#### Three exercises (Hydrogen molecule, Water and Ammonia) to practice with the basics of CPMD.

## Hydrogen Molecule

Requirements: Memory: 50-100 MB, CPU time: 1-5 min/job.

The first object of study will be a rather trivial one: an isolated
hydrogen molecule. We will treat it in the Local Density Approximation
(LDA) and use a simple norm-conserving pseudopotential. Although there
are much better ways of treating this system, the calculations are fast
and the results easy to check, so that this is an ideal testbed to
introduce and try out a lot of features in CPMD.

- Perform a wavefunction optimization (single point calculation) of a hydrogen molecule using the input file 1-h2-wave.inp and the pseudopotential file H_MT_LDA.psp. Rename the resulting restart file
**RESTART.1**to**RESTART**so that it can be used for the next calculations and will not be overwritten. Inspect the input and output files. - Calculate the Kohn-Sham Energies and calculate/write out several density or wavefunction type files using the RESTART.1 file from the previous calculation (2-h2-ksener.inp). The resulting files DENSITY, ELPOT,
etc. contain their information still in reciprocal space. You need to
use the cpmd2cube.x utility to convert them to real space file in cube
format. Usage, e.g.:

cpmd2cube.x -halfmesh -rho DENSITY cpmd2cube.x -halfmesh -psi WAVEFUNCTION.2

For the visualization of the resulting geometries and cube files, please see the VMD Visualization Tutorial. The visualization of cube files is described in Part 5. Plese note, that VMD does not consider bonds between two hydrogens (it makes it much more efficient for large biomolecules), so you have to manually set the bond with VMD scripting at the command prompt (or use a VDW representation):

set sel [atomselect 0 {name H}] $sel setbonds {{1} {0}}

Again rename the**RESTART.1**file to**RESTART**after you have verified, that the calculation was successful, so you can read it in the next step. - Calculate some more properties using the restart from the previous run using the input files: 3a-h2-prop.inp and 3b-h2-prop.inp. Have a look at the output file and the various other created files. See the CPMD manual for an explanation of their contents.
- Try
out various methods to optimize the wavefunction. The following input
files are examples for the several methods implemented in CPMD. Compare
them with respect to the final result and the convergence behavior:

- The default optimizer DIIS with a smaller vector size to conserve memory: 4a-h2-wave.inp
- Conjugate gradient PCG with line search: 4b-h2-wave.inp
- Lanczos diagonalization: 4c-h2-wave.inp
- Steepest descend: 4d-h2-wave.inp
- Davidson diagonalization: 4e-h2-wave.inp
- Simulated annealing : 4f-h2-wave.inp (NOTE: see molecular dynamics section for more info)

- Optimize the geometry of the hydrogen molecule with the default method: 5-h2-geoopt.inp If you keep this RESTART file, you can re-use it later .

**Final question**: how come you can use a pseudopotential for hydrogen, when there are no core electrons?

## Water Molecule

Requirements: Memory: 150-200 MB, CPU time: 2x 15-20 min + 1x 1 min.

In this section section we will study a slightly more ambitious
molecule: water. Since water has a dipole moment, you have to keep in
mind, that we are calculating a system with periodic boundary
conditions, so the water molecule ‘sees’ its images and interacts with
them. There are methods implemented in CPMD to compensate for this
effect, but we won’t use them here to save resources. This time we will
use a gradient corrected functional (BLYP) instead of the LDA. Also note
that in the &ATOMS section the LMAX for the oxygen is set to P
(instead of S for hydrogen) and that the keyword KLEINMAN-BYLANDER is
required for for the calculation of the nonlocal parts of the
pseudopotential.

- Optimize the geometry of a water molecule with the default geometry optimization algorithm.

1-h2o-pbc-geoopt.inp**Note**: the calculation is limited to 100 steps, so check if the optimization is converged. - Repeat the geometry optimization of a water molecule with the linear scaling geometry optimizer and adaptive convergence.

2-h2o-pbc-geo-linsc.inp**Note**: the calculation is limited to 100 steps, so check if the optimization is converged. - Do a properties calculation using the RESTART from the previous run: 3a-h2o-pbc-prop.inp and 3b-h2o-pbc-prop.inp.

## Ammonia Molecule

Requirements: Memory: 220 MB (VDB/25Ry), 600 MB (MT/70Ry), CPU time: 10-20 min (Properties: 1 min).

In this example we will diversify a little more by looking at an
ammonia molecule and using a different type of pseudopotential: a
so-called ‘ultra-soft’ (Vanderbilt) pseudopotential (USPP) both for H_VDB_BLYP.php and N_VDB_BLYP.psp.
This class of pseudopotentials can be used with a much smaller plane
wave cutoff and thus needs less memory resources than calculations with
norm-conserving pseudopotentials. However, calculations with USPPs have
to be set up more carefully and for the calculation of several
properties a single-point wavefunction optimization with norm-conserving
pseudopotentials has to be performed from the USPP restart. Also note
that in this case the FORMATTED keyword is required to have the
pseudopotential reader recognize the psedopotential file format.

- Optimize the geometry of an ammonia molecule with ultra-soft pseudopotentials: 1-nh3-geoopt-vdb.inp.
**Note**: that we now use**SYMMETRY**0 and a Poisson solver to decouple the periodic images, so that the result is closer to the calculation of an isolated molecule. See the CPMD manual for some further information. - Re-optimize the electronic structure with norm-conserving pseudopotentials and calculate some data sets for visualization: 2-nh3-wfopt-mt.inp.
**Note**: this job needs much more memory, so you may need to run it on a machine with more memory installed. - Perform a properties calculation based on the restart from the previous run, by using the input 3-nh3-prop-mt.inp.
- Perform
a geometry optimization of the (flat) transition state of the
‘umbrella’-mode of the ammonia molecule with ultra-soft
pseudopotentials: 4-nh3-geoopt-flat.inp.
In this case we ‘guide’ the geometry optimizer to the desired structure
by using a constraint, i.e. adding the following lines to the
&ATOMS section of the input file.

CONSTRAINTS FIX STRUCTURE 1 TORSION 2 3 4 1 0.0 END CONSTRAINTS

There also are geometry optimization algorithms implemented in CPMD that allow to search for a transition state, but this would go beyond the scope of this tutorial. Check out the CPMD manual and the CPMD test suite.