Merge pull request #135 from ICAMS/allow_none_pressure_for_liquid

do not allow melting when lattice is fixed

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 1.3.8
+current_version = 1.3.9
 commit = True
 tag = True
 

calphy/__init__.py

@@ -4,7 +4,7 @@
 from calphy.alchemy import Alchemy
 from calphy.routines import MeltingTemp
 
-__version__ = "1.3.8"
+__version__ = "1.3.9"
 
 def addtest(a,b):
     return a+b

calphy/input.py

@@ -40,7 +40,7 @@
 from ase.io import read, write
 import shutil
 
-__version__ = "1.3.8"
+__version__ = "1.3.9"
 
 def read_report(folder):
     """
@@ -72,7 +72,12 @@ def _to_int(val):
     if np.isscalar(val):
         return int(val)
     else:
-        return [int(x) for x in val] 
+        return [int(x) for x in val]
+
+def _to_none(val):
+    if val in ['none', 'None',]:
+        return None 
+    return val
 
 def _to_float(val):
     if np.isscalar(val):
@@ -558,6 +563,8 @@ def _read_inputfile(file):
     for count, calc in enumerate(data['calculations']):
         calc['kernel'] = count
         calc['inputfile'] = file
+        if 'pressure' in calc.keys():
+            calc['pressure'] = _to_none(calc['pressure'])
         calculations.append(Calculation(**calc))
     return calculations
 

calphy/liquid.py

@@ -56,7 +56,12 @@ def __init__(self, calculation=None, simfolder=None, log_to_screen=False):
 
     def melt_structure(self, lmp):
         """
-        """        
+        """
+        if self.calc._fix_lattice and self.calc.melting_cycle:
+
+            raise ValueError("Cannot fix lattice and melt structure (set to False) at the same time")
+
+
         melted = False
 
         #this is the multiplier for thigh to try melting routines
@@ -136,11 +141,14 @@ def run_averaging(self):
         if self.calc.melting_cycle:
             self.melt_structure(lmp)
 
-        #now assign correct temperature and equilibrate
-        self.run_zero_pressure_equilibration(lmp)
+        if not self.calc._fix_lattice:
+            #now assign correct temperature and equilibrate
+            self.run_zero_pressure_equilibration(lmp)
 
-        #converge pressure
-        self.run_pressure_convergence(lmp)
+            #converge pressure
+            self.run_pressure_convergence(lmp)
+        else:
+            self.run_constrained_pressure_convergence(lmp)
 
         #check melted error
         self.dump_current_snapshot(lmp, "traj.equilibration_stage1.dat")

calphy/phase.py

@@ -622,6 +622,7 @@ def finalise_pressure(self,):
         self.lz = np.round(np.mean(lz[-ncount+1:]), decimals=3)
         self.volatom = volatom
         self.vol = self.lx*self.ly*self.lz
+        self.rho = self.natoms/(self.lx*self.ly*self.lz)
         self.logger.info("finalized vol/atom %f at pressure %f"%(self.volatom, mean))
         self.logger.info("Avg box dimensions x: %f, y: %f, z:%f"%(self.lx, self.ly, self.lz))
 

examples/example_03/\

@@ -0,0 +1,29 @@
+calculations:
+- element: Cu
+  lattice: fcc
+  lattice_constant: 3.61
+  melting_cycle: False
+  mass: 63.546
+  md:
+    timestep: 0.001
+  mode: ts
+  n_equilibration_steps: 10000
+  n_iterations: 1
+  n_switching_steps: 25000
+  pair_coeff: '* * ../potentials/Cu01.eam.alloy Cu'
+  pair_style: eam/alloy
+  pressure: None
+  npt: False
+  queue:
+    commands:
+    - conda activate calphy-dev
+    cores: 4
+    scheduler: local
+  reference_phase: liquid
+  repeat:
+  - 5
+  - 5
+  - 5
+  temperature:
+  - 1200.0
+  - 1400.0

examples/example_03/newtest/input_file.yaml

@@ -0,0 +1,81 @@
+calculations:
+- berendsen:
+    barostat_damping: 100.0
+    thermostat_damping: 100.0
+  composition_scaling:
+    output_chemical_composition: {}
+    restrictions: []
+  element:
+  - Cu
+  equilibration_control: berendsen
+  file_format: lammps-data
+  fix_potential_path: true
+  folder_prefix: null
+  inputfile: test.input.yaml
+  kernel: 0
+  lammps_executable: null
+  lattice: /mnt/c/Users/menon/Documents/repos/projects-calphy/calphy/examples/example_03/ts-fcc-solid-1200-0.0.data
+  lattice_constant: 3.61
+  mass:
+  - 63.546
+  md:
+    barostat_damping: 0.1
+    cmdargs: ''
+    init_commands: []
+    n_cycles: 100
+    n_every_steps: 10
+    n_repeat_steps: 10
+    n_small_steps: 10000
+    thermostat_damping: 0.1
+    timestep: 0.001
+  melting_cycle: true
+  melting_temperature:
+    attempts: 5
+    guess: null
+    step: 200
+  mode: ts
+  mpi_executable: null
+  n_elements: 1
+  n_equilibration_steps: 10000
+  n_iterations: 1
+  n_print_steps: 0
+  n_switching_steps: 25000
+  nose_hoover:
+    barostat_damping: 0.1
+    thermostat_damping: 0.1
+  npt: false
+  pair_coeff:
+  - '* * /mnt/c/Users/menon/Documents/repos/projects-calphy/calphy/examples/potentials/Cu01.eam.alloy
+    Cu'
+  pair_style:
+  - eam/alloy
+  potential_file: null
+  pressure: 0.0
+  queue:
+    commands:
+    - conda activate calphy-dev
+    cores: 4
+    jobname: calphy
+    memory: 3GB
+    modules: []
+    options: []
+    queuename: ''
+    scheduler: local
+    walltime: '23:59:00'
+  reference_phase: solid
+  repeat:
+  - 5
+  - 5
+  - 5
+  script_mode: false
+  spring_constants: null
+  temperature:
+  - 1200.0
+  - 1400.0
+  temperature_high: 0.0
+  tolerance:
+    lattice_constant: 0.0002
+    liquid_fraction: 0.05
+    pressure: 0.5
+    solid_fraction: 0.7
+    spring_constant: 0.1

examples/example_03/newtest/metadata.yaml

@@ -0,0 +1,10 @@
+files:
+  input_configuration.data: input atomic configuration
+  input_file.yml: input file
+  report.yaml: results after thermodynamic integration
+software:
+  doi: 10.5281/zenodo.10527452
+  name: calphy
+  repository: https://github.com/ICAMS/calphy
+  version: 1.3.7
+  webpage: https://calphy.org/

examples/example_03/newtest/report.yaml

@@ -0,0 +1,17 @@
+average:
+  density: 0.0820695985211261
+  spring_constant: '2.3863384417846154'
+  vol_atom: 12.184090419830538
+input:
+  concentration: '1.0'
+  element: Cu
+  lattice: fcc
+  pressure: 0.0
+  temperature: 1200
+results:
+  error: 0.0
+  free_energy: -4.06638985668307
+  pv: 0.0
+  reference_system: -0.6576172684903068
+  unit: eV/atom
+  work: -3.4087725881927637

examples/example_03/oldcalc/input_file.yaml

@@ -0,0 +1,81 @@
+calculations:
+- berendsen:
+    barostat_damping: 100.0
+    thermostat_damping: 100.0
+  composition_scaling:
+    output_chemical_composition: {}
+    restrictions: []
+  element:
+  - Cu
+  equilibration_control: berendsen
+  file_format: lammps-data
+  fix_potential_path: true
+  folder_prefix: null
+  inputfile: test.input.yaml
+  kernel: 0
+  lammps_executable: null
+  lattice: /mnt/c/Users/menon/Documents/repos/projects-calphy/calphy/examples/example_03/ts-fcc-solid-1200-0.0.data
+  lattice_constant: 3.61
+  mass:
+  - 63.546
+  md:
+    barostat_damping: 0.1
+    cmdargs: ''
+    init_commands: []
+    n_cycles: 100
+    n_every_steps: 10
+    n_repeat_steps: 10
+    n_small_steps: 10000
+    thermostat_damping: 0.1
+    timestep: 0.001
+  melting_cycle: true
+  melting_temperature:
+    attempts: 5
+    guess: null
+    step: 200
+  mode: ts
+  mpi_executable: null
+  n_elements: 1
+  n_equilibration_steps: 10000
+  n_iterations: 1
+  n_print_steps: 0
+  n_switching_steps: 25000
+  nose_hoover:
+    barostat_damping: 0.1
+    thermostat_damping: 0.1
+  npt: false
+  pair_coeff:
+  - '* * /mnt/c/Users/menon/Documents/repos/projects-calphy/calphy/examples/potentials/Cu01.eam.alloy
+    Cu'
+  pair_style:
+  - eam/alloy
+  potential_file: null
+  pressure: 0.0
+  queue:
+    commands:
+    - conda activate calphy-dev
+    cores: 4
+    jobname: calphy
+    memory: 3GB
+    modules: []
+    options: []
+    queuename: ''
+    scheduler: local
+    walltime: '23:59:00'
+  reference_phase: solid
+  repeat:
+  - 5
+  - 5
+  - 5
+  script_mode: false
+  spring_constants: null
+  temperature:
+  - 1200.0
+  - 1400.0
+  temperature_high: 0.0
+  tolerance:
+    lattice_constant: 0.0002
+    liquid_fraction: 0.05
+    pressure: 0.5
+    solid_fraction: 0.7
+    spring_constant: 0.1

examples/example_03/oldcalc/metadata.yaml

@@ -0,0 +1,10 @@
+files:
+  input_configuration.data: input atomic configuration
+  input_file.yml: input file
+  report.yaml: results after thermodynamic integration
+software:
+  doi: 10.5281/zenodo.10527452
+  name: calphy
+  repository: https://github.com/ICAMS/calphy
+  version: 1.3.7
+  webpage: https://calphy.org/

examples/example_03/oldcalc/report.yaml

@@ -0,0 +1,17 @@
+average:
+  density: 0.0820695985211261
+  spring_constant: '2.3863384417846154'
+  vol_atom: 12.18403228342489
+input:
+  concentration: '1.0'
+  element: Cu
+  lattice: fcc
+  pressure: 0.0
+  temperature: 1200
+results:
+  error: 0.0
+  free_energy: -4.066892072178304
+  pv: 0.0
+  reference_system: -0.6576172684903068
+  unit: eV/atom
+  work: -3.409274803687998

examples/example_03/test.input.yaml

@@ -0,0 +1,28 @@
+calculations:
+- element: Cu
+  lattice: conf.lqd
+  melting_cycle: False
+  mass: 63.546
+  md:
+    timestep: 0.001
+  mode: ts
+  n_equilibration_steps: 10000
+  n_iterations: 1
+  n_switching_steps: 25000
+  pair_coeff: '* * ../potentials/Cu01.eam.alloy Cu'
+  pair_style: eam/alloy
+  pressure: None
+  npt: False
+  queue:
+    commands:
+    - conda activate calphy-dev
+    cores: 4
+    scheduler: local
+  reference_phase: liquid
+  repeat:
+  - 5
+  - 5
+  - 5
+  temperature:
+  - 1200.0
+  - 1400.0