From 38be602e9ac34a53486576cefdc01eb4040504c9 Mon Sep 17 00:00:00 2001 From: pee8379 Date: Wed, 8 Jun 2022 16:51:13 +0900 Subject: [PATCH] Update README.md It seems 'pert_box' dose not work as percentage. --- README.md | 42 +++++++++++++++++++++--------------------- 1 file changed, 21 insertions(+), 21 deletions(-) diff --git a/README.md b/README.md index b59725ec9..86a1998cf 100644 --- a/README.md +++ b/README.md @@ -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 @@ -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. @@ -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 @@ -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. @@ -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 @@ -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.| @@ -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 | @@ -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 | @@ -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 | @@ -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 | @@ -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 | @@ -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 | @@ -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 | @@ -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 | @@ -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 | @@ -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 | @@ -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| @@ -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 | @@ -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 | @@ -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 | @@ -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.