Reorganize files for reference manual

The files needed to build the reference manual have been moved around
such as that each chapter has its own subdirectory.

At the same time, the image files have been moved to the respective
directories as well.

CMake has been adpated to use the new directory structure.

Change-Id: I819c2168a635d23b659258f360fe1c423d2689c3

diff --git a/docs/CMakeLists.txt b/docs/CMakeLists.txt
index cc609b52ea7b50e16edb9de6e09576ee438aa3d5..9b38d75fac8f24752d9e5c2d018d2fb2d0a65ce8 100644 (file)
--- a/docs/CMakeLists.txt
+++ b/docs/CMakeLists.txt
@@ -116,76 +116,76 @@ if (SPHINX_FOUND)
         reference-manual/definitions.rst
         # Algorithms chapter
         reference-manual/algorithms.rst
-        reference-manual/periodic-boundary-conditions.rst
-        reference-manual/group-concept.rst
-        reference-manual/molecular-dynamics.rst
-        reference-manual/shell-molecular-dynamics.rst
-        reference-manual/constraint-algorithms.rst
-        reference-manual/simulated-annealing.rst
-        reference-manual/stochastic-dynamics.rst
-        reference-manual/brownian-dynamics.rst
-        reference-manual/energy-minimization.rst
-        reference-manual/normal-mode-analysis.rst
-        reference-manual/free-energy-calculations.rst
-        reference-manual/replica-exchange.rst
-        reference-manual/essential-dynamics.rst
-        reference-manual/expanded-ensemble.rst
-        reference-manual/parallelization-domain-decomp.rst
+        reference-manual/algorithms/periodic-boundary-conditions.rst
+        reference-manual/algorithms/group-concept.rst
+        reference-manual/algorithms/molecular-dynamics.rst
+        reference-manual/algorithms/shell-molecular-dynamics.rst
+        reference-manual/algorithms/constraint-algorithms.rst
+        reference-manual/algorithms/simulated-annealing.rst
+        reference-manual/algorithms/stochastic-dynamics.rst
+        reference-manual/algorithms/brownian-dynamics.rst
+        reference-manual/algorithms/energy-minimization.rst
+        reference-manual/algorithms/normal-mode-analysis.rst
+        reference-manual/algorithms/free-energy-calculations.rst
+        reference-manual/algorithms/replica-exchange.rst
+        reference-manual/algorithms/essential-dynamics.rst
+        reference-manual/algorithms/expanded-ensemble.rst
+        reference-manual/algorithms/parallelization-domain-decomp.rst
         # Interaction functions and force fields chapter
         reference-manual/functions.rst
-        reference-manual/bonded-interactions.rst
-        reference-manual/force-field.rst
-        reference-manual/free-energy-interactions.rst
-        reference-manual/interaction-methods.rst
-        reference-manual/long-range-electrostatics.rst
-        reference-manual/long-range-vdw.rst
-        reference-manual/nonbonded-interactions.rst
-        reference-manual/polarization.rst
-        reference-manual/restraints.rst
+        reference-manual/functions/bonded-interactions.rst
+        reference-manual/functions/force-field.rst
+        reference-manual/functions/free-energy-interactions.rst
+        reference-manual/functions/interaction-methods.rst
+        reference-manual/functions/long-range-electrostatics.rst
+        reference-manual/functions/long-range-vdw.rst
+        reference-manual/functions/nonbonded-interactions.rst
+        reference-manual/functions/polarization.rst
+        reference-manual/functions/restraints.rst
         # Topologies chapter
         reference-manual/topologies.rst
-        reference-manual/particle-type.rst
-        reference-manual/parameter-files.rst
-        reference-manual/molecule-definition.rst
-        reference-manual/constraint-algorithm-section.rst
-        reference-manual/pdb2gmx-input-files.rst
-        reference-manual/topology-file-formats.rst
-        reference-manual/force-field-organization.rst
+        reference-manual/topologies/particle-type.rst
+        reference-manual/topologies/parameter-files.rst
+        reference-manual/topologies/molecule-definition.rst
+        reference-manual/topologies/constraint-algorithm-section.rst
+        reference-manual/topologies/pdb2gmx-input-files.rst
+        reference-manual/topologies/topology-file-formats.rst
+        reference-manual/topologies/force-field-organization.rst
         # File formats chapter
         reference-manual/file-formats.rst
         # Special topics chapter
         reference-manual/special.rst
-        reference-manual/free-energy-implementation.rst
-        reference-manual/pulling.rst
-        reference-manual/awh.rst
-        reference-manual/enforced-rotation.rst
-        reference-manual/electric-fields.rst
-        reference-manual/comp-electrophys.rst
-        reference-manual/free-energy-pmf.rst
-        reference-manual/remove-fast-dgf.rst
-        reference-manual/viscosity-calculation.rst
-        reference-manual/tabulated-interaction-functions.rst
-        reference-manual/qmmm.rst
-        reference-manual/vmd-imd.rst
-        reference-manual/membrane-embedding.rst
+        reference-manual/special/free-energy-implementation.rst
+        reference-manual/special/pulling.rst
+        reference-manual/special/awh.rst
+        reference-manual/special/enforced-rotation.rst
+        reference-manual/special/electric-fields.rst
+        reference-manual/special/comp-electrophys.rst
+        reference-manual/special/free-energy-pmf.rst
+        reference-manual/special/remove-fast-dgf.rst
+        reference-manual/special/viscosity-calculation.rst
+        reference-manual/special/tabulated-interaction-functions.rst
+        reference-manual/special/qmmm.rst
+        reference-manual/special/vmd-imd.rst
+        reference-manual/special/membrane-embedding.rst
         # Run parameters and programs chapter
         reference-manual/run-parameters.rst
         # Analysis chapter
         reference-manual/analysis.rst
-        reference-manual/using-groups.rst
-        reference-manual/looking-at-trajectory.rst
-        reference-manual/general-properties.rst
-        reference-manual/radial-distribution-function.rst
-        reference-manual/correlation-function.rst
-        reference-manual/curve-fitting.rst
-        reference-manual/mean-square-displacement.rst
-        reference-manual/bond-angle-dihedral.rst
-        reference-manual/radius-of-gyration.rst
-        reference-manual/rmsd.rst
-        reference-manual/covariance-analysis.rst
-        reference-manual/dihedral-pca.rst
-        reference-manual/protein-related.rst
-        reference-manual/interface-related.rst
+        reference-manual/analysis/using-groups.rst
+        reference-manual/analysis/looking-at-trajectory.rst
+        reference-manual/analysis/general-properties.rst
+        reference-manual/analysis/radial-distribution-function.rst
+        reference-manual/analysis/correlation-function.rst
+        reference-manual/analysis/curve-fitting.rst
+        reference-manual/analysis/mean-square-displacement.rst
+        reference-manual/analysis/bond-angle-dihedral.rst
+        reference-manual/analysis/radius-of-gyration.rst
+        reference-manual/analysis/rmsd.rst
+        reference-manual/analysis/covariance-analysis.rst
+        reference-manual/analysis/dihedral-pca.rst
+        reference-manual/analysis/protein-related.rst
+        reference-manual/analysis/interface-related.rst
         # Implementation details chapter
         reference-manual/details.rst
         # Averages and fluctations chapter
@@ -199,81 +199,88 @@ if (SPHINX_FOUND)
         reference-manual/plots/plotje.png
         reference-manual/plots/xvgr.png
         )
-    set(REFERENCEMANUAL_IMAGE_FILES 
-        reference-manual/plots/angle.pdf
-        reference-manual/plots/awh-invN.pdf
-        reference-manual/plots/awh-pmfs.pdf
-        reference-manual/plots/awh-sampleweights.pdf
-        reference-manual/plots/awh-traj.pdf
-        reference-manual/plots/bstretch.pdf
-        reference-manual/plots/chain.pdf
-        reference-manual/plots/compelsetup.pdf
-        reference-manual/plots/dd-cells.pdf
-        reference-manual/plots/dd-tric.pdf
+    # The image files have also been ordered by the respective
+    # chapter they are included in in the reference manual
+    set(REFERENCEMANUAL_IMAGE_FILES
+        # General folder
         reference-manual/plots/decomp.pdf
-        reference-manual/plots/dih-def.pdf
         reference-manual/plots/dih.pdf
-        reference-manual/plots/distm.pdf
         reference-manual/plots/drift-all.pdf
-        reference-manual/plots/dssp.pdf
-        reference-manual/plots/dumaro.pdf
-        reference-manual/plots/dummies.pdf
-        reference-manual/plots/dumtypes.pdf
-        reference-manual/plots/equipotential.pdf
         reference-manual/plots/f-angle.pdf
-        reference-manual/plots/f-bham.pdf
         reference-manual/plots/f-bond.pdf
-        reference-manual/plots/fbposres.pdf
-        reference-manual/plots/f-dih.pdf
-        reference-manual/plots/f-dr.pdf
-        reference-manual/plots/field.pdf
-        reference-manual/plots/fig-02.pdf
-        reference-manual/plots/fig-04.pdf
-        reference-manual/plots/f-lj.pdf
-        reference-manual/plots/flowchart.pdf
-        reference-manual/plots/f-morse.pdf
         reference-manual/plots/fp-highres.pdf
-        reference-manual/plots/f-imps.pdf
-        reference-manual/plots/f-pr.pdf
-        reference-manual/plots/f-rbs.pdf
-        reference-manual/plots/free1.pdf
-        reference-manual/plots/free2.pdf
-        reference-manual/plots/gaussians.pdf
-        reference-manual/plots/hbond.pdf
-        reference-manual/plots/hbond-insert.pdf
-        reference-manual/plots/hpr-wheel.pdf
         reference-manual/plots/int-mat.pdf
-        reference-manual/plots/leapfrog.pdf
-        reference-manual/plots/lincs.pdf
-        reference-manual/plots/maxwell.pdf
         reference-manual/plots/mdpar.pdf
-        reference-manual/plots/mpmd-pme.pdf
-        reference-manual/plots/msdwater.pdf
-        reference-manual/plots/ngmxdump.pdf
-        reference-manual/plots/nstric.pdf
-        reference-manual/plots/par-lincs2.pdf
         reference-manual/plots/parsort.pdf
-        reference-manual/plots/pbctric.pdf
-        reference-manual/plots/phipsi.pdf
-        reference-manual/plots/pulldirrel.pdf
-        reference-manual/plots/pull.pdf
-        reference-manual/plots/pullref.pdf
-        reference-manual/plots/rama.pdf
-        reference-manual/plots/rdf.pdf
-        reference-manual/plots/rdfO-O.pdf
-        reference-manual/plots/rhododec.pdf
         reference-manual/plots/ring.pdf
-        reference-manual/plots/ring-imp.pdf
-        reference-manual/plots/rotation.pdf
-        reference-manual/plots/sgangle.pdf
         reference-manual/plots/shiftf.pdf
-        reference-manual/plots/softcore.pdf
-        reference-manual/plots/subst-im.pdf
-        reference-manual/plots/tetra-im.pdf
-        reference-manual/plots/truncoct.pdf
-        reference-manual/plots/vcrf.pdf
-        reference-manual/plots/verlet-drift.pdf
-        reference-manual/plots/vsite-4fdn.pdf
+        # Algorithms chapter
+        reference-manual/algorithms/plots/dd-cells.pdf
+        reference-manual/algorithms/plots/dd-tric.pdf
+        reference-manual/algorithms/plots/flowchart.pdf
+        reference-manual/algorithms/plots/free1.pdf
+        reference-manual/algorithms/plots/free2.pdf
+        reference-manual/algorithms/plots/leapfrog.pdf
+        reference-manual/algorithms/plots/lincs.pdf
+        reference-manual/algorithms/plots/maxwell.pdf
+        reference-manual/algorithms/plots/mpmd-pme.pdf
+        reference-manual/algorithms/plots/nstric.pdf
+        reference-manual/algorithms/plots/par-lincs2.pdf
+        reference-manual/algorithms/plots/pbctric.pdf
+        reference-manual/algorithms/plots/rhododec.pdf
+        reference-manual/algorithms/plots/truncoct.pdf
+        reference-manual/algorithms/plots/verlet-drift.pdf
+        # Interaction functions chapter
+        reference-manual/functions/plots/angle.pdf
+        reference-manual/functions/plots/bstretch.pdf
+        reference-manual/functions/plots/chain.pdf
+        reference-manual/functions/plots/dummies.pdf
+        reference-manual/functions/plots/f-bham.pdf
+        reference-manual/functions/plots/fbposres.pdf
+        reference-manual/functions/plots/f-dih.pdf
+        reference-manual/functions/plots/f-dr.pdf
+        reference-manual/functions/plots/fig-02.pdf
+        reference-manual/functions/plots/fig-04.pdf
+        reference-manual/functions/plots/f-imps.pdf
+        reference-manual/functions/plots/f-lj.pdf
+        reference-manual/functions/plots/f-morse.pdf
+        reference-manual/functions/plots/f-pr.pdf
+        reference-manual/functions/plots/f-rbs.pdf
+        reference-manual/functions/plots/ring-imp.pdf
+        reference-manual/functions/plots/softcore.pdf
+        reference-manual/functions/plots/subst-im.pdf
+        reference-manual/functions/plots/tetra-im.pdf
+        reference-manual/functions/plots/vcrf.pdf
+        reference-manual/functions/plots/vsite-4fdn.pdf
+        # Special topics chapter
+        reference-manual/special/plots/awh-invN.pdf
+        reference-manual/special/plots/awh-pmfs.pdf
+        reference-manual/special/plots/awh-sampleweights.pdf
+        reference-manual/special/plots/awh-traj.pdf
+        reference-manual/special/plots/compelsetup.pdf
+        reference-manual/special/plots/dumaro.pdf
+        reference-manual/special/plots/dumtypes.pdf
+        reference-manual/special/plots/equipotential.pdf
+        reference-manual/special/plots/field.pdf
+        reference-manual/special/plots/gaussians.pdf
+        reference-manual/special/plots/pulldirrel.pdf
+        reference-manual/special/plots/pull.pdf
+        reference-manual/special/plots/pullref.pdf
+        reference-manual/special/plots/rotation.pdf
+        # Analysis chapter
+        reference-manual/analysis/plots/dih-def.pdf
+        reference-manual/analysis/plots/distm.pdf
+        reference-manual/analysis/plots/dssp.pdf
+        reference-manual/analysis/plots/hbond-insert.pdf
+        reference-manual/analysis/plots/hbond.pdf
+        reference-manual/analysis/plots/hpr-wheel.pdf
+        reference-manual/analysis/plots/msdwater.pdf
+        reference-manual/analysis/plots/ngmxdump.pdf
+        reference-manual/analysis/plots/phipsi.pdf
+        reference-manual/analysis/plots/rama.pdf
+        reference-manual/analysis/plots/rdfO-O.pdf
+        reference-manual/analysis/plots/rdf.pdf
+        reference-manual/analysis/plots/sgangle.pdf 
         )
     set(SPHINX_SOURCE_FILES
         index.rst

diff --git a/docs/reference-manual/algorithms.rst b/docs/reference-manual/algorithms.rst
index f262a3f0b4a288e570ba261351d41a64c6f35ec4..a6dd4828093179af9162d3d1d95c84dd4c83f943 100644 (file)
--- a/docs/reference-manual/algorithms.rst
+++ b/docs/reference-manual/algorithms.rst
@@ -24,20 +24,20 @@ generated by an MD simulation is treated in chapter :ref:`analysis`.
 .. toctree::
    :maxdepth: 2
 
-   periodic-boundary-conditions
-   group-concept
-   molecular-dynamics
-   shell-molecular-dynamics
-   constraint-algorithms
-   simulated-annealing
-   stochastic-dynamics
-   brownian-dynamics
-   energy-minimization
-   normal-mode-analysis
-   free-energy-calculations
-   replica-exchange
-   essential-dynamics
-   expanded-ensemble
-   parallelization-domain-decomp
+   algorithms/periodic-boundary-conditions
+   algorithms/group-concept
+   algorithms/molecular-dynamics
+   algorithms/shell-molecular-dynamics
+   algorithms/constraint-algorithms
+   algorithms/simulated-annealing
+   algorithms/stochastic-dynamics
+   algorithms/brownian-dynamics
+   algorithms/energy-minimization
+   algorithms/normal-mode-analysis
+   algorithms/free-energy-calculations
+   algorithms/replica-exchange
+   algorithms/essential-dynamics
+   algorithms/expanded-ensemble
+   algorithms/parallelization-domain-decomp
 
 

diff --git a/docs/reference-manual/brownian-dynamics.rst b/docs/reference-manual/algorithms/brownian-dynamics.rst
similarity index 100%
rename from docs/reference-manual/brownian-dynamics.rst
rename to docs/reference-manual/algorithms/brownian-dynamics.rst

diff --git a/docs/reference-manual/constraint-algorithms.rst b/docs/reference-manual/algorithms/constraint-algorithms.rst
similarity index 100%
rename from docs/reference-manual/constraint-algorithms.rst
rename to docs/reference-manual/algorithms/constraint-algorithms.rst

diff --git a/docs/reference-manual/energy-minimization.rst b/docs/reference-manual/algorithms/energy-minimization.rst
similarity index 100%
rename from docs/reference-manual/energy-minimization.rst
rename to docs/reference-manual/algorithms/energy-minimization.rst

diff --git a/docs/reference-manual/essential-dynamics.rst b/docs/reference-manual/algorithms/essential-dynamics.rst
similarity index 100%
rename from docs/reference-manual/essential-dynamics.rst
rename to docs/reference-manual/algorithms/essential-dynamics.rst

diff --git a/docs/reference-manual/expanded-ensemble.rst b/docs/reference-manual/algorithms/expanded-ensemble.rst
similarity index 100%
rename from docs/reference-manual/expanded-ensemble.rst
rename to docs/reference-manual/algorithms/expanded-ensemble.rst

diff --git a/docs/reference-manual/free-energy-calculations.rst b/docs/reference-manual/algorithms/free-energy-calculations.rst
similarity index 100%
rename from docs/reference-manual/free-energy-calculations.rst
rename to docs/reference-manual/algorithms/free-energy-calculations.rst

diff --git a/docs/reference-manual/group-concept.rst b/docs/reference-manual/algorithms/group-concept.rst
similarity index 100%
rename from docs/reference-manual/group-concept.rst
rename to docs/reference-manual/algorithms/group-concept.rst

diff --git a/docs/reference-manual/molecular-dynamics.rst b/docs/reference-manual/algorithms/molecular-dynamics.rst
similarity index 100%
rename from docs/reference-manual/molecular-dynamics.rst
rename to docs/reference-manual/algorithms/molecular-dynamics.rst

diff --git a/docs/reference-manual/normal-mode-analysis.rst b/docs/reference-manual/algorithms/normal-mode-analysis.rst
similarity index 100%
rename from docs/reference-manual/normal-mode-analysis.rst
rename to docs/reference-manual/algorithms/normal-mode-analysis.rst

diff --git a/docs/reference-manual/parallelization-domain-decomp.rst b/docs/reference-manual/algorithms/parallelization-domain-decomp.rst
similarity index 100%
rename from docs/reference-manual/parallelization-domain-decomp.rst
rename to docs/reference-manual/algorithms/parallelization-domain-decomp.rst

diff --git a/docs/reference-manual/periodic-boundary-conditions.rst b/docs/reference-manual/algorithms/periodic-boundary-conditions.rst
similarity index 100%
rename from docs/reference-manual/periodic-boundary-conditions.rst
rename to docs/reference-manual/algorithms/periodic-boundary-conditions.rst

diff --git a/docs/reference-manual/plots/dd-cells.fig b/docs/reference-manual/algorithms/plots/dd-cells.fig
similarity index 100%
rename from docs/reference-manual/plots/dd-cells.fig
rename to docs/reference-manual/algorithms/plots/dd-cells.fig

diff --git a/docs/reference-manual/plots/dd-cells.pdf b/docs/reference-manual/algorithms/plots/dd-cells.pdf
similarity index 100%
rename from docs/reference-manual/plots/dd-cells.pdf
rename to docs/reference-manual/algorithms/plots/dd-cells.pdf

diff --git a/docs/reference-manual/plots/dd-cells.svg b/docs/reference-manual/algorithms/plots/dd-cells.svg
similarity index 100%
rename from docs/reference-manual/plots/dd-cells.svg
rename to docs/reference-manual/algorithms/plots/dd-cells.svg

diff --git a/docs/reference-manual/plots/dd-tric.fig b/docs/reference-manual/algorithms/plots/dd-tric.fig
similarity index 100%
rename from docs/reference-manual/plots/dd-tric.fig
rename to docs/reference-manual/algorithms/plots/dd-tric.fig

diff --git a/docs/reference-manual/plots/dd-tric.pdf b/docs/reference-manual/algorithms/plots/dd-tric.pdf
similarity index 100%
rename from docs/reference-manual/plots/dd-tric.pdf
rename to docs/reference-manual/algorithms/plots/dd-tric.pdf

diff --git a/docs/reference-manual/plots/dd-tric.svg b/docs/reference-manual/algorithms/plots/dd-tric.svg
similarity index 100%
rename from docs/reference-manual/plots/dd-tric.svg
rename to docs/reference-manual/algorithms/plots/dd-tric.svg

diff --git a/docs/reference-manual/plots/flowchart.pdf b/docs/reference-manual/algorithms/plots/flowchart.pdf
similarity index 100%
rename from docs/reference-manual/plots/flowchart.pdf
rename to docs/reference-manual/algorithms/plots/flowchart.pdf

diff --git a/docs/reference-manual/plots/flowchart.svg b/docs/reference-manual/algorithms/plots/flowchart.svg
similarity index 100%
rename from docs/reference-manual/plots/flowchart.svg
rename to docs/reference-manual/algorithms/plots/flowchart.svg

diff --git a/docs/reference-manual/plots/free1.fig b/docs/reference-manual/algorithms/plots/free1.fig
similarity index 100%
rename from docs/reference-manual/plots/free1.fig
rename to docs/reference-manual/algorithms/plots/free1.fig

diff --git a/docs/reference-manual/plots/free1.pdf b/docs/reference-manual/algorithms/plots/free1.pdf
similarity index 100%
rename from docs/reference-manual/plots/free1.pdf
rename to docs/reference-manual/algorithms/plots/free1.pdf

diff --git a/docs/reference-manual/plots/free1.svg b/docs/reference-manual/algorithms/plots/free1.svg
similarity index 100%
rename from docs/reference-manual/plots/free1.svg
rename to docs/reference-manual/algorithms/plots/free1.svg

diff --git a/docs/reference-manual/plots/free2.fig b/docs/reference-manual/algorithms/plots/free2.fig
similarity index 100%
rename from docs/reference-manual/plots/free2.fig
rename to docs/reference-manual/algorithms/plots/free2.fig

diff --git a/docs/reference-manual/plots/free2.pdf b/docs/reference-manual/algorithms/plots/free2.pdf
similarity index 100%
rename from docs/reference-manual/plots/free2.pdf
rename to docs/reference-manual/algorithms/plots/free2.pdf

diff --git a/docs/reference-manual/plots/free2.svg b/docs/reference-manual/algorithms/plots/free2.svg
similarity index 100%
rename from docs/reference-manual/plots/free2.svg
rename to docs/reference-manual/algorithms/plots/free2.svg

diff --git a/docs/reference-manual/plots/leapfrog.pdf b/docs/reference-manual/algorithms/plots/leapfrog.pdf
similarity index 100%
rename from docs/reference-manual/plots/leapfrog.pdf
rename to docs/reference-manual/algorithms/plots/leapfrog.pdf

diff --git a/docs/reference-manual/plots/leapfrog.svg b/docs/reference-manual/algorithms/plots/leapfrog.svg
similarity index 100%
rename from docs/reference-manual/plots/leapfrog.svg
rename to docs/reference-manual/algorithms/plots/leapfrog.svg

diff --git a/docs/reference-manual/plots/lincs.pdf b/docs/reference-manual/algorithms/plots/lincs.pdf
similarity index 100%
rename from docs/reference-manual/plots/lincs.pdf
rename to docs/reference-manual/algorithms/plots/lincs.pdf

diff --git a/docs/reference-manual/plots/lincs.svg b/docs/reference-manual/algorithms/plots/lincs.svg
similarity index 100%
rename from docs/reference-manual/plots/lincs.svg
rename to docs/reference-manual/algorithms/plots/lincs.svg

diff --git a/docs/reference-manual/plots/maxwell.pdf b/docs/reference-manual/algorithms/plots/maxwell.pdf
similarity index 100%
rename from docs/reference-manual/plots/maxwell.pdf
rename to docs/reference-manual/algorithms/plots/maxwell.pdf

diff --git a/docs/reference-manual/plots/maxwell.svg b/docs/reference-manual/algorithms/plots/maxwell.svg
similarity index 100%
rename from docs/reference-manual/plots/maxwell.svg
rename to docs/reference-manual/algorithms/plots/maxwell.svg

diff --git a/docs/reference-manual/plots/maxwell.xvg b/docs/reference-manual/algorithms/plots/maxwell.xvg
similarity index 100%
rename from docs/reference-manual/plots/maxwell.xvg
rename to docs/reference-manual/algorithms/plots/maxwell.xvg

diff --git a/docs/reference-manual/plots/mpmd-pme.fig b/docs/reference-manual/algorithms/plots/mpmd-pme.fig
similarity index 100%
rename from docs/reference-manual/plots/mpmd-pme.fig
rename to docs/reference-manual/algorithms/plots/mpmd-pme.fig

diff --git a/docs/reference-manual/plots/mpmd-pme.pdf b/docs/reference-manual/algorithms/plots/mpmd-pme.pdf
similarity index 100%
rename from docs/reference-manual/plots/mpmd-pme.pdf
rename to docs/reference-manual/algorithms/plots/mpmd-pme.pdf

diff --git a/docs/reference-manual/plots/mpmd-pme.svg b/docs/reference-manual/algorithms/plots/mpmd-pme.svg
similarity index 100%
rename from docs/reference-manual/plots/mpmd-pme.svg
rename to docs/reference-manual/algorithms/plots/mpmd-pme.svg

diff --git a/docs/reference-manual/plots/nstric.fig b/docs/reference-manual/algorithms/plots/nstric.fig
similarity index 100%
rename from docs/reference-manual/plots/nstric.fig
rename to docs/reference-manual/algorithms/plots/nstric.fig

diff --git a/docs/reference-manual/plots/nstric.pdf b/docs/reference-manual/algorithms/plots/nstric.pdf
similarity index 100%
rename from docs/reference-manual/plots/nstric.pdf
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diff --git a/docs/reference-manual/shell-molecular-dynamics.rst b/docs/reference-manual/algorithms/shell-molecular-dynamics.rst
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diff --git a/docs/reference-manual/simulated-annealing.rst b/docs/reference-manual/algorithms/simulated-annealing.rst
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rename from docs/reference-manual/simulated-annealing.rst
rename to docs/reference-manual/algorithms/simulated-annealing.rst

diff --git a/docs/reference-manual/stochastic-dynamics.rst b/docs/reference-manual/algorithms/stochastic-dynamics.rst
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rename to docs/reference-manual/algorithms/stochastic-dynamics.rst

diff --git a/docs/reference-manual/analysis.rst b/docs/reference-manual/analysis.rst
index 5e6b949eb0868203f06c1f1bdef969da0f45259a..4c698f9bdc7ce7057a8b314d5489316c240a6671 100644 (file)
--- a/docs/reference-manual/analysis.rst
+++ b/docs/reference-manual/analysis.rst
@@ -18,19 +18,19 @@ different analysis tools are presented.
 .. toctree::
    :maxdepth: 2
 
-   using-groups
-   looking-at-trajectory
-   general-properties
-   radial-distribution-function
-   correlation-function
-   curve-fitting
-   mean-square-displacement
-   bond-angle-dihedral
-   radius-of-gyration
-   rmsd
-   covariance-analysis
-   dihedral-pca
-   protein-related
-   interface-related
+   analysis/using-groups
+   analysis/looking-at-trajectory
+   analysis/general-properties
+   analysis/radial-distribution-function
+   analysis/correlation-function
+   analysis/curve-fitting
+   analysis/mean-square-displacement
+   analysis/bond-angle-dihedral
+   analysis/radius-of-gyration
+   analysis/rmsd
+   analysis/covariance-analysis
+   analysis/dihedral-pca
+   analysis/protein-related
+   analysis/interface-related
 
 

diff --git a/docs/reference-manual/bond-angle-dihedral.rst b/docs/reference-manual/analysis/bond-angle-dihedral.rst
similarity index 100%
rename from docs/reference-manual/bond-angle-dihedral.rst
rename to docs/reference-manual/analysis/bond-angle-dihedral.rst

diff --git a/docs/reference-manual/correlation-function.rst b/docs/reference-manual/analysis/correlation-function.rst
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diff --git a/docs/reference-manual/covariance-analysis.rst b/docs/reference-manual/analysis/covariance-analysis.rst
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diff --git a/docs/reference-manual/curve-fitting.rst b/docs/reference-manual/analysis/curve-fitting.rst
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rename from docs/reference-manual/curve-fitting.rst
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diff --git a/docs/reference-manual/dihedral-pca.rst b/docs/reference-manual/analysis/dihedral-pca.rst
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diff --git a/docs/reference-manual/radius-of-gyration.rst b/docs/reference-manual/analysis/radius-of-gyration.rst
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rename to docs/reference-manual/analysis/radius-of-gyration.rst

diff --git a/docs/reference-manual/rmsd.rst b/docs/reference-manual/analysis/rmsd.rst
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rename from docs/reference-manual/rmsd.rst
rename to docs/reference-manual/analysis/rmsd.rst

diff --git a/docs/reference-manual/using-groups.rst b/docs/reference-manual/analysis/using-groups.rst
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diff --git a/docs/reference-manual/functions.rst b/docs/reference-manual/functions.rst
index d546bfd7ae6daf01b57dcc73315f3352d94259f6..d8258910ddef662edac82802e723bcc4369ac666 100644 (file)
--- a/docs/reference-manual/functions.rst
+++ b/docs/reference-manual/functions.rst
@@ -30,14 +30,14 @@ The potential functions can be subdivided into three parts
 .. toctree::
    :maxdepth: 2
 
-   nonbonded-interactions
-   bonded-interactions
-   restraints
-   polarization
-   free-energy-interactions
-   interaction-methods
-   long-range-electrostatics
-   long-range-vdw
-   force-field
+   functions/nonbonded-interactions
+   functions/bonded-interactions
+   functions/restraints
+   functions/polarization
+   functions/free-energy-interactions
+   functions/interaction-methods
+   functions/long-range-electrostatics
+   functions/long-range-vdw
+   functions/force-field
 
 

diff --git a/docs/reference-manual/bonded-interactions.rst b/docs/reference-manual/functions/bonded-interactions.rst
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rename to docs/reference-manual/functions/bonded-interactions.rst

diff --git a/docs/reference-manual/force-field.rst b/docs/reference-manual/functions/force-field.rst
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rename to docs/reference-manual/functions/force-field.rst

diff --git a/docs/reference-manual/free-energy-interactions.rst b/docs/reference-manual/functions/free-energy-interactions.rst
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diff --git a/docs/reference-manual/interaction-methods.rst b/docs/reference-manual/functions/interaction-methods.rst
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diff --git a/docs/reference-manual/long-range-electrostatics.rst b/docs/reference-manual/functions/long-range-electrostatics.rst
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diff --git a/docs/reference-manual/polarization.rst b/docs/reference-manual/functions/polarization.rst
similarity index 100%
rename from docs/reference-manual/polarization.rst
rename to docs/reference-manual/functions/polarization.rst

diff --git a/docs/reference-manual/restraints.rst b/docs/reference-manual/functions/restraints.rst
similarity index 100%
rename from docs/reference-manual/restraints.rst
rename to docs/reference-manual/functions/restraints.rst

diff --git a/docs/reference-manual/special.rst b/docs/reference-manual/special.rst
index bc94671d8142a861213b47a2400a950e8d266ab9..45b7f1ef2ca4ac3459452d0a05e37a7d2f528ace 100644 (file)
--- a/docs/reference-manual/special.rst
+++ b/docs/reference-manual/special.rst
@@ -9,18 +9,18 @@ the use of |Gromacs| for specific scientific problems.
 .. toctree::
    :maxdepth: 2
 
-   free-energy-implementation
-   pulling
-   awh
-   enforced-rotation
-   electric-fields
-   comp-electrophys
-   free-energy-pmf
-   remove-fast-dgf
-   viscosity-calculation
-   tabulated-interaction-functions
-   qmmm
-   vmd-imd
-   membrane-embedding
+   special/free-energy-implementation
+   special/pulling
+   special/awh
+   special/enforced-rotation
+   special/electric-fields
+   special/comp-electrophys
+   special/free-energy-pmf
+   special/remove-fast-dgf
+   special/viscosity-calculation
+   special/tabulated-interaction-functions
+   special/qmmm
+   special/vmd-imd
+   special/membrane-embedding
 
 

diff --git a/docs/reference-manual/awh.rst b/docs/reference-manual/special/awh.rst
similarity index 100%
rename from docs/reference-manual/awh.rst
rename to docs/reference-manual/special/awh.rst

diff --git a/docs/reference-manual/comp-electrophys.rst b/docs/reference-manual/special/comp-electrophys.rst
similarity index 100%
rename from docs/reference-manual/comp-electrophys.rst
rename to docs/reference-manual/special/comp-electrophys.rst

diff --git a/docs/reference-manual/electric-fields.rst b/docs/reference-manual/special/electric-fields.rst
similarity index 100%
rename from docs/reference-manual/electric-fields.rst
rename to docs/reference-manual/special/electric-fields.rst

diff --git a/docs/reference-manual/enforced-rotation.rst b/docs/reference-manual/special/enforced-rotation.rst
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rename from docs/reference-manual/enforced-rotation.rst
rename to docs/reference-manual/special/enforced-rotation.rst

diff --git a/docs/reference-manual/free-energy-implementation.rst b/docs/reference-manual/special/free-energy-implementation.rst
similarity index 100%
rename from docs/reference-manual/free-energy-implementation.rst
rename to docs/reference-manual/special/free-energy-implementation.rst

diff --git a/docs/reference-manual/free-energy-pmf.rst b/docs/reference-manual/special/free-energy-pmf.rst
similarity index 100%
rename from docs/reference-manual/free-energy-pmf.rst
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diff --git a/docs/reference-manual/membrane-embedding.rst b/docs/reference-manual/special/membrane-embedding.rst
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rename from docs/reference-manual/membrane-embedding.rst
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diff --git a/docs/reference-manual/plots/awh-invN.pdf b/docs/reference-manual/special/plots/awh-invN.pdf
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diff --git a/docs/reference-manual/plots/awh-traj.pdf b/docs/reference-manual/special/plots/awh-traj.pdf
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diff --git a/docs/reference-manual/plots/compelsetup.pdf b/docs/reference-manual/special/plots/compelsetup.pdf
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similarity index 100%
rename from docs/reference-manual/plots/rotation.pdf
rename to docs/reference-manual/special/plots/rotation.pdf

diff --git a/docs/reference-manual/pulling.rst b/docs/reference-manual/special/pulling.rst
similarity index 100%
rename from docs/reference-manual/pulling.rst
rename to docs/reference-manual/special/pulling.rst

diff --git a/docs/reference-manual/qmmm.rst b/docs/reference-manual/special/qmmm.rst
similarity index 100%
rename from docs/reference-manual/qmmm.rst
rename to docs/reference-manual/special/qmmm.rst

diff --git a/docs/reference-manual/remove-fast-dgf.rst b/docs/reference-manual/special/remove-fast-dgf.rst
similarity index 100%
rename from docs/reference-manual/remove-fast-dgf.rst
rename to docs/reference-manual/special/remove-fast-dgf.rst

diff --git a/docs/reference-manual/tabulated-interaction-functions.rst b/docs/reference-manual/special/tabulated-interaction-functions.rst
similarity index 100%
rename from docs/reference-manual/tabulated-interaction-functions.rst
rename to docs/reference-manual/special/tabulated-interaction-functions.rst

diff --git a/docs/reference-manual/viscosity-calculation.rst b/docs/reference-manual/special/viscosity-calculation.rst
similarity index 100%
rename from docs/reference-manual/viscosity-calculation.rst
rename to docs/reference-manual/special/viscosity-calculation.rst

diff --git a/docs/reference-manual/vmd-imd.rst b/docs/reference-manual/special/vmd-imd.rst
similarity index 100%
rename from docs/reference-manual/vmd-imd.rst
rename to docs/reference-manual/special/vmd-imd.rst

diff --git a/docs/reference-manual/topologies.rst b/docs/reference-manual/topologies.rst
index 57b76f236a23e5cd479291396303bee28400ddd2..53bc0c2c8818a4142f7bb45fd88cf98aeb4a0828 100644 (file)
--- a/docs/reference-manual/topologies.rst
+++ b/docs/reference-manual/topologies.rst
@@ -34,12 +34,12 @@ standard force fields - contribute them to the force field archive!
 .. toctree::
    :maxdepth: 2
 
-   particle-type
-   parameter-files
-   molecule-definition
-   constraint-algorithm-section
-   pdb2gmx-input-files
-   topology-file-formats
-   force-field-organization
+   topologies/particle-type
+   topologies/parameter-files
+   topologies/molecule-definition
+   topologies/constraint-algorithm-section
+   topologies/pdb2gmx-input-files
+   topologies/topology-file-formats
+   topologies/force-field-organization
 
 

diff --git a/docs/reference-manual/constraint-algorithm-section.rst b/docs/reference-manual/topologies/constraint-algorithm-section.rst
similarity index 100%
rename from docs/reference-manual/constraint-algorithm-section.rst
rename to docs/reference-manual/topologies/constraint-algorithm-section.rst

diff --git a/docs/reference-manual/force-field-organization.rst b/docs/reference-manual/topologies/force-field-organization.rst
similarity index 100%
rename from docs/reference-manual/force-field-organization.rst
rename to docs/reference-manual/topologies/force-field-organization.rst

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diff --git a/docs/reference-manual/pdb2gmx-input-files.rst b/docs/reference-manual/topologies/pdb2gmx-input-files.rst
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