manual update; anaconda: openmpi->mpich on osx target

CMakeLists.txt

@@ -258,10 +258,10 @@ endif()
 add_library(libfaunus STATIC ${objs} ${hdrs})
 add_dependencies(libfaunus modernjson doctest eigen range-v3 docopt xdrfile progressbar pybind11)
 
-add_executable(tests EXCLUDE_FROM_ALL src/tests.cpp ${hdrs})
-add_dependencies(tests modernjson doctest eigen range-v3)
-target_link_libraries(tests libfaunus xdrfile ${LINKLIBS})
-add_test(NAME tests COMMAND tests)
+add_executable(unittests src/unittests.cpp ${hdrs})
+add_dependencies(unittests modernjson doctest eigen range-v3)
+target_link_libraries(unittests libfaunus xdrfile ${LINKLIBS})
+add_test(NAME unittests COMMAND unittests)
 
 add_executable(faunus src/faunus.cpp)
 add_dependencies(faunus modernjson doctest eigen range-v3 docopt xdrfile progressbar)

LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2018 Mikael Lund
+Copyright (c) 2019 Mikael Lund
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

README.md

@@ -24,14 +24,7 @@ On macOS or Linux, install using [conda](https://conda.io/miniconda.html):
 
     conda install -c teokem faunus
 
-Or build from source:
-
-~~~ bash
-    git clone https://github.com/mlund/faunus.git
-    cd faunus
-    cmake .
-    make
-~~~
+Or build from source, see [here](http://mlund.github.io/faunus/docs/install/).
 
 Documentation
 =============
@@ -41,7 +34,7 @@ http://mlund.github.io/faunus
 Licence
 =======
 
-Copyright 2002-2018 Mikael Lund
+Copyright 2002-2019 Mikael Lund
 
 Permission is hereby granted, free of charge, to any person obtaining a copy of this software
 and associated documentation files (the "Software"), to deal in the Software without restriction,

docs/_docs/docs.md

@@ -50,11 +50,15 @@ yason.py minimal.yml | faunus
 produces an output file, `out.json`, with move statistics, system properties etc.
 The script `yason.py` merely converts from YAML to JSON as the former, easier to read,
 is used in all examples.
-For more examples, see the `examples` folder.
+For more examples, see the [`examples` folder](https://github.com/mlund/faunus/tree/master/examples).
+
+## Getting Help
 
 To open the user-guide in a browser, type:
 
 ~~~ bash
 faunus-manual
 ~~~
 
+If you have questions, comments, or need help, create a ticket on [our Github issue page](https://github.com/mlund/faunus/issues).
+

docs/_docs/energy.md

@@ -384,7 +384,7 @@ energy:
            - harmonic: { index: [56,921], k: 10, req: 15 }
 moleculelist:
     - water: # TIP3P
-        structure: water.xyz
+        structure: "water.xyz"
         bondlist: # index relative to molecule
             - harmonic: { index: [0,1], k: 5024, req: 0.9572 }
             - harmonic: { index: [0,2], k: 5024, req: 0.9572 }

docs/_docs/install.md

@@ -40,10 +40,10 @@ but should compile on most unix operating systems and possibly under Cygwin (Win
 
 The following are optional:
 
-- Message Passing Interface (MPI)
 - `pandoc`
 - `pypandoc`
 - `BeautifulSoup4`
+- Message Passing Interface (MPI)
 
 **macOS tip:**
 Apple's developer tools, Xcode, is a quick way obtain
@@ -58,17 +58,20 @@ clang on macOS. CMake can be installed with an
 
 Download the [latest release](https://github.com/mlund/faunus/releases/latest)
 or [the developer branch](https://github.com/mlund/faunus/archive/master.zip)
-and perform the following steps in a terminal.
-Dependencies will automatically be downloaded.
+and perform the following steps in a terminal:
 
 ~~~ bash
 cd faunus
 cmake . [OPTIONS]
-make faunus
-make usagetips # optional, requires `pandoc`, `pypandoc`, `BeautifulSoup4`
+make
+make test
+make manual_html  # requires `pandoc`
+make usagetips    # requires `pandoc`, `pypandoc`, `BeautifulSoup4`
 make install
 ~~~
 
+For merely building the Faunus executable, use `make faunus` after the `cmake` command.
+
 The following options are available:
 
 CMake Option                         | Description
@@ -85,10 +88,27 @@ CMake Option                         | Description
 `-DPYTHON_INCLUDE_DIR="..."`         | Full path to python headers
 `-DPYTHON_LIBRARY="..."`             | Full path to python library, i.e. libpythonX.dylib/so
 
+### Compiling the Manual
+
+Pandoc is required to build the HTML manual: 
+
+~~~ bash
+make manual_html
+~~~
+
+In addition to pandoc, a TeX Live installation is required to build
+the PDF manual. Garamond fonts must be available:
+
+~~~ bash
+wget https://tug.org/fonts/getnonfreefonts/install-getnonfreefonts
+sudo texlua install-getnonfreefonts
+sudo getnonfreefonts garamond --sys
+make manual
+~~~
 
 ### Python libraries in odd locations
 
-Should there are multiple compilers or python distributions, be specific:
+Should there be multiple compilers or python distributions, be specific:
 
 ~~~ bash
 CC=/opt/bin/clang CXX=/opt/bin/clang++ cmake . \
@@ -115,7 +135,7 @@ make clean
 rm -fR CMakeCache.txt CMakeFiles
 ~~~
 
-## Creating a conda package (advanced usage)
+## Creating a conda package (development usage)
 
 The basic steps for creating a conda package is outlined below, albeit
 details depend on the build environment. See also the `.travis.yml`
@@ -136,13 +156,3 @@ Instead of uploading to anaconda.org, install a local copy directly after the bu
 conda install -c USER faunus --use-local
 ~~~
 
-### Requirements
-
-Building a conda package may require a TeX Live installation to create
-the PDF manual. Ensure that Garamond fonts are available:
-
-~~~ bash
-wget https://tug.org/fonts/getnonfreefonts/install-getnonfreefonts
-sudo texlua install-getnonfreefonts
-sudo getnonfreefonts garamond --sys
-~~~

docs/_docs/moves.md

@@ -210,21 +210,30 @@ The table below explains the scaling behavior in different geometries:
 `xy`         |  `cuboid`    | Scales xy, z untouched.
 `isochoric`  |  `cuboid`    | Scales xy/z, const. volume
 
-**Note:**
+**Warning:**
 Untested for cylinders, slits.
-{: .notice--info}
+{: .notice--warning}
 
 
-## Speciation / Grand Canonical
+## Speciation / Grand Canonical (beta)
 
-The speciation move handles density fluctuations and particle transformations and is the main move for particle insertion, deletion, and swapping used in (semi)-grand canonical ensembles.
+The speciation move handles density fluctuations and particle transformations and is the main move
+for particle insertion, deletion, and swapping used in (semi)-grand canonical ensembles.
 A reaction from `reactionlist` is randomly picked from the topology and is either propagated forward or backwards.
 In Faunus, the total number of atoms and molecules are constant, but these can be either _active_ or _inactive_.
 Deleting a molecule simply deactivates it, while insertion _vice versa_ activates an inactive molecule.
-Thus, it is important that the _capacity_ or reservoir of particles (active plus inactive) is sufficiently large to allow for fluctuations. This is ensured using `insertmolecules` (see Topology). A runtime warning will be given, should you run low on particles.
+Thus, it is important that the _capacity_ or reservoir of particles (active plus inactive) is
+sufficiently large to allow for fluctuations.
+This is ensured using `insertmolecules` (see Topology).
+A runtime warning will be given, should you run low on particles.
 
 For more information about reactions, see the Topology section.
 
 `speciation`    |  Description
 --------------- | ----------------------------------
 `repeat=1`      |  Average number of moves per sweep
+
+**Warning:**
+The speciation move is under construction and subject to change.
+{: .notice--warning}
+

docs/_docs/running.md

@@ -63,6 +63,12 @@ import json
 with open('out.json') as f:
     d = json.load(f) # --> dict
     print( d['atomlist'][0]["Na+"]["mw"] ) # --> 22.99
+    #             ^      ^    ^     ^
+    #             |      |    |     |
+    #             |      |    |     get mol. weight value
+    #             |      |    key is the atom name
+    #             |      fist object in array
+    #             atomlist is an array of objects
 ~~~
 
 ## Restarting
@@ -74,11 +80,14 @@ To start from the previously saved state, use:
 faunus --input in.json --state state.json
 ~~~
 
-## Message Passing Interface
+## Message Passing Interface (MPI)
+
+Only few routines in Faunus are currently parallelisable using MPI, for example
+parallel tempering, and penalty function energies.
 
 Running with MPI spawns `nproc` processes that may or may not communicate
 with each other. If `nproc>1`, input and output files are prefixed with
-`mpi{rank}.` where `{rank}` is the rank or process number.
+`mpi{rank}.` where `{rank}` is the rank or process number, starting from zero.
 
 The following starts two processes, reading input from `mpi0.in.json` and
 `mpi1.in.json`. All output files, including those from any analysis are
@@ -106,5 +115,5 @@ help(pyfaunus)
 
 For more examples, see
 [`pythontest.py`](https://github.com/mlund/faunus/blob/master/examples/pythontest.py).
-Please note that the interface is under development and subject to change.
+Note that the interface is under development and subject to change.
 

docs/_docs/topology.md

@@ -37,11 +37,11 @@ Origo ($0,0,0$) is always placed in the geometric _center_ of the simulation con
 
 `geometry` | PBC      | Required keywords
 ---------- | -------- | --------------------------------------
-type:      |          |
+`type`:    |          |
 `cuboid`   | $x,y,z$  | `length` (array or single float)
 `slit`     | $x,y$    | `length` (array or single float)
 `cylinder` | $z$      | `radius`, `length` (along $z$)
-`sphere`   | off      | `radius`
+`sphere`   | none     | `radius`
 
 ## Atom Properties
 
@@ -54,7 +54,8 @@ Atoms are the smallest possible particle entities with properties defined below.
 `dp=0`        | Translational displacement parameter [Å]
 `dprot=0`     | Rotational displacement parameter [degrees] (will be converted to radians)
 `eps=0`       | Epsilon energy scaling commonly used for Lennard-Jones interactions etc. [kJ/mol]
-`mu=[0,0,0]`  | Dipole moment vector [Debye]
+`mu=[1,0,0]`  | Dipole moment unit vector
+`mulen=0`     | Dipole moment scalar [eÅ]
 `mw=1`        | Molecular weight [g/mol]
 `q=0`         | Valency / partial charge number [$e$]
 `r=0`         | Radius = `sigma/2` [Å]
@@ -76,17 +77,22 @@ atomlist:
   - ...
 ~~~
 
+### Anisotropic Atoms
+
+By default, Faunus is currently compiled with centro-symmetric atoms, only. To add _i.e._ dipolar properties, modify the particle definition at the top of `src/faunus.cpp`.
+
+
 ## Molecule Properties
 
 A molecule is a collection of atoms, but need not be associated
 as real molecules. Two particular modes can be specified:
 
 1. If `atomic=true` the atoms in the molecule are unassociated and is
-   typically used to defined salt particles or any other non-aggregated
+   typically used to define salt particles or other non-aggregated
    species. No structure is required, and the molecular center of mass (COM) is
    unspecified.
 
-2. If `atomic=false` the molecule resembles a real molecule and a structure
+2. If `atomic=false` the molecule resembles a real molecule and a structure or trajectory
    is _required_.
 
 Properties of molecules and their default values:
@@ -176,7 +182,7 @@ container boundaries. Overlap between particles is ignored and for
 i.e. hard-sphere potentials the initial energy may be infinite.
 
 
-## Equilibrium Reactions
+## Equilibrium Reactions (beta)
 
 Faunus supports density fluctuations, coupled to chemical equilibria with
 explicit and/or implicit particles via their chemical potentials as
@@ -205,3 +211,7 @@ Available keywords:
 --------------- | ---------------------------------------------------------------
 `lnK`/`pK`      | Molar equilibrium constant either as $\ln K$ or $-\log_{10}(K)$
 
+**Warning:**
+This functionality is under construction and subject to change.
+{: .notice--warning}
+

scripts/meta.yaml

@@ -36,12 +36,12 @@ requirements:
     - pandoc 2.*
     - pypandoc 1.*
     - beautifulsoup4
-    - openmpi 1.6.3  # [osx]
+    - mpich 3.2.*    # [osx]
     - openmpi 3.1.*  # [linux64]
     - llvm-openmp    # [osx]
   run:
     - llvm-openmp    # [osx]
-    - openmpi 1.6.3  # [osx]
+    - mpich 3.2.*    # [osx]
     - openmpi 3.1.*  # [linux64]
     - ruamel_yaml
     - pygments

src/atomdata.cpp

@@ -30,11 +30,6 @@ namespace Faunus {
         for (auto it : j.items()) {
             a.name = it.key();
             xjson val = it.value();
-            //assertKeys(val, {
-            //        "activity", "alphax", "q", "dp", "dprot", "eps", "id",
-            //        "mu", "mulen", "scdir", "sclen", "mw", "sigma",
-            //        "r", "tension", "tfe", "hydrophobic"
-            //        }); // throw exception if keys other than these are given
             a.activity = val.value("activity", a.activity) * 1.0_molar;
             a.alphax   = val.value("alphax", a.alphax);
             a.charge   = val.value("q", a.charge);

src/faunus.cpp

@@ -14,13 +14,7 @@ using namespace std;
 #define FAUNUS_TIPSFILE ""
 #endif
 
-#ifdef FAUNUS_CUBOID_NOPBC
-typedef Geometry::CuboidNoPBC Tgeometry;
-#elif FAUNUS_SPHERE
-typedef Geometry::Sphere Tgeometry;
-#else
 typedef Geometry::Chameleon Tgeometry;
-#endif
 typedef Particle<Charge> Tparticle;
 
 static const char USAGE[] =