[Sat Dec 09 11:01:08 CST 2023] [MD] [warn] 'Starting MedeA Core 3.6.0' Forcefield set to: pcff+ File: Local::/home/medea/MD/Jobs/dir500/706/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/dir500/706/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 0: Angle atoms 4203 4201 4202 missing on proc 0 at step 4001416 (../ntopo_angle_all.cpp:64) ************************************** Stage 2.1: Initialize LAMMPS for a Class 2 type of forcefield 'pcff+' (from Local::/home/medea/MD/Jobs/dir500/706/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 2662 steps ending because the force tolerance Property Value Units ------------------ ---------- ----------- nSteps: 2662 Initial Fmax: 371.7 kJ/mol/Ang Fmax: 0.4 kJ/mol/Ang Initial Frms: 114.7 kJ/mol/Ang Frms: 0.0 kJ/mol/Ang P: 330065.2 atm V: 143799.6 Ang^3 rho: 1.3719 g/mL Sxx: -313320.2 atm Syy: -332578.4 atm Szz: -344297.1 atm Syz: -7177.1 atm Sxz: 2502.2 atm Sxy: 1607.3 atm Initial Epot: -672522.4 kJ/mol Epot: -725025.0 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: 12.5 kJ/mol/Ang sum_fy: 0.6 kJ/mol/Ang sum_fz: -2.2 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: 298.18 +/- 0.13 K 0 0.0% P: 335403 +/- 24 atm 0 0.0% V: 143800 +/- 0 Ang^3 0 0.0% rho: 1.3719 +/- 0 g/mL 0 0.0% Etotal: -631670 +/- 110 kJ/mol 1000 10.0% Epot: -665940 +/- 100 kJ/mol 1000 10.0% Ekin: 34257 +/- 14 kJ/mol 0 0.0% Evdw: 1135106 +/- 65 kJ/mol 0 0.0% Ecoul: -1803810 +/- 100 kJ/mol 1000 10.0% Sxx: -319013 +/- 33 atm 0 0.0% Syy: -337307 +/- 29 atm 0 0.0% Szz: -349888 +/- 39 atm 0 0.0% Syz: -7044 +/- 24 atm 0 0.0% Sxz: 2422 +/- 25 atm 0 0.0% Sxy: 1878 +/- 22 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: 298.205 +/- 0.058 K 0 0.0% P: 335424 +/- 15 atm 0 0.0% V: 143800 +/- 0 Ang^3 0 0.0% rho: 1.3719 +/- 0 g/mL 0 0.0% Etotal: -631803 +/- 44 kJ/mol 0 0.0% Epot: -666063 +/- 44 kJ/mol 0 0.0% Ekin: 34260.6 +/- 6.7 kJ/mol 0 0.0% Evdw: 1135216 +/- 42 kJ/mol 0 0.0% Ecoul: -1804034 +/- 54 kJ/mol 0 0.0% Sxx: -319046 +/- 21 atm 0 0.0% Syy: -337327 +/- 22 atm 0 0.0% Szz: -349898 +/- 18 atm 0 0.0% Syz: -7013 +/- 19 atm 0 0.0% Sxz: 2392 +/- 12 atm 0 0.0% Sxy: 1903 +/- 18 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 Mon 11 December 2023 at 12:00:42 CST after 176367 s (48:59:27) with the following error: ERROR on proc 0: Angle atoms 4203 4201 4202 missing on proc 0 at step 4001416 (../ntopo_angle_all.cpp:64) ********************************************* Entire job completed on Mon 11 December 2023 at 12:00:42 CST after 176367 s (48:59:27) and running 1 tasks.