add init-bulk in dpgen documents #907
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Signed-off-by: baihuyu12 <[email protected]>
Signed-off-by: baihuyu12 <[email protected]>
Signed-off-by: baihuyu12 <[email protected]>
Signed-off-by: baihuyu12 <[email protected]>
Signed-off-by: baihuyu12 <[email protected]>
Signed-off-by: baihuyu12 <[email protected]>
This was referenced Aug 22, 2022
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njzjz
requested changes
Aug 22, 2022
Signed-off-by: baihuyu12 <[email protected]>
Signed-off-by: baihuyu12 <[email protected]>
Codecov Report
@@ Coverage Diff @@
## devel #907 +/- ##
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+ Coverage 38.14% 38.24% +0.09%
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Files 99 99
Lines 17767 17795 +28
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+ Hits 6778 6806 +28
Misses 10989 10989
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njzjz
approved these changes
Aug 24, 2022
doc/init/init-bulk.md
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Comment on lines
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| Key | Type | Example | Description | | ||
| | :---------------- | :--------------------- | :-------------------------------------- | :-------------------------------------------------------------| | ||
| | **stages** | List of Integer | [1,2,3,4] | Stages for `init_bulk` | ||
| | **Elements** | List of String | ["Mg"] | Atom types | ||
| | cell_type | String | "hcp" | Specifying which typical structure to be generated. **Options** include fcc, hcp, bcc, sc, diamond. | ||
| | latt | Float | 4.479 | Lattice constant for single cell. | ||
| | from_poscar | Boolean | True | Deciding whether to use a given poscar as the beginning of relaxation. If it's true, keys (`cell_type`, `latt`) will be aborted. Otherwise, these two keys are **necessary**. | ||
| | from_poscar_path | String | "....../C_mp-47_conventional.POSCAR" | Path of POSCAR for VASP or STRU for ABACUS. **Necessary** if `from_poscar` is true. | ||
| | relax_incar | String | "....../INCAR" | Path of INCAR for VASP or INPUT for ABACUS for relaxation in VASP. **Necessary** if `stages` include 1. | ||
| | md_incar | String | "....../INCAR_md" | Path of INCAR for VASP or INPUT for ABACUS for MD in VASP. **Necessary** if `stages` include 3.| | ||
| | **scale** | List of float | [0.980, 1.000, 1.020] | Scales for transforming cells. | ||
| | **skip_relax** | Boolean | False | If it's true, you may directly run stage 2 (perturb and scale) using an unrelaxed POSCAR. | ||
| | **pert_numb** | Integer | 30 | Number of perturbations for each POSCAR. | ||
| | **pert_box** | Float | 0.03 | Percentage of Perturbation for cells. | ||
| | **pert_atom** | Float | 0.01 | Perturbation of each atoms (Angstrom). | ||
| | **md_nstep** | Integer | 10 | Steps of AIMD in stage 3. If it's not equal to settings via `NSW` in `md_incar`, DP-GEN will follow `NSW`. | ||
| | **coll_ndata** | Integer | 5000 | Maximal number of collected data. | ||
| | type_map | List | [ "Mg", "Al"] | The indices of elements in deepmd formats will be set in this order. | ||
| | init_fp_style | String | "ABACUS" or "VASP" | First-principle software. If this key is absent, the default value will be "VASP". | ||
| | relax_kpt | String | "....../KPT" | Path of `KPT` file for relaxation in stage 1. Only useful if `init_fp_style` is "ABACUS". | ||
| | md_kpt | String | "....../KPT" | Path of `KPT` file for MD simulations in stage 3. Only useful if `init_fp_style` is "ABACUS". | ||
| | atom_masses | List of float | [24] | List of atomic masses of elements. The order should be the same as `Elements`. Only useful if `init_fp_style` is "ABACUS". |
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This table should be generated automatically by dargs. But I don't request it done by this PR.
cc @HuangJiameng
Signed-off-by: baihuyu12 <[email protected]>
njzjz
reviewed
Aug 26, 2022
doc/init/init-bulk.md
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| "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. |
Signed-off-by: baihuyu12 <[email protected]>
AnguseZhang
approved these changes
Aug 27, 2022
njzjz
approved these changes
Aug 28, 2022
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I have the same issue but I can merge it on the app. |
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