[Thu Mar 16 15:23:04 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 700.000 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 700.00 eV VASP energy: -505.923083 eV for Mg4S4O40H48 cell Initial VASP energy: -441.512080 eV for Mg4S4O40H48 cell Relaxation energy: -64.411003 eV gained after 46 optimization steps. Electronic contributions: Empirical Formula Cell MgSO10H12 (MgSO10H12)4 ----------------- ----------------- VASP Energy -126.480771 -505.923083 eV = -12203.536 -48814.145 kJ/mol Cell parameters: Parameter Original change Final % ---------- ------------ ---------- ------------ ----- a 9.975000 0.138320 10.113320 1.4 b 6.146935 0.067886 6.214821 1.1 c 24.267000 0.474419 24.741419 2.0 alpha 97.114335 0.895338 98.009673 0.9 beta 98.780000 1.080756 99.860756 1.1 gamma 35.769016 -0.222653 35.546363 -0.6 Volume 859.541749 31.154261 890.696010 3.6 Density: 1.704 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: 52.599 MPa = 525.992 bar XX YY ZZ YZ XZ XY Stress: -51.326 -57.822 -48.650 -0.000 93.870 -0.000 MPa = -513.262 -578.216 -486.500 -0.000 938.701 -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 0.0610 0.8779 0.2500 0.0600 0.8801 0.2500 Mg4 0.9390 0.1221 0.7500 0.9400 0.1199 0.7500 S1 0.4226 0.8928 0.1231 0.4225 0.8948 0.1233 S2 0.6845 0.8928 0.3769 0.6827 0.8948 0.3767 S3 0.5774 0.1072 0.8769 0.5775 0.1052 0.8767 S4 0.3155 0.1072 0.6231 0.3173 0.1052 0.6233 O1 0.1818 0.1867 0.1360 0.1800 0.1912 0.1354 O2 0.6315 0.1867 0.3640 0.6288 0.1912 0.3646 O3 0.8182 0.8133 0.8640 0.8200 0.8088 0.8646 O4 0.3685 0.8133 0.6360 0.3712 0.8088 0.6354 O5 0.5471 0.8825 0.1664 0.5474 0.8817 0.1680 O6 0.5703 0.8825 0.3336 0.5709 0.8817 0.3320 O7 0.4529 0.1175 0.8336 0.4526 0.1183 0.8320 O8 0.4297 0.1175 0.6664 0.4291 0.1183 0.6680 O9 0.4217 0.9773 0.0683 0.4230 0.9807 0.0697 O10 0.6010 0.9773 0.4317 0.5963 0.9807 0.4303 O11 0.5783 0.0227 0.9317 0.5770 0.0193 0.9303 O12 0.3990 0.0227 0.5683 0.4037 0.0193 0.5697 O13 0.5348 0.5297 0.1192 0.5354 0.5288 0.1179 O14 0.9355 0.5297 0.3808 0.9358 0.5288 0.3821 O15 0.4652 0.4703 0.8808 0.4646 0.4712 0.8821 O16 0.0645 0.4703 0.6192 0.0642 0.4712 0.6179 O17 0.8715 0.4318 0.0468 0.8683 0.4388 0.0473 O18 0.6967 0.4318 0.4532 0.6929 0.4388 0.4527 O19 0.1285 0.5682 0.9532 0.1317 0.5612 0.9527 O20 0.3033 0.5682 0.5468 0.3071 0.5612 0.5473 H1 0.9490 0.3880 0.0748 -0.0335 0.3781 0.0798 H2 0.6630 0.3880 0.4252 0.6554 0.3781 0.4202 H3 0.0510 0.6120 0.9252 0.0335 0.6219 0.9202 H4 0.3370 0.6120 0.5748 0.3446 0.6219 0.5798 H5 0.7470 0.6040 0.0558 0.7092 0.6449 0.0570 H6 0.6490 0.6040 0.4442 0.6459 0.6449 0.4430 H7 0.2530 0.3960 0.9442 0.2908 0.3551 0.9430 H8 0.3510 0.3960 0.5558 0.3541 0.3551 0.5570 O21 0.2108 0.6494 0.0672 0.2124 0.6495 0.0676 O22 0.1398 0.6494 0.4328 0.1382 0.6495 0.4324 O23 0.7892 0.3506 0.9328 0.7876 0.3505 0.9324 O24 0.8602 0.3506 0.5672 0.8618 0.3505 0.5676 H9 0.2740 0.4540 0.0681 0.2790 0.4147 0.0670 H10 0.2720 0.4540 0.4319 0.3063 0.4147 0.4330 H11 0.7260 0.5460 0.9319 0.7210 0.5853 0.9330 H12 0.7280 0.5460 0.5681 0.6937 0.5853 0.5670 H13 0.3020 0.6180 0.0868 0.3250 0.6028 0.0896 H14 0.0800 0.6180 0.4132 0.0722 0.6028 0.4104 H15 0.6980 0.3820 0.9132 0.6750 0.3972 0.9104 H16 0.9200 0.3820 0.5868 0.9278 0.3972 0.5896 O25 0.7594 0.1042 0.0214 0.7592 0.1044 0.0207 O26 0.1364 0.1042 0.4786 0.1364 0.1044 0.4793 O27 0.2406 0.8958 0.9786 0.2408 -0.1044 0.9793 O28 0.8636 0.8958 0.5214 0.8636 -0.1044 0.5207 H17 0.6790 0.2460 0.0456 0.6663 0.2628 0.0515 H18 0.0750 0.2460 0.4544 0.0709 0.2628 0.4485 H19 0.3210 0.7540 0.9544 0.3337 0.7372 0.9485 H20 0.9250 0.7540 0.5456 0.9291 0.7372 0.5515 H21 0.7110 0.0640 0.0008 0.6915 0.0668 -0.0036 H22 0.2250 0.0640 0.4992 0.2416 0.0668 0.5036 H23 0.2890 0.9360 0.9992 0.3085 0.9332 0.0036 H24 0.7750 0.9360 0.5008 0.7584 0.9332 0.4964 O29 0.7422 0.2884 0.2819 0.7353 0.2941 0.2815 O30 0.9694 0.2884 0.2181 0.9706 0.2941 0.2185 O31 0.2578 0.7116 0.7181 0.2647 0.7059 0.7185 O32 0.0306 0.7116 0.7819 0.0294 0.7059 0.7815 H25 0.7350 0.2120 0.3027 0.7334 0.1982 0.3097 H26 0.0530 0.2120 0.1973 0.0684 0.1982 0.1903 H27 0.2650 0.7880 0.6973 0.2666 0.8018 0.6903 H28 0.9470 0.7880 0.8027 0.9316 0.8018 0.8097 H29 0.6850 0.4780 0.2957 0.6728 0.5162 0.2991 H30 0.8370 0.4780 0.2043 0.8111 0.5162 0.2009 H31 0.3150 0.5220 0.7043 0.3272 0.4838 0.7009 H32 0.1630 0.5220 0.7957 0.1889 0.4838 0.7991 O33 0.1425 0.4830 0.2806 0.1391 0.4881 0.2813 O34 0.3745 0.4830 0.2194 0.3728 0.4881 0.2187 O35 0.8575 0.5170 0.7194 0.8609 0.5119 0.7187 O36 0.6255 0.5170 0.7806 0.6272 0.5119 0.7813 H33 0.2640 0.3000 0.2958 0.2913 0.2664 0.3009 H34 0.4360 0.3000 0.2042 0.4423 0.2664 0.1991 H35 0.7360 0.7000 0.7042 0.7087 0.7336 0.6991 H36 0.5640 0.7000 0.7958 0.5577 0.7336 0.8009 H37 0.0900 0.4400 0.2715 0.0779 0.4248 0.2649 H38 0.4700 0.4400 0.2285 0.4973 0.4248 0.2351 H39 0.9100 0.5600 0.7285 -0.0779 0.5752 0.7351 H40 0.5300 0.5600 0.7715 0.5027 0.5752 0.7649 O37 0.9180 0.8810 0.1793 0.9133 0.8860 0.1792 O38 0.2010 0.8810 0.3207 0.2007 0.8860 0.3208 O39 0.0820 0.1190 0.8207 0.0867 0.1140 0.8208 O40 0.7990 0.1190 0.6793 0.7993 0.1140 0.6792 H41 0.9930 0.6900 0.1627 0.0052 0.6582 0.1575 H42 0.3170 0.6900 0.3373 0.3365 0.6582 0.3425 H43 0.0070 0.3100 0.8373 -0.0052 0.3418 0.8425 H44 0.6830 0.3100 0.6627 0.6635 0.3418 0.6575 H45 0.8070 0.0660 0.1592 0.7883 0.1023 0.1545 H46 0.1270 0.0660 0.3408 0.1095 0.1023 0.3455 H47 0.1930 0.9340 0.8408 0.2117 0.8977 0.8455 H48 0.8730 0.9340 0.6592 0.8905 0.8977 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 -0.0039 0.0078 0.0000 -0.0000 0.0281 0.0000 Mg4 0.0039 -0.0078 0.0000 0.0000 -0.0281 0.0000 S1 0.0000 0.0011 -0.0004 0.0073 0.0041 -0.0099 S2 -0.0012 0.0011 0.0004 -0.0073 0.0041 0.0099 S3 -0.0000 -0.0011 0.0004 -0.0073 -0.0041 0.0099 S4 0.0012 -0.0011 -0.0004 0.0073 -0.0041 -0.0099 O1 -0.0028 0.0003 -0.0000 -0.0261 0.0012 -0.0004 O2 0.0025 0.0003 0.0000 0.0261 0.0012 0.0004 O3 0.0028 -0.0003 0.0000 0.0261 -0.0012 0.0004 O4 -0.0025 -0.0003 -0.0000 -0.0261 -0.0012 -0.0004 O5 0.0067 -0.0071 0.0011 0.0272 -0.0256 0.0263 O6 0.0004 -0.0071 -0.0011 -0.0272 -0.0256 -0.0263 O7 -0.0067 0.0071 -0.0011 -0.0272 0.0256 -0.0263 O8 -0.0004 0.0071 0.0011 0.0272 0.0256 0.0263 O9 -0.0037 0.0099 -0.0010 0.0153 0.0354 -0.0230 O10 -0.0061 0.0099 0.0010 -0.0153 0.0354 0.0230 O11 0.0037 -0.0099 0.0010 -0.0153 -0.0354 0.0230 O12 0.0061 -0.0099 -0.0010 0.0153 -0.0354 -0.0230 O13 0.0005 -0.0068 0.0003 -0.0305 -0.0245 0.0064 O14 0.0064 -0.0068 -0.0003 0.0305 -0.0245 -0.0064 O15 -0.0005 0.0068 -0.0003 0.0305 0.0245 -0.0064 O16 -0.0064 0.0068 0.0003 -0.0305 0.0245 0.0064 O17 -0.0005 -0.0012 -0.0004 -0.0094 -0.0042 -0.0098 O18 0.0017 -0.0012 0.0004 0.0094 -0.0042 0.0098 O19 0.0005 0.0012 0.0004 0.0094 0.0042 0.0098 O20 -0.0017 0.0012 -0.0004 -0.0094 0.0042 -0.0098 H1 -0.0018 -0.0014 -0.0004 -0.0229 -0.0049 -0.0093 H2 0.0031 -0.0014 0.0004 0.0229 -0.0049 0.0093 H3 0.0018 0.0014 0.0004 0.0229 0.0049 0.0093 H4 -0.0031 0.0014 -0.0004 -0.0229 0.0049 -0.0093 H5 0.0025 -0.0042 0.0000 0.0035 -0.0151 0.0007 H6 0.0017 -0.0042 -0.0000 -0.0035 -0.0151 -0.0007 H7 -0.0025 0.0042 -0.0000 -0.0035 0.0151 -0.0007 H8 -0.0017 0.0042 0.0000 0.0035 0.0151 0.0007 O21 -0.0004 0.0024 -0.0003 0.0095 0.0087 -0.0068 O22 -0.0021 0.0024 0.0003 -0.0095 0.0087 0.0068 O23 0.0004 -0.0024 0.0003 -0.0095 -0.0087 0.0068 O24 0.0021 -0.0024 -0.0003 0.0095 -0.0087 -0.0068 H9 0.0024 -0.0060 -0.0003 -0.0051 -0.0217 -0.0062 H10 0.0036 -0.0060 0.0003 0.0051 -0.0217 0.0062 H11 -0.0024 0.0060 0.0003 0.0051 0.0217 0.0062 H12 -0.0036 0.0060 -0.0003 -0.0051 0.0217 -0.0062 H13 -0.0027 0.0021 -0.0006 -0.0145 0.0074 -0.0136 H14 0.0006 0.0021 0.0006 0.0145 0.0074 0.0136 H15 0.0027 -0.0021 0.0006 0.0145 -0.0074 0.0136 H16 -0.0006 -0.0021 -0.0006 -0.0145 -0.0074 -0.0136 O25 -0.0042 0.0013 0.0012 -0.0398 0.0046 0.0280 maximum gradient = 0.0489 O26 0.0029 0.0013 -0.0012 0.0398 0.0046 -0.0280 O27 0.0042 -0.0013 -0.0012 0.0398 -0.0046 -0.0280 O28 -0.0029 -0.0013 0.0012 -0.0398 -0.0046 0.0280 H17 0.0014 -0.0019 -0.0007 0.0074 -0.0069 -0.0178 H18 0.0005 -0.0019 0.0007 -0.0074 -0.0069 0.0178 H19 -0.0014 0.0019 0.0007 -0.0074 0.0069 0.0178 H20 -0.0005 0.0019 -0.0007 0.0074 0.0069 -0.0178 H21 0.0023 -0.0004 -0.0007 0.0235 -0.0014 -0.0176 H22 -0.0019 -0.0004 0.0007 -0.0235 -0.0014 0.0176 H23 -0.0023 0.0004 0.0007 -0.0235 0.0014 0.0176 H24 0.0019 0.0004 -0.0007 0.0235 0.0014 -0.0176 O29 -0.0057 0.0070 0.0007 -0.0250 0.0250 0.0177 O30 -0.0012 0.0070 -0.0007 0.0250 0.0250 -0.0177 O31 0.0057 -0.0070 -0.0007 0.0250 -0.0250 -0.0177 O32 0.0012 -0.0070 0.0007 -0.0250 -0.0250 0.0177 H25 0.0035 -0.0018 0.0005 0.0237 -0.0065 0.0110 H26 -0.0016 -0.0018 -0.0005 -0.0237 -0.0065 -0.0110 H27 -0.0035 0.0018 -0.0005 -0.0237 0.0065 -0.0110 H28 0.0016 0.0018 0.0005 0.0237 0.0065 0.0110 H29 0.0054 -0.0113 -0.0001 -0.0027 -0.0405 -0.0017 H30 0.0059 -0.0113 0.0001 0.0027 -0.0405 0.0017 H31 -0.0054 0.0113 0.0001 0.0027 0.0405 0.0017 H32 -0.0059 0.0113 -0.0001 -0.0027 0.0405 -0.0017 O33 0.0003 -0.0047 -0.0016 -0.0149 -0.0170 -0.0380 O34 0.0044 -0.0047 0.0016 0.0149 -0.0170 0.0380 O35 -0.0003 0.0047 0.0016 0.0149 0.0170 0.0380 O36 -0.0044 0.0047 -0.0016 -0.0149 0.0170 -0.0380 H33 -0.0025 0.0028 -0.0003 -0.0101 0.0099 -0.0078 H34 -0.0002 0.0028 0.0003 0.0101 0.0099 0.0078 H35 0.0025 -0.0028 0.0003 0.0101 -0.0099 0.0078 H36 0.0002 -0.0028 -0.0003 -0.0101 -0.0099 -0.0078 H37 -0.0000 0.0005 -0.0007 0.0046 0.0019 -0.0159 H38 -0.0005 0.0005 0.0007 -0.0046 0.0019 0.0159 H39 0.0000 -0.0005 0.0007 -0.0046 -0.0019 0.0159 H40 0.0005 -0.0005 -0.0007 0.0046 -0.0019 -0.0159 O37 0.0046 -0.0070 -0.0003 0.0119 -0.0251 -0.0075 O38 0.0024 -0.0070 0.0003 -0.0119 -0.0251 0.0075 O39 -0.0046 0.0070 0.0003 -0.0119 0.0251 0.0075 O40 -0.0024 0.0070 -0.0003 0.0119 0.0251 -0.0075 H41 -0.0006 0.0013 0.0001 0.0002 0.0047 0.0033 H42 -0.0007 0.0013 -0.0001 -0.0002 0.0047 -0.0033 H43 0.0006 -0.0013 -0.0001 -0.0002 -0.0047 -0.0033 H44 0.0007 -0.0013 0.0001 0.0002 -0.0047 0.0033 H45 -0.0004 0.0043 0.0013 0.0125 0.0154 0.0308 H46 -0.0039 0.0043 -0.0013 -0.0125 0.0154 -0.0308 H47 0.0004 -0.0043 -0.0013 -0.0125 -0.0154 -0.0308 H48 0.0039 -0.0043 0.0013 0.0125 -0.0154 0.0308 Atomic partial charges (electron charges): Atom s p d total ----- -------- -------- -------- -------- Mg1 0.260 0.398 0.258 0.916 Mg2 0.260 0.398 0.258 0.916 Mg3 0.256 0.386 0.247 0.889 Mg4 0.256 0.386 0.247 0.889 S1 1.052 1.898 0.803 3.753 S2 1.052 1.898 0.803 3.753 S3 1.052 1.898 0.803 3.753 S4 1.052 1.898 0.803 3.753 O1 1.265 2.898 0.015 4.178 O2 1.265 2.898 0.015 4.178 O3 1.265 2.898 0.015 4.178 O4 1.265 2.898 0.015 4.178 O5 1.265 2.905 0.016 4.186 O6 1.265 2.905 0.016 4.186 O7 1.265 2.905 0.016 4.186 O8 1.265 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 2.899 0.015 4.180 O14 1.266 2.899 0.015 4.180 O15 1.266 2.899 0.015 4.180 O16 1.266 2.899 0.015 4.180 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 2.986 0.012 4.231 O22 1.233 2.986 0.012 4.231 O23 1.233 2.986 0.012 4.231 O24 1.233 2.986 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 1.232 2.987 0.012 4.231 O26 1.232 2.987 0.012 4.231 O27 1.232 2.987 0.012 4.231 O28 1.232 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 0.149 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 2.987 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 4.231 O38 1.231 2.988 0.012 4.231 O39 1.231 2.988 0.012 4.231 O40 1.231 2.988 0.012 4.231 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 0.154 H46 0.147 0.006 0.000 0.154 H47 0.147 0.006 0.000 0.154 H48 0.147 0.006 0.000 0.154 Analysis of the electronic structure: The system is an insulator with an indirect gap of 5.225 eV. The valence band (#160) maximum is located near (0.33 0.00 0.00), at -0.253 eV with respect to the Fermi level. The conduction band (#161) minimum is located near (0.00 0.00 0.00), at 4.972 eV with respect to the Fermi level. The center of the gap is located at 2.359330 eV with respect to the Fermi level. The Fermi energy is used as the zero of the energy scale. Job completed on Thu 16 March 2023 at 22:51:25 CST after 26897 s (7:28:17) Entire job completed on Thu 16 March 2023 at 22:51:25 CST after 26897 s (7:28:17) and running 1 tasks.