Advance Personal Income Tax, APIT for short, is how income tax on a salary is collected in Sri Lanka. Your employer works out the tax due on each month's pay, deducts it before paying you, and sends it to the Inland Revenue Department. It is Sri Lanka's equivalent of PAYE, and the word "advance" is the point: it is tax paid during the year towards your final liability, not a separate tax.
The amount comes from tables the Inland Revenue Department publishes for each year of assessment. Table 01 covers regular monthly pay from a primary employment; other tables deal with lump sums, terminal benefits, secondary employment and non-resident employees. The tables follow the annual rates on the department's tax chart: a personal relief of 1,800,000 rupees a year, then 6% on the first 1,000,000 rupees of taxable income, 18%, 24% and 30% on each of the next three slices of 500,000, and 36% on the rest.
So a salary of 3,000,000 rupees a year leaves 1,200,000 rupees taxable after the relief. The first 1,000,000 at 6% is 60,000, and the remaining 200,000 at 18% is 36,000, a total of 96,000 rupees, or about 8,000 a month.
Table 01 takes your monthly profits from employment as its input, and this site reads that as gross remuneration. Your 8% contribution to the Employees' Provident Fund comes out of your pay but, on that reading, does not reduce the income APIT is charged on. Some payroll systems deduct it first and report less tax, which is a common source of payslip arguments.
The take-home pay calculator applies the primary employment rates to your gross salary, shows APIT and EPF as separate lines, and lists the employer's EPF and ETF contributions apart from your pay.