Squashed commits of big pdf_manual merge

This is an attempt to clean up the history before merging
geodynamics/pdf_manual back into master. It looks like we had part of
the commits already in.

This is the list of original commits:

commit c9ab3eac1eff310d7934680cda0c4d8f24b50612
Author: Timo Heister <timo.heister@gmail.com>
Date:   Fri Sep 19 12:01:43 2014 -0400

    fix citation

commit fca6fab20cf3334f91baeee8b1ddc4540d4dd059
Author: Timo Heister <timo.heister@gmail.com>
Date:   Fri Sep 19 12:00:50 2014 -0400

    add table

commit d4df85cd49794f81385cbdd5ca0803f79b01c1d8
Author: Timo Heister <timo.heister@gmail.com>
Date:   Fri Sep 19 12:00:42 2014 -0400

    formatting, typos

commit a79e6acaa88f8304a2987c3a15b9d28d5f773576
Author: Timo Heister <timo.heister@gmail.com>
Date:   Thu Sep 18 14:38:53 2014 -0400

    fix bibtex stuff

    (you need sphinxcontrib-bibtex installed)

commit 39b773c5c7d2ceb797c846b32e5b52e449681537
Author: Timo Heister <timo.heister@gmail.com>
Date:   Thu Sep 18 14:20:52 2014 -0400

    move figures in subfolder

commit a4a8fce790070f3b4c7c98db168c945107bd5266
Author: Timo Heister <timo.heister@gmail.com>
Date:   Thu Sep 18 14:16:05 2014 -0400

    center logo better

commit 362e6cd89ef68998acfa6cc20b4e44eb3295d8c8
Author: Timo Heister <timo.heister@gmail.com>
Date:   Thu Sep 18 14:13:15 2014 -0400

    smaller logo

    also clean up conf.py

commit f8d4e06a8bc987cad0e53083d5828f0da103fed4
Author: Sanne Cottaar <sanne.cottaar@gmail.com>
Date:   Thu Sep 18 18:46:44 2014 +0100

    added figures

commit cd5f32311404915f32939b83997cfefc5bd2428e
Author: Sanne Cottaar <sanne.cottaar@gmail.com>
Date:   Thu Sep 18 14:21:31 2014 +0100

    methods from paper

commit 32cf392573113caa2e4b5936707259cbd1e8f02c
Merge: 3334aa6 f47514f
Author: Sanne Cottaar <sanne.cottaar@gmail.com>
Date:   Thu Sep 18 11:55:29 2014 +0100

    merging

commit 3334aa6d94e6c08f49c1a456218409f26f184ce7
Author: Sanne Cottaar <sanne.cottaar@gmail.com>
Date:   Wed Sep 17 17:34:08 2014 +0100

    typo

commit d857182bf78ec43b31e0918b7c28dad7cbe44157
Author: Sanne Cottaar <sanne.cottaar@gmail.com>
Date:   Wed Sep 17 16:26:43 2014 +0100

    add files

commit 9d5bf04b6a2676baa5f31159edf4f57ce060266c
Author: Sanne Cottaar <sanne.cottaar@gmail.com>
Date:   Wed Sep 17 16:26:11 2014 +0100

    some methods section, broken citations, rewrite to do

commit 1b08f60419f7bd1c76b2f9f023265589d008c4be
Author: Timo Heister <timo.heister@gmail.com>
Date:   Wed Sep 10 09:10:13 2014 -0400

    write some overview

commit ab0844e9cc8716dd06d92e592df5c4acf4a5a98e
Author: Timo Heister <timo.heister@gmail.com>
Date:   Mon Sep 8 08:49:07 2014 -0400

    doc: add overview, fix examples

commit ee49c80057a0c6a64e63fb9496f880b38aec5029
Author: Timo Heister <timo.heister@gmail.com>
Date:   Mon Sep 8 08:44:45 2014 -0400

    include cig title in pdf

commit a012ce3ea1881bdcdb6efb9fbb82fda839835c04
Author: Timo Heister <timo.heister@gmail.com>
Date:   Fri Aug 29 10:11:24 2014 -0400

    play with latex format

commit dce9539ed0ebefab999c77fba774c76f5eb51e11
Author: Timo Heister <timo.heister@gmail.com>
Date:   Fri Aug 29 10:10:28 2014 -0400

    doc: move examples to beginning

commit 48bc26cdbdcff96c2177d4d7b21d44197589c71a
Author: Timo Heister <timo.heister@gmail.com>
Date:   Fri Aug 29 10:10:18 2014 -0400

    include tutorials in doc, rework text

    - tutorials are now included in Example doc section
    - for this: "if main" needed, fix finding burnman if not installed
    - Example section is somewhat work in progress
    - experiment with including code directly
    - include a picture as a test

commit 2e2b59529e8cfea3d7b57d25726da753bfae33de
Author: ian-r-rose <ian.r.rose@gmail.com>
Date:   Wed Jun 18 09:24:29 2014 -0700

    Split up onto two lines

commit 3a0ae3040cb0b71c8775d53d91f51ae0ef5c66f5
Author: ian-r-rose <ian.r.rose@gmail.com>
Date:   Wed Jun 18 09:23:54 2014 -0700

    Don't need to return mineral.

commit eb63c49d93c8748f56cf0b3d2d260c2fb28ef79a
Author: ian-r-rose <ian.r.rose@gmail.com>
Date:   Wed Jun 18 09:13:07 2014 -0700

    More text

commit b66f17029dd25d9e77dae0a8a5aa0884d862e6ad
Author: sannecottaar <sanne.cottaar@gmail.com>
Date:   Wed Jun 18 11:51:02 2014 +0100

    % to Fraction in figure label

commit d3b32c5164161846de05486a04a9d4af4156b679
Author: sannecottaar <sanne.cottaar@gmail.com>
Date:   Wed Jun 18 11:48:00 2014 +0100

    minor text changes

    changed 'mantle' to 'lower mantle'
    and added formula for stishovite and wuestite

commit b618bd4cc1114aded5912a87decb566593f66bb0
Author: ian-r-rose <ian.r.rose@gmail.com>
Date:   Tue Jun 17 20:08:34 2014 -0700

    Adjustments, text

commit ffa8d6435bd1901645ee4a9bb38effff1a916f21
Author: ian-r-rose <ian.r.rose@gmail.com>
Date:   Tue Jun 17 19:57:28 2014 -0700

    Text for step_3

commit f611903f0e5855ff2c78a3ba7f0fa12d9969864b
Author: ian-r-rose <ian.r.rose@gmail.com>
Date:   Tue Jun 17 19:11:40 2014 -0700

    Add lots of text, modifications for step_2

commit 98ac01721794fac27cf5649c3a45580e274405ff
Author: ian-r-rose <ian.r.rose@gmail.com>
Date:   Tue Jun 17 18:38:50 2014 -0700

    Add a bunch of text for step_1

commit ba438e1a6ab9f25faf08d1b470a831a22bc8d8a6
Author: ian-r-rose <ian.r.rose@gmail.com>
Date:   Tue Jun 10 18:35:26 2014 -0700

    Edits

commit e14a6686d18e0a4f66d0927a4424ac7ed3f05a2b
Author: ian-r-rose <ian.r.rose@gmail.com>
Date:   Tue Jun 10 17:33:17 2014 -0700

    Work on tutorials

commit 4baf5c9d3411e6a3d5d575b226b460d56b921d25
Author: ian-r-rose <ian.r.rose@gmail.com>
Date:   Tue Jun 10 13:21:47 2014 -0700

    Add initial versions of tutorials

commit 35f6abbb98b5ddbdb1ece912b06a30449da2ed27
Author: Timo Heister <timo.heister@gmail.com>
Date:   Fri Jul 25 09:54:49 2014 +0200

    add tests for Composite sum(fractions)!=1.0

commit 7546fd7e761833c78b8d8730fa61ec437e4838b8
Author: Timo Heister <timo.heister@gmail.com>
Date:   Tue Jul 22 15:59:18 2014 +0200

    fix composite sum of fractions

    Several things in the check if the fractions as positive and sum to
1.0
    were broken:

    - the normalization was never applied
    - if the sum was smaller than one, no warning was produced
    - 1.0-0.8-0.2 produces a negative number, but should be legal

commit 346e58aa96bfd672f8bf0bd2e778c982bf6964e5
Author: Timo Heister <timo.heister@gmail.com>
Date:   Tue Jul 22 14:28:41 2014 +0200

    update tests

commit 8ffe0f5e099d796c3cd60f8a4a8864b0c3c0743f
Author: Timo Heister <timo.heister@gmail.com>
Date:   Tue Jul 22 14:28:34 2014 +0200

    rework debug_print

    Material.debug_print was based on a current p, T given by the last
    set_state() and would return an unrolled list of minerals. This
makes it
    inconvenient to use and will provide the wrong information. Now it
will
    return a hierarchical representation independent of p,T. The old
    function is now available as print_minerals_of_current_state().

commit 55b1156f8c63a1b0f2145ea4a06e8d25192c7627
Author: Timo Heister <timo.heister@gmail.com>
Date:   Tue Jul 22 12:42:42 2014 +0200

    improve mineral database documentation

    By not displaying all the inherited member functions, the mineral
    database help page becomes useful. This commit contains some cleanup
in
    the .py files. Most notably removing redundant comments mentioning
the
    source for the minerals.

commit 683eb6c353f8078842688d88d2df69e4099b64dc
Author: Timo Heister <timo.heister@gmail.com>
Date:   Sat Jul 12 17:33:37 2014 -0700

    small homepage updates

commit 29d37840c1fe727fd60afd603f9f2a033015975e
Author: Timo Heister <timo.heister@gmail.com>
Date:   Sat Jul 12 12:30:03 2014 -0700

    remove duplicate storage of Model.avgmoduli

commit e401bc7907603d3e256ed77c3a78fbce4579a9bb
Author: Timo Heister <timo.heister@gmail.com>
Date:   Sat Jul 12 12:23:06 2014 -0700

    add tests

commit dd20f5778d3dbc7798df43d1a24e201ab0c291d5
Author: Timo Heister <timo.heister@gmail.com>
Date:   Sat Jul 12 12:23:00 2014 -0700

    fix model.density, .K, .G

commit 83f92fb0b231dbdd64d7c566184bc5012ff29676
Author: Timo Heister <timo.heister@gmail.com>
Date:   Sat Jul 12 11:54:32 2014 -0700

    add tests for model, some cleanup

commit 7da2e6797cda225662bf640f4bec2dd53e6ca41f
Author: Timo Heister <timo.heister@gmail.com>
Date:   Sat Jul 12 11:54:08 2014 -0700

    fix c_p, c_v computation

commit d50025d50ecc4e6e1b5d1d74ba64116d3d0dadaa
Author: Timo Heister <timo.heister@gmail.com>
Date:   Sat Jul 12 11:10:44 2014 -0700

    add error checking

commit 27743fc5061ce7d2f660d7076bde2a84b7a98064
Author: Timo Heister <timo.heister@gmail.com>
Date:   Fri Jul 11 09:13:02 2014 -0700

    thermal exp, c_v, c_p, Model improvements

    remove all references to main while we are at it

commit 752407a0a6e1f03db5f91b094297205fda717e0f
Author: Timo Heister <timo.heister@gmail.com>
Date:   Thu Jul 10 15:02:03 2014 -0700

    update example to use new model class

commit 4242ffbc0402af8a153aa7aabd071c094e448d4c
Author: Timo Heister <timo.heister@gmail.com>
Date:   Thu Jul 10 14:58:49 2014 -0700

    add model class

commit f47514f37d166603ef6473eac1b1b3fab823a781
Author: Timo Heister <timo.heister@gmail.com>
Date:   Wed Sep 10 09:10:13 2014 -0400

    write some overview