comsol_batch_script.java

/*
 * COMSOL Batch Processing Script (Java)
 * 
 * This script reads treatment parameters from a JSON file,
 * runs the tumor simulation model, and writes results back to JSON.
 * 
 * To use this script with COMSOL:
 * 1. Save this as comsol_batch_script.java
 * 2. Modify the parameter names to match your COMSOL model
 * 3. Run with: comsol batch -inputfile input.json -outputfile output.json
 */

import com.comsol.model.*;
import com.comsol.model.util.*;
import org.json.simple.*;
import org.json.simple.parser.*;
import java.io.*;
import java.util.*;

public class comsol_batch_script {
    
    public static void main(String[] args) {
        
        // Parse command line arguments
        String inputFile = null;
        String outputFile = null;
        String modelFile = "tumor_model.mph";  // CHANGE THIS to your model path
        
        for (int i = 0; i < args.length; i++) {
            if (args[i].equals("-inputfile") && i + 1 < args.length) {
                inputFile = args[i + 1];
            } else if (args[i].equals("-outputfile") && i + 1 < args.length) {
                outputFile = args[i + 1];
            } else if (args[i].equals("-model") && i + 1 < args.length) {
                modelFile = args[i + 1];
            }
        }
        
        if (inputFile == null || outputFile == null) {
            System.err.println("Usage: -inputfile <path> -outputfile <path> [-model <path>]");
            System.exit(1);
        }
        
        try {
            // Read input parameters from JSON
            System.out.println("Reading parameters from: " + inputFile);
            JSONParser parser = new JSONParser();
            JSONObject inputParams = (JSONObject) parser.parse(new FileReader(inputFile));
            
            JSONArray doses = (JSONArray) inputParams.get("doses");
            JSONArray intervals = (JSONArray) inputParams.get("intervals");
            double totalTime = ((Number) inputParams.get("total_time")).doubleValue();
            
            // Load COMSOL model
            System.out.println("Loading COMSOL model: " + modelFile);
            Model model = ModelUtil.load(modelFile);
            
            // Set parameters in the model
            // IMPORTANT: Adjust these parameter names to match YOUR model!
            
            int numDoses = doses.size();
            model.param().set("n_doses", String.valueOf(numDoses));
            model.param().set("total_time", String.valueOf(totalTime) + "[d]");
            
            // Set dose times and amounts
            double currentTime = 0;
            for (int i = 0; i < numDoses; i++) {
                JSONArray dose = (JSONArray) doses.get(i);
                double drug1 = ((Number) dose.get(0)).doubleValue();
                double drug2 = ((Number) dose.get(1)).doubleValue();
                double drug3 = ((Number) dose.get(2)).doubleValue();
                
                // Set parameters (ADJUST NAMES TO YOUR MODEL!)
                model.param().set("dose_time_" + i, String.valueOf(currentTime) + "[d]");
                model.param().set("dose_drug1_" + i, String.valueOf(drug1) + "[mg]");
                model.param().set("dose_drug2_" + i, String.valueOf(drug2) + "[mg]");
                model.param().set("dose_drug3_" + i, String.valueOf(drug3) + "[mg]");
                
                // Update time
                if (i < intervals.size()) {
                    currentTime += ((Number) intervals.get(i)).doubleValue();
                }
                
                System.out.println("Dose " + i + ": Drug1=" + drug1 + " Drug2=" + drug2 + " Drug3=" + drug3 + " at t=" + currentTime + "d");
            }
            
            // Run the simulation
            System.out.println("Running simulation...");
            model.study("std1").run();  // CHANGE "std1" to your study tag
            System.out.println("Simulation complete!");
            
            // Extract results
            // ADJUST THESE TO MATCH YOUR MODEL'S VARIABLES!
            double[] times = model.result().numerical("time").getData();  // time variable
            double[] tumorCells = model.result().numerical("tumor_cells").getData();  // tumor cell count variable
            
            // Prepare output JSON
            JSONObject output = new JSONObject();
            
            JSONArray timesArray = new JSONArray();
            for (double t : times) {
                timesArray.add(t);
            }
            
            JSONArray cellsArray = new JSONArray();
            for (double c : tumorCells) {
                cellsArray.add(c);
            }
            
            output.put("times", timesArray);
            output.put("tumor_cells", cellsArray);
            output.put("success", true);
            
            // Write output JSON
            System.out.println("Writing results to: " + outputFile);
            FileWriter file = new FileWriter(outputFile);
            file.write(output.toJSONString());
            file.close();
            
            System.out.println("Done!");
            
        } catch (Exception e) {
            // Write error output
            try {
                JSONObject errorOutput = new JSONObject();
                errorOutput.put("success", false);
                errorOutput.put("error", e.getMessage());
                
                FileWriter file = new FileWriter(outputFile);
                file.write(errorOutput.toJSONString());
                file.close();
            } catch (IOException ioException) {
                System.err.println("Failed to write error output: " + ioException.getMessage());
            }
            
            System.err.println("Error: " + e.getMessage());
            e.printStackTrace();
            System.exit(1);
        }
    }
}