merge TD and dev and solve conflicts

Author: maki49

.github/workflows/test.yml

@@ -27,7 +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()

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

@@ -62,7 +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) | [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)
 
@@ -919,7 +919,7 @@ This part of variables are used to control the calculation of DOS.
 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: 
     ```
@@ -933,7 +933,7 @@ 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
@@ -945,7 +945,7 @@ 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/Makefile.Objects

@@ -121,7 +121,6 @@ gint_k_init.o\
 gint_k_vl.o\
 gint_k_rho.o\
 gint_k_fvl.o\
-grid_base.o\
 grid_base_beta.o\
 ORB_control.o\
 ORB_read.o\
@@ -158,6 +157,7 @@ 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\

source/input.cpp

@@ -240,8 +240,11 @@ void Input::Default(void)
     out_charge = 0;
 	out_dm = 0;
 
-	out_descriptor = 0; // caoyu added 2020-11-24, mohan added 2021-01-03
-	lmax_descriptor = 2; // mohan added 2021-01-03
+	deepks_out_labels = 0; // caoyu added 2020-11-24, mohan added 2021-01-03
+	deepks_scf = 0;
+	deepks_bandgap = 0;
+	deepks_out_unittest = 0;
+	deepks_descriptor_lmax = 2; // mohan added 2021-01-03
 
     out_potential = 0;
     out_wf = 0;
@@ -912,22 +915,30 @@ bool Input::Read(const std::string &fn)
         {
             read_value(ifs, out_dm);
         }
-        else if (strcmp("out_descriptor", word) == 0) // caoyu added 2020-11-24, mohan modified 2021-01-03
+        else if (strcmp("deepks_out_labels", word) == 0) // caoyu added 2020-11-24, mohan modified 2021-01-03
         {
-            read_value(ifs, out_descriptor);
+            read_value(ifs, deepks_out_labels);
         }
-        else if (strcmp("lmax_descriptor", word) == 0)// mohan added 2021-01-03
-        {
-            read_value(ifs, lmax_descriptor);
-		}
-		else if (strcmp("deepks_scf", word) == 0) // caoyu added 2021-06-02
+		else if (strcmp("deepks_scf", word) == 0) // caoyu added 2020-11-24, mohan modified 2021-01-03
         {
             read_value(ifs, deepks_scf);
+        }
+		else if (strcmp("deepks_bandgap", word) == 0) // caoyu added 2020-11-24, mohan modified 2021-01-03
+        {
+            read_value(ifs, deepks_bandgap);
+        }
+        else if (strcmp("deepks_out_unittest", word) == 0)// mohan added 2021-01-03
+        {
+            read_value(ifs, deepks_out_unittest);
 		}
-		else if (strcmp("model_file", word) == 0) // caoyu added 2021-06-03
+		else if (strcmp("deepks_model", word) == 0) // caoyu added 2021-06-03
         {
-            read_value(ifs, model_file);
+            read_value(ifs, deepks_model);
         }
+		else if (strcmp("deepks_descriptor_lmax", word) == 0) // QO added 2021-12-15
+        {
+            read_value(ifs, deepks_descriptor_lmax);
+		}
 		else if (strcmp("out_potential", word) == 0)
         {
             read_value(ifs, out_potential);
@@ -1840,16 +1851,19 @@ void Input::Bcast()
     Parallel_Common::bcast_string( charge_extrap );//xiaohui modify 2015-02-01
     Parallel_Common::bcast_int( out_charge );
     Parallel_Common::bcast_int( out_dm );
-    Parallel_Common::bcast_int( out_descriptor ); // caoyu added 2020-11-24, mohan modified 2021-01-03
-    Parallel_Common::bcast_int( lmax_descriptor ); // mohan modified 2021-01-03
-    Parallel_Common::bcast_int( deepks_scf ); // caoyu add 2021-06-02
-	Parallel_Common::bcast_string( model_file ); //  caoyu add 2021-06-03
+
+    Parallel_Common::bcast_bool( deepks_out_labels ); // caoyu added 2020-11-24, mohan modified 2021-01-03
+	Parallel_Common::bcast_bool( deepks_scf );
+	Parallel_Common::bcast_bool( deepks_bandgap );
+	Parallel_Common::bcast_bool( deepks_out_unittest );
+	Parallel_Common::bcast_string( deepks_model );
+	Parallel_Common::bcast_int( deepks_descriptor_lmax );
 
 	Parallel_Common::bcast_int(out_potential);
     Parallel_Common::bcast_int( out_wf );
     Parallel_Common::bcast_int( out_wf_r );
 	Parallel_Common::bcast_int( out_dos );
-        Parallel_Common::bcast_int( out_band );
+	Parallel_Common::bcast_int( out_band );
 	Parallel_Common::bcast_int( out_hs );
 	Parallel_Common::bcast_int( out_hs2 ); //LiuXh add 2019-07-15
 	Parallel_Common::bcast_int( out_r_matrix ); // jingan add 2019-8-14

source/input.h

@@ -372,10 +372,18 @@ class Input
 //==========================================================
 // DeepKS -- added by caoyu and mohan
 //==========================================================
-    int out_descriptor; // (need libnpy) output descritpor for deepks. caoyu added 2020-11-24, mohan modified 2021-01-03
-	int lmax_descriptor; //lmax used in descriptor, mohan added 2021-01-03
-	int deepks_scf;	//(need libnpy and libtorch) if set 1, a trained model would be needed to cal V_delta and F_delta
-	string model_file;		//needed when deepks_scf=1
+    bool deepks_out_labels; // (need libnpy) prints energy and force labels and descriptors for training, wenfei 2022-1-12
+	bool deepks_scf;	//(need libnpy and libtorch) if set 1, a trained model would be needed to cal V_delta and F_delta
+	bool deepks_bandgap; //for bandgap label. QO added 2021-12-15	
+	
+	bool deepks_out_unittest; //if set 1, prints intermediate quantities that shall be used for making unit test
+
+	string deepks_model;		//needed when deepks_scf=1
+
+	//the following 3 are used when generating jle.orb
+	int deepks_descriptor_lmax; //lmax used in descriptor, mohan added 2021-01-03
+	double deepks_descriptor_rcut;
+	double deepks_descriptor_ecut;
 
 //==========================================================
 // variables for test only