[Tue Dec 12 08:58:30 CST 2023] [MD] [warn] 'Starting MedeA Core 3.6.0' Forcefield set to: pcff+ File: Local::/home/medea/MD/Jobs/dir500/709/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/dir500/709/pcff+.frc) Current system formula: K31Na2Li10Mg406S231Cl393O4892H7936 (K31Na2Li10Mg406S231Cl393O4892H7936) 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 7 7 0 2.6 0 2.6 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 3.2 0 3.2 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 3.5 0 3.5 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 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 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 timestep 1 run 150000 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 8: Bond atoms 4143 4141 missing on proc 8 at step 4002359 (../ntopo_bond_all.cpp:61) ************************************** Stage 2.1: Initialize LAMMPS for a Class 2 type of forcefield 'pcff+' (from Local::/home/medea/MD/Jobs/dir500/709/pcff+.frc) Current system formula: K31Na2Li10Mg406S231Cl393O4892H7936 (K31Na2Li10Mg406S231Cl393O4892H7936) 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 1519 steps ending because the force tolerance Property Value Units ------------------ ---------- ----------- nSteps: 1519 Initial Fmax: 371.7 kJ/mol/Ang Fmax: 0.6 kJ/mol/Ang Initial Frms: 114.7 kJ/mol/Ang Frms: 0.0 kJ/mol/Ang P: 329987.9 atm V: 143799.6 Ang^3 rho: 1.3719 g/mL Sxx: -313209.1 atm Syy: -332514.0 atm Szz: -344240.5 atm Syz: -7130.8 atm Sxz: 2492.1 atm Sxy: 1621.1 atm Initial Epot: -672522.4 kJ/mol Epot: -724888.0 kJ/mol a: 33.7899 Ang b: 48.9160 Ang c: 87.0000 Ang alpha: 90.00 degree beta: 90.00 degree gamma: 90.00 degree sum_fx: 10.0 kJ/mol/Ang sum_fy: 22.8 kJ/mol/Ang sum_fz: 1.8 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: 298.16 +/- 0.13 K 0 0.0% P: 335422 +/- 33 atm 0 0.0% V: 143800 +/- 0 Ang^3 0 0.0% rho: 1.3719 +/- 0 g/mL 0 0.0% Etotal: -631618 +/- 89 kJ/mol 0 0.0% Epot: -665873 +/- 99 kJ/mol 0 0.0% Ekin: 34255 +/- 15 kJ/mol 0 0.0% Evdw: 1135230 +/- 100 kJ/mol 0 0.0% Ecoul: -1803870 +/- 150 kJ/mol 0 0.0% Sxx: -319041 +/- 34 atm 0 0.0% Syy: -337288 +/- 56 atm 0 0.0% Szz: -349938 +/- 30 atm 0 0.0% Syz: -7032 +/- 20 atm 0 0.0% Sxz: 2400 +/- 23 atm 0 0.0% Sxy: 1891 +/- 26 atm 0 0.0% 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: 298.196 +/- 0.085 K 0 0.0% P: 335426 +/- 15 atm 0 0.0% V: 143800 +/- 0 Ang^3 0 0.0% rho: 1.3719 +/- 0 g/mL 0 0.0% Etotal: -631859 +/- 47 kJ/mol 0 0.0% Epot: -666119 +/- 50 kJ/mol 0 0.0% Ekin: 34259.5 +/- 9.8 kJ/mol 0 0.0% Evdw: 1135184 +/- 56 kJ/mol 0 0.0% Ecoul: -1804055 +/- 68 kJ/mol 0 0.0% Sxx: -319049 +/- 23 atm 0 0.0% Syy: -337326 +/- 18 atm 0 0.0% Szz: -349903 +/- 13 atm 0 0.0% Syz: -7021 +/- 16 atm 0 0.0% Sxz: 2411.8 +/- 8.1 atm 0 0.0% Sxy: 1911 +/- 14 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 2.6 0 2.6 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 3.2 0 3.2 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 3.5 0 3.5 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 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 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 timestep 1 run 150000 unfix 1 unfix ad1 unfix ad2 unfix ad3 unfix ad4 unfix ad5 unfix ad6 ********************************************* WARNING: this LAMMPS stage completed on Wed 13 December 2023 at 14:32:26 CST after 106429 s (29:33:49) with the following error: ERROR on proc 8: Bond atoms 4143 4141 missing on proc 8 at step 4002359 (../ntopo_bond_all.cpp:61) ********************************************* Entire job completed on Wed 13 December 2023 at 14:32:26 CST after 106429 s (29:33:49) and running 1 tasks.