Miscellaneous fixes

examples/hoomd-blue/spectral_abf/Butane-SpectralABF.ipynb

@@ -638,8 +638,7 @@
     "A = result[\"free_energy\"]\n",
     "# Alternatively:\n",
     "# fes_fn = result[\"fes_fn\"]\n",
-    "# A = fes_fn(mesh)\n",
-    "A = A.max() - A"
+    "# A = fes_fn(mesh)"
    ]
   },
   {

examples/hoomd-blue/spectral_abf/Butane-SpectralABF.md

@@ -386,7 +386,6 @@ A = result["free_energy"]
 # Alternatively:
 # fes_fn = result["fes_fn"]
 # A = fes_fn(mesh)
-A = A.max() - A
 ```
 
 ```python colab={"base_uri": "https://localhost:8080/", "height": 302} id="7_d_XfVLLkbI" outputId="e35db259-31f8-4a3b-b1fa-7e91a8a5c88a"

examples/hoomd-blue/spectral_abf/butane.py

@@ -257,7 +257,7 @@ def get_args(argv):
         ("time-steps", "t", int, 5e5, "Number of simulation steps"),
     ]
     parser = argparse.ArgumentParser(description="Example script to run SpectralABF")
-    for (name, short, T, val, doc) in available_args:
+    for name, short, T, val, doc in available_args:
         parser.add_argument("--" + name, "-" + short, type=T, default=T(val), help=doc)
 
     return parser.parse_args(argv)
@@ -283,7 +283,6 @@ def main(argv=[]):
     mesh = result["mesh"]
     fes_fn = result["fes_fn"]
     A = fes_fn(mesh)
-    A = A.max() - A
 
     # plot the free energy
     fig, ax = plt.subplots()

examples/hoomd3/spectral_abf/butane.py

@@ -298,7 +298,6 @@ def main(argv=[]):
     mesh = result["mesh"]
     fes_fn = result["fes_fn"]
     A = fes_fn(mesh)
-    A = A.max() - A
 
     # plot the free energy
     fig, ax = plt.subplots()

examples/openmm/spectral_abf/ADP_SpectralABF.ipynb

@@ -342,7 +342,6 @@
     "# mesh = result[\"mesh\"]\n",
     "# fes_fn = result[\"fes_fn\"]\n",
     "# A = fes_fn(mesh)\n",
-    "A = A.max() - A\n",
     "A = A.reshape(grid.shape)"
    ]
   },

examples/openmm/spectral_abf/ADP_SpectralABF.md

@@ -211,7 +211,6 @@ A = result["free_energy"]
 # mesh = result["mesh"]
 # fes_fn = result["fes_fn"]
 # A = fes_fn(mesh)
-A = A.max() - A
 A = A.reshape(grid.shape)
 ```
 

examples/openmm/spectral_abf/alanine-dipeptide.py

@@ -78,7 +78,7 @@ def get_args(argv):
         ("time-steps", "t", int, 5e5, "Number of simulation steps"),
     ]
     parser = argparse.ArgumentParser(description="Example script to run Spectral ABF")
-    for (name, short, T, val, doc) in available_args:
+    for name, short, T, val, doc in available_args:
         parser.add_argument("--" + name, "-" + short, type=T, default=T(val), help=doc)
     return parser.parse_args(argv)
 
@@ -108,7 +108,6 @@ def main(argv=[]):
 
     # Set min free energy to zero
     A = fes_fn(xi)
-    A = A.max() - A
     A = A.reshape(plot_grid.shape)
 
     # plot and save free energy to a PNG file

pysages/backends/openmm.py

@@ -157,13 +157,12 @@ def bias(snapshot, state, sync_backend):
         """Adds the computed bias to the forces."""
         if state.bias is None:
             return
-        biases = adapt(state.bias)
         # Forces may be computed asynchronously on the GPU, so we need to
         # synchronize them before applying the bias.
         sync_backend()
+        biases = adapt(state.bias)
         forces = view(snapshot.forces)
-        biases = view(biases.block_until_ready())
-        forces += biases
+        forces += view(biases.block_until_ready())
         sync_forces()
 
     def dimensionality():