MD steps and analysis steps

An analysis step, such as Diffusivity or Thermal Conductivity, needs the MD to have sampled the right things at the right rate: the heat flux every two steps, the centres of mass of the molecules, and so on. If the MD does not, the analysis fails, and in the past it failed only after all the MD had run. This page describes how MD steps and analysis steps tell each other what they provide and need, so that such mistakes are caught before the MD runs. Any MD step (LAMMPS now, GROMACS later) and any analysis step can take part by implementing the methods below.

The names are those of the H5MD file (see The H5MD file): an observable such as heat_flux or pressure_tensor, or a per-particle property as <group>/<name>, e.g. molecules/position.

Two ways to get the MD

An analysis step’s MD to analyze parameter (md source) chooses where the MD comes from:

run the MD in the sub-flowchart

The step runs the MD in its own sub-flowchart a number of times, as independent runs, and takes the errors from their spread. This is how the steps have always worked.

the last MD run

The step analyzes the last MD run earlier in the flowchart that sampled what it needs, found in the workspace variable _md_runs. One production run can then feed several analyses.

the last MD run of each loop iteration

Every run by the same MD step as the last one, which in a Loop are the runs of the iterations, analyzed as independent runs.

files

The md.h5md files given, each an independent run; job://<n>/<path> reads another job’s file.

When a single run is analyzed, it is divided into consecutive blocks (number of blocks, 5 by default), which are analyzed separately to estimate the errors. Each block must be much longer than the correlation time of what is analyzed.

The methods

MD sub-steps

md_provides()

Returns a Provides: what the run will write to md.h5md, each with its sampling Interval (in time, in steps, or both), worked out from the step’s parameters before anything runs. An interval that cannot be known yet (a variable, or a timestep that depends on the structure) is left unknown.

request_sampling(need)

Turns on the sampling a Need asks for, if it can, and returns a description of the change, or None.

Analysis steps

md_requirements()

Returns Requirements: what is needed, each with the longest acceptable interval (and the interval to use when turning it on), and whether the system must be periodic.

check_flowchart(preceding)

Called by seamm.builder.validate with the steps that run before this one. For MD from earlier in the flowchart it compares the requirements with what the last MD sub-step that samples the first need provides, and returns the problems (check_md_flowchart()). Validation runs in seamm-flowchart and the MCP tools, when the editor submits a job, and when a job starts, which stops before running any step if there are problems.

check_configuration(configuration)

Called by an MD step just before it runs, for each analysis step after it up to the next MD step. An analysis that will read this MD and cannot use the structure, such as one needing a periodic system, raises an exception, so the job stops before the MD. Periodicity is known only once the structure exists, so the flowchart check cannot catch it.

When an analysis runs its own MD, it calls request_sampling() on its sub-flowchart first, which turns on in the last MD sub-step whatever is missing and reports the changes; anything it cannot turn on stops the step before the MD.

seamm_md_analysis.step_support holds the code the analysis steps share: the parameter definitions (source_parameters), finding the MD sub-steps, the checks, finding the files to read (md_inputs), and passing results between steps.

Results for later steps

An analysis step can publish a result that later steps use. The Viscosity step calls publish_viscosity(), which stores the viscosity (in Pa s), its standard error, the temperature and the method in the workspace variable _viscosity. Diffusivity reads it with preceding_viscosity() for the Yeh–Hummer correction. A later Viscosity step replaces the record. It uses only the methods of SEAMM’s nodes and flowcharts, so the library does not depend on SEAMM.