Adding better test

src/data_parser.f90

@@ -1310,7 +1310,11 @@ subroutine repair_active_molecules(box)
         real(real64) :: dist                      ! Intramoleclar distance for sanity check
 
         ! Allocate temporary arrays for one molecule's atom positions
-        allocate(tmp_xyz(3, maxval(res%atom)))
+        if (.not. allocated(res%atom)) then
+           call  abort_run("res%atom is not allocated")
+        else
+            allocate(tmp_xyz(3, maxval(res%atom)))
+        end if
 
         k = 1  ! Global atom index
 

tests/readers/scan/run-test.sh

@@ -0,0 +1,52 @@
+#!/bin/bash
+set -euo pipefail
+
+# Path to maniac files
+BUILD_DIR="../../../build"
+MODULE_DIR="../../../include"
+
+# Path to test executables
+BIN_DIR="./build"
+mkdir -p "$BIN_DIR"
+
+# Collect Maniac object files (excluding main.o)
+shopt -s nullglob
+MANIAC_OBJS=()
+for obj in "$BUILD_DIR"/*.o; do
+    [[ $(basename "$obj") == "main.o" ]] && continue
+    MANIAC_OBJS+=("$obj")
+done
+shopt -u nullglob
+
+# COMPILE & RUN TESTS
+for TEST_SRC in test_*.f90; do
+    [[ ! -f "$TEST_SRC" ]] && {
+        echo "No test_*.f90 files found — nothing to run."
+        exit 0
+    }
+
+    TEST_NAME="${TEST_SRC%.f90}"
+    OUT_EXE="$BIN_DIR/$TEST_NAME"
+
+    if ! gfortran -O2 -I"$MODULE_DIR" -I"$BUILD_DIR" -c "$TEST_SRC" -o "$TEST_NAME.o" &>/dev/null; then
+        echo "❌ [FAIL] $TEST_NAME (compilation error)"
+        exit 1
+    fi
+
+    if ! gfortran -O2 -o "$OUT_EXE" "$TEST_NAME.o" "${MANIAC_OBJS[@]}" &>/dev/null; then
+        echo "❌ [FAIL] $TEST_NAME (linking error)"
+        exit 1
+    fi
+
+    if "$OUT_EXE" &>/dev/null; then
+    #if "$OUT_EXE"; then
+        echo "✅ [PASS] $TEST_NAME"
+    else
+        echo "❌ [FAIL] $TEST_NAME (runtime error)"
+        exit 1
+    fi
+
+    rm -f "$TEST_NAME.o"
+done
+
+rm -f fort.10 2>/dev/null || true

tests/readers/scan/test_scan_files.f90

@@ -0,0 +1,113 @@
+program test_scan_files
+
+    use, intrinsic :: iso_fortran_env, only: real64
+    use simulation_state
+    use data_parser
+    use prescan_files
+    use input_parser
+
+    implicit none
+
+    character(len=LENPATH) :: base_main     ! Path for main file
+    character(len=LENPATH) :: base_res      ! Path for reservoir file
+
+    !---------------------------------------------------------------------------
+    ! Test 1 : ZIF8-H2O without reservoir
+    !---------------------------------------------------------------------------
+    base_main = "../../../mc-topology/testcase-energy/ZIF8-H2O/"
+    base_res = ""
+    call run_test_zif8_h2o(base_main, base_res, .false.)
+
+contains
+
+    subroutine run_test_zif8_h2o(base_main, base_res, reservoir)
+
+        ! Inputs
+        character(len=*), intent(in) :: base_main
+        character(len=*), intent(in) :: base_res
+        logical, intent(in) :: reservoir
+        integer :: max_atoms_per_residue
+
+        ! Local variables
+        logical :: pass, atoms_ok, connectivity_ok
+        integer :: i, j, k
+        character(len=200) :: msg
+        real(real64), dimension(3,2) :: expected_bounds
+        integer :: expected_atoms, expected_bonds, expected_angles
+        integer :: expected_dihedrals, expected_impropers
+
+        ! Set expected values
+        expected_bounds(1,1) = -17.01162d0  ! xlo
+        expected_bounds(1,2) =  17.01162d0  ! xhi
+        expected_bounds(2,1) = -17.01162d0  ! ylo
+        expected_bounds(2,2) =  17.01162d0  ! yhi
+        expected_bounds(3,1) = -17.01162d0  ! zlo
+        expected_bounds(3,2) =  17.01162d0  ! zhi
+        expected_atoms = 2220
+        expected_bonds = 9
+        expected_angles = 9
+        expected_dihedrals = 0
+        expected_impropers = 0
+
+        !-------------------------------------------------------------------
+        ! Setup paths
+        !-------------------------------------------------------------------
+        path%input = trim(base_main) // "input.maniac"
+        path%topology = trim(base_main) // "topology.data"
+        path%parameters = trim(base_main) // "parameters.inc"
+        status%reservoir_provided = reservoir
+        if (reservoir) then
+            path%reservoir = trim(base_res) // "topology.data"
+        else
+            path%reservoir = trim(base_res)
+        end if
+
+        !-------------------------------------------------------------------
+        ! Read the system
+        !-------------------------------------------------------------------
+        call prescan_inputs()
+        call read_input_file()
+        call read_system_data()
+
+        ! Test Expected values from the LAMMPS data file
+        call assert_real_matrix_equal(primary%cell%bounds, expected_bounds, 1.0d-6)
+        call assert_int_equal(primary%num%atoms, expected_atoms, "Number of atoms")
+        call assert_int_equal(primary%num%bonds, expected_bonds, "Number of bonds")
+        call assert_int_equal(primary%num%angles, expected_angles, "Number of angles")
+        call assert_int_equal(primary%num%dihedrals, expected_dihedrals, "Number of dihedrals")
+        call assert_int_equal(primary%num%impropers, expected_impropers, "Number of impropers")
+
+    end subroutine run_test_zif8_h2o
+
+    subroutine assert_real_matrix_equal(a, b, tol)
+
+        real(real64), intent(in) :: a(:,:), b(:,:)
+        real(real64), intent(in) :: tol
+        integer :: i, j
+
+        do i = 1, size(a,1)
+            do j = 1, size(a,2)
+                if (abs(a(i,j) - b(i,j)) > tol) then
+                    print *, "ASSERTION FAILED at (", i, ",", j, ")"
+                    print *, "  got     =", a(i,j)
+                    print *, "  expected=", b(i,j)
+                    call exit(1)
+                end if
+            end do
+        end do
+    end subroutine assert_real_matrix_equal
+
+    subroutine assert_int_equal(actual, expected, msg)
+
+        integer, intent(in) :: actual, expected
+        character(len=*), intent(in) :: msg
+
+        if (actual /= expected) then
+            print *, "ASSERTION FAILED:", trim(msg)
+            print *, "  got     =", actual
+            print *, "  expected=", expected
+            call exit(1)
+        end if
+    end subroutine assert_int_equal
+
+end program test_scan_files