Added physical validation document to the dev manual.

physical_validation.rst had been written but not added to the
document generation

Unwrapped a few lines that were causing warnings

Change-Id: I99ade0d25ae3897f01a6ac57d4369c2a4e36f61b

diff --git a/docs/CMakeLists.txt b/docs/CMakeLists.txt
index 5f772b1f838d967905407b8f2eb35a024c6196de..df23f6fc98e8ac45233ad7a820a193d79e7d9ca2 100644 (file)
--- a/docs/CMakeLists.txt
+++ b/docs/CMakeLists.txt
@@ -302,6 +302,7 @@ if (SPHINX_FOUND)
         dev-manual/language-features.rst
         dev-manual/naming.rst
         dev-manual/overview.rst
+        dev-manual/physical_validation.rst
         dev-manual/redmine-states.png
         dev-manual/relocatable-binaries.rst
         dev-manual/reportstyle.rst

diff --git a/docs/dev-manual/physical_validation.rst b/docs/dev-manual/physical_validation.rst
index ea0fbe99af88971619a49a2b88089b60310c54ca..61595bfbfd16de99278e9f6ab28d4495f69d53c5 100644 (file)
--- a/docs/dev-manual/physical_validation.rst
+++ b/docs/dev-manual/physical_validation.rst
@@ -77,8 +77,7 @@ LINCS settings where applicable.
   - ``integrator = md-vv``
 * *Long-range corrections LJ*:
   - ``vdwtype = PME``
-  - ``vdwtype = cut-off``, ``vdw-modifier = force-switch``,
-    ``rvdw-switch = 0.8``
+  - ``vdwtype = cut-off``, ``vdw-modifier = force-switch``, ``rvdw-switch = 0.8``
 
 **Water**:
 
@@ -87,16 +86,14 @@ LINCS settings where applicable.
   - ``integrator = md-vv``
 * *Long-range corrections LJ*:
   - ``vdwtype = PME``
-  - ``vdwtype = cut-off``, ``vdw-modifier = force-switch``,
-    ``rvdw-switch = 0.8``
+  - ``vdwtype = cut-off``, ``vdw-modifier = force-switch``, ``rvdw-switch = 0.8``
 * *Long-range corrections electrostatics*:
   - ``coulombtype = PME``, ``fourierspacing = 0.05``
 * *Constraint algorithms*:
-  - ``constraint-algorithm = lincs``, ``lincs-order = 6``,
-    ``lincs-iter = 2``
+  - ``constraint-algorithm = lincs``, ``lincs-order = 6``, ``lincs-iter = 2``
   - ``constraint-algorithm = none``
   - SETTLE
-    
+
 
 Ensemble tests
 ^^^^^^^^^^^^^^

diff --git a/docs/dev-manual/tools.rst b/docs/dev-manual/tools.rst
index 759de07343a88cd8a26f9ce76108bb08c57e47b4..eb57c66c916d48e5370c5b29c523504efdd9e1ee 100644 (file)
--- a/docs/dev-manual/tools.rst
+++ b/docs/dev-manual/tools.rst
@@ -13,6 +13,7 @@ Several tools have their own individual pages and are listed below.
    gmxtree
    uncrustify
    testutils
+   physical_validation
 
 .. TODO: Consider what is the most reasonable structure; currently, this list
    here does not make much sense in the overall organization and creates a
@@ -171,131 +172,3 @@ git attributes
   build system dependencies for easier processing in CMake.
 
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