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Feature: add out_mat_ds to print <phi|dphi> matrix (#6149)
* Feature: add out_mat_ds to print <phi|dphi> matrix * Fix: decrease the memory of reference files --------- Co-authored-by: dyzheng <[email protected]>
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-344
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21 files changed

+231
-344
lines changed

‎docs/advanced/input_files/input-main.md‎

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@@ -153,6 +153,7 @@
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- [out\_mat\_hs2](#out_mat_hs2)
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- [out\_mat\_t](#out_mat_t)
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- [out\_mat\_dh](#out_mat_dh)
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- [out\_mat\_ds](#out_mat_ds)
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- [out\_mat\_xc](#out_mat_xc)
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- [out\_mat\_xc2](#out_mat_xc2)
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- [out\_mat\_l](#out_mat_l)
@@ -1801,6 +1802,13 @@ These variables are used to control the output of properties.
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- **Description**: Whether to print files containing the derivatives of the Hamiltonian matrix (in Ry/Bohr). The format will be the same as the Hamiltonian matrix $H(R)$ and overlap matrix $S(R)$ as mentioned in [out_mat_hs2](#out_mat_hs2). The name of the files will be `data-dHRx-sparse_SPIN0.csr` and so on. Also controled by [out_interval](#out_interval) and [out_app_flag](#out_app_flag).
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- **Default**: False
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### out_mat_ds
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- **Type**: Boolean
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- **Availability**: Numerical atomic orbital basis (not gamma-only algorithm)
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- **Description**: Whether to print files containing the derivatives of the Overlap matrix (in Ry/Bohr). The format will be the same as the Overlap matrix $dH(R)$ as mentioned in [out_mat_dh](#out_mat_dh). The name of the files will be `data-dSRx-sparse_SPIN0.csr` and so on. Also controled by [out_interval](#out_interval) and [out_app_flag](#out_app_flag). This feature can be used with `calculation get_S`.
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- **Default**: False
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### out_mat_xc
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- **Type**: Boolean

‎source/module_esolver/esolver_gets.cpp‎

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@@ -137,6 +137,20 @@ void ESolver_GetS::runner(UnitCell& ucell, const int istep)
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r_matrix.out_rR(ucell, gd, istep);
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}
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if (PARAM.inp.out_mat_ds)
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{
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LCAO_HS_Arrays HS_Arrays; // store sparse arrays
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//! Print out sparse matrix
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ModuleIO::output_dSR(istep,
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ucell,
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this->pv,
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HS_Arrays,
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gd, // mohan add 2024-04-06
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two_center_bundle_,
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orb_,
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kv);
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}
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ModuleBase::timer::tick("ESolver_GetS", "runner");
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}
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‎source/module_esolver/lcao_after_scf.cpp‎

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@@ -305,6 +305,7 @@ void ESolver_KS_LCAO<TK, TR>::after_scf(UnitCell& ucell, const int istep, const
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//! Print out sparse matrix
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ModuleIO::output_mat_sparse(PARAM.inp.out_mat_hs2,
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PARAM.inp.out_mat_dh,
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PARAM.inp.out_mat_ds,
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PARAM.inp.out_mat_t,
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PARAM.inp.out_mat_r,
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istep,

‎source/module_hamilt_lcao/hamilt_lcaodft/spar_dh.cpp‎

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@@ -4,6 +4,52 @@
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#include "module_hamilt_lcao/hamilt_lcaodft/LCAO_domain.h"
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#include <vector>
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void sparse_format::cal_dS(const UnitCell& ucell,
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const Parallel_Orbitals& pv,
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LCAO_HS_Arrays& HS_Arrays,
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const Grid_Driver& grid,
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const TwoCenterBundle& two_center_bundle,
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const LCAO_Orbitals& orb,
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const double& sparse_thr)
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{
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ModuleBase::TITLE("sparse_format", "cal_dS");
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sparse_format::set_R_range(HS_Arrays.all_R_coor, grid);
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const int nnr = pv.nnr;
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ForceStressArrays fsr_dh;
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fsr_dh.DHloc_fixedR_x = new double[nnr];
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fsr_dh.DHloc_fixedR_y = new double[nnr];
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fsr_dh.DHloc_fixedR_z = new double[nnr];
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ModuleBase::GlobalFunc::ZEROS(fsr_dh.DHloc_fixedR_x, nnr);
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ModuleBase::GlobalFunc::ZEROS(fsr_dh.DHloc_fixedR_y, nnr);
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ModuleBase::GlobalFunc::ZEROS(fsr_dh.DHloc_fixedR_z, nnr);
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// the pointers of dS is different from dH, use the dh pointers to reuse the print functions
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fsr_dh.DSloc_Rx = fsr_dh.DHloc_fixedR_x;
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fsr_dh.DSloc_Ry = fsr_dh.DHloc_fixedR_y;
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fsr_dh.DSloc_Rz = fsr_dh.DHloc_fixedR_z;
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// cal dS=<phi|dphi> in LCAO
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const bool cal_deri = true;
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const bool cal_stress = false;
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LCAO_domain::build_ST_new(fsr_dh,
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'S',
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cal_deri,
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cal_stress,
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ucell,
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orb,
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pv,
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two_center_bundle,
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&grid,
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nullptr,
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false); // delete unused parameter lm.Hloc_fixedR
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sparse_format::cal_dSTN_R(ucell,pv, HS_Arrays, fsr_dh, grid, orb.cutoffs(), 0, sparse_thr);
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delete[] fsr_dh.DHloc_fixedR_x;
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delete[] fsr_dh.DHloc_fixedR_y;
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delete[] fsr_dh.DHloc_fixedR_z;
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return;
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}
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void sparse_format::cal_dH(const UnitCell& ucell,
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const Parallel_Orbitals& pv,
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LCAO_HS_Arrays& HS_Arrays,

‎source/module_hamilt_lcao/hamilt_lcaodft/spar_dh.h‎

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@@ -21,6 +21,15 @@ void cal_dH(const UnitCell& ucell,
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const double& sparse_thr,
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Gint_k& gint_k);
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// calculated the derivative of the overlap matrix: <phi|dphi>
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void cal_dS(const UnitCell& ucell,
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const Parallel_Orbitals& pv,
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LCAO_HS_Arrays& HS_Arrays,
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const Grid_Driver& grid,
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const TwoCenterBundle& two_center_bundle,
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const LCAO_Orbitals& orb,
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const double& sparse_thr);
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// be called by 'cal_dH_sparse'
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void set_R_range(std::set<Abfs::Vector3_Order<int>>& all_R_coor, const Grid_Driver& grid);
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‎source/module_io/output_mat_sparse.cpp‎

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@@ -9,6 +9,7 @@ namespace ModuleIO
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template <>
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void output_mat_sparse(const bool& out_mat_hsR,
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const bool& out_mat_dh,
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const bool& out_mat_ds,
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const bool& out_mat_t,
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const bool& out_mat_r,
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const int& istep,
@@ -27,6 +28,7 @@ void output_mat_sparse(const bool& out_mat_hsR,
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template <>
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void output_mat_sparse(const bool& out_mat_hsR,
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const bool& out_mat_dh,
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const bool& out_mat_ds,
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const bool& out_mat_t,
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const bool& out_mat_r,
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const int& istep,
@@ -68,6 +70,18 @@ void output_mat_sparse(const bool& out_mat_hsR,
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orb,
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kv); // LiuXh add 2019-07-15
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}
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//! generate a file containing the derivatives of the overlap matrix (in Ry/Bohr)
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if (out_mat_ds)
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{
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output_dSR(istep,
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ucell,
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pv,
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HS_Arrays,
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grid, // mohan add 2024-04-06
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two_center_bundle,
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orb,
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kv);
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}
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// add by jingan for out r_R matrix 2019.8.14
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if (out_mat_r)

‎source/module_io/output_mat_sparse.h‎

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@@ -13,6 +13,7 @@ namespace ModuleIO
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template <typename T>
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void output_mat_sparse(const bool& out_mat_hsR,
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const bool& out_mat_dh,
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const bool& out_mat_ds,
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const bool& out_mat_t,
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const bool& out_mat_r,
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const int& istep,

‎source/module_io/read_input.cpp‎

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@@ -182,7 +182,7 @@ void ReadInput::create_directory(const Parameter& param)
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//----------------------------------------------------------
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bool out_dir = false;
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if (!param.input.out_app_flag
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&& (param.input.out_mat_hs2 || param.input.out_mat_r || param.input.out_mat_t || param.input.out_mat_dh))
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&& (param.input.out_mat_hs2 || param.input.out_mat_r || param.input.out_mat_t || param.input.out_mat_dh || param.input.out_mat_ds))
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{
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out_dir = true;
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}

‎source/module_io/read_input_item_output.cpp‎

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@@ -322,6 +322,18 @@ void ReadInput::item_output()
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};
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this->add_item(item);
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}
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{
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Input_Item item("out_mat_ds");
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item.annotation = "output of derivative of S(R) matrix";
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read_sync_bool(input.out_mat_ds);
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item.check_value = [](const Input_Item& item, const Parameter& para) {
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if (para.input.out_mat_ds && para.input.nspin == 4)
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{
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ModuleBase::WARNING_QUIT("ReadInput", "out_mat_ds is not available for nspin = 4");
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}
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};
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this->add_item(item);
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}
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{
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Input_Item item("out_mat_xc");
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item.annotation = "output exchange-correlation matrix in KS-orbital representation";

‎source/module_io/write_HS_R.cpp‎

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@@ -83,6 +83,37 @@ void ModuleIO::output_HSR(const UnitCell& ucell,
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return;
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}
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void ModuleIO::output_dSR(const int& istep,
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const UnitCell& ucell,
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const Parallel_Orbitals& pv,
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LCAO_HS_Arrays& HS_Arrays,
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const Grid_Driver& grid, // mohan add 2024-04-06
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const TwoCenterBundle& two_center_bundle,
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const LCAO_Orbitals& orb,
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const K_Vectors& kv,
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const bool& binary,
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const double& sparse_thr)
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{
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ModuleBase::TITLE("ModuleIO", "output_dSR");
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ModuleBase::timer::tick("ModuleIO", "output_dSR");
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sparse_format::cal_dS(ucell,
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pv,
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HS_Arrays,
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grid,
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two_center_bundle,
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orb,
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sparse_thr);
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// mohan update 2024-04-01
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ModuleIO::save_dH_sparse(istep, pv, HS_Arrays, sparse_thr, binary, "S");
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sparse_format::destroy_dH_R_sparse(HS_Arrays);
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ModuleBase::timer::tick("ModuleIO", "output_dSR");
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return;
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}
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void ModuleIO::output_dHR(const int& istep,
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const ModuleBase::matrix& v_eff,
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Gint_k& gint_k, // mohan add 2024-04-01

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