add mattersim (#37)

* add mattersim

* add `mattersim`

* run `mattersim`

* update with `mattersim` command

docs/source/recipes/energy_and_forces.rst

@@ -5,7 +5,7 @@ This recipe is used to test the performance of different models in predicting th
 
 .. code-block:: console
 
-   (.venv) $ mlipx recipes metrics --models mace_mp,sevennet,orb_v2,chgnet --datapath ../data/DODH_adsorption_dft.xyz --repro
+   (.venv) $ mlipx recipes metrics --models mace_mp,sevennet,orb_v2,chgnet,mattersim --datapath ../data/DODH_adsorption_dft.xyz --repro
 
 .. mermaid::
    :align: center

docs/source/recipes/energy_volume.rst

@@ -6,7 +6,7 @@ Compute the energy-volume curve for a given material using multiple models.
 
 .. code-block:: console
 
-   (.venv) $ mlipx recipes ev --models mace_mp,sevennet,orb_v2,chgnet --material-ids=mp-1143 --repro
+   (.venv) $ mlipx recipes ev --models mace_mp,sevennet,orb_v2,chgnet,mattersim --material-ids=mp-1143 --repro
    (.venv) $ mlipx compare --glob "*EnergyVolumeCurve"
 
 

docs/source/recipes/homonuclear_diatomics.rst

@@ -7,7 +7,7 @@ Homonuclear diatomics give a per-element information on the performance of the :
 
 .. code-block:: console
 
-   (.venv) $ mlipx recipes homonuclear-diatomics --models mace_mp,sevennet,orb_v2 --smiles="[Li+].[Cl-]" --repro
+   (.venv) $ mlipx recipes homonuclear-diatomics --models mace_mp,sevennet,orb_v2,mattersim --smiles="[Li+].[Cl-]" --repro
 
 
 You can edit the elements in the :term:`main.py` file to include the elements you want to test.

docs/source/recipes/invariances.rst

@@ -5,7 +5,7 @@ Check the rotational, translational and permutational invariance of an :term:`ml
 
 .. code-block:: console
 
-   (.venv) $ mlipx recipes invariances --models mace_mp,sevennet,orb_v2,chgnet --material-ids=mp-1143 --repro
+   (.venv) $ mlipx recipes invariances --models mace_mp,sevennet,orb_v2,chgnet,mattersim --material-ids=mp-1143 --repro
    (.venv) $ mlipx compare --glob "*TranslationalInvariance"
    (.venv) $ mlipx compare --glob "*RotationalInvariance"
    (.venv) $ mlipx compare --glob "*PermutationInvariance"

docs/source/recipes/md.rst

@@ -6,7 +6,7 @@ This recipe is used to test the performance of different models in molecular dyn
 
 .. code-block:: console
 
-   (.venv) $ mlipx recipes md --models mace_mp,sevennet,orb_v2,chgnet --material-ids=mp-1143 --repro
+   (.venv) $ mlipx recipes md --models mace_mp,sevennet,orb_v2,chgnet,mattersim --material-ids=mp-1143 --repro
    (.venv) $ mlipx compare --glob "*MolecularDynamics"
 
 

docs/source/recipes/neb.rst

@@ -8,7 +8,7 @@ You can run the following command to instantiate a test directory:
 
 .. code-block:: console
 
-   (.venv) $ mlipx recipes neb --models mace_mp,sevennet,orb_v2,chgnet --datapath ../data/neb_end_p.xyz --repro
+   (.venv) $ mlipx recipes neb --models mace_mp,sevennet,orb_v2,chgnet,mattersim --datapath ../data/neb_end_p.xyz --repro
    (.venv) $ zntrack list # show available Nodes
    (.venv) $ mlipx compare --glob "*NEBs"
 

docs/source/recipes/phase_diagram.rst

@@ -6,7 +6,7 @@ You can run the following command to instantiate a test directory:
 
 .. code-block:: console
 
-   (.venv) $ mlipx recipes phase-diagram  --models mace_mp,sevennet,orb_v2,chgnet --material-ids=mp-30084 --repro
+   (.venv) $ mlipx recipes phase-diagram  --models mace_mp,sevennet,orb_v2,chgnet,mattersim --material-ids=mp-30084 --repro
    (.venv) $ mlipx compare --glob "*PhaseDiagram"
 
 
@@ -20,6 +20,7 @@ You can run the following command to instantiate a test directory:
    plots["orb_v2_0-phase-diagram"].show()
    plots["sevennet_0-phase-diagram"].show()
    plots["chgnet_0-phase-diagram"].show()
+   plots["mattersim_0-phase-diagram"].show()
 
 
 This test uses the following Nodes together with your provided model in the :term:`models.py` file:

docs/source/recipes/pourbaix_diagram.rst

@@ -9,7 +9,7 @@ Pourbaix Diagram
 
 .. code-block:: console
 
-   (.venv) $ mlipx recipes pourbaix-diagram  --models mace_mp,sevennet,orb_v2,chgnet --material-ids=mp-1143 --repro
+   (.venv) $ mlipx recipes pourbaix-diagram  --models mace_mp,sevennet,orb_v2,chgnet,mattersim --material-ids=mp-1143 --repro
    (.venv) $ mlipx compare --glob "*PourbaixDiagram"
 
 
@@ -23,6 +23,7 @@ Pourbaix Diagram
    plots["orb_v2_0-pourbaix-diagram"].show()
    plots["sevennet_0-pourbaix-diagram"].show()
    plots["chgnet_0-pourbaix-diagram"].show()
+   plots["mattersim_0-pourbaix-diagram"].show()
 
 This test uses the following Nodes together with your provided model in the :term:`models.py` file:
 

docs/source/recipes/relax.rst

@@ -8,7 +8,7 @@ This recipe is used to test the performance of different models in performing st
 
 .. code-block:: console
 
-   (.venv) $ mlipx recipes relax --models mace_mp,sevennet,orb_v2,chgnet --material-ids=mp-1143 --repro
+   (.venv) $ mlipx recipes relax --models mace_mp,sevennet,orb_v2,chgnet,mattersim --material-ids=mp-1143 --repro
    (.venv) $ mlipx compare --glob "*StructureOptimization"
 
 .. note::

docs/source/recipes/vibrational_analysis.rst

@@ -6,7 +6,7 @@ You can run the following command to instantiate a test directory:
 
 .. code-block:: console
 
-   (.venv) $ mlipx recipes vibrational-analysis --models mace_mp,sevennet,orb_v2 --smiles=CO,CCO,CCCO,CCCCO
+   (.venv) $ mlipx recipes vibrational-analysis --models mace_mp,sevennet,orb_v2,mattersim --smiles=CO,CCO,CCCO,CCCCO
 
 The vibrational analysis method needs additional information to run.
 Please edit the ``main.py`` file and set the ``system`` parameter on the ``VibrationalAnalysis`` node.

examples/diatomics/README.md

@@ -1,4 +1,4 @@
 ```bash
-mlipx recipes homonuclear-diatomics  --models mace_mp,sevennet,orb_v2 --smiles="[Li+].[Cl-]" --repro
+mlipx recipes homonuclear-diatomics  --models mace_mp,sevennet,orb_v2,mattersim --smiles="[Li+].[Cl-]" --repro
 mlipx compare --glob "*HomonuclearDiatomics"
 ```

examples/diatomics/dvc.lock

@@ -236,3 +236,37 @@ stages:
       hash: md5
       md5: f05ba44025dbc070e740fedc0c6d2be2
       size: 64
+  mattersim_HomonuclearDiatomics:
+    cmd: zntrack run mlipx.nodes.diatomics.HomonuclearDiatomics --name mattersim_HomonuclearDiatomics
+    deps:
+    - path: nodes/initialize/Smiles2Conformers/frames.xyz
+      hash: md5
+      md5: e5492061936ed82d534cc2d7c62937ea
+      size: 153
+    params:
+      params.yaml:
+        mattersim_HomonuclearDiatomics:
+          elements: []
+          eq_distance: covalent-radiuis
+          max_distance: 2.0
+          min_distance: 0.5
+          model:
+            _cls: mlipx.nodes.generic_ase.GenericASECalculator
+            class_name: MatterSimCalculator
+            device: auto
+            kwargs:
+            module: mattersim.forcefield
+          n_points: 100
+    outs:
+    - path: nodes/mattersim/HomonuclearDiatomics/frames.json
+      hash: md5
+      md5: f27250c6ea623b2a9a38b92717cd97af
+      size: 421800
+    - path: nodes/mattersim/HomonuclearDiatomics/node-meta.json
+      hash: md5
+      md5: bc45e1ec53bd983d26b89c74fc127b40
+      size: 64
+    - path: nodes/mattersim/HomonuclearDiatomics/results.csv
+      hash: md5
+      md5: b70e500ccf4307772b390389fb6e5a1d
+      size: 5843

examples/diatomics/dvc.yaml

@@ -20,6 +20,18 @@ stages:
     - nodes/mace_mp/HomonuclearDiatomics/results.csv
     params:
     - mace_mp_HomonuclearDiatomics
+  mattersim_HomonuclearDiatomics:
+    cmd: zntrack run mlipx.nodes.diatomics.HomonuclearDiatomics --name mattersim_HomonuclearDiatomics
+    deps:
+    - nodes/initialize/Smiles2Conformers/frames.xyz
+    metrics:
+    - nodes/mattersim/HomonuclearDiatomics/node-meta.json:
+        cache: false
+    outs:
+    - nodes/mattersim/HomonuclearDiatomics/frames.json
+    - nodes/mattersim/HomonuclearDiatomics/results.csv
+    params:
+    - mattersim_HomonuclearDiatomics
   orb_v2_HomonuclearDiatomics:
     cmd: zntrack run mlipx.nodes.diatomics.HomonuclearDiatomics --name orb_v2_HomonuclearDiatomics
     deps:

examples/diatomics/main.py

@@ -16,7 +16,7 @@
     with project.group(model_name):
         neb = mlipx.HomonuclearDiatomics(
             elements=[],
-            data=sum(frames, []),
+            data=sum(frames, []),  # Use all elements from all frames
             model=model,
             n_points=100,
             min_distance=0.5,

examples/diatomics/models.py

@@ -50,6 +50,14 @@ def get_calculator(self, **kwargs):
 MODELS["orb_v2"] = OrbCalc(name="orb_v2", device="auto")
 
 
+# https://github.com/CederGroupHub/chgnet
+MODELS["mattersim"] = mlipx.GenericASECalculator(
+    module="mattersim.forcefield",
+    class_name="MatterSimCalculator",
+    device="auto",
+)
+
+
 # OPTIONAL
 # ========
 # If you have custom property names you can use the UpdatedFramesCalc

examples/diatomics/nodes/mattersim/HomonuclearDiatomics/.gitignore

@@ -0,0 +1,2 @@
+/frames.json
+/results.csv

examples/diatomics/nodes/mattersim/HomonuclearDiatomics/node-meta.json

@@ -0,0 +1 @@
+{"uuid": "c5addb02-3509-4d8c-a32a-b2908b12a680", "run_count": 1}

examples/diatomics/params.yaml

@@ -16,6 +16,18 @@ mace_mp_HomonuclearDiatomics:
       model: medium
     module: mace.calculators
   n_points: 100
+mattersim_HomonuclearDiatomics:
+  elements: []
+  eq_distance: covalent-radiuis
+  max_distance: 2.0
+  min_distance: 0.5
+  model:
+    _cls: mlipx.nodes.generic_ase.GenericASECalculator
+    class_name: MatterSimCalculator
+    device: auto
+    kwargs: null
+    module: mattersim.forcefield
+  n_points: 100
 orb_v2_HomonuclearDiatomics:
   elements: []
   eq_distance: covalent-radiuis

examples/diatomics/zntrack.json

@@ -98,5 +98,35 @@
                 "item": null
             }
         }
+    },
+    "mattersim_HomonuclearDiatomics": {
+        "nwd": {
+            "_type": "pathlib.Path",
+            "value": "nodes/mattersim/HomonuclearDiatomics"
+        },
+        "model": {
+            "_type": "@dataclasses.dataclass",
+            "value": {
+                "module": "mlipx.nodes.generic_ase",
+                "cls": "GenericASECalculator"
+            }
+        },
+        "data": {
+            "_type": "znflow.Connection",
+            "value": {
+                "instance": {
+                    "_type": "zntrack.Node",
+                    "value": {
+                        "module": "mlipx.nodes.smiles",
+                        "name": "initialize_Smiles2Conformers",
+                        "cls": "Smiles2Conformers",
+                        "remote": null,
+                        "rev": null
+                    }
+                },
+                "attribute": "frames",
+                "item": null
+            }
+        }
     }
 }

examples/energy-volume/README.md

@@ -1,4 +1,4 @@
 ```bash
-mlipx recipes ev --models mace_mp,sevennet,orb_v2,chgnet --material-ids=mp-1143 --repro
+mlipx recipes ev --models mace_mp,sevennet,orb_v2,chgnet,mattersim --material-ids=mp-1143 --repro
 mlipx compare --glob "*EnergyVolumeCurve"
 ```

examples/energy-volume/dvc.lock

@@ -149,3 +149,36 @@ stages:
       hash: md5
       md5: fa8b44ba9924d82a0487acc3e2f55a68
       size: 3509
+  mattersim_0_EnergyVolumeCurve:
+    cmd: zntrack run mlipx.nodes.energy_volume.EnergyVolumeCurve --name mattersim_0_EnergyVolumeCurve
+    deps:
+    - path: nodes/initialize/MPRester/frames.xyz
+      hash: md5
+      md5: b2aa0fb43e0b26ef88bedc082a0a2325
+      size: 866
+    params:
+      params.yaml:
+        mattersim_0_EnergyVolumeCurve:
+          data_id: -1
+          model:
+            _cls: mlipx.nodes.generic_ase.GenericASECalculator
+            class_name: MatterSimCalculator
+            device: auto
+            kwargs:
+            module: mattersim.forcefield
+          n_points: 50
+          start: 0.8
+          stop: 2.0
+    outs:
+    - path: nodes/mattersim/0/EnergyVolumeCurve/frames.xyz
+      hash: md5
+      md5: 0ad32e40ec27684ee853591e273982f2
+      size: 86946
+    - path: nodes/mattersim/0/EnergyVolumeCurve/node-meta.json
+      hash: md5
+      md5: 92019096017c6c38d3633632cb0942fc
+      size: 64
+    - path: nodes/mattersim/0/EnergyVolumeCurve/results.csv
+      hash: md5
+      md5: 1756b0048cae0710eaac8db037e20f6f
+      size: 3057

examples/energy-volume/dvc.yaml

@@ -19,6 +19,11 @@ plots:
       nodes/chgnet/0/EnergyVolumeCurve/results.csv: scale
     y:
       nodes/chgnet/0/EnergyVolumeCurve/results.csv: energy
+- mattersim_0_EnergyVolumeCurve_results:
+    x:
+      nodes/mattersim/0/EnergyVolumeCurve/results.csv: scale
+    y:
+      nodes/mattersim/0/EnergyVolumeCurve/results.csv: energy
 stages:
   chgnet_0_EnergyVolumeCurve:
     cmd: zntrack run mlipx.nodes.energy_volume.EnergyVolumeCurve --name chgnet_0_EnergyVolumeCurve
@@ -53,6 +58,18 @@ stages:
     - nodes/mace_mp/0/EnergyVolumeCurve/results.csv
     params:
     - mace_mp_0_EnergyVolumeCurve
+  mattersim_0_EnergyVolumeCurve:
+    cmd: zntrack run mlipx.nodes.energy_volume.EnergyVolumeCurve --name mattersim_0_EnergyVolumeCurve
+    deps:
+    - nodes/initialize/MPRester/frames.xyz
+    metrics:
+    - nodes/mattersim/0/EnergyVolumeCurve/node-meta.json:
+        cache: false
+    outs:
+    - nodes/mattersim/0/EnergyVolumeCurve/frames.xyz
+    - nodes/mattersim/0/EnergyVolumeCurve/results.csv
+    params:
+    - mattersim_0_EnergyVolumeCurve
   orb_v2_0_EnergyVolumeCurve:
     cmd: zntrack run mlipx.nodes.energy_volume.EnergyVolumeCurve --name orb_v2_0_EnergyVolumeCurve
     deps:

examples/energy-volume/models.py

@@ -57,6 +57,14 @@ def get_calculator(self, **kwargs):
 )
 
 
+# https://github.com/CederGroupHub/chgnet
+MODELS["mattersim"] = mlipx.GenericASECalculator(
+    module="mattersim.forcefield",
+    class_name="MatterSimCalculator",
+    device="auto",
+)
+
+
 # OPTIONAL
 # ========
 # If you have custom property names you can use the UpdatedFramesCalc

examples/energy-volume/nodes/mattersim/0/EnergyVolumeCurve/.gitignore

@@ -0,0 +1,2 @@
+/frames.xyz
+/results.csv

examples/energy-volume/nodes/mattersim/0/EnergyVolumeCurve/node-meta.json

@@ -0,0 +1 @@
+{"uuid": "b95d21a6-afe7-453b-aa44-12f636199ded", "run_count": 1}

examples/energy-volume/params.yaml

@@ -25,6 +25,17 @@ mace_mp_0_EnergyVolumeCurve:
   n_points: 50
   start: 0.8
   stop: 2.0
+mattersim_0_EnergyVolumeCurve:
+  data_id: -1
+  model:
+    _cls: mlipx.nodes.generic_ase.GenericASECalculator
+    class_name: MatterSimCalculator
+    device: auto
+    kwargs: null
+    module: mattersim.forcefield
+  n_points: 50
+  start: 0.8
+  stop: 2.0
 orb_v2_0_EnergyVolumeCurve:
   data_id: -1
   model: