Merge pull request #3 from chemle/feature_sire

Add Sire environment file and OpenMM integration documentation

MANIFEST.in

@@ -1 +1 @@
-include mlmm/*.mat
+include emle/*.mat

README.md

@@ -306,6 +306,30 @@ similar to that shown below. The columns specify the current step, the current
         50        1.000000000000     -495.725952148438       -0.020683377981     -495.725952148438
 ```
 
+## OpenMM integration
+
+We provide an interface between `emle-engine` and [OpenMM](https://openmm.org) via the
+[Sire](https://sire.openbiosim.org/) molecular simulation framework. This allows QM/MM simulations
+to be run with OpenMM using EMLE for the embedding model. This provides improved
+performance and flexibility in comparison to the `sander` interface, although
+the implementation should currently be treated as being _experimental_.
+
+To use, first create an `emle-sire` conda environment:
+
+```sh
+conda env create -f environment_sire.yaml
+conda activate emle-sire
+```
+
+Next install `emle-engine` into the environment:
+
+```sh
+python setup.py install
+```
+
+For instructions on how to use the `emle-sire` interface, see the tutorial
+documentation [here](https://github.com/OpenBioSim/sire/blob/feature_emle/doc/source/tutorial/part07/01_qmmm.rst).
+
 ## Issues
 
 The [DeePMD-kit](https://docs.deepmodeling.com/projects/deepmd/en/master/index.html) conda package pulls in a version of MPI which may cause

bin/emle-server

@@ -518,11 +518,11 @@ except:
 # Import the EMLE calculator here so that we avoid the import overhead when the
 # script is called to check if an existing server is running, e.g. when called
 # as a background process by the orca executable.
-from emle.emle import EMLECalculator
+from emle.calculator import EMLECalculator
 
 # Initialise the EMLE calculator.
 print("Initialising EMLE calculator...")
-mle_calculator = EMLECalculator(**args)
+emle_calculator = EMLECalculator(**args)
 
 while True:
     print("Waiting for a connection...")
@@ -535,7 +535,7 @@ while True:
                 # Try to run the EMLE calculation.
                 print("Running EMLE calculation...")
                 try:
-                    mle_calculator.run(path=path)
+                    emle_calculator.run(path=path)
                     msg = "7:emlefin"
                     print("Finished!")
                 except Exception as e:
@@ -549,7 +549,7 @@ while True:
                 # Try to update the interpolation lambda parameter.
                 print("Updating interpolation lambda...")
                 try:
-                    mle_calculator.set_lambda_interpolate(float(path))
+                    emle_calculator.set_lambda_interpolate(float(path))
                     msg = "13:emlelambdaset"
                     print("Lambda set!")
                 except Exception as e:

emle/sander_calculator.py

@@ -87,7 +87,7 @@ def calculate(
         # Update the positions.
         sander.set_positions(positions)
 
-        from .emle import KCAL_MOL_TO_HARTREE, BOHR_TO_ANGSTROM
+        from .calculator import KCAL_MOL_TO_HARTREE, BOHR_TO_ANGSTROM
 
         # Compute the energy and forces.
         energy, forces = sander.energy_forces()

environment_sire.yaml

@@ -0,0 +1,22 @@
+name: emle-sire
+
+channels:
+  - conda-forge
+  - openbiosim/label/emle
+
+dependencies:
+  - ambertools
+  - ase
+  - compilers
+  - deepmd-kit
+  - eigen
+  - openmm >= 8.1
+  - pip
+  - pybind11
+  - pytorch
+  - python < 3.11
+  - sire
+  - torchani
+  - xtb-python
+  - pip:
+    - git+https://github.com/lab-cosmo/librascal.git