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

Author: dyzheng

.github/workflows/test.yml

@@ -21,7 +21,7 @@ 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} ${math_libs})
+
 if(DEFINED Libxc_DIR)
   set(ENABLE_LIBXC ON)
 endif()
@@ -260,7 +263,6 @@ target_link_libraries(${ABACUS_BIN_NAME}
     cell
     symmetry
     md
-    symmetry
     neighbor
     orb
     io
@@ -272,6 +274,7 @@ target_link_libraries(${ABACUS_BIN_NAME}
     pw
     ri
     driver
+    xc
     -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/input-main.md

@@ -32,10 +32,6 @@
     - [Density of states](#density-of-states)
 
         [dos_edelta_ev](#dos-edelta-ev) | [dos_sigma](#dos-sigma) | [dos_scale](#dos-scale)
-
-    - [Electric field](#electric-field)
-    
-        [efield](#efield) | [edir](#edir) | [emaxpos](#emaxpos) | [eopreg](#eopreg) | [eamp](#eamp)
 
     - [Exact exchange](#exact-exchange) (under tests)
 
@@ -66,7 +62,7 @@
         [nurse](#nurse) | [t_in_h](#t-in-h) | [vl_in_h](#vl-in-h) | [vnl_in_h](#vnl-in-h) | [test_force](#test-force) | [test_stress](#test-stress) | [colour](#colour) | [new_dm](#new-dm) | [test_just_neighbor](#test-just-neighbor)
     - [DeePKS](#deepks)
 
-        [out_descriptor](#out-descriptor) | [lmax_descriptor](#lmax-descriptor) | [deepks_scf](#deepks-scf) | [model_file](#model-file)
+        [deepks_out_labels](#out-descriptor) | [deepks_descriptor_lmax](#lmax-descriptor) | [deepks_scf](#deepks-scf) | [deepks_model](#model-file)
 
     [back to main page](../README.md)
 
@@ -912,49 +908,12 @@ This part of variables are used to control the calculation of DOS.
 
     [back to top](#input-file)
 
-### Electric field
-This part of variables are used to control the addition of an external electric field. It is achieved by adding a saw-like potential to the local ionic potential.
-
-- efield<a id="efield"></a>
-    - *Type*: Boolean
-    - *Description*: Controls whether to add the external electric field. When set to 1, the electric field is turned on. When set to 0, there is no electric field.
-    - *Default*: 0.
-
-    [back to top](#input-file)
-
-- edir<a id="edir"></a>
-    - *Type*: Integer
-    - *Description*: Tells which reciprocal lattice vector the external electric field aligns with. Allowed values are 1,2, and 3, corresponding to the three reciprocal lattice vectors respectively.
-    - *Default*: 1
-
-    [back to top](#input-file)
-
-- emaxpos<a id="emaxpos"></a>
-    - *Type*: Real
-    - *Description*: Position of the maximum of the saw-like potential along the reciprocal lattice vector specified by edir, 0 < emaxpos < 1.
-    - *Default*: 0.5
-
-    [back to top](#input-file)
-
-- eopreg<a id="eopreg"></a>
-    - *Type*: Real
-    - *Description*: The saw-like potential increases in the region from `(emaxpos+eopreg-1)` to `(emaxpos)`, then decreases to 0 until (emaxpos+eopreg), in units of the crystal vector `edir`. Important: the change of slope of this potential must be located in the empty region, or else unphysical forces will result.
-    - *Default*: 0.1
-
-    [back to top](#input-file)
-
-- eamp<a id="eamp"></a>
-    - *Type*: Real
-    - *Description*: Amplitude of the electric field, in atomic unit: 1 a.u. = 51.4220632*10^10 V/m.
-    - *Default*: 0.001
-
-    [back to top](#input-file)
 
 ### DeePKS
 This part of variables are used to control the usage of DeePKS method (a comprehensive data-driven approach to improve accuracy of DFT).
 Warning: this function is not robust enough for version 2.2.0. Please try these variables in https://github.com/deepmodeling/abacus-develop/tree/deepks .
 
-- out_descriptor<a id="out-descriptor"></a>
+- deepks_out_labels<a id="out-descriptor"></a>
     - *Type*: Boolean
     - *Description*: when set to 1, ABACUS will calculate and output descriptor for DeePKS training. In `LCAO` calculation, a path of *.orb file is needed to be specified under `NUMERICAL_DESCRIPTOR`in `STRU`file. For example: 
     ```
@@ -968,7 +927,7 @@ Warning: this function is not robust enough for version 2.2.0. Please try these
     - *Default*: 0
 
     [back to top](#input-file)
-- lmax_descriptor<a id="lmax-descriptor"></a>
+- deepks_descriptor_lmax<a id="lmax-descriptor"></a>
     - *Type*: Integer
     - *Description*: control the max angular momentum of descriptor basis. 
     - *Default*: 0
@@ -980,7 +939,7 @@ Warning: this function is not robust enough for version 2.2.0. Please try these
     - *Default*: 0
 
     [back to top](#input-file)
-- model_file<a id="model-file"></a>
+- deepks_model<a id="model-file"></a>
     - *Type*: String
     - *Description*: the path of the trained, traced NN model file (generated by deepks-kit). used when deepks_scf is set to 1.
     - *Default*: None

examples/H2O-deepks-lcao/INPUT

@@ -26,8 +26,8 @@ mixing_beta             0.4
 #Parameters (6.Deepks)
 force			1
 test_force			1
-out_descriptor          1
-lmax_descriptor			2
+deepks_out_labels          1
+deepks_descriptor_lmax			2
 newdm		1
 deepks_scf	1
-model_file	model.ptg
+deepks_model	model.ptg

examples/H2O-deepks-pw/INPUT

@@ -25,5 +25,5 @@ mixing_beta             0.4
 
 #Parameters (6.File)
 out_band                0
-out_descriptor          1 
-lmax_descriptor			2
+deepks_out_labels          1 
+deepks_descriptor_lmax			2

source/CMakeLists.txt

@@ -5,6 +5,7 @@ add_subdirectory(module_neighbor)
 add_subdirectory(module_orbital)
 add_subdirectory(module_md)
 add_subdirectory(module_deepks)
+add_subdirectory(module_xc)
 add_subdirectory(src_io)
 add_subdirectory(src_ions)
 add_subdirectory(src_lcao)

source/Makefile

@@ -15,6 +15,7 @@ VPATH=./src_global\
 :./module_base\
 :./module_md\
 :./module_deepks\
+:./module_xc\
 :./src_pw\
 :./src_lcao\
 :./src_ions\

source/Makefile.Objects

@@ -19,8 +19,7 @@ input_conv.o\
 run_pw.o\
 run_lcao.o\
 
-OBJS_PW=xc_type.o \
-xc_functional.o\
+OBJS_PW=xc_functional.o\
 xc_3.o \
 vdwd2.o\
 vdwd2_parameters.o\
@@ -160,6 +159,7 @@ LCAO_diago.o\
 LCAO_evolve.o\
 LCAO_deepks.o\
 LCAO_deepks_fdelta.o\
+LCAO_deepks_odelta.o\
 LCAO_deepks_io.o\
 LCAO_deepks_mpi.o\
 LCAO_deepks_pdm.o\
@@ -265,7 +265,6 @@ write_HS.o\
 write_HS_R.o\
 write_dm.o\
 write_wfc_realspace.o\
-potential_libxc.o \
 potential_libxc_meta.o \
 efield.o \
 magnetism.o\