🔄 Format Conversion

This directory (Scripts/format_conversion/) contains utilities for converting between different file formats commonly used in computational materials science.

Script Location: Scripts/format_conversion/

This section covers the format conversion tools in GPUMDkit (Interactive Mode - Option 1).

Interactive Mode

gpumdkit.sh
# Select: 1) Format Conversion

You'll see the following menu:

 ------------>>
 101) Convert VASP to extxyz
 102) Convert mtp to extxyz
 103) Convert CP2K to extxyz
 104) Convert ABACUS to extxyz
 105) Convert extxyz to POSCAR
 000) Return to the main menu
 ------------>>
 Input the function number:

for 101:

 >-------------------------------------------------<
 | Calling the script in Scripts/format_conversion |
 | Script: out2xyz.sh                              |
 | Developer: Yanzhou WANG (yanzhowang@gmail.com)  |
 >-------------------------------------------------<
 Choose the type of conversion:
 1) OUTCAR to extxyz
 2) vasprun.xml to extxyz
 ------------>>

for 102:

 >-------------------------------------------------<
 | Calling the script in Scripts/format_conversion |
 | Script: mtp2xyz.py                              |
 | Developer: Ke XU (kickhsu@gmail.com)            |
 >-------------------------------------------------<
 Input <filename.cfg> <Symbol1 Symbol2 Symbol3 ...>
 Examp: train.cfg Pd Ag
 ------------>>

for 103:

 >-------------------------------------------------<
 | Calling the script in Scripts/format_conversion |
 | Script: cp2k2xyz.py                             |
 | Developer: Ke XU (kickhsu@gmail.com)            |
 >-------------------------------------------------<
 Input [pos.xyz] [frc.xyz] [cell.cell] [-shifted yes/no]
 ------------>>

for 104:

 >-------------------------------------------------<
 | Calling the script in Scripts/format_conversion |
 | Script: abacus2xyz-scf.sh/abacus2xyz-md.sh      |
 | Developer: Benrui TANG (tang070205@proton.me)   |
 >-------------------------------------------------<
 Choose the type of ABACUS calculation:
 1) SCF calculation
 2) MD calculation
 ------------>>

for 105:

 >-------------------------------------------------<
 | Calling the script in Scripts/format_conversion |
 | Script: exyz2pos.py                             |
 | Developer: Zihan YAN (yanzihan@westlake.edu.cn) |
 >-------------------------------------------------<
 Input the name of extxyz
 Examp: ./train.xyz
 ------------>>

Follow the prompts to complete the function.

---

Command-line Mode

Source Format	Target Format	Command
OUTCAR	extxyz	gpumdkit.sh -out2xyz <dir>
vasprun.xml	extxyz	gpumdkit.sh -xml2xyz <dir>
POSCAR	extxyz	gpumdkit.sh -pos2exyz <poscar> <xyz>
extxyz	POSCAR	gpumdkit.sh -exyz2pos <xyz>
POSCAR	LAMMPS	gpumdkit.sh -pos2lmp <poscar> <lmp> <elem...>
LAMMPS dump	extxyz	gpumdkit.sh -lmp2exyz <dump> <elem...>
CIF	extxyz	gpumdkit.sh -cif2exyz <cif>
CIF	POSCAR	gpumdkit.sh -cif2pos <cif>
Add groups	-	gpumdkit.sh -addgroup <poscar> <elem...>
Add weight	-	gpumdkit.sh -addweight <in> <out> <weight>
Replicate1	-	gpumdkit.sh -replicate input.vasp output.vasp 2 2 2
Replicate2	-	gpumdkit.sh -replicate input.vasp output.vasp <target_num>
Get frame	-	gpumdkit.sh -ge_frame <extxyz> <index>

---

Scripts

add_groups.py

---

This script adds group labels to structures based on specified elements.

Usage

python add_groups.py <filename> <Symbols1> <Symbols2> ...

• <filename>: The path to the input file (e.g., POSCAR).
• <Symbols>: Space-separated list of element symbols to group (e.g., Li Y Cl).

Example

python add_groups.py POSCAR Li Y Cl

Command-Line Mode Example

gpumdkit.sh -addgroup POSCAR Li Y Cl

This command will read the POSCAR file and add group labels for the elements Li, Y, and Cl. The output will be saved to a file named model.xyz.

add_weight.py

---

This script adds weight labels to structures.

Usage

python add_weight.py <input_file> <output_file> <new_weight>

• <inputfile>: The path to the input file (e.g., train.xyz).
• <outputfile>: The path to the input file (e.g., train_weighted.xyz).
• <new_weight>: The weight you need to change.

Example

python add_weight.py train.xyz train_weighted.xyz 5

Command-Line Mode Example

gpumdkit.sh -addweight train.xyz train_weighted.xyz 5

This command will read the train.xyz file and add Weight=5 labels for all structures. The output will be saved to a file named train_weighted.xyz.

exyz2pos.py

---

This script converts all frames in an extxyz file to POSCAR format.

Usage

python exyz2pos.py <extxyz_file>

Example

python exyz2pos.py structs.xyz

Command-Line Mode Example

gpumdkit.sh -exyz2pos structs.xyz

This command will convert all frames in structs.xyz to POSCAR_*.vasp files.

pos2exyz.py

---

This script converts a POSCAR file to extxyz format.

Usage

python pos2exyz.py <POSCAR_file> <extxyz_file>

• <POSCAR_file>: The path to the input POSCAR file.
• <extxyz_file>: The desired name for the output extxyz file.

Example

python pos2exyz.py POSCAR model.xyz

Command-Line Mode Example

gpumdkit.sh -pos2exyz POSCAR model.xyz

This command will read the POSCAR file and convert it to model.xyz in extxyz format.

pos2lmp.py

---

This script converts a POSCAR file to lammps-data format.

Usage

python pos2lmp.py <poscar_file> <lammps_data_file>

• <poscar_file>: The path to the input POSCAR file.
• <lammps_data_file>: The desired name for the output lammps-data file.

Example

python pos2lmp.py POSCAR lammps.data

Command-Line Mode Example

gpumdkit.sh -pos2lmp POSCAR lammps.data

This command will read the POSCAR file and convert it to lammps.data in lammps-data format.

split_single_xyz.py

---

This script splits an extxyz file into individual frames, each written to a separate file.

Usage

python split_single_xyz.py <extxyz_file>

This command will split all frames in extxyz_file into separate files named model_*.xyz.

lmp2exyz.py

---

This script will convert the lammps-dump to extxyz format.

Usage

python lmp2exyz.py <dump_file> <element1> <element2> ...

• <dump_file>: The path to the input lammps-dump file.
• <element>: The order of the specified elements.

Example

python lmp2exyz.py dump.data Li Y Cl

Command-Line Mode Example

gpumdkit.sh -lmp2exyz dump.data Li Y Cl

It will convert the dump.data to dump.xyz file

get_frame.py

---

This script will read the extxyz file and return the specified frame by index..

Usage

python get_frame.py <extxyz_file> <frame_index>

• <extxyz_file>: The path to the input extxyz file.
• <frame_index>: The index of the specified frame.

Example

python get_frame.py dump.xyz 1000

Command-Line Mode Example

gpumdkit.sh -get_frame dump.xyz 1000

You will get the frame_1000.xyz file after perform the script.

Contributing

To add new format converters:

1. Follow naming: <source>2<target>.py
2. Handle errors: Validate input format before processing
3. Document: Add usage to this README
4. Update gpumdkit.sh: Add command-line flag if appropriate

See CONTRIBUTING.md for detailed guidelines.

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Thank you for using GPUMDkit! If you have questions about format conversion, please open an issue on our GitHub repository or contact Zihan YAN (yanzihan@westlake.edu.cn).