Additinoal fixes to trajectories.

architector/io_calc.py

@@ -88,7 +88,7 @@ def __init__(self, structure, parameters={}, init_sanity_check=False,
                 fmax=0.1, maxsteps=1000, ff_preopt_run=False,
                 detect_spin_charge=False, fix_m_neighbors=False,
                 default_params=params, ase_opt_method=None, ase_opt_kwargs={}, species_run=False,
-                intermediate=False,skip_spin_assign=False,
+                intermediate=False, skip_spin_assign=False, save_trajectories=False,
                 calculator=None, debug=False):
         """CalcExecutor is the class handling all calculations of full metal-ligand complexes.
 
@@ -150,6 +150,7 @@ def __init__(self, structure, parameters={}, init_sanity_check=False,
         self.method = method
         default_params = params.copy()
         default_params['debug'] = debug
+        default_params['save_trajectories'] = save_trajectories
         default_params.update(parameters)
         self.parameters = default_params
         self.init_sanity_check = init_sanity_check
@@ -430,7 +431,7 @@ def calculate(self):
         if self.replace_trics:
             self.ase_opt_kwargs['sella_internal_trics'] = True
 
-        if self.parameters['save_trajectories'] and (self.trajectory is not None):
+        if self.parameters['save_trajectories'] and (self.trajectory is not None) and (self.parameters['dump_ase_atoms']):
             self.dump_traj()
         elif self.parameters['save_trajectories']:
             pass
@@ -442,7 +443,7 @@ def calculate(self):
     def read_traj(self):
         pwd = os.path.abspath('.')
         traj = Trajectory(os.path.join(pwd,'temp.traj'))
-        self.trajectory = traj
+        self.trajectory = [x for x in traj] # Convert to atoms
 
     def dump_traj(self):
         for i,ats in enumerate(self.trajectory):

architector/io_molecule.py

@@ -9,7 +9,7 @@
 """
 
 import ase
-from ase.io import read
+from ase.io import (read, Trajectory)
 from ase.atoms import Atoms
 from ase.atom import Atom
 import numpy as np
@@ -18,7 +18,7 @@
 import itertools
 import architector
 from architector import io_obabel
-from architector.io_core import (Geometries,calc_all_coord_atom_angles)
+from architector.io_core import (Geometries, calc_all_coord_atom_angles)
 import architector.io_ptable as io_ptable
 from io import StringIO
 from scipy.sparse.csgraph import (csgraph_from_dense, connected_components)
@@ -62,6 +62,12 @@ def convert_io_molecule(structure,
         # mol2 filename
         elif structure[-5:] == '.mol2':
             mol.read_mol2(structure,readstring=False)
+        elif structure[-5:] == '.traj': # Read in trajectory file.
+            traj = Trajectory(structure)
+            output = []
+            for ats in traj:
+                output.append(convert_io_molecule(ats))
+            return output
         elif isinstance(structure,str) and (len(structure.split('\n')) > 3) and (structure.split('\n')[0].replace(' ','').isnumeric()) \
             and ('FORCES' in structure) and ('ENERGY' in structure): # RXYZ string.
             mol.read_rxyz(structure,readstring=True)

architector/visualization.py

@@ -32,7 +32,11 @@ def type_convert(structures):
     """
     outlist = []
     if isinstance(structures,str):
-        structures = [convert_io_molecule(structures)]
+        out = convert_io_molecule(structures)
+        if isinstance(out,(np.ndarray,list)): # Read in traj.
+            structures=out
+        else:
+            structures = [out]
     elif isinstance(structures,(ase.atoms.Atoms,architector.io_molecule.Molecule)):
         structures = [convert_io_molecule(structures)]
     elif isinstance(structures,dict):