diff --git a/Makefile b/Makefile
index 3323593c68..c37fda75c2 100644
--- a/Makefile
+++ b/Makefile
@@ -6,13 +6,10 @@
DASPK=$(shell python -c 'import pydas.daspk; print pydas.daspk.__file__')
DASSL=$(shell python -c 'import pydas.dassl; print pydas.dassl.__file__')
-RDKIT_VERSION=$(shell python -c 'import rdkit; print rdkit.__version__')
-.PHONY : all minimal main solver cantherm clean decython documentation QM mopac_travis
+.PHONY : all minimal main solver check cantherm clean decython documentation mopac_travis
-all: main solver QM
-
-noQM: main solver
+all: main solver check
minimal:
python setup.py build_ext minimal --build-lib . --build-temp build --pyrex-c-in-temp
@@ -39,35 +36,32 @@ endif
cantherm:
python setup.py build_ext cantherm --build-lib . --build-temp build --pyrex-c-in-temp
-QM:
- @ echo "Checking if you have symmetry..."
- @ echo "symmetry -h"
- @ echo "Checking you have rdkit..."
- @ python -c 'import rdkit; print rdkit.__file__'
- @ echo "Checking rdkit version..."
-ifneq ($(RDKIT_VERSION),)
- @ echo "Found rdkit version $(RDKIT_VERSION)"
-else
- $(error RDKit version out of date, please install RDKit version 2015.03.1 or later with InChI support);
-endif
- @ echo "Checking rdkit has InChI support..."
- @ python -c 'from rdkit import Chem; assert Chem.inchi.INCHI_AVAILABLE, "RDKit installed without InChI Support. Please install with InChI."'
+check:
+ @ python utilities.py check-dependencies
documentation:
$(MAKE) -C documentation html
@ echo "Start at: documentation/build/html/index.html"
clean:
- python setup.py clean --build-temp build
- rm -rf build/
- find . -name '*.so' -exec rm -f '{}' \;
- find . -name '*.pyc' -exec rm -f '{}' \;
-
+ @ echo "Removing build directory..."
+ @ python setup.py clean --build-temp build
+ @ echo "Removing compiled files..."
+ @ python utilities.py clean
+ @ echo "Cleanup completed."
+
clean-solver:
- rm -r build/pyrex/rmgpy/solver/
- rm -r build/build/pyrex/rmgpy/solver/
- find rmgpy/solver/ -name '*.so' -exec rm -f '{}' \;
- find rmgpy/solver/ -name '*.pyc' -exec rm -f '{}' \;
+ @ echo "Removing solver build directories..."
+ifeq ($(OS),Windows_NT)
+ @ -rd /s /q build\pyrex\rmgpy\solver
+ @ -rd /s /q build\build\pyrex\rmgpy\solver
+else
+ @ -rm -r build/pyrex/rmgpy/solver/
+ @ -rm -r build/build/pyrex/rmgpy/solver/
+endif
+ @ echo "Removing compiled files..."
+ @ python utilities.py clean-solver
+ @ echo "Cleanup completed."
decython:
# de-cythonize all but the 'minimal'. Helpful for debugging in "pure python" mode.
@@ -75,50 +69,42 @@ decython:
find . -name *.pyc -exec rm -f '{}' \;
test-all:
-ifeq ($(OS),Windows_NT)
- nosetests --nocapture --nologcapture --all-modules --verbose --with-coverage --cover-inclusive --cover-package=rmgpy --cover-erase --cover-html --cover-html-dir=testing/coverage --exe rmgpy
-else
+ifneq ($(OS),Windows_NT)
mkdir -p testing/coverage
rm -rf testing/coverage/*
- nosetests --nocapture --nologcapture --all-modules --verbose --with-coverage --cover-inclusive --cover-package=rmgpy --cover-erase --cover-html --cover-html-dir=testing/coverage --exe rmgpy
endif
+ nosetests --nocapture --nologcapture --all-modules --verbose --with-coverage --cover-inclusive --cover-package=rmgpy --cover-erase --cover-html --cover-html-dir=testing/coverage --exe rmgpy
test-unittests:
-ifeq ($(OS),Windows_NT)
- nosetests --nocapture --nologcapture --all-modules -A 'not functional' --verbose --with-coverage --cover-inclusive --cover-package=rmgpy --cover-erase --cover-html --cover-html-dir=testing/coverage --exe rmgpy
-else
+ifneq ($(OS),Windows_NT)
mkdir -p testing/coverage
rm -rf testing/coverage/*
- nosetests --nocapture --nologcapture --all-modules -A 'not functional' --verbose --with-coverage --cover-inclusive --cover-package=rmgpy --cover-erase --cover-html --cover-html-dir=testing/coverage --exe rmgpy
endif
+ nosetests --nocapture --nologcapture --all-modules -A 'not functional' --verbose --with-coverage --cover-inclusive --cover-package=rmgpy --cover-erase --cover-html --cover-html-dir=testing/coverage --exe rmgpy
test test-unittests-non-auth:
-ifeq ($(OS),Windows_NT)
- nosetests --nocapture --nologcapture --all-modules -A 'not functional and not auth' --verbose --with-coverage --cover-inclusive --cover-package=rmgpy --cover-erase --cover-html --cover-html-dir=testing/coverage --exe rmgpy
-else
+ifneq ($(OS),Windows_NT)
mkdir -p testing/coverage
rm -rf testing/coverage/*
- nosetests --nocapture --nologcapture --all-modules -A 'not functional and not auth' --verbose --with-coverage --cover-inclusive --cover-package=rmgpy --cover-erase --cover-html --cover-html-dir=testing/coverage --exe rmgpy
endif
+ nosetests --nocapture --nologcapture --all-modules -A 'not functional and not auth' --verbose --with-coverage --cover-inclusive --cover-package=rmgpy --cover-erase --cover-html --cover-html-dir=testing/coverage --exe rmgpy
test-functional:
-ifeq ($(OS),Windows_NT)
- nosetests --nocapture --nologcapture --all-modules -A 'functional' --verbose --exe rmgpy
-else
+ifneq ($(OS),Windows_NT)
mkdir -p testing/coverage
rm -rf testing/coverage/*
- nosetests --nocapture --nologcapture --all-modules -A 'functional' --verbose --exe rmgpy
endif
+ nosetests --nocapture --nologcapture --all-modules -A 'functional' --verbose --exe rmgpy
test-database:
nosetests -v -d testing/databaseTest.py
-eg0: noQM
+eg0: all
mkdir -p testing/eg0
rm -rf testing/eg0/*
cp examples/rmg/superminimal/input.py testing/eg0/input.py
@ echo "Running eg0: superminimal (H2 oxidation) example"
python rmg.py testing/eg0/input.py
-eg1: noQM
+eg1: all
mkdir -p testing/eg1
rm -rf testing/eg1/*
cp examples/rmg/minimal/input.py testing/eg1/input.py
@@ -168,7 +154,7 @@ eg7: all
@ echo "Running eg7: gri_mech_rxn_lib example"
python rmg.py testing/eg7/input.py
-scoop: noQM
+scoop: all
mkdir -p testing/scoop
rm -rf testing/scoop/*
cp examples/rmg/minimal/input.py testing/scoop/input.py
diff --git a/documentation/source/_static/RMG-logo.pdf b/documentation/source/_static/RMG-logo.pdf
deleted file mode 100644
index 04e67a07df..0000000000
Binary files a/documentation/source/_static/RMG-logo.pdf and /dev/null differ
diff --git a/documentation/source/_static/custom.css b/documentation/source/_static/custom.css
new file mode 100644
index 0000000000..50044b6385
--- /dev/null
+++ b/documentation/source/_static/custom.css
@@ -0,0 +1,81 @@
+@import url("classic.css");
+
+/* ----- sidebar styles ----- */
+
+div.sidebarlogo {
+ text-align: center;
+ padding: 20px;
+}
+
+div.sphinxsidebarwrapper {
+ padding: 0;
+}
+
+#sidebar .icon {
+ float: left;
+ width: 40px;
+ padding: 5px;
+}
+
+#sidebar div.menuitem {
+ padding: 5px;
+}
+
+#sidebar div.menutext {
+ text-align: left;
+ margin-left: 50px;
+ padding: 1px 5px;
+}
+
+#sidebar div.menutitle {
+ color: #F04040;
+ font-size: 125%;
+ vertical-align: bottom;
+}
+
+#sidebar div.menudesc {
+ color: #FFFFFF;
+ font-size: 90%;
+ vertical-align: top;
+}
+
+#rmgsidebar a {
+ text-decoration: none;
+}
+
+#rmgsidebar div.menuitem {
+ min-height: 50px;
+}
+
+#rmgsidebar div.menuitem:hover {
+ background-color: #606060;
+}
+
+/* ----- table styles ----- */
+
+th {
+ background-color: transparent;
+}
+
+table.rmg {
+ border-top: 2px solid #000000;
+ border-bottom: 2px solid #000000;
+ border-collapse: collapse;
+ margin: 10px 10px 20px 30px;
+}
+
+table.rmg thead {
+ border-bottom: 1px solid #000000;
+}
+
+table.rmg th,
+table.rmg td {
+ padding: 5px;
+}
+
+/* ----- code block styles ----- */
+
+pre {
+ border-top: 1px solid #F04040;
+ border-bottom: 1px solid #F04040;
+}
diff --git a/documentation/source/_static/database-logo-small.png b/documentation/source/_static/database-logo-small.png
deleted file mode 100644
index 59e4508d41..0000000000
Binary files a/documentation/source/_static/database-logo-small.png and /dev/null differ
diff --git a/documentation/source/_static/documentation-icon.png b/documentation/source/_static/documentation-icon.png
deleted file mode 100644
index 88076af3ab..0000000000
Binary files a/documentation/source/_static/documentation-icon.png and /dev/null differ
diff --git a/documentation/source/_static/github-icon.png b/documentation/source/_static/github-icon.png
new file mode 100644
index 0000000000..119a56e22f
Binary files /dev/null and b/documentation/source/_static/github-icon.png differ
diff --git a/documentation/source/_static/groupdraw-logo-small.png b/documentation/source/_static/groupdraw-logo-small.png
deleted file mode 100644
index 44cef2a54c..0000000000
Binary files a/documentation/source/_static/groupdraw-logo-small.png and /dev/null differ
diff --git a/documentation/source/_static/input-logo-small.png b/documentation/source/_static/input-logo-small.png
deleted file mode 100644
index 9542994e8e..0000000000
Binary files a/documentation/source/_static/input-logo-small.png and /dev/null differ
diff --git a/documentation/source/_static/kinetics-search-logo-small.png b/documentation/source/_static/kinetics-search-logo-small.png
deleted file mode 100644
index 94dd1210e9..0000000000
Binary files a/documentation/source/_static/kinetics-search-logo-small.png and /dev/null differ
diff --git a/documentation/source/_static/moleculedraw-logo-small.png b/documentation/source/_static/moleculedraw-logo-small.png
deleted file mode 100644
index 4bb0fc055d..0000000000
Binary files a/documentation/source/_static/moleculedraw-logo-small.png and /dev/null differ
diff --git a/documentation/source/_static/pdep-logo-small.png b/documentation/source/_static/pdep-logo-small.png
deleted file mode 100644
index 6297914e67..0000000000
Binary files a/documentation/source/_static/pdep-logo-small.png and /dev/null differ
diff --git a/documentation/source/_static/rmg-icon.png b/documentation/source/_static/rmg-icon.png
new file mode 100644
index 0000000000..231a23b689
Binary files /dev/null and b/documentation/source/_static/rmg-icon.png differ
diff --git a/documentation/source/_static/rmg-logo-big.pdf b/documentation/source/_static/rmg-logo-big.pdf
new file mode 100755
index 0000000000..2023eedafc
Binary files /dev/null and b/documentation/source/_static/rmg-logo-big.pdf differ
diff --git a/documentation/source/_static/rmg-logo-small.png b/documentation/source/_static/rmg-logo-small.png
index 7e6d7742c9..741de8ed83 100644
Binary files a/documentation/source/_static/rmg-logo-small.png and b/documentation/source/_static/rmg-logo-small.png differ
diff --git a/documentation/source/_static/rmg.css b/documentation/source/_static/rmg.css
deleted file mode 100644
index f538f4b28e..0000000000
--- a/documentation/source/_static/rmg.css
+++ /dev/null
@@ -1,318 +0,0 @@
-@import url("basic.css");
-
-/* -- page layout ----------------------------------------------------------- */
-
-body {
- font-family: sans-serif;
- font-size: 100%;
- background-color: #F0F0F0;
- color: #000;
- margin: 0;
- padding: 0;
-}
-
-div.header {
- color: #993333;
- font-size: 0.8em;
- text-align: right;
- padding: 4px 10px 4px 0;
-}
-
-div.document {
-
-}
-
-div.documentwrapper {
- float: left;
- width: 100%;
-}
-
-div.bodywrapper {
- background-color: #FFFFFF;
- border: 1px solid #993333;
- border-right: 0px;
- margin: 0 0 0 230px;
-}
-
-div.body {
- color: #000000;
- padding: 0px 10px 10px 10px;
-}
-
-div.footer {
- color: #808080;
- width: 100%;
- padding: 4px 0 4px 0;
- margin: 40px 0 0 0;
- text-align: center;
- font-size: 0.7em;
-}
-
-div.footer a {
- color: #808080;
- text-decoration: underline;
-}
-
-div.related {
- color: #993333;
- font-size: 0.8em;
- padding: 4px 0 2px 0;
- border-bottom: 1px solid #993333;
-}
-
-div.related a {
- color: #993333;
-}
-
-div.related ul {
- padding: 0 0 0 0;
-}
-
-div.related ul li {
- margin-right: 0px;
- padding: 0 0 0 0;
-}
-
-div.sphinxsidebar {
-}
-
-div.sidebarlogo {
- text-align: center;
- margin: 0 0 20px 0;
-}
-
-div.sphinxsidebar h3 {
- font-family: sans-serif;
- color: #993333;
- font-size: 1.4em;
- font-weight: normal;
- margin: 0;
- padding: 0;
-}
-
-div.sphinxsidebar h3 a {
- color: #993333;
-}
-
-div.sphinxsidebar h4 {
- font-family: sans-serif;
- color: #993333;
- font-size: 1.3em;
- font-weight: normal;
- margin: 5px 0 0 0;
- padding: 0;
-}
-
-div.sphinxsidebar p {
- color: #993333;
-}
-
-div.sphinxsidebar p.topless {
- margin: 5px 10px 10px 10px;
- word-wrap: break-word;
-}
-
-div.sphinxsidebar ul {
- margin: 10px;
- padding: 0;
- color: #ffffff;
-}
-
-div.sphinxsidebar a {
- color: #993333;
-}
-
-div.sphinxsidebar input {
- border: 1px solid #993333;
- font-family: sans-serif;
- font-size: 1em;
-}
-
-
-
-/* -- hyperlink styles ------------------------------------------------------ */
-
-a {
- color: #993333;
- text-decoration: none;
-}
-
-a:visited {
- color: #993333;
- text-decoration: none;
-}
-
-a:hover {
- text-decoration: underline;
-}
-
-
-
-/* -- body styles ----------------------------------------------------------- */
-
-div.body h1,
-div.body h2,
-div.body h3,
-div.body h4,
-div.body h5,
-div.body h6 {
- font-family: sans-serif;
- font-weight: normal;
- color: #993333;
- margin: 20px 0px 10px 0px;
- padding: 3px 0px 3px 0px;
-}
-
-div.body h1 { margin-top: 0; font-size: 200%; }
-div.body h2 { font-size: 160%; }
-div.body h3 { font-size: 140%; }
-div.body h4 { font-size: 120%; }
-div.body h5 { font-size: 110%; }
-div.body h6 { font-size: 100%; }
-
-a.headerlink {
- color: #c60f0f;
- font-size: 0.8em;
- padding: 0 4px 0 4px;
- text-decoration: none;
-}
-
-a.headerlink:hover {
- background-color: #c60f0f;
- color: white;
-}
-
-div.body p, div.body dd, div.body li {
- text-align: justify;
- line-height: 130%;
-}
-
-div.admonition p.admonition-title + p {
- display: inline;
-}
-
-div.admonition p {
- margin-bottom: 5px;
-}
-
-div.admonition pre {
- margin-bottom: 5px;
-}
-
-div.admonition ul, div.admonition ol {
- margin-bottom: 5px;
-}
-
-div.note {
- background-color: #eee;
- border: 1px solid #ccc;
-}
-
-div.seealso {
- background-color: #ffc;
- border: 1px solid #ff6;
-}
-
-div.topic {
- background-color: #eee;
-}
-
-div.warning {
- background-color: #ffe4e4;
- border: 1px solid #f66;
-}
-
-p.admonition-title {
- display: inline;
-}
-
-p.admonition-title:after {
- content: ":";
-}
-
-pre {
- padding: 5px;
- background-color: #eeffcc;
- color: #333333;
- line-height: 120%;
- border: 1px solid #ac9;
- border-left: none;
- border-right: none;
-}
-
-tt {
- background-color: #ecf0f3;
- padding: 0 1px 0 1px;
- font-size: 0.95em;
-}
-
-.warning tt {
- background: #efc2c2;
-}
-
-.note tt {
- background: #d6d6d6;
-}
-
-.viewcode-back {
- font-family: sans-serif;
-}
-
-div.viewcode-block:target {
- background-color: #f4debf;
- border-top: 1px solid #ac9;
- border-bottom: 1px solid #ac9;
-}
-
-p.caption {
- font-size: 0.9em;
-}
-
-
-/* -- table styles ----------------------------------------------------------- */
-/*
-table,
-table colgroup,
-table th,
-table tr,
-table td {
- border: 0px inset #000000;
- padding: 0px
-}
-*/
-
-table.data td {
- padding-right: 3px
-}
-
-table.data, table.data thead, table.data tbody {
- border-top: 1px solid #000000;
- border-bottom: 1px solid #000000;
- padding: 20px
-}
-
-
-/* Some custom sidebar link styling */
-div.customsidebar {
- border-top: 1px solid #993333;
-}
-
-.icon_sidebar {
- float: left;
-}
-img.icon_sidebar { max-width: none;}
-
-.biglink_sidebar {
- font-size: 120%;
- font-weight: bold;
- text-align: left;
- vertical-align: bottom;
-}
-
-.linkdesc {
- font-size: 90%;
- text-align: left;
- vertical-align: top;
- font-style: italic;
-}
-
diff --git a/documentation/source/_static/solvation-search-logo-small.png b/documentation/source/_static/solvation-search-logo-small.png
deleted file mode 100644
index 6544745349..0000000000
Binary files a/documentation/source/_static/solvation-search-logo-small.png and /dev/null differ
diff --git a/documentation/source/_static/tools-icon.png b/documentation/source/_static/tools-icon.png
deleted file mode 100644
index 16e327dec4..0000000000
Binary files a/documentation/source/_static/tools-icon.png and /dev/null differ
diff --git a/documentation/source/_templates/customsidebar.html b/documentation/source/_templates/customsidebar.html
deleted file mode 100644
index b4cfc6f221..0000000000
--- a/documentation/source/_templates/customsidebar.html
+++ /dev/null
@@ -1,73 +0,0 @@
-
-
diff --git a/documentation/source/_templates/index.html b/documentation/source/_templates/index.html
index 2bab1dcab9..4b220a9ecb 100644
--- a/documentation/source/_templates/index.html
+++ b/documentation/source/_templates/index.html
@@ -2,68 +2,71 @@
{% set title = 'Overview' %}
{% block body %}
-
Reaction Mechanism Generator Documentation
+
+ Reaction Mechanism Generator (RMG) is an automatic chemical reaction mechanism generator
+ that constructs kinetic models composed of elementary chemical reaction steps using a general understanding
+ of how molecules react.
+
-
-
-
-
-
-
-
-| analyze models & search databases |
-rmg website resources (no download needed) |
-
-
-| make transition state theory calculations |
-Run Cantherm with the Canterm User's Guide |
-
-
-| create mechanisms automatically |
-Download RMG with the RMG User's Guide |
-
-
-| post an issue with RMG |
-github issues page |
-
-
-| contribute to RMG project |
-RMG developer's wiki |
-
-
-
-
+
+ This documentation site if for the newer Python version of RMG called RMG-Py.
+ It is developed on GitHub as RMG-Py.
+
-
- Reaction Mechanism Generator (RMG) is an automatic chemical reaction mechanism generator
- that constructs kinetic models composed of elementary chemical reaction
- steps using a general understanding of how molecules react.
+
+ CanTherm is developed and distributed as part of RMG-Py, but can be used as a stand-alone
+ application for Thermochemistry, Transition State Theory, and Master Equation chemical kinetics
+ calculations.
-
+
- These pages describe the newer Python version of RMG that we call RMG-Py.
- It is developed on github as RMG-Py.
+ RMG is free, open-source software, and is under active and ongoing development.
+ If you are interested in assisting with or guiding its development, please let us know.
+ Any issues, concerns, or comments can be posted to our
+ Github issues page.
-
+
- CanTherm is developed and distributed as part of RMG-Py, but can be used as a stand-alone
- application for Thermochemistry, Transition State Theory, and Master Equation chemical kinetics
- calculations.
+ While you are free to use or modify RMG components as you wish, we would like to
+ coordinate with you. Please contact Professor William H. Green,
+ Professor Richard H. West,
+ or the The RMG Development Team for further information.
-RMG is free, open-source software, and is under active and ongoing development.
-If you are interested in assisting with or guiding its development, please let us know. Any issues,
-concerns, or comments can be posted to our Github issues page.
-While you are free to use/modify RMG components as you wish, we would like to
-co-ordinate with you. Please contact Professor William H. Green,
-Professor Richard H. West,
-or the The RMG Development Team for further information.
+ Quick reference guide:
+
+
+
+ | I want to... |
+ Resource |
+
+
+
+
+ | analyze models & search databases |
+ RMG website resources (no download needed) |
+
+
+ | make transition state theory calculations |
+ Run Cantherm with the Canterm User's Guide |
+
+
+ | create mechanisms automatically |
+ Download RMG with the RMG User's Guide |
+
+
+ | post an issue with RMG |
+ GitHub issues page |
+
+
+ | contribute to RMG project |
+ RMG developer's wiki |
+
+
+
Parts of the documentation:
diff --git a/documentation/source/_templates/layout.html b/documentation/source/_templates/layout.html
index f9b27a9d06..eb1f46a9f7 100644
--- a/documentation/source/_templates/layout.html
+++ b/documentation/source/_templates/layout.html
@@ -11,39 +11,60 @@
{% endblock %}
{% block rootrellink %}
-Documentation {{ release }} »
+ RMG »
+ {{ release }} Documentation »
{% endblock %}
-{%- block header %}
-
-{%- endblock %}
-
-{%- block sidebarlogo %}
-
-{%- endblock %}
-
-{%- block relbar1 %}{% endblock %}
-
- {%- block document %}
-
- {%- if render_sidebar %}
-
- {%- endif %}
-
- {{ relbar() }}
- {% block body %} {% endblock %}
-
- {%- if render_sidebar %}
+{%- block sidebar2 %}
+ {%- if render_sidebar %}
+
- }}){kind=icon}
- }}){kind=logo}
- }}){kind=logo}
- }}){kind=logo}
- }}){kind=logo}
- }}){kind=logo}
- }}){kind=logo}
- }}){kind=icon}
- }}){kind=logo}
 }}){kind=icon}
+  }}){kind=icon}
+