./Job.out output for 1022: Structure_opt_PFA2PTFE6
Status:
finished
[Fri Jul 25 19:53:27 CST 2025] [MD] [warn] 'Starting MedeA Core 3.8.1'
MedeA version 3.8.1
#-------------------------------------------------------------------------------
# This calculation has 1 stage
#-------------------------------------------------------------------------------
Stage 1: VASP 6
#-------------------------------------------------------------------------------
# Running the calculation
#-------------------------------------------------------------------------------
Stage 1: VASP 6
Sucessfully opened MedeA database from /home/user/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.
Since no magnetic moments are in the model, this is a non-magnetic calculation using 'accurate' precision
and a default planewave cutoff energy of 400.000 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 2x2x2 mesh.
This corresponds to actual k-spacings of 0.348 x 0.348 x 0.348 per Angstrom.
The k-mesh is forced to be centered on the gamma point.
Using first order Methfessel-Paxton smearing with a width of 0.2 eV.
Other non-default parameters:
VASP version is for GPUs
==========================================
Using version 4.0 GGA-PBE / PAW potentials:
C PAW_PBE C 08Apr2002
F PAW_PBE F 08Apr2002
O PAW_PBE O 08Apr2002
H PAW_PBE H 15Jun2001
There are 8 symmetry-unique k-points
The plane wave cutoff is 400.00 eV
stdout
=========================================================
=========================================================
!!!! WARNING MESSAGES !!!!
=========================================================
WARNING: The convergence criterion for the geometry optimization is not met after 100 steps!
Whether the geometry is sufficiently converged can be assessed from the forces/stresses below and from VASP.out or OSZICAR.out.
=========================================================
=========================================================
VASP energy: -320.300606 eV for C18O2F36H2 cell
Initial VASP energy: -228.696030 eV for C18O2F36H2 cell
Relaxation energy: -91.604576 eV gained after 100 optimization steps.
Electronic contributions:
Empirical Formula Cell
C9OF18H (C9OF18H)2
----------------- -----------------
VASP Energy -160.150303 -320.300606 eV
= -15452.151 -30904.303 kJ/mol
Cell parameters:
Parameter Value
---------- ------------
a 9.039610
b 9.039610
c 9.039610
alpha 90.000000
beta 90.000000
gamma 90.000000
Volume 738.667735 Ang^3
Density: 2.100 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: -6.063 GPa
= -60.633 kbar
XX YY ZZ YZ XZ XY
Stress: 3.741 7.078 7.370 1.139 -0.054 -0.445 GPa
= 37.414 70.782 73.703 11.389 -0.537 -4.454 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
----- -------- -------- -------- -------- -------- --------
Untitled_1::C1 0.3482 0.5124 0.7803 0.3751 0.5633 0.8531
Untitled_1::C2 0.2062 0.6110 0.7965 0.2455 0.6646 0.9119
Untitled_1::F1 0.3636 0.4041 0.9034 0.4094 0.4780 0.9740
Untitled_1::F2 0.4682 0.6254 0.7817 0.4791 0.6689 0.8283
Untitled_1::F3 0.2275 0.7455 0.7039 0.2134 0.7659 0.8055
Untitled_1::O 0.1916 0.6656 0.9542 0.3031 0.7548 0.0293
Untitled_1::C3 0.2580 0.5566 0.0611 0.3108 0.7036 0.1711
Untitled_1::F4 0.1772 0.4133 0.0513 0.2084 0.5962 0.1995
Untitled_1::F5 0.2453 0.6160 0.2145 0.2869 0.8178 0.2637
Untitled_1::F6 0.4171 0.5331 0.0249 0.4469 0.6483 0.2029
Untitled_2::C1 0.2368 0.5129 0.5303 0.2710 0.4542 0.5841
Untitled_2::C2 0.3504 0.4361 0.6253 0.3911 0.4473 0.7071
Untitled_2::F1 0.2638 0.4827 0.3704 0.3363 0.4246 0.4510
Untitled_2::F2 0.2520 0.6719 0.5639 0.2220 0.5959 0.5758
Untitled_2::F3 0.5002 0.4370 0.5563 0.5163 0.4898 0.6361
Untitled_2::O 0.2887 0.2835 0.6394 0.4073 0.3028 0.7637
Untitled_2::C3 0.4116 0.1778 0.6739 0.4913 0.1888 0.7052
Untitled_2::F4 0.5430 0.2141 0.5810 0.5599 0.2222 0.5774
Untitled_2::F5 0.3625 0.0238 0.6418 0.4062 0.0687 0.6795
Untitled_2::F6 0.4517 0.1907 0.8331 0.5914 0.1488 0.8088
Untitled_3::C1 0.0648 0.3889 0.7502 0.0952 0.2875 0.7571
Untitled_3::C2 0.0770 0.4545 0.5804 0.1392 0.3390 0.5944
Untitled_3::F1 0.1502 0.2484 0.7426 0.1524 0.1505 0.7746
Untitled_3::F2 0.1398 0.4726 0.8730 0.1647 0.3827 0.8532
Untitled_3::F3 0.0524 0.3217 0.4861 0.1856 0.2161 0.5216
Untitled_3::F4 0.9596 0.5573 0.5336 0.0254 0.3991 0.5186
Untitled_4::C1 0.8113 0.4345 0.9160 0.8777 0.3987 0.9427
Untitled_4::C2 0.9013 0.3347 0.7979 0.9320 0.2766 0.8198
Untitled_4::F1 0.6776 0.3501 0.9629 0.7741 0.3213 0.0214
Untitled_4::F2 0.9098 0.4522 0.0469 0.9892 0.4300 0.0393
Untitled_4::F3 0.9259 0.1913 0.8755 0.9324 0.1486 0.9009
Untitled_4::F4 0.8124 0.2957 0.6646 0.8350 0.2569 0.7098
Untitled_5::C1 0.8895 0.6853 0.8191 0.8181 0.6841 0.8163
Untitled_5::C2 0.7604 0.5942 0.8682 0.7838 0.5459 0.9161
Untitled_5::F1 0.8507 0.8448 0.8110 0.7166 0.7905 0.8456
Untitled_5::F2 0.0092 0.6592 0.9288 -0.0492 0.7386 0.8608
Untitled_5::F3 0.6850 0.6683 0.9946 0.7679 0.6036 0.0553
Untitled_5::F4 0.6557 0.5803 0.7426 0.6533 0.4876 0.8718
Untitled_6::C1 0.8245 0.6793 0.5507 0.7208 0.7264 0.5294
Untitled_6::C2 0.9361 0.6262 0.6724 0.8234 0.6478 0.6453
Untitled_6::F1 0.8745 0.6233 0.4034 0.7151 0.6348 0.4096
Untitled_6::F2 0.6731 0.6216 0.5792 0.5812 0.7459 0.5798
Untitled_6::F3 0.9356 0.4627 0.6768 0.7948 0.5008 0.6323
Untitled_6::F4 0.0833 0.6853 0.6322 -0.0349 0.6700 0.6003
Untitled_7::C1 0.9806 0.9082 0.5286 0.9244 0.9065 0.4072
Untitled_7::C2 0.8211 0.8497 0.5445 0.7699 0.8825 0.4786
Untitled_7::F1 0.0679 0.8619 0.6603 0.0298 0.9164 0.5154
Untitled_7::F2 0.0503 0.8458 0.3930 -0.0417 0.7914 0.3162
Untitled_7::F3 0.7547 0.9083 0.6833 0.7600 0.9726 0.6000
Untitled_7::F4 0.7282 0.8979 0.4173 0.6647 0.9231 0.3783
Untitled_8::C1 0.9004 0.1285 0.3791 0.8347 0.0881 0.1889
Untitled_8::C2 0.9813 0.0778 0.5198 0.9330 0.0543 0.3224
Untitled_8::F1 0.9762 0.0649 0.2472 0.8132 -0.0361 0.1049
Untitled_8::F2 0.7444 0.0765 0.3830 0.7007 0.1468 0.2258
Untitled_8::F3 0.1373 0.1308 0.5149 0.0754 0.0654 0.2699
Untitled_8::F4 0.9075 0.1400 0.6532 0.9100 0.1650 0.4228
H_head 0.1068 0.5540 0.7590 0.1471 0.6061 0.9512
H_tail 0.9026 0.2488 0.3725 0.8963 0.1696 0.1258
Analytic Derivatives:
Atom Derivatives fractional Derivatives Cartesian (eV/Ang)
----- -------- -------- -------- -------- -------- --------
Untitled_1::C1 -0.0042 0.0030 0.0226 -0.0378 0.0271 0.2040
Untitled_1::C2 0.0000 0.0149 -0.0126 0.0001 0.1349 -0.1138
Untitled_1::F1 0.0024 0.0065 -0.0107 0.0221 0.0589 -0.0964
Untitled_1::F2 -0.0073 -0.0092 -0.0049 -0.0662 -0.0829 -0.0447
Untitled_1::F3 -0.0025 0.0064 -0.0057 -0.0228 0.0578 -0.0514
Untitled_1::O -0.0035 -0.0198 -0.0190 -0.0313 -0.1790 -0.1718
Untitled_1::C3 0.0077 -0.0127 0.0065 0.0696 -0.1144 0.0588
Untitled_1::F4 0.0079 0.0030 0.0072 0.0718 0.0269 0.0651
Untitled_1::F5 -0.0037 0.0099 -0.0008 -0.0335 0.0899 -0.0069
Untitled_1::F6 -0.0112 0.0023 0.0135 -0.1011 0.0208 0.1217
Untitled_2::C1 0.0109 -0.0024 -0.0130 0.0981 -0.0214 -0.1178
Untitled_2::C2 0.0168 0.0038 0.0115 0.1520 0.0347 0.1039
Untitled_2::F1 0.0039 -0.0072 0.0044 0.0353 -0.0649 0.0401
Untitled_2::F2 -0.0124 -0.0060 0.0092 -0.1121 -0.0538 0.0831
Untitled_2::F3 -0.0045 0.0007 0.0045 -0.0408 0.0064 0.0408
Untitled_2::O 0.0010 0.0105 -0.0014 0.0094 0.0953 -0.0123
Untitled_2::C3 0.0014 -0.0219 -0.0087 0.0129 -0.1982 -0.0784
Untitled_2::F4 0.0106 0.0075 0.0005 0.0956 0.0680 0.0043
Untitled_2::F5 -0.0037 0.0070 0.0070 -0.0331 0.0628 0.0629
Untitled_2::F6 -0.0028 0.0025 0.0039 -0.0249 0.0230 0.0356
Untitled_3::C1 -0.0020 -0.0186 0.0164 -0.0183 -0.1678 0.1483
Untitled_3::C2 0.0023 -0.0082 -0.0005 0.0206 -0.0741 -0.0048
Untitled_3::F1 0.0052 0.0126 0.0080 0.0471 0.1137 0.0721
Untitled_3::F2 -0.0014 -0.0044 -0.0051 -0.0127 -0.0398 -0.0459
Untitled_3::F3 -0.0076 -0.0031 -0.0034 -0.0683 -0.0283 -0.0310
Untitled_3::F4 -0.0080 0.0032 -0.0016 -0.0719 0.0286 -0.0149
Untitled_4::C1 -0.0132 0.0020 -0.0016 -0.1191 0.0182 -0.0148
Untitled_4::C2 0.0120 0.0164 0.0220 0.1087 0.1478 0.1991
Untitled_4::F1 0.0010 0.0040 -0.0013 0.0092 0.0363 -0.0122
Untitled_4::F2 -0.0011 -0.0084 0.0046 -0.0103 -0.0758 0.0416
Untitled_4::F3 -0.0029 0.0036 -0.0103 -0.0262 0.0325 -0.0928
Untitled_4::F4 -0.0177 0.0004 -0.0155 -0.1598 0.0039 -0.1398
Untitled_5::C1 0.0021 0.0087 -0.0066 0.0192 0.0789 -0.0594
Untitled_5::C2 -0.0259 -0.0195 0.0033 -0.2342 -0.1766 0.0294 maximum gradient = 0.2948
Untitled_5::F1 0.0062 -0.0088 0.0014 0.0565 -0.0800 0.0126
Untitled_5::F2 0.0062 -0.0005 0.0011 0.0558 -0.0049 0.0103
Untitled_5::F3 0.0016 -0.0030 -0.0086 0.0148 -0.0268 -0.0778
Untitled_5::F4 0.0299 0.0054 0.0007 0.2702 0.0485 0.0066
Untitled_6::C1 0.0132 0.0036 -0.0044 0.1190 0.0325 -0.0400
Untitled_6::C2 -0.0025 -0.0010 0.0073 -0.0227 -0.0086 0.0663
Untitled_6::F1 0.0087 0.0061 -0.0048 0.0789 0.0554 -0.0431
Untitled_6::F2 -0.0044 0.0122 0.0058 -0.0398 0.1099 0.0524
Untitled_6::F3 -0.0019 0.0038 -0.0113 -0.0174 0.0343 -0.1020
Untitled_6::F4 -0.0164 -0.0039 -0.0008 -0.1478 -0.0356 -0.0069
Untitled_7::C1 0.0102 0.0049 0.0109 0.0925 0.0447 0.0985
Untitled_7::C2 -0.0120 0.0041 0.0168 -0.1082 0.0369 0.1515
Untitled_7::F1 0.0051 0.0058 -0.0032 0.0457 0.0528 -0.0290
Untitled_7::F2 -0.0019 0.0015 -0.0080 -0.0169 0.0134 -0.0727
Untitled_7::F3 0.0020 0.0007 -0.0031 0.0184 0.0062 -0.0278
Untitled_7::F4 0.0003 0.0006 0.0051 0.0028 0.0050 0.0460
Untitled_8::C1 -0.0066 -0.0113 -0.0052 -0.0593 -0.1022 -0.0473
Untitled_8::C2 0.0028 0.0116 -0.0047 0.0253 0.1052 -0.0425
Untitled_8::F1 -0.0055 -0.0090 -0.0012 -0.0498 -0.0811 -0.0113
Untitled_8::F2 -0.0007 -0.0057 0.0074 -0.0065 -0.0512 0.0669
Untitled_8::F3 0.0056 -0.0070 0.0022 0.0507 -0.0629 0.0195
Untitled_8::F4 -0.0092 0.0020 -0.0016 -0.0832 0.0181 -0.0148
H_head 0.0143 0.0024 -0.0174 0.1294 0.0220 -0.1569
H_tail 0.0049 -0.0023 -0.0067 0.0444 -0.0208 -0.0603
Atomic partial charges (electron charges):
Atom s p d total
----- -------- -------- -------- --------
Untitled_1::C1 0.669 1.290 0.076 2.035
Untitled_1::C2 0.670 1.354 0.069 2.093
Untitled_1::F1 1.484 3.725 0.012 5.220
Untitled_1::F2 1.485 3.734 0.012 5.232
Untitled_1::F3 1.481 3.730 0.012 5.222
Untitled_1::O 1.255 2.925 0.020 4.200
Untitled_1::C3 0.636 1.290 0.135 2.062
Untitled_1::F4 1.482 3.729 0.011 5.222
Untitled_1::F5 1.483 3.730 0.012 5.225
Untitled_1::F6 1.483 3.728 0.012 5.223
Untitled_2::C1 0.667 1.339 0.082 2.088
Untitled_2::C2 0.665 1.315 0.073 2.053
Untitled_2::F1 1.484 3.720 0.012 5.216
Untitled_2::F2 1.484 3.726 0.012 5.222
Untitled_2::F3 1.485 3.736 0.013 5.233
Untitled_2::O 1.245 2.950 0.019 4.213
Untitled_2::C3 0.634 1.286 0.136 2.056
Untitled_2::F4 1.484 3.732 0.012 5.228
Untitled_2::F5 1.484 3.730 0.012 5.226
Untitled_2::F6 1.483 3.732 0.012 5.227
Untitled_3::C1 0.669 1.323 0.079 2.071
Untitled_3::C2 0.665 1.331 0.083 2.079
Untitled_3::F1 1.486 3.724 0.013 5.223
Untitled_3::F2 1.484 3.741 0.011 5.236
Untitled_3::F3 1.485 3.725 0.012 5.222
Untitled_3::F4 1.484 3.730 0.012 5.227
Untitled_4::C1 0.668 1.298 0.076 2.042
Untitled_4::C2 0.665 1.314 0.082 2.061
Untitled_4::F1 1.486 3.727 0.012 5.226
Untitled_4::F2 1.484 3.725 0.012 5.221
Untitled_4::F3 1.485 3.724 0.012 5.221
Untitled_4::F4 1.484 3.734 0.013 5.232
Untitled_5::C1 0.666 1.335 0.083 2.083
Untitled_5::C2 0.668 1.324 0.081 2.073
Untitled_5::F1 1.485 3.723 0.012 5.220
Untitled_5::F2 1.484 3.728 0.012 5.224
Untitled_5::F3 1.484 3.716 0.012 5.212
Untitled_5::F4 1.485 3.745 0.013 5.243
Untitled_6::C1 0.667 1.346 0.084 2.096
Untitled_6::C2 0.669 1.339 0.082 2.090
Untitled_6::F1 1.484 3.720 0.012 5.215
Untitled_6::F2 1.484 3.728 0.012 5.225
Untitled_6::F3 1.486 3.735 0.012 5.233
Untitled_6::F4 1.486 3.730 0.012 5.228
Untitled_7::C1 0.666 1.349 0.082 2.098
Untitled_7::C2 0.669 1.347 0.081 2.098
Untitled_7::F1 1.483 3.723 0.012 5.218
Untitled_7::F2 1.483 3.723 0.012 5.217
Untitled_7::F3 1.483 3.722 0.011 5.217
Untitled_7::F4 1.485 3.722 0.012 5.219
Untitled_8::C1 0.672 1.375 0.080 2.127
Untitled_8::C2 0.671 1.354 0.081 2.106
Untitled_8::F1 1.480 3.725 0.011 5.216
Untitled_8::F2 1.481 3.727 0.011 5.219
Untitled_8::F3 1.483 3.719 0.011 5.213
Untitled_8::F4 1.483 3.728 0.011 5.222
H_head 0.167 0.002 0.000 0.170
H_tail 0.171 0.003 0.000 0.174
Analysis of the electronic structure:
The system is an insulator with an indirect gap of 6.097 eV.
The valence band (#169) maximum is located near (0.00 0.00 0.50), at -0.148 eV with respect to the Fermi level.
The conduction band (#170) minimum is located near (0.00 0.50 0.50), at 5.950 eV with respect to the Fermi level.
The center of the gap is located at 2.900896 eV with respect to the Fermi level.
The Fermi energy is used as the zero of the energy scale.
Job completed on Fri 25 July 2025 at 20:48:51 CST after 3323 s (0:55:23)
Entire job completed on Fri 25 July 2025 at 20:48:51 CST after 3323 s (0:55:23)
and running 1 tasks.