def test_molecular_2D(): global outstructs global outstrings print( "=== Testing generation of molecular 2D crystals. This may take some time. ===" ) from time import time from pyxtal.symmetry import Group from pyxtal.molecular_crystal import molecular_crystal_2D from pymatgen.symmetry.analyzer import SpacegroupAnalyzer slow = [] failed = [] print(" Layer group # | Symbol | Time Elapsed") skip = [] for sg in range(1, 81): if sg not in skip: g = Group(sg, dim=2) multiplicity = len(g[0]) # multiplicity of the general position start = time() rand_crystal = molecular_crystal_2D(sg, ["H2O"], [multiplicity], 4.0) end = time() timespent = np.around((end - start), decimals=2) t = str(timespent) if len(t) == 3: t += "0" t += " s" if timespent >= 1.0: t += " ~" if timespent >= 3.0: t += "~" if timespent >= 10.0: t += "~" if timespent >= 60.0: t += "~" slow.append(sg) if rand_crystal.valid: if check_struct_group(rand_crystal, sg, dim=2): pass else: t += " xxxxx" outstructs.append(rand_crystal.struct) outstrings.append(str("molecular_2D_" + str(sg) + ".vasp")) symbol = g.symbol print("\t" + str(sg) + "\t|\t" + symbol + "\t|\t" + t) else: print("~~~~ Error: Could not generate layer group " + str(sg) + " after " + t) failed.append(sg) if slow != []: print( "~~~~ The following layer groups took more than 60 seconds to generate:" ) for i in slow: print(" " + str(i)) if failed != []: print("~~~~ The following layer groups failed to generate:") for i in failed: print(" " + str(i))
def test_molecular_2d(self): # print("test_molecular_2d") struc = molecular_crystal_2D(20, ["H2O"], [4], 1.0) cif = struc.to_file() self.assertTrue(struc.valid) struc = molecular_crystal_1D(20, ["H2O"], [4], 1.0) cif = struc.to_file() self.assertTrue(struc.valid)
def test_modules(): print("====== Testing functionality for pyXtal version 0.1dev ======") global failed_package failed_package = False # Record if errors occur at any level reset() print("Importing sys...") try: import sys print("Success!") except Exception as e: fail(e) sys.exit(0) print("Importing numpy...") try: import numpy as np print("Success!") except Exception as e: fail(e) sys.exit(0) I = np.array([[1, 0, 0], [0, 1, 0], [0, 0, 1]]) print("Importing pymatgen...") try: import pymatgen print("Success!") except Exception as e: fail(e) sys.exit(0) try: from pymatgen.core.operations import SymmOp except Exception as e: fail(e) sys.exit(0) print("Importing pandas...") try: import pandas print("Success!") except Exception as e: fail(e) sys.exit(0) print("Importing spglib...") try: import spglib print("Success!") except Exception as e: fail(e) sys.exit(0) print("Importing openbabel...") try: import ase print("Success!") except: print( "Error: could not import openbabel. Try reinstalling the package.") print("Importing pyxtal...") try: import pyxtal print("Success!") except Exception as e: fail(e) sys.exit(0) print("=== Testing modules ===") # =====database.element===== print("pyxtal.database.element") reset() try: import pyxtal.database.element except Exception as e: fail(e) print(" class Element") try: from pyxtal.database.element import Element except Exception as e: fail(e) if passed(): for i in range(1, 95): if passed(): try: ele = Element(i) except: fail("Could not access Element # " + str(i)) try: y = ele.sf y = ele.z y = ele.short_name y = ele.long_name y = ele.valence y = ele.valence_electrons y = ele.covalent_radius y = ele.vdw_radius y = ele.get_all(0) except: fail("Could not access attribute for element # " + str(i)) try: ele.all_z() ele.all_short_names() ele.all_long_names() ele.all_valences() ele.all_valence_electrons() ele.all_covalent_radii() ele.all_vdw_radii() except: fail("Could not access class methods") check() # =====database.hall===== print("pyxtal.database.hall") reset() try: import pyxtal.database.hall except Exception as e: fail(e) print(" hall_from_hm") try: from pyxtal.database.hall import hall_from_hm except Exception as e: fail(e) if passed(): for i in range(1, 230): if passed(): try: hall_from_hm(i) except: fail("Could not access hm # " + str(i)) check() # =====database.collection===== print("pyxtal.database.collection") reset() try: import pyxtal.database.collection except Exception as e: fail(e) print(" Collection") try: from pyxtal.database.collection import Collection except Exception as e: fail(e) if passed(): for i in range(1, 230): if passed(): try: molecule_collection = Collection("molecules") except: fail("Could not access hm # " + str(i)) check() # =====operations===== print("pyxtal.operations") reset() try: import pyxtal.operations except Exception as e: fail(e) print(" random_vector") try: from pyxtal.operations import random_vector except Exception as e: fail(e) if passed(): try: for i in range(10): random_vector() except Exception as e: fail(e) check() print(" angle") try: from pyxtal.operations import angle except Exception as e: fail(e) if passed(): try: for i in range(10): v1 = random_vector() v2 = random_vector() angle(v1, v2) except Exception as e: fail(e) check() print(" random_shear_matrix") try: from pyxtal.operations import random_shear_matrix except Exception as e: fail(e) if passed(): try: for i in range(10): random_shear_matrix() except Exception as e: fail(e) check() print(" is_orthogonal") try: from pyxtal.operations import is_orthogonal except Exception as e: fail(e) if passed(): try: a = is_orthogonal([[1, 0, 0], [0, 1, 0], [0, 0, 1]]) b = is_orthogonal([[0, 0, 1], [1, 0, 0], [1, 0, 0]]) if a is True and b is False: pass else: fail() except Exception as e: fail(e) check() print(" aa2matrix") try: from pyxtal.operations import aa2matrix except Exception as e: fail(e) if passed(): try: for i in range(10): aa2matrix(1, 1, random=True) except Exception as e: fail(e) check() print(" matrix2aa") try: from pyxtal.operations import matrix2aa except Exception as e: fail(e) if passed(): try: for i in range(10): m = aa2matrix(1, 1, random=True) aa = matrix2aa(m) except Exception as e: fail(e) check() print(" rotate_vector") try: from pyxtal.operations import rotate_vector except Exception as e: fail(e) if passed(): try: for i in range(10): v1 = random_vector() v2 = random_vector() rotate_vector(v1, v2) except Exception as e: fail(e) check() print(" are_equal") try: from pyxtal.operations import are_equal except Exception as e: fail(e) if passed(): try: op1 = SymmOp.from_xyz_string("x,y,z") op2 = SymmOp.from_xyz_string("x,y,z+1") a = are_equal(op1, op2, PBC=[0, 0, 1]) b = are_equal(op1, op2, PBC=[1, 0, 0]) if a is True and b is False: pass else: fail() except Exception as e: fail(e) check() print(" class OperationAnalyzer") try: from pyxtal.operations import OperationAnalyzer except Exception as e: fail(e) if passed(): try: for i in range(10): m = aa2matrix(1, 1, random=True) t = random_vector() op1 = SymmOp.from_rotation_and_translation(m, t) OperationAnalyzer(op1) except Exception as e: fail(e) check() print(" class Orientation") try: from pyxtal.operations import Orientation except Exception as e: fail(e) if passed(): try: for i in range(10): v1 = random_vector() c1 = random_vector() o = Orientation.from_constraint(v1, c1) except Exception as e: fail(e) check() # =====symmetry===== print("pyxtal.symmetry") reset() try: import pyxtal.symmetry except Exception as e: fail(e) print(" get_wyckoffs (may take a moment)") try: from pyxtal.symmetry import get_wyckoffs except Exception as e: fail(e) if passed(): try: for i in [1, 2, 229, 230]: get_wyckoffs(i) get_wyckoffs(i, organized=True) except: fail(" Could not access Wyckoff positions for space group # " + str(i)) check() print(" get_wyckoff_symmetry (may take a moment)") try: from pyxtal.symmetry import get_wyckoff_symmetry except Exception as e: fail(e) if passed(): try: for i in [1, 2, 229, 230]: get_wyckoff_symmetry(i) get_wyckoff_symmetry(i, molecular=True) except: fail("Could not access Wyckoff symmetry for space group # " + str(i)) check() print(" get_wyckoffs_generators (may take a moment)") try: from pyxtal.symmetry import get_wyckoff_generators except Exception as e: fail(e) if passed(): try: for i in [1, 2, 229, 230]: get_wyckoff_generators(i) except: fail("Could not access Wyckoff generators for space group # " + str(i)) check() print(" letter_from_index") try: from pyxtal.symmetry import letter_from_index except Exception as e: fail(e) if passed(): try: if letter_from_index(0, get_wyckoffs(47)) == "A": pass else: fail() except Exception as e: fail(e) check() print(" index_from_letter") try: from pyxtal.symmetry import index_from_letter except Exception as e: fail(e) if passed(): try: if index_from_letter("A", get_wyckoffs(47)) == 0: pass else: fail() except Exception as e: fail(e) check() print(" jk_from_i") try: from pyxtal.symmetry import jk_from_i except Exception as e: fail(e) if passed(): try: w = get_wyckoffs(2, organized=True) j, k = jk_from_i(1, w) if j == 1 and k == 0: pass else: print(j, k) fail() except Exception as e: fail(e) check() print(" i_from_jk") try: from pyxtal.symmetry import i_from_jk except Exception as e: fail(e) if passed(): try: w = get_wyckoffs(2, organized=True) j, k = jk_from_i(1, w) i = i_from_jk(j, k, w) if i == 1: pass else: print(j, k) fail() except Exception as e: fail(e) check() print(" ss_string_from_ops") try: from pyxtal.symmetry import ss_string_from_ops except Exception as e: fail(e) if passed(): try: strings = ["1", "4 . .", "2 3 ."] for i, sg in enumerate([1, 75, 195]): ops = get_wyckoffs(sg)[0] ss_string_from_ops(ops, sg, dim=3) except Exception as e: fail(e) check() print(" Wyckoff_position") try: from pyxtal.symmetry import Wyckoff_position except Exception as e: fail(e) if passed(): try: wp = Wyckoff_position.from_group_and_index(20, 1) except Exception as e: fail(e) check() print(" Group") try: from pyxtal.symmetry import Group except Exception as e: fail(e) if passed(): try: g3 = Group(230) g2 = Group(80, dim=2) g1 = Group(75, dim=1) except Exception as e: fail(e) check() # =====crystal===== print("pyxtal.crystal") reset() try: import pyxtal.crystal except Exception as e: fail(e) print(" random_crystal") try: from pyxtal.crystal import random_crystal except Exception as e: fail(e) if passed(): try: c = random_crystal(1, ["H"], [1], 10.0) if c.valid is True: pass else: fail() except Exception as e: fail(e) check() print(" random_crystal_2D") try: from pyxtal.crystal import random_crystal_2D except Exception as e: fail(e) if passed(): try: c = random_crystal_2D(1, ["H"], [1], 10.0) if c.valid is True: pass else: fail() except Exception as e: fail(e) check() # =====molecule===== print("pyxtal.molecule") reset() try: import pyxtal.molecule except Exception as e: fail(e) check() print(" Collections") try: from pyxtal.molecule import mol_from_collection except Exception as e: fail(e) if passed(): try: h2o = mol_from_collection("H2O") ch4 = mol_from_collection("CH4") except Exception as e: fail(e) print(" get_inertia_tensor") try: from pyxtal.molecule import get_inertia_tensor except Exception as e: fail(e) if passed(): try: get_inertia_tensor(h2o) get_inertia_tensor(ch4) except Exception as e: fail(e) check() print(" get_moment_of_inertia") try: from pyxtal.molecule import get_moment_of_inertia except Exception as e: fail(e) if passed(): try: v = random_vector() get_moment_of_inertia(h2o, v) get_moment_of_inertia(ch4, v) except Exception as e: fail(e) check() print(" reoriented_molecule") try: from pyxtal.molecule import reoriented_molecule except Exception as e: fail(e) if passed(): try: reoriented_molecule(h2o) reoriented_molecule(ch4) except Exception as e: fail(e) check() print(" orientation_in_wyckoff_position") try: from pyxtal.molecule import orientation_in_wyckoff_position except Exception as e: fail(e) if passed(): try: w = get_wyckoffs(20) ws = get_wyckoff_symmetry(20, molecular=True) wp = Wyckoff_position.from_group_and_index(20, 1) orientation_in_wyckoff_position(h2o, wp) orientation_in_wyckoff_position(ch4, wp) except Exception as e: fail(e) check() # =====molecular_crystal===== print("pyxtal.molecular_crystal") reset() try: import pyxtal.crystal except Exception as e: fail(e) print(" molecular_crystal") try: from pyxtal.molecular_crystal import molecular_crystal except Exception as e: fail(e) if passed(): try: c = molecular_crystal(1, ["H2O"], [1], 10.0) if c.valid is True: pass else: fail() except Exception as e: fail(e) check() print(" molecular_crystal_2D") try: from pyxtal.molecular_crystal import molecular_crystal_2D except Exception as e: fail(e) if passed(): try: c = molecular_crystal_2D(1, ["H2O"], [1], 10.0) if c.valid is True: pass else: fail() except Exception as e: fail(e) check() end(condition=2)
def from_random( self, dim=3, group=None, species=None, numIons=None, factor=1.1, thickness=None, area=None, lattice=None, sites=None, conventional=True, diag=False, t_factor=1.0, max_count=10, force_pass=False, ): if self.molecular: prototype = "molecular" else: prototype = "atomic" tm = Tol_matrix(prototype=prototype, factor=t_factor) count = 0 quit = False while True: count += 1 if self.molecular: if dim == 3: struc = molecular_crystal(group, species, numIons, factor, lattice=lattice, sites=sites, conventional=conventional, diag=diag, tm=tm) elif dim == 2: struc = molecular_crystal_2D(group, species, numIons, factor, thickness=thickness, sites=sites, conventional=conventional, tm=tm) elif dim == 1: struc = molecular_crystal_1D(group, species, numIons, factor, area=area, sites=sites, conventional=conventional, tm=tm) else: if dim == 3: struc = random_crystal(group, species, numIons, factor, lattice, sites, conventional, tm) elif dim == 2: struc = random_crystal_2D(group, species, numIons, factor, thickness, lattice, sites, conventional, tm) elif dim == 1: struc = random_crystal_1D(group, species, numIons, factor, area, lattice, sites, conventional, tm) else: struc = random_cluster(group, species, numIons, factor, lattice, sites, tm) if force_pass: quit = True break elif struc.valid: quit = True break if count >= max_count: raise RuntimeError( "It takes long time to generate the structure, check inputs" ) if quit: self.valid = struc.valid self.dim = dim try: self.lattice = struc.lattice if self.molecular: self.numMols = struc.numMols self.molecules = struc.molecules self.mol_sites = struc.mol_sites self.diag = struc.diag else: self.numIons = struc.numIons self.species = struc.species self.atom_sites = struc.atom_sites self.group = struc.group self.PBC = struc.PBC self.source = 'random' self.factor = struc.factor self.number = struc.number self._get_formula() except: pass
def test_molecular_2D(): global outstructs global outstrings print("=== Testing generation of molecular 2D crystals. This may take some time. ===") from time import time from spglib import get_symmetry_dataset from pyxtal.symmetry import get_layer from pyxtal.crystal import cellsize from pyxtal.molecular_crystal import molecular_crystal_2D from pyxtal.database.layergroup import Layergroup from pymatgen.symmetry.analyzer import SpacegroupAnalyzer slow = [] failed = [] print(" Layergroup | sg # Expected |Generated (SPG)|Generated (PMG)|Time Elapsed") skip = []#12, 64, 65, 80] #slow to generate for num in range(1, 81): if num not in skip: sg = Layergroup(num).sgnumber multiplicity = len(get_layer(num)[0]) / cellsize(sg) #multiplicity of the general position start = time() rand_crystal = molecular_crystal_2D(num, ['H2O'], [multiplicity], 4.0) end = time() timespent = np.around((end - start), decimals=2) t = str(timespent) if len(t) == 3: t += "0" t += " s" if timespent >= 1.0: t += " ~" if timespent >= 3.0: t += "~" if timespent >= 10.0: t += "~" if timespent >= 60.0: t += "~" slow.append(num) if rand_crystal.valid: check = False ans1 = get_symmetry_dataset(rand_crystal.spg_struct, symprec=1e-1) if ans1 is None: ans1 = "???" else: ans1 = ans1['number'] sga = SpacegroupAnalyzer(rand_crystal.struct) ans2 = "???" if sga is not None: try: ans2 = sga.get_space_group_number() except: ans2 = "???" if ans2 is None: ans2 = "???" #Compare expected and detected groups if ans1 == "???" and ans2 == "???": check = True elif ans1 == "???": if int(ans2) > sg: pass elif ans2 == "???": if int(ans1) > sg: pass else: if ans1 < sg and ans2 < sg: if compare_wyckoffs(sg, ans1) or compare_wyckoffs(sg, ans2): pass else: check = True #output cif files for incorrect space groups if check is True: if check_struct_group(rand_crystal.struct, num, dim=2): pass else: t += " xxxxx" outstructs.append(rand_crystal.struct) outstrings.append(str("2D_Molecular_"+str(num)+".vasp")) print("\t"+str(num)+"\t|\t"+str(sg)+"\t|\t"+str(ans1)+"\t|\t"+str(ans2)+"\t|\t"+t) else: print("~~~~ Error: Could not generate layer group "+str(num)+" after "+t) failed.append(num) if slow != []: print("~~~~ The following layer groups took more than 60 seconds to generate:") for i in slow: print(" "+str(i)) if failed != []: print("~~~~ The following layer groups failed to generate:") for i in failed: print(" "+str(i))
for i in range(attempts): start = time() numMols0 = np.array(numMols) if dimension == 3: print(sg, system, numMols0, factor) rand_crystal = molecular_crystal( sg, system, numMols0, factor, ) elif dimension == 2: rand_crystal = molecular_crystal_2D( sg, system, numMols0, factor, thickness, ) end = time() timespent = np.around((end - start), decimals=2) if rand_crystal.valid: pmg_struc = rand_crystal.to_pymatgen() ase_struc = rand_crystal.to_ase() comp = str(pmg_struc.composition) comp = comp.replace(" ", "") cifpath = outdir + "/" + comp + ".cif" CifWriter(pmg_struc, symprec=0.1).write_file(filename=cifpath) ans = get_symmetry_dataset(ase_struc, symprec=1e-1)["international"]