[Tue Nov 21 09:35:55 CST 2023] [MD] [warn] 'Starting MedeA Core 3.6.0' Forcefield set to: pcff+ File: Local::/home/medea/MD/Jobs/dir500/686/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/dir500/686/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: 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 2.7 0 2.7 fix ad1 subset_Layer1 ave/time 1 50000 50000 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 50000 50000 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 50000 50000 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 50000 50000 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 50000 50000 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 50000 50000 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 50000 50000 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 50000 50000 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 50000 50000 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 50000 50000 c_myADF10\[*\] file tmp10.adf mode vector timestep 1 run 50000 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 6: Angle atoms 3002 3000 3001 missing on proc 6 at step 3001027 (../ntopo_angle_all.cpp:64) ************************************** Stage 2.1: Initialize LAMMPS for a Class 2 type of forcefield 'pcff+' (from Local::/home/medea/MD/Jobs/dir500/686/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: 0.9 kJ/mol/Ang Initial Frms: 125.9 kJ/mol/Ang Frms: 0.1 kJ/mol/Ang P: -5807.4 atm V: 141184.1 Ang^3 rho: 1.4079 g/mL Sxx: 5971.2 atm Syy: 6136.9 atm Szz: 5314.1 atm Syz: 5.0 atm Sxz: 131.2 atm Sxy: 61.3 atm Initial Epot: -1200276.3 kJ/mol Epot: -1250510.9 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: 5.0 kJ/mol/Ang sum_fy: -2.9 kJ/mol/Ang sum_fz: 41.0 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: 298.11 +/- 0.17 K 0 0.0% P: -255 +/- 24 atm 0 0.0% V: 141184 +/- 0 Ang^3 0 0.0% rho: 1.40793 +/- 0 g/mL 0 0.0% Etotal: -1175009 +/- 73 kJ/mol 0 0.0% Epot: -1203529 +/- 80 kJ/mol 0 0.0% Ekin: 28520 +/- 17 kJ/mol 0 0.0% Evdw: 133683 +/- 81 kJ/mol 0 0.0% Ecoul: -1337720 +/- 130 kJ/mol 0 0.0% Sxx: -189 +/- 26 atm 0 0.0% Syy: -167 +/- 29 atm 0 0.0% Szz: 1120 +/- 31 atm 0 0.0% Syz: 11 +/- 12 atm 1000 10.0% Sxz: -2.3 +/- 8.3 atm 0 0.0% Sxy: -2 +/- 13 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: 298.233 +/- 0.059 K 0 0.0% P: -244 +/- 14 atm 0 0.0% V: 141184 +/- 0 Ang^3 0 0.0% rho: 1.40793 +/- 0 g/mL 0 0.0% Etotal: -1175146 +/- 38 kJ/mol 0 0.0% Epot: -1203678 +/- 41 kJ/mol 0 0.0% Ekin: 28532.1 +/- 5.6 kJ/mol 0 0.0% Evdw: 133660 +/- 33 kJ/mol 0 0.0% Ecoul: -1337833 +/- 65 kJ/mol 0 0.0% Sxx: -188 +/- 21 atm 0 0.0% Syy: -205 +/- 18 atm 0 0.0% Szz: 1125 +/- 11 atm 0 0.0% Syz: 1 +/- 12 atm 0 0.0% Sxz: -0.9 +/- 7.2 atm 0 0.0% Sxy: -1.1 +/- 7.5 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 2.7 0 2.7 fix ad1 subset_Layer1 ave/time 1 50000 50000 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 50000 50000 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 50000 50000 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 50000 50000 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 50000 50000 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 50000 50000 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 50000 50000 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 50000 50000 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 50000 50000 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 50000 50000 c_myADF10\[*\] file tmp10.adf mode vector timestep 1 run 50000 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 Wed 22 November 2023 at 09:40:38 CST after 86677 s (24:04:37) with the following error: ERROR on proc 6: Angle atoms 3002 3000 3001 missing on proc 6 at step 3001027 (../ntopo_angle_all.cpp:64) ********************************************* Entire job completed on Wed 22 November 2023 at 09:40:38 CST after 86677 s (24:04:37) and running 1 tasks.