Program Structure

Below is a tree diagram of the general structure for the directories and files needed to run a QXMD simulation.

├── control
│   ├── filename
│   ├── CONFIG
│   ├── IN.PARAM
│   ├── VELOC
│   └── NCPP
│       ├── H.PBE
│       └── O.PBE
├── data
└── qxmdmpi

An overview is given below, while a more detailed explanation can be found in section 4.1.

Control Directory

The control directory is where QXMD will search for all input data. The main input file, in this case named IN.PARAM, contains the settings for all input parameters for running QXMD. It is best practice to name this file ‘IN.PARAM’, though it can, in principle, be named anything. Thus, it is required to have a file named ‘filename’ which is a simple, one-line text file holding the path (relative to the QXMD executable) to the main input file, in this case ‘control/IN.PARAM’. Most QXMD runs will also require a file detailing the initial configuration of the simulation system (this may be omitted if you are restarting a QXMD run from a previous run). It is best practice to name the input configuration file ‘IN.CONFIG’, as shown above in the tree diagram. Optionally, a file defining the inital velocities of all the atoms may be defined. It is best practice to name the input velocity file ‘IN.VELOC’, as shown above in the tree diagram. If not intial velocities are provided, random initial velocities will be used corresponding to the intial temperature of the system. Finally, a directory holding pseudopotential information for all atomic species present in your simulation system is required. The PAW directory, shown above, holds pseudopotential information for hydrogen in H.PBE and oxygen in O.PBE, which would both be required for simulating, say, a water molecule.

Data directory

A directory named data is required for any QXMD run. All output data will be dumped to this directory. If there are files already present in this directory at the start of a new QXMD run, they will be overwritten. Thus, it is recommended to move files in data from a previous run to a new directory before beginning a new QXMD run. If you are restarting a QXMD run, there are some required files that must be present in data, which will be detailed in section 4.2.

QXMD executable

The QXMD executable, in this case qxmdmpi should be at the same directory level as the control and data directories.