tira/biomodels/flow.h

/*
Copyright <2017> <David Mayerich>
Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
#ifndef STIM_FLOW_H
#define STIM_FLOW_H
#include <vector>
#include <algorithm>
//STIM include
#include <stim/math/vec3.h>
#include <stim/parser/arguments.h>
#include <stim/biomodels/network.h>
#ifdef __CUDACC__
#include <cublas_v2.h>
#include <stim/cuda/cudatools/error.h>
#endif
namespace stim {
	template <typename A, typename B, typename C>
	struct triple {
		A first;
		B second;
		C third;
	};
	template <typename T>
	struct bridge {
		std::vector<unsigned> v;	// vertices' indices
		std::vector<typename stim::vec3<T> > V;	// vertices' coordinates
		T l;		// length
		T r;		// radii
		T deltaP;	// pressure drop
		T Q;		// volume flow rate
	};
	template <typename T>
	class flow {
	private:
		
		// calculate the cofactor of elemen[row][col]
		void get_minor(T** src, T** dest, int row, int col, int order) {
			// index of element to be copied
			int rowCount = 0;
			int colCount = 0;
			for (int i = 0; i < order; i++) {
				if (i != row) {
					colCount = 0;
					for (int j = 0; j < order; j++) {
						// when j is not the element
						if (j != col) {
							dest[rowCount][colCount] = src[i][j];
							colCount++;
						}
					}
					rowCount++;
				}
			}
		}
		// calculate the det()
		T determinant(T** mat, int order) {
			// degenate case when n = 1
			if (order == 1)
				return mat[0][0];
			T det = 0.0;		// determinant value
			// allocate the cofactor matrix
			T** minor = (T**)malloc((order - 1) * sizeof(T*));
			for (int i = 0; i < order - 1; i++)
				minor[i] = (T*)malloc((order - 1) * sizeof(T));
			for (int i = 0; i < order; i++) {
				// get minor of element(0, i)
				get_minor(mat, minor, 0, i, order);
				// recursion
				det += (i % 2 == 1 ? -1.0 : 1.0) * mat[0][i] * determinant(minor, order - 1);
			}
			// release memory
			for (int i = 0; i < order - 1; i++)
				free(minor[i]);
			free(minor);
			return det;
		}
	public:
		T** C;																	// Conductance
		std::vector<typename stim::triple<unsigned, unsigned, float> > Q;		// volume flow rate
		std::vector<T> QQ;														// Q' vector
		std::vector<T> P;														// initial pressure
		std::vector<T> pressure;												// final pressure
		//std::vector<typename stim::triple<unsigned, unsigned, T> > V;		 // velocity
		//std::vector<typename stim::triple<unsigned, unsigned, T> > Q;		 // volume flow rate
		//std::vector<typename stim::triple<unsigned, unsigned, T> > deltaP; // pressure drop
		flow() {}				// default constructor
		void init(unsigned n_e, unsigned n_v) {
			
			C = new T*[n_v]();
			for (unsigned i = 0; i < n_v; i++) {
				C[i] = new T[n_v]();
			}
			QQ.resize(n_v);
			P.resize(n_v);
			pressure.resize(n_v);
			Q.resize(n_e);
		}
		void reset(unsigned n_v) {
			
			for (unsigned i = 0; i < n_v; i++) {
				for (unsigned j = 0; j < n_v; j++) {
					C[i][j] = 0;
				}
			}
		}
		void clear(unsigned n_v) {
			
			for (unsigned i = 0; i < n_v; i++)
				delete[] C[i];
			delete[] C;
		}
		/// Calculate the inverse of A and store the result in C
		void inversion(T** A, int order, T* C) {
#ifdef __CUDACC__
		
			// convert from double pointer to single pointer, make it flat
			T* Aflat = (T*)malloc(order * order * sizeof(T));
			for (unsigned i = 0; i < order; i++)
				for (unsigned j = 0; j < order; j++)
					Aflat[i * order + j] = A[i][j];
			// create device pointer
			T* d_Aflat;		// flat original matrix
			T* d_Cflat;	// flat inverse matrix
			T** d_A;		// put the flat original matrix into another array of pointer
			T** d_C;
			int *d_P;
			int *d_INFO;
			// allocate memory on device
			HANDLE_ERROR(cudaMalloc((void**)&d_Aflat, order * order * sizeof(T)));
			HANDLE_ERROR(cudaMalloc((void**)&d_Cflat, order * order * sizeof(T)));
			HANDLE_ERROR(cudaMalloc((void**)&d_A, sizeof(T*)));
			HANDLE_ERROR(cudaMalloc((void**)&d_C, sizeof(T*)));
			HANDLE_ERROR(cudaMalloc((void**)&d_P, order * 1 * sizeof(int)));
			HANDLE_ERROR(cudaMalloc((void**)&d_INFO, 1 * sizeof(int)));
			// copy matrix from host to device
			HANDLE_ERROR(cudaMemcpy(d_Aflat, Aflat, order * order * sizeof(T), cudaMemcpyHostToDevice));
			
			// copy matrix from device to device
			HANDLE_ERROR(cudaMemcpy(d_A, &d_Aflat, sizeof(T*), cudaMemcpyHostToDevice));
			HANDLE_ERROR(cudaMemcpy(d_C, &d_Cflat, sizeof(T*), cudaMemcpyHostToDevice));
			// calculate the inverse of matrix based on cuBLAS
			cublasHandle_t handle;		
			CUBLAS_HANDLE_ERROR(cublasCreate_v2(&handle));	// create cuBLAS handle object
			CUBLAS_HANDLE_ERROR(cublasSgetrfBatched(handle, order, d_A, order, d_P, d_INFO, 1));
			int INFO = 0;
			HANDLE_ERROR(cudaMemcpy(&INFO, d_INFO, sizeof(int), cudaMemcpyDeviceToHost));
			if (INFO == order)
			{
				std::cout << "Factorization Failed : Matrix is singular." << std::endl;
				cudaDeviceReset();
				exit(1);
			}
			CUBLAS_HANDLE_ERROR(cublasSgetriBatched(handle, order, (const T **)d_A, order, d_P, d_C, order, d_INFO, 1));
			CUBLAS_HANDLE_ERROR(cublasDestroy_v2(handle));
			// copy inverse matrix from device to device
			HANDLE_ERROR(cudaMemcpy(&d_Cflat, d_C, sizeof(T*), cudaMemcpyDeviceToHost));
			// copy inverse matrix from device to host
			HANDLE_ERROR(cudaMemcpy(C, d_Cflat, order * order * sizeof(T), cudaMemcpyDeviceToHost));
			// clear up
			free(Aflat);
			HANDLE_ERROR(cudaFree(d_Aflat));
			HANDLE_ERROR(cudaFree(d_Cflat));
			HANDLE_ERROR(cudaFree(d_A));
			HANDLE_ERROR(cudaFree(d_C));
			HANDLE_ERROR(cudaFree(d_P));
			HANDLE_ERROR(cudaFree(d_INFO));
#else
			// get the determinant of a
			double det = 1.0 / determinant(A, order);
			// memory allocation
			T* tmp = (T*)malloc((order - 1)*(order - 1) * sizeof(T));
			T** minor = (T**)malloc((order - 1) * sizeof(T*));
			for (int i = 0; i < order - 1; i++)
				minor[i] = tmp + (i * (order - 1));
			for (int j = 0; j < order; j++) {
				for (int i = 0; i < order; i++) {
					// get the co-factor (matrix) of A(j,i)
					get_minor(A, minor, j, i, order);
					C[i][j] = det * determinant(minor, order - 1);
					if ((i + j) % 2 == 1)
						C[i][j] = -C[i][j];
				}
			}
			// release memory
			free(tmp);
			free(minor);
#endif
		}
	};
}
#endif
//// calculate the flow rate of 3D model(circle cross section)
//void calculate_flow_rate(unsigned e, T r) {
//	stim::triple<unsigned, unsigned, T> tmp_Q;
//	tmp_Q.first = V[e].first;			// copy the vertices information
//	tmp_Q.second = V[e].second;
//	tmp_Q.third = V[e].third * stim::PI * pow(r, 2);	// UNITS: uL/s
//	Q.push_back(tmp_Q);					// push back the volume flow rate information for every edge
//}
//// calculate the flow rate of 2D model(rectangular cross section)
//void calculate_flow_rate(unsigned e, T r, T h) {
//	stim::triple<unsigned, unsigned, T> tmp_Q;
//	tmp_Q.first = V[e].first;			// copy the vertices information
//	tmp_Q.second = V[e].second;
//	tmp_Q.third = V[e].third * h * r;					// UNITS: uL/s = mm^3/s
//	Q.push_back(tmp_Q);					// push back the volume flow rate information for every edge
//}
//// calculate the pressure drop of 3D model(circle cross section)
//void calculate_deltaP(unsigned e, T u, T l, T r) {
//	stim::triple<unsigned, unsigned, T> tmp_deltaP;
//	tmp_deltaP.first = V[e].first;		// copy the vertices information
//	tmp_deltaP.second = V[e].second;
//	tmp_deltaP.third = (8 * u * l * Q[e].third) / (stim::PI * pow(r, 4));		// UNITS: g/mm/s^2 = Pa
//	deltaP.push_back(tmp_deltaP);		// push back the volume flow rate information for every edge
//}
//// calculate the pressure drop of 2D model(rectangular cross section)
//void calculate_deltaP(unsigned e, T u, T l, T r, T h) {
//	stim::triple<unsigned, unsigned, T> tmp_deltaP;
//	tmp_deltaP.first = V[e].first;		// copy the vertices information
//	tmp_deltaP.second = V[e].second;
//	tmp_deltaP.third = (12 * u * l * Q[e].third) / (h * pow(r, 3));	// UNITS: g/mm/s^2 = Pa
//	deltaP.push_back(tmp_deltaP);		// push back the volume flow rate information for every edge
//}
//// better way to do this???
//// find the maximum and minimum pressure positions
//void find_max_min_pressure(size_t n_e, size_t n_v, unsigned& max, unsigned& min) {
//	std::vector<T> P(n_v, FLT_MAX);
//	// set one to reference
//	P[Q[0].first] = 0.0;
//	unsigned first = 0;
//	unsigned second = 0;
//	// calculate all the relative pressure in brute force manner
//	for (unsigned e = 0; e < n_e; e++) {
//		// assuming the obj file stores in a straight order, in other words, like swc file
//		first = Q[e].first;
//		second = Q[e].second;
//		if (P[first] != FLT_MAX)		// if pressure at start vertex is known
//			P[second] = P[first] - deltaP[e].third;
//		else if (P[second] != FLT_MAX)	// if pressure at end vertex is known
//			P[first] = P[second] + deltaP[e].third;
//	}
//	// find the maximum and minimum pressure position
//	auto m1 = std::max_element(P.begin(), P.end());		// temporarily max number
//	auto m2 = std::min_element(P.begin(), P.end());		// temporarily min number
//	max = std::distance(P.begin(), m1);
//	min = std::distance(P.begin(), m2);
//	T tmp_m = *m2;
//	// Now set the lowest pressure port to reference pressure(0.0 Pa)
//	for (unsigned i = 0; i < n_v; i++)
//		P[i] -= tmp_m;
//	for (unsigned i = 0; i < n_v; i++)
//		pressure.push_back(P[i]);
//}