Head #275

Removes one level on indentation from ghost_communicator()

…tutorial

@bindgens1

3219: Update Mac installation instructions r=jngrad a=mkuron Reported by @bindgens1 Co-authored-by: Michael Kuron <[email protected]>

3218: Update maintainer scripts, license headers, authors list r=KaiSzuttor a=jngrad Description of changes: - update maintainer scripts that process license headers - cleanup license header template: remove trailing whitespaces - cleanup license headers: fix copy-paste errors and missing asterisks in c++ files - release checklist: - add missing license headers - update year range in license headers - update authors list Co-authored-by: Jean-Noël Grad <[email protected]>

…tutorial

This commit makes the two cmake variables MPIEXEC_PREFLAGS and MPIEXEC_POSTFLAGS be taken into account in the cmdline of mpiexec-based unit tests. This commit changes

3197: LB tutorial refactoring r=jngrad a=KaiSzuttor Fixes espressomd#3205 * removed stokes drag part due to the result being possibly inconsistent under parameter changes * refactored the simulation code in the other parts Co-authored-by: Kai Szuttor <[email protected]> Co-authored-by: Jean-Noël Grad <[email protected]>

Remove obsolete warning on the rhomboid shape. Fix Sphinx syntax: `word` should be avoided (creates an HTML tag <cite>), replaced by *word* (italic via <em>), ``word`` (teletype via <span>) or :func:`word` (link). Fix math formula and function argument types.

Fix broken internal and external links, remove documentation of recently deleted Python samples, cleanup Sphinx syntax, fix typos.

…ghost-cleanup

Bump espresso version to 5.0-dev, update documentation.

…ghost-cleanup

…relation-corrected error estimates.

3225: Remove Affinity r=KaiSzuttor a=fweik Fixes espressomd#3224. Co-authored-by: Florian Weik <[email protected]>

…particle_data

fix tutorial check

… into reaction-tutorial

try fix test

Argument descriptions already in the docstrings of the linked functions.

@kosovan

Based on feedback from the ESPResSo summer school's user and developer meeting (@kosovan).

@christophlohrmann

Fix broken link, incorrect docstrings and copy-paste errors (based on inspection of the C++ code for the NPT integrator and offline discussion with @christophlohrmann).

@junghans

3234: Fix mpiio with stdlibc++ range checking r=fweik a=mkuron Fixes espressomd#3230. Reported by @junghans. When mpiio was used but no bonds were present, we would still try to copy zero bonds from a zero-length vector. This triggered an assertion when stdlibc++ range checking was enabled. Please tag for cherry-picking into 4.1.1. 3236: ESS2019 installation guide updates r=KaiSzuttor a=mkuron Lessons learned today: - We require MPI 3 because we depend on const-correctness in a few places. That means that OpenMPI 1.6.5 and lower are not supported anymore. - Installing the ROCm driver breaks access to /dev/kfd, causing hwloc initialization during `mpiexec` to hang. Rebooting helps. - Add matplotlib, ipython and jupyter to the Mac install guide. - Homebrew now defaults to Python 3, requires manually enabling cython, and it's unclear whether the hdf5 package still supports MPI (Homebrew/homebrew-core#26974) - Anaconda (~/anaconda[23]) and python.org packages (/Library/Python and /usr/local/bin) are also sources of conflict Please tag for the 4.1.1 release 3238: maintainer: Escape module python in wrapper script r=jngrad a=fweik Fixes espressomd#3237. Description of changes: - Added quotes around the module path in python wrapper script. Co-authored-by: Michael Kuron <[email protected]> Co-authored-by: Michael Kuron <[email protected]> Co-authored-by: Kai Szuttor <[email protected]> Co-authored-by: Florian Weik <[email protected]>

Note: in Python, a function taking positional arguments can take named arguments in any order.

3212: Remove unused force reduction function r=fweik a=hirschsn The function `reduce_forces_sum` was made obsolete by a538ebb Fixes # Description of changes: - Remove unused function PR Checklist ------------ - [ ] Tests? - [ ] Interface - [ ] Core - [ ] Docs? 3221: Make unit tests respect Cmake MPIEXEC_*FLAGS r=jngrad a=hirschsn There are two cmake flags called MPIEXEC_PREFLAGS and MPIEXEC_POSTFLAGS. This commit makes the unit test include these two variables in the creation of the cmdlines. These variables are useful for passing parameters to mpiexec, e.g. MPIEXEC_PREFLAGS="--bind-to;none". Fixes # Description of changes: - PR Checklist ------------ - [ ] Tests? - [ ] Interface - [ ] Core - [ ] Docs? 3232: Particle data cleanup r=KaiSzuttor a=fweik Description of changes: - Removed unused functions and macro 3240: Benchmark: Ferrofluid benchmark (derived from LJ one) r=fweik a=RudolfWeeber I did not include it into the benchmark cmake target, as it is not such a common scenario outside the ICP Co-authored-by: Steffen Hirschmann <[email protected]> Co-authored-by: Florian Weik <[email protected]> Co-authored-by: Rudolf Weeber <[email protected]>

Happens when calling `system.integrator.run(0)`. In that case the average instantaneous pressure is undefined and can only be NaN.

3202: clang-tidy: fix for empty config. r=jngrad a=KaiSzuttor we only have a CI job with maxset and clang-tidy. This PR fixes issues found with empty config. Co-authored-by: Kai Szuttor <[email protected]>

Installing ESPResSo with `make install DESTDIR="/path/to/es"` will install files in the wrong folder and set an incorrect runtime path in Cython shared objects, causing import errors. See full report: espressomd#3228 (comment)

When installing ESPResSo, the C++ shared objects and Cython shared objects are stored in the same folder. Since they have the same .so extension, when importing espressomd.cluster_analysis, the file cluster_analysis.py is loaded and the file cluster_analysis.so is automatically considered a Cython shared object, and Python fails to find the Cython-specific symbol PyInit_cluster_analysis. This is remediated by giving a different name to the C++ shared object.

Install the files in a different directory and check the python and tutorials/samples tests can still run with the installed files. Please note that pypresso will experience a major slowdown in CI when located outside the build directory, hence the 3h timeout. This job is meant to be run only during releases and in PRs that add new core modules.

Takes more than 1 hour to run in CI when pypresso is located outside the build directory.

3164: Separate quaternion algebra from particle rotation r=fweik a=jngrad Description of changes: - extract quaternion algebra from the `particle_data.hpp` and `rotation.hpp` files - removes code duplication caused by a (now resolved) circular dependency (see espressomd#3157) - makes it possible to replace the quaternion code by a dedicated library, e.g. [boost:qvm::quat](https://www.boost.org/doc/libs/1_68_0/libs/qvm/doc/index.html) or [boost::math::quaternion](https://www.boost.org/doc/libs/1_62_0/libs/math/doc/html/quaternions.html) in the core (see espressomd#2289), [rowan](https://rowan.readthedocs.io/en/latest/) in the interface (see espressomd#2964) - simplify code around call sites using Vector4d arithmetic, `std::tuple`, Particle references - documentation cleanup 3245: Fix thermostat and integrator checkpointing r=KaiSzuttor a=jngrad The checkpointing mechanism silently broke in 4.1 for the SD and NPT integrators and LB and NPT thermostats. This was fixed, and now all integrators and thermostats checkpoints are tested in CI. Co-authored-by: Jean-Noël Grad <[email protected]> Co-authored-by: Kai Szuttor <[email protected]>

3244: Update docs 4.1 r=fweik a=jngrad Provide links to Dockerfiles, fix links in 4.1 release notes, fix typos. 3250: core: virtual_sites: Removed default argument from virtual function and non-functional virtual COM feature r=jngrad a=fweik Description of changes: - Removed dead code (`VIRTUAL_SITES_COM`, `THERMOSTAT_IGNORE_NON_VIRTUAL`) - Removed default argument on virtual function Co-authored-by: Jean-Noël Grad <[email protected]> Co-authored-by: Florian Weik <[email protected]>

…possible

The installed files only exist if the Python bindings are enabled.

The clang:6.0 job fails due to undefined ASAN symbols. The logic to fix that error is in the pypresso wrapper.

3248: Fix cmake install on dev branch r=KaiSzuttor a=jngrad Porting espressomd#3228 to the dev branch Description of changes: - fix the CMake build system to include libraries in the list of installed files and test it in a dedicated CI job - fix the versioning of Cython .so shared objects - simplify the CMake tests 3251: Particle data r=jngrad a=fweik Fixes espressomd#3157. Description of changes: - Split definition of `struct Particle` from rest of particle data. Co-authored-by: Christoph Junghans <[email protected]> Co-authored-by: Jean-Noël Grad <[email protected]> Co-authored-by: Florian Weik <[email protected]>

Allow bool values in the script interface. The default value for box dimension fluctuations is now [True, True, True] instead of the counter-intuitive [0, 0, 0] that was implicitly converted to [1, 1, 1] in the core.

Average instantaneous pressure: instantaenous pressure divided by the number of steps in the integration (NaN if nsteps=0). Unused in the core and observables, inaccessible from the Python interface.

When the NpT integrator is initialized with incorrect values, halt script execution with an exception instead of initializing NVT.

Has been superseded by tutorial 12 constant pH.

They were listed as a dependencies of tutorial 06, but weren't actually included anywhere.

…f the correct resul

…:clear

… that it produces the same numbers as before).

The Python guard isn't necessary anymore because submodules are now installed in the Python package espressomd, and the testsuite itself already has a Python guard in the top-level CMakeLists.txt.

Remove the non-standard CMAKE_INSTALL_EXEC_PREFIX variable in favor of CMAKE_INSTALL_PREFIX. Install espressomd in the standard python3.X folder instead of the deprecated python3 folder. Remove duplicated code logic. Use explicit keyword arguments in calls to functions from distutils.sysconfig.

3252: Factor out ParticleList r=jngrad a=fweik Follow up on espressomd#3251. Description of changes: - Pulling `ParticleList` out of `particle_data.hpp` to get better header disentanglement. 3256: Remove tutorial 10 and unused LaTeX files r=fweik a=jngrad Closes espressomd#3211 Description of changes: - removed tutorial 10 - removed unused LaTeX preambles 3257: Remove PDB parser feature r=fweik a=jngrad The consensus offline at the ICP and online in espressomd#1441 is to drop support of the PDB parser feature in favor of the dedicated python package MDAnalysis. Co-authored-by: Florian Weik <[email protected]> Co-authored-by: Jean-Noël Grad <[email protected]>

3216: Refactor ghosts.cpp r=KaiSzuttor a=hirschsn More refactoring that builds upon espressomd#3212 Description of *major* changes: - remove GhostCommunication::mpi_comm as it is not used in ghosts.cpp, - make GhostCommunication::part_lists a std::vector, - remove static variables s_buffer and r_buffer, - factor out memory handling, - change loops to range based for, - use boost::mpi. - Replace the manual poststore and prefetch loops by find_ifs Mainly, ghosts.cpp now defines CommBuf, which is a container for the data to be sent or received as well as two classes (Archiver and BondArchiver), that insert and extract the memory from CommBuf. Some of these changes, like the removal of static variables, is necessary for my implementation of asynchronous ghost communication. PR Checklist ------------ - [ ] Tests? - [ ] Interface - [ ] Core - [ ] Docs? 3239: Added test criteria for the charged_system-2 tutorial r=RudolfWeeber,jngrad a=reinaual 3253: Refactor NpT public interface r=fweik a=jngrad Description of changes: - remove the silent conversion of the incorrect input parameter `dimension=[0,0,0]` to `[1,1,1]` in the core (bypassing sanity checks), now the checks will throw an exception for fixed-volume NpT; the original behavior was counter-intuitive and undocumented until 2 days ago - remove the automatic decay of NpT to NVT upon initialization of NpT with incorrect parameters - remove unused `p_inst_av` variable (average instantaneous pressure) - cleanup integrator documentation 3258: CMake minor fixes r=fweik a=jngrad Description of changes: - change next milestone to 4.2 - load `GNUInstallDirs` to make standard GNU paths accessible from CMake variables - simplify CMake logic and install in `python3.X` folder instead of the deprecated `python3` folder - add extra check to make sure install paths are correctly configured (all python and shared object files must be inside the package `espressomd`) Co-authored-by: Steffen Hirschmann <[email protected]> Co-authored-by: Florian Weik <[email protected]> Co-authored-by: Alexander Reinauer <[email protected]> Co-authored-by: Jean-Noël Grad <[email protected]>

According to docstring of espressomd.visualization_opengl.openGLLive the particle_type_materials needs strings

3260: OpenGL sphinx doc: particle_type_materials fix r=KaiSzuttor a=hirschsn Corrects a small bug in the OpenGL visualization tutorial: `particle_type_materials` expects strings. Also, the corresponding docstring should have an `array_like`. PR Checklist ------------ - [ ] Tests? - [ ] Interface - [ ] Core - [ ] Docs? Co-authored-by: Steffen Hirschmann <[email protected]>

Fix regression from 7f455cb.

Fix indentation, rename output variables, remove superfluous quotes around string variables. CMake quotes string variables implicitly when passed to functions, even if they contain whitespaces. Quotes are only necessary when setting a string variable.

3259: cmake: generate version.hpp at compile time to avoid rebuilds r=fweik a=junghans Make version.hpp a proper target. This prevents CMake from rebuilding all source files when a minor change is introduced anywhere in the docs, tests, or CMakeLists.txt files. Significantly reduce the number of source files including version.hpp to limit the number of objects to rebuild when the commit or branch changes. 3263: Clean up rotation flags r=jngrad a=fweik Description of changes: - Single source of truth for the rotation flags - Turned them into enum - Appropriate type - Made `ParticleProperties::rotation` exist idependent of features Co-authored-by: Christoph Junghans <[email protected]> Co-authored-by: Kai Szuttor <[email protected]> Co-authored-by: Christoph Junghans <[email protected]> Co-authored-by: Jean-Noël Grad <[email protected]> Co-authored-by: Florian Weik <[email protected]>

…ization of torque trafo

3265: Bit Mask utility function r=RudolfWeeber a=fweik Description of changes: - tuple interface for Utils::{Array, Vector} - Extract bit masking utility function to utils - Some small code modernization Co-authored-by: Florian Weik <[email protected]>

3203: Code cleanup with pylint r=KaiSzuttor a=jngrad Follow-up to espressomd#3194 Description of changes: - remove unused imports - rewrite wildcard imports as explicit imports - replace mutable optional parameters by immutable equivalents - fix LB thermostat checkpointing mechanism - cleanup and simplify conditional statements - refactor code with numpy and new espresso methods - remove unused variables/arguments - rename unused loop variables from `i` to `_` - fix broken numpy commands in parts of the testsuite that aren't executed - remove trailling whitespaces Co-authored-by: Jean-Noël Grad <[email protected]> Co-authored-by: Kai Szuttor <[email protected]>

…leanup

3268: core: Removed external force switching flags r=jngrad a=fweik Description of changes: - Removed flags to switch external force/torque on and of per particle. This does not actually improved performance and creates some noise. - Not user visible. Co-authored-by: Florian Weik <[email protected]>

…calc

3269: Move rotational thermostat out of rotation integrator r=RudolfWeeber a=fweik Description of changes: - Move rotational thermostat out of rotation integrator - Inline frame transformation - Made `ParticleForce` addable Co-authored-by: Florian Weik <[email protected]>

…ing interfaces

…ith those in the code.

3184: some modifications to constant-pH tutorial r=KaiSzuttor a=kosovan Fixes espressomd#3211 TODO (will do): - [x] First , explain how the reaction works, then discuss the acceptance - [x] Define pH, pK, activity and its relation chemical potential and concentration - [x] Refer to original literature for the acceptance, refer to review paper for discussion of peculiarities and pitfalls - [x] Include all physical parameters of the simulated system (box_l, N0, pKa, pH_range) in one block at the beginning of the script - [x] Set N0 and concentration in SI units, calculate box_l in sigma - [x] restrict the range of pH values to pH in [pK-2:pK+2] - [x] Remove the discussion of standard error of the mean, refer to Janke instead (statistical analysis is not the learning goal of this tutorial) - [x] Samples of alpha are correlated. Therefore, apply blocking method or some other analysis of correlated samples. - [x] Remove the comparison of histograms, or define a learning goal for this part. Currently, the comparison suggests that constant-pH results differ from theory, while the actual reason for this is insufficient sampling. For a sufficiently long simulations, they should not differ. This is very confusing, especially if it is not explained. Description of changes: - PR Checklist ------------ - [ ] Tests? - [ ] Interface - [ ] Core - [ ] Docs? Co-authored-by: Peter Košovan <[email protected]> Co-authored-by: Jonas Landsgesell <[email protected]> Co-authored-by: Peter Košovan <[email protected]> Co-authored-by: Peter Kosovan <[email protected]> Co-authored-by: Jean-Noël Grad <[email protected]>

3272: Ghost communicator cleanup r=RudolfWeeber a=fweik Description of changes: - Removed data_parts stored in GhostCommunicator - Removed redundant GhostCommunicators Co-authored-by: Florian Weik <[email protected]>

…flag mechanism

3276: Clean-up data_parts for ghost communication r=jngrad a=fweik Description of changes: - Removed data_parts left-overs from cell systems - Tuned GHOSTTRANS_* constants into enum - Calculate data_parts for vs relative on the fly. Co-authored-by: Florian Weik <[email protected]>

…espressomd-python

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