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Gareth Tribello
2018-10-26 22:01:05 +01:00
parent 2e79d9f340 2428c1c1f3
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5
examples/COUPLE/README
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@ -10,6 +10,7 @@ See these sections of the LAMMPS manaul for details:
2.5 Building LAMMPS as a library (doc/Section_start.html#start_5)
6.10 Coupling LAMMPS to other codes (doc/Section_howto.html#howto_10)
6.29 Using LAMMPS in client/server mode (doc/Section_howto.html#howto_29)
In all of the examples included here, LAMMPS must first be built as a
library. Basically, in the src dir you type one of
@ -33,9 +34,13 @@ 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
lammps_mc client/server coupling of Monte Carlo client
with LAMMPS server for energy evaluation
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
lammps_vasp client/server coupling of LAMMPS client with
VASP quantum DFT as server for quantum forces
library collection of useful inter-code communication routines
fortran a simple wrapper on the LAMMPS library API that
can be called from Fortran

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# Makefile for MC
SHELL = /bin/sh
SRC = mc.cpp random_park.cpp
OBJ = $(SRC:.cpp=.o)
# change this line for your machine to path for CSlib src dir
CSLIB = /home/sjplimp/lammps/lib/message/cslib/src
# compiler/linker settings
CC = g++
CCFLAGS = -g -O3 -I$(CSLIB)
LINK = g++
LINKFLAGS = -g -O -L$(CSLIB)
# targets
mc: $(OBJ)
# first line if built the CSlib within lib/message with ZMQ support
# second line if built the CSlib without ZMQ support
$(LINK) $(LINKFLAGS) $(OBJ) -lcsnompi -lzmq -o mc
# $(LINK) $(LINKFLAGS) $(OBJ) -lcsnompi -o mc
clean:
@rm -f *.o mc
# rules
%.o:%.cpp
$(CC) $(CCFLAGS) -c $<

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Sample Monte Carlo (MC) wrapper on LAMMPS via client/server coupling
See the MESSAGE package (doc/Section_messages.html#MESSAGE)
and Section_howto.html#howto10 for more details on how
client/server coupling works in LAMMPS.
In this dir, the mc.cpp/h files are a standalone "client" MC code. It
should be run on a single processor, though it could become a parallel
program at some point. LAMMPS is also run as a standalone executable
as a "server" on as many processors as desired using its "server mc"
command; see it's doc page for details.
Messages are exchanged between MC and LAMMPS via a client/server
library (CSlib), which is included in the LAMMPS distribution in
lib/message. As explained below you can choose to exchange data
between the two programs either via files or sockets (ZMQ). If the MC
program became parallel, data could also be exchanged via MPI.
The MC code makes simple MC moves, by displacing a single random atom
by a small random amount. It uses LAMMPS to calculate the energy
change, and to run dynamics between MC moves.
----------------
Build LAMMPS with its MESSAGE package installed:
See the Build extras doc page and its MESSAGE package
section for details.
CMake:
-D PKG_MESSAGE=yes # include the MESSAGE package
-D MESSAGE_ZMQ=value # build with ZeroMQ support, value = no (default) or yes
Traditional make:
% cd lammps/lib/message
% python Install.py -m -z # build CSlib with MPI and ZMQ support
% cd lammps/src
% make yes-message
% make mpi
You can leave off the -z if you do not have ZMQ on your system.
----------------
Build the MC client code
The source files for the MC code are in this dir. It links with the
CSlib library in lib/message/cslib.
You must first build the CSlib in serial mode, e.g.
% cd lammps/lib/message/cslib/src
% make lib # build serial and parallel lib with ZMQ support
% make lib zmq=no # build serial and parallel lib without ZMQ support
Then edit the Makefile in this dir. The CSLIB variable should be the
path to where the LAMMPS lib/message/cslib/src dir is on your system.
If you built the CSlib without ZMQ support you will also need to
comment/uncomment one line. Then you can just type
% make
and you should get an "mc" executable.
----------------
To run in client/server mode:
Both the client (MC) and server (LAMMPS) must use the same messaging
mode, namely file or zmq. This is an argument to the MC code; it can
be selected by setting the "mode" variable when you run LAMMPS. The
default mode = file.
Here we assume LAMMPS was built to run in parallel, and the MESSAGE
package was installed with socket (ZMQ) support. This means either of
the messaging modes can be used and LAMMPS can be run in serial or
parallel. The MC code is always run in serial.
When you run, the server should print out thermodynamic info
for every MD run it performs (between MC moves). The client
will print nothing until the simulation ends, then it will
print stats about the accepted MC moves.
The examples below are commands you should use in two different
terminal windows. The order of the two commands (client or server
launch) does not matter. You can run them both in the same window if
you append a "&" character to the first one to run it in the
background.
--------------
File mode of messaging:
% mpirun -np 1 mc in.mc file tmp.couple
% mpirun -np 1 lmp_mpi -v mode file < in.mc.server
% mpirun -np 1 mc in.mc file tmp.couple
% mpirun -np 4 lmp_mpi -v mode file < in.mc.server
ZMQ mode of messaging:
% mpirun -np 1 mc in.mc zmq localhost:5555
% mpirun -np 1 lmp_mpi -v mode zmq < in.mc.server
% mpirun -np 1 mc in.mc zmq localhost:5555
% mpirun -np 4 lmp_mpi -v mode zmq < in.mc.server
--------------
The input script for the MC program is in.mc. You can edit it to run
longer simulations.
500 nsteps = total # of steps of MD
100 ndynamics = # of MD steps between MC moves
0.1 delta = displacement size of MC move
1.0 temperature = used in MC Boltzman factor
12345 seed = random number seed
--------------
The problem size that LAMMPS is computing the MC energy for and
running dynamics on is set by the x,y,z variables in the LAMMPS
in.mc.server script. The default size is 500 particles. You can
adjust the size as follows:
lmp_mpi -v x 10 -v y 10 -v z 20 # 8000 particles

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# MC params
500 nsteps
100 ndynamics
0.1 delta
1.0 temperature
12345 seed

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examples/COUPLE/lammps_mc/in.mc.server Normal file
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# 3d Lennard-Jones Monte Carlo server script
variable mode index file
if "${mode} == file" then &
"message server mc file tmp.couple" &
elif "${mode} == zmq" &
"message server mc zmq *:5555" &
variable x index 5
variable y index 5
variable z index 5
units lj
atom_style atomic
atom_modify map yes
lattice fcc 0.8442
region box block 0 $x 0 $y 0 $z
create_box 1 box
create_atoms 1 box
mass 1 1.0
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 20 check no
velocity all create 1.44 87287 loop geom
fix 1 all nve
thermo 50
server mc

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LAMMPS (22 Aug 2018)
# 3d Lennard-Jones Monte Carlo server script
variable mode index file
if "${mode} == file" then "message server mc file tmp.couple" elif "${mode} == zmq" "message server mc zmq *:5555"
message server mc file tmp.couple
variable x index 5
variable y index 5
variable z index 5
units lj
atom_style atomic
atom_modify map yes
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
region box block 0 $x 0 $y 0 $z
region box block 0 5 0 $y 0 $z
region box block 0 5 0 5 0 $z
region box block 0 5 0 5 0 5
create_box 1 box
Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 500 atoms
Time spent = 0.000649929 secs
mass 1 1.0
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 20 check no
velocity all create 1.44 87287 loop geom
fix 1 all nve
thermo 50
server mc
run 0
Neighbor list info ...
update every 20 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 6 6 6
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -6.7733681 0 -4.6176881 -5.0221006
Loop time of 2.14577e-06 on 1 procs for 0 steps with 500 atoms
93.2% 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 | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 2.146e-06 | | |100.00
Nlocal: 500 ave 500 max 500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1956 ave 1956 max 1956 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 19500 ave 19500 max 19500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 19500
Ave neighs/atom = 39
Neighbor list builds = 0
Dangerous builds not checked
run 0
Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -6.7723127 0 -4.6166327 -5.015531
Loop time of 2.14577e-06 on 1 procs for 0 steps with 500 atoms
93.2% 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 | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 2.146e-06 | | |100.00
Nlocal: 500 ave 500 max 500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1956 ave 1956 max 1956 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 19501 ave 19501 max 19501 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 19501
Ave neighs/atom = 39.002
Neighbor list builds = 0
Dangerous builds not checked
Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -6.7723127 0 -4.6166327 -5.015531
50 0.70239211 -5.6763152 0 -4.6248342 0.59544428
100 0.7565013 -5.757431 0 -4.6249485 0.21982657
run 0
Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
Step Temp E_pair E_mol TotEng Press
100 0.7565013 -5.7565768 0 -4.6240944 0.22436405
Loop time of 1.90735e-06 on 1 procs for 0 steps with 500 atoms
157.3% 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 | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 1.907e-06 | | |100.00
Nlocal: 500 ave 500 max 500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1939 ave 1939 max 1939 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 18757 ave 18757 max 18757 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 18757
Ave neighs/atom = 37.514
Neighbor list builds = 0
Dangerous builds not checked
Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
Step Temp E_pair E_mol TotEng Press
100 0.7565013 -5.757431 0 -4.6249485 0.21982657
150 0.76110797 -5.7664315 0 -4.6270529 0.16005254
200 0.73505651 -5.7266069 0 -4.6262273 0.34189744
run 0
Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
Step Temp E_pair E_mol TotEng Press
200 0.73505651 -5.7181381 0 -4.6177585 0.37629943
Loop time of 2.14577e-06 on 1 procs for 0 steps with 500 atoms
139.8% 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 | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 2.146e-06 | | |100.00
Nlocal: 500 ave 500 max 500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1899 ave 1899 max 1899 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 18699 ave 18699 max 18699 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 18699
Ave neighs/atom = 37.398
Neighbor list builds = 0
Dangerous builds not checked
Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
Step Temp E_pair E_mol TotEng Press
200 0.73505651 -5.7266069 0 -4.6262273 0.34189744
250 0.73052476 -5.7206316 0 -4.627036 0.39287516
300 0.76300831 -5.7675007 0 -4.6252773 0.16312925
run 0
Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
Step Temp E_pair E_mol TotEng Press
300 0.76300831 -5.768304 0 -4.6260806 0.15954325
Loop time of 2.14577e-06 on 1 procs for 0 steps with 500 atoms
139.8% 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 | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 2.146e-06 | | |100.00
Nlocal: 500 ave 500 max 500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1903 ave 1903 max 1903 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 18715 ave 18715 max 18715 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 18715
Ave neighs/atom = 37.43
Neighbor list builds = 0
Dangerous builds not checked
Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
Step Temp E_pair E_mol TotEng Press
300 0.76300831 -5.768304 0 -4.6260806 0.15954325
350 0.72993309 -5.7193261 0 -4.6266162 0.3358374
400 0.72469448 -5.713463 0 -4.6285954 0.44859547
run 0
Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
Step Temp E_pair E_mol TotEng Press
400 0.72469448 -5.7077332 0 -4.6228655 0.47669832
Loop time of 1.90735e-06 on 1 procs for 0 steps with 500 atoms
157.3% 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 | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 1.907e-06 | | |100.00
Nlocal: 500 ave 500 max 500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1899 ave 1899 max 1899 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 18683 ave 18683 max 18683 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 18683
Ave neighs/atom = 37.366
Neighbor list builds = 0
Dangerous builds not checked
Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
Step Temp E_pair E_mol TotEng Press
400 0.72469448 -5.713463 0 -4.6285954 0.44859547
450 0.75305735 -5.7518283 0 -4.6245015 0.34658587
500 0.73092571 -5.7206337 0 -4.6264379 0.43715809
Total wall time: 0:00:02

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LAMMPS (22 Aug 2018)
# 3d Lennard-Jones Monte Carlo server script
variable mode index file
if "${mode} == file" then "message server mc file tmp.couple" elif "${mode} == zmq" "message server mc zmq *:5555"
message server mc file tmp.couple
variable x index 5
variable y index 5
variable z index 5
units lj
atom_style atomic
atom_modify map yes
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
region box block 0 $x 0 $y 0 $z
region box block 0 5 0 $y 0 $z
region box block 0 5 0 5 0 $z
region box block 0 5 0 5 0 5
create_box 1 box
Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 500 atoms
Time spent = 0.000592947 secs
mass 1 1.0
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 20 check no
velocity all create 1.44 87287 loop geom
fix 1 all nve
thermo 50
server mc
run 0
Neighbor list info ...
update every 20 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 6 6 6
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -6.7733681 0 -4.6176881 -5.0221006
Loop time of 3.8147e-06 on 4 procs for 0 steps with 500 atoms
59.0% CPU use with 4 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 | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 3.815e-06 | | |100.00
Nlocal: 125 ave 125 max 125 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 1099 ave 1099 max 1099 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 4875 ave 4875 max 4875 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 19500
Ave neighs/atom = 39
Neighbor list builds = 0
Dangerous builds not checked
run 0
Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -6.7723127 0 -4.6166327 -5.015531
Loop time of 3.03984e-06 on 4 procs for 0 steps with 500 atoms
106.9% CPU use with 4 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 | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 3.04e-06 | | |100.00
Nlocal: 125 ave 125 max 125 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 1099 ave 1099 max 1099 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 4875.25 ave 4885 max 4866 min
Histogram: 1 0 0 0 2 0 0 0 0 1
Total # of neighbors = 19501
Ave neighs/atom = 39.002
Neighbor list builds = 0
Dangerous builds not checked
Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -6.7723127 0 -4.6166327 -5.015531
50 0.70210225 -5.6759068 0 -4.6248598 0.59609192
100 0.75891559 -5.7611234 0 -4.6250267 0.20841608
run 0
Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
Step Temp E_pair E_mol TotEng Press
100 0.75891559 -5.7609392 0 -4.6248426 0.20981291
Loop time of 3.75509e-06 on 4 procs for 0 steps with 500 atoms
113.2% CPU use with 4 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 | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 3.755e-06 | | |100.00
Nlocal: 125 ave 126 max 124 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 1085.25 ave 1089 max 1079 min
Histogram: 1 0 0 0 0 1 0 0 0 2
Neighs: 4690.25 ave 4996 max 4401 min
Histogram: 1 0 0 1 0 1 0 0 0 1
Total # of neighbors = 18761
Ave neighs/atom = 37.522
Neighbor list builds = 0
Dangerous builds not checked
Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
Step Temp E_pair E_mol TotEng Press
100 0.75891559 -5.7609392 0 -4.6248426 0.20981291
150 0.75437991 -5.7558622 0 -4.6265555 0.20681722
200 0.73111257 -5.7193748 0 -4.6248993 0.35230715
run 0
Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
Step Temp E_pair E_mol TotEng Press
200 0.73111257 -5.7143906 0 -4.6199151 0.37126023
Loop time of 2.563e-06 on 4 procs for 0 steps with 500 atoms
117.1% CPU use with 4 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 | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 2.563e-06 | | |100.00
Nlocal: 125 ave 126 max 123 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Nghost: 1068.5 ave 1076 max 1063 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Neighs: 4674.75 ave 4938 max 4419 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Total # of neighbors = 18699
Ave neighs/atom = 37.398
Neighbor list builds = 0
Dangerous builds not checked
Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
Step Temp E_pair E_mol TotEng Press
200 0.73111257 -5.7193748 0 -4.6248993 0.35230715
250 0.73873144 -5.7312505 0 -4.6253696 0.33061033
300 0.76392796 -5.7719207 0 -4.6283206 0.18197874
run 0
Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
Step Temp E_pair E_mol TotEng Press
300 0.76392796 -5.7725589 0 -4.6289588 0.17994628
Loop time of 3.99351e-06 on 4 procs for 0 steps with 500 atoms
93.9% CPU use with 4 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 | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 3.994e-06 | | |100.00
Nlocal: 125 ave 128 max 121 min
Histogram: 1 0 0 0 0 1 0 1 0 1
Nghost: 1069 ave 1080 max 1055 min
Histogram: 1 0 0 0 0 0 2 0 0 1
Neighs: 4672 ave 4803 max 4600 min
Histogram: 2 0 0 1 0 0 0 0 0 1
Total # of neighbors = 18688
Ave neighs/atom = 37.376
Neighbor list builds = 0
Dangerous builds not checked
Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
Step Temp E_pair E_mol TotEng Press
300 0.76392796 -5.7725589 0 -4.6289588 0.17994628
350 0.71953041 -5.7041632 0 -4.6270261 0.44866153
400 0.7319047 -5.7216051 0 -4.6259438 0.46321355
run 0
Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
Step Temp E_pair E_mol TotEng Press
400 0.7319047 -5.7158168 0 -4.6201554 0.49192039
Loop time of 3.57628e-06 on 4 procs for 0 steps with 500 atoms
111.8% CPU use with 4 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 | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 3.576e-06 | | |100.00
Nlocal: 125 ave 132 max 118 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Nghost: 1057.5 ave 1068 max 1049 min
Histogram: 1 0 0 1 1 0 0 0 0 1
Neighs: 4685.75 ave 5045 max 4229 min
Histogram: 1 0 0 1 0 0 0 0 0 2
Total # of neighbors = 18743
Ave neighs/atom = 37.486
Neighbor list builds = 0
Dangerous builds not checked
Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
Step Temp E_pair E_mol TotEng Press
400 0.7319047 -5.7216051 0 -4.6259438 0.46321355
450 0.74503154 -5.7405318 0 -4.6252196 0.33211879
500 0.70570501 -5.6824439 0 -4.6260035 0.62020788
Total wall time: 0:00:02

254
examples/COUPLE/lammps_mc/log.28Aug18.zmq.g++.1 Normal file
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LAMMPS (22 Aug 2018)
# 3d Lennard-Jones Monte Carlo server script
variable mode index file
if "${mode} == file" then "message server mc file tmp.couple" elif "${mode} == zmq" "message server mc zmq *:5555"
message server mc zmq *:5555
variable x index 5
variable y index 5
variable z index 5
units lj
atom_style atomic
atom_modify map yes
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
region box block 0 $x 0 $y 0 $z
region box block 0 5 0 $y 0 $z
region box block 0 5 0 5 0 $z
region box block 0 5 0 5 0 5
create_box 1 box
Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 500 atoms
Time spent = 0.000741005 secs
mass 1 1.0
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 20 check no
velocity all create 1.44 87287 loop geom
fix 1 all nve
thermo 50
server mc
run 0
Neighbor list info ...
update every 20 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 6 6 6
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -6.7733681 0 -4.6176881 -5.0221006
Loop time of 1.90735e-06 on 1 procs for 0 steps with 500 atoms
52.4% 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 | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 1.907e-06 | | |100.00
Nlocal: 500 ave 500 max 500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1956 ave 1956 max 1956 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 19500 ave 19500 max 19500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 19500
Ave neighs/atom = 39
Neighbor list builds = 0
Dangerous builds not checked
run 0
Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -6.7723127 0 -4.6166327 -5.015531
Loop time of 1.90735e-06 on 1 procs for 0 steps with 500 atoms
52.4% 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 | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 1.907e-06 | | |100.00
Nlocal: 500 ave 500 max 500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1956 ave 1956 max 1956 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 19501 ave 19501 max 19501 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 19501
Ave neighs/atom = 39.002
Neighbor list builds = 0
Dangerous builds not checked
Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -6.7723127 0 -4.6166327 -5.015531
50 0.70239211 -5.6763152 0 -4.6248342 0.59544428
100 0.7565013 -5.757431 0 -4.6249485 0.21982657
run 0
Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
Step Temp E_pair E_mol TotEng Press
100 0.7565013 -5.7565768 0 -4.6240944 0.22436405
Loop time of 1.19209e-06 on 1 procs for 0 steps with 500 atoms
83.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 1.192e-06 | | |100.00
Nlocal: 500 ave 500 max 500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1939 ave 1939 max 1939 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 18757 ave 18757 max 18757 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 18757
Ave neighs/atom = 37.514
Neighbor list builds = 0
Dangerous builds not checked
Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
Step Temp E_pair E_mol TotEng Press
100 0.7565013 -5.757431 0 -4.6249485 0.21982657
150 0.76110797 -5.7664315 0 -4.6270529 0.16005254
200 0.73505651 -5.7266069 0 -4.6262273 0.34189744
run 0
Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
Step Temp E_pair E_mol TotEng Press
200 0.73505651 -5.7181381 0 -4.6177585 0.37629943
Loop time of 9.53674e-07 on 1 procs for 0 steps with 500 atoms
209.7% 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 | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 9.537e-07 | | |100.00
Nlocal: 500 ave 500 max 500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1899 ave 1899 max 1899 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 18699 ave 18699 max 18699 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 18699
Ave neighs/atom = 37.398
Neighbor list builds = 0
Dangerous builds not checked
Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
Step Temp E_pair E_mol TotEng Press
200 0.73505651 -5.7266069 0 -4.6262273 0.34189744
250 0.73052476 -5.7206316 0 -4.627036 0.39287516
300 0.76300831 -5.7675007 0 -4.6252773 0.16312925
run 0
Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
Step Temp E_pair E_mol TotEng Press
300 0.76300831 -5.768304 0 -4.6260806 0.15954325
Loop time of 9.53674e-07 on 1 procs for 0 steps with 500 atoms
104.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 9.537e-07 | | |100.00
Nlocal: 500 ave 500 max 500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1903 ave 1903 max 1903 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 18715 ave 18715 max 18715 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 18715
Ave neighs/atom = 37.43
Neighbor list builds = 0
Dangerous builds not checked
Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
Step Temp E_pair E_mol TotEng Press
300 0.76300831 -5.768304 0 -4.6260806 0.15954325
350 0.72993309 -5.7193261 0 -4.6266162 0.3358374
400 0.72469448 -5.713463 0 -4.6285954 0.44859547
run 0
Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
Step Temp E_pair E_mol TotEng Press
400 0.72469448 -5.7077332 0 -4.6228655 0.47669832
Loop time of 9.53674e-07 on 1 procs for 0 steps with 500 atoms
209.7% 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 | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 9.537e-07 | | |100.00
Nlocal: 500 ave 500 max 500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1899 ave 1899 max 1899 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 18683 ave 18683 max 18683 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 18683
Ave neighs/atom = 37.366
Neighbor list builds = 0
Dangerous builds not checked
Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
Step Temp E_pair E_mol TotEng Press
400 0.72469448 -5.713463 0 -4.6285954 0.44859547
450 0.75305735 -5.7518283 0 -4.6245015 0.34658587
500 0.73092571 -5.7206337 0 -4.6264379 0.43715809
Total wall time: 0:00:00

254
examples/COUPLE/lammps_mc/log.28Aug18.zmq.g++.4 Normal file
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LAMMPS (22 Aug 2018)
# 3d Lennard-Jones Monte Carlo server script
variable mode index file
if "${mode} == file" then "message server mc file tmp.couple" elif "${mode} == zmq" "message server mc zmq *:5555"
message server mc zmq *:5555
variable x index 5
variable y index 5
variable z index 5
units lj
atom_style atomic
atom_modify map yes
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
region box block 0 $x 0 $y 0 $z
region box block 0 5 0 $y 0 $z
region box block 0 5 0 5 0 $z
region box block 0 5 0 5 0 5
create_box 1 box
Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 500 atoms
Time spent = 0.000576019 secs
mass 1 1.0
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 20 check no
velocity all create 1.44 87287 loop geom
fix 1 all nve
thermo 50
server mc
run 0
Neighbor list info ...
update every 20 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 6 6 6
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -6.7733681 0 -4.6176881 -5.0221006
Loop time of 4.76837e-06 on 4 procs for 0 steps with 500 atoms
89.1% CPU use with 4 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 | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 4.768e-06 | | |100.00
Nlocal: 125 ave 125 max 125 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 1099 ave 1099 max 1099 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 4875 ave 4875 max 4875 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 19500
Ave neighs/atom = 39
Neighbor list builds = 0
Dangerous builds not checked
run 0
Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -6.7723127 0 -4.6166327 -5.015531
Loop time of 3.45707e-06 on 4 procs for 0 steps with 500 atoms
94.0% CPU use with 4 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 | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 3.457e-06 | | |100.00
Nlocal: 125 ave 125 max 125 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 1099 ave 1099 max 1099 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 4875.25 ave 4885 max 4866 min
Histogram: 1 0 0 0 2 0 0 0 0 1
Total # of neighbors = 19501
Ave neighs/atom = 39.002
Neighbor list builds = 0
Dangerous builds not checked
Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -6.7723127 0 -4.6166327 -5.015531
50 0.70210225 -5.6759068 0 -4.6248598 0.59609192
100 0.75891559 -5.7611234 0 -4.6250267 0.20841608
run 0
Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
Step Temp E_pair E_mol TotEng Press
100 0.75891559 -5.7609392 0 -4.6248426 0.20981291
Loop time of 3.03984e-06 on 4 procs for 0 steps with 500 atoms
115.1% CPU use with 4 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 | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 3.04e-06 | | |100.00
Nlocal: 125 ave 126 max 124 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 1085.25 ave 1089 max 1079 min
Histogram: 1 0 0 0 0 1 0 0 0 2
Neighs: 4690.25 ave 4996 max 4401 min
Histogram: 1 0 0 1 0 1 0 0 0 1
Total # of neighbors = 18761
Ave neighs/atom = 37.522
Neighbor list builds = 0
Dangerous builds not checked
Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
Step Temp E_pair E_mol TotEng Press
100 0.75891559 -5.7609392 0 -4.6248426 0.20981291
150 0.75437991 -5.7558622 0 -4.6265555 0.20681722
200 0.73111257 -5.7193748 0 -4.6248993 0.35230715
run 0
Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
Step Temp E_pair E_mol TotEng Press
200 0.73111257 -5.7143906 0 -4.6199151 0.37126023
Loop time of 2.38419e-06 on 4 procs for 0 steps with 500 atoms
125.8% CPU use with 4 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 | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 2.384e-06 | | |100.00
Nlocal: 125 ave 126 max 123 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Nghost: 1068.5 ave 1076 max 1063 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Neighs: 4674.75 ave 4938 max 4419 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Total # of neighbors = 18699
Ave neighs/atom = 37.398
Neighbor list builds = 0
Dangerous builds not checked
Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
Step Temp E_pair E_mol TotEng Press
200 0.73111257 -5.7193748 0 -4.6248993 0.35230715
250 0.73873144 -5.7312505 0 -4.6253696 0.33061033
300 0.76392796 -5.7719207 0 -4.6283206 0.18197874
run 0
Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
Step Temp E_pair E_mol TotEng Press
300 0.76392796 -5.7725589 0 -4.6289588 0.17994628
Loop time of 2.44379e-06 on 4 procs for 0 steps with 500 atoms
112.5% CPU use with 4 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 | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 2.444e-06 | | |100.00
Nlocal: 125 ave 128 max 121 min
Histogram: 1 0 0 0 0 1 0 1 0 1
Nghost: 1069 ave 1080 max 1055 min
Histogram: 1 0 0 0 0 0 2 0 0 1
Neighs: 4672 ave 4803 max 4600 min
Histogram: 2 0 0 1 0 0 0 0 0 1
Total # of neighbors = 18688
Ave neighs/atom = 37.376
Neighbor list builds = 0
Dangerous builds not checked
Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
Step Temp E_pair E_mol TotEng Press
300 0.76392796 -5.7725589 0 -4.6289588 0.17994628
350 0.71953041 -5.7041632 0 -4.6270261 0.44866153
400 0.7319047 -5.7216051 0 -4.6259438 0.46321355
run 0
Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
Step Temp E_pair E_mol TotEng Press
400 0.7319047 -5.7158168 0 -4.6201554 0.49192039
Loop time of 2.14577e-06 on 4 procs for 0 steps with 500 atoms
139.8% CPU use with 4 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 | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 2.146e-06 | | |100.00
Nlocal: 125 ave 132 max 118 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Nghost: 1057.5 ave 1068 max 1049 min
Histogram: 1 0 0 1 1 0 0 0 0 1
Neighs: 4685.75 ave 5045 max 4229 min
Histogram: 1 0 0 1 0 0 0 0 0 2
Total # of neighbors = 18743
Ave neighs/atom = 37.486
Neighbor list builds = 0
Dangerous builds not checked
Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
Step Temp E_pair E_mol TotEng Press
400 0.7319047 -5.7216051 0 -4.6259438 0.46321355
450 0.74503154 -5.7405318 0 -4.6252196 0.33211879
500 0.70570501 -5.6824439 0 -4.6260035 0.62020788
Total wall time: 0:00:00

263
examples/COUPLE/lammps_mc/mc.cpp Normal file
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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
------------------------------------------------------------------------- */
// MC code used with LAMMPS in client/server mode
// MC is the client, LAMMPS is the server
// Syntax: mc infile mode modearg
// mode = file, zmq
// modearg = filename for file, localhost:5555 for zmq
#include <cmath>
#include <cstdio>
#include <cstdlib>
#include <cstring>
#include "mc.h"
#include "random_park.h"
#include "cslib.h"
using namespace CSLIB_NS;
void error(const char *);
CSlib *cs_create(char *, char *);
#define MAXLINE 256
/* ---------------------------------------------------------------------- */
// main program
int main(int narg, char **arg)
{
if (narg != 4) {
error("Syntax: mc infile mode modearg");
exit(1);
}
// initialize CSlib
CSlib *cs = cs_create(arg[2],arg[3]);
// create MC class and perform run
MC *mc = new MC(arg[1],cs);
mc->run();
// final MC stats
int naccept = mc->naccept;
int nattempt = mc->nattempt;
printf("------ MC stats ------\n");
printf("MC attempts = %d\n",nattempt);
printf("MC accepts = %d\n",naccept);
printf("Acceptance ratio = %g\n",1.0*naccept/nattempt);
// clean up
delete cs;
delete mc;
}
/* ---------------------------------------------------------------------- */
void error(const char *str)
{
printf("ERROR: %s\n",str);
exit(1);
}
/* ---------------------------------------------------------------------- */
CSlib *cs_create(char *mode, char *arg)
{
CSlib *cs = new CSlib(0,mode,arg,NULL);
// initial handshake to agree on protocol
cs->send(0,1);
cs->pack_string(1,(char *) "mc");
int msgID,nfield;
int *fieldID,*fieldtype,*fieldlen;
msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen);
return cs;
}
// ----------------------------------------------------------------------
// MC class
// ----------------------------------------------------------------------
MC::MC(char *mcfile, void *cs_caller)
//MC::MC(char *mcfile, CSlib *cs_caller)
{
cs_void = cs_caller;
// setup MC params
options(mcfile);
// random # generator
random = new RanPark(seed);
}
/* ---------------------------------------------------------------------- */
MC::~MC()
{
free(x);
delete random;
}
/* ---------------------------------------------------------------------- */
void MC::run()
{
int iatom,accept,msgID,nfield;
double pe_initial,pe_final,edelta;
double dx,dy,dz;
double xold[3],xnew[3];
int *fieldID,*fieldtype,*fieldlen;
enum{NATOMS=1,EINIT,DISPLACE,ACCEPT,RUN};
CSlib *cs = (CSlib *) cs_void;
// one-time request for atom count from MD
// allocate 1d coord buffer
cs->send(NATOMS,0);
msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen);
natoms = cs->unpack_int(1);
x = (double *) malloc(3*natoms*sizeof(double));
// loop over MC moves
naccept = nattempt = 0;
for (int iloop = 0; iloop < nloop; iloop++) {
// request current energy from MD
// recv energy, coords from MD
cs->send(EINIT,0);
msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen);
pe_initial = cs->unpack_double(1);
double *x = (double *) cs->unpack(2);
// perform simple MC event
// displace a single atom by random amount
iatom = (int) natoms*random->uniform();
xold[0] = x[3*iatom+0];
xold[1] = x[3*iatom+1];
xold[2] = x[3*iatom+2];
dx = 2.0*delta*random->uniform() - delta;
dy = 2.0*delta*random->uniform() - delta;
dz = 2.0*delta*random->uniform() - delta;
xnew[0] = xold[0] + dx;
xnew[1] = xold[1] + dx;
xnew[2] = xold[2] + dx;
// send atom ID and its new coords to MD
// recv new energy
cs->send(DISPLACE,2);
cs->pack_int(1,iatom+1);
cs->pack(2,4,3,xnew);
msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen);
pe_final = cs->unpack_double(1);
// decide whether to accept/reject MC event
if (pe_final <= pe_initial) accept = 1;
else if (temperature == 0.0) accept = 0;
else if (random->uniform() >
exp(natoms*(pe_initial-pe_final)/temperature)) accept = 0;
else accept = 1;
nattempt++;
if (accept) naccept++;
// send accept (1) or reject (0) flag to MD
cs->send(ACCEPT,1);
cs->pack_int(1,accept);
msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen);
// send dynamics timesteps
cs->send(RUN,1);
cs->pack_int(1,ndynamics);
msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen);
}
// send exit message to MD
cs->send(-1,0);
msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen);
}
/* ---------------------------------------------------------------------- */
void MC::options(char *filename)
{
// default params
nsteps = 0;
ndynamics = 100;
delta = 0.1;
temperature = 1.0;
seed = 12345;
// read and parse file
FILE *fp = fopen(filename,"r");
if (fp == NULL) error("Could not open MC file");
char line[MAXLINE];
char *keyword,*value;
char *eof = fgets(line,MAXLINE,fp);
while (eof) {
if (line[0] == '#') { // comment line
eof = fgets(line,MAXLINE,fp);
continue;
}
value = strtok(line," \t\n\r\f");
if (value == NULL) { // blank line
eof = fgets(line,MAXLINE,fp);
continue;
}
keyword = strtok(NULL," \t\n\r\f");
if (keyword == NULL) error("Missing keyword in MC file");
if (strcmp(keyword,"nsteps") == 0) nsteps = atoi(value);
else if (strcmp(keyword,"ndynamics") == 0) ndynamics = atoi(value);
else if (strcmp(keyword,"delta") == 0) delta = atof(value);
else if (strcmp(keyword,"temperature") == 0) temperature = atof(value);
else if (strcmp(keyword,"seed") == 0) seed = atoi(value);
else error("Unknown param in MC file");
eof = fgets(line,MAXLINE,fp);
}
// derived params
nloop = nsteps/ndynamics;
}

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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
------------------------------------------------------------------------- */
#ifndef MC_H
#define MC_H
/* ---------------------------------------------------------------------- */
class MC {
public:
int naccept; // # of accepted MC events
int nattempt; // # of attempted MC events
MC(char *, void *);
~MC();
void run();
private:
int nsteps; // total # of MD steps
int ndynamics; // steps in one short dynamics run
int nloop; // nsteps/ndynamics
int natoms; // # of MD atoms
double delta; // MC displacement distance
double temperature; // MC temperature for Boltzmann criterion
double *x; // atom coords as 3N 1d vector
double energy; // global potential energy
int seed; // RNG seed
class RanPark *random;
void *cs_void; // messaging library
void options(char *);
};
#endif

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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
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.
------------------------------------------------------------------------- */
// Park/Miller RNG
#include <math.h>
#include "random_park.h"
//#include "error.h"
#define IA 16807
#define IM 2147483647
#define AM (1.0/IM)
#define IQ 127773
#define IR 2836
/* ---------------------------------------------------------------------- */
RanPark::RanPark(int seed_init)
{
//if (seed_init <= 0)
// error->one(FLERR,"Invalid seed for Park random # generator");
seed = seed_init;
save = 0;
}
/* ----------------------------------------------------------------------
uniform RN
------------------------------------------------------------------------- */
double RanPark::uniform()
{
int k = seed/IQ;
seed = IA*(seed-k*IQ) - IR*k;
if (seed < 0) seed += IM;
double ans = AM*seed;
return ans;
}
/* ----------------------------------------------------------------------
gaussian RN
------------------------------------------------------------------------- */
double RanPark::gaussian()
{
double first,v1,v2,rsq,fac;
if (!save) {
do {
v1 = 2.0*uniform()-1.0;
v2 = 2.0*uniform()-1.0;
rsq = v1*v1 + v2*v2;
} while ((rsq >= 1.0) || (rsq == 0.0));
fac = sqrt(-2.0*log(rsq)/rsq);
second = v1*fac;
first = v2*fac;
save = 1;
} else {
first = second;
save = 0;
}
return first;
}

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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
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.
------------------------------------------------------------------------- */
#ifndef RANPARK_H
#define RANPARK_H
class RanPark {
public:
RanPark(int);
double uniform();
double gaussian();
private:
int seed,save;
double second;
};
#endif

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# Startparameter for this run:
NWRITE = 2 write-flag & timer
PREC = normal normal or accurate (medium, high low for compatibility)
ISTART = 0 job : 0-new 1-cont 2-samecut
ICHARG = 2 charge: 1-file 2-atom 10-const
ISPIN = 1 spin polarized calculation?
LSORBIT = F spin-orbit coupling
INIWAV = 1 electr: 0-lowe 1-rand 2-diag
# Electronic Relaxation 1
ENCUT = 600.0 eV #Plane wave energy cutoff
ENINI = 600.0 initial cutoff
NELM = 100; NELMIN= 2; NELMDL= -5 # of ELM steps
EDIFF = 0.1E-05 stopping-criterion for ELM
# Ionic relaxation
EDIFFG = 0.1E-02 stopping-criterion for IOM
NSW = 0 number of steps for IOM
NBLOCK = 1; KBLOCK = 1 inner block; outer block
IBRION = -1 ionic relax: 0-MD 1-quasi-New 2-CG #No ion relaxation with -1
NFREE = 0 steps in history (QN), initial steepest desc. (CG)
ISIF = 2 stress and relaxation # 2: F-yes Sts-yes RlxIon-yes cellshape-no cellvol-no
IWAVPR = 10 prediction: 0-non 1-charg 2-wave 3-comb # 10: TMPCAR stored in memory rather than file
POTIM = 0.5000 time-step for ionic-motion
TEBEG = 3500.0; TEEND = 3500.0 temperature during run # Finite Temperature variables if AI-MD is on
SMASS = -3.00 Nose mass-parameter (am)
estimated Nose-frequenzy (Omega) = 0.10E-29 period in steps =****** mass= -0.366E-27a.u.
PSTRESS= 0.0 pullay stress
# DOS related values:
EMIN = 10.00; EMAX =-10.00 energy-range for DOS
EFERMI = 0.00
ISMEAR = 0; SIGMA = 0.10 broadening in eV -4-tet -1-fermi 0-gaus
# Electronic relaxation 2 (details)
IALGO = 48 algorithm
# Write flags
LWAVE = T write WAVECAR
LCHARG = T write CHGCAR
LVTOT = F write LOCPOT, total local potential
LVHAR = F write LOCPOT, Hartree potential only
LELF = F write electronic localiz. function (ELF)
# Dipole corrections
LMONO = F monopole corrections only (constant potential shift)
LDIPOL = F correct potential (dipole corrections)
IDIPOL = 0 1-x, 2-y, 3-z, 4-all directions
EPSILON= 1.0000000 bulk dielectric constant
# Exchange correlation treatment:
GGA = -- GGA type

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K-Points
0
Monkhorst Pack
15 15 15
0 0 0

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W unit cell
1.0
3.16 0.00000000 0.00000000
0.00000000 3.16 0.00000000
0.00000000 0.00000000 3.16
W
2
Direct
0.00000000 0.00000000 0.00000000
0.50000000 0.50000000 0.50000000

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Sample LAMMPS MD wrapper on VASP quantum DFT via client/server
coupling
See the MESSAGE package (doc/Section_messages.html#MESSAGE) and
Section_howto.html#howto10 for more details on how client/server
coupling works in LAMMPS.
In this dir, the vasp_wrap.py is a wrapper on the VASP quantum DFT
code so it can work as a "server" code which LAMMPS drives as a
"client" code to perform ab initio MD. LAMMPS performs the MD
timestepping, sends VASP a current set of coordinates each timestep,
VASP computes forces and energy and virial and returns that info to
LAMMPS.
Messages are exchanged between MC and LAMMPS via a client/server
library (CSlib), which is included in the LAMMPS distribution in
lib/message. As explained below you can choose to exchange data
between the two programs either via files or sockets (ZMQ). If the
vasp_wrap.py program became parallel, or the CSlib library calls were
integrated into VASP directly, then data could also be exchanged via
MPI.
----------------
Build LAMMPS with its MESSAGE package installed:
See the Build extras doc page and its MESSAGE package
section for details.
CMake:
-D PKG_MESSAGE=yes # include the MESSAGE package
-D MESSAGE_ZMQ=value # build with ZeroMQ support, value = no (default) or yes
Traditional make:
cd lammps/lib/message
python Install.py -m -z # build CSlib with MPI and ZMQ support
cd lammps/src
make yes-message
make mpi
You can leave off the -z if you do not have ZMQ on your system.
----------------
Build the CSlib in a form usable by the vasp_wrapper.py script:
% cd lammps/lib/message/cslib/src
% make shlib # build serial and parallel shared lib with ZMQ support
% make shlib zmq=no # build serial and parallel shared lib w/out ZMQ support
This will make a shared library versions of the CSlib, which Python
requires. Python must be able to find both the cslib.py script and
the libcsnompi.so library in your lammps/lib/message/cslib/src
directory. If it is not able to do this, you will get an error when
you run vasp_wrapper.py.
You can do this by augmenting two environment variables, either
from the command line, or in your shell start-up script.
Here is the sample syntax for the csh or tcsh shells:
setenv PYTHONPATH ${PYTHONPATH}:/home/sjplimp/lammps/lib/message/cslib/src
setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:/home/sjplimp/lammps/lib/message/cslib/src
----------------
Prepare to use VASP and the vasp_wrapper.py script
You can run the vasp_wrap.py script as-is to test that the coupling
between it and LAMMPS is functional. This will use the included
vasprun.xml file output by a previous VASP run.
But note that the as-is version of vasp_wrap.py will not attempt to
run VASP.
To do this, you must edit the 1st vaspcmd line at the top of
vasp_wrapper.py to be the launch command needed to run VASP on your
system. It can be a command to run VASP in serial or in parallel,
e.g. an mpirun command. Then comment out the 2nd vaspcmd line
immediately following it.
Insure you have the necessary VASP input files in this
directory, suitable for the VASP calculation you want to perform:
INCAR
KPOINTS
POSCAR_template
POTCAR
Examples of all but the POTCAR file are provided. As explained below,
POSCAR_W is an input file for a 2-atom unit cell of tungsten and can
be used to test the LAMMPS/VASP coupling. The POTCAR file is a
proprietary VASP file, so use one from your VASP installation.
Note that the POSCAR_template file should be matched to the LAMMPS
input script (# of atoms and atom types, box size, etc). The provided
POSCAR_W matches in.client.W.
Once you run VASP yourself, the vasprun.xml file will be overwritten.
----------------
To run in client/server mode:
NOTE: The vasp_wrap.py script must be run with Python version 2, not
3. This is because it used the CSlib python wrapper, which only
supports version 2. We plan to upgrade CSlib to support Python 3.
Both the client (LAMMPS) and server (vasp_wrap.py) must use the same
messaging mode, namely file or zmq. This is an argument to the
vasp_wrap.py code; it can be selected by setting the "mode" variable
when you run LAMMPS. The default mode = file.
Here we assume LAMMPS was built to run in parallel, and the MESSAGE
package was installed with socket (ZMQ) support. This means either of
the messaging modes can be used and LAMMPS can be run in serial or
parallel. The vasp_wrap.py code is always run in serial, but it
launches VASP from Python via an mpirun command which can run VASP
itself in parallel.
When you run, the server should print out thermodynamic info every
timestep which corresponds to the forces and virial computed by VASP.
VASP will also generate output files each timestep. The vasp_wrapper.py
script could be generalized to archive these.
The examples below are commands you should use in two different
terminal windows. The order of the two commands (client or server
launch) does not matter. You can run them both in the same window if
you append a "&" character to the first one to run it in the
background.
--------------
File mode of messaging:
% mpirun -np 1 lmp_mpi -v mode file < in.client.W
% python vasp_wrap.py file POSCAR_W
% mpirun -np 2 lmp_mpi -v mode file < in.client.W
% python vasp_wrap.py file POSCAR_W
ZMQ mode of messaging:
% mpirun -np 1 lmp_mpi -v mode zmq < in.client.W
% python vasp_wrap.py zmq POSCAR_W
% mpirun -np 2 lmp_mpi -v mode zmq < in.client.W
% python vasp_wrap.py zmq POSCAR_W

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LAMMPS W data file
2 atoms
1 atom types
0.0 3.16 xlo xhi
0.0 3.16 ylo yhi
0.0 3.16 zlo zhi
Atoms
1 1 0.000 0.000 0.000
2 1 1.58 1.58 1.58

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# small W unit cell for use with VASP
variable mode index file
if "${mode} == file" then &
"message client md file tmp.couple" &
elif "${mode} == zmq" &
"message client md zmq localhost:5555" &
variable x index 1
variable y index 1
variable z index 1
units metal
atom_style atomic
atom_modify sort 0 0.0 map yes
read_data data.W
mass 1 183.85
replicate $x $y $z
velocity all create 300.0 87287 loop geom
neighbor 0.3 bin
neigh_modify delay 0 every 10 check no
fix 1 all nve
fix 2 all client/md
fix_modify 2 energy yes
thermo 1
run 3

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LAMMPS (22 Aug 2018)
# small W unit cell for use with VASP
variable mode index file
if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555"
message client md zmq localhost:5555
variable x index 1
variable y index 1
variable z index 1
units metal
atom_style atomic
atom_modify sort 0 0.0 map yes
read_data data.W
orthogonal box = (0 0 0) to (3.16 3.16 3.16)
1 by 1 by 2 MPI processor grid
reading atoms ...
2 atoms
mass 1 183.85
replicate $x $y $z
replicate 1 $y $z
replicate 1 1 $z
replicate 1 1 1
orthogonal box = (0 0 0) to (3.16 3.16 3.16)
1 by 1 by 2 MPI processor grid
2 atoms
Time spent = 0.000148058 secs
velocity all create 300.0 87287 loop geom
neighbor 0.3 bin
neigh_modify delay 0 every 10 check no
fix 1 all nve
fix 2 all client/md
fix_modify 2 energy yes
thermo 1
run 3
Per MPI rank memory allocation (min/avg/max) = 1.8 | 1.8 | 1.8 Mbytes
Step Temp E_pair E_mol TotEng Press
0 300 0 0 -48.030793 -78159.503
1 298.24318 0 0 -48.03102 -78167.19
2 296.85584 0 0 -48.031199 -78173.26
3 295.83795 0 0 -48.031331 -78177.714
Loop time of 0.457491 on 2 procs for 3 steps with 2 atoms
Performance: 0.567 ns/day, 42.360 hours/ns, 6.558 timesteps/s
50.1% CPU use with 2 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 | 0 | 0 | 0 | 0.0 | 0.00
Comm | 1.3828e-05 | 2.9922e-05 | 4.6015e-05 | 0.0 | 0.01
Output | 7.5817e-05 | 9.3937e-05 | 0.00011206 | 0.0 | 0.02
Modify | 0.45735 | 0.45736 | 0.45736 | 0.0 | 99.97
Other | | 1.204e-05 | | | 0.00
Nlocal: 1 ave 1 max 1 min
Histogram: 2 0 0 0 0 0 0 0 0 0
Nghost: 4 ave 4 max 4 min
Histogram: 2 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 2 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 0
Dangerous builds not checked
Total wall time: 0:01:21

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#!/usr/bin/env python
# ----------------------------------------------------------------------
# LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
# http://lammps.sandia.gov, Sandia National Laboratories
# Steve Plimpton, sjplimp@sandia.gov
# ----------------------------------------------------------------------
# Syntax: vasp_wrap.py file/zmq POSCARfile
# wrapper on VASP to act as server program using CSlib
# receives message with list of coords from client
# creates VASP inputs
# invokes VASP to calculate self-consistent energy of that config
# reads VASP outputs
# sends message with energy, forces, pressure to client
# NOTES:
# check to insure basic VASP input files are in place?
# could archive VASP input/output in special filenames or dirs?
# need to check that POTCAR file is consistent with atom ordering?
# could make syntax for launching VASP more flexible
# e.g. command-line arg for # of procs
# detect if VASP had an error and return ERROR field, e.g. non-convergence ??
from __future__ import print_function
import sys
version = sys.version_info[0]
if version == 3:
sys.exit("The CSlib python wrapper does not yet support python 3")
import subprocess
import xml.etree.ElementTree as ET
from cslib import CSlib
# comment out 2nd line once 1st line is correct for your system
vaspcmd = "srun -N 1 --ntasks-per-node=4 " + \
"-n 4 /projects/vasp/2017-build/cts1/vasp5.4.4/vasp_tfermi/bin/vasp_std"
vaspcmd = "touch tmp"
# enums matching FixClientMD class in LAMMPS
SETUP,STEP = range(1,2+1)
DIM,PERIODICITY,ORIGIN,BOX,NATOMS,NTYPES,TYPES,COORDS,UNITS,CHARGE = range(1,10+1)
FORCES,ENERGY,VIRIAL,ERROR = range(1,4+1)
# -------------------------------------
# functions
# error message and exit
def error(txt):
print("ERROR:",txt)
sys.exit(1)
# -------------------------------------
# read initial VASP POSCAR file to setup problem
# return natoms,ntypes,box
def vasp_setup(poscar):
ps = open(poscar,'r').readlines()
# box size
words = ps[2].split()
xbox = float(words[0])
words = ps[3].split()
ybox = float(words[1])
words = ps[4].split()
zbox = float(words[2])
box = [xbox,ybox,zbox]
ntypes = 0
natoms = 0
words = ps[6].split()
for word in words:
if word == '#': break
ntypes += 1
natoms += int(word)
return natoms,ntypes,box
# -------------------------------------
# write a new POSCAR file for VASP
def poscar_write(poscar,natoms,ntypes,types,coords,box):
psold = open(poscar,'r').readlines()
psnew = open("POSCAR",'w')
# header, including box size
psnew.write(psold[0])
psnew.write(psold[1])
psnew.write("%g %g %g\n" % (box[0],box[1],box[2]))
psnew.write("%g %g %g\n" % (box[3],box[4],box[5]))
psnew.write("%g %g %g\n" % (box[6],box[7],box[8]))
psnew.write(psold[5])
psnew.write(psold[6])
# per-atom coords
# grouped by types
psnew.write("Cartesian\n")
for itype in range(1,ntypes+1):
for i in range(natoms):
if types[i] != itype: continue
x = coords[3*i+0]
y = coords[3*i+1]
z = coords[3*i+2]
aline = " %g %g %g\n" % (x,y,z)
psnew.write(aline)
psnew.close()
# -------------------------------------
# read a VASP output vasprun.xml file
# uses ElementTree module
# see https://docs.python.org/2/library/xml.etree.elementtree.html
def vasprun_read():
tree = ET.parse('vasprun.xml')
root = tree.getroot()
#fp = open("vasprun.xml","r")
#root = ET.parse(fp)
scsteps = root.findall('calculation/scstep')
energy = scsteps[-1].find('energy')
for child in energy:
if child.attrib["name"] == "e_0_energy":
eout = float(child.text)
fout = []
sout = []
varrays = root.findall('calculation/varray')
for varray in varrays:
if varray.attrib["name"] == "forces":
forces = varray.findall("v")
for line in forces:
fxyz = line.text.split()
fxyz = [float(value) for value in fxyz]
fout += fxyz
if varray.attrib["name"] == "stress":
tensor = varray.findall("v")
stensor = []
for line in tensor:
sxyz = line.text.split()
sxyz = [float(value) for value in sxyz]
stensor.append(sxyz)
sxx = stensor[0][0]
syy = stensor[1][1]
szz = stensor[2][2]
# symmetrize off-diagonal components
sxy = 0.5 * (stensor[0][1] + stensor[1][0])
sxz = 0.5 * (stensor[0][2] + stensor[2][0])
syz = 0.5 * (stensor[1][2] + stensor[2][1])
sout = [sxx,syy,szz,sxy,sxz,syz]
#fp.close()
return eout,fout,sout
# -------------------------------------
# main program
# command-line args
if len(sys.argv) != 3:
print("Syntax: python vasp_wrap.py file/zmq POSCARfile")
sys.exit(1)
mode = sys.argv[1]
poscar_template = sys.argv[2]
if mode == "file": cs = CSlib(1,mode,"tmp.couple",None)
elif mode == "zmq": cs = CSlib(1,mode,"*:5555",None)
else:
print("Syntax: python vasp_wrap.py file/zmq POSCARfile")
sys.exit(1)
natoms,ntypes,box = vasp_setup(poscar_template)
# initial message for MD protocol
msgID,nfield,fieldID,fieldtype,fieldlen = cs.recv()
if msgID != 0: error("Bad initial client/server handshake")
protocol = cs.unpack_string(1)
if protocol != "md": error("Mismatch in client/server protocol")
cs.send(0,0)
# endless server loop
while 1:
# recv message from client
# msgID = 0 = all-done message
msgID,nfield,fieldID,fieldtype,fieldlen = cs.recv()
if msgID < 0: break
# SETUP receive at beginning of each run
# required fields: DIM, PERIODICTY, ORIGIN, BOX,
# NATOMS, NTYPES, TYPES, COORDS
# optional fields: others in enum above, but VASP ignores them
if msgID == SETUP:
origin = []
box = []
natoms_recv = ntypes_recv = 0
types = []
coords = []
for field in fieldID:
if field == DIM:
dim = cs.unpack_int(DIM)
if dim != 3: error("VASP only performs 3d simulations")
elif field == PERIODICITY:
periodicity = cs.unpack(PERIODICITY,1)
if not periodicity[0] or not periodicity[1] or not periodicity[2]:
error("VASP wrapper only currently supports fully periodic systems")
elif field == ORIGIN:
origin = cs.unpack(ORIGIN,1)
elif field == BOX:
box = cs.unpack(BOX,1)
elif field == NATOMS:
natoms_recv = cs.unpack_int(NATOMS)
if natoms != natoms_recv:
error("VASP wrapper mis-match in number of atoms")
elif field == NTYPES:
ntypes_recv = cs.unpack_int(NTYPES)
if ntypes != ntypes_recv:
error("VASP wrapper mis-match in number of atom types")
elif field == TYPES:
types = cs.unpack(TYPES,1)
elif field == COORDS:
coords = cs.unpack(COORDS,1)
if not origin or not box or not natoms or not ntypes or \
not types or not coords:
error("Required VASP wrapper setup field not received");
# STEP receive at each timestep of run or minimization
# required fields: COORDS
# optional fields: ORIGIN, BOX
elif msgID == STEP:
coords = []
for field in fieldID:
if field == COORDS:
coords = cs.unpack(COORDS,1)
elif field == ORIGIN:
origin = cs.unpack(ORIGIN,1)
elif field == BOX:
box = cs.unpack(BOX,1)
if not coords: error("Required VASP wrapper step field not received");
else: error("VASP wrapper received unrecognized message")
# create POSCAR file
poscar_write(poscar_template,natoms,ntypes,types,coords,box)
# invoke VASP
print("\nLaunching VASP ...")
print(vaspcmd)
subprocess.check_output(vaspcmd,stderr=subprocess.STDOUT,shell=True)
# process VASP output
energy,forces,virial = vasprun_read()
# convert VASP kilobars to bars
for i,value in enumerate(virial): virial[i] *= 1000.0
# return forces, energy, pressure to client
cs.send(msgID,3);
cs.pack(FORCES,4,3*natoms,forces)
cs.pack_double(ENERGY,energy)
cs.pack(VIRIAL,4,6,virial)
# final reply to client
cs.send(0,0)
# clean-up
del cs

12329
examples/COUPLE/lammps_vasp/vasprun.xml Normal file
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File diff suppressed because it is too large Load Diff

4
examples/DIFFUSE/README
View File

@ -47,7 +47,7 @@ compute the diffusion coefficient. You can see that both measures
give roughly the same answer and rapidly become roughly constant for
the 100K step simulation.
Dcoeff = 0.36
Dcoeff = 0.33
(2) in.vacf.2d
@ -58,4 +58,4 @@ that point in time, converted into the diffusion coefficient. You can
see the VACF approach gives a more noise, fluctuating value for the
diffusion coefficient, compared to the MSD approach.
Dcoeff = 0.25 to 0.45
Dcoeff = ~0.25

245
examples/DIFFUSE/log.13Oct16.msd.2d.g++.8
View File

@ -1,245 +0,0 @@
LAMMPS (13 Oct 2016)
# sample LAMMPS input script for diffusion of 2d LJ liquid
# mean-squared displacement via compute msd
# settings
variable x equal 40
variable y equal 40
variable rho equal 0.6
variable t equal 1.0
variable rc equal 2.5
# problem setup
units lj
dimension 2
atom_style atomic
neigh_modify delay 0 every 1
lattice sq2 ${rho}
lattice sq2 0.6
Lattice spacing in x,y,z = 1.82574 1.82574 1.82574
region simbox block 0 $x 0 $y -0.1 0.1
region simbox block 0 40 0 $y -0.1 0.1
region simbox block 0 40 0 40 -0.1 0.1
create_box 1 simbox
Created orthogonal box = (0 0 -0.182574) to (73.0297 73.0297 0.182574)
4 by 2 by 1 MPI processor grid
create_atoms 1 box
Created 3200 atoms
pair_style lj/cut ${rc}
pair_style lj/cut 2.5
pair_coeff * * 1 1
mass * 1.0
velocity all create $t 97287
velocity all create 1 97287
fix 1 all nve
fix 2 all langevin $t $t 0.1 498094
fix 2 all langevin 1 $t 0.1 498094
fix 2 all langevin 1 1 0.1 498094
fix 3 all enforce2d
# equilibration run
thermo 1000
run 5000
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4 -> bins = 53 53 1
Memory usage per processor = 2.478 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1 -1.56492 0 -0.5652325 -1.5346995
1000 0.97537833 -1.5723957 0 -0.5973222 0.92877783
2000 0.99008371 -1.5748206 0 -0.58504633 1.0809416
3000 1.0111412 -1.5848987 0 -0.57407352 1.0174297
4000 1.0055417 -1.5857581 0 -0.58053054 0.95647691
5000 0.97069905 -1.5851114 0 -0.61471567 0.90108287
Loop time of 0.554412 on 8 procs for 5000 steps with 3200 atoms
Performance: 3896017.421 tau/day, 9018.559 timesteps/s
98.9% CPU use with 8 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.23992 | 0.24608 | 0.25161 | 0.7 | 44.39
Neigh | 0.063106 | 0.064417 | 0.066279 | 0.4 | 11.62
Comm | 0.072465 | 0.085066 | 0.094837 | 2.3 | 15.34
Output | 0.00013208 | 0.00013691 | 0.00014591 | 0.0 | 0.02
Modify | 0.11441 | 0.11621 | 0.11769 | 0.3 | 20.96
Other | | 0.04251 | | | 7.67
Nlocal: 400 ave 406 max 394 min
Histogram: 1 1 0 1 0 2 1 0 1 1
Nghost: 202.5 ave 212 max 191 min
Histogram: 1 0 0 0 3 1 0 2 0 1
Neighs: 2800.88 ave 2903 max 2690 min
Histogram: 1 1 0 0 1 2 1 0 1 1
Total # of neighbors = 22407
Ave neighs/atom = 7.00219
Neighbor list builds = 599
Dangerous builds = 0
unfix 2
# data gathering run
reset_timestep 0
# factor of 4 in 2 variables is for 2d
compute msd all msd com yes
variable twopoint equal c_msd[4]/4/(step*dt+1.0e-6)
fix 9 all vector 10 c_msd[4]
variable fitslope equal slope(f_9)/4/(10*dt)
thermo_style custom step temp c_msd[4] v_twopoint v_fitslope
# only need to run for 10K steps to make a good 100-frame movie
#dump 1 all custom 1 tmp.dump id type vx vy vz
#dump 2 all image 100 image.*.jpg type type zoom 1.6 adiam 1.2
thermo 1000
run 100000
Memory usage per processor = 2.853 Mbytes
Step Temp c_msd[4] v_twopoint v_fitslope
0 0.97069905 0 0 5e+20
1000 0.98138076 4.0484996 0.20242494 0.18046446
2000 0.97606079 9.2121392 0.23030346 0.2091528
3000 0.97924866 14.815034 0.24691721 0.22619184
4000 0.98568451 20.516817 0.25646019 0.23715506
5000 0.97551815 27.33922 0.27339219 0.24709999
6000 0.98482252 34.37734 0.28647782 0.25735178
7000 0.9672559 41.696689 0.29783348 0.26654059
8000 0.9836541 48.340277 0.30212673 0.27440308
9000 0.99087147 56.042692 0.31134828 0.28113047
10000 0.99663166 63.69663 0.31848314 0.28767921
11000 0.97776688 71.144109 0.32338231 0.29344527
12000 0.98246011 78.301774 0.32625739 0.29849471
13000 0.98788732 85.061923 0.32716124 0.3026655
14000 0.96872483 91.1658 0.32559214 0.30601023
15000 0.98955796 97.278388 0.32426129 0.3084275
16000 0.99855196 104.23997 0.3257499 0.31049883
17000 0.98600861 110.66055 0.3254722 0.31220348
18000 0.98696963 116.90111 0.32472531 0.31352676
19000 0.9881192 124.21305 0.32687644 0.31480062
20000 0.98527319 131.09874 0.32774685 0.31596198
21000 0.99015191 137.89263 0.32831579 0.31705324
22000 0.97972418 146.68982 0.33338595 0.31833889
23000 0.98911012 155.1264 0.33723129 0.31979515
24000 0.98810498 162.88634 0.33934653 0.32131187
25000 0.96961962 170.37907 0.34075814 0.32276215
26000 0.99118408 179.26511 0.34474059 0.32427111
27000 0.98515159 185.90764 0.3442734 0.32574529
28000 0.98951677 192.12183 0.34307469 0.32700292
29000 0.9832026 196.99457 0.33964581 0.32799023
30000 0.98449493 203.48475 0.33914124 0.3287171
31000 0.96585993 210.06193 0.33880956 0.32935775
32000 0.98758117 218.94174 0.34209646 0.33001591
33000 0.98875584 225.96489 0.34237104 0.33072947
34000 0.98007229 233.5792 0.34349882 0.3314385
35000 0.98415295 241.98148 0.34568783 0.33216634
36000 0.98101154 250.30876 0.34765106 0.33295272
37000 0.97606878 258.2127 0.34893608 0.33377673
38000 0.97220293 266.40464 0.35053242 0.33459273
39000 0.979783 272.8578 0.34981769 0.33539728
40000 0.98375673 279.87598 0.34984497 0.33609699
41000 0.97506523 288.07676 0.35131312 0.33677708
42000 0.97106749 296.11647 0.3525196 0.33751312
43000 0.97717259 304.46747 0.35403194 0.33823441
44000 0.98541435 312.57228 0.35519578 0.3389771
45000 0.97678287 321.82674 0.35758527 0.33973306
46000 0.98169719 329.78197 0.35845866 0.34051748
47000 0.99471466 337.11283 0.35863066 0.34127239
48000 0.98332437 346.0754 0.3604952 0.34202442
49000 0.98126947 356.11859 0.36338631 0.34282132
50000 0.98809751 365.65248 0.36565248 0.34368171
51000 0.95919516 373.91833 0.36658659 0.34454516
52000 0.98097913 381.26492 0.36660089 0.34538506
53000 0.97774072 388.81031 0.36680218 0.34618232
54000 0.99096915 395.56767 0.36626636 0.3469296
55000 0.97652739 401.72735 0.36520668 0.34760374
56000 0.99185306 407.28834 0.3636503 0.34819906
57000 0.96289342 414.75298 0.3638184 0.34871992
58000 0.97871716 424.69443 0.36611588 0.34927986
59000 0.98637393 433.14205 0.36706953 0.34986296
60000 0.98009845 438.14533 0.36512111 0.35040349
61000 0.99416712 446.08007 0.3656394 0.35088379
62000 0.97612483 450.90846 0.36363585 0.35132647
63000 0.97786531 455.36749 0.36140277 0.35167458
64000 0.99080668 458.04873 0.35785057 0.3519105
65000 0.97952497 461.31241 0.3548557 0.3520506
66000 0.98095955 463.91727 0.35145248 0.35207764
67000 0.98370788 468.93 0.34994776 0.35204043
68000 0.96931818 471.07765 0.34638063 0.35192685
69000 0.98512552 474.59146 0.34390685 0.35174053
70000 0.98065743 478.66071 0.3419005 0.35149002
71000 0.98971283 482.57357 0.33984054 0.35119434
72000 0.99890324 485.32018 0.3370279 0.35084345
73000 0.98649924 490.19497 0.33574998 0.35043722
74000 0.98723422 496.04991 0.33516886 0.35003351
75000 1.0025633 501.6313 0.33442087 0.34962094
76000 0.97859959 505.97813 0.33288035 0.34921013
77000 0.97973006 510.55334 0.33152814 0.3487692
78000 0.9903944 515.06966 0.33017286 0.34830833
79000 0.96847518 518.76483 0.32833217 0.3478214
80000 0.99171112 524.18127 0.32761329 0.34733349
81000 0.97202573 529.09959 0.32660468 0.3468315
82000 0.99368438 535.80271 0.32670897 0.34633058
83000 0.97932483 543.08233 0.32715803 0.34586259
84000 0.99078651 547.57861 0.32593965 0.34540839
85000 0.98973457 552.24581 0.32485048 0.34493584
86000 0.9835873 557.3493 0.32404029 0.34446152
87000 0.97180564 564.93434 0.32467491 0.34400358
88000 0.99743353 571.39837 0.32465817 0.3435667
89000 0.98993437 577.81703 0.32461631 0.3431411
90000 0.9926071 583.39378 0.32410765 0.342724
91000 0.98800458 591.08741 0.3247733 0.34232767
92000 0.98501879 596.10133 0.32396811 0.34193949
93000 0.98810082 604.02652 0.32474544 0.3415681
94000 0.97563748 609.43676 0.32416849 0.341209
95000 0.97283448 615.15754 0.32376713 0.34084828
96000 0.9883071 622.30912 0.32411933 0.34049871
97000 0.97717678 628.84457 0.32414669 0.34016355
98000 0.97190208 634.37377 0.32366009 0.3398341
99000 0.98687379 640.66666 0.32356902 0.33950845
100000 0.97559757 646.96406 0.32348203 0.33919036
Loop time of 9.58779 on 8 procs for 100000 steps with 3200 atoms
Performance: 4505729.040 tau/day, 10429.928 timesteps/s
99.4% CPU use with 8 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 4.8572 | 4.9363 | 4.9822 | 1.7 | 51.49
Neigh | 1.3583 | 1.376 | 1.3991 | 1.2 | 14.35
Comm | 1.5192 | 1.7079 | 1.8264 | 7.2 | 17.81
Output | 0.0085125 | 0.0086059 | 0.0089455 | 0.1 | 0.09
Modify | 0.77663 | 0.7903 | 0.81378 | 1.3 | 8.24
Other | | 0.7686 | | | 8.02
Nlocal: 400 ave 413 max 391 min
Histogram: 2 1 0 2 0 0 1 1 0 1
Nghost: 204.75 ave 213 max 197 min
Histogram: 1 1 0 1 0 3 0 1 0 1
Neighs: 2800.62 ave 2959 max 2661 min
Histogram: 1 1 1 2 0 0 0 1 1 1
Total # of neighbors = 22405
Ave neighs/atom = 7.00156
Neighbor list builds = 12728
Dangerous builds = 0
Total wall time: 0:00:10

251
examples/DIFFUSE/log.3Aug18.msd.2d.g++.8 Normal file
View File

@ -0,0 +1,251 @@
LAMMPS (2 Aug 2018)
# sample LAMMPS input script for diffusion of 2d LJ liquid
# mean-squared displacement via compute msd
# settings
variable x equal 40
variable y equal 40
variable rho equal 0.6
variable t equal 1.0
variable rc equal 2.5
# problem setup
units lj
dimension 2
atom_style atomic
neigh_modify delay 0 every 1
lattice sq2 ${rho}
lattice sq2 0.6
Lattice spacing in x,y,z = 1.82574 1.82574 1.82574
region simbox block 0 $x 0 $y -0.1 0.1
region simbox block 0 40 0 $y -0.1 0.1
region simbox block 0 40 0 40 -0.1 0.1
create_box 1 simbox
Created orthogonal box = (0 0 -0.182574) to (73.0297 73.0297 0.182574)
4 by 2 by 1 MPI processor grid
create_atoms 1 box
Created 3200 atoms
Time spent = 0.000706911 secs
pair_style lj/cut ${rc}
pair_style lj/cut 2.5
pair_coeff * * 1 1
mass * 1.0
velocity all create $t 97287
velocity all create 1 97287
fix 1 all nve
fix 2 all langevin $t $t 0.1 498094
fix 2 all langevin 1 $t 0.1 498094
fix 2 all langevin 1 1 0.1 498094
fix 3 all enforce2d
# equilibration run
thermo 1000
run 5000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 53 53 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/2d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.052 | 3.052 | 3.052 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1 -1.56492 0 -0.5652325 -1.5346995
1000 0.97537833 -1.5723957 0 -0.5973222 0.92877783
2000 0.99008371 -1.5748206 0 -0.58504633 1.0809416
3000 1.0111412 -1.5848987 0 -0.57407352 1.0174297
4000 1.0055417 -1.5857581 0 -0.58053054 0.95647691
5000 0.97069905 -1.5851114 0 -0.61471567 0.90108287
Loop time of 0.667446 on 8 procs for 5000 steps with 3200 atoms
Performance: 3236214.756 tau/day, 7491.238 timesteps/s
99.9% CPU use with 8 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.22913 | 0.24877 | 0.28382 | 3.6 | 37.27
Neigh | 0.064419 | 0.071256 | 0.080013 | 1.7 | 10.68
Comm | 0.103 | 0.14054 | 0.17204 | 5.5 | 21.06
Output | 0.00010705 | 0.00013995 | 0.00021911 | 0.0 | 0.02
Modify | 0.13457 | 0.14973 | 0.16887 | 2.6 | 22.43
Other | | 0.05701 | | | 8.54
Nlocal: 400 ave 406 max 394 min
Histogram: 1 1 0 1 0 2 1 0 1 1
Nghost: 202.5 ave 212 max 191 min
Histogram: 1 0 0 0 3 1 0 2 0 1
Neighs: 2800.88 ave 2903 max 2690 min
Histogram: 1 1 0 0 1 2 1 0 1 1
Total # of neighbors = 22407
Ave neighs/atom = 7.00219
Neighbor list builds = 599
Dangerous builds = 0
unfix 2
# data gathering run
reset_timestep 0
# factor of 4 in 2 variables is for 2d
compute msd all msd com yes
variable twopoint equal c_msd[4]/4/(step*dt+1.0e-6)
fix 9 all vector 10 c_msd[4]
variable fitslope equal slope(f_9)/4/(10*dt)
thermo_style custom step temp c_msd[4] v_twopoint v_fitslope
# only need to run for 10K steps to make a good 100-frame movie
#dump 1 all custom 1 tmp.dump id type vx vy vz
#dump 2 all image 100 image.*.jpg type type zoom 1.6 adiam 1.2
thermo 1000
run 100000
Per MPI rank memory allocation (min/avg/max) = 3.427 | 3.427 | 3.427 Mbytes
Step Temp c_msd[4] v_twopoint v_fitslope
0 0.97069905 0 0 5e+20
1000 0.98138076 4.0484996 0.20242494 0.20685564
2000 0.97606079 9.2121392 0.23030346 0.23687918
3000 0.97924866 14.815034 0.24691721 0.25405247
4000 0.98568451 20.516817 0.25646019 0.26353644
5000 0.97551815 27.33922 0.27339219 0.27544492
6000 0.98482252 34.37734 0.28647782 0.28966619
7000 0.9672559 41.696689 0.29783348 0.30165524
8000 0.9836541 48.340277 0.30212673 0.31085371
9000 0.99087147 56.042692 0.31134828 0.31811489
10000 0.99663166 63.69663 0.31848314 0.32589374
11000 0.97776688 71.144109 0.32338231 0.33219745
12000 0.98246011 78.301774 0.32625739 0.33723
13000 0.98788732 85.061923 0.32716124 0.34053027
14000 0.96872483 91.1658 0.32559214 0.34231162
15000 0.98955796 97.278388 0.32426129 0.34229511
16000 0.99855196 104.23997 0.3257499 0.34217252
17000 0.98600861 110.66055 0.3254722 0.34172446
18000 0.98696963 116.90111 0.32472531 0.3408227
19000 0.9881192 124.21305 0.32687644 0.34036538
20000 0.98527319 131.09874 0.32774685 0.34003478
21000 0.99015191 137.89263 0.32831579 0.33987868
22000 0.97972418 146.68982 0.33338595 0.34060035
23000 0.98911012 155.1264 0.33723129 0.34201036
24000 0.98810498 162.88634 0.33934653 0.34371488
25000 0.96961962 170.37907 0.34075814 0.34531409
26000 0.99118408 179.26511 0.34474059 0.34717195
27000 0.98515159 185.90764 0.3442734 0.34898035
28000 0.98951677 192.12183 0.34307469 0.35021808
29000 0.9832026 196.99457 0.33964581 0.35075459
30000 0.98449493 203.48475 0.33914124 0.35066186
31000 0.96585993 210.06193 0.33880956 0.35046715
32000 0.98758117 218.94174 0.34209646 0.35046623
33000 0.98875584 225.96489 0.34237104 0.35073944
34000 0.98007229 233.5792 0.34349882 0.35109188
35000 0.98415295 241.98148 0.34568783 0.35157879
36000 0.98101154 250.30876 0.34765106 0.3523013
37000 0.97606878 258.2127 0.34893608 0.35318097
38000 0.97220293 266.40464 0.35053242 0.3540743
39000 0.979783 272.8578 0.34981769 0.35496561
40000 0.98375673 279.87598 0.34984497 0.35558182
41000 0.97506523 288.07676 0.35131312 0.35618259
42000 0.97106749 296.11647 0.3525196 0.35698571
43000 0.97717259 304.46747 0.35403194 0.3577736
44000 0.98541435 312.57228 0.35519578 0.35865003
45000 0.97678287 321.82674 0.35758527 0.35958623
46000 0.98169719 329.78197 0.35845866 0.36062236
47000 0.99471466 337.11283 0.35863066 0.36158322
48000 0.98332437 346.0754 0.3604952 0.36255042
49000 0.98126947 356.11859 0.36338631 0.3636628
50000 0.98809751 365.65248 0.36565248 0.36496809
51000 0.95919516 373.91833 0.36658659 0.36628073
52000 0.98097913 381.26492 0.36660089 0.36752237
53000 0.97774072 388.81031 0.36680218 0.36863962
54000 0.99096915 395.56767 0.36626636 0.36961521
55000 0.97652739 401.72735 0.36520668 0.37038579
56000 0.99185306 407.28834 0.3636503 0.37094092
57000 0.96289342 414.75298 0.3638184 0.37130039
58000 0.97871716 424.69443 0.36611588 0.37180428
59000 0.98637393 433.14205 0.36706953 0.37239862
60000 0.98009845 438.14533 0.36512111 0.37288487
61000 0.99416712 446.08007 0.3656394 0.37321496
62000 0.97612483 450.90846 0.36363585 0.37345792
63000 0.97786531 455.36749 0.36140277 0.37344803
64000 0.99080668 458.04873 0.35785057 0.37313914
65000 0.97952497 461.31241 0.3548557 0.3725875
66000 0.98095955 463.91727 0.35145248 0.37174735
67000 0.98370788 468.93 0.34994776 0.37076942
68000 0.96931818 471.07765 0.34638063 0.36961868
69000 0.98512552 474.59146 0.34390685 0.36830908
70000 0.98065743 478.66071 0.3419005 0.36686789
71000 0.98971283 482.57357 0.33984054 0.36535224
72000 0.99890324 485.32018 0.3370279 0.36373174
73000 0.98649924 490.19497 0.33574998 0.36200692
74000 0.98723422 496.04991 0.33516886 0.36034919
75000 1.0025633 501.6313 0.33442087 0.35872052
76000 0.97859959 505.97813 0.33288035 0.35714939
77000 0.97973006 510.55334 0.33152814 0.35553808
78000 0.9903944 515.06966 0.33017286 0.35391584
79000 0.96847518 518.76483 0.32833217 0.35226287
80000 0.99171112 524.18127 0.32761329 0.35065267
81000 0.97202573 529.09959 0.32660468 0.34904364
82000 0.99368438 535.80271 0.32670897 0.34747913
83000 0.97932483 543.08233 0.32715803 0.34605097
84000 0.99078651 547.57861 0.32593965 0.34469765
85000 0.98973457 552.24581 0.32485048 0.34332115
86000 0.9835873 557.3493 0.32404029 0.34197018
87000 0.97180564 564.93434 0.32467491 0.34069702
88000 0.99743353 571.39837 0.32465817 0.33951258
89000 0.98993437 577.81703 0.32461631 0.33838511
90000 0.9926071 583.39378 0.32410765 0.33730429
91000 0.98800458 591.08741 0.3247733 0.33630505
92000 0.98501879 596.10133 0.32396811 0.33534725
93000 0.98810082 604.02652 0.32474544 0.33445545
94000 0.97563748 609.43676 0.32416849 0.33361404
95000 0.97283448 615.15754 0.32376713 0.33278044
96000 0.9883071 622.30912 0.32411933 0.33199212
97000 0.97717678 628.84457 0.32414669 0.33125729
98000 0.97190208 634.37377 0.32366009 0.33054877
99000 0.98687379 640.66666 0.32356902 0.32986014
100000 0.97559757 646.96406 0.32348203 0.32920186
Loop time of 7.61838 on 8 procs for 100000 steps with 3200 atoms
Performance: 5670494.518 tau/day, 13126.145 timesteps/s
100.0% CPU use with 8 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.5458 | 3.6709 | 3.8234 | 4.3 | 48.19
Neigh | 1.1363 | 1.1513 | 1.1753 | 1.0 | 15.11
Comm | 1.5901 | 1.7017 | 1.8664 | 6.9 | 22.34
Output | 0.0041966 | 0.0043583 | 0.0050626 | 0.4 | 0.06
Modify | 0.63816 | 0.65537 | 0.68918 | 2.0 | 8.60
Other | | 0.4348 | | | 5.71
Nlocal: 400 ave 413 max 391 min
Histogram: 2 1 0 2 0 0 1 1 0 1
Nghost: 204.75 ave 213 max 197 min
Histogram: 1 1 0 1 0 3 0 1 0 1
Neighs: 2800.62 ave 2959 max 2661 min
Histogram: 1 1 1 2 0 0 0 1 1 1
Total # of neighbors = 22405
Ave neighs/atom = 7.00156
Neighbor list builds = 12728
Dangerous builds = 0
Total wall time: 0:00:08

54
examples/DIFFUSE/log.13Oct16.vacf.2d.g++.8 → examples/DIFFUSE/log.3Aug18.vacf.2d.g++.8
View File

@ -1,4 +1,4 @@
LAMMPS (13 Oct 2016)
LAMMPS (2 Aug 2018)
# sample LAMMPS input script for diffusion of 2d LJ liquid
# mean-squared displacement via compute msd
@ -29,6 +29,7 @@ Created orthogonal box = (0 0 -0.182574) to (73.0297 73.0297 0.182574)
4 by 2 by 1 MPI processor grid
create_atoms 1 box
Created 3200 atoms
Time spent = 0.000712872 secs
pair_style lj/cut ${rc}
pair_style lj/cut 2.5
@ -49,13 +50,18 @@ fix 3 all enforce2d
thermo 1000
run 5000
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4 -> bins = 53 53 1
Memory usage per processor = 2.478 Mbytes
binsize = 1.4, bins = 53 53 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/2d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.052 | 3.052 | 3.052 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1 -1.56492 0 -0.5652325 -1.5346995
1000 0.97537833 -1.5723957 0 -0.5973222 0.92877783
@ -63,20 +69,20 @@ Step Temp E_pair E_mol TotEng Press
3000 1.0111412 -1.5848987 0 -0.57407352 1.0174297
4000 1.0055417 -1.5857581 0 -0.58053054 0.95647691
5000 0.97069905 -1.5851114 0 -0.61471567 0.90108287
Loop time of 0.557588 on 8 procs for 5000 steps with 3200 atoms
Loop time of 0.648098 on 8 procs for 5000 steps with 3200 atoms
Performance: 3873826.669 tau/day, 8967.191 timesteps/s
99.1% CPU use with 8 MPI tasks x no OpenMP threads
Performance: 3332829.949 tau/day, 7714.884 timesteps/s
99.9% CPU use with 8 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.23784 | 0.24683 | 0.25594 | 1.0 | 44.27
Neigh | 0.062975 | 0.06439 | 0.0662 | 0.4 | 11.55
Comm | 0.083826 | 0.092564 | 0.1035 | 2.1 | 16.60
Output | 0.00011778 | 0.00012615 | 0.00014257 | 0.1 | 0.02
Modify | 0.11466 | 0.11648 | 0.1187 | 0.4 | 20.89
Other | | 0.0372 | | | 6.67
Pair | 0.22614 | 0.24602 | 0.27481 | 2.8 | 37.96
Neigh | 0.066875 | 0.07135 | 0.077825 | 1.2 | 11.01
Comm | 0.098293 | 0.12744 | 0.1569 | 5.6 | 19.66
Output | 0.0001049 | 0.00012228 | 0.00014496 | 0.0 | 0.02
Modify | 0.13725 | 0.14919 | 0.16903 | 2.4 | 23.02
Other | | 0.05398 | | | 8.33
Nlocal: 400 ave 406 max 394 min
Histogram: 1 1 0 1 0 2 1 0 1 1
@ -114,7 +120,7 @@ thermo_style custom step temp c_vacf[4] v_vacf
thermo 1000
run 100000
Memory usage per processor = 2.853 Mbytes
Per MPI rank memory allocation (min/avg/max) = 3.427 | 3.427 | 3.427 Mbytes
Step Temp c_vacf[4] v_vacf
0 0.97069905 1.9407914 0
1000 0.98138076 0.029239763 0.22157396
@ -217,20 +223,20 @@ Step Temp c_vacf[4] v_vacf
98000 0.97190208 0.015065013 0.20906937
99000 0.98687379 -0.036869401 0.22993959
100000 0.97559757 0.045464091 0.23369283
Loop time of 10.8346 on 8 procs for 100000 steps with 3200 atoms
Loop time of 8.16691 on 8 procs for 100000 steps with 3200 atoms
Performance: 3987213.825 tau/day, 9229.662 timesteps/s
99.5% CPU use with 8 MPI tasks x no OpenMP threads
Performance: 5289636.190 tau/day, 12244.528 timesteps/s
100.0% CPU use with 8 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 4.8486 | 4.9469 | 5.0248 | 2.8 | 45.66
Neigh | 1.3613 | 1.374 | 1.3916 | 0.8 | 12.68
Comm | 1.8181 | 1.9534 | 2.0665 | 5.7 | 18.03
Output | 0.016565 | 0.016701 | 0.017039 | 0.1 | 0.15
Modify | 1.8395 | 1.9053 | 1.9704 | 2.8 | 17.59
Other | | 0.6383 | | | 5.89
Pair | 3.5668 | 3.6612 | 3.7867 | 4.0 | 44.83
Neigh | 1.1409 | 1.1555 | 1.1804 | 1.4 | 14.15
Comm | 1.581 | 1.711 | 1.8239 | 7.1 | 20.95
Output | 0.016626 | 0.016831 | 0.017569 | 0.2 | 0.21
Modify | 1.225 | 1.2594 | 1.3008 | 2.0 | 15.42
Other | | 0.363 | | | 4.45
Nlocal: 400 ave 413 max 391 min
Histogram: 2 1 0 2 0 0 1 1 0 1
@ -243,4 +249,4 @@ Total # of neighbors = 22405
Ave neighs/atom = 7.00156
Neighbor list builds = 12728
Dangerous builds = 0
Total wall time: 0:00:11
Total wall time: 0:00:08

2
examples/README
View File

@ -59,6 +59,7 @@ sub-directories:
accelerate: use of all the various accelerator packages
airebo: polyethylene with AIREBO potential
atm: Axilrod-Teller-Muto potential
balance: dynamic load balancing, 2d system
body: body particles, 2d system
cmap: CMAP 5-body contributions to CHARMM force field
@ -82,6 +83,7 @@ kim: use of potentials in Knowledge Base for Interatomic Models (KIM)
latte: use of LATTE density-functional tight-binding quantum code
meam: MEAM test for SiC and shear (same as shear examples)
melt: rapid melt of 3d LJ system
message: client/server coupling of 2 codes
micelle: self-assembly of small lipid-like molecules into 2d bilayers
min: energy minimization of 2d LJ melt
mscg: parameterize a multi-scale coarse-graining (MSCG) model

20
examples/SPIN/README Normal file
View File

@ -0,0 +1,20 @@
This directory contains examples and applications of the SPIN package
=====================================================================
- the iron, cobalt_hcp, cobalt_fcc and nickel directories provide
examples of spin-lattice calculations.
- the bfo repository provides an example of spin dynamics calculation
performed on a fixed lattice, and applied to the multiferroic
material bismuth-oxide.
- the read_restart directory provides examples allowing to write or
read data files, and restart magneto-mechanical simulations.
- vizualization of the dump files can be achieved using Ovito or
VMD. See the vmd repository for help vizualizing results with VMD.
** Note, the aim of this repository is mainly to provide users with
examples. Better values and tuning of the magnetic and mechanical
interactions can be achieved for more accurate materials
simulations. **

13
examples/SPIN/bfo/in.spin.bfo
View File

@ -21,9 +21,11 @@ mass 1 1.0
set group all spin/random 11 2.50
pair_style hybrid/overlay spin/exchange 6.0 spin/magelec 4.5
#pair_style hybrid/overlay spin/exchange 6.0 spin/magelec 4.5
pair_style hybrid/overlay spin/exchange 6.0 spin/magelec 4.5 spin/dmi 4.5
pair_coeff * * spin/exchange exchange 6.0 -0.01575 0.0 1.965
pair_coeff * * spin/magelec magelec 4.5 0.000109 1.0 1.0 1.0
pair_coeff * * spin/dmi dmi 4.5 0.00005 1.0 1.0 1.0
neighbor 0.1 bin
neigh_modify every 10 check yes delay 20
@ -34,7 +36,7 @@ fix 3 all nve/spin lattice no
timestep 0.0002
compute out_mag all compute/spin
compute out_mag all spin
compute out_pe all pe
compute out_ke all ke
compute out_temp all temp
@ -44,10 +46,11 @@ variable magnorm equal c_out_mag[4]
variable emag equal c_out_mag[5]
variable tmag equal c_out_mag[6]
thermo_style custom step time v_magnorm v_emag temp etotal
thermo 50
#thermo_style custom step time v_magnorm v_emag temp etotal
thermo_style custom step time v_magnorm pe ke v_emag temp etotal
thermo 10
compute outsp all property/atom spx spy spz sp fmx fmy fmz
dump 100 all custom 1 dump_bfo.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
run 5000
run 2000

2
examples/SPIN/cobalt_fcc/in.spin.cobalt_fcc
View File

@ -40,7 +40,7 @@ timestep 0.0001
# compute and output options
compute out_mag all compute/spin
compute out_mag all spin
compute out_pe all pe
compute out_ke all ke
compute out_temp all temp

12
examples/SPIN/cobalt_hcp/in.spin.cobalt_hcp
View File

@ -19,8 +19,8 @@ create_atoms 1 box
mass 1 58.93
#set group all spin/random 31 1.72
set group all spin 1.72 0.0 0.0 1.0
set group all spin/random 31 1.72
#set group all spin 1.72 0.0 0.0 1.0
velocity all create 100 4928459 rot yes dist gaussian
#pair_style hybrid/overlay eam/alloy spin/exchange 4.0 spin/neel 4.0
@ -29,18 +29,18 @@ pair_coeff * * eam/alloy Co_PurjaPun_2012.eam.alloy Co
pair_coeff * * spin/exchange exchange 4.0 0.3593 1.135028015e-05 1.064568567
#pair_coeff * * spin/neel neel 4.0 0.0048 0.234 1.168 2.6905 0.705 0.652
neighbor 0.1 bin
neigh_modify every 10 check yes delay 20
fix 1 all precession/spin zeeman 1.0 0.0 0.0 1.0
#fix 1 all precession/spin zeeman 1.0 0.0 0.0 1.0
fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0
fix 2 all langevin/spin 0.0 0.0 21
fix 3 all nve/spin lattice yes
timestep 0.0001
compute out_mag all compute/spin
compute out_mag all spin
compute out_pe all pe
compute out_ke all ke
compute out_temp all temp
@ -56,4 +56,4 @@ thermo 10
compute outsp all property/atom spx spy spz sp fmx fmy fmz
dump 100 all custom 1 dump_cobalt_hcp.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
run 2000
run 20000

2
examples/SPIN/iron/in.spin.iron
View File

@ -37,7 +37,7 @@ timestep 0.0001
# compute and output options
compute out_mag all compute/spin
compute out_mag all spin
compute out_pe all pe
compute out_ke all ke
compute out_temp all temp

2
examples/SPIN/nickel/in.spin.nickel
View File

@ -38,7 +38,7 @@ timestep 0.0001
# compute and output options
compute out_mag all compute/spin
compute out_mag all spin
compute out_pe all pe
compute out_ke all ke
compute out_temp all temp

2
examples/SPIN/read_restart/in.spin.read_data
View File

@ -25,7 +25,7 @@ timestep 0.0001
# define outputs and computes
compute out_mag all compute/spin
compute out_mag all spin
compute out_pe all pe
compute out_ke all ke
compute out_temp all temp

2
examples/SPIN/read_restart/in.spin.restart
View File

@ -29,7 +29,7 @@ timestep 0.0001
# define outputs
compute out_mag all compute/spin
compute out_mag all spin
compute out_pe all pe
compute out_ke all ke
compute out_temp all temp

2
examples/SPIN/read_restart/in.spin.write_restart
View File

@ -34,7 +34,7 @@ timestep 0.0001
# compute and output options
compute out_mag all compute/spin
compute out_mag all spin
compute out_pe all pe
compute out_ke all ke
compute out_temp all temp

7
examples/USER/diffraction/BulkNi.in
View File

@ -17,10 +17,11 @@ atom_modify sort 0 0
compute XRD all xrd 1.541838 Ni 2Theta 40 80 c 2 2 2 LP 1 echo
compute SAED all saed 0.0251 Ni Kmax 0.85 Zone 1 0 0 c 0.025 0.025 0.025 &
dR_Ewald 0.05 echo manual
compute SAED all saed 0.0251 Ni Kmax 0.85 &
Zone 0 0 0 c 0.025 0.025 0.025 &
dR_Ewald 0.01 echo manual
fix 1 all ave/histo 1 1 1 40 80 200 c_XRD[1] c_XRD[2] &
fix 1 all ave/histo/weight 1 1 1 40 80 200 c_XRD[1] c_XRD[2] &
mode vector file $A.hist.xrd
fix 2 all saed/vtk 1 1 1 c_SAED file $A_001.saed

35
examples/USER/diffraction/Output/BulkNi.in
View File

@ -1,35 +0,0 @@
variable A string bulkNi
log $A.log
boundary p p p
units metal
timestep 0.001
lattice fcc 3.52
region box block 0 20 0 20 0 20
create_box 1 box
create_atoms 1 box
pair_style none
mass * 58.71
atom_modify sort 0 0
compute XRD all xrd 1.541838 Ni 2Theta 40 80 c 2 2 2 LP 1 echo
compute SAED all saed 0.0251 Ni Kmax 0.85 &
Zone 0 0 0 c 0.025 0.025 0.025 &
dR_Ewald 0.01 echo manual
fix 1 all ave/histo/weight 1 1 1 40 80 200 c_XRD[1] c_XRD[2] &
mode vector file $A.hist.xrd
fix 2 all saed/vtk 1 1 1 c_SAED file $A_001.saed
dump 1 all custom 1 $A.dump id x y z
run 0
unfix 1
unfix 2
uncompute XRD
uncompute SAED

2467
examples/USER/misc/mop/data.mop Normal file
View File

File diff suppressed because it is too large Load Diff

40
examples/USER/misc/mop/in.compute_stress_mop Normal file
View File

@ -0,0 +1,40 @@
variable T equal 0.8
variable p_solid equal 0.05
read_data data.mop
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0
pair_coeff 1 2 0.5 1.0
pair_coeff 2 2 0.0 0.0
neigh_modify delay 0
group liquid type 1
group solid type 2
region bottom block INF INF INF INF INF 7.0
group bottom region bottom
group solid_bottom intersect solid bottom
group solid_up subtract solid solid_bottom
variable faSolid equal ${p_solid}*lx*ly/count(solid_up)
fix piston_up solid_up aveforce NULL NULL -${faSolid}
fix freeze_up solid_up setforce 0.0 0.0 NULL
fix freeze_bottom solid_bottom setforce 0.0 0.0 0.0
fix nvesol solid nve
compute Tliq liquid temp
fix nvtliq liquid nvt temp $T $T 0.5
fix_modify nvtliq temp Tliq
thermo 1000
thermo_modify flush yes temp Tliq
fix fxbal all balance 1000 1.05 shift z 10 1.05
compute mopz0 all stress/mop z center kin conf
fix mopz0t all ave/time 1 1 1 c_mopz0[*] file mopz0.time
compute moppz liquid stress/mop/profile z 0.0 0.1 kin conf
fix moppzt all ave/time 1 1 1 c_moppz[*] ave running overwrite file moppz.time mode vector
run 0

111
examples/USER/misc/mop/log.5Sep18.compute_stress_mop.g++.1 Normal file
View File

@ -0,0 +1,111 @@
LAMMPS (5 Sep 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
variable T equal 0.8
variable p_solid equal 0.05
read_data data.mop
orthogonal box = (0 0 -2) to (9.52441 9.52441 16)
1 by 1 by 1 MPI processor grid
reading atoms ...
1224 atoms
reading velocities ...
1224 velocities
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0
pair_coeff 1 2 0.5 1.0
pair_coeff 2 2 0.0 0.0
neigh_modify delay 0
group liquid type 1
792 atoms in group liquid
group solid type 2
432 atoms in group solid
region bottom block INF INF INF INF INF 7.0
group bottom region bottom
630 atoms in group bottom
group solid_bottom intersect solid bottom
216 atoms in group solid_bottom
group solid_up subtract solid solid_bottom
216 atoms in group solid_up
variable faSolid equal ${p_solid}*lx*ly/count(solid_up)
variable faSolid equal 0.05*lx*ly/count(solid_up)
fix piston_up solid_up aveforce NULL NULL -${faSolid}
fix piston_up solid_up aveforce NULL NULL -0.0209986841649146
fix freeze_up solid_up setforce 0.0 0.0 NULL
fix freeze_bottom solid_bottom setforce 0.0 0.0 0.0
fix nvesol solid nve
compute Tliq liquid temp
fix nvtliq liquid nvt temp $T $T 0.5
fix nvtliq liquid nvt temp 0.8 $T 0.5
fix nvtliq liquid nvt temp 0.8 0.8 0.5
fix_modify nvtliq temp Tliq
WARNING: Temperature for fix modify is not for group all (src/fix_nh.cpp:1404)
thermo 1000
thermo_modify flush yes temp Tliq
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:488)
fix fxbal all balance 1000 1.05 shift z 10 1.05
compute mopz0 all stress/mop z center kin conf
fix mopz0t all ave/time 1 1 1 c_mopz0[*] file mopz0.time
compute moppz liquid stress/mop/profile z 0.0 0.1 kin conf
fix moppzt all ave/time 1 1 1 c_moppz[*] ave running overwrite file moppz.time mode vector
run 0
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 7 7 13
3 neighbor lists, perpetual/occasional/extra = 1 2 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
(2) compute stress/mop, occasional, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
(3) compute stress/mop/profile, occasional, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 3.596 | 3.596 | 3.596 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 0.82011245 -3.0642111 0 -2.2692246 0.16906107 1632.8577
Loop time of 1.19209e-06 on 1 procs for 0 steps with 1224 atoms
167.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 1.192e-06 | | |100.00
Nlocal: 1224 ave 1224 max 1224 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2975 ave 2975 max 2975 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 40241 ave 40241 max 40241 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 40241
Ave neighs/atom = 32.8766
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00

111
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LAMMPS (5 Sep 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
variable T equal 0.8
variable p_solid equal 0.05
read_data data.mop
orthogonal box = (0 0 -2) to (9.52441 9.52441 16)
1 by 2 by 2 MPI processor grid
reading atoms ...
1224 atoms
reading velocities ...
1224 velocities
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0
pair_coeff 1 2 0.5 1.0
pair_coeff 2 2 0.0 0.0
neigh_modify delay 0
group liquid type 1
792 atoms in group liquid
group solid type 2
432 atoms in group solid
region bottom block INF INF INF INF INF 7.0
group bottom region bottom
630 atoms in group bottom
group solid_bottom intersect solid bottom
216 atoms in group solid_bottom
group solid_up subtract solid solid_bottom
216 atoms in group solid_up
variable faSolid equal ${p_solid}*lx*ly/count(solid_up)
variable faSolid equal 0.05*lx*ly/count(solid_up)
fix piston_up solid_up aveforce NULL NULL -${faSolid}
fix piston_up solid_up aveforce NULL NULL -0.0209986841649146
fix freeze_up solid_up setforce 0.0 0.0 NULL
fix freeze_bottom solid_bottom setforce 0.0 0.0 0.0
fix nvesol solid nve
compute Tliq liquid temp
fix nvtliq liquid nvt temp $T $T 0.5
fix nvtliq liquid nvt temp 0.8 $T 0.5
fix nvtliq liquid nvt temp 0.8 0.8 0.5
fix_modify nvtliq temp Tliq
WARNING: Temperature for fix modify is not for group all (src/fix_nh.cpp:1404)
thermo 1000
thermo_modify flush yes temp Tliq
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:488)
fix fxbal all balance 1000 1.05 shift z 10 1.05
compute mopz0 all stress/mop z center kin conf
fix mopz0t all ave/time 1 1 1 c_mopz0[*] file mopz0.time
compute moppz liquid stress/mop/profile z 0.0 0.1 kin conf
fix moppzt all ave/time 1 1 1 c_moppz[*] ave running overwrite file moppz.time mode vector
run 0
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 7 7 13
3 neighbor lists, perpetual/occasional/extra = 1 2 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
(2) compute stress/mop, occasional, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
(3) compute stress/mop/profile, occasional, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 3.509 | 3.51 | 3.511 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 0.82011245 -3.0642111 0 -2.2692246 0.16906107 1632.8577
Loop time of 4.06504e-05 on 4 procs for 0 steps with 1224 atoms
65.2% 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 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 4.065e-05 | | |100.00
Nlocal: 306 ave 320 max 295 min
Histogram: 1 1 0 0 0 0 1 0 0 1
Nghost: 1450.25 ave 1485 max 1422 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Neighs: 10060.2 ave 10866 max 9507 min
Histogram: 2 0 0 0 0 1 0 0 0 1
Total # of neighbors = 40241
Ave neighs/atom = 32.8766
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00

185
examples/USER/misc/mop/moppz.time.reference Normal file
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# Time-averaged data for fix moppzt
# TimeStep Number-of-rows
# Row c_moppz[1] c_moppz[2] c_moppz[3] c_moppz[4] c_moppz[5] c_moppz[6] c_moppz[7]
0 181
1 -2 0 0 0 0 0 0
2 -1.9 0 0 0 0 0 0
3 -1.8 0 0 0 0 0 0
4 -1.7 0 0 0 0 0 0
5 -1.6 0 0 0 0 0 0
6 -1.5 0 0 0 -9.81273e-05 0.000228605 -0.00421138
7 -1.4 0 0 0 -9.81273e-05 0.000228605 -0.00421138
8 -1.3 0 0 0 -9.81273e-05 0.000228605 -0.00421138
9 -1.2 0 0 0 -9.81273e-05 0.000228605 -0.00421138
10 -1.1 0 0 0 -9.81273e-05 0.000228605 -0.00421138
11 -1 0 0 0 -9.81273e-05 0.000228605 -0.00421138
12 -0.9 0 0 0 -9.81273e-05 0.000228605 -0.00421138
13 -0.8 0 0 0 -9.81273e-05 0.000228605 -0.00421138
14 -0.7 0 0 0 -0.000370675 -0.00240125 -0.26848
15 -0.6 0 0 0 -0.000370675 -0.00240125 -0.26848
16 -0.5 0 0 0 -0.000370675 -0.00240125 -0.26848
17 -0.4 0 0 0 -0.000370675 -0.00240125 -0.26848
18 -0.3 0 0 0 -0.000370675 -0.00240125 -0.26848
19 -0.2 0 0 0 -0.000370675 -0.00240125 -0.26848
20 -0.1 0 0 0 -0.000370675 -0.00240125 -0.26848
21 0 0 0 0 -0.000370675 -0.00240125 -0.26848
22 0.1 0 0 0 0.190761 -0.491728 0.287704
23 0.2 0 0 0 0.190761 -0.491728 0.287704
24 0.3 0 0 0 0.190761 -0.491728 0.287704
25 0.4 0 0 0 0.190761 -0.491728 0.287704
26 0.5 0 0 0 0.190761 -0.491728 0.287704
27 0.6 0 0 0 0.190761 -0.491728 0.287704
28 0.7 0 0 0 0.190761 -0.491728 0.287704
29 0.8 0 0 0 -0.181602 -0.198457 -0.0964774
30 0.9 0 0 0 -0.15138 0.183353 0.206848
31 1 0 0 0 0.174362 1.27701 0.600545
32 1.1 0 0 0 0.160987 0.563442 0.494994
33 1.2 0 0 0 0.218876 0.59796 0.398527
34 1.3 0 0 0 0.187614 0.558909 0.372353
35 1.4 0 0 0 0.118586 0.410013 0.331945
36 1.5 0 0 0 -0.0514208 0.40381 0.128097
37 1.6 3.08628 0.241189 5.90817 -0.198262 0.324128 -0.0449302
38 1.7 0 0 0 -0.104542 0.256677 -0.332854
39 1.8 0.222123 2.43524 1.10089 -0.324638 -0.168682 -1.06238
40 1.9 0 0 0 -0.175732 -0.186846 -0.163062
41 2 0 0 0 -0.137995 0.0920401 -0.260106
42 2.1 -0.179621 -2.59775 1.80077 -0.480624 -0.0439511 -0.0824913
43 2.2 0 0 0 -0.499868 -0.0106185 -0.108924
44 2.3 0 0 0 -0.703301 0.124555 -0.0880158
45 2.4 0 0 0 -0.581211 -0.244281 -0.250071
46 2.5 1.05274 -2.86043 3.36339 -0.575104 -0.148715 -0.249092
47 2.6 0 0 0 0.66061 -0.157649 -0.357141
48 2.7 0 0 0 0.299971 -0.302298 -0.572714
49 2.8 0 0 0 0.33107 -0.201699 -0.470466
50 2.9 0 0 0 0.822686 1.08427 -0.390511
51 3 0 0 0 0.716428 0.750998 -0.698174
52 3.1 0.805189 0.571878 4.31938 0.121891 0.922727 -0.932582
53 3.2 0 0 0 0.0442642 1.02537 -1.03066
54 3.3 2.54289 -1.93701 4.88355 0.0731321 1.09091 -0.83075
55 3.4 0 0 0 0.426589 0.821174 -0.765855
56 3.5 0 0 0 0.445135 0.299996 -1.48972
57 3.6 0 0 0 0.362916 -1.28673 -0.853897
58 3.7 0.952867 -1.07044 1.04141 0.12517 -1.00353 -0.785272
59 3.8 0.617661 0.991499 1.80973 -0.182369 -1.04057 -1.00435
60 3.9 0.60295 -2.41888 3.98011 0.0347345 -1.01302 -0.88314
61 4 -2.97421 -2.01531 2.98586 0.43463 -0.465643 -0.801128
62 4.1 -3.23318 -3.31281 0.956525 0.732752 0.140718 -1.10583
63 4.2 0 0 0 0.969872 0.298566 -0.823464
64 4.3 0 0 0 0.7707 0.557002 -0.836549
65 4.4 0 0 0 0.395828 0.66755 -1.53454
66 4.5 0 0 0 0.104451 0.46777 -1.32358
67 4.6 0 0 0 0.402084 0.464983 -1.22051
68 4.7 0 0 0 0.352808 0.0794986 -1.31292
69 4.8 0 0 0 0.0215512 0.284343 -0.975326
70 4.9 0 0 0 -0.133637 0.250925 -1.33918
71 5 0 0 0 -0.066208 0.104514 -1.27412
72 5.1 0 0 0 -0.184391 0.479805 -1.15139
73 5.2 0 0 0 -0.200251 0.527142 -1.34307
74 5.3 0 0 0 0.043532 -0.0788824 -0.998406
75 5.4 0 0 0 -0.531846 0.126289 -1.05818
76 5.5 0 0 0 -0.259593 0.0818463 -1.58939
77 5.6 0 0 0 -0.373828 -0.343977 -1.50908
78 5.7 -0.294161 -1.07567 3.46536 -0.0644873 -0.424333 -1.28548
79 5.8 0 0 0 -0.293233 -0.201133 -1.19085
80 5.9 0.961568 -1.44949 2.42101 -0.632816 -0.0669315 -0.85119
81 6 0 0 0 -0.0559892 -0.0194478 -1.04541
82 6.1 0 0 0 -0.339753 0.286693 -1.24366
83 6.2 0 0 0 -0.376208 0.444053 -1.7662
84 6.3 0 0 0 -0.718923 0.555398 -1.93862
85 6.4 0 0 0 -1.10631 0.263525 -1.79723
86 6.5 0 0 0 -0.217948 -0.0489491 -2.07833
87 6.6 0 0 0 -0.376248 -0.0588682 -2.45322
88 6.7 -2.12742 4.22609 2.36568 -0.236703 -0.279582 -1.56434
89 6.8 0.869072 -0.141389 3.92123 0.0540986 -0.00271606 -0.930143
90 6.9 0 0 0 1.08829 -1.11737 -0.808187
91 7 1.62633 1.08234 0.844097 1.18575 -0.408792 -0.752394
92 7.1 0 0 0 1.03324 -0.470631 -0.486767
93 7.2 0 0 0 0.950164 -0.112451 -0.479409
94 7.3 -2.66121 -0.326607 7.83093 0.359 -0.482493 0.154384
95 7.4 0 0 0 0.359089 -1.12337 0.409711
96 7.5 -1.88971 1.34806 3.56893 0.394677 -1.0109 0.548348
97 7.6 -1.34494 -0.896214 2.06959 0.231398 -0.728529 0.313513
98 7.7 0 0 0 0.415681 -0.45268 0.507181
99 7.8 0 0 0 0.259423 -0.11638 0.464208
100 7.9 -1.97572 -1.20836 3.95731 0.252257 -0.0845701 -0.249345
101 8 0 0 0 0.0688154 0.290386 -0.462467
102 8.1 0.25925 -0.458269 3.33086 0.360399 -0.0409494 -0.656911
103 8.2 0 0 0 -0.0587033 0.347698 -0.340604
104 8.3 0 0 0 -0.377192 0.153096 -0.914654
105 8.4 0 0 0 -0.431553 0.274996 -0.946252
106 8.5 0 0 0 -0.898366 0.146653 -1.36383
107 8.6 0 0 0 -0.889593 0.385951 0.125116
108 8.7 0 0 0 -0.0139171 -0.162302 -0.0287854
109 8.8 0 0 0 -0.266284 -0.148945 0.393533
110 8.9 0 0 0 -0.00920376 -0.0770818 0.334642
111 9 0 0 0 -0.0949156 0.0113352 -0.0761263
112 9.1 0 0 0 0.0688045 0.104558 -0.101891
113 9.2 3.79773 0.0255401 3.75032 0.419832 0.295402 0.652533
114 9.3 0 0 0 0.594267 0.70396 0.836434
115 9.4 0 0 0 0.174722 1.00483 1.42787
116 9.5 0 0 0 0.0626835 0.518952 0.269158
117 9.6 0 0 0 -0.302859 -0.265212 -0.0145578
118 9.7 0 0 0 -0.114026 -0.201336 -0.539522
119 9.8 0 0 0 0.104008 -0.30236 -0.0789062
120 9.9 0 0 0 -0.0482778 -0.553118 0.45214
121 10 0 0 0 -0.0554938 -0.402692 0.141112
122 10.1 0 0 0 0.174338 0.556958 -0.0922154
123 10.2 0 0 0 -1.06045 0.541565 -0.0409312
124 10.3 0 0 0 -1.20782 0.464574 -0.413871
125 10.4 0 0 0 -0.891701 0.327653 -0.286438
126 10.5 0 0 0 0.231227 -0.064277 -0.89684
127 10.6 -1.27989 -4.87365 9.40433 0.211278 0.230826 -1.23536
128 10.7 -2.1001 -0.417817 1.17745 0.425856 0.078728 -1.44229
129 10.8 0 0 0 0.30965 0.450884 -1.74985
130 10.9 0 0 0 0.36735 0.990032 -1.19971
131 11 0.253834 -1.84303 3.91828 1.01826 0.0660896 -0.481086
132 11.1 0 0 0 0.744006 0.0906555 -0.897417
133 11.2 0 0 0 0.339073 0.361038 -0.545084
134 11.3 -1.9974 -0.431998 3.46296 0.611295 0.17282 0.0341483
135 11.4 0 0 0 -0.491432 -0.958871 1.28001
136 11.5 0 0 0 0.0431048 -1.50924 1.24037
137 11.6 0 0 0 -0.684419 -0.0163951 1.06179
138 11.7 0 0 0 -0.425278 -0.127741 0.757298
139 11.8 -2.09164 0.00894897 2.22812 -0.0955178 -0.310572 0.661289
140 11.9 0 0 0 0.156959 -0.233409 0.802568
141 12 0 0 0 -0.05541 -0.346448 0.541571
142 12.1 0 0 0 0.706767 0.182767 0.25767
143 12.2 0 0 0 0.4791 0.464612 -0.212887
144 12.3 0 0 0 0.81454 0.440323 -0.461359
145 12.4 0 0 0 -0.110025 0.200698 -0.996706
146 12.5 0 0 0 -0.149791 0.165599 -1.02233
147 12.6 0 0 0 -0.170933 0.0644682 -0.866174
148 12.7 0 0 0 -0.122869 -0.0196287 -0.801348
149 12.8 0 0 0 -0.0693832 -0.0673091 -0.382802
150 12.9 0 0 0 -0.0693832 -0.0673091 -0.382802
151 13 0 0 0 -0.0693832 -0.0673091 -0.382802
152 13.1 0 0 0 -0.0693832 -0.0673091 -0.382802
153 13.2 0 0 0 -0.0693832 -0.0673091 -0.382802
154 13.3 0 0 0 -0.0693832 -0.0673091 -0.382802
155 13.4 0 0 0 -0.0693832 -0.0673091 -0.382802
156 13.5 0 0 0 -0.000502433 0.000137492 -0.227425
157 13.6 0 0 0 -0.000502433 0.000137492 -0.227425
158 13.7 0 0 0 -0.000502433 0.000137492 -0.227425
159 13.8 0 0 0 -0.000502433 0.000137492 -0.227425
160 13.9 0 0 0 -0.000502433 0.000137492 -0.227425
161 14 0 0 0 -0.000502433 0.000137492 -0.227425
162 14.1 0 0 0 -0.000502433 0.000137492 -0.227425
163 14.2 0 0 0 -0.000502433 0.000137492 -0.227425
164 14.3 0 0 0 5.79042e-05 4.68687e-05 -0.00286094
165 14.4 0 0 0 5.79042e-05 4.68687e-05 -0.00286094
166 14.5 0 0 0 5.79042e-05 4.68687e-05 -0.00286094
167 14.6 0 0 0 5.79042e-05 4.68687e-05 -0.00286094
168 14.7 0 0 0 5.79042e-05 4.68687e-05 -0.00286094
169 14.8 0 0 0 5.79042e-05 4.68687e-05 -0.00286094
170 14.9 0 0 0 5.79042e-05 4.68687e-05 -0.00286094
171 15 0 0 0 5.79042e-05 4.68687e-05 -0.00286094
172 15.1 0 0 0 0 0 0
173 15.2 0 0 0 0 0 0
174 15.3 0 0 0 0 0 0
175 15.4 0 0 0 0 0 0
176 15.5 0 0 0 0 0 0
177 15.6 0 0 0 0 0 0
178 15.7 0 0 0 0 0 0
179 15.8 0 0 0 0 0 0
180 15.9 0 0 0 0 0 0
181 16 0 0 0 0 0 0

3
examples/USER/misc/mop/mopz0.time.reference Normal file
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# Time-averaged data for fix mopz0t
# TimeStep c_mopz0[1] c_mopz0[2] c_mopz0[3] c_mopz0[4] c_mopz0[5] c_mopz0[6]
0 1.62633 1.08234 0.844097 1.18575 -0.408792 -0.752394

25
examples/USER/scafacos/data.NaCl Normal file
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LAMMPS Description
8 atoms
2 atom types
0 1 xlo xhi
0 1 ylo yhi
0 1 zlo zhi
Masses
1 22.98976928
2 35.45
Atoms
1 2 1 0.25 0.25 0.25
2 1 -1 0.75 0.25 0.25
3 1 -1 0.25 0.75 0.25
4 2 1 0.75 0.75 0.25
5 1 -1 0.25 0.25 0.75
6 2 1 0.75 0.25 0.75
7 2 1 0.25 0.75 0.75
8 1 -1 0.75 0.75 0.75

316
examples/USER/scafacos/data.cloud_wall Normal file
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@ -0,0 +1,316 @@
LAMMPS Description
300 atoms
1 atom types
0 10 xlo xhi
0 10 ylo yhi
0 10 zlo zhi
Masses
1 1.0
Atoms
1 1 1 0 0 4.5
2 1 -1 0 0 5.5
3 1 1 0 1 4.5
4 1 -1 0 1 5.5
5 1 1 0 2 4.5
6 1 -1 0 2 5.5
7 1 1 0 3 4.5
8 1 -1 0 3 5.5
9 1 1 0 4 4.5
10 1 -1 0 4 5.5
11 1 1 0 5 4.5
12 1 -1 0 5 5.5
13 1 1 0 6 4.5
14 1 -1 0 6 5.5
15 1 1 0 7 4.5
16 1 -1 0 7 5.5
17 1 1 0 8 4.5
18 1 -1 0 8 5.5
19 1 1 0 9 4.5
20 1 -1 0 9 5.5
21 1 1 1 0 4.5
22 1 -1 1 0 5.5
23 1 1 1 1 4.5
24 1 -1 1 1 5.5
25 1 1 1 2 4.5
26 1 -1 1 2 5.5
27 1 1 1 3 4.5
28 1 -1 1 3 5.5
29 1 1 1 4 4.5
30 1 -1 1 4 5.5
31 1 1 1 5 4.5
32 1 -1 1 5 5.5
33 1 1 1 6 4.5
34 1 -1 1 6 5.5
35 1 1 1 7 4.5
36 1 -1 1 7 5.5
37 1 1 1 8 4.5
38 1 -1 1 8 5.5
39 1 1 1 9 4.5
40 1 -1 1 9 5.5
41 1 1 2 0 4.5
42 1 -1 2 0 5.5
43 1 1 2 1 4.5
44 1 -1 2 1 5.5
45 1 1 2 2 4.5
46 1 -1 2 2 5.5
47 1 1 2 3 4.5
48 1 -1 2 3 5.5
49 1 1 2 4 4.5
50 1 -1 2 4 5.5
51 1 1 2 5 4.5
52 1 -1 2 5 5.5
53 1 1 2 6 4.5
54 1 -1 2 6 5.5
55 1 1 2 7 4.5
56 1 -1 2 7 5.5
57 1 1 2 8 4.5
58 1 -1 2 8 5.5
59 1 1 2 9 4.5
60 1 -1 2 9 5.5
61 1 1 3 0 4.5
62 1 -1 3 0 5.5
63 1 1 3 1 4.5
64 1 -1 3 1 5.5
65 1 1 3 2 4.5
66 1 -1 3 2 5.5
67 1 1 3 3 4.5
68 1 -1 3 3 5.5
69 1 1 3 4 4.5
70 1 -1 3 4 5.5
71 1 1 3 5 4.5
72 1 -1 3 5 5.5
73 1 1 3 6 4.5
74 1 -1 3 6 5.5
75 1 1 3 7 4.5
76 1 -1 3 7 5.5
77 1 1 3 8 4.5
78 1 -1 3 8 5.5
79 1 1 3 9 4.5
80 1 -1 3 9 5.5
81 1 1 4 0 4.5
82 1 -1 4 0 5.5
83 1 1 4 1 4.5
84 1 -1 4 1 5.5
85 1 1 4 2 4.5
86 1 -1 4 2 5.5
87 1 1 4 3 4.5
88 1 -1 4 3 5.5
89 1 1 4 4 4.5
90 1 -1 4 4 5.5
91 1 1 4 5 4.5
92 1 -1 4 5 5.5
93 1 1 4 6 4.5
94 1 -1 4 6 5.5
95 1 1 4 7 4.5
96 1 -1 4 7 5.5
97 1 1 4 8 4.5
98 1 -1 4 8 5.5
99 1 1 4 9 4.5
100 1 -1 4 9 5.5
101 1 1 5 0 4.5
102 1 -1 5 0 5.5
103 1 1 5 1 4.5
104 1 -1 5 1 5.5
105 1 1 5 2 4.5
106 1 -1 5 2 5.5
107 1 1 5 3 4.5
108 1 -1 5 3 5.5
109 1 1 5 4 4.5
110 1 -1 5 4 5.5
111 1 1 5 5 4.5
112 1 -1 5 5 5.5
113 1 1 5 6 4.5
114 1 -1 5 6 5.5
115 1 1 5 7 4.5
116 1 -1 5 7 5.5
117 1 1 5 8 4.5
118 1 -1 5 8 5.5
119 1 1 5 9 4.5
120 1 -1 5 9 5.5
121 1 1 6 0 4.5
122 1 -1 6 0 5.5
123 1 1 6 1 4.5
124 1 -1 6 1 5.5
125 1 1 6 2 4.5
126 1 -1 6 2 5.5
127 1 1 6 3 4.5
128 1 -1 6 3 5.5
129 1 1 6 4 4.5
130 1 -1 6 4 5.5
131 1 1 6 5 4.5
132 1 -1 6 5 5.5
133 1 1 6 6 4.5
134 1 -1 6 6 5.5
135 1 1 6 7 4.5
136 1 -1 6 7 5.5
137 1 1 6 8 4.5
138 1 -1 6 8 5.5
139 1 1 6 9 4.5
140 1 -1 6 9 5.5
141 1 1 7 0 4.5
142 1 -1 7 0 5.5
143 1 1 7 1 4.5
144 1 -1 7 1 5.5
145 1 1 7 2 4.5
146 1 -1 7 2 5.5
147 1 1 7 3 4.5
148 1 -1 7 3 5.5
149 1 1 7 4 4.5
150 1 -1 7 4 5.5
151 1 1 7 5 4.5
152 1 -1 7 5 5.5
153 1 1 7 6 4.5
154 1 -1 7 6 5.5
155 1 1 7 7 4.5
156 1 -1 7 7 5.5
157 1 1 7 8 4.5
158 1 -1 7 8 5.5
159 1 1 7 9 4.5
160 1 -1 7 9 5.5
161 1 1 8 0 4.5
162 1 -1 8 0 5.5
163 1 1 8 1 4.5
164 1 -1 8 1 5.5
165 1 1 8 2 4.5
166 1 -1 8 2 5.5
167 1 1 8 3 4.5
168 1 -1 8 3 5.5
169 1 1 8 4 4.5
170 1 -1 8 4 5.5
171 1 1 8 5 4.5
172 1 -1 8 5 5.5
173 1 1 8 6 4.5
174 1 -1 8 6 5.5
175 1 1 8 7 4.5
176 1 -1 8 7 5.5
177 1 1 8 8 4.5
178 1 -1 8 8 5.5
179 1 1 8 9 4.5
180 1 -1 8 9 5.5
181 1 1 9 0 4.5
182 1 -1 9 0 5.5
183 1 1 9 1 4.5
184 1 -1 9 1 5.5
185 1 1 9 2 4.5
186 1 -1 9 2 5.5
187 1 1 9 3 4.5
188 1 -1 9 3 5.5
189 1 1 9 4 4.5
190 1 -1 9 4 5.5
191 1 1 9 5 4.5
192 1 -1 9 5 5.5
193 1 1 9 6 4.5
194 1 -1 9 6 5.5
195 1 1 9 7 4.5
196 1 -1 9 7 5.5
197 1 1 9 8 4.5
198 1 -1 9 8 5.5
199 1 1 9 9 4.5
200 1 -1 9 9 5.5
201 1 -1 9.28495 2.13839 8.88019
202 1 1 4.99281 4.17459 9.83905
203 1 -1 4.91265 6.89408 2.39989
204 1 1 4.43647 3.68895 8.86086
205 1 -1 0.659075 7.07271 0.179131
206 1 1 7.791 3.40021 0.969703
207 1 -1 1.18008 3.63874 7.28751
208 1 1 8.51522 5.24681 6.37702
209 1 -1 4.24226 9.60726 3.16084
210 1 1 8.43745 8.23344 9.2883
211 1 -1 8.48509 8.84988 9.43407
212 1 1 2.81127 8.9903 0.00909212
213 1 -1 6.38283 6.20858 9.92482
214 1 1 4.59962 5.7925 7.52571
215 1 -1 7.03797 7.09336 8.15957
216 1 1 6.68103 8.04734 7.95661
217 1 -1 2.531 8.47145 1.6209
218 1 1 6.71915 8.79876 9.59581
219 1 -1 4.96758 0.0381298 0.827927
220 1 1 9.22955 1.04572 0.84722
221 1 -1 2.3224 2.57084 8.07306
222 1 1 1.94283 3.17375 3.92051
223 1 -1 2.34735 1.91295 1.29127
224 1 1 3.33928 3.30688 0.892089
225 1 -1 1.19738 4.40402 8.70835
226 1 1 7.44541 4.94803 8.28211
227 1 -1 5.93272 1.18886 1.56518
228 1 1 8.50709 8.70343 1.24939
229 1 -1 5.54016 3.38865 8.61698
230 1 1 9.47644 0.573085 3.05941
231 1 -1 9.39695 4.46542 1.84205
232 1 1 3.52268 5.60212 0.333999
233 1 -1 3.69009 9.40954 6.10446
234 1 1 3.96836 6.15307 7.57803
235 1 -1 2.02535 0.0418407 3.21642
236 1 1 2.97488 8.79711 8.33242
237 1 -1 2.4122 1.79458 3.04173
238 1 1 9.72355 3.67773 1.52435
239 1 -1 8.55216 6.1623 1.53201
240 1 1 4.98973 2.41459 9.84381
241 1 -1 8.8901 5.9006 1.97649
242 1 1 9.09932 2.23783 1.42554
243 1 -1 6.70722 8.21769 1.21953
244 1 1 6.83768 0.84508 3.25165
245 1 -1 0.222115 3.07945 0.51825
246 1 1 0.503918 9.34932 6.25278
247 1 -1 0.803159 8.7017 9.46211
248 1 1 4.88636 5.00147 9.65639
249 1 -1 1.62258 0.767285 9.63596
250 1 1 2.70143 3.01111 7.74859
251 1 -1 4.41574 5.31824 0.538729
252 1 1 1.64724 5.18097 3.59205
253 1 -1 2.33672 3.21408 6.6081
254 1 1 7.46603 1.53668 9.09844
255 1 -1 3.61269 8.44556 6.99789
256 1 1 6.95465 6.83045 9.31002
257 1 -1 5.91831 9.01549 3.4626
258 1 1 6.56503 8.42229 3.27105
259 1 -1 4.50822 9.59753 3.47025
260 1 1 4.17357 5.27384 7.34774
261 1 -1 7.70968 6.5292 3.54779
262 1 1 4.7977 4.94239 6.24947
263 1 -1 9.24016 9.36994 6.71263
264 1 1 7.36888 8.75922 0.52403
265 1 -1 9.92895 5.87551 6.21586
266 1 1 3.86308 6.71601 9.69083
267 1 -1 8.90048 0.298719 0.573852
268 1 1 6.58753 6.67768 1.83984
269 1 -1 8.672 0.367497 2.21864
270 1 1 3.44519 3.30359 6.52249
271 1 -1 7.24717 3.25113 3.41567
272 1 1 9.53447 5.81336 1.79208
273 1 -1 1.01722 6.42534 0.715
274 1 1 3.58808 4.92392 7.00979
275 1 -1 1.21399 3.56951 6.34505
276 1 1 3.50336 0.942722 2.76989
277 1 -1 9.45475 6.06299 0.659023
278 1 1 3.44464 4.03075 6.20179
279 1 -1 0.949331 5.40183 8.51385
280 1 1 6.41118 2.62135 2.31132
281 1 -1 3.58837 9.78355 7.04966
282 1 1 9.2267 3.19593 2.10384
283 1 -1 1.83092 2.35627 3.93061
284 1 1 4.97203 4.92287 1.8049
285 1 -1 7.4097 4.757 8.604
286 1 1 0.746575 7.69038 0.89134
287 1 -1 8.54862 6.59135 2.18888
288 1 1 2.18747 4.82994 0.761718
289 1 -1 5.71622 2.51116 6.85522
290 1 1 6.95554 1.83187 8.31157
291 1 -1 7.31818 6.60081 2.63208
292 1 1 0.744495 2.73429 9.86022
293 1 -1 5.1573 8.70962 2.53418
294 1 1 2.40385 1.54057 1.9297
295 1 -1 3.42609 2.25856 2.28437
296 1 1 6.66173 3.70851 9.70052
297 1 -1 7.88966 1.4343 8.91223
298 1 1 3.91118 5.22253 6.29642
299 1 -1 9.17618 3.98313 9.82158
300 1 1 4.95424 5.93521 1.3652

1016
examples/USER/scafacos/data.hammersley_sphere Normal file
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File diff suppressed because it is too large Load Diff

37
examples/USER/scafacos/in.scafacos Normal file
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@ -0,0 +1,37 @@
# Point dipoles in a 2d box
units lj
atom_style charge
read_data data.NaCl
replicate 8 8 8
velocity all create 1.5 49893
neighbor 1.0 bin
neigh_modify delay 0
fix 1 all nve
# LAMMPS computes pairwise and long-range Coulombics
#pair_style coul/long 3.0
#pair_coeff * *
#kspace_style pppm 1.0e-3
# Scafacos computes entire long-range Coulombics
# use dummy pair style to perform atom sorting
pair_style zero 1.0
pair_coeff * *
#fix 2 all scafacos p3m tolerance field 0.001
kspace_style scafacos p3m 0.001
#kspace_style scafacos tolerance field
timestep 0.005
thermo 10
run 100

31
examples/USER/scafacos/in.scafacos.cw.ewald Normal file
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@ -0,0 +1,31 @@
units lj
atom_style charge
read_data data.cloud_wall
velocity all set 0.0 0.0 0.0 mom no
pair_style zero 1.0
pair_coeff * *
neighbor 1.0 bin
neigh_modify delay 0
fix 1 all nve
kspace_style scafacos ewald 0.001
kspace_modify scafacos tolerance field
timestep 0.005
thermo_style custom step atoms cpu temp pe ke etotal ecoul press
run_style verlet
#dump simple all custom 1000 id x y z vx vy vz
#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass
#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass
#dump_modify dmpvtk pad 7
thermo 10
run 100

37
examples/USER/scafacos/in.scafacos.cw.fmm Normal file
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@ -0,0 +1,37 @@
units lj
atom_style charge
read_data data.cloud_wall
velocity all set 0.0 0.0 0.0 mom no
pair_style zero 1.0
pair_coeff * *
neighbor 1.0 bin
neigh_modify delay 0
fix 1 all nve
#pair_style coul/long 3.0
#pair_coeff * *
#kspace_style pppm 1.0e-3
kspace_style scafacos fmm 1.0e-3
kspace_modify scafacos tolerance energy_rel
kspace_modify scafacos fmm_tuning 1
timestep 0.005
thermo_style custom step atoms cpu temp pe ke etotal ecoul press
run_style verlet
#dump simple all custom 1000 id x y z vx vy vz
#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass
#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass
#dump_modify dmpvtk pad 7
thermo 10
run 100

31
examples/USER/scafacos/in.scafacos.cw.p2nfft Normal file
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@ -0,0 +1,31 @@
units lj
atom_style charge
read_data data.cloud_wall
velocity all set 0.0 0.0 0.0 mom no
pair_style zero 1.0
pair_coeff * *
neighbor 1.0 bin
neigh_modify delay 0
fix 1 all nve
kspace_style scafacos p2nfft 0.001
kspace_modify scafacos tolerance field
timestep 0.005
thermo_style custom step atoms cpu temp pe ke etotal ecoul press
run_style verlet
#dump simple all custom 1000 id x y z vx vy vz
#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass
#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass
#dump_modify dmpvtk pad 7
thermo 10
run 100

31
examples/USER/scafacos/in.scafacos.cw.p3m Normal file
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@ -0,0 +1,31 @@
units lj
atom_style charge
read_data data.cloud_wall
velocity all set 0.0 0.0 0.0 mom no
pair_style zero 1.0
pair_coeff * *
neighbor 1.0 bin
neigh_modify delay 0
fix 1 all nve
kspace_style scafacos p3m 0.001
kspace_modify scafacos tolerance field
timestep 0.005
thermo_style custom step atoms cpu temp pe ke etotal ecoul press
run_style verlet
#dump simple all custom 1000 id x y z vx vy vz
#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass
#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass
#dump_modify dmpvtk pad 7
thermo 10
run 100

37
examples/USER/scafacos/in.scafacos.ewald Normal file
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@ -0,0 +1,37 @@
# Point dipoles in a 2d box
units lj
atom_style charge
read_data data.NaCl
replicate 8 8 8
velocity all create 1.5 49893
neighbor 1.0 bin
neigh_modify delay 0
fix 1 all nve
# LAMMPS computes pairwise and long-range Coulombics
#pair_style coul/long 3.0
#pair_coeff * *
#kspace_style pppm 1.0e-3
# Scafacos computes entire long-range Coulombics
# use dummy pair style to perform atom sorting
pair_style zero 1.0
pair_coeff * *
#fix 2 all scafacos p3m tolerance field 0.001
kspace_style scafacos ewald 0.001
kspace_modify scafacos tolerance field
timestep 0.005
thermo 10
run 100

37
examples/USER/scafacos/in.scafacos.fmm Normal file
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@ -0,0 +1,37 @@
# Point dipoles in a 2d box
units lj
atom_style charge
read_data data.NaCl
replicate 8 8 8
velocity all create 1.5 49893
neighbor 1.0 bin
neigh_modify delay 0
fix 1 all nve
# LAMMPS computes pairwise and long-range Coulombics
#pair_style coul/long 3.0
#pair_coeff * *
#kspace_style pppm 1.0e-3
# Scafacos computes entire long-range Coulombics
# use dummy pair style to perform atom sorting
pair_style zero 1.0
pair_coeff * *
#fix 2 all scafacos p3m tolerance field 0.001
kspace_style scafacos fmm 0.001
kspace_modify scafacos tolerance energy
timestep 0.005
thermo 10
run 100

34
examples/USER/scafacos/in.scafacos.hsph.direct Normal file
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@ -0,0 +1,34 @@
# Point dipoles in a 2d box
units lj
atom_style charge
read_data data.hammersley_sphere
change_box all boundary f f f
velocity all create 1.5 49893
neighbor 1.0 bin
neigh_modify delay 0
fix 1 all nve
# LAMMPS computes pairwise and long-range Coulombics
#pair_style coul/long 3.0
#pair_coeff * *
#kspace_style pppm 1.0e-3
# Scafacos computes entire long-range Coulombics
# use dummy pair style to perform atom sorting
pair_style zero 1.0
pair_coeff * *
#fix 2 all scafacos p3m tolerance field 0.001
kspace_style scafacos direct 0.001
timestep 0.005
thermo 1
run 20

37
examples/USER/scafacos/in.scafacos.hsph.fmm Normal file
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@ -0,0 +1,37 @@
# Point dipoles in a 2d box
units lj
atom_style charge
read_data data.hammersley_sphere
change_box all boundary f f f
velocity all create 1.5 49893
neighbor 1.0 bin
neigh_modify delay 0
fix 1 all nve
# LAMMPS computes pairwise and long-range Coulombics
#pair_style coul/long 3.0
#pair_coeff * *
#kspace_style pppm 1.0e-3
# Scafacos computes entire long-range Coulombics
# use dummy pair style to perform atom sorting
pair_style zero 1.0
pair_coeff * *
#fix 2 all scafacos p3m tolerance field 0.001
kspace_style scafacos fmm 0.001
kspace_modify scafacos tolerance energy_rel
kspace_modify scafacos fmm_tuning 1
timestep 0.005
thermo 1
run 20

36
examples/USER/scafacos/in.scafacos.hsph.p2nfft Normal file
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@ -0,0 +1,36 @@
# Point dipoles in a 2d box
units lj
atom_style charge
read_data data.hammersley_sphere
change_box all boundary f f f
velocity all create 1.5 49893
neighbor 1.0 bin
neigh_modify delay 0
fix 1 all nve
# LAMMPS computes pairwise and long-range Coulombics
#pair_style coul/long 3.0
#pair_coeff * *
#kspace_style pppm 1.0e-3
# Scafacos computes entire long-range Coulombics
# use dummy pair style to perform atom sorting
pair_style zero 1.0
pair_coeff * *
#fix 2 all scafacos p3m tolerance field 0.001
kspace_style scafacos p2nfft 0.001
kspace_modify scafacos tolerance potential
timestep 0.005
thermo 1
run 20

37
examples/USER/scafacos/in.scafacos.p2nfft Normal file
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@ -0,0 +1,37 @@
# Point dipoles in a 2d box
units lj
atom_style charge
read_data data.NaCl
replicate 8 8 8
velocity all create 1.5 49893
neighbor 1.0 bin
neigh_modify delay 0
fix 1 all nve
# LAMMPS computes pairwise and long-range Coulombics
#pair_style coul/long 3.0
#pair_coeff * *
#kspace_style pppm 1.0e-3
# Scafacos computes entire long-range Coulombics
# use dummy pair style to perform atom sorting
pair_style zero 1.0
pair_coeff * *
#fix 2 all scafacos p3m tolerance field 0.001
kspace_style scafacos p2nfft 0.001
kspace_modify scafacos tolerance field
timestep 0.005
thermo 10
run 100

37
examples/USER/scafacos/in.scafacos.p3m Normal file
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@ -0,0 +1,37 @@
# Point dipoles in a 2d box
units lj
atom_style charge
read_data data.NaCl
replicate 8 8 8
velocity all create 1.5 49893
neighbor 1.0 bin
neigh_modify delay 0
fix 1 all nve
# LAMMPS computes pairwise and long-range Coulombics
#pair_style coul/long 3.0
#pair_coeff * *
#kspace_style pppm 1.0e-3
# Scafacos computes entire long-range Coulombics
# use dummy pair style to perform atom sorting
pair_style zero 1.0
pair_coeff * *
#fix 2 all scafacos p3m tolerance field 0.001
kspace_style scafacos p3m 0.001
kspace_modify scafacos tolerance field
timestep 0.005
thermo 10
run 100

92
examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.ewald.16 Normal file
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@ -0,0 +1,92 @@
LAMMPS (2 Aug 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
units lj
atom_style charge
read_data data.cloud_wall
orthogonal box = (0 0 0) to (10 10 10)
2 by 2 by 4 MPI processor grid
reading atoms ...
300 atoms
velocity all set 0.0 0.0 0.0 mom no
pair_style zero 1.0
pair_coeff * *
neighbor 1.0 bin
neigh_modify delay 0
fix 1 all nve
kspace_style scafacos ewald 0.001
kspace_modify scafacos tolerance field
timestep 0.005
thermo_style custom step atoms cpu temp pe ke etotal ecoul press
run_style verlet
#dump simple all custom 1000 id x y z vx vy vz
#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass
#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass
#dump_modify dmpvtk pad 7
thermo 10
run 100
Setting up ScaFaCoS with solver ewald ...
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 = 10 10 10
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.313 | 3.501 | 3.689 Mbytes
Step Atoms CPU Temp PotEng KinEng TotEng E_coul Press
0 300 0 0 0.49647271 0 0.49647271 0 0
10 300 0.051135063 0.014582562 0.44286522 0.02180093 0.46466616 0 0.0043601861
20 300 0.10210872 0.058693359 0.37869251 0.087746571 0.46643909 0 0.017549314
30 300 0.15278506 0.13468789 0.26730177 0.2013584 0.46866017 0 0.040271679
40 300 0.19430375 0.50949535 0.083356437 0.76169555 0.84505198 0 0.15233911
50 300 0.23220921 1.1731116 -0.055261984 1.7538018 1.6985399 0 0.35076037
60 300 0.27002859 1.3589639 -0.33351524 2.031651 1.6981358 0 0.4063302
70 300 0.30781388 1.6482648 -0.76570045 2.4641559 1.6984554 0 0.49283118
80 300 0.34566283 2.8640899 -2.4038488 4.2818144 1.8779656 0 0.85636288
90 300 0.38424087 93.168442 -2.5911448 139.28682 136.69568 0 27.857364
100 300 0.42331123 94.146897 -1.3480439 140.74961 139.40157 0 28.149922
Loop time of 0.423331 on 16 procs for 100 steps with 300 atoms
Performance: 102047.913 tau/day, 236.222 timesteps/s
99.2% CPU use with 16 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.5988e-05 | 3.6508e-05 | 5.5075e-05 | 0.0 | 0.01
Kspace | 0.41852 | 0.41925 | 0.41976 | 0.1 | 99.04
Neigh | 0.00023413 | 0.00056887 | 0.0012875 | 0.0 | 0.13
Comm | 0.0019519 | 0.0022772 | 0.0027158 | 0.5 | 0.54
Output | 0.00028276 | 0.00030752 | 0.0003624 | 0.0 | 0.07
Modify | 8.3685e-05 | 0.0001286 | 0.00018764 | 0.0 | 0.03
Other | | 0.000758 | | | 0.18
Nlocal: 18.75 ave 39 max 6 min
Histogram: 6 1 1 0 1 2 2 1 1 1
Nghost: 122.812 ave 195 max 63 min
Histogram: 8 0 0 0 0 0 0 1 3 4
Neighs: 160.625 ave 598 max 13 min
Histogram: 8 2 1 1 1 0 0 2 0 1
Total # of neighbors = 2570
Ave neighs/atom = 8.56667
Neighbor list builds = 23
Dangerous builds = 16
Total wall time: 0:00:00

92
examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.ewald.8 Normal file
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@ -0,0 +1,92 @@
LAMMPS (2 Aug 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
units lj
atom_style charge
read_data data.cloud_wall
orthogonal box = (0 0 0) to (10 10 10)
2 by 2 by 2 MPI processor grid
reading atoms ...
300 atoms
velocity all set 0.0 0.0 0.0 mom no
pair_style zero 1.0
pair_coeff * *
neighbor 1.0 bin
neigh_modify delay 0
fix 1 all nve
kspace_style scafacos ewald 0.001
kspace_modify scafacos tolerance field
timestep 0.005
thermo_style custom step atoms cpu temp pe ke etotal ecoul press
run_style verlet
#dump simple all custom 1000 id x y z vx vy vz
#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass
#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass
#dump_modify dmpvtk pad 7
thermo 10
run 100
Setting up ScaFaCoS with solver ewald ...
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 = 10 10 10
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.317 | 3.317 | 3.317 Mbytes
Step Atoms CPU Temp PotEng KinEng TotEng E_coul Press
0 300 0 0 0.49647271 0 0.49647271 0 0
10 300 0.057411432 0.014718629 0.45088339 0.02200435 0.47288774 0 0.00440087
20 300 0.11482716 0.05922597 0.38470912 0.088542825 0.47325194 0 0.017708565
30 300 0.17278481 0.13587829 0.27058048 0.20313804 0.47371852 0 0.040627608
40 300 0.23021507 0.51353118 0.088432648 0.76772911 0.85616176 0 0.15354582
50 300 0.28812647 1.1760001 -0.058088247 1.7581201 1.7000319 0 0.35162403
60 300 0.34651113 1.3627885 -0.33736672 2.0373688 1.7000021 0 0.40747376
70 300 0.40509939 1.6529365 -0.77082139 2.4711401 1.7003187 0 0.49422802
80 300 0.46342874 2.9569837 -2.4624654 4.4206907 1.9582253 0 0.88413814
90 300 0.52329254 81.642726 -2.5370215 122.05588 119.51885 0 24.411175
100 300 0.58335209 85.047974 -1.128107 127.14672 126.01861 0 25.429344
Loop time of 0.583369 on 8 procs for 100 steps with 300 atoms
Performance: 74052.598 tau/day, 171.418 timesteps/s
99.7% CPU use with 8 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 4.0531e-05 | 4.6492e-05 | 4.8876e-05 | 0.0 | 0.01
Kspace | 0.57805 | 0.5785 | 0.57893 | 0.0 | 99.17
Neigh | 0.00062275 | 0.00091892 | 0.0013313 | 0.0 | 0.16
Comm | 0.002604 | 0.0028289 | 0.0031538 | 0.3 | 0.48
Output | 0.0002265 | 0.0002434 | 0.00029039 | 0.0 | 0.04
Modify | 0.00016117 | 0.00017747 | 0.00019884 | 0.0 | 0.03
Other | | 0.00065 | | | 0.11
Nlocal: 37.5 ave 46 max 31 min
Histogram: 2 0 0 2 1 0 2 0 0 1
Nghost: 203.875 ave 212 max 192 min
Histogram: 1 0 1 0 0 2 1 0 0 3
Neighs: 321.625 ave 599 max 112 min
Histogram: 1 2 0 1 1 0 1 1 0 1
Total # of neighbors = 2573
Ave neighs/atom = 8.57667
Neighbor list builds = 23
Dangerous builds = 16
Total wall time: 0:00:00

99
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LAMMPS (2 Aug 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
units lj
atom_style charge
read_data data.cloud_wall
orthogonal box = (0 0 0) to (10 10 10)
1 by 1 by 1 MPI processor grid
reading atoms ...
300 atoms
velocity all set 0.0 0.0 0.0 mom no
pair_style zero 1.0
pair_coeff * *
neighbor 1.0 bin
neigh_modify delay 0
fix 1 all nve
#pair_style coul/long 3.0
#pair_coeff * *
#kspace_style pppm 1.0e-3
kspace_style scafacos fmm 1.0e-3
kspace_modify scafacos tolerance energy_rel
kspace_modify scafacos fmm_tuning 1
ScaFaCoS setting fmm inhomogen tuning ...
timestep 0.005
thermo_style custom step atoms cpu temp pe ke etotal ecoul press
run_style verlet
#dump simple all custom 1000 id x y z vx vy vz
#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass
#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass
#dump_modify dmpvtk pad 7
thermo 10
run 100
Setting up ScaFaCoS with solver fmm ...
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 = 10 10 10
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.34 | 3.34 | 3.34 Mbytes
Step Atoms CPU Temp PotEng KinEng TotEng E_coul Press
0 300 0 0 0.49646402 0 0.49646402 0 0.016548801
10 300 0.063865185 0.015455559 0.47335833 0.02310606 0.49646439 0 0.020399823
20 300 0.12760854 0.06229069 0.40334177 0.093124582 0.49646635 0 0.032069642
30 300 0.19143319 0.14310163 0.28254277 0.21393694 0.49647971 0 0.05220548
40 300 0.25553131 0.52929788 0.089669015 0.79130033 0.88096934 0 0.16124903
50 300 0.31961966 1.1963022 -0.082792461 1.7884718 1.7056794 0 0.35493462
60 300 0.38388991 1.3928167 -0.37659239 2.082261 1.7056686 0 0.40389911
70 300 0.44797421 1.7069009 -0.84571914 2.5518169 1.7060978 0 0.48217274
80 300 0.50961447 15.358343 -3.368063 22.960722 19.592659 0 4.4798757
90 300 0.57181501 42.280432 -2.1623864 63.209247 61.04686 0 12.56977
100 300 0.63501096 41.48079 -0.89904529 62.013782 61.114736 0 12.372788
Loop time of 0.635022 on 1 procs for 100 steps with 300 atoms
Performance: 68029.122 tau/day, 157.475 timesteps/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 9.0837e-05 | 9.0837e-05 | 9.0837e-05 | 0.0 | 0.01
Kspace | 0.62877 | 0.62877 | 0.62877 | 0.0 | 99.01
Neigh | 0.0035319 | 0.0035319 | 0.0035319 | 0.0 | 0.56
Comm | 0.0010211 | 0.0010211 | 0.0010211 | 0.0 | 0.16
Output | 0.00014758 | 0.00014758 | 0.00014758 | 0.0 | 0.02
Modify | 0.0010428 | 0.0010428 | 0.0010428 | 0.0 | 0.16
Other | | 0.0004218 | | | 0.07
Nlocal: 300 ave 300 max 300 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 374 ave 374 max 374 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 2459 ave 2459 max 2459 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2459
Ave neighs/atom = 8.19667
Neighbor list builds = 15
Dangerous builds = 0
Total wall time: 0:00:00

99
examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.fmm.16 Normal file
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LAMMPS (2 Aug 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
units lj
atom_style charge
read_data data.cloud_wall
orthogonal box = (0 0 0) to (10 10 10)
2 by 2 by 4 MPI processor grid
reading atoms ...
300 atoms
velocity all set 0.0 0.0 0.0 mom no
pair_style zero 1.0
pair_coeff * *
neighbor 1.0 bin
neigh_modify delay 0
fix 1 all nve
#pair_style coul/long 3.0
#pair_coeff * *
#kspace_style pppm 1.0e-3
kspace_style scafacos fmm 1.0e-3
kspace_modify scafacos tolerance energy_rel
kspace_modify scafacos fmm_tuning 1
ScaFaCoS setting fmm inhomogen tuning ...
timestep 0.005
thermo_style custom step atoms cpu temp pe ke etotal ecoul press
run_style verlet
#dump simple all custom 1000 id x y z vx vy vz
#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass
#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass
#dump_modify dmpvtk pad 7
thermo 10
run 100
Setting up ScaFaCoS with solver fmm ...
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 = 10 10 10
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.313 | 3.501 | 3.689 Mbytes
Step Atoms CPU Temp PotEng KinEng TotEng E_coul Press
0 300 0 0 0.49646402 0 0.49646402 0 0.016548801
10 300 0.023007393 0.015455559 0.47335833 0.02310606 0.49646439 0 0.020399823
20 300 0.045746088 0.06229069 0.40334177 0.093124582 0.49646635 0 0.032069642
30 300 0.068123341 0.14310163 0.28254277 0.21393694 0.49647971 0 0.05220548
40 300 0.090359211 0.52929788 0.089669015 0.79130033 0.88096934 0 0.16124903
50 300 0.11304998 1.1963022 -0.082792461 1.7884718 1.7056794 0 0.35493462
60 300 0.13585806 1.3928167 -0.37659239 2.082261 1.7056686 0 0.40389911
70 300 0.15867376 1.7069009 -0.84571914 2.5518169 1.7060978 0 0.48217274
80 300 0.18324137 15.358343 -3.368063 22.960722 19.592659 0 4.4798757
90 300 0.20960689 42.280432 -2.1623864 63.209247 61.04686 0 12.56977
100 300 0.23539281 41.48079 -0.89904529 62.013782 61.114736 0 12.372788
Loop time of 0.235411 on 16 procs for 100 steps with 300 atoms
Performance: 183509.107 tau/day, 424.790 timesteps/s
97.9% CPU use with 16 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.2425e-05 | 4.4718e-05 | 6.1274e-05 | 0.0 | 0.02
Kspace | 0.23097 | 0.23143 | 0.2318 | 0.1 | 98.31
Neigh | 0.00015116 | 0.00035347 | 0.00075746 | 0.0 | 0.15
Comm | 0.0020316 | 0.002282 | 0.0025339 | 0.3 | 0.97
Output | 0.00034404 | 0.00037053 | 0.00042701 | 0.0 | 0.16
Modify | 9.3937e-05 | 0.00014532 | 0.00018811 | 0.0 | 0.06
Other | | 0.0007878 | | | 0.33
Nlocal: 18.75 ave 36 max 6 min
Histogram: 4 3 1 0 0 1 2 1 2 2
Nghost: 127 ave 196 max 71 min
Histogram: 8 0 0 0 0 0 0 1 6 1
Neighs: 153.688 ave 491 max 10 min
Histogram: 8 1 1 1 1 1 0 0 0 3
Total # of neighbors = 2459
Ave neighs/atom = 8.19667
Neighbor list builds = 15
Dangerous builds = 0
Total wall time: 0:00:01

99
examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.fmm.2 Normal file
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LAMMPS (2 Aug 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
units lj
atom_style charge
read_data data.cloud_wall
orthogonal box = (0 0 0) to (10 10 10)
1 by 1 by 2 MPI processor grid
reading atoms ...
300 atoms
velocity all set 0.0 0.0 0.0 mom no
pair_style zero 1.0
pair_coeff * *
neighbor 1.0 bin
neigh_modify delay 0
fix 1 all nve
#pair_style coul/long 3.0
#pair_coeff * *
#kspace_style pppm 1.0e-3
kspace_style scafacos fmm 1.0e-3
kspace_modify scafacos tolerance energy_rel
kspace_modify scafacos fmm_tuning 1
ScaFaCoS setting fmm inhomogen tuning ...
timestep 0.005
thermo_style custom step atoms cpu temp pe ke etotal ecoul press
run_style verlet
#dump simple all custom 1000 id x y z vx vy vz
#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass
#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass
#dump_modify dmpvtk pad 7
thermo 10
run 100
Setting up ScaFaCoS with solver fmm ...
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 = 10 10 10
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.354 | 3.354 | 3.355 Mbytes
Step Atoms CPU Temp PotEng KinEng TotEng E_coul Press
0 300 0 0 0.49646402 0 0.49646402 0 0.016548801
10 300 0.038181543 0.015455559 0.47335833 0.02310606 0.49646439 0 0.020399823
20 300 0.076276302 0.06229069 0.40334177 0.093124582 0.49646635 0 0.032069642
30 300 0.11437607 0.14310163 0.28254277 0.21393694 0.49647971 0 0.05220548
40 300 0.15244293 0.52929788 0.089669015 0.79130033 0.88096934 0 0.16124903
50 300 0.19081283 1.1963022 -0.082792461 1.7884718 1.7056794 0 0.35493462
60 300 0.22923493 1.3928167 -0.37659239 2.082261 1.7056686 0 0.40389911
70 300 0.26754427 1.7069009 -0.84571914 2.5518169 1.7060978 0 0.48217274
80 300 0.30721259 15.358343 -3.368063 22.960722 19.592659 0 4.4798757
90 300 0.34865618 42.280432 -2.1623864 63.209247 61.04686 0 12.56977
100 300 0.39100981 41.48079 -0.89904529 62.013782 61.114736 0 12.372788
Loop time of 0.391022 on 2 procs for 100 steps with 300 atoms
Performance: 110479.760 tau/day, 255.740 timesteps/s
99.6% CPU use with 2 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 8.0109e-05 | 8.1539e-05 | 8.297e-05 | 0.0 | 0.02
Kspace | 0.38534 | 0.38582 | 0.3863 | 0.1 | 98.67
Neigh | 0.0014851 | 0.0019699 | 0.0024548 | 1.1 | 0.50
Comm | 0.0019314 | 0.0020101 | 0.0020888 | 0.2 | 0.51
Output | 0.00014496 | 0.00017297 | 0.00020099 | 0.0 | 0.04
Modify | 0.0005033 | 0.00052273 | 0.00054216 | 0.0 | 0.13
Other | | 0.0004461 | | | 0.11
Nlocal: 150 ave 159 max 141 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 392 ave 395 max 389 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 1229.5 ave 1773 max 686 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 2459
Ave neighs/atom = 8.19667
Neighbor list builds = 15
Dangerous builds = 0
Total wall time: 0:00:01

99
examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.fmm.4 Normal file
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LAMMPS (2 Aug 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
units lj
atom_style charge
read_data data.cloud_wall
orthogonal box = (0 0 0) to (10 10 10)
1 by 2 by 2 MPI processor grid
reading atoms ...
300 atoms
velocity all set 0.0 0.0 0.0 mom no
pair_style zero 1.0
pair_coeff * *
neighbor 1.0 bin
neigh_modify delay 0
fix 1 all nve
#pair_style coul/long 3.0
#pair_coeff * *
#kspace_style pppm 1.0e-3
kspace_style scafacos fmm 1.0e-3
kspace_modify scafacos tolerance energy_rel
kspace_modify scafacos fmm_tuning 1
ScaFaCoS setting fmm inhomogen tuning ...
timestep 0.005
thermo_style custom step atoms cpu temp pe ke etotal ecoul press
run_style verlet
#dump simple all custom 1000 id x y z vx vy vz
#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass
#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass
#dump_modify dmpvtk pad 7
thermo 10
run 100
Setting up ScaFaCoS with solver fmm ...
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 = 10 10 10
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.333 | 3.333 | 3.333 Mbytes
Step Atoms CPU Temp PotEng KinEng TotEng E_coul Press
0 300 0 0 0.49646402 0 0.49646402 0 0.016548801
10 300 0.029414415 0.015455559 0.47335833 0.02310606 0.49646439 0 0.020399823
20 300 0.058616877 0.06229069 0.40334177 0.093124582 0.49646635 0 0.032069642
30 300 0.087769508 0.14310163 0.28254277 0.21393694 0.49647971 0 0.05220548
40 300 0.1168611 0.52929788 0.089669015 0.79130033 0.88096934 0 0.16124903
50 300 0.14482284 1.1963022 -0.082792461 1.7884718 1.7056794 0 0.35493462
60 300 0.17198443 1.3928167 -0.37659239 2.082261 1.7056686 0 0.40389911
70 300 0.19868851 1.7069009 -0.84571914 2.5518169 1.7060978 0 0.48217274
80 300 0.22835517 15.358343 -3.368063 22.960722 19.592659 0 4.4798757
90 300 0.26023602 42.280432 -2.1623864 63.209247 61.04686 0 12.56977
100 300 0.29043221 41.48079 -0.89904529 62.013782 61.114736 0 12.372788
Loop time of 0.290448 on 4 procs for 100 steps with 300 atoms
Performance: 148735.741 tau/day, 344.296 timesteps/s
99.0% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 5.9605e-05 | 6.187e-05 | 6.4135e-05 | 0.0 | 0.02
Kspace | 0.28551 | 0.28584 | 0.28604 | 0.0 | 98.41
Neigh | 0.00077796 | 0.0010615 | 0.0013225 | 0.7 | 0.37
Comm | 0.002372 | 0.0024325 | 0.002497 | 0.1 | 0.84
Output | 0.00025368 | 0.0002659 | 0.00029516 | 0.0 | 0.09
Modify | 0.00030279 | 0.00031865 | 0.00033021 | 0.0 | 0.11
Other | | 0.0004706 | | | 0.16
Nlocal: 75 ave 81 max 70 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Nghost: 282.5 ave 290 max 274 min
Histogram: 1 0 0 1 0 0 0 0 1 1
Neighs: 614.75 ave 981 max 285 min
Histogram: 1 1 0 0 0 0 0 1 0 1
Total # of neighbors = 2459
Ave neighs/atom = 8.19667
Neighbor list builds = 15
Dangerous builds = 0
Total wall time: 0:00:01

99
examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.fmm.8 Normal file
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LAMMPS (2 Aug 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
units lj
atom_style charge
read_data data.cloud_wall
orthogonal box = (0 0 0) to (10 10 10)
2 by 2 by 2 MPI processor grid
reading atoms ...
300 atoms
velocity all set 0.0 0.0 0.0 mom no
pair_style zero 1.0
pair_coeff * *
neighbor 1.0 bin
neigh_modify delay 0
fix 1 all nve
#pair_style coul/long 3.0
#pair_coeff * *
#kspace_style pppm 1.0e-3
kspace_style scafacos fmm 1.0e-3
kspace_modify scafacos tolerance energy_rel
kspace_modify scafacos fmm_tuning 1
ScaFaCoS setting fmm inhomogen tuning ...
timestep 0.005
thermo_style custom step atoms cpu temp pe ke etotal ecoul press
run_style verlet
#dump simple all custom 1000 id x y z vx vy vz
#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass
#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass
#dump_modify dmpvtk pad 7
thermo 10
run 100
Setting up ScaFaCoS with solver fmm ...
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 = 10 10 10
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.317 | 3.317 | 3.317 Mbytes
Step Atoms CPU Temp PotEng KinEng TotEng E_coul Press
0 300 0 0 0.49646402 0 0.49646402 0 0.016548801
10 300 0.026465416 0.015455559 0.47335833 0.02310606 0.49646439 0 0.020399823
20 300 0.057377338 0.06229069 0.40334177 0.093124582 0.49646635 0 0.032069642
30 300 0.088356495 0.14310163 0.28254277 0.21393694 0.49647971 0 0.05220548
40 300 0.11900806 0.52929788 0.089669015 0.79130033 0.88096934 0 0.16124903
50 300 0.15157914 1.1963022 -0.082792461 1.7884718 1.7056794 0 0.35493462
60 300 0.18608141 1.3928167 -0.37659239 2.082261 1.7056686 0 0.40389911
70 300 0.21956491 1.7069009 -0.84571914 2.5518169 1.7060978 0 0.48217274
80 300 0.24269128 15.358343 -3.368063 22.960722 19.592659 0 4.4798757
90 300 0.26847005 42.280432 -2.1623864 63.209247 61.04686 0 12.56977
100 300 0.29283834 41.48079 -0.89904529 62.013782 61.114736 0 12.372788
Loop time of 0.292855 on 8 procs for 100 steps with 300 atoms
Performance: 147513.337 tau/day, 341.466 timesteps/s
98.4% CPU use with 8 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 4.7207e-05 | 5.5045e-05 | 6.9618e-05 | 0.0 | 0.02
Kspace | 0.28739 | 0.28773 | 0.2881 | 0.0 | 98.25
Neigh | 0.00040698 | 0.00060901 | 0.00082922 | 0.0 | 0.21
Comm | 0.0029533 | 0.0031788 | 0.0034056 | 0.3 | 1.09
Output | 0.00029063 | 0.00030866 | 0.00035119 | 0.0 | 0.11
Modify | 0.00018978 | 0.00022188 | 0.00026703 | 0.0 | 0.08
Other | | 0.0007486 | | | 0.26
Nlocal: 37.5 ave 45 max 31 min
Histogram: 1 1 1 1 1 0 1 0 1 1
Nghost: 200 ave 209 max 189 min
Histogram: 1 0 0 0 1 4 0 0 0 2
Neighs: 307.375 ave 514 max 115 min
Histogram: 2 1 0 1 1 0 0 0 1 2
Total # of neighbors = 2459
Ave neighs/atom = 8.19667
Neighbor list builds = 15
Dangerous builds = 0
Total wall time: 0:00:01

92
examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.p2nfft.1 Normal file
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@ -0,0 +1,92 @@
LAMMPS (2 Aug 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
units lj
atom_style charge
read_data data.cloud_wall
orthogonal box = (0 0 0) to (10 10 10)
1 by 1 by 1 MPI processor grid
reading atoms ...
300 atoms
velocity all set 0.0 0.0 0.0 mom no
pair_style zero 1.0
pair_coeff * *
neighbor 1.0 bin
neigh_modify delay 0
fix 1 all nve
kspace_style scafacos p2nfft 0.001
kspace_modify scafacos tolerance field
timestep 0.005
thermo_style custom step atoms cpu temp pe ke etotal ecoul press
run_style verlet
#dump simple all custom 1000 id x y z vx vy vz
#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass
#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass
#dump_modify dmpvtk pad 7
thermo 10
run 100
Setting up ScaFaCoS with solver p2nfft ...
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 = 10 10 10
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.34 | 3.34 | 3.34 Mbytes
Step Atoms CPU Temp PotEng KinEng TotEng E_coul Press
0 300 0 0 0.49683273 0 0.49683273 0 0.016561091
10 300 0.071435928 0.015479312 0.47369009 0.023141571 0.49683166 0 0.020417984
20 300 0.14302707 0.062386358 0.40356181 0.093267605 0.49682941 0 0.032105581
30 300 0.21480989 0.14331637 0.2825636 0.21425798 0.49682157 0 0.052270382
40 300 0.28638172 0.53041843 0.089505208 0.79297556 0.88248077 0 0.16157862
50 300 0.35810781 1.1948397 -0.083317439 1.7862853 1.7029679 0 0.35447982
60 300 0.42993116 1.3915614 -0.37745551 2.0803842 1.7029287 0 0.40349499
70 300 0.50181961 1.7061978 -0.84746071 2.5507657 1.703305 0 0.48190445
80 300 0.57404566 20.692093 -3.32971 30.93468 27.60497 0 6.0759456
90 300 0.64724708 48.999403 -2.1632167 73.254107 71.090891 0 14.578714
100 300 0.72128963 51.199785 -0.81127924 76.543678 75.732399 0 15.281693
Loop time of 0.721302 on 1 procs for 100 steps with 300 atoms
Performance: 59891.733 tau/day, 138.638 timesteps/s
100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 8.893e-05 | 8.893e-05 | 8.893e-05 | 0.0 | 0.01
Kspace | 0.71502 | 0.71502 | 0.71502 | 0.0 | 99.13
Neigh | 0.0035415 | 0.0035415 | 0.0035415 | 0.0 | 0.49
Comm | 0.001024 | 0.001024 | 0.001024 | 0.0 | 0.14
Output | 0.00015044 | 0.00015044 | 0.00015044 | 0.0 | 0.02
Modify | 0.0010409 | 0.0010409 | 0.0010409 | 0.0 | 0.14
Other | | 0.0004385 | | | 0.06
Nlocal: 300 ave 300 max 300 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 381 ave 381 max 381 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 2461 ave 2461 max 2461 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2461
Ave neighs/atom = 8.20333
Neighbor list builds = 15
Dangerous builds = 0
Total wall time: 0:00:00

92
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LAMMPS (2 Aug 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
units lj
atom_style charge
read_data data.cloud_wall
orthogonal box = (0 0 0) to (10 10 10)
2 by 2 by 4 MPI processor grid
reading atoms ...
300 atoms
velocity all set 0.0 0.0 0.0 mom no
pair_style zero 1.0
pair_coeff * *
neighbor 1.0 bin
neigh_modify delay 0
fix 1 all nve
kspace_style scafacos p2nfft 0.001
kspace_modify scafacos tolerance field
timestep 0.005
thermo_style custom step atoms cpu temp pe ke etotal ecoul press
run_style verlet
#dump simple all custom 1000 id x y z vx vy vz
#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass
#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass
#dump_modify dmpvtk pad 7
thermo 10
run 100
Setting up ScaFaCoS with solver p2nfft ...
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 = 10 10 10
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.313 | 3.501 | 3.689 Mbytes
Step Atoms CPU Temp PotEng KinEng TotEng E_coul Press
0 300 0 0 0.49683273 0 0.49683273 0 0.016561091
10 300 0.015678644 0.015479312 0.47369009 0.023141571 0.49683166 0 0.020417984
20 300 0.031283855 0.062386358 0.40356181 0.093267605 0.49682941 0 0.032105581
30 300 0.046878099 0.14331637 0.2825636 0.21425798 0.49682157 0 0.052270382
40 300 0.062416077 0.53041843 0.089505208 0.79297556 0.88248077 0 0.16157862
50 300 0.078029871 1.1948397 -0.083317439 1.7862853 1.7029679 0 0.35447982
60 300 0.093806505 1.3915614 -0.37745551 2.0803842 1.7029287 0 0.40349499
70 300 0.1096344 1.7061978 -0.84746071 2.5507657 1.703305 0 0.48190445
80 300 0.12532592 20.692093 -3.32971 30.93468 27.60497 0 6.0759456
90 300 0.14175463 48.999403 -2.1632167 73.254107 71.090891 0 14.578714
100 300 0.15838337 51.199785 -0.81127924 76.543678 75.732399 0 15.281693
Loop time of 0.158406 on 16 procs for 100 steps with 300 atoms
Performance: 272716.448 tau/day, 631.288 timesteps/s
99.4% CPU use with 16 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.718e-05 | 3.7491e-05 | 5.6744e-05 | 0.0 | 0.02
Kspace | 0.15435 | 0.15482 | 0.15516 | 0.1 | 97.74
Neigh | 0.00014806 | 0.0003508 | 0.00074744 | 0.0 | 0.22
Comm | 0.0016866 | 0.0019967 | 0.0023787 | 0.5 | 1.26
Output | 0.00027871 | 0.00033027 | 0.00038028 | 0.0 | 0.21
Modify | 8.0347e-05 | 0.00011933 | 0.00016522 | 0.0 | 0.08
Other | | 0.0007506 | | | 0.47
Nlocal: 18.75 ave 33 max 6 min
Histogram: 2 6 0 0 0 0 2 1 2 3
Nghost: 128.875 ave 198 max 71 min
Histogram: 7 1 0 0 0 0 0 1 5 2
Neighs: 153.812 ave 490 max 14 min
Histogram: 8 0 3 0 1 1 0 0 1 2
Total # of neighbors = 2461
Ave neighs/atom = 8.20333
Neighbor list builds = 15
Dangerous builds = 0
Total wall time: 0:00:00

92
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LAMMPS (2 Aug 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
units lj
atom_style charge
read_data data.cloud_wall
orthogonal box = (0 0 0) to (10 10 10)
1 by 1 by 2 MPI processor grid
reading atoms ...
300 atoms
velocity all set 0.0 0.0 0.0 mom no
pair_style zero 1.0
pair_coeff * *
neighbor 1.0 bin
neigh_modify delay 0
fix 1 all nve
kspace_style scafacos p2nfft 0.001
kspace_modify scafacos tolerance field
timestep 0.005
thermo_style custom step atoms cpu temp pe ke etotal ecoul press
run_style verlet
#dump simple all custom 1000 id x y z vx vy vz
#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass
#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass
#dump_modify dmpvtk pad 7
thermo 10
run 100
Setting up ScaFaCoS with solver p2nfft ...
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 = 10 10 10
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.354 | 3.354 | 3.355 Mbytes
Step Atoms CPU Temp PotEng KinEng TotEng E_coul Press
0 300 0 0 0.49683273 0 0.49683273 0 0.016561091
10 300 0.044083834 0.015479312 0.47369009 0.023141571 0.49683166 0 0.020417984
20 300 0.088379145 0.062386358 0.40356181 0.093267605 0.49682941 0 0.032105581
30 300 0.13264704 0.14331637 0.2825636 0.21425798 0.49682157 0 0.052270382
40 300 0.17687225 0.53041843 0.089505208 0.79297556 0.88248077 0 0.16157862
50 300 0.22116137 1.1948397 -0.083317439 1.7862853 1.7029679 0 0.35447982
60 300 0.26515126 1.3915614 -0.37745551 2.0803842 1.7029287 0 0.40349499
70 300 0.30891085 1.7061978 -0.84746071 2.5507657 1.703305 0 0.48190445
80 300 0.35292292 20.692093 -3.32971 30.93468 27.60497 0 6.0759456
90 300 0.39845228 48.999403 -2.1632167 73.254107 71.090891 0 14.578714
100 300 0.44492316 51.199785 -0.81127924 76.543678 75.732399 0 15.281693
Loop time of 0.444937 on 2 procs for 100 steps with 300 atoms
Performance: 97092.373 tau/day, 224.751 timesteps/s
100.0% CPU use with 2 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 7.7248e-05 | 7.844e-05 | 7.9632e-05 | 0.0 | 0.02
Kspace | 0.43932 | 0.43979 | 0.44026 | 0.1 | 98.84
Neigh | 0.0014915 | 0.0019662 | 0.0024409 | 1.1 | 0.44
Comm | 0.0019331 | 0.0019941 | 0.0020552 | 0.1 | 0.45
Output | 0.00013781 | 0.00016308 | 0.00018835 | 0.0 | 0.04
Modify | 0.00050378 | 0.00050449 | 0.00050521 | 0.0 | 0.11
Other | | 0.0004425 | | | 0.10
Nlocal: 150 ave 157 max 143 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 399 ave 402 max 396 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 1230.5 ave 1756 max 705 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 2461
Ave neighs/atom = 8.20333
Neighbor list builds = 15
Dangerous builds = 0
Total wall time: 0:00:00

92
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LAMMPS (2 Aug 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
units lj
atom_style charge
read_data data.cloud_wall
orthogonal box = (0 0 0) to (10 10 10)
1 by 2 by 2 MPI processor grid
reading atoms ...
300 atoms
velocity all set 0.0 0.0 0.0 mom no
pair_style zero 1.0
pair_coeff * *
neighbor 1.0 bin
neigh_modify delay 0
fix 1 all nve
kspace_style scafacos p2nfft 0.001
kspace_modify scafacos tolerance field
timestep 0.005
thermo_style custom step atoms cpu temp pe ke etotal ecoul press
run_style verlet
#dump simple all custom 1000 id x y z vx vy vz
#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass
#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass
#dump_modify dmpvtk pad 7
thermo 10
run 100
Setting up ScaFaCoS with solver p2nfft ...
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 = 10 10 10
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.333 | 3.333 | 3.333 Mbytes
Step Atoms CPU Temp PotEng KinEng TotEng E_coul Press
0 300 0 0 0.49683273 0 0.49683273 0 0.016561091
10 300 0.02743125 0.015479312 0.47369009 0.023141571 0.49683166 0 0.020417984
20 300 0.05494833 0.062386358 0.40356181 0.093267605 0.49682941 0 0.032105581
30 300 0.082517862 0.14331637 0.2825636 0.21425798 0.49682157 0 0.052270382
40 300 0.11015558 0.53041843 0.089505208 0.79297556 0.88248077 0 0.16157862
50 300 0.13790298 1.1948397 -0.083317439 1.7862853 1.7029679 0 0.35447982
60 300 0.1660006 1.3915614 -0.37745551 2.0803842 1.7029287 0 0.40349499
70 300 0.1937964 1.7061978 -0.84746071 2.5507657 1.703305 0 0.48190445
80 300 0.22181106 20.692093 -3.32971 30.93468 27.60497 0 6.0759456
90 300 0.25105524 48.999403 -2.1632167 73.254107 71.090891 0 14.578714
100 300 0.28086019 51.199785 -0.81127924 76.543678 75.732399 0 15.281693
Loop time of 0.280875 on 4 procs for 100 steps with 300 atoms
Performance: 153805.254 tau/day, 356.031 timesteps/s
99.7% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 5.6744e-05 | 6.0022e-05 | 6.4135e-05 | 0.0 | 0.02
Kspace | 0.27651 | 0.27682 | 0.27714 | 0.0 | 98.56
Neigh | 0.00079465 | 0.001082 | 0.0014107 | 0.8 | 0.39
Comm | 0.0019372 | 0.002014 | 0.0020835 | 0.1 | 0.72
Output | 0.00018406 | 0.00019914 | 0.00023413 | 0.0 | 0.07
Modify | 0.0002749 | 0.00028563 | 0.00029325 | 0.0 | 0.10
Other | | 0.0004173 | | | 0.15
Nlocal: 75 ave 81 max 69 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Nghost: 287 ave 296 max 278 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Neighs: 615.25 ave 964 max 286 min
Histogram: 1 1 0 0 0 0 0 1 0 1
Total # of neighbors = 2461
Ave neighs/atom = 8.20333
Neighbor list builds = 15
Dangerous builds = 0
Total wall time: 0:00:00

92
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LAMMPS (2 Aug 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
units lj
atom_style charge
read_data data.cloud_wall
orthogonal box = (0 0 0) to (10 10 10)
2 by 2 by 2 MPI processor grid
reading atoms ...
300 atoms
velocity all set 0.0 0.0 0.0 mom no
pair_style zero 1.0
pair_coeff * *
neighbor 1.0 bin
neigh_modify delay 0
fix 1 all nve
kspace_style scafacos p2nfft 0.001
kspace_modify scafacos tolerance field
timestep 0.005
thermo_style custom step atoms cpu temp pe ke etotal ecoul press
run_style verlet
#dump simple all custom 1000 id x y z vx vy vz
#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass
#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass
#dump_modify dmpvtk pad 7
thermo 10
run 100
Setting up ScaFaCoS with solver p2nfft ...
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 = 10 10 10
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.317 | 3.317 | 3.317 Mbytes
Step Atoms CPU Temp PotEng KinEng TotEng E_coul Press
0 300 0 0 0.49683273 0 0.49683273 0 0.016561091
10 300 0.01961565 0.015479312 0.47369009 0.023141571 0.49683166 0 0.020417984
20 300 0.039346695 0.062386358 0.40356181 0.093267605 0.49682941 0 0.032105581
30 300 0.059037447 0.14331637 0.2825636 0.21425798 0.49682157 0 0.052270382
40 300 0.078732729 0.53041843 0.089505208 0.79297556 0.88248077 0 0.16157862
50 300 0.098586798 1.1948397 -0.083317439 1.7862853 1.7029679 0 0.35447982
60 300 0.11857247 1.3915614 -0.37745551 2.0803842 1.7029287 0 0.40349499
70 300 0.1385541 1.7061978 -0.84746071 2.5507657 1.703305 0 0.48190445
80 300 0.15850091 20.692093 -3.32971 30.93468 27.60497 0 6.0759456
90 300 0.17892075 48.999403 -2.1632167 73.254107 71.090891 0 14.578714
100 300 0.19964767 51.199785 -0.81127924 76.543678 75.732399 0 15.281693
Loop time of 0.199664 on 8 procs for 100 steps with 300 atoms
Performance: 216363.074 tau/day, 500.840 timesteps/s
99.4% CPU use with 8 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 4.5061e-05 | 4.7535e-05 | 5.3167e-05 | 0.0 | 0.02
Kspace | 0.19551 | 0.19584 | 0.19611 | 0.0 | 98.08
Neigh | 0.00041366 | 0.00060952 | 0.00082064 | 0.0 | 0.31
Comm | 0.0021496 | 0.0022282 | 0.0024025 | 0.2 | 1.12
Output | 0.0002346 | 0.00024167 | 0.00027847 | 0.0 | 0.12
Modify | 0.00016665 | 0.00017652 | 0.0001924 | 0.0 | 0.09
Other | | 0.0005245 | | | 0.26
Nlocal: 37.5 ave 42 max 33 min
Histogram: 2 1 0 1 0 0 1 0 1 2
Nghost: 202.25 ave 212 max 194 min
Histogram: 1 0 2 1 0 2 0 1 0 1
Neighs: 307.625 ave 505 max 129 min
Histogram: 3 0 0 1 1 0 0 0 1 2
Total # of neighbors = 2461
Ave neighs/atom = 8.20333
Neighbor list builds = 15
Dangerous builds = 0
Total wall time: 0:00:00

102
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LAMMPS (2 Aug 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
# Point dipoles in a 2d box
units lj
atom_style charge
read_data data.NaCl
orthogonal box = (0 0 0) to (1 1 1)
1 by 1 by 1 MPI processor grid
reading atoms ...
8 atoms
replicate 8 8 8
orthogonal box = (0 0 0) to (8 8 8)
1 by 1 by 1 MPI processor grid
4096 atoms
Time spent = 0.000498772 secs
velocity all create 1.5 49893
neighbor 1.0 bin
neigh_modify delay 0
fix 1 all nve
# LAMMPS computes pairwise and long-range Coulombics
#pair_style coul/long 3.0
#pair_coeff * *
#kspace_style pppm 1.0e-3
# Scafacos computes entire long-range Coulombics
# use dummy pair style to perform atom sorting
pair_style zero 1.0
pair_coeff * *
#fix 2 all scafacos p3m tolerance field 0.001
kspace_style scafacos ewald 0.001
kspace_modify scafacos tolerance field
timestep 0.005
thermo 10
run 100
Setting up ScaFaCoS with solver ewald ...
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 = 8 8 8
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.813 | 5.813 | 5.813 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.5 -1.7475938 0 0.50185691 11.99707
10 1.500011 -1.747529 0 0.50193816 11.997158
20 1.5000023 -1.7475152 0 0.50193898 11.997089
30 1.4999308 -1.747404 0 0.50194285 11.996517
40 1.4997722 -1.7471622 0 0.50194686 11.995248
50 1.4995835 -1.746878 0 0.50194808 11.993739
60 1.4996054 -1.7469114 0 0.50194749 11.993914
70 1.5004341 -1.7481558 0 0.50194592 12.000543
80 1.5033218 -1.7524875 0 0.50194458 12.023638
90 1.5108306 -1.7637462 0 0.50194636 12.083694
100 1.5292479 -1.7913449 0 0.50196695 12.230996
Loop time of 1121.22 on 1 procs for 100 steps with 4096 atoms
Performance: 38.530 tau/day, 0.089 timesteps/s
100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0015197 | 0.0015197 | 0.0015197 | 0.0 | 0.00
Kspace | 1121.2 | 1121.2 | 1121.2 | 0.0 |100.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.013699 | 0.013699 | 0.013699 | 0.0 | 0.00
Output | 0.00038314 | 0.00038314 | 0.00038314 | 0.0 | 0.00
Modify | 0.011126 | 0.011126 | 0.011126 | 0.0 | 0.00
Other | | 0.00418 | | | 0.00
Nlocal: 4096 ave 4096 max 4096 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 9728 ave 9728 max 9728 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 524288 ave 524288 max 524288 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 524288
Ave neighs/atom = 128
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:18:57

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LAMMPS (2 Aug 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
# Point dipoles in a 2d box
units lj
atom_style charge
read_data data.NaCl
orthogonal box = (0 0 0) to (1 1 1)
2 by 2 by 4 MPI processor grid
reading atoms ...
8 atoms
replicate 8 8 8
orthogonal box = (0 0 0) to (8 8 8)
2 by 2 by 4 MPI processor grid
4096 atoms
Time spent = 0.000462294 secs
velocity all create 1.5 49893
neighbor 1.0 bin
neigh_modify delay 0
fix 1 all nve
# LAMMPS computes pairwise and long-range Coulombics
#pair_style coul/long 3.0
#pair_coeff * *
#kspace_style pppm 1.0e-3
# Scafacos computes entire long-range Coulombics
# use dummy pair style to perform atom sorting
pair_style zero 1.0
pair_coeff * *
#fix 2 all scafacos p3m tolerance field 0.001
kspace_style scafacos ewald 0.001
kspace_modify scafacos tolerance field
timestep 0.005
thermo 10
run 100
Setting up ScaFaCoS with solver ewald ...
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 = 8 8 8
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.501 | 3.501 | 3.501 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.5 -1.7475938 0 0.50185691 -nan
10 1.500011 -1.747529 0 0.50193816 -nan
20 1.5000023 -1.7475152 0 0.50193898 -nan
30 1.4999308 -1.747404 0 0.50194285 -nan
40 1.4997722 -1.7471622 0 0.50194686 -nan
50 1.4995835 -1.746878 0 0.50194808 -nan
60 1.4996054 -1.7469114 0 0.50194749 -nan
70 1.5004341 -1.7481558 0 0.50194592 -nan
80 1.5033218 -1.7524875 0 0.50194458 -nan
90 1.5108306 -1.7637462 0 0.50194636 -nan
100 1.5292479 -1.7913449 0 0.50196695 -nan
Loop time of 80.2777 on 16 procs for 100 steps with 4096 atoms
Performance: 538.132 tau/day, 1.246 timesteps/s
99.8% CPU use with 16 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0003705 | 0.00039807 | 0.00048542 | 0.0 | 0.00
Kspace | 80.262 | 80.263 | 80.264 | 0.0 | 99.98
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.010191 | 0.011419 | 0.012416 | 0.6 | 0.01
Output | 0.00028253 | 0.00033158 | 0.0004065 | 0.0 | 0.00
Modify | 0.00082541 | 0.0008464 | 0.00087833 | 0.0 | 0.00
Other | | 0.001511 | | | 0.00
Nlocal: 256 ave 256 max 256 min
Histogram: 16 0 0 0 0 0 0 0 0 0
Nghost: 2816 ave 2816 max 2816 min
Histogram: 16 0 0 0 0 0 0 0 0 0
Neighs: 32768 ave 32768 max 32768 min
Histogram: 16 0 0 0 0 0 0 0 0 0
Total # of neighbors = 524288
Ave neighs/atom = 128
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:01:22

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LAMMPS (2 Aug 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
# Point dipoles in a 2d box
units lj
atom_style charge
read_data data.NaCl
orthogonal box = (0 0 0) to (1 1 1)
1 by 1 by 2 MPI processor grid
reading atoms ...
8 atoms
replicate 8 8 8
orthogonal box = (0 0 0) to (8 8 8)
1 by 1 by 2 MPI processor grid
4096 atoms
Time spent = 0.000344753 secs
velocity all create 1.5 49893
neighbor 1.0 bin
neigh_modify delay 0
fix 1 all nve
# LAMMPS computes pairwise and long-range Coulombics
#pair_style coul/long 3.0
#pair_coeff * *
#kspace_style pppm 1.0e-3
# Scafacos computes entire long-range Coulombics
# use dummy pair style to perform atom sorting
pair_style zero 1.0
pair_coeff * *
#fix 2 all scafacos p3m tolerance field 0.001
kspace_style scafacos ewald 0.001
kspace_modify scafacos tolerance field
timestep 0.005
thermo 10
run 100
Setting up ScaFaCoS with solver ewald ...
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 = 8 8 8
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.574 | 4.574 | 4.574 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.5 -1.7475938 0 0.50185691 11.99707
10 1.500011 -1.747529 0 0.50193816 11.997158
20 1.5000023 -1.7475152 0 0.50193898 11.997089
30 1.4999308 -1.747404 0 0.50194285 11.996517
40 1.4997722 -1.7471622 0 0.50194686 11.995248
50 1.4995835 -1.746878 0 0.50194808 11.993739
60 1.4996054 -1.7469114 0 0.50194749 11.993914
70 1.5004341 -1.7481558 0 0.50194592 12.000543
80 1.5033218 -1.7524875 0 0.50194458 12.023638
90 1.5108306 -1.7637462 0 0.50194636 12.083694
100 1.5292479 -1.7913449 0 0.50196695 12.230996
Loop time of 566.796 on 2 procs for 100 steps with 4096 atoms
Performance: 76.218 tau/day, 0.176 timesteps/s
100.0% CPU use with 2 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0010231 | 0.0010413 | 0.0010595 | 0.1 | 0.00
Kspace | 566.77 | 566.77 | 566.77 | 0.0 | 99.99
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.019707 | 0.01982 | 0.019932 | 0.1 | 0.00
Output | 0.0002656 | 0.00029266 | 0.00031972 | 0.0 | 0.00
Modify | 0.0055575 | 0.0055707 | 0.0055838 | 0.0 | 0.00
Other | | 0.002497 | | | 0.00
Nlocal: 2048 ave 2048 max 2048 min
Histogram: 2 0 0 0 0 0 0 0 0 0
Nghost: 7168 ave 7168 max 7168 min
Histogram: 2 0 0 0 0 0 0 0 0 0
Neighs: 262144 ave 262144 max 262144 min
Histogram: 2 0 0 0 0 0 0 0 0 0
Total # of neighbors = 524288
Ave neighs/atom = 128
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:09:38

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LAMMPS (2 Aug 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
# Point dipoles in a 2d box
units lj
atom_style charge
read_data data.NaCl
orthogonal box = (0 0 0) to (1 1 1)
1 by 2 by 2 MPI processor grid
reading atoms ...
8 atoms
replicate 8 8 8
orthogonal box = (0 0 0) to (8 8 8)
1 by 2 by 2 MPI processor grid
4096 atoms
Time spent = 0.000261068 secs
velocity all create 1.5 49893
neighbor 1.0 bin
neigh_modify delay 0
fix 1 all nve
# LAMMPS computes pairwise and long-range Coulombics
#pair_style coul/long 3.0
#pair_coeff * *
#kspace_style pppm 1.0e-3
# Scafacos computes entire long-range Coulombics
# use dummy pair style to perform atom sorting
pair_style zero 1.0
pair_coeff * *
#fix 2 all scafacos p3m tolerance field 0.001
kspace_style scafacos ewald 0.001
kspace_modify scafacos tolerance field
timestep 0.005
thermo 10
run 100
Setting up ScaFaCoS with solver ewald ...
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 = 8 8 8
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.008 | 4.008 | 4.008 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.5 -1.7475938 0 0.50185691 -nan
10 1.500011 -1.747529 0 0.50193816 -nan
20 1.5000023 -1.7475152 0 0.50193898 -nan
30 1.4999308 -1.747404 0 0.50194285 -nan
40 1.4997722 -1.7471622 0 0.50194686 -nan
50 1.4995835 -1.746878 0 0.50194808 -nan
60 1.4996054 -1.7469114 0 0.50194749 -nan
70 1.5004341 -1.7481558 0 0.50194592 -nan
80 1.5033218 -1.7524875 0 0.50194458 -nan
90 1.5108306 -1.7637462 0 0.50194636 -nan
100 1.5292479 -1.7913449 0 0.50196695 -nan
Loop time of 295.996 on 4 procs for 100 steps with 4096 atoms
Performance: 145.948 tau/day, 0.338 timesteps/s
99.9% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.00071096 | 0.00071985 | 0.00072813 | 0.0 | 0.00
Kspace | 295.98 | 295.98 | 295.98 | 0.0 | 99.99
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.013666 | 0.013736 | 0.013795 | 0.0 | 0.00
Output | 0.00023484 | 0.00025135 | 0.00029254 | 0.0 | 0.00
Modify | 0.0029099 | 0.002973 | 0.0030224 | 0.1 | 0.00
Other | | 0.001821 | | | 0.00
Nlocal: 1024 ave 1024 max 1024 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 5120 ave 5120 max 5120 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 131072 ave 131072 max 131072 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 524288
Ave neighs/atom = 128
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:05:02

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LAMMPS (2 Aug 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
# Point dipoles in a 2d box
units lj
atom_style charge
read_data data.NaCl
orthogonal box = (0 0 0) to (1 1 1)
2 by 2 by 2 MPI processor grid
reading atoms ...
8 atoms
replicate 8 8 8
orthogonal box = (0 0 0) to (8 8 8)
2 by 2 by 2 MPI processor grid
4096 atoms
Time spent = 0.000232935 secs
velocity all create 1.5 49893
neighbor 1.0 bin
neigh_modify delay 0
fix 1 all nve
# LAMMPS computes pairwise and long-range Coulombics
#pair_style coul/long 3.0
#pair_coeff * *
#kspace_style pppm 1.0e-3
# Scafacos computes entire long-range Coulombics
# use dummy pair style to perform atom sorting
pair_style zero 1.0
pair_coeff * *
#fix 2 all scafacos p3m tolerance field 0.001
kspace_style scafacos ewald 0.001
kspace_modify scafacos tolerance field
timestep 0.005
thermo 10
run 100
Setting up ScaFaCoS with solver ewald ...
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 = 8 8 8
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.508 | 3.508 | 3.508 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.5 -1.7475938 0 0.50185691 -nan
10 1.500011 -1.747529 0 0.50193816 -nan
20 1.5000023 -1.7475152 0 0.50193898 -nan
30 1.4999308 -1.747404 0 0.50194285 -nan
40 1.4997722 -1.7471622 0 0.50194686 -nan
50 1.4995835 -1.746878 0 0.50194808 -nan
60 1.4996054 -1.7469114 0 0.50194749 -nan
70 1.5004341 -1.7481558 0 0.50194592 -nan
80 1.5033218 -1.7524875 0 0.50194458 -nan
90 1.5108306 -1.7637462 0 0.50194636 -nan
100 1.5292479 -1.7913449 0 0.50196695 -nan
Loop time of 154.44 on 8 procs for 100 steps with 4096 atoms
Performance: 279.720 tau/day, 0.647 timesteps/s
99.9% CPU use with 8 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.00049257 | 0.00051311 | 0.00059295 | 0.0 | 0.00
Kspace | 154.42 | 154.42 | 154.42 | 0.0 | 99.99
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.012076 | 0.013177 | 0.014308 | 0.8 | 0.01
Output | 0.00025177 | 0.00028065 | 0.00030136 | 0.0 | 0.00
Modify | 0.0015776 | 0.0017182 | 0.0018268 | 0.2 | 0.00
Other | | 0.001309 | | | 0.00
Nlocal: 512 ave 512 max 512 min
Histogram: 8 0 0 0 0 0 0 0 0 0
Nghost: 3584 ave 3584 max 3584 min
Histogram: 8 0 0 0 0 0 0 0 0 0
Neighs: 65536 ave 65536 max 65536 min
Histogram: 8 0 0 0 0 0 0 0 0 0
Total # of neighbors = 524288
Ave neighs/atom = 128
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:02:38

102
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LAMMPS (2 Aug 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
# Point dipoles in a 2d box
units lj
atom_style charge
read_data data.NaCl
orthogonal box = (0 0 0) to (1 1 1)
1 by 1 by 1 MPI processor grid
reading atoms ...
8 atoms
replicate 8 8 8
orthogonal box = (0 0 0) to (8 8 8)
1 by 1 by 1 MPI processor grid
4096 atoms
Time spent = 0.000518799 secs
velocity all create 1.5 49893
neighbor 1.0 bin
neigh_modify delay 0
fix 1 all nve
# LAMMPS computes pairwise and long-range Coulombics
#pair_style coul/long 3.0
#pair_coeff * *
#kspace_style pppm 1.0e-3
# Scafacos computes entire long-range Coulombics
# use dummy pair style to perform atom sorting
pair_style zero 1.0
pair_coeff * *
#fix 2 all scafacos p3m tolerance field 0.001
kspace_style scafacos fmm 0.001
kspace_modify scafacos tolerance energy
timestep 0.005
thermo 10
run 100
Setting up ScaFaCoS with solver fmm ...
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 = 8 8 8
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.813 | 5.813 | 5.813 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.5 -1.7475646 0 0.50188608 10.44368
10 1.5000016 -1.7475671 0 0.50188602 10.44369
20 1.4999827 -1.7475388 0 0.50188592 10.443564
30 1.4999016 -1.7474173 0 0.5018858 10.443023
40 1.4997356 -1.7471685 0 0.50188572 10.441917
50 1.4995414 -1.7468771 0 0.5018858 10.440623
60 1.4995587 -1.7469027 0 0.50188622 10.440739
70 1.5003837 -1.7481389 0 0.50188727 10.446238
80 1.5032684 -1.7524625 0 0.50188958 10.465466
90 1.5107749 -1.763714 0 0.50189507 10.515502
100 1.52919 -1.791306 0 0.50191895 10.638261
Loop time of 34.7058 on 1 procs for 100 steps with 4096 atoms
Performance: 1244.749 tau/day, 2.881 timesteps/s
100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0015228 | 0.0015228 | 0.0015228 | 0.0 | 0.00
Kspace | 34.675 | 34.675 | 34.675 | 0.0 | 99.91
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.013741 | 0.013741 | 0.013741 | 0.0 | 0.04
Output | 0.00041246 | 0.00041246 | 0.00041246 | 0.0 | 0.00
Modify | 0.01107 | 0.01107 | 0.01107 | 0.0 | 0.03
Other | | 0.004232 | | | 0.01
Nlocal: 4096 ave 4096 max 4096 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 9728 ave 9728 max 9728 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 524288 ave 524288 max 524288 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 524288
Ave neighs/atom = 128
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:35

102
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@ -0,0 +1,102 @@
LAMMPS (2 Aug 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
# Point dipoles in a 2d box
units lj
atom_style charge
read_data data.NaCl
orthogonal box = (0 0 0) to (1 1 1)
2 by 2 by 4 MPI processor grid
reading atoms ...
8 atoms
replicate 8 8 8
orthogonal box = (0 0 0) to (8 8 8)
2 by 2 by 4 MPI processor grid
4096 atoms
Time spent = 0.000400543 secs
velocity all create 1.5 49893
neighbor 1.0 bin
neigh_modify delay 0
fix 1 all nve
# LAMMPS computes pairwise and long-range Coulombics
#pair_style coul/long 3.0
#pair_coeff * *
#kspace_style pppm 1.0e-3
# Scafacos computes entire long-range Coulombics
# use dummy pair style to perform atom sorting
pair_style zero 1.0
pair_coeff * *
#fix 2 all scafacos p3m tolerance field 0.001
kspace_style scafacos fmm 0.001
kspace_modify scafacos tolerance energy
timestep 0.005
thermo 10
run 100
Setting up ScaFaCoS with solver fmm ...
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 = 8 8 8
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.501 | 3.501 | 3.501 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.5 -1.7475646 0 0.50188608 10.44368
10 1.5000016 -1.7475671 0 0.50188602 10.44369
20 1.4999827 -1.7475388 0 0.50188592 10.443564
30 1.4999016 -1.7474173 0 0.5018858 10.443023
40 1.4997356 -1.7471685 0 0.50188572 10.441917
50 1.4995414 -1.7468771 0 0.5018858 10.440623
60 1.4995587 -1.7469027 0 0.50188622 10.440739
70 1.5003837 -1.7481389 0 0.50188727 10.446238
80 1.5032684 -1.7524625 0 0.50188958 10.465466
90 1.5107749 -1.763714 0 0.50189507 10.515502
100 1.52919 -1.791306 0 0.50191895 10.638261
Loop time of 4.23774 on 16 procs for 100 steps with 4096 atoms
Performance: 10194.102 tau/day, 23.597 timesteps/s
99.6% CPU use with 16 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.00038028 | 0.00040729 | 0.00046206 | 0.0 | 0.01
Kspace | 4.2206 | 4.2211 | 4.2216 | 0.0 | 99.61
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.011439 | 0.012491 | 0.013172 | 0.4 | 0.29
Output | 0.00042915 | 0.000489 | 0.00061274 | 0.0 | 0.01
Modify | 0.00093102 | 0.00099151 | 0.0010982 | 0.0 | 0.02
Other | | 0.002255 | | | 0.05
Nlocal: 256 ave 256 max 256 min
Histogram: 16 0 0 0 0 0 0 0 0 0
Nghost: 2816 ave 2816 max 2816 min
Histogram: 16 0 0 0 0 0 0 0 0 0
Neighs: 32768 ave 32768 max 32768 min
Histogram: 16 0 0 0 0 0 0 0 0 0
Total # of neighbors = 524288
Ave neighs/atom = 128
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:06

102
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@ -0,0 +1,102 @@
LAMMPS (2 Aug 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
# Point dipoles in a 2d box
units lj
atom_style charge
read_data data.NaCl
orthogonal box = (0 0 0) to (1 1 1)
1 by 1 by 2 MPI processor grid
reading atoms ...
8 atoms
replicate 8 8 8
orthogonal box = (0 0 0) to (8 8 8)
1 by 1 by 2 MPI processor grid
4096 atoms
Time spent = 0.0003407 secs
velocity all create 1.5 49893
neighbor 1.0 bin
neigh_modify delay 0
fix 1 all nve
# LAMMPS computes pairwise and long-range Coulombics
#pair_style coul/long 3.0
#pair_coeff * *
#kspace_style pppm 1.0e-3
# Scafacos computes entire long-range Coulombics
# use dummy pair style to perform atom sorting
pair_style zero 1.0
pair_coeff * *
#fix 2 all scafacos p3m tolerance field 0.001
kspace_style scafacos fmm 0.001
kspace_modify scafacos tolerance energy
timestep 0.005
thermo 10
run 100
Setting up ScaFaCoS with solver fmm ...
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 = 8 8 8
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.574 | 4.574 | 4.574 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.5 -1.7475646 0 0.50188608 10.44368
10 1.5000016 -1.7475671 0 0.50188602 10.44369
20 1.4999827 -1.7475388 0 0.50188592 10.443564
30 1.4999016 -1.7474173 0 0.5018858 10.443023
40 1.4997356 -1.7471685 0 0.50188572 10.441917
50 1.4995414 -1.7468771 0 0.5018858 10.440623
60 1.4995587 -1.7469027 0 0.50188622 10.440739
70 1.5003837 -1.7481389 0 0.50188727 10.446238
80 1.5032684 -1.7524625 0 0.50188958 10.465466
90 1.5107749 -1.763714 0 0.50189507 10.515502
100 1.52919 -1.791306 0 0.50191895 10.638261
Loop time of 17.9401 on 2 procs for 100 steps with 4096 atoms
Performance: 2408.014 tau/day, 5.574 timesteps/s
99.9% CPU use with 2 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0010042 | 0.0010235 | 0.0010428 | 0.1 | 0.01
Kspace | 17.912 | 17.912 | 17.912 | 0.0 | 99.84
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.018252 | 0.018528 | 0.018804 | 0.2 | 0.10
Output | 0.00034094 | 0.00035989 | 0.00037885 | 0.0 | 0.00
Modify | 0.0055602 | 0.0056567 | 0.0057533 | 0.1 | 0.03
Other | | 0.002716 | | | 0.02
Nlocal: 2048 ave 2048 max 2048 min
Histogram: 2 0 0 0 0 0 0 0 0 0
Nghost: 7168 ave 7168 max 7168 min
Histogram: 2 0 0 0 0 0 0 0 0 0
Neighs: 262144 ave 262144 max 262144 min
Histogram: 2 0 0 0 0 0 0 0 0 0
Total # of neighbors = 524288
Ave neighs/atom = 128
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:19

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LAMMPS (2 Aug 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
# Point dipoles in a 2d box
units lj
atom_style charge
read_data data.NaCl
orthogonal box = (0 0 0) to (1 1 1)
1 by 2 by 2 MPI processor grid
reading atoms ...
8 atoms
replicate 8 8 8
orthogonal box = (0 0 0) to (8 8 8)
1 by 2 by 2 MPI processor grid
4096 atoms
Time spent = 0.000270367 secs
velocity all create 1.5 49893
neighbor 1.0 bin
neigh_modify delay 0
fix 1 all nve
# LAMMPS computes pairwise and long-range Coulombics
#pair_style coul/long 3.0
#pair_coeff * *
#kspace_style pppm 1.0e-3
# Scafacos computes entire long-range Coulombics
# use dummy pair style to perform atom sorting
pair_style zero 1.0
pair_coeff * *
#fix 2 all scafacos p3m tolerance field 0.001
kspace_style scafacos fmm 0.001
kspace_modify scafacos tolerance energy
timestep 0.005
thermo 10
run 100
Setting up ScaFaCoS with solver fmm ...
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 = 8 8 8
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.008 | 4.008 | 4.008 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.5 -1.7475646 0 0.50188608 10.44368
10 1.5000016 -1.7475671 0 0.50188602 10.44369
20 1.4999827 -1.7475388 0 0.50188592 10.443564
30 1.4999016 -1.7474173 0 0.5018858 10.443023
40 1.4997356 -1.7471685 0 0.50188572 10.441917
50 1.4995414 -1.7468771 0 0.5018858 10.440623
60 1.4995587 -1.7469027 0 0.50188622 10.440739
70 1.5003837 -1.7481389 0 0.50188727 10.446238
80 1.5032684 -1.7524625 0 0.50188958 10.465466
90 1.5107749 -1.763714 0 0.50189507 10.515502
100 1.52919 -1.791306 0 0.50191895 10.638261
Loop time of 10.0781 on 4 procs for 100 steps with 4096 atoms
Performance: 4286.533 tau/day, 9.923 timesteps/s
99.9% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.00071096 | 0.00073177 | 0.00075269 | 0.0 | 0.01
Kspace | 10.056 | 10.057 | 10.057 | 0.0 | 99.79
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.01492 | 0.015036 | 0.015207 | 0.1 | 0.15
Output | 0.00036311 | 0.00039428 | 0.00046515 | 0.0 | 0.00
Modify | 0.002944 | 0.0030704 | 0.0033708 | 0.3 | 0.03
Other | | 0.002214 | | | 0.02
Nlocal: 1024 ave 1024 max 1024 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 5120 ave 5120 max 5120 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 131072 ave 131072 max 131072 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 524288
Ave neighs/atom = 128
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:11

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LAMMPS (2 Aug 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
# Point dipoles in a 2d box
units lj
atom_style charge
read_data data.NaCl
orthogonal box = (0 0 0) to (1 1 1)
2 by 2 by 2 MPI processor grid
reading atoms ...
8 atoms
replicate 8 8 8
orthogonal box = (0 0 0) to (8 8 8)
2 by 2 by 2 MPI processor grid
4096 atoms
Time spent = 0.000236988 secs
velocity all create 1.5 49893
neighbor 1.0 bin
neigh_modify delay 0
fix 1 all nve
# LAMMPS computes pairwise and long-range Coulombics
#pair_style coul/long 3.0
#pair_coeff * *
#kspace_style pppm 1.0e-3
# Scafacos computes entire long-range Coulombics
# use dummy pair style to perform atom sorting
pair_style zero 1.0
pair_coeff * *
#fix 2 all scafacos p3m tolerance field 0.001
kspace_style scafacos fmm 0.001
kspace_modify scafacos tolerance energy
timestep 0.005
thermo 10
run 100
Setting up ScaFaCoS with solver fmm ...
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 = 8 8 8
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.508 | 3.508 | 3.508 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.5 -1.7475646 0 0.50188608 10.44368
10 1.5000016 -1.7475671 0 0.50188602 10.44369
20 1.4999827 -1.7475388 0 0.50188592 10.443564
30 1.4999016 -1.7474173 0 0.5018858 10.443023
40 1.4997356 -1.7471685 0 0.50188572 10.441917
50 1.4995414 -1.7468771 0 0.5018858 10.440623
60 1.4995587 -1.7469027 0 0.50188622 10.440739
70 1.5003837 -1.7481389 0 0.50188727 10.446238
80 1.5032684 -1.7524625 0 0.50188958 10.465466
90 1.5107749 -1.763714 0 0.50189507 10.515502
100 1.52919 -1.791306 0 0.50191895 10.638261
Loop time of 5.96037 on 8 procs for 100 steps with 4096 atoms
Performance: 7247.876 tau/day, 16.777 timesteps/s
99.8% CPU use with 8 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.00049591 | 0.0005368 | 0.00056005 | 0.0 | 0.01
Kspace | 5.94 | 5.941 | 5.9419 | 0.0 | 99.68
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.013702 | 0.014631 | 0.015768 | 0.6 | 0.25
Output | 0.00044751 | 0.00048846 | 0.00058961 | 0.0 | 0.01
Modify | 0.0016675 | 0.0017205 | 0.0017893 | 0.1 | 0.03
Other | | 0.001971 | | | 0.03
Nlocal: 512 ave 512 max 512 min
Histogram: 8 0 0 0 0 0 0 0 0 0
Nghost: 3584 ave 3584 max 3584 min
Histogram: 8 0 0 0 0 0 0 0 0 0
Neighs: 65536 ave 65536 max 65536 min
Histogram: 8 0 0 0 0 0 0 0 0 0
Total # of neighbors = 524288
Ave neighs/atom = 128
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:07

102
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LAMMPS (2 Aug 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
# Point dipoles in a 2d box
units lj
atom_style charge
read_data data.NaCl
orthogonal box = (0 0 0) to (1 1 1)
1 by 1 by 1 MPI processor grid
reading atoms ...
8 atoms
replicate 8 8 8
orthogonal box = (0 0 0) to (8 8 8)
1 by 1 by 1 MPI processor grid
4096 atoms
Time spent = 0.00049448 secs
velocity all create 1.5 49893
neighbor 1.0 bin
neigh_modify delay 0
fix 1 all nve
# LAMMPS computes pairwise and long-range Coulombics
#pair_style coul/long 3.0
#pair_coeff * *
#kspace_style pppm 1.0e-3
# Scafacos computes entire long-range Coulombics
# use dummy pair style to perform atom sorting
pair_style zero 1.0
pair_coeff * *
#fix 2 all scafacos p3m tolerance field 0.001
kspace_style scafacos p2nfft 0.001
kspace_modify scafacos tolerance field
timestep 0.005
thermo 10
run 100
Setting up ScaFaCoS with solver p2nfft ...
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 = 8 8 8
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.813 | 5.813 | 5.813 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.5 -1.7477245 0 0.50172614 10.443537
10 1.5000176 -1.7475898 0 0.50188725 10.443798
20 1.5000161 -1.7475262 0 0.50194874 10.443843
30 1.4999486 -1.7474019 0 0.50197176 10.443413
40 1.4997889 -1.7471525 0 0.50198161 10.442357
50 1.4995945 -1.7468614 0 0.50198122 10.441061
60 1.499609 -1.7468813 0 0.50198309 10.44116
70 1.5004314 -1.7481179 0 0.50197962 10.446638
80 1.5033149 -1.7524495 0 0.50197233 10.46585
90 1.5108219 -1.7637095 0 0.50197005 10.515883
100 1.529239 -1.7913105 0 0.501988 10.638649
Loop time of 18.1113 on 1 procs for 100 steps with 4096 atoms
Performance: 2385.257 tau/day, 5.521 timesteps/s
100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0014985 | 0.0014985 | 0.0014985 | 0.0 | 0.01
Kspace | 18.079 | 18.079 | 18.079 | 0.0 | 99.82
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.014229 | 0.014229 | 0.014229 | 0.0 | 0.08
Output | 0.0004642 | 0.0004642 | 0.0004642 | 0.0 | 0.00
Modify | 0.011227 | 0.011227 | 0.011227 | 0.0 | 0.06
Other | | 0.004455 | | | 0.02
Nlocal: 4096 ave 4096 max 4096 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 9728 ave 9728 max 9728 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 524288 ave 524288 max 524288 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 524288
Ave neighs/atom = 128
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:21

102
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LAMMPS (2 Aug 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
# Point dipoles in a 2d box
units lj
atom_style charge
read_data data.NaCl
orthogonal box = (0 0 0) to (1 1 1)
2 by 2 by 4 MPI processor grid
reading atoms ...
8 atoms
replicate 8 8 8
orthogonal box = (0 0 0) to (8 8 8)
2 by 2 by 4 MPI processor grid
4096 atoms
Time spent = 0.000361443 secs
velocity all create 1.5 49893
neighbor 1.0 bin
neigh_modify delay 0
fix 1 all nve
# LAMMPS computes pairwise and long-range Coulombics
#pair_style coul/long 3.0
#pair_coeff * *
#kspace_style pppm 1.0e-3
# Scafacos computes entire long-range Coulombics
# use dummy pair style to perform atom sorting
pair_style zero 1.0
pair_coeff * *
#fix 2 all scafacos p3m tolerance field 0.001
kspace_style scafacos p2nfft 0.001
kspace_modify scafacos tolerance field
timestep 0.005
thermo 10
run 100
Setting up ScaFaCoS with solver p2nfft ...
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 = 8 8 8
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.501 | 3.501 | 3.501 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.5 -1.7477245 0 0.50172614 10.443537
10 1.5000176 -1.7475898 0 0.50188725 10.443798
20 1.5000161 -1.7475262 0 0.50194874 10.443843
30 1.4999486 -1.7474019 0 0.50197176 10.443413
40 1.4997889 -1.7471525 0 0.50198161 10.442357
50 1.4995945 -1.7468614 0 0.50198122 10.441061
60 1.499609 -1.7468813 0 0.50198309 10.44116
70 1.5004314 -1.7481179 0 0.50197962 10.446638
80 1.5033149 -1.7524495 0 0.50197233 10.46585
90 1.5108219 -1.7637095 0 0.50197005 10.515883
100 1.529239 -1.7913105 0 0.501988 10.638649
Loop time of 1.56685 on 16 procs for 100 steps with 4096 atoms
Performance: 27571.239 tau/day, 63.822 timesteps/s
99.8% CPU use with 16 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.00036407 | 0.00040755 | 0.00047517 | 0.0 | 0.03
Kspace | 1.5521 | 1.553 | 1.5536 | 0.0 | 99.12
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.009537 | 0.010175 | 0.011894 | 0.6 | 0.65
Output | 0.000319 | 0.00039139 | 0.00052881 | 0.0 | 0.02
Modify | 0.00086999 | 0.00097834 | 0.0010362 | 0.0 | 0.06
Other | | 0.001859 | | | 0.12
Nlocal: 256 ave 256 max 256 min
Histogram: 16 0 0 0 0 0 0 0 0 0
Nghost: 2816 ave 2816 max 2816 min
Histogram: 16 0 0 0 0 0 0 0 0 0
Neighs: 32768 ave 32768 max 32768 min
Histogram: 16 0 0 0 0 0 0 0 0 0
Total # of neighbors = 524288
Ave neighs/atom = 128
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:01

102
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LAMMPS (2 Aug 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
# Point dipoles in a 2d box
units lj
atom_style charge
read_data data.NaCl
orthogonal box = (0 0 0) to (1 1 1)
1 by 1 by 2 MPI processor grid
reading atoms ...
8 atoms
replicate 8 8 8
orthogonal box = (0 0 0) to (8 8 8)
1 by 1 by 2 MPI processor grid
4096 atoms
Time spent = 0.0003438 secs
velocity all create 1.5 49893
neighbor 1.0 bin
neigh_modify delay 0
fix 1 all nve
# LAMMPS computes pairwise and long-range Coulombics
#pair_style coul/long 3.0
#pair_coeff * *
#kspace_style pppm 1.0e-3
# Scafacos computes entire long-range Coulombics
# use dummy pair style to perform atom sorting
pair_style zero 1.0
pair_coeff * *
#fix 2 all scafacos p3m tolerance field 0.001
kspace_style scafacos p2nfft 0.001
kspace_modify scafacos tolerance field
timestep 0.005
thermo 10
run 100
Setting up ScaFaCoS with solver p2nfft ...
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 = 8 8 8
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.574 | 4.574 | 4.574 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.5 -1.7477245 0 0.50172614 10.443537
10 1.5000176 -1.7475898 0 0.50188725 10.443798
20 1.5000161 -1.7475262 0 0.50194874 10.443843
30 1.4999486 -1.7474019 0 0.50197176 10.443413
40 1.4997889 -1.7471525 0 0.50198161 10.442357
50 1.4995945 -1.7468614 0 0.50198122 10.441061
60 1.499609 -1.7468813 0 0.50198309 10.44116
70 1.5004314 -1.7481179 0 0.50197962 10.446638
80 1.5033149 -1.7524495 0 0.50197233 10.46585
90 1.5108219 -1.7637095 0 0.50197005 10.515883
100 1.529239 -1.7913105 0 0.501988 10.638649
Loop time of 9.38943 on 2 procs for 100 steps with 4096 atoms
Performance: 4600.920 tau/day, 10.650 timesteps/s
99.9% CPU use with 2 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0010064 | 0.0010065 | 0.0010066 | 0.0 | 0.01
Kspace | 9.3602 | 9.3603 | 9.3604 | 0.0 | 99.69
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.019444 | 0.01968 | 0.019916 | 0.2 | 0.21
Output | 0.00033355 | 0.00035357 | 0.0003736 | 0.0 | 0.00
Modify | 0.0055819 | 0.0056176 | 0.0056534 | 0.0 | 0.06
Other | | 0.002495 | | | 0.03
Nlocal: 2048 ave 2048 max 2048 min
Histogram: 2 0 0 0 0 0 0 0 0 0
Nghost: 7168 ave 7168 max 7168 min
Histogram: 2 0 0 0 0 0 0 0 0 0
Neighs: 262144 ave 262144 max 262144 min
Histogram: 2 0 0 0 0 0 0 0 0 0
Total # of neighbors = 524288
Ave neighs/atom = 128
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:11

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LAMMPS (2 Aug 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
# Point dipoles in a 2d box
units lj
atom_style charge
read_data data.NaCl
orthogonal box = (0 0 0) to (1 1 1)
1 by 2 by 2 MPI processor grid
reading atoms ...
8 atoms
replicate 8 8 8
orthogonal box = (0 0 0) to (8 8 8)
1 by 2 by 2 MPI processor grid
4096 atoms
Time spent = 0.000260592 secs
velocity all create 1.5 49893
neighbor 1.0 bin
neigh_modify delay 0
fix 1 all nve
# LAMMPS computes pairwise and long-range Coulombics
#pair_style coul/long 3.0
#pair_coeff * *
#kspace_style pppm 1.0e-3
# Scafacos computes entire long-range Coulombics
# use dummy pair style to perform atom sorting
pair_style zero 1.0
pair_coeff * *
#fix 2 all scafacos p3m tolerance field 0.001
kspace_style scafacos p2nfft 0.001
kspace_modify scafacos tolerance field
timestep 0.005
thermo 10
run 100
Setting up ScaFaCoS with solver p2nfft ...
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 = 8 8 8
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.008 | 4.008 | 4.008 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.5 -1.7477245 0 0.50172614 10.443537
10 1.5000176 -1.7475898 0 0.50188725 10.443798
20 1.5000161 -1.7475262 0 0.50194874 10.443843
30 1.4999486 -1.7474019 0 0.50197176 10.443413
40 1.4997889 -1.7471525 0 0.50198161 10.442357
50 1.4995945 -1.7468614 0 0.50198122 10.441061
60 1.499609 -1.7468813 0 0.50198309 10.44116
70 1.5004314 -1.7481179 0 0.50197962 10.446638
80 1.5033149 -1.7524495 0 0.50197233 10.46585
90 1.5108219 -1.7637095 0 0.50197005 10.515883
100 1.529239 -1.7913105 0 0.501988 10.638649
Loop time of 5.09997 on 4 procs for 100 steps with 4096 atoms
Performance: 8470.643 tau/day, 19.608 timesteps/s
99.8% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.00069928 | 0.00071001 | 0.00073647 | 0.0 | 0.01
Kspace | 5.0795 | 5.0796 | 5.0797 | 0.0 | 99.60
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.014101 | 0.014216 | 0.014331 | 0.1 | 0.28
Output | 0.00030541 | 0.00033581 | 0.00039625 | 0.0 | 0.01
Modify | 0.0030217 | 0.0030621 | 0.0030868 | 0.0 | 0.06
Other | | 0.002036 | | | 0.04
Nlocal: 1024 ave 1024 max 1024 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 5120 ave 5120 max 5120 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 131072 ave 131072 max 131072 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 524288
Ave neighs/atom = 128
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:05

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LAMMPS (2 Aug 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
# Point dipoles in a 2d box
units lj
atom_style charge
read_data data.NaCl
orthogonal box = (0 0 0) to (1 1 1)
2 by 2 by 2 MPI processor grid
reading atoms ...
8 atoms
replicate 8 8 8
orthogonal box = (0 0 0) to (8 8 8)
2 by 2 by 2 MPI processor grid
4096 atoms
Time spent = 0.000324488 secs
velocity all create 1.5 49893
neighbor 1.0 bin
neigh_modify delay 0
fix 1 all nve
# LAMMPS computes pairwise and long-range Coulombics
#pair_style coul/long 3.0
#pair_coeff * *
#kspace_style pppm 1.0e-3
# Scafacos computes entire long-range Coulombics
# use dummy pair style to perform atom sorting
pair_style zero 1.0
pair_coeff * *
#fix 2 all scafacos p3m tolerance field 0.001
kspace_style scafacos p2nfft 0.001
kspace_modify scafacos tolerance field
timestep 0.005
thermo 10
run 100
Setting up ScaFaCoS with solver p2nfft ...
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 = 8 8 8
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.508 | 3.508 | 3.508 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.5 -1.7477245 0 0.50172614 10.443537
10 1.5000176 -1.7475898 0 0.50188725 10.443798
20 1.5000161 -1.7475262 0 0.50194874 10.443843
30 1.4999486 -1.7474019 0 0.50197176 10.443413
40 1.4997889 -1.7471525 0 0.50198161 10.442357
50 1.4995945 -1.7468614 0 0.50198122 10.441061
60 1.499609 -1.7468813 0 0.50198309 10.44116
70 1.5004314 -1.7481179 0 0.50197962 10.446638
80 1.5033149 -1.7524495 0 0.50197233 10.46585
90 1.5108219 -1.7637095 0 0.50197005 10.515883
100 1.529239 -1.7913105 0 0.501988 10.638649
Loop time of 2.88506 on 8 procs for 100 steps with 4096 atoms
Performance: 14973.700 tau/day, 34.661 timesteps/s
99.6% CPU use with 8 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.000489 | 0.00051507 | 0.00052857 | 0.0 | 0.02
Kspace | 2.8657 | 2.866 | 2.8664 | 0.0 | 99.34
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.014354 | 0.014851 | 0.015097 | 0.2 | 0.51
Output | 0.00037169 | 0.00042769 | 0.00054169 | 0.0 | 0.01
Modify | 0.0015774 | 0.0016578 | 0.0018044 | 0.2 | 0.06
Other | | 0.001645 | | | 0.06
Nlocal: 512 ave 512 max 512 min
Histogram: 8 0 0 0 0 0 0 0 0 0
Nghost: 3584 ave 3584 max 3584 min
Histogram: 8 0 0 0 0 0 0 0 0 0
Neighs: 65536 ave 65536 max 65536 min
Histogram: 8 0 0 0 0 0 0 0 0 0
Total # of neighbors = 524288
Ave neighs/atom = 128
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:03

0
examples/USER/scafacos/log.08Aug18.scafacos.g++.p3m.2 Normal file
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LAMMPS (2 Aug 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
# Point dipoles in a 2d box
units lj
atom_style charge
read_data data.hammersley_shphere
orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5)
1 by 1 by 1 MPI processor grid
reading atoms ...
1000 atoms
change_box all boundary f f f
velocity all create 1.5 49893
neighbor 1.0 bin
neigh_modify delay 0
fix 1 all nve
# LAMMPS computes pairwise and long-range Coulombics
#pair_style coul/long 3.0
#pair_coeff * *
#kspace_style pppm 1.0e-3
# Scafacos computes entire long-range Coulombics
# use dummy pair style to perform atom sorting
pair_style zero 1.0
pair_coeff * *
#fix 2 all scafacos p3m tolerance field 0.001
kspace_style scafacos direct 0.001
timestep 0.005
thermo 1
run 20
Setting up ScaFaCoS with solver direct ...
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 = 102 102 102
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 10.3 | 10.3 | 10.3 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.5 -0.62417787 0 1.6235721 0.0015678854
1 18.780041 -10.770002 0 17.371889 0.016718957
2 65.289192 -11.084705 0 86.751149 0.060353634
3 121.92987 -7.0625759 0 175.64933 0.11404974
4 185.78164 -5.8777512 0 272.51604 0.17462195
5 286.36222 -4.382053 0 424.73173 0.26918926
6 481.42206 -4.3095567 0 717.1014 0.45274088
7 488.59167 -3.8685194 0 728.2861 0.45956866
8 497.85287 -3.0417966 0 742.99073 0.46838116
9 499.61615 -3.419003 0 745.2558 0.46983345
10 502.63684 -2.8360961 0 750.36521 0.47280809
11 504.4846 -2.7628105 0 753.20736 0.47462793
12 506.54485 -2.8460356 0 756.21142 0.47651441
13 508.27211 -2.730935 0 758.91482 0.47813752
14 510.57045 -2.6094877 0 762.48033 0.48031431
15 513.14798 -2.7150827 0 766.23717 0.48275229
16 515.78124 -2.3961811 0 770.50201 0.48526333
17 515.70265 -2.2982683 0 770.48215 0.48526617
18 515.7081 -2.1515983 0 770.63699 0.48530393
19 515.74906 -2.0581436 0 770.79182 0.48530977
20 515.70883 -1.8922577 0 770.89742 0.48527105
Loop time of 0.465839 on 1 procs for 20 steps with 1000 atoms
Performance: 18547.165 tau/day, 42.933 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 | 0.00021982 | 0.00021982 | 0.00021982 | 0.0 | 0.05
Kspace | 0.3218 | 0.3218 | 0.3218 | 0.0 | 69.08
Neigh | 0.14249 | 0.14249 | 0.14249 | 0.0 | 30.59
Comm | 0.00014853 | 0.00014853 | 0.00014853 | 0.0 | 0.03
Output | 0.00026131 | 0.00026131 | 0.00026131 | 0.0 | 0.06
Modify | 0.00055146 | 0.00055146 | 0.00055146 | 0.0 | 0.12
Other | | 0.0003715 | | | 0.08
Nlocal: 1000 ave 1000 max 1000 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: 247817 ave 247817 max 247817 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 247817
Ave neighs/atom = 247.817
Neighbor list builds = 19
Dangerous builds = 18
Total wall time: 0:00:00

105
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LAMMPS (2 Aug 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
# Point dipoles in a 2d box
units lj
atom_style charge
read_data data.hammersley_shphere
orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5)
1 by 1 by 2 MPI processor grid
reading atoms ...
1000 atoms
change_box all boundary f f f
velocity all create 1.5 49893
neighbor 1.0 bin
neigh_modify delay 0
fix 1 all nve
# LAMMPS computes pairwise and long-range Coulombics
#pair_style coul/long 3.0
#pair_coeff * *
#kspace_style pppm 1.0e-3
# Scafacos computes entire long-range Coulombics
# use dummy pair style to perform atom sorting
pair_style zero 1.0
pair_coeff * *
#fix 2 all scafacos p3m tolerance field 0.001
kspace_style scafacos direct 0.001
timestep 0.005
thermo 1
run 20
Setting up ScaFaCoS with solver direct ...
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 = 102 102 102
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 6.48 | 6.861 | 7.243 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.5 -0.62417787 0 1.6235721 0.0015678854
1 18.780041 -10.770002 0 17.371889 0.016718957
2 65.289192 -11.084705 0 86.751149 0.060353634
3 121.92987 -7.0625759 0 175.64933 0.11404974
4 185.78164 -5.8777512 0 272.51604 0.17462195
5 286.36222 -4.382053 0 424.73173 0.26918926
6 481.42206 -4.3095567 0 717.1014 0.45274088
7 488.59167 -3.8685194 0 728.2861 0.45956866
8 497.85287 -3.0417966 0 742.99073 0.46838116
9 499.61615 -3.419003 0 745.2558 0.46983345
10 502.63684 -2.8360961 0 750.36521 0.47280809
11 504.4846 -2.7628105 0 753.20736 0.47462793
12 506.54485 -2.8460356 0 756.21142 0.47651441
13 508.27211 -2.730935 0 758.91482 0.47813752
14 510.57045 -2.6094877 0 762.48033 0.48031431
15 513.14798 -2.7150827 0 766.23717 0.48275229
16 515.78124 -2.3961811 0 770.50201 0.48526333
17 515.70265 -2.2982683 0 770.48215 0.48526617
18 515.7081 -2.1515983 0 770.63699 0.48530393
19 515.74906 -2.0581436 0 770.79182 0.48530977
20 515.70883 -1.8922577 0 770.89742 0.48527105
Loop time of 0.284007 on 2 procs for 20 steps with 1000 atoms
Performance: 30421.778 tau/day, 70.421 timesteps/s
99.1% CPU use with 2 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.00022578 | 0.00022626 | 0.00022674 | 0.0 | 0.08
Kspace | 0.18253 | 0.20503 | 0.22752 | 5.0 | 72.19
Neigh | 0.05363 | 0.076239 | 0.098848 | 8.2 | 26.84
Comm | 0.0014737 | 0.0016443 | 0.0018148 | 0.4 | 0.58
Output | 0.000247 | 0.00032353 | 0.00040007 | 0.0 | 0.11
Modify | 0.00029159 | 0.00029731 | 0.00030303 | 0.0 | 0.10
Other | | 0.0002506 | | | 0.09
Nlocal: 500 ave 516 max 484 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 456.5 ave 475 max 438 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 123908 ave 172139 max 75678 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 247817
Ave neighs/atom = 247.817
Neighbor list builds = 19
Dangerous builds = 18
Total wall time: 0:00:00

105
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LAMMPS (2 Aug 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
# Point dipoles in a 2d box
units lj
atom_style charge
read_data data.hammersley_shphere
orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5)
1 by 2 by 2 MPI processor grid
reading atoms ...
1000 atoms
change_box all boundary f f f
velocity all create 1.5 49893
neighbor 1.0 bin
neigh_modify delay 0
fix 1 all nve
# LAMMPS computes pairwise and long-range Coulombics
#pair_style coul/long 3.0
#pair_coeff * *
#kspace_style pppm 1.0e-3
# Scafacos computes entire long-range Coulombics
# use dummy pair style to perform atom sorting
pair_style zero 1.0
pair_coeff * *
#fix 2 all scafacos p3m tolerance field 0.001
kspace_style scafacos direct 0.001
timestep 0.005
thermo 1
run 20
Setting up ScaFaCoS with solver direct ...
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 = 102 102 102
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.837 | 5.123 | 5.6 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.5 -0.62417787 0 1.6235721 0.0015678854
1 18.780041 -10.770002 0 17.371889 0.016718957
2 65.289192 -11.084705 0 86.751149 0.060353634
3 121.92987 -7.0625759 0 175.64933 0.11404974
4 185.78164 -5.8777512 0 272.51604 0.17462195
5 286.36222 -4.382053 0 424.73173 0.26918926
6 481.42206 -4.3095567 0 717.1014 0.45274088
7 488.59167 -3.8685194 0 728.2861 0.45956866
8 497.85287 -3.0417966 0 742.99073 0.46838116
9 499.61615 -3.419003 0 745.2558 0.46983345
10 502.63684 -2.8360961 0 750.36521 0.47280809
11 504.4846 -2.7628105 0 753.20736 0.47462793
12 506.54485 -2.8460356 0 756.21142 0.47651441
13 508.27211 -2.730935 0 758.91482 0.47813752
14 510.57045 -2.6094877 0 762.48033 0.48031431
15 513.14798 -2.7150827 0 766.23717 0.48275229
16 515.78124 -2.3961811 0 770.50201 0.48526333
17 515.70265 -2.2982683 0 770.48215 0.48526617
18 515.7081 -2.1515983 0 770.63699 0.48530393
19 515.74906 -2.0581436 0 770.79182 0.48530977
20 515.70883 -1.8922577 0 770.89742 0.48527105
Loop time of 0.161335 on 4 procs for 20 steps with 1000 atoms
Performance: 53553.228 tau/day, 123.966 timesteps/s
99.5% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.00022721 | 0.00023353 | 0.000247 | 0.0 | 0.14
Kspace | 0.10295 | 0.11808 | 0.13377 | 3.5 | 73.19
Neigh | 0.023849 | 0.039717 | 0.055031 | 6.1 | 24.62
Comm | 0.0023148 | 0.0025774 | 0.0028391 | 0.4 | 1.60
Output | 0.00029063 | 0.00038403 | 0.00050664 | 0.0 | 0.24
Modify | 0.00015664 | 0.00015944 | 0.00016165 | 0.0 | 0.10
Other | | 0.0001805 | | | 0.11
Nlocal: 250 ave 259 max 238 min
Histogram: 1 0 0 1 0 0 0 0 0 2
Nghost: 672.25 ave 683 max 663 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Neighs: 61954.2 ave 97157 max 25016 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Total # of neighbors = 247817
Ave neighs/atom = 247.817
Neighbor list builds = 19
Dangerous builds = 18
Total wall time: 0:00:00

105
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LAMMPS (2 Aug 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
# Point dipoles in a 2d box
units lj
atom_style charge
read_data data.hammersley_shphere
orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5)
2 by 2 by 2 MPI processor grid
reading atoms ...
1000 atoms
change_box all boundary f f f
velocity all create 1.5 49893
neighbor 1.0 bin
neigh_modify delay 0
fix 1 all nve
# LAMMPS computes pairwise and long-range Coulombics
#pair_style coul/long 3.0
#pair_coeff * *
#kspace_style pppm 1.0e-3
# Scafacos computes entire long-range Coulombics
# use dummy pair style to perform atom sorting
pair_style zero 1.0
pair_coeff * *
#fix 2 all scafacos p3m tolerance field 0.001
kspace_style scafacos direct 0.001
timestep 0.005
thermo 1
run 20
Setting up ScaFaCoS with solver direct ...
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 = 102 102 102
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.164 | 4.26 | 4.546 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.5 -0.62417787 0 1.6235721 0.0015678854
1 18.780041 -10.770002 0 17.371889 0.016718957
2 65.289192 -11.084705 0 86.751149 0.060353634
3 121.92987 -7.0625759 0 175.64933 0.11404974
4 185.78164 -5.8777512 0 272.51604 0.17462195
5 286.36222 -4.382053 0 424.73173 0.26918926
6 481.42206 -4.3095567 0 717.1014 0.45274088
7 488.59167 -3.8685194 0 728.2861 0.45956866
8 497.85287 -3.0417966 0 742.99073 0.46838116
9 499.61615 -3.419003 0 745.2558 0.46983345
10 502.63684 -2.8360961 0 750.36521 0.47280809
11 504.4846 -2.7628105 0 753.20736 0.47462793
12 506.54485 -2.8460356 0 756.21142 0.47651441
13 508.27211 -2.730935 0 758.91482 0.47813752
14 510.57045 -2.6094877 0 762.48033 0.48031431
15 513.14798 -2.7150827 0 766.23717 0.48275229
16 515.78124 -2.3961811 0 770.50201 0.48526333
17 515.70265 -2.2982683 0 770.48215 0.48526617
18 515.7081 -2.1515983 0 770.63699 0.48530393
19 515.74906 -2.0581436 0 770.79182 0.48530977
20 515.70883 -1.8922577 0 770.89742 0.48527105
Loop time of 0.0883947 on 8 procs for 20 steps with 1000 atoms
Performance: 97743.448 tau/day, 226.258 timesteps/s
99.2% CPU use with 8 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0002284 | 0.00024167 | 0.00029922 | 0.0 | 0.27
Kspace | 0.055725 | 0.063153 | 0.071883 | 2.4 | 71.44
Neigh | 0.012251 | 0.021348 | 0.029026 | 4.3 | 24.15
Comm | 0.0025573 | 0.0029825 | 0.0034359 | 0.5 | 3.37
Output | 0.00034451 | 0.00044149 | 0.00057721 | 0.0 | 0.50
Modify | 7.8917e-05 | 8.437e-05 | 8.9407e-05 | 0.0 | 0.10
Other | | 0.0001439 | | | 0.16
Nlocal: 125 ave 133 max 113 min
Histogram: 2 0 0 0 0 1 1 0 2 2
Nghost: 773.625 ave 788 max 764 min
Histogram: 1 1 2 1 1 0 0 0 1 1
Neighs: 30977.1 ave 50690 max 10447 min
Histogram: 1 1 1 0 1 1 0 0 2 1
Total # of neighbors = 247817
Ave neighs/atom = 247.817
Neighbor list builds = 19
Dangerous builds = 18
Total wall time: 0:00:00

109
examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.fmm.1 Normal file
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LAMMPS (2 Aug 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
# Point dipoles in a 2d box
units lj
atom_style charge
read_data data.hammersley_shphere
orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5)
1 by 1 by 1 MPI processor grid
reading atoms ...
1000 atoms
change_box all boundary f f f
velocity all create 1.5 49893
neighbor 1.0 bin
neigh_modify delay 0
fix 1 all nve
# LAMMPS computes pairwise and long-range Coulombics
#pair_style coul/long 3.0
#pair_coeff * *
#kspace_style pppm 1.0e-3
# Scafacos computes entire long-range Coulombics
# use dummy pair style to perform atom sorting
pair_style zero 1.0
pair_coeff * *
#fix 2 all scafacos p3m tolerance field 0.001
kspace_style scafacos fmm 0.001
kspace_modify scafacos tolerance energy_rel
kspace_modify scafacos fmm_tuning 1
ScaFaCoS setting fmm inhomogen tuning ...
timestep 0.005
thermo 1
run 20
Setting up ScaFaCoS with solver fmm ...
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 = 102 102 102
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 10.3 | 10.3 | 10.3 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.5 -0.62417141 0 1.6235786 0.0015676581
1 18.780412 -10.770009 0 17.372438 0.016719188
2 65.294131 -11.084501 0 86.758754 0.06035827
3 121.92555 -7.0612033 0 175.64423 0.1140457
4 185.71165 -5.8781334 0 272.41077 0.17455524
5 286.28339 -4.3800108 0 424.61565 0.26911306
6 481.28097 -4.3052012 0 716.89433 0.45262045
7 487.26022 -3.8672741 0 726.29216 0.45830216
8 493.65478 -3.0242687 0 736.71742 0.46443761
9 495.66203 -3.4336343 0 739.31592 0.46613014
10 498.41831 -2.8837072 0 743.99613 0.46887706
11 499.20944 -2.7724783 0 745.29287 0.46966875
12 500.97345 -2.8281484 0 747.88057 0.47126462
13 507.46412 -2.7752775 0 757.65971 0.47728761
14 525.35729 -2.5749814 0 784.67292 0.49422171
15 563.9578 -2.9982381 0 842.09253 0.53043696
16 645.47602 -2.5519203 0 964.69389 0.60730795
17 647.09276 -2.2568468 0 967.41166 0.60891914
18 647.12596 -2.2791003 0 967.43915 0.60900309
19 647.24862 -2.2495226 0 967.65253 0.60908339
20 647.51175 -2.0239179 0 968.27244 0.60932598
Loop time of 0.797289 on 1 procs for 20 steps with 1000 atoms
Performance: 10836.721 tau/day, 25.085 timesteps/s
100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.00022364 | 0.00022364 | 0.00022364 | 0.0 | 0.03
Kspace | 0.6524 | 0.6524 | 0.6524 | 0.0 | 81.83
Neigh | 0.14312 | 0.14312 | 0.14312 | 0.0 | 17.95
Comm | 0.00020337 | 0.00020337 | 0.00020337 | 0.0 | 0.03
Output | 0.00036621 | 0.00036621 | 0.00036621 | 0.0 | 0.05
Modify | 0.00058126 | 0.00058126 | 0.00058126 | 0.0 | 0.07
Other | | 0.0003934 | | | 0.05
Nlocal: 1000 ave 1000 max 1000 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: 244342 ave 244342 max 244342 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 244342
Ave neighs/atom = 244.342
Neighbor list builds = 19
Dangerous builds = 18
Total wall time: 0:00:01

109
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LAMMPS (2 Aug 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
# Point dipoles in a 2d box
units lj
atom_style charge
read_data data.hammersley_shphere
orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5)
1 by 1 by 2 MPI processor grid
reading atoms ...
1000 atoms
change_box all boundary f f f
velocity all create 1.5 49893
neighbor 1.0 bin
neigh_modify delay 0
fix 1 all nve
# LAMMPS computes pairwise and long-range Coulombics
#pair_style coul/long 3.0
#pair_coeff * *
#kspace_style pppm 1.0e-3
# Scafacos computes entire long-range Coulombics
# use dummy pair style to perform atom sorting
pair_style zero 1.0
pair_coeff * *
#fix 2 all scafacos p3m tolerance field 0.001
kspace_style scafacos fmm 0.001
kspace_modify scafacos tolerance energy_rel
kspace_modify scafacos fmm_tuning 1
ScaFaCoS setting fmm inhomogen tuning ...
timestep 0.005
thermo 1
run 20
Setting up ScaFaCoS with solver fmm ...
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 = 102 102 102
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 6.48 | 6.861 | 7.243 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.5 -0.62417141 0 1.6235786 0.0015676581
1 18.780412 -10.770009 0 17.372438 0.016719188
2 65.294131 -11.084501 0 86.758754 0.06035827
3 121.92555 -7.0612033 0 175.64423 0.1140457
4 185.71165 -5.8781334 0 272.41077 0.17455524
5 286.28339 -4.3800108 0 424.61565 0.26911306
6 481.28097 -4.3052012 0 716.89433 0.45262045
7 487.26022 -3.8672741 0 726.29216 0.45830216
8 493.65478 -3.0242687 0 736.71742 0.46443761
9 495.66203 -3.4336343 0 739.31592 0.46613014
10 498.41831 -2.8837072 0 743.99613 0.46887706
11 499.20944 -2.7724783 0 745.29287 0.46966875
12 500.97345 -2.8281484 0 747.88057 0.47126462
13 507.46412 -2.7752775 0 757.65971 0.47728761
14 525.35729 -2.5749814 0 784.67292 0.49422171
15 563.9578 -2.9982381 0 842.09253 0.53043696
16 645.47602 -2.5519203 0 964.69389 0.60730795
17 647.09276 -2.2568468 0 967.41166 0.60891914
18 647.12596 -2.2791003 0 967.43915 0.60900309
19 647.24862 -2.2495226 0 967.65253 0.60908339
20 647.51175 -2.0239179 0 968.27244 0.60932598
Loop time of 0.701186 on 2 procs for 20 steps with 1000 atoms
Performance: 12321.981 tau/day, 28.523 timesteps/s
99.7% CPU use with 2 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.00022388 | 0.00022912 | 0.00023437 | 0.0 | 0.03
Kspace | 0.60189 | 0.62405 | 0.64621 | 2.8 | 89.00
Neigh | 0.051681 | 0.073973 | 0.096265 | 8.2 | 10.55
Comm | 0.0016983 | 0.0018919 | 0.0020854 | 0.4 | 0.27
Output | 0.00034356 | 0.00044572 | 0.00054789 | 0.0 | 0.06
Modify | 0.00031281 | 0.0003171 | 0.00032139 | 0.0 | 0.05
Other | | 0.0002786 | | | 0.04
Nlocal: 500 ave 509 max 491 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 455.5 ave 467 max 444 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 122171 ave 171834 max 72508 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 244342
Ave neighs/atom = 244.342
Neighbor list builds = 19
Dangerous builds = 18
Total wall time: 0:00:01

109
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LAMMPS (2 Aug 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
# Point dipoles in a 2d box
units lj
atom_style charge
read_data data.hammersley_shphere
orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5)
1 by 2 by 2 MPI processor grid
reading atoms ...
1000 atoms
change_box all boundary f f f
velocity all create 1.5 49893
neighbor 1.0 bin
neigh_modify delay 0
fix 1 all nve
# LAMMPS computes pairwise and long-range Coulombics
#pair_style coul/long 3.0
#pair_coeff * *
#kspace_style pppm 1.0e-3
# Scafacos computes entire long-range Coulombics
# use dummy pair style to perform atom sorting
pair_style zero 1.0
pair_coeff * *
#fix 2 all scafacos p3m tolerance field 0.001
kspace_style scafacos fmm 0.001
kspace_modify scafacos tolerance energy_rel
kspace_modify scafacos fmm_tuning 1
ScaFaCoS setting fmm inhomogen tuning ...
timestep 0.005
thermo 1
run 20
Setting up ScaFaCoS with solver fmm ...
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 = 102 102 102
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.837 | 5.123 | 5.6 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.5 -0.62417141 0 1.6235786 0.0015676581
1 18.780412 -10.770009 0 17.372438 0.016719188
2 65.294131 -11.084501 0 86.758754 0.06035827
3 121.92555 -7.0612033 0 175.64423 0.1140457
4 185.71165 -5.8781334 0 272.41077 0.17455524
5 286.28339 -4.3800108 0 424.61565 0.26911306
6 481.28097 -4.3052012 0 716.89433 0.45262045
7 487.26022 -3.8672741 0 726.29216 0.45830216
8 493.65478 -3.0242687 0 736.71742 0.46443761
9 495.66203 -3.4336343 0 739.31592 0.46613014
10 498.41831 -2.8837072 0 743.99613 0.46887706
11 499.20944 -2.7724783 0 745.29287 0.46966875
12 500.97345 -2.8281484 0 747.88057 0.47126462
13 507.46412 -2.7752775 0 757.65971 0.47728761
14 525.35729 -2.5749814 0 784.67292 0.49422171
15 563.9578 -2.9982381 0 842.09253 0.53043696
16 645.47602 -2.5519203 0 964.69389 0.60730795
17 647.09276 -2.2568468 0 967.41166 0.60891914
18 647.12596 -2.2791003 0 967.43915 0.60900309
19 647.24862 -2.2495226 0 967.65253 0.60908339
20 647.51175 -2.0239179 0 968.27244 0.60932598
Loop time of 0.666895 on 4 procs for 20 steps with 1000 atoms
Performance: 12955.555 tau/day, 29.990 timesteps/s
99.5% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0002284 | 0.00024879 | 0.00025725 | 0.0 | 0.04
Kspace | 0.6085 | 0.62278 | 0.6386 | 1.6 | 93.38
Neigh | 0.023998 | 0.040044 | 0.054552 | 6.2 | 6.00
Comm | 0.0025489 | 0.0028656 | 0.0031898 | 0.4 | 0.43
Output | 0.0004077 | 0.00053912 | 0.00071406 | 0.0 | 0.08
Modify | 0.00017953 | 0.00018525 | 0.00020218 | 0.0 | 0.03
Other | | 0.0002366 | | | 0.04
Nlocal: 250 ave 259 max 240 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Nghost: 668.75 ave 679 max 657 min
Histogram: 1 0 0 0 0 1 1 0 0 1
Neighs: 61085.5 ave 95363 max 24964 min
Histogram: 1 0 0 1 0 0 0 1 0 1
Total # of neighbors = 244342
Ave neighs/atom = 244.342
Neighbor list builds = 19
Dangerous builds = 18
Total wall time: 0:00:01

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LAMMPS (2 Aug 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
# Point dipoles in a 2d box
units lj
atom_style charge
read_data data.hammersley_shphere
orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5)
2 by 2 by 2 MPI processor grid
reading atoms ...
1000 atoms
change_box all boundary f f f
velocity all create 1.5 49893
neighbor 1.0 bin
neigh_modify delay 0
fix 1 all nve
# LAMMPS computes pairwise and long-range Coulombics
#pair_style coul/long 3.0
#pair_coeff * *
#kspace_style pppm 1.0e-3
# Scafacos computes entire long-range Coulombics
# use dummy pair style to perform atom sorting
pair_style zero 1.0
pair_coeff * *
#fix 2 all scafacos p3m tolerance field 0.001
kspace_style scafacos fmm 0.001
kspace_modify scafacos tolerance energy_rel
kspace_modify scafacos fmm_tuning 1
ScaFaCoS setting fmm inhomogen tuning ...
timestep 0.005
thermo 1
run 20
Setting up ScaFaCoS with solver fmm ...
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 = 102 102 102
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.164 | 4.26 | 4.546 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.5 -0.62417141 0 1.6235786 0.0015676581
1 18.780412 -10.770009 0 17.372438 0.016719188
2 65.294131 -11.084501 0 86.758754 0.06035827
3 121.92555 -7.0612033 0 175.64423 0.1140457
4 185.71165 -5.8781334 0 272.41077 0.17455524
5 286.28339 -4.3800108 0 424.61565 0.26911306
6 481.28097 -4.3052012 0 716.89433 0.45262045
7 487.26022 -3.8672741 0 726.29216 0.45830216
8 493.65478 -3.0242687 0 736.71742 0.46443761
9 495.66203 -3.4336343 0 739.31592 0.46613014
10 498.41831 -2.8837072 0 743.99613 0.46887706
11 499.20944 -2.7724783 0 745.29287 0.46966875
12 500.97345 -2.8281484 0 747.88057 0.47126462
13 507.46412 -2.7752775 0 757.65971 0.47728761
14 525.35729 -2.5749814 0 784.67292 0.49422171
15 563.9578 -2.9982381 0 842.09253 0.53043696
16 645.47602 -2.5519203 0 964.69389 0.60730795
17 647.09276 -2.2568468 0 967.41166 0.60891914
18 647.12596 -2.2791003 0 967.43915 0.60900309
19 647.24862 -2.2495226 0 967.65253 0.60908339
20 647.51175 -2.0239179 0 968.27244 0.60932598
Loop time of 0.569395 on 8 procs for 20 steps with 1000 atoms
Performance: 15174.000 tau/day, 35.125 timesteps/s
99.3% CPU use with 8 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.00021982 | 0.00023353 | 0.0002408 | 0.0 | 0.04
Kspace | 0.53679 | 0.54466 | 0.55292 | 0.8 | 95.66
Neigh | 0.011844 | 0.02033 | 0.028357 | 4.2 | 3.57
Comm | 0.0028894 | 0.0031579 | 0.0034704 | 0.4 | 0.55
Output | 0.0005579 | 0.00067073 | 0.0008719 | 0.0 | 0.12
Modify | 0.0001018 | 0.00011405 | 0.00012612 | 0.0 | 0.02
Other | | 0.0002268 | | | 0.04
Nlocal: 125 ave 137 max 111 min
Histogram: 1 1 0 0 0 2 2 1 0 1
Nghost: 768.875 ave 788 max 761 min
Histogram: 4 0 2 0 0 0 1 0 0 1
Neighs: 30542.8 ave 48077 max 10011 min
Histogram: 1 1 1 0 1 1 0 0 0 3
Total # of neighbors = 244342
Ave neighs/atom = 244.342
Neighbor list builds = 19
Dangerous builds = 18
Total wall time: 0:00:01

107
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LAMMPS (2 Aug 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
# Point dipoles in a 2d box
units lj
atom_style charge
read_data data.hammersley_shphere
orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5)
1 by 1 by 1 MPI processor grid
reading atoms ...
1000 atoms
change_box all boundary f f f
velocity all create 1.5 49893
neighbor 1.0 bin
neigh_modify delay 0
fix 1 all nve
# LAMMPS computes pairwise and long-range Coulombics
#pair_style coul/long 3.0
#pair_coeff * *
#kspace_style pppm 1.0e-3
# Scafacos computes entire long-range Coulombics
# use dummy pair style to perform atom sorting
pair_style zero 1.0
pair_coeff * *
#fix 2 all scafacos p3m tolerance field 0.001
kspace_style scafacos p2nfft 0.001
kspace_modify scafacos tolerance potential
timestep 0.005
thermo 1
run 20
Setting up ScaFaCoS with solver p2nfft ...
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 = 102 102 102
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 10.3 | 10.3 | 10.3 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.5 -0.62417787 0 1.6235721 0.0015678854
1 18.780041 -10.770002 0 17.371889 0.016718957
2 65.289192 -11.084705 0 86.751149 0.060353634
3 121.92987 -7.0625759 0 175.64933 0.11404974
4 185.78164 -5.8777511 0 272.51603 0.17462194
5 286.36221 -4.3820531 0 424.73172 0.26918925
6 481.42203 -4.3095567 0 717.10136 0.45274086
7 488.59165 -3.8685193 0 728.28607 0.45956865
8 497.85288 -3.0417938 0 742.99075 0.46838117
9 499.61619 -3.4190063 0 745.25585 0.46983349
10 502.63691 -2.8360951 0 750.36531 0.47280815
11 504.4847 -2.7628089 0 753.20751 0.47462802
12 506.54494 -2.8460319 0 756.21157 0.4765145
13 508.2722 -2.7309328 0 758.91497 0.47813761
14 510.57053 -2.6094792 0 762.48045 0.48031438
15 513.14804 -2.7150819 0 766.23726 0.48275234
16 515.78127 -2.3961749 0 770.50206 0.48526336
17 515.70267 -2.2982581 0 770.48219 0.48526619
18 515.70813 -2.1516075 0 770.63702 0.48530395
19 515.74908 -2.0581483 0 770.79185 0.48530979
20 515.70881 -1.892235 0 770.89742 0.48527104
Loop time of 1.06008 on 1 procs for 20 steps with 1000 atoms
Performance: 8150.306 tau/day, 18.866 timesteps/s
100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.00022078 | 0.00022078 | 0.00022078 | 0.0 | 0.02
Kspace | 0.91611 | 0.91611 | 0.91611 | 0.0 | 86.42
Neigh | 0.14232 | 0.14232 | 0.14232 | 0.0 | 13.43
Comm | 0.00015092 | 0.00015092 | 0.00015092 | 0.0 | 0.01
Output | 0.00033736 | 0.00033736 | 0.00033736 | 0.0 | 0.03
Modify | 0.00056243 | 0.00056243 | 0.00056243 | 0.0 | 0.05
Other | | 0.0003803 | | | 0.04
Nlocal: 1000 ave 1000 max 1000 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: 247817 ave 247817 max 247817 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 247817
Ave neighs/atom = 247.817
Neighbor list builds = 19
Dangerous builds = 18
Total wall time: 0:00:01

107
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LAMMPS (2 Aug 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
# Point dipoles in a 2d box
units lj
atom_style charge
read_data data.hammersley_shphere
orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5)
1 by 1 by 2 MPI processor grid
reading atoms ...
1000 atoms
change_box all boundary f f f
velocity all create 1.5 49893
neighbor 1.0 bin
neigh_modify delay 0
fix 1 all nve
# LAMMPS computes pairwise and long-range Coulombics
#pair_style coul/long 3.0
#pair_coeff * *
#kspace_style pppm 1.0e-3
# Scafacos computes entire long-range Coulombics
# use dummy pair style to perform atom sorting
pair_style zero 1.0
pair_coeff * *
#fix 2 all scafacos p3m tolerance field 0.001
kspace_style scafacos p2nfft 0.001
kspace_modify scafacos tolerance potential
timestep 0.005
thermo 1
run 20
Setting up ScaFaCoS with solver p2nfft ...
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 = 102 102 102
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 6.48 | 6.861 | 7.243 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.5 -0.62417787 0 1.6235721 0.0015678854
1 18.780041 -10.770002 0 17.371889 0.016718957
2 65.289192 -11.084705 0 86.751149 0.060353634
3 121.92987 -7.0625759 0 175.64933 0.11404974
4 185.78164 -5.8777511 0 272.51603 0.17462194
5 286.36221 -4.3820531 0 424.73172 0.26918925
6 481.42203 -4.3095567 0 717.10136 0.45274086
7 488.59165 -3.8685193 0 728.28607 0.45956865
8 497.85288 -3.0417938 0 742.99075 0.46838117
9 499.61619 -3.4190063 0 745.25585 0.46983349
10 502.63691 -2.8360951 0 750.36531 0.47280815
11 504.4847 -2.7628089 0 753.20751 0.47462802
12 506.54494 -2.8460319 0 756.21157 0.4765145
13 508.2722 -2.7309328 0 758.91497 0.47813761
14 510.57053 -2.6094792 0 762.48045 0.48031438
15 513.14804 -2.7150819 0 766.23726 0.48275234
16 515.78127 -2.3961749 0 770.50206 0.48526336
17 515.70267 -2.2982581 0 770.48219 0.48526619
18 515.70813 -2.1516075 0 770.63702 0.48530395
19 515.74908 -2.0581483 0 770.79185 0.48530979
20 515.70881 -1.892235 0 770.89742 0.48527104
Loop time of 0.701267 on 2 procs for 20 steps with 1000 atoms
Performance: 12320.557 tau/day, 28.520 timesteps/s
99.6% CPU use with 2 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0002265 | 0.00022769 | 0.00022888 | 0.0 | 0.03
Kspace | 0.60195 | 0.62374 | 0.64554 | 2.8 | 88.95
Neigh | 0.05268 | 0.074592 | 0.096504 | 8.0 | 10.64
Comm | 0.0015199 | 0.0016934 | 0.0018668 | 0.4 | 0.24
Output | 0.00031519 | 0.00041544 | 0.0005157 | 0.0 | 0.06
Modify | 0.00029492 | 0.00030565 | 0.00031638 | 0.0 | 0.04
Other | | 0.000288 | | | 0.04
Nlocal: 500 ave 516 max 484 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 456.5 ave 475 max 438 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 123908 ave 172139 max 75678 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 247817
Ave neighs/atom = 247.817
Neighbor list builds = 19
Dangerous builds = 18
Total wall time: 0:00:00

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LAMMPS (2 Aug 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
# Point dipoles in a 2d box
units lj
atom_style charge
read_data data.hammersley_shphere
orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5)
1 by 2 by 2 MPI processor grid
reading atoms ...
1000 atoms
change_box all boundary f f f
velocity all create 1.5 49893
neighbor 1.0 bin
neigh_modify delay 0
fix 1 all nve
# LAMMPS computes pairwise and long-range Coulombics
#pair_style coul/long 3.0
#pair_coeff * *
#kspace_style pppm 1.0e-3
# Scafacos computes entire long-range Coulombics
# use dummy pair style to perform atom sorting
pair_style zero 1.0
pair_coeff * *
#fix 2 all scafacos p3m tolerance field 0.001
kspace_style scafacos p2nfft 0.001
kspace_modify scafacos tolerance potential
timestep 0.005
thermo 1
run 20
Setting up ScaFaCoS with solver p2nfft ...
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 = 102 102 102
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.837 | 5.123 | 5.6 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.5 -0.62417787 0 1.6235721 0.0015678854
1 18.780041 -10.770002 0 17.371889 0.016718957
2 65.289192 -11.084705 0 86.751149 0.060353634
3 121.92987 -7.0625759 0 175.64933 0.11404974
4 185.78164 -5.8777511 0 272.51603 0.17462194
5 286.36221 -4.3820531 0 424.73172 0.26918925
6 481.42203 -4.3095567 0 717.10136 0.45274086
7 488.59165 -3.8685193 0 728.28607 0.45956865
8 497.85288 -3.0417938 0 742.99075 0.46838117
9 499.61619 -3.4190063 0 745.25585 0.46983349
10 502.63691 -2.8360951 0 750.36531 0.47280815
11 504.4847 -2.7628089 0 753.20751 0.47462802
12 506.54494 -2.8460319 0 756.21157 0.4765145
13 508.2722 -2.7309328 0 758.91497 0.47813761
14 510.57053 -2.6094792 0 762.48045 0.48031438
15 513.14804 -2.7150819 0 766.23726 0.48275234
16 515.78127 -2.3961749 0 770.50206 0.48526336
17 515.70267 -2.2982581 0 770.48219 0.48526619
18 515.70813 -2.1516075 0 770.63702 0.48530395
19 515.74908 -2.0581483 0 770.79185 0.48530979
20 515.70881 -1.892235 0 770.89742 0.48527104
Loop time of 0.427495 on 4 procs for 20 steps with 1000 atoms
Performance: 20210.785 tau/day, 46.784 timesteps/s
99.7% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0002327 | 0.00023341 | 0.00023437 | 0.0 | 0.05
Kspace | 0.36897 | 0.38411 | 0.39988 | 1.9 | 89.85
Neigh | 0.023831 | 0.039796 | 0.055124 | 6.1 | 9.31
Comm | 0.0022776 | 0.0025444 | 0.0028152 | 0.4 | 0.60
Output | 0.00033784 | 0.0004344 | 0.00057077 | 0.0 | 0.10
Modify | 0.00016117 | 0.00016713 | 0.00017095 | 0.0 | 0.04
Other | | 0.0002093 | | | 0.05
Nlocal: 250 ave 259 max 238 min
Histogram: 1 0 0 1 0 0 0 0 0 2
Nghost: 672.25 ave 683 max 663 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Neighs: 61954.2 ave 97157 max 25016 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Total # of neighbors = 247817
Ave neighs/atom = 247.817
Neighbor list builds = 19
Dangerous builds = 18
Total wall time: 0:00:00

107
examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.p2nfft.8 Normal file
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@ -0,0 +1,107 @@
LAMMPS (2 Aug 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
# Point dipoles in a 2d box
units lj
atom_style charge
read_data data.hammersley_shphere
orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5)
2 by 2 by 2 MPI processor grid
reading atoms ...
1000 atoms
change_box all boundary f f f
velocity all create 1.5 49893
neighbor 1.0 bin
neigh_modify delay 0
fix 1 all nve
# LAMMPS computes pairwise and long-range Coulombics
#pair_style coul/long 3.0
#pair_coeff * *
#kspace_style pppm 1.0e-3
# Scafacos computes entire long-range Coulombics
# use dummy pair style to perform atom sorting
pair_style zero 1.0
pair_coeff * *
#fix 2 all scafacos p3m tolerance field 0.001
kspace_style scafacos p2nfft 0.001
kspace_modify scafacos tolerance potential
timestep 0.005
thermo 1
run 20
Setting up ScaFaCoS with solver p2nfft ...
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 = 102 102 102
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.164 | 4.26 | 4.546 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.5 -0.62417787 0 1.6235721 0.0015678854
1 18.780041 -10.770002 0 17.371889 0.016718957
2 65.289192 -11.084705 0 86.751149 0.060353634
3 121.92987 -7.0625759 0 175.64933 0.11404974
4 185.78164 -5.8777511 0 272.51603 0.17462194
5 286.36221 -4.3820531 0 424.73172 0.26918925
6 481.42203 -4.3095567 0 717.10136 0.45274086
7 488.59165 -3.8685193 0 728.28607 0.45956865
8 497.85288 -3.0417938 0 742.99075 0.46838117
9 499.61619 -3.4190063 0 745.25585 0.46983349
10 502.63691 -2.8360951 0 750.36531 0.47280815
11 504.4847 -2.7628089 0 753.20751 0.47462802
12 506.54494 -2.8460319 0 756.21157 0.4765145
13 508.2722 -2.7309328 0 758.91497 0.47813761
14 510.57053 -2.6094792 0 762.48045 0.48031438
15 513.14804 -2.7150819 0 766.23726 0.48275234
16 515.78127 -2.3961749 0 770.50206 0.48526336
17 515.70267 -2.2982581 0 770.48219 0.48526619
18 515.70813 -2.1516075 0 770.63702 0.48530395
19 515.74908 -2.0581483 0 770.79185 0.48530979
20 515.70881 -1.892235 0 770.89742 0.48527104
Loop time of 0.242145 on 8 procs for 20 steps with 1000 atoms
Performance: 35681.038 tau/day, 82.595 timesteps/s
99.2% CPU use with 8 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0002315 | 0.00023672 | 0.00024652 | 0.0 | 0.10
Kspace | 0.20915 | 0.21666 | 0.22564 | 1.3 | 89.48
Neigh | 0.012218 | 0.021341 | 0.029026 | 4.3 | 8.81
Comm | 0.0028954 | 0.0031248 | 0.0033553 | 0.3 | 1.29
Output | 0.00039291 | 0.00049406 | 0.00066066 | 0.0 | 0.20
Modify | 8.7976e-05 | 9.2953e-05 | 9.7752e-05 | 0.0 | 0.04
Other | | 0.0001938 | | | 0.08
Nlocal: 125 ave 133 max 113 min
Histogram: 2 0 0 0 0 1 1 0 2 2
Nghost: 773.625 ave 788 max 764 min
Histogram: 1 1 2 1 1 0 0 0 1 1
Neighs: 30977.1 ave 50690 max 10447 min
Histogram: 1 1 1 0 1 1 0 0 2 1
Total # of neighbors = 247817
Ave neighs/atom = 247.817
Neighbor list builds = 19
Dangerous builds = 18
Total wall time: 0:00:00

2
examples/USER/smd/fluid_structure_interaction/fluid_structure_interaction.lmp
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@ -129,7 +129,7 @@ compute contact_radius all smd/contact/radius
compute S solids smd/tlsph/stress
compute nn water smd/ulsph/num/neighs
compute epl solids smd/plastic/strain
compute vol all smd/volume
compute vol all smd/vol
compute rho all smd/rho
dump dump_id all custom 100 dump.LAMMPS id type x y &

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