From 668feff676deb4b57bbee5867e9b22be8df45b0d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ole=20Sch=C3=BCtt?= Date: Sun, 10 Dec 2023 16:31:38 +0100 Subject: [PATCH] Manual: Add sub-directories to methods section --- docs/index.md | 19 +++++++++--------- docs/methods/{ => dft}/basis_sets.md | 0 .../{images => dft}/cdft-becke-atomicsize.png | Bin docs/methods/{images => dft}/cdft-becke.png | Bin .../cdft-fragment-constraint.png | Bin .../cdftci-h2-dissociation.png | Bin docs/methods/{images => dft}/cdftscf.png | Bin .../{cdft.md => dft/constrained_dft.md} | 10 ++++----- docs/methods/{ => dft}/gapw.md | 0 docs/methods/{ => dft}/gpw.md | 0 docs/methods/{ => dft}/hfx.md | 0 docs/methods/{dft.md => dft/index.md} | 6 +++--- .../{ls-dft.md => dft/linear_scaling.md} | 0 docs/methods/{lrigpw.md => dft/lri-gpw.md} | 0 docs/methods/{ => dft}/lrigpw_example.inp | 0 docs/methods/{ => dft}/pseudopotentials.md | 0 .../{embedding.md => embedding/index.md} | 0 docs/methods/{ => embedding}/kim-gordon.md | 6 +++--- docs/methods/{ => embedding}/qm_qm.md | 0 .../methods/{ => machine_learning}/allegro.md | 0 .../index.md} | 0 docs/methods/{ => machine_learning}/pao-ml.md | 0 .../index.md} | 0 docs/methods/{ => optimization}/neb.md | 0 docs/methods/{ => post_hartree_fock}/gw.md | 0 .../index.md} | 0 docs/methods/{ => post_hartree_fock}/mp2.md | 0 docs/methods/{ => post_hartree_fock}/rpa.md | 0 .../index.md} | 7 ++++++- docs/methods/{ => properties}/nmr.md | 0 docs/methods/{ => properties}/raman.md | 0 .../methods/{ => qm_mm}/implicit_solvation.md | 0 docs/methods/{qm_mm.md => qm_mm/index.md} | 0 docs/methods/{ => qm_mm}/polarizable_ff.md | 0 docs/methods/{ => sampling}/ehrenfest.md | 0 .../{sampling.md => sampling/index.md} | 0 docs/methods/{ => sampling}/metadynamics.md | 0 docs/methods/{ => sampling}/path_integrals.md | 0 docs/methods/{ => semiempiricals}/dftb.md | 0 .../index.md} | 0 docs/methods/{ => semiempiricals}/xtb.md | 0 docs/methods/spectroscopy.md | 13 ------------ 42 files changed, 26 insertions(+), 35 deletions(-) rename docs/methods/{ => dft}/basis_sets.md (100%) rename docs/methods/{images => dft}/cdft-becke-atomicsize.png (100%) rename docs/methods/{images => dft}/cdft-becke.png (100%) rename docs/methods/{images => dft}/cdft-fragment-constraint.png (100%) rename docs/methods/{images => dft}/cdftci-h2-dissociation.png (100%) rename docs/methods/{images => dft}/cdftscf.png (100%) rename docs/methods/{cdft.md => dft/constrained_dft.md} (99%) rename docs/methods/{ => dft}/gapw.md (100%) rename docs/methods/{ => dft}/gpw.md (100%) rename docs/methods/{ => dft}/hfx.md (100%) rename docs/methods/{dft.md => dft/index.md} (75%) rename docs/methods/{ls-dft.md => dft/linear_scaling.md} (100%) rename docs/methods/{lrigpw.md => dft/lri-gpw.md} (100%) rename docs/methods/{ => dft}/lrigpw_example.inp (100%) rename docs/methods/{ => dft}/pseudopotentials.md (100%) rename docs/methods/{embedding.md => embedding/index.md} (100%) rename docs/methods/{ => embedding}/kim-gordon.md (95%) rename docs/methods/{ => embedding}/qm_qm.md (100%) rename docs/methods/{ => machine_learning}/allegro.md (100%) rename docs/methods/{machine_learning.md => machine_learning/index.md} (100%) rename docs/methods/{ => machine_learning}/pao-ml.md (100%) rename docs/methods/{optimization.md => optimization/index.md} (100%) rename docs/methods/{ => optimization}/neb.md (100%) rename docs/methods/{ => post_hartree_fock}/gw.md (100%) rename docs/methods/{post_hartree_fock.md => post_hartree_fock/index.md} (100%) rename docs/methods/{ => post_hartree_fock}/mp2.md (100%) rename docs/methods/{ => post_hartree_fock}/rpa.md (100%) rename docs/methods/{other_properties.md => properties/index.md} (55%) rename docs/methods/{ => properties}/nmr.md (100%) rename docs/methods/{ => properties}/raman.md (100%) rename docs/methods/{ => qm_mm}/implicit_solvation.md (100%) rename docs/methods/{qm_mm.md => qm_mm/index.md} (100%) rename docs/methods/{ => qm_mm}/polarizable_ff.md (100%) rename docs/methods/{ => sampling}/ehrenfest.md (100%) rename docs/methods/{sampling.md => sampling/index.md} (100%) rename docs/methods/{ => sampling}/metadynamics.md (100%) rename docs/methods/{ => sampling}/path_integrals.md (100%) rename docs/methods/{ => semiempiricals}/dftb.md (100%) rename docs/methods/{semiempiricals.md => semiempiricals/index.md} (100%) rename docs/methods/{ => semiempiricals}/xtb.md (100%) delete mode 100644 docs/methods/spectroscopy.md diff --git a/docs/index.md b/docs/index.md index 684ee63a0c..86fc023b68 100644 --- a/docs/index.md +++ b/docs/index.md @@ -25,16 +25,15 @@ caption: Methods titlesonly: maxdepth: 1 --- -methods/dft -methods/post_hartree_fock -methods/semiempiricals -methods/machine_learning -methods/embedding -methods/qm_mm -methods/sampling -methods/optimization -methods/spectroscopy -methods/other_properties +methods/dft/index +methods/post_hartree_fock/index +methods/semiempiricals/index +methods/machine_learning/index +methods/embedding/index +methods/qm_mm/index +methods/sampling/index +methods/optimization/index +methods/properties/index ``` % TODO: `{toctree} % :caption: How-to guides % % dummy % ` diff --git a/docs/methods/basis_sets.md b/docs/methods/dft/basis_sets.md similarity index 100% rename from docs/methods/basis_sets.md rename to docs/methods/dft/basis_sets.md diff --git a/docs/methods/images/cdft-becke-atomicsize.png b/docs/methods/dft/cdft-becke-atomicsize.png similarity index 100% rename from docs/methods/images/cdft-becke-atomicsize.png rename to docs/methods/dft/cdft-becke-atomicsize.png diff --git a/docs/methods/images/cdft-becke.png b/docs/methods/dft/cdft-becke.png similarity index 100% rename from docs/methods/images/cdft-becke.png rename to docs/methods/dft/cdft-becke.png diff --git a/docs/methods/images/cdft-fragment-constraint.png b/docs/methods/dft/cdft-fragment-constraint.png similarity index 100% rename from docs/methods/images/cdft-fragment-constraint.png rename to docs/methods/dft/cdft-fragment-constraint.png diff --git a/docs/methods/images/cdftci-h2-dissociation.png b/docs/methods/dft/cdftci-h2-dissociation.png similarity index 100% rename from docs/methods/images/cdftci-h2-dissociation.png rename to docs/methods/dft/cdftci-h2-dissociation.png diff --git a/docs/methods/images/cdftscf.png b/docs/methods/dft/cdftscf.png similarity index 100% rename from docs/methods/images/cdftscf.png rename to docs/methods/dft/cdftscf.png diff --git a/docs/methods/cdft.md b/docs/methods/dft/constrained_dft.md similarity index 99% rename from docs/methods/cdft.md rename to docs/methods/dft/constrained_dft.md index ad07a20aad..2299fa7024 100644 --- a/docs/methods/cdft.md +++ b/docs/methods/dft/constrained_dft.md @@ -78,7 +78,7 @@ electronic structure. In practice, three SCF loops are needed to integrate CDFT which uses its own outer loop to reset the OT preconditioner. This process has been schematically illustrated in Figure 1. -![Schematic of the CDFT SCF procedure](images/cdftscf.png){align=center} +![Schematic of the CDFT SCF procedure](cdftscf.png){align=center} **Figure 1.** Schematic of the CDFT SCF procedure. The constraint Lagrangians $\vec\lambda$ are first optimized in the outer CDFT loop, their values are subsequently fixed, and the electron @@ -223,7 +223,7 @@ possible to use fragment based constraints case the constraint target value is calculated from the superposition of isolated fragment densities according to the scheme in Figure 2. -![](images/cdft-fragment-constraint.png){align=center width=350px} +![](cdft-fragment-constraint.png){align=center width=350px} **Figure 2.** Using a fragment based CDFT constraint. The system is first divided into two fragments with atomic positions fixed in the same configuration as in the full system. The electron and spin @@ -277,9 +277,9 @@ three or more atoms. The Becke cell function $P_i$ is overlayed on top of the Vo decays smoothly from 1 to 0 across the Voronoi polyhedron boundary. Using a smooth density partitioning function improves numerical stability in simulations. -![](images/cdft-becke-atomicsize.png){align=center width=400px} +![](cdft-becke-atomicsize.png){align=center width=400px} -![](images/cdft-becke.png){align=center width=400px} +![](cdft-becke.png){align=center width=400px} **Figure 3.** Comparison of the Voronoi (lines) and Becke partitioning (contours) schemes. At left, the Becke partitioning is performed without atomic size information. At right, the size of the red @@ -798,7 +798,7 @@ $\mathrm{H}_2^+ \rightarrow \mathrm{H}^+ + \mathrm{H}$. Even though this system contains only 1 electron, the dissociation profile obtained with PBE notably deviates from the exact Hartree-Fock profile as shown in Figure 4 below. -![](images/cdftci-h2-dissociation.png){align=center width=450px} +![](cdftci-h2-dissociation.png){align=center width=450px} **Figure 4.** Illustration of DFT self-interaction error for the reaction $\mathrm{H}_2^+ \rightarrow \mathrm{H}^+ + \mathrm{H}$. PBE notably deviates from the exact diff --git a/docs/methods/gapw.md b/docs/methods/dft/gapw.md similarity index 100% rename from docs/methods/gapw.md rename to docs/methods/dft/gapw.md diff --git a/docs/methods/gpw.md b/docs/methods/dft/gpw.md similarity index 100% rename from docs/methods/gpw.md rename to docs/methods/dft/gpw.md diff --git a/docs/methods/hfx.md b/docs/methods/dft/hfx.md similarity index 100% rename from docs/methods/hfx.md rename to docs/methods/dft/hfx.md diff --git a/docs/methods/dft.md b/docs/methods/dft/index.md similarity index 75% rename from docs/methods/dft.md rename to docs/methods/dft/index.md index 823a3b95a5..1efc798868 100644 --- a/docs/methods/dft.md +++ b/docs/methods/dft/index.md @@ -8,9 +8,9 @@ maxdepth: 1 gpw gapw hfx -lrigpw -cdft -ls-dft +lri-gpw +constrained_dft +linear_scaling basis_sets pseudopotentials ``` diff --git a/docs/methods/ls-dft.md b/docs/methods/dft/linear_scaling.md similarity index 100% rename from docs/methods/ls-dft.md rename to docs/methods/dft/linear_scaling.md diff --git a/docs/methods/lrigpw.md b/docs/methods/dft/lri-gpw.md similarity index 100% rename from docs/methods/lrigpw.md rename to docs/methods/dft/lri-gpw.md diff --git a/docs/methods/lrigpw_example.inp b/docs/methods/dft/lrigpw_example.inp similarity index 100% rename from docs/methods/lrigpw_example.inp rename to docs/methods/dft/lrigpw_example.inp diff --git a/docs/methods/pseudopotentials.md b/docs/methods/dft/pseudopotentials.md similarity index 100% rename from docs/methods/pseudopotentials.md rename to docs/methods/dft/pseudopotentials.md diff --git a/docs/methods/embedding.md b/docs/methods/embedding/index.md similarity index 100% rename from docs/methods/embedding.md rename to docs/methods/embedding/index.md diff --git a/docs/methods/kim-gordon.md b/docs/methods/embedding/kim-gordon.md similarity index 95% rename from docs/methods/kim-gordon.md rename to docs/methods/embedding/kim-gordon.md index 054e58a411..6b53a489fb 100644 --- a/docs/methods/kim-gordon.md +++ b/docs/methods/embedding/kim-gordon.md @@ -85,9 +85,9 @@ it is important to specify which is the 'minimum unit', that can be defined in t This strategy is based on the fourth column in the COORD section. At this point the code is able to find the best combination of 'minimum units' through the [COLORING_METHOD](#CP2K_INPUT.FORCE_EVAL.DFT.KG_METHOD.COLORING_METHOD) in order to simplify the -calculation. Another suggestion is to run KG calculations using [linear scaling DFT](./ls-dft), -replacing the [SCF](#CP2K_INPUT.FORCE_EVAL.DFT.SCF) section with the -[LS_SCF](#CP2K_INPUT.FORCE_EVAL.DFT.LS_SCF) section: +calculation. Another suggestion is to run KG calculations using +[linear scaling DFT](../dft/linear_scaling), replacing the [SCF](#CP2K_INPUT.FORCE_EVAL.DFT.SCF) +section with the [LS_SCF](#CP2K_INPUT.FORCE_EVAL.DFT.LS_SCF) section: ```none &LS_SCF diff --git a/docs/methods/qm_qm.md b/docs/methods/embedding/qm_qm.md similarity index 100% rename from docs/methods/qm_qm.md rename to docs/methods/embedding/qm_qm.md diff --git a/docs/methods/allegro.md b/docs/methods/machine_learning/allegro.md similarity index 100% rename from docs/methods/allegro.md rename to docs/methods/machine_learning/allegro.md diff --git a/docs/methods/machine_learning.md b/docs/methods/machine_learning/index.md similarity index 100% rename from docs/methods/machine_learning.md rename to docs/methods/machine_learning/index.md diff --git a/docs/methods/pao-ml.md b/docs/methods/machine_learning/pao-ml.md similarity index 100% rename from docs/methods/pao-ml.md rename to docs/methods/machine_learning/pao-ml.md diff --git a/docs/methods/optimization.md b/docs/methods/optimization/index.md similarity index 100% rename from docs/methods/optimization.md rename to docs/methods/optimization/index.md diff --git a/docs/methods/neb.md b/docs/methods/optimization/neb.md similarity index 100% rename from docs/methods/neb.md rename to docs/methods/optimization/neb.md diff --git a/docs/methods/gw.md b/docs/methods/post_hartree_fock/gw.md similarity index 100% rename from docs/methods/gw.md rename to docs/methods/post_hartree_fock/gw.md diff --git a/docs/methods/post_hartree_fock.md b/docs/methods/post_hartree_fock/index.md similarity index 100% rename from docs/methods/post_hartree_fock.md rename to docs/methods/post_hartree_fock/index.md diff --git a/docs/methods/mp2.md b/docs/methods/post_hartree_fock/mp2.md similarity index 100% rename from docs/methods/mp2.md rename to docs/methods/post_hartree_fock/mp2.md diff --git a/docs/methods/rpa.md b/docs/methods/post_hartree_fock/rpa.md similarity index 100% rename from docs/methods/rpa.md rename to docs/methods/post_hartree_fock/rpa.md diff --git a/docs/methods/other_properties.md b/docs/methods/properties/index.md similarity index 55% rename from docs/methods/other_properties.md rename to docs/methods/properties/index.md index 44f4a5a225..b83dbf925c 100644 --- a/docs/methods/other_properties.md +++ b/docs/methods/properties/index.md @@ -1,10 +1,15 @@ -# Other Properties +# Properties ```{toctree} --- titlesonly: maxdepth: 1 --- +X-Ray +Optical +Infrared +raman +nmr STM images Electron transport RESP charges diff --git a/docs/methods/nmr.md b/docs/methods/properties/nmr.md similarity index 100% rename from docs/methods/nmr.md rename to docs/methods/properties/nmr.md diff --git a/docs/methods/raman.md b/docs/methods/properties/raman.md similarity index 100% rename from docs/methods/raman.md rename to docs/methods/properties/raman.md diff --git a/docs/methods/implicit_solvation.md b/docs/methods/qm_mm/implicit_solvation.md similarity index 100% rename from docs/methods/implicit_solvation.md rename to docs/methods/qm_mm/implicit_solvation.md diff --git a/docs/methods/qm_mm.md b/docs/methods/qm_mm/index.md similarity index 100% rename from docs/methods/qm_mm.md rename to docs/methods/qm_mm/index.md diff --git a/docs/methods/polarizable_ff.md b/docs/methods/qm_mm/polarizable_ff.md similarity index 100% rename from docs/methods/polarizable_ff.md rename to docs/methods/qm_mm/polarizable_ff.md diff --git a/docs/methods/ehrenfest.md b/docs/methods/sampling/ehrenfest.md similarity index 100% rename from docs/methods/ehrenfest.md rename to docs/methods/sampling/ehrenfest.md diff --git a/docs/methods/sampling.md b/docs/methods/sampling/index.md similarity index 100% rename from docs/methods/sampling.md rename to docs/methods/sampling/index.md diff --git a/docs/methods/metadynamics.md b/docs/methods/sampling/metadynamics.md similarity index 100% rename from docs/methods/metadynamics.md rename to docs/methods/sampling/metadynamics.md diff --git a/docs/methods/path_integrals.md b/docs/methods/sampling/path_integrals.md similarity index 100% rename from docs/methods/path_integrals.md rename to docs/methods/sampling/path_integrals.md diff --git a/docs/methods/dftb.md b/docs/methods/semiempiricals/dftb.md similarity index 100% rename from docs/methods/dftb.md rename to docs/methods/semiempiricals/dftb.md diff --git a/docs/methods/semiempiricals.md b/docs/methods/semiempiricals/index.md similarity index 100% rename from docs/methods/semiempiricals.md rename to docs/methods/semiempiricals/index.md diff --git a/docs/methods/xtb.md b/docs/methods/semiempiricals/xtb.md similarity index 100% rename from docs/methods/xtb.md rename to docs/methods/semiempiricals/xtb.md diff --git a/docs/methods/spectroscopy.md b/docs/methods/spectroscopy.md deleted file mode 100644 index 21941aa832..0000000000 --- a/docs/methods/spectroscopy.md +++ /dev/null @@ -1,13 +0,0 @@ -# Spectroscopy - -```{toctree} ---- -titlesonly: -maxdepth: 1 ---- -X-Ray -Optical -Infrared -raman -nmr -```