# Open SourceMolecular Dynamics

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#### For Developers

exercises:2015_cecam_tutorial:geometry_and_cell_optimization

# Geometry optimization of NaCl clusters

Use this short script to drive CP2K

#!/bin/bash
#

for ii in 2 4 6 8 10 12
do
sed -e "s/MY_SUPERCELL/${ii}/g" template.inp > input_${ii}.inp
cp2k.popt input_${ii}.inp > NaCl_supercell_${ii}.out
done

where the template input is this geometry optimization using the classical forcefield FIST module of CP2K.

@SET NREP MY_SUPERCELL
@SET OPTIMIZER LBFGS # BFGS

&FORCE_EVAL
METHOD Fist
&MM
&FORCEFIELD
&CHARGE
ATOM Na
CHARGE +1.000
&END CHARGE
&CHARGE
ATOM Cl
CHARGE -1.000
&END CHARGE
&NONBONDED
&BMHFT
map_atoms NA NA
atoms NA NA
RCUT 10.0
&END BMHFT
&BMHFT
map_atoms NA CL
atoms NA CL
RCUT 10.0
&END BMHFT
&BMHFT
map_atoms CL CL
atoms CL CL
RCUT 10.0
&END BMHFT
&END NONBONDED
&END FORCEFIELD
&POISSON
&EWALD
EWALD_TYPE spme
ALPHA .35
GMAX 12*${NREP} O_SPLINE 6 &END EWALD &END POISSON &END MM &SUBSYS &CELL #ABC 5.620 5.620 5.620 ABC 2*5.620 2*5.620 2*5.620 MULTIPLE_UNIT_CELL${NREP} ${NREP}${NREP}
&END CELL
&TOPOLOGY
COORD_FILE_NAME NaCl.pdb
COORDINATE PDB
CONN_FILE_FORMAT OFF
MULTIPLE_UNIT_CELL ${NREP}${NREP} ${NREP} &END TOPOLOGY &END SUBSYS &END FORCE_EVAL &GLOBAL PROJECT NaCl RUN_TYPE GEO_OPT &END GLOBAL &MOTION &GEO_OPT OPTIMIZER${OPTIMIZER}
&END
&END MOTION


The script runs very quickly when the LBFGS optimizer is used. But see what happens if we switch to the BFGS optimizer instead (change the OPTIMIZER variable in the cp2k input file - you might want to reduce the size of the supercells in the driver script - NREP varying from 1 to 6 perhaps). Look at the timings that cp2k prints at the end of a run and see if you can see the culprit. Also look for warnings in your outputs (this is a good habit to get into).

How does the conjugate gradients optimizer compare to LBFGS in efficiency for this system?

# Cell optimization of NaCl

For studying many properties of solid materials it is important that the lattice parameters used in a simulation are close to equilibrium for the model chemistry (Hamiltonian) used. Otherwise, large stresses can be present that complicate comparison to experiment. Successful cell optimization requires that the energy changes smoothly with cell volume - and for this the energy cutoff is the most important parameter. The input file template below can be used with driver script to examine how the energy volume curve of NaCl changes with the PW cutoff.

@SET SCALE_FACTOR MY_SCALING
@SET NREP 1
@SET OPTIMIZER BFGS # LBFGS
@SET CUTOFF MY_CUTOFF
@SET SAFTEY_CUTOFF 1.1

&FORCE_EVAL
METHOD QS
&DFT
BASIS_SET_FILE_NAME BASIS_MOLOPT
POTENTIAL_FILE_NAME GTH_POTENTIALS
&MGRID
CUTOFF ${CUTOFF} REL_CUTOFF 60 &END MGRID &QS EPS_DEFAULT 1.0E-12 &END QS &SCF SCF_GUESS RESTART &OT ON MINIMIZER DIIS &END OT &END SCF &XC &XC_FUNCTIONAL Pade &END XC_FUNCTIONAL &END XC &END DFT &SUBSYS &CELL ABC 5.620*${SCALE_FACTOR} 5.620*${SCALE_FACTOR} 5.620*${SCALE_FACTOR}
MULTIPLE_UNIT_CELL ${NREP}${NREP} ${NREP} #&CELL_REF # ABC 5.620*${SAFETY_FACTOR} 5.620*${SAFETY_FACTOR} 5.620*${SAFETY_FACTOR}
#  MULTIPLE_UNIT_CELL ${NREP}${NREP} ${NREP} #&END &END CELL &COORD scaled Na 0.000 0.000 0.000 Cl 0.500 0.500 0.500 Na 0.000 0.500 0.500 Cl 0.500 0.000 0.000 Na 0.500 0.000 0.500 Cl 0.000 0.500 0.000 Na 0.500 0.500 0.000 Cl 0.000 0.000 0.500 &END &TOPOLOGY MULTIPLE_UNIT_CELL${NREP} ${NREP}${NREP}
&END TOPOLOGY
&KIND Na
BASIS_SET DZVP-MOLOPT-SR-GTH
&END KIND
&KIND Cl
BASIS_SET DZVP-MOLOPT-SR-GTH
&END KIND
&END SUBSYS
&END FORCE_EVAL

&GLOBAL
PROJECT NaCl
RUN_TYPE ENERGY
&END GLOBAL

&MOTION
&GEO_OPT
OPTIMIZER ${OPTIMIZER} &END &CELL_OPT KEEP_SYMMETRY &END &END MOTION The driver script could be something like #!/bin/bash # CUTOFF="280" for ii in 0.800 0.825 0.850 0.875 0.900 0.925 0.950 0.975 1.000 1.025 1.050 1.075 1.100 do #this assumes that the input template is in NaCl_QS.inp sed -e "s/MY_SCALING/${ii}/g" NaCl_QS.inp > temp.inp
sed -e "s/MY_CUTOFF/${CUTOFF}/g" temp.inp > input_${ii}.inp

#this line should changed to point to your cp2k executable
mpirun -np 2 cp2k.popt input_${ii}.inp > NaCl_${CUTOFF}_${ii}.out done  You can extract energies from the outputs with a command like grep 'ENERGY|' *out | awk '{print$10}' > NaCl_energy_volume.dat

and you can plot the results in your favourite graphing software.

What is happening here? Try changing the PW cutoff (defined in the driver script) and using the CELL_REF variable.

Copy the input template to a new file and change the RUN_TYPE to CELL_OPT. You'll also need to ask the code to calculate the stress tensor (in FORCE_EVAL section) ANALYTICALLY! Also define the CUTOFF and SCALING_FACTOR. Start the cell optimization from small cells (SCALING_FACTOR 0.85) or large cells (SCALING_FACTOR 1.10) - do you get the same results?

If you have access a machine with several cores (16 or so ideally) check whether increasing the supercell size (NREP variable) affects the results.