[Mon Nov 27 09:37:22 CST 2023] [MD] [warn] 'Starting MedeA Core 3.6.0' Forcefield set to: pcff+ File: Local::/home/medea/MD/Jobs/dir500/692/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/dir500/692/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 150000 150000 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 150000 150000 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 150000 150000 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 150000 150000 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 150000 150000 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 150000 150000 c_myADF6\[*\] file tmp6.adf mode vector compute myADF7 subset_Layer1 adf 200 4 9 9 0 3.7 0 3.7 fix ad7 subset_Layer1 ave/time 1 150000 150000 c_myADF7\[*\] file tmp7.adf mode vector compute myADF8 subset_Layer1 adf 200 6 9 9 0 4.2 0 4.2 fix ad8 subset_Layer1 ave/time 1 150000 150000 c_myADF8\[*\] file tmp8.adf mode vector compute myADF9 subset_Layer1 adf 200 3 9 9 0 4.8 0 4.8 fix ad9 subset_Layer1 ave/time 1 150000 150000 c_myADF9\[*\] file tmp9.adf mode vector compute myADF10 subset_Layer1 adf 200 5 9 9 0 3.9 0 3.9 fix ad10 subset_Layer1 ave/time 1 150000 150000 c_myADF10\[*\] file tmp10.adf mode vector timestep 1 run 150000 unfix 1 unfix ad1 unfix ad2 unfix ad3 unfix ad4 unfix ad5 unfix ad6 unfix ad7 unfix ad8 unfix ad9 unfix ad10 #------------------------------------------------------------------------------- # 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 7: Bond atoms 5761 5759 missing on proc 7 at step 3007340 (../ntopo_bond_all.cpp:61) ************************************** Stage 2.1: Initialize LAMMPS for a Class 2 type of forcefield 'pcff+' (from Local::/home/medea/MD/Jobs/dir500/692/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: 7.8 kJ/mol/Ang Initial Frms: 131.9 kJ/mol/Ang Frms: 0.5 kJ/mol/Ang P: -5290.5 atm V: 143908.1 Ang^3 rho: 1.3942 g/mL Sxx: 5597.7 atm Syy: 5298.1 atm Szz: 4975.8 atm Syz: -304.7 atm Sxz: -223.5 atm Sxy: 84.6 atm Initial Epot: -1114631.8 kJ/mol Epot: -1165831.9 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: -14.5 kJ/mol/Ang sum_fy: -21.3 kJ/mol/Ang sum_fz: 289.2 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: 298.09 +/- 0.15 K 0 0.0% P: -750 +/- 14 atm 0 0.0% V: 143908 +/- 0 Ang^3 0 0.0% rho: 1.39421 +/- 0 g/mL 0 0.0% Etotal: -1094109 +/- 59 kJ/mol 1000 10.0% Epot: -1121462 +/- 57 kJ/mol 1000 10.0% Ekin: 27347 +/- 14 kJ/mol 0 0.0% Evdw: 122401 +/- 40 kJ/mol 0 0.0% Ecoul: -1244330 +/- 110 kJ/mol 0 0.0% Sxx: 251 +/- 20 atm 0 0.0% Syy: 279 +/- 18 atm 0 0.0% Szz: 1720 +/- 16 atm 0 0.0% Syz: -17 +/- 18 atm 0 0.0% Sxz: 9 +/- 20 atm 0 0.0% Sxy: 0 +/- 18 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: 298.174 +/- 0.062 K 0 0.0% P: -759 +/- 11 atm 0 0.0% V: 143908 +/- 0 Ang^3 0 0.0% rho: 1.39421 +/- 0 g/mL 0 0.0% Etotal: -1094340 +/- 79 kJ/mol 0 0.0% Epot: -1121734 +/- 52 kJ/mol 2000 20.0% Ekin: 27355.1 +/- 5.7 kJ/mol 0 0.0% Evdw: 122398 +/- 35 kJ/mol 0 0.0% Ecoul: -1244571 +/- 95 kJ/mol 0 0.0% Sxx: 268 +/- 19 atm 0 0.0% Syy: 269 +/- 12 atm 0 0.0% Szz: 1740 +/- 16 atm 0 0.0% Syz: 5 +/- 11 atm 0 0.0% Sxz: -1 +/- 12 atm 0 0.0% Sxy: -11.6 +/- 6.9 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 150000 150000 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 150000 150000 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 150000 150000 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 150000 150000 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 150000 150000 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 150000 150000 c_myADF6\[*\] file tmp6.adf mode vector compute myADF7 subset_Layer1 adf 200 4 9 9 0 3.7 0 3.7 fix ad7 subset_Layer1 ave/time 1 150000 150000 c_myADF7\[*\] file tmp7.adf mode vector compute myADF8 subset_Layer1 adf 200 6 9 9 0 4.2 0 4.2 fix ad8 subset_Layer1 ave/time 1 150000 150000 c_myADF8\[*\] file tmp8.adf mode vector compute myADF9 subset_Layer1 adf 200 3 9 9 0 4.8 0 4.8 fix ad9 subset_Layer1 ave/time 1 150000 150000 c_myADF9\[*\] file tmp9.adf mode vector compute myADF10 subset_Layer1 adf 200 5 9 9 0 3.9 0 3.9 fix ad10 subset_Layer1 ave/time 1 150000 150000 c_myADF10\[*\] file tmp10.adf mode vector timestep 1 run 150000 unfix 1 unfix ad1 unfix ad2 unfix ad3 unfix ad4 unfix ad5 unfix ad6 unfix ad7 unfix ad8 unfix ad9 unfix ad10 ********************************************* WARNING: this LAMMPS stage completed on Tue 28 November 2023 at 02:37:16 CST after 61187 s (16:59:47) with the following error: ERROR on proc 7: Bond atoms 5761 5759 missing on proc 7 at step 3007340 (../ntopo_bond_all.cpp:61) ********************************************* Entire job completed on Tue 28 November 2023 at 02:37:16 CST after 61187 s (16:59:47) and running 1 tasks.