phydat added to automol

automol/zmatrix/_bimol_ts.py

@@ -273,7 +273,7 @@ def substitution(rct_zmas, prd_zmas):
     return ret
 
 
-def addition(rct_zmas, prd_zmas):
+def addition(rct_zmas, prd_zmas, rct_tors=()):
     """ z-matrix for an addition reaction
     """
     ret = None

phydat/__init__.py

@@ -0,0 +1,19 @@
+""" Libraries of physical data used by the drivers
+"""
+
+from phydat import phycon
+from phydat import eleclvl
+from phydat import sigmarad
+from phydat import symm
+from phydat import instab_fgrps
+from phydat import etrans
+
+
+__all__ = [
+    'phycon',
+    'eleclvl',
+    'sigmarad',
+    'symm',
+    'instab_fgrps',
+    'etrans'
+]

phydat/act_space.py

@@ -0,0 +1,18 @@
+""" Storing a dictionary of active space sizes for various species
+    DCT[(inchi, multiplicity)]
+        = (num_active_orbs, num_active_elecs, num_states)
+"""
+
+
+DCT = {
+    # Atoms
+    ('InChI=1S/O', 3): (3, 4, 3),
+    ('InChI=1S/O', 1): (3, 4, 5),
+    ('InChI=1S/N', 3): (3, 3, 1),
+    # Diatomics
+    ('InChI=1S/O2/c1-2', 3): (4, 6, 1),
+    ('InChI=1S/HO/h1H', 2): (2, 3, 2),
+    # Molecules
+    ('InChI=1S/CH2/h1H2', 3): (2, 2, 1),
+    ('InChI=1S/CH2/h1H2', 1): (2, 2, 1)
+}

phydat/bnd.py

@@ -0,0 +1,33 @@
+""" Dictionary of standard bond lengths
+"""
+
+from phydat.phycon import ANG2BOHR
+
+
+def read_len(bnd_atoms):
+    """ Read the dct
+    """
+    bnd_len = LEN_DCT.get(bnd_atoms, None)
+    if bnd_len is None:
+        bnd_atoms_flip = (bnd_atoms[1], bnd_atoms[0])
+        bnd_len = LEN_DCT.get(bnd_atoms_flip, None)
+
+    return bnd_len
+
+
+# Dictionary of A-B single bond lengths
+LEN_DCT = {
+    ('H', 'H'): 0.74 * ANG2BOHR,
+    ('H', 'C'): 1.09 * ANG2BOHR,
+    ('H', 'N'): 1.01 * ANG2BOHR,
+    ('H', 'O'): 0.95 * ANG2BOHR,
+    ('H', 'Cl'): 1.275 * ANG2BOHR,
+    ('C', 'C'): 1.54 * ANG2BOHR,
+    ('C', 'N'): 1.47 * ANG2BOHR,
+    ('C', 'O'): 1.43 * ANG2BOHR,
+    ('N', 'N'): 1.45 * ANG2BOHR,
+    ('N', 'O'): 1.45 * ANG2BOHR,
+    ('O', 'O'): 1.40 * ANG2BOHR,
+    ('C', 'Cl'): 1.74 * ANG2BOHR,
+    ('Cl', 'Cl'): 2.0 * ANG2BOHR,
+}

phydat/eleclvl.py

@@ -0,0 +1,19 @@
+"""
+Library of electronic levels for several common, small species.
+Dictionary formatted as:
+    DCT[(InChI_Key, Multiplicity)] = [[energy(cm-1), degeneracy], ...]
+"""
+
+DCT = {
+    ('InChI=1S/B', 2): [[0., 2], [16., 4]],
+    ('InChI=1S/C', 3): [[0., 1], [16.4, 3], [43.5, 5]],
+    ('InChI=1S/N', 2): [[0., 6], [8., 4]],
+    ('InChI=1S/O', 3): [[0., 5], [158.5, 3], [226.5, 1]],
+    ('InChI=1S/F', 2): [[0., 4], [404.1, 2]],
+    ('InChI=1S/Cl', 2): [[0., 4], [883.4, 2]],
+    ('InChI=1S/Br', 2): [[0., 4], [685.2, 2]],
+    ('InChI=1S/HO/h1H', 2): [[0., 2], [138.9, 2]],
+    ('InChI=1S/NO/c1-2', 2): [[0., 2], [123.1, 2]],
+    ('InChI=1S/O2/c1-2', 1): [[0., 2]],
+    ('InChI=1S/CH3O/c1-2/h1H3', 2): [[0., 3], [69.1, 1]]
+}

phydat/etrans.py

@@ -0,0 +1,167 @@
+"""
+  Values to calculate effective parameters for energy transport
+"""
+
+
+def read_lj_dct(bath, target):
+    """ Read the LJ_DCT
+    """
+
+    bath_dct = LJ_DCT.get(bath, None)
+    if bath_dct is not None:
+        lj_params = bath_dct.get(target, None)
+    else:
+        lj_params = None
+
+    return lj_params
+
+
+def read_z_alpha_dct(bath, target):
+    """ Read the LJ_DCT
+    """
+
+    target_dct = Z_ALPHA_DCT.get(bath, None)
+    if target_dct is not None:
+        z_alpha_params = target_dct.get(target, None)
+    else:
+        z_alpha_params = None
+
+    return z_alpha_params
+
+
+LJ_DCT = {
+
+    # N2 Bath Gas
+    'InChI=1S/N2/c1-2': {
+        'n-alkane': (3.68, 0.16, 100.0, 0.25),
+        '1-alkyl': (3.72, 0.15, 69.00, 0.39),
+    },
+
+    # He Bath Gas
+    'InChI=1S/He': {
+        'n-alkane': (3.33, 0.17, 21.3, 0.31),
+        'n-alcohol': (2.90, 0.21, 22.0, 0.28),
+        'n-hydroperoxide': (2.90, 0.21, 10.0, 0.75),
+        '1-alkyl': (3.20, 0.18, 20.00, 0.42),
+    },
+
+    # Ar Bath Gas
+    'InChI=1S/Ar': {
+        'n-alkane': (3.40, 0.18, 113.0, 0.31),
+        'n-alcohol': (3.05, 0.20, 150.0, 0.29),
+        'n-peroxide': (2.90, 0.25, 85.0, 0.32),
+        'epoxide': (2.90, 0.23, 75.0, 0.50),
+        'n-hydroperoxide': (3.05, 0.20, 110.0, 0.39),
+        '1-alkyl': (3.50, 0.17, 90.0, 0.38),
+        'ether': (3.15, 0.22, 110.0, 0.15) 
+    },
+
+    # H2 Bath Gas
+    'InChI=1S/H2/h1H': {
+        'n-alkane': (3.15, 0.18, 75.0, 0.30)
+    },
+}
+
+Z_ALPHA_DCT = {
+
+    # N2 Bath Gas
+    'InChI=1S/N2/c1-2': {
+        'n-alkane': {
+            300: (0.019689, -2.109835, 49.893116, 7.130308),
+            1000: (0.323108, -11.8867, 140.285802, 56.212929),
+            2000: (0.527413, -20.87865, 236.980272, 213.765542)
+        },
+        '1-alkyl': {
+            300: (0.1123, -3.9325, 44.4515, 7.3137),
+            1000: (0.2740, -9.7140, 99.5144, 93.4755),
+            2000: (0.5837, -19.3363, 181.9322, 250.0161)
+        }
+    },
+
+    # He Bath Gas
+    'InChI=1S/He': {
+        'n-alkane': {
+            300: (0.071882, -3.16556, 51.303812, 9.570797),
+            1000: (0.305537, -10.232371, 113.6291, 180.205289),
+            2000: (0.414858, -15.030357, 394911, 158, 534.047802)
+        },
+        'n-alcohol': {
+            300: (0.07044, -3.28388, 50.87526, -1.05945),
+            1000: (0.3905, -12.61792, 129.09928, 122.81934),
+            2000: (0.12611, -6.70779, 83.35158, 649.16698)
+        },
+        'n-hydroperoxide': {
+            300: (0.06934, -2.16846, 28.09786, 57.99002),
+            1000: (-0.01873, 0.9463, -9.19049, 421.53109),
+            2000: (-0.33498, 7.81371, -60.10907, 848.6624)
+        },
+        '1-alkyl': {
+            300: (0.1113, -3.6213, 36.8624, 36.1446),
+            1000: (0.1766, -5.2337, 43.6089, 261.9713),
+            2000: (0.2416, -6.7709, 47.0932, 590.3983)
+        }
+    },
+
+    # Ar Bath Gas
+    'InChI=1S/Ar': {
+        'n-alkane': {
+            300: (0.054986, -2.948084, 52.534594, -2.984767),
+            1000: (0.273835, -10.208643, 125.075803, 31.934663),
+            2000: (0.457981, -19.131921, 228.021958, 110.533659)
+        },
+        'n-alcohol': {
+            300: (0.1634, -6.39251, 83.21585, -64.1994),
+            1000: (0.22482, -9.06605, 114.55153, 63.80238),
+            2000: (0.45001, -18.13079, 206.53042, 163.72987)
+        },
+        'n-peroxide': {
+            300: (0.084, -2.9394, 31.0133, 38.0167),
+            1000: (-0.011, -0.6012, 11.7443, 280.8983),
+            2000: (-0.0117, -2.0414, 34.5284, 518.2758)
+        },
+        'n-hydroperoxide': {
+            300: (0.04706, -2.28117, 35.3249, 31.83379),
+            1000: (0.09842, -3.83485, 49.11378, 192.03656),
+            2000: (0.19506, -6.74549, 69.65477, 469.06881)
+        },
+        '1-alkyl': {
+            300: (0.0873, -3.3639, 39.6649, 8.5801),
+            1000: (0.3216, -10.2583, 98.7330, 62.6353),
+            2000: (0.4581, -16.4145, 167.6469, 178.9579)
+        },
+        'ether': {
+            300: (0.1057, -4.1378, 52.8870, 1.5181),
+            1000: (0.0116, -2.2454, 40.9493, 251.0031),
+            2000: (-0.1170, -0.4961, 40.0212, 580.5769)
+        },
+        'epoxide': {
+            300: (0.5025, -18.4928, 200.3532, -246.9419),
+            1000: (0.7488, -25.8914, 247.3055, 25.3337),
+            2000: (0.896, -30.0515, 262.9319, 412.6931)
+        },
+    },
+
+    # H2 Bath Gas
+    'InChI=1S/H2/h1H': {
+        'n-alkane': {
+            300: (0.185, -7.2964, 102.6128, 46.6884),
+            1000: (0.6173, -19.5856, 194.2888, 295.3819),
+            3000: (0.3867, 14.6607, 153.5746, 922.4951)
+        }
+    }
+}
+
+# Bond dissociation energies (kcal/mol)
+D0_DCT = {
+    'm-peroxide': 35.0,
+    'ro2_qooh': 35.0,
+    'qooh': 35.0,
+    'ketohydroperoxide': (35.0, 51.0),
+    '1-alkyl': 40.0,
+    'n-hydroperoxide': 45.0,
+    'epoxide': 60.0,
+    'm-ether': 82.0,
+    'n-alcohol': 90.0,
+    'n-alkane': 95.0,
+    'n-alkene': 95.0,
+}

phydat/instab_fgrps.py

@@ -0,0 +1,12 @@
+"""
+List of funcitonal groups attached to radical atoms that cause instabilities
+
+atm_symb: ( (instab_grp1, instab_grp2, ...),
+            (instab_prd1, instab_prd2, instab_prd3) )
+
+"""
+
+DCT = {
+    'C': (('InChI=1S/HO2/c1-2/h1H',),
+          ('InChI=1S/HO/h1H',))
+}

phydat/phycon.py

@@ -0,0 +1,33 @@
+"""
+Library of physical constants
+"""
+
+from qcelemental import constants as qcc
+
+
+# physical constants
+NAVO = 6.0221409e+23
+RC = 1.98720425864083  # gas constant in cal/(mol.K)
+RC_kcal = 1.98720425864083e-3  # gas constant in kcal/(mol.K)
+RC2 = 82.0573660809596  # gas constant in cm^3.atm/(mol.K)
+RC_cal = 1.98720425864083  # gas constant in cal/(mol.K)
+RC_atm = 82.0573660809596  # gas constant in cm^3.atm/(mol.K)
+
+# conversion factors
+KCAL2CAL = qcc.conversion_factor('kcal/mol', 'cal/mol')
+J2CAL = qcc.conversion_factor('J/mol', 'cal/mol')
+KJ2CAL = qcc.conversion_factor('kJ/mol', 'cal/mol')
+KEL2CAL = qcc.conversion_factor('kelvin', 'cal/mol')
+ANG2BOHR = qcc.conversion_factor('angstrom', 'bohr')
+BOHR2ANG = qcc.conversion_factor('bohr', 'angstrom')
+DEG2RAD = qcc.conversion_factor('degree', 'radian')
+RAD2DEG = qcc.conversion_factor('radian', 'degree')
+WAVEN2KCAL = qcc.conversion_factor('wavenumber', 'kcal/mol')
+KCAL2WAVEN = qcc.conversion_factor('kcal/mol', 'wavenumber')
+EH2KCAL = qcc.conversion_factor('hartree', 'kcal/mol')
+KCAL2EH = qcc.conversion_factor('kcal/mol', 'hartree')
+KCAL2KJ = qcc.conversion_factor('kcal/mol', 'kJ/mol')
+WAVEN2EH = qcc.conversion_factor('wavenumber', 'hartree')
+EH2WAVEN = qcc.conversion_factor('hartree', 'wavenumber')
+# AMU2KG = qcc.conversion_factor('atomic mass unit', 'kilogram')
+AMU2KG = 1.66053892173e-27

phydat/sigmarad.py

@@ -0,0 +1,7 @@
+""" Library of sigma radicals
+"""
+
+LST = [
+    'InChI=1S/CN/c1-2',
+    'InChI=1S/C2H/c1-2/h1H'
+]

phydat/symm.py

@@ -0,0 +1,13 @@
+""" Library of symmetries
+"""
+
+# Dict to store symmetry factors (change name)
+DCT = {
+    ('InChI=1S/HO/h1H', 2): 1.0
+}
+
+# Dictionary of high symmetry species w/ displacments to break sym
+# displacements are for the bonds and are in angstrom
+HIGH = {
+    'InChI=1S/CH4/h1H4': 0.0005
+}

setup.py

@@ -18,9 +18,11 @@
                 'autoread',
                 'autoread.zmatrix',
                 'autowrite',
+                'phydat',
                 'transformations'],
       package_dir={'automol': 'automol',
                    'autoread': 'autoread',
                    'autowrite': 'autowrite',
+                   'phydat': 'phydat',
                    'transformations': 'transformations'},
       package_data={'automol': ['tests/data/*.txt']})