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Added in some simulations using abTEM
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PdSiSimulations/.ipynb_checkpoints/MakeStrucuture-checkpoint.ipynb

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PdSiSimulations/MakeStrucuture.ipynb

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PdSiSimulations/PdSi.lammps (1).eam

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PdSiSimulations/Si2Pd9.cif

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# generated using pymatgen
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data_Si2Pd9
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_symmetry_space_group_name_H-M 'P 1'
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_cell_length_a 7.53468400
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_cell_length_b 9.17728400
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_cell_length_c 9.55579400
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_cell_angle_alpha 90.00000000
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_cell_angle_beta 90.00000000
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_cell_angle_gamma 90.00000000
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_symmetry_Int_Tables_number 1
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_chemical_formula_structural Si2Pd9
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_chemical_formula_sum 'Si8 Pd36'
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_cell_volume 660.76342160
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_cell_formula_units_Z 4
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loop_
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_symmetry_equiv_pos_site_id
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_symmetry_equiv_pos_as_xyz
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1 'x, y, z'
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loop_
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_atom_site_type_symbol
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_atom_site_label
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_atom_site_symmetry_multiplicity
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_atom_site_fract_x
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_atom_site_fract_y
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_atom_site_fract_z
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_atom_site_occupancy
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Si Si0 1 0.75000000 0.63212700 0.78831300 1.0
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Si Si1 1 0.25000000 0.36787300 0.21168700 1.0
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Si Si2 1 0.75000000 0.13212700 0.71168700 1.0
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Si Si3 1 0.25000000 0.86787300 0.28831300 1.0
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Si Si4 1 0.75000000 0.77264100 0.17805600 1.0
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Si Si5 1 0.25000000 0.22735900 0.82194400 1.0
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Si Si6 1 0.75000000 0.27264100 0.32194400 1.0
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Si Si7 1 0.25000000 0.72735900 0.67805600 1.0
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Pd Pd8 1 0.93396900 0.89801000 0.68106600 1.0
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Pd Pd9 1 0.43396900 0.10199000 0.31893400 1.0
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Pd Pd10 1 0.56603100 0.39801000 0.81893400 1.0
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Pd Pd11 1 0.06603100 0.60199000 0.18106600 1.0
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Pd Pd12 1 0.06603100 0.10199000 0.31893400 1.0
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Pd Pd13 1 0.56603100 0.89801000 0.68106600 1.0
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Pd Pd14 1 0.43396900 0.60199000 0.18106600 1.0
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Pd Pd15 1 0.93396900 0.39801000 0.81893400 1.0
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Pd Pd16 1 0.94242600 0.61211600 0.59362900 1.0
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Pd Pd17 1 0.44242600 0.38788400 0.40637100 1.0
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Pd Pd18 1 0.55757400 0.11211600 0.90637100 1.0
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Pd Pd19 1 0.05757400 0.88788400 0.09362900 1.0
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Pd Pd20 1 0.05757400 0.38788400 0.40637100 1.0
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Pd Pd21 1 0.55757400 0.61211600 0.59362900 1.0
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Pd Pd22 1 0.44242600 0.88788400 0.09362900 1.0
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Pd Pd23 1 0.94242600 0.11211600 0.90637100 1.0
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Pd Pd24 1 0.94102800 0.81780700 0.37738300 1.0
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Pd Pd25 1 0.44102800 0.18219300 0.62261700 1.0
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Pd Pd26 1 0.55897200 0.31780700 0.12261700 1.0
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Pd Pd27 1 0.05897200 0.68219300 0.87738300 1.0
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Pd Pd28 1 0.05897200 0.18219300 0.62261700 1.0
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Pd Pd29 1 0.55897200 0.81780700 0.37738300 1.0
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Pd Pd30 1 0.44102800 0.68219300 0.87738300 1.0
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Pd Pd31 1 0.94102800 0.31780700 0.12261700 1.0
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Pd Pd32 1 0.75000000 0.85111700 0.93267700 1.0
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Pd Pd33 1 0.25000000 0.14888300 0.06732300 1.0
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Pd Pd34 1 0.75000000 0.35111700 0.56732300 1.0
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Pd Pd35 1 0.25000000 0.64888300 0.43267700 1.0
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Pd Pd36 1 0.75000000 0.55020500 0.33487200 1.0
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Pd Pd37 1 0.25000000 0.44979500 0.66512800 1.0
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Pd Pd38 1 0.75000000 0.05020500 0.16512800 1.0
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Pd Pd39 1 0.25000000 0.94979500 0.83487200 1.0
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Pd Pd40 1 0.75000000 0.55935000 0.02962300 1.0
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Pd Pd41 1 0.25000000 0.44065000 0.97037700 1.0
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Pd Pd42 1 0.75000000 0.05935000 0.47037700 1.0
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Pd Pd43 1 0.25000000 0.94065000 0.52962300 1.0

PdSiSimulations/md.log

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Time[ps] Etot[eV] Epot[eV] Ekin[eV] T[K]

PdSiSimulations/md.traj

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PdSiSimulations/moldyn3.traj

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