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dynamics/engines/c/dynamics_lib.c
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admin 0e636e275d docs: 更新 examples/Readme.md 并新增 Readme.html
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2026-06-17 15:33:49 +08:00

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/**
* engines/c/dynamics_lib.c
* -------------------------
* 纯计算 DLL:无文件 I/O,所有数据由 Python 以 NumPy 数组传入,
* 结果直接写入 Python 预分配的输出数组。
* 算法与 main.c 和 compute.py 保持完全一致。
*
* 编译(Windows DLL:
* gcc -O3 -march=native -shared -o build/dynamics_c.dll dynamics_lib.c -lm
* 编译(Linux .so:
* gcc -O3 -march=native -shared -fPIC -o build/dynamics_c.so dynamics_lib.c -lm
* 编译(macOS .dylib:
* gcc -O3 -march=native -dynamiclib -o build/dynamics_c.dylib dynamics_lib.c -lm
*/
#ifdef _WIN32
# define EXPORT __declspec(dllexport)
#else
# define EXPORT __attribute__((visibility("default")))
#endif
#include <math.h>
#include <stdlib.h>
#include <string.h>
#include <stdio.h>
/* ── 驱动力结构体 ─────────────────────────────────────────── */
typedef struct {
int n_drivers;
const int *idx; /* [n_drivers] 0-based local atom index */
const double *amp; /* [n_drivers*3] (ax,ay,az) interleaved */
const double *freq; /* [n_drivers*3] */
const double *phi; /* [n_drivers*3] radians */
const double *eq; /* [n_drivers*3] equilibrium positions */
const double *ncycles; /* [n_drivers] 0=unlimited */
const int *has_period; /* [n_drivers] */
/* mutable freeze positions (allocated internally) */
double *freeze; /* [n_drivers*3] */
} Drivers;
/* ── 加速度:保守力(弹簧键 + 均匀重力场)────────────────── */
static void accel_conservative(
int n, const double *x, const double *y, const double *z,
const double *m,
double Gx, double Gy, double Gz,
int gravity_field, int elastic_force,
int n_bonds, const int *bond_pairs,
const double *bond_k, const double *bond_r0,
double *ax, double *ay, double *az)
{
for (int i = 0; i < n; i++) {
ax[i] = gravity_field ? Gx : 0.0;
ay[i] = gravity_field ? Gy : 0.0;
az[i] = gravity_field ? Gz : 0.0;
}
if (!elastic_force || n_bonds == 0) return;
for (int b = 0; b < n_bonds; b++) {
int ii = bond_pairs[b*2];
int jj = bond_pairs[b*2+1];
double dx = x[jj] - x[ii];
double dy = y[jj] - y[ii];
double dz = z[jj] - z[ii];
double dist = sqrt(dx*dx + dy*dy + dz*dz);
if (dist < 1e-12) continue;
double k = bond_k[b];
double r0 = bond_r0[b];
double fac = k * (dist - r0) / dist;
double fx = fac * dx, fy = fac * dy, fz_b = fac * dz;
ax[ii] += fx / m[ii]; ay[ii] += fy / m[ii]; az[ii] += fz_b / m[ii];
ax[jj] -= fx / m[jj]; ay[jj] -= fy / m[jj]; az[jj] -= fz_b / m[jj];
}
}
/* ── 完整加速度(含阻尼)────────────────────────────────── */
static void accel_full(
int n, const double *x, const double *y, const double *z,
const double *vx, const double *vy, const double *vz,
const double *m,
double Gx, double Gy, double Gz,
double Bx, double By, double Bz,
int gravity_field, int elastic_force, int damping_force,
int n_bonds, const int *bond_pairs,
const double *bond_k, const double *bond_r0,
double *ax, double *ay, double *az)
{
accel_conservative(n, x, y, z, m, Gx, Gy, Gz,
gravity_field, elastic_force,
n_bonds, bond_pairs, bond_k, bond_r0,
ax, ay, az);
if (damping_force) {
for (int i = 0; i < n; i++) {
ax[i] -= Bx * vx[i] / m[i];
ay[i] -= By * vy[i] / m[i];
az[i] -= Bz * vz[i] / m[i];
}
}
}
/* ── 边界:反弹(与 main.c limit_in_box 一致)────────────── */
static inline void _limit1(double *p, double *v, double lo, double hi) {
if (*p > hi) { *p = hi; *v = -fabs(*v); }
if (*p < lo) { *p = lo; *v = fabs(*v); }
}
/* ── 边界:回绕(与 main.c wrap_position 一致)──────────── */
static inline void _wrap1(double *p, double lo, double hi) {
if (*p > hi) *p = lo;
if (*p < lo) *p = hi;
}
/* ── 边界 + 固定约束(与 main.c apply_step 末尾一致)──────── */
static void apply_boundary_and_constraints(
int n, double *x, double *y, double *z,
double *vx, double *vy, double *vz,
const int *fixed, const double *pos_init,
double box_a)
{
double lo = -box_a, hi = box_a;
/* 反弹 */
for (int i = 0; i < n; i++) {
if (fixed[i*3] && fixed[i*3+1] && fixed[i*3+2]) continue;
_limit1(&x[i], &vx[i], lo, hi);
_limit1(&y[i], &vy[i], lo, hi);
_limit1(&z[i], &vz[i], lo, hi);
}
/* 回绕 */
for (int i = 0; i < n; i++) {
_wrap1(&x[i], lo, hi);
_wrap1(&y[i], lo, hi);
_wrap1(&z[i], lo, hi);
}
/* 逐自由度固定约束:与 main.c 和 Python apply_fixed_constraints 一致 */
for (int i = 0; i < n; i++) {
if (fixed[i*3+0]) { x[i] = pos_init[i*3+0]; vx[i] = 0.0; }
if (fixed[i*3+1]) { y[i] = pos_init[i*3+1]; vy[i] = 0.0; }
if (fixed[i*3+2]) { z[i] = pos_init[i*3+2]; vz[i] = 0.0; }
}
}
/* ══════════════════════════════════════════════════════════
* 蛙跳法(与 main.c leapfrog_step 完全一致)
* x(t), v(t-dt/2) → x(t+dt), v(t+dt/2)
* 无阻尼:纯辛积分。有阻尼:半隐式处理 α = B·dt/(2m)
* ══════════════════════════════════════════════════════════ */
static void leapfrog_step(
int n, double *x, double *y, double *z,
double *vx, double *vy, double *vz,
const double *m, const int *fixed,
double Gx, double Gy, double Gz,
double Bx, double By, double Bz,
int gravity_field, int elastic_force, int damping_force,
int n_bonds, const int *bp, const double *bk, const double *br0,
double dt)
{
double *ax = (double*)alloca(n*sizeof(double)*3);
double *ay = ax+n; double *az = ay+n;
accel_conservative(n, x, y, z, m, Gx, Gy, Gz,
gravity_field, elastic_force,
n_bonds, bp, bk, br0, ax, ay, az);
int has_damp = damping_force && (Bx != 0.0 || By != 0.0 || Bz != 0.0);
for (int i = 0; i < n; i++) {
if (fixed[i*3] && fixed[i*3+1] && fixed[i*3+2]) continue;
if (has_damp) {
double ax_ = Bx*dt/(2.0*m[i]);
double ay_ = By*dt/(2.0*m[i]);
double az_ = Bz*dt/(2.0*m[i]);
vx[i] = (vx[i]*(1.0-ax_) + ax[i]*dt) / (1.0+ax_);
vy[i] = (vy[i]*(1.0-ay_) + ay[i]*dt) / (1.0+ay_);
vz[i] = (vz[i]*(1.0-az_) + az[i]*dt) / (1.0+az_);
} else {
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;
}
}
/* ══════════════════════════════════════════════════════════
* 显式欧拉法(与 main.c explicit_euler_step 一致)
* ══════════════════════════════════════════════════════════ */
static void euler_step(
int n, double *x, double *y, double *z,
double *vx, double *vy, double *vz,
const double *m, const int *fixed,
double Gx, double Gy, double Gz,
double Bx, double By, double Bz,
int gravity_field, int elastic_force, int damping_force,
int n_bonds, const int *bp, const double *bk, const double *br0,
double dt)
{
double *ax = (double*)alloca(n*sizeof(double)*3);
double *ay = ax+n; double *az = ay+n;
accel_full(n, x, y, z, vx, vy, vz, m, Gx, Gy, Gz, Bx, By, Bz,
gravity_field, elastic_force, damping_force,
n_bonds, bp, bk, br0, ax, ay, az);
for (int i = 0; i < n; i++) {
if (fixed[i*3] && fixed[i*3+1] && fixed[i*3+2]) continue;
x[i] += vx[i]*dt; y[i] += vy[i]*dt; z[i] += vz[i]*dt;
vx[i]+= ax[i]*dt; vy[i]+= ay[i]*dt; vz[i]+= az[i]*dt;
}
}
/* ══════════════════════════════════════════════════════════
* 隐式欧拉法(与 main.c implicit_euler_step 完全一致)
*
* main.c 逻辑:
* 1. 用 v_next ≈ (v + G·dt)/(1 + γ·dt) 预测(只含重力+阻尼,不含弹簧)
* 2. 用 (x, v_next) 计算完整加速度 a_next
* 3. v += a_next·dt; x += v·dt
* ══════════════════════════════════════════════════════════ */
static void implicit_euler_step(
int n, double *x, double *y, double *z,
double *vx, double *vy, double *vz,
const double *m, const int *fixed,
double Gx, double Gy, double Gz,
double Bx, double By, double Bz,
int gravity_field, int elastic_force, int damping_force,
int n_bonds, const int *bp, const double *bk, const double *br0,
double dt)
{
double *vxn = (double*)alloca(n*sizeof(double)*3);
double *vyn = vxn+n; double *vzn = vyn+n;
for (int i = 0; i < n; i++) {
if (fixed[i*3] && fixed[i*3+1] && fixed[i*3+2]) {
vxn[i] = vyn[i] = vzn[i] = 0.0; continue;
}
double gx = Bx / m[i], gy = By / m[i], gz = Bz / m[i];
vxn[i] = (vx[i] + Gx*dt) / (1.0 + gx*dt);
vyn[i] = (vy[i] + Gy*dt) / (1.0 + gy*dt);
vzn[i] = (vz[i] + Gz*dt) / (1.0 + gz*dt);
}
double *ax = (double*)alloca(n*sizeof(double)*3);
double *ay = ax+n; double *az = ay+n;
accel_full(n, x, y, z, vxn, vyn, vzn, m, Gx, Gy, Gz, Bx, By, Bz,
gravity_field, elastic_force, damping_force,
n_bonds, bp, bk, br0, ax, ay, az);
for (int i = 0; i < n; i++) {
if (fixed[i*3] && 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(与 main.c midpoint_step 完全一致)
*
* main.c 逻辑:
* 1. a = accel(x, v)
* 2. xm = x + 0.5·v·dt; vm = v + 0.5·a·dt
* 3. x = x + vm·dt (位置更新用 vm,即中点速度)
* 4. am = accel(xm, vm)
* 5. v = v + am·dt
* ══════════════════════════════════════════════════════════ */
static void midpoint_step(
int n, double *x, double *y, double *z,
double *vx, double *vy, double *vz,
const double *m, const int *fixed,
double Gx, double Gy, double Gz,
double Bx, double By, double Bz,
int gravity_field, int elastic_force, int damping_force,
int n_bonds, const int *bp, const double *bk, const double *br0,
double dt)
{
/* Allocate in one block for cache locality */
double *buf = (double*)alloca(n*sizeof(double)*9);
double *ax = buf;
double *ay = ax+n; double *az = ay+n;
double *xm = az+n; double *ym = xm+n; double *zm = ym+n;
double *vxm = zm+n; double *vym = vxm+n; double *vzm = vym+n;
accel_full(n, x, y, z, vx, vy, vz, m, Gx, Gy, Gz, Bx, By, Bz,
gravity_field, elastic_force, damping_force,
n_bonds, bp, bk, br0, ax, ay, az);
for (int i = 0; i < n; i++) {
if (fixed[i*3] && fixed[i*3+1] && fixed[i*3+2]) {
xm[i]=x[i]; ym[i]=y[i]; zm[i]=z[i];
vxm[i]=vym[i]=vzm[i]=0.0; 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;
/* position updated with midpoint velocity (same as main.c) */
x[i] = x[i] + vxm[i]*dt;
y[i] = y[i] + vym[i]*dt;
z[i] = z[i] + vzm[i]*dt;
}
double *axm = (double*)alloca(n*sizeof(double)*3);
double *aym = axm+n; double *azm = aym+n;
accel_full(n, xm, ym, zm, vxm, vym, vzm, m, Gx, Gy, Gz, Bx, By, Bz,
gravity_field, elastic_force, damping_force,
n_bonds, bp, bk, br0, axm, aym, azm);
for (int i = 0; i < n; i++) {
if (fixed[i*3] && fixed[i*3+1] && fixed[i*3+2]) continue;
vx[i] += axm[i]*dt;
vy[i] += aym[i]*dt;
vz[i] += azm[i]*dt;
}
}
/* ── 驱动力(与 main.c apply_driving_force 一致)────────── */
static void apply_driving(
int n, double *x, double *y, double *z,
double *vx, double *vy, double *vz,
double t, int step, double dt, Drivers *drv)
{
(void)n;
if (!drv || drv->n_drivers == 0) return;
const double TWO_PI = 2.0 * 3.14159265358979323846;
for (int d = 0; d < drv->n_drivers; d++) {
int idx = drv->idx[d];
double fx = drv->freq[d*3+0];
double fy = drv->freq[d*3+1];
double fz = drv->freq[d*3+2];
if (drv->has_period[d]) {
double mf = fabs(fx) > fabs(fy) ? fabs(fx) : fabs(fy);
if (fabs(fz) > mf) mf = fabs(fz);
int period_steps = 0;
if (mf > 1e-12)
period_steps = (int)(drv->ncycles[d] / mf / dt);
if (step > period_steps) {
x[idx] = drv->freeze[d*3+0];
y[idx] = drv->freeze[d*3+1];
z[idx] = drv->freeze[d*3+2];
vx[idx] = vy[idx] = vz[idx] = 0.0;
continue;
}
double px = drv->eq[d*3+0] + drv->amp[d*3+0]*cos(TWO_PI*fx*t + drv->phi[d*3+0]);
double py = drv->eq[d*3+1] + drv->amp[d*3+1]*cos(TWO_PI*fy*t + drv->phi[d*3+1]);
double pz = drv->eq[d*3+2] + drv->amp[d*3+2]*cos(TWO_PI*fz*t + drv->phi[d*3+2]);
if (step == period_steps) {
drv->freeze[d*3+0] = px;
drv->freeze[d*3+1] = py;
drv->freeze[d*3+2] = pz;
}
}
x[idx] = drv->eq[d*3+0] + drv->amp[d*3+0]*cos(TWO_PI*fx*t + drv->phi[d*3+0]);
y[idx] = drv->eq[d*3+1] + drv->amp[d*3+1]*cos(TWO_PI*fy*t + drv->phi[d*3+1]);
z[idx] = drv->eq[d*3+2] + drv->amp[d*3+2]*cos(TWO_PI*fz*t + drv->phi[d*3+2]);
vx[idx] = -drv->amp[d*3+0]*TWO_PI*fx*sin(TWO_PI*fx*t + drv->phi[d*3+0]);
vy[idx] = -drv->amp[d*3+1]*TWO_PI*fy*sin(TWO_PI*fy*t + drv->phi[d*3+1]);
vz[idx] = -drv->amp[d*3+2]*TWO_PI*fz*sin(TWO_PI*fz*t + drv->phi[d*3+2]);
}
}
/* ══════════════════════════════════════════════════════════
* 导出函数:run_dynamics
*
* 与 main.c 的计算顺序完全一致:
* 1. leapfrog 初始化 v(-dt/2)
* 2. 初始驱动 t=0
* 3. 预热循环(不记录)
* 4. 记录循环:drive → record → step → boundary → constraints
*
* 参数说明(所有数组均为 C-contiguous 行优先 float64/int32):
* n_atoms 原子数
* pos_init 初始位置 [n_atoms*3] x0,y0,z0, x1,y1,z1, ...
* vel_init 初始速度 [n_atoms*3]
* masses 质量 [n_atoms]
* fixed 自由度约束 [n_atoms*3] int32, 1=固定
* n_bonds 键数
* bond_pairs 键对 [n_bonds*2] int32, 0-based local index
* bond_k 刚度 [n_bonds]
* bond_r0 平衡键长 [n_bonds]
* box_a 盒子半边长
* dt 时间步长
* NT 总步数(含预热)
* NSTEP 抽帧间隔
* warmup_steps 预热步数
* method_id 0=euler 1=implicit 2=midpoint 3=leapfrog
* Gx/Gy/Gz 均匀重力场加速度分量
* Bx/By/Bz 阻尼系数分量
* gravity_field / elastic_force / damping_force 力开关
* gravity_strength 原子间引力强度(暂未实现,留接口)
* n_drivers 驱动原子数
* drv_idx 驱动原子局部索引 [n_drivers] int32
* drv_amp 振幅 [n_drivers*3]
* drv_freq 频率 [n_drivers*3]
* drv_phi 初相(弧度)[n_drivers*3]
* drv_eq 平衡位置 [n_drivers*3]
* drv_ncycles 周期数 [n_drivers] 0=不限
* drv_has_period [n_drivers] int32
* n_frames 输出帧数(Python 预计算:(NT-warmup)/NSTEP 向上取整)
* out_x/y/z/vx/vy/vz 输出数组 [n_frames*n_atoms] 由 Python 预分配
* progress_cb 进度回调(可为 NULL
*
* 返回:0=成功,负数=错误
* ══════════════════════════════════════════════════════════ */
EXPORT int run_dynamics(
int n_atoms,
const double *pos_init,
const double *vel_init,
const double *masses,
const int *fixed,
int n_bonds,
const int *bond_pairs,
const double *bond_k,
const double *bond_r0,
double box_a, double dt,
int NT, int NSTEP, int warmup_steps, int method_id,
double Gx, double Gy, double Gz,
double Bx, double By, double Bz,
int gravity_field, int elastic_force, int damping_force,
double gravity_strength,
int n_drivers,
const int *drv_idx,
const double *drv_amp,
const double *drv_freq,
const double *drv_phi,
const double *drv_eq,
const double *drv_ncycles,
const int *drv_has_period,
int n_frames,
double *out_x, double *out_y, double *out_z,
double *out_vx, double *out_vy, double *out_vz,
void (*progress_cb)(int step, int total))
{
(void)gravity_strength; /* 原子间引力暂未实现 */
int n = n_atoms;
/* ── 工作数组 ── */
double *x = (double*)malloc(n*sizeof(double));
double *y = (double*)malloc(n*sizeof(double));
double *z = (double*)malloc(n*sizeof(double));
double *vx = (double*)malloc(n*sizeof(double));
double *vy = (double*)malloc(n*sizeof(double));
double *vz = (double*)malloc(n*sizeof(double));
if (!x||!y||!z||!vx||!vy||!vz) return -1;
for (int i = 0; i < n; i++) {
x[i]=pos_init[i*3+0]; y[i]=pos_init[i*3+1]; z[i]=pos_init[i*3+2];
vx[i]=vel_init[i*3+0]; vy[i]=vel_init[i*3+1]; vz[i]=vel_init[i*3+2];
}
/* ── 驱动结构 ── */
Drivers drv;
drv.n_drivers = n_drivers;
drv.idx = drv_idx;
drv.amp = drv_amp;
drv.freq = drv_freq;
drv.phi = drv_phi;
drv.eq = drv_eq;
drv.ncycles = drv_ncycles;
drv.has_period = drv_has_period;
drv.freeze = NULL;
if (n_drivers > 0) {
drv.freeze = (double*)calloc(n_drivers*3, sizeof(double));
if (!drv.freeze) { free(x);free(y);free(z);free(vx);free(vy);free(vz); return -2; }
}
/* ── 内联步进宏 ── */
#define DO_STEP() do { \
switch (method_id) { \
case 0: euler_step(n,x,y,z,vx,vy,vz,masses,fixed,Gx,Gy,Gz,Bx,By,Bz, \
gravity_field,elastic_force,damping_force, \
n_bonds,bond_pairs,bond_k,bond_r0,dt); break; \
case 1: implicit_euler_step(n,x,y,z,vx,vy,vz,masses,fixed,Gx,Gy,Gz,Bx,By,Bz, \
gravity_field,elastic_force,damping_force, \
n_bonds,bond_pairs,bond_k,bond_r0,dt); break; \
case 2: midpoint_step(n,x,y,z,vx,vy,vz,masses,fixed,Gx,Gy,Gz,Bx,By,Bz, \
gravity_field,elastic_force,damping_force, \
n_bonds,bond_pairs,bond_k,bond_r0,dt); break; \
default: leapfrog_step(n,x,y,z,vx,vy,vz,masses,fixed,Gx,Gy,Gz,Bx,By,Bz, \
gravity_field,elastic_force,damping_force, \
n_bonds,bond_pairs,bond_k,bond_r0,dt); break; \
} \
apply_boundary_and_constraints(n,x,y,z,vx,vy,vz,fixed,pos_init,box_a); \
} while(0)
/* ── 蛙跳法:初始化 v(-dt/2) = v(0) - 0.5·a_c(0)·dt ── */
if (method_id == 3) {
double *ax0 = (double*)alloca(n*sizeof(double)*3);
double *ay0 = ax0+n; double *az0 = ay0+n;
accel_conservative(n, x, y, z, masses, Gx, Gy, Gz,
gravity_field, elastic_force,
n_bonds, bond_pairs, bond_k, bond_r0,
ax0, ay0, az0);
for (int i = 0; i < n; i++) {
if (fixed[i*3] && fixed[i*3+1] && fixed[i*3+2]) continue;
vx[i] -= 0.5*ax0[i]*dt;
vy[i] -= 0.5*ay0[i]*dt;
vz[i] -= 0.5*az0[i]*dt;
}
}
/* ── 初始驱动 t=0(与 main.c 一致:leapfrog init 之后施加)── */
if (n_drivers > 0) apply_driving(n, x, y, z, vx, vy, vz, 0.0, 0, dt, &drv);
/* ── 预热(不记录)── */
for (int s = 0; s < warmup_steps; s++) {
double tw = (s + 1) * dt;
if (n_drivers > 0) apply_driving(n, x, y, z, vx, vy, vz, tw, s, dt, &drv);
DO_STEP();
}
/* ── 记录循环 ── */
int record_steps = NT - warmup_steps;
int prog_interval = record_steps / 100;
if (prog_interval < 1) prog_interval = 1;
int frame_idx = 0;
for (int s = 0; s < record_steps; s++) {
if (progress_cb && s % prog_interval == 0 && s > 0)
progress_cb(s, record_steps);
double t = (s + warmup_steps) * dt;
if (n_drivers > 0) apply_driving(n, x, y, z, vx, vy, vz, t, s, dt, &drv);
/* 抽帧记录(drive 之后,step 之前,与 main.c 一致)*/
if (s % NSTEP == 0 && frame_idx < n_frames) {
int base = frame_idx * n;
for (int i = 0; i < n; i++) {
out_x [base+i] = x[i]; out_y [base+i] = y[i]; out_z [base+i] = z[i];
out_vx[base+i] = vx[i]; out_vy[base+i] = vy[i]; out_vz[base+i] = vz[i];
}
frame_idx++;
}
DO_STEP();
}
#undef DO_STEP
free(x); free(y); free(z);
free(vx); free(vy); free(vz);
if (drv.freeze) free(drv.freeze);
return 0;
}