[Wed Dec 20 14:43:31 CST 2023] [MD] [warn] 'Starting MedeA Core 3.6.0' Forcefield set to: pcff+ File: Local::/home/medea/MD/Jobs/dir500/721/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/dir500/721/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 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 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 150000 150000 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 150000 150000 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 150000 150000 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 150000 150000 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 150000 150000 c_myADF6\[*\] file tmp6.adf mode vector timestep 1 run 150000 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 15: Angle atoms 7558 7556 7557 missing on proc 15 at step 4024347 (../ntopo_angle_all.cpp:64) ************************************** Stage 2.1: Initialize LAMMPS for a Class 2 type of forcefield 'pcff+' (from Local::/home/medea/MD/Jobs/dir500/721/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 1454 steps ending because the force tolerance Property Value Units ------------------ ---------- ----------- nSteps: 1454 Initial Fmax: 5935.3 kJ/mol/Ang Fmax: 0.7 kJ/mol/Ang Initial Frms: 171.3 kJ/mol/Ang Frms: 0.0 kJ/mol/Ang P: -12479.2 atm V: 143340.9 Ang^3 rho: 1.3114 g/mL Sxx: 11282.7 atm Syy: 12033.3 atm Szz: 14121.7 atm Syz: -93.4 atm Sxz: 15.3 atm Sxy: -23.0 atm Initial Epot: -1466346.1 kJ/mol Epot: -1525561.9 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: -15.9 kJ/mol/Ang sum_fy: -21.1 kJ/mol/Ang sum_fz: -20.4 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: 298.14 +/- 0.11 K 0 0.0% P: -7388 +/- 24 atm 0 0.0% V: 143341 +/- 0 Ang^3 0 0.0% rho: 1.31144 +/- 0 g/mL 0 0.0% Etotal: -1448880 +/- 110 kJ/mol 1000 10.0% Epot: -1478260 +/- 190 kJ/mol 0 0.0% Ekin: 29441 +/- 11 kJ/mol 0 0.0% Evdw: 154461 +/- 78 kJ/mol 0 0.0% Ecoul: -1633180 +/- 190 kJ/mol 0 0.0% Sxx: 6074 +/- 24 atm 0 0.0% Syy: 6973 +/- 50 atm 0 0.0% Szz: 9116 +/- 30 atm 0 0.0% Syz: -15 +/- 25 atm 0 0.0% Sxz: -2 +/- 15 atm 0 0.0% Sxy: 72 +/- 15 atm 1000 10.0% 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: 298.226 +/- 0.043 K 0 0.0% P: -7372 +/- 13 atm 0 0.0% V: 143341 +/- 0 Ang^3 0 0.0% rho: 1.31144 +/- 0 g/mL 0 0.0% Etotal: -1449232 +/- 73 kJ/mol 0 0.0% Epot: -1478682 +/- 72 kJ/mol 0 0.0% Ekin: 29450.1 +/- 4.3 kJ/mol 0 0.0% Evdw: 154566 +/- 30 kJ/mol 0 0.0% Ecoul: -1633659 +/- 78 kJ/mol 0 0.0% Sxx: 6088 +/- 24 atm 0 0.0% Syy: 6950 +/- 13 atm 0 0.0% Szz: 9079 +/- 32 atm 0 0.0% Syz: 0.5 +/- 8.8 atm 0 0.0% Sxz: -3 +/- 12 atm 0 0.0% Sxy: 56 +/- 12 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 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 150000 150000 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 150000 150000 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 150000 150000 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 150000 150000 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 150000 150000 c_myADF6\[*\] file tmp6.adf mode vector timestep 1 run 150000 unfix 1 unfix ad1 unfix ad3 unfix ad4 unfix ad5 unfix ad6 ********************************************* WARNING: this LAMMPS stage completed on Thu 21 December 2023 at 10:23:17 CST after 70779 s (19:39:39) with the following error: ERROR on proc 15: Angle atoms 7558 7556 7557 missing on proc 15 at step 4024347 (../ntopo_angle_all.cpp:64) ********************************************* Entire job completed on Thu 21 December 2023 at 10:23:17 CST after 70779 s (19:39:39) and running 1 tasks.