Merge pull request #69 from ICAMS/more_lammps_customisation

More lammps customisation

Author: srmnitc

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 1.2.6
+current_version = 1.2.7
 commit = True
 tag = True
 

calphy/__init__.py

@@ -4,7 +4,7 @@
 from calphy.alchemy import Alchemy
 from calphy.routines import MeltingTemp
 
-__version__ = "1.2.6"
+__version__ = "1.2.7"
 
 def addtest(a,b):
     return a+b

calphy/alchemy.py

@@ -75,7 +75,8 @@ def run_averaging(self):
         Fix lattice option is not implemented at present.
         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)
+        lmp = ph.create_object(self.cores, self.simfolder, self.calc.md.timestep, 
+            self.calc.md.cmdargs, self.calc.md.init_commands)
 
         #set up structure
         lmp = ph.create_structure(lmp, self.calc)
@@ -138,7 +139,8 @@ 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)
+        lmp = ph.create_object(self.cores, self.simfolder, self.calc.md.timestep, 
+            self.calc.md.cmdargs, self.calc.md.init_commands)
 
         # Adiabatic switching parameters.
         lmp.command("variable        li       equal   1.0")

calphy/helpers.py

@@ -33,7 +33,8 @@
 from pyscal.trajectory import Trajectory
 
 
-def create_object(cores, directory, timestep, cmdargs=None):
+def create_object(cores, directory, timestep, cmdargs=None, 
+    init_commands=None):
     """
     Create LAMMPS object
 
@@ -56,11 +57,29 @@ def create_object(cores, directory, timestep, cmdargs=None):
         mode="local", cores=cores, working_directory=directory, cmdargs=cmdargs
     )
 
-    lmp.units("metal")
-    lmp.boundary("p p p")
-    lmp.atom_style("atomic")
-    lmp.timestep(timestep)
-    lmp.command("box    tilt large")
+    commands = [["units", "metal"], 
+    ["boundary", "p p p"],
+    ["atom_style", "atomic"],
+    ["timestep", str(timestep)],
+    ["box", "tilt large"]]
+
+    if init_commands is not None:
+        #we need to replace some initial commands
+        for rc in init_commands:
+            #split the command
+            raw = rc.split()
+            for x in range(len(commands)):
+                if raw[0] == commands[x][0]:
+                    #we found a matching command
+                    commands[x] = [rc]
+                    break
+            else:
+                #its a new command, add it to the list
+                commands.append([rc])
+
+    for command in commands:
+        lmp.command(" ".join(command))
+
     return lmp
 
 
@@ -338,6 +357,7 @@ def reset_timestep(conf, file="current.data"):
         directory=os.path.dirname(file),
         timestep=0,
         cmdargs=None,
+        init_commands=None,
     )
     lmp = read_data(lmp, file)
     lmp = write_data(lmp, conf)

calphy/input.py

@@ -188,6 +188,7 @@ def __init__(self):
         self.md.thermostat_damping = 0.1
         self.md.barostat_damping = 0.1
         self.md.cmdargs = None
+        self.md.init_commands = None
 
         self.nose_hoover = InputTemplate()
         self.nose_hoover.thermostat_damping = 0.1

calphy/liquid.py

@@ -112,7 +112,8 @@ def run_averaging(self):
         At the end of the run, the averaged box dimensions are calculated. 
         """
         #create lammps object
-        lmp = ph.create_object(self.cores, self.simfolder, self.calc.md.timestep, self.calc.md.cmdargs)
+        lmp = ph.create_object(self.cores, self.simfolder, self.calc.md.timestep, 
+            self.calc.md.cmdargs, self.calc.md.init_commands)
 
         #set up structure
         lmp = ph.create_structure(lmp, self.calc, species=self.calc.n_elements+self.calc._ghost_element_count)
@@ -171,7 +172,8 @@ def run_integration(self, iteration=1):
         Run the integration routine where the initial and final systems are connected using
         the lambda parameter. See algorithm 4 in publication.
         """
-        lmp = ph.create_object(self.cores, self.simfolder, self.calc.md.timestep, self.calc.md.cmdargs)
+        lmp = ph.create_object(self.cores, self.simfolder, self.calc.md.timestep, 
+            self.calc.md.cmdargs, self.calc.md.init_commands)
 
         # Adiabatic switching parameters.
         lmp.command("variable        li       equal   1.0")

calphy/phase.py

@@ -671,7 +671,8 @@ def reversible_scaling(self, iteration=1):
         pf = lf*pi
 
         #create lammps object
-        lmp = ph.create_object(self.cores, self.simfolder, self.calc.md.timestep, self.calc.md.cmdargs)
+        lmp = ph.create_object(self.cores, self.simfolder, self.calc.md.timestep, 
+            self.calc.md.cmdargs, self.calc.md.init_commands)
 
         lmp.command("echo              log")
         lmp.command("variable          li equal %f"%li)
@@ -847,7 +848,8 @@ def temperature_scaling(self, iteration=1):
         pf = lf*p0
 
         #create lammps object
-        lmp = ph.create_object(self.cores, self.simfolder, self.calc.md.timestep, self.calc.md.cmdargs)
+        lmp = ph.create_object(self.cores, self.simfolder, self.calc.md.timestep, 
+            self.calc.md.cmdargs, self.calc.md.init_commands)
 
         lmp.command("echo              log")
         lmp.command("variable          li equal %f"%li)
@@ -932,7 +934,8 @@ def pressure_scaling(self, iteration=1):
         pf = self.calc._pressure_stop
 
         #create lammps object
-        lmp = ph.create_object(self.cores, self.simfolder, self.calc.md.timestep, self.calc.md.cmdargs)
+        lmp = ph.create_object(self.cores, self.simfolder, self.calc.md.timestep, 
+            self.calc.md.cmdargs, self.calc.md.init_commands)
 
         lmp.command("echo              log")
         lmp.command("variable          li equal %f"%li)

calphy/solid.py

@@ -136,7 +136,8 @@ def run_averaging(self):
         is calculated.
         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)
+        lmp = ph.create_object(self.cores, self.simfolder, self.calc.md.timestep, 
+            self.calc.md.cmdargs, self.calc.md.init_commands)
 
         #set up structure
         lmp = ph.create_structure(lmp, self.calc, species=self.calc.n_elements+self.calc._ghost_element_count)
@@ -206,7 +207,8 @@ def run_integration(self, iteration=1):
         Run the integration routine where the initial and final systems are connected using
         the lambda parameter. See algorithm 4 in publication.
         """
-        lmp = ph.create_object(self.cores, self.simfolder, self.calc.md.timestep, self.calc.md.cmdargs)
+        lmp = ph.create_object(self.cores, self.simfolder, self.calc.md.timestep, 
+            self.calc.md.cmdargs, self.calc.md.init_commands)
 
         #read in the conf file
         #conf = os.path.join(self.simfolder, "conf.equilibration.dump")

docs/source/inputfile.md

@@ -21,7 +21,7 @@ The inputfile is `yaml` formatted. In this section the possible keys in the inpu
 | `md` block | | | |
 | :------: | :------: | :------: | :------: |
 | [](timestep) | [](n_small_steps) | [](n_every_steps) | [](n_repeat_steps) |
-| [](n_cycles) | [](thermostat_damping) | [](barostat_damping) |
+| [](n_cycles) | [](thermostat_damping) | [](barostat_damping) | [](init_commands) |
 
 | `queue` block | | | |
 | :------: | :------: | :------: | :------: |
@@ -128,7 +128,7 @@ Calculation mode. A small description of the different modes are given below.
 - `pscale` calculates the free energy as a function of the pressure.
 
 ---
-
+self.calc.md.init_commands
 (temperature)=
 #### `temperature`  
 
@@ -542,6 +542,24 @@ n_cycles: 100
 
 Number of cycles to try converging the pressure of the system. If the pressure is not converged after `n_cycles`, an error will be raised. In each `n_cycle`, `n_small_steps` MD steps will be run.
 
+
+---
+
+(init_commands)=
+#### `init_commands`
+
+_type_: list of strings
+_default_: None
+_example_:
+```
+init_commands:
+  - timestep 0.002
+  - atom_style charge
+  - neighbor 0.6 bin
+```
+
+Provides the possibility to replace or add initial commands when the LAMMPS object is initialised. If the command is already used in calphy, for example `timestep` or `atom_style` they will be replaced. If it is a new command, it will be added. This commands receive higher priority than the ones that already exist. For examples if you provide `timestep: 0.002` in the `md` block, and `timestep 0.004` in `init_commands`, the timestep used would be 0.004.
+
 ---
 ---
 

examples/example_01/input.yaml

@@ -18,6 +18,9 @@ md:
   timestep: 0.001
   thermostat_damping: 0.1
   barostat_damping: 0.1
+  init_commands:
+     - timestep 0.002
+     - neighbor 0.6 bin
 
 queue:
   scheduler: local