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To whoever may have experience with this kind of problem.

I have recently encountered a problem in the 1.8.x versions of KSP in which a Mk3 spaceplane (stock + mk3 expansion) was struggling to break 300m/s with 11 tonnes stowed. When in previous 1.7.x versions the craft had little issue with a 40 tonne to orbit payload. This took some time to uncover as to why the plane lost so much performance over the update and it turns out that the stock mk3 cargo bay parts are no longer shielding any contained parts from aero forces during flight regardless of open or closed state.

Because this is a problem with broken stock parts I already contacted KSP support without thinking about how fundamentally even basic mods can change the functionality of the entire game. I still have yet to determine if this is a stock or a modded issue.
What could possibly cause stock aero shells to not perform their intended function?

989CC7D54907ED2EF6A9E112B180DF45F5DB3396

It is hard to depict just how much drag is coming from within the craft where it should not. So you may have to take my word for it when I say that the longest drag indicator is coming from a clamp-o-tron Sr just inside the MK3 tail section which is on the front of this aircraft body.

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5 hours ago, FletcherDragon said:

What could possibly cause stock aero shells to not perform their intended function?

If this happens right after rollout, I'd say you have a design mistake somewhere, so that the bay is not properly closed.

At any other time, I'm sorry... it is rather common for cargo bays to cease working once they've been open, or after the vessel has been loaded from a saved game. I'm not aware of any workaround to make them work again.

To clarify: stuff in the bay will still be shielded from reentry heat, extended antenas won't snap and so on. However, the parts inside are no longer exempt from drag calculations. I have on occasion put nosecones on cargo in the bay just because of this.

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10 hours ago, Laie said:

If this happens right after rollout, I'd say you have a design mistake somewhere

I've tried to rectify any improper node attachment as best as I could by simply rebuilding the entire aircraft from ground up. The cargo bay is pretty simple. one tail section, one long cargo bay section attached to a mk3 service bay. the problem persists.

10 hours ago, Laie said:

it is rather common for cargo bays to cease working once they've been open, or after the vessel has been loaded from a saved game.

All tests concerning this issue with my aircraft begin at the spawn of the aircraft. not loaded in-flight, not opened and/or closed during flight. 
 

10 hours ago, Laie said:

I have on occasion put nosecones on cargo in the bay just because of this.

While this is a partial solution, it kinda defeats the entire purpose of a cargo bay in the first place. Additionally, payloads I create often with KPBS are rather irregular in shape and cant be effectively shielded with a nose cone. particularly if the bay is packed, nosecones often clip with the front mk3 tail section and tend to invoke the kraken. It is not a practical solution. 

As for the rest. protecting from heat and antenne breakages. I can't tell if this does or doesn't work simply because with this severe drag problem the aircraft is so lame it has difficulty breaking the sound barrier. yet alone exiting the atmosphere.

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I have switched the root part to a core fuel tank and once again reassembled the plane making sure all nodes are attached properly and bays are closed before launch. Bug persists.
As suggested I uploaded the CRAFT to KerbalX, never heard of it before but looks pretty good. I went through the trouble of creating a payload similar in weight and function to the one which I discovered this bug with using just stock parts so the only mod needed is Mk3 expansion. Though my game does have more mods in it such as IFS, KIS, KAS, USI-LS which use other resources like B9, community resources and so on.  I'm still very novice at modding so its a rather arduous process still to make everything function together.

https://kerbalx.com/FletcherDragon/Gryphon-Type4

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15 hours ago, FletcherDragon said:

 I uploaded the CRAFT to KerbalX

and I downloaded it and see the same problem as you do.  There is an option in the alt-F12 menu under Physics: Aero: 'display aero data in menus' that lets us check if parts have zero drag, while still rolling on the runway.

If I move the Mk3 drone core forward to go between the Mk3 service module (from the mod) and the stock long Mk3 cargo bay, then the contents of the long cargo bay are properly shielded and show zero drag. 

KSP seems to think that the Mk3 service module from the MK3 Expansion mod is open.  When cargo bays are in a connected chain it requires that all of them are closed before it removes drag from the contents of any of the bays. (I don't know why they made this rule, but can guess the programmer had some good intentions, but in hindsight it seems overly complicated.)

The Mk3 service module from the mod never shields its contents, so it looks like KSP thinks it is always open.  I notice that the configuration file for that part has two entries of ModuleCargoBay, which seems strange.  (I'm not familiar with that mod myself, so won't point it out to the mod author unless and until I look into it a bit more.)

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32 minutes ago, OHara said:

.KSPseems to think that the Mk3 service module from the MK3 Expansion mod is open.  When cargo bays are in a connected chain it requires that all of them are closed before it removes drag from the contents of any of the bays. (I don't know why they made this rule, but can guess the programmer had some good intentions, but in hindsight it seems overly complicated.)

Of course, I can only guess. But I think that this was what replaced how things used to work before. At least on 1.4, that part must fit inside the cargo bay's collider to be shielded. This broke my legs more than once, as big cargo usually overruns one single cargo bay and then got drag no matter what.

This new way appears to be how they fixed that.

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1 hour ago, OHara said:

KSP seems to think that the Mk3 service module from the MK3 Expansion mod is open.

Wow it was that simple? attached to a buggy part? all this time and effort for that. I just exchanged the mk3 service bay for a mk3 service tank which is simply a configurable tank and the problem goes away. even with multiple open and close cycles of the main bay.
 

This issue never used to occur with the order I attached these parts in the past., so it is a new issue with the current version of the mod. I will bring it up with them next opportunity.

Thankyou very much for that. I cant tell you how frustrating this was. I will also update the build on kerbalX just because I love this plane so much.

Edited by FletcherDragon
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33 minutes ago, FletcherDragon said:

I will bring it up with them next opportunity.

@SuicidalInsanity, I don't know the history of this part, but experimentally I find that aero shielding works correctly, avoiding the problem with connected Mk3 cargo bays, if I patch your Mk3 service bay like this:

@PART[M3X_serviceBay] {
  !MODULE[ModuleCargoBay],1 {} // remove the duplicate MODULE
  @MODULE[ModuleCargoBay] {
    @closedPosition = 1
    @lookupRadius = 2
    !lookupCenter = delete // the default 0,0,0 is already in center of part
}}

Edit: even with the patch above, opening/closing the M3X service bay does not trigger KSP to update the shielded status of parts in connected cargo bays.  Maybe ModuleAnimateGeneric is the only door-opening module that works completely for cargo-bay doors.

Edited by OHara
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4 minutes ago, OHara said:

if I patch your Mk3 service bay like this

The service bay is inconsequential to the functionality of the craft. Rather than go digging into code which i'm just not comfortable with i'll use a solid piece even though it makes EC a little tight. The aircraft does now have its original grunt!

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