[Sun Mar 19 08:52:07 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, unit cell shape, unit cell volume) VASP parameters =============== This is a calculation based on density functional theory and the GGA-PBE exchange-correlation functional for describing the interactions. 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 reciprocal space projection operators. The requested k-spacing is 0.5 per Angstrom, which leads to a 3x4x1 mesh. This corresponds to actual k-spacings of 0.358 x 0.434 x 0.257 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 600 ========================================== 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 7 symmetry-unique k-points The plane wave cutoff is 750.00 eV VASP energy: -506.084267 eV for Mg4S4O40H48 cell Initial VASP energy: -506.061080 eV for Mg4S4O40H48 cell Relaxation energy: -0.023187 eV gained after 47 optimization steps. Electronic contributions: Empirical Formula Cell MgSO10H12 (MgSO10H12)4 ----------------- ----------------- VASP Energy -126.521067 -506.084267 eV = -12207.424 -48829.697 kJ/mol Cell parameters: Parameter Original change Final % ---------- ------------ ---------- ------------ ----- a 10.124269 0.033208 10.157477 0.3 b 6.220817 0.008467 6.229284 0.1 c 24.796787 0.184779 24.981566 0.7 alpha 98.042852 0.457012 98.499863 0.5 beta 99.900566 0.544429 100.444996 0.5 gamma 35.536931 -0.154012 35.382919 -0.4 Volume 894.203579 5.903136 900.106715 0.7 Density: 1.686 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: 3.438 MPa = 34.376 bar XX YY ZZ YZ XZ XY Stress: -10.899 -6.771 7.358 0.000 17.427 -0.000 MPa = -108.992 -67.711 73.575 0.000 174.275 -0.000 bar 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 0.0000 0.0000 0.0000 0.0000 Mg2 0.0000 0.0000 0.5000 0.0000 0.0000 0.5000 Mg3 0.0601 0.8797 0.2500 0.0610 0.8780 0.2500 Mg4 0.9399 0.1203 0.7500 0.9390 0.1220 0.7500 S1 0.4224 0.8950 0.1234 0.4230 0.8928 0.1234 S2 0.6826 0.8950 0.3766 0.6842 0.8928 0.3766 S3 0.5776 0.1050 0.8766 0.5770 0.1072 0.8766 S4 0.3174 0.1050 0.6234 0.3158 0.1072 0.6234 O1 0.1799 0.1914 0.1353 0.1810 0.1885 0.1354 O2 0.6288 0.1914 0.3647 0.6305 0.1885 0.3646 O3 0.8201 0.8086 0.8647 0.8190 0.8115 0.8646 O4 0.3712 0.8086 0.6353 0.3695 0.8115 0.6354 O5 0.5469 0.8822 0.1680 0.5491 0.8779 0.1679 O6 0.5709 0.8822 0.3320 0.5730 0.8779 0.3321 O7 0.4531 0.1178 0.8320 0.4509 0.1221 0.8321 O8 0.4291 0.1178 0.6680 0.4270 0.1221 0.6679 O9 0.4233 0.9802 0.0698 0.4215 0.9806 0.0703 O10 0.5965 0.9802 0.4302 0.5979 0.9806 0.4297 O11 0.5767 0.0198 0.9302 0.5785 0.0194 0.9297 O12 0.4035 0.0198 0.5698 0.4021 0.0194 0.5703 O13 0.5356 0.5288 0.1179 0.5363 0.5259 0.1177 O14 0.9356 0.5288 0.3821 0.9377 0.5259 0.3823 O15 0.4644 0.4712 0.8821 0.4637 0.4741 0.8823 O16 0.0644 0.4712 0.6179 0.0623 0.4741 0.6177 O17 0.8681 0.4384 0.0474 0.8674 0.4370 0.0478 O18 0.6935 0.4384 0.4526 0.6956 0.4370 0.4522 O19 0.1319 0.5616 0.9526 0.1326 0.5630 0.9522 O20 0.3065 0.5616 0.5474 0.3044 0.5630 0.5478 H1 0.9660 0.3783 0.0798 0.9661 0.3744 0.0802 H2 0.6556 0.3783 0.4202 0.6595 0.3744 0.4198 H3 0.0340 0.6217 0.9202 0.0339 0.6256 0.9198 H4 0.3444 0.6217 0.5798 0.3405 0.6256 0.5802 H5 0.7092 0.6441 0.0572 0.7088 0.6418 0.0575 H6 0.6467 0.6441 0.4428 0.6494 0.6418 0.4425 H7 0.2908 0.3559 0.9428 0.2912 0.3582 0.9425 H8 0.3533 0.3559 0.5572 0.3506 0.3582 0.5575 O21 0.2126 0.6489 0.0674 0.2156 0.6443 0.0664 O22 0.1384 0.6489 0.4326 0.1401 0.6443 0.4336 O23 0.7874 0.3511 0.9326 0.7844 0.3557 0.9336 O24 0.8616 0.3511 0.5674 0.8599 0.3557 0.5664 H9 0.2792 0.4144 0.0669 0.2807 0.4111 0.0665 H10 0.3064 0.4144 0.4331 0.3082 0.4111 0.4335 H11 0.7208 0.5856 0.9331 0.7193 0.5889 0.9335 H12 0.6936 0.5856 0.5669 0.6918 0.5889 0.5665 H13 0.3255 0.6019 0.0893 0.3279 0.5981 0.0886 H14 0.0726 0.6019 0.4107 0.0740 0.5981 0.4114 H15 0.6745 0.3981 0.9107 0.6721 0.4019 0.9114 H16 0.9274 0.3981 0.5893 0.9260 0.4019 0.5886 O25 0.7592 0.1044 0.0205 0.7614 0.0997 0.0200 O26 0.1363 0.1044 0.4795 0.1389 0.0997 0.4800 O27 0.2408 0.8956 0.9795 0.2386 0.9003 0.9800 O28 0.8637 0.8956 0.5205 0.8611 0.9003 0.5200 H17 0.6674 0.2616 0.0514 0.6682 0.2575 0.0504 H18 0.0710 0.2616 0.4486 0.0743 0.2575 0.4496 H19 0.3326 0.7384 0.9486 0.3318 0.7425 0.9496 H20 0.9290 0.7384 0.5514 0.9257 0.7425 0.5504 H21 0.6911 0.0676 0.9963 0.6926 0.0662 0.9949 H22 0.2412 0.0676 0.5037 0.2412 0.0662 0.5051 H23 0.3089 0.9324 0.0037 0.3074 0.9338 0.0051 H24 0.7588 0.9324 0.4963 0.7588 0.9338 0.4949 O29 0.7353 0.2939 0.2816 0.7375 0.2894 0.2822 O30 0.9708 0.2939 0.2184 0.9730 0.2894 0.2178 O31 0.2647 0.7061 0.7184 0.2625 0.7106 0.7178 O32 0.0292 0.7061 0.7816 0.0270 0.7106 0.7822 H25 0.7349 0.1968 0.3099 0.7417 0.1877 0.3104 H26 0.0683 0.1968 0.1901 0.0706 0.1877 0.1896 H27 0.2651 0.8032 0.6901 0.2583 0.8123 0.6896 H28 0.9317 0.8032 0.8099 0.9294 0.8123 0.8104 H29 0.6733 0.5152 0.2992 0.6763 0.5104 0.3000 H30 0.8115 0.5152 0.2008 0.8134 0.5104 0.2000 H31 0.3267 0.4848 0.7008 0.3237 0.4896 0.7000 H32 0.1885 0.4848 0.7992 0.1866 0.4896 0.8000 O33 0.1391 0.4879 0.2811 0.1402 0.4829 0.2790 O34 0.3730 0.4879 0.2189 0.3768 0.4829 0.2210 O35 0.8609 0.5121 0.7189 0.8598 0.5171 0.7210 O36 0.6270 0.5121 0.7811 0.6232 0.5171 0.7790 H33 0.2911 0.2669 0.3007 0.2906 0.2631 0.2992 H34 0.4419 0.2669 0.1993 0.4462 0.2631 0.2008 H35 0.7089 0.7331 0.6993 0.7094 0.7369 0.7008 H36 0.5581 0.7331 0.8007 0.5538 0.7369 0.7992 H37 0.0786 0.4238 0.2646 0.0790 0.4203 0.2621 H38 0.4976 0.4238 0.2354 0.5007 0.4203 0.2379 H39 0.9214 0.5762 0.7354 0.9210 0.5797 0.7379 H40 0.5024 0.5762 0.7646 0.4993 0.5797 0.7621 O37 0.9133 0.8866 0.1791 0.9157 0.8864 0.1790 O38 0.2001 0.8866 0.3209 0.1979 0.8864 0.3210 O39 0.0867 0.1134 0.8209 0.0843 0.1136 0.8210 O40 0.7999 0.1134 0.6791 0.8021 0.1136 0.6790 H41 0.0051 0.6588 0.1576 0.0051 0.6593 0.1575 H42 0.3360 0.6588 0.3424 0.3356 0.6593 0.3425 H43 0.9949 0.3412 0.8424 0.9949 0.3407 0.8425 H44 0.6640 0.3412 0.6576 0.6644 0.3407 0.6575 H45 0.7883 0.1028 0.1545 0.7879 0.1050 0.1550 H46 0.1089 0.1028 0.3455 0.1071 0.1050 0.3450 H47 0.2117 0.8972 0.8455 0.2121 0.8950 0.8450 H48 0.8911 0.8972 0.6545 0.8929 0.8950 0.6550 Analytic Derivatives: Atom Derivatives fractional Derivatives Cartesian (eV/Ang) ----- -------- -------- -------- -------- -------- -------- Mg1 0.0000 0.0000 0.0000 -0.0000 0.0000 0.0000 Mg2 0.0000 0.0000 0.0000 -0.0000 -0.0000 0.0000 Mg3 -0.0006 0.0012 -0.0000 0.0000 0.0044 -0.0000 Mg4 0.0006 -0.0012 0.0000 -0.0000 -0.0044 0.0000 S1 -0.0010 -0.0003 -0.0002 -0.0107 -0.0010 -0.0040 S2 0.0013 -0.0003 0.0002 0.0107 -0.0010 0.0040 S3 0.0010 0.0003 0.0002 0.0107 0.0010 0.0040 S4 -0.0013 0.0003 -0.0002 -0.0107 0.0010 -0.0040 O1 0.0010 -0.0010 0.0004 0.0038 -0.0037 0.0089 O2 -0.0000 -0.0010 -0.0004 -0.0038 -0.0037 -0.0089 O3 -0.0010 0.0010 -0.0004 -0.0038 0.0037 -0.0089 O4 0.0000 0.0010 0.0004 0.0038 0.0037 0.0089 O5 -0.0014 0.0003 -0.0006 -0.0099 0.0011 -0.0145 maximum gradient = 0.0176 O6 0.0011 0.0003 0.0006 0.0099 0.0011 0.0145 O7 0.0014 -0.0003 0.0006 0.0099 -0.0011 0.0145 O8 -0.0011 -0.0003 -0.0006 -0.0099 -0.0011 -0.0145 O9 0.0006 0.0015 0.0001 0.0136 0.0056 0.0030 O10 -0.0022 0.0015 -0.0001 -0.0136 0.0056 -0.0030 O11 -0.0006 -0.0015 -0.0001 -0.0136 -0.0056 -0.0030 O12 0.0022 -0.0015 0.0001 0.0136 -0.0056 0.0030 O13 0.0020 -0.0035 0.0004 0.0011 -0.0125 0.0102 O14 0.0015 -0.0035 -0.0004 -0.0011 -0.0125 -0.0102 O15 -0.0020 0.0035 -0.0004 -0.0011 0.0125 -0.0102 O16 -0.0015 0.0035 0.0004 0.0011 0.0125 0.0102 O17 0.0005 -0.0010 0.0002 -0.0006 -0.0035 0.0041 O18 0.0005 -0.0010 -0.0002 0.0006 -0.0035 -0.0041 O19 -0.0005 0.0010 -0.0002 0.0006 0.0035 -0.0041 O20 -0.0005 0.0010 0.0002 -0.0006 0.0035 0.0041 H1 -0.0003 0.0008 0.0002 0.0005 0.0030 0.0042 H2 -0.0005 0.0008 -0.0002 -0.0005 0.0030 -0.0042 H3 0.0003 -0.0008 -0.0002 -0.0005 -0.0030 -0.0042 H4 0.0005 -0.0008 0.0002 0.0005 -0.0030 0.0042 H5 -0.0004 0.0002 0.0001 -0.0033 0.0008 0.0022 H6 0.0002 0.0002 -0.0001 0.0033 0.0008 -0.0022 H7 0.0004 -0.0002 -0.0001 0.0033 -0.0008 -0.0022 H8 -0.0002 -0.0002 0.0001 -0.0033 -0.0008 0.0022 O21 0.0003 -0.0006 -0.0001 0.0008 -0.0020 -0.0013 O22 0.0002 -0.0006 0.0001 -0.0008 -0.0020 0.0013 O23 -0.0003 0.0006 0.0001 -0.0008 0.0020 0.0013 O24 -0.0002 0.0006 -0.0001 0.0008 0.0020 -0.0013 H9 -0.0003 0.0002 -0.0001 -0.0018 0.0007 -0.0020 H10 0.0001 0.0002 0.0001 0.0018 0.0007 0.0020 H11 0.0003 -0.0002 0.0001 0.0018 -0.0007 0.0020 H12 -0.0001 -0.0002 -0.0001 -0.0018 -0.0007 -0.0020 H13 0.0007 -0.0014 -0.0001 0.0004 -0.0050 -0.0036 H14 0.0007 -0.0014 0.0001 -0.0004 -0.0050 0.0036 H15 -0.0007 0.0014 0.0001 -0.0004 0.0050 0.0036 H16 -0.0007 0.0014 -0.0001 0.0004 0.0050 -0.0036 O25 0.0004 -0.0011 -0.0001 -0.0010 -0.0040 -0.0013 O26 0.0007 -0.0011 0.0001 0.0010 -0.0040 0.0013 O27 -0.0004 0.0011 0.0001 0.0010 0.0040 0.0013 O28 -0.0007 0.0011 -0.0001 -0.0010 0.0040 -0.0013 H17 0.0006 -0.0010 -0.0000 0.0007 -0.0036 -0.0009 H18 0.0005 -0.0010 0.0000 -0.0007 -0.0036 0.0009 H19 -0.0006 0.0010 0.0000 -0.0007 0.0036 0.0009 H20 -0.0005 0.0010 -0.0000 0.0007 0.0036 -0.0009 H21 0.0000 -0.0007 -0.0002 -0.0028 -0.0026 -0.0039 H22 0.0007 -0.0007 0.0002 0.0028 -0.0026 0.0039 H23 -0.0000 0.0007 0.0002 0.0028 0.0026 0.0039 H24 -0.0007 0.0007 -0.0002 -0.0028 0.0026 -0.0039 O29 0.0016 -0.0025 0.0002 0.0026 -0.0090 0.0054 O30 0.0009 -0.0025 -0.0002 -0.0026 -0.0090 -0.0054 O31 -0.0016 0.0025 -0.0002 -0.0026 0.0090 -0.0054 O32 -0.0009 0.0025 0.0002 0.0026 0.0090 0.0054 H25 -0.0001 -0.0000 -0.0001 -0.0013 -0.0002 -0.0024 H26 0.0002 -0.0000 0.0001 0.0013 -0.0002 0.0024 H27 0.0001 0.0000 0.0001 0.0013 0.0002 0.0024 H28 -0.0002 0.0000 -0.0001 -0.0013 0.0002 -0.0024 H29 0.0002 -0.0011 -0.0002 -0.0032 -0.0041 -0.0058 H30 0.0010 -0.0011 0.0002 0.0032 -0.0041 0.0058 H31 -0.0002 0.0011 0.0002 0.0032 0.0041 0.0058 H32 -0.0010 0.0011 -0.0002 -0.0032 0.0041 -0.0058 O33 -0.0000 -0.0008 0.0001 -0.0046 -0.0029 0.0014 O34 0.0008 -0.0008 -0.0001 0.0046 -0.0029 -0.0014 O35 0.0000 0.0008 -0.0001 0.0046 0.0029 -0.0014 O36 -0.0008 0.0008 0.0001 -0.0046 0.0029 0.0014 H33 0.0004 -0.0014 -0.0001 -0.0026 -0.0052 -0.0012 H34 0.0010 -0.0014 0.0001 0.0026 -0.0052 0.0012 H35 -0.0004 0.0014 0.0001 0.0026 0.0052 0.0012 H36 -0.0010 0.0014 -0.0001 -0.0026 0.0052 -0.0012 H37 0.0011 -0.0017 0.0001 0.0024 -0.0061 0.0029 H38 0.0006 -0.0017 -0.0001 -0.0024 -0.0061 -0.0029 H39 -0.0011 0.0017 -0.0001 -0.0024 0.0061 -0.0029 H40 -0.0006 0.0017 0.0001 0.0024 0.0061 0.0029 O37 0.0001 -0.0009 -0.0001 -0.0032 -0.0034 -0.0026 O38 0.0008 -0.0009 0.0001 0.0032 -0.0034 0.0026 O39 -0.0001 0.0009 0.0001 0.0032 0.0034 0.0026 O40 -0.0008 0.0009 -0.0001 -0.0032 0.0034 -0.0026 H41 0.0004 -0.0013 0.0000 -0.0026 -0.0046 0.0004 H42 0.0009 -0.0013 -0.0000 0.0026 -0.0046 -0.0004 H43 -0.0004 0.0013 -0.0000 0.0026 0.0046 -0.0004 H44 -0.0009 0.0013 0.0000 -0.0026 0.0046 0.0004 H45 0.0003 -0.0007 -0.0001 0.0004 -0.0024 -0.0030 H46 0.0003 -0.0007 0.0001 -0.0004 -0.0024 0.0030 H47 -0.0003 0.0007 0.0001 -0.0004 0.0024 0.0030 H48 -0.0003 0.0007 -0.0001 0.0004 0.0024 -0.0030 Atomic partial charges (electron charges): Atom s p d total ----- -------- -------- -------- -------- Mg1 0.260 0.398 0.258 0.917 Mg2 0.260 0.398 0.258 0.917 Mg3 0.256 0.386 0.246 0.888 Mg4 0.256 0.386 0.246 0.888 S1 1.052 1.896 0.800 3.748 S2 1.052 1.896 0.800 3.748 S3 1.052 1.896 0.800 3.748 S4 1.052 1.896 0.800 3.748 O1 1.265 2.896 0.015 4.177 O2 1.265 2.896 0.015 4.177 O3 1.265 2.896 0.015 4.177 O4 1.265 2.896 0.015 4.177 O5 1.265 2.903 0.016 4.184 O6 1.265 2.903 0.016 4.184 O7 1.265 2.903 0.016 4.184 O8 1.265 2.903 0.016 4.184 O9 1.267 2.894 0.015 4.176 O10 1.267 2.894 0.015 4.176 O11 1.267 2.894 0.015 4.176 O12 1.267 2.894 0.015 4.176 O13 1.266 2.897 0.015 4.179 O14 1.266 2.897 0.015 4.179 O15 1.266 2.897 0.015 4.179 O16 1.266 2.897 0.015 4.179 O17 1.233 2.986 0.012 4.230 O18 1.233 2.986 0.012 4.230 O19 1.233 2.986 0.012 4.230 O20 1.233 2.986 0.012 4.230 H1 0.148 0.006 0.000 0.155 H2 0.148 0.006 0.000 0.155 H3 0.148 0.006 0.000 0.155 H4 0.148 0.006 0.000 0.155 H5 0.147 0.006 0.000 0.154 H6 0.147 0.006 0.000 0.154 H7 0.147 0.006 0.000 0.154 H8 0.147 0.006 0.000 0.154 O21 1.233 2.987 0.012 4.231 O22 1.233 2.987 0.012 4.231 O23 1.233 2.987 0.012 4.231 O24 1.233 2.987 0.012 4.231 H9 0.146 0.006 0.000 0.153 H10 0.146 0.006 0.000 0.153 H11 0.146 0.006 0.000 0.153 H12 0.146 0.006 0.000 0.153 H13 0.149 0.006 0.000 0.155 H14 0.149 0.006 0.000 0.155 H15 0.149 0.006 0.000 0.155 H16 0.149 0.006 0.000 0.155 O25 1.232 2.987 0.012 4.230 O26 1.232 2.987 0.012 4.230 O27 1.232 2.987 0.012 4.230 O28 1.232 2.987 0.012 4.230 H17 0.150 0.006 0.000 0.157 H18 0.150 0.006 0.000 0.157 H19 0.150 0.006 0.000 0.157 H20 0.150 0.006 0.000 0.157 H21 0.150 0.006 0.000 0.156 H22 0.150 0.006 0.000 0.156 H23 0.150 0.006 0.000 0.156 H24 0.150 0.006 0.000 0.156 O29 1.236 2.972 0.012 4.220 O30 1.236 2.972 0.012 4.220 O31 1.236 2.972 0.012 4.220 O32 1.236 2.972 0.012 4.220 H25 0.148 0.006 0.000 0.154 H26 0.148 0.006 0.000 0.154 H27 0.148 0.006 0.000 0.154 H28 0.148 0.006 0.000 0.154 H29 0.143 0.006 0.000 0.149 H30 0.143 0.006 0.000 0.149 H31 0.143 0.006 0.000 0.149 H32 0.143 0.006 0.000 0.149 O33 1.231 2.988 0.012 4.230 O34 1.231 2.988 0.012 4.230 O35 1.231 2.988 0.012 4.230 O36 1.231 2.988 0.012 4.230 H33 0.146 0.006 0.000 0.153 H34 0.146 0.006 0.000 0.153 H35 0.146 0.006 0.000 0.153 H36 0.146 0.006 0.000 0.153 H37 0.149 0.006 0.000 0.155 H38 0.149 0.006 0.000 0.155 H39 0.149 0.006 0.000 0.155 H40 0.149 0.006 0.000 0.155 O37 1.230 2.990 0.011 4.232 O38 1.230 2.990 0.011 4.232 O39 1.230 2.990 0.011 4.232 O40 1.230 2.990 0.011 4.232 H41 0.148 0.006 0.000 0.155 H42 0.148 0.006 0.000 0.155 H43 0.148 0.006 0.000 0.155 H44 0.148 0.006 0.000 0.155 H45 0.147 0.006 0.000 0.153 H46 0.147 0.006 0.000 0.153 H47 0.147 0.006 0.000 0.153 H48 0.147 0.006 0.000 0.153 Analysis of the electronic structure: The system is an insulator with an indirect gap of 5.200 eV. The valence band (#160) maximum is located near (0.33 0.00 0.00), at -0.238 eV with respect to the Fermi level. The conduction band (#161) minimum is located near (0.00 0.00 0.00), at 4.962 eV with respect to the Fermi level. The center of the gap is located at 2.362191 eV with respect to the Fermi level. The Fermi energy is used as the zero of the energy scale. Job completed on Sun 19 March 2023 at 16:02:21 CST after 25810 s (7:10:10) Entire job completed on Sun 19 March 2023 at 16:02:21 CST after 25810 s (7:10:10) and running 1 tasks.