Merge remote-tracking branch 'exscientia/devel' into merge_exs_devel

lohedges · lohedges · commit 0e9c35aeb1e2 · 2023-02-03T10:06:13.000Z
diff --git a/python/BioSimSpace/Process/_gromacs.py b/python/BioSimSpace/Process/_gromacs.py
@@ -249,15 +249,11 @@ def _setup(self):
 
         # GRO87 file.
         file = _os.path.splitext(self._gro_file)[0]
-        _IO.saveMolecules(
-            file, system, "gro87", property_map=self._property_map
-        )
+        _IO.saveMolecules(file, system, "gro87", property_map=self._property_map)
 
         # TOP file.
         file = _os.path.splitext(self._top_file)[0]
-        _IO.saveMolecules(
-            file, system, "grotop", property_map=self._property_map
-        )
+        _IO.saveMolecules(file, system, "grotop", property_map=self._property_map)
 
         # Create the binary input file name.
         self._tpr_file = "%s/%s.tpr" % (self._work_dir, self._name)
diff --git a/python/BioSimSpace/Process/_namd.py b/python/BioSimSpace/Process/_namd.py
@@ -173,9 +173,7 @@ def _setup(self):
         # PSF and parameter files.
         try:
             file = _os.path.splitext(self._psf_file)[0]
-            _IO.saveMolecules(
-                file, system, "psf", property_map=self._property_map
-            )
+            _IO.saveMolecules(file, system, "psf", property_map=self._property_map)
         except Exception as e:
             msg = "Failed to write system to 'CHARMMPSF' format."
             if _isVerbose():
diff --git a/python/BioSimSpace/Process/_openmm.py b/python/BioSimSpace/Process/_openmm.py
@@ -240,9 +240,7 @@ def _setup(self):
         # RST file (coordinates).
         try:
             file = _os.path.splitext(self._rst_file)[0]
-            _IO.saveMolecules(
-                file, system, "rst7", property_map=self._property_map
-            )
+            _IO.saveMolecules(file, system, "rst7", property_map=self._property_map)
         except Exception as e:
             msg = "Failed to write system to 'RST7' format."
             if _isVerbose():
@@ -253,9 +251,7 @@ def _setup(self):
         # PRM file (topology).
         try:
             file = _os.path.splitext(self._top_file)[0]
-            _IO.saveMolecules(
-                file, system, "prm7", property_map=self._property_map
-            )
+            _IO.saveMolecules(file, system, "prm7", property_map=self._property_map)
         except Exception as e:
             msg = "Failed to write system to 'PRM7' format."
             if _isVerbose():
diff --git a/python/BioSimSpace/Process/_somd.py b/python/BioSimSpace/Process/_somd.py
@@ -318,9 +318,7 @@ def _setup(self):
         # RST file (coordinates).
         try:
             file = _os.path.splitext(self._rst_file)[0]
-            _IO.saveMolecules(
-                file, system, "rst7", property_map=self._property_map
-            )
+            _IO.saveMolecules(file, system, "rst7", property_map=self._property_map)
         except Exception as e:
             msg = "Failed to write system to 'RST7' format."
             if _isVerbose():
@@ -330,9 +328,7 @@ def _setup(self):
 
         # PRM file (topology).
         try:
-            _IO.saveMolecules(
-                file, system, "prm7", property_map=self._property_map
-            )
+            _IO.saveMolecules(file, system, "prm7", property_map=self._property_map)
         except Exception as e:
             msg = "Failed to write system to 'PRM7' format."
             if _isVerbose():
diff --git a/python/BioSimSpace/Sandpit/Exscientia/Process/_amber.py b/python/BioSimSpace/Sandpit/Exscientia/Process/_amber.py
@@ -369,9 +369,7 @@ def _write_system(self, system, coord_file=None, topol_file=None, ref_file=None)
         if coord_file is not None:
             try:
                 file = _os.path.splitext(coord_file)[0]
-                _IO.saveMolecules(
-                    file, system, "rst7", property_map=self._property_map
-                )
+                _IO.saveMolecules(file, system, "rst7", property_map=self._property_map)
             except Exception as e:
                 msg = "Failed to write system to 'RST7' format."
                 if _isVerbose():
@@ -383,9 +381,7 @@ def _write_system(self, system, coord_file=None, topol_file=None, ref_file=None)
         if ref_file is not None:
             try:
                 file = _os.path.splitext(ref_file)[0]
-                _IO.saveMolecules(
-                    file, system, "rst7", property_map=self._property_map
-                )
+                _IO.saveMolecules(file, system, "rst7", property_map=self._property_map)
             except Exception as e:
                 msg = "Failed to write system to 'RST7' format."
                 if _isVerbose():
@@ -397,9 +393,7 @@ def _write_system(self, system, coord_file=None, topol_file=None, ref_file=None)
         if topol_file is not None:
             try:
                 file = _os.path.splitext(topol_file)[0]
-                _IO.saveMolecules(
-                    file, system, "prm7", property_map=self._property_map
-                )
+                _IO.saveMolecules(file, system, "prm7", property_map=self._property_map)
             except Exception as e:
                 msg = "Failed to write system to 'PRM7' format."
                 if _isVerbose():
diff --git a/python/BioSimSpace/Sandpit/Exscientia/Process/_gromacs.py b/python/BioSimSpace/Sandpit/Exscientia/Process/_gromacs.py
@@ -334,23 +334,17 @@ def _write_system(self, system, coord_file=None, topol_file=None, ref_file=None)
         # GRO87 coordinate files.
         if coord_file is not None:
             file = _os.path.splitext(coord_file)[0]
-            _IO.saveMolecules(
-                file, system, "gro87", property_map=self._property_map
-            )
+            _IO.saveMolecules(file, system, "gro87", property_map=self._property_map)
 
         # GRO87 reference files.
         if ref_file is not None:
             file = _os.path.splitext(ref_file)[0]
-            _IO.saveMolecules(
-                file, system, "gro87", property_map=self._property_map
-            )
+            _IO.saveMolecules(file, system, "gro87", property_map=self._property_map)
 
         # TOP file.
         if topol_file is not None:
             file = _os.path.splitext(topol_file)[0]
-            _IO.saveMolecules(
-                file, system, "grotop", property_map=self._property_map
-            )
+            _IO.saveMolecules(file, system, "grotop", property_map=self._property_map)
 
             # Write the restraint to the topology file
             if self._restraint:
diff --git a/python/BioSimSpace/Sandpit/Exscientia/Process/_namd.py b/python/BioSimSpace/Sandpit/Exscientia/Process/_namd.py
@@ -168,9 +168,7 @@ def _setup(self):
         # PSF and parameter files.
         try:
             file = _os.path.splitext(self._psf_file)[0]
-            _IO.saveMolecules(
-                file, system, "psf", property_map=self._property_map
-            )
+            _IO.saveMolecules(file, system, "psf", property_map=self._property_map)
         except Exception as e:
             msg = "Failed to write system to 'CHARMMPSF' format."
             if _isVerbose():
diff --git a/python/BioSimSpace/Sandpit/Exscientia/Process/_openmm.py b/python/BioSimSpace/Sandpit/Exscientia/Process/_openmm.py
@@ -235,9 +235,7 @@ def _setup(self):
         # RST file (coordinates).
         try:
             file = _os.path.splitext(self._rst_file)[0]
-            _IO.saveMolecules(
-                file, system, "rst7", property_map=self._property_map
-            )
+            _IO.saveMolecules(file, system, "rst7", property_map=self._property_map)
         except Exception as e:
             msg = "Failed to write system to 'RST7' format."
             if _isVerbose():
@@ -248,9 +246,7 @@ def _setup(self):
         # PRM file (topology).
         try:
             file = _os.path.splitext(self._top_file)[0]
-            _IO.saveMolecules(
-                file, system, "prm7", property_map=self._property_map
-            )
+            _IO.saveMolecules(file, system, "prm7", property_map=self._property_map)
         except Exception as e:
             msg = "Failed to write system to 'PRM7' format."
             if _isVerbose():
diff --git a/python/BioSimSpace/Sandpit/Exscientia/Process/_somd.py b/python/BioSimSpace/Sandpit/Exscientia/Process/_somd.py
@@ -310,9 +310,7 @@ def _setup(self):
         # RST file (coordinates).
         try:
             file = _os.path.splitext(self._rst_file)[0]
-            _IO.saveMolecules(
-                file, system, "rst7", property_map=self._property_map
-            )
+            _IO.saveMolecules(file, system, "rst7", property_map=self._property_map)
         except Exception as e:
             msg = "Failed to write system to 'RST7' format."
             if _isVerbose():
@@ -323,9 +321,7 @@ def _setup(self):
         # PRM file (topology).
         try:
             file = _os.path.splitext(self._top_file)[0]
-            _IO.saveMolecules(
-                file, system, "prm7", property_map=self._property_map
-            )
+            _IO.saveMolecules(file, system, "prm7", property_map=self._property_map)
         except Exception as e:
             msg = "Failed to write system to 'PRM7' format."
             if _isVerbose():
diff --git a/python/BioSimSpace/Sandpit/Exscientia/Protocol/_config.py b/python/BioSimSpace/Sandpit/Exscientia/Protocol/_config.py
@@ -1,6 +1,5 @@
 import math as _math
 import warnings as _warnings
-
 from sire.legacy import Units as _SireUnits
 
 from .. import Protocol as _Protocol
@@ -294,7 +293,9 @@ def generateAmberConfig(self, extra_options=None, extra_lines=None):
         # Temperature control.
         if not isinstance(self.protocol, _Protocol.Minimisation):
             protocol_dict["ntt"] = 3  # Langevin dynamics.
-            protocol_dict["gamma_ln"] = 2  # Collision frequency (ps).
+            protocol_dict["gamma_ln"] = "{:.5f}".format(
+                1 / self.protocol.getTauT().picoseconds().value()
+            )  # Collision frequency (ps^-1).
             if isinstance(self.protocol, _Protocol.Equilibration):
                 temp0 = self.protocol.getStartTemperature().kelvin().value()
                 temp1 = self.protocol.getEndTemperature().kelvin().value()
@@ -426,9 +427,11 @@ def generateGromacsConfig(self, extra_options=None, extra_lines=None):
                 # Don't use barostat for vacuum simulations.
                 if self._has_box and self._has_water:
                     protocol_dict["pcoupl"] = "c-rescale"  # Barostat type.
-                    protocol_dict[
-                        "tau-p"
-                    ] = 1  # 1ps time constant for pressure coupling.
+                    # Do the MC move every 100 steps to be the same as AMBER.
+                    protocol_dict["nstpcouple"] = 100
+                    # 4ps time constant for pressure coupling.
+                    # As the tau-p has to be 10 times larger than nstpcouple * dt (4 fs)
+                    protocol_dict["tau-p"] = 4
                     protocol_dict[
                         "ref-p"
                     ] = f"{self.protocol.getPressure().bar().value():.5f}"  # Pressure in bar.
@@ -447,7 +450,9 @@ def generateGromacsConfig(self, extra_options=None, extra_lines=None):
             protocol_dict[
                 "tc-grps"
             ] = "system"  # A single temperature group for the entire system.
-            protocol_dict["tau-t"] = 2  # Collision frequency (ps).
+            protocol_dict["tau-t"] = "{:.5f}".format(
+                self.protocol.getTauT().picoseconds().value()
+            )  # Collision frequency (ps).
 
             if isinstance(self.protocol, _Protocol.Equilibration):
                 if self.protocol.isConstantTemp():
diff --git a/python/BioSimSpace/Sandpit/Exscientia/Protocol/_equilibration.py b/python/BioSimSpace/Sandpit/Exscientia/Protocol/_equilibration.py
@@ -50,6 +50,7 @@ def __init__(
         temperature_end=_Types.Temperature(300, "kelvin"),
         temperature=None,
         pressure=None,
+        tau_t=_Types.Time(1, "picosecond"),
         report_interval=200,
         restart_interval=1000,
         restraint=None,
@@ -82,6 +83,9 @@ def __init__(
             The pressure. If None, then the simulation is run using the NVT ensemble.
             If set to a value, then the simulation is run using the NPT ensemble.
 
+        tau_t : :class:`Time <BioSimSpace.Types.Time>`
+            Time constant for thermostat coupling.
+
         report_interval : int
             The frequency at which statistics are recorded. (In integration steps.)
 
@@ -150,6 +154,9 @@ def __init__(
         else:
             self._pressure = None
 
+        # Set the time constant for the thermostat
+        self.setTauT(tau_t)
+
         # Set the report interval.
         self.setReportInterval(report_interval)
 
@@ -306,6 +313,33 @@ def setEndTemperature(self, temperature):
                 "'temperature_end' must be of type 'BioSimSpace.Types.Temperature'"
             )
 
+    def getTauT(self):
+        """
+        Return the time constant for the thermostat.
+
+        Returns
+        -------
+
+        runtime : :class:`Time <BioSimSpace.Types.Time>`
+            The time constant for the thermostat.
+        """
+        return self._tau_t
+
+    def setTauT(self, tau_t):
+        """
+        Set the time constant for the thermostat.
+
+        Parameters
+        ----------
+
+        tau_t : :class:`Time <BioSimSpace.Types.Time>`
+            The time constant for the thermostat.
+        """
+        if isinstance(tau_t, _Types.Time):
+            self._tau_t = tau_t
+        else:
+            raise TypeError("'tau_t' must be of type 'BioSimSpace.Types.Time'")
+
     def getPressure(self):
         """
         Return the pressure.
diff --git a/python/BioSimSpace/Sandpit/Exscientia/Protocol/_free_energy.py b/python/BioSimSpace/Sandpit/Exscientia/Protocol/_free_energy.py
@@ -26,13 +26,9 @@
 
 __all__ = ["FreeEnergy"]
 
-import math as _math
-import warnings as _warnings
-
-from .. import Types as _Types
-
 from ._free_energy_mixin import _FreeEnergyMixin
 from ._production import Production as _Production
+from .. import Types as _Types
 from .. import Units as _Units
 
 
@@ -50,6 +46,7 @@ def __init__(
         runtime=_Types.Time(4, "nanosecond"),
         temperature=_Types.Temperature(300, "kelvin"),
         pressure=_Types.Pressure(1, "atmosphere"),
+        tau_t=_Types.Time(1, "picosecond"),
         report_interval=200,
         restart_interval=1000,
         first_step=0,
@@ -90,6 +87,9 @@ def __init__(
         pressure : :class:`Pressure <BioSimSpace.Types.Pressure>`
             The pressure. Pass pressure=None to use the NVT ensemble.
 
+        tau_t : :class:`Time <BioSimSpace.Types.Time>`
+            Time constant for thermostat coupling.
+
         report_interval : int
             The frequency at which statistics are recorded. (In integration steps.)
 
@@ -143,6 +143,7 @@ def __init__(
             runtime=runtime,
             temperature=temperature,
             pressure=pressure,
+            tau_t=tau_t,
             report_interval=report_interval,
             restart_interval=restart_interval,
             first_step=first_step,
diff --git a/python/BioSimSpace/Sandpit/Exscientia/Protocol/_free_energy_equilibration.py b/python/BioSimSpace/Sandpit/Exscientia/Protocol/_free_energy_equilibration.py
@@ -23,6 +23,7 @@ def __init__(
         temperature_end=_Types.Temperature(300, "kelvin"),
         temperature=None,
         pressure=None,
+        tau_t=_Types.Time(1, "picosecond"),
         report_interval=200,
         restart_interval=1000,
         restraint=None,
@@ -70,6 +71,9 @@ def __init__(
             The pressure. If this argument is omitted then the simulation
             is run using the NVT ensemble.
 
+        tau_t : :class:`Time <BioSimSpace.Types.Time>`
+            Time constant for thermostat coupling.
+
         report_interval : int
             The frequency at which statistics are recorded. (In integration steps.)
 
@@ -123,6 +127,7 @@ def __init__(
             temperature_end=temperature_end,
             temperature=temperature,
             pressure=pressure,
+            tau_t=tau_t,
             report_interval=report_interval,
             restart_interval=restart_interval,
             restraint=restraint,
diff --git a/python/BioSimSpace/Sandpit/Exscientia/Protocol/_production.py b/python/BioSimSpace/Sandpit/Exscientia/Protocol/_production.py
diff --git a/test/Sandpit/Exscientia/Protocol/test_config.py b/test/Sandpit/Exscientia/Protocol/test_config.py
