Revert to 8a827e6

cbc-univie · Aug 22, 2024 · 1e1f3e7 · 1e1f3e7
1 parent 6dab962
commit 1e1f3e7
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Showing 4 changed files with 69 additions and 100 deletions.
diff --git a/transformato/bin/drude_openmm_run.py b/transformato/bin/drude_openmm_run.py
@@ -20,7 +20,6 @@
 parser = argparse.ArgumentParser()
 parser.add_argument("-odcd", metavar="DCDFILE", dest="odcd")
 parser.add_argument("-env", metavar="ENVIRONMENT", dest="env")
-parser.add_argument("-sim", metavar="SIMULATION", dest="sim", default=True)
 args = parser.parse_args()
 
 # Load parameters
@@ -105,7 +104,6 @@
     print("Drude Hard Wall set to {}".format(integrator.getMaxDrudeDistance()))
 
 # TEST: HELLO 2!
-# another test
 
 # Set platform
 platform = Platform.getPlatformByName("CUDA")
@@ -154,76 +152,73 @@
 print("\nInitial system energy")
 print(simulation.context.getState(getEnergy=True).getPotentialEnergy())
 
-
-if args.sim.lower() == 'true':
-
-    # Drude VirtualSites
-    simulation.context.computeVirtualSites()
-
-    # Energy minimization
-    if inputs.mini_nstep > 0:
-        print("\nEnergy minimization:")
-        simulation.minimizeEnergy()
-        print(simulation.context.getState(getEnergy=True).getPotentialEnergy())
-
-    # Generate initial velocities
-    if inputs.gen_vel == "yes":
-        print("\nGenerate initial velocities")
-        if inputs.gen_seed:
-            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 * unit.picoseconds)
-    simulation.context.reinitialize(preserveState=True)
-    simulation.step(100_000)
-
-    print("Doing a third equilibration run")
-    simulation.integrator.setStepSize(0.0003 * unit.picoseconds)
-    simulation.context.reinitialize(preserveState=True)
-    simulation.step(100_000)
-
-    print("Doing a fourth equilibration run")
-    simulation.integrator.setStepSize(0.0004 * unit.picoseconds)
-    simulation.context.reinitialize(preserveState=True)
-    simulation.step(100_000)
-
-    print("Starting the actual simulation")
-    simulation.integrator.setStepSize(inputs.dt * unit.picoseconds)
-    simulation.context.reinitialize(preserveState=True)
-
-    # Production
-    print("\nMD run: %s steps" % inputs.nstep)
-    simulation.reporters.append(DCDReporter(args.odcd, inputs.nstdcd))
-    simulation.reporters.append(
-        StateDataReporter(
-            sys.stdout,
-            inputs.nstout,
-            step=True,
-            time=True,
-            potentialEnergy=True,
-            temperature=True,
-            progress=True,
-            remainingTime=True,
-            speed=True,
-            totalSteps=inputs.nstep,
-            separator="\t",
-        )
+# Drude VirtualSites
+simulation.context.computeVirtualSites()
+
+# Energy minimization
+if inputs.mini_nstep > 0:
+    print("\nEnergy minimization:")
+    simulation.minimizeEnergy()
+    print(simulation.context.getState(getEnergy=True).getPotentialEnergy())
+
+# Generate initial velocities
+if inputs.gen_vel == "yes":
+    print("\nGenerate initial velocities")
+    if inputs.gen_seed:
+        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 * unit.picoseconds)
+simulation.context.reinitialize(preserveState=True)
+simulation.step(100_000)
+
+print("Doing a third equilibration run")
+simulation.integrator.setStepSize(0.0003 * unit.picoseconds)
+simulation.context.reinitialize(preserveState=True)
+simulation.step(100_000)
+
+print("Doing a fourth equilibration run")
+simulation.integrator.setStepSize(0.0004 * unit.picoseconds)
+simulation.context.reinitialize(preserveState=True)
+simulation.step(100_000)
+
+print("Starting the actual simulation")
+simulation.integrator.setStepSize(inputs.dt * unit.picoseconds)
+simulation.context.reinitialize(preserveState=True)
+
+# Production
+print("\nMD run: %s steps" % inputs.nstep)
+simulation.reporters.append(DCDReporter(args.odcd, inputs.nstdcd))
+simulation.reporters.append(
+    StateDataReporter(
+        sys.stdout,
+        inputs.nstout,
+        step=True,
+        time=True,
+        potentialEnergy=True,
+        temperature=True,
+        progress=True,
+        remainingTime=True,
+        speed=True,
+        totalSteps=inputs.nstep,
+        separator="\t",
     )
+)
 
-    simulation.step(inputs.nstep)
-
-    # needed for later analysis
-    file_name = f"lig_in_{env}"
-    state = simulation.context.getState(getPositions=True, getVelocities=True)
-    with open(file_name + ".rst", "w") as f:
-        f.write(XmlSerializer.serialize(state))
-    with open(file_name + "_integrator.xml", "w") as outfile:
-        outfile.write(XmlSerializer.serialize(integrator))
-    with open(file_name + "_system.xml", "w") as outfile:
-        outfile.write(XmlSerializer.serialize(system))
+simulation.step(inputs.nstep)
+
+# needed for later analysis
+file_name = f"lig_in_{env}"
+state = simulation.context.getState(getPositions=True, getVelocities=True)
+with open(file_name + ".rst", "w") as f:
+    f.write(XmlSerializer.serialize(state))
+with open(file_name + "_integrator.xml", "w") as outfile:
+    outfile.write(XmlSerializer.serialize(integrator))
+with open(file_name + "_system.xml", "w") as outfile:
+    outfile.write(XmlSerializer.serialize(system))
diff --git a/transformato/bin/init_energies.sh b/transformato/bin/init_energies.sh
diff --git a/transformato/bin/simulation-rsfe.sh b/transformato/bin/simulation-rsfe.sh
@@ -12,7 +12,7 @@ hostname
 istep=lig_in_vacuum
 python openmm_run.py -env vacuum -odcd ${istep}.dcd &> vacuum_out.log
 
-# test
+
 
 istep=lig_in_waterbox
 python openmm_run.py -env waterbox -odcd ${istep}.dcd &> waterbox_out.log
diff --git a/transformato/state.py b/transformato/state.py
@@ -488,17 +488,6 @@ def _copy_omm_files(self, intermediate_state_file_path: str):
             shutil.copyfile(
                 omm_simulation_submit_script_source, omm_simulation_submit_script_target
             )
-            omm_init_energies_submit_script_source = (
-                f"{self.configuration['bin_dir']}/init_energies.sh"
-            )
-            omm_init_energies_submit_script_target = (
-                f"{intermediate_state_file_path}/init_energies.sh"
-            )
-            shutil.copyfile(
-                omm_init_energies_submit_script_source,
-                omm_init_energies_submit_script_target,
-            )
-            self._write_workload_preamble(omm_init_energies_submit_script_target)
 
         elif self.configuration["simulation"]["free-energy-type"] == "rbfe":
             # parse omm simulation paramter
@@ -524,7 +513,6 @@ def _copy_omm_files(self, intermediate_state_file_path: str):
 
         if self.multiple_runs:
             self._modify_submit_script(omm_simulation_submit_script_target)
-            self._modify_submit_script(omm_init_energies_submit_script_target)
 
         # Prepend workload manager instructions
         self._write_workload_preamble(omm_simulation_submit_script_target)