HOOMD-blue Change Log

[TOC]

v1.3.0

Released 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

Released 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

Released 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

Released 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

Released 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

Released 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

Released 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

Released 2015/03/18

Bug fixes

Enable builds with intel MPI
Silence warnings coming from boost and python headers

v1.0.2

Released 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

Released 2014/09/09

Bug fixes

Fixed bug where error messages were truncated and HOOMD exited with a segmentation fault instead (e.g. on Blue Waters)
Fixed bug where plug-ins did not load on Blue Waters
Fixed compile error with gcc4.4 and cuda5.0
Fixed syntax error in read_snapshot()
Fixed a bug where init.read_xml throwing an error (or any other command outside of run()) would hang in MPI runs
Search the install path for hoomd_script - enable the hoomd executable to be outside of the install tree (useful with cray aprun)
Fixed CMake 3.0 warnings
Removed dependancy on tr1/random
Fixed a bug where analyze.msd ignored images in the r0_file
Fixed typos in pair.gauss documentation
Fixed compile errors on Ubuntu 12.10
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.
Remove MPI from Mac OS X dmg build.
Enable import hoomd_script as ...

Other changes

Added default compile flag -march=native
Support CUDA 6.5
Binary builds for CentOS/RHEL 6, Fedora 20, Ubuntu 14.04 LTS, and Ubuntu 12.04 LTS.

Version 1.0.0

Released 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)

Version 0.11.3

Released 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

Released 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

Released 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

Support for Kepler GPUs (GTX 680)
NPH integration (integrate.nph)
Compute full pressure tensor
Example plugin for new bond potentials
New syntax for bond coefficients: bond.bond_coeff.set('type', params)
New external potential: external.periodic applies a periodic potential along one direction (uses include inducing lamellar phases in copolymer systems)
Significant performance increases when running analyze.log, analyze.msd, update.box_resize, update.rescale_temp, or update.zero_momentum with a small period
Command line options may now be overwritten by scripts, ex: options.set_gpu(2)
Added --user command line option to allow user defined options to be passed into job scripts, ex: --user="-N=5 -phi=0.56"
Added table.set_from_file method to enable reading table based pair potentials from a file
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.
Added --msg-file command line option which redirects the message output to a file
New pair potential pair.force_shifted_lj : Implements http://dx.doi.org/10.1063/1.3558787

Bug fixes

Fixed a bug where FENE bonds were sometimes computed incorrectly
Fixed a bug where pressure was computed incorrectly when using pair.dpd or pair.dpdlj
Fixed a bug where using OpenMP and CUDA at the same time caused invalid memory accesses
Fixed a bug where RPM packages did not work on systems where the CUDA toolkit was not installed
Fixed a bug where rigid body velocities were not set from python
Disabled OpenMP builds on Mac OS X. HOOMD-blue w/ openmp enabled crashes due to bugs in Apple's OpenMP implementation.
Fixed a bug that allowed users to provide invalid rigid body data and cause a seg fault.
Fixed a bug where using PPPM resulted in error messages on program exit.

API changes

Bond potentials rewritten with template evaluators
External potentials use template evaluators
Complete rewrite of ParticleData - may break existing plugins
Bond/Angle/Dihedral data structures rewritten
- The GPU specific data structures are now generated on the GPU
DPDThermo and DPDLJThermo are now processed by the same template class
Headers that cannot be included by nvcc now throw an error when they are
CUDA 4.0 is the new minimum requirement
Rewrote BoxDim to internally handle minimum image conventions
HOOMD now only compiles ptx code for the newest architecture, this halves the executable file size
New Messenger class for global control of messages printed to the screen / directed to a file.

Testing changes

Automated test suite now performs tests on OpenMPI + CUDA builds
Valgrind tests added back into automated test suite
Added CPU test in bd_ridid_updater_tests
ctest -S scripts can now set parallel makes (with cmake > 2.8.2)

Version 0.10.1

2012-02-10

Add missing entries to credits page
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).
Fix typos in ubuntu compile documentation
Add missing header files to hoomd.h
Add torque to the python particle data access API
Support boost::filesystem API v3
Expose name of executing gpu, n_cpu, hoomd version, git sha1, cuda version, and compiler version to python
Fix a bug where multiple nvt_rigid or npt_rigid integrators didn't work correctly
Fix missing pages in developer documentation

Version 0.10.0

2011-12-14

New features

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.
Additional example scripts are now present in the documentation. The example scripts are cross-linked to the commands that are used in them.
Most dump commands now accept the form: dump.ext(filename="filename.ext") which immediately writes out filename.ext.
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")

Specify rigid bodies in XML input files
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
Energy minimization of rigid bodies (integrate.mode_minimize_rigid_fire)
Existing commands are now rigid-body aware
- update.rescale_temp
- update.box_resize
- update.enforce2d
- update.zero_momentum
NVT integration using the Berendsen thermostat (integrate.berendsen)
Bonds, angles, dihedrals, and impropers can now be created and deleted with the python data access API.
Attribution clauses added to the "HOOMD-blue license":http://codeblue.umich.edu/hoomd-blue/doc/page_license.html

Changes that may break existing job scripts

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

Fixed a bug where launching hoomd on mac os X 10.5 always resulted in a bus error.
Fixed a bug where DCD output restricted to a group saved incorrect data.
force.constant may now be applied to a group of particles, not just all particles
Added C++ plugin example that demonstrates how to add a pair potential in a plugin
Fixed a bug where box.resize would always transfer particle data even in a flat portion of the variant
OpenMP builds re-enabled on Mac OS X
Initial state of integrate.nvt and integrate.npt changed to decrease oscillations at startup.
Fixed a bug where the polymer generator would fail to initialize very long polymers
Fixed a bug where images were passed to python as unsigned ints.
Fixed a bug where dump.pdb wrote coordinates in the wrong order.
Fixed a rare problem where a file written by dump.xml would not be read by init.read_xml due to round-off errors.
Increased the number of significant digits written out to dump.xml to make them more useful for ad-hoc restart files.
Potential energy and pressure computations that slow performance are now only performed on those steps where the values are actually needed.
Fixed a typo in the example C++ plugin
Mac build instructions updated to work with the latest version of macports
Fixed a bug where set_period on any dump was ineffective.
print_status_line now handles multiple lines
Fixed a bug where using bdnvt tally with per type gammas resulted in a race condition.
Fix an issue where ENABLE_CUDA=off builds gave nonsense errors when --mode=gpu was requested.
Fixed a bug where dumpl.xml could produce files that init.xml would not read
Fixed a typo in the example plugin
Fix example that uses hoomd as a library so that it compiles.
Update maintainer lines
Added message to nlist exclusions that notifies if diameter or body exclusions are set.
HOOMD-blue is now hosted in a git repository
Added bibtex bibliography to the user documentation
Converted user documentation examples to use doxygen auto cross-referencing \example commands
Fix a bug where particle data is not released in dump.binary
ENABLE_OPENMP can now be set in the ctest builds
Tuned block sizes for CUDA 4.0
Removed unsupported GPUS from CUDA_ARCH_LIST

Version 0.9.2

2011-04-04

Note: only major changes are listed here.

New features

New exclusion option: Particles can now be excluded from the neighbor list based on diameter consistent with pair.slj.
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)

New documentation: HOOMD-blue's system of units is now fully documented, and every coefficient in the documentation is labeled with the appropriate unit.
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.
CUDA 3.2 support: HOOMD-blue is now fully tested and performance tuned for use with CUDA 3.2.
CUDA 4.0 support: HOOMD-blue compiles with CUDA 4.0 and passes initial tests.
New command: tune.r_buff performs detailed auto-tuning of the r_buff neighborlist parameter.
New installation method: RPM, DEB, and app bundle packages are now built for easier installation
New command: charge.pppm computes the full long range electrostatic interaction using the PPPM method

Bug/fixes small enhancements

Fixed a bug where the python library was linked statically.
Added the PYTHON_SITEDIR setting to allow hoomd builds to install into the native python site directory.
FIRE energy minimization convergence criteria changed to require both energy and force to converge
Clarified that groups are static in the documentation
Updated doc comments for compatibility with Doxygen#7.3
system.particles.types now lists the particle types in the simulation
Creating a group of a non-existant type is no longer an error
Mention XML file format for walls in wall.lj documentation
Analyzers now profile themselves
Use "\n" for newlines in dump.xml - improves performance when writing many XML files on a NFS file system
Fixed a bug where the neighbor list build could take an exceptionally long time (several seconds) to complete the first build.
Fixed a bug where certain logged quantities always reported as 0 on the first step of the simulation.
system.box can now be used to read and set the simulation box size from python
Numerous internal API updates
Fixed a bug the resulted in incorrect behavior when using integrate.npt on the GPU.
Removed hoomd launcher shell script. In non-sitedir installs, ${HOOMD_ROOT}/bin/hoomd is now the executable itself
Creating unions of groups of non-existent types no longer produces a seg fault
hoomd now builds on all cuda architectures. Modify CUDA_ARCH_LIST in cmake to add or remove architectures from the build
hoomd now builds with boost#46.0
Updated hoomd icons to maize/blue color scheme
hoomd xml file format bumped to#3, adds support for charge.
FENE and harmonic bonds now handle 0 interaction parameters and 0 length bonds more gracefully
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

New constraint: constrain.sphere constrains a group of particles to the surface of a sphere
New pair potential/thermostat: pair.dpd implements the standard DPD conservative, random, and dissipative forces
New pair potential: pair.dpd_conservative applies just the conservative DPD potential
New pair potential: pair.eam implements the Embedded Atom Method (EAM) and supports both alloy and FS type computations.
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.
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

Pressure computation is now correct when constraints are applied.
Removed missing files from hoomd.h
pair.yukawa is no longer referred to by "gaussian" in the documentation
Fermi GPUs are now prioritized over per-Fermi GPUs in systems where both are present
HOOMD now compiles against CUDA 3.1
Momentum conservation significantly improved on compute#x hardware
hoomd plugins can now be installed into user specified directories
Setting r_buff=0 no longer triggers exclusion list updates on every step
CUDA 2.2 and older are no longer supported
Workaround for compiler bug in 3.1 that produces extremely high register usage
Disabled OpenMP compile checks on Mac OS X
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

New pair potential: Shifted LJ potential for particles of varying diameters (pair.slj)
New pair potential: Tabulated pair potential (pair.table)
New pair potential: Yukawa potential (pair.yukawa)
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.
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.
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.
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.
Plugin API : Advanced users/developers can now write, install, and use plugins for hoomd without needing to modify core hoomd source code
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.

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.
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
New script command: init.read_bin() reads restart files written by dump.bin()
New option: run() now accepts a quiet option. When True, it eliminates the status information printouts that go to stdout.
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
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.
New feature: Two dimensional simulations can now be run in hoomd: #259
New pair potential: Morse potential for particles of varying diameters (pair.morse)
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)
New feature: HOOMD on the CPU is now accelerated with OpenMP.
New feature: integrate.mode_minimize_fire performs energy minimization using the FIRE algorithm
New feature: analyze.msd can now accept an xml file specifying the initial particle positions (for restarting jobs)
Improved feature: analyze.imd now supports all IMD commands that VMD sends (pause, kill, change trate, etc.)
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.
Performance improvements: Simulation performance has been increased across the board, but especially when running systems with very low particle number densities.
New hardware support: 0.9.0 and newer support Fermi GPUs
Deprecated hardware support: 0.9.x might continue run on compute#1 GPUs but that hardware is no longer officially supported
New script command: group.tag_list() takes a python list of particle tags and creates a group
New script command: compute.thermo() computes thermodynamic properties of a group of particles for logging
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

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.

sorter.set_params no longer takes the ''bin_width'' argument. It is replaced by a new ''grid'' argument, see the documentation for details.
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

Fixed a bug where boost#38 is not found on some machines
dump.xml now has an option to write particle accelerations
Fixed a bug where periods like 1e6 were not accepted by updaters
Fixed a bug where bond.fene forces were calculated incorrectly between particles of differing diameters
Fixed a bug where bond.fene energies were computed incorrectly when running on the GPU
Fixed a bug where comments in hoomd xml files were not ignored as they aught to be: #331
It is now possible to prevent bond exclusions from ever being added to the neighbor list: #338
init.create_random_polymers can now generate extremely dense systems and will warn the user about large memory usage
variant.linear_interp now accepts a user-defined zero (handy for breaking long simulations up into many independent jobs)
Improved installation and compilation documentation
Integration methods now silently ignore when they are given an empty group
Fixed a bug where disabling all forces resulted in some forces still being applied
Integrators now behave in a reasonable way when given empty groups
Analyzers now accept a floating point period
run() now aborts immediately if limit_hours=0 is specified.
Pair potentials that diverge at r=0 will no longer result in invalid simulations when the leading coefficients are set to zero.
integrate.bdnvt can now tally the energy transferred into/out of the "reservoir", allowing energy conservation to be monitored during bd simulation runs.
Most potentials now prevent NaN results when computed for overlapping particles
Stopping a simulation from a callback or time limit no longer produces invalid simulations when continued
run() commands limited with limit_hours can now be set to only stop on given timestep multiples
Worked around a compiler bug where pair.morse would crash on Fermi GPUs
ULF stability improvements for G200 GPUs.

Version 0.8.2

2009-09-10

Note: only major changes are listed here.

New features

Quantities that vary over time can now be specified easily in scripts with the variant.linear_interp command.
Box resizing updater (update.box_resize) command that uses the time varying quantity command to grow or shrink the simulation box.
Individual run() commands can be limited by wall-clock time
Angle forces can now be specified
Dihedral forces can now be specified
Improper forces can now be specified
1-3 and 1-4 exclusions from the cutoff pair force can now be chosen
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%
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)
nlist.reset_exclusions command to control the particles that are excluded from the neighbor list

Bug/fixes small enhancements

Default block size change to improve stability on compute#3 devices
ULF workaround on GTX 280 now works with CUDA 2.2
Standalone benchmark executables have been removed and replaced by in script benchmarking commands
Block size tuning runs can now be performed automatically using the python API and results can be saved on the local machine
Fixed a bug where GTX 280 bug workarounds were not properly applied in CUDA 2.2
The time step read in from the XML file can now be optionally overwritten with a user-chosen one
Added support for CUDA 2.2
Fixed a bug where the WCA forces included in bond.fene had an improper cutoff
Added support for a python callback to be executed periodically during a run()
Removed demos from the hoomd downloads. These will be offered separately on the webpage now to keep the required download size small.
documentation improvements
Significantly increased performance of dual-GPU runs when build with CUDA 2.2 or newer
Numerous stability and performance improvements
Temperatures are now calculated based on 3N-3 degrees of freedom. See #283 for a more flexible system that is coming in the future.
Emulation mode builds now work on systems without an NVIDIA card (CUDA 2.2 or newer)
HOOMD now compiles with CUDA 2.3
Fixed a bug where uninitialized memory was written to dcd files
Fixed a bug that prevented the neighbor list on the CPU from working properly with non-cubic boxes
There is now a compile time hack to allow for more than 4 exclusions per particle
Documentation added to aid users in migrating from LAMMPS
hoomd_script now has an internal version number useful for third party scripts interfacing with it
VMD#8.7 is now found by the live demo scripts
live demos now run in vista 64-bit
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

Significant performance enhancements
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.
Particles can now be assigned a non-unit mass
init.reset() command added to allow for the creation of a looped series of simulations all in python
dump.pdb() command for writing PDB files
pair.lj now comes with an option to shift the potential energy to 0 at the cutoff
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
Gaussian pair potential computation added (pair.gauss)
update and analyze commands can now be given a function to determine a non-linear rate to run at
analyze.log, and dump.dcd can now append to existing files

Changes that will break scripts from 0.8.0

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")

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

Documentation updates
DCD file writing no longer crashes HOOMD in windows
!FindBoost.cmake is patched upstream. Use CMake 2.6.3 if you need BOOST_ROOT to work correctly
Validation tests now run with --gpu_error_checking
ULF bug workarounds are now enabled only on hardware where they are needed. This boosts performance on C1060 and newer GPUs.
!FindPythonLibs now always finds the shared python libraries, if they exist
"make package" now works fine on mac os x
Fixed erroneously reported dangerous neighbor list builds when using --mode=cpu
Small tweaks to the XML file format.
Numerous performance enhancements
Workaround for ULF on compute#1 devices in place
dump.xml can now be given the option "all=true" to write all fields
total momentum can now be logged by analyze.log
HOOMD now compiles with boost#38 (and hopefully future versions)
Updaters can now be given floating point periods such as 1e5
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
run() now shows up in the documentation index
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

Addition of FENE bond potential
Addition of update.zero_momentum command to zero a system's linear momentum
Brownian dynamics integration implemented
Multi-GPU simulations
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

analyze.log quantity names have changed

Bug/fixes small enhancements

Performance of the neighbor list has been increased significantly on the GPU (overall performance improvements are approximately 10%)
Profile option added to the run() command
Warnings are now correctly printed when negative coefficients are given to bond forces
Simulations no longer fail on G200 cards
Mac OS X binaries will be provided for download: new documentation for installing on Mac OS x has been written
Two new demos showcasing large systems
Particles leaving the simulation box due to bad initial conditions now generate an error
win64 installers will no longer attempt to install on win32 and vice-versa
neighborlist check_period now defaults to 1
The elapsed time counter in run() now continues counting time over multiple runs.
init.create_random_polymers now throws an error if the bond length is too small given the specified separation radii
Fixed a bug where a floating point value for the count field in init.create_random_polymers produced an error
Additional error checking to test if particles go NaN
Much improved status line printing for identifying hoomd_script commands
Numerous documentation updates
The VS redistributable package no longer needs to be installed to run HOOMD on windows (these files are distributed with HOOMD)
Now using new features in doxygen#5.7 to build pdf user documentation for download.
Performance enhancements of the Lennard-Jones pair force computation, thanks to David Tarjan
A header prefix can be added to log files to make them more gnuplot friendly
Log quantities completely revamped. Common quantities (i.e. kinetic energy, potential energy can now be logged in any simulation)
Particle groups can now be created. Currently only analyze.msd makes use of them.
The CUDA toolkit no longer needs to be installed to run a packaged HOOMD binary in windows.
User documentation can now be downloaded as a pdf.
Analyzers and updaters now count time 0 as being the time they were created, instead of time step 0.
Added job test scripts to aid in validating HOOMD
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

Fixed bug where extremely large box dimensions resulted in an argument error - ticket:118
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.

Stability and performance improvements.
Cleaned up the hoomd_xml file format.
Improved detection of errors in hoomd_xml files significantly.
Users no longer need to manually specify HOOMD_ROOT, unless their installation is non-standard
Particle charge can now be read in from a hoomd_xml file
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
Enabled parallel builds in MSVC for faster compilation times on multicore systems
Numerous small bug fixes
New force compute for implementing walls
Documentation updates
Support for CUDA 2.0
Bug fixed allowing simulations with no integrator
Support for boost#35.0
Cleaned up GPU code interface
NVT integrator now uses tau (period) instead of Q (the mass of the extra degree of freedom).
Added option to NVE integration to limit the distance a particle moves in a single time step
Added code to dump system snapshots in the DCD file format
Particle types can be named by strings
A snapshot of the initial configuration can now be written in the .mol2 file format
The default build settings now enable most of the optional features
Separated the user and developer documentation
Mixed polymer systems can now be generated inside HOOMD
Support for CMake 2.6.0
Wrote the user documentation
GPU selection from the command line
Implementation of the job scripting system
GPU can now handle neighbor lists that overflow
Energies are now calculated
Added a logger for logging energies during a simulation run
Code now actually compiles on Mac OS X
Benchmark and demo scripts now use the new scripting system
Consistent error message format that is more visible.
Multiple types of bonds each with the own coefficients are now supported
Added python scripts to convert from HOOMD's XML file format to LAMMPS input and dump files
Fixed a bug where empty xml nodes in input files resulted in an error message
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
Fixed erroneously reported dangerous neighbor list builds when using --mode=cpu
Small tweaks to the XML file format.
Numerous performance enhancements
Workaround for ULF on compute#1 devices in place
dump.xml can now be given the option

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