Unify output directory structure with out_app_flag=2

docs/advanced/elec_properties/hs_matrix.md

@@ -39,7 +39,7 @@ The output filenames depend on the k-point algorithm and `nspin`:
 
 Here `${k}` is the one-based k-point index. For `nspin = 2`, the overlap matrix is spin-independent, so only one overlap file is written for each physical k point. The gamma-only algorithm does not support `nspin = 4`; use the multi-k algorithm with an explicit Gamma-only `KPT` file for a noncollinear calculation at Gamma.
 
-When `out_app_flag` is false, `g${step}` is inserted before `_nao`, where `${step}` is the one-based ionic-step index. For example, the first spin channel at the first k point and first ionic step is written to `hk1s1g1_nao.txt`.
+When `out_app_flag` is not 1, `g${step}` is inserted before `_nao`, where `${step}` is the one-based ionic-step index. For example, the first spin channel at the first k point and first ionic step is written to `hk1s1g1_nao.txt`.
 
 Each output block starts with a comment header containing the one-based ionic-step index, filename, `gamma only` flag, and matrix dimensions. It is followed by `Row 1`, `Row 2`, and so on. Each row contains the matrix elements from the diagonal through the upper triangle.
 
@@ -57,7 +57,7 @@ For `out_hsk 2`, the filenames in the table above use `.dat` instead of `.txt`.
 
 The file therefore contains `sizeof(int) + N(N+1)/2 * sizeof(double)` bytes for a gamma-only record and `sizeof(int) + N(N+1) * sizeof(double)` bytes for a multi-k or spinor record. The format uses the host integer representation and byte order and is intended for readers using a compatible ABI.
 
-When `out_app_flag` is true, the first ionic step truncates the shared file and every later step appends another complete record. When it is false, each ionic step has a separate filename containing `g${step}` before `_nao`.
+When `out_app_flag` is 1, the first ionic step truncates the shared file and every later step appends another complete record. When it is not 1, each ionic step has a separate filename containing `g${step}` before `_nao`.
 
 ## out_hsr
 
@@ -95,7 +95,7 @@ In gamma-only mode, every generated file reports one Bravais lattice vector and
 
 ### Native Binary CSR Format
 
-Set `out_hsr 2` to write the same H(R) and S(R) matrix sets with a `.dat` suffix. For example, an `nspin = 2` calculation writes `hrs1_nao.dat`, `hrs2_nao.dat`, and `sr_nao.dat`. When `out_app_flag` is false, the one-based ionic step is included before `_nao`, for example `hrs1g1_nao.dat` and `srg1_nao.dat`.
+Set `out_hsr 2` to write the same H(R) and S(R) matrix sets with a `.dat` suffix. For example, an `nspin = 2` calculation writes `hrs1_nao.dat`, `hrs2_nao.dat`, and `sr_nao.dat`. When `out_app_flag` is not 1, the one-based ionic step is included before `_nao`, for example `hrs1g1_nao.dat` and `srg1_nao.dat`.
 
 Each ionic step is a complete record with no padding or self-describing header:
 
@@ -107,7 +107,7 @@ Each ionic step is a complete record with no padding or self-describing header:
 
 All R blocks stored by the internal HContainer are present, including blocks with zero nonzero values. The sparse threshold is `1e-10`, matching text CSR output. The format uses the host integer representation and byte order and therefore requires a compatible ABI. It does not contain unit-cell, spin, or matrix-label metadata; those are determined by the calculation input and filename.
 
-When `out_app_flag` is true, the first ionic step truncates the shared file and later ionic steps append complete records. Otherwise every ionic step is written to its own file.
+When `out_app_flag` is 1, the first ionic step truncates the shared file and later ionic steps append complete records. Otherwise every ionic step is written to its own file.
 
 ### NPZ Format
 

docs/advanced/elec_properties/position_matrix.md

@@ -18,7 +18,7 @@ Each file or each section of the appended file starts with "STEP: " followed by
 
 Each block here contains the matrix for the corresponding cell. There are three columns in each block, giving the matrix elements in x, y, z directions, respectively. There are altogether nbasis * nbasis lines in each block, which emulates the matrix elements.
 
-In molecular dynamics (MD) calculations, if [out_app_flag](../input_files/input-main.md#out_app_flag) is set to true, then `data-rR-tr` is written in an append manner. Otherwise, output files will be put in a separate directory, `matrix`, and named as `$x`_data-rR-tr, where `$x` is the number of MD step. In addition, the output frequency is controlled by [out_freq_ion](../input_files/input-main.md#out_freq_ion). For example, if we are running a 10-step MD with out_freq_ion = 3, then `$x` will be 0, 3, 6, and 9.
+In molecular dynamics (MD) calculations, if [out_app_flag](../input_files/input-main.md#out_app_flag) is set to 1, then `data-rR-tr` is written in an append manner. Otherwise, output files will be put in a separate directory, `matrix`, and named as `$x`_data-rR-tr, where `$x` is the number of MD step. In addition, the output frequency is controlled by [out_freq_ion](../input_files/input-main.md#out_freq_ion). For example, if we are running a 10-step MD with out_freq_ion = 3, then `$x` will be 0, 3, 6, and 9.
 
 ## get_s
 We also offer the option of only calculating the position matrix without running SCF. For that purpose, in `INPUT` file we need to set the keyword [calculation](../input_files/input-main.md#calculation) to `get_s`, and [out_mat_r](../input_files/input-main.md#out_mat_r) to `true`.

docs/advanced/elec_properties/wfc.md

@@ -18,7 +18,7 @@ The [`init_wfc file binary`](../scf/initialization.md#wavefunction) path reads o
 
 For `basis_type=lcao`, [`out_wfc_lcao`](https://abacus-rtd.readthedocs.io/en/latest/advanced/input_files/input-main.html#out-wfc-lcao) controls the output of numerical-atomic-orbital coefficients: `1` writes text files with the `.txt` suffix and `2` writes binary files with the `.dat` suffix. Multi-k calculations generate `wfs{spin}k{k-point}_nao.txt` or `.dat`, while Gamma-only calculations generate `wfs{spin}_nao.txt` or `.dat`.
 
-To reuse LCAO coefficients, point `read_file_dir` to the coefficient files and set `init_wfc file txt` for text input or `init_wfc file binary` for binary input. The selected extension is required; there is no automatic format fallback. Only independent files without geometry-step indices are supported, not files accumulated with `out_app_flag`.
+To reuse LCAO coefficients, point `read_file_dir` to the coefficient files and set `init_wfc file txt` for text input or `init_wfc file binary` for binary input. The selected extension is required; there is no automatic format fallback. Only independent files without geometry-step indices are supported, not files accumulated with `out_app_flag=1`.
 
 ## Wave Function in Real Space
 

docs/advanced/scf/initialization.md

@@ -26,7 +26,7 @@ For `basis_type=pw`, the available options are:
 * `nao+random`: Apply an approximately 5% multiplicative random perturbation to the NAO initialization; any bands not covered by NAO states are first initialized randomly.
 * `file binary`: Read binary `wf*_pw.dat` files generated with [`out_wfc_pw=2`](../elec_properties/wfc.md) from `read_file_dir`. The files must match the current k points, `nbands`, plane-wave layout, and lattice. The `txt` format is not supported for PW wavefunctions.
 
-For `basis_type=lcao`, use `init_wfc file txt` to read text `wf*_nao.txt` files generated with [`out_wfc_lcao=1`](../elec_properties/wfc.md), or `init_wfc file binary` to read binary `wf*_nao.dat` files generated with `out_wfc_lcao=2`, from `read_file_dir`. LCAO wavefunctions initialize the density matrix and real-space charge density. The selected format is required; ABACUS does not automatically detect or fall back to the other format. The files must use a compatible NAO basis, match the current k-point and spin setup, and contain enough bands. Only independent files without geometry-step indices are supported, not files accumulated with `out_app_flag`.
+For `basis_type=lcao`, use `init_wfc file txt` to read text `wf*_nao.txt` files generated with [`out_wfc_lcao=1`](../elec_properties/wfc.md), or `init_wfc file binary` to read binary `wf*_nao.dat` files generated with `out_wfc_lcao=2`, from `read_file_dir`. LCAO wavefunctions initialize the density matrix and real-space charge density. The selected format is required; ABACUS does not automatically detect or fall back to the other format. The files must use a compatible NAO basis, match the current k-point and spin setup, and contain enough bands. Only independent files without geometry-step indices are supported, not files accumulated with `out_app_flag=1`.
 
 For `basis_type=lcao_in_pw`, `init_wfc` is automatically set to `nao`.
 

examples/17_relax/04_relax_with_output_lcao/INPUT

@@ -34,11 +34,12 @@ out_dmr              1
 out_dos              1
 out_band             1
 out_stru             1
-out_app_flag         0
 
 out_mat_l 1
 out_mat_r 1
 out_mat_t 1 
 #out_mat_dh 1
 
 out_freq_ion         2
+
+out_app_flag         2

examples/18_md/02_lcao_output/INPUT

@@ -36,3 +36,5 @@ md_tchain              1
 
 dft_functional       hse
 restart_save           1
+
+out_app_flag          0

source/source_base/module_out/filename.cpp

@@ -14,7 +14,7 @@ std::string filename_output(
             const int nspin,
             const int nkstot,
             const int out_type,
-            const bool out_app_flag,
+            const int out_app_flag,
             const bool gamma_only,
             const int istep,
             const int iter)
@@ -97,14 +97,14 @@ std::string filename_output(
     }
 
     std::string istep_block
-        = (istep >= 0 && (!out_app_flag))
+        = (istep >= 0 && (out_app_flag != 1))
               ? "g" + std::to_string(istep + 1) // istep starts from 0
-              : ""; // only when istep >= 0 and out_app_flag is false will write each wfc to a separate file
+              : ""; // only when istep >= 0 and out_app_flag is not append mode will write each wfc to a separate file
 
     std::string iter_block
-        = (iter >= 0 && (!out_app_flag))
+        = (iter >= 0 && (out_app_flag != 1))
               ? "e" + std::to_string(iter) // iter starts from 1
-              : ""; // only when istep >= 0 and out_app_flag is false will write each wfc to a separate file
+              : ""; // only when istep >= 0 and out_app_flag is not append mode will write each wfc to a separate file
 
     std::string suffix_block;
     if (out_type == 1)

source/source_base/module_out/filename.h

@@ -16,7 +16,7 @@ namespace ModuleIO
  * @param nspin: number of spin channels, 1,2 or 4 
  * @param nkstot: number of total k-points 
  * @param out_type: two types of output file format, 1 for .txt and 2 for .dat (binary)
- * @param out_app_flag: whether to append to existing file.
+ * @param out_app_flag: 0=no append, 1=append to same file, 2=write to subdirectory.
  * @param gamma_only: gamma_only algorithm or not.
  * @param istep: index of the ion step starting from 0. If < 0, the step number is not included in the file name.
  * @param iter: index of the electronic step starting from 0. If < 0, the step number is not included in the file name. 
@@ -31,7 +31,7 @@ std::string filename_output(
             const int nspin,
             const int nkstot,
             const int out_type,
-            const bool out_app_flag,
+            const int out_app_flag,
             const bool gamma_only,
             const int istep=-1,
             const int iter=-1);

source/source_io/module_ctrl/ctrl_output_fp.cpp

@@ -32,10 +32,14 @@ void ctrl_output_fp(UnitCell& ucell,
     ModuleBase::TITLE("ModuleIO", "ctrl_output_fp");
     ModuleBase::timer::start("ModuleIO", "ctrl_output_fp");
 
-    const bool out_app_flag = inp.out_app_flag;
+    const int out_app_flag = inp.out_app_flag;
     const bool gamma_only = PARAM.globalv.gamma_only_local;
     const int nspin = inp.nspin;
     const std::string global_out_dir = PARAM.globalv.global_out_dir;
+    const std::string global_chg_dir = PARAM.globalv.global_chg_dir;
+    const std::string global_pot_dir = PARAM.globalv.global_pot_dir;
+    const std::string global_elf_dir = PARAM.globalv.global_elf_dir;
+    const std::string global_dip_dir = PARAM.globalv.global_dip_dir;
 
     const int output_frequency = inp.esolver_type == "tddft" ? inp.out_freq_td : inp.out_freq_ion;
     // Print the global electronic step for TDDFT and the ionic step otherwise.
@@ -61,7 +65,7 @@ void ctrl_output_fp(UnitCell& ucell,
     {
         for (int is = 0; is < nspin; ++is)
         {
-            std::string fn = PARAM.globalv.global_out_dir + "chg";
+            std::string fn = global_chg_dir + "chg";
 
             std::string spin_block;
             if (nspin == 2 || nspin == 4)
@@ -94,7 +98,7 @@ void ctrl_output_fp(UnitCell& ucell,
 
             if (XC_Functional::get_ked_flag())
             {
-                fn = PARAM.globalv.global_out_dir + "tau";
+                fn = global_chg_dir + "tau";
 
                 fn += spin_block + geom_block + ".cube";
 
@@ -123,7 +127,7 @@ void ctrl_output_fp(UnitCell& ucell,
     {
         for (int is = 0; is < nspin; is++)
         {
-            std::string fn = PARAM.globalv.global_out_dir + "pot";
+            std::string fn = global_pot_dir + "pot";
 
             std::string spin_block;
             if (nspin == 2 || nspin == 4)
@@ -157,7 +161,7 @@ void ctrl_output_fp(UnitCell& ucell,
     }
     else if (inp.out_pot[0] == 2 && should_output)
     {
-        std::string fn = PARAM.globalv.global_out_dir + "potes";
+        std::string fn = global_pot_dir + "potes";
         fn += geom_block + ".cube";
 
         const std::vector<double>* pcc_potential = pelec->pot->pcc_electron_potential();
@@ -189,7 +193,7 @@ void ctrl_output_fp(UnitCell& ucell,
             module_charge::cal_rhog_symm(is, chr, pw_rhod, ucell.symm);
         }
 
-        std::string out_dir = PARAM.globalv.global_out_dir;
+        std::string out_dir = global_elf_dir;
         ModuleIO::write_elf(out_dir,
                             istep,
                             nspin,
@@ -226,7 +230,7 @@ void ctrl_output_fp(UnitCell& ucell,
         for (int is = 0; is < nspin; ++is)
         {
             std::stringstream ss_dipole;
-            ss_dipole << global_out_dir << "dipole_s" << is + 1 << ".txt";
+            ss_dipole << global_dip_dir << "dipole_s" << is + 1 << ".txt";
             ModuleIO::write_dipole(ucell, chr.rho[is], pw_rhod, istep, ss_dipole.str(), ofs_running);
         }
     }

source/source_io/module_ctrl/ctrl_output_pw.cpp

@@ -74,7 +74,7 @@ void ModuleIO::ctrl_iter_pw(const int istep,
                                GlobalV::NPROC_IN_POOL,
                                inp.out_wfc_pw,
                                inp.ecutwfc,
-                               PARAM.globalv.global_out_dir,
+                               PARAM.globalv.global_psi_dir,
                                stp.psi_cpu[0],
                                kv,
                                pw_wfc,
@@ -174,7 +174,7 @@ void ModuleIO::ctrl_scf_pw(const int istep,
                                    PARAM.globalv.two_fermi,
                                    inp.out_app_flag,
                                    inp.bndpar,
-                                   PARAM.globalv.global_out_dir,
+                                   PARAM.globalv.global_dos_dir,
                                    ofs_running);
         }
     }
@@ -294,7 +294,7 @@ void ModuleIO::ctrl_runner_pw(UnitCell& ucell,
                               inp.out_ldos,
                               inp.stm_bias,
                               inp.nspin,
-                              PARAM.globalv.global_out_dir,
+                              PARAM.globalv.global_dos_dir,
                               PARAM.globalv.two_fermi,
                               inp.nbands,
                               inp.dos_edelta_ev,

source/source_io/module_ctrl/ctrl_runner_lcao.cpp

@@ -54,7 +54,7 @@ void ctrl_runner_lcao(UnitCell& ucell,      // unitcell
     {
         ModuleIO::Cal_ldos<TK>::cal_ldos_lcao(pelec->eferm, chr, dmat, kv,
           pelec->ekb, pelec->wg, psi[0], pgrid, pv, gd, ucell,
-          inp.stm_bias, inp.nspin, PARAM.globalv.global_out_dir,
+          inp.stm_bias, inp.nspin, PARAM.globalv.global_dos_dir,
           PARAM.globalv.two_fermi, inp.out_ldos[1], ofs_running);
     }
 

source/source_io/module_ctrl/ctrl_scf_lcao.cpp

@@ -136,10 +136,11 @@ void ModuleIO::ctrl_scf_lcao(UnitCell& ucell,
 
     //*****
 
-    const bool out_app_flag = inp.out_app_flag;
+    const int out_app_flag = inp.out_app_flag;
     const bool gamma_only = PARAM.globalv.gamma_only_local;
     const int nspin = inp.nspin;
     const std::string global_out_dir = PARAM.globalv.global_out_dir;
+    const std::string global_mat_dir = PARAM.globalv.global_mat_dir;
 
     //------------------------------------------------------------------
     //! 1) print out density of states (DOS)
@@ -168,7 +169,7 @@ void ModuleIO::ctrl_scf_lcao(UnitCell& ucell,
                                  inp.dos_emin_ev,
                                  PARAM.globalv.two_fermi,
                                  inp.bndpar,
-                                 PARAM.globalv.global_out_dir,
+                                 PARAM.globalv.global_dos_dir,
                                  ofs_running);
     }
 
@@ -179,7 +180,7 @@ void ModuleIO::ctrl_scf_lcao(UnitCell& ucell,
     {
         const int precision = inp.out_dmr[1];
 
-        ModuleIO::write_dmr(dm->get_dmr_vec(), &ucell, precision, pv, out_app_flag, 
+        ModuleIO::write_dmr(dm->get_dmr_vec(), &ucell, precision, pv, (out_app_flag == 1),
 			ucell.get_iat2iwt(), ucell.nat, istep, ofs_running);
     }
 
@@ -195,7 +196,7 @@ void ModuleIO::ctrl_scf_lcao(UnitCell& ucell,
         }
         const int precision = inp.out_dmk[1];
 
-        ModuleIO::write_dmk(dm->get_dmk_vec(), kv, precision, efermis, &(ucell), pv, global_out_dir, istep, ofs_running);
+        ModuleIO::write_dmk(dm->get_dmk_vec(), kv, precision, efermis, &(ucell), pv, global_mat_dir, istep, ofs_running);
     }
 
     //------------------------------------------------------------------
@@ -279,7 +280,7 @@ void ModuleIO::ctrl_scf_lcao(UnitCell& ucell,
         const hamilt::HContainer<TR>* sr = p_hamilt->getSR();
 
         ModuleIO::write_hsr(hr_vec, sr, &ucell, inp.out_hsr[0], precision, pv,
-                            out_app_flag, gamma_only, ucell.get_iat2iwt(), ucell.nat, istep,
+                            (out_app_flag == 1), gamma_only, ucell.get_iat2iwt(), ucell.nat, istep,
                             PARAM.globalv.global_out_dir, pelec->eferm,
                             ofs_running);
     }
@@ -399,7 +400,7 @@ void ModuleIO::ctrl_scf_lcao(UnitCell& ucell,
         dh_params.nspin = inp.nspin;
         dh_params.istep = istep;
         dh_params.gamma_only = gamma_only;
-        dh_params.append = out_app_flag;
+        dh_params.append = (out_app_flag == 1);
         dh_params.ofs_running = &ofs_running;
         if (PARAM.inp.nspin == 1 || PARAM.inp.nspin == 2)
         {
@@ -442,7 +443,7 @@ void ModuleIO::ctrl_scf_lcao(UnitCell& ucell,
         h_params.nrxx = pw_rho->nrxx;
         h_params.nspin = nspin;
         h_params.istep = istep;
-        h_params.append = out_app_flag;
+        h_params.append = (out_app_flag == 1);
         h_params.iat2iwt = ucell.get_iat2iwt();
         h_params.nat = ucell.nat;
         h_params.nlocal = PARAM.globalv.nlocal;
@@ -527,7 +528,7 @@ void ModuleIO::ctrl_scf_lcao(UnitCell& ucell,
                                false, // bit
                                inp.out_mat_tk[1],
                                1, // true for upper triangle matrix
-                               inp.out_app_flag,
+                               (inp.out_app_flag == 1),
                                t_fn,
                                pv,
                                GlobalV::DRANK,
@@ -558,7 +559,7 @@ void ModuleIO::ctrl_scf_lcao(UnitCell& ucell,
                                                           PARAM.globalv.gamma_only_local,
                                                           &ofs_running,
                                                           GlobalV::MY_RANK);
-        mylcalculator.calculate(inp.suffix, global_out_dir, ucell, inp.out_mat_l[1], GlobalV::MY_RANK, istep_in);
+        mylcalculator.calculate(inp.suffix, global_mat_dir, ucell, inp.out_mat_l[1], GlobalV::MY_RANK, istep_in);
     }
 
     //------------------------------------------------------------------