates. Moreover, the name (and location of the pseudopotential and numerical orbital files, see below) need to be specified in the STRU file.
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This is the structure file that contains the structural information about the system, e.g., lattice constant, lattice vectors, and positions of the atoms within a unit cell. The positions can be given either in direct or Cartesian coordinates. Moreover, the name of the atom (and location of the pseudopotential and numerical orbital files, see below) needs to be specified in the STRU file. The name of the structure file can be changed to a different name by explicitly specifying the name in the INPUT file.
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Specifications of the STRU file can be found in this [short instruction](docs/input-stru.md).
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- The k-point file
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The default name is KPT. It contains the information of the k-grid setting for the Brillouin zone sampling.
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-`KPT`
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This is the k-point file that contains the information of the k-grid setting for the Brillouin zone sampling.
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Specification of the k-point file can be found in this [short instruction](docs/input-kpt.md).
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- The pseudopotential files
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Norm-conserving pseudopotentials are used in ABACUS, in the UPF file format.The filename of each element’s pseudopotential needs to be specified in the `STRU` file, if the the pseudopotential files are already present in the working directory. However, in case that the pseudopotential files are stored in some other directories, then a full path to access the pseudopotential files have to be specified in the `STRU` file.
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Norm-conserving pseudopotentials are used in ABACUS, in the UPF file format.The filename of each element’s pseudopotential needs to be specified in the STRU file, together with the directory of the pseudopotential files unless they are already present in the working directory.
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More information on pseudopotentials is given [here](docs/features.md#pseudopotentials).
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- The numerical orbital files
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When performing calculations with numerical atomic orbital basis, it is necessary to prepare a numerical orbital file for each element in the system. Generally, the numerical orbital file should be prepared by the user, which will be described later. The filename for each element’s numerical orbital basis needs to be specified in the `STRU` file. However, in case that the numerical orbital files are stored in a location different from the working directory, then a full path to access the orbital files have to be specified in the `STRU` file.
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ABACUS provides numerical atomic basis sets of different accuracy levels for most elements commonly used. Users can download these basis sets from the [website](http://abacus.ustc.edu.cn/pseudo.html). Moreover, users can generate numerical atomic orbitals by themselves, and the procedure is provided in this [short introduction](docs/generate-basis.md).
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This part is only required in LCAO calculations.
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The filename for each element’s numerical orbital basis needs to be specified in the STRU file, together with the directory of the orbital files unless they are already present in the working directory.
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ABACUS provides numerical atomic basis sets of different accuracy levels for most elements commonly used. Users can download these basis sets from the [website](http://abacus.ustc.edu.cn/pseudo/list.htm). Moreover, users can generate numerical atomic orbitals by themselves, and the procedure is provided in this [short introduction](docs/generate-basis.md).
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## Run ABACUS
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After putting all required input files under one folder, enter this folder.
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```bash
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cd input_folder
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```
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Perform calculation by:
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```bash
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mpirun -np 4 abacus
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```
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You can replace `4` with your desired number of process, typically the result of the command `nproc`.
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@@ -110,21 +131,10 @@ into which the following output files will be generated:
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[back to top](#readme-top)
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# Features
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Users can refer to this [page](docs/features.md) for several features of the ABACUS code:
The following provides basic sample jobs in ABACUS. More can be found in the directories `examples/` and `tests/`, with an introduction [here](tests/README.md), and the corresponding reference outputs can be found in the file `result.ref` under each subdirectory.
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ABACUS provides a wide variety of functionalities, with explanation and examples:
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*Note that the examples there are intended as quick hands-on jobs, and the results are NOT converged with regard to basis set or k point sampling.*
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-[Basic electronic structure calculation with PW basis set](docs/examples/basic-pw.md)
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-[Basic electronic structure calculation with LCAO basis set](docs/examples/basic-lcao.md)
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-[Electric field and dipole correction](docs/examples/electric_dipole.md)
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-[Stochastic DFT and mix stochastic-deterministic DFT](docs/examples/stochastic.md)
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# Examples
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We also provide many examples in the directories examples/ and tests/.
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Note that the examples there are intended as references, and the results are not converged with regard to basis set or k point sampling.
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# Citations
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The following references are required to be cited when using ABACUS. Specifically:
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-**For general purpose:**
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In the directory tests/, each sub-directory contains a separate test example. An introduction of the examples in tests/ directory can be found [here](tests/README.md). In each subdirectory, you may also find a file named jd which contains a short job description, and for some cases you may also find a README file containing more details about the run. Also, reference output is provided in the file `result.ref`.
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[1]. Mohan Chen, G. C. Guo, and Lixin He. "Systematically improvable optimized atomic basis sets for ab initio calculations." Journal of Physics: Condensed Matter 22.44 (2010): 445501.
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[2]. Pengfei Li, et al. "Large-scale ab initio simulations based on systematically improvable atomic basis." Computational Materials Science 112 (2016): 503-517.
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-**If Stochastic DFT is used:**
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[1]. Qianrui Liu, and Mohan Chen. "Plane-Wave-Based Stochastic-Deterministic Density Functional Theory for Extended Systems." https://arxiv.org/abs/2204.05662.
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-**If DFT+U is used:**
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[1]. Xin Qu, et al. "DFT+ U within the framework of linear combination of numerical atomic orbitals." The Journal of Chemical Physics (2022).
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-**If second generation numerical orbital basis is used:**
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[1]. Peize Lin, Xinguo Ren, and Lixin He. "Strategy for constructing compact numerical atomic orbital basis sets by incorporating the gradients of reference wavefunctions." Physical Review B 103.23 (2021): 235131.
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-**If berry curvature calculation is used in LCAO base:**
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[1]. Gan Jin, Daye Zheng, and Lixin He. "Calculation of Berry curvature using non-orthogonal atomic orbitals." Journal of Physics: Condensed Matter 33.32 (2021): 325503.
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-**If DeePKS is used:**
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[1]. Wenfei Li, Qi Ou, et al. "DeePKS+ABACUS as a Bridge between Expensive Quantum Mechanical Models and Machine Learning Potentials." https://arxiv.org/abs/2206.10093.
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-**If hybrid functional is used:**
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[1]. Peize Lin, Xinguo Ren, and Lixin He. "Efficient Hybrid Density Functional Calculations for Large Periodic Systems Using Numerical Atomic Orbitals." Journal of Chemical Theory and Computation 2021, 17(1), 222–239.
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[2]. Peize Lin, Xinguo Ren, and Lixin He. "Accuracy of Localized Resolution of the Identity in Periodic Hybrid Functional Calculations with Numerical Atomic Orbitals." Journal of Physical Chemistry Letters 2020, 11, 3082-3088.
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# Development team
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The current development team consists the following research groups/affiliations:
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- University of Science and Technology of China (Dr. Lixin He)
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- Peking University (Dr. Mohan Chen)
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- Institute of Physics, Chinese Academy of Sciences (Dr. Xinguo Ren)
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- AI for Science Institute
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# For developers
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# Communicating and making contributions
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We also provide some [information](docs/CONTRIBUTING.md) on how to make contributions to ABACUS.
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If you find a bug or have some questions, please refer to our GitHub [issue tracker](https://github.com/deepmodeling/abacus-develop/issues), and our developers are willing to help. We also provide guidelines on how to make contributions to ABACUS.
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-[Structure of the package](docs/CONTRIBUTING.md#structure-of-the-package)
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-[Submitting an Issue](docs/CONTRIBUTING.md#submitting-an-issue)
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-[Submitting a Pull Request](docs/CONTRIBUTING.md#submitting-a-pull-request)
- efield_flag : If set to true, a saw-like potential simulating an electric field
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is added to the bare ionic potential.
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- dip_cor_flag : If `dip_cor_flag` == true and `efield_flag` == true, a dipole correction is also
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added to the bare ionic potential. If you want no electric field, `efield_amp` should be zero. Must be used ONLY in a slab geometry for surface calculations, with the discontinuity FALLING IN THE EMPTY SPACE.
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- efield_dir : The direction of the electric field or dipole correction is parallel to the reciprocal lattice vector, so the potential is constant in planes defined by FFT grid points, efield_dir = 0, 1 or 2. Used only if `efield_flag` == true.
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- efield_pos_max : Position of the maximum of the saw-like potential along crystal axis `efield_dir`, within the unit cell, 0 < `efield_pos_max` < 1. Used only if `efield_flag` == true.
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- efield_pos_dec : Zone in the unit cell where the saw-like potential decreases, 0 < `efield_pos_dec` < 1. Used only if `efield_flag` == true.
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- efield_amp : Amplitude of the electric field, in ***Hartree*** a.u.; 1 a.u. = 51.4220632*10^10 V/m. Used only if `efield_flag` == true. The saw-like potential increases with slope `efield_amp` in the region from (`efield_pos_max`+`efield_pos_dec`-1) to (`efield_pos_max`), then decreases until (`efield_pos_max`+`efield_pos_dec`), in units of the crystal vector `efield_dir`. Important: the change of slope of this potential must be located in the empty region, or else unphysical forces will result.
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## Dipole correction
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A dipole correction is added to the bare ionic potential.Must be used ONLY in a slab geometry, for surface calculations, with the discontinuity FALLING IN THE EMPTY SPACE.
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```
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INPUT_PARAMETERS
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efield_flag 1
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dip_cor_flag 1
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efield_dir 2
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efield_pos_max 0.5
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efield_pos_dec 0.1
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efield_amp 0
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```
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Note: *efield_amp must be zero so that there is no electric field.*
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## Electric field and Dipole correction
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Both external electric field and dipole correction are added to the bare ionic potential.
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```
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INPUT_PARAMETERS
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efield_flag 1
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dip_cor_flag 1
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efield_dir 2
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efield_pos_max 0.5
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efield_pos_dec 0.1
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efield_amp 0.001
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```
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