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Reorganize files for reference manual
author
Paul Bauer
<paul.bauer.q@gmail.com>
Thu, 26 Apr 2018 09:27:38 +0000
(11:27 +0200)
committer
Mark Abraham
<mark.j.abraham@gmail.com>
Thu, 26 Apr 2018 19:29:16 +0000
(21:29 +0200)
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
227 files changed:
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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/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
# 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/f
unctions/f
orce-field.rst
+ reference-manual/f
unctions/f
ree-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
# 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/topolog
ies/topolog
y-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
# 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
# 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
# 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
)
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/decomp.pdf
- reference-manual/plots/dih-def.pdf
reference-manual/plots/dih.pdf
reference-manual/plots/dih.pdf
- reference-manual/plots/distm.pdf
reference-manual/plots/drift-all.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-angle.pdf
- reference-manual/plots/f-bham.pdf
reference-manual/plots/f-bond.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/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/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/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/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.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/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
)
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
.. 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
rename to
docs/reference-manual/algorithms/plots/nstric.pdf
diff --git
a/docs/reference-manual/plots/nstric.svg
b/docs/reference-manual/algorithms/plots/nstric.svg
similarity index 100%
rename from
docs/reference-manual/plots/nstric.svg
rename to
docs/reference-manual/algorithms/plots/nstric.svg
diff --git
a/docs/reference-manual/plots/par-lincs2.fig
b/docs/reference-manual/algorithms/plots/par-lincs2.fig
similarity index 100%
rename from
docs/reference-manual/plots/par-lincs2.fig
rename to
docs/reference-manual/algorithms/plots/par-lincs2.fig
diff --git
a/docs/reference-manual/plots/par-lincs2.pdf
b/docs/reference-manual/algorithms/plots/par-lincs2.pdf
similarity index 100%
rename from
docs/reference-manual/plots/par-lincs2.pdf
rename to
docs/reference-manual/algorithms/plots/par-lincs2.pdf
diff --git
a/docs/reference-manual/plots/par-lincs2.svg
b/docs/reference-manual/algorithms/plots/par-lincs2.svg
similarity index 100%
rename from
docs/reference-manual/plots/par-lincs2.svg
rename to
docs/reference-manual/algorithms/plots/par-lincs2.svg
diff --git
a/docs/reference-manual/plots/pbctric.fig
b/docs/reference-manual/algorithms/plots/pbctric.fig
similarity index 100%
rename from
docs/reference-manual/plots/pbctric.fig
rename to
docs/reference-manual/algorithms/plots/pbctric.fig
diff --git
a/docs/reference-manual/plots/pbctric.pdf
b/docs/reference-manual/algorithms/plots/pbctric.pdf
similarity index 100%
rename from
docs/reference-manual/plots/pbctric.pdf
rename to
docs/reference-manual/algorithms/plots/pbctric.pdf
diff --git
a/docs/reference-manual/plots/pbctric.svg
b/docs/reference-manual/algorithms/plots/pbctric.svg
similarity index 100%
rename from
docs/reference-manual/plots/pbctric.svg
rename to
docs/reference-manual/algorithms/plots/pbctric.svg
diff --git
a/docs/reference-manual/plots/rhododec.ogl
b/docs/reference-manual/algorithms/plots/rhododec.ogl
similarity index 100%
rename from
docs/reference-manual/plots/rhododec.ogl
rename to
docs/reference-manual/algorithms/plots/rhododec.ogl
diff --git
a/docs/reference-manual/plots/rhododec.pdf
b/docs/reference-manual/algorithms/plots/rhododec.pdf
similarity index 100%
rename from
docs/reference-manual/plots/rhododec.pdf
rename to
docs/reference-manual/algorithms/plots/rhododec.pdf
diff --git
a/docs/reference-manual/plots/rhododec.svg
b/docs/reference-manual/algorithms/plots/rhododec.svg
similarity index 100%
rename from
docs/reference-manual/plots/rhododec.svg
rename to
docs/reference-manual/algorithms/plots/rhododec.svg
diff --git
a/docs/reference-manual/plots/truncoct.ogl
b/docs/reference-manual/algorithms/plots/truncoct.ogl
similarity index 100%
rename from
docs/reference-manual/plots/truncoct.ogl
rename to
docs/reference-manual/algorithms/plots/truncoct.ogl
diff --git
a/docs/reference-manual/plots/truncoct.pdf
b/docs/reference-manual/algorithms/plots/truncoct.pdf
similarity index 100%
rename from
docs/reference-manual/plots/truncoct.pdf
rename to
docs/reference-manual/algorithms/plots/truncoct.pdf
diff --git
a/docs/reference-manual/plots/truncoct.svg
b/docs/reference-manual/algorithms/plots/truncoct.svg
similarity index 100%
rename from
docs/reference-manual/plots/truncoct.svg
rename to
docs/reference-manual/algorithms/plots/truncoct.svg
diff --git
a/docs/reference-manual/plots/verlet-drift.pdf
b/docs/reference-manual/algorithms/plots/verlet-drift.pdf
similarity index 100%
rename from
docs/reference-manual/plots/verlet-drift.pdf
rename to
docs/reference-manual/algorithms/plots/verlet-drift.pdf
diff --git
a/docs/reference-manual/plots/verlet-drift.svg
b/docs/reference-manual/algorithms/plots/verlet-drift.svg
similarity index 100%
rename from
docs/reference-manual/plots/verlet-drift.svg
rename to
docs/reference-manual/algorithms/plots/verlet-drift.svg
diff --git
a/docs/reference-manual/plots/verlet-drift.xvg
b/docs/reference-manual/algorithms/plots/verlet-drift.xvg
similarity index 100%
rename from
docs/reference-manual/plots/verlet-drift.xvg
rename to
docs/reference-manual/algorithms/plots/verlet-drift.xvg
diff --git
a/docs/reference-manual/replica-exchange.rst
b/docs/reference-manual/algorithms/replica-exchange.rst
similarity index 100%
rename from
docs/reference-manual/replica-exchange.rst
rename to
docs/reference-manual/algorithms/replica-exchange.rst
diff --git
a/docs/reference-manual/shell-molecular-dynamics.rst
b/docs/reference-manual/algorithms/shell-molecular-dynamics.rst
similarity index 100%
rename from
docs/reference-manual/shell-molecular-dynamics.rst
rename to
docs/reference-manual/algorithms/shell-molecular-dynamics.rst
diff --git
a/docs/reference-manual/simulated-annealing.rst
b/docs/reference-manual/algorithms/simulated-annealing.rst
similarity index 100%
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
similarity index 100%
rename from
docs/reference-manual/stochastic-dynamics.rst
rename to
docs/reference-manual/algorithms/stochastic-dynamics.rst
diff --git
a/docs/reference-manual/analysis.rst
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(file)
--- a/
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docs/reference-manual/analysis.rst
@@
-18,19
+18,19
@@
different analysis tools are presented.
.. toctree::
:maxdepth: 2
.. 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
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a/docs/reference-manual/functions.rst
b/docs/reference-manual/functions.rst
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(file)
--- a/
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-30,14
+30,14
@@
The potential functions can be subdivided into three parts
.. toctree::
:maxdepth: 2
.. 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
+ f
unctions/f
ree-energy-interactions
+
functions/
interaction-methods
+
functions/
long-range-electrostatics
+
functions/
long-range-vdw
+ f
unctions/f
orce-field
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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
.. 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
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b/docs/reference-manual/special/viscosity-calculation.rst
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diff --git
a/docs/reference-manual/vmd-imd.rst
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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
.. 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
+ topolog
ies/topolog
y-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
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rename from
docs/reference-manual/force-field-organization.rst
rename to
docs/reference-manual/topologies/force-field-organization.rst
diff --git
a/docs/reference-manual/molecule-definition.rst
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diff --git
a/docs/reference-manual/parameter-files.rst
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docs/reference-manual/topology-file-formats.rst
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docs/reference-manual/topologies/topology-file-formats.rst