add common nonbonded force kernel

src/core/cuda/include/CudaContext.cuh

@@ -2,6 +2,10 @@
 
 #include <cuda_runtime.h>
 
+#include <array>
+#include <map>
+#include <vector>
+
 #include "system.h"
 #include "utils.h"
 
@@ -105,6 +109,27 @@ class CudaContext {
     charge_t* d_charges;
     p_atom_t* d_p_atoms;
 
+    /*
+    Other helper arrays
+    */
+    ccharge_t* d_charge_table_all;  // Device copy of h_charge_table_all
+    catype_t* d_catype_table_all;   // Device copy of h_catype_table_all
+    std::map<std::array<double, 6>, int> catype_to_type_host;
+    int* d_p_charge_types;
+    int* d_w_charge_types;
+    int* d_q_charge_types;  // [0, lambdas * n_qatoms) is the normal q_charge_type, [lambdas * n_qatoms, ... ) is the lambda-scaled q_charge_type]
+
+    int* d_p_catype_types;
+    int* d_w_catype_types;
+    int* d_q_catype_types;  // [0, lambdas * n_qatoms) is the normal q_catype_type, [lambdas * n_qatoms, ... ) is the lambda-scaled q_catype_type]
+
+    int *d_p_atoms_list;
+    int *d_w_atoms_list;
+    int *d_q_atoms_list;
+    std::vector<int> h_p_atoms_list;
+    std::vector<int> h_w_atoms_list;
+    std::vector<int> h_q_atoms_list;
+
     static CudaContext& instance() {
         static CudaContext ctx;
         return ctx;
@@ -121,6 +146,16 @@ class CudaContext {
     void sync_all_to_host();
     void reset_energies();
 
+    std::array<double, 6> get_catype_key(const catype_t& catype) {
+        return {
+            catype.aii_normal,
+            catype.bii_normal,
+            catype.aii_polar,
+            catype.bii_polar,
+            catype.aii_1_4,
+            catype.bii_1_4};
+    }
+
    private:
     CudaContext() = default;
 
@@ -129,6 +164,10 @@ class CudaContext {
     ~CudaContext() { free(); }
     CudaContext(const CudaContext&) = delete;
     CudaContext& operator=(const CudaContext&) = delete;
+
+    void initialize_charge_tables_host();
+    void initialize_catype_tables_host();
+    void initialize_atom_lists_host();
 };
 template <typename T>
 void CudaContext::sync_array_to_device(T* dst, const T* src, int count) {

src/core/cuda/include/CudaNonbondedForce.cuh

@@ -0,0 +1,22 @@
+#pragma once
+#include "system.h"
+
+void init_nonbonded_force_kernel_data();
+
+std::pair<double, double> calc_nonbonded_force_host(
+    int nx, 
+    int ny, 
+    int* x_idx_list, 
+    int* y_idx_list, 
+    bool symmetric, 
+
+    const int* x_charges_types, 
+    const int* y_charges_types,
+    const ccharge_t* ccharges_table,
+
+    const int* x_atypes_types, 
+    const int* y_atypes_types,
+    const catype_t* catypes_table
+);
+
+void cleanup_nonbonded_force();

src/core/cuda/src/CudaContext.cu

@@ -21,7 +21,6 @@ void CudaContext::init() {
     check_cudaMalloc((void**)&d_atypes, sizeof(atype_t) * n_atypes);
     check_cudaMalloc((void**)&d_catypes, sizeof(catype_t) * n_catypes);
 
-
     check_cudaMalloc((void**)&d_q_atoms, sizeof(q_atom_t) * n_qatoms);
     check_cudaMalloc((void**)&d_q_charges, sizeof(q_charge_t) * n_qatoms * n_lambdas);
     check_cudaMalloc((void**)&d_LJ_matrix, sizeof(int) * n_atoms_solute * n_atoms_solute);
@@ -54,6 +53,10 @@ void CudaContext::init() {
     check_cudaMalloc((void**)&d_charges, sizeof(charge_t) * n_charges);
     check_cudaMalloc((void**)&d_p_atoms, sizeof(p_atom_t) * n_patoms);
 
+    initialize_atom_lists_host();
+    initialize_charge_tables_host();
+    initialize_catype_tables_host();
+
     sync_all_to_device();
 }
 
@@ -208,10 +211,251 @@ void CudaContext::free() {
     cudaFree(d_ccharges);
     cudaFree(d_charges);
     cudaFree(d_p_atoms);
+    cudaFree(d_charge_table_all);
+    cudaFree(d_catype_table_all);
+    cudaFree(d_p_charge_types);
+    cudaFree(d_w_charge_types);
+    cudaFree(d_q_charge_types);
+    cudaFree(d_p_catype_types);
+    cudaFree(d_w_catype_types);
+    cudaFree(d_q_catype_types);
+
+    d_charge_table_all = nullptr;
+    d_catype_table_all = nullptr;
+    d_p_charge_types = nullptr;
+    d_w_charge_types = nullptr;
+    d_q_charge_types = nullptr;
+    d_p_catype_types = nullptr;
+    d_w_catype_types = nullptr;
+    d_q_catype_types = nullptr;
 }
 
 void CudaContext::reset_energies() {
     cudaMemset(d_dvelocities, 0, sizeof(dvel_t) * n_atoms);
     cudaMemset(d_EQ_nonbond_qq, 0, sizeof(E_nonbonded_t) * n_lambdas);
     cudaMemset(d_EQ_restraint, 0, sizeof(E_restraint_t) * n_lambdas);
 }
+
+void CudaContext::initialize_atom_lists_host() {
+    h_p_atoms_list.clear();
+    for (int i = 0; i < n_patoms; i++) {
+        int id = p_atoms[i].a - 1;
+        if (!excluded[id]) {
+            h_p_atoms_list.push_back(id);
+        }
+    }
+
+    h_w_atoms_list.clear();
+    for (int i = n_atoms_solute; i < n_atoms; i++) {
+        int id = i;
+        if (!excluded[id]) {
+            h_w_atoms_list.push_back(id);
+        }
+    }
+    printf("Number of water atoms: %d, number of all water atoms: %d\n", (int)h_w_atoms_list.size(), n_atoms - n_atoms_solute);
+
+    h_q_atoms_list.clear();
+    for (int i = 0; i < n_qatoms; i++) {
+        int id = q_atoms[i].a - 1;
+        if (!excluded[id]) {
+            h_q_atoms_list.push_back(id);
+        }
+    }
+
+    check_cudaMalloc((void**)&d_p_atoms_list, sizeof(int) * h_p_atoms_list.size());
+    cudaMemcpy(d_p_atoms_list, h_p_atoms_list.data(), sizeof(int) * h_p_atoms_list.size(), cudaMemcpyHostToDevice);
+    check_cudaMalloc((void**)&d_w_atoms_list, sizeof(int) * h_w_atoms_list.size());
+    cudaMemcpy(d_w_atoms_list, h_w_atoms_list.data(), sizeof(int) * h_w_atoms_list.size(), cudaMemcpyHostToDevice);
+    check_cudaMalloc((void**)&d_q_atoms_list, sizeof(int) * h_q_atoms_list.size());
+    cudaMemcpy(d_q_atoms_list, h_q_atoms_list.data(), sizeof(int) * h_q_atoms_list.size(), cudaMemcpyHostToDevice);
+}
+
+void CudaContext::initialize_charge_tables_host() {
+    std::map<double, int> charge_to_type_host;
+    std::vector<ccharge_t> h_charge_table_all;  // h_charge_table_all[charge type] = (code, charge)
+
+    auto add_charge = [&](double charge) {
+        if (charge_to_type_host.count(charge) == 0) {
+            int sz = h_charge_table_all.size();
+            ccharge_t new_ccharge;
+            new_ccharge.code = sz;
+            new_ccharge.charge = charge;
+            h_charge_table_all.push_back(new_ccharge);
+            charge_to_type_host[charge] = sz;
+        }
+    };
+
+    for (int i = 0; i < n_ccharges; i++) {
+        double charge = ccharges[i].charge;
+        add_charge(charge);
+    }
+    for (int state = 0; state < n_lambdas; state++) {
+        for (int i = 0; i < n_qatoms; i++) {
+            double charge = q_charges[i + n_qatoms * state].q;
+            add_charge(charge);
+            charge *= lambdas[state];
+            add_charge(charge);
+        }
+    }
+
+    std::vector<int> p_charge_types(h_p_atoms_list.size());
+    for (int i = 0; i < h_p_atoms_list.size(); i++) {
+        int id = h_p_atoms_list[i];
+        double charge = ccharges[charges[id].code - 1].charge;
+        p_charge_types[i] = charge_to_type_host[charge];
+    }
+
+    int h_q_atoms_size = h_q_atoms_list.size();
+    std::vector<int> q_charge_types(h_q_atoms_size * n_lambdas * 2);
+    std::map<int, int> q_idx;
+    for (int i = 0; i < n_qatoms; i++) {
+        int id = q_atoms[i].a - 1;
+        if (!excluded[id]) {
+            q_idx[id] = i;
+        }
+    }
+
+    for (int state = 0; state < n_lambdas; state++) {
+        for (int i = 0; i < h_q_atoms_size; i++) {
+            int id = h_q_atoms_list[i];
+            double charge = q_charges[q_idx[id] + n_qatoms * state].q;
+            q_charge_types[state * h_q_atoms_size + i] = charge_to_type_host[charge];
+            charge *= lambdas[state];
+            q_charge_types[state * h_q_atoms_size + i + h_q_atoms_size * n_lambdas] = charge_to_type_host[charge];
+        }
+    }
+
+    int h_w_atoms_size = h_w_atoms_list.size();
+    std::vector<int> w_charge_types(h_w_atoms_size);
+    for (int i = 0; i < h_w_atoms_size; i++) {
+        int id = h_w_atoms_list[i];
+        double charge = ccharges[charges[id].code - 1].charge;
+        w_charge_types[i] = charge_to_type_host[charge];
+    }
+
+    check_cudaMalloc((void**)&d_charge_table_all, sizeof(ccharge_t) * h_charge_table_all.size());
+    cudaMemcpy(d_charge_table_all, h_charge_table_all.data(), sizeof(ccharge_t) * h_charge_table_all.size(), cudaMemcpyHostToDevice);
+    check_cudaMalloc((void**)&d_p_charge_types, sizeof(int) * p_charge_types.size());
+    cudaMemcpy(d_p_charge_types, p_charge_types.data(), sizeof(int) * p_charge_types.size(), cudaMemcpyHostToDevice);
+    check_cudaMalloc((void**)&d_q_charge_types, sizeof(int) * q_charge_types.size());
+    cudaMemcpy(d_q_charge_types, q_charge_types.data(), sizeof(int) * q_charge_types.size(), cudaMemcpyHostToDevice);
+    check_cudaMalloc((void**)&d_w_charge_types, sizeof(int) * w_charge_types.size());
+    cudaMemcpy(d_w_charge_types, w_charge_types.data(), sizeof(int) * w_charge_types.size(), cudaMemcpyHostToDevice);
+}
+
+void CudaContext::initialize_catype_tables_host() {
+    std::vector<catype_t> h_catype_table_all;  // h_catype_table_all[catype code] = catype_t
+    catype_to_type_host.clear();
+
+    auto add_catype = [&](catype_t catype) {
+        auto key = get_catype_key(catype);
+        if (catype_to_type_host.count(key) == 0) {
+            int sz = h_catype_table_all.size();
+            catype.code = sz;
+            h_catype_table_all.push_back(catype);
+            catype_to_type_host[key] = sz;
+        }
+    };
+
+    for (int i = 0; i < n_catypes; i++) {
+        add_catype(catypes[i]);
+    }
+
+    for (int state = 0; state < n_lambdas; state++) {
+        for (int i = 0; i < n_qatoms; i++) {
+            const q_atype_t& qat = q_atypes[i + n_qatoms * state];
+            const q_catype_t& catype = q_catypes[qat.code - 1];
+
+            catype_t new_catype;
+            new_catype.m = catype.m;
+            new_catype.aii_normal = catype.Ai;
+            new_catype.bii_normal = catype.Bi;
+            new_catype.aii_polar = catype.Ci;
+            new_catype.bii_polar = catype.ai;
+            new_catype.aii_1_4 = catype.Ai_14;
+            new_catype.bii_1_4 = catype.Bi_14;
+
+            add_catype(new_catype);
+
+            new_catype.m *= lambdas[state];
+            new_catype.aii_normal *= lambdas[state];
+            new_catype.bii_normal *= lambdas[state];
+            new_catype.aii_polar *= lambdas[state];
+            new_catype.bii_polar *= lambdas[state];
+            new_catype.aii_1_4 *= lambdas[state];
+            new_catype.bii_1_4 *= lambdas[state];
+            add_catype(new_catype);
+        }
+    }
+
+    std::vector<int> p_catype_types(h_p_atoms_list.size());
+    for (int i = 0; i < h_p_atoms_list.size(); i++) {
+        int id = h_p_atoms_list[i];
+        auto catype = catypes[atypes[id].code - 1];
+        auto key = get_catype_key(catype);
+        p_catype_types[i] = catype_to_type_host[key];
+    }
+
+    int h_q_atoms_size = h_q_atoms_list.size();
+    std::vector<int> q_catype_types(h_q_atoms_size * n_lambdas * 2);
+    std::map<int, int> q_idx;
+    for (int i = 0; i < n_qatoms; i++) {
+        int id = q_atoms[i].a - 1;
+        if (!excluded[id]) {
+            q_idx[id] = i;
+        }
+    }
+
+
+    for (int state = 0; state < n_lambdas; state++) {
+        for (int i = 0; i < h_q_atoms_size; i++) {
+            int id = h_q_atoms_list[i];
+            const q_atype_t& qat = q_atypes[q_idx[id] + n_qatoms * state];
+            const q_catype_t& catype = q_catypes[qat.code - 1];
+
+            catype_t normal_catype;
+            normal_catype.m = catype.m;
+            normal_catype.aii_normal = catype.Ai;
+            normal_catype.bii_normal = catype.Bi;
+            normal_catype.aii_polar = catype.Ci;
+            normal_catype.bii_polar = catype.ai;
+            normal_catype.aii_1_4 = catype.Ai_14;
+            normal_catype.bii_1_4 = catype.Bi_14;
+
+            auto key_normal = get_catype_key(normal_catype);
+            q_catype_types[state * h_q_atoms_size + i] = catype_to_type_host[key_normal];
+
+            catype_t scaled_catype;
+            scaled_catype.m = catype.m * lambdas[state];
+            scaled_catype.aii_normal = catype.Ai * lambdas[state];
+            scaled_catype.bii_normal = catype.Bi * lambdas[state];
+            scaled_catype.aii_polar = catype.Ci * lambdas[state];
+            scaled_catype.bii_polar = catype.ai * lambdas[state];
+            scaled_catype.aii_1_4 = catype.Ai_14 * lambdas[state];
+            scaled_catype.bii_1_4 = catype.Bi_14 * lambdas[state];
+
+            auto key_scaled = get_catype_key(scaled_catype);
+            q_catype_types[state * h_q_atoms_size + i + h_q_atoms_size * n_lambdas] = catype_to_type_host[key_scaled];
+        }
+    }
+
+    int h_w_atoms_size = h_w_atoms_list.size();
+    std::vector<int> w_catype_types(h_w_atoms_size);
+    for (int i = 0; i < h_w_atoms_size; i++) {
+        int id = h_w_atoms_list[i];
+        auto catype = catypes[atypes[id].code - 1];
+        auto key = get_catype_key(catype);
+        w_catype_types[i] = catype_to_type_host[key];
+        // printf("Water atom %d: catype code %d mapped to %d, data: m=%f, aii_normal=%f, bii_normal=%f, aii_polar=%f, bii_polar=%f, aii_1_4=%f, bii_1_4=%f\n", id, atypes[id].code, w_catype_types[i], catype.m, catype.aii_normal, catype.bii_normal, catype.aii_polar, catype.bii_polar, catype.aii_1_4, catype.bii_1_4);
+    }
+    printf("Total water atom number: %d, w_catype_types size: %lu\n", h_w_atoms_size, w_catype_types.size());
+
+    check_cudaMalloc((void**)&d_catype_table_all, sizeof(catype_t) * h_catype_table_all.size());
+    cudaMemcpy(d_catype_table_all, h_catype_table_all.data(), sizeof(catype_t) * h_catype_table_all.size(), cudaMemcpyHostToDevice);
+    check_cudaMalloc((void**)&d_p_catype_types, sizeof(int) * p_catype_types.size());
+    cudaMemcpy(d_p_catype_types, p_catype_types.data(), sizeof(int) * p_catype_types.size(), cudaMemcpyHostToDevice);
+    check_cudaMalloc((void**)&d_q_catype_types, sizeof(int) * q_catype_types.size());
+    cudaMemcpy(d_q_catype_types, q_catype_types.data(), sizeof(int) * q_catype_types.size(), cudaMemcpyHostToDevice);
+    check_cudaMalloc((void**)&d_w_catype_types, sizeof(int) * w_catype_types.size());
+    cudaMemcpy(d_w_catype_types, w_catype_types.data(), sizeof(int) * w_catype_types.size(), cudaMemcpyHostToDevice);
+}