feat(lammps): implement to_system method for LAMMPSDumpFormat

[Copilot]

This PR implements the missing to_system method for the LAMMPSDumpFormat class, enabling conversion from LAMMPS .lmp files to .dump format.

Problem

Previously, users could not convert LAMMPS data files (.lmp) to dump format (.dump) because the LAMMPSDumpFormat class only supported reading dump files (from_system) but not writing them (to_system). This resulted in a NotImplementedError when attempting the conversion:

import dpdata
system = dpdata.System('minimized_structure.output', fmt='lammps/lmp')
system.to('lammps/dump', 'output.dump')  # Raised NotImplementedError

Solution

Added the missing functionality by:

1. Implementing from_system_data() function in dpdata/lammps/dump.py that converts system data to LAMMPS dump format string with proper:

   • Timestep headers
   • Atom count information
   • Box bounds and tilt parameters
   • Coordinate data with correct LAMMPS indexing

2. Adding to_system() method to LAMMPSDumpFormat class that uses the new conversion function

3. Adding comprehensive tests to verify the conversion works correctly and maintains data integrity

Verification

• All existing tests continue to pass (101 LAMMPS-related tests)
• Round-trip conversions (LMP → DUMP → LMP) preserve coordinates with perfect precision
• Generated dump files follow LAMMPS standard format and can be loaded back successfully
• The exact use case from the issue now works as expected

Example Usage

import dpdata

# Load LAMMPS data file
system = dpdata.System('data.lmp', fmt='lammps/lmp', type_map=['O', 'H'])

# Convert to dump format (now works!)
system.to('lammps/dump', 'output.dump')

# Generated dump file can be loaded back
system2 = dpdata.System('output.dump', fmt='lammps/dump', type_map=['O', 'H'])

Fixes #664.

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[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 85.84%. Comparing base (ab61da1) to head (69649f2).
⚠️ Report is 25 commits behind head on devel.

Additional details and impacted files

@@            Coverage Diff             @@
##            devel     #882      +/-   ##
==========================================
+ Coverage   85.45%   85.84%   +0.39%     
==========================================
  Files          82       82              
  Lines        7678     7706      +28     
==========================================
+ Hits         6561     6615      +54     
+ Misses       1117     1091      -26     

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[njzjz]

LGTM