add Widom spc/e example

This commit is contained in:
Axel Kohlmeyer 2020-07-17 21:42:00 -04:00
parent 4d4ae93ef8
commit 55c3d139c1
No known key found for this signature in database
GPG Key ID: D9B44E93BF0C375A
3 changed files with 17493 additions and 0 deletions

17322
examples/gcmc/data.spce Normal file

File diff suppressed because it is too large Load Diff

View File

@ -0,0 +1,38 @@
units real
dimension 3
boundary p p p
atom_style full
pair_style lj/cut/coul/long 10.0
bond_style harmonic
angle_style harmonic
read_data data.spce
molecule h2omol H2O.txt
### Flexible SPC/E Potential Parameters ###
### Zhang et al., Fluid Phase Equilibria, 262 (2007) 210-216 ###
pair_coeff 1 1 0.1502629 3.1169
pair_coeff 1 2 0.0341116368 2.04845
pair_coeff 2 2 0.00774378 0.98
bond_coeff 1 176.864 0.9611
angle_coeff 1 42.1845 109.4712
kspace_style pppm 1.0e-4
fix mywidom all widom 10 20 0 29494 298 mol h2omol
fix 2 all nvt temp 298.0 298.0 100.0
neighbor 2.0 bin
neigh_modify delay 10 every 2 check yes
#run variables
timestep 0.5
thermo 10
thermo_style custom step etotal pe temp press vol density f_mywidom[1] f_mywidom[2] f_mywidom[3]
run 100

View File

@ -0,0 +1,133 @@
LAMMPS (30 Jun 2020)
using 1 OpenMP thread(s) per MPI task
units real
dimension 3
boundary p p p
atom_style full
pair_style lj/cut/coul/long 10.0
bond_style harmonic
angle_style harmonic
read_data data.spce
orthogonal box = (-0.031613 -0.023523 -0.085255) to (43.234352 44.939753 42.306533)
1 by 1 by 1 MPI processor grid
reading atoms ...
8640 atoms
scanning bonds ...
2 = max bonds/atom
scanning angles ...
1 = max angles/atom
reading bonds ...
5760 bonds
reading angles ...
2880 angles
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.008 seconds
read_data CPU = 0.028 seconds
molecule h2omol H2O.txt
Read molecule template h2omol:
1 molecules
3 atoms with max type 2
2 bonds with max type 1
1 angles with max type 1
0 dihedrals with max type 0
0 impropers with max type 0
### Flexible SPC/E Potential Parameters ###
### Zhang et al., Fluid Phase Equilibria, 262 (2007) 210-216 ###
pair_coeff 1 1 0.1502629 3.1169
pair_coeff 1 2 0.0341116368 2.04845
pair_coeff 2 2 0.00774378 0.98
bond_coeff 1 176.864 0.9611
angle_coeff 1 42.1845 109.4712
kspace_style pppm 1.0e-4
fix mywidom all widom 10 20 0 29494 298 mol h2omol
fix 2 all nvt temp 298.0 298.0 100.0
neighbor 2.0 bin
neigh_modify delay 10 every 2 check yes
#run variables
timestep 0.5
thermo 10
thermo_style custom step etotal pe temp press vol density f_mywidom[1] f_mywidom[2] f_mywidom[3]
run 100
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:330)
G vector (1/distance) = 0.2690183
grid = 24 24 24
stencil order = 5
estimated absolute RMS force accuracy = 0.024843102
estimated relative force accuracy = 7.4814263e-05
using double precision FFTW3
3d grid and FFT values/proc = 29791 13824
WARNING: Fix Widom using full_energy option (src/MC/fix_widom.cpp:297)
0 atoms in group FixWidom:widom_exclusion_group:mywidom
0 atoms in group FixWidom:rotation_gas_atoms:mywidom
WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (src/neighbor.cpp:487)
Neighbor list info ...
update every 2 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 8 8 8
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 29.66 | 29.66 | 29.66 Mbytes
Step TotEng PotEng Temp Press Volume Density f_mywidom[1] f_mywidom[2] f_mywidom[3]
0 -29703.973 -29703.973 0 -4764.5901 82468.116 1.9140713 0 0 82468.116
10 -29712.131 -31110.041 54.285179 -3154.4423 82468.116 1.9140713 241.93348 3.7366217e-178 82468.116
20 -29711.939 -32614.429 112.71273 -4216.1592 82468.116 1.9140713 16.095006 1.5716469e-12 82468.116
30 -29688.142 -32368.506 104.08688 -4093.6515 82468.116 1.9140713 5.7862327 5.7086352e-05 82468.116
40 -29662.343 -32252.144 100.57005 -1458.5339 82468.116 1.9140713 126.68071 1.2467216e-93 82468.116
50 -29646.78 -32837.635 123.91081 -4607.1155 82468.116 1.9140713 74.622397 1.8790479e-55 82468.116
60 -29628.968 -33001.229 130.9554 -4589.5296 82468.116 1.9140713 3.6575433 0.0020780497 82468.116
70 -29602.78 -32816.28 124.79023 -3082.1133 82468.116 1.9140713 13.983097 5.561247e-11 82468.116
80 -29577.552 -33141.454 138.39742 -6332.8138 82468.116 1.9140713 41.98931 1.6075608e-31 82468.116
90 -29550.865 -33792.115 164.70094 -4607.6419 82468.116 1.9140713 68.690681 4.2082269e-51 82468.116
100 -29515.107 -34052.782 176.21207 -3609.5709 82468.116 1.9140713 41.090597 7.3326206e-31 82468.116
Loop time of 163.407 on 1 procs for 100 steps with 8640 atoms
Performance: 0.026 ns/day, 907.819 hours/ns, 0.612 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 8.5495 | 8.5495 | 8.5495 | 0.0 | 5.23
Bond | 0.031981 | 0.031981 | 0.031981 | 0.0 | 0.02
Kspace | 2.3995 | 2.3995 | 2.3995 | 0.0 | 1.47
Neigh | 5.0542 | 5.0542 | 5.0542 | 0.0 | 3.09
Comm | 0.051965 | 0.051965 | 0.051965 | 0.0 | 0.03
Output | 0.0018802 | 0.0018802 | 0.0018802 | 0.0 | 0.00
Modify | 147.31 | 147.31 | 147.31 | 0.0 | 90.15
Other | | 0.003614 | | | 0.00
Nlocal: 8640.00 ave 8640 max 8640 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 23499.0 ave 23499 max 23499 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3.27380e+06 ave 3.2738e+06 max 3.2738e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3273800
Ave neighs/atom = 378.91204
Ave special neighs/atom = 2.0000000
Neighbor list builds = 220
Dangerous builds = 0
Total wall time: 0:02:44