add init-bulk in dpgen documents

doc/index.rst

@@ -33,8 +33,9 @@ DPGEN's documentation
 
 .. toctree::
    :maxdepth: 2
-   :caption: Init   
-
+   :caption: Init 
+
+   init/init-bulk.md
    init/init-bulk-mdata
    init/init_surf.md
    init/init-surf-mdata

doc/init/init-bulk.md

@@ -0,0 +1,52 @@
+## Init_bulk
+
+You may prepare initial data for bulk systems with VASP by:
+
+```bash
+dpgen init_bulk PARAM [MACHINE]
+```
+The MACHINE configure file is optional. If this parameter exists, then the optimization
+tasks or MD tasks will be submitted automatically according to MACHINE.json.
+
+Basically `init_bulk` can be divided into four parts , denoted as `stages` in `PARAM`:
+1. Relax in folder `00.place_ele`
+2. Perturb and scale in folder `01.scale_pert`
+3. Run a short AIMD in folder `02.md`
+4. Collect data in folder `02.md`.
+
+All stages must be **in order**. One doesn't need to run all stages. For example, you may run stage 1 and 2, generating supercells as starting point of exploration in `dpgen run`.
+
+If MACHINE is None, there should be only one stage in stages. Corresponding tasks will be generated, but user's intervention should be involved in, to manually run the scripts.
+
+Following is an example for `PARAM`, which generates data from a typical structure hcp.
+```json
+{
+    "stages" : [1,2,3,4],
+    "cell_type":    "hcp",
+    "latt":     4.479,
+    "super_cell":   [2, 2, 2],
+    "elements":     ["Mg"],
+    "potcars":      ["....../POTCAR"],
+    "relax_incar": "....../INCAR_metal_rlx",
+    "md_incar" : "....../INCAR_metal_md",
+    "scale":        [1.00],
+    "skip_relax":   false,
+    "pert_numb":    2,
+    "md_nstep" : 5,
+    "pert_box":     0.03,
+    "pert_atom":    0.01,
+    "coll_ndata":   5000,
+    "type_map" : [ "Mg", "Al"],
+    "_comment":     "that's all"
+}
+```
+
+If you want to specify a structure as starting point for `init_bulk`, you may set in `PARAM` as follows.
+
+```json
+"from_poscar":	true,
+"from_poscar_path":	"....../C_mp-47_conventional.POSCAR",
+```
+`init_bulk` support both VASP and ABACUS for first-principle calculation. You can choose the software by specifying the key `init_fp_style`. If `init_fp_style` is not specified, the default software will be VASP. 
+
+When using ABACUS for `init_fp_style`, the keys of the paths of `INPUT` files for relaxation and MD simulations are the same as `INCAR` for VASP, which are `relax_incar` and `md_incar` respectively. Use `relax_kpt` and `md_kpt` for the relative path for `KPT` files of relaxation and MD simulations. They two can be omitted if `kspacing` (in unit of 1/Bohr) or `gamma_only` has been set in corresponding INPUT files. If `from_poscar` is set to `false`, you have to specify `atom_masses` in the same order as `elements`.