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LIDE_generator_script/default.xml

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+<?xml version="1.0" encoding="utf-8"?>
+<!--  -->
+<configuration>
+   <domain>
+      <nodeSize> 0.2 e-5 </nodeSize>
+      <nodeRatio> 16 ,16 , 1 </nodeRatio>
+      <centeredAlignment> False, False, False </centeredAlignment>
+      <boundaryConditions>
+         <material>
+            <west> Symmetry </west>
+            <east> ZeroGradient </east>
+            <south> Symmetry </south>
+            <north> ZeroGradient </north>
+            <bottom> ZeroGradient </bottom>
+            <top> ZeroGradient </top>
+         </material>
+      </boundaryConditions>
+
+      <initialConditions>
+         <treeInitializationType> LevelBased </treeInitializationType>
+         <topologyInitializationType> BottomUp </topologyInitializationType>
+
+         <material1>
+            // air
+            if ((x &lt; 0.35e-6) and (sqrt(x^2+y^2) &lt; 1e-5)) {
+               density := 998.2;
+               velocityX := 0.0;
+               velocityY := 0.0;
+               velocityZ := 0.0;
+               pressure := 10e9;
+            } else {
+               density := 0.74;
+               velocityX := 0.0;
+               velocityY := 0.0;
+               velocityZ := 0.0;
+               pressure := 1e5;
+            }
+         </material1>
+
+         <material2>
+            // water
+            density := 998.2;
+            velocityX := 0.0;
+            velocityY := 0.0;
+            velocityZ := 0.0;
+            pressure := 1e5;
+         </material2>
+
+         <interface1>
+            <levelset>
+               <type> precompiled </type>
+               <operator> or </operator>
+               <!-- <data>
+                  <function> Sphere </function>
+                  <center> 0.0, 0.0, 0.0 </center>
+                  <centerSign> -1 </centerSign>
+                  <innerRadius> 0.0 </innerRadius>
+                  <outerRadius> 1e-5 </outerRadius>
+               </data> -->
+               <data>
+                  <function> Cylinder </function>
+                  <center> 0.0, 0.0, 0.0 </center>
+                  <centerSign> 1 </centerSign>
+                  <rotation> 1.570796326794897, 0, 0 </rotation>
+                  <innerRadius> 0.0 </innerRadius>
+                  <outerRadius> 0.2e-6 </outerRadius>
+                  <height> 4e-5 </height>
+               </data>
+               <data>
+                  <function> Ellipsoid </function>
+                  <center> 0.0, 0.0, 0.0 </center>
+                  <centerSign> -1 </centerSign>
+                  <rotation> 0.0, 0.0, 0.0 </rotation>
+                  <semiAxis> 1.5e-5, 1e-5, 1e-5 </semiAxis>
+               </data>
+            </levelset>
+         </interface1>
+      </initialConditions>
+   </domain>
+
+   <materials>
+      <numberOfMaterials> 2 </numberOfMaterials>
+      <numberOfPositiveMaterials> 2 </numberOfPositiveMaterials>
+      <material1>
+         <type> Fluid </type>
+         <equationOfState>
+            <type> StiffenedGas </type>
+            <gamma> 1.33 </gamma>
+            <backgroundPressure> 0.0 </backgroundPressure>
+         </equationOfState>
+         <properties>
+            <specificHeatCapacity> 0.0 </specificHeatCapacity>
+            <thermalConductivity> 0.0 </thermalConductivity>
+            <shearViscosity> 0.0 </shearViscosity>
+            <bulkViscosity> 0.0 </bulkViscosity>
+         </properties>
+      </material1>
+
+      <material2>
+         <type> Fluid </type>
+         <equationOfState>
+            <type> StiffenedGas </type>
+            <gamma> 4.4 </gamma>
+            <backgroundPressure> 6.0e8 </backgroundPressure>
+         </equationOfState>1
+         <properties>
+            <specificHeatCapacity> 0.0 </specificHeatCapacity>
+            <thermalConductivity> 0.0 </thermalConductivity>
+            <shearViscosity> 0.0 </shearViscosity>
+            <bulkViscosity> 0.0 </bulkViscosity>
+         </properties>
+      </material2>
+   </materials>
+
+   <materialPairings>
+      <material1_2>
+         <surfaceTensionCoefficient> 0.0 </surfaceTensionCoefficient>
+      </material1_2>
+   </materialPairings>
+
+   <sourceTerms>
+      <gravity> 0, 0, 0 </gravity>
+   </sourceTerms>
+
+   <multiResolution>
+      <maximumLevel> 0 </maximumLevel>
+
+      <refinementCriterion>
+         <epsilonReference> 0.01 </epsilonReference>
+         <levelOfEpsilonReference> 0 </levelOfEpsilonReference>
+      </refinementCriterion>
+   </multiResolution>
+
+   <timeControl>
+      <startTime> 0.0 </startTime>
+      <endTime> 20e-9 </endTime>
+      <CFLNumber> 0.35 </CFLNumber>
+   </timeControl>
+
+   <dimensionalization>
+      <lengthReference> 1.0 </lengthReference>
+      <velocityReference> 1.0 </velocityReference>
+      <densityReference> 1.0 </densityReference>
+      <temperatureReference> 1.0 </temperatureReference>
+      <amountOfSubstanceReference> 1.0 </amountOfSubstanceReference>
+   </dimensionalization>
+
+   <restart>
+      <restore>
+         <mode> Off </mode>
+         <fileName> ./Alpaca/ALPACA_WORKSHOP/build/droplet_RDEMIC/restart/restart_.h5 </fileName>
+      </restore>
+      <snapshots>
+         <mode> Macro </mode>
+         <type> Interval </type>
+         <interval> 50e-9 </interval>
+         <intervalsToKeep> 2 </intervalsToKeep>
+         <stamps> </stamps>
+      </snapshots>
+   </restart>
+
+   <output>
+      <timeNamingFactor> 1.0e6 </timeNamingFactor>
+      <standard>
+         <type> Interval </type>
+         <interval> 1e-10 </interval>
+         <stamps> </stamps>
+         <minimalLevel> 0 </minimalLevel>
+      </standard>
+   </output>
+
+</configuration>

LIDE_generator_script/generator.py

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+"""
+This script generates input files for ALPACA simulations of LIDE by varying key parameters using a Sobol sequence for sampling.
+Change the parameters in the 'param_bounds' array to modify the ranges for high pressure, low pressure, laser width, and droplet radii.
+First creates a set of .xml input files using "create_alpaca_input" function, then runs ALPACA on each generated input file using "run_alpaca" function.
+For this change the number of simualtions and paths at the end of the script.
+Keep the default.xml file in the same directory as this script as the code overwrites it to create new input files.
+"""
+
+
+
+import os
+import subprocess
+import logging
+import time
+import math
+import html
+import re
+from scipy.stats.qmc import Sobol, scale
+from scipy.stats import qmc
+import xmltodict
+import numpy as np
+import warnings
+
+
+def run_alpaca(
+        xml_file,
+        output_dir: str = None,
+        mpiexec_path: str = None,
+        exec_file_path: str = None,
+        num_workers: int = 10,
+):
+    """
+    Runs ALPACA with different parameters in .xml file. 
+
+    Args:
+        xml_file (str): Path to the input .xml file to be processed.
+        mpiexec_path (str): Path to the mpiexec executable. Find using command "which mpiexec" in terminal.
+        exec_file_path (str): Path to the ALPACA executable file. Default is "./build/ALPACA".
+        num_workers (int): Number of cpu workers for parallel processing.
+        output_dir (str): Directory where output files will be saved. 
+    """
+
+     # Setup logging
+    logging.basicConfig(
+    filename=os.path.join(str(output_dir), 'data_generator.log'),
+    level=logging.INFO,
+    format='%(asctime)s [%(levelname)s] %(message)s'
+    )
+
+    # Check for executable ALAPACA location in command
+    command = [str(mpiexec_path), "-n", str(num_workers), str(exec_file_path), str(xml_file), str(output_dir)]
+
+
+    logging.info(f"Starting: {' '.join(command)}")
+    start_time = time.time()
+    result = subprocess.run(command, capture_output=True, text=True)
+    end_time = time.time()
+
+    elapsed = end_time - start_time
+    length = math.ceil(elapsed / 60)
+
+
+    if result.returncode == 0:
+        logging.info(f"Completed {xml_file} successfully in {length:.2f} minutes; [{elapsed:.2f} seconds.]")
+        logging.debug(f"Output:\n{result.stdout}")
+    else:
+        logging.error(f"ALPACA failed on {xml_file} with return code {result.returncode}")
+        logging.error(f"stderr:\n{result.stderr}")
+
+def round_sig(x, sig=5):
+    return float(f"{x:.{sig}g}")
+
+def create_alpaca_input(
+        count: int,
+        base_path: str ,
+        output_path: str 
+):
+    
+    """
+    Generates a set of ALPACA input files with varying parameters for high pressure, low pressure, laser width, and the two radii of the droplet.
+
+    Args:
+        count (int): Number of samples to generate.
+        base_path (str): Path to the base .xml file that will be modified.
+        output_path (str): Directory where the generated .xml files will be saved. Create the directory if it does not exist.
+    """
+
+    warnings.warn(f"[WARNING] Make sure the default base_input file {base_path} exists and untouched !!!.")
+    
+
+   # Define the parameters
+    param_bounds = np.array([
+        [1e10, 8e10],       # high_pressure
+        [1e5, 1e6],        # low_pressure
+        [2e-7, 15e-7],     # laser_width
+        [1e-5, 1.6e-5],    #drop_radius_1
+        [1e-5, 1.6e-5]     #drop_radius_2
+    ])
+
+    n_samples = count
+    n_dims = param_bounds.shape[0]
+
+    sampler = qmc.Sobol(d=n_dims, scramble=True, seed=10)
+    samples_unit = sampler.random(n=n_samples)
+
+    params = qmc.scale(samples_unit, param_bounds[:, 0], param_bounds[:, 1]) #[N, D] = [128, 5] 
+    params = np.vectorize(round_sig)(params, sig=5)
+
+    width = params[:, 2] + 0.15e-6
+    
+
+    # Modify default.xml file
+    for i in range(n_samples):
+        
+        with open(base_path) as f:
+            data = xmltodict.parse(f.read())
+
+
+        # Air
+        air_0 = data["configuration"]["domain"]["initialConditions"]["material1"]
+
+        air_1 = air_0.replace("0.35e-6", f"{width[i]}")
+        air_2 = air_1.replace("1e-5", f"{params[i, 4]}")
+        air_3 = air_2.replace("pressure := 10e9;", f"pressure := {params[i, 0]};")
+
+        match = re.search(r'else\s*{(.*?)}', air_0, flags=re.DOTALL)
+        else_block = match.group(1)
+        modified_else = re.sub(
+                r'pressure\s*:=\s*1e5;',
+                f'pressure := {params[i, 1]};',
+                match.group(1)
+            )
+        air_4 = air_3.replace(else_block, modified_else)
+
+        data["configuration"]["domain"]["initialConditions"]["material1"] = air_4
+
+        # Water
+        water_0 = data["configuration"]["domain"]["initialConditions"]["material2"]
+        water_1 = water_0.replace("pressure := 1e5;", f"pressure := {params[i, 1]};")
+        data["configuration"]["domain"]["initialConditions"]["material2"] = water_1
+
+
+        # Interface
+        geometry_list = data["configuration"]["domain"]["initialConditions"]["interface1"]["levelset"]["data"]
+        # print(geometry_list)
+        for geo in geometry_list:
+            func = geo["function"].strip()
+
+            if func == "Cylinder":
+                geo["outerRadius"] = f"{params[i, 2]}" 
+
+            if func == "Ellipsoid":
+                geo["semiAxis"] = f"{params[i, 3]}, {params[i, 4]}, 1e-5"
+
+
+
+        formatted_params = ["{:.4e}".format(params[i, j]) for j in range(params.shape[1])]
+
+
+        with open(output_path+ f"/hp{formatted_params[0]}_lp{formatted_params[1]}_laser{formatted_params[2]}_dropradx{formatted_params[3]}_droprady{formatted_params[4]}.xml", 'w') as f:
+            f.write(xmltodict.unparse(data, pretty=True))
+
+
+count = 2 # Number of samples to generate. keep it multiple of 2 for Sobol sequence
+inputs_output_path = "."
+data_output_path = "."
+
+
+create_alpaca_input(count=count, 
+                    base_path="./default.xml", 
+                    output_path=inputs_output_path)
+
+
+inputs = []
+for file in os.listdir(inputs_output_path):
+    if file.endswith(".xml"):
+        inputs.append(os.path.join(".", file))
+        run_alpaca(xml_file=os.path.join(str(inputs_output_path), str(inputs[-1])), 
+                   output_dir=str(data_output_path),
+                   mpiexec_path="mpiexec",
+                   exec_file_path="./build/ALPACA",
+                   num_workers=10)
+
+