Merge branch 'langevin_integrator' of github.com:cbc-univie/transformato into langevin_integrator

Author: loeflerm

.github/workflows/CI.yaml

@@ -47,7 +47,7 @@ jobs:
           #  miniforge-variant: Mambaforge-pypy3
 
     steps:
-    - uses: actions/[email protected].1
+    - uses: actions/[email protected].6
 
     - name: Additional info about the build
       shell: bash
@@ -61,7 +61,7 @@ jobs:
 
     - name: Make Cache (no worflow_dispatch)
       if: ${{ github.event_name != 'workflow_dispatch' }}
-      uses: actions/cache@v3.3.2
+      uses: actions/cache@v4.0.2
       with:
         path: ~/conda_pkgs_dir # ${{ matrix.prefix }}
         # Increase the last number (0) to reset cache manually
@@ -70,15 +70,15 @@ jobs:
 
     - name: Make Cache (worflow_dispatch)
       if: ${{ github.event_name == 'workflow_dispatch' }}
-      uses: actions/cache@v3.3.2
+      uses: actions/cache@v4.0.2
       with:
         path: ~/conda_pkgs_dir # ${{ matrix.prefix }}
         key: ${{ matrix.label }}-conda-${{ hashFiles('devtools/conda-envs/fep_env.yaml') }}-${{ env.DATE }}-${{ inputs.CACHE_NUMBER }}
       id: cache2
 
 
     # More info on options: https://github.com/conda-incubator/setup-miniconda
-    - uses: conda-incubator/[email protected].1
+    - uses: conda-incubator/[email protected].4
       with:
         python-version: ${{ matrix.python-version }}
         condarc-file: ${{ matrix.condarc-file }}
@@ -122,7 +122,7 @@ jobs:
         pytest -v --cov=transformato --cov-report=xml --color=yes transformato/tests/
 
     - name: CodeCov
-      uses: codecov/codecov-action@v3.1.4
+      uses: codecov/codecov-action@v4.4.1
       with:
         file: ./coverage.xml
         flags: unittests

devtools/conda-envs/fep_env.yaml

@@ -5,7 +5,7 @@ channels:
 dependencies:
   # Base depends
   - openmm
-  - versioneer
+  - python<3.12
   - openmmtools
   - numpy
   - ipython

transformato/bin/drude_openmm_run.py

@@ -94,7 +94,7 @@
     10 / picosecond,
     1 * kelvin,
     200 / picosecond,
-    0.0005 * picoseconds,
+    0.0001 * picoseconds,
 )
 
 integrator.setMaxDrudeDistance(0.2 * angstroms)
@@ -154,8 +154,8 @@
 
 # Energy minimization
 if inputs.mini_nstep > 0:
-    print("\nEnergy minimization: %s steps" % inputs.mini_nstep)
-    simulation.minimizeEnergy(maxIterations=inputs.mini_nstep)
+    print("\nEnergy minimization:")
+    simulation.minimizeEnergy()
     print(simulation.context.getState(getEnergy=True).getPotentialEnergy())
 
 # Generate initial velocities
@@ -165,6 +165,29 @@
         simulation.context.setVelocitiesToTemperature(inputs.gen_temp, inputs.gen_seed)
     else:
         simulation.context.setVelocitiesToTemperature(inputs.gen_temp)
+        
+## Do some additional pre-equilibration when using Drude particles
+print("Doing a first equilibration run")
+simulation.step(100_000)
+
+print("Doing a second equilibration run")
+simulation.integrator.setStepSize(0.0002 * picoseconds)
+simulation.context.reinitialize(preserveState=True)
+simulation.step(100_000)
+
+print("Doing a third equilibration run")
+simulation.integrator.setStepSize(0.0003 * picoseconds)
+simulation.context.reinitialize(preserveState=True)
+simulation.step(100_000)
+
+print("Doing a fourth equilibration run")
+simulation.integrator.setStepSize(0.0004 * picoseconds)
+simulation.context.reinitialize(preserveState=True)
+simulation.step(100_000)
+
+print("Starting the actual simulation")
+simulation.integrator.setStepSize(0.0005 * picoseconds)
+simulation.context.reinitialize(preserveState=True)
 
 # Production
 print("\nMD run: %s steps" % inputs.nstep)