Merge pull request #1667 from glotzerlab/release-4.4.0

Release 4.4.0

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 4.3.0
+current_version = 4.4.0
 commit = False
 tag = False
 parse = ^(?P<major>0|[1-9]\d*)\.(?P<minor>0|[1-9]\d*)\.(?P<patch>0|[1-9]\d*)(?:-(?P<prerelease>(?:0|[1-9]\d*|\d*[a-zA-Z-][0-9a-zA-Z-]*))(?:\.(?P<number>0|[1-9]\d*|\d*[a-zA-Z-][0-9a-zA-Z-]*)))?$

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -62,7 +62,7 @@ body:
     attributes:
       label: HOOMD-blue version
       description: What version of HOOMD-blue are you using?
-      placeholder: 4.3.0
+      placeholder: 4.4.0
     validations:
       required: true
   - type: markdown

.mailmap

@@ -174,3 +174,6 @@ Antonia Statt <[email protected]> Antonia Statt <>
 Alex Lee <[email protected]> Alex <[email protected]>
 Alex Lee <[email protected]> shihkual <[email protected]>
 Alex Lee <[email protected]> shihkual <[email protected]>
+Simone Ciarella <[email protected]> Ciarella, S <[email protected]>
+Simone Ciarella <[email protected]> SCiarella <[email protected]>
+Simone Ciarella <[email protected]> SCiarella <[email protected]>

BUILDING.rst

@@ -145,7 +145,7 @@ Clone using Git_::
 
    $ git clone --recursive https://github.com/glotzerlab/hoomd-blue
 
-Release tarballs are also available as `GitHub release`_ assets: `Download hoomd-4.3.0.tar.gz`_.
+Release tarballs are also available as `GitHub release`_ assets: `Download hoomd-4.4.0.tar.gz`_.
 
 .. seealso::
 
@@ -158,7 +158,7 @@ Release tarballs are also available as `GitHub release`_ assets: `Download hoomd
     Execute ``git submodule update --init`` to fetch the submodules each time you switch branches
     and the submodules show as modified.
 
-.. _Download hoomd-4.3.0.tar.gz: https://github.com/glotzerlab/hoomd-blue/releases/download/v4.3.0/hoomd-4.3.0.tar.gz
+.. _Download hoomd-4.4.0.tar.gz: https://github.com/glotzerlab/hoomd-blue/releases/download/v4.4.0/hoomd-4.4.0.tar.gz
 .. _GitHub release: https://github.com/glotzerlab/hoomd-blue/releases
 .. _git book: https://git-scm.com/book
 .. _Git: https://git-scm.com/

CHANGELOG.rst

@@ -7,6 +7,41 @@ Change Log
 4.x
 ---
 
+4.4.0 (2024-12-04)
+^^^^^^^^^^^^^^^^^^
+
+*Added*
+
+* ``hoomd.md.external.field.Magnetic`` computes forces and torques on particles from an external
+  magnetic field (`#1637 <https://github.com/glotzerlab/hoomd-blue/pull/1637>`__).
+* Tutorial on placing barriers
+  (`hoomd-examples/#111 <https://github.com/glotzerlab/hoomd-examples/pull/111>`__).
+
+*Fixed*
+
+* Use ``mpirun`` specific local ranks to select GPUs before checking ``SLURM_LOCALID``
+  (`#1647 <https://github.com/glotzerlab/hoomd-blue/pull/1647>`__).
+* Fix typographical errors in ``RevCross`` documentation
+  (`#1642 <https://github.com/glotzerlab/hoomd-blue/pull/1642>`__).
+* Use standards compliant ``thrust::get``
+  (`#1660 <https://github.com/glotzerlab/hoomd-blue/pull/1660>`__).
+
+*Changed*
+
+* Removed unused code
+  (`#1646 <https://github.com/glotzerlab/hoomd-blue/pull/1646>`__).
+* No longer issue a warning when ``hoomd.md.Integrator`` is used without an integration method
+  (`#1659 <https://github.com/glotzerlab/hoomd-blue/pull/1659>`__).
+* Increase performance of ``Force.forces``, ``Force.torques``, ``Force.energies``, and
+  ``Force.virials`` (`#1654 <https://github.com/glotzerlab/hoomd-blue/pull/1654>`__).
+
+*Deprecated*
+
+* ``num_cpu_threads > 1``. Use ``num_cpu_threads = 1``
+  (`#1656 <https://github.com/glotzerlab/hoomd-blue/pull/1656>`__).
+* ``HPMCIntegrator.depletant_fugacity > 0``
+  (`#1657 <https://github.com/glotzerlab/hoomd-blue/pull/1657>`__).
+
 4.3.0 (2024-10-24)
 ^^^^^^^^^^^^^^^^^^
 

CMakeLists.txt

@@ -14,7 +14,7 @@ add_subdirectory (CMake)
 
 ################################
 ## Version information
-set(HOOMD_VERSION_RAW "4.3.0")
+set(HOOMD_VERSION_RAW "4.4.0")
 string(REGEX MATCH "(.*)\\.(.*)\\.(.*)$" _hoomd_version_match ${HOOMD_VERSION_RAW})
 set(HOOMD_VERSION_MAJOR ${CMAKE_MATCH_1})
 set(HOOMD_VERSION_MINOR ${CMAKE_MATCH_2})

INSTALLING.rst

@@ -24,17 +24,17 @@ Conda package
 **HOOMD-blue** is available on conda-forge_ on the *linux-64*, *osx-64*, and *osx-arm64* platforms.
 Install the ``hoomd`` package from the conda-forge_ channel into a conda environment::
 
-    $ conda install hoomd=4.3.0
+    $ conda install hoomd=4.4.0
 
 ``conda`` auto-detects whether your system has a GPU and attempts to install the appropriate
 package. Override this and force the GPU enabled package installation with::
 
     $ export CONDA_OVERRIDE_CUDA="12.0"
-    $ conda install "hoomd=4.3.0=*gpu*" "cuda-version=12.0"
+    $ conda install "hoomd=4.4.0=*gpu*" "cuda-version=12.0"
 
 Similarly, you can force CPU only package installation with::
 
-    $ conda install "hoomd=4.3.0=*cpu*"
+    $ conda install "hoomd=4.4.0=*cpu*"
 
 .. note::
 

hoomd/data/typeparam.py

@@ -77,27 +77,31 @@ def __setitem__(self, key, value):
         Index types by name:
 
         .. skip: next if(not hoomd.version.md_built)
+
         .. code-block:: python
 
             langevin.gamma['A'] = 2.0
 
         Set parameters for multiple types:
 
         .. skip: next if(not hoomd.version.md_built)
+
         .. code-block:: python
 
             langevin.gamma[['B', 'C']] = 3.0
 
         Set type pair parameters with a tuple of names:
 
         .. skip: next if(not hoomd.version.md_built)
+
         .. code-block:: python
 
             lj.params[('A', 'A')] = dict(epsilon=1.5, sigma=2.0)
 
         Set parameters for multiple pairs (e.g. ('A', 'B') and ('A', 'C')):
 
         .. skip: next if(not hoomd.version.md_built)
+
         .. code-block:: python
 
             lj.params[('A', ['B', 'C'])] = dict(epsilon=0, sigma=0)
@@ -106,6 +110,7 @@ def __setitem__(self, key, value):
         'B'), and ('C', 'C')):
 
         .. skip: next if(not hoomd.version.md_built)
+
         .. code-block:: python
 
             lj.params[(['B', 'C'], ['B', 'C'])] = dict(epsilon=1, sigma=1)
@@ -122,11 +127,13 @@ def __getitem__(self, key):
         .. rubric:: Examples:
 
         .. skip: next if(not hoomd.version.md_built)
+
         .. code-block:: python
 
             gamma_A = langevin.gamma['A']
 
         .. skip: next if(not hoomd.version.md_built)
+
         .. code-block:: python
 
             lj_epsilon_AB = lj.params[('A', 'B')]['epsilon']
@@ -137,13 +144,15 @@ def __getitem__(self, key):
         returns multiple items in a dictionary:
 
         .. skip: next if(not hoomd.version.md_built)
+
         .. code-block:: python
 
             gammas = langevin.gamma[['A', 'B']]
 
         is equivalent to:
 
         .. skip: next if(not hoomd.version.md_built)
+
         .. code-block:: python
 
             gammas = {key: langevin.gamma[key] for key in ['A', 'B']}
@@ -170,6 +179,7 @@ def get(self, key, default):
         .. rubric:: Example:
 
         .. skip: next if(not hoomd.version.md_built)
+
         .. code-block:: python
 
             gamma_D = langevin.gamma.get('D', default=5.0)
@@ -188,6 +198,7 @@ def setdefault(self, key, default):
         .. rubric:: Example
 
         .. skip: next if(not hoomd.version.md_built)
+
         .. code-block:: python
 
             langevin.gamma.setdefault('D', default=5.0)
@@ -198,6 +209,7 @@ def __eq__(self, other):
         """Test for equality.
 
         .. skip: next if(not hoomd.version.md_built)
+
         .. code-block:: python
 
             langevin.gamma == lj.params
@@ -219,6 +231,7 @@ def default(self):
         Set a default value:
 
         .. skip: next if(not hoomd.version.md_built)
+
         .. code-block:: python
 
             langevin.gamma.default = 2.0
@@ -227,6 +240,7 @@ def default(self):
         keys in that dictionary:
 
         .. skip: next if(not hoomd.version.md_built)
+
         .. code-block:: python
 
             lj.params.default = dict(epsilon=0)
@@ -253,6 +267,7 @@ def to_base(self):
         .. rubric:: Example:
 
         .. skip: next if(not hoomd.version.md_built)
+
         .. code-block:: python
 
             plain_dict = lj.params.to_base()
@@ -265,6 +280,7 @@ def __iter__(self):
         .. rubric:: Example:
 
         .. skip: next if(not hoomd.version.md_built)
+
         .. code-block:: python
 
             for type_pair in lj.params:
@@ -278,6 +294,7 @@ def __len__(self):
         .. rubric:: Example:
 
         .. skip: next if(not hoomd.version.md_built)
+
         .. code-block:: python
 
             n_type_pairs = len(lj.params)

hoomd/hpmc/external/user.py

@@ -84,9 +84,9 @@ class CPPExternalPotential(ExternalField):
         Your code *must* return a value.
 
     .. _VectorMath.h: https://github.com/glotzerlab/hoomd-blue/blob/\
-            v4.3.0/hoomd/VectorMath.h
+            v4.4.0/hoomd/VectorMath.h
     .. _BoxDim.h: https://github.com/glotzerlab/hoomd-blue/blob/\
-            v4.3.0/hoomd/BoxDim.h
+            v4.4.0/hoomd/BoxDim.h
 
     .. rubric:: Example:
 

hoomd/hpmc/pair/user.py

@@ -76,7 +76,7 @@ class CPPPotentialBase(AutotunedObject):
                 HOOMD-blue source code.
 
     .. _VectorMath.h: https://github.com/glotzerlab/hoomd-blue/blob/\
-            v4.3.0/hoomd/VectorMath.h
+            v4.4.0/hoomd/VectorMath.h
 
     Note:
         Your code *must* return a value.

sphinx-doc/conf.py

@@ -63,8 +63,8 @@
 copyright = f'2009-{ year } The Regents of the University of Michigan'
 author = 'The Regents of the University of Michigan'
 
-version = '4.3.0'
-release = '4.3.0'
+version = '4.4.0'
+release = '4.4.0'
 
 language = 'en'
 

sphinx-doc/tutorials.rst

@@ -15,3 +15,4 @@ Tutorials
     tutorial/05-Organizing-and-Executing-Simulations/00-index
     tutorial/06-Modelling-Rigid-Bodies/00-index
     tutorial/07-Modelling-Patchy-Particles/00-index
+    tutorial/08-Placing-Barriers-in-the-Simulation-Box/00-index