[Mon Nov 06 17:54:46 CST 2023] [MD] [warn] 'Starting MedeA Core 3.6.0' Forcefield set to: pcff+ File: Local::/home/medea/MD/Jobs/dir500/665/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/dir500/665/pcff+.frc) Current system formula: K31Na2Li10Mg206S31Cl393O2892H5536 (K31Na2Li10Mg206S31Cl393O2892H5536) 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: NPT integration for 2 ns with a timestep of 1 fs P is 1 bar with cell dimensions 'a' 'b' 'alpha' 'beta' 'gamma' fixed, others relaxed 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 all nvt temp 298.2 298.2 100 drag 0.0 compute myADF1 all adf 200 4 7 7 0 2.6 0 2.6 fix ad1 all ave/time 1 10000 10000 c_myADF1\[*\] file tmp1.adf mode vector compute myADF2 all adf 200 6 7 7 0 3.3 0 3.3 fix ad2 all ave/time 1 10000 10000 c_myADF2\[*\] file tmp2.adf mode vector compute myADF3 all adf 200 3 7 7 0 3.5 0 3.5 fix ad3 all ave/time 1 10000 10000 c_myADF3\[*\] file tmp3.adf mode vector compute myADF4 all adf 200 5 7 7 0 2.7 0 2.7 fix ad4 all ave/time 1 10000 10000 c_myADF4\[*\] file tmp4.adf mode vector compute myADF5 all adf 200 1 7 7 0 3.9 0 3.9 fix ad5 all ave/time 1 10000 10000 c_myADF5\[*\] file tmp5.adf mode vector compute myADF6 all adf 200 9 7 7 0 4.8 0 4.8 fix ad6 all ave/time 1 10000 10000 c_myADF6\[*\] file tmp6.adf mode vector timestep 1 run 10000 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 13: Bond atoms 3620 3618 missing on proc 13 at step 3001796 (../ntopo_bond_all.cpp:61) ************************************** Stage 2.1: Initialize LAMMPS for a Class 2 type of forcefield 'pcff+' (from Local::/home/medea/MD/Jobs/dir500/665/pcff+.frc) Current system formula: K31Na2Li10Mg206S31Cl393O2892H5536 (K31Na2Li10Mg206S31Cl393O2892H5536) 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 36 steps ending because the linesearch alpha is zero Property Value Units ------------------ ---------- ----------- nSteps: 36 Initial Fmax: 32674.0 kJ/mol/Ang Fmax: 15995.4 kJ/mol/Ang Initial Frms: 1782.6 kJ/mol/Ang Frms: 316.7 kJ/mol/Ang P: 14570.0 atm V: 92859.5 Ang^3 rho: 1.3074 g/mL Sxx: -14873.9 atm Syy: -13844.4 atm Szz: -14991.7 atm Syz: 1041.1 atm Sxz: 349.5 atm Sxy: 250.3 atm Initial Epot: 495393.3 kJ/mol Epot: -569931.7 kJ/mol a: 33.7899 Ang b: 48.9160 Ang c: 56.1808 Ang alpha: 90.00 degree beta: 90.00 degree gamma: 90.00 degree sum_fx: 0.0 kJ/mol/Ang sum_fy: -0.0 kJ/mol/Ang sum_fz: -0.0 kJ/mol/Ang Stage 2.3: Set the velocities for 298.2 K Stage 2.4: NPT integration for 2 ns with a timestep of 1 fs P is 1 bar with cell dimensions 'a' 'b' 'alpha' 'beta' 'gamma' fixed, others relaxed T is 298.2 K Property Value +/- Uncertainty Units After Steps % Run ------------------ ---------- ----------- ------------- ------------ ------- t: 2000000.0 fs T: 298.29 +/- 0.17 K 0 0.0% P: -8 +/- 19 atm 0 0.0% V: 97469 +/- 63 Ang^3 0 0.0% rho: 1.24559 +/- 0.00081 g/mL 0 0.0% Etotal: -651530 +/- 160 kJ/mol 0 0.0% a: 33.7899 +/- 0 Ang 0 0.0% b: 48.916 +/- 0 Ang 0 0.0% c: 58.97 +/- 0.038 Ang 0 0.0% alpha: 90.00022 +/- 0 degree 0 0.0% beta: 90.00022 +/- 0 degree 0 0.0% gamma: 90.00022 +/- 0 degree 0 0.0% Epot: -675090 +/- 150 kJ/mol 0 0.0% Ekin: 23556 +/- 14 kJ/mol 0 0.0% Evdw: 88979 +/- 55 kJ/mol 0 0.0% Ecoul: -764550 +/- 180 kJ/mol 0 0.0% Sxx: 16 +/- 35 atm 0 0.0% Syy: 10 +/- 30 atm 0 0.0% Szz: -1.1 +/- 8.6 atm 0 0.0% Syz: 10 +/- 17 atm 0 0.0% Sxz: -7 +/- 14 atm 0 0.0% Sxy: 3 +/- 17 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: 298.225 +/- 0.09 K 0 0.0% P: -19 +/- 25 atm 1000 10.0% V: 97500.2 +/- 1.7e-09 Ang^3 0 0.0% rho: 1.24518 +/- 0 g/mL 0 0.0% Etotal: -651631 +/- 38 kJ/mol 0 0.0% Epot: -675182 +/- 37 kJ/mol 0 0.0% Ekin: 23551.1 +/- 7.1 kJ/mol 0 0.0% Evdw: 88949 +/- 53 kJ/mol 0 0.0% Ecoul: -764584 +/- 62 kJ/mol 0 0.0% Sxx: -6 +/- 32 atm 0 0.0% Syy: 12 +/- 24 atm 0 0.0% Szz: 30 +/- 27 atm 0 0.0% Syz: 10 +/- 11 atm 0 0.0% Sxz: 7 +/- 12 atm 0 0.0% Sxy: 2.2 +/- 9.8 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 all nvt temp 298.2 298.2 100 drag 0.0 compute myADF1 all adf 200 4 7 7 0 2.6 0 2.6 fix ad1 all ave/time 1 10000 10000 c_myADF1\[*\] file tmp1.adf mode vector compute myADF2 all adf 200 6 7 7 0 3.3 0 3.3 fix ad2 all ave/time 1 10000 10000 c_myADF2\[*\] file tmp2.adf mode vector compute myADF3 all adf 200 3 7 7 0 3.5 0 3.5 fix ad3 all ave/time 1 10000 10000 c_myADF3\[*\] file tmp3.adf mode vector compute myADF4 all adf 200 5 7 7 0 2.7 0 2.7 fix ad4 all ave/time 1 10000 10000 c_myADF4\[*\] file tmp4.adf mode vector compute myADF5 all adf 200 1 7 7 0 3.9 0 3.9 fix ad5 all ave/time 1 10000 10000 c_myADF5\[*\] file tmp5.adf mode vector compute myADF6 all adf 200 9 7 7 0 4.8 0 4.8 fix ad6 all ave/time 1 10000 10000 c_myADF6\[*\] file tmp6.adf mode vector timestep 1 run 10000 unfix 1 unfix ad1 unfix ad2 unfix ad3 unfix ad4 unfix ad5 unfix ad6 ********************************************* WARNING: this LAMMPS stage completed on Tue 07 November 2023 at 21:06:17 CST after 97878 s (27:11:18) with the following error: ERROR on proc 13: Bond atoms 3620 3618 missing on proc 13 at step 3001796 (../ntopo_bond_all.cpp:61) ********************************************* Entire job completed on Tue 07 November 2023 at 21:06:17 CST after 97878 s (27:11:18) and running 1 tasks.