View source for 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):
<pre>
BASIS_SET
BASIS_MOLOPT
POTENTIAL
</pre>

4. runscript is cp2k:
:runcp2k
<pre>
#!/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
</pre>

5. Example input files
: Example of input file for [bmim]Cl: 
<pre>
&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  
</pre>

: Example of input file for Cu water (Cu(II)+64H2O): 
<pre>
&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
</pre>