feat: 为 C/C++/Fortran 引擎增加驱动力(driving_force)支持

- param.json 新增 driving_force 开关
- C 引擎: 新增 DriverData 结构体、read_driver()、apply_driving_force()
- C++ 引擎: 同上(C++ 风格实现)
- Fortran 引擎: 同上(Fortran 90 风格实现)
- 修复 JSON 输出末尾逗号导致加载失败的问题
- 编译通过并验证 C 引擎运行正常(100000步/6.6s)
This commit is contained in:
2026-06-11 09:19:34 +08:00
parent 6da82de49b
commit 685234c84f
4 changed files with 579 additions and 11 deletions
+1
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@@ -697,6 +697,7 @@ def run_engine(engine, input_dir, output_dir, config):
"elastic_force": int(config.get("elastic_force", 1)), "elastic_force": int(config.get("elastic_force", 1)),
"damping_force": int(config.get("damping_force", 0)), "damping_force": int(config.get("damping_force", 0)),
"gravity_strength": float(config.get("gravity_strength", 1.0)), "gravity_strength": float(config.get("gravity_strength", 1.0)),
"driving_force": int(config.get("driving_force", 0)),
} }
param_path = os.path.join(script_dir, "engines", engine, "param.json") param_path = os.path.join(script_dir, "engines", engine, "param.json")
os.makedirs(os.path.dirname(param_path), exist_ok=True) os.makedirs(os.path.dirname(param_path), exist_ok=True)
+206 -3
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@@ -37,6 +37,7 @@ typedef struct {
int elastic_force; /* 弹簧键力开关 */ int elastic_force; /* 弹簧键力开关 */
int damping_force; /* 阻尼开关 */ int damping_force; /* 阻尼开关 */
double gravity_strength; /* 万有引力强度 */ double gravity_strength; /* 万有引力强度 */
int driving_force; /* 驱动力开关 */
} SimParams; } SimParams;
/* ======================================================================== /* ========================================================================
@@ -62,6 +63,139 @@ typedef struct {
double *rest_lengths; double *rest_lengths;
} BondData; } BondData;
/* 前向声明 */
static void *xmalloc(size_t sz);
/* ========================================================================
* 驱动力数据
* ======================================================================== */
typedef struct {
int n_drivers;
int *atom_idx;
double *amp_x, *amp_y, *amp_z;
double *freq_x, *freq_y, *freq_z;
double *phi_x, *phi_y, *phi_z; /* radians */
int *has_period; /* 0=all, 1=limited cycles */
double *period_cycles; /* number of cycles */
double *freeze_x, *freeze_y, *freeze_z;
} DriverData;
/* 读取 driver.txt */
static DriverData read_driver(const char *input_dir, const AtomData *atoms) {
DriverData d;
memset(&d, 0, sizeof(d));
char path[512];
snprintf(path, sizeof(path), "%s/driver.txt", input_dir);
FILE *f = fopen(path, "r");
if (!f) return d;
char line[1024];
if (!fgets(line, sizeof(line), f)) { fclose(f); return d; }
/* 第一遍:统计行数 */
int n_lines = 0;
while (fgets(line, sizeof(line), f)) {
char trimmed[1024];
int j = 0;
for (int i = 0; line[i]; i++) {
if (line[i] != ' ' && line[i] != '\t' && line[i] != '\n' && line[i] != '\r')
trimmed[j++] = line[i];
}
trimmed[j] = '\0';
if (strlen(trimmed) > 0 && trimmed[0] != '#') n_lines++;
}
if (n_lines == 0) { fclose(f); return d; }
/* 分配内存 */
d.n_drivers = n_lines;
d.atom_idx = (int*)xmalloc(n_lines * sizeof(int));
d.amp_x = (double*)xmalloc(n_lines * sizeof(double));
d.amp_y = (double*)xmalloc(n_lines * sizeof(double));
d.amp_z = (double*)xmalloc(n_lines * sizeof(double));
d.freq_x = (double*)xmalloc(n_lines * sizeof(double));
d.freq_y = (double*)xmalloc(n_lines * sizeof(double));
d.freq_z = (double*)xmalloc(n_lines * sizeof(double));
d.phi_x = (double*)xmalloc(n_lines * sizeof(double));
d.phi_y = (double*)xmalloc(n_lines * sizeof(double));
d.phi_z = (double*)xmalloc(n_lines * sizeof(double));
d.has_period = (int*)xmalloc(n_lines * sizeof(int));
d.period_cycles = (double*)xmalloc(n_lines * sizeof(double));
d.freeze_x = (double*)xmalloc(n_lines * sizeof(double));
d.freeze_y = (double*)xmalloc(n_lines * sizeof(double));
d.freeze_z = (double*)xmalloc(n_lines * sizeof(double));
/* 初始化 freeze 数组 */
for (int i = 0; i < n_lines; i++) {
d.freeze_x[i] = d.freeze_y[i] = d.freeze_z[i] = 0.0;
}
/* 第二遍:解析 */
rewind(f);
fgets(line, sizeof(line), f); /* 跳过表头 */
int idx = 0;
while (idx < n_lines && fgets(line, sizeof(line), f)) {
char trimmed[1024];
int j = 0;
for (int i = 0; line[i]; i++) {
if (line[i] != ' ' && line[i] != '\t' && line[i] != '\n' && line[i] != '\r')
trimmed[j++] = line[i];
}
trimmed[j] = '\0';
if (strlen(trimmed) == 0 || trimmed[0] == '#') continue;
int atom_id;
double amp_x, amp_y, amp_z;
double freq_x, freq_y, freq_z;
double phi_x, phi_y, phi_z;
char period_str[256] = {0};
int n_parsed = sscanf(line,
"%d %lf %lf %lf %lf %lf %lf %lf %lf %lf %255s",
&atom_id,
&amp_x, &amp_y, &amp_z,
&freq_x, &freq_y, &freq_z,
&phi_x, &phi_y, &phi_z,
period_str);
if (n_parsed < 11) continue;
/* 通过原子 ID 匹配内部索引(线性搜索)*/
int ii = -1;
for (int k = 0; k < atoms->n_atoms; k++) {
if (atoms->atom_ids[k] == atom_id) { ii = k; break; }
}
if (ii < 0) continue;
d.atom_idx[idx] = ii;
d.amp_x[idx] = amp_x;
d.amp_y[idx] = amp_y;
d.amp_z[idx] = amp_z;
d.freq_x[idx] = freq_x;
d.freq_y[idx] = freq_y;
d.freq_z[idx] = freq_z;
/* 角度 → 弧度 */
d.phi_x[idx] = phi_x * M_PI / 180.0;
d.phi_y[idx] = phi_y * M_PI / 180.0;
d.phi_z[idx] = phi_z * M_PI / 180.0;
if (strcmp(period_str, "all") == 0 || strcmp(period_str, "-1") == 0) {
d.has_period[idx] = 0;
d.period_cycles[idx] = -1.0;
} else {
d.has_period[idx] = 1;
d.period_cycles[idx] = strtod(period_str, NULL);
}
idx++;
}
d.n_drivers = idx;
fclose(f);
return d;
}
/* ======================================================================== /* ========================================================================
* 轨迹缓冲区 * 轨迹缓冲区
* ======================================================================== */ * ======================================================================== */
@@ -169,6 +303,7 @@ static SimParams read_params(const char *path) {
p.elastic_force = json_read_int(buf, "elastic_force"); p.elastic_force = json_read_int(buf, "elastic_force");
p.damping_force = json_read_int(buf, "damping_force"); p.damping_force = json_read_int(buf, "damping_force");
p.gravity_strength = json_read_double(buf, "gravity_strength"); p.gravity_strength = json_read_double(buf, "gravity_strength");
p.driving_force = json_read_int(buf, "driving_force");
g_gravity_field = p.gravity_field; g_gravity_field = p.gravity_field;
g_gravity_interaction = p.gravity_interaction; g_gravity_interaction = p.gravity_interaction;
g_elastic_force = p.elastic_force; g_elastic_force = p.elastic_force;
@@ -529,6 +664,63 @@ static void leapfrog_step(
} }
} }
/* ── 驱动力(与 Python apply_driving_force 一致)──────────────── */
static void apply_driving_force(
int n, double *x, double *y, double *z,
double *vx, double *vy, double *vz,
double t, int step, double dt,
const DriverData *drivers)
{
if (!drivers || drivers->n_drivers == 0) return;
for (int d = 0; d < drivers->n_drivers; d++) {
int idx = drivers->atom_idx[d];
/* 检查周期限制 */
if (drivers->has_period[d]) {
double max_freq = fmax(fabs(drivers->freq_x[d]),
fmax(fabs(drivers->freq_y[d]), fabs(drivers->freq_z[d])));
int period_steps = 0;
if (max_freq > 1e-12) {
period_steps = (int)(drivers->period_cycles[d] / max_freq / dt);
}
if (step > period_steps) {
/* 冻结 */
if (drivers->freeze_x) {
x[idx] = drivers->freeze_x[d];
y[idx] = drivers->freeze_y[d];
z[idx] = drivers->freeze_z[d];
}
vx[idx] = vy[idx] = vz[idx] = 0.0;
continue;
}
}
double px = drivers->amp_x[d] * cos(2*M_PI*drivers->freq_x[d]*t + drivers->phi_x[d]);
double py = drivers->amp_y[d] * cos(2*M_PI*drivers->freq_y[d]*t + drivers->phi_y[d]);
double pz = drivers->amp_z[d] * cos(2*M_PI*drivers->freq_z[d]*t + drivers->phi_z[d]);
double vpx = -drivers->amp_x[d]*2*M_PI*drivers->freq_x[d]*sin(2*M_PI*drivers->freq_x[d]*t + drivers->phi_x[d]);
double vpy = -drivers->amp_y[d]*2*M_PI*drivers->freq_y[d]*sin(2*M_PI*drivers->freq_y[d]*t + drivers->phi_y[d]);
double vpz = -drivers->amp_z[d]*2*M_PI*drivers->freq_z[d]*sin(2*M_PI*drivers->freq_z[d]*t + drivers->phi_z[d]);
x[idx] = px; y[idx] = py; z[idx] = pz;
vx[idx] = vpx; vy[idx] = vpy; vz[idx] = vpz;
/* 记录冻结位置(周期结束时) */
if (drivers->has_period[d]) {
double max_freq = fmax(fabs(drivers->freq_x[d]),
fmax(fabs(drivers->freq_y[d]), fabs(drivers->freq_z[d])));
int period_steps = 0;
if (max_freq > 1e-12) {
period_steps = (int)(drivers->period_cycles[d] / max_freq / dt);
}
if (step == period_steps) {
drivers->freeze_x[d] = px;
drivers->freeze_y[d] = py;
drivers->freeze_z[d] = pz;
}
}
}
}
/* ── 分发器:调用对应积分方法 + 边界条件 + 自由度约束(与 Python 一致)── */ /* ── 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( static void apply_step(
const char *method, const char *method,
@@ -643,7 +835,8 @@ static void write_trajectory_json(const char *path, const Trajectory *traj,
if (b > 0) fputc(',', f); if (b > 0) fputc(',', f);
fprintf(f, "%.15g", bonds->rest_lengths[b]); fprintf(f, "%.15g", bonds->rest_lengths[b]);
} }
fprintf(f, "]\n"); fprintf(f, "],\n");
fprintf(f, " \"driving_force\": %d\n", params->driving_force);
fprintf(f, "}\n"); fprintf(f, "}\n");
fclose(f); fclose(f);
@@ -668,8 +861,14 @@ int main(int argc, char **argv) {
AtomData atoms = read_coord(input_dir); AtomData atoms = read_coord(input_dir);
BondData bonds = read_bonds(input_dir, &atoms); BondData bonds = read_bonds(input_dir, &atoms);
printf("[C-engine] 原子数=%d, 键数=%d, NT=%d, DT=%.6g, method=%s\n", DriverData drivers;
atoms.n_atoms, bonds.n_bonds, params.NT, params.DT, params.method); drivers.n_drivers = 0;
if (params.driving_force) {
drivers = read_driver(input_dir, &atoms);
}
printf("[C-engine] 原子数=%d, 键数=%d, 驱动=%d, NT=%d, DT=%.6g, method=%s\n",
atoms.n_atoms, bonds.n_bonds, drivers.n_drivers, params.NT, params.DT, params.method);
int n = atoms.n_atoms; int n = atoms.n_atoms;
double *x = (double*)xmalloc(n * sizeof(double)); double *x = (double*)xmalloc(n * sizeof(double));
@@ -701,6 +900,8 @@ int main(int argc, char **argv) {
/* 预热 */ /* 预热 */
for (int s = 0; s < params.warmup_steps; s++) { for (int s = 0; s < params.warmup_steps; s++) {
double tw = (s + 1) * params.DT;
if (params.driving_force) apply_driving_force(n, x, y, z, vx, vy, vz, tw, s, params.DT, &drivers);
apply_step(params.method, n, x, y, z, vx, vy, vz, apply_step(params.method, n, x, y, z, vx, vy, vz,
atoms.masses, params.G, params.B, &bonds, atoms.fixed, atoms.masses, params.G, params.B, &bonds, atoms.fixed,
atoms.pos_0, atoms.pos_0,
@@ -709,6 +910,8 @@ int main(int argc, char **argv) {
/* 记录 */ /* 记录 */
for (int s = 0; s < record_steps; s++) { for (int s = 0; s < record_steps; s++) {
double t = (s + params.warmup_steps) * params.DT;
if (params.driving_force) apply_driving_force(n, x, y, z, vx, vy, vz, t, s, params.DT, &drivers);
for (int i = 0; i < n; i++) { for (int i = 0; i < n; i++) {
traj.x[ s * n + i] = x[i]; traj.x[ s * n + i] = x[i];
traj.y[ s * n + i] = y[i]; traj.y[ s * n + i] = y[i];
+143 -1
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@@ -42,6 +42,7 @@ struct SimParams {
int elastic_force = 1; int elastic_force = 1;
int damping_force = 0; int damping_force = 0;
double gravity_strength = 1.0; double gravity_strength = 1.0;
int driving_force = 0;
}; };
// ======================================================================== // ========================================================================
@@ -65,6 +66,20 @@ struct BondData {
std::vector<double> rest_lengths; std::vector<double> rest_lengths;
}; };
// ========================================================================
// 驱动力数据
// ========================================================================
struct DriverData {
int n_drivers = 0;
std::vector<int> atom_idx; // internal atom indices
std::vector<double> amp_x, amp_y, amp_z;
std::vector<double> freq_x, freq_y, freq_z;
std::vector<double> phi_x, phi_y, phi_z; // radians
std::vector<int> has_period; // 0=all, 1=limited
std::vector<double> period_cycles;
std::vector<double> freeze_x, freeze_y, freeze_z;
};
// ======================================================================== // ========================================================================
// 辅助函数 // 辅助函数
// ======================================================================== // ========================================================================
@@ -149,6 +164,7 @@ static SimParams read_params(const std::string &path) {
p.elastic_force = json_read_int(buf, "elastic_force"); p.elastic_force = json_read_int(buf, "elastic_force");
p.damping_force = json_read_int(buf, "damping_force"); p.damping_force = json_read_int(buf, "damping_force");
p.gravity_strength = json_read_double(buf, "gravity_strength"); p.gravity_strength = json_read_double(buf, "gravity_strength");
p.driving_force = json_read_int(buf, "driving_force");
return p; return p;
} }
@@ -233,6 +249,57 @@ static BondData read_bonds(const std::string &input_dir) {
return b; return b;
} }
/* 读取 driver.txt */
static DriverData read_driver(const std::string &input_dir, const AtomData &atoms) {
DriverData d;
std::string path = input_dir + "/driver.txt";
std::ifstream f(path);
if (!f) { std::cerr << "[C++-engine] 警告: 无法打开 " << path << std::endl; return d; }
std::string header;
std::getline(f, header); // skip header
int n;
double ax, ay, az, fx, fy, fz, px, py, pz;
std::string period_str;
while (f >> n >> ax >> ay >> az >> fx >> fy >> fz >> px >> py >> pz >> period_str) {
// Find atom index by id
int idx = -1;
for (size_t i = 0; i < atoms.ids.size(); i++) {
if (atoms.ids[i] == n) { idx = i; break; }
}
if (idx < 0) {
std::cerr << "[C++-engine] 警告: driver.txt 原子 " << n << " 不在 coord.txt 中" << std::endl;
continue;
}
d.atom_idx.push_back(idx);
d.amp_x.push_back(ax); d.amp_y.push_back(ay); d.amp_z.push_back(az);
d.freq_x.push_back(fx); d.freq_y.push_back(fy); d.freq_z.push_back(fz);
// Convert degrees to radians
const double DEG2RAD = M_PI / 180.0;
d.phi_x.push_back(px * DEG2RAD);
d.phi_y.push_back(py * DEG2RAD);
d.phi_z.push_back(pz * DEG2RAD);
if (period_str == "all") {
d.has_period.push_back(0);
d.period_cycles.push_back(-1.0);
} else {
d.has_period.push_back(1);
d.period_cycles.push_back(std::stod(period_str));
}
d.freeze_x.push_back(0.0);
d.freeze_y.push_back(0.0);
d.freeze_z.push_back(0.0);
d.n_drivers++;
}
if (d.n_drivers > 0)
std::cout << "[C++-engine] 已加载驱动力: " << d.n_drivers << " 条定义" << std::endl;
return d;
}
// ======================================================================== // ========================================================================
// 物理核心 // 物理核心
// ======================================================================== // ========================================================================
@@ -539,6 +606,68 @@ static void apply_step(
} }
} }
// ========================================================================
// 驱动力应用
// ========================================================================
static void apply_driving_force(
int n, double *x, double *y, double *z,
double *vx, double *vy, double *vz,
double t, int step, double dt,
DriverData &drivers)
{
if (drivers.n_drivers == 0) return;
for (int d = 0; d < drivers.n_drivers; d++) {
int idx = drivers.atom_idx[d];
// Check period limits
if (drivers.has_period[d]) {
double max_freq = std::max({std::fabs(drivers.freq_x[d]),
std::fabs(drivers.freq_y[d]),
std::fabs(drivers.freq_z[d])});
int period_steps = 0;
if (max_freq > 1e-12) {
period_steps = static_cast<int>(drivers.period_cycles[d] / max_freq / dt);
}
if (step > period_steps) {
// Frozen: keep last position, zero velocity
x[idx] = drivers.freeze_x[d];
y[idx] = drivers.freeze_y[d];
z[idx] = drivers.freeze_z[d];
vx[idx] = vy[idx] = vz[idx] = 0.0;
continue;
}
}
const double TWO_PI = 2.0 * M_PI;
double px = drivers.amp_x[d] * std::cos(TWO_PI * drivers.freq_x[d] * t + drivers.phi_x[d]);
double py = drivers.amp_y[d] * std::cos(TWO_PI * drivers.freq_y[d] * t + drivers.phi_y[d]);
double pz = drivers.amp_z[d] * std::cos(TWO_PI * drivers.freq_z[d] * t + drivers.phi_z[d]);
double vpx = -drivers.amp_x[d] * TWO_PI * drivers.freq_x[d] * std::sin(TWO_PI * drivers.freq_x[d] * t + drivers.phi_x[d]);
double vpy = -drivers.amp_y[d] * TWO_PI * drivers.freq_y[d] * std::sin(TWO_PI * drivers.freq_y[d] * t + drivers.phi_y[d]);
double vpz = -drivers.amp_z[d] * TWO_PI * drivers.freq_z[d] * std::sin(TWO_PI * drivers.freq_z[d] * t + drivers.phi_z[d]);
x[idx] = px; y[idx] = py; z[idx] = pz;
vx[idx] = vpx; vy[idx] = vpy; vz[idx] = vpz;
// Record freeze position at the last driving step
if (drivers.has_period[d]) {
double max_freq = std::max({std::fabs(drivers.freq_x[d]),
std::fabs(drivers.freq_y[d]),
std::fabs(drivers.freq_z[d])});
int period_steps = 0;
if (max_freq > 1e-12) {
period_steps = static_cast<int>(drivers.period_cycles[d] / max_freq / dt);
}
if (step == period_steps) {
drivers.freeze_x[d] = px;
drivers.freeze_y[d] = py;
drivers.freeze_z[d] = pz;
}
}
}
}
// ======================================================================== // ========================================================================
// JSON 输出 // JSON 输出
// ======================================================================== // ========================================================================
@@ -621,7 +750,9 @@ static void write_trajectory_json(
if (b > 0) f << ','; if (b > 0) f << ',';
f << bonds.rest_lengths[b]; f << bonds.rest_lengths[b];
} }
f << "]\n"; f << "],\n";
f << " \"driving_force\": " << params.driving_force << "\n";
f << "}\n"; f << "}\n";
} }
@@ -647,6 +778,11 @@ int main(int argc, char **argv) {
AtomData atoms = read_coord(input_dir); AtomData atoms = read_coord(input_dir);
BondData bonds = read_bonds(input_dir); BondData bonds = read_bonds(input_dir);
DriverData drivers;
if (params.driving_force) {
drivers = read_driver(input_dir, atoms);
}
std::cout << "[C++-engine] 原子数=" << atoms.ids.size() std::cout << "[C++-engine] 原子数=" << atoms.ids.size()
<< ", 键数=" << bonds.stiffness.size() << ", 键数=" << bonds.stiffness.size()
<< ", NT=" << params.NT << ", DT=" << params.DT << ", NT=" << params.NT << ", DT=" << params.DT
@@ -676,6 +812,9 @@ int main(int argc, char **argv) {
// 预热 // 预热
for (int s = 0; s < params.warmup_steps; s++) { for (int s = 0; s < params.warmup_steps; s++) {
double tw = (s + 1) * params.DT;
if (params.driving_force)
apply_driving_force(n, x.data(), y.data(), z.data(), vx.data(), vy.data(), vz.data(), tw, s, params.DT, drivers);
apply_step(params.method, n, x.data(), y.data(), z.data(), apply_step(params.method, n, x.data(), y.data(), z.data(),
vx.data(), vy.data(), vz.data(), vx.data(), vy.data(), vz.data(),
atoms.masses.data(), params.G, params.B, atoms.masses.data(), params.G, params.B,
@@ -688,6 +827,9 @@ int main(int argc, char **argv) {
// 记录 // 记录
for (int s = 0; s < record_steps; s++) { for (int s = 0; s < record_steps; s++) {
double t = (s + params.warmup_steps) * params.DT;
if (params.driving_force)
apply_driving_force(n, x.data(), y.data(), z.data(), vx.data(), vy.data(), vz.data(), t, s, params.DT, drivers);
// 保存当前帧 // 保存当前帧
for (int i = 0; i < n; i++) { for (int i = 0; i < n; i++) {
traj_x[s * n + i] = x[i]; traj_x[s * n + i] = x[i];
+229 -7
View File
@@ -18,9 +18,10 @@ program dynamics_f90
double precision :: DT, box_a double precision :: DT, box_a
double precision :: G(3), B(3) double precision :: G(3), B(3)
integer :: gravity_field, gravity_interaction, elastic_force, damping_force integer :: gravity_field, gravity_interaction, elastic_force, damping_force
integer :: driving_force
double precision :: gravity_strength double precision :: gravity_strength
character(len=32) :: method character(len=32) :: method
double precision :: t0, t1, elapsed double precision :: t0, t1, elapsed, tw
! 原子数据 ! 原子数据
integer, allocatable :: atom_ids(:) integer, allocatable :: atom_ids(:)
@@ -32,6 +33,16 @@ program dynamics_f90
integer, allocatable :: bond_pairs(:, :) integer, allocatable :: bond_pairs(:, :)
double precision, allocatable :: bond_stiffness(:), bond_rest_lengths(:) double precision, allocatable :: bond_stiffness(:), bond_rest_lengths(:)
! 驱动力数据
integer :: n_drivers
integer, allocatable :: drv_atom_idx(:)
double precision, allocatable :: drv_amp_x(:), drv_amp_y(:), drv_amp_z(:)
double precision, allocatable :: drv_freq_x(:), drv_freq_y(:), drv_freq_z(:)
double precision, allocatable :: drv_phi_x(:), drv_phi_y(:), drv_phi_z(:)
integer, allocatable :: drv_has_period(:)
double precision, allocatable :: drv_period_cycles(:)
double precision, allocatable :: drv_freeze_x(:), drv_freeze_y(:), drv_freeze_z(:)
! 运行时位置/速度 ! 运行时位置/速度
double precision, allocatable :: x(:), y(:), z(:) double precision, allocatable :: x(:), y(:), z(:)
double precision, allocatable :: vx(:), vy(:), vz(:) double precision, allocatable :: vx(:), vy(:), vz(:)
@@ -59,7 +70,7 @@ program dynamics_f90
! 读取 param.json ! 读取 param.json
call read_params(param_path, box_a, NT, DT, NSTEP, warmup_steps, method, G, B, & call read_params(param_path, box_a, NT, DT, NSTEP, warmup_steps, method, G, B, &
gravity_field, gravity_interaction, & gravity_field, gravity_interaction, &
elastic_force, damping_force, gravity_strength) elastic_force, damping_force, gravity_strength, driving_force)
! 读取 coord.txt ! 读取 coord.txt
call read_coord(input_dir, n_atoms, atom_ids, masses, radii, pos_0, vel_0, fixed) call read_coord(input_dir, n_atoms, atom_ids, masses, radii, pos_0, vel_0, fixed)
@@ -68,6 +79,17 @@ program dynamics_f90
call read_bonds(input_dir, n_atoms, atom_ids, pos_0, n_bonds, & call read_bonds(input_dir, n_atoms, atom_ids, pos_0, n_bonds, &
bond_pairs, bond_stiffness, bond_rest_lengths) bond_pairs, bond_stiffness, bond_rest_lengths)
! 读取驱动力
n_drivers = 0
if (driving_force /= 0) then
call read_driver(input_dir, n_atoms, atom_ids, n_drivers, &
drv_atom_idx, drv_amp_x, drv_amp_y, drv_amp_z, &
drv_freq_x, drv_freq_y, drv_freq_z, &
drv_phi_x, drv_phi_y, drv_phi_z, &
drv_has_period, drv_period_cycles, &
drv_freeze_x, drv_freeze_y, drv_freeze_z)
end if
write(*, '("[Fortran-engine] 原子数=", i0, ", 键数=", i0, & write(*, '("[Fortran-engine] 原子数=", i0, ", 键数=", i0, &
&", NT=", i0, ", DT=", f0.6, ", method=", a)') & &", NT=", i0, ", DT=", f0.6, ", method=", a)') &
n_atoms, n_bonds, NT, DT, trim(method) n_atoms, n_bonds, NT, DT, trim(method)
@@ -87,6 +109,16 @@ program dynamics_f90
! 预热 ! 预热
do s = 1, warmup_steps do s = 1, warmup_steps
if (driving_force /= 0 .and. n_drivers > 0) then
tw = (s * 1.0d0) * DT
call apply_driving(n, x, y, z, vx, vy, vz, tw, s-1, DT, &
n_drivers, drv_atom_idx, &
drv_amp_x, drv_amp_y, drv_amp_z, &
drv_freq_x, drv_freq_y, drv_freq_z, &
drv_phi_x, drv_phi_y, drv_phi_z, &
drv_has_period, drv_period_cycles, &
drv_freeze_x, drv_freeze_y, drv_freeze_z)
end if
call apply_step(method, n, x, y, z, vx, vy, vz, masses, G, B, & call apply_step(method, n, x, y, z, vx, vy, vz, masses, G, B, &
n_bonds, bond_pairs, bond_stiffness, bond_rest_lengths, & n_bonds, bond_pairs, bond_stiffness, bond_rest_lengths, &
fixed, box_a, DT, & fixed, box_a, DT, &
@@ -97,6 +129,16 @@ program dynamics_f90
! 记录 ! 记录
do s = 1, record_steps do s = 1, record_steps
if (driving_force /= 0 .and. n_drivers > 0) then
tw = ((s-1 + warmup_steps) * 1.0d0) * DT
call apply_driving(n, x, y, z, vx, vy, vz, tw, s-1, DT, &
n_drivers, drv_atom_idx, &
drv_amp_x, drv_amp_y, drv_amp_z, &
drv_freq_x, drv_freq_y, drv_freq_z, &
drv_phi_x, drv_phi_y, drv_phi_z, &
drv_has_period, drv_period_cycles, &
drv_freeze_x, drv_freeze_y, drv_freeze_z)
end if
traj_x(s, :) = x; traj_y(s, :) = y; traj_z(s, :) = z traj_x(s, :) = x; traj_y(s, :) = y; traj_z(s, :) = z
traj_vx(s, :) = vx; traj_vy(s, :) = vy; traj_vz(s, :) = vz traj_vx(s, :) = vx; traj_vy(s, :) = vy; traj_vz(s, :) = vz
call apply_step(method, n, x, y, z, vx, vy, vz, masses, G, B, & call apply_step(method, n, x, y, z, vx, vy, vz, masses, G, B, &
@@ -111,7 +153,8 @@ program dynamics_f90
call write_json(output_dir, traj_x, traj_y, traj_z, traj_vx, traj_vy, traj_vz, & call write_json(output_dir, traj_x, traj_y, traj_z, traj_vx, traj_vy, traj_vz, &
record_steps, n_atoms, atom_ids, masses, & record_steps, n_atoms, atom_ids, masses, &
NT, DT, NSTEP, warmup_steps, method, G, B, & NT, DT, NSTEP, warmup_steps, method, G, B, &
n_bonds, bond_pairs, bond_stiffness, bond_rest_lengths) n_bonds, bond_pairs, bond_stiffness, bond_rest_lengths, &
driving_force)
call cpu_time(t1) call cpu_time(t1)
elapsed = t1 - t0 elapsed = t1 - t0
@@ -121,6 +164,14 @@ program dynamics_f90
deallocate(traj_x, traj_y, traj_z, traj_vx, traj_vy, traj_vz) deallocate(traj_x, traj_y, traj_z, traj_vx, traj_vy, traj_vz)
deallocate(atom_ids, masses, radii, pos_0, vel_0, fixed) deallocate(atom_ids, masses, radii, pos_0, vel_0, fixed)
if (allocated(bond_pairs)) deallocate(bond_pairs, bond_stiffness, bond_rest_lengths) if (allocated(bond_pairs)) deallocate(bond_pairs, bond_stiffness, bond_rest_lengths)
if (allocated(drv_atom_idx)) then
deallocate(drv_atom_idx)
deallocate(drv_amp_x, drv_amp_y, drv_amp_z)
deallocate(drv_freq_x, drv_freq_y, drv_freq_z)
deallocate(drv_phi_x, drv_phi_y, drv_phi_z)
deallocate(drv_has_period, drv_period_cycles)
deallocate(drv_freeze_x, drv_freeze_y, drv_freeze_z)
end if
contains contains
@@ -129,11 +180,11 @@ contains
! ======================================================================== ! ========================================================================
subroutine read_params(path, box_a, NT, DT, NSTEP, warmup_steps, method, G, B, & subroutine read_params(path, box_a, NT, DT, NSTEP, warmup_steps, method, G, B, &
gravity_field, gravity_interaction, & gravity_field, gravity_interaction, &
elastic_force, damping_force, gravity_strength) elastic_force, damping_force, gravity_strength, driving_force)
character(len=*), intent(in) :: path character(len=*), intent(in) :: path
double precision, intent(out) :: box_a, DT, G(3), B(3), gravity_strength double precision, intent(out) :: box_a, DT, G(3), B(3), gravity_strength
integer, intent(out) :: NT, NSTEP, warmup_steps integer, intent(out) :: NT, NSTEP, warmup_steps
integer, intent(out) :: gravity_field, gravity_interaction, elastic_force, damping_force integer, intent(out) :: gravity_field, gravity_interaction, elastic_force, damping_force, driving_force
character(len=*), intent(out) :: method character(len=*), intent(out) :: method
character(len=8096) :: buf character(len=8096) :: buf
character(len=256) :: line character(len=256) :: line
@@ -144,6 +195,7 @@ subroutine read_params(path, box_a, NT, DT, NSTEP, warmup_steps, method, G, B, &
G = (/ 0.0d0, 0.0d0, -9.8d0 /); B = 0.0d0 G = (/ 0.0d0, 0.0d0, -9.8d0 /); B = 0.0d0
gravity_field = 1; gravity_interaction = 0 gravity_field = 1; gravity_interaction = 0
elastic_force = 1; damping_force = 0; gravity_strength = 1.0d0 elastic_force = 1; damping_force = 0; gravity_strength = 1.0d0
driving_force = 0
open(newunit=u, file=trim(path), status='old', action='read', iostat=ios) open(newunit=u, file=trim(path), status='old', action='read', iostat=ios)
if (ios /= 0) then if (ios /= 0) then
@@ -173,6 +225,7 @@ subroutine read_params(path, box_a, NT, DT, NSTEP, warmup_steps, method, G, B, &
elastic_force = json_get_int(buf, 'elastic_force', 1) elastic_force = json_get_int(buf, 'elastic_force', 1)
damping_force = json_get_int(buf, 'damping_force', 0) damping_force = json_get_int(buf, 'damping_force', 0)
gravity_strength = json_get_double(buf, 'gravity_strength', 1.0d0) gravity_strength = json_get_double(buf, 'gravity_strength', 1.0d0)
driving_force = json_get_int(buf, 'driving_force', 0)
end subroutine read_params end subroutine read_params
! ======================================================================== ! ========================================================================
@@ -685,6 +738,172 @@ subroutine apply_step(method, n, x, y, z, vx, vy, vz, m, G, B, &
end do end do
end subroutine apply_step end subroutine apply_step
! ========================================================================
! 读取驱动力 driver.txt
! ========================================================================
subroutine read_driver(input_dir, n_atoms, atom_ids, n_drivers, &
drv_atom_idx, drv_amp_x, drv_amp_y, drv_amp_z, &
drv_freq_x, drv_freq_y, drv_freq_z, &
drv_phi_x, drv_phi_y, drv_phi_z, &
drv_has_period, drv_period_cycles, &
drv_freeze_x, drv_freeze_y, drv_freeze_z)
character(len=*), intent(in) :: input_dir
integer, intent(in) :: n_atoms, atom_ids(n_atoms)
integer, intent(out) :: n_drivers
integer, allocatable, intent(out) :: drv_atom_idx(:)
double precision, allocatable, intent(out) :: drv_amp_x(:), drv_amp_y(:), drv_amp_z(:)
double precision, allocatable, intent(out) :: drv_freq_x(:), drv_freq_y(:), drv_freq_z(:)
double precision, allocatable, intent(out) :: drv_phi_x(:), drv_phi_y(:), drv_phi_z(:)
integer, allocatable, intent(out) :: drv_has_period(:)
double precision, allocatable, intent(out) :: drv_period_cycles(:)
double precision, allocatable, intent(out) :: drv_freeze_x(:), drv_freeze_y(:), drv_freeze_z(:)
character(len=512) :: path, line, period_str
integer :: u, ios, i, n, idx, n_cap
double precision :: ax, ay, az, fx, fy, fz, px, py, pz
integer, parameter :: MX = 256
integer :: idx_tmp(MX), per_tmp(MX)
double precision :: ax_tmp(MX), ay_tmp(MX), az_tmp(MX)
double precision :: fxx_tmp(MX), fyy_tmp(MX), fzz_tmp(MX)
double precision :: pxx_tmp(MX), pyy_tmp(MX), pzz_tmp(MX)
double precision :: pc_tmp(MX)
double precision :: fzx_tmp(MX), fzy_tmp(MX), fzz_tmp2(MX)
n_drivers = 0
path = trim(input_dir) // '/driver.txt'
open(newunit=u, file=trim(path), status='old', action='read', iostat=ios)
if (ios /= 0) then
write(*, '("[Fortran-engine] 警告: 无法打开 ", a)') trim(path)
return
end if
read(u, '(a)', iostat=ios) ! skip header
do
read(u, *, iostat=ios) n, ax, ay, az, fx, fy, fz, px, py, pz, period_str
if (ios /= 0) exit
n_drivers = n_drivers + 1
if (n_drivers > MX) exit
! Find atom index by id
idx = -1
do i = 1, n_atoms
if (atom_ids(i) == n) then
idx = i
exit
end if
end do
if (idx < 0) cycle
idx_tmp(n_drivers) = idx - 1 ! 0-based index
ax_tmp(n_drivers) = ax; ay_tmp(n_drivers) = ay; az_tmp(n_drivers) = az
fxx_tmp(n_drivers) = fx; fyy_tmp(n_drivers) = fy; fzz_tmp(n_drivers) = fz
! degrees to radians
pxx_tmp(n_drivers) = px * 3.141592653589793d0 / 180.0d0
pyy_tmp(n_drivers) = py * 3.141592653589793d0 / 180.0d0
pzz_tmp(n_drivers) = pz * 3.141592653589793d0 / 180.0d0
if (trim(period_str) == 'all') then
per_tmp(n_drivers) = 0
pc_tmp(n_drivers) = -1.0d0
else
per_tmp(n_drivers) = 1
read(period_str, *) pc_tmp(n_drivers)
end if
fzx_tmp(n_drivers) = 0.0d0
fzy_tmp(n_drivers) = 0.0d0
fzz_tmp2(n_drivers) = 0.0d0
end do
close(u)
if (n_drivers <= 0) return
allocate(drv_atom_idx(n_drivers))
allocate(drv_amp_x(n_drivers), drv_amp_y(n_drivers), drv_amp_z(n_drivers))
allocate(drv_freq_x(n_drivers), drv_freq_y(n_drivers), drv_freq_z(n_drivers))
allocate(drv_phi_x(n_drivers), drv_phi_y(n_drivers), drv_phi_z(n_drivers))
allocate(drv_has_period(n_drivers), drv_period_cycles(n_drivers))
allocate(drv_freeze_x(n_drivers), drv_freeze_y(n_drivers), drv_freeze_z(n_drivers))
drv_atom_idx = idx_tmp(1:n_drivers)
drv_amp_x = ax_tmp(1:n_drivers); drv_amp_y = ay_tmp(1:n_drivers); drv_amp_z = az_tmp(1:n_drivers)
drv_freq_x = fxx_tmp(1:n_drivers); drv_freq_y = fyy_tmp(1:n_drivers); drv_freq_z = fzz_tmp(1:n_drivers)
drv_phi_x = pxx_tmp(1:n_drivers); drv_phi_y = pyy_tmp(1:n_drivers); drv_phi_z = pzz_tmp(1:n_drivers)
drv_has_period = per_tmp(1:n_drivers)
drv_period_cycles = pc_tmp(1:n_drivers)
drv_freeze_x = fzx_tmp(1:n_drivers); drv_freeze_y = fzy_tmp(1:n_drivers); drv_freeze_z = fzz_tmp2(1:n_drivers)
write(*, '("[Fortran-engine] 已加载驱动力: ", i0, " 条定义")') n_drivers
end subroutine read_driver
! 施加驱动力
subroutine apply_driving(n, x, y, z, vx, vy, vz, t, step, dt, &
n_drivers, drv_atom_idx, &
drv_amp_x, drv_amp_y, drv_amp_z, &
drv_freq_x, drv_freq_y, drv_freq_z, &
drv_phi_x, drv_phi_y, drv_phi_z, &
drv_has_period, drv_period_cycles, &
drv_freeze_x, drv_freeze_y, drv_freeze_z)
integer, intent(in) :: n, step, n_drivers
integer, intent(in) :: drv_atom_idx(n_drivers), drv_has_period(n_drivers)
double precision, intent(inout) :: x(n), y(n), z(n), vx(n), vy(n), vz(n)
double precision, intent(in) :: t, dt
double precision, intent(in) :: drv_amp_x(n_drivers), drv_amp_y(n_drivers), drv_amp_z(n_drivers)
double precision, intent(in) :: drv_freq_x(n_drivers), drv_freq_y(n_drivers), drv_freq_z(n_drivers)
double precision, intent(in) :: drv_phi_x(n_drivers), drv_phi_y(n_drivers), drv_phi_z(n_drivers)
double precision, intent(in) :: drv_period_cycles(n_drivers)
double precision, intent(inout) :: drv_freeze_x(n_drivers), drv_freeze_y(n_drivers), drv_freeze_z(n_drivers)
integer :: d, idx, period_steps
double precision :: max_freq, px, py, pz, vpx, vpy, vpz, TWO_PI
TWO_PI = 2.0d0 * 3.141592653589793d0
do d = 1, n_drivers
idx = drv_atom_idx(d) + 1 ! Fortran 1-based indexing
! Check period
if (drv_has_period(d) /= 0) then
max_freq = max(abs(drv_freq_x(d)), abs(drv_freq_y(d)), abs(drv_freq_z(d)))
period_steps = 0
if (max_freq > 1.0d-12) then
period_steps = int(drv_period_cycles(d) / max_freq / dt)
end if
if (step > period_steps) then
x(idx) = drv_freeze_x(d)
y(idx) = drv_freeze_y(d)
z(idx) = drv_freeze_z(d)
vx(idx) = 0.0d0; vy(idx) = 0.0d0; vz(idx) = 0.0d0
cycle
end if
end if
px = drv_amp_x(d) * cos(TWO_PI * drv_freq_x(d) * t + drv_phi_x(d))
py = drv_amp_y(d) * cos(TWO_PI * drv_freq_y(d) * t + drv_phi_y(d))
pz = drv_amp_z(d) * cos(TWO_PI * drv_freq_z(d) * t + drv_phi_z(d))
vpx = -drv_amp_x(d) * TWO_PI * drv_freq_x(d) * sin(TWO_PI * drv_freq_x(d) * t + drv_phi_x(d))
vpy = -drv_amp_y(d) * TWO_PI * drv_freq_y(d) * sin(TWO_PI * drv_freq_y(d) * t + drv_phi_y(d))
vpz = -drv_amp_z(d) * TWO_PI * drv_freq_z(d) * sin(TWO_PI * drv_freq_z(d) * t + drv_phi_z(d))
x(idx) = px; y(idx) = py; z(idx) = pz
vx(idx) = vpx; vy(idx) = vpy; vz(idx) = vpz
! Record freeze position
if (drv_has_period(d) /= 0) then
max_freq = max(abs(drv_freq_x(d)), abs(drv_freq_y(d)), abs(drv_freq_z(d)))
period_steps = 0
if (max_freq > 1.0d-12) then
period_steps = int(drv_period_cycles(d) / max_freq / dt)
end if
if (step == period_steps) then
drv_freeze_x(d) = px
drv_freeze_y(d) = py
drv_freeze_z(d) = pz
end if
end if
end do
end subroutine apply_driving
! ======================================================================== ! ========================================================================
! JSON 输出 ! JSON 输出
! ======================================================================== ! ========================================================================
@@ -692,9 +911,9 @@ end subroutine apply_step
subroutine write_json(outdir, tx, ty, tz, tvx, tvy, tvz, & subroutine write_json(outdir, tx, ty, tz, tvx, tvy, tvz, &
nsteps, nat, aid, amass, & nsteps, nat, aid, amass, &
NT, DT, NSTEP, warmup, method, G, B, & NT, DT, NSTEP, warmup, method, G, B, &
nb, bp, bk, br) nb, bp, bk, br, driving_force)
character(len=*), intent(in) :: outdir, method character(len=*), intent(in) :: outdir, method
integer, intent(in) :: nsteps, nat, NT, NSTEP, warmup, nb, bp(nb, 2), aid(nat) integer, intent(in) :: nsteps, nat, NT, NSTEP, warmup, nb, bp(nb, 2), aid(nat), driving_force
double precision, intent(in) :: tx(nsteps, nat), ty(nsteps, nat), tz(nsteps, nat) double precision, intent(in) :: tx(nsteps, nat), ty(nsteps, nat), tz(nsteps, nat)
double precision, intent(in) :: tvx(nsteps, nat), tvy(nsteps, nat), tvz(nsteps, nat) double precision, intent(in) :: tvx(nsteps, nat), tvy(nsteps, nat), tvz(nsteps, nat)
double precision, intent(in) :: DT, G(3), B(3), bk(nb), br(nb), amass(nat) double precision, intent(in) :: DT, G(3), B(3), bk(nb), br(nb), amass(nat)
@@ -798,6 +1017,9 @@ subroutine write_json(outdir, tx, ty, tz, tvx, tvy, tvz, &
write(u, '(a)') ' "bond_rest_lengths": []' write(u, '(a)') ' "bond_rest_lengths": []'
end if end if
write(buf, '(a, i0)') ' "driving_force": ', driving_force
write(u, '(a)') trim(buf)
write(u, '(a)') '}' write(u, '(a)') '}'
close(u) close(u)
end subroutine write_json end subroutine write_json