3.3. Build atom Input

abcinp is used to generate input files for atom. Just run abcinp without any argument and it will print help information:

abcinp filename kind_of_atoms forcefield amplitude sn gmax glimit nsaves natoms1 symbol1 ...
 -- For atomic clusters:
forcefield = LennardJones:              sigma epsilon
forcefield = CoulombLennardJones:       q sigma epsilon
forcefield = Morse:                     power epsilon beta r0
forcefield = CoulombBornMayer:          q B rho
forcefield = CoulombMorseRepulsion:     q D alpha rho C
forcefield = Girifalco:                 nC A B d
forcefield = Dzugutov:                  a alpha kF b sigma m rC V0
forcefield = Gupta:                     A xi d p q
forcefield = SuttonChen:                p q epsilon a c
forcefield = SuttonChenMJB:             p epsilon a c alpha
forcefield = Tersoff:                   A B lambda mu beta m c d h R S chi omega
forcefield = ExLennardJones:            maxk c6 c7 ... cmaxk

You need to input several arguments. I will explain them one by one:

• filename The job file name. The generated input files will be named as filename.inp, filename.par and filenamei.xyz.

• kind_of_atoms The number of atomic types. For \(\left(\mathrm{MgO}\right)_{10}\) clusters, this should be 2; For \(\mathrm{B}_{20}\), this should be 1.

• forcefield The force field you want to use. All supported ones are listed in Supported Model Force Fields. Available choices: LennardJones, CoulombLennardJones, Morse, CoulombBornMayer, CoulombMorseRepulsion, Girifalco, Dzugutov, Gupta, SuttonChen, SuttonChenMJB, Tersoff, ExLennardJones.

Attention

You must input exactly the names listed above. For example, if you want to use Gupta potential, you must input Gupta. Both gupta or GUPTA will raise errors!

• amplitude The estimated size of the cluster in Angstrom. See Theoretical Background for details.

• sn The population size \(SN\). See Theoretical Background for details.

• gmax The maximum cycle number \(g_{\mathrm{max}}\). See Theoretical Background for details.

• glimit The scout limit \(g_{\mathrm{limit}}\). See Theoretical Background for details.

• nasves The number of local minima you want to save.

• natoms1 symbol1 ... For each kind of atoms, its number and symbol must be given. For \(\left(\mathrm{MgO}\right)_{10}\) clusters, this should be 10 Mg 10 O; For \(\mathrm{B}_{20}\), this should be 20 B.

After this, abcinp will ask for force field parameters. It will hint you the order of parameters, and the parameter names are exactly the same as shown in the formulas in Supported Model Force Fields. For references, below we give the correspondence between computer characters and mathematical symbols:

Potential	Computer Characters and Mathematical Symbols
Coulomb-Born-Mayer	q - \(q\), B - \(B\), rho - \(\rho\)
Lennard-Jones	sigma - \(\sigma\), epsilon - \(\epsilon\)
Coulomb-Lennard-Jones	q - \(q\), sigma - \(\sigma\), epsilon - \(\epsilon\)
Morse	power - \(n\), epsilon - \(\epsilon\), beta - \(\beta\), r0 - \(r^{0}\)
Coulomb-Morse-Repulsion	q - \(q\), D - \(D\), alpha - \(\alpha\), rho - \(\rho\), C - \(C\)
Girifalco	nC - \(N_{\mathrm{C}}\), A - \(A\), B - \(B\), d - \(d\)
Dzugutov	a - \(a\), alpha - \(\alpha\), kF - \(k_{\mathrm{F}}\), b - \(b\), sigma - \(\sigma\), m - \(m\), rC - \(r_{\mathrm{C}}\), V0 - \(V_0\)
Gupta	A - \(A\), xi - \(\xi\), d - \(d\), p - \(p\), q - \(q\)
Sutton–Chen	p - \(p\), q - \(q\), epsilon - \(\epsilon\), a - \(a\), c - \(c\)
Modified Sutton-Chen (by Januszko–Bose)	p - \(p\), epsilon - \(\epsilon\), a - \(a\), c - \(c\), alpha - \(\alpha\)
Tersoff	A - \(A\), B - \(B\), lambda - \(\lambda\), mu - \(\mu\), beta - \(\beta\), m - \(m\), c - \(c\), d - \(d\), h - \(h\), R - \(R\), S - \(S\), chi - \(\chi\), omega - \(\omega\)
Extended Lennard-Jones	maxk - \(k_{\mathrm{max}}\), c6 - \(c_6\), …

Let’s explain this with the example in Example: 38 Lennard-Jones Particles:

$ abcinp lj38 1 LennardJones 5.0 30 300 5 30 38 C
Parameters for atom 0: sigma epsilon > 1.4 1.0

This means: Perform a global optimization on a LennardJones cluster, with \(L\) = 5.0, \(SN\) = 30, \(g_{\mathrm{max}}\) = 300, \(g_{\mathrm{limit}}\) = 5, 30 local minima will be saved. We have 1 kind of particles, its number and symbol is 38 and C, respectively. The generated files will be named as lj38*.

After this, you will get three files:

• lj38.inp The main input file.

• lj38.par The parameter file.

• lj38i.xyz Initial guess of the cluster.

Let’s examine lj38.inp:

lj38.inp

38           # number of atoms
lj38i.xyz    # initial guess file ; * - random guess
LennardJones # force field types
lj38.par     # force field parameters
30           # population size
300          # maximal generations
5            # scout limit
5.00000000   # amplitude
lj38         # save optimized configuration to .xyz and .gjf
30           # number of LMs to be saved

All texts after # are comments and can be arbitrary. The meaning of each line is explained by its comment. If you do not have an initial guess, you can change line 2 to * then atom will automatically generate an initial guess.