Merge branch 'python' of git://github.com/espressomd/espresso into ch…

…eckpointing

doc/sphinx/analysis.rst

@@ -62,7 +62,7 @@ For example, ::
 
 Momentum of the System
 ~~~~~~~~~~~~~~~~~~~~~~
-:meth:`espressomd.analyze.Analysis.analyze_linear_momentum`
+:meth:`espressomd.analyze.Analysis.linear_momentum`
 
 This command returns the total linear momentum of the particles and the
 lattice Boltzmann (LB) fluid, if one exists. Giving the optional

doc/sphinx/installation.rst

@@ -44,6 +44,7 @@ C++ Compiler
 
 Boost
     A number of advanced C++ features used by ESPResSo is provided by Boost.
+    We strongly recommend to use at least boost 1.67.
 
 FFTW
     For some algorithms (P\ :math:`^3`\ M), ESPResSo needs the FFTW library
@@ -55,24 +56,31 @@ MPI
     environment that implements the MPI standard version 1.2.
 
 Python
-    ESPResSo's main user interface is via the Python scripting interface. Both, Python 2 and 3 are supported.
+    ESPResSo's main user interface is via the Python scripting interface.
+    We strongly recommend Python 3. Python 2 support is about to be removed.
 
 Cython
-    Cython is used for connecting the C++ core to Python
+    Cython is used for connecting the C++ core to Python.
+    At least version 0.23 is required.
+
 
 .. _Installing Requirements on Ubuntu Linux:
 
 Installing Requirements on Ubuntu Linux
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+These instructions pertain to Python 3. If you need to use the deprecated
+Python 2 support, leave out the `3` in the Python package names.
+I.e., use `python-numpy` rather than `python3-numpy`.
+
 
-To make ESPResSo run on Ubuntu 16.04 LTS or 18.04 LTS, its dependencies can be
+To make ESPResSo run on 18.04 LTS, its dependencies can be
 installed with:
 
 .. code-block:: bash
 
-    sudo apt install build-essential cmake cython python-numpy \
+    sudo apt install build-essential cmake cython python3-numpy \
     libboost-all-dev openmpi-common fftw3-dev libhdf5-dev libhdf5-openmpi-dev \
-    doxygen python-opengl python-sphinx python-pip libgsl-dev
+    doxygen python3-opengl python3-sphinx python3-pip libgsl-dev
 
 
 Optionally the ccmake utility can be installed for easier configuration:
@@ -166,9 +174,9 @@ command in |es| 's source directory:
 
 .. code-block:: bash
 
-    pip install -r requirements.txt --user --upgrade
+    pip3 install -r requirements.txt --user --upgrade
 
-Please note that on some systems, ``pip`` has to be replaced by ``pip2`` to install Python 2 versions of the packages.
+Please note that on some systems, ``pip3`` has to be replaced by ``pip`` or ``pip2`` to install Python 2 versions of the packages.
 
 .. _Quick installation:
 
@@ -178,15 +186,24 @@ Quick installation
 If you have installed the requirements (see section :ref:`Requirements
 <requirements>` ) in standard locations, to compile, it is usually enough to
 create a build directory and call ``cmake`` and ``make`` (optional steps
-which modify the build process are commented out):
+which modify the build process are commented out).
+To chose the correct Python version, run
+
+.. code-block:: bash
+
+    python -V
+    python3 -V
+
+This shows which Python version the binaries are for. Then pass the one you'd like to use in the cmake command line, below.
+
 
 .. code-block:: bash
 
     mkdir build
     cd build
     #cp myconfig-default.hpp myconfig.hpp # use the default configuration as template
     #nano myconfig.hpp                    # edit to add/remove features as desired
-    cmake ..
+    cmake -DPYTHON_EXECUTABLE=`which python3` ..
     #ccmake . // in order to add/remove features like SCAFACOS or CUDA
     make
 
@@ -219,7 +236,7 @@ command:
 
     ./pypresso <SCRIPT>
 
-where is ``<SCRIPT>`` is a ``python`` script which has to
+where ``<SCRIPT>`` is a ``python`` script which has to
 be written by the user. You can find some examples in the :file:`samples`
 folder of the source code directory. If you want to run in parallel, you should
 have compiled with *Open MPI*, and need to tell MPI to run in parallel. The actual

doc/sphinx/magnetostatics.rst

@@ -44,7 +44,7 @@ completely unphysical simulations.
 Dipolar P3M
 ~~~~~~~~~~~
 This is the dipolar version of the P3M algorithm, described in :cite:`cerda08d`.
-It is interfaced via :class:`espressomd.magnetostatics.DipolarP3M`.
+It is interfaced via :class:`~espressomd.magnetostatics.DipolarP3M`.
 
 Make sure that you know the relevance of the P3M parameters before using
 P3M! If you are not sure, read the following references
@@ -94,7 +94,7 @@ The method is used as follows::
 
 
 
-.. _Dipolar direct sum on gpu:
+.. _Dipolar direct sum:
 
 Dipolar direct sum
 ------------------
@@ -111,31 +111,34 @@ Due to the long-range nature of dipolar interactions, Direct summation with mini
 
 Two methods are available:
 
-* :class:`espressomd.magnetostatics.DipolarDirectSumCpu`
+* :class:`~espressomd.magnetostatics.DipolarDirectSumCpu`
   performs the calculation in double precision on the Cpu.
 
 
-* :class:`espressomd.magnetostatics.DipolarDirectSumGpu`
+* :class:`~espressomd.magnetostatics.DipolarDirectSumGpu`
   performs the calculations in single precision on a Cuda-capable graphics card.
   The implementation is optimized for large systems of several thousand
   particles. It makes use of one thread per particle. When there are fewer
   particles than the number of threads the gpu can execute simultaneously,
   the rest of the gpu remains idle. Hence, the method will perform poorly
   for small systems.
 
-To use the methods, create an instance of either :class:`espressomd.magnetostatics.DipolarDirectSumCpu` or :class:`espressomd.magnetostatics.DipolarDirectSumGpu` and add it to the system's list of active actors. The only required parameter is the Prefactor :eq:`dipolar_prefactor`::
+To use the methods, create an instance of either :class:`~espressomd.magnetostatics.DipolarDirectSumCpu` or :class:`~espressomd.magnetostatics.DipolarDirectSumGpu` and add it to the system's list of active actors. The only required parameter is the Prefactor :eq:`dipolar_prefactor`::
 
   from espressomd.magnetostatics import DipolarDirectSumGpu
   dds = DipolarDirectSumGpu(bjerrum_length=1)
   system.actors.add(dds)
 
 
-For testing purposes, a variant of the dipolar direct sum is available which adds periodic copies to the system in periodic directions (:class:`espressomd.magnetostatics.DipolarDirectSumWithReplicaCpu`).
-
+For testing purposes, a variant of the dipolar direct sum is available which
+adds periodic copies to the system in periodic directions:
+:class:`~espressomd.magnetostatics.DipolarDirectSumWithReplicaCpu`.
 As it is very slow, this method is not intended to do simulations, but
-rather to check the results you get from more efficient methods like
-P3M.
+rather to check the results you get from more efficient methods like P3M.
 
+:class:`~espressomd.magnetostatics.DipolarDirectSumCpu` and
+:class:`~espressomd.magnetostatics.DipolarDirectSumWithReplicaCpu`
+do not support MPI parallelization.
 
 
 
@@ -154,7 +157,7 @@ an additive distance respectively. For the detailed description of the
 Barnes-Hut method application to the dipole-dipole interactions, please
 refer to :cite:`Polyakov2013`.
 
-To use the method, create an instance of :class:`espressomd.magnetostatics.DipolarBarnesHutGpu` and add it to the system's list of active actors::
+To use the method, create an instance of :class:`~espressomd.magnetostatics.DipolarBarnesHutGpu` and add it to the system's list of active actors::
 
   from espressomd.magnetostatics import DipolarBarnesHutGpu
   bh = DipolarBarnesHutGpu(prefactor=pf_dds_gpu, epssq=200.0, itolsq=8.0)
@@ -171,7 +174,7 @@ library for dipoles, if the methods support dipolar calculations. The feature
 feature. Dipolar calculations are only included in the ``dipolar`` branch of
 the Scafacos code.
 
-To use SCAFACOS, create an instance of :class:`espressomd.magnetostatics.Scafacos`
+To use SCAFACOS, create an instance of :class:`~espressomd.magnetostatics.Scafacos`
 and add it to the list of active actors. Three parameters have to be specified:
 
 * ``method_name``: name of the SCAFACOS method being used.

maintainer/CI/doc_warnings.sh

@@ -32,7 +32,7 @@
 regex_sphinx_broken_link='<code class=\"xref py py-[a-z]+ docutils literal notranslate\"><span class=\"pre\">(?!(int|float|bool|str|object|list|tuple|dict)<)[^<>]+?</span></code>(?!</a>)'
 
 # list of espresso modules not compiled in CI (visualization, scafacos)
-regex_ignored_es_features_ci='(visualization|[a-z]+\.[sS]cafacos)'
+regex_ignored_es_features_ci='^(espressomd\.)?(visualization|([a-z]+\.)?[sS]cafacos)'
 
 if [ ! -f doc/sphinx/html/index.html ]; then
     echo "Please run Sphinx first."
@@ -57,7 +57,7 @@ if [ $? = "0" ]; then
         # skip espresso modules not compiled in CI (visualization, scafacos)
         is_es_feature_skipped="false"
         if [ "${CI}" != "" ]; then
-            grep -Pq "^espressomd\.${regex_ignored_es_features_ci}" <<< "${reference}"
+            grep -Pq "${regex_ignored_es_features_ci}" <<< "${reference}"
             [ "$?" = "0" ] && is_es_feature_skipped="true"
         fi
         # private objects are not documented and cannot be linked
@@ -77,11 +77,22 @@ if [ $? = "0" ]; then
         filepath_rst=$(echo "${filepath_html}" | sed 's|/html/|/|')
         filepath_rst="${filepath_rst%.html}.rst"
         if [ -f "${filepath_rst}" ]; then
+            # look for the reference
             grep -q -F "\`${reference}\`" "${filepath_rst}"
             if [ $? = "0" ]; then
                 grep --color -FnHo -m 1 "\`${reference}\`" "${filepath_rst}" | tee -a doc_warnings.log~
                 continue
             fi
+            # if not found, check if reference was shortened, for example
+            # :class:`~espressomd.system.System` outputs a link named `System`
+            grep -q -P "^[a-zA-Z0-9_]+$" <<< "${reference}"
+            if [ $? = "0" ]; then
+                grep -q -P "\`~.+${reference}\`" "${filepath_rst}"
+                if [ $? = "0" ]; then
+                    grep --color -PnHo -m 1 "\`~.+${reference}\`" "${filepath_rst}" | tee -a doc_warnings.log~
+                    continue
+                fi
+            fi
         fi
         # if not in a .rst file, show the .html file without line number
         echo "${filepath_html}:\`${reference}\`" | tee -a doc_warnings.log~
@@ -92,7 +103,7 @@ if [ $? = "0" ]; then
     cat doc_warnings.log~ >> doc_warnings.log
     rm doc_warnings.log~
     # warn user about ignored features in CI
-    grep -Pq "espressomd\.${regex_ignored_es_features_ci}" doc_warnings.log
+    grep -Pq "${regex_ignored_es_features_ci}" doc_warnings.log
     if [ "$?" = "0" ] && [ "${CI}" = "" ]; then
         echo "(Note that features visualization and Scafacos are ignored in CI)"
     fi

samples/lj_liquid.py

@@ -186,7 +186,7 @@
     energies = system.analysis.energy()
     print(energies)
     obs_file.write('{ time %s } %s\n' % (system.time, energies))
-    linear_momentum = system.analysis.analyze_linear_momentum()
+    linear_momentum = system.analysis.linear_momentum()
     print(linear_momentum)
 
 #   write observables

samples/lj_liquid_distribution.py

@@ -217,7 +217,7 @@
     energies = system.analysis.energy()
     print(energies)
     obs_file.write('{ time %s } %s\n' % (system.time, energies))
-    linear_momentum = system.analysis.analyze_linear_momentum()
+    linear_momentum = system.analysis.linear_momentum()
     print(linear_momentum)
 
 #   write observables

samples/lj_liquid_structurefactor.py

@@ -194,7 +194,7 @@
     energies = system.analysis.energy()
     print(energies)
     obs_file.write('{ time %s } %s\n' % (system.time, energies))
-    linear_momentum = system.analysis.analyze_linear_momentum()
+    linear_momentum = system.analysis.linear_momentum()
     print(linear_momentum)
 
 

src/core/cells.cpp

@@ -382,13 +382,13 @@ void cells_resort_particles(int global_flag) {
       resort_particles = Cells::RESORT_GLOBAL;
       append_indexed_particle(local_cells.cell[0], std::move(part));
     }
-  }
-
+  } else {
 #ifdef ADDITIONAL_CHECKS
-  /* at the end of the day, everything should be consistent again */
-  check_particle_consistency();
-  check_particle_sorting();
+    /* at the end of the day, everything should be consistent again */
+    check_particle_consistency();
+    check_particle_sorting();
 #endif
+  }
 
   ghost_communicator(&cell_structure.ghost_cells_comm);
   ghost_communicator(&cell_structure.exchange_ghosts_comm);