Skip to content

Commit d78df7f

Browse files
niccolotubininiccolotubini
committed
Add new classes and update existing
1 parent 7a5c3f2 commit d78df7f

10 files changed

+2337
-10
lines changed

‎src/main/java/it/geoframe/blogpsot/netcdf/monodimensionalproblemtimedependent/ReadNetCDFHeatAdvectionDiffusionGrid1D.java‎

Lines changed: 356 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,356 @@
1+
/*
2+
// * GNU GPL v3 License
3+
*
4+
* Copyright 2019 Niccolo` Tubini
5+
*
6+
* This program is free software: you can redistribute it and/or modify
7+
* it under the terms of the GNU General Public License as published by
8+
* the Free Software Foundation, either version 3 of the License, or
9+
* (at your option) any later version.
10+
*
11+
* This program is distributed in the hope that it will be useful,
12+
* but WITHOUT ANY WARRANTY; without even the implied warranty of
13+
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
14+
* GNU General Public License for more details.
15+
*
16+
* You should have received a copy of the GNU General Public License
17+
* along with this program. If not, see <http://www.gnu.org/licenses/>.
18+
*/
19+
20+
package it.geoframe.blogpsot.netcdf.monodimensionalproblemtimedependent;
21+
22+
import java.io.IOException;
23+
import oms3.annotations.Author;
24+
import oms3.annotations.Description;
25+
import oms3.annotations.Documentation;
26+
import oms3.annotations.Execute;
27+
import oms3.annotations.In;
28+
import oms3.annotations.Keywords;
29+
import oms3.annotations.Label;
30+
import oms3.annotations.License;
31+
import oms3.annotations.Name;
32+
import oms3.annotations.Out;
33+
import oms3.annotations.Status;
34+
import oms3.annotations.Unit;
35+
import ucar.ma2.ArrayDouble;
36+
import ucar.ma2.ArrayDouble.D1;
37+
import ucar.ma2.ArrayInt;
38+
import ucar.ma2.InvalidRangeException;
39+
import ucar.nc2.NetcdfFile;
40+
import ucar.nc2.Variable;
41+
42+
@Description("This class reads a NetCDF containing 1D grid data.")
43+
@Documentation("")
44+
@Author(name = "Niccolo' Tubini", contact = "[email protected]")
45+
@Keywords("Soil heat conduction, phase change, frozen soil, GEOframe, Permafrostnet")
46+
@Label("GEOframe.NETCDF")
47+
@Name("readFreezingThawing1Dgrid")
48+
@Status(Status.CERTIFIED)
49+
@License("General Public License Version 3 (GPLv3)")
50+
51+
public class ReadNetCDFHeatAdvectionDiffusionGrid1D {
52+
53+
@Description("File name of NetCDF containing grid data")
54+
@In
55+
public String gridFilename;
56+
57+
@Description("Number of control volume")
58+
@Out
59+
@Unit("-")
60+
public int KMAX;
61+
62+
@Description("eta coordinate of volume centroids: zero is at soil surface and and positive upward")
63+
@Out
64+
@Unit("m")
65+
public double[] eta;
66+
67+
@Description("eta coordinate of volume interfaces: zero is at soil surface and and positive upward.")
68+
@Out
69+
@Unit("m")
70+
public double[] etaDual;
71+
72+
@Description("z coordinate of volume centroids: zero is at the bottom of the column and and positive upward")
73+
@Out
74+
@Unit("m")
75+
public double[] z;
76+
77+
@Description("z coordinate of volume interfaces: zero is at soil surface and and positive upward.")
78+
@Out
79+
@Unit("m")
80+
public double[] zDual;
81+
82+
@Description("Water suction profile")
83+
@Out
84+
@Unit("m")
85+
public double[] psi;
86+
87+
@Description("Initial condition for temperature")
88+
@Out
89+
@Unit("K")
90+
public double[] temperatureIC;
91+
92+
@Description("Distance between consecutive controids, is used to compute gradients")
93+
@Out
94+
@Unit("m")
95+
public double[] spaceDelta;
96+
97+
@Description("Dimension of the control volume. It is used to integrate enthalpy function")
98+
@Out
99+
@Unit("m")
100+
public double[] controlVolume;
101+
102+
@Description("Control volume label identifying the equation state")
103+
@Out
104+
@Unit("-")
105+
public int[] equationStateID;
106+
107+
@Description("Control volume label identifying the set of paremeters describing the soil")
108+
@Out
109+
@Unit("-")
110+
public int[] parameterID;
111+
112+
@Description("Soil particles density")
113+
@Out
114+
@Unit("kg m-3")
115+
public double[] soilParticlesDensity;
116+
117+
@Description("Soil particles thermal conductivity")
118+
@Out
119+
@Unit("W m-2 K-1")
120+
public double[] soilParticlesThermalConductivity;
121+
122+
@Description("Soil particles specific heat capacity")
123+
@Out
124+
@Unit("J kg-1 m-3")
125+
public double[] soilParticlesSpecificHeatCapacity;
126+
127+
@Description("Adimensional water content at saturation")
128+
@Out
129+
@Unit("-")
130+
public double[] thetaS;
131+
132+
@Description("Adimensional residual water content")
133+
@Out
134+
@Unit("-")
135+
public double[] thetaR;
136+
137+
@Description("Melting temperature")
138+
@Out
139+
@Unit("K")
140+
public double[] meltingTemperature;
141+
142+
@Description("Hydraulic conductivity at saturation")
143+
@Out
144+
@Unit("m/s")
145+
public double[] Ks;
146+
147+
@Description("Aquitard compressibility")
148+
@Out
149+
@Unit("1/Pa")
150+
public double[] alphaSS;
151+
152+
@Description("Water compressibility")
153+
@Out
154+
@Unit("1/Pa")
155+
public double[] betaSS;
156+
157+
@Description("SWRC parameter 1. This depends on the SWRC used, look at the documentation.")
158+
@Out
159+
@Unit("-")
160+
public double[] par1SWRC;
161+
162+
@Description("SWRC parameter 2. This depends on the SWRC used, look at the documentation.")
163+
@Out
164+
@Unit("-")
165+
public double[] par2SWRC;
166+
167+
@Description("SWRC parameter 3. This depends on the SWRC used, look at the documentation.")
168+
@Out
169+
@Unit("-")
170+
public double[] par3SWRC;
171+
172+
@Description("SWRC parameter 4. This depends on the SWRC used, look at the documentation.")
173+
@Out
174+
@Unit("-")
175+
public double[] par4SWRC;
176+
177+
@Description("Fifth SWRC parameter. This depends on the SWRC used, look at the documentation.")
178+
@Out
179+
@Unit(" ")
180+
public double[] par5SWRC;
181+
182+
private int[] size;
183+
private int[] size1;
184+
private int[] sizeParameter;
185+
// private int[] sizeCellSize;
186+
private int step = 0;
187+
188+
@Execute
189+
/**
190+
* Read the computational grid.
191+
**/
192+
public void read() throws IOException {
193+
194+
if (step == 0) {
195+
196+
// Open the file. The ReadOnly parameter tells netCDF we want
197+
// read-only access to the file.
198+
NetcdfFile dataFile = null;
199+
String filename = gridFilename;
200+
// Open the file.
201+
try {
202+
203+
dataFile = NetcdfFile.open(filename, null);
204+
205+
// Retrieve the variables named "___"
206+
Variable dataKMAX = dataFile.findVariable("KMAX");
207+
Variable dataEta = dataFile.findVariable("eta");
208+
Variable dataEtaDual = dataFile.findVariable("etaDual");
209+
Variable dataZ = dataFile.findVariable("z");
210+
Variable dataZDual = dataFile.findVariable("zDual");
211+
Variable dataPsiIC = dataFile.findVariable("psi0");
212+
Variable dataTemperatureIC = dataFile.findVariable("T0");
213+
Variable dataSpaceDelta = dataFile.findVariable("spaceDelta");
214+
Variable dataControlVolume = dataFile.findVariable("controlVolume");
215+
Variable dataEquationStateID = dataFile.findVariable("equationStateID");
216+
Variable dataParameterID = dataFile.findVariable("parameterID");
217+
218+
Variable dataSoilParticlesDensity = dataFile.findVariable("soilParticlesDensity");
219+
Variable dataThermalConductivitySoilParticles = dataFile.findVariable("thermalConductivitySoilParticles");
220+
Variable dataSpecificThermalCapacitySoilParticles = dataFile.findVariable("specificThermalCapacitySoilParticles");
221+
Variable dataThetaS = dataFile.findVariable("thetaS");
222+
Variable dataThetaR = dataFile.findVariable("thetaR");
223+
Variable dataMeltingTemperature = dataFile.findVariable("meltingTemperature");
224+
Variable dataKs = dataFile.findVariable("ks");
225+
Variable dataAlphaSS = dataFile.findVariable("alphaSpecificStorage");
226+
Variable dataBetaSS = dataFile.findVariable("betaSpecificStorage");
227+
Variable dataPar1SWRC = dataFile.findVariable("par1SWRC");
228+
Variable dataPar2SWRC = dataFile.findVariable("par2SWRC");
229+
Variable dataPar3SWRC = dataFile.findVariable("par3SWRC");
230+
Variable dataPar4SWRC = dataFile.findVariable("par4SWRC");
231+
Variable dataPar5SWRC = dataFile.findVariable("par5SWRC");
232+
233+
234+
size = dataEta.getShape();
235+
236+
KMAX = 0;
237+
eta = new double[size[0]];
238+
etaDual = new double[size[0]];
239+
z = new double[size[0]];
240+
zDual = new double[size[0]];
241+
controlVolume = new double[size[0]];
242+
psi = new double[size[0]];
243+
temperatureIC = new double[size[0]];
244+
equationStateID = new int[size[0]];
245+
parameterID = new int[size[0]];
246+
247+
size1 = dataSpaceDelta.getShape();
248+
spaceDelta = new double[size1[0]];
249+
250+
251+
sizeParameter = dataPar1SWRC.getShape();
252+
soilParticlesDensity = new double[sizeParameter[0]];
253+
soilParticlesThermalConductivity = new double[sizeParameter[0]];
254+
soilParticlesSpecificHeatCapacity = new double[sizeParameter[0]];
255+
thetaS = new double[sizeParameter[0]];
256+
thetaR = new double[sizeParameter[0]];
257+
meltingTemperature = new double[sizeParameter[0]];
258+
par1SWRC = new double[sizeParameter[0]];
259+
par2SWRC = new double[sizeParameter[0]];
260+
par3SWRC = new double[sizeParameter[0]];
261+
par4SWRC = new double[sizeParameter[0]];
262+
par5SWRC = new double[sizeParameter[0]];
263+
Ks = new double[sizeParameter[0]];
264+
alphaSS = new double[sizeParameter[0]];
265+
betaSS = new double[sizeParameter[0]];
266+
267+
ArrayDouble.D1 dataArrayEta = (ArrayDouble.D1) dataEta.read(null, size);
268+
ArrayDouble.D1 dataArrayEtaDual= (ArrayDouble.D1) dataEtaDual.read(null, size);
269+
ArrayDouble.D1 dataArrayZ = (ArrayDouble.D1) dataZ.read(null, size);
270+
ArrayDouble.D1 dataArrayZDual = (ArrayDouble.D1) dataZDual.read(null, size);
271+
ArrayDouble.D1 dataArrayPsiIC = (ArrayDouble.D1) dataPsiIC.read(null, size);
272+
ArrayDouble.D1 dataArrayTemperatureIC = (ArrayDouble.D1) dataTemperatureIC.read(null, size);
273+
ArrayDouble.D1 dataArraySpaceDelta = (ArrayDouble.D1) dataSpaceDelta.read(null, size1);
274+
ArrayDouble.D1 dataArrayControlVolume = (ArrayDouble.D1) dataControlVolume.read(null, size);
275+
ArrayInt.D1 dataArrayEquationStateID = (ArrayInt.D1) dataEquationStateID.read(null, size);
276+
ArrayInt.D1 dataArrayParameterID= (ArrayInt.D1) dataParameterID.read(null, size);
277+
ArrayDouble.D1 dataArraySoilParticlesDensity = (ArrayDouble.D1) dataSoilParticlesDensity.read(null, sizeParameter);
278+
ArrayDouble.D1 dataArrayThermalConductivitySoilParticles = (ArrayDouble.D1) dataThermalConductivitySoilParticles.read(null, sizeParameter);
279+
ArrayDouble.D1 dataArraySpecificThermalCapacitySoilParticles = (ArrayDouble.D1) dataSpecificThermalCapacitySoilParticles.read(null, sizeParameter);
280+
ArrayDouble.D1 dataArrayThetaS = (ArrayDouble.D1) dataThetaS.read(null, sizeParameter);
281+
ArrayDouble.D1 dataArrayThetaR = (ArrayDouble.D1) dataThetaR.read(null, sizeParameter);
282+
ArrayDouble.D1 dataArrayMeltingTemperature = (ArrayDouble.D1) dataMeltingTemperature.read(null, sizeParameter);
283+
ArrayDouble.D1 dataArrayKs = (ArrayDouble.D1) dataKs.read(null, sizeParameter);
284+
ArrayDouble.D1 dataArrayAlphaSS = (ArrayDouble.D1) dataAlphaSS.read(null, sizeParameter);
285+
ArrayDouble.D1 dataArrayBetaSS = (ArrayDouble.D1) dataBetaSS.read(null, sizeParameter);
286+
ArrayDouble.D1 dataArrayPar1SWRC = (ArrayDouble.D1) dataPar1SWRC.read(null, sizeParameter);
287+
ArrayDouble.D1 dataArrayPar2SWRC = (ArrayDouble.D1) dataPar2SWRC.read(null, sizeParameter);
288+
ArrayDouble.D1 dataArrayPar3SWRC = (ArrayDouble.D1) dataPar3SWRC.read(null, sizeParameter);
289+
ArrayDouble.D1 dataArrayPar4SWRC = (ArrayDouble.D1) dataPar4SWRC.read(null, sizeParameter);
290+
ArrayDouble.D1 dataArrayPar5SWRC = (ArrayDouble.D1) dataPar5SWRC.read(null, sizeParameter);
291+
292+
293+
294+
295+
296+
297+
KMAX = dataKMAX.readScalarInt();
298+
for (int i = 0; i < size[0]; i++) {
299+
300+
eta[i] = dataArrayEta.get(i);
301+
etaDual[i] = dataArrayEtaDual.get(i);
302+
z[i] = dataArrayZ.get(i);
303+
zDual[i] = dataArrayZDual.get(i);
304+
psi[i] = dataArrayPsiIC.get(i);
305+
temperatureIC[i] = dataArrayTemperatureIC.get(i);
306+
controlVolume[i] = dataArrayControlVolume.get(i);
307+
equationStateID[i] = (int) dataArrayEquationStateID.get(i);
308+
parameterID[i] = (int) dataArrayParameterID.get(i);
309+
310+
}
311+
312+
for (int i = 0; i < size1[0]; i++) {
313+
314+
spaceDelta[i] = dataArraySpaceDelta.get(i);
315+
316+
}
317+
318+
for (int i = 0; i < sizeParameter[0]; i++) {
319+
320+
soilParticlesDensity[i] = dataArraySoilParticlesDensity.get(i);
321+
soilParticlesThermalConductivity[i] = dataArrayThermalConductivitySoilParticles.get(i);
322+
soilParticlesSpecificHeatCapacity[i] = dataArraySpecificThermalCapacitySoilParticles.get(i);
323+
thetaS[i] = dataArrayThetaS.get(i);
324+
thetaR[i] = dataArrayThetaR.get(i);
325+
meltingTemperature[i] = dataArrayMeltingTemperature.get(i);
326+
Ks[i] = dataArrayKs.get(i);
327+
alphaSS[i] = dataArrayAlphaSS.get(i);
328+
betaSS[i] = dataArrayBetaSS.get(i);
329+
par1SWRC[i] = dataArrayPar1SWRC.get(i);
330+
par2SWRC[i] = dataArrayPar2SWRC.get(i);
331+
par3SWRC[i] = dataArrayPar3SWRC.get(i);
332+
par4SWRC[i] = dataArrayPar4SWRC.get(i);
333+
par5SWRC[i] = dataArrayPar5SWRC.get(i);
334+
335+
}
336+
337+
338+
} catch (InvalidRangeException e) {
339+
e.printStackTrace();
340+
341+
} finally {
342+
if (dataFile != null)
343+
try {
344+
dataFile.close();
345+
} catch (IOException ioe) {
346+
ioe.printStackTrace();
347+
}
348+
}
349+
350+
System.out.println("*** SUCCESS reading file " + gridFilename);
351+
352+
}
353+
step++;
354+
355+
}
356+
}

0 commit comments

Comments
 (0)