diff --git a/.vscode/settings.json b/.vscode/settings.json
index b9cbf89..5d1101b 100644
--- a/.vscode/settings.json
+++ b/.vscode/settings.json
@@ -14,6 +14,7 @@
         "threadpool.h": "c",
         "electrosphere_fluidsim.h": "c",
         "type_traits": "c",
-        "mainfunctions.h": "c"
+        "mainfunctions.h": "c",
+        "chunk.h": "c"
     }
 }
\ No newline at end of file
diff --git a/src/main/c/chunkmask.c b/src/main/c/chunkmask.c
index 5e38a17..a588b00 100644
--- a/src/main/c/chunkmask.c
+++ b/src/main/c/chunkmask.c
@@ -3,46 +3,6 @@
 #include "includes/utilities.h"
 #include "includes/chunkmask.h"
 
-uint32_t matrix_transform(JNIEnv * env, jobjectArray jrx);
-
-/**
- * Calculates the bitmask for available chunks for the provided chunk's neighbor array
-*/
-int calculateChunkMask(JNIEnv * env, jobjectArray jrx){
-    return matrix_transform(env,jrx);
-}
-
-/**
- * Calculates a mask that represents all nearby chunks that are actually accessible and exist
-*/
-uint32_t matrix_transform(JNIEnv * env, jobjectArray jrx){
-
-    //The returned value, an availability mask that contains the availability of each neighbor chunk
-    uint32_t rVal = 0;
-
-    //Add to maks for initial chunks
-    for(int i = 0; i < CENTER_LOC; i++){
-        if((*env)->GetObjectArrayElement(env,jrx,i)!=NULL){
-            rVal = rVal + 1;
-        }
-        rVal = rVal << 1;
-    }
-    //add 1 for center chunk because we already have that
-    rVal = rVal + 1;
-    rVal = rVal << 1;
-    //continue on for remaining chunks
-    for(int i = CENTER_LOC+1; i < 27; i++){
-        if((*env)->GetObjectArrayElement(env,jrx,i)!=NULL){
-            rVal = rVal + 1;
-        }
-        if(i < 26){
-            rVal = rVal << 1;
-        }
-    }
-
-    return rVal;
-}
-
 const uint32_t CHUNK_INDEX_ARR[] = {
     CHUNK_000, CHUNK_100, CHUNK_200,
     CHUNK_010, CHUNK_110, CHUNK_210,
diff --git a/src/main/c/compile.sh b/src/main/c/compile.sh
index b0337a5..dd40d53 100644
--- a/src/main/c/compile.sh
+++ b/src/main/c/compile.sh
@@ -51,10 +51,10 @@ rm -f ./*.dll
 # OUTPUT_FILE="./velocitystep.o"
 # gcc $COMPILE_FLAGS -I"$BASE_INCLUDE_DIR" -I"$OS_INCLUDE_DIR" $INPUT_FILES -o $OUTPUT_FILE
 
-# COMPILE_FLAGS="-c -fPIC -m64 -mavx -mavx2 -march=native -Ofast -msse -msse2 -msse3 -mmmx -m3dnow"
-# INPUT_FILES="./chunkmask.c"
-# OUTPUT_FILE="./chunkmask.o"
-# gcc $COMPILE_FLAGS -I"$BASE_INCLUDE_DIR" -I"$OS_INCLUDE_DIR" $INPUT_FILES -o $OUTPUT_FILE
+COMPILE_FLAGS="-c -fPIC -m64 -mavx -mavx2 -march=native -Ofast -msse -msse2 -msse3 -mmmx -m3dnow"
+INPUT_FILES="./javainterface.c"
+OUTPUT_FILE="./javainterface.o"
+gcc $COMPILE_FLAGS -I"$BASE_INCLUDE_DIR" -I"$OS_INCLUDE_DIR" $INPUT_FILES -o $OUTPUT_FILE
 
 COMPILE_FLAGS="-c -fPIC -m64 -mavx -mavx2 -march=native -Ofast -msse -msse2 -msse3 -mmmx -m3dnow"
 INPUT_FILES="./fluidsim.c"
@@ -66,7 +66,7 @@ gcc $COMPILE_FLAGS -I"$BASE_INCLUDE_DIR" -I"$OS_INCLUDE_DIR" $INPUT_FILES -o $OU
 #compile shared object file
 OUTPUT_FILE="libfluidsim$LIB_ENDING"
 COMPILE_FLAGS="-shared"
-INPUT_FILES="fluidsim.o"
+INPUT_FILES="fluidsim.o javainterface.o"
 gcc $COMPILE_FLAGS $INPUT_FILES -o $OUTPUT_FILE
 
 #move to resources
diff --git a/src/main/c/fluidsim.c b/src/main/c/fluidsim.c
index a91efe4..ae84c19 100644
--- a/src/main/c/fluidsim.c
+++ b/src/main/c/fluidsim.c
@@ -4,14 +4,12 @@
 #include "includes/chunkmask.h"
 #include "includes/electrosphere_FluidSim.h"
 #include "includes/mainFunctions.h"
+#include "includes/chunk.h"
 
 #include "./chunkmask.c"
 #include "./velocitystep.c"
 #include "./densitystep.c"
 
-//include stb ds
-#define STB_DS_IMPLEMENTATION
-#include "./lib/stb/stb_ds.h"
 
 #define DIM 18
 #define LINEARSOLVERTIMES 20
@@ -23,126 +21,20 @@
 
 char fileNameBuff[50];
 
-/**
- * A chunk
-*/
-typedef struct {
-    float * d[27];
-    float * d0[27];
-    float * u[27];
-    float * v[27];
-    float * w[27];
-    float * u0[27];
-    float * v0[27];
-    float * w0[27];
-    int chunkMask;
-} Chunk;
-
 //all chunks
 Chunk ** chunks = NULL;
 
-#define getChunk(i) (*env)->CallObjectMethod(env,chunkList,jListGet,i)
-#define getBuffArr(buffId) (*env)->GetObjectField(env,chunkJRaw,buffId)
-#define setBuffArr(buffId,value) (*env)->SetObjectField(env,chunkJRaw,buffId,value)
-
 //jni help:
 //https://stackoverflow.com/questions/39823375/clarification-about-getfieldid
 
 void saveStep(float * values, const char * name);
 
-JNIEXPORT void JNICALL Java_electrosphere_FluidSim_simulate(
-    JNIEnv * env,
-    jclass class,
-    jobject chunkList,
+void simulate(
+    int numChunks,
+    Chunk ** passedInChunks,
     jfloat timestep
 ){
-    jclass listClass = (*env)->FindClass(env,"java/util/List");
-    jclass fluidSimClass = (*env)->FindClass(env,"electrosphere/FluidSim");
-    //JNIEnv *env, jclass clazz, const char *name, const char *sig
-    jmethodID jListSize = (*env)->GetMethodID(env, listClass, "size", "()I");
-    jmethodID jListGet  = (*env)->GetMethodID(env, listClass, "get", "(I)Ljava/lang/Object;");
-    jmethodID jListAdd  = (*env)->GetMethodID(env, listClass, "add", "(Ljava/lang/Object;)Z");
-
-    //ByteBuffer[]
-    jfieldID dJId = (*env)->GetFieldID(env,fluidSimClass,"density","[Ljava/nio/ByteBuffer;");
-    jfieldID d0JId = (*env)->GetFieldID(env,fluidSimClass,"densityAddition","[Ljava/nio/ByteBuffer;");
-    jfieldID uJId = (*env)->GetFieldID(env,fluidSimClass,"uVector","[Ljava/nio/ByteBuffer;");
-    jfieldID vJId = (*env)->GetFieldID(env,fluidSimClass,"vVector","[Ljava/nio/ByteBuffer;");
-    jfieldID wJId = (*env)->GetFieldID(env,fluidSimClass,"wVector","[Ljava/nio/ByteBuffer;");
-    jfieldID u0JId = (*env)->GetFieldID(env,fluidSimClass,"uAdditionVector","[Ljava/nio/ByteBuffer;");
-    jfieldID v0JId = (*env)->GetFieldID(env,fluidSimClass,"vAdditionVector","[Ljava/nio/ByteBuffer;");
-    jfieldID w0JId = (*env)->GetFieldID(env,fluidSimClass,"wAdditionVector","[Ljava/nio/ByteBuffer;");
-    jfieldID chunkmaskJId = (*env)->GetFieldID(env,fluidSimClass,"chunkMask","I");
-
-    //the number of chunks
-    int numChunks = (*env)->CallIntMethod(env,chunkList,jListSize);
-
-    //current chunk (this)
-    jobject chunkJRaw;
-    //current chunk fields
-    jobjectArray jd;
-    jobjectArray jd0;
-    jobjectArray u;
-    jobjectArray v;
-    jobjectArray w;
-    jobjectArray u0;
-    jobjectArray v0;
-    jobjectArray w0;
-    int chunkMask;
-
-    //solve chunk mask
-    for(int i = 0; i < numChunks; i++){
-        chunkJRaw = getChunk(i);
-        chunkMask = Java_electrosphere_FluidSim_calculateChunkMask(env,chunkJRaw,getBuffArr(dJId));
-        (*env)->SetIntField(env,chunkJRaw,chunkmaskJId,chunkMask);
-
-        Chunk * newChunk;
-        if(i >= stbds_arrlen(chunks)){
-            // printf("allocate chunk %d\n",i);
-            // fflush(stdout);
-            newChunk = (Chunk *)malloc(sizeof(Chunk));
-            // printf("new chunk %p\n",newChunk);
-            // fflush(stdout);
-            stbds_arrput(chunks,newChunk);
-            // printf("new chunk %p\n",chunks[i]);
-            // fflush(stdout);
-        } else {
-            newChunk = chunks[i];
-            // printf("get chunk %d: %p\n",i,newChunk);
-            // fflush(stdout);
-        }
-        jd = (*env)->GetObjectField(env,chunkJRaw,dJId);
-        jd0 = (*env)->GetObjectField(env,chunkJRaw,d0JId);
-        u = (*env)->GetObjectField(env,chunkJRaw,uJId);
-        v = (*env)->GetObjectField(env,chunkJRaw,vJId);
-        w = (*env)->GetObjectField(env,chunkJRaw,wJId);
-        u0 = (*env)->GetObjectField(env,chunkJRaw,u0JId);
-        v0 = (*env)->GetObjectField(env,chunkJRaw,v0JId);
-        w0 = (*env)->GetObjectField(env,chunkJRaw,w0JId);
-        newChunk->chunkMask = chunkMask;
-        for(int j = 0; j < 27; j++){
-            if((chunkMask & CHUNK_INDEX_ARR[j]) > 0){
-                newChunk->d[j] = GET_ARR(env,jd,j);
-                newChunk->d0[j] = GET_ARR(env,jd0,j);
-                newChunk->u[j] = GET_ARR(env,u,j);
-                newChunk->v[j] = GET_ARR(env,v,j);
-                newChunk->w[j] = GET_ARR(env,w,j);
-                newChunk->u0[j] = GET_ARR(env,u0,j);
-                newChunk->v0[j] = GET_ARR(env,v0,j);
-                newChunk->w0[j] = GET_ARR(env,w0,j);
-            }
-        }
-        // for(int j = 0; j < 27; j++){
-        //     newChunk.d[j] = GET_ARR(env,d,j);
-        // }
-        // chunks[i].d0 = getBuffArr(d0JId);
-        // chunks[i].u = getBuffArr(uJId);
-        // chunks[i].v = getBuffArr(vJId);
-        // chunks[i].w = getBuffArr(wJId);
-        // chunks[i].u0 = getBuffArr(u0JId);
-        // chunks[i].v0 = getBuffArr(v0JId);
-        // chunks[i].w0 = getBuffArr(w0JId);
-    }
+    chunks = passedInChunks;
 
     // printf("%p\n",chunks[0].d);
     saveStep(chunks[0]->u[CENTER_LOC], "./chunks/beginU");
@@ -155,10 +47,9 @@ JNIEXPORT void JNICALL Java_electrosphere_FluidSim_simulate(
     //solve chunk mask
     for(int i = 0; i < numChunks; i++){
         Chunk * currentChunk = chunks[i];
-        chunkMask = currentChunk->chunkMask;
         addSourceToVectors(
             DIM,
-            chunkMask,
+            currentChunk->chunkMask,
             currentChunk->u,
             currentChunk->v,
             currentChunk->w,
@@ -181,7 +72,6 @@ JNIEXPORT void JNICALL Java_electrosphere_FluidSim_simulate(
         //swap vector fields
         for(int i = 0; i < numChunks; i++){
             Chunk * currentChunk = chunks[i];
-            chunkMask = currentChunk->chunkMask;
 
             float * tmpArr;
             for(int j = 0; j < 27; j++){
@@ -203,13 +93,12 @@ JNIEXPORT void JNICALL Java_electrosphere_FluidSim_simulate(
         //copy neighbors
         for(int i = 0; i < numChunks; i++){
             Chunk * currentChunk = chunks[i];
-            chunkMask = currentChunk->chunkMask;
-            copyNeighborsRaw(DIM,chunkMask,0,1,currentChunk->u);
-            copyNeighborsRaw(DIM,chunkMask,0,2,currentChunk->v);
-            copyNeighborsRaw(DIM,chunkMask,0,3,currentChunk->w);
-            copyNeighborsRaw(DIM,chunkMask,0,1,currentChunk->u0);
-            copyNeighborsRaw(DIM,chunkMask,0,2,currentChunk->v0);
-            copyNeighborsRaw(DIM,chunkMask,0,3,currentChunk->w0);
+            copyNeighborsRaw(DIM,currentChunk->chunkMask,0,1,currentChunk->u);
+            copyNeighborsRaw(DIM,currentChunk->chunkMask,0,2,currentChunk->v);
+            copyNeighborsRaw(DIM,currentChunk->chunkMask,0,3,currentChunk->w);
+            copyNeighborsRaw(DIM,currentChunk->chunkMask,0,1,currentChunk->u0);
+            copyNeighborsRaw(DIM,currentChunk->chunkMask,0,2,currentChunk->v0);
+            copyNeighborsRaw(DIM,currentChunk->chunkMask,0,3,currentChunk->w0);
         }
     }
     saveStep(chunks[0]->u[CENTER_LOC], "./chunks/swapU");
@@ -228,8 +117,7 @@ JNIEXPORT void JNICALL Java_electrosphere_FluidSim_simulate(
             //solve vector diffusion
             for(int i = 0; i < numChunks; i++){
                 Chunk * currentChunk = chunks[i];
-                chunkMask = currentChunk->chunkMask;
-                solveVectorDiffuse(DIM,chunkMask,currentChunk->u,currentChunk->v,currentChunk->w,currentChunk->u0,currentChunk->v0,currentChunk->w0,DIFFUSION_CONSTANT,VISCOSITY_CONSTANT,timestep);
+                solveVectorDiffuse(DIM,currentChunk->chunkMask,currentChunk->u,currentChunk->v,currentChunk->w,currentChunk->u0,currentChunk->v0,currentChunk->w0,DIFFUSION_CONSTANT,VISCOSITY_CONSTANT,timestep);
             }
             if(SAVE_STEPS){
                 sprintf(fileNameBuff, "./chunks/diffuseUStep%dx", l);
@@ -248,19 +136,18 @@ JNIEXPORT void JNICALL Java_electrosphere_FluidSim_simulate(
             //update array for vectors
             for(int i = 0; i < numChunks; i++){
                 Chunk * currentChunk = chunks[i];
-                chunkMask = currentChunk->chunkMask;
-                setBoundsToNeighborsRaw(DIM,chunkMask,1,currentChunk->u);
-                setBoundsToNeighborsRaw(DIM,chunkMask,2,currentChunk->v);
-                setBoundsToNeighborsRaw(DIM,chunkMask,3,currentChunk->w);
+                setBoundsToNeighborsRaw(DIM,currentChunk->chunkMask,1,currentChunk->u);
+                setBoundsToNeighborsRaw(DIM,currentChunk->chunkMask,2,currentChunk->v);
+                setBoundsToNeighborsRaw(DIM,currentChunk->chunkMask,3,currentChunk->w);
                 // setBoundsToNeighborsRaw(DIM,chunkMask,1,currentChunk->u0);
                 // setBoundsToNeighborsRaw(DIM,chunkMask,2,currentChunk->v0);
                 // setBoundsToNeighborsRaw(DIM,chunkMask,3,currentChunk->w0);
-                copyNeighborsRaw(DIM,chunkMask,0,0,currentChunk->u);
-                copyNeighborsRaw(DIM,chunkMask,0,0,currentChunk->v);
-                copyNeighborsRaw(DIM,chunkMask,0,0,currentChunk->w);
-                copyNeighborsRaw(DIM,chunkMask,0,0,currentChunk->u0);
-                copyNeighborsRaw(DIM,chunkMask,0,0,currentChunk->v0);
-                copyNeighborsRaw(DIM,chunkMask,0,0,currentChunk->w0);
+                copyNeighborsRaw(DIM,currentChunk->chunkMask,0,0,currentChunk->u);
+                copyNeighborsRaw(DIM,currentChunk->chunkMask,0,0,currentChunk->v);
+                copyNeighborsRaw(DIM,currentChunk->chunkMask,0,0,currentChunk->w);
+                copyNeighborsRaw(DIM,currentChunk->chunkMask,0,0,currentChunk->u0);
+                copyNeighborsRaw(DIM,currentChunk->chunkMask,0,0,currentChunk->v0);
+                copyNeighborsRaw(DIM,currentChunk->chunkMask,0,0,currentChunk->w0);
             }
             if(SAVE_STEPS){
                 sprintf(fileNameBuff, "./chunks/diffuseUStep%dxBnd", l);
@@ -289,23 +176,21 @@ JNIEXPORT void JNICALL Java_electrosphere_FluidSim_simulate(
         //update array for vectors
         for(int i = 0; i < numChunks; i++){
             Chunk * currentChunk = chunks[i];
-            chunkMask = currentChunk->chunkMask;
             // setBoundsToNeighborsRaw(DIM,chunkMask,1,currentChunk->u);
             // setBoundsToNeighborsRaw(DIM,chunkMask,2,currentChunk->v);
             // setBoundsToNeighborsRaw(DIM,chunkMask,3,currentChunk->w);
             // setBoundsToNeighborsRaw(DIM,chunkMask,1,currentChunk->u0);
             // setBoundsToNeighborsRaw(DIM,chunkMask,2,currentChunk->v0);
-            copyNeighborsRaw(DIM,chunkMask,0,1,currentChunk->u);
-            copyNeighborsRaw(DIM,chunkMask,0,2,currentChunk->v);
-            copyNeighborsRaw(DIM,chunkMask,0,3,currentChunk->w);
-            copyNeighborsRaw(DIM,chunkMask,0,1,currentChunk->u0);
-            copyNeighborsRaw(DIM,chunkMask,0,2,currentChunk->v0);
+            copyNeighborsRaw(DIM,currentChunk->chunkMask,0,1,currentChunk->u);
+            copyNeighborsRaw(DIM,currentChunk->chunkMask,0,2,currentChunk->v);
+            copyNeighborsRaw(DIM,currentChunk->chunkMask,0,3,currentChunk->w);
+            copyNeighborsRaw(DIM,currentChunk->chunkMask,0,1,currentChunk->u0);
+            copyNeighborsRaw(DIM,currentChunk->chunkMask,0,2,currentChunk->v0);
         }
         //setup projection
         for(int i = 0; i < numChunks; i++){
             Chunk * currentChunk = chunks[i];
-            chunkMask = currentChunk->chunkMask;
-            setupProjection(DIM,chunkMask,currentChunk->u,currentChunk->v,currentChunk->w,currentChunk->u0,currentChunk->v0,DIFFUSION_CONSTANT,VISCOSITY_CONSTANT,timestep);
+            setupProjection(DIM,currentChunk->chunkMask,currentChunk->u,currentChunk->v,currentChunk->w,currentChunk->u0,currentChunk->v0,DIFFUSION_CONSTANT,VISCOSITY_CONSTANT,timestep);
         }
 
         saveStep(chunks[0]->v0[CENTER_LOC], "./chunks/setupProj1Div");
@@ -314,11 +199,10 @@ JNIEXPORT void JNICALL Java_electrosphere_FluidSim_simulate(
         //update array for vectors
         for(int i = 0; i < numChunks; i++){
             Chunk * currentChunk = chunks[i];
-            chunkMask = currentChunk->chunkMask;
-            setBoundsToNeighborsRaw(DIM,chunkMask,0,currentChunk->u0);
-            setBoundsToNeighborsRaw(DIM,chunkMask,0,currentChunk->v0);
-            copyNeighborsRaw(DIM,chunkMask,0,0,currentChunk->u0);
-            copyNeighborsRaw(DIM,chunkMask,0,0,currentChunk->v0);
+            setBoundsToNeighborsRaw(DIM,currentChunk->chunkMask,0,currentChunk->u0);
+            setBoundsToNeighborsRaw(DIM,currentChunk->chunkMask,0,currentChunk->v0);
+            copyNeighborsRaw(DIM,currentChunk->chunkMask,0,0,currentChunk->u0);
+            copyNeighborsRaw(DIM,currentChunk->chunkMask,0,0,currentChunk->v0);
         }
 
         saveStep(chunks[0]->v0[CENTER_LOC], "./chunks/setupProj1DivBnd");
@@ -332,8 +216,7 @@ JNIEXPORT void JNICALL Java_electrosphere_FluidSim_simulate(
         for(int l = 0; l < LINEARSOLVERTIMES; l++){
             for(int i = 0; i < numChunks; i++){
                 Chunk * currentChunk = chunks[i];
-                chunkMask = currentChunk->chunkMask;
-                solveProjection(DIM,chunkMask,currentChunk->u,currentChunk->v,currentChunk->w,currentChunk->u0,currentChunk->v0,currentChunk->w0,DIFFUSION_CONSTANT,VISCOSITY_CONSTANT,timestep);
+                solveProjection(DIM,currentChunk->chunkMask,currentChunk->u,currentChunk->v,currentChunk->w,currentChunk->u0,currentChunk->v0,currentChunk->w0,DIFFUSION_CONSTANT,VISCOSITY_CONSTANT,timestep);
             }
             if(SAVE_STEPS){
                 sprintf(fileNameBuff, "./chunks/proj1Step%dx", l);
@@ -343,9 +226,8 @@ JNIEXPORT void JNICALL Java_electrosphere_FluidSim_simulate(
             }
             for(int i = 0; i < numChunks; i++){
                 Chunk * currentChunk = chunks[i];
-                chunkMask = currentChunk->chunkMask;
-                setBoundsToNeighborsRaw(DIM,chunkMask,0,currentChunk->u0);
-                copyNeighborsRaw(DIM,chunkMask,0,0,currentChunk->u0);
+                setBoundsToNeighborsRaw(DIM,currentChunk->chunkMask,0,currentChunk->u0);
+                copyNeighborsRaw(DIM,currentChunk->chunkMask,0,0,currentChunk->u0);
             }
             if(SAVE_STEPS){
                 sprintf(fileNameBuff, "./chunks/proj1Step%dxBnd", l);
@@ -359,8 +241,7 @@ JNIEXPORT void JNICALL Java_electrosphere_FluidSim_simulate(
         //Finalize projection
         for(int i = 0; i < numChunks; i++){
             Chunk * currentChunk = chunks[i];
-            chunkMask = currentChunk->chunkMask;
-            finalizeProjection(DIM,chunkMask,currentChunk->u,currentChunk->v,currentChunk->w,currentChunk->u0,currentChunk->v0,currentChunk->w0,DIFFUSION_CONSTANT,VISCOSITY_CONSTANT,timestep);
+            finalizeProjection(DIM,currentChunk->chunkMask,currentChunk->u,currentChunk->v,currentChunk->w,currentChunk->u0,currentChunk->v0,currentChunk->w0,DIFFUSION_CONSTANT,VISCOSITY_CONSTANT,timestep);
         }
 
         saveStep(chunks[0]->u[CENTER_LOC], "./chunks/finalizeProj1U");
@@ -371,19 +252,18 @@ JNIEXPORT void JNICALL Java_electrosphere_FluidSim_simulate(
         //...
         for(int i = 0; i < numChunks; i++){
             Chunk * currentChunk = chunks[i];
-            chunkMask = currentChunk->chunkMask;
-            setBoundsToNeighborsRaw(DIM,chunkMask,1,currentChunk->u);
-            setBoundsToNeighborsRaw(DIM,chunkMask,2,currentChunk->v);
-            setBoundsToNeighborsRaw(DIM,chunkMask,3,currentChunk->w);
-            setBoundsToNeighborsRaw(DIM,chunkMask,1,currentChunk->u0);
-            setBoundsToNeighborsRaw(DIM,chunkMask,2,currentChunk->v0);
-            setBoundsToNeighborsRaw(DIM,chunkMask,3,currentChunk->w0);
-            copyNeighborsRaw(DIM,chunkMask,0,1,currentChunk->u);
-            copyNeighborsRaw(DIM,chunkMask,0,2,currentChunk->v);
-            copyNeighborsRaw(DIM,chunkMask,0,3,currentChunk->w);
-            copyNeighborsRaw(DIM,chunkMask,0,1,currentChunk->u0);
-            copyNeighborsRaw(DIM,chunkMask,0,2,currentChunk->v0);
-            copyNeighborsRaw(DIM,chunkMask,0,3,currentChunk->w0);
+            setBoundsToNeighborsRaw(DIM,currentChunk->chunkMask,1,currentChunk->u);
+            setBoundsToNeighborsRaw(DIM,currentChunk->chunkMask,2,currentChunk->v);
+            setBoundsToNeighborsRaw(DIM,currentChunk->chunkMask,3,currentChunk->w);
+            setBoundsToNeighborsRaw(DIM,currentChunk->chunkMask,1,currentChunk->u0);
+            setBoundsToNeighborsRaw(DIM,currentChunk->chunkMask,2,currentChunk->v0);
+            setBoundsToNeighborsRaw(DIM,currentChunk->chunkMask,3,currentChunk->w0);
+            copyNeighborsRaw(DIM,currentChunk->chunkMask,0,1,currentChunk->u);
+            copyNeighborsRaw(DIM,currentChunk->chunkMask,0,2,currentChunk->v);
+            copyNeighborsRaw(DIM,currentChunk->chunkMask,0,3,currentChunk->w);
+            copyNeighborsRaw(DIM,currentChunk->chunkMask,0,1,currentChunk->u0);
+            copyNeighborsRaw(DIM,currentChunk->chunkMask,0,2,currentChunk->v0);
+            copyNeighborsRaw(DIM,currentChunk->chunkMask,0,3,currentChunk->w0);
         }
     }
     saveStep(chunks[0]->u[CENTER_LOC], "./chunks/projU");
@@ -398,7 +278,6 @@ JNIEXPORT void JNICALL Java_electrosphere_FluidSim_simulate(
         //swap vector fields
         for(int i = 0; i < numChunks; i++){
             Chunk * currentChunk = chunks[i];
-            chunkMask = currentChunk->chunkMask;
 
             float * tmpArr;
             for(int j = 0; j < 27; j++){
@@ -420,13 +299,12 @@ JNIEXPORT void JNICALL Java_electrosphere_FluidSim_simulate(
         //copy neighbors
         for(int i = 0; i < numChunks; i++){
             Chunk * currentChunk = chunks[i];
-            chunkMask = currentChunk->chunkMask;
-            copyNeighborsRaw(DIM,chunkMask,0,1,currentChunk->u);
-            copyNeighborsRaw(DIM,chunkMask,0,2,currentChunk->v);
-            copyNeighborsRaw(DIM,chunkMask,0,3,currentChunk->w);
-            copyNeighborsRaw(DIM,chunkMask,0,1,currentChunk->u0);
-            copyNeighborsRaw(DIM,chunkMask,0,2,currentChunk->v0);
-            copyNeighborsRaw(DIM,chunkMask,0,3,currentChunk->w0);
+            copyNeighborsRaw(DIM,currentChunk->chunkMask,0,1,currentChunk->u);
+            copyNeighborsRaw(DIM,currentChunk->chunkMask,0,2,currentChunk->v);
+            copyNeighborsRaw(DIM,currentChunk->chunkMask,0,3,currentChunk->w);
+            copyNeighborsRaw(DIM,currentChunk->chunkMask,0,1,currentChunk->u0);
+            copyNeighborsRaw(DIM,currentChunk->chunkMask,0,2,currentChunk->v0);
+            copyNeighborsRaw(DIM,currentChunk->chunkMask,0,3,currentChunk->w0);
         }
     }
     saveStep(chunks[0]->u[CENTER_LOC], "./chunks/swap2U");
@@ -440,36 +318,33 @@ JNIEXPORT void JNICALL Java_electrosphere_FluidSim_simulate(
         //update border arrs
         for(int i = 0; i < numChunks; i++){
             Chunk * currentChunk = chunks[i];
-            chunkMask = currentChunk->chunkMask;
-            setBoundsToNeighborsRaw(DIM,chunkMask,1,currentChunk->u);
-            setBoundsToNeighborsRaw(DIM,chunkMask,2,currentChunk->v);
-            setBoundsToNeighborsRaw(DIM,chunkMask,3,currentChunk->w);
-            setBoundsToNeighborsRaw(DIM,chunkMask,1,currentChunk->u0);
-            setBoundsToNeighborsRaw(DIM,chunkMask,2,currentChunk->v0);
-            setBoundsToNeighborsRaw(DIM,chunkMask,3,currentChunk->w0);
-            copyNeighborsRaw(DIM,chunkMask,0,1,currentChunk->u);
-            copyNeighborsRaw(DIM,chunkMask,0,2,currentChunk->v);
-            copyNeighborsRaw(DIM,chunkMask,0,3,currentChunk->w);
-            copyNeighborsRaw(DIM,chunkMask,0,1,currentChunk->u0);
-            copyNeighborsRaw(DIM,chunkMask,0,2,currentChunk->v0);
-            copyNeighborsRaw(DIM,chunkMask,0,3,currentChunk->w0);
+            setBoundsToNeighborsRaw(DIM,currentChunk->chunkMask,1,currentChunk->u);
+            setBoundsToNeighborsRaw(DIM,currentChunk->chunkMask,2,currentChunk->v);
+            setBoundsToNeighborsRaw(DIM,currentChunk->chunkMask,3,currentChunk->w);
+            setBoundsToNeighborsRaw(DIM,currentChunk->chunkMask,1,currentChunk->u0);
+            setBoundsToNeighborsRaw(DIM,currentChunk->chunkMask,2,currentChunk->v0);
+            setBoundsToNeighborsRaw(DIM,currentChunk->chunkMask,3,currentChunk->w0);
+            copyNeighborsRaw(DIM,currentChunk->chunkMask,0,1,currentChunk->u);
+            copyNeighborsRaw(DIM,currentChunk->chunkMask,0,2,currentChunk->v);
+            copyNeighborsRaw(DIM,currentChunk->chunkMask,0,3,currentChunk->w);
+            copyNeighborsRaw(DIM,currentChunk->chunkMask,0,1,currentChunk->u0);
+            copyNeighborsRaw(DIM,currentChunk->chunkMask,0,2,currentChunk->v0);
+            copyNeighborsRaw(DIM,currentChunk->chunkMask,0,3,currentChunk->w0);
         }
         //advect
         for(int i = 0; i < numChunks; i++){
             Chunk * currentChunk = chunks[i];
-            chunkMask = currentChunk->chunkMask;
-            advectVectors(DIM,chunkMask,currentChunk->u,currentChunk->v,currentChunk->w,currentChunk->u0,currentChunk->v0,currentChunk->w0,DIFFUSION_CONSTANT,VISCOSITY_CONSTANT,timestep);
+            advectVectors(DIM,currentChunk->chunkMask,currentChunk->u,currentChunk->v,currentChunk->w,currentChunk->u0,currentChunk->v0,currentChunk->w0,DIFFUSION_CONSTANT,VISCOSITY_CONSTANT,timestep);
         }
         //update neighbor arr
         for(int i = 0; i < numChunks; i++){
             Chunk * currentChunk = chunks[i];
-            chunkMask = currentChunk->chunkMask;
-            setBoundsToNeighborsRaw(DIM,chunkMask,1,currentChunk->u);
-            setBoundsToNeighborsRaw(DIM,chunkMask,2,currentChunk->v);
-            setBoundsToNeighborsRaw(DIM,chunkMask,3,currentChunk->w);
-            copyNeighborsRaw(DIM,chunkMask,0,1,currentChunk->u);
-            copyNeighborsRaw(DIM,chunkMask,0,2,currentChunk->v);
-            copyNeighborsRaw(DIM,chunkMask,0,3,currentChunk->w);
+            setBoundsToNeighborsRaw(DIM,currentChunk->chunkMask,1,currentChunk->u);
+            setBoundsToNeighborsRaw(DIM,currentChunk->chunkMask,2,currentChunk->v);
+            setBoundsToNeighborsRaw(DIM,currentChunk->chunkMask,3,currentChunk->w);
+            copyNeighborsRaw(DIM,currentChunk->chunkMask,0,1,currentChunk->u);
+            copyNeighborsRaw(DIM,currentChunk->chunkMask,0,2,currentChunk->v);
+            copyNeighborsRaw(DIM,currentChunk->chunkMask,0,3,currentChunk->w);
         }
     }
     saveStep(chunks[0]->u[CENTER_LOC], "./chunks/advectU");
@@ -483,32 +358,29 @@ JNIEXPORT void JNICALL Java_electrosphere_FluidSim_simulate(
         //update array for vectors
         for(int i = 0; i < numChunks; i++){
             Chunk * currentChunk = chunks[i];
-            chunkMask = currentChunk->chunkMask;
-            setBoundsToNeighborsRaw(DIM,chunkMask,1,currentChunk->u);
-            setBoundsToNeighborsRaw(DIM,chunkMask,2,currentChunk->v);
-            setBoundsToNeighborsRaw(DIM,chunkMask,3,currentChunk->w);
-            setBoundsToNeighborsRaw(DIM,chunkMask,1,currentChunk->u0);
-            setBoundsToNeighborsRaw(DIM,chunkMask,2,currentChunk->v0);
-            copyNeighborsRaw(DIM,chunkMask,0,1,currentChunk->u);
-            copyNeighborsRaw(DIM,chunkMask,0,2,currentChunk->v);
-            copyNeighborsRaw(DIM,chunkMask,0,3,currentChunk->w);
-            copyNeighborsRaw(DIM,chunkMask,0,1,currentChunk->u0);
-            copyNeighborsRaw(DIM,chunkMask,0,2,currentChunk->v0);
+            setBoundsToNeighborsRaw(DIM,currentChunk->chunkMask,1,currentChunk->u);
+            setBoundsToNeighborsRaw(DIM,currentChunk->chunkMask,2,currentChunk->v);
+            setBoundsToNeighborsRaw(DIM,currentChunk->chunkMask,3,currentChunk->w);
+            setBoundsToNeighborsRaw(DIM,currentChunk->chunkMask,1,currentChunk->u0);
+            setBoundsToNeighborsRaw(DIM,currentChunk->chunkMask,2,currentChunk->v0);
+            copyNeighborsRaw(DIM,currentChunk->chunkMask,0,1,currentChunk->u);
+            copyNeighborsRaw(DIM,currentChunk->chunkMask,0,2,currentChunk->v);
+            copyNeighborsRaw(DIM,currentChunk->chunkMask,0,3,currentChunk->w);
+            copyNeighborsRaw(DIM,currentChunk->chunkMask,0,1,currentChunk->u0);
+            copyNeighborsRaw(DIM,currentChunk->chunkMask,0,2,currentChunk->v0);
         }
         //setup projection
         for(int i = 0; i < numChunks; i++){
             Chunk * currentChunk = chunks[i];
-            chunkMask = currentChunk->chunkMask;
-            setupProjection(DIM,chunkMask,currentChunk->u,currentChunk->v,currentChunk->w,currentChunk->u0,currentChunk->v0,DIFFUSION_CONSTANT,VISCOSITY_CONSTANT,timestep);
+            setupProjection(DIM,currentChunk->chunkMask,currentChunk->u,currentChunk->v,currentChunk->w,currentChunk->u0,currentChunk->v0,DIFFUSION_CONSTANT,VISCOSITY_CONSTANT,timestep);
         }
         //update array for vectors
         for(int i = 0; i < numChunks; i++){
             Chunk * currentChunk = chunks[i];
-            chunkMask = currentChunk->chunkMask;
-            setBoundsToNeighborsRaw(DIM,chunkMask,1,currentChunk->u0);
-            setBoundsToNeighborsRaw(DIM,chunkMask,2,currentChunk->v0);
-            copyNeighborsRaw(DIM,chunkMask,0,1,currentChunk->u0);
-            copyNeighborsRaw(DIM,chunkMask,0,2,currentChunk->v0);
+            setBoundsToNeighborsRaw(DIM,currentChunk->chunkMask,1,currentChunk->u0);
+            setBoundsToNeighborsRaw(DIM,currentChunk->chunkMask,2,currentChunk->v0);
+            copyNeighborsRaw(DIM,currentChunk->chunkMask,0,1,currentChunk->u0);
+            copyNeighborsRaw(DIM,currentChunk->chunkMask,0,2,currentChunk->v0);
         }
         //samples u0, v0
         //sets u0
@@ -518,14 +390,12 @@ JNIEXPORT void JNICALL Java_electrosphere_FluidSim_simulate(
         for(int l = 0; l < LINEARSOLVERTIMES; l++){
             for(int i = 0; i < numChunks; i++){
                 Chunk * currentChunk = chunks[i];
-                chunkMask = currentChunk->chunkMask;
-                solveProjection(DIM,chunkMask,currentChunk->u,currentChunk->v,currentChunk->w,currentChunk->u0,currentChunk->v0,currentChunk->w0,DIFFUSION_CONSTANT,VISCOSITY_CONSTANT,timestep);
+                solveProjection(DIM,currentChunk->chunkMask,currentChunk->u,currentChunk->v,currentChunk->w,currentChunk->u0,currentChunk->v0,currentChunk->w0,DIFFUSION_CONSTANT,VISCOSITY_CONSTANT,timestep);
             }
             for(int i = 0; i < numChunks; i++){
                 Chunk * currentChunk = chunks[i];
-                chunkMask = currentChunk->chunkMask;
-                setBoundsToNeighborsRaw(DIM,chunkMask,0,currentChunk->u0);
-                copyNeighborsRaw(DIM,chunkMask,0,0,currentChunk->u0);
+                setBoundsToNeighborsRaw(DIM,currentChunk->chunkMask,0,currentChunk->u0);
+                copyNeighborsRaw(DIM,currentChunk->chunkMask,0,0,currentChunk->u0);
             }
         }
         //samples u,v,w,u0
@@ -533,26 +403,24 @@ JNIEXPORT void JNICALL Java_electrosphere_FluidSim_simulate(
         //Finalize projection
         for(int i = 0; i < numChunks; i++){
             Chunk * currentChunk = chunks[i];
-            chunkMask = currentChunk->chunkMask;
-            finalizeProjection(DIM,chunkMask,currentChunk->u,currentChunk->v,currentChunk->w,currentChunk->u0,currentChunk->v0,currentChunk->w0,DIFFUSION_CONSTANT,VISCOSITY_CONSTANT,timestep);
+            finalizeProjection(DIM,currentChunk->chunkMask,currentChunk->u,currentChunk->v,currentChunk->w,currentChunk->u0,currentChunk->v0,currentChunk->w0,DIFFUSION_CONSTANT,VISCOSITY_CONSTANT,timestep);
         }
         //set boundaries a final time for u,v,w
         //...
         for(int i = 0; i < numChunks; i++){
             Chunk * currentChunk = chunks[i];
-            chunkMask = currentChunk->chunkMask;
-            setBoundsToNeighborsRaw(DIM,chunkMask,1,currentChunk->u);
-            setBoundsToNeighborsRaw(DIM,chunkMask,2,currentChunk->v);
-            setBoundsToNeighborsRaw(DIM,chunkMask,3,currentChunk->w);
-            setBoundsToNeighborsRaw(DIM,chunkMask,1,currentChunk->u0);
-            setBoundsToNeighborsRaw(DIM,chunkMask,2,currentChunk->v0);
-            setBoundsToNeighborsRaw(DIM,chunkMask,3,currentChunk->w0);
-            copyNeighborsRaw(DIM,chunkMask,0,1,currentChunk->u);
-            copyNeighborsRaw(DIM,chunkMask,0,2,currentChunk->v);
-            copyNeighborsRaw(DIM,chunkMask,0,3,currentChunk->w);
-            copyNeighborsRaw(DIM,chunkMask,0,1,currentChunk->u0);
-            copyNeighborsRaw(DIM,chunkMask,0,2,currentChunk->v0);
-            copyNeighborsRaw(DIM,chunkMask,0,3,currentChunk->w0);
+            setBoundsToNeighborsRaw(DIM,currentChunk->chunkMask,1,currentChunk->u);
+            setBoundsToNeighborsRaw(DIM,currentChunk->chunkMask,2,currentChunk->v);
+            setBoundsToNeighborsRaw(DIM,currentChunk->chunkMask,3,currentChunk->w);
+            setBoundsToNeighborsRaw(DIM,currentChunk->chunkMask,1,currentChunk->u0);
+            setBoundsToNeighborsRaw(DIM,currentChunk->chunkMask,2,currentChunk->v0);
+            setBoundsToNeighborsRaw(DIM,currentChunk->chunkMask,3,currentChunk->w0);
+            copyNeighborsRaw(DIM,currentChunk->chunkMask,0,1,currentChunk->u);
+            copyNeighborsRaw(DIM,currentChunk->chunkMask,0,2,currentChunk->v);
+            copyNeighborsRaw(DIM,currentChunk->chunkMask,0,3,currentChunk->w);
+            copyNeighborsRaw(DIM,currentChunk->chunkMask,0,1,currentChunk->u0);
+            copyNeighborsRaw(DIM,currentChunk->chunkMask,0,2,currentChunk->v0);
+            copyNeighborsRaw(DIM,currentChunk->chunkMask,0,3,currentChunk->w0);
         }
     }
 
@@ -572,8 +440,7 @@ JNIEXPORT void JNICALL Java_electrosphere_FluidSim_simulate(
     {
         for(int i = 0; i < numChunks; i++){
             Chunk * currentChunk = chunks[i];
-            chunkMask = currentChunk->chunkMask;
-            addDensity(DIM,chunkMask,currentChunk->d,currentChunk->d0,timestep);
+            addDensity(DIM,currentChunk->chunkMask,currentChunk->d,currentChunk->d0,timestep);
         }
     }
     //swap all density arrays
@@ -591,9 +458,8 @@ JNIEXPORT void JNICALL Java_electrosphere_FluidSim_simulate(
         }
         for(int i = 0; i < numChunks; i++){
             Chunk * currentChunk = chunks[i];
-            chunkMask = currentChunk->chunkMask;
-            copyNeighborsRaw(DIM,chunkMask,0,0,currentChunk->d);
-            copyNeighborsRaw(DIM,chunkMask,0,0,currentChunk->d0);
+            copyNeighborsRaw(DIM,currentChunk->chunkMask,0,0,currentChunk->d);
+            copyNeighborsRaw(DIM,currentChunk->chunkMask,0,0,currentChunk->d0);
         }
     }
     //diffuse density
@@ -601,13 +467,11 @@ JNIEXPORT void JNICALL Java_electrosphere_FluidSim_simulate(
         for(int l = 0; l < LINEARSOLVERTIMES; l++){
             for(int i = 0; i < numChunks; i++){
                 Chunk * currentChunk = chunks[i];
-                chunkMask = currentChunk->chunkMask;
-                solveDiffuseDensity(DIM,chunkMask,currentChunk->d,currentChunk->d0,currentChunk->u,currentChunk->v,currentChunk->w,DIFFUSION_CONSTANT,VISCOSITY_CONSTANT,timestep);
+                solveDiffuseDensity(DIM,currentChunk->chunkMask,currentChunk->d,currentChunk->d0,currentChunk->u,currentChunk->v,currentChunk->w,DIFFUSION_CONSTANT,VISCOSITY_CONSTANT,timestep);
             }
             for(int i = 0; i < numChunks; i++){
                 Chunk * currentChunk = chunks[i];
-                chunkMask = currentChunk->chunkMask;
-                setBoundsToNeighborsRaw(DIM,chunkMask,0,currentChunk->d);
+                setBoundsToNeighborsRaw(DIM,currentChunk->chunkMask,0,currentChunk->d);
             }
         }
     }
@@ -625,25 +489,22 @@ JNIEXPORT void JNICALL Java_electrosphere_FluidSim_simulate(
         }
         for(int i = 0; i < numChunks; i++){
             Chunk * currentChunk = chunks[i];
-            chunkMask = currentChunk->chunkMask;
-            copyNeighborsRaw(DIM,chunkMask,0,0,currentChunk->d);
-            copyNeighborsRaw(DIM,chunkMask,0,0,currentChunk->d0);
+            copyNeighborsRaw(DIM,currentChunk->chunkMask,0,0,currentChunk->d);
+            copyNeighborsRaw(DIM,currentChunk->chunkMask,0,0,currentChunk->d0);
         }
     }
     //advect density
     {
         for(int i = 0; i < numChunks; i++){
             Chunk * currentChunk = chunks[i];
-            chunkMask = currentChunk->chunkMask;
-            advectDensity(chunkMask,DIM,currentChunk->d,currentChunk->d0,currentChunk->u,currentChunk->v,currentChunk->w,timestep);
+            advectDensity(currentChunk->chunkMask,DIM,currentChunk->d,currentChunk->d0,currentChunk->u,currentChunk->v,currentChunk->w,timestep);
         }
     }
     //mirror densities
     {
         for(int i = 0; i < numChunks; i++){
             Chunk * currentChunk = chunks[i];
-            chunkMask = currentChunk->chunkMask;
-            setBoundsToNeighborsRaw(DIM,chunkMask,0,currentChunk->d);
+            setBoundsToNeighborsRaw(DIM,currentChunk->chunkMask,0,currentChunk->d);
         }
     }
 }
diff --git a/src/main/c/includes/chunk.h b/src/main/c/includes/chunk.h
new file mode 100644
index 0000000..586f37e
--- /dev/null
+++ b/src/main/c/includes/chunk.h
@@ -0,0 +1,19 @@
+#ifndef CHUNK_H
+#define CHUNK_H
+
+/**
+ * A chunk
+*/
+typedef struct {
+    float * d[27];
+    float * d0[27];
+    float * u[27];
+    float * v[27];
+    float * w[27];
+    float * u0[27];
+    float * v0[27];
+    float * w0[27];
+    int chunkMask;
+} Chunk;
+
+#endif
\ No newline at end of file
diff --git a/src/main/c/includes/mainFunctions.h b/src/main/c/includes/mainFunctions.h
index 32e5bab..13d4354 100644
--- a/src/main/c/includes/mainFunctions.h
+++ b/src/main/c/includes/mainFunctions.h
@@ -3,13 +3,9 @@
 
 #include <jni.h>
 
-/*
- * Class:     electrosphere_FluidSim
- * Method:    calculateChunkMask
- * Signature: ([Ljava/nio/ByteBuffer;)I
- */
-JNIEXPORT jint JNICALL Java_electrosphere_FluidSim_calculateChunkMask
-  (JNIEnv *, jobject, jobjectArray);
+#include "./chunk.h"
+
+void simulate(int numChunks, Chunk ** passedInChunks, jfloat timestep);
 
 /*
  * Class:     electrosphere_FluidSim
diff --git a/src/main/c/javainterface.c b/src/main/c/javainterface.c
new file mode 100644
index 0000000..cd68b07
--- /dev/null
+++ b/src/main/c/javainterface.c
@@ -0,0 +1,169 @@
+#include <jni.h>
+
+//library includes
+//include stb ds
+#define STB_DS_IMPLEMENTATION
+#include "./lib/stb/stb_ds.h"
+
+//local includes
+#include "./includes/chunk.h"
+#include "./includes/chunkmask.h"
+#include "./includes/mainFunctions.h"
+#include "./includes/utilities.h"
+
+
+//defines
+
+
+//function defines
+#define getChunk(i) (*env)->CallObjectMethod(env,chunkList,jListGet,i)
+#define getBuffArr(buffId) (*env)->GetObjectField(env,chunkJRaw,buffId)
+#define setBuffArr(buffId,value) (*env)->SetObjectField(env,chunkJRaw,buffId,value)
+
+
+
+//declarations
+void readInChunks(JNIEnv * env, jobject chunkList);
+int calculateChunkMask(JNIEnv * env, jobjectArray jrx);
+uint32_t matrix_transform(JNIEnv * env, jobjectArray jrx);
+
+
+
+//the list of chunks
+Chunk ** javaChunkView = NULL;
+//the number of chunks
+int numChunks = 0;
+
+
+JNIEXPORT void JNICALL Java_electrosphere_FluidSim_simulate(
+    JNIEnv * env,
+    jclass fluidSimClass,
+    jobject chunkList,
+    jfloat dt
+    ){
+    readInChunks(env,chunkList);
+    simulate(numChunks,javaChunkView,dt);
+}
+
+
+/**
+ * Reads chunks into the dynamic array
+*/
+void readInChunks(JNIEnv * env, jobject chunkList){
+    jclass listClass = (*env)->FindClass(env,"java/util/List");
+    jclass fluidSimClass = (*env)->FindClass(env,"electrosphere/FluidSim");
+    //JNIEnv *env, jclass clazz, const char *name, const char *sig
+    jmethodID jListSize = (*env)->GetMethodID(env, listClass, "size", "()I");
+    jmethodID jListGet  = (*env)->GetMethodID(env, listClass, "get", "(I)Ljava/lang/Object;");
+    jmethodID jListAdd  = (*env)->GetMethodID(env, listClass, "add", "(Ljava/lang/Object;)Z");
+
+    //ByteBuffer[]
+    jfieldID dJId = (*env)->GetFieldID(env,fluidSimClass,"density","[Ljava/nio/ByteBuffer;");
+    jfieldID d0JId = (*env)->GetFieldID(env,fluidSimClass,"densityAddition","[Ljava/nio/ByteBuffer;");
+    jfieldID uJId = (*env)->GetFieldID(env,fluidSimClass,"uVector","[Ljava/nio/ByteBuffer;");
+    jfieldID vJId = (*env)->GetFieldID(env,fluidSimClass,"vVector","[Ljava/nio/ByteBuffer;");
+    jfieldID wJId = (*env)->GetFieldID(env,fluidSimClass,"wVector","[Ljava/nio/ByteBuffer;");
+    jfieldID u0JId = (*env)->GetFieldID(env,fluidSimClass,"uAdditionVector","[Ljava/nio/ByteBuffer;");
+    jfieldID v0JId = (*env)->GetFieldID(env,fluidSimClass,"vAdditionVector","[Ljava/nio/ByteBuffer;");
+    jfieldID w0JId = (*env)->GetFieldID(env,fluidSimClass,"wAdditionVector","[Ljava/nio/ByteBuffer;");
+    jfieldID chunkmaskJId = (*env)->GetFieldID(env,fluidSimClass,"chunkMask","I");
+
+    //the number of chunks
+    numChunks = (*env)->CallIntMethod(env,chunkList,jListSize);
+
+    //current chunk (this)
+    jobject chunkJRaw;
+    //current chunk fields
+    jobjectArray jd;
+    jobjectArray jd0;
+    jobjectArray u;
+    jobjectArray v;
+    jobjectArray w;
+    jobjectArray u0;
+    jobjectArray v0;
+    jobjectArray w0;
+    int chunkMask;
+
+    //solve chunk mask
+    for(int i = 0; i < numChunks; i++){
+        chunkJRaw = getChunk(i);
+        chunkMask = calculateChunkMask(env,getBuffArr(dJId));
+        (*env)->SetIntField(env,chunkJRaw,chunkmaskJId,chunkMask);
+
+        Chunk * newChunk;
+        if(i >= stbds_arrlen(javaChunkView)){
+            // printf("allocate chunk %d\n",i);
+            // fflush(stdout);
+            newChunk = (Chunk *)malloc(sizeof(Chunk));
+            // printf("new chunk %p\n",newChunk);
+            // fflush(stdout);
+            stbds_arrput(javaChunkView,newChunk);
+            // printf("new chunk %p\n",chunks[i]);
+            // fflush(stdout);
+        } else {
+            newChunk = javaChunkView[i];
+            // printf("get chunk %d: %p\n",i,newChunk);
+            // fflush(stdout);
+        }
+        jd = (*env)->GetObjectField(env,chunkJRaw,dJId);
+        jd0 = (*env)->GetObjectField(env,chunkJRaw,d0JId);
+        u = (*env)->GetObjectField(env,chunkJRaw,uJId);
+        v = (*env)->GetObjectField(env,chunkJRaw,vJId);
+        w = (*env)->GetObjectField(env,chunkJRaw,wJId);
+        u0 = (*env)->GetObjectField(env,chunkJRaw,u0JId);
+        v0 = (*env)->GetObjectField(env,chunkJRaw,v0JId);
+        w0 = (*env)->GetObjectField(env,chunkJRaw,w0JId);
+        newChunk->chunkMask = chunkMask;
+        for(int j = 0; j < 27; j++){
+            if((chunkMask & CHUNK_INDEX_ARR[j]) > 0){
+                newChunk->d[j] = GET_ARR(env,jd,j);
+                newChunk->d0[j] = GET_ARR(env,jd0,j);
+                newChunk->u[j] = GET_ARR(env,u,j);
+                newChunk->v[j] = GET_ARR(env,v,j);
+                newChunk->w[j] = GET_ARR(env,w,j);
+                newChunk->u0[j] = GET_ARR(env,u0,j);
+                newChunk->v0[j] = GET_ARR(env,v0,j);
+                newChunk->w0[j] = GET_ARR(env,w0,j);
+            }
+        }
+    }
+}
+
+
+/**
+ * Calculates the bitmask for available chunks for the provided chunk's neighbor array
+*/
+int calculateChunkMask(JNIEnv * env, jobjectArray jrx){
+    return matrix_transform(env,jrx);
+}
+
+/**
+ * Calculates a mask that represents all nearby chunks that are actually accessible and exist
+*/
+uint32_t matrix_transform(JNIEnv * env, jobjectArray jrx){
+
+    //The returned value, an availability mask that contains the availability of each neighbor chunk
+    uint32_t rVal = 0;
+
+    //Add to maks for initial chunks
+    for(int i = 0; i < CENTER_LOC; i++){
+        if((*env)->GetObjectArrayElement(env,jrx,i)!=NULL){
+            rVal = rVal + 1;
+        }
+        rVal = rVal << 1;
+    }
+    //add 1 for center chunk because we already have that
+    rVal = rVal + 1;
+    rVal = rVal << 1;
+    //continue on for remaining chunks
+    for(int i = CENTER_LOC+1; i < 27; i++){
+        if((*env)->GetObjectArrayElement(env,jrx,i)!=NULL){
+            rVal = rVal + 1;
+        }
+        if(i < 26){
+            rVal = rVal << 1;
+        }
+    }
+
+    return rVal;
+}
\ No newline at end of file