Package: lammps-step
SEAMM LAMMPS Plug-inA SEAMM plug-in for LAMMPS, a forcefield-based molecular dynamics code.This plug-in provides a graphical user interface (GUI) for setting up
complex simulations using LAMMPS. It uses a sub-flowchart that
provides steps such as constant pressure and temperature (NPT)
dynamics which give access to the functionality in LAMMPS in a more
consistent and understandable way than the inscrutable fixes that
LAMMPS uses.These sub-flowcharts mirror the main flowchart in form and function
and can use the same variables such as temperature and pressure that
are accessible anywhere in the flowcharts. This allows “programming” a
LAMMPS workflow in the same familiar way that SEAMM uses to represent
the overall workflow.Free software: BSD licenseDocumentation:https://molssi-seamm.github.io/lammps_step/index.htmlCode:https://github.com/molssi-seamm/lammps_stepFeaturesUse of any forcefield supported by the forcefield plug-in:PCFFOpenKIM: EAM, MEAM, LJ, ReaxFFMolecular statics: minimizationMolecular dynamics: NVE, NVT, and NPT with any of the approaches
supported in LAMMPSAutomatic statistical analysis of averages from MDDetection of equilibrationMean and standard error of the mean for the sampling after
equilibrationAutocorrelation function and timeStatistical inefficiencyPlotting of results in the DashboardUsing property values to drive MD. Rather than running MD for a
length of time, automatically run long enough to determine a set of
properties within given error bars.AcknowledgementsThis package was created withCookiecutterand themolssi-seamm/cookiecutter-seamm-pluginproject template.Developed by the Molecular Sciences Software Institute (MolSSI),
which receives funding from theNational Science Foundationunder
award ACI-1547580History2024.1.18 – Restructured to support running in containers.2023.11.7 – Bugfix: properties that are constantA property, such as the total energy, can be a constant over an MD run due to
precision of the trajectory. This caused errors because the autocorrelation
function is not defined. These cases are now detected and the ACF not calculated
for them.2023.11.6 – Bugfix in thermal conductivityDue to change in input file name.2023.9.6 – Corrected issues with final coordinates; added velocitiesThere was a problem with getting the final coordinates from a dump file.Added saving and reusing velocities so now a second LAMMPS step will by default use
the velocities from the previous step, which is what you would expect.2023.8.31 – Bugfix: not reading structure correctly after dynamics2023.8.27 – Added support for tabulated angle potentials.Support for the CL&P-OPLSAA potential for octahedral PF6-2023.8.21 – Bugfix: x-axes length on graphics incorrectThe size of the x-axes of the trajectory graphs were wrong, often much too large,
compressing the actual data near the beginning of the graph.Fixed an issue with systems with no non-bonds.2023.6.17 – Bugfix: more centroid/stress/atom issuesAvoided using centroid/stress/atom for heat flux in standard NVE, NVT, … dynamics
with Class 2 forcefield.Added option to not use centroid/stress/atom for any forcefield.2023.6.16 – Heat flux with PCFFcentroid/stress/atom does not work with Class 2 forcefields, so don’t use for PCFF.2023.5.29 – Self diffusion and other improvementsAdded trajectory panel to support diffusion, viscosity and simple thermal
conductivity.Added support for separate GPU versions of LAMMPS.Added support for command-line arguments to LAMMPS, mainly used for accelerators.Added support for using modules.2023.4.24 – Support for thermal conductivityInternal changes to support thermal conductivity with its embedded flowchart.Added the heat flux substep.Now delete output and reference files when rerunning, so the output is clean.Internal changes to support running LAMMPS from a Python driver.Corrected units of properties returned from LAMMPS when e.g. metal units used.Added support for Buckingham potentialsFixed issues with and cleaned up the use of hybrid types for bonds, angles, ….Fixed issues with the alignment of some of the widgets in the GUI.2023.4.9 – Hid the warning from pymbarImporting pymbar timeseries writes a warning to the terminal about its proper
usage. SEAMM already handles the warned case, so the message is simply confusing to
users and hence this release hides it.2023.4.6 – Better forcefield handling.Added correct molecule numbers for valence forcefields.Correctly handle ReaxFF from OpenKimUpdated for some minor changes in OpenKim2023.2.6 – Added handling of OPLS-AA forcefieldAdded handling of the OPLS-AA forcefieldMoved documentation to new MolSSI theme and diátaxis layoutCleaned up internale dependencies and workflows for GitHub2022.10.31 – Bugfix: properties with commasProperties with commas in their name in data/properties.csv need to have quotes to
protect the property name!2022.10.27 – Added propertiesAdded properties to be saved in the database.Updated calls topymbarbecause the names of methods were changed.Add the missing references forpymbar2021.2.11 (11 February 2021)Updated the README file to give a better description.Updated the short description in setup.py to work with the new installer.Added keywords for better searchability.2021.2.4.1 (4 February 2021)Internal patch to fix CI; no changes for users.2021.2.4 (4 February 2021)Updated for compatibility with the new system classes in MolSystem
2021.2.2 release.2020.12.4 (4 December 2020)Internal: switching CI from TravisCI to GitHub Actions, and in the
process moving documentation from ReadTheDocs to GitHub Pages where
it is consolidated with the main SEAMM documentation.2020.11.2 (2 November 2020)Updated to be compatible with the new command-line argument
handling.2020.10.13 (13 October 2020)Added capability to run MD until a set of user-selected properties
are converged to requested accuracy.2020.9.25 (25 September 2020)Updated to be compatible with the new system classes in MolSystem.2020.8.2.1 (2 August 2020)Bugfix: Fixed problem with nonbonds and charges just introduced.2020.8.2 (2 August 2020)Bugfix: Corrected the time units when usingmetalunits with
e.g. EAM potentials.2020.8.1 (1 August 2020)Added support for OpenKIM potentials.0.9.4 (29 May 2020)Cleaned up the output for the statistical analysis.0.9.3 (29 May 2020)Fixed issue with settings for bins in LAMMPS for small nonperiodic
systems with just a few atoms.0.9.2 (25 May 2020)Switched to using PYMBAR for detecting covergence to equilibrium for
MD runs. This is a more robust solution than the previous approach.0.9.1 (24 May 2020)Support for rigid water models, such as TIP-3P.0.9 (15 April 2020)Support for plots in the dashboard of properties from MD.
Added option to produce local HTML for the above plots.0.8.2 (2020-01-25)No significant changes in functionality.Incorporating changes to the SEAMM infrastructure, which simplify
the code for plug-ins.Updating the Travis CI to handle incompatible changes in Travis, and
to use Conda environments in all steps.0.7.1 (18 December 2019)Fixed problem with assigning charges to the system.0.7.0 (17 December 2019)General clean-up of code and output.0.6 (8 September 2019)Switched to ConfigArgParse for handling command-line arguments.Added the locations of LAMMPS executables to a configuration file
for easier access.0.5.2 (31 August 2019)Defined the correct requirements for installation.0.5.1 (30 August 2019)Bugfix: corrected the name of the LAMMPS executable.0.5.0 (30 August 2019)Added ability to use serial or parallel versions of LAMMPS based on
an environment variable.0.3.1 (27 August 2019)Added initial, fairly reasonable output.0.2.1 (29 July 2019)First release on PyPI.