public release 3.0.0 - see README and CHANGES for details

projects/twoatom/twoatom-energy.json

@@ -0,0 +1,93 @@
+{
+  // line comments using // or # prefix are allowed as an extension of JSON syntax
+  "project": {
+    "__module__": "projects.twoatom.twoatom",
+    "__class__": "TwoatomProject",
+    "job_name": "twoatom0002",
+    "job_tags": [],
+    "description": "",
+    "mode": "single",
+    "directories": {
+      "data": "",
+      "output": ""
+    },
+    "keep_files": [
+      "cluster",
+      "model",
+      "scan",
+      "report",
+      "population"
+    ],
+    "keep_best": 10,
+    "keep_levels": 1,
+    "time_limit": 24,
+    "log_file": "",
+    "log_level": "WARNING",
+    "cluster_generator": {
+      "__class__": "TwoatomCluster",
+      "atom_types": {
+        "A": "N",
+        "B": "Ni"
+      },
+      "model_dict": {
+        "dAB": "dNNi",
+        "th": "pNNi",
+        "ph": "aNNi"
+      }
+    },
+    "atomic_scattering_factory": "InternalAtomicCalculator",
+    "multiple_scattering_factory": "EdacCalculator",
+    "model_space": {
+      "dNNi": {
+        "start": 2.109,
+        "min": 2.0,
+        "max": 2.25,
+        "step": 0.05
+      },
+      "pNNi": {
+        "start": 15.0,
+        "min": 0.0,
+        "max": 30.0,
+        "step": 1.0
+      },
+      "V0": {
+        "start": 21.966,
+        "min": 15.0,
+        "max": 25.0,
+        "step": 1.0
+      },
+      "Zsurf": {
+        "start": 1.449,
+        "min": 0.5,
+        "max": 2.0,
+        "step": 0.25
+      }
+    },
+    "domains": [
+      {
+        "default": 0.0
+      }
+    ],
+    "scans": [
+      {
+        "__class__": "mp.ScanCreator",
+        "filename": "twoatom_energy_alpha.etpai",
+        "emitter": "N",
+        "initial_state": "1s",
+        "positions": {
+          "e": "np.arange(10, 400, 5)",
+          "t": "0",
+          "p": "0",
+          "a": "np.linspace(-30, 30, 31)"
+        }
+      }
+    ],
+    "optimizer_params": {
+      "pop_size": 0,
+      "seed_file": "",
+      "seed_limit": 0,
+      "recalc_seed": true,
+      "table_file": ""
+    }
+  }
+}

projects/twoatom/twoatom-hemi.json

@@ -0,0 +1,90 @@
+{
+  // line comments using // or # prefix are allowed as an extension of JSON syntax
+  "project": {
+    "__module__": "projects.twoatom.twoatom",
+    "__class__": "TwoatomProject",
+    "job_name": "twoatom0001",
+    "job_tags": [],
+    "description": "",
+    "mode": "single",
+    "directories": {
+      "data": "",
+      "output": ""
+    },
+    "keep_files": [
+      "cluster",
+      "model",
+      "scan",
+      "report",
+      "population"
+    ],
+    "keep_best": 10,
+    "keep_levels": 1,
+    "time_limit": 24,
+    "log_file": "",
+    "log_level": "WARNING",
+    "cluster_generator": {
+      "__class__": "TwoatomCluster",
+      "atom_types": {
+        "A": "N",
+        "B": "Ni"
+      },
+      "model_dict": {
+        "dAB": "dNNi",
+        "th": "pNNi",
+        "ph": "aNNi"
+      }
+    },
+    "atomic_scattering_factory": "InternalAtomicCalculator",
+    "multiple_scattering_factory": "EdacCalculator",
+    "model_space": {
+        "dNNi": {
+          "start": 2.109,
+          "min": 2.0,
+          "max": 2.25,
+          "step": 0.05
+        },
+        "pNNi": {
+          "start": 15.0,
+          "min": 0.0,
+          "max": 30.0,
+          "step": 1.0
+        },
+        "V0": {
+          "start": 21.966,
+          "min": 15.0,
+          "max": 25.0,
+          "step": 1.0
+        },
+        "Zsurf": {
+          "start": 1.449,
+          "min": 0.5,
+          "max": 2.0,
+          "step": 0.25
+        }
+    },
+    "domains": [
+      {
+        "default": 0.0
+      }
+    ],
+    "scans": [
+      {
+        // class name as it would be used in the project module
+        "__class__": "mp.ScanLoader",
+        // any placeholder key from project.directories can be used
+        "filename": "{project}/twoatom_hemi_250e.etpi",
+        "emitter": "N",
+        "initial_state": "1s",
+        "is_modf": false
+      }
+    ],
+    "optimizer_params": {
+      "pop_size": 0,
+      "seed_file": "",
+      "seed_limit": 0,
+      "recalc_seed": true,
+      "table_file": ""
+    }
+  }
+}

projects/twoatom/twoatom.py

@@ -308,14 +308,12 @@ def set_project_args(project, project_args):
     @param project_args: (Namespace object) project arguments.
     """
 
-    scans = ['tp250e']
+    scans = []
     try:
         if project_args.scans:
             scans = project_args.scans
-        else:
-            logger.warning(BMsg("missing scan argument, using {0}", scans[0]))
     except AttributeError:
-        logger.warning(BMsg("missing scan argument, using {0}", scans[0]))
+        pass
 
     for scan_key in scans:
         scan_spec = project.scan_dict[scan_key]
@@ -337,7 +335,7 @@ def parse_project_args(_args):
     parser = argparse.ArgumentParser()
 
     # main arguments
-    parser.add_argument('-s', '--scans', nargs="*", default=['tp250e'],
+    parser.add_argument('-s', '--scans', nargs="*",
                         help="nick names of scans to use in calculation (see create_project function)")
 
     parsed_args = parser.parse_args(_args)