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modified: INSTALL.md modified: README.md modified: build_release_zip.py modified: compute.py new file: doc/index.html modified: dynamics.py modified: engines/c/main.c modified: engines/cpp/main.cpp modified: engines/fortran/main.f90 modified: examples/case01/input/coord.txt renamed: examples/case01/input/parameters.yaml -> examples/case01/input/input.txt modified: examples/case01/run_dynamics.py new file: examples/case02/input/bond.txt new file: examples/case02/input/connection.txt new file: examples/case02/input/coord.txt new file: examples/case02/input/input.txt new file: examples/case02/run_dynamics.py
746 lines
26 KiB
C
746 lines
26 KiB
C
/**
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* engines/c/main.c
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* -----------------
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* C 语言动力学模拟引擎。
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* 与 Python 版 (compute.py) 算法保持一致。
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*
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* 输入: param.json 数值参数（Python 从 YAML 转换得来）
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* <input_dir>/coord.txt
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* <input_dir>/connection.txt
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* <input_dir>/bond.txt
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* 输出: <output_dir>/trajectory.txt (JSON 格式，与 Python 版兼容)
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*
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* 编译: cmake --build build --target dynamics_c
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* 用法: ./build/dynamics_c <input_dir> <output_dir> <param_json_path>
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*/
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#include <stdio.h>
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#include <stdlib.h>
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#include <string.h>
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#include <math.h>
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#include <time.h>
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/* ========================================================================
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* 配置参数（从 param.json 读取）
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* ======================================================================== */
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typedef struct {
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double box_a; /* 盒子半边长 */
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int NT; /* 总步数 */
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double DT; /* 时间步长 */
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int NSTEP; /* 抽帧间隔 */
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int warmup_steps; /* 预热步数 */
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char method[32]; /* 算法名称 */
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double G[3]; /* 重力分量 */
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double B[3]; /* 阻尼分量 */
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int gravity_field; /* 均匀重力场开关 */
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int gravity_interaction; /* 原子间万有引力开关 */
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int elastic_force; /* 弹簧键力开关 */
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int damping_force; /* 阻尼开关 */
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double gravity_strength; /* 万有引力强度 */
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} SimParams;
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/* ========================================================================
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* 原子数据
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* ======================================================================== */
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typedef struct {
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int n_atoms;
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int *atom_ids;
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double *masses;
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double *radii;
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double *pos_0; /* 初始位置 (n_atoms*3) */
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double *vel_0; /* 初始速度 (n_atoms*3) */
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int *fixed; /* 固定约束 (n_atoms*3) */
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} AtomData;
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/* ========================================================================
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* 成键数据
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* ======================================================================== */
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typedef struct {
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int n_bonds;
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int *pairs; /* (n_bonds*2) */
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double *stiffness;
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double *rest_lengths;
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} BondData;
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/* ========================================================================
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* 轨迹缓冲区
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* ======================================================================== */
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typedef struct {
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int n_steps;
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int n_atoms;
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double *x, *y, *z;
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double *vx, *vy, *vz;
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} Trajectory;
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/* ========================================================================
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* 辅助函数
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* ======================================================================== */
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static void die(const char *msg) {
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fprintf(stderr, "[C-engine] 错误: %s\n", msg);
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exit(1);
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}
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static void *xmalloc(size_t sz) {
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void *p = malloc(sz);
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if (!p) die("内存分配失败");
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return p;
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}
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/* 从 JSON 中读取 double 值 */
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static double json_read_double(const char *json, const char *key) {
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char search[256];
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snprintf(search, sizeof(search), "\"%s\"", key);
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const char *p = strstr(json, search);
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if (!p) return 0.0;
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p = strchr(p, ':');
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if (!p) return 0.0;
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p++;
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while (*p == ' ' || *p == '\t' || *p == '\n') p++;
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return strtod(p, NULL);
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}
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static int json_read_int(const char *json, const char *key) {
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return (int)json_read_double(json, key);
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}
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/* 从 JSON 中读取字符串值（写入 dst，最多 dst_sz 字节） */
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static void json_read_string(const char *json, const char *key, char *dst, int dst_sz) {
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char search[256];
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snprintf(search, sizeof(search), "\"%s\"", key);
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const char *p = strstr(json, search);
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if (!p) { dst[0] = '\0'; return; }
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p = strchr(p, ':');
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if (!p) { dst[0] = '\0'; return; }
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p++;
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while (*p == ' ' || *p == '\t' || *p == '\n') p++;
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if (*p != '"') { dst[0] = '\0'; return; }
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p++;
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int i = 0;
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while (*p && *p != '"' && i < dst_sz - 1) { dst[i++] = *p++; }
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dst[i] = '\0';
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}
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/* 读取 JSON 数组 (如 "G": [0, 0, -9.8]) 到 double[3] */
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static void json_read_double3(const char *json, const char *key, double out[3]) {
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char search[256];
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snprintf(search, sizeof(search), "\"%s\"", key);
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const char *p = strstr(json, search);
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if (!p) { out[0]=out[1]=out[2]=0; return; }
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p = strchr(p, '[');
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if (!p) { out[0]=out[1]=out[2]=0; return; }
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p++;
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for (int i = 0; i < 3; i++) {
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while (*p == ' ' || *p == '\t' || *p == '\n' || *p == ',') p++;
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out[i] = strtod(p, (char**)&p);
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}
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}
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/* 读取 param.json */
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static int g_gravity_field = 1;
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static int g_gravity_interaction = 0;
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static int g_elastic_force = 1;
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static int g_damping_force = 0;
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static double g_gravity_strength = 1.0;
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static SimParams read_params(const char *path) {
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FILE *f = fopen(path, "rb");
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if (!f) die("无法打开 param.json");
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fseek(f, 0, SEEK_END);
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long sz = ftell(f);
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fseek(f, 0, SEEK_SET);
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char *buf = (char*)xmalloc(sz + 1);
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fread(buf, 1, sz, f);
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buf[sz] = '\0';
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fclose(f);
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SimParams p;
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p.box_a = json_read_double(buf, "box_a");
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p.NT = json_read_int(buf, "NT");
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p.DT = json_read_double(buf, "DT");
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p.NSTEP = json_read_int(buf, "NSTEP");
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p.warmup_steps = json_read_int(buf, "warmup_steps");
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strcpy(p.method, "leapfrog"); /* 默认 */
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json_read_string(buf, "method", p.method, sizeof(p.method));
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json_read_double3(buf, "G", p.G);
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json_read_double3(buf, "B", p.B);
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p.gravity_field = json_read_int(buf, "gravity_field");
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p.gravity_interaction = json_read_int(buf, "gravity_interaction");
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p.elastic_force = json_read_int(buf, "elastic_force");
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p.damping_force = json_read_int(buf, "damping_force");
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p.gravity_strength = json_read_double(buf, "gravity_strength");
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g_gravity_field = p.gravity_field;
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g_gravity_interaction = p.gravity_interaction;
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g_elastic_force = p.elastic_force;
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g_damping_force = p.damping_force;
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g_gravity_strength = p.gravity_strength;
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free(buf);
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return p;
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}
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/* 读取 coord.txt */
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static AtomData read_coord(const char *input_dir) {
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char path[512];
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snprintf(path, sizeof(path), "%s/coord.txt", input_dir);
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FILE *f = fopen(path, "r");
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if (!f) die("无法打开 coord.txt");
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/* 跳过第一行表头 */
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char line[1024];
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if (!fgets(line, sizeof(line), f)) die("coord.txt 为空");
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int capacity = 16;
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AtomData a;
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a.n_atoms = 0;
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a.atom_ids = (int*)xmalloc(capacity * sizeof(int));
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a.masses = (double*)xmalloc(capacity * sizeof(double));
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a.radii = (double*)xmalloc(capacity * sizeof(double));
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a.pos_0 = (double*)xmalloc(capacity * 3 * sizeof(double));
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a.vel_0 = (double*)xmalloc(capacity * 3 * sizeof(double));
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a.fixed = (int*)xmalloc(capacity * 3 * sizeof(int));
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while (fgets(line, sizeof(line), f)) {
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if (a.n_atoms >= capacity) {
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capacity *= 2;
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a.atom_ids = realloc(a.atom_ids, capacity * sizeof(int));
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a.masses = realloc(a.masses, capacity * sizeof(double));
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a.radii = realloc(a.radii, capacity * sizeof(double));
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a.pos_0 = realloc(a.pos_0, capacity * 3 * sizeof(double));
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a.vel_0 = realloc(a.vel_0, capacity * 3 * sizeof(double));
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a.fixed = realloc(a.fixed, capacity * 3 * sizeof(int));
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}
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int id, fx, fy, fz;
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double mass, rad, px, py, pz, vx, vy, vz;
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int n_parsed = sscanf(line, "%d %lf %lf %lf %lf %lf %lf %lf %lf %d %d %d",
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&id, &mass, &rad, &px, &py, &pz, &vx, &vy, &vz, &fx, &fy, &fz);
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if (n_parsed == 9) {
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fx = fy = fz = 0;
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} else if (n_parsed != 12) {
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continue;
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}
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int i = a.n_atoms;
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a.atom_ids[i] = id;
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a.masses[i] = mass;
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a.radii[i] = rad;
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a.pos_0[i*3+0] = px; a.pos_0[i*3+1] = py; a.pos_0[i*3+2] = pz;
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a.vel_0[i*3+0] = vx; a.vel_0[i*3+1] = vy; a.vel_0[i*3+2] = vz;
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a.fixed[i*3+0] = fx; a.fixed[i*3+1] = fy; a.fixed[i*3+2] = fz;
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a.n_atoms++;
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}
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fclose(f);
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if (a.n_atoms <= 0) die("coord.txt 原子数无效");
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return a;
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}
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/* 读取 connection.txt */
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static BondData read_bonds(const char *input_dir, const AtomData *atoms) {
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char path[512];
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BondData b;
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b.n_bonds = 0;
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b.pairs = NULL;
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b.stiffness = NULL;
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b.rest_lengths = NULL;
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snprintf(path, sizeof(path), "%s/connection.txt", input_dir);
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FILE *f = fopen(path, "r");
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if (!f) return b;
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char line[256];
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if (!fgets(line, sizeof(line), f)) { fclose(f); return b; }
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int n_lines = 0, tmp_a, tmp_b;
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char bond_name[256];
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while (fscanf(f, "%d %d %s", &tmp_a, &tmp_b, bond_name) == 3) n_lines++;
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rewind(f);
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if (n_lines == 0) { fclose(f); return b; }
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b.n_bonds = n_lines;
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b.pairs = (int*)xmalloc(n_lines * 2 * sizeof(int));
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b.stiffness = (double*)xmalloc(n_lines * sizeof(double));
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b.rest_lengths = (double*)xmalloc(n_lines * sizeof(double));
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char bond_path[512];
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snprintf(bond_path, sizeof(bond_path), "%s/bond.txt", input_dir);
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FILE *fb = fopen(bond_path, "r");
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for (int i = 0; i < n_lines; i++) {
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fscanf(f, "%d %d %s", &tmp_a, &tmp_b, bond_name);
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b.pairs[i*2+0] = tmp_a - 1;
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b.pairs[i*2+1] = tmp_b - 1;
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b.stiffness[i] = 1.0;
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b.rest_lengths[i] = 2.0;
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if (fb) {
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char name[256], header[256];
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double k, r0;
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rewind(fb);
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fgets(header, sizeof(header), fb); // 跳过表头行
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while (fscanf(fb, "%s %lf %lf", name, &k, &r0) == 3) {
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if (strcmp(name, bond_name) == 0) {
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b.stiffness[i] = k;
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b.rest_lengths[i] = r0;
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break;
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}
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}
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}
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}
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fclose(f);
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if (fb) fclose(fb);
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return b;
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}
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/* ========================================================================
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* 物理核心（与 Python compute.py 对应）
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* ======================================================================== */
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/* 加速度计算（各力独立开关控制） */
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static void compute_acceleration(
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int n, const double *x, const double *y, const double *z,
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const double *vx, const double *vy, const double *vz,
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const double *m, const double G[3], const double B[3],
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const BondData *bonds,
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double *ax, double *ay, double *az)
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{
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/* 先清零 */
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for (int i = 0; i < n; i++) {
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ax[i] = 0.0; ay[i] = 0.0; az[i] = 0.0;
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}
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/* 均匀重力场 */
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if (g_gravity_field) {
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for (int i = 0; i < n; i++) {
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ax[i] += G[0];
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ay[i] += G[1];
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az[i] += G[2];
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}
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}
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/* 阻尼 */
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if (g_damping_force) {
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for (int i = 0; i < n; i++) {
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ax[i] -= B[0] * vx[i] / m[i];
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ay[i] -= B[1] * vy[i] / m[i];
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az[i] -= B[2] * vz[i] / m[i];
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}
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}
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/* 弹簧键力 */
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if (g_elastic_force) {
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for (int b = 0; b < bonds->n_bonds; b++) {
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int i = bonds->pairs[b*2+0];
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int j = bonds->pairs[b*2+1];
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double dx = x[j] - x[i];
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double dy = y[j] - y[i];
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double dz = z[j] - z[i];
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double dist = sqrt(dx*dx + dy*dy + dz*dz);
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if (dist < 1e-12) continue;
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double stretch = dist - bonds->rest_lengths[b];
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double fmag = bonds->stiffness[b] * stretch;
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double ux = dx / dist, uy = dy / dist, uz = dz / dist;
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double fx = fmag * ux, fy = fmag * uy, fz = fmag * uz;
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ax[i] += fx / m[i]; ay[i] += fy / m[i]; az[i] += fz / m[i];
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ax[j] -= fx / m[j]; ay[j] -= fy / m[j]; az[j] -= fz / m[j];
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}
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}
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/* 万有引力（所有原子对之间） */
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if (g_gravity_interaction) {
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for (int i = 0; i < n; i++) {
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for (int j = i + 1; j < n; j++) {
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double dx = x[j] - x[i];
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double dy = y[j] - y[i];
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double dz = z[j] - z[i];
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double r2 = dx*dx + dy*dy + dz*dz;
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if (r2 <= 1e-12) continue;
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double r = sqrt(r2);
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double f_mag = g_gravity_strength * m[i] * m[j] / r2;
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double fx_g = f_mag * dx / r;
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double fy_g = f_mag * dy / r;
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double fz_g = f_mag * dz / r;
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ax[i] += fx_g / m[i]; ay[i] += fy_g / m[i]; az[i] += fz_g / m[i];
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ax[j] -= fx_g / m[j]; ay[j] -= fy_g / m[j]; az[j] -= fz_g / m[j];
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}
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}
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}
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}
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/* 边界条件：clamp 位置 + 速度反转 ——与 Python Limit_in_box 一致 */
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static void limit_in_box(double *pos, double *vel, double lo, double hi) {
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if (*pos > hi) { *pos = hi; *vel = -*vel; }
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if (*pos < lo) { *pos = lo; *vel = -*vel; }
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}
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/* ── 显式欧拉法 ──────────── */
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static void explicit_euler_step(
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int n, double *x, double *y, double *z,
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double *vx, double *vy, double *vz,
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const double *m, const double G[3], const double B[3],
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const BondData *bonds, const int *fixed, double dt)
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{
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double *ax = (double*)alloca(n * sizeof(double));
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double *ay = (double*)alloca(n * sizeof(double));
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double *az = (double*)alloca(n * sizeof(double));
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compute_acceleration(n, x, y, z, vx, vy, vz, m, G, B, bonds, ax, ay, az);
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for (int i = 0; i < n; i++) {
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if (fixed[i*3+0] && fixed[i*3+1] && fixed[i*3+2]) continue;
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x[i] += vx[i] * dt;
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y[i] += vy[i] * dt;
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z[i] += vz[i] * dt;
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vx[i] += ax[i] * dt;
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vy[i] += ay[i] * dt;
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vz[i] += az[i] * dt;
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}
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}
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/* ── 隐式欧拉法 ──────────── */
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static void implicit_euler_step(
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int n, double *x, double *y, double *z,
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double *vx, double *vy, double *vz,
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const double *m, const double G[3], const double B[3],
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const BondData *bonds, const int *fixed, double dt)
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{
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double *vxn = (double*)alloca(n * sizeof(double));
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double *vyn = (double*)alloca(n * sizeof(double));
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double *vzn = (double*)alloca(n * sizeof(double));
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for (int i = 0; i < n; i++) {
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if (fixed[i*3+0] && fixed[i*3+1] && fixed[i*3+2]) {
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vxn[i] = 0; vyn[i] = 0; vzn[i] = 0; continue;
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}
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double gx = B[0] / m[i], gy = B[1] / m[i], gz = B[2] / m[i];
|
|
vxn[i] = (vx[i] + G[0] * dt) / (1.0 + gx * dt);
|
|
vyn[i] = (vy[i] + G[1] * dt) / (1.0 + gy * dt);
|
|
vzn[i] = (vz[i] + G[2] * dt) / (1.0 + gz * 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, vxn, vyn, vzn, 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;
|
|
}
|
|
}
|
|
|
|
/* ── 中点法 ──────────── */
|
|
static void midpoint_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 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);
|
|
|
|
double *xm = (double*)alloca(n * sizeof(double));
|
|
double *ym = (double*)alloca(n * sizeof(double));
|
|
double *zm = (double*)alloca(n * sizeof(double));
|
|
double *vxm = (double*)alloca(n * sizeof(double));
|
|
double *vym = (double*)alloca(n * sizeof(double));
|
|
double *vzm = (double*)alloca(n * sizeof(double));
|
|
|
|
for (int i = 0; i < n; i++) {
|
|
if (fixed[i*3+0] && fixed[i*3+1] && fixed[i*3+2]) {
|
|
xm[i]=ym[i]=zm[i]=vxm[i]=vym[i]=vzm[i]=0; continue;
|
|
}
|
|
xm[i] = x[i] + 0.5 * vx[i] * dt;
|
|
ym[i] = y[i] + 0.5 * vy[i] * dt;
|
|
zm[i] = z[i] + 0.5 * vz[i] * dt;
|
|
vxm[i] = vx[i] + 0.5 * ax[i] * dt;
|
|
vym[i] = vy[i] + 0.5 * ay[i] * dt;
|
|
vzm[i] = vz[i] + 0.5 * az[i] * dt;
|
|
x[i] = x[i] + vxm[i] * dt;
|
|
y[i] = y[i] + vym[i] * dt;
|
|
z[i] = z[i] + vzm[i] * dt;
|
|
}
|
|
|
|
compute_acceleration(n, xm, ym, zm, vxm, vym, vzm, 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;
|
|
}
|
|
}
|
|
|
|
/* ── 蛙跳法（Velocity-Verlet）── */
|
|
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 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);
|
|
|
|
/* 半推速度：v_half = v + 0.5*a*dt */
|
|
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 * 0.5;
|
|
vy[i] += ay[i] * dt * 0.5;
|
|
vz[i] += az[i] * dt * 0.5;
|
|
}
|
|
|
|
/* 全推位置（不含边界）*/
|
|
for (int i = 0; i < n; i++) {
|
|
if (fixed[i*3+0] && fixed[i*3+1] && fixed[i*3+2]) continue;
|
|
x[i] += vx[i] * dt; /* vx 此时是 v_half */
|
|
y[i] += vy[i] * dt;
|
|
z[i] += vz[i] * dt;
|
|
}
|
|
|
|
/* 显式预测器：v_pred = v_half + 0.5*a_old*dt，用第一次加速度外推半步
|
|
包含重力+阻尼+弹簧的所有贡献（标准 Velocity-Verlet 预测步）*/
|
|
double *pred_vx = (double*)alloca(n * sizeof(double));
|
|
double *pred_vy = (double*)alloca(n * sizeof(double));
|
|
double *pred_vz = (double*)alloca(n * sizeof(double));
|
|
for (int i = 0; i < n; i++) {
|
|
if (fixed[i*3+0] && fixed[i*3+1] && fixed[i*3+2]) continue;
|
|
pred_vx[i] = vx[i] + 0.5 * ax[i] * dt;
|
|
pred_vy[i] = vy[i] + 0.5 * ay[i] * dt;
|
|
pred_vz[i] = vz[i] + 0.5 * az[i] * dt;
|
|
}
|
|
|
|
/* 用新位置 + 预测速度重算加速度 */
|
|
compute_acceleration(n, x, y, z, pred_vx, pred_vy, pred_vz, m, G, B, bonds, ax, ay, az);
|
|
|
|
/* 速度后半步：v = v_half + 0.5*a_next*dt
|
|
vx 仍为 v_half（未被覆盖）*/
|
|
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 * 0.5;
|
|
vy[i] += ay[i] * dt * 0.5;
|
|
vz[i] += az[i] * dt * 0.5;
|
|
}
|
|
}
|
|
|
|
/* ── 分发器：调用对应积分方法 + 边界条件 + 自由度约束（与 Python 一致）── */
|
|
static void apply_step(
|
|
const char *method,
|
|
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,
|
|
const double *pos_0,
|
|
double box_a, double dt)
|
|
{
|
|
if (strcmp(method, "explicit_euler") == 0) {
|
|
explicit_euler_step(n, x, y, z, vx, vy, vz, m, G, B, bonds, fixed, dt);
|
|
} else if (strcmp(method, "implicit_euler") == 0) {
|
|
implicit_euler_step(n, x, y, z, vx, vy, vz, m, G, B, bonds, fixed, dt);
|
|
} else if (strcmp(method, "midpoint") == 0) {
|
|
midpoint_step(n, x, y, z, vx, vy, vz, m, G, B, bonds, fixed, dt);
|
|
} else if (strcmp(method, "leapfrog") == 0) {
|
|
leapfrog_step(n, x, y, z, vx, vy, vz, m, G, B, bonds, fixed, dt);
|
|
} else {
|
|
fprintf(stderr, "[C-engine] 未知算法: %s\n", method);
|
|
exit(1);
|
|
}
|
|
|
|
/* 边界条件（与 Python Limit_in_box 一致） */
|
|
for (int i = 0; i < n; i++) {
|
|
if (fixed[i*3+0] && fixed[i*3+1] && fixed[i*3+2]) continue;
|
|
limit_in_box(&x[i], &vx[i], -box_a, box_a);
|
|
limit_in_box(&y[i], &vy[i], -box_a, box_a);
|
|
limit_in_box(&z[i], &vz[i], -box_a, box_a);
|
|
}
|
|
|
|
/* 逐自由度固定约束（与 Python apply_fixed_constraints 一致） */
|
|
for (int i = 0; i < n; i++) {
|
|
if (fixed[i*3+0]) { x[i] = pos_0[i*3+0]; vx[i] = 0.0; }
|
|
if (fixed[i*3+1]) { y[i] = pos_0[i*3+1]; vy[i] = 0.0; }
|
|
if (fixed[i*3+2]) { z[i] = pos_0[i*3+2]; vz[i] = 0.0; }
|
|
}
|
|
}
|
|
|
|
// ========================================================================
|
|
// 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");
|
|
|
|
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, " ]");
|
|
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\": \"%s\",\n", params->method);
|
|
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]);
|
|
|
|
fprintf(f, " \"atom_ids\": [");
|
|
for (int i = 0; i < atoms->n_atoms; i++) {
|
|
if (i > 0) fputc(',', f);
|
|
fprintf(f, "%d", atoms->atom_ids[i]);
|
|
}
|
|
fprintf(f, "],\n");
|
|
|
|
fprintf(f, " \"atom_masses\": [");
|
|
for (int i = 0; i < atoms->n_atoms; i++) {
|
|
if (i > 0) fputc(',', f);
|
|
fprintf(f, "%.15g", atoms->masses[i]);
|
|
}
|
|
fprintf(f, "],\n");
|
|
|
|
fprintf(f, " \"bond_pairs\": [");
|
|
for (int b = 0; b < bonds->n_bonds; b++) {
|
|
if (b > 0) fputc(',', f);
|
|
fprintf(f, "[%d, %d]", bonds->pairs[b*2], bonds->pairs[b*2+1]);
|
|
}
|
|
fprintf(f, "],\n");
|
|
|
|
fprintf(f, " \"bond_stiffness\": [");
|
|
for (int b = 0; b < bonds->n_bonds; b++) {
|
|
if (b > 0) fputc(',', f);
|
|
fprintf(f, "%.15g", bonds->stiffness[b]);
|
|
}
|
|
fprintf(f, "],\n");
|
|
|
|
fprintf(f, " \"bond_rest_lengths\": [");
|
|
for (int b = 0; b < bonds->n_bonds; b++) {
|
|
if (b > 0) fputc(',', f);
|
|
fprintf(f, "%.15g", bonds->rest_lengths[b]);
|
|
}
|
|
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();
|
|
|
|
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, method=%s\n",
|
|
atoms.n_atoms, bonds.n_bonds, params.NT, params.DT, params.method);
|
|
|
|
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：改用 record_steps */
|
|
int record_steps = params.NT - params.warmup_steps;
|
|
Trajectory traj;
|
|
traj.n_steps = record_steps;
|
|
traj.n_atoms = n;
|
|
traj.x = (double*)xmalloc(record_steps * n * sizeof(double) * 6);
|
|
traj.y = traj.x + record_steps * n;
|
|
traj.z = traj.y + record_steps * n;
|
|
traj.vx = traj.z + record_steps * n;
|
|
traj.vy = traj.vx + record_steps * n;
|
|
traj.vz = traj.vy + record_steps * n;
|
|
|
|
/* 预热 */
|
|
for (int s = 0; s < params.warmup_steps; s++) {
|
|
apply_step(params.method, n, x, y, z, vx, vy, vz,
|
|
atoms.masses, params.G, params.B, &bonds, atoms.fixed,
|
|
atoms.pos_0,
|
|
params.box_a, params.DT);
|
|
}
|
|
|
|
/* 记录 */
|
|
for (int s = 0; s < record_steps; s++) {
|
|
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];
|
|
}
|
|
apply_step(params.method, n, x, y, z, vx, vy, vz,
|
|
atoms.masses, params.G, params.B, &bonds, atoms.fixed,
|
|
atoms.pos_0,
|
|
params.box_a, params.DT);
|
|
}
|
|
|
|
char out_path[512];
|
|
snprintf(out_path, sizeof(out_path), "%s/trajectory.txt", output_dir);
|
|
write_trajectory_json(out_path, &traj, ¶ms, &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", record_steps, 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;
|
|
}
|