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

 into refactor

docs/advanced/input_files/input-main.md

@@ -423,6 +423,7 @@
     - [pexsi\_zero\_thr](#pexsi_zero_thr)
   - [Linear Response TDDFT](#linear-response-tddft)
     - [xc\_kernel](#xc_kernel)
+    - [lr\_init\_xc\_kernel](#lr_init_xc_kernel)
     - [lr\_solver](#lr_solver)
     - [lr\_thr](#lr_thr)
     - [nocc](#nocc)
@@ -3943,6 +3944,15 @@ These parameters are used to solve the excited states using. e.g. LR-TDDFT.
 Currently supported: `RPA`, `LDA`, `PBE`, `HSE`, `HF`.
 - **Default**: LDA
 
+### lr_init_xc_kernel
+
+- **Type**: String
+- **Description**: The method to initalize the xc kernel. 
+  - "default": Calculate xc kerenel ($f_\text{xc}$) from the ground-state charge density.
+  - "file": Read the xc kernel $f_\text{xc}$ on grid from the provided files. The following words should be the paths of ".cube" files, where the first 1 (*[nspin](#nspin)==1*) or 3 (*[nspin](#nspin)==2*, namely spin-aa, spin-ab and spin-bb) will be read in. The parameter [xc_kernel](#xc_kernel) will be invalid. Now only LDA-type kernel is supproted as the potential will be calculated by directly multiplying the transition density.
+  - "from_charge_file": Calculate fxc from the charge density read from the provided files. The following words should be the paths of ".cube" files, where the first [nspin]($nspin) files will be read in. 
+- **Default**: "default"
+
 ### lr_solver
 
 - **Type**: String

examples/bsse/water/result.ref

@@ -1,5 +1,5 @@
--13.31798074740440
-E_H2O: -466.1225988776397
-E_O: -427.6271689751553
-E_H1: -12.58872469295076
-E_H2: -12.58872446212924
+-13.49968292248493
+E_H2O: -466.1225988772539
+E_O: -427.5222287307378
+E_H1: -12.55034372743879
+E_H2: -12.55034349659238

examples/scf/lcao_Cu/INPUT

@@ -4,7 +4,6 @@ orbital_dir                 ../../../tests/PP_ORB
 nbands		10
 
 calculation	scf
-ecutwfc		100 
 ecutwfc		100 ###Energy cutoff needs to be tested to ensure your calculation is reliable.[1]
 scf_thr		1.0e-8
 scf_nmax	100

source/Makefile.Objects

@@ -725,7 +725,7 @@ OBJS_TENSOR=tensor.o\
     dmr_complex.o\
     operator_lr_hxc.o\
     operator_lr_exx.o\
-    kernel_xc.o\
+    xc_kernel.o\
     pot_hxc_lrtd.o\
     lr_spectrum.o\
     hamilt_casida.o\

source/module_base/module_mixing/mixing_data.cpp

@@ -3,7 +3,7 @@
 namespace Base_Mixing
 {
 
-Mixing_Data::Mixing_Data(const int& ndim, const int& length, const size_t& type_size)
+Mixing_Data::Mixing_Data(const int& ndim, const std::size_t& length, const size_t& type_size)
 {
     this->ndim_tot = ndim;
     this->length = length;
@@ -15,16 +15,18 @@ Mixing_Data::Mixing_Data(const int& ndim, const int& length, const size_t& type_
 
 Mixing_Data::~Mixing_Data()
 {
-    if (this->data != nullptr)
+    if (this->data != nullptr) {
         free(this->data);
 }
+}
 
-void Mixing_Data::resize(const int& ndim, const int& length, const size_t& type_size)
+void Mixing_Data::resize(const int& ndim, const std::size_t& length, const size_t& type_size)
 {
     this->ndim_tot = ndim;
     this->length = length;
-    if (this->data != nullptr)
+    if (this->data != nullptr) {
         free(this->data);
+}
     if (ndim * length > 0)
     {
         this->data = malloc(ndim * length * type_size);

source/module_base/module_mixing/mixing_data.h

@@ -22,7 +22,7 @@ class Mixing_Data
      * @param type_size size of type
      *
      */
-    Mixing_Data(const int& ndim, const int& length, const size_t& type_size);
+    Mixing_Data(const int& ndim, const std::size_t& length, const size_t& type_size);
 
     /**
      * @brief Destroy the Mixing_Data object
@@ -38,7 +38,7 @@ class Mixing_Data
      * @param type_size size of type
      *
      */
-    void resize(const int& ndim, const int& length, const size_t& type_size);
+    void resize(const int& ndim, const std::size_t& length, const size_t& type_size);
 
     /**
      * @brief push data to the tensor
@@ -54,7 +54,7 @@ class Mixing_Data
 #ifdef _OPENMP
 #pragma omp parallel for schedule(static, 4096/sizeof(FPTYPE))
 #endif
-        for (int i = 0; i < length; ++i)
+        for (std::size_t i = 0; i < length; ++i)
         {
             FP_startdata[i] = data_in[i];
         }
@@ -86,7 +86,7 @@ class Mixing_Data
     // the number of vectors for mixing
     int ndim_tot = 0;
     // the length of each vector
-    int length = 0;
+    std::size_t length = 0;
     // the start index for vector: start = this->index_move(0)
     int start = -1;
     // the number of used vectors for mixing

source/module_base/module_mixing/pulay_mixing.cpp

@@ -28,13 +28,13 @@ void Pulay_Mixing::tem_push_data(Mixing_Data& mdata,
                                  std::function<void(FPTYPE*, const FPTYPE*, const FPTYPE*)> mix,
                                  const bool& need_calcoef)
 {
-    const size_t length = mdata.length;
+    const std::size_t length = mdata.length;
     std::vector<FPTYPE> F_tmp(length);
 
 #ifdef _OPENMP
 #pragma omp parallel for schedule(static, 4096 / sizeof(FPTYPE))
 #endif
-    for (int i = 0; i < length; ++i)
+    for (std::size_t i = 0; i < length; ++i)
     {
         F_tmp[i] = data_out[i] - data_in[i];
     }
@@ -69,7 +69,7 @@ void Pulay_Mixing::tem_push_data(Mixing_Data& mdata,
 #ifdef _OPENMP
 #pragma omp parallel for schedule(static, 4096 / sizeof(FPTYPE))
 #endif
-        for (int i = 0; i < length; ++i)
+        for (std::size_t i = 0; i < length; ++i)
         {
             FP_F[i] = F_tmp[i];
         }
@@ -81,7 +81,7 @@ void Pulay_Mixing::tem_push_data(Mixing_Data& mdata,
 #ifdef _OPENMP
 #pragma omp parallel for schedule(static, 4096 / sizeof(FPTYPE))
 #endif
-        for (int i = 0; i < length; ++i)
+        for (std::size_t i = 0; i < length; ++i)
         {
             FP_startF[i] = F_tmp[i];
         }
@@ -103,7 +103,7 @@ void Pulay_Mixing::tem_cal_coef(const Mixing_Data& mdata, std::function<double(F
         ModuleBase::WARNING_QUIT(
             "Pulay_mixing",
             "One Pulay_Mixing object can only bind one Mixing_Data object to calculate coefficients");
-    const int length = mdata.length;
+    const std::size_t length = mdata.length;
     FPTYPE* FP_F = static_cast<FPTYPE*>(F);
 
     if (mdata.ndim_use > 1)

source/module_cell/module_neighbor/sltk_atom.h

@@ -20,15 +20,31 @@ class FAtom
 	int type;
 	int natom;
 
+	int cell_x;
+	int cell_y;
+	int cell_z;
 public:
 //==========================================================
 // Default Constructor and deconstructor
 //==========================================================
 
 	FAtom();
+	FAtom(const double& x_in, const double& y_in, const double& z_in, 
+			const int& type_in, const int& natom_in, 
+			const int& cell_x_in, const int& cell_y_in, const int& cell_z_in)
+	{
+		d_x = x_in;
+		d_y = y_in;
+		d_z = z_in;
+		type = type_in;
+		natom = natom_in;
+		cell_x = cell_x_in;
+		cell_y = cell_y_in;
+		cell_z = cell_z_in;
+	}
 	~FAtom();
 //2015-05-07
-	void delete_vector(void);
+	void delete_vector();
 
 //	static int count1;
 //	static int count2;
@@ -47,7 +63,7 @@ class FAtom
 	std::shared_ptr<AdjacentSet> getAdjacentSet() const
 	{ return this->as; }
 
-	void allocate_AdjacentSet(void)
+	void allocate_AdjacentSet()
 	{ this->as = std::make_shared<AdjacentSet>(); }
 
 //==========================================================
@@ -59,16 +75,9 @@ class FAtom
 	const double& z() const { return d_z; }
 	const int& getType() const { return type;}
 	const int& getNatom() const { return natom;}
-
-//==========================================================
-// MEMBER FUNCTION :
-// EXPLAIN : set value
-//==========================================================
-	void setX(const double& r) { d_x = r; }
-	void setY(const double& r) { d_y = r; }
-	void setZ(const double& r) { d_z = r; }
-	void setType(const int ntype) {type = ntype;}
-	void setNatom(const int atom) {natom = atom;}
+	const int& getCellX() const { return cell_x; }
+	const int& getCellY() const { return cell_y; }
+	const int& getCellZ() const { return cell_z; }	
 };
 
 #endif