diff --git a/examples/PACKAGES/ipi/README b/examples/PACKAGES/ipi/README.md similarity index 64% rename from examples/PACKAGES/ipi/README rename to examples/PACKAGES/ipi/README.md index d093cea4c5..4b192aa776 100644 --- a/examples/PACKAGES/ipi/README +++ b/examples/PACKAGES/ipi/README.md @@ -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. - - - diff --git a/examples/PACKAGES/ipi/i-pi_input.xml b/examples/PACKAGES/ipi/i-pi_input.xml index 310c909338..7cbf559322 100644 --- a/examples/PACKAGES/ipi/i-pi_input.xml +++ b/examples/PACKAGES/ipi/i-pi_input.xml @@ -1,31 +1,37 @@ - - - i-pi_positions.xyz - [ 51.8,0,0,0, 49.84,0,0,0, 200 ] - 300 - - - [ step, time{picosecond}, conserved{electronvolt}, temperature{kelvin}, kinetic_cv{electronvolt}, potential{electronvolt}, pressure_cv{megapascal}] + + + [ step, time{picosecond}, conserved{kelvin}, temperature{kelvin}, kinetic_cv{kelvin}, potential{kelvin}, pressure_cv{megapascal}] [ isotope_tdfep(1.167;C), isotope_scfep(1.167;0) ] - positions{angstrom} - - - 1000 - 128000 - 8417 - - -
graphene
-
-
- - - - [ 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] - - - 1.0 - 300 - True - + [ kinetic_cv{kelvin}(C) ] + positions{angstrom} + kinetic_cv + +
+ 1000000 + + 31415 + + +
graphene
+
+ + + i-pi_positions.xyz + 300 + + + + + + + 1.0 + + 100 + + + + + 300 + +