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This umbrella "enhancement" issue is to organize various tasks related to inspecting and setting simulation inputs with stand-alone tools and as data flow operations.
generate TPR data from inputs other than existing TPR (e.g. grompp)
abstractly produce simulation input objects (make_input())
insert graph node to transform simulation input from one source to simulation input with modified parameters (most simple, a new tpr file with updated parameters for the simulation node) (e.g. modify_input()): Modify simulation parameter #85
Along the way, encapsulation will lead to a distinction between file data and data flow abstractions.
Add TPR file class to gmx.core
Add checkpoint file awareness to gmx.core
Add "simulationState" abstraction to gmx.core to capture full simulator state restored from checkpoint files, including configuration, topology, parameters, and numerical state with hysteresis.
Fixeskassonlab#86
gmx.fileio.read_tpr() and gmx.fileio.write_tpr_file() work as standalone tools to read, manipulate, and rewrite a TPR file.
We defer several enhancements to other issues, including:
* use in work graphs (see kassonlab#85)
* integration with checkpoint data (see kassonlab#71)
* several missing parameters that should be added to tprfile.cpp (kassonlab#192)
See kassonlab#187 for more discussion.
This umbrella "enhancement" issue is to organize various tasks related to inspecting and setting simulation inputs with stand-alone tools and as data flow operations.
Tools and core functionality:
grompp
)make_input()
)modify_input()
): Modify simulation parameter #85Along the way, encapsulation will lead to a distinction between file data and data flow abstractions.
gmx.core
to capture full simulator state restored from checkpoint files, including configuration, topology, parameters, and numerical state with hysteresis.In the near term, C++ classes map fairly directly to TPX inputs and outputs.
Commit ae15738 added
gmx.core.copy_tprfile
with an argument to set thensteps
in the new TPR file toend_time
, which is kind of clunky.To do: update and incorporate issues from #56 into more granular tasks and close #56
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