[Sun Dec 24 11:44:53 CST 2023] [MD] [warn] 'Starting MedeA Core 3.6.0' Forcefield set to: pcff+ File: Local::/home/medea/MD/Jobs/dir500/725/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/dir500/725/pcff+.frc) Current system formula: K6Na810Li14Mg240S27Cl1256O2807H5398 (K6Na810Li14Mg240S27Cl1256O2807H5398) 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 4 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 7 7 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 7 7 0 3.6 0 3.6 fix ad3 subset_Layer1 ave/time 1 200000 200000 c_myADF3\[*\] file tmp3.adf mode vector compute myADF4 all adf 100 5 7 7 0 3.0 0 3.0 fix ad4 subset_Layer1 ave/time 1 200000 200000 c_myADF4\[*\] file tmp4.adf mode vector compute myADF5 all adf 100 1 7 7 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 9 7 7 0 4.9 0 4.9 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 3: Bond atoms 8631 8630 missing on proc 3 at step 4012236 (../ntopo_bond_all.cpp:61) ************************************** Stage 2.1: Initialize LAMMPS for a Class 2 type of forcefield 'pcff+' (from Local::/home/medea/MD/Jobs/dir500/725/pcff+.frc) Current system formula: K6Na810Li14Mg240S27Cl1256O2807H5398 (K6Na810Li14Mg240S27Cl1256O2807H5398) 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 1711 steps ending because the force tolerance Property Value Units ------------------ ---------- ----------- nSteps: 1711 Initial Fmax: 722.4 kJ/mol/Ang Fmax: 0.6 kJ/mol/Ang Initial Frms: 131.9 kJ/mol/Ang Frms: 0.0 kJ/mol/Ang P: -6499.1 atm V: 138878.5 Ang^3 rho: 1.4412 g/mL Sxx: 6691.0 atm Syy: 6682.6 atm Szz: 6123.7 atm Syz: -285.0 atm Sxz: -95.6 atm Sxy: 76.7 atm Initial Epot: -1343178.4 kJ/mol Epot: -1394152.8 kJ/mol a: 36.8271 Ang b: 36.8271 Ang c: 102.4000 Ang alpha: 90.00 degree beta: 90.00 degree gamma: 90.00 degree sum_fx: 21.6 kJ/mol/Ang sum_fy: 4.4 kJ/mol/Ang sum_fz: 2.0 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 +/- 0.13 K 0 0.0% P: -11 +/- 24 atm 0 0.0% V: 138878 +/- 0 Ang^3 0 0.0% rho: 1.44119 +/- 0 g/mL 0 0.0% Etotal: -1322312 +/- 42 kJ/mol 2000 20.0% Epot: -1350334 +/- 41 kJ/mol 2000 20.0% Ekin: 28017 +/- 12 kJ/mol 0 0.0% Evdw: 151368 +/- 83 kJ/mol 0 0.0% Ecoul: -1502050 +/- 110 kJ/mol 1000 10.0% Sxx: -432 +/- 22 atm 0 0.0% Syy: -370 +/- 26 atm 0 0.0% Szz: 834 +/- 45 atm 0 0.0% Syz: 3 +/- 20 atm 0 0.0% Sxz: -9 +/- 30 atm 0 0.0% Sxy: -8 +/- 18 atm 0 0.0% Stage 2.5: NVT integration for 4 ns with a timestep of 1 fs T is 298.2 K Property Value +/- Uncertainty Units After Steps % Run ------------------ ---------- ----------- ------------- ------------ ------- t: 4000000.0 fs T: 298.217 +/- 0.072 K 0 0.0% P: 6 +/- 15 atm 0 0.0% V: 138878 +/- 0 Ang^3 0 0.0% rho: 1.44119 +/- 0 g/mL 0 0.0% Etotal: -1322462 +/- 77 kJ/mol 0 0.0% Epot: -1350483 +/- 74 kJ/mol 0 0.0% Ekin: 28021 +/- 6.7 kJ/mol 0 0.0% Evdw: 151372 +/- 49 kJ/mol 0 0.0% Ecoul: -1502220 +/- 110 kJ/mol 0 0.0% Sxx: -428 +/- 19 atm 0 0.0% Syy: -433 +/- 18 atm 0 0.0% Szz: 843 +/- 16 atm 0 0.0% Syz: -6 +/- 13 atm 0 0.0% Sxz: 0 +/- 11 atm 0 0.0% Sxy: -1 +/- 14 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 7 7 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 7 7 0 3.6 0 3.6 fix ad3 subset_Layer1 ave/time 1 200000 200000 c_myADF3\[*\] file tmp3.adf mode vector compute myADF4 all adf 100 5 7 7 0 3.0 0 3.0 fix ad4 subset_Layer1 ave/time 1 200000 200000 c_myADF4\[*\] file tmp4.adf mode vector compute myADF5 all adf 100 1 7 7 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 9 7 7 0 4.9 0 4.9 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 Mon 25 December 2023 at 21:10:08 CST after 120309 s (33:25:09) with the following error: ERROR on proc 3: Bond atoms 8631 8630 missing on proc 3 at step 4012236 (../ntopo_bond_all.cpp:61) ********************************************* Entire job completed on Mon 25 December 2023 at 21:10:08 CST after 120309 s (33:25:09) and running 1 tasks.