├── LICENSE ├── README.md ├── doc ├── .keep ├── I-ReaxFF_Manual.md ├── gulp │ ├── .keep │ ├── GULP分子动力学模拟.md │ └── GULP并行安装.md ├── lammps │ ├── .keep │ └── 并行安装lammps.md ├── octave.md ├── qe │ ├── .keep │ └── 并行编译qe.md ├── siesta │ ├── .keep │ ├── Al.psf │ ├── C.psf │ ├── F.psf │ ├── H.psf │ ├── N.psf │ ├── O.psf │ ├── in.fdf │ └── 并行编译siesta.md ├── 图1.png ├── 图2.png └── 图3.png ├── examples ├── Readme.md ├── example_al │ └── .keep ├── example_ch4h2o │ ├── .keep │ ├── Readme.md │ ├── aimd_ch4w2 │ │ ├── .keep │ │ ├── ch4w2-0 │ │ │ ├── SinglePointEnergies.log │ │ │ ├── ch4w2.traj │ │ │ └── in.fdf │ │ ├── ch4w2-1 │ │ │ ├── SinglePointEnergies.log │ │ │ ├── ch4w2.traj │ │ │ └── in.fdf │ │ └── ch4w2-2 │ │ │ ├── SinglePointEnergies.log │ │ │ ├── ch4w2.traj │ │ │ └── in.fdf │ ├── aimd_h22 │ │ ├── .keep │ │ ├── h22-0.traj │ │ ├── h22-0 │ │ │ ├── SinglePointEnergies.log │ │ │ ├── h22.traj │ │ │ ├── md.traj │ │ │ └── siesta_h22.out │ │ ├── h22-1 │ │ │ ├── SinglePointEnergies.log │ │ │ ├── h22.traj │ │ │ ├── siesta.bib │ │ │ └── siesta.out │ │ ├── h22-2 │ │ │ ├── SinglePointEnergies.log │ │ │ ├── h22.traj │ │ │ ├── md.traj │ │ │ └── siesta.out │ │ ├── h22-3 │ │ │ ├── SinglePointEnergies.log │ │ │ ├── ffield.json │ │ │ ├── h22.traj │ │ │ ├── in.fdf │ │ │ ├── md.traj │ │ │ └── siesta.out │ │ ├── h22-4 │ │ │ ├── SinglePointEnergies.log │ │ │ ├── h22.traj │ │ │ └── siesta.out │ │ ├── h22-5 │ │ │ ├── SinglePointEnergies.log │ │ │ ├── h22.traj │ │ │ └── siesta.out │ │ ├── h22-6 │ │ │ ├── SinglePointEnergies.log │ │ │ └── h22.traj │ │ ├── h22-7 │ │ │ ├── SinglePointEnergies.log │ │ │ └── h22.traj │ │ ├── h22-8 │ │ │ ├── SinglePointEnergies.log │ │ │ ├── h22.traj │ │ │ └── md.traj │ │ └── h22-v.traj │ ├── aimd_h2o16 │ │ ├── .keep │ │ ├── h2o16-0 │ │ │ ├── C.psf │ │ │ ├── Cl.psf │ │ │ ├── H.psf │ │ │ ├── N.psf │ │ │ ├── O.psf │ │ │ ├── SinglePointEnergies.log │ │ │ ├── h2o16.traj │ │ │ └── in.fdf │ │ ├── h2o16-1 │ │ │ ├── SinglePointEnergies.log │ │ │ ├── h2o16.traj │ │ │ └── in.fdf │ │ ├── h2o16-2 │ │ │ ├── SinglePointEnergies.log │ │ │ ├── h2o16.traj │ │ │ └── in.fdf │ │ ├── h2o16-3 │ │ │ ├── SinglePointEnergies.log │ │ │ ├── h2o16.traj │ │ │ └── in.fdf │ │ └── h2o16-4 │ │ │ ├── SinglePointEnergies.log │ │ │ ├── h2o16.traj │ │ │ └── in.fdf │ ├── aimd_h2o2 │ │ ├── .keep │ │ ├── h2o2-0 │ │ │ ├── SinglePointEnergies.log │ │ │ ├── h2o2.traj │ │ │ ├── siesta-1.out │ │ │ ├── siesta-11.out │ │ │ ├── siesta-2.out │ │ │ ├── siesta-4.out │ │ │ ├── siesta-6.out │ │ │ └── siesta-8.out │ │ ├── h2o2-1 │ │ │ ├── SinglePointEnergies.log │ │ │ ├── h2o2.traj │ │ │ └── siesta-50.out │ │ ├── h2o2-2 │ │ │ ├── SinglePointEnergies.log │ │ │ ├── h2o2.traj │ │ │ └── siesta-50.out │ │ ├── h2o2-3 │ │ │ ├── SinglePointEnergies.log │ │ │ ├── h2o2.traj │ │ │ └── siesta-50.out │ │ └── h2o2-4 │ │ │ ├── SinglePointEnergies.log │ │ │ ├── h2o2.traj │ │ │ ├── in.fdf │ │ │ └── siesta-31.out │ ├── ch4w2.gen │ ├── ffield.json │ ├── gmd.py │ ├── h22.gen │ ├── h2o16.gen │ ├── h2o2.gen │ ├── json_to_ffield.py │ ├── json_to_lib.py │ ├── lm.py │ ├── ml_train.py │ ├── pseudo │ │ ├── .keep │ │ ├── C.psf │ │ ├── H.psf │ │ ├── N.psf │ │ └── O.psf │ ├── rotate.py │ ├── stretch.py │ ├── train.py │ └── train_without_force.py ├── example_fc_lammps │ └── .keep ├── example_fox │ ├── .keep │ ├── README.md │ ├── aimd_fox7 │ │ ├── fox7-0 │ │ │ ├── C.psf │ │ │ ├── H.psf │ │ │ ├── N.psf │ │ │ ├── O.psf │ │ │ ├── fox7.traj │ │ │ └── in.fdf │ │ ├── fox7-1 │ │ │ ├── SinglePointEnergies.log │ │ │ └── fox7.traj │ │ └── fox7-2 │ │ │ ├── C.psf │ │ │ ├── H.psf │ │ │ ├── N.psf │ │ │ ├── O.psf │ │ │ ├── SinglePointEnergies.log │ │ │ ├── fox7.traj │ │ │ └── siesta-18.out │ ├── ffield.json │ ├── fox7.png │ ├── lm.py │ ├── pseudo │ │ ├── .keep │ │ ├── Al.psf │ │ ├── C.psf │ │ ├── Cl.psf │ │ ├── H.psf │ │ ├── N.psf │ │ └── O.psf │ └── train.py ├── example_graph │ ├── .keep │ └── ml_train_reax.py ├── example_phonon │ ├── .keep │ ├── ph_gulp.py │ ├── readme.md │ └── reaxff_nn.lib ├── example_reax │ ├── .keep │ ├── aimd_tkx │ │ ├── tkx-0 │ │ │ └── tkx.traj │ │ ├── tkx-1 │ │ │ └── tkx.traj │ │ ├── tkx-2 │ │ │ └── tkx.traj │ │ ├── tkx-3 │ │ │ └── tkx.traj │ │ ├── tkx-4 │ │ │ └── tkx.traj │ │ ├── tkx-5 │ │ │ └── tkx.traj │ │ └── tkx-6 │ │ │ ├── SinglePointEnergies.log │ │ │ ├── in.fdf │ │ │ └── tkx.traj │ ├── aimd_tkx2 │ │ ├── tkx2-0 │ │ │ └── tkx2.traj │ │ ├── tkx2-1 │ │ │ └── tkx2.traj │ │ ├── tkx2-2 │ │ │ └── tkx2.traj │ │ ├── tkx2-3 │ │ │ └── tkx2.traj │ │ └── tkx2-4 │ │ │ └── tkx2.traj │ ├── ffield.json │ ├── ffield_to_json.py │ ├── json_to_ffield.py │ ├── lmd.py │ ├── ml_train_reax.py │ ├── readme.md │ ├── tkx2.gen │ └── train_reax.py ├── example_torch │ ├── .keep │ ├── aimd_ch4w2 │ │ ├── ch4w2-0 │ │ │ ├── SinglePointEnergies.log │ │ │ ├── ch4w2.traj │ │ │ └── in.fdf │ │ ├── ch4w2-1 │ │ │ ├── SinglePointEnergies.log │ │ │ ├── ch4w2.traj │ │ │ └── in.fdf │ │ └── ch4w2-2 │ │ │ ├── SinglePointEnergies.log │ │ │ ├── ch4w2.traj │ │ │ └── in.fdf │ └── train.py └── train.png ├── irff ├── .keep ├── AtomDance.py ├── LearningMachine.py ├── RadiusCutOff.py ├── __init__.py ├── data │ ├── .keep │ ├── ColData.py │ ├── __init__.py │ ├── dpdata.py │ ├── mdtodata.py │ ├── prep_data.py │ └── qeout_to_traj.py ├── deb │ ├── .keep │ ├── __init__.py │ ├── compare_energies.py │ ├── deb_bde.py │ ├── hbdeb.py │ ├── ird.py │ ├── irdeb.py │ ├── irffdeb.py │ ├── irnan.py │ ├── mpdeb.py │ ├── reax_debug.py │ ├── reax_gulp.py │ └── theta.py ├── dft │ ├── .keep │ ├── CheckEmol.py │ ├── SinglePointEnergy.py │ ├── __init__.py │ ├── cpmd.py │ ├── dftb.py │ ├── nwchem.py │ ├── qe.py │ ├── siesta.py │ ├── siesta_zmatix_constrain.py │ └── smd_server.py ├── dingtalk.py ├── emdk.py ├── getNeighbor.pyx ├── getNeighbors.py ├── intCheck.py ├── irff.py ├── irff_autograd.py ├── irff_np.py ├── link.py ├── md │ ├── .keep │ ├── ReactionCapture.py │ ├── __init__.py │ ├── gofr.py │ ├── gulp.py │ ├── hugoniot.py │ ├── irmd.py │ └── lammps.py ├── ml │ ├── .keep │ ├── __init__.py │ ├── data.py │ ├── evaluate_data.py │ ├── evolution.py │ ├── ffield.py │ ├── fit.py │ ├── fluctuation.py │ ├── gaqeq.py │ ├── genetic.py │ ├── gpfit_tfv2.py │ ├── harmonic.py │ ├── nn.py │ ├── reax_funcs.py │ └── train.py ├── mlqeq.py ├── molecule.py ├── mpnn.py ├── neighbor.pyx ├── neighbors.py ├── plot │ ├── .keep │ ├── BondEnergy.py │ ├── CheckAng.py │ ├── LearningResults.py │ ├── LearningResultsAng.py │ ├── MessagePassing.py │ ├── __init__.py │ ├── abc.py │ ├── angel_to_bond.py │ ├── bde.py │ ├── compare_energies.py │ ├── fingerprint.py │ ├── gofr.py │ ├── irnn_plot.py │ ├── label_md.py │ ├── labels.py │ ├── morse.py │ ├── morse_taper.py │ ├── mpbd.py │ ├── mpnn_plbd.py │ ├── nx.py │ ├── pdf.py │ ├── plbd.py │ ├── plbo.py │ ├── ple.py │ ├── plea.py │ ├── pleb.py │ ├── pleo.py │ ├── plev.py │ ├── plevdw.py │ ├── plf.py │ ├── plot_atoms.py │ ├── plot_atoms_matplot.py │ ├── plot_atoms_momenta.py │ ├── plot_bond_energy.py │ ├── plot_charge.py │ ├── plot_energy.py │ ├── plot_eover.py │ ├── plot_eover_atom.py │ ├── plot_functions.py │ ├── plot_morse.py │ ├── plot_pes.py │ ├── plot_pressure.py │ ├── plot_zmat_pes.py │ ├── plotenergy.py │ ├── plotenergy_bond.py │ ├── pltp.py │ ├── reax_plbd.py │ ├── reax_pldd.py │ ├── reax_plot.py │ ├── reax_plov.py │ ├── rffbd.py │ ├── sigmoid.py │ ├── vdw_taper.py │ └── view.py ├── potentials │ ├── .keep │ ├── __init__.py │ ├── ffield_CHNO.json │ ├── ffield_CarbonSp2.json │ ├── ffield_SiN.json │ └── json_to_ffield.py ├── prop │ ├── .keep │ ├── __init__.py │ └── gofr.py ├── qeq.py ├── reax.py ├── reax_data.py ├── reax_force_data.py ├── reax_nn.py ├── reaxff_jax.py ├── reaxff_torch.py ├── reaxfflib.py ├── set_matrix_tensor.py ├── spectra.py ├── structures │ ├── .keep │ ├── Al.gen │ ├── C2C4.gen │ ├── HMX_MOL.gen │ ├── NM.gen │ ├── __init__.py │ ├── ball.py │ ├── ball_bulk.py │ ├── diamond.py │ ├── fox7.gen │ └── nm3.gen ├── tools │ ├── .keep │ ├── __init__.py │ ├── eos_opt.py │ ├── epstopdf.py │ ├── ffieldtolib.py │ ├── fingerprint.py │ ├── fit_hugoniot_state.py │ ├── fitnn.py │ ├── json_to_ffield.py │ ├── load_individuals.py │ ├── morse_taper.py │ ├── pre_opt.py │ ├── prepare_ffield.py │ ├── pressure.py │ ├── pseudo_gen.py │ ├── rsetff.py │ ├── setwb.py │ ├── vdw.py │ └── zmat_to_atoms.py ├── trainer.py └── zmatrix.py ├── setup.py ├── test ├── .keep ├── ffield.json ├── gp4-0.traj ├── gp4-1.traj ├── md.traj ├── test_force_nn.py ├── test_reax_force.py ├── test_reax_gulp.py ├── test_reax_nn.py ├── test_train_tf_force.py └── train_with_force.py └── tools ├── .keep ├── README.md ├── add_element.py ├── add_layer.py ├── apprun.py ├── atoms_to_poscar.py ├── atoms_to_yaml.py ├── axial_strain.py ├── bend.py ├── c3_zmat_pes.py ├── checkoffd.py ├── cif_to_poscar.py ├── cifs_to_traj.py ├── cnt.py ├── collision.py ├── coltraj.py ├── compare_dft.py ├── continous.py ├── control_to_poscar.py ├── cplib.py ├── data ├── .keep ├── ase_convert_dpmd.py ├── ase_to_mtp.py ├── gen_to_csv.py └── md_to_traj.py ├── de.py ├── deb ├── .keep ├── compare_energies.py ├── deb_bd.py ├── deb_bo.py ├── deb_delta.py ├── deb_energies.py ├── deb_eover.py ├── deb_thet.py ├── dinfo.py ├── mp_deb.py └── theta.py ├── dft ├── .keep ├── ebind_smd.py ├── nw.py ├── qmd.py ├── singlepoint.py └── smd.py ├── diff_fnn.py ├── ffield_to_csv.py ├── ffield_to_json.py ├── fitmorse.py ├── fitnn.py ├── gaussian.py ├── get_forces.py ├── gp.py ├── gulp_time.py ├── harmonic.py ├── init_ffield_fit.py ├── integrate.py ├── json_to_ffield.py ├── json_to_lib.py ├── md ├── .keep ├── dmd.py ├── get_md_time.py ├── gmd.py ├── lam2xyz.f ├── lmd.py ├── lopt.py ├── lopt_ace.py ├── lopt_dp.py ├── lopt_gap.py ├── lopt_mtp.py ├── md.py ├── pack_poscar.py ├── scale.py └── scale_mol.py ├── merge.py ├── ml ├── .keep ├── gp_uncertainty.py ├── invariance.py └── invariance_info.py ├── ml_optimize_coulomb.py ├── ml_train.py ├── ml_train_coul.py ├── ml_train_reax.py ├── moment.py ├── nomb.py ├── notebooks ├── .keep ├── deb_angle.ipynb ├── deb_bo.ipynb ├── deb_energies.ipynb └── deb_manybody.ipynb ├── out_to_traj.py ├── pes ├── .keep ├── zmat_stretch.py ├── zmatpes.py └── zmatpes_cbd2.py ├── phonopy ├── .keep ├── af_flow_scale.py ├── generate_displacements.py ├── ph_flow.py ├── ph_flow_lammps.py ├── phonon_siesta.ipynb └── plotband.py ├── plot ├── .keep ├── hbond.py ├── hbond_component.py ├── kappa_plot.py ├── plevdw.py ├── plot_convergence_af.py ├── plot_ebind.py ├── plot_msd.py ├── plot_result.py ├── plot_thermal.py ├── plot_time.py ├── plotatoms.py ├── plotatoms_bondorder.py ├── trajplot.py ├── trajplot_gulp.py └── trajplot_lammps.py ├── pm.py ├── prior_bo_fit.py ├── qeout_to_traj.py ├── rmsave.py ├── rotate.py ├── rotator.py ├── select_element.py ├── single_point.py ├── sort_atoms.py ├── stretch.py ├── stretch_zmat.py ├── structure.py ├── supercell.py ├── swing.py ├── test_reax.py ├── torsion.py ├── train_nn.py ├── train_reax.py ├── uspex ├── .keep ├── calc_individuals.py ├── density.py ├── ebind_gulp.py ├── ebind_smd.py ├── gen_to_csv.py ├── hbond.py ├── 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