Merge pull request #116 from dyzheng/new

Merge deepmodeling/abacus-develop to abacusmodeling

Author: dyzheng

.github/workflows/dynamic.yml

@@ -2,7 +2,7 @@ name: Dynamic Analysis
 
 on:
   schedule:
-    - cron: '0 20 * * *'
+    - cron: '0 3 * * *'
   workflow_dispatch:
     inputs:
       name:
@@ -14,6 +14,7 @@ jobs:
   test:
     name: Do the job on the runner
     runs-on: self-hosted
+    if: github.repository_owner == 'deepmodeling'
     container: ghcr.io/deepmodeling/abacus-development-kit:gnu
     steps:
       - name: Checkout

.github/workflows/static.yaml

@@ -6,6 +6,7 @@ on:
 jobs:
   clang-tidy:
     runs-on: self-hosted
+    if: github.repository_owner == 'deepmodeling'
     container: ghcr.io/deepmodeling/abacus-development-kit:gnu
     steps:
       - name: Checkout Pull Request

.github/workflows/test.yml

@@ -4,15 +4,19 @@ on:
   pull_request_target:
     branches:
       - develop
+      - tryEigen
       - update_MD
       - ABACUS_2.2.0_beta
       - deepks
       - planewave
-jobs:
+      - pw_refactor
+      - TDDFT
 
+jobs:
   test:
     name: Do the job on the runner
     runs-on: self-hosted
+    if: github.repository_owner == 'deepmodeling'
     container: ghcr.io/deepmodeling/abacus-development-kit:gnu
     steps:
       - name: Checkout
@@ -23,7 +27,7 @@ jobs:
         env:
           GTEST_COLOR: 'yes'
         run: |
-          cmake -B build -DBUILD_TESTING=ON
+          cmake -B build -DBUILD_TESTING=ON -DENABLE_DEEPKS=ON
           cmake --build build -j8
           cmake --install build
           cmake --build build --target test ARGS="-V"

CMakeLists.txt

@@ -167,13 +167,14 @@ else()
     message(WARNING "Cannot find the correct library for Fortran.")
   endif()
 endif()
-target_link_libraries(${ABACUS_BIN_NAME} ${math_libs})
 
 if(ENABLE_DEEPKS)
   set(CMAKE_CXX_STANDARD 14)
   find_package(Torch REQUIRED)
   include_directories(${TORCH_INCLUDE_DIRS})
-  target_link_libraries(${ABACUS_BIN_NAME} ${TORCH_LIBRARIES})
+  target_link_libraries(${ABACUS_BIN_NAME} deepks)
+  list(APPEND math_libs ${TORCH_LIBRARIES})
+
   add_compile_options(${TORCH_CXX_FLAGS})
 
   find_path(libnpy_SOURCE_DIR
@@ -192,6 +193,8 @@ if(ENABLE_DEEPKS)
   add_compile_definitions(__DEEPKS)
 endif()
 
+target_link_libraries(${ABACUS_BIN_NAME} ${math_libs})
+
 if(DEFINED Libxc_DIR)
   set(ENABLE_LIBXC ON)
 endif()
@@ -226,7 +229,7 @@ IF (BUILD_TESTING)
   find_package(Threads)
   set(CMAKE_CXX_STANDARD_REQUIRED ON)
   find_package(GTest HINTS /usr/local/lib/ ${GTEST_DIR})
-  if(NOT DEFINED ${GTest_FOUND})
+  if(NOT ${GTest_FOUND})
     include(FetchContent)
     FetchContent_Declare(
       googletest
@@ -260,7 +263,6 @@ target_link_libraries(${ABACUS_BIN_NAME}
     cell
     symmetry
     md
-    symmetry
     neighbor
     orb
     io
@@ -272,6 +274,8 @@ target_link_libraries(${ABACUS_BIN_NAME}
     pw
     ri
     driver
+    xc
+    esolver
     -lm
 )
 

Dockerfile.intel

@@ -38,7 +38,7 @@ RUN source /opt/intel/oneapi/setvars.sh \
 	&& wget https://elpa.mpcdf.mpg.de/software/tarball-archive/Releases/2021.05.002/elpa-2021.05.002.tar.gz \
 	&& tar xzf elpa-2021.05.002.tar.gz  && rm elpa-2021.05.002.tar.gz \
 	&& cd elpa-2021.05.002 && mkdir build && cd build \
-	&& ../configure FCFLAGS="-mkl=cluster" \
+	&& ../configure FCFLAGS="-qmkl=cluster" \
 	&& make -j8 \
 	&& make PREFIX=/usr/local install \
 	&& ln -s /usr/local/include/elpa-2021.05.002/elpa /usr/local/include/ \

doc/developers.md

@@ -46,6 +46,9 @@ To add a unit test:
 AddTest(
   TARGET <module_name>_<test_name> # this is the executable file name of the test
   SOURCES <test_name>.cpp
+
+  # OPTIONAL: if this test requires external libraries, add them with "LIBS" statement.
+  LIBS math_libs # `math_libs` includes all math libraries in ABACUS.
 )
 ```
 

doc/examples/band-struc.md

@@ -5,7 +5,7 @@
 This example shows how to calculate the energy band structure. Similar to the [DOS case](#dos.md), we first, do a ground-state energy calculation as in [this example](#basic-lcao.md) ***with one additional keyword in the INPUT file***:
 
 ```
-out_charge              1
+out_chg              1
 ```
 
 this will produce the converged charge density, which is contained in the file SPIN1_CHG. Copy the file along with the `STRU` file, the pseudopotential file and the atomic orbital file (and the local density matrix file onsite.dm if DFT+U is used) to the new working directory where we will do a non-self-consistent calculation. In this example, the potential is constructed from the ground-state charge density from the proceeding calculation. Now the INPUT file is like:
@@ -20,17 +20,17 @@ read_file_dir   ./
 
 #Parameters (Accuracy)
 ecutwfc 60
-niter 50
-dr2 1.0e-9
-ethr 1.0e-7
+scf_nmax 50
+scf_thr 1.0e-9
+pw_diag_thr 1.0e-7
 
 #Parameters (File)
-start_charge file
+init_chg file
 out_band 1
 
 #Parameters (Smearing)
-smearing gaussian
-sigma 0.02
+smearing_method gaussian
+smearing_sigma 0.02
 ```
 
 Here the the relevant k-point file KPT looks like,

doc/examples/basic-lcao.md

@@ -52,7 +52,7 @@ basis:
  ---------------------------------------------------------
  SELF-CONSISTENT : 
  ---------------------------------------------------------
- ITER   ETOT(eV)       EDIFF(eV)      DRHO2      TIME(s)    
+ ITER   ETOT(eV)       EDIFF(eV)      SCF_THR      TIME(s)    
  GE1    -2.138667e+02  0.000000e+00   1.652e-01  4.690e+00  
  GE2    -2.139153e+02  -4.859216e-02  3.480e-02  4.970e+00  
  GE3    -2.139161e+02  -8.407097e-04  4.131e-03  4.760e+00  

doc/examples/basic-pw.md

@@ -15,9 +15,9 @@ For this example, the input files are:
     basis_type pw
     suffix Si2_diamond
     symmetry 1
-    niter 60
-    dr2 1.0e-9
-    out_charge 1
+    scf_nmax 60
+    scf_thr 1.0e-9
+    out_chg 1
     ```
 
     The meanings of the above parameters are:
@@ -48,11 +48,11 @@ For this example, the input files are:
 
         Use symmetry(=1) or not(=0) in the calculation. The default value is 0.
 
-    - niter
+    - scf_nmax
         The maximal iteration number for electronic-structure calculations.
-    - dr2
+    - scf_thr
         Tolerance of the difference of charge density, below which the self-consistent calculation is considered to be converged.
-    - out_charge
+    - out_chg
         Print out the charge density(=1) or not(=0).
 
     A complete list of INPUT keyewords can be found in the [instruction](../input-main.md).
@@ -131,7 +131,7 @@ The following typical output information will be printed to the screen:
  -------------------------------------------
  SELF-CONSISTENT : 
  -------------------------------------------
- ITER   ETOT(eV)       EDIFF(eV)      DRHO2      CG_ITER    TIME(S)    
+ ITER   ETOT(eV)       EDIFF(eV)      SCF_THR      CG_ITER    TIME(S)    
  CG1    -2.154524e+02  0.000000e+00   6.855e-02  1.000e+00  1.290e+00  
  CG2    -2.154992e+02  -4.673475e-02  2.378e-03  2.000e+00  8.400e-01  
  CG3    -2.155050e+02  -5.882715e-03  8.220e-05  2.594e+00  9.000e-01  

doc/examples/berry-phase.md

@@ -25,14 +25,14 @@ suffix        PbTiO3
 ntype         3
 nbands        25 // number of bands
 ecutwfc       50 // Ry
-niter         20
+scf_nmax         20
 symmetry      0 // turn off symmetry
-ethr          1e-10
-smearing      gaussian // gaussian smearing
-sigma         0.002 // Ry
+pw_diag_thr          1e-10
+smearing_method      gaussian // gaussian smearing
+smearing_sigma         0.002 // Ry
 calculation   nscf // non-self-consistent calculation
 basis_type    lcao // atomic basis
-start_charge  file // read charge from files
+init_chg  file // read charge from files
 berry_phase   1 // calculate Berry phase
 gdir          3 // calculate polarization along c axis
 ```