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DrPaulSharpDrPaulSharp
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Addresses review comments
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13 files changed

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-606
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13 files changed

+391
-606
lines changed

‎RATapi/examples/absorption/absorption.ipynb‎

Lines changed: 17 additions & 546 deletions
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‎RATapi/examples/absorption/absorption.py‎

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@@ -1,4 +1,3 @@
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import os
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import pathlib
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import numpy as np
@@ -78,18 +77,18 @@ def absorption():
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problem.resolution_parameters.set_fields(0, fit=True)
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# Now add the data we need
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data_path = os.path.join(pathlib.Path(__file__).parents[1].resolve(), "data")
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data_path = pathlib.Path(__file__).parents[1] / "data"
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83-
data_1 = np.loadtxt(os.path.join(data_path, "D2O_spin_down.dat"))
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data_1 = np.loadtxt(data_path / "D2O_spin_down.dat")
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problem.data.append(name="D2O_dn", data=data_1)
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86-
data_2 = np.loadtxt(os.path.join(data_path, "D2O_spin_up.dat"))
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data_2 = np.loadtxt(data_path / "D2O_spin_up.dat")
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problem.data.append(name="D2O_up", data=data_2)
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89-
data_3 = np.loadtxt(os.path.join(data_path, "H2O_spin_down.dat"))
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data_3 = np.loadtxt(data_path / "H2O_spin_down.dat")
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problem.data.append(name="H2O_dn", data=data_3)
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92-
data_4 = np.loadtxt(os.path.join(data_path, "H2O_spin_up.dat"))
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data_4 = np.loadtxt(data_path / "H2O_spin_up.dat")
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problem.data.append(name="H2O_up", data=data_4)
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# Add the custom file

‎RATapi/examples/convert_rascal_project/convert_rascal.ipynb‎

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‎RATapi/examples/domains/domains_custom_XY.ipynb‎

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@@ -17,8 +17,6 @@
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"[IMAGES!]\n",
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"\n",
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"# Simple example of a layer containing domains using a custom XY model\n",
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"\n",
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"Domains custom XY models operate in the same way as domains custom layer models, in that there is an additional input to the custom model specifying the domain to be calculated:\n",
@@ -456,7 +454,7 @@
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"text": [
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"Starting RAT ───────────────────────────────────────────────────────────────────────────────────────────────────────────\n",
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"\n",
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"Elapsed time is 0.058 seconds\n",
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"Elapsed time is 0.071 seconds\n",
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"\n",
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"Finished RAT ───────────────────────────────────────────────────────────────────────────────────────────────────────────\n",
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"\n"

‎RATapi/examples/languages/run_custom_file_languages.py‎

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@@ -11,6 +11,7 @@
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project = setup_problem.make_example_problem()
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controls = RAT.Controls()
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controls.calcSldDuringFit = True
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# Python
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start = time.time()

‎RATapi/examples/languages/setup_problem.py‎

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Original file line numberDiff line numberDiff line change
@@ -1,4 +1,3 @@
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import os
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import pathlib
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import numpy as np
@@ -39,10 +38,10 @@ def make_example_problem():
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# and H2O. Load these datafiles in and put them in the data block
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# Read in the datafiles
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data_path = os.path.join(pathlib.Path(__file__).parents[1].resolve(), "data")
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D2O_data = np.loadtxt(os.path.join(data_path, "c_PLP0016596.dat"), delimiter=",")
44-
SMW_data = np.loadtxt(os.path.join(data_path, "c_PLP0016601.dat"), delimiter=",")
45-
H2O_data = np.loadtxt(os.path.join(data_path, "c_PLP0016607.dat"), delimiter=",")
41+
data_path = pathlib.Path("../data")
42+
D2O_data = np.loadtxt(data_path / "c_PLP0016596.dat", delimiter=",")
43+
SMW_data = np.loadtxt(data_path / "c_PLP0016601.dat", delimiter=",")
44+
H2O_data = np.loadtxt(data_path / "c_PLP0016607.dat", delimiter=",")
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# Add the data to the project - note this data has a resolution 4th column
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problem.data.append(name="Bilayer / D2O", data=D2O_data)

‎RATapi/examples/non_polarised/DSPC_custom_XY.py‎

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Original file line numberDiff line numberDiff line change
@@ -1,4 +1,3 @@
1-
import os
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import pathlib
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import numpy as np
@@ -59,10 +58,10 @@ def DSPC_custom_XY():
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# Water and H2O. Load these datafiles in and put them in the data block
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# Read in the datafiles
62-
data_path = os.path.join(pathlib.Path(__file__).parents[1].resolve(), "data")
63-
D2O_data = np.loadtxt(os.path.join(data_path, "c_PLP0016596.dat"), delimiter=",")
64-
SMW_data = np.loadtxt(os.path.join(data_path, "c_PLP0016601.dat"), delimiter=",")
65-
H2O_data = np.loadtxt(os.path.join(data_path, "c_PLP0016607.dat"), delimiter=",")
61+
data_path = pathlib.Path(__file__).parents[1] / "data"
62+
D2O_data = np.loadtxt(data_path / "c_PLP0016596.dat", delimiter=",")
63+
SMW_data = np.loadtxt(data_path / "c_PLP0016601.dat", delimiter=",")
64+
H2O_data = np.loadtxt(data_path / "c_PLP0016607.dat", delimiter=",")
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# Add the data to the project - note this data has a resolution 4th column
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problem.data.append(name="Bilayer / D2O", data=D2O_data)

‎RATapi/examples/non_polarised/DSPC_custom_layers.ipynb‎

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Original file line numberDiff line numberDiff line change
@@ -7,7 +7,6 @@
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"metadata": {},
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"outputs": [],
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"source": [
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"import os\n",
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"import pathlib\n",
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"\n",
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"import numpy as np\n",
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"outputs": [],
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"source": [
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"# Read in the datafiles\n",
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"data_path = os.path.join(pathlib.Path.cwd().parents[0].resolve(), \"data\")\n",
489-
"D2O_data = np.loadtxt(os.path.join(data_path, \"c_PLP0016596.dat\"), delimiter=\",\")\n",
490-
"SMW_data = np.loadtxt(os.path.join(data_path, \"c_PLP0016601.dat\"), delimiter=\",\")\n",
491-
"H2O_data = np.loadtxt(os.path.join(data_path, \"c_PLP0016607.dat\"), delimiter=\",\")\n",
487+
"data_path = pathlib.Path(\"../data\")\n",
488+
"D2O_data = np.loadtxt(data_path / \"c_PLP0016596.dat\", delimiter=\",\")\n",
489+
"SMW_data = np.loadtxt(data_path / \"c_PLP0016601.dat\", delimiter=\",\")\n",
490+
"H2O_data = np.loadtxt(data_path / \"c_PLP0016607.dat\", delimiter=\",\")\n",
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"\n",
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"# Add the data to the project - note this data has a resolution 4th column\n",
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"problem.data.append(name=\"Bilayer / D2O\", data=D2O_data, data_range=[0.013, 0.37])\n",
@@ -819,7 +818,7 @@
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"text": [
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"Starting RAT ───────────────────────────────────────────────────────────────────────────────────────────────────────────\n",
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"\n",
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"Elapsed time is 0.023 seconds\n",
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"Elapsed time is 0.020 seconds\n",
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"\n",
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"Finished RAT ───────────────────────────────────────────────────────────────────────────────────────────────────────────\n",
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"\n"

‎RATapi/examples/non_polarised/DSPC_custom_layers.py‎

Lines changed: 4 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,3 @@
1-
import os
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import pathlib
32

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import numpy as np
@@ -39,10 +38,10 @@ def DSPC_custom_layers():
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# Water and H2O. Load these datafiles in and put them in the data block
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# Read in the datafiles
42-
data_path = os.path.join(pathlib.Path(__file__).parents[1].resolve(), "data")
43-
D2O_data = np.loadtxt(os.path.join(data_path, "c_PLP0016596.dat"), delimiter=",")
44-
SMW_data = np.loadtxt(os.path.join(data_path, "c_PLP0016601.dat"), delimiter=",")
45-
H2O_data = np.loadtxt(os.path.join(data_path, "c_PLP0016607.dat"), delimiter=",")
41+
data_path = pathlib.Path(__file__).parents[1] / "data"
42+
D2O_data = np.loadtxt(data_path / "c_PLP0016596.dat", delimiter=",")
43+
SMW_data = np.loadtxt(data_path / "c_PLP0016601.dat", delimiter=",")
44+
H2O_data = np.loadtxt(data_path / "c_PLP0016607.dat", delimiter=",")
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4746
# Add the data to the project - note this data has a resolution 4th column
4847
problem.data.append(name="Bilayer / D2O", data=D2O_data, data_range=[0.013, 0.37])

‎RATapi/examples/non_polarised/DSPC_custom_xy.ipynb‎

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@@ -7,7 +7,6 @@
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"metadata": {},
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"outputs": [],
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"source": [
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"import os\n",
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"import pathlib\n",
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"\n",
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"import numpy as np\n",
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"outputs": [],
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"source": [
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"# Read in the datafiles\n",
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"data_path = os.path.join(pathlib.Path.cwd().parents[0].resolve(), \"data\")\n",
129-
"D2O_data = np.loadtxt(os.path.join(data_path, \"c_PLP0016596.dat\"), delimiter=\",\")\n",
130-
"SMW_data = np.loadtxt(os.path.join(data_path, \"c_PLP0016601.dat\"), delimiter=\",\")\n",
131-
"H2O_data = np.loadtxt(os.path.join(data_path, \"c_PLP0016607.dat\"), delimiter=\",\")\n",
127+
"data_path = pathlib.Path(\"../data\")\n",
128+
"D2O_data = np.loadtxt(data_path / \"c_PLP0016596.dat\", delimiter=\",\")\n",
129+
"SMW_data = np.loadtxt(data_path / \"c_PLP0016601.dat\", delimiter=\",\")\n",
130+
"H2O_data = np.loadtxt(data_path / \"c_PLP0016607.dat\", delimiter=\",\")\n",
132131
"\n",
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"# Add the data to the project - note this data has a resolution 4th column\n",
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"problem.data.append(name=\"Bilayer / D2O\", data=D2O_data)\n",
@@ -245,7 +244,7 @@
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"source": [
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"## Running the Model\n",
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"\n",
248-
"We do this by first making a controls block as previously. We'll run a Differential Evolution, and then a Bayesian analysis:"
247+
"We do this by first making a controls block as previously. We'll run a Differential Evolution:"
249248
]
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},
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{
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264263
"Running Differential Evolution\n",
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"\n",
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"Final chi squared is 8.39155\n",
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"Elapsed time is 127.146 seconds\n",
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"Elapsed time is 108.162 seconds\n",
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"\n",
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"Finished RAT ───────────────────────────────────────────────────────────────────────────────────────────────────────────\n",
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"\n"

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