dpdata-cli

Name: dpdata-cli
Author: jinzhezenggroup

113stars23forks

How to install dpdata-cli?

jinzhezenggroup/computational-chemistry-agent-skills/dpdata-cli

$npx -y skills add jinzhezenggroup/computational-chemistry-agent-skills --skill dpdata-cli

Installs into the current project.

Summary

A command-line utility for converting and manipulating over 50 atomic simulation data formats, including outputs from DFT and MD software (VASP, LAMMPS, Gaussian, QE, CP2K, ABACUS, etc.). USE WHEN you need to convert structural or trajectory files between different computational

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SKILL.md

1	# dpdata CLI
2
3	dpdata is a tool for manipulating multiple atomic simulation data formats. This skill enables format conversion between various DFT/MD software outputs via command line.
4
5	## Quick Start
6
7	Run dpdata via uvx:
8
9	```bash
10	uvx dpdata <from_file> [options]
11	```
12
13	## Command Line Usage
14
15	```text
16	dpdata: Manipulating multiple atomic simulation data formats
17	usage: dpdata [-h] [--to_file TO_FILE] [--from_format FROM_FORMAT]
18	[--to_format TO_FORMAT] [--no-labeled] [--multi]
19	[--type-map TYPE_MAP [TYPE_MAP ...]] [--version]
20	from_file
21	```
22
23	### Arguments
24
25	\| Argument \| Description \|
26	\| --------------------- \| ----------------------------------------------------- \|
27	\| `from_file` \| Read data from a file (positional) \|
28	\| `--to_file`, `-O` \| Dump data to a file \|
29	\| `--from_format`, `-i` \| Format of from_file (default: "auto") \|
30	\| `--to_format`, `-o` \| Format of to_file \|
31	\| `--no-labeled`, `-n` \| Labels aren't provided (default: False) \|
32	\| `--multi`, `-m` \| System contains multiple directories (default: False) \|
33	\| `--type-map`, `-t` \| Type map for atom types \|
34	\| `--version` \| Show dpdata version and exit \|
35
36	## Common Examples
37
38	### Convert VASP OUTCAR to deepmd format
39
40	```bash
41	uvx dpdata OUTCAR -i vasp/outcar -O deepmd_data -o deepmd/raw
42	```
43
44	### Convert LAMMPS dump to VASP POSCAR
45
46	```bash
47	uvx dpdata dump.lammps -i lammps/dump -O POSCAR -o vasp/poscar
48	```
49
50	### Convert with type map
51
52	```bash
53	uvx dpdata OUTCAR -i vasp/outcar -O deepmd_data -o deepmd/raw -t C H O N
54	```
55
56	### Convert multiple systems
57
58	```bash
59	uvx dpdata data_dir -i vasp/outcar -O output_dir -o deepmd/comp --multi
60	```
61
62	### Convert to deepmd/npy (compressed format)
63
64	```bash
65	uvx dpdata OUTCAR -i vasp/outcar -O deepmd_npy -o deepmd/npy
66	```
67
68	### Convert to deepmd/hdf5
69
70	```bash
71	uvx dpdata OUTCAR -i vasp/outcar -O data.h5 -o deepmd/hdf5
72	```
73
74	## Supported Formats
75
76	Formats may be updated. For the complete and latest list, see:
77
78	- [Formats Reference (stable)](https://docs.deepmodeling.com/projects/dpdata/en/stable/formats.html)
79
80	### DeePMD-kit Formats
81
82	\| Format Name \| Description \|
83	\| ---------------------------- \| ---------------------------------- \|
84	\| `deepmd/raw` \| DeePMD-kit raw text format \|
85	\| `deepmd/comp` / `deepmd/npy` \| DeePMD-kit compressed numpy format \|
86	\| `deepmd/npy/mixed` \| DeePMD-kit mixed type format \|
87	\| `deepmd/hdf5` \| DeePMD-kit HDF5 format \|
88
89	### VASP Formats
90
91	\| Format Name \| Description \|
92	\| ----------------------------------------------------- \| -------------------- \|
93	\| `vasp/poscar` / `vasp/contcar` / `poscar` / `contcar` \| VASP structure files \|
94	\| `vasp/outcar` / `outcar` \| VASP OUTCAR output \|
95	\| `vasp/xml` / `xml` \| VASP XML output \|
96	\| `vasp/string` \| VASP string format \|
97
98	### LAMMPS Formats
99
100	\| Format Name \| Description \|
101	\| ---------------------- \| ---------------- \|
102	\| `lammps/lmp` / `lmp` \| LAMMPS data file \|
103	\| `lammps/dump` / `dump` \| LAMMPS dump file \|
104
105	### ABACUS Formats
106
107	\| Format Name \| Description \|
108	\| -------------------------------------------------------- \| --------------------- \|
109	\| `stru` / `abacus/stru` \| ABACUS structure file \|
110	\| `abacus/lcao/scf` / `abacus/pw/scf` / `abacus/scf` \| ABACUS SCF output \|
111	\| `abacus/lcao/md` / `abacus/pw/md` / `abacus/md` \| ABACUS MD output \|
112	\| `abacus/lcao/relax` / `abacus/pw/relax` / `abacus/relax` \| ABACUS relax output \|
113
114	### Quantum ESPRESSO Formats
115
116	\| Format Name \| Description \|
117	\| ------------ \| ---------------- \|
118	\| `qe/cp/traj` \| QE CP trajectory \|
119	\| `qe/pw/scf` \| QE PWscf output \|
120
121	### CP2K Formats
122
123	\| Format Name \| Description \|
124	\| ------------------ \| ---------------- \|
125	\| `cp2k/output` \| CP2K output \|
126	\| `cp2k/aimd_output` \| CP2K AIMD output \|
127
128	### Gaussian Fo

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dpdata-cli

113stars23forks

View on GitHub

How to install dpdata-cli?

jinzhezenggroup/computational-chemistry-agent-skills/dpdata-cli

$npx -y skills add jinzhezenggroup/computational-chemistry-agent-skills --skill dpdata-cli

Installs into the current project.

Summary

Files · 1

View on GitHub

SKILL.md

1	# dpdata CLI
2
3	dpdata is a tool for manipulating multiple atomic simulation data formats. This skill enables format conversion between various DFT/MD software outputs via command line.
4
5	## Quick Start
6
7	Run dpdata via uvx:
8
9	```bash
10	uvx dpdata <from_file> [options]
11	```
12
13	## Command Line Usage
14
15	```text
16	dpdata: Manipulating multiple atomic simulation data formats
17	usage: dpdata [-h] [--to_file TO_FILE] [--from_format FROM_FORMAT]
18	[--to_format TO_FORMAT] [--no-labeled] [--multi]
19	[--type-map TYPE_MAP [TYPE_MAP ...]] [--version]
20	from_file
21	```
22
23	### Arguments
24
25	\| Argument \| Description \|
26	\| --------------------- \| ----------------------------------------------------- \|
27	\| `from_file` \| Read data from a file (positional) \|
28	\| `--to_file`, `-O` \| Dump data to a file \|
29	\| `--from_format`, `-i` \| Format of from_file (default: "auto") \|
30	\| `--to_format`, `-o` \| Format of to_file \|
31	\| `--no-labeled`, `-n` \| Labels aren't provided (default: False) \|
32	\| `--multi`, `-m` \| System contains multiple directories (default: False) \|
33	\| `--type-map`, `-t` \| Type map for atom types \|
34	\| `--version` \| Show dpdata version and exit \|
35
36	## Common Examples
37
38	### Convert VASP OUTCAR to deepmd format
39
40	```bash
41	uvx dpdata OUTCAR -i vasp/outcar -O deepmd_data -o deepmd/raw
42	```
43
44	### Convert LAMMPS dump to VASP POSCAR
45
46	```bash
47	uvx dpdata dump.lammps -i lammps/dump -O POSCAR -o vasp/poscar
48	```
49
50	### Convert with type map
51
52	```bash
53	uvx dpdata OUTCAR -i vasp/outcar -O deepmd_data -o deepmd/raw -t C H O N
54	```
55
56	### Convert multiple systems
57
58	```bash
59	uvx dpdata data_dir -i vasp/outcar -O output_dir -o deepmd/comp --multi
60	```
61
62	### Convert to deepmd/npy (compressed format)
63
64	```bash
65	uvx dpdata OUTCAR -i vasp/outcar -O deepmd_npy -o deepmd/npy
66	```
67
68	### Convert to deepmd/hdf5
69
70	```bash
71	uvx dpdata OUTCAR -i vasp/outcar -O data.h5 -o deepmd/hdf5
72	```
73
74	## Supported Formats
75
76	Formats may be updated. For the complete and latest list, see:
77
78	- [Formats Reference (stable)](https://docs.deepmodeling.com/projects/dpdata/en/stable/formats.html)
79
80	### DeePMD-kit Formats
81
82	\| Format Name \| Description \|
83	\| ---------------------------- \| ---------------------------------- \|
84	\| `deepmd/raw` \| DeePMD-kit raw text format \|
85	\| `deepmd/comp` / `deepmd/npy` \| DeePMD-kit compressed numpy format \|
86	\| `deepmd/npy/mixed` \| DeePMD-kit mixed type format \|
87	\| `deepmd/hdf5` \| DeePMD-kit HDF5 format \|
88
89	### VASP Formats
90
91	\| Format Name \| Description \|
92	\| ----------------------------------------------------- \| -------------------- \|
93	\| `vasp/poscar` / `vasp/contcar` / `poscar` / `contcar` \| VASP structure files \|
94	\| `vasp/outcar` / `outcar` \| VASP OUTCAR output \|
95	\| `vasp/xml` / `xml` \| VASP XML output \|
96	\| `vasp/string` \| VASP string format \|
97
98	### LAMMPS Formats
99
100	\| Format Name \| Description \|
101	\| ---------------------- \| ---------------- \|
102	\| `lammps/lmp` / `lmp` \| LAMMPS data file \|
103	\| `lammps/dump` / `dump` \| LAMMPS dump file \|
104
105	### ABACUS Formats
106
107	\| Format Name \| Description \|
108	\| -------------------------------------------------------- \| --------------------- \|
109	\| `stru` / `abacus/stru` \| ABACUS structure file \|
110	\| `abacus/lcao/scf` / `abacus/pw/scf` / `abacus/scf` \| ABACUS SCF output \|
111	\| `abacus/lcao/md` / `abacus/pw/md` / `abacus/md` \| ABACUS MD output \|
112	\| `abacus/lcao/relax` / `abacus/pw/relax` / `abacus/relax` \| ABACUS relax output \|
113
114	### Quantum ESPRESSO Formats
115
116	\| Format Name \| Description \|
117	\| ------------ \| ---------------- \|
118	\| `qe/cp/traj` \| QE CP trajectory \|
119	\| `qe/pw/scf` \| QE PWscf output \|
120
121	### CP2K Formats
122
123	\| Format Name \| Description \|
124	\| ------------------ \| ---------------- \|
125	\| `cp2k/output` \| CP2K output \|
126	\| `cp2k/aimd_output` \| CP2K AIMD output \|
127
128	### Gaussian Fo

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