[Fri Dec 29 23:55:51 CST 2023] [MD] [warn] 'Starting MedeA Core 3.6.0' Forcefield set to: pcff+ File: Local::/home/medea/MD/Jobs/dir500/733/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/dir500/733/pcff+.frc) Current system formula: K6Li14Mg440S227Cl446O4807H7798 (K6Li14Mg440S227Cl446O4807H7798) 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 1 ns with a timestep of 1 fs T is 298.2 K Stage 2.5: NVT integration for 3 ns 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 subset_Layer1 nvt temp 298.2 298.2 100 drag 0.0 compute myADF1 all adf 100 4 6 6 0 2.7 0 2.7 fix ad1 subset_Layer1 ave/time 1 200000 200000 c_myADF1\[*\] file tmp1.adf mode vector compute myADF3 all adf 100 3 6 6 0 3.4 0 3.4 fix ad3 subset_Layer1 ave/time 1 200000 200000 c_myADF3\[*\] file tmp3.adf mode vector compute myADF4 all adf 100 5 6 6 0 2.7 0 2.7 fix ad4 subset_Layer1 ave/time 1 200000 200000 c_myADF4\[*\] file tmp4.adf mode vector compute myADF5 all adf 100 1 6 6 0 3.9 0 3.9 fix ad5 subset_Layer1 ave/time 1 200000 200000 c_myADF5\[*\] file tmp5.adf mode vector compute myADF6 all adf 100 8 6 6 0 4.8 0 4.8 fix ad6 subset_Layer1 ave/time 1 200000 200000 c_myADF6\[*\] file tmp6.adf mode vector timestep 1 run 200000 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 9: Bond atoms 10374 10373 missing on proc 9 at step 3007627 (../ntopo_bond_all.cpp:61) ************************************** Stage 2.1: Initialize LAMMPS for a Class 2 type of forcefield 'pcff+' (from Local::/home/medea/MD/Jobs/dir500/733/pcff+.frc) Current system formula: K6Li14Mg440S227Cl446O4807H7798 (K6Li14Mg440S227Cl446O4807H7798) 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 1685 steps ending because the force tolerance Property Value Units ------------------ ---------- ----------- nSteps: 1685 Initial Fmax: 785.4 kJ/mol/Ang Fmax: 0.6 kJ/mol/Ang Initial Frms: 115.3 kJ/mol/Ang Frms: 0.0 kJ/mol/Ang P: 332766.7 atm V: 142807.9 Ang^3 rho: 1.3824 g/mL Sxx: -315813.0 atm Syy: -334972.3 atm Szz: -347514.7 atm Syz: -7061.9 atm Sxz: 2509.2 atm Sxy: 1883.7 atm Initial Epot: -734737.9 kJ/mol Epot: -785267.8 kJ/mol a: 33.7899 Ang b: 48.9160 Ang c: 86.4000 Ang alpha: 90.00 degree beta: 90.00 degree gamma: 90.00 degree sum_fx: 19.6 kJ/mol/Ang sum_fy: -9.0 kJ/mol/Ang sum_fz: -7.7 kJ/mol/Ang Stage 2.3: Set the velocities for 298.2 K Stage 2.4: NVT integration for 1 ns with a timestep of 1 fs T is 298.2 K Property Value +/- Uncertainty Units After Steps % Run ------------------ ---------- ----------- ------------- ------------ ------- t: 1000000.0 fs T: 298.17 +/- 0.15 K 0 0.0% P: 337801 +/- 24 atm 0 0.0% V: 142808 +/- 0 Ang^3 0 0.0% rho: 1.38238 +/- 0 g/mL 0 0.0% Etotal: -692822 +/- 64 kJ/mol 1000 10.0% Epot: -726736 +/- 63 kJ/mol 1000 10.0% Ekin: 33907 +/- 17 kJ/mol 0 0.0% Evdw: 1142200 +/- 74 kJ/mol 0 0.0% Ecoul: -1871700 +/- 120 kJ/mol 0 0.0% Sxx: -321388 +/- 30 atm 0 0.0% Syy: -339707 +/- 39 atm 0 0.0% Szz: -352307 +/- 46 atm 0 0.0% Syz: -7037 +/- 18 atm 0 0.0% Sxz: 2447 +/- 25 atm 0 0.0% Sxy: 1934 +/- 16 atm 0 0.0% Stage 2.5: NVT integration for 3 ns with a timestep of 1 fs T is 298.2 K Property Value +/- Uncertainty Units After Steps % Run ------------------ ---------- ----------- ------------- ------------ ------- t: 3000000.0 fs T: 298.188 +/- 0.062 K 0 0.0% P: 337794 +/- 23 atm 0 0.0% V: 142808 +/- 0 Ang^3 0 0.0% rho: 1.38238 +/- 0 g/mL 0 0.0% Etotal: -693050 +/- 54 kJ/mol 0 0.0% Epot: -726959 +/- 55 kJ/mol 0 0.0% Ekin: 33909.1 +/- 7.1 kJ/mol 0 0.0% Evdw: 1142213 +/- 54 kJ/mol 0 0.0% Ecoul: -1871915 +/- 69 kJ/mol 0 0.0% Sxx: -321359 +/- 29 atm 0 0.0% Syy: -339749 +/- 22 atm 0 0.0% Szz: -352275 +/- 34 atm 0 0.0% Syz: -7028 +/- 16 atm 0 0.0% Sxz: 2430 +/- 19 atm 0 0.0% Sxy: 1947 +/- 24 atm 0 0.0% 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 subset_Layer1 nvt temp 298.2 298.2 100 drag 0.0 compute myADF1 all adf 100 4 6 6 0 2.7 0 2.7 fix ad1 subset_Layer1 ave/time 1 200000 200000 c_myADF1\[*\] file tmp1.adf mode vector compute myADF3 all adf 100 3 6 6 0 3.4 0 3.4 fix ad3 subset_Layer1 ave/time 1 200000 200000 c_myADF3\[*\] file tmp3.adf mode vector compute myADF4 all adf 100 5 6 6 0 2.7 0 2.7 fix ad4 subset_Layer1 ave/time 1 200000 200000 c_myADF4\[*\] file tmp4.adf mode vector compute myADF5 all adf 100 1 6 6 0 3.9 0 3.9 fix ad5 subset_Layer1 ave/time 1 200000 200000 c_myADF5\[*\] file tmp5.adf mode vector compute myADF6 all adf 100 8 6 6 0 4.8 0 4.8 fix ad6 subset_Layer1 ave/time 1 200000 200000 c_myADF6\[*\] file tmp6.adf mode vector timestep 1 run 200000 unfix 1 unfix ad1 unfix ad3 unfix ad4 unfix ad5 unfix ad6 ********************************************* WARNING: this LAMMPS stage completed on Sat 30 December 2023 at 22:57:06 CST after 82868 s (23:01:08) with the following error: ERROR on proc 9: Bond atoms 10374 10373 missing on proc 9 at step 3007627 (../ntopo_bond_all.cpp:61) ********************************************* Entire job completed on Sat 30 December 2023 at 22:57:06 CST after 82868 s (23:01:08) and running 1 tasks.