Began reorganizing project

notes.org

-
-* TODO active
-** Fix wrapping routines (trouble with machine precision
-
-** make units and kT more uniform (references to 295 K are hardcoded into RB code and Temperature code) 
-*** I would prefer to specify temperature in K, rather than specifying a scaling factor to be applied to all energies to make them kT
-
-** handle periodic boundaries for RBs
-** RB read restart file
-** RB throw exception if an RB type uses a grid key multiple times
-** RB each RB gets temperature from grid
-
-
-* TODO eventually
-** enable flag to disable physics-checking assertions in kernels (also write these assertions)
-** split computation into multiple regions
-*** simulate regions, also in overlap
-**** atoms at edge of overlap can have DoF frozen
-*** periodically synchronize positions
-*** optimize to minimize communication & error
-**** monitor energy jumps associated with this process
-
-
-** organize code a bit better
-** increase cells/cutoff
-
-** improve pairlist algorithm
-http://arxiv.org/pdf/1306.1737.pdf
-** RB optionally don't eval forces every ts
-
-** pairlists for rigid bodies 
-*** maybe for grids, depending on parallel structure of code
-
-* Organization of code
-** RgidBodyController (RBC) holds device pointers, manages force evaluation and integration
-
-
-* other ideas
-** interpolate density grid?
-
-BaseGrid.h:	// RBTODO Fix?
-BaseGrid.h-	BaseGrid(); // cmaffeo2 (2015) moved this out of protected, cause I wanted BaseGrid in a struct
-BaseGrid.h-  // The most obvious of constructors.
-BaseGrid.h-		BaseGrid(Matrix3 basis0, Vector3 origin0, int nx0, int ny0, int nz0);
-BaseGrid.h-
---
-BaseGrid.h-    float a0, a1, a2, a3;
-BaseGrid.h-
-BaseGrid.h:		// RBTODO parallelize loops?
-BaseGrid.h-		
-BaseGrid.h-    // Mix along x, taking the derivative.
-BaseGrid.h-    float g2[4][4];
-BaseGrid.h-    for (int iy = 0; iy < 4; iy++) {
---
-BaseGrid.h-  }
-BaseGrid.h-
-BaseGrid.h:	// RBTODO overload with optimized algorithm
-BaseGrid.h-	//  skip transforms (assume identity basis)
-BaseGrid.h-  HOST DEVICE inline float interpolatePotential(Vector3 pos) const {
-BaseGrid.h-    // Find the home node.
-BaseGrid.h-    Vector3 l = basisInv.transform(pos - origin);
---
-BaseGrid.h-
-BaseGrid.h-		// out of grid? return 0
-BaseGrid.h:		// RBTODO
-BaseGrid.h-			
-BaseGrid.h-    // Get the array jumps.
-BaseGrid.h-    int jump[3];
-BaseGrid.h-    jump[0] = nz*ny;
---
-BaseGrid.h-		// Find the values at the neighbors.
-BaseGrid.h-		float g1[4][4][4];
-BaseGrid.h:		//RBTODO parallelize?
-BaseGrid.h-		for (int ix = 0; ix < 4; ix++) {
-BaseGrid.h-			for (int iy = 0; iy < 4; iy++) {
-BaseGrid.h-				for (int iz = 0; iz < 4; iz++) {
-BaseGrid.h-	  			// Wrap around the periodic boundaries. 
---
-ComputeGridGrid.cuh-													Matrix3 basis_rho, Vector3 origin_rho,
-ComputeGridGrid.cuh-													Matrix3 basis_u,   Vector3 origin_u) {
-ComputeGridGrid.cuh:  // RBTODO http://devblogs.nvidia.com/parallelforall/cuda-pro-tip-write-flexible-kernels-grid-stride-loops/
-ComputeGridGrid.cuh-	const unsigned int r_id = blockIdx.x * blockDim.x + threadIdx.x;
-ComputeGridGrid.cuh-	
-ComputeGridGrid.cuh:	// RBTODO parallelize transform
-ComputeGridGrid.cuh-	if (r_id > rho->size)					// skip threads with no data 
-ComputeGridGrid.cuh-		return;
-ComputeGridGrid.cuh-	
-ComputeGridGrid.cuh-	// Maybe: Tile grid data into shared memory
-ComputeGridGrid.cuh:	//   RBTODO: think about localizing regions of grid data
-ComputeGridGrid.cuh-	Vector3 p = rho->getPosition(r_id, basis, origin);
-ComputeGridGrid.cuh-	float val = rho->val[r_id];
-ComputeGridGrid.cuh-
-ComputeGridGrid.cuh:	// RBTODO reduce forces and torques
-ComputeGridGrid.cuh-	// http://www.cuvilib.com/Reduction.pdf
-ComputeGridGrid.cuh-
-ComputeGridGrid.cuh:	// RBTODO combine interp methods and reduce repetition! 
-ComputeGridGrid.cuh-	float energy = u->interpolatePotential(p); 
-ComputeGridGrid.cuh-	Vector3 f = u->interpolateForceD(p);
-ComputeGridGrid.cuh-	Vector3 t = cross(p,f);				// test if sign is correct!
-ComputeGridGrid.cuh-
-ComputeGridGrid.cuh:	// RBTODO 3rd-law forces + torques
-ComputeGridGrid.cuh-}
---
-Configuration.cpp-				cudaMemcpyHostToDevice));
-Configuration.cpp-	}
-Configuration.cpp:	// RBTODO: moved this out of preceding loop; was that correct?
-Configuration.cpp-	gpuErrchk(cudaMemcpyAsync(part_d, part_addr, sizeof(BrownianParticleType*) * numParts,
-Configuration.cpp-				cudaMemcpyHostToDevice));
-Configuration.cpp-
-Configuration.cpp-
---
-Configuration.cpp-			sz = sizeof(float) * len;
-Configuration.cpp-			gpuErrchk(cudaMemcpy( tmpData, g->val, sz, cudaMemcpyHostToDevice));
-Configuration.cpp:			// RBTODO: why can't this be deleted? 
-Configuration.cpp-			// delete[] tmpData;
-Configuration.cpp-		}
-Configuration.cpp-	}
-Configuration.cpp-
---
-Configuration.cpp-			sz = sizeof(float) * len;
-Configuration.cpp-			gpuErrchk(cudaMemcpy( tmpData, g->val, sz, cudaMemcpyHostToDevice));
-Configuration.cpp:			// RBTODO: why can't this be deleted? 
-Configuration.cpp-			// delete[] tmpData;
-Configuration.cpp-		}
-Configuration.cpp-		
-Configuration.cpp-  }
---
-RigidBodyGrid.h-	\===============================*/
-RigidBodyGrid.h-	
-RigidBodyGrid.h:	// RBTODO Fix?
-RigidBodyGrid.h-	RigidBodyGrid(); // cmaffeo2 (2015) moved this out of protected, cause I wanted RigidBodyGrid in a struct
-RigidBodyGrid.h-  // The most obvious of constructors.
-RigidBodyGrid.h-		RigidBodyGrid(int nx0, int ny0, int nz0);
-RigidBodyGrid.h-
---
-RigidBodyGrid.h-    float a0, a1, a2, a3;
-RigidBodyGrid.h-
-RigidBodyGrid.h:		// RBTODO further parallelize loops? unlikely?
-RigidBodyGrid.h-		
-RigidBodyGrid.h-    // Mix along x, taking the derivative.
-RigidBodyGrid.h-    float g2[4][4];
-RigidBodyGrid.h-    for (int iy = 0; iy < 4; iy++) {
---
-RigidBodyGrid.h-
-RigidBodyGrid.h-		// out of grid? return 0
-RigidBodyGrid.h:		// RBTODO
-RigidBodyGrid.h-			
-RigidBodyGrid.h-    // Get the array jumps.
-RigidBodyGrid.h-    int jump[3];
-RigidBodyGrid.h-    jump[0] = nz*ny;
---
-RigidBodyGrid.h-		w[2] = l.z - homeZ;
-RigidBodyGrid.h-		// Find the values at the neighbors.
-RigidBodyGrid.h:		float g1[4][4][4];					/* RBTODO: inefficient for my algorithm? */
-RigidBodyGrid.h-		for (int ix = 0; ix < 4; ix++) {
-RigidBodyGrid.h-			int jx = ix-1 + home[0];
-RigidBodyGrid.h-			for (int iy = 0; iy < 4; iy++) {
-RigidBodyGrid.h-				int jy = iy-1 + home[1];
---
-RigidBodyGrid.h-	  			// Assume zero value at edges
-RigidBodyGrid.h-					int jz = iz-1 + home[2];
-RigidBodyGrid.h:					// RBTODO: possible branch divergence in warp?
-RigidBodyGrid.h-					if (jx <  0  ||  jy < 0  ||  jz < 0  ||
-RigidBodyGrid.h-							jx >= nx || jz >= nz || jz >= nz) {
-RigidBodyGrid.h-						g1[ix][iy][iz] = 0;
-RigidBodyGrid.h-					} else {
---
-RigidBodyGrid.h-		// Find the values at the neighbors.
-RigidBodyGrid.h-		float g1[4][4][4];
-RigidBodyGrid.h:		//RBTODO parallelize?
-RigidBodyGrid.h-		for (int ix = 0; ix < 4; ix++) {
-RigidBodyGrid.h-			for (int iy = 0; iy < 4; iy++) {
-RigidBodyGrid.h-				for (int iz = 0; iz < 4; iz++) {
-RigidBodyGrid.h-	  			// Wrap around the periodic boundaries.