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NPT validation and MD checkpoints #208

Merged
merged 26 commits into from
Nov 29, 2023
Merged

NPT validation and MD checkpoints #208

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40a4961
made cell explicit in simulation loop
M-R-Schaefer Nov 13, 2023
71e9029
h5trajhanderl now records actual sim time
M-R-Schaefer Nov 14, 2023
f9d5375
imported logging setup from trianing into MD
M-R-Schaefer Nov 14, 2023
797d5b4
pulled trajectory handelr out of `run_nvt`
M-R-Schaefer Nov 14, 2023
17570a5
removed old sampling interval check comment
M-R-Schaefer Nov 14, 2023
cf1f058
moved directory creation to top level
M-R-Schaefer Nov 14, 2023
e67c561
fixed nvt apply fn calling signature and sim dir creation
M-R-Schaefer Nov 14, 2023
9d1860a
removed log gile CLI and MD option
M-R-Schaefer Nov 14, 2023
6ef18aa
removed unused box arg from create energy fn
M-R-Schaefer Nov 14, 2023
37b7ebf
Merge branch 'dev' into npt_validation
M-R-Schaefer Nov 14, 2023
bd6cac3
added checkpoint interval to md config and md code
M-R-Schaefer Nov 14, 2023
5bd0b24
removed duplicate docs makefiles
M-R-Schaefer Nov 14, 2023
83607a9
implemented saving and loading of MD checkpoints
M-R-Schaefer Nov 15, 2023
c4a670e
pbar now correctly shows 100 percent on completion
M-R-Schaefer Nov 15, 2023
a0341ec
removed debug statements
M-R-Schaefer Nov 15, 2023
6e84d19
set default md log level to info
M-R-Schaefer Nov 15, 2023
94eb969
refactored checkpoint and momenta loading into separete function
M-R-Schaefer Nov 15, 2023
ccc39d1
moved System and SimFunctions to separate submodule
M-R-Schaefer Nov 15, 2023
b571222
utility logging redirect for logs during tqdm pbar
M-R-Schaefer Nov 15, 2023
81af8ee
H5TrajHandler now appends to trajectory if an existing one is found
M-R-Schaefer Nov 15, 2023
56d942d
DSTruncater now initializes chunked datasets, added TrajHandler type …
M-R-Schaefer Nov 15, 2023
1a61a7b
added trajectory truncation on checkpoint loading and time printing i…
M-R-Schaefer Nov 15, 2023
be9a134
linting
M-R-Schaefer Nov 15, 2023
b8bb72f
added explicit buffer size argument to TrajHandler
M-R-Schaefer Nov 15, 2023
2db1501
added checkpoint loading to MD integration test
M-R-Schaefer Nov 15, 2023
10b6061
linting
M-R-Schaefer Nov 15, 2023
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removed unused box arg from create energy fn
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@M-R-Schaefer
M-R-Schaefer committed Nov 14, 2023
commit 6ef18aa691e2e3a281071122cb05f379ff3b0fe0
4 changes: 2 additions & 2 deletions apax/md/nvt.py
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Original file line number Diff line number Diff line change
Expand Up @@ -30,7 +30,7 @@
log = logging.getLogger(__name__)


def create_energy_fn(model, params, numbers, box, n_models):
def create_energy_fn(model, params, numbers, n_models):
def ensemble(params, R, Z, neighbor, box, offsets):
vmodel = jax.vmap(model, (0, None, None, None, None, None), 0)
energies = vmodel(params, R, Z, neighbor, box, offsets)
Expand Down Expand Up @@ -377,7 +377,7 @@ def md_setup(model_config: Config, md_config: MDConfig):
_, params = restore_parameters(model_config.data.model_version_path())
params = canonicalize_energy_model_parameters(params)
energy_fn = create_energy_fn(
model.apply, params, system.atomic_numbers, system.box, model_config.n_models
model.apply, params, system.atomic_numbers, model_config.n_models
)
sim_fns = SimulationFunctions(energy_fn, shift_fn, neighbor_fn)
return system, sim_fns
Expand Down