diff --git a/examples-mechanical-simulations/LixSi/2-MD Simulation/Li_13-Si_4-bulk-stretch.in b/examples-mechanical-simulations/LixSi/2-MD Simulation/Li_13-Si_4-bulk-stretch.in new file mode 100644 index 0000000..f04f635 --- /dev/null +++ b/examples-mechanical-simulations/LixSi/2-MD Simulation/Li_13-Si_4-bulk-stretch.in @@ -0,0 +1,99 @@ +#========== Basic Settings ========== + +units metal +dimension 3 +boundary p p p +atom_style atomic +atom_modify map yes +variable dt equal 0.001 +timestep ${dt} + +#========== Model ========== + +read_data LiSi.data +variable voll equal 1.6e6 +variable Vol equal vol + +#========== Force Fields ========== + +pair_style aenet Li.pytorch.nn Si.pytorch.nn +pair_coeff * * + +#========== Neighbor Lists ========== + +neighbor 2.0 bin +neigh_modify every 10 delay 10 check yes + +#========== Computes ========== + +compute 1 all stress/atom NULL +compute 2 all reduce sum c_1[1] c_1[2] c_1[3] + +#========== Energy Minimization ========== + +min_style cg +minimize 1.0e-7 1.0e-7 1000 1000 + +#========== Equalibration ========== + +variable Tdamp equal "v_dt*100" +fix 1 all nvt temp 300.0 300.0 ${Tdamp} +thermo 100 +thermo_style custom step pxx pyy pzz temp press pe ke lx ly lz c_2[1] c_2[2] c_2[3] +dump 1 all xyz 100 relax.xyz +run 20000 +write_restart restart_hpc.20000 +unfix 1 +undump 1 +variable tem equal "ly" +variable L0 equal ${tem} + +#========== Deformation ========== + +reset_timestep 0 +#read_restart restart.10000 +variable Pdamp equal "v_dt*1000" +fix 1 all npt temp 300.0 300.0 ${Tdamp} x 1 1 ${Pdamp} z 1 1 ${Pdamp} drag 1 +variable srate equal 1.0e10 +variable srate1 equal "v_srate/1.0e12" + +fix add1 all ave/time 1 10 10 c_2[1] c_2[2] c_2[3] +#fix add2 all ave/time 1 10 10 v_Vol +#fix add3 all ave/time 1 10 10 c_1[1] c_1[2] c_1[3] + + +fix 2 all deform 1 y erate ${srate1} units box remap x + +#========== Outputs ========== + +variable ConvCoeff equal 1.0e-4 +variable sigmaxx1 equal "c_2[1]/v_voll*v_ConvCoeff" +variable sigmayy1 equal "c_2[2]/v_voll*v_ConvCoeff" +variable sigmazz1 equal "c_2[3]/v_voll*v_ConvCoeff" + +variable sigmaxx2 equal "f_add1[1]/v_Vol*v_ConvCoeff" +variable sigmayy2 equal "f_add1[2]/v_Vol*v_ConvCoeff" +variable sigmazz2 equal "f_add1[3]/v_Vol*v_ConvCoeff" + + +variable strain2perDT equal "1.0e10*v_dt*1.0e-12" +variable strain2 equal "v_strain2perDT*(step)" + +variable strain1 equal "(ly-v_L0)/v_L0" +variable p1 equal "-pxx/10000" +variable p2 equal "-pyy/10000" +variable p3 equal "-pzz/10000" + +thermo 200 +thermo_style custom step temp v_strain1 v_p1 v_p2 v_p3 ke pe press ly v_strain2 v_sigmaxx1 v_sigmayy1 v_sigmazz1 v_sigmaxx2 v_sigmayy2 v_sigmazz2 +dump 1 all atom 200 tensile_movie.lammpstrj + +#dump 2 all custom 5000 dump.stress.* id type x y z f_add3[1] f_add3[2] f_add3[3] + +fix 3 all print 10 "${strain1} ${p1} ${p2} ${p3}" file strain1-stress1.txt screen no +fix 4 all print 10 "${strain2} ${sigmaxx1} ${sigmayy1} ${sigmazz1}" file strain2-stress2.txt screen no +fix 42 all print 10 "${strain2} ${sigmaxx2} ${sigmayy2} ${sigmazz2}" file strain3-stress3.txt screen no +run 60000 +write_restart restart_hpc.deform.60000 + +