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feat: support remove solvents in structure_generator #661

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Merged
Rasic2 merged 1 commit into from
Jan 19, 2026
+22 −0
Merged

feat: support remove solvents in structure_generator #661

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1 change: 1 addition & 0 deletions agents/matmaster_agent/sub_agents/structure_generate_agent/agent.py
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Original file line number Diff line number Diff line change
Expand Up @@ -60,6 +60,7 @@ def __init__(self, llm_config: LLMConfig, name_suffix=''):
sync_tools=[
'add_hydrogens',
'generate_ordered_replicas',
'remove_solvents',
'build_bulk_structure_by_template',
'build_bulk_structure_by_wyckoff',
'make_supercell_structure',
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21 changes: 21 additions & 0 deletions agents/matmaster_agent/sub_agents/tools.py
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Expand Up @@ -1231,6 +1231,27 @@
'bypass_confirmation': True,
'self_check': False,
},
'remove_solvents': {
'belonging_agent': StructureGenerateAgentName,
'scene': [SceneEnum.STRUCTURE_GENERATE, SceneEnum.STRUCTURE_SANITIZE],
'description': (
'What it does: Remove specified solvent molecules from a molecular crystal structure.\n'
'When to use: When desolvating molecular crystals to obtain solvent-free or partially desolvated structures for analysis or simulation.\n'
'Prerequisites / Inputs: CIF structure file containing identifiable solvent molecules; target solvent names or formulas.\n'
'Outputs: Path to the desolvated structure file.\n'
'Cannot do / Limits: Only removes whole solvent molecules that can be identified by composition; does not modify framework atoms or resolve disorder.\n'
'Prior step: It is recommended to call get_structure_info first to inspect molecular components and confirm solvent identities.\n'
'Cost / Notes: Low. Recommended to inspect molecular components first.'
),
'args_setting': (
'Parameter guidance: structure_path: Required. Input CIF file containing solvent molecules. '
'output_file: Required. Path to save the desolvated structure. '
'targets: Required. List of solvent names or chemical formulas to remove (e.g., "H2O", "DMF"). '
),
'alternative': [],
'bypass_confirmation': True,
'self_check': False,
},
'run_superconductor_optimization': {
'belonging_agent': SuperconductorAgentName,
'scene': [SceneEnum.SUPERCONDUCTOR],
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