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Merge remote-tracking branch 'origin/veloxchem' into sankey_diagram
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@guser40
guser40 committed Aug 16, 2024
2 parents a7532f7 + a1df42e commit 09fd716
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Showing 2 changed files with 41 additions and 25 deletions.
2 changes: 1 addition & 1 deletion ext/mdlib
Submodule mdlib updated 36 files
+9 −0 .github/workflows/ubuntu22.yml
+1 −0 CMakeLists.txt
+1 −1 benchmark/bench_util.c
+4 −4 src/core/md_allocator.c
+2 −2 src/core/md_arena_allocator.c
+1 −1 src/core/md_hash.c
+1 −1 src/core/md_hash.h
+3 −3 src/core/md_os.c
+2 −2 src/core/md_os.h
+18 −18 src/core/md_unit.c
+18 −18 src/core/md_unit.h
+6 −6 src/core/md_vec_math.h
+0 −3 src/md_frame_cache.c
+6 −6 src/md_gfx.c
+5 −5 src/md_gfx.h
+3 −3 src/md_gl.c
+2 −2 src/md_gl.h
+1 −1 src/md_gro.c
+1 −1 src/md_gro.h
+5 −5 src/md_lammps.c
+4 −4 src/md_lammps.h
+1 −1 src/md_mmcif.c
+1 −1 src/md_mmcif.h
+2 −2 src/md_pdb.c
+2 −2 src/md_pdb.h
+227 −96 src/md_script.c
+1 −1 src/md_script_functions.inl
+3 −3 src/md_util.c
+3 −3 src/md_util.h
+1 −1 src/md_vlx.c
+1 −1 src/md_vlx.h
+2 −2 src/md_xyz.c
+2 −2 src/md_xyz.h
+1 −1 test_data
+14 −4 unittest/test_lammps.c
+30 −0 unittest/test_script.c
64 changes: 40 additions & 24 deletions src/components/veloxchem/veloxchem.cpp
View file
Original file line number Diff line number Diff line change
Expand Up @@ -168,6 +168,9 @@ struct VeloxChem : viamd::EventHandler {
double* osc_points;
double* cgs_points;
const char* x_unit;

bool first_plot_rot_ecd = true;
bool first_plot_vib = true;
} rsp;

// Arena for persistent allocations for the veloxchem module (tied to the lifetime of the VLX object)
Expand Down Expand Up @@ -600,6 +603,8 @@ struct VeloxChem : viamd::EventHandler {
return async_task;
}



static inline double axis_conversion_multiplier(const double* y1_array, const double* y2_array, size_t y1_array_size, size_t y2_array_size) {
double y1_max = 0;
double y2_max = 0;
Expand Down Expand Up @@ -1083,7 +1088,7 @@ struct VeloxChem : viamd::EventHandler {
int num_properties = ARRAY_SIZE(properties);

if (ImGui::Begin("Spectra Export", &rsp.show_export_window)) {
static int table_format = 1;
static int table_format = 0;
static int property_idx = 0;
const char* x_unit = "DEBUG";

Expand All @@ -1094,7 +1099,7 @@ struct VeloxChem : viamd::EventHandler {
str_t file_extension = {};
if (ImGui::BeginCombo("File Format", table_formats[table_format].lbl.ptr)) {
//TODO: Start at 0 when XVG is implemented
for (int i = 1; i < (int)ARRAY_SIZE(table_formats); ++i) {
for (int i = 0; i < (int)ARRAY_SIZE(table_formats); ++i) {
if (ImGui::Selectable(table_formats[i].lbl.ptr, table_format == i)) {
table_format = i;
}
Expand Down Expand Up @@ -1153,6 +1158,18 @@ struct VeloxChem : viamd::EventHandler {
if (table_format == 0) {
//md_xvg_write
//TODO: Implement md_xvg_write_to_file
str_t header = md_xvg_format_header(properties[property_idx].lable, str_from_cstr(x_unit), properties[property_idx].y_unit, 0, legends, arena);
str_t xvg = md_xvg_format(header, 2, 1024, column_data, arena);
md_file_o* file = md_file_open(path, MD_FILE_WRITE | MD_FILE_BINARY);
if (file) {
const size_t written_bytes = md_file_write(file, xvg.ptr, xvg.len);
if (written_bytes != xvg.len) {
MD_LOG_ERROR("CSV: Unexpected error, some bytes were not written");
}
}
else {
MD_LOG_ERROR("CSV: File could not be opened for writing: '%.*s'", (int)path.len, path.ptr);
}

}
else if (table_format == 1) {
Expand Down Expand Up @@ -1194,8 +1211,8 @@ struct VeloxChem : viamd::EventHandler {
}
ImGui::EndMenuBar();
}
static bool first_plot1 = true;
if (first_plot1) { ImGui::SetNextItemOpen(true); }

if (rsp.first_plot_rot_ecd) { ImGui::SetNextItemOpen(true); }
if (ImGui::TreeNode("Absorption & ECD")) {
bool refit1 = false;
bool recalculate1 = false;
Expand All @@ -1214,7 +1231,7 @@ struct VeloxChem : viamd::EventHandler {
const double* y_osc_peaks = vlx.rsp.absorption_osc_str;
const double* y_cgs_peaks = vlx.rsp.electronic_circular_dichroism_cgs;

if (first_plot1) {
if (rsp.first_plot_rot_ecd) {
rsp.x_ev_samples = md_array_create(double, num_samples, arena);
rsp.x_unit_samples = md_array_create(double, num_samples, arena);
rsp.x_unit_peaks = md_array_create(double, num_peaks, arena);
Expand Down Expand Up @@ -1254,14 +1271,14 @@ struct VeloxChem : viamd::EventHandler {
break;
}

if (recalculate1 || first_plot1) {
if (recalculate1 || rsp.first_plot_rot_ecd) {
osc_to_eps(rsp.eps, rsp.x_ev_samples, num_samples, y_osc_peaks, vlx.rsp.absorption_ev, num_peaks, distr_func, gamma1 * 2);
rot_to_eps_delta(rsp.ecd, rsp.x_ev_samples, num_samples, y_cgs_peaks, vlx.rsp.absorption_ev, num_peaks, distr_func, gamma1 * 2);
}

static ImPlotRect osc_lim_constraint = {0, 0, 0, 0};
static ImPlotRect cgs_lim_constraint = {0, 0, 0, 0};
if (refit1 || first_plot1) {
if (refit1 || rsp.first_plot_rot_ecd) {
// Do conversions
convert_values(rsp.x_unit_peaks, vlx.rsp.absorption_ev, num_peaks, x_unit);
convert_values(rsp.x_unit_samples, rsp.x_ev_samples, num_samples, x_unit);
Expand All @@ -1278,7 +1295,7 @@ struct VeloxChem : viamd::EventHandler {
}
}

if (first_plot1) {
if (rsp.first_plot_rot_ecd) {
rsp.osc_points = md_array_create(double, num_peaks, arena);
rsp.cgs_points = md_array_create(double, num_peaks, arena);
max_points(rsp.osc_points, y_osc_peaks, num_peaks);
Expand Down Expand Up @@ -1311,20 +1328,20 @@ struct VeloxChem : viamd::EventHandler {
if (ImPlot::BeginSubplots("##AxisLinking", 2, 1, ImVec2(-1, -1), ImPlotSubplotFlags_LinkCols)) {
// Absorption
static double osc_to_eps_mult = 1;
if (recalculate1 || first_plot1) {
if (recalculate1 || rsp.first_plot_rot_ecd) {
osc_to_eps_mult = is_all_zero(y_osc_peaks, num_peaks) ? 1 : axis_conversion_multiplier(y_osc_peaks, rsp.eps, num_peaks, num_samples);
}

static ImPlotRect cur_osc_lims = {0, 1, 0, 1};
if (refit1 || first_plot1) {
if (refit1 || rsp.first_plot_rot_ecd) {
ImPlot::SetNextAxisToFit(ImAxis_X1);
}
if (ImPlot::BeginPlot("Absorption")) {
ImPlot::SetupLegend(ImPlotLocation_NorthEast, ImPlotLegendFlags_None);
ImPlot::SetupAxis(ImAxis_X1, x_unit_str[x_unit]);
ImPlot::SetupAxis(ImAxis_Y1, "f", ImPlotAxisFlags_AuxDefault);
ImPlot::SetupAxis(ImAxis_Y2, (const char*)u8"ε (L mol⁻¹ cm⁻¹)");
if (refit1 || first_plot1) {
if (refit1 || rsp.first_plot_rot_ecd) {
ImPlot::SetupAxisLimits(ImAxis_X1, osc_lim_constraint.X.Min, osc_lim_constraint.X.Max);
ImPlot::SetupAxisLimits(ImAxis_Y1, osc_lim_constraint.Y.Min, osc_lim_constraint.Y.Max);
cur_osc_lims = osc_lim_constraint;
Expand Down Expand Up @@ -1376,11 +1393,11 @@ struct VeloxChem : viamd::EventHandler {

// Rotatory ECD
static double cgs_to_ecd_mult = 1;
if (recalculate1 || first_plot1) {
if (recalculate1 || rsp.first_plot_rot_ecd) {
cgs_to_ecd_mult = is_all_zero(y_cgs_peaks, num_peaks) ? 1 : axis_conversion_multiplier(y_cgs_peaks, rsp.ecd, num_peaks, num_samples);
}
static ImPlotRect cur_cgs_lims = {0, 1, 0, 1};
if (refit1 || first_plot1) {
if (refit1 || rsp.first_plot_rot_ecd) {
ImPlot::SetNextAxisToFit(ImAxis_X1);
}

Expand All @@ -1389,7 +1406,7 @@ struct VeloxChem : viamd::EventHandler {
ImPlot::SetupAxis(ImAxis_X1, x_unit_str[x_unit]);
ImPlot::SetupAxis(ImAxis_Y1, (const char*)u8"R (10⁻⁴⁰ cgs)", ImPlotAxisFlags_AuxDefault);
ImPlot::SetupAxis(ImAxis_Y2, (const char*)u8"Δε(ω) (L mol⁻¹ cm⁻¹)");
if (refit1 || first_plot1) {
if (refit1 || rsp.first_plot_rot_ecd) {
ImPlot::SetupAxisLimits(ImAxis_X1, cgs_lim_constraint.X.Min, cgs_lim_constraint.X.Max);
ImPlot::SetupAxisLimits(ImAxis_Y1, cgs_lim_constraint.Y.Min, cgs_lim_constraint.Y.Max);
cur_cgs_lims = cgs_lim_constraint;
Expand Down Expand Up @@ -1440,12 +1457,11 @@ struct VeloxChem : viamd::EventHandler {
}
ImPlot::EndSubplots();
}
first_plot1 = false;
rsp.first_plot_rot_ecd = false;
ImGui::TreePop();
}

static bool first_plot2 = true;
if (first_plot2) { ImGui::SetNextItemOpen(true); }

if (rsp.first_plot_vib) { ImGui::SetNextItemOpen(true); }
if (ImGui::TreeNode("Vibrational Analysis")) {
// draw the vibrational analysis
double har_freqs[3] = {1562.20, 3663.36, 3677.39};
Expand Down Expand Up @@ -1505,7 +1521,7 @@ struct VeloxChem : viamd::EventHandler {
break;
}

if (first_plot2) {
if (rsp.first_plot_vib) {
rsp.vib_x = md_array_create(double, num_samples, arena);
rsp.vib_y = md_array_create(double, num_samples, arena);

Expand All @@ -1520,11 +1536,11 @@ struct VeloxChem : viamd::EventHandler {
}
}

if (first_plot2 || recalculate2 || refit2) {
if (rsp.first_plot_vib || recalculate2 || refit2) {
general_broadening(rsp.vib_y, rsp.vib_x, num_samples, irs, har_freqs, num_vibs, distr_func, gamma2 * 2);
}

if (first_plot2) {
if (rsp.first_plot_vib) {
rsp.vib_points = md_array_create(double, num_vibs, arena);
max_points(rsp.vib_points, irs, num_vibs);
}
Expand All @@ -1537,7 +1553,7 @@ struct VeloxChem : viamd::EventHandler {
ImPlotAxisFlags y_flag = invert_y ? ImPlotAxisFlags_Invert : 0;

static ImPlotRect lim_constraint = { 0, 0, 0, 0 };
if (refit2 || first_plot2) {
if (refit2 || rsp.first_plot_vib) {
lim_constraint = get_plot_limits(rsp.vib_x, irs, num_vibs, num_samples);
}

Expand All @@ -1546,7 +1562,7 @@ struct VeloxChem : viamd::EventHandler {
ImPlot::SetupLegend(ImPlotLocation_NorthEast, ImPlotLegendFlags_None);
ImPlot::SetupAxis(ImAxis_X1, (const char*)u8"Harmonic Frequency (cm⁻¹)", x_flag);
ImPlot::SetupAxis(ImAxis_Y1, "IR Intensity (km/mol)", y_flag);
if (refit2 || first_plot2) {
if (refit2 || rsp.first_plot_vib) {
ImPlot::SetupAxisLimits(ImAxis_X1, lim_constraint.X.Min, lim_constraint.X.Max);
ImPlot::SetupAxisLimits(ImAxis_Y1, lim_constraint.Y.Min, lim_constraint.Y.Max);
}
Expand Down Expand Up @@ -1605,7 +1621,7 @@ struct VeloxChem : viamd::EventHandler {
state.mold.dirty_buffers |= MolBit_DirtyPosition | MolBit_ClearVelocity;
coord_modified = false;
}
first_plot2 = false;
rsp.first_plot_vib = false;
ImPlot::EndPlot();
}

Expand Down

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