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
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+82
-174
@@ -49,7 +49,7 @@ program dynamics_f90
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double precision, allocatable :: vx(:), vy(:), vz(:)
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! 轨迹缓冲区
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integer :: record_steps
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integer :: record_steps, n_frames, frame_idx
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double precision, allocatable :: traj_x(:, :), traj_y(:, :), traj_z(:, :)
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double precision, allocatable :: traj_vx(:, :), traj_vy(:, :), traj_vz(:, :)
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@@ -104,10 +104,11 @@ program dynamics_f90
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vx(i) = vel_0(i, 1); vy(i) = vel_0(i, 2); vz(i) = vel_0(i, 3)
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end do
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! 分配轨迹缓冲区
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! 分配轨迹缓冲区（只保存采样帧，不保存每一步）
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record_steps = NT - warmup_steps
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allocate(traj_x(record_steps, n), traj_y(record_steps, n), traj_z(record_steps, n))
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allocate(traj_vx(record_steps, n), traj_vy(record_steps, n), traj_vz(record_steps, n))
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n_frames = max(1, record_steps / max(1, NSTEP))
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allocate(traj_x(n_frames, n), traj_y(n_frames, n), traj_z(n_frames, n))
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allocate(traj_vx(n_frames, n), traj_vy(n_frames, n), traj_vz(n_frames, n))
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! 真蛙跳初始化：v(0) 反推 v(-dt/2) = v(0) - 0.5*a_c(0)*dt
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if (trim(method) == 'leapfrog') then
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@@ -160,12 +161,19 @@ program dynamics_f90
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pos_0)
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end do
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! 记录
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prog_step = record_steps / 100
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if (prog_step < 1) prog_step = 1
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! 记录（每 NSTEP 步采一帧）
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prog_step = max(1, record_steps / 100)
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frame_idx = 0
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do s = 1, record_steps
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if (mod(s, prog_step) == 0 .and. s > 0) then
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if (mod(s, prog_step) == 0) then
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write(*, '("[Fortran-engine] progress: ", i0, "/", i0)') s, record_steps
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flush(6)
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end if
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! 采帧：在每个 NSTEP 区间的起始时刻记录
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if (mod(s-1, max(1, NSTEP)) == 0 .and. frame_idx < n_frames) then
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frame_idx = frame_idx + 1
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traj_x(frame_idx, :) = x; traj_y(frame_idx, :) = y; traj_z(frame_idx, :) = z
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traj_vx(frame_idx, :) = vx; traj_vy(frame_idx, :) = vy; traj_vz(frame_idx, :) = vz
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end if
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if (driving_force /= 0 .and. n_drivers > 0) then
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tw = ((s-1 + warmup_steps) * 1.0d0) * DT
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@@ -178,8 +186,6 @@ program dynamics_f90
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drv_eq_x, drv_eq_y, drv_eq_z, &
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drv_freeze_x, drv_freeze_y, drv_freeze_z)
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end if
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traj_x(s, :) = x; traj_y(s, :) = y; traj_z(s, :) = z
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traj_vx(s, :) = vx; traj_vy(s, :) = vy; traj_vz(s, :) = vz
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call apply_step(method, n, x, y, z, vx, vy, vz, masses, G, B, &
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n_bonds, bond_pairs, bond_stiffness, bond_rest_lengths, &
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fixed, box_a, DT, &
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@@ -188,13 +194,14 @@ program dynamics_f90
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pos_0)
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end do
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! 输出轨迹
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write(*, '("[Fortran-engine] 正在写入轨迹数据…")')
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call write_json(output_dir, traj_x, traj_y, traj_z, traj_vx, traj_vy, traj_vz, &
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record_steps, n_atoms, atom_ids, masses, &
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NT, DT, NSTEP, warmup_steps, method, G, B, &
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n_bonds, bond_pairs, bond_stiffness, bond_rest_lengths, &
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driving_force)
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! 输出 display.txt
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write(*, '("[Fortran-engine] 正在写入 display.txt (", i0, " 帧)…")') n_frames
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flush(6)
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call write_display_txt(output_dir, n_frames, n_atoms, atom_ids, &
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traj_x, traj_y, traj_z, traj_vx, traj_vy, traj_vz, &
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NT, DT, NSTEP, warmup_steps, method, G, B, &
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n_bonds, gravity_field, elastic_force, damping_force, &
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driving_force, box_a, gravity_strength)
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call cpu_time(t1)
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elapsed = t1 - t0
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@@ -985,179 +992,80 @@ subroutine apply_driving(n, x, y, z, vx, vy, vz, t, step, dt, &
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end subroutine apply_driving
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! ========================================================================
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! JSON 输出
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! display.txt 输出（与 compute.py save_display_txt 格式一致）
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! ========================================================================
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subroutine write_json(outdir, tx, ty, tz, tvx, tvy, tvz, &
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nsteps, nat, aid, amass, &
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NT, DT, NSTEP, warmup, method, G, B, &
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nb, bp, bk, br, driving_force)
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subroutine write_display_txt(outdir, n_frames, nat, aid, &
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tx, ty, tz, tvx, tvy, tvz, &
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NT, DT, NSTEP, warmup, method, G, B, &
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nb, gravity_field, elastic_force, damping_force, &
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driving_force, box_a, gravity_strength)
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character(len=*), intent(in) :: outdir, method
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integer, intent(in) :: nsteps, nat, NT, NSTEP, warmup, nb, bp(nb, 2), aid(nat), driving_force
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double precision, intent(in) :: tx(nsteps, nat), ty(nsteps, nat), tz(nsteps, nat)
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double precision, intent(in) :: tvx(nsteps, nat), tvy(nsteps, nat), tvz(nsteps, nat)
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double precision, intent(in) :: DT, G(3), B(3), bk(nb), br(nb), amass(nat)
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integer, intent(in) :: n_frames, nat, NT, NSTEP, warmup, nb
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integer, intent(in) :: gravity_field, elastic_force, damping_force, driving_force
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integer, intent(in) :: aid(nat)
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double precision, intent(in) :: tx(n_frames, nat), ty(n_frames, nat), tz(n_frames, nat)
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double precision, intent(in) :: tvx(n_frames, nat), tvy(n_frames, nat), tvz(n_frames, nat)
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double precision, intent(in) :: DT, G(3), B(3), box_a, gravity_strength
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character(len=512) :: path, buf
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integer :: u, s, i, ib, ios
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integer :: u, f, a, ios
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integer :: dynamic_steps
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double precision :: T_total
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path = trim(outdir) // '/trajectory.txt'
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dynamic_steps = NT - warmup
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T_total = NT * DT
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path = trim(outdir) // '/display.txt'
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open(newunit=u, file=trim(path), status='replace', action='write', iostat=ios)
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if (ios /= 0) then
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write(*, '("[Fortran-engine] 错误: 无法写入 ", a)') trim(path)
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stop
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return
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end if
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write(u, '(a)') '{'
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! traj_x
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write(u, '(a)') ' "traj_x": ['
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do s = 1, nsteps
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call json_arr(u, tx(s, :), nat, s < nsteps, ' ')
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end do
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write(u, '(a)') ' ],'
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! traj_y
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write(u, '(a)') ' "traj_y": ['
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do s = 1, nsteps
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call json_arr(u, ty(s, :), nat, s < nsteps, ' ')
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end do
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write(u, '(a)') ' ],'
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! traj_z
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write(u, '(a)') ' "traj_z": ['
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do s = 1, nsteps
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call json_arr(u, tz(s, :), nat, s < nsteps, ' ')
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end do
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write(u, '(a)') ' ],'
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! traj_vx
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write(u, '(a)') ' "traj_vx": ['
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do s = 1, nsteps
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call json_arr(u, tvx(s, :), nat, s < nsteps, ' ')
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end do
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write(u, '(a)') ' ],'
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! traj_vy
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write(u, '(a)') ' "traj_vy": ['
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do s = 1, nsteps
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call json_arr(u, tvy(s, :), nat, s < nsteps, ' ')
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end do
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write(u, '(a)') ' ],'
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! traj_vz
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write(u, '(a)') ' "traj_vz": ['
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do s = 1, nsteps
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call json_arr(u, tvz(s, :), nat, s < nsteps, ' ')
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end do
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write(u, '(a)') ' ],'
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! 标量参数
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write(buf, '(a, i0, a)') ' "NT": ', NT, ','
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! ── header ────────────────────────────────────────────────────────────
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write(u, '("number of frames: ", i0)') n_frames
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write(u, '("number of particles: ", i0)') nat
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write(u, '("DT: ", g0)') DT
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write(u, '("NSTEP: ", i0)') NSTEP
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write(u, '("method: ", a)') trim(method)
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write(u, '("NT: ", i0)') NT
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write(u, '("warmup_steps: ", i0)') warmup
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write(u, '("dynamic_steps: ", i0)') dynamic_steps
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write(u, '("T_total: ", g0)') T_total
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write(u, '("box_a: ", g0)') box_a
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write(u, '("gravity_field: ", i0)') gravity_field
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write(u, '("elastic_force: ", i0)') elastic_force
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write(u, '("damping_force: ", i0)') damping_force
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write(u, '("driving_force: ", i0)') driving_force
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write(u, '("gravity_strength: ", g0)') gravity_strength
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write(buf, '("G: [", g0, ", ", g0, ", ", g0, "]")') G(1), G(2), G(3)
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write(u, '(a)') trim(buf)
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write(buf, '(a, g0, a)') ' "DT": ', DT, ','
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write(u, '(a)') trim(buf)
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write(buf, '(a, i0, a)') ' "NSTEP": ', NSTEP, ','
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write(u, '(a)') trim(buf)
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write(buf, '(a, a, a)') ' "method": "', trim(method), '",'
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write(u, '(a)') trim(buf)
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write(buf, '(a, i0, a)') ' "warmup_steps": ', warmup, ','
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write(buf, '("B: [", g0, ", ", g0, ", ", g0, "]")') B(1), B(2), B(3)
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write(u, '(a)') trim(buf)
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write(u, '("number_of_frames: ", i0)') n_frames
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write(u, '("number_of_particles: ", i0)') nat
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write(buf, '("X_MIN: ", g0)') -box_a; write(u, '(a)') trim(buf)
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write(buf, '("X_MAX: ", g0)') box_a; write(u, '(a)') trim(buf)
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write(buf, '("Y_MIN: ", g0)') -box_a; write(u, '(a)') trim(buf)
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write(buf, '("Y_MAX: ", g0)') box_a; write(u, '(a)') trim(buf)
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write(buf, '("Z_MIN: ", g0)') -box_a; write(u, '(a)') trim(buf)
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write(buf, '("Z_MAX: ", g0)') box_a; write(u, '(a)') trim(buf)
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write(buf, '(a, g0, a, g0, a, g0, a)') &
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' "G": [', G(1), ', ', G(2), ', ', G(3), '],'
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write(u, '(a)') trim(buf)
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write(buf, '(a, g0, a, g0, a, g0, a)') &
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' "B": [', B(1), ', ', B(2), ', ', B(3), '],'
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write(u, '(a)') trim(buf)
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! 原子信息
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write(u, '(a)', advance='no') ' "atom_ids": ['
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do i = 1, nat
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if (i > 1) write(u, '(a)', advance='no') ','
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write(u, '(i0)', advance='no') aid(i)
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! ── frame data ────────────────────────────────────────────────────────
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do f = 1, n_frames
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write(u, '()') ! 空行
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write(u, '("frame: ", i0)') f
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write(u, '("n x y z vx vy vz")')
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do a = 1, nat
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write(u, '(i0, 6(f13.6))') aid(a), &
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tx(f,a), ty(f,a), tz(f,a), tvx(f,a), tvy(f,a), tvz(f,a)
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end do
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end do
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write(u, '(a)') '],'
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write(u, '(a)', advance='no') ' "atom_masses": ['
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do i = 1, nat
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if (i > 1) write(u, '(a)', advance='no') ','
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write(u, '(g0)', advance='no') amass(i)
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end do
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write(u, '(a)') '],'
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! 成键
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if (nb > 0) then
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call write_int2_arr(u, 'bond_pairs', bp, nb, .true.)
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call write_dbl_arr(u, 'bond_stiffness', bk, nb, .true.)
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call write_dbl_arr(u, 'bond_rest_lengths', br, nb, .true.)
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else
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write(u, '(a)') ' "bond_pairs": [],'
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write(u, '(a)') ' "bond_stiffness": [],'
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write(u, '(a)') ' "bond_rest_lengths": [],'
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end if
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write(buf, '(a, i0)') ' "driving_force": ', driving_force
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write(u, '(a)') trim(buf)
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write(u, '(a)') '}'
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close(u)
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end subroutine write_json
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! 写出单行 JSON 数组 [v1, v2, ...]
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subroutine json_arr(u, vals, n, has_next, indent)
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integer, intent(in) :: u, n
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double precision, intent(in) :: vals(n)
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logical, intent(in) :: has_next
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character(len=*), intent(in) :: indent
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integer :: i
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write(u, '(a)', advance='no') indent // '['
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do i = 1, n
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if (i > 1) write(u, '(a)', advance='no') ','
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write(u, '(g0.8)', advance='no') vals(i)
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end do
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if (has_next) then
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write(u, '(a)') '],'
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else
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write(u, '(a)') ']'
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end if
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end subroutine json_arr
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subroutine write_int2_arr(u, name, arr, n, has_next)
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integer, intent(in) :: u, n, arr(n, 2)
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character(len=*), intent(in) :: name
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logical, intent(in) :: has_next
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character(len=65536) :: buf
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integer :: i, pos
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write(u, '(a)', advance='no') ' "' // trim(name) // '": ['
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do i = 1, n
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if (i > 1) write(u, '(a)', advance='no') ','
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write(buf, '(a, i0, a, i0, a)') '[', arr(i, 1), ',', arr(i, 2), ']'
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write(u, '(a)', advance='no') trim(buf)
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end do
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if (has_next) then
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write(u, '(a)') '],'
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else
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write(u, '(a)') ']'
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end if
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end subroutine write_int2_arr
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subroutine write_dbl_arr(u, name, arr, n, has_next)
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integer, intent(in) :: u, n
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double precision, intent(in) :: arr(n)
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character(len=*), intent(in) :: name
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logical, intent(in) :: has_next
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integer :: i
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write(u, '(a)', advance='no') ' "' // trim(name) // '": ['
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do i = 1, n
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if (i > 1) write(u, '(a)', advance='no') ','
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write(u, '(g0.8)', advance='no') arr(i)
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end do
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if (has_next) then
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write(u, '(a)') '],'
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else
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write(u, '(a)') ']'
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end if
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end subroutine write_dbl_arr
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write(*, '("[Fortran-engine] display.txt 已保存: ", a)') trim(path)
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flush(6)
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end subroutine write_display_txt
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end program dynamics_f90
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