mlatom 3.5.0__tar.gz → 3.6.0__tar.gz

{mlatom-3.5.0/src/mlatom.egg-info → mlatom-3.6.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: mlatom
-Version: 3.5.0
+Version: 3.6.0
 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 3.5.0
+Version 3.6.0
 
 **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, Sebastian V. Pios, Yanchi Ou, MLatom: A Package for Atomistic Simulations with Machine Learning,  version 3.5.0, 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 3.6.0, Xiamen University, Xiamen, China, 2013-2024.
   [MLatom.com](http://mlatom.com).
                                                                       
 The citations for MLatom's interfaces and features shall be eventually

{mlatom-3.5.0 → mlatom-3.6.0}/README.md

@@ -1,7 +1,7 @@
 # About Program
 MLatom: a Package for Atomistic Simulations with Machine Learning
 
-Version 3.5.0
+Version 3.6.0
 
 **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, Sebastian V. Pios, Yanchi Ou, MLatom: A Package for Atomistic Simulations with Machine Learning,  version 3.5.0, 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 3.6.0, Xiamen University, Xiamen, China, 2013-2024.
   [MLatom.com](http://mlatom.com).
                                                                       
 The citations for MLatom's interfaces and features shall be eventually

{mlatom-3.5.0 → mlatom-3.6.0}/setup.py

@@ -43,7 +43,7 @@ with open(os.path.join(here, 'README.md')) as f:
 
 setup(
     name = pkg_name,
-    version = "3.5.0",
+    version = "3.6.0",
     author = "Pavlo O. Dral",
     author_email = "admin@mlatom.com",
     license = 'MIT (modified)',

{mlatom-3.5.0 → mlatom-3.6.0}/src/mlatom/MLatom.py

@@ -4,7 +4,7 @@
   !---------------------------------------------------------------------------!
   !                                                                           !
   !     MLatom: a Package for Atomistic Simulations with Machine Learning     !
-  !                             MLatom 3.5.0                                  !
+  !                             MLatom 3.6.0                                  !
   !                                   @                                       !
   !                 Xiamen Atomistic Computing Suite (XACS)                   !
   !                                                                           !
@@ -36,7 +36,7 @@
   ! 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 3.5.0, Xiamen University, Xiamen, China, 2013-2024.               !
+  ! version 3.6.0, 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-3.5.0 → mlatom-3.6.0}/src/mlatom/args_class.py

@@ -462,6 +462,9 @@ class mlatom_args(ArgsBase):
         self.set_keyword_alias('ANI-2x', ['ani2x'])
         self.set_keyword_alias('ANI-1x-D4', ['ani1xd4'])
         self.set_keyword_alias('ANI-2x-D4', ['ani2xd4'])
+        self.set_keyword_alias('ANI-1xnr', ['ani1xnr'])
+        self.set_keyword_alias('AIMNet2@B973c', ['aimnet2atb973c'])
+        self.set_keyword_alias('AIMNet2@wb97M-D3', ['aimnet2atwb97md3'])
         self.set_keyword_alias('GFN2-xTB', ['gfn2xtb'])
         self.set_keyword_alias('MNDO/dH', ['mndodh'])
         self.set_keyword_alias('MNDO/H', ['mndoh'])

{mlatom-3.5.0 → mlatom-3.6.0}/src/mlatom/data.py

@@ -1486,6 +1486,7 @@ class molecular_trajectory():
             moldb.write_file_with_properties(filename+'.ekin',property_to_write='kinetic_energy')
             moldb.write_file_with_properties(filename+'.epot',property_to_write='energy')
             moldb.write_file_with_properties(filename+'.etot',property_to_write='total_energy')
+            moldb.write_file_with_properties(filename+'.temp',property_to_write='temperature')
             if 'dipole_moment' in moldb.molecules[0].__dict__.keys():
                 with open(filename+'.dp','w') as dpf:
                     for imolecule in moldb.molecules:

{mlatom-3.5.0 → mlatom-3.6.0}/src/mlatom/doc.py

@@ -179,6 +179,9 @@ class Doc():
       ANI-2x                   perform ANI-2x      calculations
       ANI-1x-D4                perform ANI-1x-D4   calculations
       ANI-2x-D4                perform ANI-2x-D4   calculations
+      ANI-1xnr                 perform ANI-1xnr    calculations
+      AIMNet2@B973c            perform AIMNet2@B97-3c calculations
+      AIMNet2@wB97M-D3         perform AIMNet2@wB97M-D3 calculations
       ODM2
       ODM2*
       GFN2-xTB

{mlatom-3.5.0 → mlatom-3.6.0}/src/mlatom/header.py

@@ -128,6 +128,18 @@ def printHeader(args):
         if args.ani2xd4:
             refItems['D4']  = refs['D4']
             refItems['D4 program']  = refs['D4prog']
+
+    if args.method:
+        if 'DM21' in args.method.upper():
+            refItems['DM21'] = refs['DM21']
+    
+    if args.ani1xnr:
+        refItems['ANI-1xnr'] = refs['ANI-1xnr']
+    if args.aimnet2atb973c:
+        refItems['AIMNet2@B973c'] = refs['AIMNet2']
+    if args.aimnet2atwb97md3:
+        refItems['AIMNet2@wb97M-D3'] = refs['AIMNet2']
+
     
     if args.geomopt:
         if 'optprog=ase' in ' '.join(args.args2pass).lower():

{mlatom-3.5.0 → mlatom-3.6.0}/src/mlatom/initial_conditions.py

@@ -202,7 +202,7 @@ def generate_initial_conditions(molecule=None, generation_method=None, number_of
             mass = mass_.reshape(Natoms,1)
             total_mass = np.sum(mass_)
             for irepeat in range(number_of_initial_conditions):
-                if eliminate_angular_momentum:
+                if eliminate_angular_momentum and not molecule.is_it_linear():
                     velocities_all[irepeat] = getridofang(coordinates_all[irepeat],velocities_all[irepeat],mass_)
                     v_cm = sum(velocities_all[irepeat]*mass)/total_mass
                     velocities_all[irepeat] -= v_cm

{mlatom-3.5.0 → mlatom-3.6.0}/src/mlatom/interfaces/__init__.py

@@ -10,6 +10,10 @@ def ani(**kwargs):
     from .torchani_interface import ani_methods as interface
     return interface(**kwargs)
 
+def aimnet2(**kwargs):
+    from .torchani_interface import aimnet2_methods as interface 
+    return interface(**kwargs)
+
 def mndo(**kwargs):
     from .mndo_interface import mndo_methods as interface
     return interface(**kwargs)

{mlatom-3.5.0 → mlatom-3.6.0}/src/mlatom/interfaces/gaussian_interface.py

@@ -186,13 +186,18 @@ def run_gaussian_job(**kwargs):
         memory = f"%mem={kwargs['memory']}\n"
     gaussian_keywords = f'{memory}%nproc={nthreads}\n' + gaussian_keywords 
     
+    if 'cwd' in kwargs:
+        cwd = kwargs['cwd']
+    else:
+        cwd='.'
+        
     if 'model_predict_kwargs' in kwargs:
         model_predict_kwargs_str = str(kwargs['model_predict_kwargs'])
     else:
         model_predict_kwargs_str = "{}"
     
     model_predict_kwargs_str_file = 'model_predict_kwargs'
-    with open(model_predict_kwargs_str_file, 'w') as f:
+    with open(os.path.join(cwd, model_predict_kwargs_str_file), 'w') as f:
         f.write(model_predict_kwargs_str)
     
     if 'external_task' in kwargs:
@@ -227,11 +232,6 @@ def run_gaussian_job(**kwargs):
                 kwargs['method'] = 'p ' + kwargs['method']
             gaussian_keywords += '# '+kwargs['method']+'\n'
 
-    if 'cwd' in kwargs:
-        cwd = kwargs['cwd']
-    else:
-        cwd='.'
-
     if 'writechk' in kwargs:
         writechk = kwargs['writechk']
     else:

{mlatom-3.5.0 → mlatom-3.6.0}/src/mlatom/interfaces/pyscf_interface.py

@@ -72,6 +72,10 @@ class pyscf_methods(OMP_pyscf):
         pyscf_mol.unit = 'Ang'
         pyscf_mol.build()
 
+        # DM21
+        if 'DM21' in self.method.upper():
+            self.predict_for_molecule_DM21(molecule=molecule, pyscf_mol=pyscf_mol, calculate_energy=calculate_energy, calculate_energy_gradients=calculate_energy_gradients, calculate_hessian=calculate_hessian, **kwargs)
+            return
 
         # HF
         if 'HF' == self.method.upper():
@@ -193,8 +197,50 @@ class pyscf_methods(OMP_pyscf):
                     h[ii*3:(ii+1)*3, jj*3:(jj+1)*3] = hess[ii][jj]
             molecule.hessian = h / constants.Bohr2Angstrom**2
 
-       
-    
+    def predict_for_molecule_DM21(self, molecule=None, pyscf_mol=None, calculate_energy=True, calculate_energy_gradients=False, calculate_hessian=False, **kwargs):
+        # reference: https://github.com/google-deepmind/deepmind-research/tree/f5de0ede8430809180254ee957abf36ed62579ef/density_functional_approximation_dm21
+        # METHODS AVAILABE:
+        # DM21 - trained on molecules dataset, and fractional charge, and fractional spin constraints.
+        # DM21m - trained on molecules dataset.
+        # DM21mc - trained on molecules dataset, and fractional charge constraints.
+        # DM21mu - trained on molecules dataset, and electron gas constraints.
+
+        from pyscf import dft
+        try:
+            import density_functional_approximation_dm21 as dm21
+        except:
+            errmsg = 'Please install required packages for DM21. For more details, please refer to https://github.com/google-deepmind/deepmind-research/tree/master/density_functional_approximation_dm21.'
+            raise ModuleNotFoundError(errmsg)
+        
+        if pyscf_mol.spin == 0:
+            pyscf_method = dft.RKS(pyscf_mol)
+        else:
+            pyscf_method = dft.UKS(pyscf_mol)
+
+        pyscf_method.xc = 'B3LYP'
+        pyscf_method.run()
+        dm0 = pyscf_method.make_rdm1()
+        pyscf_method._numint = dm21.NeuralNumInt(dm21.Functional.__dict__[self.method])
+        # relax convergence tolerances to increase success to convergence
+        pyscf_method.conv_tol = 1E-6
+        pyscf_method.conv_tol_grad = 1E-3
+        try:
+            pyscf_method.kernel(dm0=dm0)
+        except:
+            errmsg = 'DM21 cannot converge properly'
+            stopper.stopMLatom(errmsg)
+                
+        if calculate_energy:
+            molecule.energy = pyscf_method.e_tot
+
+        if calculate_energy_gradients:           
+            errmsg = 'DM21 by pyscf does not support gradients calculation'
+            raise ValueError(errmsg)
+
+        if calculate_hessian:
+            errmsg = 'DM21 by pyscf does not support hessian calculation'
+            raise ValueError(errmsg)
+
     @doc_inherit
     def predict(self, molecule=None, molecular_database=None, calculate_energy=True, calculate_energy_gradients=False, calculate_hessian=False, **kwargs):
         '''

{mlatom-3.5.0 → mlatom-3.6.0}/src/mlatom/interfaces/torchani_interface.py

@@ -15,8 +15,11 @@ import numpy as np
 import tqdm
 from collections import OrderedDict
 import torch
+from torch import nn, Tensor
 import torchani
 from torchani.data import TransformableIterable, IterableAdapter
+from typing import Dict, List
+
 
 from .. import data
 from .. import models
@@ -649,7 +652,9 @@ class ani_methods(models.torchani_model):
 
     def model_setup(self, method):
         self.method = method
-        if 'ANI-1x'.casefold() in method.casefold():
+        if 'ANI-1xnr'.casefold() in method.casefold():
+            self.model = load_ani1xnr_model()
+        elif 'ANI-1x'.casefold() in method.casefold():
             self.model = torchani.models.ANI1x(periodic_table_index=True).to(self.device).double()
         elif 'ANI-1ccx'.casefold() in method.casefold():
             self.model = torchani.models.ANI1ccx(periodic_table_index=True).to(self.device).double()
@@ -726,6 +731,132 @@ class ani_methods(models.torchani_model):
             modelname = self.method.lower().replace('-','')
         molecule.__dict__[f'{modelname}'].standard_deviation(properties=properties+atomic_properties)
 
+def load_ani1xnr_model():
+    # ANI-1xnr https://github.com/atomistic-ml/ani-1xnr/
+    # Universal reactive ML potential ANI-1xnr: https://doi.org/10.1038/s41557-023-01427-3
+    species = ['H', 'C', 'N', 'O']
+    def parse_ani1xnr_resources():
+        import requests
+        import zipfile
+        import io
+        local_dir = os.path.expanduser('~/.local/ANI1xnr/')
+        url = "https://github.com/atomistic-ml/ani-1xnr/archive/refs/heads/main.zip"
+        if not os.path.exists(local_dir+'ani-1xnr-main'):
+            os.makedirs(local_dir, exist_ok=True)
+            print(f'Downloading ANI-1xnr model parameters ...')
+            resource_res = requests.get(url)
+            resource_zip = zipfile.ZipFile(io.BytesIO(resource_res.content))
+            resource_zip.extractall(local_dir)
+        return local_dir
+    model_prefix = parse_ani1xnr_resources() + 'ani-1xnr-main/model/ani-1xnr/'
+    # const_file, sae_file, ensemble_prefix, ensemble_size = parse_ani1xnr_resources()
+    const_file = model_prefix + 'rHCNO-5.2R_32-3.5A_a8-4.params'
+    sae_file = model_prefix + 'sae_linfit.dat'
+    consts = torchani.neurochem.Constants(const_file)
+    aev_computer = torchani.AEVComputer(**consts)
+    energy_shifter = torchani.neurochem.load_sae(sae_file)
+    species_converter = torchani.nn.SpeciesConverter(species)
+
+    neural_networks = []
+    for ii in range(8):
+        neural_network = torchani.neurochem.load_model(consts.species, model_prefix + f'train{ii}/networks')
+        neural_networks.append(torchani.nn.Sequential(species_converter, aev_computer, neural_network, energy_shifter))
+
+    model_ensemble = torchani.nn.Ensemble(modules=neural_networks)
+    model_ensemble.species = species
+
+    return model_ensemble
+
+class aimnet2_methods(models.torchani_model):
+    '''
+    Universal ML methods with AIMNet2: https://doi.org/10.26434/chemrxiv-2023-296ch
+
+    Arguments:
+        method (str): A string that specifies the method. Available choices: ``'AIMNet2@b973c'`` and ``'AIMNet2@wb97m-d3'``.
+        device (str, optional): Indicate which device the calculation will be run on, i.e. 'cpu' for CPU, 'cuda' for Nvidia GPUs. When not speficied, it will try to use CUDA if there exists valid ``CUDA_VISIBLE_DEVICES`` in the environ of system.
+
+    '''
+    
+    available_methods = models.methods.methods_map['aimnet2']
+    element_symbols_available = ['H', 'B', 'C', 'N', 'O', 'F', 'Si', 'P', 'S', 'Cl', 'As', 'Se', 'Br', 'I']
+
+    def __init__(self, method: str = 'AIMNet2@b973c', device: str = 'cuda' if torch.cuda.is_available() else 'cpu', **kwargs):
+        self.device = torch.device(device)
+        self.model_path = self.parse_aimnet2_resources(method)
+        self.model = torch.jit.load(self.model_path)
+        
+    @doc_inherit
+    def predict(
+            self, 
+            molecular_database: data.molecular_database = None, 
+            molecule: data.molecule = None,
+            calculate_energy: bool = False,
+            calculate_energy_gradients: bool = False, 
+            calculate_hessian: bool = False,
+            batch_size: int = 2**16,
+        ) -> None:
+
+        molDB = super().predict(molecular_database=molecular_database, molecule=molecule)
+
+        for element_symbol in np.unique(np.concatenate(molDB.element_symbols)):
+            if element_symbol not in self.element_symbols_available:
+                print(f' * Warning * Molecule contains elements \'{element_symbol}\', which is not supported by method \'{self.method}\' that only supports {self.element_symbols_available}, no calculations performed')
+                return
+
+        for mol in molDB:
+            self.predict_for_molecule(
+                molecule=mol, 
+                calculate_energy=calculate_energy, 
+                calculate_energy_gradients=calculate_energy_gradients, 
+                calculate_hessian=calculate_hessian)
+
+    def predict_for_molecule(
+        self,
+        molecule, 
+        calculate_energy: bool = False, 
+        calculate_energy_gradients: bool = False, 
+        calculate_hessian: bool = False):
+
+        coord = torch.as_tensor(molecule.xyz_coordinates).to(torch.float).to(self.device).unsqueeze(0)
+        numbers = torch.as_tensor(molecule.atomic_numbers).to(torch.long).to(self.device).unsqueeze(0)
+        charge = torch.tensor([molecule.charge], dtype=torch.float, device=self.device)
+        nninput = dict(coord=coord, numbers=numbers, charge=charge)
+        prev = torch.is_grad_enabled()
+        torch._C._set_grad_enabled(calculate_energy_gradients)
+        if calculate_energy_gradients:
+            nninput['coord'].requires_grad_(True)
+        nnoutput = self.model(nninput)
+        if calculate_energy:
+            molecule.energy = nnoutput['energy'].item()
+        if calculate_energy_gradients:
+            if 'forces' in nnoutput:
+                f = nnoutput['forces'][0]
+            else:
+                f = - torch.autograd.grad(nnoutput['energy'], nninput['coord'])[0][0]
+            forces = f.detach().cpu().numpy()
+            molecule.add_xyz_vectorial_property(forces, 'energy_gradients')
+
+        if calculate_hessian:
+            print('Hessian not available yet')
+            molecule.hessian = np.zeros((len(molecule),)*2)
+        
+        torch._C._set_grad_enabled(prev)
+
+    @staticmethod
+    def parse_aimnet2_resources(method):
+        import requests
+        local_dir = os.path.expanduser('~/.local/AIMNet2/')
+        repo_name = "AIMNet2"
+        tag_name = method.lower().replace('@', '_')
+        url = "https://github.com/isayevlab/{}/raw/main/models/{}_ens.jpt".format(repo_name, tag_name)
+        if not os.path.exists(local_dir+f'{tag_name}_ens.jpt'):
+            os.makedirs(local_dir, exist_ok=True)
+            print(f'Downloading {method} model parameters ...')
+            resource_res = requests.get(url)
+            with open(local_dir+f'{tag_name}_ens.jpt', 'wb') as f:
+                f.write(resource_res.content)
+        return local_dir + f'{tag_name}_ens.jpt'
+
 def printHelp():
     helpText = __doc__.replace('.. code-block::\n\n', '') + '''
   To use Interface_ANI, please install TorchANI and its dependencies

{mlatom-3.5.0 → mlatom-3.6.0}/src/mlatom/md.py

@@ -141,6 +141,12 @@ class md():
         
         self.stop_function = stop_function
         self.stop_function_kwargs = stop_function_kwargs
+
+        self.linearity = self.molecule_with_initial_conditions.is_it_linear()
+        if self.linearity:
+            self.degrees_of_freedom = 3 * self.Natoms - 5
+        else:
+            self.degrees_of_freedom = 3 * self.Natoms - 6
         self.propagate()
         
     def propagate(self):
@@ -200,6 +206,7 @@ class md():
             velocity = np.copy(molecule.get_xyz_vectorial_properties('xyz_velocities'))
             
             molecule.total_energy = molecule.energy + molecule.kinetic_energy
+            molecule.temperature = molecule.kinetic_energy / (constants.kB_in_Hartree*self.degrees_of_freedom/2)
             trajectory_step.step = istep 
             trajectory_step.time = istep * self.time_step
             trajectory_step.molecule = molecule 

{mlatom-3.5.0 → mlatom-3.6.0}/src/mlatom/md_cmd.py

@@ -90,9 +90,20 @@ class MD_CMD():
                 stopMLatom('User-defined initial XYZ file %s does not exist'%(args.initXYZ))
             mol = data.molecule()
             mol.read_from_xyz_file(args.initXYZ)
+        else:
+            mol = data.molecule()
+            mol.load(args.normalModefile)
 
         # Deal with degrees of freedom
-        if args.initConditions.lower() == 'random':
+        if args.initConditions == '' or args.initConditions.lower() == 'user-defined' or args.initConditions.lower() == 'random':
+            if mol.is_it_linear():
+                linear = 1 
+                print('    Linear molecule detected')
+            else:
+                linear = 0
+            Natoms = len(mol.atoms)
+            DOF = 3*Natoms-6+linear 
+        else:
             if mol.is_it_linear():
                 linear = 1 
                 print('    Linear molecule detected')
@@ -100,6 +111,7 @@ class MD_CMD():
                 linear = 0
             Natoms = len(mol.atoms)
             DOF = 3*Natoms-6+linear 
+        
         # print('    Degrees of freedom: %d'%(DOF))
 
         # Generate initial conditions
@@ -117,8 +129,7 @@ class MD_CMD():
                                                           file_with_initial_xyz_coordinates = args.initXYZ,
                                                           file_with_initial_xyz_velocities  = args.initVXYZ)
         elif args.initConditions.lower() == 'random':
-            if args.initTemperature == 0:
-                initTemperature = 300
+            initTemperature = args.initTemperature
             print('    Use random sampling to generate initial condition')
             print(f'      Initial XYZ coordinates file: {args.initXYZ}')
             print(f'      Initial instantaneous temperature: {initTemperature}')

{mlatom-3.5.0 → mlatom-3.6.0}/src/mlatom/models.py

@@ -162,7 +162,7 @@ class methods(model):
             ===============  ==========================================================================================================================================================================
             Program          Methods                                                                                                                                                                   
             ===============  ==========================================================================================================================================================================
-            TorchANI         ``'AIQM1'``, ``'AIQM1@DFT'``, ``'AIQM1@DFT*'``, ``'ANI-1ccx'``, ``'ANI-1x'``, ``'ANI-1x-D4'``, ``'ANI-2x'``, ``'ANI-2x-D4'``                                              
+            TorchANI         ``'AIQM1'``, ``'AIQM1@DFT'``, ``'AIQM1@DFT*'``, ``'ANI-1ccx'``, ``'ANI-1x'``, ``'ANI-1x-D4'``, ``'ANI-2x'``, ``'ANI-2x-D4'``, ``'ANI-1xnr'``                                              
             dftd4            ``'AIQM1'``, ``'AIQM1@DFT'``, ``'ANI-1x-D4'``, ``'ANI-2x-D4'``, ``'D4'``                                                                                                  
             MNDO or Sparrow  ``'AIQM1'``, ``'AIQM1@DFT'``, ``'AIQM1@DFT*'``, ``'MNDO'``, ``'MNDO/d'``, ``'ODM2*'``, ``'ODM3*'``,  ``'OM2'``, ``'OM3'``, ``'PM3'``, ``'SCC-DFTB'``, ``'SCC-DFTB-heats'``
             MNDO             ``'CNDO/2'``, ``'MINDO/3'``, ``'MNDO/H'``, ``'MNDO/dH'``, ``'MNDOC'``, ``'ODM2'``, ``'ODM3'``, ``'OM1'``, semiempirical OMx, DFTB, NDDO-type methods                                                                  
@@ -177,7 +177,8 @@ class methods(model):
 
     methods_map = {
     'aiqm1': ['AIQM1', 'AIQM1@DFT', 'AIQM1@DFT*'],
-    'ani': ["ANI-1x", "ANI-1ccx", "ANI-2x", 'ANI-1x-D4', 'ANI-2x-D4'],
+    'ani': ["ANI-1x", "ANI-1ccx", "ANI-2x", 'ANI-1x-D4', 'ANI-2x-D4', 'ANI-1xnr'], 
+    'aimnet2': ["AIMNet2@b973c", "AIMNet2@wb97m-d3"],
     'mndo': ['ODM2*', 'ODM2', 'ODM3', 'OM3', 'OM2', 'OM1', 'PM3', 'AM1', 'MNDO/d', 'MNDOC', 'MNDO', 'MINDO/3', 'CNDO/2', 'SCC-DFTB', 'SCC-DFTB-heats', 'MNDO/H', 'MNDO/dH'],
     'sparrow': ['DFTB0', 'DFTB2', 'DFTB3', 'MNDO', 'MNDO/d', 'AM1', 'RM1', 'PM3', 'PM6', 'OM2', 'OM3', 'ODM2*', 'ODM3*', 'AIQM1'],
     'xtb': ['GFN2-xTB'],

{mlatom-3.5.0 → mlatom-3.6.0}/src/mlatom/ref.json

@@ -46,5 +46,9 @@
     "KREGgrads":             "Y.-F. Hou, F. Ge, P. O. Dral.\nJ. Chem. Theory Comput. 2023, 19, 2369",
     "MLTPA":                 "Y. Su, Y. Dai, Y. Zeng, C. Wei, Y. Chen, F. Ge, P. Zheng,\nD. Zhou, P. O. Dral, C. Wang. Adv. Sci. 2023, 2204902",
     "MLQDprog": "A. Ullah, P. O. Dral.\nMLQD: A package for machine learning-based quantum dissipative dynamics.\nChemRxiv. 2023. DOI: 10.26434/chemrxiv-2023-0xkv1\nSee MLatom.com for reference updates",
-    "geometric":             "L.-P. Wang, C. C. Song,\nJ. Chem. Phys. 2016, 144, 214108"
+    "geometric":             "L.-P. Wang, C. C. Song,\nJ. Chem. Phys. 2016, 144, 214108",
+    "DM21": "J. Kirkpatrick, ; B. McMorrow, D. H. P. Turban, A. L. Gaunt, J. S. Spencer, \nA. G. D. G. Matthews, A. Obika, L. Thiry, M. Fortunato, D. Pfau, et al.,\nScience 2021, 374, 1385",
+    "AIMNet2": "D. Anstine, R. Zubatyuk , O. Isayev \nAIMNet2: A Neural Network Potential to Meet your Neutral, \nCharged, Organic, and Elemental-Organic Needs. \nChemRxiv. 2024; DOI:10.26434/chemrxiv-2023-296ch-v2",
+    "ANI-1xnr": "S. Zhang, M.Z. Makoś, R.B. Jadrich, E. Kraka, K. Barros, \nB. T. Nebgen,S. Tretiak, O. Isayev, N. Lubbers, R. A. Messerly,\nJ. S. Smith, Nat. Chem. 2024, 16, 727"
 }
+

{mlatom-3.5.0 → mlatom-3.6.0}/src/mlatom/simulations.py

@@ -477,7 +477,7 @@ class freq():
 
     def freq_pyscf(self):
         self.successful = False
-        self.model.interface.predict(molecule=self.molecule, calculate_energy=True, calculate_hessian=True, **self.model_predict_kwargs)
+        self.model.predict(molecule=self.molecule, calculate_energy=True, calculate_hessian=True, **self.model_predict_kwargs)
         from .interfaces import pyscf_interface
         self.successful = pyscf_interface.thermo_calculation(molecule=self.molecule)
     

{mlatom-3.5.0 → mlatom-3.6.0/src/mlatom.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: mlatom
-Version: 3.5.0
+Version: 3.6.0
 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 3.5.0
+Version 3.6.0
 
 **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, Sebastian V. Pios, Yanchi Ou, MLatom: A Package for Atomistic Simulations with Machine Learning,  version 3.5.0, 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 3.6.0, Xiamen University, Xiamen, China, 2013-2024.
   [MLatom.com](http://mlatom.com).
                                                                       
 The citations for MLatom's interfaces and features shall be eventually