flashmd 0.2.0__tar.gz → 0.2.1__tar.gz
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- {flashmd-0.2.0/src/flashmd.egg-info → flashmd-0.2.1}/PKG-INFO +1 -1
- {flashmd-0.2.0 → flashmd-0.2.1}/pyproject.toml +1 -1
- {flashmd-0.2.0 → flashmd-0.2.1}/src/flashmd/ipi.py +6 -5
- {flashmd-0.2.0 → flashmd-0.2.1/src/flashmd.egg-info}/PKG-INFO +1 -1
- {flashmd-0.2.0 → flashmd-0.2.1}/LICENSE +0 -0
- {flashmd-0.2.0 → flashmd-0.2.1}/README.md +0 -0
- {flashmd-0.2.0 → flashmd-0.2.1}/setup.cfg +0 -0
- {flashmd-0.2.0 → flashmd-0.2.1}/src/flashmd/__init__.py +0 -0
- {flashmd-0.2.0 → flashmd-0.2.1}/src/flashmd/ase/__init__.py +0 -0
- {flashmd-0.2.0 → flashmd-0.2.1}/src/flashmd/ase/bussi.py +0 -0
- {flashmd-0.2.0 → flashmd-0.2.1}/src/flashmd/ase/langevin.py +0 -0
- {flashmd-0.2.0 → flashmd-0.2.1}/src/flashmd/ase/npt.py +0 -0
- {flashmd-0.2.0 → flashmd-0.2.1}/src/flashmd/ase/velocity_verlet.py +0 -0
- {flashmd-0.2.0 → flashmd-0.2.1}/src/flashmd/models.py +0 -0
- {flashmd-0.2.0 → flashmd-0.2.1}/src/flashmd/stepper.py +0 -0
- {flashmd-0.2.0 → flashmd-0.2.1}/src/flashmd.egg-info/SOURCES.txt +0 -0
- {flashmd-0.2.0 → flashmd-0.2.1}/src/flashmd.egg-info/dependency_links.txt +0 -0
- {flashmd-0.2.0 → flashmd-0.2.1}/src/flashmd.egg-info/requires.txt +0 -0
- {flashmd-0.2.0 → flashmd-0.2.1}/src/flashmd.egg-info/top_level.txt +0 -0
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@@ -37,7 +37,7 @@ def get_standard_vv_step(
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if rescale_energy:
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info("@flashmd: Old energy", verbosity.debug)
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old_energy = sim.properties("
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old_energy = sim.properties("conserved")
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motion.integrator.pstep(level=0)
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motion.integrator.pconstraints()
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@@ -48,7 +48,7 @@ def get_standard_vv_step(
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if rescale_energy:
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info("@flashmd: Energy rescale", verbosity.debug)
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new_energy = sim.properties("
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new_energy = sim.properties("conserved")
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kinetic_energy = sim.properties("kinetic_md")
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alpha = np.sqrt(1.0 - (new_energy - old_energy) / kinetic_energy)
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motion.beads.p[:] = alpha * dstrip(motion.beads.p)
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@@ -76,7 +76,7 @@ def get_flashmd_vv_step(sim, model, device, rescale_energy=True, random_rotation
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info("@flashmd: Starting VV", verbosity.debug)
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if rescale_energy:
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info("@flashmd: Old energy", verbosity.debug)
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old_energy = sim.properties("
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old_energy = sim.properties("conserved")
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info("@flashmd: Stepper", verbosity.debug)
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system = ipi_to_system(motion, device, dtype)
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@@ -109,11 +109,12 @@ def get_flashmd_vv_step(sim, model, device, rescale_energy=True, random_rotation
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if rescale_energy:
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info("@flashmd: Energy rescale", verbosity.debug)
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new_energy = sim.properties("
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new_energy = sim.properties("conserved")
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kinetic_energy = sim.properties("kinetic_md")
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alpha = np.sqrt(1.0 - (new_energy - old_energy) / kinetic_energy)
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motion.beads.p[:] = alpha * dstrip(motion.beads.p)
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motion.integrator.pconstraints() # just to make sure; should be cheap
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info("@flashmd: End of VV step", verbosity.debug)
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return flashmd_vv
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