Merge branch 'develop' of github.com:deepmodeling/abacus-develop into develop

Author: dyzheng

Dockerfile

@@ -1,5 +1,10 @@
 # To build this Dockerfile, run `docker build -t abacus - < Dockerfile`.
-# Pull image with `docker pull ghcr.io/deepmodeling/abacus:latest`.
+# Alternatively, pull the image with `docker pull ghcr.io/deepmodeling/abacus:latest`.
+# Also available at `docker pull registry.dp.tech/deepmodeling/abacus:latest`.
+
+# Docker images are aimed for evaluating ABACUS.
+# For production use, please compile ABACUS from source code and run in bare-metal for a better performace.
+
 FROM ubuntu:22.04
 RUN apt update && apt install -y --no-install-recommends \
     libopenblas-dev liblapack-dev libscalapack-mpi-dev libelpa-dev libfftw3-dev libcereal-dev libxc-dev \
@@ -17,10 +22,11 @@ RUN git clone https://github.com/deepmodeling/abacus-develop.git --depth 1 && \
 # If you have trouble cloning repo, replace "github.com" with "gitee.com".
 CMD mpirun --use-hwthread-cpus abacus
 
-# To run ABACUS built by this image with all available threads, execute `docker run -v <host>:<wd> -w <wd/input> abacus`.
+# To run ABACUS built by this image with all available threads, execute `docker run -v <host>:<wd> -w <wd/input> abacus:latest`.
 # Replace '<host>' with the path to all files(including pseudopotential files), '<wd>' with a path to working directory, and '<wd/input>' with the path to input folder(containing 'INPUT', 'STRU', etc.).
-# e.g. after clone the repo to `$HOME` and pulled this image, execute `docker run -v ~/abacus-develop/tests/integrate:/workspace -w /workspace/101_PW_15_f_pseudopots abacus`.
-# To run ABACUS with a given MPI process number, execute `docker run -v <host>:<wd> -w <wd/input> -it --entrypoint mpirun abacus -np <processes> abacus`. Note: the first "abacus" is the name of the image, the second "abacus" is the name of the executable file. Do not use '--cpus' flag of 'docker run' to specify the number of processes.
+# e.g. after cloning the repo to `$HOME` and pulling image, execute `docker run -v ~/abacus-develop/tests/integrate:/workspace -w /workspace/101_PW_15_f_pseudopots abacus:latest`.
+# To run ABACUS with a given MPI process number, execute `docker run -v <host>:<wd> -w <wd/input> -it --entrypoint mpirun abacus:latest -np <processes> abacus`.
+# Note: It would be better using all available CPUs. Docker uses CFS to share the CPU resources, which will result in bad CPU affinity.
 
 # To use this image as developing environment, execute `docker run -it --entrypoint /bin/bash abacus`.
 # Please refer to https://docs.docker.com/engine/reference/commandline/run/ for more details.

Dockerfile.gnu

@@ -16,3 +16,10 @@ RUN wget https://download.pytorch.org/libtorch/cpu/libtorch-cxx11-abi-shared-wit
     unzip -q libtorch.zip && rm libtorch.zip && \
     cd libtorch && cp -r . /usr/local && \
     cd .. && rm -r libtorch
+
+RUN git clone https://github.com/deepmodeling/abacus-develop.git --depth 1 && \
+    cd abacus-develop && \
+    cmake -B build -DENABLE_DEEPKS=ON && \
+    cmake --build build -j`nproc` && \
+    cmake --install build && \
+    cd .. && rm -rf abacus-develop

Dockerfile.intel

@@ -47,3 +47,16 @@ RUN source /opt/intel/oneapi/setvars.sh \
 	&& make PREFIX=/usr/local install \
 	&& ln -s /usr/local/include/elpa-2021.05.002/elpa /usr/local/include/ \
 	&& cd /tmp && rm -rf elpa-2021.05.002
+
+RUN wget https://download.pytorch.org/libtorch/cpu/libtorch-cxx11-abi-shared-with-deps-1.9.1%2Bcpu.zip \
+        --no-check-certificate --quiet -O libtorch.zip && \
+    unzip -q libtorch.zip && rm libtorch.zip && \
+    cd libtorch && cp -r . /usr/local && \
+    cd .. && rm -r libtorch
+
+RUN git clone https://github.com/deepmodeling/abacus-develop.git --depth 1 && \
+    cd abacus-develop && \
+    cmake -B build -DENABLE_DEEPKS=ON && \
+    cmake --build build -j`nproc` && \
+    cmake --install build && \
+    cd .. && rm -rf abacus-develop

README.md

@@ -95,7 +95,7 @@ The following files are the central input files for ABACUS. Before executing the
 
 - The numerical orbital files
 
-    This part is only required in LCAO calculations. 
+    This part is only required in LCAO calculations.
     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.
     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).
 
@@ -136,7 +136,7 @@ into which the following output files will be generated:
 [back to top](#readme-top)
 
 ## Hands-on examples
-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.
+The following provides basic sample jobs in ABACUS. More can be found in the directories `examples/` and `tests/`, and the corresponding reference outputs can be found in the file `result.ref` under each subdirectory.
 
 *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.*
 
@@ -171,13 +171,13 @@ The following references are required to be cited when using ABACUS. Specificall
 - **For general purpose:**
 
     [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.
-    
+
     [2]. Pengfei Li, et al. "Large-scale ab initio simulations based on systematically improvable atomic basis." Computational Materials Science 112 (2016): 503-517.
 
 - **If Stochastic DFT is used:**
 
     [1]. Qianrui Liu, and Mohan Chen. "Plane-Wave-Based Stochastic-Deterministic Density Functional Theory for Extended Systems." https://arxiv.org/abs/2204.05662.
-    
+
 - **If DFT+U is used:**
 
     [1]. Xin Qu, et al. "DFT+ U within the framework of linear combination of numerical atomic orbitals." The Journal of Chemical Physics (2022).
@@ -189,17 +189,17 @@ The following references are required to be cited when using ABACUS. Specificall
 - **If berry curvature calculation is used in LCAO base:**
 
     [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.
-    
+
 - **If DeePKS is used:**
 
     [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.
-    
+
 - **If hybrid functional is used:**
-    
+
     [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.
-    
+
     [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.
-    
+
 [back to top](#readme-top)
 
 # Development team
@@ -232,4 +232,3 @@ If you find a bug or have some questions, please refer to our GitHub [issue trac
 - [Exchange-correlation functionals](docs/features.md#exchange-correlation-functionals)
 
 [back to top](#readme-top)
-

docs/examples/dpgen.md

@@ -163,6 +163,7 @@ Next, for the "dpgen run" step, the following `run_param.json` should be provide
     "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.
     "ecutwfc": 80,      
@@ -175,7 +176,6 @@ Next, for the "dpgen run" step, the following `run_param.json` should be provide
     "smearing_sigma": 0.002,
     "scf_thr":1e-8,
     "cal_force":1,        # calculate force must be set to 1 in dpgen calculation
-    "k_points":[2, 2, 2, 0, 0, 0],  # k-mesh setting
     "kspacing": 0.01  # when KSPACING is set, the above k_points setting becomes invalid.
     }
 }
@@ -186,4 +186,4 @@ Notes:
 - The ABACUS-DPGEN interface can be used in both pw and lcao basis.
 
 
-[back to top](#abacus-wannier90-interface)
+[back to top](#abacus-wannier90-interface)

docs/features.md

@@ -34,7 +34,7 @@ In the INPUT file, the keyword basis_type controls what basis type to use:
 
 The default value of basis_type is pw. When choosing lcao or lcao_in_pw, the user should prepare atomic orbitals first.
 
-Information on the keyword basis_type can also be found in [the list of input keywords](input-main.md#basis-type).
+Information on the keyword basis_type can also be found in [the list of input keywords](input-main.md#basis_type).
 
 We also provide a [detailed instruction](generate-basis.md) on generating basis functions.
 
@@ -43,7 +43,7 @@ We also provide a [detailed instruction](generate-basis.md) on generating basis
 ## Pseudopotentials
 
 Currently ABACUS uses norm-conserving pseudopotentials in the (old) format of UPF, which
-is the standard pseudopotential format for uantum ESPRESSO. To run a calculation, the pseudopotential needs to be set in STRU file. For example:
+is the standard pseudopotential format for Quantum ESPRESSO. To run a calculation, the pseudopotential needs to be set in STRU file. For example:
 
 ```
 ATOMIC_SPECIES
@@ -63,7 +63,7 @@ vectors of the supercell are set in the STRU file.
 
 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.
 
-More information on k-points is provided in this [instruction](#docs/input-kpt.md)
+More information on k-points is provided in this [instruction](input-kpt.md)
 
 [back to top](#features)
 
@@ -86,7 +86,7 @@ hpseps can not be used with plane wave basis.
 
 Then the user has to correct the input file and restart the calculation.
 
-Information on the keyword ks_solver is also given in the [list of input variables](input-main.md#ks-solver).
+Information on the keyword ks_solver is also given in the [list of input variables](input-main.md#ks_solver).
 
 [back to top](#features)
 
@@ -126,6 +126,6 @@ The user can set the XC functional type in INPUT file with the parameter, dft_fu
 
 If the functional specified by the user is not consistent with the pseudopotential file, the program will stop with an error message.
 
-Information on the keyword ks_solver is also given in the [list of input variables](input-main.md#dft-functional).
+Information on the keyword ks_solver is also given in the [list of input variables](input-main.md#dft_functional).
 
 [back to top](#features)