MultiOptPy 1.20.2__py3-none-any.whl

multioptpy/Parameters/gnb.py

@@ -0,0 +1,104 @@
+from multioptpy.Parameters.atomic_number import number_element, element_number
+from multioptpy.Parameters.unit_values import UnitValueLib
+
+
+
+def GNB_s_lib(element):
+    #ref.: DOI: 10.1021/acs.jctc.4c01435
+    if element is int:
+        element = number_element(element)
+    # C is C_3
+    # N is N_3
+    # The parameters of Lanthanides are same as La. (The parameters of Lanthanides except for La are not available in the paper.)
+    GNB_s = {'H' : 0.2772, 'He': 0.2425,
+             'Li': 0.3266, 'Be': 0.3964, 'B' : 0.3121, 'C' : 0.2455, 'N': 0.2743, 'O' : 0.2577, 'F' : 0.2791, 'Ne': 0.2378,
+             'Na': 0.2592, 'Mg': 0.3837, 'Al': 0.3013, 'Si': 0.3202, 'P': 0.3399, 'S' : 0.3215, 'Cl': 0.3071, 'Ar': 0.2752,
+             'K' : 0.2264, 'Ca': 0.4015, 'Sc': 0.9388, 'Ti': 0.6048, 'V': 0.3678, 'Cr': 0.2848, 'Mn': 0.3550, 'Fe': 0.4406, 'Co': 0.4124, 'Ni': 0.3139, 'Cu': 0.3345, 'Zn': 0.3391, 'Ga': 0.3146, 'Ge': 0.3327, 'As': 0.4040, 'Se': 0.3343, 'Br': 0.3242, 'Kr': 0.2920,
+             'Rb': 0.2677, 'Sr': 0.3446, 'Y': 1.0038, 'Zr': 0.6146, 'Nb': 0.4244, 'Mo': 0.4882, 'Tc': 0.4439, 'Ru': 0.4736, 'Rh': 0.4039, 'Pd': 0.3188, 'Ag': 0.2948, 'Cd': 0.3012, 'In': 0.3351, 'Sn': 0.3134, 'Sb': 0.4081, 'Te': 0.3585, 'I': 0.3574, 'Xe': 0.3134,
+             'Cs': 0.2872, 'Ba': 0.3788, 'La': 1.0851, 'Ce': 1.0851, 'Pr': 1.0851, 'Nd': 1.0851, 'Pm': 1.0851, 'Sm': 1.0851, 'Eu': 1.0851, 'Gd': 1.0851, 'Tb': 1.0851, 'Dy': 1.0851, 'Ho': 1.0851, 'Er': 1.0851, 'Tm': 1.0851, 'Yb': 1.0851, 'Lu': 1.0851, 'Hf': 0.5577, 'Ta': 0.5308, 'W': 0.3926, 'Re': 0.5351, 'Os': 0.4701, 'Ir': 0.3661, 'Pt': 0.3411, 'Au': 0.3164, 'Hg': 0.3047, 'Tl': 0.2802, 'Pb': 0.2682, 'Bi': 0.3876, 'Po': 0.3679, 'At': 0.3680, 'Rn': 0.3195, 'X': 1.000}#ang.
+    
+    return GNB_s[element] / UnitValueLib().bohr2angstroms #Bohr
+
+def GNB_beta_lib(element):
+    #ref.: DOI: 10.1021/acs.jctc.4c01435
+    if element is int:
+        element = number_element(element)
+    # C is C_3
+    # N is N_3
+    # The parameters of Lanthanides are same as La. (The parameters of Lanthanides except for La are not available in the paper.)
+    GNB_beta = {'H': 1.7504, 'He': 2.0870,
+                'Li': 2.3073, 'Be': 2.8811, 'B': 2.6366, 'C': 3.0189, 'N': 2.9432, 'O': 2.7407, 'F': 2.5863, 'Ne': 2.5307,
+                'Na': 2.5679, 'Mg': 2.9679, 'Al': 3.2377, 'Si': 3.2749, 'P': 3.7491, 'S': 3.6718, 'Cl': 3.4180, 'Ar': 3.3306,
+                'K': 2.9736, 'Ca': 3.4464, 'Sc': 4.5955, 'Ti': 3.5334, 'V': 3.0680, 'Cr': 2.8393, 'Mn': 3.0550, 'Fe': 3.2628, 'Co': 3.2622, 'Ni': 2.7490, 'Cu': 2.9097, 'Zn': 2.9024, 'Ga': 3.3924, 'Ge': 3.2804, 'As': 3.8757, 'Se': 3.8562, 'Br': 3.7067, 'Kr': 3.6457,
+                'Rb': 3.4421, 'Sr': 3.5590, 'Y': 5.7293, 'Zr': 5.0750, 'Nb': 3.7156, 'Mo': 3.6853, 'Tc': 3.6987, 'Ru': 3.7826, 'Rh': 3.4706, 'Pd': 3.3433, 'Ag': 3.1186, 'Cd': 3.0853, 'In': 3.5452, 'Sn': 3.2997, 'Sb': 4.1277, 'Te': 4.1795, 'I': 4.0988, 'Xe': 4.0387,
+                'Cs': 3.8468, 'Ba': 4.0368, 'La': 6.1365, 'Ce': 6.1365, 'Pr': 6.1365, 'Nd': 6.1365, 'Pm': 6.1365, 'Sm': 6.1365, 'Eu': 6.1365, 'Gd': 6.1365, 'Tb': 6.1365, 'Dy': 6.1365, 'Ho': 6.1365, 'Er': 6.1365, 'Tm': 6.1365, 'Yb': 6.1365, 'Lu': 6.1365, 'Hf': 5.2130, 'Ta': 4.7637, 'W': 3.6018, 'Re': 3.9552, 'Os': 4.0278, 'Ir': 3.6123, 'Pt': 3.6066, 'Au': 3.3822, 'Hg': 3.3750, 'Tl': 3.3964, 'Pb': 3.2481, 'Bi': 4.1225, 'Po': 4.2313, 'At': 4.2455, 'Rn': 4.1784, 'X': 0.000}#ang.
+    
+    return GNB_beta[element] / UnitValueLib().bohr2angstroms #Bohr
+
+
+def GNB_radii_lib(element):
+    #ref.: DOI: 10.1021/acs.jctc.4c01435
+    if element is int:
+        element = number_element(element)
+    # C is C_3
+    # N is N_3
+    # The parameters of Lanthanides are same as La. (The parameters of Lanthanides except for La are not available in the paper.) 
+    GNB_radii = {'H': 3.6516, 'He': 2.1843,
+             'Li': 1.2711, 'Be': 3.3497, 'B': 2.7079, 'C': 1.8219, 'N': 2.4667, 'O': 2.3650, 'F': 1.5062, 'Ne': 1.8233,
+             'Na': 1.3974, 'Mg': 3.3515, 'Al': 3.0102, 'Si': 3.1629, 'P': 3.2554, 'S': 2.9539, 'Cl': 3.0368, 'Ar': 2.6598,
+             'K': 4.0877, 'Ca': 4.1275, 'Sc': 9.7282, 'Ti': 8.5322, 'V': 7.2344, 'Cr': 5.3605, 'Mn': 3.7180, 'Fe': 3.6408, 'Co': 3.4961, 'Ni': 3.5108, 'Cu': 3.0537, 'Zn': 3.0261, 'Ga': 3.1735, 'Ge': 3.1773, 'As': 3.8357, 'Se': 3.1109, 'Br': 3.2122, 'Kr': 2.8263,
+             'Rb': 2.4120, 'Sr': 1.8940, 'Y': 11.2061, 'Zr': 6.8210, 'Nb': 7.2367, 'Mo': 3.9010, 'Tc': 4.0857, 'Ru': 4.0450, 'Rh': 3.4813, 'Pd': 3.0487, 'Ag': 2.7795, 'Cd': 2.8673, 'In': 3.3339, 'Sn': 3.0086, 'Sb': 3.9919, 'Te': 3.4209, 'I': 3.5649, 'Xe': 3.0288,
+             'Cs': 2.2620, 'Ba': 1.3837, 'La': 12.1710, 'Ce': 12.1710, 'Pr': 12.1710, 'Nd': 12.1710, 'Pm': 12.1710, 'Sm': 12.1710, 'Eu': 12.1710, 'Gd': 12.1710, 'Tb': 12.1710, 'Dy': 12.1710, 'Ho': 12.1710, 'Er': 12.1710, 'Tm': 12.1710, 'Yb': 12.1710, 'Lu': 12.1710, 'Hf': 6.0791, 'Ta': 5.7661, 'W': 3.6366, 'Re': 4.2410, 'Os': 4.1348, 'Ir': 3.4213, 'Pt': 3.2486, 'Au': 2.9588, 'Hg': 2.9381, 'Tl': 2.7711, 'Pb': 2.5816, 'Bi': 3.7850, 'Po': 3.5381, 'At': 3.6985, 'Rn': 3.0551, 'X': 0.000}#ang.
+    
+    return GNB_radii[element] / UnitValueLib().bohr2angstroms #Bohr
+
+def GNB_C6_lib(element):
+    #ref.: DOI: 10.1021/acs.jctc.4c01435
+    if element is int:
+        element = number_element(element)
+    # C is C_3
+    # N is N_3
+    # The parameters of Lanthanides are same as La. (The parameters of Lanthanides except for La are not available in the paper.)   
+    GNB_C6 = {'H': 95.99, 'He': 40.67,
+             'Li': 70.21, 'Be': 114.51, 'B': 152.36, 'C': 184.28, 'N': 482.54, 'O': 405.57, 'F': 218.45, 'Ne': 174.81,
+             'Na': 181.70, 'Mg': 263.02, 'Al': 228.10, 'Si': 359.43, 'P': 3222.12, 'S': 2144.49, 'Cl': 2072.46, 'Ar': 1357.42,
+             'K': 1406.65, 'Ca': 1058.36, 'Sc': 11498.73, 'Ti': 3361.33, 'V': 2095.91, 'Cr': 1049.31, 'Mn': 966.27, 'Fe': 1571.36, 'Co': 1183.59, 'Ni': 787.76, 'Cu': 563.93, 'Zn': 592.91, 'Ga': 430.82, 'Ge': 812.57, 'As': 4533.53, 'Se': 3440.92, 'Br': 3859.82, 'Kr': 2729.60,
+             'Rb': 1864.19, 'Sr': 1175.73, 'Y': 32141.18, 'Zr': 27655.14, 'Nb': 2864.20, 'Mo': 3563.45, 'Tc': 3266.43, 'Ru': 3967.23, 'Rh': 2233.82, 'Pd': 1393.49, 'Ag': 1315.09, 'Cd': 1311.47, 'In': 1460.56, 'Sn': 1662.99, 'Sb': 8089.97, 'Te': 6887.05, 'I': 8799.32, 'Xe': 6136.50,
+             'Cs': 3757.31, 'Ba': 2561.18, 'La': 66580.83, 'Ce': 66580.83, 'Pr': 66580.83, 'Nd': 66580.83, 'Pm': 66580.83, 'Sm': 66580.83, 'Eu': 66580.83, 'Gd': 66580.83, 'Tb': 66580.83, 'Dy': 66580.83, 'Ho': 66580.83, 'Er': 66580.83, 'Tm': 66580.83, 'Yb': 66580.83, 'Lu': 66580.83, 'Hf': 27593.76, 'Ta': 15364.65, 'W': 2734.50, 'Re': 4801.82, 'Os': 5685.94, 'Ir': 2786.00, 'Pt': 2699.79, 'Au': 2282.60, 'Hg': 2476.79, 'Tl': 2988.70, 'Pb': 2506.63, 'Bi': 8916.84, 'Po': 8694.22, 'At': 11821.61, 'Rn': 8410.64, 'X': 0.000}#kcal ang^6 mol^-1
+    
+    return GNB_C6[element] / UnitValueLib().hartree2kcalmol / (UnitValueLib().bohr2angstroms) ** 6 #hartree bohr^6
+
+def GNB_VDW_radii_lib(element):
+    #ref.: DOI: 10.1021/acs.jctc.4c01435
+    if element is int:
+        element = number_element(element)
+    # C is C_3
+    # N is N_3
+    # The parameters of Lanthanides are same as La. (The parameters of Lanthanides except for La are not available in the paper.)
+    # Please check the SI of the paper for the details of the parameters.
+    GNB_VDW_distance = {'H':3.2431,'He':3.0533,
+                        'Li' : 3.6711 ,'Be': 5.3659, 'B': 3.9219,'C': 4.0516, 'N':3.6456,'O':3.3001, 'F': 3.2433,'Ne': 3.1416, 
+                        'Na': 3.2429,'Mg': 4.8010 ,'Al':4.7457 ,'Si': 4.7121, 'P': 4.3825, 'S': 4.3735,'Cl':3.9557,'Ar': 3.8692,
+                        'K': 3.8025 ,'Ca':5.0620 ,'Sc': 10.586 ,'Ti':7.7490 ,'V': 5.6617, 'Cr': 4.4761,'Mn': 4.1887, 'Fe': 4.4113,'Co':4.4575 ,'Ni': 3.6711,'Cu': 3.8716,'Zn': 3.8327,'Ga': 4.7820,'Ge': 4.3316,'As': 4.7036 ,'Se': 4.4826,'Br':4.1816,'Kr':4.1261,
+                        'Rb': 3.8623,'Sr': 4.5095,'Y': 11.9894,'Zr': 7.1388,'Nb': 6.4121,'Mo': 4.757,'Tc': 4.8495,'Ru': 4.8882,'Rh':4.3388 ,'Pd': 4.061,'Ag':3.5832 ,'Cd': 3.5717,'In': 4.5002,'Sn': 3.8721,'Sb': 4.8066,'Te': 4.7337, 'I': 4.5014, 'Xe': 4.4360, 
+                        'Cs': 4.2468,'Ba': 5.0441, 'La': 12.586, 'Ce': 12.586,'Pr': 12.586,'Nd': 12.586,'Pm': 12.586,'Sm': 12.586,'Eu': 12.586,'Gd': 12.586,'Tb': 12.586,'Dy': 12.586,'Ho': 12.586,'Er': 12.586,'Tm': 12.586,'Yb': 12.586,'Lu': 12.586,'Hf': 6.7740,
+                        'Ta': 6.3793,'W': 4.4757,'Re': 5.2841,'Os': 5.0541,'Ir': 4.339,'Pt': 4.2436,'Au': 3.8280,'Hg': 3.7598,'Tl': 3.6437,'Pb': 3.4216,'Bi': 4.6308,'Po': 4.7192,'At': 4.6158,'Rn': 4.5115}
+    return GNB_VDW_distance[element] / UnitValueLib().bohr2angstroms#Bohr
+
+def GNB_VDW_well_depth_lib(element):
+    #ref.: DOI: 10.1021/acs.jctc.4c01435
+    if element is int:
+        element = number_element(element)    
+    # C is C_3
+    # N is N_3
+    # The parameters of Lanthanides are same as La. (The parameters of Lanthanides except for La are not available in the paper.)
+    # Please check the SI of the paper for the details of the parameters.    
+    GNB_VDW_well_depth = {'H':0.0226, 'He':0.0257,
+                          'Li':0.0133 ,'Be':0.0026 ,'B':0.0215,'C': 0.0264, 'N':0.1103, 'O':0.1624,'F':0.0908,'Ne':0.0985, 
+                          'Na':0.0813, 'Mg':0.0110 ,'Al':0.0120,'Si': 0.0188, 'P':0.2342, 'S':0.1671, 'Cl':0.2754,  'Ar':0.2247,
+                          'K':0.1573,'Ca':0.0307,'Sc':0.0034,'Ti': 0.0046,'V': 0.0110, 'Cr':0.0298, 'Mn':0.0791,'Fe': 0.0883,'Co':0.0673,'Ni':0.1293,'Cu':0.0786,'Zn':0.0862,'Ga':0.0211 ,'Ge':0.0640, 'As':0.1947,'Se':0.2280,'Br':0.3678,'Kr':0.3084,
+                          'Rb':0.3220,'Sr':0.0756,'Y':0.0045 ,'Zr':0.0838,'Nb':0.0117,'Mo':0.1245,'Tc':0.1101,'Ru':0.1233 ,'Rh':0.1478,'Pd':0.1582,'Ag':0.3034,'Cd':0.2994,'In':0.0930,'Sn':0.2434,'Sb':0.3045,'Te':0.3227, 'I':0.5242,'Xe':0.4498, 
+                          'Cs':0.3778,'Ba':0.0854 , 'La':0.0066 , 'Ce':0.0066 ,'Pr':0.0066 ,'Nd':0.0066 ,'Pm':0.0066 ,'Sm':0.0066 ,'Eu':0.0066 ,'Gd':0.0066 ,'Tb':0.0066 ,'Dy':0.0066 ,'Ho':0.0066 ,'Er':0.0066 ,'Tm':0.0066 ,'Yb':0.0066 ,'Lu':0.0066,'Hf':0.1267 ,
+                          'Ta':0.0999 ,'W':0.1562 ,'Re':0.0906 ,'Os':0.1498,'Ir':0.1992,'Pt':0.2303,'Au':0.3535 ,'Hg':0.4313 ,'Tl':0.6563 ,'Pb':0.7952 ,'Bi':0.4271 ,'Po':0.4029 ,'At':0.6010 ,'Rn':0.5572, 'X':0.000}
+                
+    return GNB_VDW_well_depth[element] / UnitValueLib().hartree2kcalmol #hartree

multioptpy/Parameters/parameter.py

@@ -0,0 +1,22 @@
+
+### General Nonbonded Force Field Parameters ###
+from multioptpy.Parameters.gnb import *
+
+### Universal Force Field Parameters ###
+from multioptpy.Parameters.uff import *
+
+### D2 Dispersion Model Parameters ###
+from multioptpy.Parameters.d2 import *
+
+from multioptpy.Parameters.gfnff_param import *
+from multioptpy.Parameters.gfn0xtb_param import *
+from multioptpy.Parameters.d4 import *
+from multioptpy.Parameters.d3 import *
+
+from multioptpy.Parameters.dreiding import *
+from multioptpy.Parameters.covalent_radii import *
+
+
+from multioptpy.Parameters.atomic_mass import *
+from multioptpy.Parameters.unit_values import *
+

multioptpy/Parameters/uff.py

@@ -0,0 +1,72 @@
+from multioptpy.Parameters.atomic_number import number_element, element_number
+from multioptpy.Parameters.unit_values import UnitValueLib
+
+
+def UFF_bond_distance_lib(element):
+    if element is int:
+        element = number_element(element)
+    UFF_bond_distance = {'H_':0.354, 'H_b':0.460, 'He':0.849,
+                        'Li' : 1.336, 'Be': 1.074, 'B_3':0.838, 'B_2':0.828, 'C_3': 0.757, 'C_R': 0.729, 'C_2': 0.732, 'C_1': 0.706,###
+                          'N':3.660,'O':3.500 , 'F':3.364,'Ne': 3.243, 
+                        'Na':2.983,'Mg': 3.021 ,'Al':4.499 ,'Si': 4.295, 'P':4.147, 'S':4.035 ,'Cl':3.947,'Ar':3.868 ,
+                        'K':3.812 ,'Ca':3.399 ,'Sc':3.295 ,'Ti':3.175 ,'V': 3.144, 'Cr':3.023 ,'Mn': 2.961, 'Fe': 2.912,'Co':2.872 ,'Ni':2.834 ,'Cu':3.495 ,'Zn':2.763 ,'Ga': 4.383,'Ge':4.280,'As':4.230 ,'Se':4.205,'Br':4.189,'Kr':4.141 ,
+                        'Rb':4.114 ,'Sr': 3.641,'Y':3.345 ,'Zr':3.124 ,'Nb':3.165 ,'Mo':3.052 ,'Tc':2.998 ,'Ru':2.963 ,'Rh':2.929 ,'Pd':2.899 ,'Ag':3.148 ,'Cd':2.848 ,'In':4.463 ,'Sn':4.392 ,'Sb':4.420 ,'Te':4.470 , 'I':4.50, 'Xe':4.404 , 
+                        'Cs':4.517 ,'Ba':3.703 , 'La':3.522 , 'Ce':3.556 ,'Pr':3.606 ,'Nd':3.575 ,'Pm':3.547 ,'Sm':3.520 ,'Eu':3.493 ,'Gd':3.368 ,'Tb':3.451 ,'Dy':3.428 ,'Ho':3.409 ,'Er':3.391 ,'Tm':3.374 ,'Yb':3.355,'Lu':3.640 ,'Hf': 3.141,
+                        'Ta':3.170 ,'W':3.069 ,'Re':2.954 ,'Os':3.120 ,'Ir':2.840 ,'Pt':2.754 ,'Au':3.293 ,'Hg':2.705 ,'Tl':4.347 ,'Pb':4.297 ,'Bi':4.370 ,'Po':4.709 ,'At':4.750 ,'Rn': 4.765}#H...Rn J. Am. Chem. Soc., 1992, 114, 10024 #ang.
+                
+    return UFF_bond_distance[element] / UnitValueLib().bohr2angstroms#Bohr
+
+
+
+def UFF_bondangle_lib(element):# not implemented
+    if element is int:
+        element = number_element(element)
+    UFF_bondangle = {'H_':180.0, 'H_b':83.5, 'He':90.0,
+                        'Li' : 180.0, 'Be': 109.47, 'B_3':109.47, 'B_2':120.0, 'C_3': 109.47, 'C_R': 120.0, 'C_2': 120.0, 'C_1': 180.0,###
+                          'N':3.660,'O':3.500 , 'F':3.364,'Ne': 3.243, 
+                        'Na':2.983,'Mg': 3.021 ,'Al':4.499 ,'Si': 4.295, 'P':4.147, 'S':4.035 ,'Cl':3.947,'Ar':3.868 ,
+                        'K':3.812 ,'Ca':3.399 ,'Sc':3.295 ,'Ti':3.175 ,'V': 3.144, 'Cr':3.023 ,'Mn': 2.961, 'Fe': 2.912,'Co':2.872 ,'Ni':2.834 ,'Cu':3.495 ,'Zn':2.763 ,'Ga': 4.383,'Ge':4.280,'As':4.230 ,'Se':4.205,'Br':4.189,'Kr':4.141 ,
+                        'Rb':4.114 ,'Sr': 3.641,'Y':3.345 ,'Zr':3.124 ,'Nb':3.165 ,'Mo':3.052 ,'Tc':2.998 ,'Ru':2.963 ,'Rh':2.929 ,'Pd':2.899 ,'Ag':3.148 ,'Cd':2.848 ,'In':4.463 ,'Sn':4.392 ,'Sb':4.420 ,'Te':4.470 , 'I':4.50, 'Xe':4.404 , 
+                        'Cs':4.517 ,'Ba':3.703 , 'La':3.522 , 'Ce':3.556 ,'Pr':3.606 ,'Nd':3.575 ,'Pm':3.547 ,'Sm':3.520 ,'Eu':3.493 ,'Gd':3.368 ,'Tb':3.451 ,'Dy':3.428 ,'Ho':3.409 ,'Er':3.391 ,'Tm':3.374 ,'Yb':3.355,'Lu':3.640 ,'Hf': 3.141,
+                        'Ta':3.170 ,'W':3.069 ,'Re':2.954 ,'Os':3.120 ,'Ir':2.840 ,'Pt':2.754 ,'Au':3.293 ,'Hg':2.705 ,'Tl':4.347 ,'Pb':4.297 ,'Bi':4.370 ,'Po':4.709 ,'At':4.750 ,'Rn': 4.765}#H...Rn J. Am. Chem. Soc., 1992, 114, 10024 #ang.
+                
+    return UFF_bondangle[element] * UnitValueLib().deg2rad #rad
+
+
+def UFF_effective_charge_lib(element):
+    if element is int:
+        element = number_element(element)
+    UFF_EC = {'H':0.712,'He': 0.098,
+                        'Li' : 1.026 ,'Be': 1.565, 'B': 1.755,'C': 1.912, 'N': 2.544,'O': 2.300, 'F': 1.735,'Ne': 0.194, 
+                        'Na': 1.081, 'Mg': 1.787,'Al': 1.792,'Si': 2.323, 'P': 2.863, 'S': 2.703,'Cl': 2.348,'Ar': 0.300,
+                        'K': 1.165 ,'Ca': 2.141,'Sc': 2.592,'Ti': 2.659,'V': 2.679, 'Cr': 2.463,'Mn': 2.430, 'Fe': 2.430,'Co': 2.430 ,'Ni': 2.430 ,'Cu': 1.756 ,'Zn': 1.308,'Ga': 1.821, 'Ge': 2.789,'As': 2.864,'Se': 2.764,'Br': 2.519,'Kr': 0.452,
+                        'Rb': 1.592,'Sr': 2.449,'Y': 3.257,'Zr': 3.667,'Nb': 3.618,'Mo': 3.400, 'Tc': 3.400,'Ru': 3.400,'Rh': 3.508, 'Pd': 3.210,'Ag': 1.956,'Cd': 1.650,'In': 2.070,'Sn': 2.961,'Sb': 2.704,'Te': 2.882, 'I': 2.650, 'Xe': 0.556, 
+                        'Cs': 1.573,'Ba': 2.727, 'La': 3.300, 'Ce': 3.300,'Pr': 3.300,'Nd':3.300,'Pm':3.300,'Sm':3.300,'Eu':3.300,'Gd':3.300,'Tb':3.300,'Dy':3.300,'Ho': 3.416 ,'Er': 3.300,'Tm': 3.300,'Yb': 2.618,'Lu': 3.271,'Hf': 3.921,
+                        'Ta': 4.075,'W': 3.70,'Re': 3.70,'Os': 3.70,'Ir': 3.731,'Pt': 3.382,'Au': 2.625,'Hg': 1.750,'Tl': 2.068,'Pb': 2.846,'Bi': 2.470,'Po': 2.330,'At': 2.240,'Rn': 0.583}#H...Rn J. Am. Chem. Soc., 1992, 114, 10024 #charge
+    return UFF_EC[element]
+
+def UFF_VDW_distance_lib(element):
+    if element is int:
+        element = number_element(element)
+    UFF_VDW_distance = {'H':2.886,'He':2.362 ,
+                        'Li' : 2.451 ,'Be': 2.745, 'B':4.083 ,'C': 3.851, 'N':3.660,'O':3.500 , 'F':3.364,'Ne': 3.243, 
+                        'Na':2.983,'Mg': 3.021 ,'Al':4.499 ,'Si': 4.295, 'P':4.147, 'S':4.035 ,'Cl':3.947,'Ar':3.868 ,
+                        'K':3.812 ,'Ca':3.399 ,'Sc':3.295 ,'Ti':3.175 ,'V': 3.144, 'Cr':3.023 ,'Mn': 2.961, 'Fe': 2.912,'Co':2.872 ,'Ni':2.834 ,'Cu':3.495 ,'Zn':2.763 ,'Ga': 4.383,'Ge':4.280,'As':4.230 ,'Se':4.205,'Br':4.189,'Kr':4.141 ,
+                        'Rb':4.114 ,'Sr': 3.641,'Y':3.345 ,'Zr':3.124 ,'Nb':3.165 ,'Mo':3.052 ,'Tc':2.998 ,'Ru':2.963 ,'Rh':2.929 ,'Pd':2.899 ,'Ag':3.148 ,'Cd':2.848 ,'In':4.463 ,'Sn':4.392 ,'Sb':4.420 ,'Te':4.470 , 'I':4.50, 'Xe':4.404 , 
+                        'Cs':4.517 ,'Ba':3.703 , 'La':3.522 , 'Ce':3.556 ,'Pr':3.606 ,'Nd':3.575 ,'Pm':3.547 ,'Sm':3.520 ,'Eu':3.493 ,'Gd':3.368 ,'Tb':3.451 ,'Dy':3.428 ,'Ho':3.409 ,'Er':3.391 ,'Tm':3.374 ,'Yb':3.355,'Lu':3.640 ,'Hf': 3.141,
+                        'Ta':3.170 ,'W':3.069 ,'Re':2.954 ,'Os':3.120 ,'Ir':2.840 ,'Pt':2.754 ,'Au':3.293 ,'Hg':2.705 ,'Tl':4.347 ,'Pb':4.297 ,'Bi':4.370 ,'Po':4.709 ,'At':4.750 ,'Rn': 4.765}#H...Rn J. Am. Chem. Soc., 1992, 114, 10024 #ang.
+                
+    return UFF_VDW_distance[element] / UnitValueLib().bohr2angstroms#Bohr
+
+def UFF_VDW_well_depth_lib(element):
+    if element is int:
+        element = number_element(element)         
+    UFF_VDW_well_depth = {'H':0.0152, 'He':0.056 ,
+                          'Li':0.025 ,'Be':0.085 ,'B':0.095,'C': 0.0951, 'N':0.0774, 'O':0.0957,'F':0.0725,'Ne':0.042 , 
+                          'Na':0.50, 'Mg':0.111 ,'Al':0.31 ,'Si': 0.31, 'P':0.3200, 'S':0.3440, 'Cl':0.2833,  'Ar':0.185 ,
+                          'K':0.035 ,'Ca':0.05 ,'Sc':0.019 ,'Ti':0.0550 ,'V':0.016 , 'Cr':0.015, 'Mn':0.013 ,'Fe': 0.0550,'Co':0.014 ,'Ni':0.015 ,'Cu':0.005 ,'Zn':0.055 ,'Ga':0.40 ,'Ge':0.40, 'As':0.41 ,'Se':0.43,'Br':0.37,'Kr':0.220 ,
+                          'Rb':0.04 ,'Sr':0.235 ,'Y':0.072 ,'Zr':0.069 ,'Nb':0.059 ,'Mo':0.056 ,'Tc':0.048 ,'Ru':0.0500 ,'Rh':0.053 ,'Pd':0.048 ,'Ag':0.036 ,'Cd':0.228 ,'In':0.55 ,'Sn':0.55 ,'Sb':0.55 ,'Te':0.57 , 'I':0.51,'Xe':0.332 , 
+                          'Cs':0.045 ,'Ba':0.364 , 'La':0.017 , 'Ce':0.013 ,'Pr':0.010 ,'Nd':0.010 ,'Pm':0.009 ,'Sm':0.008 ,'Eu':0.008 ,'Gd':0.009 ,'Tb':0.007 ,'Dy':0.007 ,'Ho':0.007 ,'Er':0.007 ,'Tm':0.006 ,'Yb':0.228 ,'Lu':0.041 ,'Hf':0.072 ,
+                          'Ta':0.081 ,'W':0.067 ,'Re':0.066 ,'Os':0.037 ,'Ir':0.073 ,'Pt':0.080 ,'Au':0.039 ,'Hg':0.385 ,'Tl':0.680 ,'Pb':0.663 ,'Bi':0.518 ,'Po':0.325 ,'At':0.284 ,'Rn':0.248, 'X':0.010}#H...Rn J. Am. Chem. Soc., 1992, 114, 10024 # kcal/mol
+                
+    return UFF_VDW_well_depth[element] / UnitValueLib().hartree2kcalmol #hartree

multioptpy/Parameters/unit_values.py

@@ -0,0 +1,20 @@
+
+class UnitValueLib: 
+    def __init__(self):
+        self.hartree2kcalmol = 627.509 #
+        self.bohr2angstroms = 0.52917721067 #
+        self.hartree2kjmol = 2625.500 #
+        self.hartree2eV = 27.211396127707
+        self.amu2kg = 1.66053906660 * 10 ** (-27)
+        self.au2kg = 9.1093837015 * 10 ** (-31)
+        self.hartree2j =  4.3597447222071 * 10 ** (-18) 
+        self.bohr2m = 5.29177210903 * 10 ** (-11)
+        self.mol2au = 6.02214076 * 10 ** 23
+        self.deg2rad = 0.017453292519943295
+        self.au2sec = 2.418884326505 * 10 ** (-17)
+        self.boltzmann_constant = 1.380649 * 10 ** (-23) # J/K
+        self.planck_constant = 6.62607015 * 10 ** (-34) # J.s
+        self.vacume_light_speed = 2.99792458 * 10 ** 8 # m/s
+        
+        return
+        

multioptpy/Potential/AFIR_potential.py

@@ -0,0 +1,55 @@
+from multioptpy.Parameters.parameter import UnitValueLib, covalent_radii_lib
+
+import math
+import torch
+
+        
+class AFIRPotential:
+    def __init__(self, **kwarg):
+        self.config = kwarg
+        UVL = UnitValueLib()
+        self.hartree2kcalmol = UVL.hartree2kcalmol 
+        self.bohr2angstroms = UVL.bohr2angstroms 
+        self.hartree2kjmol = UVL.hartree2kjmol 
+        self.R_0 = 3.8164/self.bohr2angstroms #ang.→bohr
+        self.EPSIRON = 1.0061/self.hartree2kjmol #kj/mol→hartree
+        self.p = 6.0
+        return
+    def calc_energy(self, geom_num_list, bias_pot_params):
+        """
+        # required variables: 
+                             self.config["AFIR_Fragm_1"], 
+                             self.config["AFIR_Fragm_2"],
+                             self.config["element_list"]
+                             bias_pot_params[0] : AFIR_gamma
+        """
+        """
+        ###  Reference  ###
+            Chem. Rec., 2016, 16, 2232
+            J. Comput. Chem., 2018, 39, 233
+            WIREs Comput. Mol. Sci., 2021, 11, e1538
+        """
+
+        if bias_pot_params[0] > 0.0 or bias_pot_params[0] < 0.0:
+            alpha = (bias_pot_params[0]/self.hartree2kjmol) / ((2 ** (-1/6) - (1 + math.sqrt(1 + (abs(bias_pot_params[0]/self.hartree2kjmol) / self.EPSIRON))) ** (-1/6))*self.R_0) #hartree/Bohr
+        else:
+            alpha = 0.0
+        A = 0.0
+        B = 0.0
+        
+        i_indices = torch.tensor(self.config["AFIR_Fragm_1"]) - 1  # 0-based index
+        j_indices = torch.tensor(self.config["AFIR_Fragm_2"]) - 1  # 0-based index
+
+        R_i = torch.tensor([covalent_radii_lib(self.config["element_list"][i.item()]) for i in i_indices])  # shape: (M,)
+        R_j = torch.tensor([covalent_radii_lib(self.config["element_list"][j.item()]) for j in j_indices])  # shape: (M,)
+
+        geom_diff = geom_num_list[i_indices].unsqueeze(1) - geom_num_list[j_indices].unsqueeze(0)  # shape: (M, N, 3)
+        vector = torch.linalg.norm(geom_diff, dim=2)  # shape: (M, N)
+
+        omega = ((R_i.unsqueeze(1) + R_j.unsqueeze(0)) / vector) ** self.p  # shape: (M, N)
+
+        A = (omega * vector).sum() 
+        B = omega.sum()  
+        
+        energy = alpha*(A/B)#A/B:Bohr
+        return energy #hartree

multioptpy/Potential/LJ_repulsive_potential.py

@@ -0,0 +1,345 @@
+
+from multioptpy.Parameters.parameter import UnitValueLib, UFF_VDW_distance_lib, UFF_VDW_well_depth_lib
+
+import itertools
+import math
+import torch
+
+
+class LJRepulsivePotentialScale:
+    def __init__(self, mm_pot_type="UFF", **kwarg):
+        if mm_pot_type == "UFF":
+            self.VDW_distance_lib = UFF_VDW_distance_lib #function
+            self.VDW_well_depth_lib = UFF_VDW_well_depth_lib #function
+        else:
+            raise "No MM potential type"
+        self.config = kwarg
+        
+        UVL = UnitValueLib()
+        self.hartree2kcalmol = UVL.hartree2kcalmol 
+        self.bohr2angstroms = UVL.bohr2angstroms 
+        self.hartree2kjmol = UVL.hartree2kjmol
+        
+        indices_1 = torch.tensor(self.config["repulsive_potential_Fragm_1"]) - 1
+        indices_2 = torch.tensor(self.config["repulsive_potential_Fragm_2"]) - 1
+        self.pairs_1, self.pairs_2 = torch.meshgrid(indices_1, indices_2, indexing='ij')
+        self.pairs_1 = self.pairs_1.flatten()
+        self.pairs_2 = self.pairs_2.flatten()
+   
+        VDW_well_depth_1 = [self.VDW_well_depth_lib(self.config["element_list"][elem]) for elem in self.pairs_1]
+        VDW_well_depth_2 = [self.VDW_well_depth_lib(self.config["element_list"][elem]) for elem in self.pairs_2]
+        
+        self.VDW_well_depth_1 = torch.tensor(VDW_well_depth_1)
+        self.VDW_well_depth_2 = torch.tensor(VDW_well_depth_2)
+        
+        VDW_distance_1 = [self.VDW_distance_lib(self.config["element_list"][elem]) for elem in self.pairs_1]
+        VDW_distance_2 = [self.VDW_distance_lib(self.config["element_list"][elem]) for elem in self.pairs_2]
+        
+        self.VDW_distance_1 = torch.tensor(VDW_distance_1)
+        self.VDW_distance_2 = torch.tensor(VDW_distance_2)
+        
+        return
+    def calc_energy(self, geom_num_list, bias_pot_params=[]):#geom_num_list: torch.float32
+        """
+        # required variables: self.config["repulsive_potential_well_scale"], 
+                             self.config["repulsive_potential_dist_scale"], 
+                             self.config["repulsive_potential_Fragm_1"],
+                             self.config["repulsive_potential_Fragm_2"]
+                             self.config["element_list"]
+        """
+        energy = 0.0
+        UFF_VDW_well_depth = torch.sqrt(
+            self.config["repulsive_potential_well_scale"] ** 2 * self.VDW_well_depth_1 * self.VDW_well_depth_2)
+        UFF_VDW_distance = torch.sqrt(
+            self.config["repulsive_potential_dist_scale"] ** 2 * self.VDW_distance_1 * self.VDW_distance_2)
+        
+        vectors = torch.linalg.norm(geom_num_list[self.pairs_1] - geom_num_list[self.pairs_2], dim=1)
+        
+        tot_energy = UFF_VDW_well_depth * (
+            -2 * (UFF_VDW_distance / vectors) ** 6
+            + (UFF_VDW_distance / vectors) ** 12)
+        energy = torch.sum(tot_energy)
+        return energy
+
+class LJRepulsivePotentialValue:
+    def __init__(self, mm_pot_type="UFF", **kwarg):
+        if mm_pot_type == "UFF":
+            self.VDW_distance_lib = UFF_VDW_distance_lib #function
+            self.VDW_well_depth_lib = UFF_VDW_well_depth_lib #function
+        else:
+            raise "No MM potential type"
+        self.config = kwarg
+        
+        UVL = UnitValueLib()
+        self.hartree2kcalmol = UVL.hartree2kcalmol 
+        self.bohr2angstroms = UVL.bohr2angstroms 
+        self.hartree2kjmol = UVL.hartree2kjmol 
+
+        indices_1 = torch.tensor(self.config["repulsive_potential_Fragm_1"]) - 1
+        indices_2 = torch.tensor(self.config["repulsive_potential_Fragm_2"]) - 1
+        self.pairs_1, self.pairs_2 = torch.meshgrid(indices_1, indices_2, indexing='ij')
+        self.pairs_1 = self.pairs_1.flatten()
+        self.pairs_2 = self.pairs_2.flatten()
+   
+        VDW_well_depth_1 = [self.VDW_well_depth_lib(self.config["element_list"][elem]) for elem in self.pairs_1]
+        VDW_well_depth_2 = [self.VDW_well_depth_lib(self.config["element_list"][elem]) for elem in self.pairs_2]
+        
+        self.VDW_well_depth_1 = torch.tensor(VDW_well_depth_1)
+        self.VDW_well_depth_2 = torch.tensor(VDW_well_depth_2)
+        
+        VDW_distance_1 = [self.VDW_distance_lib(self.config["element_list"][elem]) for elem in self.pairs_1]
+        VDW_distance_2 = [self.VDW_distance_lib(self.config["element_list"][elem]) for elem in self.pairs_2]
+        
+        self.VDW_distance_1 = torch.tensor(VDW_distance_1)
+        self.VDW_distance_2 = torch.tensor(VDW_distance_2)
+        
+        return
+    def calc_energy(self, geom_num_list, bias_pot_params=[]):#geom_num_list: torch.float32
+        """
+        # required variables: self.config["repulsive_potential_well_value"], 
+                             self.config["repulsive_potential_dist_value"], 
+                             self.config["repulsive_potential_Fragm_1"],
+                             self.config["repulsive_potential_Fragm_2"]
+                             self.config["element_list"]
+        """
+        
+        energy = 0.0
+        UFF_VDW_well_depth = self.config["repulsive_potential_well_value"]/self.hartree2kjmol
+        UFF_VDW_distance = self.config["repulsive_potential_dist_value"]/self.bohr2angstroms
+        vectors = torch.linalg.norm(geom_num_list[self.pairs_1] - geom_num_list[self.pairs_2], dim=1)
+        tot_energy = UFF_VDW_well_depth * (
+            -2 * (UFF_VDW_distance / vectors) ** 6
+            + (UFF_VDW_distance / vectors) ** 12)
+        energy = torch.sum(tot_energy)
+        return energy
+
+
+class LJRepulsivePotentialv2Scale:
+    def __init__(self, mm_pot_type="UFF", **kwarg):
+        if mm_pot_type == "UFF":
+            self.VDW_distance_lib = UFF_VDW_distance_lib #function
+            self.VDW_well_depth_lib = UFF_VDW_well_depth_lib #function
+        else:
+            raise "No MM potential type"
+        self.config = kwarg
+        
+        UVL = UnitValueLib()
+        self.hartree2kcalmol = UVL.hartree2kcalmol 
+        self.bohr2angstroms = UVL.bohr2angstroms 
+        self.hartree2kjmol = UVL.hartree2kjmol 
+        
+        self.center1 = self.config["repulsive_potential_v2_center"][1] - 1
+        self.center0 = self.config["repulsive_potential_v2_center"][0] - 1
+
+        self.target_indices = torch.tensor(self.config["repulsive_potential_v2_target"]) - 1
+
+        VDW_well_depth_center = self.VDW_well_depth_lib(self.config["element_list"][self.center1])
+        VDW_distance_center = self.VDW_distance_lib(self.config["element_list"][self.center1])
+
+        VDW_well_depth_target = [self.VDW_well_depth_lib(self.config["element_list"][tgt]) for tgt in self.target_indices]
+        VDW_distance_target = [self.VDW_distance_lib(self.config["element_list"][tgt]) for tgt in self.target_indices]
+        
+        self.VDW_well_depth_center = torch.tensor(VDW_well_depth_center)
+        self.VDW_distance_center = torch.tensor(VDW_distance_center)
+        self.VDW_well_depth_target = torch.tensor(VDW_well_depth_target)
+        self.VDW_distance_target = torch.tensor(VDW_distance_target)
+                
+        
+    def calc_energy(self, geom_num_list, bias_pot_params=[]):
+        """
+        # required variables: self.config["repulsive_potential_v2_well_scale"], 
+                             self.config["repulsive_potential_v2_dist_scale"], 
+                             self.config["repulsive_potential_v2_length"],
+                             self.config["repulsive_potential_v2_const_rep"]
+                             self.config["repulsive_potential_v2_const_attr"], 
+                             self.config["repulsive_potential_v2_order_rep"], 
+                             self.config["repulsive_potential_v2_order_attr"],
+                             self.config["repulsive_potential_v2_center"]
+                             self.config["repulsive_potential_v2_target"]
+                             self.config["element_list"]
+        """
+        energy = 0.0
+        
+     
+        center_vector = geom_num_list[self.center1] - geom_num_list[self.center0]
+        center_norm = torch.linalg.norm(center_vector)
+        LJ_pot_center = (
+            geom_num_list[self.center1]
+            + (self.config["repulsive_potential_v2_length"] / self.bohr2angstroms) * (center_vector / center_norm))
+
+        UFF_VDW_well_depth = torch.sqrt(
+            self.config["repulsive_potential_v2_well_scale"] * self.VDW_well_depth_center * self.VDW_well_depth_target)
+        UFF_VDW_distance = torch.sqrt(
+            self.config["repulsive_potential_v2_dist_scale"] * self.VDW_distance_center * self.VDW_distance_target)
+
+        vectors = geom_num_list[self.target_indices] - LJ_pot_center
+        distances = torch.linalg.norm(vectors, dim=1)
+
+        rep_term = (
+            abs(self.config["repulsive_potential_v2_const_rep"])
+            * (UFF_VDW_distance / distances) ** self.config["repulsive_potential_v2_order_rep"])
+        attr_term = (
+            -1
+            * abs(self.config["repulsive_potential_v2_const_attr"])
+            * (UFF_VDW_distance / distances) ** self.config["repulsive_potential_v2_order_attr"])
+
+        tot_energy = UFF_VDW_well_depth * (rep_term + attr_term)
+        energy = torch.sum(tot_energy)
+        return energy
+    
+class LJRepulsivePotentialv2Value:
+    def __init__(self, mm_pot_type="UFF", **kwarg):
+        if mm_pot_type == "UFF":
+            self.VDW_distance_lib = UFF_VDW_distance_lib  # function
+            self.VDW_well_depth_lib = UFF_VDW_well_depth_lib  # function
+        else:
+            raise ValueError("No MM potential type")
+        self.config = kwarg
+
+        UVL = UnitValueLib()
+        self.hartree2kcalmol = UVL.hartree2kcalmol
+        self.bohr2angstroms = UVL.bohr2angstroms
+        self.hartree2kjmol = UVL.hartree2kjmol
+        
+        self.center1 = self.config["repulsive_potential_v2_center"][1] - 1
+        self.center0 = self.config["repulsive_potential_v2_center"][0] - 1
+        self.target_indices = torch.tensor(self.config["repulsive_potential_v2_target"]) - 1
+        
+        target_elements = [self.config["element_list"][idx] for idx in self.target_indices]
+        self.VDW_well_depth_target = torch.tensor([
+            math.sqrt(self.config["repulsive_potential_v2_well_value"] / self.hartree2kjmol
+                      * self.VDW_well_depth_lib(element))
+            for element in target_elements
+        ])
+        self.VDW_distance_target = torch.tensor([
+            math.sqrt(self.config["repulsive_potential_v2_dist_value"] / self.bohr2angstroms
+                      * self.VDW_distance_lib(element))
+            for element in target_elements
+        ])
+
+        
+    def calc_energy(self, geom_num_list, bias_pot_params=[]):
+        """
+        # required variables: self.config["repulsive_potential_v2_well_value"], 
+                             self.config["repulsive_potential_v2_dist_value"], 
+                             self.config["repulsive_potential_v2_length"],
+                             self.config["repulsive_potential_v2_const_rep"],
+                             self.config["repulsive_potential_v2_const_attr"], 
+                             self.config["repulsive_potential_v2_order_rep"], 
+                             self.config["repulsive_potential_v2_order_attr"],
+                             self.config["repulsive_potential_v2_center"],
+                             self.config["repulsive_potential_v2_target"],
+                             self.config["element_list"]
+        """
+        energy = 0.0
+        center_vector = geom_num_list[self.center1] - geom_num_list[self.center0]
+        center_norm = torch.linalg.norm(center_vector)
+        LJ_pot_center = (
+            geom_num_list[self.center1]
+            + (self.config["repulsive_potential_v2_length"] / self.bohr2angstroms)
+            * (center_vector / center_norm))
+
+        vectors = geom_num_list[self.target_indices] - LJ_pot_center
+        distances = torch.linalg.norm(vectors, dim=1)
+
+        rep_term = (
+            abs(self.config["repulsive_potential_v2_const_rep"])
+            * (self.VDW_distance_target / distances) ** self.config["repulsive_potential_v2_order_rep"])
+        attr_term = (
+            -1
+            * abs(self.config["repulsive_potential_v2_const_attr"])
+            * (self.VDW_distance_target / distances) ** self.config["repulsive_potential_v2_order_attr"])
+
+        energy = torch.sum(self.VDW_well_depth_target * (rep_term + attr_term))
+        return energy
+    
+class LJRepulsivePotentialGaussian:
+    def __init__(self, mm_pot_type="UFF", **kwarg):
+        if mm_pot_type == "UFF":
+            self.VDW_distance_lib = UFF_VDW_distance_lib #function
+            self.VDW_well_depth_lib = UFF_VDW_well_depth_lib #function
+        else:
+            raise "No MM potential type"
+        self.config = kwarg
+        
+        UVL = UnitValueLib()
+        self.hartree2kcalmol = UVL.hartree2kcalmol 
+        self.bohr2angstroms = UVL.bohr2angstroms 
+        self.hartree2kjmol = UVL.hartree2kjmol 
+        
+        return
+    #calc_energy_gau
+    def calc_energy(self, geom_num_list, bias_pot_params=[]):
+
+        """
+        # required variables: self.config["repulsive_potential_gaussian_LJ_well_depth"], 
+                             self.config["repulsive_potential_gaussian_LJ_dist"], 
+                             self.config["repulsive_potential_gaussian_gau_well_depth"],
+                             self.config["repulsive_potential_gaussian_gau_dist"]
+                             self.config["repulsive_potential_gaussian_gau_range"], 
+                             self.config["repulsive_potential_gaussian_fragm_1"], 
+                             self.config["repulsive_potential_gaussian_fragm_2"],
+                             self.config["element_list"]
+        """
+        energy = 0.0
+        gau_range_const = 0.03
+        for i, j in itertools.product(self.config["repulsive_potential_gaussian_fragm_1"], self.config["repulsive_potential_gaussian_fragm_2"]):
+            LJ_well_depth = self.config["repulsive_potential_gaussian_LJ_well_depth"]/self.hartree2kjmol
+            LJ_distance = self.config["repulsive_potential_gaussian_LJ_dist"]/self.bohr2angstroms
+            Gau_well_depth = self.config["repulsive_potential_gaussian_gau_well_depth"]/self.hartree2kjmol
+            Gau_distance = self.config["repulsive_potential_gaussian_gau_dist"]/self.bohr2angstroms
+            Gau_range = self.config["repulsive_potential_gaussian_gau_range"]/self.bohr2angstroms
+            vector = torch.linalg.norm(geom_num_list[i-1] - geom_num_list[j-1], ord=2) #bohr
+            energy += LJ_well_depth * ( -2 * ( LJ_distance / vector ) ** 6 + ( LJ_distance / vector ) ** 12) -1 * Gau_well_depth * torch.exp(-1 * (vector - Gau_distance) ** 2 / (gau_range_const * (Gau_range) ** 2))
+       
+        return energy
+
+class LJRepulsivePotentialCone:
+    def __init__(self, mm_pot_type="UFF", **kwarg):
+        if mm_pot_type == "UFF":
+            self.VDW_distance_lib = UFF_VDW_distance_lib #function
+            self.VDW_well_depth_lib = UFF_VDW_well_depth_lib #function
+        else:
+            raise "No MM potential type"
+        self.config = kwarg
+        
+        UVL = UnitValueLib()
+        self.hartree2kcalmol = UVL.hartree2kcalmol 
+        self.bohr2angstroms = UVL.bohr2angstroms 
+        self.hartree2kjmol = UVL.hartree2kjmol 
+        
+        return
+    def calc_energy(self, geom_num_list, bias_pot_params=[]):
+
+        a_value = 1.0
+        """
+        # ref.  ACS Catal. 2022, 12, 7, 3752–3766
+        # required variables: self.config["cone_potential_well_value"], 
+                             self.config["cone_potential_dist_value"], 
+                             self.config["cone_potential_cone_angle"],
+                             self.config["cone_potential_center"], 
+                             self.config["cone_potential_three_atoms"]
+                             self.config["cone_potential_target"]   
+                             self.config["element_list"]
+        """
+        apex_vector = geom_num_list[self.config["cone_potential_center"]-1] - (2.28/self.bohr2angstroms) * ((geom_num_list[self.config["cone_potential_three_atoms"][0]-1] + geom_num_list[self.config["cone_potential_three_atoms"][1]-1] + geom_num_list[self.config["cone_potential_three_atoms"][2]-1] -3.0 * geom_num_list[self.config["cone_potential_center"]-1]) / torch.linalg.norm(geom_num_list[self.config["cone_potential_three_atoms"][0]-1] + geom_num_list[self.config["cone_potential_three_atoms"][1]-1] + geom_num_list[self.config["cone_potential_three_atoms"][2]-1] -3.0 * geom_num_list[self.config["cone_potential_center"]-1]))
+        cone_angle = torch.deg2rad(torch.tensor(self.config["cone_potential_cone_angle"], dtype=torch.float32))
+        energy = 0.0
+        for i in self.config["cone_potential_target"]:
+            UFF_VDW_well_depth = math.sqrt(self.config["cone_potential_well_value"]/self.hartree2kjmol * self.VDW_well_depth_lib(self.config["element_list"][i-1]))
+            UFF_VDW_distance = math.sqrt(self.config["cone_potential_dist_value"]/self.bohr2angstroms * self.VDW_distance_lib(self.config["element_list"][i-1]))
+            s_a_length = (geom_num_list[i-1] - apex_vector).view(1,3)
+            c_a_length = (geom_num_list[self.config["cone_potential_center"]-1] - apex_vector).view(1,3)
+            sub_angle = torch.arccos((torch.matmul(c_a_length, s_a_length.T)) / (torch.linalg.norm(c_a_length) * torch.linalg.norm(s_a_length)))#rad
+            dist = torch.linalg.norm(s_a_length)
+            
+            if sub_angle - cone_angle / 2 <= torch.pi / 2:
+                length = (dist * torch.sin(sub_angle - cone_angle / 2)).view(1,1)
+            
+            else:
+                length = dist.view(1,1)
+            
+            energy += 4 * UFF_VDW_well_depth * ((UFF_VDW_distance / (length + a_value * UFF_VDW_distance)) ** 12 - (UFF_VDW_distance / (length + a_value * UFF_VDW_distance)) ** 6)
+            
+        
+        return energy