[Wed Dec 13 17:37:41 CST 2023] [MD] [warn] 'Starting MedeA Core 3.6.0' Forcefield set to: pcff+ File: Local::/home/medea/MD/Jobs/dir500/711/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 5 stages: Stage 2.1: Initialize LAMMPS for a Class 2 type of forcefield 'pcff+' (from Local::/home/medea/MD/Jobs/dir500/711/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 3 ns with a timestep of 1 fs T is 298.2 K Stage 2.5: 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 5 stages: ***** LAMMPS error in LAMMPS.out ***** ERROR on proc 6: Bond atoms 13772 13770 missing on proc 6 at step 3001769 (../ntopo_bond_all.cpp:61) ************************************** Stage 2.1: Initialize LAMMPS for a Class 2 type of forcefield 'pcff+' (from Local::/home/medea/MD/Jobs/dir500/711/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 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: 298.204 +/- 0.054 K 0 0.0% P: 335420 +/- 15 atm 0 0.0% V: 143800 +/- 0 Ang^3 0 0.0% rho: 1.3719 +/- 0 g/mL 0 0.0% Etotal: -631703 +/- 73 kJ/mol 0 0.0% Epot: -665964 +/- 73 kJ/mol 0 0.0% Ekin: 34260.4 +/- 6.2 kJ/mol 0 0.0% Evdw: 1135198 +/- 51 kJ/mol 0 0.0% Ecoul: -1803921 +/- 71 kJ/mol 0 0.0% Sxx: -319033 +/- 18 atm 0 0.0% Syy: -337316 +/- 32 atm 0 0.0% Szz: -349911 +/- 30 atm 0 0.0% Syz: -7034 +/- 9.2 atm 0 0.0% Sxz: 2406 +/- 13 atm 0 0.0% Sxy: 1898 +/- 11 atm 0 0.0% Stage 2.5: 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 Thu 14 December 2023 at 11:11:56 CST after 63248 s (17:34:08) with the following error: ERROR on proc 6: Bond atoms 13772 13770 missing on proc 6 at step 3001769 (../ntopo_bond_all.cpp:61) ********************************************* Entire job completed on Thu 14 December 2023 at 11:11:56 CST after 63248 s (17:34:08) and running 1 tasks.