Change Log

5.x

5.1.1 (2025-03-19)

Fixed

• Prevent warnings about forces that provide torques (or not) (#2015).

• Compile without errors or warnings with CUDA 12.8 (#2019).

• force.Active applies torques correctly when the filter is not All (#2020).

• MD integrators no longer integrate the z degree of freedom in 2D simulation boxes (#2021).

• HPMC integrators no longer miss pairwise interactions when updaters, such as RemoveDrift move particles (#2022).

5.1.0 (2025-02-20)

Added

• The WangFrenkel potential (#1970).

• mpcd.update.ReverseNonequilibriumShearFlow (#1983).

• Support rocm 6 (#2002).

Fixed

• Correctly reference TriggeredOperation in inherited documentation (#1990).

Removed

• Support for rocm5 (#2002).

5.0.1 (2025-01-20)

Fixed

• Prevent missing 1 required positional argument: 'kT' errors when using NEC integrators (#1965).

• Note the current version of CUDA in the micromamba installation instructions (#1972).

• Provide a navigation bar on the 404 not found page in the documentation (#1986).

5.0.0 (2024-12-02)

Fixed

• Ensure that users set unique seeds on all partitions when performing Gibbs ensemble simulations (#1925)

• Mesh potentials return only one volume or area when ignore_type == True (#1928)

• Ensure correct methods are used by hoomd.mpcd.fill.VirtualParticleFiller for certain geometries, improving performance on the GPU in these cases (#1934).

• Correctly apply HPMCIntegrator.external_potentials in hoomd.hpmc.update.MuVT (#1941).

• Ensure GPU autotuners for MPCD methods are included in hoomd.Operations.is_tuning_complete and hoomd.Operations.tune_kernel_parameters through hoomd.mpcd.Integrator (#1951).

• Read after write hazard in the GPU implementation of Dipole, ALJ, and all Patchy potentials in hoomd.md.pair.ansiso (#1944).

• Read after write hazard in the GPU implementation of hoomd.md.mesh.conservation.Volume (#1953).

• hoomd.hpmc.pair.Pair.energy now computes the correct energy when there are multiple pair potentials with different r_cut values (#1955).

• Initializing large numbers (~100+ million) of MPCD particles with domain decomposition no longer causes a segmentation fault (#1897).

Added

• mpcd.geometry.ConcentricCylinders (#1894).

• kT parameter to all HPMC integrators. All HPMC-related operations respect the set kT (#1869).

• P property of hoomd.hpmc.compute.SDF (#1869).

• MPCD supports non-cubic collision cells, including both orthorhombic and triclinic cell shapes. The cell size is controlled by the number of cells along each lattice vector that defines the simulation box (#1950).

Changed

• betaP is replaced by P in hoomd.hpmc.update.BoxMC (#1869)

• hoomd.update.Clusters is now hoomd.update.GCA (#1926)

• hoomd.hpmc.external.wall.WallPotential is now hoomd.hpmc.external.WallPotential and can be added to IntegratorHPMC.external_potentials (#1941)

• hoomd.hpmc.external.field.Harmonic is now hoomd.hpmc.external.Harmonic and can be added to IntegratorHPMC.external_potentials (#1941).

• Document one class per html page and show inherited members in class documentation (#1952).

Removed

• _InternalCustomUpdater.update. (#1699).

• _InternalCustomTuner.tune. (#1699).

• _InternalCustomWriter.write. (#1699).

• HDF5Log.write. (#1699).

• hoomd.util.GPUNotAvailableError (#1708).

• Snapshot.from_gsd_snapshot (#1888).

• box1, box2, and variant arguments to hoomd.update.BoxResize (#1888).

• hpmc.pair.user.CPPPotentialBase, hpmc.pair.user.CPPPotential, hpmc.pair.user.CPPPotentialUnion, and hpmc.integrate.HPMCIntegrator.pair_potential (#1888).

• hoomd.hpmc.external.user.CPPExternalPotential (#1888).

• Implicit depletants from HPMC. (#1931).

• Device.num_cpu_threads. (#1932).

• Device.gpu_ids and the single-process multi-GPU feature (#1936).

• [c++] GlobalArray and GlobalVector (#1938).

• IntegratorHPMC.external_potential (#1941).

4.x

4.9.1 (2024-10-31)

Fixed

• Correct compile errors with -DENABLE_GPU=on -DHOOMD_GPU_PLATFORM=HIP (#1920)

4.9.0 (2024-10-29)

Added

• Support Python 3.13 (#1915)

• Patchy potentials for MD simulations: hoomd.md.pair.aniso.PatchyExpandedGaussian, hoomd.md.pair.aniso.PatchyExpandedLJ, hoomd.md.pair.aniso.PatchyExpandedMie, hoomd.md.pair.aniso.PatchyGaussian, hoomd.md.pair.aniso.PatchyLJ, hoomd.md.pair.aniso.PatchyMie, and hoomd.md.pair.aniso.PatchyYukawa (#1412).

• Double-well potentials in HPMC: hoomd.hpmc.pair.LJGauss and hoomd.hpmc.pair.OPP (#1889).

• Mesh potentials: hoomd.md.mesh.bending.BendingRigidity, hoomd.md.mesh.bending.Helfrich, hoomd.md.mesh.conservation.Area, hoomd.md.mesh.conservation.TriangleArea, and hoomd.md.mesh.conservation.Volume (#1792, #1793, #1794, #1795).

• start and end arguments to hoomd.write.Burst.dump (#1870)

• hoomd.mpcd.geometry.CosineChannel for a serpentine (cosine) channel (#1836).

• hoomd.mpcd.geometry.CosineExpansionContraction for an expansion-contraction channel (#1836).

Fixed

• Errors in the documentation (#1830, #1861, #1872, #1884, #1896).

• Thermalize momenta of particles with floppy body tags (#1891).

• Spheropolyhedra with two vertices can now be saved as a valid gsd_shape_spec (#1898).

Changed

• Improved build instructions (#1909).

4.8.2 (2024-07-23)

Fixed

• Correct citation to Langevin piston paper (#1849).

• External walls, external fields, and constrains can now be implemented via external plugins (#1849).

• Prevent compile errors with -DENABLE_GPU=on -DHOOMD_GPU_PLATFORM=HIP (#1851).

• Prevent /usr/lib64/slurm/auth_munge.so: undefined symbol: slurm_conf error on Purdue Anvil (#1850).

4.8.1 (2024-07-18)

Fixed

• Prevent illegal instruction when accessing 0 length snapshot arrays (#1846)

• Fix MPCD compiler warning. (#1845)

4.8.0 (2024-07-11)

Added

• hoomd.mpcd reimplements the MPCD method for simulating hydrodynamic interactions. See the migrating page for an overview and individual class and method documentation for more information (#1784).

• MPCD tutorial.

• Support numpy 2.0 (#1797)

• hoomd.hpmc.external.External provides an abstract interface to external potentials (#1811).

• hoomd.hpmc.external.Linear computes the potential as a linear function of the distance from a point to a plane (#1811).

• HPMCIntegrator.external_potentials sets the list of external potentials applied to the system (#1811).

• hpmc.pair.ExpandedGaussian computes the expanded Gaussian pair potential in HPMC (#1817).

Changed

• Miscellaneous documentation improvements (#1786, #1800, #1820).

• Provide an error message for invalid Ellipsoid shape parameters (#1785).

• Provide the full CUDA error message when scanning devices (#1803).

• Test with gcc14, clang17, and clang18. No longer test with clang10, clang11, or clang12. (#1798, #1816).

• Ensure that Gaussian-type pair potentials have positive sigma values (#1810).

• Demonstrate Step and AngularStep in the tutorial “Modelling Patchy Particles”.

• Fixed typographical errors in all tutorials.

Fixed

• Issue the proper error message when ALJ.shape is not set for all particle types (#1808).

• Correctly apply Brownian torque when elements of the inertia tensor are 0 (#1825).

Deprecated

• HPMCIntegrator.external_potential - use HPMCIntegrator.external_potentials (#1811).

• hoomd.hpmc.external.user.CPPExternalPotential - use hoomd.hpmc.external.Linear or write a custom component in C++ (#1811).

Removed

• Support for Python 3.8 (#1797).

4.7.0 (2024-05-16)

Fixed

• md.methods.rattle.Brownian executes without causing a segmentation fault on the CPU with domain decomposition (#1748).

• Compile BoxDim.h without warnings (#1756).

• Do not compute dipole-dipole interactions that are not necessary (#1758).

• Correctly define the units of gamma in md.methods.Langevin (#1771).

• Fix compile errors with external components that use the Expanded Mie potential (#1781).

• Allow HPMC pair potentials to be subclassed in external components (#1780).

Added

• “How to tune move sizes in multicomponent HPMC systems” documentation page (#1750).

• hoomd.box.from_basis_vectors - construct a box from arbitrary basis vectors (#1769).

Changed

• Make readthedocs builds more reproducible (#1758).

4.6.0 (2024-03-19)

Fixed

• create_state_from_gsd reads bond/angle/dihedral/improper/pair types when there are no corresponding groups (#1729).

Added

• hoomd.variant.box.BoxVariant - Describe boxes that change as a function of timestep (#1685).

• hoomd.variant.box.Constant - A constant box (#1685).

• hoomd.variant.box.Interpolate - Linearly interpolate between two boxes (#1685).

• hoomd.variant.box.InverseVolumeRamp - Linearly ramp the inverse volume of the system (#1685).

• hoomd.hpmc.update.QuickCompress now accepts a hoomd.variant.box.BoxVariant object for target_box (#1736).

• box argument to hoomd.update.BoxResize that accepts a hoomd.variant.box.BoxVariant (#1740).

• hoomd.hpmc.pair.Union computes pair potentials between unions of points. Replaces CPPPotentialUnion (#1725).

• hoomd.hpmc.pair.Step - A step function potential (#1732).

• hoomd.hpmc.pair.AngularStep - Angular patches on particles with step function interactions (e.g. Kern-Frenkel) (#1728).

Changed

• Use FindPython on modern CMake installations. You may need to adjust build scripts in cases where the new behavior does not exactly match the old (i.e. use -DPython_EXECUTABLE in place of -DPYTHON_EXECUTABLE) (#1730).

• External components must switch from pybind11_add_module to hoomd_add_module (#1730).

Deprecated

• box1, box2, and variant arguments to hoomd.update.BoxResize (#1740).

4.5.0 (2024-02-13)

Fixed

• hoomd.hpmc.update.Shape properly restores shape alchemy parameters on rejected trial moves (#1696).

• hoomd.hpmc.update.Shape now functions with hoomd.device.GPU (#1696).

• hoomd.hpmc.update.MuVT applies external potentials (#1711).

• hoomd.hpmc.update.QuickCompress can now reshape boxes with tilt factors <= 0 (#1709).

Added

• Improve component build documentation and link to the hoomd-component-template repository (#1668).

• hoomd.md.improper.Periodic - CHARMM-like periodic improper potential (#1662).

• allow_unsafe_resize flag to hoomd.hpmc.update.QuickCompress (#1678).

• hoomd.error.GPUNotAvailableError (#1694).

• HPMC compile time pair potential framework (CPU only). Allows potential energy in HPMC simulations without CPPPotential.

  • hoomd.hpmc.pair.LennardJones - Evaluate Lennard Jones energy between particles (#1676).

  • HPMCIntegrator.pair_potentials - Set a list of pair potentials to evaluate (#1676).

  • HPMCIntegrator.pair_energy (loggable) - Total pair energy from all pair potentials. (#1676).

Deprecated

• _InternalCustomUpdater.update. (#1692).

• _InternalCustomTuner.tune. (#1692).

• _InternalCustomWriter.write. (#1692).

• HDF5Log.write. (#1692).

• hoomd.util.GPUNotAvailableError (#1694).

• hoomd.hpmc.pair.user.CPPPotentialBase (#1676).

• hoomd.hpmc.pair.user.CPPPotential - Use a built-in potential or compile your code in a component (#1676).

• hoomd.hpmc.pair.user.CPPPotentialUnion - Use a built-in potential or compile your code in a component (#1676).

• HPMCIntegrator.pair_potential - Use compiled potentials with pair_potentials (#1676).

• Single-process multi-gpu code path (#1706).

Changed

• Refactored the C++ API for PatchEnergy potentials (#1676).

• Removed unused Operation._children methods (#1713).

4.4.1 (2023-12-18)

Fixed

• Correct net_virial values in local snapshots (#1672).

• Improve HPMC performance on the CPU when using a pair potential (#1679).

• Improve HPMC performance with 3D hard shapes (#1679).

• Improve HPMC performance on the CPU (#1687).

Changed

• Provide support via GitHub discussions (#1671).

4.4.0 (2023-12-04)

Added

• hoomd.md.external.field.Magnetic computes forces and torques on particles from an external magnetic field (#1637).

• Tutorial on placing barriers (hoomd-examples/#111).

Fixed

• Use mpirun specific local ranks to select GPUs before checking SLURM_LOCALID (#1647).

• Fix typographical errors in RevCross documentation (#1642).

• Use standards compliant thrust::get (#1660).

Changed

• Removed unused code (#1646).

• No longer issue a warning when hoomd.md.Integrator is used without an integration method (#1659).

• Increase performance of Force.forces, Force.torques, Force.energies, and Force.virials (#1654).

Deprecated

• num_cpu_threads > 1. Use num_cpu_threads = 1 (#1656).

• HPMCIntegrator.depletant_fugacity > 0 (#1657).

4.3.0 (2023-10-24)

Fixed

• md.alchemy.methods.NVT now evolves the elements provided in alchemical_dof (#1633).

• More consistent notice messages regarding MPI ranks used in GPU selection (#1635).

• hoomd.hpmc.compute.SDF computes correct pressures with patchy potentials. (#1636).

Added

• Support GCC 13 (#1634).

• Support Python 3.12 (#1634).

• tau parameter to hoomd.md.methods.thermostats.Bussi (#1619).

Changed

• Revise class documentation. (#1628).

• Add more code snippets to the class documentation (#1628).

4.2.1 (2023-10-02)

Fixed

• hoomd.write.Table correctly displays floating point values that are exactly 0.0 (#1625).

• hoomd.write.HDF5Log defaults to "f8" formatting except when the value is an int, or a numpy.number (#1620).

• Attempt to workaround PMI_Init returned 1 error on OLCF Frontier (#1629).

• Apple clang 15 compiles HOOMD-blue without errors (#1626).

4.2.0 (2023-09-20)

Fixed

• Make HDF5Log example more visible (#1602).

• Access valid GPU memory in hoomd.hpmc.update.Clusters (#1607).

• Test suite passes on the ROCm GPU platform (#1607).

• Provide an error message when using md.external.field.Periodic in 2D (#1603).

• hoomd.write.GSD reports “File exists” in the exception description when using the 'xb' mode and the file exists (#1609).

• Write small numbers correctly in hoomd.write.Table (#1617).

• Make examples in hoomd.md.methods.NVE and hoomd.md.methods.DisplacementCapped more visible (#1601).

Added

• Documentation page: “How to apply arbitrary forces in MD” (#1610).

• Documentation page: “How to prevent particles from moving” (#1611).

• Documentation page: “How to minimize the potential energy of a system” (#1614).

• Documentation page: “How to continuously vary potential parameters” (#1612).

• Documentation page: “How to determine the most efficient device” (#1616).

• Documentation page: “How to choose the neighbor list buffer distance” (#1615).

• Documentation page: “How to compute the free energy of solids” (#1613).

• MPCD particle data is now available included in Snapshot (#1580).

• Add variable parameters to hpmc.external.user.CPPExternalPotential (#1608).

Changed

• Removed the unused ExternalFieldComposite.h and all the related ExternalFieldComposite* (#1604).

4.1.0 (2023-08-07)

Fixed

• Improved documentation (#1585).

• Update mesh documentation (#1587).

• Follow detailed balance in hoomd.hpmc.update.Shape (#1595).

• pre-commit environment installs correctly on macos-arm64 (#1597).

• Install all HPMC headers for use by plugins (#1573).

• Bond potentials can now be implemented via external plugins (#1591).

Added

• Tested example code snippets in select modules (#1574) (#1586).

• hoomd.util.make_example_simulation - create an example Simulation object (#1574) (#1586).

• hoomd.write.Burst now has a __len__ method (#1575).

• Support clang 15 and 16 on Linux (#1593).

• hoomd.write.HDF5Logger - write log quantities to HDF5 files (#1588).

• default_gamma and default_gamma_r arguments to hoomd.md.methods.rattle.Brownian hoomd.md.methods.rattle.Langevin, and hoomd.md.methods.rattle.OverdampedViscous (#1589).

4.0.1 (2023-06-27)

Fixed

• Prevent ValueError: signal only works in main thread of the main interpreter when importing hoomd in a non-main thread (#1576).

• The recommended conda install commands find the documented version (#1578).

• CMake completes without error when HOOMD_GPU_PLATFORM=HIP (#1579).

• Tests pass with GSD 3.0.0 installed (#1577).

• Provide full CUDA error message when possible (#1581).

• Notice level 4 gives additional GPU initialization details (#1581).

• Show particle out of bounds error messages in exception description (#1581).

Changed

• Package source in hoomd-x.y.z.tar.gz (previously hoomd-vx.y.z.tar.gz) (#1572).

4.0.0 (2023-06-06)

Fixed

• Fix error with MPI_Allreduce on OLCF Frontier (#1547).

• Correct equations in virial pressure documentation (#1548).

• Work around cases where Python’s garbage collector fails to collect Operation objects (#1457).

• Incorrect behavior with hpmc.external.user.CPPExternalPotential in MPI domain decomposition simulations (#1562).

Added

• hoomd.md.ConstantVolume integration method (#1419).

• hoomd.md.ConstantPressure integration method, implementing the Langevin piston barostat (#1419).

• Thermostats in hoomd.md.methods.thermostats that work with ConstantVolume and ConstantPressure, including the new Bussi-Donadio-Parrinello thermostat (#1419).

• hoomd.md.external.wall.Gaussian (#1499).

• hoomd.write.GSD.maximum_write_buffer_size - Set the maximum size of the GSD write buffer (#1541).

• hoomd.write.GSD.flush - flush the write buffer of an open GSD file (#1541).

• On importing hoomd, install a SIGTERM handler that calls sys.exit(1) (#1541).

• More descriptive error messages when calling Simulation.run (#1552).

• hoomd.Snapshot.from_gsd_frame - convert a gsd.hoomd.Frame object to hoomd.Snapshot (#1559).

• hoomd.device.NoticeFile - a file-like object that writes to hoomd.device.Device.notice (#1449).

• hoomd.write.Burst - selective high-frequency frame writing to GSD files (#1543).

• Support LLVM 16 (#1568).

• More detailed status message for found CUDA libraries (#1566).

Changed

• hoomd.md.constrain.Rigid no longer takes diameters or charges as keys in the body parameters. create_bodies method now takes an optional charges argument to set charges (#1350).

• Control the precision with the CMake options HOOMD_LONGREAL_SIZE (default: 64) and HOOMD_SHORTREAL_SIZE (default: 32) (#355).

• [developers] ShortReal and LongReal types enable mixed precision implementations (#355).

• hoomd.md.constrain.Rigid now updates constituent particle types each step (#1440).

• Moved hoomd.mesh.Mesh.triangles to hoomd.mesh.Mesh.triangulation (#1464).

• hoomd.write.GSD does not write particles/diameter by default (#1266).

• Updated tutorials to use HOOMD-blue v4 API, work with up to date releases of freud, gsd, and signac. Also make general improvements to the tutorials.

• Document changes needed to migrate from v3 to v4 in the migration guide.

• More descriptive error messages when calling Simulation.run (#1552).

• Increase performance of hoomd.write.GSD (#1538).

• Increase performance of hoomd.State.get_snapshot in serial (#1538).

• hoomd.write.GSD.dynamic now allows fine grained control over individual particle fields (#1538).

• No longer test with GCC 7-8, Python 3.6-3.7, or Clang 6-9) (#1544).

• Improved error messages with NVRTC compiled code (#1567).

Deprecated

• Scalar, Scalar2, Scalar3, and Scalar4 data types. Use LongReal[N] instead in new code (#355).

• hoomd.Snapshot.from_gsd_snapshot - use hoomd.Snapshot.from_gsd_frame (#1559).

Removed

• fix_cudart_rpath CMake macro (#1383).

• ENABLE_MPI_CUDA CMake option (#1401).

• Berendsen, NPH, NPT, NVE, NVT MD integration methods (#1419).

• hoomd.write.GSD.log (#1480).

• CMake option and compiler definition SINGLE_PRECISION (#355).

• charges key in hoomd.md.constrain.Rigid.body (#1496).

• diameter key in hoomd.md.constrain.Rigid.body. (#1496).

• hoomd.md.dihedral.Harmonic. (#1496).

• hoomd.device.GPU.memory_traceback parameter. (#1496).

• hoomd.md.pair.aniso.Dipole.mode parameter. (#1496).

• hoomd.md.pair.aniso.ALJ.mode parameter (#1496).

• hoomd.md.pair.Gauss (#1499).

• hoomd.md.external.wall.Gauss (#1499).

• msg_file property and argument in hoomd.device.Device. (#1499).

• The sdf attribute of hoomd.hpmc.compute.SDF - use sdf_compression (#1523).

• alpha parameter and attribute in Langevin, BD, and OverdampedViscous integration methods (#1266).

• needsDiameter and setDiameter API in C++ potential evaluators (#1266).

v3.x

v3.11.0 (2023-04-14)

Added:

• hoomd.md.Integrator.validate_groups verifies that MD integration methods are applied to distinct subsets of the system and that those subsets consist of integrable particles (automatically called when attached) (#1466).

Changed:

• hoomd.hpmc.compute.SDF computes pressures for systems of concave and non-monotonic patch interactions (#1391).

• Reorganize documentation contents to fit in the sidebar, including landing pages for tutorials and how-to guides (#1526).

Fixed:

• Improved readability of images in the documentation (#1521).

• hoomd.write.Table now raises a meaningful error when given incorrect logger categories (#1510).

• Correctly document the 1/2 scaling factor in the pairwise virial computation (#1525).

• thermalize_particle_momenta now sets 0 velocity and angular momentum for rigid constituent particles (#1472).

• Reduce likelihood of data corruption when writing GSD files (#1531).

• Clarify migration process for hoomd.md.pair.ExpandedLJ (#1501).

Deprecated:

• The sdf attribute of hoomd.hpmc.compute.SDF - use sdf_compression (#1391).

v3.10.0 (2023-03-14)

Added:

• The message_filename property and argument to Device, CPU, and GPU to replace msg_file (#1497).

• hoomd.md.pair.Gaussian to replace hoomd.md.pair.Gauss (#1497).

• hoomd.md.pair.ExpandedGaussian - the expanded Gaussian pair force (#1493).

• Guide: How to apply arbitrary pair potentials in HPMC (#1505).

Changed:

• Use furo style for HTML documentation (#1498).

Fixed:

• The hoomd.md.pair potentials ExpandedLJ, ExpandedMie, LJGauss, and TWF now shift V(r_cut) to 0 properly when mode == 'shift' (#1504).

• Corrected errors in the pair potential documentation (#1504).

• Note that the 'body' exclusion should be used with hoomd.md.constrain.Rigid (#1465).

• Correctly identify the 'xyz' mode in hoomd.md.methods.NPH (#1509).

Deprecated:

• The msg_file property and argument to Device, CPU, and GPU.

• hoomd.md.pair.Gauss.

v3.9.0 (2023-02-15)

Added:

• GPU code path for hoomd.update.BoxResize (#1462).

• logger keyword argument and property to hoomd.write.GSD (#1481).

Changed:

• Issue FutureWarning warnings when using deprecated APIs (#1485).

• Reformat the list of deprecated features. (#1490).

• In simulations with rigid bodies, remove D degrees of freedom when the system is momentum conserving (#1467).

Fixed:

• Compile without errors using hipcc and ROCM 5.1.0 (#1478).

• Document that hoomd.md.force.Force can be added to Operations.computes (#1489).

• hoomd.md.constrain.Rigid.create_bodies completes without segmentation faults when particle body tags are not -1 (#1476).

• hoomd.hpmc.compute.FreeVolume computes the free area correctly in 2D simulations (#1473).

Deprecated:

• Deprecate write.GSD log keyword argument and property in favor of logger (#1481).

v3.8.1 (2023-01-27)

Fixed:

• #1468: Conserve linear momentum in simulations using hoomd.md.constrain.Rigid on more than 1 MPI rank.

v3.8.0 (2023-01-12)

Added

• Support Python 3.11.

• Support CUDA 11.8.

• Support CUDA 12.0.0 final.

Fixed

• Improve numerical stability of orientation quaternions when using hoomd.md.update.ActiveRotationalDiffusion

• Reduced memory usage and fix spurious failures in test_nlist.py.

• Avoid triggering TypeError("expected x and y to have same length") in hoomd.hpmc.compute.SDF.betaP.

Deprecated

• The following integration methods are deprecated. Starting in v4.0.0, the same functionalities will be available via hoomd.md.methods.ConstantVolume/ hoomd.md.methods.ConstantPressure with an appropriately chosen thermostat argument.

  • hoomd.md.methods.NVE

  • hoomd.md.methods.NVT

  • hoomd.md.methods.Berendsen

  • hoomd.md.methods.NPH

  • hoomd.md.methods.NPT

Removed

• Support for CUDA 10.

v3.7.0 (2022-11-29)

Added

• Neighborlist.r_cut sets the base cutoff radius for neighbor search - for use when the neighbor list is used for analysis or custom Python code.

• Neighborlist.cpu_local_nlist_arrays provides zero-copy access to the computed neighbor list.

• Neighborlist.gpu_local_nlist_arrays provides zero-copy access to the computed neighbor list.

• Neighborlist.local_pair_list provides the rank local pair list by index.

• Neighborlist.pair_list provides the global pair list by tag on rank 0.

• hoomd.md.dihedral.Periodic - a new name for the previous Harmonic potential.

• default_gamma and default_gamma_r arguments to the hoomd.md.methods: Brownian, Langevin, and OverdampedViscous.

• reservoir_energy loggable in hoomd.md.methods.Langevin.

• hoomd.md.force.Constant applies constant forces and torques to particles.

Changed

• [plugin developers] Refactored the LocalDataAccess C++ classes to add flexibility.

Fixed

• hoomd.hpmc.nec integrators compute non-infinite virial pressures for 2D simulations.

• Raise an exception when attempting to get the shape specification of shapes with 0 elements.

• Box conversion error message now names hoomd.Box.

Deprecated

• hoomd.md.dihedral.Harmonic - use the functionally equivalent hoomd.md.dihedral.Periodic.

• charges key in hoomd.md.constrain.Rigid.body.

• diameters key in hoomd.md.constrain.Rigid.body.

v3.6.0 (2022-10-25)

Changed

• In hoomd.md.pair.aniso.ALJ, shape.rounding_radii now defaults to (0.0, 0.0, 0.0).

• Revise hoomd.md.pair.aniso.ALJ documentation.

• hoomd.md.force.Force instances can now be added to the Operations list allowing users to compute force, torque, energy, and virials of forces that are not included in the dynamics of the system.

• [developers]: Removed internal methods _remove and _add from the data model.

Fixed

• Increase the performance of md.pair.Table on the CPU.

• Improve accuracy of hoomd.hpmc.update.BoxMC when used with patch potentials.

• Provide an accurate warning message when creating the state with many bond/angle/… types.

• Add missing documentation for hoomd.md.methods.Berendsen.

• CVE-2007-4559

v3.5.0 (2022-09-14)

Added

• Example plugin that demonstrates how to add a MD pair potential.

• Support a large number of particle and bond types (subject to available GPU memory and user patience) for the Cell neighbor list, MD pair potentials, MD bond potentials, Brownian, and Langevin integration methods.

Changed

• Raise an error when initializing with duplicate types.

• hpmc.compute.SDF now computes pressures of systems with patch interactions.

• Raise descriptive error messages when the shared memory request exceeds that available on the GPU.

Fixed

• Include all Neighborlist attributes in the documentation.

• Memory allocation errors in C++ now result in MemoryError exceptions in Python.

• Add missing Autotuned.h header file.

• External components build correctly when ENABLE_MPI=on or ENABLE_GPU=on.

• Type parameter validation when items contain numpy.ndarray elements.

• Compile with CUDA 12.0.

Deprecated

• Device.memory_traceback attribute. This attribute has no effect.

v3.4.0 (2022-08-15)

Added

• The new HOOMD-blue logo is now available in the documentation.

• hoomd.md.methods.DisplacementCapped class for relaxing configurations with overlaps.

• hoomd.md.methods.rattle.DisplacementCapped class for relaxing configurations with overlaps.

• hoomd.device.Device.notice - print user-defined messages to the configured message output stream.

• Tutorial: Modelling Rigid Bodies.

• AutotunedObject class that provides an interface to read and write tuned kernel parameters, query whether tuning is complete, and start tuning again at the object level.

• is_tuning_complete method to Operations. Check whether kernel parameter tuning is complete for all operations.

• tune_kernel_parameters methods to Operations and many other classes. Start tuning kernel parameters in all operations.

• hoomd.md.HalfStepHook - extensible hook class called between step 1 and 2 of MD integration.

• hoomd.md.Integrator.half_step_hook - property to get/set the half step hook.

Fixed

• Active forces on manifolds now attach to the Simulation correctly.

• hoomd.update.FilterUpdater now accepts hoomd.filter.CustomFilter subclasses.

• Correct error message is given when a sequence like parameter is not given to a type parameter.

• Fix non-axis-aligned Cylinder walls in MD.

• hoomd.md.constrain.Constraint now has hoomd.md.force.Force as a base class.

• Provide a warning instead of an error when passing an out of range seed to the Simulation constructor.

• Compile with current versions of HIP and ROCm.

• Compilation errors with CUDA >=11.8.

v3.3.0 (2022-07-08)

Added

• A decorator that modifies the namespace of operation and custom action classes hoomd.logging.modify_namespace.

• Tuner for the neighbor list buffer size hoomd.md.tune.NeighborListBuffer.

• Solver infrastructure for optimization problems.

• Simulation.initial_timestep: the timestep on which the last call to run started.

• variant_like, trigger_like, and filter_like typing objects for documentation.

Changed

• Removed "__main__" from some user custom action logging namespaces.

Fixed

• Improve documentation.

• Non-default loggables can now be explicitly specified with Logger.add.

• Iteration of Logger instances.

• The logging category of hoomd.md.Integrate.linear_momentum

v3.2.0 (2022-05-18)

Added

• hoomd.md.nlist.Neighborlist.num_builds property - The number of neighbor list builds since the last call to Simulation.run.

• hoomd.md.nlist.Cell.dimensions property - The dimensions of the cell list.

• hoomd.md.nlist.Cell.allocated_particles_per_cell property - The number of particle slots allocated per cell.

• hoomd.mesh.Mesh - Triangular mesh data structure.

• hoomd.md.mesh.bond - Bond potentials on mesh edges.

• Support gcc 12.

• Support clang 14.

• Set ENABLE_LLVM=on in conda binary builds.

Fixed

• Clarify documentation.

• Box.dimension reports the correct value when reading in 2D boxes from GSD files generated in HOOMD v2.

• Improve performance of run time compiled HPMC potentials on the CPU.

• Pressing Ctrl-C or interrupting the kernel in Jupyter stops the run at the end of the current timestep.

v3.1.0 (2022-04-27)

Added

• Support LLVM 13 when ENABLE_LLVM=on.

• hoomd.md.pair.LJGauss - Lennard-Jones-Gaussian pair potential.

• hoomd.md.alchemy.methods.NVT - Alchemical molecular dynamics integration method.

• hoomd.md.alchemy.pair.LJGauss - Lennard-Jones-Gaussian pair potential with alchemical degrees of freedom.

• hoomd.hpmc.update.Shape - Alchemical hard particle Monte Carlo through shape change moves.

• hoomd.hpmc.shape_move.Elastic - Shape move with elastic potential energy penalty.

• hoomd.hpmc.shape_move.ShapeSpace - Moves in a user defined shape space.

• hoomd.hpmc.shape_move.Vertex - Translate shape vertices.

Changed

• HPMC fugacity is now a per-type quantity.

• Improved documentation.

• [developers] Reduced the time needed for incremental builds.

• [developers] Reduced memory needed to compile HOOMD.

Fixed

• ALJ unit test passes in Debug builds.

• Add quotes to conda-forge gpu package installation example.

• hoomd.md.force.Custom zeroes forces, torques, energies, and virials before calling set_forces.

• Point tarball download link to https://github.com/glotzerlab/hoomd-blue/releases.

Deprecated

• hoomd.md.pair.aniso.ALJ.mode - parameter has no effect.

• hoomd.md.pair.aniso.Dipole.mode - parameter has no effect.

v3.0.1 (2022-04-08)

Fixed

• Display status of trunk-patch branch in the GitHub actions badge.

• Add EvaluatorPairTable.h to installation directory.

• Add hoomd.filter.Rigid to the documentation.

• Prevent TypeError: 'bool' object is not iterable errors when comparing Tag filters with different lengths arrays.

• Simulation.tps and Simulation.walltime update every step of the run.

v3.0.0 (2022-03-22)

Overview

HOOMD-blue v3.0.0 is the first production release with the new API that has been developed and implemented over more than 2 years. Those still using v2.x will need to make changes to their scripts to use v3. See the Migrating to the latest version page for an overview and individual class and method documentation for more information. To summarize, the new API is object oriented, allows HOOMD-blue to work effectively as a Python package, and provides more hooks for Python code to directly interface with the simulation.

New features in v3 since v2.9.7:

• Zero-copy data access through numpy and cupy.

• Triggers determine what timesteps operations execute on.

• User-defined operations, triggers, particle filters, variants, and forces.

• Logging subsystem supports array quantities.

• Implicit depletants for 2D shapes in HPMC.

• Harmonically mapped averaging for MD thermodynamic quantities of crystals.

• TWF and OPP pair potentials.

• Tether bond potential.

• Manifold constraints for MD integration methods (using RATTLE) and active forces.

• Document code architecture in ARCHITECTURE.md.

• Overdamped viscous MD integration method.

• User-defined pair potentials work with HPMC on the GPU.

• Long range tail correction for Lennard-Jones potential.

• Anisotropic Lennard-Jones-like pair potential for polyhedra and ellipsoids.

• Newtownian event chain Monte Carlo for spheres and convex polyhedra.

See the full change log below for all v3 beta releases.

Changes from v3.0.0-beta.14:

Added

• hoomd.hpmc.tune.BoxMCMoveSize - Tune BoxMC move sizes to meet target acceptance ratios.

• hoomd.hpmc.nec.integrate.Sphere - Newtonian event chain Monte Carlo for hard spheres.

• hoomd.hpmc.nec.integrate.ConvexPolyhedron - Newtonian event chain Monte Carlo for hard convex polyhedra.

• hoomd.hpmc.nec.tune.ChainTime - Tune chain times in newtonian event chain Monte Carlo method.

Changed

• Improve documentation.

• [breaking] Renamed the hoomd.md.bond.Table energy parameter from V to U.

• [breaking] Renamed the hoomd.md.pair.Table energy parameter from V to U.

• [breaking] Renamed the hoomd.md.angle.Table energy parameter from V to U.

• [breaking] Renamed the hoomd.md.dihedral.Table energy parameter from V to U.

• [breaking] Renamed hoomd.md.nlist.Nlist to hoomd.md.nlist.NeighborList.

• [developer] Updater and Analyzer in C++ have a m_trigger member now.

• [developer] _TriggeredOperation has been moved to TriggeredOperation and custom trigger setting and getting logic removed.

Fixed

• FIRE.converged may be queried before calling Simulation.run.

• Bug where using __iadd__ to certain attributes would fail with an exception.

• Bug where hoomd.md.pair.LJ.additional_energy is NaN when tail_correction is enabled and some pairs have r_cut=0.

• Compile error with CUDA 11.7.

• Compile errors on native ubuntu 20.04 systems.

• Compile errors with ENABLE_GPU=on and clang as a host compiler.

Removed

• [developers] Removed IntegratorData class. It is replaced by structs that are defined in the integrator classes.

• get_ordered_vertices from hoomd.md.pair.aniso.ALJ.

• Removed optional coxeter dependency.

• The limit parameter from hoomd.md.methods.NVE.

• The limit parameter from hoomd.md.methods.rattle.NVE.

• The diameter_shift parameter from hoomd.md.nlist.NeighborList.

• The max_diameter parameter from hoomd.md.nlist.NeighborList.

v3.0.0-beta.14 (2022-02-18)

Added

• hoomd.hpmc.external.field.Harmonic - harmonic potential of particles to specific sites in the simulation box and orientations.

• Support cereal 1.3.1

• Guide on how to model molecular systems.

• version.floating_point_precision - Floating point width in bits for the particle properties and local calculations.

• hoomd.md.pair.LJ.tail_correction - Option to enable the isotropic integrated long range tail correction.

• hoomd.md.Integrator.linear_momentum - Compute the total system linear momentum. Loggable.

• hoomd.md.bond.Table - Tabulated bond potential.

• hoomd.md.angle.Table - Tabulated angle potential.

• hoomd.md.dihedral.Table - Tabulated dihedral potential.

• hoomd.md.improper.Harmonic - Compute the harmonic improper potential and forces.

• Tutorial on Organizing and executing simulations.

• C++ and build system overview in ARCHITECTURE.md.

• hoomd.hpmc.external.wall - Overlap checks between particles and wall surfaces.

• hoomd.md.pair.ansio.ALJ - an anisotropic Lennard-Jones-like pair potential for polyhedra and ellipsoids.

• New optional dependency: coxeter, needed for some ALJ methods.

Changed

• Support variant translational and rotational spring constants in hoomd.hpmc.external.field.Harmonic.

• [breaking] Renamed hoomd.md.angle.Cosinesq to hoomd.md.angle.CosineSquared.

• [breaking] hoomd.Box no longer has a matrix property use to_matrix and from_matrix.

Fixed

• Compilation errors on FreeBSD.

• TypeError when instantiating special pair forces.

• Inconsistent state when using the walls setter of a hoomd.md.external.wall.WallPotential.

Removed

• [breaking] Removed hoomd.md.pair.SLJ potential and wall. Use hoomd.md.pair.ExpandedLJ.

• [breaking] hoomd.Box.lattice_vectors property no longer exists.

v3.0.0-beta.13 (2022-01-18)

Added

• md.pair.ExpandedLJ - A Lennard-Jones potential where r is replaced with r-delta.

• Support nested modification of operation parameters.

• wall - Define wall surfaces in the simulation box.

• md.external.wall - Pair interactions between particles and wall surfaces.

• Communicator.walltime - the wall clock time since creating the Communicator.

• md.force.Custom - user defined forces in Python.

Changed

• Call update_group_dof implicitly in set_snapshot, when changing integrators or integration methods, and on steps where FilterUpdater acts on the system.

• [breaking] update_group_dof defers counting the degrees of freedom until the next timestep or the next call to Simulation.run.

• [breaking] Renamed md.bond.FENE to md.bond.FENEWCA.

• md.bond.FENEWCA takes a user provided delta parameter and ignores the particle diameters.

• [breaking] md.pair.DLVO takes user provided a1 and a2 parameters and ignores the particle diameters.

• Removed invalid linker options when using gcc on Apple systems.

• Removed the r_on attribute and default_r_on constructor argument from pair potentials that do not use it.

• Building from source requires a C++17 compatible compiler.

Fixed

• Compile error with Apple clang clang-1300.0.29.30.

• Incorrect OPLS dihedral forces when compiled with Apple clang clang-1300.0.29.30.

Deprecated

• md.pair.SLJ - Replaced with md.pair.ExpandedLJ.

Removed

• Leftover state logging category.

v3.0.0-beta.12 (2021-12-14)

Added

• Support simulations with arbitrarily large or small scales (within the limits of the floating point representation).

Changed

• Report full error details in the exception message.

• Improved documentation.

• [breaking]: buffer is now a required argument when constructing a neighbor list.

• [breaking]: force_tol, angmom_tol, and energy_tol are now required arguments to md.minimize.FIRE

Fixed

• Allow neighbor lists to store more than 2**32-1 total neighbors.

• Return expected parameter values instead of NaN when potential parameters are set to 0.

v3.0.0-beta.11 (2021-11-18)

Added

• Support Python 3.10.

• Support clang 13.

Changed

• [developers] Place all all HOOMD C++ classes in the hoomd and nested namespaces.

• [developers] Use official pre-commit clang-format repository.

v3.0.0-beta.10 (2021-10-25)

Added

• md.minimize.FIRE - MD integrator that minimizes the system’s potential energy.

• Include example AKMA and MD unit conversion factors in the documentation.

• BUILD_LLVM CMake option (defaults off) to enable features that require LLVM.

• hpmc.pair.user.CPPPotential - user-defined pair potentials between particles in HPMC.

• hpmc.pair.user.CPPPotentialUnion - user-defined site-site pair potentials between shapes in HPMC.

• hpmc.external.user.CPPExternalPotential - user-defined external potentials in HPMC.

• Support user-defined pair potentials in HPMC on the GPU.

Changed

• Improved documentation.

• Improved error messages when setting operation parameters.

• Noted some dependencies of dependencies for building documentation.

• [developers] Removed m_comm from most classes. Use m_sysdef->isDomainDecomposed() instead.

• Add support for LLVM 12

• ENABLE_LLVM=on requires the clang development libraries.

• [breaking] Renamed the Integrator attribute aniso to integrate_rotational_dof and removed the 'auto' option. Users must now explicitly choose integrate_rotational_dof=True to integrate the rotational degrees of freedom in the system.

Fixed

• Calling Operations.__len__ no longer raises a RecursionError.

• RATTLE integration methods execute on the GPU.

• Include EvaluatorPairDLVO.h in the installation for plugins.

• Bug in setting zero sized ManagedArrays.

• Kernel launch errors when one process uses different GPU devices.

• Race condition that lead to incorrect simulations with md.pair.Table.

• Bug where some particle filers would have 0 rotational degrees of freedom.

Removed

• The BUILD_JIT CMake option.

• Support for LLVM <= 9.

v3.0.0-beta.9 (2021-09-08)

Added

• Communicator.num_partitions - the number of partitions in the communicator.

• domain_decomposition argument to State factory methods - set the parameters of the MPI domain decomposition

• State.domain_decomposition - number of domains in the x, y, and z directions in the domain decomposition.

• State.domain_decomposition_split_fractions - the fractional positions of the split planes in the domain decomposition.

• hoomd.update.FilterUpdater - an updater that evaluates the particles associated with a hoomd.filter.ParticleFilter instance.

• hoomd.update.RemoveDrift - Remove the average drift from a system restrained on a lattice.

• Developer documentation for HOOMD-blue’s Python object data model in ARCHITECTURE.md.

• Autocomplete support for interactive notebooks.

• hoomd.md.methods.OverdampedViscous - Overdamped integrator with a drag force but no random force .

• MutabilityError exception when setting read-only operation parameters.

Changed

• Improved documentation.

• [breaking] Moved manifold_constrant to separate integration method classes in hoomd.md.methods.rattle.

• [breaking] Moved trigger to first argument position in hoomd.update.BoxResize, hoomd.write.DCD, and hoomd.write.GSD.

• [breaking] hoomd.data.LocalSnapshot particle data API now matches Snapshot. Changes to angular momentum, moment of intertia, and rigid body id attributes.

• hoomd.write.CustomWriter now exposes action through the writer attribute.

• [breaking] Active force rotational diffusion is managed by hoomd.md.update.ActiveRotationalDiffusion.

Fixed

• TypeParameter can set multiple parameters after calling hoomd.Simulation.run.

• tune.LoadBalancer can be used in a simulation.

• hoomd.md.pair.Pair r_cut type parameter can be set to 0.

• MD integration methods can be removed from the integrator’s method list.

• Neighborlist exclusions update when the number of bonds change.

• Errors related to equality checks between HOOMD operations.

• The integrator can be removed from a simulation after running.

• hoomd.md.constrain.Rigid.create_bodies method correctly assigns the body attribute.

• Setting rigid attribute of a MD integrator to None is allowed.

Deprecated

Removed

• Snapshot.exists - use snapshot.communicator.rank == 0

• State.snapshot - use get_snapshot and set_snapshot

• The State.box property setter - use State.set_box

v3.0.0-beta.8 (2021-08-03)

Added

• Consistent documentation of parameter dimensions and units reference documentation.

• md.update.ReversePerturbationFlow - implementation of mueller_plathe_flow from v2.

• md.pair.ExpandedMie - Mie potential where r is replaced with r - delta.

• md.pair.Table - Pair potential evaluated using the given tabulated values.

• md.constrain.Distance - fix distances between pairs of particles.

• hpmc.compute.SDF - compute the pressure of convex hard particle systems.

• Snapshot.wrap() - wrap snapshot particles back into the box.

• Support gcc11.

• md.bond.Tether - A bond with minimum and maximum lengths.

• State.get_snapshot and State.set_snapshot - methods to access the global snapshot.

• State.set_box set a new simulation box without modifying particle properties.

• md.long_range.pppm.make_pppm_coulomb_forces - Long range electrostatics evaluated by PPPM.

• md.long_range.pppm.Coulomb - The reciprocal part of PPPM electrostatics.

• md.force.ActiveOnManifold - Active forces constrained to manifolds.

Changed

• Improved documentation.

• [breaking] Constructor arguments that set a default value per type or pair of types now have default in their name (e.g. r_cut to default_r_cut for pair potentials and a to default_a for HPMC integrators).

• [developer] Support git worktree checkouts.

• [breaking] Rename nrank to ranks_per_partition in Communicator.

• rowan is now an optional dependency when running unit tests.

• Snapshot and Box methods that make in-place modifications return the object.

Fixed

• Bug where ThermdynamicQuantities.volume returned 0 in 2D simulations.

• Update neighbor list exclusions after the number of particles changes.

• Test failures with the CMake option BUILD_MD=off.

• write.Table can now display MD pressures.

Deprecated

• State.snapshot - use get_snapshot and set_snapshot.

• The ability to set boxes with the property State.box - use set_box.

Removed

• [breaking] Simulation.write_debug_data.

• [breaking] shared_msg_file option to Device. msg_file now has the same behavior as shared_msg_file.

• [developers] C++ and Python implementations of constraint_ellipsoid, from hoomd.md.update and sphere and oneD from hoomd.md.constrain.

• [developers] Doxygen configuration files.

v3.0.0-beta.7 (2021-06-16)

Added

• md.constrain.Rigid - Rigid body constraints.

• dem_built, hpmc_built, md_built, and mpcd_built to hoomd.version - flags that indicate when optional submodules have been built.

• GPU.compute_capability property.

• [developers] pre-commit enforced style guidelines for the codebase.

• [developers] Validation tests for MD Lennard-Jones simulations.

• [developers] Unit tests for bond, angle, and dihedral potentials.

Changed

• Improved documentation on compiling HOOMD.

• Operations raise a DataAccessError when accessing properties that are not available because Simulation.run has not been called.

• TypeConversionError is now in the hoomd.error package.

• from_gsd_snapshot only accesses the GSD snapshot on MPI rank 0.

Fixed

• Some broken references in the documentation.

• Missing documentation for md.pair.TWF.

• Inconsistent documentation in md.pair.

• Correctly identify GPUs by ID in GPU.devices.

• Don’t initialize contexts on extra GPUs on MPI ranks.

• Support 2D inputs in from_gsd_snapshot.

Deprecated

• Snapshot.exists - use Snapshot.communicator.rank == 0 instead.

Removed

• [developers] C++ implementations of rescale_temp and enforce2d.

• [developers] Unused methods of Integrator.

v3.0.0-beta.6 (2021-05-17)

Added

• md.pair.LJ0804 - 8,4 Lennard-Jones pair potential.

• md.nlist.Stencil - Stencil algorithm to generate neighbor lists.

• md.nlist.Tree - BVH algorithm to generate neighbor lists.

• hoomd.md.Force, hoomd.md.Operation, and hoomd.md.Operations objects are now picklable.

• Manifold constraints using RATTLE with md.methods.NVE, md.methods.Langevin and md.methods.Brownian - Supporting sphere, ellipsoid, plane, cylinder, gyroid, diamond, and primitive manifolds.

• md.compute.HarmonicAveragedThermodynamicQuantities - More accurate thermodynamic quantities for crystals

Changed

• Raise an exception when initializing systems with invalid particle type ids.

Fixed

• Setting the operations attribute in Simulation objects in specific circumstances.

• Misc documentation updates.

• 'sim' is not defined error when using md.dihedral potentials.

Removed

• C++ implemtation of v2 logging infrastructure.

v3.0.0-beta.5 (2021-03-23)

Added

• filter parameter to update.BoxResize - A ParticleFilter that identifies the particles to scale with the box.

• Simulation.seed - one place to set random number seeds for all operations.

• net_force, net_torque, and net_energy per-particle arrays in local snapshots.

• Support hpmc.update.Clusters on the GPU.

• hpmc.update.MuVT - Gibbs ensemble simulations with HPMC.

• md.update.ZeroMomentum - Remove linear momentum from the system.

• hpmc.compute.FreeVolume - Compute free volume available to test particles.

• Custom action tutorials.

Changed

• [breaking] Removed the parameter scale_particles in update.BoxResize

• [internal] Modified signature of data.typeconverter.OnlyTypes

• Remove use of deprecated numpy APIs.

• Added more details to the migration guide.

• Support timestep values in the range [0,2**64-1].

• [breaking] Removed seed argument from State.thermalize_particle_momenta

• [breaking] Removed seed argument from md.methods.NVT.thermalize_thermostat_dof

• [breaking] Removed seed argument from md.methods.NPT.thermalize_thermostat_and_barostat_dof

• [breaking] Removed seed argument from md.methods.NPH.thermalize_barostat_dof

• [breaking] Removed seed argument from md.methods.Langevin

• [breaking] Removed seed argument from md.methods.Brownian

• [breaking] Removed seed argument from md.force.Active

• [breaking] Removed seed argument from md.pair.DPD

• [breaking] Removed seed argument from md.pair.DPDLJ

• [breaking] Removed seed argument from all HPMC integrators.

• [breaking] Removed seed argument from hpmc.update.Clusters

• [breaking] Removed seed argument from hpmc.update.BoxMC

• [breaking] Removed seed argument from hpmc.update.QuickCompress

• Use latest version of getar library.

• Improve documentation.

• Improve performance of md.pair.Mie.

• [breaking] hpmc.update.Clusters re-implemented with a rejection free, but not ergodic, algorithm for anisotropic particles. The new algorithm does not run in parallel over MPI ranks.

• [breaking] HPMC depletion algorithm rewritten.

• [breaking, temporary] HPMC depletant fugacity is now set for type pairs. This change will be reverted in a future release.

• Tutorials require fresnel 0.13.

• Support TBB 2021.

Fixed

• Install ParticleFilter header files for external plugins.

• md.force.Active keeps floating point values set for active_force and active_torque.

• create_state_from_snapshot accepts gsd.hoomd.Snapshot objects without error.

• HOOMD compiles on Apple silicon macOS systems.

• Memory leak in PPPM force compute.

• Segmentation fault that occurred when dumping GSD shapes for spheropolygons and spheropolyhedra with 0 vertices.

• Incorrect MD neighbor lists in MPI simulations with more than 1 rank.

• md.bond.FENE accepts parameters.

Removed

• Testing with CUDA 9, GCC 4.8, GCC 5.x, GCC 6.x, clang 5

v3.0.0-beta.4 (2021-02-16)

Added

• hoomd.write.DCD - DCD trajectory writer.

• hoomd.md.many_body - RevCross, SquareDensity, and Tersoff triplet potentials.

• hoomd.md.methods.Berendsen - Berendsen integration method.

• hoomd.md.methods.NPH - Constant pressure constant enthalpy integration method.

• hoomd.md.pair.TWF - Potential for modeling globular proteins by Pieter Rein ten Wolde and Daan Frenkel.

• Custom particle filters in Python via hoomd.filter.CustomFilter.

Changed

• Documentation improvements.

Fixed

• Correctly determine the maximum r_cut in simulations with more than one pair potential and more than one type.

v3.0.0-beta.3 (2021-01-11)

Added

• hoomd.variant.Variant objects are picklable.

• hoomd.filter.ParticleFilter objects are picklable.

• hoomd.trigger.Trigger objects are picklable.

• hoomd.Snapshot.from_gsd_snapshot - Convert GSD snapshots to HOOMD.

• hoomd.md.pair.aniso.GayBerne - Uniaxial ellipsoid pair potential.

• hoomd.md.pair.aniso.Dipole - Dipole pair potential.

• hoomd.md.pair.OPP - Oscillating pair potential.

Changed

• Improved compilation docs.

• Box equality checking now returns NotImplemented for non-hoomd.Box objects.

• Simulation.create_state_from_snapshot now accepts gsd.hoomd.Snapshot objects.

• Attempting to run in a local snapshot context manager will now raise a RuntimeError.

• Attempting to set the state to a new snapshot in a local snapshot context manager will now raise a RuntimeError.

Fixed

• hoomd.variant.Power objects now have a t_ramp attribute as documented.

• Enable memory buffers larger than 2-4 GiB.

• Correctly write large image flags to GSD files.

• Support more than 26 default type names.

• Correctly represent fractional degrees of freedom.

• Compute the minimum image in double precision.

v3.0.0-beta.2 (2020-12-15)

Added

• Support pybind11 2.6.0

• Exclusive creation file mode for write.GSD.

• hpmc.update.BoxMC.

• walltime and final_timestep loggable properties in Simulation.

• Null particle filter.

• Logging tutorial.

Changed

• [breaking] Replace write.GSD argument overwrite with mode.

• [breaking] Rename flags to categories in Logger

• hoomd.snapshot.ConfigurationData.dimensions is not settable and is determined by the snapshot box. If box.Lz == 0, the dimensions are 2 otherwise 3.

• Building from source requires a C++14 compatible compiler.

• Improved documentation.

• hpmc.integrate.FacetedEllipsoid’s shape specification now has a default origin of (0, 0, 0).

• Document loggable quantities in property docstrings.

• Skip GPU tests when no GPU is present.

• write.Table writes integers with integer formatting.

Fixed

• Simulation.run now ends with a KeyboardInterrupt exception when Jupyter interrupts the kernel.

• Logging the state of specific objects with nested attributes.

• Broken relative RPATHs.

• Add missing documentation for version.version

• Error when removing specific operations from a simulation’s operations attribute.

• Find CUDA libraries on additional Linux distributions.

• hpmc.update.Clusters now works with all HPMC integrators.

• Simulation.timestep reports the correct value when analyzers are called.

• Logger names quantities with the documented namespace name.

v3.0.0-beta.1 (2020-10-15)

Overview

v3 has a completely new Python API. See the tutorials, migration guide and new API documentation learn about it. The API documentation serves as the complete list of all features currently implemented in v3.0.0-beta.1. Not all features in v2 have been ported in v3.0.0-beta.1. Future beta releases will add additional functionality.

Added

• Zero-copy data access through numpy (CPU) and cupy (GPU).

• User-defined operations in Python.

• User-defined triggers determine what time steps operations execute on.

• New logging subsystem supports array quantities and binary log files.

• Implicit depletants are now supported by any hpmc integrator through mc.set_fugacity('type', fugacity).

• Enable implicit depletants for two-dimensional shapes in hpmc.

• jit.patch.user() and jit.patch.user_union() now support GPUs via NVRTC.

• Add harmonically mapped averaging.

• Add Visual Studio Code workspace

Changed

• The run method has minimal overhead

• All loggable quantities are directly accessible as object properties.

• Operation parameters are always synchronized.

• Operations can be instantiated without a device or MPI communicator.

• Writers write output for step+1 at the bottom of the run loop.

• HOOMD writes minimal output to stdout/stderr by default.

• CMake >=3.9, cereal, eigen, and pybind11 are required to compile HOOMD.

• Plugins must be updated to build against v3.

• By default, HOOMD installs to the site-packages directory associated with the python executable given, which may be inside a virtual environment.

• Refactored CMake code.

• git submodule update no longer runs when during CMake configuration.

• Use random123 library for implicit depletants in hpmc.

• HOOMD requires a GPU that supports concurrent managed memory access (Pascal or newer).

Bug fixes

• Improved accuracy of DLVO potential on the GPU.

• Improved performance of HPMC simulations on the CPU in non-cubic boxes.

Removed

• HOOMD-blue no longer parses command line options.

• Type swap moves in hpmc.update.muvt() are no longer supported (transfer_ratio option to muvt.set_params())

• The option implicit=True to hpmc.integrate.* is no longer available (use set_fugacity).

• static parameter in dump.gsd

• util.quiet_status and util.unquiet_status.

• deprecated.analyze.msd.

• deprecated.dump.xml.

• deprecated.dump.pos.

• deprecated.init.read_xml.

• deprecated.init.create_random.

• deprecated.init.create_random_polymers.

• hpmc ignore_overlaps parameter.

• hpmc sphere_union::max_members parameter.

• hpmc convex_polyhedron_union.

• hpmc setup_pos_writer method.

• hpmc depletant_mode='circumsphere'.

• hpmc max_verts parameter.

• hpmc depletant_mode parameter.

• hpmc ntrial parameter.

• hpmc implicit boolean parameter.

• group parameter to md.integrate.mode_minimize_fire

• cgcmm.angle.cgcmm

• cgcmm.pair.cgcmm

• COPY_HEADERS CMake option.

• Many other python modules have been removed or re-implemented with new names. See the migration guide and new API documentation for a complete list.

• Support for NVIDIA GPUS with compute capability < 6.0.

v2.x

v2.9.7 (2021-08-03)

Bug fixes

• Support CUDA 11.5. A bug in CUDA 11.4 may result in the error __global__ function call is not configured when running HOOMD.

v2.9.6 (2021-03-16)

Bug fixes

• Support TBB 2021.

v2.9.5 (2021-03-15)

Bug fixes

• Support macos-arm64.

• Support TBB 2021.

• Fix memory leak in PPPM.

v2.9.4 (2021-02-05)

Bug fixes

• Support thrust 1.10

• Support LLVM11

• Fix Python syntax warnings

• Fix compile errors with gcc 10

v2.9.3 (2020-08-05)

Bug fixes

• Fix a compile error with CUDA 11

v2.9.2 (2020-06-26)

Bug fixes

• Fix a bug where repeatedly using objects with period=None would use significant amounts of memory.

• Support CUDA 11.

• Reccomend citing the 2020 Computational Materials Science paper 10.1016/j.commatsci.2019.109363.

v2.9.1 (2020-05-28)

Bug fixes

• Fixed a minor bug where the variable period timestep would be off by one when the timestep got sufficiently large.

• Updated collections API to hide DeprecationWarning.

• Fix scaling of cutoff in Gay-Berne potential to scale the current maximum distance based on the orientations of the particles, ensuring ellipsoidal energy isocontours.

• Misc documentation fixes.

v2.9.0 (2020-02-03)

New features

• General

  • Read and write GSD 2.0 files.

    • HOOMD >=2.9 can read and write GSD files created by HOOMD <= 2.8 or GSD 1.x. HOOMD <= 2.8 cannot read GSD files created by HOOMD >=2.9 or GSD >= 2.0.

    • OVITO >=3.0.0-dev652 reads GSD 2.0 files.

    • A future release of the gsd-vmd plugin will read GSD 2.0 files.

• HPMC

  • User-settable parameters in jit.patch.

  • 2D system support in muVT updater.

  • Fix bug in HPMC where overlaps were not checked after adding new particle types.

• MD

  • The performance of nlist.tree has been drastically improved for a variety of systems.

v2.8.2 (2019-12-20)

Bug fixes

• Fix randomization of barostat and thermostat velocities with randomize_velocities() for non-unit temperatures.

• Improve MPCD documentation.

• Fix uninitialized memory in some locations which could have led to unreproducible results with HPMC in MPI, in particular with ALWAYS_USE_MANAGED_MEMORY=ON.

• Fix calculation of cell widths in HPMC (GPU) and nlist.cell() with MPI.

• Fix potential memory-management issue in MPI for migrating MPCD particles and cell energy.

• Fix bug where exclusions were sometimes ignored when charge.pppm() is the only potential using the neighbor list.

• Fix bug where exclusions were not accounted for properly in the pppm_energy log quantity.

• Fix a bug where MD simulations with MPI start off without a ghost layer, leading to crashes or dangerous builds shortly after run().

• hpmc.update.remove_drift now communicates particle positions after updating them.

v2.8.1 (2019-11-26)

Bug fixes

• Fix a rare divide-by-zero in the collide.srd thermostat.

• Improve performance of first frame written by dump.gsd.

• Support Python 3.8.

• Fix an error triggering migration of embedded particles for MPCD with MPI + GPU configurations.

v2.8.0 (2019-10-30)

New Features

• MD:

  • hoomd.md.dihedral.harmonic now accepts phase offsets, phi_0, for CHARMM-style periodic dihedrals.

  • Enable per-type shape information for anisotropic pair potentials that complements the existing pair parameters struct.

• HPMC:

  • Enable the use of an array with adjustable parameters within the user defined pair potential.

  • Add muVT updater for 2D systems.

Bug fixes

• Fix missing header in external plugin builds.

• Enable couple='none' option to md.integrate.npt() when randomly initializing velocities.

• Documentation improvements.

• Skip gsd shape unit test when required modules are not compiled.

• Fix default particle properties when new particles are added to the system (e.g., via the muVT updater).

• Fix charge.pppm() execution on multiple GPUs.

• Enable with SimulationContext() as c.

• Fix a bug for mpcd.collide.at with embedded particles, which may have given incorrect results or simulation crashes.

v2.7.0 (2019-10-01)

New features

• General:

  • Allow components to use Logger at the C++ level.

  • Drop support for python 2.7.

  • User-defined log quantities in dump.gsd.

  • Add hoomd.dump.gsd.dump_shape to save particle shape information in GSD files.

• HPMC:

  • Add get_type_shapes to ellipsoid.

• MPCD:

  • mpcd.stream.slit_pore allows for simulations through parallel-plate (lamellar) pores.

  • mpcd.integrate supports integration of MD (solute) particles with bounce-back rules in MPCD streaming geometries.

Bug fixes

• hoomd.hdf5.log.query works with matrix quantities.

• test_group_rigid.py is run out of the md module.

• Fix a bug in md.integrate.langevin() and md.integrate.bd() where on the GPU the value of gamma would be ignored.

• Fix documentation about interoperability between md.mode_minimize_fire() and MPI.

• Clarify dump.gsd documentation.

• Improve documentation of lattice_field and frenkel_ladd_energy classes.

• Clarify singularity image download documentation.

• Correctly document the functional form of the Buckingham pair potential.

• Correct typos in HPMC example snippets.

• Support compilation in WSL.

v2.6.0 (2019-05-28)

New features

• General:

  • Enable HPMC plugins.

  • Fix plug-in builds when ENABLE_TBB or ALWAYS_USE_MANAGED_MEMORY CMake parameters are set.

  • Remove support for compute 3.0 GPUs.

  • Report detailed CUDA errors on initialization.

  • Document upcoming feature removals and API changes.

• MD:

  • Exclude neighbors that belong to the same floppy molecule.

  • Add fourier potential.

• HPMC:

  • New shape class: hpmc.integrate.faceted_ellipsoid_union().

  • Store the orientable shape state.

• MPCD:

  • mpcd.stream.slit allows for simulations in parallel-plate channels. Users can implement other geometries as a plugin.

  • MPCD supports virtual particle filling in bounded geometries through the set_filler method of mpcd.stream classes.

  • mpcd.stream includes an external mpcd.force acting on the MPCD particles. A block force, a constant force, and a sine force are implemented.

Bug fixes

• Fix compile errors with LLVM 8 and -DBUILD_JIT=on.

• Allow simulations with 0 bonds to specify bond potentials.

• Fix a problem where HOOMD could not be imported in mpi4py jobs.

• Validate snapshot input in restore_snapshot.

• Fix a bug where rigid body energy and pressure deviated on the first time step after run().

• Fix a bug which could lead to invalid MPI simulations with nlist.cell() and nlist.stencil().

C++ API changes

• Refactor handling of MPI_Comm inside library

• Use random123 for random number generation

• CMake version 2.8.10.1 is now a minimum requirement for compiling from source

v2.5.2 (2019-04-30)

Bug fixes

• Support LLVM 9 in jit

• Fix error when importing jit before hpmc

• HPMC integrators raise errors when restore_state=True and state information is missing

• Send messages to replaced sys.stdout and sys.stderr streams

• Add hpmc.update.clusters to documentation index

• Fix a bug in the MPCD Gaussian random number generator that could lead to NaN values

• Fix issue where an initially cubic box can become non-cubic with integrate.npt() and randomize_velocities()

• Fix illegal memory access in NeighborListGPU with -DALWAYS_USE_MANAGED_MEMORY=ON on single GPUs

• Improve pair.table performance with multi-GPU execution

• Improve charge.pppm performance with multi-GPU execution

• Improve rigid body performance with multi-GPU execution

• Display correct cell list statistics with the -DALWAYS_USE_MANAGED_MEMORY=ON compile option

• Fix a sporadic data corruption / bus error issue when data structures are dynamically resized in simulations that use unified memory (multi-GPU, or with -DALWAYS_USE_MANAGED_MEMORY=ON compile time option)

• Improve integrate.nve and integrate.npt performance with multi-GPU execution

• Improve some angular degrees of freedom integrators with multi-GPU execution

• Improve rigid body pressure calculation performance with multi-GPU execution

v2.5.1 (2019-03-14)

Bug fixes

• fix out-of-range memory access in hpmc.integrate.convex_polyheron

• Remove support for clang3.8 and 4.0

• Documentation improvements

• Fix a segfault when using SLURM_LOCALID

v2.5.0 (2019-02-05)

New features

• General:

  • Fix BondedGroupData and CommunicatorGPU compile errors in certain build configurations

• MD:

  • Generalize md.integrate.brownian and md.integrate.langevin to support anisotropic friction coefficients for rotational Brownian motion.

  • Improve NVLINK performance with rigid bodies

  • randomize_velocities now chooses random values for the internal integrator thermostat and barostat variables.

  • get_net_force returns the net force on a group of particles due to a specific force compute

• HPMC:

  • Fix a bug where external fields were ignored with the HPMC implicit integrator unless a patch potential was also in use.

• JIT:

  • Add jit.external.user to specify user-defined external fields in HPMC.

  • Use -DHOOMD_LLVMJIT_BUILD now instead of -DHOOMD_NOPYTHON

v2.4.2 (2018-12-20)

Bug fixes

• Miscellaneous documentation updates

• Fix compile error with with -DALWAYS_USE_MANAGED_MEMORY=ON

• Fix MuellerPlatheFlow, cast input parameter to int to avoid C++ constructor type mismatch

• Improve startup time with multi-GPU simulations

• Correctly assign GPUs to MPI processes on Summit when launching with more than one GPU per resource set

• Optimize multi-GPU performance with NVLINK

• Do not use mapped memory with MPI/GPU anymore

• Fix some cases where a multi-GPU simulation fails with an alignment error

• Eliminate remaining instance of unsafe __shfl

• Hide CMake warnings regarding missing CPU math libraries

• Hide CMake warning regarding missing MPI<->CUDA interoperability

• Refactor memory management to fix linker errors with some compilers

C++ API Changes

• May break some plug-ins which rely on GPUArray data type being returned from ParticleData and other classes (replace by GlobalArray)

v2.4.1 (2018-11-27)

Bug fixes

• Install WarpTools.cuh for use by plugins

• Fix potential violation of detailed balance with anisotropic particles with hpmc.update.clusters in periodic boundary conditions

• Support llvm 7.0

v2.4.0 (2018-11-07)

New features

• General:

  • Misc documentation updates

  • Accept mpi4py communicators in context.initialize.

  • CUDA 10 support and testing

  • Sphinx 1.8 support

  • Flush message output so that python -u is no longer required to obtain output on some batch job systems

  • Support multi-GPU execution on dense nodes using CUDA managed memory. Execute with --gpu=0,1,..,n-1 command line option to run on the first n GPUs (Pascal and above).

    • Node-local acceleration is implemented for a subset of kernels. Performance improvements may vary.

    • Improvements are only expected with NVLINK hardware. Use MPI when NVLINK is not available.

    • Combine the --gpu=.. command line option with mpirun to execute on many dense nodes

  • Bundle libgetar v0.7.0 and remove sqlite3 dependency

  • When building with ENABLE_CUDA=on, CUDA 8.0 is now a minimum requirement

• MD:

  • no changes.

• HPMC:

  • Add convex_spheropolyhedron_union shape class.

  • Correctly count acceptance rate when maximum particle move is is zero in hpmc.integrate.*.

  • Correctly count acceptance rate when maximum box move size is zero in hpmc.update.boxmc.

  • Fix a bug that may have led to overlaps between polygon soups with hpmc.integrate.polyhedron.

  • Improve performance in sphere trees used in hpmc.integrate.sphere_union.

  • Add test_overlap method to python API

• API:

  • Allow external callers of HOOMD to set the MPI communicator

  • Removed all custom warp reduction and scan operations. These are now performed by CUB.

  • Separate compilation of pair potentials into multiple files.

  • Removed compute 2.0 workaround implementations. Compute 3.0 is now a hard minimum requirement to run HOOMD.

  • Support and enable compilation for sm70 with CUDA 9 and newer.

• Deprecated:

  • HPMC: The implicit depletant mode circumsphere with ntrial > 0 does not support compute 7.0 (Volta) and newer GPUs and is now disabled by default. To enable this functionality, configure HOOMD with option the -DENABLE_HPMC_REINSERT=ON, which will not function properly on compute 7.0 (Volta) and newer GPUs.

  • HPMC: convex_polyhedron_union is replaced by convex_spheropolyhedron_union (when sweep_radii are 0 for all particles)

v2.3.5 (2018-10-07)

Bug fixes

• Document --single-mpi command line option.

• HPMC: Fix a bug where hpmc.field.lattice_field did not resize 2D systems properly in combination with update.box_resize.

v2.3.4 (2018-07-30)

Bug fixes

• init.read_gsd no longer applies the time_step override when reading the restart file

• HPMC: Add hpmc_patch_energy and hpmc_patch_rcut loggable quantities to the documentation

v2.3.3 (2018-07-03)

Bug fixes

• Fix libquickhull.so not found regression on Mac OS X

v2.3.2 (2018-06-29)

Bug fixes

• Fix a bug where gsd_snapshot would segfault when called without an execution context.

• Compile warning free with gcc8.

• Fix compile error when TBB include files are in non-system directory.

• Fix libquickhull.so not found error on additional platforms.

• HOOMD-blue is now available on conda-forge and the docker hub.

• MPCD: Default value for kT parameter is removed for mpcd.collide.at. Scripts that are correctly running are not affected by this change.

• MPCD: mpcd notifies the user of the appropriate citation.

• MD: Correct force calculation between dipoles and point charge in pair.dipole

Deprecated

• The anaconda channel glotzer will no longer be updated. Use conda-forge to upgrade to v2.3.2 and newer versions.

v2.3.1 (2018-05-25)

Bug fixes

• Fix doxygen documentation syntax errors

• Fix libquickhull.so not found error on some platforms

• HPMC: Fix bug that allowed particles to pas through walls

• HPMC: Check spheropolyhedra with 0 vertices against walls correctly

• HPMC: Fix plane wall/spheropolyhedra overlap test

• HPMC: Restore detailed balance in implicit depletant integrator

• HPMC: Correctly choose between volume and lnV moves in hpmc.update.boxmc

• HPMC: Fix name of log quantity hpmc_clusters_pivot_acceptance

• MD: Fix image list for tree neighbor lists in 2d

v2.3.0 (2018-04-25)

New features

• General:

  • Store BUILD_* CMake variables in the hoomd cmake cache for use in external plugins.

  • init.read_gsd and data.gsd_snapshot now accept negative frame indices to index from the end of the trajectory.

  • Faster reinitialization from snapshots when done frequently.

  • New command line option --single-mpi allows non-mpi builds of hoomd to launch within mpirun (i.e. for use with mpi4py managed pools of jobs)

  • For users of the University of Michigan Flux system: A --mode option is no longer required to run hoomd.

• MD:

  • Improve performance with md.constrain.rigid in multi-GPU simulations.

  • New command integrator.randomize_velocities() sets a particle group’s linear and angular velocities to random values consistent with a given kinetic temperature.

  • md.force.constant() now supports setting the force per particle and inside a callback

• HPMC:

  • Enabled simulations involving spherical walls and convex spheropolyhedral particle shapes.

  • Support patchy energetic interactions between particles (CPU only)

  • New command hpmc.update.clusters() supports geometric cluster moves with anisotropic particles and/or depletants and/or patch potentials. Supported move types: pivot and line reflection (geometric), and AB type swap.

• JIT:

  • Add new experimental jit module that uses LLVM to compile and execute user provided C++ code at runtime. (CPU only)

  • Add jit.patch.user: Compute arbitrary patch energy between particles in HPMC (CPU only)

  • Add jit.patch.user_union: Compute arbitrary patch energy between rigid unions of points in HPMC (CPU only)

  • Patch energies operate with implicit depletant and normal HPMC integration modes.

  • jit.patch.user_union operates efficiently with additive contributions to the cutoff.

• MPCD:

  • The mpcd component adds support for simulating hydrodynamics using the multiparticle collision dynamics method.

Beta feature

• Node local parallelism (optional, build with ENABLE_TBB=on):

  • The Intel TBB library is required to enable this feature.

  • The command line option --nthreads limits the number of threads HOOMD will use. The default is all CPU cores in the system.

  • Only the following methods in HOOMD will take advantage of multiple threads:

    • hpmc.update.clusters()

    • HPMC integrators with implicit depletants enabled

    • jit.patch.user_union

Node local parallelism is still under development. It is not enabled in builds by default and only a few methods utilize multiple threads. In future versions, additional methods in HOOMD may support multiple threads.

To ensure future workflow compatibility as future versions enable threading in more components, explicitly set –nthreads=1.

Bug fixes

• Fixed a problem with periodic boundary conditions and implicit depletants when depletant_mode=circumsphere

• Fixed a rare segmentation fault with hpmc.integrate.*_union() and hpmc.integrate.polyhedron

• md.force.active and md.force.dipole now record metadata properly.

• Fixed a bug where HPMC restore state did not set ignore flags properly.

• hpmc_boxmc_ln_volume_acceptance is now available for logging.

Other changes

• Eigen is now provided as a submodule. Plugins that use Eigen headers need to update include paths.

• HOOMD now builds with pybind 2.2. Minor changes to source and cmake scripts in plugins may be necessary. See the updated example plugin.

• HOOMD now builds without compiler warnings on modern compilers (gcc6, gcc7, clang5, clang6).

• HOOMD now uses pybind11 for numpy arrays instead of num_util.

• HOOMD versions v2.3.x will be the last available on the anaconda channel glotzer.

v2.2.5 (2018-04-20)

Bug fixes

• Pin cuda compatible version in conda package to resolve libcu*.so not found errors in conda installations.

v2.2.4 (2018-03-05)

Bug fixes

• Fix a rare error in md.nlist.tree when particles are very close to each other.

• Fix deadlock when `init.read_getar` is given different file names on different ranks.

• Sample from the correct uniform distribution of depletants in a sphere cap with depletant_mode='overlap_regions' on the CPU

• Fix a bug where ternary (or higher order) mixtures of small and large particles were not correctly handled with depletant_mode='overlap_regions' on the CPU

• Improve acceptance rate in depletant simulations with depletant_mode='overlap_regions'

v2.2.3 (2018-01-25)

Bug fixes

• Write default values to gsd frames when non-default values are present in frame 0.

• md.wall.force_shifted_lj now works.

• Fix a bug in HPMC where run() would not start after restore_state unless shape parameters were also set from python.

• Fix a bug in HPMC Box MC updater where moves were attempted with zero weight.

• dump.gsd() now writes hpmc shape state correctly when there are multiple particle types.

• hpmc.integrate.polyhedron() now produces correct results on the GPU.

• Fix binary compatibility across python minor versions.

v2.2.2 (2017-12-04)

Bug fixes

• md.dihedral.table.set_from_file now works.

• Fix a critical bug where forces in MPI simulations with rigid bodies or anisotropic particles were incorrectly calculated

• Ensure that ghost particles are updated after load balancing.

• meta.dump_metadata no longer reports an error when used with md.constrain.rigid

• Miscellaneous documentation fixes

• dump.gsd can now write GSD files with 0 particles in a frame

• Explicitly report MPI synchronization delays due to load imbalance with profile=True

• Correctly compute net torque of rigid bodies with anisotropic constituent particles in MPI execution on multiple ranks

• Fix PotentialPairDPDThermoGPU.h for use in external plugins

• Use correct ghost region with constrain.rigid in MPI execution on multiple ranks

• hpmc.update.muvt() now works with depletant_mode='overlap_regions'

• Fix the sampling of configurations with in hpmc.update.muvt with depletants

• Fix simulation crash after modifying a snapshot and re-initializing from it

• The pressure in simulations with rigid bodies (md.constrain.rigid()) and MPI on multiple ranks is now computed correctly

v2.2.1 (2017-10-04)

Bug fixes

• Add special pair headers to install target

• Fix a bug where hpmc.integrate.convex_polyhedron, hpmc.integrate.convex_spheropolyhedron, hpmc.integrate.polyedron, hpmc.integrate.faceted_sphere, hpmc.integrate.sphere_union and hpmc.integrate.convex_polyhedron_union produced spurious overlaps on the GPU

v2.2.0 (2017-09-08)

New features

• General:

  • Add hoomd.hdf5.log to log quantities in hdf5 format. Matrix quantities can be logged.

  • dump.gsd can now save internal state to gsd files. Call dump_state(object) to save the state for a particular object. The following objects are supported:

    • HPMC integrators save shape and trial move size state.

  • Add dynamic argument to hoomd.dump.gsd to specify which quantity categories should be written every frame.

  • HOOMD now inter-operates with other python libraries that set the active CUDA device.

  • Add generic capability for bidirectional ghost communication, enabling multi body potentials in MPI simulation.

• MD:

  • Added support for a 3 body potential that is harmonic in the local density.

  • force.constant and force.active can now apply torques.

  • quiet option to nlist.tune to quiet the output of the embedded run() commands.

  • Add special pairs as exclusions from neighbor lists.

  • Add cosine squared angle potential md.angle.cosinesq.

  • Add md.pair.DLVO() for evaluation of colloidal dispersion and electrostatic forces.

  • Add Lennard-Jones 12-8 pair potential.

  • Add Buckingham (exp-6) pair potential.

  • Add Coulomb 1-4 special_pair potential.

  • Check that composite body dimensions are consistent with minimum image convention and generate an error if they are not.

  • md.integrate.mode.minimize_fire() now supports anisotropic particles (i.e. composite bodies)

  • md.integrate.mode.minimize_fire() now supports flexible specification of integration methods

  • md.integrate.npt()/md.integrate.nph() now accept a friction parameter (gamma) for damping out box fluctuations during minimization runs

  • Add new command integrate.mode_standard.reset_methods() to clear NVT and NPT integrator variables

• HPMC:

  • hpmc.integrate.sphere_union() takes new capacity parameter to optimize performance for different shape sizes

  • hpmc.integrate.polyhedron() takes new capacity parameter to optimize performance for different shape sizes

  • hpmc.integrate.convex_polyhedron and convex_spheropolyhedron now support arbitrary numbers of vertices, subject only to memory limitations (max_verts is now ignored).

  • HPMC integrators restore state from a gsd file read by init.read_gsd when the option restore_state is True.

  • Deterministic HPMC integration on the GPU (optional): mc.set_params(deterministic=True).

  • New hpmc.update.boxmc.ln_volume() move allows logarithmic volume moves for fast equilibration.

  • New shape: hpmc.integrate.convex_polyhedron_union performs simulations of unions of convex polyhedra.

  • hpmc.field.callback() now enables MC energy evaluation in a python function

  • The option depletant_mode='overlap_regions' for hpmc.integrate.* allows the selection of a new depletion algorithm that restores the diffusivity of dilute colloids in dense depletant baths

Deprecated

• HPMC: hpmc.integrate.sphere_union() no longer needs the max_members parameter.

• HPMC: hpmc.integrate.convex_polyhedron and convex_spheropolyhedron no longer needs the max_verts parameter.

• The static argument to hoomd.dump.gsd should no longer be used. Use dynamic instead.

Bug fixes

• HPMC:

  • hpmc.integrate.sphere_union() and hpmc.integrate.polyhedron() missed overlaps.

  • Fix alignment error when running implicit depletants on GPU with ntrial > 0.

  • HPMC integrators now behave correctly when the user provides different RNG seeds on different ranks.

  • Fix a bug where overlapping configurations were produced with hpmc.integrate.faceted_sphere()

• MD:

  • charge.pppm() with order=7 now gives correct results

  • The PPPM energy for particles excluded as part of rigid bodies now correctly takes into account the periodic boundary conditions

• EAM:

  • metal.pair.eam now produces correct results.

Other changes

• Optimized performance of HPMC sphere union overlap check and polyhedron shape

• Improved performance of rigid bodies in MPI simulations

• Support triclinic boxes with rigid bodies

• Raise an error when an updater is given a period of 0

• Revised compilation instructions

• Misc documentation improvements

• Fully document constrain.rigid

• -march=native is no longer set by default (this is now a suggestion in the documentation)

• Compiler flags now default to CMake defaults

• ENABLE_CUDA and ENABLE_MPI CMake options default OFF. User must explicitly choose to enable optional dependencies.

• HOOMD now builds on powerpc+CUDA platforms (tested on summitdev)

• Improve performance of GPU PPPM force calculation

• Use sphere tree to further improve performance of hpmc.integrate.sphere_union()

v2.1.9 (2017-08-22)

Bug fixes

• Fix a bug where the log quantity momentum was incorrectly reported in MPI simulations.

• Raise an error when the user provides inconsistent charge or diameter lists to md.constrain.rigid.

• Fix a bug where pair.compute_energy() did not report correct results in MPI parallel simulations.

• Fix a bug where make rigid bodies with anisotropic constituent particles did not work on the GPU.

• Fix hoomd compilation after the rebase in the cub repository.

• deprecated.dump.xml() now writes correct results when particles have been added or deleted from the simulation.

• Fix a critical bug where charge.pppm() calculated invalid forces on the GPU

v2.1.8 (2017-07-19)

Bug fixes

• `init.read_getar` now correctly restores static quantities when given a particular frame.

• Fix bug where many short calls to run() caused incorrect results when using md.integrate.langevin.

• Fix a bug in the Saru pseudo-random number generator that caused some double-precision values to be drawn outside the valid range [0,1) by a small amount. Both floats and doubles are now drawn on [0,1).

• Fix a bug where coefficients for multi-character unicode type names failed to process in Python 2.

Other changes

• The Saru generator has been moved into hoomd/Saru.h, and plugins depending on Saru or SaruGPU will need to update their includes. The SaruGPU class has been removed. Use hoomd::detail::Saru instead for both CPU and GPU plugins.

v2.1.7 (2017-05-11)

Bug fixes

• Fix PPM exclusion handling on the CPU

• Handle r_cut for special pairs correctly

• Fix tauP reference in NPH documentation

• Fixed constrain.rigid on compute 5.x.

• Fixed random seg faults when using sqlite getar archives with LZ4 compression

• Fixed XZ coupling with hoomd.md.integrate.npt integration

• Fixed aspect ratio with non-cubic boxes in hoomd.hpmc.update.boxmc

v2.1.6 (2017-04-12)

Bug fixes

• Document hpmc.util.tune_npt

• Fix dump.getar.writeJSON usage with MPI execution

• Fix a bug where integrate.langevin and integrate.brownian correlated RNGs between ranks in multiple CPU execution

• Bump CUB to version 1.6.4 for improved performance on Pascal architectures. CUB is now embedded using a git submodule. Users upgrading existing git repositories should reinitialize their git submodules with git submodule update --init

• CMake no longer complains when it finds a partial MKL installation.

v2.1.5 (2017-03-09)

Bug fixes

• Fixed a compile error on Mac

v2.1.4 (2017-03-09)

Bug fixes

• Fixed a bug re-enabling disabled integration methods

• Fixed a bug where adding particle types to the system failed for anisotropic pair potentials

• scipy is no longer required to execute DEM component unit tests

• Issue a warning when a subsequent call to context.initialize is given different arguments

• DPD now uses the seed from rank 0 to avoid incorrect simulations when users provide different seeds on different ranks

• Miscellaneous documentation updates

• Defer initialization message until context.initialize

• Fixed a problem where a momentary dip in TPS would cause walltime limited jobs to exit prematurely

• HPMC and DEM components now correctly print citation notices

v2.1.3 (2017-02-07)

Bug fixes

• Fixed a bug where the WalltimeLimitReached was ignored

v2.1.2 (2017-01-11)

Bug fixes

• (HPMC) Implicit depletants with spheres and faceted spheres now produces correct ensembles

• (HPMC) Implicit depletants with ntrial > 0 now produces correct ensembles

• (HPMC) NPT ensemble in HPMC (hpmc.update.boxmc) now produces correct ensembles

• Fix a bug where multiple nvt/npt integrators caused warnings from analyze.log.

• update.balance() is properly ignored when only one rank is available

• Add missing headers to plugin install build

• Fix a bug where charge.pppm calculated an incorrect pressure

• Other changes *

• Drop support for compute 2.0 GPU devices

• Support cusolver with CUDA 8.0

v2.1.1 (2016-10-23)

Bug fixes

• Fix force.active memory allocation bug

• Quiet Python.h warnigns when building (python 2.7)

• Allow multi-character particle types in HPMC (python 2.7)

• Enable dump.getar.writeJSON in MPI

• Allow the flow to change directions in md.update.mueller_plathe_flow

• Fix critical bug in MPI communication when using HPMC integrators

v2.1.0 (2016-10-04)

New features

• enable/disable overlap checks between pairs of constituent particles for hpmc.integrate.sphere_union()

• Support for non-additive mixtures in HPMC, overlap checks can now be enabled/disabled per type-pair

• Add md.constrain.oned to constrain particles to move in one dimension

• hpmc.integrate.sphere_union() now takes max_members as an optional argument, allowing to use GPU memory more efficiently

• Add md.special_pair.lj() to support scaled 1-4 (or other) exclusions in all-atom force fields

• md.update.mueller_plathe_flow(): Method to create shear flows in MD simulations

• use_charge option for md.pair.reaction_field

• md.charge.pppm() takes a Debye screening length as an optional parameter

• md.charge.pppm() now computes the rigid body correction to the PPPM energy

Deprecated

• HPMC: the ignore_overlaps flag is replaced by hpmc.integrate.interaction_matrix

Other changes

• Optimized MPI simulations of mixed systems with rigid and non-rigid bodies

• Removed dependency on all boost libraries. Boost is no longer needed to build hoomd

• Intel compiler builds are no longer supported due to c++11 bugs

• Shorter compile time for HPMC GPU kernels

• Include symlinked external components in the build process

• Add template for external components

• Optimized dense depletant simulations with HPMC on CPU

Bug fixes

• fix invalid mesh energy in non-neutral systems with md.charge.pppm()

• Fix invalid forces in simulations with many bond types (on GPU)

• fix rare cases where analyze.log() would report a wrong pressure

• fix possible illegal memory access when using md.constrain.rigid() in GPU MPI simulations

• fix a bug where the potential energy is misreported on the first step with md.constrain.rigid()

• Fix a bug where the potential energy is misreported in MPI simulations with md.constrain.rigid()

• Fix a bug where the potential energy is misreported on the first step with md.constrain.rigid()

• md.charge.pppm() computed invalid forces

• Fix a bug where PPPM interactions on CPU where not computed correctly

• Match logged quantitites between MPI and non-MPI runs on first time step

• Fix md.pair.dpd and md.pair.dpdlj set_params

• Fix diameter handling in DEM shifted WCA potential

• Correctly handle particle type names in lattice.unitcell

• Validate md.group.tag_list is consistent across MPI ranks

v2.0.3 (2016-08-30)

• hpmc.util.tune now works with particle types as documented

• Fix pressure computation with pair.dpd() on the GPU

• Fix a bug where dump.dcd corrupted files on job restart

• Fix a bug where HPMC walls did not work correctly with MPI

• Fix a bug where stdout/stderr did not appear in MPI execution

• HOOMD will now report an human readable error when users forget context.initialize()

• Fix syntax errors in frenkel ladd field

v2.0.2 (2016-08-09)

• Support CUDA Toolkit 8.0

• group.rigid()/nonrigid() did not work in MPI simulations

• Fix builds with ENABLE_DOXYGEN=on

• Always add -std=c++11 to the compiler command line arguments

• Fix rare infinite loops when using hpmc.integrate.faceted_sphere

• Fix hpmc.util.tune to work with more than one tunable

• Fix a bug where dump.gsd() would write invalid data in simulations with changing number of particles

• replicate() sometimes did not work when restarting a simulation

v2.0.1 (2016-07-15)

Bug fixes

• Fix acceptance criterion in mu-V-T simulations with implicit depletants (HPMC).

• References to disabled analyzers, computes, updaters, etc. are properly freed from the simulation context.

• Fix a bug where init.read_gsd ignored the restart argument.

• Report an error when HPMC kernels run out of memory.

• Fix ghost layer when using rigid constraints in MPI runs.

• Clarify definition of the dihedral angle.

v2.0.0 (2016-06-22)

HOOMD-blue v2.0 is released under a clean BSD 3-clause license.

New packages

• dem - simulate faceted shapes with dynamics

• hpmc - hard particle Monte Carlo of a variety of shape classes.

Bug fixes

• Angles, dihedrals, and impropers no longer initialize with one default type.

• Fixed a bug where integrate.brownian gave the same x,y, and z velocity components.

• Data proxies verify input types and vector lengths.

• dump.dcd no longer generates excessive metadata traffic on lustre file systems

New features

• Distance constraints constrain.distance - constrain pairs of particles to a fixed separation distance

• Rigid body constraints constrain.rigid - rigid bodies now have central particles, and support MPI and replication

• Multi-GPU electrostatics charge.pppm - the long range electrostatic forces are now supported in MPI runs

• context.initialize() can now be called multiple times - useful in jupyter notebooks

• Manage multiple simulations in a single job script with SimulationContext as a python context manager.

• util.quiet_status() / util.unquiet_status() allow users to control if line status messages are output.

• Support executing hoomd in Jupyter (ipython) notebooks. Notice, warning, and error messages now show up in the notebook output blocks.

• analyze.log can now register python callback functions as sources for logged quantities.

• The GSD file format (https://gsd.readthedocs.io) is fully implemented in hoomd

  • dump.gsd writes GSD trajectories and restart files (use truncate=true for restarts).

  • init.read_gsd reads GSD file and initializes the system, and can start the simulation from any frame in the GSD file.

  • data.gsd_snapshot reads a GSD file into a snapshot which can be modified before system initialization with init.read_snapshot.

  • The GSD file format is capable of storing all particle and topology data fields in hoomd, either static at frame 0, or varying over the course of the trajectory. The number of particles, types, bonds, etc. can also vary over the trajectory.

• force.active applies an active force (optionally with rotational diffusion) to a group of particles

• update.constrain_ellipsoid constrains particles to an ellipsoid

• integrate.langevin and integrate.brownian now apply rotational noise and damping to anisotropic particles

• Support dynamically updating groups. group.force_update() forces the group to rebuild according to the original selection criteria. For example, this can be used to periodically update a cuboid group to include particles only in the specified region.

• pair.reaction_field implements a pair force for a screened electrostatic interaction of a charge pair in a dielectric medium.

• force.get_energy allows querying the potential energy of a particle group for a specific force

• init.create_lattice initializes particles on a lattice.

  • lattice.unitcell provides a generic unit cell definition for create_lattice

  • Convenience functions for common lattices: sq, hex, sc, bcc, fcc.

• Dump and initialize commands for the GTAR file format (https://libgetar.readthedocs.io).

  • GTAR can store trajectory data in zip, tar, sqlite, or bare directories

  • The current version stores system properties, later versions will be able to capture log, metadata, and other output to reduce the number of files that a job script produces.

• integrate.npt can now apply a constant stress tensor to the simulation box.

• Faceted shapes can now be simulated through the dem component.

Changes that require job script modifications

• context.initialize() is now required before any other hoomd script command.

• init.reset() no longer exists. Use context.initialize() or activate a SimulationContext.

• Any scripts that relied on undocumented members of the globals module will fail. These variables have been moved to the context module and members of the currently active SimulationContext.

• bonds, angles, dihedrals, and impropers no longer use the set_coeff syntax. Use bond_coeff.set, angle_coeff.set, dihedral_coeff.set, and improper_coeff.set instead.

• hoomd_script no longer exists, python commands are now spread across hoomd, hoomd.md, and other sub packages.

• integrate.\*_rigid() no longer exists. Use a standard integrator on group.rigid_center(), and define rigid bodies using constrain.rigid()

• All neighbor lists must be explicitly created using nlist.\*, and each pair potential must be attached explicitly to a neighbor list. A default global neighbor list is no longer created.

• Moved cgcmm into its own package.

• Moved eam into the metal package.

• Integrators now take kT arguments for temperature instead of T to avoid confusion on the units of temperature.

• phase defaults to 0 for updaters and analyzers so that restartable jobs are more easily enabled by default.

• dump.xml (deprecated) requires a particle group, and can dump subsets of particles.

Other changes

• CMake minimum version is now 2.8

• Convert particle type names to str to allow unicode type name input

• __version__ is now available in the top level package

• boost::iostreams is no longer a build dependency

• boost::filesystem is no longer a build dependency

• New concepts page explaining the different styles of neighbor lists

• Default neighbor list buffer radius is more clearly shown to be r_buff = 0.4

• Memory usage of nlist.stencil is significantly reduced

• A C++11 compliant compiler is now required to build HOOMD-blue

Removed

• Removed integrate.bdnvt: use integrate.langevin

• Removed mtk=False option from integrate.nvt - The MTK NVT integrator is now the only implementation.

• Removed integrate.\*_rigid(): rigid body functionality is now contained in the standard integration methods

• Removed the global neighbor list, and thin wrappers to the neighbor list in nlist.

• Removed PDB and MOL2 dump writers.

• Removed init.create_empty

Deprecated

• Deprecated analyze.msd.

• Deprecated dump.xml.

• Deprecated dump.pos.

• Deprecated init.read_xml.

• Deprecated init.create_random.

• Deprecated init.create_random_polymers.

v1.x

v1.3.3 (2016-03-06)

Bug fixes

• Fix problem incluing hoomd.h in plugins

• Fix random memory errors when using walls

v1.3.2 (2016-02-08)

Bug fixes

• Fix wrong access to system.box

• Fix kinetic energy logging in MPI

• Fix particle out of box error if particles are initialized on the boundary in MPI

• Add integrate.brownian to the documentation index

• Fix misc doc typos

• Fix runtime errors with boost 1.60.0

• Fix corrupt metadata dumps in MPI runs

v1.3.1 (2016-1-14)

Bug fixes

• Fix invalid MPI communicator error with Intel MPI

• Fix python 3.5.1 seg fault

v1.3.0 (2015-12-8)

New features

• Automatically load balanced domain decomposition simulations.

• Anisotropic particle integrators.

• Gay-Berne pair potential.

• Dipole pair potential.

• Brownian dynamics integrate.brownian

• Langevin dynamics integrate.langevin (formerly bdnvt)

• nlist.stencil to compute neighbor lists using stencilled cell lists.

• Add single value scale, min_image, and make_fraction to data.boxdim

• analyze.log can optionally not write a file and now supports querying current quantity values.

• Rewritten wall potentials.

  • Walls are now sums of planar, cylindrical, and spherical half-spaces.

  • Walls are defined and can be modified in job scripts.

  • Walls execute on the GPU.

  • Walls support per type interaction parameters.

  • Implemented for: lj, gauss, slj, yukawa, morse, force_shifted_lj, and mie potentials.

• External electric field potential: external.e_field

Bug fixes

• Fixed a bug where NVT integration hung when there were 0 particles in some domains.

• Check SLURM environment variables for local MPI rank identification

• Fixed a typo in the box math documentation

• Fixed a bug where exceptions weren’t properly passed up to the user script

• Fixed a bug in the velocity initialization example

• Fixed an openmpi fork() warning on some systems

• Fixed segfaults in PPPM

• Fixed a bug where compute.thermo failed after reinitializing a system

• Support list and dict-like objects in init.create_random_polymers.

• Fall back to global rank to assign GPUs if local rank is not available

Deprecated commands

• integrate.bdnvt is deprecated. Use integrate.langevin instead.

• dump.bin and init.bin are now removed. Use XML files for restartable jobs.

Changes that may break existing scripts

• boxdim.wrap now returns the position and image in a tuple, where it used to return just the position.

• wall.lj has a new API

• dump.bin and init.bin have been removed.

v1.2.1 (2015-10-22)

Bug fixes

• Fix a crash when adding or removing particles and reinitializing

• Fix a bug where simulations hung on sm 5.x GPUs with CUDA 7.5

• Fix compile error with long tests enabled

• Issue a warning instead of an error for memory allocations greater than 4 GiB.

• Fix invalid RPATH when building inside zsh.

• Fix incorrect simulations with integrate.npt_rigid

• Label mie potential correctly in user documentation

v1.2.0 (2015-09-30)

New features

• Performance improvements for systems with large particle size disparity

• Bounding volume hierarchy (tree) neighbor list computation

• Neighbor lists have separate r_cut values for each pair of types

• addInfo callback for dump.pos allows user specified information in pos files

Bug fixes

• Fix test_pair_set_energy unit test, which failed on numpy < 1.9.0

• Analyze.log now accepts unicode strings.

• Fixed a bug where calling restore_snapshot() during a run zeroed potential parameters.

• Fix segfault on exit with python 3.4

• Add cite.save() to documentation

• Fix a problem were bond forces are computed incorrectly in some MPI configurations

• Fix bug in pair.zbl

• Add pair.zbl to the documentation

• Use HOOMD_PYTHON_LIBRARY to avoid problems with modified CMake builds that preset PYTHON_LIBRARY

v1.1.1 (2015-07-21)

Bug fixes

• dump.xml(restart=True) now works with MPI execution

• Added missing documentation for meta.dump_metadata

• Build all unit tests by default

• Run all script unit tests through mpirun -n 1

v1.1.0 (2015-07-14)

New features

• Allow builds with ninja.

• Allow K=0 FENE bonds.

• Allow number of particles types to change after initialization.

  system.particles.types.add('newtype')
  

• Allow number of particles to change after initialization.

  system.particles.add(‘A’)
  del system.particles[0]
  

• OPLS dihedral

• Add phase keyword to analyzers and dumps to make restartable jobs easier.

• HOOMD_WALLTIME_STOP environment variable to stop simulation runs before they hit a wall clock limit.

• init.read_xml() Now accepts an initialization and restart file.

• dump.xml() can now write restart files.

• Added documentation concepts page on writing restartable jobs.

• New citation management infrastructure. cite.save() writes .bib files with a list of references to features actively used in the current job script.

• Snapshots expose data as numpy arrays for high performance access to particle properties.

• data.make_snapshot() makes a new empty snapshot.

• analyze.callback() allows multiple python callbacks to operate at different periods.

• comm.barrier()``and comm.barrier_all()``allow users to insert barriers into their scripts.

• Mie pair potential.

• meta.dump_metadata() writes job metadata information out to a json file.

• context.initialize() initializes the execution context.

• Restart option for dump.xml()

Bug fixes

• Fix slow performance when initializing pair.slj()in MPI runs.

• Properly update particle image when setting position from python.

• PYTHON_SITEDIR hoomd shell launcher now calls the python interpreter used at build time.

• Fix compile error on older gcc versions.

• Fix a bug where rigid bodies had 0 velocity when restarting jobs.

• Enable -march=native builds in OS X clang builds.

• Fix group.rigid() and group.nonrigid().

• Fix image access from the python data access proxies.

• Gracefully exit when launching MPI jobs with mixed execution configurations.

Changes that may require updated job scripts

• context.initialize() must be called before any comm method that queries the MPI rank. Call it as early as possible in your job script (right after importing hoomd_script) to avoid problems.

Deprecated

• init.create_empty() is deprecated and will be removed in a future version. Use data.make_snapshot() and init.read_snapshot() instead.

• Job scripts that do not call context.initialize() will result in a warning message. A future version of HOOMD will require that you call context.initialize().

Removed

• Several option commands for controlling the execution configuration. Replaced with context.initialize.

v1.0.5 (2015-05-19)

Bug fixes

• Fix segfault when changing integrators

• Fix system.box to indicate the correct number of dimensions

• Fix syntax error in comm.get_rank with –nrank

• Enable CUDA enabled builds with the intel compiler

• Use CMake builtin FindCUDA on recent versions of CMake

• GCC_ARCH env var sets the -march command line option to gcc at configure time

• Auto-assign GPU-ids on non-compute exclusive systems even with –mode=gpu

• Support python 3.5 alpha

• Fix a bug where particle types were doubled with boost 1.58.0

• Fix a bug where angle_z=true dcd output was inaccurate near 0 angles

• Properly handle lj.wall potentials with epsilon=0.0 and particles on top of the walls

v1.0.4 (2015-04-07)

Bug fixes

• Fix invalid virials computed in rigid body simulations when multi-particle bodies crossed box boundaries

• Fix invalid forces/torques for rigid body simulations caused by race conditions

• Fix compile errors on Mac OS X 10.10

• Fix invalid pair force computations caused by race conditions

• Fix invalid neighbour list computations caused by race conditions on Fermi generation GPUs

Other

• Extremely long running unit tests are now off by default. Enable with -DHOOMD_SKIP_LONG_TESTS=OFF

• Add additional tests to detect race conditions and memory errors in kernels

v1.0.3 (2015-03-18)

Bug fixes

• Enable builds with intel MPI

• Silence warnings coming from boost and python headers

v1.0.2 (2015-01-21)

Bug fixes

• Fixed a bug where linear_interp would not take a floating point value for zero

• Provide more useful error messages when cuda drivers are not present

• Assume device count is 0 when cudaGetDeviceCount() returns an error

• Link to python statically when ENABLE_STATIC=on

• Misc documentation updates

v1.0.1 (2014-09-09)

Bug fixes

1. Fixed bug where error messages were truncated and HOOMD exited with a segmentation fault instead (e.g. on Blue Waters)

2. Fixed bug where plug-ins did not load on Blue Waters

3. Fixed compile error with gcc4.4 and cuda5.0

4. Fixed syntax error in read_snapshot()

5. Fixed a bug where init.read_xml throwing an error (or any other command outside of run()) would hang in MPI runs

6. Search the install path for hoomd_script - enable the hoomd executable to be outside of the install tree (useful with cray aprun)

7. Fixed CMake 3.0 warnings

8. Removed dependancy on tr1/random

9. Fixed a bug where analyze.msd ignored images in the r0_file

10. Fixed typos in pair.gauss documentation

11. Fixed compile errors on Ubuntu 12.10

12. Fix failure of integrate.nvt to reach target temperature in analyze.log. The fix is a new symplectic MTK integrate.nvt integrator. Simulation results in hoomd v1.0.0 are correct, just the temperature and velocity outputs are off slightly.

13. Remove MPI from Mac OS X dmg build.

14. Enable import hoomd_script as ...

Other changes

1. Added default compile flag -march=native

2. Support CUDA 6.5

3. Binary builds for CentOS/RHEL 6, Fedora 20, Ubuntu 14.04 LTS, and Ubuntu 12.04 LTS.

Version 1.0.0 (2014-05-25)

New features

• Support for python 3

• New NPT integrator capable of flexible coupling schemes

• Triclinic unit cell support

• MPI domain decomposition

• Snapshot save/restore

• Autotune block sizes at run time

• Improve performance in small simulation boxes

• Improve performance with smaller numbers of particles per GPU

• Full double precision computations on the GPU (compile time option must be enabled, binary builds provided on the download page are single precision)

• Tabulated bond potential bond.table

• Tabulated angle potential angle.table

• Tabulated dihedral potental dihedral.table

• update.box_resize now accepts period=None to trigger an immediate update of the box without creating a periodic updater

• update.box_resize now replaces None arguments with the current box parameters

• init.create_random and init.create_random_polymers can now create random configurations in triclinc and 2D boxes

• init.create_empty can now create triclinic boxes

• particle, bond, angle, dihedral, and impropers types can now be named in init.create_empty

• system.replicate command replicates the simulation box

Bug fixes

• Fixed a bug where init.create_random_polymers failed when lx,ly,lz were not equal.

• Fixed a bug in init.create_random_polymers and init.create_random where the separation radius was not accounted for correctly

• Fixed a bug in bond.* where random crashes would occur when more than one bond type was defined

• Fixed a bug where dump.dcd did not write the period to the file

Changes that may require updated job scripts

• integrate.nph: A time scale tau_p for the relaxation of the barostat is now required instead of the barostat mass W of the previous release. The time scale is the relaxation time the barostat would have at an average temperature T_0 = 1, and it is related to the internally used (Andersen) Barostat mass W via W = d N T_0 tau_p^2, where d is the dimensionsality and N the number of particles.

• sorter and nlist are now modules, not variables in the __main__ namespace.

• Data proxies function correctly in MPI simulations, but are extremely slow. If you use init.create_empty, consider separating the generation step out to a single rank short execution that writes an XML file for the main run.

• update.box_resize(Lx=...) no longer makes cubic box updates, instead it will keep the current Ly and Lz. Use the L=... shorthand for cubic box updates.

• All init.* commands now take data.boxdim objects, instead of hoomd.boxdim (or 3-tuples). We strongly encourage the use of explicit argument names for data.boxdim(). In particular, if hoomd.boxdim(123) was previously used to create a cubic box, it is now required to use data.boxdim(L=123) (CORRECT) instead of data.boxdim(123) (INCORRECT), otherwise a box with unit dimensions along the y and z axes will be created.

• system.dimensions can no longer be set after initialization. System dimensions are now set during initialization via the data.boxdim interface. The dimensionality of the system can now be queried through system.box.

• system.box no longer accepts 3-tuples. It takes data.boxdim objects.

• system.dimensions no longer exists. Query the dimensionality of the system from system.box. Set the dimensionality of the system by passing an appropriate data.boxdim to an init method.

• init.create_empty no longer accepts n_*_types. Instead, it now takes a list of strings to name the types.

Deprecated

• Support for G80, G200 GPUs.

• dump.bin and read.bin. These will be removed in v1.1 and replaced with a new binary format.

Removed

• OpenMP mult-core execution (replaced with MPI domain decomposition)

• tune.find_optimal_block_size (replaced by Autotuner)

v0.x

Version 0.11.3 (2013-05-10)

Bug fixes

• Fixed a bug where charge.pppm could not be used after init.reset()

• Data proxies can now set body angular momentum before the first run()

• Fixed a bug where PPPM forces were incorrect on the GPU

Version 0.11.2 (2012-12-19)

New features

• Block sizes tuned for K20

Bug fixes

• Warn user that PPPM ignores rigid body exclusions

• Document that proxy iterators need to be deleted before init.reset()

• Fixed a bug where body angular momentum could not be set

• Fixed a bug where analyze.log would report nan for the pressure tensor in nve and nvt simulations

Version 0.11.1 (2012-11-2)

New features

• Support for CUDA 5.0

• Binary builds for Fedora 16 and OpenSUSE 12.1

• Automatically specify /usr/bin/gcc to nvcc when the configured gcc is not supported

Bug fixes

• Fixed a compile error with gcc 4.7

• Fixed a bug where PPPM forces were incorrect with neighborlist exclusions

• Fixed an issue where boost 1.50 and newer were not detected properly when BOOST_ROOT is set

• Fixed a bug where accessing force data in python prevented init.reset() from working

• Fixed a bug that prevented pair.external from logging energy

• Fixed a unit test that failed randomly

Version 0.11.0 (2012-07-27)

New features

1. Support for Kepler GPUs (GTX 680)

2. NPH integration (integrate.nph)

3. Compute full pressure tensor

4. Example plugin for new bond potentials

5. New syntax for bond coefficients: bond.bond_coeff.set(‘type’, params)

6. New external potential: external.periodic applies a periodic potential along one direction (uses include inducing lamellar phases in copolymer systems)

7. Significant performance increases when running analyze.log, analyze.msd, update.box_resize, update.rescale_temp, or update.zero_momentum with a small period

8. Command line options may now be overwritten by scripts, ex: options.set_gpu(2)

9. Added –user command line option to allow user defined options to be passed into job scripts, ex: –user=“-N=5 -phi=0.56”

10. Added table.set_from_file method to enable reading table based pair potentials from a file

11. Added –notice-level command line option to control how much extra information is printed during a run. Set to 0 to disable, or any value up to 10. At 10, verbose debugging information is printed.

12. Added –msg-file command line option which redirects the message output to a file

13. New pair potential pair.force_shifted_lj : Implements https://dx.doi.org/10.1063/1.3558787

Bug fixes

1. Fixed a bug where FENE bonds were sometimes computed incorrectly

2. Fixed a bug where pressure was computed incorrectly when using pair.dpd or pair.dpdlj

3. Fixed a bug where using OpenMP and CUDA at the same time caused invalid memory accesses

4. Fixed a bug where RPM packages did not work on systems where the CUDA toolkit was not installed

5. Fixed a bug where rigid body velocities were not set from python

6. Disabled OpenMP builds on Mac OS X. HOOMD-blue w/ openmp enabled crashes due to bugs in Apple’s OpenMP implementation.

7. Fixed a bug that allowed users to provide invalid rigid body data and cause a seg fault.

8. Fixed a bug where using PPPM resulted in error messages on program exit.

API changes

1. Bond potentials rewritten with template evaluators

2. External potentials use template evaluators

3. Complete rewrite of ParticleData - may break existing plugins

4. Bond/Angle/Dihedral data structures rewritten

   • The GPU specific data structures are now generated on the GPU

5. DPDThermo and DPDLJThermo are now processed by the same template class

6. Headers that cannot be included by nvcc now throw an error when they are

7. CUDA 4.0 is the new minimum requirement

8. Rewrote BoxDim to internally handle minimum image conventions

9. HOOMD now only compiles ptx code for the newest architecture, this halves the executable file size

10. New Messenger class for global control of messages printed to the screen / directed to a file.

Testing changes

1. Automated test suite now performs tests on OpenMPI + CUDA builds

2. Valgrind tests added back into automated test suite

3. Added CPU test in bd_ridid_updater_tests

4. ctest -S scripts can now set parallel makes (with cmake > 2.8.2)

Version 0.10.1 (2012-02-10)

1. Add missing entries to credits page

2. Add dist_check option to neighbor list. Can be used to force neighbor list builds at a specified frequency (useful in profiling runs with nvvp).

3. Fix typos in ubuntu compile documentation

4. Add missing header files to hoomd.h

5. Add torque to the python particle data access API

6. Support boost::filesystem API v3

7. Expose name of executing gpu, n_cpu, hoomd version, git sha1, cuda version, and compiler version to python

8. Fix a bug where multiple nvt_rigid or npt_rigid integrators didn’t work correctly

9. Fix missing pages in developer documentation

Version 0.10.0 (2011-12-14)

New features

1. Added pair.dpdlj which uses the DPD thermostat and the Lennard-Jones potential. In previous versions, this could be accomplished by using two pair commands but at the cost of reduced performance.

2. Additional example scripts are now present in the documentation. The example scripts are cross-linked to the commands that are used in them.

3. Most dump commands now accept the form: dump.ext(filename=“filename.ext”) which immediately writes out filename.ext.

4. Added vis parameter to dump.xml which enables output options commonly used in files written for the purposes of visulization. dump.xml also now accepts parameters on the instantiation line. Combined with the previous feature, dump.xml(filename=“file.xml”, vis=True) is now a convenient short hand for what was previously

   xml = dump.xml()
   xml.set_params(position = True, mass = True, diameter = True,
                         type = True, bond = True, angle = True,
                         dihedral = True, improper = True, charge = True)
   xml.write(filename="file.xml")
   

5. Specify rigid bodies in XML input files

6. Simulations that contain rigid body constraints applied to groups of particles in BDNVT, NVE, NVT, and NPT ensembles.

   • integrate.bdnvt_rigid

   • integrate.nve_rigid

   • integrate.nvt_rigid

   • integrate.npt_rigid

7. Energy minimization of rigid bodies (integrate.mode_minimize_rigid_fire)

8. Existing commands are now rigid-body aware

   • update.rescale_temp

   • update.box_resize

   • update.enforce2d

   • update.zero_momentum

9. NVT integration using the Berendsen thermostat (integrate.berendsen)

10. Bonds, angles, dihedrals, and impropers can now be created and deleted with the python data access API.

11. Attribution clauses added to the HOOMD-blue license.

Changes that may break existing job scripts

1. The wrap option to dump.dcd has been changed to unwrap_full and its meaning inverted. dump.dcd now offers two options for unwrapping particles, unwrap_full fully unwraps particles into their box image and unwrap_rigid unwraps particles in rigid bodies so that bodies are not broken up across a box boundary.

Bug/fixes small enhancements

1. Fixed a bug where launching hoomd on mac os X 10.5 always resulted in a bus error.

2. Fixed a bug where DCD output restricted to a group saved incorrect data.

3. force.constant may now be applied to a group of particles, not just all particles

4. Added C++ plugin example that demonstrates how to add a pair potential in a plugin

5. Fixed a bug where box.resize would always transfer particle data even in a flat portion of the variant

6. OpenMP builds re-enabled on Mac OS X

7. Initial state of integrate.nvt and integrate.npt changed to decrease oscillations at startup.

8. Fixed a bug where the polymer generator would fail to initialize very long polymers

9. Fixed a bug where images were passed to python as unsigned ints.

10. Fixed a bug where dump.pdb wrote coordinates in the wrong order.

11. Fixed a rare problem where a file written by dump.xml would not be read by init.read_xml due to round-off errors.

12. Increased the number of significant digits written out to dump.xml to make them more useful for ad-hoc restart files.

13. Potential energy and pressure computations that slow performance are now only performed on those steps where the values are actually needed.

14. Fixed a typo in the example C++ plugin

15. Mac build instructions updated to work with the latest version of macports

16. Fixed a bug where set_period on any dump was ineffective.

17. print_status_line now handles multiple lines

18. Fixed a bug where using bdnvt tally with per type gammas resulted in a race condition.

19. Fix an issue where ENABLE_CUDA=off builds gave nonsense errors when –mode=gpu was requested.

20. Fixed a bug where dumpl.xml could produce files that init.xml would not read

21. Fixed a typo in the example plugin

22. Fix example that uses hoomd as a library so that it compiles.

23. Update maintainer lines

24. Added message to nlist exclusions that notifies if diameter or body exclusions are set.

25. HOOMD-blue is now hosted in a git repository

26. Added bibtex bibliography to the user documentation

27. Converted user documentation examples to use doxygen auto cross-referencing \example commands

28. Fix a bug where particle data is not released in dump.binary

29. ENABLE_OPENMP can now be set in the ctest builds

30. Tuned block sizes for CUDA 4.0

31. Removed unsupported GPUS from CUDA_ARCH_LIST

Version 0.9.2 (2011-04-04)

Note: only major changes are listed here.

New features

1. New exclusion option: Particles can now be excluded from the neighbor list based on diameter consistent with pair.slj.

2. New pair coeff syntax: Coefficients for multiple type pairs can be specified conveniently on a single line.

   coeff.set(['A', 'B', 'C', 'D'], ['A', 'B', 'C', 'D'], epsilon=1.0)
   

3. New documentation: HOOMD-blue’s system of units is now fully documented, and every coefficient in the documentation is labeled with the appropriate unit.

4. Performance improvements: Performance has been significantly boosted for simulations of medium sized systems (5,000-20,000 particles). Smaller performance boosts were made to larger runs.

5. CUDA 3.2 support: HOOMD-blue is now fully tested and performance tuned for use with CUDA 3.2.

6. CUDA 4.0 support: HOOMD-blue compiles with CUDA 4.0 and passes initial tests.

7. New command: tune.r_buff performs detailed auto-tuning of the r_buff neighborlist parameter.

8. New installation method: RPM, DEB, and app bundle packages are now built for easier installation

9. New command: charge.pppm computes the full long range electrostatic interaction using the PPPM method

Bug/fixes small enhancements

1. Fixed a bug where the python library was linked statically.

2. Added the PYTHON_SITEDIR setting to allow hoomd builds to install into the native python site directory.

3. FIRE energy minimization convergence criteria changed to require both energy and force to converge

4. Clarified that groups are static in the documentation

5. Updated doc comments for compatibility with Doxygen#7.3

6. system.particles.types now lists the particle types in the simulation

7. Creating a group of a non-existant type is no longer an error

8. Mention XML file format for walls in wall.lj documentation

9. Analyzers now profile themselves

10. Use \n for newlines in dump.xml - improves performance when writing many XML files on a NFS file system

11. Fixed a bug where the neighbor list build could take an exceptionally long time (several seconds) to complete the first build.

12. Fixed a bug where certain logged quantities always reported as 0 on the first step of the simulation.

13. system.box can now be used to read and set the simulation box size from python

14. Numerous internal API updates

15. Fixed a bug the resulted in incorrect behavior when using integrate.npt on the GPU.

16. Removed hoomd launcher shell script. In non-sitedir installs, ${HOOMD_ROOT}/bin/hoomd is now the executable itself

17. Creating unions of groups of non-existent types no longer produces a seg fault

18. hoomd now builds on all cuda architectures. Modify CUDA_ARCH_LIST in cmake to add or remove architectures from the build

19. hoomd now builds with boost#46.0

20. Updated hoomd icons to maize/blue color scheme

21. hoomd xml file format bumped to#3, adds support for charge.

22. FENE and harmonic bonds now handle 0 interaction parameters and 0 length bonds more gracefully

23. The packaged plugin template now actually builds and installs into a recent build of hoomd

Version 0.9.1 (2010-10-08)

Note: only major changes are listed here.

New features

1. New constraint: constrain.sphere constrains a group of particles to the surface of a sphere

2. New pair potential/thermostat: pair.dpd implements the standard DPD conservative, random, and dissipative forces

3. New pair potential: pair.dpd_conservative applies just the conservative DPD potential

4. New pair potential: pair.eam implements the Embedded Atom Method (EAM) and supports both alloy and FS type computations.

5. Faster performance: Cell list and neighbor list code has been rewritten for performance.

   • In our benchmarks, performance increases ranged from 10-50% over HOOMD-blue 0.9.0. Simulations with shorter cutoffs tend to attain a higher performance boost than those with longer cutoffs.

   • We recommended that you re-tune r_buff values for optimal performance with 0.9.1.

   • Due to the nature of the changes, identical runs may produce different trajectories.

6. Removed limitation: The limit on the number of neighbor list exclusions per particle has been removed. Any number of exclusions can now be added per particle. Expect reduced performance when adding excessive numbers of exclusions.

Bug/fixes small enhancements

1. Pressure computation is now correct when constraints are applied.

2. Removed missing files from hoomd.h

3. pair.yukawa is no longer referred to by “gaussian” in the documentation

4. Fermi GPUs are now prioritized over per-Fermi GPUs in systems where both are present

5. HOOMD now compiles against CUDA 3.1

6. Momentum conservation significantly improved on compute#x hardware

7. hoomd plugins can now be installed into user specified directories

8. Setting r_buff=0 no longer triggers exclusion list updates on every step

9. CUDA 2.2 and older are no longer supported

10. Workaround for compiler bug in 3.1 that produces extremely high register usage

11. Disabled OpenMP compile checks on Mac OS X

12. Support for compute 2.1 devices (such as the GTX 460)

Version 0.9.0 (2010-05-18)

Note: only major changes are listed here.

New features

1. New pair potential: Shifted LJ potential for particles of varying diameters (pair.slj)

2. New pair potential: Tabulated pair potential (pair.table)

3. New pair potential: Yukawa potential (pair.yukawa)

4. Update to pair potentials: Most pair potentials can now accept different values of r_cut for different type pairs. The r_cut specified in the initial pair.*** command is now treated as the default r_cut, so no changes to scripts are necessary.

5. Update to pair potentials: Default pair coeff values are now supported. The parameter alpha for lj now defaults to#0, so there is no longer a need to specify it for a majority of simulations.

6. Update to pair potentials: The maximum r_cut needed for the neighbor list is now determined at the start of each run(). In simulations where r_cut may decrease over time, increased performance will result.

7. Update to pair potentials: Pair potentials are now specified via template evaluator classes. Adding a new pair potential to hoomd now only requires a small amount of additional code.

8. Plugin API : Advanced users/developers can now write, install, and use plugins for hoomd without needing to modify core hoomd source code

9. Particle data access: User-level hoomd scripts can now directly access the particle data. For example, one can change all particles in the top half of the box to be type B:

   top = group.cuboid(name="top", zmin=0)
   for p in top:
       p.type = 'B'
   

   . All particle data including position, velocity, type, ‘’et cetera’’, can be read and written in this manner. Computed forces and energies can also be accessed in a similar way.

10. New script command: init.create_empty() can be used in conjunction with the particle data access above to completely initialize a system within the hoomd script.

11. New script command: dump.bin() writes full binary restart files with the entire system state, including the internal state of integrators.

    • File output can be gzip compressed (if zlib is available) to save space

    • Output can alternate between two different output files for safe crash recovery

12. New script command: init.read_bin() reads restart files written by dump.bin()

13. New option: run() now accepts a quiet option. When True, it eliminates the status information printouts that go to stdout.

14. New example script: Example 6 demonstrates the use of the particle data access routines to initialize a system. It also demonstrates how to initialize velocities from a gaussian distribution

15. New example script: Example 7 plots the pair.lj potential energy and force as evaluated by hoomd. It can trivially be modified to plot any potential in hoomd.

16. New feature: Two dimensional simulations can now be run in hoomd: #259

17. New pair potential: Morse potential for particles of varying diameters (pair.morse)

18. New command: run_upto will run a simulation up to a given time step number (handy for breaking long simulations up into many independent jobs)

19. New feature: HOOMD on the CPU is now accelerated with OpenMP.

20. New feature: integrate.mode_minimize_fire performs energy minimization using the FIRE algorithm

21. New feature: analyze.msd can now accept an xml file specifying the initial particle positions (for restarting jobs)

22. Improved feature: analyze.imd now supports all IMD commands that VMD sends (pause, kill, change trate, etc.)

23. New feature: Pair potentials can now be given names, allowing multiple potentials of the same type to be logged separately. Additionally, potentials that are disabled and not applied to the system dynamics can be optionally logged.

24. Performance improvements: Simulation performance has been increased across the board, but especially when running systems with very low particle number densities.

25. New hardware support: 0.9.0 and newer support Fermi GPUs

26. Deprecated hardware support: 0.9.x might continue run on compute#1 GPUs but that hardware is no longer officially supported

27. New script command: group.tag_list() takes a python list of particle tags and creates a group

28. New script command: compute.thermo() computes thermodynamic properties of a group of particles for logging

29. New feature: dump.dcd can now optionally write out only those particles that belong to a specified group

Changes that will break jobs scripts written for 0.8.x

1. Integration routines have changed significantly to enable new use cases. Where scripts previously had commands like:

   integrate.nve(dt=0.005)
   

   they now need

   all = group.all()
   integrate.mode_standard(dt=0.005)
   integrate.nve(group=all)
   

   . Integrating only specific groups of particles enables simulations to fix certain particles in place or integrate different parts of the system at different temperatures, among many other possibilities.

2. sorter.set_params no longer takes the ‘’bin_width’’ argument. It is replaced by a new ‘’grid’’ argument, see the documentation for details.

3. conserved_quantity is no longer a quantity available for logging. Instead log the nvt reservoir energy and compute the total conserved quantity in post processing.

Bug/fixes small enhancements

1. Fixed a bug where boost#38 is not found on some machines

2. dump.xml now has an option to write particle accelerations

3. Fixed a bug where periods like 1e6 were not accepted by updaters

4. Fixed a bug where bond.fene forces were calculated incorrectly between particles of differing diameters

5. Fixed a bug where bond.fene energies were computed incorrectly when running on the GPU

6. Fixed a bug where comments in hoomd xml files were not ignored as they aught to be: #331

7. It is now possible to prevent bond exclusions from ever being added to the neighbor list: #338

8. init.create_random_polymers can now generate extremely dense systems and will warn the user about large memory usage

9. variant.linear_interp now accepts a user-defined zero (handy for breaking long simulations up into many independent jobs)

10. Improved installation and compilation documentation

11. Integration methods now silently ignore when they are given an empty group

12. Fixed a bug where disabling all forces resulted in some forces still being applied

13. Integrators now behave in a reasonable way when given empty groups

14. Analyzers now accept a floating point period

15. run() now aborts immediately if limit_hours=0 is specified.

16. Pair potentials that diverge at r=0 will no longer result in invalid simulations when the leading coefficients are set to zero.

17. integrate.bdnvt can now tally the energy transferred into/out of the “reservoir”, allowing energy conservation to be monitored during bd simulation runs.

18. Most potentials now prevent NaN results when computed for overlapping particles

19. Stopping a simulation from a callback or time limit no longer produces invalid simulations when continued

20. run() commands limited with limit_hours can now be set to only stop on given timestep multiples

21. Worked around a compiler bug where pair.morse would crash on Fermi GPUs

22. ULF stability improvements for G200 GPUs.

Version 0.8.2 (2009-09-10)

Note: only major changes are listed here.

New features

1. Quantities that vary over time can now be specified easily in scripts with the variant.linear_interp command.

2. Box resizing updater (update.box_resize) command that uses the time varying quantity command to grow or shrink the simulation box.

3. Individual run() commands can be limited by wall-clock time

4. Angle forces can now be specified

5. Dihedral forces can now be specified

6. Improper forces can now be specified

7. 1-3 and 1-4 exclusions from the cutoff pair force can now be chosen

8. New command line option: –minimize-cpu-usage cuts the CPU usage of HOOMD down to 10% of one CPU core while only decreasing overall performance by 10%

9. Major changes have been made in the way HOOMD chooses the device on which to run (all require CUDA 2.2 or newer)

   • there are now checks that an appropriate NVIDIA drivers is installed

   • running without any command line options will now correctly revert to running on the CPU if no capable GPUs are installed

   • when no gpu is explicitly specified, the default choice is now prioritized to choose the fastest GPU and one that is not attached to a display first

   • new command line option: –ignore-display-gpu will prevent HOOMD from executing on any GPU attached to a display

   • HOOMD now prints out a short description of the GPU(s) it is running on

   • on linux, devices can be set to compute-exclusive mode and HOOMD will then automatically choose the first free GPU (see the documentation for details)

10. nlist.reset_exclusions command to control the particles that are excluded from the neighbor list

Bug/fixes small enhancements

1. Default block size change to improve stability on compute#3 devices

2. ULF workaround on GTX 280 now works with CUDA 2.2

3. Standalone benchmark executables have been removed and replaced by in script benchmarking commands

4. Block size tuning runs can now be performed automatically using the python API and results can be saved on the local machine

5. Fixed a bug where GTX 280 bug workarounds were not properly applied in CUDA 2.2

6. The time step read in from the XML file can now be optionally overwritten with a user-chosen one

7. Added support for CUDA 2.2

8. Fixed a bug where the WCA forces included in bond.fene had an improper cutoff

9. Added support for a python callback to be executed periodically during a run()

10. Removed demos from the hoomd downloads. These will be offered separately on the webpage now to keep the required download size small.

11. documentation improvements

12. Significantly increased performance of dual-GPU runs when build with CUDA 2.2 or newer

13. Numerous stability and performance improvements

14. Temperatures are now calculated based on 3N-3 degrees of freedom. See #283 for a more flexible system that is coming in the future.

15. Emulation mode builds now work on systems without an NVIDIA card (CUDA 2.2 or newer)

16. HOOMD now compiles with CUDA 2.3

17. Fixed a bug where uninitialized memory was written to dcd files

18. Fixed a bug that prevented the neighbor list on the CPU from working properly with non-cubic boxes

19. There is now a compile time hack to allow for more than 4 exclusions per particle

20. Documentation added to aid users in migrating from LAMMPS

21. hoomd_script now has an internal version number useful for third party scripts interfacing with it

22. VMD#8.7 is now found by the live demo scripts

23. live demos now run in vista 64-bit

24. init.create_random_polymers can now create polymers with more than one type of bond

Version 0.8.1 (2009-03-24)

Note: only major changes are listed here.

New features

1. Significant performance enhancements

2. New build option for compiling on UMich CAC clusters: ENABLE_CAC_GPU_ID compiles HOOMD to read in the $CAC_GPU_ID environment variable and use it to determine which GPUs to execute on. No –gpu command line required in job scripts any more.

3. Particles can now be assigned a non-unit mass

4. init.reset() command added to allow for the creation of a looped series of simulations all in python

5. dump.pdb() command for writing PDB files

6. pair.lj now comes with an option to shift the potential energy to 0 at the cutoff

7. pair.lj now comes with an opiton to smoothly switch both the potential and force to 0 at the cutoff with the XPLOR smoothing function

8. Gaussian pair potential computation added (pair.gauss)

9. update and analyze commands can now be given a function to determine a non-linear rate to run at

10. analyze.log, and dump.dcd can now append to existing files

Changes that will break scripts from 0.8.0

1. dump.mol2() has been changed to be more consistent with other dump commands. In order to get the same result as the previous behavior, replace

   dump.mol2(filename="file.mol2")
   

   with

   mol2 = dump.mol2()
   mol2.write(filename="file.mol2")
   

2. Grouping commands have been moved to their own package for organizational purposes. group_all() must now be called as group.all() and similarly for tags and type.

Bug/fixes small enhancements

1. Documentation updates

2. DCD file writing no longer crashes HOOMD in windows

3. !FindBoost.cmake is patched upstream. Use CMake 2.6.3 if you need BOOST_ROOT to work correctly

4. Validation tests now run with –gpu_error_checking

5. ULF bug workarounds are now enabled only on hardware where they are needed. This boosts performance on C1060 and newer GPUs.

6. !FindPythonLibs now always finds the shared python libraries, if they exist

7. “make package” now works fine on mac os x

8. Fixed erroneously reported dangerous neighbor list builds when using –mode=cpu

9. Small tweaks to the XML file format.

10. Numerous performance enhancements

11. Workaround for ULF on compute#1 devices in place

12. dump.xml can now be given the option “all=true” to write all fields

13. total momentum can now be logged by analyze.log

14. HOOMD now compiles with boost#38 (and hopefully future versions)

15. Updaters can now be given floating point periods such as 1e5

16. Additional warnings are now printed when HOOMD is about to allocate a large amount of memory due to the specification of an extremely large box size

17. run() now shows up in the documentation index

18. Default sorter period is now 100 on CPUs to improve performance on chips with small caches

Version 0.8.0 (2008-12-22)

Note: only major changes are listed here.

New features

1. Addition of FENE bond potential

2. Addition of update.zero_momentum command to zero a system’s linear momentum

3. Brownian dynamics integration implemented

4. Multi-GPU simulations

5. Particle image flags are now tracked. analyze.msd command added to calculate the mean squared displacement.

Changes that will break scripts from 0.7.x

1. analyze.log quantity names have changed

Bug/fixes small enhancements

1. Performance of the neighbor list has been increased significantly on the GPU (overall performance improvements are approximately 10%)

2. Profile option added to the run() command

3. Warnings are now correctly printed when negative coefficients are given to bond forces

4. Simulations no longer fail on G200 cards

5. Mac OS X binaries will be provided for download: new documentation for installing on Mac OS x has been written

6. Two new demos showcasing large systems

7. Particles leaving the simulation box due to bad initial conditions now generate an error

8. win64 installers will no longer attempt to install on win32 and vice-versa

9. neighborlist check_period now defaults to 1

10. The elapsed time counter in run() now continues counting time over multiple runs.

11. init.create_random_polymers now throws an error if the bond length is too small given the specified separation radii

12. Fixed a bug where a floating point value for the count field in init.create_random_polymers produced an error

13. Additional error checking to test if particles go NaN

14. Much improved status line printing for identifying hoomd_script commands

15. Numerous documentation updates

16. The VS redistributable package no longer needs to be installed to run HOOMD on windows (these files are distributed with HOOMD)

17. Now using new features in doxygen#5.7 to build pdf user documentation for download.

18. Performance enhancements of the Lennard-Jones pair force computation, thanks to David Tarjan

19. A header prefix can be added to log files to make them more gnuplot friendly

20. Log quantities completely revamped. Common quantities (i.e. kinetic energy, potential energy can now be logged in any simulation)

21. Particle groups can now be created. Currently only analyze.msd makes use of them.

22. The CUDA toolkit no longer needs to be installed to run a packaged HOOMD binary in windows.

23. User documentation can now be downloaded as a pdf.

24. Analyzers and updaters now count time 0 as being the time they were created, instead of time step 0.

25. Added job test scripts to aid in validating HOOMD

26. HOOMD will now build with default settings on a linux/unix-like OS where the boost static libraries are not installed, but the dynamic ones are.

Version 0.7.1 (2008-09-12)

1. Fixed bug where extremely large box dimensions resulted in an argument error - ticket:118

2. Fixed bug where simulations ran incorrectly with extremely small box dimensions - ticket:138

Version 0.7.0 (2008-08-12)

Note: only major changes are listed here.

1. Stability and performance improvements.

2. Cleaned up the hoomd_xml file format.

3. Improved detection of errors in hoomd_xml files significantly.

4. Users no longer need to manually specify HOOMD_ROOT, unless their installation is non-standard

5. Particle charge can now be read in from a hoomd_xml file

6. Consistency changes in the hoomd_xml file format: HOOMD 0.6.0 XML files are not compatible. No more compatibility breaking changes are planned after 0.7.0

7. Enabled parallel builds in MSVC for faster compilation times on multicore systems

8. Numerous small bug fixes

9. New force compute for implementing walls

10. Documentation updates

11. Support for CUDA 2.0

12. Bug fixed allowing simulations with no integrator

13. Support for boost#35.0

14. Cleaned up GPU code interface

15. NVT integrator now uses tau (period) instead of Q (the mass of the extra degree of freedom).

16. Added option to NVE integration to limit the distance a particle moves in a single time step

17. Added code to dump system snapshots in the DCD file format

18. Particle types can be named by strings

19. A snapshot of the initial configuration can now be written in the .mol2 file format

20. The default build settings now enable most of the optional features

21. Separated the user and developer documentation

22. Mixed polymer systems can now be generated inside HOOMD

23. Support for CMake 2.6.0

24. Wrote the user documentation

25. GPU selection from the command line

26. Implementation of the job scripting system

27. GPU can now handle neighbor lists that overflow

28. Energies are now calculated

29. Added a logger for logging energies during a simulation run

30. Code now actually compiles on Mac OS X

31. Benchmark and demo scripts now use the new scripting system

32. Consistent error message format that is more visible.

33. Multiple types of bonds each with the own coefficients are now supported

34. Added python scripts to convert from HOOMD’s XML file format to LAMMPS input and dump files

35. Fixed a bug where empty xml nodes in input files resulted in an error message

36. Fixed a bug where HOOMD seg faulted when a particle left the simulation , vis=True)* is now a convenient short hand for what was previously box now works fine on mac os x

37. Fixed erroneously reported dangerous neighbor list builds when using –mode=cpu

38. Small tweaks to the XML file format.

39. Numerous performance enhancements

40. Workaround for ULF on compute#1 devices in place

41. dump.xml can now be given the option