Hi, lammps-user,
I was about to replace the H2O defined by UFF to TIP3P water model to introduce interaction like Hydrogen bond.
The script works fine for H2O defined by UFF.
To use TIP3P water model, I changed coeffs for H2O after minimization and before run dynamics along with fix shake command.
Minimization seems to run normally because highly overlapped water molecules caused by create_atoms command get dispersive properly.
But after minimization, the whole calculation gets stuck.
After killing the calculation (lammps was call by lsf job server), the log file stacked at:
“SHAKE stats (type/ave/delta) on step 348
10 1.00663 2.5901 10800
18 103.549 135.39”
I’ve tried to change the number of H2O, the calculation gets stuck if the number of water molecules is more than 100.
- I doubt that there is something wrong with fix shake command.
- E_pair and Energy seem wrong because they are positive. But I doubt it is because I hold fix for graphene and MOF at a very close position.
Please help me.
Zhongming.
#content: in.test
variable chargeall equal charge(all)
variable chargeMOF equal charge(MOF)
variable chargeGraphene equal charge(Graphene)
variable chargewater equal charge(water)
variable chargeNi equal charge(Ni)
variable chargeKNO3 equal charge(KNO3)
log log.HfBTB-MOL-Graphene-Ni0 append
units real
atom_style full
boundary p p p
pair_style lj/cut/coul/long 12.500
bond_style harmonic
angle_style hybrid fourier cosine/periodic harmonic
dihedral_style harmonic
improper_style fourier
kspace_style ewald 0.000001
dielectric 1.0
pair_modify tail yes mix arithmetic
special_bonds lj/coul 0.0 0.0 1.0
box tilt large
read_data data.HfBTB-MOL-Graphene-Ni0 extra/atom/types 5 extra/bond/types 2 extra/angle/types 2 extra/improper/types 1
## insert H2O ##
molecule h2o H2O.txt offset 9 9 17 3 1
create_atoms 0 random 1800 1 NULL mol h2o 1
mass 10 15.9994 # O
mass 11 1.008 # H
pair_coeff 10 10 0.060000 3.118146
pair_coeff 11 11 0.044000 2.571134
bond_coeff 10 559.995206 0.990254
angle_coeff 18 fourier 122.883342 0.300235 0.267331 0.266745
## insert H2O ##
## insert KNO3 ##
molecule kno3 KNO3.txt offset 11 10 18 3 1
create_atoms 0 random 25 1 NULL mol kno3 1
create_atoms 14 random 6 1 NULL
mass 12 14.006700000
mass 13 15.999400000
mass 14 39.098300000
set type 12 charge 0.0554
set type 13 charge -0.3518
set type 14 charge 1.0
pair_coeff 12 12 0.069000 3.260689
pair_coeff 13 13 0.060000 3.118146
pair_coeff 14 14 0.035000 3.396106
bond_coeff 11 810.558119 1.338317
angle_coeff 19 cosine/periodic 240.205081 -1 3
improper_coeff 2 2.000000 1.000000 -1.000000 0.000000 0
## insert KNO3 ##
#### Atom Groupings ####
group MOF id 1:550
group Graphene id 551:1078
group Ni id 1079:1085
group water type 10 11
group KNO3 type 12:14
group NO3 type 12:13
#### END Atom Groupings ####
#### QEQ ####
set atom 10 charge -2 # O on MOL
set group Graphene charge -0.01264
fix qeqNi Ni qeq/dynamic 1 10 1.0e-3 200 param.qeq1
fix qeqMOF MOF qeq/dynamic 1 10 1.0e-3 200 param.qeq1
run 0
unfix qeqNi
unfix qeqMOF
#### QEQ ####
velocity all create 298.0 12345689 dist uniform
fix 1 all nve temp 298.0 298.0 100.0
neighbor 1 bin
neigh_modify delay 0 every 1 check yes
thermo 200
thermo_style custom step time temp press epair emol v_chargeall v_chargeMOF v_chargeGraphene v_chargewater v_chargeNi v_chargeKNO3 density
thermo_modify norm no flush yes
timestep 0.1 # fs
#### fix Graphene while md ####
fix graphene Graphene setforce 0 0 0
velocity Graphene set 0 0 0
#### fix Graphene while md ####
dump trjmini all xyz 1 mini.xyz
dump_modify trjmini element Hf C O O O H Ni O H O H N O K
minimize 1.0e-8 1.0e-8 10000 10000
write_data data.aftermini
undump trjmini
#### fix MOF while md ####
fix mof MOF setforce 0 0 0
velocity MOF set 0 0 0
#### fix MOF while md ####
## change H2O to TIP3P ##
set type 10 charge -0.830
set type 11 charge 0.415
pair_coeff 10 10 0.102 3.188
pair_coeff 11 11 0.0 0.0
bond_coeff 10 450 0.9572
angle_coeff 18 harmonic 55 104.52
fix water water shake 0.0001 20 2000 b 10 a 18
## change TIP3P ##
timestep 0.1
dump trj all xyz 2000 MD-result.xyz
dump_modify trj element Hf C O O O H Ni O H O H N O K
run 20000000 # run md for 10ns
# content: log.lammps
This job begins at: Sat Mar 31 11:00:38 CST 2018
job runs at the following node:
c067 c067 c067 c067 c067 c067 c067 c067
Number of processor: 8
1 Nodes allocated
LAMMPS (11 Aug 2017)
using 1 OpenMP thread(s) per MPI task
Reading data file ...
triclinic box = (0 0 0) to (34.5385 40.6066 60) with tilt (0 0 0)
2 by 2 by 2 MPI processor grid
reading atoms ...
1085 atoms
scanning bonds ...
8 = max bonds/atom
scanning angles ...
28 = max angles/atom
scanning dihedrals ...
12 = max dihedrals/atom
scanning impropers ...
3 = max impropers/atom
reading bonds ...
1452 bonds
reading angles ...
3089 angles
reading dihedrals ...
3956 dihedrals
reading impropers ...
2112 impropers
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 1
special bond factors coul: 0 0 1
8 = max # of 1-2 neighbors
21 = max # of 1-3 neighbors
22 = max # of special neighbors
Read molecule h2o:
3 atoms with 11 types
2 bonds with 10 types
1 angles with 18 types
0 dihedrals with 0 types
0 impropers with 0 types
WARNING: Molecule attributes do not match system attributes (../molecule.cpp:1369)
Created 5400 atoms
Read molecule kno3:
5 atoms with 14 types
3 bonds with 11 types
3 angles with 19 types
0 dihedrals with 0 types
3 impropers with 2 types
WARNING: Molecule attributes do not match system attributes (../molecule.cpp:1369)
Created 125 atoms
Created 6 atoms
Setting atom values ...
25 settings made for charge
Setting atom values ...
75 settings made for charge
Setting atom values ...
31 settings made for charge
550 atoms in group MOF
528 atoms in group Graphene
7 atoms in group Ni
5400 atoms in group water
131 atoms in group KNO3
100 atoms in group NO3
Setting atom values ...
1 settings made for charge
Setting atom values ...
528 settings made for charge
Ewald initialization ...
WARNING: System is not charge neutral, net charge = -2.67392 (../kspace.cpp:302)
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.24987
estimated absolute RMS force accuracy = 0.00036409
estimated relative force accuracy = 1.09645e-06
KSpace vectors: actual max1d max3d = 3511 15 14895
kxmax kymax kzmax = 9 11 15
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 14.5
ghost atom cutoff = 14.5
binsize = 7.25, bins = 5 6 9
3 neighbor lists, perpetual/occasional/extra = 3 0 0
(1) pair lj/cut/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton/tri
stencil: half/bin/3d/newton/tri
bin: standard
(2) fix qeq/dynamic, perpetual, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
(3) fix qeq/dynamic, perpetual, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
Setting up Verlet run ...
Unit style : real
Current step : 0
Time step : 1
WARNING: Inconsistent image flags (../domain.cpp:786)
Per MPI rank memory allocation (min/avg/max) = 61.58 | 68.61 | 76.83 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 4.960651e+15 7043.4173 4.960651e+15 1.6168563e+16
Loop time of 4.52995e-06 on 8 procs for 0 steps with 6616 atoms
63.5% CPU use with 8 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total