[lammps-users] various questions on input data an fix command

I’ve some questions on LAMMPS as follows.

  1. Would you tell me how I can build LAMMPS-formatted file containing atomic positions data and topology information and force field parameter data (such as “in.peptide file” in peptide subdirectory of examples directory of LAMMPS), using a usual file (pdb,mol etc.) for positional data and topological information and a force field parameter file in PARAMS directory of LAMMPS?
    I think it is one of main works for running jobs using LAMMPS and I hope your answer as in detail as possible, please.

Can I also build it using pizza.py?
If so, would you let me know what I should do for it in pizza.py, please?

  1. Is it possible that I insert three information as described in question 1 to input file by reading two files (one is for positional data and topology data which may be formmated in LAMMPS data style and the other is force field parameter file such as those of PARAMS directory) rather than one single file?

If it is possible, what I should do for it?
Which is more usual way, reading one single file or two separated files?

  1. What does “ID (that is, user-assigned name for the fix)” of fix command mean? In what case, is it used?
    If I’d like to Langevin temperature control instead of Nose/Noover temperature thermostat in NVT ensemble, what should I write in input file with respect to fix command?
    Should I override fix nvt command as follows?

fix 1 all nvt
fix 1 all langevin (arguments)

Incidentally asking, in example input file at the page 35 of manual file described below,

units lj
atom_style bond
pair_style lj/cut 1.12
pair_modify shift yes
bond_style fene
special_bonds 0.0 1.0 1.0
read_data tmp.restart.data
neighbor 0.4 bin
neigh_modify every 1 delay 1
fix 1 all nve
fix 2 all langevin 1.0 1.0 10.0 904297
timestep 0.012
reset_timestep 50
run 50

What does mean “the use of different ID names” (and why should we write them in this way)
in
“fix 1 all nve
fix 2 all langevin 1.0 1.0 10.0 904297” of this input file?

  1. Is there any recommendable book or files for tutorial course to learn LAMMPS except for manual file?
    It seems that it is not so easy to learn lAMMPS.

  2. It is hard to find “search box” for “the keyword search” on question and answer contents in archive section. If it is available, where can I find it?

Thanks for ther reading and I hope your answer as in detail as possible, please.
With best regards,

Sincerely
Luke

Answers below.

Steve

2010/4/27 JhonY. I. <[email protected]...>:

I've some questions on LAMMPS as follows.

1. Would you tell me how I can build LAMMPS-formatted file containing atomic
positions data and topology information and force field parameter data (such
as "in.peptide file" in peptide subdirectory of examples directory of
LAMMPS), using a usual file (pdb,mol etc.) for positional data and
topological information and a force field parameter file in PARAMS directory
of LAMMPS?
I think it is one of main works for running jobs using LAMMPS and I hope
your answer as in detail as possible, please.

Can I also build it using pizza.py?
If so, would you let me know what I should do for it in pizza.py, please?

You have to pre-process the PDB file, using a tool like tools/ch2lmp
or tools/msi2lmp.

2. Is it possible that I insert three information as described in question 1
to input file by reading two files (one is for positional data and topology
data which may be formmated in LAMMPS data style and the other is force
field parameter file such as those of PARAMS directory) rather than one
single file?

If it is possible, what I should do for it?
Which is more usual way, reading one single file or two separated files?

See the README files for those tools.

3. What does "ID (that is, user-assigned name for the fix)" of fix command
mean? In what case, is it used?
If I'd like to Langevin temperature control instead of Nose/Noover
temperature thermostat in NVT ensemble, what should I write in input file
with respect to fix command?
Should I override fix nvt command as follows?

fix 1 all nvt
fix 1 all langevin (arguments)

That will invoke both fixes, which you probably don't want. Every fix
should have its own ID, so you can refer to them later with other
commands, like unfix 1, or fix modify, or to ouput their values.

Incidentally asking, in example input file at the page 35 of manual file
described below,

units lj
atom_style bond
pair_style lj/cut 1.12
pair_modify shift yes
bond_style fene
special_bonds 0.0 1.0 1.0
read_data tmp.restart.data
neighbor 0.4 bin
neigh_modify every 1 delay 1
fix 1 all nve
fix 2 all langevin 1.0 1.0 10.0 904297
timestep 0.012
reset_timestep 50
run 50

What does mean "the use of different ID names" (and why should we write them
in this way)
in
"fix 1 all nve
fix 2 all langevin 1.0 1.0 10.0 904297" of this input file?

Answered that above. You can't give 2 different fixes the same ID.

4. Is there any recommendable book or files for tutorial course to learn
LAMMPS except for manual file?
It seems that it is not so easy to learn lAMMPS.

That and the example files are all there is. You might also check
the workshop WWW page, which might have a few intro PPT slides.

5. It is hard to find "search box" for "the keyword search" on question and
answer contents in archive section. If it is available, where can I find
it?

If you mean search the mail list, then lammps/sandia.gov/mail.html
has several methods to do that.