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 0 1.000000e-10 5000 500000
fix 1 all box/relax aniso 0.0
minimize 0 1.000000e-10 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.