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Refactor trajectory frame caching, align Dataset-owned state access, fix dataset lifecycle, enforce state vs dataset API boundaries, and introduce System architecture #139

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Refactor trajectory frame caching, align Dataset-owned state access, fix dataset lifecycle, enforce state vs dataset API boundaries, and introduce System architecture #139

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e034d42
Initial plan
Copilot Mar 12, 2026
e3c3d07
refactor trajectory cache to state-owned lru8 cache
Copilot Mar 12, 2026
cfcd7f8
cleanup remove stale md_frame_cache references
Copilot Mar 12, 2026
b226da1
Removed unwanted things in loader and refactored portions of Applicat…
scanberg Mar 13, 2026
391bcd9
fix dataset state accesses after refactor
Copilot Mar 13, 2026
97cdb3c
wip
scanberg Mar 13, 2026
a69c3ed
mdlib update
scanberg Mar 13, 2026
9180ef1
fix: dataset loading/unloading, compile errors, bitfield safety
Copilot Mar 13, 2026
6a88a97
refactor: make state vs dataset distinction explicit in procedure sig…
Copilot Mar 13, 2026
bf8fc34
architecture: introduce System struct as pure data container separate…
Copilot Mar 14, 2026
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2 changes: 0 additions & 2 deletions CMakeLists.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -47,7 +47,6 @@ option(VIAMD_IMGUI_ENABLE_DOCKSPACE "Enable ImGui Dockspace in main window" OFF)
option(VIAMD_CREATE_MACOSX_BUNDLE "Build a macosx bundle instead of just an executable" OFF)
option(VIAMD_LINK_STDLIB_STATIC "Link against stdlib statically" ON)
option(VIAMD_ENABLE_VELOXCHEM "Enable Veloxchem Module" OFF)
set(VIAMD_FRAME_CACHE_SIZE_MB "2048" CACHE STRING "Reserved frame cache size in Megabytes")
set(VIAMD_NUM_WORKER_THREADS "8" CACHE STRING "Number of worker threads (Decrease if you run out of memory during evaluation)")

# MDLIB OPTIONS
Expand Down Expand Up @@ -203,7 +202,6 @@ endif()
target_compile_definitions(viamd PRIVATE
${VIAMD_DEFINES}
VIAMD_NUM_WORKER_THREADS=${VIAMD_NUM_WORKER_THREADS}
VIAMD_FRAME_CACHE_SIZE=${VIAMD_FRAME_CACHE_SIZE_MB}
VIAMD_IMGUI_ENABLE_VIEWPORTS=$<BOOL:${VIAMD_IMGUI_ENABLE_VIEWPORTS}>
VIAMD_IMGUI_ENABLE_DOCKSPACE=$<BOOL:${VIAMD_IMGUI_ENABLE_DOCKSPACE}>
${MD_DEFINES}
Expand Down
2 changes: 1 addition & 1 deletion ext/mdlib
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Submodule mdlib updated 4 files
+3 −1 src/core/md_bitfield.c
+2 −2 src/md_system.h
+3 −3 src/md_trajectory.h
+1 −1 src/md_xtc.c
160 changes: 80 additions & 80 deletions src/components/dataset/dataset.cpp
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30 changes: 15 additions & 15 deletions src/components/ramachandran/ramachandran.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -634,8 +634,8 @@ struct Ramachandran : viamd::EventHandler {
md_array_shrink(rama_type_indices[2], 0);
md_array_shrink(rama_type_indices[3], 0);

for (uint32_t i = 0; i < (uint32_t)md_array_size(state.mold.sys.protein_backbone.segment.rama_type); ++i) {
switch (state.mold.sys.protein_backbone.segment.rama_type[i]) {
for (uint32_t i = 0; i < (uint32_t)md_array_size(current_dataset(state).system.sys.protein_backbone.segment.rama_type); ++i) {
switch (current_dataset(state).system.sys.protein_backbone.segment.rama_type[i]) {
case MD_RAMACHANDRAN_TYPE_GENERAL: md_array_push(rama_type_indices[0], i, arena); break;
case MD_RAMACHANDRAN_TYPE_GLYCINE: md_array_push(rama_type_indices[1], i, arena); break;
case MD_RAMACHANDRAN_TYPE_PROLINE: md_array_push(rama_type_indices[2], i, arena); break;
Expand All @@ -650,18 +650,18 @@ struct Ramachandran : viamd::EventHandler {
}

void update(ApplicationState& state) {
if (show_window && state.mold.sys.protein_backbone.segment.count > 0) {
const size_t num_frames = md_trajectory_num_frames(state.mold.traj);
if (show_window && current_dataset(state).system.sys.protein_backbone.segment.count > 0) {
const size_t num_frames = md_trajectory_num_frames(current_dataset(state).system.traj);
if (num_frames > 0) {
if (full_fingerprint != state.trajectory_data.backbone_angles.fingerprint) {
if (full_fingerprint != current_dataset(state).system.trajectory_data.backbone_angles.fingerprint) {
if (!task_system::task_is_running(compute_density_full)) {
full_fingerprint = state.trajectory_data.backbone_angles.fingerprint;
full_fingerprint = current_dataset(state).system.trajectory_data.backbone_angles.fingerprint;

const uint32_t frame_beg = 0;
const uint32_t frame_end = (uint32_t)num_frames;
const uint32_t frame_stride = (uint32_t)state.trajectory_data.backbone_angles.stride;
const uint32_t frame_stride = (uint32_t)current_dataset(state).system.trajectory_data.backbone_angles.stride;

compute_density_full = rama_rep_compute_density(&rama_data.full, state.trajectory_data.backbone_angles.data, frame_beg, frame_end, frame_stride);
compute_density_full = rama_rep_compute_density(&rama_data.full, current_dataset(state).system.trajectory_data.backbone_angles.data, frame_beg, frame_end, frame_stride);
} else {
task_system::task_interrupt(compute_density_full);
}
Expand All @@ -673,9 +673,9 @@ struct Ramachandran : viamd::EventHandler {

const uint32_t frame_beg = MIN((uint32_t)state.timeline.filter.beg_frame, (uint32_t)num_frames - 1);
const uint32_t frame_end = MIN((uint32_t)state.timeline.filter.end_frame + 1, (uint32_t)num_frames);
const uint32_t frame_stride = (uint32_t)state.trajectory_data.backbone_angles.stride;
const uint32_t frame_stride = (uint32_t)current_dataset(state).system.trajectory_data.backbone_angles.stride;

compute_density_filt = rama_rep_compute_density(&rama_data.filt, state.trajectory_data.backbone_angles.data, frame_beg, frame_end, frame_stride);
compute_density_filt = rama_rep_compute_density(&rama_data.filt, current_dataset(state).system.trajectory_data.backbone_angles.data, frame_beg, frame_end, frame_stride);
}
else {
task_system::task_interrupt(compute_density_filt);
Expand Down Expand Up @@ -762,9 +762,9 @@ struct Ramachandran : viamd::EventHandler {
ImGui::EndMenuBar();
}

const auto& sys = state.mold.sys;
md_bitfield_t* selection_mask = &state.selection.selection_mask;
md_bitfield_t* highlight_mask = &state.selection.highlight_mask;
const auto& sys = current_dataset(state).system.sys;
md_bitfield_t* selection_mask = &current_dataset(state).selection.selection_mask;
md_bitfield_t* highlight_mask = &current_dataset(state).selection.highlight_mask;

const int plot_offset = MAX(0, layout_mode - 1);
const int plot_cols = (layout_mode == 0) ? 2 : 1;
Expand Down Expand Up @@ -919,7 +919,7 @@ struct Ramachandran : viamd::EventHandler {
}

if (is_selecting[plot_idx]) {
grow_mask_by_selection_granularity(highlight_mask, state.selection.granularity, sys);
grow_mask_by_selection_granularity(highlight_mask, current_dataset(state).selection.granularity, sys);
}

if (mouse_hover_idx != -1) {
Expand All @@ -928,7 +928,7 @@ struct Ramachandran : viamd::EventHandler {
md_urange_t range = md_component_atom_range(&sys.component, comp_idx);
if (range.beg != range.end) {
modify_field(highlight_mask, range, SelectionOperator::Or);
grow_mask_by_selection_granularity(highlight_mask, state.selection.granularity, sys);
grow_mask_by_selection_granularity(highlight_mask, current_dataset(state).selection.granularity, sys);
}
str_t lbl = md_component_name(&sys.component, comp_idx);
md_sequence_id_t seq_id = md_component_seq_id(&sys.component, comp_idx);
Expand Down
24 changes: 12 additions & 12 deletions src/components/shapespace/shapespace.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -176,7 +176,7 @@ struct Shapespace : viamd::EventHandler {
ImGui::PopItemWidth();
if (ImGui::IsItemHovered()) {
if (input_valid) {
md_bitfield_copy(&app_state->selection.highlight_mask, &joined_bitfield);
md_bitfield_copy(&current_dataset(*app_state).selection.highlight_mask, &joined_bitfield);
} else if (error[0] != '\0') {
ImGui::SetTooltip("%s", error);
}
Expand Down Expand Up @@ -291,7 +291,7 @@ struct Shapespace : viamd::EventHandler {
ImPlot::PopStyleVar(2);

if (ImPlot::IsPlotHovered()) {
md_bitfield_clear(&app_state->selection.highlight_mask);
md_bitfield_clear(&current_dataset(*app_state).selection.highlight_mask);
}

// Redraw hovered index
Expand All @@ -308,7 +308,7 @@ struct Shapespace : viamd::EventHandler {
vec2_t* coordinates = coords + offset;
ImPlot::PlotScatterG("##hovered structure", getter, coordinates, count);
if (hovered_structure_idx < (int)md_array_size(bitfields)) {
md_bitfield_copy(&app_state->selection.highlight_mask, &bitfields[hovered_structure_idx]);
md_bitfield_copy(&current_dataset(*app_state).selection.highlight_mask, &bitfields[hovered_structure_idx]);
}
}
if (hovered_point_idx != -1) {
Expand All @@ -326,11 +326,11 @@ struct Shapespace : viamd::EventHandler {
ImGui::SetTooltip("%s", buf);

if (structure_idx < (int)md_array_size(bitfields)) {
md_bitfield_copy(&app_state->selection.highlight_mask, &bitfields[structure_idx]);
md_bitfield_copy(&current_dataset(*app_state).selection.highlight_mask, &bitfields[structure_idx]);
}

if (ImGui::IsWindowFocused() && ImPlot::IsPlotHovered() && ImGui::GetIO().MouseClicked[0]) {
app_state->animation.frame = frame_idx;
current_dataset(*app_state).animation.frame = frame_idx;
}
}
ImPlot::PopStyleColor();
Expand All @@ -356,11 +356,11 @@ struct Shapespace : viamd::EventHandler {
joined_bitfield = {0};
md_bitfield_init(&joined_bitfield, arena);

md_trajectory_i* traj = load::traj::get_raw_trajectory(app_state->mold.traj);
md_trajectory_i* traj = current_dataset(*app_state).system.traj;

input_valid = false;
MEMSET(error, 0, sizeof(error));
if (md_filter_evaluate(&bitfields, str_from_cstr(input), &app_state->mold.sys, app_state->mold.sys.atom.x, app_state->mold.sys.atom.y, app_state->mold.sys.atom.z, app_state->script.ir, NULL, error, sizeof(error), arena)) {
if (md_filter_evaluate(&bitfields, str_from_cstr(input), &current_dataset(*app_state).system.sys, current_dataset(*app_state).system.sys.atom.x, current_dataset(*app_state).system.sys.atom.y, current_dataset(*app_state).system.sys.atom.z, app_state->script.ir, NULL, error, sizeof(error), arena)) {
eval_hash = hash;

input_valid = true;
Expand All @@ -385,7 +385,7 @@ struct Shapespace : viamd::EventHandler {
evaluate_task = task_system::create_pool_task(STR_LIT("Eval Shape Space"), (uint32_t)num_frames, [shapespace = this, traj](uint32_t range_beg, uint32_t range_end, uint32_t thread_num) {
(void)thread_num;
ApplicationState* app_state = shapespace->app_state;
const size_t stride = ALIGN_TO(app_state->mold.sys.atom.count, 8);
const size_t stride = ALIGN_TO(current_dataset(*app_state).system.sys.atom.count, 8);
const size_t bytes = stride * 3 * sizeof(float);
md_allocator_i* alloc = md_arena_allocator_create(md_get_heap_allocator(), MEGABYTES(1));
defer { md_arena_allocator_destroy(alloc); };
Expand All @@ -397,7 +397,7 @@ struct Shapespace : viamd::EventHandler {
float* w = 0;
if (shapespace->use_mass) {
w = (float*)md_arena_allocator_push(alloc, stride * sizeof(float));
md_atom_extract_masses(w, 0, app_state->mold.sys.atom.count, &app_state->mold.sys.atom);
md_atom_extract_masses(w, 0, current_dataset(*app_state).system.sys.atom.count, &current_dataset(*app_state).system.sys.atom);
}

const vec2_t p[3] = {{0.0f, 0.0f}, {1.0f, 0.0f}, {0.5f, 0.86602540378f}};
Expand All @@ -419,8 +419,8 @@ struct Shapespace : viamd::EventHandler {
xyzw[dst_idx++] = vec4_set(x[src_idx], y[src_idx], z[src_idx], w ? w[src_idx] : 1.0f);
}

vec3_t com = md_util_com_compute_vec4(xyzw, 0, count, &app_state->mold.sys.unitcell);
md_util_deperiodize_vec4(xyzw, count, com, &app_state->mold.sys.unitcell);
vec3_t com = md_util_com_compute_vec4(xyzw, 0, count, &current_dataset(*app_state).system.sys.unitcell);
md_util_deperiodize_vec4(xyzw, count, com, &current_dataset(*app_state).system.sys.unitcell);

const mat3_t M = mat3_covariance_matrix_vec4(xyzw, 0, count, com);
const vec3_t weights = md_util_shape_weights(&M);
Expand Down Expand Up @@ -449,7 +449,7 @@ struct Shapespace : viamd::EventHandler {
defer { md_arena_allocator_destroy(temp_arena); };

// @TODO: add unit to time (if available)
md_unit_t time_unit = md_trajectory_time_unit(app_state->mold.traj);
md_unit_t time_unit = md_trajectory_time_unit(current_dataset(*app_state).system.traj);

str_t x_label = STR_LIT("Frame");
if (!md_unit_empty(time_unit)) {
Expand Down
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