[Sat Apr 29 14:33:00 CST 2023] [MD] [warn] 'Starting MedeA Core 3.6.0' MedeA version 3.6.0 #------------------------------------------------------------------------------- # This calculation has 1 stage #------------------------------------------------------------------------------- Stage 1: VASP 6 #------------------------------------------------------------------------------- # Running the calculation #------------------------------------------------------------------------------- Stage 1: VASP 6 Sucessfully opened MedeA database from /home/medea/MD/Databases/MedeA.db VASP 6 CALCULATION PROTOCOL: ============================ 1. Geometry optimization (atom positions) VASP parameters =============== This is a calculation based on density functional theory and the GGA-PBE exchange-correlation functional for describing the interactions. Van der Waals interactions are added by means of a forcefield (DFT+D2 approach of S. Grimme). Since no magnetic moments are in the model, this is a non-magnetic calculation using 'accurate' precision and a user-defined planewave cutoff energy of 750.000 eV. The electronic iterations convergence is 1.00E-05 eV using the Normal (blocked Davidson) algorithm and real space projection operators. The requested k-spacing is 0.4 per Angstrom, which leads to a 3x2x1 mesh. This corresponds to actual k-spacings of 0.290 x 0.317 x 0.242 per Angstrom. The k-mesh is forced to be centered on the gamma point. Using Gaussian smearing with a width of 0.05 eV. Other non-default parameters: Number of steps is 800 ========================================== Using version 4.0 GGA-PBE / PAW potentials: Mg PAW_PBE Mg 13Apr2007 S PAW_PBE S 06Sep2000 O PAW_PBE O 08Apr2002 H PAW_PBE H 15Jun2001 There are 4 symmetry-unique k-points The plane wave cutoff is 750.00 eV VASP energy: -504.789431 eV for Mg4S4O40H48 cell Non-dispersive: -499.476851 eV Van der Waals: -5.312580 eV Initial VASP energy: -500.591910 eV for Mg4S4O40H48 cell Relaxation energy: -4.197521 eV gained after 396 optimization steps. Electronic contributions: Empirical Formula Cell MgSO10H12 (MgSO10H12)4 ----------------- ----------------- VASP Energy -126.197358 -504.789431 eV = -12176.191 -48704.764 kJ/mol Cell parameters: Parameter Value ---------- ------------ a 7.210470 b 9.900590 c 26.000000 alpha 90.000000 beta 90.000000 gamma 90.000000 Volume 1856.085587 Ang^3 Density: 0.818 Mg/m^3 The pressure given below is exerted by the system according to its volume. Positive pressure would cause expansion during full geometry optimization. Pressure: 21.000 MPa = 210.000 bar XX YY ZZ YZ XZ XY Stress: -272.500 -59.569 267.949 -13.674 75.105 -51.239 MPa = -2.725 -0.596 2.679 -0.137 0.751 -0.512 kbar The stress tensor above is imposed on the system, i.e. negative values of diagonal components would cause expansion of the corresponding lattice parameter upon full geometry optimization. The pressure and stress include only electronic terms, i.e. the vibrational, temperature and other terms are not included here. Fractional Coordinates: Atom Initial Coordinates Final Coordinates ----- -------- -------- -------- -------- -------- -------- Mg1 0.0000 0.0000 0.5883 -0.0269 -0.0132 0.5819 Mg2 0.5000 0.5000 0.5883 0.4731 0.4868 0.5819 Mg3 0.9387 0.9000 0.8182 0.9606 0.9231 0.8163 Mg4 0.4387 0.4000 0.8182 0.4606 0.4231 0.8163 S1 0.4465 0.8209 0.7016 0.4482 0.8275 0.7312 S2 0.5535 0.1791 0.4750 0.5339 0.1533 0.4856 S3 0.9465 0.3209 0.7016 0.9482 0.3275 0.7312 S4 0.0535 0.6791 0.4750 0.0339 0.6533 0.4856 O1 0.0943 0.2189 0.7131 0.1205 0.2476 0.7227 O2 0.9057 0.7811 0.4635 0.8822 0.7485 0.4735 O3 0.5943 0.7189 0.7131 0.6205 0.7476 0.7227 O4 0.4057 0.2811 0.4635 0.3822 0.2485 0.4735 O6 0.4410 0.9239 0.7427 0.4593 0.8824 0.7879 O7 0.5590 0.0761 0.4338 0.5449 0.0368 0.4524 O9 0.9410 0.4239 0.7427 0.9593 0.3824 0.7879 O10 0.0590 0.5761 0.4338 0.0449 0.5368 0.4524 O11 0.4905 0.8861 0.6508 0.4309 0.9437 0.6979 O12 0.5095 0.1139 0.5257 0.4999 0.1003 0.5420 O13 0.9905 0.3861 0.6508 0.9309 0.4437 0.6979 O14 0.0095 0.6139 0.5257 -0.0001 0.6003 0.5420 O15 0.2629 0.7520 0.6970 0.2865 0.7353 0.7289 O16 0.7371 0.2480 0.4795 0.7148 0.2304 0.4886 O17 0.7629 0.2520 0.6970 0.7865 0.2353 0.7289 O18 0.2371 0.7480 0.4795 0.2148 0.7304 0.4886 O19 0.2203 0.0715 0.6304 0.1601 0.0633 0.6367 O20 0.7797 0.9285 0.5462 0.7548 0.8876 0.5467 O21 0.7203 0.5715 0.6304 0.6601 0.5633 0.6367 O22 0.2797 0.4285 0.5462 0.2548 0.3876 0.5467 H1 0.1885 0.1238 0.6613 0.1305 0.1361 0.6604 H2 0.8115 0.8762 0.5152 0.8012 0.8339 0.5146 H3 0.6885 0.6238 0.6613 0.6305 0.6361 0.6604 H4 0.3115 0.3762 0.5152 0.3012 0.3339 0.5146 H5 0.3238 0.0098 0.6389 0.2593 0.0110 0.6528 H6 0.6762 0.9902 0.5376 0.6601 0.9539 0.5353 H7 0.8238 0.5098 0.6389 0.7593 0.5110 0.6528 H8 0.1762 0.4902 0.5376 0.1601 0.4539 0.5353 O23 0.3295 0.5053 0.6522 0.2596 0.5194 0.6401 O24 0.6705 0.4947 0.5243 0.6800 0.4674 0.5327 O25 0.8295 0.0053 0.6522 0.7596 0.0194 0.6401 O26 0.1705 0.9947 0.5243 0.1800 0.9674 0.5327 H9 0.2103 0.4564 0.6491 0.1613 0.4619 0.6264 H10 0.7897 0.5436 0.5274 0.7990 0.5193 0.5345 H11 0.7103 0.9564 0.6491 0.6613 0.9619 0.6264 H12 0.2897 0.0436 0.5274 0.2990 0.0193 0.5345 H13 0.3031 0.5878 0.6720 0.2072 0.6111 0.6368 H14 0.6969 0.4122 0.5046 0.6949 0.3895 0.5085 H15 0.8031 0.0878 0.6720 0.7072 0.1111 0.6368 H16 0.1969 0.9122 0.5046 0.1949 0.8895 0.5085 O27 0.0556 0.8007 0.6074 0.0762 0.7809 0.6101 O28 0.9444 0.1993 0.5692 0.9309 0.1912 0.5638 O29 0.5556 0.3007 0.6074 0.5762 0.2809 0.6101 O30 0.4444 0.6993 0.5692 0.4309 0.6912 0.5638 H17 0.1372 0.7740 0.6359 0.2020 0.7943 0.5962 H18 0.8628 0.2260 0.5407 0.8481 0.2019 0.5311 H19 0.6372 0.2740 0.6359 0.7020 0.2943 0.5962 H20 0.3628 0.7260 0.5407 0.3481 0.7019 0.5311 H21 0.0369 0.7241 0.5840 0.0268 0.7111 0.5834 H22 0.9631 0.2759 0.5925 0.0463 0.2399 0.5559 H23 0.5369 0.2241 0.5840 0.5268 0.2111 0.5834 H24 0.4631 0.7759 0.5925 0.5463 0.7399 0.5559 O31 0.1468 0.0316 0.7898 0.1738 0.0589 0.7945 O32 0.1468 0.7684 0.8467 0.1708 0.7967 0.8462 O33 0.6468 0.5316 0.7898 0.6738 0.5589 0.7945 O34 0.6468 0.2684 0.8467 0.6708 0.2967 0.8462 H25 0.0980 0.0931 0.7628 0.1521 0.1189 0.7638 H26 0.0980 0.7069 0.8737 0.1656 0.7020 0.8335 H27 0.5980 0.5931 0.7628 0.6521 0.6189 0.7638 H28 0.5980 0.2069 0.8737 0.6656 0.2020 0.8335 H29 0.2579 0.9891 0.7737 0.2876 0.0055 0.7868 H30 0.2579 0.8109 0.8628 0.2877 0.8280 0.8294 H31 0.7579 0.4891 0.7737 0.7876 0.5055 0.7868 H32 0.7579 0.3109 0.8628 0.7877 0.3280 0.8294 O35 0.2459 0.5338 0.7894 0.2420 0.5560 0.7990 O36 0.2459 0.2662 0.8471 0.2535 0.2942 0.8455 O37 0.7459 0.0338 0.7894 0.7420 0.0560 0.7990 O38 0.7459 0.7662 0.8471 0.7535 0.7942 0.8455 H33 0.1348 0.5004 0.7711 0.1299 0.5009 0.7905 H34 0.1348 0.2996 0.8654 0.1356 0.3243 0.8293 H35 0.6348 0.0004 0.7711 0.6299 0.0009 0.7905 H36 0.6348 0.7996 0.8654 0.6356 0.8243 0.8293 H37 0.2135 0.6200 0.8060 0.2651 0.6163 0.7678 H38 0.2135 0.1800 0.8305 0.2542 0.1981 0.8348 H39 0.7135 0.1200 0.8060 0.7651 0.1163 0.7678 H40 0.7135 0.6800 0.8305 0.7542 0.6981 0.8348 O39 0.4414 0.5159 0.8838 0.4748 0.5166 0.8908 O40 0.4414 0.2841 0.7527 0.4562 0.3414 0.7460 O42 0.9414 0.0159 0.8838 0.9748 0.0166 0.8908 O43 0.9414 0.7841 0.7527 0.9562 0.8414 0.7460 H41 0.3283 0.5281 0.9045 0.3744 0.5757 0.9016 H42 0.3283 0.2719 0.7320 0.3422 0.3205 0.7266 H44 0.8283 0.0281 0.9045 0.8744 0.0757 0.9016 H45 0.8283 0.7719 0.7320 0.8422 0.8205 0.7266 H47 0.0515 0.0218 0.9062 -0.0093 -0.0503 0.9179 H48 0.0515 0.7782 0.7303 0.0655 0.8069 0.7273 H50 0.5515 0.5218 0.9062 0.4907 0.4497 0.9179 H51 0.5515 0.2782 0.7303 0.5655 0.3069 0.7273 Analytic Derivatives: Atom Derivatives fractional Derivatives Cartesian (eV/Ang) ----- -------- -------- -------- -------- -------- -------- Mg1 0.0002 0.0002 0.0001 0.0014 0.0016 0.0033 Mg2 0.0002 0.0002 0.0001 0.0014 0.0016 0.0033 Mg3 0.0009 0.0002 0.0003 0.0067 0.0018 0.0066 Mg4 0.0009 0.0002 0.0003 0.0067 0.0018 0.0066 S1 0.0003 -0.0008 -0.0006 0.0023 -0.0077 -0.0149 S2 -0.0001 -0.0000 0.0001 -0.0009 -0.0001 0.0025 S3 0.0003 -0.0008 -0.0006 0.0023 -0.0077 -0.0149 S4 -0.0001 -0.0000 0.0001 -0.0009 -0.0001 0.0025 O1 0.0012 -0.0005 -0.0000 0.0088 -0.0050 -0.0003 O2 -0.0006 -0.0005 0.0001 -0.0047 -0.0047 0.0026 O3 0.0012 -0.0005 -0.0000 0.0088 -0.0050 -0.0003 O4 -0.0006 -0.0005 0.0001 -0.0047 -0.0047 0.0026 O6 0.0008 0.0001 0.0001 0.0055 0.0013 0.0038 O7 0.0011 -0.0003 -0.0002 0.0079 -0.0029 -0.0051 O9 0.0008 0.0001 0.0001 0.0055 0.0013 0.0038 O10 0.0011 -0.0003 -0.0002 0.0079 -0.0029 -0.0051 O11 -0.0001 0.0014 -0.0000 -0.0007 0.0141 -0.0000 O12 -0.0009 -0.0002 0.0000 -0.0066 -0.0019 0.0010 O13 -0.0001 0.0014 -0.0000 -0.0007 0.0141 -0.0000 O14 -0.0009 -0.0002 0.0000 -0.0066 -0.0019 0.0010 O15 -0.0020 -0.0002 0.0001 -0.0141 -0.0023 0.0019 O16 0.0014 0.0001 -0.0001 0.0102 0.0005 -0.0033 O17 -0.0020 -0.0002 0.0001 -0.0141 -0.0023 0.0019 O18 0.0014 0.0001 -0.0001 0.0102 0.0005 -0.0033 O19 -0.0004 0.0005 0.0002 -0.0027 0.0053 0.0062 O20 -0.0001 0.0001 0.0005 -0.0008 0.0008 0.0134 O21 -0.0004 0.0005 0.0002 -0.0027 0.0053 0.0062 O22 -0.0001 0.0001 0.0005 -0.0008 0.0008 0.0134 H1 -0.0002 -0.0000 -0.0001 -0.0014 -0.0004 -0.0037 H2 0.0001 -0.0006 -0.0005 0.0007 -0.0057 -0.0137 H3 -0.0002 -0.0000 -0.0001 -0.0014 -0.0004 -0.0037 H4 0.0001 -0.0006 -0.0005 0.0007 -0.0057 -0.0137 H5 0.0007 -0.0006 0.0003 0.0048 -0.0058 0.0085 H6 0.0002 0.0000 -0.0002 0.0011 0.0001 -0.0040 H7 0.0007 -0.0006 0.0003 0.0048 -0.0058 0.0085 H8 0.0002 0.0000 -0.0002 0.0011 0.0001 -0.0040 O23 -0.0006 -0.0001 0.0001 -0.0047 -0.0012 0.0016 O24 0.0009 -0.0001 -0.0001 0.0065 -0.0013 -0.0033 O25 -0.0006 -0.0001 0.0001 -0.0047 -0.0012 0.0016 O26 0.0009 -0.0001 -0.0001 0.0065 -0.0013 -0.0033 H9 0.0002 -0.0000 -0.0000 0.0012 -0.0003 -0.0006 H10 -0.0003 0.0003 0.0002 -0.0020 0.0033 0.0048 H11 0.0002 -0.0000 -0.0000 0.0012 -0.0003 -0.0006 H12 -0.0003 0.0003 0.0002 -0.0020 0.0033 0.0048 H13 0.0011 -0.0015 0.0002 0.0076 -0.0151 0.0042 maximum gradient = 0.0174 H14 -0.0004 -0.0001 -0.0000 -0.0028 -0.0007 -0.0007 H15 0.0011 -0.0015 0.0002 0.0076 -0.0151 0.0042 H16 -0.0004 -0.0001 -0.0000 -0.0028 -0.0007 -0.0007 O27 -0.0002 0.0004 0.0004 -0.0012 0.0043 0.0095 O28 -0.0004 0.0003 -0.0003 -0.0028 0.0031 -0.0081 O29 -0.0002 0.0004 0.0004 -0.0012 0.0043 0.0095 O30 -0.0004 0.0003 -0.0003 -0.0028 0.0031 -0.0081 H17 -0.0002 0.0003 0.0001 -0.0016 0.0029 0.0035 H18 0.0007 -0.0001 0.0002 0.0052 -0.0011 0.0064 H19 -0.0002 0.0003 0.0001 -0.0016 0.0029 0.0035 H20 0.0007 -0.0001 0.0002 0.0052 -0.0011 0.0064 H21 0.0004 -0.0007 -0.0001 0.0028 -0.0065 -0.0025 H22 0.0000 -0.0001 0.0002 0.0000 -0.0007 0.0046 H23 0.0004 -0.0007 -0.0001 0.0028 -0.0065 -0.0025 H24 0.0000 -0.0001 0.0002 0.0000 -0.0007 0.0046 O31 -0.0004 0.0000 -0.0000 -0.0030 0.0001 -0.0006 O32 -0.0007 -0.0006 -0.0000 -0.0053 -0.0063 -0.0008 O33 -0.0004 0.0000 -0.0000 -0.0030 0.0001 -0.0006 O34 -0.0007 -0.0006 -0.0000 -0.0053 -0.0063 -0.0008 H25 -0.0000 0.0003 0.0000 -0.0000 0.0026 0.0006 H26 -0.0003 0.0002 -0.0000 -0.0024 0.0019 -0.0010 H27 -0.0000 0.0003 0.0000 -0.0000 0.0026 0.0006 H28 -0.0003 0.0002 -0.0000 -0.0024 0.0019 -0.0010 H29 0.0001 0.0001 0.0000 0.0008 0.0013 0.0012 H30 -0.0000 0.0008 0.0001 -0.0003 0.0082 0.0019 H31 0.0001 0.0001 0.0000 0.0008 0.0013 0.0012 H32 -0.0000 0.0008 0.0001 -0.0003 0.0082 0.0019 O35 0.0001 -0.0000 -0.0001 0.0006 -0.0001 -0.0031 O36 -0.0011 -0.0006 -0.0003 -0.0077 -0.0058 -0.0079 O37 0.0001 -0.0000 -0.0001 0.0006 -0.0001 -0.0031 O38 -0.0011 -0.0006 -0.0003 -0.0077 -0.0058 -0.0079 H33 -0.0007 0.0000 0.0001 -0.0049 0.0000 0.0017 H34 0.0003 -0.0000 0.0001 0.0022 -0.0001 0.0020 H35 -0.0007 0.0000 0.0001 -0.0049 0.0000 0.0017 H36 0.0003 -0.0000 0.0001 0.0022 -0.0001 0.0020 H37 0.0002 0.0006 -0.0004 0.0016 0.0056 -0.0093 H38 -0.0002 0.0009 -0.0001 -0.0013 0.0089 -0.0022 H39 0.0002 0.0006 -0.0004 0.0016 0.0056 -0.0093 H40 -0.0002 0.0009 -0.0001 -0.0013 0.0089 -0.0022 O39 -0.0002 -0.0004 0.0001 -0.0012 -0.0041 0.0024 O40 0.0002 0.0002 -0.0000 0.0015 0.0015 -0.0012 O42 -0.0002 -0.0004 0.0001 -0.0012 -0.0041 0.0024 O43 0.0002 0.0002 -0.0000 0.0015 0.0015 -0.0012 H41 0.0003 0.0011 -0.0003 0.0024 0.0110 -0.0084 H42 0.0011 -0.0001 0.0001 0.0080 -0.0008 0.0018 H44 0.0003 0.0011 -0.0003 0.0024 0.0110 -0.0084 H45 0.0011 -0.0001 0.0001 0.0080 -0.0008 0.0018 H47 -0.0013 0.0001 0.0000 -0.0094 0.0011 0.0009 H48 -0.0010 -0.0000 -0.0001 -0.0073 -0.0005 -0.0019 H50 -0.0013 0.0001 0.0000 -0.0094 0.0011 0.0009 H51 -0.0010 -0.0000 -0.0001 -0.0073 -0.0005 -0.0019 Atomic partial charges (electron charges): Atom s p d total ----- -------- -------- -------- -------- Mg1 0.267 0.392 0.246 0.905 Mg2 0.267 0.392 0.246 0.905 Mg3 0.268 0.402 0.255 0.925 Mg4 0.268 0.402 0.255 0.925 S1 1.055 1.907 0.809 3.770 S2 1.056 1.901 0.796 3.753 S3 1.055 1.907 0.809 3.770 S4 1.056 1.901 0.796 3.753 O1 1.268 2.903 0.016 4.187 O2 1.271 2.896 0.017 4.184 O3 1.268 2.903 0.016 4.187 O4 1.271 2.896 0.017 4.184 O6 1.262 2.886 0.011 4.159 O7 1.283 2.875 0.021 4.179 O9 1.262 2.886 0.011 4.159 O10 1.283 2.875 0.021 4.179 O11 1.279 2.894 0.020 4.192 O12 1.263 2.879 0.011 4.153 O13 1.279 2.894 0.020 4.192 O14 1.263 2.879 0.011 4.153 O15 1.269 2.908 0.017 4.193 O16 1.265 2.900 0.015 4.180 O17 1.269 2.908 0.017 4.193 O18 1.265 2.900 0.015 4.180 O19 1.236 2.985 0.013 4.234 O20 1.235 2.970 0.010 4.215 O21 1.236 2.985 0.013 4.234 O22 1.235 2.970 0.010 4.215 H1 0.155 0.006 0.000 0.162 H2 0.129 0.006 0.000 0.135 H3 0.155 0.006 0.000 0.162 H4 0.129 0.006 0.000 0.135 H5 0.153 0.006 0.000 0.159 H6 0.146 0.006 0.000 0.152 H7 0.153 0.006 0.000 0.159 H8 0.146 0.006 0.000 0.152 O23 1.242 2.962 0.014 4.219 O24 1.229 3.000 0.010 4.239 O25 1.242 2.962 0.014 4.219 O26 1.229 3.000 0.010 4.239 H9 0.155 0.006 0.000 0.162 H10 0.142 0.006 0.000 0.148 H11 0.155 0.006 0.000 0.162 H12 0.142 0.006 0.000 0.148 H13 0.150 0.006 0.000 0.156 H14 0.141 0.006 0.000 0.147 H15 0.150 0.006 0.000 0.156 H16 0.141 0.006 0.000 0.147 O27 1.244 2.940 0.012 4.197 O28 1.236 2.967 0.011 4.214 O29 1.244 2.940 0.012 4.197 O30 1.236 2.967 0.011 4.214 H17 0.152 0.006 0.000 0.158 H18 0.130 0.006 0.000 0.136 H19 0.152 0.006 0.000 0.158 H20 0.130 0.006 0.000 0.136 H21 0.132 0.006 0.000 0.138 H22 0.151 0.006 0.000 0.157 H23 0.132 0.006 0.000 0.138 H24 0.151 0.006 0.000 0.157 O31 1.236 2.979 0.011 4.226 O32 1.239 2.968 0.013 4.219 O33 1.236 2.979 0.011 4.226 O34 1.239 2.968 0.013 4.219 H25 0.140 0.006 0.000 0.147 H26 0.147 0.006 0.000 0.153 H27 0.140 0.006 0.000 0.147 H28 0.147 0.006 0.000 0.153 H29 0.145 0.006 0.000 0.152 H30 0.146 0.006 0.000 0.152 H31 0.145 0.006 0.000 0.152 H32 0.146 0.006 0.000 0.152 O35 1.236 2.977 0.011 4.224 O36 1.239 2.970 0.013 4.222 O37 1.236 2.977 0.011 4.224 O38 1.239 2.970 0.013 4.222 H33 0.144 0.006 0.000 0.151 H34 0.148 0.006 0.000 0.154 H35 0.144 0.006 0.000 0.151 H36 0.148 0.006 0.000 0.154 H37 0.136 0.006 0.000 0.142 H38 0.148 0.006 0.000 0.154 H39 0.136 0.006 0.000 0.142 H40 0.148 0.006 0.000 0.154 O39 1.240 2.967 0.014 4.222 O40 1.228 3.005 0.011 4.244 O42 1.240 2.967 0.014 4.222 O43 1.228 3.005 0.011 4.244 H41 0.156 0.006 0.000 0.162 H42 0.146 0.006 0.000 0.153 H44 0.156 0.006 0.000 0.162 H45 0.146 0.006 0.000 0.153 H47 0.156 0.006 0.000 0.162 H48 0.145 0.006 0.000 0.152 H50 0.156 0.006 0.000 0.162 H51 0.145 0.006 0.000 0.152 Analysis of the electronic structure: The system is a semiconductor with a direct gap of 0.387 eV. The valence band (#160) maximum is located near (0.00 0.00 0.00), at -0.195 eV with respect to the Fermi level. The conduction band (#161) minimum is located near (0.00 0.00 0.00), at 0.192 eV with respect to the Fermi level. The center of the gap is located at -0.001747 eV with respect to the Fermi level. The Fermi energy is used as the zero of the energy scale. Job completed on Mon 01 May 2023 at 13:07:06 CST after 167641 s (46:34:01) Entire job completed on Mon 01 May 2023 at 13:07:06 CST after 167641 s (46:34:01) and running 1 tasks.