ASE on your local PC

2025 July 11, updated for v1.4.2

ASE provides interfaces to different codes. ASE also includes Pure Python EMT calculator, which is suitable for testing CrySPY because of its fast and easy structure optimization.

In this tutorial, we try to use CrySPY in your local PC (Mac or Linux). The target system is Cu 8 atoms.

Assumption

Here, we assume the following conditions:

CrySPY 1.2.0 or later in your local PC
CrySPY job filename: job_cryspy
ase input filename: ase_in.py

Input files

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

Download from CrySPY_utility/examples/ase_Cu8_RS
Copy from CrySPY utility that you installed

cd ase_Cu8_RS
tree

.
├── calc_in
│   ├── ase_in.py
│   └── job_cryspy
└── cryspy.in

cryspy.in

cryspy.in is the input file of CrySPY.

[basic]
algo = RS
calc_code = ASE
tot_struc = 5
nstage = 1
njob = 5
jobcmd = zsh
jobfile = job_cryspy

[structure]
atype = Cu
nat = 8

[ASE]
ase_python = ase_in.py

[option]

In [basic] section, jobcmd = zsh can be changed to jobcmd = sh or jobcmd = bash in accordance with your environment. CrySPY runs zsh job_cryspy as a background job internally.

[ASE] section is required when you use ASE.

You can name the following files whatever you want:

jobfile: job_cryspy
ase_python: ase_in.py

The other input variables are discussed later.

calc_in directory

The job file and input files for ASE are prepared in this directory.

Job file

The name of the job file must match the value of jobfile in cryspy.in. The example of job file (here, job_cryspy) is shown below.

#!/bin/sh

# ---------- ASE
python3 ase_in.py

You can specify the input (ase_in.py) file names, but it must match the values of ase_python in cryspy.in. ~~You must add sed -i -e ‘3 s/^.*$/done/’ stat_job at the end of the file in CrySPY.~~ Starting from version 1.4.2, CrySPY automatically appends the following line to the end of the job file. (See also: Features > Job file auto-rewriting)

# ---------- CrySPY
sed -i -e '3s/^sub.*/done/' stat_job

Note

For versions older than 1.4.2, the last line of the job file must be written as sed -i -e '3s/^sub.*/done/' stat_job. If you use a job file with this sed command in version 1.4.2 or later, it will simply be executed twice, which does not cause any problems.
The meaning of the above sed command is to change the part starting with “sub” in the third line of the file stat_job to “done”.

Tip

(Detail: Features > Job file auto-rewriting)
In the job file of CrySPY, the string CrySPY_ID is automatically replaced with the structure ID. When you use a job scheduler such as PBS and SLURM, it is useful to set the structure ID to the job name. For example, in the PBS system, #PBS -N Si_CrySPY_ID in ID 10 is replaced with #PBS -N Si_10. Note that starting with a number will result in an error. You should add a prefix like Si_.

Input for ASE

Input files corresponding to the number of stages (nstage in cryspy.in) are required. Prepare the input file names by adding x_ as a prefix or _x as a suffix, where x is the stage number.

CrySPY searches for input files in the following order of priority:

x_ase_in.py
ase_in.py_x
ase_in.py

If you use the same input for all stages, you can omit x_ or _x.

In this ASE tutorial, since nstage = 1 is used, only one ASE input file, ase_in.py, is needed. You can omit x_ or _x. An example of ase_in.py is shown below (for details on how to use ASE, refer to the official documentation).

from ase.constraints import FixSymmetry
from ase.filters import FrechetCellFilter
from ase.calculators.emt import EMT
from ase.optimize import BFGS
from ase.io import read, write

# ---------- input structure
# CrySPY outputs 'POSCAR' as an input file in work/xxxxxx directory
atoms = read('POSCAR', format='vasp')

# ---------- setting and run
atoms.calc = EMT()
atoms.set_constraint([FixSymmetry(atoms)])
cell_filter = FrechetCellFilter(atoms, hydrostatic_strain=False)
opt = BFGS(cell_filter)

# ---------- run
converged = opt.run(fmax=0.01, steps=2000)

# ---------- rule in ASE interface
# output file for energy: 'log.tote' in eV/cell
#                         CrySPY reads the last line of 'log.tote' file
# outimized structure: 'CONTCAR' file in vasp format
# check_opt: 'out_check_opt' file ('done' or 'not yet')
#                         CrySPY reads the last line of 'out_check_opt' file

# ------ energy
e = cell_filter.atoms.get_total_energy()    # eV/cell
with open('log.tote', mode='w') as f:
    f.write(str(e))

# ------ struc
opt_atoms = cell_filter.atoms.copy()
opt_atoms.set_constraint(None)    # remove constraint for pymatgen
write('CONTCAR', opt_atoms, format='vasp', direct=True)

# ------ check_opt
with open('out_check_opt', mode='w') as f:
    if converged:
        f.write('done\n')
    else:
        f.write('not yet\n')

Unlike VASP and QE, the ASE input (python script) is more flexible. CrySPY has three rules:

Energy is output in units of eV/cell to log.tote file. CrySPY reads the last line of it.
Optimized structure is output to CONTCAR file in the VASP format.
The result of the optimization convergence check should be written as either done or not_yet in a file named out_check_opt. CrySPY reads the last line of this file.

Running CrySPY

Go to Running CrySPY