Enable XYZ format and Z'=2

0.py

@@ -0,0 +1,8 @@
+from pyxtal import pyxtal
+from pyxtal.lattice import Lattice
+struc = pyxtal(molecular=True)
+sites = [{"4e": [0.77, 0.57, 0.53]}]
+lat = Lattice.from_para(11.43, 6.49, 11.19, 90, 83.31, 90, ltype="monoclinic")
+for i in range(200):
+    struc.from_random(3, 14, ["aspirin"], [4], lattice=lat, sites=sites)
+    print(i, struc.lattice)                                

CTMTNA.cif

@@ -0,0 +1,101 @@
+smiles: O=N(=O)N1CN(CN(C1)N(=O)=O)N(=O)=O
+# Refcode: CTMTNA
+
+#######################################################################
+#
+#                 Cambridge Crystallographic Data Centre
+#                                CCDC 
+#
+#######################################################################
+#
+# If this CIF has been generated from an entry in the Cambridge 
+# Structural Database, then it will include bibliographic, chemical, 
+# crystal, experimental, refinement or atomic coordinate data resulting 
+# from the CCDC's data processing and validation procedures.
+#
+#######################################################################
+
+data_CTMTNA
+_chemical_name_common            1,3,5-trinitro-1,3,5-triazinane
+_chemical_formula_moiety         'C3 H6 N6 O6'
+_chemical_name_systematic        Cyclotrimethylene-trinitramine
+_symmetry_cell_setting           orthorhombic
+_symmetry_space_group_name_H-M   'P b c a'
+_symmetry_Int_Tables_number      61
+_space_group_name_Hall           '-P 2ac 2ab'
+loop_
+_symmetry_equiv_pos_site_id
+_symmetry_equiv_pos_as_xyz
+1 x,y,z
+2 1/2-x,-y,1/2+z
+3 1/2+x,1/2-y,-z
+4 -x,1/2+y,1/2-z
+5 -x,-y,-z
+6 1/2+x,y,1/2-z
+7 1/2-x,1/2+y,z
+8 x,1/2-y,1/2+z
+_cell_length_a                   13.182(2)
+_cell_length_b                   11.574(2)
+_cell_length_c                   10.709(2)
+_cell_angle_alpha                90
+_cell_angle_beta                 90
+_cell_angle_gamma                90
+_cell_volume                     1633.86
+_chemical_melting_point          '478 K'
+_cell_formula_units_Z            8
+_chemical_properties_physical    explosive
+loop_
+_atom_site_label
+_atom_site_type_symbol
+_atom_site_fract_x
+_atom_site_fract_y
+_atom_site_fract_z
+C1 C 0.18390 0.35780 0.44000
+C2 C 0.05030 0.24400 0.33950
+C3 C 0.14870 0.38130 0.21590
+H1 H 0.24010 0.29440 0.42260
+H2 H 0.20130 0.40680 0.52440
+H3 H -0.02610 0.21170 0.35400
+H4 H 0.10150 0.17280 0.31920
+H5 H 0.20520 0.31660 0.19170
+H6 H 0.14400 0.44320 0.14130
+N1 N 0.17610 0.43600 0.33300
+N2 N 0.08770 0.29960 0.45370
+N3 N 0.05360 0.32220 0.23290
+N4 N 0.22600 0.53790 0.33460
+N5 N 0.01550 0.35250 0.52940
+N6 N -0.03330 0.38750 0.20780
+O1 O 0.22700 0.59320 0.23880
+O2 O 0.26490 0.56870 0.43380
+O3 O -0.06930 0.31420 0.52620
+O4 O 0.04540 0.42710 0.59900
+O5 O -0.11210 0.35340 0.25040
+O6 O -0.02360 0.46910 0.13900
+loop_
+_geom_bond_atom_site_label_1
+_geom_bond_atom_site_label_2
+_geom_bond_site_symmetry_1
+_geom_bond_site_symmetry_2
+C1 H1 1_555 1_555
+C2 H3 1_555 1_555
+C3 H5 1_555 1_555
+H2 C1 1_555 1_555
+H4 C2 1_555 1_555
+H6 C3 1_555 1_555
+N1 C1 1_555 1_555
+N2 C1 1_555 1_555
+N3 C2 1_555 1_555
+N4 N1 1_555 1_555
+N5 N2 1_555 1_555
+N6 N3 1_555 1_555
+O1 N4 1_555 1_555
+O2 N4 1_555 1_555
+O3 N5 1_555 1_555
+O4 N5 1_555 1_555
+O5 N6 1_555 1_555
+O6 N6 1_555 1_555
+C2 N2 1_555 1_555
+C3 N1 1_555 1_555
+C3 N3 1_555 1_555
+
+#END

CTMTNA.xyz

@@ -0,0 +1,23 @@
+21
+Cyclotrimethylene-trinitramine
+C          2.42417        4.14118        4.71196
+C          0.66305        2.82406        3.63571
+C          1.96016        4.41317        2.31207
+H          3.16500        3.40739        4.52562
+H          2.65354        4.70830        5.61580
+H         -0.34405        2.45022        3.79099
+H          1.33797        1.99999        3.41831
+H          2.70495        3.66433        2.05292
+H          1.89821        5.12960        1.51318
+N          2.32135        5.04626        3.56610
+N          1.15606        3.46757        4.85867
+N          0.70656        3.72914        2.49413
+N          2.97913        6.22565        3.58323
+N          0.20432        4.07984        5.66934
+N         -0.43896        4.48493        2.22533
+O          2.99231        6.86570        2.55731
+O          3.49191        6.58213        4.64556
+O         -0.91351        3.63655        5.63508
+O          0.59846        4.94326        6.41469
+O         -1.47770        4.09025        2.68153
+O         -0.31110        5.42936        1.48855

csp_xyz.py

@@ -0,0 +1,184 @@
+"""
+This is an example to perform CSP based on a reference crystal.
+The structures with good matches will be output to *-matched.cif.
+Supports molecule input as .xyz or .smi.
+"""
+from pyxtal import pyxtal
+from pyxtal.optimize import WFS, DFS, QRS
+from pyxtal.molecule import pyxtal_molecule, compare_mol_connectivity
+import argparse
+import os
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser()
+    parser.add_argument("-g", "--gen", dest="gen", type=int, default=1,
+                        help="Number of generation, default: 1")
+    parser.add_argument("-p", "--pop", dest="pop", type=int, default=10,
+                        help="Population size, default: 10")
+    parser.add_argument("-n", "--ncpu", dest="ncpu", type=int, default=1,
+                        help="cpu number, default: 1")
+    parser.add_argument("-a", "--algo", dest="algo", default="WFS",
+                        help="algorithm, default: WFS")
+    parser.add_argument("--mlp", dest="mlp", default="MACE",
+                        help="MLP backend for xyz-only relaxation (MACE/ANI/UMA), default: MACE")
+    parser.add_argument("--preopt", dest="preopt", action="store_true",
+                        help="preoptimize the lattice and rotation")
+    parser.add_argument("--parameters", dest="parameters", default="parameters.xml",
+                        help="forcefield parameter xml file, default: parameters.xml")
+    parser.add_argument("--ffstyle", dest="ffstyle", default="gaff",
+                        help="forcefield style, default: gaff")
+
+    # New: molecule + reference inputs
+    parser.add_argument("--mol", dest="mol", default="CTMTNA.xyz",
+                        help="Molecule input (.xyz or .smi), default: CTMTNA.xyz")
+    parser.add_argument("--smiles", dest="smiles", default=None,
+                        help="Optional SMILES for force-field mode; not needed for .xyz MLP-only runs")
+    parser.add_argument("--xyz-only", dest="xyz_only", action="store_true",
+                        help="Force MLP-only mode (selected automatically for .xyz without --smiles)")
+    parser.add_argument("--nconf", dest="nconf", type=int, default=1,
+                        help="Number of conformers generated from --smiles, default: 1")
+    parser.add_argument("--niter-conf", dest="niter_conf", type=int, default=5,
+                        help="Embedding iterations for conformer generation, default: 5")
+    parser.add_argument("--conf-tol", dest="conf_tol", type=float, default=0.5,
+                        help="RMSD tolerance for unique conformers, default: 0.5")
+    parser.add_argument("--uff", dest="use_uff", action="store_true",
+                        help="Use UFF (instead of MMFF) in conformer generation")
+    parser.add_argument("--seed", dest="seed", default=None,
+                        help="Optional reference crystal CIF used only for match checking")
+    parser.add_argument("--wdir", dest="wdir", default="ctmtna-simple",
+                        help="Working directory, default: ctmtna-simple")
+    parser.add_argument("--sg", dest="sg", type=int, nargs="+", default=[61],
+                        help="Space group list, default: 61")
+    # add CLI arg
+    parser.add_argument(
+        "--active-sites",
+        dest="active_sites",
+        type=int,
+        nargs=3,
+        metavar=("DONOR", "ACCEPTOR", "H"),
+        default=None,
+        help="Optional atom indices for active sites, e.g. --active-sites 11 12 20",
+    )
+
+    options = parser.parse_args()
+
+    # build active_sites only if provided
+    active_sites = None
+    if options.active_sites is not None:
+        d, a, h = options.active_sites
+        active_sites = [[d], [a], [h]]
+
+    mol_paths = [x.strip() for x in options.mol.split(",") if len(x.strip()) > 0]
+    if len(mol_paths) == 0:
+        raise ValueError("Please provide at least one molecule path via --mol")
+    mol_ext = os.path.splitext(mol_paths[0])[1].lower()
+    for mpath in mol_paths:
+        ext = os.path.splitext(mpath)[1].lower()
+        if ext != ".smi" and not os.path.exists(mpath):
+            raise FileNotFoundError(f"Cannot find molecule file: {mpath}")
+    if options.seed is not None and not os.path.exists(options.seed):
+        raise FileNotFoundError(f"Cannot find reference CIF: {options.seed}")
+
+    xyz_only = options.xyz_only or (
+        options.smiles is None
+        and all(os.path.splitext(path)[1].lower() == ".xyz" for path in mol_paths)
+    )
+
+    # Optimizer currently requires a valid SMILES string internally
+    if xyz_only:
+        if options.algo != "WFS":
+            raise ValueError("xyz-only mode currently supports --algo WFS only")
+        smiles_opt = options.smiles if options.smiles is not None else "xyz_only"
+    elif options.smiles is not None:
+        smiles_opt = options.smiles
+    elif mol_ext == ".smi":
+        smiles_opt = os.path.splitext(os.path.basename(mol_paths[0]))[0]
+    else:
+        raise ValueError(
+            "For .xyz input, please also provide --smiles '<SMILES>' "
+            "so optimizer torsion/FF initialization can proceed."
+        )
+
+    # Build molecule pool:
+    # - single geometry from --mol
+    # - or multiple conformers generated from --smiles
+    if xyz_only:
+        mol_objs = [pyxtal_molecule(mpath, active_sites=active_sites) for mpath in mol_paths]
+        molecules_for_opt = [mol_objs]
+        seed_molecules = [mol_objs[0]]
+    elif options.nconf > 1:
+        if options.smiles is None:
+            raise ValueError("Please provide --smiles when --nconf > 1")
+        confs = pyxtal_molecule.get_conformers_from_smiles(
+            options.smiles,
+            N_iter=options.niter_conf,
+            N_conf=options.nconf,
+            tol=options.conf_tol,
+            use_uff=options.use_uff,
+        )
+        if len(confs) == 0:
+            raise RuntimeError("No conformers were generated from --smiles")
+        if active_sites is not None:
+            for m in confs:
+                m.active_sites = active_sites
+        molecules_for_opt = [confs]
+        seed_molecules = [confs[0]]
+    else:
+        m1 = pyxtal_molecule(mol_paths[0], active_sites=active_sites)
+        # For xyz input, verify topology matches the SMILES-based template used
+        # by optimizer internals (torsion/FF typing).
+        if mol_ext == ".xyz":
+            m_smi = pyxtal_molecule(smiles_opt + ".smi")
+            ok, _ = compare_mol_connectivity(m1.mol, m_smi.mol, ignore_HH=True)
+            if not ok:
+                raise ValueError(
+                    "Input .xyz connectivity does not match --smiles template. "
+                    "HTOCSP force-field/torsion setup is SMILES-driven, so xyz-only "
+                    "input is not currently sufficient for robust optimization. "
+                    "Use --mol '<SMILES>.smi' (or --nconf from SMILES), or provide "
+                    "an xyz generated with the same atom/bond topology convention."
+                )
+        molecules_for_opt = [[m1]]
+        seed_molecules = [m1]
+
+    # A reference CIF is optional. It is used for match checking, not for
+    # defining the molecule; molecular geometry comes from --mol.
+    pmg = None
+    if options.seed is not None:
+        xtal = pyxtal(molecular=True)
+        xtal.from_seed(options.seed, molecules=seed_molecules)
+        pmg = xtal.to_pymatgen()
+
+    # Sampling
+    fun = globals().get(options.algo)
+    if fun is None:
+        raise ValueError(f"Unknown algorithm: {options.algo}. Choose from WFS, DFS, QRS.")
+
+    run_kwargs = dict(
+        tag="csp_run",
+        N_gen=options.gen,
+        N_pop=options.pop,
+        N_cpu=options.ncpu,
+        mlp=options.mlp,
+        skip_mlp=False if xyz_only else True,
+        ff_style=options.ffstyle,
+        ff_parameters=options.parameters,
+        molecules=molecules_for_opt,
+        xyz_only=xyz_only,
+    )
+    if options.algo != "QRS":
+        run_kwargs["pre_opt"] = options.preopt
+    if xyz_only and options.algo == "WFS":
+        run_kwargs["fracs"] = [1.0, 0.0]
+
+    go = fun(
+        smiles_opt,
+        options.wdir,
+        options.sg,
+        **run_kwargs,
+    )
+
+    go.run(ref_pmg=pmg)
+    if pmg is not None:
+        go.print_matches(header="Ref_match")
+    go.plot_results()

pyxtal/optimize/WFS.py

@@ -92,6 +92,7 @@ def __init__(
         use_mpi: bool = False,
         pre_opt: bool = False,
         check: bool = True,
+        xyz_only: bool = False,
     ):
         if isinstance(random_state, Generator):
             self.random_state = random_state.spawn(1)[0]
@@ -142,6 +143,7 @@ def __init__(
             check_stable,
             use_mpi,
             pre_opt,
+            xyz_only=xyz_only,
         )
 
         if fracs is None: