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4. How-to discussions

The following sections describe what commands can be used to perform certain kinds of LAMMPS simulations.

4.1 Restarting a simulation
4.2 2d simulations
4.3 CHARMM and AMBER force fields
4.4 Running multiple simulations from one input script
4.5 Parallel tempering
4.6 Granular models
4.7 TIP3P water model
4.8 TIP4P water model

The example input scripts included in the LAMMPS distribution and highlighted in this section also show how to setup and run various kinds of problems.


4.1 Restarting a simulation

There are 3 ways to continue a long LAMMPS simulation. Multiple run commands can be used in the same input script. Each run will continue from where the previous run left off. Or binary restart files can be saved to disk using the restart command. At a later time, these binary files can be read via a read_restart command in a new script. Or they can be converted to text data files and read by a read_data command in a new script. This section discusses the restart2data tool that is used to perform the conversion.

Here we give examples of 2 scripts that read either a binary restart file or a converted data file and then issue a new run command to continue where the previous run left off. They illustrate what settings must be made in the new script. Details are discussed in the documentation for the read_restart and read_data commands.

Look at the in.chain input script provided in the bench directory of the LAMMPS distribution to see the original script that these 2 scripts are based on. If that script had the line

restart	        50 tmp.restart 

added to it, it would produce 2 binary restart files (tmp.restart.50 and tmp.restart.100) as it ran.

This script could be used to read the 1st restart file and re-run the last 50 timesteps:

read_restart	tmp.restart.50 
neighbor	0.4 bin
neigh_modify	every 1 delay 1 
fix		1 all nve
fix		2 all langevin 1.0 1.0 10.0 904297 
timestep	0.012 
run		50 

Note that the following commands do not need to be repeated because their settings are included in the restart file: units, atom_style, special_bonds, pair_style, bond_style. However these commands do need to be used, since their settings are not in the restart file: neighbor, fix, timestep.

If you actually use this script to perform a restarted run, you will notice that the thermodynamic data match at step 50 (if you also put a "thermo 50" command in the original script), but do not match at step 100. This is because the fix langevin command uses random numbers in a way that does not allow for perfect restarts.

As an alternate approach, the restart file could be converted to a data file using this tool:

restart2data tmp.restart.50 tmp.restart.data 

Then, this script could be used to re-run the last 50 steps:

units		lj
atom_style	bond
pair_style	lj/cut 1.12
pair_modify	shift yes
bond_style	fene
special_bonds   0.0 1.0 1.0 
read_data	tmp.restart.data 
neighbor	0.4 bin
neigh_modify	every 1 delay 1 
fix		1 all nve
fix		2 all langevin 1.0 1.0 10.0 904297 
timestep	0.012 
reset_timestep	50
run		50 

Note that nearly all the settings specified in the original in.chain script must be repeated, except the pair_coeff and bond_coeff commands since the new data file lists the force field coefficients. Also, the reset_timestep command is used to tell LAMMPS the current timestep. This value is stored in restart files, but not in data files.


4.2 2d simulations

Use the dimension command to specify a 2d simulation.

Make the simulation box periodic in z via the boundary command. This is the default.

If using the create box command to define a simulation box, set the z dimensions narrow, but finite, so that the create_atoms command will tile the 3d simulation box with a single z plane of atoms - e.g.

create box 1 -10 10 -10 10 -0.25 0.25 

If using the read data command to read in a file of atom coordinates, set the "zlo zhi" values to be finite but narrow, similar to the create_box command settings just described. For each atom in the file, assign a z coordinate so it falls inside the z-boundaries of the box - e.g. 0.0.

Use the fix enforce2d command as the last defined fix to insure that the z-components of velocities and forces are zeroed out every timestep. The reason to make it the last fix is so that any forces induced by other fixes will be zeroed out.

Many of the example input scripts included in the LAMMPS distribution are for 2d models.


4.3 CHARMM and AMBER force fields

There are many different ways to compute forces in the CHARMM and AMBER molecular dynamics codes, only some of which are available as options in LAMMPS. A force field has 2 parts: the formulas that define it and the coefficients used for a particular system. Here we only discuss formulas implemented in LAMMPS. Setting coefficients is done in the input data file via the read_data command or in the input script with commands like pair_coeff or bond_coeff. See this section for additional tools that can use CHARMM or AMBER to assign force field coefficients and convert their output into LAMMPS input.

These style choices compute force field formulas that are consistent with common options in CHARMM or AMBER. See each command's documentation for the formula it computes.


4.4 Running multiple simulations from one input script

This can be done in several ways. See the documentation for individual commands for more details on how these examples work.

If "multiple simulations" means continue a previous simulation for more timesteps, then you simply use the run command multiple times. For example, this script

units lj
atom_style atomic
read_data data.lj
run 10000
run 10000
run 10000
run 10000
run 10000 

would run 5 successive simulations of the same system for a total of 50,000 timesteps.

If you wish to run totally different simulations, one after the other, the clear command can be used in between them to re-initialize LAMMPS. For example, this script

units lj
atom_style atomic
read_data data.lj
run 10000
clear
units lj
atom_style atomic
read_data data.lj.new
run 10000 

would run 2 independent simulations, one after the other.

For large numbers of independent simulations, you can use variables and the next and jump commands to loop over the same input script multiple times with different settings. For example, this script, named in.polymer

variable d index run1 run2 run3 run4 run5 run6 run7 run8
cd $d
read_data data.polymer
run 10000
cd ..
clear
next d
jump in.polymer 

would run 8 simulations in different directories, using a data.polymer file in each directory. The same concept could be used to run the same system at 8 different temperatures, using a temperature variable and storing the output in different log and dump files, for example

variable a loop 8
variable t index 0.8 0.85 0.9 0.95 1.0 1.05 1.1 1.15
log log.$a
read data.polymer
velocity all create $t 352839
fix 1 all nvt $t $t 100.0
dump 1 all atom 1000 dump.$a
run 100000
next t
next a
jump in.polymer 

All of the above examples work whether you are running on 1 or multiple processors, but assumed you are running LAMMPS on a single partition of processors. LAMMPS can be run on multiple partitions via the "-partition" command-line switch as described in this section of the manual.

In the last 2 examples, if LAMMPS were run on 3 partitions, the same scripts could be used if the "index" and "loop" variables were replaced with universe-style variables, as described in the variable command. Also, the "next t" and "next a" commands would need to be replaced with a single "next a t" command. With these modifications, the 8 simulations of each script would run on the 3 partitions one after the other until all were finished. Initially, 3 simulations would be started simultaneously, one on each partition. When one finished, that partition would then start the 4th simulation, and so forth, until all 8 were completed.


4.5 Parallel tempering

The temper command can be used to perform a parallel tempering or replica-exchange simulation where multiple copies of a simulation are run at different temperatures on different sets of processors, and Monte Carlo temperature swaps are performed between pairs of copies.

Use the -procs and -in command-line switches to launch LAMMPS on multiple partitions.

In your input script, define a set of temperatures, one for each processor partition, using the variable command:

variable t proc 300.0 310.0 320.0 330.0 

Define a fix of style nvt or langevin to control the temperature of each simulation:

fix myfix all nvt $t $t 100.0 

Use the temper command in place of a run command to perform a simulation where tempering exchanges will take place:

temper 100000 100 $t myfix 3847 58382 

4.6 Granular models

To run a simulation of a granular model, you will want to use the following commands:

Use one of these 3 pair potentials:

These commands implement fix options specific to granular systems:

The fix style freeze zeroes both the force and torque of frozen atoms, and should be used for granular system instead of the fix style setforce.

For computational efficiency, you can eliminate needless pairwise computations between frozen atoms by using this command:


4.7 TIP3P water model

The TIP3P water model as implemented in CHARMM (MacKerell) specifies a 3-site rigid water molecule with charges and Lennard-Jones parameters assigned to each of the 3 atoms. In LAMMPS the fix shake command can be used to hold the two O-H bonds and the H-O-H angle rigid. A bond style of harmonic and an angle style of harmonic or charmm should also be used. These are the additional parameters (in real units) to set for O and H atoms and the water molecule to run a TIP3P model:

O charge = -0.834
H charge = 0.417

O mass = 15.9994
H mass = 1.008

LJ epsilon of O = 0.1521
LJ sigma of O = 3.15057
LJ epsilon of H = 0.046
LJ sigma of H = 0.400014

K of O-H bond = 450
r0 of O-H bond = 0.9572

K of H-O-H angle = 55
theta of H-O-H angle = 104.52

Note: If the LJ epsilon and sigma for H are set to 0.0, it corresponds to the original 1983 TIP3P model (Jorgensen).


4.7 TIP4P water model

The four-point TIP4P water model extends the traditional three-point TIP3P model by adding an additional site, usually massless, where the charge associated with the oxygen atom is placed. This M site is located at a fixed distance away from the oxygen along the bisector of the HOH bond angle.

Two different four-point models can be implemented using the pair styles with tip4p in their style name. For both these models, the bond lengths and bond angles should be held fixed using the fix shake command. The following parameters, in real units, should be used to specify the other parameters that match the original TIP4P model (Jorgensen).

O mass = 15.9994
H mass = 1.008

O charge = -1.040
H charge = 0.520

OH bond length = 0.9572
HOH bond angle = 104.52

OM distance = 0.15

LJ epsilon of O-O = 0.1550
LJ sigma of O-O = 3.1526

LJ epsilon, sigma of O-H, H-H = 0.0

An alternate four-point model, the TIP4P-Ew model (Horn), is identical, except for the following parameters:

O charge = -1.084
H charge = 0.5242

OM distance = 0.1250

LJ epsilon of O-O = 0.16275
LJ sigma of O-O = 3.16435

Note that the OM distance is specified in the pair_style command, not as part of the pair coefficients.


(Horn) Horn, Swope, Pitera, Madura, Dick, Hura, and Head-Gordon, J Chem Phys, 120, 9665 (2004).

(MacKerell) MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field, Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).

(Jorgensen) Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem Phys, 79, 926 (1983).