This repository will contain validation and application data to the paper Automated Exploration of Complex Reaction Networks Accelerated by a Data-Efficient Machine Learning Potential, by S. Li et al.
- deepmd-kit >= 3.1.0
- ase >= 3.25.0
Once deepmd-kit is successfully installed, the MDCD-NN models can be invoked by the calculators provided by deepmd-kit or Gaussian interfaces provided by this repository.
This folder contains MDCD-NN model ensembles (4 models).
This folder contains the interface scripts for MDCD-NN to Gaussian 16.
To use these scripts, first, launch DPA3_Server.py:
Usage: DPA3_Server.py model_1 model_2 ... model_N &
The DPA3_Server.py will be initialized with models provided by model_1 to model_N. After the initialization succeeded, a suggestive line DPA-3 server initialized on $(hostname):${port} will be printed
Then, MDCD-NN-based energy, gradient and hessian (numerical) calculations can be invoked by Gaussian 16 with the DPA3_Client.py script through the external keyword (https://gaussian.com/external/).
Example: #p opt=(nomicro,calcfc,recalc=10) nosymm external='DPA3_Client.py'
Finally, after all the calculations complete, one can terminate DPA3_Server.py simply by execuating DPA3_Terminator.py.
RGD1_s.wB97XD4.xyz: gCP(TZ)-wB97X-D4/def2-TZVP calculated elementary reaction steps selected from the RGD1 dataset. Structures are sequenced by the order of reactant_i, product_i, TS_i, reactant_i+1, ...
Cyclo_s.wB97XD4.xyz: gCP(TZ)-wB97X-D4/def2-TZVP calculated elementary reaction steps selected from the Cyclo[3+2] dataset. Structures are sequenced by the order of reactant_A_i, reactant_B_i, product_i, TS_i, reactant_A_i+1, ...
RGD1_s.MDCD-NN.xyz: MDCD-NN evaluated results for RGD1_s in the same order
Cyclo_s.MDCD-NN.xyz: MDCD-NN evaluated results in Cyclo_s the same order
All files with the name neutral_{Tag:03d}.gjf are starting reactant structures for 100 neutral textbook elementary reactions investigated in this work, while radical_{Tag:03d}.gjf are the starting 81 radical reactant structures. The files are in the Gaussian input gjf format except several additional lines behind the cartesian coordinates to specify the reaction coordinate (RC) used in CD calculations.
For example, the file neutral_001.gjf contains three additional lines:
Refene: Auto
FixBond1: 2 15 3.19 3.04 2.89 2.74 2.58 2.43 2.28 2.13 1.98 1.82 1.67 1.52
FixBond2: 3 18 3.19 3.04 2.89 2.74 2.58 2.43 2.28 2.13 1.98 1.82 1.67 1.52
The first line specifies the reference energy in a.u. for this CD calculation, where Auto means to perform free optimization for the starting structure to obtain its reference energy.
The following lines starting with FixBond{i}: have N+2 parameters in each line, with N as the number of a series of constrained optimization jobs in this CD calculation. The first two parameters indicate the atom pair (i,j) (starting from 1) and the resting N float numbers Angstrom during CD optimization.
In this case, we perform 12 constrained optimization jobs. The atomic distances Angstrom, respectively.
The subdirectory mdcdnn contains the Gaussian 16 outputs of MDCD-NN computed optimization and frequency analysis jobs for each reactant, product and transition state (TS) of the 181 elementary reactions.
The subdirectory dft contains the Gaussian 16 outputs of gCP(TZ)-wB97X-D4/def2-TZVP computed optimization and frequency analysis jobs for each reactant, product and transition state (TS) of the 181 elementary reactions.
All files with the suffix cfms.xyz are MDCD-NN-optimized conformers of intermediates and TSs. Each file represents one structural isomer, with multiple frames of structures within representing all conformational isomers of this isomer, sorted in order of relative Gibbs free energy from lowest to highest. The xyz-formatted comment line for each conformational isomer contains four numbers, from left to right, the electronic and Gibbs free energies in a.u., and the relative electronic and Gibbs free energies in kcal/mol over the lowest-energy conformer of this structural isomer calculated with MDCD-NN, respectively.
All files with the name DFT.xyz are gCP(TZ)-wB97X-D4/def2-TZVP optimized structures for the lowest-energy conformers involved in the MDCD-NN-calculated reaction networks. The name of each structure is noted in the xyz-formatted comment line.
dasa_dft.xyz: gCP(TZ)-wB97X-D4/def2-TZVP optimized structures.
dasa_mdcdnn.xyz: MDCD-NN optimized structures involved in the DASA reaction.
dasa.lammps.in: Lammps input file for committor-based OPES simulation of DASA reaction with MDCD-NN.
dasa.plumed.in: Plumed input file for committor-based OPES simulation of DASA reaction with MDCD-NN.
geom.lmp: Input geometry for committor-based OPES simulation of DASA reaction with MDCD-NN.
lmp-model_6_z_700K.pt: Committor model file for committor-based OPES simulation of DASA reaction with MDCD-NN.
FES-data.dat: Free energy surface and uncertainties for committor-based OPES simulation of DASA reaction with MDCD-NN.
This project is covered under the Apache 2.0 License.