From 002bafb72104b751a58073e0ffd3474ac214c82b Mon Sep 17 00:00:00 2001 From: SY Wang Date: Sun, 13 Sep 2026 23:50:30 +0800 Subject: [PATCH] Docs: Fix Sphinx build warnings --- .readthedocs.yaml | 2 +- docs/CONTRIBUTING.md | 2 +- docs/Makefile | 2 +- docs/advanced/elec_properties/Mulliken.md | 2 +- docs/advanced/elec_properties/index.rst | 1 + docs/advanced/elec_properties/wfc.md | 2 +- docs/advanced/input_files/input-main.md | 2 +- docs/advanced/input_files/stru.md | 14 +++++----- docs/advanced/install.md | 14 +++++----- docs/advanced/interface/dpgen.md | 28 +++++++++++++------ docs/advanced/interface/index.rst | 1 + .../interface/migration-guide-csr-format.md | 6 ++-- docs/advanced/json/index.rst | 7 +++++ docs/advanced/md.md | 2 +- docs/advanced/output_files/running_scf.log.md | 2 +- docs/advanced/pp_orb.md | 3 +- docs/advanced/scf/construct_H.md | 4 +-- docs/advanced/scf/performance.md | 2 +- docs/community/contribution_guide.md | 2 +- docs/conf.py | 1 + docs/generate_input_main.py | 0 docs/index.rst | 1 + docs/parameters.yaml | 2 +- docs/quick_start/easy_install.md | 4 +-- docs/quick_start/input.md | 6 ++-- .../module_parameter/read_input_item_md.cpp | 2 +- 26 files changed, 67 insertions(+), 47 deletions(-) create mode 100644 docs/advanced/json/index.rst mode change 100644 => 100755 docs/generate_input_main.py diff --git a/.readthedocs.yaml b/.readthedocs.yaml index db95d725eba..ef9ef1e47d3 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -16,7 +16,7 @@ sphinx: # You can configure Sphinx to use a different builder, for instance use the dirhtml builder for simpler URLs # builder: "dirhtml" # Fail on all warnings to avoid broken references - # fail_on_warning: true + fail_on_warning: true # Optionally build your docs in additional formats such as PDF and ePub formats: all diff --git a/docs/CONTRIBUTING.md b/docs/CONTRIBUTING.md index 428190292f5..c53846664c5 100644 --- a/docs/CONTRIBUTING.md +++ b/docs/CONTRIBUTING.md @@ -95,7 +95,7 @@ To help us reproduce and confirm a bug, please provide a test case and building ## Agent governance and automated review Before coding or requesting review, read the repository governance entry point -[`AGENTS.md`](../AGENTS.md) and the full +[`AGENTS.md`](https://github.com/deepmodeling/abacus-develop/blob/develop/AGENTS.md) and the full [ABACUS Agent Governance](./developers_guide/agent_governance.md) guide. These rules apply to human contributors, AI agents, GitHub CI, and CodeRabbit. diff --git a/docs/Makefile b/docs/Makefile index d7b9e870f7a..c1d81852ef6 100644 --- a/docs/Makefile +++ b/docs/Makefile @@ -3,7 +3,7 @@ # You can set these variables from the command line, and also # from the environment for the first two. -SPHINXOPTS ?= +SPHINXOPTS ?= -W -n --keep-going SPHINXBUILD ?= sphinx-build SOURCEDIR = $(PWD) BUILDDIR = build diff --git a/docs/advanced/elec_properties/Mulliken.md b/docs/advanced/elec_properties/Mulliken.md index a34bca5d07a..686c4670bd2 100644 --- a/docs/advanced/elec_properties/Mulliken.md +++ b/docs/advanced/elec_properties/Mulliken.md @@ -1,7 +1,7 @@ # Mulliken Charge Analysis From version 2.1.0, ABACUS has the function of Mulliken population analysis. The example can be found in [examples/mulliken](https://github.com/deepmodeling/abacus-develop/tree/develop/examples/mulliken). \ -To use this function, set [out_mul](./input-main.md#out_mul) to `1` in the INPUT file. After calculation, there will be an output file named `mulliken.txt` in the output directory. In MD calculations, the output interval is controlled by the keyword [out_freq_ion](./input-main.md#out_freq_ion). In the file, there are contents like (`nspin 1`): +To use this function, set [out_mul](../input_files/input-main.md#out_mul) to `1` in the INPUT file. After calculation, there will be an output file named `mulliken.txt` in the output directory. In MD calculations, the output interval is controlled by the keyword [out_freq_ion](../input_files/input-main.md#out_freq_ion). In the file, there are contents like (`nspin 1`): ``` STEP: 0 diff --git a/docs/advanced/elec_properties/index.rst b/docs/advanced/elec_properties/index.rst index ad032d392a4..d75e28e28c1 100644 --- a/docs/advanced/elec_properties/index.rst +++ b/docs/advanced/elec_properties/index.rst @@ -11,4 +11,5 @@ Electronic Properties and Outputs charge hs_matrix density_matrix + position_matrix Berry_phase diff --git a/docs/advanced/elec_properties/wfc.md b/docs/advanced/elec_properties/wfc.md index a3f6d52f6c8..354d8844fc4 100644 --- a/docs/advanced/elec_properties/wfc.md +++ b/docs/advanced/elec_properties/wfc.md @@ -14,7 +14,7 @@ The files are stored in `OUT.${suffix}/`. Their pattern is `wfk{k}[s{spin}][g{ge With `out_freq_ion=0`, files are written only when the electronic calculation converges or reaches `scf_nmax`, and the names contain neither `g*` nor `e*`. During structural relaxation or molecular dynamics, each later ionic step overwrites the same files. With `out_freq_ion>0`, output is restricted to the ionic steps selected by `out_freq_ion` and occurs at multiples of `out_freq_elec`, at convergence, or at `scf_nmax`; both `g*` and `e*` are included in the file names. A static `calculation=scf` or `calculation=nscf` run also receives `g1e*` indices when `out_freq_ion>0`. -The [`init_wfc file binary`](../scf/initialization.md#wave-function) path reads only unindexed binary `wf*_pw.dat` files from `read_file_dir`. Generate directly reusable files with `out_wfc_pw=2` and normally `out_freq_ion=0`. Text `wf*_pw.txt` files and files containing `g*` or `e*` indices are not matched automatically. +The [`init_wfc file binary`](../scf/initialization.md#wavefunction) path reads only unindexed binary `wf*_pw.dat` files from `read_file_dir`. Generate directly reusable files with `out_wfc_pw=2` and normally `out_freq_ion=0`. Text `wf*_pw.txt` files and files containing `g*` or `e*` indices are not matched automatically. For `basis_type=lcao`, [`out_wfc_lcao`](https://abacus-rtd.readthedocs.io/en/latest/advanced/input_files/input-main.html#out-wfc-lcao) controls the output of numerical-atomic-orbital coefficients: `1` writes text files with the `.txt` suffix and `2` writes binary files with the `.dat` suffix. Multi-k calculations generate `wfs{spin}k{k-point}_nao.txt` or `.dat`, while Gamma-only calculations generate `wfs{spin}_nao.txt` or `.dat`. diff --git a/docs/advanced/input_files/input-main.md b/docs/advanced/input_files/input-main.md index 428f38fd01d..e85b0e2b818 100644 --- a/docs/advanced/input_files/input-main.md +++ b/docs/advanced/input_files/input-main.md @@ -3800,7 +3800,7 @@ ### cal_syns -- **Type**: Boolean [Integer](optional) +- **Type**: Boolean \[Integer\](optional) - **Description**: Whether to calculate and output asynchronous overlap matrix for Hefei-NAMD interface. When enabled, calculates <phi(t-1)|phi(t)> by computing overlap between basis functions at atomic positions from previous time step and current time step. The overlap is calculated by shifting atom positions backward by velocity x md_dt. Output file: OUT.*/syns_nao.csr in CSR format. - 0 or false: disable diff --git a/docs/advanced/input_files/stru.md b/docs/advanced/input_files/stru.md index 37ae64d8712..3730c5bec51 100644 --- a/docs/advanced/input_files/stru.md +++ b/docs/advanced/input_files/stru.md @@ -4,13 +4,13 @@ - [no latname](#no-latname) - [latname fcc](#latname-fcc) - [Structure of the file](#structure-of-the-file) - - [ATOMIC_SPECIES](#ATOMIC_SPECIES) - - [NUMERICAL_ORBITAL](#NUMERICAL_ORBITAL) - - [LATTICE_CONSTANT](#LATTICE_CONSTANT) - - [LATTICE_VECTORS](#LATTICE_VECTORS) - - [LATTICE_PARAMETERS](#LATTICE_PARAMETERS) - - [ATOMIC_POSITIONS](#ATOMIC_POSITIONS) - - [More Key Words](#More-Key-Words) + - [ATOMIC_SPECIES](#atomic_species) + - [NUMERICAL_ORBITAL](#numerical_orbital) + - [LATTICE_CONSTANT](#lattice_constant) + - [LATTICE_VECTORS](#lattice_vectors) + - [LATTICE_PARAMETERS](#lattice_parameters) + - [ATOMIC_POSITIONS](#atomic_positions) + - [More Key Words](#more-key-words) ## Examples diff --git a/docs/advanced/install.md b/docs/advanced/install.md index 71319e737d3..ab1939181be 100644 --- a/docs/advanced/install.md +++ b/docs/advanced/install.md @@ -287,7 +287,7 @@ When `CXX=mpicxx`, a parallel version will be compiled. When `CXX=g++`, a sequen Except modifying `Makefile.vars`, you can also directly use -```makefile +```bash make CXX=mpiicpc ELPA_DIR=/public/soft/elpa_21.05.002 \ ELPA_INCLUDE_DIR=${ELPA_DIR}/include/elpa-2021.05.002 \ CEREAL_DIR=/public/soft/cereal @@ -305,7 +305,7 @@ The program compiled using the above instructions do not link with LIBXC and use To compile ABACUS with LIBXC, you need to define `LIBXC_DIR` in the file `Makefile.vars` or use -```makefile +```bash make LIBXC_DIR=/pulic/soft/libxc ``` @@ -315,7 +315,7 @@ directly. To compile ABACUS with machine learning algorithms, you need to set `ENABLE_MLALGO = ON`, and define `LIBTORCH_DIR` and `LIBNPY_DIR` in the file `Makefile.vars` or use -```makefile +```bash make ENABLE_MLALGO=ON LIBTORCH_DIR=/opt/libtorch/ LIBNPY_DIR=/opt/libnpy/ ``` @@ -329,22 +329,22 @@ directly. To compile ABACUS with DeePMD-kit, you need to define `DeePMD_DIR` and `TensorFlow_DIR` (TensorFlow Backend, optional) and/or `LIBTORCH_DIR` (PyTorch Backend, optional) in the file `Makefile.vars`. Or the `tensorflow_cc` and `torch` libraries are in the same directory as the `deepmd_c`/`deepmd_cc` libraries, then -```makefile +```bash make DeePMD_DIR=/dir_to_deepmd-kit ``` DeePMD-kit supports TensorFlow backend but its libraries are placed at another directory, then -```makefile +```bash make DeePMD_DIR=/dir_to_deepmd-kit TensorFlow_DIR=/dir_to_tensorflow ``` Similarly, DeePMD-kit supports PyTorch backend but its libraries are placed at another directory, then -```makefile +```bash make DeePMD_DIR=/dir_to_deepmd-kit Torch_DIR=/dir_to_pytorch ``` ### Add LibRI Support To use new EXX, you need two libraries: [LibRI](https://github.com/abacusmodeling/LibRI) and [LibComm](https://github.com/abacusmodeling/LibComm) and need to define `LIBRI_DIR` and `LIBCOMM_DIR` in the file `Makefile.vars` or use -```makefile +```bash make LIBRI_DIR=/public/software/LibRI LIBCOMM_DIR=/public/software/LibComm ``` directly. diff --git a/docs/advanced/interface/dpgen.md b/docs/advanced/interface/dpgen.md index bcfb1b1cb79..554daf80bf8 100644 --- a/docs/advanced/interface/dpgen.md +++ b/docs/advanced/interface/dpgen.md @@ -14,7 +14,7 @@ Secondly, for the "dpgen init_bulk" step, an `init.json` file should be provided ```json { - "init_fp_style": "ABACUS", # abacus interface + "init_fp_style": "ABACUS", "stages": [1,2,3,4], "cell_type": "fcc", "super_cell": [2, 1, 1], @@ -49,7 +49,7 @@ Next, for the "dpgen run" step, the following `run_param.json` should be provide "init_data_sys": [ "Al.STRU.01x01x01/02.md/sys-0004/deepmd" ], - "sys_format": "abacus/stru", # the initial structures are in ABACUS/STRU formate + "sys_format": "abacus/stru", "sys_configs_prefix": "./", "sys_configs": [ [ @@ -162,11 +162,11 @@ Next, for the "dpgen run" step, the following `run_param.json` should be provide "fp_task_max": 20, "fp_task_min": 5, "fp_pp_path": "./", - "fp_pp_files": ["Al_ONCV_PBE-1.0.upf"], # the pseudopotential file - "fp_orb_files": ["Al_gga_9au_100Ry_4s4p1d.orb"], # the orbital file (use only in LCAO calculation) - "k_points":[2, 2, 2, 0, 0, 0], # k-mesh setting - "user_fp_params":{ # All the ABACUS input paramters are defined here - "ntype": 1, # defining input parameters from INPUT files is not supported yet. + "fp_pp_files": ["Al_ONCV_PBE-1.0.upf"], + "fp_orb_files": ["Al_gga_9au_100Ry_4s4p1d.orb"], + "k_points":[2, 2, 2, 0, 0, 0], + "user_fp_params":{ + "ntype": 1, "ecutwfc": 80, "mixing_type": "broyden", "mixing_beta": 0.8, @@ -176,12 +176,22 @@ Next, for the "dpgen run" step, the following `run_param.json` should be provide "smearing_method": "mp", "smearing_sigma": 0.002, "scf_thr":1e-8, - "cal_force":1, # calculate force must be set to 1 in dpgen calculation - "kspacing": 0.01 # when KSPACING is set, the above k_points setting becomes invalid. + "cal_force":1, + "kspacing": 0.01 } } ``` +```{important} +Some ABACUS-specific parameters in this example require additional attention: + +- `sys_format`: Set to `"abacus/stru"` when the initial structures are provided in the ABACUS `STRU` format. +- `fp_orb_files`: Orbital files are required only for LCAO calculations. +- `user_fp_params`: ABACUS input parameters for first-principles calculations are specified here; specifying them through an `INPUT` file is not supported. +- `cal_force`: Must be set to `1` for DP-GEN calculations. +- `k_points` and `kspacing`: `k_points` specifies the k-point mesh. If `kspacing` is set in `user_fp_params`, it takes precedence over `k_points`. +``` + ## autotest This example can be found in examples/dpgen-example/autotest directory. diff --git a/docs/advanced/interface/index.rst b/docs/advanced/interface/index.rst index 6622e821b7e..1033502a281 100644 --- a/docs/advanced/interface/index.rst +++ b/docs/advanced/interface/index.rst @@ -19,3 +19,4 @@ Interfaces to Other Softwares ShengBTE candela TB2J + migration-guide-csr-format diff --git a/docs/advanced/interface/migration-guide-csr-format.md b/docs/advanced/interface/migration-guide-csr-format.md index d1300690b56..0703ed22980 100644 --- a/docs/advanced/interface/migration-guide-csr-format.md +++ b/docs/advanced/interface/migration-guide-csr-format.md @@ -1,10 +1,10 @@ -# Migration Guide: New CSR Format for H(R) and S(R) Matrices +# Migration Guide: New CSR Format for H\(R\) and S\(R\) Matrices ## Overview -Starting from ABACUS v3.9.0.25, the output format for Hamiltonian H(R) and overlap S(R) matrices has been unified to use standard CSR (Compressed Sparse Row) format, matching the format used by `out_dmr` for density matrices. +Starting from ABACUS v3.9.0.25, the output format for Hamiltonian H\(R\) and overlap S\(R\) matrices has been unified to use standard CSR (Compressed Sparse Row) format, matching the format used by `out_dmr` for density matrices. -This change affects downstream tools that read H(R) and S(R) matrices, including: +This change affects downstream tools that read H\(R\) and S\(R\) matrices, including: - TB2J (magnetic exchange parameters) - DeepH (machine learning Hamiltonian) - pyATB (tight-binding analysis) diff --git a/docs/advanced/json/index.rst b/docs/advanced/json/index.rst new file mode 100644 index 00000000000..172481781d8 --- /dev/null +++ b/docs/advanced/json/index.rst @@ -0,0 +1,7 @@ +================================================= +JSON Usage +================================================= + +.. toctree:: + json_add + json_para diff --git a/docs/advanced/md.md b/docs/advanced/md.md index c66243a362e..cd42e9c2680 100644 --- a/docs/advanced/md.md +++ b/docs/advanced/md.md @@ -30,7 +30,7 @@ Furthermore, ABACUS also provides a [list of keywords](./input_files/input-main. The MD output information will be written into the file `MD_dump`， in which the atomic forces, atomic velocities, and lattice virial are controlled by keyword [dump_force](./input_files/input-main.md#dump_force), [dump_vel](./input_files/input-main.md#dump_vel), and [dump_virial](./input_files/input-main.md#dump_virial), respectively. -[Examples](../../examples/md/lcao_gammaonly_Si8/) of MD simulations are also provided. +[Examples](https://github.com/deepmodeling/abacus-develop/tree/develop/examples/md/lcao_gammaonly_Si8) of MD simulations are also provided. There are eight INPUT files corresponding to eight different MD evolution methods in the directory. For examlpe, `INPUT_0` shows how to employ the NVE simulation. diff --git a/docs/advanced/output_files/running_scf.log.md b/docs/advanced/output_files/running_scf.log.md index 07d16a4f545..50064c7c2df 100644 --- a/docs/advanced/output_files/running_scf.log.md +++ b/docs/advanced/output_files/running_scf.log.md @@ -1,6 +1,6 @@ # The running_scf.log file -- [The running\_scf.log file](#the-running_scf.log-file) +- [The running\_scf.log file](#the-running_scflog-file) - [Reading information](#reading-information) - [Reading version information](#reading-version-information) - [Reading general information](#reading-general-information) diff --git a/docs/advanced/pp_orb.md b/docs/advanced/pp_orb.md index 4cfe750096b..e3e285f2a90 100644 --- a/docs/advanced/pp_orb.md +++ b/docs/advanced/pp_orb.md @@ -76,11 +76,10 @@ When performing spin-orbit coupling (SOC) calculations with `lspinorb=1`, specif Full-relativistic pseudopotentials suitable for SOC calculations can be identified by checking the UPF file header (`PP_HEADER` section): ```xml + ``` diff --git a/docs/advanced/scf/construct_H.md b/docs/advanced/scf/construct_H.md index 69a22ad80e9..1c3f8dba38e 100644 --- a/docs/advanced/scf/construct_H.md +++ b/docs/advanced/scf/construct_H.md @@ -4,7 +4,7 @@ In our package, the XC functional can be set explicitly using the `dft_functional` keyword in `INPUT` file. If `dft_functional` is not specified, ABACUS will use the xc functional indicated in the pseudopotential file. -Several common functionals are implemented in ABACUS, such as PZ and PBE. Users can check out this [file](../../../source/source_hamilt/module_xc/xc_funcs.h) for a complete list of functionals implemented in ABACUS. Furthermore, if ABACUS is compiled with LIBXC, we also support all the LDA, GGA and meta-GGA functionals provided therein. +Several common functionals are implemented in ABACUS, such as PZ and PBE. Users can check out this [file](https://github.com/deepmodeling/abacus-develop/blob/develop/source/source_hamilt/module_xc/xc_funcs.h) for a complete list of functionals implemented in ABACUS. Furthermore, if ABACUS is compiled with LIBXC, we also support all the LDA, GGA and meta-GGA functionals provided therein. Here, we use a simple [example calculation](https://github.com/deepmodeling/abacus-develop/tree/develop/examples/scf/lcao_Si2) for illustration. @@ -69,7 +69,7 @@ Here, we use a simple [example calculation](https://github.com/deepmodeling/abac ABACUS supports functionals with exact Hartree-Fock exchange in LCAO basis set only. The old INPUT parameter exx_hybrid_type for hybrid functionals has been absorbed into `dft_functional`. Options are `hf` (pure Hartree-Fock), `pbe0`(PBE0), `hse`, and `scan0`(SCAN0) (Note: in order to use HSE or SCAN0 functional, LIBXC is required). Note also that only HSE has been tested while other hybrid functionals have NOT been fully tested yet, and the maximum parallel cpus for running exx is N^4, with N being the number of atoms. - More information on the hybrid functional can be found from the section [Exact Exchange](../input_files/input-main.md#exact-exchange) in the list of input variables for more information. + More information on the hybrid functional can be found from the section [Exact Exchange](../input_files/input-main.md#exact-exchange-common) in the list of input variables for more information. An example HSE calculation is provided in this [directory](https://github.com/deepmodeling/abacus-develop/tree/develop/examples/hse/lcao_Si2). Apart from the input files (`INPUT`, `STRU`, `KPT`), we further provide two files: running_scf.log_ref and log_ref, which contains reference for running_scf.log and standard output from the program, respectively. diff --git a/docs/advanced/scf/performance.md b/docs/advanced/scf/performance.md index cf3ebb907f3..49e9d38d4dd 100644 --- a/docs/advanced/scf/performance.md +++ b/docs/advanced/scf/performance.md @@ -20,7 +20,7 @@ Inclusion of k-point symmetry helps increasing the efficiency of calculations by For LCAO calculation, the matrix elements of the local potential is evaluated using grid integration. In grid integration, we group real-space FFT grid points into boxes of dimension bx * by * bz, and then proceed with the boxes as the basis unit of calculation. -Setting [bx, by, bz](../input_files/input-main.md#bx-by-bz) to be values other than default might help with the efficiency of grid integration. +Setting [bx](../input_files/input-main.md#bx), [by](../input_files/input-main.md#by), and [bz](../input_files/input-main.md#bz) to values other than default might help with the efficiency of grid integration. > Note: the choice of bx, by, bz should be integer factors of the dimension of the real space FFT grid in each direction. diff --git a/docs/community/contribution_guide.md b/docs/community/contribution_guide.md index 33fc82e8400..7f37664cde4 100644 --- a/docs/community/contribution_guide.md +++ b/docs/community/contribution_guide.md @@ -11,7 +11,7 @@ We assume you already have a good idea on what to do, otherwise the [issue track It is suggested to [submit new issues](https://github.com/deepmodeling/abacus-develop/issues/new/choose) before coding out changes to involve more discussions and suggestions from development team. Refer to the technical guide in [Contributing to ABACUS](../CONTRIBUTING.md) when needed. - **Follow governance rules.** -Before implementation and review, read [`AGENTS.md`](../../AGENTS.md) and the +Before implementation and review, read [`AGENTS.md`](https://github.com/deepmodeling/abacus-develop/blob/develop/AGENTS.md) and the [ABACUS Agent Governance](../developers_guide/agent_governance.md) guide. New code is reviewed against the shared rules for global dependencies, default parameters, header dependencies, tests, INPUT documentation linkage, LF line diff --git a/docs/conf.py b/docs/conf.py index bf96df8cb7b..96f3c814fc1 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -50,6 +50,7 @@ "tasklist", ] myst_heading_anchors = 4 +nitpicky = True # Add any paths that contain templates here, relative to this directory. templates_path = ['_templates'] diff --git a/docs/generate_input_main.py b/docs/generate_input_main.py old mode 100644 new mode 100755 diff --git a/docs/index.rst b/docs/index.rst index dd0b5968c4c..f0d34d3242e 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -45,6 +45,7 @@ the developments and applications of novel machine-learning-assisted DFT methods advanced/interface/index advanced/input_files/index advanced/windows_installer + advanced/json/index .. toctree:: :maxdepth: 2 diff --git a/docs/parameters.yaml b/docs/parameters.yaml index a0f76236e86..7f6871f7003 100644 --- a/docs/parameters.yaml +++ b/docs/parameters.yaml @@ -1780,7 +1780,7 @@ parameters: availability: "" - name: cal_syns category: Molecular dynamics - type: "Boolean [Integer](optional)" + type: "Boolean \\[Integer\\](optional)" description: | Whether to calculate and output asynchronous overlap matrix for Hefei-NAMD interface. When enabled, calculates by computing overlap between basis functions at atomic positions from previous time step and current time step. The overlap is calculated by shifting atom positions backward by velocity x md_dt. Output file: OUT.*/syns_nao.csr in CSR format. diff --git a/docs/quick_start/easy_install.md b/docs/quick_start/easy_install.md index 474f31c1c16..637b4bb54fb 100644 --- a/docs/quick_start/easy_install.md +++ b/docs/quick_start/easy_install.md @@ -1,6 +1,6 @@ # Easy Installation -This guide helps you install ABACUS with basic features. **For DeePKS, DeePMD and Libxc support, or building with `make`, please refer to [the advanced installation guide](../advanced/install.md)** after going through this page. We recommend building ABACUS with `cmake` to avoid dependency issues. We recommend compiling ABACUS (and possibly its requirements) from the source code using the latest compiler for the best performace. You can use [toolchain](#install-by-toolchain) to install ABACUS and dependencies in a source-code compilation way with convience. You can also deploy ABACUS **without building** by [Docker](#container-deployment) or [conda](#install-by-conda). Please note that ABACUS only supports Linux; for Windows users, please consider using [WSL](https://learn.microsoft.com/en-us/windows/wsl/) or docker. For a scripted one-click setup that provisions WSL2 and installs ABACUS inside it automatically, see [Windows One-Click Installer](./advanced/windows_installer.md). +This guide helps you install ABACUS with basic features. **For DeePKS, DeePMD and Libxc support, or building with `make`, please refer to [the advanced installation guide](../advanced/install.md)** after going through this page. We recommend building ABACUS with `cmake` to avoid dependency issues. We recommend compiling ABACUS (and possibly its requirements) from the source code using the latest compiler for the best performace. You can use [toolchain](#install-by-toolchain) to install ABACUS and dependencies in a source-code compilation way with convience. You can also deploy ABACUS **without building** by [Docker](#container-deployment) or [conda](#install-by-conda). Please note that ABACUS only supports Linux; for Windows users, please consider using [WSL](https://learn.microsoft.com/en-us/windows/wsl/) or docker. For a scripted one-click setup that provisions WSL2 and installs ABACUS inside it automatically, see [Windows One-Click Installer](../advanced/windows_installer.md). ## Get ABACUS source code @@ -272,7 +272,7 @@ Usually a CPU has a feature named Hyper-Threading(HT). This feature enables one > Please note that containers target at developing and testing, but not massively parallel computing for production. Docker has a bad support to MPI, which may cause performance degradation. -We've built a ready-for-use version of ABACUS with docker [here](https://github.com/deepmodeling/abacus-develop/pkgs/container/abacus). For a quick start: pull the image, prepare the data, run container. Instructions on using the image can be accessed in [Dockerfile](../../Dockerfile). A mirror is available by `docker pull registry.dp.tech/deepmodeling/abacus`. +We've built a ready-for-use version of ABACUS with docker [here](https://github.com/deepmodeling/abacus-develop/pkgs/container/abacus). For a quick start: pull the image, prepare the data, run container. Instructions on using the image can be accessed in [Dockerfile](https://github.com/deepmodeling/abacus-develop/blob/develop/Dockerfile). A mirror is available by `docker pull registry.dp.tech/deepmodeling/abacus`. We also offer a pre-built docker image containing all the requirements for development. Please refer to our [Package Page](https://github.com/orgs/deepmodeling/packages?repo_name=abacus-develop). diff --git a/docs/quick_start/input.md b/docs/quick_start/input.md index f4dfe068afc..1f0ac33c640 100644 --- a/docs/quick_start/input.md +++ b/docs/quick_start/input.md @@ -8,7 +8,7 @@ The `INPUT` file contains parameters that control the type of calculation as wel Below is an example `INPUT` file with some of the most important parameters that need to be set: -```plaintext +```text INPUT_PARAMETERS suffix MgO # the output files will be in OUT.{suffix} directory pseudo_dir ./ # where the pseudopotential for each element is @@ -103,7 +103,7 @@ The structure file contains structural information about the system, e.g., latti An example of the `STRU` file is given as follows : -```plaintext +```text #This is the atom file containing all the information #about the lattice structure. @@ -152,7 +152,7 @@ This file contains information of the kpoint grid setting for the Brillouin zone An example of the `KPT` file is given below: -```plaintext +```text K_POINTS 0 Gamma diff --git a/source/source_io/module_parameter/read_input_item_md.cpp b/source/source_io/module_parameter/read_input_item_md.cpp index cebe8d7d944..97744202193 100644 --- a/source/source_io/module_parameter/read_input_item_md.cpp +++ b/source/source_io/module_parameter/read_input_item_md.cpp @@ -695,7 +695,7 @@ Note: It is a system-dependent empirical parameter. An improper choice might lea Input_Item item("cal_syns"); item.annotation = "calculate asynchronous overlap matrix to output for Hefei-NAMD"; item.category = "Molecular dynamics"; - item.type = R"(Boolean [Integer](optional))"; + item.type = R"(Boolean \[Integer\](optional))"; item.description = R"(Whether to calculate and output asynchronous overlap matrix for Hefei-NAMD interface. When enabled, calculates by computing overlap between basis functions at atomic positions from previous time step and current time step. The overlap is calculated by shifting atom positions backward by velocity x md_dt. Output file: OUT.*/syns_nao.csr in CSR format. * 0 or false: disable