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12
benchmarks/QS/check-release-comparison.py
View file

@ -92,11 +92,9 @@ def run_benchmark(cp2k_exe_dir, input_file, mpi_wrapper="mpiexec -np {mpi_ranks}
allok = True
print(
"""
print("""
CP2K | # Threads | # Ranks | Energy
-----+-----------+---------+------------------------"""
)
-----+-----------+---------+------------------------""")
for (omp_num_threads, mpi_ranks), energy in zip(TEST_COMBINATIONS, energies):
version = cp2k_version(omp_num_threads, mpi_ranks)
@ -109,11 +107,9 @@ CP2K | # Threads | # Ranks | Energy
f"{version} | {omp_num_threads:9d} | {mpi_ranks:7d} | {energy:20.14f} {mark}"
)
print(
f"""\
print(f"""\
----------------------------------------------------
mean: {mean:20.14f} +/- {var:16.12e}"""
)
mean: {mean:20.14f} +/- {var:16.12e}""")
return allok

18
benchmarks/QS_LiH_HFX/README.md
View file

@ -119,12 +119,12 @@ with later ones.
Running on ORNL's Cray XT5 (Jaguar) the following runtime has been obtained in a setup using 8 OMP
threads per node (8 cores per node / 16 Gb per node).
| Cores | Full CP2K\[s\] | HFX\[s\] | local HFX\[s\] | Mem/node\[Mb\] |
| ----: | -------------: | -------: | -------------: | -------------: |
| 1024 | 6569.07 | 6488.24 | 6406.99 | 14845.00 |
| 2048 | 1369.92 | 1314.86 | 1259.82 | 13468.00 |
| 4096 | 722.24 | 670.18 | 631.11 | 7293.00 |
| 8192 | 402.18 | 352.21 | 317.59 | 4306.00 |
| 16384 | 274.41 | 213.88 | 172.88 | 2801.00 |
| 32768 | 201.71 | 135.47 | 85.29 | 2046.00 |
| 65536 | 255.97 | 117.33 | 41.43 | 1673.00 |
| Cores | Full CP2K[s] | HFX[s] | local HFX[s] | Mem/node[Mb] |
| ----: | -----------: | ------: | -----------: | -----------: |
| 1024 | 6569.07 | 6488.24 | 6406.99 | 14845.00 |
| 2048 | 1369.92 | 1314.86 | 1259.82 | 13468.00 |
| 4096 | 722.24 | 670.18 | 631.11 | 7293.00 |
| 8192 | 402.18 | 352.21 | 317.59 | 4306.00 |
| 16384 | 274.41 | 213.88 | 172.88 | 2801.00 |
| 32768 | 201.71 | 135.47 | 85.29 | 2046.00 |
| 65536 | 255.97 | 117.33 | 41.43 | 1673.00 |

6
benchmarks/QS_low_scaling_GW/README.md
View file

@ -18,8 +18,8 @@ To run the benchmark, CP2K needs to be compiled with libint support (`-D__LIBINT
## Results on Piz Dora, CSCS
| Input File | Configuration | Total Number of Cores | Runtime \[s\] |
| ---------- | ------------------------: | --------------------: | ------------: |
| GW.inp | 16 nodes x 36 MPI x 1 OMP | 576 | 305 |
| Input File | Configuration | Total Number of Cores | Runtime [s] |
| ---------- | ------------------------: | --------------------: | ----------: |
| GW.inp | 16 nodes x 36 MPI x 1 OMP | 576 | 305 |
The timings have been obtained on CRAY-XC40 (PizDora@CSCS)

8
benchmarks/QS_mp2_rpa/32-H2O/README.md
View file

@ -28,9 +28,9 @@ the additional files [`t_c_g.dat`](../../../data/t_c_g.dat) and
### Results on Piz Dora, CSCS
| Input File | Configuration | Total Number of Cores | Runtime \[s\] |
| ---------- | ------------------------: | --------------------: | ------------: |
| RI-MP2.inp | 16 nodes x 16 MPI x 1 OMP | 256 | 392 |
| RI-RPA.inp | 16 nodes x 16 MPI x 1 OMP | 256 | 221 |
| Input File | Configuration | Total Number of Cores | Runtime [s] |
| ---------- | ------------------------: | --------------------: | ----------: |
| RI-MP2.inp | 16 nodes x 16 MPI x 1 OMP | 256 | 392 |
| RI-RPA.inp | 16 nodes x 16 MPI x 1 OMP | 256 | 221 |
\*) The timings have been obtained on CRAY-XC40 (PizDora@CSCS)

2
benchmarks/QS_single_node/README.md
View file

@ -1,5 +1,5 @@
# Quickstep Single Node Regression Tests
The purpose of these tests is to give a quick idea of the performance of a system, when only a
single node is available. The tests should run in \< 5 minutes on a modern node, and require less
single node is available. The tests should run in < 5 minutes on a modern node, and require less
than 16Gb of memory.

2
docs/README.md
View file

@ -38,7 +38,7 @@ To build a local version of the manual perform the following steps:
1. Browse the HTML output in the `_build/html` directory.
> \[!TIP\]
> [!TIP]
>
> While the first invocation of Sphinx can be quite slow, subsequent builds are significantly faster
> thanks to its doctree cache. Nevertheless, a build with the full input reference can take several

1
docs/generate_input_reference.py
View file

@ -11,7 +11,6 @@ from datetime import datetime
from collections import defaultdict
from functools import cache
SectionPath = Tuple[str, ...]

422
docs/methods/post_hartree_fock/low-scaling.md
View file

@ -62,7 +62,7 @@ operator with a cutoff radius of 1.5-2.0 Angstroms as a RI metric is safer.
All post-HF calculations need an accurate and well converged SCF as a starting point. In this case,
a pure Hartree-Fock calculation is performed. Note the use of the truncated Coulomb operator as HFX
potential, with cutoff radius \< L/2, as always required in periodic HF. Here, the value of 4.5
potential, with cutoff radius < L/2, as always required in periodic HF. Here, the value of 4.5
Angstroms is somewhat small, and simulating a larger water box would be advised.
A numerical Laplace transform is used to reduce the scaling of the method. The integral is replaced
@ -73,99 +73,99 @@ band gap of the system and the total spread of the SCF eigenvalues. If the selec
point is innapropriate, a warning is issued.
```none
&GLOBAL
PROJECT water32
RUN_TYPE MD
PRINT_LEVEL MEDIUM
&END GLOBAL
&MOTION
&MD
STEPS 3
&END MD
&END MOTION
&FORCE_EVAL
&DFT
!cc-TZ: RI-MP2 optimized basis sets
BASIS_SET_FILE_NAME BASIS_RI_cc-TZ
POTENTIAL_FILE_NAME POTENTIAL
SORT_BASIS EXP
&MGRID
CUTOFF 600
REL_CUTOFF 50
NGRIDS 5
&END MGRID
&SCF
SCF_GUESS RESTART
EPS_SCF 1.0E-6
MAX_SCF 40
&END SCF
&XC
&XC_FUNCTIONAL NONE
&END XC_FUNCTIONAL
&HF
FRACTION 1.0
&INTERACTION_POTENTIAL
!TC potential with cutoff < L/2 for periodic HFX
POTENTIAL_TYPE TRUNCATED
CUTOFF_RADIUS 4.5
&END INTERACTION_POTENTIAL
&MEMORY
!maximum memory allocated to HFX ERI storage, per MPI rank
!the optimal number depends on the specifics of the computer
MAX_MEMORY 4000
&END MEMORY
&GLOBAL
PROJECT water32
RUN_TYPE MD
PRINT_LEVEL MEDIUM
&END GLOBAL
&MOTION
&MD
STEPS 3
&END MD
&END MOTION
&FORCE_EVAL
&DFT
!cc-TZ: RI-MP2 optimized basis sets
BASIS_SET_FILE_NAME BASIS_RI_cc-TZ
POTENTIAL_FILE_NAME POTENTIAL
SORT_BASIS EXP
&MGRID
CUTOFF 600
REL_CUTOFF 50
NGRIDS 5
&END MGRID
&SCF
SCF_GUESS RESTART
EPS_SCF 1.0E-6
MAX_SCF 40
&END SCF
&XC
&XC_FUNCTIONAL NONE
&END XC_FUNCTIONAL
&HF
FRACTION 1.0
&INTERACTION_POTENTIAL
!TC potential with cutoff < L/2 for periodic HFX
POTENTIAL_TYPE TRUNCATED
CUTOFF_RADIUS 4.5
&END INTERACTION_POTENTIAL
&MEMORY
!maximum memory allocated to HFX ERI storage, per MPI rank
!the optimal number depends on the specifics of the computer
MAX_MEMORY 4000
&END MEMORY
&END HF
&WF_CORRELATION
!explicit opposite-spin scaling
SCALE_S 1.3
&RI_SOS_MP2
!MINIMAX quadrature by default
QUADRATURE_POINTS 6
&WF_CORRELATION
!explicit opposite-spin scaling
SCALE_S 1.3
&RI_SOS_MP2
!MINIMAX quadrature by default
QUADRATURE_POINTS 6
&END RI_SOS_MP2
!Enabling low-scaling
&LOW_SCALING
MEMORY_CUT 3
&END LOW_SCALING
&RI
&RI_METRIC
!Short range RI metric for SOS-MP2
POTENTIAL_TYPE TRUNCATED
CUTOFF_RADIUS 1.5
&END RI_METRIC
&END RI
&INTEGRALS
ERI_METHOD GPW
&WFC_GPW
!Safe yet faster than default values
CUTOFF 200
REL_CUTOFF 40
!Enabling low-scaling
&LOW_SCALING
MEMORY_CUT 3
&END LOW_SCALING
&RI
&RI_METRIC
!Short range RI metric for SOS-MP2
POTENTIAL_TYPE TRUNCATED
CUTOFF_RADIUS 1.5
&END RI_METRIC
&END RI
&INTEGRALS
ERI_METHOD GPW
&WFC_GPW
!Safe yet faster than default values
CUTOFF 200
REL_CUTOFF 40
&END WFC_GPW
&END INTEGRALS
&END WF_CORRELATION
&END XC
&END DFT
&SUBSYS
&CELL
ABC 9.8528 9.8528 9.8528
&END CELL
&TOPOLOGY
COORD_FILE_FORMAT XYZ
COORD_FILE_NAME ./H2O-32.xyz
&END TOPOLOGY
&KIND H
BASIS_SET cc-DZ
BASIS_SET RI_AUX RI_DZ
POTENTIAL GTH-HF
&END KIND
&KIND O
BASIS_SET cc-DZ
BASIS_SET RI_AUX RI_DZ
POTENTIAL GTH-HF
&END KIND
&END SUBSYS
&END WF_CORRELATION
&END XC
&END DFT
&SUBSYS
&CELL
ABC 9.8528 9.8528 9.8528
&END CELL
&TOPOLOGY
COORD_FILE_FORMAT XYZ
COORD_FILE_NAME ./H2O-32.xyz
&END TOPOLOGY
&KIND H
BASIS_SET cc-DZ
BASIS_SET RI_AUX RI_DZ
POTENTIAL GTH-HF
&END KIND
&KIND O
BASIS_SET cc-DZ
BASIS_SET RI_AUX RI_DZ
POTENTIAL GTH-HF
&END KIND
&END SUBSYS
&END FORCE_EVAL
```
@ -186,7 +186,7 @@ exchange energy (EXX) calculated with the same orbitals. The `&HF` section in RP
last step. If taken to be the same as the SCF (except for `FRACTION` and `MEMORY`), the stored ERIs
can be reused and rescaled instead of recomputed, thus saving precious computational time. The
`ADMM` keyword in RPA specifies that the EXX should be calculated within the ADMM approximation.
Note the truncated Coulomb potential used for HFX, and its cutoff radius of 4.5 Angstroms (\< L/2),
Note the truncated Coulomb potential used for HFX, and its cutoff radius of 4.5 Angstroms (< L/2),
necessary for periodic HFX calculations. This cutoff radius is on the shorter size, and using a
larger simulation cell would be advised.
@ -195,126 +195,126 @@ efficiency, as the default grid follows a Clenshaw-Curtis scheme, which requires
integration points for the same accuracy.
```none
&GLOBAL
PROJECT TiO2
RUN_TYPE CELL_OPT
PRINT_LEVEL MEDIUM
&END GLOBAL
&MOTION
&CELL_OPT
MAX_ITER 2
&END CELL_OPT
&END MOTION
&FORCE_EVAL
STRESS_TENSOR ANALYTICAL
&DFT
BASIS_SET_FILE_NAME BASIS_ccGRB_UZH
BASIS_SET_FILE_NAME BASIS_ADMM_UZH
POTENTIAL_FILE_NAME POTENTIAL_UZH
SORT_BASIS EXP
!automatically generated RI basis set
AUTO_BASIS RI_AUX SMALL
!enabling the ADMM2 approximation
&AUXILIARY_DENSITY_MATRIX_METHOD
METHOD BASIS_PROJECTION
ADMM_PURIFICATION_METHOD NONE
EXCH_CORRECTION_FUNC PBEX
&END AUXILIARY_DENSITY_MATRIX_METHOD
&MGRID
CUTOFF 600
REL_CUTOFF 50
NGRIDS 5
&END MGRID
&SCF
EPS_SCF 1.0E-6
MAX_SCF 20
&OT
PRECONDITIONER FULL_ALL
MINIMIZER DIIS
&END OT
&OUTER_SCF
MAX_SCF 5
EPS_SCF 1.0E-6
&END OUTER_SCF
&END SCF
&XC
&XC_FUNCTIONAL
&PBE
SCALE_X 0.75
&END PBE
&END XC_FUNCTIONAL
&HF
FRACTION 0.25
!always use a short range potential < L/2 in periodic HFX
&INTERACTION_POTENTIAL
POTENTIAL_TYPE TRUNCATED
CUTOFF_RADIUS 4.5
&END INTERACTION_POTENTIAL
&MEMORY
!maximum memory allocated to HFX ERI storage, per MPI rank
!the optimal number depends on the specifics of the computer
MAX_MEMORY 4000
&END MEMORY
&GLOBAL
PROJECT TiO2
RUN_TYPE CELL_OPT
PRINT_LEVEL MEDIUM
&END GLOBAL
&MOTION
&CELL_OPT
MAX_ITER 2
&END CELL_OPT
&END MOTION
&FORCE_EVAL
STRESS_TENSOR ANALYTICAL
&DFT
BASIS_SET_FILE_NAME BASIS_ccGRB_UZH
BASIS_SET_FILE_NAME BASIS_ADMM_UZH
POTENTIAL_FILE_NAME POTENTIAL_UZH
SORT_BASIS EXP
!automatically generated RI basis set
AUTO_BASIS RI_AUX SMALL
!enabling the ADMM2 approximation
&AUXILIARY_DENSITY_MATRIX_METHOD
METHOD BASIS_PROJECTION
ADMM_PURIFICATION_METHOD NONE
EXCH_CORRECTION_FUNC PBEX
&END AUXILIARY_DENSITY_MATRIX_METHOD
&MGRID
CUTOFF 600
REL_CUTOFF 50
NGRIDS 5
&END MGRID
&SCF
EPS_SCF 1.0E-6
MAX_SCF 20
&OT
PRECONDITIONER FULL_ALL
MINIMIZER DIIS
&END OT
&OUTER_SCF
MAX_SCF 5
EPS_SCF 1.0E-6
&END OUTER_SCF
&END SCF
&XC
&XC_FUNCTIONAL
&PBE
SCALE_X 0.75
&END PBE
&END XC_FUNCTIONAL
&HF
FRACTION 0.25
!always use a short range potential < L/2 in periodic HFX
&INTERACTION_POTENTIAL
POTENTIAL_TYPE TRUNCATED
CUTOFF_RADIUS 4.5
&END INTERACTION_POTENTIAL
&MEMORY
!maximum memory allocated to HFX ERI storage, per MPI rank
!the optimal number depends on the specifics of the computer
MAX_MEMORY 4000
&END MEMORY
&END HF
&WF_CORRELATION
&RI_RPA
MINIMAX_QUADRATURE
QUADRATURE_POINTS 6
!calculate EXX with ADMM, using the same HF section as in SCF
!so that the integrals can be resued without recomputing
ADMM
&HF
FRACTION 1.0
&INTERACTION_POTENTIAL
POTENTIAL_TYPE TRUNCATED
CUTOFF_RADIUS 4.5
&END INTERACTION_POTENTIAL
&END HF
&END RI_RPA
!enabling low-scaling
&LOW_SCALING
MEMORY_CUT 3
&WF_CORRELATION
&RI_RPA
MINIMAX_QUADRATURE
QUADRATURE_POINTS 6
!calculate EXX with ADMM, using the same HF section as in SCF
!so that the integrals can be resued without recomputing
ADMM
&HF
FRACTION 1.0
&INTERACTION_POTENTIAL
POTENTIAL_TYPE TRUNCATED
CUTOFF_RADIUS 4.5
&END INTERACTION_POTENTIAL
&END HF
&END RI_RPA
!enabling low-scaling
&LOW_SCALING
MEMORY_CUT 3
&END LOW_SCALING
&RI
!overlap RI metric is appropriate for dense systems
&RI_METRIC
POTENTIAL_TYPE IDENTITY
&END RI_METRIC
&END RI
&INTEGRALS
ERI_METHOD GPW
!Safe yet faster than default values
&WFC_GPW
CUTOFF 200
REL_CUTOFF 40
&END WFC_GPW
&END INTEGRALS
&RI
!overlap RI metric is appropriate for dense systems
&RI_METRIC
POTENTIAL_TYPE IDENTITY
&END RI_METRIC
&END RI
&INTEGRALS
ERI_METHOD GPW
!Safe yet faster than default values
&WFC_GPW
CUTOFF 200
REL_CUTOFF 40
&END WFC_GPW
&END INTEGRALS
&END WF_CORRELATION
&END XC
&END DFT
&SUBSYS
&CELL
ABC 9.330 9.330 9.107
&END CELL
&TOPOLOGY
COORD_FILE_FORMAT XYZ
COORD_FILE_NAME ./TiO2.xyz
&END TOPOLOGY
&KIND Ti
BASIS_SET ccGRB-D-q12
BASIS_SET AUX_FIT admm-dz-q12
POTENTIAL GTH-PBE0-q12
&END KIND
&KIND O
BASIS_SET ccGRB-D-q6
BASIS_SET AUX_FIT admm-dz-q6
POTENTIAL GTH-PBE0-q6
&END KIND
&END SUBSYS
&END XC
&END DFT
&SUBSYS
&CELL
ABC 9.330 9.330 9.107
&END CELL
&TOPOLOGY
COORD_FILE_FORMAT XYZ
COORD_FILE_NAME ./TiO2.xyz
&END TOPOLOGY
&KIND Ti
BASIS_SET ccGRB-D-q12
BASIS_SET AUX_FIT admm-dz-q12
POTENTIAL GTH-PBE0-q12
&END KIND
&KIND O
BASIS_SET ccGRB-D-q6
BASIS_SET AUX_FIT admm-dz-q6
POTENTIAL GTH-PBE0-q6
&END KIND
&END SUBSYS
&END FORCE_EVAL
```
@ -336,9 +336,7 @@ There are a few importnat input parameters for low-scaling post-HF calculations:
consumption of the program is divided by three (initial and final tensors are not affected, as
well as the data concerning the rest of the calculation). A higher value reduces the memory
footprint, but leads to performance overheads.
- `RI METRIC`: the choice of RI metric is crucial for performance in periodic calculations.
A\
shorter ranged RI metric will generally be more efficient, while a longer ranged metric (e.g.
TC\
- `RI METRIC`: the choice of RI metric is crucial for performance in periodic calculations. A
shorter ranged RI metric will generally be more efficient, while a longer ranged metric (e.g. TC
with a cutoff radius of 1.5 Angstrom) can be more accurate. See [](#Bussy2023) for a full
discussion.

6
docs/methods/properties/bandstructure_gw.md
View file

@ -74,10 +74,8 @@ $$ \varepsilon_{n\mathbf{k}}^{G_0W_0} = \varepsilon_{n\mathbf{k}}^\text{DFT} + \
We might interpret that we remove the spurious xc contribution from DFT,
$\braket{\psi_{n\mathbf{k}}|
v_\text{xc}|\psi_{n\mathbf{k}}}$, from the DFT eigenvalue
$\varepsilon_{n\mathbf{k}}^\text{DFT}$ and we add the xc contribution from
*G*<sub>0</sub>*W*<sub>0</sub>,
$\braket{\psi_{n\mathbf{k}}|
v_\text{xc}|\psi_{n\mathbf{k}}}$, from the DFT eigenvalue $\varepsilon_{n\mathbf{k}}^\text{DFT}$ and
we add the xc contribution from *G*<sub>0</sub>*W*<sub>0</sub>, $\braket{\psi_{n\mathbf{k}}|
\Sigma^{G_0W_0}(\varepsilon_{n\mathbf{k}}^{G_0W_0}) |\psi_{n\mathbf{k}}}$.
CP2K also allows to perform eigenvalue-selfconsistency in $G$ (ev*GW*<sub>0</sub>) and

10
docs/methods/properties/optical/vibronicspec.md
View file

@ -156,8 +156,8 @@ basis set, and convergence settings, across all calculations. The optimized geom
the chosen computational setup, so using different parameters in vibrational analysis and spectrum
calculation could mean the geometry is no longer at the true minimum for those new settings. The
geometry in this tutorial is optimized using `PBE0` functional and `TZVP-MOLOPT-PBE0-GTH` basis
sets. [ADMM](#CP2K_INPUT.FORCE_EVAL.DFT.AUXILIARY_DENSITY_MATRIX_METHOD)[](#Guidon2010)
approximation is also used with `admm-dzp` basis to reduce the cost of exchange integrals.
sets. The [ADMM](#CP2K_INPUT.FORCE_EVAL.DFT.AUXILIARY_DENSITY_MATRIX_METHOD) approximation
([](#Guidon2010)) is also used with `admm-dzp` basis to reduce the cost of exchange integrals.
### 1. Vibrational modes and frequencies
@ -327,8 +327,8 @@ than the default, to ensure more accurate excitation energies. We also ask to pr
we set a [THRESHOLD](#CP2K_INPUT.FORCE_EVAL.PROPERTIES.TDDFPT.PRINT.FORCES.THRESHOLD) of 0.001. This
means forces are only calculated for states whose oscillator strength is above that value. Filtering
out weak states helps keep the calculation efficient. You can also list specific states explicitly
with the [LIST](#CP2K_INPUT.FORCE_EVAL.PROPERTIES.TDDFPT.PRINT.FORCES.LIST) keyword (\[Strand2019\],
[](#Iannuzzi2005), \[Hehn2022\]).
with the [LIST](#CP2K_INPUT.FORCE_EVAL.PROPERTIES.TDDFPT.PRINT.FORCES.LIST) keyword
([Strand2019](https://doi.org/10.1063/1.5078682), [](#Iannuzzi2005), [](#Hehn2022)).
The output file we need is `so2-TDFORCE-1_0.tdfrc` file, which contains the spectrum data and the
forces in this format:
@ -425,7 +425,7 @@ calculation parameters are:
- Spectrum type (absorption or fluorescence)
- States to include, it can take different arguments:
- "all", includes all states that have forces in TDFORCE file
- a list like \[1, 2, 5\] to explicitly give state numbers
- a list like [1, 2, 5] to explicitly give state numbers
- "threshold:0.001", this option works like the THRESHOLD filter we used in the TDDFT force
calculation, including only states with oscillator strength above 0.001.

7
docs/methods/properties/x-ray/delta-kick.md
View file

@ -92,10 +92,9 @@ efficiency the propagation parameters are set to focus only on one specific part
### Absorption spectrum
Under the assumption of linear response to the perturbation,\
the real and imaginary part of the
calculated frequency-dependent polarizability define the nature of the response. If the frequency is
at an electronic resonance, then the polarizability has an imaginary part. The polarizability is
pure real off resonances.
the real and imaginary part of the calculated frequency-dependent polarizability define the nature
of the response. If the frequency is at an electronic resonance, then the polarizability has an
imaginary part. The polarizability is pure real off resonances.
From one Real-Time propagation, one can obtain three components of the polarizability tensor. For
instance, applying a $\delta$-kick along $x$ provides the components $\alpha_{xx}$, $\alpha_{yx}$

2
docs/methods/properties/x-ray/tddft.md
View file

@ -543,7 +543,7 @@ for 2px, 2py and 2pz. To avoid cancelling contributions, the sum of the absolute
Hybrid functionals with high fraction of Hartree-Fock exchange are know to perform well for core
spectroscopy. PBEh($\alpha=0.45$) and BHandHLYP have had success with this particular
implementation. In periodic boundary conditions, the truncated Coulomb operator should be used (with
truncation radius \< half cell parameter).
truncation radius < half cell parameter).
For appropriate description of core states, all-electron basis sets should be used for the excited
atom(s). MOLOPT basis sets and pseudopotentials can be used on all other atoms. There exist core

2
docs/methods/qm_mm/builtin.md
View file

@ -90,7 +90,7 @@ input file.
We can now move on to actually running CP2K. We will first run 1000 steps of energy minimization (or
fewer, depending on the convergence) with the input file `em.inp` to eliminate bad contacts. For
quantities like cell size, for instance, CP2K allows you to specify your units by placing them in
brackets, for instance [TIMESTEP](#CP2K_INPUT.MOTION.MD.TIMESTEP) \[fs\] 0.5.
brackets, for instance [TIMESTEP](#CP2K_INPUT.MOTION.MD.TIMESTEP) [fs] 0.5.
```none
cp2k can be run using a single process:

15
docs/methods/sampling/ehrenfest.md
View file

@ -89,7 +89,7 @@ the matrix in the exponential of the propagator becomes fully complex.
## Running real time time dependend DFT in CP2K
To run RTP or Ehrenfest MD with CP2K, the corresponding [RUN_TYPE](#CP2K_INPUT.GLOBAL.RUN_TYPE) in
the \[GLOBAL\] (#CP2K_INPUT.GLOBAL) section has to be selected, and the [MD](#CP2K_INPUT.MOTION.MD)
the [GLOBAL](#CP2K_INPUT.GLOBAL) section has to be selected, and the [MD](#CP2K_INPUT.MOTION.MD)
section has to be present to specify the time step length `TIMESTEP` and the desired number of steps
(`STEPS`). It is crucial to set an appropriate time step to propagate the electronic degrees of
freedom, i.e., in the order of atto-seconds. All other input parameters related to the RT-TDDFT run
@ -188,13 +188,12 @@ This equation is propagated for each $i$ electron with a time step $\delta t$: t
collectively over time in a **continuous manner**. Especially, the energy evolution is continuous:
the electrons cannot absorb exactly one photon at a given frequency to instantaneously go from one
electronic state to another.\
If one applies a field resonant with a given electronic transition,
the MOs involved in this transition will gradually be transformed from their initial state to the
corresponding excited state. This will happen in real-time without defining any specific electronic
transition before starting the simulation. Some preliminary calculations to determine the spectral
features of the system under study are in general useful to better define the desired properties of
the perturbing field. For core state excitations these information can be obtained by XAS
simulations.
If one applies a field resonant with a given electronic transition, the MOs involved in this
transition will gradually be transformed from their initial state to the corresponding excited
state. This will happen in real-time without defining any specific electronic transition before
starting the simulation. Some preliminary calculations to determine the spectral features of the
system under study are in general useful to better define the desired properties of the perturbing
field. For core state excitations these information can be obtained by XAS simulations.
Once the RTP has started, the evolution of the electronic structure can be monitored by means of
several descriptors, like the time dependent dipole moment, current density, total electronic

2
docs/methods/sampling/molecular_dynamics.md
View file

@ -94,7 +94,7 @@ specific heat and are inversely proportional with sqrt(N) where N is the system
A faster way to equilibrate the system is to use `LANGEVIN` as
[ENSEMBLE](#CP2K_INPUT.MOTION.MD.ENSEMBLE), and use a [GAMMA](#CP2K_INPUT.MOTION.MD.LANGEVIN.GAMMA)
of 0.001 \[1/fs\] (or larger if you want to equilibrate faster). Langevin introduces a viscous
of 0.001 [1/fs] (or larger if you want to equilibrate faster). Langevin introduces a viscous
dissipative force and a random forces that are in equilibrioum at the given temperature. For
equilibration purposes (and not to simulate removed degrees of freedom, like a solvent), the smaller
gamma the longer it takes to equilibrate, and the closer the trajectory is to an NVE trajectory, the

2
docs/technologies/eigensolvers/cusolvermp.md
View file

@ -5,7 +5,7 @@ tools for the solution of dense linear systems and eigenvalue problems.
## Dependencies
[cuSOLVERmp] \< 0.7
[cuSOLVERmp] < 0.7
- [CAL]: requires `libcal.\*` in the `$PATH`
- [UCC]: requires `libucc.\*` and `libucs.\*` in the `$PATH`

1
src/start/python/sample_force_env.py
View file

@ -6,7 +6,6 @@ import numpy as np
import cp2k
TEST_FILE_CONTENT = """
&FORCE_EVAL
METHOD Quickstep

1
tools/benchmark_plots/plot_benchmark.py
View file

@ -4,6 +4,7 @@
"""
Make a plot of CP2K benchmark data.
"""
import numpy as np
import matplotlib.pyplot as plt
import matplotlib.ticker

1
tools/benchmark_plots/plot_comparison.py
View file

@ -4,6 +4,7 @@
"""
Make a plot of CP2K benchmark data.
"""
import numpy as np
import matplotlib.pyplot as plt
import matplotlib.ticker

4
tools/build_utils/makedep.py
View file

@ -123,9 +123,7 @@ $(LIBDIR)/{archive}{ext} : {objs}
# Public modules for package {pkg}
install: PUBLICFILES += {pubfiles}
""".format(
pkg=pkg, pubfiles=" ".join(mod for mod in packages[pkg]["public"])
)
""".format(pkg=pkg, pubfiles=" ".join(mod for mod in packages[pkg]["public"]))
# write rules for executables
archive_postfix = archive_ext.rsplit(".", 1)[0]

1
tools/conventions/analyze_gfortran_ast.py
View file

@ -8,7 +8,6 @@ import collections
from os import path
from typing import Dict, TextIO, List
USE_EXCEPTIONS = ("omp_lib", "omp_lib_kinds", "lapack")
# precompile regex

54
tools/docker/generate_dockerfiles.py
View file

@ -233,9 +233,7 @@ def main() -> None:
# ======================================================================================
def regtest(profile: str, version: str, testopts: str = "") -> str:
return (
install_cp2k(profile=profile, version=version)
+ rf"""
return install_cp2k(profile=profile, version=version) + rf"""
# Run regression tests.
ARG TESTOPTS="{testopts}"
COPY ./tests ./tests
@ -244,29 +242,21 @@ RUN /bin/bash -o pipefail -c " \
TESTOPTS='${{TESTOPTS}}' \
./test_regtest.sh {profile} {version} |& tee report.log && \
rm -rf regtesting"
"""
+ print_cached_report()
)
""" + print_cached_report()
# ======================================================================================
def test_build(profile: str, version: str) -> str:
return (
install_cp2k(profile=profile, version=version)
+ rf"""
return install_cp2k(profile=profile, version=version) + rf"""
# Run build test.
COPY ./tools/docker/scripts/test_build.sh .
RUN ./test_build.sh "{profile}" "{version}" 2>&1 | tee report.log
"""
+ print_cached_report()
)
""" + print_cached_report()
# ======================================================================================
def performance(profile: str) -> str:
return (
install_cp2k(profile=profile, version="psmp")
+ rf"""
return install_cp2k(profile=profile, version="psmp") + rf"""
# Run performance test for {profile}.
COPY ./benchmarks ./benchmarks
COPY ./tools/regtesting ./tools/regtesting
@ -274,9 +264,7 @@ COPY ./tools/docker/scripts/test_performance.sh \
./tools/docker/scripts/plot_performance.py \
./
RUN ./test_performance.sh "{profile}" 2>&1 | tee report.log
"""
+ print_cached_report()
)
""" + print_cached_report()
# ======================================================================================
@ -311,24 +299,19 @@ RUN /bin/bash -ec "./tools/conventions/test_conventions.sh |& tee report.log"
# ======================================================================================
def manual() -> str:
return (
install_cp2k(profile="toolchain", version="psmp", revision=True)
+ rf"""
return install_cp2k(profile="toolchain", version="psmp", revision=True) + rf"""
# Generate manual.
COPY ./docs ./docs
COPY ./tools/input_editing ./tools/input_editing
COPY ./tools/docker/scripts/test_manual.sh .
ARG ADD_EDIT_LINKS=yes
RUN ./test_manual.sh "${{ADD_EDIT_LINKS}}" 2>&1 | tee report.log
"""
+ print_cached_report()
)
""" + print_cached_report()
# ======================================================================================
def precommit() -> str:
return (
rf"""
return rf"""
FROM ubuntu:24.04
# Install dependencies.
@ -343,29 +326,22 @@ COPY ./ ./
# Run precommit test.
RUN ./tools/docker/scripts/test_precommit.sh 2>&1 | tee report.log
"""
+ print_cached_report()
)
""" + print_cached_report()
# ======================================================================================
def test_3rd_party(name: str) -> str:
return (
install_cp2k(profile="toolchain", version="ssmp")
+ rf"""
return install_cp2k(profile="toolchain", version="ssmp") + rf"""
# Run test for {name}.
COPY ./tests ./tests
COPY ./tools/docker/scripts/test_{name}.sh ./
RUN ./test_{name}.sh 2>&1 | tee report.log
"""
+ print_cached_report()
)
""" + print_cached_report()
# ======================================================================================
def test_without_build(name: str) -> str:
return (
rf"""
return rf"""
FROM ubuntu:24.04
# Install dependencies.
@ -390,9 +366,7 @@ RUN bash -c "if [ -n "${{GIT_COMMIT_SHA}}" ] ; then echo "git:\${{GIT_COMMIT_SHA
# Run test for {name}.
COPY ./tools/docker/scripts/test_{name}.sh .
RUN ./test_{name}.sh 2>&1 | tee report.log
"""
+ print_cached_report()
)
""" + print_cached_report()
# ======================================================================================

2
tools/docker/scripts/test_precommit.sh
View file

@ -5,7 +5,7 @@
echo -e "\n========== Starting Precommit Server =========="
cd ./tools/precommit/ || exit 1
export REVISION="unknown revision"
gunicorn --bind=:8080 --workers=1 --threads=8 --timeout=0 precommit_server:app &> /var/tmp/precommit_server.logs &
gunicorn --bind=:8080 --workers=1 --threads=8 --timeout=0 --no-control-socket precommit_server:app &> /var/tmp/precommit_server.logs &
sleep 3
cat /var/tmp/precommit_server.logs

1
tools/precommit/format_fortran.py
View file

@ -18,7 +18,6 @@ from prettify_cp2k import replacer
sys.path.insert(0, path.join(path.dirname(path.abspath(__file__)), "fprettify"))
from fprettify import reformat_ffile, fparse_utils, log_exception
TO_UPCASE_RE = re.compile(
r"""
(?P<toUpcase>

4
tools/precommit/install_requirements.sh
View file

@ -26,8 +26,10 @@ rm -rf /var/lib/apt/lists/*
python3 -m venv /opt/venv
export PATH="/opt/venv/bin:$PATH"
# TODO Add a pylock.toml file (https://peps.python.org/pep-0751/)
# Install Python packages. Upgrade via:
# pip3 install black flask gunicorn mdformat-gfm cmake-format
# pip3 install black flask gunicorn cmake-format fortitude-lint \
# mdformat mdformat-gfm mdformat_frontmatter mdformat_myst mdformat_tables
# pip3 freeze > requirements.txt
pip3 install --quiet -r requirements.txt

14
tools/precommit/prettify_cp2k/normalizeFortranFile.py
View file

@ -305,7 +305,7 @@ def parseRoutine(inFile, logger):
}
stream = InputStream(inFile)
while True:
(jline, _, lines) = stream.nextFortranLine()
jline, _, lines = stream.nextFortranLine()
if len(lines) == 0:
break
if FCT_RE.match(jline) or SUBR_RE.match(jline):
@ -317,7 +317,7 @@ def parseRoutine(inFile, logger):
subF = open(m.group("file"), "r", encoding="utf8")
subStream = InputStream(subF)
while True:
(subjline, _, sublines) = subStream.nextFortranLine()
subjline, _, sublines = subStream.nextFortranLine()
if not sublines:
break
routine["strippedCore"].append(subjline)
@ -351,7 +351,7 @@ def parseRoutine(inFile, logger):
routine["result"] = routine["name"]
while True:
(jline, comment_list, lines) = stream.nextFortranLine()
jline, comment_list, lines = stream.nextFortranLine()
comments = "\n".join(_ for _ in comment_list)
if len(lines) == 0:
break
@ -422,7 +422,7 @@ def parseRoutine(inFile, logger):
istart = lines
interfaceDeclFile = StringIO()
while True:
(jline, _, lines) = stream.nextFortranLine()
jline, _, lines = stream.nextFortranLine()
if INTERFACE_END_RE.match(jline):
iend = lines
break
@ -481,7 +481,7 @@ def parseRoutine(inFile, logger):
subF = open(m.group("file"), "r", encoding="utf8")
subStream = InputStream(subF)
while True:
(subjline, _, sublines) = subStream.nextFortranLine()
subjline, _, sublines = subStream.nextFortranLine()
if not sublines:
break
routine["strippedCore"].append(subjline)
@ -498,7 +498,7 @@ def parseRoutine(inFile, logger):
if logger.isEnabledFor(logging.DEBUG):
traceback.print_exc()
(jline, _, lines) = stream.nextFortranLine()
jline, _, lines = stream.nextFortranLine()
return routine
@ -1021,7 +1021,7 @@ def parseUse(inFile):
commonUses = ""
stream = InputStream(inFile)
while True:
(jline, comment_list, lines) = stream.nextFortranLine()
jline, comment_list, lines = stream.nextFortranLine()
comments = "\n".join(_ for _ in comment_list if _)
lineNr = lineNr + len(lines)
if not lines:

52
tools/precommit/requirements.txt
View file

@ -1,31 +1,31 @@
black==24.3.0
blinker==1.7.0
click==8.1.7
black==26.1.0
blinker==1.9.0
click==8.3.1
cmake-format==0.6.13
cmakelang==0.6.13
Flask==3.0.0
Flask==3.1.3
fortitude-lint==0.7.5
gunicorn==23.0.0
itsdangerous==2.1.2
gunicorn==25.1.0
itsdangerous==2.2.0
Jinja2==3.1.6
linkify-it-py==2.0.2
markdown-it-py==2.2.0
MarkupSafe==2.1.3
mdformat==0.7.17
mdformat-gfm==0.3.5
mdformat_frontmatter==2.0.1
mdformat_myst==0.1.5
mdformat_tables==0.4.1
mdit-py-plugins==0.3.5
markdown-it-py==3.0.0
MarkupSafe==3.0.3
mdformat==0.7.22
mdformat-gfm==1.0.0
mdformat_footnote==0.1.3
mdformat_front_matters==2.0.0
mdformat_frontmatter==2.0.10
mdformat_myst==0.3.0
mdformat_tables==1.0.0
mdit-py-plugins==0.5.0
mdurl==0.1.2
mypy-extensions==1.0.0
packaging==23.2
pathspec==0.11.2
platformdirs==4.0.0
ruamel.yaml==0.18.5
ruamel.yaml.clib==0.2.8
six==1.16.0
tomli==2.0.1
typing_extensions==4.8.0
uc-micro-py==1.0.2
Werkzeug==3.1.5
mypy_extensions==1.1.0
packaging==26.0
pathspec==1.0.4
platformdirs==4.9.2
pytokens==0.4.1
ruamel.yaml==0.19.1
six==1.17.0
toml==0.10.2
wcwidth==0.6.0
Werkzeug==3.1.6