CP2K¶
(contributed by Felipe Zapata, extended by Patrick Melix)
Settings¶
The cp2k input is rather complex one compared to other computational codes, but its input is structured as a set of nested block and sub-blocks that can be easily represented by the Settings
class.
Like the other interfaces, the CP2K input file is generated using the input branch of the job settings.
For instance, a single point calculation for pentacene:
penta = Settings()
penta.input.force_eval.dft.basis_set_file_name = "/path/to/basis"
penta.input.force_eval.dft.potential_set_file_name = "/path/to/potential"
penta.input.force_eval.dft.mgrid.cutoff = 400
penta.input.force_eval.dft.mgrid.ngrids = 4
penta.input.force_eval.dft.poisson = Settings()
penta.input.force_eval.dft.localize._h = "T"
penta.input.force_eval.dft.qs.method = "GPW"
penta.input.force_eval.dft.scf.eps_scf = 1e-6
penta.input.force_eval.dft.scf.max_scf = 200
penta.input.force_eval.dft.xc.xc_functional._h = "PBE"
penta.input.force_eval.subsys.cell.A = '16.11886919 0.07814137 -0.697284243'
penta.input.force_eval.subsys.cell.B = '-0.215317662 4.389405268 1.408951791'
penta.input.force_eval.subsys.cell.C = '-0.216126961 1.732808365 9.74896108'
penta.input.force_eval.subsys.cell.periodic = 'XYZ'
penta.input.force_eval.subsys.kind.C.basis_set = "DZVP-MOLOPT-SR-GTH-Q4"
penta.input.force_eval.subsys.kind.C.potential = "GTH-PBE-Q4"
penta.input.force_eval.subsys.kind.H.basis_set = "DZVP-MOLOPT-SR-GTH-Q1"
penta.input.force_eval.subsys.kind.H.potential = "GTH-PBE-q1"
penta.input.force_eval.subsys.topology.coord_file_name = "./penta.xyz"
penta.input.force_eval.subsys.topology.coordinate = "xyz"
penta.input['global'].print_level = "low"
penta.input['global'].project = "example"
penta.input['global'].run_type = "energy_force"
The input generated during the execution of the cp2k job is similar to:
&FORCE_EVAL
&DFT
BASIS_SET_FILE_NAME /path/to/basis
&MGRID
CUTOFF 400
NGRIDS 4
&END
&POISSON
&END
&LOCALIZE T
&END
POTENTIAL_FILE_NAME /path/to/potential
&QS
METHOD GPW
&END
&SCF
EPS_SCF 1e-06
MAX_SCF 200
&END
&XC
&XC_FUNCTIONAL PBE
&END
&END
&END
&SUBSYS
&CELL
A 16.11886919 0.07814137 -0.697284243
B -0.215317662 4.389405268 1.408951791
C -0.216126961 1.732808365 9.748961085
PERIODIC XYZ
&END
&KIND C
BASIS_SET DZVP-MOLOPT-SR-GTH-q4
POTENTIAL GTH-PBE-q4
&END
&KIND H
BASIS_SET DZVP-MOLOPT-SR-GTH-q1
POTENTIAL GTH-PBE-q1
&END
&TOPOLOGY
COORD_FILE_NAME ./geometry.xyz
COORDINATE XYZ
&END
&END
&END
&GLOBAL
PRINT_LEVEL LOW
PROJECT example
RUN_TYPE ENERGY_FORCE
&END
PLAMS automatically creates the indented structure of the previous example together with the special character & at the beginning and end of each section, and finally the keyword END at the end of each section.
Notice that CP2K requires the explicit declaration of the basis set together with the charge and the name of the potential used for each one of the atoms. In the previous example the basis for the carbon is DZVP-MOLOPT-SR-GTH, while the potential is GTH-PBE and the charge q4.
The input parser also allows for header values like in this example &LOCALIZE T &END by using the <some_section>._h
(for header) notation in the Settings
instance (just like in ADFJob
).
Inclusion of external files by using the @INCLUDE notation of Cp2k is supported. Also the @SET and @IF keys can be used, just replace the @ sign by at_
in the definition of your Settings
.
If you need some files to be copied to the actual execution directory, pass them to the constructor using the copy=
option. See the API below.
Molecule parsing¶
Molecules can be parsed into the input automatically by passing them to the Cp2kJob
constructor.
Leaving the molecule unset is supported, make sure you then set your molecule by hand (e.g. using the TOPOLOGY section).
Parsing of the molecule can be avoided by setting job.settings.ignore_molecule = True
in the Settings
of the job.
Also, the simulation cell can be specified using the x, y, z vectors like in the previous example. A cubic box can be easily specified by:
penta.input.force_eval.subsys.cell.ABC = "[angstrom] 50 50 50"
That results in a simulation cube of 50 cubic angstroms. For a more detailed description of the cp2k input see manual.
Loading jobs¶
Calculations done without PLAMS can be loaded using the load_external()
functionality. The Cp2kResults
class supports reading input files into Settings
objects.
Just do Cp2kJob.load_external(path)
to get the settings from the file.
Molecule loading¶
A Molecule
can be recreated from a Settings
instance using the Cp2kSettings2Mol
function.
API¶
-
class
Cp2kJob
[source]¶ A class representing a single computational job with CP2K.
In addition to the arguments of
SingleJob
,Cp2kJob
takes acopy
argument.copy
can be a list or string, containing paths to files to be copied to the jobs directory. This might e.g. be a molecule, further input files etc.-
_result_type
¶
-
__init__
(copy=None, **kwargs)[source]¶ Initialize self. See help(type(self)) for accurate signature.
-
get_input
()[source]¶ Transform all contents of
input
branch ofSettings
into string with blocks, subblocks, keys and values.
-
get_runscript
()[source]¶ Run a parallel version of CP2K.
The exact CP2K executable, and whether or not one wants to use
srun
ormpirun
can be specified underself.settings.executable
. Currently supported executables are:"sdbg"
: Serial single core testing and debugging"sopt"
: Serial general single core usage"ssmp"
: Parallel (only OpenMP), single node, multi core"pdbg"
: Parallel (only MPI) multi-node testing and debugging"popt"
: Parallel (only MPI) general usage, no threads"psmp"
: parallel (MPI + OpenMP) general usage, threading mightimprove scalability and memory usage
For example:
>>> from scm.plams import Cp2kJob
>>> job = Cp2kJob(...) >>> job.settings.executable = "cp2k.popt" >>> job.settings.executable = "c2pk.ssmp" >>> job.settings.executable = "mpirun -np 24 cp2k.psmp"
-
-
class
Cp2kResults
[source]¶ A class for CP2K results.
-
recreate_settings
()[source]¶ Recreate job for
load_external()
.If a keyword and a section with the same name appear, only the keyword is used. This happens e.g. when reading restart files where
kind.symbol.potential
is given as Potential ABCD and &POTENTIAL …. &END POTENTIAL.Limited support of sections that have different formatting like KIND and COORD. Check the resulting
Settings
instance if the information you want is there. Be careful with reading restart files, since they are automatically generated and not every case is handled well here. You should get all the information but not sure if I know about all special cases of input.
-
get_energy
(index=- 1, unit='a.u.')[source]¶ Returns ‘Total energy:’ from the output file.
Set
index
to choose the n-th occurence of the total energy in the output, e.g. to choose an optimization step. Also supports slices. Defaults to the last occurence.
-
get_dispersion
(index=- 1, unit='a.u.')[source]¶ Returns ‘Dispersion energy:’ from the output file.
Set
index
to choose the n-th occurence of the dispersion energy in the output, e.g. to choose an optimization step. Also supports slices. Defaults to the last occurence.
-
get_forces
(file=None, index=- 1)[source]¶ Returns list of ndarrays with forces for each atom.
Set
file
to use other than the main output file.Set
index
to choose the n-th occurence of the forces in the output, e.g. to choose an optimization step. Set to None to return all as a list. Defaults to the last occurence.
-
get_mulliken_charges
(return_spin=False, index=- 1)[source]¶ Get Mulliken charges (and spin moments).
Set
index
to choose the n-th occurence of the Charges in the output, e.g. to choose an optimization step. Set to None to return all as a list. Defaults to the last occurence.Returns list of charges. If
return_spin
is True returns tuple of charges and spins.
-
get_hirshfeld_charges
(return_spin=False, index=- 1)[source]¶ Get Hirshfeld charges (and spin moments).
Set
index
to choose the n-th occurence of the Charges in the output , e.g. to choose an optimization step. Set to None to return all as a list. Defaults to the last occurence.Returns list of charges. If
return_spin
is True returns tuple of charges and spins.
-
get_multigrid_info
()[source]¶ Get Information on multigrids.
Usefull for converging cutoffs. Needs ‘Medium’ global print level.
Returns a dict with keys ‘counts’ and ‘cutoffs’.
-
get_md_infos
(file=None, cache=False)[source]¶ Read the MD-info sections.
Returns a list with descriptors and a nested list containing the values for each timestep.
Set
cache
to save the results inself.md_infos
to speed up analysis by avoiding I/O.
-
get_md_cell_volumes
(file=None, unit='angstrom')[source]¶ Get cell Volumes using the
get_md_infos()
function.
-
get_md_pressure
(file=None)[source]¶ Get pressures using the
get_md_infos()
function.
-