Index based connectivity #131
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Extended the code to incorporate two-particle bonds.
clog() only logs on the root rank. Probably add ArgumentParser for --verbose to control logging output.
1. echos the conf key value pairs 2. add --destdir, --profile, --verbose 3. reformat output files to standard 5 digit beam shard names: https://beam.apache.org/releases/javadoc/2.2.0/org/apache/beam/sdk/io/ShardNameTemplate.html (assuming we will run to 1M ranks)
This is buggy but at least allows me to run the code.
Logging exchange cost and use new pmesh exchange routines.
Use the standard python package directory layout. Add utils/ directory for auxiliary scripts. Add a placeholder docs/ directory for future sphinx autodoc deployment.
Adds a requirements.txt file to manage python package dependencies.
Also update the README with how to build for different use cases.
Also update build instructions in README
Ensure that github-linguist does not incorrectly classify any OCCAM input/output files as ROFF text-formatting files
Revert commit 29a56a4940d71db8ca25450d868ed769ccef88c4. Turns out it is necessary that test/ is a python module in order to test without installing the main source as a package with `pip install -e .` first. Need to add setup.py, clean up main.py, and make a proper package before this file can be removed.
This way we avoid opening/closing the file an extra time when reading the data in main.py.
Remove all the (2.479 / 298) approximations in different places, absorbing the definition of the constant into Config. Also change all instances of (3 / 2) to 1.5.
Implement separate thermostat coupling groups
Splits molecules after the charmm-gui Martini equilibration makes everything one giant molecule with all the particles.
Add split_gro_molecules.py
Instead of only removing the linear center of mass momentum at the beginning of the simulation if cancel_com_momentum is True, we remove the linear momentum at the start *and* every cancel_com_momentum steps if an integer value is specified.
Add option to remove linear center of mass momentum every N steps
* Move to tomli, drop nested lists in config.toml * Update test * Update requirements * Update conftest * Update nesting for bonds, angles and chi
I vote for YES |
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@mortele, @xinmeng2020 when you have free time, can you guys give a quick look at/test this PR, check if it works and if I missed anything? |
mortele
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Closing this one, opening a new one without the bloated history. |
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This PR implements what's proposed in #126. The core part of this pull request was written by @xinmeng2020 in the ElecPE branch.
One last issue: do we want to keep the old routines for backward compatibility/systems that don't need fancy connectivity?