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small changes to last LATTE PR, including xControl to upper case

This commit is contained in:
Steven J. Plimpton 2018-06-25 17:43:31 -06:00
parent 5e48565761
commit 49a91db0b2
5 changed files with 175 additions and 3 deletions

0
examples/latte/in.latte.water.ch4.consecutive.md → examples/latte/in.latte.multiple
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2
examples/latte/latte.in
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@ -9,7 +9,7 @@ LATTE INPUT FILE
#General controls
CONTROL{
xControl= 1
XCONTROL= 1
BASISTYPE= NONORTHO
PARAMPATH= "./TBparam"
KBT= 0.0

171
examples/latte/log.21Jun18.latte.multiple.g++.1 Normal file
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@ -0,0 +1,171 @@
LAMMPS (22 Jun 2018)
units metal
atom_style full
atom_modify sort 0 0.0 # turn off sorting of the coordinates
read_data data.water
orthogonal box = (0 0 0) to (6.267 6.267 6.267)
1 by 1 by 1 MPI processor grid
reading atoms ...
24 atoms
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
# initialize system
velocity all create 0.0 87287 loop geom
pair_style zero 1.0
pair_coeff * *
neighbor 1.0 bin
neigh_modify every 1 delay 0 check yes
timestep 0.00025
fix 1 all nve
fix 2 all latte NULL
fix_modify 2 energy yes
thermo_style custom step temp pe etotal press
# dynamics
thermo 10
run 10
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2
ghost atom cutoff = 2
binsize = 1, bins = 7 7 7
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.629 | 5.629 | 5.629 Mbytes
Step Temp PotEng TotEng Press
0 0 -104.95596 -104.95596 48235.442
10 336.53107 -105.96027 -104.95977 97996.851
Loop time of 0.912921 on 1 procs for 10 steps with 24 atoms
Performance: 0.237 ns/day, 101.436 hours/ns, 10.954 timesteps/s
6614.5% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 4.3392e-05 | 4.3392e-05 | 4.3392e-05 | 0.0 | 0.00
Bond | 3.8862e-05 | 3.8862e-05 | 3.8862e-05 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00036955 | 0.00036955 | 0.00036955 | 0.0 | 0.04
Output | 9.799e-05 | 9.799e-05 | 9.799e-05 | 0.0 | 0.01
Modify | 0.91199 | 0.91199 | 0.91199 | 0.0 | 99.90
Other | | 0.0003812 | | | 0.04
Nlocal: 24 ave 24 max 24 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 71 ave 71 max 71 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 37 ave 37 max 37 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 37
Ave neighs/atom = 1.54167
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
# Clear up previus calculation
clear
# simple CH4 molecule with LATTE
units metal
atom_style full
atom_modify sort 0 0.0 # turn off sorting of the coordinates
read_data data.ch4
triclinic box = (0 0 0) to (19.523 12.758 11.692) with tilt (0 0 0)
1 by 1 by 1 MPI processor grid
reading atoms ...
5 atoms
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
# initialize system
velocity all create 0.0 87287 loop geom
pair_style zero 1.0
pair_coeff * *
neighbor 1.0 bin
neigh_modify every 1 delay 0 check yes
timestep 0.00025
fix 1 all nve
fix 2 all latte NULL
fix_modify 2 energy yes
thermo_style custom step temp pe etotal press
# dynamics
thermo 10
run 10
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2
ghost atom cutoff = 2
binsize = 1, bins = 20 13 12
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/newton/tri
stencil: half/bin/3d/newton/tri
bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.651 | 5.651 | 5.651 Mbytes
Step Temp PotEng TotEng Press
0 0 -23.980353 -23.980353 348.02716
10 19.123149 -23.990297 -23.98041 18.774332
Loop time of 0.0415399 on 1 procs for 10 steps with 5 atoms
Performance: 5.200 ns/day, 4.616 hours/ns, 240.732 timesteps/s
6674.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 5.722e-06 | 5.722e-06 | 5.722e-06 | 0.0 | 0.01
Bond | 7.6294e-06 | 7.6294e-06 | 7.6294e-06 | 0.0 | 0.02
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 1.8358e-05 | 1.8358e-05 | 1.8358e-05 | 0.0 | 0.04
Output | 2.0981e-05 | 2.0981e-05 | 2.0981e-05 | 0.0 | 0.05
Modify | 0.041394 | 0.041394 | 0.041394 | 0.0 | 99.65
Other | | 9.322e-05 | | | 0.22
Nlocal: 5 ave 5 max 5 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 7 ave 7 max 7 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 10 ave 10 max 10 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 10
Ave neighs/atom = 2
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:01

2
lib/latte/Install.py
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@ -144,7 +144,7 @@ if buildflag:
print("Downloading LATTE ...")
geturl(url,"LATTE.tar.gz")
print("Unpacking LATTE zipfile ...")
print("Unpacking LATTE ...")
if os.path.exists(lattedir):
cmd = 'rm -rf "%s"' % lattedir
subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)

3
src/LATTE/fix_latte.cpp
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@ -42,6 +42,7 @@ extern "C" {
int latte_abiversion();
}
#define ABIVERSION 20180622
#define INVOKED_PERATOM 8
/* ---------------------------------------------------------------------- */
@ -55,7 +56,7 @@ FixLatte::FixLatte(LAMMPS *lmp, int narg, char **arg) :
if (comm->nprocs != 1)
error->all(FLERR,"Fix latte currently runs only in serial");
if (20180622 != latte_abiversion())
if (latte_abiversion() != ABIVERSION)
error->all(FLERR,"LAMMPS is linked against incompatible LATTE library");
if (narg != 4) error->all(FLERR,"Illegal fix latte command");