LUNAR: Automated input generation and analysis for reactive LAMMPS simulations input and output files
Data files
May 30, 2024 version files 1.43 GB
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AroCy_L10_cell_builder_random_replicate_1_intial_configuration.data
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AroCy_L10_cell_builder_random_replicate_2_intial_configuration.data
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AroCy_L10_cell_builder_random_replicate_3_intial_configuration.data
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AroCy_L10_cell_builder_random_replicate_4_intial_configuration.data
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AroCy_L10_cell_builder_random_replicate_5_intial_configuration.data
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AroCy_L10_LAMMPS_replicated_intial_configuration.data
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AroCy_L10_packmol_gas_intial_configuration.data
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AroCy_L10_packmol_liquid_intial_configuration.data
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detda_typed_IFF_tag_data1_merged.data
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dgebf_typed_IFF_tag_data2_merged.data
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EPON_862_cell_builder_grouped_replicate_intial_configuration.data
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EPON_862_cell_builder_random_replicate_1_intial_configuration.data
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EPON_862_cell_builder_random_replicate_2_intial_configuration.data
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EPON_862_cell_builder_random_replicate_3_intial_configuration.data
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EPON_862_cell_builder_random_replicate_4_intial_configuration.data
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EPON_862_cell_builder_random_replicate_5_intial_configuration.data
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EPON_862_LAMMPS_replicated_intial_configuration.data
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EPON_862_packmol_gas_intial_configuration.data
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EPON_862_packmol_liquid_intial_configuration.data
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generalized_lmp_input.script
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L10_IFF_typed_IFF_tag_data1_merged.data
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n1_densify_AroCy_L10.script
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n1_densify_EPON_862.script
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n2_relax_liquid_AroCy_L10.script
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n2_relax_liquid_EPON_862.script
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n3_react_step_seq_AroCy_L10.script
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n3_react_step_seq_EPON_862.script
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n4_relax_xld_AroCy_L10.script
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n4_relax_xld_EPON_862.script
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post_reaction_1_typed_IFF_tag_post1_merged.lmpmol
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post_reaction_2_typed_IFF_tag_post2_merged.lmpmol
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post1_IFF_typed_IFF_tag_post1_merged.lmpmol
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post2_IFF_typed_IFF_tag_post2_merged.lmpmol
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pre_reaction_1_typed_IFF_tag_pre1_merged.lmpmol
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pre_reaction_2_typed_IFF_tag_pre2_merged.lmpmol
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pre1_IFF_typed_IFF_tag_pre1_merged.lmpmol
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pre1-post1_rxn-map_uncommented.txt
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pre2_IFF_typed_IFF_tag_pre2_merged.lmpmol
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pre2-post2_rxn-map_uncommented.txt
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README.md
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relax_AroCy_L10_cell_builder_random_replicate_1_pxld_0_IFF_hc_2.995.data
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relax_AroCy_L10_cell_builder_random_replicate_1_pxld_0_IFF.data
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relax_AroCy_L10_cell_builder_random_replicate_1_pxld_10_IFF.data
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relax_AroCy_L10_cell_builder_random_replicate_1_pxld_20_IFF.data
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relax_AroCy_L10_cell_builder_random_replicate_1_pxld_30_IFF.data
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relax_AroCy_L10_cell_builder_random_replicate_1_pxld_40_IFF.data
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relax_AroCy_L10_cell_builder_random_replicate_1_pxld_50_IFF.data
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relax_AroCy_L10_cell_builder_random_replicate_1_pxld_60_IFF.data
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relax_AroCy_L10_cell_builder_random_replicate_1_pxld_70_IFF.data
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relax_AroCy_L10_cell_builder_random_replicate_1_pxld_80_IFF.data
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relax_AroCy_L10_cell_builder_random_replicate_1_pxld_90_IFF.data
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relax_AroCy_L10_cell_builder_random_replicate_1_pxld_97_IFF_hc_2.995.data
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relax_AroCy_L10_cell_builder_random_replicate_1_pxld_97_IFF.data
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relax_AroCy_L10_cell_builder_random_replicate_2_pxld_0_IFF.data
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relax_AroCy_L10_cell_builder_random_replicate_2_pxld_10_IFF.data
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relax_AroCy_L10_cell_builder_random_replicate_2_pxld_20_IFF.data
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relax_AroCy_L10_cell_builder_random_replicate_2_pxld_30_IFF.data
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relax_AroCy_L10_cell_builder_random_replicate_2_pxld_40_IFF.data
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relax_AroCy_L10_cell_builder_random_replicate_2_pxld_50_IFF.data
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relax_AroCy_L10_cell_builder_random_replicate_2_pxld_60_IFF.data
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relax_AroCy_L10_cell_builder_random_replicate_2_pxld_70_IFF.data
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relax_AroCy_L10_cell_builder_random_replicate_2_pxld_80_IFF.data
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relax_AroCy_L10_cell_builder_random_replicate_2_pxld_90_IFF.data
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relax_AroCy_L10_cell_builder_random_replicate_2_pxld_97_IFF.data
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relax_AroCy_L10_cell_builder_random_replicate_3_pxld_0_IFF.data
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relax_AroCy_L10_cell_builder_random_replicate_3_pxld_10_IFF.data
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relax_AroCy_L10_cell_builder_random_replicate_3_pxld_20_IFF.data
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relax_AroCy_L10_cell_builder_random_replicate_3_pxld_30_IFF.data
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relax_AroCy_L10_cell_builder_random_replicate_3_pxld_40_IFF.data
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relax_AroCy_L10_cell_builder_random_replicate_3_pxld_50_IFF.data
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relax_AroCy_L10_cell_builder_random_replicate_3_pxld_60_IFF.data
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relax_AroCy_L10_cell_builder_random_replicate_3_pxld_70_IFF.data
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relax_AroCy_L10_cell_builder_random_replicate_3_pxld_80_IFF.data
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relax_AroCy_L10_cell_builder_random_replicate_3_pxld_90_IFF.data
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relax_AroCy_L10_cell_builder_random_replicate_3_pxld_97_IFF.data
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relax_AroCy_L10_cell_builder_random_replicate_4_pxld_0_IFF.data
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relax_AroCy_L10_cell_builder_random_replicate_4_pxld_10_IFF.data
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relax_AroCy_L10_cell_builder_random_replicate_4_pxld_20_IFF.data
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relax_AroCy_L10_cell_builder_random_replicate_4_pxld_30_IFF.data
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relax_AroCy_L10_cell_builder_random_replicate_4_pxld_40_IFF.data
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relax_AroCy_L10_cell_builder_random_replicate_4_pxld_50_IFF.data
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relax_AroCy_L10_cell_builder_random_replicate_4_pxld_60_IFF.data
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relax_AroCy_L10_cell_builder_random_replicate_4_pxld_70_IFF.data
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relax_AroCy_L10_cell_builder_random_replicate_4_pxld_80_IFF.data
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relax_AroCy_L10_cell_builder_random_replicate_4_pxld_90_IFF.data
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relax_AroCy_L10_cell_builder_random_replicate_4_pxld_96_IFF.data
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relax_AroCy_L10_cell_builder_random_replicate_5_pxld_0_IFF.data
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relax_AroCy_L10_cell_builder_random_replicate_5_pxld_10_IFF.data
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relax_AroCy_L10_cell_builder_random_replicate_5_pxld_20_IFF.data
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relax_AroCy_L10_cell_builder_random_replicate_5_pxld_30_IFF.data
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relax_AroCy_L10_cell_builder_random_replicate_5_pxld_40_IFF.data
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relax_AroCy_L10_cell_builder_random_replicate_5_pxld_50_IFF.data
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relax_AroCy_L10_cell_builder_random_replicate_5_pxld_60_IFF.data
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relax_AroCy_L10_cell_builder_random_replicate_5_pxld_70_IFF.data
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relax_AroCy_L10_cell_builder_random_replicate_5_pxld_80_IFF.data
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relax_AroCy_L10_cell_builder_random_replicate_5_pxld_90_IFF.data
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relax_AroCy_L10_cell_builder_random_replicate_5_pxld_96_IFF.data
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relax_AroCy_L10_LAMMPS_create_atoms_pxld_0_IFF.data
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relax_AroCy_L10_LAMMPS_create_atoms_pxld_10_IFF.data
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relax_AroCy_L10_LAMMPS_create_atoms_pxld_20_IFF.data
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relax_AroCy_L10_LAMMPS_create_atoms_pxld_30_IFF.data
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relax_AroCy_L10_LAMMPS_create_atoms_pxld_40_IFF.data
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relax_AroCy_L10_LAMMPS_create_atoms_pxld_50_IFF.data
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relax_AroCy_L10_LAMMPS_create_atoms_pxld_60_IFF.data
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relax_AroCy_L10_LAMMPS_create_atoms_pxld_70_IFF.data
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relax_AroCy_L10_LAMMPS_create_atoms_pxld_80_IFF.data
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relax_AroCy_L10_LAMMPS_create_atoms_pxld_90_IFF.data
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relax_AroCy_L10_LAMMPS_create_atoms_pxld_97_IFF.data
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relax_AroCy_L10_LAMMPS_replicated_pxld_0_IFF.data
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relax_AroCy_L10_LAMMPS_replicated_pxld_10_IFF.data
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relax_AroCy_L10_LAMMPS_replicated_pxld_20_IFF.data
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relax_AroCy_L10_LAMMPS_replicated_pxld_30_IFF.data
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relax_AroCy_L10_LAMMPS_replicated_pxld_40_IFF.data
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relax_AroCy_L10_LAMMPS_replicated_pxld_50_IFF.data
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relax_AroCy_L10_LAMMPS_replicated_pxld_60_IFF.data
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relax_AroCy_L10_LAMMPS_replicated_pxld_70_IFF.data
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relax_AroCy_L10_LAMMPS_replicated_pxld_80_IFF.data
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relax_AroCy_L10_LAMMPS_replicated_pxld_90_IFF.data
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relax_AroCy_L10_LAMMPS_replicated_pxld_97.85_IFF.data
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relax_AroCy_L10_packmol_gas_pxld_0_IFF.data
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relax_AroCy_L10_packmol_gas_pxld_10_IFF.data
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relax_AroCy_L10_packmol_gas_pxld_20_IFF.data
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relax_AroCy_L10_packmol_gas_pxld_30_IFF.data
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relax_AroCy_L10_packmol_gas_pxld_40_IFF.data
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relax_AroCy_L10_packmol_gas_pxld_50_IFF.data
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relax_AroCy_L10_packmol_gas_pxld_60_IFF.data
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relax_AroCy_L10_packmol_gas_pxld_70_IFF.data
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relax_AroCy_L10_packmol_gas_pxld_80_IFF.data
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relax_AroCy_L10_packmol_gas_pxld_90_IFF.data
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relax_AroCy_L10_packmol_gas_pxld_96.89_IFF.data
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relax_AroCy_L10_packmol_liquid_pxld_0_IFF.data
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relax_AroCy_L10_packmol_liquid_pxld_10_IFF.data
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relax_AroCy_L10_packmol_liquid_pxld_20_IFF.data
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relax_AroCy_L10_packmol_liquid_pxld_30_IFF.data
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relax_AroCy_L10_packmol_liquid_pxld_40_IFF.data
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relax_AroCy_L10_packmol_liquid_pxld_50_IFF.data
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relax_AroCy_L10_packmol_liquid_pxld_60_IFF.data
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relax_AroCy_L10_packmol_liquid_pxld_70_IFF.data
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relax_AroCy_L10_packmol_liquid_pxld_80_IFF.data
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relax_AroCy_L10_packmol_liquid_pxld_90_IFF.data
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relax_AroCy_L10_packmol_liquid_pxld_95.93_IFF.data
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relax_EPON_862_cell_builder_grouped_replicate_pxld_0_IFF.data
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relax_EPON_862_cell_builder_grouped_replicate_pxld_10_IFF.data
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relax_EPON_862_cell_builder_grouped_replicate_pxld_20_IFF.data
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relax_EPON_862_cell_builder_grouped_replicate_pxld_30_IFF.data
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relax_EPON_862_cell_builder_grouped_replicate_pxld_40_IFF.data
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relax_EPON_862_cell_builder_grouped_replicate_pxld_50_IFF.data
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relax_EPON_862_cell_builder_grouped_replicate_pxld_60_IFF.data
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relax_EPON_862_cell_builder_grouped_replicate_pxld_70_IFF.data
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relax_EPON_862_cell_builder_grouped_replicate_pxld_80_IFF.data
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relax_EPON_862_cell_builder_grouped_replicate_pxld_90_IFF.data
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relax_EPON_862_cell_builder_random_replicate_1_pxld_0_IFF_hc_2.995.data
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relax_EPON_862_cell_builder_random_replicate_1_pxld_0_IFF.data
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relax_EPON_862_cell_builder_random_replicate_1_pxld_10_IFF.data
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relax_EPON_862_cell_builder_random_replicate_1_pxld_20_IFF.data
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relax_EPON_862_cell_builder_random_replicate_1_pxld_30_IFF.data
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relax_EPON_862_cell_builder_random_replicate_1_pxld_40_IFF.data
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relax_EPON_862_cell_builder_random_replicate_1_pxld_50_IFF.data
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relax_EPON_862_cell_builder_random_replicate_1_pxld_60_IFF.data
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relax_EPON_862_cell_builder_random_replicate_1_pxld_70_IFF.data
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relax_EPON_862_cell_builder_random_replicate_1_pxld_80_IFF.data
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relax_EPON_862_cell_builder_random_replicate_1_pxld_88.2_IFF_hc_2.995.data
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relax_EPON_862_cell_builder_random_replicate_1_pxld_88.2_IFF.data
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relax_EPON_862_cell_builder_random_replicate_2_pxld_0_IFF.data
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relax_EPON_862_cell_builder_random_replicate_2_pxld_10_IFF.data
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relax_EPON_862_cell_builder_random_replicate_2_pxld_20_IFF.data
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relax_EPON_862_cell_builder_random_replicate_2_pxld_30_IFF.data
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relax_EPON_862_cell_builder_random_replicate_2_pxld_40_IFF.data
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relax_EPON_862_cell_builder_random_replicate_2_pxld_50_IFF.data
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relax_EPON_862_cell_builder_random_replicate_2_pxld_60_IFF.data
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relax_EPON_862_cell_builder_random_replicate_2_pxld_70_IFF.data
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relax_EPON_862_cell_builder_random_replicate_2_pxld_80_IFF.data
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relax_EPON_862_cell_builder_random_replicate_2_pxld_85.7_IFF.data
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relax_EPON_862_cell_builder_random_replicate_3_pxld_0_IFF.data
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relax_EPON_862_cell_builder_random_replicate_3_pxld_10_IFF.data
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relax_EPON_862_cell_builder_random_replicate_3_pxld_20_IFF.data
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relax_EPON_862_cell_builder_random_replicate_3_pxld_30_IFF.data
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relax_EPON_862_cell_builder_random_replicate_3_pxld_40_IFF.data
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relax_EPON_862_cell_builder_random_replicate_3_pxld_50_IFF.data
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relax_EPON_862_cell_builder_random_replicate_3_pxld_60_IFF.data
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relax_EPON_862_cell_builder_random_replicate_3_pxld_70_IFF.data
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relax_EPON_862_cell_builder_random_replicate_3_pxld_80_IFF.data
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relax_EPON_862_cell_builder_random_replicate_3_pxld_88.5_IFF.data
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relax_EPON_862_cell_builder_random_replicate_4_pxld_0_IFF.data
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relax_EPON_862_cell_builder_random_replicate_4_pxld_10_IFF.data
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relax_EPON_862_cell_builder_random_replicate_4_pxld_20_IFF.data
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relax_EPON_862_cell_builder_random_replicate_4_pxld_30_IFF.data
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relax_EPON_862_cell_builder_random_replicate_4_pxld_40_IFF.data
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relax_EPON_862_cell_builder_random_replicate_4_pxld_50_IFF.data
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relax_EPON_862_cell_builder_random_replicate_4_pxld_60_IFF.data
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relax_EPON_862_cell_builder_random_replicate_4_pxld_70_IFF.data
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relax_EPON_862_cell_builder_random_replicate_4_pxld_80_IFF.data
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relax_EPON_862_cell_builder_random_replicate_4_pxld_86.8_IFF.data
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relax_EPON_862_cell_builder_random_replicate_5_pxld_0_IFF.data
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relax_EPON_862_cell_builder_random_replicate_5_pxld_10_IFF.data
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relax_EPON_862_cell_builder_random_replicate_5_pxld_20_IFF.data
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relax_EPON_862_cell_builder_random_replicate_5_pxld_30_IFF.data
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relax_EPON_862_cell_builder_random_replicate_5_pxld_40_IFF.data
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relax_EPON_862_cell_builder_random_replicate_5_pxld_50_IFF.data
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relax_EPON_862_cell_builder_random_replicate_5_pxld_60_IFF.data
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relax_EPON_862_cell_builder_random_replicate_5_pxld_70_IFF.data
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relax_EPON_862_cell_builder_random_replicate_5_pxld_80_IFF.data
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relax_EPON_862_cell_builder_random_replicate_5_pxld_88.7_IFF.data
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relax_EPON_862_LAMMPS_create_atoms_pxld_0_IFF.data
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relax_EPON_862_LAMMPS_create_atoms_pxld_10_IFF.data
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relax_EPON_862_LAMMPS_create_atoms_pxld_20_IFF.data
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relax_EPON_862_LAMMPS_create_atoms_pxld_30_IFF.data
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relax_EPON_862_LAMMPS_create_atoms_pxld_40_IFF.data
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relax_EPON_862_LAMMPS_create_atoms_pxld_50_IFF.data
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relax_EPON_862_LAMMPS_create_atoms_pxld_60_IFF.data
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relax_EPON_862_LAMMPS_create_atoms_pxld_70_IFF.data
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relax_EPON_862_LAMMPS_create_atoms_pxld_80_IFF.data
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relax_EPON_862_LAMMPS_create_atoms_pxld_87.22_IFF.data
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relax_EPON_862_LAMMPS_replicated_pxld_0_IFF.data
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relax_EPON_862_LAMMPS_replicated_pxld_10_IFF.data
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relax_EPON_862_LAMMPS_replicated_pxld_20_IFF.data
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relax_EPON_862_LAMMPS_replicated_pxld_30_IFF.data
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relax_EPON_862_LAMMPS_replicated_pxld_40_IFF.data
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relax_EPON_862_LAMMPS_replicated_pxld_50_IFF.data
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relax_EPON_862_LAMMPS_replicated_pxld_60_IFF.data
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relax_EPON_862_LAMMPS_replicated_pxld_70_IFF.data
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relax_EPON_862_LAMMPS_replicated_pxld_80_IFF.data
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relax_EPON_862_LAMMPS_replicated_pxld_88.88_IFF.data
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relax_EPON_862_packmol_gas_pxld_0_IFF.data
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relax_EPON_862_packmol_gas_pxld_10_IFF.data
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relax_EPON_862_packmol_gas_pxld_20_IFF.data
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relax_EPON_862_packmol_gas_pxld_30_IFF.data
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relax_EPON_862_packmol_gas_pxld_40_IFF.data
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relax_EPON_862_packmol_gas_pxld_50_IFF.data
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relax_EPON_862_packmol_gas_pxld_60_IFF.data
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relax_EPON_862_packmol_gas_pxld_70_IFF.data
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relax_EPON_862_packmol_gas_pxld_80_IFF.data
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relax_EPON_862_packmol_gas_pxld_85.97_IFF.data
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relax_EPON_862_packmol_liquid_pxld_0_IFF.data
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relax_EPON_862_packmol_liquid_pxld_10_IFF.data
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relax_EPON_862_packmol_liquid_pxld_20_IFF.data
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relax_EPON_862_packmol_liquid_pxld_30_IFF.data
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relax_EPON_862_packmol_liquid_pxld_40_IFF.data
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relax_EPON_862_packmol_liquid_pxld_50_IFF.data
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relax_EPON_862_packmol_liquid_pxld_60_IFF.data
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relax_EPON_862_packmol_liquid_pxld_70_IFF.data
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relax_EPON_862_packmol_liquid_pxld_80_IFF.data
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relax_EPON_862_packmol_liquid_pxld_90_IFF.data
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relax_EPON_862_packmol_liquid_pxld_93.47_IFF.data
Jun 10, 2024 version files 1.43 GB
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AroCy_L10_cell_builder_random_replicate_1_intial_configuration.data
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AroCy_L10_cell_builder_random_replicate_2_intial_configuration.data
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AroCy_L10_cell_builder_random_replicate_3_intial_configuration.data
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AroCy_L10_cell_builder_random_replicate_4_intial_configuration.data
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AroCy_L10_cell_builder_random_replicate_5_intial_configuration.data
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AroCy_L10_LAMMPS_replicated_intial_configuration.data
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AroCy_L10_packmol_gas_intial_configuration.data
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AroCy_L10_packmol_liquid_intial_configuration.data
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detda_typed_IFF_tag_data1_merged.data
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dgebf_typed_IFF_tag_data2_merged.data
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EPON_862_cell_builder_grouped_replicate_intial_configuration.data
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EPON_862_cell_builder_random_replicate_1_intial_configuration.data
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EPON_862_cell_builder_random_replicate_2_intial_configuration.data
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EPON_862_cell_builder_random_replicate_3_intial_configuration.data
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EPON_862_cell_builder_random_replicate_4_intial_configuration.data
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EPON_862_cell_builder_random_replicate_5_intial_configuration.data
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EPON_862_LAMMPS_replicated_intial_configuration.data
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EPON_862_packmol_gas_intial_configuration.data
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EPON_862_packmol_liquid_intial_configuration.data
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generalized_lmp_input.script
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L10_IFF_typed_IFF_tag_data1_merged.data
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n1_densify_AroCy_L10.script
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n1_densify_EPON_862.script
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n2_relax_liquid_AroCy_L10.script
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n2_relax_liquid_EPON_862.script
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n3_react_step_seq_AroCy_L10.script
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n3_react_step_seq_EPON_862.script
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n4_relax_xld_AroCy_L10.script
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n4_relax_xld_EPON_862.script
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post_reaction_1_typed_IFF_tag_post1_merged.lmpmol
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post_reaction_2_typed_IFF_tag_post2_merged.lmpmol
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post1_IFF_typed_IFF_tag_post1_merged.lmpmol
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post2_IFF_typed_IFF_tag_post2_merged.lmpmol
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pre_reaction_1_typed_IFF_tag_pre1_merged.lmpmol
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pre_reaction_2_typed_IFF_tag_pre2_merged.lmpmol
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pre1_IFF_typed_IFF_tag_pre1_merged.lmpmol
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pre1-post1_rxn-map_uncommented.txt
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pre2_IFF_typed_IFF_tag_pre2_merged.lmpmol
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pre2-post2_rxn-map_uncommented.txt
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README.md
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relax_AroCy_L10_cell_builder_random_replicate_1_pxld_0_IFF_hc_2.995.data
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Abstract
Generating molecular models for the LAMMPS molecular dynamics (MD) simulation software package is a difficult task and is an impediment to the more widespread and efficient use of MD in materials design and development. Fixed-bond force fields generally require manual assignment of atom types, bonded interactions, charges, and simulation domain sizes. A new LAMMPS pre- and post-processing toolkit (LUNAR) is presented that efficiently builds molecular systems for LAMMPS. LUNAR automatically assigns atom types, generates bonded interactions, assigns charges, and provides initial configuration methods to generate large molecular systems. LUNAR can also incorporate chemical reactivity into simulations using fixed-bond force fields by facilitating the use of the REACTER protocol. Additionally, LUNAR provides post-processing for free volume calculations, cure characterization calculations, and property predictions from LAMMPS thermodynamic outputs. LUNAR has been validated via building and simulation of pure epoxy and cyanate ester polymer systems with a comparison of the corresponding predicted structures and properties to benchmark values, including experimental results from the literature. LUNAR provides the tools for the computationally-driven development of next-generation composite materials in the Integrated Computational Materials Engineering (ICME) and Materials Genome Initiative (MGI) frameworks.
README: LUNAR: Automated Input Generation and Analysis for Reactive LAMMPS Simulations Input and Output files
https://doi.org/10.5061/dryad.h18931zv1
This dataset contains all LAMMPS output data files generated during the benchmarking of the LUNAR software.
Description of the data and file structure
The naming of the files should provide enough guidance on what each file is. Here are a few notes about the naming convention:
- The "pxld" stands for percent crosslinked where the trailing number is the crosslinking percent (i.e. "pxld_10", means 10% crosslinked).
- The "replicate" stands for the replicate identifier (i.e. "replicate_1", means it is replicate 1 from the manuscript).
- The "initial_configuration" means this file was input to LAMMPS to start the first MD simulation with LAMMPS.
- All ".data" file extensions are LAMMPS data files
- All ".script" extensions are LAMMPS input files
- All ".lmpmol" extensions are LAMMPS molecule templates for "fix bond/react"
- All ".txt" extensions are LAMMPS map files for "fix bond/react"
Code/Software
The LUNAR software can be accessed at https://github.com/CMMRLab/LUNAR and LAMMPS can be accessed at https://www.lammps.org/download.html.
Methods
The data was collected using LAMMPS version April 7th, 2022