10 thoughts on “fftool

  1. olá primeiramente parabéns pelo belíssimo trabalho no desenvolvimento de campos de forças para líquidos iônicos. Sou estudante de engenharia e gostaria de utilizar o seu programa fftool, mas , estou com problemas com a seguinte mensagem de erro : not created

    estou escrevendo da seguinte forma

    python fftool.py 1 spc.zmat -b 40
    python fftool.py 1 spc.zmat -lammps 40

    poderia me ajudar ?

    obrigado pela atenção

    • Hi,
      The command you issued creates one box of 40 A side containing water molecules (only 1 in your case):
      $ python fftool.py 1 spc.zmat -b 40
      This generates xyz files with atomic coordinates for the molecules and an input file for packmol. You need to use packmol to actually pack the molecules in the box:
      $ packmol < pack.inp And then run fftool once again to finally create the lammps input files from those coordinates: $ python fftool.py 1 spc.zmat -b 40 -l Hope this helps. Agilio

  2. Hi,

    I am a beginner at Molecular Dynamics. I am trying to obtain the XYZ file from zmat file in fftool and also see the charges in the molecule. Could you help me with this?

    • fftool generates xyz files for use by packmol to create an initial configuration (positions of atoms in a simulation box). To see the charges on atoms you have to proceed to create datafilee in LAMMPS (or DLPOLY or Gromacs) format. This is explained in the README. To put 1 molecule in a 30 A box and create lammps input files use the following 3 commands:
      $ fftool 1 molecule.zmat -b 30
      $ packmol < pack.inp $ fftool 1 molecule.zmat -b 30 -l

  3. hello sir.
    Respected sir,
    I want to ask , if i have c3c1im_pack.xyz,PF6_pack.xyz and gold.xyz(radius-15Amstrong) and want to put all of this in a same box .can i use fftool or xyztool??also if i give the lj parameters in il.ff file for gold can i do this.
    #gold
    i j pot re/A kr/kJmol-1
    Au Au 196.967 0.00 lj 3.2 0.75

    regards

    • Yes, fftool can do what you want.
      You need to create a simple .ff file with the Lennard-Jones parameters for gold atoms.
      Then you need to describe with care the interactions between gold atoms and the ionic liquids, and this is not trivial.
      I did something similar with ruthenium and iron:
      A.S. Pensado, A.A.H. Padua, Solvation and Stabilization of Metallic Nanoparticles in Ionic Liquids, Angew Chem Int Edit. 50 (2011) 8683–8687. doi:10.1002/anie.201103096.
      A.C.F. Mendonça, P. Malfreyt, A.A.H. Padua, Interactions and Ordering of Ionic Liquids at a Metal Surface, J Chem Theory Comput. 8 (2012) 3348–3355. doi:10.1021/ct300452u.

  4. Hello sir,

    I Have a mixture of c2mimpf6 and c6mimpf6 in a box . Using the fftool and il.ff , i got the lammps input file below having paircoefficients but I want to group seperatly c2mim and c6mim using the group command of lammps.(group cation type 1 2…like this),is there any option using fftool i can get seperate atomtype for both the cation(c2mim and c6mim)??

    pair_coeff 1 1 lj/cut/coul/long 0.170000 3.250000 # NA NA
    pair_coeff 2 2 lj/cut/coul/long 0.070000 3.550000 # CR CR
    pair_coeff 3 3 lj/cut/coul/long 0.070000 3.550000 # CW CW
    pair_coeff 4 4 lj/cut/coul/long 0.065999 3.500000 # C1 C1
    pair_coeff 5 5 lj/cut/coul/long 0.030000 2.420000 # HCR HCR
    pair_coeff 6 6 lj/cut/coul/long 0.030000 2.420000 # HCW HCW
    pair_coeff 7 7 lj/cut/coul/long 0.030000 2.500000 # H1 H1
    pair_coeff 8 8 lj/cut/coul/long 0.065999 3.500000 # CE CE
    pair_coeff 9 9 lj/cut/coul/long 0.030000 2.500000 # HC HC
    pair_coeff 10 10 lj/cut/coul/long 0.065999 3.500000 # C2 C2
    pair_coeff 11 11 lj/cut/coul/long 0.065999 3.500000 # CS CS
    pair_coeff 12 12 lj/cut/coul/long 0.065999 3.500000 # CT CT

  5. It’s a good question. Maybe the easiest way is to edit one of the files (c2c1im) and give atoms new names. Then copy il.ff to another name and change the same atom types; use the new il.ff with the modified molecule/ion. This is very simple because only the non-bonded types matter.

  6. thank you sir .but i have tried to do edit the c2c1im.zmat file but as soon i tried to do that its showing me error
    ./fftool 100 c2c1im.zmat 100 c6c1im.zmat -b 60
    c2c1im.zmat
    error in c2c1im+: no parameters for atom Cr
    error in c2c1im+: no parameters for atom Cw
    error in c2c1im+: no parameters for atom Cw
    error in c2c1im+: no parameters for atom Ca
    error in c2c1im+: no parameters for atom Hcr
    error in c2c1im+: no parameters for atom Ca
    error in c2c1im+: no parameters for atom Hcw
    error in c2c1im+: no parameters for atom Hcw
    error in c2c1im+: no parameters for atom Ha
    error in c2c1im+: no parameters for atom Ha
    error in c2c1im+: no parameters for atom Ha
    error in c2c1im+: no parameters for atom Ce
    error in c2c1im+: no parameters for atom Ha
    error in c2c1im+: no parameters for atom Ha
    error in c2c1im+: no parameters for atom Hc
    error in c2c1im+: no parameters for atom Hc
    error in c2c1im+: no parameters for atom Hc

    • I suppose you have to modify the force field file (*.ff) accordingly for the new atom names.

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