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Yeah, I that value should just be the hard cap on breakthroughs that can be researched. I'm guessing when at 0 it went all buggy because the game expects you to research some breakthrough techs. Also, if you want more breakthrough anomalies on the map I can put that in the mod also. I just quickly put together the mod for you now and I will be adding stuff to it as updates later on. I don't know if I will change how many breakthrough's you get by scanning the map though. I will probably implement a way to get more breakthroughs for mid game and late game as I don't want people having a bunch of breakthrough's early on. I have already implemented a way to get breakthroughs late game by simply having one of the wonders unlock more breakthroughs.

const.BreakThroughTechsPerGame is used only once: To set a variable which is used to determine the number of breakthrough anomalies that are spawned. That number is then added with BonusCountBreakthrough for final number of breakthrough anomalies. BonusCountBreakthrough is set from a sponsor/commander variable:
Code:
'anomaly_bonus_breakthrough', range(min, max),

Also getting a bunch of breakthrough tech unlocks early isn't a problem since the research costs increase so dramatically.

EDIT: const.BreakThroughTechsPerGame is used only in random maps. I'm not still not 100% on when a map is random vs non random but I think non-random is any named map area, IE Viking 1 Landing Area, while random is any "Colony Site" map.
 
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const.BreakThroughTechsPerGame is used only once: To set a variable which is used to determine the number of breakthrough anomalies that are spawned. That number is then added with BonusCountBreakthrough for final number of breakthrough anomalies. BonusCountBreakthrough is set from a sponsor/commander variable:
Code:
'anomaly_bonus_breakthrough', range(min, max),

Also getting a bunch of breakthrough tech unlocks early isn't a problem since the research costs increase so dramatically.

EDIT: const.BreakThroughTechsPerGame is used only in random maps. I'm not still not 100% on when a map is random vs nonrandom but I think non-random is any named map area, IE Viking 1 Landing Area, while random is any "Colony Site" map.

Thanks for the info. Myself and the OP are working on looking into all of this in great detail. The mod that I made is just the framework for now, and we will be building upon it in the near future. Any other info you come across would be highly useful if you can post it in here. Again, thank you for the info.
 
I made a mod that disabled breathroughs alltogether.
the anomalies are still there but the effect of them is changed. you could use the same code and just have a different trigger for it. for example having more than 4 breakthrough techs unlocked locks changes the effect of the anomalies. so the only way to get more breakthroughs would be building the omega telescope then, restircting it to 7 total

http://steamcommunity.com/sharedfiles/filedetails/?id=1340547177