[Fri Mar 17 08:33:39 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-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 0.435 x 0.258 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 700.00 eV VASP energy: -506.021707 eV for Mg4S4O40H48 cell Initial VASP energy: -505.999680 eV for Mg4S4O40H48 cell Relaxation energy: -0.022027 eV gained after 44 optimization steps. Electronic contributions: Empirical Formula Cell MgSO10H12 (MgSO10H12)4 ----------------- ----------------- VASP Energy -126.505427 -506.021707 eV = -12205.915 -48823.661 kJ/mol Cell parameters: Parameter Original change Final % ---------- ------------ ---------- ------------ ----- a 10.113320 0.020675 10.133996 0.2 b 6.214821 0.004948 6.219769 0.1 c 24.741419 0.189340 24.930759 0.8 alpha 98.009673 0.386779 98.396452 0.4 beta 99.860756 0.464890 100.325645 0.5 gamma 35.546363 -0.100129 35.446234 -0.3 Volume 890.696010 5.868590 896.564600 0.7 Density: 1.693 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: -18.229 MPa = -182.293 bar XX YY ZZ YZ XZ XY Stress: 0.521 16.847 37.320 -0.000 20.454 0.000 MPa = 5.207 168.470 373.201 -0.000 204.544 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 0.0600 0.8801 0.2500 0.0607 0.8786 0.2500 Mg4 0.9400 0.1199 0.7500 0.9393 0.1214 0.7500 S1 0.4225 0.8948 0.1233 0.4229 0.8930 0.1234 S2 0.6827 0.8948 0.3767 0.6841 0.8930 0.3766 S3 0.5775 0.1052 0.8767 0.5771 0.1070 0.8766 S4 0.3173 0.1052 0.6233 0.3159 0.1070 0.6234 O1 0.1800 0.1912 0.1354 0.1806 0.1889 0.1354 O2 0.6288 0.1912 0.3646 0.6305 0.1889 0.3646 O3 0.8200 0.8088 0.8646 0.8194 0.8111 0.8646 O4 0.3712 0.8088 0.6354 0.3695 0.8111 0.6354 O5 0.5474 0.8817 0.1680 0.5488 0.8787 0.1680 O6 0.5709 0.8817 0.3320 0.5725 0.8787 0.3320 O7 0.4526 0.1183 0.8320 0.4512 0.1213 0.8320 O8 0.4291 0.1183 0.6680 0.4275 0.1213 0.6680 O9 0.4230 0.9807 0.0697 0.4219 0.9806 0.0702 O10 0.5963 0.9807 0.4303 0.5975 0.9806 0.4298 O11 0.5770 0.0193 0.9303 0.5781 0.0194 0.9298 O12 0.4037 0.0193 0.5697 0.4025 0.0194 0.5702 O13 0.5354 0.5288 0.1179 0.5364 0.5260 0.1177 O14 0.9358 0.5288 0.3821 0.9376 0.5260 0.3823 O15 0.4646 0.4712 0.8821 0.4636 0.4740 0.8823 O16 0.0642 0.4712 0.6179 0.0624 0.4740 0.6177 O17 0.8683 0.4388 0.0473 0.8675 0.4372 0.0477 O18 0.6929 0.4388 0.4527 0.6953 0.4372 0.4523 O19 0.1317 0.5612 0.9527 0.1325 0.5628 0.9523 O20 0.3071 0.5612 0.5473 0.3047 0.5628 0.5477 H1 0.9665 0.3781 0.0798 0.9660 0.3749 0.0802 H2 0.6554 0.3781 0.4202 0.6591 0.3749 0.4198 H3 0.0335 0.6219 0.9202 0.0340 0.6251 0.9198 H4 0.3446 0.6219 0.5798 0.3409 0.6251 0.5802 H5 0.7092 0.6449 0.0570 0.7086 0.6421 0.0572 H6 0.6459 0.6449 0.4430 0.6493 0.6421 0.4428 H7 0.2908 0.3551 0.9430 0.2914 0.3579 0.9428 H8 0.3541 0.3551 0.5570 0.3507 0.3579 0.5572 O21 0.2124 0.6495 0.0676 0.2147 0.6457 0.0666 O22 0.1382 0.6495 0.4324 0.1397 0.6457 0.4334 O23 0.7876 0.3505 0.9324 0.7853 0.3543 0.9334 O24 0.8618 0.3505 0.5676 0.8603 0.3543 0.5666 H9 0.2790 0.4147 0.0670 0.2800 0.4121 0.0665 H10 0.3063 0.4147 0.4330 0.3079 0.4121 0.4335 H11 0.7210 0.5853 0.9330 0.7200 0.5879 0.9335 H12 0.6937 0.5853 0.5670 0.6921 0.5879 0.5665 H13 0.3250 0.6028 0.0896 0.3271 0.5992 0.0888 H14 0.0722 0.6028 0.4104 0.0737 0.5992 0.4112 H15 0.6750 0.3972 0.9104 0.6729 0.4008 0.9112 H16 0.9278 0.3972 0.5896 0.9263 0.4008 0.5888 O25 0.7592 0.1044 0.0207 0.7609 0.1000 0.0201 O26 0.1364 0.1044 0.4793 0.1391 0.1000 0.4799 O27 0.2408 0.8956 0.9793 0.2391 0.9000 0.9799 O28 0.8636 0.8956 0.5207 0.8609 0.9000 0.5201 H17 0.6663 0.2628 0.0515 0.6675 0.2585 0.0506 H18 0.0709 0.2628 0.4485 0.0740 0.2585 0.4494 H19 0.3337 0.7372 0.9485 0.3325 0.7415 0.9494 H20 0.9291 0.7372 0.5515 0.9260 0.7415 0.5506 H21 0.6915 0.0668 0.9964 0.6918 0.0668 0.9950 H22 0.2416 0.0668 0.5036 0.2414 0.0668 0.5050 H23 0.3085 0.9332 0.0036 0.3082 0.9332 0.0050 H24 0.7584 0.9332 0.4964 0.7586 0.9332 0.4950 O29 0.7353 0.2941 0.2815 0.7372 0.2897 0.2822 O30 0.9706 0.2941 0.2185 0.9731 0.2897 0.2178 O31 0.2647 0.7059 0.7185 0.2628 0.7103 0.7178 O32 0.0294 0.7059 0.7815 0.0269 0.7103 0.7822 H25 0.7334 0.1982 0.3097 0.7415 0.1877 0.3106 H26 0.0684 0.1982 0.1903 0.0708 0.1877 0.1894 H27 0.2666 0.8018 0.6903 0.2585 0.8123 0.6894 H28 0.9316 0.8018 0.8097 0.9292 0.8123 0.8106 H29 0.6728 0.5162 0.2991 0.6761 0.5106 0.2999 H30 0.8111 0.5162 0.2009 0.8134 0.5106 0.2001 H31 0.3272 0.4838 0.7009 0.3239 0.4894 0.7001 H32 0.1889 0.4838 0.7991 0.1866 0.4894 0.7999 O33 0.1391 0.4881 0.2813 0.1393 0.4838 0.2791 O34 0.3728 0.4881 0.2187 0.3769 0.4838 0.2209 O35 0.8609 0.5119 0.7187 0.8607 0.5162 0.7209 O36 0.6272 0.5119 0.7813 0.6231 0.5162 0.7791 H33 0.2913 0.2664 0.3009 0.2899 0.2635 0.2993 H34 0.4423 0.2664 0.1991 0.4465 0.2635 0.2007 H35 0.7087 0.7336 0.6991 0.7101 0.7365 0.7007 H36 0.5577 0.7336 0.8009 0.5535 0.7365 0.7993 H37 0.0779 0.4248 0.2649 0.0785 0.4205 0.2619 H38 0.4973 0.4248 0.2351 0.5010 0.4205 0.2381 H39 0.9221 0.5752 0.7351 0.9215 0.5795 0.7381 H40 0.5027 0.5752 0.7649 0.4990 0.5795 0.7619 O37 0.9133 0.8860 0.1792 0.9153 0.8869 0.1788 O38 0.2007 0.8860 0.3208 0.1978 0.8869 0.3212 O39 0.0867 0.1140 0.8208 0.0847 0.1131 0.8212 O40 0.7993 0.1140 0.6792 0.8022 0.1131 0.6788 H41 0.0052 0.6582 0.1575 0.0049 0.6599 0.1573 H42 0.3365 0.6582 0.3425 0.3352 0.6599 0.3427 H43 0.9948 0.3418 0.8425 0.9951 0.3401 0.8427 H44 0.6635 0.3418 0.6575 0.6648 0.3401 0.6573 H45 0.7883 0.1023 0.1545 0.7876 0.1058 0.1548 H46 0.1095 0.1023 0.3455 0.1066 0.1058 0.3452 H47 0.2117 0.8977 0.8455 0.2124 0.8942 0.8452 H48 0.8905 0.8977 0.6545 0.8934 0.8942 0.6548 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 0.0018 -0.0036 0.0000 -0.0000 -0.0129 0.0000 Mg4 -0.0018 0.0036 -0.0000 0.0000 0.0129 -0.0000 S1 0.0007 0.0009 0.0001 0.0116 0.0031 0.0011 S2 -0.0016 0.0009 -0.0001 -0.0116 0.0031 -0.0011 S3 -0.0007 -0.0009 -0.0001 -0.0116 -0.0031 -0.0011 S4 0.0016 -0.0009 0.0001 0.0116 -0.0031 0.0011 O1 0.0000 -0.0013 0.0001 -0.0066 -0.0047 0.0013 O2 0.0013 -0.0013 -0.0001 0.0066 -0.0047 -0.0013 O3 -0.0000 0.0013 -0.0001 0.0066 0.0047 -0.0013 O4 -0.0013 0.0013 0.0001 -0.0066 0.0047 0.0013 O5 0.0018 -0.0025 0.0001 0.0055 -0.0089 0.0021 O6 0.0006 -0.0025 -0.0001 -0.0055 -0.0089 -0.0021 O7 -0.0018 0.0025 -0.0001 -0.0055 0.0089 -0.0021 O8 -0.0006 0.0025 0.0001 0.0055 0.0089 0.0021 O9 -0.0008 0.0009 0.0001 -0.0037 0.0032 0.0020 O10 -0.0001 0.0009 -0.0001 0.0037 0.0032 -0.0020 O11 0.0008 -0.0009 -0.0001 0.0037 -0.0032 -0.0020 O12 0.0001 -0.0009 0.0001 -0.0037 -0.0032 0.0020 O13 -0.0002 -0.0011 -0.0001 -0.0068 -0.0040 -0.0031 O14 0.0013 -0.0011 0.0001 0.0068 -0.0040 0.0031 O15 0.0002 0.0011 0.0001 0.0068 0.0040 0.0031 O16 -0.0013 0.0011 -0.0001 -0.0068 0.0040 -0.0031 O17 -0.0009 0.0008 0.0001 -0.0055 0.0030 0.0018 O18 0.0001 0.0008 -0.0001 0.0055 0.0030 -0.0018 O19 0.0009 -0.0008 -0.0001 0.0055 -0.0030 -0.0018 O20 -0.0001 -0.0008 0.0001 -0.0055 -0.0030 0.0018 H1 -0.0000 0.0007 0.0002 0.0022 0.0025 0.0047 H2 -0.0006 0.0007 -0.0002 -0.0022 0.0025 -0.0047 H3 0.0000 -0.0007 -0.0002 -0.0022 -0.0025 -0.0047 H4 0.0006 -0.0007 0.0002 0.0022 -0.0025 0.0047 H5 0.0002 0.0004 0.0003 0.0032 0.0015 0.0061 H6 -0.0006 0.0004 -0.0003 -0.0032 0.0015 -0.0061 H7 -0.0002 -0.0004 -0.0003 -0.0032 -0.0015 -0.0061 H8 0.0006 -0.0004 0.0003 0.0032 -0.0015 0.0061 O21 -0.0001 -0.0001 0.0000 -0.0020 -0.0003 0.0004 O22 0.0002 -0.0001 -0.0000 0.0020 -0.0003 -0.0004 O23 0.0001 0.0001 -0.0000 0.0020 0.0003 -0.0004 O24 -0.0002 0.0001 0.0000 -0.0020 0.0003 0.0004 H9 0.0010 -0.0016 0.0002 0.0019 -0.0056 0.0045 H10 0.0005 -0.0016 -0.0002 -0.0019 -0.0056 -0.0045 H11 -0.0010 0.0016 -0.0002 -0.0019 0.0056 -0.0045 H12 -0.0005 0.0016 0.0002 0.0019 0.0056 0.0045 H13 0.0010 -0.0025 -0.0002 -0.0013 -0.0090 -0.0060 H14 0.0015 -0.0025 0.0002 0.0013 -0.0090 0.0060 H15 -0.0010 0.0025 0.0002 0.0013 0.0090 0.0060 H16 -0.0015 0.0025 -0.0002 -0.0013 0.0090 -0.0060 O25 0.0005 -0.0008 -0.0001 0.0019 -0.0027 -0.0019 O26 0.0002 -0.0008 0.0001 -0.0019 -0.0027 0.0019 O27 -0.0005 0.0008 0.0001 -0.0019 0.0027 0.0019 O28 -0.0002 0.0008 -0.0001 0.0019 0.0027 -0.0019 H17 0.0000 -0.0019 -0.0003 -0.0080 -0.0068 -0.0069 H18 0.0018 -0.0019 0.0003 0.0080 -0.0068 0.0069 H19 -0.0000 0.0019 0.0003 0.0080 0.0068 0.0069 H20 -0.0018 0.0019 -0.0003 -0.0080 0.0068 -0.0069 H21 -0.0002 0.0000 0.0002 -0.0024 0.0000 0.0057 H22 0.0001 0.0000 -0.0002 0.0024 0.0000 -0.0057 H23 0.0002 -0.0000 -0.0002 0.0024 -0.0000 -0.0057 H24 -0.0001 -0.0000 0.0002 -0.0024 -0.0000 0.0057 O29 0.0023 -0.0035 0.0003 0.0048 -0.0127 0.0064 maximum gradient = 0.0150 O30 0.0012 -0.0035 -0.0003 -0.0048 -0.0127 -0.0064 O31 -0.0023 0.0035 -0.0003 -0.0048 0.0127 -0.0064 O32 -0.0012 0.0035 0.0003 0.0048 0.0127 0.0064 H25 -0.0012 0.0018 -0.0001 -0.0027 0.0064 -0.0027 H26 -0.0006 0.0018 0.0001 0.0027 0.0064 0.0027 H27 0.0012 -0.0018 0.0001 0.0027 -0.0064 0.0027 H28 0.0006 -0.0018 -0.0001 -0.0027 -0.0064 -0.0027 H29 -0.0011 0.0012 0.0000 -0.0049 0.0044 0.0001 H30 -0.0001 0.0012 -0.0000 0.0049 0.0044 -0.0001 H31 0.0011 -0.0012 -0.0000 0.0049 -0.0044 -0.0001 H32 0.0001 -0.0012 0.0000 -0.0049 -0.0044 0.0001 O33 -0.0004 0.0003 -0.0003 -0.0011 0.0011 -0.0078 O34 0.0001 0.0003 0.0003 0.0011 0.0011 0.0078 O35 0.0004 -0.0003 0.0003 0.0011 -0.0011 0.0078 O36 -0.0001 -0.0003 -0.0003 -0.0011 -0.0011 -0.0078 H33 0.0007 -0.0012 0.0001 0.0005 -0.0042 0.0022 H34 0.0005 -0.0012 -0.0001 -0.0005 -0.0042 -0.0022 H35 -0.0007 0.0012 -0.0001 -0.0005 0.0042 -0.0022 H36 -0.0005 0.0012 0.0001 0.0005 0.0042 0.0022 H37 0.0009 -0.0013 0.0003 0.0007 -0.0048 0.0083 H38 0.0005 -0.0013 -0.0003 -0.0007 -0.0048 -0.0083 H39 -0.0009 0.0013 -0.0003 -0.0007 0.0048 -0.0083 H40 -0.0005 0.0013 0.0003 0.0007 0.0048 0.0083 O37 0.0012 -0.0013 0.0003 0.0044 -0.0047 0.0076 O38 0.0001 -0.0013 -0.0003 -0.0044 -0.0047 -0.0076 O39 -0.0012 0.0013 -0.0003 -0.0044 0.0047 -0.0076 O40 -0.0001 0.0013 0.0003 0.0044 0.0047 0.0076 H41 -0.0004 0.0002 0.0001 -0.0031 0.0008 0.0019 H42 0.0002 0.0002 -0.0001 0.0031 0.0008 -0.0019 H43 0.0004 -0.0002 -0.0001 0.0031 -0.0008 -0.0019 H44 -0.0002 -0.0002 0.0001 -0.0031 -0.0008 0.0019 H45 0.0012 -0.0027 0.0000 -0.0016 -0.0097 0.0010 H46 0.0015 -0.0027 -0.0000 0.0016 -0.0097 -0.0010 H47 -0.0012 0.0027 -0.0000 0.0016 0.0097 -0.0010 H48 -0.0015 0.0027 0.0000 -0.0016 0.0097 0.0010 Atomic partial charges (electron charges): Atom s p d total ----- -------- -------- -------- -------- Mg1 0.261 0.400 0.260 0.921 Mg2 0.261 0.400 0.260 0.921 Mg3 0.256 0.386 0.246 0.888 Mg4 0.256 0.386 0.246 0.888 S1 1.052 1.897 0.801 3.749 S2 1.052 1.897 0.801 3.749 S3 1.052 1.897 0.801 3.749 S4 1.052 1.897 0.801 3.749 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 2.903 0.016 4.185 O6 1.266 2.903 0.016 4.185 O7 1.266 2.903 0.016 4.185 O8 1.266 2.903 0.016 4.185 O9 1.267 2.894 0.015 4.177 O10 1.267 2.894 0.015 4.177 O11 1.267 2.894 0.015 4.177 O12 1.267 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 2.986 0.012 4.231 O18 1.233 2.986 0.012 4.231 O19 1.233 2.986 0.012 4.231 O20 1.233 2.986 0.012 4.231 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 2.987 0.012 4.232 O22 1.233 2.987 0.012 4.232 O23 1.233 2.987 0.012 4.232 O24 1.233 2.987 0.012 4.232 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 4.230 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 0.149 0.006 0.000 0.156 H22 0.149 0.006 0.000 0.156 H23 0.149 0.006 0.000 0.156 H24 0.149 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 5.212 eV. The valence band (#160) maximum is located near (0.33 -0.00 0.00), at -0.248 eV with respect to the Fermi level. The conduction band (#161) minimum is located near (0.00 0.00 0.00), at 4.964 eV with respect to the Fermi level. The center of the gap is located at 2.357787 eV with respect to the Fermi level. The Fermi energy is used as the zero of the energy scale. Job completed on Fri 17 March 2023 at 14:27:32 CST after 21229 s (5:53:49) Entire job completed on Fri 17 March 2023 at 14:27:32 CST after 21229 s (5:53:49) and running 1 tasks.