Molecular crystal structure prediction

情報

First, see Tutorial > Random Search (RS) for basic usage of CrySPY.

In this section, we give a tutorial on the molecular structure generation part only. Since version 0.9.0, CrySPY has been able to generate random molecular crystal structures using PyXtal.

You need to use a pre-defined molecular by PyXtal’s database (see, https://pyxtal.readthedocs.io/en/latest/Usage.html?highlight=benzene#pyxtal-molecule-pyxtal-molecule)) or create molecule files that define molecular structures.

Pre-defined molecule

PyXtal currently supports C60, H2O, CH4, NH3, benzene, naphthalene, anthracene, tetracene, pentacene, coumarin, resorcinol, benzamide, aspirin, ddt, lindane, glycine, glucose, and ROY.

Let us generate molecular crystal structures that consist of 2 benzenes.

Move to your working directory, and copy input example files by one of the following methods.

Take a look at cryspy.in.

$ cat cryspy.in
[basic]
algo = RS
calc_code = QE
tot_struc = 6
nstage = 2
njob = 2
jobcmd = qsub
jobfile = job_cryspy

[structure]
struc_mode = mol
natot = 24
atype = H C
nat = 12 12
mol_file = benzene
nmol = 2

[QE]
qe_infile = pwscf.in
qe_outfile = pwscf.out
kppvol = 40  60

[option]

In generating molecular crystal structures, you have to set struc_mode = mol in the [structure] section. Molecule file(s) and the number of molecule(s) are specified as:

  • mol_file = benzene
  • nmol = 2

Run CrySPY and see the initial structures (./data/init_POSCARS).

User-defined molecule

Move to your working directory, and copy input example files for 2 formula units of Li3PS4.

  • version 1.0.0 or later
    • Copy from CrySPY utility
  • version 0.10.3 or earlier
    • cp -r ~/CrySPY_root/CrySPY-0.9.0/example/QE_Li3PS4_2fu_RS_mol .
$ cd QE_Li3PS4_2fu_RS_mol
$ ls
Li.xyz  PS4.xyz  calc_in/  cryspy.in

Molecule files of Li and PS4 are included. Supported formats in PyXtal are .xyz, .gjf, .g03, .g09, .com, .inp, .out, and pymatgen’s JSON serialized molecules.

$ cat Li.xyz
1
New structure
 Li  0.000  0.000  0.000

$ cat PS4.xyz
5
New structure
 P    0.000000    0.000000    0.000000
 S    1.200000    1.200000   -1.200000
 S    1.200000   -1.200000    1.200000
 S   -1.200000    1.200000    1.200000
 S   -1.200000   -1.200000   -1.200000

Check cryspy.in.

$ cat cryspy.in
[basic]
algo = RS
calc_code = QE
tot_struc = 4
nstage = 2
njob = 1
jobcmd = qsub
jobfile = job_cryspy

[structure]
struc_mode = mol
natot = 16
atype = Li P S
nat = 6 2 8
mol_file = ./Li.xyz  ./PS4.xyz
nmol = 6 2

[QE]
qe_infile = pwscf.in
qe_outfile = pwscf.out
kppvol = 40  60

[option]

A single atom (Li atom in this case) is treated as a molecule in the molecular crystal structure generation mode. In this example, a random molecular structure is composed of six Li molecules (atoms) and two PS4 molecules specified as:

  • mol_file = ./Li.xyz ./PS4.xyz
  • nmol = 6 2

In mol_file, set relative path of molecule files from cryspy.in. Here the molecule files are placed in the same directory.

Run CrySPY and see the initial structures (./data/init_POSCARS).

timeout_mol

Molecular crystal structure generation can be time consuming because PyXtal calculates the molecule directions according to a specified space group. Sometimes molecular crystal structure generation gets stuck. So we set a time limit on the single structure generation. The time limit (timeout_mol) is set to 120 seconds by default. If the limit is insufficient, you have to increase it as (see last line):

struc_mode = mol
natot = 16
atype = Li P S
nat = 6 2 8
mol_file = ./Li.xyz  ./PS4.xyz
nmol = 6 2
timeout_mol = 300.0

Volume of unit cell

You can control the volume of unit cells by changing the value(s) of scaling factor, vol_factor, in cryspy.in. By default, vol_factor is set to 1.0. It is also possible to specify a range of factors. Set minimum and maximum values as follows:

struc_mode = mol
natot = 16
atype = Li P S
nat = 6 2 8
mol_file = ./Li.xyz  ./PS4.xyz
nmol = 6 2
timeout_mol = 300.0
vol_factor = 0.8 1.5