flashmd 0.2.2__tar.gz → 0.2.3__tar.gz

{flashmd-0.2.2/src/flashmd.egg-info → flashmd-0.2.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: flashmd
-Version: 0.2.2
+Version: 0.2.3
 Summary: Accelerated molecular dynamics with large-time-step predictions
 Author: flashmd developers
 License: Apache-2.0
@@ -60,12 +60,14 @@ from flashmd.ase.langevin import Langevin
 
 
 # Choose your time step (go for 10-30x what you would use in normal MD for your system)
-time_step = 16  # 16 fs; also available: 1, 2, 4, 8, 32, 64, 128 fs
+time_step = 64  # 64 fs; also available: 1, 2, 4, 8, 16, 32, 128 fs
 
 # Create a structure and initialize velocities
 atoms = ase.build.bulk("Al", "fcc", cubic=True)
 MaxwellBoltzmannDistribution(atoms, temperature_K=300)
-atoms.set_velocities(atoms.get_velocities() - atoms.get_velocities().mean(axis=0))
+
+# It is generally a good idea to remove any net velocity from the system
+atoms.set_velocities(atoms.get_velocities() - atoms.get_momenta().sum(axis=0) / atoms.get_masses().sum())
 
 # Load models
 device="cuda" if torch.cuda.is_available() else "cpu"
@@ -132,3 +134,6 @@ pip install flashmd==0.1.2 ase==3.24.0 pet-mad==1.4.3
 
 and using the "PET-MAD" models (PBEsol) from https://huggingface.co/lab-cosmo/flashmd.
 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.

{flashmd-0.2.2 → flashmd-0.2.3}/README.md

@@ -31,12 +31,14 @@ from flashmd.ase.langevin import Langevin
 
 
 # Choose your time step (go for 10-30x what you would use in normal MD for your system)
-time_step = 16  # 16 fs; also available: 1, 2, 4, 8, 32, 64, 128 fs
+time_step = 64  # 64 fs; also available: 1, 2, 4, 8, 16, 32, 128 fs
 
 # Create a structure and initialize velocities
 atoms = ase.build.bulk("Al", "fcc", cubic=True)
 MaxwellBoltzmannDistribution(atoms, temperature_K=300)
-atoms.set_velocities(atoms.get_velocities() - atoms.get_velocities().mean(axis=0))
+
+# It is generally a good idea to remove any net velocity from the system
+atoms.set_velocities(atoms.get_velocities() - atoms.get_momenta().sum(axis=0) / atoms.get_masses().sum())
 
 # Load models
 device="cuda" if torch.cuda.is_available() else "cpu"
@@ -103,3 +105,6 @@ pip install flashmd==0.1.2 ase==3.24.0 pet-mad==1.4.3
 
 and using the "PET-MAD" models (PBEsol) from https://huggingface.co/lab-cosmo/flashmd.
 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.

{flashmd-0.2.2 → flashmd-0.2.3}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "flashmd"
-version = "0.2.2"
+version = "0.2.3"
 requires-python = ">=3.9"
 
 readme = "README.md"

{flashmd-0.2.2 → flashmd-0.2.3}/src/flashmd/ase/langevin.py

@@ -27,7 +27,7 @@ class Langevin(VelocityVerlet):
         self.friction = 1.0 / time_constant
         self.fixcm = fixcm
         if self.fixcm:
-            self.atoms.set_velocities(self.atoms.get_velocities() - self.atoms.get_velocities().mean(axis=0))
+            self.atoms.set_velocities(self.atoms.get_velocities() - self.atoms.get_momenta().sum(axis=0) / self.atoms.get_masses().sum())
 
     def step(self):
         self.apply_langevin_half_step()
@@ -43,4 +43,4 @@ class Langevin(VelocityVerlet):
         ) * np.random.randn(*old_momenta.shape)
         self.atoms.set_momenta(new_momenta)
         if self.fixcm:
-            self.atoms.set_velocities(self.atoms.get_velocities() - self.atoms.get_velocities().mean(axis=0))
+            self.atoms.set_velocities(self.atoms.get_velocities() - self.atoms.get_momenta().sum(axis=0) / self.atoms.get_masses().sum())

{flashmd-0.2.2 → flashmd-0.2.3/src/flashmd.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: flashmd
-Version: 0.2.2
+Version: 0.2.3
 Summary: Accelerated molecular dynamics with large-time-step predictions
 Author: flashmd developers
 License: Apache-2.0
@@ -60,12 +60,14 @@ from flashmd.ase.langevin import Langevin
 
 
 # Choose your time step (go for 10-30x what you would use in normal MD for your system)
-time_step = 16  # 16 fs; also available: 1, 2, 4, 8, 32, 64, 128 fs
+time_step = 64  # 64 fs; also available: 1, 2, 4, 8, 16, 32, 128 fs
 
 # Create a structure and initialize velocities
 atoms = ase.build.bulk("Al", "fcc", cubic=True)
 MaxwellBoltzmannDistribution(atoms, temperature_K=300)
-atoms.set_velocities(atoms.get_velocities() - atoms.get_velocities().mean(axis=0))
+
+# It is generally a good idea to remove any net velocity from the system
+atoms.set_velocities(atoms.get_velocities() - atoms.get_momenta().sum(axis=0) / atoms.get_masses().sum())
 
 # Load models
 device="cuda" if torch.cuda.is_available() else "cpu"
@@ -132,3 +134,6 @@ pip install flashmd==0.1.2 ase==3.24.0 pet-mad==1.4.3
 
 and using the "PET-MAD" models (PBEsol) from https://huggingface.co/lab-cosmo/flashmd.
 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.