[Fri Nov 10 17:58:33 CST 2023] [MD] [warn] 'Starting MedeA Core 3.6.0' Forcefield set to: pcff+ File: Local::/home/medea/MD/Jobs/dir500/674/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/dir500/674/pcff+.frc) Current system formula: K671Na2Li10Mg206S31Cl1033O2892H5536 (K671Na2Li10Mg206S31Cl1033O2892H5536) 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: 1000 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 movable nvt temp 298.2 298.2 100 drag 0.0 compute myADF1 subset_Layer1 adf 200 4 7 7 0 2.8 0 2.8 fix ad1 subset_Layer1 ave/time 1 10000 10000 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 10000 10000 c_myADF2\[*\] file tmp2.adf mode vector compute myADF3 subset_Layer1 adf 200 3 7 7 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 7 7 0 3.0 0 3.0 fix ad4 subset_Layer1 ave/time 1 10000 10000 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 10000 10000 c_myADF5\[*\] file tmp5.adf mode vector compute myADF6 subset_Layer1 adf 200 9 7 7 0 4.7 0 4.7 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 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 6 stages: ***** LAMMPS error in LAMMPS.out ***** ERROR on proc 13: Angle atoms 3037 3035 3036 missing on proc 13 at step 3003402 (../ntopo_angle_all.cpp:64) ************************************** Stage 2.1: Initialize LAMMPS for a Class 2 type of forcefield 'pcff+' (from Local::/home/medea/MD/Jobs/dir500/674/pcff+.frc) Current system formula: K671Na2Li10Mg206S31Cl1033O2892H5536 (K671Na2Li10Mg206S31Cl1033O2892H5536) 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: 1000 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 1000 steps ending because the max iterations Property Value Units ------------------ ---------- ----------- nSteps: 1000 Initial Fmax: 407.0 kJ/mol/Ang Fmax: 8.9 kJ/mol/Ang Initial Frms: 131.9 kJ/mol/Ang Frms: 0.5 kJ/mol/Ang P: -5275.5 atm V: 143908.1 Ang^3 rho: 1.3942 g/mL Sxx: 5568.8 atm Syy: 5294.2 atm Szz: 4963.6 atm Syz: -300.1 atm Sxz: -218.8 atm Sxy: 94.8 atm Initial Epot: -1114631.8 kJ/mol Epot: -1165829.9 kJ/mol a: 35.8935 Ang b: 35.8935 Ang c: 111.7000 Ang alpha: 90.00 degree beta: 90.00 degree gamma: 90.00 degree sum_fx: -20.6 kJ/mol/Ang sum_fy: -23.4 kJ/mol/Ang sum_fz: 299.2 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: 298.15 +/- 0.12 K 0 0.0% P: -775 +/- 21 atm 0 0.0% V: 143908 +/- 0 Ang^3 0 0.0% rho: 1.39421 +/- 0 g/mL 0 0.0% Etotal: -1094135 +/- 94 kJ/mol 0 0.0% Epot: -1121511 +/- 88 kJ/mol 1000 10.0% Ekin: 27353 +/- 11 kJ/mol 0 0.0% Evdw: 122328 +/- 70 kJ/mol 0 0.0% Ecoul: -1244320 +/- 150 kJ/mol 0 0.0% Sxx: 293 +/- 20 atm 0 0.0% Syy: 273 +/- 21 atm 0 0.0% Szz: 1760 +/- 36 atm 0 0.0% Syz: -12 +/- 12 atm 0 0.0% Sxz: -15 +/- 16 atm 0 0.0% Sxy: -2 +/- 15 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: 298.21 +/- 0.05 K 0 0.0% P: -771 +/- 16 atm 0 0.0% V: 143908 +/- 0 Ang^3 0 0.0% rho: 1.39421 +/- 0 g/mL 0 0.0% Etotal: -1094390 +/- 110 kJ/mol 0 0.0% Epot: -1121750 +/- 100 kJ/mol 0 0.0% Ekin: 27358.4 +/- 4.6 kJ/mol 0 0.0% Evdw: 122365 +/- 45 kJ/mol 0 0.0% Ecoul: -1244590 +/- 100 kJ/mol 0 0.0% Sxx: 271 +/- 19 atm 0 0.0% Syy: 274 +/- 18 atm 0 0.0% Szz: 1769 +/- 25 atm 0 0.0% Syz: 3.3 +/- 9.4 atm 0 0.0% Sxz: -3 +/- 12 atm 0 0.0% Sxy: -4.9 +/- 9.1 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 7 7 0 2.8 0 2.8 fix ad1 subset_Layer1 ave/time 1 10000 10000 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 10000 10000 c_myADF2\[*\] file tmp2.adf mode vector compute myADF3 subset_Layer1 adf 200 3 7 7 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 7 7 0 3.0 0 3.0 fix ad4 subset_Layer1 ave/time 1 10000 10000 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 10000 10000 c_myADF5\[*\] file tmp5.adf mode vector compute myADF6 subset_Layer1 adf 200 9 7 7 0 4.7 0 4.7 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 ad2 unfix ad3 unfix ad4 unfix ad5 unfix ad6 ********************************************* WARNING: this LAMMPS stage completed on Sat 11 November 2023 at 09:00:55 CST after 54128 s (15:02:08) with the following error: ERROR on proc 13: Angle atoms 3037 3035 3036 missing on proc 13 at step 3003402 (../ntopo_angle_all.cpp:64) ********************************************* Entire job completed on Sat 11 November 2023 at 09:00:55 CST after 54128 s (15:02:08) and running 1 tasks.