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Merge branch 'clean-master2' of github.com:julient31/lammps into pppm_spin

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Conflicts:
	src/SPIN/pair_spin_exchange.cpp
	src/atom.cpp
	src/pair.cpp
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julient31
2019-04-19 15:02:25 -06:00
parent 7a2d326103 898860328b
commit a696b26301
4475 changed files with 423708 additions and 327416 deletions
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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

36
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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examples/COUPLE/lammps_mc/log.28Aug18.file.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 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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3
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
@ -77,11 +78,13 @@ friction: frictional contact of spherical asperities between 2d surfaces
gcmc: Grand Canonical Monte Carlo (GCMC) via the fix gcmc command
granregion: use of fix wall/region/gran as boundary on granular particles
hugoniostat: Hugoniostat shock dynamics
hyper: global and local hyperdynamics of diffusion on Pt surface
indent: spherical indenter into a 2d solid
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

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

@ -36,7 +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

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

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

@ -42,7 +42,7 @@ 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

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

@ -39,7 +39,7 @@ 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

55
examples/SPIN/spinmin/in.spinmin.bfo Normal file
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@ -0,0 +1,55 @@
# bfo in a 3d periodic box
units metal
dimension 3
boundary p p f
atom_style spin
# necessary for the serial algorithm (sametag)
atom_modify map array
lattice sc 3.96
region box block 0.0 34.0 0.0 34.0 0.0 1.0
create_box 1 box
create_atoms 1 box
# setting mass, mag. moments, and interactions for bcc iron
mass 1 1.0
set group all spin/random 11 2.50
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/magelec magelec 4.5 0.00109 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
#fix 1 all precession/spin zeeman 0.001 0.0 0.0 1.0 anisotropy 0.01 1.0 0.0 0.0
fix 1 all precession/spin anisotropy 0.0000033 0.0 0.0 1.0
fix_modify 1 energy yes
timestep 0.0001
compute out_mag all spin
compute out_pe all pe
compute out_ke all ke
compute out_temp all temp
variable magz equal c_out_mag[3]
variable magnorm equal c_out_mag[4]
variable emag equal c_out_mag[5]
variable tmag equal c_out_mag[6]
thermo 50
thermo_style custom step time v_magnorm v_emag v_tmag temp etotal
thermo_modify format float %20.15g
compute outsp all property/atom spx spy spz sp fmx fmy fmz
dump 1 all custom 50 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
min_style spin
min_modify alpha_damp 1.0 discrete_factor 10.0
minimize 1.0e-10 0.0 1000 100

55
examples/SPIN/spinmin/in.spinmin.iron Normal file
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@ -0,0 +1,55 @@
# bcc iron in a 3d periodic box
units metal
dimension 3
boundary p p f
atom_style spin
# necessary for the serial algorithm (sametag)
atom_modify map array
lattice bcc 2.8665
region box block 0.0 4.0 0.0 4.0 0.0 4.0
create_box 1 box
create_atoms 1 box
# setting mass, mag. moments, and interactions for bcc iron
mass 1 55.845
set group all spin/random 31 2.2
#set group all spin 2.2 1.0 1.0 -1.0
pair_style spin/exchange 3.5
pair_coeff * * exchange 3.4 0.02726 0.2171 1.841
neighbor 0.1 bin
neigh_modify every 10 check yes delay 20
#fix 1 all precession/spin zeeman 0.001 0.0 0.0 1.0 anisotropy 0.01 1.0 0.0 0.0
fix 1 all precession/spin anisotropy 0.0001 0.0 0.0 1.0
fix_modify 1 energy yes
timestep 0.0001
compute out_mag all spin
compute out_pe all pe
compute out_ke all ke
compute out_temp all temp
variable magx equal c_out_mag[1]
variable magy equal c_out_mag[2]
variable magz equal c_out_mag[3]
variable magnorm equal c_out_mag[4]
variable emag equal c_out_mag[5]
variable tmag equal c_out_mag[6]
thermo 100
thermo_style custom step time v_magx v_magz v_magnorm v_tmag etotal
thermo_modify format float %20.15g
compute outsp all property/atom spx spy spz sp fmx fmy fmz
dump 1 all custom 100 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
min_style spin
min_modify alpha_damp 1.0 discrete_factor 10.0
minimize 1.0e-10 1.0e-10 100000 1000

41
examples/USER/adios/adios2_config.xml Normal file
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@ -0,0 +1,41 @@
<?xml version="1.0"?>
<adios-config>
<!-- example engines
<engine type="BPFile">
<parameter key="substreams" value="10"/>
</engine>
<engine type="HDF5">
The 'substreams' parameter in BPFile controls how many
files on disk are created. This number should be proportional
to the number of servers in the parallel file system,
NOT to the number of processes.
substreams=1 is generally a very inefficient setting for large parallel runs.
-->
<!--====================================================
Configuration for the dump atom/adios command
====================================================-->
<io name="atom">
<engine type="BPFile">
<parameter key="substreams" value="1"/>
</engine>
</io>
<!--====================================================
Configuration for the dump custom/adios command
====================================================-->
<io name="custom">
<engine type="BPFile">
<parameter key="substreams" value="1"/>
</engine>
</io>
</adios-config>

57
examples/USER/adios/in.adios_balance Normal file
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@ -0,0 +1,57 @@
# 2d circle of particles inside a box with LJ walls
variable b index 0
variable x index 50
variable y index 20
variable d index 20
variable v index 5
variable w index 2
units lj
dimension 2
atom_style atomic
boundary f f p
lattice hex 0.85
region box block 0 $x 0 $y -0.5 0.5
create_box 1 box
region circle sphere $(v_d/2+1) $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
create_atoms 1 region circle
mass 1 1.0
velocity all create 0.5 87287 loop geom
velocity all set $v $w 0 sum yes
pair_style lj/cut 2.5
pair_coeff 1 1 10.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi $x 1 1 2.5
fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi $y 1 1 2.5
comm_style tiled
fix 10 all balance 50 0.9 rcb
compute 1 all property/atom proc
variable p atom c_1%10
dump 2 all custom 50 balance.dump id v_p x y z
dump 3 all custom/adios 50 balance_custom.bp id v_p x y z
dump 4 all atom/adios 50 balance_atom.bp
#dump 3 all image 50 image.*.jpg v_p type &
# adiam 1.0 view 0 0 zoom 1.8 subbox yes 0.02
#variable colors string &
# "red green blue yellow white &
# purple pink orange lime gray"
#dump_modify 3 pad 5 amap 0 10 sa 1 10 ${colors}
thermo_style custom step temp epair press f_10[3] f_10
thermo 100
run 200
write_dump all atom/adios balance_atom_final.bp

114
examples/USER/adios/log.balance Normal file
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@ -0,0 +1,114 @@
LAMMPS (4 Jan 2019)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
# 2d circle of particles inside a box with LJ walls
variable b index 0
variable x index 50
variable y index 20
variable d index 20
variable v index 5
variable w index 2
units lj
dimension 2
atom_style atomic
boundary f f p
lattice hex 0.85
Lattice spacing in x,y,z = 1.16553 2.01877 1.16553
region box block 0 $x 0 $y -0.5 0.5
region box block 0 50 0 $y -0.5 0.5
region box block 0 50 0 20 -0.5 0.5
create_box 1 box
Created orthogonal box = (0 0 -0.582767) to (58.2767 40.3753 0.582767)
2 by 2 by 1 MPI processor grid
region circle sphere $(v_d/2+1) $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
region circle sphere 11 $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
region circle sphere 11 6.7735026918962581988 0.0 $(v_d/2)
region circle sphere 11 6.7735026918962581988 0.0 10
create_atoms 1 region circle
Created 361 atoms
Time spent = 0.00171804 secs
mass 1 1.0
velocity all create 0.5 87287 loop geom
velocity all set $v $w 0 sum yes
velocity all set 5 $w 0 sum yes
velocity all set 5 2 0 sum yes
pair_style lj/cut 2.5
pair_coeff 1 1 10.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi $x 1 1 2.5
fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi 50 1 1 2.5
fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi $y 1 1 2.5
fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi 20 1 1 2.5
comm_style tiled
fix 10 all balance 50 0.9 rcb
compute 1 all property/atom proc
variable p atom c_1%10
dump 2 all custom 50 balance.dump id v_p x y z
dump 3 all custom/adios 50 balance_custom.bp id v_p x y z
dump 4 all atom/adios 50 balance_atom.bp
#dump 3 all image 50 image.*.jpg v_p type # adiam 1.0 view 0 0 zoom 1.8 subbox yes 0.02
#variable colors string # "red green blue yellow white # purple pink orange lime gray"
#dump_modify 3 pad 5 amap 0 10 sa 1 10 ${colors}
thermo_style custom step temp epair press f_10[3] f_10
thermo 100
run 200
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 = 42 29 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) = 4.926 | 4.933 | 4.944 Mbytes
Step Temp E_pair Press f_10[3] f_10
0 25.701528 -29.143179 -1.2407285 3.2354571 1.0526316
100 26.269576 -29.713313 7.9052334 1.2742382 1.0304709
200 26.368336 -29.809962 1.6412462 1.2520776 1.0083102
Loop time of 0.0992351 on 4 procs for 200 steps with 361 atoms
Performance: 870660.046 tau/day, 2015.417 timesteps/s
32.2% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0078368 | 0.0081607 | 0.0085468 | 0.3 | 8.22
Neigh | 0.002804 | 0.0045915 | 0.0092173 | 3.9 | 4.63
Comm | 0.044407 | 0.05352 | 0.062051 | 3.0 | 53.93
Output | 0.011406 | 0.012025 | 0.01342 | 0.7 | 12.12
Modify | 0.006305 | 0.0064294 | 0.0066617 | 0.2 | 6.48
Other | | 0.01451 | | | 14.62
Nlocal: 90.25 ave 91 max 90 min
Histogram: 3 0 0 0 0 0 0 0 0 1
Nghost: 58.25 ave 64 max 51 min
Histogram: 1 0 0 0 0 0 2 0 0 1
Neighs: 730.75 ave 801 max 671 min
Histogram: 1 0 1 0 0 1 0 0 0 1
Total # of neighbors = 2923
Ave neighs/atom = 8.09695
Neighbor list builds = 60
Dangerous builds = 0
Total wall time: 0:00:00

1
examples/USER/atc/cauchy_born/Au_u3.eam Symbolic link
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@ -0,0 +1 @@
../../../../potentials/Au_u3.eam

1751
examples/USER/atc/cauchy_born/ftcb_constV_setup.init Normal file
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535
examples/USER/atc/cauchy_born/read_xref_0.data Normal file
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@ -0,0 +1,535 @@
LAMMPS data file from restart file: timestep = 0, procs = 1
256 atoms
1 atom types
0.0000000000000000e+00 2.1024909948000001e+01 xlo xhi
0.0000000000000000e+00 2.1024909948000001e+01 ylo yhi
0.0000000000000000e+00 2.1024909948000001e+01 zlo zhi
Masses
1 39.95
Pair Coeffs
1 0.238 3.405
Atoms
1 1 1.3140568717500001e+00 1.3140568717500001e+00 1.3140568717500001e+00 0 0 0
2 1 3.9421706152500002e+00 3.9421706152500002e+00 1.3140568717500001e+00 0 0 0
3 1 3.9421706152500002e+00 1.3140568717500001e+00 3.9421706152500002e+00 0 0 0
4 1 1.3140568717500001e+00 3.9421706152500002e+00 3.9421706152500002e+00 0 0 0
5 1 6.5702843587500004e+00 1.3140568717500001e+00 1.3140568717500001e+00 0 0 0
6 1 9.1983981022499997e+00 3.9421706152500002e+00 1.3140568717500001e+00 0 0 0
7 1 9.1983981022499997e+00 1.3140568717500001e+00 3.9421706152500002e+00 0 0 0
8 1 6.5702843587500004e+00 3.9421706152500002e+00 3.9421706152500002e+00 0 0 0
9 1 1.1826511845750002e+01 1.3140568717500001e+00 1.3140568717500001e+00 0 0 0
10 1 1.4454625589250000e+01 3.9421706152500002e+00 1.3140568717500001e+00 0 0 0
11 1 1.4454625589250000e+01 1.3140568717500001e+00 3.9421706152500002e+00 0 0 0
12 1 1.1826511845750002e+01 3.9421706152500002e+00 3.9421706152500002e+00 0 0 0
13 1 1.7082739332750002e+01 1.3140568717500001e+00 1.3140568717500001e+00 0 0 0
14 1 1.9710853076250000e+01 3.9421706152500002e+00 1.3140568717500001e+00 0 0 0
15 1 1.9710853076250000e+01 1.3140568717500001e+00 3.9421706152500002e+00 0 0 0
16 1 1.7082739332750002e+01 3.9421706152500002e+00 3.9421706152500002e+00 0 0 0
17 1 1.3140568717500001e+00 6.5702843587500004e+00 1.3140568717500001e+00 0 0 0
18 1 3.9421706152500002e+00 9.1983981022499997e+00 1.3140568717500001e+00 0 0 0
19 1 3.9421706152500002e+00 6.5702843587500004e+00 3.9421706152500002e+00 0 0 0
20 1 1.3140568717500001e+00 9.1983981022499997e+00 3.9421706152500002e+00 0 0 0
21 1 6.5702843587500004e+00 6.5702843587500004e+00 1.3140568717500001e+00 0 0 0
22 1 9.1983981022499997e+00 9.1983981022499997e+00 1.3140568717500001e+00 0 0 0
23 1 9.1983981022499997e+00 6.5702843587500004e+00 3.9421706152500002e+00 0 0 0
24 1 6.5702843587500004e+00 9.1983981022499997e+00 3.9421706152500002e+00 0 0 0
25 1 1.1826511845750002e+01 6.5702843587500004e+00 1.3140568717500001e+00 0 0 0
26 1 1.4454625589250000e+01 9.1983981022499997e+00 1.3140568717500001e+00 0 0 0
27 1 1.4454625589250000e+01 6.5702843587500004e+00 3.9421706152500002e+00 0 0 0
28 1 1.1826511845750002e+01 9.1983981022499997e+00 3.9421706152500002e+00 0 0 0
29 1 1.7082739332750002e+01 6.5702843587500004e+00 1.3140568717500001e+00 0 0 0
30 1 1.9710853076250000e+01 9.1983981022499997e+00 1.3140568717500001e+00 0 0 0
31 1 1.9710853076250000e+01 6.5702843587500004e+00 3.9421706152500002e+00 0 0 0
32 1 1.7082739332750002e+01 9.1983981022499997e+00 3.9421706152500002e+00 0 0 0
33 1 1.3140568717500001e+00 1.1826511845750002e+01 1.3140568717500001e+00 0 0 0
34 1 3.9421706152500002e+00 1.4454625589250000e+01 1.3140568717500001e+00 0 0 0
35 1 3.9421706152500002e+00 1.1826511845750002e+01 3.9421706152500002e+00 0 0 0
36 1 1.3140568717500001e+00 1.4454625589250000e+01 3.9421706152500002e+00 0 0 0
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531
examples/USER/atc/cauchy_born/read_xref_1.init Normal file
View File

@ -0,0 +1,531 @@
LAMMPS data file from restart file: timestep = 1, procs = 1
256 atoms
1 atom types
-1.0512454974000009e+00 2.2076155445400001e+01 xlo xhi
-1.0512454974000009e+00 2.2076155445400001e+01 ylo yhi
-1.0512454974000009e+00 2.2076155445400001e+01 zlo zhi
Masses
1 39.95
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@ -0,0 +1,407 @@
LAMMPS data file from restart file: timestep = 0, procs = 1
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@ -1,5 +1,4 @@
variable sname index h_atom
log ${sname}.spe.log
units real
newton on
@ -37,4 +36,4 @@ variable press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol)
thermo 1
thermo_style custom step etotal pe ke v_eke v_epauli v_estatics v_errestrain temp press v_press
run 0
run 10

3
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@ -1,5 +1,4 @@
variable sname index h_molecule
log ${sname}.spe.log
units real
newton on
@ -37,4 +36,4 @@ variable press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol)
thermo 1
thermo_style custom step etotal pe ke v_eke v_epauli v_estatics v_errestrain temp press v_press
run 0
run 10

100
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LAMMPS (27 Nov 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 sname index h_atom
units real
newton on
boundary p p p
processors 1 * *
atom_style wavepacket
read_data data.${sname}
read_data data.h_atom
orthogonal box = (-0.529177 -0.529177 -0.529177) to (0.529177 0.529177 0.529177)
1 by 1 by 1 MPI processor grid
reading atoms ...
2 atoms
#neighbor 2.0 nsq
pair_style awpmd/cut -1. hartree ermscale 0.99 free flex_press
pair_coeff * *
timestep 0.001
fix 1 all nve/awpmd
comm_modify vel yes
compute energies all pair awpmd/cut
variable eke equal c_energies[1]
variable epauli equal c_energies[2]
variable estatics equal c_energies[3]
variable errestrain equal c_energies[4]
compute peratom all stress/atom NULL
compute p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3]
variable press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol)
thermo 1
thermo_style custom step etotal pe ke v_eke v_epauli v_estatics v_errestrain temp press v_press
run 10
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.52918
ghost atom cutoff = 2.52918
binsize = 1.26459, bins = 1 1 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair awpmd/cut, perpetual
attributes: half, newton off
pair build: half/bin/newtoff
stencil: half/bin/3d/newtoff
bin: standard
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (src/domain.cpp:933)
Per MPI rank memory allocation (min/avg/max) = 5.111 | 5.111 | 5.111 Mbytes
Step TotEng PotEng KinEng v_eke v_epauli v_estatics v_errestrain Temp Press v_press
0 -266.3192 -266.3192 0 266.32732 0 -532.64652 0 0 156.59865 -0
1 -266.3192 -266.3192 0 266.32746 0 -532.64666 0 0 159.30733 -0
2 -266.3192 -266.3192 1.7273458e-17 266.32797 0 -532.64718 0 5.7948873e-15 169.14686 6.6606909e-13
3 -266.3192 -266.3192 4.6899813e-15 266.32927 0 -532.64847 0 1.5733915e-12 194.06892 1.8084691e-10
4 -266.3192 -266.3192 1.4824973e-13 266.33199 0 -532.6512 0 4.9734712e-11 246.65762 5.7165485e-09
5 -266.3192 -266.3192 1.9298888e-12 266.33712 0 -532.65632 0 6.4743771e-10 345.53056 7.441702e-08
6 -266.3192 -266.3192 1.5343223e-11 266.34601 0 -532.66521 0 5.1473332e-09 516.91949 5.9163869e-07
7 -266.3192 -266.3192 8.8661674e-11 266.36051 0 -532.6797 0 2.9744154e-08 796.4357 3.4188175e-06
8 -266.31919 -266.31919 4.0865149e-10 266.38304 0 -532.70223 0 1.3709411e-07 1231.0302 1.5757709e-05
9 -266.31918 -266.31918 1.5889509e-09 266.41674 0 -532.73592 0 5.3306012e-07 1881.1652 6.1270366e-05
10 -266.31916 -266.31916 5.4070747e-09 266.46554 0 -532.7847 0 1.8139615e-06 2823.2238 0.00020849822
Loop time of 0.000725031 on 1 procs for 10 steps with 2 atoms
Performance: 1.192 ns/day, 20.140 hours/ns, 13792.516 timesteps/s
99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.00030851 | 0.00030851 | 0.00030851 | 0.0 | 42.55
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0001204 | 0.0001204 | 0.0001204 | 0.0 | 16.61
Output | 0.00028038 | 0.00028038 | 0.00028038 | 0.0 | 38.67
Modify | 6.1989e-06 | 6.1989e-06 | 6.1989e-06 | 0.0 | 0.85
Other | | 9.537e-06 | | | 1.32
Nlocal: 2 ave 2 max 2 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 248 ave 248 max 248 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 225 ave 225 max 225 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 225
Ave neighs/atom = 112.5
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00

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LAMMPS (27 Nov 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 sname index h_atom
units real
newton on
boundary p p p
processors 1 * *
atom_style wavepacket
read_data data.${sname}
read_data data.h_atom
orthogonal box = (-0.529177 -0.529177 -0.529177) to (0.529177 0.529177 0.529177)
1 by 2 by 2 MPI processor grid
reading atoms ...
2 atoms
#neighbor 2.0 nsq
pair_style awpmd/cut -1. hartree ermscale 0.99 free flex_press
pair_coeff * *
timestep 0.001
fix 1 all nve/awpmd
comm_modify vel yes
compute energies all pair awpmd/cut
variable eke equal c_energies[1]
variable epauli equal c_energies[2]
variable estatics equal c_energies[3]
variable errestrain equal c_energies[4]
compute peratom all stress/atom NULL
compute p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3]
variable press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol)
thermo 1
thermo_style custom step etotal pe ke v_eke v_epauli v_estatics v_errestrain temp press v_press
run 10
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.52918
ghost atom cutoff = 2.52918
binsize = 1.26459, bins = 1 1 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair awpmd/cut, perpetual
attributes: half, newton off
pair build: half/bin/newtoff
stencil: half/bin/3d/newtoff
bin: standard
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (src/domain.cpp:933)
Per MPI rank memory allocation (min/avg/max) = 5.391 | 5.391 | 5.391 Mbytes
Step TotEng PotEng KinEng v_eke v_epauli v_estatics v_errestrain Temp Press v_press
0 -266.3192 -266.3192 0 266.32732 0 -532.64652 0 0 156.59865 -0
1 -266.3192 -266.3192 0 266.32789 0 -532.64709 0 0 167.49891 -0
2 -266.3192 -266.3192 1.219316e-15 266.3314 0 -532.6506 0 4.0905525e-13 235.2267 4.7017146e-11
3 -266.3192 -266.3192 8.3179871e-14 266.34548 0 -532.66468 0 2.7905123e-11 506.68594 3.2074377e-09
4 -266.3192 -266.3192 4.4091748e-12 266.39036 0 -532.70955 0 1.4791868e-09 1372.0565 1.7001894e-07
5 -266.31916 -266.31916 9.8904198e-11 266.51357 0 -532.83273 0 3.3180309e-08 3748.6725 3.8137718e-06
6 -266.31893 -266.31893 1.3132578e-09 266.81733 0 -533.13626 0 4.4057077e-07 9611.8807 5.0639565e-05
7 -266.31762 -266.31762 1.2317167e-08 267.50719 0 -533.82481 0 4.1321544e-06 22950.26 0.00047495321
8 -266.31123 -266.31123 9.0048883e-08 268.97689 0 -535.28812 0 3.0209534e-05 51470.197 0.0034723086
9 -266.28324 -266.28324 5.4612621e-07 271.95757 0 -538.24082 0 0.00018321403 109735.25 0.02105877
10 -266.17113 -266.17114 2.8729529e-06 277.79384 0 -543.96498 0 0.00096381615 225424.02 0.11078182
Loop time of 0.00176561 on 4 procs for 10 steps with 2 atoms
Performance: 0.489 ns/day, 49.045 hours/ns, 5663.769 timesteps/s
87.0% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 6.3419e-05 | 0.00012642 | 0.00030923 | 0.0 | 7.16
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00073171 | 0.00086534 | 0.001025 | 0.0 | 49.01
Output | 0.00063562 | 0.00075388 | 0.00094962 | 0.0 | 42.70
Modify | 3.8147e-06 | 4.4703e-06 | 6.1989e-06 | 0.0 | 0.25
Other | | 1.55e-05 | | | 0.88
Nlocal: 0.5 ave 2 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 1
Nghost: 249.5 ave 250 max 248 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Neighs: 56.25 ave 225 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 1
Total # of neighbors = 225
Ave neighs/atom = 112.5
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00

100
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LAMMPS (27 Nov 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 sname index h_molecule
units real
newton on
boundary p p p
processors 1 * *
atom_style wavepacket
read_data data.${sname}
read_data data.h_molecule
orthogonal box = (-0.529177 -0.529177 -0.529177) to (0.529177 0.529177 0.529177)
1 by 1 by 1 MPI processor grid
reading atoms ...
4 atoms
#neighbor 2.0 nsq
pair_style awpmd/cut -1. hartree ermscale 0.99 free flex_press
pair_coeff * *
timestep 0.001
fix 1 all nve/awpmd
comm_modify vel yes
compute energies all pair awpmd/cut
variable eke equal c_energies[1]
variable epauli equal c_energies[2]
variable estatics equal c_energies[3]
variable errestrain equal c_energies[4]
compute peratom all stress/atom NULL
compute p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3]
variable press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol)
thermo 1
thermo_style custom step etotal pe ke v_eke v_epauli v_estatics v_errestrain temp press v_press
run 10
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.52918
ghost atom cutoff = 2.52918
binsize = 1.26459, bins = 1 1 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair awpmd/cut, perpetual
attributes: half, newton off
pair build: half/bin/newtoff
stencil: half/bin/3d/newtoff
bin: standard
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (src/domain.cpp:933)
Per MPI rank memory allocation (min/avg/max) = 5.142 | 5.142 | 5.142 Mbytes
Step TotEng PotEng KinEng v_eke v_epauli v_estatics v_errestrain Temp Press v_press
0 30358.159 30358.159 0 39537.73 -1.5916157e-12 -9179.5713 0 0 1.3475994e+09 -0
1 30360.49 30360.489 0.0009272222 39540.081 2.0463631e-12 -9179.5926 0 0.10368794 1.3476061e+09 35.753932
2 67447.779 67447.776 0.00370884 80547.07 -1.1368684e-12 -13099.294 0 0.41474633 2.8529839e+09 143.01385
3 3713046.5 3713046.5 0.0041850026 3803060.3 -1.29603e-10 -90013.788 0 0.46799388 1.4486958e+11 161.3748
4 2445632.1 2445620 12.171486 2452194.4 -9.777068e-11 -6574.4062 0 1361.0937 -6.5572589e+08 469335.68
5 2434860.1 2434845.9 14.215419 2433638.8 -1.0663825e-10 1207.1541 0 1589.6595 -359380.29 548150.31
6 2444984.1 2444969.8 14.215428 2451100 5.1841198e-11 -6130.1373 0 1589.6605 -5.6327282e+08 548150.63
7 2436128.7 2436110.9 17.793789 2434903.7 2.0190782e-10 1207.154 0 1989.8158 -221406.77 686133.18
8 2444786.5 2444768.7 17.793798 2450583.8 -1.1027623e-10 -5815.0651 0 1989.8169 -5.0227031e+08 686133.54
9 2437198.9 2437175.9 22.942086 2435968.8 2.2600943e-10 1207.1538 0 2565.5315 -22903.736 884652.88
10 2444787.1 2444764.2 22.942097 2450333.1 -3.1832315e-11 -5568.9214 0 2565.5327 -4.5741803e+08 884653.3
Loop time of 0.00158453 on 1 procs for 10 steps with 4 atoms
Performance: 0.545 ns/day, 44.015 hours/ns, 6311.020 timesteps/s
85.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.00088882 | 0.00088882 | 0.00088882 | 0.0 | 56.09
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00031352 | 0.00031352 | 0.00031352 | 0.0 | 19.79
Output | 0.00036216 | 0.00036216 | 0.00036216 | 0.0 | 22.86
Modify | 5.9605e-06 | 5.9605e-06 | 5.9605e-06 | 0.0 | 0.38
Other | | 1.407e-05 | | | 0.89
Nlocal: 4 ave 4 max 4 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 596 ave 596 max 596 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 966 ave 966 max 966 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 966
Ave neighs/atom = 241.5
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00

100
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LAMMPS (27 Nov 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 sname index h_molecule
units real
newton on
boundary p p p
processors 1 * *
atom_style wavepacket
read_data data.${sname}
read_data data.h_molecule
orthogonal box = (-0.529177 -0.529177 -0.529177) to (0.529177 0.529177 0.529177)
1 by 2 by 2 MPI processor grid
reading atoms ...
4 atoms
#neighbor 2.0 nsq
pair_style awpmd/cut -1. hartree ermscale 0.99 free flex_press
pair_coeff * *
timestep 0.001
fix 1 all nve/awpmd
comm_modify vel yes
compute energies all pair awpmd/cut
variable eke equal c_energies[1]
variable epauli equal c_energies[2]
variable estatics equal c_energies[3]
variable errestrain equal c_energies[4]
compute peratom all stress/atom NULL
compute p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3]
variable press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol)
thermo 1
thermo_style custom step etotal pe ke v_eke v_epauli v_estatics v_errestrain temp press v_press
run 10
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.52918
ghost atom cutoff = 2.52918
binsize = 1.26459, bins = 1 1 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair awpmd/cut, perpetual
attributes: half, newton off
pair build: half/bin/newtoff
stencil: half/bin/3d/newtoff
bin: standard
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (src/domain.cpp:933)
Per MPI rank memory allocation (min/avg/max) = 5.172 | 5.234 | 5.422 Mbytes
Step TotEng PotEng KinEng v_eke v_epauli v_estatics v_errestrain Temp Press v_press
0 30358.159 30358.159 0 39537.73 -1.5916157e-12 -9179.5713 0 0 1.3475994e+09 -0
1 30360.982 30360.981 0.0009272222 39540.638 -1.1368684e-12 -9179.6571 0 0.10368794 1.3476263e+09 35.753932
2 67459.392 67459.388 0.0037086548 80559.71 6.5938366e-12 -13100.322 0 0.41472561 2.8534514e+09 143.0067
3 3732209.2 3732209.2 0.0041861902 3822452.2 -3.1604941e-11 -90242.984 0 0.46812669 1.4561246e+11 161.42059
4 2482974.7 2482961.9 12.860712 2489531.2 -2.2896529e-10 -6569.2968 0 1438.1675 -6.5458119e+08 495912.44
5 2472238.2 2472223.2 14.933049 2471015.7 -1.6120794e-10 1207.5188 0 1669.9095 -324992.65 575822.3
6 2482233.1 2482218.1 14.933057 2488321.7 -2.0691004e-11 -6103.5677 0 1669.9104 -5.5786438e+08 575822.62
7 2473498.5 2473479.8 18.61401 2472272.3 1.459739e-10 1207.5167 0 2081.5382 -183348.11 717761.12
8 2481621.3 2481602.6 18.614019 2487299.1 7.0258466e-11 -5696.4589 0 2081.5393 -4.7962801e+08 717761.48
9 2474506.2 2474482.2 24.021181 2473274.7 2.1395863e-10 1207.508 0 2686.2029 24318.554 926263.07
10 2480376.3 2480352.2 24.021192 2485505 -8.5719876e-11 -5152.7478 0 2686.2041 -3.8355089e+08 926263.48
Loop time of 0.00267726 on 4 procs for 10 steps with 4 atoms
Performance: 0.323 ns/day, 74.368 hours/ns, 3735.160 timesteps/s
91.1% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.00011826 | 0.00027376 | 0.00073862 | 0.0 | 10.23
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00080514 | 0.0011864 | 0.001574 | 0.9 | 44.31
Output | 0.00094914 | 0.0011944 | 0.0017326 | 0.9 | 44.61
Modify | 3.3379e-06 | 4.4703e-06 | 6.1989e-06 | 0.0 | 0.17
Other | | 1.824e-05 | | | 0.68
Nlocal: 1 ave 4 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 1
Nghost: 599 ave 600 max 596 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Neighs: 241.5 ave 966 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 1
Total # of neighbors = 966
Ave neighs/atom = 241.5
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00

71
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@ -1,5 +1,4 @@
LAMMPS (20 Apr 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
units real
dimension 3
@ -21,7 +20,7 @@ pair_style table spline 15000
pair_coeff 1 1 lammps_nb_MET-MET.table nb_METMET 12.0
WARNING: 78 of 2500 force values in table are inconsistent with -dE/dr.
Should only be flagged at inflection points (../pair_table.cpp:481)
Should only be flagged at inflection points (src/pair_table.cpp:481)
neigh_modify delay 0 every 1 check yes one 10000
neighbor 12.0 bin
@ -90,54 +89,54 @@ Neighbor list info ...
Per MPI rank memory allocation (min/avg/max) = 4.691 | 4.691 | 4.691 Mbytes
Step Temp PotEng TotEng Press Volume
0 300 1061.5961 1926.3291 107.006 66250.679
500 314.54728 1034.1091 1940.7738 194.42689 65660.282
1000 301.41603 1030.7027 1899.5173 -91.966709 66262.543
1500 298.8308 1014.8276 1876.1905 -80.178606 67053.605
2000 294.78476 1046.8207 1896.521 50.592942 66316.735
2500 301.18564 1033.9214 1902.0719 40.48255 66607.667
3000 301.06632 1022.0381 1889.8447 47.582344 66341.947
3500 297.98361 989.80983 1848.7307 -204.69879 67462.078
4000 299.03493 1034.6571 1896.6083 89.188888 66457.385
4500 306.03351 985.4121 1867.5363 -51.102407 67519.446
5000 305.6903 1013.8613 1894.9963 -141.13704 67240.467
5500 292.23444 1029.5558 1871.905 20.764579 66683.876
6000 287.87735 1017.7325 1847.5226 -35.288049 66630.031
6500 305.26461 960.08118 1839.9891 -352.42596 67612.317
7000 300.34449 1055.0664 1920.7923 22.04027 66187.27
7500 305.48612 1038.6651 1919.2115 17.807254 66324.168
8000 316.03232 1034.6809 1945.6262 27.482857 66502.198
8500 294.28636 1038.8213 1887.085 -72.840559 66851.661
9000 316.69029 1065.7481 1978.5899 245.61677 65678.385
9500 297.46127 1034.5547 1891.97 54.23428 66892.627
10000 301.24799 1036.5432 1904.8735 7.7134029 66150.506
Loop time of 34.426 on 1 procs for 10000 steps with 968 atoms
500 314.70267 1036.3305 1943.4431 205.83301 65603.85
1000 304.99804 1034.15 1913.2896 -79.521176 66268.87
1500 305.2621 996.9303 1876.831 -97.93992 67090.442
2000 311.29317 1083.9171 1981.2021 119.28085 65589.674
2500 305.51905 1051.59 1932.2314 -34.076658 66487.327
3000 291.76224 1053.524 1894.5121 45.522865 65879.535
3500 297.65795 1017.1028 1875.085 -79.41965 67185.19
4000 285.98779 1042.3622 1866.7058 88.549172 66357.051
4500 295.35 1071.4505 1922.7801 -16.75965 65378.949
5000 293.20958 1009.9943 1855.1543 -270.58058 67555.38
5500 292.40422 1085.3901 1928.2287 161.88502 65677.644
6000 318.79663 1012.4832 1931.3964 -65.692451 67458.05
6500 308.03807 1046.1413 1934.0436 249.70237 66052.045
7000 289.33716 1037.9657 1871.9636 47.662734 66782.578
7500 297.3092 1032.356 1889.3329 -24.049617 66129.95
8000 298.27827 1044.118 1903.8882 -26.61809 66720.381
8500 299.52706 1026.7068 1890.0766 -128.14995 67695.559
9000 304.67694 1018.2095 1896.4236 -61.360724 65942.4
9500 293.81117 1019.2221 1866.1162 -47.726496 66843.848
10000 309.9256 1043.5321 1936.875 -103.81403 66222.21
Loop time of 42.5056 on 1 procs for 10000 steps with 968 atoms
Performance: 25.097 ns/day, 0.956 hours/ns, 290.478 timesteps/s
Performance: 20.327 ns/day, 1.181 hours/ns, 235.263 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 33.324 | 33.324 | 33.324 | 0.0 | 96.80
Neigh | 0.12198 | 0.12198 | 0.12198 | 0.0 | 0.35
Comm | 0.42865 | 0.42865 | 0.42865 | 0.0 | 1.25
Output | 0.00059938 | 0.00059938 | 0.00059938 | 0.0 | 0.00
Modify | 0.42553 | 0.42553 | 0.42553 | 0.0 | 1.24
Other | | 0.1252 | | | 0.36
Pair | 40.972 | 40.972 | 40.972 | 0.0 | 96.39
Neigh | 0.18576 | 0.18576 | 0.18576 | 0.0 | 0.44
Comm | 0.71338 | 0.71338 | 0.71338 | 0.0 | 1.68
Output | 0.00050306 | 0.00050306 | 0.00050306 | 0.0 | 0.00
Modify | 0.52926 | 0.52926 | 0.52926 | 0.0 | 1.25
Other | | 0.1042 | | | 0.25
Nlocal: 968 ave 968 max 968 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 9112 ave 9112 max 9112 min
Nghost: 9215 ave 9215 max 9215 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 404392 ave 404392 max 404392 min
Neighs: 411837 ave 411837 max 411837 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 404392
Ave neighs/atom = 417.76
Total # of neighbors = 411837
Ave neighs/atom = 425.451
Neighbor list builds = 13
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:34
Total wall time: 0:00:42

81
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@ -1,5 +1,4 @@
LAMMPS (20 Apr 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
units real
dimension 3
@ -21,7 +20,7 @@ pair_style table spline 15000
pair_coeff 1 1 lammps_nb_MET-MET.table nb_METMET 12.0
WARNING: 78 of 2500 force values in table are inconsistent with -dE/dr.
Should only be flagged at inflection points (../pair_table.cpp:481)
Should only be flagged at inflection points (src/pair_table.cpp:481)
neigh_modify delay 0 every 1 check yes one 10000
neighbor 12.0 bin
@ -90,54 +89,54 @@ Neighbor list info ...
Per MPI rank memory allocation (min/avg/max) = 3.37 | 3.37 | 3.371 Mbytes
Step Temp PotEng TotEng Press Volume
0 300 1061.5961 1926.3291 107.006 66250.679
500 314.54728 1034.1091 1940.7738 194.42689 65660.282
1000 301.41603 1030.7027 1899.5173 -91.966709 66262.543
1500 298.8308 1014.8276 1876.1905 -80.178606 67053.605
2000 294.78476 1046.8207 1896.521 50.592942 66316.735
2500 301.18564 1033.9214 1902.0719 40.482557 66607.667
3000 301.06631 1022.0381 1889.8447 47.582403 66341.947
3500 297.98353 989.81011 1848.7308 -204.69823 67462.076
4000 299.03465 1034.6603 1896.6108 89.196235 66457.338
4500 306.04532 985.37017 1867.5285 -51.094929 67519.735
5000 304.72903 1014.9543 1893.3184 -127.04402 67238.517
5500 292.52622 1025.6599 1868.8502 -19.753932 66716.551
6000 296.82719 1031.5184 1887.1059 -1.2609328 66368.611
6500 298.63312 1018.4299 1879.2229 -24.75835 66524.898
7000 303.25389 1005.9283 1880.0404 -96.273504 67349.674
7500 292.45089 1068.2863 1911.2595 103.23295 65778.08
8000 301.22765 1040.6294 1908.9011 -0.83635353 66831.038
8500 300.19765 1047.5856 1912.8883 -31.582343 66316.305
9000 295.1108 1023.8234 1874.4635 -88.165532 67192.344
9500 302.1087 1003.6348 1874.4459 -18.707065 66369.361
10000 296.3083 1004.126 1858.2178 -28.293045 66862.576
Loop time of 28.8053 on 4 procs for 10000 steps with 968 atoms
500 314.70267 1036.3305 1943.4431 205.83301 65603.85
1000 304.99804 1034.15 1913.2896 -79.521176 66268.87
1500 305.2621 996.9303 1876.831 -97.93992 67090.442
2000 311.29317 1083.9171 1981.2021 119.28085 65589.674
2500 305.51905 1051.59 1932.2314 -34.076657 66487.327
3000 291.76224 1053.524 1894.5121 45.522919 65879.535
3500 297.65792 1017.1041 1875.0862 -79.411904 67185.183
4000 285.99141 1042.379 1866.733 88.735986 66356.756
4500 295.34218 1071.2977 1922.6048 -17.479073 65381.597
5000 292.47 1012.3769 1855.405 -255.07433 67527.215
5500 294.04431 1080.4547 1928.0208 192.6588 65811.742
6000 300.45893 986.16669 1852.2225 -167.3405 67858.175
6500 305.59738 1022.5276 1903.3947 -116.41298 66612.704
7000 312.11968 1032.7392 1932.4065 152.17956 66016.299
7500 306.80585 1032.1157 1916.4662 51.07705 66875.727
8000 292.30957 1048.9003 1891.4661 61.280503 65894.103
8500 297.79592 1013.4061 1871.786 -133.01136 66842.574
9000 290.36753 1043.7732 1880.7412 65.208248 66010.86
9500 288.92211 1077.8835 1910.6851 46.291982 65674.639
10000 311.51608 1015.3567 1913.2842 -146.49492 66882.692
Loop time of 13.9823 on 4 procs for 10000 steps with 968 atoms
Performance: 29.994 ns/day, 0.800 hours/ns, 347.159 timesteps/s
95.2% CPU use with 4 MPI tasks x 1 OpenMP threads
Performance: 61.792 ns/day, 0.388 hours/ns, 715.190 timesteps/s
98.2% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 19.929 | 21.765 | 23.391 | 27.8 | 75.56
Neigh | 0.067397 | 0.071231 | 0.077313 | 1.5 | 0.25
Comm | 3.9226 | 5.5183 | 7.3214 | 53.7 | 19.16
Output | 0.00069928 | 0.0016099 | 0.0043275 | 3.9 | 0.01
Modify | 1.0874 | 1.1376 | 1.1888 | 4.2 | 3.95
Other | | 0.3112 | | | 1.08
Pair | 10.131 | 11.235 | 12.333 | 23.2 | 80.35
Neigh | 0.044854 | 0.046303 | 0.047541 | 0.5 | 0.33
Comm | 1.1939 | 2.2964 | 3.4087 | 51.7 | 16.42
Output | 0.0004735 | 0.0032033 | 0.01137 | 8.3 | 0.02
Modify | 0.30542 | 0.31846 | 0.32508 | 1.4 | 2.28
Other | | 0.08323 | | | 0.60
Nlocal: 242 ave 244 max 239 min
Nlocal: 242 ave 248 max 232 min
Histogram: 1 0 0 0 0 0 1 0 1 1
Nghost: 5718.5 ave 5736 max 5702 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Neighs: 100703 ave 108064 max 93454 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Nghost: 5845.75 ave 5877 max 5808 min
Histogram: 1 0 0 0 1 0 0 1 0 1
Neighs: 104313 ave 113860 max 95507 min
Histogram: 1 1 0 0 0 0 0 1 0 1
Total # of neighbors = 402813
Ave neighs/atom = 416.129
Neighbor list builds = 14
Total # of neighbors = 417252
Ave neighs/atom = 431.045
Neighbor list builds = 13
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:28
Total wall time: 0:00:14

2
examples/USER/cgdna/examples/oxDNA/duplex1/input.duplex1 → examples/USER/cgdna/examples/oxDNA/duplex1/in.duplex1
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@ -72,6 +72,6 @@ fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${e
#dump_modify out sort id
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
run 1000000
run 10000
#write_restart config.${number}.*

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@ -0,0 +1,172 @@
LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
variable number equal 1
variable ofreq equal 1000
variable efreq equal 1000
units lj
dimension 3
newton off
boundary p p p
atom_style hybrid bond ellipsoid
atom_modify sort 0 1.0
# Pair interactions require lists of neighbours to be calculated
neighbor 1.0 bin
neigh_modify every 1 delay 0 check yes
read_data data.duplex1
orthogonal box = (-20 -20 -20) to (20 20 20)
1 by 1 by 1 MPI processor grid
reading atoms ...
10 atoms
reading velocities ...
10 velocities
10 ellipsoids
scanning bonds ...
2 = max bonds/atom
reading bonds ...
8 bonds
2 = max # of 1-2 neighbors
2 = max # of 1-3 neighbors
2 = max # of 1-4 neighbors
4 = max # of special neighbors
set atom * mass 3.1575
10 settings made for mass
group all type 1 4
10 atoms in group all
# oxDNA bond interactions - FENE backbone
bond_style oxdna/fene
bond_coeff * 2.0 0.25 0.7525
# oxDNA pair interactions
pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
pair_coeff * * oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
pair_coeff * * oxdna/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
pair_coeff * * oxdna/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff 1 4 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff 2 3 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff * * oxdna/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65
# NVE ensemble
fix 1 all nve/dot
#fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
#fix 1 all nve/asphere
#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10
timestep 1e-5
#comm_style tiled
#fix 3 all balance 10000 1.1 rcb
#compute mol all chunk/atom molecule
#compute mychunk all vcm/chunk mol
#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
#dump pos all xyz ${ofreq} traj.${number}.xyz
#compute quat all property/atom quatw quati quatj quatk
#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
#dump_modify quat sort id
#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le"
compute erot all erotate/asphere
compute ekin all ke
compute epot all pe
variable erot equal c_erot
variable ekin equal c_ekin
variable epot equal c_epot
variable etot equal c_erot+c_ekin+c_epot
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
#dump_modify out sort id
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
run 10000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.92828
ghost atom cutoff = 1.92828
binsize = 0.964142, bins = 42 42 42
5 neighbor lists, perpetual/occasional/extra = 5 0 0
(1) pair oxdna/excv, perpetual
attributes: half, newton off
pair build: half/bin/newtoff
stencil: half/bin/3d/newtoff
bin: standard
(2) pair oxdna/stk, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
(3) pair oxdna/hbond, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
(4) pair oxdna/xstk, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
(5) pair oxdna/coaxstk, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 2.859 | 2.859 | 2.859 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -1.4711818 0.0069384985 -1.4642433 -6.2745089e-05
1000 ekin = 0.00113448721737003 | erot = 0.00413455947734281 | epot = -14.6477022915193 | etot = -14.6424332448246
2000 ekin = 0.00449927223902336 | erot = 0.0164446434455805 | epot = -14.6633771605337 | etot = -14.6424332448491
3000 ekin = 0.00997964450841065 | erot = 0.0366523356056461 | epot = -14.6890652250033 | etot = -14.6424332448892
4000 ekin = 0.0173888111295073 | erot = 0.0643039804300221 | epot = -14.7241260365031 | etot = -14.6424332449436
5000 ekin = 0.0264744514136619 | erot = 0.0987844033142066 | epot = -14.7676920997383 | etot = -14.6424332450104
6000 ekin = 0.0369277948556079 | erot = 0.139336571052565 | epot = -14.8186976109956 | etot = -14.6424332450875
7000 ekin = 0.04839505571915 | erot = 0.18508629569208 | epot = -14.8759145965832 | etot = -14.642433245172
8000 ekin = 0.0604909336920643 | erot = 0.23507130752353 | epot = -14.9379954864767 | etot = -14.6424332452611
9000 ekin = 0.0728137406440561 | erot = 0.288273694501537 | epot = -15.003520680497 | etot = -14.6424332453514
10000 ekin = 0.0849615563085879 | erot = 0.343654369293472 | epot = -15.0710491710418 | etot = -14.6424332454398
10000 0.0062934486 -1.5138305 0.0067255788 -1.4986088 -9.9021593e-05
Loop time of 0.141929 on 1 procs for 10000 steps with 10 atoms
Performance: 60875.649 tau/day, 70457.927 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 | 0.11467 | 0.11467 | 0.11467 | 0.0 | 80.79
Bond | 0.0050094 | 0.0050094 | 0.0050094 | 0.0 | 3.53
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0013616 | 0.0013616 | 0.0013616 | 0.0 | 0.96
Output | 4.0531e-06 | 4.0531e-06 | 4.0531e-06 | 0.0 | 0.00
Modify | 0.017901 | 0.017901 | 0.017901 | 0.0 | 12.61
Other | | 0.002982 | | | 2.10
Nlocal: 10 ave 10 max 10 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: 43 ave 43 max 43 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 43
Ave neighs/atom = 4.3
Ave special neighs/atom = 3.6
Neighbor list builds = 0
Dangerous builds = 0
#write_restart config.${number}.*
Total wall time: 0:00:00

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@ -0,0 +1,172 @@
LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
variable number equal 1
variable ofreq equal 1000
variable efreq equal 1000
units lj
dimension 3
newton off
boundary p p p
atom_style hybrid bond ellipsoid
atom_modify sort 0 1.0
# Pair interactions require lists of neighbours to be calculated
neighbor 1.0 bin
neigh_modify every 1 delay 0 check yes
read_data data.duplex1
orthogonal box = (-20 -20 -20) to (20 20 20)
1 by 2 by 2 MPI processor grid
reading atoms ...
10 atoms
reading velocities ...
10 velocities
10 ellipsoids
scanning bonds ...
2 = max bonds/atom
reading bonds ...
8 bonds
2 = max # of 1-2 neighbors
2 = max # of 1-3 neighbors
2 = max # of 1-4 neighbors
4 = max # of special neighbors
set atom * mass 3.1575
10 settings made for mass
group all type 1 4
10 atoms in group all
# oxDNA bond interactions - FENE backbone
bond_style oxdna/fene
bond_coeff * 2.0 0.25 0.7525
# oxDNA pair interactions
pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
pair_coeff * * oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
pair_coeff * * oxdna/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
pair_coeff * * oxdna/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff 1 4 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff 2 3 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff * * oxdna/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65
# NVE ensemble
fix 1 all nve/dot
#fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
#fix 1 all nve/asphere
#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10
timestep 1e-5
#comm_style tiled
#fix 3 all balance 10000 1.1 rcb
#compute mol all chunk/atom molecule
#compute mychunk all vcm/chunk mol
#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
#dump pos all xyz ${ofreq} traj.${number}.xyz
#compute quat all property/atom quatw quati quatj quatk
#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
#dump_modify quat sort id
#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le"
compute erot all erotate/asphere
compute ekin all ke
compute epot all pe
variable erot equal c_erot
variable ekin equal c_ekin
variable epot equal c_epot
variable etot equal c_erot+c_ekin+c_epot
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
#dump_modify out sort id
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
run 10000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.92828
ghost atom cutoff = 1.92828
binsize = 0.964142, bins = 42 42 42
5 neighbor lists, perpetual/occasional/extra = 5 0 0
(1) pair oxdna/excv, perpetual
attributes: half, newton off
pair build: half/bin/newtoff
stencil: half/bin/3d/newtoff
bin: standard
(2) pair oxdna/stk, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
(3) pair oxdna/hbond, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
(4) pair oxdna/xstk, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
(5) pair oxdna/coaxstk, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 7.341 | 7.523 | 7.705 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -1.4711818 0.0069384985 -1.4642433 -6.2745089e-05
1000 ekin = 0.00113448721737009 | erot = 0.0041345594773427 | epot = -14.6477022915193 | etot = -14.6424332448246
2000 ekin = 0.00449927223902292 | erot = 0.0164446434455803 | epot = -14.6633771605337 | etot = -14.6424332448491
3000 ekin = 0.00997964450840756 | erot = 0.0366523356056465 | epot = -14.6890652250033 | etot = -14.6424332448892
4000 ekin = 0.017388811129498 | erot = 0.0643039804300254 | epot = -14.7241260365031 | etot = -14.6424332449436
5000 ekin = 0.0264744514136422 | erot = 0.098784403314214 | epot = -14.7676920997383 | etot = -14.6424332450104
6000 ekin = 0.0369277948555727 | erot = 0.139336571052581 | epot = -14.8186976109956 | etot = -14.6424332450875
7000 ekin = 0.0483950557190949 | erot = 0.185086295692111 | epot = -14.8759145965832 | etot = -14.642433245172
8000 ekin = 0.0604909336919856 | erot = 0.235071307523583 | epot = -14.9379954864767 | etot = -14.6424332452611
9000 ekin = 0.0728137406439517 | erot = 0.288273694501617 | epot = -15.003520680497 | etot = -14.6424332453514
10000 ekin = 0.0849615563084573 | erot = 0.34365436929359 | epot = -15.0710491710418 | etot = -14.6424332454398
10000 0.0062934486 -1.5138305 0.0067255788 -1.4986088 -0.00010196899
Loop time of 0.134536 on 4 procs for 10000 steps with 10 atoms
Performance: 64220.659 tau/day, 74329.466 timesteps/s
97.3% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0030077 | 0.052212 | 0.093066 | 17.4 | 38.81
Bond | 0.00061846 | 0.00234 | 0.0039451 | 2.8 | 1.74
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.013431 | 0.014091 | 0.014596 | 0.4 | 10.47
Output | 5.0783e-05 | 5.1141e-05 | 5.1498e-05 | 0.0 | 0.04
Modify | 0.0011578 | 0.0059478 | 0.010331 | 4.8 | 4.42
Other | | 0.05989 | | | 44.52
Nlocal: 2.5 ave 5 max 0 min
Histogram: 1 0 1 0 0 0 0 0 1 1
Nghost: 7.5 ave 10 max 5 min
Histogram: 1 0 1 0 0 0 0 0 1 1
Neighs: 17.5 ave 33 max 0 min
Histogram: 1 0 1 0 0 0 0 0 1 1
Total # of neighbors = 70
Ave neighs/atom = 7
Ave special neighs/atom = 3.6
Neighbor list builds = 0
Dangerous builds = 0
#write_restart config.${number}.*
Total wall time: 0:00:00

2
examples/USER/cgdna/examples/oxDNA/duplex2/input.duplex2 → examples/USER/cgdna/examples/oxDNA/duplex2/in.duplex2
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@ -72,6 +72,6 @@ fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${e
#dump_modify out sort id
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
run 1000000
run 10000
#write_restart config.${number}.*

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LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
variable number equal 2
variable ofreq equal 1000
variable efreq equal 1000
units lj
dimension 3
newton off
boundary p p p
atom_style hybrid bond ellipsoid
atom_modify sort 0 1.0
# Pair interactions require lists of neighbours to be calculated
neighbor 1.0 bin
neigh_modify every 1 delay 0 check yes
read_data data.duplex2
orthogonal box = (-20 -20 -20) to (20 20 20)
1 by 1 by 1 MPI processor grid
reading atoms ...
16 atoms
reading velocities ...
16 velocities
16 ellipsoids
scanning bonds ...
2 = max bonds/atom
reading bonds ...
13 bonds
2 = max # of 1-2 neighbors
2 = max # of 1-3 neighbors
4 = max # of 1-4 neighbors
6 = max # of special neighbors
set atom * mass 3.1575
16 settings made for mass
group all type 1 4
16 atoms in group all
# oxDNA bond interactions - FENE backbone
bond_style oxdna/fene
bond_coeff * 2.0 0.25 0.7525
# oxDNA pair interactions
pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
pair_coeff * * oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
pair_coeff * * oxdna/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
pair_coeff * * oxdna/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff 1 4 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff 2 3 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff * * oxdna/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65
# NVE ensemble
#fix 1 all nve/dot
fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
#fix 1 all nve/asphere
#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10
timestep 1e-5
#comm_style tiled
#fix 3 all balance 10000 1.1 rcb
#compute mol all chunk/atom molecule
#compute mychunk all vcm/chunk mol
#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
#dump pos all xyz ${ofreq} traj.${number}.xyz
#compute quat all property/atom quatw quati quatj quatk
#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
#dump_modify quat sort id
#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le"
compute erot all erotate/asphere
compute ekin all ke
compute epot all pe
variable erot equal c_erot
variable ekin equal c_ekin
variable epot equal c_epot
variable etot equal c_erot+c_ekin+c_epot
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
#dump_modify out sort id
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
run 10000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.92828
ghost atom cutoff = 1.92828
binsize = 0.964142, bins = 42 42 42
5 neighbor lists, perpetual/occasional/extra = 5 0 0
(1) pair oxdna/excv, perpetual
attributes: half, newton off
pair build: half/bin/newtoff
stencil: half/bin/3d/newtoff
bin: standard
(2) pair oxdna/stk, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
(3) pair oxdna/hbond, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
(4) pair oxdna/xstk, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
(5) pair oxdna/coaxstk, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 2.861 | 2.861 | 2.861 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -1.5402493 0.0070469125 -1.5332024 -8.5641987e-05
1000 ekin = 1.54234964773389 | erot = 1.71563526070267 | epot = -24.5477045187653 | etot = -21.2897196103287
2000 ekin = 1.85988866919215 | erot = 1.9424302796508 | epot = -24.4843044999595 | etot = -20.6819855511165
3000 ekin = 2.68354339452998 | erot = 2.14216528317607 | epot = -24.4019350693561 | etot = -19.57622639165
4000 ekin = 2.04461800191989 | erot = 1.49015219763162 | epot = -24.2959428773347 | etot = -20.7611726777832
5000 ekin = 1.76794859210155 | erot = 2.54289684465818 | epot = -24.2337587736863 | etot = -19.9229133369266
6000 ekin = 3.1106424806079 | erot = 2.04409805200892 | epot = -24.1585729744133 | etot = -19.0038324417964
7000 ekin = 3.21360097519306 | erot = 2.71941303605722 | epot = -24.0566262531609 | etot = -18.1236122419107
8000 ekin = 2.82489935901743 | erot = 2.66790555575696 | epot = -24.0194805097633 | etot = -18.526675594989
9000 ekin = 2.69381302856378 | erot = 2.59107820129446 | epot = -23.9216126050554 | etot = -18.6367213751972
10000 ekin = 2.65765007662471 | erot = 1.95562671446597 | epot = -23.7978334881241 | etot = -19.1845566970334
10000 0.11811778 -1.4992295 0.011864944 -1.3212615 -0.00013416809
Loop time of 0.295538 on 1 procs for 10000 steps with 16 atoms
Performance: 29234.801 tau/day, 33836.575 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 | 0.20959 | 0.20959 | 0.20959 | 0.0 | 70.92
Bond | 0.0073669 | 0.0073669 | 0.0073669 | 0.0 | 2.49
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0016472 | 0.0016472 | 0.0016472 | 0.0 | 0.56
Output | 5.0068e-06 | 5.0068e-06 | 5.0068e-06 | 0.0 | 0.00
Modify | 0.073117 | 0.073117 | 0.073117 | 0.0 | 24.74
Other | | 0.003813 | | | 1.29
Nlocal: 16 ave 16 max 16 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: 88 ave 88 max 88 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 88
Ave neighs/atom = 5.5
Ave special neighs/atom = 3.75
Neighbor list builds = 0
Dangerous builds = 0
#write_restart config.${number}.*
Total wall time: 0:00:00

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LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
variable number equal 2
variable ofreq equal 1000
variable efreq equal 1000
units lj
dimension 3
newton off
boundary p p p
atom_style hybrid bond ellipsoid
atom_modify sort 0 1.0
# Pair interactions require lists of neighbours to be calculated
neighbor 1.0 bin
neigh_modify every 1 delay 0 check yes
read_data data.duplex2
orthogonal box = (-20 -20 -20) to (20 20 20)
1 by 2 by 2 MPI processor grid
reading atoms ...
16 atoms
reading velocities ...
16 velocities
16 ellipsoids
scanning bonds ...
2 = max bonds/atom
reading bonds ...
13 bonds
2 = max # of 1-2 neighbors
2 = max # of 1-3 neighbors
4 = max # of 1-4 neighbors
6 = max # of special neighbors
set atom * mass 3.1575
16 settings made for mass
group all type 1 4
16 atoms in group all
# oxDNA bond interactions - FENE backbone
bond_style oxdna/fene
bond_coeff * 2.0 0.25 0.7525
# oxDNA pair interactions
pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
pair_coeff * * oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
pair_coeff * * oxdna/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
pair_coeff * * oxdna/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff 1 4 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff 2 3 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff * * oxdna/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65
# NVE ensemble
#fix 1 all nve/dot
fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
#fix 1 all nve/asphere
#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10
timestep 1e-5
#comm_style tiled
#fix 3 all balance 10000 1.1 rcb
#compute mol all chunk/atom molecule
#compute mychunk all vcm/chunk mol
#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
#dump pos all xyz ${ofreq} traj.${number}.xyz
#compute quat all property/atom quatw quati quatj quatk
#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
#dump_modify quat sort id
#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le"
compute erot all erotate/asphere
compute ekin all ke
compute epot all pe
variable erot equal c_erot
variable ekin equal c_ekin
variable epot equal c_epot
variable etot equal c_erot+c_ekin+c_epot
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
#dump_modify out sort id
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
run 10000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.92828
ghost atom cutoff = 1.92828
binsize = 0.964142, bins = 42 42 42
5 neighbor lists, perpetual/occasional/extra = 5 0 0
(1) pair oxdna/excv, perpetual
attributes: half, newton off
pair build: half/bin/newtoff
stencil: half/bin/3d/newtoff
bin: standard
(2) pair oxdna/stk, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
(3) pair oxdna/hbond, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
(4) pair oxdna/xstk, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
(5) pair oxdna/coaxstk, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 7.466 | 7.648 | 7.83 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -1.5402493 0.0070469125 -1.5332024 -8.5641987e-05
1000 ekin = 1.34565986428024 | erot = 2.31051421234078 | epot = -24.5061991591502 | etot = -20.8500250825292
2000 ekin = 2.15911766687235 | erot = 2.16031365874707 | epot = -24.4723177103698 | etot = -20.1528863847504
3000 ekin = 3.26561948796015 | erot = 2.75651822936604 | epot = -24.412573068346 | etot = -18.3904353510198
4000 ekin = 1.92438809241066 | erot = 2.12016940074985 | epot = -24.3496233970111 | etot = -20.3050659038506
5000 ekin = 1.35986357015476 | erot = 1.99413493074226 | epot = -24.2789445616949 | etot = -20.9249460607979
6000 ekin = 2.19432475124593 | erot = 1.74281260409078 | epot = -24.2128064295788 | etot = -20.2756690742421
7000 ekin = 2.65619274477635 | erot = 1.74094257048458 | epot = -24.1673462333493 | etot = -19.7702109180883
8000 ekin = 2.51333548501168 | erot = 2.34649854571051 | epot = -24.0812769481836 | etot = -19.2214429174614
9000 ekin = 2.24506493169711 | erot = 2.0652555461504 | epot = -23.9906736063989 | etot = -19.6803531285514
10000 ekin = 2.36632635249862 | erot = 1.7959247176153 | epot = -23.9002627850602 | etot = -19.7380117149463
10000 0.10517006 -1.5057137 0.011947302 -1.345871 -9.5924016e-05
Loop time of 0.251867 on 4 procs for 10000 steps with 16 atoms
Performance: 34303.820 tau/day, 39703.495 timesteps/s
97.8% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0035377 | 0.092047 | 0.17435 | 26.0 | 36.55
Bond | 0.00065637 | 0.0031857 | 0.0053554 | 3.8 | 1.26
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.013929 | 0.01497 | 0.015733 | 0.6 | 5.94
Output | 5.0783e-05 | 5.2691e-05 | 5.3883e-05 | 0.0 | 0.02
Modify | 0.0013576 | 0.020825 | 0.040231 | 11.8 | 8.27
Other | | 0.1208 | | | 47.96
Nlocal: 4 ave 8 max 0 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Nghost: 9 ave 10 max 8 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Neighs: 34.5 ave 67 max 0 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Total # of neighbors = 138
Ave neighs/atom = 8.625
Ave special neighs/atom = 3.75
Neighbor list builds = 0
Dangerous builds = 0
#write_restart config.${number}.*
Total wall time: 0:00:00

2
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@ -73,6 +73,6 @@ fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${e
#dump_modify out sort id
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
run 1000000
run 10000
#write_restart config.${number}.*

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LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
variable number equal 1
variable ofreq equal 1000
variable efreq equal 1000
units lj
dimension 3
newton off
boundary p p p
atom_style hybrid bond ellipsoid
atom_modify sort 0 1.0
# Pair interactions require lists of neighbours to be calculated
neighbor 1.0 bin
neigh_modify every 1 delay 0 check yes
read_data data.duplex1
orthogonal box = (-20 -20 -20) to (20 20 20)
1 by 1 by 1 MPI processor grid
reading atoms ...
10 atoms
reading velocities ...
10 velocities
10 ellipsoids
scanning bonds ...
2 = max bonds/atom
reading bonds ...
8 bonds
2 = max # of 1-2 neighbors
2 = max # of 1-3 neighbors
2 = max # of 1-4 neighbors
4 = max # of special neighbors
set atom * mass 3.1575
10 settings made for mass
group all type 1 4
10 atoms in group all
# oxDNA bond interactions - FENE backbone
bond_style oxdna2/fene
bond_coeff * 2.0 0.25 0.7564
# oxDNA pair interactions
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
pair_coeff * * oxdna2/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
pair_coeff * * oxdna2/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff 1 4 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff 2 3 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
pair_coeff * * oxdna2/dh 0.1 1.0 0.815
# NVE ensemble
fix 1 all nve/dot
#fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
#fix 1 all nve/asphere
#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10
timestep 1e-5
#comm_style tiled
#fix 3 all balance 10000 1.1 rcb
#compute mol all chunk/atom molecule
#compute mychunk all vcm/chunk mol
#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
#dump pos all xyz ${ofreq} traj.${number}.xyz
#compute quat all property/atom quatw quati quatj quatk
#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
#dump_modify quat sort id
#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le"
compute erot all erotate/asphere
compute ekin all ke
compute epot all pe
variable erot equal c_erot
variable ekin equal c_ekin
variable epot equal c_epot
variable etot equal c_erot+c_ekin+c_epot
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
#dump_modify out sort id
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
run 10000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.6274
ghost atom cutoff = 2.6274
binsize = 1.3137, bins = 31 31 31
6 neighbor lists, perpetual/occasional/extra = 6 0 0
(1) pair oxdna2/excv, perpetual
attributes: half, newton off
pair build: half/bin/newtoff
stencil: half/bin/3d/newtoff
bin: standard
(2) pair oxdna2/stk, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
(3) pair oxdna2/hbond, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
(4) pair oxdna2/xstk, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
(5) pair oxdna2/coaxstk, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
(6) pair oxdna2/dh, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 3.023 | 3.023 | 3.023 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -1.4712768 0.009525411 -1.4617514 -5.8922361e-05
1000 ekin = 0.00113086229080528 | erot = 0.0043101016040658 | epot = -14.6229549982368 | etot = -14.617514034342
2000 ekin = 0.0044853322434243 | erot = 0.0171407706505008 | epot = -14.6391401372615 | etot = -14.6175140343675
3000 ekin = 0.00995035259649284 | erot = 0.0381961780846485 | epot = -14.6656605650904 | etot = -14.6175140344093
4000 ekin = 0.0173418024862054 | erot = 0.0669935184860634 | epot = -14.7018493554381 | etot = -14.6175140344659
5000 ekin = 0.0264109356286075 | erot = 0.102878288094517 | epot = -14.7468032582586 | etot = -14.6175140345355
6000 ekin = 0.0368533113591442 | erot = 0.14504542056987 | epot = -14.7994127665447 | etot = -14.6175140346157
7000 ekin = 0.0483200640564843 | erot = 0.19256586251551 | epot = -14.8583999612756 | etot = -14.6175140347036
8000 ekin = 0.0604312317605998 | erot = 0.24441787013151 | epot = -14.9223631366883 | etot = -14.6175140347962
9000 ekin = 0.0727907119671751 | erot = 0.299521949931843 | epot = -14.989826696789 | etot = -14.6175140348899
10000 ekin = 0.0850022498875221 | erot = 0.356777997217908 | epot = -15.0592942820869 | etot = -14.6175140349815
10000 0.006296463 -1.5144685 0.0085391004 -1.4974292 -0.00010794792
Loop time of 0.149406 on 1 procs for 10000 steps with 10 atoms
Performance: 57828.835 tau/day, 66931.522 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 | 0.11971 | 0.11971 | 0.11971 | 0.0 | 80.12
Bond | 0.0051196 | 0.0051196 | 0.0051196 | 0.0 | 3.43
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0013614 | 0.0013614 | 0.0013614 | 0.0 | 0.91
Output | 5.0068e-06 | 5.0068e-06 | 5.0068e-06 | 0.0 | 0.00
Modify | 0.018941 | 0.018941 | 0.018941 | 0.0 | 12.68
Other | | 0.004268 | | | 2.86
Nlocal: 10 ave 10 max 10 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: 45 ave 45 max 45 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 45
Ave neighs/atom = 4.5
Ave special neighs/atom = 3.6
Neighbor list builds = 0
Dangerous builds = 0
#write_restart config.${number}.*
Total wall time: 0:00:00

178
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LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
variable number equal 1
variable ofreq equal 1000
variable efreq equal 1000
units lj
dimension 3
newton off
boundary p p p
atom_style hybrid bond ellipsoid
atom_modify sort 0 1.0
# Pair interactions require lists of neighbours to be calculated
neighbor 1.0 bin
neigh_modify every 1 delay 0 check yes
read_data data.duplex1
orthogonal box = (-20 -20 -20) to (20 20 20)
1 by 2 by 2 MPI processor grid
reading atoms ...
10 atoms
reading velocities ...
10 velocities
10 ellipsoids
scanning bonds ...
2 = max bonds/atom
reading bonds ...
8 bonds
2 = max # of 1-2 neighbors
2 = max # of 1-3 neighbors
2 = max # of 1-4 neighbors
4 = max # of special neighbors
set atom * mass 3.1575
10 settings made for mass
group all type 1 4
10 atoms in group all
# oxDNA bond interactions - FENE backbone
bond_style oxdna2/fene
bond_coeff * 2.0 0.25 0.7564
# oxDNA pair interactions
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
pair_coeff * * oxdna2/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
pair_coeff * * oxdna2/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff 1 4 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff 2 3 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
pair_coeff * * oxdna2/dh 0.1 1.0 0.815
# NVE ensemble
fix 1 all nve/dot
#fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
#fix 1 all nve/asphere
#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10
timestep 1e-5
#comm_style tiled
#fix 3 all balance 10000 1.1 rcb
#compute mol all chunk/atom molecule
#compute mychunk all vcm/chunk mol
#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
#dump pos all xyz ${ofreq} traj.${number}.xyz
#compute quat all property/atom quatw quati quatj quatk
#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
#dump_modify quat sort id
#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le"
compute erot all erotate/asphere
compute ekin all ke
compute epot all pe
variable erot equal c_erot
variable ekin equal c_ekin
variable epot equal c_epot
variable etot equal c_erot+c_ekin+c_epot
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
#dump_modify out sort id
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
run 10000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.6274
ghost atom cutoff = 2.6274
binsize = 1.3137, bins = 31 31 31
6 neighbor lists, perpetual/occasional/extra = 6 0 0
(1) pair oxdna2/excv, perpetual
attributes: half, newton off
pair build: half/bin/newtoff
stencil: half/bin/3d/newtoff
bin: standard
(2) pair oxdna2/stk, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
(3) pair oxdna2/hbond, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
(4) pair oxdna2/xstk, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
(5) pair oxdna2/coaxstk, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
(6) pair oxdna2/dh, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 7.652 | 7.834 | 8.016 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -1.4712768 0.009525411 -1.4617514 -5.8922361e-05
1000 ekin = 0.00113086229080478 | erot = 0.00431010160406708 | epot = -14.6229549982368 | etot = -14.617514034342
2000 ekin = 0.00448533224342286 | erot = 0.0171407706505013 | epot = -14.6391401372615 | etot = -14.6175140343675
3000 ekin = 0.0099503525964896 | erot = 0.0381961780846438 | epot = -14.6656605650904 | etot = -14.6175140344093
4000 ekin = 0.0173418024861991 | erot = 0.0669935184860479 | epot = -14.7018493554381 | etot = -14.6175140344659
5000 ekin = 0.0264109356285965 | erot = 0.102878288094482 | epot = -14.7468032582586 | etot = -14.6175140345355
6000 ekin = 0.0368533113591268 | erot = 0.145045420569809 | epot = -14.7994127665446 | etot = -14.6175140346156
7000 ekin = 0.0483200640564584 | erot = 0.192565862515413 | epot = -14.8583999612755 | etot = -14.6175140347036
8000 ekin = 0.0604312317605635 | erot = 0.24441787013137 | epot = -14.9223631366881 | etot = -14.6175140347962
9000 ekin = 0.072790711967127 | erot = 0.299521949931654 | epot = -14.9898266967887 | etot = -14.6175140348899
10000 ekin = 0.0850022498874609 | erot = 0.356777997217666 | epot = -15.0592942820866 | etot = -14.6175140349815
10000 0.006296463 -1.5144685 0.0085391004 -1.4974292 -0.00010794792
Loop time of 0.14583 on 4 procs for 10000 steps with 10 atoms
Performance: 59247.054 tau/day, 68572.979 timesteps/s
97.5% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0034175 | 0.055587 | 0.10059 | 17.9 | 38.12
Bond | 0.00064635 | 0.002131 | 0.0035357 | 2.5 | 1.46
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.014538 | 0.014932 | 0.015271 | 0.2 | 10.24
Output | 5.7459e-05 | 5.7697e-05 | 5.7936e-05 | 0.0 | 0.04
Modify | 0.0012829 | 0.0063873 | 0.011321 | 5.2 | 4.38
Other | | 0.06674 | | | 45.76
Nlocal: 2.5 ave 5 max 0 min
Histogram: 1 0 1 0 0 0 0 0 1 1
Nghost: 7.5 ave 10 max 5 min
Histogram: 1 0 1 0 0 0 0 0 1 1
Neighs: 18.5 ave 35 max 0 min
Histogram: 1 0 1 0 0 0 0 0 1 1
Total # of neighbors = 74
Ave neighs/atom = 7.4
Ave special neighs/atom = 3.6
Neighbor list builds = 0
Dangerous builds = 0
#write_restart config.${number}.*
Total wall time: 0:00:00

2
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@ -73,6 +73,6 @@ fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${e
#dump_modify out sort id
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
run 1000000
run 10000
#write_restart config.${number}.*

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LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
variable number equal 2
variable ofreq equal 1000
variable efreq equal 1000
units lj
dimension 3
newton off
boundary p p p
atom_style hybrid bond ellipsoid
atom_modify sort 0 1.0
# Pair interactions require lists of neighbours to be calculated
neighbor 1.0 bin
neigh_modify every 1 delay 0 check yes
read_data data.duplex2
orthogonal box = (-20 -20 -20) to (20 20 20)
1 by 1 by 1 MPI processor grid
reading atoms ...
16 atoms
reading velocities ...
16 velocities
16 ellipsoids
scanning bonds ...
2 = max bonds/atom
reading bonds ...
13 bonds
2 = max # of 1-2 neighbors
2 = max # of 1-3 neighbors
4 = max # of 1-4 neighbors
6 = max # of special neighbors
set atom * mass 3.1575
16 settings made for mass
group all type 1 4
16 atoms in group all
# oxDNA bond interactions - FENE backbone
bond_style oxdna2/fene
bond_coeff * 2.0 0.25 0.7564
# oxDNA pair interactions
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
pair_coeff * * oxdna2/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
pair_coeff * * oxdna2/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff 1 4 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff 2 3 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
pair_coeff * * oxdna2/dh 0.1 1.0 0.815
# NVE ensemble
#fix 1 all nve/dot
fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
#fix 1 all nve/asphere
#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10
timestep 1e-5
#comm_style tiled
#fix 3 all balance 10000 1.1 rcb
#compute mol all chunk/atom molecule
#compute mychunk all vcm/chunk mol
#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
#dump pos all xyz ${ofreq} traj.${number}.xyz
#compute quat all property/atom quatw quati quatj quatk
#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
#dump_modify quat sort id
#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le"
compute erot all erotate/asphere
compute ekin all ke
compute epot all pe
variable erot equal c_erot
variable ekin equal c_ekin
variable epot equal c_epot
variable etot equal c_erot+c_ekin+c_epot
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
#dump_modify out sort id
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
run 10000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.6274
ghost atom cutoff = 2.6274
binsize = 1.3137, bins = 31 31 31
6 neighbor lists, perpetual/occasional/extra = 6 0 0
(1) pair oxdna2/excv, perpetual
attributes: half, newton off
pair build: half/bin/newtoff
stencil: half/bin/3d/newtoff
bin: standard
(2) pair oxdna2/stk, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
(3) pair oxdna2/hbond, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
(4) pair oxdna2/xstk, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
(5) pair oxdna2/coaxstk, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
(6) pair oxdna2/dh, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 3.025 | 3.025 | 3.025 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -1.5358787 0.0096742456 -1.5262045 -7.9568629e-05
1000 ekin = 1.54282272464468 | erot = 1.71757897250772 | epot = -24.4403527731341 | etot = -21.1799510759817
2000 ekin = 1.86109566690716 | erot = 1.93804145796026 | epot = -24.3759816748265 | etot = -20.5768445499591
3000 ekin = 2.68769182431188 | erot = 2.14559269500086 | epot = -24.2916556822451 | etot = -19.4583711629324
4000 ekin = 2.04710303757243 | erot = 1.48774072590987 | epot = -24.190371461807 | etot = -20.6555276983247
5000 ekin = 1.77654023802719 | erot = 2.534186505221 | epot = -24.1246365663843 | etot = -19.8139098231361
6000 ekin = 3.12253137872527 | erot = 2.04028266818831 | epot = -24.0491248750916 | etot = -18.886310828178
7000 ekin = 3.22418765752177 | erot = 2.72037570174023 | epot = -23.9458569915548 | etot = -18.0012936322928
8000 ekin = 2.83204202112963 | erot = 2.67060276413777 | epot = -23.9211291529766 | etot = -18.4184843677092
9000 ekin = 2.69585642754481 | erot = 2.59559820250212 | epot = -23.8340823338302 | etot = -18.5426277037833
10000 ekin = 2.66058119525512 | erot = 1.95965933336077 | epot = -23.7132443170725 | etot = -19.0930037884566
10000 0.11824805 -1.4953627 0.013284973 -1.3157914 -0.00012999454
Loop time of 0.32781 on 1 procs for 10000 steps with 16 atoms
Performance: 26356.746 tau/day, 30505.493 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 | 0.24211 | 0.24211 | 0.24211 | 0.0 | 73.86
Bond | 0.0075173 | 0.0075173 | 0.0075173 | 0.0 | 2.29
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0014515 | 0.0014515 | 0.0014515 | 0.0 | 0.44
Output | 5.4836e-06 | 5.4836e-06 | 5.4836e-06 | 0.0 | 0.00
Modify | 0.073331 | 0.073331 | 0.073331 | 0.0 | 22.37
Other | | 0.003398 | | | 1.04
Nlocal: 16 ave 16 max 16 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: 116 ave 116 max 116 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 116
Ave neighs/atom = 7.25
Ave special neighs/atom = 3.75
Neighbor list builds = 0
Dangerous builds = 0
#write_restart config.${number}.*
Total wall time: 0:00:00

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LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
variable number equal 2
variable ofreq equal 1000
variable efreq equal 1000
units lj
dimension 3
newton off
boundary p p p
atom_style hybrid bond ellipsoid
atom_modify sort 0 1.0
# Pair interactions require lists of neighbours to be calculated
neighbor 1.0 bin
neigh_modify every 1 delay 0 check yes
read_data data.duplex2
orthogonal box = (-20 -20 -20) to (20 20 20)
1 by 2 by 2 MPI processor grid
reading atoms ...
16 atoms
reading velocities ...
16 velocities
16 ellipsoids
scanning bonds ...
2 = max bonds/atom
reading bonds ...
13 bonds
2 = max # of 1-2 neighbors
2 = max # of 1-3 neighbors
4 = max # of 1-4 neighbors
6 = max # of special neighbors
set atom * mass 3.1575
16 settings made for mass
group all type 1 4
16 atoms in group all
# oxDNA bond interactions - FENE backbone
bond_style oxdna2/fene
bond_coeff * 2.0 0.25 0.7564
# oxDNA pair interactions
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
pair_coeff * * oxdna2/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
pair_coeff * * oxdna2/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff 1 4 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff 2 3 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
pair_coeff * * oxdna2/dh 0.1 1.0 0.815
# NVE ensemble
#fix 1 all nve/dot
fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
#fix 1 all nve/asphere
#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10
timestep 1e-5
#comm_style tiled
#fix 3 all balance 10000 1.1 rcb
#compute mol all chunk/atom molecule
#compute mychunk all vcm/chunk mol
#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
#dump pos all xyz ${ofreq} traj.${number}.xyz
#compute quat all property/atom quatw quati quatj quatk
#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
#dump_modify quat sort id
#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le"
compute erot all erotate/asphere
compute ekin all ke
compute epot all pe
variable erot equal c_erot
variable ekin equal c_ekin
variable epot equal c_epot
variable etot equal c_erot+c_ekin+c_epot
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
#dump_modify out sort id
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
run 10000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.6274
ghost atom cutoff = 2.6274
binsize = 1.3137, bins = 31 31 31
6 neighbor lists, perpetual/occasional/extra = 6 0 0
(1) pair oxdna2/excv, perpetual
attributes: half, newton off
pair build: half/bin/newtoff
stencil: half/bin/3d/newtoff
bin: standard
(2) pair oxdna2/stk, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
(3) pair oxdna2/hbond, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
(4) pair oxdna2/xstk, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
(5) pair oxdna2/coaxstk, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
(6) pair oxdna2/dh, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 7.777 | 7.959 | 8.142 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -1.5358787 0.0096742456 -1.5262045 -7.9568629e-05
1000 ekin = 1.34554291364716 | erot = 2.30525041754444 | epot = -24.3924150888896 | etot = -20.741621757698
2000 ekin = 2.15972469811184 | erot = 2.1628675965276 | epot = -24.3548203354875 | etot = -20.0322280408481
3000 ekin = 3.26433550542939 | erot = 2.76107866472085 | epot = -24.2947953202752 | etot = -18.269381150125
4000 ekin = 1.9203212531997 | erot = 2.13339438425299 | epot = -24.234098584123 | etot = -20.1803829466703
5000 ekin = 1.35481075814721 | erot = 2.00854026688447 | epot = -24.1768963201279 | etot = -20.8135452950963
6000 ekin = 2.18974627635306 | erot = 1.73271671162435 | epot = -24.1096616118305 | etot = -20.1871986238531
7000 ekin = 2.65472853187395 | erot = 1.73258720631296 | epot = -24.0561118130561 | etot = -19.6687960748691
8000 ekin = 2.51192327964357 | erot = 2.34132844779952 | epot = -23.9708695663488 | etot = -19.1176178389058
9000 ekin = 2.24554900802464 | erot = 2.0522939078286 | epot = -23.874757758319 | etot = -19.5769148424658
10000 ekin = 2.36227360512089 | erot = 1.80185994066737 | epot = -23.7793375260418 | etot = -19.6152039802535
10000 0.10498994 -1.5020657 0.015857071 -1.3385665 -8.8930899e-05
Loop time of 0.291642 on 4 procs for 10000 steps with 16 atoms
Performance: 29625.313 tau/day, 34288.557 timesteps/s
96.6% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0035026 | 0.1107 | 0.20674 | 28.3 | 37.96
Bond | 0.00062203 | 0.0029532 | 0.0049176 | 3.6 | 1.01
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.016712 | 0.018041 | 0.01914 | 0.7 | 6.19
Output | 5.0306e-05 | 5.424e-05 | 5.579e-05 | 0.0 | 0.02
Modify | 0.0013862 | 0.020914 | 0.039594 | 11.7 | 7.17
Other | | 0.139 | | | 47.65
Nlocal: 4 ave 8 max 0 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Nghost: 11 ave 14 max 8 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Neighs: 46 ave 89 max 0 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Total # of neighbors = 184
Ave neighs/atom = 11.5
Ave special neighs/atom = 3.75
Neighbor list builds = 0
Dangerous builds = 0
#write_restart config.${number}.*
Total wall time: 0:00:00

64
examples/USER/cgsdk/peg-verlet/log.pegc12e8-angle → examples/USER/cgsdk/peg-verlet/log.27Nov18.pegc12e8-angle.g++.1
View File

@ -1,5 +1,4 @@
LAMMPS (20 Mar 2014-ICMS)
WARNING: OMP_NUM_THREADS environment is not set. (../comm.cpp:100)
LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# Solvated 5-mer peptide
@ -19,7 +18,7 @@ special_bonds lj/coul 0.0 0.0 1.0
read_data data.pegc12e8.gz
orthogonal box = (-63.7 -63.7 -200) to (63.7 63.7 200)
2 by 1 by 1 MPI processor grid
1 by 1 by 1 MPI processor grid
reading atoms ...
40140 atoms
reading velocities ...
@ -52,59 +51,71 @@ fix 1 all nvt temp 303.0 303.0 100.0
thermo_style multi
thermo 200
run 1000
Memory usage per processor = 12.4188 Mbytes
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 18
ghost atom cutoff = 18
binsize = 9, bins = 15 15 45
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/sdk, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 47.18 | 47.18 | 47.18 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = -217835.8659 KinEng = 36252.9606 Temp = 303.0000
PotEng = -254088.8265 E_bond = 4468.5931 E_angle = 3565.0955
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262122.5151
E_coul = 0.0000 E_long = 0.0000 Press = 114.4952
---------------- Step 200 ----- CPU = 8.7547 (sec) ----------------
---------------- Step 200 ----- CPU = 11.2079 (sec) ----------------
TotEng = -217870.2208 KinEng = 36451.9852 Temp = 304.6634
PotEng = -254322.2060 E_bond = 4534.3652 E_angle = 3349.2174
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262205.7887
E_coul = 0.0000 E_long = 0.0000 Press = 39.4030
---------------- Step 400 ----- CPU = 17.7479 (sec) ----------------
---------------- Step 400 ----- CPU = 22.6137 (sec) ----------------
TotEng = -218169.7022 KinEng = 36263.1022 Temp = 303.0848
PotEng = -254432.8045 E_bond = 4598.1819 E_angle = 3416.3763
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262447.3627
E_coul = 0.0000 E_long = 0.0000 Press = 9.8923
---------------- Step 600 ----- CPU = 26.7299 (sec) ----------------
---------------- Step 600 ----- CPU = 33.9441 (sec) ----------------
TotEng = -217912.9317 KinEng = 36465.5757 Temp = 304.7770
PotEng = -254378.5074 E_bond = 4648.1881 E_angle = 3412.8346
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262439.5301
E_coul = 0.0000 E_long = 0.0000 Press = 25.6392
---------------- Step 800 ----- CPU = 35.8941 (sec) ----------------
---------------- Step 800 ----- CPU = 45.4291 (sec) ----------------
TotEng = -218439.8078 KinEng = 36035.8518 Temp = 301.1854
PotEng = -254475.6596 E_bond = 4557.5842 E_angle = 3438.5605
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262471.8043
E_coul = 0.0000 E_long = 0.0000 Press = -1.6281
---------------- Step 1000 ----- CPU = 45.1542 (sec) ----------------
---------------- Step 1000 ----- CPU = 56.9328 (sec) ----------------
TotEng = -217925.0543 KinEng = 36271.3928 Temp = 303.1541
PotEng = -254196.4471 E_bond = 4624.7673 E_angle = 3487.7805
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262308.9949
E_coul = 0.0000 E_long = 0.0000 Press = -7.3081
Loop time of 56.9329 on 1 procs for 1000 steps with 40140 atoms
Loop time of 45.1542 on 2 procs for 1000 steps with 40140 atoms
99.5% CPU use with 2 MPI tasks x 1 OpenMP threads
Performance: 9.567 ns/day 2.509 hours/ns 22.146 timesteps/s
Performance: 7.588 ns/day, 3.163 hours/ns, 17.565 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timings breakdown:
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 38.906 | 38.953 | 39.001 | 0.8 | 86.27
Bond | 0.90927 | 0.96844 | 1.0276 | 6.0 | 2.14
Neigh | 3.7623 | 3.7641 | 3.766 | 0.1 | 8.34
Comm | 0.56974 | 0.67309 | 0.77643 | 12.6 | 1.49
Output | 0.00067949 | 0.00072169 | 0.00076389 | 0.2 | 0.00
Modify | 0.52627 | 0.53756 | 0.54885 | 1.5 | 1.19
Other | | 0.2571 | | | 0.57
Pair | 50.734 | 50.734 | 50.734 | 0.0 | 89.11
Bond | 0.94032 | 0.94032 | 0.94032 | 0.0 | 1.65
Neigh | 4.5195 | 4.5195 | 4.5195 | 0.0 | 7.94
Comm | 0.15045 | 0.15045 | 0.15045 | 0.0 | 0.26
Output | 0.00056767 | 0.00056767 | 0.00056767 | 0.0 | 0.00
Modify | 0.47228 | 0.47228 | 0.47228 | 0.0 | 0.83
Other | | 0.1154 | | | 0.20
Nlocal: 20070 ave 20100 max 20040 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 20230.5 ave 20241 max 20220 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 2.84338e+06 ave 2.85198e+06 max 2.83477e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nlocal: 40140 ave 40140 max 40140 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 25966 ave 25966 max 25966 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 5.68676e+06 ave 5.68676e+06 max 5.68676e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 5686756
Ave neighs/atom = 141.673
@ -113,3 +124,4 @@ Neighbor list builds = 38
Dangerous builds = 0
#write_restart pegc12e8-1.restart
Total wall time: 0:00:57

127
examples/USER/cgsdk/peg-verlet/log.27Nov18.pegc12e8-angle.g++.4 Normal file
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@ -0,0 +1,127 @@
LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# Solvated 5-mer peptide
units real
dimension 3
atom_style angle
# enforce that in z-direction there is only one
# processor (could be two) for optimal performance
processors * * 1
# read topology and force field
pair_style lj/sdk 15.0
bond_style harmonic
angle_style sdk
special_bonds lj/coul 0.0 0.0 1.0
read_data data.pegc12e8.gz
orthogonal box = (-63.7 -63.7 -200) to (63.7 63.7 200)
2 by 2 by 1 MPI processor grid
reading atoms ...
40140 atoms
reading velocities ...
40140 velocities
scanning bonds ...
1 = max bonds/atom
scanning angles ...
1 = max angles/atom
reading bonds ...
13284 bonds
reading angles ...
12177 angles
2 = max # of 1-2 neighbors
2 = max # of 1-3 neighbors
4 = max # of special neighbors
neighbor 3.0 bin
neigh_modify delay 5
timestep 5.0
#dump 1 all xtc 200 pegc12e8-1.xtc
#dump_modify 1 unwrap yes
#dump 2 all dcd 200 pegc12e8-1.dcd unwrap
#dump_modify 2 unwrap yes
velocity all create 303.0 46659 mom yes rot yes dist gaussian
fix 1 all nvt temp 303.0 303.0 100.0
thermo_style multi
thermo 200
run 1000
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 18
ghost atom cutoff = 18
binsize = 9, bins = 15 15 45
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/sdk, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 15.87 | 15.87 | 15.87 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = -217835.8659 KinEng = 36252.9606 Temp = 303.0000
PotEng = -254088.8265 E_bond = 4468.5931 E_angle = 3565.0955
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262122.5151
E_coul = 0.0000 E_long = 0.0000 Press = 114.4952
---------------- Step 200 ----- CPU = 3.0597 (sec) ----------------
TotEng = -217870.2208 KinEng = 36451.9852 Temp = 304.6634
PotEng = -254322.2060 E_bond = 4534.3652 E_angle = 3349.2174
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262205.7887
E_coul = 0.0000 E_long = 0.0000 Press = 39.4030
---------------- Step 400 ----- CPU = 6.2514 (sec) ----------------
TotEng = -218169.7022 KinEng = 36263.1022 Temp = 303.0848
PotEng = -254432.8045 E_bond = 4598.1819 E_angle = 3416.3763
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262447.3627
E_coul = 0.0000 E_long = 0.0000 Press = 9.8923
---------------- Step 600 ----- CPU = 9.4073 (sec) ----------------
TotEng = -217912.9317 KinEng = 36465.5757 Temp = 304.7770
PotEng = -254378.5074 E_bond = 4648.1881 E_angle = 3412.8346
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262439.5301
E_coul = 0.0000 E_long = 0.0000 Press = 25.6392
---------------- Step 800 ----- CPU = 12.6096 (sec) ----------------
TotEng = -218439.8078 KinEng = 36035.8518 Temp = 301.1854
PotEng = -254475.6596 E_bond = 4557.5842 E_angle = 3438.5605
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262471.8043
E_coul = 0.0000 E_long = 0.0000 Press = -1.6281
---------------- Step 1000 ----- CPU = 15.9134 (sec) ----------------
TotEng = -217925.0543 KinEng = 36271.3928 Temp = 303.1541
PotEng = -254196.4471 E_bond = 4624.7673 E_angle = 3487.7805
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262308.9949
E_coul = 0.0000 E_long = 0.0000 Press = -7.3081
Loop time of 15.9135 on 4 procs for 1000 steps with 40140 atoms
Performance: 27.147 ns/day, 0.884 hours/ns, 62.840 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 | 13.325 | 13.6 | 13.755 | 4.7 | 85.46
Bond | 0.2432 | 0.25007 | 0.25671 | 1.0 | 1.57
Neigh | 1.2394 | 1.2399 | 1.2402 | 0.0 | 7.79
Comm | 0.41026 | 0.5737 | 0.85471 | 23.4 | 3.61
Output | 0.00025368 | 0.0004195 | 0.00091338 | 0.0 | 0.00
Modify | 0.17159 | 0.17316 | 0.17459 | 0.3 | 1.09
Other | | 0.0768 | | | 0.48
Nlocal: 10035 ave 10084 max 9971 min
Histogram: 1 0 0 1 0 0 0 0 1 1
Nghost: 14548.8 ave 14610 max 14509 min
Histogram: 1 0 1 1 0 0 0 0 0 1
Neighs: 1.42169e+06 ave 1.42961e+06 max 1.40922e+06 min
Histogram: 1 0 0 0 0 0 1 0 1 1
Total # of neighbors = 5686756
Ave neighs/atom = 141.673
Ave special neighs/atom = 1.26861
Neighbor list builds = 38
Dangerous builds = 0
#write_restart pegc12e8-1.restart
Total wall time: 0:00:16

64
examples/USER/cgsdk/peg-verlet/log.pegc12e8 → examples/USER/cgsdk/peg-verlet/log.27Nov18.pegc12e8.g++.1
View File

@ -1,5 +1,4 @@
LAMMPS (20 Mar 2014-ICMS)
WARNING: OMP_NUM_THREADS environment is not set. (../comm.cpp:100)
LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# Solvated 5-mer peptide
@ -19,7 +18,7 @@ special_bonds lj/coul 0.0 0.0 1.0
read_data data.pegc12e8.gz
orthogonal box = (-63.7 -63.7 -200) to (63.7 63.7 200)
2 by 1 by 1 MPI processor grid
1 by 1 by 1 MPI processor grid
reading atoms ...
40140 atoms
reading velocities ...
@ -52,59 +51,71 @@ fix 1 all nvt temp 303.0 303.0 100.0
thermo_style multi
thermo 200
run 1000
Memory usage per processor = 12.4188 Mbytes
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 18
ghost atom cutoff = 18
binsize = 9, bins = 15 15 45
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/sdk, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 47.18 | 47.18 | 47.18 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = -217990.7972 KinEng = 36252.9606 Temp = 303.0000
PotEng = -254243.7577 E_bond = 4468.5931 E_angle = 3410.1642
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262122.5151
E_coul = 0.0000 E_long = 0.0000 Press = 105.8245
---------------- Step 200 ----- CPU = 8.6552 (sec) ----------------
---------------- Step 200 ----- CPU = 11.2074 (sec) ----------------
TotEng = -218203.1886 KinEng = 36162.5201 Temp = 302.2441
PotEng = -254365.7087 E_bond = 4568.6683 E_angle = 3409.8838
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262344.2608
E_coul = 0.0000 E_long = 0.0000 Press = 29.3660
---------------- Step 400 ----- CPU = 17.5807 (sec) ----------------
---------------- Step 400 ----- CPU = 22.6113 (sec) ----------------
TotEng = -217955.7366 KinEng = 36340.4946 Temp = 303.7316
PotEng = -254296.2312 E_bond = 4621.0208 E_angle = 3512.1547
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262429.4067
E_coul = 0.0000 E_long = 0.0000 Press = 16.4419
---------------- Step 600 ----- CPU = 28.1043 (sec) ----------------
---------------- Step 600 ----- CPU = 34.0551 (sec) ----------------
TotEng = -218291.9151 KinEng = 36079.2122 Temp = 301.5478
PotEng = -254371.1273 E_bond = 4626.3494 E_angle = 3476.1668
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262473.6435
E_coul = 0.0000 E_long = 0.0000 Press = 14.0304
---------------- Step 800 ----- CPU = 40.5132 (sec) ----------------
---------------- Step 800 ----- CPU = 45.5316 (sec) ----------------
TotEng = -218539.5667 KinEng = 36042.0419 Temp = 301.2372
PotEng = -254581.6086 E_bond = 4563.0010 E_angle = 3616.1814
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262760.7910
E_coul = 0.0000 E_long = 0.0000 Press = -6.8312
---------------- Step 1000 ----- CPU = 52.8166 (sec) ----------------
---------------- Step 1000 ----- CPU = 56.9111 (sec) ----------------
TotEng = -217783.9370 KinEng = 36453.9620 Temp = 304.6800
PotEng = -254237.8990 E_bond = 4693.8725 E_angle = 3528.1925
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262459.9639
E_coul = 0.0000 E_long = 0.0000 Press = 0.0980
Loop time of 56.9112 on 1 procs for 1000 steps with 40140 atoms
Loop time of 52.8166 on 2 procs for 1000 steps with 40140 atoms
99.6% CPU use with 2 MPI tasks x 1 OpenMP threads
Performance: 8.179 ns/day 2.934 hours/ns 18.933 timesteps/s
Performance: 7.591 ns/day, 3.162 hours/ns, 17.571 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timings breakdown:
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 45.657 | 45.84 | 46.022 | 2.7 | 86.79
Bond | 0.98427 | 0.99283 | 1.0014 | 0.9 | 1.88
Neigh | 4.4454 | 4.4458 | 4.4462 | 0.0 | 8.42
Comm | 0.49872 | 0.6719 | 0.84508 | 21.1 | 1.27
Output | 0.00076818 | 0.00083113 | 0.00089407 | 0.2 | 0.00
Modify | 0.59218 | 0.59264 | 0.5931 | 0.1 | 1.12
Other | | 0.2731 | | | 0.52
Pair | 50.775 | 50.775 | 50.775 | 0.0 | 89.22
Bond | 0.88358 | 0.88358 | 0.88358 | 0.0 | 1.55
Neigh | 4.5176 | 4.5176 | 4.5176 | 0.0 | 7.94
Comm | 0.14942 | 0.14942 | 0.14942 | 0.0 | 0.26
Output | 0.00057101 | 0.00057101 | 0.00057101 | 0.0 | 0.00
Modify | 0.4728 | 0.4728 | 0.4728 | 0.0 | 0.83
Other | | 0.1127 | | | 0.20
Nlocal: 20070 ave 20109 max 20031 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 20234 ave 20281 max 20187 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 2.84584e+06 ave 2.85375e+06 max 2.83793e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nlocal: 40140 ave 40140 max 40140 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 25968 ave 25968 max 25968 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 5.69168e+06 ave 5.69168e+06 max 5.69168e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 5691680
Ave neighs/atom = 141.796
@ -113,3 +124,4 @@ Neighbor list builds = 38
Dangerous builds = 0
#write_restart pegc12e8-1.restart
Total wall time: 0:00:57

127
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LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# Solvated 5-mer peptide
units real
dimension 3
atom_style angle
# enforce that in z-direction there is only one
# processor (could be two) for optimal performance
processors * * 1
# read topology and force field
pair_style lj/sdk 15.0
bond_style harmonic
angle_style harmonic
special_bonds lj/coul 0.0 0.0 1.0
read_data data.pegc12e8.gz
orthogonal box = (-63.7 -63.7 -200) to (63.7 63.7 200)
2 by 2 by 1 MPI processor grid
reading atoms ...
40140 atoms
reading velocities ...
40140 velocities
scanning bonds ...
1 = max bonds/atom
scanning angles ...
1 = max angles/atom
reading bonds ...
13284 bonds
reading angles ...
12177 angles
2 = max # of 1-2 neighbors
2 = max # of 1-3 neighbors
4 = max # of special neighbors
neighbor 3.0 bin
neigh_modify delay 5
timestep 5.0
#dump 1 all xtc 200 pegc12e8-1.xtc
#dump_modify 1 unwrap yes
#dump 2 all dcd 200 pegc12e8-1.dcd unwrap
#dump_modify 2 unwrap yes
velocity all create 303.0 46659 mom yes rot yes dist gaussian
fix 1 all nvt temp 303.0 303.0 100.0
thermo_style multi
thermo 200
run 1000
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 18
ghost atom cutoff = 18
binsize = 9, bins = 15 15 45
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/sdk, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 15.87 | 15.87 | 15.87 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = -217990.7972 KinEng = 36252.9606 Temp = 303.0000
PotEng = -254243.7577 E_bond = 4468.5931 E_angle = 3410.1642
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262122.5151
E_coul = 0.0000 E_long = 0.0000 Press = 105.8245
---------------- Step 200 ----- CPU = 3.0107 (sec) ----------------
TotEng = -218203.1886 KinEng = 36162.5201 Temp = 302.2441
PotEng = -254365.7087 E_bond = 4568.6683 E_angle = 3409.8838
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262344.2608
E_coul = 0.0000 E_long = 0.0000 Press = 29.3660
---------------- Step 400 ----- CPU = 6.1324 (sec) ----------------
TotEng = -217955.7366 KinEng = 36340.4946 Temp = 303.7316
PotEng = -254296.2312 E_bond = 4621.0208 E_angle = 3512.1547
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262429.4067
E_coul = 0.0000 E_long = 0.0000 Press = 16.4419
---------------- Step 600 ----- CPU = 9.3443 (sec) ----------------
TotEng = -218291.9151 KinEng = 36079.2122 Temp = 301.5478
PotEng = -254371.1273 E_bond = 4626.3494 E_angle = 3476.1668
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262473.6435
E_coul = 0.0000 E_long = 0.0000 Press = 14.0304
---------------- Step 800 ----- CPU = 12.5388 (sec) ----------------
TotEng = -218539.5667 KinEng = 36042.0419 Temp = 301.2372
PotEng = -254581.6086 E_bond = 4563.0010 E_angle = 3616.1814
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262760.7910
E_coul = 0.0000 E_long = 0.0000 Press = -6.8312
---------------- Step 1000 ----- CPU = 15.7416 (sec) ----------------
TotEng = -217783.9370 KinEng = 36453.9620 Temp = 304.6800
PotEng = -254237.8990 E_bond = 4693.8725 E_angle = 3528.1925
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262459.9639
E_coul = 0.0000 E_long = 0.0000 Press = 0.0980
Loop time of 15.7417 on 4 procs for 1000 steps with 40140 atoms
Performance: 27.443 ns/day, 0.875 hours/ns, 63.525 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 | 13.591 | 13.612 | 13.626 | 0.4 | 86.47
Bond | 0.22508 | 0.23213 | 0.23791 | 1.0 | 1.47
Neigh | 1.2257 | 1.2261 | 1.2266 | 0.0 | 7.79
Comm | 0.39628 | 0.41769 | 0.44666 | 2.9 | 2.65
Output | 0.000247 | 0.00041109 | 0.00090098 | 0.0 | 0.00
Modify | 0.17674 | 0.17803 | 0.17952 | 0.2 | 1.13
Other | | 0.07576 | | | 0.48
Nlocal: 10035 ave 10098 max 10004 min
Histogram: 2 0 1 0 0 0 0 0 0 1
Nghost: 14546.5 ave 14564 max 14503 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Neighs: 1.42292e+06 ave 1.43408e+06 max 1.41615e+06 min
Histogram: 1 1 0 1 0 0 0 0 0 1
Total # of neighbors = 5691680
Ave neighs/atom = 141.796
Ave special neighs/atom = 1.26861
Neighbor list builds = 38
Dangerous builds = 0
#write_restart pegc12e8-1.restart
Total wall time: 0:00:15

145
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LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# coarse grained SDS surfactant monolayer
units real
dimension 3
atom_style full
processors * * 1
pair_style hybrid/overlay lj/sdk 15.0 coul/long 26.5
bond_style harmonic
angle_style sdk
special_bonds lj/coul 0.0 0.0 1.0
read_data data.sds.gz
orthogonal box = (-27.713 -27.713 -200) to (193.991 83.139 200)
1 by 1 by 1 MPI processor grid
reading atoms ...
31280 atoms
reading velocities ...
31280 velocities
scanning bonds ...
1 = max bonds/atom
scanning angles ...
1 = max angles/atom
reading bonds ...
4096 bonds
reading angles ...
3072 angles
2 = max # of 1-2 neighbors
2 = max # of 1-3 neighbors
4 = max # of special neighbors
pair_coeff 1 4 coul/long # SO4 SOD
pair_coeff 4 4 coul/long # SOD SOD
pair_coeff 1 1 lj/sdk lj9_6 0.7000 4.3210 # SO4 SO4
pair_coeff 1 2 lj/sdk lj9_6 0.3830 4.4135 # SO4 CM
pair_coeff 1 3 lj/sdk lj9_6 0.4050 4.4530 # SO4 CT
pair_coeff 1 4 lj/sdk lj12_4 1.1000 4.1000 # SO4 SOD
pair_coeff 1 5 lj/sdk lj12_4 1.1000 4.1000 # SO4 W
pair_coeff 2 2 lj/sdk lj9_6 0.4200 4.5060 # CM CM
pair_coeff 2 3 lj/sdk lj9_6 0.4440 4.5455 # CT CM
pair_coeff 2 4 lj/sdk lj12_4 0.3400 4.4385 # SOD CM
pair_coeff 2 5 lj/sdk lj12_4 0.3400 4.4385 # W CM
pair_coeff 3 3 lj/sdk lj9_6 0.4690 4.5850 # CT CT
pair_coeff 3 4 lj/sdk lj12_4 0.3600 4.4780 # SOD CT
pair_coeff 3 5 lj/sdk lj12_4 0.3600 4.4780 # W CT
pair_coeff 4 4 lj/sdk lj12_4 0.3500 4.3710 # SOD SOD
pair_coeff 4 5 lj/sdk lj12_4 0.8950 4.3710 # SOD W
pair_coeff 5 5 lj/sdk lj12_4 0.8950 4.3710 # W W
group charged type 1 4
2048 atoms in group charged
atom_modify first charged
kspace_style pppm/cg 0.00001
kspace_modify order 3
comm_modify mode multi
neighbor 2.0 multi
neigh_modify delay 4 every 2 check yes
timestep 10.0
fix 1 all nvt temp 310.0 310.0 100.0
thermo 10
run 100
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
G vector (1/distance) = 0.0416781
grid = 8 4 12
stencil order = 3
estimated absolute RMS force accuracy = 0.00248777
estimated relative force accuracy = 7.49185e-06
using double precision FFTs
3d grid and FFT values/proc = 1155 384
Neighbor list info ...
update every 2 steps, delay 4 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 28.5
ghost atom cutoff = 28.5
binsize = 8.5, bins = 27 14 48
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair lj/sdk, perpetual
attributes: half, newton on
pair build: half/multi/newton
stencil: half/multi/3d/newton
bin: standard
(2) pair coul/long, perpetual, skip from (1)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
PPPM/cg optimization cutoff: 1e-05
Total charged atoms: 6.5%
Min/max charged atoms/proc: 6.5% 6.5%
Per MPI rank memory allocation (min/avg/max) = 35.49 | 35.49 | 35.49 Mbytes
Step Temp E_pair E_mol TotEng Press
0 310.0934 -249339.72 2566.2036 -217861.41 -25.664516
10 310.88051 -249369.1 2549.1166 -217834.49 -29.095262
20 310.33025 -249325.09 2543.0138 -217847.89 -30.069751
30 308.24273 -249331.54 2604.3227 -217987.66 -28.033129
40 309.41339 -249363.5 2560.6727 -217954.13 -25.802838
50 309.16857 -249071.94 2571.9117 -217674.15 -17.946457
60 312.67237 -249288.77 2621.0185 -217515.19 -25.723545
70 310.13623 -249262.32 2595.874 -217750.35 -26.276067
80 310.60448 -249415.99 2596.6752 -217859.56 -27.942924
90 309.63209 -249403.14 2606.3186 -217927.73 -24.456575
100 309.40793 -249341.62 2599.6402 -217893.79 -22.554823
Loop time of 9.61984 on 1 procs for 100 steps with 31280 atoms
Performance: 8.981 ns/day, 2.672 hours/ns, 10.395 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 | 7.2928 | 7.2928 | 7.2928 | 0.0 | 75.81
Bond | 0.036198 | 0.036198 | 0.036198 | 0.0 | 0.38
Kspace | 0.053125 | 0.053125 | 0.053125 | 0.0 | 0.55
Neigh | 2.117 | 2.117 | 2.117 | 0.0 | 22.01
Comm | 0.029731 | 0.029731 | 0.029731 | 0.0 | 0.31
Output | 0.0014369 | 0.0014369 | 0.0014369 | 0.0 | 0.01
Modify | 0.079014 | 0.079014 | 0.079014 | 0.0 | 0.82
Other | | 0.01051 | | | 0.11
Nlocal: 31280 ave 31280 max 31280 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 16629 ave 16629 max 16629 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3.40168e+06 ave 3.40168e+06 max 3.40168e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3401676
Ave neighs/atom = 108.749
Ave special neighs/atom = 0.458312
Neighbor list builds = 10
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:10

50
examples/USER/cgsdk/sds-monolayer/log.sds-hybrid → examples/USER/cgsdk/sds-monolayer/log.27Nov18.sds-hybrid.g++.4
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@ -1,5 +1,4 @@
LAMMPS (20 Mar 2014-ICMS)
WARNING: OMP_NUM_THREADS environment is not set. (../comm.cpp:100)
LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# coarse grained SDS surfactant monolayer
@ -58,7 +57,7 @@ atom_modify first charged
kspace_style pppm/cg 0.00001
kspace_modify order 3
communicate multi
comm_modify mode multi
neighbor 2.0 multi
neigh_modify delay 4 every 2 check yes
@ -70,6 +69,7 @@ thermo 10
run 100
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
G vector (1/distance) = 0.0416781
grid = 8 4 12
stencil order = 3
@ -77,10 +77,27 @@ PPPM initialization ...
estimated relative force accuracy = 7.49185e-06
using double precision FFTs
3d grid and FFT values/proc = 525 96
Neighbor list info ...
update every 2 steps, delay 4 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 28.5
ghost atom cutoff = 28.5
binsize = 8.5, bins = 27 14 48
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair lj/sdk, perpetual
attributes: half, newton on
pair build: half/multi/newton
stencil: half/multi/3d/newton
bin: standard
(2) pair coul/long, perpetual, skip from (1)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
PPPM/cg optimization cutoff: 1e-05
Total charged atoms: 6.5%
Min/max charged atoms/proc: 6.4% 6.7%
Memory usage per processor = 7.66668 Mbytes
Per MPI rank memory allocation (min/avg/max) = 17.48 | 17.48 | 17.48 Mbytes
Step Temp E_pair E_mol TotEng Press
0 310.0934 -249339.72 2566.2036 -217861.41 -25.664516
10 310.88051 -249369.1 2549.1166 -217834.49 -29.095262
@ -93,22 +110,22 @@ Step Temp E_pair E_mol TotEng Press
80 310.60448 -249415.99 2596.6752 -217859.56 -27.942924
90 309.63209 -249403.14 2606.3186 -217927.73 -24.456575
100 309.40793 -249341.62 2599.6402 -217893.79 -22.554823
Loop time of 2.54454 on 4 procs for 100 steps with 31280 atoms
Loop time of 4.07239 on 4 procs for 100 steps with 31280 atoms
98.6% CPU use with 4 MPI tasks x 1 OpenMP threads
Performance: 21.216 ns/day 1.131 hours/ns 24.556 timesteps/s
Performance: 33.955 ns/day, 0.707 hours/ns, 39.300 timesteps/s
98.9% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timings breakdown:
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.082 | 3.0928 | 3.1091 | 0.6 | 75.95
Bond | 0.021077 | 0.021421 | 0.021823 | 0.2 | 0.53
Kspace | 0.042646 | 0.058859 | 0.069797 | 4.1 | 1.45
Neigh | 0.79689 | 0.79696 | 0.79711 | 0.0 | 19.57
Comm | 0.048668 | 0.049552 | 0.050446 | 0.3 | 1.22
Output | 0.00072145 | 0.00095147 | 0.0016341 | 1.3 | 0.02
Modify | 0.034767 | 0.035175 | 0.035714 | 0.2 | 0.86
Other | | 0.01665 | | | 0.41
Pair | 1.8639 | 1.8913 | 1.9283 | 1.8 | 74.33
Bond | 0.0092797 | 0.0094567 | 0.0095828 | 0.1 | 0.37
Kspace | 0.018389 | 0.056616 | 0.084424 | 10.7 | 2.23
Neigh | 0.53553 | 0.53569 | 0.53605 | 0.0 | 21.05
Comm | 0.023819 | 0.02433 | 0.02506 | 0.3 | 0.96
Output | 0.00058866 | 0.00084978 | 0.0016243 | 0.0 | 0.03
Modify | 0.021841 | 0.022059 | 0.022308 | 0.1 | 0.87
Other | | 0.004233 | | | 0.17
Nlocal: 7820 ave 7866 max 7774 min
Histogram: 1 1 0 0 0 0 0 0 1 1
@ -125,3 +142,4 @@ Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:02

129
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LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# coarse grained SDS surfactant monolayer
units real
dimension 3
atom_style full
processors * * 1
pair_style lj/sdk/coul/long 15.0
bond_style harmonic
angle_style sdk
special_bonds lj/coul 0.0 0.0 1.0
read_data data.sds.gz
orthogonal box = (-27.713 -27.713 -200) to (193.991 83.139 200)
1 by 1 by 1 MPI processor grid
reading atoms ...
31280 atoms
reading velocities ...
31280 velocities
scanning bonds ...
1 = max bonds/atom
scanning angles ...
1 = max angles/atom
reading bonds ...
4096 bonds
reading angles ...
3072 angles
2 = max # of 1-2 neighbors
2 = max # of 1-3 neighbors
4 = max # of special neighbors
pair_coeff 1 1 lj9_6 0.7000 4.3210 # SO4 SO4
pair_coeff 1 2 lj9_6 0.3830 4.4135 # SO4 CM
pair_coeff 1 3 lj9_6 0.4050 4.4530 # SO4 CT
pair_coeff 1 4 lj12_4 1.1000 4.1000 # SO4 SOD
pair_coeff 1 5 lj12_4 1.1000 4.1000 # SO4 W
pair_coeff 2 2 lj9_6 0.4200 4.5060 # CM CM
pair_coeff 2 3 lj9_6 0.4440 4.5455 # CT CM
pair_coeff 2 4 lj12_4 0.3400 4.4385 # SOD CM
pair_coeff 2 5 lj12_4 0.3400 4.4385 # W CM
pair_coeff 3 3 lj9_6 0.4690 4.5850 # CT CT
pair_coeff 3 4 lj12_4 0.3600 4.4780 # SOD CT
pair_coeff 3 5 lj12_4 0.3600 4.4780 # W CT
pair_coeff 4 4 lj12_4 0.3500 4.3710 # SOD SOD
pair_coeff 4 5 lj12_4 0.8950 4.3710 # SOD W
pair_coeff 5 5 lj12_4 0.8950 4.3710 # W W
kspace_style pppm/cg 0.00001
kspace_modify order 3
neighbor 2.0 bin
neigh_modify delay 4 every 2 check yes
timestep 10.0
fix 1 all nvt temp 310.0 310.0 100.0
thermo 10
run 100
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
G vector (1/distance) = 0.0789325
grid = 15 8 25
stencil order = 3
estimated absolute RMS force accuracy = 0.00275556
estimated relative force accuracy = 8.29828e-06
using double precision FFTs
3d grid and FFT values/proc = 5544 3000
Neighbor list info ...
update every 2 steps, delay 4 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 17
ghost atom cutoff = 17
binsize = 8.5, bins = 27 14 48
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/sdk/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
PPPM/cg optimization cutoff: 1e-05
Total charged atoms: 6.5%
Min/max charged atoms/proc: 6.5% 6.5%
Per MPI rank memory allocation (min/avg/max) = 35.36 | 35.36 | 35.36 Mbytes
Step Temp E_pair E_mol TotEng Press
0 310.0934 -247030.21 2566.2036 -215551.9 -14.547393
10 310.89138 -247061.61 2549.4854 -215525.62 -18.043512
20 310.29287 -247017.8 2542.4491 -215544.65 -19.148631
30 308.13371 -247024.82 2602.1061 -215693.32 -17.390902
40 309.40426 -247058.41 2558.7402 -215651.82 -15.445066
50 309.11317 -246753.92 2570.8603 -215362.36 -7.4232007
60 312.52974 -246964.73 2618.8108 -215206.66 -15.23965
70 310.11675 -246941.68 2591.8668 -215435.53 -16.153691
80 310.48262 -247090.02 2595.0493 -215546.58 -18.080368
90 309.60017 -247067.1 2604.6545 -215596.33 -14.583764
100 309.7356 -247004.05 2604.8729 -215520.43 -12.78624
Loop time of 9.23618 on 1 procs for 100 steps with 31280 atoms
Performance: 9.355 ns/day, 2.566 hours/ns, 10.827 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 7.7363 | 7.7363 | 7.7363 | 0.0 | 83.76
Bond | 0.032901 | 0.032901 | 0.032901 | 0.0 | 0.36
Kspace | 0.078907 | 0.078907 | 0.078907 | 0.0 | 0.85
Neigh | 1.2706 | 1.2706 | 1.2706 | 0.0 | 13.76
Comm | 0.026005 | 0.026005 | 0.026005 | 0.0 | 0.28
Output | 0.0014131 | 0.0014131 | 0.0014131 | 0.0 | 0.02
Modify | 0.079446 | 0.079446 | 0.079446 | 0.0 | 0.86
Other | | 0.01055 | | | 0.11
Nlocal: 31280 ave 31280 max 31280 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 15812 ave 15812 max 15812 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3.3521e+06 ave 3.3521e+06 max 3.3521e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3352103
Ave neighs/atom = 107.164
Ave special neighs/atom = 0.458312
Neighbor list builds = 10
Dangerous builds = 0
Total wall time: 0:00:09

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