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Merge branch 'lammps:develop' into cg-dna

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Oliver Henrich
2024-06-12 17:38:20 +01:00
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23
examples/PACKAGES/ipi/README → examples/PACKAGES/ipi/README.md
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@ -1,17 +1,17 @@
i-PI path integral interface examples
=====================================
This folder contains a couple of examples to run LAMMPS as a client,
This folder contains an example to run LAMMPS as a client,
exchanging information on the atomic configurations, energy and forces
with the i-PI Python interface
[http://epfl-cosmo.github.io/gle4md/index.html?page=ipi]. These
with the [http://ipi-code.org](i-PI Python interface). These
examples require a working copy of i-PI and compiling LAMMPS in a UNIX
environment. Note that a copy of i-PI is provided with LAMMPS, in the
tools/i-pi directory.
environment.
i-PI can be installed from source or from `pip`. Please refer to the
documentation for up-to-date installation instruction.
Note that the i-PI examples listed here are designed for the public V1.0
version of i-PI. Refer to the LAMMPS examples distributed with i-PI if you
are using a development version.
Note that the i-PI examples listed here have been tested to work with the
3.0 version of i-PI. Refer to the LAMMPS examples distributed with i-PI if you
are using a different version.
Path integral simulation of graphene
------------------------------------
@ -25,7 +25,7 @@ and the format of the output.
How to run i-PI
---------------
You should have a relatively recent (>=2.5) version of Python and Numpy,
You should have a relatively recent (>=3.5) version of Python and Numpy,
and the public version of i-PI. You can then run i-PI by executing
```bash
@ -33,7 +33,7 @@ and the public version of i-PI. You can then run i-PI by executing
```
In a separate terminal, then, you should run LAMMPS compiled to provide
fix_ipi functionalities.
`fix_ipi` functionalities.
```bash
$LAMMPS -in in.graphene
@ -41,6 +41,3 @@ fix_ipi functionalities.
You can run multiple instances of LAMMPS if you want to exploit the
parallelism over the path integral beads.

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examples/PACKAGES/ipi/i-pi_input.xml
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<simulation verbosity="medium">
<initialize nbeads='8'>
<file mode='xyz' units="angstrom"> i-pi_positions.xyz </file>
<cell mode='manual' units="angstrom"> [ 51.8,0,0,0, 49.84,0,0,0, 200 ] </cell>
<velocities mode='thermal' units='kelvin'> 300 </velocities>
</initialize>
<output prefix='graphene'>
<properties stride='5' filename='out' flush="10" > [ step, time{picosecond}, conserved{electronvolt}, temperature{kelvin}, kinetic_cv{electronvolt}, potential{electronvolt}, pressure_cv{megapascal}] </properties>
<simulation verbosity='medium'>
<output prefix='simulation'>
<properties stride='5' filename='out' flush="10" > [ step, time{picosecond}, conserved{kelvin}, temperature{kelvin}, kinetic_cv{kelvin}, potential{kelvin}, pressure_cv{megapascal}] </properties>
<properties stride='5' filename='iso' flush="10" > [ isotope_tdfep(1.167;C), isotope_scfep(1.167;0) ] </properties>
<trajectory stride='20' filename='pos' flush="100"> positions{angstrom}</trajectory>
<checkpoint stride='2000' />
</output>
<total_steps>1000</total_steps>
<total_time>128000</total_time>
<prng><seed>8417</seed></prng>
<forces>
<socket mode="unix">
<address>graphene</address>
</socket>
</forces>
<ensemble mode='nvt'>
<thermostat mode='gle'>
<A shape='(5,5)'>
[ 1.124524713863e-3, 1.648702679619e-6, 6.970075857471e-5, -2.202066291263e-4, 1.401342873485e-3, -1.681700567912e-6, 5.197673899653e-10, 4.365423872046e-6, -1.200041116490e-6, 2.564577183580e-6, -8.965478630849e-5, -4.365423872046e-6, 8.218704940997e-6, 3.114246791997e-5, -6.044142906315e-5, -6.272281358913e-5, 1.200041116490e-6, -3.114246791997e-5, 1.612301941566e-4, 6.958958085115e-5, 1.318373360752e-3, -2.564577183580e-6, 6.044142906315e-5, -6.958958085115e-5, 1.872119364197e-3]
</A>
</thermostat>
<timestep units="femtosecond">1.0</timestep>
<temperature units='kelvin'>300</temperature>
<fixcom> True </fixcom>
</ensemble>
<properties stride='1' filename='kc'> [ kinetic_cv{kelvin}(C) ] </properties>
<trajectory stride='5' filename='pos' flush="100">positions{angstrom}</trajectory>
<trajectory stride='5' filename='kin' flush="100"> kinetic_cv </trajectory>
<checkpoint stride='20000'/>
</output>
<total_steps>1000000</total_steps>
<prng>
<seed>31415</seed>
</prng>
<ffsocket name='lammps' mode='unix'>
<address> graphene </address>
</ffsocket>
<system>
<initialize nbeads='8'>
<file mode='xyz'> i-pi_positions.xyz </file>
<velocities mode='thermal' units='kelvin'> 300 </velocities>
</initialize>
<forces>
<force forcefield='lammps'> </force>
</forces>
<motion mode='dynamics'>
<dynamics mode='nvt'>
<timestep units='femtosecond'> 1.0 </timestep>
<thermostat mode='langevin'>
<tau units='femtosecond'> 100 </tau>
</thermostat>
</dynamics>
</motion>
<ensemble>
<temperature units='kelvin'> 300 </temperature>
</ensemble>
</system>
</simulation>