From 78735e7fcf9d0109fed2434a9b5797f602c1f3ca Mon Sep 17 00:00:00 2001 From: Paul Bauer Date: Thu, 26 Apr 2018 11:27:38 +0200 Subject: [PATCH] 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 --- docs/CMakeLists.txt | 251 +++++++++--------- docs/reference-manual/algorithms.rst | 30 +-- .../{ => algorithms}/brownian-dynamics.rst | 0 .../constraint-algorithms.rst | 0 .../{ => algorithms}/energy-minimization.rst | 0 .../{ => algorithms}/essential-dynamics.rst | 0 .../{ => algorithms}/expanded-ensemble.rst | 0 .../free-energy-calculations.rst | 0 .../{ => algorithms}/group-concept.rst | 0 .../{ => algorithms}/molecular-dynamics.rst | 0 .../{ => algorithms}/normal-mode-analysis.rst | 0 .../parallelization-domain-decomp.rst | 0 .../periodic-boundary-conditions.rst | 0 .../{ => algorithms}/plots/dd-cells.fig | 0 .../{ => algorithms}/plots/dd-cells.pdf | Bin .../{ => algorithms}/plots/dd-cells.svg | 0 .../{ => algorithms}/plots/dd-tric.fig | 0 .../{ => algorithms}/plots/dd-tric.pdf | Bin .../{ => algorithms}/plots/dd-tric.svg | 0 .../{ => algorithms}/plots/flowchart.pdf | Bin .../{ => algorithms}/plots/flowchart.svg | 0 .../{ => algorithms}/plots/free1.fig | 0 .../{ => algorithms}/plots/free1.pdf | Bin .../{ => algorithms}/plots/free1.svg | 0 .../{ => algorithms}/plots/free2.fig | 0 .../{ => algorithms}/plots/free2.pdf | Bin .../{ => algorithms}/plots/free2.svg | 0 .../{ => algorithms}/plots/leapfrog.pdf | Bin .../{ => algorithms}/plots/leapfrog.svg | 0 .../{ => algorithms}/plots/lincs.pdf | Bin .../{ => algorithms}/plots/lincs.svg | 0 .../{ => algorithms}/plots/maxwell.pdf | Bin .../{ => algorithms}/plots/maxwell.svg | 0 .../{ => algorithms}/plots/maxwell.xvg | 0 .../{ => algorithms}/plots/mpmd-pme.fig | 0 .../{ => algorithms}/plots/mpmd-pme.pdf | Bin .../{ => algorithms}/plots/mpmd-pme.svg | 0 .../{ => algorithms}/plots/nstric.fig | 0 .../{ => algorithms}/plots/nstric.pdf | Bin .../{ => algorithms}/plots/nstric.svg | 0 .../{ => algorithms}/plots/par-lincs2.fig | 0 .../{ => algorithms}/plots/par-lincs2.pdf | Bin .../{ => algorithms}/plots/par-lincs2.svg | 0 .../{ => algorithms}/plots/pbctric.fig | 0 .../{ => algorithms}/plots/pbctric.pdf | Bin .../{ => algorithms}/plots/pbctric.svg | 0 .../{ => algorithms}/plots/rhododec.ogl | 0 .../{ => algorithms}/plots/rhododec.pdf | Bin .../{ => algorithms}/plots/rhododec.svg | 0 .../{ => algorithms}/plots/truncoct.ogl | 0 .../{ => algorithms}/plots/truncoct.pdf | Bin .../{ => algorithms}/plots/truncoct.svg | 0 .../{ => algorithms}/plots/verlet-drift.pdf | Bin .../{ => algorithms}/plots/verlet-drift.svg | 0 .../{ => algorithms}/plots/verlet-drift.xvg | 0 .../{ => algorithms}/replica-exchange.rst | 0 .../shell-molecular-dynamics.rst | 0 .../{ => algorithms}/simulated-annealing.rst | 0 .../{ => algorithms}/stochastic-dynamics.rst | 0 docs/reference-manual/analysis.rst | 28 +- .../{ => analysis}/bond-angle-dihedral.rst | 0 .../{ => analysis}/correlation-function.rst | 0 .../{ => analysis}/covariance-analysis.rst | 0 .../{ => analysis}/curve-fitting.rst | 0 .../{ => analysis}/dihedral-pca.rst | 0 .../{ => analysis}/general-properties.rst | 0 .../{ => analysis}/interface-related.rst | 0 .../{ => analysis}/looking-at-trajectory.rst | 0 .../mean-square-displacement.rst | 0 .../{ => analysis}/plots/dih-def.fig | 0 .../{ => analysis}/plots/dih-def.pdf | Bin .../{ => analysis}/plots/dih-def.svg | 0 .../{ => analysis}/plots/distm.pdf | Bin .../{ => analysis}/plots/distm.svg | 0 .../{ => analysis}/plots/dssp.pdf | Bin .../{ => analysis}/plots/dssp.svg | 0 .../{ => analysis}/plots/hbond-insert.fig | 0 .../{ => analysis}/plots/hbond-insert.pdf | Bin .../{ => analysis}/plots/hbond-insert.svg | 0 .../{ => analysis}/plots/hbond.fig | 0 .../{ => analysis}/plots/hbond.pdf | Bin .../{ => analysis}/plots/hbond.svg | 0 .../{ => analysis}/plots/hpr-wheel.pdf | Bin .../{ => analysis}/plots/hpr-wheel.svg | 0 .../{ => analysis}/plots/msdwater.pdf | Bin .../{ => analysis}/plots/msdwater.svg | 0 .../{ => analysis}/plots/msdwater.xvg | 0 .../{ => analysis}/plots/ngmxdump.pdf | Bin .../{ => analysis}/plots/ngmxdump.svg | 0 .../{ => analysis}/plots/phipsi.fig | 0 .../{ => analysis}/plots/phipsi.pdf | Bin .../{ => analysis}/plots/phipsi.svg | 0 .../{ => analysis}/plots/rama.pdf | Bin .../{ => analysis}/plots/rama.svg | 0 .../{ => analysis}/plots/rama.xvg | 0 .../{ => analysis}/plots/rdf.fig | 0 .../{ => analysis}/plots/rdf.pdf | Bin .../{ => analysis}/plots/rdf.svg | 0 .../{ => analysis}/plots/rdfO-O.pdf | Bin .../{ => analysis}/plots/rdfO-O.svg | 0 .../{ => analysis}/plots/rdfO-O.xvg | 0 .../{ => analysis}/plots/sgangle.pdf | Bin .../{ => analysis}/plots/sgangle.svg | 0 .../{ => analysis}/protein-related.rst | 0 .../radial-distribution-function.rst | 0 .../{ => analysis}/radius-of-gyration.rst | 0 docs/reference-manual/{ => analysis}/rmsd.rst | 0 .../{ => analysis}/using-groups.rst | 0 docs/reference-manual/functions.rst | 18 +- .../{ => functions}/bonded-interactions.rst | 0 .../{ => functions}/force-field.rst | 0 .../free-energy-interactions.rst | 0 .../{ => functions}/interaction-methods.rst | 0 .../long-range-electrostatics.rst | 0 .../{ => functions}/long-range-vdw.rst | 0 .../nonbonded-interactions.rst | 0 .../{ => functions}/plots/angle.fig | 0 .../{ => functions}/plots/angle.pdf | Bin .../{ => functions}/plots/angle.svg | 0 .../{ => functions}/plots/bstretch.fig | 0 .../{ => functions}/plots/bstretch.pdf | Bin .../{ => functions}/plots/bstretch.svg | 0 .../{ => functions}/plots/chain.fig | 0 .../{ => functions}/plots/chain.pdf | Bin .../{ => functions}/plots/chain.svg | 0 .../{ => functions}/plots/dummies.fig | 0 .../{ => functions}/plots/dummies.pdf | Bin .../{ => functions}/plots/dummies.svg | 0 .../{ => functions}/plots/f-bham.pdf | Bin .../{ => functions}/plots/f-bham.svg | 0 .../{ => functions}/plots/f-bham.xvg | 0 .../{ => functions}/plots/f-dih.pdf | Bin .../{ => functions}/plots/f-dih.svg | 0 .../{ => functions}/plots/f-dih.xvg | 0 .../{ => functions}/plots/f-dr.pdf | Bin .../{ => functions}/plots/f-dr.svg | 0 .../{ => functions}/plots/f-dr.xvg | 0 .../{ => functions}/plots/f-imps.pdf | Bin .../{ => functions}/plots/f-imps.xvg | 0 .../{ => functions}/plots/f-lj.pdf | Bin .../{ => functions}/plots/f-lj.svg | 0 .../{ => functions}/plots/f-lj.xvg | 0 .../{ => functions}/plots/f-morse.pdf | Bin .../{ => functions}/plots/f-morse.svg | 0 .../{ => functions}/plots/f-morse.xvg | 0 .../{ => functions}/plots/f-pr.pdf | Bin .../{ => functions}/plots/f-pr.svg | 0 .../{ => functions}/plots/f-pr.xvg | 0 .../{ => functions}/plots/f-rbs.pdf | Bin .../{ => functions}/plots/f-rbs.svg | 0 .../{ => functions}/plots/f-rbs.xvg | 0 .../{ => functions}/plots/fbposres.pdf | Bin .../{ => functions}/plots/fbposres.svg | 0 .../{ => functions}/plots/fbposres.xvg | 0 .../{ => functions}/plots/fig-02.pdf | Bin .../{ => functions}/plots/fig-02.svg | 0 .../{ => functions}/plots/fig-04.pdf | Bin .../{ => functions}/plots/fig-04.svg | 0 .../{ => functions}/plots/ring-imp.fig | 0 .../{ => functions}/plots/ring-imp.pdf | Bin .../{ => functions}/plots/ring-imp.svg | 0 .../{ => functions}/plots/softcore.pdf | Bin .../{ => functions}/plots/softcore.svg | 0 .../{ => functions}/plots/softcore.xvg | 0 .../{ => functions}/plots/subst-im.fig | 0 .../{ => functions}/plots/subst-im.pdf | Bin .../{ => functions}/plots/subst-im.svg | 0 .../{ => functions}/plots/tetra-im.fig | 0 .../{ => functions}/plots/tetra-im.pdf | Bin .../{ => functions}/plots/tetra-im.svg | 0 .../{ => functions}/plots/vcrf.pdf | Bin .../{ => functions}/plots/vcrf.svg | 0 .../{ => functions}/plots/vcrf.xvg | 0 .../{ => functions}/plots/vsite-4fdn.pdf | Bin .../{ => functions}/plots/vsite-4fdn.svg | 0 .../{ => functions}/polarization.rst | 0 .../{ => functions}/restraints.rst | 0 docs/reference-manual/special.rst | 26 +- docs/reference-manual/{ => special}/awh.rst | 0 .../{ => special}/comp-electrophys.rst | 0 .../{ => special}/electric-fields.rst | 0 .../{ => special}/enforced-rotation.rst | 0 .../free-energy-implementation.rst | 0 .../{ => special}/free-energy-pmf.rst | 0 .../{ => special}/membrane-embedding.rst | 0 .../{ => special}/plots/awh-invN.pdf | Bin .../{ => special}/plots/awh-invN.svg | 0 .../{ => special}/plots/awh-pmfs.pdf | Bin .../{ => special}/plots/awh-pmfs.svg | 0 .../{ => special}/plots/awh-sampleweights.pdf | Bin .../{ => special}/plots/awh-sampleweights.svg | 0 .../{ => special}/plots/awh-traj.pdf | Bin .../{ => special}/plots/awh-traj.svg | 0 .../{ => special}/plots/compelsetup.pdf | Bin .../{ => special}/plots/dumaro.fig | 0 .../{ => special}/plots/dumaro.pdf | Bin .../{ => special}/plots/dumaro.svg | 0 .../{ => special}/plots/dumtypes.fig | 0 .../{ => special}/plots/dumtypes.pdf | Bin .../{ => special}/plots/dumtypes.svg | 0 .../{ => special}/plots/equipotential.pdf | 0 .../{ => special}/plots/field.pdf | Bin .../{ => special}/plots/field.svg | 0 .../{ => special}/plots/field.xvg | 0 .../{ => special}/plots/gaussians.pdf | 0 .../{ => special}/plots/pull.pdf | Bin .../{ => special}/plots/pull.svg | 0 .../{ => special}/plots/pulldirrel.fig | 0 .../{ => special}/plots/pulldirrel.pdf | Bin .../{ => special}/plots/pulldirrel.svg | 0 .../{ => special}/plots/pullref.pdf | Bin .../{ => special}/plots/pullref.svg | 0 .../{ => special}/plots/rotation.pdf | 0 .../{ => special}/pulling.rst | 0 docs/reference-manual/{ => special}/qmmm.rst | 0 .../{ => special}/remove-fast-dgf.rst | 0 .../tabulated-interaction-functions.rst | 0 .../{ => special}/viscosity-calculation.rst | 0 .../{ => special}/vmd-imd.rst | 0 docs/reference-manual/topologies.rst | 14 +- .../constraint-algorithm-section.rst | 0 .../force-field-organization.rst | 0 .../{ => topologies}/molecule-definition.rst | 0 .../{ => topologies}/parameter-files.rst | 0 .../{ => topologies}/particle-type.rst | 0 .../{ => topologies}/pdb2gmx-input-files.rst | 0 .../topology-file-formats.rst | 0 227 files changed, 187 insertions(+), 180 deletions(-) rename docs/reference-manual/{ => algorithms}/brownian-dynamics.rst (100%) rename docs/reference-manual/{ => algorithms}/constraint-algorithms.rst (100%) rename docs/reference-manual/{ => algorithms}/energy-minimization.rst (100%) rename docs/reference-manual/{ => algorithms}/essential-dynamics.rst (100%) rename docs/reference-manual/{ => algorithms}/expanded-ensemble.rst (100%) rename docs/reference-manual/{ => algorithms}/free-energy-calculations.rst (100%) rename docs/reference-manual/{ => algorithms}/group-concept.rst (100%) rename docs/reference-manual/{ => algorithms}/molecular-dynamics.rst (100%) rename docs/reference-manual/{ => algorithms}/normal-mode-analysis.rst (100%) rename docs/reference-manual/{ => algorithms}/parallelization-domain-decomp.rst (100%) rename docs/reference-manual/{ => algorithms}/periodic-boundary-conditions.rst (100%) rename docs/reference-manual/{ => algorithms}/plots/dd-cells.fig (100%) rename docs/reference-manual/{ => algorithms}/plots/dd-cells.pdf (100%) rename docs/reference-manual/{ => algorithms}/plots/dd-cells.svg (100%) rename docs/reference-manual/{ 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rename docs/reference-manual/{ => algorithms}/stochastic-dynamics.rst (100%) rename docs/reference-manual/{ => analysis}/bond-angle-dihedral.rst (100%) rename docs/reference-manual/{ => analysis}/correlation-function.rst (100%) rename docs/reference-manual/{ => analysis}/covariance-analysis.rst (100%) rename docs/reference-manual/{ => analysis}/curve-fitting.rst (100%) rename docs/reference-manual/{ => analysis}/dihedral-pca.rst (100%) rename docs/reference-manual/{ => analysis}/general-properties.rst (100%) rename docs/reference-manual/{ => analysis}/interface-related.rst (100%) rename docs/reference-manual/{ => analysis}/looking-at-trajectory.rst (100%) rename docs/reference-manual/{ => analysis}/mean-square-displacement.rst (100%) rename docs/reference-manual/{ => analysis}/plots/dih-def.fig (100%) rename docs/reference-manual/{ => analysis}/plots/dih-def.pdf (100%) rename docs/reference-manual/{ => analysis}/plots/dih-def.svg (100%) rename docs/reference-manual/{ => 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special}/plots/field.svg (100%) rename docs/reference-manual/{ => special}/plots/field.xvg (100%) rename docs/reference-manual/{ => special}/plots/gaussians.pdf (100%) rename docs/reference-manual/{ => special}/plots/pull.pdf (100%) rename docs/reference-manual/{ => special}/plots/pull.svg (100%) rename docs/reference-manual/{ => special}/plots/pulldirrel.fig (100%) rename docs/reference-manual/{ => special}/plots/pulldirrel.pdf (100%) rename docs/reference-manual/{ => special}/plots/pulldirrel.svg (100%) rename docs/reference-manual/{ => special}/plots/pullref.pdf (100%) rename docs/reference-manual/{ => special}/plots/pullref.svg (100%) rename docs/reference-manual/{ => special}/plots/rotation.pdf (100%) rename docs/reference-manual/{ => special}/pulling.rst (100%) rename docs/reference-manual/{ => special}/qmmm.rst (100%) rename docs/reference-manual/{ => special}/remove-fast-dgf.rst (100%) rename docs/reference-manual/{ => special}/tabulated-interaction-functions.rst (100%) rename docs/reference-manual/{ => special}/viscosity-calculation.rst (100%) rename docs/reference-manual/{ => special}/vmd-imd.rst (100%) rename docs/reference-manual/{ => topologies}/constraint-algorithm-section.rst (100%) rename docs/reference-manual/{ => topologies}/force-field-organization.rst (100%) rename docs/reference-manual/{ => topologies}/molecule-definition.rst (100%) rename docs/reference-manual/{ => topologies}/parameter-files.rst (100%) rename docs/reference-manual/{ => topologies}/particle-type.rst (100%) rename docs/reference-manual/{ => topologies}/pdb2gmx-input-files.rst (100%) rename docs/reference-manual/{ => topologies}/topology-file-formats.rst (100%) diff --git a/docs/CMakeLists.txt b/docs/CMakeLists.txt index cc609b52ea..9b38d75fac 100644 --- 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 f262a3f0b4..a6dd482809 100644 --- 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 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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 b/docs/reference-manual/analysis.rst index 5e6b949eb0..4c698f9bdc 100644 --- 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 similarity index 100% rename from docs/reference-manual/correlation-function.rst rename to docs/reference-manual/analysis/correlation-function.rst diff --git a/docs/reference-manual/covariance-analysis.rst b/docs/reference-manual/analysis/covariance-analysis.rst similarity index 100% rename from docs/reference-manual/covariance-analysis.rst rename to docs/reference-manual/analysis/covariance-analysis.rst diff --git a/docs/reference-manual/curve-fitting.rst b/docs/reference-manual/analysis/curve-fitting.rst similarity index 100% rename from docs/reference-manual/curve-fitting.rst rename to docs/reference-manual/analysis/curve-fitting.rst diff --git a/docs/reference-manual/dihedral-pca.rst b/docs/reference-manual/analysis/dihedral-pca.rst similarity index 100% rename from docs/reference-manual/dihedral-pca.rst rename to docs/reference-manual/analysis/dihedral-pca.rst diff --git a/docs/reference-manual/general-properties.rst b/docs/reference-manual/analysis/general-properties.rst similarity index 100% rename from docs/reference-manual/general-properties.rst rename to docs/reference-manual/analysis/general-properties.rst diff --git a/docs/reference-manual/interface-related.rst b/docs/reference-manual/analysis/interface-related.rst similarity index 100% rename from docs/reference-manual/interface-related.rst rename to docs/reference-manual/analysis/interface-related.rst diff --git a/docs/reference-manual/looking-at-trajectory.rst b/docs/reference-manual/analysis/looking-at-trajectory.rst similarity index 100% rename from docs/reference-manual/looking-at-trajectory.rst rename to docs/reference-manual/analysis/looking-at-trajectory.rst diff --git a/docs/reference-manual/mean-square-displacement.rst b/docs/reference-manual/analysis/mean-square-displacement.rst similarity index 100% rename from docs/reference-manual/mean-square-displacement.rst rename to docs/reference-manual/analysis/mean-square-displacement.rst diff --git a/docs/reference-manual/plots/dih-def.fig b/docs/reference-manual/analysis/plots/dih-def.fig similarity index 100% rename from docs/reference-manual/plots/dih-def.fig rename to docs/reference-manual/analysis/plots/dih-def.fig diff --git a/docs/reference-manual/plots/dih-def.pdf b/docs/reference-manual/analysis/plots/dih-def.pdf similarity index 100% rename from docs/reference-manual/plots/dih-def.pdf rename to docs/reference-manual/analysis/plots/dih-def.pdf diff --git a/docs/reference-manual/plots/dih-def.svg b/docs/reference-manual/analysis/plots/dih-def.svg similarity index 100% rename from docs/reference-manual/plots/dih-def.svg rename to docs/reference-manual/analysis/plots/dih-def.svg diff --git a/docs/reference-manual/plots/distm.pdf 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docs/reference-manual/radius-of-gyration.rst 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 similarity index 100% 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 similarity index 100% rename from docs/reference-manual/using-groups.rst rename to docs/reference-manual/analysis/using-groups.rst diff --git a/docs/reference-manual/functions.rst b/docs/reference-manual/functions.rst index d546bfd7ae..d8258910dd 100644 --- 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 similarity index 100% rename from docs/reference-manual/bonded-interactions.rst 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 similarity index 100% rename from docs/reference-manual/force-field.rst 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 similarity index 100% rename from docs/reference-manual/free-energy-interactions.rst rename to docs/reference-manual/functions/free-energy-interactions.rst diff --git a/docs/reference-manual/interaction-methods.rst b/docs/reference-manual/functions/interaction-methods.rst similarity index 100% rename from docs/reference-manual/interaction-methods.rst rename to docs/reference-manual/functions/interaction-methods.rst diff --git a/docs/reference-manual/long-range-electrostatics.rst b/docs/reference-manual/functions/long-range-electrostatics.rst similarity index 100% rename from docs/reference-manual/long-range-electrostatics.rst rename to docs/reference-manual/functions/long-range-electrostatics.rst diff --git a/docs/reference-manual/long-range-vdw.rst b/docs/reference-manual/functions/long-range-vdw.rst similarity index 100% rename from docs/reference-manual/long-range-vdw.rst rename to docs/reference-manual/functions/long-range-vdw.rst diff --git a/docs/reference-manual/nonbonded-interactions.rst 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bc94671d81..45b7f1ef2c 100644 --- 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 similarity index 100% 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 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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 57b76f236a..53bc0c2c88 100644 --- 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 diff --git a/docs/reference-manual/molecule-definition.rst b/docs/reference-manual/topologies/molecule-definition.rst similarity index 100% rename from docs/reference-manual/molecule-definition.rst rename to docs/reference-manual/topologies/molecule-definition.rst diff --git a/docs/reference-manual/parameter-files.rst b/docs/reference-manual/topologies/parameter-files.rst similarity index 100% rename from docs/reference-manual/parameter-files.rst rename to docs/reference-manual/topologies/parameter-files.rst diff --git a/docs/reference-manual/particle-type.rst b/docs/reference-manual/topologies/particle-type.rst similarity index 100% rename from docs/reference-manual/particle-type.rst rename to docs/reference-manual/topologies/particle-type.rst diff --git a/docs/reference-manual/pdb2gmx-input-files.rst b/docs/reference-manual/topologies/pdb2gmx-input-files.rst similarity index 100% rename from docs/reference-manual/pdb2gmx-input-files.rst rename to docs/reference-manual/topologies/pdb2gmx-input-files.rst diff --git a/docs/reference-manual/topology-file-formats.rst b/docs/reference-manual/topologies/topology-file-formats.rst similarity index 100% rename from docs/reference-manual/topology-file-formats.rst rename to docs/reference-manual/topologies/topology-file-formats.rst -- 2.22.0