RunProperties.java

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package com.scottishseafarms.particle_track;

import java.io.*;
import java.util.Properties;
import static com.scottishseafarms.particle_track.ISO_datestr.dateIntParse;

/**
 *
 * @author sa01ta
 */
public class RunProperties {
    String basedir, sitedir, // Location of code and site data files
            datadir, datadirPrefix, datadirSuffix, // Location of default hydrodynamic data, with prefix and suffix for finding annual subdirectories
            datadir2, datadir2Prefix, datadir2Suffix, // Location of secondary (larger domain) hydrodynamic data, with prefix and suffix for finding annual subdirectories 
            mesh1, mesh2, // Full path to the mesh files used describing spatial structure of the hydrodynamic data (
            mesh1Type, mesh2Type, // What type of meshes are being read in (FVCOM or ROMS)
            restartParticles, // Full path to file containing locations of particles for a hot restart (matches last hour of locations file)
            location, sitefile, sitefileEnd, habitat, suffix, species, // Descriptive strings
            coordRef; // Coordinate reference system
            
            
    boolean backwards, // run model backwards? Needs some work on loops to make this work correctly
            timeInterpolate, spatialInterpolate, // interpolate between hydro file data values?
            rk4, // use RK4 numerical integration (alternative is Euler; need about 10 times as many steps)
            parallel, // use multiple cores to speed up run?
            diffusion, variableDiff, // include random walk, use diffusion parameter from hydro output?
            salinityMort, // mortality calculated based on local salinity (sea lice - doesn't presently do anything)?
            endOnArrival, // stop at first suitable habitat site, or simply note arrival and move on?
            setStartDepth, fixDepth, // set particle depth at initiation?
            readHydroVelocityOnly, // read only u,v from hydro files (saves RAM, ignores random extra variables)
            recordPsteps, splitPsteps, // record particle element densities? split by source site?
            recordConnectivity, recordLocations, recordArrivals, // record connectivity? particle locations? arrivals at sites?
            duplicateLastDay, // Should hydro file for last day be duplicated for interpolation puproses during last hour of simulation (false except when in operational mode)    
            checkOpenBoundaries, // Should open boundaries be checked? If reading hydro mesh from file directly, the answer is currently NO (open boundaries treated as closed boundaries).
            vertInterp; // Should layer velocities be interpolated vertically to particle depth (alternative - old behaviour - is to pick nearest depth)
    
    int start_ymd, end_ymd, numberOfDays, // Start and end of run. If numberOfDays = 0, it is ignored and end_ymd is used instead
            releaseScenario, // 0 release all at "releaseTime", 1 continuous release ("nparts" per hour per site)
            nparts, // Number of particles released per site (per hour in releaseScenario == 1
            recordsPerFile1, // Number of records per velocity file (allow two velocity files with different sizes)
            stepsPerStep, // Number of increments between each velocity record (also for time interpolations)
            //depthLayers, // Number of depth layers in hydro output - IDEALLY DEPRECATE
            thresh, // Threshold distance for "settlement" (m)
            behaviour, // Particle behaviour - see Particle.java
            parallelThreads, // Number of threads to use in parallel execution
            minchVersion, // Another element of the filename for hydrodynamic files
            pstepsInterval, connectivityInterval; // Interval in hours between recording element density summaries, and connectivity

    double releaseTime, releaseTimeEnd, viabletime, // Time of particle release (if releaseScenario == "0") and end of particle release (if releaseScenario == 2), Time to attain settlement competency
            dt, // Timestep (s) per record
            D_h, // Horizontal diffuision parameter
            D_hVert, // Vertical diffuision parameter
            mortalityRate, // Hourly mortality rate of particles
            maxParticleAge, // Maximum age for particles. Set to <=0 and it will be ignored.
            viableDegreeDays,maxDegreeDays, // Degree x days to use for settlement viability time and mortality 
            sinkingRateMean, sinkingRateStd, // Particle sinking distribution parameters
            vertSwimSpeedMean, vertSwimSpeedStd,
            salinityThreshold,
            startDepth, // Particle initiation depth
            restartParticlesCutoffDays, // when reading the specified restart particles file, cutoff in particle start date to apply (days before start date of run)
            velocityScale; // Numerical scaling of velocity for horizontal particle movement
  
    /**
     * 
     * @param filename 
     */
    public RunProperties(String filename)
    {
        System.out.println("GETTING PROPERTIES FROM "+filename);
        Properties properties = new Properties();
        try 
        {
            properties.load(new FileInputStream(filename));
        } 
        catch (IOException e) 
        {
            System.err.println("!!!Could not find properties file!!!");
        }
        
        for(String key : properties.stringPropertyNames()) {
            String value = properties.getProperty(key);
            System.out.println(key + " => " + value);
        }
        
        basedir = properties.getProperty("basedir","/home/sa01ta/particle_track/");
        sitedir = properties.getProperty("sitedir","/home/sa01ta/particle_track/minch_sites/");
        datadir = properties.getProperty("datadir","/home/sa01da/work/minch2/Archive/");
        datadirPrefix = properties.getProperty("datadirPrefix","netcdf_");
        datadirSuffix = properties.getProperty("datadirSuffix","");
        datadir2 = properties.getProperty("datadir2","/home/sa01da/data/oss/");
        datadir2Prefix = properties.getProperty("datadirPrefix","");
        datadir2Suffix = properties.getProperty("datadirSuffix","_OLD");
        
        minchVersion = Integer.parseInt(properties.getProperty("minchVersion","2"));
        
        mesh1 = properties.getProperty("mesh1","/home/sa01ta/particle_track/WestCOMS_mesh.nc");
        mesh2 = properties.getProperty("mesh2","");
        mesh1Type = properties.getProperty("mesh1Type","");
        mesh2Type = properties.getProperty("mesh2Type","");
        
        checkOpenBoundaries = Boolean.parseBoolean(properties.getProperty("checkOpenBoundaries","false"));
        
        restartParticles = properties.getProperty("restartParticles",""); 
        restartParticlesCutoffDays = Double.parseDouble(properties.getProperty("restartParticlesCutoffDays","21"));
        
        sitefile = properties.getProperty("sitefile","startlocations.dat");
        sitefileEnd = properties.getProperty("sitefileEnd",sitefile);
        
        location = properties.getProperty("location","minch");
        habitat = properties.getProperty("habitat","");
        suffix = properties.getProperty("suffix",""); 
        
        coordRef = properties.getProperty("coordRef","WGS84"); 
        
        start_ymd = Integer.parseInt(properties.getProperty("start_ymd","20180101"));
        numberOfDays = Integer.parseInt(properties.getProperty("numberOfDays","0"));
        if (numberOfDays>0)
        {
            int[] startDate = ISO_datestr.dateIntParse(start_ymd);
            ISO_datestr tempIsoDate = new ISO_datestr(startDate[0], startDate[1], startDate[2]);
            for (int i = 1; i < numberOfDays; i++)
            {
                tempIsoDate.addDay();
            }
            end_ymd = Integer.parseInt(tempIsoDate.getDateStr());
        }
        else
        {
            end_ymd = Integer.parseInt(properties.getProperty("end_ymd","20180102"));
        }
        if (end_ymd<start_ymd)
        {
            System.err.println("***** End date before start date! *****");
            System.exit(1);
        }
        
        // Set variable values based on contents of the properties object
        backwards = Boolean.parseBoolean(properties.getProperty("backwards","false"));
        // DEPRECATED
        //timeInterpolate = Boolean.parseBoolean(properties.getProperty("timeInterpolate","true"));
        //spatialInterpolate = Boolean.parseBoolean(properties.getProperty("spatialInterpolate","true"));
    
        rk4 = Boolean.parseBoolean(properties.getProperty("rk4","true"));
        
        diffusion = Boolean.parseBoolean(properties.getProperty("diffusion","true"));
        variableDiff = Boolean.parseBoolean(properties.getProperty("variableDiff","false"));
        salinityMort = Boolean.parseBoolean(properties.getProperty("salinityMort","false"));
        endOnArrival = Boolean.parseBoolean(properties.getProperty("endOnArrival","false"));
        // DEPRECATED
        //tidalRelease = Boolean.parseBoolean(properties.getProperty("tidalRelease","false"));
        setStartDepth = Boolean.parseBoolean(properties.getProperty("setStartDepth","false"));
        fixDepth = Boolean.parseBoolean(properties.getProperty("fixDepth","false"));
        startDepth = Integer.parseInt(properties.getProperty("startDepth","0"));
        
        vertInterp = Boolean.parseBoolean(properties.getProperty("vertInterp","true"));
        readHydroVelocityOnly = Boolean.parseBoolean(properties.getProperty("readHydroVelocityOnly","false"));
        if (vertInterp == true && readHydroVelocityOnly == true)
        {
            System.err.println("If using vertical interpolation, must read all hydro fields; setting readHydroVelocityOnly to FALSE");
            readHydroVelocityOnly = false;
        }
        velocityScale = Double.parseDouble(properties.getProperty("velocityScale","1"));
        
        duplicateLastDay = Boolean.parseBoolean(properties.getProperty("duplicateLastDay","false"));
        
        parallel = Boolean.parseBoolean(properties.getProperty("parallel","true"));
        parallelThreads = Integer.parseInt(properties.getProperty("parallelThreads","4"));
        // DEPRECATED
        //oldOutput = Boolean.parseBoolean(properties.getProperty("oldOutput"));
    
        recordPsteps = Boolean.parseBoolean(properties.getProperty("recordPsteps","true"));
        splitPsteps = Boolean.parseBoolean(properties.getProperty("splitPsteps","true"));
        pstepsInterval = Integer.parseInt(properties.getProperty("pstepsInterval","24"));
        recordConnectivity = Boolean.parseBoolean(properties.getProperty("recordConnectivity","true"));
        connectivityInterval = Integer.parseInt(properties.getProperty("connectivityInterval","24"));
        recordLocations = Boolean.parseBoolean(properties.getProperty("recordLocations","true"));
        recordArrivals = Boolean.parseBoolean(properties.getProperty("recordArrivals","true"));
        
        releaseScenario = Integer.parseInt(properties.getProperty("releaseScenario","0"));
        nparts = Integer.parseInt(properties.getProperty("nparts","5"));
        releaseTime = Double.parseDouble(properties.getProperty("releaseTime","0"));
        releaseTimeEnd = Double.parseDouble(properties.getProperty("releaseTimeEnd","24"));

        dt = Double.parseDouble(properties.getProperty("dt","3600"));
        
        // 21/11/2018 --- Ideally want to remove this. If using two models for hydro 
        // would ideally sense from the hydro file
        recordsPerFile1 = Integer.parseInt(properties.getProperty("recordsPerFile1","25"));
        //recordsPerFile2 = Integer.parseInt(properties.getProperty("recordsPerFile2","4"));
        
        stepsPerStep = Integer.parseInt(properties.getProperty("stepsPerStep","25"));
        
        // 21/11/2018 --- possible to remove? If using two models for hydro 
        // would ideally sense from the hydro file
        //depthLayers = Integer.parseInt(properties.getProperty("depthLayers","10"));       

        thresh = Integer.parseInt(properties.getProperty("thresh","500"));
        behaviour = Integer.parseInt(properties.getProperty("behaviour","1"));
        
        D_h = Double.parseDouble(properties.getProperty("D_h","0.1"));
        D_hVert = Double.parseDouble(properties.getProperty("D_hVert","0.005"));
        mortalityRate = Double.parseDouble(properties.getProperty("mortalityRate","0.01"));
        
        species = properties.getProperty("species","none"); 
        viabletime = Double.parseDouble(properties.getProperty("viabletime","86"));
        maxParticleAge = Double.parseDouble(properties.getProperty("maxParticleAge","336"));
        
        viableDegreeDays = Double.parseDouble(properties.getProperty("viableDegreeDays","-1"));
        maxDegreeDays = Double.parseDouble(properties.getProperty("maxDegreeDays","-1"));
        if (viableDegreeDays != -1)
        {
            //viabletime = viableDegreeDays*20;
            viabletime = -1;
            System.out.println("viableDegreeDays entered; set viabletime="+viabletime+" so won't be used at 56N!");
        }
        if (maxDegreeDays != -1)
        {
            //maxParticleAge = maxDegreeDays*20;
            maxParticleAge = -1;
            System.out.println("maxDegreeDays entered; set maxParticleAge="+maxParticleAge+" so won't be used at 56N!");
        }
        if ((viableDegreeDays != -1 || maxParticleAge != -1) && readHydroVelocityOnly == true)
        {
            System.err.println("readHydroVelocityOnly==true AND trying to use degree-days for development => won't develop or die!");
        }
        
        vertSwimSpeedMean = Double.parseDouble(properties.getProperty("vertSwimSpeedMean","0"));
        vertSwimSpeedStd = Double.parseDouble(properties.getProperty("vertSwimSpeedStd","0"));
                
        sinkingRateMean = Double.parseDouble(properties.getProperty("sinkingRateMean","0"));
        sinkingRateStd = Double.parseDouble(properties.getProperty("sinkingRateStd","0"));
        
        salinityThreshold = Double.parseDouble(properties.getProperty("salinityThreshold","0"));
                
        properties.list(System.out);
        
    }

}