A notebook for non-conservative MTS dynamics with PET-MAD

INSTALLING.rst

@@ -36,6 +36,7 @@ Whenever you want to run the recipe you just need to activate the environment
 and run the recipe file. 
 
 .. code-block:: bash
+
    # When you want to use the environment
    conda env activate --name <recipe-env-path>
 

README.rst

@@ -1,10 +1,10 @@
-The Atomistic Cookbook repository
-=================================
+Source code for the Atomistic Cookbook
+======================================
 
 .. image:: ./docs/src/_static/cookbook-icon.svg
    :alt: A cookbook with a cover showing a water molecule and mathematical symbols
    :align: center
-   :width: 50%
+   :width: 30%
 
 
 This repository contains the source code for a collection of software recipes,

docs/requirements.txt

@@ -5,4 +5,4 @@ sphinx-gallery
 sphinx-toggleprompt
 docutils
 furo
-chemiscope>=0.7
+chemiscope>=0.8.5

docs/src/software/chemiscope.sec

@@ -21,3 +21,4 @@ repository <https://github.com/lab-cosmo/chemiscope>`_.
 - examples/water-model/water-model
 - examples/polarizability/polarizability
 - examples/pet-mad/pet-mad
+- examples/pet-mad/pet-mad-nc  

docs/src/software/i-pi.sec

@@ -15,3 +15,4 @@ it on the `ipi-code website <http://ipi-code.org>`_, the `documentation pages
 - examples/pi-mts-rpc/mts-rpc
 - examples/water-model/water-model
 - examples/pet-mad/pet-mad
+- examples/pet-mad-nc/pet-mad-nc

docs/src/software/metatensor.sec

@@ -12,3 +12,4 @@ training and evaluating ML models.
 - examples/water-model/water-model
 - examples/polarizability/polarizability
 - examples/pet-mad/pet-mad
+- examples/pet-mad-nc/pet-mad-nc

docs/src/topics/ml-models.sec

@@ -11,3 +11,4 @@ data.
 - examples/periodic-hamiltonian/periodic-hamiltonian
 - examples/polarizability/polarizability
 - examples/pet-mad/pet-mad
+- examples/pet-mad/pet-mad-nc

examples/pet-mad-nc/README.rst

@@ -0,0 +1,5 @@
+Non-conservative MTS MD 
+=======================
+
+An example of running hybrid conservative/non-conservative MD
+using PET-MAD and i-PI.

examples/pet-mad-nc/data/input-nc-nve-mts.xml

@@ -0,0 +1,45 @@
+<simulation verbosity="high">
+<output prefix="nve-nc-mts">
+    <properties stride="1" filename="out">
+		[step, time{picosecond}, conserved{electronvolt}, temperature{kelvin},
+        kinetic_md{electronvolt}, potential{electronvolt}, 
+        pot_component(0){electronvolt}, pot_component(1){electronvolt}
+		]
+    </properties>
+    <trajectory filename="pos" stride="2" format="ase"> positions </trajectory>
+    <trajectory filename="forces_c" stride="2" format="ase"> forces_component(0) </trajectory>
+    <trajectory filename="forces_nc" stride="2" format="ase"> forces_component(1) </trajectory>
+    <checkpoint stride="1000"/>
+</output>
+<total_steps>50</total_steps>
+<prng><seed>12345</seed></prng>
+
+<ffdirect  name='cons' pbc="false">
+    <pes>metatensor</pes>
+    <parameters>{template:data/bmimcl.xyz,model:pet-mad-latest.pt,device:cpu,non_conservative:False} </parameters>
+</ffdirect>
+<ffdirect  name='nocons' pbc="false">
+    <pes>metatensor</pes>
+    <parameters>{template:data/bmimcl.xyz,model:pet-mad-latest.pt,device:cpu,non_conservative:True} </parameters>
+</ffdirect>
+<system>
+    <initialize nbeads="1">
+        <file mode="ase"> data/bmimcl.xyz </file>
+        <velocities mode="thermal" units="kelvin"> 400.0 </velocities>
+    </initialize>
+    <forces>
+        <force forcefield="cons">
+            <mts_weights>[1,0]</mts_weights>
+        </force>
+        <force forcefield="nocons">
+            <mts_weights>[-1,1]</mts_weights>
+        </force>
+    </forces>
+    <motion mode="dynamics">
+    	<dynamics mode="nve">
+        	<timestep units="femtosecond"> 4 </timestep>
+            <nmts>[1,8]</nmts>
+        </dynamics>
+    </motion>
+</system>
+</simulation>

examples/pet-mad-nc/data/input-nc-nve.xml

@@ -0,0 +1,36 @@
+<simulation verbosity="high">
+<output prefix="nve-nc">
+    <properties stride="8" filename="out">
+		[step, time{picosecond}, conserved{electronvolt}, temperature{kelvin},
+        kinetic_md{electronvolt}, potential{electronvolt}, 
+        pot_component(0){electronvolt}
+		]
+    </properties>
+    <trajectory filename="pos" stride="16" format="ase"> positions </trajectory>
+    <trajectory filename="forces_nc" stride="16" format="ase"> forces_component(0) </trajectory>
+    <checkpoint stride="1000"/>
+</output>
+<total_steps>160</total_steps>
+<prng><seed>12345</seed></prng>
+<ffdirect  name='nocons' pbc="false">
+    <pes>metatensor</pes>
+    <parameters>{template:data/bmimcl.xyz,model:pet-mad-latest.pt,device:cpu,non_conservative:True} </parameters>
+</ffdirect>
+<system>
+    <initialize nbeads="1">
+        <file mode="ase"> data/bmimcl.xyz </file>
+        <velocities mode="thermal" units="kelvin"> 400.0 </velocities>
+    </initialize>
+    <forces>
+        <force forcefield="nocons">
+        </force>
+    </forces>
+
+    <motion mode="dynamics">
+    	<dynamics mode="nve">
+        	<timestep units="femtosecond"> 0.5 </timestep>
+        </dynamics>
+    </motion>
+
+</system>
+</simulation>

examples/pet-mad-nc/data/input-nve.xml

@@ -0,0 +1,36 @@
+<simulation verbosity="high">
+<output prefix="nve-c">
+    <properties stride="8" filename="out">
+		[step, time{picosecond}, conserved{electronvolt}, temperature{kelvin},
+        kinetic_md{electronvolt}, potential{electronvolt}, 
+        pot_component(0){electronvolt}
+		]
+    </properties>
+    <trajectory filename="pos" stride="16" format="ase"> positions </trajectory>
+    <trajectory filename="forces_c" stride="16" format="ase"> forces_component(0) </trajectory>
+    <checkpoint stride="1000"/>
+</output>
+<total_steps>32</total_steps>
+<prng><seed>12345</seed></prng>
+<ffdirect  name='cons' pbc="false">
+    <pes>metatensor</pes>
+    <parameters>{template:data/bmimcl.xyz,model:pet-mad-latest.pt,device:cpu,non_conservative:False} </parameters>
+</ffdirect>
+<system>
+    <initialize nbeads="1">
+        <file mode="ase"> data/bmimcl.xyz </file>
+        <velocities mode="thermal" units="kelvin"> 400.0 </velocities>
+    </initialize>
+    <forces>
+        <force forcefield="cons">
+        </force>
+    </forces>
+
+    <motion mode="dynamics">
+    	<dynamics mode="nve">
+        	<timestep units="femtosecond"> 0.5 </timestep>
+        </dynamics>
+    </motion>
+
+</system>
+</simulation>

examples/pet-mad-nc/environment.yml

@@ -0,0 +1,13 @@
+channels:
+  - metatensor
+  - conda-forge
+dependencies:
+  - python=3.12
+  - pip
+  - pip:
+    - ase>=3.23
+    - pet-mad>=1.1.0rc4,<2.0  
+    - ipi>=3.1.4,<4.0
+    - chemiscope>=0.8.5,<0.9
+    - matplotlib>=3.10,<4.0
+    - vesin[torch]>=0.3.2,<0.4