The initial coordinates of the isobutane molecule are given below. You can copy and paste the information in a file named isobutane.dat.
# Sample LAMMPS data file for isobutane (methylpropane) (C4H10) # This file is used with the LAMMPS input file isobutane.in # Reference: Physical Chemistry Chemical Physics, 16(13) (2014):6233-6249. # Will reproduce the uncorrected MEAM value for Isobutane in Table 3, Column 4 of the paper. 14 atoms -1000.000000 1000.000000 xlo xhi -1000.000000 1000.000000 ylo yhi -1000.000000 1000.000000 zlo zhi 2 atom types Masses 1 12.0111 2 1.0079 Atoms 1 1 -3.562470 -0.260470 -0.116530 2 1 -2.438430 0.633300 0.403110 3 1 -1.077080 0.080400 -0.013190 4 1 -2.613790 2.064060 -0.101360 5 2 -4.540900 0.132060 0.180090 6 2 -3.471380 -1.273370 0.290050 7 2 -3.542640 -0.331510 -1.209220 8 2 -2.485530 0.645380 1.498590 9 2 -0.947440 -0.946270 0.345340 10 2 -0.267740 0.686240 0.408140 11 2 -0.964560 0.076010 -1.102550 12 2 -1.807410 2.708080 0.265230 13 2 -3.562660 2.484470 0.248610 14 2 -2.609090 2.104430 -1.195780
The following script performs energy minimization of the isobutane structure. You can save the information in an input file named isobutane.in.
# Sample LAMMPS input script for the energy minimization of isobutane (methylpropane) (C4H10) # This file is used with the isobutane.dat file and the MEAM parameter files. # Reference: Physical Chemistry Chemical Physics, 16(13) (2014):6233-6249. # Will reproduce the uncorrected MEAM value for Isobutane in Table 3, Column 4 of the paper. # ------------------ Initialize Simulation ----------------------- clear units metal boundary p p p atom_style atomic read_data Isobutane.dat # --------------- Define Interatomic Potential ------------------- pair_style meam pair_coeff * * CH_library.meam C H CH.meam C H # -------------------- Define Output ----------------------------- dump coord all custom 1 Isobutane.dump id type x y z # ------------------- Run Minimization --------------------------- minimize 1e-25 1e-25 10000 10000