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Running cp2k Calculations PDF

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191 views23 pages

Running cp2k Calculations PDF

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Anonymous G4wKZ9w
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RUNNING CP2K

CALCULATIONS
Iain Bethune ([email protected])
Overview
•  How to run CP2K

•  CP2K Input file


•  The Basics
•  The How – FORCE_EVAL
•  The What – MOTION

•  Basis Sets and Pseudopotential libraries

•  CP2K Output
•  Controlling what gets written
•  Overview of an output file

•  Restarting a calculation
How to run CP2K
•  CP2K binaries:
•  cp2k.version where version is usually one of:
•  sopt – Serial, optimised
•  ssmp – Single process + symmetric multiprocessor (OpenMP)
•  popt – Parallel (MPI), optimised
•  psmp – Parallel (MPI) + symmetric multiprocessor (OpenMP)

•  Available from http://www.cp2k.org/download


•  Linux binaries (released versions)
•  Also in Linux package managers
•  Source code (released versions and latest trunk), GPL
•  May be pre-installed, e.g. NSCCS, ARCHER …
How to run CP2K
•  Basic command line options:
•  cp2k.sopt –i input_file –o output_file

•  By default, output goes to the standard output


•  Output to file appends (beware!)
•  Input file is the last argument if not otherwise specified

•  Other useful options:


•  cp2k.sopt –-version
•  cp2k.sopt –-check input_file
•  cp2k.sopt –-html-manual
•  cp2k.sopt --help
How to run CP2K
•  Typical files associated with a CP2K run:
•  Input (required):
•  e.g. H2O-32.inp (main input file, name and extension are arbitrary)
•  Optional inputs:
•  POTENTIAL (psuedopotential library)
•  BASIS_SET (basis set library)
•  Structure file (e.g. psf, xyz, crd …)
•  …
•  Outputs:
•  PROJECT-1.restart (input file to restart calculation)
•  PROJECT-pos-1.xyz (trajectory for MD or GEO_OPT)
•  PROJECT-1.ener (MD energies, temperature, cons. Q …)
•  PROJECT-1.cell (cell parameters for NPT MD or CELL_OPT)
•  PROJECT-RESTART.wfn (orbitals for restart)
CP2K Input file: The Basics
•  Full documentation available online:
•  http://manual.cp2k.org
•  Or generate with --html-manual

•  Sections – 13 (optional) top level sections


&BEGIN section_name [params]
…
&END [section_name]

•  Keywords
KEYWORD value
KEYWORD [ON|OFF] [YES|NO] [TRUE|FALSE] …
KEYWORD

•  Nesting
•  Sections may others sections and keywords
CP2K Input file: The Basics
•  Basic pre-processing syntax
@INCLUDE ‘filename’ – copy in text from file
@SET VAR value – define a variable
$VAR – replaced with variable value
@IF / @ENDIF – simple logic
! or # – comments

•  Units
•  Numerical entries have a default unit (see manual)
•  Specify other units by hand e.g.
ABC [nm] 100 100 100 (or bohr, default is angstrom)
EMAX_SPLINE [eV] 50 (or Ry, joule, default is hartree)
•  Also combinations e.g. [hartree*bohr^-2]
CP2K Input file: The Basics
•  GLOBAL section (required)
&GLOBAL
PROJECT H2O-32
RUN_TYPE MD
PRINT_LEVEL HIGH
&TIMINGS
THRESHOLD 0.000001
&END
WALLTIME 3600
&END GLOBAL
CP2K Input file: The How
•  FORCE_EVAL section (required)
&FORCE_EVAL
METHOD QS (or FIST, QMMM …)
&DFT
…
&END DFT
&SUBSYS
…
&END SUBSYS
&END FORCE_EVAL
CP2K Input file: The How
&DFT
BASIS_SET_FILE_NAME GTH_BASIS_SETS Basis and PP library files
POTENTIAL_FILE_NAME POTENTIAL
&MGRID
CUTOFF 280
REL_CUTOFF 30 Parameters for the realspace multi-grids
&END MGRID
&QS
EPS_DEFAULT 1.0E-12
WF_INTERPOLATION PS
Quickstep options
EXTRAPOLATION_ORDER 3
&END QS
&SCF
SCF_GUESS ATOMIC Control of SCF procedure, including
&OT ON
MINIMIZER DIIS minimisation scheme
&END OT
&PRINT
&RESTART OFF
&END
&END
&END SCF
&XC Exchange-Correlation Functional (LDA)
&XC_FUNCTIONAL Pade
&END XC_FUNCTIONAL
&END XC
&END DFT
CP2K Input file: The How
&SUBSYS
&CELL Cell definition
ABC 9.8528 9.8528 9.8528
&END CELL
# 32 H2O (TIP5P,1bar,300K) a = 9.8528 Particle coordinates
&COORD
O 2.280398 9.146539 5.088696
O 1.251703 2.406261 7.769908 Could also @include an external file
O 1.596302 6.920128 0.656695 or parse other formats via
...
H 0.837635 8.186808 8.987268
&TOPOLOGY
H 8.314696 10.115534 2.212519 COORD_FILE_NAME
H 8.687134 8.667252 2.448452 &END TOPOLOGY
&END COORD
&KIND H
BASIS_SET TZV2P-GTH
POTENTIAL GTH-PADE-q1 Definitions of atomic kinds
&END KIND
&KIND O
BASIS_SET TZV2P-GTH
Could specify charge, mass …
POTENTIAL GTH-PADE-q6
&END KIND
&END SUBSYS
CP2K Input file: The What
•  MOTION section
&MOTION
&MD
ENSEMBLE NVE
STEPS 10
TIMESTEP 0.5
TEMPERATURE 300.0
&END MD
&END MOTION

•  Also used to control Geometry Optimisation, NEB, Monte Carlo, …


Basis Sets and PP libraries
•  CP2K uses Goedecker-Teter-Hutter, seperable
Pseudopotentials
•  Several sets of PPs and corresponding optimised basis sets are
available
•  See cp2k/data or online:
http://sourceforge.net/p/cp2k/code/HEAD/tree/trunk/cp2k/data

•  POTENTIAL, GTH_POTENTIALS
•  Wide range of PPs for at many elements - LDA (PADE), PBE, BLYP …

•  BASIS_SET, GTH_BASIS_SET, BASIS_MOLOPT


•  Various qualities / size of basis
•  Make sure Basis and PP match (functional and number of electrons)
•  Some documentation and references at head of each file
CP2K Output: Controlling what gets written
•  The PRINT_LEVEL keyword in &GLOBAL

•  SILENT, LOW, MEDIUM (default), HIGH, DEBUG

•  HIGH can give more information if you are interested


•  Also gives some per-process logging in parallel jobs
•  For long MD runs (e.g. classical), recommend using LOW

•  Fine grained control is available via print-keys


•  Most input sections contain a &PRINT sub-section
•  Each &PRINT sub-section has further subsections for each
quantity that may be printed
CP2K Output: Controlling what gets written
•  For example, the &PRINT section in &MOTION contains
&CELL
&FORCES
&TRAJECTORY
&VELOCITIES
...
•  Each section has parameters (and defaults) for which
print level it is output
•  &TRAJECTORY defaults to LOW
•  &VELOCITIES defaults to HIGH
CP2K Output: Controlling what gets written
•  Can also specify frequency of printing via &EACH sub-
section e.g.
&PRINT
&CELL
&EACH
MD 100
&END EACH
&END CELL
&END PRINT

•  Control over filenames, file formats etc. at each &PRINT


section
CP2K Output: Overview of an output file
…
Restarting a calculation
•  If you need to restart your job…
•  Hardware failure
•  Batch system time limit
•  Need more MD sampling
•  …

•  CP2K dumps a restart input file which can be directly re-


run
•  cp2k.sopt –i PROJECT-1.restart
•  Continuous numbering of MD steps
•  Stores all state variables (incl. extended system)
•  Use SCF_GUESS RESTART
Tools for building CP2K input
•  Plugins are available for your favourite(!) text editors:
•  https://www.cp2k.org/tools:vim
•  https://www.cp2k.org/tools:emacs
•  Syntax highlighting, indentation, show/hide sections, keywords
Tools for building CP2K input
•  Python interfaces
•  Atomic Simulation Environment (ASE) – see tomorrow

•  PyCP2K (https://github.com/SINGROUP/pycp2k)
•  Object-oriented wrapper following the CP2K input format
•  Auto-completion (for e.g. Spyder IDE)
•  E.g. GLOBAL%RUN_TYPE is GLOBAL.Run_type
•  May use ASE for execution
Tools for building CP2K input
•  CP2K Input Editor
•  Browser-based:
•  http://cp2k-www.epcc.ed.ac.uk/cp2k-input-editor
•  Show/hide sections
•  Dropdowns for option selection
•  Tooltip help on every keyword
•  Basic input validation
•  Library of example input template files
•  Supports CP2K releases 2.5-2.7, 3.0, 4.0
Tools for building CP2K input
Running a CP2K Calculation

Questions?

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