calphy 1.2.14__py3-none-any.whl → 1.3.0__py3-none-any.whl

calphy/lattice.py

@@ -1,180 +0,0 @@
-"""
-calphy: a Python library and command line interface for automated free
-energy calculations.
-
-Copyright 2021  (c) Sarath Menon^1, Yury Lysogorskiy^2, Ralf Drautz^2
-^1: Max Planck Institut für Eisenforschung, Dusseldorf, Germany 
-^2: Ruhr-University Bochum, Bochum, Germany
-
-calphy is published and distributed under the Academic Software License v1.0 (ASL). 
-calphy is distributed in the hope that it will be useful for non-commercial academic research, 
-but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  
-calphy API is published and distributed under the BSD 3-Clause "New" or "Revised" License
-See the LICENSE FILE for more details. 
-
-More information about the program can be found in:
-Menon, Sarath, Yury Lysogorskiy, Jutta Rogal, and Ralf Drautz.
-“Automated Free Energy Calculation from Atomistic Simulations.” Physical Review Materials 5(10), 2021
-DOI: 10.1103/PhysRevMaterials.5.103801
-
-For more information contact:
-sarath.menon@ruhr-uni-bochum.de/yury.lysogorskiy@icams.rub.de
-"""
-
-from mendeleev import element
-import os
-from pylammpsmpi import LammpsLibrary
-import numpy as np
-import pyscal.core as pc
-from ase.io import read
-
-"""
-Conversion factors for creating initial lattices
-"""
-latticedict = {
-    "BCC" :{"LQD": 1.00000, "BCC":1.00000, "FCC":0.79370, "HCP":1.12246, "DIA":0.62996, "SC":1.25992, "N":2},
-    "FCC" :{"LQD": 1.00000, "BCC":1.25992, "FCC":1.00000, "HCP":1.78179, "DIA":0.79370, "SC":1.58740, "N":4},
-    "HCP" :{"LQD": 1.00000, "BCC":0.89090, "FCC":0.79370, "HCP":1.00000, "DIA":0.62996, "SC":0.89089, "N":4},
-    "DIA" :{"LQD": 1.00000, "BCC":1.58740, "FCC":0.79370, "HCP":1.25992, "DIA":1.00000, "SC":2.00000, "N":8},
-    "SC"  :{"LQD": 1.00000, "BCC":0.79370, "FCC":0.62996, "HCP":1.12247, "DIA":0.50000, "SC":1.00000, "N":1},
-}
-
-def get_lattice(symbol, lat):
-    """
-    Find lattice constants of an element
-
-    Parameters
-    ----------
-    symbol : string
-        symbol of chemical element
-
-    lattice_list : list of strings
-        list of lattices
-
-    Returns
-    -------
-    lattice_constants : list of floats
-        list of lattice constant values
-
-    atoms_per_cell : list of ints
-        number of atoms per cell
-
-    lammps_lattice : list of strings
-        the main lattice to be used in lammps
-    """
-
-    chem = element(symbol)
-    
-    mainlat = chem.lattice_structure
-    
-    if mainlat == "HEX":
-        mainlat = "HCP"
-
-    mainalat = chem.lattice_constant
-
-    #print(mainlat, lat)
-    newlat = latticedict[mainlat][lat]*mainalat
-    lattice_constant = newlat
-
-    if lat == "LQD":
-        atoms_per_cell = latticedict[mainlat]["N"]
-        lammps_lattice = mainlat.lower()    
-    else:
-        atoms_per_cell = latticedict[lat]["N"]
-        lammps_lattice = lat.lower()
-
-    return lattice_constant, atoms_per_cell, lammps_lattice
-
-def check_dump_file(infile):
-    try:
-        #now use pyscal to read it in,
-        sys = pc.System()
-        sys.read_inputfile(infile)
-        atoms = sys.atoms
-        natoms = len(atoms)
-        types = [atom.type for atom in atoms]
-        xx, xxcounts = np.unique(types, return_counts=True)
-        conc = xxcounts/np.sum(xxcounts)
-        return (natoms, conc)
-    except:
-        return None
-
-def check_data_file(infile, script_mode=False):
-    try:
-        if not script_mode:
-            lmp = LammpsLibrary(cores=1, 
-                working_directory=os.getcwd())
-            lmp.units("metal")
-            lmp.boundary("p p p")
-            lmp.atom_style("atomic")
-            lmp.timestep(0.001)            
-            lmp.read_data(infile)
-            natoms = lmp.natoms
-            #now we convert to a dump file and read the concentration
-            trajfile = ".".join([infile, "dump"])
-            lmp.command("mass * 1.0")
-            lmp.dump("2 all custom", 1, trajfile,"id type x y z")
-            lmp.run(0)
-            lmp.undump(2)
-            lmp.close()
-            format = 'lammps-dump'
-        else:
-            trajfile = read(infile, format='lammps-data', style='atomic')
-            format = 'ase'
-        #now use pyscal to read it in,
-        sys = pc.System()
-        sys.read_inputfile(trajfile, format=format)
-        atoms = sys.atoms
-        types = [atom.type for atom in atoms]
-        xx, xxcounts = np.unique(types, return_counts=True)
-        conc = xxcounts/np.sum(xxcounts)
-        return (natoms, conc)
-    except:
-        return None
-
-def prepare_lattice(calc):
-    #process lattice
-    lattice = calc.lattice.upper()
-    dumpfile = False
-
-    if lattice in ["BCC", "FCC", "HCP", "DIA", "SC", "LQD"]:
-        #process lattice
-        #throw error for multicomponent
-        if calc.n_elements > 1:
-            raise ValueError("Only files supported for multicomponent")
-
-        alat, apc, l = get_lattice(calc.element[0], calc.lattice)
-
-        #replace lattice constant
-        if calc.lattice_constant != 0:
-            alat = calc.lattice_constant
-        
-        conc = [1,]
-
-    elif os.path.exists(calc.lattice):
-        calc.lattice = os.path.abspath(calc.lattice)
-
-        res = check_dump_file(calc.lattice)
-        dumpfile = True
-
-        if res is None:
-            res = check_data_file(calc.lattice)
-            dumpfile = False
-
-        if res is not None:
-            natoms = res[0]
-            conc = res[1]
-            l = "file"
-            alat = 1.00
-            apc = natoms
-        else:
-            raise ValueError("An input file was provided but it was neither data or dump file")
-
-    else:
-        raise ValueError("Unknown lattice found. Allowed options are BCC, FCC, HCP, DIA, SC or LQD; or an input file.")
-    
-    if l == "dia":
-        l = "diamond"
-
-    return l, alat, apc, conc, dumpfile 
-

calphy-1.2.14.dist-info/RECORD

@@ -1,25 +0,0 @@
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-calphy/solid.py,sha256=D-FDcHaHgxoDMqBKThdi1cVJbYTh_PxdQmcf_60itdY,19585
-calphy/splines.py,sha256=BGwUVz_qXQxUzpUCuZo6CsELcd5JVNWzI-Ttcz22G_E,61627
-calphy-1.2.14.dist-info/LICENSE,sha256=XIHGB5RZLIhOjjoO1bPf0II-qDbjhP5Cv5HJMRE9v1g,16651
-calphy-1.2.14.dist-info/METADATA,sha256=Ab20D6XMm3B-WnvtIztATit9YmPxWYDLxYJrpvNa1BQ,4238
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