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wanghan-iapcm merged 2 commits into from
Feb 24, 2023
Merged

Correct the headers in README.md #424

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5d7fae0
Correct the header of `Mixed Type Format` in README.md
iProzd Feb 23, 2023
3bcad48
Fix headers in README.md
iProzd Feb 23, 2023
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24 changes: 12 additions & 12 deletions README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@
dpdata only works with python 3.7 or above.


# Installation
## Installation
One can download the source code of dpdata by
```bash
git clone https://github.com/deepmodeling/dpdata.git dpdata
Expand All @@ -19,7 +19,7 @@ pip install dpdata
```


# Quick start
## Quick start

This section gives some examples on how dpdata works. Firstly one needs to import the module in a python 3.x compatible code.
```python
Expand All @@ -32,7 +32,7 @@ The typicall workflow of `dpdata` is
3. Dump data to in a desired format


## Load data
### Load data
```python
d_poscar = dpdata.System("POSCAR", fmt="vasp/poscar")
```
Expand Down Expand Up @@ -150,7 +150,7 @@ ms.to_deepmd_raw("deepmd")
ms.to_deepmd_npy("deepmd")
```

## Access data
### Access data
These properties stored in `System` and `LabeledSystem` can be accessed by operator `[]` with the key of the property supplied, for example
```python
coords = d_outcar["coords"]
Expand All @@ -169,7 +169,7 @@ Available properties are (nframe: number of frames in the system, natoms: total
| 'virials' | np.ndarray | nframes x 3 x 3 | True | The virial tensor of each frame


## Dump data
### Dump data
The data stored in `System` or `LabeledSystem` can be dumped in 'lammps/lmp' or 'vasp/poscar' format, for example:
```python
d_outcar.to("lammps/lmp", "conf.lmp", frame_idx=0)
Expand All @@ -195,7 +195,7 @@ dpdata.LabeledSystem("OUTCAR").sub_system([0, -1]).to("deepmd/raw", "dpmd_raw")
by which only the first and last frames are dumped to `dpmd_raw`.


## replicate
### replicate
dpdata will create a super cell of the current atom configuration.
```python
dpdata.System("./POSCAR").replicate(
Expand All @@ -209,7 +209,7 @@ dpdata.System("./POSCAR").replicate(
tuple(1,2,3) means don't copy atom configuration in x direction, make 2 copys in y direction, make 3 copys in z direction.


## perturb
### perturb
By the following example, each frame of the original system (`dpdata.System('./POSCAR')`) is perturbed to generate three new frames. For each frame, the cell is perturbed by 5% and the atom positions are perturbed by 0.6 Angstrom. `atom_pert_style` indicates that the perturbation to the atom positions is subject to normal distribution. Other available options to `atom_pert_style` are`uniform` (uniform in a ball), and `const` (uniform on a sphere).
```python
perturbed_system = dpdata.System("./POSCAR").perturb(
Expand All @@ -221,15 +221,15 @@ perturbed_system = dpdata.System("./POSCAR").perturb(
print(perturbed_system.data)
```

## replace
### replace
By the following example, Random 8 Hf atoms in the system will be replaced by Zr atoms with the atom postion unchanged.
```python
s = dpdata.System("tests/poscars/POSCAR.P42nmc", fmt="vasp/poscar")
s.replace("Hf", "Zr", 8)
s.to_vasp_poscar("POSCAR.P42nmc.replace")
```

# BondOrderSystem
## BondOrderSystem
A new class `BondOrderSystem` which inherits from class `System` is introduced in dpdata. This new class contains information of chemical bonds and formal charges (stored in `BondOrderSystem.data['bonds']`, `BondOrderSystem.data['formal_charges']`). Now BondOrderSystem can only read from .mol/.sdf formats, because of its dependency on rdkit (which means rdkit must be installed if you want to use this function). Other formats, such as pdb, must be converted to .mol/.sdf format (maybe with software like open babel).
```python
import dpdata
Expand All @@ -254,7 +254,7 @@ AllChem.EmbedMultipleConfs(mol, 10)
system = dpdata.BondOrderSystem(rdkit_mol=mol)
```

## Bond Order Assignment
### Bond Order Assignment
The `BondOrderSystem` implements a more robust sanitize procedure for rdkit Mol, as defined in `dpdata.rdkit.santizie.Sanitizer`. This class defines 3 level of sanitization process by: low, medium and high. (default is medium).
+ low: use `rdkit.Chem.SanitizeMol()` function to sanitize molecule.
+ medium: before using rdkit, the programm will first assign formal charge of each atom to avoid inappropriate valence exceptions. However, this mode requires the rightness of the bond order information in the given molecule.
Expand All @@ -268,7 +268,7 @@ import dpdata
for sdf_file in glob.glob("bond_order/refined-set-ligands/obabel/*sdf"):
syst = dpdata.BondOrderSystem(sdf_file, sanitize_level="high", verbose=False)
```
## Formal Charge Assignment
### Formal Charge Assignment
BondOrderSystem implement a method to assign formal charge for each atom based on the 8-electron rule (see below). Note that it only supports common elements in bio-system: B,C,N,O,P,S,As
```python
import dpdata
Expand Down Expand Up @@ -304,7 +304,7 @@ import dpdata
dpdata.MultiSystems().load_systems_from_file("mixed_dir", fmt="deepmd/npy/mixed")
```

# Plugins
## Plugins

One can follow [a simple example](plugin_example/) to add their own format by creating and installing plugins. It's critical to add the [Format](dpdata/format.py) class to `entry_points['dpdata.plugins']` in [`pyproject.toml`](plugin_example/pyproject.toml):
```toml
Expand Down