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

Author: Qianruipku

.gitignore

@@ -9,3 +9,4 @@ result.out
 .cache
 .vscode
 html
+run.log

CMakeLists.txt

@@ -114,7 +114,7 @@ if(MKLROOT)
   find_package(IntelMKL REQUIRED)
   add_definitions(-D__MKL -DMKL_ILP64)
   include_directories(${MKL_INCLUDE_DIRS} ${MKL_INCLUDE_DIRS}/fftw)
-  
+
   # Since libtorch will find its own MKL, the fftw part conflicts with the original one.
   # When enable deepks, mkl will be linked within ${TORCH_LIBRARIES}.
   if(ENABLE_DEEPKS)
@@ -138,6 +138,11 @@ else()
     LAPACK::LAPACK
     ScaLAPACK::ScaLAPACK
   )
+  if(CMAKE_COMPILER_IS_GNUCXX)
+  target_link_libraries(${ABACUS_BIN_NAME}
+    -lgfortran
+  )
+  endif()
 endif()
 
 if(ENABLE_DEEPKS)
@@ -155,7 +160,7 @@ if(ENABLE_DEEPKS)
   include(FetchContent)
     FetchContent_Declare(
       libnpy
-      GIT_REPOSITORY https://github.com.cnpmjs.org/llohse/libnpy.git
+      GIT_REPOSITORY https://github.com/llohse/libnpy.git
     )
     FetchContent_MakeAvailable(libnpy)
   endif()
@@ -191,6 +196,39 @@ add_compile_definitions(
   TEST_EXX_RADIAL=1
 )
 
+IF (BUILD_TESTING)
+  include(CTest)
+  enable_testing()
+  find_package(Threads)
+  set(CMAKE_CXX_STANDARD_REQUIRED ON)
+  include(FetchContent)
+  FetchContent_Declare(
+    googletest
+    GIT_REPOSITORY https://github.com/google/googletest.git
+    GIT_TAG "origin/main"
+  )
+  FetchContent_MakeAvailable(googletest)
+  # TODO: Find GoogleTest Locally
+
+  add_subdirectory(tests) # Contains integration tests
+
+endif()
+function(AddTest)
+  cmake_parse_arguments(UT "DYN" "TARGET" "LIBS;DYN_LIBS;STATIC_LIBS;SOURCES;DEPENDS" ${ARGN})
+  add_executable(${UT_TARGET} ${UT_SOURCES})
+  #dependencies & link library
+  get_target_property(ABACUS_LINK_LIBRARIES ${ABACUS_BIN_NAME} LINK_LIBRARIES)
+  target_link_libraries(${UT_TARGET} ${UT_LIBS} ${ABACUS_LINK_LIBRARIES}
+    base cell symmetry md symmetry
+    neighbor orb io ions lcao parallel mrrr pdiag pw ri driver
+    pthread gtest_main)
+  install(TARGETS ${UT_TARGET} DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/../../../tests )
+  add_test(NAME ${UT_TARGET}
+    COMMAND ${UT_TARGET}
+    WORKING_DIRECTORY $<TARGET_FILE_DIR:${UT_TARGET}>
+  )
+endfunction(AddTest)
+
 add_subdirectory(source)
 
 target_link_libraries(${ABACUS_BIN_NAME}
@@ -212,19 +250,8 @@ target_link_libraries(${ABACUS_BIN_NAME}
     driver
     -lm
 )
-if(CMAKE_COMPILER_IS_GNUCXX)
-target_link_libraries(${ABACUS_BIN_NAME}
-  -lgfortran
-)
-endif()
 
 install(PROGRAMS ${ABACUS_BIN_PATH}
     TYPE BIN
     #DESTINATION ${CMAKE_INSTALL_BINDIR}
 )
-
-include(CTest)
-enable_testing()
-IF (BUILD_TESTING)
-  add_subdirectory(tests)
-endif()

doc/developers.md

@@ -19,7 +19,38 @@ Raising issues on GitHub is a convernient way to notify the develper team about
 
 ## Modularization and module tests
 
-The ABACUS code is reconstructed to form several self-contained modules. A description of modules can be found in the [installation guide](install.md#structure-of-source-code). We also provide module tests for the modules.
+The ABACUS code is refactored to several self-contained modules. A description of modules can be found in the [installation guide](install.md#structure-of-source-code). We also provide module unit tests.
+
+### Add a unit test
+
+If there are currently no unit tests provided for the module, do as follows. `module_base` provides a simple demonstration.
+
+- Add a folder named `test` under the module.
+- Append the content below to `CMakeLists.txt` of the module:
+
+```cmake
+IF (BUILD_TESTING)
+  add_subdirectory(test)
+endif()
+```
+
+- Add a blank `CMakeLists.txt` under `module*/test`.
+
+To add a unit test:
+
+- Write your test under `GoogleTest` framework.
+- Add your testing source code with suffix `*_test.cpp` in `test` directory.
+- Append the content below to `CMakeLists.txt` of the module:
+
+```cmake
+AddTest(
+  TARGET <module_name>_<test_name> # this is the executable file name of the test
+  SOURCES <test_name>.cpp
+)
+```
+
+- Build with `-D BUILD_TESTING=1` flag. You can find built testing programs under `build/source/<module_name>/test`.
+- Follow the installing procedure of CMake. The tests will move to `build/test`.
 
 [back to top](#for-developers)
 
@@ -91,7 +122,7 @@ For comments that need to be shown in documents, these formats should be used --
 
 A helpful VS Code extension -- Doxygen Documentation Generator, can help you formating comments.
 
-An practical example is class [LCAO_Descriptor](https://github.com/deepmodeling/abacus-develop/blob/deepks/source/src_lcao/LCAO_descriptor.h), the effects can be seen on [readthedocs page](https://abacus-deepks.readthedocs.io/en/latest/DeePKS_API/classLCAO__Descriptor.html#exhale-class-classLCAO-Descriptor)
+An practical example is class [LCAO_Deepks](https://github.com/deepmodeling/abacus-develop/blob/deepks/source/module_deepks/LCAO_deepks.h), the effects can be seen on [readthedocs page](https://abacus-deepks.readthedocs.io/en/latest/DeePKS_API/classLCAO__Descriptor.html#exhale-class-classLCAO-Descriptor)
 
 - Detailed Comment Block
 

doc/examples/md.md

@@ -38,7 +38,7 @@ md_dt               1    //time step
 md_tfirst           700  //the first target temperature
 md_rstmd            0    //whether restart md
 md_qmass            1    //mass of themostat
-md_dumpmdfred       10   //The period to dump MD information for monitoring and restarting MD
+md_dumpfred       10   //The period to dump MD information for monitoring and restarting MD
 ```
 
 These MD parameters means that ABACUS will use NVT ensemble with Nosé-hoover themostat; the time step is 1fs, and target temperature is 700K; start renew without restart file, set the mass of themostat as 1g/mol, and calculate the MSD and diffusion coefficent from first step.
@@ -50,7 +50,7 @@ Note: *Please turn off symmetry when do MD simulation.*
 - md_tfirst : target temperature in md simulation(K), you should set parameter md_tlast and md_fixtemperature when you want to change temperature during md simulation.
 - md_rstmd : 0, no need of restart ; 1, restart with restart file, you must repalce STRU file with STRU_MD before you run the restart task.
 - md_qmass : mass of thermostat, set by experience, if you don’t know how to set, set it to 0 will have a number autosetted by ABACUS
-- md_dumpmdfred : frequency for output consequence of md simulation
+- md_dumpfred : frequency for output consequence of md simulation
 
 The STRU file is:
 ```

doc/examples/tddft.md

@@ -35,7 +35,7 @@ md_nresn 3
 md_nyosh 3
 md_qmass 0
 md_tlast 30
-md_dumpmdfred 1
+md_dumpfred 1
 md_domsd 0
 md_domsdatom 0
 md_outputstressperiod 0

doc/input-main.md

@@ -43,7 +43,7 @@
 
     - [Molecular dynamics](#molecular-dynamics)
 
-        [md_type](#md-type) | [md_potential](#md-potential) | [md_rstmd](#md-rstmd) | [md_dt](#md_dt) | [md_t](#md-t) | [md_qmass](#md-qmass) | [md_dumpmdfred](#md-dumpmdfred) | [md_tfreq](#md-tfreq) | [md_fixtemperature](#md-fixtemperature) | [NVT_control](#nvt-control) | [NVT_tau](#nvt-tau) | [MNHC](#mnhc) | [md_ediff](#md-ediff) | [md_ediffg](#md-ediffg) | [rcut_lj](#rcut_lj) | [epsilon_lj](#epsilon_lj) | [sigma_lj](#sigma_lj) | [direction](#direction) | [velocity](#velocity) | [viscosity](#viscosity) | [tscale](#tscale) | [damp](#damp)
+        [md_type](#md-type) | [md_potential](#md-potential) | [md_rstmd](#md-rstmd) | [md_dt](#md_dt) | [md_t](#md-t) | [md_qmass](#md-qmass) | [md_dumpfred](#md-dumpfred) | [md_rstfred](#md-rstfred) | [md_tfreq](#md-tfreq) | [MNHC](#mnhc) | [rcut_lj](#rcut_lj) | [epsilon_lj](#epsilon_lj) | [sigma_lj](#sigma_lj) | [direction](#direction) | [velocity](#velocity) | [viscosity](#viscosity) | [tscale](#tscale) | [damp](#damp)
 
     - [DFT+U correction](#DFT_U-correction)
 
@@ -1157,45 +1157,26 @@ This part of variables are used to control the molecular dynamics calculations.
     - *Default*: No default
 
     [back to top](#input-file)
-- md_dumpmdfred<a id="md-dumpmdfred"></a>
+- md_dumpfred<a id="md-dumpfred"></a>
     - *Type*: Integer
-    - *Description*:This is the steps to control the frequence to output md information
+    - *Description*:This is the frequence to dump md information.
     - *Default*: 1
 
     [back to top](#input-file)
 
-- md_tfreq<a id="md-tfreq"></a>
-    - *Type*: Real
-    - *Description*: 
-        - Oscillation frequency, used to determine Qmass of NHC; 
-        - 1/(md_tfreq*md_dt) is collision probability in Anderson method.
-    - *Default*: 1.0
-
-    [back to top](#input-file)
-
-- md_fixtemperature<a id="md-fixtemperature"></a>
-    - *Type*: Integer
-    - *Description*:
-        - n:when set to n (n > 1), ABACUS will read the file "ChangeTemp.dat" and change system’s temperature every n steps
-        - 0,1:When set to 0 or 1, ABACUS won’t change the temperature during running MD.
-    - *Default*: 1
-
-    [back to top](#input-file)
-
-- NVT_control<a id="nvt-control"></a> 
+- md_rstfred<a id="md-rstfred"></a>
     - *Type*: Integer
-    - *Description*: Specifies which type of thermostat is used.
-        - 1: Nose-Hoover-chains
-        - 2: Langevin
-        - 3: Andersen
+    - *Description*:This is the frequence to output restart information.
     - *Default*: 1
 
     [back to top](#input-file)
 
-- NVT_tau<a id="nvt-tau"></a>
+- md_tfreq<a id="md-tfreq"></a>
     - *Type*: Real
-    - *Description*: Parameter for adjust effect of thermostat corresponding to the time scale of collision, in fs. If te input value is less than 1d-10, then it is automatically set in ABACUS.
-    - *Default*: 0 
+    - *Description*: 
+        - Oscillation frequency, used to determine Qmass of NHC; 
+        - 1/(md_tfreq*md_dt) is collision probability in Anderson method.
+    - *Default*: 1.0
 
     [back to top](#input-file)
 
@@ -1206,20 +1187,6 @@ This part of variables are used to control the molecular dynamics calculations.
 
     [back to top](#input-file)
 
-- md_ediff<a id="md-ediff"></a>
-    - *Type*: Real
-    - *Description*: Parameter for constraining total energy change.
-    - *Default*: 0.0001
-
-    [back to top](#input-file)
-
-- md_ediffg<a id="md-ediffg"></a>
-    - *Type*: Real
-    - *Description*: Parameter for constraining max force change
-    - *Default*: 0.001
-
-    [back to top](#input-file)
-
 - rcut_lj<a id="rcut_lj"></a>
     - *Type*: Real
     - *Description*: Cut-off radius for Leonard Jones potential (angstrom).

source/CMakeLists.txt

@@ -4,6 +4,7 @@ add_subdirectory(module_symmetry)
 add_subdirectory(module_neighbor)
 add_subdirectory(module_orbital)
 add_subdirectory(module_md)
+add_subdirectory(module_deepks)
 add_subdirectory(src_io)
 add_subdirectory(src_ions)
 add_subdirectory(src_lcao)

source/Makefile

@@ -14,6 +14,7 @@ VPATH=./src_global\
 :./module_cell\
 :./module_base\
 :./module_md\
+:./module_deepks\
 :./src_pw\
 :./src_lcao\
 :./src_ions\

source/Makefile.Objects

@@ -160,10 +160,14 @@ LCAO_matrix.o\
 LCAO_nnr.o \
 LCAO_diago.o\
 LCAO_evolve.o\
-LCAO_descriptor.o\
-LCAO_descriptor_old.o\
-LCAO_descriptor_io.o\
-LCAO_descriptor_dV.o\
+LCAO_deepks.o\
+LCAO_deepks_fdelta.o\
+LCAO_deepks_io.o\
+LCAO_deepks_mpi.o\
+LCAO_deepks_pdm.o\
+LCAO_deepks_psialpha.o\
+LCAO_deepks_torch.o\
+LCAO_deepks_vdelta.o\
 ylm.o\
 FORCE_STRESS.o\
 FORCE_gamma.o\
@@ -226,7 +230,6 @@ parallel_reduce.o\
 parallel_pw.o\
 ft.o\
 parallel_grid.o\
-parallel_deepks.o \
 
 OBJS_FIRST_PRINCIPLES=$(OBJS_MAIN)\
 $(OBJS_PW)\
@@ -246,6 +249,16 @@ read_rho.o\
 read_atoms.o\
 read_cell_pseudopots.o\
 read_dm.o\
+read_txt_tools.o\
+read_txt_stru.o\
+read_txt_input_value.o\
+read_txt_input_item.o\
+read_txt_input_list.o\
+read_txt_input_process.o\
+read_txt_input_process_global.o\
+read_txt_input-general.o\
+read_txt_input-pw.o\
+read_txt_input-spectrum.o\
 write_pot.o\
 write_rho.o\
 write_rho_cube.o\

source/input.cpp

@@ -1145,14 +1145,6 @@ bool Input::Read(const std::string &fn)
 		{
 			read_value(ifs, mdp.mdtype);
 		}
-		else if (strcmp("nvt_tau",word) == 0)
-		{
-			read_value(ifs, mdp.NVT_tau);
-		}
-		else if (strcmp("nvt_control",word) == 0)
-		{
-			read_value(ifs,mdp.NVT_control );
-		}
 		else if (strcmp("md_dt",word) == 0)
 		{
 			read_value(ifs, mdp.dt);
@@ -1173,30 +1165,18 @@ bool Input::Read(const std::string &fn)
 		{
 			read_value(ifs,mdp.tlast );
 		}
-		else if (strcmp("md_dumpmdfred",word) == 0)
+		else if (strcmp("md_dumpfred",word) == 0)
 		{
-			read_value(ifs, mdp.recordFreq);
+			read_value(ifs, mdp.dumpfreq);
 		}
-		else if (strcmp("md_mdoutpath",word) == 0)
+		else if (strcmp("md_rstfred",word) == 0)
 		{
-			read_value(ifs,mdp.mdoutputpath );
+			read_value(ifs, mdp.rstfreq);
 		}
 		else if (strcmp("md_rstmd",word) == 0)
 		{
 			read_value(ifs,mdp.rstMD );
 		}
-		else if (strcmp("md_fixtemperature",word) == 0)
-		{
-			read_value(ifs,mdp.fixTemperature );
-		}
-		else if (strcmp("md_ediff",word) == 0)
-		{
-			read_value(ifs,mdp.ediff );
-		}
-		else if (strcmp("md_ediffg",word) == 0)
-		{
-			read_value(ifs,mdp.ediffg );
-		}
 		//added by zheng daye
 //----------------------------------------------------------
 // Classic MD
@@ -2153,19 +2133,14 @@ void Input::Bcast()
 */
 	//zheng daye add 2014/5/5
         Parallel_Common::bcast_int(mdp.mdtype);
-        Parallel_Common::bcast_double(mdp.NVT_tau);
-        Parallel_Common::bcast_int(mdp.NVT_control);
         Parallel_Common::bcast_double(mdp.dt);
         Parallel_Common::bcast_int(mdp.MNHC);
         Parallel_Common::bcast_double(mdp.Qmass);
         Parallel_Common::bcast_double(mdp.tfirst);
         Parallel_Common::bcast_double(mdp.tlast);
-        Parallel_Common::bcast_int(mdp.recordFreq);
-        Parallel_Common::bcast_string(mdp.mdoutputpath);
+        Parallel_Common::bcast_int(mdp.dumpfreq);
+		Parallel_Common::bcast_int(mdp.rstfreq);
         Parallel_Common::bcast_int(mdp.rstMD);
-        Parallel_Common::bcast_int(mdp.fixTemperature);
-        Parallel_Common::bcast_double(mdp.ediff);
-        Parallel_Common::bcast_double(mdp.ediffg);
 		Parallel_Common::bcast_double(mdp.rcut_lj);
 		Parallel_Common::bcast_double(mdp.epsilon_lj);
 		Parallel_Common::bcast_double(mdp.sigma_lj);