LAMMPS from scratch · 20 min

How LAMMPS reads one line

Before LAMMPS does anything with a line, it joins continued lines, cuts off comments, replaces variables with their values and splits the result into words. You follow these six steps in the real source, run any line through a line reader that predicts each step, and check the prediction against LAMMPS.

The six steps between a line of text and a command being run, in input.cpp
The rules for &, #, $x, ${name} and $(formula), including a 15-digit trap
Use variables in the melt script and confirm by hand that nothing changes

1 · Understand: six steps for every line

Step	What happens	Where in input.cpp
1. read	take the next line of the file	`Input::file()`, line 196
2. join	a line ending in `&` is joined to the next (the & becomes a space)	line 205: "if line ends in continuation char '&'"
3. strip	everything from `#` on is a comment, unless the # is inside quotes	lines 444–472
4. substitute	`$x`, `${name}` and `$(formula)` are replaced by values, except inside quotes (a command such as print substitutes its quoted text itself, later)	line 488: `substitute(copy,…)`
5. split	cut into words at spaces; text in quotes stays one word (quotes removed)	`nextword()`, line 525
6. run	the first word is the command; LAMMPS looks it up and runs it with the other words	`execute_command()`, line 764

The comment step in the real code, translated:

// strip a # comment by replacing it with 0 // do not treat a # inside single/double/triple quotes as a comment while (*ptr) { walk along the line, one character at a time if (*ptr == '#') { found a # outside quotes: *ptr = '\0'; end the line here break; } if (*ptr == '\'') { … } a quote: jump to the matching quote

Step 6 is a long list of names (if (mycmd == "clear") … else if (mycmd == "units") …), followed by a lookup table for commands such as run and velocity. A name in neither gives the error "Unknown command".

Write	Means	Example (rc = 2.0)
`$x`	the variable with the one-letter name x	`$n` → 10
`${name}`	the variable called name; an equal-style formula is printed with 15 digits	`${rc}` → 2
`$(formula)`	work out the formula now, print with up to 20 digits	`$(v_rc+0.5)` → 2.5
`$(formula:%.4f)`	the same, with your own format	`$(v_rc/3:%.4f)` → 0.6667

2 · Modify and observe: the line reader

Pick an example or type your own line and variables. The page predicts every step; "Check with LAMMPS" asks the real LAMMPS to print the substituted line.

Variables defined earlier in the script The line (or lines) LAMMPS reads

3 · Match: variables change nothing when the values are the same

Here is melt with the temperature and the cutoff written as variables: T = 2*1.5 and the cutoff $(v_rc+0.5) with rc = 2.0. Step 4 turns them into 3 and 2.5, so the hand prediction for step 0 is exactly the original line.

variable T equal 2*1.5 variable rc equal 2.0 … velocity all create ${T} 87287 loop geom → create 3 87287 pair_style lj/cut $(v_rc+0.5) → lj/cut 2.5 pair_coeff 1 1 1.0 1.0 $(v_rc+0.5) # same cutoff → 1 1 1.0 1.0 2.5 predicted step 0: E_pair −6.7733681 TotEng −2.2744931 Press −3.7033504

Your turn

1. What does LAMMPS make of pair_coeff 1 1 1.0 1.0 2.5#cutoff?

The # starts a comment even with no space before it, so the line becomes pair_coeff 1 1 1.0 1.0 2.5. Try it in the line reader.

2. With variable third equal 1/3, why does $(v_third) print 0.33333333333333298176 but $(1/3) prints 0.33333333333333331483?

3. You write variable rc equal 2.5 and then pair_style lj/cut $rc. What goes wrong?

$rc means the one-letter variable r followed by the letter c. If r is not defined LAMMPS stops with an error; if it is, you get a wrong number. Names longer than one letter need braces: ${rc}.