Hii, I am planning to simulate the adsorption in HPLC with the caffeine and water for finding the concentration of adsorbate in absorbent. But I am getting this error. can anyone help me to fix this error?
Reading data file …
orthogonal box = (-100 -100 -100) to (100 100 100)
1 by 2 by 5 MPI processor grid
reading atoms …
576 atoms
reading velocities …
576 velocities
Finding 1-2 1-3 1-4 neighbors …
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
21 = max # of special neighbors
special bonds CPU = 0.001 seconds
read_data CPU = 0.006 seconds
Read molecule template h2omol:
Water molecule.
1 molecules
0 fragments
3 atoms with max type 4
2 bonds with max type 1
1 angles with max type 1
0 dihedrals with max type 0
0 impropers with max type 0
Read molecule template caffeine:
#Caffiene molecule
1 molecules
0 fragments
24 atoms with max type 8
25 bonds with max type 5
11 angles with max type 3
0 dihedrals with max type 0
0 impropers with max type 0
Created 15 atoms
using lattice units in orthogonal box = (-100 -100 -100) to (100 100 100)
create_atoms CPU = 0.000 seconds
Created 120 atoms
using lattice units in orthogonal box = (-100 -100 -100) to (100 100 100)
create_atoms CPU = 0.000 seconds
576 atoms in group SiO
15 atoms in group H2O
120 atoms in group Caffeine
Reading vashishta potential file …/…/Potential/SiO.1990.vashishta with DATE: 2015-10-14
dynamic group oxygen defined
dynamic group carbon defined
Finding SHAKE clusters …
0 = # of size 2 clusters
0 = # of size 3 clusters
0 = # of size 4 clusters
5 = # of frozen angles
find clusters CPU = 0.000 seconds
WARNING: Temperature for fix modify is not for group all (…/fix_nh.cpp:1397)
WARNING: Temperature for fix modify is not for group all (…/fix_nh.cpp:1397)
WARNING: Temperature for fix modify is not for group all (…/fix_nh.cpp:1397)
PPPM initialization …
extracting TIP4P info from pair style
WARNING: System is not charge neutral, net charge = -0.001 (…/kspace.cpp:327)
using 12-bit tables for long-range coulomb (…/kspace.cpp:342)
G vector (1/distance) = 0.19311378
grid = 48 48 48
stencil order = 5
estimated absolute RMS force accuracy = 0.0015334965
estimated relative force accuracy = 0.00010649544
using double precision KISS FFT
3d grid and FFT values/proc = 23055 11520
WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (…/pair.cpp:242)
WARNING: Communication cutoff 0 is shorter than a bond length based estimate of 2.755. This may lead to errors. (…/comm.cpp:723)
WARNING: Increasing communication cutoff to 12.1118 for TIP4P pair style (…/pair_lj_cut_tip4p_long.cpp:478)
Neighbor list info …
update: every = 1 steps, delay = 1 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 11.3092
ghost atom cutoff = 12.1118
binsize = 5.6546, bins = 36 36 36
3 neighbor lists, perpetual/occasional/extra = 3 0 0
(1) pair vashishta, perpetual, skip from (3)
attributes: full, newton on, cut 11
pair build: skip
stencil: none
bin: none
(2) pair lj/cut/tip4p/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
(3) neighbor class addition, perpetual
attributes: full, newton on, cut 11
pair build: full/bin
stencil: full/bin/3d
bin: standard
Setting up Verlet run …
Unit style : metal
Current step : 0
Time step : 0.001
Per MPI rank memory allocation (min/avg/max) = 19.48 | 19.84 | 20.68 Mbytes
Step Temp E_pair E_mol TotEng Press
0 248.27296 -6697.5762 329.79898 -6345.1525 -180.95
ERROR on proc 4: Bond atoms 627 632 missing on proc 4 at step 57 (…/ntopo_bond_partial.cpp:60)
Last command: run 5000