Run PTCDA_single example with pytest

.github/workflows/ci.yml

@@ -7,7 +7,7 @@ jobs:
         runs-on: ubuntu-latest
         strategy:
             matrix:
-                python-version: ['3.7', '3.8', '3.9', '3.10', '3.11', '3.12']
+                python-version: ['3.7', '3.9', '3.10', '3.11', '3.12']
 
         steps:
             - name: Check out repository
@@ -20,11 +20,11 @@ jobs:
 
             - name: Install package and its dependencies
               run: |
-                  pip install .[dev,opencl]
+                  pip install -e .[dev,opencl]
                   pip install pocl-binary-distribution
 
             - name: Run pytest
-              run: pytest tests -v --cov
+              run: PPAFM_RECOMPILE=1 pytest tests examples -v --cov -s
 
             - name: Save test images
               uses: actions/upload-artifact@v3

.gitignore

@@ -28,3 +28,5 @@ dist/
 
 # Sphinx documentation
 doc/sphinx/build/
+
+.coverage

examples/PTCDA_Hartree_dz2/example_ptcda_hartree.py

@@ -0,0 +1,27 @@
+import os
+import subprocess
+from pathlib import Path
+
+from ppafm.cli.generateElFF import main as generate_elff
+from ppafm.cli.generateLJFF import main as generate_ljff
+from ppafm.cli.plot_results import main as plot_results
+from ppafm.cli.relaxed_scan import main as relaxed_scan
+
+
+def example_ptcda_hartree():
+    script_location = Path(__file__).absolute().parent
+
+    # Change directory to the location of this script
+    os.chdir(script_location)
+
+    subprocess.run(["wget", "--no-check-certificate", "https://www.dropbox.com/s/18eg89l89npll8x/LOCPOT.xsf.zip"])
+    subprocess.run(["unzip", "LOCPOT.xsf.zip"])
+
+    generate_ljff(["--input", "LOCPOT.xsf"])
+    generate_elff(["--input", "LOCPOT.xsf", "--tip", "dz2"])
+    relaxed_scan(["--klat", "0.5", "--charge", "-0.10"])
+    plot_results(["--klat", "0.5", "--charge", "-0.10", "--Amplitude", "0.5", "--df"])
+
+
+if __name__ == "__main__":
+    example_ptcda_singe()

examples/PTCDA_single/example_ptcda.py

@@ -0,0 +1,23 @@
+import os
+from pathlib import Path
+
+from ppafm.cli.generateElFF_point_charges import main as generate_elff_point_charges
+from ppafm.cli.generateLJFF import main as generate_ljff
+from ppafm.cli.plot_results import main as plot_results
+from ppafm.cli.relaxed_scan import main as relaxed_scan
+
+
+def example_ptcda_singe():
+    script_location = Path(__file__).absolute().parent
+
+    # Change directory to the location of this script
+    os.chdir(script_location)
+
+    generate_ljff(["--input", "PTCDA.xyz"])
+    generate_elff_point_charges(["--input", "PTCDA.xyz", "--tip", "s"])
+    relaxed_scan(["--klat", "0.5", "--charge", "-0.10"])
+    plot_results(["--klat", "0.5", "--charge", "-0.10", "--arange", "0.5", "2.0", "2", "--df"])
+
+
+if __name__ == "__main__":
+    example_ptcda_singe()

ppafm/cli/generateElFF.py

@@ -13,7 +13,7 @@
 )
 
 
-def main():
+def main(argv=None):
     parser = common.CLIParser(
         description="Generate electrostatic force field by cross-correlation of sample Hartree potential with tip charge density. "
         "The generated force field is saved to FFel_{x,y,z}.[ext]."
@@ -29,7 +29,7 @@ def main():
     parser.add_argument("--Vref",       action="store", type=float,                help="Field under the KPFM dens. and Vh was calculated in V/Ang")
     parser.add_argument("--z0",         action="store", type=float, default=0.0,   help="Heigth of the topmost layer of metallic substrate for E to V conversion (Ang)")
     # fmt: on
-    args = parser.parse_args()
+    args = parser.parse_args(argv)
 
     # Load parameters.
     params_path = Path("params.ini") if Path("params.ini").is_file() else cpp_utils.PACKAGE_PATH / "defaults" / "params.ini"

ppafm/cli/generateElFF_point_charges.py

@@ -4,10 +4,10 @@
 from ..HighLevel import computeELFF_pointCharge
 
 
-def main():
+def main(argv=None):
     parser = common.CLIParser(description="Generate electrostatic force field by Coulomb interaction of point charges. The generated force field is saved to FFel_{x,y,z}.[ext].")
     parser.add_arguments(["input", "input_format", "output_format", "tip", "energy", "noPBC"])
-    args = parser.parse_args()
+    args = parser.parse_args(argv)
 
     common.loadParams("params.ini")
     common.apply_options(vars(args))

ppafm/cli/generateLJFF.py

@@ -5,11 +5,11 @@
 from ..HighLevel import computeLJ
 
 
-def main():
+def main(argv=None):
     parser = common.CLIParser(description="Generate a Lennard-Jones, Morse, or vdW force field. The generated force field is saved to FFLJ_{x,y,z}.[ext].")
 
     parser.add_arguments(["input", "input_format", "output_format", "ffModel", "energy", "noPBC"])
-    args = parser.parse_args()
+    args = parser.parse_args(argv)
 
     try:
         common.loadParams("params.ini")

ppafm/cli/plot_results.py

@@ -17,7 +17,7 @@
 atom_size = 0.15
 
 
-def main():
+def main(argv=None):
     # fmt: off
     parser = common.CLIParser( description="Plot results for a scan with a specified charge, amplitude, and spring constant.Images are saved in folder Q{charge}K{klat}/Amp{Amplitude}." )
     parser.add_arguments(["output_format","Amplitude","arange","klat","krange","charge", "qrange", "Vbias", "Vrange", "noPBC", ])
@@ -36,7 +36,7 @@ def main():
     parser.add_argument( "--bI",        action="store_true",                           help="Plot images for Boltzmann current"    )
     # fmt: on
 
-    args = parser.parse_args()
+    args = parser.parse_args(argv)
     opt_dict = vars(args)
 
     common.loadParams("params.ini")

ppafm/cli/relaxed_scan.py

@@ -28,7 +28,7 @@ def rotate_ff(fx, fy, a):
     return new_fx, new_fy
 
 
-def main():
+def main(argv=None):
     parser = common.CLIParser(
         description="Perform a scan, relaxing the probe particle in a precalculated force field. The generated force field is saved to Q{charge}K{klat}/OutFz.xsf."
     )
@@ -46,7 +46,7 @@ def main():
     parser.add_argument("--pol_t",          action="store",      type=float, default=1.0, help="Scaling factor for tip polarization")
     parser.add_argument("--pol_s",          action="store",      type=float, default=1.0, help="Scaling factor for sample polarization")
     # fmt: on
-    args = parser.parse_args()
+    args = parser.parse_args(argv)
 
     opt_dict = vars(args)
     common.loadParams("params.ini")

ppafm/io.py

@@ -1,5 +1,6 @@
 #!/usr/bin/python
 
+import copy
 import os
 import re
 
@@ -459,7 +460,7 @@ def loadGeometry(fname=None, format=None, params=None):
         if qs is None:
             qs = np.zeros(len(Zs))
         atoms = [list(Zs), list(xyzs[:, 0]), list(xyzs[:, 1]), list(xyzs[:, 2]), list(qs)]
-        nDim = params["gridN"].copy()
+        nDim = copy.copy(params["gridN"])
 
     # Make sure lvec is a 4x3 array. Use default grid parameters if needed
     if (lvec is None) or (len(lvec) == 0):
@@ -503,11 +504,12 @@ def loadGeometry(fname=None, format=None, params=None):
 
     # Copy lattice vectors and grid dimensions to the global parameters
     # so as to guarantee compatibility between the local variables and global parameters
+
     for i in range(3):
         params["gridA"][i] = lvec[1][i]
         params["gridB"][i] = lvec[2][i]
         params["gridC"][i] = lvec[3][i]
-        params["gridN"][i] = nDim[i]
+    params["gridN"] = nDim
 
     return atoms, nDim, lvec
 

pyproject.toml

@@ -80,3 +80,8 @@ skip = ["pp*", "*-manylinux_i686", "*-musllinux*", '*-win32']
 line-length = 180
 target-version = ['py37', 'py38', 'py39', 'py310', 'py311']
 extend-exclude = "ppafm/dev"
+
+[tool.pytest.ini_options]
+testpaths = ["tests", "examples"]
+python_files = ["test_*.py", "example_*.py"]
+python_functions = ["test_*", "example_*"]