Tuned disposition further

aibergman · aibergman · commit 34a833759bd9 · 2026-01-11T10:02:58.000+01:00
diff --git a/content/examples.rst b/content/examples.rst
@@ -43,3 +43,13 @@ SKKR Input
 ----------
 
 The ``xctensortest`` directory contains the same data as in the bccFe directory, but set up in the tensorial format that arises from the Vienna-Budapest SKKR code [Udvardi2003]_ .
+
+
+**References**
+
+See the centralized :doc:`references` for full bibliographic entries:
+
+- [Bergman2010]_ - Magnon softening in ferromagnetic monolayers
+- [Hellsvik2008]_ - Dynamics of diluted magnetic semiconductors from atomistic spin-dynamics simulations
+- [Udvardi2003]_ - First-principles relativistic study of spin waves in thin magnetic films
+
diff --git a/content/input-keywords-ams.rst b/content/input-keywords-ams.rst
@@ -874,11 +874,15 @@ Planned extensions:
 * **Time-resolved spectroscopy**: Pump-probe magnon dynamics after laser excitation
 
 References
-==========
+----------
+
+See the centralized :doc:`references` for full bibliographic entries:
+
+- [TothLake2015]_ - Linear spin wave theory for single-Q incommensurate magnetic structures
+- [Colpa1978]_ - Diagonalization of the quadratic boson Hamiltonian
+- [Holstein1940]_ - Holstein-Primakoff transformation and ferromagnetic field dependence
+- [Halilov1998]_ - Adiabatic spin dynamics from spin-density-functional theory
 
-.. [TothLake2015] Tóth, S., and Lake, B. "Linear spin wave theory for single-Q incommensurate magnetic structures." *J. Phys.: Condens. Matter* **27**, 166002 (2015).
-.. [Colpa1978] Colpa, J. H. P. "Diagonalization of the quadratic boson Hamiltonian." *Physica A* **93**, 327 (1978).
-.. note:: The full bibliographic entries for Holstein1940 and Halilov1998 have been moved to the centralized references page.
 
 See Also
 ========
diff --git a/content/input-keywords-autocorrelation.rst b/content/input-keywords-autocorrelation.rst
@@ -62,8 +62,7 @@ Spatial binning and macrocell averaging
 -------------------------------------------------
 
 For spatially-resolved analysis, autocorrelation can be computed separately within
-each **macrocell** (computational domain subdivision). This enables characterization
-of spatial inhomogeneities in relaxation dynamics [Holian1995]_.
+each **macrocell** (computational domain subdivision). 
 
 When ``do_macro_cells Y`` is set in the input, the code:
 
@@ -331,3 +330,13 @@ Related keywords and cross-references
 - ``do_avrg``, ``avrg_step``: Companion average magnetization measurements (see :doc:`input-keywords-averages`)
 
 Output files use the simulation identifier ``simid`` (see :doc:`input-keywords-system`).
+
+
+References
+----------
+
+See the centralized :doc:`references` for full bibliographic entries:
+
+- [Reif1965]_ - Statistical and thermal physics fundamentals
+- [Evans2000]_ - Statistical mechanics of nonequilibrium systems
+
diff --git a/content/input-keywords-averages.rst b/content/input-keywords-averages.rst
@@ -348,6 +348,17 @@ Example inpsd.dat snippet
    # Enable type-projected averages (ferrimagnetic system)
    do_proj_avrg  Y
 
+
+References
+----------
+
+See the centralized :doc:`references` for full bibliographic entries:
+
+- [Binder1981]_ - Fourth order Binder cumulants for phase transition identification
+- [Landau2014]_ - Monte Carlo simulation methods and statistical mechanics
+- [Evans1985]_ - Nose-Hoover thermostat implementation
+
+
    # Enable cumulants for phase transition study
    do_cumu       Y
    cumu_step     100        # Sample every 100 steps for statistics
diff --git a/content/input-keywords-clusters.rst b/content/input-keywords-clusters.rst
@@ -8,8 +8,7 @@ The UppASD code provides functionality to **embed magnetic impurity clusters**
 within a host system, allowing users to study local properties of defects, interfaces,
 and heterostructures without breaking full system symmetries. The cluster method enables
 different magnetic moments, exchange interactions, Dzyaloshinskii-Moriya (DM) interactions,
-anisotropies, and gyromagnetic ratios inside the cluster compared to the host
-[Chico2014]_.
+anisotropies, and gyromagnetic ratios inside the cluster compared to the host.
 
 --------------------------------------------------
 Cluster embedding: concept and use cases
@@ -391,7 +390,6 @@ References and further reading
 
 For the cluster embedding methodology and applications:
 
-.. [Chico2014] J. Chico, L. E. F. Foa Torres, R. H. Barco, O. Eriksson, and A. Bergman, "Unraveling novel quantum critical behavior in a two-dimensional Heisenberg antiferromagnet," *Phys. Rev. B* **90**, 064425 (2014).
 
 See also
 --------
diff --git a/content/input-keywords-correlations.rst b/content/input-keywords-correlations.rst
@@ -324,3 +324,13 @@ See also
 - :doc:`input-keywords-autocorrelation` (local autocorrelation sampling)
 - :doc:`input-keywords-montecarlo` (Monte Carlo sampling methods)
 - :doc:`input-keywords-system` (system setup and q-points)
+
+
+References
+----------
+
+See the centralized :doc:`references` for full bibliographic entries:
+
+- [Bergman2010]_ - Magnon softening in ferromagnetic monolayers
+- [Squires1978]_ - Introduction to thermal neutron scattering theory
+
diff --git a/content/input-keywords-currents.rst b/content/input-keywords-currents.rst
@@ -252,3 +252,19 @@ Notes on usage
   intended for thin-film bilayer systems.
 - For thick samples, care should be taken when using interfacial torque models.
 
+
+References
+----------
+
+See the centralized :doc:`references` for full bibliographic entries:
+
+- [ZhangLi2004]_ - Zhang-Li spin-transfer torque formulation
+- [Slonczewski1996]_ - Current-driven excitation of magnetic multilayers
+- [RalphStiles2008]_ - Comprehensive review of spin transfer torques
+- [Meo2023]_ - Spin-transfer and spin-orbit torques in LLG equation
+- [Manchon2019]_ - Current-induced spin-orbit torques review
+- [Haney2013]_ - Current-induced torques and interfacial spin-orbit coupling
+- [Liu2012]_ - Spin-torque switching with giant spin Hall effect
+- [GambardellaMiron2011]_ - Current-induced spin-orbit torques
+
+
diff --git a/content/input-keywords-fields.rst b/content/input-keywords-fields.rst
@@ -7,8 +7,7 @@ Parameters for applying time and space-dependent magnetic fields
 The UppASD code supports a comprehensive suite of **time and space-dependent magnetic field
 profiles** that can be applied to the system during simulations. These include pulsed
 fields with various temporal shapes, monochromatic and broadened microwave fields with
-spatial and temporal modulation, moving field profiles, and demagnetization effects
-[Pereiro2014]_ [Chico2015]_.
+spatial and temporal modulation, moving field profiles, and demagnetization effects.
 
 --------------------------------------------------
 Field overview and use cases
@@ -512,20 +511,17 @@ Technical considerations
 - Volume: Ų for demagnetization
 
 --------------------------------------------------
-References and further reading
---------------------------------------------------
-
-For microwave field implementations and FMR:
 
-.. [Pereiro2014] M. Pereiro, D. Yudin, J. Chico, C. Etz, O. Eriksson, and A. Bergman, "Topological properties of slowly relaxing excitations in thin films of magnetic topological insulators," *Nature Communications* **5**, 4144 (2014).
+References
+----------
 
-For ultrafast magnetization dynamics:
+See the centralized :doc:`references` for full bibliographic entries:
 
-.. [Chico2015] J. Chico, L. E. F. Foa Torres, R. H. Barco, O. Eriksson, and A. Bergman, "Unraveling quantum critical behavior in a two-dimensional Heisenberg antiferromagnet," *Phys. Rev. B* **90**, 064425 (2014).
+- [Pereiro2014]_ - Topological properties in magnetic topological insulators
 
 See also
 --------
 
 - :doc:`input-keywords-system` (system geometry for demagnetization)
 - :doc:`input-keywords-hamiltonian` (static exchange interactions)
-- :doc:`input-core-files` (core file formats: ``posfile``, ``momfile``, etc.)
+- :doc:`input-core-files` (core file formats: ``posfile``, ``momfile``, etc.)
diff --git a/content/input-keywords-gneb.rst b/content/input-keywords-gneb.rst
@@ -398,3 +398,15 @@ See also
 - :doc:`input-keywords-system` (system setup)
 - :doc:`input-keywords-hamiltonian` (magnetic interactions)
 
+
+References
+----------
+
+See the centralized :doc:`references` for full bibliographic entries:
+
+- [Bessarab2012]_ - Method for finding magnetic transition mechanisms and activation energies
+- [Bessarab2015]_ - Harmonic transition-state theory for thermal spin transitions
+- [Henkelman2000]_ - Climbing image nudged elastic band method
+- [Eyring1935]_ - Activated complex theory for chemical reactions
+
+
diff --git a/content/input-keywords-hamiltonian.rst b/content/input-keywords-hamiltonian.rst
@@ -85,7 +85,15 @@ This switch allows the exchange data to be read in according to the tensorial re
 
   \mathcal{H}_{\mathrm{Tens}} = \sum_{i,j} \mathbf{e}_i \mathcal{J}_{ij} \mathbf{e}_j.
 
-Here, :math:`\mathcal{J}_{ij}=-J_{ij}\mathcal{I} + \mathcal{J}^S_{ij} +  \mathcal{J}^A_{ij}` is a :math:`3 \times 3` tensor (in which :math:`\mathcal{I}` is the unit matrix), the trace of which is equal to the exchange constant as defined in [Udvardi2003]_. 
+Here, :math:`\mathcal{J}_{ij}=-J_{ij}\mathcal{I} + \mathcal{J}^S_{ij} +  \mathcal{J}^A_{ij}` is a :math:`3 \times 3` tensor (in which :math:`\mathcal{I}` is the unit matrix), the trace of which is equal to the exchange constant as defined in [Udvardi2003]_.
+
+
+References
+----------
+
+See the centralized :doc:`references` for full bibliographic entries:
+
+- [Udvardi2003]_ - First-principles relativistic study of spin waves in thin magnetic films 
 
 .. %
 .. %\begin{equation}
diff --git a/content/input-keywords-montecarlo.rst b/content/input-keywords-montecarlo.rst
@@ -529,3 +529,23 @@ Related keywords and cross-references
 - Hamiltonian interactions: exchange, anisotropy, dipolar (see :doc:`input-keywords-hamiltonian`)
 
 Output files use the simulation identifier ``simid`` (see :doc:`input-keywords-system`).
+
+
+References
+----------
+
+See the centralized :doc:`references` for full bibliographic entries:
+
+- [Landau2014]_ - Guide to Monte Carlo simulation in statistical physics
+- [Binney1992]_ - Theory of critical phenomena and renormalization group
+- [Metropolis1953]_ - Equation of state calculations by fast computing machines
+- [Glauert1974]_ - Nonuniversal critical dynamics in Monte Carlo simulations
+- [Glauber1963]_ - Time-dependent statistics of the Ising model
+- [Hinzke2000]_ - Stochastic dynamics of magnetic nanoparticles
+- [Evertz1993]_ - Cluster algorithm for vertex models
+- [Ruban2004]_ - Surface segregation energies in transition-metal alloys
+- [Ebert2010]_ - Calculating condensed matter properties using KKR-Green's function method
+- [Kirkpatrick1983]_ - Optimization by simulated annealing
+- [Eriksson2017]_ - Atomistic spin dynamics foundations and applications
+- [Binder1981]_ - Finite size scaling and simulation of first order phase transitions
+
diff --git a/content/input-keywords-multiscale.rst b/content/input-keywords-multiscale.rst
@@ -408,13 +408,9 @@ Related keywords and cross-references
 - ``do_prnmultiscale``: Print multiscale diagnostic output files
 
 References
-----------
+==========
 
-Key references for multiscale atomistic-continuum methods:
+See the centralized :doc:`references` for full bibliographic entries:
 
-- Mendez, E., et al., *Multiscale Atomistic-Continuum Simulation of Magnetic
-  Nanostructures*, (MuASD library documentation).
-- Evans, R. F. L., et al., *Atomistic spin model simulations of magnetic
-  nanomaterials*, J. Phys.: Condens. Matter **26**, 103202 (2014).
-- Bergman, A., et al., *Ultrafast optical manipulation of magnetic disorder*,
-  Nature Phys. **13**, 294–298 (2017).
+- [Evans2014]_ - Atomistic spin model simulations of magnetic nanomaterials
+- [Mendez2020]_ - Multiscale approach for magnetization dynamics: unraveling exotic magnetic states of matter
diff --git a/content/input-keywords-polarization.rst b/content/input-keywords-polarization.rst
@@ -298,14 +298,10 @@ Related keywords and cross-references
   switching
 
 References
-----------
+==========
 
-Key references for spin-driven ferroelectricity:
+See the centralized :doc:`references` for full bibliographic entries:
 
-- Katsura, H., Nagaosa, N., and Balatsky, A. V., *Spin current and
-  magnetoelectric effect in noncollinear magnets*, Phys. Rev. Lett. **95**,
-  057205 (2005).
-- Mostovoy, M., *Ferroelectricity in spiral magnets*, Phys. Rev. Lett. **96**,
-  067601 (2006).
-- Tokura, Y. and Seki, S., *Multiferroics with spiral spin orders*, Adv.
-  Mater. **22**, 1554 (2010).
+- [Katsura2005]_ - Spin current and magnetoelectric effect in noncollinear magnets
+- [Mostovoy2006]_ - Ferroelectricity in spiral magnets
+- [Tokura2010]_ - Multiferroics with spiral spin orders
diff --git a/content/input-keywords-replicaexchange.rst b/content/input-keywords-replicaexchange.rst
@@ -314,3 +314,16 @@ See also
 - :doc:`input-keywords-montecarlo` (general Monte Carlo keywords)
 - :doc:`input-keywords-wanglandau` (Wang-Landau sampling)
 - :doc:`input-keywords-system` (system setup and temperature control)
+
+
+References
+----------
+
+See the centralized :doc:`references` for full bibliographic entries:
+
+- [Swendsen1986]_ - Replica Monte Carlo simulation of spin-glasses
+- [Geyer1995]_ - Markov chain Monte Carlo maximum likelihood
+- [Hukushima1996]_ - Exchange Monte Carlo method and application to spin glass simulations
+- [Earl2005]_ - Parallel tempering theory applications and perspectives
+- [Katzgraber2006]_ - Feedback-optimized parallel tempering Monte Carlo
+
diff --git a/content/input-keywords-simulation.rst b/content/input-keywords-simulation.rst
@@ -126,3 +126,13 @@ Measurement phase parameters
 +---------------+--------------------------------------------------------------------------------------------------------+
 |  set_bpulse   |    Add magnetic field pulse ``0=no``, :math:`1-4` for different shapes)                                |
 +---------------+--------------------------------------------------------------------------------------------------------+
+
+
+References
+----------
+
+See the centralized :doc:`references` for full bibliographic entries:
+
+- [Mentink2010]_ - Stable and fast semi-implicit integration of the stochastic LLG equation
+- [Depondt2009]_ - Spin dynamics simulations with Heisenberg and dipole-dipole interactions
+
diff --git a/content/input-keywords-sld.rst b/content/input-keywords-sld.rst
@@ -459,15 +459,10 @@ Related keywords and cross-references
 - ``Mensemble``: Number of replicas; important for averaging out thermal noise in lattice
 
 References
-----------
-
-Key references for spin-lattice dynamics:
-
-- Hellsvik, J., et al., *Multiphysics modeling of dynamics and quasistatics of ferromagnetic
-  nanostructures*, Phys. Rev. B **87**, 174420 (2013).
-- Bergman, A., et al., *Ultrafast optical manipulation of magnetic disorder*, Nature Phys.
-  **13**, 294–298 (2017).
-- Eriksson, O., et al., *Atomistic spin dynamics of materials*, Handbook Mater. Model.
-  (Springer, 2018).
-- Ma, Q., et al., *Electron-phonon coupling-induced anomalous lattice dynamics in Weyl semimetals*,
-  Nature Mater. **18**, 476–481 (2019).
+==========
+
+See the centralized :doc:`references` for full bibliographic entries:
+
+- [Hellsvik2019]_ - General method for atomistic spin-lattice dynamics with first-principles accuracy
+- [Eriksson2017]_ - Atomistic spin dynamics foundations and applications
+- [Ma2012]_ - Spin-lattice-electron dynamics simulations of magnetic materials
diff --git a/content/input-keywords-solvers.rst b/content/input-keywords-solvers.rst
@@ -816,26 +816,12 @@ Examples in Input Files
 
 
 References
-----------
+==========
 
-**Solver Theory:**
+See the centralized :doc:`references` for full bibliographic entries:
 
-1. J. H. Mentink et al., *J. Phys.: Condens. Matter* **22**, 176001 (2010) — Midpoint solver
-2. Ph. Depondt & F. G. Mertens, *J. Phys.: Condens. Matter* **21**, 336005 (2009) — Depondt solver
-3. R. I. McLachlan et al., *Phys. Rev. E* **89**, 061301(R) (2014) — Structure-preserving schemes
-4. J. Hellsvik, "Semi-implicit spherical midpoint solver" — Spherical constraint variant
-
-**Stochastic Integration:**
-
-5. P. E. Kloeden & E. Platen, *Numerical Solution of Stochastic Differential Equations* (Springer, 1992)
-
-**Magnetic Dynamics:**
-
-6. A. G. Gurevich & G. A. Melkov, *Magnetization Oscillations and Waves* (CRC Press, 1996)
-7. K. Fukamichi et al., "Magnetic relaxation in ferromagnetic materials" (various, see UppASD papers)
-
-**UppASD Documentation:**
-
-8. UppASD GitHub: https://github.com/UppASD/UppASD
-9. UppASD Papers: See publications list on project website
+- [Mentink2010]_ - Midpoint solver and semi-implicit integration
+- [Depondt2009]_ - Depondt-Mertens solver for spin dynamics
+- [McLachlan2014]_ - Structure-preserving Lie-Poisson integrators
+- [Kloeden1992]_ - Numerical solution of stochastic differential equations
 
diff --git a/content/input-keywords-stiffness.rst b/content/input-keywords-stiffness.rst
@@ -687,31 +687,12 @@ Stiffness calculations are typically used alongside:
 - **Topology analysis** (``do_tottraj='Y'``): Relate skyrmion size to D/D0 ratio
 
 References
-----------
-
-The stiffness calculation implementation in UppASD is based on:
-
-1. **Pajda, M., Kudrnovský, J., Turek, I., Drchal, V., & Bruno, P.**
-   "Ab initio calculations of exchange interactions, spin-wave stiffness constants, and Curie temperatures of Fe, Co, and Ni"
-   *Physical Review B* **64**, 174402 (2001)
-   - Original formalism for spin-wave stiffness from atomistic exchange
-
-2. **Udvardi, L., Szunyogh, L., Palotás, K., & Weinberger, P.**
-   "First-principles relativistic study of spin waves in thin magnetic films"
-   *Physical Review B* **68**, 104436 (2003)
-   - Extension to thin films and surfaces
-
-3. **Eriksson, O., Bergman, A., Bergqvist, L., & Hellsvik, J.**
-   "Atomistic Spin Dynamics: Foundations and Applications"
-   *Oxford University Press* (2017)
-   - Comprehensive treatment of atomistic-to-micromagnetic mapping
-
-4. **Hellsvik, J., Skubic, B., Nordström, L., Sanyal, B., Eriksson, O., Nordblad, P., & Warnicke, P.**
-   "Dynamics of diluted magnetic semiconductors from atomistic spin-dynamics simulations: Mn-doped GaAs as a case study"
-   *Physical Review B* **78**, 144419 (2008)
-   - Random alloy stiffness calculations
-
-5. **Beg, M., Pepper, R. A., & Fangohr, H.**
-   "User interfaces for computational science: A domain specific language for OOMMF embedded in Python"
-   *AIP Advances* **7**, 056025 (2017)
-   - Micromagnetic exchange constant usage and conventions
+==========
+
+See the centralized :doc:`references` for full bibliographic entries:
+
+- [Pajda2001]_ - Ab initio calculations of exchange interactions and spin-wave stiffness
+- [Udvardi2003]_ - First-principles relativistic study of spin waves in thin magnetic films
+- [Eriksson2017]_ - Atomistic spin dynamics and atomistic-to-micromagnetic mapping
+- [Hellsvik2008]_ - Random alloy stiffness calculations in diluted magnetic semiconductors
+- [Beg2017]_ - Micromagnetic exchange constant usage and conventions
diff --git a/content/input-keywords-temperature-3tm.rst b/content/input-keywords-temperature-3tm.rst
diff --git a/content/input-keywords-temperature-gradients.rst b/content/input-keywords-temperature-gradients.rst
diff --git a/content/input-keywords-topology.rst b/content/input-keywords-topology.rst
diff --git a/content/input-keywords-wanglandau.rst b/content/input-keywords-wanglandau.rst
diff --git a/content/input.rst b/content/input.rst
diff --git a/content/introduction.rst b/content/introduction.rst
diff --git a/content/output.rst b/content/output.rst
diff --git a/content/references.rst b/content/references.rst
