Move manual repo into code repo, and make it build
authorMark Abraham <mark.j.abraham@gmail.com>
Fri, 11 Oct 2013 15:38:38 +0000 (17:38 +0200)
committerGerrit Code Review <gerrit@gerrit.gromacs.org>
Wed, 16 Oct 2013 18:39:41 +0000 (20:39 +0200)
commit6876e9d9c2b776bccd72ac280b8d8d04ab22324f
treeee9f10402fd13316263159c765418e540950a8ef
parent0b23449442ad0b0c1cc827bcb90d698f00292be3
Move manual repo into code repo, and make it build

Supersedes I12066943a1. Contains all the manual content from
Ic1f74befee88. Manual history is lost - nobody was super
keen on keeping it, and the git repos still exist if we
care later on.

If the user opts in with cmake .. -DGMX_BUILD_MANUAL=on, this patch
detects whether a manual build is possible. If so, creates a make
target called "manual" which will build the PDF manual in the manual
sub-directory. The manual is never automatically made, and the
supporting detection is never automatically run. Thus, a normal
GROMACS user or developer never has any problems.

Appendix D (compendium of man pages) is removed. The header of chapter
7 always contained advice on where to get that content. That advice
is updated.

Also
* streamlined manual CMakeLists.txt for new context
* removed outdated \gmxmajor{} LaTeX macro
* noted some TODOs for future work

Refs #1177

Change-Id: I7e56a01182fbd9803222c8d47cb8a9c88d7b932a
209 files changed:
CMakeLists.txt
manual/CMakeLists.txt [new file with mode: 0644]
manual/README [new file with mode: 0644]
manual/UseLATEX.cmake [new file with mode: 0755]
manual/algorithms.tex [new file with mode: 0644]
manual/analyse.tex [new file with mode: 0644]
manual/averages.tex [new file with mode: 0644]
manual/defunits.tex [new file with mode: 0644]
manual/fancy.sty [new file with mode: 0644]
manual/files.tex [new file with mode: 0644]
manual/forcefield.tex [new file with mode: 0644]
manual/gmxmanual.cls [new file with mode: 0644]
manual/gmxpar.tex [new file with mode: 0644]
manual/gromacs.tex [new file with mode: 0644]
manual/here.sty [new file with mode: 0644]
manual/hfill.ist [new file with mode: 0644]
manual/implement.tex [new file with mode: 0644]
manual/index.gmx [new file with mode: 0644]
manual/install.tex [new file with mode: 0644]
manual/intro.tex [new file with mode: 0644]
manual/macros.tex [new file with mode: 0644]
manual/mkmdp [new file with mode: 0755]
manual/mkproglist [new file with mode: 0755]
manual/monster.bib [new file with mode: 0644]
manual/picins.sty [new file with mode: 0644]
manual/plots/adress.png [new file with mode: 0644]
manual/plots/angle.eps [new file with mode: 0644]
manual/plots/angle.fig [new file with mode: 0644]
manual/plots/angle.pdf [new file with mode: 0644]
manual/plots/bstretch.eps [new file with mode: 0644]
manual/plots/bstretch.fig [new file with mode: 0644]
manual/plots/bstretch.pdf [new file with mode: 0644]
manual/plots/chain.eps [new file with mode: 0644]
manual/plots/chain.fig [new file with mode: 0644]
manual/plots/chain.pdf [new file with mode: 0644]
manual/plots/dd-cells.eps [new file with mode: 0644]
manual/plots/dd-cells.fig [new file with mode: 0644]
manual/plots/dd-cells.pdf [new file with mode: 0644]
manual/plots/dd-tric.eps [new file with mode: 0644]
manual/plots/dd-tric.fig [new file with mode: 0644]
manual/plots/dd-tric.pdf [new file with mode: 0644]
manual/plots/decomp.eps [new file with mode: 0644]
manual/plots/decomp.fig [new file with mode: 0644]
manual/plots/decomp.pdf [new file with mode: 0644]
manual/plots/dih-def.eps [new file with mode: 0644]
manual/plots/dih-def.fig [new file with mode: 0644]
manual/plots/dih-def.pdf [new file with mode: 0644]
manual/plots/dih.eps [new file with mode: 0644]
manual/plots/dih.fig [new file with mode: 0644]
manual/plots/dih.pdf [new file with mode: 0644]
manual/plots/distm.eps [new file with mode: 0644]
manual/plots/distm.pdf [new file with mode: 0644]
manual/plots/drift-all.eps [new file with mode: 0644]
manual/plots/drift-all.pdf [new file with mode: 0644]
manual/plots/drift-all.xvg [new file with mode: 0644]
manual/plots/dssp.eps [new file with mode: 0644]
manual/plots/dssp.pdf [new file with mode: 0644]
manual/plots/dumaro.eps [new file with mode: 0644]
manual/plots/dumaro.fig [new file with mode: 0644]
manual/plots/dumaro.pdf [new file with mode: 0644]
manual/plots/dummies.eps [new file with mode: 0644]
manual/plots/dummies.fig [new file with mode: 0644]
manual/plots/dummies.pdf [new file with mode: 0644]
manual/plots/dumtypes.eps [new file with mode: 0644]
manual/plots/dumtypes.fig [new file with mode: 0644]
manual/plots/dumtypes.pdf [new file with mode: 0644]
manual/plots/equipotential.pdf [new file with mode: 0644]
manual/plots/f-angle.eps [new file with mode: 0644]
manual/plots/f-angle.pdf [new file with mode: 0644]
manual/plots/f-angle.xvg [new file with mode: 0644]
manual/plots/f-bham.eps [new file with mode: 0644]
manual/plots/f-bham.pdf [new file with mode: 0644]
manual/plots/f-bham.xvg [new file with mode: 0644]
manual/plots/f-bond.eps [new file with mode: 0644]
manual/plots/f-bond.pdf [new file with mode: 0644]
manual/plots/f-bond.xvg [new file with mode: 0644]
manual/plots/f-dih.eps [new file with mode: 0644]
manual/plots/f-dih.pdf [new file with mode: 0644]
manual/plots/f-dih.xvg [new file with mode: 0644]
manual/plots/f-dr.eps [new file with mode: 0644]
manual/plots/f-dr.pdf [new file with mode: 0644]
manual/plots/f-dr.xvg [new file with mode: 0644]
manual/plots/f-imps.eps [new file with mode: 0644]
manual/plots/f-imps.pdf [new file with mode: 0644]
manual/plots/f-imps.xvg [new file with mode: 0644]
manual/plots/f-lj.eps [new file with mode: 0644]
manual/plots/f-lj.pdf [new file with mode: 0644]
manual/plots/f-lj.xvg [new file with mode: 0644]
manual/plots/f-morse.eps [new file with mode: 0644]
manual/plots/f-morse.pdf [new file with mode: 0644]
manual/plots/f-morse.xvg [new file with mode: 0644]
manual/plots/f-pr.eps [new file with mode: 0644]
manual/plots/f-pr.pdf [new file with mode: 0644]
manual/plots/f-pr.xvg [new file with mode: 0644]
manual/plots/f-rbs.eps [new file with mode: 0644]
manual/plots/f-rbs.pdf [new file with mode: 0644]
manual/plots/f-rbs.xvg [new file with mode: 0644]
manual/plots/fbposres.eps [new file with mode: 0644]
manual/plots/fbposres.pdf [new file with mode: 0644]
manual/plots/fbposres.xvg [new file with mode: 0644]
manual/plots/flowchart.eps [new file with mode: 0644]
manual/plots/flowchart.pdf [new file with mode: 0644]
manual/plots/fp-highres.eps [new file with mode: 0644]
manual/plots/fp-highres.jpg [new file with mode: 0644]
manual/plots/free1.eps [new file with mode: 0644]
manual/plots/free1.fig [new file with mode: 0644]
manual/plots/free1.pdf [new file with mode: 0644]
manual/plots/free2.eps [new file with mode: 0644]
manual/plots/free2.fig [new file with mode: 0644]
manual/plots/free2.pdf [new file with mode: 0644]
manual/plots/gaussians.pdf [new file with mode: 0644]
manual/plots/hbond-insert.eps [new file with mode: 0644]
manual/plots/hbond-insert.fig [new file with mode: 0644]
manual/plots/hbond-insert.pdf [new file with mode: 0644]
manual/plots/hbond.eps [new file with mode: 0644]
manual/plots/hbond.fig [new file with mode: 0644]
manual/plots/hbond.pdf [new file with mode: 0644]
manual/plots/hpr-wheel.eps [new file with mode: 0644]
manual/plots/hpr-wheel.pdf [new file with mode: 0644]
manual/plots/int-mat.eps [new file with mode: 0644]
manual/plots/int-mat.pdf [new file with mode: 0644]
manual/plots/leapfrog.eps [new file with mode: 0644]
manual/plots/leapfrog.pdf [new file with mode: 0644]
manual/plots/lincs.eps [new file with mode: 0644]
manual/plots/lincs.pdf [new file with mode: 0644]
manual/plots/maxwell.eps [new file with mode: 0644]
manual/plots/maxwell.pdf [new file with mode: 0644]
manual/plots/maxwell.xvg [new file with mode: 0644]
manual/plots/mdpar.eps [new file with mode: 0644]
manual/plots/mdpar.pdf [new file with mode: 0644]
manual/plots/mpmd-pme.eps [new file with mode: 0644]
manual/plots/mpmd-pme.fig [new file with mode: 0644]
manual/plots/mpmd-pme.pdf [new file with mode: 0644]
manual/plots/msdwater.eps [new file with mode: 0644]
manual/plots/msdwater.pdf [new file with mode: 0644]
manual/plots/msdwater.xvg [new file with mode: 0644]
manual/plots/myvi [new file with mode: 0755]
manual/plots/ngmxdump.eps [new file with mode: 0644]
manual/plots/ngmxdump.pdf [new file with mode: 0644]
manual/plots/nstric.eps [new file with mode: 0644]
manual/plots/nstric.fig [new file with mode: 0644]
manual/plots/nstric.pdf [new file with mode: 0644]
manual/plots/par-lincs2.eps [new file with mode: 0644]
manual/plots/par-lincs2.fig [new file with mode: 0644]
manual/plots/par-lincs2.pdf [new file with mode: 0644]
manual/plots/parsort.eps [new file with mode: 0644]
manual/plots/parsort.fig [new file with mode: 0644]
manual/plots/parsort.pdf [new file with mode: 0644]
manual/plots/pbctric.eps [new file with mode: 0644]
manual/plots/pbctric.fig [new file with mode: 0644]
manual/plots/pbctric.pdf [new file with mode: 0644]
manual/plots/peregrine.jpg [new file with mode: 0644]
manual/plots/phipsi.eps [new file with mode: 0644]
manual/plots/phipsi.fig [new file with mode: 0644]
manual/plots/phipsi.pdf [new file with mode: 0644]
manual/plots/pull.eps [new file with mode: 0644]
manual/plots/pull.pdf [new file with mode: 0644]
manual/plots/pullref.eps [new file with mode: 0644]
manual/plots/pullref.pdf [new file with mode: 0644]
manual/plots/rama.eps [new file with mode: 0644]
manual/plots/rama.pdf [new file with mode: 0644]
manual/plots/rama.xvg [new file with mode: 0644]
manual/plots/rdf.eps [new file with mode: 0644]
manual/plots/rdf.fig [new file with mode: 0644]
manual/plots/rdf.pdf [new file with mode: 0644]
manual/plots/rdfO-O.eps [new file with mode: 0644]
manual/plots/rdfO-O.pdf [new file with mode: 0644]
manual/plots/rdfO-O.xvg [new file with mode: 0644]
manual/plots/rhododec.eps [new file with mode: 0644]
manual/plots/rhododec.ogl [new file with mode: 0644]
manual/plots/rhododec.pdf [new file with mode: 0644]
manual/plots/ring-imp.eps [new file with mode: 0644]
manual/plots/ring-imp.fig [new file with mode: 0644]
manual/plots/ring-imp.pdf [new file with mode: 0644]
manual/plots/ring.eps [new file with mode: 0644]
manual/plots/ring.pdf [new file with mode: 0644]
manual/plots/rotation.pdf [new file with mode: 0644]
manual/plots/sgangle.eps [new file with mode: 0644]
manual/plots/sgangle.fig [new file with mode: 0644]
manual/plots/sgangle.pdf [new file with mode: 0644]
manual/plots/shiftf.eps [new file with mode: 0644]
manual/plots/shiftf.pdf [new file with mode: 0644]
manual/plots/softcore.eps [new file with mode: 0644]
manual/plots/softcore.pdf [new file with mode: 0644]
manual/plots/softcore.xvg [new file with mode: 0644]
manual/plots/subst-im.eps [new file with mode: 0644]
manual/plots/subst-im.fig [new file with mode: 0644]
manual/plots/subst-im.pdf [new file with mode: 0644]
manual/plots/tetra-im.eps [new file with mode: 0644]
manual/plots/tetra-im.fig [new file with mode: 0644]
manual/plots/tetra-im.pdf [new file with mode: 0644]
manual/plots/truncoct.eps [new file with mode: 0644]
manual/plots/truncoct.ogl [new file with mode: 0644]
manual/plots/truncoct.pdf [new file with mode: 0644]
manual/plots/vcrf.eps [new file with mode: 0644]
manual/plots/vcrf.pdf [new file with mode: 0644]
manual/plots/vcrf.xvg [new file with mode: 0644]
manual/plots/verlet-drift.eps [new file with mode: 0644]
manual/plots/verlet-drift.pdf [new file with mode: 0644]
manual/plots/verlet-drift.xvg [new file with mode: 0644]
manual/plots/vsite-4fdn.eps [new file with mode: 0644]
manual/plots/vsite-4fdn.pdf [new file with mode: 0644]
manual/programs.tex [new file with mode: 0644]
manual/proteins.bst [new file with mode: 0644]
manual/special.tex [new file with mode: 0644]
manual/subindex [new file with mode: 0755]
manual/topology.tex [new file with mode: 0644]
manual/underscore.sty [new file with mode: 0644]
manual/unpubl.bib [new file with mode: 0644]