Feat pt: Support multi structures input for single frame #3566
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Signed-off-by: Chenqqian Zhang <100290172+Chengqian-Zhang@users.noreply.github.com>
deepmd/utils/data.py
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| if self.multistru: | ||
| size = frames["coord"].shape[1] | ||
| rng = np.random.default_rng() | ||
| sample_idx = rng.integers(low=0, high=size, size=1)[0] |
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Is it really random?
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We use the random generator in deepmd.utils.rndom. The generator here cannot be controlled.
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I have change it to
from deepmd.utils import random as dp_random
sample_idx = dp_random.choice(range(num_stru), size=1)[0]
But I find that when num_stru = 11, the sample_idx is 1,4,8,10 all the time. I hope that the value is randomly selected from range(0--10). How can I solve it? @njzjz
Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## devel #3566 +/- ##
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- Coverage 77.49% 77.47% -0.02%
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Files 432 432
Lines 37164 37185 +21
Branches 1620 1620
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+ Hits 28801 28810 +9
- Misses 7495 7507 +12
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Shouldn't it be documented? Otherwise no one knows how to use it.
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I add doc to deepmd/doc. Should I add doc to other places?
deepmd/utils/data.py
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| if self.multistru: | ||
| size = frames["coord"].shape[1] | ||
| rng = np.random.default_rng() | ||
| sample_idx = rng.integers(low=0, high=size, size=1)[0] |
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We use the random generator in deepmd.utils.rndom. The generator here cannot be controlled.
| elif data.size == nframes * natoms * ndof_: | ||
| if output_natoms_for_type_sel: | ||
| pass | ||
| if key == "coord" and self.multistru: |
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Do we assume aparam and other properties are the same for all conformations?
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I haven't thought of a situation where there are different other properties(aparam fparam) of all conformations. The reason I add this feature is that when one only have molecules in SMILES format, one may generate several possible conformations using tools such as rdkit. Do you have more better ideas?
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@wanghan-iapcm Different 3D conformations of a molecule have exactly the same label, and each epoch takes one of all 3D conformations of this molecule. Because molecule may only has SMILES, the exact 3D sturcture is unknown. |
I do not find any reason why different 3D configurations cannot be place in one batch. |
Support multi structures input for one frame:
background:
When we predict the properties of small molecules, sometimes multiple 3D conformations are generated from the SMILES format structure, but their targets are the same. In each epoch we would like to pick only one of the 3D configurations as input.
Impletation:
When the file "multistru" is present in the data folder (like nopbc), "coord.npy" can be written in the format (nframe * struc_num * natom * 3), where struc_num is the number of 3D conformations for each structure.