feat(con): use readcon

.github/workflows/ci_benchmark.yml

@@ -35,7 +35,7 @@ jobs:
           cp -r /tmp/_bench_preserve/benchmarks/ benchmarks/
           cp /tmp/_bench_preserve/asv.conf.json asv.conf.json
 
-      - uses: prefix-dev/setup-pixi@v0.8.10
+      - uses: prefix-dev/setup-pixi@v0.9.4
         with:
           cache: true
           cache-write: false
@@ -50,6 +50,10 @@ jobs:
             core.exportVariable('ACTIONS_CACHE_URL', process.env.ACTIONS_CACHE_URL || '');
             core.exportVariable('ACTIONS_RUNTIME_TOKEN', process.env.ACTIONS_RUNTIME_TOKEN || '');
 
+      - name: Install cbindgen
+        shell: bash
+        run: command -v cbindgen || cargo install cbindgen
+
       - name: Build
         run: |
           pixi run bash -c "meson setup bbdir \

.github/workflows/ci_build_akmc.yml

@@ -17,7 +17,7 @@ jobs:
         os: [ubuntu-22.04, macos-14, windows-latest]
     steps:
       - uses: actions/checkout@v4
-      - uses: prefix-dev/setup-pixi@v0.8.10
+      - uses: prefix-dev/setup-pixi@v0.9.4
         with:
           cache: true
           cache-write: ${{ github.event_name == 'push' && github.ref_name == 'main' }}
@@ -27,6 +27,10 @@ jobs:
           script: |
             core.exportVariable('ACTIONS_CACHE_URL', process.env.ACTIONS_CACHE_URL || '');
             core.exportVariable('ACTIONS_RUNTIME_TOKEN', process.env.ACTIONS_RUNTIME_TOKEN || '');
+      - name: Install cbindgen
+        shell: bash
+        run: command -v cbindgen || cargo install cbindgen
+
       - name: Use Homebrew gfortran (macOS)
         if: runner.os == 'macOS'
         run: |

.github/workflows/ci_build_gprd.yml

@@ -24,7 +24,7 @@ jobs:
           git clone git@github.com:TheochemUI/gpr_optim.git subprojects/gpr_optim
           cd subprojects/gpr_optim
           git checkout 26242c8e94569ef81103ece4662008c3250ada55
-      - uses: prefix-dev/setup-pixi@v0.8.10
+      - uses: prefix-dev/setup-pixi@v0.9.4
         with:
           cache: true
           cache-write: ${{ github.event_name == 'push' && github.ref_name == 'main' }}
@@ -37,6 +37,10 @@ jobs:
           script: |
             core.exportVariable('ACTIONS_CACHE_URL', process.env.ACTIONS_CACHE_URL || '');
             core.exportVariable('ACTIONS_RUNTIME_TOKEN', process.env.ACTIONS_RUNTIME_TOKEN || '');
+      - name: Install cbindgen
+        shell: bash
+        run: command -v cbindgen || cargo install cbindgen
+
       - name: Install eon
         shell: pixi run bash -e {0}
         run: |

.github/workflows/ci_docs.yml

@@ -25,23 +25,15 @@ jobs:
         with:
           fetch-depth: 0
 
-      - uses: prefix-dev/setup-pixi@v0.8.10
+      - uses: prefix-dev/setup-pixi@v0.9.4
         with:
           cache: true
           cache-write: ${{ github.event_name == 'push' && github.ref_name == 'main' }}
-          activate-environment: true
           environments: >-
             docs
 
-      - name: Install uv
-        uses: astral-sh/setup-uv@v6
-
       - name: Generate Docs
-        shell: pixi run bash -e {0}
-        run: |
-          uvx pdm sync
-          uvx pdm run pip install . -vvv
-          uvx pdm run sphinx-build -b html docs/source docs/build/html
+        run: pixi run -e docs makedocs
 
       - name: Upload artifact
         uses: actions/upload-artifact@v4

.github/workflows/ci_metatomic.yml

@@ -18,7 +18,7 @@ jobs:
         os: [ubuntu-22.04, macos-14]
     steps:
       - uses: actions/checkout@v4
-      - uses: prefix-dev/setup-pixi@v0.8.10
+      - uses: prefix-dev/setup-pixi@v0.9.4
         with:
           cache: true
           cache-write: ${{ github.event_name == 'push' && github.ref_name == 'main' }}
@@ -31,6 +31,10 @@ jobs:
           script: |
             core.exportVariable('ACTIONS_CACHE_URL', process.env.ACTIONS_CACHE_URL || '');
             core.exportVariable('ACTIONS_RUNTIME_TOKEN', process.env.ACTIONS_RUNTIME_TOKEN || '');
+      - name: Install cbindgen
+        shell: bash
+        run: command -v cbindgen || cargo install cbindgen
+
       - name: Use Homebrew gfortran (macOS)
         if: runner.os == 'macOS'
         run: |

.github/workflows/ci_serve.yml

@@ -17,7 +17,7 @@ jobs:
         os: [ubuntu-22.04]
     steps:
       - uses: actions/checkout@v4
-      - uses: prefix-dev/setup-pixi@v0.8.10
+      - uses: prefix-dev/setup-pixi@v0.9.4
         with:
           cache: true
           cache-write: ${{ github.event_name == 'push' && github.ref_name == 'main' }}
@@ -30,6 +30,10 @@ jobs:
           script: |
             core.exportVariable('ACTIONS_CACHE_URL', process.env.ACTIONS_CACHE_URL || '');
             core.exportVariable('ACTIONS_RUNTIME_TOKEN', process.env.ACTIONS_RUNTIME_TOKEN || '');
+      - name: Install cbindgen
+        shell: bash
+        run: command -v cbindgen || cargo install cbindgen
+
       - name: Build with serve mode
         shell: pixi run bash -e {0}
         run: |

.github/workflows/ci_xtb.yml

@@ -20,7 +20,7 @@ jobs:
         os: [ubuntu-22.04]
     steps:
       - uses: actions/checkout@v4
-      - uses: prefix-dev/setup-pixi@v0.8.10
+      - uses: prefix-dev/setup-pixi@v0.9.4
         with:
           cache: true
           cache-write: ${{ github.event_name == 'push' && github.ref_name == 'main' }}
@@ -33,6 +33,10 @@ jobs:
           script: |
             core.exportVariable('ACTIONS_CACHE_URL', process.env.ACTIONS_CACHE_URL || '');
             core.exportVariable('ACTIONS_RUNTIME_TOKEN', process.env.ACTIONS_RUNTIME_TOKEN || '');
+      - name: Install cbindgen
+        shell: bash
+        run: command -v cbindgen || cargo install cbindgen
+
       - name: Install eon
         shell: pixi run bash -e {0}
         run: |

client/BasinHoppingJob.cpp

@@ -10,8 +10,8 @@
 ** https://github.com/TheochemUI/eOn
 */
 
-#include <math.h>
-#include <stdio.h>
+#include <cmath>
+#include <filesystem>
 #include <string>
 
 #include "BasinHoppingJob.h"
@@ -82,9 +82,7 @@ std::vector<std::string> BasinHoppingJob::run(void) {
   *minimumEnergyStructure = *current;
   int nsteps = params.basin_hopping_options.steps +
                params.basin_hopping_options.quenching_steps;
-  long totalfc;
-  FILE *pFile;
-  pFile = fopen("bh.dat", "w");
+  auto bhFile = fmt::output_file("bh.dat");
 
   SPDLOG_LOGGER_DEBUG(
       log, "[Basin Hopping] {:4s} {:12s} {:12s} {:12s} {:4s} {:5s} {:5s}",
@@ -190,9 +188,10 @@ std::vector<std::string> BasinHoppingJob::run(void) {
 
           snprintf(fname, 128, "energy_%.5i.dat", step + 1);
           returnFiles.push_back(fname);
-          FILE *fh = fopen(fname, "w");
-          fprintf(fh, "%.10e\n", currentEnergy);
-          fclose(fh);
+          {
+            auto efh = fmt::output_file(fname);
+            efh.print("{:.10e}\n", currentEnergy);
+          }
         }
       }
 
@@ -205,21 +204,15 @@ std::vector<std::string> BasinHoppingJob::run(void) {
       minTrial->matter2con("movie", true);
     }
 
-    // totalfc = Potential::fcallsTotal;
-    char acceptReject[2];
-    acceptReject[1] = '\0';
-    if (accepted) {
-      acceptReject[0] = 'A';
-    } else {
-      acceptReject[0] = 'R';
-    }
-    // SPDLOG_LOGGER_DEBUG(log, "[Basin Hopping] %5i %12.3f %12.3f %12.3f %4i
-    // %5.3f %5.3f %1s\n",
-    //        step+1, currentEnergy, minTrial->getPotentialEnergy(),
-    //        minimumEnergy, minfcalls, totalAccept/((double)step+1),
-    //        curDisplacement, acceptReject);
-    // fprintf(pFile, "%6i %9ld %12.4e %12.4e\n",step+1,totalfc,currentEnergy,
-    // minTrial->getPotentialEnergy());
+    SPDLOG_LOGGER_DEBUG(log,
+                        "[Basin Hopping] {:5d} {:12.3f} {:12.3f} {:12.3f} "
+                        "{:5.3f} {:5.3f} {:1s}",
+                        step + 1, currentEnergy, minTrial->getPotentialEnergy(),
+                        minimumEnergy,
+                        totalAccept / (static_cast<double>(step) + 1),
+                        curDisplacement, accepted ? "A" : "R");
+    bhFile.print("{:6d} {:12.4e} {:12.4e}\n", step + 1, currentEnergy,
+                 minTrial->getPotentialEnergy());
 
     if (minimumEnergy < params.basin_hopping_options.stop_energy) {
       break;
@@ -261,43 +254,38 @@ std::vector<std::string> BasinHoppingJob::run(void) {
       recentAccept = 0;
     }
   }
-  fclose(pFile);
 
   /* Save Results */
 
-  FILE *fileResults, *fileProduct;
-
   std::string resultsFilename("results.dat");
   returnFiles.push_back(resultsFilename);
-  fileResults = fopen(resultsFilename.c_str(), "wb");
+  {
+    auto out = fmt::output_file(resultsFilename);
 
-  if (params.debug_options.write_movies == true) {
-    std::string movieFilename("movie.xyz");
-    returnFiles.push_back(movieFilename);
-  }
+    if (params.debug_options.write_movies == true) {
+      std::string movieFilename("movie.xyz");
+      returnFiles.push_back(movieFilename);
+    }
 
-  fprintf(fileResults, "%d termination_reason\n", 0);
-  fprintf(fileResults, "%.6f minimum_energy\n", minimumEnergy);
-  fprintf(fileResults, "%ld random_seed\n", params.main_options.randomSeed);
-  fprintf(fileResults, "%.3f acceptance_ratio\n",
-          totalAccept / params.basin_hopping_options.steps);
-  if (params.basin_hopping_options.swap_probability > 0) {
-    fprintf(fileResults, "%.3f swap_acceptance_ratio\n",
-            swap_accept / double(swap_count));
+    out.print("{} termination_reason\n", 0);
+    out.print("{:.6f} minimum_energy\n", minimumEnergy);
+    out.print("{} random_seed\n", params.main_options.randomSeed);
+    out.print("{:.3f} acceptance_ratio\n",
+              totalAccept / params.basin_hopping_options.steps);
+    if (params.basin_hopping_options.swap_probability > 0) {
+      out.print("{:.3f} swap_acceptance_ratio\n",
+                swap_accept / double(swap_count));
+    }
+    out.print("{} total_normal_displacement_steps\n",
+              disp_count - jump_count -
+                  params.basin_hopping_options.quenching_steps);
+    out.print("{} total_jump_steps\n", jump_count);
+    out.print("{} total_swap_steps\n", swap_count);
   }
-  fprintf(fileResults, "%ld total_normal_displacement_steps\n",
-          disp_count - jump_count -
-              params.basin_hopping_options.quenching_steps);
-  fprintf(fileResults, "%d total_jump_steps\n", jump_count);
-  fprintf(fileResults, "%d total_swap_steps\n", swap_count);
-  // fprintf(fileResults, "%d total_force_calls\n", Potential::fcallsTotal);
-  fclose(fileResults);
 
   std::string productFilename("min.con");
   returnFiles.push_back(productFilename);
-  fileProduct = fopen(productFilename.c_str(), "wb");
-  minimumEnergyStructure->matter2con(fileProduct);
-  fclose(fileProduct);
+  minimumEnergyStructure->matter2con(productFilename);
 
   std::string bhFilename("bh.dat");
   returnFiles.push_back(bhFilename);

client/DynamicsJob.cpp

@@ -9,7 +9,6 @@
 ** Repo:
 ** https://github.com/TheochemUI/eOn
 */
-#include <stdio.h>
 #include <string>
 
 #include "Dynamics.h"
@@ -30,13 +29,9 @@ std::vector<std::string> DynamicsJob::run(void) {
   d->run();
 
   *F = *R;
-  FILE *fileProduct;
   std::string productFilename("final.con");
   returnFiles.push_back(productFilename);
-
-  fileProduct = fopen(productFilename.c_str(), "wb");
-  F->matter2con(fileProduct);
-  fclose(fileProduct);
+  F->matter2con(productFilename);
 
   delete d;
 

client/FiniteDifferenceJob.cpp

@@ -36,24 +36,23 @@ std::vector<std::string> FiniteDifferenceJob::run(void) {
   AtomMatrix displacement;
   displacement.resize(reactant->numberOfAtoms(), 3);
   displacement.setZero();
-  printf("displacing atoms:");
+  SPDLOG_DEBUG("displacing atoms:");
   for (int i = 0; i < reactant->numberOfAtoms(); i++) {
     if (reactant->distance(epicenter, i) <= 3.3) {
-      printf(" %i", i);
+      SPDLOG_DEBUG(" {}", i);
       for (int j = 0; j < 3; j++) {
         if (!reactant->getFixed(i)) {
           displacement(i, j) = randomDouble(1.0);
         }
       }
     }
   }
-  printf("\n");
   displacement.normalize();
 
   // Loop over values of dimer dR and print the output to results.dat.
-  FILE *results = fopen("results.dat", "w");
-  fprintf(results, "%14s    %14s\n", "dR", "curvature");
-  printf("%14s    %14s\n", "dR", "curvature");
+  auto results = fmt::output_file("results.dat");
+  results.print("{:>14s}    {:>14s}\n", "dR", "curvature");
+  SPDLOG_DEBUG("{:>14s}    {:>14s}", "dR", "curvature");
   AtomMatrix posB;
   AtomMatrix forceB;
   double curvature = 0.0;
@@ -63,11 +62,9 @@ std::vector<std::string> FiniteDifferenceJob::run(void) {
     forceB = reactant->getForces();
     curvature =
         ((forceB - forceA).array() * displacement.array()).sum() / dRs[dRi];
-    fprintf(results, "%14.8f    %14.8f\n", dRs[dRi], curvature);
-    printf("%14.8f    %14.8f\n", dRs[dRi], curvature);
-    fflush(results);
+    results.print("{:14.8f}    {:14.8f}\n", dRs[dRi], curvature);
+    SPDLOG_DEBUG("{:14.8f}    {:14.8f}", dRs[dRi], curvature);
   }
-  fclose(results);
 
   std::vector<std::string> empty;
   return empty;

client/GPSurrogateJob.cpp

@@ -89,11 +89,9 @@ std::vector<std::string> GPSurrogateJob::run(void) {
 
     std::string nebFilename(fmt::format("neb_final_gpr_{:03d}.con", n_gp));
     returnFiles.push_back(nebFilename);
-    FILE *fileNEB = fopen(nebFilename.c_str(), "wb");
     for (long i = 0; i <= neb->numImages + 1; i++) {
-      neb->path[i]->matter2con(fileNEB);
+      neb->path[i]->matter2con(nebFilename, /*append=*/i > 0);
     }
-    fclose(fileNEB);
     // } else
     if (status_neb == NudgedElasticBand::NEBStatus::GOOD &&
         helper_functions::surrogate::accuratePES(neb->path, pot)) {

client/GlobalOptimizationJob.cpp

@@ -72,8 +72,8 @@ std::vector<std::string> GlobalOptimizationJob::run(void) {
     } else {
       earrim1 = earr[i - 1];
     }
-    fprintf(earrfile, "%5zu  %15.5f  %15.5f  %15.5f  ", i + 1, earr[i],
-            earr[i] - earr[0], earr[i] - earrim1);
+    earrfile.print("{:5d}  {:15.5f}  {:15.5f}  {:15.5f}  ", i + 1, earr[i],
+                   earr[i] - earr[0], earr[i] - earrim1);
   }
   // globopt.run();
   return returnFiles;
@@ -191,8 +191,10 @@ void GlobalOptimizationJob::report(Matter *matter_hop) {
   double epot_hop = matter_hop->getPotentialEnergy();
   double temp = (2.0 * ekin_p / params.constants.kB);
   double dt = params.dynamics_options.time_step;
-  fprintf(monfile, "%15.5f  %15.5f  %11zu  %12.2f         %c%c  %5ld  %5ld",
-          epot_hop, ediff, (size_t)temp, dt, C1, C2, fcallsMove, fcallsRelax);
+  monfile.print(
+      "{:15.5f}  {:15.5f}  {:11d}  {:12.2f}         {:c}{:c}  {:5d}  {:5d}",
+      epot_hop, ediff, static_cast<size_t>(temp), dt, C1, C2, fcallsMove,
+      fcallsRelax);
 }
 
 void GlobalOptimizationJob::decisionStep(Matter *matter_cur,