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Update README.md #750

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0767dce
Merge pull request #720 from amcadmus/master
amcadmus Apr 26, 2022
38be602
Update README.md
pee8379 Jun 8, 2022
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42 changes: 21 additions & 21 deletions README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -153,7 +153,7 @@ The following table gives explicit descriptions on keys in `PARAM`.

The bold notation of key (such as **Elements**) means that it's a necessary key.

Key | Type | Example | Discription |
Key | Type | Example | Description |
| :---------------- | :--------------------- | :-------------------------------------- | :-------------------------------------------------------------|
| **stages** | List of Integer | [1,2,3,4] | Stages for `init_bulk`
| **Elements** | List of String | ["Mg"] | Atom types
Expand All @@ -166,7 +166,7 @@ The bold notation of key (such as **Elements**) means that it's a necessary key.
| **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 (pertub and scale) using an unrelaxed POSCAR.
| **pert_numb** | Integer | 30 | Number of pertubations for each POSCAR.
| **pert_box** | Float | 0.03 | Percentage of Perturbation for cells.
| **pert_box** | Float | 0.03 | Pertubation of lattice vector component (Angstrom).
| **pert_atom** | Float | 0.01 | Pertubation 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.
Expand Down Expand Up @@ -300,7 +300,7 @@ The following table gives explicit descriptions on keys in `PARAM`.

The bold notation of key (such as **Elements**) means that it's a necessary key.

Key | Type | Example | Discription |
Key | Type | Example | Description |
| :---------------- | :--------------------- | :-------------------------------------- | :-------------------------------------------------------------|
| **stages** | List of Integer | [1,2,3,4] | Stages for `init_surf`
| **Elements** | List of String | ["Mg"] | Atom types
Expand All @@ -316,7 +316,7 @@ The bold notation of key (such as **Elements**) means that it's a necessary key.
| **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 (pertub and scale) using an unrelaxed POSCAR.
| **pert_numb** | Integer | 30 | Number of pertubations for each POSCAR.
| **pert_box** | Float | 0.03 | Percentage of Perturbation for cells.
| **pert_box** | Float | 0.03 | Pertubation of lattice vector component (Angstrom).
| **pert_atom** | Float | 0.01 | Pertubation of each atoms (Angstrom).
| **coll_ndata** | Integer | 5000 | Maximal number of collected data.

Expand Down Expand Up @@ -491,7 +491,7 @@ The following table gives explicit descriptions on keys in `PARAM`.

The bold notation of key (such aas **type_map**) means that it's a necessary key.

Key | Type | Example | Discription |
Key | Type | Example | Description |
| :---------------- | :--------------------- | :-------------------------------------- | :-------------------------------------------------------------|
| *#Basics*
| **type_map** | List of string | ["H", "C"] | Atom types
Expand Down Expand Up @@ -581,7 +581,7 @@ There are some new keys needed to be added into `param` and `machine` if CALYPSO

The bold notation of key (such as **calypso_path**) means that it's a necessary key.

Key | Type | Example | Discription |
Key | Type | Example | Description |
| :---------------- | :--------------------- | :-------------------------------------- | :-------------------------------------------------------------|
| *in param file*
| **model_devi_engine** | string | "calypso" | CALYPSO as model-deviation engine.|
Expand Down Expand Up @@ -768,7 +768,7 @@ The last part is the optional settings for various tasks mentioned above. You ca

param.json in a dictionary.

| Fields | Type | Example | Discription |
| Fields | Type | Example | Description |
| :---------------- | :--------------------- | :------------- | :----------------|
| potcar_map | dict | {"Al": "example/POTCAR"} |a dict like { "element" : "position of POTCAR" } |
| conf_dir | path like string | "confs/Al/std-fcc" | the dir which contains vasp's POSCAR |
Expand All @@ -780,7 +780,7 @@ param.json in a dictionary.

The keys in param["vasp_params"] is shown below.

| Fields | Type | Example | Discription |
| Fields | Type | Example | Description |
| :---------------- | :--------------------- | :---------------- | :----------------|
| ecut | real number | 650 | the plane wave cutoff for grid. |
| ediff | real number | 1e-6 |Tolerance of Density Matrix |
Expand All @@ -791,7 +791,7 @@ The keys in param["vasp_params"] is shown below.

the keys in param["lammps_params"].

| Key | Type | Example | Discription |
| Key | Type | Example | Description |
| :---------------- | :--------------------- | :-------------------------------------- | :-------------------------------------------------------------|
| model_dir | path like string | "example/Al_model" | the model dir which contains .pb file |
| type_map | list of string | ["Al"] | a list contains the element, usually useful for multiple element situation |
Expand All @@ -808,7 +808,7 @@ the keys in param["lammps_params"].

param.json.

| Field | Type | Example | Discription |
| Field | Type | Example | Description |
| :---------------- | :--------------------- | :-------------------------------------- | :-------------------------------------------------------------|
| EpA(eV) | real number | -3.7468 | the potential energy of a atom|
| VpA(A^3)| real number | 16.511| theEquilibrium volume of a atom |
Expand All @@ -819,7 +819,7 @@ conf_dir: EpA(eV) VpA(A^3)
confs/Al/std-fcc -3.7468 16.511
```

| Field | Type | Example | Discription |
| Field | Type | Example | Description |
| :---------------- | :--------------------- | :-------------------------------------- | :-------------------------------------------------------------|
| EpA(eV) | real number | -3.7468 | the potential energy of a atom|
| VpA(A^3)| real number | 16.511| theEquilibrium volume of a atom |
Expand All @@ -844,7 +844,7 @@ VpA(A^3) EpA(eV)
```


| Field | Type| Example| Discription |
| Field | Type| Example| Description |
| :---------------- | :--------------------- | :-------------------------------------- | :-------------------------------------------------------------|
| EpA(eV) | list of real number | [15.5,16.0,16.5,17.0] | the potential energy of a atom in quilibrium state|
| VpA(A^3)| list of real number |[-3.7306, -3.7429, -3.746762, -3.7430] | the equilibrium volume of a atom |
Expand All @@ -858,7 +858,7 @@ VpA(A^3) EpA(eV)
+ `norm_deform` and `shear_deform` are the scales of material deformation.
This task uses the stress-strain relationship to calculate the elastic constant.

|Key | Type | Example | Discription |
|Key | Type | Example | Description |
| :---------------- | :--------------------- | :-------------------------------------- | :-------------------------------------------------------------|
| norm_deform | real number | 0.02 | uniaxial deformation range |
| shear_deform | real number | 0.05| shear deformation range |
Expand All @@ -878,7 +878,7 @@ conf_dir:confs/Al/std-fcc
# Poission Ratio uV = 0.31
```

| Field | Type | Example | Discription |
| Field | Type | Example | Description |
| :---------------- | :--------------------- | :-------------------------------------- | :-------------------------------------------------------------|
| elastic module(GPa)| 6*6 matrix of real number| [[130.50 57.45 54.45 4.24 0.00 0.00] [57.61 130.31 54.45 -4.29 -0.00 -0.00] [54.48 54.48 133.32 -0.00 -0.00 -0.00] [4.49 -4.02 -0.89 33.78 0.00 -0.00] [-0.00 -0.00 -0.00 -0.00 33.77 4.29] [0.00 -0.00 -0.00 -0.00 4.62 36.86]]| Voigt-notation elastic module;sequence of row and column is (xx, yy, zz, yz, zx, xy)|
| bulk modulus(GPa) | real number | 80.78 | bulk modulus |
Expand All @@ -895,7 +895,7 @@ conf_dir:confs/Al/std-fcc
```
+ `supercell`:(list of integer) the supercell size used to generate vacancy defect and interstitial defect

|Key | Type | Example | Discription |
|Key | Type | Example | Description |
| :---------------- | :--------------------- | :-------------------------------------- | :-------------------------------------------------------------|
| supercell | list of integer | [3,3,3] | the supercell size used to generate vacancy defect and interstitial defect |

Expand All @@ -905,7 +905,7 @@ conf_dir:confs/Al/std-fcc
Structure: Vac_E(eV) E(eV) equi_E(eV)
struct-3x3x3-000: 0.859 -96.557 -97.416
```
| Field | Type | Example | Discription |
| Field | Type | Example | Description |
| :---------------- | :--------------------- | :-------------------------------------- | :-------------------------------------------------------------|
|Structure| list of string |['struct-3x3x3-000'] | structure name|
| Vac_E(eV) | real number |0.723 | the vacancy formation energy |
Expand All @@ -921,7 +921,7 @@ struct-3x3x3-000: 0.859 -96.557 -97.416
+ `insert_ele`:(list of string) the elements used to generate point interstitial defect
+ `repord-opt`:(boolean) whether to reproduce trajectories of interstitial defect

|Key | Type | Example | Discription |
|Key | Type | Example | Description |
| :---------------- | :--------------------- | :-------------------------------------- | :-------------------------------------------------------------|
| insert_ele | list of string | ["Al"] | the elements used to generate point interstitial defect |
| reprod-opt | boolean | false | whether to reproduce trajectories of interstitial defect|
Expand All @@ -933,7 +933,7 @@ Insert_ele-Struct: Inter_E(eV) E(eV) equi_E(eV)
struct-Al-3x3x3-000: 3.919 -100.991 -104.909
struct-Al-3x3x3-001: 2.681 -102.229 -104.909
```
| Field | Type | Example | Discription |
| Field | Type | Example | Description |
| :---------------- | :--------------------- | :-------------------------------------- | :-------------------------------------------------------------|
|Structure| string |'struct-Al-3x3x3-000' | structure name|
| Inter_E(eV) | real number |0.723 | the interstitial formation energy |
Expand All @@ -958,7 +958,7 @@ struct-Al-3x3x3-001: 2.681 -102.229 -104.909
+ `static-opt`:(boolean) whether to use atomic relaxation to compute surface energy. if false, the structure will be relaxed.
+ `relax_box`:(boolean) set true if the box is relaxed, otherwise only relax atom positions.

|Key | Type | Example | Discription |
|Key | Type | Example | Description |
| :---------------- | :--------------------- | :-------------------------------------- | :-------------------------------------------------------------|
| min_slab_size| real number| 10 | the minimum size of slab thickness |
|min_vacuum_size | real number| 11 | the minimum size of the vacuume width |
Expand All @@ -974,7 +974,7 @@ Miller_Indices: Surf_E(J/m^2) EpA(eV) equi_EpA(eV)
struct-000-m1.1.1m: 0.673 -3.628 -3.747
struct-001-m2.2.1m: 0.917 -3.592 -3.747
```
| Field | Type | Example| Discription|
| Field | Type | Example| Description|
| :---------------- | :--------------------- | :-------------------------------------- | :-------------------------------------------------------------|
|Miller_Indices| string | struct-000-m1.1.1m | Miller Indices|
|Surf_E(J/m^2)| real number | 0.673 | the surface formation energy |
Expand Down Expand Up @@ -1315,7 +1315,7 @@ Following table illustrates which key is needed for three types of machine: `tra
The following table gives explicit descriptions on keys in param.json.


Key | Type | Example | Discription |
Key | Type | Example | Description |
| :---------------- | :--------------------- | :-------------------------------------- | :-------------------------------------------------------------|
| machine | Dict | | Settings of the machine for TASK.
| resources | Dict | | Resources needed for calculation.
Expand Down