Merge pull request #216 from dyzheng/abacusmodeling

Merge: update to v3.0.1

Author: dyzheng

.readthedocs.yaml

@@ -5,6 +5,8 @@
 # Required
 version: 2
 
+formats: all
+
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
    configuration: docs/conf.py

CMakeLists.txt

@@ -1,8 +1,7 @@
-########################################
-# CMake build system
-# This file is part of ABACUS
 cmake_minimum_required(VERSION 3.16)
-########################################
+if(POLICY CMP0131) # From CMake 3.24
+    cmake_policy(SET CMP0135 NEW)
+endif()
 
 project(ABACUS
     VERSION 3.0.0
@@ -250,6 +249,32 @@ if(ENABLE_LIBXC)
   endif()
 endif()
 
+if(DEFINED DeePMD_DIR)
+  add_compile_definitions(
+    __DPMD 
+    HIGH_PREC
+  )
+  add_compile_options(-Wl,--no-as-needed)
+  find_package(DeePMD REQUIRED)
+  include_directories(${DeePMD_DIR}/include)
+  target_link_libraries(${ABACUS_BIN_NAME} 
+    DeePMD::deepmd_cc
+    DeePMD::deepmd_op
+    DeePMD::deepmd_op_cuda
+    DeePMD::tensorflow_cc
+  )
+  if(NOT DEFINED TensorFlow_DIR)
+    message(FATAL_ERROR "Please define TensorFlow_DIR!")
+  endif()
+endif()
+
+if(DEFINED TensorFlow_DIR)
+  include_directories(${TensorFlow_DIR}/include)
+  if(NOT DEFINED DeePMD_DIR)
+    message(FATAL_ERROR "Please define DeePMD_DIR!")
+  endif()
+endif()
+
 add_compile_definitions(
   __EXX
   __FFTW3
@@ -333,6 +358,7 @@ target_link_libraries(${ABACUS_BIN_NAME}
     hamilt
     psi
     esolver
+    rpa
 )
 
 install(PROGRAMS ${ABACUS_BIN_PATH}

Dockerfile.gnu

@@ -13,9 +13,9 @@ RUN git clone https://github.com/llohse/libnpy.git && \
 
 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
+    unzip -q libtorch.zip -d /opt  && rm libtorch.zip
+
+ENV CMAKE_PREFIX_PATH=/opt/libtorch/share/cmake
 
 RUN git clone https://github.com/deepmodeling/abacus-develop.git --depth 1 && \
     cd abacus-develop && \

Dockerfile.intel

@@ -50,9 +50,9 @@ RUN source /opt/intel/oneapi/setvars.sh \
 
 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
+    unzip -q libtorch.zip -d /opt  && rm libtorch.zip
+
+ENV CMAKE_PREFIX_PATH=/opt/libtorch/share/cmake
 
 RUN git clone https://github.com/deepmodeling/abacus-develop.git --depth 1 && \
     cd abacus-develop && \

conda/conda_build_config.yaml

@@ -0,0 +1,8 @@
+channel_sources:
+  - conda-forge
+  - defaults
+channel_targets:
+  - deepmodeling
+mpi:
+  - mpich
+  # - openmpi

conda/meta.yaml

@@ -0,0 +1,80 @@
+{% set version = os.popen('git describe --tags --abbrev=0').read().strip('\n').lstrip('v').replace('-', '_') %}
+
+package:
+  name: abacus
+  version: {{ version }}
+
+# This conda package may be built locally with
+# conda build . -c conda-forge
+source:
+  path: ..
+  # git_url: https://github.com/deepmodeling/abacus-develop.git
+  # git_rev: v3.0.0
+
+build:
+  skip: true  # [not linux]
+  script: |
+    cmake -B conda_build ${CMAKE_ARGS} -DCMAKE_BUILD_TYPE=Release
+    cmake --build conda_build -j`nproc`
+    cmake --install conda_build
+  # ${CMAKE_ARGS} applys restrictions for CMake to search libs under conda building env.
+  # See https://conda-forge.org/docs/maintainer/knowledge_base.html#using-cmake .
+  string: {{ GIT_BUILD_STR }}
+  number: {{ GIT_DESCRIBE_NUMBER }}
+
+requirements:
+  build:
+    - {{ compiler('cxx') }}
+    - make
+    - cmake
+
+  host:
+    - {{ mpi }}
+    - openblas=*=openmp*
+    - elpa=*=mpi*
+    - fftw=*=mpi*
+
+  run:
+    - libopenblas=*=openmp*
+    - scalapack
+    - elpa=*=mpi*
+    - fftw=*=mpi*
+
+test:
+  commands:
+  # Dry run ABACUS to verify dynamic libs are present.
+    - abacus
+    - mpirun -n 2 abacus
+
+  # Run end-to-end tests. This may take long time; disabled by default.
+  # Unit tests are not built here.
+  # Hence, some tests(ienvelope) requiring additional validation components are expected to fail.
+  # Please uncomment the codes below if necessary.
+
+  #   - cd tests/integrate && bash Autotest.sh
+  # source_files:
+  #   - tests/integrate
+  #   - tests/PP_ORB
+
+# Locally built package can be installed by
+# conda create -n my_abacus_env abacus -c local -c conda-forge
+
+# Feedstock: https://github.com/deepmd-kit-recipes/abacus-feedstock
+# Package:   https://anaconda.org/deepmodeling/abacus
+about:
+  home: http://abacus.ustc.edu.cn/
+  doc_url: https://abacus.deepmodeling.com/
+  dev_url: https://github.com/deepmodeling/abacus-develop
+  license: LGPL-3.0
+  license_family: LGPL
+  license_file: LICENSE
+  summary: An electronic structure package based on plane wave and numerical atomic basis sets.
+  description: >
+    ABACUS (Atomic-orbital Based Ab-initio Computation at UStc) is an open-source package based on density functional theory (DFT).
+    The package utilizes both plane wave and numerical atomic basis sets with the usage of norm-conserving pseudopotentials
+    to describe the interactions between nuclear ions and valence electrons. ABACUS supports LDA, GGA, meta-GGA, and hybrid functionals.
+    Apart from single-point calculations, the package allows geometry optimizations and ab-initio molecular dynamics with various ensembles.
+
+extra:
+  recipe-maintainers:
+    - caic99

docs/advanced/input_files/input-main.md

@@ -30,7 +30,7 @@
 
 - [Variables related to output information](#variables-related-to-output-information)
 
-    [out_force](#out_force) | [out_mul](#out_mul) | [out_freq_elec](#out_freq_elec) | [out_freq_ion](#out_freq_ion) | [out_chg](#out_chg) | [out_pot](#out_pot) | [out_dm](#out_dm) | [out_wfc_pw](#out_wfc_pw) | [out_wfc_r](#out_wfc_r) | [out_wfc_lcao](#out_wfc_lcao) | [out_dos](#out_dos) | [out_band](#out_band) | [out_proj_band](#out_proj_band) | [out_stru](#out_stru) | [out_level](#out_level) | [out_alllog](#out_alllog) | [out_mat_hs](#out_mat_hs) | [out_mat_r](#out_mat_r) | [out_mat_hs2](#out_mat_hs2) | [out_element_info](#out_element_info) | [restart_save](#restart_save) | [restart_load](#restart_load) | [dft_plus_dmft](#dft_plus_dmft)
+    [out_force](#out_force) | [out_mul](#out_mul) | [out_freq_elec](#out_freq_elec) | [out_freq_ion](#out_freq_ion) | [out_chg](#out_chg) | [out_pot](#out_pot) | [out_dm](#out_dm) | [out_wfc_pw](#out_wfc_pw) | [out_wfc_r](#out_wfc_r) | [out_wfc_lcao](#out_wfc_lcao) | [out_dos](#out_dos) | [out_band](#out_band) | [out_proj_band](#out_proj_band) | [out_stru](#out_stru) | [out_level](#out_level) | [out_alllog](#out_alllog) | [out_mat_hs](#out_mat_hs) | [out_mat_r](#out_mat_r) | [out_mat_hs2](#out_mat_hs2) | [out_element_info](#out_element_info) | [restart_save](#restart_save) | [restart_load](#restart_load) | [dft_plus_dmft](#dft_plus_dmft) | [rpa](#rpa)
 
 - [Density of states](#density-of-states)
 
@@ -42,7 +42,7 @@
 
 - [Molecular dynamics](#molecular-dynamics)
 
-    [md_type](#md_type) | [md_nstep](#md_nstep) | [md_ensolver](#md_ensolver) | [md_restart](#md_restart) | [md_dt](#md_dt) | [md_tfirst, md_tlast](#md_tfirst-md_tlast) | [md_dumpfreq](#md_dumpfreq) | [md_restartfreq](#md_restartfreq) | [md_seed](#md_seed) | [md_tfreq](#md_tfreq) | [md_mnhc](#md_mnhc) | [lj_rcut](#lj_rcut) | [lj_epsilon](#lj_epsilon) | [lj_sigma](#lj_sigma) | [msst_direction](#msst_direction) | [msst_vel](#msst_vel) | [msst_vis](#msst_vis) | [msst_tscale](#msst_tscale) | [msst_qmass](#msst_qmass) | [md_damp](#md_damp)
+    [md_type](#md_type) | [md_nstep](#md_nstep) | [md_ensolver](#md_ensolver) | [md_restart](#md_restart) | [md_dt](#md_dt) | [md_tfirst, md_tlast](#md_tfirst-md_tlast) | [md_dumpfreq](#md_dumpfreq) | [md_restartfreq](#md_restartfreq) | [md_seed](#md_seed) | [md_tfreq](#md_tfreq) | [md_mnhc](#md_mnhc) | [lj_rcut](#lj_rcut) | [lj_epsilon](#lj_epsilon) | [lj_sigma](#lj_sigma) | [pot_file](#pot_file) | [msst_direction](#msst_direction) | [msst_vel](#msst_vel) | [msst_vis](#msst_vis) | [msst_tscale](#msst_tscale) | [msst_qmass](#msst_qmass) | [md_damp](#md_damp)
 
 - [vdW correction](#vdw-correction)
 
@@ -78,7 +78,7 @@
 
 - [Electronic conductivities](#electronic-conductivities)
 
-    [cal_cond](#cal_cond) | [cond_nche](#cond_nche) | [cond_dw](#cond_dw) | [cond_wcut](#cond_wcut) | [cond_wenlarge](#cond_wenlarge) | [cond_fwhm](#cond_fwhm)
+    [cal_cond](#cal_cond) | [cond_nche](#cond_nche) | [cond_dw](#cond_dw) | [cond_wcut](#cond_wcut) | [cond_wenlarge](#cond_wenlarge) | [cond_fwhm](#cond_fwhm) | [cond_nonlocal](#cond_nonlocal)
 
 - [Implicit solvation model](#implicit-solvation-model)
 
@@ -471,7 +471,7 @@ calculations.
 ### nspin
 
 - **Type**: Integer
-- **Description**: Number of spin components of wave functions. There are only two choices now: 1 or 2, meaning non spin or collinear spin.
+- **Description**: Number of spin components of wave functions. There are only two choices now: 1 or 2, meaning non spin or collinear spin. For case of [noncollinear polarized](../scf/spin.md#noncollinear-spin-polarized-calculations), nspin will be automatically set to 4 without being specified in user input.
 - **Default**: 1
 
 ### smearing_method
@@ -967,6 +967,11 @@ Si-p2-orbital-dru.dat  Si-s1-orbital-ru.dat" for example.
 - **Description**: Whether to generate output to be used in dmft. It seems this functionality is not working anymore.
 - **Default**: 0
 
+### rpa
+- **Type**: Boolean
+- **Description**: Generate output files used in rpa calculation.
+- **Default**: 0
+
 [back to top](#full-list-of-input-keywords)
 
 ## Density of states
@@ -1375,6 +1380,12 @@ temperature will fluctuate violently; if it is too small, the temperature will t
 - **Description**: The value of sigma for Leonard Jones potential (angstrom).
 - **Default**: 3.405 (for He)
 
+### pot_file
+
+- **Type**: String
+- **Description**: The filename of potential files for CMD such as DP.
+- **Default**: graph.pb
+
 ### msst_direction
 
 - **Type**: Integer
@@ -1859,6 +1870,12 @@ Thermal conductivities: $\kappa = \lim_{\omega\to 0}\kappa(\omega)$.
 - **Description**: We use gaussian functions to approxiamte $\delta(E)\approx \frac{1}{\sqrt{2\pi}\Delta E}e^{-\frac{E^2}{2{\Delta E}^2}}$. FWHM for conductivities, $FWHM=2*\sqrt{2\ln2}\cdot \Delta E$. The unit is eV.
 - **Default**: 0.3
 
+### cond_nonlocal
+
+- **Type**: Boolean
+- **Description**: Conductivities need to calculate velocity matrix $\bra{\psi_i}\hat{v}\ket{\psi_j}$ and $m\hat{v}=\hat{p}+\frac{im}{\hbar}[\hat{V}_{NL},\hat{r}]$. If `cond_nonlocal` is false, $m\hat{v}\approx\hat{p}$.
+- **Default**: True
+
 [back to top](#full-list-of-input-keywords)
 
 ## Implicit solvation model

docs/advanced/install.md

@@ -6,10 +6,10 @@ ABACUS use exchange-correlation functionals by default. However, for some functi
 
 Dependency: [Libxc](https://tddft.org/programs/libxc/)>=5.1.7 .
 
-If Libxc is not installed in standard path (i.e. installed with a custom prefix path), you can set `LIBXC_DIR` to the corresponding directory.
+If Libxc is not installed in standard path (i.e. installed with a custom prefix path), you can set `Libxc_DIR` to the corresponding directory.
 
 ```bash
-cmake -B build -DLIBXC_DIR=~/libxc
+cmake -B build -DLibxc_DIR=~/libxc
 ```
 
 ## Build with DeePKS
@@ -26,6 +26,18 @@ If DeePKS feature is requied for [DeePKS-kit](https://github.com/deepmodeling/de
 cmake -B build -DENABLE_DEEPKS=1 -DTorch_DIR=~/libtorch/share/cmake/Torch/ -Dlibnpy_INCLUDE_DIR=~/libnpy/include
 ```
 
+## Build with DeePMD-kit
+If the Deep Potential model is employed in Molecule Dynamics calculations, the following prerequisites and steps are needed:
+
+### Extra prerequisites
+
+- [DeePMD-kit](https://github.com/deepmodeling/deepmd-kit)
+- [TensorFlow](https://www.tensorflow.org/)
+
+```bash
+cmake -B build -DDeePMD_DIR=~/deepmd-kit -DTensorFlow_DIR=~/tensorflow
+```
+
 ## Build Unit Tests
 To build tests for ABACUS, define `BUILD_TESTING` flag. You can also specify path to local installation of [Googletest](https://github.com/google/googletest) by setting `GTEST_DIR` flags. If not found in local, the configuration process will try to download it automatically.
 
@@ -55,11 +67,15 @@ CC = mpiicpc
 # icpc:      compile intel serial version
 # make: ELPA_DIR, ELPA_INCLUDE_DIR, CEREAL_DIR must also be set.
 # make pw: nothing need to be set except LIBXC_DIR
-# 
+#
 # mpicxx:    compile gnu parallel version
 # g++:       compile gnu serial version
 # make: FFTW_DIR, OPENBLAS_LIB_DIR, SCALAPACK_LIB_DIR, ELPA_DIR, ELPA_INCLUDE_DIR, CEREAL_DIR must also be set.
 # make pw: FFTW_DIR, OPENBLAS_LIB_DIR must be set.
+
+# GPU = OFF  #We do not support GPU yet
+# OFF:  do not use GPU
+# CUDA: use CUDA
 #======================================================================
 
 #-------  FOR INTEL COMPILER  ------------
@@ -96,6 +112,17 @@ CEREAL_DIR    = /public/soft/cereal
 # LIBXC_DIR    		= /public/soft/libxc
 # directory of libxc(>5.1.7), which contains include and lib/libxc.a
 # add LIBXC_DIR to use libxc to compile ABACUS
+
+# DeePMD_DIR = ${deepmd_root}
+# TensorFlow_DIR = ${tensorflow_root}
+# add them to use DEEPMD
+
+# NP = 14 # It is not supported. use make -j14 or make -j to parallelly compile
+
+# DEBUG = OFF
+# Only for developers
+# ON:   use gnu compiler and check segmental defaults
+# OFF:  nothing
 #======================================================================
 ```
 
@@ -132,7 +159,7 @@ CEREAL_DIR=/public/soft/cereal
 ```
 ABACUS now support full version and pw version. Use `make` or `make abacus` to compile full version which supports LCAO calculations. Use `make pw` to compile pw version which only supports pw calculations. For pw version, `make pw CC=mpiicpc`, you do not need to provide any libs. For `make pw CC=mpicxx`, you need provide `FFTW_DIR` and `OPENBLAS_LIB_DIR`.
 
-Besides, libxc and deepks are optional libs to compile abacus. 
+Besides, libxc and deepks are optional libs to compile abacus.
 They will be used when `LIBXC_DIR` is defined like
 ```
 LIBXC_DIR    		= /public/soft/libxc
@@ -151,16 +178,24 @@ After the compilation finishes without error messages (except perhaps for some w
 
 The program compiled using the above instructions do not link with LIBXC and use exchange-correlation functionals as written in the ABACUS program. However, for some functionals (such as HSE hybrid functional), LIBXC is required.
 
-To compile ABACUS with LIBXC, you need to define `LIBXC_DIR` in the file `Makefile.vars` or use 
+To compile ABACUS with LIBXC, you need to define `LIBXC_DIR` in the file `Makefile.vars` or use
 ```makefile
 make LIBXC_DIR=/pulic/soft/libxc
-``` 
+```
 directly.
 
 ### Add DeePKS Support
 
-To compile ABACUS with DEEPKS, you need to define `LIBTORCH_DIR` and `LIBNPY_DIR` in the file `Makefile.vars` or use 
+To compile ABACUS with DEEPKS, you need to define `LIBTORCH_DIR` and `LIBNPY_DIR` in the file `Makefile.vars` or use
 ```makefile
 make LIBTORCH_DIR=/opt/libtorch/ LIBNPY_DIR=/opt/libnpy/
-``` 
+```
 directly.
+
+### Add DeePMD-kit Support
+
+To compile ABACUS with DeePMD-kit, you need to define `DeePMD_DIR` and `TensorFlow_DIR` in the file `Makefile.vars` or use 
+```makefile
+make DeePMD_DIR=~/deepmd-kit TensorFlow_DIR=~/tensorflow
+``` 
+directly.

docs/advanced/md.md

@@ -13,6 +13,9 @@ By setting `calculation` to be `md` or `sto-md`, ABACUS currently provides six d
 
 Furthermore, ABACUS also provides a [list of keywords](./input_files/input-main.md#molecular-dynamics) to control relevant parmeters used in MD simulations.
 
+To employ CMD calculations, `md_ensolver` should be set to be `LJ` or `DP`.
+If DP model is selected, the filename of DP model is specified by keyword `pot_file`.
+
 [Examples](https://github.com/deepmodeling/abacus-develop/tree/develop/examples/md/lcao_gammaonly_Sn64) of MD simulations are also provided.
 There are six INPUT files corresponding to six different MD evolution methods in the directory.
 For examlpe, `INPUT_0` shows how to employ the NVE simulation.

docs/conf.py

@@ -75,3 +75,6 @@
 latex_engine = 'xelatex'
 mathjax_path = 'https://cdnjs.cloudflare.com/ajax/libs/mathjax/3.2.0/es5/tex-mml-chtml.min.js'
 #deepmodeling_current_site = 'Tutorials'
+latex_elements = {
+    'extraclassoptions':'openany,oneside'
+}