flashmd 0.2.8__tar.gz → 0.2.9__tar.gz

{flashmd-0.2.8 → flashmd-0.2.9}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: flashmd
-Version: 0.2.8
+Version: 0.2.9
 Summary: Accelerated molecular dynamics with large-time-step predictions
 Author: flashmd developers
 License: Apache-2.0
@@ -19,10 +19,13 @@ Classifier: Topic :: Scientific/Engineering :: Chemistry
 Classifier: Topic :: Scientific/Engineering :: Physics
 Classifier: Topic :: Software Development :: Libraries
 Classifier: Topic :: Software Development :: Libraries :: Python Modules
-Requires-Python: >=3.10
+Requires-Python: >=3.11
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: metatrain==2026.2
+Requires-Dist: metatomic-ase
+Requires-Dist: vesin>=0.5.4
+Requires-Dist: nvalchemi-toolkit-ops==0.3.0
 Requires-Dist: ase
 Requires-Dist: huggingface_hub
 Provides-Extra: dev
@@ -128,7 +131,7 @@ Using FlashMD in i-PI
 ---------------------
 
 You can see
-[this cookbook recipe](https://atomistic-cookbook.org/examples/flashmd/flashmd-demo.html) 
+[this cookbook recipe](https://atomistic-cookbook.org/examples/flashmd/flashmd-demo.html)
 for usage examples. i-PI is our most mature interface, and the one that was used to
 generate all our published results.
 
@@ -191,3 +194,8 @@ Note that the results were obtained through the i-PI interface.
 
 Instructions and material to reproduce the results in the paper are available on
 Materials Cloud at https://doi.org/10.24435/materialscloud:b7-xq.
+
+Maintainers
+-----------
+
+This project is [maintained](https://github.com/lab-cosmo/.github/blob/main/Maintainers.md) by [@frostedoyster](https://github.com/frostedoyster) and [@johannes-spies](https://github.com/johannes-spies), who will reply to issues and pull requests opened on this repository as soon as possible. You can mention them directly if you haven't received an answer after a couple of days.

{flashmd-0.2.8 → flashmd-0.2.9}/README.md

@@ -95,7 +95,7 @@ Using FlashMD in i-PI
 ---------------------
 
 You can see
-[this cookbook recipe](https://atomistic-cookbook.org/examples/flashmd/flashmd-demo.html) 
+[this cookbook recipe](https://atomistic-cookbook.org/examples/flashmd/flashmd-demo.html)
 for usage examples. i-PI is our most mature interface, and the one that was used to
 generate all our published results.
 
@@ -158,3 +158,8 @@ Note that the results were obtained through the i-PI interface.
 
 Instructions and material to reproduce the results in the paper are available on
 Materials Cloud at https://doi.org/10.24435/materialscloud:b7-xq.
+
+Maintainers
+-----------
+
+This project is [maintained](https://github.com/lab-cosmo/.github/blob/main/Maintainers.md) by [@frostedoyster](https://github.com/frostedoyster) and [@johannes-spies](https://github.com/johannes-spies), who will reply to issues and pull requests opened on this repository as soon as possible. You can mention them directly if you haven't received an answer after a couple of days.

{flashmd-0.2.8 → flashmd-0.2.9}/pyproject.toml

@@ -1,7 +1,7 @@
 [project]
 name = "flashmd"
-version = "0.2.8"
-requires-python = ">=3.10"
+version = "0.2.9"
+requires-python = ">=3.11"
 
 readme = "README.md"
 license = {text = "Apache-2.0"}
@@ -10,6 +10,9 @@ authors = [{name = "flashmd developers"}]
 
 dependencies = [
     "metatrain==2026.2",
+    "metatomic-ase",
+    "vesin>=0.5.4",
+    "nvalchemi-toolkit-ops==0.3.0",  # tricks metatomic-ase into avoiding buggy vesin
     "ase",
     "huggingface_hub",
 ]
@@ -79,4 +82,13 @@ filterwarnings = [
     "ignore:custom data:UserWarning",
     "ignore:`torch.jit.script` is deprecated:DeprecationWarning",
     "ignore:`torch.jit.load` is deprecated:DeprecationWarning",
+    "ignore:`compute_requested_neighbors_from_options` is deprecated and will be removed in a future version:UserWarning",
+    "ignore:hf_xet\\.download_files\\(\\) is deprecated:DeprecationWarning",
+    "ignore:Due to '_pack_', the 'APICLaunchParamRecord' Structure will use memory layout compatible with MSVC:DeprecationWarning",
+    "ignore:`torch.jit.script` is not supported:DeprecationWarning",
+    "ignore:`torch.jit.script_method` is not supported:DeprecationWarning",
+    "ignore:`torch.jit.script_method` is deprecated:DeprecationWarning",
+    "ignore:`torch.jit.load` is not supported:DeprecationWarning",
+    "ignore:The 'nvalchemiops.neighborlist' module has been renamed to 'nvalchemiops.neighbors':DeprecationWarning",
+    "ignore:From version 0.3.0 onwards, PyTorch is now an optional dependency:DeprecationWarning",
 ]

{flashmd-0.2.8 → flashmd-0.2.9}/src/flashmd/ase/__init__.py

@@ -1,4 +1,4 @@
-from metatomic.torch.ase_calculator import MetatomicCalculator
+from metatomic_ase import MetatomicCalculator
 
 
 class EnergyCalculator(MetatomicCalculator):

{flashmd-0.2.8 → flashmd-0.2.9}/src/flashmd/stepper.py

@@ -28,6 +28,15 @@ class FlashMDStepper:
 
         self.dtype = getattr(torch, self.model.capabilities().dtype)
         self.device = device
+        self.neighbor_list_calculators = vesin.metatomic.neighbor_lists_for_model(
+            "angstrom", self.model
+        )
+
+        # vesin's CUDA brute_force algorithm is broken for triclinic cells,
+        # so we use cell_list for all CUDA calculations to avoid potential issues. See
+        # https://github.com/Luthaf/vesin/issues/157
+        for neighbor_list in self.neighbor_list_calculators:
+            neighbor_list._nl.algorithm = "cell_list"
 
     def step(self, system: System):
         if system.device.type != self.device.type:
@@ -35,7 +44,8 @@ class FlashMDStepper:
         if system.positions.dtype != self.dtype:
             raise ValueError("System dtype does not match stepper dtype.")
 
-        vesin.metatomic.compute_requested_neighbors([system], "angstrom", self.model)
+        for calculator in self.neighbor_list_calculators:
+            calculator.add_neighbor_list(system)
 
         masses = system.get_data("masses").block().values
         model_outputs = self.model(

{flashmd-0.2.8 → flashmd-0.2.9}/src/flashmd.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: flashmd
-Version: 0.2.8
+Version: 0.2.9
 Summary: Accelerated molecular dynamics with large-time-step predictions
 Author: flashmd developers
 License: Apache-2.0
@@ -19,10 +19,13 @@ Classifier: Topic :: Scientific/Engineering :: Chemistry
 Classifier: Topic :: Scientific/Engineering :: Physics
 Classifier: Topic :: Software Development :: Libraries
 Classifier: Topic :: Software Development :: Libraries :: Python Modules
-Requires-Python: >=3.10
+Requires-Python: >=3.11
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: metatrain==2026.2
+Requires-Dist: metatomic-ase
+Requires-Dist: vesin>=0.5.4
+Requires-Dist: nvalchemi-toolkit-ops==0.3.0
 Requires-Dist: ase
 Requires-Dist: huggingface_hub
 Provides-Extra: dev
@@ -128,7 +131,7 @@ Using FlashMD in i-PI
 ---------------------
 
 You can see
-[this cookbook recipe](https://atomistic-cookbook.org/examples/flashmd/flashmd-demo.html) 
+[this cookbook recipe](https://atomistic-cookbook.org/examples/flashmd/flashmd-demo.html)
 for usage examples. i-PI is our most mature interface, and the one that was used to
 generate all our published results.
 
@@ -191,3 +194,8 @@ Note that the results were obtained through the i-PI interface.
 
 Instructions and material to reproduce the results in the paper are available on
 Materials Cloud at https://doi.org/10.24435/materialscloud:b7-xq.
+
+Maintainers
+-----------
+
+This project is [maintained](https://github.com/lab-cosmo/.github/blob/main/Maintainers.md) by [@frostedoyster](https://github.com/frostedoyster) and [@johannes-spies](https://github.com/johannes-spies), who will reply to issues and pull requests opened on this repository as soon as possible. You can mention them directly if you haven't received an answer after a couple of days.

{flashmd-0.2.8 → flashmd-0.2.9}/src/flashmd.egg-info/requires.txt

@@ -1,4 +1,7 @@
 metatrain==2026.2
+metatomic-ase
+vesin>=0.5.4
+nvalchemi-toolkit-ops==0.3.0
 ase
 huggingface_hub