External Lammps Library

To provide more flexiblity in terms of scheduling the Lammps Library, it would be great to allow the user to set the Lammps Library object.

Author: jan-janssen

calphy/alchemy.py

@@ -53,11 +53,11 @@ class Alchemy(cph.Phase):
 
     """
 
-    def __init__(self, calculation=None, simfolder=None, log_to_screen=False):
+    def __init__(self, calculation=None, simfolder=None, log_to_screen=False, lmp=None):
 
         # call base class
         super().__init__(
-            calculation=calculation, simfolder=simfolder, log_to_screen=log_to_screen
+            calculation=calculation, simfolder=simfolder, log_to_screen=log_to_screen, lmp=lmp,
         )
 
     def run_averaging(self):
@@ -82,11 +82,12 @@ def run_averaging(self):
         At the end of the run, the averaged box dimensions are calculated.
         """
         lmp = ph.create_object(
-            self.cores,
-            self.simfolder,
-            self.calc.md.timestep,
-            self.calc.md.cmdargs,
-            self.calc.md.init_commands,
+            cores=self.cores,
+            directory=self.simfolder, 
+            timestep=self.calc.md.timestep, 
+            cmdargs=self.calc.md.cmdargs, 
+            init_commands=self.calc.md.init_commands, 
+            lmp=self._lmp,
         )
 
         lmp.command(f"pair_style {self.calc._pair_style_with_options[0]}")
@@ -156,11 +157,12 @@ def run_integration(self, iteration=1):
 
         # create lammps object
         lmp = ph.create_object(
-            self.cores,
-            self.simfolder,
-            self.calc.md.timestep,
-            self.calc.md.cmdargs,
-            self.calc.md.init_commands,
+            cores=self.cores,
+            directory=self.simfolder, 
+            timestep=self.calc.md.timestep, 
+            cmdargs=self.calc.md.cmdargs, 
+            init_commands=self.calc.md.init_commands, 
+            lmp=self._lmp,
         )
 
         # Adiabatic switching parameters.

calphy/helpers.py

@@ -49,7 +49,7 @@ def write(self, infile):
 
 
 def create_object(
-    cores, directory, timestep, cmdargs="", init_commands=(), script_mode=False
+    cores, directory, timestep, cmdargs="", init_commands=(), script_mode=False, lmp=None,
 ):
     """
     Create LAMMPS object
@@ -71,7 +71,7 @@ def create_object(
     """
     if script_mode:
         lmp = LammpsScript()
-    else:
+    elif lmp is None:
         if cmdargs == "":
             cmdargs = None
         elif isinstance(cmdargs, str):

calphy/liquid.py

@@ -49,13 +49,13 @@ class Liquid(cph.Phase):
 
     """
 
-    def __init__(self, calculation=None, simfolder=None, log_to_screen=False):
+    def __init__(self, calculation=None, simfolder=None, log_to_screen=False, lmp=None):
         """
         Set up class
         """
         # call base class
         super().__init__(
-            calculation=calculation, simfolder=simfolder, log_to_screen=log_to_screen
+            calculation=calculation, simfolder=simfolder, log_to_screen=log_to_screen, lmp=lmp,
         )
 
     def rattle_structure(self, lmp):
@@ -166,11 +166,12 @@ def run_averaging(self):
         """
         # create lammps object
         lmp = ph.create_object(
-            self.cores,
-            self.simfolder,
-            self.calc.md.timestep,
-            self.calc.md.cmdargs,
-            self.calc.md.init_commands,
+            cores=self.cores,
+            directory=self.simfolder, 
+            timestep=self.calc.md.timestep, 
+            cmdargs=self.calc.md.cmdargs, 
+            init_commands=self.calc.md.init_commands, 
+            lmp=self._lmp,
         )
 
         lmp.command(f"pair_style {self.calc._pair_style_with_options[0]}")
@@ -241,11 +242,12 @@ def run_integration(self, iteration=1):
         the lambda parameter. See algorithm 4 in publication.
         """
         lmp = ph.create_object(
-            self.cores,
-            self.simfolder,
-            self.calc.md.timestep,
-            self.calc.md.cmdargs,
-            self.calc.md.init_commands,
+            cores=self.cores,
+            directory=self.simfolder, 
+            timestep=self.calc.md.timestep, 
+            cmdargs=self.calc.md.cmdargs, 
+            init_commands=self.calc.md.init_commands, 
+            lmp=self._lmp,
         )
 
         # Adiabatic switching parameters.

calphy/phase.py

@@ -53,7 +53,7 @@ class Phase:
 
     """
 
-    def __init__(self, calculation=None, simfolder=None, log_to_screen=False):
+    def __init__(self, calculation=None, simfolder=None, log_to_screen=False, lmp=None):
 
         self.calc = copy.deepcopy(calculation)
 
@@ -225,6 +225,7 @@ def __init__(self, calculation=None, simfolder=None, log_to_screen=False):
             self.logger.info("pair_style or pair_coeff not provided")
             if self.calc.potential_file is not None:
                 self.logger.info("potential is being loaded from file instead")
+        self._lmp = lmp
 
     def __repr__(self):
         """
@@ -944,11 +945,13 @@ def reversible_scaling(self, iteration=1):
 
         # create lammps object
         lmp = ph.create_object(
-            self.cores,
-            self.simfolder,
-            self.calc.md.timestep,
-            self.calc.md.cmdargs,
-            self.calc.md.init_commands,
+            cores=self.cores,
+            directory=self.simfolder, 
+            timestep=self.calc.md.timestep, 
+            cmdargs=self.calc.md.cmdargs, 
+            init_commands=self.calc.md.init_commands, 
+            script_mode=False, 
+            lmp=self._lmp,
         )
 
         lmp.command("echo              log")
@@ -1327,11 +1330,13 @@ def temperature_scaling(self, iteration=1):
 
         # create lammps object
         lmp = ph.create_object(
-            self.cores,
-            self.simfolder,
-            self.calc.md.timestep,
-            self.calc.md.cmdargs,
-            self.calc.md.init_commands,
+            cores=self.cores,
+            directory=self.simfolder, 
+            timestep=self.calc.md.timestep, 
+            cmdargs=self.calc.md.cmdargs, 
+            init_commands=self.calc.md.init_commands, 
+            script_mode=False, 
+            lmp=self._lmp,
         )
 
         lmp.command("echo              log")
@@ -1473,11 +1478,13 @@ def pressure_scaling(self, iteration=1):
 
         # create lammps object
         lmp = ph.create_object(
-            self.cores,
-            self.simfolder,
-            self.calc.md.timestep,
-            self.calc.md.cmdargs,
-            self.calc.md.init_commands,
+            cores=self.cores,
+            directory=self.simfolder, 
+            timestep=self.calc.md.timestep, 
+            cmdargs=self.calc.md.cmdargs, 
+            init_commands=self.calc.md.init_commands, 
+            script_mode=False, 
+            lmp=self._lmp,
         )
 
         lmp.command("echo              log")

calphy/solid.py

@@ -51,11 +51,11 @@ class Solid(cph.Phase):
 
     """
 
-    def __init__(self, calculation=None, simfolder=None, log_to_screen=False):
+    def __init__(self, calculation=None, simfolder=None, log_to_screen=False, lmp=None):
 
         # call base class
         super().__init__(
-            calculation=calculation, simfolder=simfolder, log_to_screen=log_to_screen
+            calculation=calculation, simfolder=simfolder, log_to_screen=log_to_screen, lmp=lmp,
         )
 
     def run_spring_constant_convergence(self, lmp):
@@ -236,12 +236,13 @@ def run_interactive_averaging(self):
         """
 
         lmp = ph.create_object(
-            self.cores,
-            self.simfolder,
-            self.calc.md.timestep,
-            self.calc.md.cmdargs,
-            init_commands=self.calc.md.init_commands,
+            cores=self.cores,
+            directory=self.simfolder, 
+            timestep=self.calc.md.timestep, 
+            cmdargs=self.calc.md.cmdargs, 
+            init_commands=self.calc.md.init_commands, 
             script_mode=self.calc.script_mode,
+            lmp=self._lmp,
         )
 
         # set up potential
@@ -324,12 +325,13 @@ def run_minimal_averaging(self):
         At the end of the run, the averaged box dimensions are calculated.
         """
         lmp = ph.create_object(
-            self.cores,
-            self.simfolder,
-            self.calc.md.timestep,
-            self.calc.md.cmdargs,
-            init_commands=self.calc.md.init_commands,
+            cores=self.cores,
+            directory=self.simfolder, 
+            timestep=self.calc.md.timestep, 
+            cmdargs=self.calc.md.cmdargs, 
+            init_commands=self.calc.md.init_commands, 
             script_mode=self.calc.script_mode,
+            lmp=self._lmp,
         )
 
         # set up potential
@@ -407,12 +409,13 @@ def run_integration(self, iteration=1):
         the lambda parameter. See algorithm 4 in publication.
         """
         lmp = ph.create_object(
-            self.cores,
-            self.simfolder,
-            self.calc.md.timestep,
-            self.calc.md.cmdargs,
-            init_commands=self.calc.md.init_commands,
+            cores=self.cores,
+            directory=self.simfolder, 
+            timestep=self.calc.md.timestep, 
+            cmdargs=self.calc.md.cmdargs, 
+            init_commands=self.calc.md.init_commands, 
             script_mode=self.calc.script_mode,
+            lmp=self._lmp,
         )
 
         # set up potential