mlatom 3.2.0__tar.gz → 3.3.0__tar.gz

{mlatom-3.2.0/src/mlatom.egg-info → mlatom-3.3.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: mlatom
-Version: 3.2.0
+Version: 3.3.0
 Summary: A Package for Atomistic Simulations with Machine Learning
 Home-page: http://mlatom.com
 Author: Pavlo O. Dral
@@ -27,7 +27,7 @@ Requires-Dist: tqdm
 # About Program
 MLatom: a Package for Atomistic Simulations with Machine Learning
 
-Version 3.2.0
+Version 3.3.0
 
 **Official website**: http://mlatom.com/    
 **Manual**: http://mlatom.com/manual/  
@@ -60,7 +60,7 @@ When this Software or its derivatives are used in scientific publications, it sh
 * Pavlo O. Dral, Fuchun Ge, Yi-Fan Hou, Peikun Zheng, Yuxinxin Chen, Mario Barbatti, Olexandr Isayev, Cheng Wang, Bao-Xin Xue, Max Pinheiro Jr, Yuming Su, Yiheng Dai, Yangtao Chen, Lina Zhang, Shuang Zhang, Arif Ullah, Quanhao Zhang, Yanchi Ou. [MLatom 3: A Platform for Machine Learning-enhanced Computational Chemistry Simulations and Workflows](https://doi.org/10.1021/acs.jctc.3c01203).   *J. Chem. Theory Comput.* **2024**, *20*, 1193--1213.                                                                                               
 * Pavlo O. Dral, Fuchun Ge, Bao-Xin Xue, Yi-Fan Hou, Max Pinheiro Jr, Jianxing Huang, Mario Barbatti. [MLatom 2: An Integrative Platform for Atomistic Machine Learning](http://doi.org/10.1007/s41061-021-00339-5). *Top. Curr. Chem.* **2021**, *379*, 27.       
 * Pavlo O. Dral. [MLatom: A Program Package for Quantum Chemical Research Assisted by Machine Learning](http://dx.doi.org/10.1002/jcc.26004). *J. Comput. Chem.* **2019**, *40*, 2339--2347.                                                                                      
-* Pavlo O. Dral, Fuchun Ge, Yi-Fan Hou, Peikun Zheng, Yuxinxin Chen, Bao-Xin Xue, Max Pinheiro Jr, Yuming Su, Yiheng Dai, Yangtao Chen, Shuang Zhang, Lina Zhang, Arif Ullah, Quanhao Zhang, Yanchi Ou, MLatom: A Package for Atomistic Simulations with Machine Learning,  version 3.2.0, Xiamen University, Xiamen, China, 2013-2024.
+* Pavlo O. Dral, Fuchun Ge, Yi-Fan Hou, Peikun Zheng, Yuxinxin Chen, Bao-Xin Xue, Max Pinheiro Jr, Yuming Su, Yiheng Dai, Yangtao Chen, Shuang Zhang, Lina Zhang, Arif Ullah, Quanhao Zhang, Sebastian V. Pios, Yanchi Ou, MLatom: A Package for Atomistic Simulations with Machine Learning,  version 3.3.0, Xiamen University, Xiamen, China, 2013-2024.
   [MLatom.com](http://mlatom.com).
                                                                       
 The citations for MLatom's interfaces and features shall be eventually
@@ -109,7 +109,7 @@ Citations mentioned above should be included. For convenience, below we provide
     }
 
     @misc{MLatomProg,
-    author = {Dral, Pavlo O. and Ge, Fuchun and Hou, Yi-Fan and Zheng, Peikun and Chen, Yuxinxin and Xue, Bao-Xin and Pinheiro Jr, Max and Su, Yuming and Dai, Yiheng and Chen, Yangtao and Zhang, Shuang and Zhang, Lina and Ullah, Arif and Zhang, Quanhao and Ou, Yanchi},
+    author = {Dral, Pavlo O. and Ge, Fuchun and Hou, Yi-Fan and Zheng, Peikun and Chen, Yuxinxin and Xue, Bao-Xin and Pinheiro Jr, Max and Su, Yuming and Dai, Yiheng and Chen, Yangtao and Zhang, Shuang and Zhang, Lina and Ullah, Arif and Zhang, Quanhao and Pios, Sebastian V. and Ou, Yanchi},
     title = {MLatom: A Package for Atomistic Simulations with Machine Learning},
     year = {2013--2024},
     type = {Computer Program}

{mlatom-3.2.0 → mlatom-3.3.0}/README.md

@@ -1,7 +1,7 @@
 # About Program
 MLatom: a Package for Atomistic Simulations with Machine Learning
 
-Version 3.2.0
+Version 3.3.0
 
 **Official website**: http://mlatom.com/    
 **Manual**: http://mlatom.com/manual/  
@@ -34,7 +34,7 @@ When this Software or its derivatives are used in scientific publications, it sh
 * Pavlo O. Dral, Fuchun Ge, Yi-Fan Hou, Peikun Zheng, Yuxinxin Chen, Mario Barbatti, Olexandr Isayev, Cheng Wang, Bao-Xin Xue, Max Pinheiro Jr, Yuming Su, Yiheng Dai, Yangtao Chen, Lina Zhang, Shuang Zhang, Arif Ullah, Quanhao Zhang, Yanchi Ou. [MLatom 3: A Platform for Machine Learning-enhanced Computational Chemistry Simulations and Workflows](https://doi.org/10.1021/acs.jctc.3c01203).   *J. Chem. Theory Comput.* **2024**, *20*, 1193--1213.                                                                                               
 * Pavlo O. Dral, Fuchun Ge, Bao-Xin Xue, Yi-Fan Hou, Max Pinheiro Jr, Jianxing Huang, Mario Barbatti. [MLatom 2: An Integrative Platform for Atomistic Machine Learning](http://doi.org/10.1007/s41061-021-00339-5). *Top. Curr. Chem.* **2021**, *379*, 27.       
 * Pavlo O. Dral. [MLatom: A Program Package for Quantum Chemical Research Assisted by Machine Learning](http://dx.doi.org/10.1002/jcc.26004). *J. Comput. Chem.* **2019**, *40*, 2339--2347.                                                                                      
-* Pavlo O. Dral, Fuchun Ge, Yi-Fan Hou, Peikun Zheng, Yuxinxin Chen, Bao-Xin Xue, Max Pinheiro Jr, Yuming Su, Yiheng Dai, Yangtao Chen, Shuang Zhang, Lina Zhang, Arif Ullah, Quanhao Zhang, Yanchi Ou, MLatom: A Package for Atomistic Simulations with Machine Learning,  version 3.2.0, Xiamen University, Xiamen, China, 2013-2024.
+* Pavlo O. Dral, Fuchun Ge, Yi-Fan Hou, Peikun Zheng, Yuxinxin Chen, Bao-Xin Xue, Max Pinheiro Jr, Yuming Su, Yiheng Dai, Yangtao Chen, Shuang Zhang, Lina Zhang, Arif Ullah, Quanhao Zhang, Sebastian V. Pios, Yanchi Ou, MLatom: A Package for Atomistic Simulations with Machine Learning,  version 3.3.0, Xiamen University, Xiamen, China, 2013-2024.
   [MLatom.com](http://mlatom.com).
                                                                       
 The citations for MLatom's interfaces and features shall be eventually
@@ -83,7 +83,7 @@ Citations mentioned above should be included. For convenience, below we provide
     }
 
     @misc{MLatomProg,
-    author = {Dral, Pavlo O. and Ge, Fuchun and Hou, Yi-Fan and Zheng, Peikun and Chen, Yuxinxin and Xue, Bao-Xin and Pinheiro Jr, Max and Su, Yuming and Dai, Yiheng and Chen, Yangtao and Zhang, Shuang and Zhang, Lina and Ullah, Arif and Zhang, Quanhao and Ou, Yanchi},
+    author = {Dral, Pavlo O. and Ge, Fuchun and Hou, Yi-Fan and Zheng, Peikun and Chen, Yuxinxin and Xue, Bao-Xin and Pinheiro Jr, Max and Su, Yuming and Dai, Yiheng and Chen, Yangtao and Zhang, Shuang and Zhang, Lina and Ullah, Arif and Zhang, Quanhao and Pios, Sebastian V. and Ou, Yanchi},
     title = {MLatom: A Package for Atomistic Simulations with Machine Learning},
     year = {2013--2024},
     type = {Computer Program}

{mlatom-3.2.0 → mlatom-3.3.0}/setup.py

@@ -43,7 +43,7 @@ with open(os.path.join(here, 'README.md')) as f:
 
 setup(
     name = pkg_name,
-    version = "3.2.0",
+    version = "3.3.0",
     author = "Pavlo O. Dral",
     author_email = "admin@mlatom.com",
     license = 'MIT (modified)',

{mlatom-3.2.0 → mlatom-3.3.0}/src/mlatom/MLatom.py

@@ -4,7 +4,7 @@
   !---------------------------------------------------------------------------!
   !                                                                           !
   !     MLatom: a Package for Atomistic Simulations with Machine Learning     !
-  !                             MLatom 3.2.0                                  !
+  !                             MLatom 3.3.0                                  !
   !                                   @                                       !
   !                 Xiamen Atomistic Computing Suite (XACS)                   !
   !                                                                           !
@@ -32,15 +32,11 @@
   ! Shuang Zhang, Arif Ullah, Quanhao Zhang, Yanchi Ou.                       !
   ! J. Chem. Theory Comput. 2024, 20, 1193-1213.                              !
   !                                                                           !
-  ! Pavlo O. Dral, Fuchun Ge, Bao-Xin Xue, Yi-Fan Hou, Max Pinheiro Jr,       !
-  ! Jianxing Huang, Mario Barbatti, Top. Curr. Chem. 2021, 379, 27            !
-  ! Pavlo O. Dral, J. Comput. Chem. 2019, 40, 2339-2347.                      !
-  !                                                                           !
-  ! Pavlo O. Dral, Fuchun Ge, Yi-Fan Hou, Peikun Zheng, Yuxinxin Chen,        !
-  ! Bao-Xin Xue, Max Pinheiro Jr, Yuming Su, Yiheng Dai, Yangtao Chen,        !
-  ! Shuang Zhang, Lina Zhang, Arif Ullah, Quanhao Zhang, Yanchi Ou,           !
+  ! Pavlo O. Dral, Fuchun Ge, Yi-Fan Hou, Peikun Zheng, Yuxinxin Chen, Bao-Xin!
+  ! Xue, Max Pinheiro Jr, Yuming Su, Yiheng Dai, Yangtao Chen, Shuang Zhang,  !
+  ! Lina Zhang, Arif Ullah, Quanhao Zhang, Sebastian V. Pios, Yanchi Ou,      !
   ! MLatom: A Package for Atomistic Simulations with Machine Learning,        !
-  ! version 3.2.0, Xiamen University, Xiamen, China, 2013-2024.               !
+  ! version 3.3.0, Xiamen University, Xiamen, China, 2013-2024.               !
   !                                                                           !
   ! The citations for MLatom's interfaces and features shall be eventually    !
   ! included too. See header.py, ref.json and http://mlatom.com.              !

{mlatom-3.2.0 → mlatom-3.3.0}/src/mlatom/__init__.py

@@ -1,5 +1,5 @@
 #!/usr/bin/env python3
-from . import data, models, plot, simulations, stats, xyz
+from . import data, models, plot, simulations, stats, xyz, namd, constants
 from .simulations import optimize_geometry, irc, freq, thermochemistry, md, generate_initial_conditions, vibrational_spectrum
 from .data import atom, molecule, molecular_database
 from .models import methods

{mlatom-3.2.0 → mlatom-3.3.0}/src/mlatom/aiqm1.py

@@ -11,16 +11,13 @@ import numpy as np
 import os
 from . import data, models, stopper
 
-try: 
-    import torch
-    import torchani
-    from torchani.utils import ChemicalSymbolsToInts
-except:
-    raise ValueError('Please install all Python modules required for TorchANI')
+import torch
+import torchani
+from torchani.utils import ChemicalSymbolsToInts
 
 class aiqm1(models.torchani_model):
     """
-    The Artificial intelligence–quantum mechanical method as in the `AIQM1 paper`_.
+    The Artificial intelligence-quantum mechanical method as in the `AIQM1 paper`_.
 
     Arguments:
         method (str, optional): AIQM method used. Currently supports AIQM1, AIQM1\@DFT*, and AIQM1\@DFT. Default value: AIQM1.
@@ -69,50 +66,66 @@ class aiqm1(models.torchani_model):
         self.aiqm1_model = models.model_tree_node(name=modelname, children=aiqm1_children, operator='sum')
     
     def predict(self, molecular_database=None, molecule=None,
-                calculate_energy=True, calculate_energy_gradients=False, calculate_hessian=False):
-        if molecular_database != None:
-            molDB = molecular_database
-        elif molecule != None:
-            molDB = data.molecular_database()
-            molDB.molecules.append(molecule)
-        else:
-            errmsg = 'Either molecule or molecular_database should be provided in input'
-            raise ValueError(errmsg)
-        
+                calculate_energy=True, calculate_energy_gradients=False, calculate_hessian=False, nstates=1, current_state=0, **kwargs):
+        molDB = super().predict(molecular_database=molecular_database, molecule=molecule)
+        if 'nthreads' in self.__dict__: self.aiqm1_model.nthreads = self.nthreads
         for mol in molDB.molecules:
             self.predict_for_molecule(molecule=mol,
-                                    calculate_energy=calculate_energy, calculate_energy_gradients=calculate_energy_gradients, calculate_hessian=calculate_hessian)
+                                    calculate_energy=calculate_energy, calculate_energy_gradients=calculate_energy_gradients, calculate_hessian=calculate_hessian, nstates=nstates, 
+                                    current_state=current_state,
+                                    **kwargs)
         
     def predict_for_molecule(self, molecule=None,
-                calculate_energy=True, calculate_energy_gradients=False, calculate_hessian=False):
+                calculate_energy=True, calculate_energy_gradients=False, calculate_hessian=False, nstates=1, current_state=0, **kwargs):
         
         for atom in molecule.atoms:
             if not atom.atomic_number in [1, 6, 7, 8]:
                 print(' * Warning * Molecule contains elements other than CHNO, no calculations performed')
                 return
         
+        if nstates >1:
+            mol_copy = molecule.copy()
+            mol_copy.electronic_states = []
+            for _ in range(nstates - len(molecule.electronic_states)):
+                molecule.electronic_states.append(mol_copy.copy())
+        
+        # for molecule in molecules:
         if len(molecule.atoms) == 1:
             molecule.energy = self.atomic_energies[self.method][molecule.atoms[0].atomic_number]
             standard_atom = data.atom(atomic_number=molecule.atoms[0].atomic_number)
             if molecule.charge != 0 or molecule.multiplicity != standard_atom.multiplicity:
                 odm2model = models.methods(method='ODM2*', program=self.qm_program)
                 mol_odm2 = molecule.copy()
-                odm2model.predict(molecule=mol_odm2)
+                odm2model.predict(molecule=mol_odm2, nstates=nstates, **kwargs)
                 mol_standard_odm2 = molecule.copy() ; mol_standard_odm2.charge = 0; mol_standard_odm2.multiplicity=standard_atom.multiplicity
-                odm2model.predict(molecule=mol_standard_odm2)
+                odm2model.predict(molecule=mol_standard_odm2, nstates=nstates, **kwargs)
                 molecule.energy = molecule.energy + mol_odm2.energy - mol_standard_odm2.energy
         else:
+            if nstates > 1 and isinstance(calculate_energy_gradients, list): 
+                if any(calculate_energy_gradients):
+                    calculate_energy_gradients = [True] * nstates
             self.aiqm1_model.predict(molecule=molecule,
-                                    calculate_energy=calculate_energy, calculate_energy_gradients=calculate_energy_gradients, calculate_hessian=calculate_hessian)
+                                    calculate_energy=calculate_energy, calculate_energy_gradients=calculate_energy_gradients, calculate_hessian=calculate_hessian, nstates=nstates, 
+                                    current_state=current_state,
+                                    **kwargs)
             
             properties = [] ; atomic_properties = []
+            
+            calculate_energy_gradients = bool(np.array(calculate_energy_gradients).any())
+            calculate_hessian = bool(np.array(calculate_hessian).any())
             if calculate_energy: properties.append('energy')
             if calculate_energy_gradients: atomic_properties.append('energy_gradients')
             if calculate_hessian: properties.append('hessian')
             modelname = self.method.lower().replace('*','star').replace('@','at')
-            molecule.__dict__[f'{modelname}_nn'].standard_deviation(properties=properties+atomic_properties)
 
-class atomic_energy_shift():
+            if nstates >1:
+                for mol_el_st in molecule.electronic_states:
+                    mol_el_st.__dict__[f'{modelname}_nn'].standard_deviation(properties=properties+atomic_properties)
+            else:
+                molecule.__dict__[f'{modelname}_nn'].standard_deviation(properties=properties+atomic_properties)
+            
+
+class atomic_energy_shift(models.model):
     atomic_energy_shifts = {'AIQM1': {1: -4.29365862e-02, 6: -3.34329586e+01, 7: -4.69301173e+01, 8: -6.29634763e+01},
                             'AIQM1@DFT': {1: -4.27888067e-02, 6: -3.34869833e+01, 7: -4.69896148e+01, 8: -6.30294433e+01}}
     atomic_energy_shifts['AIQM1@DFT*'] = atomic_energy_shifts['AIQM1@DFT']
@@ -121,30 +134,35 @@ class atomic_energy_shift():
         self.method = method
         
     def predict(self, molecular_database=None, molecule=None,
-                calculate_energy=True, calculate_energy_gradients=False, calculate_hessian=False):
-        if molecular_database != None:
-            molDB = molecular_database
-        elif molecule != None:
-            molDB = data.molecular_database()
-            molDB.molecules.append(molecule)
-        else:
-            errmsg = 'Either molecule or molecular_database should be provided in input'
-            raise ValueError(errmsg)
+                calculate_energy=True, calculate_energy_gradients=False, calculate_hessian=False, nstates=1, **kwargs):
+        molDB = super().predict(molecular_database=molecular_database, molecule=molecule)
+        calculate_energy_gradients = bool(np.array(calculate_energy_gradients).any())
+        calculate_hessian = bool(np.array(calculate_hessian).any())
          
         for mol in molDB.molecules:
-            if calculate_energy:
-                sae = 0.0
-                for atom in mol.atoms:
-                    sae += self.atomic_energy_shifts[self.method][atom.atomic_number]
-                mol.energy = sae
-            if calculate_energy_gradients:
-                for atom in mol.atoms:
-                    atom.energy_gradients = np.zeros(3)
-            if calculate_hessian:
-                ndim = len(mol.atoms) * 3
-                mol.hessian = np.zeros(ndim*ndim).reshape(ndim,ndim)
+            molecules = [mol]
 
-class ani_nns_in_aiqm1():
+            if nstates >1:
+                mol_copy = mol.copy()
+                mol_copy.electronic_states = []
+                for _ in range(nstates - len(mol.electronic_states)):
+                    mol.electronic_states.append(mol_copy.copy())
+                molecules = mol.electronic_states
+            
+            for mol in molecules:
+                if calculate_energy:
+                    sae = 0.0
+                    for atom in mol.atoms:
+                        sae += self.atomic_energy_shifts[self.method][atom.atomic_number]
+                    mol.energy = sae
+                if calculate_energy_gradients:
+                    for atom in mol.atoms:
+                        atom.energy_gradients = np.zeros(3)
+                if calculate_hessian:
+                    ndim = len(mol.atoms) * 3
+                    mol.hessian = np.zeros(ndim*ndim).reshape(ndim,ndim)
+
+class ani_nns_in_aiqm1(models.torchani_model):
     species_order = [1, 6, 7, 8]
     
     def __init__(self, method='AIQM1', model_index = 0):
@@ -225,34 +243,39 @@ class ani_nns_in_aiqm1():
         self.nn = nn
     
     def predict(self, molecular_database=None, molecule=None,
-                calculate_energy=True, calculate_energy_gradients=False, calculate_hessian=False):
-        if molecular_database != None:
-            molDB = molecular_database
-        elif molecule != None:
-            molDB = data.molecular_database()
-            molDB.molecules.append(molecule)
-        else:
-            errmsg = 'Either molecule or molecular_database should be provided in input'
-            raise ValueError(errmsg)
+                calculate_energy=True, calculate_energy_gradients=False, calculate_hessian=False, nstates=1, **kwargs):
+        molDB = super().predict(molecular_database=molecular_database, molecule=molecule)
         
+        calculate_energy_gradients = bool(np.array(calculate_energy_gradients).any())
+        calculate_hessian = bool(np.array(calculate_hessian).any())
         species_to_tensor = ChemicalSymbolsToInts(self.species_order)
         
         for mol in molDB.molecules:
-            atomic_numbers = np.array([atom.atomic_number for atom in mol.atoms])
-            xyz_coordinates = torch.tensor(np.array(mol.xyz_coordinates).astype('float')).to(self.device).requires_grad_(calculate_energy_gradients or calculate_hessian)
-            xyz_coordinates = xyz_coordinates.unsqueeze(0)
-            species = species_to_tensor(atomic_numbers).to(self.device).unsqueeze(0)
-            ANI_NN_energy = self.model((species, xyz_coordinates)).energies
-            if calculate_energy: mol.energy = float(ANI_NN_energy)
-            if calculate_energy_gradients or calculate_hessian:
-                ANI_NN_energy_gradients = torch.autograd.grad(ANI_NN_energy.sum(), xyz_coordinates, create_graph=True, retain_graph=True)[0]
-                if calculate_energy_gradients:
-                    grads = ANI_NN_energy_gradients[0].detach().cpu().numpy()
-                    for iatom in range(len(mol.atoms)):
-                        mol.atoms[iatom].energy_gradients = grads[iatom]
-            if calculate_hessian:
-                ANI_NN_hessian = torchani.utils.hessian(xyz_coordinates, energies=ANI_NN_energy)
-                mol.hessian = ANI_NN_hessian[0].detach().cpu().numpy()
+            molecules = [mol]
+
+            if nstates >1:
+                mol_copy = mol.copy()
+                mol_copy.electronic_states = []
+                for _ in range(nstates - len(mol.electronic_states)):
+                    mol.electronic_states.append(mol_copy.copy())
+                molecules = mol.electronic_states
+            
+            for mol in molecules:
+                atomic_numbers = np.array([atom.atomic_number for atom in mol.atoms])
+                xyz_coordinates = torch.tensor(np.array(mol.xyz_coordinates).astype('float')).to(self.device).requires_grad_(calculate_energy_gradients or calculate_hessian)
+                xyz_coordinates = xyz_coordinates.unsqueeze(0)
+                species = species_to_tensor(atomic_numbers).to(self.device).unsqueeze(0)
+                ANI_NN_energy = self.model((species, xyz_coordinates)).energies
+                if calculate_energy: mol.energy = float(ANI_NN_energy)
+                if calculate_energy_gradients or calculate_hessian:
+                    ANI_NN_energy_gradients = torch.autograd.grad(ANI_NN_energy.sum(), xyz_coordinates, create_graph=True, retain_graph=True)[0]
+                    if calculate_energy_gradients:
+                        grads = ANI_NN_energy_gradients[0].detach().cpu().numpy()
+                        for iatom in range(len(mol.atoms)):
+                            mol.atoms[iatom].energy_gradients = grads[iatom]
+                if calculate_hessian:
+                    ANI_NN_hessian = torchani.utils.hessian(xyz_coordinates, energies=ANI_NN_energy)
+                    mol.hessian = ANI_NN_hessian[0].detach().cpu().numpy()
 
 if __name__ == '__main__':
     pass

{mlatom-3.2.0 → mlatom-3.3.0}/src/mlatom/data.py

@@ -125,6 +125,8 @@ class molecule:
             self.atoms = []
         else:
             self.atoms = atoms
+        
+        self.electronic_states = []
 
     def read_from_xyz_file(self, filename: str, format: Union[str, None] = None) -> molecule:
         '''
@@ -137,6 +139,8 @@ class molecule:
             - ``'COLUMBUS'``
 
             - ``'NEWTON-X'`` or ``'NX'``
+
+            - ``'turbomol'``
             
         Arguments:
             filename (str): The name of the file to be read.
@@ -159,6 +163,8 @@ class molecule:
 
             - ``'NEWTON-X'`` or ``'NX'``
 
+            - ``'turbomol'``
+            
         Arguments:
             string (str): The string input.
             format (str, optional): The format of the string.
@@ -187,6 +193,15 @@ class molecule:
                                     nuclear_charge=float(yy[1]),
                                     xyz_coordinates=coords,
                                     nuclear_mass=float(yy[-1])))
+        elif format.casefold() == 'turbomole':
+            for line in fxyz:
+                yy = line.split()
+                if len(yy) != 4:
+                    continue 
+                else:
+                    coords = array([float(xx)*constants.Bohr2Angstrom for xx in yy[0:3]]).astype(float)                    
+                    self.atoms.append(atom(element_symbol=yy[3].capitalize(),
+                                      xyz_coordinates=coords))
         return self
 
     def read_from_numpy(self, coordinates: np.ndarray, species: np.ndarray) -> molecule:
@@ -308,6 +323,8 @@ class molecule:
 
             - ``'NEWTON-X'`` or ``'NX'``
 
+            - ``'turbomol'``
+
         Arguments:
             filename (str): The name of the file to be written.
             format (str, optional): The format of the file.
@@ -330,6 +347,12 @@ class molecule:
                                                                       atom.xyz_coordinates[1] * constants.Angstrom2Bohr,
                                                                       atom.xyz_coordinates[2] * constants.Angstrom2Bohr,
                                                                       atom.nuclear_mass))
+            elif format.casefold() in ['TURBOMOLE'.casefold()]:
+                fw.writelines('$coord\n')
+                for atom in self.atoms:
+                    fw.writelines('%25.13f %25.13f %25.13f %-3s \n' % (atom.xyz_coordinates[0] * constants.Angstrom2Bohr, atom.xyz_coordinates[1] * constants.Angstrom2Bohr, atom.xyz_coordinates[2] * constants.Angstrom2Bohr, atom.element_symbol))
+                fw.writelines('$user-defined bonds\n')
+                fw.writelines('$end\n')
 
 
     def get_xyz_string(self) -> str:
@@ -391,6 +414,14 @@ class molecule:
 
     def get_energy_gradients(self):
         return self.get_xyz_vectorial_properties('energy_gradients')
+    
+    @property
+    def energy_gradients(self):
+        return self.get_energy_gradients()
+    
+    @energy_gradients.setter
+    def energy_gradients(self, value):
+        self.add_xyz_derivative_property(value, property_name='energy', xyz_derivative_property='energy_gradients')
 
     def get_number_of_atoms(self):
         return len(self)
@@ -573,7 +604,35 @@ class molecule:
         
     def __getitem__(self, item):
         return self.atoms[item]
+
+    @property 
+    def state_energies(self) -> np.ndarray:
+        '''
+        The electronic state energies of the molecule.
+        '''
+        return np.array([state.energy for state in self.electronic_states])
         
+    @property 
+    def state_gradients(self) -> np.ndarray:
+        '''
+        The electronic state energy gradients of the molecule.
+        '''
+        return np.array([state.energy_gradients for state in self.electronic_states])
+        
+    @property 
+    def energy_gaps(self) -> np.ndarray:
+        '''
+        The energy gaps of different states.
+        '''
+        return self.state_energies - self.state_energies[:, np.newaxis]
+    
+    @property 
+    def excitation_energies(self) -> np.ndarray:
+        '''
+        The excitation energies of the molecule from ground state.
+        '''
+        return self.state_energies[1:] - self.electronic_states[0].energy if len(self.electronic_states) > 1 else []
+
 class properties_tree_node():
     def __init__(self, name=None, parent=None, children=None, properties=None):
         self.name = name
@@ -1269,6 +1328,8 @@ def dict_to_molecule_class_instance(dd):
         if key == 'atoms':
             for aa in dd[key]:
                 mol.atoms.append(dict_to_atom_class_instance(aa))
+        elif key == 'electronic_states':
+            mol.electronic_states = [dict_to_molecule_class_instance(state_dict) for state_dict in dd[key]]
         elif type(dd[key]) == dict:
             if 'parent' in dd[key].keys():
                 dict_to_properties_tree_node_class_instance(dd, key, mol)    
@@ -1330,6 +1391,13 @@ class molecular_trajectory():
                     'mass':None,
                     'species':None,
                     }
+            data['state_energies'] = []
+            data['state_gradients'] = []
+            if 'nonadiabatic_coupling_vectors' in self.steps[0].molecule.atoms[0].__dict__: data['nonadiabatic_coupling_vectors'] = []
+            data['random_number'] = []
+            data['hopping_probabilities'] = []
+            if 'current_state' in self.steps[0].__dict__: data['current_state'] = []
+            #'state_gradients'
             dp_flag = True
             for istep in self.steps:
                 if not 'dipole_moment' in istep.molecule.__dict__.keys():
@@ -1343,9 +1411,34 @@ class molecular_trajectory():
                 data['position'].append(istep.molecule.xyz_coordinates)
                 data['velocities'].append(istep.molecule.get_xyz_vectorial_properties('xyz_velocities'))
                 data['gradients'].append(istep.molecule.get_energy_gradients())
+                if len(istep.molecule.electronic_states) > 1:
+                    data['state_energies'].append(istep.molecule.state_energies)
+                    state_gradients = []
+                    for i in range(0, len(istep.molecule.electronic_states)):
+                        if 'energy_gradients' in istep.molecule.electronic_states[i].atoms[0].__dict__:
+                            state_gradients.append(istep.molecule.electronic_states[i].get_energy_gradients())
+                        else:
+                            state_gradients.append(None)
+                    data['state_gradients'].append(np.array(state_gradients))
+                if 'nonadiabatic_coupling_vectors' in data.keys(): data['nonadiabatic_coupling_vectors'].append(istep.molecule.get_xyz_vectorial_properties('nonadiabatic_coupling_vectors'))
                 data['kinetic_energy'].append(istep.molecule.kinetic_energy)
                 data['potential_energy'].append(istep.molecule.energy)
                 data['total_energy'].append(istep.molecule.kinetic_energy+istep.molecule.energy)
+                if 'random_number' in data.keys():
+                    try:
+                        data['random_number'].append(istep.random_number)
+                    except AttributeError:
+                        data['random_number'].append(np.nan)
+                if 'hopping_probabilities' in data.keys():
+                    try:
+                        data['hopping_probabilities'].append(max(istep.hopping_probabilities))
+                    except AttributeError:
+                        data['hopping_probabilities'].append(np.nan)
+                if 'current_state' in data.keys():
+                    try:
+                        data['current_state'].append(istep.current_state)
+                    except AttributeError:
+                        data['current_state'].append(np.nan)
                 if dp_flag:
                     data['dipole_moment'].append(istep.molecule.dipole_moment)
             with h5md(filename) as trajH5:
@@ -1394,6 +1487,22 @@ class molecular_trajectory():
                 # gradients
                 for iatom in range(Natoms):
                     molecule_istep.atoms[iatom].energy_gradients = data['gradients'][istep][iatom]
+
+                if 'state_energies' in data.keys():
+                    molecule_istep.electronic_states=[]
+                    molecule_istep.electronic_states.extend([molecule_istep.copy() for _ in range(len(data['state_energies'][istep]))])
+                    for i in range(0, len(data['state_energies'][istep])):
+                        molecule_istep.electronic_states[i].energy = data['state_energies'][istep][i]
+                if 'state_gradients' in data.keys():
+                    if not molecule_istep.electronic_states:
+                        molecule_istep.electronic_states=[]
+                        molecule_istep.electronic_states.extend([molecule_istep.copy() for _ in range(len(data['state_gradients'][istep]))])
+                    for i in range(0, len(data['state_gradients'][istep])):
+                        if data['state_gradients'][istep][i] is not None:
+                            molecule_istep.electronic_states[i].add_xyz_derivative_property(np.array(data['state_gradients'][istep][i]).astype(float), 'energy', 'energy_gradients')
+                if 'nonadiabatic_coupling_vectors' in data.keys():
+                    for iatom in range(Natoms):
+                        molecule_istep.atoms[iatom].nonadiabatic_coupling_vectors = data['nonadiabatic_coupling_vectors'][istep][iatom]
                 # kinetic_energy 
                 # molecule_istep.kinetic_energy = data['kinetic_energy'][istep]
                 # potential_energy 
@@ -1406,6 +1515,15 @@ class molecular_trajectory():
                 trajectory_step.molecule = molecule_istep
                 trajectory_step.step = istep 
                 trajectory_step.time = data['time'][istep]
+                # random_number
+                if 'random_number' in data.keys():
+                    trajectory_step.random_number = data['random_number'][istep]
+                # prob
+                if 'hopping_probabilities' in data.keys():
+                    trajectory_step.hopping_probabilities = data['hopping_probabilities'][istep]
+                # current_state
+                if 'current_state' in data.keys():
+                    trajectory_step.current_state = data['current_state'][istep]
                 self.steps.append(trajectory_step)
         
         elif format.casefold() == 'json'.casefold():