src/autodock/autodock_gpu.cu

/**
 * @file autodock_gpu.cu
 * @brief Implementation of GPU-accelerated AutoDock
 * 
 * @authors OpenPeer AI, Riemann Computing Inc., Bleunomics, Andrew Magdy Kamal
 */

#include "autodock_gpu.cuh"
#include <iostream>
#include <fstream>
#include <algorithm>
#include <cmath>
#include <curand_kernel.h>

namespace docking_at_home {
namespace autodock {

// CUDA error checking macro
#define CUDA_CHECK(call) \
    do { \
        cudaError_t err = call; \
        if (err != cudaSuccess) { \
            std::cerr << "CUDA error in " << __FILE__ << ":" << __LINE__ \
                      << " - " << cudaGetErrorString(err) << std::endl; \
            return false; \
        } \
    } while(0)

// AutoDockGPU Implementation

AutoDockGPU::AutoDockGPU() 
    : is_initialized_(false), device_id_(0),
      d_ligand_atoms_(nullptr), d_receptor_atoms_(nullptr),
      d_energy_grid_(nullptr), d_population_(nullptr), d_energies_(nullptr),
      ligand_atoms_size_(0), receptor_atoms_size_(0),
      total_computation_time_(0.0f), total_evaluations_(0) {
}

AutoDockGPU::~AutoDockGPU() {
    cleanup();
}

bool AutoDockGPU::initialize(int device_id) {
    device_id_ = device_id;

    // Check CUDA device
    int device_count;
    CUDA_CHECK(cudaGetDeviceCount(&device_count));
    
    if (device_id_ >= device_count) {
        std::cerr << "Invalid device ID: " << device_id_ << std::endl;
        return false;
    }

    CUDA_CHECK(cudaSetDevice(device_id_));
    CUDA_CHECK(cudaGetDeviceProperties(&device_prop_, device_id_));

    std::cout << "Initialized GPU: " << device_prop_.name << std::endl;
    std::cout << "Compute Capability: " << device_prop_.major << "." 
              << device_prop_.minor << std::endl;
    std::cout << "Total Global Memory: " << device_prop_.totalGlobalMem / (1024*1024) 
              << " MB" << std::endl;

    // Initialize CUDPP
    CUDPPConfiguration config;
    config.algorithm = CUDPP_SORT_RADIX;
    config.datatype = CUDPP_FLOAT;
    config.op = CUDPP_ADD;
    config.options = CUDPP_OPTION_FORWARD | CUDPP_OPTION_EXCLUSIVE;

    CUDPPResult result = cudppCreate(&cudpp_handle_);
    if (result != CUDPP_SUCCESS) {
        std::cerr << "CUDPP initialization failed" << std::endl;
        return false;
    }

    is_initialized_ = true;
    return true;
}

bool AutoDockGPU::load_ligand(const std::string& filename, Ligand& ligand) {
    std::ifstream file(filename);
    if (!file.is_open()) {
        std::cerr << "Failed to open ligand file: " << filename << std::endl;
        return false;
    }

    ligand.atoms.clear();
    ligand.name = filename;
    ligand.num_rotatable_bonds = 0;

    std::string line;
    while (std::getline(file, line)) {
        if (line.substr(0, 4) == "ATOM" || line.substr(0, 6) == "HETATM") {
            Atom atom;
            // Parse PDBQT format (simplified)
            // In production, use proper PDBQT parser
            atom.x = std::stof(line.substr(30, 8));
            atom.y = std::stof(line.substr(38, 8));
            atom.z = std::stof(line.substr(46, 8));
            atom.charge = 0.0f;
            atom.radius = 1.5f;
            atom.type = 0;
            
            ligand.atoms.push_back(atom);
        }
    }

    file.close();

    // Calculate geometric center
    ligand.center_x = ligand.center_y = ligand.center_z = 0.0f;
    for (const auto& atom : ligand.atoms) {
        ligand.center_x += atom.x;
        ligand.center_y += atom.y;
        ligand.center_z += atom.z;
    }
    int n = ligand.atoms.size();
    if (n > 0) {
        ligand.center_x /= n;
        ligand.center_y /= n;
        ligand.center_z /= n;
    }

    std::cout << "Loaded ligand: " << ligand.atoms.size() << " atoms" << std::endl;
    return true;
}

bool AutoDockGPU::load_receptor(const std::string& filename, Receptor& receptor) {
    std::ifstream file(filename);
    if (!file.is_open()) {
        std::cerr << "Failed to open receptor file: " << filename << std::endl;
        return false;
    }

    receptor.atoms.clear();
    receptor.name = filename;

    std::string line;
    while (std::getline(file, line)) {
        if (line.substr(0, 4) == "ATOM" || line.substr(0, 6) == "HETATM") {
            Atom atom;
            atom.x = std::stof(line.substr(30, 8));
            atom.y = std::stof(line.substr(38, 8));
            atom.z = std::stof(line.substr(46, 8));
            atom.charge = 0.0f;
            atom.radius = 1.5f;
            atom.type = 0;
            
            receptor.atoms.push_back(atom);
        }
    }

    file.close();

    // Calculate grid bounds
    if (!receptor.atoms.empty()) {
        float min_x = receptor.atoms[0].x, max_x = receptor.atoms[0].x;
        float min_y = receptor.atoms[0].y, max_y = receptor.atoms[0].y;
        float min_z = receptor.atoms[0].z, max_z = receptor.atoms[0].z;

        for (const auto& atom : receptor.atoms) {
            min_x = std::min(min_x, atom.x);
            max_x = std::max(max_x, atom.x);
            min_y = std::min(min_y, atom.y);
            max_y = std::max(max_y, atom.y);
            min_z = std::min(min_z, atom.z);
            max_z = std::max(max_z, atom.z);
        }

        // Add padding
        float padding = 10.0f;
        receptor.grid_min_x = min_x - padding;
        receptor.grid_max_x = max_x + padding;
        receptor.grid_min_y = min_y - padding;
        receptor.grid_max_y = max_y + padding;
        receptor.grid_min_z = min_z - padding;
        receptor.grid_max_z = max_z + padding;
        receptor.grid_spacing = 0.375f; // Standard AutoDock grid spacing
    }

    std::cout << "Loaded receptor: " << receptor.atoms.size() << " atoms" << std::endl;
    return true;
}

bool AutoDockGPU::dock(const Ligand& ligand, 
                       const Receptor& receptor,
                       const DockingParameters& params,
                       std::vector<DockingPose>& poses) {
    if (!is_initialized_) {
        std::cerr << "GPU not initialized" << std::endl;
        return false;
    }

    std::cout << "Starting GPU-accelerated docking..." << std::endl;
    std::cout << "Ligand: " << ligand.atoms.size() << " atoms" << std::endl;
    std::cout << "Receptor: " << receptor.atoms.size() << " atoms" << std::endl;
    std::cout << "Parameters: " << params.num_runs << " runs, " 
              << params.population_size << " population size" << std::endl;

    cudaEvent_t start, stop;
    cudaEventCreate(&start);
    cudaEventCreate(&stop);
    cudaEventRecord(start);

    // Allocate and transfer memory
    if (!allocate_device_memory(ligand, receptor)) {
        return false;
    }
    
    if (!transfer_to_device(ligand, receptor)) {
        return false;
    }

    // Compute energy grid
    if (!compute_energy_grid(receptor)) {
        return false;
    }

    // Run genetic algorithm
    if (!run_genetic_algorithm(params, poses)) {
        return false;
    }

    // Cluster results
    if (!cluster_results(poses, params.rmsd_tolerance)) {
        return false;
    }

    cudaEventRecord(stop);
    cudaEventSynchronize(stop);
    
    float milliseconds = 0;
    cudaEventElapsedTime(&milliseconds, start, stop);
    total_computation_time_ = milliseconds / 1000.0f;

    std::cout << "Docking completed in " << total_computation_time_ << " seconds" << std::endl;
    std::cout << "Generated " << poses.size() << " unique poses" << std::endl;

    cudaEventDestroy(start);
    cudaEventDestroy(stop);

    return true;
}

std::string AutoDockGPU::get_device_info() {
    if (!is_initialized_) {
        return "GPU not initialized";
    }

    std::stringstream ss;
    ss << "Device: " << device_prop_.name << "\n"
       << "Compute Capability: " << device_prop_.major << "." << device_prop_.minor << "\n"
       << "Total Memory: " << device_prop_.totalGlobalMem / (1024*1024) << " MB\n"
       << "Multiprocessors: " << device_prop_.multiProcessorCount << "\n"
       << "Max Threads per Block: " << device_prop_.maxThreadsPerBlock;
    
    return ss.str();
}

std::string AutoDockGPU::get_performance_metrics() {
    std::stringstream ss;
    ss << "Total Computation Time: " << total_computation_time_ << " seconds\n"
       << "Total Evaluations: " << total_evaluations_ << "\n"
       << "Evaluations per Second: " 
       << (total_computation_time_ > 0 ? total_evaluations_ / total_computation_time_ : 0);
    
    return ss.str();
}

void AutoDockGPU::cleanup() {
    if (is_initialized_) {
        free_device_memory();
        cudppDestroy(cudpp_handle_);
        cudaDeviceReset();
        is_initialized_ = false;
    }
}

// Private methods

bool AutoDockGPU::allocate_device_memory(const Ligand& ligand, const Receptor& receptor) {
    ligand_atoms_size_ = ligand.atoms.size() * sizeof(Atom);
    receptor_atoms_size_ = receptor.atoms.size() * sizeof(Atom);

    CUDA_CHECK(cudaMalloc(&d_ligand_atoms_, ligand_atoms_size_));
    CUDA_CHECK(cudaMalloc(&d_receptor_atoms_, receptor_atoms_size_));

    // Allocate energy grid (simplified)
    size_t grid_size = 100 * 100 * 100 * sizeof(float);
    CUDA_CHECK(cudaMalloc(&d_energy_grid_, grid_size));

    return true;
}

bool AutoDockGPU::transfer_to_device(const Ligand& ligand, const Receptor& receptor) {
    CUDA_CHECK(cudaMemcpy(d_ligand_atoms_, ligand.atoms.data(), 
                          ligand_atoms_size_, cudaMemcpyHostToDevice));
    CUDA_CHECK(cudaMemcpy(d_receptor_atoms_, receptor.atoms.data(), 
                          receptor_atoms_size_, cudaMemcpyHostToDevice));
    return true;
}

bool AutoDockGPU::compute_energy_grid(const Receptor& receptor) {
    // Simplified energy grid computation
    std::cout << "Computing energy grid on GPU..." << std::endl;
    return true;
}

bool AutoDockGPU::run_genetic_algorithm(const DockingParameters& params, 
                                        std::vector<DockingPose>& poses) {
    std::cout << "Running genetic algorithm on GPU..." << std::endl;
    
    // Create sample poses (in production, this would run actual GA)
    for (int i = 0; i < params.num_runs; ++i) {
        DockingPose pose;
        pose.translation[0] = pose.translation[1] = pose.translation[2] = 0.0f;
        pose.rotation[0] = 1.0f; pose.rotation[1] = pose.rotation[2] = pose.rotation[3] = 0.0f;
        pose.binding_energy = -5.0f + (rand() % 100) / 10.0f;
        pose.rank = i + 1;
        poses.push_back(pose);
    }
    
    total_evaluations_ = params.num_runs * params.num_evals;
    
    return true;
}

bool AutoDockGPU::cluster_results(std::vector<DockingPose>& poses, float rmsd_tolerance) {
    // Sort by energy
    std::sort(poses.begin(), poses.end(), 
              [](const DockingPose& a, const DockingPose& b) {
                  return a.binding_energy < b.binding_energy;
              });
    
    // Simplified clustering (in production, use RMSD-based clustering)
    return true;
}

void AutoDockGPU::free_device_memory() {
    if (d_ligand_atoms_) cudaFree(d_ligand_atoms_);
    if (d_receptor_atoms_) cudaFree(d_receptor_atoms_);
    if (d_energy_grid_) cudaFree(d_energy_grid_);
    if (d_population_) cudaFree(d_population_);
    if (d_energies_) cudaFree(d_energies_);
}

// CUDA Kernel Implementations

__global__ void calculate_energy_kernel(
    const Atom* ligand_atoms,
    const Atom* receptor_atoms,
    int num_ligand_atoms,
    int num_receptor_atoms,
    float* energies) {
    
    int idx = blockIdx.x * blockDim.x + threadIdx.x;
    if (idx >= num_ligand_atoms * num_receptor_atoms) return;

    int lig_idx = idx / num_receptor_atoms;
    int rec_idx = idx % num_receptor_atoms;

    Atom lig = ligand_atoms[lig_idx];
    Atom rec = receptor_atoms[rec_idx];

    // Calculate distance
    float dx = lig.x - rec.x;
    float dy = lig.y - rec.y;
    float dz = lig.z - rec.z;
    float r2 = dx*dx + dy*dy + dz*dz;
    float r = sqrtf(r2);

    // Simplified Lennard-Jones potential
    float r6 = r2 * r2 * r2;
    float r12 = r6 * r6;
    float energy = 4.0f * ((1.0f / r12) - (1.0f / r6));

    energies[idx] = energy;
}

__global__ void evaluate_population_kernel(
    const float* population,
    const Atom* ligand_atoms,
    const Atom* receptor_atoms,
    const float* energy_grid,
    float* fitness_values,
    int population_size,
    int num_genes) {
    
    int idx = blockIdx.x * blockDim.x + threadIdx.x;
    if (idx >= population_size) return;

    // Simplified fitness evaluation
    fitness_values[idx] = population[idx * num_genes];
}

__global__ void crossover_kernel(
    float* population,
    const float* parent_indices,
    float crossover_rate,
    int population_size,
    int num_genes,
    unsigned long long seed) {
    
    int idx = blockIdx.x * blockDim.x + threadIdx.x;
    if (idx >= population_size / 2) return;

    curandState state;
    curand_init(seed, idx, 0, &state);

    if (curand_uniform(&state) < crossover_rate) {
        // Perform crossover
        int crossover_point = curand(&state) % num_genes;
        // Swap genes after crossover point
    }
}

__global__ void mutation_kernel(
    float* population,
    float mutation_rate,
    int population_size,
    int num_genes,
    unsigned long long seed) {
    
    int idx = blockIdx.x * blockDim.x + threadIdx.x;
    int total_genes = population_size * num_genes;
    if (idx >= total_genes) return;

    curandState state;
    curand_init(seed, idx, 0, &state);

    if (curand_uniform(&state) < mutation_rate) {
        // Mutate gene
        population[idx] += curand_normal(&state) * 0.1f;
    }
}

} // namespace autodock
} // namespace docking_at_home