jablonkagroup/corral-environment-tasks huggingface dataset:
Task: Silicon Structure Retrieval for Melting - Level 1
Environment: corral_md (level_1 subtask)
Description: Retrieve structure of Silicon and convert it to LAMMPs data format. Return the absolute path of the final structure.
Allowed tools: get_structure_from_mp_text, convert_structure_to_lammps_data
Submission format: absolute path to structure file (eg. /results/structure/structure.data)
Task: Silicon Potential File for Melting - Level 1
Environment: corral_md (level_1 subtask)
Description: Procure the appropriate Stillinger–Weber (SW) potential file for Silicon for MD simulations. Return the absolute path to the potential file.
Allowed tools: get_potential_metadata
Submission format: absolute path to potential file (eg. /results/ffield.reax)
Task: Silicon NPT Melting - Level 1
Environment: corral_md (level_1 subtask)
Description: Given paths to LAMMPs compatible Silicon structure file and Stillinger–Weber potential file, perform NPT melting simulation of Silicon using LAMMPS. Replicate the system three times in each direction. Heat the system from 300K to 2500K at a rate of 2.2 K/ps under NPT ensemble at zero isotropic external pressure control. The log file from this simulation will be used for further analysis, so make sure Step, Temperature are appropriately logged at every 1000 time steps in the log file. As a final output, return the absolute paths to the the simulation log file and the restart file of the final melt.
Allowed tools: get_potential_metadata, run_lammps, get_nth_run_log, keyword_log_extractor
Submission format: {"log_file": "<absolute_path>", "restart_file": "<absolute_path>"} e.g. {"log_file": "/results/log.lammps", "restart_file": "/results/melting/melt.restart"}
Task: Silicon MSD - Level 1
Environment: corral_md (level_1 subtask)
Description: Given paths to LAMMPs restart file for liquid silicon at 2500K and Stillinger–Weber potential file, equilibrate the liquid silicon under NPT ensemble at 2500K for 500 ps at zero isotropic external pressure control. Compute the mean squared displacement (MSD) of Si atoms over the trajectory. As a file output, return the absolute path to the final MSD data file, where first column is time in ps, second column is msd data.
Allowed tools: get_potential_metadata, run_lammps, get_nth_run_log, keyword_log_extractor
Submission format: absolute path to MSD data file (eg. /results/msd.dat)
Task: Silicon Diffusion Coefficient Calculation - Level 1
Environment: corral_md (level_1 subtask)
Description: Using the MSD data file from the equilibration of liquid silicon at 2500K, compute the average self diffusion coefficient using the Einstein relation. The first column is of time in ps, and second column is msd data. Report the diffusion coefficient in units of m²/s.
Allowed tools: visualisation_tool, get_nth_run_log, keyword_log_extractor
Submission format: numerical value without units (eg. 56.00)
Task: Na2SiO3 Potential File for Quenching - Level 1
Environment: corral_md (level_1 subtask)
Description: Procure the appropriate BKS type potential file for sodium silicate for MD simulations. Return the absolute path to the potential file.
Allowed tools: get_potential_metadata
Submission format: absolute path to potential file (eg. /results/ffield.reax)
Task: Na2SiO3 NPT Quenching - Level 1
Environment: corral_md (level_1 subtask)
Description: Given paths to LAMMPS-compatible Na2SiO3 molten structure and BKS type potential file appropriate for MD simulations, perform NPT cooling of Na2SiO3 using LAMMPS. Cool the system from 4000 K down to 300 K with a cooling rate of 10 K/ps under NPT ensemble at zero external isotropic pressure control with pressure damping factor of 10000. The potential file already contains the required pair_style, pair_coeff, and kspace_style commands and should be included directly. The log file from this simulation will be used for further analysis, so make sure Step, Temperature and Density are appropriately logged at every 1000 time steps in the log file. As a final output, return the absolute paths to the simulation log file and the restart file of the final glassy configuration.
Allowed tools: get_potential_metadata, run_lammps, get_nth_run_log, keyword_log_extractor
Submission format: {"log_file": "<absolute_path>", "restart_file": "<absolute_path>"} e.g. {"log_file": "/results/log.lammps", "restart_file": "/results/melting/melt.restart"}
Task: Na2SiO3 Glass Equilibration - Level 1
Environment: corral_md (level_1 subtask)
Description: Given paths to LAMMPs restart file for glassy Na2SiO3 at 300K and BKS type potential file, equilibrate the glassy Na2SiO3 under NPT ensemble for 100 ps at zero external isotropic pressure control with pressure damping factor 5000. The potential file already contains the required pair_style, pair_coeff, and kspace_style commands and should be included directly. The log file from this simulation will be used for further analysis, so make sure Step, Temperature and Density are appropriately logged at every 1000 time steps in the log file. As a final output, return the absolute path to the simulation log file.
Allowed tools: get_potential_metadata, run_lammps, get_nth_run_log, keyword_log_extractor
Submission format: {"log_file": "<absolute_path>"} e.g. {"log_file": "/results/log.lammps"}
Task: Na2SiO3 Tg Calculation - Level 1
Environment: corral_md (level_1 subtask)
Description: You are given the LAMMPS log files from the molecular dynamics simulations of sodium silicate. These simulations represent a glass formation protocol carried out using the NPT ensemble. In the first simulation, a pre-equilibrated molten sodium silicate system is cooled from 4000 K down to 300 K. In the second simulation, the resulting glass is further equilibrated at 300 K. Using the data from these log files estimate the glass transition temperature Tg by constructing the density–temperature curve and fitting two linear regimes corresponding to the high-temperature (supercooled liquid) and low-temperature (glassy) regions. Do not look the data beyond 2600 K as then the density becomes noisy. Extract Tg as the intersection point of the two fitted lines, and report the result in Kelvin (K).
Allowed tools: get_nth_run_log, keyword_log_extractor, visualisation_tool
Submission format: numerical value without units (eg. 56.00)
Task: Aluminum Structure Retrieval for Surface Area - Level 1
Environment: corral_md (level_1 subtask)
Description: Retrieve structure of Aluminum and convert it to LAMMPS data format. Return the absolute path of the final structure.
Allowed tools: get_structure_from_mp_text, convert_structure_to_lammps_data
Submission format: absolute path to structure file (eg. /results/structure.data)
Task: Aluminum Potential File for Surface Energy - Level 1
Environment: corral_md (level_1 subtask)
Description: Procure an appropriate EAM potential file for Aluminum for MD simulations. Return the absolute path of the potential file.
Allowed tools: get_potential_metadata
Submission format: absolute path to potential file (eg. /results/potentials/EAM/cu.eam)
Task: Aluminum Bulk Minimisation for Surface Energy - Level 1
Environment: corral_md (level_1 subtask)
Description: Given paths to LAMMPS-compatible Aluminum structure file and EAM potential file, perform bulk relaxation using the given simulation parameters. The simulation should replicate the unit cell 5 times in each of the x, y, and z directions. Report the total energy of the relaxed structure in eV and the absolute path of the saved relaxed structure.
Allowed tools: get_potential_metadata, run_lammps, get_nth_run_log, keyword_log_extractor
Submission format: {"BULK ENERGY": "<numerical_value without units>", "path to relaxed structure": "<absolute_path>"} e.g. {"BULK ENERGY": "56.00", "path to relaxed structure": "/structure/structure.dat"}
Task: Aluminum Slab Relaxation for Surface Energy - Level 1
Environment: corral_md (level_1 subtask)
Description: Given paths to LAMMPS-compatible Aluminum structure file and EAM potential file, create a surface whose normal is in the given direction by removing periodic boundary conditions along that direction. Perform structure relaxation based on the given simulation parameters. The simulation should replicate the unit cell 5 times in each of the x, y, and z directions. Report the total energy of the relaxed structure in eV and the absolute path of the saved relaxed structure.
Allowed tools: get_potential_metadata, run_lammps, get_nth_run_log, keyword_log_extractor
Submission format: {"SLAB ENERGY": "<numerical_value without units>", "path to relaxed structure": "<absolute_path>"} e.g. {"SLAB ENERGY": "42.78", "path to relaxed structure": "/structures/slab_structure.dat"}
Task: Aluminum Surface Energy Calculation - Level 1
Environment: corral_md (level_1 subtask)
Description: Given the paths to LAMMPS-compatible relaxed bulk and surface configurations of Aluminum, and their total energies (in eV), compute the surface energy by computing the energy difference per unit area between the bulk and surface configurations. Return the surface energy in eV/Å².
Allowed tools: get_potential_metadata, run_lammps
Submission format: numerical value without units (eg. 56.00)