mlatom 3.18.2__tar.gz → 3.19.0__tar.gz

{mlatom-3.18.2/src/mlatom.egg-info → mlatom-3.19.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: mlatom
-Version: 3.18.2
+Version: 3.19.0
 Summary: A Package for AI-enhanced computational chemistry
 Home-page: http://mlatom.com
 Author: Pavlo O. Dral
@@ -14,20 +14,11 @@ Classifier: Environment :: Console
 Requires-Python: >=3.8
 Description-Content-Type: text/markdown
 License-File: LICENSE.txt
-Requires-Dist: numpy
-Requires-Dist: scipy
-Requires-Dist: h5py
-Requires-Dist: pyh5md
-Requires-Dist: torch
-Requires-Dist: torchani
-Requires-Dist: matplotlib
-Requires-Dist: statsmodels
-Requires-Dist: tqdm
 
 # About Program
 MLatom: a Package for Atomistic Simulations with Machine Learning
 
-Version 3.18.2
+Version 3.19.0
 
 **Official website**: http://mlatom.com/    
 **Documentation**: http://mlatom.com/docs/                     
@@ -56,7 +47,7 @@ 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, Yuxinxin Chen, Peikun Zheng, Bao-Xin Xue, Mikolaj Martyka, Lina Zhang, Jakub Martinka, Quanhao Zhang, Xin-Yu Tong, Arif Ullah, Sebastian V. Pios, Vignesh B. Kumar, Yanchi Ou, Max Pinheiro Jr, Yuming Su, Yiheng Dai, Yangtao Chen, Shuang Zhang, Matheus O. Bispo, MLatom: A Package for Atomistic Simulations with Machine Learning,  version 3.18.2, Xiamen University, Xiamen, China, 2013-2025. [MLatom.com](http://mlatom.com).
+* Pavlo O. Dral, Fuchun Ge, Yi-Fan Hou, Yuxinxin Chen, Peikun Zheng, Bao-Xin Xue, Mikolaj Martyka, Lina Zhang, Jakub Martinka, Quanhao Zhang, Xin-Yu Tong, Arif Ullah, Sebastian V. Pios, Vignesh B. Kumar, Yanchi Ou, Max Pinheiro Jr, Yuming Su, Yiheng Dai, Yangtao Chen, Shuang Zhang, Jinming Hu, Matheus O. Bispo, MLatom: A Package for Atomistic Simulations with Machine Learning,  version 3.19.0, Xiamen University, Xiamen, China, 2013-2025. [MLatom.com](http://mlatom.com).
                                                                       
 The citations for MLatom's interfaces and features shall be eventually
 included too. See program output, header.py, ref.json, and [MLatom.com](http://mlatom.com).          
@@ -104,7 +95,7 @@ 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 Chen, Yuxinxin and Zheng, Peikun and Xue, Bao-Xin and Martyka, Mikolaj and Zhang, Lina and Martinka, Jakub and Zhang, Quanhao and Tong, Xin-Yu and Ullah, Arif and Pios, Sebastian V. and Kumar, Vignesh B. and Ou, Yanchi and Jr, Max Pinheiro and Su, Yuming and Dai, Yiheng and Chen, Yangtao and Zhang, Shuang and Bispo, Matheus O.},
+    author = {Dral, Pavlo O. and Ge, Fuchun and Hou, Yi-Fan and Chen, Yuxinxin and Zheng, Peikun and Xue, Bao-Xin and Martyka, Mikolaj and Zhang, Lina and Martinka, Jakub and Zhang, Quanhao and Tong, Xin-Yu and Ullah, Arif and Pios, Sebastian V. and Kumar, Vignesh B. and Ou, Yanchi and Jr, Max Pinheiro and Su, Yuming and Dai, Yiheng and Chen, Yangtao and Zhang, Shuang and Hu, Jinming and Bispo, Matheus O.},
     title = {MLatom: A Package for Atomistic Simulations with Machine Learning},
     year = {2013--2025},
     type = {Computer Program}

{mlatom-3.18.2 → mlatom-3.19.0}/README.md

@@ -1,7 +1,7 @@
 # About Program
 MLatom: a Package for Atomistic Simulations with Machine Learning
 
-Version 3.18.2
+Version 3.19.0
 
 **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, Yuxinxin Chen, Peikun Zheng, Bao-Xin Xue, Mikolaj Martyka, Lina Zhang, Jakub Martinka, Quanhao Zhang, Xin-Yu Tong, Arif Ullah, Sebastian V. Pios, Vignesh B. Kumar, Yanchi Ou, Max Pinheiro Jr, Yuming Su, Yiheng Dai, Yangtao Chen, Shuang Zhang, Matheus O. Bispo, MLatom: A Package for Atomistic Simulations with Machine Learning,  version 3.18.2, Xiamen University, Xiamen, China, 2013-2025. [MLatom.com](http://mlatom.com).
+* Pavlo O. Dral, Fuchun Ge, Yi-Fan Hou, Yuxinxin Chen, Peikun Zheng, Bao-Xin Xue, Mikolaj Martyka, Lina Zhang, Jakub Martinka, Quanhao Zhang, Xin-Yu Tong, Arif Ullah, Sebastian V. Pios, Vignesh B. Kumar, Yanchi Ou, Max Pinheiro Jr, Yuming Su, Yiheng Dai, Yangtao Chen, Shuang Zhang, Jinming Hu, Matheus O. Bispo, MLatom: A Package for Atomistic Simulations with Machine Learning,  version 3.19.0, Xiamen University, Xiamen, China, 2013-2025. [MLatom.com](http://mlatom.com).
                                                                       
 The citations for MLatom's interfaces and features shall be eventually
 included too. See program output, header.py, ref.json, and [MLatom.com](http://mlatom.com).          
@@ -78,7 +78,7 @@ 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 Chen, Yuxinxin and Zheng, Peikun and Xue, Bao-Xin and Martyka, Mikolaj and Zhang, Lina and Martinka, Jakub and Zhang, Quanhao and Tong, Xin-Yu and Ullah, Arif and Pios, Sebastian V. and Kumar, Vignesh B. and Ou, Yanchi and Jr, Max Pinheiro and Su, Yuming and Dai, Yiheng and Chen, Yangtao and Zhang, Shuang and Bispo, Matheus O.},
+    author = {Dral, Pavlo O. and Ge, Fuchun and Hou, Yi-Fan and Chen, Yuxinxin and Zheng, Peikun and Xue, Bao-Xin and Martyka, Mikolaj and Zhang, Lina and Martinka, Jakub and Zhang, Quanhao and Tong, Xin-Yu and Ullah, Arif and Pios, Sebastian V. and Kumar, Vignesh B. and Ou, Yanchi and Jr, Max Pinheiro and Su, Yuming and Dai, Yiheng and Chen, Yangtao and Zhang, Shuang and Hu, Jinming and Bispo, Matheus O.},
     title = {MLatom: A Package for Atomistic Simulations with Machine Learning},
     year = {2013--2025},
     type = {Computer Program}

{mlatom-3.18.2 → mlatom-3.19.0}/setup.py

@@ -43,7 +43,7 @@ with open(os.path.join(here, 'README.md')) as f:
 
 setup(
     name = pkg_name,
-    version = "3.18.2",
+    version = "3.19.0",
     author = "Pavlo O. Dral",
     author_email = "admin@mlatom.com",
     license = 'MIT (modified)',

{mlatom-3.18.2 → mlatom-3.19.0}/src/mlatom/EEEDDDD.py

@@ -18,6 +18,8 @@ from .EEEDDDD_nn import batch_jacobian, MLP, ModelEnsemble, StackModelEnsemble,
 from .EEEDDDD_descriptor import self_edge_vector_matrix, self_distance_matrix
 from typing import Any, List, Dict, Union, Iterable, Optional
 
+torch.set_default_dtype(torch.float32)
+
 # torch.autograd.set_detect_anomaly(True)
 
 @compile_mode("script")
@@ -278,6 +280,7 @@ class EEEDDDD(model_cls.ml_model, model_cls.torch_model,model_cls.downloadable_m
         self.species = model_dict['args'].pop('species')
         model = self._new_model(model_dict['args'])
         model.load_state_dict(model_dict['state'])
+        model = model.to(torch.float32)
         model.eval()
         if self.verbose:
             print(f"model loaded from {model_file}")
@@ -294,10 +297,18 @@ class EEEDDDD(model_cls.ml_model, model_cls.torch_model,model_cls.downloadable_m
                 kwargs['reset_base'] = reset_base
             self.model = ensemble(models=models, **kwargs)
     
-    def load_special(self,model_file):
-        model_name, model_path, download = self.check_model_path(model_file)
-        if download: self.download(model_name,model_path)
-        model_paths = [os.path.join(model_path,f'MDtrajNet-1.{ii}.pt') for ii in range(4)]
+    def load_special(self, model_file):
+
+        download_links = [
+            'https://zenodo.org/records/15877717/files/mdtrajnet1_model.zip?download=1',
+            'https://aitomistic.xyz/model/mdtrajnet1_model.zip']
+        model_dir = 'mdtrajnet1_model'
+        model_files = [f'MDtrajNet-1.{ii}.pt' for ii in range(4)]
+
+        mlatom_model_dir, to_download = self.check_model_path(model_dir, model_files)
+        if to_download: self.download(download_links, mlatom_model_dir)
+
+        model_paths = [os.path.join(mlatom_model_dir,f'MDtrajNet-1.{ii}.pt') for ii in range(4)]
         self.load(model_paths)
 
     def specie_to_index(self, species: np.ndarray) -> torch.Tensor:

{mlatom-3.18.2 → mlatom-3.19.0}/src/mlatom/MLTPA.py

@@ -1,11 +1,13 @@
 #!/usr/bin/env python
 # coding: utf-8
 
-
 '''
   !---------------------------------------------------------------------------! 
   ! mltpa: Machine learning prediction of the Two-photon absorption           ! 
-  ! Implementations by: Yuming Su, Yiheng Dai, Yangtao Chen, Fuchun Ge        ! 
+  ! Implementations by: Yuming Su, Yiheng Dai, Yangtao Chen, Fuchun Ge        !
+  !                                                                           !
+  ! Modified on 2025.07.30 by Yuming Su, to make it work,                     !
+  ! if one does NOT have conjugation structure                                !
   !---------------------------------------------------------------------------! 
 '''
 
@@ -345,6 +347,52 @@ class MLTPA(object):
         mol = Chem.MolFromSmiles(smiles)
         d_m = Chem.rdmolops.GetDistanceMatrix(mol)
         ring_list, f_a = self.find_conj(smiles)
+        
+        # 处理没有共轭结构的情况
+        if len(ring_list) == 0:
+            # 没有共轭结构时，最大共轭距离为0
+            feature_vector[0] = 0
+            
+            # 计算所有原子的PEOE电荷、logP和MR
+            AllChem.ComputeGasteigerCharges(mol, nIter=25)
+            peoe_charge = [mol.GetAtomWithIdx(i).GetDoubleProp('_GasteigerCharge') for i in range(mol.GetNumAtoms())]
+            contribs = rdMolDescriptors._CalcCrippenContribs(mol)
+            logp = [contribs[i][0] for i in range(len(contribs))]
+            mr = [contribs[i][1] for i in range(len(contribs))]
+            
+            # 使用整个分子的原子进行片段匹配
+            all_atoms = list(range(mol.GetNumAtoms()))
+            atom_props = [peoe_charge, logp, mr]
+            
+            for prop_idx in range(len(atom_props)):
+                atom_props_list = atom_props[prop_idx]
+                frag_x = []
+                
+                # 在整个分子中寻找匹配的片段
+                for i in range(len(mff_title)):
+                    patt = mff_title[i]
+                    f = Chem.MolFromSmarts(patt)
+                    atomids = mol.GetSubstructMatches(f)
+                    if len(atomids) > 0:
+                        for atomid_group in atomids:
+                            x_temp = 0
+                            for k in atomid_group:
+                                x_temp += atom_props_list[k]
+                            frag_x.append(x_temp)
+                
+                if len(frag_x) == 0:
+                    frag_x = [0]
+                
+                if prop_idx == 0 or prop_idx == 2:  # PEOE电荷和MR取最大值
+                    feature_vector[prop_idx + 1] = max(frag_x)
+                else:  # logP取最小值
+                    feature_vector[prop_idx + 1] = min(frag_x)
+            
+            feature_vector[4] = et30
+            feature_vector[5] = wavelength
+            return feature_vector
+        
+        # 原有的有共轭结构的处理逻辑
         lstmax = sorted(ring_list, key=len)[-1]
 
         # calculate max conju-distance

{mlatom-3.18.2 → mlatom-3.19.0}/src/mlatom/MLatom.py

@@ -4,11 +4,9 @@
   !---------------------------------------------------------------------------!
   !                                                                           !
   !     MLatom: a Package for Atomistic Simulations with Machine Learning     !
-  !                             MLatom 3.18.2                                 !
-  !                                   @                                       !
-  !                 Xiamen Atomistic Computing Suite (XACS)                   !
+  !                             MLatom 3.19.0                                 !
   !                                                                           !
-  !                http://mlatom.com/ @ https://XACScloud.com                 !
+  !                           http://mlatom.com/                              !
   !                                                                           !
   !            MIT License (modified to request proper citations)             !
   !                   Copyright (c) 2013- Pavlo O. Dral                       !
@@ -36,9 +34,9 @@
   ! Bao-Xin Xue, Mikolaj Martyka, Lina Zhang, Jakub Martinka, Quanhao Zhang,  !
   ! Xin-Yu Tong, Arif Ullah, Sebastian V. Pios, Vignesh B. Kumar, Yanchi Ou,  !
   ! Max Pinheiro Jr, Yuming Su, Yiheng Dai, Yangtao Chen, Shuang Zhang,       !
-  ! Matheus O. Bispo                                                          !
+  ! Jinming Hu, Matheus O. Bispo                                              !
   ! MLatom: A Package for Atomistic Simulations with Machine Learning,        !
-  ! version 3.18.2, Xiamen University, Xiamen, China, 2013-2025.              !
+  ! version 3.19.0, Xiamen University, Xiamen, China, 2013-2025.              !
   !                                                                           !
   ! The citations for MLatom's interfaces and features shall be eventually    !
   ! included too. See header.py, ref.json and http://mlatom.com.              !

{mlatom-3.18.2 → mlatom-3.19.0}/src/mlatom/MLtasks.py

@@ -46,12 +46,12 @@ def useMLmodel(args):
     if args.uaiqm:
         get_uaiqm_args(args)
     model = loading_model(args)
-    molecular_database = loading_data(args.XYZfile, args.Yfile, args.YgradXYZfile, charges=args.charges, multiplicities=args.multiplicities)
+    molecular_database = loading_data(args.XYZfile, args.jsonfile, args.Yfile, args.YgradXYZfile, charges=args.charges, multiplicities=args.multiplicities)
     t_predict = predicting(model=model, molecular_database=molecular_database, value=bool(args.YestFile), gradient=bool(args.YgradXYZestFile), hessian=bool(args.hessianEstFile), ismethod=args.method)
     saving_predictions(molecular_database, YestFile=args.YestFile, YgradXYZestFile=args.YgradXYZestFile, hessianEstFile=args.hessianEstFile, method=args.method)
     if args.method:
         print('')
-        if args.AIQM1 or args.AIQM1DFT or args.AIQM1DFTstar or args.AIQM2 or args.AIQM2DFT or args.ani1ccx or args.ani1x or args.ani2x or args.ani1xd4 or args.ani2xd4 or args.ani1ccxgelu or args.ani1xgelu or args.ani1ccxgelud4 or args.ani1xgelud4:
+        if args.AIQM1 or args.AIQM1DFT or args.AIQM1DFTstar or args.AIQM2 or args.AIQM2DFT or args.AIQM3 or args.AIQM3DFT or args.ani1ccx or args.ani1x or args.ani2x or args.ani1xd4 or args.ani2xd4 or args.ani1ccxgelu or args.ani1xgelu or args.ani1ccxgelud4 or args.ani1xgelud4:
             nmol = 0
             for mol in molecular_database:
                 nmol += 1
@@ -60,6 +60,8 @@ def useMLmodel(args):
                     printing_aiqm1_results(aiqm1=args.AIQM1, molecule=mol)
                 if args.AIQM2 or args.AIQM2DFT:
                     printing_aiqm2_results(molecule=mol)
+                if args.AIQM3 or args.AIQM3DFT:
+                    printing_aiqm3_results(molecule=mol)
                 elif args.ani1ccx or args.ani1x or args.ani2x or args.ani1xd4 or args.ani2xd4 or args.ani1ccxgelu or args.ani1xgelu or args.ani1ccxgelud4 or args.ani1xgelud4:
                     printing_animethod_results(methodname=model.method, molecule=mol)
         elif 'uaiqm' in args.method:
@@ -79,7 +81,7 @@ def useMLmodel(args):
 def createMLmodel(args):
     if args.deltaLearn:
         pre_delta_learning(args)
-    molecular_database = loading_data(args.XYZfile, args.Yfile, args.YgradXYZfile, charges=args.charges, multiplicities=args.multiplicities)
+    molecular_database = loading_data(args.XYZfile, args.jsonfile, args.Yfile, args.YgradXYZfile, charges=args.charges, multiplicities=args.multiplicities)
     i_train, i_subtrain, i_validate, i_test, i_cvtest, i_cvopt = sampling(args=args)
     model = loading_model(args)
     result = training(
@@ -95,7 +97,7 @@ def createMLmodel(args):
 def estAccMLmodel(args):
     if args.deltaLearn:
         pre_delta_learning(args)
-    molecular_database = loading_data(args.XYZfile, args.Yfile, args.YgradXYZfile)
+    molecular_database = loading_data(args.XYZfile,args.jsonfile, args.Yfile, args.YgradXYZfile)
     i_train, i_subtrain, i_validate, i_test, i_cvtest, i_cvopt = sampling(args=args)
     model = loading_model(args)
     if args.CVtest:
@@ -212,7 +214,7 @@ def selfCorrect(args):
                     fylayer.writelines('%25.13f\n' % (ylayerm1[ii] + yestlayer[ii]))
 
 def learningCurve(args):
-    molecular_database = loading_data(args.XYZfile, args.Yfile, args.YgradXYZfile, charges=args.charges, multiplicities=args.multiplicities)
+    molecular_database = loading_data(args.XYZfile, args.jsonfile, args.Yfile, args.YgradXYZfile, charges=args.charges, multiplicities=args.multiplicities)
     if args.XfileIn:
         args.XfileIn = os.path.abspath(args.Xfilein)
     else:
@@ -385,7 +387,7 @@ def geomopt(args, return_moldb=False):
     from . import simulations
     if args.uaiqm:
         get_uaiqm_args(args)
-    molDB = loading_data(XYZfile=args.XYZfile, charges=args.charges, multiplicities=args.multiplicities)
+    molDB = loading_data(XYZfile=args.XYZfile, jsonfile=args.jsonfile, charges=args.charges, multiplicities=args.multiplicities)
     model = loading_model(args)
     fname = args.optXYZ
     # if os.path.exists(fname): stopper.stopMLatom(f'File {fname} already exists; please delete or rename it')
@@ -431,6 +433,10 @@ def geomopt(args, return_moldb=False):
             print('\n\n Final properties of molecule %d\n' % (imol+1))
             printing_aiqm2_results(molecule=geomopt.optimized_molecule)
             print('\n')
+        if args.AIQM3 or args.AIQM3DFT:
+            print('\n\n Final properties of molecule %d\n' % (imol+1))
+            printing_aiqm3_results(molecule=geomopt.optimized_molecule)
+            print('\n')
         elif args.method and 'uaiqm' in args.method:
             print('\n\n Final properties of molecule %d\n' % (imol+1))
             uversion = None if not args.uversion else args.uversion
@@ -456,7 +462,7 @@ def ts(args, return_moldb=False):
 def freq(args, molDB=None):
     from . import simulations
     if molDB is None:
-        molDB = loading_data(args.XYZfile, charges=args.charges, multiplicities=args.multiplicities)
+        molDB = loading_data(args.XYZfile, jsonfile=args.jsonfile, charges=args.charges, multiplicities=args.multiplicities)
     if args.uaiqm:
         get_uaiqm_args(args)
     model = loading_model(args)
@@ -557,6 +563,9 @@ def freq(args, molDB=None):
         if args.AIQM2 or args.AIQM2DFT:
             printing_aiqm2_results(molecule=mol)
             print('')
+        if args.AIQM3 or args.AIQM3DFT:
+            printing_aiqm3_results(molecule=mol)
+            print('')
         elif args.method and 'uaiqm' in args.method:
             uversion = None if not args.uversion else args.uversion
             printing_uaiqm_results(molecule=mol, method=args.method, uversion=args.uversion)
@@ -579,13 +588,13 @@ def freq(args, molDB=None):
             # To-do: make it work for ANI-1ccx
             if args.AIQM1:
                 if mol.aiqm1_nn.energy_standard_deviation > 0.41*constants.kcalpermol2Hartree:
-                    print(' * Warning * Heat of formation have high uncertainty!')
+                    print(' * Warning * Heat of formation has high uncertainty!')
             if args.AIQM2:
                 if mol.aiqm2_nn.energy_standard_deviation > 0.36*constants.kcalpermol2Hartree:
-                    print(' * Warning * Heat of formation have high uncertainty!')
+                    print(' * Warning * Heat of formation has high uncertainty!')
             if args.ani1ccx:
                 if mol.ani1ccx.energy_standard_deviation > 1.68*constants.kcalpermol2Hartree:
-                    print(' * Warning * Heat of formation have high uncertainty!')
+                    print(' * Warning * Heat of formation has high uncertainty!')
         print('')
 
 def ir(args):
@@ -596,13 +605,20 @@ def raman(args):
     freq(args)
 
 def irc(args):
-    from . import simulations
-    molDB = loading_data(args.XYZfile, charges=args.charges, multiplicities=args.multiplicities)
+    from .irc import irc
+    molDB = loading_data(XYZfile=args.XYZfile, jsonfile=args.jsonfile, charges=args.charges, multiplicities=args.multiplicities)
     model = loading_model(args)
     for imol, mol in enumerate(molDB):
         mol.number = imol+1
-        geomopt = simulations.irc(model=model,
-                                    ts_molecule=mol)
+        if len(molDB) == 1: wd = 'irc'
+        else: wd = f'irc{imol}'
+        forward=False; backward=False
+        if args.forward: forward=True
+        if args.backward: backward=True 
+        results = irc(
+            model=model, molecule=mol, program=args.ircprog, working_directory=wd,
+            forward=forward, backward=backward)
+        print(results); sys.stdout.flush()
 
 def MD(args):
     from . import md_cmd
@@ -641,7 +657,7 @@ def MLTPA(args):
 
 def al(args):
     from .al import active_learning
-    molDB = loading_data(args.XYZfile, charges=args.charges, multiplicities=args.multiplicities)
+    molDB = loading_data(args.XYZfile, jsonfile=args.jsonfile, charges=args.charges, multiplicities=args.multiplicities)
     args.nthreads = 1
     model = loading_model(args)
     active_learning(
@@ -650,11 +666,22 @@ def al(args):
     )
 
 # Reusable functions below. Name with -ing form
-def loading_data(XYZfile, Yfile=None, YgradXYZfile=None, charges=None, multiplicities=None):
-    assert XYZfile, 'please provide data file(s) needed.'
-    if not os.path.exists(XYZfile):
+def loading_data(XYZfile=None, jsonfile=None, Yfile=None, YgradXYZfile=None, charges=None, multiplicities=None):
+    
+    assert XYZfile or jsonfile, 'please provide data file(s) needed.'
+    if XYZfile and jsonfile:
+        print("Both xyz file and .json file are specified. Only json file will be loaded!")
+        XYZfile = None 
+
+    if XYZfile and not os.path.exists(XYZfile):
         stopper.stopMLatom(f'xyz file {XYZfile} is not found!')
-    molecular_database = data.molecular_database.from_xyz_file(XYZfile)
+    if jsonfile and not os.path.exists(jsonfile):
+        stopper.stopMLatom(f'json file {jsonfile} is not found!')
+    
+    if XYZfile:
+        molecular_database = data.molecular_database.from_xyz_file(XYZfile)
+    if jsonfile:
+        molecular_database = data.molecular_database.load(jsonfile, format='json')
     if Yfile: 
         molecular_database.add_scalar_properties_from_file(Yfile)
     if YgradXYZfile:
@@ -688,6 +715,8 @@ def loading_method(args):
         kwargs['warning'] = args.uwarning
     method = models.methods(**kwargs)
     method.set_num_threads(args.nthreads)
+    if args.calcdir:
+        method.working_directory = args.calcdir # some methods don't have working_directory arguments
     return method
 
 def loading_model(args):
@@ -1080,7 +1109,7 @@ def post_delta_learning(args):
                     fyestt.writelines('%s\n' % strtmp)
 
 def get_uaiqm_args(args):
-    molecular_database = loading_data(args.XYZfile, args.Yfile, args.YgradXYZfile, charges=args.charges, multiplicities=args.multiplicities)
+    molecular_database = loading_data(args.XYZfile, args.jsonfile, args.Yfile, args.YgradXYZfile, charges=args.charges, multiplicities=args.multiplicities)
     model = models.uaiqm(method='uaiqm_optimal')
     if not args.ncpus:
         args.ncpus = 8
@@ -1123,6 +1152,20 @@ def printing_aiqm2_results(molecule=None):
     print(fmt % ('D4 contribution', molecule.d4wb97x.energy))
     print(fmt % ('Total energy', molecule.energy))
 
+def printing_aiqm3_results(molecule=None):
+    fmt = ' %-41s: %15.8f Hartree'
+    # find aiqm1 keyword
+    for kk,_ in molecule.__dict__.items():
+        if 'aiqm3' in kk and kk[-2:]=='nn':
+            aiqm3method = kk.replace('_nn','')
+            break
+    print(fmt % ('Standard deviation of NN contribution', molecule.__dict__[aiqm3method+'_nn'].energy_standard_deviation), end='')
+    print(' %15.5f kcal/mol' % (molecule.__dict__[aiqm3method+'_nn'].energy_standard_deviation * constants.Hartree2kcalpermol))
+    print(fmt % ('NN contribution', molecule.__dict__[aiqm3method+'_nn'].energy))
+    print(fmt % ('GFN2-xTB* contribution', molecule.gfn2xtbstar.energy), file=sys.stdout)
+    print(fmt % ('D3 contribution', molecule.d3b973c.energy))
+    print(fmt % ('Total energy', molecule.energy))
+
 def printing_uaiqm_results(molecule=None, method=None, uversion=None):
     print(f' Selected UAIQM method: {method}')
     if uversion:

{mlatom-3.18.2 → mlatom-3.19.0}/src/mlatom/__init__.py

@@ -4,12 +4,12 @@ from .MLatom import run
 from .simulations import optimize_geometry, irc, freq, thermochemistry, md, generate_initial_conditions, vibrational_spectrum, md_parallel
 from .data import atom, molecule, molecular_database
 from .models import kreg, ani, msani
-from .models import methods, aiqm1, aiqm2, dens, ani_methods, aimnet2_methods, gaussian_methods, pyscf_methods, orca_methods, turbomole_methods, mndo_methods, sparrow_methods, xtb_methods, dftbplus_methods, columbus_methods, dftd3_methods, dftd4_methods
+from .models import methods, aiqm1, aiqm2, aiqm3, dens, ani_methods, aimnet2_methods, gaussian_methods, pyscf_methods, orca_methods, turbomole_methods, mndo_methods, sparrow_methods, xtb_methods, dftbplus_methods, columbus_methods, dftd3_methods, dftd4_methods
 from .models import MDtrajNet
 from . import al_utils
 from .al import al
 from .gap_md import gap_md, gap_model
 # add-ons
-from .models import uaiqm, omnip2x, vecmsani
+from .models import uaiqm, omnip1, omnip2x, vecmsani
 
-__version__ = '3.18.2'
+__version__ = '3.19.0'

mlatom-3.19.0/src/mlatom/addons/aiqm3/aiqm3.py

@@ -0,0 +1,47 @@
+import os
+from ... import data, models, constants
+from ...model_cls import method_model, model_tree_node, downloadable_model
+
+class aiqm3(method_model, downloadable_model):
+
+    """ 
+    GFN2-xTB based artificial intelligence quantum-mechanical method 3 (AIQM3)
+
+    Arguments:
+
+        method (str, optional): Currently supports AIQM3, AIQM3@DFT, AIQM3@DFT*
+        working_directory (str, optional): The path to save temporary calculation file. By default, current directory will be choosed.
+        baseline_kwargs (dict, optional): Keywords passed to GFN2-xTB
+        dispersion_kwargs (dict, optional): 
+
+    .. code-block:: 
+
+        # Initialize molecule
+        mol = ml.molecule.from_xyz_file(filename='ethanol.xyz')
+        # Run AIQM3 calculation
+        aiqm3 = ml.methods(method='aiqm3')
+        aiqm3.predict(molecule=mol, calculate_energy=True, calculate_energy_gradients=True, calculate_hessian=True)
+        # Get energy, gradient, and uncertainty of AIQM3 
+        energy = mol.energy
+        gradient = mol.get_energy_gradients()
+        hess = mol.hessian
+        std = mol.aiqm3_model_nn.energy_standard_deviation
+
+    """ 
+    
+    supported_methods = ['AIQM3', 'AIQM3@DFT']
+
+    def __init__(
+        self,
+        method: str = 'AIQM3',
+        working_directory: str = None,
+        baseline_kwargs: dict = None,
+        dispersion_kwargs: dict = None,
+        nthreads: int = 1
+    ):
+
+        if self.is_method_supported(method=method):
+            raise ValueError(f'The requested method "{method}" is supported as an add-on in Aitomic, please refer to http://MLatom.com/aitomic for the instructions on how to obtain it.')
+        else:
+            self.raise_unsupported_method_error(method)
+

{mlatom-3.18.2 → mlatom-3.19.0}/src/mlatom/aiqm1.py

@@ -200,25 +200,30 @@ class ani_nns_in_aiqm1(torchani_model, downloadable_model):
 
     def load_model(self):
         import torch
-        mlatomdir=os.path.dirname(__file__)
-        dirname = os.path.join(mlatomdir, 'aiqm1_model')
+        # mlatomdir = os.path.dirname(__file__)
+        # dirname = os.path.join(mlatomdir, 'aiqm1_model')
         method = 'aiqm1_' + self.level
         self.define_nn()
 
-        # check model file
-        # if 'dft' in method.lower():
-        #     if 'MODELSPATH' in os.environ:
-        #         modelspath = os.environ['MODELSPATH']
-        #     else:
-        #         raise ValueError(f'Please set environment variable MODELSPATH for using this method and put NN model files under $MODELSPATH/{method}_model/')
-        # dirname = os.path.join(os.environ['MODELSPATH'], f'{method}_model')
-        # if not os.path.exists(dirname):
-        #     raise ValueError(f'Please put model files under $MODELSPATH/{method}_model/')
-        model_name, model_path, download = self.check_model_path(self.method)
-        if download: self.download(model_name, model_path)
+        if method == 'aiqm1_cc':
+            download_links = [
+                'https://zenodo.org/records/15383390/files/aiqm1_cc_model.zip?download=1',
+                'https://aitomistic.xyz/model/uaiqm_odm2star_cc_20211202.zip']
+            model_dir = 'aiqm1_model'
+            model_files = [f'cv{ii}.pt' for ii in range(8)]
+
+        elif method == 'aiqm1_dft':
+            download_links = [
+                'https://zenodo.org/records/15383390/files/aiqm1_dft_model.zip?download=1',
+                'https://aitomistic.xyz/model/uaiqm_odm2star_dft_20211202.zip']
+            model_dir = 'aiqm1_dft_model'
+            model_files = [f'cv{ii}.pt' for ii in range(8)]
+
+        mlatom_model_dir, to_download = self.check_model_path(model_dir, model_files)
+        if to_download: self.download(download_links, mlatom_model_dir)
         
         # checkpoint = torch.load(os.path.join(dirname, f'{method}_cv{self.model_index}.pt'), map_location=self.device)
-        checkpoint = torch.load(os.path.join(model_path, f'cv{self.model_index}.pt'), map_location=self.device, weights_only=False)
+        checkpoint = torch.load(os.path.join(mlatom_model_dir, f'cv{self.model_index}.pt'), map_location=self.device, weights_only=False)
         self.nn.load_state_dict(checkpoint['nn'])
         import torchani
         self.model  = torchani.nn.Sequential(self.aev_computer, self.nn).to(self.device).double()