cleanup java side somewhat

src/main/c/fluidsim.c

@@ -3,6 +3,7 @@
 #include "includes/utilities.h"
 #include "includes/chunkmask.h"
 #include "includes/electrosphere_FluidSim.h"
+#include "includes/mainFunctions.h"
 
 #define DIM 18
 #define LINEARSOLVERTIMES 20

src/main/c/includes/electrosphere_FluidSim.h

@@ -17,102 +17,6 @@ extern "C" {
 #define electrosphere_FluidSim_LINEARSOLVERTIMES 20L
 #undef electrosphere_FluidSim_GRAVITY
 #define electrosphere_FluidSim_GRAVITY -100.0f
-/*
- * Class:     electrosphere_FluidSim
- * Method:    calculateChunkMask
- * Signature: ([Ljava/nio/ByteBuffer;)I
- */
-JNIEXPORT jint JNICALL Java_electrosphere_FluidSim_calculateChunkMask
-  (JNIEnv *, jobject, jobjectArray);
-
-/*
- * Class:     electrosphere_FluidSim
- * Method:    addSourceToVectors
- * Signature: (II[Ljava/nio/ByteBuffer;[Ljava/nio/ByteBuffer;[Ljava/nio/ByteBuffer;[Ljava/nio/ByteBuffer;[Ljava/nio/ByteBuffer;[Ljava/nio/ByteBuffer;FFF)V
- */
-JNIEXPORT void JNICALL Java_electrosphere_FluidSim_addSourceToVectors
-  (JNIEnv *, jobject, jint, jint, jobjectArray, jobjectArray, jobjectArray, jobjectArray, jobjectArray, jobjectArray, jfloat, jfloat, jfloat);
-
-/*
- * Class:     electrosphere_FluidSim
- * Method:    solveVectorDiffuse
- * Signature: (II[Ljava/nio/ByteBuffer;[Ljava/nio/ByteBuffer;[Ljava/nio/ByteBuffer;[Ljava/nio/ByteBuffer;[Ljava/nio/ByteBuffer;[Ljava/nio/ByteBuffer;FFF)V
- */
-JNIEXPORT void JNICALL Java_electrosphere_FluidSim_solveVectorDiffuse
-  (JNIEnv *, jobject, jint, jint, jobjectArray, jobjectArray, jobjectArray, jobjectArray, jobjectArray, jobjectArray, jfloat, jfloat, jfloat);
-
-/*
- * Class:     electrosphere_FluidSim
- * Method:    setupProjection
- * Signature: (II[Ljava/nio/ByteBuffer;[Ljava/nio/ByteBuffer;[Ljava/nio/ByteBuffer;[Ljava/nio/ByteBuffer;[Ljava/nio/ByteBuffer;[Ljava/nio/ByteBuffer;FFF)V
- */
-JNIEXPORT void JNICALL Java_electrosphere_FluidSim_setupProjection
-  (JNIEnv *, jobject, jint, jint, jobjectArray, jobjectArray, jobjectArray, jobjectArray, jobjectArray, jobjectArray, jfloat, jfloat, jfloat);
-
-/*
- * Class:     electrosphere_FluidSim
- * Method:    solveProjection
- * Signature: (II[Ljava/nio/ByteBuffer;[Ljava/nio/ByteBuffer;[Ljava/nio/ByteBuffer;[Ljava/nio/ByteBuffer;[Ljava/nio/ByteBuffer;[Ljava/nio/ByteBuffer;FFF)V
- */
-JNIEXPORT void JNICALL Java_electrosphere_FluidSim_solveProjection
-  (JNIEnv *, jobject, jint, jint, jobjectArray, jobjectArray, jobjectArray, jobjectArray, jobjectArray, jobjectArray, jfloat, jfloat, jfloat);
-
-/*
- * Class:     electrosphere_FluidSim
- * Method:    finalizeProjection
- * Signature: (II[Ljava/nio/ByteBuffer;[Ljava/nio/ByteBuffer;[Ljava/nio/ByteBuffer;[Ljava/nio/ByteBuffer;[Ljava/nio/ByteBuffer;[Ljava/nio/ByteBuffer;FFF)V
- */
-JNIEXPORT void JNICALL Java_electrosphere_FluidSim_finalizeProjection
-  (JNIEnv *, jobject, jint, jint, jobjectArray, jobjectArray, jobjectArray, jobjectArray, jobjectArray, jobjectArray, jfloat, jfloat, jfloat);
-
-/*
- * Class:     electrosphere_FluidSim
- * Method:    advectVectors
- * Signature: (II[Ljava/nio/ByteBuffer;[Ljava/nio/ByteBuffer;[Ljava/nio/ByteBuffer;[Ljava/nio/ByteBuffer;[Ljava/nio/ByteBuffer;[Ljava/nio/ByteBuffer;FFF)V
- */
-JNIEXPORT void JNICALL Java_electrosphere_FluidSim_advectVectors
-  (JNIEnv *, jobject, jint, jint, jobjectArray, jobjectArray, jobjectArray, jobjectArray, jobjectArray, jobjectArray, jfloat, jfloat, jfloat);
-
-/*
- * Class:     electrosphere_FluidSim
- * Method:    addDensity
- * Signature: (II[Ljava/nio/ByteBuffer;[Ljava/nio/ByteBuffer;F)V
- */
-JNIEXPORT void JNICALL Java_electrosphere_FluidSim_addDensity
-  (JNIEnv *, jobject, jint, jint, jobjectArray, jobjectArray, jfloat);
-
-/*
- * Class:     electrosphere_FluidSim
- * Method:    solveDiffuseDensity
- * Signature: (II[Ljava/nio/ByteBuffer;[Ljava/nio/ByteBuffer;[Ljava/nio/ByteBuffer;[Ljava/nio/ByteBuffer;[Ljava/nio/ByteBuffer;FFF)V
- */
-JNIEXPORT void JNICALL Java_electrosphere_FluidSim_solveDiffuseDensity
-  (JNIEnv *, jobject, jint, jint, jobjectArray, jobjectArray, jobjectArray, jobjectArray, jobjectArray, jfloat, jfloat, jfloat);
-
-/*
- * Class:     electrosphere_FluidSim
- * Method:    advectDensity
- * Signature: (II[Ljava/nio/ByteBuffer;[Ljava/nio/ByteBuffer;[Ljava/nio/ByteBuffer;[Ljava/nio/ByteBuffer;[Ljava/nio/ByteBuffer;FFF)V
- */
-JNIEXPORT void JNICALL Java_electrosphere_FluidSim_advectDensity
-  (JNIEnv *, jobject, jint, jint, jobjectArray, jobjectArray, jobjectArray, jobjectArray, jobjectArray, jfloat, jfloat, jfloat);
-
-/*
- * Class:     electrosphere_FluidSim
- * Method:    setBoundsToNeighbors
- * Signature: (III[Ljava/nio/ByteBuffer;)V
- */
-JNIEXPORT void JNICALL Java_electrosphere_FluidSim_setBoundsToNeighbors
-  (JNIEnv *, jobject, jint, jint, jint, jobjectArray);
-
-/*
- * Class:     electrosphere_FluidSim
- * Method:    copyNeighbors
- * Signature: (IIII[Ljava/nio/ByteBuffer;)V
- */
-JNIEXPORT void JNICALL Java_electrosphere_FluidSim_copyNeighbors
-  (JNIEnv *, jobject, jint, jint, jint, jint, jobjectArray);
-
 /*
  * Class:     electrosphere_FluidSim
  * Method:    simulate

src/main/c/includes/mainFunctions.h

@@ -0,0 +1,102 @@
+#ifndef MAINFUNC
+#define MAINFUNC
+
+#include <jni.h>
+
+/*
+ * Class:     electrosphere_FluidSim
+ * Method:    calculateChunkMask
+ * Signature: ([Ljava/nio/ByteBuffer;)I
+ */
+JNIEXPORT jint JNICALL Java_electrosphere_FluidSim_calculateChunkMask
+  (JNIEnv *, jobject, jobjectArray);
+
+/*
+ * Class:     electrosphere_FluidSim
+ * Method:    addSourceToVectors
+ * Signature: (II[Ljava/nio/ByteBuffer;[Ljava/nio/ByteBuffer;[Ljava/nio/ByteBuffer;[Ljava/nio/ByteBuffer;[Ljava/nio/ByteBuffer;[Ljava/nio/ByteBuffer;FFF)V
+ */
+JNIEXPORT void JNICALL Java_electrosphere_FluidSim_addSourceToVectors
+  (JNIEnv *, jobject, jint, jint, jobjectArray, jobjectArray, jobjectArray, jobjectArray, jobjectArray, jobjectArray, jfloat, jfloat, jfloat);
+
+/*
+ * Class:     electrosphere_FluidSim
+ * Method:    solveVectorDiffuse
+ * Signature: (II[Ljava/nio/ByteBuffer;[Ljava/nio/ByteBuffer;[Ljava/nio/ByteBuffer;[Ljava/nio/ByteBuffer;[Ljava/nio/ByteBuffer;[Ljava/nio/ByteBuffer;FFF)V
+ */
+JNIEXPORT void JNICALL Java_electrosphere_FluidSim_solveVectorDiffuse
+  (JNIEnv *, jobject, jint, jint, jobjectArray, jobjectArray, jobjectArray, jobjectArray, jobjectArray, jobjectArray, jfloat, jfloat, jfloat);
+
+/*
+ * Class:     electrosphere_FluidSim
+ * Method:    setupProjection
+ * Signature: (II[Ljava/nio/ByteBuffer;[Ljava/nio/ByteBuffer;[Ljava/nio/ByteBuffer;[Ljava/nio/ByteBuffer;[Ljava/nio/ByteBuffer;[Ljava/nio/ByteBuffer;FFF)V
+ */
+JNIEXPORT void JNICALL Java_electrosphere_FluidSim_setupProjection
+  (JNIEnv *, jobject, jint, jint, jobjectArray, jobjectArray, jobjectArray, jobjectArray, jobjectArray, jobjectArray, jfloat, jfloat, jfloat);
+
+/*
+ * Class:     electrosphere_FluidSim
+ * Method:    solveProjection
+ * Signature: (II[Ljava/nio/ByteBuffer;[Ljava/nio/ByteBuffer;[Ljava/nio/ByteBuffer;[Ljava/nio/ByteBuffer;[Ljava/nio/ByteBuffer;[Ljava/nio/ByteBuffer;FFF)V
+ */
+JNIEXPORT void JNICALL Java_electrosphere_FluidSim_solveProjection
+  (JNIEnv *, jobject, jint, jint, jobjectArray, jobjectArray, jobjectArray, jobjectArray, jobjectArray, jobjectArray, jfloat, jfloat, jfloat);
+
+/*
+ * Class:     electrosphere_FluidSim
+ * Method:    finalizeProjection
+ * Signature: (II[Ljava/nio/ByteBuffer;[Ljava/nio/ByteBuffer;[Ljava/nio/ByteBuffer;[Ljava/nio/ByteBuffer;[Ljava/nio/ByteBuffer;[Ljava/nio/ByteBuffer;FFF)V
+ */
+JNIEXPORT void JNICALL Java_electrosphere_FluidSim_finalizeProjection
+  (JNIEnv *, jobject, jint, jint, jobjectArray, jobjectArray, jobjectArray, jobjectArray, jobjectArray, jobjectArray, jfloat, jfloat, jfloat);
+
+/*
+ * Class:     electrosphere_FluidSim
+ * Method:    advectVectors
+ * Signature: (II[Ljava/nio/ByteBuffer;[Ljava/nio/ByteBuffer;[Ljava/nio/ByteBuffer;[Ljava/nio/ByteBuffer;[Ljava/nio/ByteBuffer;[Ljava/nio/ByteBuffer;FFF)V
+ */
+JNIEXPORT void JNICALL Java_electrosphere_FluidSim_advectVectors
+  (JNIEnv *, jobject, jint, jint, jobjectArray, jobjectArray, jobjectArray, jobjectArray, jobjectArray, jobjectArray, jfloat, jfloat, jfloat);
+
+/*
+ * Class:     electrosphere_FluidSim
+ * Method:    addDensity
+ * Signature: (II[Ljava/nio/ByteBuffer;[Ljava/nio/ByteBuffer;F)V
+ */
+JNIEXPORT void JNICALL Java_electrosphere_FluidSim_addDensity
+  (JNIEnv *, jobject, jint, jint, jobjectArray, jobjectArray, jfloat);
+
+/*
+ * Class:     electrosphere_FluidSim
+ * Method:    solveDiffuseDensity
+ * Signature: (II[Ljava/nio/ByteBuffer;[Ljava/nio/ByteBuffer;[Ljava/nio/ByteBuffer;[Ljava/nio/ByteBuffer;[Ljava/nio/ByteBuffer;FFF)V
+ */
+JNIEXPORT void JNICALL Java_electrosphere_FluidSim_solveDiffuseDensity
+  (JNIEnv *, jobject, jint, jint, jobjectArray, jobjectArray, jobjectArray, jobjectArray, jobjectArray, jfloat, jfloat, jfloat);
+
+/*
+ * Class:     electrosphere_FluidSim
+ * Method:    advectDensity
+ * Signature: (II[Ljava/nio/ByteBuffer;[Ljava/nio/ByteBuffer;[Ljava/nio/ByteBuffer;[Ljava/nio/ByteBuffer;[Ljava/nio/ByteBuffer;FFF)V
+ */
+JNIEXPORT void JNICALL Java_electrosphere_FluidSim_advectDensity
+  (JNIEnv *, jobject, jint, jint, jobjectArray, jobjectArray, jobjectArray, jobjectArray, jobjectArray, jfloat, jfloat, jfloat);
+
+/*
+ * Class:     electrosphere_FluidSim
+ * Method:    setBoundsToNeighbors
+ * Signature: (III[Ljava/nio/ByteBuffer;)V
+ */
+JNIEXPORT void JNICALL Java_electrosphere_FluidSim_setBoundsToNeighbors
+  (JNIEnv *, jobject, jint, jint, jint, jobjectArray);
+
+/*
+ * Class:     electrosphere_FluidSim
+ * Method:    copyNeighbors
+ * Signature: (IIII[Ljava/nio/ByteBuffer;)V
+ */
+JNIEXPORT void JNICALL Java_electrosphere_FluidSim_copyNeighbors
+  (JNIEnv *, jobject, jint, jint, jint, jint, jobjectArray);
+
+#endif

src/main/java/electrosphere/FluidSim.java

@@ -184,25 +184,9 @@ public class FluidSim {
 
         lastTime = GLFW.glfwGetTime();
         //
-        //Vector stage
+        //simulate
         simulateWrapper(chunksToSim,timestep);
-        // solveChunkMask(simArray);
+        //clock
-        // addVectorSources(simArray, timestep);
-        // swapAllVectorFields(simArray, timestep);
-        // solveVectorDiffusion(simArray, timestep);
-        // solveProjection(simArray, step, timestep);
-        // swapAllVectorFields(simArray, timestep);
-        // advectVectorsAcrossBoundaries(simArray, timestep);
-        // solveProjection(simArray, step, timestep);
-
-        //
-        //Density stage
-        // addDensity(simArray, timestep);
-        // swapAllDensityArrays(simArray, timestep);
-        // diffuseDensity(simArray, timestep);
-        // swapAllDensityArrays(simArray, timestep);
-        // advectDensity(simArray, timestep);
-        // mirrorNeighborDensities(simArray, timestep);
         time = time + (GLFW.glfwGetTime() - lastTime);
         i++;
         if(i == 100){
@@ -350,524 +334,6 @@ public class FluidSim {
         return rVal;
     }
 
-    private static void solveChunkMask(FluidSim[][][] simArray){
-        for(int x = 0; x < simArray.length; x++){
-            for(int y = 0; y < simArray[0].length; y++){
-                for(int z = 0; z < simArray[0][0].length; z++){
-                    simArray[x][y][z].calculateChunkMaskWrapper();
-                }
-            }
-        }
-    }
-
-    private static void addVectorSources(FluidSim[][][] simArray, float timestep){
-        for(int x = 0; x < simArray.length; x++){
-            for(int y = 0; y < simArray[0].length; y++){
-                for(int z = 0; z < simArray[0][0].length; z++){
-
-                    //Add source to all 3 vectors
-                    // add_source(N, u, u0, dt);
-                    // add_source(N, v, v0, dt);
-                    // add_source(N, w, w0, dt);
-                    simArray[x][y][z].addSourceToVectorsWrapper(timestep);
-                }
-            }
-        }
-        //swap
-        //u <=> u0 etc for u, v, and w
-        
-    }
-
-    private static void solveVectorDiffusion(FluidSim[][][] simArray, float timestep){
-        //samples u,v,w,u0,v0,w0
-        //sets u,v,w
-        // for(int x = 0; x < simArray.length; x++){
-        //     for(int y = 0; y < simArray[0].length; y++){
-        //         for(int z = 0; z < simArray[0][0].length; z++){
-        //             simArray[x][y][z].copyNeighborsWrapper(1, simArray[x][y][z].uVector);
-        //             simArray[x][y][z].copyNeighborsWrapper(2, simArray[x][y][z].vVector);
-        //             simArray[x][y][z].copyNeighborsWrapper(3, simArray[x][y][z].wVector);
-        //             simArray[x][y][z].copyNeighborsWrapper(1, simArray[x][y][z].uAdditionVector);
-        //             simArray[x][y][z].copyNeighborsWrapper(2, simArray[x][y][z].vAdditionVector);
-        //             simArray[x][y][z].copyNeighborsWrapper(3, simArray[x][y][z].wAdditionVector);
-        //         }
-        //     }
-        // }
-        for(int l = 0; l < LINEARSOLVERTIMES; l++){
-            for(int x = 0; x < simArray.length; x++){
-                for(int y = 0; y < simArray[0].length; y++){
-                    for(int z = 0; z < simArray[0][0].length; z++){
-                        //lin_solve(env, chunk_mask, N, b, x, x0, a, 1+6*a);
-                        //+
-                        //set_bnd(env, chunk_mask, N, b, x);
-                        //for u, v, and w all in 1 shot
-                        simArray[x][y][z].solveVectorDiffuseWrapper(timestep);
-                    }
-                }
-            }
-            for(int x = 0; x < simArray.length; x++){
-                for(int y = 0; y < simArray[0].length; y++){
-                    for(int z = 0; z < simArray[0][0].length; z++){
-                        simArray[x][y][z].setBoundsToNeighborsWrapper(1, simArray[x][y][z].uVector);
-                        simArray[x][y][z].setBoundsToNeighborsWrapper(2, simArray[x][y][z].vVector);
-                        simArray[x][y][z].setBoundsToNeighborsWrapper(3, simArray[x][y][z].wVector);
-                        simArray[x][y][z].copyNeighborsWrapper(1, x, simArray[x][y][z].uVector);
-                        simArray[x][y][z].copyNeighborsWrapper(2, x, simArray[x][y][z].vVector);
-                        simArray[x][y][z].copyNeighborsWrapper(3, x, simArray[x][y][z].wVector);
-                    }
-                }
-            }
-        }
-    }
-
-    private static void solveProjection(FluidSim[][][] simArray, int step, float timestep){
-        //samples u,v,w
-        //sets u0,v0
-        for(int x = 0; x < simArray.length; x++){
-            for(int y = 0; y < simArray[0].length; y++){
-                for(int z = 0; z < simArray[0][0].length; z++){
-                    simArray[x][y][z].setBoundsToNeighborsWrapper(1, simArray[x][y][z].uVector);
-                    simArray[x][y][z].setBoundsToNeighborsWrapper(2, simArray[x][y][z].vVector);
-                    simArray[x][y][z].setBoundsToNeighborsWrapper(3, simArray[x][y][z].wVector);
-                    simArray[x][y][z].setBoundsToNeighborsWrapper(1, simArray[x][y][z].uAdditionVector);
-                    simArray[x][y][z].setBoundsToNeighborsWrapper(2, simArray[x][y][z].vAdditionVector);
-                    simArray[x][y][z].copyNeighborsWrapper(1, x, simArray[x][y][z].uVector);
-                    simArray[x][y][z].copyNeighborsWrapper(2, x, simArray[x][y][z].vVector);
-                    simArray[x][y][z].copyNeighborsWrapper(3, x, simArray[x][y][z].wVector);
-                    simArray[x][y][z].copyNeighborsWrapper(1, x, simArray[x][y][z].uAdditionVector);
-                    simArray[x][y][z].copyNeighborsWrapper(2, x, simArray[x][y][z].vAdditionVector);
-                }
-            }
-        }
-        for(int x = 0; x < simArray.length; x++){
-            for(int y = 0; y < simArray[0].length; y++){
-                for(int z = 0; z < simArray[0][0].length; z++){
-                    // System.out.println("Setup " + x + " " +  y + " " + z);
-                    //setup projection across boundaries
-                    //...
-                    //set boundaries appropriately
-                    //...
-                    simArray[x][y][z].setupProjectionWrapper(timestep);
-                }
-            }
-        }
-        for(int x = 0; x < simArray.length; x++){
-            for(int y = 0; y < simArray[0].length; y++){
-                for(int z = 0; z < simArray[0][0].length; z++){
-                    simArray[x][y][z].setBoundsToNeighborsWrapper(0, simArray[x][y][z].uAdditionVector);
-                    simArray[x][y][z].setBoundsToNeighborsWrapper(0, simArray[x][y][z].vAdditionVector);
-                    simArray[x][y][z].copyNeighborsWrapper(0, x, simArray[x][y][z].uAdditionVector);
-                    simArray[x][y][z].copyNeighborsWrapper(0, x, simArray[x][y][z].vAdditionVector);
-                }
-            }
-        }
-        //samples u0, v0
-        //sets u0
-        //these should have just been mirrored in the above
-        //
-        //Perform main projection solver
-        for(int l = 0; l < LINEARSOLVERTIMES; l++){
-            for(int x = 0; x < simArray.length; x++){
-                for(int y = 0; y < simArray[0].length; y++){
-                    for(int z = 0; z < simArray[0][0].length; z++){
-                        //lin_solve(env, chunk_mask, N, b, x, x0, a, 1+6*a);
-                        //for u, v, and w all in 1 shot
-                        simArray[x][y][z].solveProjectionWrapper(timestep);
-                    }
-                }
-            }
-            //be sure to set boundaries to neighbor chunk values where appropriate
-            for(int x = 0; x < simArray.length; x++){
-                for(int y = 0; y < simArray[0].length; y++){
-                    for(int z = 0; z < simArray[0][0].length; z++){
-                        simArray[x][y][z].setBoundsToNeighborsWrapper(0, simArray[x][y][z].uAdditionVector);
-                        simArray[x][y][z].copyNeighborsWrapper(0, x, simArray[x][y][z].uAdditionVector);
-                    }
-                }
-            }
-        }
-        //samples u,v,w,u0
-        //sets u,v,w
-        //Finalize projection
-        for(int x = 0; x < simArray.length; x++){
-            for(int y = 0; y < simArray[0].length; y++){
-                for(int z = 0; z < simArray[0][0].length; z++){
-                    //Subtract curl field from current vector field
-                    //...
-                    simArray[x][y][z].finalizeProjectionWrapper(timestep);
-                }
-            }
-        }
-        //set boundaries a final time for u,v,w
-        //...
-        for(int x = 0; x < simArray.length; x++){
-            for(int y = 0; y < simArray[0].length; y++){
-                for(int z = 0; z < simArray[0][0].length; z++){
-                    simArray[x][y][z].setBoundsToNeighborsWrapper(1, simArray[x][y][z].uVector);
-                    simArray[x][y][z].setBoundsToNeighborsWrapper(2, simArray[x][y][z].vVector);
-                    simArray[x][y][z].setBoundsToNeighborsWrapper(3, simArray[x][y][z].wVector);
-                    simArray[x][y][z].copyNeighborsWrapper(1, x, simArray[x][y][z].uVector);
-                    simArray[x][y][z].copyNeighborsWrapper(2, x, simArray[x][y][z].vVector);
-                    simArray[x][y][z].copyNeighborsWrapper(3, x, simArray[x][y][z].wVector);
-                    simArray[x][y][z].setBoundsToNeighborsWrapper(1, simArray[x][y][z].uAdditionVector);
-                    simArray[x][y][z].setBoundsToNeighborsWrapper(2, simArray[x][y][z].vAdditionVector);
-                    simArray[x][y][z].setBoundsToNeighborsWrapper(3, simArray[x][y][z].wAdditionVector);
-                    simArray[x][y][z].copyNeighborsWrapper(0, x, simArray[x][y][z].uAdditionVector);
-                    simArray[x][y][z].copyNeighborsWrapper(0, x, simArray[x][y][z].vAdditionVector);
-                    simArray[x][y][z].copyNeighborsWrapper(0, x, simArray[x][y][z].wAdditionVector);
-                }
-            }
-        }
-    }
-
-    private static void mirrorNeighborDensities(FluidSim[][][] simArray, float timestep){
-        for(int x = 0; x < simArray.length; x++){
-            for(int y = 0; y < simArray[0].length; y++){
-                for(int z = 0; z < simArray[0][0].length; z++){
-                    simArray[x][y][z].setBoundsToNeighborsWrapper(0, simArray[x][y][z].density);
-                }
-            }
-        }
-    }
-
-    private static void swapAllVectorFields(FluidSim[][][] simArray, float timestep){
-        for(int x = 0; x < simArray.length; x++){
-            for(int y = 0; y < simArray[0].length; y++){
-                for(int z = 0; z < simArray[0][0].length; z++){
-                    simArray[x][y][z].swapVectorFields();
-                }
-            }
-        }
-        //then need to mirror each array as relevant
-        for(int x = 0; x < simArray.length; x++){
-            for(int y = 0; y < simArray[0].length; y++){
-                for(int z = 0; z < simArray[0][0].length; z++){
-                    simArray[x][y][z].copyNeighborsWrapper(1, x, simArray[x][y][z].uVector);
-                    simArray[x][y][z].copyNeighborsWrapper(2, x, simArray[x][y][z].vVector);
-                    simArray[x][y][z].copyNeighborsWrapper(3, x, simArray[x][y][z].wVector);
-                    simArray[x][y][z].copyNeighborsWrapper(1, x, simArray[x][y][z].uAdditionVector);
-                    simArray[x][y][z].copyNeighborsWrapper(2, x, simArray[x][y][z].vAdditionVector);
-                    simArray[x][y][z].copyNeighborsWrapper(2, x, simArray[x][y][z].wAdditionVector);
-                }
-            }
-        }
-    }
-
-    private void swapVectorFields(){
-        ByteBuffer tmp;
-        //swap x0 <-> x
-        // tmp = densityAddition;
-        // densityAddition = density[13];
-        // density[13] = tmp;
-        //swap u0 <-> u
-        for(int i = 0; i < 27; i++){
-            tmp = uAdditionVector[i];
-            uAdditionVector[i] = uVector[i];
-            uVector[i] = tmp;
-            //swap v0 <-> v
-            tmp = vAdditionVector[i];
-            vAdditionVector[i] = vVector[i];
-            vVector[i] = tmp;
-            //swap w0 <-> w
-            tmp = wAdditionVector[i];
-            wAdditionVector[i] = wVector[i];
-            wVector[i] = tmp;
-        }
-        //...
-    }
-
-    private static void advectVectorsAcrossBoundaries(FluidSim[][][] simArray, float timestep){
-        for(int x = 0; x < simArray.length; x++){
-            for(int y = 0; y < simArray[0].length; y++){
-                for(int z = 0; z < simArray[0][0].length; z++){
-                    simArray[x][y][z].setBoundsToNeighborsWrapper(1, simArray[x][y][z].uVector);
-                    simArray[x][y][z].setBoundsToNeighborsWrapper(2, simArray[x][y][z].vVector);
-                    simArray[x][y][z].setBoundsToNeighborsWrapper(3, simArray[x][y][z].wVector);
-                    simArray[x][y][z].setBoundsToNeighborsWrapper(1, simArray[x][y][z].uAdditionVector);
-                    simArray[x][y][z].setBoundsToNeighborsWrapper(2, simArray[x][y][z].vAdditionVector);
-                    simArray[x][y][z].setBoundsToNeighborsWrapper(3, simArray[x][y][z].wAdditionVector);
-                    simArray[x][y][z].copyNeighborsWrapper(1, x, simArray[x][y][z].uVector);
-                    simArray[x][y][z].copyNeighborsWrapper(2, x, simArray[x][y][z].vVector);
-                    simArray[x][y][z].copyNeighborsWrapper(3, x, simArray[x][y][z].wVector);
-                    simArray[x][y][z].copyNeighborsWrapper(1, x, simArray[x][y][z].uAdditionVector);
-                    simArray[x][y][z].copyNeighborsWrapper(2, x, simArray[x][y][z].vAdditionVector);
-                    simArray[x][y][z].copyNeighborsWrapper(3, x, simArray[x][y][z].wAdditionVector);
-                }
-            }
-        }
-        //samples u,v,w,u0,v0,w0
-        for(int x = 0; x < simArray.length; x++){
-            for(int y = 0; y < simArray[0].length; y++){
-                for(int z = 0; z < simArray[0][0].length; z++){
-                    // advect(env, chunk_mask, N, 1, jru, u0, u0, v0, w0, dt);
-                    // advect(env, chunk_mask, N, 2, jrv, v0, u0, v0, w0, dt);
-                    // advect(env, chunk_mask, N, 3, jrw, w0, u0, v0, w0, dt);
-                    //...
-                    simArray[x][y][z].advectVectorsWrapper(timestep);
-                }
-            }
-        }
-        //mirror neighbor data
-        for(int x = 0; x < simArray.length; x++){
-            for(int y = 0; y < simArray[0].length; y++){
-                for(int z = 0; z < simArray[0][0].length; z++){
-                    simArray[x][y][z].setBoundsToNeighborsWrapper(1, simArray[x][y][z].uVector);
-                    simArray[x][y][z].setBoundsToNeighborsWrapper(2, simArray[x][y][z].vVector);
-                    simArray[x][y][z].setBoundsToNeighborsWrapper(3, simArray[x][y][z].wVector);
-                    simArray[x][y][z].copyNeighborsWrapper(1, x, simArray[x][y][z].uVector);
-                    simArray[x][y][z].copyNeighborsWrapper(2, x, simArray[x][y][z].vVector);
-                    simArray[x][y][z].copyNeighborsWrapper(3, x, simArray[x][y][z].wVector);
-                }
-            }
-        }
-    }
-
-    private static void addDensity(FluidSim[][][] simArray, float timestep){
-        for(int x = 0; x < simArray.length; x++){
-            for(int y = 0; y < simArray[0].length; y++){
-                for(int z = 0; z < simArray[0][0].length; z++){
-                    //add_source(N, x, x0, dt);
-                    simArray[x][y][z].addDensityWrapper(timestep);
-                    //swap x <=> x0
-                    //swap arrays in java side...
-                    // simArray[x][y][z].swapDensityArrays();
-                }
-            }
-        }
-    }
-
-    private static void swapAllDensityArrays(FluidSim[][][] simArray, float timestep){
-        for(int x = 0; x < simArray.length; x++){
-            for(int y = 0; y < simArray[0].length; y++){
-                for(int z = 0; z < simArray[0][0].length; z++){
-                    simArray[x][y][z].swapDensityArrays();
-                }
-            }
-        }
-        for(int x = 0; x < simArray.length; x++){
-            for(int y = 0; y < simArray[0].length; y++){
-                for(int z = 0; z < simArray[0][0].length; z++){
-                    simArray[x][y][z].copyNeighborsWrapper(0, x, simArray[x][y][z].density);
-                    simArray[x][y][z].copyNeighborsWrapper(0, x, simArray[x][y][z].densityAddition);
-                }
-            }
-        }
-    }
-
-    private void swapDensityArrays(){
-        for(int i = 0; i < 27; i++){
-            ByteBuffer tmp = density[i];
-            density[i] = densityAddition[i];
-            densityAddition[i] = tmp;
-        }
-    }
-
-    private static void diffuseDensity(FluidSim[][][] simArray, float timestep){
-        for(int l = 0; l < LINEARSOLVERTIMES; l++){
-            for(int x = 0; x < simArray.length; x++){
-                for(int y = 0; y < simArray[0].length; y++){
-                    for(int z = 0; z < simArray[0][0].length; z++){
-                        //lin_solve(env, chunk_mask, N, b, x, x0, a, 1+6*a);
-                        //+
-                        //set_bnd(env, chunk_mask, N, b, x);
-                        simArray[x][y][z].solveDiffuseDensityWrapper(timestep);
-                    }
-                }
-            }
-            for(int x = 0; x < simArray.length; x++){
-                for(int y = 0; y < simArray[0].length; y++){
-                    for(int z = 0; z < simArray[0][0].length; z++){
-                        simArray[x][y][z].setBoundsToNeighborsWrapper(0, simArray[x][y][z].density);
-                    }
-                }
-            }
-        }
-    }
-
-    private static void advectDensity(FluidSim[][][] simArray, float timestep){
-        for(int x = 0; x < simArray.length; x++){
-            for(int y = 0; y < simArray[0].length; y++){
-                for(int z = 0; z < simArray[0][0].length; z++){
-                    //swap x <=> x0 again
-                    // simArray[x][y][z].swapDensityArrays();
-                    //advect density
-                    simArray[x][y][z].advectDensityWrapper(timestep);
-                }
-            }
-        }
-    }
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-    
-
-    // /**
-    //  * The native function call to simulate a frame of fluid
-    //  * @param DIM_X
-    //  * @param DIM_Y
-    //  * @param DIM_Z
-    //  * @param x
-    //  * @param x0
-    //  * @param u
-    //  * @param v
-    //  * @param w
-    //  * @param u0
-    //  * @param v0
-    //  * @param w0
-    //  * @param DIFFUSION_CONSTANT
-    //  * @param VISCOSITY_CONSTANT
-    //  * @param timestep
-    //  */
-    // private native void simulate(
-    //     int DIM_X,
-    //     int chunkMask,
-    //     ByteBuffer[] x,
-    //     ByteBuffer x0,
-    //     ByteBuffer[] u,
-    //     ByteBuffer[] v,
-    //     ByteBuffer[] w,
-    //     ByteBuffer[] u0,
-    //     ByteBuffer[] v0,
-    //     ByteBuffer[] w0,
-    //     float DIFFUSION_CONSTANT,
-    //     float VISCOSITY_CONSTANT,
-    //     float timestep
-    // );
-
-    private void calculateChunkMaskWrapper(){
-        this.chunkMask = this.calculateChunkMask(density);
-    }
-    /**
-     * Calculates the mask of chunk neighbors
-     * @param densityBuffers The neighbor array
-     * @return The mask
-     */
-    private native int calculateChunkMask(ByteBuffer[] densityBuffers);
-
-    /**
-     * Add vector values to u, v, and w all at once
-     */
-    private void addSourceToVectorsWrapper(float timestep){
-        addSourceToVectors(DIM, chunkMask, uVector, vVector, wVector, uAdditionVector, vAdditionVector, wAdditionVector, DIFFUSION_CONSTANT, VISCOSITY_CONSTANT, timestep);
-    }
-    private native void addSourceToVectors(int DIM_X, int chunkMask, ByteBuffer[] u, ByteBuffer v[], ByteBuffer w[], ByteBuffer u0[], ByteBuffer v0[], ByteBuffer w0[], float DIFFUSION_CONSTANT, float VISCOSITY_CONSTANT, float timestep);
-
-    /**
-     * Solves u, v, and w diffusion systems of equations
-     */
-    private void solveVectorDiffuseWrapper(float timestep){
-        solveVectorDiffuse(DIM, chunkMask, uVector, vVector, wVector, uAdditionVector, vAdditionVector, wAdditionVector, DIFFUSION_CONSTANT, VISCOSITY_CONSTANT, timestep);
-    }
-    private native void solveVectorDiffuse(int DIM_X, int chunkMask, ByteBuffer[] u, ByteBuffer v[], ByteBuffer w[], ByteBuffer u0[], ByteBuffer v0[], ByteBuffer w0[], float DIFFUSION_CONSTANT, float VISCOSITY_CONSTANT, float timestep);
-
-    /**
-     * Setup projection system
-     */
-    private void setupProjectionWrapper(float timestep){
-        setupProjection(DIM, chunkMask, uVector, vVector, wVector, uAdditionVector, vAdditionVector, wAdditionVector, DIFFUSION_CONSTANT, VISCOSITY_CONSTANT, timestep);
-    }
-    private native void setupProjection(int DIM_X, int chunkMask, ByteBuffer[] u, ByteBuffer v[], ByteBuffer w[], ByteBuffer u0[], ByteBuffer v0[], ByteBuffer w0[], float DIFFUSION_CONSTANT, float VISCOSITY_CONSTANT, float timestep);
-
-    /**
-     * Solve projection system
-     */
-    private void solveProjectionWrapper(float timestep){
-        solveProjection(DIM, chunkMask, uVector, vVector, wVector, uAdditionVector, vAdditionVector, wAdditionVector, DIFFUSION_CONSTANT, VISCOSITY_CONSTANT, timestep);
-    }
-    private native void solveProjection(int DIM_X, int chunkMask, ByteBuffer[] u, ByteBuffer v[], ByteBuffer w[], ByteBuffer u0[], ByteBuffer v0[], ByteBuffer w0[], float DIFFUSION_CONSTANT, float VISCOSITY_CONSTANT, float timestep);
-
-    /**
-     * Does work like subtracting curl from vector field, setting boundaries, etc
-     */
-    private void finalizeProjectionWrapper(float timestep){
-        finalizeProjection(DIM, chunkMask, uVector, vVector, wVector, uAdditionVector, vAdditionVector, wAdditionVector, DIFFUSION_CONSTANT, VISCOSITY_CONSTANT, timestep);
-    }
-    private native void finalizeProjection(int DIM_X, int chunkMask, ByteBuffer[] u, ByteBuffer v[], ByteBuffer w[], ByteBuffer u0[], ByteBuffer v0[], ByteBuffer w0[], float DIFFUSION_CONSTANT, float VISCOSITY_CONSTANT, float timestep);
-
-    /**
-     * Advects vectors
-     */
-    private void advectVectorsWrapper(float timestep){
-        advectVectors(DIM, chunkMask, uVector, vVector, wVector, uAdditionVector, vAdditionVector, wAdditionVector, DIFFUSION_CONSTANT, VISCOSITY_CONSTANT, timestep);
-    }
-    private native void advectVectors(int DIM_X, int chunkMask, ByteBuffer[] u, ByteBuffer v[], ByteBuffer w[], ByteBuffer u0[], ByteBuffer v0[], ByteBuffer w0[], float DIFFUSION_CONSTANT, float VISCOSITY_CONSTANT, float timestep);
-
-    /**
-     * Adds density to the simulation
-     */
-    private void addDensityWrapper(float timestep){
-        addDensity(DIM, chunkMask, density, densityAddition, timestep);
-    }
-    private native void addDensity(int DIM_X, int chunkMask, ByteBuffer[] x, ByteBuffer[] x0, float timestep);
-
-    /**
-     * Solve density diffusion
-     */
-    private void solveDiffuseDensityWrapper(float timestep){
-        solveDiffuseDensity(DIM, chunkMask, density, densityAddition, uVector, vVector, wVector, DIFFUSION_CONSTANT, VISCOSITY_CONSTANT, timestep);
-    }
-    private native void solveDiffuseDensity(int DIM_X, int chunkMask, ByteBuffer[] x, ByteBuffer[] x0, ByteBuffer[] u, ByteBuffer v[], ByteBuffer w[], float DIFFUSION_CONSTANT, float VISCOSITY_CONSTANT, float timestep);
-
-    /**
-     * Solve density diffusion
-     */
-    private void advectDensityWrapper(float timestep){
-        advectDensity(DIM, chunkMask, density, densityAddition, uVector, vVector, wVector, DIFFUSION_CONSTANT, VISCOSITY_CONSTANT, timestep);
-    }
-    private native void advectDensity(int DIM_X, int chunkMask, ByteBuffer[] x, ByteBuffer[] x0, ByteBuffer[] u, ByteBuffer v[], ByteBuffer w[], float DIFFUSION_CONSTANT, float VISCOSITY_CONSTANT, float timestep);
-
-
-    /**
-     * Sets the bounds of the neighbormap to neighbor values if available
-     */
-    private void setBoundsToNeighborsWrapper(int vectorDir, ByteBuffer[] neighborMap){
-        setBoundsToNeighbors(DIM, chunkMask, vectorDir, neighborMap);
-    }
-    private native void setBoundsToNeighbors(int DIM_X, int chunkMask, int vectorDir, ByteBuffer[] neighborMap);
-
-    /**
-     * Sets the bounds of the neighbormap to neighbor values if available, otherwise doesn't mess with them.
-     * This is to make sure zeroing out doesn't mess up the sim
-     */
-    private void copyNeighborsWrapper(int vectorDir, int x, ByteBuffer[] neighborMap){
-        copyNeighbors(DIM, chunkMask, x, vectorDir, neighborMap);
-    }
-    private native void copyNeighbors(int DIM_X, int chunkMask, int x, int vectorDir, ByteBuffer[] neighborMap);
-
-
-
-
 
 
     /**