├── 2d_diffusion.gif ├── README.md ├── Supplementary_Information_Theory.pdf ├── examples ├── README.md ├── Si_800atoms │ ├── 1_make_structure │ │ ├── BOX │ │ ├── DATA │ │ ├── structure │ │ ├── structure.cpp │ │ └── structure.xyz │ ├── 2_run_md │ │ ├── DATA │ │ ├── Si.tersoff │ │ ├── dump.forces │ │ ├── dump.xyz │ │ ├── in.run │ │ └── log.lammps │ ├── 3_mode_calculations │ │ ├── DATA │ │ ├── INPUT │ │ ├── Si.tersoff │ │ ├── calc_eig.py │ │ └── run.sh │ └── 4_run_md │ │ ├── DATA │ │ ├── D_FIX_WP_0 │ │ ├── D_FIX_WP_1 │ │ ├── D_FIX_WP_2 │ │ ├── D_FIX_WP_3 │ │ ├── Si.tersoff │ │ ├── in.run │ │ └── log.lammps ├── Si_8atoms │ ├── 1_get_modes │ │ ├── .README.md.swp │ │ ├── DATA │ │ ├── DEBUG_ASR │ │ ├── DEBUG_IFC2MCC │ │ ├── EMAT │ │ ├── FC2 │ │ ├── FC2_ASR │ │ ├── FC3 │ │ ├── FC4 │ │ ├── FREQUENCIES │ │ ├── INPUT │ │ ├── MCC2_PYTHON │ │ ├── MCC3 │ │ ├── MCC3_10 │ │ ├── MCC3_10_unique │ │ ├── MCC3_all │ │ ├── README.md │ │ ├── Si.tersoff │ │ ├── calc_eig.py │ │ ├── get_unique.py │ │ ├── job-fd2.err │ │ ├── job-fd2.out │ │ ├── log.lammps │ │ ├── mcc4 │ │ │ └── MCC4_0 │ │ ├── outfile_ifc2 │ │ ├── outfile_ifc3 │ │ ├── outfile_ifc4 │ │ └── run.sh │ ├── 2_energy_transfer_ensembles │ │ ├── EMAT │ │ ├── MCC3 │ │ ├── README.md │ │ ├── em_house │ │ │ ├── analyze.py │ │ │ └── gnuplot_em_compare │ │ ├── files │ │ │ ├── DATA │ │ │ ├── EQUIL │ │ │ ├── FREQUENCIES │ │ │ ├── INDICES │ │ │ ├── MODECOOR │ │ │ ├── MODETEMP │ │ │ ├── README.md │ │ │ ├── Si.tersoff │ │ │ ├── in.run_template │ │ │ ├── integrate6.py │ │ │ └── rando_vel.py │ │ └── run_ensembles.sh │ ├── 3_heat_flux_md │ │ ├── EMAT │ │ ├── GV │ │ ├── README.md │ │ ├── e1 │ │ │ ├── DATA │ │ │ ├── D_MODE_HEATFLUX │ │ │ ├── EQUIL │ │ │ ├── FREQUENCIES │ │ │ ├── INDICES │ │ │ ├── MODECOOR │ │ │ ├── MODETEMP │ │ │ ├── README.md │ │ │ ├── Si.tersoff │ │ │ ├── dump.xyz │ │ │ ├── fv.dat │ │ │ ├── in.run │ │ │ ├── in.run_template │ │ │ ├── integrate6.py │ │ │ ├── log.lammps │ │ │ ├── qnm.dat │ │ │ ├── qtot.dat │ │ │ └── rando_vel.py │ │ ├── files │ │ │ ├── DATA │ │ │ ├── EQUIL │ │ │ ├── FREQUENCIES │ │ │ ├── INDICES │ │ │ ├── MODECOOR │ │ │ ├── MODETEMP │ │ │ ├── README.md │ │ │ ├── Si.tersoff │ │ │ ├── in.run │ │ │ ├── in.run_template │ │ │ ├── integrate6.py │ │ │ └── rando_vel.py │ │ ├── qtot_house │ │ │ └── qtot1.dat │ │ └── run_ensembles.sh │ └── README.md ├── heat_flux │ ├── README.md │ ├── Si_8atoms │ │ ├── EMAT │ │ ├── GV │ │ ├── README.md │ │ ├── e1 │ │ │ ├── DATA │ │ │ ├── D_MODE_HEATFLUX │ │ │ ├── EQUIL │ │ │ ├── FREQUENCIES │ │ │ ├── INDICES │ │ │ ├── MODECOOR │ │ │ ├── MODETEMP │ │ │ ├── README.md │ │ │ ├── Si.tersoff │ │ │ ├── fv.dat │ │ │ ├── in.run │ │ │ ├── in.run_template │ │ │ ├── integrate6.py │ │ │ ├── log.lammps │ │ │ ├── qnm.dat │ │ │ ├── qtot.dat │ │ │ └── rando_vel.py │ │ ├── files │ │ │ ├── DATA │ │ │ ├── EQUIL │ │ │ ├── FREQUENCIES │ │ │ ├── INDICES │ │ │ ├── MODECOOR │ │ │ ├── MODETEMP │ │ │ ├── README.md │ │ │ ├── Si.tersoff │ │ │ ├── in.run │ │ │ ├── in.run_template │ │ │ ├── integrate6.py │ │ │ └── rando_vel.py │ │ ├── qtot_house │ │ │ └── qtot1.dat │ │ └── run_ensembles.sh │ ├── Si_Ge_alloy_x=10 │ │ ├── 1_make_structure │ │ │ ├── BOX │ │ │ ├── DATA │ │ │ ├── README.md │ │ │ ├── structure │ │ │ ├── structure.cpp │ │ │ └── structure.xyz │ │ ├── 2_relax_and_md │ │ │ ├── DATA │ │ │ ├── DATA_RELAXED │ │ │ ├── DATA_RELAXED_SORTED │ │ │ ├── README.md │ │ │ ├── Si.tersoff │ │ │ ├── SiCGe.tersoff │ │ │ ├── in.relax │ │ │ ├── in.run │ │ │ └── sort_positons_id.py │ │ ├── 3_mode_calculations │ │ │ ├── DATA_RELAXED_SORTED │ │ │ ├── INPUT │ │ │ ├── SiCGe.tersoff │ │ │ ├── calc_eig.py │ │ │ └── run.sh │ │ ├── 4_run_md_heatflux │ │ │ ├── DATA_RELAXED_SORTED │ │ │ ├── EQUIL │ │ │ ├── data2equil.py │ │ │ └── in.run │ │ └── README.md │ ├── Si_Ge_alloy_x=30 │ │ ├── 1_make_structure │ │ │ ├── BOX │ │ │ ├── DATA │ │ │ ├── README.md │ │ │ ├── structure │ │ │ ├── structure.cpp │ │ │ └── structure.xyz │ │ ├── 2_relax_and_md │ │ │ ├── DATA │ │ │ ├── DATA_RELAXED │ │ │ ├── DATA_RELAXED_SORTED │ │ │ ├── POSITIONS_RELAXED_SORTED │ │ │ ├── README.md │ │ │ ├── Si.tersoff │ │ │ ├── SiCGe.tersoff │ │ │ ├── in.relax │ │ │ ├── in.run │ │ │ ├── log.lammps │ │ │ └── sort_positons_id.py │ │ ├── 3_mode_calculations │ │ │ ├── DATA_RELAXED_SORTED │ │ │ ├── INPUT │ │ │ ├── SiCGe.tersoff │ │ │ ├── calc_eig.py │ │ │ └── run.sh │ │ └── README.md │ ├── Si_pure │ │ ├── 1_make_structure │ │ │ ├── BOX │ │ │ ├── DATA │ │ │ ├── structure │ │ │ ├── structure.cpp │ │ │ └── structure.xyz │ │ ├── 2_run_md │ │ │ ├── DATA │ │ │ ├── Si.tersoff │ │ │ └── in.run │ │ ├── 3_mode_calculations │ │ │ ├── DATA │ │ │ ├── INPUT │ │ │ ├── Si.tersoff │ │ │ ├── calc_eig.py │ │ │ └── run.sh │ │ ├── 4_run_md │ │ │ ├── DATA │ │ │ ├── README.md │ │ │ ├── equilbrium │ │ │ │ ├── 2dplot.jpg │ │ │ │ ├── DATA │ │ │ │ ├── EQUIL │ │ │ │ ├── FREQUENCIES │ │ │ │ ├── README.md │ │ │ │ ├── Si.tersoff │ │ │ │ ├── gnuplot_em_gif │ │ │ │ ├── gnuplot_fv │ │ │ │ ├── gnuplot_script │ │ │ │ ├── in.run │ │ │ │ └── sort.py │ │ │ └── single_wp │ │ │ │ ├── 2dplot.jpg │ │ │ │ ├── DATA │ │ │ │ ├── EQUIL │ │ │ │ ├── FREQUENCIES │ │ │ │ ├── README.md │ │ │ │ ├── Si.tersoff │ │ │ │ ├── em2.gif │ │ │ │ ├── gnuplot_em_gif │ │ │ │ ├── gnuplot_fv │ │ │ │ ├── gnuplot_script │ │ │ │ ├── in.run │ │ │ │ ├── tol=1e-5.gif │ │ │ │ ├── tol=1e-8.gif │ │ │ │ ├── tol=2.6e-5.gif │ │ │ │ ├── tol=2e-5.gif │ │ │ │ └── view_twotype.py │ │ ├── README.md │ │ └── visualize │ │ │ ├── DATA │ │ │ ├── FREQUENCIES │ │ │ ├── INPUT │ │ │ ├── README.md │ │ │ ├── Si.tersoff │ │ │ ├── disp.xyz │ │ │ ├── gnuplot_hf │ │ │ └── log.lammps │ └── Si_with_Ge_impurity │ │ └── equilbrium │ │ ├── 2dplot.jpg │ │ ├── DATA │ │ ├── DATA_RELAXED │ │ ├── DATA_RELAXED_SORTED │ │ ├── EQUIL │ │ ├── FREQUENCIES │ │ ├── POSITIONS_RELAXED │ │ ├── POSITIONS_RELAXED_SORTED │ │ ├── README │ │ ├── README.md │ │ ├── Si.tersoff │ │ ├── SiCGe.tersoff │ │ ├── gnuplot_em_gif │ │ ├── gnuplot_fv │ │ ├── gnuplot_script │ │ ├── in.relax │ │ ├── in.run │ │ ├── sort_mode_hf.py │ │ ├── sort_positons_id.py │ │ └── view_twotype.py ├── interface_transfer │ ├── 1_get_modes │ │ ├── 2dplot.jpg │ │ ├── DATA │ │ ├── DEBUG_ASR │ │ ├── DEBUG_IFC2MCC │ │ ├── FC2 │ │ ├── ILIST │ │ ├── INPUT │ │ ├── MCC2_PYTHON │ │ ├── README.md │ │ ├── Si.tersoff │ │ ├── calc_eig.py │ │ ├── gnuplot_mcc3 │ │ ├── gnuplot_mcc3_avg │ │ ├── gnuplot_script │ │ ├── graph.jpg │ │ ├── log.lammps │ │ ├── outfile_ifc2 │ │ └── smcc2 │ │ │ ├── SMCC2_0 │ │ │ ├── SMCC2_1 │ │ │ ├── SMCC2_2 │ │ │ └── SMCC2_3 │ ├── 2_simulate_energy_transfer │ │ ├── DATA │ │ ├── EQUIL │ │ ├── FREQUENCIES │ │ ├── README.md │ │ ├── Si.tersoff │ │ └── in.run │ └── README.md ├── mode_action │ ├── EMAT │ ├── README.md │ ├── files │ │ ├── DATA │ │ ├── EQUIL │ │ ├── FREQUENCIES │ │ ├── INDICES │ │ ├── MODECOOR │ │ ├── MODETEMP │ │ ├── PAIRS │ │ ├── README.md │ │ ├── Si.tersoff │ │ ├── in.run │ │ ├── in.run_template │ │ ├── integrate6.py │ │ └── rando_vel.py │ ├── jnm_house │ │ ├── README.md │ │ ├── cor_fft.cpp │ │ ├── cor_fft2.cpp │ │ ├── gnuplot_script │ │ ├── gnuplot_script_ave │ │ ├── gnuplot_script_tnm │ │ ├── gnuplot_script_tnm_avg │ │ ├── integrate.cpp │ │ ├── integrate_ave.cpp │ │ ├── plot_20ensembles.png │ │ ├── plot_34_35.png │ │ ├── plot_34_45.png │ │ ├── plot_34_56.png │ │ ├── plot_ave.png │ │ └── postproc.sh │ └── run_ensembles.sh ├── mode_flux_correlation │ ├── EMAT │ ├── README.md │ ├── files │ │ ├── DATA │ │ ├── EQUIL │ │ ├── FREQUENCIES │ │ ├── INDICES │ │ ├── MODECOOR │ │ ├── MODETEMP │ │ ├── PAIRS │ │ ├── README.md │ │ ├── Si.tersoff │ │ ├── in.run │ │ ├── in.run_template │ │ ├── integrate6.py │ │ └── rando_vel.py │ ├── jnm_house │ │ ├── README.md │ │ ├── average_ensembles.py │ │ ├── calc │ │ ├── cor_fft.cpp │ │ ├── gnuplot_script │ │ ├── gnuplot_script_ave │ │ ├── integrate │ │ ├── integrate.cpp │ │ ├── integrate_ave │ │ ├── integrate_ave.cpp │ │ ├── plot.png │ │ ├── plot_ave.png │ │ └── postproc.sh │ └── run_ensembles.sh ├── power_transfer │ ├── EMAT │ ├── MCC3 │ ├── MCC3_unique │ ├── MCC4 │ ├── README.md │ ├── e1 │ │ ├── DATA │ │ ├── D_FIX_MODE_0 │ │ ├── D_TEP │ │ ├── EQUIL │ │ ├── FC2 │ │ ├── FC3 │ │ ├── FC4 │ │ ├── FREQUENCIES │ │ ├── INDICES │ │ ├── MODECOOR │ │ ├── MODETEMP │ │ ├── Si.tersoff │ │ ├── disp.dat │ │ ├── dump.xyz │ │ ├── em.dat │ │ ├── em2.dat │ │ ├── em_compare.png │ │ ├── fm.dat │ │ ├── fv.dat │ │ ├── gnuplot_em_compare │ │ ├── gnuplot_em_time │ │ ├── ht.dat │ │ ├── ht2.dat │ │ ├── ht3.dat │ │ ├── in.run │ │ ├── in.run_template │ │ ├── integrate5.py │ │ ├── integrate6.py │ │ ├── integrated_fv.dat │ │ ├── log.lammps │ │ ├── mc.dat │ │ ├── pe.dat │ │ ├── pe3.dat │ │ ├── rando_vel.py │ │ ├── tm.dat │ │ ├── vm.dat │ │ └── xm.dat │ ├── em_house │ │ ├── analyze.py │ │ ├── em1.dat │ │ ├── em10.dat │ │ ├── em2.dat │ │ ├── em3.dat │ │ ├── em4.dat │ │ ├── em5.dat │ │ ├── em6.dat │ │ ├── em7.dat │ │ ├── em8.dat │ │ ├── em9.dat │ │ ├── em_avg.dat │ │ ├── em_compare.png │ │ ├── gnuplot_em_compare │ │ ├── summ1.dat │ │ ├── summ10.dat │ │ ├── summ2.dat │ │ ├── summ3.dat │ │ ├── summ4.dat │ │ ├── summ5.dat │ │ ├── summ6.dat │ │ ├── summ7.dat │ │ ├── summ8.dat │ │ ├── summ9.dat │ │ └── summ_avg.dat │ ├── files │ │ ├── DATA │ │ ├── EQUIL │ │ ├── FC2 │ │ ├── FC3 │ │ ├── FC4 │ │ ├── FREQUENCIES │ │ ├── INDICES │ │ ├── MODECOOR │ │ ├── MODETEMP │ │ ├── Si.tersoff │ │ ├── gnuplot_em_compare │ │ ├── gnuplot_em_time │ │ ├── in.run_template │ │ ├── integrate5.py │ │ ├── integrate6.py │ │ └── rando_vel.py │ ├── lammps_files │ │ ├── compute_mode_fv.cpp │ │ ├── compute_mode_fv.h │ │ ├── pair_tep.cpp │ │ └── pair_tep.h │ └── run_ensembles.sh ├── simple_transfer │ ├── MCC3 │ ├── MCC3-orig │ ├── README.md │ └── files │ │ ├── DATA_1x1x100 │ │ ├── EQUIL │ │ ├── FREQUENCIES │ │ ├── INDICES │ │ ├── MODECOOR │ │ ├── MODETEMP │ │ ├── README.md │ │ ├── Si.tersoff │ │ ├── em.png │ │ ├── em_compare.png │ │ ├── gnuplot_em_compare │ │ ├── gnuplot_em_gif │ │ ├── gnuplot_em_time │ │ ├── in.run │ │ ├── integrate2.py │ │ └── integrate5.py └── verify_spatial_transfer │ ├── 1_get_modes │ ├── 2dplot.jpg │ ├── DATA │ ├── FREQUENCIES │ ├── ILIST │ ├── INPUT │ ├── README.md │ ├── Si.tersoff │ ├── calc_eig.py │ ├── gnuplot_mcc3 │ ├── gnuplot_mcc3_avg │ ├── gnuplot_script │ └── graph.jpg │ ├── 2_simulate_energy_transfer │ ├── DATA │ ├── EMAT │ ├── EQUIL │ ├── FC2 │ ├── FC3 │ ├── FREQUENCIES │ ├── README.md │ ├── echange.png │ ├── extract_de.py │ ├── extract_de3.py │ ├── files │ │ ├── compute_mode_hf.cpp │ │ ├── compute_mode_hf.h │ │ ├── pair_tep.cpp │ │ └── pair_tep.h │ ├── gnuplot_echange │ ├── gnuplot_echange3 │ ├── gnuplot_echange_compare │ ├── in.run2 │ ├── in.run3 │ ├── integrate2.py │ ├── integrate3.py │ └── run.sh │ └── README.md ├── extended_mode.gif ├── lammps ├── README.md ├── compute_mode.cpp ├── compute_mode.h ├── compute_mode_fv.cpp ├── compute_mode_fv.h ├── compute_mode_heatflux.cpp ├── compute_mode_heatflux.h ├── compute_mode_heatflux2.cpp ├── compute_mode_heatflux2.h ├── compute_mode_hf.cpp ├── compute_mode_hf.h ├── fix_mode.cpp ├── fix_mode.h ├── fix_wp.cpp ├── fix_wp.h └── lammps │ ├── README │ ├── compute_mode.cpp │ ├── compute_mode.h │ ├── fix_mode.cpp │ └── fix_mode.h ├── mode_decomposition.gif ├── nmd ├── README.md ├── power_transfer │ ├── CONFIG │ ├── DEBUG_input │ ├── DEBUG_potential │ ├── DEBUG_update │ ├── DFILE │ ├── EMAT │ ├── EMAT_old │ ├── EQUIL │ ├── FC2_FD │ ├── FC2_FD_old │ ├── FC3_FD │ ├── FC4_FD │ ├── FFILE │ ├── FREQ │ ├── INPUT │ ├── MCC2 │ ├── MCC3 │ ├── MCC3_orig │ ├── MCC4 │ ├── MPE dump_atom_harmonic.xyz │ ├── MPE dump_mode.xyz │ ├── README.md │ ├── calc_traj_mpe.py │ ├── dump.forces │ ├── dump.forces2 │ ├── dump.forces3 │ ├── dump.forces4 │ ├── dump.forces_mta │ ├── dump.forces_mta2 │ ├── dump.forces_mta3 │ ├── dump.forces_mta4 │ ├── dump.xyz │ ├── dump_atom.xyz │ ├── dump_atom_harmonic.xyz │ ├── dump_mode.xyz │ ├── em.dat │ ├── em_compare.png │ ├── frequencies.txt │ ├── fv.dat │ ├── gnuplot_em_compare │ ├── integrate5.py │ ├── integrated_fv.dat │ ├── nmd │ ├── output │ ├── output_mode │ ├── plot_trajectory │ │ ├── dump.forces2 │ │ ├── dump.forces3 │ │ ├── dump.forces4 │ │ ├── dump.forces_mta2 │ │ ├── dump.forces_mta3 │ │ ├── dump.forces_mta4 │ │ └── plot.py │ └── run.sh ├── src │ ├── Makefile │ ├── compute.cpp │ ├── compute.h │ ├── compute.o │ ├── em3.cpp │ ├── em3.h │ ├── em3.o │ ├── input.cpp │ ├── input.h │ ├── input.o │ ├── main.cpp │ ├── main.o │ ├── memory.cpp │ ├── memory.h │ ├── memory.o │ ├── mode.cpp │ ├── mode.h │ ├── mode.o │ ├── nmd │ ├── output.cpp │ ├── output.h │ ├── output.o │ ├── pointers.h │ ├── potential.cpp │ ├── potential.h │ ├── potential.o │ ├── timer.cpp │ ├── timer.h │ ├── timer.o │ ├── update.cpp │ ├── update.h │ └── update.o └── trajectory │ ├── CONFIG │ ├── DEBUG_input │ ├── DEBUG_potential │ ├── DEBUG_update │ ├── DFILE │ ├── EMAT │ ├── EMAT_old │ ├── EQUIL │ ├── FC2_FD │ ├── FC2_FD_old │ ├── FC3_FD │ ├── FC4_FD │ ├── FFILE │ ├── FREQ │ ├── INPUT │ ├── MCC2 │ ├── MCC3 │ ├── MCC3_orig │ ├── MCC4 │ ├── MPE dump_atom_harmonic.xyz │ ├── MPE dump_atom_integrate0.xyz │ ├── MPE dump_mode.xyz │ ├── calc_traj_mpe.py │ ├── dump.forces │ ├── dump.forces2 │ ├── dump.forces3 │ ├── dump.forces4 │ ├── dump.forces_mta │ ├── dump.forces_mta2 │ ├── dump.forces_mta3 │ ├── dump.forces_mta4 │ ├── dump.xyz │ ├── em.dat │ ├── em_compare.png │ ├── frequencies.txt │ ├── fv.dat │ ├── gnuplot_em_compare │ ├── gnuplot_traj_err │ ├── integrate5.py │ ├── integrated_fv.dat │ ├── nmd │ ├── output │ ├── output_mode │ ├── plot_trajectory │ ├── dump.forces2 │ ├── dump.forces3 │ ├── dump.forces4 │ ├── dump.forces_mta2 │ ├── dump.forces_mta3 │ ├── dump.forces_mta4 │ └── plot.py │ ├── traj_err.dat │ ├── traj_err.png │ └── traj_err_integrate0.dat ├── src ├── Makefile ├── asr.cpp ├── asr.h ├── asr.o ├── compute.cpp ├── compute.h ├── compute.o ├── fcfd ├── ifc2mcc.cpp ├── ifc2mcc.h ├── ifc2mcc.o ├── in.cpp ├── in.h ├── in.o ├── main.cpp ├── main.o ├── mc ├── mc.cpp ├── mc.h ├── mc.o ├── mem.cpp ├── mem.h ├── mem.o ├── 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