addressed compiler warnings

CMakeLists.txt

@@ -245,14 +245,13 @@ set(hdrs
     )
 
 # Compiler spacific flagg
-
 ## GCC
 if (CMAKE_CXX_COMPILER_ID MATCHES "GNU")
-    add_compile_options(-Wall -Wextra -pedantic-errors -Werror -Wunreachable-code
+    add_compile_options(-Wall -Wextra -Wpedantic -Wunreachable-code -Wstrict-aliasing
         -Wno-sign-compare -Wno-unused-local-typedefs -Wno-unknown-pragmas)
 ## Clang
 elseif (CMAKE_CXX_COMPILER_ID MATCHES "Clang")
-    add_compile_options(-Wall -Wextra -pedantic-errors -Werror -Wunreachable-code
+    add_compile_options(-Wall -Wextra -Wpedantic -Wunreachable-code
         -Wstrict-aliasing -Wno-sign-compare -Wno-unused-local-typedef -Wno-unknown-pragmas)
 endif()
 

docs/_docs/install.md

@@ -35,12 +35,15 @@ but should compile on most unix operating systems and possibly under Cygwin (Win
 
 - CMake 3.9+
 - C/C++14 compiler (Clang 3.5+, GCC 6+, etc.)
-- Python 3.6+ with `ruamel_yaml` or `yaml`
+- Python 3.6+ with the following packages:
+  - `ruamel_yaml` or `yaml`
 
 The following are optional:
 
 - Message Passing Interface (MPI)
-- Pandoc (for building documentation)
+- `pandoc`
+- `pypandoc`
+- `BeautifulSoup4`
 
 **macOS tip:**
 Apple's developer tools, Xcode, is a quick way obtain
@@ -61,8 +64,8 @@ Dependencies will automatically be downloaded.
 ~~~ bash
 cd faunus
 cmake . [OPTIONS]
-make
-make test
+make faunus
+make usagetips # optional, requires `pandoc`, `pypandoc`, `BeautifulSoup4`
 make install
 ~~~
 
@@ -71,22 +74,21 @@ The following options are available:
 CMake Option                         | Description
 ------------------------------------ | ---------------------------------------
 `-DENABLE_MPI=OFF`                   | Enable MPI
-`-DENABLE_OPENMP=OFF`                | Enable OpenMP support
+`-DENABLE_OPENMP=ON`                 | Enable OpenMP support
 `-DENABLE_PYTHON=ON`                 | Build python bindings (experimental)
 `-DENABLE_POWERSASA=ON`              | Enable SASA routines (external download)
 `-DCMAKE_BUILD_TYPE=RelWithDebInfo`  | Alternatives: `Debug` or `Release` (faster)
 `-DCMAKE_CXX_FLAGS_RELEASE="..."`    | Compiler options for Release mode
 `-DCMAKE_CXX_FLAGS_DEBUG="..."`      | Compiler options for Debug mode
 `-DCMAKE_INSTALL_PREFIX:PATH="..."`  | Install location (default: `/usr/local`)
-`-DMYPLAYGROUND="absolute path"`     | Add additional source directory
 `-DPYTHON_EXECUTABLE="..."`          | Full path to Python executable
 `-DPYTHON_INCLUDE_DIR="..."`         | Full path to python headers
 `-DPYTHON_LIBRARY="..."`             | Full path to python library, i.e. libpythonX.dylib/so
 
 
 ### Python libraries in odd locations
 
-Should you have multiple compilers or python distributions, be specific:
+Should there are multiple compilers or python distributions, be specific:
 
 ~~~ bash
 CC=/opt/bin/clang CXX=/opt/bin/clang++ cmake . \
@@ -116,7 +118,7 @@ rm -fR CMakeCache.txt CMakeFiles
 ## Creating a conda package (advanced usage)
 
 The basic steps for creating a conda package is outlined below, albeit
-details may depend on your build environment. See also the `.travis.yml`
+details depend on the build environment. See also the `.travis.yml`
 configuration file in the main repository.
 
 ~~~ bash
@@ -128,8 +130,7 @@ anaconda login
 anaconda upload -u USER ... # see output from build step
 ~~~
 
-Instead of uploading to anaconda.org you
-can install a local copy directly after the build step above:
+Instead of uploading to anaconda.org, install a local copy directly after the build step above:
 
 ~~~ bash
 conda install -c USER faunus --use-local

scripts/extracttips.py

@@ -17,12 +17,6 @@
 import pypandoc
 import re
 
-from sympy.external import import_module
-#from .errors import LaTeXParsingError  # noqa
-from sympy.parsing.latex import parse_latex
-from sympy import init_printing
-from sympy import pprint, pretty
-
 with open('manual.html', 'r') as f:
     data=f.read()
     soup = BeautifulSoup(data)

src/geometry.cpp

@@ -167,8 +167,7 @@ namespace Faunus {
             }
         }
 
-        bool Chameleon::collision(const Point &a, double r) const {
-            assert(std::fabs(r)<1e-6 && "collision test w. radius unimplemented.");
+        bool Chameleon::collision(const Point &a) const {
             double r2 = radius*radius;
             switch (type) {
                 case SPHERE:

src/geometry.h

@@ -77,7 +77,7 @@ namespace Faunus {
             virtual void randompos( Point&, Random& ) const=0; //!< Generate random position
             virtual Point vdist( const Point&, const Point& ) const=0; //!< (Minimum) distance between two points
             virtual void boundary( Point& ) const=0; //!< Apply boundary conditions
-            virtual bool collision( const Point&, double=0) const=0; //!< Overlap with boundaries
+            virtual bool collision(const Point&) const=0; //!< Overlap with boundaries
             virtual Point getLength() const=0; //!< Side lengths
 
             inline double sqdist( const Point &a, const Point &b ) const {
@@ -131,7 +131,7 @@ namespace Faunus {
                 Point setVolume(double V, VolumeMethod method=ISOTROPIC) override;
                 Point getLength() const override; //!< Enscribed box
                 void randompos( Point &m, Random &rand ) const override;
-                bool collision(const Point &a, double r=0) const override;
+                bool collision(const Point &a) const override;
                 void from_json(const json &j);
                 void to_json(json &j) const;
 

src/molecule.h

@@ -63,7 +63,7 @@ namespace Faunus {
                     else { // insert molecule
                         if ( keeppos ) {                     // keep original positions (no rotation/trans)
                             for ( auto &i : v )              // ...but let's make sure it fits
-                                if ( geo.collision(i.pos, 0))
+                                if (geo.collision(i.pos))
                                     throw std::runtime_error("Error: Inserted molecule does not fit in container");
                         } else {
                             Point cm;                       // new mass center position

src/move.h

@@ -1263,8 +1263,10 @@ namespace Faunus {
                 public:
                     using BasePointerVector<Movebase>::vec;
                     inline Propagator() {}
-                    inline Propagator(const json &j, Tspace &spc, MPI::MPIController&) {
-
+#pragma GCC diagnostic push
+#pragma GCC diagnostic ignored "-Wunused-parameter"
+                    inline Propagator(const json &j, Tspace &spc, MPI::MPIController &mpi) {
+#pragma GCC diagnostic pop
                         if (j.count("random")==1)
                             Movebase::slump = j["random"]; // slump is static --> shared for all moves
 
@@ -1280,11 +1282,11 @@ namespace Faunus {
                                     else if (it.key()=="charge") this->template push_back<Move::ChargeMove<Tspace>>(spc);
                                     else if (it.key()=="speciation") this->template push_back<Move::SpeciationMove<Tspace>>(spc);
                                     else if (it.key()=="cluster") this->template push_back<Move::Cluster<Tspace>>(spc);
-                                    // more moves go here...
+                                    // new moves go here...
 #ifdef ENABLE_MPI
                                     else if (it.key()=="temper") this->template push_back<Move::ParallelTempering<Tspace>>(spc, mpi);
+                                    // new moves requiring MPI go here...
 #endif
-
                                     if (vec.size()==oldsize+1) {
                                         vec.back()->from_json( it.value() );
                                         addWeight(vec.back()->repeat);

src/pyfaunus.cpp

@@ -72,7 +72,7 @@ PYBIND11_MODULE(pyfaunus, m)
         .def("getVolume", &Geometry::GeometryBase::getVolume, "Get container volume", "dim"_a=3)
         .def("setVolume", &Geometry::GeometryBase::setVolume, "Set container volume", "volume"_a,
                 "method"_a=Geometry::ISOTROPIC)
-        .def("collision", &Geometry::GeometryBase::collision, "pos"_a, "radius"_a=0, "Checks if point is inside container")
+        .def("collision", &Geometry::GeometryBase::collision, "pos"_a, "Checks if point is inside container")
         .def("getLength", &Geometry::GeometryBase::getLength, "Get cuboid sidelengths")
         .def("vdist", &Geometry::GeometryBase::vdist, "Minimum vector distance, a-b", "a"_a, "b"_a)
         .def("sqdist", &Geometry::GeometryBase::sqdist, "Squared minimum distance, |a-b|^2", "a"_a, "b"_a)

src/space.h

@@ -292,7 +292,9 @@ namespace Faunus {
                             for (auto& i : g)
                                 i.pos = i.pos.cwiseProduct(scale);
                         else { // scale mass center and translate
+#ifndef NDEBUG
                             Point oldcm = g.cm;
+#endif
                             Point delta = g.cm.cwiseProduct(scale) - g.cm;
                             g.cm = g.cm.cwiseProduct(scale);
                             for (auto &i : g) {