============================================= Variable Ionic Masses ============================================= :Author: Harry Brough, University of Manchester Introduction =================================== ONETEP [Skylaris2005]_ assigns every ionic species a default mass, taken from an internal table and determined by the element. The ``species_mass`` block, introduced in v8.2, overrides these defaults on a per-species basis, allowing isotopic substitution without altering the electronic structure of the calculation. This is of use for: * **Molecular dynamics** — isotope effects on diffusion and rates of barrier crossing. * **Vibrational and phonon calculations** — isotopic shifts of harmonic frequencies, zero-point energies, thermochemical corrections, and hence kinetic isotope effects. Because the Born-Oppenheimer potential energy surface does not depend on the ionic masses, no aspect of the electronic structure calculation is changed: total energies, forces, NGWFs, the density kernel and the locations of stationary points are all identical to those obtained with the default masses. Only mass-dependent nuclear properties are affected. Keywords =================================== The atomic masses can be specified with the ``species_mass`` block keyword, as shown: :: %block species_mass H 2.014102 C 13.00335 O 17.99916 %endblock species_mass This requests a calculation with deuterium instead of protium, and with :sup:`13`\ C and :sup:`18`\ O nuclei. The first entry on each line is the species label, exactly as it appears in the first column of the ``species`` block. Not every atomic species needs to be listed in ``species_mass``; any species omitted retains its default mass. By default, the mass units are atomic mass units (amu) — this can be changed in the same way as other block keywords. Other possible units are grams (g) and kilograms (kg). Selective Isotopic Substitution ============================================= Because ``species_mass`` acts on species labels rather than on elements, distinct labels must be introduced in the ``species`` block in order to substitute only some atoms of a given element. To deuterate a single hydroxyl hydrogen, for instance: :: %block species H H 1 1 8.0 H_D H 1 1 8.0 O O 8 4 8.0 %endblock species %block species_mass H_D 2.014102 %endblock species_mass Both hydrogen labels share the same element, atomic number and pseudopotential, and only the mass differs. Atoms are then assigned to one label or the other in the ``positions_abs`` block. Default Masses =================================== The ionic masses that ONETEP uses by default are tabulated here, which are generally natural abundance standard atomic weights. === === ========== === === ========== === === ========== Z El. Mass / amu Z El. Mass / amu Z El. Mass / amu === === ========== === === ========== === === ========== 1 H 1.00794 38 Sr 87.62 75 Re 186.207 2 He 4.00260 39 Y 88.90585 76 Os 190.23 3 Li 6.941 40 Zr 91.224 77 Ir 192.217 4 Be 9.012187 41 Nb 92.90638 78 Pt 195.078 5 B 10.811 42 Mo 95.94 79 Au 196.96655 6 C 12.0107 43 Tc 98.0 80 Hg 200.59 7 N 14.00674 44 Ru 101.07 81 Tl 204.3833 8 O 15.9994 45 Rh 102.90550 82 Pb 207.2 9 F 18.99840 46 Pd 106.42 83 Bi 208.98038 10 Ne 20.1797 47 Ag 107.8682 84 Po 209.0 11 Na 22.98977 48 Cd 112.411 85 At 210.0 12 Mg 24.3050 49 In 114.818 86 Rn 222.0 13 Al 26.98154 50 Sn 118.710 87 Fr 223.0 14 Si 28.0855 51 Sb 121.760 88 Ra 226.0 15 P 30.97376 52 Te 127.60 89 Ac 227.0 16 S 32.066 53 I 126.90447 90 Th 232.0381 17 Cl 35.4527 54 Xe 131.29 91 Pa 231.03588 18 Ar 39.948 55 Cs 132.90545 92 U 238.0289 19 K 39.0983 56 Ba 137.327 93 Np 237.0 20 Ca 40.078 57 La 138.9055 94 Pu 244.0 21 Sc 44.95591 58 Ce 140.116 95 Am 243.0 22 Ti 47.867 59 Pr 140.90765 96 Cm 247.0 23 V 50.9415 60 Nd 144.24 97 Bk 247.0 24 Cr 51.9961 61 Pm 145.0 98 Cf 251.0 25 Mn 54.93805 62 Sm 150.36 99 Es 252.0 26 Fe 55.845 63 Eu 151.964 100 Fm 257.0 27 Co 58.93320 64 Gd 157.25 101 Md 258.0 28 Ni 58.6934 65 Tb 158.92534 102 No 259.0 29 Cu 63.546 66 Dy 162.50 103 Lr 262.0 30 Zn 65.39 67 Ho 164.93032 104 Rf 261.0 31 Ga 69.723 68 Er 167.26 105 Db 262.0 32 Ge 72.61 69 Tm 168.93421 106 Sg 263.0 33 As 74.92160 70 Yb 173.04 107 Bh 264.0 34 Se 78.96 71 Lu 174.967 108 Hs 265.0 35 Br 79.904 72 Hf 178.49 109 Mt 268.0 36 Kr 83.80 73 Ta 180.9479 37 Rb 85.4678 74 W 183.84 === === ========== === === ========== === === ========== References =================================== .. [Skylaris2005] C.-K. Skylaris et al., J. Chem. Phys. **122**, 084119 (2005).