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Atom-configuration file

Original file format described here is used in pmd .

File format

Note

File format, particulary H-matrix part, changed since rev240307.

An example of the pmd file is as follows.

1 :!
2 :! specorder:  W  H
3 :!    
4 :  2.855300000E+000
5 :  3.00000000000000E+000  0.00000000000000E+000  0.00000000000000E+000   0.00  0.00  0.00
6 :  0.00000000000000E+000  3.00000000000000E+000  0.00000000000000E+000   0.00  0.00  0.00
7 :  0.00000000000000E+000  0.00000000000000E+000  3.00000000000000E+000   0.00  0.00  0.00
8 :        55
9 :  1.10000000000001  1.000E-007  1.000E-007  1.000E-007  3.62E-004  1.60E-004  9.60E-004
10:  1.10000000000002  1.666E-001  1.666E-001  1.666E-001  3.62E-004  1.60E-004  9.60E-004
11:  ...
12:  1.10000000000054  9.00E-001  9.00E-007  9.00E-001  3.62E-004  1.60E-004  9.60E-004
13:  2.10000000000055  5.33E-001  5.33E-001  5.33E-001  3.62E-004  1.60E-004  9.60E-004

Here, line numbers are shown for the ease of explanation.

  • Line 1-3: Lines begin with ! or # are treated as comment lines. There are some keywords that are used to specify some additional data to pmd when they are at a comment line at the beginning.

    • specorder: specifies the species order used in pmd.

    Note

    specorder must be specified in the current pmd (since rev190515), as the masses and the interatomic potentials are determined using this information.

  • Line 4: The lattie constant value that is multiplied to the cell vectors below to obtain absolute cell vectors.

  • Line 5 to 7: Lattice vectors and their velocities. The 2nd line is a1 vector, 3rd line for a2, and 4th line for a3. Columns 1, 2, and 3 are x , y , z components of each vector. Velocities follow these vectors, since rev240307.
  • Line 8: Number of atoms in the system or decomposed region.
  • After line 9: One atom information per one line.
  • 1st column after line 9: Tag of an atom. The digit in the one's place means species of the atom. The digit in the tenth's place is ifmv value which controls the direction of motion of the atom.
  • 2-4th column after line 9: x , y , and z coordinates of the atom normalized by the lattice vectors. Thus they should be in (0:1]
  • 5-7th column after line 9: x , y , and z components of the atom velocities that are also normalized.

Sample Fortran code

open(ionum,file=cfname,status='replace')
write(ionum,'(es23.14e3)') hunit
write(ionum,'(3es23.14e3)') ((h(ia,1,l)/hunit,ia=1,3),l=0,1)
write(ionum,'(3es23.14e3)') ((h(ia,2,l)/hunit,ia=1,3),l=0,1)
write(ionum,'(3es23.14e3)') ((h(ia,3,l)/hunit,ia=1,3),l=0,1)
write(ionum,'(i10)') natm
do i=1,ntot
  write(ionum,'(7es23.14e3)') tag(i), rtot(1:3,i), vtot(1:3,i)
  close(ionum)
enddo

Detail explanations of variables are omitted. Users can write their own code by following this sample Fortran code.

Format conversion

There is a python utility, napsys.py that can convert files amoung the following formats,

  • pmd: input format for pmd program.
  • POSCAR: input format of VASP program.
  • dump: output format of LAMMPS-dump command.

You can use like following, :

$ python /path/to/nap/nappy/napsys.py convert pmdini POSCAR

Here pmdini file will be converted to POSCAR file in POSCAR format, where the file format is determined automatically from file names. Users can also specify input/output file format by the options --in-format and --out-format.

See the help message for more details as, :

$ python /path/to/nap/nappy/napsys.py -h

Make crystalline structures

There is also a python utility, cell_maker.py, which makes typical conventional crystalline structures. You can make a pmd format file of diamond structured cubic system with 8 atoms as,

$ python /path/to/nap/nappy/mkcell/cell_maker.py dia -l 5.473 -o pmdini

The option -l specifies the lattice constant of the lattice. Output format is automatically detected from the file name. You can also make fcc, bcc, sc (simple cubic), and hcp structures as well.