Merge branch 'develop' into deepks_append_npy

Author: xuan112358

docs/CONTRIBUTING.md

@@ -46,11 +46,11 @@ For those who are interested in the source code, the following figure shows the
 |   |                           (4) Utility functions: timer, random number generator, etc.
 |   |                           (5) Global parameters: input parameters, element names, mathematical and physical constants.
 |   |-- module_container        The container module for storing data and performing operations on them and on different architectures.
-|-- module_basis                Basis means the basis set to expand the wave function.
+|-- source_basis                Basis means the basis set to expand the wave function.
 |   |-- module_ao               Atomic orbital basis set to be refactored.
 |   |-- module_nao              New numerical atomic orbital basis set for two-center integrals in LCAO calculations
 |   `-- module_pw               Data structures and relevant methods for planewave involved calculations
-|-- module_cell                 The module for defining the unit cell and its operations, and reading pseudopotentials.
+|-- source_cell                 The module for defining the unit cell and its operations, and reading pseudopotentials.
 |   |-- module_neighbor         The module for finding the neighbors of each atom in the unit cell.
 |   |-- module_paw              The module for performing PAW calculations.
 |   |-- module_symmetry         The module for finding the symmetry operations of the unit cell.
@@ -257,7 +257,7 @@ To add a unit test:
     ./cell_unitcell_test
     ```
 
-    under the directory of `build/source/module_cell/test` to run the test `cell_unitcell_test`.
+    under the directory of `build/source/source_cell/test` to run the test `cell_unitcell_test`.
     However, it is more convenient to run unit tests with `ctest` command under the `build` directory. You can check all unit tests by
 
     ```bash

docs/advanced/input_files/input-main.md

@@ -2146,7 +2146,7 @@ Warning: this function is not robust enough for the current version. Please try
 - **Description**: Print labels and descriptors for DeePKS in OUT.${suffix}. The names of these files start with "deepks".
   - 0 : No output.
   - 1 : Output intermediate files needed during DeePKS training.
-  - 2 : Output target labels for label preperation. The label files are named as `deepks_<property>.npy`, where the units and formats are the same as label files `<property>.npy` required for training, except that the first dimension (`nframes`) is excluded. System structrue files are also given in `deepks_atom.npy` and `deepks_box.npy` in the unit of *Bohr*, which means `lattice_constant` should be set to 1 when training. 
+  - 2 : Output target labels for label preperation. The label files are named as `deepks_<property>.npy` or `deepks_<property>.csr`, where the units and formats are the same as label files `<property>.npy` or `<property>.csr` required for training, except that the first dimension (`nframes`) is excluded. System structrue files are also given in `deepks_atom.npy` and `deepks_box.npy` in the unit of *Bohr*, which means `lattice_constant` should be set to 1 when training. 
 - **Note**: When `deepks_out_labels` equals **1**, the path of a numerical descriptor (an `orb` file) is needed to be specified under the `NUMERICAL_DESCRIPTOR` tag in the `STRU` file. For example:
 
   ```text
@@ -2260,8 +2260,11 @@ Warning: this function is not robust enough for the current version. Please try
 
 - **Type**: int
 - **Availability**: numerical atomic orbital basis
-- **Description**: Include V_delta label for DeePKS training. When `deepks_out_labels` is true and `deepks_v_delta` > 0, ABACUS will output h_base.npy, v_delta.npy and h_tot.npy(h_tot=h_base+v_delta). 
-  Meanwhile, when `deepks_v_delta` equals 1, ABACUS will also output v_delta_precalc.npy, which is used to calculate V_delta during DeePKS training. However, when the number of atoms grows, the size of v_delta_precalc.npy will be very large. In this case, it's recommended to set `deepks_v_delta` as 2, and ABACUS will output phialpha.npy and grad_evdm.npy but not v_delta_precalc.npy. These two files are small and can be used to calculate v_delta_precalc in the procedure of training DeePKS.
+- **Description**: Include V_delta/V_delta_R (Hamiltonian in k/real space) label for DeePKS training. When `deepks_out_labels` is true and `deepks_v_delta` > 0 (k space), ABACUS will output `deepks_hbase.npy`, `deepks_vdelta.npy` and `deepks_htot.npy`(htot=hbase+vdelta). When `deepks_out_labels` is true and `deepks_v_delta` < 0 (real space), ABACUS will output `deepks_hrtot.csr`, `deepks_hrdelta.csr`. Some more files output for different settings.
+  - `deepks_v_delta` = 1: `deepks_vdpre.npy`, which is used to calculate V_delta during DeePKS training.
+  - `deepks_v_delta` = 2: `deepks_phialpha.npy` and `deepks_gevdm.npy`, which can be used to calculate `deepks_vdpre.npy`. A recommanded method for memory saving.
+  - `deepks_v_delta` = -1: `deepks_vdrpre.npy`, which is used to calculate V_delta_R during DeePKS training.
+  - `deepks_v_delta` = -2: `deepks_phialpha_r.npy` and `deepks_gevdm.npy`, which can be used to calculate `deepks_vdrpre.npy`. A recommanded method for memory saving.
 - **Default**: 0
 
 ### deepks_out_unittest

python/pyabacus/CMakeLists.txt

@@ -13,7 +13,7 @@ find_package(pybind11 CONFIG REQUIRED)
 # set source path
 set(ABACUS_SOURCE_DIR "${PROJECT_SOURCE_DIR}/../../source")
 set(BASE_PATH "${ABACUS_SOURCE_DIR}/source_base")
-set(NAO_PATH "${ABACUS_SOURCE_DIR}/module_basis/module_nao")
+set(NAO_PATH "${ABACUS_SOURCE_DIR}/source_basis/module_nao")
 set(HSOLVER_PATH "${ABACUS_SOURCE_DIR}/source_hsolver")
 set(PSI_PATH "${ABACUS_SOURCE_DIR}/module_psi")
 set(ENABLE_LCAO ON)
@@ -82,7 +82,7 @@ set(PARAMETER_BINARY_DIR "${PROJECT_SOURCE_DIR}/build/parameter")
 add_subdirectory(${ABACUS_SOURCE_DIR}/module_parameter ${PARAMETER_BINARY_DIR})
 # add orb
 set(ORB_BINARY_DIR "${PROJECT_SOURCE_DIR}/build/orb")
-add_subdirectory(${ABACUS_SOURCE_DIR}/module_basis/module_ao ${ORB_BINARY_DIR})
+add_subdirectory(${ABACUS_SOURCE_DIR}/source_basis/module_ao ${ORB_BINARY_DIR})
 # set(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE)
 
 # set RPATH

python/pyabacus/CONTRIBUTING.md

@@ -73,7 +73,7 @@ find_package(pybind11 CONFIG REQUIRED)
 # Set source path
 set(ABACUS_SOURCE_DIR "${PROJECT_SOURCE_DIR}/../../source")
 set(BASE_PATH "${ABACUS_SOURCE_DIR}/source_base")
-set(NAO_PATH "${ABACUS_SOURCE_DIR}/module_basis/module_nao")
+set(NAO_PATH "${ABACUS_SOURCE_DIR}/source_basis/module_nao")
 set(HSOLVER_PATH "${ABACUS_SOURCE_DIR}/source_hsolver")
 set(PSI_PATH "${ABACUS_SOURCE_DIR}/module_psi")
 set(ENABLE_LCAO ON)
@@ -147,7 +147,7 @@ set(PARAMETER_BINARY_DIR "${PROJECT_SOURCE_DIR}/build/parameter")
 add_subdirectory(${ABACUS_SOURCE_DIR}/module_parameter ${PARAMETER_BINARY_DIR})
 # Add orb
 set(ORB_BINARY_DIR "${PROJECT_SOURCE_DIR}/build/orb")
-add_subdirectory(${ABACUS_SOURCE_DIR}/module_basis/module_ao ${ORB_BINARY_DIR})
+add_subdirectory(${ABACUS_SOURCE_DIR}/source_basis/module_ao ${ORB_BINARY_DIR})
 ```
 - This section sets the position-independent code flag and adds subdirectories for the base, parameter, and orb modules. It specifies the build directories for these modules.
 

python/pyabacus/src/ModuleNAO/py_m_nao.cpp

@@ -3,8 +3,8 @@
 #include <pybind11/stl.h>
 
 #include "source_base/vector3.h"
-#include "module_basis/module_nao/radial_collection.h"
-#include "module_basis/module_nao/two_center_integrator.h"
+#include "source_basis/module_nao/radial_collection.h"
+#include "source_basis/module_nao/two_center_integrator.h"
 
 namespace py = pybind11;
 using namespace pybind11::literals;

python/pyabacus/src/py_numerical_radial.cpp

@@ -1,7 +1,7 @@
 #include <pybind11/numpy.h>
 #include <pybind11/pybind11.h>
 
-#include "module_basis/module_nao/numerical_radial.h"
+#include "source_basis/module_nao/numerical_radial.h"
 
 namespace py = pybind11;
 using namespace pybind11::literals;

source/CMakeLists.txt

@@ -1,15 +1,15 @@
 add_subdirectory(source_base)
-add_subdirectory(module_cell)
+add_subdirectory(source_cell)
 add_subdirectory(module_psi)
 add_subdirectory(module_elecstate)
 add_subdirectory(module_hamilt_general)
 add_subdirectory(module_hamilt_pw)
 add_subdirectory(module_hamilt_lcao)
 add_subdirectory(source_hsolver)
-add_subdirectory(module_basis/module_ao)
-add_subdirectory(module_basis/module_nao)
+add_subdirectory(source_basis/module_ao)
+add_subdirectory(source_basis/module_nao)
 add_subdirectory(module_md)
-add_subdirectory(module_basis/module_pw)
+add_subdirectory(source_basis/module_pw)
 add_subdirectory(source_esolver)
 add_subdirectory(module_hamilt_lcao/module_gint)
 add_subdirectory(module_io)
@@ -34,7 +34,7 @@ list(APPEND device_srcs
   module_hamilt_pw/hamilt_pwdft/kernels/ekinetic_op.cpp
   module_hamilt_pw/hamilt_pwdft/kernels/meta_op.cpp
   module_hamilt_pw/hamilt_stodft/kernels/hpsi_norm_op.cpp
-  module_basis/module_pw/kernels/pw_op.cpp
+  source_basis/module_pw/kernels/pw_op.cpp
   source_hsolver/kernels/dngvd_op.cpp
   source_hsolver/kernels/bpcg_kernel_op.cpp
   module_elecstate/kernels/elecstate_op.cpp
@@ -64,7 +64,7 @@ if(USE_CUDA)
     module_hamilt_pw/hamilt_pwdft/kernels/cuda/meta_op.cu
     module_hamilt_pw/hamilt_stodft/kernels/cuda/hpsi_norm_op.cu
     module_hamilt_pw/hamilt_pwdft/kernels/cuda/onsite_op.cu
-    module_basis/module_pw/kernels/cuda/pw_op.cu
+    source_basis/module_pw/kernels/cuda/pw_op.cu
     source_hsolver/kernels/cuda/dngvd_op.cu
     source_hsolver/kernels/cuda/bpcg_kernel_op.cu
     module_elecstate/kernels/cuda/elecstate_op.cu
@@ -91,7 +91,7 @@ if(USE_ROCM)
     module_hamilt_pw/hamilt_pwdft/kernels/rocm/meta_op.hip.cu
     module_hamilt_pw/hamilt_pwdft/kernels/rocm/onsite_op.hip.cu
     module_hamilt_pw/hamilt_stodft/kernels/rocm/hpsi_norm_op.hip.cu
-    module_basis/module_pw/kernels/rocm/pw_op.hip.cu
+    source_basis/module_pw/kernels/rocm/pw_op.hip.cu
     source_hsolver/kernels/rocm/dngvd_op.hip.cu
     source_hsolver/kernels/rocm/bpcg_kernel_op.hip.cu
     module_elecstate/kernels/rocm/elecstate_op.hip.cu

source/Makefile.Objects

@@ -13,11 +13,11 @@ HEADERS = source_main/*.h
 
 VPATH=./src_global:\
 ./source_main:\
-./module_basis/module_ao:\
-./module_basis/module_nao:\
-./module_cell/module_neighbor:\
-./module_cell/module_symmetry:\
-./module_cell:\
+./source_basis/module_ao:\
+./source_basis/module_nao:\
+./source_cell/module_neighbor:\
+./source_cell/module_symmetry:\
+./source_cell:\
 ./source_base:\
 ./source_base/kernels:\
 ./source_base/module_container/base/core:\
@@ -27,8 +27,8 @@ VPATH=./src_global:\
 ./source_base/module_device:\
 ./source_base/module_mixing:\
 ./module_md:\
-./module_basis/module_pw:\
-./module_basis/module_pw/module_fft:\
+./source_basis/module_pw:\
+./source_basis/module_pw/module_fft:\
 ./source_esolver:\
 ./source_hsolver:\
 ./source_hsolver/kernels:\

source/module_elecstate/cal_nelec_nband.h

@@ -1,7 +1,7 @@
 #ifndef CAL_NELEC_NBAND_H
 #define CAL_NELEC_NBAND_H
 
-#include "module_cell/atom_spec.h"
+#include "source_cell/atom_spec.h"
 
 namespace elecstate {
 

source/module_elecstate/cal_ux.h

@@ -1,7 +1,7 @@
 #ifndef CAL_UX_H
 #define CAL_UX_H
 
-#include "module_cell/unitcell.h"
+#include "source_cell/unitcell.h"
 
 namespace elecstate {