limit the filename length dumped by MultiSystems (#554)

Fix #553.

---------

Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

dpdata/system.py

@@ -1,5 +1,6 @@
 # %%
 import glob
+import hashlib
 import os
 import warnings
 from copy import deepcopy
@@ -19,7 +20,13 @@
 from dpdata.driver import Driver, Minimizer
 from dpdata.format import Format
 from dpdata.plugin import Plugin
-from dpdata.utils import add_atom_names, elements_index_map, remove_pbc, sort_atom_names
+from dpdata.utils import (
+    add_atom_names,
+    elements_index_map,
+    remove_pbc,
+    sort_atom_names,
+    utf8len,
+)
 
 
 def load_format(fmt):
@@ -562,6 +569,42 @@ def uniq_formula(self):
             ]
         )
 
+    @property
+    def short_formula(self) -> str:
+        """Return the short formula of this system. Elements with zero number
+        will be removed.
+        """
+        return "".join(
+            [
+                f"{symbol}{numb}"
+                for symbol, numb in zip(
+                    self.data["atom_names"], self.data["atom_numbs"]
+                )
+                if numb
+            ]
+        )
+
+    @property
+    def formula_hash(self) -> str:
+        """Return the hash of the formula of this system."""
+        return hashlib.sha256(self.formula.encode("utf-8")).hexdigest()
+
+    @property
+    def short_name(self) -> str:
+        """Return the short name of this system (no more than 255 bytes), in
+        the following order:
+            - formula
+            - short_formula
+            - formula_hash.
+        """
+        formula = self.formula
+        if utf8len(formula) <= 255:
+            return formula
+        short_formula = self.short_formula
+        if utf8len(short_formula) <= 255:
+            return short_formula
+        return self.formula_hash
+
     def extend(self, systems):
         """Extend a system list to this system.
 
@@ -1247,7 +1290,9 @@ def from_fmt_obj(self, fmtobj, directory, labeled=True, **kwargs):
     def to_fmt_obj(self, fmtobj, directory, *args, **kwargs):
         if not isinstance(fmtobj, dpdata.plugins.deepmd.DeePMDMixedFormat):
             for fn, ss in zip(
-                fmtobj.to_multi_systems(self.systems.keys(), directory, **kwargs),
+                fmtobj.to_multi_systems(
+                    [ss.short_name for ss in self.systems.values()], directory, **kwargs
+                ),
                 self.systems.values(),
             ):
                 ss.to_fmt_obj(fmtobj, fn, *args, **kwargs)

dpdata/utils.py

@@ -99,3 +99,8 @@ def uniq_atom_names(data):
         sum(ii == data["atom_types"]) for ii in range(len(data["atom_names"]))
     ]
     return data
+
+
+def utf8len(s: str) -> int:
+    """Return the byte length of a string."""
+    return len(s.encode("utf-8"))

tests/test_multisystems.py

@@ -1,7 +1,9 @@
 import os
+import tempfile
 import unittest
 from itertools import permutations
 
+import numpy as np
 from comp_sys import CompLabeledSys, IsNoPBC, MultiSystems
 from context import dpdata
 
@@ -200,5 +202,37 @@ def setUp(self):
         self.atom_names = ["C", "H", "O"]
 
 
+class TestLongFilename(unittest.TestCase):
+    def test_long_filename1(self):
+        system = dpdata.System(
+            data={
+                "atom_names": [f"TYPE{ii}" for ii in range(200)],
+                "atom_numbs": [1] + [0 for _ in range(199)],
+                "atom_types": np.arange(1),
+                "coords": np.zeros((1, 1, 3)),
+                "orig": np.zeros(3),
+                "cells": np.zeros((1, 3, 3)),
+            }
+        )
+        ms = dpdata.MultiSystems(system)
+        with tempfile.TemporaryDirectory() as tmpdir:
+            ms.to_deepmd_npy(tmpdir)
+
+    def test_long_filename2(self):
+        system = dpdata.System(
+            data={
+                "atom_names": [f"TYPE{ii}" for ii in range(200)],
+                "atom_numbs": [1 for _ in range(200)],
+                "atom_types": np.arange(200),
+                "coords": np.zeros((1, 200, 3)),
+                "orig": np.zeros(3),
+                "cells": np.zeros((1, 3, 3)),
+            }
+        )
+        ms = dpdata.MultiSystems(system)
+        with tempfile.TemporaryDirectory() as tmpdir:
+            ms.to_deepmd_npy(tmpdir)
+
+
 if __name__ == "__main__":
     unittest.main()