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Add pickling (instead of writing to .dat) #14

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ebac1d2
Pickle instead of writing to DAT (butane_ANN.py)
ricalessandri Jul 25, 2023
c0d45bf
Remove `A = A.max() - A` from ANN, butane (not needed anymore)
ricalessandri Jul 25, 2023
ebd02e1
run_result --> raw_result
ricalessandri Jul 25, 2023
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7 changes: 3 additions & 4 deletions hoomd-blue/classic/butane/ann/butane_ANN.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -662,7 +662,7 @@
}
],
"source": [
"run_result = pysages.run(method, generate_context, int(5e5))"
"raw_result = pysages.run(method, generate_context, int(5e5))"
]
},
{
Expand Down Expand Up @@ -694,11 +694,10 @@
},
"outputs": [],
"source": [
"result = pysages.analyze(run_result)\n",
"result = pysages.analyze(raw_result)\n",
"\n",
"mesh = result[\"mesh\"]\n",
"A = result[\"free_energy\"]\n",
"A = A.max() - A"
"A = result[\"free_energy\"]"
]
},
{
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5 changes: 2 additions & 3 deletions hoomd-blue/classic/butane/ann/butane_ANN.md
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Expand Up @@ -368,7 +368,7 @@ Make sure to run with GPU support, otherwise, it can take a very long time.
<!-- #endregion -->

```python colab={"base_uri": "https://localhost:8080/"} id="K951m4BbpUar" outputId="f01ca7e3-69f4-4218-9eb5-cdc022f877b8"
run_result = pysages.run(method, generate_context, int(5e5))
raw_result = pysages.run(method, generate_context, int(5e5))
```

<!-- #region id="PXBKUfK0p9T2" -->
Expand All @@ -382,11 +382,10 @@ import matplotlib.pyplot as plt
```

```python id="6W7Xf0ilqAcm"
result = pysages.analyze(run_result)
result = pysages.analyze(raw_result)

mesh = result["mesh"]
A = result["free_energy"]
A = A.max() - A
```

```python colab={"base_uri": "https://localhost:8080/", "height": 300} id="TBiPAnMwqEIF" outputId="de1e6c26-0dc9-48ef-cecd-6f94bf11c25c"
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8 changes: 3 additions & 5 deletions hoomd-blue/classic/butane/ann/butane_ANN.py
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Original file line number Diff line number Diff line change
Expand Up @@ -22,7 +22,7 @@
from pysages.methods import ANN

# %%
kT = 0.596161
kT = 0.596161 # kcal/mol
dt = 0.02045


Expand Down Expand Up @@ -284,7 +284,6 @@ def main(argv=[]):

mesh = result["mesh"]
A = result["free_energy"]
A = A.max() - A

fig, ax = plt.subplots()

Expand All @@ -295,9 +294,8 @@ def main(argv=[]):
plt.gca()
fig.savefig("butane-fe.png")

# write free energy to file
dih_vs_A = np.stack([mesh[:, 0], A[:, 0]], axis=1)
np.savetxt("butane-fe.dat", dih_vs_A, header='"dih" "Free energy"')
# write results to pickle file
pickle.dump( raw_result, open("raw_result.pickle", "wb") )

return result["free_energy"]

Expand Down