docs: 更新 examples/Readme.md 并新增 Readme.html
- 覆盖全部 10 个案例（原 Readme 只到 case06） - 新增案例选择指南表格 - Readme.html 为深色主题独立 HTML 页面 （含卡片布局、标签分类、代码高亮、响应式设计） - 各案例详情对齐最新配置参数
This commit is contained in:
+20
-1
@@ -8,6 +8,7 @@ CC = gcc
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CFLAGS = -O3 -march=native -Wall -Wextra
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LDFLAGS = -lm
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SRCS = main.c
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LIB_SRC = dynamics_lib.c
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# 自动检测系统
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UNAME_S := $(shell uname -s 2>/dev/null || echo Windows)
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@@ -15,15 +16,33 @@ UNAME_S := $(shell uname -s 2>/dev/null || echo Windows)
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# 目标文件名：统一使用 .exe 后缀（方便 Python 跨平台调用）
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TARGET = build/dynamics_c.exe
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# DLL 目标（平台自动选择后缀）
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ifeq ($(UNAME_S),Linux)
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DLL_TARGET = build/dynamics_c.so
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DLL_FLAGS = -shared -fPIC
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else ifeq ($(UNAME_S),Darwin)
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DLL_TARGET = build/dynamics_c.dylib
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DLL_FLAGS = -dynamiclib
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else
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DLL_TARGET = build/dynamics_c.dll
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DLL_FLAGS = -shared
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endif
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# ── 本地编译 ─────────────────────────────────
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.PHONY: all clean linux windows macos
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.PHONY: all dll clean linux windows macos
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all: $(TARGET)
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dll: $(DLL_TARGET)
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$(TARGET): $(SRCS) | build
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$(CC) $(CFLAGS) -o $@ $(SRCS) $(LDFLAGS)
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@echo " === C engine built: $@ ==="
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$(DLL_TARGET): $(LIB_SRC) | build
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$(CC) $(CFLAGS) $(DLL_FLAGS) -o $@ $(LIB_SRC) $(LDFLAGS)
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@echo " === C DLL built: $@ ==="
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build:
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mkdir -p build
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@@ -0,0 +1 @@
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{"n_atoms": 40, "nt": 200000, "step_time": 2.5352442264556887e-05}
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@@ -0,0 +1,554 @@
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/**
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* engines/c/dynamics_lib.c
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* -------------------------
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* 纯计算 DLL：无文件 I/O，所有数据由 Python 以 NumPy 数组传入，
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* 结果直接写入 Python 预分配的输出数组。
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* 算法与 main.c 和 compute.py 保持完全一致。
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*
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* 编译（Windows DLL）:
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* gcc -O3 -march=native -shared -o build/dynamics_c.dll dynamics_lib.c -lm
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* 编译（Linux .so）:
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* gcc -O3 -march=native -shared -fPIC -o build/dynamics_c.so dynamics_lib.c -lm
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* 编译（macOS .dylib）:
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* gcc -O3 -march=native -dynamiclib -o build/dynamics_c.dylib dynamics_lib.c -lm
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*/
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#ifdef _WIN32
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# define EXPORT __declspec(dllexport)
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#else
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# define EXPORT __attribute__((visibility("default")))
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#endif
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#include <math.h>
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#include <stdlib.h>
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#include <string.h>
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#include <stdio.h>
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/* ── 驱动力结构体 ─────────────────────────────────────────── */
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typedef struct {
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int n_drivers;
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const int *idx; /* [n_drivers] 0-based local atom index */
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const double *amp; /* [n_drivers*3] (ax,ay,az) interleaved */
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const double *freq; /* [n_drivers*3] */
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const double *phi; /* [n_drivers*3] radians */
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const double *eq; /* [n_drivers*3] equilibrium positions */
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const double *ncycles; /* [n_drivers] 0=unlimited */
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const int *has_period; /* [n_drivers] */
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/* mutable freeze positions (allocated internally) */
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double *freeze; /* [n_drivers*3] */
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} Drivers;
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/* ── 加速度：保守力（弹簧键 + 均匀重力场）────────────────── */
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static void accel_conservative(
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int n, const double *x, const double *y, const double *z,
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const double *m,
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double Gx, double Gy, double Gz,
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int gravity_field, int elastic_force,
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int n_bonds, const int *bond_pairs,
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const double *bond_k, const double *bond_r0,
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double *ax, double *ay, double *az)
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{
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for (int i = 0; i < n; i++) {
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ax[i] = gravity_field ? Gx : 0.0;
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ay[i] = gravity_field ? Gy : 0.0;
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az[i] = gravity_field ? Gz : 0.0;
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}
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if (!elastic_force || n_bonds == 0) return;
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for (int b = 0; b < n_bonds; b++) {
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int ii = bond_pairs[b*2];
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int jj = bond_pairs[b*2+1];
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double dx = x[jj] - x[ii];
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double dy = y[jj] - y[ii];
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double dz = z[jj] - z[ii];
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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 k = bond_k[b];
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double r0 = bond_r0[b];
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double fac = k * (dist - r0) / dist;
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double fx = fac * dx, fy = fac * dy, fz_b = fac * dz;
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ax[ii] += fx / m[ii]; ay[ii] += fy / m[ii]; az[ii] += fz_b / m[ii];
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ax[jj] -= fx / m[jj]; ay[jj] -= fy / m[jj]; az[jj] -= fz_b / m[jj];
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}
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}
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/* ── 完整加速度（含阻尼）────────────────────────────────── */
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static void accel_full(
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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,
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double Gx, double Gy, double Gz,
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double Bx, double By, double Bz,
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int gravity_field, int elastic_force, int damping_force,
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int n_bonds, const int *bond_pairs,
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const double *bond_k, const double *bond_r0,
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double *ax, double *ay, double *az)
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{
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accel_conservative(n, x, y, z, m, Gx, Gy, Gz,
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gravity_field, elastic_force,
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n_bonds, bond_pairs, bond_k, bond_r0,
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ax, ay, az);
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if (damping_force) {
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for (int i = 0; i < n; i++) {
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ax[i] -= Bx * vx[i] / m[i];
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ay[i] -= By * vy[i] / m[i];
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az[i] -= Bz * vz[i] / m[i];
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}
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}
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}
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/* ── 边界：反弹（与 main.c limit_in_box 一致）────────────── */
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static inline void _limit1(double *p, double *v, double lo, double hi) {
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if (*p > hi) { *p = hi; *v = -fabs(*v); }
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if (*p < lo) { *p = lo; *v = fabs(*v); }
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}
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/* ── 边界：回绕（与 main.c wrap_position 一致）──────────── */
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static inline void _wrap1(double *p, double lo, double hi) {
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if (*p > hi) *p = lo;
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if (*p < lo) *p = hi;
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}
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/* ── 边界 + 固定约束（与 main.c apply_step 末尾一致）──────── */
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static void apply_boundary_and_constraints(
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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 int *fixed, const double *pos_init,
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double box_a)
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{
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double lo = -box_a, hi = box_a;
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/* 反弹 */
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for (int i = 0; i < n; i++) {
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if (fixed[i*3] && fixed[i*3+1] && fixed[i*3+2]) continue;
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_limit1(&x[i], &vx[i], lo, hi);
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_limit1(&y[i], &vy[i], lo, hi);
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_limit1(&z[i], &vz[i], lo, hi);
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}
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/* 回绕 */
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for (int i = 0; i < n; i++) {
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_wrap1(&x[i], lo, hi);
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_wrap1(&y[i], lo, hi);
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_wrap1(&z[i], lo, hi);
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}
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/* 逐自由度固定约束：与 main.c 和 Python apply_fixed_constraints 一致 */
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for (int i = 0; i < n; i++) {
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if (fixed[i*3+0]) { x[i] = pos_init[i*3+0]; vx[i] = 0.0; }
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if (fixed[i*3+1]) { y[i] = pos_init[i*3+1]; vy[i] = 0.0; }
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if (fixed[i*3+2]) { z[i] = pos_init[i*3+2]; vz[i] = 0.0; }
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}
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}
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/* ══════════════════════════════════════════════════════════
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* 蛙跳法（与 main.c leapfrog_step 完全一致）
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* x(t), v(t-dt/2) → x(t+dt), v(t+dt/2)
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* 无阻尼：纯辛积分。有阻尼：半隐式处理 α = B·dt/(2m)
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* ══════════════════════════════════════════════════════════ */
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static void leapfrog_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 int *fixed,
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double Gx, double Gy, double Gz,
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double Bx, double By, double Bz,
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int gravity_field, int elastic_force, int damping_force,
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int n_bonds, const int *bp, const double *bk, const double *br0,
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double dt)
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{
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double *ax = (double*)alloca(n*sizeof(double)*3);
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double *ay = ax+n; double *az = ay+n;
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accel_conservative(n, x, y, z, m, Gx, Gy, Gz,
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gravity_field, elastic_force,
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n_bonds, bp, bk, br0, ax, ay, az);
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int has_damp = damping_force && (Bx != 0.0 || By != 0.0 || Bz != 0.0);
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for (int i = 0; i < n; i++) {
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if (fixed[i*3] && fixed[i*3+1] && fixed[i*3+2]) continue;
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if (has_damp) {
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double ax_ = Bx*dt/(2.0*m[i]);
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double ay_ = By*dt/(2.0*m[i]);
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double az_ = Bz*dt/(2.0*m[i]);
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vx[i] = (vx[i]*(1.0-ax_) + ax[i]*dt) / (1.0+ax_);
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vy[i] = (vy[i]*(1.0-ay_) + ay[i]*dt) / (1.0+ay_);
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vz[i] = (vz[i]*(1.0-az_) + az[i]*dt) / (1.0+az_);
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} else {
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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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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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}
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}
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/* ══════════════════════════════════════════════════════════
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* 显式欧拉法（与 main.c explicit_euler_step 一致）
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* ══════════════════════════════════════════════════════════ */
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static void 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 int *fixed,
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double Gx, double Gy, double Gz,
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double Bx, double By, double Bz,
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int gravity_field, int elastic_force, int damping_force,
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int n_bonds, const int *bp, const double *bk, const double *br0,
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double dt)
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{
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double *ax = (double*)alloca(n*sizeof(double)*3);
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double *ay = ax+n; double *az = ay+n;
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accel_full(n, x, y, z, vx, vy, vz, m, Gx, Gy, Gz, Bx, By, Bz,
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gravity_field, elastic_force, damping_force,
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n_bonds, bp, bk, br0, ax, ay, az);
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for (int i = 0; i < n; i++) {
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if (fixed[i*3] && fixed[i*3+1] && fixed[i*3+2]) continue;
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x[i] += vx[i]*dt; y[i] += vy[i]*dt; z[i] += vz[i]*dt;
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vx[i]+= ax[i]*dt; vy[i]+= ay[i]*dt; vz[i]+= az[i]*dt;
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}
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}
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/* ══════════════════════════════════════════════════════════
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* 隐式欧拉法（与 main.c implicit_euler_step 完全一致）
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*
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* main.c 逻辑：
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* 1. 用 v_next ≈ (v + G·dt)/(1 + γ·dt) 预测（只含重力+阻尼，不含弹簧）
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* 2. 用 (x, v_next) 计算完整加速度 a_next
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* 3. v += a_next·dt; x += v·dt
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* ══════════════════════════════════════════════════════════ */
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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 int *fixed,
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double Gx, double Gy, double Gz,
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double Bx, double By, double Bz,
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int gravity_field, int elastic_force, int damping_force,
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int n_bonds, const int *bp, const double *bk, const double *br0,
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double dt)
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{
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double *vxn = (double*)alloca(n*sizeof(double)*3);
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double *vyn = vxn+n; double *vzn = vyn+n;
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for (int i = 0; i < n; i++) {
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if (fixed[i*3] && fixed[i*3+1] && fixed[i*3+2]) {
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vxn[i] = vyn[i] = vzn[i] = 0.0; continue;
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}
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double gx = Bx / m[i], gy = By / m[i], gz = Bz / m[i];
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vxn[i] = (vx[i] + Gx*dt) / (1.0 + gx*dt);
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vyn[i] = (vy[i] + Gy*dt) / (1.0 + gy*dt);
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vzn[i] = (vz[i] + Gz*dt) / (1.0 + gz*dt);
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}
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double *ax = (double*)alloca(n*sizeof(double)*3);
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double *ay = ax+n; double *az = ay+n;
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accel_full(n, x, y, z, vxn, vyn, vzn, m, Gx, Gy, Gz, Bx, By, Bz,
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gravity_field, elastic_force, damping_force,
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n_bonds, bp, bk, br0, ax, ay, az);
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for (int i = 0; i < n; i++) {
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if (fixed[i*3] && fixed[i*3+1] && fixed[i*3+2]) continue;
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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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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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}
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}
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/* ══════════════════════════════════════════════════════════
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* 中点法（与 main.c midpoint_step 完全一致）
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*
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* main.c 逻辑：
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* 1. a = accel(x, v)
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* 2. xm = x + 0.5·v·dt; vm = v + 0.5·a·dt
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* 3. x = x + vm·dt (位置更新用 vm，即中点速度)
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* 4. am = accel(xm, vm)
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* 5. v = v + am·dt
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* ══════════════════════════════════════════════════════════ */
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static void midpoint_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 int *fixed,
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double Gx, double Gy, double Gz,
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double Bx, double By, double Bz,
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int gravity_field, int elastic_force, int damping_force,
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int n_bonds, const int *bp, const double *bk, const double *br0,
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double dt)
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{
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/* Allocate in one block for cache locality */
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double *buf = (double*)alloca(n*sizeof(double)*9);
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double *ax = buf;
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double *ay = ax+n; double *az = ay+n;
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double *xm = az+n; double *ym = xm+n; double *zm = ym+n;
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double *vxm = zm+n; double *vym = vxm+n; double *vzm = vym+n;
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accel_full(n, x, y, z, vx, vy, vz, m, Gx, Gy, Gz, Bx, By, Bz,
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gravity_field, elastic_force, damping_force,
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n_bonds, bp, bk, br0, ax, ay, az);
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for (int i = 0; i < n; i++) {
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if (fixed[i*3] && fixed[i*3+1] && fixed[i*3+2]) {
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xm[i]=x[i]; ym[i]=y[i]; zm[i]=z[i];
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vxm[i]=vym[i]=vzm[i]=0.0; continue;
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}
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xm[i] = x[i] + 0.5*vx[i]*dt;
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ym[i] = y[i] + 0.5*vy[i]*dt;
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zm[i] = z[i] + 0.5*vz[i]*dt;
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vxm[i] = vx[i] + 0.5*ax[i]*dt;
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vym[i] = vy[i] + 0.5*ay[i]*dt;
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vzm[i] = vz[i] + 0.5*az[i]*dt;
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/* position updated with midpoint velocity (same as main.c) */
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x[i] = x[i] + vxm[i]*dt;
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y[i] = y[i] + vym[i]*dt;
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z[i] = z[i] + vzm[i]*dt;
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}
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double *axm = (double*)alloca(n*sizeof(double)*3);
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double *aym = axm+n; double *azm = aym+n;
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accel_full(n, xm, ym, zm, vxm, vym, vzm, m, Gx, Gy, Gz, Bx, By, Bz,
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gravity_field, elastic_force, damping_force,
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n_bonds, bp, bk, br0, axm, aym, azm);
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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;
|
||||
}
|
||||
Reference in New Issue
Block a user