[Fri Apr 14 19:37:41 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 '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 0.4 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: Number of steps is 500 ========================================== 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: -505.367449 eV for Mg4S4O40H48 cell Non-dispersive: -499.956569 eV Van der Waals: -5.410880 eV Initial VASP energy: -505.102070 eV for Mg4S4O40H48 cell Relaxation energy: -0.265379 eV gained after 187 optimization steps. Electronic contributions: Empirical Formula Cell MgSO10H12 (MgSO10H12)4 ----------------- ----------------- VASP Energy -126.341862 -505.367449 eV = -12190.134 -48760.534 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: 216.000 MPa = 2.160 kbar XX YY ZZ YZ XZ XY Stress: -464.589 -337.977 155.890 -54.856 -22.534 309.473 MPa = -4.646 -3.380 1.559 -0.549 -0.225 3.095 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 0.9962 0.9816 0.5827 0.9851 0.9757 0.5821 Mg2 0.4962 0.4816 0.5827 0.4851 0.4757 0.5821 Mg3 0.9323 0.9284 0.8158 0.9391 0.9316 0.8172 Mg4 0.4323 0.4284 0.8158 0.4391 0.4316 0.8172 S1 0.4379 0.8273 0.7314 0.4400 0.8362 0.7324 S2 0.5759 0.1321 0.4950 0.5744 0.1258 0.4924 S3 0.9379 0.3273 0.7314 0.9400 0.3362 0.7324 S4 0.0759 0.6321 0.4950 0.0744 0.6258 0.4924 O1 0.1095 0.2451 0.7275 0.1127 0.2558 0.7278 O2 0.9194 0.7044 0.4717 0.9196 0.6974 0.4683 O3 0.6095 0.7451 0.7275 0.6127 0.7558 0.7278 O4 0.4194 0.2044 0.4717 0.4196 0.1974 0.4683 O6 0.4288 0.8757 0.7891 0.4337 0.8877 0.7898 O7 0.6159 0.0023 0.4704 0.6144 -0.0052 0.4688 O9 0.9288 0.3757 0.7891 0.9337 0.3877 0.7898 O10 0.1159 0.5023 0.4704 0.1144 0.4948 0.4688 O11 0.4437 0.9494 0.7007 0.4373 0.9560 0.7004 O12 0.5244 0.1004 0.5519 0.5176 0.0963 0.5496 O13 0.9437 0.4494 0.7007 0.9373 0.4560 0.7004 O14 0.0244 0.6004 0.5519 0.0176 0.5963 0.5496 O15 0.2744 0.7407 0.7217 0.2778 0.7461 0.7247 O16 0.7451 0.2212 0.4968 0.7428 0.2142 0.4946 O17 0.7744 0.2407 0.7217 0.7778 0.2461 0.7247 O18 0.2451 0.7212 0.4968 0.2428 0.7142 0.4946 O19 0.1672 0.0588 0.6415 0.1381 0.0534 0.6459 O20 0.8052 0.8736 0.5399 0.7989 0.8627 0.5374 O21 0.6672 0.5588 0.6415 0.6381 0.5534 0.6459 O22 0.3052 0.3736 0.5399 0.2989 0.3627 0.5374 H1 0.1458 0.1469 0.6570 0.1543 0.1507 0.6437 H2 0.8570 0.8045 0.5145 0.8541 0.7965 0.5116 H3 0.6458 0.6469 0.6570 0.6543 0.6507 0.6437 H4 0.3570 0.3045 0.5145 0.3541 0.2965 0.5116 H5 0.2692 0.0155 0.6601 0.2521 0.0162 0.6608 H6 0.7290 0.9284 0.5142 0.7217 0.9173 0.5120 H7 0.7692 0.5155 0.6601 0.7521 0.5162 0.6608 H8 0.2290 0.4284 0.5142 0.2217 0.4173 0.5120 O23 0.2598 0.5016 0.6325 0.2420 0.5031 0.6245 O24 0.7045 0.4713 0.5335 0.6998 0.4603 0.5346 O25 0.7598 0.0016 0.6325 0.7420 0.0031 0.6245 O26 0.2045 0.9713 0.5335 0.1998 0.9603 0.5346 H9 0.1622 0.4860 0.6065 0.1489 0.5219 0.5965 H10 0.8238 0.5189 0.5393 0.8181 0.5108 0.5387 H11 0.6622 0.9860 0.6065 0.6489 0.0219 0.5965 H12 0.3238 0.0189 0.5393 0.3181 0.0108 0.5387 H13 0.2368 0.5951 0.6427 0.2355 0.5826 0.6465 H14 0.7265 0.3919 0.5111 0.7204 0.3800 0.5124 H15 0.7368 0.0951 0.6427 0.7355 0.0826 0.6465 H16 0.2265 0.8919 0.5111 0.2204 0.8800 0.5124 O27 0.0940 0.7919 0.6153 0.0802 0.7877 0.6152 O28 0.9668 0.1961 0.5712 0.9767 0.1905 0.5678 O29 0.5940 0.2919 0.6153 0.5802 0.2877 0.6152 O30 0.4668 0.6961 0.5712 0.4767 0.6905 0.5678 H17 0.2253 0.8001 0.6057 0.2129 0.7946 0.6074 H18 0.8801 0.2057 0.5397 0.8887 0.2006 0.5372 H19 0.7253 0.3001 0.6057 0.7129 0.2946 0.6074 H20 0.3801 0.7057 0.5397 0.3887 0.7006 0.5372 H21 0.0514 0.7181 0.5898 0.0397 0.7167 0.5889 H22 0.0818 0.2431 0.5611 0.0904 0.2393 0.5573 H23 0.5514 0.2181 0.5898 0.5397 0.2167 0.5889 H24 0.5818 0.7431 0.5611 0.5904 0.7393 0.5573 O31 0.1540 0.0589 0.7994 0.1538 0.0661 0.7979 O32 0.1365 0.7890 0.8439 0.1462 0.7981 0.8464 O33 0.6540 0.5589 0.7994 0.6538 0.5661 0.7979 O34 0.6365 0.2890 0.8439 0.6462 0.2981 0.8464 H25 0.1362 0.1204 0.7688 0.1344 0.1266 0.7670 H26 0.1250 0.6996 0.8268 0.1379 0.7071 0.8304 H27 0.6362 0.6204 0.7688 0.6344 0.6266 0.7670 H28 0.6250 0.1996 0.8268 0.6379 0.2071 0.8304 H29 0.2654 0.0025 0.7917 0.2665 0.0109 0.7904 H30 0.2536 0.8213 0.8272 0.2627 0.8314 0.8298 H31 0.7654 0.5025 0.7917 0.7665 0.5109 0.7904 H32 0.7536 0.3213 0.8272 0.7627 0.3314 0.8298 O35 0.2141 0.5575 0.7904 0.2213 0.5642 0.7949 O36 0.2243 0.3039 0.8449 0.2285 0.3061 0.8465 O37 0.7141 0.0575 0.7904 0.7213 0.0642 0.7949 O38 0.7243 0.8039 0.8449 0.7285 0.8061 0.8465 H33 0.1011 0.5035 0.7834 0.1076 0.5105 0.7875 H34 0.1072 0.3273 0.8261 0.1112 0.3353 0.8294 H35 0.6011 0.0035 0.7834 0.6076 0.0105 0.7875 H36 0.6072 0.8273 0.8261 0.6112 0.8353 0.8294 H37 0.2383 0.6157 0.7590 0.2454 0.6233 0.7636 H38 0.2311 0.2054 0.8387 0.2308 0.2092 0.8368 H39 0.7383 0.1157 0.7590 0.7454 0.1233 0.7636 H40 0.7311 0.7054 0.8387 0.7308 0.7092 0.8368 O39 0.4014 0.5393 0.8868 0.4215 0.5322 0.8902 O40 0.4456 0.3471 0.7448 0.4451 0.3480 0.7472 O42 0.9014 0.0393 0.8868 0.9215 0.0322 0.8902 O43 0.9456 0.8471 0.7448 0.9451 0.8480 0.7472 H41 0.3403 0.6272 0.8841 0.3501 0.6160 0.8902 H42 0.3322 0.3232 0.7257 0.3293 0.3210 0.7296 H44 0.8403 0.1272 0.8841 0.8501 0.1160 0.8902 H45 0.8322 0.8232 0.7257 0.8293 0.8210 0.7296 H47 0.8228 0.9856 0.9094 0.8616 0.9730 0.9151 H48 0.0555 0.8167 0.7253 0.0538 0.8184 0.7272 H50 0.3228 0.4856 0.9094 0.3616 0.4730 0.9151 H51 0.5555 0.3167 0.7253 0.5538 0.3184 0.7272 Analytic Derivatives: Atom Derivatives fractional Derivatives Cartesian (eV/Ang) ----- -------- -------- -------- -------- -------- -------- Mg1 -0.0001 -0.0002 0.0002 -0.0007 -0.0021 0.0048 Mg2 -0.0001 -0.0002 0.0002 -0.0007 -0.0021 0.0048 Mg3 0.0003 0.0004 0.0003 0.0018 0.0044 0.0085 Mg4 0.0003 0.0004 0.0003 0.0018 0.0044 0.0085 S1 0.0001 0.0003 -0.0001 0.0007 0.0025 -0.0020 S2 -0.0008 0.0001 -0.0002 -0.0058 0.0007 -0.0059 S3 0.0001 0.0003 -0.0001 0.0007 0.0025 -0.0020 S4 -0.0008 0.0001 -0.0002 -0.0058 0.0007 -0.0059 O1 0.0005 -0.0003 0.0000 0.0035 -0.0026 0.0009 O2 0.0004 0.0003 -0.0001 0.0026 0.0032 -0.0031 O3 0.0005 -0.0003 0.0000 0.0035 -0.0026 0.0009 O4 0.0004 0.0003 -0.0001 0.0026 0.0032 -0.0031 O6 0.0001 0.0001 0.0003 0.0007 0.0011 0.0073 O7 0.0006 -0.0005 -0.0002 0.0040 -0.0054 -0.0051 O9 0.0001 0.0001 0.0003 0.0007 0.0011 0.0073 O10 0.0006 -0.0005 -0.0002 0.0040 -0.0054 -0.0051 O11 -0.0004 0.0003 -0.0000 -0.0032 0.0025 -0.0008 O12 0.0001 -0.0002 0.0002 0.0010 -0.0016 0.0053 O13 -0.0004 0.0003 -0.0000 -0.0032 0.0025 -0.0008 O14 0.0001 -0.0002 0.0002 0.0010 -0.0016 0.0053 O15 -0.0003 -0.0004 0.0002 -0.0020 -0.0036 0.0042 O16 0.0006 0.0002 0.0001 0.0040 0.0020 0.0028 O17 -0.0003 -0.0004 0.0002 -0.0020 -0.0036 0.0042 O18 0.0006 0.0002 0.0001 0.0040 0.0020 0.0028 O19 -0.0017 -0.0003 -0.0002 -0.0126 -0.0034 -0.0053 O20 -0.0001 0.0003 0.0001 -0.0006 0.0033 0.0034 O21 -0.0017 -0.0003 -0.0002 -0.0126 -0.0034 -0.0053 O22 -0.0001 0.0003 0.0001 -0.0006 0.0033 0.0034 H1 0.0003 -0.0001 -0.0000 0.0025 -0.0015 -0.0003 H2 -0.0000 -0.0005 -0.0001 -0.0003 -0.0054 -0.0038 H3 0.0003 -0.0001 -0.0000 0.0025 -0.0015 -0.0003 H4 -0.0000 -0.0005 -0.0001 -0.0003 -0.0054 -0.0038 H5 -0.0001 0.0008 -0.0001 -0.0009 0.0083 -0.0029 H6 0.0003 -0.0002 0.0000 0.0025 -0.0022 0.0003 H7 -0.0001 0.0008 -0.0001 -0.0009 0.0083 -0.0029 H8 0.0003 -0.0002 0.0000 0.0025 -0.0022 0.0003 O23 0.0005 0.0007 0.0003 0.0037 0.0071 0.0083 O24 -0.0024 -0.0006 0.0001 -0.0171 -0.0058 0.0034 maximum gradient = 0.0184 O25 0.0005 0.0007 0.0003 0.0037 0.0071 0.0083 O26 -0.0024 -0.0006 0.0001 -0.0171 -0.0058 0.0034 H9 -0.0014 0.0001 -0.0003 -0.0103 0.0006 -0.0075 H10 0.0019 0.0005 0.0000 0.0139 0.0049 0.0009 H11 -0.0014 0.0001 -0.0003 -0.0103 0.0006 -0.0075 H12 0.0019 0.0005 0.0000 0.0139 0.0049 0.0009 H13 -0.0004 -0.0011 -0.0003 -0.0029 -0.0107 -0.0084 H14 -0.0002 -0.0014 -0.0003 -0.0017 -0.0142 -0.0090 H15 -0.0004 -0.0011 -0.0003 -0.0029 -0.0107 -0.0084 H16 -0.0002 -0.0014 -0.0003 -0.0017 -0.0142 -0.0090 O27 0.0007 -0.0006 -0.0003 0.0053 -0.0061 -0.0069 O28 0.0001 -0.0004 0.0001 0.0004 -0.0035 0.0018 O29 0.0007 -0.0006 -0.0003 0.0053 -0.0061 -0.0069 O30 0.0001 -0.0004 0.0001 0.0004 -0.0035 0.0018 H17 -0.0005 -0.0002 0.0000 -0.0035 -0.0017 0.0001 H18 -0.0003 -0.0004 -0.0001 -0.0024 -0.0035 -0.0028 H19 -0.0005 -0.0002 0.0000 -0.0035 -0.0017 0.0001 H20 -0.0003 -0.0004 -0.0001 -0.0024 -0.0035 -0.0028 H21 -0.0005 -0.0001 0.0002 -0.0033 -0.0013 0.0053 H22 0.0004 0.0001 -0.0002 0.0026 0.0007 -0.0045 H23 -0.0005 -0.0001 0.0002 -0.0033 -0.0013 0.0053 H24 0.0004 0.0001 -0.0002 0.0026 0.0007 -0.0045 O31 0.0001 0.0009 0.0001 0.0011 0.0090 0.0019 O32 0.0010 0.0012 0.0000 0.0075 0.0115 0.0009 O33 0.0001 0.0009 0.0001 0.0011 0.0090 0.0019 O34 0.0010 0.0012 0.0000 0.0075 0.0115 0.0009 H25 0.0002 -0.0002 0.0000 0.0017 -0.0021 0.0009 H26 -0.0001 -0.0007 0.0000 -0.0006 -0.0065 0.0008 H27 0.0002 -0.0002 0.0000 0.0017 -0.0021 0.0009 H28 -0.0001 -0.0007 0.0000 -0.0006 -0.0065 0.0008 H29 0.0003 0.0000 -0.0001 0.0024 0.0004 -0.0039 H30 -0.0004 -0.0000 0.0002 -0.0032 -0.0002 0.0041 H31 0.0003 0.0000 -0.0001 0.0024 0.0004 -0.0039 H32 -0.0004 -0.0000 0.0002 -0.0032 -0.0002 0.0041 O35 0.0004 0.0006 -0.0000 0.0032 0.0064 -0.0006 O36 -0.0000 0.0007 -0.0000 -0.0001 0.0074 -0.0007 O37 0.0004 0.0006 -0.0000 0.0032 0.0064 -0.0006 O38 -0.0000 0.0007 -0.0000 -0.0001 0.0074 -0.0007 H33 -0.0001 -0.0001 0.0000 -0.0005 -0.0011 0.0004 H34 0.0004 0.0002 0.0001 0.0028 0.0016 0.0017 H35 -0.0001 -0.0001 0.0000 -0.0005 -0.0011 0.0004 H36 0.0004 0.0002 0.0001 0.0028 0.0016 0.0017 H37 0.0002 0.0002 0.0001 0.0018 0.0017 0.0023 H38 -0.0001 -0.0002 0.0000 -0.0008 -0.0018 0.0007 H39 0.0002 0.0002 0.0001 0.0018 0.0017 0.0023 H40 -0.0001 -0.0002 0.0000 -0.0008 -0.0018 0.0007 O39 -0.0009 0.0008 0.0002 -0.0065 0.0079 0.0051 O40 -0.0001 -0.0000 0.0000 -0.0011 -0.0003 0.0001 O42 -0.0009 0.0008 0.0002 -0.0065 0.0079 0.0051 O43 -0.0001 -0.0000 0.0000 -0.0011 -0.0003 0.0001 H41 0.0009 -0.0009 -0.0000 0.0063 -0.0084 -0.0003 H42 -0.0006 0.0003 -0.0001 -0.0046 0.0029 -0.0017 H44 0.0009 -0.0009 -0.0000 0.0063 -0.0084 -0.0003 H45 -0.0006 0.0003 -0.0001 -0.0046 0.0029 -0.0017 H47 0.0005 0.0006 -0.0000 0.0036 0.0063 -0.0005 H48 0.0007 -0.0002 -0.0000 0.0053 -0.0016 -0.0000 H50 0.0005 0.0006 -0.0000 0.0036 0.0063 -0.0005 H51 0.0007 -0.0002 -0.0000 0.0053 -0.0016 -0.0000 Atomic partial charges (electron charges): Atom s p d total ----- -------- -------- -------- -------- Mg1 0.267 0.396 0.250 0.914 Mg2 0.267 0.396 0.250 0.914 Mg3 0.267 0.398 0.251 0.916 Mg4 0.267 0.398 0.251 0.916 S1 1.055 1.906 0.807 3.768 S2 1.056 1.906 0.804 3.766 S3 1.055 1.906 0.807 3.768 S4 1.056 1.906 0.804 3.766 O1 1.269 2.907 0.016 4.192 O2 1.278 2.889 0.019 4.186 O3 1.269 2.907 0.016 4.192 O4 1.278 2.889 0.019 4.186 O6 1.262 2.884 0.011 4.157 O7 1.278 2.888 0.019 4.185 O9 1.262 2.884 0.011 4.157 O10 1.278 2.888 0.019 4.185 O11 1.279 2.891 0.020 4.190 O12 1.261 2.888 0.011 4.161 O13 1.279 2.891 0.020 4.190 O14 1.261 2.888 0.011 4.161 O15 1.269 2.902 0.016 4.188 O16 1.266 2.903 0.015 4.185 O17 1.269 2.902 0.016 4.188 O18 1.266 2.903 0.015 4.185 O19 1.238 2.978 0.013 4.230 O20 1.237 2.969 0.011 4.217 O21 1.238 2.978 0.013 4.230 O22 1.237 2.969 0.011 4.217 H1 0.156 0.006 0.000 0.163 H2 0.139 0.006 0.000 0.145 H3 0.156 0.006 0.000 0.163 H4 0.139 0.006 0.000 0.145 H5 0.151 0.006 0.000 0.157 H6 0.138 0.006 0.000 0.145 H7 0.151 0.006 0.000 0.157 H8 0.138 0.006 0.000 0.145 O23 1.241 2.967 0.013 4.221 O24 1.229 3.001 0.011 4.241 O25 1.241 2.967 0.013 4.221 O26 1.229 3.001 0.011 4.241 H9 0.142 0.006 0.000 0.148 H10 0.144 0.006 0.000 0.151 H11 0.142 0.006 0.000 0.148 H12 0.144 0.006 0.000 0.151 H13 0.157 0.006 0.000 0.163 H14 0.144 0.006 0.000 0.150 H15 0.157 0.006 0.000 0.163 H16 0.144 0.006 0.000 0.150 O27 1.243 2.955 0.013 4.211 O28 1.236 2.968 0.011 4.215 O29 1.243 2.955 0.013 4.211 O30 1.236 2.968 0.011 4.215 H17 0.154 0.006 0.000 0.161 H18 0.136 0.006 0.000 0.143 H19 0.154 0.006 0.000 0.161 H20 0.136 0.006 0.000 0.143 H21 0.137 0.006 0.000 0.143 H22 0.148 0.006 0.000 0.154 H23 0.137 0.006 0.000 0.143 H24 0.148 0.006 0.000 0.154 O31 1.236 2.978 0.011 4.225 O32 1.241 2.962 0.013 4.215 O33 1.236 2.978 0.011 4.225 O34 1.241 2.962 0.013 4.215 H25 0.139 0.006 0.000 0.145 H26 0.147 0.006 0.000 0.154 H27 0.139 0.006 0.000 0.145 H28 0.147 0.006 0.000 0.154 H29 0.145 0.006 0.000 0.151 H30 0.145 0.006 0.000 0.152 H31 0.145 0.006 0.000 0.151 H32 0.145 0.006 0.000 0.152 O35 1.236 2.978 0.011 4.225 O36 1.238 2.971 0.012 4.222 O37 1.236 2.978 0.011 4.225 O38 1.238 2.971 0.012 4.222 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 0.137 0.006 0.000 0.144 H38 0.148 0.006 0.000 0.154 H39 0.137 0.006 0.000 0.144 H40 0.148 0.006 0.000 0.154 O39 1.240 2.965 0.014 4.220 O40 1.228 3.005 0.011 4.244 O42 1.240 2.965 0.014 4.220 O43 1.228 3.005 0.011 4.244 H41 0.154 0.006 0.000 0.161 H42 0.145 0.006 0.000 0.152 H44 0.154 0.006 0.000 0.161 H45 0.145 0.006 0.000 0.152 H47 0.155 0.006 0.000 0.162 H48 0.146 0.006 0.000 0.152 H50 0.155 0.006 0.000 0.162 H51 0.146 0.006 0.000 0.152 Analysis of the electronic structure: The system is a semiconductor with an indirect gap of 1.476 eV. The valence band (#160) maximum is located near (0.33 0.50 0.00), at -0.260 eV with respect to the Fermi level. The conduction band (#161) minimum is located near (0.00 0.00 0.00), at 1.216 eV with respect to the Fermi level. The center of the gap is located at 0.477654 eV with respect to the Fermi level. The Fermi energy is used as the zero of the energy scale. Job completed on Sun 16 April 2023 at 16:53:50 CST after 162965 s (45:16:05) Entire job completed on Sun 16 April 2023 at 16:53:50 CST after 162965 s (45:16:05) and running 1 tasks.