First working version of cleed called from Python.

empa-scientific-it · Jul 24, 2024 · c704a9f · c704a9f
1 parent b35f9bf
commit c704a9f
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Showing 9 changed files with 456 additions and 13 deletions.
diff --git a/.gitignore b/.gitignore
@@ -213,6 +213,7 @@ dkms.conf
 
 # CMake builds
 cmake-build*/
+cleedpy/cleed/bin/
 
 # Vscode
 .vscode/
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -23,7 +23,7 @@ repos:
           - id: autoflake
 
     - repo: https://github.com/psf/black
-      rev: 23.3.0
+      rev: 24.4.2
       hooks:
           - id: black
             language_version: python3

diff --git a/cleedpy/cleed/src/leed.c b/cleedpy/cleed/src/leed.c
@@ -1,8 +1,8 @@
 #include "leed.h"
 
 real ** leed(
-    char * bul_file,
     char * par_file,
+    char * bul_file,
     char *res_file
     ){
     struct cryst_str *bulk=NULL;

diff --git a/cleedpy/cli/leed.py b/cleedpy/cli/leed.py
@@ -3,11 +3,12 @@
 import typer
 
 from ..config import load_parameters
+from ..interface.cleed import call_cleed
 from ..physics.constants import BOHR_TO_ANGSTROM
 from ..preprocess import extract_bulk_parameters, transform_cells
 
 
-def leed(inptut_file: Path):
+def leed_bak(inptut_file: Path):
     """Leed CLI."""
     config = load_parameters(inptut_file)
     transformation_matrix = transform_cells(config)
@@ -24,6 +25,20 @@ def leed(inptut_file: Path):
     )
 
 
+def leed(
+    parameters_file: str = typer.Option(  # noqa: B008
+        "leed.inp", "--input", "-i", help="Input file with parameters"
+    ),
+    bulk_file: str = typer.Option(None, "--bulk", "-b", help="Bulk file"),  # noqa: B008
+    output_file: str = typer.Option(  # noqa: B008
+        "leed.out", "--output", "-o", help="Output file"
+    ),  # noqa: B008
+):
+    """Leed CLI."""
+    result = call_cleed(parameters_file, bulk_file, output_file)
+    print(result)
+
+
 def cli():
     """Leed CLI."""
     typer.run(leed)

diff --git a/cleedpy/interface/cleed.py b/cleedpy/interface/cleed.py
@@ -210,20 +210,17 @@ def get_cleed_lib() -> CDLL:
     return cdll.LoadLibrary(cleed_lib)
 
 
-def call_cleed() -> None:
+def call_cleed(parameters_file, bulk_file, output_file):
     lib = get_cleed_lib()
 
-    lib.my_test_function.argtypes = [c_int, c_int, POINTER(Crystal)]
-    lib.my_test_function.restype = c_int
+    lib.leed.argtypes = [c_char_p, c_char_p, c_char_p]
+    lib.leed.restype = POINTER(POINTER(c_double))
 
-    bulk = Crystal()
-    bulk.vr = 1.0
-    bulk.vi = 2.0
-    bulk.temp = 300.0
-
-    bulk.a = (0.0, 1.0, 2.0, 3.0, 4.0)
+    result = lib.leed(
+        parameters_file.encode(), bulk_file.encode(), output_file.encode()
+    )
 
-    print("Result is ", lib.my_test_function(1, 2, bulk))
+    return result
 
 
 if __name__ == "__main__":

diff --git a/examples/cleedpy_example_intermediate/PHASE/Cu_BVH.phs b/examples/cleedpy_example_intermediate/PHASE/Cu_BVH.phs
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+100 9 neng lmax (Cu, 60.70 amu, potential (WAKOH) from potpsb., zero at MT radius)
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