How to fix i-ip NameError: Tag name 'initialize' is not a recognized property of 'simulation' objects

LAMMPS LAMMPS Beginners
1

I try to run this example to learn i-pi: lammps-git-tutorial/tools/i-pi/examples/lammps/h2o-pimd at master · lammps/lammps-git-tutorial (github.com)

But whenever I run

i-pi input.xml

where the input.xml is

<simulation>
   <initialize nbeads='32'>
      <file mode='pdb'> water_298K.pdb </file>
      <velocities mode="thermal" units='kelvin'> 298 </velocities>
   </initialize>
   <output prefix='no_rpc'>
      <properties stride='1' filename='out'>  [ step, time{picosecond}, conserved, temperature{kelvin}, kinetic_cv, potential, pressure_cv{megapascal}] </properties>
      <trajectory filename='pos' stride='20'> positions </trajectory>
   </output>
   <total_steps>500000</total_steps>
   <prng><seed>32345</seed></prng>
   <forces>
      <socket mode='unix'>
         <address>no_rpc</address>
      </socket>
   </forces>
   <ensemble mode='nvt'>
      <thermostat mode='svr'>
         <tau units='femtosecond'>25</tau>
      </thermostat>
      <timestep units='femtosecond'> 0.25</timestep>
      <temperature units='kelvin'>298</temperature>
   </ensemble>
</simulation>

I get the following error:

Traceback (most recent call last):
  File "/data/share/apps/deepmd/2.2.9/bin/i-pi", line 112, in <module>
    main(args[0], options)
  File "/data/share/apps/deepmd/2.2.9/bin/i-pi", line 61, in main
    simulation = Simulation.load_from_xml(fn_input, request_banner=True, custom_verbosity=options.verbosity)
  File "/data/share/apps/deepmd/2.2.9/lib/python3.10/site-packages/ipi/engine/simulation.py", line 81, in load_from_xml
    input_simulation.parse(xmlrestart.fields[0][1])
  File "/data/share/apps/deepmd/2.2.9/lib/python3.10/site-packages/ipi/utils/inputvalue.py", line 359, in parse
    raise NameError(
NameError: Tag name 'initialize' is not a recognized property of 'simulation' objects

The version of i-pi is 2.6.3. I am new to this and have no idea how to fix it.

2

This is really not a LAMMPS problem but an i-PI problem, so you should discuss it in their forum(s).

I suspect that the examples bundled with LAMMPS need to be updated, since they were made for a much older i-PI version that is bundled with LAMMPS. We very recently had some updates to fix ipi and removed the outdated version of the i-PI package and added instructions to install i-PI via pip instead.

3

You are right, the examples in LAMMPS is out of date. Examples in i-pi project work fine.

4

Also, you had been using a git repo that was clearly indicated as a demo copy make for a tutorial for people learning to use git with LAMMPS that was held some 5 years ago and that had not been updated since. The real LAMMPS git repo is a GitHub - lammps/lammps: Public development project of the LAMMPS MD software package

This is the right location to look for files to learn i-PI. The interface to LAMMPS has been essentially unchanged. There are some recent changes to fix ipi that will improve the performance when using i-PI with LAMMPS. You can look for them in the next feature release which may happen this month or the next.