John Duke joined the Atlas on 12 May 1819. His Medical Journal began on that day. He provided a day by day entry describing weather conditions, punishments and illnesses. On 21 May 1819 prisoners were received on board. On 22nd and 25th May more were received more from Justitia hulk at Woolwich, making a total of 156 men.
On the 9 June 1819, they dropped down to Gravesend and on the 10 June 1819, got underway. They came to anchor at the Downs on 11 June 1819 and the prison and hospital were cleaned. 
Departure from England
On the 12th June 1819 they weighed anchor at 5 am. The convicts were allowed on deck in rotation and they anchored off Dungeness at 7:30. They sailed down the Channel on 18th June 1819 and on the 20th all prisoners were brought on deck for 2 hours under armed guard while the prisons were thoroughly cleaned, ventilated and fumigated. Efforts to keep the prisons well ventilated and the prisoners clean continued for the rest of the voyage under directions from surgeon Duke. 
Plan of Mutiny
On 23 June several prisoners were overheard planning to take the ship, two were handcuffed for being out of bed. At 10 am Alexander L. Hayes, Edward Mills and Jonathan White received a dozen lashes each for having broken through the prison into the hospital and having two steel saws in their possession. Prisoners were then allowed on deck only 40 at a time. 
The weather was warm on the 27 June when Madeira was sighted 16 leagues to NNW and on the 4 July when the prisoners were mustered and inspected, the island of St Antonio was sighted 8 leagues to the west. By early July the weather had turned sultry with heavy showers. These conditions continued for the next few weeks and John Duke was unable to keep the prisoners as dry as he could have wished. 
They passed the equator on 23 July, but did not observe the usual ceremony on the occasion as the heavy showers continued.
The following entry in the surgeon's journal reveals that the prisoners were defrauded of their allowances for a part of the voyage:
Prisons scraped, cleaned and ventilated. The usual number of prisoners on deck throughout the day. Windsails at each hatchway.
It was this morning discovered that Evan Griffiths a man who had been engaged to serve out the provisions to the Guard and Prisoners during the voyage has been in the habit of adulterating the wine before it was issued to the prisoners. It was proved that he first measured out four gallons of wine which he divided into two buckets but as each prisoner was allowed one gill of wine twice a week it required five gallons each issuing day to give this allowance; therefore instead of measuring off five gallons he measured off only four and to make up the deficiency he added half a gallon of water to the quantity of wine in each bucket. Have also proved that he was in the habit of adulterating the rum allowance for the guard and the manner in which he managed this discovered no less ingenuity than cunning and duplicity. As the Sergeant of the Guard attended daily and saw the proper allowance pumped from the cask it was impossible that he could openly adulterate it but he uniformly contrived to introduce the pump into the cask previously filled with water and when so fitted he pumped off the soldier's allowance. It appeared that he had been in the habit of abstracting butter, wine and rum from the casks and converting them to his own purposes. He had the dexterity to carry on these nefarious practices for a considerable time notwithstanding a certain number of the prisoners daily attended to see that they weighed their just and proper allowance. I am sorry to add that Mr. Watson the Chief Mate was implicated in these disgraceful proceedings. Griffiths was immediately dismissed from his situation and put in irons; and the Chief Mate was suspended from his duty. 
Land was sighted at daylight on 26 August and at 3 pm they anchored in Table Bay, Cape Town, where they remained until 6th September. Twelve more prisoners were taken on at the Cape. They also took on fresh meat and vegetables, however the prisoners complained of the condition of it. Although the Master of the ship and Lieutenant of the Guard declared it to be good and wholesome, still the prisoners threw some of it overboard.
Arrival in Port Jackson
On 19 October 1819 at 3 am the light on Port Jackson was sighted, and a Pilot came on board at 10 am. At 1:30 they came to anchor in Sydney Cove after a voyage of 124 days. One prisoner by the name of Solomon Hill died on the voyage.
On the 27 October, the Colonial Secretary inspected the prisoners and enquired of each if they had any grievances. Several complained that Griffiths had been withholding part of their daily allowances and the Secretary promised it would be enquired into and redressed. The following two days, the prisoners were allowed on deck as they pleased and they were issued with new clothes to land in.
After 154 days on board the Atlas, they were landed and inspected by Governor Lachlan Macquarie on the 30 October, who according to the Sydney Gazette was afterwards pleased to return a polite compliment to the Commanders and Superintendent Surgeons, requiring the acceptance of his thanks for the very fine and healthy appearance of their people.
In the usual mode of enquiry His Excellency applied to the men individually whether they had any cause of complaint as respected their treatment or allowance on the passage; but the men looked so well and hearty, and appeared to have been so very well used, as to deserve His Excellency's congratulations.
The surgeon reported that Governor Macquarie ordered the amount of daily allowance defrauded by Griffiths should be calculated and made good either in kind or in money.
Departure from the Colony
The Atlas departed Sydney on 10th January and Hobart on 2nd February bound for Madras where she arrived on 3rd April.....
April 3. Atlas, Short, from New South Wales; Sydney, 10th Jan; Hobart Town 2nd Feb. - Passengers: Lieut. Marsh 45 foot, commanding; Lieut. Ramus 30th foot; Lieut. Ashurst 34rd foot; Lieut. Wilton, 53rd foot; Lieut. Prior 46th foot; Ensign Harrison 45th; Mr Duke, surg, R.N., and Mrs. Brady with detachments of H.M. 1st,46 and 89th regiments. 
The Atlas was wrecked near India on 9th May 1820 .- On the forenoon of May the 9th, 1820, the ship riding heavy, and the sea breaking with great force over her, hove gears overboard ; she then parted from her small bower cable and being observed to be drifting fast on shore, owing to the breakers, slipt her chain cable, and put to sea under the storm stay sails, which were instantly blown to pieces ; the ship at the same time falling upon her beam ends. It was then found necessary to cut away the mizen-mast in hopes of her righting, which carried away both her quarter-boat wheels, binnacle, and nearly one third of the round-house. At half-past 3 p. m. the main mast went with a heavy crash, close by the board; the ship still righted, but would not wear ; the main-mast, in falling, disabled the lee pumps, and tore away the planks in the wake of the channel bolts, which occasioned her to leak considerably. It now blew a hurricane ; the ship, being entirely upon her beam ends, was quite unmanageable. At 5 P. M. experienced a sudden shift of wind to the S. W. and found the ship drifting fast towards Ponlieat Shoal.
At half-past 11 P. M. the ship struck, with a heavy crash, amongst the breakers on Poulicat Sands; immediately cut way the foremast, she being inclined to swing broadside on the water, which, at that time, was rising as high as her main deck beams. At 1 A. M. the ship, being struck with a heavy sea, parted in two, in the wake of the mizen chains ; the crew endeavouring to save themselves, upon the quarter deck ; which at about two A. M. separated from her lower works and was drove by the breakers towards the shore; the crew closely clinging to it, as their only resource At about half past 3 it struck the beach ; and, upon mustering the crew found five deficient ; viz. two men and one boy (European), and two natives. The Commander, Officers, and crew, return their most sincere thanks to Dr. Bronnickam, resident at Poulicat, for his attention towards them in their then helpless state ; and take this opportunity of paying the public tribute of gratitude, which they consider so justly due to his humanity, and the hospitable manner in which they were received and treated by that Gentleman 
4). Edward Smith, born in Tipperary and a teacher of languages was tried at the Old Bailey on 2nd December 1818 for pocketpicking. He was 30 years of age and was sentenced to transportation for life. (Old Bailey Online). On arrival he was assigned to Mr. Eyre at Parramatta as a Clerk. He was assigned to William Lawson at Prospect in 1822
5). William Chadwick was transported on the Atlas - On Saturday and Sunday nights last, the following convicts left our County Gaol, for Sheerness and Woolwich preparatory to being shipped for New South Wales: Thomas Walton, Joseph Walton, Robert Chorlton, Peter Blackshaw, Thomas Mellor, William Birkin, Robert Roberts, Thomas Forrester, William Dormody, John Stretch, for Sheerness...- William Chadwick, Isaac White, Robert Joule, Thomas Bingham, Samuel Kenrick, Peter Hardy, John Johnson, James Smith and John Smith for Woolwich. - (Chester Chronicle and Cheshire and North Wales General Advertiser. 14 May 1819.). He was tried at Chester 12 April 1819 for larceny and sentenced to 14 years transportation. William Chadwick was admitted to the Justitia Hulk on 10th May 1819 . On arrival in NSW William Chadwick was assigned to Lieutenant Lawson at Bathurst, to be employed as Surgeon in the Bathurst district. (Colonial Secretary's Correspondence). He absconded from Bathurst in August 1820 and in 1824 was posted as having absconded from Patrick Sheals gang at Rooty Hill.
6). The twelve convicts embarked at the Cape of Good Hope were:
Pierre Moussiee. Calling Tailor
Joseph Lafleur. Native Place Nantz. Calling Tailor
John Cockross/ Cobcroft. Native Place Manchester. Calling Painter
John Holland. Native Place Carlow. Calling Bricklayer
John Morrow. Native Place Co. Derry. Calling Labourer
Edward Rawlings Native Place Reading. Calling Seaman
Michael Coogan. Native Place Gloucestershire. Calling Clerk
William Hitchcock, Native Place Lincolnshire. Calling Stone cutter
John Singleton. Native Place Yorkshire. Calling Stone Cutter
William Parkins. Native Place Essex. Calling Stone Cutter
Thomas Maddin. Native Place Longford. Calling Soldier
Albert Wynyard Louw. Calling Blacksmith