For everyone familiar with Warhammer 40k the input should be self explaining. The highlighted area is where you fill in the stats of you units and weapons. The left column is for the attacking unit, the right column for the defending unit. You may use values like D6 or 2D3 in the fields for "Shots", "AP" and "D". This input type of input is not supported by the other fields.
If your unit has any ability that allows to perform re-rolls this can be chosen from the drop-down menus. Also rules that allow the attacker to cause mortal wounds on specific wound rolls can be chosen from a drop down menu.
ProbHammer simulates a large number of dice rolls to calculate the probability distribution. You can choose how many of those simulation runs ProbHammer should use. If you see that the result changes alot from one simulation to the next, even if you don't change the parameters, you should choose the next higher number of simulations from the "# Simulations" drop down menu. Usually 100.000 simulations should be enough for every possible case. Depending on your platform the number of simulations affects the computation time needed to finish the simulation.
If you want to see the probability of slain models instead of the caused wounds you need to check "Plot Slain Models".
The upper bar graph shows the probability to cause a minimum of X wounds. Where X is the corresponding value on the x-axis. For example: If the bar for 4 wounds has a height of 70%, you have a 70% chance to cause 4 or more wounds.
The bottom bar graph show shows the probability to cause a specific number of wounds. For example: If the bar for 6 wounds has a height of 12%, the probability to cause exactly 6 wounds is 12%.
As an overview also some average values are plotted on the left side of the upper bar plot. There you see average values of each combat stage. Like the number of successful hit rolls, wound rolls or the number of saved wounds and even the average number of mortal wounds. The last value is the average value of lost wounds or slain models depending if you put a checkmark at "Plot Slain Models". This is the average value of the probability functions shown in the bar graphs.
If you want to save a simulation result for later comparison you need to type a name next to the save result button then press "Save Result". The simulation will them be shown in the list below. After you added at least two simulations to the result list you can select the ones you would like to compare, then press "Compare Selected". The bar graph will then update to show the selected simulations. A legend for the graph will be displayed in the top right corner. Should the graph not update properly try to click "Compare Selected" again. This is a known bug which will be resolved soon.