Relaxation: make

The list of the directories storing structures are ["confs/std-*"] in the previous example. For single element system, if POSCAR doesn't exist in the directories: std-fcc, std-hcp, std-dhcp, std-bcc, std-diamond, and std-sc, the package will automatically generate the standard crystal structures fcc, hcp, dhcp, bcc, diamond, and sc in the corresponding directories, respectively. In other conditions and for multi-component system (more than 1), if POSCAR doesn't exist, the package will terminate and print the error "no configuration for autotest".

VASP relaxation

Take the input example of Al in the previous section, when we do make as follows:

dpgen autotest make relaxation.json

the following files would be generated:

tree confs/std-fcc/relaxation/

confs/std-fcc/relaxation/
|-- INCAR
|-- POTCAR
`-- relax_task
    |-- INCAR -> ../INCAR
    |-- inter.json
    |-- KPOINTS
    |-- POSCAR -> ../../POSCAR
    |-- POTCAR -> ../POTCAR
    `-- task.json

inter.json records the information in the interaction dictionary and task.json records the information in the relaxation dictionary.

LAMMPS relaxation

dpgen autotest make relaxation.json
tree confs/std-fcc/

the output would be:

confs/std-fcc/
|-- POSCAR
`-- relaxation
    |-- frozen_model.pb -> ../../../frozen_model.pb
    |-- in.lammps
    `-- relax_task
        |-- conf.lmp
        |-- frozen_model.pb -> ../frozen_model.pb
        |-- in.lammps -> ../in.lammps
        |-- inter.json
        |-- POSCAR -> ../../POSCAR
        `-- task.json

the conf.lmp is the input configuration and in.lammps is the input command file for lammps.

in.lammps: the package would generate the file confs/mp-*/relaxation/in.lammps as follows and we refer the user to the further information of fix box/relax function in lammps:

clear
units 	          metal
dimension	  3
boundary	  p p p
atom_style	  atomic
box               tilt large
read_data         conf.lmp
mass              1 26.982
neigh_modify      every 1 delay 0 check no
pair_style deepmd frozen_model.pb
pair_coeff
compute           mype all pe
thermo            100
thermo_style      custom step pe pxx pyy pzz pxy pxz pyz lx ly lz vol c_mype
dump              1 all custom 100 dump.relax id type xs ys zs fx fy fz
min_style         cg
fix               1 all box/relax iso 0.0
minimize          1.000000e-12 1.000000e-06 5000 500000
fix               1 all box/relax aniso 0.0
minimize          1.000000e-12 1.000000e-06 5000 500000
variable          N equal count(all)
variable          V equal vol
variable          E equal "c_mype"
variable          tmplx equal lx
variable          tmply equal ly
variable          Pxx equal pxx
variable          Pyy equal pyy
variable          Pzz equal pzz
variable          Pxy equal pxy
variable          Pxz equal pxz
variable          Pyz equal pyz
variable          Epa equal ${E}/${N}
variable          Vpa equal ${V}/${N}
variable          AA equal (${tmplx}*${tmply})
print "All done"
print "Total number of atoms = ${N}"
print "Final energy per atoms = ${Epa}"
print "Final volume per atoms = ${Vpa}"
print "Final Base area = ${AA}"
print "Final Stress (xx yy zz xy xz yz) = ${Pxx} ${Pyy} ${Pzz} ${Pxy} ${Pxz} ${Pyz}"

If user provides lammps input command file in.lammps, the thermo_style and dump commands should be the same as the above file.

interatomic potential model: the frozen_model.pb in confs/mp-*/relaxation would link to the frozen_model.pb file given in the input.