Reorganize files for reference manual
authorPaul Bauer <paul.bauer.q@gmail.com>
Thu, 26 Apr 2018 09:27:38 +0000 (11:27 +0200)
committerMark Abraham <mark.j.abraham@gmail.com>
Thu, 26 Apr 2018 19:29:16 +0000 (21:29 +0200)
commit78735e7fcf9d0109fed2434a9b5797f602c1f3ca
tree0f23d8750fb376114612ea3a76231d9bea88e66d
parentc29a096c54c47e304d4887c19e6c2d7c5ee40e5c
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
227 files changed:
docs/CMakeLists.txt
docs/reference-manual/algorithms.rst
docs/reference-manual/algorithms/brownian-dynamics.rst [moved from docs/reference-manual/brownian-dynamics.rst with 100% similarity]
docs/reference-manual/algorithms/constraint-algorithms.rst [moved from docs/reference-manual/constraint-algorithms.rst with 100% similarity]
docs/reference-manual/algorithms/energy-minimization.rst [moved from docs/reference-manual/energy-minimization.rst with 100% similarity]
docs/reference-manual/algorithms/essential-dynamics.rst [moved from docs/reference-manual/essential-dynamics.rst with 100% similarity]
docs/reference-manual/algorithms/expanded-ensemble.rst [moved from docs/reference-manual/expanded-ensemble.rst with 100% similarity]
docs/reference-manual/algorithms/free-energy-calculations.rst [moved from docs/reference-manual/free-energy-calculations.rst with 100% similarity]
docs/reference-manual/algorithms/group-concept.rst [moved from docs/reference-manual/group-concept.rst with 100% similarity]
docs/reference-manual/algorithms/molecular-dynamics.rst [moved from docs/reference-manual/molecular-dynamics.rst with 100% similarity]
docs/reference-manual/algorithms/normal-mode-analysis.rst [moved from docs/reference-manual/normal-mode-analysis.rst with 100% similarity]
docs/reference-manual/algorithms/parallelization-domain-decomp.rst [moved from docs/reference-manual/parallelization-domain-decomp.rst with 100% similarity]
docs/reference-manual/algorithms/periodic-boundary-conditions.rst [moved from docs/reference-manual/periodic-boundary-conditions.rst with 100% similarity]
docs/reference-manual/algorithms/plots/dd-cells.fig [moved from docs/reference-manual/plots/dd-cells.fig with 100% similarity]
docs/reference-manual/algorithms/plots/dd-cells.pdf [moved from docs/reference-manual/plots/dd-cells.pdf with 100% similarity]
docs/reference-manual/algorithms/plots/dd-cells.svg [moved from docs/reference-manual/plots/dd-cells.svg with 100% similarity]
docs/reference-manual/algorithms/plots/dd-tric.fig [moved from docs/reference-manual/plots/dd-tric.fig with 100% similarity]
docs/reference-manual/algorithms/plots/dd-tric.pdf [moved from docs/reference-manual/plots/dd-tric.pdf with 100% similarity]
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docs/reference-manual/algorithms/plots/flowchart.pdf [moved from docs/reference-manual/plots/flowchart.pdf with 100% similarity]
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docs/reference-manual/algorithms/plots/free1.fig [moved from docs/reference-manual/plots/free1.fig with 100% similarity]
docs/reference-manual/algorithms/plots/free1.pdf [moved from docs/reference-manual/plots/free1.pdf with 100% similarity]
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docs/reference-manual/algorithms/plots/free2.fig [moved from docs/reference-manual/plots/free2.fig with 100% similarity]
docs/reference-manual/algorithms/plots/free2.pdf [moved from docs/reference-manual/plots/free2.pdf with 100% similarity]
docs/reference-manual/algorithms/plots/free2.svg [moved from docs/reference-manual/plots/free2.svg with 100% similarity]
docs/reference-manual/algorithms/plots/leapfrog.pdf [moved from docs/reference-manual/plots/leapfrog.pdf with 100% similarity]
docs/reference-manual/algorithms/plots/leapfrog.svg [moved from docs/reference-manual/plots/leapfrog.svg with 100% similarity]
docs/reference-manual/algorithms/plots/lincs.pdf [moved from docs/reference-manual/plots/lincs.pdf with 100% similarity]
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docs/reference-manual/algorithms/plots/maxwell.pdf [moved from docs/reference-manual/plots/maxwell.pdf with 100% similarity]
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docs/reference-manual/algorithms/plots/maxwell.xvg [moved from docs/reference-manual/plots/maxwell.xvg with 100% similarity]
docs/reference-manual/algorithms/plots/mpmd-pme.fig [moved from docs/reference-manual/plots/mpmd-pme.fig with 100% similarity]
docs/reference-manual/algorithms/plots/mpmd-pme.pdf [moved from docs/reference-manual/plots/mpmd-pme.pdf with 100% similarity]
docs/reference-manual/algorithms/plots/mpmd-pme.svg [moved from docs/reference-manual/plots/mpmd-pme.svg with 100% similarity]
docs/reference-manual/algorithms/plots/nstric.fig [moved from docs/reference-manual/plots/nstric.fig with 100% similarity]
docs/reference-manual/algorithms/plots/nstric.pdf [moved from docs/reference-manual/plots/nstric.pdf with 100% similarity]
docs/reference-manual/algorithms/plots/nstric.svg [moved from docs/reference-manual/plots/nstric.svg with 100% similarity]
docs/reference-manual/algorithms/plots/par-lincs2.fig [moved from docs/reference-manual/plots/par-lincs2.fig with 100% similarity]
docs/reference-manual/algorithms/plots/par-lincs2.pdf [moved from docs/reference-manual/plots/par-lincs2.pdf with 100% similarity]
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docs/reference-manual/algorithms/plots/pbctric.fig [moved from docs/reference-manual/plots/pbctric.fig with 100% similarity]
docs/reference-manual/algorithms/plots/pbctric.pdf [moved from docs/reference-manual/plots/pbctric.pdf with 100% similarity]
docs/reference-manual/algorithms/plots/pbctric.svg [moved from docs/reference-manual/plots/pbctric.svg with 100% similarity]
docs/reference-manual/algorithms/plots/rhododec.ogl [moved from docs/reference-manual/plots/rhododec.ogl with 100% similarity]
docs/reference-manual/algorithms/plots/rhododec.pdf [moved from docs/reference-manual/plots/rhododec.pdf with 100% similarity]
docs/reference-manual/algorithms/plots/rhododec.svg [moved from docs/reference-manual/plots/rhododec.svg with 100% similarity]
docs/reference-manual/algorithms/plots/truncoct.ogl [moved from docs/reference-manual/plots/truncoct.ogl with 100% similarity]
docs/reference-manual/algorithms/plots/truncoct.pdf [moved from docs/reference-manual/plots/truncoct.pdf with 100% similarity]
docs/reference-manual/algorithms/plots/truncoct.svg [moved from docs/reference-manual/plots/truncoct.svg with 100% similarity]
docs/reference-manual/algorithms/plots/verlet-drift.pdf [moved from docs/reference-manual/plots/verlet-drift.pdf with 100% similarity]
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docs/reference-manual/algorithms/plots/verlet-drift.xvg [moved from docs/reference-manual/plots/verlet-drift.xvg with 100% similarity]
docs/reference-manual/algorithms/replica-exchange.rst [moved from docs/reference-manual/replica-exchange.rst with 100% similarity]
docs/reference-manual/algorithms/shell-molecular-dynamics.rst [moved from docs/reference-manual/shell-molecular-dynamics.rst with 100% similarity]
docs/reference-manual/algorithms/simulated-annealing.rst [moved from docs/reference-manual/simulated-annealing.rst with 100% similarity]
docs/reference-manual/algorithms/stochastic-dynamics.rst [moved from docs/reference-manual/stochastic-dynamics.rst with 100% similarity]
docs/reference-manual/analysis.rst
docs/reference-manual/analysis/bond-angle-dihedral.rst [moved from docs/reference-manual/bond-angle-dihedral.rst with 100% similarity]
docs/reference-manual/analysis/correlation-function.rst [moved from docs/reference-manual/correlation-function.rst with 100% similarity]
docs/reference-manual/analysis/covariance-analysis.rst [moved from docs/reference-manual/covariance-analysis.rst with 100% similarity]
docs/reference-manual/analysis/curve-fitting.rst [moved from docs/reference-manual/curve-fitting.rst with 100% similarity]
docs/reference-manual/analysis/dihedral-pca.rst [moved from docs/reference-manual/dihedral-pca.rst with 100% similarity]
docs/reference-manual/analysis/general-properties.rst [moved from docs/reference-manual/general-properties.rst with 100% similarity]
docs/reference-manual/analysis/interface-related.rst [moved from docs/reference-manual/interface-related.rst with 100% similarity]
docs/reference-manual/analysis/looking-at-trajectory.rst [moved from docs/reference-manual/looking-at-trajectory.rst with 100% similarity]
docs/reference-manual/analysis/mean-square-displacement.rst [moved from docs/reference-manual/mean-square-displacement.rst with 100% similarity]
docs/reference-manual/analysis/plots/dih-def.fig [moved from docs/reference-manual/plots/dih-def.fig with 100% similarity]
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docs/reference-manual/analysis/plots/distm.pdf [moved from docs/reference-manual/plots/distm.pdf with 100% similarity]
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docs/reference-manual/analysis/plots/dssp.pdf [moved from docs/reference-manual/plots/dssp.pdf with 100% similarity]
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docs/reference-manual/analysis/plots/hbond-insert.fig [moved from docs/reference-manual/plots/hbond-insert.fig with 100% similarity]
docs/reference-manual/analysis/plots/hbond-insert.pdf [moved from docs/reference-manual/plots/hbond-insert.pdf with 100% similarity]
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docs/reference-manual/analysis/plots/hbond.fig [moved from docs/reference-manual/plots/hbond.fig with 100% similarity]
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docs/reference-manual/analysis/plots/phipsi.fig [moved from docs/reference-manual/plots/phipsi.fig with 100% similarity]
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docs/reference-manual/analysis/plots/rama.pdf [moved from docs/reference-manual/plots/rama.pdf with 100% similarity]
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docs/reference-manual/analysis/plots/rdf.fig [moved from docs/reference-manual/plots/rdf.fig with 100% similarity]
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docs/reference-manual/analysis/plots/sgangle.pdf [moved from docs/reference-manual/plots/sgangle.pdf with 100% similarity]
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docs/reference-manual/analysis/protein-related.rst [moved from docs/reference-manual/protein-related.rst with 100% similarity]
docs/reference-manual/analysis/radial-distribution-function.rst [moved from docs/reference-manual/radial-distribution-function.rst with 100% similarity]
docs/reference-manual/analysis/radius-of-gyration.rst [moved from docs/reference-manual/radius-of-gyration.rst with 100% similarity]
docs/reference-manual/analysis/rmsd.rst [moved from docs/reference-manual/rmsd.rst with 100% similarity]
docs/reference-manual/analysis/using-groups.rst [moved from docs/reference-manual/using-groups.rst with 100% similarity]
docs/reference-manual/functions.rst
docs/reference-manual/functions/bonded-interactions.rst [moved from docs/reference-manual/bonded-interactions.rst with 100% similarity]
docs/reference-manual/functions/force-field.rst [moved from docs/reference-manual/force-field.rst with 100% similarity]
docs/reference-manual/functions/free-energy-interactions.rst [moved from docs/reference-manual/free-energy-interactions.rst with 100% similarity]
docs/reference-manual/functions/interaction-methods.rst [moved from docs/reference-manual/interaction-methods.rst with 100% similarity]
docs/reference-manual/functions/long-range-electrostatics.rst [moved from docs/reference-manual/long-range-electrostatics.rst with 100% similarity]
docs/reference-manual/functions/long-range-vdw.rst [moved from docs/reference-manual/long-range-vdw.rst with 100% similarity]
docs/reference-manual/functions/nonbonded-interactions.rst [moved from docs/reference-manual/nonbonded-interactions.rst with 100% similarity]
docs/reference-manual/functions/plots/angle.fig [moved from docs/reference-manual/plots/angle.fig with 100% similarity]
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