<?php
    $username = "*****";
    $password = "******";
    $host = "localhost";
    $database="db";

    $server = mysql_connect($host, $username, $password);
    $connection = mysql_select_db($database, $server);

    $myquery = "
SELECT  `this`, `that` FROM  `table`
";
    $query = mysql_query($myquery);

    if ( ! $query ) {
        echo mysql_error();
        die;
    }

    $data = array();

    for ($x = 0; $x < mysql_num_rows($query); $x++) {
        $data[] = mysql_fetch_assoc($query);
    }

    $fp = fopen('empdata.json', 'w');
    fwrite($fp, json_encode($data));
    fclose($fp);

    mysql_close($server);
?>

d3.json("mypreviouslygeneratedjson.json", function (error, data) {

    data.forEach(function (d)
    {
        ...
    }

echo json_encode($data);