How to use x and width in a bar chart with scaleTime?

The problem with your question has nothing to do with programming, or JavaScript, or D3… the problem is a basic dataviz concept (that’s why I added the data-visualization tag in your question):

What you’re trying to do is not correct! You should not use bars with a time scale. Time scales are for time series (in which we use dots, or dots connected by lines).

If you use bars with time in the x axis you’ll face problems:

Positioning the bar: the left margin of the bar will be always at the date you set. The whole bar will lie after that date;
Setting the width of the bar: in a real bar chart, which uses categorical variables for the x axis, the width has no meaning. But in a time scale the width represents time.

However, just for the sake of explanation, let’s create this bar chart with a time scale (despite the fact that this is a wrong choice)… Here is how to do it:

First, set the “width” of the bars in time. Let’s say, each bar will have 10 days of width:

.attr("width", function(d){
    return x(d3.timeDay.offset(d.date, 10)) - x(d.date)
})

Then, set the x position of the bar to the current date less half its width (that is, less 5 days in our example):

.attr('x', function(d, i) {
    return x(d3.timeDay.offset(d.date, -5));
})

Finally, don’t forget to create a “padding” in the time scale:

var x = d3.scaleTime()
  .domain([d3.min(data, function(d) {
    return d3.timeDay.offset(d.date, -10);
  }), d3.max(data, function(d) {
    return d3.timeDay.offset(d.date, 10);
  })])
  .range([0, width]);

Here is your code with those changes:

var keys = [];
var legendKeys = [];

var maxVal = [];

var w = 800;
var h = 450;

var margin = {
  top: 30,
  bottom: 40,
  left: 50,
  right: 20,
};

var width = w - margin.left - margin.right;
var height = h - margin.top - margin.bottom;

var colors = ['#FF9A00', '#FFEBB6', '#FFC400', '#B4EDA0', '#FF4436'];

var data = [{
    "one": 4306,
    "two": 2465,
    "three": 2299,
    "four": 988,
    "five": 554,
    "six": 1841,
    "date": "2015-05-31T00:00:00"
  }, {
    "one": 4378,
    "two": 2457,
    "three": 2348,
    "four": 1021,
    "five": 498,
    "six": 1921,
    "date": "2015-06-30T00:00:00"
  }, {
    "one": 3404,
    "two": 2348,
    "three": 1655,
    "four": 809,
    "five": 473,
    "six": 1056,
    "date": "2015-07-31T00:00:00"
  },

];

data.forEach(function(d) {
  d.date = new Date(d.date)
})

for (var i = 0; i < data.length; i++) {
  for (var key in data[i]) {
    if (!data.hasOwnProperty(key) && key !== "date")
      maxVal.push(data[i][key]);
  }
}

var x = d3.scaleTime()
  .domain([d3.min(data, function(d) {
    return d3.timeDay.offset(d.date, -10);
  }), d3.max(data, function(d) {
    return d3.timeDay.offset(d.date, 10);
  })])
  .range([0, width]);

var y = d3.scaleLinear()
  .domain([0, d3.max(maxVal, function(d) {
    return d;
  })])
  .range([height, 0]);

var svg = d3.select('body').append('svg')
  .attr('class', 'chart')
  .attr('width', w)
  .attr('height', h);

var chart = svg.append('g')
  .classed('graph', true)
  .attr('transform', 'translate(' + margin.left + ',' + margin.top + ')');

var layersArea = chart.append('g')
  .attr('class', 'layers');


var layers = layersArea.append('g')
  .attr('class', 'layer');

layers.selectAll('rect')
  .data(data)
  .enter()
  .append('rect')

.attr('height', function(d, i) {
  return height - y(d.one);
})

.attr('y', function(d, i) {
  return y(d.one);
})

// .attr('width', function(d, i) {
//   return 50;
// })

.attr("width", function(d) {
  return x(d3.timeDay.offset(d.date, 10)) - x(d.date)
})

.attr('x', function(d, i) {
  return x(d3.timeDay.offset(d.date, -5));
})

.style('fill', (d, i) => {
  return colors[i];
});

chart.append('g')
  .classed('x axis', true)
  .attr("transform", "translate(0," + height + ")")
  .call(d3.axisBottom(x)
    .tickFormat(d3.timeFormat("%Y-%m-%d")).tickValues(data.map(function(d) {
      return new Date(d.date)
    })));

chart.append('g')
  .classed('y axis', true)
  .call(d3.axisLeft(y)
    .ticks(10));

<script src="https://d3js.org/d3.v4.min.js"></script>

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