calphy 1.3.1__tar.gz → 1.3.2__tar.gz

{calphy-1.3.1/calphy.egg-info → calphy-1.3.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: calphy
-Version: 1.3.1
+Version: 1.3.2
 Summary: free energy calculation for python
 Home-page: https://github.com/ICAMS/calphy
 Author: Sarath Menon, Yury Lysogorskiy, Ralf Drautz

{calphy-1.3.1 → calphy-1.3.2}/calphy/__init__.py

@@ -4,7 +4,7 @@ from calphy.solid import Solid
 from calphy.alchemy import Alchemy
 from calphy.routines import MeltingTemp
 
-__version__ = "1.3.1"
+__version__ = "1.3.2"
 
 def addtest(a,b):
     return a+b

{calphy-1.3.1 → calphy-1.3.2}/calphy/helpers.py

@@ -46,8 +46,8 @@ class LammpsScript:
             for line in self.script:
                 fout.write(f'{line}\n')
 
-def create_object(cores, directory, timestep, cmdargs=None, 
-    init_commands=None, script_mode=False):
+def create_object(cores, directory, timestep, cmdargs="", 
+    init_commands=(), script_mode=False):
     """
     Create LAMMPS object
 
@@ -69,6 +69,8 @@ def create_object(cores, directory, timestep, cmdargs=None,
     if script_mode:
         lmp = LammpsScript()
     else:
+        if cmdargs == "":
+            cmdargs = None
         lmp = LammpsLibrary(
             cores=cores, working_directory=directory, cmdargs=cmdargs
         )
@@ -79,7 +81,7 @@ def create_object(cores, directory, timestep, cmdargs=None,
     ["timestep", str(timestep)],
     ["box", "tilt large"]]
 
-    if init_commands is not None:
+    if len(init_commands) > 0:
         #we need to replace some initial commands
         for rc in init_commands:
             #split the command

{calphy-1.3.1 → calphy-1.3.2}/calphy/input.py

@@ -40,6 +40,7 @@ from pyscal3.core import structure_dict, element_dict, _make_crystal
 from ase.io import read, write
 import shutil
 
+__version__ = "1.3.2"
 
 def read_report(folder):
     """
@@ -95,8 +96,8 @@ class MD(BaseModel, title='MD specific input options'):
     n_cycles: Annotated[int, Field(default=100, gt=0)]
     thermostat_damping: Annotated[Union[float, conlist(float, min_length=2, max_length=2)], Field(default=0.1, gt=0)]
     barostat_damping: Annotated[Union[float, conlist(float, min_length=2, max_length=2)], Field(default=0.1, gt=0)]
-    cmdargs: Annotated[Union[None, str], Field(default=None)]
-    init_commands: Annotated[Union[None, List[str]], Field(default=None)]
+    cmdargs: Annotated[str, Field(default="")]
+    init_commands: Annotated[List, Field(default=[])]
 
 
 class NoseHoover(BaseModel, title='Specific input options for Nose-Hoover thermostat'):
@@ -111,12 +112,12 @@ class Queue(BaseModel, title='Options for configuring queue'):
     scheduler: Annotated[str, Field(default='local')]
     cores: Annotated[int, Field(default=1, gt=0)]
     jobname: Annotated[str, Field(default='calphy')]
-    walltime: Annotated[Union[str, None], Field(default=None)]
-    queuename: Annotated[Union[str,None], Field(default=None)]
+    walltime: Annotated[str, Field(default="23:59:00")]
+    queuename: Annotated[str, Field(default="")]
     memory: Annotated[str, Field(default="3GB")]
-    commands: Annotated[Union[List[str],None], Field(default=None)]
-    options: Annotated[Union[List[str],None], Field(default=None)]
-    modules: Annotated[Union[List[str],None], Field(default=None)]
+    commands: Annotated[List, Field(default=[])]
+    options: Annotated[List, Field(default=[])]
+    modules: Annotated[List, Field(default=[])]
 
 class Tolerance(BaseModel, title='Tolerance settings for convergence'):
     lattice_constant: Annotated[float, Field(default=0.0002, ge=0)]
@@ -656,4 +657,21 @@ def _convert_legacy_inputfile(file, return_calcs=False):
         warnings.warn(f'Old style input file calphy < v2 found. Converted input in {outfile}. Please check!')
         with open(outfile, 'w') as fout:
             yaml.safe_dump(newdata, fout)
-        return outfile
+        return outfile
+
+
+def generate_metadata():
+    metadata = {}
+    metadata["software"] = {}
+    metadata["software"]["name"] = "calphy"
+    metadata["software"]["doi"] = "10.5281/zenodo.10527452"
+    metadata["software"]["version"] = __version__
+    metadata["software"]["repository"] = "https://github.com/ICAMS/calphy"
+    metadata["software"]["webpage"] = "https://calphy.org/"
+
+    metadata["files"] = {}
+    metadata["files"]["input_file.yml"] = "input file"
+    metadata["files"]["report.yaml"] = "results after thermodynamic integration"
+    metadata["files"]["input_configuration.data"] = "input atomic configuration"
+
+    return metadata

{calphy-1.3.1 → calphy-1.3.2}/calphy/phase.py

@@ -28,11 +28,14 @@ sarath.menon@ruhr-uni-bochum.de/yury.lysogorskiy@icams.rub.de
 import numpy as np
 import yaml
 import copy
+import os
+import shutil
 
 import pyscal3.traj_process as ptp
 from calphy.integrators import *
 import calphy.helpers as ph
 from calphy.errors import *
+from calphy.input import generate_metadata
 
 class Phase:
     """
@@ -50,6 +53,20 @@ class Phase:
     def __init__(self, calculation=None, simfolder=None, log_to_screen=False):
 
         self.calc = copy.deepcopy(calculation)
+        
+        #serialise input
+        indict = {"calculations": [self.calc.dict()]}
+        with open(os.path.join(simfolder, 'input_file.yaml'), 'w') as fout:
+            yaml.safe_dump(indict, fout)
+
+        #serialise input configuration
+        shutil.copy(self.calc.lattice, os.path.join(simfolder, 'input_configuration.data'))
+
+        #write simple metadata
+        with open(os.path.join(simfolder, 'metadata.yaml'), 'w') as fout:
+            yaml.safe_dump(generate_metadata(), fout)
+        
+
         self.simfolder = simfolder
         self.log_to_screen = log_to_screen
         

{calphy-1.3.1 → calphy-1.3.2}/calphy/scheduler.py

@@ -32,7 +32,6 @@ class Local:
     def __init__(self, options, cores=1, directory=os.getcwd()):
         self.queueoptions = {"scheduler": "local",
                              "jobname": "tis",
-                             "walltime": None,
                              "queuename": None,
                              "memory": None,
                              "cores": cores,
@@ -92,7 +91,6 @@ class SLURM:
         self.queueoptions = {"scheduler": "slurm",
                              "jobname": "tis",
                              "walltime": "23:59:00",
-                             "queuename": "shorttime",
                              "memory": "3GB",
                              "cores": cores,
                              "hint": "nomultithread",
@@ -108,7 +106,8 @@ class SLURM:
         for (key, val) in options.items():
             if key in self.queueoptions.keys():
                 if val is not None:
-                    self.queueoptions[key] = val
+                    if val is not "":
+                        self.queueoptions[key] = val
         self.maincommand = ""
 
 

{calphy-1.3.1 → calphy-1.3.2/calphy.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: calphy
-Version: 1.3.1
+Version: 1.3.2
 Summary: free energy calculation for python
 Home-page: https://github.com/ICAMS/calphy
 Author: Sarath Menon, Yury Lysogorskiy, Ralf Drautz

{calphy-1.3.1 → calphy-1.3.2}/setup.py

@@ -53,7 +53,7 @@ setup(
     packages=find_packages(include=['calphy', 'calphy.*']),
     test_suite='tests',
     url='https://github.com/ICAMS/calphy',
-    version='1.3.1',
+    version='1.3.2',
     zip_safe=False,
     entry_points={
         'console_scripts': [