# Fileset

[README.md](https://mdr.nims.go.jp/filesets/8aeb52f6-ffba-43ef-b6d8-659f136b0201/download)

## Creator

[Kosuke Nakano](https://orcid.org/0000-0001-7756-4355), Benjamin X. Shi, Dario Alfè, Andrea Zen

## Rights



## Other metadata

[LRDMC Benchmark Dataset for Noncovalent Interaction Systems](https://mdr.nims.go.jp/datasets/1c0a3318-ae25-4b93-8a18-c6da6261c845)

## Fulltext

# LRDMC Benchmark Dataset for Noncovalent Interaction SystemsThis repository provides the **structures**, **wavefunctions**, **pseudopotentials**, and **LRDMC energy data** used for benchmark calculations on a set of noncovalent interaction systems.The dataset is organized by molecular system, structure type (monomers, dimers, and faraway dimers), trial wavefunction, and lattice spacing.---## OverviewThe repository contains directories for the following 12 molecular systems:- `water-dimer/`- `acetic-acid-dimer/`- `formic-acid-dimer/`- `uracil-cyclopentane/`- `methylamine-dimer/`- `water-peptide/`- `MeOH-pyridine/`- `ethene-ethyne/`- `ethyne-dimer/`- `peptide-pentane/`- `pentane_AcNH2/`- `benzene-dimer/`Each molecular-system directory contains structure-specific subdirectories corresponding to monomers, bound dimers, and faraway dimers.For example, `water-dimer/` contains:- `water_monomer_1/`- `water_monomer_2/`- `water_water/`- `water_water_faraway/`and `acetic-acid-dimer/` contains:- `AcOH_mon1/`- `AcOH-AcOH/`- `AcOH-AcOH-faraway/`The leading numeric prefixes used in the original calculation directories are omitted in this archive for readability.---## Molecular structure sourcesThe molecular systems included in this repository correspond to the following entries in the original benchmark datasets:### 1) `water-dimer/`- No. 1 in **S66**### 2) `acetic-acid-dimer/`- No. 20 in **S66**### 3) `formic-acid-dimer/`- No. 3 in **S22**### 4) `uracil-cyclopentane/`- No. 42 in **S66**### 5) `methylamine-dimer/`- No. 10 in **S66**### 6) `water-peptide/`- No. 4 in **S66**### 7) `MeOH-pyridine/`- No. 19 in **S66**### 8) `ethene-ethyne/`- No. 22 in **A24**### 9) `ethyne-dimer/`- No. 24 in **A24**### 10) `peptide-pentane/`- No. 46 in **S66**### 11) `pentane_AcNH2/`- No. 62 in **S66**### 12) `benzene-dimer/`- No. 24 in **S66**The original benchmark datasets are:- **S22**    Jurečka, P.; Šponer, J.; Černý, J.; Hobza, P. *Benchmark Database of Accurate (MP2 and CCSD(T) Complete Basis Set Limit) Interaction Energies of Small Model Complexes, DNA Base Pairs, and Amino Acid Pairs.* *Phys. Chem. Chem. Phys.* **2006**, *8*, 1985-1993.- **S66**    Řezáč, J.; Riley, K. E.; Hobza, P. *S66: A Well-Balanced Database of Benchmark Interaction Energies Relevant to Biomolecular Structures.* *J. Chem. Theory Comput.* **2011**, *7*, 2427-2438.- **A24**    Řezáč, J.; Hobza, P. *Describing Noncovalent Interactions beyond the Common Approximations: How Accurate Is the “Gold Standard,” CCSD(T) at the Complete Basis Set Limit?* *J. Chem. Theory Comput.* **2013**, *9*, 2151-2155.The molecular structures in this dataset can also be obtained from the **Benchmark Energy & Geometry Database (BEGDB)**:- BEGDB: `http://www.begdb.org`Řezáč, J.; Jurečka, P.; Riley, K. E.; Černý, J.; Valdes, H.; Pluháčková, K.; Berka, K.; Řezáč, T.; Pitoňák, M.; Vondrášek, J.; Hobza, P. *Collect. Czech. Chem. Commun.* **2008**, *73*, 1261-1270. `http://dx.doi.org/10.1135/cccc20081261`---## Directory structureEach structure directory contains:- `*.xyz`    Structure used for the calculation in XYZ format.- `lrdmc-ext-SD-workflow/`- `lrdmc-ext-AGPn-workflow/`These correspond to LRDMC calculations performed with two different trial wavefunctions:- `lrdmc-ext-SD-workflow/`    LRDMC calculations using an SD trial wavefunction.- `lrdmc-ext-AGPn-workflow/`    LRDMC calculations using an AGPn trial wavefunction.---## Lattice-spacing directoriesEach workflow directory contains subdirectories for different lattice spacings:- `alat_-0.1/`- `alat_-0.2/`- `alat_-0.25/`- `alat_-0.30/`Each `alat_-0.xx/` directory corresponds to one LRDMC calculation at the given lattice spacing.---## Files in each `alat_-0.xx/` directoryEach lattice-spacing directory contains the following files:- `wavefunction.dat`    Many-body wavefunction in the TurboRVB format.- `pseudopotential.dat`    Pseudopotential file in the TurboRVB format.- `energy.dat`    Energy output file obtained from the corresponding LRDMC calculation.These files were renamed from the original workflow outputs as follows:- `fort.10` -> `wavefunction.dat`- `pseudo.dat` -> `pseudopotential.dat`- `pip0_fn.d` -> `energy.dat`To reproduce the original LRDMC calculations directly, these filenames should be converted back to their original names.---## Notes on the dataset organization- Only the structure files (`*.xyz`) and the two selected LRDMC workflow results are included in this archive.- Other workflow directories from the original calculation tree are omitted.- The directory names were simplified from the original source layout by removing leading numeric identifiers from structure-directory names.- The directory `lrdmc-ext-AGPn-workflow/` in this archive originates from `lrdmc-ext-AGPn-MP2-lrdmcopt-workflow/` in the original calculation tree.---## License- This data is distributed under the CC0 LICENSE.