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new MESSAGE package for client/server/coupling

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This commit is contained in:
Steven J. Plimpton
2018-07-23 15:58:33 -06:00
parent 5c21d2aff9
commit 2f55981224
97 changed files with 8885 additions and 104 deletions
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3
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 +34,11 @@ 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 Monte Carlo with LAMMPS MD
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 LAMMPS MD with VASP quantum DFT
library collection of useful inter-code communication routines
fortran a simple wrapper on the LAMMPS library API that
can be called from Fortran

34
examples/COUPLE/lammps_mc/Makefile Normal file
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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)
# this line if built the CSlib within lib/message with ZMQ support
# note this is using the serial (no-mpi) version of the CSlib
$(LINK) $(LINKFLAGS) $(OBJ) -lcsnompi -lzmq -o mc
# this line if built the CSlib without ZMQ support
# $(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 and the MC client code
First, build LAMMPS with its MESSAGE package installed:
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.
Next build the MC client code:
First edit the Makefile in this dir. The CSLIB variable should be the
path to where the LAMMPS lib/message dir is on your system. If you
built the CSlib without ZMQ support you will also need to
comment/uncomment two lines. 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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examples/COUPLE/lammps_mc/in.mc Normal file
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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.23Jul18.file.g++.1 Normal file
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LAMMPS (16 Jul 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 = 0.000633001 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 2.14577e-06 on 1 procs for 0 steps with 500 atoms
46.6% 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 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
314.6% 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
314.6% 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: 0:00:02

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LAMMPS (16 Jul 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 = 0.000604868 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 3.09944e-06 on 4 procs for 0 steps with 500 atoms
72.6% 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 | | 3.099e-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 3.33786e-06 on 4 procs for 0 steps with 500 atoms
119.8% 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 | | 3.338e-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 3.51667e-06 on 4 procs for 0 steps with 500 atoms
113.7% 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 | | 3.517e-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 2.92063e-06 on 4 procs for 0 steps with 500 atoms
119.8% 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 | | 2.921e-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 3.39746e-06 on 4 procs for 0 steps with 500 atoms
117.7% 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 | | 3.397e-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 3.39746e-06 on 4 procs for 0 steps with 500 atoms
117.7% 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 | | 3.397e-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
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LAMMPS (16 Jul 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 = 0.000612974 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
46.6% 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 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: 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 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: 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 0 on 1 procs for 0 steps with 500 atoms
0.0% 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 | | 0 | | | 0.00
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 0 on 1 procs for 0 steps with 500 atoms
0.0% 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 | | 0 | | | 0.00
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.23Jul18.zmq.g++.4 Normal file
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LAMMPS (16 Jul 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 = 0.000566006 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 4.29153e-06 on 4 procs for 0 steps with 500 atoms
99.0% 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 | | 4.292e-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 3.57628e-06 on 4 procs for 0 steps with 500 atoms
97.9% 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 | | 3.576e-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 3.09944e-06 on 4 procs for 0 steps with 500 atoms
121.0% 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 | | 3.099e-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 2.14577e-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 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 1.90735e-06 on 4 procs for 0 steps with 500 atoms
157.3% 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 | | 1.907e-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
151.5% 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 | | 2.146e-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

261
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 <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "cslib.h"
using namespace CSLIB_NS;
#include "mc.h"
#include "random_park.h"
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, CSlib *cs_caller)
{
cs = 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};
// 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 *, class CSlib *);
~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;
class CSlib *cs; // 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_warp.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:
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.
----------------
To run in client/server mode:
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
--------------
The provided data.W file (for LAMMPS) and POSCAR_W file (for VASP) are
for a simple 2-atom unit cell of bcc tungsten (W). You could
replicate this with LAMMPS to create a larger system. The
vasp_wrap.py script needs to be generalized to create an appropriate
POSCAR_W file for a larger box.
VASP input file include the sample INCAR and KPOINTS files provided.
A POTCAR file is also needed, which should come from your VASP package
installation.

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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 (20 Apr 2018)
# small W unit cell for use with VASP
#message client aimd file tmp.couple
message client aimd zmq localhost:5555
#message client aimd mpi/two tmp.couple
#message client aimd mpi/one tmp.couple
units real
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 1 MPI processor grid
reading atoms ...
2 atoms
mass 1 1.0
#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 message/aimd
fix_modify 2 energy yes
thermo 1
run 2
Per MPI rank memory allocation (min/avg/max) = 1.8 | 1.8 | 1.8 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 0 0 -48.069571 -172694.2
1 0.063865861 0 0 -48.069381 -172693.93
2 0.25546344 0 0 -48.06881 -172693.1
Loop time of 0.281842 on 1 procs for 2 steps with 2 atoms
Performance: 0.613 ns/day, 39.145 hours/ns, 7.096 timesteps/s
0.0% 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 | 3.0994e-06 | 3.0994e-06 | 3.0994e-06 | 0.0 | 0.00
Output | 8.9169e-05 | 8.9169e-05 | 8.9169e-05 | 0.0 | 0.03
Modify | 0.28174 | 0.28174 | 0.28174 | 0.0 | 99.97
Other | | 5.96e-06 | | | 0.00
Nlocal: 2 ave 2 max 2 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 7 ave 7 max 7 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 0
Dangerous builds not checked
Total wall time: 0:00:06

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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, virial to client
# NOTES:
# check to insure basic VASP input files are in place?
# worry about archiving VASP input/output in special filenames or dirs?
# how to get ordering (by type) of VASP atoms vs LAMMPS atoms
# create one initial permutation vector?
# could make syntax for launching VASP more flexible
# e.g. command-line arg for # of procs
import sys
import commands
import xml.etree.ElementTree as ET
from cslib import CSlib
vaspcmd = "srun -N 1 --ntasks-per-node=4 " + \
"-n 4 /projects/vasp/2017-build/cts1/vasp5.4.4/vasp_tfermi/bin/vasp_std"
# enums matching FixClientMD class in LAMMPS
SETUP,STEP = range(1,2+1)
UNITS,DIM,NATOMS,NTYPES,BOXLO,BOXHI,BOXTILT,TYPES,COORDS,CHARGE = range(1,10+1)
FORCES,ENERGY,VIRIAL = range(1,3+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
print >>psnew,psold[0],
print >>psnew,psold[1],
print >>psnew,"%g 0.0 0.0" % box[0]
print >>psnew,"0.0 %g 0.0" % box[1]
print >>psnew,"0.0 0.0 %g" % box[2]
print >>psnew,psold[5],
print >>psnew,psold[6],
# per-atom coords
# grouped by types
print >>psnew,"Cartesian"
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" % (x,y,z)
print >>psnew,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]
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
# could generalize this to be more like ServerMD class
# allow for box size, atom types, natoms, etc
# unpack coords from client
# create VASP input
# NOTE: generalize this for general list of atom types
coords = cs.unpack(COORDS,1)
#types = cs.unpack(2);
types = 2*[1]
poscar_write(poscar_template,natoms,ntypes,types,coords,box)
# invoke VASP
print "Launching VASP ..."
print vaspcmd
out = commands.getoutput(vaspcmd)
print out
# process VASP output
energy,forces,virial = vasprun_read()
# return forces, energy, virial 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