[Wed Nov 08 10:51:13 CST 2023] [MD] [warn] 'Starting MedeA Core 3.6.0' Forcefield set to: pcff+ File: Local::/home/medea/MD/Jobs/dir500/669/pcff+.frc md5 sum: 271FB553B535FE0449E31A6F8A0898D3 MedeA version 3.6.0 #------------------------------------------------------------------------------- # This calculation has 2 stages #------------------------------------------------------------------------------- Stage 1: Variables tstep = 1 fs T = 298.2 K P = 1 bar Stage 2: This LAMMPS calculation has 6 stages: Stage 2.1: Initialize LAMMPS for a Class 2 type of forcefield 'pcff+' (from Local::/home/medea/MD/Jobs/dir500/669/pcff+.frc) Current system formula: K150Li14Mg384S27Cl878O3671H7126 (K150Li14Mg384S27Cl878O3671H7126) The nonbond terms are handled with a cutoff at 12 Angstrom. The long-range Coulomb interactions are handled with the pppm method to a precision of 0.00001. The long-range van der Waals interactions are included via tail corrections. Stage 2.2: Minimize using conjugate gradients and linesearch fast Relative energy convergence: 0.0 Force convergence: 1.0 Maximum atomic motion: 0.05 Maximum number of iterations: 3000 Maximum number of force evaluations: 10000 Stage 2.3: Set the velocities for 298.2 K Stage 2.4: NVT integration for 10 ps with a timestep of 1 fs T is 298.2 K Stage 2.5: NVT integration for 10 ps with a timestep of 1 fs T is 298.2 K Stage 2.6: Custom code -- Custom code reset_timestep 0 thermo_style custom step v_time press vol v_sysdensity temp ebond eangle edihed eimp evdwl ecoul etail elong pe ke thermo 100 fix 1 movable nvt temp 298.2 298.2 100 drag 0.0 compute myADF1 subset_Layer1 adf 200 4 6 6 0 2.6 0 2.6 fix ad1 subset_Layer1 ave/time 1 10000 10000 c_myADF1\[*\] file tmp1.adf mode vector compute myADF3 subset_Layer1 adf 200 3 6 6 0 3.6 0 3.6 fix ad3 subset_Layer1 ave/time 1 10000 10000 c_myADF3\[*\] file tmp3.adf mode vector compute myADF4 subset_Layer1 adf 200 5 6 6 0 2.7 0 2.7 fix ad4 subset_Layer1 ave/time 1 10000 10000 c_myADF4\[*\] file tmp4.adf mode vector compute myADF5 subset_Layer1 adf 200 1 6 6 0 3.9 0 3.9 fix ad5 subset_Layer1 ave/time 1 10000 10000 c_myADF5\[*\] file tmp5.adf mode vector compute myADF6 subset_Layer1 adf 200 8 6 6 0 4.8 0 4.8 fix ad6 subset_Layer1 ave/time 1 10000 10000 c_myADF6\[*\] file tmp6.adf mode vector timestep 1 run 10000 unfix 1 unfix ad1 unfix ad3 unfix ad4 unfix ad5 unfix ad6 #------------------------------------------------------------------------------- # Running the calculation #------------------------------------------------------------------------------- Stage 1: Variables tstep = 1 fs T = 298.2 K P = 1 bar Stage 2: This LAMMPS calculation has 6 stages: ***** LAMMPS error in LAMMPS.out ***** ERROR on proc 26: Angle atoms 4900 4898 4899 missing on proc 26 at step 16691 (../ntopo_angle_all.cpp:64) ************************************** Stage 2.1: Initialize LAMMPS for a Class 2 type of forcefield 'pcff+' (from Local::/home/medea/MD/Jobs/dir500/669/pcff+.frc) Current system formula: K150Li14Mg384S27Cl878O3671H7126 (K150Li14Mg384S27Cl878O3671H7126) The nonbond terms are handled with a cutoff at 12 Angstrom. The long-range Coulomb interactions are handled with the pppm method to a precision of 0.00001. The long-range van der Waals interactions are included via tail corrections. Stage 2.2: Minimize using conjugate gradients and linesearch fast Relative energy convergence: 0.0 Force convergence: 1.0 Maximum atomic motion: 0.05 Maximum number of iterations: 3000 Maximum number of force evaluations: 10000 Note: 2.2_Minimization.out contains warning messages from LAMMPS - examine this file for additional information. The minimization finished after 2436 steps ending because the force tolerance Property Value Units ------------------ ---------- ----------- nSteps: 2436 Initial Fmax: 5935.3 kJ/mol/Ang Fmax: 0.8 kJ/mol/Ang Initial Frms: 171.3 kJ/mol/Ang Frms: 0.0 kJ/mol/Ang P: -12404.2 atm V: 143340.9 Ang^3 rho: 1.3114 g/mL Sxx: 11262.5 atm Syy: 11966.3 atm Szz: 13983.8 atm Syz: -143.5 atm Sxz: -15.7 atm Sxy: -59.7 atm Initial Epot: -1466346.1 kJ/mol Epot: -1525701.6 kJ/mol a: 45.4020 Ang b: 32.1502 Ang c: 98.2000 Ang alpha: 90.00 degree beta: 90.00 degree gamma: 90.00 degree sum_fx: -5.2 kJ/mol/Ang sum_fy: -6.9 kJ/mol/Ang sum_fz: 0.5 kJ/mol/Ang Stage 2.3: Set the velocities for 298.2 K Stage 2.4: NVT integration for 10 ps with a timestep of 1 fs T is 298.2 K Property Value +/- Uncertainty Units After Steps % Run ------------------ ---------- ----------- ------------- ------------ ------- t: 10000 fs T: 292 +/- 14 K 0 0.0% P: -7030 +/- 130 atm 0 0.0% V: 143341 +/- 0 Ang^3 0 0.0% rho: 1.31144 +/- 0 g/mL 0 0.0% Etotal: -1447900 +/- 2500 kJ/mol 0 0.0% Epot: -1476700 +/- 1200 kJ/mol 0 0.0% Ekin: 28800 +/- 1400 kJ/mol 0 0.0% Evdw: 155270 +/- 190 kJ/mol 2000 20.0% Ecoul: -1632900 +/- 2000 kJ/mol 0 0.0% Sxx: 5760 +/- 120 atm 0 0.0% Syy: 6590 +/- 110 atm 0 0.0% Szz: 8760 +/- 180 atm 0 0.0% Syz: -77 +/- 48 atm 0 0.0% Sxz: -3 +/- 56 atm 0 0.0% Sxy: 43 +/- 31 atm 0 0.0% Stage 2.5: NVT integration for 10 ps with a timestep of 1 fs T is 298.2 K Property Value +/- Uncertainty Units After Steps % Run ------------------ ---------- ----------- ------------- ------------ ------- t: 10000 fs T: 297.8 +/- 0.57 K 0 0.0% P: -7246 +/- 77 atm 0 0.0% V: 143341 +/- 0 Ang^3 0 0.0% rho: 1.31144 +/- 0 g/mL 0 0.0% Etotal: -1448150 +/- 140 kJ/mol 3000 30.0% Epot: -1477520 +/- 120 kJ/mol 3000 30.0% Ekin: 29408 +/- 56 kJ/mol 0 0.0% Evdw: 154910 +/- 190 kJ/mol 0 0.0% Ecoul: -1632770 +/- 200 kJ/mol 1000 10.0% Sxx: 5992 +/- 78 atm 0 0.0% Syy: 6837 +/- 87 atm 0 0.0% Szz: 8910 +/- 100 atm 0 0.0% Syz: 58 +/- 43 atm 0 0.0% Sxz: 78 +/- 42 atm 0 0.0% Sxy: 50 +/- 55 atm 0 0.0% Group Interactions analysis for groups Layer2/Li_1 (total interaction energy evaluations = 100) -------------------------------------------------------------------- smallest E_ab = -171.9 kJ/mol largest E_ab = -130.7 kJ/mol mean = -153.7 kJ/mol mean of squares = 2.368e+04 (kJ/mol)^2 standard deviation = 7.526 kJ/mol -------------------------------------------------------------------- Group Interactions analysis for groups Layer2/K_1 (total interaction energy evaluations = 100) -------------------------------------------------------------------- smallest E_ab = -64.64 kJ/mol largest E_ab = -47.22 kJ/mol mean = -57.25 kJ/mol mean of squares = 3288 (kJ/mol)^2 standard deviation = 3.318 kJ/mol -------------------------------------------------------------------- Group Interactions analysis for groups Layer2/Mg_1 (total interaction energy evaluations = 100) -------------------------------------------------------------------- smallest E_ab = -4914 kJ/mol largest E_ab = -3676 kJ/mol mean = -4297 kJ/mol mean of squares = 1.852e+07 (kJ/mol)^2 standard deviation = 238.3 kJ/mol -------------------------------------------------------------------- Group Interactions analysis for groups Layer2/Cl_1 (total interaction energy evaluations = 100) -------------------------------------------------------------------- smallest E_ab = 1626 kJ/mol largest E_ab = 2726 kJ/mol mean = 2175 kJ/mol mean of squares = 4.773e+06 (kJ/mol)^2 standard deviation = 211.8 kJ/mol -------------------------------------------------------------------- Group Interactions analysis for groups Layer2/SO4 (total interaction energy evaluations = 100) -------------------------------------------------------------------- smallest E_ab = 48.15 kJ/mol largest E_ab = 198.6 kJ/mol mean = 112.1 kJ/mol mean of squares = 1.345e+04 (kJ/mol)^2 standard deviation = 29.84 kJ/mol -------------------------------------------------------------------- Group Interactions analysis for groups Layer2/H2O (total interaction energy evaluations = 100) -------------------------------------------------------------------- smallest E_ab = -1996 kJ/mol largest E_ab = -1741 kJ/mol mean = -1865 kJ/mol mean of squares = 3.479e+06 (kJ/mol)^2 standard deviation = 55.6 kJ/mol -------------------------------------------------------------------- Stage 2.6: Custom code -- Custom code reset_timestep 0 thermo_style custom step v_time press vol v_sysdensity temp ebond eangle edihed eimp evdwl ecoul etail elong pe ke thermo 100 fix 1 movable nvt temp 298.2 298.2 100 drag 0.0 compute myADF1 subset_Layer1 adf 200 4 6 6 0 2.6 0 2.6 fix ad1 subset_Layer1 ave/time 1 10000 10000 c_myADF1\[*\] file tmp1.adf mode vector compute myADF3 subset_Layer1 adf 200 3 6 6 0 3.6 0 3.6 fix ad3 subset_Layer1 ave/time 1 10000 10000 c_myADF3\[*\] file tmp3.adf mode vector compute myADF4 subset_Layer1 adf 200 5 6 6 0 2.7 0 2.7 fix ad4 subset_Layer1 ave/time 1 10000 10000 c_myADF4\[*\] file tmp4.adf mode vector compute myADF5 subset_Layer1 adf 200 1 6 6 0 3.9 0 3.9 fix ad5 subset_Layer1 ave/time 1 10000 10000 c_myADF5\[*\] file tmp5.adf mode vector compute myADF6 subset_Layer1 adf 200 8 6 6 0 4.8 0 4.8 fix ad6 subset_Layer1 ave/time 1 10000 10000 c_myADF6\[*\] file tmp6.adf mode vector timestep 1 run 10000 unfix 1 unfix ad1 unfix ad3 unfix ad4 unfix ad5 unfix ad6 ********************************************* WARNING: this LAMMPS stage completed on Wed 08 November 2023 at 11:01:55 CST after 635 s (0:10:35) with the following error: ERROR on proc 26: Angle atoms 4900 4898 4899 missing on proc 26 at step 16691 (../ntopo_angle_all.cpp:64) ********************************************* Entire job completed on Wed 08 November 2023 at 11:01:55 CST after 635 s (0:10:35) and running 1 tasks.