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|---|---|---|
| @@ -1,65 +1,139 @@ | ||
| bibtex: | ||
| - "@article{afzal2021, | ||
| author = {Afzal, Mohammad Atif Faiz and Browning, Andrea R. and Goldberg, Alexander | ||
| and Halls, Mathew D. and Gavartin, Jacob L. and Morisato, | ||
| Tsuguo and Hughes, Thomas F. and Giesen, David J. and Goose, Joseph E.}, | ||
| title = {High-Throughput Molecular Dynamics Simulations and Validation of Thermophysical | ||
| Properties of Polymers for Various Applications}, | ||
| journal = {ACS Applied Polymer Materials}, | ||
| volume = {3}, | ||
| number = {2}, | ||
| pages = {620-630}, | ||
| year = {2021}, | ||
| doi = {10.1021/acsapm.0c00524}}" | ||
| description: | ||
| "This paper outlines a MD simulation workflow based on GPU MD simulation | ||
| and the refined optimized potentials for liquid simulation (OPLS) OPLS3e force field to calculate glass transition temperatures (Tgs) of 315 polymers for which Bicerano reported experimental values." | ||
| identifiers: | ||
| - description: PSMILES | ||
| id: PSMILES | ||
| type: PSMILES | ||
| - description: polymer name | ||
| id: compound_name | ||
| names: | ||
| - noun: comxpound name | ||
| type: Other | ||
| license: CC BY 4.0 | ||
| links: | ||
| - description: corresponding publication | ||
| url: https://pubs.acs.org/doi/10.1021/acsapm.0c00524# | ||
| - description: data source | ||
| url: | ||
| - https://raw.githubusercontent.com/AdrianM0/chemnlp/main/data/tabular/bicerano_dataset/HT_MD_polymer_properties.csv | ||
| name: bicerano_dataset | ||
| description: |- | ||
| This paper outlines a MD simulation workflow based on GPU MD simulation and the | ||
| refined optimized potentials for liquid simulation (OPLS) OPLS3e force field to | ||
| calculate glass transition temperatures (Tgs) of 315 polymers for which Bicerano | ||
| reported experimental values. | ||
| num_points: 315 | ||
| targets: | ||
| - id: Tg_exp | ||
| description: experimental glass transition temperature | ||
| units: K | ||
| type: float | ||
| - description: experimental glass transition temperature | ||
| id: Tg_exp | ||
| names: | ||
| - noun: experimental glass transition temperature | ||
| uris: | ||
| - id: Tg_calc | ||
| description: calculated glass transition T | ||
| units: K | ||
| type: float | ||
| units: K | ||
| uris: null | ||
| - description: calculated glass transition temperature | ||
| id: Tg_calc | ||
| names: | ||
| - noun: computed glass transition temperature | ||
| - id: rho_300K_calc | ||
| description: computed density at 300K | ||
| units: g/cm^3 | ||
| - noun: MD-computed glass transition temperature (OPLS3e force field) | ||
| - noun: computed glass transition temperature (using MD with OPLS3e force field) | ||
| type: float | ||
| units: K | ||
| - description: computed density at 300K | ||
| id: rho_300K_calc | ||
| names: | ||
| - noun: computed polymer density at 300K | ||
| identifiers: | ||
| - id: PSMILES | ||
| type: PSMILES | ||
| description: PSMILES | ||
| - id: compound_name | ||
| type: Other | ||
| names: | ||
| - noun: compound name | ||
| description: polymer name | ||
| license: CC BY 4.0 | ||
| links: | ||
| - url: https://pubs.acs.org/doi/10.1021/acsapm.0c00524# | ||
| description: corresponding publication | ||
| - url: | ||
| - https://raw.githubusercontent.com/AdrianM0/chemnlp/main/data/tabular/bicerano_dataset/HT_MD_polymer_properties.csv | ||
| description: data source | ||
| num_points: 315 | ||
| bibtex: | ||
| - |- | ||
| @article{afzal2021, | ||
| author = {Afzal, Mohammad Atif Faiz and Browning, Andrea R. and Goldberg, Alexander and Halls, Mathew D. and Gavartin, Jacob L. and Morisato, | ||
| Tsuguo and Hughes, Thomas F. and Giesen, David J. and Goose, Joseph E.}, | ||
| title = {High-Throughput Molecular Dynamics Simulations and Validation of Thermophysical Properties of Polymers for Various Applications}, | ||
| journal = {ACS Applied Polymer Materials}, | ||
| volume = {3}, | ||
| number = {2}, | ||
| pages = {620-630}, | ||
| year = {2021}, | ||
| doi = {10.1021/acsapm.0c00524}} | ||
| - noun: computed polymer density at 300K (using MD with OPLS3e force field) | ||
| - noun: computed density at 300K (using MD with OPLS3e force field) | ||
| type: float | ||
| units: g/cm^3 | ||
| templates: | ||
| - The polymer with the {PSMILES__description} of {PSMILES#} has an experimental glass transition temperature of {Tg_exp#} {Tg_exp__units}. | ||
| - The polymer with the {PSMILES__description} of {PSMILES#} has a computed glass transition temperature of {Tg_calc#} {Tg_exp__units}. | ||
| - The polymer with the {PSMILES__description} of {PSMILES#} has a computed density at 300 K of {rho_300K_calc#} {rho_300K_calc__units}. | ||
| - The polymer with the {compound_name__names__noun} of {compound_name#} has an experimental glass transition temperature of {Tg_exp#} {Tg_exp__units}. | ||
| - The polymer with the {compound_name__names__noun} of {compound_name#} has a computed glass transition temperature of {Tg_calc#} {Tg_calc__units}. | ||
| - The polymer with the {compound_name__names__noun} of {compound_name#} has a computed density at 300 K of {rho_300K_calc#} {rho_300K_calc__units}. | ||
| - The polymer with the {PSMILES__description} of {PSMILES#} has an {Tg_exp__names__noun} of {Tg_exp#} {Tg_exp__units}. | ||
| - The polymer with the {PSMILES__description} of {PSMILES#} has a {Tg_calc__names__noun} of {Tg_calc#} {Tg_exp__units}. | ||
| - The polymer with the {PSMILES__description} of {PSMILES#} has a {rho_300K_calc__names__noun} of {rho_300K_calc#} {rho_300K_calc__units}. | ||
| - The polymer with the {compound_name__names__noun} of {compound_name#} has an {Tg_exp__names__noun} of {Tg_exp#} {Tg_exp__units}. | ||
| - The polymer with the {compound_name__names__noun} of {compound_name#} has a {Tg_calc__names__noun} of {Tg_calc#} {Tg_calc__units}. | ||
| - The polymer with the {compound_name__names__noun} of {compound_name#} has a {rho_300K_calc__names__noun} of {rho_300K_calc#} {rho_300K_calc__units}. | ||
| - What is the {Tg_exp__names__noun} of the polymer with the {PSMILES__description} {PSMILES#}? Answer:<EOI> {Tg_exp#} {Tg_exp__units}. | ||
| - What is the {Tg_calc__names__noun} of the polymer with the {PSMILES__description} {PSMILES#}? Answer:<EOI> {Tg_calc#} {Tg_calc__units}. | ||
| - What is the {rho_300K_calc__names__noun} of the polymer with the {PSMILES__description} {PSMILES#}? Answer:<EOI> {rho_300K_calc#} {rho_300K_calc__units}. | ||
| - What is the {Tg_exp__names__noun} of the polymer with the {compound_name__names__noun} {compound_name#}? Answer:<EOI> {Tg_exp#} {Tg_exp__units}. | ||
| - What is the {Tg_calc__names__noun} of the polymer with the {compound_name__names__noun} {compound_name#}? Answer:<EOI> {Tg_calc#} {Tg_calc__units}. | ||
| - What is the {rho_300K_calc__names__noun} of the polymer with the {compound_name__names__noun} {compound_name#}? Answer:<EOI> {rho_300K_calc#} {rho_300K_calc__units}. | ||
| - The polymer with the {PSMILES__description} {PSMILES#} has an {Tg_exp__names__noun} of {Tg_exp#} {Tg_exp__units} and a {Tg_calc__names__noun} of {Tg_calc#} {Tg_calc__units}. | ||
| - The polymer with the {compound_name__names__noun} {compound_name#} has an {Tg_exp__names__noun} of {Tg_exp#} {Tg_exp__units} and a {Tg_calc__names__noun} of {Tg_calc#} {Tg_calc__units}. | ||
| - Compare the {Tg_exp__names__noun} and {Tg_calc__names__noun} for the polymer with the {PSMILES__description} {PSMILES#}. Answer:<EOI> {Tg_exp#} {Tg_exp__units}, {Tg_calc#} {Tg_calc__units}. | ||
| - Compare the {Tg_exp__names__noun} and {Tg_calc__names__noun} for the polymer with the {compound_name__names__noun} {compound_name#}. Answer:<EOI> {Tg_exp#} {Tg_exp__units}, {Tg_calc#} {Tg_calc__units}. | ||
| - What is the {rho_300K_calc__names__noun} of the polymer with the {PSMILES__description} {PSMILES#} at 300K? Answer:<EOI> {rho_300K_calc#} {rho_300K_calc__units}. | ||
| - What is the {rho_300K_calc__names__noun} of the polymer with the {compound_name__names__noun} {compound_name#} at 300K? Answer:<EOI> {rho_300K_calc#} {rho_300K_calc__units}. | ||
| - |- | ||
| Task: Please answer the multiple choice question. | ||
| Question: What is the {Tg_exp__names__noun} of the polymer with the {PSMILES__description} {PSMILES#}? | ||
| Constraint: You must pick one of {%multiple_choice_enum%3%aA1}. | ||
| Options: | ||
| {Tg_exp#} | ||
| Answer:<EOI> {%multiple_choice_result} | ||
| - |- | ||
| Task: Please answer the multiple choice question. | ||
| Question: What is the {Tg_calc__names__noun} of the polymer with the {compound_name__names__noun} | ||
| {compound_name#}? | ||
| Constraint: You must pick one of {%multiple_choice_enum%3%aA1}. | ||
| Options: | ||
| {Tg_calc#} | ||
| Answer:<EOI> {%multiple_choice_result} | ||
| - |- | ||
| Task: Please answer the multiple choice question. | ||
| Question: What is the {rho_300K_calc__names__noun} of the polymer with the {PSMILES__description} {PSMILES#}? | ||
| Constraint: You must pick one of {%multiple_choice_enum%3%aA1}. | ||
| Options: | ||
| {%multiple_choice_enum%3%aA1} | ||
| {rho_300K_calc#} | ||
| Answer:<EOI> {%multiple_choice_result} | ||
| - |- | ||
| Task: Please answer the multiple choice question. | ||
| Question: What is the {Tg_exp__names__noun} of the polymer with the {compound_name__names__noun} {compound_name#}? | ||
| Constraint: You must pick one of {%multiple_choice_enum%3%aA1}. | ||
| Options: | ||
| {Tg_exp#} | ||
| Answer:<EOI> {%multiple_choice_result} | ||
| - |- | ||
| Question: What is a polymer with a computed glass transition temperature of {Tg_calc#} {Tg_calc__units} and a computed density at 300 K of {rho_300K_calc#} {rho_300K_calc__units}. | ||
| Answer: A polymer with {PSMILES__description} {PSMILES#} | ||
| Task: Please answer the multiple choice question. | ||
| Question: What is the {Tg_calc__names__noun} of the polymer with the {PSMILES__description} | ||
| {PSMILES#}? | ||
| Constraint: You must pick one of {%multiple_choice_enum%3%aA1}. | ||
| Options: | ||
| {Tg_calc#} | ||
| Answer:<EOI> {%multiple_choice_result} |
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