# LJ Fluid In this hands-on guide, we'll use LAMMPS to simulate a mixture of two fluids (binary fluid) and study the phase separation. The fluids are modeled as Lennard-Jones particles confined within a cubic box with continuous boundaries (periodic boundary conditions). We'll employ a Langevin thermostat to control the temperature, and calculate fundamental properties like potential and kinetic energies. This tutorial serves as a stepping stone, showcasing essential elements of molecular dynamics simulations, including setting up the system, minimizing energy, solving the equations of motion, and visualizing the resulting particle trajectories. ## Introduction to simple LAMMPS script In order to go through step by step lets consider the simulation framework. Simulation might contains several files. But here we mainly focus on: - a) `run.in` -- it cpntains mostly all the informations - b) `system.data` -- particles, positions, velocities, bonds, angles, information `````{admonition} run.in :class: tip - **1) Initialization:** units, dimension, atom_style, pair_style boundary _etc._ - **2a) System definition:** either load `system.data` or `create_atoms` - **2b) Bond and Angle information:** `pair_coeff`, `angle_coeff`, `mass` - **3) Minimization:** to avoid initial overlaps - **4) Visualization:** Check whether particles are in the box _etc._ - **5) Dummy Run:** Initially run for small timesteps _i.e.,_ $\sim 10^5$ - **6) Reset time:** `write_data` , `reset_timesteps` - **7) Final Run:** ````` `````{admonition} With the help of ChatGPT you can built your first simulation :class: note ``` `Promt:` I am a beginner looking to learn the LAMMPS package from scratch. Could you provide me with step-by-step instructions on how to set up and run basic simulations? Specifically, I'd like: - 1. Detailed instructions on installing LAMMPS on my operating system. - 2. An overview of the structure of a LAMMPS input script. - 3. A couple of simple example simulations, including the full input script for each. - 4. Instructions on how to run these simulations. - 5. Tips on how to analyze the output and visualize the results. - 6. Recommendations for further learning resources or tutorials. Please provide the input scripts and any necessary commands to run the simulations. ``` ````` `````{admonition} [system.data:](https://shuvo-dip.github.io/MD_Simulation/lj_fluid.html) an example of lammps generated system file :class: tip ``` LAMMPS data file via write_data, version 3 Mar 2020, timestep = 0 200 atoms 5 atom types 199 bonds 1 bond types 198 angles 1 angle types 0.0000000000000000e+00 5.0000000000000000e+01 xlo xhi 0.0000000000000000e+00 5.0000000000000000e+01 ylo yhi 0.0000000000000000e+00 5.0000000000000000e+01 zlo zhi Masses 1 1 2 1 3 1 4 1 5 1 Atoms # full 35 1 4 0.0000000000000000e+00 4.6927442356735957e-04 2.5917304644577136e+01 9.2446343214115345e-01 1 0 1 24 1 3 0.0000000000000000e+00 4.4738596798170382e+00 2.7817888523819551e+01 5.6717976560832186e+00 1 0 1 200 1 1 0.0000000000000000e+00 5.9147516604228179e-01 1.8162531643029414e+01 4.7691758446364831e+00 1 0 1 166 1 5 0.0000000000000000e+00 1.4206564943257913e-01 2.5387383075812657e+01 4.9959602477906309e+01 1 0 0 168 1 3 0.0000000000000000e+00 5.9831302455988533e-01 2.7059222183708062e+01 4.9375698118072819e+01 1 0 0 167 . . . 198 1 3 0.0000000000000000e+00 4.9886372673067399e+01 1.9279039503505089e+01 3.3634226785821535e+00 0 0 1 188 1 3 0.0000000000000000e+00 4.9545910789376187e+01 2.5180567455466711e+01 4.8987638671791863e+01 0 0 0 89 1 2 0.0000000000000000e+00 4.9901224571757616e+01 1.5141601528783990e+01 4.6754960184097342e+01 0 0 0 114 1 3 0.0000000000000000e+00 4.9958704483647480e+01 2.1674563605430009e+01 1.3738041526491067e+01 0 0 1 Velocities 35 -8.7770147801311138e-01 1.5101693717367606e+00 6.0446096933556570e-01 24 -9.9424974102245878e-01 1.3375187903264580e+00 2.5207278347123672e+00 200 1.1303805073183029e+00 6.5838908974304966e-01 1.6455895349853347e+00 166 -2.1711562280283929e+00 5.5739576720902884e-01 -2.4101260924931348e-01 168 3.9698835008419225e-02 5.8955871401596471e-01 2.3171435957398314e+00 . . . 188 -1.8696257894080665e-01 -1.1207437904225968e+00 -3.9930018404493181e-03 89 2.9740209786705213e-01 7.0494417493173855e-01 7.4736174728733051e-01 114 -4.7738544094380891e-01 5.8646358115481168e-01 -1.3337631131086364e-01 Bonds 1 1 35 36 2 1 24 25 3 1 166 167 4 1 168 169 5 1 167 168 . . 198 1 89 90 199 1 114 115 Angles 1 1 34 35 36 2 1 23 24 25 3 1 165 166 167 4 1 167 168 169 . . ``` ````` ### What do these numbers mean? `````{admonition} [system.data:](https://shuvo-dip.github.io/MD_Simulation/lj_fluid.html) an example of lammps generated system file :class: tip ``` LAMMPS data file via write_data, version 3 Mar 2020, timestep = 0 200 atoms 5 atom types 199 bonds 1 bond types 198 angles 1 angle types X_low X_high xlo xhi :box dimension along x Y_low Y_high ylo yhi :box dimension along y Z_low Z_high zlo zhi :box dimension along z Masses atom_type mass 1 1 2 1 Atoms # full atom_ID molecular_ID atom_type charge x y z ix iy iz(image in the periodic boundary) 1 1 1 0 2 3 4 0 0 0 2 1 2 0 3 5 1 0 0 0 Velocities atom_ID vx vy vz 1 0.5 0.4 0.33 Bonds ID Bond_type atom1 atom2 (atom1 atom2 are sequentially connected via a bond) 1 1 1 2 2 1 2 3 Angles ID Angle_type atom1 atom2 atom3 (atom1 atom2 and atom3 are sequentially connected) 1 1 1 2 3 2 1 2 3 4 ``` :::{important} Please make sure you always keep the format fixed No space between different segements might leads to syntax error ::: ````` Lets pick an example of LJ fluid. `````{admonition} What are the parameters we need to specify :class: tip :::{important} - a) Numer of particles - b) Non-bonded interactions - c) Mass - d) Bonds, angle, dihedrals etc. - e) What type of bonds, angles, dihedrals etc. and their corresponding parameters - f) Boundaries - g) How long simulation would run - h) timesteps, otherwise defult - i) How frequently dump the configurations ::: ````` `````{admonition} Method 1: [run.in:](https://shuvo-dip.github.io/MD_Simulation/lj_fluid.html) LAMMPS script for a 10-particle LJ fluid :class: tip ``` units lj dimension 3 atom_style full pair_style lj/cut 1.112 boundary p p p region simulation_box block 0 20 0 20 0 20 create_box 1 simulation_box create_atoms 1 random 10 12345 NULL overlap 2.0 maxtry 50 mass 1 1 pair_coeff * * 1.0 1.0 thermo 100 thermo_style custom step temp pe ke etotal press timestep 0.005 fix mynve all nve fix mylgv all langevin 1.0 1.0 0.1 1530917 run 10000 reset_timestep 0 dump mydmp all atom 1000 dump.lammpstrj run 1000000 ````` ![movie](LJ_fluid/method_01/lj_fluid_method_01.gif) `````{admonition} log file :class: tip ``` . . . . 999100 1.3074207 0 1.765018 1.765018 0.0014708483 999200 1.4026846 0 1.8936242 1.8936242 0.0015780201 999300 0.72046866 0 0.9726327 0.9726327 0.00081052725 999400 0.78655881 0 1.0618544 1.0618544 0.00088487866 999500 1.0822006 0 1.4609708 1.4609708 0.0012174757 999600 0.90615892 0 1.2233145 1.2233145 0.0010194288 999700 0.985891 0 1.3309528 1.3309528 0.0011091274 999800 1.2901643 0 1.7417218 1.7417218 0.0014514348 999900 0.67689256 0 0.91380495 0.91380495 0.00076150413 1000000 0.78634406 0 1.0615645 1.0615645 0.00088463707 Loop time of 19.87 on 8 procs for 1000000 steps with 10 atoms Performance: 21741277.904 tau/day, 50327.032 timesteps/s, 503.270 katom-step/s 80.1% CPU use with 8 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.054741 | 0.057883 | 0.064233 | 1.2 | 0.29 Bond | 0.04021 | 0.042227 | 0.044459 | 0.8 | 0.21 Neigh | 0.34606 | 0.35955 | 0.37062 | 1.3 | 1.81 Comm | 7.498 | 8.0589 | 8.8711 | 16.4 | 40.56 Output | 0.57603 | 0.61785 | 0.73808 | 6.0 | 3.11 Modify | 0.16301 | 0.17659 | 0.1904 | 2.4 | 0.89 Other | | 10.56 | | | 53.13 Nlocal: 1.25 ave 4 max 0 min Histogram: 4 0 1 0 0 1 0 1 0 1 Nghost: 2.125 ave 4 max 0 min Histogram: 2 0 0 0 0 2 0 3 0 1 Neighs: 0 ave 0 max 0 min Histogram: 8 0 0 0 0 0 0 0 0 0 Total # of neighbors = 0 Ave neighs/atom = 0 Ave special neighs/atom = 0 Neighbor list builds = 78413 Dangerous builds = 0 Total wall time: 0:00:20 ````` `````{admonition} Method 2: [run.in:](https://shuvo-dip.github.io/MD_Simulation/lj_fluid.html) LAMMPS script read_data from *system_specific.data* file :class: tip ``` units lj dimension 3 atom_style full pair_style lj/cut 1.112 boundary p p p read_data system_box.data pair_coeff * * 1.0 1.0 thermo 100 thermo_style custom step temp pe ke etotal press timestep 0.005 fix mynve all nve fix mylgv all langevin 1.0 1.0 0.1 1530917 run 10000 reset_timestep 0 thermo 1000 dump mydmp all atom 1000 dump.lammpstrj run 1000000 ````` `````{admonition} Method 2: [system_box.data:](https://shuvo-dip.github.io/MD_Simulation/lj_fluid.html) LAMMPS script *system_box.data* file :class: tip ``` LAMMPS data file via write_data, version 3 Mar 2020 10 atoms 1 atom types 0 10 xlo xhi 0 10 ylo yhi 0 10 zlo zhi Masses 1 1 Atoms # full 1 1 1 0 1 1 1 2 1 1 0 2 2 2 3 1 1 0 3 1 1 4 1 1 0 4 2 2 5 1 1 0 5 1 1 6 1 1 0 6 2 2 7 1 1 0 7 1 1 8 1 1 0 8 2 2 9 1 1 0 9 1 1 10 1 1 0 1 5 2 ````` ![movie](LJ_fluid/method_02/lj_fluid_method_02.gif) `````{admonition} Method 3: [run.in:](https://shuvo-dip.github.io/MD_Simulation/lj_fluid.html) LAMMPS script read_data from *system_specific.data* file populate the box with molecules replication :class: tip ``` units lj dimension 3 atom_style full pair_style lj/cut 1.112 boundary p p p read_data system_box.data replicate 3 3 3 pair_coeff * * 1.0 1.0 thermo 100 thermo_style custom step temp pe ke etotal press timestep 0.005 fix mynve all nve fix mylgv all langevin 1.0 1.0 0.1 1530917 run 10000 reset_timestep 0 thermo 1000 dump mydmp all atom 1000 dump.lammpstrj run 1000000 ````` `````{admonition} Method 3: [system_box.data:](https://shuvo-dip.github.io/MD_Simulation/lj_fluid.html) LAMMPS script *system_box.data* file specify only one molecule and replicate it :class: tip ``` LAMMPS data file via write_data, version 3 Mar 2020, 1 atoms 1 atom types 0 2 xlo xhi 0 2 ylo yhi 0 2 zlo zhi Masses 1 1 Atoms # full 1 1 1 0 1 1 1 ````` ![movie](LJ_fluid/method_03/lj_fluid_method_03.gif) Lets pick an example of Binary mixture of LJ fluid. `````{admonition} Binary immiscible fluid :class: tip :::{important} - a) Intermolecular interaction between Phase A and Phase A attract each other - b) Intermolecular interaction between Phase B and Phase B attract each other - c) Phase A and Phase B dislike each other - d) Box is filled with Phase A and Phase B around 50%:50% ::: ````` `````{admonition} [run.in:](https://shuvo-dip.github.io/MD_Simulation/lj_fluid.html) LAMMPS script for a binary mixture of LJ fluid :class: tip ``` units lj dimension 3 atom_style full pair_style lj/smooth/linear 3.5 boundary p p p region simulation_box block 0 30 0 30 0 30 region simulation_box_sidea block 0 30 0 30 0 14.5 region simulation_box_sideb block 0 30 0 30 15 30 create_box 2 simulation_box lattice fcc 1.0 create_atoms 1 region simulation_box_sidea ratio 0.63 5478952 create_atoms 2 region simulation_box_sideb ratio 0.63 5478952 mass * 1 pair_coeff 1 1 1.0 1.0 #AA pair_coeff 1 2 1.0 0.5 #AB pair_coeff 2 2 1.0 1.0 #BB write_data system_formation.data thermo 500 thermo_style custom step temp pe ke etotal density press timestep 0.005 fix mynve all nve fix mylgv all langevin 1.0 1.0 0.1 1530917 run 10000 write_data system_after_equilibrium.data reset_timestep 0 thermo 5000 dump mydmp all atom 1000 dump.lammpstrj run 1000000 write_data system_after_longtime.data ````` ![movie](LJ_fluid/method_04/lj_binary_fluid_method_04.gif)