Graphics Processing Units Molecular Dynamics
ensemble ti_rs keyword to enable nonequilibrium free-energy calculations along an isobaric path.ensemble ti_as keyword to enable nonequilibrium free-energy calculations along an isothermal path.ensemble ti_spring, eliminating the need for post-processing.ensemble ti_spring.compute_shc.compute_shc.New features
ensemble ti: This keyword is used to set up an equilibrium thermodynamic integration integrator. It is for testing purpose and its only differece from ti_spring keyword is that the lambda value is fixed instead of changing.ensemble nphug: This keyword sets up a Hugoniot thermostat integrator.ensemble mirror: This keyword is employed to configure a momentum mirror shock wave simulation, where atoms are deflected by a moving momentum mirror to generate a shock wave.ensemble piston: This keyword is employed to configure a piston shock wave simulation, where a fixed wall of atoms is displaced at a specified velocity to generate a shock wave.dump_piston: Piston simulations commonly involve millions of atoms. Dumping all the virial and velocity data for each atom can lead to excessively large output files, making data processing cumbersome. The dump_piston command addresses this by calculating spatial thermo information during the simulation.dump_dipole: Predicts the dipole on the fly using a TNEP model, see https://doi.org/10.1021/acs.jctc.3c01343
dump_polarizability: Predicts the polarizability on the fly using a TNEP model, see https://doi.org/10.1021/acs.jctc.3c01343
Enhancements and changes
basis_size for NEP training from (12, 12) to (8, 8).stress_train.out and stress_test.out during NEP trainingcompute_shc to calculate the SHC for all the groups in a grouping method simultaneously.replicate, see #523 for detailselectron_stop in run.in to apply electron stopping.compte_rdf in run.in to compute the radial distribution function (RDF).mc in run.in to perform efficient MCMD simulations in canonical, semi-grand canonical, and variance-constraint semi-grand canonical ensembles with a NEP model (only).dftd3 in run.in to add the D3 dispersion correction to a NEP model (only).replicate in run.in to replicate the initial model.ensemble options npt_mttk, nph_mttk, and nvt_mttk.ensemble ti_spring for free-energy calculations using the nonequilibrium thermodynamic integration method.ensemble msst for multi-scale shock technique (MSST) simulations.compute_lsqt to compute the electronic transport properties by coupling MD and linear scaling quantum transport (LSQT).fire for the keyword minimize in run.in.has_potential for the keyword dump_exyz in run.in.ensemble nvt_lan keeps to be the initial one, not changing linearly from the initial one to the final one.model_type keyword in nep.in, which can be set to 0, 1, or 2, corresponding to NEP models for potential, dipole, and polarizability, respectively. Tutorials for training dipole and polarizability NEP models are created.ensemble pimd, ensemble rpmd, ensemble trpmd, and dump_beads.compute_hnemdec and the related output file is onsager.out.dump_netcdf command.plumed interface #395prediction mode in nep.in. #391 #366basis_size from 8 8 to 12 12 #402plumed interface #394virial_train.out and virial_test.out file format: they have 12 instead of 2 columns now. #399plumed interface when the number of atoms exceeds 1024 #339filesize mismatch bug #310compute_msd keyword for mean-square displacement calculation #324compute_viscosity keyword for viscosity calculation #325dump_observer keyword for running MD with the average of an ensemble of NEP models or reporting model uncertainty #332lambda_shear keyword in nep.in #320version keyword in nep.in. It is now the default version for NEP training as it is much better than NEP2 and NEP3 for multi-component systems. #277INT_MAX. #276NEP_CPU to a separate repo (https://github.com/brucefan1983/NEP_CPU), where a NEP-LAMMPS interface is also created.GPUMD-v3.3.1 will be the best choice.potential keyword.potential keyword once and only once in run.in.neighbor keyword in run.in. The code will build the neighbor list at each step with the potential cutoff. The user does not need to estimate a neighbor list size now. For NEP models, the information of neighbor list size will be recorded into nep.txt. For empirical potentials, the code has chosen reasonable neighbor list sizes.gpumd and nep executables.xyz.in to model.xyz, and changed train.in/test.in to train.xyz/test.xyz. All the .xyz files are in the extended XYZ format. See the manual pages https://gpumd.zheyongfan.org/index.php/The_model.xyz_input_file and https://gpumd.zheyongfan.org/index.php/The_train.xyz_input_file for details on the extended XYZ format.export CUDA_VISIBLE_DEVICES=0,1 (0 and 1 are the IDs of the GPUs to be used) in the command line or by specifying something in a job-submission script in a cluster.