path: root/python-dpdata.spec

%global _empty_manifest_terminate_build 0
Name:		python-dpdata
Version:	0.2.15
Release:	1
Summary:	Manipulating data formats of DeePMD-kit, VASP, QE, PWmat, and LAMMPS, etc.
License:	GNU LESSER GENERAL PUBLIC LICENSE Version 3, 29 June 2007  Copyright (C) 2007 Free Software Foundation, Inc. <https://fsf.org/> Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed.   This version of the GNU Lesser General Public License incorporates the terms and conditions of version 3 of the GNU General Public License, supplemented by the additional permissions listed below.  0. Additional Definitions.  As used herein, "this License" refers to version 3 of the GNU Lesser General Public License, and the "GNU GPL" refers to version 3 of the GNU General Public License.  "The Library" refers to a covered work governed by this License, other than an Application or a Combined Work as defined below.  An "Application" is any work that makes use of an interface provided by the Library, but which is not otherwise based on the Library. 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Each version is given a distinguishing version number. If the Library as you received it specifies that a certain numbered version of the GNU Lesser General Public License "or any later version" applies to it, you have the option of following the terms and conditions either of that published version or of any later version published by the Free Software Foundation. If the Library as you received it does not specify a version number of the GNU Lesser General Public License, you may choose any version of the GNU Lesser General Public License ever published by the Free Software Foundation.  If the Library as you received it specifies that a proxy can decide whether future versions of the GNU Lesser General Public License shall apply, that proxy's public statement of acceptance of any version is permanent authorization for you to choose that version for the Library. 
URL:		https://github.com/deepmodeling/dpdata
Source0:	https://mirrors.nju.edu.cn/pypi/web/packages/b2/fd/fb65e3e1d7a183848135f019cef536e91d5ac9b9b87008c3bb83d5e6ce6e/dpdata-0.2.15.tar.gz
BuildArch:	noarch

Requires:	python3-numpy
Requires:	python3-monty
Requires:	python3-scipy
Requires:	python3-h5py
Requires:	python3-wcmatch
Requires:	python3-importlib-metadata
Requires:	python3-parmed
Requires:	python3-parmed
Requires:	python3-ase
Requires:	python3-sphinx
Requires:	python3-recommonmark
Requires:	python3-sphinx-rtd-theme
Requires:	python3-numpydoc
Requires:	python3-m2r2
Requires:	python3-deepmodeling-sphinx
Requires:	python3-sphinx-argparse
Requires:	python3-pymatgen

%description
**dpdata** is a python package for manipulating data formats of software in computational science, including DeePMD-kit, VASP, LAMMPS, GROMACS, Gaussian.
dpdata only works with python 3.7 or above.


## Installation
One can download the source code of dpdata by
```bash
git clone https://github.com/deepmodeling/dpdata.git dpdata
```
then use `pip` to install the module from source
```bash
cd dpdata
pip install .
```

`dpdata` can also by install via pip without source
```bash
pip install dpdata
```


## 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
import dpdata
```
The typicall workflow of `dpdata` is

1. Load data from vasp or lammps or deepmd-kit data files.
2. Manipulate data
3. Dump data to in a desired format


### Load data
```python
d_poscar = dpdata.System("POSCAR", fmt="vasp/poscar")
```
or let dpdata infer the format (`vasp/poscar`) of the file from the file name extension
```python
d_poscar = dpdata.System("my.POSCAR")
```
The number of atoms, atom types, coordinates are loaded from the `POSCAR` and stored to a data `System` called `d_poscar`.
A data `System` (a concept used by [deepmd-kit](https://github.com/deepmodeling/deepmd-kit)) contains frames that has the same number of atoms of the same type. The order of the atoms should be consistent among the frames in one `System`.
It is noted that `POSCAR` only contains one frame.
If the multiple frames stored in, for example, a `OUTCAR` is wanted,
```python
d_outcar = dpdata.LabeledSystem("OUTCAR")
```
The labels provided in the `OUTCAR`, i.e. energies, forces and virials (if any), are loaded by `LabeledSystem`. It is noted that the forces of atoms are always assumed to exist. `LabeledSystem` is a derived class of `System`.

The `System` or `LabeledSystem` can be constructed from the following file formats with the `format key` in the table passed to argument `fmt`:

| Software| format | multi frames | labeled | class	    | format key    |
| ------- | :---   | :---:        | :---:   | :---          | :---          |
| vasp	  | poscar | False        | False   | System	    | 'vasp/poscar' |
| vasp    | outcar | True         | True    | LabeledSystem | 'vasp/outcar' |
| vasp    | xml    | True         | True    | LabeledSystem | 'vasp/xml'    |
| lammps  | lmp    | False        | False   | System        | 'lammps/lmp'  |
| lammps  | dump   | True         | False   | System        | 'lammps/dump' |
| deepmd  | raw    | True         | False   | System	    | 'deepmd/raw'  |
| deepmd  | npy    | True         | False   | System        | 'deepmd/npy'  |
| deepmd  | raw    | True         | True    | LabeledSystem | 'deepmd/raw'  |
| deepmd  | npy    | True         | True    | LabeledSystem | 'deepmd/npy'  |
| deepmd  | npy    | True         | True    | MultiSystems | 'deepmd/npy/mixed'  |
| deepmd  | npy    | True         | False    | MultiSystems | 'deepmd/npy/mixed'  |
| gaussian| log    | False        | True    | LabeledSystem | 'gaussian/log'|
| gaussian| log    | True         | True    | LabeledSystem | 'gaussian/md' |
| siesta  | output | False        | True    | LabeledSystem | 'siesta/output'|
| siesta  | aimd_output  | True         | True    | LabeledSystem | 'siesta/aimd_output' |
| cp2k    | output | False        | True    | LabeledSystem | 'cp2k/output' |
| cp2k    | aimd_output  | True         | True    | LabeledSystem | 'cp2k/aimd_output' |
| QE      | log    | False        | True    | LabeledSystem | 'qe/pw/scf'   |
| QE      | log    | True         | False   | System        | 'qe/cp/traj'  |
| QE      | log    | True         | True    | LabeledSystem | 'qe/cp/traj'  |
| Fhi-aims| output | True         | True    | LabeledSystem | 'fhi_aims/md'  |
| Fhi-aims| output | False        | True    | LabeledSystem | 'fhi_aims/scf'  |
|quip/gap|xyz|True|True|MultiSystems|'quip/gap/xyz'|
| PWmat   | atom.config | False        | False   | System        | 'pwmat/atom.config'  |
| PWmat   | movement    | True         | True    | LabeledSystem | 'pwmat/movement'     |
| PWmat   | OUT.MLMD    | True         | True    | LabeledSystem | 'pwmat/out.mlmd'     |
| Amber   | multi       | True         | True    | LabeledSystem | 'amber/md'           |
| Amber/sqm | sqm.out   | False        | False   | System        | 'sqm/out'            |
| Gromacs | gro         | True         | False   | System        | 'gromacs/gro'        |
| ABACUS  | STRU        | False        | False   | System        | 'abacus/stru'         |
| ABACUS  | STRU        | False        | True    | LabeledSystem | 'abacus/scf'         |
| ABACUS  | cif         | True         | True    | LabeledSystem | 'abacus/md'          |
| ABACUS  | STRU        | True         | True    | LabeledSystem | 'abacus/relax'       |
| ase     | structure   | True         | True    | MultiSystems  | 'ase/structure'      |


The Class `dpdata.MultiSystems`  can read data  from a dir which may contains many files of different systems, or from single xyz file which contains different systems.

Use `dpdata.MultiSystems.from_dir` to read from a  directory, `dpdata.MultiSystems` will walk in the directory
Recursively  and  find all file with specific file_name. Supports all the file formats that `dpdata.LabeledSystem` supports.

Use  `dpdata.MultiSystems.from_file` to read from single file. Single-file support is available for the `quip/gap/xyz` and `ase/structure` formats.

For example, for `quip/gap xyz` files, single .xyz file may contain many different configurations with different atom numbers and atom type.

The following commands relating to `Class dpdata.MultiSystems` may be useful.
```python
# load data

xyz_multi_systems = dpdata.MultiSystems.from_file(
    file_name="tests/xyz/xyz_unittest.xyz", fmt="quip/gap/xyz"
)
vasp_multi_systems = dpdata.MultiSystems.from_dir(
    dir_name="./mgal_outcar", file_name="OUTCAR", fmt="vasp/outcar"
)

# use wildcard
vasp_multi_systems = dpdata.MultiSystems.from_dir(
    dir_name="./mgal_outcar", file_name="*OUTCAR", fmt="vasp/outcar"
)

# print the multi_system infomation
print(xyz_multi_systems)
print(xyz_multi_systems.systems)  # return a dictionaries

# print the system infomation
print(xyz_multi_systems.systems["B1C9"].data)

# dump a system's data to ./my_work_dir/B1C9_raw folder
xyz_multi_systems.systems["B1C9"].to_deepmd_raw("./my_work_dir/B1C9_raw")

# dump all systems
xyz_multi_systems.to_deepmd_raw("./my_deepmd_data/")
```

You may also use the following code to parse muti-system:
```python
from dpdata import LabeledSystem, MultiSystems
from glob import glob

"""
process multi systems
"""
fs = glob("./*/OUTCAR")  # remeber to change here !!!
ms = MultiSystems()
for f in fs:
    try:
        ls = LabeledSystem(f)
    except:
        print(f)
    if len(ls) > 0:
        ms.append(ls)

ms.to_deepmd_raw("deepmd")
ms.to_deepmd_npy("deepmd")
```

### 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"]
```
Available properties are (nframe: number of frames in the system, natoms: total number of atoms in the system)

| key		|  type		| dimension		| are labels	| description
| ---		| ---		| ---			| ---		| ---
| 'atom_names'	| list of str	| ntypes		| False		| The name of each atom type
| 'atom_numbs'	| list of int	| ntypes		| False		| The number of atoms of each atom type
| 'atom_types'	| np.ndarray	| natoms		| False		| Array assigning type to each atom
| 'cells'	| np.ndarray	| nframes x 3 x 3	| False		| The cell tensor of each frame
| 'coords'	| np.ndarray	| nframes x natoms x 3	| False		| The atom coordinates
| 'energies'	| np.ndarray	| nframes		| True		| The frame energies
| 'forces'	| np.ndarray	| nframes x natoms x 3	| True		| The atom forces
| 'virials'	| np.ndarray	| nframes x 3 x 3	| True		| The virial tensor of each frame


### 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)
```
The first frames of `d_outcar` will be dumped to 'conf.lmp'
```python
d_outcar.to("vasp/poscar", "POSCAR", frame_idx=-1)
```
The last frames of `d_outcar` will be dumped to 'POSCAR'.

The data stored in `LabeledSystem` can be dumped to deepmd-kit raw format, for example
```python
d_outcar.to("deepmd/raw", "dpmd_raw")
```
Or a simpler command:
```python
dpdata.LabeledSystem("OUTCAR").to("deepmd/raw", "dpmd_raw")
```
Frame selection can be implemented by
```python
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
dpdata will create a super cell of the current atom configuration.
```python
dpdata.System("./POSCAR").replicate(
    (
        1,
        2,
        3,
    )
)
```
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
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(
    pert_num=3,
    cell_pert_fraction=0.05,
    atom_pert_distance=0.6,
    atom_pert_style="normal",
)
print(perturbed_system.data)
```

### 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
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

system_1 = dpdata.BondOrderSystem(
    "tests/bond_order/CH3OH.mol", fmt="mol"
)  # read from .mol file
system_2 = dpdata.BondOrderSystem(
    "tests/bond_order/methane.sdf", fmt="sdf"
)  # read from .sdf file
```
In sdf file, all molecules must be of the same topology (i.e. conformers of the same molecular configuration).
`BondOrderSystem` also supports initialize from a `rdkit.Chem.rdchem.Mol` object directly.
```python
from rdkit import Chem
from rdkit.Chem import AllChem
import dpdata

mol = Chem.MolFromSmiles("CC")
mol = Chem.AddHs(mol)
AllChem.EmbedMultipleConfs(mol, 10)
system = dpdata.BondOrderSystem(rdkit_mol=mol)
```

### 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.
+ high: the program will try to fix inappropriate bond orders in aromatic hetreocycles, phosphate, sulfate, carboxyl, nitro, nitrine, guanidine groups. If this procedure fails to sanitize the given molecule, the program will then try to call `obabel` to pre-process the mol and repeat the sanitization procedure. **That is to say, if you wan't to use this level of sanitization, please ensure `obabel` is installed in the environment.**
According to our test, our sanitization procedure can successfully read 4852 small molecules in the PDBBind-refined-set. It is necessary to point out that the in the molecule file (mol/sdf), the number of explicit hydrogens has to be correct. Thus, we recommend to use
 `obabel xxx -O xxx -h` to pre-process the file. The reason why we do not implement this hydrogen-adding procedure in dpdata is that we can not ensure its correctness.

```python
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
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

syst = dpdata.BondOrderSystem("tests/bond_order/CH3NH3+.mol", fmt="mol")
print(syst.get_formal_charges())  # return the formal charge on each atom
print(syst.get_charge())  # return the total charge of the system
```

If a valence of 3 is detected on carbon, the formal charge will be assigned to -1. Because for most cases (in alkynyl anion, isonitrile, cyclopentadienyl anion), the formal charge on 3-valence carbon is -1, and this is also consisent with the 8-electron rule.

## Mixed Type Format
The format `deepmd/npy/mixed` is the mixed type numpy format for DeePMD-kit, and can be loaded or dumped through class `dpdata.MultiSystems`.

Under this format, systems with the same number of atoms but different formula can be put together
for a larger system, especially when the frame numbers in systems are sparse.

This also helps to mixture the type information together for model training with type embedding network.

Here are examples using `deepmd/npy/mixed` format:

- Dump a MultiSystems into a mixed type numpy directory:
```python
import dpdata

dpdata.MultiSystems(*systems).to_deepmd_npy_mixed("mixed_dir")
```

- Load a mixed type data into a MultiSystems:
```python
import dpdata

dpdata.MultiSystems().load_systems_from_file("mixed_dir", fmt="deepmd/npy/mixed")
```

## 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
[project.entry-points.'dpdata.plugins']
random = "dpdata_random:RandomFormat"
```


%package -n python3-dpdata
Summary:	Manipulating data formats of DeePMD-kit, VASP, QE, PWmat, and LAMMPS, etc.
Provides:	python-dpdata
BuildRequires:	python3-devel
BuildRequires:	python3-setuptools
BuildRequires:	python3-pip
%description -n python3-dpdata
**dpdata** is a python package for manipulating data formats of software in computational science, including DeePMD-kit, VASP, LAMMPS, GROMACS, Gaussian.
dpdata only works with python 3.7 or above.


## Installation
One can download the source code of dpdata by
```bash
git clone https://github.com/deepmodeling/dpdata.git dpdata
```
then use `pip` to install the module from source
```bash
cd dpdata
pip install .
```

`dpdata` can also by install via pip without source
```bash
pip install dpdata
```


## 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
import dpdata
```
The typicall workflow of `dpdata` is

1. Load data from vasp or lammps or deepmd-kit data files.
2. Manipulate data
3. Dump data to in a desired format


### Load data
```python
d_poscar = dpdata.System("POSCAR", fmt="vasp/poscar")
```
or let dpdata infer the format (`vasp/poscar`) of the file from the file name extension
```python
d_poscar = dpdata.System("my.POSCAR")
```
The number of atoms, atom types, coordinates are loaded from the `POSCAR` and stored to a data `System` called `d_poscar`.
A data `System` (a concept used by [deepmd-kit](https://github.com/deepmodeling/deepmd-kit)) contains frames that has the same number of atoms of the same type. The order of the atoms should be consistent among the frames in one `System`.
It is noted that `POSCAR` only contains one frame.
If the multiple frames stored in, for example, a `OUTCAR` is wanted,
```python
d_outcar = dpdata.LabeledSystem("OUTCAR")
```
The labels provided in the `OUTCAR`, i.e. energies, forces and virials (if any), are loaded by `LabeledSystem`. It is noted that the forces of atoms are always assumed to exist. `LabeledSystem` is a derived class of `System`.

The `System` or `LabeledSystem` can be constructed from the following file formats with the `format key` in the table passed to argument `fmt`:

| Software| format | multi frames | labeled | class	    | format key    |
| ------- | :---   | :---:        | :---:   | :---          | :---          |
| vasp	  | poscar | False        | False   | System	    | 'vasp/poscar' |
| vasp    | outcar | True         | True    | LabeledSystem | 'vasp/outcar' |
| vasp    | xml    | True         | True    | LabeledSystem | 'vasp/xml'    |
| lammps  | lmp    | False        | False   | System        | 'lammps/lmp'  |
| lammps  | dump   | True         | False   | System        | 'lammps/dump' |
| deepmd  | raw    | True         | False   | System	    | 'deepmd/raw'  |
| deepmd  | npy    | True         | False   | System        | 'deepmd/npy'  |
| deepmd  | raw    | True         | True    | LabeledSystem | 'deepmd/raw'  |
| deepmd  | npy    | True         | True    | LabeledSystem | 'deepmd/npy'  |
| deepmd  | npy    | True         | True    | MultiSystems | 'deepmd/npy/mixed'  |
| deepmd  | npy    | True         | False    | MultiSystems | 'deepmd/npy/mixed'  |
| gaussian| log    | False        | True    | LabeledSystem | 'gaussian/log'|
| gaussian| log    | True         | True    | LabeledSystem | 'gaussian/md' |
| siesta  | output | False        | True    | LabeledSystem | 'siesta/output'|
| siesta  | aimd_output  | True         | True    | LabeledSystem | 'siesta/aimd_output' |
| cp2k    | output | False        | True    | LabeledSystem | 'cp2k/output' |
| cp2k    | aimd_output  | True         | True    | LabeledSystem | 'cp2k/aimd_output' |
| QE      | log    | False        | True    | LabeledSystem | 'qe/pw/scf'   |
| QE      | log    | True         | False   | System        | 'qe/cp/traj'  |
| QE      | log    | True         | True    | LabeledSystem | 'qe/cp/traj'  |
| Fhi-aims| output | True         | True    | LabeledSystem | 'fhi_aims/md'  |
| Fhi-aims| output | False        | True    | LabeledSystem | 'fhi_aims/scf'  |
|quip/gap|xyz|True|True|MultiSystems|'quip/gap/xyz'|
| PWmat   | atom.config | False        | False   | System        | 'pwmat/atom.config'  |
| PWmat   | movement    | True         | True    | LabeledSystem | 'pwmat/movement'     |
| PWmat   | OUT.MLMD    | True         | True    | LabeledSystem | 'pwmat/out.mlmd'     |
| Amber   | multi       | True         | True    | LabeledSystem | 'amber/md'           |
| Amber/sqm | sqm.out   | False        | False   | System        | 'sqm/out'            |
| Gromacs | gro         | True         | False   | System        | 'gromacs/gro'        |
| ABACUS  | STRU        | False        | False   | System        | 'abacus/stru'         |
| ABACUS  | STRU        | False        | True    | LabeledSystem | 'abacus/scf'         |
| ABACUS  | cif         | True         | True    | LabeledSystem | 'abacus/md'          |
| ABACUS  | STRU        | True         | True    | LabeledSystem | 'abacus/relax'       |
| ase     | structure   | True         | True    | MultiSystems  | 'ase/structure'      |


The Class `dpdata.MultiSystems`  can read data  from a dir which may contains many files of different systems, or from single xyz file which contains different systems.

Use `dpdata.MultiSystems.from_dir` to read from a  directory, `dpdata.MultiSystems` will walk in the directory
Recursively  and  find all file with specific file_name. Supports all the file formats that `dpdata.LabeledSystem` supports.

Use  `dpdata.MultiSystems.from_file` to read from single file. Single-file support is available for the `quip/gap/xyz` and `ase/structure` formats.

For example, for `quip/gap xyz` files, single .xyz file may contain many different configurations with different atom numbers and atom type.

The following commands relating to `Class dpdata.MultiSystems` may be useful.
```python
# load data

xyz_multi_systems = dpdata.MultiSystems.from_file(
    file_name="tests/xyz/xyz_unittest.xyz", fmt="quip/gap/xyz"
)
vasp_multi_systems = dpdata.MultiSystems.from_dir(
    dir_name="./mgal_outcar", file_name="OUTCAR", fmt="vasp/outcar"
)

# use wildcard
vasp_multi_systems = dpdata.MultiSystems.from_dir(
    dir_name="./mgal_outcar", file_name="*OUTCAR", fmt="vasp/outcar"
)

# print the multi_system infomation
print(xyz_multi_systems)
print(xyz_multi_systems.systems)  # return a dictionaries

# print the system infomation
print(xyz_multi_systems.systems["B1C9"].data)

# dump a system's data to ./my_work_dir/B1C9_raw folder
xyz_multi_systems.systems["B1C9"].to_deepmd_raw("./my_work_dir/B1C9_raw")

# dump all systems
xyz_multi_systems.to_deepmd_raw("./my_deepmd_data/")
```

You may also use the following code to parse muti-system:
```python
from dpdata import LabeledSystem, MultiSystems
from glob import glob

"""
process multi systems
"""
fs = glob("./*/OUTCAR")  # remeber to change here !!!
ms = MultiSystems()
for f in fs:
    try:
        ls = LabeledSystem(f)
    except:
        print(f)
    if len(ls) > 0:
        ms.append(ls)

ms.to_deepmd_raw("deepmd")
ms.to_deepmd_npy("deepmd")
```

### 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"]
```
Available properties are (nframe: number of frames in the system, natoms: total number of atoms in the system)

| key		|  type		| dimension		| are labels	| description
| ---		| ---		| ---			| ---		| ---
| 'atom_names'	| list of str	| ntypes		| False		| The name of each atom type
| 'atom_numbs'	| list of int	| ntypes		| False		| The number of atoms of each atom type
| 'atom_types'	| np.ndarray	| natoms		| False		| Array assigning type to each atom
| 'cells'	| np.ndarray	| nframes x 3 x 3	| False		| The cell tensor of each frame
| 'coords'	| np.ndarray	| nframes x natoms x 3	| False		| The atom coordinates
| 'energies'	| np.ndarray	| nframes		| True		| The frame energies
| 'forces'	| np.ndarray	| nframes x natoms x 3	| True		| The atom forces
| 'virials'	| np.ndarray	| nframes x 3 x 3	| True		| The virial tensor of each frame


### 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)
```
The first frames of `d_outcar` will be dumped to 'conf.lmp'
```python
d_outcar.to("vasp/poscar", "POSCAR", frame_idx=-1)
```
The last frames of `d_outcar` will be dumped to 'POSCAR'.

The data stored in `LabeledSystem` can be dumped to deepmd-kit raw format, for example
```python
d_outcar.to("deepmd/raw", "dpmd_raw")
```
Or a simpler command:
```python
dpdata.LabeledSystem("OUTCAR").to("deepmd/raw", "dpmd_raw")
```
Frame selection can be implemented by
```python
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
dpdata will create a super cell of the current atom configuration.
```python
dpdata.System("./POSCAR").replicate(
    (
        1,
        2,
        3,
    )
)
```
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
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(
    pert_num=3,
    cell_pert_fraction=0.05,
    atom_pert_distance=0.6,
    atom_pert_style="normal",
)
print(perturbed_system.data)
```

### 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
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

system_1 = dpdata.BondOrderSystem(
    "tests/bond_order/CH3OH.mol", fmt="mol"
)  # read from .mol file
system_2 = dpdata.BondOrderSystem(
    "tests/bond_order/methane.sdf", fmt="sdf"
)  # read from .sdf file
```
In sdf file, all molecules must be of the same topology (i.e. conformers of the same molecular configuration).
`BondOrderSystem` also supports initialize from a `rdkit.Chem.rdchem.Mol` object directly.
```python
from rdkit import Chem
from rdkit.Chem import AllChem
import dpdata

mol = Chem.MolFromSmiles("CC")
mol = Chem.AddHs(mol)
AllChem.EmbedMultipleConfs(mol, 10)
system = dpdata.BondOrderSystem(rdkit_mol=mol)
```

### 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.
+ high: the program will try to fix inappropriate bond orders in aromatic hetreocycles, phosphate, sulfate, carboxyl, nitro, nitrine, guanidine groups. If this procedure fails to sanitize the given molecule, the program will then try to call `obabel` to pre-process the mol and repeat the sanitization procedure. **That is to say, if you wan't to use this level of sanitization, please ensure `obabel` is installed in the environment.**
According to our test, our sanitization procedure can successfully read 4852 small molecules in the PDBBind-refined-set. It is necessary to point out that the in the molecule file (mol/sdf), the number of explicit hydrogens has to be correct. Thus, we recommend to use
 `obabel xxx -O xxx -h` to pre-process the file. The reason why we do not implement this hydrogen-adding procedure in dpdata is that we can not ensure its correctness.

```python
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
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

syst = dpdata.BondOrderSystem("tests/bond_order/CH3NH3+.mol", fmt="mol")
print(syst.get_formal_charges())  # return the formal charge on each atom
print(syst.get_charge())  # return the total charge of the system
```

If a valence of 3 is detected on carbon, the formal charge will be assigned to -1. Because for most cases (in alkynyl anion, isonitrile, cyclopentadienyl anion), the formal charge on 3-valence carbon is -1, and this is also consisent with the 8-electron rule.

## Mixed Type Format
The format `deepmd/npy/mixed` is the mixed type numpy format for DeePMD-kit, and can be loaded or dumped through class `dpdata.MultiSystems`.

Under this format, systems with the same number of atoms but different formula can be put together
for a larger system, especially when the frame numbers in systems are sparse.

This also helps to mixture the type information together for model training with type embedding network.

Here are examples using `deepmd/npy/mixed` format:

- Dump a MultiSystems into a mixed type numpy directory:
```python
import dpdata

dpdata.MultiSystems(*systems).to_deepmd_npy_mixed("mixed_dir")
```

- Load a mixed type data into a MultiSystems:
```python
import dpdata

dpdata.MultiSystems().load_systems_from_file("mixed_dir", fmt="deepmd/npy/mixed")
```

## 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
[project.entry-points.'dpdata.plugins']
random = "dpdata_random:RandomFormat"
```


%package help
Summary:	Development documents and examples for dpdata
Provides:	python3-dpdata-doc
%description help
**dpdata** is a python package for manipulating data formats of software in computational science, including DeePMD-kit, VASP, LAMMPS, GROMACS, Gaussian.
dpdata only works with python 3.7 or above.


## Installation
One can download the source code of dpdata by
```bash
git clone https://github.com/deepmodeling/dpdata.git dpdata
```
then use `pip` to install the module from source
```bash
cd dpdata
pip install .
```

`dpdata` can also by install via pip without source
```bash
pip install dpdata
```


## 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
import dpdata
```
The typicall workflow of `dpdata` is

1. Load data from vasp or lammps or deepmd-kit data files.
2. Manipulate data
3. Dump data to in a desired format


### Load data
```python
d_poscar = dpdata.System("POSCAR", fmt="vasp/poscar")
```
or let dpdata infer the format (`vasp/poscar`) of the file from the file name extension
```python
d_poscar = dpdata.System("my.POSCAR")
```
The number of atoms, atom types, coordinates are loaded from the `POSCAR` and stored to a data `System` called `d_poscar`.
A data `System` (a concept used by [deepmd-kit](https://github.com/deepmodeling/deepmd-kit)) contains frames that has the same number of atoms of the same type. The order of the atoms should be consistent among the frames in one `System`.
It is noted that `POSCAR` only contains one frame.
If the multiple frames stored in, for example, a `OUTCAR` is wanted,
```python
d_outcar = dpdata.LabeledSystem("OUTCAR")
```
The labels provided in the `OUTCAR`, i.e. energies, forces and virials (if any), are loaded by `LabeledSystem`. It is noted that the forces of atoms are always assumed to exist. `LabeledSystem` is a derived class of `System`.

The `System` or `LabeledSystem` can be constructed from the following file formats with the `format key` in the table passed to argument `fmt`:

| Software| format | multi frames | labeled | class	    | format key    |
| ------- | :---   | :---:        | :---:   | :---          | :---          |
| vasp	  | poscar | False        | False   | System	    | 'vasp/poscar' |
| vasp    | outcar | True         | True    | LabeledSystem | 'vasp/outcar' |
| vasp    | xml    | True         | True    | LabeledSystem | 'vasp/xml'    |
| lammps  | lmp    | False        | False   | System        | 'lammps/lmp'  |
| lammps  | dump   | True         | False   | System        | 'lammps/dump' |
| deepmd  | raw    | True         | False   | System	    | 'deepmd/raw'  |
| deepmd  | npy    | True         | False   | System        | 'deepmd/npy'  |
| deepmd  | raw    | True         | True    | LabeledSystem | 'deepmd/raw'  |
| deepmd  | npy    | True         | True    | LabeledSystem | 'deepmd/npy'  |
| deepmd  | npy    | True         | True    | MultiSystems | 'deepmd/npy/mixed'  |
| deepmd  | npy    | True         | False    | MultiSystems | 'deepmd/npy/mixed'  |
| gaussian| log    | False        | True    | LabeledSystem | 'gaussian/log'|
| gaussian| log    | True         | True    | LabeledSystem | 'gaussian/md' |
| siesta  | output | False        | True    | LabeledSystem | 'siesta/output'|
| siesta  | aimd_output  | True         | True    | LabeledSystem | 'siesta/aimd_output' |
| cp2k    | output | False        | True    | LabeledSystem | 'cp2k/output' |
| cp2k    | aimd_output  | True         | True    | LabeledSystem | 'cp2k/aimd_output' |
| QE      | log    | False        | True    | LabeledSystem | 'qe/pw/scf'   |
| QE      | log    | True         | False   | System        | 'qe/cp/traj'  |
| QE      | log    | True         | True    | LabeledSystem | 'qe/cp/traj'  |
| Fhi-aims| output | True         | True    | LabeledSystem | 'fhi_aims/md'  |
| Fhi-aims| output | False        | True    | LabeledSystem | 'fhi_aims/scf'  |
|quip/gap|xyz|True|True|MultiSystems|'quip/gap/xyz'|
| PWmat   | atom.config | False        | False   | System        | 'pwmat/atom.config'  |
| PWmat   | movement    | True         | True    | LabeledSystem | 'pwmat/movement'     |
| PWmat   | OUT.MLMD    | True         | True    | LabeledSystem | 'pwmat/out.mlmd'     |
| Amber   | multi       | True         | True    | LabeledSystem | 'amber/md'           |
| Amber/sqm | sqm.out   | False        | False   | System        | 'sqm/out'            |
| Gromacs | gro         | True         | False   | System        | 'gromacs/gro'        |
| ABACUS  | STRU        | False        | False   | System        | 'abacus/stru'         |
| ABACUS  | STRU        | False        | True    | LabeledSystem | 'abacus/scf'         |
| ABACUS  | cif         | True         | True    | LabeledSystem | 'abacus/md'          |
| ABACUS  | STRU        | True         | True    | LabeledSystem | 'abacus/relax'       |
| ase     | structure   | True         | True    | MultiSystems  | 'ase/structure'      |


The Class `dpdata.MultiSystems`  can read data  from a dir which may contains many files of different systems, or from single xyz file which contains different systems.

Use `dpdata.MultiSystems.from_dir` to read from a  directory, `dpdata.MultiSystems` will walk in the directory
Recursively  and  find all file with specific file_name. Supports all the file formats that `dpdata.LabeledSystem` supports.

Use  `dpdata.MultiSystems.from_file` to read from single file. Single-file support is available for the `quip/gap/xyz` and `ase/structure` formats.

For example, for `quip/gap xyz` files, single .xyz file may contain many different configurations with different atom numbers and atom type.

The following commands relating to `Class dpdata.MultiSystems` may be useful.
```python
# load data

xyz_multi_systems = dpdata.MultiSystems.from_file(
    file_name="tests/xyz/xyz_unittest.xyz", fmt="quip/gap/xyz"
)
vasp_multi_systems = dpdata.MultiSystems.from_dir(
    dir_name="./mgal_outcar", file_name="OUTCAR", fmt="vasp/outcar"
)

# use wildcard
vasp_multi_systems = dpdata.MultiSystems.from_dir(
    dir_name="./mgal_outcar", file_name="*OUTCAR", fmt="vasp/outcar"
)

# print the multi_system infomation
print(xyz_multi_systems)
print(xyz_multi_systems.systems)  # return a dictionaries

# print the system infomation
print(xyz_multi_systems.systems["B1C9"].data)

# dump a system's data to ./my_work_dir/B1C9_raw folder
xyz_multi_systems.systems["B1C9"].to_deepmd_raw("./my_work_dir/B1C9_raw")

# dump all systems
xyz_multi_systems.to_deepmd_raw("./my_deepmd_data/")
```

You may also use the following code to parse muti-system:
```python
from dpdata import LabeledSystem, MultiSystems
from glob import glob

"""
process multi systems
"""
fs = glob("./*/OUTCAR")  # remeber to change here !!!
ms = MultiSystems()
for f in fs:
    try:
        ls = LabeledSystem(f)
    except:
        print(f)
    if len(ls) > 0:
        ms.append(ls)

ms.to_deepmd_raw("deepmd")
ms.to_deepmd_npy("deepmd")
```

### 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"]
```
Available properties are (nframe: number of frames in the system, natoms: total number of atoms in the system)

| key		|  type		| dimension		| are labels	| description
| ---		| ---		| ---			| ---		| ---
| 'atom_names'	| list of str	| ntypes		| False		| The name of each atom type
| 'atom_numbs'	| list of int	| ntypes		| False		| The number of atoms of each atom type
| 'atom_types'	| np.ndarray	| natoms		| False		| Array assigning type to each atom
| 'cells'	| np.ndarray	| nframes x 3 x 3	| False		| The cell tensor of each frame
| 'coords'	| np.ndarray	| nframes x natoms x 3	| False		| The atom coordinates
| 'energies'	| np.ndarray	| nframes		| True		| The frame energies
| 'forces'	| np.ndarray	| nframes x natoms x 3	| True		| The atom forces
| 'virials'	| np.ndarray	| nframes x 3 x 3	| True		| The virial tensor of each frame


### 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)
```
The first frames of `d_outcar` will be dumped to 'conf.lmp'
```python
d_outcar.to("vasp/poscar", "POSCAR", frame_idx=-1)
```
The last frames of `d_outcar` will be dumped to 'POSCAR'.

The data stored in `LabeledSystem` can be dumped to deepmd-kit raw format, for example
```python
d_outcar.to("deepmd/raw", "dpmd_raw")
```
Or a simpler command:
```python
dpdata.LabeledSystem("OUTCAR").to("deepmd/raw", "dpmd_raw")
```
Frame selection can be implemented by
```python
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
dpdata will create a super cell of the current atom configuration.
```python
dpdata.System("./POSCAR").replicate(
    (
        1,
        2,
        3,
    )
)
```
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
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(
    pert_num=3,
    cell_pert_fraction=0.05,
    atom_pert_distance=0.6,
    atom_pert_style="normal",
)
print(perturbed_system.data)
```

### 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
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

system_1 = dpdata.BondOrderSystem(
    "tests/bond_order/CH3OH.mol", fmt="mol"
)  # read from .mol file
system_2 = dpdata.BondOrderSystem(
    "tests/bond_order/methane.sdf", fmt="sdf"
)  # read from .sdf file
```
In sdf file, all molecules must be of the same topology (i.e. conformers of the same molecular configuration).
`BondOrderSystem` also supports initialize from a `rdkit.Chem.rdchem.Mol` object directly.
```python
from rdkit import Chem
from rdkit.Chem import AllChem
import dpdata

mol = Chem.MolFromSmiles("CC")
mol = Chem.AddHs(mol)
AllChem.EmbedMultipleConfs(mol, 10)
system = dpdata.BondOrderSystem(rdkit_mol=mol)
```

### 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.
+ high: the program will try to fix inappropriate bond orders in aromatic hetreocycles, phosphate, sulfate, carboxyl, nitro, nitrine, guanidine groups. If this procedure fails to sanitize the given molecule, the program will then try to call `obabel` to pre-process the mol and repeat the sanitization procedure. **That is to say, if you wan't to use this level of sanitization, please ensure `obabel` is installed in the environment.**
According to our test, our sanitization procedure can successfully read 4852 small molecules in the PDBBind-refined-set. It is necessary to point out that the in the molecule file (mol/sdf), the number of explicit hydrogens has to be correct. Thus, we recommend to use
 `obabel xxx -O xxx -h` to pre-process the file. The reason why we do not implement this hydrogen-adding procedure in dpdata is that we can not ensure its correctness.

```python
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
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

syst = dpdata.BondOrderSystem("tests/bond_order/CH3NH3+.mol", fmt="mol")
print(syst.get_formal_charges())  # return the formal charge on each atom
print(syst.get_charge())  # return the total charge of the system
```

If a valence of 3 is detected on carbon, the formal charge will be assigned to -1. Because for most cases (in alkynyl anion, isonitrile, cyclopentadienyl anion), the formal charge on 3-valence carbon is -1, and this is also consisent with the 8-electron rule.

## Mixed Type Format
The format `deepmd/npy/mixed` is the mixed type numpy format for DeePMD-kit, and can be loaded or dumped through class `dpdata.MultiSystems`.

Under this format, systems with the same number of atoms but different formula can be put together
for a larger system, especially when the frame numbers in systems are sparse.

This also helps to mixture the type information together for model training with type embedding network.

Here are examples using `deepmd/npy/mixed` format:

- Dump a MultiSystems into a mixed type numpy directory:
```python
import dpdata

dpdata.MultiSystems(*systems).to_deepmd_npy_mixed("mixed_dir")
```

- Load a mixed type data into a MultiSystems:
```python
import dpdata

dpdata.MultiSystems().load_systems_from_file("mixed_dir", fmt="deepmd/npy/mixed")
```

## 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
[project.entry-points.'dpdata.plugins']
random = "dpdata_random:RandomFormat"
```


%prep
%autosetup -n dpdata-0.2.15

%build
%py3_build

%install
%py3_install
install -d -m755 %{buildroot}/%{_pkgdocdir}
if [ -d doc ]; then cp -arf doc %{buildroot}/%{_pkgdocdir}; fi
if [ -d docs ]; then cp -arf docs %{buildroot}/%{_pkgdocdir}; fi
if [ -d example ]; then cp -arf example %{buildroot}/%{_pkgdocdir}; fi
if [ -d examples ]; then cp -arf examples %{buildroot}/%{_pkgdocdir}; fi
pushd %{buildroot}
if [ -d usr/lib ]; then
	find usr/lib -type f -printf "/%h/%f\n" >> filelist.lst
fi
if [ -d usr/lib64 ]; then
	find usr/lib64 -type f -printf "/%h/%f\n" >> filelist.lst
fi
if [ -d usr/bin ]; then
	find usr/bin -type f -printf "/%h/%f\n" >> filelist.lst
fi
if [ -d usr/sbin ]; then
	find usr/sbin -type f -printf "/%h/%f\n" >> filelist.lst
fi
touch doclist.lst
if [ -d usr/share/man ]; then
	find usr/share/man -type f -printf "/%h/%f.gz\n" >> doclist.lst
fi
popd
mv %{buildroot}/filelist.lst .
mv %{buildroot}/doclist.lst .

%files -n python3-dpdata -f filelist.lst
%dir %{python3_sitelib}/*

%files help -f doclist.lst
%{_docdir}/*

%changelog
* Tue May 30 2023 Python_Bot <Python_Bot@openeuler.org> - 0.2.15-1
- Package Spec generated