[Thu Mar 30 10:14:43 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 '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 0.4 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: Convergence criterion for ionic relaxations is 0.08 eV/Ang Number of steps is 200 ========================================== 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: -504.554093 eV for Mg4S4O40H48 cell Non-dispersive: -499.345593 eV Van der Waals: -5.208500 eV Initial VASP energy: -500.123870 eV for Mg4S4O40H48 cell Relaxation energy: -4.430223 eV gained after 154 optimization steps. Electronic contributions: Empirical Formula Cell MgSO10H12 (MgSO10H12)4 ----------------- ----------------- VASP Energy -126.138523 -504.554093 eV = -12170.514 -48682.058 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: -135.000 MPa = -1.350 kbar XX YY ZZ YZ XZ XY Stress: -199.048 287.271 315.744 -18.212 -57.485 17.243 MPa = -1.990 2.873 3.157 -0.182 -0.575 0.172 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 -0.0155 -0.0107 0.5811 Mg2 0.5000 0.5000 0.5883 0.4845 0.4893 0.5811 Mg3 0.9387 0.9000 0.8182 0.9542 0.9192 0.8156 Mg4 0.4387 0.4000 0.8182 0.4542 0.4192 0.8156 S1 0.4465 0.8209 0.7016 0.4348 0.8209 0.7260 S2 0.5535 0.1791 0.4750 0.5356 0.1666 0.4838 S3 0.9465 0.3209 0.7016 0.9348 0.3209 0.7260 S4 0.0535 0.6791 0.4750 0.0356 0.6666 0.4838 O1 0.0943 0.2189 0.7131 0.1075 0.2393 0.7195 O2 0.9057 0.7811 0.4635 0.8909 0.7705 0.4763 O3 0.5943 0.7189 0.7131 0.6075 0.7393 0.7195 O4 0.4057 0.2811 0.4635 0.3909 0.2705 0.4763 O6 0.4410 0.9239 0.7427 0.4429 0.8866 0.7801 O7 0.5590 0.0761 0.4338 0.5358 0.0600 0.4460 O9 0.9410 0.4239 0.7427 0.9429 0.3866 0.7801 O10 0.0590 0.5761 0.4338 0.0358 0.5600 0.4460 O11 0.4905 0.8861 0.6508 0.4193 0.9266 0.6879 O12 0.5095 0.1139 0.5257 0.5024 0.1027 0.5384 O13 0.9905 0.3861 0.6508 0.9193 0.4266 0.6879 O14 0.0095 0.6139 0.5257 0.0024 0.6027 0.5384 O15 0.2629 0.7520 0.6970 0.2738 0.7266 0.7265 O16 0.7371 0.2480 0.4795 0.7225 0.2358 0.4882 O17 0.7629 0.2520 0.6970 0.7738 0.2266 0.7265 O18 0.2371 0.7480 0.4795 0.2225 0.7358 0.4882 O19 0.2203 0.0715 0.6304 0.1834 0.0787 0.6297 O20 0.7797 0.9285 0.5462 0.7463 0.9008 0.5511 O21 0.7203 0.5715 0.6304 0.6834 0.5787 0.6297 O22 0.2797 0.4285 0.5462 0.2463 0.4008 0.5511 H1 0.1885 0.1238 0.6613 0.1473 0.1436 0.6561 H2 0.8115 0.8762 0.5152 0.7912 0.8494 0.5189 H3 0.6885 0.6238 0.6613 0.6473 0.6436 0.6561 H4 0.3115 0.3762 0.5152 0.2912 0.3494 0.5189 H5 0.3238 0.0098 0.6389 0.2728 0.0185 0.6462 H6 0.6762 0.9902 0.5376 0.6526 0.9712 0.5406 H7 0.8238 0.5098 0.6389 0.7728 0.5185 0.6462 H8 0.1762 0.4902 0.5376 0.1526 0.4712 0.5406 O23 0.3295 0.5053 0.6522 0.2957 0.4997 0.6491 O24 0.6705 0.4947 0.5243 0.6723 0.4826 0.5258 O25 0.8295 0.0053 0.6522 0.7957 -0.0003 0.6491 O26 0.1705 0.9947 0.5243 0.1723 0.9826 0.5258 H9 0.2103 0.4564 0.6491 0.1928 0.4511 0.6329 H10 0.7897 0.5436 0.5274 0.7944 0.5296 0.5292 H11 0.7103 0.9564 0.6491 0.6928 0.9511 0.6329 H12 0.2897 0.0436 0.5274 0.2944 0.0296 0.5292 H13 0.3031 0.5878 0.6720 0.2481 0.5912 0.6540 H14 0.6969 0.4122 0.5046 0.6911 0.4012 0.5038 H15 0.8031 0.0878 0.6720 0.7481 0.0912 0.6540 H16 0.1969 0.9122 0.5046 0.1911 0.9012 0.5038 O27 0.0556 0.8007 0.6074 0.0763 0.7909 0.6077 O28 0.9444 0.1993 0.5692 0.9186 0.1949 0.5671 O29 0.5556 0.3007 0.6074 0.5763 0.2909 0.6077 O30 0.4444 0.6993 0.5692 0.4186 0.6949 0.5671 H17 0.1372 0.7740 0.6359 0.2094 0.7849 0.5987 H18 0.8628 0.2260 0.5407 0.8416 0.2061 0.5329 H19 0.6372 0.2740 0.6359 0.7094 0.2849 0.5987 H20 0.3628 0.7260 0.5407 0.3416 0.7061 0.5329 H21 0.0369 0.7241 0.5840 0.0255 0.7195 0.5831 H22 0.9631 0.2759 0.5925 0.0324 0.2473 0.5611 H23 0.5369 0.2241 0.5840 0.5255 0.2195 0.5831 H24 0.4631 0.7759 0.5925 0.5324 0.7473 0.5611 O31 0.1468 0.0316 0.7898 0.1587 0.0610 0.7919 O32 0.1468 0.7684 0.8467 0.1772 0.8011 0.8431 O33 0.6468 0.5316 0.7898 0.6587 0.5610 0.7919 O34 0.6468 0.2684 0.8467 0.6772 0.3011 0.8431 H25 0.0980 0.0931 0.7628 0.1321 0.1197 0.7607 H26 0.0980 0.7069 0.8737 0.1633 0.7041 0.8348 H27 0.5980 0.5931 0.7628 0.6321 0.6197 0.7607 H28 0.5980 0.2069 0.8737 0.6633 0.2041 0.8348 H29 0.2579 0.9891 0.7737 0.2724 0.0077 0.7831 H30 0.2579 0.8109 0.8628 0.2882 0.8272 0.8219 H31 0.7579 0.4891 0.7737 0.7724 0.5077 0.7831 H32 0.7579 0.3109 0.8628 0.7882 0.3272 0.8219 O35 0.2459 0.5338 0.7894 0.2318 0.5450 0.7992 O36 0.2459 0.2662 0.8471 0.2727 0.2751 0.8492 O37 0.7459 0.0338 0.7894 0.7318 0.0450 0.7992 O38 0.7459 0.7662 0.8471 0.7727 0.7751 0.8492 H33 0.1348 0.5004 0.7711 0.1215 0.4872 0.7901 H34 0.1348 0.2996 0.8654 0.1571 0.3038 0.8651 H35 0.6348 0.0004 0.7711 0.6215 -0.0128 0.7901 H36 0.6348 0.7996 0.8654 0.6571 0.8038 0.8651 H37 0.2135 0.6200 0.8060 0.2537 0.6052 0.7682 H38 0.2135 0.1800 0.8305 0.2363 0.1946 0.8281 H39 0.7135 0.1200 0.8060 0.7537 0.1052 0.7682 H40 0.7135 0.6800 0.8305 0.7363 0.6946 0.8281 O39 0.4414 0.5159 0.8838 0.4732 0.5166 0.8895 O40 0.4414 0.2841 0.7527 0.4443 0.3247 0.7481 O42 0.9414 0.0159 0.8838 0.9732 0.0166 0.8895 O43 0.9414 0.7841 0.7527 0.9443 0.8247 0.7481 H41 0.3283 0.5281 0.9045 0.3649 0.5513 0.9076 H42 0.3283 0.2719 0.7320 0.3347 0.3174 0.7257 H44 0.8283 0.0281 0.9045 0.8649 0.0513 0.9076 H45 0.8283 0.7719 0.7320 0.8347 0.8174 0.7257 H47 0.0515 0.0218 0.9062 0.0418 -0.0398 0.9137 H48 0.0515 0.7782 0.7303 0.0550 0.7925 0.7291 H50 0.5515 0.5218 0.9062 0.5418 0.4602 0.9137 H51 0.5515 0.2782 0.7303 0.5550 0.2925 0.7291 Analytic Derivatives: Atom Derivatives fractional Derivatives Cartesian (eV/Ang) ----- -------- -------- -------- -------- -------- -------- Mg1 0.0033 -0.0021 0.0003 0.0237 -0.0211 0.0070 Mg2 0.0033 -0.0021 0.0003 0.0237 -0.0211 0.0070 Mg3 -0.0030 -0.0007 0.0004 -0.0217 -0.0065 0.0108 Mg4 -0.0030 -0.0007 0.0004 -0.0217 -0.0065 0.0108 S1 0.0017 -0.0011 -0.0010 0.0121 -0.0106 -0.0260 S2 0.0028 -0.0001 0.0015 0.0202 -0.0006 0.0386 S3 0.0017 -0.0011 -0.0010 0.0121 -0.0106 -0.0260 S4 0.0028 -0.0001 0.0015 0.0202 -0.0006 0.0386 O1 -0.0007 0.0038 0.0012 -0.0051 0.0376 0.0303 O2 -0.0017 -0.0006 -0.0004 -0.0126 -0.0063 -0.0095 O3 -0.0007 0.0038 0.0012 -0.0051 0.0376 0.0303 O4 -0.0017 -0.0006 -0.0004 -0.0126 -0.0063 -0.0095 O6 0.0055 -0.0008 -0.0004 0.0399 -0.0082 -0.0113 O7 -0.0019 -0.0000 0.0003 -0.0139 -0.0001 0.0075 O9 0.0055 -0.0008 -0.0004 0.0399 -0.0082 -0.0113 O10 -0.0019 -0.0000 0.0003 -0.0139 -0.0001 0.0075 O11 0.0081 0.0025 -0.0002 0.0583 0.0248 -0.0039 O12 0.0000 -0.0002 -0.0000 0.0004 -0.0021 -0.0012 O13 0.0081 0.0025 -0.0002 0.0583 0.0248 -0.0039 O14 0.0000 -0.0002 -0.0000 0.0004 -0.0021 -0.0012 O15 -0.0081 -0.0045 -0.0005 -0.0582 -0.0448 -0.0125 maximum gradient = 0.0745 O16 0.0016 0.0008 -0.0002 0.0114 0.0081 -0.0043 O17 -0.0081 -0.0045 -0.0005 -0.0582 -0.0448 -0.0125 O18 0.0016 0.0008 -0.0002 0.0114 0.0081 -0.0043 O19 -0.0030 0.0024 0.0004 -0.0215 0.0240 0.0096 O20 0.0012 0.0024 0.0005 0.0083 0.0236 0.0117 O21 -0.0030 0.0024 0.0004 -0.0215 0.0240 0.0096 O22 0.0012 0.0024 0.0005 0.0083 0.0236 0.0117 H1 -0.0029 -0.0024 -0.0004 -0.0212 -0.0236 -0.0114 H2 0.0005 -0.0029 -0.0008 0.0038 -0.0283 -0.0209 H3 -0.0029 -0.0024 -0.0004 -0.0212 -0.0236 -0.0114 H4 0.0005 -0.0029 -0.0008 0.0038 -0.0283 -0.0209 H5 0.0006 -0.0010 0.0004 0.0040 -0.0102 0.0101 H6 -0.0008 -0.0005 -0.0002 -0.0061 -0.0054 -0.0059 H7 0.0006 -0.0010 0.0004 0.0040 -0.0102 0.0101 H8 -0.0008 -0.0005 -0.0002 -0.0061 -0.0054 -0.0059 O23 -0.0022 0.0005 -0.0000 -0.0156 0.0046 -0.0007 O24 -0.0032 0.0009 0.0008 -0.0227 0.0090 0.0200 O25 -0.0022 0.0005 -0.0000 -0.0156 0.0046 -0.0007 O26 -0.0032 0.0009 0.0008 -0.0227 0.0090 0.0200 H9 -0.0011 -0.0011 -0.0004 -0.0076 -0.0110 -0.0108 H10 -0.0006 -0.0013 0.0008 -0.0045 -0.0129 0.0205 H11 -0.0011 -0.0011 -0.0004 -0.0076 -0.0110 -0.0108 H12 -0.0006 -0.0013 0.0008 -0.0045 -0.0129 0.0205 H13 -0.0033 0.0011 -0.0011 -0.0235 0.0111 -0.0291 H14 0.0011 0.0008 0.0001 0.0082 0.0077 0.0015 H15 -0.0033 0.0011 -0.0011 -0.0235 0.0111 -0.0291 H16 0.0011 0.0008 0.0001 0.0082 0.0077 0.0015 O27 0.0007 -0.0002 0.0006 0.0053 -0.0020 0.0167 O28 -0.0049 -0.0014 -0.0018 -0.0354 -0.0137 -0.0456 O29 0.0007 -0.0002 0.0006 0.0053 -0.0020 0.0167 O30 -0.0049 -0.0014 -0.0018 -0.0354 -0.0137 -0.0456 H17 -0.0034 0.0017 -0.0005 -0.0244 0.0163 -0.0133 H18 0.0008 0.0003 0.0007 0.0058 0.0027 0.0182 H19 -0.0034 0.0017 -0.0005 -0.0244 0.0163 -0.0133 H20 0.0008 0.0003 0.0007 0.0058 0.0027 0.0182 H21 -0.0012 -0.0015 0.0003 -0.0086 -0.0149 0.0068 H22 0.0021 0.0016 -0.0001 0.0151 0.0158 -0.0036 H23 -0.0012 -0.0015 0.0003 -0.0086 -0.0149 0.0068 H24 0.0021 0.0016 -0.0001 0.0151 0.0158 -0.0036 O31 0.0009 0.0008 -0.0013 0.0068 0.0082 -0.0334 O32 0.0018 0.0007 -0.0001 0.0131 0.0072 -0.0014 O33 0.0009 0.0008 -0.0013 0.0068 0.0082 -0.0334 O34 0.0018 0.0007 -0.0001 0.0131 0.0072 -0.0014 H25 0.0043 0.0021 -0.0001 0.0307 0.0206 -0.0020 H26 0.0017 0.0003 -0.0006 0.0122 0.0031 -0.0147 H27 0.0043 0.0021 -0.0001 0.0307 0.0206 -0.0020 H28 0.0017 0.0003 -0.0006 0.0122 0.0031 -0.0147 H29 0.0020 0.0009 -0.0016 0.0146 0.0092 -0.0421 H30 -0.0008 -0.0017 0.0013 -0.0055 -0.0170 0.0348 H31 0.0020 0.0009 -0.0016 0.0146 0.0092 -0.0421 H32 -0.0008 -0.0017 0.0013 -0.0055 -0.0170 0.0348 O35 0.0005 0.0008 -0.0010 0.0037 0.0082 -0.0264 O36 0.0028 0.0018 0.0007 0.0201 0.0180 0.0178 O37 0.0005 0.0008 -0.0010 0.0037 0.0082 -0.0264 O38 0.0028 0.0018 0.0007 0.0201 0.0180 0.0178 H33 -0.0049 -0.0020 0.0003 -0.0354 -0.0203 0.0086 H34 0.0019 0.0025 -0.0003 0.0140 0.0250 -0.0079 H35 -0.0049 -0.0020 0.0003 -0.0354 -0.0203 0.0086 H36 0.0019 0.0025 -0.0003 0.0140 0.0250 -0.0079 H37 -0.0015 0.0024 0.0017 -0.0106 0.0241 0.0434 H38 0.0008 -0.0024 -0.0000 0.0058 -0.0237 -0.0001 H39 -0.0015 0.0024 0.0017 -0.0106 0.0241 0.0434 H40 0.0008 -0.0024 -0.0000 0.0058 -0.0237 -0.0001 O39 -0.0043 -0.0016 0.0002 -0.0311 -0.0159 0.0064 O40 0.0004 -0.0029 -0.0022 0.0032 -0.0284 -0.0577 O42 -0.0043 -0.0016 0.0002 -0.0311 -0.0159 0.0064 O43 0.0004 -0.0029 -0.0022 0.0032 -0.0284 -0.0577 H41 0.0033 -0.0003 0.0004 0.0237 -0.0028 0.0092 H42 -0.0012 -0.0003 0.0012 -0.0087 -0.0030 0.0305 H44 0.0033 -0.0003 0.0004 0.0237 -0.0028 0.0092 H45 -0.0012 -0.0003 0.0012 -0.0087 -0.0030 0.0305 H47 -0.0027 -0.0006 0.0004 -0.0193 -0.0060 0.0091 H48 0.0068 0.0031 0.0010 0.0490 0.0302 0.0267 H50 -0.0027 -0.0006 0.0004 -0.0193 -0.0060 0.0091 H51 0.0068 0.0031 0.0010 0.0490 0.0302 0.0267 Atomic partial charges (electron charges): Atom s p d total ----- -------- -------- -------- -------- Mg1 0.268 0.393 0.246 0.907 Mg2 0.268 0.393 0.246 0.907 Mg3 0.268 0.402 0.255 0.925 Mg4 0.268 0.402 0.255 0.925 S1 1.053 1.906 0.811 3.770 S2 1.056 1.901 0.797 3.755 S3 1.053 1.906 0.811 3.770 S4 1.056 1.902 0.797 3.755 O1 1.268 2.904 0.016 4.187 O2 1.271 2.889 0.017 4.176 O3 1.268 2.904 0.016 4.187 O4 1.271 2.894 0.017 4.182 O6 1.262 2.890 0.012 4.165 O7 1.285 2.870 0.021 4.176 O9 1.262 2.890 0.012 4.165 O10 1.285 2.862 0.021 4.168 O11 1.276 2.901 0.020 4.196 O12 1.264 2.878 0.012 4.154 O13 1.276 2.901 0.020 4.196 O14 1.264 2.878 0.012 4.154 O15 1.267 2.907 0.016 4.190 O16 1.266 2.896 0.015 4.177 O17 1.267 2.907 0.016 4.190 O18 1.266 2.891 0.015 4.172 O19 1.238 2.982 0.013 4.233 O20 1.235 2.969 0.010 4.214 O21 1.238 2.982 0.013 4.233 O22 1.235 2.969 0.010 4.214 H1 0.155 0.006 0.000 0.161 H2 0.132 0.006 0.000 0.138 H3 0.155 0.006 0.000 0.161 H4 0.132 0.006 0.000 0.138 H5 0.152 0.006 0.000 0.159 H6 0.140 0.006 0.000 0.147 H7 0.152 0.006 0.000 0.159 H8 0.140 0.006 0.000 0.147 O23 1.244 2.959 0.014 4.217 O24 1.230 2.998 0.010 4.238 O25 1.244 2.959 0.014 4.217 O26 1.230 2.997 0.010 4.237 H9 0.154 0.006 0.000 0.160 H10 0.143 0.006 0.000 0.149 H11 0.154 0.006 0.000 0.160 H12 0.143 0.006 0.000 0.149 H13 0.154 0.006 0.000 0.161 H14 0.143 0.006 0.000 0.149 H15 0.154 0.006 0.000 0.161 H16 0.143 0.006 0.000 0.149 O27 1.241 2.953 0.012 4.206 O28 1.237 2.963 0.011 4.210 O29 1.241 2.953 0.012 4.206 O30 1.237 2.963 0.011 4.210 H17 0.150 0.006 0.000 0.157 H18 0.128 0.006 0.000 0.134 H19 0.150 0.006 0.000 0.157 H20 0.128 0.006 0.000 0.134 H21 0.137 0.006 0.000 0.143 H22 0.151 0.006 0.000 0.158 H23 0.137 0.006 0.000 0.143 H24 0.151 0.006 0.000 0.158 O31 1.237 2.975 0.011 4.223 O32 1.239 2.967 0.012 4.218 O33 1.237 2.975 0.011 4.223 O34 1.239 2.967 0.012 4.218 H25 0.137 0.006 0.000 0.144 H26 0.149 0.006 0.000 0.155 H27 0.137 0.006 0.000 0.144 H28 0.149 0.006 0.000 0.155 H29 0.144 0.006 0.000 0.150 H30 0.143 0.006 0.000 0.149 H31 0.144 0.006 0.000 0.150 H32 0.143 0.006 0.000 0.149 O35 1.236 2.976 0.011 4.222 O36 1.238 2.970 0.013 4.220 O37 1.236 2.976 0.011 4.222 O38 1.238 2.970 0.013 4.220 H33 0.140 0.006 0.000 0.147 H34 0.158 0.006 0.000 0.164 H35 0.140 0.006 0.000 0.147 H36 0.158 0.006 0.000 0.164 H37 0.138 0.006 0.000 0.145 H38 0.142 0.006 0.000 0.148 H39 0.138 0.006 0.000 0.145 H40 0.142 0.006 0.000 0.148 O39 1.242 2.964 0.014 4.219 O40 1.228 3.005 0.011 4.244 O42 1.242 2.964 0.014 4.219 O43 1.228 3.005 0.011 4.244 H41 0.156 0.006 0.000 0.162 H42 0.147 0.006 0.000 0.153 H44 0.156 0.006 0.000 0.162 H45 0.147 0.006 0.000 0.153 H47 0.155 0.006 0.000 0.161 H48 0.144 0.006 0.000 0.151 H50 0.155 0.006 0.000 0.161 H51 0.144 0.006 0.000 0.151 Analysis of the electronic structure: The system is a semiconductor with a direct gap of 0.044 eV. The valence band (#160) maximum is located near (0.00 0.00 0.00), at -0.043 eV with respect to the Fermi level. The conduction band (#161) minimum is located near (0.00 0.00 0.00), at 0.001 eV with respect to the Fermi level. The center of the gap is located at -0.021248 eV with respect to the Fermi level. The Fermi energy is used as the zero of the energy scale. Job completed on Sat 01 April 2023 at 21:51:49 CST after 214602 s (59:36:42) Entire job completed on Sat 01 April 2023 at 21:51:49 CST after 214603 s (59:36:43) and running 1 tasks.