[Sat Mar 18 14:33:49 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 'normal' precision and a user-defined planewave cutoff energy of 750.000 eV. The electronic iterations convergence is 1.00E-04 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 0.361 x 0.437 x 0.262 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: Convergence criterion for ionic relaxations is 0.05 eV/Ang 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: -506.000218 eV for Mg4S4O40H48 cell Initial VASP energy: -441.577490 eV for Mg4S4O40H48 cell Relaxation energy: -64.422728 eV gained after 47 optimization steps. Electronic contributions: Empirical Formula Cell MgSO10H12 (MgSO10H12)4 ----------------- ----------------- VASP Energy -126.500055 -506.000218 eV = -12205.397 -48821.587 kJ/mol Cell parameters: Parameter Original change Final % ---------- ------------ ---------- ------------ ----- a 9.975000 0.149269 10.124269 1.5 b 6.146935 0.073883 6.220817 1.2 c 24.267000 0.529787 24.796787 2.2 alpha 97.114335 0.928516 98.042852 1.0 beta 98.780000 1.120566 99.900566 1.1 gamma 35.769016 -0.232085 35.536931 -0.6 Volume 859.541749 34.661830 894.203579 4.0 Density: 1.697 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: 25.347 MPa = 253.468 bar XX YY ZZ YZ XZ XY Stress: -70.251 5.334 -11.123 -0.000 106.634 -0.000 MPa = -0.703 0.053 -0.111 -0.000 1.066 -0.000 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 0.0000 0.0000 0.0000 0.0000 Mg2 0.0000 0.0000 0.5000 0.0000 0.0000 0.5000 Mg3 0.0610 0.8779 0.2500 0.0601 0.8797 0.2500 Mg4 0.9390 0.1221 0.7500 0.9399 0.1203 0.7500 S1 0.4226 0.8928 0.1231 0.4224 0.8950 0.1234 S2 0.6845 0.8928 0.3769 0.6826 0.8950 0.3766 S3 0.5774 0.1072 0.8769 0.5776 0.1050 0.8766 S4 0.3155 0.1072 0.6231 0.3174 0.1050 0.6234 O1 0.1818 0.1867 0.1360 0.1799 0.1914 0.1353 O2 0.6315 0.1867 0.3640 0.6288 0.1914 0.3647 O3 0.8182 0.8133 0.8640 0.8201 0.8086 0.8647 O4 0.3685 0.8133 0.6360 0.3712 0.8086 0.6353 O5 0.5471 0.8825 0.1664 0.5469 0.8822 0.1680 O6 0.5703 0.8825 0.3336 0.5709 0.8822 0.3320 O7 0.4529 0.1175 0.8336 0.4531 0.1178 0.8320 O8 0.4297 0.1175 0.6664 0.4291 0.1178 0.6680 O9 0.4217 0.9773 0.0683 0.4233 0.9802 0.0698 O10 0.6010 0.9773 0.4317 0.5965 0.9802 0.4302 O11 0.5783 0.0227 0.9317 0.5767 0.0198 0.9302 O12 0.3990 0.0227 0.5683 0.4035 0.0198 0.5698 O13 0.5348 0.5297 0.1192 0.5356 0.5288 0.1179 O14 0.9355 0.5297 0.3808 0.9356 0.5288 0.3821 O15 0.4652 0.4703 0.8808 0.4644 0.4712 0.8821 O16 0.0645 0.4703 0.6192 0.0644 0.4712 0.6179 O17 0.8715 0.4318 0.0468 0.8681 0.4384 0.0474 O18 0.6967 0.4318 0.4532 0.6935 0.4384 0.4526 O19 0.1285 0.5682 0.9532 0.1319 0.5616 0.9526 O20 0.3033 0.5682 0.5468 0.3065 0.5616 0.5474 H1 0.9490 0.3880 0.0748 -0.0340 0.3783 0.0798 H2 0.6630 0.3880 0.4252 0.6556 0.3783 0.4202 H3 0.0510 0.6120 0.9252 0.0340 0.6217 0.9202 H4 0.3370 0.6120 0.5748 0.3444 0.6217 0.5798 H5 0.7470 0.6040 0.0558 0.7092 0.6441 0.0572 H6 0.6490 0.6040 0.4442 0.6467 0.6441 0.4428 H7 0.2530 0.3960 0.9442 0.2908 0.3559 0.9428 H8 0.3510 0.3960 0.5558 0.3533 0.3559 0.5572 O21 0.2108 0.6494 0.0672 0.2126 0.6489 0.0674 O22 0.1398 0.6494 0.4328 0.1384 0.6489 0.4326 O23 0.7892 0.3506 0.9328 0.7874 0.3511 0.9326 O24 0.8602 0.3506 0.5672 0.8616 0.3511 0.5674 H9 0.2740 0.4540 0.0681 0.2792 0.4144 0.0669 H10 0.2720 0.4540 0.4319 0.3064 0.4144 0.4331 H11 0.7260 0.5460 0.9319 0.7208 0.5856 0.9331 H12 0.7280 0.5460 0.5681 0.6936 0.5856 0.5669 H13 0.3020 0.6180 0.0868 0.3255 0.6019 0.0893 H14 0.0800 0.6180 0.4132 0.0726 0.6019 0.4107 H15 0.6980 0.3820 0.9132 0.6745 0.3981 0.9107 H16 0.9200 0.3820 0.5868 0.9274 0.3981 0.5893 O25 0.7594 0.1042 0.0214 0.7592 0.1044 0.0205 O26 0.1364 0.1042 0.4786 0.1363 0.1044 0.4795 O27 0.2406 0.8958 0.9786 0.2408 -0.1044 0.9795 O28 0.8636 0.8958 0.5214 0.8637 -0.1044 0.5205 H17 0.6790 0.2460 0.0456 0.6674 0.2616 0.0514 H18 0.0750 0.2460 0.4544 0.0710 0.2616 0.4486 H19 0.3210 0.7540 0.9544 0.3326 0.7384 0.9486 H20 0.9250 0.7540 0.5456 0.9290 0.7384 0.5514 H21 0.7110 0.0640 0.0008 0.6911 0.0676 -0.0037 H22 0.2250 0.0640 0.4992 0.2412 0.0676 0.5037 H23 0.2890 0.9360 0.9992 0.3089 0.9324 0.0037 H24 0.7750 0.9360 0.5008 0.7588 0.9324 0.4963 O29 0.7422 0.2884 0.2819 0.7353 0.2939 0.2816 O30 0.9694 0.2884 0.2181 0.9708 0.2939 0.2184 O31 0.2578 0.7116 0.7181 0.2647 0.7061 0.7184 O32 0.0306 0.7116 0.7819 0.0292 0.7061 0.7816 H25 0.7350 0.2120 0.3027 0.7349 0.1968 0.3099 H26 0.0530 0.2120 0.1973 0.0683 0.1968 0.1901 H27 0.2650 0.7880 0.6973 0.2651 0.8032 0.6901 H28 0.9470 0.7880 0.8027 0.9317 0.8032 0.8099 H29 0.6850 0.4780 0.2957 0.6733 0.5152 0.2992 H30 0.8370 0.4780 0.2043 0.8115 0.5152 0.2008 H31 0.3150 0.5220 0.7043 0.3267 0.4848 0.7008 H32 0.1630 0.5220 0.7957 0.1885 0.4848 0.7992 O33 0.1425 0.4830 0.2806 0.1391 0.4879 0.2811 O34 0.3745 0.4830 0.2194 0.3730 0.4879 0.2189 O35 0.8575 0.5170 0.7194 0.8609 0.5121 0.7189 O36 0.6255 0.5170 0.7806 0.6270 0.5121 0.7811 H33 0.2640 0.3000 0.2958 0.2911 0.2669 0.3007 H34 0.4360 0.3000 0.2042 0.4419 0.2669 0.1993 H35 0.7360 0.7000 0.7042 0.7089 0.7331 0.6993 H36 0.5640 0.7000 0.7958 0.5581 0.7331 0.8007 H37 0.0900 0.4400 0.2715 0.0786 0.4238 0.2646 H38 0.4700 0.4400 0.2285 0.4976 0.4238 0.2354 H39 0.9100 0.5600 0.7285 -0.0786 0.5762 0.7354 H40 0.5300 0.5600 0.7715 0.5024 0.5762 0.7646 O37 0.9180 0.8810 0.1793 0.9133 0.8866 0.1791 O38 0.2010 0.8810 0.3207 0.2001 0.8866 0.3209 O39 0.0820 0.1190 0.8207 0.0867 0.1134 0.8209 O40 0.7990 0.1190 0.6793 0.7999 0.1134 0.6791 H41 0.9930 0.6900 0.1627 0.0051 0.6588 0.1576 H42 0.3170 0.6900 0.3373 0.3360 0.6588 0.3424 H43 0.0070 0.3100 0.8373 -0.0051 0.3412 0.8424 H44 0.6830 0.3100 0.6627 0.6640 0.3412 0.6576 H45 0.8070 0.0660 0.1592 0.7883 0.1028 0.1545 H46 0.1270 0.0660 0.3408 0.1089 0.1028 0.3455 H47 0.1930 0.9340 0.8408 0.2117 0.8972 0.8455 H48 0.8730 0.9340 0.6592 0.8911 0.8972 0.6545 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 -0.0054 0.0108 0.0000 -0.0000 0.0388 0.0000 Mg4 0.0054 -0.0108 0.0000 0.0000 -0.0388 0.0000 S1 0.0006 0.0001 -0.0014 0.0116 0.0005 -0.0332 S2 -0.0007 0.0001 0.0014 -0.0116 0.0005 0.0332 S3 -0.0006 -0.0001 0.0014 -0.0116 -0.0005 0.0332 S4 0.0007 -0.0001 -0.0014 0.0116 -0.0005 -0.0332 O1 0.0021 -0.0066 -0.0001 -0.0118 -0.0237 -0.0023 O2 0.0045 -0.0066 0.0001 0.0118 -0.0237 0.0023 O3 -0.0021 0.0066 0.0001 0.0118 0.0237 0.0023 O4 -0.0045 0.0066 -0.0001 -0.0118 0.0237 -0.0023 O5 0.0065 -0.0074 0.0013 0.0227 -0.0266 0.0315 O6 0.0009 -0.0074 -0.0013 -0.0227 -0.0266 -0.0315 O7 -0.0065 0.0074 -0.0013 -0.0227 0.0266 -0.0315 O8 -0.0009 0.0074 0.0013 0.0227 0.0266 0.0315 O9 -0.0061 0.0130 -0.0005 0.0060 0.0469 -0.0112 maximum gradient = 0.0486 O10 -0.0069 0.0130 0.0005 -0.0060 0.0469 0.0112 O11 0.0061 -0.0130 0.0005 -0.0060 -0.0469 0.0112 O12 0.0069 -0.0130 -0.0005 0.0060 -0.0469 -0.0112 O13 -0.0027 -0.0025 0.0004 -0.0405 -0.0090 0.0100 O14 0.0052 -0.0025 -0.0004 0.0405 -0.0090 -0.0100 O15 0.0027 0.0025 -0.0004 0.0405 0.0090 -0.0100 O16 -0.0052 0.0025 0.0004 -0.0405 0.0090 0.0100 O17 0.0005 -0.0011 0.0001 -0.0008 -0.0040 0.0016 O18 0.0006 -0.0011 -0.0001 0.0008 -0.0040 -0.0016 O19 -0.0005 0.0011 -0.0001 0.0008 0.0040 -0.0016 O20 -0.0006 0.0011 0.0001 -0.0008 0.0040 0.0016 H1 0.0005 -0.0048 -0.0005 -0.0166 -0.0173 -0.0127 H2 0.0043 -0.0048 0.0005 0.0166 -0.0173 0.0127 H3 -0.0005 0.0048 0.0005 0.0166 0.0173 0.0127 H4 -0.0043 0.0048 -0.0005 -0.0166 0.0173 -0.0127 H5 0.0005 -0.0025 -0.0004 -0.0057 -0.0089 -0.0094 H6 0.0020 -0.0025 0.0004 0.0057 -0.0089 0.0094 H7 -0.0005 0.0025 0.0004 0.0057 0.0089 0.0094 H8 -0.0020 0.0025 -0.0004 -0.0057 0.0089 -0.0094 O21 0.0028 -0.0029 0.0001 0.0134 -0.0103 0.0021 O22 0.0001 -0.0029 -0.0001 -0.0134 -0.0103 -0.0021 O23 -0.0028 0.0029 -0.0001 -0.0134 0.0103 -0.0021 O24 -0.0001 0.0029 0.0001 0.0134 0.0103 0.0021 H9 0.0014 -0.0041 -0.0004 -0.0053 -0.0148 -0.0094 H10 0.0027 -0.0041 0.0004 0.0053 -0.0148 0.0094 H11 -0.0014 0.0041 0.0004 0.0053 0.0148 0.0094 H12 -0.0027 0.0041 -0.0004 -0.0053 0.0148 -0.0094 H13 -0.0040 0.0046 -0.0006 -0.0148 0.0165 -0.0133 H14 -0.0006 0.0046 0.0006 0.0148 0.0165 0.0133 H15 0.0040 -0.0046 0.0006 0.0148 -0.0165 0.0133 H16 0.0006 -0.0046 -0.0006 -0.0148 -0.0165 -0.0133 O25 -0.0016 -0.0011 0.0012 -0.0251 -0.0038 0.0282 O26 0.0026 -0.0011 -0.0012 0.0251 -0.0038 -0.0282 O27 0.0016 0.0011 -0.0012 0.0251 0.0038 -0.0282 O28 -0.0026 0.0011 0.0012 -0.0251 0.0038 0.0282 H17 -0.0008 -0.0001 -0.0007 -0.0062 -0.0004 -0.0176 H18 0.0010 -0.0001 0.0007 0.0062 -0.0004 0.0176 H19 0.0008 0.0001 0.0007 0.0062 0.0004 0.0176 H20 -0.0010 0.0001 -0.0007 -0.0062 0.0004 -0.0176 H21 0.0018 0.0004 -0.0006 0.0225 0.0013 -0.0146 H22 -0.0022 0.0004 0.0006 -0.0225 0.0013 0.0146 H23 -0.0018 -0.0004 0.0006 -0.0225 -0.0013 0.0146 H24 0.0022 -0.0004 -0.0006 0.0225 -0.0013 -0.0146 O29 -0.0001 -0.0022 -0.0002 -0.0116 -0.0080 -0.0047 O30 0.0023 -0.0022 0.0002 0.0116 -0.0080 0.0047 O31 0.0001 0.0022 0.0002 0.0116 0.0080 0.0047 O32 -0.0023 0.0022 -0.0002 -0.0116 0.0080 -0.0047 H25 0.0018 -0.0023 0.0008 0.0032 -0.0084 0.0181 H26 0.0006 -0.0023 -0.0008 -0.0032 -0.0084 -0.0181 H27 -0.0018 0.0023 -0.0008 -0.0032 0.0084 -0.0181 H28 -0.0006 0.0023 0.0008 0.0032 0.0084 0.0181 H29 0.0018 -0.0014 0.0003 0.0102 -0.0050 0.0072 H30 -0.0004 -0.0014 -0.0003 -0.0102 -0.0050 -0.0072 H31 -0.0018 0.0014 -0.0003 -0.0102 0.0050 -0.0072 H32 0.0004 0.0014 0.0003 0.0102 0.0050 0.0072 O33 0.0003 -0.0021 -0.0016 -0.0014 -0.0076 -0.0391 O34 0.0018 -0.0021 0.0016 0.0014 -0.0076 0.0391 O35 -0.0003 0.0021 0.0016 0.0014 0.0076 0.0391 O36 -0.0018 0.0021 -0.0016 -0.0014 0.0076 -0.0391 H33 -0.0023 0.0009 -0.0003 -0.0169 0.0032 -0.0076 H34 0.0014 0.0009 0.0003 0.0169 0.0032 0.0076 H35 0.0023 -0.0009 0.0003 0.0169 -0.0032 0.0076 H36 -0.0014 -0.0009 -0.0003 -0.0169 -0.0032 -0.0076 H37 0.0003 0.0003 -0.0005 0.0061 0.0010 -0.0116 H38 -0.0006 0.0003 0.0005 -0.0061 0.0010 0.0116 H39 -0.0003 -0.0003 0.0005 -0.0061 -0.0010 0.0116 H40 0.0006 -0.0003 -0.0005 0.0061 -0.0010 -0.0116 O37 0.0051 -0.0068 -0.0003 0.0181 -0.0243 -0.0064 O38 0.0017 -0.0068 0.0003 -0.0181 -0.0243 0.0064 O39 -0.0051 0.0068 0.0003 -0.0181 0.0243 0.0064 O40 -0.0017 0.0068 -0.0003 0.0181 0.0243 -0.0064 H41 -0.0022 0.0043 0.0003 -0.0020 0.0154 0.0071 H42 -0.0020 0.0043 -0.0003 0.0020 0.0154 -0.0071 H43 0.0022 -0.0043 -0.0003 0.0020 -0.0154 -0.0071 H44 0.0020 -0.0043 0.0003 -0.0020 -0.0154 0.0071 H45 0.0016 0.0002 0.0017 0.0106 0.0008 0.0416 H46 -0.0018 0.0002 -0.0017 -0.0106 0.0008 -0.0416 H47 -0.0016 -0.0002 -0.0017 -0.0106 -0.0008 -0.0416 H48 0.0018 -0.0002 0.0017 0.0106 -0.0008 0.0416 Atomic partial charges (electron charges): Atom s p d total ----- -------- -------- -------- -------- Mg1 0.259 0.397 0.258 0.914 Mg2 0.259 0.397 0.258 0.914 Mg3 0.255 0.384 0.244 0.884 Mg4 0.255 0.384 0.244 0.884 S1 1.052 1.897 0.802 3.751 S2 1.052 1.897 0.802 3.751 S3 1.052 1.897 0.802 3.751 S4 1.052 1.897 0.802 3.751 O1 1.265 2.897 0.015 4.177 O2 1.265 2.897 0.015 4.177 O3 1.265 2.897 0.015 4.177 O4 1.265 2.897 0.015 4.177 O5 1.266 2.905 0.016 4.186 O6 1.266 2.905 0.016 4.186 O7 1.266 2.905 0.016 4.186 O8 1.266 2.905 0.016 4.186 O9 1.268 2.894 0.015 4.177 O10 1.268 2.894 0.015 4.177 O11 1.268 2.894 0.015 4.177 O12 1.268 2.894 0.015 4.177 O13 1.266 2.898 0.015 4.179 O14 1.266 2.898 0.015 4.179 O15 1.266 2.898 0.015 4.179 O16 1.266 2.898 0.015 4.179 O17 1.233 2.985 0.012 4.230 O18 1.233 2.985 0.012 4.230 O19 1.233 2.985 0.012 4.230 O20 1.233 2.985 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 0.153 H6 0.147 0.006 0.000 0.153 H7 0.147 0.006 0.000 0.153 H8 0.147 0.006 0.000 0.153 O21 1.233 2.985 0.012 4.231 O22 1.233 2.985 0.012 4.231 O23 1.233 2.985 0.012 4.231 O24 1.233 2.985 0.012 4.231 H9 0.147 0.006 0.000 0.153 H10 0.147 0.006 0.000 0.153 H11 0.147 0.006 0.000 0.153 H12 0.147 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 1.231 2.987 0.012 4.231 O26 1.231 2.987 0.012 4.231 O27 1.231 2.987 0.012 4.231 O28 1.231 2.987 0.012 4.231 H17 0.150 0.006 0.000 0.156 H18 0.150 0.006 0.000 0.156 H19 0.150 0.006 0.000 0.156 H20 0.150 0.006 0.000 0.156 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 2.973 0.012 4.221 O30 1.236 2.973 0.012 4.221 O31 1.236 2.973 0.012 4.221 O32 1.236 2.973 0.012 4.221 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 0.150 H30 0.143 0.006 0.000 0.150 H31 0.143 0.006 0.000 0.150 H32 0.143 0.006 0.000 0.150 O33 1.231 2.987 0.012 4.230 O34 1.231 2.987 0.012 4.230 O35 1.231 2.987 0.012 4.230 O36 1.231 2.987 0.012 4.230 H33 0.146 0.006 0.000 0.152 H34 0.146 0.006 0.000 0.152 H35 0.146 0.006 0.000 0.152 H36 0.146 0.006 0.000 0.152 H37 0.149 0.006 0.000 0.156 H38 0.149 0.006 0.000 0.156 H39 0.149 0.006 0.000 0.156 H40 0.149 0.006 0.000 0.156 O37 1.231 2.988 0.012 4.230 O38 1.231 2.988 0.012 4.230 O39 1.231 2.988 0.012 4.230 O40 1.231 2.988 0.012 4.230 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 5.208 eV. The valence band (#160) maximum is located near (0.33 0.00 0.00), at -0.242 eV with respect to the Fermi level. The conduction band (#161) minimum is located near (0.00 0.00 0.00), at 4.966 eV with respect to the Fermi level. The center of the gap is located at 2.362033 eV with respect to the Fermi level. The Fermi energy is used as the zero of the energy scale. Job completed on Sat 18 March 2023 at 22:21:53 CST after 28080 s (7:48:00) Entire job completed on Sat 18 March 2023 at 22:21:53 CST after 28080 s (7:48:00) and running 1 tasks.