From 339534c03edc3897f5c51a1dfcdd25c97371c185 Mon Sep 17 00:00:00 2001 From: Kevin Boyd Date: Wed, 8 Aug 2018 20:33:14 -0400 Subject: [PATCH] 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 --- docs/CMakeLists.txt | 1 + docs/dev-manual/physical_validation.rst | 11 +- docs/dev-manual/tools.rst | 129 +----------------------- 3 files changed, 6 insertions(+), 135 deletions(-) diff --git a/docs/CMakeLists.txt b/docs/CMakeLists.txt index 5f772b1f83..df23f6fc98 100644 --- 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 ea0fbe99af..61595bfbfd 100644 --- 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 759de07343..eb57c66c91 100644 --- 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. include-what-you-use - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -- 2.22.0