# Using deformations with user defined structures¶

This example demonstrates the use of the deformations. It employs the embedded atom method (EAM) potential routine together with user defined functions [MisMehPap01]. The example also illustrates the use of XML Inclusions.

## Location¶

examples/imposing_a_deformation

## Input files¶

• main.xml: main input file

  1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72  Demonstrating the usage of deformations maximum Cu 3.615 3.615 lattice_constant tetragonal_strain 
• potential.xml: initial parameter set (included in main input file via XML Inclusions)

  1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109  r (E1*(exp(-2*alpha1*(r-r01)) - 2*exp(-alpha1*(r-r01))) + E2*(exp(-2*alpha2*(r-r02)) - 2*exp(-alpha2*(r-r02))) + delta) E1*(2*alpha1*exp(-alpha1*(r-r01)) - 2*alpha1*exp(-2*alpha1*(r-r01))) + E2*(2*alpha2*exp(-alpha2*(r-r02)) - 2*alpha2*exp(-2*alpha2*(r-r02))) 2.01458e2 2.97758 0.83591 6.59288e-3 1.54927 4.46867 0.86225e-2 5.50679 r 1 - 1/(1 + ((r - cutoff) / h)^4) 4 * h^4 * (r-cutoff)^3 / ((h^4 + (r-cutoff)^4)^2) 0.50037 5.50679 r - (r < rs1 ? S1*(rs1-r)^4 : 0) - (r < rs2 ? S2*(rs2-r)^4 : 0) - (r < rs3 ? S3*(rs3-r)^4 : 0) - (r < rs1 ? -4*S1*(rs1-r)^3 : 0) - (r < rs2 ? -4*S2*(rs2-r)^3 : 0) - (r < rs3 ? -4*S3*(rs3-r)^3 : 0) 2.24000 1.80000 1.20000 4.00000 40.00000 1.15000e3 r a * exp(-beta1*(r - r03)^2) + exp(-beta2*(r - r04)) beta2*(-exp(-beta1*(r-r04))) - 2*a*beta1*(r-r03)*exp(-beta1*(r-r03)^2) 3.80362 -2.19885 -2.61984e2 0.17394 5.35661e2 5.50679 r 1 - 1/(1 + ((r - cutoff) / h)^4) 4 * h^4 * (r-cutoff)^3 / ((h^4 + (r-cutoff)^4)^2) 0.5 rho (rho < 1) ? (F0 + 0.5*F2*(rho - 1)^2 + q1*(rho-1)^3 + q2*(rho-1)^4 + q3*(rho-1)^5 + q4*(rho-1)^6) : (F0 + 0.5*F2*(rho - 1)^2 + q1*(rho-1)^3 + Q1*(rho-1)^4) / (1 + Q2*(rho-1)^3) (rho < 1) ? (rho - 1)*(F2 + 3*q1*(rho-1) + 4*q2*(rho-1)^2 + 5*q3*(rho-1)^3 + 6*q4*(rho-1)^4) : (F2*(rho-1) + 3*q1*(rho-1)^2 + 4*Q1*(rho-1)^3)/(Q2*(rho-1)^3 + 1) - (3*Q2*(rho-1)^2 * (F0 + 0.5*F2*(rho-1)^2 + q1*(rho-1)^3 + Q1*(rho-1)^4)) / ((Q2*(rho-1)^3 + 1)^2) -2.3 1.4 -1.3 -0.9 1.8 3.0 0.4 0.3 

## Output¶

• The final properties (as well as parameters) are written to standard output.

  1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 This is program version 0.1.6 Reading job file main.xml ------------------------------------------------------- Parsing input file(s) ------------------------------------------------------- EAM potential - maximum cutoff : 5.50679 Neighbor lists of structure 'conventional_fcc_cell1' will be built for the first time. Neighbor lists of structure 'conventional_fcc_cell2' will be built for the first time. ------------------------------------------------------- Computing structure properties Relaxing atomic d.o.f. of structure conventional_fcc_cell1 (#dof=9): Neighbor lists of structure 'conventional_fcc_cell1' need to be rebuilt because of cell deformation (skin=0, cell_def=0 threshold=0). force_rlx_iter=1 E=-14.2315 fnorm=9.68342e-17 Structure 'conventional_fcc_cell1': total-energy: -14.2315 eV atomic-energy: -3.55787 eV/atom total-volume: 47.2416 A^3 atomic-volume: 11.8104 A^3/atom Relaxing atomic d.o.f. of structure conventional_fcc_cell2 (#dof=9): Neighbor lists of structure 'conventional_fcc_cell2' need to be rebuilt because of cell deformation (skin=0, cell_def=0 threshold=0). force_rlx_iter=1 E=-14.17 fnorm=5.74558e-17 Structure 'conventional_fcc_cell2': total-energy: -14.17 eV atomic-energy: -3.54249 eV/atom total-volume: 49.6037 A^3 atomic-volume: 12.4009 A^3/atom ------------------------------------------------------- -------------------------------------------------------