document code path in logs

improve docs
MFTabriz · May 29, 2023 · ff1d72f · ff1d72f
1 parent 2973f78
commit ff1d72f
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Showing 6 changed files with 24 additions and 18 deletions.
diff --git a/src/general_io.cpp b/src/general_io.cpp
@@ -56,10 +56,10 @@ void cli_params::parse(int argc, char *argv[]) {
            "To calculate the charge correction, slabcc needs the following "
            "files:\n"
            " 1. Input parameters file (default: slabcc.in)\n"
-           " 2. CHGCAR of the neutral system\n"
-           " 3. CHGCAR of the charged system\n"
-           " 4. LOCPOT of the neutral system\n"
-           " 5. LOCPOT of the charged system\n\n"
+           " 2. CHGCAR of the neutral system (default: CHGCAR.N)\n"
+           " 3. CHGCAR of the charged system (default: CHGCAR.C)\n"
+           " 4. LOCPOT of the neutral system (default: LOCPOT.N)\n"
+           " 5. LOCPOT of the charged system (default: LOCPOT.C)\n\n"
            "The input parameters file for a slab should minimally include:\n"
            " - charge_position : approximate position of the localized charge "
            "center\n"

diff --git a/src/slabcc.cpp b/src/slabcc.cpp
@@ -163,7 +163,7 @@ int main(int argc, char *argv[]) {
   }
   log->debug("Slab normal direction index (0-2): {}", model.normal_direction);
   log->trace("Shift to center done!");
-
+  log->trace("----calculating difference of input files---");
   supercell Defect_supercell = Neutral_supercell;
   Defect_supercell.potential =
       Charged_supercell.potential - Neutral_supercell.potential;
@@ -186,7 +186,7 @@ int main(int argc, char *argv[]) {
   model.POT_target_on_input_grid = Defect_supercell.potential;
 
   if (output_diffs_only) {
-    log->debug("Only the extra charge and the potential difference calculation "
+    log->trace("Only the extra charge and the potential difference calculation "
                "have been requested!");
     write_planar_avg(Defect_supercell.potential,
                      Defect_supercell.charge * model.voxel_vol, "D",
@@ -214,7 +214,7 @@ int main(int argc, char *argv[]) {
   model.defect_charge = accu(Defect_supercell.charge) * model.voxel_vol;
 
   if (std::abs(model.defect_charge) < 0.001) {
-    log->debug("Total extra charge: {}", model.defect_charge);
+    log->trace("Total extra charge: {}", model.defect_charge);
     log->warn("Total extra charge seems to be very small. Please make sure the "
               "path to the input CHGCAR files are "
               "set properly!");
@@ -227,6 +227,8 @@ int main(int argc, char *argv[]) {
                             optimize_charge_fraction || optimize_interfaces;
 
   if (optimize_any) {
+    log->info("--------------------optimizing model "
+              "parameters------------------------");
     const arma::rowvec2 shifted_interfaces0 = model.interfaces;
     const arma::mat charge_position0 = model.charge_position;
     const arma::urowvec3 cell_grid0 = model.cell_grid;
@@ -314,17 +316,17 @@ int main(int argc, char *argv[]) {
       model.update_V_target();
     }
   }
-
+  log->info("--------Calculating periodic energy---------");
   model.gaussian_charges_gen();
   model.dielectric_profiles_gen();
   auto local_param = model.data_packer();
   std::vector<double> gradients = {};
   model.potential_RMSE =
       potential_error(std::get<0>(local_param), gradients, &model);
 
-  log->debug("Cell dimensions (bohr): " +
+  log->trace("Cell dimensions (bohr): " +
              to_string(model.cell_vectors_lengths));
-  log->debug("Volume (bohr^3): {}", model.cell_volume);
+  log->trace("Volume (bohr^3): {}", model.cell_volume);
 
   if (is_active(verbosity::write_defect_file)) {
     supercell Model_supercell = Neutral_supercell;
@@ -403,11 +405,12 @@ int main(int argc, char *argv[]) {
   log->debug("Difference of the charge in the input files: {}",
              to_string(model.defect_charge));
   log->debug("Total charge of the model: {}", to_string(model.total_charge));
-
+  log->info("-------calculating isolated energy----------");
   double E_isolated = 0;
   double E_correction = 0;
   if (extrapolate) {
-
+    log->debug("extrapolation steps size: {}", extrapol_steps_size);
+    log->debug("extrapolation steps number: {}", extrapol_steps_num);
     const arma::rowvec3 extrapolation_grid_size =
         extrapol_grid_x * arma::conv_to<arma::rowvec>::from(model.cell_grid);
     const arma::urowvec3 extrapolation_grid = {

diff --git a/src/slabcc_input.cpp b/src/slabcc_input.cpp
@@ -6,6 +6,7 @@
 
 void input_data::verify() const {
   auto log = spdlog::get("loggers");
+  log->debug("----------verifying input parameters--------");
   charge_sigma = arma::abs(charge_sigma);
   max_eval = std::abs(max_eval);
   max_time = std::abs(max_time);

diff --git a/src/slabcc_model.cpp b/src/slabcc_model.cpp
@@ -5,6 +5,8 @@
 #include "slabcc_model.hpp"
 
 void slabcc_model::set_input_variables(const input_data &inputfile_variables) {
+  auto log = spdlog::get("loggers");
+  log->debug("-------------initializing model-------------");
   normal_direction = inputfile_variables.normal_direction;
   interfaces = inputfile_variables.interfaces;
   diel_in = inputfile_variables.diel_in;
@@ -472,10 +474,11 @@ void slabcc_model::update_V_target() {
     const arma::rowvec new_grid_z = arma::linspace<arma::rowvec>(
         1.0, POT_target_on_input_grid.n_slices, cell_grid(2));
 
+    log->debug("Calculating target potential on grid size: " +
+               to_string(SizeVec(POT_target)));
     POT_target =
         interp3(POT_target_on_input_grid, new_grid_x, new_grid_y, new_grid_z);
     POT_target -= arma::accu(POT_target) / POT_target.n_elem;
-    log->debug("New potential grid size: " + to_string(SizeVec(POT_target)));
   }
 }
 
@@ -681,7 +684,6 @@ double slabcc_model::potential_error(const std::vector<double> &x,
     initial_potential_RMSE = potential_RMSE;
   }
 
-  log->debug("-----------------------------------------");
   if (this->type != model_type::bulk) {
     const arma::rowvec2 unshifted_interfaces =
         fmod_p(interfaces - rounded_relative_shift(normal_direction), 1);

diff --git a/utils/build_pages.sh b/utils/build_pages.sh
@@ -12,8 +12,8 @@ if [ -z "$STAGE_PATH" ]; then
 fi
 
 mkdir -p "$STAGE_PATH"
-
-SOURCE_LINK="${CI_COMMIT_LINK/%commit\/${CI_COMMIT_SHA}/src\/commit\/${CI_COMMIT_SHA}\/docs/manual.rst}"
+INDEX_HTML=docs/manual.rst
+SOURCE_LINK="https://codeberg.org/meisam/slabcc/src/commit/${CI_COMMIT_SHA}/${INDEX_HTML}"
 
 echo "SOURCE LINK: $SOURCE_LINK"
-tail -n +2 < docs/manual.rst | rst2html.py --title="SLABCC" -g --source-url="$SOURCE_LINK" > "$STAGE_PATH"/index.html
+tail -n +2 < "$INDEX_HTML" | rst2html.py --title="SLABCC" -g --source-url="$SOURCE_LINK" > "$STAGE_PATH"/index.html
diff --git a/utils/git_commit.sh b/utils/git_commit.sh
@@ -43,4 +43,4 @@ if [ "$GITHASH" = "?" ]; then
 fi
 
 
-echo "$GITHASH (status: $GIT_STATE)"
+echo "$GITHASH (repo status: $GIT_STATE)"
Original file line number	Diff line number	Diff line change
Expand Up		@@ -43,4 +43,4 @@ if [ "$GITHASH" = "?" ]; then
		fi


		echo "$GITHASH (status: $GIT_STATE)"
		echo "$GITHASH (repo status: $GIT_STATE)"