[Wed Nov 29 17:01:43 CST 2023] [MD] [warn] 'Starting MedeA Core 3.6.0' Forcefield set to: pcff+ File: Local::/home/medea/MD/Jobs/dir500/698/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/dir500/698/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 2 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 3: Bond atoms 8007 8006 missing on proc 3 at step 2010698 (../ntopo_bond_all.cpp:61) ************************************** Stage 2.1: Initialize LAMMPS for a Class 2 type of forcefield 'pcff+' (from Local::/home/medea/MD/Jobs/dir500/698/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: 6.4 kJ/mol/Ang Initial Frms: 131.9 kJ/mol/Ang Frms: 0.4 kJ/mol/Ang P: -5280.7 atm V: 143908.1 Ang^3 rho: 1.3942 g/mL Sxx: 5576.0 atm Syy: 5265.1 atm Szz: 5001.0 atm Syz: -295.7 atm Sxz: -212.5 atm Sxy: 78.1 atm Initial Epot: -1114631.8 kJ/mol Epot: -1165839.6 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: -15.3 kJ/mol/Ang sum_fy: -24.2 kJ/mol/Ang sum_fz: 304.7 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 +/- 0.16 K 0 0.0% P: -759 +/- 20 atm 0 0.0% V: 143908 +/- 0 Ang^3 0 0.0% rho: 1.39421 +/- 0 g/mL 0 0.0% Etotal: -1094152 +/- 80 kJ/mol 0 0.0% Epot: -1121504 +/- 87 kJ/mol 0 0.0% Ekin: 27352 +/- 15 kJ/mol 0 0.0% Evdw: 122336 +/- 47 kJ/mol 0 0.0% Ecoul: -1244364 +/- 97 kJ/mol 0 0.0% Sxx: 256 +/- 22 atm 0 0.0% Syy: 274 +/- 22 atm 0 0.0% Szz: 1747 +/- 31 atm 0 0.0% Syz: -8 +/- 14 atm 0 0.0% Sxz: -2 +/- 15 atm 0 0.0% Sxy: -8 +/- 15 atm 0 0.0% Stage 2.5: NVT integration for 2 ns with a timestep of 1 fs T is 298.2 K Property Value +/- Uncertainty Units After Steps % Run ------------------ ---------- ----------- ------------- ------------ ------- t: 2000000.0 fs T: 298.216 +/- 0.069 K 0 0.0% P: -767 +/- 16 atm 0 0.0% V: 143908 +/- 0 Ang^3 0 0.0% rho: 1.39421 +/- 0 g/mL 0 0.0% Etotal: -1094333 +/- 36 kJ/mol 0 0.0% Epot: -1121692 +/- 35 kJ/mol 0 0.0% Ekin: 27358.9 +/- 6.3 kJ/mol 0 0.0% Evdw: 122313 +/- 46 kJ/mol 0 0.0% Ecoul: -1244505 +/- 54 kJ/mol 0 0.0% Sxx: 264 +/- 19 atm 0 0.0% Syy: 281 +/- 21 atm 0 0.0% Szz: 1756 +/- 25 atm 0 0.0% Syz: -2 +/- 14 atm 0 0.0% Sxz: 7 +/- 17 atm 0 0.0% Sxy: -2.6 +/- 8.6 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 Thu 30 November 2023 at 14:04:00 CST after 75730 s (21:02:10) with the following error: ERROR on proc 3: Bond atoms 8007 8006 missing on proc 3 at step 2010698 (../ntopo_bond_all.cpp:61) ********************************************* Entire job completed on Thu 30 November 2023 at 14:04:00 CST after 75730 s (21:02:10) and running 1 tasks.