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Merge branch 'develop' into replicate_periodic_box

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This commit is contained in:
Jacob Gissinger
2024-01-10 20:01:42 -05:00
committed by GitHub
parent f024abfe34 7ca2dcac62
commit ad7b5e38ab
9108 changed files with 1151239 additions and 445815 deletions
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2
examples/ASPHERE/README
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@ -29,8 +29,10 @@ stochastic rotation dynamics solvent, using the fix srd command.
box = 2d rigid box particles in SRDs, self-diffusion and viscosity
dimer = 2d rigid dimers in SRDs, self-diffusion and viscosity
ellipsoid = 2d ellipsoids in SRDs, self-diffusion and viscosity
flat_membrane = 2d flat membrane in NVE, self-diffusion and viscosity
line = 2d line-faceted rigid particles, NEMD shearing for viscosity,
implicit and in SRDs
poly = 2d poly-disperse spheroids in SRDs, self-diffusion and viscosity
star = 2d rigid star particles in SRDs, self-diffusion and viscosity
tri = 3d triangle-faceted rigid particles in SRDs, NEMD shearing for viscosity
vesicle = 3d vesicle in NVE, self-diffusionand viscosity

125
examples/ASPHERE/ellipsoid/in.ellipsoid
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@ -1,23 +1,23 @@
# SRD diffusion demo - ellipsoids
units lj
atom_style ellipsoid
atom_modify first big
dimension 2
units lj
atom_style ellipsoid
atom_modify first big
dimension 2
# create big ellipsoidal particles
lattice sq 0.14
region box block 0 10 0 10 -0.5 0.5
create_box 2 box
create_atoms 1 region box
lattice sq 0.14
region box block 0 10 0 10 -0.5 0.5
create_box 2 box
create_atoms 1 region box
set type 1 mass 1.0
set type 1 shape 3.0 1.0 1.0
group big type 1
set group big quat/random 29898
set type 1 mass 1.0
set type 1 shape 3.0 1.0 1.0
group big type 1
set group big quat/random 29898
velocity big create 1.44 87287 loop geom
velocity big create 1.44 87287 loop geom
# equilibrate big particles
@ -26,57 +26,59 @@ pair_coeff 1 1 1.0 1.0 1 1 1 1 1 1
pair_coeff 1 2 1.0 1.0 1 1 1 1 1 1 0.0
pair_coeff 2 2 1.0 1.0 1 1 1 1 1 1 0.0
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 big nve/asphere
fix 2 all enforce2d
fix 1 big nve/asphere
fix 2 all enforce2d
compute rot big temp/asphere
compute rot big temp/asphere
compute 0 all property/atom quatw quati quatj quatk shapex shapey shapez
#dump 1 all custom 10 dump.ellipsoid.equil id type x y z &
# quatw quati quatj quatk
#dump 1 all custom 10 dump.ellipsoid.equil id type x y z c_0[*]
#dump_modify 1 colname c_0[1] quatw colname c_0[2] quati colname c_0[3] quatj colname c_0[4] quatk &
# colname c_0[5] shapex colname c_0[6] shapey colname c_0[7] shapez
thermo_style custom step temp c_rot epair etotal press
thermo 100
thermo_style custom step temp c_rot epair etotal press
thermo 100
run 1000
run 1000
#undump 1
unfix 1
unfix 2
#undump 1
unfix 1
unfix 2
# add small particles as hi density lattice
region plane block INF INF INF INF -0.001 0.001 units box
lattice sq 120.0
create_atoms 2 region plane
region plane block INF INF INF INF -0.001 0.001 units box
lattice sq 120.0
create_atoms 2 region plane
set type 2 mass 0.01
group small type 2
velocity small create 1.0 593849 loop geom
set type 2 mass 0.01
group small type 2
velocity small create 1.0 593849 loop geom
# delete overlaps
# must set 1-2 cutoff to non-zero value
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0
pair_coeff 2 2 0.0 1.0 0.0
pair_coeff 1 2 0.0 1.0 2.0
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0
pair_coeff 2 2 0.0 1.0 0.0
pair_coeff 1 2 0.0 1.0 2.0
neigh_modify one 10000
neigh_modify one 10000
delete_atoms overlap 1.6 small big
delete_atoms overlap 1.6 small big
# SRD run
reset_timestep 0
reset_timestep 0
neighbor 0.3 multi
neigh_modify delay 0 every 1 check yes
neighbor 0.3 multi
neigh_modify delay 0 every 1 check yes
comm_modify mode multi group big vel yes
neigh_modify include big
comm_modify mode multi group big vel yes
neigh_modify include big
# no pairwise interactions with small particles
@ -88,29 +90,30 @@ pair_coeff 2 2 1.0 1.0 1 1 1 1 1 1 0.0
# use fix SRD to push small particles out from inside big ones
# if comment out, big particles won't see SRD particles
timestep 0.0005
timestep 0.0005
fix 1 big nve/asphere
fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 &
collision noslip search 0.2 inside ignore exact no bounce 50
fix 3 all enforce2d
fix 1 big nve/asphere
fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 &
collision noslip search 0.2 inside ignore exact no bounce 50
fix 3 all enforce2d
# diagnostics
compute tbig big temp/asphere
variable pebig equal pe*atoms/count(big)
variable ebig equal etotal*atoms/count(big)
thermo_style custom step temp c_rot f_2[9] etotal v_pebig v_ebig press &
f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] &
f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]
compute tbig big temp/asphere
variable pebig equal pe*atoms/count(big)
variable ebig equal etotal*atoms/count(big)
thermo_style custom step temp c_rot f_2[9] etotal v_pebig v_ebig press &
f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] &
f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]
thermo_modify temp tbig
thermo 1000
thermo_modify temp tbig
thermo 1000
#dump 1 all custom 1000 dump.ellipsoid id type x y z &
# quatw quati quatj quatk
#dump 1 all custom 1000 dump.ellipsoid id type x y z c_0[*]
#dump_modify 1 colname c_0[1] quatw colname c_0[2] quati colname c_0[3] quatj colname c_0[4] quatk &
# colname c_0[5] shapex colname c_0[6] shapey colname c_0[7] shapez
#dump 1 all image 1000 image.*.jpg type type zoom 1.6
#dump_modify 1 pad 6 adiam 1 1 adiam 2 0.2
#dump 2 all image 1000 image.*.jpg type type zoom 1.6
#dump_modify 2 pad 6 adiam 1 1 adiam 2 0.2
run 100000
run 100000

125
examples/ASPHERE/ellipsoid/in.ellipsoid.mp
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@ -1,23 +1,23 @@
# SRD viscosity demo - ellipsoids
units lj
atom_style ellipsoid
atom_modify first big
dimension 2
units lj
atom_style ellipsoid
atom_modify first big
dimension 2
# create big ellipsoidal particles
lattice sq 0.14
region box block 0 10 0 10 -0.5 0.5
create_box 2 box
create_atoms 1 region box
lattice sq 0.14
region box block 0 10 0 10 -0.5 0.5
create_box 2 box
create_atoms 1 region box
set type 1 mass 1.0
set type 1 shape 3.0 1.0 1.0
group big type 1
set group big quat/random 29898
set type 1 mass 1.0
set type 1 shape 3.0 1.0 1.0
group big type 1
set group big quat/random 29898
velocity big create 1.44 87287 loop geom
velocity big create 1.44 87287 loop geom
# equilibrate big particles
@ -26,57 +26,59 @@ pair_coeff 1 1 1.0 1.0 1 1 1 1 1 1
pair_coeff 1 2 1.0 1.0 1 1 1 1 1 1 0.0
pair_coeff 2 2 1.0 1.0 1 1 1 1 1 1 0.0
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 big nve/asphere
fix 2 all enforce2d
fix 1 big nve/asphere
fix 2 all enforce2d
compute rot big temp/asphere
compute rot big temp/asphere
compute 0 all property/atom quatw quati quatj quatk shapex shapey shapez
#dump 1 all custom 10 dump.ellipsoid.equil id type x y z &
# quatw quati quatj quatk
#dump 1 all custom 10 dump.ellipsoid.equil id type x y z c_0[*]
#dump_modify 1 colname c_0[1] quatw colname c_0[2] quati colname c_0[3] quatj colname c_0[4] quatk &
# colname c_0[5] shapex colname c_0[6] shapey colname c_0[7] shapez
thermo_style custom step temp c_rot epair etotal press
thermo 100
thermo_style custom step temp c_rot epair etotal press
thermo 100
run 1000
run 1000
#undump 1
unfix 1
unfix 2
#undump 1
unfix 1
unfix 2
# add small particles as hi density lattice
region plane block INF INF INF INF -0.001 0.001 units box
lattice sq 120.0
create_atoms 2 region plane
region plane block INF INF INF INF -0.001 0.001 units box
lattice sq 120.0
create_atoms 2 region plane
set type 2 mass 0.01
group small type 2
velocity small create 1.0 593849 loop geom
set type 2 mass 0.01
group small type 2
velocity small create 1.0 593849 loop geom
# delete overlaps
# must set 1-2 cutoff to non-zero value
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0
pair_coeff 2 2 0.0 1.0 0.0
pair_coeff 1 2 0.0 1.0 2.0
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0
pair_coeff 2 2 0.0 1.0 0.0
pair_coeff 1 2 0.0 1.0 2.0
neigh_modify one 10000
neigh_modify one 10000
delete_atoms overlap 1.6 small big
delete_atoms overlap 1.6 small big
# SRD run
reset_timestep 0
reset_timestep 0
neighbor 0.3 multi
neigh_modify delay 0 every 1 check yes
neighbor 0.3 multi
neigh_modify delay 0 every 1 check yes
comm_modify mode multi group big vel yes
neigh_modify include big
comm_modify mode multi group big vel yes
neigh_modify include big
# no pairwise interactions with small particles
@ -88,30 +90,31 @@ pair_coeff 2 2 1.0 1.0 1 1 1 1 1 1 0.0
# use fix SRD to push small particles out from inside big ones
# if comment out, big particles won't see SRD particles
timestep 0.0005
timestep 0.0005
fix 1 big nve/asphere
fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 &
fix 1 big nve/asphere
fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 &
collision noslip search 0.2 inside ignore exact no bounce 50
fix 3 small viscosity 20 x y 50
fix 4 all enforce2d
fix 3 small viscosity 20 x y 50
fix 4 all enforce2d
# diagnostics
compute tbig big temp/asphere
variable pebig equal pe*atoms/count(big)
variable ebig equal etotal*atoms/count(big)
thermo_style custom step temp c_rot f_2[9] etotal v_pebig v_ebig press &
f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] &
f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]
compute tbig big temp/asphere
variable pebig equal pe*atoms/count(big)
variable ebig equal etotal*atoms/count(big)
thermo_style custom step temp c_rot f_2[9] etotal v_pebig v_ebig press &
f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] &
f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]
thermo_modify temp tbig
thermo 1000
thermo_modify temp tbig
thermo 1000
#dump 1 all custom 500 dump.ellipsoid.mp id type x y z &
# quatw quati quatj quatk
#dump 1 all custom 500 dump.ellipsoid id type x y z c_0[*]
#dump_modify 1 colname c_0[1] quatw colname c_0[2] quati colname c_0[3] quatj colname c_0[4] quatk &
# colname c_0[5] shapex colname c_0[6] shapey colname c_0[7] shapez
#dump 1 all image 500 image.*.jpg type type zoom 1.6
#dump_modify 1 pad 6 adiam 1 1 adiam 2 0.2
#dump 1 all image 500 image.*.jpg type type zoom 1.6
#dump_modify 1 pad 6 adiam 1 1 adiam 2 0.2
run 50000
run 50000

55
examples/ASPHERE/flat_membrane/in.flat_membrane Normal file
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@ -0,0 +1,55 @@
# flat membrane demo
variable r0 equal 0.97
variable d1 equal ${r0}
variable d2 equal sqrt(3.0)*${r0}
variable d3 equal 3.0*${r0}
variable ro equal 2./${d1}/${d2}/${d3}
variable T equal 0.23
variable LD equal 1.0
units lj
atom_style ellipsoid
boundary p p p
lattice custom ${ro} a1 ${d1} 0.0 0.0 a2 0.0 ${d2} 0.0 &
a3 0.0 0.0 ${d3} basis 0.0 0.0 0.0 basis 0.5 0.5 0.0
region box block 0 40 0 24 -20 20
create_box 1 box
region membrane block 0 40 0 24 -0.5 0.5
create_atoms 1 region membrane
group membrane region membrane
set type 1 mass 1.0
set type 1 shape 1 0.99 0.99
set group all quat 0 -1 0 90
#compute memb all temp/com
#compute rot all temp/asphere bias memb
velocity all create ${T} 87287 loop geom
pair_style ylz 2.6
pair_coeff * * 1.0 1.0 4 3 0.0 2.6
neighbor 1.0 bin
thermo_style custom step temp press pxx pyy
thermo 200
timestep 0.01
#dump 1 all atom 10 dump_onlymembrane.lammpstrj
fix 1 all langevin ${T} ${T} ${LD} 48279
fix 2 all nve/asphere
run 3000

159
examples/ASPHERE/flat_membrane/log.18Oct22.flat_membrane.g++.1 Normal file
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@ -0,0 +1,159 @@
LAMMPS (15 Sep 2022)
using 1 OpenMP thread(s) per MPI task
# flat membrane demo
variable r0 equal 0.97
variable d1 equal ${r0}
variable d1 equal 0.97
variable d2 equal sqrt(3.0)*${r0}
variable d2 equal sqrt(3.0)*0.97
variable d3 equal 3.0*${r0}
variable d3 equal 3.0*0.97
variable ro equal 2./${d1}/${d2}/${d3}
variable ro equal 2./0.97/${d2}/${d3}
variable ro equal 2./0.97/1.68008928334181/${d3}
variable ro equal 2./0.97/1.68008928334181/2.91
variable T equal 0.23
variable LD equal 1.0
units lj
atom_style ellipsoid
boundary p p p
lattice custom ${ro} a1 ${d1} 0.0 0.0 a2 0.0 ${d2} 0.0 a3 0.0 0.0 ${d3} basis 0.0 0.0 0.0 basis 0.5 0.5 0.0
lattice custom 0.421728460751825 a1 ${d1} 0.0 0.0 a2 0.0 ${d2} 0.0 a3 0.0 0.0 ${d3} basis 0.0 0.0 0.0 basis 0.5 0.5 0.0
lattice custom 0.421728460751825 a1 0.97 0.0 0.0 a2 0.0 ${d2} 0.0 a3 0.0 0.0 ${d3} basis 0.0 0.0 0.0 basis 0.5 0.5 0.0
lattice custom 0.421728460751825 a1 0.97 0.0 0.0 a2 0.0 1.68008928334181 0.0 a3 0.0 0.0 ${d3} basis 0.0 0.0 0.0 basis 0.5 0.5 0.0
lattice custom 0.421728460751825 a1 0.97 0.0 0.0 a2 0.0 1.68008928334181 0.0 a3 0.0 0.0 2.91 basis 0.0 0.0 0.0 basis 0.5 0.5 0.0
Lattice spacing in x,y,z = 0.97 1.6800893 2.91
region box block 0 40 0 24 -20 20
create_box 1 box
Created orthogonal box = (0 0 -58.2) to (38.8 40.322143 58.2)
1 by 1 by 1 MPI processor grid
region membrane block 0 40 0 24 -0.5 0.5
create_atoms 1 region membrane
Created 1920 atoms
using lattice units in orthogonal box = (0 0 -58.2) to (38.8 40.322143 58.2)
create_atoms CPU = 0.001 seconds
group membrane region membrane
1920 atoms in group membrane
set type 1 mass 1.0
Setting atom values ...
1920 settings made for mass
set type 1 shape 1 1 1
Setting atom values ...
1920 settings made for shape
set group all quat 0 -1 0 90
Setting atom values ...
1920 settings made for quat
#compute memb all temp/com
#compute rot all temp/asphere bias memb
velocity all create ${T} 87287 loop geom
velocity all create 0.23 87287 loop geom
pair_style ylz 2.6
pair_coeff * * 1.0 1.0 4 3 0.0 2.6
neighbor 1.0 bin
thermo_style custom step temp press pxx pyy
thermo 200
timestep 0.01
#dump 1 all atom 10 dump_onlymembrane.lammpstrj
fix 1 all langevin ${T} ${T} ${LD} 48279
fix 1 all langevin 0.23 ${T} ${LD} 48279
fix 1 all langevin 0.23 0.23 ${LD} 48279
fix 1 all langevin 0.23 0.23 1 48279
fix 2 all nve/asphere
run 3000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- pair ylz command:
@Article{Yuan10,
author = {H. Yuan, C. Huang, J. Li, G. Lykotrafitis, and S. Zhang},
title = {One-particle-thick, solvent-free, coarse-grained model for biological and biomimetic fluid membranes},
journal = {Phys. Rev. E},
year = 2010,
volume = 82,
pages = {011905}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 10 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 3.6
ghost atom cutoff = 3.6
binsize = 1.8, bins = 22 23 65
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair ylz, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.024 | 5.024 | 5.024 Mbytes
Step Temp Press Pxx Pyy
0 0.23 -0.0073508785 -0.012283389 -0.012234574
200 0.20903886 -0.0010605951 -0.0011885957 -0.00198842
400 0.21898026 -0.00069250685 -0.0013217981 -0.00073225707
600 0.22689361 -0.00057919328 -0.00076880503 -0.0010242283
800 0.22983221 -0.00032145682 -0.00051928834 -0.00059337525
1000 0.23819392 -0.00027969126 -0.00088082301 -5.2666567e-05
1200 0.22053795 -0.00029571329 -0.0004446455 -0.00035529929
1400 0.22285021 -0.0002690371 -0.00068896571 -3.6258442e-05
1600 0.22687044 2.8599875e-05 -0.00032651798 0.0004056081
1800 0.23356905 -2.28742e-05 -0.00027073251 0.00025081131
2000 0.22499821 8.8230586e-06 -7.5750159e-05 0.0001988705
2200 0.23162995 -9.026855e-05 -0.00025832535 5.4904927e-05
2400 0.22920223 0.00016700455 3.5283125e-05 0.00034955857
2600 0.2260299 5.3095557e-05 0.00025691786 0.00013353467
2800 0.2296401 0.00043234854 0.00058344966 0.00063645193
3000 0.22564577 2.6423111e-05 8.9918406e-05 0.00022146229
Loop time of 6.76659 on 1 procs for 3000 steps with 1920 atoms
Performance: 383058.431 tau/day, 443.355 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 | 5.7968 | 5.7968 | 5.7968 | 0.0 | 85.67
Neigh | 0.086077 | 0.086077 | 0.086077 | 0.0 | 1.27
Comm | 0.034761 | 0.034761 | 0.034761 | 0.0 | 0.51
Output | 0.00038014 | 0.00038014 | 0.00038014 | 0.0 | 0.01
Modify | 0.8268 | 0.8268 | 0.8268 | 0.0 | 12.22
Other | | 0.02181 | | | 0.32
Nlocal: 1920 ave 1920 max 1920 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 772 ave 772 max 772 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 46804 ave 46804 max 46804 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 46804
Ave neighs/atom = 24.377083
Neighbor list builds = 99
Dangerous builds = 0
Total wall time: 0:00:06

159
examples/ASPHERE/flat_membrane/log.18Oct22.flat_membrane.g++.4 Normal file
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@ -0,0 +1,159 @@
LAMMPS (15 Sep 2022)
using 1 OpenMP thread(s) per MPI task
# flat membrane demo
variable r0 equal 0.97
variable d1 equal ${r0}
variable d1 equal 0.97
variable d2 equal sqrt(3.0)*${r0}
variable d2 equal sqrt(3.0)*0.97
variable d3 equal 3.0*${r0}
variable d3 equal 3.0*0.97
variable ro equal 2./${d1}/${d2}/${d3}
variable ro equal 2./0.97/${d2}/${d3}
variable ro equal 2./0.97/1.68008928334181/${d3}
variable ro equal 2./0.97/1.68008928334181/2.91
variable T equal 0.23
variable LD equal 1.0
units lj
atom_style ellipsoid
boundary p p p
lattice custom ${ro} a1 ${d1} 0.0 0.0 a2 0.0 ${d2} 0.0 a3 0.0 0.0 ${d3} basis 0.0 0.0 0.0 basis 0.5 0.5 0.0
lattice custom 0.421728460751825 a1 ${d1} 0.0 0.0 a2 0.0 ${d2} 0.0 a3 0.0 0.0 ${d3} basis 0.0 0.0 0.0 basis 0.5 0.5 0.0
lattice custom 0.421728460751825 a1 0.97 0.0 0.0 a2 0.0 ${d2} 0.0 a3 0.0 0.0 ${d3} basis 0.0 0.0 0.0 basis 0.5 0.5 0.0
lattice custom 0.421728460751825 a1 0.97 0.0 0.0 a2 0.0 1.68008928334181 0.0 a3 0.0 0.0 ${d3} basis 0.0 0.0 0.0 basis 0.5 0.5 0.0
lattice custom 0.421728460751825 a1 0.97 0.0 0.0 a2 0.0 1.68008928334181 0.0 a3 0.0 0.0 2.91 basis 0.0 0.0 0.0 basis 0.5 0.5 0.0
Lattice spacing in x,y,z = 0.97 1.6800893 2.91
region box block 0 40 0 24 -20 20
create_box 1 box
Created orthogonal box = (0 0 -58.2) to (38.8 40.322143 58.2)
1 by 1 by 4 MPI processor grid
region membrane block 0 40 0 24 -0.5 0.5
create_atoms 1 region membrane
Created 1920 atoms
using lattice units in orthogonal box = (0 0 -58.2) to (38.8 40.322143 58.2)
create_atoms CPU = 0.001 seconds
group membrane region membrane
1920 atoms in group membrane
set type 1 mass 1.0
Setting atom values ...
1920 settings made for mass
set type 1 shape 1 1 1
Setting atom values ...
1920 settings made for shape
set group all quat 0 -1 0 90
Setting atom values ...
1920 settings made for quat
#compute memb all temp/com
#compute rot all temp/asphere bias memb
velocity all create ${T} 87287 loop geom
velocity all create 0.23 87287 loop geom
pair_style ylz 2.6
pair_coeff * * 1.0 1.0 4 3 0.0 2.6
neighbor 1.0 bin
thermo_style custom step temp press pxx pyy
thermo 200
timestep 0.01
#dump 1 all atom 10 dump_onlymembrane.lammpstrj
fix 1 all langevin ${T} ${T} ${LD} 48279
fix 1 all langevin 0.23 ${T} ${LD} 48279
fix 1 all langevin 0.23 0.23 ${LD} 48279
fix 1 all langevin 0.23 0.23 1 48279
fix 2 all nve/asphere
run 3000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- pair ylz command:
@Article{Yuan10,
author = {H. Yuan, C. Huang, J. Li, G. Lykotrafitis, and S. Zhang},
title = {One-particle-thick, solvent-free, coarse-grained model for biological and biomimetic fluid membranes},
journal = {Phys. Rev. E},
year = 2010,
volume = 82,
pages = {011905}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 10 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 3.6
ghost atom cutoff = 3.6
binsize = 1.8, bins = 22 23 65
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair ylz, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.182 | 4.794 | 5.472 Mbytes
Step Temp Press Pxx Pyy
0 0.23 -0.0073508785 -0.012283389 -0.012234574
200 0.20647718 -0.0012368074 -0.0021167303 -0.0015343502
400 0.21648371 -0.00085695085 -0.0015627331 -0.0011177093
600 0.22929515 -0.00050218657 -0.0008332 -0.00062622609
800 0.22062664 -0.00049172378 -0.000611884 -0.00075089294
1000 0.22422425 -0.00039405068 -0.00037600355 -0.00070786572
1200 0.2298767 -0.00025939082 -0.00021616578 -0.00053125505
1400 0.2335927 5.8028332e-05 0.00017530192 -3.1675138e-05
1600 0.22884878 -0.0001733902 -0.0008056431 0.00014276754
1800 0.22813498 0.00019873459 0.00051040124 5.8860949e-05
2000 0.2273166 -3.3595127e-05 0.0001705632 -0.00026498213
2200 0.2251643 -2.4517311e-05 -4.0618888e-05 1.066658e-05
2400 0.22460629 -4.5661259e-05 -0.00019144039 -1.6649099e-05
2600 0.23085675 0.00014029405 0.00017983536 0.00017895001
2800 0.22364591 4.2999164e-05 -0.00011000466 0.00024363243
3000 0.23421357 0.00023505702 0.00020752013 0.00053567111
Loop time of 4.68577 on 4 procs for 3000 steps with 1920 atoms
Performance: 553164.568 tau/day, 640.237 timesteps/s
95.6% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.00015072 | 1.6029 | 3.8573 | 131.7 | 34.21
Neigh | 0.00055747 | 0.025423 | 0.065858 | 17.0 | 0.54
Comm | 0.0052259 | 0.48173 | 1.624 | 96.5 | 10.28
Output | 0.0003894 | 0.023428 | 0.047223 | 15.0 | 0.50
Modify | 0.00037337 | 0.2141 | 0.44595 | 46.3 | 4.57
Other | | 2.338 | | | 49.90
Nlocal: 480 ave 1011 max 0 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Nghost: 860 ave 1771 max 0 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 11697.8 ave 30095 max 0 min
Histogram: 2 0 0 0 0 1 0 0 0 1
Total # of neighbors = 46791
Ave neighs/atom = 24.370313
Neighbor list builds = 99
Dangerous builds = 0
Total wall time: 0:00:04

18
examples/ASPHERE/tri/in.tri.srd
View File

@ -2,7 +2,7 @@
units lj
atom_style tri
atom_modify first big
atom_modify first big map yes
read_data data.tri.srd
@ -52,12 +52,12 @@ pair_coeff 1 2 0.0 1.0 0.0
timestep 0.001
fix 1 big rigid molecule #langevin 1.0 1.0 0.1 12398
fix 2 small srd 20 big 1.0 0.25 49894 &
fix 1 big rigid/small molecule #langevin 1.0 1.0 0.1 12398
fix 2 small srd 20 big 1.0 1.0 49894 &
search 0.2 cubic warn 0.0001 shift yes 49829 &
overlap yes collision noslip
overlap yes collision noslip inside ignore
fix 3 all deform 1 x scale 0.6 y scale 0.6 z scale 0.6
fix 3 all deform 1 x scale 0.8 y scale 0.8 z scale 0.8
# diagnostics
@ -73,8 +73,8 @@ compute 2 all ke
compute 3 all pe
variable toteng equal (c_1+c_2+c_3)/atoms
thermo 1000
thermo_style custom step f_1 c_tsmall f_2[9] temp press
thermo 100
thermo_style custom step f_1 c_tsmall temp press f_2[9] f_2[4]
thermo_modify temp tbig
compute 10 all property/atom corner1x corner1y corner1z &
@ -93,9 +93,9 @@ unfix 3
change_box all triclinic
fix 2 small srd 20 big 1.0 0.25 49894 &
fix 2 small srd 20 big 1.0 1.0 49894 &
search 0.2 cubic warn 0.0001 shift yes 49829 &
overlap yes collision noslip tstat yes
overlap yes collision noslip tstat yes inside ignore
#dump 1 all custom 500 dump2.atom.srd id type x y z ix iy iz
#dump 2 all custom 500 dump2.tri.srd id type &

812
examples/ASPHERE/tri/log.15Aug23.tri.srd.g++.8 Normal file
View File

@ -0,0 +1,812 @@
LAMMPS (2 Aug 2023 - Development - patch_2Aug2023-114-gdad8081d55-modified)
WARNING: Using I/O redirection is unreliable with parallel runs. Better to use the -in switch to read input files. (../lammps.cpp:537)
# Aspherical shear demo - 3d triangle boxes, solvated by SRD particles
units lj
atom_style tri
atom_modify first big map yes
read_data data.tri.srd
Reading data file ...
orthogonal box = (-8.4373405 -8.4373405 -8.4373405) to (8.4373405 8.4373405 8.4373405)
2 by 2 by 2 MPI processor grid
reading atoms ...
1500 atoms
1500 triangles
read_data CPU = 0.007 seconds
# add small particles as hi density lattice
lattice sc 0.4
Lattice spacing in x,y,z = 1.3572088 1.3572088 1.3572088
region box block INF INF INF INF INF INF
lattice sc 20.0
Lattice spacing in x,y,z = 0.36840315 0.36840315 0.36840315
create_atoms 2 region box
Created 91125 atoms
using lattice units in orthogonal box = (-8.4373405 -8.4373405 -8.4373405) to (8.4373405 8.4373405 8.4373405)
create_atoms CPU = 0.002 seconds
group big type 1
1500 atoms in group big
group small type 2
91125 atoms in group small
set group small mass 0.01
Setting atom values ...
91125 settings made for mass
# delete overlaps
# must set 1-2 cutoff to non-zero value
pair_style lj/cut 1.5
pair_coeff 1 1 1.0 1.0
pair_coeff 2 2 0.0 1.0 0.0
pair_coeff 1 2 0.0 1.0
delete_atoms overlap 1.5 small big
System init for delete_atoms ...
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.8
ghost atom cutoff = 1.8
binsize = 0.9, bins = 19 19 19
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) command delete_atoms, occasional
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
(2) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
WARNING: Delete_atoms cutoff > minimum neighbor cutoff (../delete_atoms.cpp:312)
Deleted 76354 atoms, new total = 16271
# SRD run
reset_timestep 0
velocity small create 1.44 87287 loop geom
neighbor 0.3 multi
neigh_modify delay 0 every 1 check yes
neigh_modify exclude molecule/intra big include big
comm_modify mode multi group big vel yes
neigh_modify include big
# no pairwise interactions with small particles
pair_style tri/lj 3.5
pair_coeff 1 1 0.1 1.0
pair_coeff 2 2 0.0 1.0 0.0
pair_coeff 1 2 0.0 1.0 0.0
# use fix SRD to push small particles out from inside big ones
# if comment out, big particles won't see SRD particles
timestep 0.001
fix 1 big rigid/small molecule #langevin 1.0 1.0 0.1 12398
create bodies CPU = 0.000 seconds
125 rigid bodies with 1500 atoms
1.8601881 = max distance from body owner to body atom
fix 2 small srd 20 big 1.0 1.0 49894 search 0.2 cubic warn 0.0001 shift yes 49829 overlap yes collision noslip inside ignore
fix 3 all deform 1 x scale 0.8 y scale 0.8 z scale 0.8
# diagnostics
compute tsmall small temp/deform
compute tbig big temp
variable pebig equal pe*atoms/count(big)
variable ebig equal etotal*atoms/count(big)
compute_modify tbig extra/dof -4500
compute 1 big erotate/asphere
compute 2 all ke
compute 3 all pe
variable toteng equal (c_1+c_2+c_3)/atoms
thermo 100
thermo_style custom step f_1 c_tsmall temp press f_2[9] f_2[4]
thermo_modify temp tbig
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:527)
compute 10 all property/atom corner1x corner1y corner1z corner2x corner2y corner2z corner3x corner3y corner3z
#dump 1 all custom 500 dump1.atom.srd id type x y z ix iy iz
#dump 2 all custom 500 dump1.tri.srd id type # c_10[1] c_10[2] c_10[3] c_10[4] c_10[5] c_10[6] # c_10[7] c_10[8] c_10[9]
run 10000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- neighbor multi command: doi:10.1016/j.cpc.2008.03.005, doi:10.1007/s40571-020-00361-2
@Article{Intveld08,
author = {in 't Veld, P. J. and S. J.~Plimpton and G. S. Grest},
title = {Accurate and Efficient Methods for Modeling Colloidal
Mixtures in an Explicit Solvent using Molecular Dynamics},
journal = {Comput.\ Phys.\ Commut.},
year = 2008,
volume = 179,
pages = {320--329}
}
@article{Shire2020,
author = {Shire, Tom and Hanley, Kevin J. and Stratford, Kevin},
title = {{DEM} Simulations of Polydisperse Media: Efficient Contact
Detection Applied to Investigate the Quasi-Static Limit},
journal = {Computational Particle Mechanics},
year = {2020}
@article{Monti2022,
author = {Monti, Joseph M. and Clemmer, Joel T. and Srivastava,
Ishan and Silbert, Leonardo E. and Grest, Gary S.
and Lechman, Jeremy B.},
title = {Large-scale frictionless jamming with power-law particle
size distributions},
journal = {Phys. Rev. E},
volume = {106}
issue = {3}
year = {2022}
}
- fix srd command: doi:10.1063/1.3419070
@Article{Petersen10,
author = {M. K. Petersen and J. B. Lechman and S. J. Plimpton and
G. S. Grest and in 't Veld, P. J. and P. R. Schunk},
title = {Mesoscale Hydrodynamics via Stochastic Rotation
Dynamics: Comparison with {L}ennard-{J}ones Fluid},
journal = {J.~Chem.\ Phys.},
year = 2010,
volume = 132,
pages = 174106
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
WARNING: Using compute temp/deform with inconsistent fix deform remap option (../compute_temp_deform.cpp:71)
WARNING: Using fix srd with box deformation but no SRD thermostat (../fix_srd.cpp:405)
SRD info:
SRD/big particles = 14771 1500
big particle diameter max/min = 2.9202881 0.87320391
SRD temperature & lamda = 1 0.2
SRD max distance & max velocity = 0.8 40
SRD grid counts: 17 17 17
SRD grid size: request, actual (xyz) = 1, 0.99262829 0.99262829 0.99262829
SRD per actual grid cell = -3.9971745
SRD viscosity = -34.162587
big/SRD mass density ratio = -3.3753691
WARNING: SRD bin size for fix srd differs from user request (../fix_srd.cpp:2805)
WARNING: Fix srd grid size > 1/4 of big particle diameter (../fix_srd.cpp:2826)
WARNING: Fix srd viscosity < 0.0 due to low SRD density (../fix_srd.cpp:2828)
# of rescaled SRD velocities = 0
ave/max small velocity = 19.970837 35.150443
ave/max big velocity = 0 0
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 3.8
ghost atom cutoff = 3.8
binsize = 16.874681, bins = 1 1 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair tri/lj, perpetual
attributes: half, newton on
pair build: half/multi/newton
stencil: half/multi/3d
bin: multi
Per MPI rank memory allocation (min/avg/max) = 125.9 | 126.4 | 126.7 Mbytes
Step f_1 c_tsmall Temp Press f_2[9] f_2[4]
0 0 1.4401779 0 -0.15917996 0 0
100 0.36662911 1.1475389 0.24585067 1.0290503 1.1382325 18
200 0.73133134 1.0558153 0.49986673 0.73932383 1.049638 34
300 1.1229361 1.0218621 0.82641583 0.7589689 1.0205369 40
400 1.5826262 0.99541508 1.2201293 0.69171726 0.99190857 52
500 1.8834563 0.99351667 1.4778822 1.0147794 1.0005581 63
600 2.4225372 0.98954834 1.8740966 1.1362893 0.99760042 61
700 3.0172772 0.99153625 2.3351502 1.3284877 0.98731355 39
800 3.5307913 1.0012521 2.6477224 1.1404922 0.9846605 52
900 3.757064 0.99743944 2.7220653 1.4078087 0.97538456 55
1000 4.3165268 1.002214 3.055501 1.2252972 0.99123745 63
1100 4.2796945 1.0075233 3.1022956 1.1893685 1.0139864 69
1200 4.3719315 1.0037271 3.0054509 1.3886162 1.002661 64
1300 4.5628012 0.99368316 3.2690604 1.3621012 0.9810568 56
1400 4.6954389 0.99365088 3.1940001 1.8485712 0.99571089 71
1500 5.0270163 0.99455258 3.4120396 1.5992539 0.98294263 77
1600 5.5897797 1.0021621 3.647347 1.7796904 0.98967622 66
1700 5.5330194 1.0130853 3.6407996 1.8005429 1.0068955 62
1800 5.3606928 1.0090284 3.5863618 1.3308757 1.0214092 59
1900 5.6086195 1.0071865 3.7427101 1.5296314 0.99886937 55
2000 5.3726474 1.0064207 3.603621 1.9473142 0.99999816 54
2100 5.836183 1.0124553 3.7321841 1.7889397 1.0188986 59
2200 5.5090061 1.0113832 3.5884963 1.6617781 1.0071583 59
2300 5.4011211 1.0095947 3.520406 1.8937582 0.99689983 61
2400 5.2219281 1.0053246 3.3699458 1.7231672 0.99899754 59
2500 5.7695275 1.0141459 3.6211469 1.7767598 1.0143133 65
2600 5.4206253 1.0182828 3.521774 2.0800518 1.0081603 70
2700 5.1401099 1.0085209 3.4200563 2.4019836 1.0107652 59
2800 6.5420721 1.0159876 4.1996904 1.863842 1.0160738 61
2900 5.9082962 1.0106921 3.7223419 2.0586998 1.0073885 67
3000 5.6556123 1.0099021 3.6768976 1.921987 1.0068962 76
3100 5.2913762 1.0008567 3.4103831 1.9831969 0.99187526 80
3200 5.1032361 0.99756662 3.1967156 2.2448433 0.99743574 93
3300 5.2622386 1.0024934 3.3325614 2.0078097 1.0047789 86
3400 5.1247527 0.99810102 3.1363556 1.8907269 0.98936508 82
3500 4.9424333 1.0009344 3.2153968 1.9002728 0.99161849 71
3600 5.1243735 1.0037377 3.3117313 2.1267438 1.0078943 65
3700 5.5045819 1.0006119 3.5686193 2.3466538 0.99876164 68
3800 5.5355384 1.0022639 3.6701457 2.0383269 1.0008683 76
3900 6.4915796 1.0137733 4.3225864 2.6996933 1.0064787 79
4000 6.6631737 1.0236248 4.3057163 2.6352666 1.0255232 75
4100 6.2999507 1.0263876 4.0101385 2.5479077 1.0168303 79
4200 6.7902489 1.0247392 4.4616158 2.4926177 1.0191403 91
4300 6.505908 1.0182073 4.0675428 2.168754 1.0177101 74
4400 5.9554283 1.0115938 3.5787297 2.9258144 1.0133896 72
4500 6.2276609 1.0202416 3.8211204 2.5308249 1.0174385 74
4600 6.0485727 1.0195757 3.8217434 2.6421797 1.0201441 78
4700 6.511063 1.0220764 3.933486 2.8591093 1.0147269 83
4800 6.9478172 1.0106414 4.345402 3.3257663 1.00469 85
4900 6.7547045 1.0211842 4.1874576 3.6503845 1.022873 94
5000 7.2603949 1.0234313 4.5393985 3.4667806 1.0222306 105
5100 7.1899652 1.0256566 4.5421834 3.8137207 1.0317242 99
5200 7.1960739 1.026746 4.4288606 3.5523675 1.0242269 97
5300 7.1294458 1.017883 4.5799808 3.3917274 1.0145317 99
5400 6.2810892 1.0291953 4.0109229 2.8604571 1.0289438 97
5500 6.15246 1.0288734 3.8714587 3.2760394 1.0210757 89
5600 6.5860526 1.0192882 4.0272883 3.3124298 1.0096258 93
5700 7.0296116 1.0097293 4.2652722 3.6049788 1.012463 82
5800 6.8372302 1.0140065 4.2205065 4.3686183 1.0088542 93
5900 7.8887098 1.0090612 4.9724078 4.457317 1.0045137 92
6000 10.120663 1.0312443 6.3025192 4.72018 1.0374722 91
6100 9.1318265 1.0304199 5.7084296 4.244548 1.0259056 97
6200 8.9758903 1.0295285 5.1842704 4.870955 1.0178851 95
6300 9.0088218 1.022484 5.3742805 5.1554352 1.0138365 101
6400 10.470322 1.0287848 6.4602103 4.5461489 1.0335978 105
6500 11.100779 1.0347405 6.9630121 4.9840664 1.0339044 99
6600 10.139333 1.0476079 6.4284839 4.5523893 1.0433517 104
6700 8.9706766 1.0386262 5.8387485 4.247024 1.0408151 101
6800 7.7799532 1.0362651 4.9946283 4.6093924 1.0274763 102
6900 8.0866551 1.0337743 4.9942769 4.1679939 1.0454805 102
7000 8.0224277 1.0193598 4.9380527 3.9173115 1.0185001 109
7100 7.8361001 1.0211143 4.872673 5.3471479 1.024779 110
7200 7.8542147 1.0057183 4.8666653 4.668317 0.99980296 122
7300 7.9313852 1.0159181 5.0062527 4.1410294 1.0195705 114
7400 7.2769846 1.0155245 4.6349779 4.9138895 1.0005886 119
7500 7.5974523 1.0196295 4.7918247 4.2525935 1.0211412 124
7600 6.7835063 1.0203187 4.2674694 4.9251624 1.0218296 113
7700 6.4039017 1.0119494 4.1086667 5.5240525 1.0078246 118
7800 7.0715134 1.0149015 4.2450776 4.8796778 1.0164737 125
7900 6.3626535 1.02294 4.202778 4.482164 1.0235878 136
8000 6.2423869 1.0212553 4.0460303 5.2753307 1.0124884 132
8100 6.550891 1.0223318 4.2993545 5.2634985 1.0163244 143
8200 6.9122202 1.008347 4.3551124 5.4108909 1.0084913 142
8300 6.9104634 1.0103936 4.4622206 5.6762373 0.99559355 143
8400 6.4918879 1.0084381 4.1050732 5.8389788 1.0036021 135
8500 7.4377218 1.0216662 4.5229841 5.5431311 1.0260799 123
8600 7.572198 1.0228381 4.9058913 7.1028185 1.0015164 116
8700 8.204675 1.03457 5.2231696 6.4790244 1.0214635 132
8800 8.3118914 1.0381333 5.1795799 6.7437722 1.0290086 132
8900 8.2559198 1.0268665 5.218352 7.2191395 1.019804 138
9000 8.0403128 1.0339414 4.9310394 6.4942331 1.041527 156
9100 7.1773079 1.0397062 4.4993688 7.0272109 1.0388012 167
9200 7.1793935 1.0373589 4.3481663 7.4894459 1.0078785 157
9300 8.3705146 1.0248112 5.1036971 8.2173072 1.010168 156
9400 9.4935002 1.0252907 5.7846951 9.7466018 1.028941 170
9500 9.5208037 1.0371093 5.9635099 7.6444933 1.022673 165
9600 8.9992217 1.0292895 5.6224192 8.8071452 1.0101362 169
9700 8.682661 1.0422224 5.3997636 8.6827834 1.0337928 149
9800 7.6191562 1.0350948 4.7198842 8.6125595 1.0300395 151
9900 8.0910913 1.0319432 4.8843183 7.9013334 1.0272495 167
10000 7.4438347 1.0186098 4.7184985 8.999795 0.99762661 177
Loop time of 162.325 on 8 procs for 10000 steps with 16271 atoms
Performance: 5322.658 tau/day, 61.605 timesteps/s, 1.002 Matom-step/s
99.3% CPU use with 8 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 33.647 | 64.106 | 79.639 | 169.5 | 39.49
Neigh | 0.30808 | 0.44033 | 0.50863 | 9.8 | 0.27
Comm | 26.611 | 43.438 | 74.998 | 215.7 | 26.76
Output | 0.0072573 | 0.0087791 | 0.0097993 | 0.9 | 0.01
Modify | 53.171 | 54.121 | 55.362 | 12.3 | 33.34
Other | | 0.2104 | | | 0.13
Nlocal: 2033.88 ave 2601 max 1413 min
Histogram: 1 2 0 0 0 0 2 1 1 1
Nghost: 1647.25 ave 1714 max 1617 min
Histogram: 4 0 1 0 0 1 1 0 0 1
Neighs: 12482.8 ave 17009 max 8679 min
Histogram: 1 1 1 0 1 1 2 0 0 1
Total # of neighbors = 99862
Ave neighs/atom = 6.1374224
Neighbor list builds = 562
Dangerous builds = 0
#undump 1
#undump 2
unfix 3
change_box all triclinic
Changing box ...
triclinic box = (-6.7498724 -6.7498724 -6.7498724) to (6.7498724 6.7498724 6.7498724) with tilt (0 0 0)
fix 2 small srd 20 big 1.0 1.0 49894 search 0.2 cubic warn 0.0001 shift yes 49829 overlap yes collision noslip tstat yes inside ignore
#dump 1 all custom 500 dump2.atom.srd id type x y z ix iy iz
#dump 2 all custom 500 dump2.tri.srd id type # c_10[1] c_10[2] c_10[3] c_10[4] c_10[5] c_10[6] # c_10[7] c_10[8] c_10[9]
fix 3 all deform 1 xy erate 0.05 units box remap v
run 40000
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
SRD info:
SRD/big particles = 14771 1500
big particle diameter max/min = 2.9202881 0.87320391
SRD temperature & lamda = 1 0.2
SRD max distance & max velocity = 0.8 40
SRD grid counts: 13 13 13
SRD grid size: request, actual (xyz) = 1, 1.0384419 1.0384419 1.0384419
SRD per actual grid cell = -2.775698
SRD viscosity = -12.180602
big/SRD mass density ratio = -5.5653033
WARNING: SRD bin size for fix srd differs from user request (../fix_srd.cpp:2805)
WARNING: Fix srd grid size > 1/4 of big particle diameter (../fix_srd.cpp:2826)
WARNING: Fix srd viscosity < 0.0 due to low SRD density (../fix_srd.cpp:2828)
# of rescaled SRD velocities = 1
ave/max small velocity = 16.14994 40
ave/max big velocity = 1.6952661 5.2200074
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 3.8
ghost atom cutoff = 3.8
binsize = 13.499745, bins = 1 1 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair tri/lj, perpetual
attributes: half, newton on
pair build: half/multi/newton/tri
stencil: half/multi/3d/tri
bin: multi
Per MPI rank memory allocation (min/avg/max) = 106.9 | 107.5 | 107.7 Mbytes
Step f_1 c_tsmall Temp Press f_2[9] f_2[4]
10000 7.4438347 1.0189789 4.7184481 7.9505614 0 0
10100 7.0770142 1.0021471 4.4491455 6.606701 1 141
10200 6.7628072 1.002308 4.152988 8.5190386 1 125
10300 6.5333319 1.0007472 4.1295404 8.2341747 1 109
10400 6.3237519 1.0024029 3.8636034 9.4058128 1 95
10500 6.6411054 1.0026261 4.2975997 7.6122304 1 82
10600 5.7470775 1.0004827 3.7959947 7.3091777 1 67
10700 5.9744919 1.0014977 3.6885649 7.5517197 1 59
10800 5.8028731 1.0029627 3.7553961 6.2787087 1 49
10900 5.3755286 1.0019318 3.5334739 7.1318348 1 41
11000 5.3915962 1.001463 3.483172 7.6362496 1 40
11100 5.8683672 1.0022459 3.6697589 6.9711866 1 33
11200 5.4351801 0.99956703 3.4548447 7.0745257 1 29
11300 4.9397513 1.0008287 3.1990325 6.0917337 1 27
11400 4.9159845 1.0017862 3.0005677 7.653817 1 26
11500 4.9243103 1.0013135 3.1799841 7.744414 1 23
11600 5.2036357 1.0017984 3.2963749 7.540477 1 22
11700 4.8991892 1.0020757 3.1773032 8.7218471 1 27
11800 4.9489399 1.003438 3.1679764 7.1605486 1 26
11900 4.82398 1.0019946 3.1939566 7.1397869 1 21
12000 4.3531411 1.000532 2.8321416 7.6672501 1 23
12100 4.8226081 1.0018898 3.0382137 6.8343432 1 25
12200 4.7456418 1.0032116 2.9186038 7.3067818 1 20
12300 4.4280468 1.0005857 2.734593 8.0365684 1 22
12400 4.7311239 1.0000982 2.8898839 7.9231831 1 22
12500 4.7261054 1.0016127 2.9090517 7.6085854 1 24
12600 4.7719025 1.0016702 2.9736761 7.6101796 1 26
12700 4.386248 1.001394 2.8508378 6.4765102 1 28
12800 4.3313538 1.0019737 2.6258221 6.3164681 1 19
12900 4.2219861 1.0007469 2.5345699 7.0901077 1 22
13000 4.1775643 1.0011891 2.5807017 7.3579938 1 25
13100 4.3060837 1.0008671 2.5974066 6.9301328 1 22
13200 4.3529062 0.99996469 2.7571632 6.7806287 1 21
13300 4.2178709 1.000673 2.7819091 7.6449064 1 18
13400 4.2714169 1.0021294 2.7280794 8.0986691 1 18
13500 4.3430969 1.0037732 2.6768429 8.1267941 1 18
13600 4.3664374 1.0016083 2.6470186 6.2797727 1 20
13700 4.4904769 1.0008993 2.7885718 7.7410193 1 22
13800 4.2966193 1.001532 2.73862 7.9651302 1 21
13900 4.4003185 1.0009984 2.7484129 8.7160439 1 24
14000 4.5948292 1.0011748 2.9051777 7.842121 1 22
14100 4.6901122 1.0001265 2.9404111 8.9953816 1 20
14200 4.8517518 0.99998743 2.9647625 6.6450509 1 22
14300 4.889628 1.0018051 3.0891097 7.2671824 1 20
14400 4.578862 1.0010629 2.8239776 6.1317183 1 23
14500 4.0865406 1.0013917 2.5119661 6.864665 1 19
14600 4.30688 1.0009041 2.6817814 6.9007433 1 18
14700 4.1295726 1.002342 2.6032093 7.1441648 1 15
14800 4.2176021 1.0015157 2.7332903 6.8394683 1 16
14900 4.2012664 0.99986345 2.6498409 7.4568241 1 15
15000 4.6124269 1.0014751 2.9584178 7.9341875 1 16
15100 4.947327 1.0010615 3.0784409 7.6241305 1 21
15200 5.253281 1.002095 3.3093754 8.1872718 1 25
15300 5.2642369 1.0017799 3.1511136 7.4668389 1 25
15400 5.1967916 1.0029407 3.247548 8.0840111 1 23
15500 5.7465412 1.001896 3.468834 9.5990471 1 15
15600 6.2245772 1.0021086 3.6127689 7.8242016 1 19
15700 5.5626191 0.99984979 3.3893723 7.8124588 1 20
15800 5.5945727 1.0010291 3.3442448 7.0116922 1 17
15900 5.4450219 1.0006248 3.3132381 8.4803413 1 15
16000 5.7800459 1.001449 3.5002534 8.7989456 1 19
16100 6.1168718 1.0008109 3.8081142 8.0119729 1 18
16200 5.4901649 1.0020643 3.3673653 7.3483134 1 17
16300 5.4051694 1.0015652 3.3560012 7.4641983 1 19
16400 5.4237612 1.0012686 3.3816406 7.3845086 1 14
16500 5.1935593 1.001754 3.3340381 7.8607712 1 16
16600 5.539343 1.0021073 3.4164309 8.1541097 1 12
16700 5.8922923 1.0013792 3.553426 7.5220576 1 14
16800 5.956937 1.0005959 3.7630589 8.7417987 1 13
16900 5.469721 1.0016219 3.5531223 8.6721994 1 13
17000 5.3110154 1.001142 3.4167244 7.4644182 1 15
17100 5.9226035 0.99918238 4.0244287 6.5172028 1 16
17200 5.4897042 0.99981565 3.4350691 5.6840394 1 20
17300 5.4302636 1.0021571 3.421473 6.4317025 1 21
17400 5.5559131 1.0013807 3.4951403 6.874191 1 24
17500 5.4068006 1.0010448 3.4506835 7.7069504 1 22
17600 4.9283792 1.0007628 3.1736308 7.3098058 1 20
17700 4.9319722 0.99935896 3.0956257 8.2120111 1 15
17800 4.6842391 1.00037 2.9602433 7.4116352 1 17
17900 4.7714682 1.0009332 2.9666778 7.5925131 1 17
18000 4.7233188 1.0035687 3.0991778 7.1636357 1 10
18100 4.6487958 1.0020255 3.10781 6.8468658 1 12
18200 4.6284129 1.0012617 3.089724 6.3082275 1 13
18300 4.7136404 0.99962415 3.1261978 7.3359556 1 15
18400 5.0367681 1.0011016 3.2413493 8.3910633 1 14
18500 4.9658104 1.0025407 3.2420827 7.4701216 1 17
18600 4.6100059 1.0014508 3.0216884 6.553483 1 17
18700 4.3246452 1.0016721 2.7810363 6.7450293 1 19
18800 4.9415788 1.0012406 3.1661907 7.5544034 1 18
18900 5.3930915 1.000138 3.2557456 7.350955 1 21
19000 5.1938599 1.0007364 3.2398733 6.5397956 1 22
19100 5.4433048 1.0019191 3.2699245 8.3625772 1 22
19200 6.1303261 1.0004005 3.7823203 8.0537369 1 22
19300 5.5762518 1.0008117 3.5689121 8.3714373 1 22
19400 5.1316743 0.9999834 3.099381 7.405287 1 23
19500 5.2064799 1.0012007 3.3059455 7.3499127 1 25
19600 5.1650099 1.0023314 3.3759492 7.3637616 1 21
19700 5.8316278 1.0023317 3.601564 7.153887 1 19
19800 5.6435147 1.0010657 3.4967581 6.8899334 1 21
19900 5.4071193 0.99961357 3.4977894 6.1068438 1 20
20000 5.5058495 1.000982 3.5185057 8.5657603 1 19
20100 5.6551271 1.0025852 3.5672369 7.8242273 1 20
20200 5.7196886 1.002283 3.6010925 7.1449072 1 22
20300 5.5593553 1.0009987 3.4363398 8.4141755 1 21
20400 5.5550247 1.001081 3.3950874 8.0222131 1 20
20500 5.4510415 0.99997273 3.5505093 7.5243655 1 18
20600 5.8014064 1.0007611 3.8084579 7.6583499 1 18
20700 5.7337315 1.0020309 3.7973684 8.7376766 1 17
20800 5.2512898 0.99901254 3.5027763 7.8902791 1 14
20900 5.3245034 1.0014504 3.3354615 6.7030716 1 17
21000 5.2071731 1.0020459 3.3881369 5.8616999 1 20
21100 5.3187535 1.0010762 3.2845672 8.1422146 1 21
21200 5.5298545 0.99942313 3.4393978 7.1183144 1 22
21300 5.8430744 1.0008652 3.719408 7.8522038 1 20
21400 5.8190457 1.0017046 3.5624252 7.8150165 1 20
21500 6.004585 1.0035276 3.9161914 7.7719377 1 21
21600 6.7202635 0.99970072 3.9642141 8.7934294 1 18
21700 6.8590346 1.0007883 4.4285217 8.9014638 1 20
21800 6.627638 1.0012117 4.1154082 8.3153026 1 22
21900 7.8281047 1.0008299 4.8842343 8.4016227 1 20
22000 7.200038 1.0014681 4.4141419 9.4091956 1 18
22100 7.7442011 1.0018051 4.7850371 8.9885489 1 15
22200 7.4770203 1.0033558 4.7512643 8.4898148 1 17
22300 8.1080801 1.0000019 5.2725185 9.2314625 1 14
22400 7.8068311 1.0020672 4.9055683 8.4064748 1 12
22500 7.4594636 1.0008427 4.6586396 8.5102986 1 11
22600 6.9380609 1.0024634 4.2435619 10.395118 1 16
22700 6.9338066 1.001056 4.3436179 7.9126284 1 18
22800 6.8049493 1.0020052 4.1443407 7.8228868 1 18
22900 6.2280158 1.0021474 3.7695343 7.3179647 1 20
23000 5.649403 1.0017128 3.5941976 7.2964709 1 19
23100 5.3203116 1.001912 3.3807399 6.6454551 1 15
23200 5.8172882 1.0005742 3.6625896 8.4256312 1 15
23300 5.9647182 1.0015466 3.9106019 8.3303303 1 14
23400 5.9784055 1.0034542 3.7229235 7.7934273 1 14
23500 5.377627 1.00192 3.5481778 6.8195124 1 17
23600 5.4807136 1.0014662 3.563123 7.6356376 1 18
23700 5.8896329 1.0013553 3.7990694 8.5513408 1 13
23800 6.3463707 0.9999403 3.9609397 8.5741923 1 11
23900 6.656669 1.0014998 4.1993183 9.0862996 1 13
24000 7.583723 1.0025057 4.7628652 7.5007245 1 20
24100 6.9868359 1.0014089 4.4369841 7.692833 1 25
24200 7.1966062 1.0013149 4.4384528 9.5264821 1 18
24300 6.7765706 1.0007065 4.3500477 9.4974154 1 16
24400 7.0853466 1.0013246 4.409163 9.2215823 1 17
24500 6.9603823 1.0004247 4.4866051 7.7870058 1 20
24600 6.9208291 0.99953329 4.2298144 6.5732392 1 21
24700 6.5005518 1.0026848 4.0003505 7.8094715 1 22
24800 5.8421948 1.0012055 3.6686768 7.6078157 1 26
24900 5.8410604 1.0023428 3.746177 6.8971309 1 22
25000 5.8728511 1.0001747 3.7170134 7.4456816 1 19
25100 6.0217168 1.000624 3.7756108 6.6542452 1 20
25200 6.1939015 1.0017861 3.8943084 9.395821 1 25
25300 6.161998 1.0010373 3.9255122 6.2228884 1 28
25400 5.5850406 1.0018505 3.5129832 7.2551309 1 24
25500 6.0286276 1.0009028 3.8580887 6.8065265 1 24
25600 5.6262228 1.0005097 3.4574446 7.5061246 1 21
25700 6.1348187 1.0009828 3.8073512 7.4818375 1 17
25800 6.09781 1.0026426 3.9585383 9.0915939 1 21
25900 6.2673667 1.0002269 3.8182813 9.2134822 1 21
26000 6.6001776 1.0020444 4.041386 8.0403555 1 18
26100 6.3063025 1.0016633 3.8649839 8.8149734 1 19
26200 6.0046983 1.002332 3.5380766 8.6145656 1 17
26300 5.9627788 1.0005401 3.56864 6.7821213 1 15
26400 5.0547314 0.9998295 3.2106781 9.2935351 1 15
26500 5.256781 1.0013131 3.2946631 8.8590275 1 15
26600 5.6250355 1.0023929 3.5243033 8.8985058 1 17
26700 6.0197165 1.0018323 3.7973947 7.3093402 1 17
26800 5.4556541 1.0015309 3.4295107 8.2342049 1 18
26900 5.420428 1.0024996 3.4374201 7.1444636 1 16
27000 6.165624 1.0019174 3.8726016 8.6588275 1 20
27100 6.7131697 1.0006541 4.266264 8.7063389 1 24
27200 6.4855163 1.0016139 4.2029778 7.667611 1 29
27300 6.0525608 1.000478 3.9169723 7.4515279 1 25
27400 6.1426194 1.0014522 3.9176108 6.8689671 1 24
27500 6.5981349 1.0001143 4.0620686 8.6804552 1 27
27600 6.7827138 1.0016694 4.2764286 9.3912843 1 21
27700 6.6368902 1.0025149 4.1452128 9.1814523 1 24
27800 6.9791025 1.0019486 4.3989933 7.9446882 1 24
27900 6.617142 1.0015736 4.360571 9.3732108 1 26
28000 7.2818263 1.0014101 4.6041512 8.2398587 1 28
28100 7.2543709 1.0007625 4.5724787 7.7373488 1 22
28200 7.0631847 1.0023922 4.4021705 8.3290554 1 29
28300 7.2999952 1.0012593 4.4655563 8.612666 1 27
28400 7.4124538 1.0014043 4.5011335 8.379391 1 29
28500 7.0350937 1.0011392 4.3528091 7.8167375 1 24
28600 7.9659642 1.0031684 4.8732467 8.0661929 1 30
28700 7.2865919 1.0010958 4.6650146 8.0325989 1 32
28800 7.7039529 1.0027912 4.8299888 9.5471747 1 30
28900 8.3288847 1.0012438 5.0785288 8.8964877 1 31
29000 7.9348665 1.0021794 4.9393968 9.5531767 1 31
29100 8.2473389 1.0013795 4.9890359 9.7697184 1 29
29200 8.6383362 1.0018356 4.9856954 7.6402719 1 25
29300 8.2504592 1.0011048 4.9631793 7.9466724 1 24
29400 8.0502922 1.0010516 5.2521065 8.4515028 1 26
29500 7.9475896 1.0012951 4.8584644 9.1225463 1 19
29600 8.5641641 1.0016228 5.4361335 9.2045399 1 23
29700 8.9932021 1.0011848 5.5727205 8.6045729 1 23
29800 8.0320178 1.0019073 5.2837013 8.9335413 1 22
29900 8.2676522 1.0012734 5.2213798 8.8966896 1 24
30000 9.1848984 1.001747 5.9147628 12.096129 1 27
30100 10.184519 0.99977427 6.4260136 11.140491 1 27
30200 9.271472 1.0023983 6.0252189 9.6954338 1 30
30300 9.0751572 1.000851 5.6010295 9.734426 1 28
30400 9.4581261 1.0018449 5.6987258 9.70456 1 34
30500 9.1574751 0.99944001 5.582217 9.300318 1 27
30600 8.619312 1.001388 5.3503985 8.2759155 1 26
30700 7.9370031 1.0026674 5.0702831 8.5368014 1 28
30800 7.9221619 1.0019077 5.1278637 11.046922 1 26
30900 9.9722884 1.0025903 6.4055506 10.167311 1 25
31000 8.8648667 0.99962676 5.4777514 10.142102 1 21
31100 8.576344 1.000906 5.3216342 8.7984921 1 18
31200 7.8480974 1.0010341 4.9584917 9.0696437 1 16
31300 8.3536183 1.0005758 5.208516 9.7971514 1 15
31400 8.5301933 1.0007603 5.2241536 9.0257241 1 17
31500 8.5196226 1.0018215 5.0576064 8.8847294 1 19
31600 8.1470823 1.0023147 4.9182956 9.0205413 1 20
31700 8.1475888 1.0005764 5.1814113 9.0603162 1 16
31800 7.8629717 1.0014194 4.9221218 9.366291 1 16
31900 7.7206559 1.0021082 4.9167636 7.4136735 1 16
32000 7.5152809 1.0004752 4.6330638 8.830959 1 16
32100 8.2693974 1.0011751 4.9094804 9.427636 1 13
32200 8.3067661 0.9997006 4.9036865 9.0374633 1 17
32300 7.2068514 1.0007866 4.3580755 8.6445065 1 17
32400 6.885063 1.0011887 4.1528011 8.1199454 1 16
32500 6.9147014 1.0020825 4.160405 7.5398034 1 19
32600 6.8809668 1.000971 4.3312782 8.2157688 1 16
32700 6.4818892 1.0000885 3.9433899 7.309605 1 22
32800 6.6875555 1.0018674 4.1017504 7.2327183 1 22
32900 7.6118502 0.99975736 4.4498951 8.5072395 1 19
33000 7.7576909 1.0022061 4.7239551 9.2132467 1 22
33100 7.8616235 1.000482 5.0031322 9.349805 1 20
33200 8.2620563 1.0015059 5.2482188 10.286446 1 17
33300 8.0217099 1.0015466 5.1166876 9.1381844 1 20
33400 7.6565746 1.0024855 4.7594208 9.2646824 1 22
33500 7.9633887 1.0010334 4.6754116 9.1085184 1 23
33600 7.9566834 1.0024542 4.6712679 9.2046594 1 25
33700 8.2639384 1.0003021 5.1326892 8.0930215 1 24
33800 8.5648917 1.0000947 5.2099387 8.8127486 1 21
33900 8.3593557 1.0002488 5.1291354 8.5938391 1 25
34000 8.1922068 1.0030011 5.1441189 7.1529563 1 24
34100 8.4260308 1.0004639 5.5876122 9.0450303 1 28
34200 8.3014654 1.0002204 5.1964772 8.4920822 1 33
34300 7.4736545 1.0010306 4.7932244 7.8442244 1 30
34400 7.0023126 1.0024002 4.5665168 8.4702188 1 29
34500 7.3797703 1.000813 4.7224014 8.4098954 1 30
34600 7.7158761 0.99973161 4.7441628 8.5818592 1 29
34700 7.6135895 1.0015768 4.6612844 7.2195952 1 28
34800 7.0458078 0.99992638 4.2805357 7.4162305 1 32
34900 7.6190708 1.0007146 4.8064968 8.2709405 1 27
35000 7.4614294 1.0006051 4.7807207 7.7137359 1 28
35100 7.7008336 1.0008263 4.6823621 7.0208513 1 26
35200 8.1510766 1.000271 5.1781834 7.3231692 1 24
35300 7.5106275 1.0010438 4.6988185 8.9418343 1 25
35400 7.8116652 1.0009688 4.8622216 7.4624002 1 17
35500 7.2159785 1.0027484 4.543984 8.3177043 1 21
35600 7.6978875 1.0004834 4.7021203 8.3706905 1 20
35700 7.7827655 1.0019919 4.775879 8.6083292 1 15
35800 7.8433537 1.001844 4.7506574 7.3250009 1 15
35900 7.9456497 1.0004336 4.7925775 7.9824359 1 18
36000 8.1044513 1.0022261 5.1213755 9.211699 1 16
36100 7.6657532 1.0025661 4.751804 8.9770412 1 19
36200 7.909323 1.0035462 4.8435293 10.232493 1 21
36300 8.4188244 1.0016775 5.4337725 9.2060079 1 24
36400 8.7352689 1.0011274 5.6313351 8.6202832 1 24
36500 8.3459273 1.0005659 5.187336 6.9333716 1 21
36600 7.7118105 1.0018769 4.9293347 8.2789615 1 14
36700 7.8069879 1.0014021 4.7782709 8.4841233 1 15
36800 7.862085 1.0005342 4.8680692 8.1055023 1 16
36900 7.9469362 1.0027815 4.9339095 9.157722 1 16
37000 7.9085375 1.0024851 5.0921374 8.9374239 1 16
37100 8.9464869 1.0005734 5.6837772 8.806998 1 16
37200 8.1482632 1.0021175 5.1266453 8.5772094 1 18
37300 7.7958072 1.0026336 4.788431 8.3233372 1 19
37400 7.3647655 1.0015482 4.4786134 9.6606112 1 23
37500 7.3071882 1.0003912 4.681549 8.6319438 1 17
37600 7.8672509 1.0000478 4.7981944 8.3051478 1 14
37700 7.9306696 0.99923102 4.9316544 9.3672856 1 15
37800 7.7397949 0.99948557 5.1168552 8.5978047 1 17
37900 7.9121039 1.0020122 4.9866234 7.640888 1 14
38000 7.433451 1.0007901 4.6254894 8.0853539 1 14
38100 7.4636908 1.0021552 4.8472833 8.1975615 1 10
38200 7.4453077 1.0010305 4.6910943 7.8192603 1 13
38300 7.0488536 1.0012587 4.5490462 8.190036 1 16
38400 8.0686748 1.0016782 5.0747029 7.7242015 1 15
38500 7.9575875 1.0007137 4.8361776 8.05268 1 15
38600 7.6690498 1.0027522 4.8823286 9.1926516 1 20
38700 7.1567 1.002374 4.5600354 10.098089 1 19
38800 6.9100518 1.0008695 4.4101446 7.8832032 1 19
38900 6.8021882 1.0017647 4.1844125 8.1858761 1 21
39000 8.3996464 1.0010263 4.8183813 8.0997387 1 16
39100 8.4533834 1.0021643 5.074254 11.291904 1 19
39200 8.2406701 1.002062 5.0117425 8.778159 1 24
39300 8.3134114 1.0008218 5.0067136 7.9871787 1 22
39400 7.4307571 1.0014205 4.5858283 8.8596594 1 25
39500 7.1146821 1.0016367 4.5021057 7.4890018 1 22
39600 8.0048978 0.99992107 4.9235747 7.8770845 1 24
39700 8.070853 1.0029024 5.0842957 9.020664 1 21
39800 7.6939108 1.0012543 4.8986595 8.3306129 1 20
39900 7.2915444 1.00267 4.5038291 8.3844384 1 20
40000 7.3023994 1.0020441 4.4960911 8.1023709 1 18
40100 7.0221648 1.0033695 4.6374149 8.3756822 1 24
40200 7.4114756 1.0019246 4.6733475 7.6547258 1 23
40300 7.5323108 1.0005472 4.8284493 8.2820085 1 26
40400 7.3890772 1.0010491 4.6599273 8.9203575 1 19
40500 7.5786764 1.0016114 4.8166885 8.6760107 1 25
40600 8.165763 1.0006961 5.1488995 7.9321524 1 22
40700 8.1277597 0.99933464 5.0441567 10.069551 1 16
40800 8.1050904 1.0024705 5.4408599 8.3244459 1 21
40900 7.805318 1.0022992 4.9965408 9.7193723 1 21
41000 9.0130932 1.0006842 5.7931112 6.1646073 1 20
41100 8.0387975 1.0017359 5.3355655 9.6123191 1 21
41200 8.4484723 1.0014151 5.4461007 8.5146504 1 27
41300 8.6181909 1.0007562 5.2963876 9.1122306 1 30
41400 9.6762899 1.0010931 5.950456 9.2851025 1 25
41500 9.9414226 1.0016186 6.1433384 10.741453 1 24
41600 9.3348435 1.0003483 5.9291766 11.460717 1 20
41700 9.6125587 1.0013661 5.8530052 9.2105722 1 19
41800 11.383056 1.0032034 7.1988684 10.312945 1 22
41900 10.884524 1.0034888 6.9126707 10.775457 1 20
42000 11.071218 1.0026753 7.0004189 10.740627 1 20
42100 11.054304 1.0008347 6.9602414 8.9885498 1 22
42200 22.478691 1.0020466 14.997099 12.72513 1 19
42300 18.303508 1.0027626 11.336523 12.638769 1 18
42400 15.998712 1.0030312 9.4092725 11.070501 1 24
42500 15.034488 1.0024472 9.3543751 11.48052 1 28
42600 14.538257 1.0033153 9.2523745 10.909576 1 27
42700 13.986613 1.001458 8.5544184 10.765136 1 29
42800 13.240256 1.0027899 8.2014429 10.506497 1 32
42900 12.784336 1.0001406 8.0823431 12.258209 1 33
43000 13.374145 1.0012996 8.4207155 10.32817 1 31
43100 13.142334 1.0022503 8.5908808 10.152205 1 32
43200 12.669284 1.0018944 7.8511966 10.580104 1 32
43300 13.155032 1.001144 8.0337768 10.6652 1 39
43400 12.155928 1.0019472 7.5886584 11.234772 1 35
43500 12.385603 1.0007639 7.8865245 9.3868914 1 32
43600 12.236179 1.0027456 7.7521353 10.456701 1 42
43700 11.49535 1.0008758 7.3633144 8.8490079 1 40
43800 11.469157 1.0015845 7.0035577 10.594522 1 41
43900 11.228266 1.0013014 7.0137223 8.0653711 1 38
44000 10.56742 1.0016631 6.6908938 8.1094154 1 35
44100 9.8964699 1.0008351 6.3550438 8.6578181 1 36
44200 9.041539 1.0019541 5.6721401 8.6518043 1 38
44300 9.0767434 1.0034191 5.7446596 8.3838528 1 38
44400 9.2299608 1.0019526 5.7117964 8.3106491 1 37
44500 9.458981 1.0030409 5.7612138 7.7679755 1 37
44600 8.9611997 1.0014848 5.6490756 6.9224078 1 37
44700 8.0853184 1.0018894 5.2288749 8.0910912 1 32
44800 7.9999755 1.0015853 4.8088312 7.1854304 1 30
44900 7.6598023 1.0009751 4.6690664 7.1999858 1 28
45000 7.4939315 1.0010307 4.8119666 7.9615769 1 26
45100 7.4690079 0.99913423 4.9704428 7.6026835 1 32
45200 7.7001199 1.001626 4.9315953 7.4926686 1 25
45300 7.8794405 1.0011648 4.8624857 8.0804457 1 26
45400 7.493909 1.0016257 4.7631808 8.0330626 1 26
45500 7.5963141 1.0005825 4.7220659 7.0971298 1 23
45600 7.9028612 1.0017008 4.9561022 8.440428 1 23
45700 7.2285584 1.0006033 4.5521456 9.385579 1 23
45800 7.5687284 1.0024318 4.8557498 8.3052658 1 23
45900 7.8938604 1.0013937 5.1393944 5.5323667 1 26
46000 8.318466 1.0020803 5.4761811 8.2227801 1 25
46100 7.9169512 1.0024598 5.0406355 8.64365 1 27
46200 7.5535458 1.0016318 4.8010133 9.370726 1 26
46300 7.8926896 1.0001525 5.18463 7.9830196 1 27
46400 7.487145 1.002671 4.7718312 8.300134 1 29
46500 7.3564658 1.0006114 4.6762189 7.34947 1 26
46600 7.2261291 1.0005569 4.4751221 6.5847138 1 27
46700 7.2943203 1.0020164 4.3335327 7.7296507 1 25
46800 8.5849411 1.0014634 5.4501531 9.0933014 1 25
46900 10.176752 1.0023799 6.0456779 9.4050423 1 16
47000 9.1913098 1.0029076 5.7577256 9.1826215 1 22
47100 9.5479771 1.0022102 6.1100973 8.9440056 1 28
47200 9.9944172 1.0004924 6.3649417 9.1507264 1 25
47300 9.3543283 1.0013246 6.0873147 10.41657 1 24
47400 8.594101 1.0020068 5.6864295 9.2388304 1 24
47500 9.3191964 1.002411 6.0537511 9.3506828 1 23
47600 8.1615734 1.001364 5.3757905 10.303962 1 30
47700 8.3615046 1.0003075 5.2727936 9.3162209 1 32
47800 8.3566467 1.0026031 5.4379524 7.7644422 1 33
47900 8.4062556 1.0006471 5.3098736 8.0181121 1 33
48000 8.2233307 1.0012304 4.9650027 9.2644288 1 34
48100 8.4495256 1.000088 4.9940422 10.01023 1 27
48200 8.8068097 1.0014275 5.4732649 8.410093 1 31
48300 8.0008187 1.0017459 4.7732764 9.25726 1 27
48400 7.7242529 1.0026909 4.9084505 8.7147295 1 30
48500 8.3752816 1.001333 5.1071228 8.2267308 1 32
48600 9.0777805 1.0019328 5.7331841 9.6679383 1 29
48700 9.3623061 1.0001767 5.7117062 8.396895 1 25
48800 8.1186637 1.0013185 5.2697427 8.6058372 1 27
48900 7.3685497 1.0007173 4.6097553 7.8047228 1 24
49000 7.1661421 1.0023152 4.5389038 8.8759552 1 22
49100 6.9857144 1.0016394 4.6489319 8.2022359 1 24
49200 6.7160336 1.0018413 4.2488082 8.3393245 1 25
49300 7.9703755 1.0010628 5.2328567 7.968278 1 28
49400 8.2628465 1.0010877 5.2292977 8.0196533 1 27
49500 8.1436558 1.0015175 5.0344712 8.0712037 1 30
49600 8.5182498 1.0021589 5.1029028 8.6869789 1 28
49700 8.3604444 1.0015016 5.0333696 9.4861656 1 25
49800 7.336335 1.0020055 4.6365173 8.7210022 1 30
49900 7.432996 1.0016415 4.7090587 8.7033033 1 29
50000 7.4937053 1.001014 4.7212573 9.0890363 1 29
Loop time of 999.576 on 8 procs for 40000 steps with 16271 atoms
Performance: 3457.466 tau/day, 40.017 timesteps/s, 651.116 katom-step/s
99.3% CPU use with 8 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 293.48 | 403.7 | 545.29 | 357.5 | 40.39
Neigh | 2.4176 | 3.2721 | 3.8303 | 25.2 | 0.33
Comm | 163.58 | 305.88 | 419.83 | 416.7 | 30.60
Output | 0.032483 | 0.034794 | 0.040514 | 1.2 | 0.00
Modify | 281.15 | 285.67 | 293.8 | 24.3 | 28.58
Other | | 1.023 | | | 0.10
Nlocal: 2033.88 ave 2657 max 1198 min
Histogram: 2 0 0 0 0 2 1 0 1 2
Nghost: 1628.12 ave 1719 max 1569 min
Histogram: 2 0 1 1 2 1 0 0 0 1
Neighs: 13566 ave 18212 max 8488 min
Histogram: 1 0 0 1 2 1 2 0 0 1
Total # of neighbors = 108528
Ave neighs/atom = 6.6700264
Neighbor list builds = 2447
Dangerous builds = 2
Total wall time: 0:19:22

243
examples/ASPHERE/tri/log.1Feb14.tri.srd.g++.8
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LAMMPS (1 Feb 2014)
# Aspherical shear demo - 3d triangle boxes, solvated by SRD particles
units lj
atom_style tri
atom_modify first big
read_data data.tri.srd
orthogonal box = (-8.43734 -8.43734 -8.43734) to (8.43734 8.43734 8.43734)
2 by 2 by 2 MPI processor grid
reading atoms ...
1500 atoms
1500 triangles
# add small particles as hi density lattice
lattice sc 0.4
Lattice spacing in x,y,z = 1.35721 1.35721 1.35721
region box block INF INF INF INF INF INF
lattice sc 20.0
Lattice spacing in x,y,z = 0.368403 0.368403 0.368403
create_atoms 2 region box
Created 91125 atoms
group big type 1
1500 atoms in group big
group small type 2
91125 atoms in group small
set group small mass 0.01
91125 settings made for mass
# delete overlaps
# must set 1-2 cutoff to non-zero value
pair_style lj/cut 1.5
pair_coeff 1 1 1.0 1.0
pair_coeff 2 2 0.0 1.0 0.0
pair_coeff 1 2 0.0 1.0
delete_atoms overlap 1.5 small big
Deleted 76354 atoms, new total = 16271
# SRD run
reset_timestep 0
velocity small create 1.44 87287 loop geom
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
neigh_modify exclude molecule big include big
communicate multi group big vel yes
neigh_modify include big
# no pairwise interactions with small particles
pair_style tri/lj 3.5
pair_coeff 1 1 0.1 1.0
pair_coeff 2 2 0.0 1.0 0.0
pair_coeff 1 2 0.0 1.0 0.0
# use fix SRD to push small particles out from inside big ones
# if comment out, big particles won't see SRD particles
timestep 0.001
fix 1 big rigid molecule #langevin 1.0 1.0 0.1 12398
125 rigid bodies with 1500 atoms
fix 2 small srd 20 big 1.0 0.25 49894 search 0.2 cubic warn 0.0001 shift yes 49829 overlap yes collision noslip
fix 3 all deform 1 x scale 0.6 y scale 0.6 z scale 0.6
# diagnostics
compute tsmall small temp/deform
compute tbig big temp
variable pebig equal pe*atoms/count(big)
variable ebig equal etotal*atoms/count(big)
compute 1 big erotate/asphere
compute 2 all ke
compute 3 all pe
variable toteng equal (c_1+c_2+c_3)/atoms
thermo 1000
thermo_style custom step f_1 c_tsmall f_2[9] temp press
thermo_modify temp tbig
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:439)
compute 10 all property/atom corner1x corner1y corner1z corner2x corner2y corner2z corner3x corner3y corner3z
#dump 1 all custom 500 dump1.atom.srd id type x y z ix iy iz
#dump 2 all custom 500 dump1.tri.srd id type # c_10[1] c_10[2] c_10[3] c_10[4] c_10[5] c_10[6] # c_10[7] c_10[8] c_10[9]
run 10000
WARNING: Using fix srd with box deformation but no SRD thermostat (../fix_srd.cpp:385)
SRD info:
SRD/big particles = 14771 1500
big particle diameter max/min = 1.46014 0.436602
SRD temperature & lamda = 1 0.2
SRD max distance & max velocity = 0.8 40
SRD grid counts: 67 67 67
SRD grid size: request, actual (xyz) = 0.25, 0.251861 0.251861 0.251861
SRD per actual grid cell = 0.0647662
SRD viscosity = -1.09837
big/SRD mass density ratio = 24.668
WARNING: SRD bin size for fix srd differs from user request (../fix_srd.cpp:2853)
WARNING: Fix srd grid size > 1/4 of big particle diameter (../fix_srd.cpp:2875)
WARNING: Fix srd viscosity < 0.0 due to low SRD density (../fix_srd.cpp:2877)
# of rescaled SRD velocities = 0
ave/max small velocity = 19.9708 35.1504
ave/max big velocity = 0 0
WARNING: Using compute temp/deform with inconsistent fix deform remap option (../compute_temp_deform.cpp:76)
Memory usage per processor = 116.135 Mbytes
Step 1 tsmall 2[9] Temp Press
0 0 1.4405441 0 0 -0.15917996
1000 1.0535509 1.1241378 1.1224038 0 0.15526438
2000 2.4635987 1.0240667 0.94231519 0 0.011069846
3000 3.1093028 1.0070585 1.0176028 0 0.34124888
4000 2.9524179 1.0101774 1.0311733 0 -0.22118101
5000 2.9175438 1.0109144 1.0284445 0 0.1839507
6000 3.3200928 0.99108983 0.95968219 0 1.0229339
7000 3.3020156 0.99661428 0.98000621 0 2.3333851
8000 4.1500999 0.99129645 0.99723707 0 4.3054414
9000 6.537028 1.0074533 1.0251098 0 18.782913
10000 16.233245 1.0145766 1.0219787 0 147.83787
Loop time of 228.558 on 8 procs for 10000 steps with 16271 atoms
Pair time (%) = 145.018 (63.4492)
Neigh time (%) = 32.6283 (14.2757)
Comm time (%) = 43.3283 (18.9572)
Outpt time (%) = 0.000848889 (0.00037141)
Other time (%) = 7.58254 (3.31755)
Nlocal: 2033.88 ave 2092 max 1902 min
Histogram: 1 0 0 0 1 1 0 1 1 3
Nghost: 2805 ave 2855 max 2751 min
Histogram: 1 0 2 1 0 0 0 2 1 1
Neighs: 30026.5 ave 38700 max 24367 min
Histogram: 1 0 2 1 3 0 0 0 0 1
Total # of neighbors = 240212
Ave neighs/atom = 14.7632
Neighbor list builds = 501
Dangerous builds = 0
#undump 1
#undump 2
unfix 3
change_box all triclinic
triclinic box = (-5.0624 -5.0624 -5.0624) to (5.0624 5.0624 5.0624) with tilt (0 0 0)
fix 2 small srd 20 big 1.0 0.25 49894 search 0.2 cubic warn 0.0001 shift yes 49829 overlap yes collision noslip tstat yes
#dump 1 all custom 500 dump2.atom.srd id type x y z ix iy iz
#dump 2 all custom 500 dump2.tri.srd id type # c_10[1] c_10[2] c_10[3] c_10[4] c_10[5] c_10[6] # c_10[7] c_10[8] c_10[9]
fix 3 all deform 1 xy erate 0.05 units box remap v
run 40000
SRD info:
SRD/big particles = 14771 1500
big particle diameter max/min = 1.46014 0.436602
SRD temperature & lamda = 1 0.2
SRD max distance & max velocity = 0.8 40
SRD grid counts: 40 40 40
SRD grid size: request, actual (xyz) = 0.25, 0.25312 0.25312 0.25312
SRD per actual grid cell = -1.93929
SRD viscosity = -0.36972
big/SRD mass density ratio = -0.836253
WARNING: SRD bin size for fix srd differs from user request (../fix_srd.cpp:2853)
WARNING: Fix srd grid size > 1/4 of big particle diameter (../fix_srd.cpp:2875)
WARNING: Fix srd viscosity < 0.0 due to low SRD density (../fix_srd.cpp:2877)
# of rescaled SRD velocities = 1
ave/max small velocity = 16.0639 40
ave/max big velocity = 2.05735 6.73052
Memory usage per processor = 65.2471 Mbytes
Step 1 tsmall 2[9] Temp Press
10000 16.233245 1.0144194 0 0 146.27032
11000 17.301043 1.0619209 1 0 84.226323
12000 13.481177 1.063945 1 0 80.42834
13000 12.616615 1.0536125 1 0 68.365053
14000 12.16592 1.0581344 1 0 59.709941
15000 10.811557 1.0650453 1 0 59.869798
16000 9.9303081 1.0641012 1 0 59.289126
17000 10.452639 1.0589904 1 0 52.680235
18000 9.2488947 1.0556713 1 0 51.044123
19000 8.7179788 1.0566791 1 0 50.927924
20000 7.8641299 1.0668891 1 0 53.961014
21000 8.4333975 1.0628003 1 0 54.677068
22000 8.554623 1.0591872 1 0 51.784737
23000 7.895462 1.0598512 1 0 53.26885
24000 7.7014869 1.055569 1 0 54.236941
25000 7.508138 1.0581539 1 0 53.297709
26000 8.0707381 1.0586451 1 0 51.411341
27000 8.224223 1.0585509 1 0 52.775784
28000 8.8720461 1.0648837 1 0 49.681447
29000 8.503895 1.0538278 1 0 52.478556
30000 8.2272425 1.0625583 1 0 52.795709
31000 8.4626161 1.0599557 1 0 52.905343
32000 7.7410527 1.0587681 1 0 57.464472
33000 7.2765481 1.0677531 1 0 59.46728
34000 7.036016 1.0640728 1 0 60.636828
35000 8.497203 1.0577458 1 0 55.257312
36000 8.9218761 1.0585038 1 0 55.668201
37000 8.0469115 1.0561193 1 0 58.711565
38000 8.6456966 1.0663818 1 0 53.691658
39000 8.566667 1.0616928 1 0 52.866468
40000 7.7081259 1.0577046 1 0 54.105829
41000 7.4051952 1.0570277 1 0 56.094997
42000 7.331432 1.0632261 1 0 55.661067
43000 7.5587053 1.0602077 1 0 54.30762
44000 7.4521497 1.0594391 1 0 52.993548
45000 7.6234559 1.0641992 1 0 53.352202
46000 8.0659693 1.0609367 1 0 50.302682
47000 7.5227882 1.0563543 1 0 50.43551
48000 8.0798684 1.0628968 1 0 48.419201
49000 7.130784 1.0594143 1 0 50.656081
50000 7.3219268 1.0608236 1 0 54.808358
Loop time of 1651.84 on 8 procs for 40000 steps with 16271 atoms
Pair time (%) = 1232.76 (74.6296)
Neigh time (%) = 171.893 (10.4061)
Comm time (%) = 193.625 (11.7218)
Outpt time (%) = 0.00338289 (0.000204795)
Other time (%) = 53.5578 (3.24231)
Nlocal: 2033.88 ave 2229 max 1953 min
Histogram: 2 1 2 2 0 0 0 0 0 1
Nghost: 2757.88 ave 2810 max 2692 min
Histogram: 1 1 1 0 1 0 0 1 1 2
Neighs: 30098.6 ave 37369 max 25592 min
Histogram: 1 3 0 1 0 1 1 0 0 1
Total # of neighbors = 240789
Ave neighs/atom = 14.7987
Neighbor list builds = 2007
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation

33
examples/ASPHERE/vesicle/in.vesicle Normal file
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# Vesicle demo
variable T equal 0.2
variable LD equal 1.0
units lj
atom_style ellipsoid
boundary p p p
read_data read_data.vesicle1026
compute ali all temp/com
compute rott all temp/asphere bias ali
velocity all create ${T} 87287 loop geom
pair_style ylz 2.6
pair_coeff * * 1.0 1.0 4 3 0.0 2.6
neighbor 1.0 bin
thermo_style custom step temp press pxx pyy
thermo 200
timestep 0.001
#dump 1 all atom 10 onlymembrane2.lammpstrj
fix 1 all langevin ${T} ${T} ${LD} 48279
fix 2 all nve/asphere
run 3000

122
examples/ASPHERE/vesicle/log.18Oct22.vesicle.g++.1 Normal file
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LAMMPS (15 Sep 2022)
using 1 OpenMP thread(s) per MPI task
# Vesicle demo
variable T equal 0.2
variable LD equal 1.0
units lj
atom_style ellipsoid
boundary p p p
read_data read_data.vesicle1026
Reading data file ...
orthogonal box = (-35 -35 -35) to (35 35 35)
1 by 1 by 1 MPI processor grid
reading atoms ...
2938 atoms
2938 ellipsoids
read_data CPU = 0.010 seconds
compute ali all temp/com
compute rott all temp/asphere bias ali
velocity all create ${T} 87287 loop geom
velocity all create 0.2 87287 loop geom
pair_style ylz 2.6
pair_coeff * * 1.0 1.0 4 3 0.0 2.6
neighbor 1.0 bin
thermo_style custom step temp press pxx pyy
thermo 200
timestep 0.001
#dump 1 all atom 10 onlymembrane2.lammpstrj
fix 1 all langevin ${T} ${T} ${LD} 48279
fix 1 all langevin 0.2 ${T} ${LD} 48279
fix 1 all langevin 0.2 0.2 ${LD} 48279
fix 1 all langevin 0.2 0.2 1 48279
fix 2 all nve/asphere
run 3000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- pair ylz command:
@Article{Yuan10,
author = {H. Yuan, C. Huang, J. Li, G. Lykotrafitis, and S. Zhang},
title = {One-particle-thick, solvent-free, coarse-grained model for biological and biomimetic fluid membranes},
journal = {Phys. Rev. E},
year = 2010,
volume = 82,
pages = {011905}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 10 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 3.6
ghost atom cutoff = 3.6
binsize = 1.8, bins = 39 39 39
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair ylz, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.091 | 5.091 | 5.091 Mbytes
Step Temp Press Pxx Pyy
0 0.2 -0.0054891414 -0.0052713616 -0.0053641136
200 0.12816247 -0.0051288861 -0.0048542514 -0.0049847561
400 0.1377632 -0.0048071582 -0.0045651263 -0.0048444087
600 0.14983781 -0.0045305725 -0.0043305994 -0.0046127777
800 0.16205271 -0.0041176346 -0.0040534483 -0.0041351779
1000 0.17462122 -0.0037000069 -0.0034938539 -0.0037915494
1200 0.18335448 -0.0032674318 -0.0032790248 -0.0031967931
1400 0.19195613 -0.0029332101 -0.0030823703 -0.0028287799
1600 0.19261762 -0.0025263447 -0.0025152249 -0.0026205398
1800 0.19758674 -0.0021087725 -0.001981333 -0.002309048
2000 0.19748896 -0.0017662369 -0.0019316344 -0.0016696035
2200 0.20196986 -0.0013363214 -0.0015581191 -0.0013384961
2400 0.20109248 -0.0009190831 -0.0010331417 -0.0010664316
2600 0.20228664 -0.00053590675 -0.00071808747 -0.00050218533
2800 0.20512955 -0.00030845899 -0.00016244901 -0.00047877516
3000 0.19855941 -7.9520073e-05 -0.00014969215 -5.4724226e-06
Loop time of 9.6866 on 1 procs for 3000 steps with 2938 atoms
Performance: 26758.610 tau/day, 309.706 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 8.3097 | 8.3097 | 8.3097 | 0.0 | 85.79
Neigh | 0.039037 | 0.039037 | 0.039037 | 0.0 | 0.40
Comm | 0.0021766 | 0.0021766 | 0.0021766 | 0.0 | 0.02
Output | 0.00048628 | 0.00048628 | 0.00048628 | 0.0 | 0.01
Modify | 1.3043 | 1.3043 | 1.3043 | 0.0 | 13.47
Other | | 0.0309 | | | 0.32
Nlocal: 2938 ave 2938 max 2938 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 73242 ave 73242 max 73242 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 73242
Ave neighs/atom = 24.929204
Neighbor list builds = 26
Dangerous builds = 0
Total wall time: 0:00:09

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LAMMPS (15 Sep 2022)
using 1 OpenMP thread(s) per MPI task
# Vesicle demo
variable T equal 0.2
variable LD equal 1.0
units lj
atom_style ellipsoid
boundary p p p
read_data read_data.vesicle1026
Reading data file ...
orthogonal box = (-35 -35 -35) to (35 35 35)
1 by 2 by 2 MPI processor grid
reading atoms ...
2938 atoms
2938 ellipsoids
read_data CPU = 0.137 seconds
compute ali all temp/com
compute rott all temp/asphere bias ali
velocity all create ${T} 87287 loop geom
velocity all create 0.2 87287 loop geom
pair_style ylz 2.6
pair_coeff * * 1.0 1.0 4 3 0.0 2.6
neighbor 1.0 bin
thermo_style custom step temp press pxx pyy
thermo 200
timestep 0.001
#dump 1 all atom 10 onlymembrane2.lammpstrj
fix 1 all langevin ${T} ${T} ${LD} 48279
fix 1 all langevin 0.2 ${T} ${LD} 48279
fix 1 all langevin 0.2 0.2 ${LD} 48279
fix 1 all langevin 0.2 0.2 1 48279
fix 2 all nve/asphere
run 3000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- pair ylz command:
@Article{Yuan10,
author = {H. Yuan, C. Huang, J. Li, G. Lykotrafitis, and S. Zhang},
title = {One-particle-thick, solvent-free, coarse-grained model for biological and biomimetic fluid membranes},
journal = {Phys. Rev. E},
year = 2010,
volume = 82,
pages = {011905}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 10 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 3.6
ghost atom cutoff = 3.6
binsize = 1.8, bins = 39 39 39
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair ylz, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.899 | 4.9 | 4.902 Mbytes
Step Temp Press Pxx Pyy
0 0.2 -0.0054891414 -0.0052713616 -0.0053641136
200 0.12893798 -0.0051492794 -0.0048734875 -0.0049624005
400 0.13798694 -0.004875313 -0.0047071897 -0.0049305051
600 0.14725193 -0.0046349542 -0.004719983 -0.0045791451
800 0.16146954 -0.0042232199 -0.0040789193 -0.0043672895
1000 0.17268468 -0.0037146703 -0.0036270393 -0.0039169034
1200 0.18266242 -0.0032749755 -0.0032971704 -0.0033323855
1400 0.18500165 -0.0028179031 -0.0030659821 -0.0027519633
1600 0.19513132 -0.0023407512 -0.0025109801 -0.0023416835
1800 0.19645259 -0.0019995412 -0.0019064341 -0.0021757747
2000 0.19658104 -0.0015897919 -0.0015850523 -0.0016828478
2200 0.1989936 -0.0011794062 -0.0011779716 -0.0012070706
2400 0.20011525 -0.0009147432 -0.00094040885 -0.001073922
2600 0.2013975 -0.00059253676 -0.00051920304 -0.00075138934
2800 0.19715513 -0.00020995605 -0.00024386426 -0.0005475745
3000 0.1976782 -0.0001308553 5.693004e-05 -0.00034478469
Loop time of 8.46954 on 4 procs for 3000 steps with 2938 atoms
Performance: 30603.800 tau/day, 354.211 timesteps/s
77.9% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.1751 | 2.4162 | 2.6707 | 13.2 | 28.53
Neigh | 0.0090503 | 0.0098389 | 0.010503 | 0.6 | 0.12
Comm | 3.5807 | 4.1526 | 4.9283 | 24.3 | 49.03
Output | 0.00032165 | 0.0029648 | 0.010842 | 8.4 | 0.04
Modify | 0.34554 | 0.37442 | 0.39198 | 2.8 | 4.42
Other | | 1.514 | | | 17.87
Nlocal: 734.5 ave 739 max 730 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Nghost: 420.25 ave 424 max 415 min
Histogram: 1 0 0 0 0 1 0 1 0 1
Neighs: 18304.5 ave 19839 max 16636 min
Histogram: 1 0 0 0 1 0 1 0 0 1
Total # of neighbors = 73218
Ave neighs/atom = 24.921035
Neighbor list builds = 25
Dangerous builds = 0
Total wall time: 0:00:08

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16
examples/COUPLE/README
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@ -19,12 +19,12 @@ See these sections of the LAMMPS manual for details:
Build LAMMPS as a library (doc/html/Build_basics.html)
Link LAMMPS as a library to another code (doc/html/Build_link.html)
Coupling LAMMPS to other codes (doc/html/Howto_couple.html)
Using LAMMPS in client/server mode (doc/html/Howto_client_server.html)
Library interface to LAMMPS (doc/html/Howto_library.html)
Detailed documentation of the LAMMPS interfaces (doc/html/Library.html)
The library interface to LAMMPS is in src/library.cpp. Routines can
be easily added to this file so an external program can perform the
LAMMPS tasks desired.
The core library interface to LAMMPS is in src/library.cpp. Routines
can be easily added to this file so an external program can perform
the LAMMPS tasks desired.
-------------------------------------------------------------------
@ -33,16 +33,8 @@ These are the sub-directories included in this directory:
simple simple example of driver code calling LAMMPS as a lib
multiple example of driver code calling multiple instances of LAMMPS
plugin example for loading LAMMPS at runtime from a shared library
lammps_quest MD with quantum forces, coupling to Quest DFT code
lammps_spparks grain-growth Monte Carlo with strain via MD,
coupling to SPPARKS kinetic MC code
library collection of useful inter-code communication routines
fortran a simple wrapper on the LAMMPS library API that
can be called from Fortran
fortran2 a more sophisticated wrapper on the LAMMPS library API that
can be called from Fortran
fortran_dftb wrapper written by Nir Goldman (LLNL), as an
extension to fortran2, used for calling LAMMPS
from Fortran DFTB+ tight-binding code
Each sub-directory has its own README with more details.

11
examples/COUPLE/fortran/README
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@ -1,11 +0,0 @@
libfwrapper.c is a C file that wraps a few functions of the LAMMPS
library API in src/library.h so that it can be called from Fortran.
See the couple/simple/simple_f77.f90 program for an example of a Fortran
code that does this.
See the README file in that dir for instructions on how to build a
Fortran code that uses this wrapper and links to the LAMMPS library.
This legacy wrapper is deprecated and will be removed in a future
release of LAMMPS. Please use the Fortran 90 module instead.

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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* libwrapper = fortran wrappers for LAMMPS library functions.
See README for compilation instructions */
#include "mpi.h"
#include "stdio.h"
#include "stdlib.h"
#include "string.h"
#include "stdint.h"
#include "library.h" /* this is a LAMMPS include file */
/* wrapper for creating a lammps instance from fortran.
since fortran has no simple way to emit a C-compatible
argument array, we don't support it. for simplicity,
the address of the pointer to the lammps object is
stored in a 64-bit integer on all platforms. */
void lammps_open_(MPI_Fint *comm, int64_t *ptr)
{
*ptr = (int64_t) lammps_open_fortran(0,NULL,*comm);
}
/* no-MPI version of the wrapper from above. */
void lammps_open_no_mpi_(int64_t *ptr)
{
void *obj;
lammps_open_no_mpi(0,NULL,&obj);
*ptr = (int64_t) obj;
}
/* wrapper for shutting down a lammps instance from fortran. */
void lammps_close_(int64_t *ptr)
{
void *obj;
obj = (void *) *ptr;
lammps_close(obj);
}
/* wrapper for passing an input file to lammps from fortran.
since fortran strings are not zero terminated, we have
to pass the length explicitly and make a copy that is. */
void lammps_file_(int64_t *ptr, char *fname, MPI_Fint *len)
{
void *obj;
char *cpy;
obj = (void *) *ptr;
cpy = (char *)calloc(*len + 1,sizeof(char));
memcpy(cpy,fname,*len);
lammps_file(obj,cpy);
free(cpy);
}
/* wrapper for passing a line input to lammps from fortran.
since fortran strings are not zero terminated, we have
to pass the length explicitly and make a copy that is. */
void lammps_command_(int64_t *ptr, char *line, MPI_Fint *len)
{
void *obj;
char *cpy;
obj = (void *) *ptr;
cpy = (char *)calloc(*len + 1,sizeof(char));
memcpy(cpy,line,*len);
lammps_command(obj,cpy);
free(cpy);
}
/* fortran wrapper to get the number of atoms from lammps.
return values require an interface in fortran, so we
make the wrapper into a procedure. */
void lammps_get_natoms_(int64_t *ptr, MPI_Fint *natoms)
{
void *obj;
obj = (void *) *ptr;
*natoms = lammps_get_natoms(obj);
}

1
examples/COUPLE/fortran2/.gitignore vendored
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@ -1 +0,0 @@
*.mod

236
examples/COUPLE/fortran2/LAMMPS-wrapper.cpp
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@ -1,236 +0,0 @@
/* -----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ------------------------------------------------------------------------
Contributing author: Karl D. Hammond <karlh@ugcs.caltech.edu>
University of Tennessee, Knoxville (USA), 2012
------------------------------------------------------------------------- */
/* This is set of "wrapper" functions to assist LAMMPS.F90, which itself
provides a (I hope) robust Fortran interface to library.cpp and
library.h. All functions herein COULD be added to library.cpp instead of
including this as a separate file. See the README for instructions. */
#include <mpi.h>
#include "LAMMPS-wrapper.h"
#include <library.h>
#include <lammps.h>
#include <atom.h>
#include <fix.h>
#include <compute.h>
#include <modify.h>
#include <error.h>
#include <cstdlib>
using namespace LAMMPS_NS;
void lammps_open_fortran_wrapper (int argc, char **argv,
MPI_Fint communicator, void **ptr)
{
MPI_Comm C_communicator = MPI_Comm_f2c (communicator);
lammps_open (argc, argv, C_communicator, ptr);
}
int lammps_get_ntypes (void *ptr)
{
class LAMMPS *lmp = (class LAMMPS *) ptr;
int ntypes = lmp->atom->ntypes;
return ntypes;
}
void lammps_error_all (void *ptr, const char *file, int line, const char *str)
{
class LAMMPS *lmp = (class LAMMPS *) ptr;
lmp->error->all (file, line, str);
}
int lammps_extract_compute_vectorsize (void *ptr, char *id, int style)
{
class LAMMPS *lmp = (class LAMMPS *) ptr;
int icompute = lmp->modify->find_compute(id);
if ( icompute < 0 ) return 0;
class Compute *compute = lmp->modify->compute[icompute];
if ( style == 0 )
{
if ( !compute->vector_flag )
return 0;
else
return compute->size_vector;
}
else if ( style == 1 )
{
return lammps_get_natoms (ptr);
}
else if ( style == 2 )
{
if ( !compute->local_flag )
return 0;
else
return compute->size_local_rows;
}
else
return 0;
}
void lammps_extract_compute_arraysize (void *ptr, char *id, int style,
int *nrows, int *ncols)
{
class LAMMPS *lmp = (class LAMMPS *) ptr;
int icompute = lmp->modify->find_compute(id);
if ( icompute < 0 )
{
*nrows = 0;
*ncols = 0;
}
class Compute *compute = lmp->modify->compute[icompute];
if ( style == 0 )
{
if ( !compute->array_flag )
{
*nrows = 0;
*ncols = 0;
}
else
{
*nrows = compute->size_array_rows;
*ncols = compute->size_array_cols;
}
}
else if ( style == 1 )
{
if ( !compute->peratom_flag )
{
*nrows = 0;
*ncols = 0;
}
else
{
*nrows = lammps_get_natoms (ptr);
*ncols = compute->size_peratom_cols;
}
}
else if ( style == 2 )
{
if ( !compute->local_flag )
{
*nrows = 0;
*ncols = 0;
}
else
{
*nrows = compute->size_local_rows;
*ncols = compute->size_local_cols;
}
}
else
{
*nrows = 0;
*ncols = 0;
}
return;
}
int lammps_extract_fix_vectorsize (void *ptr, char *id, int style)
{
class LAMMPS *lmp = (class LAMMPS *) ptr;
int ifix = lmp->modify->find_fix(id);
if ( ifix < 0 ) return 0;
class Fix *fix = lmp->modify->fix[ifix];
if ( style == 0 )
{
if ( !fix->vector_flag )
return 0;
else
return fix->size_vector;
}
else if ( style == 1 )
{
return lammps_get_natoms (ptr);
}
else if ( style == 2 )
{
if ( !fix->local_flag )
return 0;
else
return fix->size_local_rows;
}
else
return 0;
}
void lammps_extract_fix_arraysize (void *ptr, char *id, int style,
int *nrows, int *ncols)
{
class LAMMPS *lmp = (class LAMMPS *) ptr;
int ifix = lmp->modify->find_fix(id);
if ( ifix < 0 )
{
*nrows = 0;
*ncols = 0;
}
class Fix *fix = lmp->modify->fix[ifix];
if ( style == 0 )
{
if ( !fix->array_flag )
{
*nrows = 0;
*ncols = 0;
}
else
{
*nrows = fix->size_array_rows;
*ncols = fix->size_array_cols;
}
}
else if ( style == 1 )
{
if ( !fix->peratom_flag )
{
*nrows = 0;
*ncols = 0;
}
else
{
*nrows = lammps_get_natoms (ptr);
*ncols = fix->size_peratom_cols;
}
}
else if ( style == 2 )
{
if ( !fix->local_flag )
{
*nrows = 0;
*ncols = 0;
}
else
{
*nrows = fix->size_local_rows;
*ncols = fix->size_local_cols;
}
}
else
{
*nrows = 0;
*ncols = 0;
}
return;
}
/* vim: set ts=3 sts=3 expandtab: */

41
examples/COUPLE/fortran2/LAMMPS-wrapper.h
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@ -1,41 +0,0 @@
/* -----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ------------------------------------------------------------------------
Contributing author: Karl D. Hammond <karlh@ugcs.caltech.edu>
University of Tennessee, Knoxville (USA), 2012
------------------------------------------------------------------------- */
/* This is set of "wrapper" functions to assist LAMMPS.F90, which itself
provides a (I hope) robust Fortran interface to library.cpp and
library.h. All prototypes herein COULD be added to library.h instead of
including this as a separate file. See the README for instructions. */
#ifdef __cplusplus
extern "C" {
#endif
/* Prototypes for auxiliary functions */
void lammps_open_fortran_wrapper (int, char**, MPI_Fint, void**);
int lammps_get_ntypes (void*);
int lammps_extract_compute_vectorsize (void*, char*, int);
void lammps_extract_compute_arraysize (void*, char*, int, int*, int*);
int lammps_extract_fix_vectorsize (void*, char*, int);
void lammps_extract_fix_arraysize (void*, char*, int, int*, int*);
void lammps_error_all (void*, const char*, int, const char*);
#ifdef __cplusplus
}
#endif
/* vim: set ts=3 sts=3 expandtab: */

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@ -1,37 +0,0 @@
SHELL = /bin/sh
# Path to LAMMPS extraction directory
LAMMPS_ROOT = ../../..
LAMMPS_SRC = $(LAMMPS_ROOT)/src
# Uncomment the line below if using the MPI stubs library
MPI_STUBS = #-I$(LAMMPS_SRC)/STUBS
FC = mpifort # replace with your Fortran compiler
CXX = mpicxx # replace with your C++ compiler
CXXLIB = -lstdc++ # replace with your C++ runtime libs
# Flags for Fortran compiler, C++ compiler, and C preprocessor, respectively
FFLAGS = -O2 -fPIC
CXXFLAGS = -O2 -fPIC
CPPFLAGS = -DOMPI_SKIP_MPICXX=1 -DMPICH_SKIP_MPICXX -DLAMMPS_LIB_MPI
all : liblammps_fortran.a liblammps_fortran.so
liblammps_fortran.so : LAMMPS.o LAMMPS-wrapper.o
$(FC) $(FFLAGS) -shared -o $@ $^ $(CXXLIB)
liblammps_fortran.a : LAMMPS.o LAMMPS-wrapper.o
$(AR) rs $@ $^
LAMMPS.o lammps.mod : LAMMPS.F90
$(FC) $(CPPFLAGS) $(FFLAGS) -c $<
LAMMPS-wrapper.o : LAMMPS-wrapper.cpp LAMMPS-wrapper.h
$(CXX) $(CPPFLAGS) $(CXXFLAGS) -c $< -I$(LAMMPS_SRC) $(MPI_STUBS)
clean :
$(RM) *.o *.mod liblammps_fortran.a liblammps_fortran.so
dist :
tar -czf Fortran-interface.tar.gz LAMMPS-wrapper.h LAMMPS-wrapper.cpp LAMMPS.F90 makefile README

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LAMMPS.F90 defines a Fortran 2003 module, LAMMPS, which wraps all functions in
src/library.h so they can be used directly from Fortran-encoded programs.
All functions in src/library.h that use and/or return C-style pointers have
Fortran wrapper functions that use Fortran-style arrays, pointers, and
strings; all C-style memory management is handled internally with no user
intervention. See --USE-- for notes on how this interface differs from the
C interface (and the Python interface).
This interface was created by Karl Hammond who you can contact with
questions:
Karl D. Hammond
University of Tennessee, Knoxville
karlh at ugcs.caltech.edu
karlh at utk.edu
-------------------------------------
--COMPILATION--
First, be advised that mixed-language programming is not trivial. It requires
you to link in the required libraries of all languages you use (in this case,
those for Fortran, C, and C++), as well as any other libraries required.
You are also advised to read the --USE-- section below before trying to
compile.
The following steps will work to compile this module (replace ${LAMMPS_SRC}
with the path to your LAMMPS source directory).
Steps 3-5 are accomplished, possibly after some modifications to
the makefile, by make using the attached makefile. Said makefile also builds
the dynamically-linkable library (liblammps_fortran.so).
** STATIC LIBRARY INSTRUCTIONS **
(1) Compile LAMMPS as a static library.
Call the resulting file ${LAMMPS_LIB}, which will have an actual name
like liblmp_openmpi.a. If compiling using the MPI stubs in
${LAMMPS_SRC}/STUBS, you will need to know where libmpi_stubs.a
is as well (I'll call it ${MPI_STUBS} hereafter)
(2) Copy said library to your Fortran program's source directory or replace
${LAMMPS_LIB} with its full path in the instructions below.
(3) Compile (but don't link!) LAMMPS.F90. Example:
mpif90 -c LAMMPS.f90
OR
gfortran -c LAMMPS.F90
NOTE: you may get a warning such as,
subroutine lammps_open_wrapper (argc, argv, communicator, ptr) &
Variable 'communicator' at (1) is a parameter to the BIND(C)
procedure 'lammps_open_wrapper' but may not be C interoperable
This is normal (see --IMPLEMENTATION NOTES--).
(4) Compile (but don't link) LAMMPS-wrapper.cpp. You will need its header
file as well. You will have to provide the locations of LAMMPS's
header files. For example,
mpicxx -c -I${LAMMPS_SRC} LAMMPS-wrapper.cpp
OR
g++ -c -I${LAMMPS_SRC} -I${LAMMPS_SRC}/STUBS LAMMPS-wrapper.cpp
OR
icpc -c -I${LAMMPS_SRC} -I${LAMMPS_SRC}/STUBS LAMMPS-wrapper.cpp
(5) OPTIONAL: Make a library from the object files so you can carry around
two files instead of three. Example:
ar rs liblammps_fortran.a LAMMPS.o LAMMPS-wrapper.o
This will create the file liblammps_fortran.a that you can use in place
of "LAMMPS.o LAMMPS-wrapper.o" later. Note that you will still
need to have the .mod file from part (3).
It is also possible to add LAMMPS.o and LAMMPS-wrapper.o into the
LAMMPS library (e.g., liblmp_openmpi.a) instead of creating a separate
library, like so:
ar rs ${LAMMPS_LIB} LAMMPS.o LAMMPS-wrapper.o
In this case, you can now use the Fortran wrapper functions as if they
were part of the usual LAMMPS library interface (if you have the module
file visible to the compiler, that is).
(6) Compile (but don't link) your Fortran program. Example:
mpif90 -c myfreeformatfile.f90
mpif90 -c myfixedformatfile.f
OR
gfortran -c myfreeformatfile.f90
gfortran -c myfixedformatfile.f
The object files generated by these steps are collectively referred to
as ${my_object_files} in the next step(s).
IMPORTANT: If the Fortran module from part (3) is not in the current
directory or in one searched by the compiler for module files, you will
need to include that location via the -I flag to the compiler, like so:
mpif90 -I${LAMMPS_SRC}/examples/COUPLE/fortran2 -c myfreeformatfile.f90
(7) Link everything together, including any libraries needed by LAMMPS (such
as the C++ standard library, the C math library, the JPEG library, fftw,
etc.) For example,
mpif90 LAMMPS.o LAMMPS-wrapper.o ${my_object_files} \
${LAMMPS_LIB} -lmpi_cxx -lstdc++ -lm
OR
gfortran LAMMPS.o LAMMPS-wrapper.o ${my_object_files} \
${LAMMPS_LIB} ${MPI_STUBS} -lstdc++ -lm
OR
ifort LAMMPS.o LAMMPS-wrapper.o ${my_object_files} \
${LAMMPS_LIB} ${MPI_STUBS} -cxxlib -lm
Any other required libraries (e.g. -ljpeg, -lfftw) should be added to
the end of this line.
You should now have a working executable.
** DYNAMIC LIBRARY INSTRUCTIONS **
(1) Compile LAMMPS as a dynamic library
(make makeshlib && make -f Makefile.shlib [targetname]).
(2) Compile, but don't link, LAMMPS.F90 using the -fPIC flag, such as
mpif90 -fPIC -c LAMMPS.f90
(3) Compile, but don't link, LAMMPS-wrapper.cpp in the same manner, e.g.
mpicxx -fPIC -c LAMMPS-wrapper.cpp
(4) Make the dynamic library, like so:
mpif90 -fPIC -shared -o liblammps_fortran.so LAMMPS.o LAMMPS-wrapper.o
(5) Compile your program, such as,
mpif90 -I${LAMMPS_SRC}/examples/COUPLE/fortran2 -c myfreeformatfile.f90
where ${LAMMPS_SRC}/examples/COUPLE/fortran2 contains the .mod file from
step (3)
(6) Link everything together, such as
mpif90 ${my_object_files} -L${LAMMPS_SRC} \
-L${LAMMPS_SRC}/examples/COUPLE/fortran2 -llammps_fortran \
-llammps_openmpi -lmpi_cxx -lstdc++ -lm
If you wish to avoid the -L flags, add the directories containing your
shared libraries to the LIBRARY_PATH environment variable. At run time, you
will have to add these directories to LD_LIBRARY_PATH as well; otherwise,
your executable will not find the libraries it needs.
-------------------------------------
--USAGE--
To use this API, your program unit (PROGRAM/SUBROUTINE/FUNCTION/MODULE/etc.)
should look something like this:
program call_lammps
use LAMMPS
! Other modules, etc.
implicit none
type (lammps_instance) :: lmp ! This is a pointer to your LAMMPS instance
real (C_double) :: fix
real (C_double), dimension(:), pointer :: fix2
! Rest of declarations
call lammps_open_no_mpi ('lmp -in /dev/null -screen out.lammps',lmp)
! Set up rest of program here
call lammps_file (lmp, 'in.example')
call lammps_extract_fix (fix, lmp, '2', 0, 1, 1, 1)
call lammps_extract_fix (fix2, lmp, '4', 0, 2, 1, 1)
call lammps_close (lmp)
end program call_lammps
Important notes:
* Though I dislike the use of pointers, they are necessary when communicating
with C and C++, which do not support Fortran's ALLOCATABLE attribute.
* There is no need to deallocate C-allocated memory; this is done for you in
the cases when it is done (which are all cases when pointers are not
accepted, such as global fix data)
* All arguments which are char* variables in library.cpp are character (len=*)
variables here. For example,
call lammps_command (lmp, 'units metal')
will work as expected.
* The public functions (the only ones you can use) have interfaces as
described in the comments at the top of LAMMPS.F90. They are not always
the same as those in library.h, since C strings are replaced by Fortran
strings and the like.
* The module attempts to check whether you have done something stupid (such
as assign a 2D array to a scalar), but it's not perfect. For example, the
command
call lammps_extract_global (nlocal, ptr, 'nlocal')
will give nlocal correctly if nlocal is a pointer to type INTEGER, but it
will give the wrong answer if nlocal is a pointer to type REAL. This is a
feature of the (void*) type cast in library.cpp. There is no way I can
check this for you! It WILL catch you if you pass it an allocatable or
fixed-size array when it expects a pointer.
* Arrays constructed from temporary data from LAMMPS are ALLOCATABLE, and
represent COPIES of data, not the originals. Functions like
lammps_extract_atom, which return actual LAMMPS data, are pointers.
* IMPORTANT: Due to the differences between C and Fortran arrays (C uses
row-major vectors, Fortran uses column-major vectors), all arrays returned
from LAMMPS have their indices swapped.
* An example of a complete program, simple.f90, is included with this
package.
-------------------------------------
--TROUBLESHOOTING--
Compile-time errors (when compiling LAMMPS.F90, that is) probably indicate
that your compiler is not new enough to support Fortran 2003 features. For
example, GCC 4.1.2 will not compile this module, but GCC 4.4.0 will.
If your compiler balks at 'use, intrinsic :: ISO_C_binding,' try removing the
intrinsic part so it looks like an ordinary module. However, it is likely
that such a compiler will also have problems with everything else in the
file as well.
If you get a segfault as soon as the lammps_open call is made, check that you
compiled your program AND LAMMPS-wrapper.cpp using the same MPI headers. Using
the stubs for one and the actual MPI library for the other will cause Bad
Things to happen.
If you find run-time errors, please pass them along via the LAMMPS Users
mailing list (please CC me as well; address above). Please provide a minimal
working example along with the names and versions of the compilers you are
using. Please make sure the error is repeatable and is in MY code, not yours
(generating a minimal working example will usually ensure this anyway).
-------------------------------------
--IMPLEMENTATION NOTES--
The Fortran procedures have the same names as the C procedures, and
their purpose is the same, but they may take different arguments. Here are
some of the important differences:
* lammps_open and lammps_open_no_mpi take a string instead of argc and
argv. This is necessary because C and C++ have a very different way
of treating strings than Fortran. If you want the command line to be
passed to lammps_open (as it often would be from C/C++), use the
GET_COMMAND intrinsic to obtain it.
* All C++ functions that accept char* pointers now accept Fortran-style
strings within this interface instead.
* All of the lammps_extract_[something] functions, which return void*
C-style pointers, have been replaced by generic subroutines that return
Fortran variables (which may be arrays). The first argument houses the
variable/pointer to be returned (pretend it's on the left-hand side); all
other arguments are identical except as stipulated above.
Note that it is not possible to declare generic functions that are selected
based solely on the type/kind/rank (TKR) signature of the return value,
only based on the TKR of the arguments.
* The SHAPE of the first argument to lammps_extract_[something] is checked
against the "shape" of the C array (e.g., double vs. double* vs. double**).
Calling a subroutine with arguments of inappropriate rank will result in an
error at run time.
* The indices i and j in lammps_extract_fix are used the same way they
are in f_ID[i][j] references in LAMMPS (i.e., starting from 1). This is
different than the way library.cpp uses these numbers, but is more
consistent with the way arrays are accessed in LAMMPS and in Fortran.
* The char* pointer normally returned by lammps_command is thrown away
in this version; note also that lammps_command is now a subroutine
instead of a function.
* The pointer to LAMMPS itself is of type(lammps_instance), which is itself
a synonym for type(C_ptr), part of ISO_C_BINDING. Type (C_ptr) is
C's void* data type.
* This module will almost certainly generate a compile-time warning,
such as,
subroutine lammps_open_wrapper (argc, argv, communicator, ptr) &
Variable 'communicator' at (1) is a parameter to the BIND(C)
procedure 'lammps_open_wrapper' but may not be C interoperable
This happens because lammps_open_wrapper actually takes a Fortran
INTEGER argument, whose type is defined by the MPI library itself. The
Fortran integer is converted to a C integer by the MPI library (if such
conversion is actually necessary).
* lammps_extract_global returns COPIES of the (scalar) data, as does the
C version.
* lammps_extract_atom, lammps_extract_compute, and lammps_extract_fix
have a first argument that will be associated with ACTUAL LAMMPS DATA.
This means the first argument must be:
* The right rank (via the DIMENSION modifier)
* A C-interoperable POINTER type (i.e., INTEGER (C_int) or
REAL (C_double)).
* lammps_extract_variable returns COPIES of the data, as the C library
interface does. There is no need to deallocate using lammps_free.
* The 'data' argument to lammps_gather_atoms and lammps_scatter atoms must
be ALLOCATABLE. It should be of type INTEGER or DOUBLE PRECISION. It
does NOT need to be C inter-operable (and indeed should not be).
* The 'count' argument of lammps_scatter_atoms is unnecessary; the shape of
the array determines the number of elements LAMMPS will read.

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@ -1,16 +0,0 @@
units lj
atom_modify map array
lattice bcc 1.0
region simbox block 0 10 0 10 0 10
create_box 2 simbox
create_atoms 1 region simbox
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0
mass 1 58.2 # These are made-up numbers
mass 2 28.3
velocity all create 1200.0 7474848 dist gaussian
fix 1 all nve
fix 2 all dt/reset 1 1E-5 1E-3 0.01 units box
fix 4 all ave/histo 10 5 100 0.5 1.5 50 f_2 file temp.histo ave running
thermo_style custom step dt temp press etotal f_4[1][1]
thermo 100

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program simple
use MPI
use LAMMPS
! The following line is unnecessary, as I have included these three entities
! with the LAMMPS module, but I leave them in anyway to remind people where
! they came from
use, intrinsic :: ISO_C_binding, only : C_double, C_ptr, C_int
implicit none
! Notes:
! * If LAMMPS returns a scalar that is allocated by the library interface
! (see library.cpp), then that memory is deallocated automatically and
! the argument to lammps_extract_fix must be a SCALAR.
! * If LAMMPS returns a pointer to an array, consisting of internal LAMMPS
! data, then the argument must be an interoperable Fortran pointer.
! Interoperable means it is of type INTEGER (C_INT) or of type
! REAL (C_DOUBLE) in this context.
! * Pointers should NEVER be deallocated, as that would deallocate internal
! LAMMPS data!
! * Note that just because you can read the values of, say, a compute at
! any time does not mean those values represent the "correct" values.
! LAMMPS will abort you if you try to grab a pointer to a non-current
! entity, but once it's bound, it's your responsibility to check that
! it's current before evaluating.
! * IMPORTANT: Two-dimensional arrays (such as 'x' from extract_atom)
! will be transposed from what they might look like in C++. This is
! because of different bookkeeping conventions between Fortran and C
! that date back to about 1970 or so (when C was written).
! * Arrays start from 1, EXCEPT for mass from extract_atom, which
! starts from 0. This is because the C array actually has a blank
! first element (and thus mass[1] corresponds to the mass of type 1)
type (C_ptr) :: lmp
real (C_double), pointer :: compute => NULL()
real (C_double) :: fix, fix2
real (C_double), dimension(:), pointer :: compute_v => NULL()
real (C_double), dimension(:,:), pointer :: x => NULL()
real (C_double), dimension(:), pointer :: mass => NULL()
integer, dimension(:), allocatable :: types
double precision, dimension(:), allocatable :: r
integer :: error, narg, me, nprocs
character (len=1024) :: command_line
call MPI_Init (error)
call MPI_Comm_rank (MPI_COMM_WORLD, me, error)
call MPI_Comm_size (MPI_COMM_WORLD, nprocs, error)
! You are free to pass any string you like to lammps_open or
! lammps_open_no_mpi; here is how you pass it the command line
!call get_command (command_line)
!call lammps_open (command_line, MPI_COMM_WORLD, lmp)
! And here's how to to it with a string constant of your choice
call lammps_open_no_mpi ('lmp -log log.simple', lmp)
call lammps_file (lmp, 'in.simple')
call lammps_command (lmp, 'run 500')
! This extracts f_2 as a scalar (the last two arguments can be arbitrary)
call lammps_extract_fix (fix, lmp, '2', LMP_STYLE_GLOBAL, LMP_TYPE_SCALAR, 1, 1)
print *, 'Fix is ', fix
! This extracts f_4[1][1] as a scalar
call lammps_extract_fix (fix2, lmp, '4', LMP_STYLE_GLOBAL, LMP_TYPE_ARRAY, 1, 1)
print *, 'Fix 2 is ', fix2
! This extracts the scalar compute of compute thermo_temp
call lammps_extract_compute (compute, lmp, 'thermo_temp', LMP_STYLE_GLOBAL, LMP_TYPE_SCALAR)
print *, 'Compute is ', compute
! This extracts the vector compute of compute thermo_temp
call lammps_extract_compute (compute_v, lmp, 'thermo_temp', LMP_STYLE_GLOBAL, LMP_TYPE_VECTOR)
print *, 'Vector is ', compute_v
! This extracts the masses
call lammps_extract_atom (mass, lmp, 'mass')
print *, 'Mass is ', mass(1:)
! Extracts a pointer to the arrays of positions for all atoms
call lammps_extract_atom (x, lmp, 'x')
if ( .not. associated (x) ) print *, 'x is not associated'
print *, 'x is ', x(:,1) ! Prints x, y, z for atom 1
! Extracts pointer to atom types
call lammps_gather_atoms (lmp, 'type', 1, types)
print *, 'types is ', types(1:3)
! Allocates an array and assigns all positions to it
call lammps_gather_atoms (lmp, 'x', 3, r)
print *, 'natoms = ', int(lammps_get_natoms(lmp))
print *, 'size(r) = ', size(r)
print *, 'r is ', r(1:6)
! Puts those position data back
call lammps_scatter_atoms (lmp, 'x', r)
call lammps_command (lmp, 'run 1')
print *, 'x is ', x(:,1) ! Note that the position updates!
print *, 'Compute is ', compute ! This did only because "temp" is part of
! the thermo output; the vector part did
! not, and won't until we give LAMMPS a
! thermo output or other command that
! requires its value
call lammps_close (lmp)
call MPI_Finalize (error)
end program simple

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/* -----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ------------------------------------------------------------------------
Contributing author: Karl D. Hammond <karlh@ugcs.caltech.edu>
University of Tennessee, Knoxville (USA), 2012
------------------------------------------------------------------------- */
/* This is set of "wrapper" functions to assist LAMMPS.F90, which itself
provides a (I hope) robust Fortran interface to library.cpp and
library.h. All functions herein COULD be added to library.cpp instead of
including this as a separate file. See the README for instructions. */
#include <mpi.h>
#include "LAMMPS-wrapper.h"
#include <library.h>
#include <lammps.h>
#include <atom.h>
#include <fix.h>
#include <compute.h>
#include <modify.h>
#include <error.h>
#include <cstdlib>
using namespace LAMMPS_NS;
void lammps_open_fortran_wrapper (int argc, char **argv,
MPI_Fint communicator, void **ptr)
{
MPI_Comm C_communicator = MPI_Comm_f2c (communicator);
lammps_open (argc, argv, C_communicator, ptr);
}
int lammps_get_ntypes (void *ptr)
{
class LAMMPS *lmp = (class LAMMPS *) ptr;
int ntypes = lmp->atom->ntypes;
return ntypes;
}
void lammps_error_all (void *ptr, const char *file, int line, const char *str)
{
class LAMMPS *lmp = (class LAMMPS *) ptr;
lmp->error->all (file, line, str);
}
int lammps_extract_compute_vectorsize (void *ptr, char *id, int style)
{
class LAMMPS *lmp = (class LAMMPS *) ptr;
int icompute = lmp->modify->find_compute(id);
if ( icompute < 0 ) return 0;
class Compute *compute = lmp->modify->compute[icompute];
if ( style == 0 )
{
if ( !compute->vector_flag )
return 0;
else
return compute->size_vector;
}
else if ( style == 1 )
{
return lammps_get_natoms (ptr);
}
else if ( style == 2 )
{
if ( !compute->local_flag )
return 0;
else
return compute->size_local_rows;
}
else
return 0;
}
void lammps_extract_compute_arraysize (void *ptr, char *id, int style,
int *nrows, int *ncols)
{
class LAMMPS *lmp = (class LAMMPS *) ptr;
int icompute = lmp->modify->find_compute(id);
if ( icompute < 0 )
{
*nrows = 0;
*ncols = 0;
}
class Compute *compute = lmp->modify->compute[icompute];
if ( style == 0 )
{
if ( !compute->array_flag )
{
*nrows = 0;
*ncols = 0;
}
else
{
*nrows = compute->size_array_rows;
*ncols = compute->size_array_cols;
}
}
else if ( style == 1 )
{
if ( !compute->peratom_flag )
{
*nrows = 0;
*ncols = 0;
}
else
{
*nrows = lammps_get_natoms (ptr);
*ncols = compute->size_peratom_cols;
}
}
else if ( style == 2 )
{
if ( !compute->local_flag )
{
*nrows = 0;
*ncols = 0;
}
else
{
*nrows = compute->size_local_rows;
*ncols = compute->size_local_cols;
}
}
else
{
*nrows = 0;
*ncols = 0;
}
return;
}
int lammps_extract_fix_vectorsize (void *ptr, char *id, int style)
{
class LAMMPS *lmp = (class LAMMPS *) ptr;
int ifix = lmp->modify->find_fix(id);
if ( ifix < 0 ) return 0;
class Fix *fix = lmp->modify->fix[ifix];
if ( style == 0 )
{
if ( !fix->vector_flag )
return 0;
else
return fix->size_vector;
}
else if ( style == 1 )
{
return lammps_get_natoms (ptr);
}
else if ( style == 2 )
{
if ( !fix->local_flag )
return 0;
else
return fix->size_local_rows;
}
else
return 0;
}
void lammps_extract_fix_arraysize (void *ptr, char *id, int style,
int *nrows, int *ncols)
{
class LAMMPS *lmp = (class LAMMPS *) ptr;
int ifix = lmp->modify->find_fix(id);
if ( ifix < 0 )
{
*nrows = 0;
*ncols = 0;
}
class Fix *fix = lmp->modify->fix[ifix];
if ( style == 0 )
{
if ( !fix->array_flag )
{
*nrows = 0;
*ncols = 0;
}
else
{
*nrows = fix->size_array_rows;
*ncols = fix->size_array_cols;
}
}
else if ( style == 1 )
{
if ( !fix->peratom_flag )
{
*nrows = 0;
*ncols = 0;
}
else
{
*nrows = lammps_get_natoms (ptr);
*ncols = fix->size_peratom_cols;
}
}
else if ( style == 2 )
{
if ( !fix->local_flag )
{
*nrows = 0;
*ncols = 0;
}
else
{
*nrows = fix->size_local_rows;
*ncols = fix->size_local_cols;
}
}
else
{
*nrows = 0;
*ncols = 0;
}
return;
}
/* vim: set ts=3 sts=3 expandtab: */

40
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/* -----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ------------------------------------------------------------------------
Contributing author: Karl D. Hammond <karlh@ugcs.caltech.edu>
University of Tennessee, Knoxville (USA), 2012
------------------------------------------------------------------------- */
/* This is set of "wrapper" functions to assist LAMMPS.F90, which itself
provides a (I hope) robust Fortran interface to library.cpp and
library.h. All prototypes herein COULD be added to library.h instead of
including this as a separate file. See the README for instructions. */
#ifdef __cplusplus
extern "C" {
#endif
/* Prototypes for auxiliary functions */
void lammps_open_fortran_wrapper (int, char**, MPI_Fint, void**);
int lammps_get_ntypes (void*);
int lammps_extract_compute_vectorsize (void*, char*, int);
void lammps_extract_compute_arraysize (void*, char*, int, int*, int*);
int lammps_extract_fix_vectorsize (void*, char*, int);
void lammps_extract_fix_arraysize (void*, char*, int, int*, int*);
void lammps_error_all (void*, const char*, int, const char*);
#ifdef __cplusplus
}
#endif
/* vim: set ts=3 sts=3 expandtab: */

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/* -----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ------------------------------------------------------------------------
Contributing author: Karl D. Hammond <karlh@ugcs.caltech.edu>
University of Tennessee, Knoxville (USA), 2012
------------------------------------------------------------------------- */
/* This is set of "wrapper" functions to assist LAMMPS.F90, which itself
provides a (I hope) robust Fortran interface to library.cpp and
library.h. All functions herein COULD be added to library.cpp instead of
including this as a separate file. See the README for instructions. */
#include <mpi.h>
#include "LAMMPS-wrapper2.h"
#include <library.h>
#include <lammps.h>
#include <atom.h>
#include <input.h>
#include <modify.h>
#include <fix.h>
#include <fix_external.h>
#include <compute.h>
#include <modify.h>
#include <error.h>
#include <cstdlib>
using namespace LAMMPS_NS;
extern "C" void f_callback(void *, bigint, int, tagint *, double **, double **);
void lammps_set_callback (void *ptr) {
class LAMMPS *lmp = (class LAMMPS *) ptr;
int ifix = lmp->modify->find_fix_by_style("external");
FixExternal *fix = (FixExternal *) lmp->modify->fix[ifix];
fix->set_callback(f_callback, ptr);
return;
}
void lammps_set_external_vector_length (void *ptr, int n) {
class LAMMPS *lmp = (class LAMMPS *) ptr;
int ifix = lmp->modify->find_fix_by_style("external");
FixExternal *fix = (FixExternal *) lmp->modify->fix[ifix];
fix->set_vector_length(n);
return;
}
void lammps_set_external_vector (void *ptr, int n, double val) {
class LAMMPS *lmp = (class LAMMPS *) ptr;
int ifix = lmp->modify->find_fix_by_style("external");
FixExternal *fix = (FixExternal *) lmp->modify->fix[ifix];
fix->set_vector (n, val);
return;
}
void lammps_set_user_energy (void *ptr, double energy) {
class LAMMPS *lmp = (class LAMMPS *) ptr;
int ifix = lmp->modify->find_fix_by_style("external");
FixExternal *fix = (FixExternal *) lmp->modify->fix[ifix];
fix->set_energy_global(energy);
return;
}
void lammps_set_user_virial (void *ptr, double *virial) {
class LAMMPS *lmp = (class LAMMPS *) ptr;
int ifix = lmp->modify->find_fix_by_style("external");
FixExternal *fix = (FixExternal *) lmp->modify->fix[ifix];
fix->set_virial_global(virial);
return;
}

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/* -----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ------------------------------------------------------------------------
Contributing author: Nir Goldman, ngoldman@llnl.gov, Oct. 19th, 2016
------------------------------------------------------------------------- */
/* This is set of "wrapper" functions to assist LAMMPS.F90, which itself
provides a (I hope) robust Fortran interface to library.cpp and
library.h. All prototypes herein COULD be added to library.h instead of
including this as a separate file. See the README for instructions. */
#ifdef __cplusplus
extern "C" {
#endif
/* Prototypes for auxiliary functions */
void lammps_set_callback (void *);
void lammps_set_user_energy (void*, double);
void lammps_set_user_virial (void*, double*);
void lammps_set_external_vector_length (void*, int);
void lammps_set_external_vector (void*, int, double);
#ifdef __cplusplus
}
#endif
/* vim: set ts=3 sts=3 expandtab: */

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!! -----------------------------------------------------------------------
! LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
! www.cs.sandia.gov/~sjplimp/lammps.html
! Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
!
! Copyright (2003) Sandia Corporation. Under the terms of Contract
! DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
! certain rights in this software. This software is distributed under
! the GNU General Public License.
!
! See the README file in the top-level LAMMPS directory.
!--------------------------------------------------------------------------
!! ------------------------------------------------------------------------
! Contributing author: Karl D. Hammond <karlh@ugcs.caltech.edu>
! University of Tennessee, Knoxville (USA), 2012
!--------------------------------------------------------------------------
!! LAMMPS, a Fortran 2003 module containing an interface between Fortran
!! programs and the C-style functions in library.cpp that ship with LAMMPS.
!! This file should be accompanied by LAMMPS-wrapper.cpp and LAMMPS-wrapper.h,
!! which define wrapper functions that ease portability and enforce array
!! dimensions.
!!
!! Everything in this module should be 100% portable by way of Fortran 2003's
!! ISO_C_BINDING intrinsic module. See the README for instructions for
!! compilation and use.
!!
!! Here are the PUBLIC functions and subroutines included in this module.
!! subroutine lammps_open (command_line, communicator, ptr)
!! subroutine lammps_open_no_mpi (command_line, ptr)
!! subroutine lammps_close (ptr)
!! subroutine lammps_file (ptr, str)
!! subroutine lammps_command (ptr, str)
!! subroutine lammps_free (ptr)
!! subroutine lammps_extract_global (global, ptr, name)
!! subroutine lammps_extract_atom (atom, ptr, name)
!! subroutine lammps_extract_fix (fix, ptr, id, style, type, i, j)
!! subroutine lammps_extract_compute (compute, ptr, id, style, type)
!! subroutine lammps_extract_variable (variable, ptr, name, group)
!! function lammps_get_natoms (ptr)
!! subroutine lammps_gather_atoms (ptr, name, count, data)
!! subroutine lammps_scatter_atoms (ptr, name, data)
#define FLERR __FILE__,__LINE__
! The above line allows for similar error checking as is done with standard
! LAMMPS files.
module LAMMPS
use, intrinsic :: ISO_C_binding, only : C_double, C_int, C_ptr, C_char, &
C_NULL_CHAR, C_loc, C_F_pointer, lammps_instance => C_ptr
implicit none
private
public :: lammps_set_user_virial
public :: lammps_set_external_vector_length
public :: lammps_set_external_vector
public :: lammps_set_user_energy
public :: lammps_open, lammps_open_no_mpi, lammps_close, lammps_file, &
lammps_command, lammps_free, lammps_extract_global, &
lammps_extract_atom, lammps_extract_compute, lammps_extract_fix, &
lammps_extract_variable, lammps_get_natoms, lammps_gather_atoms, &
lammps_set_callback
public :: lammps_scatter_atoms, lammps_instance, C_ptr, C_double, C_int
!! Functions supplemental to the prototypes in library.h. {{{1
!! The function definitions (in C++) are contained in LAMMPS-wrapper.cpp.
!! I would have written the first in Fortran, but the MPI libraries (which
!! were written in C) have C-based functions to convert from Fortran MPI
!! handles to C MPI handles, and there is no Fortran equivalent for those
!! functions.
interface
subroutine lammps_open_wrapper (argc, argv, communicator, ptr) &
bind (C, name='lammps_open_fortran_wrapper')
import :: C_int, C_ptr
integer (C_int), value :: argc
type (C_ptr), dimension(*) :: argv
integer, value :: communicator
type (C_ptr) :: ptr
end subroutine lammps_open_wrapper
subroutine lammps_actual_error_all (ptr, file, line, str) &
bind (C, name='lammps_error_all')
import :: C_int, C_char, C_ptr
type (C_ptr), value :: ptr
character (kind=C_char), dimension(*), intent(in) :: file, str
integer (C_int), value :: line
end subroutine lammps_actual_error_all
function lammps_get_ntypes (ptr) result (ntypes) &
bind (C, name='lammps_get_ntypes')
import :: C_int, C_ptr
type (C_ptr), value :: ptr
integer (C_int) :: ntypes
end function lammps_get_ntypes
function lammps_actual_extract_compute_vectorsize (ptr, id, style) &
result (vectorsize) bind (C, name='lammps_extract_compute_vectorsize')
import :: C_int, C_char, C_ptr
integer (C_int) :: vectorsize
type (C_ptr), value :: ptr
character (kind=C_char), dimension(*) :: id
integer (C_int), value :: style
end function lammps_actual_extract_compute_vectorsize
subroutine lammps_actual_extract_compute_arraysize (ptr, id, style, &
nrows, ncols) bind (C, name='lammps_extract_compute_arraysize')
import :: C_int, C_char, C_ptr
integer (C_int) :: arraysize
type (C_ptr), value :: ptr
character (kind=C_char), dimension(*) :: id
integer (C_int), value :: style
integer (C_int) :: nrows, ncols
end subroutine lammps_actual_extract_compute_arraysize
function lammps_actual_extract_fix_vectorsize (ptr, id, style) &
result (vectorsize) bind (C, name='lammps_extract_fix_vectorsize')
import :: C_int, C_char, C_ptr
integer (C_int) :: vectorsize
type (C_ptr), value :: ptr
character (kind=C_char), dimension(*) :: id
integer (C_int), value :: style
end function lammps_actual_extract_fix_vectorsize
subroutine lammps_actual_extract_fix_arraysize (ptr, id, style, &
nrows, ncols) bind (C, name='lammps_extract_fix_arraysize')
import :: C_int, C_char, C_ptr
type (C_ptr), value :: ptr
character (kind=C_char), dimension(*) :: id
integer (C_int), value :: style
integer (C_int) :: nrows, ncols
end subroutine lammps_actual_extract_fix_arraysize
end interface
!! Functions/subroutines defined in library.h and library.cpp {{{1
interface
subroutine lammps_actual_open_no_mpi (argc, argv, ptr) &
bind (C, name='lammps_open_no_mpi')
import :: C_int, C_ptr
integer (C_int), value :: argc
type (C_ptr), dimension(*) :: argv
type (C_ptr) :: ptr
end subroutine lammps_actual_open_no_mpi
subroutine lammps_close (ptr) bind (C, name='lammps_close')
import :: C_ptr
type (C_ptr), value :: ptr
end subroutine lammps_close
subroutine lammps_actual_file (ptr, str) bind (C, name='lammps_file')
import :: C_ptr, C_char
type (C_ptr), value :: ptr
character (kind=C_char), dimension(*) :: str
end subroutine lammps_actual_file
function lammps_actual_command (ptr, str) result (command) &
bind (C, name='lammps_command')
import :: C_ptr, C_char
type (C_ptr), value :: ptr
character (kind=C_char), dimension(*) :: str
type (C_ptr) :: command
end function lammps_actual_command
subroutine lammps_free (ptr) bind (C, name='lammps_free')
import :: C_ptr
type (C_ptr), value :: ptr
end subroutine lammps_free
function lammps_actual_extract_global (ptr, name) &
bind (C, name='lammps_extract_global') result (global)
import :: C_ptr, C_char
type (C_ptr), value :: ptr
character (kind=C_char), dimension(*) :: name
type (C_ptr) :: global
end function lammps_actual_extract_global
function lammps_actual_extract_atom (ptr, name) &
bind (C, name='lammps_extract_atom') result (atom)
import :: C_ptr, C_char
type (C_ptr), value :: ptr
character (kind=C_char), dimension(*) :: name
type (C_ptr) :: atom
end function lammps_actual_extract_atom
function lammps_actual_extract_compute (ptr, id, style, type) &
result (compute) bind (C, name='lammps_extract_compute')
import :: C_ptr, C_char, C_int
type (C_ptr), value :: ptr
character (kind=C_char), dimension(*) :: id
integer (C_int), value :: style, type
type (C_ptr) :: compute
end function lammps_actual_extract_compute
function lammps_actual_extract_fix (ptr, id, style, type, i, j) &
result (fix) bind (C, name='lammps_extract_fix')
import :: C_ptr, C_char, C_int
type (C_ptr), value :: ptr
character (kind=C_char), dimension(*) :: id
integer (C_int), value :: style, type, i, j
type (C_ptr) :: fix
end function lammps_actual_extract_fix
function lammps_actual_extract_variable (ptr, name, group) &
result (variable) bind (C, name='lammps_extract_variable')
import :: C_ptr, C_char
type (C_ptr), value :: ptr
character (kind=C_char), dimension(*) :: name, group
type (C_ptr) :: variable
end function lammps_actual_extract_variable
function lammps_get_natoms (ptr) result (natoms) &
bind (C, name='lammps_get_natoms')
import :: C_ptr, C_int
type (C_ptr), value :: ptr
integer (C_int) :: natoms
end function lammps_get_natoms
subroutine lammps_set_callback (ptr) &
bind (C, name='lammps_set_callback')
import :: C_ptr
type (C_ptr), value :: ptr
end subroutine lammps_set_callback
subroutine lammps_set_user_energy (ptr, energy) &
bind (C, name='lammps_set_user_energy')
import :: C_ptr, C_double
type (C_ptr), value :: ptr
real(C_double), value :: energy
end subroutine lammps_set_user_energy
subroutine lammps_set_user_virial (ptr, virial) &
bind (C, name='lammps_set_user_virial')
import :: C_ptr, C_double
type (C_ptr), value :: ptr
real(C_double) :: virial(6)
end subroutine lammps_set_user_virial
subroutine lammps_set_external_vector_length (ptr, n) &
bind (C, name='lammps_set_external_vector_length')
import :: C_ptr, C_double, C_int
type(C_ptr), value :: ptr
integer (C_int), value :: n
end subroutine lammps_set_external_vector_length
subroutine lammps_set_external_vector (ptr, n, val) &
bind (C, name='lammps_set_external_vector')
import :: C_ptr, C_int, C_double
type (C_ptr), value :: ptr
integer (C_int), value :: n
real(C_double), value :: val
end subroutine lammps_set_external_vector
subroutine lammps_actual_gather_atoms (ptr, name, type, count, data) &
bind (C, name='lammps_gather_atoms')
import :: C_ptr, C_int, C_char
type (C_ptr), value :: ptr, data
character (kind=C_char), dimension(*) :: name
integer (C_int), value :: type, count
end subroutine lammps_actual_gather_atoms
subroutine lammps_actual_scatter_atoms (ptr, name, type, count, data) &
bind (C, name='lammps_scatter_atoms')
import :: C_ptr, C_int, C_char
type (C_ptr), value :: ptr, data
character (kind=C_char), dimension(*) :: name
integer (C_int), value :: type, count
end subroutine lammps_actual_scatter_atoms
end interface
! Generic functions for the wrappers below {{{1
interface lammps_extract_global
module procedure lammps_extract_global_i, &
lammps_extract_global_dp
end interface lammps_extract_global
interface lammps_extract_atom
module procedure lammps_extract_atom_ia, &
lammps_extract_atom_dpa, &
lammps_extract_atom_dp2a
end interface lammps_extract_atom
interface lammps_extract_compute
module procedure lammps_extract_compute_dp, &
lammps_extract_compute_dpa, &
lammps_extract_compute_dp2a
end interface lammps_extract_compute
interface lammps_extract_fix
module procedure lammps_extract_fix_dp, &
lammps_extract_fix_dpa, &
lammps_extract_fix_dp2a
end interface lammps_extract_fix
interface lammps_extract_variable
module procedure lammps_extract_variable_dp, &
lammps_extract_variable_dpa
end interface lammps_extract_variable
interface lammps_gather_atoms
module procedure lammps_gather_atoms_ia, lammps_gather_atoms_dpa
end interface lammps_gather_atoms
interface lammps_scatter_atoms
module procedure lammps_scatter_atoms_ia, lammps_scatter_atoms_dpa
end interface lammps_scatter_atoms
contains !! Wrapper functions local to this module {{{1
subroutine lammps_open (command_line, communicator, ptr)
character (len=*), intent(in) :: command_line
integer, intent(in) :: communicator
type (C_ptr) :: ptr
integer (C_int) :: argc
type (C_ptr), dimension(:), allocatable :: argv
character (kind=C_char), dimension(len_trim(command_line)+1), target :: &
c_command_line
c_command_line = string2Cstring (command_line)
call Cstring2argcargv (c_command_line, argc, argv)
call lammps_open_wrapper (argc, argv, communicator, ptr)
deallocate (argv)
end subroutine lammps_open
!-----------------------------------------------------------------------------
subroutine lammps_open_no_mpi (command_line, ptr)
character (len=*), intent(in) :: command_line
type (C_ptr) :: ptr
integer (C_int) :: argc
type (C_ptr), dimension(:), allocatable :: argv
character (kind=C_char), dimension(len_trim(command_line)+1), target :: &
c_command_line
c_command_line = string2Cstring (command_line)
call Cstring2argcargv (c_command_line, argc, argv)
call lammps_actual_open_no_mpi (argc, argv, ptr)
deallocate (argv)
end subroutine lammps_open_no_mpi
!-----------------------------------------------------------------------------
subroutine lammps_file (ptr, str)
type (C_ptr) :: ptr
character (len=*) :: str
character (kind=C_char), dimension(len_trim(str)+1) :: Cstr
Cstr = string2Cstring (str)
call lammps_actual_file (ptr, Cstr)
end subroutine lammps_file
!-----------------------------------------------------------------------------
subroutine lammps_command (ptr, str)
type (C_ptr) :: ptr
character (len=*) :: str
character (kind=C_char), dimension(len_trim(str)+1) :: Cstr
type (C_ptr) :: dummy
Cstr = string2Cstring (str)
dummy = lammps_actual_command (ptr, Cstr)
end subroutine lammps_command
!-----------------------------------------------------------------------------
! lammps_extract_global {{{2
function lammps_extract_global_Cptr (ptr, name) result (global)
type (C_ptr) :: global
type (C_ptr), intent(in) :: ptr
character (len=*), intent(in) :: name
character (kind=C_char), dimension(len_trim(name)+1) :: Cname
Cname = string2Cstring (name)
global = lammps_actual_extract_global (ptr, Cname)
end function lammps_extract_global_Cptr
subroutine lammps_extract_global_i (global, ptr, name)
integer (C_int), pointer, intent(out) :: global
type (C_ptr), intent(in) :: ptr
character (len=*), intent(in) :: name
type (C_ptr) :: Cptr
Cptr = lammps_extract_global_Cptr (ptr, name)
call C_F_pointer (Cptr, global)
end subroutine lammps_extract_global_i
subroutine lammps_extract_global_dp (global, ptr, name)
real (C_double), pointer, intent(out) :: global
type (C_ptr), intent(in) :: ptr
character (len=*), intent(in) :: name
type (C_ptr) :: Cptr
Cptr = lammps_extract_global_Cptr (ptr, name)
call C_F_pointer (Cptr, global)
end subroutine lammps_extract_global_dp
!-----------------------------------------------------------------------------
! lammps_extract_atom {{{2
function lammps_extract_atom_Cptr (ptr, name) result (atom)
type (C_ptr) :: atom
type (C_ptr), intent(in) :: ptr
character (len=*), intent(in) :: name
character (kind=C_char), dimension(len_trim(name)+1) :: Cname
Cname = string2Cstring (name)
atom = lammps_actual_extract_atom (ptr, Cname)
end function lammps_extract_atom_Cptr
subroutine lammps_extract_atom_ia (atom, ptr, name)
integer (C_int), dimension(:), pointer, intent(out) :: atom
type (C_ptr), intent(in) :: ptr
character (len=*), intent(in) :: name
type (C_ptr) :: Cptr
integer (C_int), pointer :: nelements
call lammps_extract_global_i (nelements, ptr, 'nlocal')
Cptr = lammps_extract_atom_Cptr (ptr, name)
call C_F_pointer (Cptr, atom, (/nelements/))
end subroutine lammps_extract_atom_ia
subroutine lammps_extract_atom_dpa (atom, ptr, name)
real (C_double), dimension(:), pointer, intent(out) :: atom
type (C_ptr), intent(in) :: ptr
character (len=*), intent(in) :: name
type (C_ptr) :: Cptr
integer (C_int), pointer :: nlocal
integer :: nelements
real (C_double), dimension(:), pointer :: Fptr
if ( name == 'mass' ) then
nelements = lammps_get_ntypes (ptr) + 1
else if ( name == 'x' .or. name == 'v' .or. name == 'f' .or. &
name == 'mu' .or. name == 'omega' .or. name == 'torque' .or. &
name == 'angmom' ) then
! We should not be getting a rank-2 array here!
call lammps_error_all (ptr, FLERR, 'You cannot extract those atom&
& data (' // trim(name) // ') into a rank 1 array.')
return
else
! Everything else we can get is probably nlocal units long
call lammps_extract_global_i (nlocal, ptr, 'nlocal')
nelements = nlocal
end if
Cptr = lammps_extract_atom_Cptr (ptr, name)
call C_F_pointer (Cptr, Fptr, (/nelements/))
if ( name == 'mass' ) then
!atom(0:) => Fptr
atom => Fptr
else
atom => Fptr
end if
end subroutine lammps_extract_atom_dpa
subroutine lammps_extract_atom_dp2a (atom, ptr, name)
real (C_double), dimension(:,:), pointer, intent(out) :: atom
type (C_ptr), intent(in) :: ptr
character (len=*), intent(in) :: name
type (C_ptr) :: Cptr
type (C_ptr), pointer, dimension(:) :: Catom
integer (C_int), pointer :: nelements
if ( name /= 'x' .and. name /= 'v' .and. name /= 'f' .and. &
name /= 'mu' .and. name /= 'omega' .and. name /= 'tandque' .and. &
name /= 'angmom' .and. name /= 'fexternal' ) then
! We should not be getting a rank-2 array here!
call lammps_error_all (ptr, FLERR, 'You cannot extract those atom&
& data (' // trim(name) // ') into a rank 2 array.')
return
end if
Cptr = lammps_extract_atom_Cptr (ptr, name)
call lammps_extract_global_i (nelements, ptr, 'nlocal')
! Catom will now be the array of void* pointers that the void** pointer
! pointed to. Catom(1) is now the pointer to the first element.
call C_F_pointer (Cptr, Catom, (/nelements/))
! Now get the actual array, which has its shape transposed from what we
! might think of it in C
call C_F_pointer (Catom(1), atom, (/3, nelements/))
end subroutine lammps_extract_atom_dp2a
!-----------------------------------------------------------------------------
! lammps_extract_compute {{{2
function lammps_extract_compute_Cptr (ptr, id, style, type) result (compute)
type (C_ptr) :: compute
type (C_ptr), intent(in) :: ptr
character (len=*), intent(in) :: id
integer, intent(in) :: style, type
integer (kind=C_int) :: Cstyle, Ctype
character (kind=C_char), dimension(len_trim(id)+1) :: Cid
Cid = string2Cstring (id)
Cstyle = style
Ctype = type
compute = lammps_actual_extract_compute (ptr, Cid, Cstyle, Ctype)
end function lammps_extract_compute_Cptr
subroutine lammps_extract_compute_dp (compute, ptr, id, style, type)
real (C_double), pointer, intent(out) :: compute
type (C_ptr), intent(in) :: ptr
character (len=*), intent(in) :: id
integer, intent(in) :: style, type
type (C_ptr) :: Cptr
! The only valid values of (style,type) are (0,0) for scalar 'compute'
if ( style /= 0 ) then
call lammps_error_all (ptr, FLERR, 'You cannot pack per-atom/local&
& data into a scalar.')
return
end if
if ( type == 1 ) then
call lammps_error_all (ptr, FLERR, 'You cannot extract a compute&
& vector (rank 1) into a scalar.')
return
else if ( type == 2 ) then
call lammps_error_all (ptr, FLERR, 'You cannot extract a compute&
& array (rank 2) into a scalar.')
return
end if
Cptr = lammps_extract_compute_Cptr (ptr, id, style, type)
call C_F_pointer (Cptr, compute)
end subroutine lammps_extract_compute_dp
subroutine lammps_extract_compute_dpa (compute, ptr, id, style, type)
real (C_double), dimension(:), pointer, intent(out) :: compute
type (C_ptr), intent(in) :: ptr
character (len=*), intent(in) :: id
integer, intent(in) :: style, type
type (C_ptr) :: Cptr
integer :: nelements
! Check for the correct dimensionality
if ( type == 0 ) then
call lammps_error_all (ptr, FLERR, 'You cannot extract a compute&
& scalar (rank 0) into a rank 1 variable.')
return
else if ( type == 2 ) then
call lammps_error_all (ptr, FLERR, 'You cannot extract a compute&
& array (rank 2) into a rank 1 variable.')
return
end if
nelements = lammps_extract_compute_vectorsize (ptr, id, style)
Cptr = lammps_extract_compute_Cptr (ptr, id, style, type)
call C_F_pointer (Cptr, compute, (/nelements/))
end subroutine lammps_extract_compute_dpa
subroutine lammps_extract_compute_dp2a (compute, ptr, id, style, type)
real (C_double), dimension(:,:), pointer, intent(out) :: compute
type (C_ptr), intent(in) :: ptr
character (len=*), intent(in) :: id
integer, intent(in) :: style, type
type (C_ptr) :: Cptr
type (C_ptr), pointer, dimension(:) :: Ccompute
integer :: nr, nc
! Check for the correct dimensionality
if ( type == 0 ) then
call lammps_error_all (ptr, FLERR, 'You cannot extract a compute&
& scalar (rank 0) into a rank 2 variable.')
return
else if ( type == 1 ) then
call lammps_error_all (ptr, FLERR, 'You cannot extract a compute&
& array (rank 1) into a rank 2 variable.')
return
end if
call lammps_extract_compute_arraysize (ptr, id, style, nr, nc)
Cptr = lammps_extract_compute_Cptr (ptr, id, style, type)
call C_F_pointer (Cptr, Ccompute, (/nr/))
! Note that the matrix is transposed, from Fortran's perspective
call C_F_pointer (Ccompute(1), compute, (/nc, nr/))
end subroutine lammps_extract_compute_dp2a
!-----------------------------------------------------------------------------
! lammps_extract_fix {{{2
function lammps_extract_fix_Cptr (ptr, id, style, type, i, j) &
result (fix)
type (C_ptr) :: fix
type (C_ptr), intent(in) :: ptr
character (len=*), intent(in) :: id
integer, intent(in) :: style, type, i, j
character (kind=C_char), dimension(len_trim(id)+1) :: Cid
integer (kind=C_int) :: Cstyle, Ctype, Ci, Cj
Cid = string2Cstring (id)
Cstyle = style
Ctype = type
Ci = i - 1 ! This is for consistency with the values from f_ID[i],
Cj = j - 1 ! which is different from what library.cpp uses!
if ( (type >= 1 .and. Ci < 0) .or. &
(type == 2 .and. (Ci < 0 .or. Cj < 0) ) ) then
call lammps_error_all (ptr, FLERR, 'Index out of range in&
& lammps_extract_fix')
end if
fix = lammps_actual_extract_fix (ptr, Cid, Cstyle, Ctype, Ci, Cj)
end function lammps_extract_fix_Cptr
subroutine lammps_extract_fix_dp (fix, ptr, id, style, type, i, j)
real (C_double), intent(out) :: fix
type (C_ptr), intent(in) :: ptr
character (len=*), intent(in) :: id
integer, intent(in) :: style, type, i, j
type (C_ptr) :: Cptr
real (C_double), pointer :: Fptr
! Check for the correct dimensionality
if ( style /= 0 ) then
select case (type)
case (0)
call lammps_error_all (ptr, FLERR, 'There is no per-atom or local&
& scalar data available from fixes.')
case (1)
call lammps_error_all (ptr, FLERR, 'You cannot extract a fix''s &
&per-atom/local vector (rank 1) into a scalar.')
case (2)
call lammps_error_all (ptr, FLERR, 'You cannot extract a fix''s &
&per-atom/local array (rank 2) into a scalar.')
case default
call lammps_error_all (ptr, FLERR, 'Invalid extract_fix style/&
&type combination.')
end select
return
end if
Cptr = lammps_extract_fix_Cptr (ptr, id, style, type, i, j)
call C_F_pointer (Cptr, Fptr)
fix = Fptr
nullify (Fptr)
! Memory is only allocated for "global" fix variables
if ( style == 0 ) call lammps_free (Cptr)
end subroutine lammps_extract_fix_dp
subroutine lammps_extract_fix_dpa (fix, ptr, id, style, type, i, j)
real (C_double), dimension(:), pointer, intent(out) :: fix
type (C_ptr), intent(in) :: ptr
character (len=*), intent(in) :: id
integer, intent(in) :: style, type, i, j
type (C_ptr) :: Cptr
integer :: fix_len
! Check for the correct dimensionality
if ( style == 0 ) then
call lammps_error_all (ptr, FLERR, 'You can''t extract the&
& whole vector from global fix data')
return
else if ( type == 0 ) then
call lammps_error_all (ptr, FLERR, 'You can''t extract a fix&
& scalar into a rank 1 variable')
return
else if ( type == 2 ) then
call lammps_error_all (ptr, FLERR, 'You cannot extract a fix&
& array into a rank 1 variable.')
return
else if ( type /= 1 ) then
call lammps_error_all (ptr, FLERR, 'Invalid type for fix extraction.')
return
end if
fix_len = lammps_extract_fix_vectorsize (ptr, id, style)
call C_F_pointer (Cptr, fix, (/fix_len/))
! Memory is only allocated for "global" fix variables, which we should
! never get here, so no need to call lammps_free!
end subroutine lammps_extract_fix_dpa
subroutine lammps_extract_fix_dp2a (fix, ptr, id, style, type, i, j)
real (C_double), dimension(:,:), pointer, intent(out) :: fix
type (C_ptr), intent(in) :: ptr
character (len=*), intent(in) :: id
integer, intent(in) :: style, type, i, j
type (C_ptr) :: Cptr
type (C_ptr), pointer, dimension(:) :: Cfix
integer :: nr, nc
! Check for the correct dimensionality
if ( style == 0 ) then
call lammps_error_all (ptr, FLERR, 'It is not possible to extract the&
& entire array from global fix data.')
return
else if ( type == 0 ) then
call lammps_error_all (ptr, FLERR, 'You cannot extract a fix&
& scalar (rank 0) into a rank 2 variable.')
return
else if ( type == 1 ) then
call lammps_error_all (ptr, FLERR, 'You cannot extract a fix&
& vector (rank 1) into a rank 2 variable.')
return
end if
call lammps_extract_fix_arraysize (ptr, id, style, nr, nc)
! Extract pointer to first element as Cfix(1)
call C_F_pointer (Cptr, Cfix, (/nr/))
! Now extract the array, which is transposed
call C_F_pointer (Cfix(1), fix, (/nc, nr/))
end subroutine lammps_extract_fix_dp2a
!-----------------------------------------------------------------------------
! lammps_extract_variable {{{2
function lammps_extract_variable_Cptr (ptr, name, group) result (variable)
type (C_ptr) :: ptr, variable
character (len=*) :: name
character (len=*), optional :: group
character (kind=C_char), dimension(len_trim(name)+1) :: Cname
character (kind=C_char), dimension(:), allocatable :: Cgroup
Cname = string2Cstring (name)
if ( present(group) ) then
allocate (Cgroup(len_trim(group)+1))
Cgroup = string2Cstring (group)
else
allocate (Cgroup(1))
Cgroup(1) = C_NULL_CHAR
end if
variable = lammps_actual_extract_variable (ptr, Cname, Cgroup)
deallocate (Cgroup)
end function lammps_extract_variable_Cptr
subroutine lammps_extract_variable_dp (variable, ptr, name, group)
real (C_double), intent(out) :: variable
type (C_ptr), intent(in) :: ptr
character (len=*), intent(in) :: name
character (len=*), intent(in), optional :: group
type (C_ptr) :: Cptr
real (C_double), pointer :: Fptr
if ( present(group) ) then
Cptr = lammps_extract_variable_Cptr (ptr, name, group)
else
Cptr = lammps_extract_variable_Cptr (ptr, name)
end if
call C_F_pointer (Cptr, Fptr)
variable = Fptr
nullify (Fptr)
call lammps_free (Cptr)
end subroutine lammps_extract_variable_dp
subroutine lammps_extract_variable_dpa (variable, ptr, name, group)
real (C_double), dimension(:), allocatable, intent(out) :: variable
type (C_ptr), intent(in) :: ptr
character (len=*), intent(in) :: name
character (len=*), intent(in), optional :: group
type (C_ptr) :: Cptr
real (C_double), dimension(:), pointer :: Fptr
integer :: natoms
if ( present(group) ) then
Cptr = lammps_extract_variable_Cptr (ptr, name, group)
else
Cptr = lammps_extract_variable_Cptr (ptr, name)
end if
natoms = lammps_get_natoms (ptr)
allocate (variable(natoms))
call C_F_pointer (Cptr, Fptr, (/natoms/))
variable = Fptr
nullify (Fptr)
call lammps_free (Cptr)
end subroutine lammps_extract_variable_dpa
!-------------------------------------------------------------------------2}}}
subroutine lammps_gather_atoms_ia (ptr, name, count, data)
type (C_ptr), intent(in) :: ptr
character (len=*), intent(in) :: name
integer, intent(in) :: count
integer, dimension(:), allocatable, intent(out) :: data
type (C_ptr) :: Cdata
integer (C_int), dimension(:), pointer :: Fdata
integer (C_int) :: natoms
character (kind=C_char), dimension(len_trim(name)+1) :: Cname
integer (C_int), parameter :: Ctype = 0_C_int
integer (C_int) :: Ccount
natoms = lammps_get_natoms (ptr)
Cname = string2Cstring (name)
if ( count /= 1 .and. count /= 3 ) then
call lammps_error_all (ptr, FLERR, 'lammps_gather_atoms requires&
& count to be either 1 or 3')
else
Ccount = count
end if
allocate ( Fdata(count*natoms) )
allocate ( data(count*natoms) )
Cdata = C_loc (Fdata(1))
call lammps_actual_gather_atoms (ptr, Cname, Ctype, Ccount, Cdata)
data = Fdata
deallocate (Fdata)
end subroutine lammps_gather_atoms_ia
subroutine lammps_gather_atoms_dpa (ptr, name, count, data)
type (C_ptr), intent(in) :: ptr
character (len=*), intent(in) :: name
integer, intent(in) :: count
double precision, dimension(:), allocatable, intent(out) :: data
type (C_ptr) :: Cdata
real (C_double), dimension(:), pointer :: Fdata
integer (C_int) :: natoms
character (kind=C_char), dimension(len_trim(name)+1) :: Cname
integer (C_int), parameter :: Ctype = 1_C_int
integer (C_int) :: Ccount
natoms = lammps_get_natoms (ptr)
Cname = string2Cstring (name)
if ( count /= 1 .and. count /= 3 ) then
call lammps_error_all (ptr, FLERR, 'lammps_gather_atoms requires&
& count to be either 1 or 3')
else
Ccount = count
end if
allocate ( Fdata(count*natoms) )
allocate ( data(count*natoms) )
Cdata = C_loc (Fdata(1))
call lammps_actual_gather_atoms (ptr, Cname, Ctype, Ccount, Cdata)
data = Fdata(:)
deallocate (Fdata)
end subroutine lammps_gather_atoms_dpa
!-----------------------------------------------------------------------------
subroutine lammps_scatter_atoms_ia (ptr, name, data)
type (C_ptr), intent(in) :: ptr
character (len=*), intent(in) :: name
integer, dimension(:), intent(in) :: data
integer (kind=C_int) :: natoms, Ccount
integer (kind=C_int), parameter :: Ctype = 0_C_int
character (kind=C_char), dimension(len_trim(name)+1) :: Cname
integer (C_int), dimension(size(data)), target :: Fdata
type (C_ptr) :: Cdata
natoms = lammps_get_natoms (ptr)
Cname = string2Cstring (name)
Ccount = size(data) / natoms
if ( Ccount /= 1 .and. Ccount /= 3 ) &
call lammps_error_all (ptr, FLERR, 'lammps_gather_atoms requires&
& count to be either 1 or 3')
Fdata = data
Cdata = C_loc (Fdata(1))
call lammps_actual_scatter_atoms (ptr, Cname, Ctype, Ccount, Cdata)
end subroutine lammps_scatter_atoms_ia
subroutine lammps_scatter_atoms_dpa (ptr, name, data)
type (C_ptr), intent(in) :: ptr
character (len=*), intent(in) :: name
double precision, dimension(:), intent(in) :: data
integer (kind=C_int) :: natoms, Ccount
integer (kind=C_int), parameter :: Ctype = 1_C_int
character (kind=C_char), dimension(len_trim(name)+1) :: Cname
real (C_double), dimension(size(data)), target :: Fdata
type (C_ptr) :: Cdata
natoms = lammps_get_natoms (ptr)
Cname = string2Cstring (name)
Ccount = size(data) / natoms
if ( Ccount /= 1 .and. Ccount /= 3 ) &
call lammps_error_all (ptr, FLERR, 'lammps_gather_atoms requires&
& count to be either 1 or 3')
Fdata = data
Cdata = C_loc (Fdata(1))
call lammps_actual_scatter_atoms (ptr, Cname, Ctype, Ccount, Cdata)
end subroutine lammps_scatter_atoms_dpa
!-----------------------------------------------------------------------------
function lammps_extract_compute_vectorsize (ptr, id, style) &
result (vectorsize)
integer :: vectorsize
type (C_ptr), intent(in) :: ptr
character (len=*), intent(in) :: id
integer, intent(in) :: style
integer (C_int) :: Cvectorsize, Cstyle
character (kind=C_char), dimension(len_trim(id)+1) :: Cid
Cid = string2Cstring (id)
Cstyle = int(style, C_int)
Cvectorsize = lammps_actual_extract_compute_vectorsize (ptr, Cid, Cstyle)
vectorsize = int(Cvectorsize, kind(vectorsize))
end function lammps_extract_compute_vectorsize
!-----------------------------------------------------------------------------
function lammps_extract_fix_vectorsize (ptr, id, style) &
result (vectorsize)
integer :: vectorsize
type (C_ptr), intent(in) :: ptr
character (len=*), intent(in) :: id
integer, intent(in) :: style
integer (C_int) :: Cvectorsize, Cstyle
character (kind=C_char), dimension(len_trim(id)+1) :: Cid
Cid = string2Cstring (id)
Cstyle = int(style, C_int)
Cvectorsize = lammps_actual_extract_fix_vectorsize (ptr, Cid, Cstyle)
vectorsize = int(Cvectorsize, kind(vectorsize))
end function lammps_extract_fix_vectorsize
!-----------------------------------------------------------------------------
subroutine lammps_extract_compute_arraysize (ptr, id, style, nrows, ncols)
type (C_ptr), intent(in) :: ptr
character (len=*), intent(in) :: id
integer, intent(in) :: style
integer, intent(out) :: nrows, ncols
integer (C_int) :: Cstyle, Cnrows, Cncols
character (kind=C_char), dimension(len_trim(id)+1) :: Cid
Cid = string2Cstring (id)
Cstyle = int (style, C_int)
call lammps_actual_extract_compute_arraysize (ptr, Cid, Cstyle, &
Cnrows, Cncols)
nrows = int (Cnrows, kind(nrows))
ncols = int (Cncols, kind(ncols))
end subroutine lammps_extract_compute_arraysize
!-----------------------------------------------------------------------------
subroutine lammps_extract_fix_arraysize (ptr, id, style, nrows, ncols)
type (C_ptr), intent(in) :: ptr
character (len=*), intent(in) :: id
integer, intent(in) :: style
integer, intent(out) :: nrows, ncols
integer (C_int) :: Cstyle, Cnrows, Cncols
character (kind=C_char), dimension(len_trim(id)+1) :: Cid
Cid = string2Cstring (id)
Cstyle = int (style, kind(Cstyle))
call lammps_actual_extract_fix_arraysize (ptr, Cid, Cstyle, &
Cnrows, Cncols)
nrows = int (Cnrows, kind(nrows))
ncols = int (Cncols, kind(ncols))
end subroutine lammps_extract_fix_arraysize
!-----------------------------------------------------------------------------
subroutine lammps_error_all (ptr, file, line, str)
type (C_ptr), intent(in) :: ptr
character (len=*), intent(in) :: file, str
integer, intent(in) :: line
character (kind=C_char), dimension(len_trim(file)+1) :: Cfile
character (kind=C_char), dimension(len_trim(str)+1) :: Cstr
integer (C_int) :: Cline
Cline = int(line, kind(Cline))
Cfile = string2Cstring (file)
Cstr = string2Cstring (str)
call lammps_actual_error_all (ptr, Cfile, Cline, Cstr)
end subroutine lammps_error_all
!-----------------------------------------------------------------------------
! Locally defined helper functions {{{1
pure function string2Cstring (string) result (C_string)
use, intrinsic :: ISO_C_binding, only : C_char, C_NULL_CHAR
character (len=*), intent(in) :: string
character (len=1, kind=C_char) :: C_string (len_trim(string)+1)
integer :: i, n
n = len_trim (string)
forall (i = 1:n)
C_string(i) = string(i:i)
end forall
C_string(n+1) = C_NULL_CHAR
end function string2Cstring
!-----------------------------------------------------------------------------
subroutine Cstring2argcargv (Cstring, argc, argv)
!! Converts a C-style string to argc and argv, that is, words in Cstring
!! become C-style strings in argv. IMPORTANT: Cstring is modified by
!! this routine! I would make Cstring local TO this routine and accept
!! a Fortran-style string instead, but we run into scoping and
!! allocation problems that way. This routine assumes the string is
!! null-terminated, as all C-style strings must be.
character (kind=C_char), dimension(*), target, intent(inout) :: Cstring
integer (C_int), intent(out) :: argc
type (C_ptr), dimension(:), allocatable, intent(out) :: argv
integer :: StringStart, SpaceIndex, strlen, argnum
argc = 1_C_int
! Find the length of the string
strlen = 1
do while ( Cstring(strlen) /= C_NULL_CHAR )
strlen = strlen + 1
end do
! Find the number of non-escaped spaces
SpaceIndex = 2
do while ( SpaceIndex < strlen )
if ( Cstring(SpaceIndex) == ' ' .and. &
Cstring(SpaceIndex-1) /= '\' ) then
argc = argc + 1_C_int
! Find the next non-space character
do while ( Cstring(SpaceIndex+1) == ' ')
SpaceIndex = SpaceIndex + 1
end do
end if
SpaceIndex = SpaceIndex + 1
end do
! Now allocate memory for argv
allocate (argv(argc))
! Now find the string starting and ending locations
StringStart = 1
SpaceIndex = 2
argnum = 1
do while ( SpaceIndex < strlen )
if ( Cstring(SpaceIndex) == ' ' .and. &
Cstring(SpaceIndex-1) /= '\' ) then
! Found a real space => split strings and store this one
Cstring(Spaceindex) = C_NULL_CHAR ! Replaces space with NULL
argv(argnum) = C_loc(Cstring(StringStart))
argnum = argnum + 1
! Find the next non-space character
do while ( Cstring(SpaceIndex+1) == ' ')
SpaceIndex = SpaceIndex + 1
end do
StringStart = SpaceIndex + 1
else if ( Cstring(SpaceIndex) == ' ' .and. &
Cstring(SpaceIndex-1) == '\' ) then
! Escaped space => remove backslash and move rest of array
Cstring(SpaceIndex-1:strlen-1) = Cstring(SpaceIndex:strlen)
strlen = strlen - 1 ! Last character is still C_NULL_CHAR
end if
SpaceIndex = SpaceIndex + 1
end do
! Now handle the last argument
argv(argnum) = C_loc(Cstring(StringStart))
end subroutine Cstring2argcargv
! 1}}}
end module LAMMPS
! vim: foldmethod=marker tabstop=3 softtabstop=3 shiftwidth=3 expandtab

37
examples/COUPLE/fortran_dftb/README
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@ -1,37 +0,0 @@
This directory has an example of using a callback function to obtain
forces from a fortran code for a LAMMPS simulation. The reader should
refer to the README file in COUPLE/fortran2 before proceeding. Here,
the LAMMPS.F90 file has been modified slightly and additional files
named LAMMPS-wrapper2.h and LAMMPS-wrapper2.cpp have been included in
order to supply wrapper functions to set the LAMMPS callback function,
total energy, virial, and electronic entropy contribution (needed for
MSST simulations with a quantum code).
In this example, the callback function is set to run the
semi-empirical quantum code DFTB+ in serial and then read in the total
energy, forces, and stress tensor from file. In this case, nlocal =
the total number of atoms in the system, so particle positions can be
read from the pos array directly, and DFTB+ forces can simply be
included via the fext array. The user should take care in the case of
a parallel calculation, where LAMMPS can assign different particules
to each processor. For example, the user should use functions such as
lammps_gather_atoms() and lammps_scatter_atoms() in the case where the
fortran force calculating code requires the positions of all atoms,
etc.
A few more important notes:
-Calling the subroutine lammps_set_callback() is required in order to set
a pointer to the callback function in LAMMPS.
-The subroutine lammps_set_user_energy() passes in the potential energy
from DFTB+ to LAMMPS. Similarly, lammps_set_user_virial passes the stress tensor.
-The electronic entropy contribution is set via lammps_set_external_vector(). Their needs
to be a call to lammps_set_external_vector_length() before this value can be
passed to LAMMPS.
This example was created by Nir Goldman, whom you can contact with
questions:
Nir Goldman, LLNL
ngoldman@llnl.gov

148
examples/COUPLE/fortran_dftb/data.diamond
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@ -1,148 +0,0 @@
# Position data file
64 atoms
1 atom types
0 7.134 xlo xhi
0 7.134 ylo yhi
0 7.134 zlo zhi
0.00000000 0.00000000 0.00000000 xy xz yz
Masses
1 12.010000
Atoms
1 1 0 0 0 0
2 1 0 0.89175 0.89175 0.89175
3 1 0 1.7835 1.7835 0
4 1 0 2.67525 2.67525 0.89175
5 1 0 0 1.7835 1.7835
6 1 0 0.89175 2.67525 2.67525
7 1 0 1.7835 0 1.7835
8 1 0 2.67525 0.89175 2.67525
9 1 0 0 0 3.567
10 1 0 0.89175 0.89175 4.45875
11 1 0 1.7835 1.7835 3.567
12 1 0 2.67525 2.67525 4.45875
13 1 0 0 1.7835 5.3505
14 1 0 0.89175 2.67525 6.24225
15 1 0 1.7835 0 5.3505
16 1 0 2.67525 0.89175 6.24225
17 1 0 0 3.567 0
18 1 0 0.89175 4.45875 0.89175
19 1 0 1.7835 5.3505 0
20 1 0 2.67525 6.24225 0.89175
21 1 0 0 5.3505 1.7835
22 1 0 0.89175 6.24225 2.67525
23 1 0 1.7835 3.567 1.7835
24 1 0 2.67525 4.45875 2.67525
25 1 0 0 3.567 3.567
26 1 0 0.89175 4.45875 4.45875
27 1 0 1.7835 5.3505 3.567
28 1 0 2.67525 6.24225 4.45875
29 1 0 0 5.3505 5.3505
30 1 0 0.89175 6.24225 6.24225
31 1 0 1.7835 3.567 5.3505
32 1 0 2.67525 4.45875 6.24225
33 1 0 3.567 0 0
34 1 0 4.45875 0.89175 0.89175
35 1 0 5.3505 1.7835 0
36 1 0 6.24225 2.67525 0.89175
37 1 0 3.567 1.7835 1.7835
38 1 0 4.45875 2.67525 2.67525
39 1 0 5.3505 0 1.7835
40 1 0 6.24225 0.89175 2.67525
41 1 0 3.567 0 3.567
42 1 0 4.45875 0.89175 4.45875
43 1 0 5.3505 1.7835 3.567
44 1 0 6.24225 2.67525 4.45875
45 1 0 3.567 1.7835 5.3505
46 1 0 4.45875 2.67525 6.24225
47 1 0 5.3505 0 5.3505
48 1 0 6.24225 0.89175 6.24225
49 1 0 3.567 3.567 0
50 1 0 4.45875 4.45875 0.89175
51 1 0 5.3505 5.3505 0
52 1 0 6.24225 6.24225 0.89175
53 1 0 3.567 5.3505 1.7835
54 1 0 4.45875 6.24225 2.67525
55 1 0 5.3505 3.567 1.7835
56 1 0 6.24225 4.45875 2.67525
57 1 0 3.567 3.567 3.567
58 1 0 4.45875 4.45875 4.45875
59 1 0 5.3505 5.3505 3.567
60 1 0 6.24225 6.24225 4.45875
61 1 0 3.567 5.3505 5.3505
62 1 0 4.45875 6.24225 6.24225
63 1 0 5.3505 3.567 5.3505
64 1 0 6.24225 4.45875 6.24225
Velocities
1 -0.00733742 -0.0040297 -0.00315229
2 -0.00788609 -0.00567535 -0.00199152
3 -0.00239042 0.00710139 -0.00335049
4 0.00678551 0.0019976 0.00219289
5 0.00413717 0.00275709 0.000937637
6 -0.00126313 0.00485636 0.00727862
7 0.00337547 -0.00234623 -0.000922223
8 -0.00792183 -0.00509186 -0.00104168
9 0.00414091 0.00390285 0.000845961
10 -0.000284543 0.0010771 -0.00458404
11 -0.00394968 -0.00446363 -0.00361688
12 0.00067088 -0.00655175 -0.00752464
13 0.00306632 -0.00245545 -0.00183867
14 -0.0082145 -0.00564127 0.000281191
15 0.00504454 0.0045835 0.000495763
16 0.0035767 0.00320441 -0.00486426
17 0.00420597 0.00262005 -0.0049459
18 0.00440579 -1.76783e-05 0.00449311
19 -0.00406463 0.00613304 0.00285599
20 0.00171215 -0.00517887 0.00124326
21 0.0011118 0.00334129 -0.0015222
22 -0.00838394 -0.00112906 -0.00353379
23 -0.00578527 -0.00415501 0.00297043
24 -0.00211466 0.000964108 -0.00716523
25 -0.000204107 -0.00380986 0.00681648
26 0.00677838 0.00540935 0.0044354
27 -0.00266809 -0.00358382 -0.00241889
28 -0.0003973 0.00236566 0.00558871
29 0.000754103 0.00457797 0.000105531
30 -0.00246049 0.00110428 0.00511088
31 0.00248891 0.00623314 0.00461597
32 -0.00509423 0.000570503 0.00720856
33 -0.00244427 -0.00374384 0.00618767
34 -0.000360752 -8.10558e-05 0.00314052
35 0.00435313 -0.00630587 -0.0070309
36 0.00651087 -0.00389833 3.72525e-05
37 0.00631828 -0.00316064 0.00231522
38 -0.00579624 -0.00345068 -0.000277486
39 0.00483974 0.000715028 0.000206355
40 -0.00388164 -0.00189242 -0.00554862
41 0.00398115 0.00152915 0.00756919
42 -0.000552263 0.00352025 -0.000246143
43 -0.00800284 0.00555703 0.00425716
44 -0.00734405 -0.00752512 0.00667173
45 -0.00545636 0.00421035 0.00399552
46 0.00480246 0.00621147 -0.00492715
47 -0.00424168 0.00621818 -9.37733e-05
48 -0.00649561 0.00612908 -0.0020753
49 -0.0075007 -0.00384737 -0.00687913
50 -0.00203903 -0.00764372 0.0023883
51 0.00442642 0.00744072 -0.0049344
52 -0.00280486 -0.00509128 -0.00678045
53 0.00679491 0.00583493 0.00333875
54 0.00574665 -0.00521074 0.00523475
55 0.00305618 -0.00320094 0.00341297
56 0.004304 0.000615544 -0.00668787
57 0.00564532 0.00327373 0.00388611
58 0.000676899 0.00210326 0.00495295
59 0.000160781 -0.00744313 -0.00279828
60 0.00623521 0.00371301 0.00178015
61 0.00520759 0.000642669 0.00207913
62 0.00398042 0.0046438 -0.00359978
63 -0.00478071 -0.00304932 -0.00765125
64 0.00282671 -0.00548392 -0.00692691

40
examples/COUPLE/fortran_dftb/dftb_in.hsd
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@ -1,40 +0,0 @@
#sample DFTB+ script to run this test code
Geometry = GenFormat {
<<< "lammps.gen"
}
Driver = {
}
Hamiltonian = DFTB {
LAMMPS = Yes # keyword to print energy, forces, and stress tensor to file(results.out)
SCC = No
MaxAngularMomentum = {
C = "p"
}
Charge = 0.0
Eigensolver = Standard {}
Filling = Fermi {
Temperature [Kelvin] = 298.0
}
SlaterKosterFiles = Type2FileNames {
Prefix = "~/slako/mio-1-1/" # the user must define the location of the skf files
Separator = "-"
Suffix = ".skf"
LowerCaseTypeName = No
}
KPointsAndWeights = {
0.0000000000000 0.0000000000000 0.0000000000000 1.00000000000000
}
}
Options = {
CalculateForces = Yes
WriteDetailedOut = No
WriteBandOut = No
RandomSeed = 12345
}
ParserOptions = {
ParserVersion = 3
}

129
examples/COUPLE/fortran_dftb/dftb_pin.hsd
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Geometry = GenFormat {
64 S
C
1 1 7.099007 7.117657 7.119139
2 1 0.858709 0.867233 0.882294
3 1 1.772527 1.811776 7.120239
4 1 2.702145 2.681271 0.901362
5 1 0.017539 1.794455 1.788454
6 1 0.885593 2.694118 2.707994
7 1 1.795055 7.120787 1.777896
8 1 2.642849 0.868278 2.670699
9 1 0.016060 0.017156 3.568644
10 1 0.891891 0.896406 4.439286
11 1 1.766086 1.764402 3.550134
12 1 2.677349 2.648926 4.427174
13 1 0.010133 1.771283 5.342173
14 1 0.858153 2.653565 6.241596
15 1 1.804087 0.020636 5.353268
16 1 2.689680 0.907188 6.224575
17 1 0.017845 3.577563 7.113016
18 1 0.910027 4.459286 0.910286
19 1 1.766394 5.376046 0.015526
20 1 2.683727 6.220728 0.898553
21 1 0.003357 5.363423 1.774139
22 1 0.856735 6.238324 2.660213
23 1 1.761079 3.549776 1.797054
24 1 2.667227 4.463441 2.646074
25 1 7.132499 3.551558 3.599764
26 1 0.920387 4.482191 4.479257
27 1 1.772194 5.337132 3.555569
28 1 2.675010 6.251629 4.483124
29 1 0.005702 5.371095 5.351147
30 1 0.880807 6.249819 6.264231
31 1 1.793177 3.592396 5.369939
32 1 2.653179 4.463595 6.274044
33 1 3.557243 7.118913 0.026006
34 1 4.458971 0.889331 0.904950
35 1 5.367903 1.759757 7.104941
36 1 6.271565 2.658454 0.890168
37 1 3.591915 1.768681 1.793880
38 1 4.435612 2.662184 2.676722
39 1 5.371040 0.000196 1.783464
40 1 6.226453 0.886640 2.653384
41 1 3.583339 0.005449 3.600177
42 1 4.453692 0.909417 4.459713
43 1 5.314554 1.805409 3.584215
44 1 6.210181 2.642660 4.486206
45 1 3.545704 1.802745 5.365369
46 1 4.476660 2.701226 6.220451
47 1 5.332820 0.029557 5.347965
48 1 6.215725 0.915081 6.230289
49 1 3.536446 3.551469 7.106600
50 1 4.451181 4.426439 0.900180
51 1 5.368735 5.377996 7.109524
52 1 6.230666 6.220985 0.862175
53 1 3.596626 5.372822 1.797613
54 1 4.485613 6.221252 2.699652
55 1 5.364421 3.549838 1.796281
56 1 6.261739 4.459046 2.648152
57 1 3.588752 3.581054 3.581755
58 1 4.462342 4.467270 4.478800
59 1 5.355202 5.318323 3.556531
60 1 6.268570 6.259831 4.465795
61 1 3.588636 5.354278 5.362327
62 1 4.475747 6.263866 6.227803
63 1 5.331158 3.554349 5.318368
64 1 6.254581 4.436344 6.209681
0.0 0.0 0.0
7.13400000000000 0 0
0 7.13400000000000 0
0 0 7.13400000000000
}
Driver = {}
Hamiltonian = DFTB {
LAMMPS = Yes
SCC = No
MaxAngularMomentum = {
C = "p"
}
Charge = 0.0
Eigensolver = Standard {}
Filling = Fermi {
Temperature [Kelvin] = 298.0
IndependentKFilling = No
}
SlaterKosterFiles = Type2FileNames {
Prefix = "~/slako/mio-1-1/"
Separator = "-"
Suffix = ".skf"
LowerCaseTypeName = No
}
KPointsAndWeights = {
0.0000000000000 0.0000000000000 0.0000000000000 1.00000000000000
}
PolynomialRepulsive = {}
OldRepulsiveSum = No
OrbitalResolvedSCC = No
OldSKInterpolation = No
NoErep = No
Dispersion = {}
ThirdOrder = No
ThirdOrderFull = No
}
Options = {
CalculateForces = Yes
WriteDetailedOut = No
WriteBandOut = No
RandomSeed = 12345
MullikenAnalysis = No
WriteEigenvectors = No
WriteAutotestTag = No
WriteDetailedXML = No
WriteResultsTag = No
AtomResolvedEnergies = No
WriteHS = No
WriteRealHS = No
MinimiseMemoryUsage = No
ShowFoldedCoords = No
}
ParserOptions = {
ParserVersion = 3
WriteHSDInput = Yes
WriteXMLInput = No
StopAfterParsing = No
IgnoreUnprocessedNodes = No
}
Analysis = {
ProjectStates = {}
}

16
examples/COUPLE/fortran_dftb/in.simple
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units real
atom_style charge
atom_modify map array
atom_modify sort 0 0.0
read_data data.diamond
neighbor 1.0 bin
neigh_modify delay 0 every 5 check no
fix 1 all nve
fix 2 all external pf/callback 1 1
fix_modify 2 energy yes
thermo_style custom step temp etotal ke pe lx ly lz pxx pyy pzz press
thermo 1
timestep 0.5

71
examples/COUPLE/fortran_dftb/log.simple
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LAMMPS (6 Jul 2017)
units real
atom_style charge
atom_modify map array
atom_modify sort 0 0.0
read_data data.diamond
triclinic box = (0 0 0) to (7.134 7.134 7.134) with tilt (0 0 0)
1 by 1 by 1 MPI processor grid
reading atoms ...
64 atoms
reading velocities ...
64 velocities
neighbor 1.0 bin
neigh_modify delay 0 every 5 check no
fix 1 all nve
fix 2 all external pf/callback 1 1
fix_modify 2 energy yes
thermo_style custom step temp etotal ke pe lx ly lz pxx pyy pzz press
thermo 1
timestep 0.5
run 10
Neighbor list info ...
update every 5 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 0
ghost atom cutoff = 0
binsize = 7.134, bins = 1 1 1
0 neighbor lists, perpetual/occasional/extra = 0 0 0
Per MPI rank memory allocation (min/avg/max) = 2.3 | 2.3 | 2.3 Mbytes
Step Temp TotEng KinEng PotEng Lx Ly Lz Pxx Pyy Pzz Press
0 298.24835 -69593.587 56.008365 -69649.595 7.134 7.134 7.134 -19980.19 -21024.038 -21097.458 -20700.562
1 295.24358 -69593.585 55.444098 -69649.029 7.134 7.134 7.134 -19778.833 -20799.657 -20854.156 -20477.549
2 286.37211 -69593.58 53.778115 -69647.358 7.134 7.134 7.134 -19227.52 -20177.28 -20176.12 -19860.306
3 272.062 -69593.572 51.090804 -69644.663 7.134 7.134 7.134 -18360.869 -19189.684 -19100.021 -18883.525
4 253.01834 -69593.561 47.514575 -69641.075 7.134 7.134 7.134 -17198.143 -17855.03 -17652.036 -17568.403
5 230.19242 -69593.547 43.228073 -69636.775 7.134 7.134 7.134 -15750.247 -16183.764 -15854.145 -15929.386
6 204.71787 -69593.533 38.44418 -69631.977 7.134 7.134 7.134 -14083.498 -14247.434 -13789.835 -14040.256
7 177.82397 -69593.518 33.393748 -69626.911 7.134 7.134 7.134 -12340.963 -12202.878 -11623.171 -12055.671
8 150.76736 -69593.503 28.312758 -69621.816 7.134 7.134 7.134 -10637.824 -10180.827 -9495.0496 -10104.567
9 124.7737 -69593.49 23.431383 -69616.921 7.134 7.134 7.134 -9113.3842 -8339.0492 -7572.8076 -8341.747
10 100.98183 -69593.478 18.963481 -69612.442 7.134 7.134 7.134 -7833.9349 -6756.9749 -5945.8968 -6845.6022
Loop time of 2.20497 on 1 procs for 10 steps with 64 atoms
Performance: 0.196 ns/day, 122.499 hours/ns, 4.535 timesteps/s
0.2% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 1.4305e-06 | 1.4305e-06 | 1.4305e-06 | 0.0 | 0.00
Comm | 4.22e-05 | 4.22e-05 | 4.22e-05 | 0.0 | 0.00
Output | 0.00067687 | 0.00067687 | 0.00067687 | 0.0 | 0.03
Modify | 2.2042 | 2.2042 | 2.2042 | 0.0 | 99.96
Other | | 6.533e-05 | | | 0.00
Nlocal: 64 ave 64 max 64 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 2
Dangerous builds not checked
Total wall time: 0:00:02

45
examples/COUPLE/fortran_dftb/makefile
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SHELL = /bin/sh
# Path to LAMMPS extraction directory
LAMMPS_ROOT = ../../..
LAMMPS_SRC = $(LAMMPS_ROOT)/src
# Uncomment the line below if using the MPI stubs library
MPI_STUBS = #-I$(LAMMPS_SRC)/STUBS
FC = mpif90 # replace with your Fortran compiler
CXX = mpicc # replace with your C++ compiler
# Flags for Fortran compiler, C++ compiler, and C preprocessor, respectively
FFLAGS = -O2 -fPIC
CXXFLAGS = -O2 -fPIC
CPPFLAGS = -DOMPI_SKIP_MPICXX=1 -DMPICH_SKIP_MPICXX
all : liblammps_fortran.a liblammps_fortran.so simpleF.x
liblammps_fortran.so : LAMMPS.o LAMMPS-wrapper.o LAMMPS-wrapper2.o
$(FC) $(FFLAGS) -shared -o $@ $^
simpleF.x: simple.o LAMMPS.o LAMMPS-wrapper.o LAMMPS-wrapper2.o
$(FC) $(FFLAGS) simple.o -o simpleF.x liblammps_fortran.a $(LAMMPS_SRC)/liblammps_mvapich.a -lstdc++ /usr/lib64/libfftw3.a
liblammps_fortran.a : LAMMPS.o LAMMPS-wrapper.o LAMMPS-wrapper2.o
$(AR) rs $@ $^
LAMMPS.o lammps.mod : LAMMPS.F90
$(FC) $(CPPFLAGS) $(FFLAGS) -c $<
simple.o : simple.f90
$(FC) $(FFLAGS) -c $<
LAMMPS-wrapper.o : LAMMPS-wrapper.cpp LAMMPS-wrapper.h
$(CXX) $(CPPFLAGS) $(CXXFLAGS) -c $< -I$(LAMMPS_SRC) $(MPI_STUBS)
LAMMPS-wrapper2.o : LAMMPS-wrapper2.cpp LAMMPS-wrapper2.h
$(CXX) $(CPPFLAGS) $(CXXFLAGS) -c $< -I$(LAMMPS_SRC) $(MPI_STUBS)
clean :
$(RM) *.o *.mod liblammps_fortran.a liblammps_fortran.so
dist :
tar -czvf fortran-interface-callback.tar.gz LAMMPS-wrapper.h LAMMPS-wrapper.cpp LAMMPS-wrapper2.h LAMMPS-wrapper2.cpp LAMMPS.F90 makefile README simple.f90

110
examples/COUPLE/fortran_dftb/simple.f90
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@ -1,110 +0,0 @@
module callback
implicit none
contains
subroutine fortran_callback(lmp, timestep, nlocal, ids, c_pos, c_fext) &
& bind(C, name='f_callback')
use, intrinsic :: ISO_C_binding
use LAMMPS
implicit none
type (C_ptr), value :: lmp
integer(C_int64_t), intent(in), value :: timestep
integer(C_int), intent(in), value :: nlocal
real (C_double), dimension(:,:), pointer :: x
type(c_ptr) :: c_pos, c_fext, c_ids
double precision, pointer :: fext(:,:), pos(:,:)
integer, intent(in) :: ids(nlocal)
real(C_double) :: virial(6)
real (C_double) :: etot
real(C_double), pointer :: ts_lmp
double precision :: stress(3,3), ts_dftb
integer :: natom , i
real (C_double), parameter :: econv = 627.4947284155114 ! converts from Ha to
double precision, parameter :: fconv = 1185.793095983065 ! converts from Ha/bohr to
double precision, parameter :: autoatm = 2.9037166638E8
double precision lx, ly, lz
real (C_double), pointer :: boxxlo, boxxhi
real (C_double), pointer :: boxylo, boxyhi
real (C_double), pointer :: boxzlo, boxzhi
double precision, parameter :: nktv2p = 68568.4149999999935972
double precision :: volume
type (C_ptr) :: Cptr
type (C_ptr), pointer, dimension(:) :: Catom
call c_f_pointer(c_pos, pos, [3,nlocal])
call c_f_pointer(c_fext, fext, [3,nlocal])
call lammps_extract_global(boxxlo, lmp, 'boxxlo')
call lammps_extract_global(boxxhi, lmp, 'boxxhi')
call lammps_extract_global(boxylo, lmp, 'boxylo')
call lammps_extract_global(boxyhi, lmp, 'boxyhi')
call lammps_extract_global(boxzlo, lmp, 'boxzlo')
call lammps_extract_global(boxzhi, lmp, 'boxzhi')
lx = boxxhi - boxxlo
ly = boxyhi - boxylo
lz = boxzhi - boxzlo
volume = lx*ly*lz
open (unit = 10, status = 'replace', action = 'write', file='lammps.gen')
write(10,*)nlocal,"S"
write(10,*) "C"
do i = 1, nlocal
write(10,'(2I,3F15.6)')i,1,pos(:,ids(i))
enddo
write(10,*)"0.0 0.0 0.0"
write(10,*)lx,0,0
write(10,*)0,ly,0
write(10,*)0,0,lz
close(10)
call system("./dftb+ > dftb.out")
open (unit = 10, status = 'old', file = 'results.out')
read(10,*)etot
read(10,*)ts_dftb
do i = 1, 3
read(10,*)stress(i,:)
enddo
stress (:,:) = stress(:,:)*autoatm
virial(1) = stress(1,1)/(nktv2p/volume)
virial(2) = stress(2,2)/(nktv2p/volume)
virial(3) = stress(3,3)/(nktv2p/volume)
virial(4) = stress(1,2)/(nktv2p/volume)
virial(5) = stress(1,3)/(nktv2p/volume)
virial(6) = stress(2,3)/(nktv2p/volume)
etot = etot*econv
call lammps_set_external_vector(lmp,1,ts_dftb*econv)
do i = 1, nlocal
read(10,*)fext(:,ids(i))
fext(:,ids(i)) = fext(:,ids(i))*fconv
enddo
close(10)
call lammps_set_user_energy (lmp, etot)
call lammps_set_user_virial (lmp, virial)
end subroutine
end module callback
program simple_fortran_callback
use MPI
use LAMMPS
use callback
use, intrinsic :: ISO_C_binding, only : C_double, C_ptr, C_int, C_FUNPTR
implicit none
type (C_ptr) :: lmp
integer :: error, narg, me, nprocs
call MPI_Init (error)
call MPI_Comm_rank (MPI_COMM_WORLD, me, error)
call MPI_Comm_size (MPI_COMM_WORLD, nprocs, error)
call lammps_open_no_mpi ('lmp -log log.simple', lmp)
call lammps_file (lmp, 'in.simple')
call lammps_set_callback(lmp)
call lammps_set_external_vector_length(lmp,2)
call lammps_command (lmp, 'run 10')
call lammps_close (lmp)
call MPI_Finalize (error)
end program simple_fortran_callback

47
examples/COUPLE/lammps_quest/Makefile.g++
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# Makefile for MD with quantum forces via LAMMPS <-> Quest coupling
SHELL = /bin/sh
# System-specific settings
LAMMPS = /home/sjplimp/lammps
CC = g++
CCFLAGS = -g -O -DMPICH_IGNORE_CXX_SEEK -I../library
DEPFLAGS = -M
LINK = g++
LINKFLAGS = -g -O -L../library -L${LAMMPS}/src
USRLIB = -lcouple -llammps_g++
SYSLIB = -lfftw -lmpich -lpthread
ARCHIVE = ar
ARFLAGS = -rc
SIZE = size
# Files
EXE = lmpqst
SRC = $(wildcard *.cpp)
INC = $(wildcard *.h)
OBJ = $(SRC:.cpp=.o)
# Targets
$(EXE): $(OBJ)
$(LINK) $(LINKFLAGS) $(OBJ) $(USRLIB) $(SYSLIB) -o $(EXE)
$(SIZE) $(EXE)
clean:
rm $(EXE) *.o
# Compilation rules
%.o:%.cpp
$(CC) $(CCFLAGS) -c $<
%.d:%.cpp
$(CC) $(CCFLAGS) $(DEPFLAGS) $< > $@
# Individual dependencies
DEPENDS = $(OBJ:.o=.d)
include $(DEPENDS)

70
examples/COUPLE/lammps_quest/README
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IMPORTANT NOTE: This example has not been updated since 2014,
so it is not likely to work anymore out of the box. There have
been changes to LAMMPS and its library interface that would need
to be applied. Please see the manual for the documentation of
the library interface.
This directory has an application that runs classical MD via LAMMPS,
but uses quantum forces calculated by the Quest DFT (density
functional) code in place of the usual classical MD forces calculated
by a pair style in LAMMPS.
lmpqst.cpp main program
it links LAMMPS as a library
it invokes Quest as an executable
in.lammps LAMMPS input script, without the run command
si_111.in Quest input script for an 8-atom Si unit cell
lmppath.h contains path to LAMMPS home directory
qstexe.h contains full pathname to Quest executable
After editing the Makefile, lmppath.h, and qstexe.h to make them
suitable for your box, type:
make -f Makefile.g++
and you should get the lmpqst executable.
NOTE: To run this coupled application, you must of course, have Quest
built on your system. It's WWW site is http://dft.sandia.gov/Quest.
It is not an open-source code, buy you can contact its authors to
obtain a copy.
You can run lmpqst in serial or parallel as:
% lmpqst Niter in.lammps in.quest
% mpirun -np 4 lmpqst Niter in.lammps in.quest
where
Niter = # of MD iterations
in.lammps = LAMMPS input script
in.quest = Quest input script
The log files are for this run:
% lmpqst 10 in.lammps si_111.in
This application is an example of a coupling where the driver code
(lmpqst) runs one code (LAMMPS) as an outer code and facilitates it
calling the other code (Quest) as an inner code. Specifically, the
driver (lmpqst) invokes one code (LAMMPS) to perform its timestep
loop, and grabs information from the other code (Quest) during its
timestep. This is done in LAMMPS using the fix external command,
which makes a "callback" to the driver application (lmpqst), which in
turn invokes Quest with new atom coordinates, lets Quest compute
forces, and returns those forces to the LAMMPS fix external.
The driver code launches LAMMPS in parallel. But Quest is only run on
a single processor. It would be possible to change this by using a
parallel build of Quest.
Since Quest does not currently have a library interface, the driver
code interfaces with Quest via input and output files.
Note that essentially 100% of the run time for this coupled
application is spent in Quest, as the quantum calculation of forces
dominates the calculation.
You can look at the log files in the directory to see sample LAMMPS
output for this simulation. Dump files produced by LAMMPS are stored
as dump.md.

20
examples/COUPLE/lammps_quest/in.lammps
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# LAMMPS input for coupling MD/Quantum
units metal
dimension 3
atom_style atomic
atom_modify sort 0 0.0
lattice diamond 5.43
region box block 0 1 0 1 0 1
create_box 1 box
create_atoms 1 box
mass 1 28.08
velocity all create 300.0 87293 loop geom
fix 1 all nve
fix 2 all external pf/callback 1 1
dump 1 all custom 1 dump.md id type x y z fx fy fz
thermo 1

1
examples/COUPLE/lammps_quest/lmppath.h
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#define LMPPATH /home/sjplimp/lammps

270
examples/COUPLE/lammps_quest/lmpqst.cpp
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// lmpqst = umbrella driver to couple LAMMPS + Quest
// for MD using quantum forces
// Syntax: lmpqst Niter in.lammps in.quest
// Niter = # of MD iterations
// in.lammps = LAMMPS input script
// in.quest = Quest input script
#include <mpi.h>
#include <cstdio>
#include <cstdlib>
#include <cstring>
#include "stdint.h"
#include "many2one.h"
#include "one2many.h"
#include "files.h"
#include "memory.h"
#include "error.h"
#define QUOTE_(x) #x
#define QUOTE(x) QUOTE_(x)
#include "lmppath.h"
#include QUOTE(LMPPATH/src/lammps.h)
#include QUOTE(LMPPATH/src/library.h)
#include QUOTE(LMPPATH/src/input.h)
#include QUOTE(LMPPATH/src/modify.h)
#include QUOTE(LMPPATH/src/fix.h)
#include QUOTE(LMPPATH/src/fix_external.h)
#include "qstexe.h"
using namespace LAMMPS_NS;
#define ANGSTROM_per_BOHR 0.529
#define EV_per_RYDBERG 13.6056923
void quest_callback(void *, bigint, int, int *, double **, double **);
struct Info {
int me;
Memory *memory;
LAMMPS *lmp;
char *quest_input;
};
/* ---------------------------------------------------------------------- */
int main(int narg, char **arg)
{
int n;
char str[128];
// setup MPI
MPI_Init(&narg,&arg);
MPI_Comm comm = MPI_COMM_WORLD;
int me,nprocs;
MPI_Comm_rank(comm,&me);
MPI_Comm_size(comm,&nprocs);
Memory *memory = new Memory(comm);
Error *error = new Error(comm);
// command-line args
if (narg != 4) error->all("Syntax: lmpqst Niter in.lammps in.quest");
int niter = atoi(arg[1]);
n = strlen(arg[2]) + 1;
char *lammps_input = new char[n];
strcpy(lammps_input,arg[2]);
n = strlen(arg[3]) + 1;
char *quest_input = new char[n];
strcpy(quest_input,arg[3]);
// instantiate LAMMPS
LAMMPS *lmp = new LAMMPS(0,NULL,MPI_COMM_WORLD);
// create simulation in LAMMPS from in.lammps
lmp->input->file(lammps_input);
// make info available to callback function
Info info;
info.me = me;
info.memory = memory;
info.lmp = lmp;
info.quest_input = quest_input;
// set callback to Quest inside fix external
// this could also be done thru Python, using a ctypes callback
int ifix = lmp->modify->find_fix("2");
FixExternal *fix = (FixExternal *) lmp->modify->fix[ifix];
fix->set_callback(quest_callback,&info);
// run LAMMPS for Niter
// each time it needs forces, it will invoke quest_callback
sprintf(str,"run %d",niter);
lmp->input->one(str);
// clean up
delete lmp;
delete memory;
delete error;
delete [] lammps_input;
delete [] quest_input;
MPI_Finalize();
}
/* ----------------------------------------------------------------------
callback to Quest with atom IDs and coords from each proc
invoke Quest to compute forces, load them into f for LAMMPS to use
f can be NULL if proc owns no atoms
------------------------------------------------------------------------- */
void quest_callback(void *ptr, bigint ntimestep,
int nlocal, int *id, double **x, double **f)
{
int i,j;
char str[128];
Info *info = (Info *) ptr;
// boxlines = LAMMPS box size converted into Quest lattice vectors
char **boxlines = NULL;
if (info->me == 0) {
boxlines = new char*[3];
for (i = 0; i < 3; i++) boxlines[i] = new char[128];
}
double boxxlo = *((double *) lammps_extract_global(info->lmp,"boxxlo"));
double boxxhi = *((double *) lammps_extract_global(info->lmp,"boxxhi"));
double boxylo = *((double *) lammps_extract_global(info->lmp,"boxylo"));
double boxyhi = *((double *) lammps_extract_global(info->lmp,"boxyhi"));
double boxzlo = *((double *) lammps_extract_global(info->lmp,"boxzlo"));
double boxzhi = *((double *) lammps_extract_global(info->lmp,"boxzhi"));
double boxxy = *((double *) lammps_extract_global(info->lmp,"xy"));
double boxxz = *((double *) lammps_extract_global(info->lmp,"xz"));
double boxyz = *((double *) lammps_extract_global(info->lmp,"yz"));
double xprd = (boxxhi-boxxlo)/ANGSTROM_per_BOHR;
double yprd = (boxyhi-boxylo)/ANGSTROM_per_BOHR;
double zprd = (boxzhi-boxzlo)/ANGSTROM_per_BOHR;
double xy = boxxy/ANGSTROM_per_BOHR;
double xz = boxxz/ANGSTROM_per_BOHR;
double yz = boxyz/ANGSTROM_per_BOHR;
if (info->me == 0) {
sprintf(boxlines[0],"%g %g %g\n",xprd,0.0,0.0);
sprintf(boxlines[1],"%g %g %g\n",xy,yprd,0.0);
sprintf(boxlines[2],"%g %g %g\n",xz,yz,zprd);
}
// xlines = x for atoms on each proc converted to text lines
// xlines is suitable for insertion into Quest input file
// convert LAMMPS Angstroms to Quest bohr
int natoms;
MPI_Allreduce(&nlocal,&natoms,1,MPI_INT,MPI_SUM,MPI_COMM_WORLD);
Many2One *lmp2qst = new Many2One(MPI_COMM_WORLD);
lmp2qst->setup(nlocal,id,natoms);
char **xlines = NULL;
double **xquest = NULL;
if (info->me == 0) {
xquest = info->memory->create_2d_double_array(natoms,3,"lmpqst:xquest");
xlines = new char*[natoms];
for (i = 0; i < natoms; i++) xlines[i] = new char[128];
}
if (info->me == 0) lmp2qst->gather(&x[0][0],3,&xquest[0][0]);
else lmp2qst->gather(&x[0][0],3,NULL);
if (info->me == 0) {
for (i = 0; i < natoms; i++) {
xquest[i][0] /= ANGSTROM_per_BOHR;
xquest[i][1] /= ANGSTROM_per_BOHR;
xquest[i][2] /= ANGSTROM_per_BOHR;
}
for (i = 0; i < natoms; i++) {
sprintf(xlines[i],"%d %d %g %g %g\n",i+1,1,
xquest[i][0],xquest[i][1],xquest[i][2]);
}
}
// one-processor tasks:
// whack all lcao.* files
// cp quest_input to lcao.in
// replace atom coords section of lcao.in with new atom coords
// run Quest on one proc, save screen output to file
// flines = atom forces extracted from Quest screen file
// fquest = atom forces
// convert Quest Ryd/bohr to LAMMPS eV/Angstrom
char **flines = NULL;
double **fquest = NULL;
if (info->me == 0) {
fquest = info->memory->create_2d_double_array(natoms,3,"lmpqst:fquest");
flines = new char*[natoms];
for (i = 0; i < natoms; i++) flines[i] = new char[128];
}
if (info->me == 0) {
system("rm lcao.*");
sprintf(str,"cp %s lcao.in",info->quest_input);
system(str);
sprintf(str,"cp %s lcao.x",QUOTE(QUEST));
system(str);
replace("lcao.in","primitive lattice vectors",3,boxlines);
replace("lcao.in","atom, type, position vector",natoms,xlines);
system("lcao.x > lcao.screen");
extract("lcao.screen","atom x force "
"y force z force",natoms,flines);
int itmp;
for (i = 0; i < natoms; i++)
sscanf(flines[i],"%d %lg %lg %lg",&itmp,
&fquest[i][0],&fquest[i][1],&fquest[i][2]);
for (i = 0; i < natoms; i++) {
fquest[i][0] *= EV_per_RYDBERG / ANGSTROM_per_BOHR;
fquest[i][1] *= EV_per_RYDBERG / ANGSTROM_per_BOHR;
fquest[i][2] *= EV_per_RYDBERG / ANGSTROM_per_BOHR;
}
}
// convert fquest on one proc into f for atoms on each proc
One2Many *qst2lmp = new One2Many(MPI_COMM_WORLD);
qst2lmp->setup(natoms,nlocal,id);
double *fvec = NULL;
if (f) fvec = &f[0][0];
if (info->me == 0) qst2lmp->scatter(&fquest[0][0],3,fvec);
else qst2lmp->scatter(NULL,3,fvec);
// clean up
// some data only exists on proc 0
delete lmp2qst;
delete qst2lmp;
info->memory->destroy_2d_double_array(xquest);
info->memory->destroy_2d_double_array(fquest);
if (boxlines) {
for (i = 0; i < 3; i++) delete [] boxlines[i];
delete [] boxlines;
}
if (xlines) {
for (i = 0; i < natoms; i++) delete [] xlines[i];
delete [] xlines;
}
if (flines) {
for (i = 0; i < natoms; i++) delete [] flines[i];
delete [] flines;
}
}

58
examples/COUPLE/lammps_quest/log.lammps.1
View File

@ -1,58 +0,0 @@
LAMMPS (20 Sep 2010)
# LAMMPS input for coupling MD/Quantum
units metal
dimension 3
atom_style atomic
atom_modify sort 0 0.0
lattice diamond 5.43
Lattice spacing in x,y,z = 5.43 5.43 5.43
region box block 0 1 0 1 0 1
create_box 1 box
Created orthogonal box = (0 0 0) to (5.43 5.43 5.43)
1 by 1 by 1 processor grid
create_atoms 1 box
Created 8 atoms
mass 1 28.08
velocity all create 300.0 87293 loop geom
fix 1 all nve
fix 2 all external
dump 1 all custom 1 dump.md id type x y z fx fy fz
thermo 1
run 10
Memory usage per processor = 1.25982 Mbytes
Step Temp E_pair E_mol TotEng Press
0 300 0 0 0.2714463 1810.9378
1 298.22165 0 0 0.26983722 1800.2029
2 293.2839 0 0 0.26536943 1770.3964
3 286.18537 0 0 0.25894654 1727.5464
4 277.61576 0 0 0.25119258 1675.8163
5 267.3325 0 0 0.24188807 1613.7418
6 254.94702 0 0 0.23068142 1538.9774
7 240.91176 0 0 0.21798202 1454.2541
8 226.27996 0 0 0.20474287 1365.9298
9 212.1059 0 0 0.19191788 1280.3687
10 199.27609 0 0 0.18030919 1202.922
Loop time of 80.663 on 1 procs for 10 steps with 8 atoms
Pair time (%) = 0 (0)
Neigh time (%) = 0 (0)
Comm time (%) = 4.91142e-05 (6.08882e-05)
Outpt time (%) = 0.00111485 (0.0013821)
Other time (%) = 80.6618 (99.9986)
Nlocal: 8 ave 8 max 8 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 10 ave 10 max 10 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0

58
examples/COUPLE/lammps_quest/log.lammps.4
View File

@ -1,58 +0,0 @@
LAMMPS (20 Sep 2010)
# LAMMPS input for coupling MD/Quantum
units metal
dimension 3
atom_style atomic
atom_modify sort 0 0.0
lattice diamond 5.43
Lattice spacing in x,y,z = 5.43 5.43 5.43
region box block 0 1 0 1 0 1
create_box 1 box
Created orthogonal box = (0 0 0) to (5.43 5.43 5.43)
1 by 2 by 2 processor grid
create_atoms 1 box
Created 8 atoms
mass 1 28.08
velocity all create 300.0 87293 loop geom
fix 1 all nve
fix 2 all external
dump 1 all custom 1 dump.md id type x y z fx fy fz
thermo 1
run 10
Memory usage per processor = 1.25928 Mbytes
Step Temp E_pair E_mol TotEng Press
0 300 0 0 0.2714463 1810.9378
1 298.22166 0 0 0.26983722 1800.2029
2 293.28391 0 0 0.26536944 1770.3964
3 286.18538 0 0 0.25894655 1727.5464
4 277.61578 0 0 0.25119259 1675.8164
5 267.33252 0 0 0.24188809 1613.7419
6 254.94703 0 0 0.23068143 1538.9774
7 240.91175 0 0 0.21798202 1454.254
8 226.27997 0 0 0.20474287 1365.9299
9 212.10594 0 0 0.19191791 1280.3689
10 199.27613 0 0 0.18030923 1202.9223
Loop time of 79.8256 on 4 procs for 10 steps with 8 atoms
Pair time (%) = 0 (0)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000365376 (0.000457718)
Outpt time (%) = 0.00169969 (0.00212925)
Other time (%) = 79.8236 (99.9974)
Nlocal: 2 ave 2 max 2 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 5 ave 5 max 5 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0

1
examples/COUPLE/lammps_quest/qstexe.h
View File

@ -1 +0,0 @@
#define QUEST /home/sjplimp/csrf/quest/src/lcao.x

161
examples/COUPLE/lammps_quest/si_111.in
View File

@ -1,161 +0,0 @@
do setup
do iters
do force
no relax
setup data
title
Si 1x1x1 unit cell
functional
PBE
dimensions of system (0=cluster ... 3=bulk)
3
primitive lattice vectors
10.261212 0.000000 0.000000
0.000000 10.261212 0.000000
0.000000 0.000000 10.261212
grid dimensions
10 10 10
atom types
1
type number, label:
1 Si_pbe
notes5
Originally constructed by Peter A. Schultz, 12Apr01
potential generated by new Hamann program PUNSLDX
Cite use with: D.R. Hamann, unpublished.
Potential: "standard" setting out to l=2
Basis: amended Jun05 for better (2d/1d not 1d/1d) d-function
effective nuclear charge (s2p2 to 10.0)
4.00000000d+00
pseudopotentials: Lmax, and effective gaussian range
2 0.86000000d+00
functional type used in generating potential:
PBE
radial mesh: number of points for local and non-local pot integrals
80 67
mesh points for nuclear potential; ham2dh
0.02500000 0.02696978 0.02909477 0.03138719 0.03386023 0.03652812
0.03940622 0.04251109 0.04586060 0.04947402 0.05337215 0.05757741
0.06211402 0.06700807 0.07228773 0.07798338 0.08412779 0.09075634
0.09790716 0.10562140 0.11394345 0.12292121 0.13260635 0.14305458
0.15432605 0.16648562 0.17960325 0.19375443 0.20902061 0.22548964
0.24325628 0.26242278 0.28309943 0.30540522 0.32946852 0.35542780
0.38343245 0.41364362 0.44623518 0.48139466 0.51932441 0.56024270
0.60438500 0.65200533 0.70337773 0.75879783 0.81858456 0.88308197
0.95266121 1.02772271 1.10869840 1.19605428 1.29029305 1.39195702
1.50163124 1.61994684 1.74758469 1.88527930 2.03382306 2.19407079
2.36694466 2.55343950 2.75462852 2.97166951 3.20581145 3.45840177
3.73089402 4.02485632 4.34198031 4.68409093 5.05315693 5.45130215
5.88081777 6.34417553 6.84404189 7.38329340 7.96503329 8.59260927
9.26963282 10.00000000
radwts: weights for radial points
0.00189603 0.00204542 0.00220659 0.00238045 0.00256800 0.00277034
0.00298862 0.00322410 0.00347813 0.00375218 0.00404781 0.00436675
0.00471081 0.00508198 0.00548240 0.00591436 0.00638036 0.00688308
0.00742541 0.00801047 0.00864162 0.00932251 0.01005704 0.01084945
0.01170429 0.01262649 0.01362135 0.01469459 0.01585240 0.01710143
0.01844888 0.01990249 0.02147064 0.02316234 0.02498733 0.02695611
0.02908002 0.03137128 0.03384307 0.03650961 0.03938625 0.04248955
0.04583736 0.04944895 0.05334510 0.05754823 0.06208254 0.06697411
0.07225109 0.07794385 0.08408515 0.09071034 0.09785753 0.10556786
0.11388570 0.12285891 0.13253914 0.14298208 0.15424783 0.16640123
0.17951222 0.19365623 0.20891467 0.22537535 0.24313298 0.26228977
0.28295594 0.30525043 0.32930153 0.35524766 0.38323811 0.41343397
0.44600900 0.48115067 0.51906119 0.55995874 0.60407867 0.65167486
0.70302122 0.75841323
non-local potential: l,potential*integration weight
0 0.62022930 0.62128855 0.62243016 0.62366033 0.62498568 0.62641328
0.62795061 0.62960563 0.63138673 0.63330275 0.63536294 0.63757692
0.63995464 0.64250630 0.64524218 0.64817253 0.65130735 0.65465605
0.65822713 0.66202767 0.66606269 0.67033437 0.67484108 0.67957602
0.68452576 0.68966817 0.69497006 0.70038419 0.70584566 0.71126756
0.71653578 0.72150290 0.72598113 0.72973436 0.73246932 0.73382636
0.73337030 0.73058243 0.72485505 0.71549107 0.70171167 0.68267654
0.65752236 0.62542611 0.58570073 0.53792896 0.48213811 0.41900888
0.35009536 0.27800640 0.20646172 0.14009458 0.08384960 0.04186877
0.01596164 0.00423035 0.00115036 0.00066636 0.00047879 0.00029939
0.00016329 0.00007995 0.00003517 0.00001362 0.00000445 0.00000111
0.00000016 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
0.00000000 0.00000000
non-local potential: l,potential*integration weight
1 0.59551624 0.59463303 0.59368033 0.59265268 0.59154422 0.59034862
0.58905906 0.58766819 0.58616811 0.58455033 0.58280567 0.58092430
0.57889565 0.57670833 0.57435015 0.57180802 0.56906791 0.56611482
0.56293268 0.55950435 0.55581158 0.55183493 0.54755377 0.54294628
0.53798942 0.53265896 0.52692951 0.52077458 0.51416671 0.50707751
0.49947790 0.49133817 0.48262822 0.47331766 0.46337588 0.45277197
0.44147437 0.42945016 0.41666374 0.40307468 0.38863443 0.37328165
0.35693601 0.33949042 0.32080256 0.30068740 0.27891443 0.25521609
0.22931791 0.20100526 0.17024474 0.13737521 0.10336405 0.07007167
0.04035673 0.01767907 0.00470635 0.00076638 0.00047880 0.00029939
0.00016329 0.00007995 0.00003517 0.00001362 0.00000445 0.00000111
0.00000016 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
0.00000000 0.00000000
non-local potential: l,potential*integration weight
2 0.56305372 0.55961728 0.55591134 0.55191498 0.54760572 0.54295941
0.53795013 0.53255008 0.52672947 0.52045641 0.51369682 0.50641433
0.49857022 0.49012333 0.48103004 0.47124429 0.46071759 0.44939919
0.43723624 0.42417413 0.41015690 0.39512792 0.37903070 0.36181001
0.34341340 0.32379300 0.30290805 0.28072780 0.25723539 0.23243242
0.20634465 0.17902876 0.15058041 0.12114359 0.09092117 0.06018665
0.02929636 -0.00129833 -0.03104046 -0.05926034 -0.08517498 -0.10789810
-0.12646610 -0.13988656 -0.14721657 -0.14767751 -0.14080976 -0.12666296
-0.10600305 -0.08049270 -0.05276798 -0.02629475 -0.00486427 0.00837657
0.01228139 0.00892332 0.00342796 0.00074936 0.00047880 0.00029939
0.00016329 0.00007995 0.00003517 0.00001362 0.00000445 0.00000111
0.00000016 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
0.00000000 0.00000000
number of radial functions **** Si PBE Ham-II basis 20Feb01-PAS ****
5
angular momentum, number of alphas
0 4
alphas - s - 4s/2/4s407 (bulk Si dzp Eopt+reopt c1)
0.10460000d+00 0.27226300d+00 1.30050800d+00 2.60103000d+00
wave function coefficients
0.20995300d+00 0.55978200d+00 -0.99128200d+00 0.33487100d+00
angular momentum, number of alphas
1 3
alphas - p - 3p/2/3p492 (bulk Si dzp Eopt + reopt c1)
0.09424100d+00 0.31767900d+00 1.56114500d+00
wave function coefficients
0.06761600d+00 0.31821200d+00 -0.06638300d+00
angular momentum, number of alphas
0 1
alphas - s - second zeta s polarization
0.10460000d+00
wave function coefficients
1.00000000d+00
angular momentum, number of alphas
1 1
alphas - p - second zeta p polarization
0.09424100d+00
wave function coefficients
1.00000000d+00
angular momentum, number of alphas
2 2
alphas - d - angular polarization (dzp Eopt)
0.32000000d+00 1.40000000d+00
wave function coefficients
0.31557000d+00 1.00000000d+00
shell occupancies for this silicon, Si: s(2.00)p(2.00)
2.00000000 2.00000000 0.00000000 0.00000000 0.00000000 0.00000000
end atom file
number of atoms in unit cell
8
atom, type, position vector
1 1 0.0000000000 0.0000000000 0.0000000000
2 1 5.1306060590 5.1306060590 0.0000000000
3 1 5.1306060590 0.0000000000 5.1306060590
4 1 0.0000000000 5.1306060590 5.1306060590
5 1 2.5653030295 2.5653030295 2.5653030295
6 1 7.6959090885 7.6959090885 2.5653030295
7 1 7.6959090885 2.5653030295 7.6959090885
8 1 2.5653030295 7.6959090885 7.6959090885
kgrid
0 0 0
end setup phase data
run phase input data
end of run phase data

16
examples/COUPLE/lammps_spparks/Makefile.g++ → examples/COUPLE/lammps_spparks/Makefile.mpi
View File

@ -2,18 +2,20 @@
SHELL = /bin/sh
# Paths to your local LAMMPS and SPPARKS home directories
LAMMPS = /home/sjplimp/lammps/git
SPPARKS = /home/sjplimp/spparks/git
# System-specific settings
LAMMPS = /home/sjplimp/lammps
SPPARKS = /home/sjplimp/spparks
CC = g++
CC = mpicxx
CCFLAGS = -g -O -DMPICH_IGNORE_CXX_SEEK -I../library
DEPFLAGS = -M
LINK = g++
LINK = mpicxx
LINKFLAGS = -g -O -L../library -L${LAMMPS}/src -L${SPPARKS}/src
USRLIB = -lcouple -llmp_g++ -lspk_g++
SYSLIB = -lfftw -lmpich -lpthread
USRLIB = -lcouple -llammps_mpi -lspparks_mpi
SYSLIB =
ARCHIVE = ar
ARFLAGS = -rc
SIZE = size

97
examples/COUPLE/lammps_spparks/README
View File

@ -1,44 +1,67 @@
IMPORTANT NOTE: This example has not been updated since 2013,
so it is not likely to work anymore out of the box. There have
been changes to LAMMPS and its library interface that would need
to be applied. Please see the manual for the documentation of
the library interface.
This directory has an application that models grain growth in the
presence of strain.
The grain growth is simulated by a Potts model in a kinetic Monte
Carlo code SPPARKS. Clusters of like spins on a lattice represent
grains. The Hamiltonian for the energy due of a collection of spins
includes a strain term and is described on this page in the SPPARKS
documentation:
The grain growth is simulated by a Potts model in the kinetic Monte
Carlo code SPPARKS -- https://spparks.github.io
http://spparks.sandia.gov/doc/app_potts_strain.html.
Clusters of like spins on a lattice represent grains. The Hamiltonian
for the energy due of a collection of spins includes a strain term and
is described on this page in the SPPARKS documentation:
The strain is computed by the molecular dynamics code LAMMPS as a
particle displacement where pairs of atoms across a grain boundary are
of different types and thus push off from each other due to a
Lennard-Jones sigma between particles of different types that is
larger than the sigma between particles of the same type (interior to
grains).
https://spparks.github.io/doc/app_potts_strain.html
The strain is computed by the LAMMPS molecular dynamics code --
https://www.lammps.org -- as a particle displacement where pairs of
atoms across a grain boundary are of different types and thus push off
from each other due to a Lennard-Jones sigma between particles of
different types that is larger than the sigma between particles of the
same type (interior to grains).
lmpspk.cpp main program
it links LAMMPS and SPPARKS as libraries
it links to LAMMPS and SPPARKS as libraries
in.spparks SPPARKS input script, without the run command
lmppath.h contains path to LAMMPS home directory
spkpath.h contains path to SPPARKS home directory
After editing the Makefile, lmppath.h, and spkpath.h to make them
suitable for your box, type:
-----------------------------------
g++ -f Makefile.g++
(1) To build and run this coupled application, you must have SPPARKS
built on your system. It's WWW site is https://spparks.github.io and
it can be downloaded as a tarball or cloned as a local Git repo.
and you should get the lmpspk executable.
To build SPPARKS, do the following:
NOTE: To build and run this coupled application, you must of course,
have SPPARKS built on your system. It's WWW site is
http://www.sandia.gov/~sjplimp/spparks.html. It is an open-source
code, written by two of the LAMMPS authors.
% cd spparks/src
% make mpi
% make mode=lib mpi # build SPPARKS as a library
-----------------------------------
(2) You must also build the coupling library in
lammps/examples/COUPLE/library.
To build the coupling library, do the following:
% cd lammps/examples/COUPLE/library
% make -f Makefile.mpi
-----------------------------------
(3) Edit the Makefile.mpi, lmppath.h, and spkpath.h files in this
directory to make them suitable for your box. Each of the 3 files
has a comment telling you what to do.
-----------------------------------
(4) Build the coupled lmpspk application in this directory.
% make -f Makefile.mpi
This should give you a lmpspk executable.
-----------------------------------
(5) Run the test simulation
You can run lmpspk in serial or parallel as:
@ -52,7 +75,7 @@ Ndelta = time to run MC in each iteration
Sfactor = multiplier on strain effect
in.spparks = SPPARKS input script
The log files are for this run:
The log files included in this directory are for this run:
% lmpspk 20 10.0 1 in.spparks
@ -70,11 +93,15 @@ The driver code launches both SPPARKS and LAMMPS in parallel and they
both decompose their spatial domains in the same manner. The datums
in SPPARKS (lattice sites) are the same as the datums in LAMMPS
(coarse-grained particles). If this were not the case, more
sophisticated inter-code communication could be performed.
sophisticated inter-code communication could be performed. Note that
the in.lammps and data.lammps files are not inputs; they are generated
by the lmpspk driver.
You can look at the log files in the directory to see sample LAMMPS
and SPPARKS output for this simulation. Dump files produced by the
run are stored as dump.mc and dump.md. The image*.png files show
snapshots from both the LAMMPS and SPPARKS output. Note that the
in.lammps and data.lammps files are not inputs; they are generated by
the lmpspk driver.
You can look at the log files in the directory to see LAMMPS and
SPPARKS output for this simulation run on 1 and 4 processors. Dump
files produced by the run are named dump.mc and dump.md. The image
PPM files show snapshots from the SPPARKS and LAMMPS output. Compare
the image_spparks.0019.ppm and image_lammps.0190.ppm file. They were
written at the same point in the simulation by both codes. The color
maps for the 2 codes are not the same, but the morphology of the
grains is.

2
examples/COUPLE/lammps_spparks/in.lammps
View File

@ -111,4 +111,6 @@ pair_coeff 100 100 1.0 1.0
compute da all displace/atom
dump 1 all atom 10 dump.md
dump 2 all image 10 image_lammps.*.ppm type type zoom 1.6
dump_modify 2 pad 4 acolor * red/green/blue/aqua/magenta/yellow
thermo 1

6
examples/COUPLE/lammps_spparks/in.spparks
View File

@ -20,4 +20,8 @@ diag_style energy
temperature 1.0
stats 10.0
dump 1 10.0 dump.mc
dump 1 text 10.0 dump.mc id site x y
dump 2 image 1000 image_spparks.*.ppm site site view 0 0 box no 0.1 &
crange 1 100 drange 1 1 shape cube zoom 1.5 size 512 512
dump_modify 2 pad 4

4
examples/COUPLE/lammps_spparks/lmppath.h
View File

@ -1 +1,3 @@
#define LMPPATH /home/sjplimp/lammps
// path to your LAMMPS home directory
#define LMPPATH /home/sjplimp/lammps/git

54
examples/COUPLE/lammps_spparks/lmpspk.cpp
View File

@ -14,8 +14,8 @@
#include "lammps_data_write.h"
#include "many2many.h"
#include "memory.h"
#include "error.h"
#include "memorylib.h"
#include "errorlib.h"
#define QUOTE_(x) #x
#define QUOTE(x) QUOTE_(x)
@ -51,8 +51,8 @@ int main(int narg, char **arg)
MPI_Comm_rank(comm,&me);
MPI_Comm_size(comm,&nprocs);
Memory *memory = new Memory(comm);
Error *error = new Error(comm);
MemoryLib *memory = new MemoryLib(comm);
ErrorLib *error = new ErrorLib(comm);
// command-line args
@ -83,28 +83,28 @@ int main(int narg, char **arg)
double **xyz;
double *strain;
dimension = *((int *) spparks_extract(spk,"dimension"));
nglobal = *((int *) spparks_extract(spk,"nglobal"));
nlocal_spparks = *((int *) spparks_extract(spk,"nlocal"));
dimension = *((int *) spparks_extract(spk,(char *) "dimension"));
nglobal = *((int *) spparks_extract(spk,(char *) "nglobal"));
nlocal_spparks = *((int *) spparks_extract(spk,(char *) "nlocal"));
boxxlo = *((double *) spparks_extract(spk,"boxxlo"));
boxxhi = *((double *) spparks_extract(spk,"boxxhi"));
boxylo = *((double *) spparks_extract(spk,"boxylo"));
boxyhi = *((double *) spparks_extract(spk,"boxyhi"));
boxxlo = *((double *) spparks_extract(spk,(char *) "boxxlo"));
boxxhi = *((double *) spparks_extract(spk,(char *) "boxxhi"));
boxylo = *((double *) spparks_extract(spk,(char *) "boxylo"));
boxyhi = *((double *) spparks_extract(spk,(char *) "boxyhi"));
if (dimension == 3) {
boxzlo = *((double *) spparks_extract(spk,"boxzlo"));
boxzhi = *((double *) spparks_extract(spk,"boxzhi"));
boxzlo = *((double *) spparks_extract(spk,(char *) "boxzlo"));
boxzhi = *((double *) spparks_extract(spk,(char *) "boxzhi"));
} else {
boxzlo = -0.5;
boxzhi = 0.5;
}
id_spparks = (int *) spparks_extract(spk,"id");
spins = (int *) spparks_extract(spk,"site");
xyz = (double **) spparks_extract(spk,"xyz");
id_spparks = (int *) spparks_extract(spk,(char *) "id");
spins = (int *) spparks_extract(spk,(char *) "site");
xyz = (double **) spparks_extract(spk,(char *) "xyz");
nspins = *((int *) spparks_extract(spk,"nspins"));
strain = (double *) spparks_extract(spk,"strain");
nspins = *((int *) spparks_extract(spk,(char *) "nspins"));
strain = (double *) spparks_extract(spk,(char *) "strain");
// write a LAMMPS input script using SPPARKS params
@ -114,7 +114,7 @@ int main(int narg, char **arg)
fprintf(fp,"units lj\n");
sprintf(str,"dimension %d\n",dimension);
fprintf(fp,str);
fprintf(fp,"%s",str);
fprintf(fp,"atom_style atomic\n\n");
fprintf(fp,"read_data data.lammps\n");
@ -124,12 +124,14 @@ int main(int narg, char **arg)
fprintf(fp,"pair_coeff * * 1.0 1.2\n");
for (i = 0; i < nspins; i++) {
sprintf(str,"pair_coeff %d %d 1.0 1.0\n",i+1,i+1);
fprintf(fp,str);
fprintf(fp,"%s",str);
}
fprintf(fp,"\n");
fprintf(fp,"compute da all displace/atom\n\n");
fprintf(fp,"dump 1 all atom 10 dump.md\n");
fprintf(fp,"dump 2 all image 10 image_lammps.*.ppm type type zoom 1.6\n");
fprintf(fp,"dump_modify 2 pad 4 acolor * red/green/blue/aqua/magenta/yellow\n");
fprintf(fp,"thermo 1\n");
fclose(fp);
@ -138,12 +140,12 @@ int main(int narg, char **arg)
// write a LAMMPS data file using SPPARKS data
LAMMPSDataWrite *lwd = new LAMMPSDataWrite(MPI_COMM_WORLD);
lwd->file("data.lammps");
lwd->header("%d atoms",nglobal);
lwd->header("%d atom types",nspins);
lwd->header("%g %g xlo xhi",boxxlo,boxxhi);
lwd->header("%g %g ylo yhi",boxylo,boxyhi);
lwd->header("%g %g zlo zhi",boxzlo,boxzhi);
lwd->file((char *) "data.lammps");
lwd->header((char *) "%d atoms",nglobal);
lwd->header((char *) "%d atom types",nspins);
lwd->header((char *) "%g %g xlo xhi",boxxlo,boxxhi);
lwd->header((char *) "%g %g ylo yhi",boxylo,boxyhi);
lwd->header((char *) "%g %g zlo zhi",boxzlo,boxzhi);
lwd->atoms(nlocal_spparks);
lwd->atoms(id_spparks);
lwd->atoms(spins);

1618
examples/COUPLE/lammps_spparks/log.lammps.1
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File diff suppressed because it is too large Load Diff

1815
examples/COUPLE/lammps_spparks/log.lammps.4
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File diff suppressed because it is too large Load Diff

324
examples/COUPLE/lammps_spparks/log.spparks.1
View File

@ -1,4 +1,4 @@
SPPARKS (26 Aug 2010)
SPPARKS (19 Sept 2022)
# SPPARKS input for coupling MD/MC
seed 56789
@ -28,244 +28,246 @@ diag_style energy
temperature 1.0
stats 10.0
dump 1 10.0 dump.mc
dump 1 text 10.0 dump.mc id site x y
run 10Setting up run ...
Running with 32-bit site IDs
Memory usage per processor = 2.375 Mbytes
Time Naccept Nreject Nsweeps CPU Energy
0 0 0 0 0 19766
10 17929 0 0 0.0776 5324
Loop time of 0.077626 on 1 procs
10 18978 0 13 0.0259 5500
Loop time of 0.0258905 on 1 procs
Solve time (%) = 0.0070138 (9.03537)
Solve time (%) = 0.00155363 (6.00079)
Update time (%) = 0 (0)
Comm time (%) = 0.00146031 (1.88122)
Outpt time (%) = 0.00415015 (5.34634)
App time (%) = 0.0614648 (79.1807)
Other time (%) = 0.00353694 (4.55639)
Comm time (%) = 0.000642316 (2.4809)
Outpt time (%) = 0.000680321 (2.62769)
App time (%) = 0.0226682 (87.5542)
Other time (%) = 0.000346003 (1.33641)
run 10Setting up run ...
Time Naccept Nreject Nsweeps CPU Energy
10 17929 0 0 0 5324
20 24582 0 0 0.0279 4750
Loop time of 0.027904 on 1 procs
10 18978 0 13 0 5500
20 25374 0 18 0.00709 4552
Loop time of 0.00708869 on 1 procs
Solve time (%) = 0.00271416 (9.72676)
Solve time (%) = 0.000496193 (6.99978)
Update time (%) = 0 (0)
Comm time (%) = 0.000461817 (1.65502)
Outpt time (%) = 0.0042181 (15.1165)
App time (%) = 0.0191288 (68.5521)
Other time (%) = 0.00138116 (4.94967)
Comm time (%) = 0.000158039 (2.22945)
Outpt time (%) = 0.0006739 (9.50669)
App time (%) = 0.00564639 (79.6535)
Other time (%) = 0.000114167 (1.61055)
run 10Setting up run ...
Time Naccept Nreject Nsweeps CPU Energy
20 24582 0 0 0 4750
30 30109 0 0 0.0234 4264
Loop time of 0.023375 on 1 procs
20 25374 0 18 0 4552
30 30752 0 23 0.00575 4096
Loop time of 0.00575649 on 1 procs
Solve time (%) = 0.00216675 (9.2695)
Solve time (%) = 0.000415252 (7.21363)
Update time (%) = 0 (0)
Comm time (%) = 0.000342846 (1.46672)
Outpt time (%) = 0.00416183 (17.8046)
App time (%) = 0.015563 (66.5796)
Other time (%) = 0.00114059 (4.87954)
Comm time (%) = 0.00013092 (2.2743)
Outpt time (%) = 0.000662723 (11.5126)
App time (%) = 0.00445117 (77.3244)
Other time (%) = 9.6422e-05 (1.67501)
run 10Setting up run ...
Time Naccept Nreject Nsweeps CPU Energy
30 30109 0 0 0 4264
40 35032 0 0 0.0208 3880
Loop time of 0.020786 on 1 procs
30 30752 0 23 0 4096
40 35529 0 27 0.00589 3596
Loop time of 0.00589801 on 1 procs
Solve time (%) = 0.0019896 (9.57182)
Solve time (%) = 0.000424563 (7.19841)
Update time (%) = 0 (0)
Comm time (%) = 0.000316858 (1.52438)
Outpt time (%) = 0.00413609 (19.8984)
App time (%) = 0.0132952 (63.962)
Other time (%) = 0.00104833 (5.04341)
Comm time (%) = 0.000114131 (1.93508)
Outpt time (%) = 0.000763593 (12.9466)
App time (%) = 0.0044969 (76.2443)
Other time (%) = 9.8828e-05 (1.67562)
run 10Setting up run ...
Time Naccept Nreject Nsweeps CPU Energy
40 35032 0 0 0 3880
50 39543 0 0 0.0193 3784
Loop time of 0.0193491 on 1 procs
40 35529 0 27 0 3596
50 39736 0 31 0.00444 3298
Loop time of 0.00444854 on 1 procs
Solve time (%) = 0.00185919 (9.60865)
Solve time (%) = 0.000323247 (7.26637)
Update time (%) = 0 (0)
Comm time (%) = 0.000333071 (1.72138)
Outpt time (%) = 0.00412297 (21.3083)
App time (%) = 0.0120728 (62.3946)
Other time (%) = 0.000961065 (4.96698)
Comm time (%) = 9.6777e-05 (2.17548)
Outpt time (%) = 0.000637529 (14.3312)
App time (%) = 0.00331502 (74.5193)
Other time (%) = 7.5967e-05 (1.70769)
run 10Setting up run ...
Time Naccept Nreject Nsweeps CPU Energy
50 39543 0 0 0 3784
60 43899 0 0 0.0187 3706
Loop time of 0.018713 on 1 procs
50 39736 0 31 0 3298
60 43567 0 35 0.00507 3296
Loop time of 0.0050729 on 1 procs
Solve time (%) = 0.00176001 (9.40526)
Solve time (%) = 0.000354098 (6.98019)
Update time (%) = 0 (0)
Comm time (%) = 0.000314474 (1.68051)
Outpt time (%) = 0.00413895 (22.118)
App time (%) = 0.0116153 (62.0706)
Other time (%) = 0.000884295 (4.72556)
Comm time (%) = 0.000114818 (2.26336)
Outpt time (%) = 0.000893366 (17.6106)
App time (%) = 0.00362051 (71.3697)
Other time (%) = 9.0105e-05 (1.7762)
run 10Setting up run ...
Time Naccept Nreject Nsweeps CPU Energy
60 43899 0 0 0 3706
70 48028 0 0 0.0179 3392
Loop time of 0.0178769 on 1 procs
60 43567 0 35 0 3296
70 47305 0 39 0.00417 3174
Loop time of 0.00417405 on 1 procs
Solve time (%) = 0.00174618 (9.76781)
Solve time (%) = 0.00030627 (7.33747)
Update time (%) = 0 (0)
Comm time (%) = 0.000296593 (1.65909)
Outpt time (%) = 0.00414801 (23.2032)
App time (%) = 0.0108221 (60.5367)
Other time (%) = 0.000864029 (4.83322)
Comm time (%) = 9.1156e-05 (2.18387)
Outpt time (%) = 0.000689193 (16.5114)
App time (%) = 0.00301511 (72.2347)
Other time (%) = 7.232e-05 (1.73261)
run 10Setting up run ...
Time Naccept Nreject Nsweeps CPU Energy
70 48028 0 0 0 3392
80 51900 0 0 0.017 3208
Loop time of 0.0169971 on 1 procs
70 47305 0 39 0 3174
80 51214 0 43 0.00437 3252
Loop time of 0.00437516 on 1 procs
Solve time (%) = 0.00157022 (9.23819)
Solve time (%) = 0.000332427 (7.59805)
Update time (%) = 0 (0)
Comm time (%) = 0.000290394 (1.70849)
Outpt time (%) = 0.00416803 (24.522)
App time (%) = 0.0101995 (60.0076)
Other time (%) = 0.0007689 (4.52371)
Comm time (%) = 9.1593e-05 (2.09348)
Outpt time (%) = 0.00064481 (14.738)
App time (%) = 0.00323051 (73.8375)
Other time (%) = 7.5822e-05 (1.73301)
run 10Setting up run ...
Time Naccept Nreject Nsweeps CPU Energy
80 51900 0 0 0 3208
90 55450 0 0 0.0159 3162
Loop time of 0.0158761 on 1 procs
80 51214 0 43 0 3252
90 54863 0 47 0.00417 3016
Loop time of 0.00417621 on 1 procs
Solve time (%) = 0.0014894 (9.38143)
Solve time (%) = 0.000285188 (6.82887)
Update time (%) = 0 (0)
Comm time (%) = 0.000301123 (1.89671)
Outpt time (%) = 0.00413799 (26.0644)
App time (%) = 0.00924802 (58.2514)
Other time (%) = 0.00069952 (4.40613)
Comm time (%) = 9.0115e-05 (2.15782)
Outpt time (%) = 0.000719767 (17.2349)
App time (%) = 0.00301373 (72.1642)
Other time (%) = 6.7413e-05 (1.61421)
run 10Setting up run ...
Time Naccept Nreject Nsweeps CPU Energy
90 55450 0 0 0 3162
100 59009 0 0 0.0158 3038
Loop time of 0.0158172 on 1 procs
90 54863 0 47 0 3016
100 58060 0 51 0.00369 2766
Loop time of 0.00369187 on 1 procs
Solve time (%) = 0.00142503 (9.00938)
Solve time (%) = 0.000253511 (6.86674)
Update time (%) = 0 (0)
Comm time (%) = 0.000296831 (1.87664)
Outpt time (%) = 0.00412178 (26.0589)
App time (%) = 0.00923729 (58.4004)
Other time (%) = 0.000736237 (4.65467)
Comm time (%) = 8.878e-05 (2.40475)
Outpt time (%) = 0.000686238 (18.5878)
App time (%) = 0.00260318 (70.5111)
Other time (%) = 6.0163e-05 (1.62961)
run 10Setting up run ...
Time Naccept Nreject Nsweeps CPU Energy
100 59009 0 0 0 3038
110 62454 0 0 0.0155 3066
Loop time of 0.015537 on 1 procs
100 58060 0 51 0 2766
110 61110 0 55 0.00349 2840
Loop time of 0.00349695 on 1 procs
Solve time (%) = 0.00135612 (8.72834)
Solve time (%) = 0.000239587 (6.85131)
Update time (%) = 0 (0)
Comm time (%) = 0.000293732 (1.89053)
Outpt time (%) = 0.00415182 (26.7221)
App time (%) = 0.00904965 (58.2457)
Other time (%) = 0.000685692 (4.41328)
Comm time (%) = 8.1517e-05 (2.33109)
Outpt time (%) = 0.000719507 (20.5753)
App time (%) = 0.0023994 (68.614)
Other time (%) = 5.6943e-05 (1.62836)
run 10Setting up run ...
Time Naccept Nreject Nsweeps CPU Energy
110 62454 0 0 0 3066
120 65856 0 0 0.0152 2898
Loop time of 0.0152211 on 1 procs
110 61110 0 55 0 2840
120 64087 0 59 0.00325 2714
Loop time of 0.00324861 on 1 procs
Solve time (%) = 0.00139046 (9.13505)
Solve time (%) = 0.000225271 (6.93437)
Update time (%) = 0 (0)
Comm time (%) = 0.000291109 (1.91253)
Outpt time (%) = 0.0041492 (27.2595)
App time (%) = 0.00871038 (57.2257)
Other time (%) = 0.00067997 (4.46728)
Comm time (%) = 8.3445e-05 (2.56863)
Outpt time (%) = 0.000647543 (19.9329)
App time (%) = 0.00223748 (68.8748)
Other time (%) = 5.4877e-05 (1.68924)
run 10Setting up run ...
Time Naccept Nreject Nsweeps CPU Energy
120 65856 0 0 0 2898
130 68856 0 0 0.0137 2798
Loop time of 0.0137191 on 1 procs
120 64087 0 59 0 2714
130 67004 0 63 0.00333 2664
Loop time of 0.00333198 on 1 procs
Solve time (%) = 0.00130701 (9.52695)
Solve time (%) = 0.00022963 (6.89169)
Update time (%) = 0 (0)
Comm time (%) = 0.000296831 (2.16364)
Outpt time (%) = 0.00412989 (30.1032)
App time (%) = 0.00742817 (54.1448)
Other time (%) = 0.000557184 (4.06138)
Comm time (%) = 9.0368e-05 (2.71214)
Outpt time (%) = 0.000650383 (19.5194)
App time (%) = 0.00230627 (69.2163)
Other time (%) = 5.5328e-05 (1.66051)
run 10Setting up run ...
Time Naccept Nreject Nsweeps CPU Energy
130 68856 0 0 0 2798
140 71967 0 0 0.0141 2700
Loop time of 0.0141542 on 1 procs
130 67004 0 63 0 2664
140 69933 0 67 0.00324 2680
Loop time of 0.00324401 on 1 procs
Solve time (%) = 0.00132799 (9.38232)
Solve time (%) = 0.000227399 (7.00982)
Update time (%) = 0 (0)
Comm time (%) = 0.000284195 (2.00785)
Outpt time (%) = 0.00414681 (29.2974)
App time (%) = 0.00777125 (54.9042)
Other time (%) = 0.000623941 (4.40817)
Comm time (%) = 8.818e-05 (2.71824)
Outpt time (%) = 0.000638812 (19.6921)
App time (%) = 0.00223398 (68.8649)
Other time (%) = 5.5635e-05 (1.71501)
run 10Setting up run ...
Time Naccept Nreject Nsweeps CPU Energy
140 71967 0 0 0 2700
150 74773 0 0 0.0132 2644
Loop time of 0.0131881 on 1 procs
140 69933 0 67 0 2680
150 72830 0 71 0.00314 2664
Loop time of 0.0031476 on 1 procs
Solve time (%) = 0.00111961 (8.48956)
Solve time (%) = 0.000213509 (6.78324)
Update time (%) = 0 (0)
Comm time (%) = 0.000277758 (2.10612)
Outpt time (%) = 0.00413394 (31.3459)
App time (%) = 0.00711513 (53.951)
Other time (%) = 0.000541687 (4.10738)
Comm time (%) = 8.6263e-05 (2.7406)
Outpt time (%) = 0.000676177 (21.4823)
App time (%) = 0.00211915 (67.326)
Other time (%) = 5.2495e-05 (1.66778)
run 10Setting up run ...
Time Naccept Nreject Nsweeps CPU Energy
150 74773 0 0 0 2644
160 77662 0 0 0.0134 2616
Loop time of 0.0133891 on 1 procs
150 72830 0 71 0 2664
160 75877 0 75 0.00386 2640
Loop time of 0.00386614 on 1 procs
Solve time (%) = 0.00116301 (8.68621)
Solve time (%) = 0.000262699 (6.79487)
Update time (%) = 0 (0)
Comm time (%) = 0.00027895 (2.08341)
Outpt time (%) = 0.00415397 (31.025)
App time (%) = 0.00725079 (54.1544)
Other time (%) = 0.000542402 (4.05107)
Comm time (%) = 0.000115859 (2.99676)
Outpt time (%) = 0.000745615 (19.2858)
App time (%) = 0.00267785 (69.2643)
Other time (%) = 6.4111e-05 (1.65827)
run 10Setting up run ...
Time Naccept Nreject Nsweeps CPU Energy
160 77662 0 0 0 2616
170 80475 0 0 0.0131 2538
Loop time of 0.0130939 on 1 procs
160 75877 0 75 0 2640
170 78733 0 79 0.00555 2486
Loop time of 0.0055484 on 1 procs
Solve time (%) = 0.00108457 (8.28296)
Solve time (%) = 0.000407211 (7.33925)
Update time (%) = 0 (0)
Comm time (%) = 0.000279665 (2.13583)
Outpt time (%) = 0.00412798 (31.5259)
App time (%) = 0.00700951 (53.5324)
Other time (%) = 0.000592232 (4.52294)
Comm time (%) = 0.000168943 (3.04489)
Outpt time (%) = 0.000823976 (14.8507)
App time (%) = 0.00404893 (72.9746)
Other time (%) = 9.9346e-05 (1.79053)
run 10Setting up run ...
Time Naccept Nreject Nsweeps CPU Energy
170 80475 0 0 0 2538
180 83407 0 0 0.0136 2660
Loop time of 0.0136199 on 1 procs
170 78733 0 79 0 2486
180 81400 0 83 0.00291 2396
Loop time of 0.00291697 on 1 procs
Solve time (%) = 0.00117278 (8.61079)
Solve time (%) = 0.000197105 (6.75718)
Update time (%) = 0 (0)
Comm time (%) = 0.000262737 (1.92907)
Outpt time (%) = 0.00413108 (30.3312)
App time (%) = 0.0074532 (54.7229)
Other time (%) = 0.0006001 (4.40605)
Comm time (%) = 8.6733e-05 (2.97339)
Outpt time (%) = 0.000641861 (22.0044)
App time (%) = 0.00194335 (66.6221)
Other time (%) = 4.7923e-05 (1.6429)
run 10Setting up run ...
Time Naccept Nreject Nsweeps CPU Energy
180 83407 0 0 0 2660
190 86407 0 0 0.0138 2656
Loop time of 0.013859 on 1 procs
180 81400 0 83 0 2396
190 84097 0 86 0.00291 2418
Loop time of 0.00290961 on 1 procs
Solve time (%) = 0.00119066 (8.59124)
Solve time (%) = 0.000198685 (6.82859)
Update time (%) = 0 (0)
Comm time (%) = 0.000247717 (1.7874)
Outpt time (%) = 0.00414801 (29.93)
App time (%) = 0.00767326 (55.3665)
Other time (%) = 0.000599384 (4.32486)
Comm time (%) = 6.5496e-05 (2.25103)
Outpt time (%) = 0.000671627 (23.0831)
App time (%) = 0.00192582 (66.1883)
Other time (%) = 4.7978e-05 (1.64895)
run 10Setting up run ...
Time Naccept Nreject Nsweeps CPU Energy
190 86407 0 0 0 2656
200 88961 0 0 0.0124 2374
Loop time of 0.0124531 on 1 procs
190 84097 0 86 0 2418
200 86656 0 90 0.00332 2442
Loop time of 0.00332468 on 1 procs
Solve time (%) = 0.00107932 (8.6671)
Solve time (%) = 0.000220838 (6.64238)
Update time (%) = 0 (0)
Comm time (%) = 0.000233412 (1.87433)
Outpt time (%) = 0.00414777 (33.3072)
App time (%) = 0.00648117 (52.0447)
Other time (%) = 0.000511408 (4.10668)
Comm time (%) = 9.3912e-05 (2.82469)
Outpt time (%) = 0.000744786 (22.4017)
App time (%) = 0.00221113 (66.5064)
Other time (%) = 5.402e-05 (1.62482)

324
examples/COUPLE/lammps_spparks/log.spparks.4
View File

@ -1,4 +1,4 @@
SPPARKS (26 Aug 2010)
SPPARKS (19 Sept 2022)
# SPPARKS input for coupling MD/MC
seed 56789
@ -28,244 +28,246 @@ diag_style energy
temperature 1.0
stats 10.0
dump 1 10.0 dump.mc
dump 1 text 10.0 dump.mc id site x y
run 10Setting up run ...
Running with 32-bit site IDs
Memory usage per processor = 2.375 Mbytes
Time Naccept Nreject Nsweeps CPU Energy
0 0 0 0 0 19766
10 18695 0 0 0.024 5696
Loop time of 0.0240365 on 4 procs
10 18709 0 14 0.00995 5410
Loop time of 0.00996147 on 4 procs
Solve time (%) = 0.0017997 (7.48737)
Solve time (%) = 0.000401817 (4.03371)
Update time (%) = 0 (0)
Comm time (%) = 0.00263286 (10.9536)
Outpt time (%) = 0.00416493 (17.3275)
App time (%) = 0.0137114 (57.044)
Other time (%) = 0.00172764 (7.18756)
Comm time (%) = 0.00184758 (18.5473)
Outpt time (%) = 0.000835493 (8.38724)
App time (%) = 0.00643178 (64.5665)
Other time (%) = 0.000444804 (4.46524)
run 10Setting up run ...
Time Naccept Nreject Nsweeps CPU Energy
10 18695 0 0 0 5696
20 25730 0 0 0.0114 4806
Loop time of 0.0113776 on 4 procs
10 18709 0 14 0 5410
20 25405 0 20 0.00348 4414
Loop time of 0.00348928 on 4 procs
Solve time (%) = 0.000647247 (5.68877)
Solve time (%) = 0.000145149 (4.15985)
Update time (%) = 0 (0)
Comm time (%) = 0.0013088 (11.5033)
Outpt time (%) = 0.00417346 (36.6812)
App time (%) = 0.0045594 (40.0733)
Other time (%) = 0.000688732 (6.05338)
Comm time (%) = 0.000562263 (16.114)
Outpt time (%) = 0.0007944 (22.7669)
App time (%) = 0.00176801 (50.6697)
Other time (%) = 0.000219463 (6.28963)
run 10Setting up run ...
Time Naccept Nreject Nsweeps CPU Energy
20 25730 0 0 0 4806
30 31377 0 0 0.00985 4308
Loop time of 0.00987101 on 4 procs
20 25405 0 20 0 4414
30 30724 0 25 0.00314 4092
Loop time of 0.00314216 on 4 procs
Solve time (%) = 0.000525832 (5.32704)
Solve time (%) = 0.000123228 (3.92176)
Update time (%) = 0 (0)
Comm time (%) = 0.0012235 (12.3949)
Outpt time (%) = 0.00415748 (42.1181)
App time (%) = 0.00343758 (34.825)
Other time (%) = 0.000526607 (5.33489)
Comm time (%) = 0.000561445 (17.8681)
Outpt time (%) = 0.00079681 (25.3586)
App time (%) = 0.00146373 (46.5835)
Other time (%) = 0.000196952 (6.26804)
run 10Setting up run ...
Time Naccept Nreject Nsweeps CPU Energy
30 31377 0 0 0 4308
40 36311 0 0 0.0092 3840
Loop time of 0.00922179 on 4 procs
30 30724 0 25 0 4092
40 35289 0 30 0.00256 3496
Loop time of 0.0025659 on 4 procs
Solve time (%) = 0.000474155 (5.14168)
Solve time (%) = 9.47535e-05 (3.6928)
Update time (%) = 0 (0)
Comm time (%) = 0.00114667 (12.4344)
Outpt time (%) = 0.00414455 (44.943)
App time (%) = 0.00293165 (31.7905)
Other time (%) = 0.000524759 (5.69043)
Comm time (%) = 0.000508415 (19.8143)
Outpt time (%) = 0.000788757 (30.74)
App time (%) = 0.00106383 (41.4604)
Other time (%) = 0.000110143 (4.29259)
run 10Setting up run ...
Time Naccept Nreject Nsweeps CPU Energy
40 36311 0 0 0 3840
50 40886 0 0 0.00891 3534
Loop time of 0.0089252 on 4 procs
40 35289 0 30 0 3496
50 39511 0 35 0.00252 3294
Loop time of 0.00252512 on 4 procs
Solve time (%) = 0.000433862 (4.86109)
Solve time (%) = 8.7092e-05 (3.44903)
Update time (%) = 0 (0)
Comm time (%) = 0.00113171 (12.68)
Outpt time (%) = 0.00413698 (46.3517)
App time (%) = 0.00268257 (30.0561)
Other time (%) = 0.000540078 (6.05116)
Comm time (%) = 0.000631729 (25.0178)
Outpt time (%) = 0.000780138 (30.8952)
App time (%) = 0.000963016 (38.1375)
Other time (%) = 6.31405e-05 (2.5005)
run 10Setting up run ...
Time Naccept Nreject Nsweeps CPU Energy
50 40886 0 0 0 3534
60 44888 0 0 0.00831 3306
Loop time of 0.00833625 on 4 procs
50 39511 0 35 0 3294
60 43241 0 40 0.00254 3158
Loop time of 0.00254794 on 4 procs
Solve time (%) = 0.000383437 (4.59963)
Solve time (%) = 8.5528e-05 (3.35675)
Update time (%) = 0 (0)
Comm time (%) = 0.00106108 (12.7285)
Outpt time (%) = 0.00413227 (49.5699)
App time (%) = 0.00232393 (27.8774)
Other time (%) = 0.000435531 (5.22455)
Comm time (%) = 0.000598337 (23.4831)
Outpt time (%) = 0.000777931 (30.5317)
App time (%) = 0.000940118 (36.8971)
Other time (%) = 0.00014603 (5.73128)
run 10Setting up run ...
Time Naccept Nreject Nsweeps CPU Energy
60 44888 0 0 0 3306
70 48583 0 0 0.00806 3078
Loop time of 0.0080772 on 4 procs
60 43241 0 40 0 3158
70 46797 0 44 0.00248 3060
Loop time of 0.00248266 on 4 procs
Solve time (%) = 0.000353277 (4.37375)
Solve time (%) = 8.14515e-05 (3.28081)
Update time (%) = 0 (0)
Comm time (%) = 0.00102895 (12.739)
Outpt time (%) = 0.0041061 (50.8357)
App time (%) = 0.00213838 (26.4742)
Other time (%) = 0.000450492 (5.57732)
Comm time (%) = 0.000482648 (19.4407)
Outpt time (%) = 0.000991271 (39.9277)
App time (%) = 0.00085854 (34.5814)
Other time (%) = 6.87532e-05 (2.76933)
run 10Setting up run ...
Time Naccept Nreject Nsweeps CPU Energy
70 48583 0 0 0 3078
80 52044 0 0 0.00786 2998
Loop time of 0.00788343 on 4 procs
70 46797 0 44 0 3060
80 50183 0 48 0.0024 3102
Loop time of 0.00240397 on 4 procs
Solve time (%) = 0.000333607 (4.23175)
Solve time (%) = 8.22802e-05 (3.42268)
Update time (%) = 0 (0)
Comm time (%) = 0.00101435 (12.8669)
Outpt time (%) = 0.00420028 (53.2799)
App time (%) = 0.00198931 (25.234)
Other time (%) = 0.000345886 (4.3875)
Comm time (%) = 0.000494873 (20.5856)
Outpt time (%) = 0.00085299 (35.4825)
App time (%) = 0.000883469 (36.7504)
Other time (%) = 9.03613e-05 (3.75883)
run 10Setting up run ...
Time Naccept Nreject Nsweeps CPU Energy
80 52044 0 0 0 2998
90 55352 0 0 0.0083 3026
Loop time of 0.00831437 on 4 procs
80 50183 0 48 0 3102
90 53732 0 52 0.00272 3028
Loop time of 0.00272017 on 4 procs
Solve time (%) = 0.00031358 (3.77154)
Solve time (%) = 9.94713e-05 (3.6568)
Update time (%) = 0 (0)
Comm time (%) = 0.00111783 (13.4445)
Outpt time (%) = 0.00467652 (56.2462)
App time (%) = 0.00188529 (22.6751)
Other time (%) = 0.00032115 (3.86259)
Comm time (%) = 0.000613542 (22.5553)
Outpt time (%) = 0.000800183 (29.4166)
App time (%) = 0.00108281 (39.8067)
Other time (%) = 0.000124164 (4.56456)
run 10Setting up run ...
Time Naccept Nreject Nsweeps CPU Energy
90 55352 0 0 0 3026
100 58494 0 0 0.00733 2742
Loop time of 0.00735307 on 4 procs
90 53732 0 52 0 3028
100 57112 0 56 0.0023 2942
Loop time of 0.00230787 on 4 procs
Solve time (%) = 0.000297189 (4.0417)
Solve time (%) = 7.58975e-05 (3.28864)
Update time (%) = 0 (0)
Comm time (%) = 0.000801027 (10.8938)
Outpt time (%) = 0.00418043 (56.8529)
App time (%) = 0.00179577 (24.422)
Other time (%) = 0.000278652 (3.7896)
Comm time (%) = 0.000502726 (21.7831)
Outpt time (%) = 0.000796114 (34.4956)
App time (%) = 0.000828819 (35.9127)
Other time (%) = 0.000104316 (4.51999)
run 10Setting up run ...
Time Naccept Nreject Nsweeps CPU Energy
100 58494 0 0 0 2742
110 61498 0 0 0.00732 2636
Loop time of 0.00733691 on 4 procs
100 57112 0 56 0 2942
110 60445 0 60 0.00192 2850
Loop time of 0.00192261 on 4 procs
Solve time (%) = 0.000282168 (3.84587)
Solve time (%) = 6.89883e-05 (3.58826)
Update time (%) = 0 (0)
Comm time (%) = 0.000877678 (11.9625)
Outpt time (%) = 0.00414526 (56.4987)
App time (%) = 0.00174332 (23.7609)
Other time (%) = 0.000288486 (3.93199)
Comm time (%) = 0.000257782 (13.4079)
Outpt time (%) = 0.000791242 (41.1545)
App time (%) = 0.000735212 (38.2403)
Other time (%) = 6.9388e-05 (3.60905)
run 10Setting up run ...
Time Naccept Nreject Nsweeps CPU Energy
110 61498 0 0 0 2636
120 64343 0 0 0.00719 2518
Loop time of 0.00721735 on 4 procs
110 60445 0 60 0 2850
120 63603 0 64 0.00193 2866
Loop time of 0.00193198 on 4 procs
Solve time (%) = 0.000270605 (3.74937)
Solve time (%) = 6.44032e-05 (3.33354)
Update time (%) = 0 (0)
Comm time (%) = 0.00078702 (10.9046)
Outpt time (%) = 0.00416625 (57.7254)
App time (%) = 0.00162369 (22.497)
Other time (%) = 0.000369787 (5.12359)
Comm time (%) = 0.00027428 (14.1969)
Outpt time (%) = 0.000812462 (42.0534)
App time (%) = 0.000682923 (35.3484)
Other time (%) = 9.79088e-05 (5.0678)
run 10Setting up run ...
Time Naccept Nreject Nsweeps CPU Energy
120 64343 0 0 0 2518
130 66901 0 0 0.00709 2480
Loop time of 0.00710845 on 4 procs
120 63603 0 64 0 2866
130 66749 0 68 0.0022 2710
Loop time of 0.00220226 on 4 procs
Solve time (%) = 0.000247002 (3.47476)
Solve time (%) = 8.013e-05 (3.63854)
Update time (%) = 0 (0)
Comm time (%) = 0.00100386 (14.1221)
Outpt time (%) = 0.00416774 (58.6307)
App time (%) = 0.00143349 (20.166)
Other time (%) = 0.00025636 (3.60641)
Comm time (%) = 0.000362387 (16.4552)
Outpt time (%) = 0.000819649 (37.2186)
App time (%) = 0.000844146 (38.3309)
Other time (%) = 9.59462e-05 (4.35672)
run 10Setting up run ...
Time Naccept Nreject Nsweeps CPU Energy
130 66901 0 0 0 2480
140 69617 0 0 0.00723 2462
Loop time of 0.00725645 on 4 procs
130 66749 0 68 0 2710
140 69868 0 72 0.00276 2822
Loop time of 0.00276561 on 4 procs
Solve time (%) = 0.000262678 (3.61992)
Solve time (%) = 8.8444e-05 (3.19799)
Update time (%) = 0 (0)
Comm time (%) = 0.000848353 (11.691)
Outpt time (%) = 0.00418752 (57.7076)
App time (%) = 0.00152171 (20.9704)
Other time (%) = 0.000436187 (6.01102)
Comm time (%) = 0.000566006 (20.4659)
Outpt time (%) = 0.00100224 (36.2395)
App time (%) = 0.000938724 (33.9427)
Other time (%) = 0.000170192 (6.15388)
run 10Setting up run ...
Time Naccept Nreject Nsweeps CPU Energy
140 69617 0 0 0 2462
150 72516 0 0 0.0077 2368
Loop time of 0.00771403 on 4 procs
140 69868 0 72 0 2822
150 72809 0 77 0.00203 2530
Loop time of 0.00203296 on 4 procs
Solve time (%) = 0.000279188 (3.61922)
Solve time (%) = 6.10922e-05 (3.00508)
Update time (%) = 0 (0)
Comm time (%) = 0.00115103 (14.9212)
Outpt time (%) = 0.00420797 (54.5495)
App time (%) = 0.00164241 (21.2911)
Other time (%) = 0.000433445 (5.61892)
Comm time (%) = 0.000430907 (21.196)
Outpt time (%) = 0.000773949 (38.07)
App time (%) = 0.000649508 (31.9488)
Other time (%) = 0.000117508 (5.78011)
run 10Setting up run ...
Time Naccept Nreject Nsweeps CPU Energy
150 72516 0 0 0 2368
160 75201 0 0 0.00745 2384
Loop time of 0.00747746 on 4 procs
150 72809 0 77 0 2530
160 75490 0 82 0.00243 2560
Loop time of 0.00243939 on 4 procs
Solve time (%) = 0.00026089 (3.48901)
Solve time (%) = 7.29237e-05 (2.98943)
Update time (%) = 0 (0)
Comm time (%) = 0.00115579 (15.457)
Outpt time (%) = 0.00416714 (55.7293)
App time (%) = 0.0015164 (20.2796)
Other time (%) = 0.000377238 (5.045)
Comm time (%) = 0.000533877 (21.8857)
Outpt time (%) = 0.000900521 (36.9159)
App time (%) = 0.000753532 (30.8902)
Other time (%) = 0.000178534 (7.31879)
run 10Setting up run ...
Time Naccept Nreject Nsweeps CPU Energy
160 75201 0 0 0 2384
170 77794 0 0 0.00709 2286
Loop time of 0.00710869 on 4 procs
160 75490 0 82 0 2560
170 78382 0 86 0.00203 2424
Loop time of 0.00203432 on 4 procs
Solve time (%) = 0.000261724 (3.68175)
Solve time (%) = 6.05745e-05 (2.97762)
Update time (%) = 0 (0)
Comm time (%) = 0.000879705 (12.3751)
Outpt time (%) = 0.00419676 (59.0371)
App time (%) = 0.00145274 (20.4362)
Other time (%) = 0.000317752 (4.46992)
Comm time (%) = 0.000357404 (17.5687)
Outpt time (%) = 0.000830967 (40.8473)
App time (%) = 0.000642883 (31.6018)
Other time (%) = 0.000142495 (7.00454)
run 10Setting up run ...
Time Naccept Nreject Nsweeps CPU Energy
170 77794 0 0 0 2286
180 80320 0 0 0.00723 2186
Loop time of 0.00725418 on 4 procs
170 78382 0 86 0 2424
180 81046 0 90 0.00266 2450
Loop time of 0.00266286 on 4 procs
Solve time (%) = 0.000241041 (3.32279)
Solve time (%) = 7.05732e-05 (2.65028)
Update time (%) = 0 (0)
Comm time (%) = 0.00100464 (13.8491)
Outpt time (%) = 0.00413877 (57.0535)
App time (%) = 0.00144053 (19.8579)
Other time (%) = 0.000429213 (5.91677)
Comm time (%) = 0.000638214 (23.9672)
Outpt time (%) = 0.00102986 (38.6749)
App time (%) = 0.000760398 (28.5557)
Other time (%) = 0.000163817 (6.15191)
run 10Setting up run ...
Time Naccept Nreject Nsweeps CPU Energy
180 80320 0 0 0 2186
190 82621 0 0 0.00686 2204
Loop time of 0.00687295 on 4 procs
180 81046 0 90 0 2450
190 83562 0 94 0.00216 2402
Loop time of 0.0021675 on 4 procs
Solve time (%) = 0.000222385 (3.23565)
Solve time (%) = 6.2358e-05 (2.87696)
Update time (%) = 0 (0)
Comm time (%) = 0.000860512 (12.5203)
Outpt time (%) = 0.00418121 (60.8357)
App time (%) = 0.00126499 (18.4053)
Other time (%) = 0.000343859 (5.00308)
Comm time (%) = 0.000536287 (24.7422)
Outpt time (%) = 0.000802317 (37.0158)
App time (%) = 0.000649124 (29.9481)
Other time (%) = 0.000117412 (5.41694)
run 10Setting up run ...
Time Naccept Nreject Nsweeps CPU Energy
190 82621 0 0 0 2204
200 84907 0 0 0.00681 2276
Loop time of 0.0068413 on 4 procs
190 83562 0 94 0 2402
200 86036 0 98 0.0021 2306
Loop time of 0.00210625 on 4 procs
Solve time (%) = 0.000233412 (3.4118)
Solve time (%) = 5.94018e-05 (2.82026)
Update time (%) = 0 (0)
Comm time (%) = 0.000758171 (11.0823)
Outpt time (%) = 0.00421125 (61.5562)
App time (%) = 0.00125164 (18.2953)
Other time (%) = 0.000386834 (5.65439)
Comm time (%) = 0.000492842 (23.399)
Outpt time (%) = 0.000817012 (38.7899)
App time (%) = 0.000597335 (28.3601)
Other time (%) = 0.00013966 (6.63072)

4
examples/COUPLE/lammps_spparks/spkpath.h
View File

@ -1 +1,3 @@
#define SPKPATH /home/sjplimp/spparks
// path to your SPPARKS home directory
#define SPKPATH /home/sjplimp/spparks/git

0
examples/COUPLE/library/Makefile.g++ → examples/COUPLE/library/Makefile.mpi
View File

2
examples/COUPLE/library/README
View File

@ -6,7 +6,7 @@ SPPARKS applications in 2 sister directories.
The library dir has a Makefile (which you may need to edit for your
box). If you type
g++ -f Makefile.g++
make -f Makefile.mpi
you should create libcouple.a, which the other coupled applications
link to.

10
examples/COUPLE/library/error.cpp → examples/COUPLE/library/errorlib.cpp
View File

@ -1,11 +1,11 @@
#include <mpi.h>
#include <cstdio>
#include <cstdlib>
#include "error.h"
#include "errorlib.h"
/* ---------------------------------------------------------------------- */
Error::Error(MPI_Comm caller)
ErrorLib::ErrorLib(MPI_Comm caller)
{
comm = caller;
MPI_Comm_rank(comm,&me);
@ -15,7 +15,7 @@ Error::Error(MPI_Comm caller)
called by all procs
------------------------------------------------------------------------- */
void Error::all(const char *str)
void ErrorLib::all(const char *str)
{
if (me == 0) printf("ERROR: %s\n",str);
MPI_Finalize();
@ -26,7 +26,7 @@ void Error::all(const char *str)
called by one proc
------------------------------------------------------------------------- */
void Error::one(const char *str)
void ErrorLib::one(const char *str)
{
printf("ERROR on proc %d: %s\n",me,str);
MPI_Abort(comm,1);
@ -36,7 +36,7 @@ void Error::one(const char *str)
called by one proc
------------------------------------------------------------------------- */
void Error::warning(const char *str)
void ErrorLib::warning(const char *str)
{
printf("WARNING: %s\n",str);
}

8
examples/COUPLE/library/error.h → examples/COUPLE/library/errorlib.h
View File

@ -1,11 +1,11 @@
#ifndef ERROR_H
#define ERROR_H
#ifndef ERRORLIB_H
#define ERRORLIB_H
#include <mpi.h>
class Error {
class ErrorLib {
public:
Error(MPI_Comm);
ErrorLib(MPI_Comm);
void all(const char *);
void one(const char *);

2
examples/COUPLE/library/files.cpp
View File

@ -29,7 +29,7 @@ void replace(char *file, char *header, int n, char **lines)
/* ---------------------------------------------------------------------- */
char **extract(char *file, char *header, int n, char **lines)
void extract(char *file, char *header, int n, char **lines)
{
FILE *fp = fopen(file,"r");

2
examples/COUPLE/library/files.h
View File

@ -1,5 +1,5 @@
#ifndef FILES_H
#define FILES_H
void replace(char *, char *, int, char **);
char **extract(char *, char *, int, char **);
void extract(char *, char *, int, char **);
#endif

16
examples/COUPLE/library/irregular.cpp
View File

@ -2,8 +2,8 @@
#include <cstdlib>
#include <cstring>
#include "irregular.h"
#include "memory.h"
#include "error.h"
#include "memorylib.h"
#include "errorlib.h"
#define MAX(A,B) ((A) > (B)) ? (A) : (B)
@ -18,8 +18,8 @@ Irregular::Irregular(MPI_Comm caller)
MPI_Comm_rank(comm,&me);
MPI_Comm_size(comm,&nprocs);
memory = new Memory(comm);
error = new Error(comm);
memory = new MemoryLib(comm);
error = new ErrorLib(comm);
init();
@ -119,7 +119,7 @@ void Irregular::pattern(int n, int *proclist)
for (int i = 0; i < nrecv; i++)
MPI_Irecv(&recvcount[i],1,MPI_INT,MPI_ANY_SOURCE,0,comm,&request[i]);
// barrier to insure receives are posted
// barrier to ensure receives are posted
MPI_Barrier(comm);
@ -128,7 +128,7 @@ void Irregular::pattern(int n, int *proclist)
for (int i = 0; i < nsend; i++)
MPI_Send(&sendcount[i],1,MPI_INT,sendproc[i],0,comm);
// insure all MPI_ANY_SOURCE messages are received
// ensure all MPI_ANY_SOURCE messages are received
// set recvproc
if (nrecv) MPI_Waitall(nrecv,request,status);
@ -270,7 +270,7 @@ void Irregular::exchange_same(char *sendbuf, char *recvbuf)
char *buf = (char *) memory->smalloc(nsendmax,"buf");
// barrier to insure receives are posted
// barrier to ensure receives are posted
MPI_Barrier(comm);
@ -325,7 +325,7 @@ void Irregular::exchange_varying(char *sendbuf, char *recvbuf)
char *buf = (char *) memory->smalloc(nsendmax,"buf");
// barrier to insure receives are posted
// barrier to ensure receives are posted
MPI_Barrier(comm);

4
examples/COUPLE/library/irregular.h
View File

@ -46,8 +46,8 @@ class Irregular {
MPI_Status *status; // MPI statuses for Waitall
MPI_Comm comm; // MPI communicator for all communication
class Memory *memory;
class Error *error;
class MemoryLib *memory;
class ErrorLib *error;
void exchange_same(char *, char *);
void exchange_varying(char *, char *);

4
examples/COUPLE/library/lammps_data_write.cpp
View File

@ -2,8 +2,8 @@
#include <cstdlib>
#include <cstring>
#include "lammps_data_write.h"
#include "memory.h"
#include "error.h"
#include "memorylib.h"
#include "errorlib.h"
#define DELTA 4;

8
examples/COUPLE/library/many2many.cpp
View File

@ -3,8 +3,8 @@
#include <cstdio>
#include "many2many.h"
#include "irregular.h"
#include "memory.h"
#include "error.h"
#include "memorylib.h"
#include "errorlib.h"
#include <map>
@ -18,8 +18,8 @@ Many2Many::Many2Many(MPI_Comm caller)
MPI_Comm_rank(comm,&me);
MPI_Comm_size(comm,&nprocs);
memory = new Memory(comm);
error = new Error(comm);
memory = new MemoryLib(comm);
error = new ErrorLib(comm);
src_own = dest_own = NULL;
src_off = dest_off = NULL;

4
examples/COUPLE/library/many2many.h
View File

@ -15,8 +15,8 @@ class Many2Many {
protected:
int me,nprocs;
MPI_Comm comm;
class Memory *memory;
class Error *error;
class MemoryLib *memory;
class ErrorLib *error;
int nown; // # of IDs common to src and dest
int nsrc_off,ndest_off; // # of off-processor IDs

4
examples/COUPLE/library/many2one.cpp
View File

@ -2,7 +2,7 @@
#include <cstdio>
#include <cstdlib>
#include "many2one.h"
#include "memory.h"
#include "memorylib.h"
/* ---------------------------------------------------------------------- */
@ -12,7 +12,7 @@ Many2One::Many2One(MPI_Comm caller_comm)
MPI_Comm_rank(comm,&me);
MPI_Comm_size(comm,&nprocs);
memory = new Memory(comm);
memory = new MemoryLib(comm);
if (me == 0) {
counts = new int[nprocs];

2
examples/COUPLE/library/many2one.h
View File

@ -14,7 +14,7 @@ class Many2One {
protected:
int me,nprocs;
MPI_Comm comm;
class Memory *memory;
class MemoryLib *memory;
int nsrc,nall;
int *counts,*multicounts;

22
examples/COUPLE/library/memory.cpp → examples/COUPLE/library/memorylib.cpp
View File

@ -1,19 +1,19 @@
#include <mpi.h>
#include <cstdlib>
#include <cstdio>
#include "memory.h"
#include "error.h"
#include "memorylib.h"
#include "errorlib.h"
/* ---------------------------------------------------------------------- */
Memory::Memory(MPI_Comm comm)
MemoryLib::MemoryLib(MPI_Comm comm)
{
error = new Error(comm);
error = new ErrorLib(comm);
}
/* ---------------------------------------------------------------------- */
Memory::~Memory()
MemoryLib::~MemoryLib()
{
delete error;
}
@ -22,7 +22,7 @@ Memory::~Memory()
safe malloc
------------------------------------------------------------------------- */
void *Memory::smalloc(int n, const char *name)
void *MemoryLib::smalloc(int n, const char *name)
{
if (n == 0) return NULL;
void *ptr = malloc(n);
@ -38,7 +38,7 @@ void *Memory::smalloc(int n, const char *name)
safe free
------------------------------------------------------------------------- */
void Memory::sfree(void *ptr)
void MemoryLib::sfree(void *ptr)
{
if (ptr == NULL) return;
free(ptr);
@ -48,7 +48,7 @@ void Memory::sfree(void *ptr)
safe realloc
------------------------------------------------------------------------- */
void *Memory::srealloc(void *ptr, int n, const char *name)
void *MemoryLib::srealloc(void *ptr, int n, const char *name)
{
if (n == 0) {
sfree(ptr);
@ -68,7 +68,7 @@ void *Memory::srealloc(void *ptr, int n, const char *name)
create a 2d double array
------------------------------------------------------------------------- */
double **Memory::create_2d_double_array(int n1, int n2, const char *name)
double **MemoryLib::create_2d_double_array(int n1, int n2, const char *name)
{
double *data = (double *) smalloc(n1*n2*sizeof(double),name);
@ -89,7 +89,7 @@ double **Memory::create_2d_double_array(int n1, int n2, const char *name)
if either dim is 0, return NULL
------------------------------------------------------------------------- */
double **Memory::grow_2d_double_array(double **array,
double **MemoryLib::grow_2d_double_array(double **array,
int n1, int n2, const char *name)
{
@ -111,7 +111,7 @@ double **Memory::grow_2d_double_array(double **array,
free a 2d double array
------------------------------------------------------------------------- */
void Memory::destroy_2d_double_array(double **array)
void MemoryLib::destroy_2d_double_array(double **array)
{
if (array == NULL) return;

12
examples/COUPLE/library/memory.h → examples/COUPLE/library/memorylib.h
View File

@ -1,12 +1,12 @@
#ifndef MEMORY_H
#define MEMORY_H
#ifndef MEMORY_LIB_H
#define MEMORY_LIB_H
#include <mpi.h>
class Memory {
class MemoryLib {
public:
Memory(MPI_Comm);
~Memory();
MemoryLib(MPI_Comm);
~MemoryLib();
void *smalloc(int n, const char *);
void sfree(void *);
@ -17,7 +17,7 @@ class Memory {
void destroy_2d_double_array(double **);
private:
class Error *error;
class ErrorLib *error;
};
#endif

4
examples/COUPLE/library/one2many.cpp
View File

@ -1,7 +1,7 @@
#include <mpi.h>
#include <cstdlib>
#include "one2many.h"
#include "memory.h"
#include "memorylib.h"
#include <map>
@ -13,7 +13,7 @@ One2Many::One2Many(MPI_Comm caller_comm)
MPI_Comm_rank(comm,&me);
MPI_Comm_size(comm,&nprocs);
memory = new Memory(comm);
memory = new MemoryLib(comm);
hash = new std::map<int,int>();
}

2
examples/COUPLE/library/one2many.h
View File

@ -16,7 +16,7 @@ class One2Many {
protected:
int me,nprocs;
MPI_Comm comm;
class Memory *memory;
class MemoryLib *memory;
std::map<int,int> *hash;
int nsrc;
};

8
examples/COUPLE/library/send2one.cpp
View File

@ -2,8 +2,8 @@
#include <cstdlib>
#include <cstdio>
#include "send2one.h"
#include "memory.h"
#include "error.h"
#include "memorylib.h"
#include "errorlib.h"
/* ---------------------------------------------------------------------- */
@ -13,8 +13,8 @@ Send2One::Send2One(MPI_Comm caller_comm)
MPI_Comm_rank(comm,&me);
MPI_Comm_size(comm,&nprocs);
memory = new Memory(comm);
error = new Error(comm);
memory = new MemoryLib(comm);
error = new ErrorLib(comm);
buf = NULL;
maxbuf = 0;

4
examples/COUPLE/library/send2one.h
View File

@ -13,8 +13,8 @@ class Send2One {
protected:
int me,nprocs;
MPI_Comm comm;
class Memory *memory;
class Error *error;
class MemoryLib *memory;
class ErrorLib *error;
int maxbuf;
char *buf;

4
examples/COUPLE/multiple/multiple.cpp
View File

@ -1,7 +1,7 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
https://www.lammps.org/, Sandia National Laboratories
LAMMPS development team: developers@lammps.org
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains

1
examples/COUPLE/plugin/.gitignore vendored Normal file
View File

@ -0,0 +1 @@
/build

44
examples/COUPLE/plugin/CMakeLists.txt Normal file
View File

@ -0,0 +1,44 @@
# -*- CMake -*- file for example programs that use the LAMMPS library
# where the library is loaded dynamically at runtime.
##########################################
cmake_minimum_required(VERSION 3.16)
# enforce out-of-source build
if(${CMAKE_SOURCE_DIR} STREQUAL ${CMAKE_BINARY_DIR})
message(FATAL_ERROR "In-source builds are not allowed. You must create and use a build directory. "
"Please remove CMakeCache.txt and CMakeFiles first.")
endif()
project(liblammpsplugin VERSION 1.0 LANGUAGES C)
# by default, install into $HOME/.local (not /usr/local),
# so that no root access (and sudo) is needed
if(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)
set(CMAKE_INSTALL_PREFIX "$ENV{HOME}/.local" CACHE PATH "Default install path" FORCE)
endif()
# ugly hacks for MSVC which by default always reports an old C++ standard in the __cplusplus macro
# and prints lots of pointless warnings about "unsafe" functions
if(MSVC)
if(CMAKE_C_COMPILER_ID STREQUAL "MSVC")
add_compile_options(/EHsc)
endif()
add_compile_definitions(_CRT_SECURE_NO_WARNINGS)
endif()
find_package(MPI REQUIRED)
# do not include the (obsolete) MPI C++ bindings which makes
# for leaner object files and avoids namespace conflicts
set(MPI_CXX_SKIP_MPICXX TRUE)
##########################
add_executable(simple-plugin simple.c liblammpsplugin.c)
target_link_libraries(simple-plugin PRIVATE MPI::MPI_C)
target_compile_definitions(simple-plugin PRIVATE LAMMPS_LIB_MPI)
# link with -ldl or equivalent for plugin loading; except on Windows
if(NOT ${CMAKE_SYSTEM_NAME} STREQUAL "Windows")
target_link_libraries(simple-plugin PRIVATE ${CMAKE_DL_LIBS})
endif()

25
examples/COUPLE/plugin/README
View File

@ -11,32 +11,39 @@ liblammpsplugin.c is the LAMMPS library plugin loader
You can then build the driver executable codes with a compile line
like below.
mpicc -c -O -Wall -g -I$HOME/lammps/src liblammpsplugin.c
mpicc -c -O -Wall -g simple.c
mpicc simple.o liblammpsplugin.o -ldl -o simpleC
mpicc -c -O -DLAMMPS_LIB_MPI -Wall -g liblammpsplugin.c
mpicc -c -O -DLAMMPS_LIB_MPI -Wall -g simple.c
mpicc simple.o liblammpsplugin.o -ldl -o simple-plugin
or using the provided CMake file with:
mkdir build
cd build
cmake ../
cmake --build .
You also need to build LAMMPS as a shared library
(see examples/COUPLE/README), e.g.
(see examples/COUPLE/README), e.g.
cd $HOME/lammps/src
make mode=shlib mpi
or
or
cd $HOME/lammps
mkdir build-shared
cd build-shared
cmake -D BUILD_LIB=on -D BUILD_SHARED_LIBS=on ../cmake
cmake -D BUILD_MPI=on -D BUILD_SHARED_LIBS=on ../cmake
make
You then run simpleC on a parallel machine
You then run simple-plugin on a parallel machine
on some number of processors Q with 3 arguments:
% mpirun -np Q simpleC P in.lj $HOME/lammps/src/liblammps.so
% mpirun -np Q simple-plugin P in.lj $HOME/lammps/src/liblammps.so
or
% mpirun -np Q simpleC P in.lj $HOME/lammps/build-shared/liblammps.so
% mpirun -np Q simple-plugin P in.lj $HOME/lammps/build-shared/liblammps.so
P is the number of procs you want LAMMPS to run on (must be <= Q) and
in.lj is a LAMMPS input script and the last argument is the path to

87
examples/COUPLE/plugin/liblammpsplugin.c
View File

@ -1,7 +1,7 @@
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/ Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
https://www.lammps.org/, Sandia National Laboratories
LAMMPS development team: developers@lammps.org
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
@ -18,10 +18,29 @@
a LAMMPS plugin to some other software.
*/
#include "library.h"
#include "liblammpsplugin.h"
#include <stdlib.h>
#if defined(_WIN32)
#ifndef WIN32_LEAN_AND_MEAN
#define WIN32_LEAN_AND_MEAN
#endif
#if defined(_WIN32_WINNT)
#undef _WIN32_WINNT
#endif
// target Windows version is windows 7 and later
#define _WIN32_WINNT _WIN32_WINNT_WIN7
#define PSAPI_VERSION 2
#include <windows.h>
#else
#include <dlfcn.h>
#endif
#include <stdlib.h>
liblammpsplugin_t *liblammpsplugin_load(const char *lib)
{
@ -29,14 +48,30 @@ liblammpsplugin_t *liblammpsplugin_load(const char *lib)
void *handle;
if (lib == NULL) return NULL;
#ifdef _WIN32
handle = (void *) LoadLibrary(lib);
#else
handle = dlopen(lib,RTLD_NOW|RTLD_GLOBAL);
#endif
if (handle == NULL) return NULL;
lmp = (liblammpsplugin_t *) malloc(sizeof(liblammpsplugin_t));
lmp = (liblammpsplugin_t *) calloc(1, sizeof(liblammpsplugin_t));
lmp->abiversion = LAMMPSPLUGIN_ABI_VERSION;
lmp->handle = handle;
#define ADDSYM(symbol) lmp->symbol = dlsym(handle,"lammps_" #symbol)
#ifdef _WIN32
#define ADDSYM(symbol) *(void **) (&lmp->symbol) = (void *) GetProcAddress((HINSTANCE) handle, "lammps_" #symbol)
#else
#define ADDSYM(symbol) *(void **) (&lmp->symbol) = dlsym(handle,"lammps_" #symbol)
#endif
#if defined(LAMMPS_LIB_MPI)
ADDSYM(open);
#else
lmp->open = NULL;
#endif
ADDSYM(open_no_mpi);
ADDSYM(open_fortran);
ADDSYM(close);
@ -46,6 +81,8 @@ liblammpsplugin_t *liblammpsplugin_load(const char *lib)
ADDSYM(kokkos_finalize);
ADDSYM(python_finalize);
ADDSYM(error);
ADDSYM(file);
ADDSYM(command);
ADDSYM(commands_list);
@ -53,6 +90,7 @@ liblammpsplugin_t *liblammpsplugin_load(const char *lib)
ADDSYM(get_natoms);
ADDSYM(get_thermo);
ADDSYM(last_thermo);
ADDSYM(extract_box);
ADDSYM(reset_box);
@ -70,14 +108,26 @@ liblammpsplugin_t *liblammpsplugin_load(const char *lib)
ADDSYM(extract_compute);
ADDSYM(extract_fix);
ADDSYM(extract_variable);
ADDSYM(extract_variable_datatype);
ADDSYM(set_variable);
ADDSYM(variable_info);
ADDSYM(gather_atoms);
ADDSYM(gather_atoms_concat);
ADDSYM(gather_atoms_subset);
ADDSYM(scatter_atoms);
ADDSYM(scatter_atoms_subset);
ADDSYM(gather_bonds);
ADDSYM(gather_angles);
ADDSYM(gather_dihedrals);
ADDSYM(gather_impropers);
ADDSYM(gather);
ADDSYM(gather_concat);
ADDSYM(gather_subset);
ADDSYM(scatter);
ADDSYM(scatter_subset);
ADDSYM(create_atoms);
@ -116,6 +166,9 @@ liblammpsplugin_t *liblammpsplugin_load(const char *lib)
ADDSYM(plugin_count);
ADDSYM(plugin_name);
ADDSYM(encode_image_flags);
ADDSYM(decode_image_flags);
ADDSYM(set_fix_external_callback);
ADDSYM(fix_external_get_force);
ADDSYM(fix_external_set_energy_global);
@ -125,20 +178,20 @@ liblammpsplugin_t *liblammpsplugin_load(const char *lib)
ADDSYM(fix_external_set_vector_length);
ADDSYM(fix_external_set_vector);
ADDSYM(flush_buffers);
ADDSYM(free);
ADDSYM(is_running);
ADDSYM(force_timeout);
#ifdef LAMMPS_EXCEPTIONS
lmp->has_exceptions = 1;
ADDSYM(has_error);
ADDSYM(get_last_error_message);
#else
lmp->has_exceptions = 0;
lmp->has_error = NULL;
lmp->get_last_error_message = NULL;
#endif
lmp->has_exceptions = lmp->config_has_exceptions();
if (lmp->has_exceptions) {
ADDSYM(has_error);
ADDSYM(get_last_error_message);
}
ADDSYM(python_api_version);
return lmp;
}
@ -147,7 +200,11 @@ int liblammpsplugin_release(liblammpsplugin_t *lmp)
if (lmp == NULL) return 1;
if (lmp->handle == NULL) return 2;
#ifdef _WIN32
FreeLibrary((HINSTANCE) lmp->handle);
#else
dlclose(lmp->handle);
#endif
free((void *)lmp);
return 0;
}

138
examples/COUPLE/plugin/liblammpsplugin.h
View File

@ -1,7 +1,7 @@
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/ Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
https://www.lammps.org/, Sandia National Laboratories
LAMMPS development team: developers@lammps.org
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
@ -28,11 +28,72 @@
#define LAMMPS_SMALLBIG
#endif
#if defined(LAMMPS_LIB_MPI)
#include <mpi.h>
#if defined(LAMMPS_BIGBIG) || defined(LAMMPS_SMALLBIG)
#include <inttypes.h> /* for int64_t */
#endif
#if defined(LAMMPS_BIGBIG) || defined(LAMMPS_SMALLBIG)
#include <stdint.h> /* for int64_t */
#endif
/* The following enums must be kept in sync with the equivalent enums
* or constants in src/library.h, src/lmptype.h, python/lammps/constants.py,
* fortran/lammps.f90, and tools/swig/lammps.i */
/* Data type constants for extracting data from atoms, computes and fixes */
enum _LMP_DATATYPE_CONST {
LAMMPS_NONE = -1, /*!< no data type assigned (yet) */
LAMMPS_INT = 0, /*!< 32-bit integer (array) */
LAMMPS_INT_2D = 1, /*!< two-dimensional 32-bit integer array */
LAMMPS_DOUBLE = 2, /*!< 64-bit double (array) */
LAMMPS_DOUBLE_2D = 3, /*!< two-dimensional 64-bit double array */
LAMMPS_INT64 = 4, /*!< 64-bit integer (array) */
LAMMPS_INT64_2D = 5, /*!< two-dimensional 64-bit integer array */
LAMMPS_STRING = 6 /*!< C-String */
};
/* Style constants for extracting data from computes and fixes. */
enum _LMP_STYLE_CONST {
LMP_STYLE_GLOBAL = 0, /*!< return global data */
LMP_STYLE_ATOM = 1, /*!< return per-atom data */
LMP_STYLE_LOCAL = 2 /*!< return local data */
};
/* Type and size constants for extracting data from computes and fixes. */
enum _LMP_TYPE_CONST {
LMP_TYPE_SCALAR = 0, /*!< return scalar */
LMP_TYPE_VECTOR = 1, /*!< return vector */
LMP_TYPE_ARRAY = 2, /*!< return array */
LMP_SIZE_VECTOR = 3, /*!< return length of vector */
LMP_SIZE_ROWS = 4, /*!< return number of rows */
LMP_SIZE_COLS = 5 /*!< return number of columns */
};
/* Error codes to select the suitable function in the Error class */
enum _LMP_ERROR_CONST {
LMP_ERROR_WARNING = 0, /*!< call Error::warning() */
LMP_ERROR_ONE = 1, /*!< called from one MPI rank */
LMP_ERROR_ALL = 2, /*!< called from all MPI ranks */
LMP_ERROR_WORLD = 4, /*!< error on Comm::world */
LMP_ERROR_UNIVERSE = 8 /*!< error on Comm::universe */
};
/** Variable style constants for extracting data from variables.
*
* Must be kept in sync with the equivalent constants in python/lammps/constants.py,
* fortran/lammps.f90, and tools/swig/lammps.i */
enum _LMP_VAR_CONST {
LMP_VAR_EQUAL = 0, /*!< compatible with equal-style variables */
LMP_VAR_ATOM = 1, /*!< compatible with atom-style variables */
LMP_VAR_VECTOR = 2, /*!< compatible with vector-style variables */
LMP_VAR_STRING = 3 /*!< return value will be a string (catch-all) */
};
#ifdef __cplusplus
extern "C" {
#endif
@ -45,11 +106,16 @@ typedef void (*FixExternalFnPtr)(void *, int, int, int *, double **, double **);
typedef void (*FixExternalFnPtr)(void *, int64_t, int, int *, double **, double **);
#endif
#define LAMMPSPLUGIN_ABI_VERSION 2
struct _liblammpsplugin {
int abiversion;
int has_exceptions;
void *handle;
#if defined(LAMMPS_LIB_MPI)
void *(*open)(int, char **, MPI_Comm, void **);
#else
void *open;
#endif
void *(*open_no_mpi)(int, char **, void **);
void *(*open_fortran)(int, char **, void **, int);
void (*close)(void *);
@ -59,13 +125,16 @@ struct _liblammpsplugin {
void (*kokkos_finalize)();
void (*python_finalize)();
void (*file)(void *, char *);
void (*error)(void *, int, const char *);
void (*file)(void *, const char *);
char *(*command)(void *, const char *);
void (*commands_list)(void *, int, const char **);
void (*commands_string)(void *, const char *);
double (*get_natoms)(void *);
double (*get_thermo)(void *, char *);
double (*get_thermo)(void *, const char *);
void *(*last_thermo)(void *, const char *, int);
void (*extract_box)(void *, double *, double *,
double *, double *, double *, int *, int *);
@ -78,37 +147,46 @@ struct _liblammpsplugin {
int *(*extract_global_datatype)(void *, const char *);
void *(*extract_global)(void *, const char *);
void *(*extract_atom_datatype)(void *, const char *);
int *(*extract_atom_datatype)(void *, const char *);
void *(*extract_atom)(void *, const char *);
void *(*extract_compute)(void *, const char *, int, int);
void *(*extract_fix)(void *, const char *, int, int, int, int);
void *(*extract_variable)(void *, const char *, char *);
int (*extract_variable_datatype)(void *, const char *);
int (*set_variable)(void *, char *, char *);
int (*variable_info)(void *, int, char *, int);
void (*gather_atoms)(void *, char *, int, int, void *);
void (*gather_atoms_concat)(void *, char *, int, int, void *);
void (*gather_atoms_subset)(void *, char *, int, int, int, int *, void *);
void (*scatter_atoms)(void *, char *, int, int, void *);
void (*scatter_atoms_subset)(void *, char *, int, int, int, int *, void *);
void (*gather_atoms)(void *, const char *, int, int, void *);
void (*gather_atoms_concat)(void *, const char *, int, int, void *);
void (*gather_atoms_subset)(void *, const char *, int, int, int, int *, void *);
void (*scatter_atoms)(void *, const char *, int, int, void *);
void (*scatter_atoms_subset)(void *, const char *, int, int, int, int *, void *);
void (*gather_bonds)(void *, void *);
// lammps_create_atoms() takes tagint and imageint as args
// ifdef insures they are compatible with rest of LAMMPS
// caller must match to how LAMMPS library is built
void (*gather_angles)(void *, void *);
void (*gather_dihedrals)(void *, void *);
void (*gather_impropers)(void *, void *);
void (*gather)(void *, const char *, int, int, void *);
void (*gather_concat)(void *, const char *, int, int, void *);
void (*gather_subset)(void *, const char *, int, int, int, int *,void *);
void (*scatter)(void *, const char *, int, int, void *);
void (*scatter_subset)(void *, const char *, int, int, int, int *, void *);
/* lammps_create_atoms() takes tagint and imageint as args
* the ifdef ensures they are compatible with rest of LAMMPS
* caller must match to how LAMMPS library is built */
#ifndef LAMMPS_BIGBIG
void (*create_atoms)(void *, int, int *, int *, double *,
double *, int *, int);
int (*create_atoms)(void *, int, int *, int *, double *, double *, int *, int);
#else
void (*create_atoms)(void *, int, int64_t *, int *, double *,
double *, int64_t *, int);
int (*create_atoms)(void *, int, int64_t *, int *, double *, double *, int64_t *, int);
#endif
int (*find_pair_neighlist)(void *, const char *, int, int, int);
int (*find_fix_neighlist)(void *, const char *, int);
int (*find_compute_neighlist)(void *, char *, int);
int (*find_compute_neighlist)(void *, const char *, int);
int (*neighlist_num_elements)(void *, int);
void (*neighlist_element_neighbors)(void *, int, int, int *, int *, int **);
@ -141,8 +219,16 @@ struct _liblammpsplugin {
int (*plugin_count)();
int (*plugin_name)(int, char *, char *, int);
void (*set_fix_external_callback)(void *, const char *, FixExternalFnPtr, void*);
void (*fix_external_get_force)(void *, const char *);
#if !defined(LAMMPS_BIGBIG)
int (*encode_image_flags)(int, int, int);
void (*decode_image_flags)(int, int *);
#else
int64_t (*encode_image_flags)(int, int, int);
void (*decode_image_flags)(int64_t, int *);
#endif
void (*set_fix_external_callback)(void *, const char *, FixExternalFnPtr, void *);
double **(*fix_external_get_force)(void *, const char *);
void (*fix_external_set_energy_global)(void *, const char *, double);
void (*fix_external_set_energy_peratom)(void *, const char *, double *);
void (*fix_external_set_virial_global)(void *, const char *, double *);
@ -150,13 +236,17 @@ struct _liblammpsplugin {
void (*fix_external_set_vector_length)(void *, const char *, int);
void (*fix_external_set_vector)(void *, const char *, int, double);
void (*flush_buffers)(void *);
void (*free)(void *);
void (*is_running)(void *);
int (*is_running)(void *);
void (*force_timeout)(void *);
int (*has_error)(void *);
int (*get_last_error_message)(void *, char *, int);
int (*python_api_version)();
};
typedef struct _liblammpsplugin liblammpsplugin_t;

41
examples/COUPLE/plugin/simple.c
View File

@ -1,7 +1,7 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
https://www.lammps.org, Sandia National Laboratories
LAMMPS development team: developers@lammps.org
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
@ -19,10 +19,16 @@
in.lammps = LAMMPS input script
See README for compilation instructions */
#include <mpi.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <mpi.h>
/* define so interface to lammps_open() is available,
since we will run on split communicator */
#define LAMMPS_LIB_MPI 1
#include "liblammpsplugin.h" /* this is the include for the plugin loader */
int main(int narg, char **arg)
@ -47,7 +53,7 @@ int main(int narg, char **arg)
MPI_Init(&narg,&arg);
if (narg != 4) {
printf("Syntax: simpleC P in.lammps /path/to/liblammps.so\n");
printf("Syntax: %s P in.lammps /path/to/liblammps.so\n", arg[0]);
exit(1);
}
@ -86,8 +92,20 @@ int main(int narg, char **arg)
if (me == 0) printf("ERROR: Could not load shared LAMMPS library\n");
MPI_Abort(MPI_COMM_WORLD,1);
}
/* must match the plugin ABI version */
if (plugin->abiversion != LAMMPSPLUGIN_ABI_VERSION) {
if (me == 0) printf("ERROR: Plugin abi version does not match: %d vs %d\n",
plugin->abiversion, LAMMPSPLUGIN_ABI_VERSION);
MPI_Abort(MPI_COMM_WORLD,1);
}
}
if (lammps == 1) {
if (plugin->open == NULL) {
printf("ERROR: liblammpsmpi.c must be compiled with -DLAMMPS_LIB_MPI=1 for this program\n");
MPI_Abort(MPI_COMM_WORLD,2);
}
lmp = plugin->open(0,NULL,comm_lammps,NULL);
}
if (lammps == 1) lmp = plugin->open(0,NULL,comm_lammps,NULL);
while (1) {
if (me == 0) {
@ -112,24 +130,25 @@ int main(int narg, char **arg)
int natoms = plugin->get_natoms(lmp);
x = (double *) malloc(3*natoms*sizeof(double));
plugin->gather_atoms(lmp,"x",1,3,x);
plugin->gather_atoms(lmp,(char *)"x",1,3,x);
v = (double *) malloc(3*natoms*sizeof(double));
plugin->gather_atoms(lmp,"v",1,3,v);
plugin->gather_atoms(lmp,(char *)"v",1,3,v);
double epsilon = 0.1;
x[0] += epsilon;
plugin->scatter_atoms(lmp,"x",1,3,x);
plugin->scatter_atoms(lmp,(char *)"x",1,3,x);
plugin->command(lmp,"run 1");
}
// extract force on single atom two different ways
/* extract force on single atom two different ways */
if (lammps == 1) {
double **f = (double **) plugin->extract_atom(lmp,"f");
printf("Force on 1 atom via extract_atom: %g\n",f[0][0]);
double *fx = (double *) plugin->extract_variable(lmp,"fx","all");
double *fx = (double *) plugin->extract_variable(lmp,"fx",(char *)"all");
printf("Force on 1 atom via extract_variable: %g\n",fx[0]);
plugin->free(fx);
}
/* use commands_string() and commands_list() to invoke more commands */
@ -160,7 +179,7 @@ int main(int narg, char **arg)
if (v) free(v);
if (type) free(type);
// close down LAMMPS
/* close down LAMMPS */
if (lammps == 1) {
plugin->close(lmp);

91
examples/COUPLE/simple/CMakeLists.txt
View File

@ -1,17 +1,88 @@
cmake_minimum_required(VERSION 3.10)
project(simple CXX)
# -*- CMake -*- file for simple examples using the LAMMPS library interface
set(LAMMPS_SRC_DIRECTORY "" CACHE PATH "Path for lammps source")
if(NOT LAMMPS_SRC_DIRECTORY STREQUAL "" AND EXISTS ${LAMMPS_SRC_DIRECTORY}/cmake/CMakeLists.txt)
option(BUILD_LIB "Build LAMMPS library" ON)
add_subdirectory(${LAMMPS_SRC_DIRECTORY}/cmake lammps)
else()
cmake_minimum_required(VERSION 3.16)
# enforce out-of-source build
if(${CMAKE_SOURCE_DIR} STREQUAL ${CMAKE_BINARY_DIR})
message(FATAL_ERROR "In-source builds are not allowed. You must create and use a build directory. "
"Please remove CMakeCache.txt and CMakeFiles first.")
endif()
project(couple-simple VERSION 1.0 LANGUAGES C CXX)
# by default, install into $HOME/.local (not /usr/local),
# so that no root access (and sudo) is needed
if(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)
set(CMAKE_INSTALL_PREFIX "$ENV{HOME}/.local" CACHE PATH "Default install path" FORCE)
endif()
# ugly hacks for MSVC which by default always reports an old C++ standard in the __cplusplus macro
# and prints lots of pointless warnings about "unsafe" functions
if(MSVC)
if(CMAKE_C_COMPILER_ID STREQUAL "MSVC")
add_compile_options(/EHsc)
endif()
add_compile_definitions(_CRT_SECURE_NO_WARNINGS)
endif()
find_package(MPI QUIET)
# do not include the (obsolete) MPI C++ bindings which makes
# for leaner object files and avoids namespace conflicts
set(MPI_CXX_SKIP_MPICXX TRUE)
##########################
# build within LAMMPS build system
if(NOT LAMMPS_SOURCE_DIR)
find_package(LAMMPS REQUIRED)
endif()
add_executable(simpleCC simple.cpp)
target_link_libraries(simpleCC LAMMPS::lammps)
target_link_libraries(simpleCC PRIVATE LAMMPS::lammps MPI::MPI_CXX)
enable_language(C)
add_executable(simpleC simple.c)
target_link_libraries(simpleC LAMMPS::lammps)
target_link_libraries(simpleC PRIVATE LAMMPS::lammps MPI::MPI_C)
if(LAMMPS_SOURCE_DIR)
include(CheckGeneratorSupport)
if(NOT CMAKE_GENERATOR_SUPPORT_FORTRAN)
message(STATUS "Skipping Test for the LAMMPS Fortran Module Coupling: no Fortran support in build tool")
return()
endif()
include(CheckLanguage)
check_language(Fortran)
if(CMAKE_Fortran_COMPILER)
enable_language(Fortran)
# need to check for MPI again to include Fortran components, since Fortran wasn't enabled before
find_package(MPI QUIET COMPONENTS Fortran)
if(NOT (MPI_Fortran_FOUND AND MPI_Fortran_HAVE_F90_MODULE))
message(STATUS "Insufficient MPI Fortran support. Skipping building simpleF90")
return()
endif()
# GNU Fortran 4.8.x on RHEL/CentOS 7.x is not sufficient to compile the Fortran module.
# GNU Fortran 7.x on Ubuntu 18.04LTS fails as well.
# Work around flang being detected as GNU
get_filename_component(_tmp_fc ${CMAKE_Fortran_COMPILER} NAME)
if((CMAKE_Fortran_COMPILER_ID STREQUAL "GNU") AND (CMAKE_Fortran_COMPILER_VERSION VERSION_LESS 9.0) AND NOT (_tmp_fc STREQUAL "flang"))
message(STATUS "Need GNU Fortran compiler version 9.x or later for LAMMPS Fortran module")
return()
endif()
get_filename_component(LAMMPS_FORTRAN_MODULE ${LAMMPS_SOURCE_DIR}/../fortran/lammps.f90 ABSOLUTE)
add_executable(simpleF90 ${LAMMPS_FORTRAN_MODULE} simple.f90)
target_link_libraries(simpleF90 PRIVATE MPI::MPI_Fortran LAMMPS::lammps)
get_filename_component(_tmp_fc ${CMAKE_Fortran_COMPILER} NAME)
if (_tmp_fc STREQUAL "flang")
target_link_libraries(simpleF90 PRIVATE gfortran)
endif()
include(CheckFortranCompilerFlag)
check_fortran_compiler_flag(-fallow-argument-mismatch HAS_MISMATCH)
if(HAS_MISMATCH)
target_compile_options(simpleF90 PRIVATE -fallow-argument-mismatch)
endif()
endif()
endif()

13
examples/COUPLE/simple/README
View File

@ -8,9 +8,8 @@ code to perform a coupled calculation.
simple.cpp is the C++ driver
simple.c is the C driver
simple.f90 is the Fortran driver using the new Fortran module
simple_f77.f90 is the Fortran driver using the legacy Fortran wrapper
The 4 codes do the same thing, so you can compare them to see how to
The 3 codes do the same thing, so you can compare them to see how to
drive LAMMPS from each language. See python/example/simple.py
to do something similar from Python. The new Fortran driver requires
a Fortran module that uses the Fortran 03 ISO_C_BINDING module to
@ -45,12 +44,7 @@ the fortran directory:
mpifort -L${HOME}/lammps/src ../../../fortran/lammps.f90 simple.f90 -llammps -o simpleF
This builds the legacy Fortran wrapper and driver with the LAMMPS library
using the mpifort (Fortran) MPI compiler wrapper (assuming GNU gfortran).
mpifort -std=legacy -L${HOME}/lammps/src ../fortran/libfwrapper.c simple.f90 -llammps -o simpleF77
You then run simpleCC, simpleC, simpleF, or simpleF77 on a parallel machine
You then run simpleCC, simpleC, or simpleF on a parallel machine
on some number of processors Q with 2 arguments:
% mpirun -np Q simpleCC P in.lj
@ -72,8 +66,7 @@ of LAMMPS. You could add any functions you wish to this file to
manipulate LAMMPS data however you wish.
The Fortran driver is using the Fortran 03 module which uses a derived
type with type bound subroutines. Only a small subset of the C library
functions are currently accessible through the Fortran module.
type with type bound subroutines.
The C++ driver does the same thing, except that it instantiates LAMMPS
as an object first. Some of the functions in src/library.cpp can be

7
examples/COUPLE/simple/simple.c
View File

@ -1,7 +1,7 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
https://www.lammps.org/, Sandia National Laboratories
LAMMPS development team: developers@lammps.org
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
@ -35,7 +35,7 @@ int main(int narg, char **arg)
MPI_Init(&narg,&arg);
if (narg != 3) {
printf("Syntax: simpleC P in.lammps\n");
printf("Syntax: %s P in.lammps\n", arg[0]);
exit(1);
}
@ -121,6 +121,7 @@ int main(int narg, char **arg)
double *fx = (double *) lammps_extract_variable(lmp,"fx","all");
printf("Force on 1 atom via extract_variable: %g\n",fx[0]);
lammps_free(fx);
}
/* use commands_string() and commands_list() to invoke more commands */

30
examples/COUPLE/simple/simple.cpp
View File

@ -1,7 +1,7 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
https://www.lammps.org/, Sandia National Laboratories
LAMMPS development team: developers@lammps.org
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
@ -41,7 +41,7 @@ int main(int narg, char **arg)
MPI_Init(&narg,&arg);
if (narg != 3) {
printf("Syntax: simpleCC P in.lammps\n");
printf("Syntax: %s P in.lammps\n", arg[0]);
exit(1);
}
@ -67,7 +67,7 @@ int main(int narg, char **arg)
FILE *fp;
if (me == 0) {
fp = fopen(arg[2],"r");
if (fp == NULL) {
if (fp == nullptr) {
printf("ERROR: Could not open LAMMPS input script\n");
MPI_Abort(MPI_COMM_WORLD,1);
}
@ -78,14 +78,14 @@ int main(int narg, char **arg)
// (could just send it to proc 0 of comm_lammps and let it Bcast)
// all LAMMPS procs call input->one() on the line
LAMMPS *lmp = NULL;
if (lammps == 1) lmp = new LAMMPS(0,NULL,comm_lammps);
LAMMPS *lmp = nullptr;
if (lammps == 1) lmp = new LAMMPS(0,nullptr,comm_lammps);
int n;
char line[1024];
while (1) {
while (true) {
if (me == 0) {
if (fgets(line,1024,fp) == NULL) n = 0;
if (fgets(line,1024,fp) == nullptr) n = 0;
else n = strlen(line) + 1;
if (n == 0) fclose(fp);
}
@ -101,8 +101,8 @@ int main(int narg, char **arg)
// put coords back into LAMMPS
// run a single step with changed coords
double *x = NULL;
double *v = NULL;
double *x = nullptr;
double *v = nullptr;
if (lammps == 1) {
lmp->input->one("run 10");
@ -125,12 +125,12 @@ int main(int narg, char **arg)
// extract force on single atom two different ways
if (lammps == 1) {
double **f = (double **) lammps_extract_atom(lmp,(char *) "f");
double **f = (double **) lammps_extract_atom(lmp, "f");
printf("Force on 1 atom via extract_atom: %g\n",f[0][0]);
double *fx = (double *)
lammps_extract_variable(lmp,(char *) "fx",(char *) "all");
double *fx = (double *) lammps_extract_variable(lmp, "fx", "all");
printf("Force on 1 atom via extract_variable: %g\n",fx[0]);
lammps_free(fx);
}
// use commands_string() and commands_list() to invoke more commands
@ -147,7 +147,7 @@ int main(int narg, char **arg)
// create_atoms() to create new ones with old coords, vels
// initial thermo should be same as step 20
int *type = NULL;
int *type = nullptr;
if (lammps == 1) {
int natoms = static_cast<int> (lmp->atom->natoms);
@ -155,7 +155,7 @@ int main(int narg, char **arg)
for (int i = 0; i < natoms; i++) type[i] = 1;
lmp->input->one("delete_atoms group all");
lammps_create_atoms(lmp,natoms,NULL,type,x,v,NULL,0);
lammps_create_atoms(lmp,natoms,nullptr,type,x,v,nullptr,0);
lmp->input->one("run 10");
}

13
examples/COUPLE/simple/simple.f90
View File

@ -1,6 +1,6 @@
! LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
! www.cs.sandia.gov/~sjplimp/lammps.html
! Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
! https://www.lammps.org/, Sandia National Laboratories
! LAMMPS development team: developers@lammps.org
!
! Copyright (2003) Sandia Corporation. Under the terms of Contract
! DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
@ -18,8 +18,8 @@
! See README for compilation instructions
PROGRAM f_driver
USE mpi
USE liblammps
USE mpi
IMPLICIT NONE
INTEGER, PARAMETER :: fp=20
@ -30,7 +30,7 @@ PROGRAM f_driver
REAL (kind=8), ALLOCATABLE :: x(:)
REAL (kind=8), PARAMETER :: epsilon=0.1
CHARACTER (len=64) :: arg
CHARACTER (len=1024) :: arg
CHARACTER (len=1024) :: line
! setup MPI and various communicators
@ -129,7 +129,10 @@ PROGRAM f_driver
! free LAMMPS object
IF (color == 1) CALL lmp%close()
IF (color == 1) THEN
CALL lmp%CLOSE()
CALL mpi_comm_free(comm_lammps,ierr)
END IF
! close down MPI

125
examples/COUPLE/simple/simple_f77.f90
View File

@ -1,125 +0,0 @@
! LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
! www.cs.sandia.gov/~sjplimp/lammps.html
! Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
!
! Copyright (2003) Sandia Corporation. Under the terms of Contract
! DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
! certain rights in this software. This software is distributed under
! the GNU General Public License.
!
! See the README file in the top-level LAMMPS directory.
! f_driver = simple example of how an umbrella program
! can invoke LAMMPS as a library on some subset of procs
! Syntax: simpleF P in.lammps
! P = # of procs to run LAMMPS on
! must be <= # of procs the driver code itself runs on
! in.lammps = LAMMPS input script
! See README for compilation instructions
PROGRAM f_driver
IMPLICIT NONE
INCLUDE 'mpif.h'
INTEGER, PARAMETER :: fp=20
INTEGER :: n, narg, ierr, me, nprocs, natoms
INTEGER :: lammps, nprocs_lammps, comm_lammps
INTEGER (kind=8) :: ptr
REAL (kind=8), ALLOCATABLE :: x(:)
REAL (kind=8), PARAMETER :: epsilon=0.1
CHARACTER (len=64) :: arg
CHARACTER (len=1024) :: line
! setup MPI and various communicators
! driver runs on all procs in MPI_COMM_WORLD
! comm_lammps only has 1st P procs (could be all or any subset)
CALL mpi_init(ierr)
narg = command_argument_count()
IF (narg /= 2) THEN
PRINT *, 'Syntax: simpleF P in.lammps'
CALL mpi_abort(MPI_COMM_WORLD,1,ierr)
END IF
CALL mpi_comm_rank(MPI_COMM_WORLD,me,ierr);
CALL mpi_comm_size(MPI_COMM_WORLD,nprocs,ierr);
CALL get_command_argument(1,arg)
READ (arg,'(I10)') nprocs_lammps
IF (nprocs_lammps > nprocs) THEN
IF (me == 0) THEN
PRINT *, 'ERROR: LAMMPS cannot use more procs than available'
CALL mpi_abort(MPI_COMM_WORLD,2,ierr)
END IF
END IF
lammps = 0
IF (me < nprocs_lammps) THEN
lammps = 1
ELSE
lammps = MPI_UNDEFINED
END IF
CALL mpi_comm_split(MPI_COMM_WORLD,lammps,0,comm_lammps,ierr)
! open LAMMPS input script on rank zero
CALL get_command_argument(2,arg)
OPEN(UNIT=fp, FILE=arg, ACTION='READ', STATUS='OLD', IOSTAT=ierr)
IF (ierr /= 0) THEN
PRINT *, 'ERROR: Could not open LAMMPS input script'
CALL mpi_abort(MPI_COMM_WORLD,3,ierr);
END IF
! run the input script thru LAMMPS one line at a time until end-of-file
! driver proc 0 reads a line, Bcasts it to all procs
! (could just send it to proc 0 of comm_lammps and let it Bcast)
! all LAMMPS procs call lammps_command() on the line */
IF (lammps == 1) CALL lammps_open(comm_lammps,ptr)
n = 0
DO
IF (me == 0) THEN
READ (UNIT=fp, FMT='(A)', IOSTAT=ierr) line
n = 0
IF (ierr == 0) THEN
n = LEN(TRIM(line))
IF (n == 0 ) THEN
line = ' '
n = 1
END IF
END IF
END IF
CALL mpi_bcast(n,1,MPI_INTEGER,0,MPI_COMM_WORLD,ierr)
IF (n == 0) EXIT
CALL mpi_bcast(line,n,MPI_CHARACTER,0,MPI_COMM_WORLD,ierr)
IF (lammps == 1) CALL lammps_command(ptr,line,n)
END DO
CLOSE(UNIT=fp)
! run 10 more steps followed by a single step */
IF (lammps == 1) THEN
CALL lammps_command(ptr,'run 10',6)
CALL lammps_get_natoms(ptr,natoms)
print*,'natoms=',natoms
CALL lammps_command(ptr,'run 1',5);
END IF
! free LAMMPS object
IF (lammps == 1) CALL lammps_close(ptr);
! close down MPI
CALL mpi_finalize(ierr)
END PROGRAM f_driver

1
examples/ELASTIC_T/BORN_MATRIX/Argon/Analytical/compute_born.py
View File

@ -1,7 +1,6 @@
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
import sys
import numpy as np
def reduce_Born(Cf):

1
examples/ELASTIC_T/BORN_MATRIX/Argon/Numdiff/compute_born.py
View File

@ -1,7 +1,6 @@
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
import sys
import numpy as np
def reduce_Born(Cf):

2
examples/ELASTIC_T/BORN_MATRIX/Silicon/elastic_utils.py
View File

@ -1,5 +1,5 @@
import numpy as np
from lammps import lammps, LAMMPS_INT, LMP_STYLE_GLOBAL, LMP_VAR_EQUAL, LMP_VAR_ATOM
from lammps import lammps, LMP_VAR_EQUAL
# method for rotating elastic constants

1
examples/PACKAGES/alchemy/AlCu.eam.alloy Symbolic link
View File

@ -0,0 +1 @@
../../../potentials/AlCu.eam.alloy

62
examples/PACKAGES/alchemy/h2o.mol Normal file
View File

@ -0,0 +1,62 @@
# Water molecule. SPC/E model.
3 atoms
2 bonds
1 angles
Coords
1 1.12456 0.09298 1.27452
2 1.53683 0.75606 1.89928
3 0.49482 0.56390 0.65678
Types
1 1
2 2
3 2
Charges
1 -0.8472
2 0.4236
3 0.4236
Bonds
1 1 1 2
2 1 1 3
Angles
1 1 2 1 3
Shake Flags
1 1
2 1
3 1
Shake Atoms
1 1 2 3
2 1 2 3
3 1 2 3
Shake Bond Types
1 1 1 1
2 1 1 1
3 1 1 1
Special Bond Counts
1 2 0 0
2 1 1 0
3 1 1 0
Special Bonds
1 2 3
2 1 3
3 1 2

45
examples/PACKAGES/alchemy/in.alloy Normal file
View File

@ -0,0 +1,45 @@
# Example for an alchemical transformation simulation of pure copper into an aluminium bronze
# set up different names for two partitions
variable name world pure alloy
# create pure copper system
units metal
lattice fcc 3.75
region box block 0 6 0 6 0 6
create_box 2 box
timestep 0.002
create_atoms 1 box
displace_atoms all random 0.3 0.3 0.3 57845645
pair_style eam/alloy
pair_coeff * * AlCu.eam.alloy Cu Al
# replace 5% of copper with aluminium on the second partition only
if "${name} == alloy" then &
"set type 1 type/fraction 2 0.05 6745234"
# define ramp variable to combine the two different partitions
if "${name} == pure" then &
"variable ramp equal ramp(1.0,0.0)" &
else &
"variable ramp equal ramp(0.0,1.0)"
velocity all create 5000.0 6567345
fix 1 all nvt temp 2500.0 500.0 0.002
fix 2 all alchemy v_ramp
compute pressure all pressure/alchemy 2
# only need to output a dump file from one partition
#if "${name} == alloy" then &
# "dump 1 all custom 100 ${name}.lammpstrj id type element x y z" &
# "dump_modify 1 element Cu Al"
thermo_style custom step temp press etotal density pe ke f_2 f_2[3]
thermo_modify colname f_2 lambda colname f_2[3] EPot_mixed
thermo_modify press pressure
thermo 100
run 10000 post no

100
examples/PACKAGES/alchemy/in.twowater Normal file
View File

@ -0,0 +1,100 @@
# Example for an alchemical transformation of two water molecules into a hydronium and hydroxyl ion
# WARNING: This input is intended for demonstrating the method only,
# the force field parameters are mostly made up and NOT suitable for production simulations.
# set up different names for two partitions
variable name world twowater twoions
units real
atom_style full
atom_modify map array
region box block -5 5 -5 5 -5 5
boundary p p p
create_box 2 box bond/types 2 angle/types 2 &
extra/bond/per/atom 3 extra/angle/per/atom 3 extra/special/per/atom 3
mass 1 15.9994
mass 2 1.008
pair_style lj/cut/coul/cut 10.0
pair_coeff 1 1 0.1553 3.166
pair_coeff 1 2 0.0 1.0
pair_coeff 2 2 0.0 1.0
bond_style harmonic
bond_coeff * 1000.0 1.0
angle_style harmonic
angle_coeff * 100.0 109.47
molecule water h2o.mol
# create the two molecules we want to transform ...
create_atoms 0 single -2.0 0.0 0.0 mol water 453624
create_atoms 0 single 2.0 0.0 0.0 mol water 767353
# ... and put them in a group
group transform id 1:6
# now fill the rest of the box with more water
create_atoms 0 random 32 34564 NULL mol water 25367 overlap 1.33
# change topology and settings for the two states
# we cannot simply create a different topology directly or
# load a different data file because the order and position
# of all atoms must be maintained across both replica
# we first have to remove all topology data in the transform group
delete_bonds transform bond 1
delete_bonds transform angle 1 remove
# then generate different topologies for the two partitions. select by name.
if "${name} == twowater" then &
"create_bonds single/bond 2 1 2" &
"create_bonds single/bond 2 1 3" &
"create_bonds single/bond 2 4 5" &
"create_bonds single/bond 2 4 6" &
"create_bonds single/angle 2 2 1 3" &
"create_bonds single/angle 2 5 4 6" &
else &
"create_bonds single/bond 2 1 2" &
"create_bonds single/bond 2 3 4" &
"create_bonds single/bond 2 4 5" &
"create_bonds single/bond 2 4 6" &
"create_bonds single/angle 2 3 4 5" &
"create_bonds single/angle 2 5 4 6" &
"create_bonds single/angle 2 3 4 6" &
"set atom 1 charge -1.1354" &
"set atom 2 charge 0.1354" &
"set atom 3 charge 0.56775" &
"set atom 4 charge -0.70305" &
"set atom 5*6 charge 0.56775"
velocity all create 300.0 5463576
timestep 0.2
# define ramp variable to combine the two different partitions
if "${name} == twowater" then &
"variable ramp equal ramp(1.0,0.0)" &
else &
"variable ramp equal ramp(0.0,1.0)"
# since the trajectory and forces are kept identical through fix alchemy,
# we can do fix npt simulations, but we must use the "mixed" pressure
fix integrate all npt temp 300 300 1.0 iso 1.0 1.0 10.0
fix transform all alchemy v_ramp
compute pressure all pressure/alchemy transform
fix_modify integrate press pressure
# only need to output a dump file from one partition
# if "${name} == twowater" then &
# "dump 1 all atom 100 ${name}.lammpstrj" &
# "dump_modify 1 sort id"
thermo_style custom step temp press etotal density pe ke f_transform f_transform[3]
thermo_modify colname f_transform lambda colname f_transform[3] EPot_mixed
thermo_modify press pressure
thermo 100
run 20000

13
examples/PACKAGES/alchemy/log.25Feb23.alloy.g++.4 Normal file
View File

@ -0,0 +1,13 @@
LAMMPS (8 Feb 2023)
Running on 2 partitions of processors
Starting alchemical transformation at 0%
Alchemical transformation progress: 10%
Alchemical transformation progress: 20%
Alchemical transformation progress: 30%
Alchemical transformation progress: 40%
Alchemical transformation progress: 50%
Alchemical transformation progress: 60%
Alchemical transformation progress: 70%
Alchemical transformation progress: 80%
Alchemical transformation progress: 90%
Alchemical transformation progress: 100%

169
examples/PACKAGES/alchemy/log.25Feb23.alloy.g++.4.0 Normal file
View File

@ -0,0 +1,169 @@
LAMMPS (8 Feb 2023)
Processor partition = 0
using 1 OpenMP thread(s) per MPI task
# Example for an alchemical transformation simulation of pure copper into an aluminium bronze
# set up different names for two partitions
variable name world pure alloy
# create pure copper system
units metal
lattice fcc 3.75
Lattice spacing in x,y,z = 3.75 3.75 3.75
region box block 0 6 0 6 0 6
create_box 2 box
Created orthogonal box = (0 0 0) to (22.5 22.5 22.5)
1 by 1 by 2 MPI processor grid
timestep 0.002
create_atoms 1 box
Created 864 atoms
using lattice units in orthogonal box = (0 0 0) to (22.5 22.5 22.5)
create_atoms CPU = 0.001 seconds
displace_atoms all random 0.3 0.3 0.3 57845645
Displacing atoms ...
pair_style eam/alloy
pair_coeff * * AlCu.eam.alloy Cu Al
Reading eam/alloy potential file AlCu.eam.alloy with DATE: 2008-10-01
# replace 5% of copper with aluminium on the second partition only
if "${name} == alloy" then "set type 1 type/fraction 2 0.05 6745234"
# define ramp variable to combine the two different partitions
if "${name} == pure" then "variable ramp equal ramp(1.0,0.0)" else "variable ramp equal ramp(0.0,1.0)"
variable ramp equal ramp(1.0,0.0)
velocity all create 5000.0 6567345
fix 1 all nvt temp 2500.0 500.0 0.002
fix 2 all alchemy v_ramp
compute pressure all pressure/alchemy 2
# only need to output a dump file from one partition
#if "${name} == alloy" then # "dump 1 all custom 100 ${name}.lammpstrj id type element x y z" # "dump_modify 1 element Cu Al"
thermo_style custom step temp press etotal density pe ke f_2 f_2[3]
thermo_modify colname f_2 lambda colname f_2[3] EPot_mixed
thermo_modify press pressure
thermo 100
run 10000 post no
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 8.6825
ghost atom cutoff = 8.6825
binsize = 4.34125, bins = 6 6 6
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair eam/alloy, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.474 | 3.474 | 3.474 Mbytes
Step Temp Press TotEng Density PotEng KinEng lambda EPot_mixed
0 5000 2135632.8 10911.637 8.0039334 10353.88 557.75753 1 10353.88
100 2424.8703 98461.445 -2402.724 8.0039334 -2673.222 270.49793 0.99 -2673.3837
200 2404.4922 111478.55 -2381.5114 8.0039334 -2649.7361 268.22473 0.98 -2650.057
300 2388.2899 109429.75 -2387.7985 8.0039334 -2654.2158 266.41733 0.97 -2654.7075
400 2377.6418 97114.07 -2409.7114 8.0039334 -2674.9409 265.22953 0.96 -2675.755
500 2371.5028 98285.746 -2408.3248 8.0039334 -2672.8695 264.54471 0.95 -2673.6895
600 2368.0363 101125.13 -2402.9816 8.0039334 -2667.1396 264.15802 0.94 -2668.238
700 2364.8386 96916.491 -2410.1795 8.0039334 -2673.9808 263.80131 0.93 -2675.3394
800 2361.5815 101050.97 -2404.7579 8.0039334 -2668.1958 263.43797 0.92 -2669.6797
900 2355.1085 95290.542 -2416.4508 8.0039334 -2679.1667 262.7159 0.91 -2681.0381
1000 2344.579 90348.199 -2430.3553 8.0039334 -2691.8966 261.54132 0.9 -2693.7969
1100 2328.7808 87089.44 -2435.1426 8.0039334 -2694.9216 259.779 0.89 -2696.9199
1200 2310.0924 89628.642 -2438.4943 8.0039334 -2696.1886 257.69429 0.88 -2698.4983
1300 2288.2762 92771.824 -2430.0042 8.0039334 -2685.2648 255.26065 0.87 -2687.6406
1400 2258.3028 83029.221 -2451.9432 8.0039334 -2703.8603 251.91707 0.86 -2706.638
1500 2226.5131 83386 -2452.9658 8.0039334 -2701.3367 248.37089 0.85 -2704.0915
1600 2192.5777 81801.467 -2460.6692 8.0039334 -2705.2546 244.58535 0.84 -2708.3304
1700 2158.7421 84933.294 -2456.2782 8.0039334 -2697.0891 240.81093 0.83 -2700.142
1800 2123.8912 76700.779 -2474.2534 8.0039334 -2711.1767 236.92327 0.82 -2714.6978
1900 2091.3912 82568.985 -2469.6316 8.0039334 -2702.9295 233.29783 0.81 -2706.5643
2000 2061.868 79024.983 -2476.3262 8.0039334 -2706.3307 230.00448 0.8 -2710.7
2100 2036.179 72408.502 -2493.6936 8.0039334 -2720.8324 227.13884 0.79 -2725.1617
2200 2014.0161 81172.694 -2479.0525 8.0039334 -2703.719 224.66652 0.78 -2708.4618
2300 1996.2707 78029.129 -2485.3835 8.0039334 -2708.0706 222.687 0.77 -2712.5894
2400 1982.6409 79691.571 -2483.2441 8.0039334 -2704.4107 221.16658 0.76 -2709.4434
2500 1971.6774 75015.359 -2493.8754 8.0039334 -2713.819 219.94358 0.75 -2719.4159
2600 1963.0369 74845.99 -2493.3203 8.0039334 -2712.3 218.97972 0.74 -2718.1619
2700 1955.2025 76756.042 -2491.6282 8.0039334 -2709.7339 218.10578 0.73 -2716.0963
2800 1947.4326 70627.84 -2507.5853 8.0039334 -2724.8243 217.23904 0.72 -2730.7999
2900 1939.4308 70852.114 -2508.8277 8.0039334 -2725.1742 216.34642 0.71 -2731.5024
3000 1929.3184 75867.616 -2497.0826 8.0039334 -2712.301 215.21837 0.7 -2718.4146
3100 1916.202 68984.855 -2517.8316 8.0039334 -2731.5868 213.75522 0.69 -2738.0966
3200 1901.363 73304.621 -2508.0281 8.0039334 -2720.128 212.09991 0.68 -2727.1933
3300 1881.196 69447.29 -2513.9782 8.0039334 -2723.8285 209.85024 0.67 -2730.768
3400 1856.1833 64973.868 -2526.8095 8.0039334 -2733.8695 207.06004 0.66 -2741.4173
3500 1829.7246 64688.566 -2528.8664 8.0039334 -2732.9749 204.10853 0.65 -2740.986
3600 1800.1245 56451.766 -2547.6377 8.0039334 -2748.4443 200.80659 0.64 -2756.4626
3700 1771.5886 68268.147 -2530.5906 8.0039334 -2728.214 197.62337 0.63 -2735.8618
3800 1740.3894 64187.24 -2539.0772 8.0039334 -2733.2202 194.14306 0.62 -2742.67
3900 1709.6971 61697.296 -2548.5651 8.0039334 -2739.2844 190.71928 0.61 -2748.648
4000 1680.6126 58960.336 -2557.3154 8.0039334 -2744.7902 187.47487 0.6 -2753.7317
4100 1653.386 49607.708 -2575.5217 8.0039334 -2759.9594 184.43769 0.59 -2769.1633
4200 1628.5806 59615.376 -2562.3155 8.0039334 -2743.9861 181.67062 0.58 -2753.41
4300 1605.7638 57213.496 -2568.9241 8.0039334 -2748.0495 179.12536 0.57 -2758.0401
4400 1586.3539 57319.854 -2567.3656 8.0039334 -2744.3258 176.96016 0.56 -2754.0451
4500 1569.1762 51130.713 -2581.1996 8.0039334 -2756.2435 175.04397 0.55 -2767.0321
4600 1554.2279 51209.179 -2582.5415 8.0039334 -2755.918 173.37646 0.54 -2767.2662
4700 1541.2064 51391.73 -2584.9958 8.0039334 -2756.9197 171.92389 0.53 -2768.7565
4800 1529.3566 48164.466 -2590.6042 8.0039334 -2761.2062 170.60203 0.52 -2773.7243
4900 1517.8359 47270.397 -2595.8724 8.0039334 -2765.1893 169.31688 0.51 -2777.023
5000 1506.2157 46127.507 -2595.6789 8.0039334 -2763.6995 168.02063 0.5 -2777.2298
5100 1494.4675 45092.69 -2600.075 8.0039334 -2766.7851 166.7101 0.49 -2779.7181
5200 1480.2051 41485.775 -2607.0151 8.0039334 -2772.1342 165.1191 0.48 -2785.5483
5300 1465.1748 39849.775 -2612.3292 8.0039334 -2775.7716 163.44246 0.47 -2788.9493
5400 1447.9857 39330.898 -2615.0485 8.0039334 -2776.5735 161.52498 0.46 -2790.3996
5500 1427.9752 35674.647 -2624.4226 8.0039334 -2783.7154 159.29278 0.45 -2797.922
5600 1406.1138 33960.907 -2630.1163 8.0039334 -2786.9704 156.85411 0.44 -2801.8887
5700 1383.2834 39122.559 -2621.0951 8.0039334 -2775.4025 154.30734 0.43 -2790.3487
5800 1357.4953 34996.372 -2632.2759 8.0039334 -2783.7065 151.43064 0.42 -2798.8306
5900 1331.345 30380.598 -2640.9488 8.0039334 -2789.4624 148.51354 0.41 -2804.9873
6000 1304.5621 26910.214 -2652.7787 8.0039334 -2798.3046 145.52587 0.4 -2814.8623
6100 1278.2361 34273.343 -2642.9208 8.0039334 -2785.51 142.58917 0.39 -2801.9949
6200 1251.7315 29640.216 -2651.6543 8.0039334 -2791.2868 139.63253 0.38 -2807.555
6300 1226.3243 25302.881 -2660.8448 8.0039334 -2797.6431 136.79832 0.37 -2815.3412
6400 1202.0501 23978.218 -2668.9812 8.0039334 -2803.0717 134.09049 0.36 -2820.0498
6500 1178.656 25315.547 -2668.8266 8.0039334 -2800.3074 131.48085 0.35 -2817.3114
6600 1156.9362 22676.36 -2673.1256 8.0039334 -2802.1835 129.05797 0.34 -2819.6239
6700 1163.8953 22497.41 -2674.4164 8.0039334 -2804.2506 129.83427 0.33 -2821.3556
6800 1123.3867 18193.925 -2685.3997 8.0039334 -2810.7152 125.31548 0.32 -2830.2267
6900 1147.6164 19451.295 -2682.5112 8.0039334 -2810.5295 128.01834 0.31 -2830.1189
7000 1096.0437 16757.031 -2689.5567 8.0039334 -2811.822 122.26532 0.3 -2832.475
7100 1065.1232 11734.429 -2703.0123 8.0039334 -2821.8284 118.8161 0.29 -2841.8886
7200 1048.459 15187.579 -2697.6953 8.0039334 -2814.6525 116.95718 0.28 -2834.2885
7300 1067.9311 13697.721 -2698.4027 8.0039334 -2817.532 119.12932 0.27 -2838.9073
7400 998.4963 13330.213 -2707.915 8.0039334 -2819.2987 111.38377 0.26 -2840.2979
7500 1023.6105 7070.7227 -2712.3293 8.0039334 -2826.5146 114.18529 0.25 -2848.8706
7600 970.8256 7694.074 -2717.03 8.0039334 -2825.3271 108.29706 0.24 -2848.0154
7700 966.64807 2336.6244 -2727.1914 8.0039334 -2835.0224 107.83105 0.23 -2858.6468
7800 961.41051 564.58952 -2731.2826 8.0039334 -2838.5294 107.24679 0.22 -2862.4362
7900 880.63112 3569.7496 -2734.8614 8.0039334 -2833.0971 98.235727 0.21 -2857.2329
8000 904.4189 -883.03123 -2738.386 8.0039334 -2839.2753 100.88929 0.2 -2864.1778
8100 901.36129 -977.71992 -2739.797 8.0039334 -2840.3452 100.54821 0.19 -2864.7239
8200 834.53102 2535.4088 -2741.7378 8.0039334 -2834.831 93.093191 0.18 -2859.9007
8300 830.12299 -6039.909 -2755.2151 8.0039334 -2847.8166 92.601469 0.17 -2873.9613
8400 807.63492 -5386.015 -2755.7433 8.0039334 -2845.8362 90.092891 0.16 -2872.8494
8500 792.64609 -6372.4363 -2758.8515 8.0039334 -2847.2724 88.420864 0.15 -2874.8424
8600 758.58937 -11610.225 -2770.2002 8.0039334 -2854.822 84.621786 0.14 -2882.1413
8700 758.23023 -10178.597 -2769.9169 8.0039334 -2854.4986 84.581724 0.13 -2881.6683
8800 743.6008 -12026.268 -2776.0268 8.0039334 -2858.9766 82.949788 0.12 -2886.1335
8900 734.90694 -17472.954 -2783.3532 8.0039334 -2865.3332 81.979975 0.11 -2893.7244
9000 707.10989 -17006.609 -2785.8037 8.0039334 -2864.6829 78.879173 0.1 -2893.2911
9100 695.13334 -20282.325 -2793.2101 8.0039334 -2870.7532 77.543171 0.09 -2899.891
9200 642.26078 -20368.748 -2798.1031 8.0039334 -2869.7483 71.645157 0.08 -2899.7706
9300 641.79203 -21031.839 -2798.6175 8.0039334 -2870.2104 71.592866 0.07 -2901.0899
9400 640.84125 -20243.066 -2799.2216 8.0039334 -2870.7084 71.486807 0.06 -2901.4655
9500 609.96498 -23936.746 -2809.3896 8.0039334 -2877.4321 68.042512 0.05 -2908.2797
9600 574.1911 -26956.034 -2817.6178 8.0039334 -2881.6696 64.051882 0.04 -2912.6742
9700 567.47641 -28321.949 -2818.8602 8.0039334 -2882.163 63.302848 0.03 -2914.4223
9800 520.37758 -31000.6 -2828.0252 8.0039334 -2886.0741 58.048903 0.02 -2918.4921
9900 506.49368 -32223.744 -2830.1705 8.0039334 -2886.6706 56.500132 0.01 -2920.4741
10000 507.13597 -33930.476 -2834.3236 8.0039334 -2890.8954 56.571781 0 -2924.5423
Loop time of 17.7279 on 2 procs for 10000 steps with 864 atoms
Total wall time: 0:00:17

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examples/PACKAGES/alchemy/log.25Feb23.alloy.g++.4.1 Normal file
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LAMMPS (8 Feb 2023)
Processor partition = 1
using 1 OpenMP thread(s) per MPI task
# Example for an alchemical transformation simulation of pure copper into an aluminium bronze
# set up different names for two partitions
variable name world pure alloy
# create pure copper system
units metal
lattice fcc 3.75
Lattice spacing in x,y,z = 3.75 3.75 3.75
region box block 0 6 0 6 0 6
create_box 2 box
Created orthogonal box = (0 0 0) to (22.5 22.5 22.5)
1 by 1 by 2 MPI processor grid
timestep 0.002
create_atoms 1 box
Created 864 atoms
using lattice units in orthogonal box = (0 0 0) to (22.5 22.5 22.5)
create_atoms CPU = 0.000 seconds
displace_atoms all random 0.3 0.3 0.3 57845645
Displacing atoms ...
pair_style eam/alloy
pair_coeff * * AlCu.eam.alloy Cu Al
Reading eam/alloy potential file AlCu.eam.alloy with DATE: 2008-10-01
# replace 5% of copper with aluminium on the second partition only
if "${name} == alloy" then "set type 1 type/fraction 2 0.05 6745234"
set type 1 type/fraction 2 0.05 6745234
Setting atom values ...
37 settings made for type/fraction
# define ramp variable to combine the two different partitions
if "${name} == pure" then "variable ramp equal ramp(1.0,0.0)" else "variable ramp equal ramp(0.0,1.0)"
variable ramp equal ramp(0.0,1.0)
velocity all create 5000.0 6567345
fix 1 all nvt temp 2500.0 500.0 0.002
fix 2 all alchemy v_ramp
compute pressure all pressure/alchemy 2
# only need to output a dump file from one partition
#if "${name} == alloy" then # "dump 1 all custom 100 ${name}.lammpstrj id type element x y z" # "dump_modify 1 element Cu Al"
thermo_style custom step temp press etotal density pe ke f_2 f_2[3]
thermo_modify colname f_2 lambda colname f_2[3] EPot_mixed
thermo_modify press pressure
thermo 100
run 10000 post no
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 8.6825
ghost atom cutoff = 8.6825
binsize = 4.34125, bins = 6 6 6
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair eam/alloy, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.474 | 3.474 | 3.474 Mbytes
Step Temp Press TotEng Density PotEng KinEng lambda EPot_mixed
0 5000 2135632.8 11134.401 7.8067107 10576.643 557.75753 0 10353.88
100 2502.4638 98461.445 -2410.2394 7.8067107 -2689.393 279.1536 0.01 -2673.3837
200 2471.2133 111478.55 -2390.1144 7.8067107 -2665.7819 275.66756 0.02 -2650.057
300 2442.869 109429.75 -2398.101 7.8067107 -2670.6067 272.50571 0.03 -2654.7075
400 2420.4514 97114.07 -2425.2882 7.8067107 -2695.2932 270.005 0.04 -2675.755
500 2403.3496 98285.746 -2421.1707 7.8067107 -2689.268 268.09727 0.05 -2673.6895
600 2388.6644 101125.13 -2418.9873 7.8067107 -2685.4464 266.45911 0.06 -2668.238
700 2372.4091 96916.491 -2428.7444 7.8067107 -2693.3902 264.64581 0.07 -2675.3394
800 2356.5786 101050.97 -2423.8648 7.8067107 -2686.7446 262.87989 0.08 -2669.6797
900 2337.3256 95290.542 -2439.2282 7.8067107 -2699.9604 260.73219 0.09 -2681.0381
1000 2314.6552 90348.199 -2452.6965 7.8067107 -2710.8998 258.20327 0.1 -2693.7969
1100 2288.9862 87089.44 -2457.7481 7.8067107 -2713.088 255.33986 0.11 -2696.9199
1200 2263.1553 89628.642 -2462.9772 7.8067107 -2715.4356 252.45838 0.12 -2698.4983
1300 2238.1696 92771.824 -2453.8691 7.8067107 -2703.5403 249.67118 0.13 -2687.6406
1400 2209.3333 83029.221 -2477.2462 7.8067107 -2723.7006 246.45446 0.14 -2706.638
1500 2181.9468 83386 -2476.3027 7.8067107 -2719.7022 243.39945 0.15 -2704.0915
1600 2156.3929 81801.467 -2483.9294 7.8067107 -2724.4783 240.54887 0.16 -2708.3304
1700 2133.221 84933.294 -2477.0832 7.8067107 -2715.0473 237.96401 0.17 -2700.142
1800 2110.4496 76700.779 -2495.3147 7.8067107 -2730.7386 235.42383 0.18 -2714.6978
1900 2091.8774 82568.985 -2488.7082 7.8067107 -2722.0603 233.35207 0.19 -2706.5643
2000 2074.8972 79024.983 -2496.7194 7.8067107 -2728.1773 231.45791 0.2 -2710.7
2100 2059.7023 72408.502 -2511.6849 7.8067107 -2741.4478 229.76289 0.21 -2725.1617
2200 2046.5649 81172.694 -2496.9796 7.8067107 -2725.277 228.2974 0.22 -2708.4618
2300 2033.9024 78029.129 -2500.8329 7.8067107 -2727.7178 226.88488 0.23 -2712.5894
2400 2022.0535 79691.571 -2499.8173 7.8067107 -2725.3804 225.56311 0.24 -2709.4434
2500 2008.7841 75015.359 -2512.1238 7.8067107 -2736.2067 224.08289 0.25 -2719.4159
2600 1995.175 74845.99 -2512.2807 7.8067107 -2734.8455 222.56477 0.26 -2718.1619
2700 1979.2542 76756.042 -2512.5095 7.8067107 -2733.2983 220.78879 0.27 -2716.0963
2800 1961.2518 70627.84 -2527.3853 7.8067107 -2746.1659 218.78059 0.28 -2730.7999
2900 1942.4706 70852.114 -2530.3101 7.8067107 -2746.9956 216.68552 0.29 -2731.5024
3000 1922.0973 75867.616 -2518.2668 7.8067107 -2732.6796 214.41284 0.3 -2718.4146
3100 1898.9538 68984.855 -2540.7552 7.8067107 -2752.5863 211.83116 0.31 -2738.0966
3200 1874.9107 73304.621 -2533.0578 7.8067107 -2742.2069 209.14911 0.32 -2727.1933
3300 1848.9824 69447.29 -2538.6006 7.8067107 -2744.8574 206.25677 0.33 -2730.768
3400 1821.4108 64973.868 -2552.8877 7.8067107 -2756.0688 203.18111 0.34 -2741.4173
3500 1795.4926 64688.566 -2555.5739 7.8067107 -2755.8638 200.2899 0.35 -2740.986
3600 1769.4009 56451.766 -2573.338 7.8067107 -2770.7174 197.37934 0.36 -2756.4626
3700 1745.5646 68268.147 -2554.1634 7.8067107 -2748.8838 194.72036 0.37 -2735.8618
3800 1721.4956 64187.24 -2566.0526 7.8067107 -2758.088 192.03542 0.38 -2742.67
3900 1699.517 61697.296 -2573.7098 7.8067107 -2763.2935 189.58368 0.39 -2748.648
4000 1680.2819 58960.336 -2579.7058 7.8067107 -2767.1438 187.43798 0.4 -2753.7317
4100 1662.2079 49607.708 -2596.9862 7.8067107 -2782.408 185.42179 0.41 -2769.1633
4200 1645.509 59615.376 -2582.865 7.8067107 -2766.424 183.55901 0.42 -2753.41
4300 1628.9336 57213.496 -2589.5734 7.8067107 -2771.2834 181.71 0.43 -2758.0401
4400 1614.2369 57319.854 -2586.3446 7.8067107 -2766.4151 180.07055 0.44 -2754.0451
4500 1598.6946 51130.713 -2601.8813 7.8067107 -2780.2181 178.33679 0.45 -2767.0321
4600 1583.2816 51209.179 -2603.9706 7.8067107 -2780.5881 176.61745 0.46 -2767.2662
4700 1567.3743 51391.73 -2607.2614 7.8067107 -2782.1044 174.84296 0.47 -2768.7565
4800 1550.9245 48164.466 -2614.2775 7.8067107 -2787.2854 173.00797 0.48 -2773.7243
4900 1532.697 47270.397 -2618.365 7.8067107 -2789.3397 170.97466 0.49 -2777.023
5000 1513.7604 46127.507 -2621.8979 7.8067107 -2790.7601 168.86225 0.5 -2777.2298
5100 1494.431 45092.69 -2625.438 7.8067107 -2792.144 166.70602 0.51 -2779.7181
5200 1472.5263 41485.775 -2633.6681 7.8067107 -2797.9306 164.26252 0.52 -2785.5483
5300 1450.7978 39849.775 -2638.7965 7.8067107 -2800.6352 161.83868 0.53 -2788.9493
5400 1428.063 39330.898 -2642.8749 7.8067107 -2802.1774 159.30258 0.54 -2790.3996
5500 1404.4139 35674.647 -2652.8811 7.8067107 -2809.5456 156.66449 0.55 -2797.922
5600 1380.8619 33960.907 -2659.5731 7.8067107 -2813.6103 154.03722 0.56 -2801.8887
5700 1357.9957 39122.559 -2650.1374 7.8067107 -2801.6239 151.48646 0.57 -2790.3487
5800 1334.8385 34996.372 -2660.8794 7.8067107 -2809.7826 148.90324 0.58 -2798.8306
5900 1312.6203 30380.598 -2669.3511 7.8067107 -2815.7758 146.42476 0.59 -2804.9873
6000 1290.7337 26910.214 -2681.9175 7.8067107 -2825.9008 143.98328 0.6 -2814.8623
6100 1269.6552 34273.343 -2670.9025 7.8067107 -2812.5345 141.63195 0.61 -2801.9949
6200 1249.4502 29640.216 -2678.1477 7.8067107 -2817.5258 139.37805 0.62 -2807.555
6300 1229.8377 25302.881 -2688.545 7.8067107 -2825.7352 137.19025 0.63 -2815.3412
6400 1211.0142 23978.218 -2694.5096 7.8067107 -2829.6 135.09045 0.64 -2820.0498
6500 1192.3094 25315.547 -2693.4635 7.8067107 -2826.4674 133.0039 0.65 -2817.3114
6600 1174.741 22676.36 -2697.5642 7.8067107 -2828.6083 131.04413 0.66 -2819.6239
6700 1117.0829 22497.41 -2705.1682 7.8067107 -2829.7804 124.61228 0.67 -2821.3556
6800 1125.4062 18193.925 -2713.8679 7.8067107 -2839.4086 125.54075 0.68 -2830.2267
6900 1142.0728 19451.295 -2711.5199 7.8067107 -2838.9199 127.39994 0.69 -2830.1189
7000 1148.9469 16757.031 -2713.1595 7.8067107 -2841.3263 128.16676 0.7 -2832.475
7100 1044.2332 11734.429 -2733.5965 7.8067107 -2850.0822 116.48578 0.71 -2841.8886
7200 1052.3967 15187.579 -2724.5284 7.8067107 -2841.9248 117.39644 0.72 -2834.2885
7300 1045.9123 13697.721 -2730.1401 7.8067107 -2846.8132 116.67309 0.73 -2838.9073
7400 1082.9806 13330.213 -2726.8679 7.8067107 -2847.676 120.80812 0.74 -2840.2979
7500 980.30736 7070.7227 -2746.9678 7.8067107 -2856.3226 109.35476 0.75 -2848.8706
7600 982.86602 7694.074 -2745.5399 7.8067107 -2855.1801 109.64018 0.76 -2848.0154
7700 958.27863 2336.6244 -2758.806 7.8067107 -2865.7035 106.89742 0.77 -2858.6468
7800 991.25495 564.58952 -2758.6032 7.8067107 -2869.1791 110.57598 0.78 -2862.4362
7900 901.65217 3569.7496 -2763.0681 7.8067107 -2863.6488 100.58066 0.79 -2857.2329
8000 871.00782 -883.03123 -2773.2412 7.8067107 -2870.4035 97.162233 0.8 -2864.1778
8100 873.73598 -977.71992 -2772.9758 7.8067107 -2870.4424 97.466563 0.81 -2864.7239
8200 859.27838 2535.4088 -2769.5501 7.8067107 -2865.4039 95.853797 0.82 -2859.9007
8300 874.88664 -6039.909 -2781.7213 7.8067107 -2879.3163 97.594921 0.83 -2873.9613
8400 810.33098 -5386.015 -2787.6011 7.8067107 -2877.9947 90.393641 0.84 -2872.8494
8500 812.50682 -6372.4363 -2789.0713 7.8067107 -2879.7077 90.636359 0.85 -2874.8424
8600 792.27145 -11610.225 -2798.2095 7.8067107 -2886.5886 88.379073 0.86 -2882.1413
8700 737.92522 -10178.597 -2803.4114 7.8067107 -2885.7281 82.316669 0.87 -2881.6683
8800 744.31065 -12026.268 -2806.8078 7.8067107 -2889.8367 83.028973 0.88 -2886.1335
8900 709.31385 -17472.954 -2818.1084 7.8067107 -2897.2334 79.125027 0.89 -2893.7244
9000 704.20763 -17006.609 -2817.9144 7.8067107 -2896.4698 78.555422 0.9 -2893.2911
9100 697.72956 -20282.325 -2824.94 7.8067107 -2902.7728 77.832782 0.91 -2899.891
9200 696.15397 -20368.748 -2824.7243 7.8067107 -2902.3813 77.657023 0.92 -2899.7706
9300 627.98752 -21031.839 -2833.3613 7.8067107 -2903.4142 70.052953 0.93 -2901.0899
9400 603.4933 -20243.066 -2836.1082 7.8067107 -2903.4288 67.320586 0.94 -2901.4655
9500 599.69375 -23936.746 -2843.0066 7.8067107 -2909.9033 66.89674 0.95 -2908.2797
9600 587.42611 -26956.034 -2848.4377 7.8067107 -2913.966 65.528267 0.96 -2912.6742
9700 567.47718 -28321.949 -2852.1171 7.8067107 -2915.42 63.302933 0.97 -2914.4223
9800 524.81105 -31000.6 -2860.6103 7.8067107 -2919.1537 58.543462 0.98 -2918.4921
9900 507.60008 -32223.744 -2864.192 7.8067107 -2920.8155 56.623552 0.99 -2920.4741
10000 521.28866 -33930.476 -2866.3918 7.8067107 -2924.5423 58.150534 1 -2924.5423
Loop time of 17.7277 on 2 procs for 10000 steps with 864 atoms
Total wall time: 0:00:17

13
examples/PACKAGES/alchemy/log.25Feb23.twowater.g++.4 Normal file
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LAMMPS (8 Feb 2023)
Running on 2 partitions of processors
Starting alchemical transformation at 0%
Alchemical transformation progress: 10%
Alchemical transformation progress: 20%
Alchemical transformation progress: 30%
Alchemical transformation progress: 40%
Alchemical transformation progress: 50%
Alchemical transformation progress: 60%
Alchemical transformation progress: 70%
Alchemical transformation progress: 80%
Alchemical transformation progress: 90%
Alchemical transformation progress: 100%

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