[lammps-users] Questions on isobaric simulation and phonon dispersion analysis

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1

First many thanks to all the people who answered to my previous questions really.

My current questions are as follows.

  1. What does Tstart or Pstart mean in thermostat and barostat?
    Is it initial targeted temperature or pressure during early period of simulation (e.g. that of a few hundred steps from starting)?

  2. I’d like to perform NPT simulation using anisotropic barostat (three length dimensions of box may be controlled independently to each other).

I used the command of
“fix 1 all npt temp 298. 298. 100. aniso 1. 1. 1000.” for it.

Is it correct for my purpose?
If not, would you let me know what it should be in detail,please?

  1. I plan to run NVT or NVE simulation after appropriate box size corresponding to 1 atm is determined using NPT simulation.
    For this, average values of width, depth, and height of box should be obtained from sample data in which they are varied dynamically during NPT simulation
    .
    How can I obtain the information on these averages values from NPT simulation in LAMMPS?
    Can I use built-variables of NPT for them?
    Otherwise, should I use additional command for them?

  2. I use LAMMPS-April-10 version program.
    Is fix/NVT command available in this version still?
    I ask this qeustion since the use of fix/NVT command gave error message.

  3. Is phonon dispersion analysis available using LAMMPS?
    If so, what should I do for it?
    I suppose that I should use a certain script file and atomic positional data, if it is possible.

Incidentally asking, if there is recommendable softwares (even if it is commercial software) for phonon analysis which gives detailed information on phonon dispersion relation and offers graphical output of high level, using atomic positional data (of classical MD simulation) as
input data, would you let me know of them, please?

Best regards,

Luke

2

2010/6/28 JhonY. I. <yijhon@…8…>

First many thanks to all the people who answered to my previous questions really.

My current questions are as follows.

  1. What does Tstart or Pstart mean in thermostat and barostat?
    Is it initial targeted temperature or pressure during early period of simulation (e.g. that of a few hundred steps from starting)?

See http://lammps.sandia.gov/doc/fix_nh.html

  1. I’d like to perform NPT simulation using anisotropic barostat (three length dimensions of box may be controlled independently to each other).

I used the command of
“fix 1 all npt temp 298. 298. 100. aniso 1. 1. 1000.” for it.

Is it correct for my purpose?
If not, would you let me know what it should be in detail,please?

See http://lammps.sandia.gov/doc/fix_nh.html

  1. I plan to run NVT or NVE simulation after appropriate box size corresponding to 1 atm is determined using NPT simulation.
    For this, average values of width, depth, and height of box should be obtained from sample data in which they are varied dynamically during NPT simulation
    .
    How can I obtain the information on these averages values from NPT simulation in LAMMPS?
    Can I use built-variables of NPT for them?
    Otherwise, should I use additional command for them?

See:

http://lammps.sandia.gov/doc/Section_howto.html#4_15
http://lammps.sandia.gov/doc/Section_howto.html#4_16

  1. I use LAMMPS-April-10 version program.
    Is fix/NVT command available in this version still?
    I ask this qeustion since the use of fix/NVT command gave error message.

See http://lammps.sandia.gov/doc/fix_nh.html ; fix nvt still exists.

(If you were using a previous version of LAMMPS and then upgraded to the more recent version, some of the syntaxes for commands may have changed—read the manual to see the latest formats to use.)

–AEI