Update outdated software dependencies - removes MatGL engine

.binder/environment.yml

@@ -12,35 +12,34 @@ dependencies:
 - ipytree =0.2.2
 - ipywidgets =8.1.6
 - jupyterlab =4.4.1
-- numpy =1.26.4
+- numpy =2.3.4
 - sqlalchemy =2.0.38
 - traitlets =5.14.3
-- ase =3.24.0
-- assyst =0.3.0
+- ase =3.26.0
+- assyst =0.9.0
 - bayesian-optimization =2.0.3
-- calphy =1.3.13
-- grace-tensorpotential =0.5.1
+- calphy =1.4.3
+- grace-tensorpotential =0.5.3
 - iprpy-data =2023.07.25
 - lammps =2024.08.29=*openmpi*
-- landau =1.3.4
-- matgl =1.1.3
-- matplotlib =3.10.0
+- landau =1.5.2
+- matplotlib =3.10.7
 - nglview =3.1.4
-- pandas =2.2.3
-- phonopy =2.43.2
-- pint =0.24.4
-- psycopg2 =2.9.9
-- pyiron_atomistics =0.7.18
-- pyiron_base =0.14.3
+- pandas =2.3.3
+- phonopy =2.43.6
+- pint =0.25.0
+- psycopg2 =2.9.10
+- pyiron_atomistics =0.8.4
+- pyiron_base =0.15.9
 - pyiron-data =0.0.30
-- pyiron_lammps =0.4.1
+- pyiron_lammps =0.4.9
 - python-ace =0.3.1
 - python-ternary =1.0.8
 - pyxtal =1.1.0
 - scikit-image =0.25.2
 - scikit-learn =1.6.1
-- scipy =1.15.2
+- scipy =1.16.2
 - seaborn =0.13.2
-- structuretoolkit = 0.0.32
+- structuretoolkit = 0.0.37
 - nodejs=18
 - postgresql

notebooks/development/Calphad.ipynb

@@ -309,7 +309,7 @@
    "source": [
     "from pyiron_core.pyiron_workflow import as_function_node\n",
     "from pyiron_core.pyiron_nodes.atomistic.structure.build import Bulk\n",
-    "from pyiron_core.pyiron_nodes.atomistic.engine.ase import M3GNet\n",
+    "from pyiron_core.pyiron_nodes.atomistic.engine.ase import GRACE\n",
     "from pyiron_core.pyiron_nodes.atomistic.calculator.ase import StaticEnergy\n",
     "from pyiron_core.pyiron_nodes.atomistic.property.elastic import InputElasticTensor\n",
     "\n",
@@ -356,7 +356,7 @@
     "    return elastic_constants\n",
     "\n",
     "bulk = Bulk(\"Al\", cubic=True).run()\n",
-    "engine = M3GNet().run()\n",
+    "engine = GRACE().run()\n",
     "calculator = StaticEnergy(bulk, engine=engine) #.run()\n",
     "ComputeElasticConstants(bulk, engine, calculator).run()    "
    ]
@@ -524,12 +524,12 @@
     "\n",
     "from pyiron_core.pyiron_workflow import as_macro_node, as_function_node, Node\n",
     "from pyiron_core.pyiron_nodes.atomistic.structure.build import Bulk\n",
-    "from pyiron_core.pyiron_nodes.atomistic.engine.ase import M3GNet\n",
+    "from pyiron_core.pyiron_nodes.atomistic.engine.ase import GRACE\n",
     "from pyiron_core.pyiron_nodes.atomistic.calculator.ase import StaticEnergy\n",
     "from pyiron_core.pyiron_nodes.atomistic.property.elastic import InputElasticTensor, SymmetryAnalysis, GenerateStructures, AnalyseStructures\n",
     "\n",
     "structure = Bulk(\"Al\", cubic=True).run()\n",
-    "engine = M3GNet().run()\n",
+    "engine = GRACE().run()\n",
     "calculator = StaticEnergy(structure, engine=engine)\n",
     "calculator = GetFreeEnergy(structure=structure, engine=engine)\n",
     "parameters = InputElasticTensor(num_of_point=6)\n",

notebooks/development/Murnaghan.json

@@ -19,19 +19,19 @@
                 }
             }
         },
-        "M3GNet": {
-            "id": "M3GNet",
-            "import_path": "pyiron_nodes.atomistic.engine.ase.M3GNet",
-            "label": "M3GNet",
+        "GRACE": {
+            "id": "GRACE",
+            "import_path": "pyiron_nodes.atomistic.engine.ase.GRACE",
+            "label": "GRACE",
             "parent_id": null,
             "level": 0,
             "graph": null,
             "node_type": "node",
             "widget_type": "customNode",
             "expanded": false,
             "node": {
-                "label": "M3GNet",
-                "function": "pyiron_nodes.atomistic.engine.ase.M3GNet",
+                "label": "GRACE",
+                "function": "pyiron_nodes.atomistic.engine.ase.GRACE",
                 "inputs": {}
             }
         },
@@ -109,7 +109,7 @@
     "edges": {
         "values": [
             {
-                "source": "M3GNet",
+                "source": "GRACE",
                 "target": "Static",
                 "sourceHandle": "out",
                 "targetHandle": "engine"
@@ -141,4 +141,4 @@
         ],
         "obj_type": "pyiron_core.pyiron_workflow.graph.base.GraphEdge"
     }
-}
+}

notebooks/development/cecam.ipynb

@@ -188,10 +188,10 @@
      "evalue": "name 'xx' is not defined",
      "output_type": "error",
      "traceback": [
-      "\u001b[31m---------------------------------------------------------------------------\u001b[39m",
-      "\u001b[31mNameError\u001b[39m                                 Traceback (most recent call last)",
-      "\u001b[36mCell\u001b[39m\u001b[36m \u001b[39m\u001b[32mIn[6]\u001b[39m\u001b[32m, line 1\u001b[39m\n\u001b[32m----> \u001b[39m\u001b[32m1\u001b[39m \u001b[43mxx\u001b[49m\n",
-      "\u001b[31mNameError\u001b[39m: name 'xx' is not defined"
+      "\u001B[31m---------------------------------------------------------------------------\u001B[39m",
+      "\u001B[31mNameError\u001B[39m                                 Traceback (most recent call last)",
+      "\u001B[36mCell\u001B[39m\u001B[36m \u001B[39m\u001B[32mIn[6]\u001B[39m\u001B[32m, line 1\u001B[39m\n\u001B[32m----> \u001B[39m\u001B[32m1\u001B[39m \u001B[43mxx\u001B[49m\n",
+      "\u001B[31mNameError\u001B[39m: name 'xx' is not defined"
      ]
     }
    ],
@@ -330,8 +330,8 @@
     "    wf = Workflow('subgraph')\n",
     "\n",
     "    wf.Bulk = pyiron_nodes.atomistic.structure.build.Bulk(name=name, a=a) \n",
-    "    wf.M3GNet = pyiron_nodes.atomistic.engine.ase.M3GNet() \n",
-    "    wf.Static = pyiron_nodes.atomistic.calculator.ase.Static(structure=wf.Bulk, engine=wf.M3GNet) \n",
+    "    wf.GRACE = pyiron_nodes.atomistic.engine.ase.GRACE()\n",
+    "    wf.Static = pyiron_nodes.atomistic.calculator.ase.Static(structure=wf.Bulk, engine=wf.GRACE)\n",
     "    wf.GetEnergyLast = pyiron_nodes.atomistic.calculator.output.GetEnergyLast(calculator=wf.Static) \n",
     "\n",
     "    out = wf.GetEnergyLast.pull()\n",
@@ -357,13 +357,13 @@
     "    wf = Workflow('subgraph')\n",
     "\n",
     "    wf.Bulk = pyiron_nodes.atomistic.structure.build.Bulk(name=name, a=a) \n",
-    "    wf.M3GNet = pyiron_nodes.atomistic.engine.ase.M3GNet() \n",
-    "    wf.Static = pyiron_nodes.atomistic.calculator.ase.Static(structure=wf.Bulk, engine=wf.M3GNet) \n",
+    "    wf.GRACE = pyiron_nodes.atomistic.engine.ase.GRACE()\n",
+    "    wf.Static = pyiron_nodes.atomistic.calculator.ase.Static(structure=wf.Bulk, engine=wf.GRACE)\n",
     "    wf.GetEnergyLast = pyiron_nodes.atomistic.calculator.output.GetEnergyLast(calculator=wf.Static) \n",
     "\n",
     "    return wf.GetEnergyLast.outputs.energy_last, wf.Bulk"
    ],
-   "id": "6042e7fa09f9372d"
+   "id": "c9ac77afac0eaf0f"
   },
   {
    "metadata": {},
@@ -379,7 +379,7 @@
     "    output_labels = None\n",
     "output_labels"
    ],
-   "id": "68591839823902e7"
+   "id": "e87bcf34197c623c"
   },
   {
    "cell_type": "code",
@@ -927,19 +927,18 @@
    ]
   },
   {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "c8d4528e-a91c-4a7c-bc34-8b3401d3924b",
    "metadata": {},
+   "cell_type": "code",
    "outputs": [],
+   "execution_count": null,
    "source": [
     "base.Graph(id=None, \n",
     "      label='subgraph', \n",
     "      root_node=None, \n",
     "      nodes=NestedDict({'Bulk': GraphNode(id='Bulk', import_path='pyiron_nodes.atomistic.structure.build.Bulk', label='Bulk', \n",
     "                                          parent_id=None, level=0, node=<pyiron_core.pyiron_workflow.simple_workflow.Node object at 0x17372c3e0>,\n",
     "                                          graph=None, node_type='node', widget_type='customNode', expanded=False), \n",
-    "                        'M3GNet': GraphNode(id='M3GNet', import_path='pyiron_nodes.atomistic.engine.ase.M3GNet', label='M3GNet', \n",
+    "                        'GRACE': GraphNode(id='GRACE', import_path='pyiron_nodes.atomistic.engine.ase.GRACE', label='GRACE',\n",
     "                                            parent_id=None, level=0, node=<pyiron_core.pyiron_workflow.simple_workflow.Node object at 0x17372c410>,\n",
     "                                            graph=None, node_type='node', widget_type='customNode', expanded=False), \n",
     "                        'Static': GraphNode(id='Static', import_path='pyiron_nodes.atomistic.calculator.ase.Static', label='Static', \n",
@@ -950,18 +949,17 @@
     "                                                   graph=None, node_type='node', widget_type='customNode', expanded=False)}), \n",
     "      edges=[GraphEdge(source='Static', target='GetEnergyLast', sourceHandle='out', targetHandle='calculator'), \n",
     "             GraphEdge(source='Bulk', target='Static', sourceHandle='structure', targetHandle='structure'), \n",
-    "             GraphEdge(source='M3GNet', target='Static', sourceHandle='out', targetHandle='engine')], graph={})"
-   ]
+    "             GraphEdge(source='GRACE', target='Static', sourceHandle='out', targetHandle='engine')], graph={})"
+   ],
+   "id": "855cb2b37f204e80"
   },
   {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "826876b1-c68e-4751-8779-dac8ef719904",
    "metadata": {},
+   "cell_type": "code",
    "outputs": [],
-   "source": [
-    "subgraph.graph"
-   ]
+   "execution_count": null,
+   "source": "subgraph.graph",
+   "id": "819e6e4e7951dba2"
   },
   {
    "cell_type": "code",

notebooks/development/elastic.json

@@ -68,19 +68,19 @@
                 }
             }
         },
-        "M3GNet": {
-            "id": "M3GNet",
-            "import_path": "pyiron_nodes.atomistic.engine.ase.M3GNet",
-            "label": "M3GNet",
+        "GRACE": {
+            "id": "GRACE",
+            "import_path": "pyiron_nodes.atomistic.engine.ase.GRACE",
+            "label": "GRACE",
             "parent_id": null,
             "level": 0,
             "graph": null,
             "node_type": "node",
             "widget_type": "customNode",
             "expanded": false,
             "node": {
-                "label": "M3GNet",
-                "function": "pyiron_nodes.atomistic.engine.ase.M3GNet",
+                "label": "GRACE",
+                "function": "pyiron_nodes.atomistic.engine.ase.GRACE",
                 "inputs": {}
             }
         },
@@ -196,7 +196,7 @@
                 "targetHandle": "values"
             },
             {
-                "source": "M3GNet",
+                "source": "GRACE",
                 "target": "StaticEnergy",
                 "sourceHandle": "out",
                 "targetHandle": "engine"

notebooks/development/elastic_m3gnet.json

@@ -1,5 +1,5 @@
 {
-    "label": "elastic_m3gnet",
+    "label": "elastic_GRACE",
     "nodes": {
         "CubicBulkCell": {
             "id": "CubicBulkCell",
@@ -326,19 +326,19 @@
                 "inputs": {}
             }
         },
-        "M3GNet": {
-            "id": "M3GNet",
-            "import_path": "pyiron_nodes.atomistic.engine.ase.M3GNet",
-            "label": "M3GNet",
+        "GRACE": {
+            "id": "GRACE",
+            "import_path": "pyiron_nodes.atomistic.engine.ase.GRACE",
+            "label": "GRACE",
             "parent_id": null,
             "level": 0,
             "graph": null,
             "node_type": "node",
             "widget_type": "customNode",
             "expanded": false,
             "node": {
-                "label": "M3GNet",
-                "function": "pyiron_nodes.atomistic.engine.ase.M3GNet",
+                "label": "GRACE",
+                "function": "pyiron_nodes.atomistic.engine.ase.GRACE",
                 "inputs": {}
             }
         },
@@ -471,7 +471,7 @@
                 "targetHandle": "dataclass"
             },
             {
-                "source": "M3GNet",
+                "source": "GRACE",
                 "target": "Static",
                 "sourceHandle": "out",
                 "targetHandle": "engine"

notebooks/development/energy.json

@@ -19,19 +19,19 @@
                 }
             }
         },
-        "M3GNet": {
-            "id": "M3GNet",
-            "import_path": "pyiron_nodes.atomistic.engine.ase.M3GNet",
-            "label": "M3GNet",
+        "GRACE": {
+            "id": "GRACE",
+            "import_path": "pyiron_nodes.atomistic.engine.ase.GRACE",
+            "label": "GRACE",
             "parent_id": null,
             "level": 0,
             "graph": null,
             "node_type": "node",
             "widget_type": "customNode",
             "expanded": false,
             "node": {
-                "label": "M3GNet",
-                "function": "pyiron_nodes.atomistic.engine.ase.M3GNet",
+                "label": "GRACE",
+                "function": "pyiron_nodes.atomistic.engine.ase.GRACE",
                 "inputs": {}
             }
         },
@@ -110,7 +110,7 @@
                 "targetHandle": "structure"
             },
             {
-                "source": "M3GNet",
+                "source": "GRACE",
                 "target": "Static",
                 "sourceHandle": "out",
                 "targetHandle": "engine"
@@ -136,4 +136,4 @@
         ],
         "obj_type": "pyiron_core.pyiron_workflow.graph.base.GraphEdge"
     }
-}
+}

notebooks/development/minimize.json

@@ -216,19 +216,19 @@
                 "inputs": {}
             }
         },
-        "M3GNet": {
-            "id": "M3GNet",
-            "import_path": "pyiron_nodes.atomistic.engine.ase.M3GNet",
-            "label": "M3GNet",
+        "GRACE": {
+            "id": "GRACE",
+            "import_path": "pyiron_nodes.atomistic.engine.ase.GRACE",
+            "label": "GRACE",
             "parent_id": null,
             "level": 0,
             "graph": null,
             "node_type": "node",
             "widget_type": "customNode",
             "expanded": false,
             "node": {
-                "label": "M3GNet",
-                "function": "pyiron_nodes.atomistic.engine.ase.M3GNet",
+                "label": "GRACE",
+                "function": "pyiron_nodes.atomistic.engine.ase.GRACE",
                 "inputs": {}
             }
         },
@@ -311,7 +311,7 @@
                 "targetHandle": "structure"
             },
             {
-                "source": "M3GNet",
+                "source": "GRACE",
                 "target": "Minimize",
                 "sourceHandle": "out",
                 "targetHandle": "engine"