Use sum_cube.py in place of sum_cube.cpp (#6948)

Author: Cstandardlib

tests/integrate/CMakeLists.txt

@@ -1,14 +1,6 @@
 find_program(BASH bash)
 find_package(Python3 REQUIRED)
-
-add_executable(sum_cube ${ABACUS_TEST_DIR}/integrate/tools/sum_cube.cpp)
-install(TARGETS sum_cube DESTINATION ${ABACUS_TEST_DIR}/integrate/tools/)
-message(STATUS "Target sum_cube has been defined in ${CMAKE_CURRENT_SOURCE_DIR}") # 添加此行
-    
-if(ENABLE_COVERAGE)
-  add_coverage(sum_cube)
-endif()
-
+   
 if(ENABLE_ASAN)
     add_test(
         NAME integrated_test_with_asan

tests/integrate/tools/catch_properties.sh

@@ -4,7 +4,7 @@
 # this compare script is used in different integrate tests
 COMPARE_SCRIPT="../../integrate/tools/CompareFile.py"
 #COMPARE_SCRIPT="../../integrate/tools/compare_file.py"
-SUM_CUBE_EXE="../../integrate/tools/sum_cube"
+SUM_CUBE_EXE="python3 ../../integrate/tools/sum_cube.py"
 
 
 sum_file(){

tests/integrate/tools/sum_cube.py

@@ -0,0 +1,96 @@
+#!/usr/bin/env python3
+import sys
+
+def main():
+    if len(sys.argv) < 2:
+        print(f"Can't find {sys.argv[1] if len(sys.argv) > 1 else 'file'} !")
+        sys.exit(1)
+
+    input_file = sys.argv[1]
+
+    try:
+        with open(input_file, 'r') as inp:
+            # skip the first two lines
+            inp.readline()
+            inp.readline()
+
+            # read the 3rd line: number of atoms + origin coordinates
+            line = inp.readline().split()
+            if not line:
+                return
+            natom = int(line[0])
+            # origin_x = float(line[1])
+            # origin_y = float(line[2])
+            # origin_z = float(line[3])
+
+            # read the grid vectors (support non-orthogonal)
+            line = inp.readline().split()
+            nx = int(line[0])
+            v1 = [float(line[1]), float(line[2]), float(line[3])]
+
+            line = inp.readline().split()
+            ny = int(line[0])
+            v2 = [float(line[1]), float(line[2]), float(line[3])]
+
+            line = inp.readline().split()
+            nz = int(line[0])
+            v3 = [float(line[1]), float(line[2]), float(line[3])]
+
+            # calculate the volume element |v1 · (v2 × v3)|
+            val0 = v2[1] * v3[2] - v2[2] * v3[1]
+            val1 = v2[0] * v3[2] - v2[2] * v3[0]
+            val2 = v2[0] * v3[1] - v2[1] * v3[0]
+            
+            volume = abs(v1[0] * val0 - v1[1] * val1 + v1[2] * val2)
+
+            # skip the atom coordinates
+            # natom can be negative in cube files sometimes?
+            # C++ code: for (int i = 0; i < natom; ++i)
+            # If natom is negative, loop doesn't run.
+            
+            atoms_to_skip = natom
+            if atoms_to_skip < 0:
+                 # In some cube formats, negative natom means second line of header contains units or something?
+                 # Standard: "If the number of atoms is negative, that indicates that the file contains input lines... One line for each non-zero E value."
+                 # But the C++ code simple loops < natom. If natom < 0, it skips 0 lines.
+                 # We will mimic C++ behavior assuming it works for the files they have.
+                 atoms_to_skip = 0 # Loop won't run if natom < 0
+
+            for _ in range(atoms_to_skip):
+                inp.readline()
+
+            nr = nx * ny * nz
+            
+            total_sum = 0.0
+            count = 0
+            
+            # Read grid values
+            # iterate over remaining lines to handle values spread across lines
+            for line in inp:
+                parts = line.split()
+                for part in parts:
+                    total_sum += float(part)
+                    count += 1
+                    if count >= nr:
+                        break
+                if count >= nr:
+                    break
+            
+            ne = total_sum * volume
+            # cout default precision is 6, but setprecision(10) changes it.
+            # Python's default float printing is usually sufficient, but let's use formatting to be sure.
+            # {:.10g} prints up to 10 significant digits.
+            print(f"{ne:.10g}")
+
+    except FileNotFoundError:
+        print(f"Can't find {input_file} !")
+        sys.exit(1)
+    except Exception as e:
+        # C++ doesn't print other errors generally, but let's be safe.
+        # But to be functionally equivalent, maybe we shouldn't.
+        # The C++ code crashes or behaves weirdly on bad input.
+        # Let's just exit 1.
+        sys.exit(1)
+
+if __name__ == "__main__":
+    main()