modified: CMakeLists.txt
modified: INSTALL.md modified: README.md modified: build_release_zip.py modified: compute.py new file: doc/index.html modified: dynamics.py modified: engines/c/main.c modified: engines/cpp/main.cpp modified: engines/fortran/main.f90 modified: examples/case01/input/coord.txt renamed: examples/case01/input/parameters.yaml -> examples/case01/input/input.txt modified: examples/case01/run_dynamics.py new file: examples/case02/input/bond.txt new file: examples/case02/input/connection.txt new file: examples/case02/input/coord.txt new file: examples/case02/input/input.txt new file: examples/case02/run_dynamics.py
This commit is contained in:
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@@ -1,22 +1,49 @@
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! engines/fortran/main.f90
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! ------------------------
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! Fortran 动力学模拟引擎（模板/参考实现）。
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! Fortran 动力学模拟引擎。
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! 与 Python 版 (compute.py) 算法保持一致。
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!
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! 接口与 C 引擎一致：
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! 输入: param.json, <input_dir>/coord.txt, connection.txt, bond.txt
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! 输出: <output_dir>/trajectory.txt (JSON)
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! 输入: param.json, <input_dir>/coord.txt, connection.txt, bond.txt
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! 输出: <output_dir>/trajectory.txt (JSON)
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!
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! 编译:
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! gfortran -O3 -march=native -o build/dynamics_f90 main.f90
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!
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! 用法:
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! ./build/dynamics_f90 <input_dir> <output_dir> <param_json>
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! 编译: cmake --build build --target dynamics_f90
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! 用法: ./build/dynamics_f90 <input_dir> <output_dir> <param_json>
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program dynamics_f90
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implicit none
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character(len=256) :: input_dir, output_dir, param_path
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integer :: narg
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character(len=256) :: input_dir, output_dir, param_path
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integer :: narg, i, n, s
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integer :: NT, NSTEP, warmup_steps, n_atoms, n_bonds
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double precision :: DT, box_a
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double precision :: G(3), B(3)
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integer :: gravity_field, gravity_interaction, elastic_force, damping_force
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double precision :: gravity_strength
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character(len=32) :: method
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double precision :: t0, t1, elapsed
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! 原子数据
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integer, allocatable :: atom_ids(:)
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double precision, allocatable :: masses(:), radii(:)
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double precision, allocatable :: pos_0(:, :), vel_0(:, :)
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integer, allocatable :: fixed(:, :)
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! 成键数据
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integer, allocatable :: bond_pairs(:, :)
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double precision, allocatable :: bond_stiffness(:), bond_rest_lengths(:)
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! 运行时位置/速度
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double precision, allocatable :: x(:), y(:), z(:)
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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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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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! ========================================================================
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! 主流程
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! ========================================================================
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narg = command_argument_count()
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if (narg < 3) then
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write(*,*) "用法: dynamics_f90 <input_dir> <output_dir> <param_json>"
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@@ -27,14 +54,808 @@ program dynamics_f90
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call get_command_argument(2, output_dir)
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call get_command_argument(3, param_path)
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! TODO: 实现与 C 引擎相同的物理模拟
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!
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! 参考实现:
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! 1. 读取 param.json → NT, DT, G, B, ...
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! 2. 读取 coord.txt → 原子数, 质量, 位置, 速度
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! 3. 读取 connection.txt + bond.txt → 成键参数
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! 4. Leapfrog 循环 NT 步
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! 5. 输出 trajectory.txt (JSON 格式)
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call cpu_time(t0)
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! 读取 param.json
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call read_params(param_path, box_a, NT, DT, NSTEP, warmup_steps, method, G, B, &
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gravity_field, gravity_interaction, &
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elastic_force, damping_force, gravity_strength)
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! 读取 coord.txt
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call read_coord(input_dir, n_atoms, atom_ids, masses, radii, pos_0, vel_0, fixed)
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! 读取成键信息
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call read_bonds(input_dir, n_atoms, atom_ids, pos_0, n_bonds, &
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bond_pairs, bond_stiffness, bond_rest_lengths)
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write(*, '("[Fortran-engine] 原子数=", i0, ", 键数=", i0, &
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&", NT=", i0, ", DT=", f0.6, ", method=", a)') &
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n_atoms, n_bonds, NT, DT, trim(method)
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! 初始化位置/速度
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n = n_atoms
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allocate(x(n), y(n), z(n), vx(n), vy(n), vz(n))
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do i = 1, n
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x(i) = pos_0(i, 1); y(i) = pos_0(i, 2); z(i) = pos_0(i, 3)
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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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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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! 预热
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do s = 1, warmup_steps
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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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gravity_field, gravity_interaction, &
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elastic_force, damping_force, gravity_strength, &
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pos_0)
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end do
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! 记录
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do s = 1, record_steps
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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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gravity_field, gravity_interaction, &
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elastic_force, damping_force, gravity_strength, &
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pos_0)
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end do
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! 输出轨迹
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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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call cpu_time(t1)
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elapsed = t1 - t0
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write(*, '("[Fortran-engine] 计算完成: ", i0, " 步, ", f0.6, " s")') record_steps, elapsed
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deallocate(x, y, z, vx, vy, vz)
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deallocate(traj_x, traj_y, traj_z, traj_vx, traj_vy, traj_vz)
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deallocate(atom_ids, masses, radii, pos_0, vel_0, fixed)
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if (allocated(bond_pairs)) deallocate(bond_pairs, bond_stiffness, bond_rest_lengths)
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contains
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! ========================================================================
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! 读取 param.json
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! ========================================================================
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subroutine read_params(path, box_a, NT, DT, NSTEP, warmup_steps, method, G, B, &
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gravity_field, gravity_interaction, &
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elastic_force, damping_force, gravity_strength)
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character(len=*), intent(in) :: path
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double precision, intent(out) :: box_a, DT, G(3), B(3), gravity_strength
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integer, intent(out) :: NT, NSTEP, warmup_steps
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integer, intent(out) :: gravity_field, gravity_interaction, elastic_force, damping_force
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character(len=*), intent(out) :: method
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character(len=8096) :: buf
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character(len=256) :: line
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integer :: u, ios
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box_a = 10.0d0; NT = 10000; DT = 0.001d0; NSTEP = 100; warmup_steps = 0
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method = 'leapfrog'
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G = (/ 0.0d0, 0.0d0, -9.8d0 /); B = 0.0d0
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gravity_field = 1; gravity_interaction = 0
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elastic_force = 1; damping_force = 0; gravity_strength = 1.0d0
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open(newunit=u, file=trim(path), status='old', action='read', iostat=ios)
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if (ios /= 0) then
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write(*, '("[Fortran-engine] 警告: 无法打开 ", a, ", 使用默认值")') trim(path)
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return
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end if
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buf = ''
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do
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read(u, '(a)', iostat=ios) line
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if (ios /= 0) exit
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buf = trim(buf) // trim(line) // char(10)
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end do
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close(u)
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if (ios > 0) return
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box_a = json_get_double(buf, 'box_a', box_a)
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NT = json_get_int(buf, 'NT', NT)
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DT = json_get_double(buf, 'DT', DT)
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NSTEP = json_get_int(buf, 'NSTEP', NSTEP)
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warmup_steps = json_get_int(buf, 'warmup_steps', warmup_steps)
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call json_get_string(buf, 'method', method)
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if (len_trim(method) == 0) method = 'leapfrog'
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call json_get_double3(buf, 'G', G)
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call json_get_double3(buf, 'B', B)
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gravity_field = json_get_int(buf, 'gravity_field', 1)
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gravity_interaction = json_get_int(buf, 'gravity_interaction', 0)
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elastic_force = json_get_int(buf, 'elastic_force', 1)
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damping_force = json_get_int(buf, 'damping_force', 0)
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gravity_strength = json_get_double(buf, 'gravity_strength', 1.0d0)
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end subroutine read_params
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! ========================================================================
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! JSON 辅助解析
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! ========================================================================
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function json_get_double(buf, key, default) result(val)
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character(len=*), intent(in) :: buf, key
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double precision, intent(in) :: default
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double precision :: val
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integer :: p, ios
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val = default
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p = index(buf, '"' // key // '"')
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if (p == 0) return
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p = index(buf(p:), ':') + p
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do while (p <= len(buf) .and. (buf(p:p) == ':' .or. buf(p:p) == ' ' &
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.or. buf(p:p) == char(9) .or. buf(p:p) == char(10)))
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p = p + 1
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end do
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read(buf(p:), *, iostat=ios) val
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end function json_get_double
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function json_get_int(buf, key, default) result(val)
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character(len=*), intent(in) :: buf, key
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integer, intent(in) :: default
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integer :: val
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val = nint(json_get_double(buf, key, dble(default)))
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end function json_get_int
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subroutine json_get_double3(buf, key, vals)
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character(len=*), intent(in) :: buf, key
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double precision, intent(out) :: vals(3)
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integer :: p, i, ios
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vals = 0.0d0
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p = index(buf, '"' // key // '"')
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if (p == 0) return
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p = index(buf(p:), '[') + p
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do i = 1, 3
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do while (buf(p:p) == ' ' .or. buf(p:p) == ',' .or. &
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buf(p:p) == char(9) .or. buf(p:p) == char(10))
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p = p + 1
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end do
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read(buf(p:), *, iostat=ios) vals(i)
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if (ios /= 0) exit
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do while (p <= len(buf) .and. buf(p:p) /= ',' .and. buf(p:p) /= ']')
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p = p + 1
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end do
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end do
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end subroutine json_get_double3
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! 从 JSON 中读取字符串值
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subroutine json_get_string(buf, key, val)
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character(len=*), intent(in) :: buf, key
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character(len=*), intent(out) :: val
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integer :: p, i, j
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val = ''
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p = index(buf, '"' // key // '"')
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if (p == 0) return
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p = index(buf(p:), ':') + p
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do while (p <= len(buf) .and. (buf(p:p) == ':' .or. buf(p:p) == ' ' &
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.or. buf(p:p) == char(9) .or. buf(p:p) == char(10)))
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p = p + 1
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end do
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if (buf(p:p) /= '"') return
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p = p + 1
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i = 1
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do while (p <= len(buf) .and. buf(p:p) /= '"' .and. i <= len(val))
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val(i:i) = buf(p:p)
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i = i + 1; p = p + 1
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end do
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end subroutine json_get_string
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! ========================================================================
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! 读取 coord.txt
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! ========================================================================
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subroutine read_coord(input_dir, n_atoms, atom_ids, masses, radii, pos_0, vel_0, fixed)
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character(len=*), intent(in) :: input_dir
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integer, intent(out) :: n_atoms
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integer, allocatable, intent(out) :: atom_ids(:)
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double precision, allocatable, intent(out) :: masses(:), radii(:)
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double precision, allocatable, intent(out) :: pos_0(:, :), vel_0(:, :)
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integer, allocatable, intent(out) :: fixed(:, :)
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character(len=512) :: path, line
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integer :: u, ios, ncols, n_cap, id, fx, fy, fz, i
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double precision :: mass, rad, px, py, pz, vx, vy, vz
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integer, parameter :: MX = 4096
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integer :: ids_tmp(MX), fix_tmp(MX, 3)
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double precision :: m_tmp(MX), r_tmp(MX), p_tmp(MX, 3), v_tmp(MX, 3)
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n_atoms = 0
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path = trim(input_dir) // '/coord.txt'
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open(newunit=u, file=trim(path), status='old', action='read', iostat=ios)
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if (ios /= 0) then; write(*, '("[Fortran-engine] 错误: 无法打开 ", a)') trim(path); stop; end if
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read(u, '(a)', iostat=ios) line
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ncols = 0
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do i = 1, len_trim(line)
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if (line(i:i) /= ' ' .and. (i == 1 .or. line(i-1:i-1) == ' ')) ncols = ncols + 1
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end do
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do
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read(u, '(a)', iostat=ios) line
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if (ios /= 0) exit
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if (len_trim(line) == 0 .or. line(1:1) == '#') cycle
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n_atoms = n_atoms + 1
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if (n_atoms > MX) exit
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if (ncols >= 12) then
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read(line, *) id, mass, rad, px, py, pz, vx, vy, vz, fx, fy, fz
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else
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read(line, *) id, mass, rad, px, py, pz, vx, vy, vz
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fx = 0; fy = 0; fz = 0
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end if
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ids_tmp(n_atoms) = id
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m_tmp(n_atoms) = mass; r_tmp(n_atoms) = rad
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p_tmp(n_atoms, :) = (/ px, py, pz /)
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v_tmp(n_atoms, :) = (/ vx, vy, vz /)
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fix_tmp(n_atoms, :) = (/ fx, fy, fz /)
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end do
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close(u)
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if (n_atoms <= 0) then; write(*, '("[Fortran-engine] 错误: coord.txt 为空")') ; stop; end if
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allocate(atom_ids(n_atoms), masses(n_atoms), radii(n_atoms))
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allocate(pos_0(n_atoms, 3), vel_0(n_atoms, 3), fixed(n_atoms, 3))
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atom_ids = ids_tmp(1:n_atoms)
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masses = m_tmp(1:n_atoms); radii = r_tmp(1:n_atoms)
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pos_0 = p_tmp(1:n_atoms, :); vel_0 = v_tmp(1:n_atoms, :)
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fixed = fix_tmp(1:n_atoms, :)
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end subroutine read_coord
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! ========================================================================
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! 读取成键信息 (connection.txt + bond.txt)
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! ========================================================================
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subroutine read_bonds(input_dir, n_atoms, atom_ids, pos_0, n_bonds, &
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bond_pairs, bond_stiffness, bond_rest_lengths)
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character(len=*), intent(in) :: input_dir
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integer, intent(in) :: n_atoms, atom_ids(n_atoms)
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double precision, intent(in) :: pos_0(n_atoms, 3)
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integer, intent(out) :: n_bonds
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integer, allocatable, intent(out) :: bond_pairs(:, :)
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double precision, allocatable, intent(out) :: bond_stiffness(:), bond_rest_lengths(:)
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character(len=512) :: conn_path
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integer :: u, ios, a1, a2, idx1, idx2, i
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integer, parameter :: MX = 4096
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integer :: ptmp(MX, 2), idx_map(9999)
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double precision :: ktmp(MX), r0tmp(MX), dx, dy, dz
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character(len=64) :: name
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n_bonds = 0; idx_map = -1
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do i = 1, n_atoms
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if (atom_ids(i) > 0 .and. atom_ids(i) <= 9998) idx_map(atom_ids(i)) = i
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end do
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conn_path = trim(input_dir) // '/connection.txt'
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open(newunit=u, file=trim(conn_path), status='old', action='read', iostat=ios)
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if (ios /= 0) return
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read(u, *, iostat=ios)
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do
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read(u, *, iostat=ios) a1, a2, name
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if (ios /= 0) exit
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call find_bond(trim(input_dir), trim(name), ktmp(n_bonds+1), r0tmp(n_bonds+1))
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idx1 = idx_map(a1); idx2 = idx_map(a2)
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if (idx1 < 1 .or. idx2 < 1) cycle
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if (r0tmp(n_bonds+1) <= 0.0d0) then
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dx = pos_0(idx2, 1) - pos_0(idx1, 1)
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dy = pos_0(idx2, 2) - pos_0(idx1, 2)
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dz = pos_0(idx2, 3) - pos_0(idx1, 3)
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r0tmp(n_bonds+1) = sqrt(dx*dx + dy*dy + dz*dz)
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end if
|
||||
n_bonds = n_bonds + 1
|
||||
ptmp(n_bonds, :) = (/ idx1 - 1, idx2 - 1 /)
|
||||
if (n_bonds >= MX) exit
|
||||
end do
|
||||
close(u)
|
||||
|
||||
if (n_bonds <= 0) return
|
||||
allocate(bond_pairs(n_bonds, 2), bond_stiffness(n_bonds), bond_rest_lengths(n_bonds))
|
||||
bond_pairs(:, :) = ptmp(1:n_bonds, :)
|
||||
bond_stiffness = ktmp(1:n_bonds)
|
||||
bond_rest_lengths = r0tmp(1:n_bonds)
|
||||
end subroutine read_bonds
|
||||
|
||||
subroutine find_bond(bond_dir, bond_name, k, r0)
|
||||
character(len=*), intent(in) :: bond_dir, bond_name
|
||||
double precision, intent(out) :: k, r0
|
||||
character(len=512) :: path, bn
|
||||
integer :: u, ios
|
||||
double precision :: bk, br
|
||||
k = 1.0d0; r0 = -1.0d0
|
||||
path = trim(bond_dir) // '/bond.txt'
|
||||
open(newunit=u, file=trim(path), status='old', action='read', iostat=ios)
|
||||
if (ios /= 0) return
|
||||
read(u, *, iostat=ios)
|
||||
do
|
||||
read(u, *, iostat=ios) bn, bk, br
|
||||
if (ios /= 0) exit
|
||||
if (trim(bn) == trim(bond_name)) then
|
||||
k = bk
|
||||
if (br > 0.0d0) r0 = br
|
||||
exit
|
||||
end if
|
||||
end do
|
||||
close(u)
|
||||
end subroutine find_bond
|
||||
|
||||
! ========================================================================
|
||||
! 物理核心
|
||||
! ========================================================================
|
||||
|
||||
! 加速度计算（各力独立开关控制）
|
||||
pure subroutine accel(n, x, y, z, vx, vy, vz, m, G, B, &
|
||||
nb, bp, bk, br, &
|
||||
gravity_field, gravity_interaction, &
|
||||
elastic_force, damping_force, gravity_strength, &
|
||||
ax, ay, az)
|
||||
integer, intent(in) :: n, nb, bp(nb, 2)
|
||||
integer, intent(in) :: gravity_field, gravity_interaction, elastic_force, damping_force
|
||||
double precision, intent(in) :: x(n), y(n), z(n), vx(n), vy(n), vz(n)
|
||||
double precision, intent(in) :: m(n), G(3), B(3), bk(nb), br(nb), gravity_strength
|
||||
double precision, intent(out) :: ax(n), ay(n), az(n)
|
||||
integer :: i, j, ib
|
||||
double precision :: dx, dy, dz, dist, s, fm, ux, uy, uz, r2, fg
|
||||
|
||||
! 清零
|
||||
ax = 0.0d0; ay = 0.0d0; az = 0.0d0
|
||||
|
||||
! 均匀重力场
|
||||
if (gravity_field /= 0) then
|
||||
do i = 1, n
|
||||
ax(i) = G(1); ay(i) = G(2); az(i) = G(3)
|
||||
end do
|
||||
end if
|
||||
|
||||
! 阻尼
|
||||
if (damping_force /= 0) then
|
||||
do i = 1, n
|
||||
ax(i) = ax(i) - B(1) * vx(i) / m(i)
|
||||
ay(i) = ay(i) - B(2) * vy(i) / m(i)
|
||||
az(i) = az(i) - B(3) * vz(i) / m(i)
|
||||
end do
|
||||
end if
|
||||
|
||||
! 弹簧键力
|
||||
if (elastic_force /= 0) then
|
||||
do ib = 1, nb
|
||||
i = bp(ib, 1) + 1; j = bp(ib, 2) + 1
|
||||
dx = x(j) - x(i); dy = y(j) - y(i); dz = z(j) - z(i)
|
||||
dist = sqrt(dx*dx + dy*dy + dz*dz)
|
||||
if (dist < 1.0d-12) cycle
|
||||
s = (dist - br(ib)) / dist
|
||||
fm = bk(ib) * s
|
||||
ux = fm * dx; uy = fm * dy; uz = fm * dz
|
||||
ax(i) = ax(i) + ux / m(i); ay(i) = ay(i) + uy / m(i); az(i) = az(i) + uz / m(i)
|
||||
ax(j) = ax(j) - ux / m(j); ay(j) = ay(j) - uy / m(j); az(j) = az(j) - uz / m(j)
|
||||
end do
|
||||
end if
|
||||
|
||||
! 万有引力（所有原子对之间）
|
||||
if (gravity_interaction /= 0) then
|
||||
do i = 1, n - 1
|
||||
do j = i + 1, n
|
||||
dx = x(j) - x(i); dy = y(j) - y(i); dz = z(j) - z(i)
|
||||
r2 = dx*dx + dy*dy + dz*dz
|
||||
if (r2 <= 1.0d-12) cycle
|
||||
dist = sqrt(r2)
|
||||
fg = gravity_strength * m(i) * m(j) / r2
|
||||
ux = fg * dx / dist; uy = fg * dy / dist; uz = fg * dz / dist
|
||||
ax(i) = ax(i) + ux / m(i); ay(i) = ay(i) + uy / m(i); az(i) = az(i) + uz / m(i)
|
||||
ax(j) = ax(j) - ux / m(j); ay(j) = ay(j) - uy / m(j); az(j) = az(j) - uz / m(j)
|
||||
end do
|
||||
end do
|
||||
end if
|
||||
end subroutine accel
|
||||
|
||||
! 边界条件：clamp 位置 + 速度反转
|
||||
subroutine limit_in_box(pos, vel, lo, hi)
|
||||
double precision, intent(inout) :: pos, vel
|
||||
double precision, intent(in) :: lo, hi
|
||||
if (pos > hi) then
|
||||
pos = hi; vel = -vel
|
||||
else if (pos < lo) then
|
||||
pos = lo; vel = -vel
|
||||
end if
|
||||
end subroutine limit_in_box
|
||||
|
||||
! ── 显式欧拉法 ────────────
|
||||
subroutine explicit_euler_step(n, x, y, z, vx, vy, vz, m, G, B, &
|
||||
nb, bp, bk, br, fixed, dt, &
|
||||
gravity_field, gravity_interaction, &
|
||||
elastic_force, damping_force, gravity_strength)
|
||||
integer, intent(in) :: n, nb, bp(nb, 2), fixed(n, 3)
|
||||
integer, intent(in) :: gravity_field, gravity_interaction, elastic_force, damping_force
|
||||
double precision, intent(inout) :: x(n), y(n), z(n), vx(n), vy(n), vz(n)
|
||||
double precision, intent(in) :: m(n), G(3), B(3), bk(nb), br(nb), dt, gravity_strength
|
||||
double precision :: ax(n), ay(n), az(n)
|
||||
integer :: i
|
||||
|
||||
call accel(n, x, y, z, vx, vy, vz, m, G, B, nb, bp, bk, br, &
|
||||
gravity_field, gravity_interaction, &
|
||||
elastic_force, damping_force, gravity_strength, ax, ay, az)
|
||||
do i = 1, n
|
||||
if (fixed(i,1) /= 0 .and. fixed(i,2) /= 0 .and. fixed(i,3) /= 0) cycle
|
||||
x(i) = x(i) + vx(i) * dt
|
||||
y(i) = y(i) + vy(i) * dt
|
||||
z(i) = z(i) + vz(i) * dt
|
||||
vx(i) = vx(i) + ax(i) * dt
|
||||
vy(i) = vy(i) + ay(i) * dt
|
||||
vz(i) = vz(i) + az(i) * dt
|
||||
end do
|
||||
end subroutine explicit_euler_step
|
||||
|
||||
! ── 隐式欧拉法 ────────────
|
||||
subroutine implicit_euler_step(n, x, y, z, vx, vy, vz, m, G, B, &
|
||||
nb, bp, bk, br, fixed, dt, &
|
||||
gravity_field, gravity_interaction, &
|
||||
elastic_force, damping_force, gravity_strength)
|
||||
integer, intent(in) :: n, nb, bp(nb, 2), fixed(n, 3)
|
||||
integer, intent(in) :: gravity_field, gravity_interaction, elastic_force, damping_force
|
||||
double precision, intent(inout) :: x(n), y(n), z(n), vx(n), vy(n), vz(n)
|
||||
double precision, intent(in) :: m(n), G(3), B(3), bk(nb), br(nb), dt, gravity_strength
|
||||
double precision :: ax(n), ay(n), az(n)
|
||||
double precision :: vxn(n), vyn(n), vzn(n)
|
||||
double precision :: gx, gy, gz
|
||||
integer :: i
|
||||
|
||||
! 隐式速度（重力 + 阻尼）
|
||||
do i = 1, n
|
||||
if (fixed(i,1) /= 0 .and. fixed(i,2) /= 0 .and. fixed(i,3) /= 0) then
|
||||
vxn(i) = 0; vyn(i) = 0; vzn(i) = 0; cycle
|
||||
end if
|
||||
gx = B(1) / m(i); gy = B(2) / m(i); gz = B(3) / m(i)
|
||||
vxn(i) = (vx(i) + G(1) * dt) / (1.0d0 + gx * dt)
|
||||
vyn(i) = (vy(i) + G(2) * dt) / (1.0d0 + gy * dt)
|
||||
vzn(i) = (vz(i) + G(3) * dt) / (1.0d0 + gz * dt)
|
||||
end do
|
||||
|
||||
! 用当前位 + 隐式速度算完整加速度
|
||||
call accel(n, x, y, z, vxn, vyn, vzn, m, G, B, nb, bp, bk, br, &
|
||||
gravity_field, gravity_interaction, &
|
||||
elastic_force, damping_force, gravity_strength, ax, ay, az)
|
||||
|
||||
do i = 1, n
|
||||
if (fixed(i,1) /= 0 .and. fixed(i,2) /= 0 .and. fixed(i,3) /= 0) cycle
|
||||
vx(i) = vx(i) + ax(i) * dt
|
||||
vy(i) = vy(i) + ay(i) * dt
|
||||
vz(i) = vz(i) + az(i) * dt
|
||||
x(i) = x(i) + vx(i) * dt
|
||||
y(i) = y(i) + vy(i) * dt
|
||||
z(i) = z(i) + vz(i) * dt
|
||||
end do
|
||||
end subroutine implicit_euler_step
|
||||
|
||||
! ── 中点法 ────────────
|
||||
subroutine midpoint_step(n, x, y, z, vx, vy, vz, m, G, B, &
|
||||
nb, bp, bk, br, fixed, dt, &
|
||||
gravity_field, gravity_interaction, &
|
||||
elastic_force, damping_force, gravity_strength)
|
||||
integer, intent(in) :: n, nb, bp(nb, 2), fixed(n, 3)
|
||||
integer, intent(in) :: gravity_field, gravity_interaction, elastic_force, damping_force
|
||||
double precision, intent(inout) :: x(n), y(n), z(n), vx(n), vy(n), vz(n)
|
||||
double precision, intent(in) :: m(n), G(3), B(3), bk(nb), br(nb), dt, gravity_strength
|
||||
double precision :: ax(n), ay(n), az(n)
|
||||
double precision :: xm(n), ym(n), zm(n), vxm(n), vym(n), vzm(n)
|
||||
integer :: i
|
||||
|
||||
call accel(n, x, y, z, vx, vy, vz, m, G, B, nb, bp, bk, br, &
|
||||
gravity_field, gravity_interaction, &
|
||||
elastic_force, damping_force, gravity_strength, ax, ay, az)
|
||||
do i = 1, n
|
||||
if (fixed(i,1) /= 0 .and. fixed(i,2) /= 0 .and. fixed(i,3) /= 0) then
|
||||
xm(i)=0; ym(i)=0; zm(i)=0; vxm(i)=0; vym(i)=0; vzm(i)=0; cycle
|
||||
end if
|
||||
xm(i) = x(i) + 0.5d0 * vx(i) * dt
|
||||
ym(i) = y(i) + 0.5d0 * vy(i) * dt
|
||||
zm(i) = z(i) + 0.5d0 * vz(i) * dt
|
||||
vxm(i) = vx(i) + 0.5d0 * ax(i) * dt
|
||||
vym(i) = vy(i) + 0.5d0 * ay(i) * dt
|
||||
vzm(i) = vz(i) + 0.5d0 * az(i) * dt
|
||||
x(i) = x(i) + vxm(i) * dt
|
||||
y(i) = y(i) + vym(i) * dt
|
||||
z(i) = z(i) + vzm(i) * dt
|
||||
end do
|
||||
|
||||
call accel(n, xm, ym, zm, vxm, vym, vzm, m, G, B, nb, bp, bk, br, &
|
||||
gravity_field, gravity_interaction, &
|
||||
elastic_force, damping_force, gravity_strength, ax, ay, az)
|
||||
do i = 1, n
|
||||
if (fixed(i,1) /= 0 .and. fixed(i,2) /= 0 .and. fixed(i,3) /= 0) cycle
|
||||
vx(i) = vx(i) + ax(i) * dt
|
||||
vy(i) = vy(i) + ay(i) * dt
|
||||
vz(i) = vz(i) + az(i) * dt
|
||||
end do
|
||||
end subroutine midpoint_step
|
||||
|
||||
! ── 蛙跳法（Velocity-Verlet）──
|
||||
subroutine leapfrog_full(n, x, y, z, vx, vy, vz, m, G, B, &
|
||||
nb, bp, bk, br, fixed, dt, &
|
||||
gravity_field, gravity_interaction, &
|
||||
elastic_force, damping_force, gravity_strength)
|
||||
integer, intent(in) :: n, nb, bp(nb, 2), fixed(n, 3)
|
||||
integer, intent(in) :: gravity_field, gravity_interaction, elastic_force, damping_force
|
||||
double precision, intent(inout) :: x(n), y(n), z(n), vx(n), vy(n), vz(n)
|
||||
double precision, intent(in) :: m(n), G(3), B(3), bk(nb), br(nb), dt, gravity_strength
|
||||
double precision :: ax(n), ay(n), az(n)
|
||||
double precision :: dmp_vx(n), dmp_vy(n), dmp_vz(n)
|
||||
double precision :: gx, gy, gz
|
||||
integer :: i
|
||||
|
||||
call accel(n, x, y, z, vx, vy, vz, m, G, B, nb, bp, bk, br, &
|
||||
gravity_field, gravity_interaction, &
|
||||
elastic_force, damping_force, gravity_strength, ax, ay, az)
|
||||
|
||||
! 速度半步推
|
||||
do i = 1, n
|
||||
if (fixed(i,1) /= 0 .and. fixed(i,2) /= 0 .and. fixed(i,3) /= 0) cycle
|
||||
vx(i) = vx(i) + ax(i) * dt * 0.5d0
|
||||
vy(i) = vy(i) + ay(i) * dt * 0.5d0
|
||||
vz(i) = vz(i) + az(i) * dt * 0.5d0
|
||||
end do
|
||||
|
||||
! 全推位置（不含边界）
|
||||
do i = 1, n
|
||||
if (fixed(i,1) /= 0 .and. fixed(i,2) /= 0 .and. fixed(i,3) /= 0) cycle
|
||||
x(i) = x(i) + vx(i) * dt
|
||||
y(i) = y(i) + vy(i) * dt
|
||||
z(i) = z(i) + vz(i) * dt
|
||||
end do
|
||||
|
||||
! 隐式阻尼处理（用临时数组 dmp_v，不覆盖 vx/vy/vz）
|
||||
do i = 1, n
|
||||
if (fixed(i,1) /= 0 .and. fixed(i,2) /= 0 .and. fixed(i,3) /= 0) then
|
||||
dmp_vx(i) = 0; dmp_vy(i) = 0; dmp_vz(i) = 0; cycle
|
||||
end if
|
||||
gx = B(1) / m(i); gy = B(2) / m(i); gz = B(3) / m(i)
|
||||
dmp_vx(i) = (vx(i) + 0.5d0 * G(1) * dt) / (1.0d0 + 0.5d0 * gx * dt)
|
||||
dmp_vy(i) = (vy(i) + 0.5d0 * G(2) * dt) / (1.0d0 + 0.5d0 * gy * dt)
|
||||
dmp_vz(i) = (vz(i) + 0.5d0 * G(3) * dt) / (1.0d0 + 0.5d0 * gz * dt)
|
||||
end do
|
||||
|
||||
! 用新位置 + 阻尼速度重算加速度
|
||||
call accel(n, x, y, z, dmp_vx, dmp_vy, dmp_vz, m, G, B, nb, bp, bk, br, &
|
||||
gravity_field, gravity_interaction, &
|
||||
elastic_force, damping_force, gravity_strength, ax, ay, az)
|
||||
|
||||
! 速度后半步：v = v_half + 0.5*a_next*dt（vx 仍为 v_half）
|
||||
do i = 1, n
|
||||
if (fixed(i,1) /= 0 .and. fixed(i,2) /= 0 .and. fixed(i,3) /= 0) cycle
|
||||
vx(i) = vx(i) + ax(i) * dt * 0.5d0
|
||||
vy(i) = vy(i) + ay(i) * dt * 0.5d0
|
||||
vz(i) = vz(i) + az(i) * dt * 0.5d0
|
||||
end do
|
||||
end subroutine leapfrog_full
|
||||
|
||||
! ── 分发器 + 边界条件 + 自由度约束 ──
|
||||
subroutine apply_step(method, n, x, y, z, vx, vy, vz, m, G, B, &
|
||||
nb, bp, bk, br, fixed, box_a, dt, &
|
||||
gravity_field, gravity_interaction, &
|
||||
elastic_force, damping_force, gravity_strength, &
|
||||
pos_0)
|
||||
character(len=*), intent(in) :: method
|
||||
integer, intent(in) :: n, nb, bp(nb, 2), fixed(n, 3)
|
||||
integer, intent(in) :: gravity_field, gravity_interaction, elastic_force, damping_force
|
||||
double precision, intent(inout) :: x(n), y(n), z(n), vx(n), vy(n), vz(n)
|
||||
double precision, intent(in) :: m(n), G(3), B(3), bk(nb), br(nb), box_a, dt, gravity_strength
|
||||
double precision, intent(in) :: pos_0(n, 3)
|
||||
double precision :: mm(n)
|
||||
integer :: i
|
||||
|
||||
mm = m
|
||||
|
||||
if (trim(method) == 'explicit_euler') then
|
||||
call explicit_euler_step(n, x, y, z, vx, vy, vz, mm, G, B, &
|
||||
nb, bp, bk, br, fixed, dt, &
|
||||
gravity_field, gravity_interaction, &
|
||||
elastic_force, damping_force, gravity_strength)
|
||||
else if (trim(method) == 'implicit_euler') then
|
||||
call implicit_euler_step(n, x, y, z, vx, vy, vz, mm, G, B, &
|
||||
nb, bp, bk, br, fixed, dt, &
|
||||
gravity_field, gravity_interaction, &
|
||||
elastic_force, damping_force, gravity_strength)
|
||||
else if (trim(method) == 'midpoint') then
|
||||
call midpoint_step(n, x, y, z, vx, vy, vz, mm, G, B, &
|
||||
nb, bp, bk, br, fixed, dt, &
|
||||
gravity_field, gravity_interaction, &
|
||||
elastic_force, damping_force, gravity_strength)
|
||||
else if (trim(method) == 'leapfrog') then
|
||||
call leapfrog_full(n, x, y, z, vx, vy, vz, mm, G, B, &
|
||||
nb, bp, bk, br, fixed, dt, &
|
||||
gravity_field, gravity_interaction, &
|
||||
elastic_force, damping_force, gravity_strength)
|
||||
else
|
||||
write(*, '("[Fortran-engine] 未知算法: ", a)') trim(method)
|
||||
stop
|
||||
end if
|
||||
|
||||
! 边界条件
|
||||
do i = 1, n
|
||||
if (fixed(i,1) /= 0 .and. fixed(i,2) /= 0 .and. fixed(i,3) /= 0) cycle
|
||||
call limit_in_box(x(i), vx(i), -box_a, box_a)
|
||||
call limit_in_box(y(i), vy(i), -box_a, box_a)
|
||||
call limit_in_box(z(i), vz(i), -box_a, box_a)
|
||||
end do
|
||||
|
||||
! 逐自由度固定约束（与 Python apply_fixed_constraints 一致）
|
||||
do i = 1, n
|
||||
if (fixed(i,1) /= 0) then; x(i) = pos_0(i, 1); vx(i) = 0.0d0; end if
|
||||
if (fixed(i,2) /= 0) then; y(i) = pos_0(i, 2); vy(i) = 0.0d0; end if
|
||||
if (fixed(i,3) /= 0) then; z(i) = pos_0(i, 3); vz(i) = 0.0d0; end if
|
||||
end do
|
||||
end subroutine apply_step
|
||||
|
||||
! ========================================================================
|
||||
! JSON 输出
|
||||
! ========================================================================
|
||||
|
||||
subroutine write_json(outdir, tx, ty, tz, tvx, tvy, tvz, &
|
||||
nsteps, nat, aid, amass, &
|
||||
NT, DT, NSTEP, warmup, method, G, B, &
|
||||
nb, bp, bk, br)
|
||||
character(len=*), intent(in) :: outdir, method
|
||||
integer, intent(in) :: nsteps, nat, NT, NSTEP, warmup, nb, bp(nb, 2), aid(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) :: DT, G(3), B(3), bk(nb), br(nb), amass(nat)
|
||||
|
||||
character(len=512) :: path, buf
|
||||
integer :: u, s, i, ib, ios
|
||||
|
||||
path = trim(outdir) // '/trajectory.txt'
|
||||
open(newunit=u, file=trim(path), status='replace', action='write', iostat=ios)
|
||||
if (ios /= 0) then
|
||||
write(*, '("[Fortran-engine] 错误: 无法写入 ", a)') trim(path)
|
||||
stop
|
||||
end if
|
||||
|
||||
write(u, '(a)') '{'
|
||||
|
||||
! traj_x
|
||||
write(u, '(a)') ' "traj_x": ['
|
||||
do s = 1, nsteps
|
||||
call json_arr(u, tx(s, :), nat, s < nsteps, ' ')
|
||||
end do
|
||||
write(u, '(a)') ' ],'
|
||||
|
||||
! traj_y
|
||||
write(u, '(a)') ' "traj_y": ['
|
||||
do s = 1, nsteps
|
||||
call json_arr(u, ty(s, :), nat, s < nsteps, ' ')
|
||||
end do
|
||||
write(u, '(a)') ' ],'
|
||||
|
||||
! traj_z
|
||||
write(u, '(a)') ' "traj_z": ['
|
||||
do s = 1, nsteps
|
||||
call json_arr(u, tz(s, :), nat, s < nsteps, ' ')
|
||||
end do
|
||||
write(u, '(a)') ' ],'
|
||||
|
||||
! traj_vx
|
||||
write(u, '(a)') ' "traj_vx": ['
|
||||
do s = 1, nsteps
|
||||
call json_arr(u, tvx(s, :), nat, s < nsteps, ' ')
|
||||
end do
|
||||
write(u, '(a)') ' ],'
|
||||
|
||||
! traj_vy
|
||||
write(u, '(a)') ' "traj_vy": ['
|
||||
do s = 1, nsteps
|
||||
call json_arr(u, tvy(s, :), nat, s < nsteps, ' ')
|
||||
end do
|
||||
write(u, '(a)') ' ],'
|
||||
|
||||
! traj_vz
|
||||
write(u, '(a)') ' "traj_vz": ['
|
||||
do s = 1, nsteps
|
||||
call json_arr(u, tvz(s, :), nat, s < nsteps, ' ')
|
||||
end do
|
||||
write(u, '(a)') ' ],'
|
||||
|
||||
! 标量参数
|
||||
write(buf, '(a, i0, a)') ' "NT": ', NT, ','
|
||||
write(u, '(a)') trim(buf)
|
||||
write(buf, '(a, g0, a)') ' "DT": ', DT, ','
|
||||
write(u, '(a)') trim(buf)
|
||||
write(buf, '(a, i0, a)') ' "NSTEP": ', NSTEP, ','
|
||||
write(u, '(a)') trim(buf)
|
||||
write(buf, '(a, a, a)') ' "method": "', trim(method), '",'
|
||||
write(u, '(a)') trim(buf)
|
||||
write(buf, '(a, i0, a)') ' "warmup_steps": ', warmup, ','
|
||||
write(u, '(a)') trim(buf)
|
||||
|
||||
write(buf, '(a, g0, a, g0, a, g0, a)') &
|
||||
' "G": [', G(1), ', ', G(2), ', ', G(3), '],'
|
||||
write(u, '(a)') trim(buf)
|
||||
write(buf, '(a, g0, a, g0, a, g0, a)') &
|
||||
' "B": [', B(1), ', ', B(2), ', ', B(3), '],'
|
||||
write(u, '(a)') trim(buf)
|
||||
|
||||
! 原子信息
|
||||
write(u, '(a)', advance='no') ' "atom_ids": ['
|
||||
do i = 1, nat
|
||||
if (i > 1) write(u, '(a)', advance='no') ','
|
||||
write(u, '(i0)', advance='no') aid(i)
|
||||
end do
|
||||
write(u, '(a)') '],'
|
||||
|
||||
write(u, '(a)', advance='no') ' "atom_masses": ['
|
||||
do i = 1, nat
|
||||
if (i > 1) write(u, '(a)', advance='no') ','
|
||||
write(u, '(g0)', advance='no') amass(i)
|
||||
end do
|
||||
write(u, '(a)') '],'
|
||||
|
||||
! 成键
|
||||
if (nb > 0) then
|
||||
call write_int2_arr(u, 'bond_pairs', bp, nb, .true.)
|
||||
call write_dbl_arr(u, 'bond_stiffness', bk, nb, .true.)
|
||||
call write_dbl_arr(u, 'bond_rest_lengths', br, nb, .false.)
|
||||
else
|
||||
write(u, '(a)') ' "bond_pairs": [],'
|
||||
write(u, '(a)') ' "bond_stiffness": [],'
|
||||
write(u, '(a)') ' "bond_rest_lengths": []'
|
||||
end if
|
||||
|
||||
write(u, '(a)') '}'
|
||||
close(u)
|
||||
end subroutine write_json
|
||||
|
||||
! 写出单行 JSON 数组 [v1, v2, ...]
|
||||
subroutine json_arr(u, vals, n, has_next, indent)
|
||||
integer, intent(in) :: u, n
|
||||
double precision, intent(in) :: vals(n)
|
||||
logical, intent(in) :: has_next
|
||||
character(len=*), intent(in) :: indent
|
||||
integer :: i
|
||||
write(u, '(a)', advance='no') indent // '['
|
||||
do i = 1, n
|
||||
if (i > 1) write(u, '(a)', advance='no') ','
|
||||
write(u, '(g0)', advance='no') vals(i)
|
||||
end do
|
||||
if (has_next) then
|
||||
write(u, '(a)') '],'
|
||||
else
|
||||
write(u, '(a)') ']'
|
||||
end if
|
||||
end subroutine json_arr
|
||||
|
||||
subroutine write_int2_arr(u, name, arr, n, has_next)
|
||||
integer, intent(in) :: u, n, arr(n, 2)
|
||||
character(len=*), intent(in) :: name
|
||||
logical, intent(in) :: has_next
|
||||
character(len=65536) :: buf
|
||||
integer :: i, pos
|
||||
write(u, '(a)', advance='no') ' "' // trim(name) // '": ['
|
||||
do i = 1, n
|
||||
if (i > 1) write(u, '(a)', advance='no') ','
|
||||
write(buf, '(a, i0, a, i0, a)') '[', arr(i, 1), ',', arr(i, 2), ']'
|
||||
write(u, '(a)', advance='no') trim(buf)
|
||||
end do
|
||||
if (has_next) then
|
||||
write(u, '(a)') '],'
|
||||
else
|
||||
write(u, '(a)') ']'
|
||||
end if
|
||||
end subroutine write_int2_arr
|
||||
|
||||
subroutine write_dbl_arr(u, name, arr, n, has_next)
|
||||
integer, intent(in) :: u, n
|
||||
double precision, intent(in) :: arr(n)
|
||||
character(len=*), intent(in) :: name
|
||||
logical, intent(in) :: has_next
|
||||
integer :: i
|
||||
write(u, '(a)', advance='no') ' "' // trim(name) // '": ['
|
||||
do i = 1, n
|
||||
if (i > 1) write(u, '(a)', advance='no') ','
|
||||
write(u, '(g0)', advance='no') arr(i)
|
||||
end do
|
||||
if (has_next) then
|
||||
write(u, '(a)') '],'
|
||||
else
|
||||
write(u, '(a)') ']'
|
||||
end if
|
||||
end subroutine write_dbl_arr
|
||||
|
||||
write(*,*) "[Fortran-engine] 待实现"
|
||||
end program dynamics_f90
|
||||
|
||||
Reference in New Issue
Block a user