mlatom 3.16.0__tar.gz → 3.16.2__tar.gz

{mlatom-3.16.0/src/mlatom.egg-info → mlatom-3.16.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: mlatom
-Version: 3.16.0
+Version: 3.16.2
 Summary: A Package for AI-enhanced computational chemistry
 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 3.16.0
+Version 3.16.2
 
 **Official website**: http://mlatom.com/    
 **Documentation**: http://mlatom.com/docs/                     
@@ -56,7 +56,7 @@ 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, Mikolaj Martyka, Max Pinheiro Jr, Yuming Su, Yiheng Dai, Yangtao Chen, Shuang Zhang, Lina Zhang, Arif Ullah, Quanhao Zhang, Sebastian V. Pios, Yanchi Ou, Matheus O. Bispo, Vignesh B. Kumar, MLatom: A Package for Atomistic Simulations with Machine Learning,  version 3.16.0, Xiamen University, Xiamen, China, 2013-2024.
+* Pavlo O. Dral, Fuchun Ge, Yi-Fan Hou, Peikun Zheng, Yuxinxin Chen, Bao-Xin Xue, Mikolaj Martyka, Max Pinheiro Jr, Yuming Su, Yiheng Dai, Yangtao Chen, Shuang Zhang, Lina Zhang, Arif Ullah, Quanhao Zhang, Sebastian V. Pios, Yanchi Ou, Matheus O. Bispo, Vignesh B. Kumar, Xin-Yu Tong, MLatom: A Package for Atomistic Simulations with Machine Learning,  version 3.16.2, Xiamen University, Xiamen, China, 2013-2024.
   [MLatom.com](http://mlatom.com).
                                                                       
 The citations for MLatom's interfaces and features shall be eventually
@@ -105,7 +105,7 @@ 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 Martyka, Mikolaj 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 and Bispo, Matheus O. and Kumar, Vignesh B.},
+    author = {Dral, Pavlo O. and Ge, Fuchun and Hou, Yi-Fan and Zheng, Peikun and Chen, Yuxinxin and Xue, Bao-Xin and Martyka, Mikolaj 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 and Bispo, Matheus O. and Kumar, Vignesh B. and Tong, Xin-Yu},
     title = {MLatom: A Package for Atomistic Simulations with Machine Learning},
     year = {2013--2024},
     type = {Computer Program}

{mlatom-3.16.0 → mlatom-3.16.2}/README.md

@@ -1,7 +1,7 @@
 # About Program
 MLatom: a Package for Atomistic Simulations with Machine Learning
 
-Version 3.16.0
+Version 3.16.2
 
 **Official website**: http://mlatom.com/    
 **Documentation**: http://mlatom.com/docs/                     
@@ -30,7 +30,7 @@ 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, Mikolaj Martyka, Max Pinheiro Jr, Yuming Su, Yiheng Dai, Yangtao Chen, Shuang Zhang, Lina Zhang, Arif Ullah, Quanhao Zhang, Sebastian V. Pios, Yanchi Ou, Matheus O. Bispo, Vignesh B. Kumar, MLatom: A Package for Atomistic Simulations with Machine Learning,  version 3.16.0, Xiamen University, Xiamen, China, 2013-2024.
+* Pavlo O. Dral, Fuchun Ge, Yi-Fan Hou, Peikun Zheng, Yuxinxin Chen, Bao-Xin Xue, Mikolaj Martyka, Max Pinheiro Jr, Yuming Su, Yiheng Dai, Yangtao Chen, Shuang Zhang, Lina Zhang, Arif Ullah, Quanhao Zhang, Sebastian V. Pios, Yanchi Ou, Matheus O. Bispo, Vignesh B. Kumar, Xin-Yu Tong, MLatom: A Package for Atomistic Simulations with Machine Learning,  version 3.16.2, Xiamen University, Xiamen, China, 2013-2024.
   [MLatom.com](http://mlatom.com).
                                                                       
 The citations for MLatom's interfaces and features shall be eventually
@@ -79,7 +79,7 @@ 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 Martyka, Mikolaj 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 and Bispo, Matheus O. and Kumar, Vignesh B.},
+    author = {Dral, Pavlo O. and Ge, Fuchun and Hou, Yi-Fan and Zheng, Peikun and Chen, Yuxinxin and Xue, Bao-Xin and Martyka, Mikolaj 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 and Bispo, Matheus O. and Kumar, Vignesh B. and Tong, Xin-Yu},
     title = {MLatom: A Package for Atomistic Simulations with Machine Learning},
     year = {2013--2024},
     type = {Computer Program}

{mlatom-3.16.0 → mlatom-3.16.2}/setup.py

@@ -43,7 +43,7 @@ with open(os.path.join(here, 'README.md')) as f:
 
 setup(
     name = pkg_name,
-    version = "3.16.0",
+    version = "3.16.2",
     author = "Pavlo O. Dral",
     author_email = "admin@mlatom.com",
     license = 'MIT (modified)',

{mlatom-3.16.0 → mlatom-3.16.2}/src/mlatom/MLatom.py

@@ -4,7 +4,7 @@
   !---------------------------------------------------------------------------!
   !                                                                           !
   !     MLatom: a Package for Atomistic Simulations with Machine Learning     !
-  !                             MLatom 3.16.0                                 !
+  !                             MLatom 3.16.2                                 !
   !                                   @                                       !
   !                 Xiamen Atomistic Computing Suite (XACS)                   !
   !                                                                           !
@@ -36,8 +36,9 @@
   ! Bao-Xin Xue, Mikolaj Martyka, Max Pinheiro Jr, Yuming Su, Yiheng Dai,     !
   ! Yangtao Chen, Shuang Zhang, Lina Zhang, Arif Ullah, Quanhao Zhang,        !
   ! Sebastian V. Pios, Yanchi Ou, Matheus O. Bispo, Vignesh B. Kumar,         !
+  ! Xin-Yu Tong,                                                              !
   ! MLatom: A Package for Atomistic Simulations with Machine Learning,        !
-  ! version 3.16.0, Xiamen University, Xiamen, China, 2013-2024.              !
+  ! version 3.16.2, 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-3.16.0 → mlatom-3.16.2}/src/mlatom/MLtasks.py

@@ -364,7 +364,15 @@ def slice(args):
     from . import sliceData
     sliceData.sliceDataCls(argsSD = args.args2pass)
 
-def geomopt(args):
+def optfreq(args):
+    molDB = geomopt(args, return_moldb=True)
+    freq(args, molDB=molDB)
+    
+def tsfreq(args):
+    molDB = ts(args, return_moldb=True)
+    freq(args, molDB=molDB)
+
+def geomopt(args, return_moldb=False):
     from . import simulations
     molDB = loading_data(XYZfile=args.XYZfile, charges=args.charges, multiplicities=args.multiplicities)
     model = loading_model(args)
@@ -419,13 +427,20 @@ def geomopt(args):
         else:
             print('\n Final energy of molecule %6d: %25.13f Hartree\n\n' % (imol+1, geomopt.optimized_molecule.energy))
     db_opt.write_file_with_xyz_coordinates(filename=fname)
+    if return_moldb:
+        return db_opt
 
-def ts(args):
-    geomopt(args)
+def ts(args, return_moldb=False):
+    if return_moldb:
+        molDB = geomopt(args, return_moldb=return_moldb)
+        return molDB
+    else:
+        geomopt(args, return_moldb=return_moldb)
 
-def freq(args):
+def freq(args, molDB=None):
     from . import simulations
-    molDB = loading_data(args.XYZfile, charges=args.charges, multiplicities=args.multiplicities)
+    if molDB is None:
+        molDB = loading_data(args.XYZfile, charges=args.charges, multiplicities=args.multiplicities)
     model = loading_model(args)
     kwargs = {}
     if args.freqProg:       kwargs['program'] = args.freqProg

{mlatom-3.16.0 → mlatom-3.16.2}/src/mlatom/al.py

@@ -1,20 +1,13 @@
 import sys
-from . import data, stats, models, optimize_geometry, freq, md, md_parallel, generate_initial_conditions
-from .al_utils import *
+from . import data, stats, models, simulations, optimize_geometry, freq, md, md_parallel, generate_initial_conditions
+from .simulations import run_in_parallel 
+from .al_utils import Sampler, ml_model_trainer, ml_model, ml_model_msani, stopper
 import numpy as np 
 import os 
-import matplotlib.pyplot as plt 
-import scipy 
-import torch
-import random 
-import joblib 
-from joblib import Parallel, delayed 
-from multiprocessing.pool import ThreadPool as Pool
-import timeit 
-import json
+import random
+import timeit
 import copy
 
-
 class al():
     '''
     Active learning procedure 
@@ -141,6 +134,7 @@ class al():
         elif 'nthreads' in kwargs:
             self.label_nthreads = kwargs['nthreads']
         else:
+            import joblib
             self.label_nthreads = joblib.cpu_count()
         
         if 'refmethod_kwargs' in kwargs:
@@ -186,6 +180,8 @@ class al():
         if 'device' in kwargs:
             self.device = kwargs['device']
         else:
+            # to-do: that should be done just for the models using torch, otherwise loading takes time
+            import torch
             self.device = 'cuda' if torch.cuda.is_available() else 'cpu'
         # ..property_to_learn: A list of properties to learn with ML
         #   ...Note:
@@ -233,6 +229,7 @@ class al():
             if 'nthreads' in kwargs:
                 self.sampler_kwargs['nthreads'] = kwargs['nthreads']
             elif 'nthreads' not in self.sampler_kwargs.keys():
+                import joblib
                 self.sampler_kwargs['nthreads'] = joblib.cpu_count()
             if 'initcond_sampler' in self.sampler_kwargs.keys():
                 self.sampler_kwargs['initcond_sampler'] = Sampler(sampler_function=self.sampler_kwargs['initcond_sampler'])
@@ -314,6 +311,7 @@ class al():
 
     # Dump AL info
     def dump(self):
+        import json
         jsonfile = open('al_info.json','w') 
         json.dump(self.dict_to_json_dict(self.al_info),jsonfile,indent=4)
         jsonfile.close()
@@ -321,6 +319,7 @@ class al():
     # Load AL info
     def load(self):
         if os.path.exists('al_info.json'):
+            import json
             jsonfile = open('al_info.json','r') 
             al_info = json.load(jsonfile)
         else:
@@ -472,6 +471,7 @@ class al():
                 if len(Ntrain_list) > 1 and len(Ntrain_list) >= self.minimum_number_of_fitting_points:
                     x = np.log(Ntrain_list)
                     y = np.log(eRMSE_list)
+                    import scipy
                     linreg = scipy.stats.linregress(x,y)
                     slope = linreg.slope 
                     intercept = linreg.intercept 
@@ -701,7 +701,7 @@ class al():
             return molecule
         nmols = len(moldb)
         if nthreads > 1:
-            newmols = simulations.run_in_parallel(molecular_database=moldb,
+            newmols = run_in_parallel(molecular_database=moldb,
                 task=sptask,
                 task_kwargs={'model': method, 'refmethod_kwargs': {'calculate_energy': calculate_energy, 'calculate_energy_gradients':calculate_energy_gradients, 'calculate_hessian':calculate_hessian, **model_predict_kwargs}},
                 nthreads=nthreads,
@@ -709,8 +709,10 @@ class al():
             for imol in range(len(moldb)):
                 moldb.molecules[imol] = newmols[imol]
             
+            # from multiprocessing.pool import ThreadPool as Pool
             #pool = Pool(processes=nthreads)
             #mols = pool.map(label,list(range(nmols)))
+            # from joblib import Parallel, delayed 
             # mols = Parallel(n_jobs=nthreads)(delayed(label)(i) for i in range(nmols))
         else:
             moldb2label = data.molecular_database()

{mlatom-3.16.0 → mlatom-3.16.2}/src/mlatom/al_utils.py

@@ -1,20 +1,9 @@
 import sys
 from . import data, stats, models, simulations, optimize_geometry, md, md_parallel, constants, generate_initial_conditions
 import numpy as np 
-import os 
-import matplotlib.pyplot as plt 
-import scipy 
-import torch
-from scipy.optimize import fsolve
+import os
 import random 
-import joblib 
-from joblib import Parallel, delayed 
-import timeit 
-import json
 from . import gap_md, namd
-from time import sleep
-
-
 
 class Sampler():
     def __init__(self,sampler_function=None):
@@ -200,6 +189,7 @@ class Sampler():
         else:
             initial_molecular_database = initcond_sampler.sample(**initcond_sampler_kwargs)
         if nthreads is None:
+            import joblib
             nthreads = joblib.cpu_count()
         if stop_function is None:
             stop_function = internal_stop_function
@@ -278,6 +268,7 @@ class Sampler():
         else:
             initial_molecular_database = initcond_sampler.sample(**initcond_sampler_kwargs)
         if nthreads is None:
+            import joblib
             nthreads = joblib.cpu_count()
         if stop_function is None:
             stop_function = internal_stop_function
@@ -356,6 +347,7 @@ class Sampler():
         else:
             initial_molecular_database = initcond_sampler.sample(**initcond_sampler_kwargs)
         if nthreads is None:
+            import joblib
             nthreads = joblib.cpu_count()
         if stop_function is None:
             stop_function = internal_stop_function
@@ -426,6 +418,7 @@ class Sampler():
                 traj = dyn.molecular_trajectory 
                 return traj 
             
+            from joblib import Parallel, delayed 
             trajs = Parallel(n_jobs=nthreads)(delayed(run_traj)(i) for i in range(len(initial_molecular_database)))
             sys.stdout.flush() 
 
@@ -598,6 +591,7 @@ class Sampler():
         if 'nthreads' in kwargs:
             nthreads = kwargs['nthreads']
         else:
+            import joblib
             nthreads = joblib.cpu_count()
         if 'uq_tresholds' in kwargs:
             uq_tresholds = kwargs['uq_tresholds']
@@ -846,7 +840,8 @@ class Sampler():
             for i in range(N_gapMD):
                 if os.path.exists("gapMD_traj{}.h5".format(i)):
                     os.system("rm gapMD_traj{}.h5".format(i))
-                
+            
+            from joblib import Parallel, delayed 
             gapMD_trajs_down = Parallel(n_jobs=nthreads)(delayed(run_gapMD)(init_cond_for_gapMD_down,i, lower_surface=lower_surface_list[i], current_surface=lower_surface_list[i]) for i in range(len(init_cond_for_gapMD_down)))
             
             sys.stdout.flush()
@@ -886,6 +881,7 @@ class Sampler():
             upper_surface_list = []
             for i in range(N_gapMD):
                 upper_surface_list.append(random.randrange(1,nstates))
+            from joblib import Parallel, delayed 
             gapMD_trajs_up = Parallel(n_jobs=nthreads)(delayed(run_gapMD)(init_cond_for_gapMD_up,i, lower_surface=upper_surface_list[i]-1, current_surface=upper_surface_list[i]) for i in range(len(init_cond_for_gapMD_up)))
             sys.stdout.flush()
             itraj=0 
@@ -959,6 +955,7 @@ class excess_energy_generator():
                 bb = 7*aa 
                 aa = min(aa,0.3)
                 return self.get_average_IEE(aa,bb,self.number_of_valence_electrons) - target 
+            from scipy.optimize import fsolve
             self.aa = fsolve(func,[0.2])[0]
             self.bb = 7*self.aa
             self.aa = min(self.aa,0.3)
@@ -1210,6 +1207,8 @@ class delta_ml_model_trainer(ml_model_trainer):
 class ml_model(models.ml_model):
     def __init__(self,al_info={},model_file=None,device=None,verbose=False,ml_model_type='ANI',**kwargs):
         if device is None:
+            # to-do: that should be done just for the models using torch, otherwise loading takes time
+            import torch
             device = 'cuda' if torch.cuda.is_available() else 'cpu'
         self.ml_model_type = ml_model_type
         if model_file is None:
@@ -1470,6 +1469,7 @@ class ml_model(models.ml_model):
         print(f"                Correlation coefficient = {aux_model_validate_vPCC}")
 
         # Value scatter plot of the main model
+        import matplotlib.pyplot as plt
         fig,ax = plt.subplots() 
         fig.set_size_inches(15,12)
         diagonal_line = [min([min(values),min(estimated_values)]),max([max(values),max(estimated_values)])]
@@ -1883,6 +1883,7 @@ class ml_model_msani(models.ml_model):
         print(f"                Correlation coefficient = {aux_model_validate_vPCC}")
 
         # Value scatter plot of the main model
+        import matplotlib.pyplot as plt 
         fig,ax = plt.subplots() 
         fig.set_size_inches(15,12)
         diagonal_line = [min([min(values),min(estimated_values)]),max([max(values),max(estimated_values)])]

{mlatom-3.16.0 → mlatom-3.16.2}/src/mlatom/args_class.py

@@ -695,6 +695,10 @@ class mlatom_args(ArgsBase):
             elif len(tasks) > 1:
                 if self.selfCorrect:
                     self._task = 'selfCorrect'
+                elif 'geomopt' in tasks and 'freq' in tasks:
+                    self._task = 'optfreq'
+                elif 'ts' in tasks and 'freq' in tasks:
+                    self._task = 'tsfreq'
                 else:
                     if 'useMLmodel' in tasks:
                         tasks.remove('useMLmodel')

{mlatom-3.16.0 → mlatom-3.16.2}/src/mlatom/data.py

@@ -5,7 +5,7 @@
   !---------------------------------------------------------------------------! 
   ! data: Module for working with data                                        ! 
   ! Implementations by: Pavlo O. Dral, Fuchun Ge,                             !
-  !                     Shuang Zhang, Yi-Fan Hou, Yanchi Ou                   !
+  !                     Shuang Zhang, Yi-Fan Hou, Yanchi Ou, Mikołaj Martyka  !
   !---------------------------------------------------------------------------! 
 '''
 
@@ -13,6 +13,7 @@ from __future__ import annotations
 from typing import Any, Union, Dict, List, Optional, Iterable
 import uuid, copy, os, json
 import numpy as np
+import math
 import h5py
 import functools
 from . import constants
@@ -142,6 +143,10 @@ def load_return_molecule(filename=None, format='json'):
         jsonfile = open(filename, 'r')
         moldict = json.load(jsonfile)
         newmol = dict_to_molecule_class_instance(moldict)
+    elif format.casefold() == 'xyz'.casefold():
+        newmol = molecule.from_xyz_file(filename)
+    elif format.casefold() == 'xyzstring'.casefold():
+        newmol = molecule.from_xyz_string(filename)
     elif format.casefold() == 'gaussian'.casefold():
         from .interfaces import gaussian_interface
         newmol = gaussian_interface.parse_gaussian_output(filename=filename)
@@ -663,7 +668,78 @@ class molecule:
             new_molecule = copy.deepcopy(self)
         new_molecule.id = str(uuid.uuid4())
         return new_molecule
+    def bond_length(self, a1, a2):
+        """Return the distance between atom numbers a1 and a2.
     
+        Atoms are numbered from zero.
+    
+        """
+        diff = self.atoms[a1].xyz_coordinates - self.atoms[a2].xyz_coordinates
+        return np.linalg.norm(diff)
+        
+    def bond_angle(self, a1, a2, a3, degrees=True):
+            """Return the bond angle a1-a2-a3.
+    
+            The angle is defined by the vectors a1-a2 and a2-a3.
+            Atoms are numbered from zero.
+            based on Tom Keal MNDOtools.py, October 2007
+            degrees - if true, return angle in degrees, else radians.
+    
+            """
+            # Based on the bond angle routine from geoman.f90 by Eduardo Fabiano
+            # vector 1 = 1->2
+            v1 = self.atoms[a2].xyz_coordinates - self.atoms[a1].xyz_coordinates
+            v1 = v1/np.linalg.norm(v1)
+    
+            # vector 2 = 2->3
+            v2 = self.atoms[a3].xyz_coordinates - self.atoms[a2].xyz_coordinates
+            v2 = v2/np.linalg.norm(v2)
+    
+            # dot product
+            dotp = np.dot(v1, v2)
+            # angle in radians
+            ang = math.pi - math.acos(dotp)
+            if degrees:
+                ang *= (180.0 / math.pi)
+            return ang
+    def dihedral_angle(self, a1, a2, a3, a4, degrees=True):
+        """Return the dihedral angle a1-a2-a3-a4.
+    
+        The angle is defined between the planes a1-a2-a3 and a2-a3-a4.
+        Atoms are numbered from zero.
+        based on Tom Keal MNDOtools.py, October 2007
+    
+        degrees - if true, return angle in degrees, else radians.
+    
+        """
+        # Based on the dihedral routine from geoman.f90 by Eduardo Fabiano
+        # vector 1 = 1->2
+        v1 = self.atoms[a2].xyz_coordinates - self.atoms[a1].xyz_coordinates
+        v1 = v1/np.linalg.norm(v1)
+    
+        # vector 2 = 2->3
+        v2 = self.atoms[a3].xyz_coordinates - self.atoms[a2].xyz_coordinates
+        v2 = v2/np.linalg.norm(v2)
+    
+        # vector 3 = 3->4
+        v3 = self.atoms[a4].xyz_coordinates - self.atoms[a3].xyz_coordinates
+        v3 = v3/np.linalg.norm(v3)
+    
+        # vector product 1 = v1^v2
+        w1 = np.cross(v1,v2)
+        w1 = w1/np.linalg.norm(w1)
+    
+        # vector product 2 = v3^v2
+        w2 = np.cross(v3,v2)
+        w2 = w2/np.linalg.norm(w2)
+    
+        # dot product
+        dotp = np.dot(w1,w2)
+        # angle in radians
+        ang = math.pi - math.acos(dotp)
+        if degrees:
+            ang *= (180.0 / math.pi)
+        return ang    
     def proliferate(
             self, 
             shifts: Optional[Iterable] = None, 
@@ -1647,7 +1723,7 @@ class molecular_database:
         '''
         return molecular_database([mol.proliferate(*args, **kwargs) for mol in self])
     
-    def dump(self, filename=None, format=None):
+    def dump(self, filename=None, format='json'):
         '''
         Dump the molecular database to a file.
         '''
@@ -1663,14 +1739,21 @@ class molecular_database:
             jsonfile = open(filename, 'r')
             data = json.load(jsonfile)
             self.molecules = []
-            for molecule in data['molecules']:
-                self.molecules.append(dict_to_molecule_class_instance(molecule))
-        if format.casefold() == 'npz'.casefold():
+            for mol in data['molecules']:
+                self.molecules.append(dict_to_molecule_class_instance(mol))
+        elif format.casefold() == 'npz'.casefold():
             with np.load(filename, allow_pickle=True) as npz:
                 data = dict(npz)
                 self.molecules = []
-                for molecule in data['molecules']:
-                    self.molecules.append(dict_to_molecule_class_instance(molecule))
+                for mol in data['molecules']:
+                    self.molecules.append(dict_to_molecule_class_instance(mol))
+        elif format.casefold() == 'gaussian'.casefold():
+            mol = molecule.load(filename, format=format)
+            if 'molecular_database' in mol.__dict__.keys():
+                for key in mol.molecular_database.__dict__.keys():
+                    self.__dict__[key] = mol.molecular_database.__dict__[key]
+            else:
+                self.molecules.append(mol)
         return self
     
     @classmethod
@@ -1887,6 +1970,14 @@ def dict_to_molecule_class_instance(dd):
                 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 key == 'molecular_database':
+            mol.molecular_database = molecular_database()
+            mol.molecular_database.molecules = [dict_to_molecule_class_instance(state_dict) for state_dict in dd[key]['molecules']]
+        elif key == 'optimization_trajectory':
+            mol.optimization_trajectory = molecular_trajectory()
+            mol.optimization_trajectory.steps = [molecular_trajectory_step(step=state_dict['step'],
+                                                                           molecule=dict_to_molecule_class_instance(state_dict['molecule']))
+                                                 for state_dict in dd[key]['steps']]
         elif type(dd[key]) == dict:
             if 'parent' in dd[key].keys():
                 dict_to_properties_tree_node_class_instance(dd, key, mol)    
@@ -2134,6 +2225,13 @@ class molecular_trajectory():
                     if not key in ['step', 'molecule']:
                         self.steps[-1].__dict__[key] = step[key]
     
+        elif format.casefold() == 'gaussian'.casefold():
+            mol = molecule.load(filename, format=format)
+            if 'optimization_trajectory' in mol.__dict__.keys():
+                for key in mol.optimization_trajectory.__dict__.keys():
+                    self.__dict__[key] = mol.optimization_trajectory.__dict__[key]
+            else:
+                raise ValueError('No optimization trajectory could be parsed from the Gaussian output file')
    
     def get_xyz_string(self) -> str:
         '''

{mlatom-3.16.0 → mlatom-3.16.2}/src/mlatom/interfaces/__init__.py

@@ -64,4 +64,8 @@ def pyscf():
 
 def orca():
     from .orca_interface import orca_methods as interface
-    return interface
+    return interface
+
+def dftbplus():
+    from .dftbplus_interface import dftbplus_methods as interface
+    return interface

{mlatom-3.16.0 → mlatom-3.16.2}/src/mlatom/interfaces/ase_interface.py

@@ -129,9 +129,11 @@ def dimer_method(initial_molecule, model,
     atoms.calc = MLatomCalculator(model=model,  model_predict_kwargs= model_predict_kwargs, save_optimization_trajectory=True)
 
     from ase.dimer import DimerControl, MinModeAtoms, MinModeTranslate
+    
+    random_seed = kwargs.pop('random_seed') if 'random_seed' in kwargs else None
 
     with DimerControl(**kwargs) as d_control:
-        d_atoms = MinModeAtoms(atoms, d_control, random_seed = kwargs['random_seed'] if 'random_seed' in kwargs else 0)
+        d_atoms = MinModeAtoms(atoms, d_control, random_seed = random_seed)
         d_atoms.displace()
         with MinModeTranslate(d_atoms) as dim_rlx:
             dim_rlx.run(fmax=convergence_criterion_for_forces,