initialize.slim

initialize() {
    if (!exists("JSON_FILE")) {
        stop("must define JSON_FILE");
    }
    if (!exists("DRY_RUN")) {
        defineConstant("DRY_RUN", 0);
    }
    defineConstant("SCALING_FACTOR", 10.0);
    defineConstant("MUTATION_RATE", 0);
    defineConstant("RECOMBINATION_RATE", 0);
    defineConstant("CONTIG_LENGTH", 100);
    defineConstant("TREES_FILE", "/tmp/slim_out.trees");
    initializeTreeSeq();
    initializeMutationRate(SCALING_FACTOR * MUTATION_RATE);
    initializeMutationType("m1", 0.5, "f", 0.0);
    initializeGenomicElementType("g1", m1, 1.0);
    initializeGenomicElement(g1, 0, CONTIG_LENGTH - 1);
    initializeRecombinationRate((1 - (1 - 2 * RECOMBINATION_RATE)^SCALING_FACTOR) / 2);

    source("demes.slim");
}

1 {
    model = demes_load(JSON_FILE, scaling_factor=SCALING_FACTOR, burn_in=10.0);
    demes_schedule_events(model);
    g_end = model.getValue("end_time");
    sim.rescheduleScriptBlock(s1, g_end, g_end);

    if (DRY_RUN) {
        // Just print out the script blocks that are scheduled and then exit.
        for (sb in sortBy(sim.scriptBlocks, "start")) {
            if (sb.type != "initialize" & sb != self) { 
                print_scriptblock(sb);
            }
        }
        sim.scriptBlocks.active = F;
        sim.simulationFinished();
    }
}

// Output the tree sequence file at the end of the simulation.
s1 late() {
    dbg(self);  // Print the current script block as it's executed.
    sim.treeSeqOutput(TREES_FILE);
}