Talk:Mod:Hunt Research Group/cp2k how
1. Website: http://manual.cp2k.org/trunk/
2. Lecture notes: http://www.cecam.org/workshop-4-529.html
3. Basis/Potential Files (can be downloaded together with the CP2K package):
BASIS_SET BASIS_MOLOPT POTENTIAL
4. runscript is cp2k:
- runcp2k
#!/bin/sh
#PBS -l walltime=120:00:00
#PBS -lselect=1:ncpus=8:mem=8000MB
#PBS -j oe
#PBS -q pqph
# make sure you manage your cpus and memory
# above are PBS directives
# -l lines specify resource requirements.
# walltime, mem and ncpus should be considered manadatory.
# -j oe merges stdout and stderr
# submit jobs to the que with this script using the following command:
# qsub -N jobname -v in=name runcp2k
# load modules
#
module load intel-suite mpi cp2k/2.3
# run cp2k
#
# set the name of the basis set file, and of the pseudopotential file in the cp2k input.
# Or else copy those files in the working directory.
# variable PBS_O_WORKDIR=directory from which the job was sumbited.
# variable TMPDIR=directory in which job is run
echo workdir $PBS_0_WORKDIR
echo tmpdir $TMPDIR
# mpiexec {PATH_TO_CP2K_EXECUTABLE}/cp2k.popt file.inp
# {PATH_TO_CP2K_EXECUTABLE} is the directory where the parallel executable of cp2k is
# file.inp is an input file defined in variable in
mpiexec cp2k.popt $PBS_O_WORKDIR/${in}.inp >$PBS_O_WORKDIR/${in}.out 2>&1
# check for a checkpoint file
#
test -r $TMPDIR/*restart*
if [ $? -eq 0 ]
then
cp -f $TMPDIR/*restart* $PBS_O_WORKDIR/
else
echo "no restart file"
fi
test -r $TMPDIR/*pos*
if [ $? -eq 0 ]
then
cp -f $TMPDIR/*pos* $PBS_O_WORKDIR/
else
echo "no pos file"
fi
# exit
5. Example input files
- Example of input file for [bmim]Cl:
&GLOBAL --> Section that contains general information about the simulation and parameters for the whole program.
PROJECT bmimcl --> Name of the project, used to determine the name of the files generated by the program.
PRINT_LEVEL MEDIUM --> How much output is written out.
RUN_TYPE MD --> Type of run that to perform (e.g. MD, GeoOpt, MC).
&END --> End of section.
&FORCE_EVAL --> Parameters used to calculate energy and forces and to describe the system.
METHOD Quickstep --> Method used to compute forces. (Quickstep is for electronic structure methods, e.g. DFT).
&DFT --> Parameters for DFT.
BASIS_SET_FILE_NAME /work/lge/cp2ktest/BASIS_MOLOPT --> Path of basis set file.
POTENTIAL_FILE_NAME /work/lge/cp2ktest/POTENTIAL --> Path of pseudopotential file.
&XC --> Parameters to calculate the xc (exchange-correlation) potential.
&XC_FUNCTIONAL BLYP --> The xc functional to be used.
&END XC_FUNCTIONAL
&XC_GRID --> xc parameters used when calculating the xc on the grid.
XC_DERIV NN10_SMOOTH --> Method used to compute the derivatives.
XC_SMOOTH_RHO NN10 --> Density smoothing used for the xc calculation.
&END XC_GRID
&vdW_POTENTIAL --> Section for all additional dispersion corrections to the xc functionals.
DISPERSION_FUNCTIONAL PAIR_POTENTIAL --> (or POTENTIAL_TYPE, specifies the type of dispersion functional or potential to use).
&PAIR_POTENTIAL --> Info on the pair potential used to calculate dispersion.
TYPE DFTD3 --> Type of potential.
REFERENCE_FUNCTIONAL BLYP --> Use parameters for this specific density functional
&END PAIR_POTENTIAL
&END vdW_POTENTIAL
&END XC
&MGRID --> Multigrid information
CUTOFF 280 --> Cutoff of the finest grid level in Ry.
NGRIDS 5 --> Number of multigrids.
&END
&SCF --> Parameters for the SCF run.
SCF_GUESS ATOMIC --> Initial guess for the wavefunction (ATOMIC generates an atomic density using the atomic code).
MAX_SCF 300 --> Maximum number of SCF iterations for one optimisation.
&OT --> Various options for the orbtial transformation (OT) method.
PRECONDITIONER FULL_SINGLE_INVERSE --> Type of preconditioner to be used with all minimisation schemes (FULL_SINGLE_INVERSE based on H-eS cholesky inversion).
MINIMIZER DIIS --> Minimiser to be used with the OT method (e.g. CG, SD).
&END OT
&END SCF
&PRINT --> turn off printing of the Mulliken charges
&MULLIKEN SILENT
&END
&END
&END SECTION DFT
&SUBSYS --> Defines a subsystem: coordinates, topology, molecules and cell.
&CELL --> Input parameters needed to set up the cell.
ABC 19.522 19.522 19.522 --> Specifies the lengths of the cell vectors A, B and C in Angstroms.
&END CELL
&KIND H --> Description of H atoms.
BASIS_SET DZVP-MOLOPT-SR-GTH --> Primary Gaussian basis set.
POTENTIAL GTH-BLYP-q1 --> Name of pseudopotential.
&END
&KIND C --> Description of C atoms.
BASIS_SET DZVP-MOLOPT-SR-GTH --> Primary Gaussian basis set.
POTENTIAL GTH-BLYP-q4 --> Name of pseudopotential.
&END
&KIND N --> Description of N atoms.
BASIS_SET DZVP-MOLOPT-SR-GTH --> Primary Gaussian basis set.
POTENTIAL GTH-BLYP-q5 --> Name of pseudopotential.
&END
&KIND CL --> Description of Cl atoms.
BASIS_SET DZVP-MOLOPT-SR-GTH --> Primary Gaussian basis set.
POTENTIAL GTH-BLYP-q7 --> Name of pseudopotential.
&END
&COORD --> Coordinates of the atoms in xyz format, in Angstroms (by default).
.....
&END
&END SUBSYS
&END FORCE_EVAL
&MOTION --> Defines tools connected with motion of the nuclei.
&MD --> Parameters to perform an MD run.
ENSEMBLE NVT --> Ensemble to be used.
STEPS 2000 --> Number of MD steps
TIMESTEP 0.5 --> Length of integration step in fs.
&THERMOSTAT --> Specify the thermostat and related parameters.
TYPE NOSE --> Thermostat to be used (NOSE is for the Nose-Hoover thermostat).
&NOSE --> Parameters of the Nose-Hoover thermostat chain.
TIMECON 100 --> Time constant of the thermostat chain in fs.
&END NOSE
&END THERMOSTAT
TEMPERATURE 353 --> Temperature in K used to initialise the velocities with init and pos restart, and in the NPT/NVT simulations.
&END MD
&END MOTION
- Example of input file for Cu water (Cu(II)+64H2O):
&GLOBAL --> Section that contains general information about the simulation and parameters for the whole program.
PROJECT cuwater --> Name of the project, used to determine the name of the files generated by the program.
PRINT_LEVEL MEDIUM --> How much output is written out.
RUN_TYPE MD --> Type of run that to perform (e.g. MD, GeoOpt, MC).
&END --> End of section.
&FORCE_EVAL --> Parameters used to calculate energy and forces and to describe the system.
METHOD Quickstep --> Method used to compute forces. (Quickstep is for electronic structure methods, e.g. DFT).
&DFT --> Parameters for DFT.
BASIS_SET_FILE_NAME /work/lge/cp2kcuwater/BASIS_MOLOPT --> Path of basis set file.
POTENTIAL_FILE_NAME /work/lge/cp2kcuwater/POTENTIAL --> Path of pseudopotential file.
LSD --> or UKS, requests a spin-polarised calculation using alpha and beta orbtials, i.e. no spin restriction is applied.
CHARGE 2 --> Total charge of the system
MULTIPLICITY 2 --> Two times the total spin plus one.
&PRINT --> Printing options.
&LOCALIZATION --> Printing options related to the Wannier centers and properties computed with Wannier centers.
&WANNIER_CENTERS --> Controls the printing of the wannier functions.
IONS+CENTERS --> Prints out the wannier centers together with the particles.
&END
&END
&END
&MGRID --> Multigrid information
CUTOFF 280 --> Cutoff of the finest grid level in Ry.
&END MGRID
&QS --> Parameters needed to set up the Quickstep framework
EXTRAPOLATION PS --> Extrapolation strategy for the wavefunction during e.g. MD (PS is higher order extrapolation of the density matrix times the overlap matrix).
EXTRAPOLATION_ORDER 2 --> Order for the PS or ASPC extrapolation.
&END QS
&SCF --> Parameters for the SCF run.
CHOLESKY OFF --> If the cholesky method should be used for computing the inverse of S, and in this case calling which Lapack routines (OFF means do not use cholesky).
SCF_GUESS ATOMIC --> Initial guess for the wavefunction (ATOMIC generates an atomic density using the atomic code).
EPS_SCF 3.0E-6 --> Target accuracy for the scf convergence.
MAX_SCF 20 --> Maximum number of SCF iterations for one optimisation.
&OUTER_SCF --> Parameters controlling the outer SCF loop.
EPS_SCF 3.0E-6 --> Target gradient (not accuracy?) of the outer SCF variables. Notice that the EPS_SCF of the inner loop also determines the value that can be reached in the outer loop, typically EPS_SCF of the outer loop must be smaller than the EPS_SCF of the inner loop.
MAX_SCF 20 --> The maximum number of outer loops.
&END
&OT --> Various options for the orbtial transformation (OT) method.
MINIMIZER DIIS --> Minimiser to be used with the OT method (e.g. CG, SD).
PRECONDITIONER FULL_ALL --> Type of preconditioner to be used with all minimisation schemes (FULL_ALL is the most effective state selective preconditioner based on diagonalisation, requires the ENERGY_GAP parameters to be an underestimate of the HOMO-LUMO gap).
ENERGY_GAP 0.01 --> Should be an estimate for the HOMO-LUMO energy gap in a.u. and is used in preconditioning.
&END OT
&END SCF
&XC --> Parameters to calculate the xc (exchange-correlation) potential.
&XC_FUNCTIONAL BLYP --> The xc functional to be used.
&END XC_FUNCTIONAL
&END XC
&END DFT
&SUBSYS --> Defines a subsystem: coordinates, topology, molecules and cell.
&CELL --> Input parameters needed to set up the cell.
ABC 12.535 12.535 12.535 --> Specifies the lengths of the cell vectors A, B and C in Angstroms.
&END CELL
&KIND H --> Description of H atoms.
BASIS_SET DZVP-MOLOPT-SR-GTH --> Primary Gaussian basis set.
POTENTIAL GTH-BLYP-q1 --> Name of pseudopotential.
&END
&KIND O --> Description of O atoms.
BASIS_SET DZVP-MOLOPT-SR-GTH --> Primary Gaussian basis set.
POTENTIAL GTH-BLYP-q6 --> Name of pseudopotential.
&END
&KIND Cu --> Description of Cu atoms.
BASIS_SET DZVP-MOLOPT-SR-GTH --> Primary Gaussian basis set.
POTENTIAL GTH-BLYP-q11 --> Name of pseudopotential.
&END
&COORD --> Coordinates of the atoms in xyz format, in Angstroms (by default).
.....
&END
&END SUBSYS
&END FORCE_EVAL
&MOTION --> Defines tools connected with motion of the nuclei.
&MD --> Parameters to perform an MD run.
ENSEMBLE NVT --> Ensemble to be used.
STEPS 2000 --> Number of MD steps
TIMESTEP 0.5 --> Length of integration step in fs.
&THERMOSTAT --> Specify the thermostat and related parameters.
TYPE NOSE --> Thermostat to be used (NOSE is for the Nose-Hoover thermostat).
&NOSE --> Parameters of the Nose-Hoover thermostat chain.
TIMECON 100 --> Time constant of the thermostat chain in fs.
&END NOSE
&END THERMOSTAT
TEMPERATURE 298 --> Temperature in K used to initialise the velocities with init and pos restart, and in the NPT/NVT simulations.
&END MD
&END MOTION