Merge branch 'fleur-example' into 'master'

Add running example for Fleur

See merge request !389

content/applications/app_specific/running_fleur.md

++++
+title = "Running Fleur/7.1  at HCC"
+description = "How to run Fleur V7.0 on HCC resources."
++++
+The FLEUR project provides a simulation tool for materials properties using density functional theory and related methods.
+
+
+Performing Fleur calculations on some material always starts with the specification of a (prototype) unit cell. With this basic specification the Fleur input generator inpgen then generates a Fleur input file with a reasonable parametrization for the provided unit cell. In this section we discuss the basic usage of the input generator.
+
+In general the input for the Fleur input generator consists of the definition of the unit cell shape as well as the definition of the atoms and atom positions in the cell. Optionally some additional parameters can be set to override or modify the automatic procedure used to determine the parametrization in the Fleur input file.
+
+
+Using the input generator starts by writing a small text file containing the configuration of the unit cell. For a simple Si crystal such a file might look like:
+
+
+**Step 1:** Create "inpSi.txt" file with this content:
+
+{{% panel theme="info" header="Create  inpSi.txt file" %}}
+{{< highlight bash >}}
+Si bulk
+&lattice latsys='cF', a0=1.8897269, a=5.43 /
+2
+14 0.125 0.125 0.125
+14 -0.125 -0.125 -0.125
+
+{{< /highlight >}}
+{{% /panel %}}
+
+
+The first line of the file contains a comment. Here this comment is Si bulk. Next comes the definition of the crystal lattice. This is done in the &lattice line. It starts with the specification of the lattice system in latsys='cF'. cf specifies an fcc lattice. The line is completed with the setting of some parameters. In this case the parameter a is the lattice parameter of the fcc lattice and a0 is a factor that is multipied to all lattice parameters. Note that the input generator expects the lattice specification in units of Bohr radii (a0
+). But since in this example a is provided in Angstrom we need the factor a0 to convert it to units of a0.
+
+
+In the next part of the inpgen input the atom positions are specified. This starts by providing the number of atoms in the next line. For this example system there are 2 atoms in the unit cell. The following lines define the atomic numbers and related atom positions in internal coordinates, i.e., in coordinates of the Bravais lattice vectors. 14 is the atomic number of Si and the two atoms are at (1/8,1/8,1/8) and (−1/8,−1/8,−1/8).
+
+**Step 2:** Call input file "inpSi.txt" to inpgen:
+
+{{% panel theme="info" header="Call inpSi.txt input file" %}}
+{{< highlight bash >}}
+
+inpgen -f inpSi.txt
+
+{{< /highlight >}}
+{{% /panel %}}
+
+
+With this command inpgen will generate a basic Fleur input file inp.xml. In addition a file sym.xml containing the symmetry operations and a file kpts.xml containing sets of k-points will be generated. These additional xml file are actually included into inp.xml by the parser and can also be included directly in the file. Furthermore a file struct.xsf is generated. This is an XCrysden structure file that can be used to visualize the just defined unit cell, e.g., to check for complex structures whether the setup is as expected. The output of the input generator can be found in the file out. If there are problems in generating the Fleur input file hints for the reason might be found in this file or directly on the terminal. The generated file FleurInputSchema.xsd is temporary. It is generated in every inpgen and fleur run and only contains the formal specification of the Fleur input file format.
+
+
+
+**Step 3:** Create a job file "fleur_Job.sh" as the following:
+
+{{% panel theme="info" header="Create job file for Fleur" %}}
+{{< highlight bash >}}
+
+#!/bin/sh
+#SBATCH --nodes=1 
+#SBATCH --ntasks-per-node=16
+#SBATCH --mem-per-cpu=8192
+#SBATCH --time=0:30:00
+#SBATCH --partition=batch
+#SBATCH --error=TestJob.%J.stderr
+#SBATCH --output=TestJob.%J.stdout
+
+module load compiler/gcc/9  openmpi/4.1 fleur/7.0
+mpirun -np 16 fleur_MPI
+
+{{< /highlight >}}
+{{% /panel %}}
+
+
+**Step 3:** Submit the job to the cluster using "sbatch" command as the following:
+
+{{% panel theme="info" header="Submit Fleur  job to the cluster" %}}
+{{< highlight bash >}}
+
+sbatch fleur_Job.sh
+
+{{< /highlight >}}
+{{% /panel %}}
+
+
+{{% notice info %}}
+After your job is finished running, the output and errors will be written to the files TestJob.%J.stdout and TestJob.%J.stderr files.
+{{% /notice %}}