[Mon Oct 09 14:32:25 CST 2023] [MD] [warn] 'Starting MedeA Core 3.6.0' Forcefield set to: pcff+ File: Local::/home/medea/MD/Jobs/dir500/638/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 5 stages: Stage 2.1: Initialize LAMMPS for a Class 2 type of forcefield 'pcff+' (from Local::/home/medea/MD/Jobs/dir500/638/pcff+.frc) Current system formula: K40Na866Li7Mg151S31Cl1153O2936H5624 (K40Na866Li7Mg151S31Cl1153O2936H5624) 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: 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 7 7 0 2.7 0 2.7 fix ad1 subset_Layer1 ave/time 1 3000000 3000000 c_myADF1\[*\] file tmp1.adf mode vector compute myADF2 subset_Layer1 adf 200 6 7 7 0 3.3 0 3.3 fix ad2 subset_Layer1 ave/time 1 3000000 3000000 c_myADF2\[*\] file tmp2.adf mode vector compute myADF3 subset_Layer1 adf 200 3 7 7 0 3.5 0 3.5 fix ad3 subset_Layer1 ave/time 1 3000000 3000000 c_myADF3\[*\] file tmp3.adf mode vector compute myADF4 subset_Layer1 adf 200 5 7 7 0 3.0 0 3.0 fix ad4 subset_Layer1 ave/time 1 3000000 3000000 c_myADF4\[*\] file tmp4.adf mode vector compute myADF5 subset_Layer1 adf 200 1 7 7 0 3.9 0 3.9 fix ad5 subset_Layer1 ave/time 1 3000000 3000000 c_myADF5\[*\] file tmp5.adf mode vector compute myADF6 subset_Layer1 adf 200 9 7 7 0 4.8 0 4.8 fix ad6 subset_Layer1 ave/time 1 3000000 3000000 c_myADF6\[*\] file tmp6.adf mode vector timestep 0.5 run 3000000 unfix 1 unfix ad1 unfix ad2 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 5 stages: ***** LAMMPS error in LAMMPS.out ***** ERROR on proc 2: Angle atoms 2429 2427 2428 missing on proc 2 at step 1043633 (../ntopo_angle_all.cpp:64) ************************************** Stage 2.1: Initialize LAMMPS for a Class 2 type of forcefield 'pcff+' (from Local::/home/medea/MD/Jobs/dir500/638/pcff+.frc) Current system formula: K40Na866Li7Mg151S31Cl1153O2936H5624 (K40Na866Li7Mg151S31Cl1153O2936H5624) 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 3000 steps ending because the max iterations Property Value Units ------------------ ---------- ----------- nSteps: 3000 Initial Fmax: 361.1 kJ/mol/Ang Fmax: 3.0 kJ/mol/Ang Initial Frms: 125.9 kJ/mol/Ang Frms: 0.2 kJ/mol/Ang P: -5943.5 atm V: 141184.1 Ang^3 rho: 1.4079 g/mL Sxx: 6083.5 atm Syy: 6234.2 atm Szz: 5512.9 atm Syz: -23.9 atm Sxz: 181.8 atm Sxy: 28.2 atm Initial Epot: -1200276.3 kJ/mol Epot: -1250512.4 kJ/mol a: 36.8271 Ang b: 36.8271 Ang c: 104.1000 Ang alpha: 90.00 degree beta: 90.00 degree gamma: 90.00 degree sum_fx: 8.6 kJ/mol/Ang sum_fy: -1.7 kJ/mol/Ang sum_fz: 59.5 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: 298.13 +/- 0.13 K 0 0.0% P: -275 +/- 17 atm 0 0.0% V: 141184 +/- 0 Ang^3 0 0.0% rho: 1.40793 +/- 0 g/mL 0 0.0% Etotal: -1175026 +/- 61 kJ/mol 0 0.0% Epot: -1203548 +/- 64 kJ/mol 0 0.0% Ekin: 28522 +/- 12 kJ/mol 0 0.0% Evdw: 133638 +/- 58 kJ/mol 0 0.0% Ecoul: -1337690 +/- 110 kJ/mol 0 0.0% Sxx: -169 +/- 17 atm 0 0.0% Syy: -158 +/- 28 atm 0 0.0% Szz: 1151 +/- 16 atm 0 0.0% Syz: -6 +/- 16 atm 0 0.0% Sxz: 14 +/- 15 atm 0 0.0% Sxy: -2 +/- 13 atm 0 0.0% Stage 2.5: 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 7 7 0 2.7 0 2.7 fix ad1 subset_Layer1 ave/time 1 3000000 3000000 c_myADF1\[*\] file tmp1.adf mode vector compute myADF2 subset_Layer1 adf 200 6 7 7 0 3.3 0 3.3 fix ad2 subset_Layer1 ave/time 1 3000000 3000000 c_myADF2\[*\] file tmp2.adf mode vector compute myADF3 subset_Layer1 adf 200 3 7 7 0 3.5 0 3.5 fix ad3 subset_Layer1 ave/time 1 3000000 3000000 c_myADF3\[*\] file tmp3.adf mode vector compute myADF4 subset_Layer1 adf 200 5 7 7 0 3.0 0 3.0 fix ad4 subset_Layer1 ave/time 1 3000000 3000000 c_myADF4\[*\] file tmp4.adf mode vector compute myADF5 subset_Layer1 adf 200 1 7 7 0 3.9 0 3.9 fix ad5 subset_Layer1 ave/time 1 3000000 3000000 c_myADF5\[*\] file tmp5.adf mode vector compute myADF6 subset_Layer1 adf 200 9 7 7 0 4.8 0 4.8 fix ad6 subset_Layer1 ave/time 1 3000000 3000000 c_myADF6\[*\] file tmp6.adf mode vector timestep 0.5 run 3000000 unfix 1 unfix ad1 unfix ad2 unfix ad3 unfix ad4 unfix ad5 unfix ad6 ********************************************* WARNING: this LAMMPS stage completed on Mon 09 October 2023 at 18:58:25 CST after 15952 s (4:25:52) with the following error: ERROR on proc 2: Angle atoms 2429 2427 2428 missing on proc 2 at step 1043633 (../ntopo_angle_all.cpp:64) ********************************************* Entire job completed on Mon 09 October 2023 at 18:58:25 CST after 15952 s (4:25:52) and running 1 tasks.