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Molecular Dynamics: a client/server approach

Timing: \(\sim\) 20 minutes total

In this exercise we are going to familiarize ourselves with the syntax of i-PI input files. As mentioned previously, the i-PI program works through a client-server architecture. It can use INTERNET or UNIX sockets, that allow the system to be simulated on the same machine or on a different machine, as long as the calculation can communicate with the server.

Let's take a look at the input files. The simulation example here will consist of one Zundel cation in the canonical (NVT) ensemble at 300 K.

i-PI communication channels

Server

An example of an input file for i-PI can be found in input.xml. It is an xml file, which is quite intuitive to learn. Please take your time to understand the keywords that are there and consult the i-PI manual. We will be using UNIX sockets here, which is the most convenient way to use the code when running both servers and clients in small desktop (or laptop) machines. For that, we have to specify only the <address>, which can simply be a string containing a name of your choice. For internet sockets, one would have to provide the relevant IP address for the <address> field and a number for the <port> field.

Client

The keyword to add to the control.in file of FHI-aims is

use_pimd_wrapper UNIX:<address> <portnumber>

where <address> should be substituted by the name of the socket you choose, and the port can be any number since it does not play a role for UNIX sockets. The address that goes in the control.in file should match the one in the input.xml file of i-PI. The geometry.in is only provided for the initialization of FHI-aims, and in this mode FHI-aims does not use the atomic positions in this file (except to initialize numerical quantities). However, it is very important to note that:

Matching species order in geometry.in and i-PI input

In order to avoid inconsistencies, the order of atomic species in the geometry.in file of FHI-aims and the file containing the initial geometry read by i-PI (normally something like init.xyz) must match.

Note

In all subsequent exercises you will be free to choose <address> as you want, and you should please change it in your input files (control.in and input.xml) so that your server and your client always match!*

Running i-PI with FHI-aims

Let's run an i-PI+FHI-aims Molecular Dynamics simulation!

  • Open a terminal at the current directory and launch i-PI by typing

    i-pi input.xml
    

    At this point i-PI should start and parse the input file. At the bottom of the output on the screen it should say:

    Created unix socket with address EX1   
    @ForceField: Starting the polling thread main loop.
    

    This means i-PI has started properly, has created the UNIX socket, and is waiting for the communications from the clients that take care of the force evaluations.

  • Now we can launch FHI-aims. Open a second terminal, either manually or by typing ctrl+shift+t, and enter the command

    aims.x
    

    Then FHI-aims should start and you will see some outputs.

  • Now switch to the terminal where i-PI is running, notice that i-PI has built the connection with FHI-aims with the following message,

    @SOCKET:   Client asked for connection from . Now hand-shaking.
    @SOCKET:   Handshaking was successful. Added to the client list.
    

    and started the Molecular Dynamics simulation. It should also print on screen information about the time taken for each MD step.

  • What we are going to do now is to kill FHI-aims (don't worry, you will not be sued for that). Simply switch to the terminal where FHI-aims is running and press ctrl + c. Now look at whether i-PI is still running. Notice that although the evolution of the MD is paused, i-PI itself does not die but instead continues to run and waits for a new client to take over. Now start FHI-aims again by typing:

    aims.x
    

    What happens to i-PI now?

Answer

i-PI restarts the dynamics and continues printing the corresponding steps on the original output.

  • What if one stops i-PI? Trigger a soft exit of i-PI by typing ctrl + c at the terminal where it is running, or create a file named EXIT in the folder where i-PI is running (you can use the bash command touch EXIT). Watch how i-PI responds, and how FHI-aims reacts. Think about what are the advantages of a clean exit when a MD program stops unexpectedly.
Answer

When i-PI is stopped the client-server connection dies, i-PI stops at the subsequent step with a "SOFT EXIT" procedure, while FHI-aims does not run a new SCF cycle. Advantages of such an approach include saving the output files for the future, creating a RESTART file that can be used to rerun/continue the simulation from the current state.

  • Take a look at all the output files written by i-PI. You should have the file ex1.out that describes the system properties, ex1.pos.xyz that records the atomic trajectories, and RESTART that contains all the information to restart the simulation.

  • Last (and tricky) question: We are dealing with a charged system. Can you find where the total charge in the input.xml file is specified? Why?

Answer

The charge is not specified in input.xml. The charge (+1 for the zundel cation) is carried by the lack of an electron, and therefore needs to be specified in the electronic structure code (it is in control.in). i-PI is concerned with the dynamics of the nuclei which are given by the forces calculated by FHI-aims in this case!