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THE PROJECT STARTS FROM https://github.com/abacusmodeling/abacus-develop,
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WHERE MORE INFORMATION CAN BE FOUND.
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ABACUS is an electronic structure package based on density functional theory(DFT), adopting either plane wave basis or numerical atomic orbitals.
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Please refer to our [GitHub repository](https://github.com/deepmodeling/abacus-develop) for more information and support.
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# Table of contents
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-[About ABACUS](#about-abacus)
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-[Features](#features)
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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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-[Examples](#examples)
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-[For developers](#for-developers)
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# About ABACUS
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ABACUS IS AN ELECTRONIC STRUCTURE PACKAGE BASED ON DENSITY FUNCTIONAL THEORY.
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ABACUS ADOPTS EITHER PLANE WAVE BASIS OR NUMERICAL ATOMIC ORBITALS.
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---
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# Features
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ABACUS provides the following features and functionalities:
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[back to top](#readme-top)
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# Download and install
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ABACUS can be downloaded from its [official website](http://abacus.ustc.edu.cn/) or our [github website](https://github.com/deepmodeling/abacus-develop.git).
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Please refer to the [installation guide](doc/install.md) for instruction on the structure of the package and how to install ABACUS.
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ABACUS can be downloaded from our [official website](http://abacus.ustc.edu.cn/) or [GitHub release page](https://github.com/deepmodeling/abacus-develop/releases) for stable versions. You can also get the developing version from our [GitHub repository](https://github.com/deepmodeling/abacus-develop).
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Please refer to the [installation guide](docs/install.md) for instruction on the structure of the package and how to install ABACUS.
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[back to top](#readme-top)
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# Quickstart guide
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## Input files
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The following files are the central input files for ABACUS. Before executing the program, please
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make sure these files are prepared and stored in the working directory.
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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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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](doc/input-main.md).
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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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*Attention: Users cannot change the filename “INPUT” to other names.*
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- The structure file
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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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Specifications of the STRU file can be found in this [short instruction](doc/input-stru.md).
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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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Specification of the k-point file can be found in this [short instruction](doc/input-kpt.md).
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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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More information on pseudopotentials is given [here](doc/features.md#pseudopotentials).
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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](doc/generate-basis.md).
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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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[back to top](#readme-top)
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## Output files
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When the calculation finishes, the program will create an output directory (default: OUT.ABACUS/),
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into which the following output files will be generated:
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1.`INPUT`: contains all input parameters, user’s input and default.
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2.`istate.info`: information of energy eigenvalues.
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3.`running_${calculation}.log`: contains the running details. Information on the variable calculation is found in the [list of keywords](doc/input-main.md#calculation). For example, if we are doing a SCF calculation, the log files will be named running_scf.log.
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3.`running_${calculation}.log`: contains the running details. Information on the variable calculation is found in the [list of keywords](docs/input-main.md#calculation). For example, if we are doing a SCF calculation, the log files will be named running_scf.log.
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4.`STRU_READIN_ADJUST.cif`: structure file in the cif formatter.
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5.`warning.log`: errors and warning messages.
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6. directories containing element information. For example, Si/:
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# Features
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Users can refer to this [page](doc/features.md) for several features of the ABACUS code:
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Users can refer to this [page](docs/features.md) for several features of the ABACUS code:
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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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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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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[back to top](#readme-top)
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# For developers
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We also provide some [information](doc/developers.md) for developers.
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-[Raising issues on GitHub](doc/developers.md#raising-issues-on-github)
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-[Modularization and module tests](doc/developers.md#modularization-and-module-tests)
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-[Contributing to ABACUS](doc/developers.md#contributing-to-abacus)
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For the input k-point (KPT) file, the file should either contain the k-point coordinates and weights or the mesh size for creating the k-point gird. Both options are allowed in ABACUS.
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More information on k-points is provided in this [instruction](#doc/input-kpt.md)
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More information on k-points is provided in this [instruction](#docs/input-kpt.md)
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#### dft_functional
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-**Type**: String
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-**Description**: In our package, the XC functional can either be set explicitly using the dft_functional keyword as explained below, or set implicitly according to the XC functional information read from pseudopotential file. The user should ensure that the XC functional set in the INPUT file and the pseudopotential file are consistent. If more than one element is present in the system, make sure all of pseudopotentials have the same XC functional. **Currently only LDA and GGA are supported.**
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To be specific, we briefly explain the format of the pseudopotential file and the key information it contains. There are a few lines in Si`s GGA pseudopotential file Si_ONCV_PBE-1.0.upf:
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```
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...
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<PP_HEADER
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generated="Generated using ONCVPSP code by D. R. Hamann"
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author="Martin Schlipf and Francois Gygi"
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date="150105"
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comment=""
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element="Si"
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pseudo_type="NC"
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relativistic="scalar"
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is_ultrasoft="F"
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is_paw="F"
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is_coulomb="F"
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has_so="F"
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has_wfc="F"
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has_gipaw="F"
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core_correction="F"
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functional="PBE"
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z_valence=" 4.00"
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total_psenergy=" -3.74274958433E+00"
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rho_cutoff=" 6.01000000000E+00"
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```
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Possible values of this variable are:
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- none: the functional is specified implicity by the input pseudopotential file
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- lda: Perdew-Zunger local density approximation
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- pbe: Perdew-Burke-Ernzerhof general gradient approximation
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If the functional specified by the user is not consistent with the pseudopotential file, the program will stop with an error message.
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- **Default**: none
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-**Description**: type of exchange-correlation functional used in calculation. If dft_functional is not set, the program will adopt the functional used to generate pseudopotential files, provided all of them are generated using the same functional. For example, we present a few lines in Si’s GGA pseudopotential file Si_ONCV_PBE-1.0.upf:
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```
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...
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<PP_HEADER
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generated="Generated using ONCVPSP code by D. R. Hamann"
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author="Martin Schlipf and Francois Gygi"
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date="150105"
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comment=""
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element="Si"
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pseudo_type="NC"
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relativistic="scalar"
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is_ultrasoft="F"
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is_paw="F"
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is_coulomb="F"
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has_so="F"
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has_wfc="F"
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has_gipaw="F"
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core_correction="F"
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functional="PBE"
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z_valence=" 4.00"
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total_psenergy=" -3.74274958433E+00"
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rho_cutoff=" 6.01000000000E+00"
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```
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According to the information above, this pseudopotential is generated using PBE functional.
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On the other hand, if dft_functional is specified, it will overwrite the functional from pseudopotentials and performs calculation with whichever functional the user prefers. We further offer two ways of supplying exchange-correlation functional. The first is using 'short-hand' names such as 'LDA', 'PBE', 'SCAN'. A complete list of 'short-hand' expressions can be found in [source code](../source/module_xc/xc_functional.cpp). The other way is only available when ***compiling with LIBXC***, and it allows for supplying exchange-correlation functionals as combinations of LIBXC keywords for functional components, joined by plus sign, for example, 'dft_functional='LDA_X_1D_EXPONENTIAL+LDA_C_1D_CSC'. The list of LIBXC keywords can be found on its [website](https://www.tddft.org/programs/libxc/functionals/). In this way, **we support all the LDA,GGA and mGGA functionals provided by LIBXC**.
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We also provides (under test) two hybrid functionals: PBE0 and HSE. For more information about hybrid functionals, refer to the [section](#exact-exchange) on its input variables.
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-**Default**: same as UPF file.
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#### pseudo_type
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- 2: NVT ensemble with Langevin method;
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- 3: NVT ensemble with Anderson thermostat;
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- 4: MSST method;
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***Note: when md_type is set to 1, md_tfreq is required to stablize temperature. It is an empirical parameter whose value is system-dependent, ranging from 1/(40\*md_dt) to 1/(100\*md_dt). An improper choice of its value might lead to failure of job.***
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- **Default**: 1
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#### md_nstep
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- **Type**: Real
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- **Description**:
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- Oscillation frequency, used to determine Qmass of NHC;
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- 1/(md_tfreq*md_dt) is collision probability in Anderson method.
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- **Default**: 1.0
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- When md_type = 1, md_tfreq controls the frequency of the temperature oscillations during the simulation. If it is too large, the
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temperature will fluctuate violently; if it is too small, the temperature will take a very long time to equilibrate with the atomic system.
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- When md_type = 3, md_tfreq*md_dt is the collision probability in Anderson method.
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- If md_tfreq is not set in INPUT, md_tfreq will be autoset to be 1/40/md_dt.
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