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Ying-Li Niu
2026-05-17 08:47:25 +08:00
parent 1159d86b8b
commit 45513fe334
27 changed files with 4734 additions and 2 deletions
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engines/c/main.c
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/**
* engines/c/main.c
* -----------------
* C 语言动力学模拟引擎。
* 输入: param.json 数值参数（Python 从 YAML 转换得来）
* <input_dir>/coord.txt
* <input_dir>/connection.txt
* <input_dir>/bond.txt
* 输出: <output_dir>/trajectory.txt (JSON 格式，与 Python 版兼容)
*
* 编译: make
* 用法: ./build/dynamics_c <input_dir> <output_dir> <param_json_path>
*/
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <math.h>
#include <time.h>
/* ========================================================================
* 配置参数（从 param.json 读取）
* ======================================================================== */
typedef struct {
double box_a; /* 盒子半边长 */
int NT; /* 总步数 */
double DT; /* 时间步长 */
int NSTEP; /* 抽帧间隔 */
int warmup_steps; /* 预热步数 */
double G[3]; /* 重力分量 */
double B[3]; /* 阻尼分量 */
} SimParams;
/* ========================================================================
* 原子数据
* ======================================================================== */
typedef struct {
int n_atoms;
int *atom_ids;
double *masses;
double *radii;
double *pos_0; /* 初始位置 (n_atoms*3) */
double *vel_0; /* 初始速度 (n_atoms*3) */
int *fixed; /* 固定约束 (n_atoms*3) */
} AtomData;
/* ========================================================================
* 成键数据
* ======================================================================== */
typedef struct {
int n_bonds;
int *pairs; /* (n_bonds*2) */
double *stiffness;
double *rest_lengths;
} BondData;
/* ========================================================================
* 轨迹缓冲区
* ======================================================================== */
typedef struct {
int n_steps;
int n_atoms;
double *x, *y, *z;
double *vx, *vy, *vz;
} Trajectory;
/* ========================================================================
* 辅助函数
* ======================================================================== */
static void die(const char *msg) {
fprintf(stderr, "[C-engine] 错误: %s\n", msg);
exit(1);
}
static void *xmalloc(size_t sz) {
void *p = malloc(sz);
if (!p) die("内存分配失败");
return p;
}
/* 从 JSON 中读取 double 值。简单实现：搜索 key 并解析 */
static double json_read_double(const char *json, const char *key) {
char search[256];
snprintf(search, sizeof(search), "\"%s\"", key);
const char *p = strstr(json, search);
if (!p) return 0.0;
p = strchr(p, ':');
if (!p) return 0.0;
p++;
while (*p == ' ' || *p == '\t' || *p == '\n') p++;
return strtod(p, NULL);
}
static int json_read_int(const char *json, const char *key) {
return (int)json_read_double(json, key);
}
/* 读取 JSON 数组 (如 "G": [0, 0, -9.8]) 到 double[3] */
static void json_read_double3(const char *json, const char *key, double out[3]) {
char search[256];
snprintf(search, sizeof(search), "\"%s\"", key);
const char *p = strstr(json, search);
if (!p) { out[0]=out[1]=out[2]=0; return; }
p = strchr(p, '[');
if (!p) { out[0]=out[1]=out[2]=0; return; }
p++;
for (int i = 0; i < 3; i++) {
while (*p == ' ' || *p == '\t' || *p == '\n' || *p == ',') p++;
out[i] = strtod(p, (char**)&p);
}
}
/* 读取 param.json */
static SimParams read_params(const char *path) {
FILE *f = fopen(path, "rb");
if (!f) die("无法打开 param.json");
fseek(f, 0, SEEK_END);
long sz = ftell(f);
fseek(f, 0, SEEK_SET);
char *buf = (char*)xmalloc(sz + 1);
fread(buf, 1, sz, f);
buf[sz] = '\0';
fclose(f);
SimParams p;
p.box_a = json_read_double(buf, "box_a");
p.NT = json_read_int(buf, "NT");
p.DT = json_read_double(buf, "DT");
p.NSTEP = json_read_int(buf, "NSTEP");
p.warmup_steps = json_read_int(buf, "warmup_steps");
json_read_double3(buf, "G", p.G);
json_read_double3(buf, "B", p.B);
free(buf);
return p;
}
/* 读取 coord.txt */
static AtomData read_coord(const char *input_dir) {
char path[512];
snprintf(path, sizeof(path), "%s/coord.txt", input_dir);
FILE *f = fopen(path, "r");
if (!f) die("无法打开 coord.txt");
/* 跳过第一行表头 */
char line[1024];
if (!fgets(line, sizeof(line), f)) die("coord.txt 为空");
/* 先读入所有行到内存 */
int capacity = 16;
AtomData a;
a.n_atoms = 0;
a.atom_ids = (int*)xmalloc(capacity * sizeof(int));
a.masses = (double*)xmalloc(capacity * sizeof(double));
a.radii = (double*)xmalloc(capacity * sizeof(double));
a.pos_0 = (double*)xmalloc(capacity * 3 * sizeof(double));
a.vel_0 = (double*)xmalloc(capacity * 3 * sizeof(double));
a.fixed = (int*)xmalloc(capacity * 3 * sizeof(int));
while (fgets(line, sizeof(line), f)) {
if (a.n_atoms >= capacity) {
capacity *= 2;
a.atom_ids = realloc(a.atom_ids, capacity * sizeof(int));
a.masses = realloc(a.masses, capacity * sizeof(double));
a.radii = realloc(a.radii, capacity * sizeof(double));
a.pos_0 = realloc(a.pos_0, capacity * 3 * sizeof(double));
a.vel_0 = realloc(a.vel_0, capacity * 3 * sizeof(double));
a.fixed = realloc(a.fixed, capacity * 3 * sizeof(int));
}
int id, fx, fy, fz;
double mass, rad, px, py, pz, vx, vy, vz;
int n_parsed = sscanf(line, "%d %lf %lf %lf %lf %lf %lf %lf %lf %d %d %d",
&id, &mass, &rad, &px, &py, &pz, &vx, &vy, &vz, &fx, &fy, &fz);
if (n_parsed == 9) {
/* 无固定约束列 */
fx = fy = fz = 0;
} else if (n_parsed != 12) {
continue; /* 跳过空行/格式不符的行 */
}
int i = a.n_atoms;
a.atom_ids[i] = id;
a.masses[i] = mass;
a.radii[i] = rad;
a.pos_0[i*3+0] = px; a.pos_0[i*3+1] = py; a.pos_0[i*3+2] = pz;
a.vel_0[i*3+0] = vx; a.vel_0[i*3+1] = vy; a.vel_0[i*3+2] = vz;
a.fixed[i*3+0] = fx; a.fixed[i*3+1] = fy; a.fixed[i*3+2] = fz;
a.n_atoms++;
}
fclose(f);
if (a.n_atoms <= 0) die("coord.txt 原子数无效");
return a;
}
/* 读取 connection.txt */
static BondData read_bonds(const char *input_dir, const AtomData *atoms) {
char path[512];
BondData b;
b.n_bonds = 0;
b.pairs = NULL;
b.stiffness = NULL;
b.rest_lengths = NULL;
snprintf(path, sizeof(path), "%s/connection.txt", input_dir);
FILE *f = fopen(path, "r");
if (!f) return b; /* 无成键 */
/* 跳过第一行表头 */
char line[256];
if (!fgets(line, sizeof(line), f)) { fclose(f); return b; }
/* 先数行数 */
int n_lines = 0, tmp_a, tmp_b;
char bond_name[256];
while (fscanf(f, "%d %d %s", &tmp_a, &tmp_b, bond_name) == 3) n_lines++;
rewind(f);
if (n_lines == 0) { fclose(f); return b; }
b.n_bonds = n_lines;
b.pairs = (int*)xmalloc(n_lines * 2 * sizeof(int));
b.stiffness = (double*)xmalloc(n_lines * sizeof(double));
b.rest_lengths = (double*)xmalloc(n_lines * sizeof(double));
/* 读取 bond.txt 获取劲度系数和平衡长度 */
char bond_path[512];
snprintf(bond_path, sizeof(bond_path), "%s/bond.txt", input_dir);
FILE *fb = fopen(bond_path, "r");
/* bond.txt 格式: name stiffness rest_length */
for (int i = 0; i < n_lines; i++) {
fscanf(f, "%d %d %s", &tmp_a, &tmp_b, bond_name);
/* 转换原子编号为 0-based 索引 */
b.pairs[i*2+0] = tmp_a - 1;
b.pairs[i*2+1] = tmp_b - 1;
/* 查找 bond.txt 中对应的参数 */
b.stiffness[i] = 1.0;
b.rest_lengths[i] = 2.0; /* 默认值 */
if (fb) {
char name[256];
double k, r0;
rewind(fb);
while (fscanf(fb, "%s %lf %lf", name, &k, &r0) == 3) {
if (strcmp(name, bond_name) == 0) {
b.stiffness[i] = k;
b.rest_lengths[i] = r0;
break;
}
}
}
}
fclose(f);
if (fb) fclose(fb);
return b;
}
/* ========================================================================
* 物理核心
* ======================================================================== */
static void compute_acceleration(
int n, const double *x, const double *y, const double *z,
const double *vx, const double *vy, const double *vz,
const double *m, const double G[3], const double B[3],
const BondData *bonds,
double *ax, double *ay, double *az)
{
for (int i = 0; i < n; i++) {
double inv_m = 1.0 / m[i];
ax[i] = (m[i] * G[0] - B[0] * vx[i]) * inv_m;
ay[i] = (m[i] * G[1] - B[1] * vy[i]) * inv_m;
az[i] = (m[i] * G[2] - B[2] * vz[i]) * inv_m;
}
/* 弹簧力 */
for (int b = 0; b < bonds->n_bonds; b++) {
int i = bonds->pairs[b*2+0];
int j = bonds->pairs[b*2+1];
double dx = x[j] - x[i];
double dy = y[j] - y[i];
double dz = z[j] - z[i];
double dist = sqrt(dx*dx + dy*dy + dz*dz);
if (dist < 1e-12) continue;
double stretch = dist - bonds->rest_lengths[b];
double fmag = bonds->stiffness[b] * stretch;
double ux = dx / dist, uy = dy / dist, uz = dz / dist;
double fx = fmag * ux, fy = fmag * uy, fz = fmag * uz;
ax[i] += fx / m[i]; ay[i] += fy / m[i]; az[i] += fz / m[i];
ax[j] -= fx / m[j]; ay[j] -= fy / m[j]; az[j] -= fz / m[j];
}
}
/* clamp */
static double clamp(double v, double lo, double hi) {
return fmin(fmax(v, lo), hi);
}
/* 蛙跳法一步 */
static void leapfrog_step(
int n, double *x, double *y, double *z,
double *vx, double *vy, double *vz,
const double *m, const double G[3], const double B[3],
const BondData *bonds, const int *fixed,
double box_a, double dt)
{
double *ax = (double*)alloca(n * sizeof(double));
double *ay = (double*)alloca(n * sizeof(double));
double *az = (double*)alloca(n * sizeof(double));
compute_acceleration(n, x, y, z, vx, vy, vz, m, G, B, bonds, ax, ay, az);
for (int i = 0; i < n; i++) {
if (fixed[i*3+0] && fixed[i*3+1] && fixed[i*3+2]) continue;
vx[i] += ax[i] * dt;
vy[i] += ay[i] * dt;
vz[i] += az[i] * dt;
x[i] += vx[i] * dt;
y[i] += vy[i] * dt;
z[i] += vz[i] * dt;
/* wrap */
x[i] = clamp(x[i], -box_a, box_a);
y[i] = clamp(y[i], -box_a, box_a);
z[i] = clamp(z[i], -box_a, box_a);
}
}
/* ========================================================================
* JSON 输出
* ======================================================================== */
static void write_trajectory_json(const char *path, const Trajectory *traj,
const SimParams *params, const AtomData *atoms,
const BondData *bonds)
{
FILE *f = fopen(path, "w");
if (!f) die("无法写入 trajectory.txt");
fprintf(f, "{\n");
/* traj_x, traj_y, ... */
const char *names[] = {"traj_x","traj_y","traj_z","traj_vx","traj_vy","traj_vz"};
double *arrs[] = {traj->x, traj->y, traj->z, traj->vx, traj->vy, traj->vz};
for (int a = 0; a < 6; a++) {
fprintf(f, " \"%s\": [\n", names[a]);
for (int t = 0; t < traj->n_steps; t++) {
fprintf(f, " [");
for (int i = 0; i < traj->n_atoms; i++) {
fprintf(f, "%.15g", arrs[a][t * traj->n_atoms + i]);
if (i < traj->n_atoms - 1) fputc(',', f);
}
fprintf(f, "]");
if (t < traj->n_steps - 1) fputc(',', f);
fputc('\n', f);
}
fprintf(f, " ]");
// 每个轨迹数组后加逗号（后面还有标量参数）
fputc(',', f);
fputc('\n', f);
}
/* 标量参数 */
fprintf(f, " \"NT\": %d,\n", params->NT);
fprintf(f, " \"DT\": %.15g,\n", params->DT);
fprintf(f, " \"NSTEP\": %d,\n", params->NSTEP);
fprintf(f, " \"method\": \"leapfrog\",\n");
fprintf(f, " \"warmup_steps\": %d,\n", params->warmup_steps);
fprintf(f, " \"G\": [%.15g, %.15g, %.15g],\n", params->G[0], params->G[1], params->G[2]);
fprintf(f, " \"B\": [%.15g, %.15g, %.15g],\n", params->B[0], params->B[1], params->B[2]);
/* 原子信息 */
fprintf(f, " \"atom_ids\": [");
for (int i = 0; i < atoms->n_atoms; i++) {
fprintf(f, "%d", atoms->atom_ids[i]);
if (i < atoms->n_atoms - 1) fputc(',', f);
}
fprintf(f, "],\n");
fprintf(f, " \"atom_masses\": [");
for (int i = 0; i < atoms->n_atoms; i++) {
fprintf(f, "%.15g", atoms->masses[i]);
if (i < atoms->n_atoms - 1) fputc(',', f);
}
fprintf(f, "],\n");
/* 成键 */
fprintf(f, " \"bond_pairs\": [");
for (int b = 0; b < bonds->n_bonds; b++) {
fprintf(f, "[%d, %d]", bonds->pairs[b*2], bonds->pairs[b*2+1]);
if (b < bonds->n_bonds - 1) fputc(',', f);
}
fprintf(f, "],\n");
fprintf(f, " \"bond_stiffness\": [");
for (int b = 0; b < bonds->n_bonds; b++) {
fprintf(f, "%.15g", bonds->stiffness[b]);
if (b < bonds->n_bonds - 1) fputc(',', f);
}
fprintf(f, "],\n");
fprintf(f, " \"bond_rest_lengths\": [");
for (int b = 0; b < bonds->n_bonds; b++) {
fprintf(f, "%.15g", bonds->rest_lengths[b]);
if (b < bonds->n_bonds - 1) fputc(',', f);
}
fprintf(f, "]\n");
fprintf(f, "}\n");
fclose(f);
}
/* ========================================================================
* 主函数
* ======================================================================== */
int main(int argc, char **argv) {
if (argc < 4) {
fprintf(stderr, "用法: %s <input_dir> <output_dir> <param_json>\n", argv[0]);
return 1;
}
const char *input_dir = argv[1];
const char *output_dir = argv[2];
const char *param_path = argv[3];
clock_t t0 = clock();
/* 读取参数和输入 */
SimParams params = read_params(param_path);
AtomData atoms = read_coord(input_dir);
BondData bonds = read_bonds(input_dir, &atoms);
printf("[C-engine] 原子数=%d, 键数=%d, NT=%d, DT=%.6g\n",
atoms.n_atoms, bonds.n_bonds, params.NT, params.DT);
/* 初始化位置/速度 */
int n = atoms.n_atoms;
double *x = (double*)xmalloc(n * sizeof(double));
double *y = (double*)xmalloc(n * sizeof(double));
double *z = (double*)xmalloc(n * sizeof(double));
double *vx = (double*)xmalloc(n * sizeof(double));
double *vy = (double*)xmalloc(n * sizeof(double));
double *vz = (double*)xmalloc(n * sizeof(double));
for (int i = 0; i < n; i++) {
x[i] = atoms.pos_0[i*3+0];
y[i] = atoms.pos_0[i*3+1];
z[i] = atoms.pos_0[i*3+2];
vx[i] = atoms.vel_0[i*3+0];
vy[i] = atoms.vel_0[i*3+1];
vz[i] = atoms.vel_0[i*3+2];
}
/* 分配轨迹缓冲区 */
Trajectory traj;
traj.n_steps = params.NT;
traj.n_atoms = n;
traj.x = (double*)xmalloc(params.NT * n * sizeof(double) * 6);
traj.y = traj.x + params.NT * n;
traj.z = traj.y + params.NT * n;
traj.vx = traj.z + params.NT * n;
traj.vy = traj.vx + params.NT * n;
traj.vz = traj.vy + params.NT * n;
/* 预热 */
for (int s = 0; s < params.warmup_steps; s++) {
leapfrog_step(n, x, y, z, vx, vy, vz,
atoms.masses, params.G, params.B, &bonds, atoms.fixed,
params.box_a, params.DT);
}
/* 记录 */
for (int s = 0; s < params.NT; s++) {
leapfrog_step(n, x, y, z, vx, vy, vz,
atoms.masses, params.G, params.B, &bonds, atoms.fixed,
params.box_a, params.DT);
/* 保存这一帧 */
for (int i = 0; i < n; i++) {
traj.x[ s * n + i] = x[i];
traj.y[ s * n + i] = y[i];
traj.z[ s * n + i] = z[i];
traj.vx[s * n + i] = vx[i];
traj.vy[s * n + i] = vy[i];
traj.vz[s * n + i] = vz[i];
}
}
/* 输出轨迹 */
char out_path[512];
snprintf(out_path, sizeof(out_path), "%s/trajectory.txt", output_dir);
write_trajectory_json(out_path, &traj, &params, &atoms, &bonds);
clock_t t1 = clock();
double elapsed = (double)(t1 - t0) / CLOCKS_PER_SEC;
printf("[C-engine] 计算完成: %d 步, %.3f s\n", params.NT, elapsed);
/* 清理 */
free(traj.x);
free(x); free(y); free(z);
free(vx); free(vy); free(vz);
free(atoms.atom_ids);
free(atoms.masses); free(atoms.radii);
free(atoms.pos_0); free(atoms.vel_0);
free(atoms.fixed);
if (bonds.pairs) { free(bonds.pairs); free(bonds.stiffness); free(bonds.rest_lengths); }
return 0;
}