From c078969bf945a475acf73b54de8647dac0b903ea Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ole=20Sch=C3=BCtt?= Date: Thu, 28 Dec 2023 12:40:03 +0100 Subject: [PATCH] Manual: Touch up page names and titles --- .../dft/{constrained_dft.md => constrained.md} | 0 docs/methods/dft/{hfx.md => hartree-fock.md} | 2 +- docs/methods/dft/index.md | 6 +++--- docs/methods/dft/{lri-gpw.md => local_ri.md} | 0 docs/methods/machine_learning/index.md | 2 +- .../machine_learning/{allegro.md => nequip.md} | 0 docs/methods/optimization/index.md | 2 +- .../optimization/{neb.md => nudged_elastic_band.md} | 0 docs/methods/post_hartree_fock/gw.md | 2 +- docs/methods/post_hartree_fock/mp2.md | 2 +- docs/methods/properties/index.md | 12 ++++++------ docs/methods/properties/{tddft.md => optical.md} | 0 docs/methods/properties/raman.md | 2 +- docs/methods/qm_mm/builtin.md | 2 +- docs/methods/qm_mm/image_charges.md | 2 +- docs/methods/qm_mm/index.md | 2 +- ...{polarizable_ff.md => polarizable_force_field.md} | 2 +- docs/methods/sampling/index.md | 2 +- docs/methods/sampling/{gemc.md => monte_carlo.md} | 2 +- docs/methods/sampling/newton-x.md | 4 ++-- 20 files changed, 23 insertions(+), 23 deletions(-) rename docs/methods/dft/{constrained_dft.md => constrained.md} (100%) rename docs/methods/dft/{hfx.md => hartree-fock.md} (87%) rename docs/methods/dft/{lri-gpw.md => local_ri.md} (100%) rename docs/methods/machine_learning/{allegro.md => nequip.md} (100%) rename docs/methods/optimization/{neb.md => nudged_elastic_band.md} (100%) rename docs/methods/properties/{tddft.md => optical.md} (100%) rename docs/methods/qm_mm/{polarizable_ff.md => polarizable_force_field.md} (84%) rename docs/methods/sampling/{gemc.md => monte_carlo.md} (99%) diff --git a/docs/methods/dft/constrained_dft.md b/docs/methods/dft/constrained.md similarity index 100% rename from docs/methods/dft/constrained_dft.md rename to docs/methods/dft/constrained.md diff --git a/docs/methods/dft/hfx.md b/docs/methods/dft/hartree-fock.md similarity index 87% rename from docs/methods/dft/hfx.md rename to docs/methods/dft/hartree-fock.md index 2ba5c241de..68fe927103 100644 --- a/docs/methods/dft/hfx.md +++ b/docs/methods/dft/hartree-fock.md @@ -1,4 +1,4 @@ -# Hartree-Fock eXchange +# Hartree-Fock Exchange Unfortunately no one has gotten around to writing this page yet :-( diff --git a/docs/methods/dft/index.md b/docs/methods/dft/index.md index 1efc798868..301b68ce2a 100644 --- a/docs/methods/dft/index.md +++ b/docs/methods/dft/index.md @@ -7,9 +7,9 @@ maxdepth: 1 --- gpw gapw -hfx -lri-gpw -constrained_dft +hartree-fock +local_ri +constrained linear_scaling basis_sets pseudopotentials diff --git a/docs/methods/dft/lri-gpw.md b/docs/methods/dft/local_ri.md similarity index 100% rename from docs/methods/dft/lri-gpw.md rename to docs/methods/dft/local_ri.md diff --git a/docs/methods/machine_learning/index.md b/docs/methods/machine_learning/index.md index 178ebb5252..d9281e2541 100644 --- a/docs/methods/machine_learning/index.md +++ b/docs/methods/machine_learning/index.md @@ -5,7 +5,7 @@ titlesonly: maxdepth: 1 --- -allegro +nequip nnp pao-ml ``` diff --git a/docs/methods/machine_learning/allegro.md b/docs/methods/machine_learning/nequip.md similarity index 100% rename from docs/methods/machine_learning/allegro.md rename to docs/methods/machine_learning/nequip.md diff --git a/docs/methods/optimization/index.md b/docs/methods/optimization/index.md index ebeb365865..f3f49805c7 100644 --- a/docs/methods/optimization/index.md +++ b/docs/methods/optimization/index.md @@ -6,5 +6,5 @@ titlesonly: maxdepth: 1 --- Geometry Optimization -neb +nudged_elastic_band ``` diff --git a/docs/methods/optimization/neb.md b/docs/methods/optimization/nudged_elastic_band.md similarity index 100% rename from docs/methods/optimization/neb.md rename to docs/methods/optimization/nudged_elastic_band.md diff --git a/docs/methods/post_hartree_fock/gw.md b/docs/methods/post_hartree_fock/gw.md index db54f69b29..03eaf9746e 100644 --- a/docs/methods/post_hartree_fock/gw.md +++ b/docs/methods/post_hartree_fock/gw.md @@ -1,4 +1,4 @@ -# GW approximation +# GW Approximation The purpose of this section is to explain how to compute the energy of molecular orbitals/bands from GW for molecules/condensed phase systems with CP2K. In DFT, the energy of a molecular orbital diff --git a/docs/methods/post_hartree_fock/mp2.md b/docs/methods/post_hartree_fock/mp2.md index 69080499d1..00bcee842c 100644 --- a/docs/methods/post_hartree_fock/mp2.md +++ b/docs/methods/post_hartree_fock/mp2.md @@ -1,4 +1,4 @@ -# Møller–Plesset perturbation theory +# Møller–Plesset Perturbation Theory The MP2 method computes diff --git a/docs/methods/properties/index.md b/docs/methods/properties/index.md index b40b9d3283..fcd71c37db 100644 --- a/docs/methods/properties/index.md +++ b/docs/methods/properties/index.md @@ -5,12 +5,12 @@ titlesonly: maxdepth: 1 --- -X-Ray -tddft -Infrared +X-Ray Spectroscopy +optical +Infrared Spectroscopy raman nmr -STM images -Electron transport -RESP charges +STM Images +Electron Transport +RESP Charges ``` diff --git a/docs/methods/properties/tddft.md b/docs/methods/properties/optical.md similarity index 100% rename from docs/methods/properties/tddft.md rename to docs/methods/properties/optical.md diff --git a/docs/methods/properties/raman.md b/docs/methods/properties/raman.md index 0214e0403f..e8275ccb96 100644 --- a/docs/methods/properties/raman.md +++ b/docs/methods/properties/raman.md @@ -1,3 +1,3 @@ -# Raman +# Raman Spectroscopy Unfortunately, nobody has gotten around to writing this page yet :-( diff --git a/docs/methods/qm_mm/builtin.md b/docs/methods/qm_mm/builtin.md index d831947f94..ba173c3a50 100644 --- a/docs/methods/qm_mm/builtin.md +++ b/docs/methods/qm_mm/builtin.md @@ -1,4 +1,4 @@ -# QM/MM with built-in force-field +# QM/MM with Built-in Force Field This tutorial will illustrate the setup process of a QM/MM protein - substrate system. The model system we will be using is chorismate mutase, an enzyme that catalyzes the conversion of chorismate diff --git a/docs/methods/qm_mm/image_charges.md b/docs/methods/qm_mm/image_charges.md index 3fbc56f39a..62833c40b7 100644 --- a/docs/methods/qm_mm/image_charges.md +++ b/docs/methods/qm_mm/image_charges.md @@ -1,4 +1,4 @@ -# Image charges +# Image Charges ## Introduction diff --git a/docs/methods/qm_mm/index.md b/docs/methods/qm_mm/index.md index ac0af78147..28aeb7d2e1 100644 --- a/docs/methods/qm_mm/index.md +++ b/docs/methods/qm_mm/index.md @@ -7,7 +7,7 @@ maxdepth: 1 --- builtin gromacs -polarizable_ff +polarizable_force_field implicit_solvation image_charges ``` diff --git a/docs/methods/qm_mm/polarizable_ff.md b/docs/methods/qm_mm/polarizable_force_field.md similarity index 84% rename from docs/methods/qm_mm/polarizable_ff.md rename to docs/methods/qm_mm/polarizable_force_field.md index 23f8ecf8a7..b42e0a8590 100644 --- a/docs/methods/qm_mm/polarizable_ff.md +++ b/docs/methods/qm_mm/polarizable_force_field.md @@ -1,4 +1,4 @@ -# Polarizable Force-Fields +# Polarizable Force Field Unfortunately no one has gotten around to writing this page yet :-( diff --git a/docs/methods/sampling/index.md b/docs/methods/sampling/index.md index 886bd18449..619b659583 100644 --- a/docs/methods/sampling/index.md +++ b/docs/methods/sampling/index.md @@ -10,7 +10,7 @@ metadynamics path_integrals newton-x i-pi -gemc +monte_carlo Langevin Dynamics ehrenfest ``` diff --git a/docs/methods/sampling/gemc.md b/docs/methods/sampling/monte_carlo.md similarity index 99% rename from docs/methods/sampling/gemc.md rename to docs/methods/sampling/monte_carlo.md index ee778f54b6..a106736454 100644 --- a/docs/methods/sampling/gemc.md +++ b/docs/methods/sampling/monte_carlo.md @@ -1,4 +1,4 @@ -# Gibbs Ensemble Monte Carlo +# Monte Carlo In the most common set up of Gibbs Ensemble Monte Carlo (GEMC) simulation, 2 boxes are utilized to represent vapor and liquid phases. In order to equilibrate the system, different types of moves are diff --git a/docs/methods/sampling/newton-x.md b/docs/methods/sampling/newton-x.md index af83a24124..66f6bd89b9 100644 --- a/docs/methods/sampling/newton-x.md +++ b/docs/methods/sampling/newton-x.md @@ -24,7 +24,7 @@ Coulomb, exchange and exchange-correlation contributions, and $\mathbf{C}$ the m coefficients. $\mu, \nu, \dots$ denote atomic orbitals, $i, j, \dots$ occupied molecular orbitals. The corresponding excited-state gradient is obtained setting up a variational Lagrangian and taking the derivative with respect to the nuclear coordinates $\mathbf{R}$ (see also -[](../properties/tddft)). +[](../properties/optical)). By performing a TDDFPT computation, excitation energies $\Omega^M (\mathbf{R}(t))$, excited-state eigenvectors $\mathbf{X}^M (\mathbf{R}(t))$ and corresponding excited-state gradients @@ -66,7 +66,7 @@ $a,b, \dots$ denote virtual molecular orbitals. ## General input setup The input sections for TDDFPT energy and gradient computations are described in -[](../properties/tddft). To furthermore provide the required CP2K output, subsequently read in by +[](../properties/optical). To furthermore provide the required CP2K output, subsequently read in by NEWTONX, the following print statements have to be added to the CP2K input files: - [FORCE_EVAL.PRINT.FORCES](#CP2K_INPUT.FORCE_EVAL.PRINT.FORCES): prints the excited-state forces