├── .examples ├── Cu_210_tilt │ ├── Cu.eam.alloy │ ├── best_grip_data_Cu210.csv │ ├── best_grip_plot_Cu210.png │ ├── lammps_0.936_0.455_0.97_1.76_1_11_900_1000 │ ├── lammps_0.951_0.000_0.62_0.01_1_1_900_24000 │ ├── lammps_0.953_0.857_1.18_2.59_2_7_500_12000 │ └── params.yaml ├── Si_310_twist │ ├── Si.sw │ ├── lammps_1.049_0.800_3.17_3.41_1_1_1100_6000 │ ├── lammps_1.081_0.20_2.91_2.38_1_2_1400_100000 │ ├── lammps_1.102_0.300_4.44_2.18_1_1_1300_61000 │ └── params.yaml ├── Ti_2130_tilt │ ├── POSCAR_LOWER │ ├── POSCAR_UPPER │ ├── Ti.meam.spline │ ├── lammps_0.462_0.000_2.51_0.59_2_1_500_7000 │ ├── lammps_0.508_0.500_2.06_2.51_2_1_700_20000 │ └── params.yaml ├── W_310_twist │ ├── W.eam.alloy │ ├── lammps_2.297_0.200_0.59_0.60_1_1_1100_3000 │ ├── lammps_2.469_0.400_5.56_5.36_2_1_1300_6000 │ └── params.yaml ├── W_552_tilt │ ├── Marinica_2013 │ │ ├── W.eam.fs │ │ ├── best_grip_W_552_Marinica.csv │ │ ├── lammps_2.731_0.571_0.71_0.80_2_7_1600_88000 │ │ ├── lammps_2.732_0.500_0.83_2.47_1_2_3300_24000 │ │ ├── lammps_2.732_0.571_6.41_1.31_2_7_2200_66000 │ │ ├── lammps_2.734_0.571_1.65_4.01_4_7_2300_174000 │ │ ├── lammps_2.734_0.600_5.70_3.35_2_5_1400_113000 │ │ ├── lammps_2.735_0.600_4.87_4.16_2_5_2700_0 │ │ ├── lammps_2.736_0.500_1.94_3.91_1_6_1900_166000 │ │ ├── lammps_2.736_0.600_0.19_3.66_2_5_3100_78000 │ │ ├── lammps_3.047_0.000_1.37_1.49_1_1_1700_0 │ │ └── params.yaml │ └── Zhou_2004 │ │ ├── W.eam.alloy │ │ ├── best_grip_W_552_Zhou.csv │ │ ├── lammps_2.446_0.50_0.14_0.09_1_4_1600_57000 │ │ ├── lammps_2.467_0.33_4.38_0.05_3_3_1900_154000 │ │ ├── lammps_2.497_0.00_0.14_0.11_2_2_1300_3000 │ │ ├── lammps_2.869_0.00_2.40_0.03_1_1_2700_0 │ │ └── params.yaml ├── sample_pbs_submit.sh └── sample_slurm_submit.sh ├── .gitignore ├── LICENSE ├── NOTICE ├── README.md ├── core ├── __init__.py ├── bicrystal.py ├── interstitial.py └── simulation.py ├── main.py ├── params.yaml ├── simul_files ├── lammps.in_1 └── lammps.in_2 └── utils ├── __init__.py ├── clean.sh ├── constants.py ├── dump2poscar.py ├── plot_gco.py ├── tests.py ├── unique.py └── utils.py /.examples/Cu_210_tilt/best_grip_plot_Cu210.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/enze-chen/grip/596c17dff5bef9b7638020a5200daf1abb3a56d0/.examples/Cu_210_tilt/best_grip_plot_Cu210.png -------------------------------------------------------------------------------- /.examples/Cu_210_tilt/lammps_0.951_0.000_0.62_0.01_1_1_900_24000: -------------------------------------------------------------------------------- 1 | ITEM: TIMESTEP 2 | 0 3 | ITEM: NUMBER OF ATOMS 4 | 176 5 | ITEM: BOX BOUNDS pp pp ss 6 | 0.0000000000000000e+00 8.0833857386617396e+00 7 | 0.0000000000000000e+00 3.6150000000000002e+00 8 | -7.0728035473001209e-03 7.0654125907192736e+01 9 | ITEM: ATOMS id type x y z c_eng 10 | 1 1 6.49763 0.00500657 35.5588 -3.49376 11 | 2 1 1.58793 0.00500704 36.9925 -3.24339 12 | 3 1 4.03051 0.00500705 36.5272 -3.48517 13 | 4 1 7.05964 0.0050089 38.1581 -3.50605 14 | 5 1 8.0722 1.81251 36.5272 -3.48517 15 | 6 1 3.01795 1.81251 38.1581 -3.50605 16 | 7 1 5.40061 1.81251 39.2821 -3.28142 17 | 8 1 1.35891 0.00501144 39.2821 -3.28142 18 | 9 1 3.80717 0.00501104 39.8347 -3.47416 19 | 10 1 6.2668 0.00501158 40.7359 -3.50146 20 | 11 1 7.84887 1.81251 39.8347 -3.47416 21 | 12 1 2.22511 1.81251 40.7359 -3.50146 22 | 13 1 4.60971 1.81251 41.5853 -3.50988 23 | 14 1 7.05125 1.81251 42.3333 -3.54245 24 | 15 1 0.568014 0.00501182 41.5853 -3.50988 25 | 16 1 3.00955 0.00501205 42.3333 -3.54245 26 | 17 1 5.43755 0.00501234 43.1643 -3.54021 27 | 18 1 1.39585 1.81251 43.1643 -3.54021 28 | 19 1 2.45594 1.81251 35.5588 -3.49376 29 | 20 1 5.62963 1.81251 36.9925 -3.24339 30 | 21 1 7.85411 0.00501252 43.9792 -3.53618 31 | 22 1 2.20012 0.00501278 44.7751 -3.54202 32 | 23 1 4.62528 0.00501305 45.5891 -3.54004 33 | 24 1 7.04866 0.0050133 46.3982 -3.53928 34 | 25 1 0.58359 1.81251 45.5891 -3.54004 35 | 26 1 3.00697 1.81251 46.3982 -3.53928 36 | 27 1 5.43302 1.81251 47.2041 -3.54046 37 | 28 1 1.39132 0.00501354 47.2041 -3.54046 38 | 29 1 3.81626 0.0050137 48.0138 -3.53996 39 | 30 1 6.24097 0.00501397 48.8221 -3.53986 40 | 31 1 7.85795 1.81251 48.0138 -3.53996 41 | 32 1 2.19927 1.81251 48.8221 -3.53986 42 | 33 1 4.62451 1.81251 49.63 -3.5401 43 | 34 1 7.0495 1.81251 50.4386 -3.53998 44 | 35 1 0.582818 0.00501421 49.63 -3.5401 45 | 36 1 3.00781 0.00501431 50.4386 -3.53998 46 | 37 1 5.43277 0.0050146 51.2469 -3.53998 47 | 38 1 1.39107 1.81251 51.2469 -3.53998 48 | 39 1 3.81242 1.81251 43.9792 -3.53618 49 | 40 1 6.24182 1.81251 44.7751 -3.54202 50 | 41 1 7.85778 0.0050146 52.0552 -3.54002 51 | 42 1 2.19941 0.0050146 52.8636 -3.53999 52 | 43 1 4.62443 0.0050146 53.6719 -3.54 53 | 44 1 7.04944 0.0050146 54.4802 -3.54 54 | 45 1 0.582734 1.81251 53.6719 -3.54 55 | 46 1 3.00775 1.81251 54.4802 -3.54 56 | 47 1 5.43277 1.81251 55.2886 -3.54 57 | 48 1 1.39107 0.0050146 55.2886 -3.54 58 | 49 1 3.81609 0.0050146 56.0969 -3.54 59 | 50 1 6.2411 0.0050146 56.9052 -3.54 60 | 51 1 7.85778 1.81251 56.0969 -3.54 61 | 52 1 2.19941 1.81251 56.9052 -3.54 62 | 53 1 4.62443 1.81251 57.7136 -3.54 63 | 54 1 7.04944 1.81251 58.5219 -3.54 64 | 55 1 0.582734 0.0050146 57.7136 -3.54 65 | 56 1 3.00775 0.0050146 58.5219 -3.54 66 | 57 1 5.43277 0.0050146 59.3303 -3.54 67 | 58 1 1.39107 1.81251 59.3303 -3.54 68 | 59 1 3.81609 1.81251 52.0552 -3.54002 69 | 60 1 6.2411 1.81251 52.8636 -3.53999 70 | 61 1 7.85778 0.0050146 60.1386 -3.54 71 | 62 1 2.19941 0.0050146 60.9469 -3.54 72 | 63 1 4.62443 0.0050146 61.7553 -3.54 73 | 64 1 7.04944 0.0050146 62.5636 -3.54 74 | 65 1 0.582734 1.81251 61.7553 -3.54 75 | 66 1 3.00775 1.81251 62.5636 -3.54 76 | 67 1 5.43277 1.81251 63.372 -3.54 77 | 68 1 1.39107 0.0050146 63.372 -3.54 78 | 69 1 3.81609 0.0050146 64.1803 -3.54 79 | 70 1 6.2411 0.0050146 64.9886 -3.54 80 | 71 1 7.85778 1.81251 64.1803 -3.54 81 | 72 1 2.19941 1.81251 64.9886 -3.54 82 | 73 1 4.62443 1.81251 65.797 -3.54 83 | 74 1 7.04944 1.81251 66.6053 -3.54048 84 | 75 1 0.582734 0.0050146 65.797 -3.54 85 | 76 1 3.00775 0.0050146 66.6053 -3.54048 86 | 77 1 5.43277 0.0050146 67.4136 -3.53371 87 | 78 1 1.39107 1.81251 67.4136 -3.53371 88 | 79 1 3.81609 1.81251 60.1386 -3.54 89 | 80 1 6.2411 1.81251 60.9469 -3.54 90 | 81 1 7.85778 0.0050146 68.222 -3.50249 91 | 82 1 2.19941 0.0050146 69.0303 -3.39542 92 | 83 1 4.62443 0.0050146 69.8387 -3.14502 93 | 84 1 7.04944 0.0050146 70.647 -2.6938 94 | 85 1 0.582734 1.81251 69.8387 -3.14502 95 | 86 1 3.00775 1.81251 70.647 -2.6938 96 | 87 1 3.81609 1.81251 68.222 -3.50249 97 | 88 1 6.2411 1.81251 69.0303 -3.39542 98 | 89 1 0 0.005 5e-05 -2.6938 99 | 90 1 0.808339 0.005 2.42507 -3.50249 100 | 91 1 1.61668 0.005 4.85008 -3.54 101 | 92 1 2.42502 0.005 7.2751 -3.54 102 | 93 1 0 1.8125 4.04174 -3.54048 103 | 94 1 0.808339 1.8125 6.46676 -3.54 104 | 95 1 1.61668 1.8125 0.808389 -3.14502 105 | 96 1 2.42502 1.8125 3.2334 -3.53371 106 | 97 1 3.23335 1.8125 5.65842 -3.54 107 | 98 1 3.23335 0.005 1.61673 -3.39542 108 | 99 1 4.04169 0.005 4.04174 -3.54048 109 | 100 1 4.85003 0.005 6.46676 -3.54 110 | 101 1 4.04169 1.8125 5e-05 -2.6938 111 | 102 1 4.85003 1.8125 2.42507 -3.50249 112 | 103 1 5.65837 1.8125 4.85008 -3.54 113 | 104 1 6.46671 1.8125 7.2751 -3.54 114 | 105 1 5.65837 0.005 0.808389 -3.14502 115 | 106 1 6.46671 0.005 3.2334 -3.53371 116 | 107 1 7.27505 0.005 5.65842 -3.54 117 | 108 1 7.27505 1.8125 1.61673 -3.39542 118 | 109 1 0 0.005 8.08344 -3.54 119 | 110 1 0.808339 0.005 10.5085 -3.54 120 | 111 1 1.61668 0.005 12.9335 -3.54 121 | 112 1 2.42502 0.005 15.3585 -3.54 122 | 113 1 0 1.8125 12.1251 -3.54 123 | 114 1 0.808339 1.8125 14.5501 -3.54 124 | 115 1 1.61668 1.8125 8.89177 -3.54 125 | 116 1 2.42502 1.8125 11.3168 -3.54 126 | 117 1 3.23335 1.8125 13.7418 -3.54 127 | 118 1 3.23335 0.005 9.70011 -3.54 128 | 119 1 4.04169 0.005 12.1251 -3.54 129 | 120 1 4.85003 0.005 14.5501 -3.54 130 | 121 1 4.04169 1.8125 8.08344 -3.54 131 | 122 1 4.85003 1.8125 10.5085 -3.54 132 | 123 1 5.65837 1.8125 12.9335 -3.54 133 | 124 1 6.46671 1.8125 15.3585 -3.54 134 | 125 1 5.65837 0.005 8.89177 -3.54 135 | 126 1 6.46671 0.005 11.3168 -3.54 136 | 127 1 7.27505 0.005 13.7418 -3.54 137 | 128 1 7.27505 1.8125 9.70011 -3.54 138 | 129 1 0 0.005 16.1668 -3.54 139 | 130 1 0.808339 0.005 18.5918 -3.54 140 | 131 1 1.61668 0.00500079 21.0168 -3.54 141 | 132 1 2.42502 0.00500186 23.4418 -3.53999 142 | 133 1 8.08338 1.8125 20.2085 -3.54 143 | 134 1 0.80833 1.8125 22.6335 -3.54 144 | 135 1 1.61668 1.8125 16.9752 -3.54 145 | 136 1 2.42502 1.8125 19.4002 -3.54 146 | 137 1 3.23336 1.8125 21.8252 -3.54001 147 | 138 1 3.23335 0.005 17.7835 -3.54 148 | 139 1 4.04169 0.00500047 20.2085 -3.54 149 | 140 1 4.85002 0.00500152 22.6335 -3.54 150 | 141 1 4.04169 1.8125 16.1668 -3.54 151 | 142 1 4.85003 1.8125 18.5918 -3.54 152 | 143 1 5.65837 1.8125 21.0168 -3.54 153 | 144 1 6.46671 1.8125 23.4418 -3.53999 154 | 145 1 5.65837 0.005 16.9752 -3.54 155 | 146 1 6.46671 0.005 19.4002 -3.54 156 | 147 1 7.27505 0.00500117 21.8252 -3.54001 157 | 148 1 7.27505 1.8125 17.7835 -3.54 158 | 149 1 2.11072e-05 0.00500217 24.2503 -3.54003 159 | 150 1 0.808427 0.00500324 26.6755 -3.54013 160 | 151 1 1.61702 0.00500419 29.1016 -3.5406 161 | 152 1 2.42623 0.00500508 31.5318 -3.54258 162 | 153 1 0.000128602 1.8125 28.2915 -3.53989 163 | 154 1 0.809175 1.8125 30.7156 -3.53981 164 | 155 1 1.61664 1.8125 25.0585 -3.53997 165 | 156 1 2.42481 1.8125 27.4833 -3.53985 166 | 157 1 3.23233 1.8125 29.9071 -3.5392 167 | 158 1 3.23337 0.00500288 25.8668 -3.53997 168 | 159 1 4.04182 0.00500382 28.2915 -3.53989 169 | 160 1 4.85087 0.00500473 30.7156 -3.53981 170 | 161 1 4.04171 1.8125 24.2503 -3.54003 171 | 162 1 4.85012 1.8125 26.6755 -3.54013 172 | 163 1 5.65872 1.8125 29.1016 -3.5406 173 | 164 1 6.46792 1.81251 31.5318 -3.54258 174 | 165 1 5.65833 0.00500254 25.0585 -3.53997 175 | 166 1 6.4665 0.0050035 27.4833 -3.53985 176 | 167 1 7.27402 0.00500446 29.9071 -3.5392 177 | 168 1 7.27506 1.8125 25.8668 -3.53997 178 | 169 1 8.07871 0.00500537 32.3253 -3.53516 179 | 170 1 0.789216 0.00500618 34.7149 -3.50065 180 | 171 1 1.62154 1.81251 33.1385 -3.53857 181 | 172 1 3.23717 0.00500604 33.9789 -3.54048 182 | 173 1 4.03701 1.81251 32.3253 -3.53516 183 | 174 1 4.83091 1.81251 34.7149 -3.50065 184 | 175 1 5.66323 0.00500566 33.1385 -3.53857 185 | 176 1 7.27886 1.81251 33.9789 -3.54048 186 | Egb = 0.951019002161011 187 | -------------------------------------------------------------------------------- /.examples/Cu_210_tilt/params.yaml: -------------------------------------------------------------------------------- 1 | # Input data for the GRand canonical Interface Predictor (GRIP). Format is YAML. 2 | 3 | # Parameters for the algorithm 4 | algo: 5 | dir_struct: 'best' # Folder to store best structures. 6 | dir_calcs: 'calc_procs' # Folder to store temporary calculation files. 7 | ngrid: 100 # Number of grid points in each dim = ngrid * nprocs. 8 | frac_min: 0.00 # Minimum fraction of atoms on a plane (0 <= n <= 1). 9 | frac_max: 1.00 # Maximum fraction of atoms on a plane. Set both to 1.0 for gamma-surface. 10 | gb_gap: 0.3 # Initial gap between slabs prior to MD/relaxation (in Ang.). 11 | perturb_u: 0.3 # Maximum random perturbation (A) of atoms above GB 12 | perturb_l: 0.0 # Maximum random perturbation (A) of atoms below GB 13 | gb_thick: 10 # Thickness of GB region (in Angstrom) on either side of interface. 14 | pad: 10 # Extra padding (A) on top of gb_thick for relaxation / energy calculations. 15 | vacuum: 1 # Vacuum to add on top for MD (A); less needed for s boundary. 16 | 17 | inter_p: 0.0 # Probability of swapping with interstitial sites. [0.0, 1.0] = [Never, Always]. 18 | inter_s: 'Cu' # species of atom to insert. 19 | inter_n: 2 # Number of GB interstitial sites to swap with atoms in GB region. 20 | inter_t: 1.5 # Thickness of region (A) on either side of GB to search for interstitials. 21 | inter_u: False # Only choose unique interstitial sites. 22 | inter_r: True # Randomly choose interstitial sites vs. largest volume 23 | inter_w: 2 # How to swap: 1 = only subs, 2 = only inter, 3 = uniform, 4 = mostly subs, 5 = mostly inter 24 | 25 | MD_run: 0.95 # Probability of running MD simulation before relaxing. [0.0, 1.0] = [Never, Always]. 26 | Tmin: 300 # Temperature lower bound for MD simulation. 27 | Tmax: 1200 # Temperature upper bound, vary in multiple of 100s. 28 | MD_min: 5000 # Min steps for MD simulation. 29 | MD_max: 300000 # Max steps for MD simulation. 30 | var_steps: 2 # 0 = Min steps only; 1 = linear sample; 2 = exponential sample 31 | 32 | lammps_bin: '/g/g16/chen120/bin/lammps_serial' # Path to [serial] LAMMPS binary. 33 | Emult: 2 # Maximum energy threshold * Egb_min to keep; at least 1.0. 34 | nruns: 0 # Number of iterations in total (each processor). Set 0 for infinite loop. 35 | clear_freq: 50 # Number of iterations before clearing duplicates. Set 0 to never clear. 36 | 37 | 38 | # Parameters for the material 39 | struct: 40 | user: False # True: read existing cells (POSCAR_*), False: generate w/ ase. 41 | cutoff: 35 # Max height (A) to cut slabs if user=False; speed up calcs. Set to 0 to ignore. 42 | write: True # Write generated cells to POSCAR_* 43 | size0: [1, 1, 1] # Minimum replications in [x, y, z] to create supercells. 44 | size: [3, 12, 15] # Replications in [x, y, z] to create supercells. z is not used if user=True. 45 | reps: 2 # Sample replications (1) exactly, (2) uniform, (3) weighted smaller, (4) weighted larger. 46 | 47 | # Basic info - potential dependent!! 48 | upper_dirs: [ [2, 1, 0], [0, 0, -1], [-1, 2, 0] ] # Cu(210) tilt 49 | lower_dirs: [ [2, -1, 0], [0, 0, -1], [1, 2, 0] ] 50 | symbol: 'Cu' # Chemical formula 51 | crystal: 'fcc' # fcc, bcc, hcp, or dc 52 | mass: 63.546 # Atomic mass 53 | a: 3.615 # a lattice constant; 54 | c: 3.615 # c lattice constant; only used for hcp 55 | dlat: 0 # Minimal normal component of lattice vector to calculate Nplane. Set 0 to ignore. 56 | Ecoh: -3.54 # Energy per atom in bulk 57 | pair_style: 'eam/alloy' # pair_style for LAMMPS 58 | pair_coeff: '* * /g/g16/chen120/lammps/pots/Cu.eam.alloy Cu' # pair_coeff for LAMMPS 59 | 60 | -------------------------------------------------------------------------------- /.examples/Si_310_twist/Si.sw: -------------------------------------------------------------------------------- 1 | # DATE: 2007-06-11 CONTRIBUTOR: Aidan Thompson, athomps@sandia.gov CITATION: Stillinger and Weber, Phys Rev B, 31, 5262, (1985) 2 | # Stillinger-Weber parameters for various elements and mixtures 3 | # multiple entries can be added to this file, LAMMPS reads the ones it needs 4 | # these entries are in LAMMPS "metal" units: 5 | # epsilon = eV; sigma = Angstroms 6 | # other quantities are unitless 7 | 8 | # format of a single entry (one or more lines): 9 | # element 1, element 2, element 3, 10 | # epsilon, sigma, a, lambda, gamma, costheta0, A, B, p, q, tol 11 | 12 | # Here are the original parameters in metal units, for Silicon from: 13 | # 14 | # Stillinger and Weber, Phys. Rev. B, v. 31, p. 5262, (1985) 15 | # 16 | 17 | Si Si Si 2.1683 2.0951 1.80 21.0 1.20 -0.333333333333 18 | 7.049556277 0.6022245584 4.0 0.0 0.0 19 | -------------------------------------------------------------------------------- /.examples/Si_310_twist/lammps_1.049_0.800_3.17_3.41_1_1_1100_6000: -------------------------------------------------------------------------------- 1 | ITEM: TIMESTEP 2 | 0 3 | ITEM: NUMBER OF ATOMS 4 | 278 5 | ITEM: BOX BOUNDS pp pp ss 6 | 0.0000000000000000e+00 8.5870068723042259e+00 7 | 0.0000000000000000e+00 8.5870068723042259e+00 8 | -7.4115936535697488e-03 7.4463094887121130e+01 9 | ITEM: ATOMS id type x y z c_eng 10 | 1 1 1.85963 3.77023 37.8509 -4.13517 11 | 2 1 3.11571 5.75953 38.4589 -4.08838 12 | 3 1 6.72738 4.82678 37.8509 -4.13517 13 | 4 1 8.05874 6.15813 39.3203 -4.13517 14 | 5 1 1.46103 7.41421 38.7123 -4.08838 15 | 6 1 3.03749e-06 4.2985 40.6568 -4.24994 16 | 7 1 1.7837 5.07311 41.949 -4.27346 17 | 8 1 3.76173 5.36137 40.6843 -4.2251 18 | 9 1 5.20898 6.91821 41.7626 -4.18705 19 | 10 1 6.91598 7.9126 40.3653 -4.11895 20 | 11 1 3.11698e-06 0.00499789 41.8837 -4.25662 21 | 12 1 1.67103 0.684401 40.3653 -4.11895 22 | 13 1 3.37803 1.67879 41.7626 -4.18705 23 | 14 1 7.12598 1.1828 38.7123 -4.08838 24 | 15 1 7.52414 0.536772 36.4869 -4.2251 25 | 16 1 0.528277 2.43888 39.3203 -4.13517 26 | 17 1 4.82528 3.23564 40.6843 -4.2251 27 | 18 1 6.80331 3.5239 41.949 -4.27346 28 | 19 1 2.5698 3.33258 43.2684 -4.26803 29 | 20 1 4.29351 4.2985 44.5784 -4.32206 30 | 21 1 6.01721 5.26442 43.2684 -4.26803 31 | 22 1 7.76628 6.04758 44.6065 -4.33124 32 | 23 1 0.898936 6.86447 43.2226 -4.31225 33 | 24 1 2.60518 7.73689 44.5671 -4.33271 34 | 25 1 3.0638e-06 4.2985 45.9492 -4.33574 35 | 26 1 1.72105 5.15588 47.3008 -4.33624 36 | 27 1 3.4371 6.01441 45.9381 -4.33486 37 | 28 1 5.1536 6.87597 47.2976 -4.33651 38 | 29 1 6.86832 7.75207 45.9451 -4.33387 39 | 30 1 3.13105e-06 0.00499757 47.3079 -4.3355 40 | 31 1 1.7187 0.844931 45.9451 -4.33387 41 | 32 1 3.43341 1.72103 47.2976 -4.33651 42 | 33 1 4.29351 0.00499792 43.1536 -4.30403 43 | 34 1 5.98184 0.860111 44.5671 -4.33271 44 | 35 1 7.68808 1.73254 43.2226 -4.31225 45 | 36 1 0.820732 2.54942 44.6065 -4.33124 46 | 37 1 5.14992 2.58259 45.9381 -4.33486 47 | 38 1 6.86596 3.44112 47.3008 -4.33624 48 | 39 1 2.5769 3.43787 48.658 -4.33657 49 | 40 1 4.29351 4.2985 50.0158 -4.33659 50 | 41 1 6.01011 5.15913 48.658 -4.33657 51 | 42 1 7.72791 6.01534 50.0169 -4.33659 52 | 43 1 0.859597 6.87178 48.6602 -4.33654 53 | 44 1 2.5768 7.73293 50.0163 -4.33659 54 | 45 1 2.77577e-06 4.2985 51.3748 -4.3366 55 | 46 1 1.71758 5.15728 52.7321 -4.3366 56 | 47 1 3.43509 6.01563 51.3742 -4.3366 57 | 48 1 5.15233 6.87464 52.7319 -4.3366 58 | 49 1 6.8695 7.73356 51.374 -4.3366 59 | 50 1 2.88832e-06 0.00499696 52.7318 -4.3366 60 | 51 1 1.71751 0.863443 51.374 -4.3366 61 | 52 1 3.43468 1.72236 52.7319 -4.3366 62 | 53 1 4.29351 0.00499751 48.6571 -4.33656 63 | 54 1 6.01022 0.864072 50.0163 -4.33659 64 | 55 1 7.72742 1.72523 48.6602 -4.33654 65 | 56 1 0.859103 2.58166 50.0169 -4.33659 66 | 57 1 5.15193 2.58137 51.3742 -4.3366 67 | 58 1 6.86943 3.43972 52.7321 -4.3366 68 | 59 1 2.5761 3.43976 54.0898 -4.3366 69 | 60 1 4.29351 4.2985 55.4475 -4.3366 70 | 61 1 6.01091 5.15724 54.0898 -4.3366 71 | 62 1 7.72835 6.01593 55.4475 -4.3366 72 | 63 1 0.858714 6.87469 54.0897 -4.3366 73 | 64 1 2.57613 7.73332 55.4474 -4.3366 74 | 65 1 2.53185e-06 4.2985 56.8052 -4.3366 75 | 66 1 1.7174 5.1572 58.1629 -4.3366 76 | 67 1 3.43481 6.0159 56.8052 -4.3366 77 | 68 1 5.15221 6.8746 58.1629 -4.3366 78 | 69 1 6.86961 7.7333 56.8052 -4.3366 79 | 70 1 2.53185e-06 0.00499671 58.1629 -4.3366 80 | 71 1 1.7174 0.863697 56.8052 -4.3366 81 | 72 1 3.43481 1.7224 58.1629 -4.3366 82 | 73 1 4.29351 0.00499689 54.0896 -4.3366 83 | 74 1 6.01089 0.863677 55.4474 -4.3366 84 | 75 1 7.7283 1.72231 54.0897 -4.3366 85 | 76 1 0.858664 2.58107 55.4475 -4.3366 86 | 77 1 5.15221 2.5811 56.8052 -4.3366 87 | 78 1 6.86961 3.4398 58.1629 -4.3366 88 | 79 1 2.5761 3.4398 59.5207 -4.3366 89 | 80 1 4.29351 4.2985 60.8784 -4.3366 90 | 81 1 6.01091 5.1572 59.5207 -4.3366 91 | 82 1 7.72831 6.0159 60.8784 -4.3366 92 | 83 1 0.858703 6.8746 59.5207 -4.3366 93 | 84 1 2.5761 7.7333 60.8784 -4.3366 94 | 85 1 2.53185e-06 4.2985 62.2361 -4.3366 95 | 86 1 1.7174 5.1572 63.5938 -4.3366 96 | 87 1 3.43481 6.0159 62.2361 -4.3366 97 | 88 1 5.15221 6.8746 63.5938 -4.3366 98 | 89 1 6.86961 7.7333 62.2361 -4.3366 99 | 90 1 2.53185e-06 0.00499671 63.5938 -4.3366 100 | 91 1 1.7174 0.863697 62.2361 -4.3366 101 | 92 1 3.43481 1.7224 63.5938 -4.3366 102 | 93 1 4.29351 0.00499671 59.5207 -4.3366 103 | 94 1 6.01091 0.863697 60.8784 -4.3366 104 | 95 1 7.72831 1.7224 59.5207 -4.3366 105 | 96 1 0.858703 2.5811 60.8784 -4.3366 106 | 97 1 5.15221 2.5811 62.2361 -4.3366 107 | 98 1 6.86961 3.4398 63.5938 -4.3366 108 | 99 1 2.5761 3.4398 64.9516 -4.3366 109 | 100 1 4.29351 4.2985 66.3093 -4.3366 110 | 101 1 6.01091 5.1572 64.9516 -4.3366 111 | 102 1 7.72831 6.0159 66.3093 -4.3366 112 | 103 1 0.858703 6.8746 64.9516 -4.3366 113 | 104 1 2.5761 7.7333 66.3093 -4.3366 114 | 105 1 2.53185e-06 4.2985 67.667 -4.3366 115 | 106 1 1.7174 5.1572 69.0247 -4.3366 116 | 107 1 3.43481 6.0159 67.667 -4.3366 117 | 108 1 5.15221 6.8746 69.0247 -4.3366 118 | 109 1 6.86961 7.7333 67.667 -4.3366 119 | 110 1 2.53185e-06 0.00499671 69.0247 -4.3366 120 | 111 1 1.7174 0.863697 67.667 -4.3366 121 | 112 1 3.43481 1.7224 69.0247 -4.3366 122 | 113 1 4.29351 0.00499671 64.9516 -4.3366 123 | 114 1 6.01091 0.863697 66.3093 -4.3366 124 | 115 1 7.72831 1.7224 64.9516 -4.3366 125 | 116 1 0.858703 2.5811 66.3093 -4.3366 126 | 117 1 5.15221 2.5811 67.667 -4.3366 127 | 118 1 6.86961 3.4398 69.0247 -4.3366 128 | 119 1 2.5761 3.4398 70.3825 -4.3366 129 | 120 1 4.29351 4.2985 71.7402 -4.3366 130 | 121 1 6.01091 5.1572 70.3825 -4.3366 131 | 122 1 7.72831 6.0159 71.7402 -4.3366 132 | 123 1 0.858703 6.8746 70.3825 -4.3366 133 | 124 1 2.5761 7.7333 71.7402 -4.3366 134 | 125 1 2.53185e-06 4.2985 73.0979 -4.3366 135 | 126 1 1.7174 5.1572 74.4556 -2.1683 136 | 127 1 3.43481 6.0159 73.0979 -4.3366 137 | 128 1 5.15221 6.8746 74.4556 -2.1683 138 | 129 1 6.86961 7.7333 73.0979 -4.3366 139 | 130 1 2.53185e-06 0.00499671 74.4556 -2.1683 140 | 131 1 1.7174 0.863697 73.0979 -4.3366 141 | 132 1 3.43481 1.7224 74.4556 -2.1683 142 | 133 1 4.29351 0.00499671 70.3825 -4.3366 143 | 134 1 6.01091 0.863697 71.7402 -4.3366 144 | 135 1 7.72831 1.7224 70.3825 -4.3366 145 | 136 1 0.858703 2.5811 71.7402 -4.3366 146 | 137 1 5.15221 2.5811 73.0979 -4.3366 147 | 138 1 6.86961 3.4398 74.4556 -2.1683 148 | 139 1 0 0.005 5e-05 -2.1683 149 | 140 1 0.858701 1.7224 1.35778 -4.3366 150 | 141 1 1.7174 3.4398 5e-05 -2.1683 151 | 142 1 2.5761 5.1572 1.35778 -4.3366 152 | 143 1 3.4348 6.87461 5e-05 -2.1683 153 | 144 1 4.2935 0.005 1.35778 -4.3366 154 | 145 1 2.5761 0.863701 2.7155 -4.3366 155 | 146 1 3.4348 2.5811 4.07322 -4.3366 156 | 147 1 4.2935 4.2985 2.7155 -4.3366 157 | 148 1 5.1522 6.0159 4.07322 -4.3366 158 | 149 1 6.0109 7.73331 2.7155 -4.3366 159 | 150 1 6.86961 0.863701 4.07322 -4.3366 160 | 151 1 0.858701 6.0159 2.7155 -4.3366 161 | 152 1 1.7174 7.73331 4.07322 -4.3366 162 | 153 1 5.1522 1.7224 5e-05 -2.1683 163 | 154 1 6.0109 3.4398 1.35778 -4.3366 164 | 155 1 6.86961 5.1572 5e-05 -2.1683 165 | 156 1 7.72831 6.87461 1.35778 -4.3366 166 | 157 1 7.72831 2.5811 2.7155 -4.3366 167 | 158 1 5.01367e-16 4.2985 4.07322 -4.3366 168 | 159 1 0 0.005 5.43095 -4.3366 169 | 160 1 0.858701 1.7224 6.78868 -4.3366 170 | 161 1 1.7174 3.4398 5.43095 -4.3366 171 | 162 1 2.5761 5.1572 6.78868 -4.3366 172 | 163 1 3.4348 6.87461 5.43095 -4.3366 173 | 164 1 4.2935 0.005 6.78868 -4.3366 174 | 165 1 2.5761 0.863701 8.1464 -4.3366 175 | 166 1 3.4348 2.5811 9.50413 -4.3366 176 | 167 1 4.2935 4.2985 8.1464 -4.3366 177 | 168 1 5.1522 6.0159 9.50413 -4.3366 178 | 169 1 6.0109 7.73331 8.1464 -4.3366 179 | 170 1 6.86961 0.863701 9.50413 -4.3366 180 | 171 1 0.858701 6.0159 8.1464 -4.3366 181 | 172 1 1.7174 7.73331 9.50413 -4.3366 182 | 173 1 5.1522 1.7224 5.43095 -4.3366 183 | 174 1 6.0109 3.4398 6.78868 -4.3366 184 | 175 1 6.86961 5.1572 5.43095 -4.3366 185 | 176 1 7.72831 6.87461 6.78868 -4.3366 186 | 177 1 7.72831 2.5811 8.1464 -4.3366 187 | 178 1 5.01367e-16 4.2985 9.50413 -4.3366 188 | 179 1 0 0.005 10.8619 -4.3366 189 | 180 1 0.858701 1.7224 12.2196 -4.3366 190 | 181 1 1.7174 3.4398 10.8619 -4.3366 191 | 182 1 2.5761 5.1572 12.2196 -4.3366 192 | 183 1 3.4348 6.87461 10.8619 -4.3366 193 | 184 1 4.2935 0.005 12.2196 -4.3366 194 | 185 1 2.5761 0.863701 13.5773 -4.3366 195 | 186 1 3.4348 2.5811 14.935 -4.3366 196 | 187 1 4.2935 4.2985 13.5773 -4.3366 197 | 188 1 5.1522 6.0159 14.935 -4.3366 198 | 189 1 6.0109 7.73331 13.5773 -4.3366 199 | 190 1 6.86961 0.863701 14.935 -4.3366 200 | 191 1 0.858701 6.0159 13.5773 -4.3366 201 | 192 1 1.7174 7.73331 14.935 -4.3366 202 | 193 1 5.1522 1.7224 10.8619 -4.3366 203 | 194 1 6.0109 3.4398 12.2196 -4.3366 204 | 195 1 6.86961 5.1572 10.8619 -4.3366 205 | 196 1 7.72831 6.87461 12.2196 -4.3366 206 | 197 1 7.72831 2.5811 13.5773 -4.3366 207 | 198 1 5.01367e-16 4.2985 14.935 -4.3366 208 | 199 1 0 0.005 16.2928 -4.3366 209 | 200 1 0.858701 1.7224 17.6505 -4.3366 210 | 201 1 1.7174 3.4398 16.2928 -4.3366 211 | 202 1 2.5761 5.1572 17.6505 -4.3366 212 | 203 1 3.4348 6.87461 16.2928 -4.3366 213 | 204 1 4.2935 0.005 17.6505 -4.3366 214 | 205 1 2.5761 0.863699 19.0082 -4.3366 215 | 206 1 3.4348 2.5811 20.366 -4.3366 216 | 207 1 4.2935 4.2985 19.0082 -4.3366 217 | 208 1 5.15221 6.0159 20.366 -4.3366 218 | 209 1 6.01091 7.73331 19.0082 -4.3366 219 | 210 1 6.86959 0.863709 20.366 -4.3366 220 | 211 1 0.858701 6.0159 19.0082 -4.3366 221 | 212 1 1.71742 7.7333 20.366 -4.3366 222 | 213 1 5.1522 1.7224 16.2928 -4.3366 223 | 214 1 6.0109 3.4398 17.6505 -4.3366 224 | 215 1 6.86961 5.1572 16.2928 -4.3366 225 | 216 1 7.72831 6.87461 17.6505 -4.3366 226 | 217 1 7.72831 2.5811 19.0082 -4.3366 227 | 218 1 4.9931e-07 4.2985 20.366 -4.3366 228 | 219 1 6.46247e-07 0.00499992 21.7237 -4.3366 229 | 220 1 0.858741 1.7224 23.0814 -4.3366 230 | 221 1 1.71743 3.43984 21.7237 -4.3366 231 | 222 1 2.57619 5.15721 23.0815 -4.3366 232 | 223 1 3.43483 6.87462 21.7237 -4.3366 233 | 224 1 4.2935 0.00499988 23.0815 -4.3366 234 | 225 1 2.57614 0.863826 24.4393 -4.3366 235 | 226 1 3.43506 2.58099 25.7972 -4.3366 236 | 227 1 4.2935 4.2985 24.4394 -4.3366 237 | 228 1 5.15195 6.01601 25.7972 -4.3366 238 | 229 1 6.01087 7.73318 24.4393 -4.3366 239 | 230 1 6.86988 0.863419 25.797 -4.3366 240 | 231 1 0.858783 6.01609 24.4391 -4.3366 241 | 232 1 1.71713 7.73359 25.797 -4.3366 242 | 233 1 5.15218 1.72238 21.7237 -4.3366 243 | 234 1 6.01082 3.43979 23.0815 -4.3366 244 | 235 1 6.86958 5.15717 21.7237 -4.3366 245 | 236 1 7.72827 6.8746 23.0814 -4.3366 246 | 237 1 7.72823 2.58092 24.4391 -4.3366 247 | 238 1 1.39196e-06 4.2985 25.7964 -4.3366 248 | 239 1 1.49443e-06 0.00499958 27.1554 -4.33659 249 | 240 1 0.860634 1.7216 28.5132 -4.33657 250 | 241 1 1.71684 3.4394 27.1542 -4.33659 251 | 242 1 2.57328 5.1581 28.511 -4.33654 252 | 243 1 3.43443 6.8753 27.1549 -4.33659 253 | 244 1 4.29351 0.00499941 28.514 -4.33656 254 | 245 1 2.57747 0.865095 29.8736 -4.33651 255 | 246 1 3.45357 2.57981 31.2261 -4.33387 256 | 247 1 4.29351 4.2985 29.8633 -4.3355 257 | 248 1 5.13344 6.0172 31.2261 -4.33387 258 | 249 1 6.00954 7.73191 29.8736 -4.33651 259 | 250 1 6.8711 0.861408 31.2331 -4.33486 260 | 251 1 0.857382 6.01955 29.8703 -4.33624 261 | 252 1 1.71591 7.7356 31.2331 -4.33486 262 | 253 1 5.15258 1.72171 27.1549 -4.33659 263 | 254 1 6.01373 3.43891 28.511 -4.33654 264 | 255 1 6.87017 5.1576 27.1542 -4.33659 265 | 256 1 7.72638 6.8754 28.5132 -4.33657 266 | 257 1 7.72963 2.57745 29.8703 -4.33624 267 | 258 1 2.55612e-06 4.2985 31.222 -4.33574 268 | 259 1 2.61302e-06 0.00499898 32.5928 -4.32206 269 | 260 1 0.965924 1.7287 33.9028 -4.26803 270 | 261 1 1.74908 3.47777 32.5647 -4.33124 271 | 262 1 2.56597 5.19744 33.9486 -4.31225 272 | 263 1 3.43839 6.90368 32.6041 -4.33271 273 | 264 1 4.29351 0.00499883 34.0176 -4.30403 274 | 265 1 2.61971 0.920477 35.4086 -4.18705 275 | 266 1 3.6141 2.62748 36.8059 -4.11895 276 | 267 1 4.29351 4.2985 35.2875 -4.25662 277 | 268 1 4.97291 5.96953 36.8059 -4.11895 278 | 269 1 5.9673 7.67653 35.4086 -4.18705 279 | 270 1 5.47131 2.83747 38.4589 -4.08838 280 | 271 1 0.774607 6.0822 35.2222 -4.27346 281 | 272 1 1.06287 8.06023 36.4869 -4.2251 282 | 273 1 5.14862 1.69333 32.6041 -4.33271 283 | 274 1 6.02104 3.39957 33.9486 -4.31225 284 | 275 1 6.83793 5.11923 32.5647 -4.33124 285 | 276 1 7.62109 6.8683 33.9028 -4.26803 286 | 277 1 7.81241 2.5148 35.2222 -4.27346 287 | 278 1 3.06449e-06 4.2985 36.5144 -4.24994 288 | Egb = 1.04861023564184 289 | -------------------------------------------------------------------------------- /.examples/Si_310_twist/lammps_1.102_0.300_4.44_2.18_1_1_1300_61000: -------------------------------------------------------------------------------- 1 | ITEM: TIMESTEP 2 | 0 3 | ITEM: NUMBER OF ATOMS 4 | 273 5 | ITEM: BOX BOUNDS pp pp ss 6 | 0.0000000000000000e+00 8.5870068723042259e+00 7 | 0.0000000000000000e+00 8.5870068723042259e+00 8 | -7.2402452733085244e-03 7.2734039483436732e+01 9 | ITEM: ATOMS id type x y z c_eng 10 | 1 1 0.807918 5.67001 37.4339 -4.1885 11 | 2 1 3.67215 8.09702 38.1883 -4.05095 12 | 3 1 1.27159 6.43342 35.2812 -4.16913 13 | 4 1 2.25795 4.2888 38.686 -4.20858 14 | 5 1 3.85933 5.15866 40.1461 -4.23279 15 | 6 1 5.2415 6.43342 38.8034 -4.16913 16 | 7 1 7.16687 6.8837 40.1619 -4.25136 17 | 8 1 0.350217 7.51631 38.8231 -4.22501 18 | 9 1 2.16054 8.36205 40.045 -4.15468 19 | 10 1 7.55005 4.27398 37.0423 -4.13812 20 | 11 1 5.8229 1.90416 40.0768 -4.15842 21 | 12 1 7.69331 2.74907 38.8809 -4.15061 22 | 13 1 0.720139 3.49101 40.2754 -4.19443 23 | 14 1 4.81255 3.48327 41.4762 -4.30649 24 | 15 1 6.50426 4.30991 42.872 -4.33047 25 | 16 1 8.19056 5.1838 41.5093 -4.27686 26 | 17 1 1.3078 6.00079 42.9023 -4.3228 27 | 18 1 3.02444 6.81768 41.5578 -4.2934 28 | 19 1 4.77878 7.75475 42.8398 -4.32213 29 | 20 1 2.22131 4.26921 44.2064 -4.33254 30 | 21 1 3.93069 5.15553 45.5641 -4.33621 31 | 22 1 5.64223 6.03791 44.2106 -4.33487 32 | 23 1 7.35936 6.88114 45.5784 -4.33564 33 | 24 1 0.48567 7.7465 44.2275 -4.33397 34 | 25 1 2.2189 0.00508268 45.575 -4.33634 35 | 26 1 3.94792 0.860917 44.227 -4.33352 36 | 27 1 5.67045 1.72573 45.5696 -4.336 37 | 28 1 6.48602 0.0938555 41.4786 -4.30318 38 | 29 1 8.26266 0.868939 42.8259 -4.33043 39 | 30 1 1.46423 1.6223 41.4609 -4.23532 40 | 31 1 3.12361 2.5571 42.841 -4.31874 41 | 32 1 7.38792 2.57844 44.1998 -4.33335 42 | 33 1 0.505515 3.43145 45.5732 -4.33557 43 | 34 1 4.79952 3.4419 46.9238 -4.33645 44 | 35 1 6.51372 4.29964 48.2858 -4.33655 45 | 36 1 8.22893 5.15637 46.9244 -4.33641 46 | 37 1 1.35783 6.01384 48.2861 -4.33658 47 | 38 1 3.0749 6.87099 46.9283 -4.33646 48 | 39 1 4.79177 7.73275 48.2876 -4.33652 49 | 40 1 2.22014 4.29796 49.6439 -4.33658 50 | 41 1 3.93676 5.15715 51.0025 -4.3366 51 | 42 1 5.6537 6.01612 49.6444 -4.33659 52 | 43 1 7.37092 6.87416 51.0033 -4.3366 53 | 44 1 0.502281 7.7314 49.6465 -4.33658 54 | 45 1 2.21957 0.00476865 51.0033 -4.33659 55 | 46 1 3.93695 0.864123 49.6458 -4.33657 56 | 47 1 5.65461 1.72275 51.0033 -4.3366 57 | 48 1 6.51169 0.00992654 46.9374 -4.33636 58 | 49 1 8.23188 0.864008 48.2923 -4.33656 59 | 50 1 1.36337 1.71982 46.9351 -4.33651 60 | 51 1 3.0832 2.58226 48.286 -4.33655 61 | 52 1 7.37184 2.5829 49.6461 -4.33658 62 | 53 1 0.503038 3.44018 51.0031 -4.33659 63 | 54 1 4.79557 3.44003 52.3608 -4.3366 64 | 55 1 6.51306 4.29849 53.7186 -4.3366 65 | 56 1 8.23051 5.15714 52.3609 -4.3366 66 | 57 1 1.36089 6.01591 53.7186 -4.3366 67 | 58 1 3.07837 6.8744 52.3608 -4.3366 68 | 59 1 4.79566 7.7333 53.7186 -4.3366 69 | 60 1 2.21958 4.2985 55.0763 -4.3366 70 | 61 1 3.93698 5.1572 56.434 -4.3366 71 | 62 1 5.65438 6.0159 55.0763 -4.3366 72 | 63 1 7.37179 6.8746 56.434 -4.3366 73 | 64 1 0.50218 7.7333 55.0763 -4.3366 74 | 65 1 2.21958 0.00499661 56.434 -4.3366 75 | 66 1 3.93698 0.863697 55.0763 -4.3366 76 | 67 1 5.65438 1.7224 56.434 -4.3366 77 | 68 1 6.51303 0.00506466 52.3609 -4.3366 78 | 69 1 8.2305 0.863702 53.7186 -4.3366 79 | 70 1 1.36094 1.72236 52.3608 -4.3366 80 | 71 1 3.0783 2.58111 53.7186 -4.3366 81 | 72 1 7.37179 2.5811 55.0763 -4.3366 82 | 73 1 0.50218 3.4398 56.434 -4.3366 83 | 74 1 4.79568 3.4398 57.7918 -4.3366 84 | 75 1 6.51308 4.2985 59.1495 -4.3366 85 | 76 1 8.23049 5.1572 57.7918 -4.3366 86 | 77 1 1.36088 6.0159 59.1495 -4.3366 87 | 78 1 3.07828 6.8746 57.7918 -4.3366 88 | 79 1 4.79568 7.7333 59.1495 -4.3366 89 | 80 1 2.21958 4.2985 60.5072 -4.3366 90 | 81 1 3.93698 5.1572 61.8649 -4.3366 91 | 82 1 5.65438 6.0159 60.5072 -4.3366 92 | 83 1 7.37179 6.8746 61.8649 -4.3366 93 | 84 1 0.50218 7.7333 60.5072 -4.3366 94 | 85 1 2.21958 0.00499661 61.8649 -4.3366 95 | 86 1 3.93698 0.863697 60.5072 -4.3366 96 | 87 1 5.65438 1.7224 61.8649 -4.3366 97 | 88 1 6.51308 0.00499661 57.7918 -4.3366 98 | 89 1 8.23049 0.863697 59.1495 -4.3366 99 | 90 1 1.36088 1.7224 57.7918 -4.3366 100 | 91 1 3.07828 2.5811 59.1495 -4.3366 101 | 92 1 7.37179 2.5811 60.5072 -4.3366 102 | 93 1 0.50218 3.4398 61.8649 -4.3366 103 | 94 1 4.79568 3.4398 63.2227 -4.3366 104 | 95 1 6.51308 4.2985 64.5804 -4.3366 105 | 96 1 8.23049 5.1572 63.2227 -4.3366 106 | 97 1 1.36088 6.0159 64.5804 -4.3366 107 | 98 1 3.07828 6.8746 63.2227 -4.3366 108 | 99 1 4.79568 7.7333 64.5804 -4.3366 109 | 100 1 2.21958 4.2985 65.9381 -4.3366 110 | 101 1 3.93698 5.1572 67.2958 -4.3366 111 | 102 1 5.65438 6.0159 65.9381 -4.3366 112 | 103 1 7.37179 6.8746 67.2958 -4.3366 113 | 104 1 0.50218 7.7333 65.9381 -4.3366 114 | 105 1 2.21958 0.00499661 67.2958 -4.3366 115 | 106 1 3.93698 0.863697 65.9381 -4.3366 116 | 107 1 5.65438 1.7224 67.2958 -4.3366 117 | 108 1 6.51308 0.00499661 63.2227 -4.3366 118 | 109 1 8.23049 0.863697 64.5804 -4.3366 119 | 110 1 1.36088 1.7224 63.2227 -4.3366 120 | 111 1 3.07828 2.5811 64.5804 -4.3366 121 | 112 1 7.37179 2.5811 65.9381 -4.3366 122 | 113 1 0.50218 3.4398 67.2958 -4.3366 123 | 114 1 4.79568 3.4398 68.6536 -4.3366 124 | 115 1 6.51308 4.2985 70.0113 -4.3366 125 | 116 1 8.23049 5.1572 68.6536 -4.3366 126 | 117 1 1.36088 6.0159 70.0113 -4.3366 127 | 118 1 3.07828 6.8746 68.6536 -4.3366 128 | 119 1 4.79568 7.7333 70.0113 -4.3366 129 | 120 1 2.21958 4.2985 71.369 -4.3366 130 | 121 1 3.93698 5.1572 72.7267 -2.1683 131 | 122 1 5.65438 6.0159 71.369 -4.3366 132 | 123 1 7.37179 6.8746 72.7267 -2.1683 133 | 124 1 0.50218 7.7333 71.369 -4.3366 134 | 125 1 2.21958 0.00499661 72.7267 -2.1683 135 | 126 1 3.93698 0.863697 71.369 -4.3366 136 | 127 1 5.65438 1.7224 72.7267 -2.1683 137 | 128 1 6.51308 0.00499661 68.6536 -4.3366 138 | 129 1 8.23049 0.863697 70.0113 -4.3366 139 | 130 1 1.36088 1.7224 68.6536 -4.3366 140 | 131 1 3.07828 2.5811 70.0113 -4.3366 141 | 132 1 7.37179 2.5811 71.369 -4.3366 142 | 133 1 0.50218 3.4398 72.7267 -2.1683 143 | 134 1 0 0.005 5e-05 -2.1683 144 | 135 1 0.858701 1.7224 1.35778 -4.3366 145 | 136 1 1.7174 3.4398 5e-05 -2.1683 146 | 137 1 2.5761 5.1572 1.35778 -4.3366 147 | 138 1 3.4348 6.87461 5e-05 -2.1683 148 | 139 1 4.2935 0.005 1.35778 -4.3366 149 | 140 1 2.5761 0.863701 2.7155 -4.3366 150 | 141 1 3.4348 2.5811 4.07322 -4.3366 151 | 142 1 4.2935 4.2985 2.7155 -4.3366 152 | 143 1 5.1522 6.0159 4.07322 -4.3366 153 | 144 1 6.0109 7.73331 2.7155 -4.3366 154 | 145 1 6.86961 0.863701 4.07322 -4.3366 155 | 146 1 0.858701 6.0159 2.7155 -4.3366 156 | 147 1 1.7174 7.73331 4.07322 -4.3366 157 | 148 1 5.1522 1.7224 5e-05 -2.1683 158 | 149 1 6.0109 3.4398 1.35778 -4.3366 159 | 150 1 6.86961 5.1572 5e-05 -2.1683 160 | 151 1 7.72831 6.87461 1.35778 -4.3366 161 | 152 1 7.72831 2.5811 2.7155 -4.3366 162 | 153 1 5.01367e-16 4.2985 4.07322 -4.3366 163 | 154 1 0 0.005 5.43095 -4.3366 164 | 155 1 0.858701 1.7224 6.78868 -4.3366 165 | 156 1 1.7174 3.4398 5.43095 -4.3366 166 | 157 1 2.5761 5.1572 6.78868 -4.3366 167 | 158 1 3.4348 6.87461 5.43095 -4.3366 168 | 159 1 4.2935 0.005 6.78868 -4.3366 169 | 160 1 2.5761 0.863701 8.1464 -4.3366 170 | 161 1 3.4348 2.5811 9.50413 -4.3366 171 | 162 1 4.2935 4.2985 8.1464 -4.3366 172 | 163 1 5.1522 6.0159 9.50413 -4.3366 173 | 164 1 6.0109 7.73331 8.1464 -4.3366 174 | 165 1 6.86961 0.863701 9.50413 -4.3366 175 | 166 1 0.858701 6.0159 8.1464 -4.3366 176 | 167 1 1.7174 7.73331 9.50413 -4.3366 177 | 168 1 5.1522 1.7224 5.43095 -4.3366 178 | 169 1 6.0109 3.4398 6.78868 -4.3366 179 | 170 1 6.86961 5.1572 5.43095 -4.3366 180 | 171 1 7.72831 6.87461 6.78868 -4.3366 181 | 172 1 7.72831 2.5811 8.1464 -4.3366 182 | 173 1 5.01367e-16 4.2985 9.50413 -4.3366 183 | 174 1 0 0.005 10.8619 -4.3366 184 | 175 1 0.858701 1.7224 12.2196 -4.3366 185 | 176 1 1.7174 3.4398 10.8619 -4.3366 186 | 177 1 2.5761 5.1572 12.2196 -4.3366 187 | 178 1 3.4348 6.87461 10.8619 -4.3366 188 | 179 1 4.2935 0.005 12.2196 -4.3366 189 | 180 1 2.5761 0.863701 13.5773 -4.3366 190 | 181 1 3.4348 2.5811 14.935 -4.3366 191 | 182 1 4.2935 4.2985 13.5773 -4.3366 192 | 183 1 5.1522 6.0159 14.935 -4.3366 193 | 184 1 6.0109 7.73331 13.5773 -4.3366 194 | 185 1 6.86961 0.863701 14.935 -4.3366 195 | 186 1 0.858701 6.0159 13.5773 -4.3366 196 | 187 1 1.7174 7.73331 14.935 -4.3366 197 | 188 1 5.1522 1.7224 10.8619 -4.3366 198 | 189 1 6.0109 3.4398 12.2196 -4.3366 199 | 190 1 6.86961 5.1572 10.8619 -4.3366 200 | 191 1 7.72831 6.87461 12.2196 -4.3366 201 | 192 1 7.72831 2.5811 13.5773 -4.3366 202 | 193 1 5.01367e-16 4.2985 14.935 -4.3366 203 | 194 1 0 0.005 16.2928 -4.3366 204 | 195 1 0.858701 1.7224 17.6505 -4.3366 205 | 196 1 1.7174 3.4398 16.2928 -4.3366 206 | 197 1 2.5761 5.1572 17.6505 -4.3366 207 | 198 1 3.4348 6.87461 16.2928 -4.3366 208 | 199 1 4.2935 0.005 17.6505 -4.3366 209 | 200 1 2.5761 0.863703 19.0082 -4.3366 210 | 201 1 3.43478 2.58111 20.366 -4.3366 211 | 202 1 4.29351 4.2985 19.0082 -4.3366 212 | 203 1 5.15219 6.01592 20.366 -4.3366 213 | 204 1 6.01091 7.73332 19.0082 -4.3366 214 | 205 1 6.8696 0.863707 20.366 -4.3366 215 | 206 1 0.858695 6.0159 19.0082 -4.3366 216 | 207 1 1.71742 7.7333 20.366 -4.3366 217 | 208 1 5.1522 1.7224 16.2928 -4.3366 218 | 209 1 6.0109 3.4398 17.6505 -4.3366 219 | 210 1 6.86961 5.1572 16.2928 -4.3366 220 | 211 1 7.72831 6.87461 17.6505 -4.3366 221 | 212 1 7.72831 2.58109 19.0082 -4.3366 222 | 213 1 2.41361e-05 4.29849 20.366 -4.3366 223 | 214 1 6.1486e-05 0.00506585 21.7237 -4.3366 224 | 215 1 0.858471 1.72275 23.0813 -4.3366 225 | 216 1 1.71751 3.44003 21.7238 -4.3366 226 | 217 1 2.57633 5.15715 23.082 -4.3366 227 | 218 1 3.43472 6.8744 21.7238 -4.3366 228 | 219 1 4.29351 0.00477 23.0813 -4.33659 229 | 220 1 2.57614 0.864125 24.4388 -4.33657 230 | 221 1 3.42988 2.58227 25.7986 -4.33655 231 | 222 1 4.29295 4.29796 24.4407 -4.33658 232 | 223 1 5.15525 6.01384 25.7984 -4.33658 233 | 224 1 6.0108 7.7314 24.4381 -4.33658 234 | 225 1 6.86821 0.86401 25.7922 -4.33656 235 | 226 1 0.85938 6.01612 24.4401 -4.33659 236 | 227 1 1.72131 7.73275 25.7969 -4.33652 237 | 228 1 5.15214 1.72237 21.7237 -4.3366 238 | 229 1 6.01005 3.44018 23.0815 -4.33659 239 | 230 1 6.86958 5.15714 21.7237 -4.3366 240 | 231 1 7.72917 6.87416 23.0813 -4.3366 241 | 232 1 7.72825 2.5829 24.4385 -4.33658 242 | 233 1 8.58637 4.29964 25.7987 -4.33655 243 | 234 1 0.00139145 0.00992859 27.1471 -4.33636 244 | 235 1 0.842635 1.72573 28.515 -4.336 245 | 236 1 1.71356 3.4419 27.1607 -4.33645 246 | 237 1 2.5824 5.15553 28.5204 -4.33621 247 | 238 1 3.43818 6.87099 27.1563 -4.33646 248 | 239 1 4.29418 0.00508457 28.5096 -4.33634 249 | 240 1 2.56517 0.860919 29.8576 -4.33352 250 | 241 1 3.38948 2.5571 31.2435 -4.31874 251 | 242 1 4.29177 4.26921 29.8782 -4.33254 252 | 243 1 5.20529 6.0008 31.1823 -4.3228 253 | 244 1 6.02741 7.7465 29.8571 -4.33397 254 | 245 1 6.83743 0.86894 31.2587 -4.33043 255 | 246 1 0.87085 6.03792 29.8739 -4.33487 256 | 247 1 1.73431 7.75475 31.2448 -4.32213 257 | 248 1 5.14972 1.71982 27.1494 -4.33651 258 | 249 1 6.00757 3.43146 28.5114 -4.33557 259 | 250 1 6.87116 5.15637 27.1601 -4.33641 260 | 251 1 7.74073 6.88115 28.5061 -4.33564 261 | 252 1 7.71217 2.57844 29.8847 -4.33335 262 | 253 1 0.0088276 4.30991 31.2125 -4.33047 263 | 254 1 0.0270645 0.0938565 32.606 -4.30318 264 | 255 1 0.690188 1.90416 34.0077 -4.15842 265 | 256 1 1.70053 3.48327 32.6084 -4.30649 266 | 257 1 2.65376 5.15867 33.9384 -4.23279 267 | 258 1 3.48864 6.81768 32.5268 -4.2934 268 | 259 1 4.35254 8.36205 34.0396 -4.15468 269 | 260 1 1.67035 1.45459 36.1286 -4.21404 270 | 261 1 3.25654 2.92026 37.0423 -4.23684 271 | 262 1 4.25513 4.2888 35.3985 -4.20858 272 | 263 1 5.70517 5.67001 36.6506 -4.1885 273 | 264 1 2.84093 8.09703 35.8963 -4.05095 274 | 265 1 4.84274 1.45459 37.9559 -4.21404 275 | 266 1 6.16287 7.51631 35.2615 -4.22501 276 | 267 1 8.54464 0.899515 37.6685 -4.1358 277 | 268 1 5.04886 1.6223 32.6236 -4.23532 278 | 269 1 5.79295 3.49101 33.8092 -4.19443 279 | 270 1 6.90954 5.1838 32.5753 -4.27686 280 | 271 1 7.93322 6.8837 33.9226 -4.25136 281 | 272 1 6.55546 0.899515 36.416 -4.1358 282 | 273 1 7.40678 2.74907 35.2036 -4.15061 283 | Egb = 1.10199384945264 284 | -------------------------------------------------------------------------------- /.examples/Si_310_twist/params.yaml: -------------------------------------------------------------------------------- 1 | # Input data for the GRand canonical Interface Predictor (GRIP). Format is YAML. 2 | 3 | # Parameters for the algorithm 4 | algo: 5 | dir_struct: 'best' # Folder to store best structures. 6 | dir_calcs: 'calc_procs' # Folder to store temporary calculation files. 7 | ngrid: 100 # Number of grid points in each dim = ngrid * nprocs. 8 | frac_min: 0.00 # Minimum fraction of atoms on a plane (0 <= n <= 1). 9 | frac_max: 1.00 # Maximum fraction of atoms on a plane. Set both to 1.0 for gamma-surface. 10 | gb_gap: 0.3 # Initial gap between slabs prior to MD/relaxation (in Ang.). 11 | perturb_u: 0.3 # Maximum random perturbation (A) of atoms above GB 12 | perturb_l: 0.0 # Maximum random perturbation (A) of atoms below GB 13 | gb_thick: 10 # Thickness of GB region (in Angstrom) on either side of interface. 14 | pad: 10 # Extra padding (A) on top of gb_thick for relaxation / energy calculations. 15 | vacuum: 1 # Vacuum to add on top for MD (A); less needed for s boundary. 16 | 17 | inter_p: 0.0 # Probability of swapping with interstitial sites. [0.0, 1.0] = [Never, Always]. 18 | inter_s: 'Si' # species of atom to insert. 19 | inter_n: 2 # Number of GB interstitial sites to swap with atoms in GB region. 20 | inter_t: 1.5 # Thickness of region (A) on either side of GB to search for interstitials. 21 | inter_u: False # Only choose unique interstitial sites. 22 | inter_r: True # Randomly choose interstitial sites vs. largest volume 23 | inter_w: 2 # How to swap: 1 = only subs, 2 = only inter, 3 = uniform, 4 = mostly subs, 5 = mostly inter 24 | 25 | MD_run: 0.95 # Probability of running MD simulation before relaxing. [0.0, 1.0] = [Never, Always]. 26 | Tmin: 300 # Temperature lower bound for MD simulation. 27 | Tmax: 1500 # Temperature upper bound, vary in multiple of 100s. 28 | MD_min: 5000 # Min steps for MD simulation. 29 | MD_max: 300000 # Max steps for MD simulation. 30 | var_steps: 2 # 0 = Min steps only; 1 = linear sample; 2 = exponential sample 31 | 32 | lammps_bin: '/g/g16/chen120/bin/lammps_serial' # Path to [serial] LAMMPS binary. 33 | Emult: 2 # Maximum energy threshold * Egb_min to keep; at least 1.0. 34 | nruns: 0 # Number of iterations in total (each processor). Set 0 for infinite loop. 35 | clear_freq: 50 # Number of iterations before clearing duplicates. Set 0 to never clear. 36 | 37 | 38 | # Parameters for the material 39 | struct: 40 | user: False # True: read existing cells (POSCAR_*), False: generate w/ ase. 41 | cutoff: 35 # Max height (A) to cut slabs if user=False; speed up calcs. Set to 0 to ignore. 42 | write: True # Write generated cells to POSCAR_* 43 | size0: [1, 1, 1] # Minimum replications in [x, y, z] to create supercells. 44 | size: [2, 2, 15] # Replications in [x, y, z] to create supercells. z is not used if user=True. 45 | reps: 2 # Sample replications (1) exactly, (2) uniform, (3) weighted smaller, (4) weighted larger. 46 | 47 | # Basic info - potential dependent! 48 | upper_dirs: [ [3, 1, 0], [-1, 3, 0], [0, 0, 1] ] # W(310) twist 49 | lower_dirs: [ [3, -1, 0], [1, 3, 0], [0, 0, 1] ] 50 | symbol: 'Si' # Chemical formula 51 | crystal: 'dc' # fcc, bcc, hcp, or dc 52 | mass: 28.09 # Atomic mass 53 | a: 5.4309 # a lattice constant 54 | c: 5.4309 # c lattice constant; only used for hcp 55 | dlat: 0 # Minimal normal component of lattice vector to calculate Nplane. Set 0 to ignore. 56 | Ecoh: -4.3366 # Energy per atom in bulk 57 | pair_style: 'sw' # pair_style for LAMMPS 58 | pair_coeff: '* * /g/g16/chen120/lammps/pots/Si.sw Si' # pair_coeff for LAMMPS 59 | 60 | -------------------------------------------------------------------------------- /.examples/Ti_2130_tilt/POSCAR_LOWER: -------------------------------------------------------------------------------- 1 | Ti lower [[5, -1, -4, 0], [0, 0, 0, -1], [-1, 3, -2, 0]] 2 | 1.0000000000000000 3 | 7.7533742170747830 0.0000000000000000 0.0000000000000000 4 | 0.0000000000000000 4.6782999999999992 0.0000000000000000 5 | 0.0000000000000000 0.0000000000000000 35.4915077671799537 6 | Ti 7 | 74 8 | Direct 9 | 0.0000000000000000 0.0010687642947224 0.0000014087877114 10 | 0.7857142857142871 0.0010687642947217 0.6216239061422346 11 | 0.9285714285714298 0.5010687642947216 0.5855878193390738 12 | 0.8571428571428582 0.0010687642947218 0.5405427108351228 13 | 0.0000000000000014 0.5010687642947219 0.5045066240319620 14 | 0.9285714285714296 0.0010687642947219 0.4594615155280111 15 | 0.4285714285714302 0.5010687642947214 0.7747772750556678 16 | 0.8571428571428584 0.5010687642947216 0.6666690146461856 17 | 0.3571428571428585 0.0010687642947216 0.7297321665517167 18 | 0.4285714285714299 0.0010687642947217 0.6486509712446051 19 | 0.5714285714285727 0.5010687642947216 0.6126148844414443 20 | 0.5000000000000011 0.0010687642947217 0.5675697759374934 21 | 0.6428571428571441 0.5010687642947219 0.5315336891343326 22 | 0.5714285714285724 0.0010687642947218 0.4864885806303816 23 | 0.7142857142857154 0.5010687642947219 0.4504524938272209 24 | 0.5000000000000013 0.5010687642947216 0.6936960797485561 25 | 0.7142857142857157 0.0010687642947216 0.7027051014493462 26 | 0.7857142857142874 0.5010687642947214 0.7477502099532972 27 | 0.0000000000000014 0.0010687642947215 0.7567592316540873 28 | 0.8571428571428591 0.0010687642947213 0.9189216222683109 29 | 0.0000000000000021 0.5010687642947214 0.8828855354651500 30 | 0.9285714285714302 0.0010687642947214 0.8378404269611991 31 | 0.5714285714285734 0.5010687642947212 0.9909937958746323 32 | 0.5000000000000019 0.0010687642947213 0.9459486873706814 33 | 0.6428571428571447 0.5010687642947214 0.9099126005675205 34 | 0.5714285714285731 0.0010687642947214 0.8648674920635697 35 | 0.7142857142857161 0.5010687642947214 0.8288314052604088 36 | 0.6428571428571445 0.0010687642947215 0.7837862967564578 37 | 0.1428571428571447 0.0010687642947213 0.9729757524730521 38 | 0.2857142857142876 0.5010687642947212 0.9369396656698913 39 | 0.2142857142857160 0.0010687642947214 0.8918945571659402 40 | 0.3571428571428588 0.5010687642947214 0.8558584703627795 41 | 0.2857142857142874 0.0010687642947215 0.8108133618588285 42 | 0.0714285714285730 0.5010687642947214 0.8018043401580383 43 | 0.6428571428571438 0.0010687642947219 0.4054073853232699 44 | 0.1428571428571441 0.5010687642947214 0.7207231448509266 45 | 0.0714285714285726 0.0010687642947216 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Reference: R. G. Hennig, T. J. Lenosky, D. R. Trinkle, S. P. Rudin, and J. W. Wilkins, Phys. Rev. B 78, 054121 (2008) 2 | 13 3 | -20.0 0.0 4 | 1 0 1 0 5 | 1.742692837163632546e+00 3.744277175966389349e+00 0.0e+00 6 | 2.055801767399996649e+00 9.108397309055012991e-01 1.087025233010940539e+01 7 | 2.368910697636360752e+00 3.880458966341450711e-01 -1.553224188359566327e+00 8 | 2.682019627872724410e+00 -1.884090653346989427e-02 2.436300413714785229e+00 9 | 2.995128558109088512e+00 -2.480989296390785637e-01 2.679127139950259640e+00 10 | 3.308237488345452615e+00 -2.644895502965277645e-01 -1.250563846088559861e-01 11 | 3.621346418581816273e+00 -2.271961892825972718e-01 1.106625553693794339e+00 12 | 3.934455348818180376e+00 -1.292930901760148965e-01 -5.920536767960294933e-01 13 | 4.247564279054544478e+00 -5.968536693320936753e-02 -4.701234146338039155e-01 14 | 4.560673209290908581e+00 -3.110002556084055444e-02 -3.807399733552661869e-02 15 | 4.873782139527271795e+00 -1.384736320244591042e-02 -7.115479604519592272e-02 16 | 5.186891069763635898e+00 -3.203412727856397215e-03 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87 | 78 1 14.9518 2.34415 61.9273 -4.83118 88 | 79 1 8.85988 2.34415 57.1311 -4.83001 89 | 80 1 13.8442 0.0049998 60.6483 -4.83118 90 | 81 1 13.2904 0.0049998 57.7706 -4.8311 91 | 82 1 13.8442 2.34415 56.1719 -4.83215 92 | 83 1 12.7366 0.0049998 54.8929 -4.83041 93 | 84 1 13.2882 2.34415 53.292 -4.83337 94 | 85 1 12.1809 0.0049999 52.0165 -4.82822 95 | 86 1 12.733 2.34415 50.4125 -4.83365 96 | 87 1 14.398 2.34415 59.0496 -4.83118 97 | 88 1 0.552694 0.0049998 58.7298 -4.83109 98 | 89 1 9.41369 2.34415 60.0088 -4.83118 99 | 90 1 8.85988 0.0049998 61.6075 -4.83118 100 | 91 1 0.552694 2.34415 67.6826 -4.54858 101 | 92 1 14.9518 0.0049998 66.4037 -4.81816 102 | 93 1 15.5056 2.34415 64.8049 -4.83118 103 | 94 1 14.398 0.0049998 63.526 -4.83118 104 | 95 1 13.8442 2.34415 69.6011 -3.69294 105 | 96 1 12.7366 0.0049998 68.3221 -4.37289 106 | 97 1 13.2904 2.34415 66.7234 -4.81125 107 | 98 1 12.1828 0.0049998 65.4444 -4.82813 108 | 99 1 12.7366 2.34415 63.8457 -4.83118 109 | 100 1 11.6289 0.0049998 62.5667 -4.83118 110 | 101 1 11.0751 2.34415 68.6419 -4.0641 111 | 102 1 9.96751 0.0049998 67.3629 -4.55549 112 | 103 1 10.5213 2.34415 65.7642 -4.82122 113 | 104 1 9.41369 0.0049998 64.4852 -4.83118 114 | 105 1 9.96751 2.34415 62.8865 -4.83118 115 | 106 1 11.6277 0.00499958 49.1405 -4.8282 116 | 107 1 12.1828 2.34415 60.968 -4.83118 117 | 108 1 11.0751 0.0049998 59.689 -4.83118 118 | 109 1 11.6289 2.34415 58.0903 -4.83098 119 | 110 1 13.8589 2.34415 42.849 -4.79401 120 | 111 1 12.7745 0.00499874 41.5443 -4.79391 121 | 112 1 13.3661 2.34415 40.0169 -4.73456 122 | 113 1 12.1557 0.00499913 38.7805 -4.77235 123 | 114 1 12.9167 2.34415 37.289 -4.69542 124 | 115 1 11.7687 0.00499788 35.9897 -4.68639 125 | 116 1 12.1806 2.34415 47.5297 -4.83708 126 | 117 1 11.0695 0.00499919 46.2691 -4.82299 127 | 118 1 11.6199 2.34415 44.6511 -4.83246 128 | 119 1 10.5267 0.00499894 43.3898 -4.82302 129 | 120 1 11.0941 2.34415 41.7475 -4.85455 130 | 121 1 9.94557 0.0049985 40.531 -4.79394 131 | 122 1 10.5631 2.34415 38.8888 -4.82184 132 | 123 1 9.4499 0.00499864 37.5917 -4.78847 133 | 124 1 10.3131 2.34415 36.0469 -4.78373 134 | 125 1 13.3 0.00499892 44.3953 -4.80929 135 | 126 1 15.5056 0.0049998 69.2814 -3.81005 136 | 127 1 14.4131 2.34415 45.671 -4.80729 137 | 128 1 14.9562 2.34415 48.5265 -4.81638 138 | 129 1 10.5213 0.0049998 56.8114 -4.83181 139 | 130 1 11.0751 2.34415 55.2126 -4.83363 140 | 131 1 9.96659 0.00499981 53.927 -4.83606 141 | 132 1 10.5207 2.34415 52.3258 -4.83447 142 | 133 1 9.41093 0.00499973 51.0396 -4.83986 143 | 134 1 9.96696 2.34415 49.4366 -4.83839 144 | 135 1 8.8523 0.00499932 48.1458 -4.84326 145 | 136 1 9.40989 2.34415 46.5439 -4.83918 146 | 137 1 0.547286 0.0049993 45.2329 -4.85778 147 | 138 1 8.86933 2.34415 43.6242 -4.85528 148 | 139 1 15.4837 0.00499886 42.31 -4.86226 149 | 140 1 0.563381 2.34415 40.7015 -4.8365 150 | 141 1 14.9603 0.00499843 39.2941 -4.92627 151 | 142 1 0.139339 2.34415 37.6851 -4.85284 152 | 143 1 14.5385 0.00499799 36.1456 -4.99008 153 | 144 1 13.8546 0.00499942 47.2455 -4.82149 154 | 145 1 0 0.005 5e-05 -2.91263 155 | 146 1 6.10169 0.00499882 22.0349 -4.82146 156 | 147 1 7.20303 2.34415 20.7542 -4.81622 157 | 148 1 6.64874 0.00499935 19.1697 -4.82472 158 | 149 1 0.00208504 2.34415 17.8939 -4.82219 159 | 150 1 7.20201 0.00499976 16.3015 -4.82717 160 | 151 1 3.34079 2.34415 27.5325 -4.85456 161 | 152 1 6.65992 2.34415 23.6095 -4.80708 162 | 153 1 2.77355 0.00499838 25.8903 -4.82299 163 | 154 1 3.31625 0.00499877 23.0111 -4.82295 164 | 155 1 4.42746 2.34415 21.7505 -4.83705 165 | 156 1 3.87474 0.00499912 20.1398 -4.82802 166 | 157 1 4.97974 2.34415 18.8677 -4.8335 167 | 158 1 4.42805 0.00499955 17.2638 -4.82892 168 | 159 1 5.53626 2.34415 15.9894 -4.83354 169 | 160 1 3.86658 2.34415 24.629 -4.83248 170 | 161 1 5.54685 0.00499855 24.8849 -4.8093 171 | 162 1 6.10563 2.34415 26.4312 -4.79391 172 | 163 1 15.4839 0.00499824 26.9698 -4.86233 173 | 164 1 6.78516 0.00499786 33.1344 -4.99008 174 | 165 1 0.139365 2.34415 31.5949 -4.85285 175 | 166 1 7.20704 0.00499827 29.9859 -4.92629 176 | 167 1 5.21836 2.34415 34.64 -4.6238 177 | 168 1 4.01537 0.00499777 33.2904 -4.6864 178 | 169 1 5.16337 2.34415 31.9911 -4.6954 179 | 170 1 4.40246 0.00499737 30.4996 -4.77235 180 | 171 1 5.61283 2.34415 29.2632 -4.73449 181 | 172 1 5.02136 0.00499832 27.7358 -4.7939 182 | 173 1 1.44851 0.00499759 34.64 -4.72105 183 | 174 1 2.55976 2.34415 33.2331 -4.78373 184 | 175 1 1.69658 0.00499777 31.6884 -4.78847 185 | 176 1 2.80977 2.34415 30.3913 -4.82185 186 | 177 1 2.19227 0.00499796 28.749 -4.79394 187 | 178 1 0.563466 2.34415 28.5784 -4.83655 188 | 179 1 4.98431 0.005 14.3885 -4.8302 189 | 180 1 1.11615 2.34415 25.6556 -4.85534 190 | 181 1 0.547625 0.00499863 24.0468 -4.85787 191 | 182 1 1.6568 2.34415 22.7357 -4.83931 192 | 183 1 4.4305 2.34415 8.31339 -4.83118 193 | 184 1 3.87669 0.005 6.71467 -4.83118 194 | 185 1 4.98431 2.34415 5.43569 -4.83118 195 | 186 1 4.4305 0.005 3.83698 -4.82122 196 | 187 1 5.53812 2.34415 2.558 -4.64741 197 | 188 1 4.98431 0.005 0.959281 -4.00031 198 | 189 1 1.10762 2.34415 12.1503 -4.83122 199 | 190 1 0.553812 0.005 10.5516 -4.83118 200 | 191 1 1.66144 2.34415 9.27262 -4.83118 201 | 192 1 1.10762 0.005 7.6739 -4.83118 202 | 193 1 2.21525 2.34415 6.39493 -4.83118 203 | 194 1 1.66144 0.005 4.79621 -4.83118 204 | 195 1 2.76906 2.34415 3.51723 -4.81816 205 | 196 1 2.21525 0.005 1.91851 -4.54167 206 | 197 1 0.553812 2.34415 1.59877 -4.39166 207 | 198 1 3.32287 0.005 9.59236 -4.83118 208 | 199 1 7.83958 2.34415 34.64 -4.74324 209 | 200 1 3.87669 2.34415 11.1911 -4.83116 210 | 201 1 3.32287 2.34415 14.0688 -4.83255 211 | 202 1 1.09934 0.00499905 21.1335 -4.84361 212 | 203 1 2.2143 2.34415 19.8428 -4.83832 213 | 204 1 1.65848 0.00499945 18.2395 -4.8405 214 | 205 1 2.76774 2.34415 16.9533 -4.83529 215 | 206 1 2.21525 0.005 15.3478 -4.83503 216 | 207 1 0.553812 2.34415 15.028 -4.82709 217 | 208 1 5.42736e-15 0.005 13.4293 -4.82992 218 | 209 1 6.09194 2.34415 13.1095 -4.83241 219 | 210 1 5.53812 0.005 11.5108 -4.83119 220 | 211 1 6.64575 2.34415 10.2319 -4.83118 221 | 212 1 6.09194 0.005 8.63313 -4.83118 222 | 213 1 7.19956 2.34415 7.35416 -4.83118 223 | 214 1 6.64575 0.005 5.75544 -4.83118 224 | 215 1 3.87669e-15 2.34415 4.47646 -4.82813 225 | 216 1 7.19956 0.005 2.87774 -4.72768 226 | 217 1 2.76906 0.005 12.4701 -4.83111 227 | 218 1 3.32287 2.34415 0.639538 -3.81696 228 | 219 1 7.75337 0.005 5e-05 -2.91263 229 | 220 1 13.8551 0.00499887 22.0349 -4.82146 230 | 221 1 14.9564 2.34415 20.7542 -4.81622 231 | 222 1 14.4021 0.00499953 19.1697 -4.82472 232 | 223 1 7.75546 2.34415 17.8939 -4.82219 233 | 224 1 14.9554 0.00499977 16.3015 -4.82717 234 | 225 1 11.0942 2.34415 27.5325 -4.85456 235 | 226 1 14.4133 2.34415 23.6095 -4.80708 236 | 227 1 10.5269 0.00499855 25.8903 -4.82299 237 | 228 1 11.0696 0.0049989 23.0111 -4.82295 238 | 229 1 12.1808 2.34415 21.7505 -4.83705 239 | 230 1 11.6281 0.00499928 20.1398 -4.82802 240 | 231 1 12.7331 2.34415 18.8677 -4.8335 241 | 232 1 12.1814 0.00499965 17.2638 -4.82892 242 | 233 1 13.2896 2.34415 15.9894 -4.83354 243 | 234 1 11.62 2.34415 24.629 -4.83248 244 | 235 1 13.3002 0.0049986 24.8849 -4.8093 245 | 236 1 13.859 2.34415 26.4312 -4.79391 246 | 237 1 7.73052 0.0049986 26.9698 -4.86233 247 | 238 1 14.5385 0.00499793 33.1344 -4.99008 248 | 239 1 7.89274 2.34415 31.5949 -4.85285 249 | 240 1 14.9604 0.00499811 29.9859 -4.92629 250 | 241 1 12.9717 2.34415 34.64 -4.6238 251 | 242 1 11.7687 0.00499894 33.2904 -4.6864 252 | 243 1 12.9167 2.34415 31.9911 -4.6954 253 | 244 1 12.1558 0.00499861 30.4996 -4.77235 254 | 245 1 13.3662 2.34415 29.2632 -4.73449 255 | 246 1 12.7747 0.00499843 27.7358 -4.7939 256 | 247 1 9.20189 0.0049981 34.64 -4.72105 257 | 248 1 10.3131 2.34415 33.2331 -4.78373 258 | 249 1 9.44996 0.00499844 31.6884 -4.78847 259 | 250 1 10.5631 2.34415 30.3913 -4.82185 260 | 251 1 9.94565 0.00499847 28.749 -4.79394 261 | 252 1 8.31684 2.34415 28.5784 -4.83655 262 | 253 1 12.7377 0.005 14.3885 -4.8302 263 | 254 1 8.86953 2.34415 25.6556 -4.85534 264 | 255 1 8.301 0.00499888 24.0468 -4.85787 265 | 256 1 9.41018 2.34415 22.7357 -4.83931 266 | 257 1 12.1839 2.34415 8.31339 -4.83118 267 | 258 1 11.6301 0.005 6.71467 -4.83118 268 | 259 1 12.7377 2.34415 5.43569 -4.83118 269 | 260 1 12.1839 0.005 3.83698 -4.82122 270 | 261 1 13.2915 2.34415 2.558 -4.64741 271 | 262 1 12.7377 0.005 0.959281 -4.00031 272 | 263 1 8.861 2.34415 12.1503 -4.83122 273 | 264 1 8.30719 0.005 10.5516 -4.83118 274 | 265 1 9.41481 2.34415 9.27262 -4.83118 275 | 266 1 8.861 0.005 7.6739 -4.83118 276 | 267 1 9.96862 2.34415 6.39493 -4.83118 277 | 268 1 9.41481 0.005 4.79621 -4.83118 278 | 269 1 10.5224 2.34415 3.51723 -4.81816 279 | 270 1 9.96862 0.005 1.91851 -4.54167 280 | 271 1 8.30719 2.34415 1.59877 -4.39166 281 | 272 1 11.0762 0.005 9.59236 -4.83118 282 | 273 1 0.0862106 2.34415 34.64 -4.74324 283 | 274 1 11.6301 2.34415 11.1911 -4.83116 284 | 275 1 11.0762 2.34415 14.0688 -4.83255 285 | 276 1 8.85272 0.00499906 21.1335 -4.84361 286 | 277 1 9.96767 2.34415 19.8428 -4.83832 287 | 278 1 9.41185 0.00499971 18.2395 -4.8405 288 | 279 1 10.5211 2.34415 16.9533 -4.83529 289 | 280 1 9.96862 0.005 15.3478 -4.83503 290 | 281 1 8.30719 2.34415 15.028 -4.82709 291 | 282 1 7.75337 0.005 13.4293 -4.82992 292 | 283 1 13.8453 2.34415 13.1095 -4.83241 293 | 284 1 13.2915 0.005 11.5108 -4.83119 294 | 285 1 14.3991 2.34415 10.2319 -4.83118 295 | 286 1 13.8453 0.005 8.63313 -4.83118 296 | 287 1 14.9529 2.34415 7.35416 -4.83118 297 | 288 1 14.3991 0.005 5.75544 -4.83118 298 | 289 1 7.75337 2.34415 4.47646 -4.82813 299 | 290 1 14.9529 0.005 2.87774 -4.72768 300 | 291 1 10.5224 0.005 12.4701 -4.83111 301 | 292 1 11.0762 2.34415 0.639538 -3.81696 302 | Egb = 0.461926308725685 303 | -------------------------------------------------------------------------------- /.examples/Ti_2130_tilt/lammps_0.508_0.500_2.06_2.51_2_1_700_20000: -------------------------------------------------------------------------------- 1 | ITEM: TIMESTEP 2 | 0 3 | ITEM: NUMBER OF ATOMS 4 | 294 5 | ITEM: BOX BOUNDS pp pp ss 6 | 0.0000000000000000e+00 1.5506748434149568e+01 7 | 0.0000000000000000e+00 4.6783000000000001e+00 8 | -6.9722435625482046e-03 7.0076465334096383e+01 9 | ITEM: ATOMS id type x y z c_eng 10 | 1 1 1.39575 2.34416 35.9056 -4.54822 11 | 2 1 8.30782 2.34417 56.3205 -4.83147 12 | 3 1 8.86163 0.00502093 54.7217 -4.82808 13 | 4 1 7.75647 2.34417 53.4418 -4.83179 14 | 5 1 8.31255 0.00502017 51.8469 -4.82873 15 | 6 1 7.19827 2.34417 50.5685 -4.82855 16 | 7 1 7.75401 0.00502093 62.3956 -4.83118 17 | 8 1 1.66207 0.00502093 57.5994 -4.83039 18 | 9 1 6.64638 2.34417 61.1166 -4.83118 19 | 10 1 6.09257 2.34417 58.2389 -4.83115 20 | 11 1 6.64638 0.00502093 56.6402 -4.83054 21 | 12 1 5.53876 2.34417 55.3612 -4.82895 22 | 13 1 6.09303 0.00502059 53.765 -4.83008 23 | 14 1 4.98404 2.34417 52.4933 -4.8232 24 | 15 1 5.53476 0.00501994 50.8964 -4.82613 25 | 16 1 7.2002 0.00502093 59.5179 -4.83118 26 | 17 1 8.86163 2.34417 59.1982 -4.83113 27 | 18 1 2.21589 0.00502093 60.4771 -4.83118 28 | 19 1 1.66207 2.34417 62.0758 -4.83118 29 | 20 1 8.86163 0.00502093 68.151 -4.54858 30 | 21 1 7.75401 2.34417 66.872 -4.81816 31 | 22 1 8.30782 0.00502093 65.2733 -4.83118 32 | 23 1 7.2002 2.34417 63.9943 -4.83118 33 | 24 1 6.64638 0.00502093 70.0694 -3.69294 34 | 25 1 5.53876 2.34417 68.7905 -4.37289 35 | 26 1 6.09257 0.00502093 67.1917 -4.81125 36 | 27 1 4.98495 2.34417 65.9128 -4.82813 37 | 28 1 5.53876 0.00502093 64.3141 -4.83118 38 | 29 1 4.43114 2.34417 63.0351 -4.83118 39 | 30 1 3.87732 0.00502093 69.1102 -4.0641 40 | 31 1 2.7697 2.34417 67.8312 -4.55549 41 | 32 1 3.32351 0.00502093 66.2325 -4.82122 42 | 33 1 2.21589 2.34417 64.9535 -4.83118 43 | 34 1 2.7697 0.00502093 63.3548 -4.83118 44 | 35 1 4.43903 2.34417 49.6222 -4.82342 45 | 36 1 4.98495 0.00502093 61.4364 -4.83118 46 | 37 1 3.87732 2.34417 60.1574 -4.83118 47 | 38 1 4.43114 0.00502093 58.5587 -4.83106 48 | 39 1 6.60702 0.00501733 43.2876 -4.80159 49 | 40 1 5.58799 2.34417 41.9146 -4.83835 50 | 41 1 6.1651 0.00501547 40.272 -4.77748 51 | 42 1 4.8577 2.34416 39.2421 -4.7067 52 | 43 1 6.27043 0.00501206 35.3527 -4.68206 53 | 44 1 5.27243 0.00501346 37.6803 -4.54823 54 | 45 1 4.99383 0.00501907 48.0175 -4.83162 55 | 46 1 3.8688 2.34417 46.7776 -4.80706 56 | 47 1 4.40449 0.00501805 45.1746 -4.81006 57 | 48 1 3.36415 2.34417 43.9107 -4.809 58 | 49 1 3.91622 0.00501658 42.2613 -4.8499 59 | 50 1 2.68634 2.34417 41.1484 -4.76896 60 | 51 1 3.18517 0.00501412 39.5401 -4.74651 61 | 52 1 2.39373 2.34416 38.2333 -4.682 62 | 53 1 2.88881 0.00501251 36.5316 -4.72749 63 | 54 1 6.07112 2.34417 44.8335 -4.80713 64 | 55 1 8.30782 2.34417 69.7497 -3.81005 65 | 56 1 7.22035 0.00501863 46.0944 -4.82553 66 | 57 1 7.75097 0.00501951 48.9829 -4.81933 67 | 58 1 3.32351 2.34417 57.2797 -4.8318 68 | 59 1 3.87732 0.00502093 55.681 -4.8349 69 | 60 1 2.76697 2.34417 54.3971 -4.8343 70 | 61 1 3.3202 0.00502034 52.7941 -4.83627 71 | 62 1 2.21457 2.34417 51.5089 -4.8392 72 | 63 1 2.76984 0.00501973 49.8969 -4.84604 73 | 64 1 1.64495 2.34417 48.6249 -4.83517 74 | 65 1 2.19291 0.00501884 47.0114 -4.84041 75 | 66 1 8.86175 2.34417 45.7018 -4.85877 76 | 67 1 1.66278 0.00501779 44.0482 -4.89686 77 | 68 1 8.2216 2.34417 42.8422 -4.80618 78 | 69 1 8.72357 0.00501613 41.1627 -4.77883 79 | 70 1 7.74615 2.34417 39.7235 -4.93108 80 | 71 1 8.25607 0.00501374 37.9613 -5.09395 81 | 72 1 6.76552 2.34416 37.0544 -4.72752 82 | 73 1 6.65954 2.34417 47.6844 -4.83498 83 | 74 1 9.14913 2.34416 35.9056 -4.54822 84 | 75 1 0.554448 2.34417 56.3205 -4.83147 85 | 76 1 1.10826 0.00502093 54.7217 -4.82808 86 | 77 1 0.00309136 2.34417 53.4418 -4.83179 87 | 78 1 0.55918 0.00502014 51.8469 -4.82873 88 | 79 1 14.9516 2.34417 50.5685 -4.82855 89 | 80 1 0.000635509 0.00502093 62.3956 -4.83118 90 | 81 1 9.41545 0.00502093 57.5994 -4.83039 91 | 82 1 14.3998 2.34417 61.1166 -4.83118 92 | 83 1 13.8459 2.34417 58.2389 -4.83115 93 | 84 1 14.3998 0.00502093 56.6402 -4.83054 94 | 85 1 13.2921 2.34417 55.3612 -4.82895 95 | 86 1 13.8464 0.00502046 53.765 -4.83008 96 | 87 1 12.7374 2.34417 52.4933 -4.8232 97 | 88 1 13.2881 0.00501985 50.8964 -4.82613 98 | 89 1 14.9536 0.00502093 59.5179 -4.83118 99 | 90 1 1.10826 2.34417 59.1982 -4.83113 100 | 91 1 9.96926 0.00502093 60.4771 -4.83118 101 | 92 1 9.41545 2.34417 62.0758 -4.83118 102 | 93 1 1.10826 0.00502093 68.151 -4.54858 103 | 94 1 0.000635509 2.34417 66.872 -4.81816 104 | 95 1 0.554448 0.00502093 65.2733 -4.83118 105 | 96 1 14.9536 2.34417 63.9943 -4.83118 106 | 97 1 14.3998 0.00502093 70.0694 -3.69294 107 | 98 1 13.2921 2.34417 68.7905 -4.37289 108 | 99 1 13.8459 0.00502093 67.1917 -4.81125 109 | 100 1 12.7383 2.34417 65.9128 -4.82813 110 | 101 1 13.2921 0.00502093 64.3141 -4.83118 111 | 102 1 12.1845 2.34417 63.0351 -4.83118 112 | 103 1 11.6307 0.00502093 69.1102 -4.0641 113 | 104 1 10.5231 2.34417 67.8312 -4.55549 114 | 105 1 11.0769 0.00502093 66.2325 -4.82122 115 | 106 1 9.96926 2.34417 64.9535 -4.83118 116 | 107 1 10.5231 0.00502093 63.3548 -4.83118 117 | 108 1 12.1924 2.34417 49.6222 -4.82342 118 | 109 1 12.7383 0.00502093 61.4364 -4.83118 119 | 110 1 11.6307 2.34417 60.1574 -4.83118 120 | 111 1 12.1845 0.00502093 58.5587 -4.83106 121 | 112 1 14.3604 0.0050173 43.2876 -4.80159 122 | 113 1 13.3414 2.34417 41.9146 -4.83835 123 | 114 1 13.9185 0.00501531 40.272 -4.77748 124 | 115 1 12.6111 2.34416 39.2421 -4.7067 125 | 116 1 14.0238 0.00501218 35.3527 -4.68206 126 | 117 1 13.0258 0.00501385 37.6803 -4.54823 127 | 118 1 12.7472 0.00501912 48.0175 -4.83162 128 | 119 1 11.6222 2.34417 46.7776 -4.80706 129 | 120 1 12.1579 0.00501803 45.1746 -4.81006 130 | 121 1 11.1175 2.34417 43.9107 -4.809 131 | 122 1 11.6696 0.00501684 42.2613 -4.8499 132 | 123 1 10.4397 2.34417 41.1484 -4.76896 133 | 124 1 10.9385 0.00501417 39.5401 -4.74651 134 | 125 1 10.1471 2.34416 38.2333 -4.682 135 | 126 1 10.6422 0.00501233 36.5316 -4.72749 136 | 127 1 13.8245 2.34417 44.8335 -4.80713 137 | 128 1 0.554448 2.34417 69.7497 -3.81005 138 | 129 1 14.9737 0.00501858 46.0944 -4.82553 139 | 130 1 15.5043 0.0050193 48.9829 -4.81933 140 | 131 1 11.0769 2.34417 57.2797 -4.8318 141 | 132 1 11.6307 0.00502093 55.681 -4.8349 142 | 133 1 10.5203 2.34417 54.3971 -4.8343 143 | 134 1 11.0736 0.00502034 52.7941 -4.83627 144 | 135 1 9.96794 2.34417 51.5089 -4.83921 145 | 136 1 10.5232 0.00501966 49.8969 -4.84604 146 | 137 1 9.39833 2.34417 48.6249 -4.83517 147 | 138 1 9.94628 0.00501888 47.0114 -4.84041 148 | 139 1 1.10837 2.34417 45.7018 -4.85877 149 | 140 1 9.41615 0.00501779 44.0482 -4.89686 150 | 141 1 0.468225 2.34417 42.8422 -4.80618 151 | 142 1 0.970195 0.00501605 41.1627 -4.77883 152 | 143 1 15.4995 2.34417 39.7235 -4.93108 153 | 144 1 0.502699 0.00501374 37.9613 -5.09395 154 | 145 1 14.5189 2.34416 37.0544 -4.72752 155 | 146 1 14.4129 2.34417 47.6844 -4.83498 156 | 147 1 0 0.005 5e-05 -2.91263 157 | 148 1 6.0912 0.0050036 22.0794 -4.83842 158 | 149 1 7.19582 2.34415 20.7942 -4.8354 159 | 150 1 6.6428 0.00500225 19.1912 -4.83346 160 | 151 1 0.000364353 2.34415 17.9119 -4.83554 161 | 152 1 7.19928 0.00500084 16.3102 -4.83368 162 | 153 1 3.34372 2.34416 27.4913 -4.82558 163 | 154 1 6.64648 2.34415 23.6907 -4.84548 164 | 155 1 2.78283 0.00500565 25.9015 -4.83486 165 | 156 1 3.32123 0.00500413 23.0169 -4.82855 166 | 157 1 4.43629 2.34415 21.7384 -4.82899 167 | 158 1 3.88039 0.00500275 20.1443 -4.83216 168 | 159 1 4.98521 2.34415 18.8607 -4.82821 169 | 160 1 4.43121 0.00500146 17.2655 -4.83073 170 | 161 1 5.53957 2.34415 15.9859 -4.83017 171 | 162 1 3.87419 2.34415 24.6024 -4.81976 172 | 163 1 5.5213 0.00500498 24.962 -4.8349 173 | 164 1 6.06935 2.34416 26.5754 -4.84017 174 | 165 1 15.4989 0.00500617 26.8078 -4.80746 175 | 166 1 6.56305 0.00500927 32.4375 -4.76909 176 | 167 1 0.0396427 2.34416 31.3245 -4.84989 177 | 168 1 7.24093 0.00500723 29.675 -4.80912 178 | 169 1 4.3794 2.34416 35.6247 -5.09397 179 | 170 1 3.86944 0.00501016 33.8626 -4.93107 180 | 171 1 4.84687 2.34416 32.4235 -4.77877 181 | 172 1 4.34479 0.00500803 30.7441 -4.80608 182 | 173 1 5.53941 2.34416 29.5382 -4.89677 183 | 174 1 4.98499 0.00500638 27.8848 -4.85858 184 | 175 1 0.981004 0.00501126 34.3438 -4.70667 185 | 176 1 2.28842 2.34416 33.3139 -4.7775 186 | 177 1 1.7112 0.00500893 31.6713 -4.83828 187 | 178 1 2.73035 2.34416 30.2983 -4.8017 188 | 179 1 2.19436 0.00500714 28.7524 -4.80714 189 | 180 1 0.527938 2.34416 28.4112 -4.81015 190 | 181 1 4.98431 0.005 14.3885 -4.83139 191 | 182 1 1.11752 2.34416 25.5682 -4.8316 192 | 183 1 0.562819 0.0050046 23.9629 -4.82375 193 | 184 1 1.65819 2.34415 22.6887 -4.82637 194 | 185 1 4.4305 2.34415 8.31339 -4.83118 195 | 186 1 3.87669 0.005 6.71467 -4.83118 196 | 187 1 4.98431 2.34415 5.43569 -4.83118 197 | 188 1 4.4305 0.005 3.83698 -4.82122 198 | 189 1 5.53812 2.34415 2.558 -4.64741 199 | 190 1 4.98431 0.005 0.959281 -4.00031 200 | 191 1 1.10762 2.34415 12.1503 -4.83116 201 | 192 1 0.553812 0.005 10.5516 -4.83118 202 | 193 1 1.66144 2.34415 9.27262 -4.83118 203 | 194 1 1.10762 0.005 7.6739 -4.83118 204 | 195 1 2.21525 2.34415 6.39493 -4.83118 205 | 196 1 1.66144 0.005 4.79621 -4.83118 206 | 197 1 2.76906 2.34415 3.51723 -4.81816 207 | 198 1 2.21525 0.005 1.91851 -4.54167 208 | 199 1 0.553812 2.34415 1.59877 -4.39166 209 | 200 1 3.32287 0.005 9.59236 -4.83118 210 | 201 1 7.06194 2.34416 34.0458 -4.74652 211 | 202 1 3.87669 2.34415 11.1911 -4.8312 212 | 203 1 3.32287 2.34415 14.0688 -4.83099 213 | 204 1 1.1074 0.00500322 21.0905 -4.82462 214 | 205 1 2.21735 2.34415 19.8204 -4.83056 215 | 206 1 1.66353 0.00500168 18.2212 -4.82827 216 | 207 1 2.76885 2.34415 16.944 -4.82966 217 | 208 1 2.21525 0.005 15.3478 -4.82937 218 | 209 1 0.553812 2.34415 15.028 -4.83254 219 | 210 1 5.42736e-15 0.005 13.4293 -4.83189 220 | 211 1 6.09194 2.34415 13.1095 -4.83042 221 | 212 1 5.53812 0.005 11.5108 -4.83118 222 | 213 1 6.64575 2.34415 10.2319 -4.83118 223 | 214 1 6.09194 0.005 8.63313 -4.83118 224 | 215 1 7.19956 2.34415 7.35416 -4.83118 225 | 216 1 6.64575 0.005 5.75544 -4.83118 226 | 217 1 3.87669e-15 2.34415 4.47646 -4.82813 227 | 218 1 7.19956 0.005 2.87774 -4.72768 228 | 219 1 2.76906 0.005 12.4701 -4.83123 229 | 220 1 3.32287 2.34415 0.639538 -3.81696 230 | 221 1 7.75337 0.005 5e-05 -2.91263 231 | 222 1 13.8446 0.0050036 22.0794 -4.83842 232 | 223 1 14.9492 2.34415 20.7942 -4.8354 233 | 224 1 14.3962 0.00500209 19.1912 -4.83346 234 | 225 1 7.75374 2.34415 17.9119 -4.83554 235 | 226 1 14.9527 0.00500077 16.3102 -4.83368 236 | 227 1 11.0971 2.34416 27.4913 -4.82558 237 | 228 1 14.3999 2.34415 23.6907 -4.84548 238 | 229 1 10.5362 0.0050054 25.9015 -4.83486 239 | 230 1 11.0746 0.00500411 23.0169 -4.82855 240 | 231 1 12.1897 2.34415 21.7384 -4.82899 241 | 232 1 11.6338 0.00500269 20.1443 -4.83216 242 | 233 1 12.7386 2.34415 18.8607 -4.82821 243 | 234 1 12.1846 0.0050013 17.2655 -4.83073 244 | 235 1 13.2929 2.34415 15.9859 -4.83017 245 | 236 1 11.6276 2.34415 24.6024 -4.81976 246 | 237 1 13.2747 0.00500497 24.962 -4.8349 247 | 238 1 13.8227 2.34416 26.5754 -4.84017 248 | 239 1 7.74556 0.0050059 26.8078 -4.80746 249 | 240 1 14.3164 0.00500996 32.4375 -4.76909 250 | 241 1 7.79302 2.34416 31.3245 -4.84989 251 | 242 1 14.9943 0.00500766 29.675 -4.80912 252 | 243 1 12.1328 2.34416 35.6247 -5.09397 253 | 244 1 11.6228 0.00501037 33.8626 -4.93107 254 | 245 1 12.6002 2.34416 32.4235 -4.77877 255 | 246 1 12.0982 0.00500821 30.7441 -4.80608 256 | 247 1 13.2928 2.34416 29.5382 -4.89677 257 | 248 1 12.7384 0.00500639 27.8848 -4.85858 258 | 249 1 8.73438 0.00501143 34.3438 -4.70666 259 | 250 1 10.0418 2.34416 33.3139 -4.7775 260 | 251 1 9.46457 0.00500864 31.6713 -4.83828 261 | 252 1 10.4837 2.34416 30.2983 -4.8017 262 | 253 1 9.94773 0.00500701 28.7524 -4.80714 263 | 254 1 8.28131 2.34416 28.4112 -4.81015 264 | 255 1 12.7377 0.005 14.3885 -4.83139 265 | 256 1 8.8709 2.34416 25.5682 -4.8316 266 | 257 1 8.31619 0.0050044 23.9629 -4.82375 267 | 258 1 9.41156 2.34415 22.6887 -4.82637 268 | 259 1 12.1839 2.34415 8.31339 -4.83118 269 | 260 1 11.6301 0.005 6.71467 -4.83118 270 | 261 1 12.7377 2.34415 5.43569 -4.83118 271 | 262 1 12.1839 0.005 3.83698 -4.82122 272 | 263 1 13.2915 2.34415 2.558 -4.64741 273 | 264 1 12.7377 0.005 0.959281 -4.00031 274 | 265 1 8.861 2.34415 12.1503 -4.83116 275 | 266 1 8.30719 0.005 10.5516 -4.83118 276 | 267 1 9.41481 2.34415 9.27262 -4.83118 277 | 268 1 8.861 0.005 7.6739 -4.83118 278 | 269 1 9.96862 2.34415 6.39493 -4.83118 279 | 270 1 9.41481 0.005 4.79621 -4.83118 280 | 271 1 10.5224 2.34415 3.51723 -4.81816 281 | 272 1 9.96862 0.005 1.91851 -4.54167 282 | 273 1 8.30719 2.34415 1.59877 -4.39166 283 | 274 1 11.0762 0.005 9.59236 -4.83118 284 | 275 1 14.8153 2.34416 34.0458 -4.74652 285 | 276 1 11.6301 2.34415 11.1911 -4.8312 286 | 277 1 11.0762 2.34415 14.0688 -4.83099 287 | 278 1 8.86078 0.00500312 21.0905 -4.82462 288 | 279 1 9.97072 2.34415 19.8204 -4.83056 289 | 280 1 9.41691 0.0050017 18.2212 -4.82827 290 | 281 1 10.5222 2.34415 16.944 -4.82966 291 | 282 1 9.96862 0.005 15.3478 -4.82937 292 | 283 1 8.30719 2.34415 15.028 -4.83254 293 | 284 1 7.75337 0.005 13.4293 -4.83189 294 | 285 1 13.8453 2.34415 13.1095 -4.83042 295 | 286 1 13.2915 0.005 11.5108 -4.83118 296 | 287 1 14.3991 2.34415 10.2319 -4.83118 297 | 288 1 13.8453 0.005 8.63313 -4.83118 298 | 289 1 14.9529 2.34415 7.35416 -4.83118 299 | 290 1 14.3991 0.005 5.75544 -4.83118 300 | 291 1 7.75337 2.34415 4.47646 -4.82813 301 | 292 1 14.9529 0.005 2.87774 -4.72768 302 | 293 1 10.5224 0.005 12.4701 -4.83123 303 | 294 1 11.0762 2.34415 0.639538 -3.81696 304 | Egb = 0.50840658447605 305 | -------------------------------------------------------------------------------- /.examples/Ti_2130_tilt/params.yaml: -------------------------------------------------------------------------------- 1 | # Input data for the GRand canonical Interface Predictor (GRIP). Format is YAML. 2 | 3 | # Parameters for the algorithm 4 | algo: 5 | dir_struct: 'best' # Folder to store best structures. 6 | dir_calcs: 'calc_procs' # Folder to store temporary calculation files. 7 | ngrid: 100 # Number of grid points in each dim = ngrid * nprocs. 8 | frac_min: 0.00 # Minimum fraction of atoms on a plane (0 <= n <= 1). 9 | frac_max: 1.00 # Maximum fraction of atoms on a plane. Set both to 1.0 for gamma-surface. 10 | gb_gap: 0.3 # Initial gap between slabs prior to MD/relaxation (in Ang.). 11 | perturb_u: 0.3 # Maximum random perturbation (A) of atoms above GB 12 | perturb_l: 0.0 # Maximum random perturbation (A) of atoms below GB 13 | gb_thick: 10 # Thickness of GB region (in Angstrom) on either side of interface. 14 | pad: 10 # Extra padding (A) on top of gb_thick for relaxation / energy calculations. 15 | vacuum: 1 # Vacuum to add on top for MD (A); less needed for s boundary. 16 | 17 | inter_p: 0.0 # Probability of swapping with interstitial sites. [0.0, 1.0] = [Never, Always]. 18 | inter_s: 'Ti' # species of atom to insert. 19 | inter_n: 2 # Number of GB interstitial sites to swap with atoms in GB region. 20 | inter_t: 1.5 # Thickness of region (A) on either side of GB to search for interstitials. 21 | inter_u: False # Only choose unique interstitial sites. 22 | inter_r: True # Randomly choose interstitial sites vs. largest volume 23 | inter_w: 2 # How to swap: 1 = only subs, 2 = only inter, 3 = uniform, 4 = mostly subs, 5 = mostly inter 24 | 25 | MD_run: 0.95 # Probability of running MD simulation before relaxing. [0.0, 1.0] = [Never, Always]. 26 | Tmin: 300 # Temperature lower bound for MD simulation. 27 | Tmax: 1200 # Temperature upper bound, vary in multiple of 100s. 28 | MD_min: 5000 # Min steps for MD simulation. 29 | MD_max: 300000 # Max steps for MD simulation. 30 | var_steps: 2 # 0 = Min steps only; 1 = linear sample; 2 = exponential sample 31 | 32 | lammps_bin: '/g/g16/chen120/bin/lammps_serial' # Path to [serial] LAMMPS binary. 33 | Emult: 2 # Maximum energy threshold * Egb_min to keep; at least 1.0. 34 | nruns: 0 # Number of iterations in total (each processor). Set 0 for infinite loop. 35 | clear_freq: 50 # Number of iterations before clearing duplicates. Set 0 to never clear. 36 | 37 | 38 | # Parameters for the material 39 | struct: 40 | user: True # True: read existing cells (POSCAR_*), False: generate w/ ase. 41 | cutoff: 35 # Max height (A) to cut slabs if user=False; speed up calcs. Set to 0 to ignore. 42 | write: False # Write generated cells to POSCAR_* 43 | size0: [1, 1, 1] # Minimum replications in [x, y, z] to create supercells. 44 | size: [3, 5, 15] # Replications in [x, y, z] to create supercells. z is not used if user=True. 45 | reps: 2 # Sample replications (1) exactly, (2) uniform, (3) weighted towards smaller. 46 | 47 | upper_dirs: [ [4, 1, -5, 0], [0, 0, 0, -1], [-2, 3, -1, 0] ] # Ti(21-30) tilt 48 | lower_dirs: [ [5, -1, -4, 0], [0, 0, 0, -1], [-1, 3, -2, 0] ] 49 | symbol: 'Ti' # Chemical formula 50 | crystal: 'hcp' # fcc, bcc, hcp, or dc 51 | mass: 47.867 # Atomic mass 52 | a: 2.9305 # a lattice constant 53 | c: 4.6783 # c lattice constant; hcp only, ignored for others 54 | dlat: 0.959231 # Minimal normal component of lattice vector to calculate Nplane. Set 0 to ignore. 55 | Ecoh: -4.8312 # Energy per atom in bulk 56 | pair_style: 'meam/spline' # pair_style for LAMMPS 57 | pair_coeff: '* * /g/g16/chen120/lammps/pots/Ti.meam.spline Ti' # pair_coeff for LAMMPS 58 | 59 | -------------------------------------------------------------------------------- /.examples/W_310_twist/lammps_2.297_0.200_0.59_0.60_1_1_1100_3000: -------------------------------------------------------------------------------- 1 | ITEM: TIMESTEP 2 | 0 3 | ITEM: NUMBER OF ATOMS 4 | 472 5 | ITEM: BOX BOUNDS pp pp ss 6 | 0.0000000000000000e+00 1.0008131290506235e+01 7 | 0.0000000000000000e+00 1.0008131290506235e+01 8 | -7.3245617200455226e-03 7.3613713916192907e+01 9 | ITEM: ATOMS id type x y z c_eng 10 | 1 1 3.07182 1.01456 38.1963 -8.32913 11 | 2 1 5.54666 1.15019 37.2205 -8.38844 12 | 3 1 6.88448 8.97744 38.3761 -8.88801 13 | 4 1 1.88042 3.97337 38.3761 -8.88801 14 | 5 1 4.66051 3.28284 38.8578 -8.38629 15 | 6 1 7.51173 2.07096 38.8852 -8.27237 16 | 7 1 9.36551 3.66712 37.3755 -8.40981 17 | 8 1 0.353863 1.18412 38.7266 -8.55524 18 | 9 1 2.50767 7.07503 38.8852 -8.27237 19 | 10 1 5.35793 6.18819 38.7266 -8.55524 20 | 11 1 8.07588 6.01863 38.1963 -8.32913 21 | 12 1 9.66458 8.28691 38.8578 -8.38629 22 | 13 1 1.6628 9.28843 40.2543 -8.50223 23 | 14 1 2.52462 2.23636 40.4663 -8.54817 24 | 15 1 3.54507 0.198648 42.0166 -8.48511 25 | 16 1 5.45223 1.05592 40.242 -8.63234 26 | 17 1 6.53518 9.21312 42.0018 -8.46201 27 | 18 1 8.52255 0.165873 40.4539 -8.3579 28 | 19 1 1.53112 4.20905 42.0018 -8.46201 29 | 20 1 3.51849 5.16994 40.4539 -8.3579 30 | 21 1 4.59374 3.18517 41.94 -8.80652 31 | 22 1 6.66686 4.28436 40.2543 -8.50223 32 | 23 1 7.52887 2.20974 41.9298 -8.86368 33 | 24 1 9.58673 3.2487 40.3154 -8.59354 34 | 25 1 0.529147 1.19617 41.9354 -8.7255 35 | 26 1 2.52481 7.2138 41.9298 -8.86368 36 | 27 1 4.58266 8.25277 40.3154 -8.59354 37 | 28 1 5.53321 6.20024 41.9354 -8.7255 38 | 29 1 7.52869 7.24042 40.4663 -8.54817 39 | 30 1 8.54914 5.20271 42.0166 -8.48511 40 | 31 1 0.448161 6.05998 40.242 -8.63234 41 | 32 1 9.59781 8.18924 41.94 -8.80652 42 | 33 1 1.54298 9.21072 43.5237 -8.68968 43 | 34 1 2.54595 2.20601 43.5567 -8.79212 44 | 35 1 3.54705 0.195758 45.1309 -8.78827 45 | 36 1 5.55 1.20088 43.5303 -8.65811 46 | 37 1 6.54388 9.20718 45.1311 -8.77457 47 | 38 1 8.55221 0.196044 43.5479 -8.80714 48 | 39 1 1.53981 4.20311 45.1311 -8.77457 49 | 40 1 3.54815 5.20011 43.5479 -8.80714 50 | 41 1 4.55066 3.20004 45.1196 -8.75028 51 | 42 1 6.54704 4.20665 43.5237 -8.68968 52 | 43 1 7.54654 2.20143 45.1153 -8.75336 53 | 44 1 9.54465 3.18839 43.5319 -8.72226 54 | 45 1 0.544015 1.19787 45.1196 -8.74665 55 | 46 1 2.54247 7.2055 45.1153 -8.75336 56 | 47 1 4.54059 8.19245 43.5319 -8.72226 57 | 48 1 5.54808 6.20193 45.1196 -8.74665 58 | 49 1 7.55002 7.21008 43.5567 -8.79212 59 | 50 1 8.55111 5.19982 45.1309 -8.78827 60 | 51 1 0.545931 6.20495 43.5303 -8.65811 61 | 52 1 9.55473 8.20411 45.1196 -8.75028 62 | 53 1 1.54368 9.20542 46.7023 -8.75292 63 | 54 1 2.54539 2.20029 46.7082 -8.7666 64 | 55 1 3.5459 0.197428 48.2886 -8.76445 65 | 56 1 5.54778 1.20041 46.7047 -8.75211 66 | 57 1 6.54738 9.20568 48.289 -8.7637 67 | 58 1 8.54994 0.198431 46.7051 -8.76732 68 | 59 1 1.54331 4.20161 48.289 -8.7637 69 | 60 1 3.54587 5.2025 46.7051 -8.76732 70 | 61 1 4.54678 3.20088 48.2872 -8.75811 71 | 62 1 6.54775 4.20135 46.7023 -8.75292 72 | 63 1 7.54856 2.19986 48.2862 -8.75696 73 | 64 1 9.54932 3.19766 46.7044 -8.75421 74 | 65 1 0.543449 1.19838 48.2871 -8.75826 75 | 66 1 2.5445 7.20392 48.2862 -8.75696 76 | 67 1 4.54526 8.20173 46.7044 -8.75421 77 | 68 1 5.54751 6.20244 48.2871 -8.75826 78 | 69 1 7.54945 7.20436 46.7082 -8.7666 79 | 70 1 8.54996 5.20149 48.2886 -8.76445 80 | 71 1 0.543719 6.20447 46.7047 -8.75211 81 | 72 1 9.55084 8.20495 48.2872 -8.75811 82 | 73 1 1.54399 9.20524 49.8695 -8.75876 83 | 74 1 2.5449 2.19967 49.8705 -8.76133 84 | 75 1 3.54563 0.197889 51.4525 -8.76054 85 | 76 1 5.54725 1.19917 49.87 -8.75946 86 | 77 1 6.54796 9.20539 51.4526 -8.76061 87 | 78 1 8.54965 0.198188 49.8698 -8.76044 88 | 79 1 1.5439 4.20133 51.4526 -8.76061 89 | 80 1 3.54559 5.20225 49.8698 -8.76044 90 | 81 1 4.54646 3.20058 51.4524 -8.75977 91 | 82 1 6.54806 4.20118 49.8695 -8.75876 92 | 83 1 7.54882 2.19966 51.4522 -8.75942 93 | 84 1 9.55033 3.19995 49.8699 -8.75943 94 | 85 1 0.543191 1.1987 51.4523 -8.75979 95 | 86 1 2.54475 7.20373 51.4522 -8.75942 96 | 87 1 4.54627 8.20401 49.8699 -8.75943 97 | 88 1 5.54726 6.20277 51.4523 -8.75979 98 | 89 1 7.54897 7.20374 49.8705 -8.76133 99 | 90 1 8.5497 5.20195 51.4525 -8.76054 100 | 91 1 0.543187 6.20324 49.87 -8.75946 101 | 92 1 9.55053 8.20464 51.4524 -8.75977 102 | 93 1 1.54397 9.20532 53.0348 -8.75977 103 | 94 1 2.54479 2.19963 53.0348 -8.76023 104 | 95 1 3.5456 0.198005 54.6172 -8.76004 105 | 96 1 5.54723 1.19882 53.0348 -8.75999 106 | 97 1 6.54804 9.20532 54.6172 -8.76007 107 | 98 1 8.54967 0.198005 53.0348 -8.75995 108 | 99 1 1.54397 4.20126 54.6172 -8.76007 109 | 100 1 3.5456 5.20207 53.0348 -8.75995 110 | 101 1 4.54641 3.20044 54.6172 -8.75998 111 | 102 1 6.54804 4.20126 53.0348 -8.75977 112 | 103 1 7.54885 2.19963 54.6172 -8.75992 113 | 104 1 9.55048 3.20044 53.0348 -8.75997 114 | 105 1 0.543161 1.19882 54.6172 -8.75997 115 | 106 1 2.54479 7.2037 54.6172 -8.75992 116 | 107 1 4.54641 8.20451 53.0348 -8.75997 117 | 108 1 5.54723 6.20288 54.6172 -8.75997 118 | 109 1 7.54885 7.2037 53.0348 -8.76023 119 | 110 1 8.54967 5.20207 54.6172 -8.76004 120 | 111 1 0.543161 6.20288 53.0348 -8.75999 121 | 112 1 9.55048 8.20451 54.6172 -8.75998 122 | 113 1 1.54397 9.20532 56.1997 -8.75999 123 | 114 1 2.54479 2.19963 56.1997 -8.75999 124 | 115 1 3.5456 0.198005 57.7821 -8.75999 125 | 116 1 5.54723 1.19882 56.1997 -8.75999 126 | 117 1 6.54804 9.20532 57.7821 -8.75999 127 | 118 1 8.54967 0.198005 56.1997 -8.75999 128 | 119 1 1.54397 4.20126 57.7821 -8.75999 129 | 120 1 3.5456 5.20207 56.1997 -8.75999 130 | 121 1 4.54641 3.20044 57.7821 -8.75999 131 | 122 1 6.54804 4.20126 56.1997 -8.75999 132 | 123 1 7.54885 2.19963 57.7821 -8.75999 133 | 124 1 9.55048 3.20044 56.1997 -8.75999 134 | 125 1 0.543161 1.19882 57.7821 -8.75999 135 | 126 1 2.54479 7.2037 57.7821 -8.75999 136 | 127 1 4.54641 8.20451 56.1997 -8.75999 137 | 128 1 5.54723 6.20288 57.7821 -8.75999 138 | 129 1 7.54885 7.2037 56.1997 -8.75999 139 | 130 1 8.54967 5.20207 57.7821 -8.75999 140 | 131 1 0.543161 6.20288 56.1997 -8.75999 141 | 132 1 9.55048 8.20451 57.7821 -8.75999 142 | 133 1 1.54397 9.20532 59.3645 -8.75999 143 | 134 1 2.54479 2.19963 59.3645 -8.75999 144 | 135 1 3.5456 0.198005 60.9469 -8.75999 145 | 136 1 5.54723 1.19882 59.3645 -8.75999 146 | 137 1 6.54804 9.20532 60.9469 -8.75999 147 | 138 1 8.54967 0.198005 59.3645 -8.75999 148 | 139 1 1.54397 4.20126 60.9469 -8.75999 149 | 140 1 3.5456 5.20207 59.3645 -8.75999 150 | 141 1 4.54641 3.20044 60.9469 -8.75999 151 | 142 1 6.54804 4.20126 59.3645 -8.75999 152 | 143 1 7.54885 2.19963 60.9469 -8.75999 153 | 144 1 9.55048 3.20044 59.3645 -8.75999 154 | 145 1 0.543161 1.19882 60.9469 -8.75999 155 | 146 1 2.54479 7.2037 60.9469 -8.75999 156 | 147 1 4.54641 8.20451 59.3645 -8.75999 157 | 148 1 5.54723 6.20288 60.9469 -8.75999 158 | 149 1 7.54885 7.2037 59.3645 -8.75999 159 | 150 1 8.54967 5.20207 60.9469 -8.75999 160 | 151 1 0.543161 6.20288 59.3645 -8.75999 161 | 152 1 9.55048 8.20451 60.9469 -8.75999 162 | 153 1 1.54397 9.20532 62.5294 -8.75999 163 | 154 1 2.54479 2.19963 62.5294 -8.75999 164 | 155 1 3.5456 0.198005 64.1118 -8.75999 165 | 156 1 5.54723 1.19882 62.5294 -8.75999 166 | 157 1 6.54804 9.20532 64.1118 -8.75999 167 | 158 1 8.54967 0.198005 62.5294 -8.75999 168 | 159 1 1.54397 4.20126 64.1118 -8.75999 169 | 160 1 3.5456 5.20207 62.5294 -8.75999 170 | 161 1 4.54641 3.20044 64.1118 -8.75999 171 | 162 1 6.54804 4.20126 62.5294 -8.75999 172 | 163 1 7.54885 2.19963 64.1118 -8.75999 173 | 164 1 9.55048 3.20044 62.5294 -8.75999 174 | 165 1 0.543161 1.19882 64.1118 -8.75999 175 | 166 1 2.54479 7.2037 64.1118 -8.75999 176 | 167 1 4.54641 8.20451 62.5294 -8.75999 177 | 168 1 5.54723 6.20288 64.1118 -8.75999 178 | 169 1 7.54885 7.2037 62.5294 -8.75999 179 | 170 1 8.54967 5.20207 64.1118 -8.75999 180 | 171 1 0.543161 6.20288 62.5294 -8.75999 181 | 172 1 9.55048 8.20451 64.1118 -8.75999 182 | 173 1 1.54397 9.20532 65.6942 -8.75999 183 | 174 1 2.54479 2.19963 65.6942 -8.75999 184 | 175 1 3.5456 0.198005 67.2766 -8.75999 185 | 176 1 5.54723 1.19882 65.6942 -8.75999 186 | 177 1 6.54804 9.20532 67.2766 -8.75999 187 | 178 1 8.54967 0.198005 65.6942 -8.75999 188 | 179 1 1.54397 4.20126 67.2766 -8.75999 189 | 180 1 3.5456 5.20207 65.6942 -8.75999 190 | 181 1 4.54641 3.20044 67.2766 -8.75999 191 | 182 1 6.54804 4.20126 65.6942 -8.75999 192 | 183 1 7.54885 2.19963 67.2766 -8.75999 193 | 184 1 9.55048 3.20044 65.6942 -8.75999 194 | 185 1 0.543161 1.19882 67.2766 -8.75999 195 | 186 1 2.54479 7.2037 67.2766 -8.75999 196 | 187 1 4.54641 8.20451 65.6942 -8.75999 197 | 188 1 5.54723 6.20288 67.2766 -8.75999 198 | 189 1 7.54885 7.2037 65.6942 -8.75999 199 | 190 1 8.54967 5.20207 67.2766 -8.75999 200 | 191 1 0.543161 6.20288 65.6942 -8.75999 201 | 192 1 9.55048 8.20451 67.2766 -8.75999 202 | 193 1 1.54397 9.20532 68.8591 -8.75999 203 | 194 1 2.54479 2.19963 68.8591 -8.75999 204 | 195 1 3.5456 0.198005 70.4415 -8.75999 205 | 196 1 5.54723 1.19882 68.8591 -8.75999 206 | 197 1 6.54804 9.20532 70.4415 -8.75999 207 | 198 1 8.54967 0.198005 68.8591 -8.75999 208 | 199 1 1.54397 4.20126 70.4415 -8.75999 209 | 200 1 3.5456 5.20207 68.8591 -8.75999 210 | 201 1 4.54641 3.20044 70.4415 -8.75999 211 | 202 1 6.54804 4.20126 68.8591 -8.75999 212 | 203 1 7.54885 2.19963 70.4415 -8.75999 213 | 204 1 9.55048 3.20044 68.8591 -8.75999 214 | 205 1 0.543161 1.19882 70.4415 -8.75999 215 | 206 1 2.54479 7.2037 70.4415 -8.75999 216 | 207 1 4.54641 8.20451 68.8591 -8.75999 217 | 208 1 5.54723 6.20288 70.4415 -8.75999 218 | 209 1 7.54885 7.2037 68.8591 -8.75999 219 | 210 1 8.54967 5.20207 70.4415 -8.75999 220 | 211 1 0.543161 6.20288 68.8591 -8.75999 221 | 212 1 9.55048 8.20451 70.4415 -8.75999 222 | 213 1 1.54397 9.20532 72.0239 -8.49339 223 | 214 1 2.54479 2.19963 72.0239 -8.49339 224 | 215 1 3.5456 0.198005 73.6063 -7.15841 225 | 216 1 5.54723 1.19882 72.0239 -8.49339 226 | 217 1 6.54804 9.20532 73.6063 -7.15841 227 | 218 1 8.54967 0.198005 72.0239 -8.49339 228 | 219 1 1.54397 4.20126 73.6063 -7.15841 229 | 220 1 3.5456 5.20207 72.0239 -8.49339 230 | 221 1 4.54641 3.20044 73.6063 -7.15841 231 | 222 1 6.54804 4.20126 72.0239 -8.49339 232 | 223 1 7.54885 2.19963 73.6063 -7.15841 233 | 224 1 9.55048 3.20044 72.0239 -8.49339 234 | 225 1 0.543161 1.19882 73.6063 -7.15841 235 | 226 1 2.54479 7.2037 73.6063 -7.15841 236 | 227 1 4.54641 8.20451 72.0239 -8.49339 237 | 228 1 5.54723 6.20288 73.6063 -7.15841 238 | 229 1 7.54885 7.2037 72.0239 -8.49339 239 | 230 1 8.54967 5.20207 73.6063 -7.15841 240 | 231 1 0.543161 6.20288 72.0239 -8.49339 241 | 232 1 9.55048 8.20451 73.6063 -7.15841 242 | 233 1 0 0.005 5e-05 -7.15841 243 | 234 1 3.00244 1.00581 5e-05 -7.15841 244 | 235 1 5.00407 0.005 1.58247 -8.49339 245 | 236 1 6.00488 2.00663 5e-05 -7.15841 246 | 237 1 8.00651 1.00581 1.58247 -8.49339 247 | 238 1 9.00732 3.00744 5e-05 -7.15841 248 | 239 1 1.00081 2.00663 1.58247 -8.49339 249 | 240 1 2.00163 4.00825 5e-05 -7.15841 250 | 241 1 4.00325 3.00744 1.58247 -8.49339 251 | 242 1 5.00407 5.00907 5e-05 -7.15841 252 | 243 1 7.00569 4.00825 1.58247 -8.49339 253 | 244 1 8.00651 6.00988 5e-05 -7.15841 254 | 245 1 0 5.00907 1.58247 -8.49339 255 | 246 1 1.00081 7.01069 5e-05 -7.15841 256 | 247 1 3.00244 6.00988 1.58247 -8.49339 257 | 248 1 4.00325 8.01151 5e-05 -7.15841 258 | 249 1 6.00488 7.01069 1.58247 -8.49339 259 | 250 1 7.00569 9.01232 5e-05 -7.15841 260 | 251 1 9.00732 8.01151 1.58247 -8.49339 261 | 252 1 2.00163 9.01232 1.58247 -8.49339 262 | 253 1 0 0.005 3.1649 -8.75999 263 | 254 1 3.00244 1.00581 3.1649 -8.75999 264 | 255 1 5.00407 0.005 4.74732 -8.75999 265 | 256 1 6.00488 2.00663 3.1649 -8.75999 266 | 257 1 8.00651 1.00581 4.74732 -8.75999 267 | 258 1 9.00732 3.00744 3.1649 -8.75999 268 | 259 1 1.00081 2.00663 4.74732 -8.75999 269 | 260 1 2.00163 4.00825 3.1649 -8.75999 270 | 261 1 4.00325 3.00744 4.74732 -8.75999 271 | 262 1 5.00407 5.00907 3.1649 -8.75999 272 | 263 1 7.00569 4.00825 4.74732 -8.75999 273 | 264 1 8.00651 6.00988 3.1649 -8.75999 274 | 265 1 0 5.00907 4.74732 -8.75999 275 | 266 1 1.00081 7.01069 3.1649 -8.75999 276 | 267 1 3.00244 6.00988 4.74732 -8.75999 277 | 268 1 4.00325 8.01151 3.1649 -8.75999 278 | 269 1 6.00488 7.01069 4.74732 -8.75999 279 | 270 1 7.00569 9.01232 3.1649 -8.75999 280 | 271 1 9.00732 8.01151 4.74732 -8.75999 281 | 272 1 2.00163 9.01232 4.74732 -8.75999 282 | 273 1 0 0.005 6.32975 -8.75999 283 | 274 1 3.00244 1.00581 6.32975 -8.75999 284 | 275 1 5.00407 0.005 7.91217 -8.75999 285 | 276 1 6.00488 2.00663 6.32975 -8.75999 286 | 277 1 8.00651 1.00581 7.91217 -8.75999 287 | 278 1 9.00732 3.00744 6.32975 -8.75999 288 | 279 1 1.00081 2.00663 7.91217 -8.75999 289 | 280 1 2.00163 4.00825 6.32975 -8.75999 290 | 281 1 4.00325 3.00744 7.91217 -8.75999 291 | 282 1 5.00407 5.00907 6.32975 -8.75999 292 | 283 1 7.00569 4.00825 7.91217 -8.75999 293 | 284 1 8.00651 6.00988 6.32975 -8.75999 294 | 285 1 0 5.00907 7.91217 -8.75999 295 | 286 1 1.00081 7.01069 6.32975 -8.75999 296 | 287 1 3.00244 6.00988 7.91217 -8.75999 297 | 288 1 4.00325 8.01151 6.32975 -8.75999 298 | 289 1 6.00488 7.01069 7.91217 -8.75999 299 | 290 1 7.00569 9.01232 6.32975 -8.75999 300 | 291 1 9.00732 8.01151 7.91217 -8.75999 301 | 292 1 2.00163 9.01232 7.91217 -8.75999 302 | 293 1 0 0.005 9.4946 -8.75999 303 | 294 1 3.00244 1.00581 9.4946 -8.75999 304 | 295 1 5.00407 0.005 11.077 -8.75999 305 | 296 1 6.00488 2.00663 9.4946 -8.75999 306 | 297 1 8.00651 1.00581 11.077 -8.75999 307 | 298 1 9.00732 3.00744 9.4946 -8.75999 308 | 299 1 1.00081 2.00663 11.077 -8.75999 309 | 300 1 2.00163 4.00825 9.4946 -8.75999 310 | 301 1 4.00325 3.00744 11.077 -8.75999 311 | 302 1 5.00407 5.00907 9.4946 -8.75999 312 | 303 1 7.00569 4.00825 11.077 -8.75999 313 | 304 1 8.00651 6.00988 9.4946 -8.75999 314 | 305 1 0 5.00907 11.077 -8.75999 315 | 306 1 1.00081 7.01069 9.4946 -8.75999 316 | 307 1 3.00244 6.00988 11.077 -8.75999 317 | 308 1 4.00325 8.01151 9.4946 -8.75999 318 | 309 1 6.00488 7.01069 11.077 -8.75999 319 | 310 1 7.00569 9.01232 9.4946 -8.75999 320 | 311 1 9.00732 8.01151 11.077 -8.75999 321 | 312 1 2.00163 9.01232 11.077 -8.75999 322 | 313 1 0 0.005 12.6594 -8.75999 323 | 314 1 3.00244 1.00581 12.6594 -8.75999 324 | 315 1 5.00407 0.005 14.2419 -8.75999 325 | 316 1 6.00488 2.00663 12.6594 -8.75999 326 | 317 1 8.00651 1.00581 14.2419 -8.75999 327 | 318 1 9.00732 3.00744 12.6594 -8.75999 328 | 319 1 1.00081 2.00663 14.2419 -8.75999 329 | 320 1 2.00163 4.00825 12.6594 -8.75999 330 | 321 1 4.00325 3.00744 14.2419 -8.75999 331 | 322 1 5.00407 5.00907 12.6594 -8.75999 332 | 323 1 7.00569 4.00825 14.2419 -8.75999 333 | 324 1 8.00651 6.00988 12.6594 -8.75999 334 | 325 1 0 5.00907 14.2419 -8.75999 335 | 326 1 1.00081 7.01069 12.6594 -8.75999 336 | 327 1 3.00244 6.00988 14.2419 -8.75999 337 | 328 1 4.00325 8.01151 12.6594 -8.75999 338 | 329 1 6.00488 7.01069 14.2419 -8.75999 339 | 330 1 7.00569 9.01232 12.6594 -8.75999 340 | 331 1 9.00732 8.01151 14.2419 -8.75999 341 | 332 1 2.00163 9.01232 14.2419 -8.75999 342 | 333 1 0 0.005 15.8243 -8.75999 343 | 334 1 3.00244 1.00581 15.8243 -8.75999 344 | 335 1 5.00407 0.005 17.4067 -8.75999 345 | 336 1 6.00488 2.00663 15.8243 -8.75999 346 | 337 1 8.00651 1.00581 17.4067 -8.75999 347 | 338 1 9.00732 3.00744 15.8243 -8.75999 348 | 339 1 1.00081 2.00663 17.4067 -8.75999 349 | 340 1 2.00163 4.00825 15.8243 -8.75999 350 | 341 1 4.00325 3.00744 17.4067 -8.75999 351 | 342 1 5.00407 5.00907 15.8243 -8.75999 352 | 343 1 7.00569 4.00825 17.4067 -8.75999 353 | 344 1 8.00651 6.00988 15.8243 -8.75999 354 | 345 1 0 5.00907 17.4067 -8.75999 355 | 346 1 1.00081 7.01069 15.8243 -8.75999 356 | 347 1 3.00244 6.00988 17.4067 -8.75999 357 | 348 1 4.00325 8.01151 15.8243 -8.75999 358 | 349 1 6.00488 7.01069 17.4067 -8.75999 359 | 350 1 7.00569 9.01232 15.8243 -8.75999 360 | 351 1 9.00732 8.01151 17.4067 -8.75999 361 | 352 1 2.00163 9.01232 17.4067 -8.75999 362 | 353 1 0 0.005 18.9891 -8.75992 363 | 354 1 3.00244 1.00581 18.9891 -8.76005 364 | 355 1 5.00407 0.005 20.5716 -8.76028 365 | 356 1 6.00488 2.00663 18.9891 -8.75999 366 | 357 1 8.00651 1.00581 20.5716 -8.75983 367 | 358 1 9.00732 3.00744 18.9891 -8.76001 368 | 359 1 1.00081 2.00663 20.5716 -8.75994 369 | 360 1 2.00163 4.00825 18.9891 -8.76001 370 | 361 1 4.00325 3.00744 20.5716 -8.75987 371 | 362 1 5.00407 5.00907 18.9891 -8.75992 372 | 363 1 7.00569 4.00825 20.5716 -8.76003 373 | 364 1 8.00651 6.00988 18.9891 -8.76005 374 | 365 1 0 5.00907 20.5716 -8.76028 375 | 366 1 1.00081 7.01069 18.9891 -8.75999 376 | 367 1 3.00244 6.00988 20.5716 -8.75983 377 | 368 1 4.00325 8.01151 18.9891 -8.76001 378 | 369 1 6.00488 7.01069 20.5716 -8.75994 379 | 370 1 7.00569 9.01232 18.9891 -8.76001 380 | 371 1 9.00732 8.01151 20.5716 -8.75987 381 | 372 1 2.00163 9.01232 20.5716 -8.76003 382 | 373 1 10.0081 0.00502958 22.1542 -8.7595 383 | 374 1 3.00241 1.00593 22.1538 -8.76037 384 | 375 1 5.00409 0.00490322 23.7358 -8.76168 385 | 376 1 6.00495 2.00665 22.154 -8.75994 386 | 377 1 8.00646 1.00568 23.7368 -8.75916 387 | 378 1 9.00723 3.00734 22.154 -8.76001 388 | 379 1 1.0006 2.00652 23.7365 -8.75927 389 | 380 1 2.00172 4.00817 22.1539 -8.76022 390 | 381 1 4.00358 3.00764 23.7367 -8.75886 391 | 382 1 5.00402 5.0091 22.1542 -8.7595 392 | 383 1 7.00561 4.00839 23.7364 -8.76072 393 | 384 1 8.00647 6.01 22.1538 -8.76037 394 | 385 1 2.01401e-05 5.00897 23.7358 -8.76168 395 | 386 1 1.00088 7.01072 22.154 -8.75994 396 | 387 1 3.00239 6.00974 23.7368 -8.75916 397 | 388 1 4.00317 8.01141 22.154 -8.76001 398 | 389 1 6.00466 7.01059 23.7365 -8.75927 399 | 390 1 7.00579 9.01224 22.1539 -8.76022 400 | 391 1 9.00765 8.0117 23.7367 -8.75886 401 | 392 1 2.00154 9.01246 23.7364 -8.76072 402 | 393 1 10.0078 0.00515406 25.3202 -8.75781 403 | 394 1 3.0023 1.00661 25.3179 -8.76193 404 | 395 1 5.00383 0.00454918 26.8976 -8.76887 405 | 396 1 6.00505 2.00676 25.3189 -8.75942 406 | 397 1 8.00594 1.00554 26.9033 -8.75591 407 | 398 1 9.00712 3.00683 25.3187 -8.7594 408 | 399 1 0.999982 2.00576 26.9023 -8.75316 409 | 400 1 2.00209 4.00778 25.3184 -8.76212 410 | 401 1 4.00473 3.00862 26.9032 -8.751 411 | 402 1 5.00378 5.00922 25.3202 -8.75781 412 | 403 1 7.00585 4.00867 26.9004 -8.76709 413 | 404 1 8.00636 6.01068 25.3179 -8.76193 414 | 405 1 10.0079 5.00861 26.8976 -8.76887 415 | 406 1 1.00098 7.01082 25.3189 -8.75942 416 | 407 1 3.00187 6.0096 26.9033 -8.75591 417 | 408 1 4.00305 8.01089 25.3187 -8.7594 418 | 409 1 6.00405 7.00983 26.9023 -8.75316 419 | 410 1 7.00615 9.01185 25.3184 -8.76212 420 | 411 1 9.0088 8.01269 26.9032 -8.751 421 | 412 1 2.00178 9.01274 26.9004 -8.76709 422 | 413 1 10.0064 0.00548322 28.4901 -8.75807 423 | 414 1 3.00162 1.01025 28.4787 -8.76472 424 | 415 1 5.00096 0.00392477 30.0452 -8.79516 425 | 416 1 6.00422 2.00816 28.4845 -8.75715 426 | 417 1 8.00252 1.00562 30.0768 -8.7294 427 | 418 1 9.00862 3.00269 28.4837 -8.75378 428 | 419 1 1.00181 2.00181 30.0767 -8.70539 429 | 420 1 2.00347 4.00651 28.4801 -8.77435 430 | 421 1 4.00485 3.01319 30.0817 -8.69324 431 | 422 1 5.00236 5.00955 28.4901 -8.75807 432 | 423 1 7.01026 4.0088 30.0558 -8.79795 433 | 424 1 8.00568 6.01431 28.4787 -8.76472 434 | 425 1 10.005 5.00799 30.0452 -8.79516 435 | 426 1 1.00015 7.01223 28.4845 -8.75715 436 | 427 1 2.99846 6.00968 30.0768 -8.7294 437 | 428 1 4.00456 8.00675 28.4837 -8.75378 438 | 429 1 6.00587 7.00587 30.0767 -8.70539 439 | 430 1 7.00754 9.01058 28.4801 -8.77435 440 | 431 1 9.00892 8.01726 30.0817 -8.69324 441 | 432 1 2.00619 9.01287 30.0558 -8.79795 442 | 433 1 10.003 0.00567218 31.6693 -8.83515 443 | 434 1 3.00478 1.01817 31.6266 -8.49459 444 | 435 1 4.99676 0.0167976 33.1209 -8.44211 445 | 436 1 5.997 2.02642 31.6528 -8.78843 446 | 437 1 7.99749 0.945184 33.2943 -8.69781 447 | 438 1 9.02255 2.97076 31.654 -8.77277 448 | 439 1 1.10029 2.03307 33.317 -8.7507 449 | 440 1 1.99816 4.01186 31.621 -8.50896 450 | 441 1 3.87658 3.00775 33.3447 -8.72512 451 | 442 1 4.99898 5.00974 31.6693 -8.83515 452 | 443 1 7.03907 4.02706 33.1548 -8.35521 453 | 444 1 8.00885 6.02224 31.6266 -8.49459 454 | 445 1 10.0008 5.02086 33.1209 -8.44211 455 | 446 1 0.992937 7.03049 31.6528 -8.78843 456 | 447 1 2.99342 5.94925 33.2943 -8.69781 457 | 448 1 4.01848 7.97482 31.654 -8.77277 458 | 449 1 6.10436 7.03714 33.317 -8.7507 459 | 450 1 7.00222 9.01592 31.621 -8.50896 460 | 451 1 8.88064 8.01182 33.3447 -8.72512 461 | 452 1 2.035 9.03112 33.1548 -8.35521 462 | 453 1 0.152793 0.00224348 34.7607 -8.18684 463 | 454 1 3.3402 0.639511 35.1603 -8.76996 464 | 455 1 4.36145 8.67119 37.3755 -8.40981 465 | 456 1 6.01973 2.11238 34.7646 -8.69013 466 | 457 1 8.25158 1.05238 36.5091 -8.55452 467 | 458 1 8.93517 2.95735 34.7825 -8.51986 468 | 459 1 1.18692 1.87897 36.3083 -8.32546 469 | 460 1 1.48395 4.30787 35.2093 -8.46835 470 | 461 1 3.78656 3.175 36.2866 -8.50176 471 | 462 1 5.15686 5.00631 34.7607 -8.18684 472 | 463 1 6.67121 3.902 36.9292 -8.78372 473 | 464 1 8.34426 5.64358 35.1603 -8.76996 474 | 465 1 0.542591 6.15426 37.2205 -8.38844 475 | 466 1 1.01567 7.11645 34.7646 -8.69013 476 | 467 1 3.24751 6.05645 36.5091 -8.55452 477 | 468 1 3.9311 7.96141 34.7825 -8.51986 478 | 469 1 6.19098 6.88304 36.3083 -8.32546 479 | 470 1 6.48801 9.31194 35.2093 -8.46835 480 | 471 1 8.79062 8.17907 36.2866 -8.50176 481 | 472 1 1.66714 8.90607 36.9292 -8.78372 482 | Egb = 2.29691598776671 483 | -------------------------------------------------------------------------------- /.examples/W_310_twist/params.yaml: -------------------------------------------------------------------------------- 1 | # Input data for the GRand canonical Interface Predictor (GRIP). Format is YAML. 2 | 3 | # Parameters for the algorithm 4 | algo: 5 | dir_struct: 'best' # Folder to store best structures. 6 | dir_calcs: 'calc_procs' # Folder to store temporary calculation files. 7 | ngrid: 100 # Number of grid points in each dim = ngrid * nprocs. 8 | frac_min: 0.00 # Minimum fraction of atoms on a plane (0 <= n <= 1). 9 | frac_max: 1.00 # Maximum fraction of atoms on a plane. Set both to 1.0 for gamma-surface. 10 | gb_gap: 0.3 # Initial gap between slabs prior to MD/relaxation (in Ang.). 11 | perturb_u: 0.3 # Maximum random perturbation (A) of atoms above GB 12 | perturb_l: 0.0 # Maximum random perturbation (A) of atoms below GB 13 | gb_thick: 10 # Thickness of GB region (in Angstrom) on either side of interface. 14 | pad: 10 # Extra padding (A) on top of gb_thick for relaxation / energy calculations. 15 | vacuum: 1 # Vacuum to add on top for MD (A); less needed for s boundary. 16 | 17 | inter_p: 0.0 # Probability of swapping with interstitial sites. [0.0, 1.0] = [Never, Always]. 18 | inter_s: 'W' # species of atom to insert. 19 | inter_n: 2 # Number of GB interstitial sites to swap with atoms in GB region. 20 | inter_t: 1.5 # Thickness of region (A) on either side of GB to search for interstitials. 21 | inter_u: False # Only choose unique interstitial sites. 22 | inter_r: True # Randomly choose interstitial sites vs. largest volume 23 | inter_w: 2 # How to swap: 1 = only subs, 2 = only inter, 3 = uniform, 4 = mostly subs, 5 = mostly inter 24 | 25 | MD_run: 0.95 # Probability of running MD simulation before relaxing. [0.0, 1.0] = [Never, Always]. 26 | Tmin: 1000 # Temperature lower bound for MD simulation. 27 | Tmax: 2500 # Temperature upper bound, vary in multiple of 100s. 28 | MD_min: 5000 # Min steps for MD simulation. 29 | MD_max: 300000 # Max steps for MD simulation. 30 | var_steps: 2 # 0 = Min steps only; 1 = linear sample; 2 = exponential sample 31 | 32 | lammps_bin: '/g/g16/chen120/bin/lammps_serial' # Path to [serial] LAMMPS binary. 33 | Emult: 2 # Maximum energy threshold * Egb_min to keep; at least 1.0. 34 | nruns: 0 # Number of iterations in total (each processor). Set 0 for infinite loop. 35 | clear_freq: 50 # Number of iterations before clearing duplicates. Set 0 to never clear. 36 | 37 | 38 | # Parameters for the material 39 | struct: 40 | user: False # True: read existing cells (POSCAR_*), False: generate w/ ase. 41 | cutoff: 35 # Max height (A) to cut slabs if user=False; speed up calcs. Set to 0 to ignore. 42 | write: True # Write generated cells to POSCAR_* 43 | size0: [1, 1, 1] # Minimum replications in [x, y, z] to create supercells. 44 | size: [3, 3, 15] # Replications in [x, y, z] to create supercells. z is not used if user=True. 45 | reps: 2 # Sample replications (1) exactly, (2) uniform, (3) weighted smaller, (4) weighted larger. 46 | 47 | # Basic info - potential dependent! 48 | upper_dirs: [ [3, 1, 0], [-1, 3, 0], [0, 0, 1] ] # W(310) twist 49 | lower_dirs: [ [3, -1, 0], [1, 3, 0], [0, 0, 1] ] 50 | symbol: 'W' # Chemical formula 51 | crystal: 'bcc' # fcc, bcc, hcp, or dc 52 | mass: 183.84 # Atomic mass 53 | a: 3.164849 # a lattice constant 54 | c: 3.164849 # c lattice constant; only used for hcp 55 | dlat: 0 # Minimal normal component of lattice vector to calculate Nplane. Set 0 to ignore. 56 | Ecoh: -8.76 # Energy per atom in bulk 57 | pair_style: 'eam/alloy' # pair_style for LAMMPS 58 | pair_coeff: '* * /g/g16/chen120/lammps/pots/W.eam.alloy W' # pair_coeff for LAMMPS 59 | 60 | -------------------------------------------------------------------------------- /.examples/W_552_tilt/Marinica_2013/lammps_2.732_0.500_0.83_2.47_1_2_3300_24000: -------------------------------------------------------------------------------- 1 | ITEM: TIMESTEP 2 | 0 3 | ITEM: NUMBER OF ATOMS 4 | 471 5 | ITEM: BOX BOUNDS pp pp ss 6 | 0.0000000000000000e+00 8.1579593036494149e+00 7 | 0.0000000000000000e+00 8.8812611717030396e+00 8 | -1.0026682790216613e-02 1.0042982056374944e+02 9 | ITEM: ATOMS id type x y z c_eng 10 | 1 1 0.516804 4.35259 52.2835 -8.13156 11 | 2 1 3.61507 4.47005 52.8024 -8.89383 12 | 3 1 4.49524 4.45682 55.5335 -8.8747 13 | 4 1 5.43482 4.45074 58.1188 -8.91524 14 | 5 1 6.34498 4.44901 60.6819 -8.90078 15 | 6 1 7.25156 4.44844 63.245 -8.89989 16 | 7 1 2.72672e-05 4.44828 65.8085 -8.89994 17 | 8 1 0.90645 4.44823 68.3723 -8.89997 18 | 9 1 1.81288 4.44823 70.9361 -8.89998 19 | 10 1 3.03461 6.67101 55.1069 -8.73259 20 | 11 1 3.92367 6.67356 57.6736 -8.88514 21 | 12 1 4.83302 6.66974 60.2496 -8.90319 22 | 13 1 5.74049 6.66878 62.8165 -8.90084 23 | 14 1 6.64715 6.66859 65.381 -8.90016 24 | 15 1 7.55365 6.66855 67.9449 -8.90002 25 | 16 1 0.302145 6.66854 70.5087 -8.89999 26 | 17 1 1.20859 6.66854 73.0726 -8.89998 27 | 18 1 1.86975 7.7774 50.2099 -8.41109 28 | 19 1 5.19796 6.68135 53.36 -8.87044 29 | 20 1 6.02989 6.67118 55.9911 -8.89847 30 | 21 1 6.94925 6.67046 58.544 -8.89792 31 | 22 1 7.85556 6.66915 61.1078 -8.89868 32 | 23 1 0.604201 6.66869 63.6718 -8.8999 33 | 24 1 1.51071 6.66857 66.2357 -8.89999 34 | 25 1 2.41717 6.66854 68.7995 -8.89998 35 | 26 1 4.12981 6.60695 50.9372 -8.59194 36 | 27 1 6.61384 4.43464 53.9354 -8.51973 37 | 28 1 7.55374 4.45104 56.4304 -8.8606 38 | 29 1 0.302388 4.44983 58.975 -8.89039 39 | 30 1 1.20871 4.44875 61.5361 -8.89953 40 | 31 1 2.11509 4.44835 64.0994 -8.89996 41 | 32 1 5.97939 4.49864 51.3621 -8.53826 42 | 33 1 8.11312 6.66361 54.2209 -8.89889 43 | 34 1 0.90765 6.67458 56.8175 -8.91265 44 | 35 1 1.81241 6.67057 59.3957 -8.90645 45 | 36 1 7.32913 2.21007 51.4793 -8.54783 46 | 37 1 1.53229 4.45523 54.7347 -8.94639 47 | 38 1 2.41789 4.45257 57.2748 -8.89036 48 | 39 1 2.07059 6.64006 52.6237 -8.69788 49 | 40 1 3.32386 4.45013 59.8297 -8.89201 50 | 41 1 4.23021 4.44874 62.3905 -8.89887 51 | 42 1 5.13653 4.44833 64.9539 -8.89986 52 | 43 1 6.04294 4.44825 67.5177 -8.89997 53 | 44 1 6.94938 4.44823 70.0815 -8.89998 54 | 45 1 7.85581 4.44822 72.6453 -8.89998 55 | 46 1 2.7192 6.66902 61.9621 -8.90115 56 | 47 1 3.62572 6.66864 64.5264 -8.90007 57 | 48 1 4.53219 6.66856 67.0903 -8.9 58 | 49 1 5.43864 6.66854 69.6541 -8.89998 59 | 50 1 6.34508 6.66854 72.218 -8.89998 60 | 51 1 3.02149 4.44825 66.6631 -8.89996 61 | 52 1 3.92791 4.44823 69.2269 -8.89997 62 | 53 1 4.83435 4.44822 71.7907 -8.89998 63 | 54 1 3.32361 6.66854 71.3634 -8.89998 64 | 55 1 2.71932 4.44822 73.4999 -8.89998 65 | 56 1 3.62576 4.44822 76.0637 -8.89998 66 | 57 1 4.5322 4.44822 78.6275 -8.89998 67 | 58 1 5.43864 4.44822 81.1912 -8.89998 68 | 59 1 6.34508 4.44822 83.755 -8.89998 69 | 60 1 7.25152 4.44822 86.3188 -8.89998 70 | 61 1 1.81772e-06 4.44822 88.8826 -8.89998 71 | 62 1 0.906442 4.44822 91.4464 -8.89998 72 | 63 1 1.81288 4.44822 94.0102 -8.89998 73 | 64 1 3.02147 6.66854 78.2002 -8.89998 74 | 65 1 3.92791 6.66854 80.7639 -8.89998 75 | 66 1 4.83435 6.66854 83.3277 -8.89998 76 | 67 1 5.74079 6.66854 85.8915 -8.89998 77 | 68 1 6.64723 6.66854 88.4553 -8.89998 78 | 69 1 7.55367 6.66854 91.0191 -8.89998 79 | 70 1 0.302148 6.66854 93.5829 -8.89998 80 | 71 1 1.20859 6.66854 96.1467 -8.91055 81 | 72 1 4.23005 6.66854 73.9272 -8.89998 82 | 73 1 5.13649 6.66854 76.491 -8.89998 83 | 74 1 6.04293 6.66854 79.0548 -8.89998 84 | 75 1 6.94937 6.66854 81.6185 -8.89998 85 | 76 1 7.85581 6.66854 84.1823 -8.89998 86 | 77 1 0.604295 6.66854 86.7461 -8.89998 87 | 78 1 1.51074 6.66854 89.3099 -8.89998 88 | 79 1 2.41717 6.66854 91.8737 -8.89998 89 | 80 1 5.74079 4.44822 74.3545 -8.89998 90 | 81 1 6.64723 4.44822 76.9183 -8.89998 91 | 82 1 7.55367 4.44822 79.482 -8.89998 92 | 83 1 0.302148 4.44822 82.0458 -8.89998 93 | 84 1 1.20859 4.44822 84.6096 -8.89998 94 | 85 1 2.11503 4.44822 87.1734 -8.89998 95 | 86 1 7.25152 6.66854 74.7818 -8.89998 96 | 87 1 1.81772e-06 6.66854 77.3456 -8.89998 97 | 88 1 0.906442 6.66854 79.9093 -8.89998 98 | 89 1 1.81288 6.66854 82.4731 -8.89998 99 | 90 1 0.604295 4.44822 75.2091 -8.89998 100 | 91 1 1.51074 4.44822 77.7729 -8.89998 101 | 92 1 2.41717 4.44822 80.3366 -8.89998 102 | 93 1 2.11503 6.66854 75.6364 -8.89998 103 | 94 1 3.32361 4.44822 82.9004 -8.89998 104 | 95 1 4.23005 4.44822 85.4642 -8.89998 105 | 96 1 5.13649 4.44822 88.028 -8.89998 106 | 97 1 6.04293 4.44822 90.5918 -8.89998 107 | 98 1 6.94937 4.44822 93.1556 -8.89998 108 | 99 1 7.85581 4.44822 95.7194 -8.89999 109 | 100 1 2.71932 6.66854 85.0369 -8.89998 110 | 101 1 3.62576 6.66854 87.6007 -8.89998 111 | 102 1 4.5322 6.66854 90.1645 -8.89998 112 | 103 1 5.43864 6.66854 92.7283 -8.89998 113 | 104 1 6.34508 6.66854 95.2921 -8.89998 114 | 105 1 3.02147 4.44822 89.7372 -8.89998 115 | 106 1 3.92791 4.44822 92.301 -8.89998 116 | 107 1 4.83435 4.44822 94.8648 -8.89998 117 | 108 1 3.32361 6.66854 94.4375 -8.89998 118 | 109 1 2.71932 4.44822 96.574 -8.91611 119 | 110 1 3.62576 4.44822 99.1378 -7.83773 120 | 111 1 4.23005 6.66854 97.0013 -8.92667 121 | 112 1 5.13649 6.66854 99.5651 -7.85861 122 | 113 1 5.74079 4.44822 97.4286 -8.93195 123 | 114 1 6.64723 4.44822 99.9924 -7.60504 124 | 115 1 7.25152 6.66854 97.8559 -8.94308 125 | 116 1 1.81772e-06 6.66854 100.42 -6.80401 126 | 117 1 0.604295 4.44822 98.2832 -8.6482 127 | 118 1 2.11503 6.66854 98.7105 -8.16469 128 | 119 1 3.5514 0.00675854 52.6566 -8.99722 129 | 120 1 4.51008 8.8803 55.4843 -8.87505 130 | 121 1 5.43396 0.00490351 58.1079 -8.91886 131 | 122 1 6.34482 0.0067315 60.6797 -8.90261 132 | 123 1 7.25142 0.00736262 63.2445 -8.9003 133 | 124 1 8.15794 0.00753778 65.8084 -8.90002 134 | 125 1 0.906437 0.00758008 68.3723 -8.89998 135 | 126 1 1.81288 0.00758944 70.9361 -8.89998 136 | 127 1 3.04947 2.22699 55.1829 -8.69041 137 | 128 1 3.93237 2.22421 57.7027 -8.86733 138 | 129 1 4.83516 2.22672 60.2559 -8.89907 139 | 130 1 5.74095 2.22765 62.8179 -8.89996 140 | 131 1 6.64726 2.22785 65.3813 -8.89996 141 | 132 1 7.55368 2.2279 67.945 -8.89998 142 | 133 1 0.302152 2.22791 70.5088 -8.89998 143 | 134 1 1.20859 2.22791 73.0726 -8.89998 144 | 135 1 4.12981 0.0665897 49.4826 -8.59194 145 | 136 1 5.19397 2.21244 53.4491 -8.87315 146 | 137 1 6.03719 2.22363 56.0066 -8.90909 147 | 138 1 6.95185 2.22555 58.5509 -8.89589 148 | 139 1 7.85646 2.22724 61.1098 -8.8976 149 | 140 1 0.604456 2.22776 63.6723 -8.89956 150 | 141 1 1.51078 2.22788 66.2358 -8.89992 151 | 142 1 2.41719 2.2279 68.7996 -8.89997 152 | 143 1 2.11884 4.40456 47.7022 -8.31194 153 | 144 1 6.6544 0.0113296 53.8936 -8.49169 154 | 145 1 7.55583 0.00220452 56.4075 -8.87235 155 | 146 1 0.302541 0.00589552 58.9684 -8.89678 156 | 147 1 1.20844 0.00707282 61.5346 -8.90121 157 | 148 1 2.11499 0.00746498 64.0991 -8.90024 158 | 149 1 5.95708 8.8215 51.3427 -8.59335 159 | 150 1 8.11943 2.22299 54.2645 -8.97636 160 | 151 1 0.910723 2.22277 56.8327 -8.89645 161 | 152 1 1.81288 2.22595 59.4002 -8.90257 162 | 153 1 0.544827 0.0453365 52.1743 -8.71139 163 | 154 1 1.53193 0.00466756 54.6625 -8.93356 164 | 155 1 2.41952 0.0032361 57.2535 -8.89586 165 | 156 1 2.11884 2.26897 52.7176 -8.31194 166 | 157 1 3.32334 0.00583091 59.8244 -8.89659 167 | 158 1 4.22995 0.00708136 62.3895 -8.89981 168 | 159 1 5.13644 0.00747803 64.9537 -8.90002 169 | 160 1 6.04292 0.00756747 67.5176 -8.9 170 | 161 1 6.94937 0.00758684 70.0814 -8.89999 171 | 162 1 7.85581 0.00759241 72.6453 -8.89998 172 | 163 1 2.71946 2.22746 61.9633 -8.89992 173 | 164 1 3.62582 2.22781 64.5267 -8.89974 174 | 165 1 4.53222 2.22789 67.0904 -8.89994 175 | 166 1 5.43864 2.2279 69.6542 -8.89997 176 | 167 1 6.34508 2.22791 72.218 -8.89998 177 | 168 1 3.02146 0.00756234 66.663 -8.90002 178 | 169 1 3.9279 0.00758552 69.2268 -8.89999 179 | 170 1 4.83435 0.00759067 71.7907 -8.89998 180 | 171 1 3.32362 2.22791 71.3634 -8.89998 181 | 172 1 2.71932 0.00759241 73.4999 -8.89998 182 | 173 1 3.62576 0.00759241 76.0637 -8.89998 183 | 174 1 4.5322 0.00759241 78.6275 -8.89998 184 | 175 1 5.43864 0.00759241 81.1912 -8.89998 185 | 176 1 6.34508 0.00759241 83.755 -8.89998 186 | 177 1 7.25152 0.00759241 86.3188 -8.89998 187 | 178 1 1.81772e-06 0.00759241 88.8826 -8.89998 188 | 179 1 0.906442 0.00759241 91.4464 -8.89998 189 | 180 1 1.81288 0.00759241 94.0102 -8.89998 190 | 181 1 3.02147 2.22791 78.2002 -8.89998 191 | 182 1 3.92791 2.22791 80.7639 -8.89998 192 | 183 1 4.83435 2.22791 83.3277 -8.89998 193 | 184 1 5.74079 2.22791 85.8915 -8.89998 194 | 185 1 6.64723 2.22791 88.4553 -8.89998 195 | 186 1 7.55367 2.22791 91.0191 -8.89998 196 | 187 1 0.302148 2.22791 93.5829 -8.89998 197 | 188 1 1.20859 2.22791 96.1467 -8.91055 198 | 189 1 4.23005 2.22791 73.9272 -8.89998 199 | 190 1 5.13649 2.22791 76.491 -8.89998 200 | 191 1 6.04293 2.22791 79.0548 -8.89998 201 | 192 1 6.94937 2.22791 81.6185 -8.89998 202 | 193 1 7.85581 2.22791 84.1823 -8.89998 203 | 194 1 0.604295 2.22791 86.7461 -8.89998 204 | 195 1 1.51074 2.22791 89.3099 -8.89998 205 | 196 1 2.41717 2.22791 91.8737 -8.89998 206 | 197 1 5.74079 0.00759241 74.3545 -8.89998 207 | 198 1 6.64723 0.00759241 76.9183 -8.89998 208 | 199 1 7.55367 0.00759241 79.482 -8.89998 209 | 200 1 0.302148 0.00759241 82.0458 -8.89998 210 | 201 1 1.20859 0.00759241 84.6096 -8.89998 211 | 202 1 2.11503 0.00759241 87.1734 -8.89998 212 | 203 1 7.25152 2.22791 74.7818 -8.89998 213 | 204 1 1.81772e-06 2.22791 77.3456 -8.89998 214 | 205 1 0.906442 2.22791 79.9093 -8.89998 215 | 206 1 1.81288 2.22791 82.4731 -8.89998 216 | 207 1 0.604295 0.00759241 75.2091 -8.89998 217 | 208 1 1.51074 0.00759241 77.7729 -8.89998 218 | 209 1 2.41717 0.00759241 80.3366 -8.89998 219 | 210 1 2.11503 2.22791 75.6364 -8.89998 220 | 211 1 3.32361 0.00759241 82.9004 -8.89998 221 | 212 1 4.23005 0.00759241 85.4642 -8.89998 222 | 213 1 5.13649 0.00759241 88.028 -8.89998 223 | 214 1 6.04293 0.00759241 90.5918 -8.89998 224 | 215 1 6.94937 0.00759241 93.1556 -8.89998 225 | 216 1 7.85581 0.00759241 95.7194 -8.89999 226 | 217 1 2.71932 2.22791 85.0369 -8.89998 227 | 218 1 3.62576 2.22791 87.6007 -8.89998 228 | 219 1 4.5322 2.22791 90.1645 -8.89998 229 | 220 1 5.43864 2.22791 92.7283 -8.89998 230 | 221 1 6.34508 2.22791 95.2921 -8.89998 231 | 222 1 3.02147 0.00759241 89.7372 -8.89998 232 | 223 1 3.92791 0.00759241 92.301 -8.89998 233 | 224 1 4.83435 0.00759241 94.8648 -8.89998 234 | 225 1 3.32361 2.22791 94.4375 -8.89998 235 | 226 1 2.71932 0.00759241 96.574 -8.91611 236 | 227 1 3.62576 0.00759241 99.1378 -7.83773 237 | 228 1 4.23005 2.22791 97.0013 -8.92667 238 | 229 1 5.13649 2.22791 99.5651 -7.85861 239 | 230 1 5.74079 0.00759241 97.4286 -8.93195 240 | 231 1 6.64723 0.00759241 99.9924 -7.60504 241 | 232 1 7.25152 2.22791 97.8559 -8.94308 242 | 233 1 1.81772e-06 2.22791 100.42 -6.80401 243 | 234 1 0.604295 0.00759241 98.2832 -8.6482 244 | 235 1 2.11503 2.22791 98.7105 -8.16469 245 | 236 1 0 0.005 5e-05 -6.80401 246 | 237 1 2.11503 0.005 1.70925 -8.16469 247 | 238 1 4.23005 0.005 3.41845 -8.92667 248 | 239 1 6.34508 0.005 5.12765 -8.89998 249 | 240 1 3.62576 2.22532 1.28195 -7.83773 250 | 241 1 5.74079 2.22532 2.99115 -8.93195 251 | 242 1 7.85581 2.22532 4.70035 -8.89999 252 | 243 1 0.604293 2.22532 2.13655 -8.6482 253 | 244 1 2.71932 2.22532 3.84575 -8.91611 254 | 245 1 4.83435 2.22532 5.55495 -8.89998 255 | 246 1 6.94937 2.22532 7.26415 -8.89998 256 | 247 1 1.20859 0.005 4.27305 -8.91055 257 | 248 1 3.32361 0.005 5.98225 -8.89998 258 | 249 1 5.43864 0.005 7.69145 -8.89998 259 | 250 1 7.55367 0.005 9.40065 -8.89998 260 | 251 1 1.81288 2.22532 6.40955 -8.89998 261 | 252 1 3.92791 2.22532 8.11875 -8.89998 262 | 253 1 6.04293 2.22532 9.82795 -8.89998 263 | 254 1 0.302147 0.005 6.83685 -8.89998 264 | 255 1 2.41717 0.005 8.54605 -8.89998 265 | 256 1 4.5322 0.005 10.2552 -8.89998 266 | 257 1 6.64723 0.005 11.9644 -8.89998 267 | 258 1 0.90644 2.22532 8.97335 -8.89998 268 | 259 1 3.02147 2.22532 10.6825 -8.89998 269 | 260 1 5.13649 2.22532 12.3917 -8.89998 270 | 261 1 7.25152 2.22532 14.1009 -8.89998 271 | 262 1 1.51073 0.005 11.1098 -8.89998 272 | 263 1 3.62576 0.005 12.819 -8.89998 273 | 264 1 5.74079 0.005 14.5282 -8.89998 274 | 265 1 7.85581 0.005 16.2374 -8.89998 275 | 266 1 0 2.22532 11.5371 -8.89998 276 | 267 1 2.11503 2.22532 13.2463 -8.89998 277 | 268 1 4.23005 2.22532 14.9555 -8.89998 278 | 269 1 6.34508 2.22532 16.6647 -8.89998 279 | 270 1 0.604293 0.005 13.6736 -8.89998 280 | 271 1 2.71932 0.005 15.3828 -8.89998 281 | 272 1 4.83435 0.005 17.092 -8.89998 282 | 273 1 6.94937 0.005 18.8012 -8.89998 283 | 274 1 1.20859 2.22532 15.8101 -8.89998 284 | 275 1 3.32361 2.22532 17.5193 -8.89998 285 | 276 1 5.43864 2.22532 19.2285 -8.89998 286 | 277 1 7.55367 2.22532 20.9377 -8.89998 287 | 278 1 1.81288 0.005 17.9466 -8.89998 288 | 279 1 3.92791 0.005 19.6558 -8.89998 289 | 280 1 6.04293 0.005 21.365 -8.89998 290 | 281 1 0.302147 2.22532 18.3739 -8.89998 291 | 282 1 2.41717 2.22532 20.0831 -8.89998 292 | 283 1 4.5322 2.22532 21.7923 -8.89998 293 | 284 1 0.90644 0.005 20.5104 -8.89998 294 | 285 1 3.02147 0.005 22.2196 -8.89998 295 | 286 1 1.51073 2.22532 22.6469 -8.89998 296 | 287 1 5.13649 0.005 0.85465 -7.85861 297 | 288 1 7.25152 0.005 2.56385 -8.94308 298 | 289 1 6.64723 2.22532 0.42735 -7.60504 299 | 290 1 0 0.005 23.0742 -8.89998 300 | 291 1 2.11503 0.005 24.7834 -8.89998 301 | 292 1 4.23005 0.005 26.4926 -8.89998 302 | 293 1 6.34508 0.005 28.2018 -8.89998 303 | 294 1 3.62576 2.22532 24.3561 -8.89998 304 | 295 1 5.74079 2.22532 26.0653 -8.89998 305 | 296 1 7.85581 2.22532 27.7745 -8.89998 306 | 297 1 0.604293 2.22532 25.2107 -8.89998 307 | 298 1 2.71932 2.22532 26.9199 -8.89998 308 | 299 1 4.83435 2.22531 28.6291 -8.89998 309 | 300 1 6.94937 2.22531 30.3383 -8.89998 310 | 301 1 1.20859 0.005 27.3472 -8.89998 311 | 302 1 3.32361 0.00499885 29.0564 -8.89998 312 | 303 1 5.43864 0.0049964 30.7656 -8.89998 313 | 304 1 7.55365 0.00499023 32.4749 -8.90002 314 | 305 1 1.81288 2.22531 29.4837 -8.89998 315 | 306 1 3.92791 2.22531 31.1929 -8.89997 316 | 307 1 6.04294 2.22529 32.9021 -8.89997 317 | 308 1 0.302144 0.00499807 29.911 -8.89999 318 | 309 1 2.41717 0.00499407 31.6203 -8.89998 319 | 310 1 4.53218 0.00498066 33.3295 -8.9 320 | 311 1 6.64715 0.0049513 35.0388 -8.90016 321 | 312 1 0.906449 2.2253 32.0475 -8.89997 322 | 313 1 3.02149 2.22529 33.7567 -8.89996 323 | 314 1 5.13653 2.2252 35.4659 -8.89986 324 | 315 1 7.25156 2.2251 37.1748 -8.89989 325 | 316 1 1.51071 0.0049686 34.1841 -8.89999 326 | 317 1 3.62572 0.0048979 35.8934 -8.90007 327 | 318 1 5.74049 0.00475622 37.6033 -8.90084 328 | 319 1 7.85556 0.00438268 39.312 -8.89868 329 | 320 1 2.66624e-05 2.22526 34.6113 -8.89994 330 | 321 1 2.11509 2.22518 36.3204 -8.89996 331 | 322 1 4.23021 2.22479 38.0293 -8.89887 332 | 323 1 6.34498 2.22453 39.7379 -8.90078 333 | 324 1 0.604201 0.00484913 36.748 -8.8999 334 | 325 1 2.7192 0.00451754 38.4577 -8.90115 335 | 326 1 4.83302 0.00380143 40.1702 -8.90319 336 | 327 1 6.94925 0.00307895 41.8758 -8.89792 337 | 328 1 1.20871 2.22478 38.8837 -8.89953 338 | 329 1 3.32386 2.22341 40.5901 -8.89201 339 | 330 1 5.43482 2.2228 42.3009 -8.91524 340 | 331 1 7.55374 2.22249 43.9894 -8.8606 341 | 332 1 1.81242 0.0029646 41.0241 -8.90645 342 | 333 1 3.92367 8.88124 42.7461 -8.88514 343 | 334 1 6.02989 0.00235389 44.4286 -8.89847 344 | 335 1 0.302388 2.22371 41.4448 -8.89039 345 | 336 1 2.41789 2.22097 43.145 -8.89036 346 | 337 1 4.49524 2.21672 44.8863 -8.8747 347 | 338 1 0.90765 8.88022 43.6023 -8.91265 348 | 339 1 3.03461 0.0025267 45.3129 -8.73259 349 | 340 1 1.53229 2.21831 45.6851 -8.94639 350 | 341 1 5.13649 0.005 23.9288 -8.89998 351 | 342 1 7.25152 0.005 25.638 -8.89998 352 | 343 1 6.64723 2.22532 23.5015 -8.89998 353 | 344 1 8.11312 0.00992372 46.1988 -8.89889 354 | 345 1 2.07059 0.0334768 47.7961 -8.69788 355 | 346 1 5.95708 6.7333 49.0771 -8.59335 356 | 347 1 5.19796 8.87345 47.0598 -8.87044 357 | 348 1 1.84501 5.13921 50.2107 -7.96316 358 | 349 1 1.84501 1.53433 50.2091 -7.96316 359 | 350 1 4.23615 2.27748 51.0051 -8.25126 360 | 351 1 6.65441 6.66221 46.5261 -8.49169 361 | 352 1 5.97939 2.1749 49.0577 -8.53826 362 | 353 1 6.61384 2.2389 46.4844 -8.51973 363 | 354 1 0 4.44563 5e-05 -6.80401 364 | 355 1 2.11503 4.44563 1.70925 -8.16469 365 | 356 1 4.23005 4.44563 3.41845 -8.92667 366 | 357 1 6.34508 4.44563 5.12765 -8.89998 367 | 358 1 3.62576 6.66595 1.28195 -7.83773 368 | 359 1 5.74079 6.66595 2.99115 -8.93195 369 | 360 1 7.85581 6.66595 4.70035 -8.89999 370 | 361 1 0.604293 6.66595 2.13655 -8.6482 371 | 362 1 2.71932 6.66595 3.84575 -8.91611 372 | 363 1 4.83435 6.66595 5.55495 -8.89998 373 | 364 1 6.94937 6.66595 7.26415 -8.89998 374 | 365 1 1.20859 4.44563 4.27305 -8.91055 375 | 366 1 3.32361 4.44563 5.98225 -8.89998 376 | 367 1 5.43864 4.44563 7.69145 -8.89998 377 | 368 1 7.55367 4.44563 9.40065 -8.89998 378 | 369 1 1.81288 6.66595 6.40955 -8.89998 379 | 370 1 3.92791 6.66595 8.11875 -8.89998 380 | 371 1 6.04293 6.66595 9.82795 -8.89998 381 | 372 1 0.302147 4.44563 6.83685 -8.89998 382 | 373 1 2.41717 4.44563 8.54605 -8.89998 383 | 374 1 4.5322 4.44563 10.2552 -8.89998 384 | 375 1 6.64723 4.44563 11.9644 -8.89998 385 | 376 1 0.90644 6.66595 8.97335 -8.89998 386 | 377 1 3.02147 6.66595 10.6825 -8.89998 387 | 378 1 5.13649 6.66595 12.3917 -8.89998 388 | 379 1 7.25152 6.66595 14.1009 -8.89998 389 | 380 1 1.51073 4.44563 11.1098 -8.89998 390 | 381 1 3.62576 4.44563 12.819 -8.89998 391 | 382 1 5.74079 4.44563 14.5282 -8.89998 392 | 383 1 7.85581 4.44563 16.2374 -8.89998 393 | 384 1 0 6.66595 11.5371 -8.89998 394 | 385 1 2.11503 6.66595 13.2463 -8.89998 395 | 386 1 4.23005 6.66595 14.9555 -8.89998 396 | 387 1 6.34508 6.66595 16.6647 -8.89998 397 | 388 1 0.604293 4.44563 13.6736 -8.89998 398 | 389 1 2.71932 4.44563 15.3828 -8.89998 399 | 390 1 4.83435 4.44563 17.092 -8.89998 400 | 391 1 6.94937 4.44563 18.8012 -8.89998 401 | 392 1 1.20859 6.66595 15.8101 -8.89998 402 | 393 1 3.32361 6.66595 17.5193 -8.89998 403 | 394 1 5.43864 6.66595 19.2285 -8.89998 404 | 395 1 7.55367 6.66595 20.9377 -8.89998 405 | 396 1 1.81288 4.44563 17.9466 -8.89998 406 | 397 1 3.92791 4.44563 19.6558 -8.89998 407 | 398 1 6.04293 4.44563 21.365 -8.89998 408 | 399 1 0.302147 6.66595 18.3739 -8.89998 409 | 400 1 2.41717 6.66595 20.0831 -8.89998 410 | 401 1 4.5322 6.66595 21.7923 -8.89998 411 | 402 1 0.90644 4.44563 20.5104 -8.89998 412 | 403 1 3.02147 4.44563 22.2196 -8.89998 413 | 404 1 1.51073 6.66595 22.6469 -8.89998 414 | 405 1 5.13649 4.44563 0.85465 -7.85861 415 | 406 1 7.25152 4.44563 2.56385 -8.94308 416 | 407 1 6.64723 6.66595 0.42735 -7.60504 417 | 408 1 0 4.44563 23.0742 -8.89998 418 | 409 1 2.11503 4.44563 24.7834 -8.89998 419 | 410 1 4.23005 4.44563 26.4926 -8.89998 420 | 411 1 6.34508 4.44563 28.2018 -8.89998 421 | 412 1 3.62576 6.66595 24.3561 -8.89998 422 | 413 1 5.74079 6.66595 26.0653 -8.89998 423 | 414 1 7.85581 6.66595 27.7745 -8.89998 424 | 415 1 0.604293 6.66595 25.2107 -8.89998 425 | 416 1 2.71932 6.66595 26.9199 -8.89998 426 | 417 1 4.83435 6.66595 28.6291 -8.89998 427 | 418 1 6.94937 6.66595 30.3383 -8.89999 428 | 419 1 1.20859 4.44563 27.3472 -8.89998 429 | 420 1 3.32362 4.44563 29.0564 -8.89998 430 | 421 1 5.43864 4.44563 30.7656 -8.89997 431 | 422 1 7.55368 4.44564 32.4748 -8.89998 432 | 423 1 1.81288 6.66595 29.4837 -8.89998 433 | 424 1 3.9279 6.66595 31.1929 -8.89999 434 | 425 1 6.04292 6.66597 32.9022 -8.9 435 | 426 1 0.30215 4.44563 29.911 -8.89998 436 | 427 1 2.41718 4.44564 31.6202 -8.89997 437 | 428 1 4.53222 4.44565 33.3294 -8.89994 438 | 429 1 6.64726 4.44568 35.0385 -8.89996 439 | 430 1 0.906436 6.66596 32.0475 -8.89998 440 | 431 1 3.02146 6.66598 33.7568 -8.90002 441 | 432 1 5.13644 6.66606 35.4661 -8.90002 442 | 433 1 7.25142 6.66618 37.1753 -8.9003 443 | 434 1 1.51078 4.44566 34.184 -8.89992 444 | 435 1 3.62582 4.44573 35.8931 -8.89974 445 | 436 1 5.74095 4.44589 37.6019 -8.89996 446 | 437 1 7.85647 4.4463 39.31 -8.8976 447 | 438 1 8.15794 6.666 34.6114 -8.90002 448 | 439 1 2.11499 6.66607 36.3207 -8.90024 449 | 440 1 4.22995 6.66646 38.0303 -8.89981 450 | 441 1 6.34482 6.66681 39.7401 -8.90261 451 | 442 1 0.604456 4.44578 36.7475 -8.89956 452 | 443 1 2.71946 4.44608 38.4565 -8.89992 453 | 444 1 4.83516 4.44682 40.1639 -8.89907 454 | 445 1 6.95185 4.44799 41.8688 -8.89589 455 | 446 1 1.20844 6.66646 38.8852 -8.90121 456 | 447 1 3.32334 6.66771 40.5954 -8.89659 457 | 448 1 5.43396 6.66863 42.3119 -8.91886 458 | 449 1 7.55583 6.67133 44.0123 -8.87235 459 | 450 1 1.81288 4.44758 41.0195 -8.90257 460 | 451 1 3.93237 4.44932 42.7171 -8.86733 461 | 452 1 6.03719 4.44991 44.4131 -8.90909 462 | 453 1 0.302541 6.66764 41.4514 -8.89678 463 | 454 1 2.41952 6.6703 43.1663 -8.89586 464 | 455 1 4.51008 6.67449 44.9355 -8.87505 465 | 456 1 0.910723 4.45076 43.5871 -8.89645 466 | 457 1 3.04947 4.44655 45.2369 -8.69041 467 | 458 1 1.53193 6.66887 45.7573 -8.93356 468 | 459 1 5.13649 4.44563 23.9288 -8.89998 469 | 460 1 7.25152 4.44563 25.638 -8.89998 470 | 461 1 6.64723 6.66595 23.5015 -8.89998 471 | 462 1 8.11943 4.45055 46.1553 -8.97636 472 | 463 1 3.61507 2.20349 47.6174 -8.89383 473 | 464 1 4.23615 4.39606 49.4147 -8.25126 474 | 465 1 3.5514 6.66678 47.7632 -8.99722 475 | 466 1 7.32913 4.46347 48.9405 -8.54783 476 | 467 1 7.56221 0.0239834 49.1328 -8.75225 477 | 468 1 7.56221 6.64955 51.287 -8.75225 478 | 469 1 5.19398 4.4611 46.9707 -8.87315 479 | 470 1 0.516804 2.32095 48.1363 -8.13156 480 | 471 1 0.544827 6.6282 48.2455 -8.71139 481 | Egb = 2.73154631318894 482 | -------------------------------------------------------------------------------- /.examples/W_552_tilt/Marinica_2013/lammps_3.047_0.000_1.37_1.49_1_1_1700_0: -------------------------------------------------------------------------------- 1 | ITEM: TIMESTEP 2 | 0 3 | ITEM: NUMBER OF ATOMS 4 | 236 5 | ITEM: BOX BOUNDS pp pp ss 6 | 0.0000000000000000e+00 8.1579593036494149e+00 7 | 0.0000000000000000e+00 4.4406305858515198e+00 8 | -1.0164277105511370e-02 1.0077228911022334e+02 9 | ITEM: ATOMS id type x y z c_eng 10 | 1 1 0.344432 1.13071 50.5947 -7.64676 11 | 2 1 2.08242 2.23547 53.1151 -8.91434 12 | 3 1 2.99877 2.2547 55.8495 -8.89411 13 | 4 1 3.92315 2.2565 58.4568 -8.91621 14 | 5 1 4.83386 2.25648 61.0236 -8.90187 15 | 6 1 5.74073 2.25643 63.5872 -8.90023 16 | 7 1 6.64724 2.25642 66.1509 -8.9 17 | 8 1 7.55368 2.25642 68.7146 -8.89997 18 | 9 1 0.302157 2.25642 71.2784 -8.89998 19 | 10 1 1.53085 0.0335489 55.4845 -8.74384 20 | 11 1 2.41569 0.0354609 58.0237 -8.87854 21 | 12 1 3.32275 0.0360844 60.5941 -8.90282 22 | 13 1 4.2298 0.0361136 63.1594 -8.90063 23 | 14 1 5.13644 0.0361067 65.7235 -8.90012 24 | 15 1 6.04293 0.0361034 68.2873 -8.90001 25 | 16 1 6.94938 0.0361019 70.8511 -8.89998 26 | 17 1 7.85582 0.0361008 73.4149 -8.89998 27 | 18 1 2.62825 0.0165222 51.3408 -8.25966 28 | 19 1 3.68555 0.0356632 53.7583 -8.92086 29 | 20 1 4.52524 0.037098 56.3424 -8.90295 30 | 21 1 5.43933 0.0364217 58.8916 -8.89822 31 | 22 1 6.34535 0.0361496 61.4518 -8.89871 32 | 23 1 7.25163 0.036107 64.0146 -8.89972 33 | 24 1 4.16968e-05 0.0361033 66.5781 -8.89993 34 | 25 1 0.906457 0.0361025 69.1419 -8.89997 35 | 26 1 4.43521 2.26814 51.7155 -8.5832 36 | 27 1 5.14018 2.26227 54.2595 -8.56208 37 | 28 1 6.04592 2.25802 56.7679 -8.8741 38 | 29 1 6.95055 2.25656 59.3163 -8.89403 39 | 30 1 7.85621 2.25642 61.8781 -8.9 40 | 31 1 0.604403 2.25642 64.4416 -8.89994 41 | 32 1 5.8953 0.0577411 51.7843 -8.57106 42 | 33 1 6.60269 0.0442905 54.6006 -8.93448 43 | 34 1 7.55735 0.0362924 57.1717 -8.90314 44 | 35 1 0.302866 0.03604 59.7403 -8.90442 45 | 36 1 7.17983 2.29522 52.5441 -8.30439 46 | 37 1 0.0122891 2.25563 55.0321 -8.95942 47 | 38 1 0.908675 2.25596 57.604 -8.89771 48 | 39 1 0.566466 0.027303 53.0147 -8.3694 49 | 40 1 1.8129 2.25629 60.1678 -8.89222 50 | 41 1 2.71924 2.25641 62.7319 -8.89962 51 | 42 1 3.62571 2.25642 65.2961 -8.9 52 | 43 1 4.53219 2.25642 67.86 -8.9 53 | 44 1 5.43864 2.25642 70.4238 -8.89999 54 | 45 1 6.34509 2.25642 72.9876 -8.89998 55 | 46 1 1.20875 0.03608 62.3048 -8.89989 56 | 47 1 2.11506 0.0361013 64.8688 -8.89982 57 | 48 1 3.02147 0.0361034 67.4326 -8.89996 58 | 49 1 3.92791 0.0361024 69.9965 -8.89998 59 | 50 1 4.83435 0.0361008 72.5603 -8.89998 60 | 51 1 1.51076 2.25642 67.0054 -8.89995 61 | 52 1 2.41718 2.25642 69.5692 -8.89997 62 | 53 1 3.32362 2.25642 72.133 -8.89998 63 | 54 1 1.81289 0.0361016 71.7057 -8.89998 64 | 55 1 1.20859 2.25642 73.8422 -8.89998 65 | 56 1 2.11503 2.25642 76.406 -8.89998 66 | 57 1 3.02147 2.25642 78.9698 -8.89998 67 | 58 1 3.92791 2.25642 81.5336 -8.89998 68 | 59 1 4.83435 2.25642 84.0974 -8.89998 69 | 60 1 5.74079 2.25642 86.6612 -8.89998 70 | 61 1 6.64723 2.25642 89.225 -8.89998 71 | 62 1 7.55367 2.25642 91.7888 -8.89998 72 | 63 1 0.302154 2.25642 94.3526 -8.89998 73 | 64 1 1.51074 0.0361008 78.5425 -8.89998 74 | 65 1 2.41718 0.0361008 81.1063 -8.89998 75 | 66 1 3.32362 0.0361008 83.6701 -8.89998 76 | 67 1 4.23006 0.0361008 86.2339 -8.89998 77 | 68 1 5.1365 0.0361008 88.7977 -8.89998 78 | 69 1 6.04294 0.0361008 91.3615 -8.89998 79 | 70 1 6.94938 0.0361008 93.9253 -8.89998 80 | 71 1 7.85582 0.0361008 96.4891 -8.91055 81 | 72 1 2.71933 0.0361008 74.2695 -8.89998 82 | 73 1 3.62577 0.0361008 76.8333 -8.89998 83 | 74 1 4.53221 0.0361008 79.3971 -8.89998 84 | 75 1 5.43865 0.0361008 81.9609 -8.89998 85 | 76 1 6.34509 0.0361008 84.5247 -8.89998 86 | 77 1 7.25153 0.0361008 87.0885 -8.89998 87 | 78 1 7.60458e-06 0.0361008 89.6523 -8.89998 88 | 79 1 0.906448 0.0361008 92.2161 -8.89998 89 | 80 1 4.23006 2.25642 74.6968 -8.89998 90 | 81 1 5.1365 2.25642 77.2606 -8.89998 91 | 82 1 6.04294 2.25642 79.8244 -8.89998 92 | 83 1 6.94938 2.25642 82.3882 -8.89998 93 | 84 1 7.85582 2.25642 84.952 -8.89998 94 | 85 1 0.604301 2.25642 87.5158 -8.89998 95 | 86 1 5.74079 0.0361008 75.1241 -8.89998 96 | 87 1 6.64723 0.0361008 77.6879 -8.89998 97 | 88 1 7.55367 0.0361008 80.2517 -8.89998 98 | 89 1 0.302154 0.0361008 82.8155 -8.89998 99 | 90 1 7.25153 2.25642 75.5514 -8.89998 100 | 91 1 7.60458e-06 2.25642 78.1152 -8.89998 101 | 92 1 0.906448 2.25642 80.679 -8.89998 102 | 93 1 0.604301 0.0361008 75.9787 -8.89998 103 | 94 1 1.81289 2.25642 83.2428 -8.89998 104 | 95 1 2.71933 2.25642 85.8066 -8.89998 105 | 96 1 3.62577 2.25642 88.3704 -8.89998 106 | 97 1 4.53221 2.25642 90.9342 -8.89998 107 | 98 1 5.43865 2.25642 93.498 -8.89998 108 | 99 1 6.34509 2.25642 96.0618 -8.89999 109 | 100 1 1.20859 0.0361008 85.3793 -8.89998 110 | 101 1 2.11503 0.0361008 87.9431 -8.89998 111 | 102 1 3.02147 0.0361008 90.5069 -8.89998 112 | 103 1 3.92791 0.0361008 93.0707 -8.89998 113 | 104 1 4.83435 0.0361008 95.6345 -8.89998 114 | 105 1 1.51074 2.25642 90.0796 -8.89998 115 | 106 1 2.41718 2.25642 92.6434 -8.89998 116 | 107 1 3.32362 2.25642 95.2072 -8.89998 117 | 108 1 1.81289 0.0361008 94.7799 -8.89998 118 | 109 1 1.20859 2.25642 96.9164 -8.91611 119 | 110 1 2.11503 2.25642 99.4802 -7.83773 120 | 111 1 2.71933 0.0361008 97.3437 -8.92667 121 | 112 1 3.62577 0.0361008 99.9075 -7.85861 122 | 113 1 4.23006 2.25642 97.771 -8.93195 123 | 114 1 5.1365 2.25642 100.335 -7.60504 124 | 115 1 5.74079 0.0361008 98.1983 -8.94308 125 | 116 1 6.64723 0.0361008 100.762 -6.80401 126 | 117 1 7.25153 2.25642 98.6256 -8.6482 127 | 118 1 0.604301 0.0361008 99.0529 -8.16469 128 | 119 1 0 0.005 5e-05 -6.80401 129 | 120 1 2.11503 0.005 1.70925 -8.16469 130 | 121 1 4.23005 0.005 3.41845 -8.92667 131 | 122 1 6.34508 0.005 5.12765 -8.89998 132 | 123 1 3.62576 2.22532 1.28195 -7.83773 133 | 124 1 5.74079 2.22532 2.99115 -8.93195 134 | 125 1 7.85581 2.22532 4.70035 -8.89999 135 | 126 1 0.604293 2.22532 2.13655 -8.6482 136 | 127 1 2.71932 2.22532 3.84575 -8.91611 137 | 128 1 4.83435 2.22532 5.55495 -8.89998 138 | 129 1 6.94937 2.22532 7.26415 -8.89998 139 | 130 1 1.20859 0.005 4.27305 -8.91055 140 | 131 1 3.32361 0.005 5.98225 -8.89998 141 | 132 1 5.43864 0.005 7.69145 -8.89998 142 | 133 1 7.55367 0.005 9.40065 -8.89998 143 | 134 1 1.81288 2.22532 6.40955 -8.89998 144 | 135 1 3.92791 2.22532 8.11875 -8.89998 145 | 136 1 6.04293 2.22532 9.82795 -8.89998 146 | 137 1 0.302147 0.005 6.83685 -8.89998 147 | 138 1 2.41717 0.005 8.54605 -8.89998 148 | 139 1 4.5322 0.005 10.2552 -8.89998 149 | 140 1 6.64723 0.005 11.9644 -8.89998 150 | 141 1 0.90644 2.22532 8.97335 -8.89998 151 | 142 1 3.02147 2.22532 10.6825 -8.89998 152 | 143 1 5.13649 2.22532 12.3917 -8.89998 153 | 144 1 7.25152 2.22532 14.1009 -8.89998 154 | 145 1 1.51073 0.005 11.1098 -8.89998 155 | 146 1 3.62576 0.005 12.819 -8.89998 156 | 147 1 5.74079 0.005 14.5282 -8.89998 157 | 148 1 7.85581 0.005 16.2374 -8.89998 158 | 149 1 0 2.22532 11.5371 -8.89998 159 | 150 1 2.11503 2.22532 13.2463 -8.89998 160 | 151 1 4.23005 2.22532 14.9555 -8.89998 161 | 152 1 6.34508 2.22532 16.6647 -8.89998 162 | 153 1 0.604293 0.005 13.6736 -8.89998 163 | 154 1 2.71932 0.005 15.3828 -8.89998 164 | 155 1 4.83435 0.005 17.092 -8.89998 165 | 156 1 6.94937 0.005 18.8012 -8.89998 166 | 157 1 1.20859 2.22532 15.8101 -8.89998 167 | 158 1 3.32361 2.22532 17.5193 -8.89998 168 | 159 1 5.43864 2.22532 19.2285 -8.89998 169 | 160 1 7.55367 2.22532 20.9377 -8.89998 170 | 161 1 1.81288 0.005 17.9466 -8.89998 171 | 162 1 3.92791 0.005 19.6558 -8.89998 172 | 163 1 6.04293 0.005 21.365 -8.89998 173 | 164 1 0.302147 2.22532 18.3739 -8.89998 174 | 165 1 2.41717 2.22532 20.0831 -8.89998 175 | 166 1 4.5322 2.22532 21.7923 -8.89998 176 | 167 1 0.90644 0.005 20.5104 -8.89998 177 | 168 1 3.02147 0.005 22.2196 -8.89998 178 | 169 1 1.51073 2.22532 22.6469 -8.89998 179 | 170 1 5.13649 0.005 0.85465 -7.85861 180 | 171 1 7.25152 0.005 2.56385 -8.94308 181 | 172 1 6.64723 2.22532 0.42735 -7.60504 182 | 173 1 0 0.005 23.0742 -8.89998 183 | 174 1 2.11503 0.005 24.7834 -8.89998 184 | 175 1 4.23005 0.005 26.4926 -8.89998 185 | 176 1 6.34508 0.005 28.2018 -8.89998 186 | 177 1 3.62576 2.22532 24.3561 -8.89998 187 | 178 1 5.74079 2.22532 26.0653 -8.89998 188 | 179 1 7.85581 2.22532 27.7745 -8.89998 189 | 180 1 0.604293 2.22532 25.2107 -8.89998 190 | 181 1 2.71932 2.22532 26.9199 -8.89998 191 | 182 1 4.83435 2.22531 28.6291 -8.89998 192 | 183 1 6.94937 2.22531 30.3383 -8.89998 193 | 184 1 1.20859 0.005 27.3472 -8.89998 194 | 185 1 3.32361 0.00499919 29.0564 -8.89998 195 | 186 1 5.43864 0.00499846 30.7656 -8.89999 196 | 187 1 7.55367 0.00499784 32.4748 -8.89997 197 | 188 1 1.81288 2.22531 29.4837 -8.89998 198 | 189 1 3.9279 2.22531 31.193 -8.89998 199 | 190 1 6.04292 2.22531 32.9021 -8.90001 200 | 191 1 0.30215 0.00499897 29.911 -8.89998 201 | 192 1 2.41718 0.00499823 31.6202 -8.89997 202 | 193 1 4.53218 0.00499697 33.3295 -8.9 203 | 194 1 6.64723 0.00499571 35.0386 -8.9 204 | 195 1 0.906451 2.22531 32.0475 -8.89997 205 | 196 1 3.02146 2.22531 33.7568 -8.89996 206 | 197 1 5.13644 2.22531 35.466 -8.90012 207 | 198 1 7.25162 2.22531 37.1748 -8.89972 208 | 199 1 1.51076 0.00499789 34.1841 -8.89995 209 | 200 1 3.62571 0.00499559 35.8934 -8.9 210 | 201 1 5.74072 0.00498495 37.6022 -8.90023 211 | 202 1 7.8562 0.00499949 39.3113 -8.9 212 | 203 1 3.61405e-05 2.22531 34.6113 -8.89993 213 | 204 1 2.11505 2.22531 36.3207 -8.89982 214 | 205 1 4.2298 2.2253 38.03 -8.90063 215 | 206 1 6.34535 2.22527 39.7376 -8.89871 216 | 207 1 0.604398 0.00500058 36.7478 -8.89994 217 | 208 1 2.71924 0.00500705 38.4575 -8.89962 218 | 209 1 4.83386 0.0049402 40.1658 -8.90187 219 | 210 1 6.95054 0.00485191 41.8731 -8.89403 220 | 211 1 1.20875 2.22534 38.8847 -8.89989 221 | 212 1 3.32275 2.22533 40.5953 -8.90282 222 | 213 1 5.43933 2.225 42.2978 -8.89822 223 | 214 1 7.55735 2.22512 44.0178 -8.90314 224 | 215 1 1.8129 0.0051269 41.0216 -8.89222 225 | 216 1 3.92315 0.0049191 42.7326 -8.91621 226 | 217 1 6.04591 0.00339757 44.4215 -8.8741 227 | 218 1 0.302863 2.22538 41.4492 -8.90442 228 | 219 1 2.41569 2.22596 43.1657 -8.87854 229 | 220 1 4.52524 2.22432 44.847 -8.90295 230 | 221 1 0.908673 0.00545699 43.5854 -8.89771 231 | 222 1 2.99876 0.00671565 45.3399 -8.89411 232 | 223 1 1.53085 2.22787 45.7049 -8.74384 233 | 224 1 5.13649 0.005 23.9288 -8.89998 234 | 225 1 7.25152 0.005 25.638 -8.89998 235 | 226 1 6.64723 2.22532 23.5015 -8.89998 236 | 227 1 0.0122875 0.0057901 46.1573 -8.95942 237 | 228 1 2.08242 0.0259508 48.0744 -8.91434 238 | 229 1 4.43521 4.43391 49.4739 -8.5832 239 | 230 1 3.68555 2.22575 47.4312 -8.92086 240 | 231 1 5.8953 2.20368 49.4051 -8.57106 241 | 232 1 0.566465 2.23411 48.1747 -8.3694 242 | 233 1 2.62825 2.2449 49.8486 -8.25966 243 | 234 1 5.14018 4.43978 46.9299 -8.56208 244 | 235 1 7.17983 4.40683 48.6454 -8.30439 245 | 236 1 6.60269 2.21713 46.5888 -8.93448 246 | Egb = 3.04731230584712 247 | -------------------------------------------------------------------------------- /.examples/W_552_tilt/Marinica_2013/params.yaml: -------------------------------------------------------------------------------- 1 | # Input data for the GRand canonical Interface Predictor (GRIP). Format is YAML. 2 | 3 | # Parameters for the algorithm 4 | algo: 5 | dir_struct: 'best' # Folder to store best structures. 6 | dir_calcs: 'calc_procs' # Folder to store temporary calculation files. 7 | ngrid: 100 # Number of grid points in each dim = ngrid * nprocs. 8 | frac_min: 0.00 # Minimum fraction of atoms on a plane (0 <= n <= 1). 9 | frac_max: 1.00 # Maximum fraction of atoms on a plane. Set both to 1.0 for gamma-surface. 10 | gb_gap: 0.3 # Initial gap between slabs prior to MD/relaxation (in Ang.). 11 | perturb_u: 0.3 # Maximum random perturbation (A) of atoms above GB 12 | perturb_l: 0.0 # Maximum random perturbation (A) of atoms below GB 13 | gb_thick: 10 # Thickness of GB region (in Angstrom) on either side of interface. 14 | pad: 10 # Extra padding (A) on top of gb_thick for relaxation / energy calculations. 15 | vacuum: 1 # Vacuum to add on top for MD (A); less needed for s boundary. 16 | 17 | inter_p: 0.0 # Probability of swapping with interstitial sites. [0.0, 1.0] = [Never, Always]. 18 | inter_s: 'W' # species of atom to insert. 19 | inter_n: 2 # Number of GB interstitial sites to swap with atoms in GB region. 20 | inter_t: 1.5 # Thickness of region (A) on either side of GB to search for interstitials. 21 | inter_u: False # Only choose unique interstitial sites. 22 | inter_r: True # Randomly choose interstitial sites vs. largest volume 23 | inter_w: 2 # How to swap: 1 = only subs, 2 = only inter, 3 = uniform, 4 = mostly subs, 5 = mostly inter 24 | 25 | MD_run: 0.95 # Probability of running MD simulation before relaxing. [0.0, 1.0] = [Never, Always]. 26 | Tmin: 1000 # Temperature lower bound for MD simulation. 27 | Tmax: 2500 # Temperature upper bound, vary in multiple of 100s. 28 | MD_min: 5000 # Min steps for MD simulation. 29 | MD_max: 300000 # Max steps for MD simulation. 30 | var_steps: 2 # 0 = Min steps only; 1 = linear sample; 2 = exponential sample 31 | 32 | lammps_bin: '/g/g16/chen120/bin/lammps_serial' # Path to [serial] LAMMPS binary. 33 | Emult: 2 # Maximum energy threshold * Egb_min to keep; at least 1.0. 34 | nruns: 0 # Number of iterations in total (each processor). Set 0 for infinite loop. 35 | clear_freq: 50 # Number of iterations before clearing duplicates. Set 0 to never clear. 36 | 37 | 38 | # Parameters for the material 39 | struct: 40 | user: False # True: read existing cells (POSCAR_*), False: generate w/ ase. 41 | cutoff: 50 # Max height (A) to cut slabs if user=False; speed up calcs. Set to 0 to ignore. 42 | write: True # Write generated cells to POSCAR_* 43 | size0: [1, 1, 1] # Minimum replications in [x, y, z] to create supercells. 44 | size: [4, 7, 15] # Replications in [x, y, z] to create supercells. z is not used if user=True. 45 | reps: 2 # Sample replications (1) exactly, (2) uniform, (3) weighted smaller, (4) weighted larger. 46 | 47 | # Basic info - potential dependent! 48 | upper_dirs: [ [1, 1, 5], [-1, 1, 0], [-5, -5, 2] ] # W(552) tilt 49 | lower_dirs: [ [1, 1, -5], [-1, 1, 0], [5, 5, 2] ] 50 | symbol: 'W' # Chemical formula 51 | crystal: 'bcc' # fcc, bcc, hcp, or dc 52 | mass: 183.84 # Atomic mass 53 | a: 3.14 # a lattice constant 54 | c: 3.14 # c lattice constant; only used for hcp 55 | dlat: 0 # Minimal normal component of lattice vector to calculate Nplane. Set 0 to ignore. 56 | Ecoh: -8.9 # Energy per atom in bulk 57 | pair_style: 'eam/fs' # pair_style for LAMMPS 58 | pair_coeff: '* * /g/g16/chen120/lammps/pots/W.eam.fs W' # pair_coeff for LAMMPS 59 | 60 | 61 | -------------------------------------------------------------------------------- /.examples/W_552_tilt/Zhou_2004/lammps_2.869_0.00_2.40_0.03_1_1_2700_0: -------------------------------------------------------------------------------- 1 | ITEM: TIMESTEP 2 | 0 3 | ITEM: NUMBER OF ATOMS 4 | 164 5 | ITEM: BOX BOUNDS pp pp ss 6 | 0.0000000000000000e+00 8.2225188994253315e+00 7 | 0.0000000000000000e+00 4.4757723786629278e+00 8 | -7.3131749262502557e-03 7.0464569430593116e+01 9 | ITEM: ATOMS id type x y z c_eng 10 | 1 1 3.53892 0.00500126 35.8665 -7.74216 11 | 2 1 4.56663 0.00500169 38.1379 -8.16365 12 | 3 1 5.24169 0.00500177 40.7855 -8.8305 13 | 4 1 6.17127 0.00500177 43.3356 -8.76218 14 | 5 1 7.08222 0.00500189 45.9115 -8.75681 15 | 6 1 7.99509 0.00500204 48.4933 -8.75921 16 | 7 1 0.686006 0.00500227 51.0767 -8.75967 17 | 8 1 1.5995 0.00500241 53.6606 -8.75993 18 | 9 1 2.51312 0.00500241 56.2447 -8.75999 19 | 10 1 3.69126 2.24289 40.2991 -8.65731 20 | 11 1 4.63894 2.24289 42.8983 -8.79662 21 | 12 1 5.55838 2.24289 45.4797 -8.76622 22 | 13 1 6.47207 2.24289 48.0627 -8.76105 23 | 14 1 7.38574 2.24289 50.6462 -8.76018 24 | 15 1 0.0768133 2.24289 53.23 -8.75997 25 | 16 1 0.990426 2.24289 55.814 -8.75999 26 | 17 1 1.90404 2.24289 58.3981 -8.75999 27 | 18 1 5.20444 2.24289 35.9104 -8.67266 28 | 19 1 5.77414 2.24289 38.7595 -7.92288 29 | 20 1 6.78821 2.24289 41.202 -8.67645 30 | 21 1 7.69572 2.24289 43.759 -8.737 31 | 22 1 0.382218 2.24289 46.3399 -8.75624 32 | 23 1 1.29524 2.24289 48.9232 -8.75919 33 | 24 1 2.20858 2.24289 51.5072 -8.75974 34 | 25 1 3.12219 2.24289 54.0913 -8.75999 35 | 26 1 6.71025 0.00500113 35.6192 -8.81557 36 | 27 1 7.3687 0.00500173 38.9908 -8.73634 37 | 28 1 0.0907173 0.00500178 41.5859 -8.80553 38 | 29 1 0.991029 0.00500183 44.1823 -8.75941 39 | 30 1 1.90414 0.00500194 46.7686 -8.76012 40 | 31 1 2.81766 0.00500211 49.3534 -8.75977 41 | 32 1 7.8115 2.24289 37.202 -7.6356 42 | 33 1 0.720613 2.24289 39.4849 -8.52899 43 | 34 1 1.6059 2.24289 42.0254 -8.64798 44 | 35 1 2.51203 2.24289 44.6135 -8.75217 45 | 36 1 1.08947 0.00500154 37.0877 -8.2771 46 | 37 1 2.23116 0.00500179 39.7463 -8.71987 47 | 38 1 3.10698 0.00500182 42.4437 -8.76939 48 | 39 1 2.78837 2.24289 37.5606 -8.78199 49 | 40 1 4.03286 0.00500187 45.0428 -8.76874 50 | 41 1 4.94871 0.005002 47.6304 -8.76227 51 | 42 1 5.86283 0.00500218 50.2152 -8.76072 52 | 43 1 6.77664 0.00500241 52.7993 -8.76016 53 | 44 1 7.69026 0.00500241 55.3834 -8.75999 54 | 45 1 0.381351 0.00500241 57.9674 -8.75999 55 | 46 1 3.42638 2.24289 47.1992 -8.75893 56 | 47 1 4.34014 2.24289 49.7842 -8.75996 57 | 48 1 5.25395 2.24289 52.3686 -8.76007 58 | 49 1 6.16757 2.24289 54.9527 -8.75999 59 | 50 1 7.08118 2.24289 57.5368 -8.75999 60 | 51 1 3.73127 0.00500241 51.9379 -8.76 61 | 52 1 4.64488 0.00500241 54.522 -8.75999 62 | 53 1 5.55849 0.00500241 57.1061 -8.75999 63 | 54 1 4.0358 2.24289 56.6754 -8.75999 64 | 55 1 3.42673 0.00500241 58.8288 -8.75999 65 | 56 1 4.34034 0.00500241 61.4129 -8.75999 66 | 57 1 5.25395 0.00500241 63.997 -8.75999 67 | 58 1 6.16757 0.00500241 66.5811 -8.75991 68 | 59 1 7.08118 0.00500241 69.1652 -7.62235 69 | 60 1 3.73127 2.24289 63.5663 -8.75999 70 | 61 1 4.64488 2.24289 66.1504 -8.75999 71 | 62 1 5.55849 2.24289 68.7345 -7.93439 72 | 63 1 4.94942 2.24289 59.2595 -8.75999 73 | 64 1 5.86303 2.24289 61.8436 -8.75999 74 | 65 1 6.77664 2.24289 64.4277 -8.75999 75 | 66 1 7.69026 2.24289 67.0118 -8.75991 76 | 67 1 0.381351 2.24289 69.5958 -7.62218 77 | 68 1 6.47211 0.00500241 59.6902 -8.75999 78 | 69 1 7.38572 0.00500241 62.2743 -8.75999 79 | 70 1 0.0768133 0.00500241 64.8583 -8.75999 80 | 71 1 0.990426 0.00500241 67.4424 -8.75991 81 | 72 1 1.90404 0.00500241 70.0265 -7.32523 82 | 73 1 7.99479 2.24289 60.1209 -8.75999 83 | 74 1 0.685889 2.24289 62.7049 -8.75999 84 | 75 1 1.5995 2.24289 65.289 -8.75999 85 | 76 1 2.51312 2.24289 67.8731 -8.75975 86 | 77 1 1.29496 0.00500241 60.5515 -8.75999 87 | 78 1 2.20858 0.00500241 63.1356 -8.75999 88 | 79 1 3.12219 0.00500241 65.7197 -8.75999 89 | 80 1 2.81765 2.24289 60.9822 -8.75999 90 | 81 1 4.0358 0.00500241 68.3038 -8.47822 91 | 82 1 3.42673 2.24289 70.4572 -6.41377 92 | 83 1 0 0.005 5e-05 -6.41377 93 | 84 1 2.13176 0.005 1.72278 -7.93439 94 | 85 1 4.26353 0.005 3.4455 -8.75991 95 | 86 1 6.39529 0.005 5.16823 -8.75999 96 | 87 1 3.65445 2.24289 1.29209 -7.62235 97 | 88 1 5.78622 2.24289 3.01482 -8.75991 98 | 89 1 7.91798 2.24289 4.73755 -8.75999 99 | 90 1 0.609075 2.24289 2.15346 -8.47822 100 | 91 1 2.74084 2.24289 3.87618 -8.75991 101 | 92 1 4.8726 2.24289 5.59891 -8.75999 102 | 93 1 7.00437 2.24289 7.32163 -8.75999 103 | 94 1 1.21815 0.005 4.30686 -8.75999 104 | 95 1 3.34992 0.005 6.02959 -8.75999 105 | 96 1 5.48168 0.005 7.75232 -8.75999 106 | 97 1 7.61344 0.005 9.47504 -8.75999 107 | 98 1 1.82723 2.24289 6.46027 -8.75999 108 | 99 1 3.95899 2.24289 8.183 -8.75999 109 | 100 1 6.09075 2.24289 9.90572 -8.75999 110 | 101 1 0.304538 0.005 6.89095 -8.75999 111 | 102 1 2.4363 0.005 8.61368 -8.75999 112 | 103 1 4.56807 0.005 10.3364 -8.75999 113 | 104 1 6.69983 0.005 12.0591 -8.75999 114 | 105 1 0.913613 2.24289 9.04436 -8.75999 115 | 106 1 3.04538 2.24289 10.7671 -8.75999 116 | 107 1 5.17714 2.24289 12.4898 -8.75999 117 | 108 1 7.30891 2.24289 14.2125 -8.75999 118 | 109 1 1.52269 0.005 11.1978 -8.75999 119 | 110 1 3.65445 0.005 12.9205 -8.75999 120 | 111 1 5.78622 0.005 14.6432 -8.75999 121 | 112 1 7.91798 0.005 16.3659 -8.75999 122 | 113 1 0 2.24289 11.6284 -8.75999 123 | 114 1 2.13176 2.24289 13.3512 -8.75999 124 | 115 1 4.26353 2.24289 15.0739 -8.75999 125 | 116 1 6.39529 2.24289 16.7966 -8.75999 126 | 117 1 0.609075 0.005 13.7819 -8.75999 127 | 118 1 2.74084 0.005 15.5046 -8.75999 128 | 119 1 4.8726 0.005 17.2273 -8.75997 129 | 120 1 7.00437 0.005 18.95 -8.75998 130 | 121 1 1.21815 2.24289 15.9353 -8.75999 131 | 122 1 3.34992 2.24289 17.658 -8.76002 132 | 123 1 5.48171 2.24289 19.3807 -8.7599 133 | 124 1 7.61341 2.24289 21.1035 -8.76001 134 | 125 1 1.82723 0.005 18.0887 -8.76003 135 | 126 1 3.95903 0.00500008 19.8113 -8.75995 136 | 127 1 6.09078 0.00500021 21.5342 -8.7599 137 | 128 1 0.304538 2.24289 18.5194 -8.76002 138 | 129 1 2.43629 2.24289 20.242 -8.76014 139 | 130 1 4.56817 2.24289 21.9647 -8.75962 140 | 131 1 0.913564 0.00500019 20.6728 -8.76007 141 | 132 1 3.04546 0.00500025 22.3952 -8.76004 142 | 133 1 1.52258 2.24289 22.8261 -8.76064 143 | 134 1 5.17714 0.005 0.861413 -7.62218 144 | 135 1 7.30891 0.005 2.58414 -8.75975 145 | 136 1 6.69983 2.24289 0.430731 -7.32523 146 | 137 1 8.22236 0.0050003 23.257 -8.75995 147 | 138 1 2.13188 0.0050003 24.9786 -8.76088 148 | 139 1 4.26385 0.00500033 26.7026 -8.75785 149 | 140 1 6.39438 0.00500036 28.4262 -8.75419 150 | 141 1 3.65478 2.24289 24.5483 -8.7587 151 | 142 1 5.78618 2.24289 26.2727 -8.76154 152 | 143 1 7.91597 2.24289 27.9974 -8.76672 153 | 144 1 0.608548 2.24289 25.4107 -8.76194 154 | 145 1 2.74195 2.24289 27.1302 -8.75417 155 | 146 1 4.87156 2.24289 28.8593 -8.76807 156 | 147 1 6.99031 2.24289 30.5911 -8.77116 157 | 148 1 1.21854 0.00500033 27.5614 -8.76557 158 | 149 1 3.35278 0.00500045 29.287 -8.73652 159 | 150 1 5.48227 0.00500057 31.009 -8.67838 160 | 151 1 7.56665 0.00500065 32.7324 -8.77677 161 | 152 1 1.83377 2.24289 29.706 -8.7446 162 | 153 1 3.96725 2.24289 31.4638 -8.80356 163 | 154 1 6.08886 2.24289 33.2573 -8.52102 164 | 155 1 0.302 0.00500048 30.1426 -8.80289 165 | 156 1 2.45296 0.00500062 31.8607 -8.65189 166 | 157 1 4.62591 0.00500078 33.5706 -8.52563 167 | 158 1 0.914657 2.24289 32.2455 -8.79998 168 | 159 1 3.03738 2.24289 34.1033 -8.74232 169 | 160 1 1.43721 0.00500073 34.3069 -8.00803 170 | 161 1 0.0682914 2.24289 34.7774 -7.99951 171 | 162 1 5.17728 0.00500029 24.1184 -8.75958 172 | 163 1 7.30864 0.0050003 25.8417 -8.75867 173 | 164 1 6.69979 2.24289 23.6879 -8.76004 174 | Egb = 2.86852169460812 175 | -------------------------------------------------------------------------------- /.examples/W_552_tilt/Zhou_2004/params.yaml: -------------------------------------------------------------------------------- 1 | # Input data for the GRand canonical Interface Predictor (GRIP). Format is YAML. 2 | 3 | # Parameters for the algorithm 4 | algo: 5 | dir_struct: 'best' # Folder to store best structures. 6 | dir_calcs: 'calc_procs' # Folder to store temporary calculation files. 7 | ngrid: 100 # Number of grid points in each dim = ngrid * nprocs. 8 | frac_min: 0.00 # Minimum fraction of atoms on a plane (0 <= n <= 1). 9 | frac_max: 1.00 # Maximum fraction of atoms on a plane. Set both to 1.0 for gamma-surface. 10 | gb_gap: 0.3 # Initial gap between slabs prior to MD/relaxation (in Ang.). 11 | perturb_u: 0.3 # Maximum random perturbation (A) of atoms above GB 12 | perturb_l: 0.0 # Maximum random perturbation (A) of atoms below GB 13 | gb_thick: 10 # Thickness of GB region (in Angstrom) on either side of interface. 14 | pad: 10 # Extra padding (A) on top of gb_thick for relaxation / energy calculations. 15 | vacuum: 1 # Vacuum to add on top for MD (A); less needed for s boundary. 16 | 17 | inter_p: 0.0 # Probability of swapping with interstitial sites. [0.0, 1.0] = [Never, Always]. 18 | inter_s: 'W' # species of atom to insert. 19 | inter_n: 2 # Number of GB interstitial sites to swap with atoms in GB region. 20 | inter_t: 1.5 # Thickness of region (A) on either side of GB to search for interstitials. 21 | inter_u: False # Only choose unique interstitial sites. 22 | inter_r: True # Randomly choose interstitial sites vs. largest volume 23 | inter_w: 2 # How to swap: 1 = only subs, 2 = only inter, 3 = uniform, 4 = mostly subs, 5 = mostly inter 24 | 25 | MD_run: 0.95 # Probability of running MD simulation before relaxing. [0.0, 1.0] = [Never, Always]. 26 | Tmin: 1000 # Temperature lower bound for MD simulation. 27 | Tmax: 2500 # Temperature upper bound, vary in multiple of 100s. 28 | MD_min: 5000 # Min steps for MD simulation. 29 | MD_max: 300000 # Max steps for MD simulation. 30 | var_steps: 2 # 0 = Min steps only; 1 = linear sample; 2 = exponential sample 31 | 32 | lammps_bin: '/g/g16/chen120/bin/lammps_serial' # Path to [serial] LAMMPS binary. 33 | Emult: 2 # Maximum energy threshold * Egb_min to keep; at least 1.0. 34 | nruns: 0 # Number of iterations in total (each processor). Set 0 for infinite loop. 35 | clear_freq: 50 # Number of iterations before clearing duplicates. Set 0 to never clear. 36 | 37 | 38 | # Parameters for the material 39 | struct: 40 | user: False # True: read existing cells (POSCAR_*), False: generate w/ ase. 41 | cutoff: 35 # Max height (A) to cut slabs if user=False; speed up calcs. Set to 0 to ignore. 42 | write: True # Write generated cells to POSCAR_* 43 | size0: [1, 1, 1] # Minimum replications in [x, y, z] to create supercells. 44 | size: [3, 3, 15] # Replications in [x, y, z] to create supercells. z is not used if user=True. 45 | reps: 2 # Sample replications (1) exactly, (2) uniform, (3) weighted smaller, (4) weighted larger. 46 | 47 | # Basic info - potential dependent! 48 | upper_dirs: [ [1, 1, 5], [-1, 1, 0], [-5, -5, 2] ] # W(552) tilt 49 | lower_dirs: [ [1, 1, -5], [-1, 1, 0], [5, 5, 2] ] 50 | symbol: 'W' # Chemical formula 51 | crystal: 'bcc' # fcc, bcc, hcp, or dc 52 | mass: 183.84 # Atomic mass 53 | a: 3.164849 # a lattice constant 54 | c: 3.164849 # c lattice constant; only used for hcp 55 | dlat: 0 # Minimal normal component of lattice vector to calculate Nplane. Set 0 to ignore. 56 | Ecoh: -8.76 # Energy per atom in bulk 57 | pair_style: 'eam/alloy' # pair_style for LAMMPS 58 | pair_coeff: '* * /g/g16/chen120/lammps/pots/W.eam.alloy W' # pair_coeff for LAMMPS 59 | -------------------------------------------------------------------------------- /.examples/sample_pbs_submit.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash -l 2 | #PBS -A account 3 | #PBS -l nodes=1:ppn=24 4 | #PBS -N GRIP 5 | #PBS -l walltime=12:00:00 6 | #PBS -q prod 7 | #PBS -j oe 8 | #PBS -o zjob.out 9 | 10 | # ------------------------------------------------ 11 | 12 | cd ${PBS_O_WORKDIR} 13 | 14 | NNODES=`wc -l < $PBS_NODEFILE` 15 | NRANKS=24 16 | 17 | NTOTRANKS=$(( NNODES * NRANKS )) 18 | echo "Running GRIP on" $NTOTRANKS "cores." 19 | 20 | mpiexec -n ${NTOTRANKS} -ppn ${NRANKS} python3 main.py 21 | 22 | -------------------------------------------------------------------------------- /.examples/sample_slurm_submit.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | #SBATCH -A account 3 | #SBATCH -N 1 4 | #SBATCH -n 24 5 | #SBATCH -J GRIP 6 | #SBATCH -t 12:00:00 7 | #SBATCH -p pbatch 8 | #SBATCH -o zjob.o%j 9 | 10 | ########################### 11 | 12 | echo "Running GRIP on" $SLURM_NTASKS "cores on" $SLURM_CLUSTER_NAME 13 | srun -N1 -n$SLURM_NTASKS --wait=0 --kill-on-bad-exit=0 python3 main.py 14 | 15 | -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 1 | # Byte-compiled / optimized / DLL files 2 | **/__pycache__/ 3 | *.py[cod] 4 | *$py.class 5 | 6 | # User additions 7 | best* 8 | calc_procs* 9 | sub_*.sh 10 | POSCAR_* 11 | my_params.yaml 12 | zjob.* 13 | -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 1 | MIT License 2 | 3 | Copyright (c) 2024, Lawrence Livermore National Security, LLC 4 | 5 | Permission is hereby granted, free of charge, to any person obtaining a copy 6 | of this software and associated documentation files (the "Software"), to deal 7 | in the Software without restriction, including without limitation the rights 8 | to use, copy, modify, merge, publish, distribute, sublicense, and/or sell 9 | copies of the Software, and to permit persons to whom the Software is 10 | furnished to do so, subject to the following conditions: 11 | 12 | The above copyright notice and this permission notice shall be included in all 13 | copies or substantial portions of the Software. 14 | 15 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 16 | IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 17 | FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE 18 | AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 19 | LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, 20 | OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE 21 | SOFTWARE. 22 | 23 | -------------------------------------------------------------------------------- /NOTICE: -------------------------------------------------------------------------------- 1 | This work was produced under the auspices of the U.S. Department of Energy by 2 | Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344. 3 | 4 | This work was prepared as an account of work sponsored by an agency of the 5 | United States Government. Neither the United States Government nor Lawrence 6 | Livermore National Security, LLC, nor any of their employees makes any warranty, 7 | expressed or implied, or assumes any legal liability or responsibility for the 8 | accuracy, completeness, or usefulness of any information, apparatus, product, or 9 | process disclosed, or represents that its use would not infringe privately owned 10 | rights. Reference herein to any specific commercial product, process, or service 11 | by trade name, trademark, manufacturer, or otherwise does not necessarily 12 | constitute or imply its endorsement, recommendation, or favoring by the United 13 | States Government or Lawrence Livermore National Security, LLC. The views and 14 | opinions of authors expressed herein do not necessarily state or reflect those 15 | of the United States Government or Lawrence Livermore National Security, LLC, 16 | and shall not be used for advertising or product endorsement purposes. -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | # GRand canonical Interface Predictor (GRIP) 2 | 3 | _Authors: [Enze Chen](https://enze-chen.github.io/) (Stanford University) and 4 | [Timofey Frolov](https://people.llnl.gov/frolov2) (Lawrence Livermore National Laboratory)_ 5 | _Version: 0.2025.05.08_ 6 | 7 | An algorithm for performing grand canonical optimization (GCO) of interfacial 8 | structure (e.g., grain boundaries) in crystalline materials. 9 | It automates sampling of microscopic degrees of freedom and finite-temperature rearrangements. 10 | The algorithm repeatedly samples different structures in two phases: 11 | 1. Structure generation and manipulation is largely handled using the 12 | [Atomic Simulation Environment (ASE)](https://wiki.fysik.dtu.dk/ase/). 13 | 2. Dynamic sampling at finite temperatures followed by relaxation is performed using 14 | [LAMMPS](https://www.lammps.org), although in principle other energy 15 | evaluation methods (e.g., density functional theory in [VASP](https://www.vasp.at)) 16 | may be used. 17 | 18 | Video tutorials for some of the capabilities and usage patterns can be found on YouTube in our 19 | [2025 TMS presentation](https://youtu.be/QtuUdnOl1k4) and [command line examples](https://youtu.be/5BwtWnQ-JR8). 🎥 20 | 21 | ------ 22 | 23 | 24 | ## Dependencies 25 | - [Python](https://www.python.org/) (3.11.5+) 26 | - [PyYAML](https://pyyaml.org/) (6.0.1) 27 | - [NumPy](https://numpy.org/) (1.24.4) 28 | - [ASE](https://wiki.fysik.dtu.dk/ase/) (3.22.1) 29 | - [LAMMPS](https://www.lammps.org) (**serial** binary only) 30 | - [MPI for Python](https://mpi4py.readthedocs.io/en/stable) (3.1.4, for PBS resource managers only) 31 | 32 | _Optional_ 33 | - [pandas](https://pandas.pydata.org/) (1.5.3) 34 | - [Matplotlib](https://matplotlib.org/stable/index.html) (3.10.1) 35 | 36 | 37 | ## Usage 38 | 39 | GRIP functions as a collection of scripts, there's no binary that you need to install or compile. 40 | Assuming the above Python libraries are installed, clone the repo and make the 41 | appropriate modifications in `params.yaml` (see file for detailed comments), 42 | including the **path** to the LAMMPS binary on your system. 43 | You will also need the **path** to the interatomic potential file, 44 | as the code reads it from disk to avoid making unnecessary copies. 45 | 46 | If you wish, you can supply your own slabs for the bicrystal configuration as 47 | POSCAR_LOWER and POSCAR_UPPER (in the [POSCAR](https://www.vasp.at/wiki/index.php/POSCAR) 48 | file format). 49 | Then call: 50 | ```python 51 | python main.py 52 | ``` 53 | If you don't have LAMMPS or just want to test the script, you can run it with the `-d` flag. 54 | In fact, it is recommended you run it in debug mode first to ensure the proper configuration. 55 | 56 | See the `.examples` folder for a Slurm submission script for parallel execution (preferred). 57 | Note that GRIP can use multiple cores, but only those on a single node (for now). 58 | 59 | 60 | ## File structure 61 | - `main.py`: Script to launch everything. 62 | - `params.yaml`: Simulation parameters; **you'll want to edit this.** 63 | - `core`: Folder containing main classes (`Bicrystal`, `Simulation`, etc.) 64 | - `utils`: Folder containing helper functions (`utils.py`, `unique.py`, etc.) 65 | - `simul_files`: Folder containing simulation files (LAMMPS input files, etc.) 66 | - `best`: GRIP creates this folder. All relaxed structures are stored here. The naming convention is: 67 | `lammps_Egb_n_X-SHIFT_Y-SHIFT_X-REPS_Y-REPS_TEMP_STEPS` 68 | 69 | 70 | Duplicate files are periodically deleted by calling `clear_best()` in `utils/unique.py`. 71 | The default method cleans about 1-3% of files on average. 72 | Use the `-e` flag for more aggressive cleaning (>50%). 73 | Use the `-s` flag to save the processed results to CSV from a pandas DataFrame. 74 | 75 | Results can be visualized by running `python utils/plot_gco.py` and it generates a 76 | GCO plot of $E_{\mathrm{gb}}$ vs. $[n]$. 77 | The `.examples` folder has this plot for several boundaries. 78 | By default executing this file will save both the results (CSV) and the figure (PNG) 79 | to the same folder as the GRIP output files. 80 | Adding the `--file` flag with a filename will visualize the structure down the y-axis. 81 | 82 | 83 | ------ 84 | 85 | 86 | ## Areas for improvement 87 | - [x] Add parallelism for other job schedulers besides SLURM. 88 | - [ ] Create more flexible workflow classes for Monte Carlo moves, energy minimization options, etc. 89 | - [ ] Extend the code to be compatible with the parallel build of LAMMPS. 90 | - [ ] Extend the code to work on cores across multiple compute nodes. 91 | - [ ] Extend the compositional DOF to work with multi-component systems. 92 | - [ ] Add in Bayesian optimization to narrow down simulation parameters. 93 | - [ ] Incorporate ways to identify the GB atoms on the fly. 94 | - [ ] Optimize the saving of files to reduce the memory footprint (sometimes > 1 GB). 95 | - [ ] Improve the error handling if LAMMPS crashes (and resubmit?) 96 | 97 | 98 | ## Common errors 99 | 100 | - `KeyError` - GRIP is expecting a key that does not exist in your `params.yaml` file. 101 | You may have an outdated parameters file, potentially from the `.examples` folder. 102 | Check the current `params.yaml` file on GitHub for the up-to-date list. 103 | - `FileNotFoundError: No such file or directory: 'lammps_end_STRUC'` - Likely because 104 | LAMMPS failed to run correctly, so the anticipated `STRUC` files weren't generated. 105 | See log files for details. 106 | - Incorrect number of atom types - By default the STRUC file will show the number of 107 | atom types equal to the unique species in the system. Some potentials require all 108 | parameterized species to be specified even if fewer species are actually present. 109 | One solution on older ASE version is to add the `specorder` parameter to 110 | [`write_lammps_data()`](https://wiki.fysik.dtu.dk/ase/ase/io/formatoptions.html#ase.io.lammpsdata.write_lammps_data) 111 | to enforce the proper atom type assignments. 112 | 113 | 114 | ## Contributing 115 | 116 | If you encounter any errors or have a suggestion, feel free to raise an Issue or Pull Request. 117 | We'll try to respond as soon as possible! 118 | 119 | 120 | ## Citation 121 | If you use GRIP in your work, we would appreciate a citation to the [original manuscript](https://www.nature.com/articles/s41467-024-51330-9): 122 | 123 | > Enze Chen, Tae Wook Heo, Brandon C. Wood, Mark Asta, and Timofey Frolov. 124 | "Grand canonically optimized grain boundary phases in hexagonal close-packed titanium." 125 | _Nature Communications_, **15**, 7049, 2024. 126 | 127 | or in BibTeX format: 128 | 129 | ``` 130 | @article{chen_2024_grip, 131 | author = {Chen, Enze and Heo, Tae Wook and Wood, Brandon C. and Asta, Mark and Frolov, Timofey}, 132 | title = {Grand canonically optimized grain boundary phases in hexagonal close-packed titanium}, 133 | year = {2024}, 134 | journal = {Nature Communications}, 135 | volume = {15}, 136 | number = {1}, 137 | pages = {7049}, 138 | doi = {10.1038/s41467-024-51330-9}, 139 | } 140 | ``` 141 | 142 | 143 | ## License 144 | GRIP is distributed under the terms of the MIT license. 145 | All new contributions must be made under this license. 146 | 147 | SPDX-License-Identifier: MIT 148 | 149 | LLNL-CODE-XXXXXX 150 | -------------------------------------------------------------------------------- /core/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/enze-chen/grip/596c17dff5bef9b7638020a5200daf1abb3a56d0/core/__init__.py -------------------------------------------------------------------------------- /core/interstitial.py: -------------------------------------------------------------------------------- 1 | from typing import Sequence 2 | 3 | import numpy as np 4 | 5 | class Interstitial(): 6 | """ 7 | A class for constructing Interstitial site objects. 8 | 9 | Attributes: 10 | p (np.ndarray): xyz positions of the site. 11 | 12 | symbol (str): Atomic species in the interstitial. 13 | 14 | nn (n): Number of nearest neighbors to the interstitial. 15 | 16 | nnd (list): Distances to neighbors. 17 | 18 | label (str): Name of interstitial (e.g., tetrahedral) 19 | """ 20 | 21 | def __init__(self, 22 | p: Sequence[float], 23 | symbol: str=None, 24 | nn: int=None, 25 | nnd: Sequence[float]=None, 26 | label: str=None): 27 | self.p = np.asarray(p) 28 | self.symbol = symbol 29 | self.nn = nn 30 | self.nnd = np.asarray(nnd) 31 | self.label = label 32 | 33 | 34 | @classmethod 35 | def from_df(cls, df): 36 | sites = [] 37 | for a in df.itertuples(): 38 | site = cls(p=[a.x, a.y, a.z], nn=a.nn, nnd=a.nnd, label=a.label) 39 | sites.append(site) 40 | return sites 41 | 42 | def __repr__(self): 43 | return f"{self.__class__.__name__}(symbol={self.symbol}, p={self.p})" 44 | 45 | def position(self): 46 | return self.p 47 | -------------------------------------------------------------------------------- /core/simulation.py: -------------------------------------------------------------------------------- 1 | import os 2 | from subprocess import Popen, PIPE, getstatusoutput 3 | 4 | import numpy as np 5 | from ase.io.lammpsrun import read_lammps_dump 6 | 7 | from core.bicrystal import Bicrystal 8 | from utils.unique import clear_best 9 | 10 | class Simulation(): 11 | """ 12 | A class for organizing LAMMPS parameters and running LAMMPS. 13 | 14 | Attributes: 15 | root (str): The base path for the simulation. 16 | 17 | debug (bool): Flag for running in DEBUG mode. 18 | 19 | pid (int): The current process ID. 20 | 21 | cfold (str): The subfolder for the current process. 22 | 23 | Emult (float): Multiplicative factor for GB energy to save. 24 | 25 | clear_freq (int): Number of iterations before clearing duplicates. 26 | 27 | counter (int): Counter for tracking when to clear duplicates. 28 | 29 | best_Egb (float): Best GB energy value found so far. 30 | 31 | lmp (str): The path to the LAMMPS executable. 32 | 33 | md_run (float): Probably of running finite-temperature MD. 34 | 35 | md_steps0 (int): Minimum number of MD steps to run from input file. 36 | 37 | md_steps1 (int): Maximum number of MD steps to run from input file. 38 | 39 | md_steps (int): Sampled number of MD steps to run (if md_run=True). 40 | 41 | md_var (bool): Whether to vary the number of MD steps. 42 | 43 | Tmin (int): Minimum temperature of the MD simulation. 44 | 45 | Tmax (int): Maximum temperature of the MD simulation. 46 | 47 | md_T (int): Sampled temperature of the MD simulation (if md_run=True). 48 | 49 | md_style (str): Pair style argument in LAMMPS for a specific potential. 50 | 51 | md_coeff (str): Pair coeff argument in LAMMPS for a specific potential. 52 | 53 | Ecoh (float): Bulk cohesive energy for the specific potential. 54 | 55 | mass (float): Mass of the species. 56 | """ 57 | 58 | fname_final = "lammps_end_STRUC" # Final filename when relaxation is done 59 | 60 | def __init__(self, 61 | struct: dict, 62 | algo: dict, 63 | debug: bool=False): 64 | """ 65 | Constructs a Simulation object. 66 | 67 | Args: 68 | struct (dict): Dictionary of structure parameters. 69 | 70 | algo (dict): Dictionary of algorithm parameters. 71 | 72 | debug (bool, optional): Flag for running in DEBUG mode. 73 | Defaults to False. 74 | 75 | Returns: 76 | Simulation object 77 | """ 78 | self.root = os.getcwd() 79 | self.debug = debug 80 | if not self.debug: 81 | if "SLURM_PROCID" in os.environ: 82 | self.pid = int(os.environ["SLURM_PROCID"]) 83 | elif "PBS_TASKNUM" in os.environ: 84 | from mpi4py import MPI 85 | comm = MPI.COMM_WORLD 86 | self.pid = comm.Get_rank() 87 | else: 88 | self.pid = 0 89 | else: 90 | self.pid = 0 91 | self.cfold = os.path.join(algo["dir_calcs"], f"{algo['dir_calcs']}_{self.pid + 1}") 92 | self.Emult = algo["Emult"] # for saving later 93 | self.counter = 0 94 | self.best_Egb = 1000 95 | self.nruns = algo["nruns"] 96 | self.clear_freq = algo["clear_freq"] 97 | 98 | self.lmp = algo["lammps_bin"] 99 | self.md_run = algo["MD_run"] 100 | if self.debug: 101 | self.md_steps0 = 1000 102 | else: 103 | self.md_steps0 = algo["MD_min"] 104 | self.md_steps1 = algo["MD_max"] 105 | self.md_steps = None 106 | self.md_var = algo["var_steps"] 107 | self.md_T = None 108 | self.Tmin = algo["Tmin"] 109 | self.Tmax = algo["Tmax"] 110 | 111 | # These definitions will have to change with binary systems 112 | self.symbol = struct["symbol"] 113 | self.md_style = struct["pair_style"] 114 | self.md_coeff = struct["pair_coeff"] 115 | self.Ecoh = struct["Ecoh"] 116 | self.mass = struct["mass"] # keep in separate data file? 117 | 118 | 119 | def sample_params(self, rng: np.random.Generator) -> None: 120 | """ 121 | Selects a random MD temperature and numsteps. 122 | 123 | Args: 124 | rng (np.random.Generator): Random number generator from NumPy. 125 | 126 | Returns: 127 | None 128 | """ 129 | # Randomly choose a temperature in multiples of 100 130 | self.md_T = rng.choice(np.arange(self.Tmin, self.Tmax + 1, 100)) 131 | if rng.random() > self.md_run: 132 | self.md_steps = 0 133 | elif self.md_var == 1 and not self.debug: 134 | # Linearly scale the number of MD steps 135 | self.md_steps = int(np.round(rng.integers(self.md_steps0, self.md_steps1, 136 | endpoint=True), -3)) 137 | elif self.md_var == 2 and not self.debug: 138 | # Exponentially scale the number of MD steps 139 | C = np.log(self.md_steps1 / self.md_steps0) 140 | self.md_steps = int(np.round(self.md_steps0 * 141 | np.exp(C * rng.random()), -3)) 142 | else: 143 | self.md_steps = self.md_steps0 144 | 145 | 146 | def run_md(self, system: Bicrystal, update_gb: bool=True) -> None: 147 | """ 148 | Run a LAMMPS simulation in two steps: Optional high-temperature MD 149 | then relaxation. Writes the input structure with dummy GB energy 150 | if the LAMMPS executable path doesn't exist. 151 | 152 | Args: 153 | system (Bicrystal): Bicrystal object with a GB. 154 | 155 | update_gb (bool): Store the relaxed GB structure into Bicrystal object. 156 | 157 | Raises: 158 | Assertion: Temperature and num steps must be set first. 159 | 160 | Assertion: Bounds in the Bicrystal must be set first. 161 | 162 | Returns: 163 | None. 164 | """ 165 | assert self.md_T is not None and self.md_steps is not None, \ 166 | "Must set a temperature and number of steps first!" 167 | assert system.bounds is not None, "Compute GB boundaries using " + \ 168 | "bicrystal.get_bounds() before running a simulation!" 169 | 170 | # Enter the calculation directory 171 | run_dir = os.path.join(self.root, self.cfold) 172 | os.chdir(run_dir) 173 | 174 | if os.path.exists(self.lmp) or getstatusoutput(self.lmp + " -h")[0] == 0: 175 | # First perform MD run 176 | if self.md_steps > 0: 177 | input1 = [self.lmp, "-i", "lammps.in_1", "-v", "T1", str(self.md_T), 178 | "-v", "MDsteps", str(self.md_steps), "-v", "SEED", str(self.pid+1), 179 | "-v", "STYLE", self.md_style, "-v", "COEFF", self.md_coeff, 180 | "-v", "Lowerb", str(system.bounds[0]), 181 | "-v", "Upperb", str(system.bounds[1]), 182 | "-v", "MASS", str(self.mass), "-log", "log.lammps_1"] 183 | p1 = Popen(input1, stdout=PIPE, stderr=PIPE) 184 | p1.wait() 185 | else: 186 | # If no MD, copy the initial structure for part 2 187 | os.system("cp STRUC STRUC_temp") 188 | 189 | # Second perform static relaxation 190 | input2 = [self.lmp, "-i", "lammps.in_2", 191 | "-v", "STYLE", self.md_style, "-v", "COEFF", self.md_coeff, 192 | "-v", "Ecoh", str(self.Ecoh), "-v", "MASS", str(self.mass), 193 | "-v", "Lowerb", str(system.bounds[0]), 194 | "-v", "Upperb", str(system.bounds[1]), 195 | "-v", "Pad", str(system.bounds[2]), 196 | "-v", "f", self.fname_final, "-log", "log.lammps_2"] 197 | p2 = Popen(input2, stdout=PIPE, stderr=PIPE) 198 | p2.wait() 199 | else: 200 | print("Cannot find LAMMPS executable! Check path.") 201 | # If LAMMPS doesn't exist, just write a dummy output file 202 | self.write_dummy_lammps_dump(self.fname_final, system) 203 | with open(self.fname_final, "a") as f: 204 | f.write("Egb = 12.3456789\n") 205 | 206 | if update_gb: 207 | system.gb = read_lammps_dump(self.fname_final) 208 | type_list_init = system.gb.get_chemical_symbols() 209 | if len(set(type_list_init)) == 1: 210 | for a in system.gb: 211 | a.symbol = self.symbol 212 | system.relaxed = True 213 | 214 | # Iterate counter to keep track of when to clear duplicates 215 | self.counter += 1 216 | os.chdir(self.root) 217 | 218 | 219 | def get_gb_energy(self, system: Bicrystal) -> float: 220 | """ 221 | Calculate the GB energy printed on the last line of the output file. 222 | 223 | Args: 224 | system (Bicrystal): Bicrystal object with a GB. 225 | 226 | Raises: 227 | Assertion: File must exist. 228 | 229 | Returns: 230 | Egb (float): GB energy in Joules per meter squared. 231 | """ 232 | filename = os.path.join(self.cfold, "lammps_end_STRUC") 233 | assert os.path.exists(filename), "Final structure not found! " + \ 234 | "Check log files from LAMMPS." 235 | 236 | with open(os.path.join(self.cfold, "lammps_end_STRUC"), "rb") as f: 237 | try: # catch OSError in case of a one line file 238 | f.seek(-2, os.SEEK_END) 239 | while f.read(1) != b'\n': 240 | f.seek(-2, os.SEEK_CUR) 241 | except OSError: 242 | f.seek(0) 243 | last_line = f.readline().decode() 244 | 245 | tokens = last_line.split(' ') #Example: "Egb = 3.419154496\n" 246 | assert tokens[0] == "Egb", print("No GB energy was written! 😞") 247 | Egb = float(tokens[2]) 248 | system.Egb = Egb # save energy into Bicrystal attribute 249 | return Egb 250 | 251 | 252 | def write_dummy_lammps_dump(self, filename: str, system: Bicrystal) -> None: 253 | """ 254 | Write a Bicrystal structure to LAMMPS dump format (for debugging). 255 | 256 | Args: 257 | filename (str): Name of final LAMMPS dump file. 258 | 259 | system (Bicrystal): Bicrystal object with a GB. 260 | 261 | Raises: 262 | Assertion: GB must first be created using join_gb(). 263 | 264 | Returns: 265 | None 266 | """ 267 | assert system.gb is not None, "GB hasn't been created yet! " + \ 268 | "Use the join_gb() method before writing." 269 | 270 | with open(filename, "w") as f: 271 | f.write("ITEM: TIMESTEP\n") 272 | f.write("0\n") 273 | f.write("ITEM: NUMBER OF ATOMS\n") 274 | f.write(f"{system.natoms}\n") 275 | f.write("ITEM: BOX BOUNDS pp pp ss\n") 276 | for i in range(3): 277 | f.write(f"0.0 {system.gb.cell[i, i]}\n") 278 | f.write("ITEM: ATOMS id type x y z c_eng\n") 279 | s = system.gb.get_chemical_symbols() # might need for binary 280 | s_unique_sorted = sorted(list(dict.fromkeys(s))) 281 | p = system.gb.get_positions() 282 | for i in range(system.natoms): 283 | idx = s_unique_sorted.index(s[i]) 284 | f.write(f"{i+1} {idx+1} {p[i,0]} {p[i,1]} {p[i,2]} 0.0\n") 285 | 286 | 287 | def store_best_structs(self, system: Bicrystal, best_dir: str = "best") -> None: 288 | """ 289 | Store the best structures from the simulations. 290 | 291 | Args: 292 | system (Bicrystal): Bicrystal object with GB. 293 | 294 | best_dir (str, optional): Directory to save structures to. 295 | Defaults to "best." 296 | 297 | Returns: 298 | None 299 | """ 300 | if system.Egb < self.best_Egb * self.Emult: 301 | if system.Egb < self.best_Egb: 302 | self.best_Egb = system.Egb 303 | 304 | # Custom file name to differentiate results 305 | fname2best = f"lammps_{system.Egb:.3f}_{system.n:.3f}_" + \ 306 | f"{system.dxyz[0]:.2f}_{system.dxyz[1]:.2f}_" + \ 307 | f"{system.rxyz[0]:d}_{system.rxyz[1]:d}_" + \ 308 | f"{self.md_T:d}_{self.md_steps:d}" 309 | 310 | if os.name == 'nt': 311 | ccommand = "copy" 312 | else: 313 | ccommand = "cp" 314 | os.system(f"{ccommand} {os.path.join(self.cfold, self.fname_final)} " + \ 315 | f"{os.path.join(best_dir, fname2best)}") 316 | 317 | # Periodically remove duplicate structures 318 | if self.clear_freq: 319 | if len(os.listdir(best_dir)) > 4000: 320 | print(f"Clearing highest energy from {best_dir} now\n") 321 | clear_best(best_dir, extra=True, alpha=0.5) 322 | elif self.counter % self.clear_freq == 0: 323 | print(f"Clearing {best_dir} now\n") 324 | clear_best(best_dir) 325 | 326 | -------------------------------------------------------------------------------- /main.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python3 2 | import os 3 | from argparse import ArgumentParser 4 | import numpy as np 5 | 6 | from core.bicrystal import Bicrystal 7 | from core.simulation import Simulation 8 | from utils.utils import make_dirs, get_inputs, make_crystals, compute_weights, \ 9 | get_xy_translation, get_xy_replications 10 | 11 | ############################################################################## 12 | 13 | def main(infile: str, debug: bool) -> None: 14 | """ 15 | Performs grand canonical optimization of GB structures. 16 | 17 | Args: 18 | infile (str): YAML file of simulation parameters. 19 | Defaults to params.yaml. 20 | 21 | debug (bool): Flag for running in DEBUG mode. 22 | Defaults to False. 23 | 24 | Returns: 25 | None. 26 | """ 27 | 28 | # Read in parameters from YAML file. 29 | struct, algo = get_inputs(infile, debug) 30 | 31 | # Create a Simulation object to orchestrate the simulation 32 | sim = Simulation(struct, algo, debug) 33 | if debug: print(f"Starting GRIP calculations from {sim.root}") 34 | if debug: print(f"This process is running in {sim.cfold}") 35 | # Note: The logging package might make debugging print statements easier. 36 | 37 | # Create relevant directories like "best," "calc_proc#," etc 38 | make_dirs(sim.pid, algo["dir_struct"], algo["dir_calcs"]) 39 | 40 | # Use structure parameters to create upper and lower bulk slabs 41 | lower_0, upper_0, dlat = make_crystals(struct, debug) 42 | 43 | # Compute the weights for replications 44 | weights = compute_weights(struct) 45 | if debug: print(f"The weight are: {weights}") 46 | 47 | # Create a Bicrystal object from the two bulk slabs 48 | bicrystal = Bicrystal(lower_0, upper_0, struct, algo, dlat, 49 | make_copy=False, debug=debug) 50 | 51 | ########################################################################## 52 | 53 | # This loop samples different GB structures 54 | while sim.counter < sim.nruns or not sim.nruns: 55 | 56 | if debug: print(f"\n~~~~~ Starting simulation iteration {sim.counter+1} ~~~~~\n") 57 | 58 | # Make a copy of the parent slabs for each run 59 | bicrystal.copy_ul() 60 | 61 | # Sample a random translation and shift the upper slab 62 | dx, dy = get_xy_translation(upper_0, rng, algo["ngrid"], sim.pid, debug) 63 | bicrystal.shift_upper(dx, dy) 64 | if debug: print(f"Translation in (x, y) = [{dx:.4f}, {dy:.4f}]") 65 | 66 | # Get the bounds of the GB region for MD 67 | bicrystal.get_bounds(algo) 68 | if debug: print(f"Bounds for MD simulation (lower, upper, pad): \n{bicrystal.bounds}\n") 69 | 70 | # Sample a replication amount and replicate bicrystal in xy directions 71 | rx, ry = get_xy_replications(rng, weights) 72 | bicrystal.replicate(rx, ry) 73 | if debug: print(f"Replication in (x, y) = [{rx}, {ry}]") 74 | 75 | # Get the number of grain boundary atoms in the upper slab 76 | bicrystal.get_gbplane_atoms_u() 77 | if debug: print(f"Num atoms per plane in upper: {bicrystal.npp_u}\n") 78 | if debug: print(f"Num atoms in bicrystal: {bicrystal.natoms}") 79 | 80 | # Create vacancies in those grain boundary atoms in the upper slab 81 | bicrystal.defect_upper(algo, rng) 82 | 83 | if debug: print(f"{bicrystal} \n") 84 | if debug: print(f"Num atoms in bicrystal: {bicrystal.natoms}") 85 | if debug: print(f"n frac = {bicrystal.n}\n") 86 | 87 | # Perturb the GB atoms randomly 88 | bicrystal.perturb_atoms(rng) 89 | if debug: print(f"Perturbing GB atoms by {algo['perturb_u']} and {algo['perturb_l']}\n") 90 | 91 | # Combine the two slabs (upper w/ defects) into a single GB structure 92 | bicrystal.join_gb(algo) 93 | 94 | # Find interstitial sites and swap atoms in GB region 95 | swapped_n = bicrystal.find_and_swap_inters(rng) 96 | if debug: print(f"Swapping {swapped_n} GB atoms with interstitial sites.\n") 97 | 98 | # Write the GB structure to a file that is the initial structure for LAMMPS 99 | input_struct_file = os.path.join(algo["dir_calcs"], f"{algo['dir_calcs']}_{sim.pid+1}", "STRUC") 100 | bicrystal.write_gb(input_struct_file) 101 | 102 | if debug: print(bicrystal) 103 | if debug: print(f"GB structure is {bicrystal.gb}\n") 104 | 105 | # Sample parameters like Temperature and Numsteps for this iteration 106 | sim.sample_params(rng) 107 | if debug: print(f"The simulation parameters are T={sim.md_T}, N={sim.md_steps}") 108 | 109 | # Run the MD simulation to produce a final, relaxed GB structure 110 | if debug: print(f"Running MD sampling") 111 | sim.run_md(bicrystal, update_gb=True) 112 | 113 | # Get the GB energy from the last line in the final file (lammps_end_STRUC) 114 | sim.get_gb_energy(bicrystal) 115 | 116 | if debug: print(bicrystal) 117 | if debug: print(f"GB structure is {bicrystal.gb}\n") 118 | if debug: print(f"The GB energy is {bicrystal.Egb} J/m^2\n") 119 | 120 | # Store the energy in a list and save the file to the "best" folder 121 | sim.store_best_structs(bicrystal) 122 | 123 | if debug:# and sim.counter == 3: 124 | assert False, "Terminated early in DEBUG mode." 125 | 126 | ############################################################################## 127 | 128 | if __name__ == "__main__": 129 | parser = ArgumentParser(description="Perform grand canonical optimization of GBs.") 130 | parser.add_argument("-i", "--input", type=str, default="params.yaml", 131 | help="File containing structure & algorithm parameters.") 132 | parser.add_argument("-d", "--debug", action="store_true", 133 | help="Run in DEBUG mode, which prints variables and terminates early.") 134 | parser.add_argument("-s", "--seed", type=int, default=1, 135 | help="Random seed for debugging.") 136 | args = parser.parse_args() 137 | infile = args.input 138 | debug = args.debug 139 | seed = args.seed 140 | 141 | if debug: 142 | rng = np.random.default_rng(seed=seed) 143 | else: 144 | rng = np.random.default_rng() 145 | 146 | main(infile, debug) 147 | -------------------------------------------------------------------------------- /params.yaml: -------------------------------------------------------------------------------- 1 | # Input data for the GRand canonical Interface Predictor (GRIP). Format is YAML. 2 | 3 | # Parameters for the algorithm 4 | algo: 5 | dir_struct: 'best' # Folder to store best structures. 6 | dir_calcs: 'calc_procs' # Folder to store temporary calculation files. 7 | ngrid: 100 # Number of grid points in each dim = ngrid * nprocs. 8 | frac_min: 0.00 # Minimum fraction of atoms on a plane (0 <= n <= 1). 9 | frac_max: 1.00 # Maximum fraction of atoms on a plane. Set both to 1.0 for gamma-surface. 10 | gb_gap: 0.3 # Initial gap between slabs prior to MD/relaxation (in Ang.). 11 | perturb_u: 0.0 # Maximum random perturbation (A) of atoms above GB 12 | perturb_l: 0.0 # Maximum random perturbation (A) of atoms below GB 13 | gb_thick: 10 # Thickness of GB region (in Angstrom) on either side of interface. 14 | pad: 10 # Extra padding (A) on top of gb_thick for relaxation / energy calculations. 15 | vacuum: 1 # Vacuum to add on top for MD (A); less needed for s boundary. 16 | 17 | inter_p: 0.0 # Probability of swapping with interstitial sites. [0.0, 1.0] = [Never, Always]. 18 | inter_s: 'Ti' # species of atom to insert. 19 | inter_n: 2 # Number of GB interstitial sites to swap with atoms in GB region. 20 | inter_t: 1.5 # Thickness of region (A) on either side of GB to search for interstitials. 21 | inter_u: False # Only choose unique interstitial sites. 22 | inter_r: True # True = randomly choose sites; False = largest volume 23 | inter_w: 2 # How to swap: 1 = only subs, 2 = only inter, 3 = uniform, 4 = mostly subs, 5 = mostly inter 24 | 25 | MD_run: 0.95 # Probability of running MD simulation before relaxing. [0.0, 1.0] = [Never, Always]. 26 | Tmin: 300 # Temperature lower bound for MD simulation. Min ~0.3 Tm. 27 | Tmax: 1200 # Temperature upper bound, vary in multiple of 100s. Max ~0.9 Tm. 28 | MD_min: 5000 # Min steps for MD simulation. 29 | MD_max: 500000 # Max steps for MD simulation. 30 | var_steps: 2 # 0 = Min steps only; 1 = linear sample; 2 = exponential sample 31 | 32 | lammps_bin: '/g/g16/chen120/bin/lammps_serial' # Absolute path to [serial] LAMMPS binary or shell command. 33 | Emult: 2 # Maximum energy threshold * Egb_min to keep; at least 1.0. 34 | nruns: 0 # Number of iterations in total (each processor). Set 0 for infinite loop. 35 | clear_freq: 50 # Number of iterations before clearing duplicates. Set 0 to never clear. 36 | 37 | 38 | # Parameters for the material 39 | struct: 40 | user: False # True: read existing cells (POSCAR_*), False: generate w/ ase. 41 | cutoff: 35 # Max height (A) to cut slabs if user=False; speed up calcs. Set to 0 to ignore. 42 | write: True # Write generated cells to POSCAR_* 43 | size0: [1, 1, 1] # Minimum replications in [x, y, z] to create supercells. 44 | size: [2, 4, 15] # Replications in [x, y, z] to create supercells. z is not used if user=True. 45 | reps: 2 # Sample replications (1) exactly, (2) uniform, (3) weighted smaller, (4) weighted larger. 46 | 47 | # Basic info - potential dependent! 48 | upper_dirs: [ [5, 2, -7, 0], [0, 0, 0, -1], [-3, 4, -1, 0] ] # Ti(31-40) tilt 49 | lower_dirs: [ [7, -2, -5, 0], [0, 0, 0, -1], [-1, 4, -3, 0] ] 50 | symbol: 'Ti' # Chemical formula 51 | crystal: 'hcp' # fcc, bcc, hcp, or dc 52 | mass: 47.867 # Atomic mass 53 | # HENNIG 54 | a: 2.9305 # a lattice constant at 0K; potential dependent; provide to 4 decimal places. 55 | c: 4.6783 # c lattice constant at 0K; hcp only, ignored for others 56 | dlat: 0.703883 # Minimal normal component of lattice vector to calculate Nplane. Required if user=True. Set 0 to ignore. 57 | Ecoh: -4.8312 # Energy per atom in bulk; potential dependent; provide to 4 decimal places. 58 | pair_style: 'meam/spline' # pair_style for LAMMPS 59 | pair_coeff: '* * /g/g16/chen120/lammps/pots/Ti.meam.spline Ti' # pair_coeff for LAMMPS 60 | # ZOPE 61 | #a: 2.9527 # a lattice constant at 0K; potential dependent; provide to 4 decimal places. 62 | #c: 4.6808 # c lattice constant; hcp only, ignored for others 63 | #dlat: 0.0 # Minimal normal component of lattice vector to calculate Nplane. Required if user=True. Set 0 to ignore. 64 | #Ecoh: -4.8500 # Energy per atom in bulk; potential dependent; provide to 4 decimal places. 65 | #pair_style: 'eam/alloy' # pair_style for LAMMPS 66 | #pair_coeff: '* * /g/g16/chen120/lammps/pots/TiAl.eam.alloy Ti' # pair_coeff for LAMMPS 67 | 68 | -------------------------------------------------------------------------------- /simul_files/lammps.in_1: -------------------------------------------------------------------------------- 1 | 2 | # ---------- Initialize Simulation --------------------- 3 | clear 4 | units metal 5 | dimension 3 6 | boundary p p s 7 | atom_style atomic 8 | 9 | variable T0 equal 50 # Tm W=3695 Ti=1941 10 | variable velT equal "v_T1 * 2" 11 | #variable MDsteps equal 5000 12 | #variable SEED equal 1 13 | 14 | 15 | # ---------- Create Atomistic Structure --------------------- 16 | read_data STRUC 17 | mass * ${MASS} # W=183.84 Ti=47.867 Cu=63.546 # for some potentials (e.g., MEAM) 18 | 19 | variable Lower1 equal "bound(all, zmin) + v_Lowerb" 20 | variable Upper1 equal "bound(all, zmax) - v_Upperb" 21 | print "${Lower1}" screen yes 22 | print "${Upper1}" screen yes 23 | 24 | region lowlayer block INF INF INF INF INF ${Lower1} units box 25 | group lowlayer region lowlayer 26 | 27 | region gbregion block INF INF INF INF ${Lower1} ${Upper1} units box 28 | group gbregion region gbregion 29 | 30 | region uplayer block INF INF INF INF ${Upper1} INF units box 31 | group uplayer region uplayer 32 | 33 | 34 | # ---------- Define Interatomic Potential --------------------- 35 | 36 | pair_style ${STYLE} 37 | pair_coeff ${COEFF} 38 | 39 | neighbor 1.0 bin 40 | neigh_modify every 1 delay 1 check yes 41 | 42 | 43 | # ---------- MD simulation --------------------- 44 | # fix upper and lower blocks 45 | fix f1 lowlayer setforce 0.0 0.0 0.0 46 | fix f2 uplayer aveforce 0.0 0.0 0.0 47 | min_style cg 48 | minimize 1e-15 1e-15 100000 100000 49 | 50 | # Stage 1: High-temperature MD 51 | velocity gbregion create ${velT} ${SEED} dist gaussian rot yes 52 | fix r1 all nve 53 | fix r2 gbregion langevin ${T1} ${T1} $(100*dt) ${SEED} 54 | #fix r2 gbregion nvt temp ${T1} ${T1} $(100*dt) 55 | #fix r3 uplayer nvt temp ${T1} ${T1} $(100*dt) 56 | 57 | timestep 0.002 58 | run ${MDsteps} 59 | 60 | # Stage 2: Ramp down the system 61 | unfix r2 62 | fix r3 gbregion langevin ${T1} ${T0} $(100*dt) ${SEED} 63 | #fix r4 gbregion nvt temp ${T1} ${T0} $(100*dt) 64 | run 1000 65 | 66 | # write output 67 | write_data STRUC_temp nocoeff 68 | print "MD is DONE" 69 | 70 | -------------------------------------------------------------------------------- /simul_files/lammps.in_2: -------------------------------------------------------------------------------- 1 | 2 | # ---------- Initialize Simulation --------------------- 3 | clear 4 | units metal 5 | dimension 3 6 | boundary p p s 7 | atom_style atomic 8 | #variable f string lammps_end_STRUC 9 | 10 | 11 | # ---------- Create Atomistic Structure --------------------- 12 | read_data STRUC_temp 13 | mass * ${MASS} # W=183.84 Ti=47.867 Cu=63.546 # for some potentials (e.g., MEAM) 14 | 15 | variable Lower1 equal "bound(all, zmin) + v_Lowerb - v_Pad" 16 | variable Upper1 equal "bound(all, zmax) - v_Upperb + v_Pad" 17 | print "${Lower1}" screen yes 18 | print "${Upper1}" screen yes 19 | 20 | region lowlayer block INF INF INF INF INF ${Lower1} units box 21 | group lowlayer region lowlayer 22 | 23 | region gbregion block INF INF INF INF ${Lower1} ${Upper1} units box 24 | group gbregion region gbregion 25 | 26 | region uplayer block INF INF INF INF ${Upper1} INF units box 27 | group uplayer region uplayer 28 | 29 | 30 | # ---------- Define Interatomic Potential --------------------- 31 | pair_style ${STYLE} 32 | pair_coeff ${COEFF} 33 | 34 | neighbor 2.0 bin 35 | neigh_modify delay 10 check yes 36 | 37 | 38 | # ---------- Run Minimization --------------------- 39 | fix f1 lowlayer setforce 0.0 0.0 0.0 40 | fix f2 uplayer aveforce 0.0 0.0 0.0 41 | min_style cg 42 | minimize 1e-15 1e-15 100000 100000 43 | 44 | 45 | # ---------- Regroup to compute energies ---------------- 46 | variable EPad equal 1.5 47 | variable Lower2 equal "v_Lower1 - v_EPad" 48 | variable Upper2 equal "v_Upper1 + v_EPad" 49 | region gbregion2 block INF INF INF INF ${Lower2} ${Upper2} units box 50 | group gbregion2 region gbregion2 51 | 52 | compute eng all pe/atom 53 | compute eatoms gbregion2 reduce sum c_eng 54 | reset_timestep 0 55 | thermo 0 56 | thermo_style custom step pe lx ly lz press pxx pyy pzz c_eatoms 57 | dump d1 all custom 100 ${f} id type x y z c_eng 58 | dump_modify d1 sort id 59 | run 0 60 | 61 | 62 | # ---------- Compute properties --------------------- 63 | #variable Ecoh equal -4.85 64 | variable Ntot equal "count(gbregion2)" 65 | variable Ebulk equal "v_Ecoh * count(gbregion2)" 66 | variable Etot equal "c_eatoms" 67 | variable GBarea equal "lx * ly" 68 | variable Egb equal "(v_Etot - v_Ebulk)/ v_GBarea * 16.021" 69 | 70 | if "(${Egb} < 0.0) " then "variable Egb equal 100" 71 | 72 | print "Energy per atom = ${Ecoh}" 73 | print "Bulk energy ${Ebulk}" 74 | print "Etot ${Etot}" 75 | print "AreaXY = ${GBarea}" 76 | print "N total atoms = ${Ntot}" 77 | print "Egb = ${Egb}" append ${f} screen yes 78 | print "RELAXATION is DONE" 79 | -------------------------------------------------------------------------------- /utils/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/enze-chen/grip/596c17dff5bef9b7638020a5200daf1abb3a56d0/utils/__init__.py -------------------------------------------------------------------------------- /utils/clean.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | rm -rf zjob.o* calc_proc* **/__pycache__ #best 4 | -------------------------------------------------------------------------------- /utils/constants.py: -------------------------------------------------------------------------------- 1 | P_SHIFT = 0.005 2 | Z_THRESH = 0.00005 -------------------------------------------------------------------------------- /utils/dump2poscar.py: -------------------------------------------------------------------------------- 1 | import os 2 | import argparse 3 | import yaml 4 | import shutil 5 | 6 | import numpy as np 7 | import pandas as pd 8 | 9 | import ase.io 10 | 11 | 12 | def create_ref_dft(ref_file, gb_struct, vacuum): 13 | ngb = len(gb_struct) 14 | aa, bb, cc = gb_struct.cell 15 | s = ase.io.read(ref_file, format="vasp") 16 | 17 | # First replicate as needed 18 | ar, br, cr = s.cell 19 | rx = round(aa[0] / ar[0]) 20 | ry = round(bb[1] / br[1]) 21 | s *= (rx, ry, 1) 22 | 23 | # Now guess a cutoff 24 | z_guess = gb_struct.cell[2, 2] * 0.8 25 | s_guess = s.copy() 26 | del s_guess[[a.index for a in s_guess if a.position[2] > z_guess]] 27 | while len(s_guess) < ngb: 28 | z_guess += 0.05 29 | s_guess = s.copy() 30 | del s_guess[[a.index for a in s_guess if a.position[2] > z_guess]] 31 | 32 | if len(gb_dft) != len(s_guess): 33 | print(f"Beware, number of atoms in GB ({len(gb_dft)}) does not equal number of atoms in the reference ({len(s_guess)})!") 34 | 35 | s_guess.cell[2, 2] = z_guess + vacuum 36 | return s_guess 37 | 38 | 39 | 40 | def create_gb_struct(gb_file, thickness, vacuum, symb): 41 | df = pd.read_csv(gb_file, skiprows=9, names=['id', 'type', 'x', 'y', 'z', 'c_eng'], sep=' ') 42 | zmax = df['z'].max() 43 | sub = df[(df['z'] > 10) & (df['z'] < zmax - 10)] 44 | zmid = np.mean(sub[sub['c_eng'] > 1.02 * sub['c_eng'].max()].z) 45 | 46 | s = ase.io.read(gb_file, format="lammps-dump-text") 47 | s.positions -= [0, 0, zmid - thickness/2] 48 | s.cell[2, 2] = thickness + vacuum 49 | del s[[a.index for a in s if (a.position[2] < 0) or (a.position[2] > thickness)]] 50 | for a in s: 51 | a.symbol = symb 52 | return s 53 | 54 | 55 | if __name__ == '__main__': 56 | 57 | parser = argparse.ArgumentParser(description="Convert GRIP outputs to POSCARs.") 58 | parser.add_argument("-f", "--folder", type=str, default="best", 59 | help="Folder containing GRIP outputs.") 60 | parser.add_argument("-o", "--out_folder", type=str, default="best_poscars", 61 | help="Folder containing POSCAR files.") 62 | parser.add_argument("-i", "--infile", type=str, default="params.yaml", 63 | help="GRIP input parameters.") 64 | parser.add_argument("-s", "--scale", type=float, default=1.0, 65 | help="Ratio of DFT to MD lattice constants.") 66 | parser.add_argument("-E", "--energy", type=float, default=1000., 67 | help="Grain boundary energy threshold to convert.") 68 | parser.add_argument("-N", "--natoms", type=int, default=200, 69 | help="Number of atoms threshold for final POSCAR.") 70 | parser.add_argument("-t", "--thickness", type=float, default=30.0, 71 | help="Height in Angstroms for the GB slice.") 72 | parser.add_argument("-v", "--vacuum", type=float, default=10.0, 73 | help="Vacuum to add on top of POSCAR.") 74 | args = parser.parse_args() 75 | folder = args.folder 76 | outfolder = args.out_folder 77 | infile = args.infile 78 | scale = args.scale 79 | Ethresh = args.energy 80 | Nthresh = args.natoms 81 | t = args.thickness 82 | v = args.vacuum 83 | 84 | os.makedirs(outfolder, exist_ok=True) 85 | 86 | files = [x for x in os.listdir(folder) if x.startswith('lammps_')] 87 | with open(infile, 'r') as ff: 88 | params = yaml.safe_load(ff) 89 | 90 | cell_scaling = [scale, scale, 1] 91 | 92 | for f in files: 93 | tokens = f.split('_') 94 | Egb = float(tokens[1]) 95 | 96 | s = create_gb_struct(os.path.join(folder, f), t, v, params['struct']['symbol']) 97 | N = len(s) 98 | s.set_cell(s.get_cell() * cell_scaling, scale_atoms=True) 99 | 100 | if N < Nthresh and Egb < Ethresh: 101 | final_file = os.path.join(outfolder, f"POSCAR_{N}_{'_'.join(tokens[1:])}") 102 | ase.io.write(final_file, s, format="vasp") 103 | 104 | -------------------------------------------------------------------------------- /utils/plot_gco.py: -------------------------------------------------------------------------------- 1 | import argparse 2 | import numpy as np 3 | import matplotlib.pyplot as plt 4 | from ase.io.lammpsrun import read_lammps_dump 5 | from ase.visualize.plot import plot_atoms 6 | 7 | from unique import clear_best, process_output 8 | 9 | ############################################################################# 10 | 11 | def make_plot(dir_best: str = "best", Emax: float = 0.0, hide: bool = False) -> None: 12 | """ 13 | Make a GCO plot (Egb vs. n) for the best structures. 14 | 15 | Args: 16 | dir_best (str, optional): Folder to save structures in. 17 | Defaults to "best". 18 | 19 | Emax (float, optiona): Maximum value on y-axis. 20 | 21 | hide (bool, optional): Whether to hide the rendered Pyplot. 22 | Defaults to False. 23 | 24 | Returns: 25 | None, but a Pyplot might be displayed. 26 | """ 27 | file_list, ngb_list, Egb_list = process_output(dir_best)[:3] 28 | Egbmaxmin = max([min(Egb_list[ngb_list==n]) for n in set(ngb_list)]) 29 | 30 | plt.rcParams.update({"font.size":12}) 31 | fig, ax = plt.subplots(layout="constrained") 32 | ax.plot(ngb_list, Egb_list, 'o', c='k', ms=3, clip_on=True) 33 | ymin = ax.get_ylim()[0] 34 | ymax = Emax if Emax else Egbmaxmin + 0.2 * (Egbmaxmin - ymin) 35 | ax.set(xlim=(0, 1), 36 | ylim=(ymin, ymax), 37 | xlabel=r"$[n]$", ylabel=r"$E_{\mathrm{gb}}$ (J m$^{-2}$)") 38 | 39 | fig.savefig(f"{dir_best}/best_grip_plot.png", dpi=300, bbox_inches="tight") 40 | if not hide: 41 | plt.show() 42 | 43 | 44 | def view_struct(filename: str) -> None: 45 | """ 46 | Use ASE and Matplotlib to visualize a GB structure. 47 | 48 | Args: 49 | filename (str): Name of the LAMMPS dump file. 50 | """ 51 | s = read_lammps_dump(filename) 52 | zmid = np.mean([min(s.positions[:,2]), max(s.positions[:,2])]) 53 | gb_thick = 20 54 | 55 | fig, ax = plt.subplots(figsize=(7,7)) 56 | plot_atoms(atoms=s, ax=ax, radii=1.6, rotation=("90x,0y,0z")) 57 | ax.set_ylim(zmid - gb_thick, zmid + gb_thick) 58 | ax.set_axis_off() 59 | plt.tight_layout() 60 | plt.show() 61 | 62 | 63 | if __name__ == "__main__": 64 | parser = argparse.ArgumentParser(description="Plot GCO plot (Egb vs. n) for GRIP results.") 65 | parser.add_argument("-f", "--folder", type=str, default="best", 66 | help="Folder where GB structs are stored.") 67 | parser.add_argument("-E", "--Emax", type=float, 68 | help="Max Egb for y axis of plot.") 69 | parser.add_argument("-s", "--silent", action="store_true", 70 | help="Do not show the plot.") 71 | parser.add_argument("-e", "--extra", action="store_true", 72 | help="Remove additional higher energy structs.") 73 | parser.add_argument("--file", type=str, default="", 74 | help="View a structure instead of the GCO plot.") 75 | args = parser.parse_args() 76 | dir_best = args.folder 77 | Emax = args.Emax 78 | hide = args.silent 79 | extra = args.extra 80 | filename = args.file 81 | 82 | clear_best(dir_best, extra, save=True) 83 | 84 | if filename: 85 | view_struct(filename) 86 | else: 87 | make_plot(dir_best, Emax, hide) 88 | -------------------------------------------------------------------------------- /utils/tests.py: -------------------------------------------------------------------------------- 1 | import unittest 2 | 3 | class TestBicrystalMethods(unittest.TestCase): 4 | 5 | # STUB TODO 6 | 7 | def test_upper(self): 8 | pass 9 | 10 | 11 | if __name__ == '__main__': 12 | unittest.main() 13 | -------------------------------------------------------------------------------- /utils/unique.py: -------------------------------------------------------------------------------- 1 | import os 2 | import argparse 3 | from subprocess import call 4 | from typing import Tuple 5 | 6 | import numpy as np 7 | from numpy import ndarray 8 | import pandas as pd 9 | 10 | ############################################################################# 11 | 12 | def process_output(dir_best: str = 'best') -> Tuple[list, ndarray, ndarray]: 13 | """ 14 | Process the output files and get the Egb and n values. 15 | 16 | Args: 17 | dir_best (str, optional): Folder to save structures in. 18 | Defaults to 'best'. 19 | 20 | Returns: 21 | The list of file names and NumPy arrays for the GB energy and n. 22 | """ 23 | file_list = sorted([x for x in os.listdir(dir_best) if x.startswith('lammps_')]) 24 | Egb_list, ngb_list, dx_list, dy_list = [], [], [], [] 25 | rx_list, ry_list, T_list, steps_list = [], [], [], [] 26 | 27 | print(f"Found {len(file_list)} files.") 28 | 29 | for f in file_list: 30 | features = f.split('_') 31 | Egb_list.append(float(features[1])) 32 | ngb_list.append(float(features[2])) 33 | dx_list.append(float(features[3])) 34 | dy_list.append(float(features[4])) 35 | rx_list.append(int(features[5])) 36 | ry_list.append(int(features[6])) 37 | T_list.append(int(features[7])) 38 | steps_list.append(int(features[8])) 39 | 40 | return file_list, np.array(ngb_list), np.array(Egb_list), \ 41 | np.array(dx_list), np.array(dy_list), np.array(rx_list), np.array(ry_list), \ 42 | np.array(T_list), np.array(steps_list) 43 | 44 | 45 | def clear_best(dir_best: str = 'best', extra: bool = False, thresh: float = 0.003, 46 | alpha: float = 0.25, save: bool = False) -> None: 47 | """ 48 | Periodically remove duplicate structures that are saved. 49 | 50 | Args: 51 | dir_best (str, optional): Folder that structures are saved in. 52 | Defaults to 'best'. 53 | 54 | extra (bool, optional): Whether to remove additional duplicates. 55 | Defaults to False. 56 | 57 | thresh (float, optional): Energy difference below which to remove duplicates. 58 | Defaults to 0.003 J/m^2. 59 | 60 | alpha (float, optional): Multiplicative factor of Emax to set thresholds. 61 | Defaults to 0.25. 62 | 63 | save (bool, optional): Whether to save structures into CSV. 64 | Defaults to False. 65 | 66 | Returns: 67 | None 68 | """ 69 | # First filter by unique Egb and n, minimizing replications and translations 70 | file_list = sorted([x for x in os.listdir(dir_best) if x.startswith('lammps_')]) 71 | print(f"Found {len(file_list)} files.") 72 | 73 | unique_dir = {} 74 | for fx in file_list: 75 | features = fx.split('_') 76 | Egb = features[1] 77 | ngb = features[2] 78 | dx = float(features[3]) 79 | dy = float(features[4]) 80 | rx = int(features[5]) 81 | ry = int(features[6]) 82 | 83 | # Create keys for filtering unique structures 84 | key1 = f"{Egb}_{ngb}" 85 | key2 = rx * ry 86 | key3 = dx**2 + dy**2 87 | 88 | if key1 not in unique_dir.keys(): 89 | unique_dir[key1] = [key2, key3, fx] 90 | else: 91 | key2_old, key3_old = unique_dir[key1][0:2] 92 | if key2 < key2_old: 93 | unique_dir[key1] = [key2, key3_old, fx] 94 | elif (key2 == key2_old) and (key3 < key3_old): 95 | unique_dir[key1] = [key2, key3, fx] 96 | 97 | unique_files = [] 98 | for k,v in unique_dir.items(): 99 | unique_files.append(v[-1]) 100 | 101 | # Determine which files are redundant then delete them 102 | files_to_delete = set(file_list) - set(unique_files) 103 | print(f"Removing {len(files_to_delete)} files.") 104 | for d in files_to_delete: 105 | try: 106 | os.remove(os.path.join(dir_best, d)) 107 | except FileNotFoundError: 108 | pass 109 | 110 | # Put lists into a pandas DataFrame 111 | lists = process_output(dir_best) 112 | file_list, ngb_list, Egb_list = lists[:3] 113 | df = pd.DataFrame({'n':ngb_list, 'Egb':Egb_list, 'dx':lists[3], 'dy':lists[4], 114 | 'rx':lists[5], 'ry':lists[6], 'T':lists[7], 'steps':lists[8], 115 | 'f':file_list}) 116 | 117 | # If specified, then further remove files with high energy 118 | if extra: 119 | # remove files with really high energy 120 | Emin = min(Egb_list) 121 | Egbmaxmin = max([min(Egb_list[ngb_list==n]) for n in set(ngb_list)]) 122 | max_thresh = Egbmaxmin + alpha * (Egbmaxmin - Emin) 123 | print(f"Max threshold: {max_thresh}") 124 | to_delete = df[df['Egb'] > max_thresh]['f'].tolist() 125 | 126 | # remove those close in energy for same value of n 127 | groups = df.groupby('n') 128 | for name,group in groups: 129 | group.sort_values('Egb', inplace=True) 130 | Emin0 = min(group['Egb']) 131 | Emax0 = min(max_thresh, max(group['Egb'])) 132 | min_thresh = alpha * (Emax0 - Emin0) 133 | Emin = Emin0 134 | for ind,row in group.iterrows(): 135 | Ecurr = row['Egb'] 136 | if Ecurr > Emin0 + min_thresh and Emin < Ecurr <= Emin + thresh: 137 | to_delete.append(row['f']) 138 | else: 139 | Emin = Ecurr 140 | 141 | to_delete = set(to_delete) 142 | print(f"Removing {len(to_delete)} files.") 143 | for f in to_delete: 144 | try: 145 | os.remove(os.path.join(dir_best, f)) 146 | except FileNotFoundError: 147 | pass 148 | 149 | df.sort_values('Egb', inplace=True) 150 | if save: 151 | df.to_csv(f"{dir_best}/best_grip_data.csv", index=False) 152 | 153 | return df 154 | 155 | 156 | if __name__ == "__main__": 157 | parser = argparse.ArgumentParser(description="Clean up files from GRIP.") 158 | parser.add_argument("-f", "--folder", type=str, default="best", 159 | help="Folder where GB structs are stored.") 160 | parser.add_argument("-e", "--extra", action="store_true", 161 | help="Remove additional higher energy structs.") 162 | parser.add_argument("-t", "--thresh", type=float, default=0.003, 163 | help="Egb difference to remove.") 164 | parser.add_argument("--alpha", type=float, default=0.25, 165 | help="Fraction of Emax to set thresholds.") 166 | parser.add_argument("-s", "--save", action="store_true", 167 | help="Save results to CSV.") 168 | args = parser.parse_args() 169 | dir_best = args.folder 170 | extra = args.extra 171 | thresh = args.thresh 172 | alpha = args.alpha 173 | save = args.save 174 | 175 | df = clear_best(dir_best, extra, thresh, alpha, save) 176 | print(df.head(15)) 177 | 178 | -------------------------------------------------------------------------------- /utils/utils.py: -------------------------------------------------------------------------------- 1 | import os 2 | import shutil 3 | import time 4 | import yaml 5 | from typing import Tuple 6 | 7 | import numpy as np 8 | from ase.lattice.bravais import Lattice 9 | from ase.lattice.hexagonal import HexagonalClosedPacked, Hexagonal 10 | from ase.lattice.cubic import FaceCenteredCubic, BodyCenteredCubic, Diamond, SimpleCubic 11 | import ase.io 12 | 13 | from utils.constants import P_SHIFT, Z_THRESH 14 | 15 | ############################################################################# 16 | 17 | def get_inputs(input_data: str = "params.yaml", debug: bool = False) -> Tuple[dict, dict]: 18 | """ 19 | Gather structure and system information from user. 20 | 21 | Args: 22 | input_data (str, optional): YAML file of simulation parameters. 23 | Defaults to params.yaml. 24 | 25 | debug (bool, optional): Flag for running in DEBUG mode. 26 | Defaults to False. 27 | 28 | Raises: 29 | Assertions: A few sanity checks on parameter values (e.g., T > 0) 30 | 31 | Returns: 32 | struct (dict): Dictionary with structure parameters. 33 | 34 | algo (dict): Dictionary with algorithm parameters. 35 | """ 36 | with open(input_data, "r") as file: 37 | data = yaml.safe_load(file) 38 | if debug: print(f"Input params: {data}\n") 39 | 40 | # Validate inputs for algorithm parameters 41 | algo = data["algo"] 42 | assert isinstance(algo["ngrid"], int), "Invalid data type for ngrid, should be int." 43 | assert 0 <= algo["frac_min"] <= 1, "Invalid value for 'frac_min', should be float in [0,1]." 44 | assert 0 <= algo["frac_max"] <= 1, "Invalid value for 'frac_max', should be float in [0,1]." 45 | assert algo["frac_min"] <= algo["frac_max"], "Invalid; 'frac_min' must be <= 'frac_max'." 46 | 47 | assert algo["gb_gap"] >= 0, "Bicrystal slabs require non-negative separation." 48 | if algo["gb_thick"] < 5: 49 | print("Warning: GB region is a little thin, consider increasing 'gb_thick'.") 50 | if algo["pad"] < 3: 51 | print("Warning: Padding around GB is a little thin, consider increasing 'pad'.") 52 | 53 | assert algo["vacuum"] >= 0, "Bicrystal slabs require non-negative vacuum on top." 54 | assert algo["Emult"] >= 1, "Egb multiplier must be >= 1!" 55 | 56 | assert 0 <= algo["inter_p"] <= 1, "Invalid value for 'inter_p', should be float in [0,1]." 57 | assert algo["inter_n"] >= 0, "Number of interstitials must be non-negative!" 58 | if algo["inter_n"] > 0: 59 | assert algo["inter_t"] > 0, "Interstitial thickness must be positive for swapping!" 60 | 61 | assert 0 < algo["Tmin"] <= algo["Tmax"], "Invalid temperatures, should be 0 < Tmin <= Tmax!" 62 | assert algo["MD_min"] >= 0, "Number of MD steps must be >= 0!" 63 | assert algo["MD_max"] >= algo["MD_min"], "Max MD steps must be >= min steps!" 64 | 65 | # Validate inputs for structure parameters 66 | struct = data["struct"] 67 | if struct["cutoff"] < 20: 68 | print("Warning: User-generated slab might be too short to avoid interface effects.") 69 | assert struct["mass"] > 0, "Mass of species must be positive!" 70 | assert struct["a"] > 0, "Cell length must be positive!" 71 | assert struct["c"] > 0, "Cell length must be positive!" 72 | if struct["Ecoh"] > 0: 73 | print("Warning: Supplied Ecoh was positive! Double check?") 74 | 75 | for i in range(3): 76 | assert isinstance(struct["size0"][i], int) and struct["size0"][i] > 0, \ 77 | f"Minimum replications in dim {i} must be integer >= 1." 78 | assert isinstance(struct["size"][i], int) and struct["size"][i] > 0, \ 79 | f"Number of replications in dim {i} must be integer >= 1." 80 | assert struct["size0"][i] <= struct["size"][i], \ 81 | f"size0 in dim {i} cannot be larger than size!" 82 | 83 | assert struct["reps"] in [1, 2, 3, 4], \ 84 | f"Repetitions flag {struct['reps']} not yet supported! Choose from [1, 2, 3, 4]." 85 | 86 | return struct, algo 87 | 88 | 89 | def make_dirs(pid: int, dir_struct: str = "best", dir_calcs: str = "calc_procs") -> None: 90 | """ 91 | Make a directory to store the best unique structures. 92 | 93 | Args: 94 | pid (int): Current process ID. 95 | 96 | dir_struct (str, optional): Name of folder to store best structures. 97 | Defaults to "best". 98 | 99 | dir_calcs (str, optional): Name of folder to store calculation files. 100 | Defaults to "calc_procs". 101 | 102 | Returns: 103 | None, but folders are created. 104 | """ 105 | # Delete old calculation folders 106 | shutil.rmtree(dir_calcs, ignore_errors=True) 107 | time.sleep(1) 108 | 109 | # Make new folders for parallel calculations 110 | os.makedirs(dir_struct, exist_ok=True) 111 | os.makedirs(dir_calcs, exist_ok=True) 112 | time.sleep(1) 113 | 114 | shutil.copytree("simul_files", 115 | os.path.join(dir_calcs, f"{dir_calcs}_{pid+1}"), 116 | dirs_exist_ok=True) 117 | time.sleep(2) 118 | 119 | 120 | def compute_dhkl(crystal: str, plane: list, a: float, c: float = 0) -> float: 121 | """ 122 | Compute the interplanar spacing. 123 | 124 | Args: 125 | crystal (str): The base crystal structure. 126 | 127 | plane (list): The indices of the plane. 128 | 129 | a (float): The lattice constant. 130 | 131 | c (float): The lattice constant (only used for HCP). 132 | Default is 0. 133 | 134 | Raises: 135 | Exception: Structure must be {fcc, bcc, dc, hcp}. 136 | 137 | Returns: 138 | dhkl (float): Distance between hkl planes. 139 | """ 140 | if crystal.lower() in ["fcc", "bcc", "dc"]: 141 | return a / np.sqrt(plane[0]**2 + plane[1]**2 + plane[2]**2) 142 | elif crystal.lower() in ["hcp"]: 143 | return 1 / np.sqrt(4/3 * (plane[0]**2 + plane[0]*plane[1] + plane[1]**2) / a**2 + \ 144 | plane[3]**2 / c**2) 145 | else: 146 | raise Exception(f"Crystal structure '{crystal}' is not yet supported.") 147 | 148 | 149 | def make_crystals(struct: dict, debug: bool = False) -> Tuple[Lattice, Lattice, float]: 150 | """ 151 | Make the two crystallites or read in from files. Assumes z-axis is GB normal. 152 | 153 | Args: 154 | struct (dict): Dictionary with structure parameters. 155 | 156 | debug (bool, optional): Flag for running in DEBUG mode. 157 | Defaults to False. 158 | 159 | Raises: 160 | Exception: Structure must be {fcc, bcc, dc, hcp}. 161 | 162 | Returns: 163 | Tuple[Lattice, Lattice, float]: The lower and upper slabs, respectively. 164 | Also returns the minimum normal component of a lattice vector. 165 | """ 166 | init_size = (1, 1, struct["size"][2]) 167 | if struct["user"]: 168 | upper_crystal = ase.io.read("POSCAR_UPPER", format="vasp") 169 | lower_crystal = ase.io.read("POSCAR_LOWER", format="vasp") 170 | dlat = struct["dlat"] 171 | else: 172 | if struct["crystal"] == "fcc": 173 | upper_crystal = FaceCenteredCubic( 174 | symbol=struct["symbol"], 175 | latticeconstant=struct["a"], 176 | directions=struct["upper_dirs"], 177 | size=init_size) 178 | lower_crystal = FaceCenteredCubic( 179 | symbol=struct["symbol"], 180 | latticeconstant=struct["a"], 181 | directions=struct["lower_dirs"], 182 | size=init_size) 183 | elif struct["crystal"] == "bcc": 184 | upper_crystal = BodyCenteredCubic( 185 | symbol=struct["symbol"], 186 | latticeconstant=struct["a"], 187 | directions=struct["upper_dirs"], 188 | size=init_size) 189 | lower_crystal = BodyCenteredCubic( 190 | symbol=struct["symbol"], 191 | latticeconstant=struct["a"], 192 | directions=struct["lower_dirs"], 193 | size=init_size) 194 | elif struct["crystal"] == "dc": 195 | upper_crystal = Diamond( 196 | symbol=struct["symbol"], 197 | latticeconstant=struct["a"], 198 | directions=struct["upper_dirs"], 199 | size=init_size) 200 | lower_crystal = Diamond( 201 | symbol=struct["symbol"], 202 | latticeconstant=struct["a"], 203 | directions=struct["lower_dirs"], 204 | size=init_size) 205 | elif struct["crystal"] == "sc": 206 | upper_crystal = SimpleCubic( 207 | symbol=struct["symbol"], 208 | latticeconstant=struct["a"], 209 | directions=struct["upper_dirs"], 210 | size=init_size) 211 | lower_crystal = SimpleCubic( 212 | symbol=struct["symbol"], 213 | latticeconstant=struct["a"], 214 | directions=struct["lower_dirs"], 215 | size=init_size) 216 | elif struct["crystal"] == "hcp": 217 | upper_crystal = HexagonalClosedPacked( 218 | symbol=struct["symbol"], 219 | latticeconstant=(struct["a"], struct["c"]), 220 | directions=struct["upper_dirs"], 221 | size=init_size) 222 | lower_crystal = HexagonalClosedPacked( 223 | symbol=struct["symbol"], 224 | latticeconstant=(struct["a"], struct["c"]), 225 | directions=struct["lower_dirs"], 226 | size=init_size) 227 | else: 228 | raise Exception(f"Crystal structure '{struct['crystal']}' is not yet supported.") 229 | 230 | # Shift atoms slightly to add tolerance 231 | upper_crystal.positions += [0, P_SHIFT, Z_THRESH] 232 | upper_crystal.wrap() 233 | lower_crystal.positions += [0, P_SHIFT, Z_THRESH] 234 | lower_crystal.wrap() 235 | 236 | # Chop off excess crystal to speed up simulations 237 | names = ["lower", "upper"] 238 | for i,c in enumerate([lower_crystal, upper_crystal]): 239 | if c.cell[2, 2] > struct["cutoff"] and struct["cutoff"]: 240 | nvec = struct[f"{names[i]}_dirs"][2] 241 | dspace = compute_dhkl(struct["crystal"], nvec, struct["a"], struct["c"]) 242 | if debug: print(f"Interplanar spacing for {names[i]} is {dspace:.6f} A.") 243 | zmax = (struct["cutoff"] // dspace + 1) * dspace - Z_THRESH + min(c.positions[:, 2].round(6)) 244 | del c[[a.index for a in c if a.position[2] > zmax]] 245 | c.cell[2, 2] = zmax 246 | 247 | # Calculate dlat for later calculation of Nplane 248 | if struct["crystal"] in ["fcc", "bcc", "sc"]: 249 | unique_z = sorted(list(set(lower_crystal.positions[:, 2].round(6)))) 250 | elif struct["crystal"] == "dc": 251 | parentlat = FaceCenteredCubic( 252 | symbol=struct["symbol"], 253 | latticeconstant=struct["a"], 254 | directions=struct["lower_dirs"], 255 | size=init_size) 256 | unique_z = sorted(list(set(parentlat.positions[:, 2].round(6)))) 257 | elif struct["crystal"] == "hcp": 258 | parentlat = Hexagonal( 259 | symbol=struct["symbol"], 260 | latticeconstant=(struct["a"], struct["c"]), 261 | directions=struct["lower_dirs"], 262 | size=init_size) 263 | unique_z = sorted(list(set(parentlat.positions[:, 2].round(6)))) 264 | dlat = abs(unique_z[1] - unique_z[0]) 265 | 266 | # Save the structures (POSCAR_*) to the current directory 267 | if struct["write"]: 268 | ase.io.write("POSCAR_UPPER", upper_crystal, format="vasp") 269 | ase.io.write("POSCAR_LOWER", lower_crystal, format="vasp") 270 | 271 | # Warn if slabs are too short in z direction (arbitrarily chosen) 272 | if upper_crystal.cell[2, 2] < 20: 273 | print(f"WARNING!! Upper slab has height {upper_crystal.cell[2, 2]:.2f}A, " + \ 274 | "which is small. Results may be inaccurate.") 275 | if lower_crystal.cell[2, 2] < 20: 276 | print(f"WARNING!! Lower slab has height {upper_crystal.cell[2, 2]:.2f}A, " + \ 277 | "which is small. Results may be inaccurate.") 278 | 279 | return lower_crystal, upper_crystal, dlat 280 | 281 | 282 | def compute_unit_props(slab: Lattice) -> Tuple[int, int]: 283 | """ 284 | Compute ngb for unit plane and the number of planes in one d-spacing. 285 | 286 | Args: 287 | slab (Lattice): One of the slabs in the bicrystal. 288 | 289 | Returns: 290 | npp_unit (int): Number of atoms in one plane in unit cell. 291 | 292 | npl_unit (int): Number of different planes in unit cell. 293 | """ 294 | npp_unit = sum(slab.positions[:, 2] < min(slab.positions[:, 2]) + Z_THRESH) 295 | zpos = np.sort(np.unique((np.round(slab.positions[:,2], 5)))) 296 | diff = [zpos[i+1] - zpos[i] for i in range(len(zpos)-1)] 297 | npl_unit = len(np.unique(np.round(diff, 2))) 298 | return npp_unit, npl_unit 299 | 300 | 301 | def compute_weights(struct: dict) -> dict: 302 | """ 303 | Compute the weights for sampling repetitions. 304 | 305 | Args: 306 | struct (dict): Dictionary with structure parameters. 307 | 308 | Returns: 309 | weights (dict): Dictionary of weights for sampling repetitions. 310 | """ 311 | nx = np.arange(struct["size0"][0], struct["size"][0] + 1) 312 | ny = np.arange(struct["size0"][1], struct["size"][1] + 1) 313 | nnx = struct["size"][0] - struct["size0"][0] + 1 314 | nny = struct["size"][1] - struct["size0"][1] + 1 315 | if struct["reps"] == 1: # sample exact replications 316 | wx = np.zeros(nnx) 317 | wx[-1] = 1 318 | wy = np.zeros(nny) 319 | wy[-1] = 1 320 | elif struct["reps"] == 2: # uniformly sample replications 321 | wx = np.ones(nnx) / nnx 322 | wy = np.ones(nny) / nny 323 | elif struct["reps"] == 3: # weighted negative exponential smaller 324 | wx = np.exp(-nx) / sum(np.exp(-nx)) 325 | wy = np.exp(-ny) / sum(np.exp(-ny)) 326 | else: # weighted negative exponential larger 327 | wx = np.exp(-nx) / sum(np.exp(-nx)) 328 | wy = np.exp(-ny) / sum(np.exp(-ny)) 329 | wx = wx[::-1] 330 | wy = wy[::-1] 331 | weights = {'nx':nx, 'wx':wx, 'ny':ny, 'wy':wy} 332 | 333 | return weights 334 | 335 | 336 | def get_xy_translation(slab: Lattice, rng: np.random.Generator, ngrid: int, 337 | pid: int, debug: bool = False) -> Tuple[float, float]: 338 | """ 339 | Calculate translations in x and y. 340 | 341 | Args: 342 | slab (Lattice): One of the slabs in the bicrystal. 343 | 344 | rng (Generator): Random number generator from NumPy. 345 | 346 | ngrid (int): Number of grid points in one dimension. 347 | 348 | pid (int): Current process ID. 349 | 350 | debug (bool, optional): Flag for running in DEBUG mode. 351 | Defaults to False. 352 | 353 | Returns: 354 | Tuple[float, float]: Translations in x and y, respectively. 355 | """ 356 | if not debug: 357 | if "SLURM_NPROCS" in os.environ: 358 | nproc = int(os.environ["SLURM_NPROCS"]) 359 | elif "PBS_TASKNUM" in os.environ: 360 | nproc = int(os.environ["NCPUS"]) 361 | else: 362 | nproc = 1 363 | else: 364 | nproc = 1 365 | 366 | # Create grid for translations 367 | grid = {"x": nproc * ngrid, 368 | "y": nproc * ngrid} 369 | 370 | dx = rng.uniform(0.0, slab.cell[0, 0]) 371 | y_translation = np.linspace(0, slab.cell[1, 1], grid["y"] + 1) 372 | first = int(pid / nproc * grid["y"]) 373 | last = int((pid + 1) / nproc * grid["y"]) 374 | dy = rng.uniform(y_translation[first], y_translation[last]) 375 | return dx, dy 376 | 377 | 378 | def get_xy_replications(rng: np.random.Generator, weights: dict) -> Tuple[int, int]: 379 | """ 380 | Make replications in x and y with weight probabilities. 381 | 382 | Args: 383 | rng (Generator): Random number generator from NumPy. 384 | 385 | weights (dict): Dictionary of weights for sampling repetitions. 386 | 387 | Returns: 388 | Tuple[int, int]: Replications in x and y, respectively. 389 | """ 390 | rx = rng.choice(weights['nx'], p=weights['wx']) 391 | ry = rng.choice(weights['ny'], p=weights['wy']) 392 | return rx, ry 393 | 394 | --------------------------------------------------------------------------------