Pulled develop. Solved false_positives.txt bond.cpp and bond.h files conflict.
This commit is contained in:
Germain Clavier
@ -9,6 +9,11 @@ model a realistic problem.
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In many of the examples included here, LAMMPS must first be built as a
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library.
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Also see the Howto_mdi doc page in the LAMMPS manual for a description
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of how LAMMPS can be coupled to other codes in a client/server fashion
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using the MDI Library created by the MolSSI consortium. The MDI
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package in LAMMPS has support for this style of code coupling.
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See these sections of the LAMMPS manual for details:
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Build LAMMPS as a library (doc/html/Build_basics.html)
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@ -28,15 +33,9 @@ These are the sub-directories included in this directory:
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simple simple example of driver code calling LAMMPS as a lib
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multiple example of driver code calling multiple instances of LAMMPS
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plugin example for loading LAMMPS at runtime from a shared library
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lammps_mc client/server coupling of Monte Carlo client
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with LAMMPS server for energy evaluation
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lammps_nwchem client/server coupling of LAMMPS client with
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NWChem quantum DFT as server for quantum forces
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lammps_quest MD with quantum forces, coupling to Quest DFT code
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lammps_spparks grain-growth Monte Carlo with strain via MD,
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coupling to SPPARKS kinetic MC code
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lammps_vasp client/server coupling of LAMMPS client with
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VASP quantum DFT as server for quantum forces
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library collection of useful inter-code communication routines
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fortran a simple wrapper on the LAMMPS library API that
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can be called from Fortran
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@ -1,33 +0,0 @@
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# Makefile for MC
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SHELL = /bin/sh
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SRC = mc.cpp random_park.cpp
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OBJ = $(SRC:.cpp=.o)
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# change this line for your machine to path for CSlib src dir
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CSLIB = /home/sjplimp/lammps/lib/message/cslib/src
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# compiler/linker settings
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CC = g++
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CCFLAGS = -g -O3 -I$(CSLIB)
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LINK = g++
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LINKFLAGS = -g -O -L$(CSLIB)
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# targets
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mc: $(OBJ)
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# first line if built the CSlib within lib/message with ZMQ support
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# second line if built the CSlib without ZMQ support
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$(LINK) $(LINKFLAGS) $(OBJ) -lcsnompi -lzmq -o mc
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# $(LINK) $(LINKFLAGS) $(OBJ) -lcsnompi -o mc
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clean:
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@rm -f *.o mc
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# rules
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%.o:%.cpp
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$(CC) $(CCFLAGS) -c $<
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@ -1,128 +0,0 @@
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Sample Monte Carlo (MC) wrapper on LAMMPS via client/server coupling
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See the MESSAGE package documentation Build_extras.html#message
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and Build_extras.html#message for more details on how client/server
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coupling works in LAMMPS.
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In this dir, the mc.cpp/h files are a standalone "client" MC code. It
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should be run on a single processor, though it could become a parallel
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program at some point. LAMMPS is also run as a standalone executable
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as a "server" on as many processors as desired using its "server mc"
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command; see it's doc page for details.
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Messages are exchanged between MC and LAMMPS via a client/server
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library (CSlib), which is included in the LAMMPS distribution in
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lib/message. As explained below you can choose to exchange data
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between the two programs either via files or sockets (ZMQ). If the MC
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program became parallel, data could also be exchanged via MPI.
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The MC code makes simple MC moves, by displacing a single random atom
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by a small random amount. It uses LAMMPS to calculate the energy
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change, and to run dynamics between MC moves.
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----------------
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Build LAMMPS with its MESSAGE package installed:
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See the Build extras doc page and its MESSAGE package
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section for details.
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CMake:
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-D PKG_MESSAGE=yes # include the MESSAGE package
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-D MESSAGE_ZMQ=value # build with ZeroMQ support, value = no (default) or yes
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Traditional make:
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% cd lammps/lib/message
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% python Install.py -m -z # build CSlib with MPI and ZMQ support
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% cd lammps/src
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% make yes-message
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% make mpi
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You can leave off the -z if you do not have ZMQ on your system.
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----------------
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Build the MC client code
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The source files for the MC code are in this dir. It links with the
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CSlib library in lib/message/cslib.
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You must first build the CSlib in serial mode, e.g.
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% cd lammps/lib/message/cslib/src
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% make lib # build serial and parallel lib with ZMQ support
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% make lib zmq=no # build serial and parallel lib without ZMQ support
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Then edit the Makefile in this dir. The CSLIB variable should be the
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path to where the LAMMPS lib/message/cslib/src dir is on your system.
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If you built the CSlib without ZMQ support you will also need to
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comment/uncomment one line. Then you can just type
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% make
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and you should get an "mc" executable.
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----------------
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To run in client/server mode:
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Both the client (MC) and server (LAMMPS) must use the same messaging
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mode, namely file or zmq. This is an argument to the MC code; it can
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be selected by setting the "mode" variable when you run LAMMPS. The
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default mode = file.
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Here we assume LAMMPS was built to run in parallel, and the MESSAGE
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package was installed with socket (ZMQ) support. This means either of
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the messaging modes can be used and LAMMPS can be run in serial or
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parallel. The MC code is always run in serial.
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When you run, the server should print out thermodynamic info
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for every MD run it performs (between MC moves). The client
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will print nothing until the simulation ends, then it will
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print stats about the accepted MC moves.
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The examples below are commands you should use in two different
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terminal windows. The order of the two commands (client or server
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launch) does not matter. You can run them both in the same window if
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you append a "&" character to the first one to run it in the
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background.
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--------------
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File mode of messaging:
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% mpirun -np 1 mc in.mc file tmp.couple
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% mpirun -np 1 lmp_mpi -v mode file -in in.mc.server
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% mpirun -np 1 mc in.mc file tmp.couple
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% mpirun -np 4 lmp_mpi -v mode file -in in.mc.server
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ZMQ mode of messaging:
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% mpirun -np 1 mc in.mc zmq localhost:5555
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% mpirun -np 1 lmp_mpi -v mode zmq -in in.mc.server
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% mpirun -np 1 mc in.mc zmq localhost:5555
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% mpirun -np 4 lmp_mpi -v mode zmq -in in.mc.server
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--------------
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The input script for the MC program is in.mc. You can edit it to run
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longer simulations.
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500 nsteps = total # of steps of MD
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100 ndynamics = # of MD steps between MC moves
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0.1 delta = displacement size of MC move
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1.0 temperature = used in MC Boltzman factor
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12345 seed = random number seed
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--------------
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The problem size that LAMMPS is computing the MC energy for and
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running dynamics on is set by the x,y,z variables in the LAMMPS
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in.mc.server script. The default size is 500 particles. You can
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adjust the size as follows:
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lmp_mpi -v x 10 -v y 10 -v z 20 # 8000 particles
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@ -1,7 +0,0 @@
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# MC params
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500 nsteps
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100 ndynamics
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0.1 delta
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1.0 temperature
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12345 seed
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@ -1,36 +0,0 @@
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# 3d Lennard-Jones Monte Carlo server script
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variable mode index file
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if "${mode} == file" then &
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"message server mc file tmp.couple" &
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elif "${mode} == zmq" &
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"message server mc zmq *:5555" &
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variable x index 5
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variable y index 5
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variable z index 5
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units lj
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atom_style atomic
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atom_modify map yes
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lattice fcc 0.8442
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region box block 0 $x 0 $y 0 $z
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create_box 1 box
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create_atoms 1 box
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mass 1 1.0
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pair_style lj/cut 2.5
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pair_coeff 1 1 1.0 1.0 2.5
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neighbor 0.3 bin
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neigh_modify delay 0 every 20 check no
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velocity all create 1.44 87287 loop geom
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fix 1 all nve
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thermo 50
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server mc
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@ -1,254 +0,0 @@
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LAMMPS (22 Aug 2018)
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# 3d Lennard-Jones Monte Carlo server script
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variable mode index file
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if "${mode} == file" then "message server mc file tmp.couple" elif "${mode} == zmq" "message server mc zmq *:5555"
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message server mc file tmp.couple
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variable x index 5
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variable y index 5
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variable z index 5
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units lj
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atom_style atomic
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atom_modify map yes
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lattice fcc 0.8442
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Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
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region box block 0 $x 0 $y 0 $z
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region box block 0 5 0 $y 0 $z
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region box block 0 5 0 5 0 $z
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region box block 0 5 0 5 0 5
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create_box 1 box
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Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798)
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1 by 1 by 1 MPI processor grid
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create_atoms 1 box
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Created 500 atoms
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Time spent = 0.000649929 secs
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mass 1 1.0
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pair_style lj/cut 2.5
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pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
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neighbor 0.3 bin
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neigh_modify delay 0 every 20 check no
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|
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velocity all create 1.44 87287 loop geom
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||||
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fix 1 all nve
|
||||
|
||||
thermo 50
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|
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server mc
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||||
run 0
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||||
Neighbor list info ...
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||||
update every 20 steps, delay 0 steps, check no
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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
|
||||
@ -1,254 +0,0 @@
|
||||
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
|
||||
@ -1,254 +0,0 @@
|
||||
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
|
||||
@ -1,254 +0,0 @@
|
||||
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
|
||||
@ -1,263 +0,0 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/, 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;
|
||||
}
|
||||
@ -1,40 +0,0 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/ 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
|
||||
@ -1,72 +0,0 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/, 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;
|
||||
}
|
||||
@ -1,28 +0,0 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/ 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
|
||||
@ -1,197 +0,0 @@
|
||||
Sample LAMMPS MD wrapper on NWChem via client/server coupling
|
||||
|
||||
See the MESSAGE package documentation Build_extras.html#message
|
||||
and Build_extras.html#message for more details on how client/server
|
||||
coupling works in LAMMPS.
|
||||
|
||||
In this dir, the nwchem_wrap.py is a wrapper on the NWChem electronic
|
||||
structure 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 NWChem a current set of coordinates each timestep,
|
||||
NWChem computes forces and energy (and virial) and returns that info
|
||||
to LAMMPS.
|
||||
|
||||
Messages are exchanged between NWChem 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
|
||||
nwchem_wrap.py program became parallel, or the CSlib library calls were
|
||||
integrated into NWChem directly, then data could also be exchanged via
|
||||
MPI.
|
||||
|
||||
There are 2 examples provided in the planeware and ao_basis
|
||||
sub-directories. See details below.
|
||||
|
||||
----------------
|
||||
|
||||
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 nwchem_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 nwchem_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 NWChem and the nwchem_wrap.py script
|
||||
|
||||
You can run the nwchem_wrap.py script as-is to test that the coupling
|
||||
between it and LAMMPS is functional. This will use the included
|
||||
nwchem_lammps.out files output by a previous NWChem run.
|
||||
|
||||
But note that the as-is version of nwchem_wrap.py will not attempt to
|
||||
run NWChem.
|
||||
|
||||
To do this, you must edit the 1st nwchemcmd line at the top of
|
||||
nwchem_wrapper.py to be the launch command needed to run NWChem on
|
||||
your system. It can be a command to run NWChem in serial or in
|
||||
parallel, e.g. an mpirun command. Then comment out the 2nd nwchemcmd
|
||||
line immediately following it.
|
||||
|
||||
Ensure you have the necessary NWChem input file in this directory,
|
||||
suitable for the NWChem calculation you want to perform.
|
||||
|
||||
Example input files are provided for both atom-centered AO basis sets
|
||||
and plane-wave basis sets. Note that the NWChem template file should
|
||||
be matched to the LAMMPS input script (# of atoms and atom types, box
|
||||
size, etc).
|
||||
|
||||
Once you run NWChem yourself, the nwchem_lammps.out file will be
|
||||
overwritten.
|
||||
|
||||
The syntax of the wrapper is:
|
||||
nwchem_wrap.py file/zmq ao/pw input_template
|
||||
* file/zmg = messaging mode, must match LAMMPS messaging mode
|
||||
* ao/pw = basis set mode, selects between atom-centered and plane-wave
|
||||
the input_template file must correspond to the appropriate basis set mode:
|
||||
the "ao" mode supports the scf and dft modules in NWChem,
|
||||
the "pw" mode supports the nwpw module.
|
||||
* input_template = NWChem input file used as template, must include a
|
||||
"geometry" block with the atoms in the simulation, dummy
|
||||
xyz coordinates should be included (but are not used).
|
||||
Atom ordering must match LAMMPS input.
|
||||
|
||||
During a simulation, the molecular orbitals from the previous timestep
|
||||
will be used as the initial guess for the next NWChem calculation. If
|
||||
a file named "nwchem_lammps.movecs" is in the directory the wrapper is
|
||||
called from, these orbitals will be used as the initial guess orbitals
|
||||
in the first step of the simulation.
|
||||
|
||||
----------------
|
||||
|
||||
Example directories
|
||||
|
||||
(1) planewave
|
||||
|
||||
Demonstrates coupling of the nwpw module in NWChem with LAMMPS. Only fully
|
||||
periodic boundary conditions and orthogonal simulation boxes are currently
|
||||
supported by the wrapper. The included files provide an example run using a
|
||||
2 atom unit cell of tungsten.
|
||||
|
||||
Files:
|
||||
* data.W LAMMPS input with geometry information
|
||||
* in.client.W LAMMPS simulation input
|
||||
* log.client.output LAMMPS simulation output
|
||||
* w.nw NWChem template input file
|
||||
* nwchem_lammps.out NWChem output
|
||||
|
||||
(2) ao_basis
|
||||
|
||||
Demonstrates coupling of the scf (or dft) modules in NWChem with
|
||||
LAMMPS. Only fully aperiodic boundary conditions are currently
|
||||
supported by the wrapper. The included files provide an example run
|
||||
using a single water molecule.
|
||||
|
||||
Files:
|
||||
* data.h2o LAMMPS input with geometry information
|
||||
* in.client.h2o LAMMPS simulation input
|
||||
* log.client.output LAMMPS simulation output
|
||||
* h2o.nw NWChem template input file
|
||||
* nwchem_lammps.out NWChem output
|
||||
|
||||
As noted above, you can run the nwchem_wrap.py script as-is to test that
|
||||
the coupling between it and LAMMPS is functional. This will use the included
|
||||
nwchem_lammps.out files.
|
||||
|
||||
----------------
|
||||
|
||||
To run in client/server mode:
|
||||
|
||||
NOTE: The nwchem_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 (nwchem_wrap.py) must use the same
|
||||
messaging mode, namely file or zmq. This is an argument to the
|
||||
nwchem_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 nwchem_wrap.py code is always run in serial, but it
|
||||
launches NWChem from Python via an mpirun command which can run NWChem
|
||||
itself in parallel.
|
||||
|
||||
When you run, the server should print out thermodynamic info every
|
||||
timestep which corresponds to the forces and virial computed by NWChem.
|
||||
NWChem will also generate output files each timestep. Output files from
|
||||
previous timesteps are archived in a "nwchem_logs" directory.
|
||||
|
||||
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 in.client.W
|
||||
% python nwchem_wrap.py file pw w.nw
|
||||
|
||||
% mpirun -np 2 lmp_mpi -v mode file -in in.client.h2o
|
||||
% python nwchem_wrap.py file ao h2o.nw
|
||||
|
||||
ZMQ mode of messaging:
|
||||
|
||||
% mpirun -np 1 lmp_mpi -v mode zmq -in in.client.W
|
||||
% python nwchem_wrap.py zmq pw w.nw
|
||||
|
||||
% mpirun -np 2 lmp_mpi -v mode zmq -in in.client.h2o
|
||||
% python nwchem_wrap.py zmq ao h2o.nw
|
||||
@ -1,20 +0,0 @@
|
||||
LAMMPS H2O data file
|
||||
|
||||
3 atoms
|
||||
|
||||
2 atom types
|
||||
|
||||
-10.0 10.0 xlo xhi
|
||||
-10.0 10.0 ylo yhi
|
||||
-10.0 10.0 zlo zhi
|
||||
|
||||
Masses
|
||||
|
||||
1 15.994915008544922
|
||||
2 1.0078250169754028
|
||||
|
||||
Atoms
|
||||
|
||||
1 1 0.0 0.0 0.0
|
||||
2 2 0.0 0.756723 -0.585799
|
||||
3 2 0.0 -0.756723 -0.585799
|
||||
@ -1,25 +0,0 @@
|
||||
echo
|
||||
|
||||
memory global 40 mb stack 23 mb heap 5 mb
|
||||
|
||||
geometry units angstrom noautosym
|
||||
O 0.0 0.0 0.0
|
||||
H 1.0 0.5 0.0
|
||||
H -1.0 0.5 0.0
|
||||
end
|
||||
|
||||
basis
|
||||
O library 6-31g*
|
||||
H library 6-31g*
|
||||
end
|
||||
|
||||
scf
|
||||
maxiter 100
|
||||
end
|
||||
|
||||
#dft
|
||||
# xc b3lyp
|
||||
#end
|
||||
|
||||
task scf gradient
|
||||
#task dft gradient
|
||||
@ -1,27 +0,0 @@
|
||||
# H2O with NWChem
|
||||
|
||||
variable mode index file
|
||||
|
||||
if "${mode} == file" then &
|
||||
"message client md file tmp.couple" &
|
||||
elif "${mode} == zmq" &
|
||||
"message client md zmq localhost:5555" &
|
||||
|
||||
units metal
|
||||
atom_style atomic
|
||||
atom_modify sort 0 0.0 map yes
|
||||
|
||||
boundary m m m
|
||||
read_data data.h2o
|
||||
|
||||
velocity all create 300.0 87287 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 10 check no
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all client/md
|
||||
fix_modify 2 energy yes
|
||||
|
||||
thermo 1
|
||||
run 3
|
||||
@ -1,30 +0,0 @@
|
||||
# H2O with NWChem
|
||||
|
||||
variable mode index file
|
||||
|
||||
if "${mode} == file" then &
|
||||
"message client md file tmp.couple" &
|
||||
elif "${mode} == zmq" &
|
||||
"message client md zmq localhost:5555" &
|
||||
|
||||
units metal
|
||||
atom_style atomic
|
||||
atom_modify sort 0 0.0 map yes
|
||||
|
||||
boundary m m m
|
||||
read_data data.h2o
|
||||
|
||||
group one id 2
|
||||
displace_atoms one move 0.1 0.2 0.3
|
||||
|
||||
velocity all create 300.0 87287 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 10 check no
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all client/md
|
||||
fix_modify 2 energy yes
|
||||
|
||||
thermo 1
|
||||
minimize 1.0e-6 1.0e-6 10 50
|
||||
@ -1,66 +0,0 @@
|
||||
LAMMPS (19 Sep 2019)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# H2O with NWChem
|
||||
|
||||
variable mode index file
|
||||
|
||||
if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555"
|
||||
message client md file tmp.couple
|
||||
units metal
|
||||
atom_style atomic
|
||||
atom_modify sort 0 0.0 map yes
|
||||
|
||||
boundary m m m
|
||||
read_data data.h2o
|
||||
orthogonal box = (-10 -10 -10) to (10 10 10)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
3 atoms
|
||||
read_data CPU = 0.000627125 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
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:166)
|
||||
Per MPI rank memory allocation (min/avg/max) = 0.0276 | 0.0276 | 0.0276 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
0 300 0 0 0.077556087 10.354878 8000
|
||||
1 300 0 0 0.077556087 10.354878 8000
|
||||
2 300 0 0 0.077556087 10.354878 8000
|
||||
3 300 0 0 0.077556087 10.354878 8000
|
||||
Loop time of 0.30198 on 1 procs for 3 steps with 3 atoms
|
||||
|
||||
Performance: 0.858 ns/day, 27.961 hours/ns, 9.934 timesteps/s
|
||||
0.0% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 2.5979e-06 | 2.5979e-06 | 2.5979e-06 | 0.0 | 0.00
|
||||
Output | 0.00012053 | 0.00012053 | 0.00012053 | 0.0 | 0.04
|
||||
Modify | 0.30185 | 0.30185 | 0.30185 | 0.0 | 99.96
|
||||
Other | | 8.211e-06 | | | 0.00
|
||||
|
||||
Nlocal: 3 ave 3 max 3 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds not checked
|
||||
Total wall time: 0:00:07
|
||||
@ -1,66 +0,0 @@
|
||||
LAMMPS (19 Sep 2019)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# H2O with NWChem
|
||||
|
||||
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 file tmp.couple
|
||||
units metal
|
||||
atom_style atomic
|
||||
atom_modify sort 0 0.0 map yes
|
||||
|
||||
boundary m m m
|
||||
read_data data.h2o
|
||||
orthogonal box = (-10 -10 -10) to (10 10 10)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
3 atoms
|
||||
read_data CPU = 0.000608759 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
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:166)
|
||||
Per MPI rank memory allocation (min/avg/max) = 0.0276 | 0.0276 | 0.0276 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
0 300 0 0 -2068.2746 10.354878 8000
|
||||
1 200.33191 0 0 -2068.2704 6.9147085 8000
|
||||
2 152.36218 0 0 -2068.269 5.2589726 8000
|
||||
3 227.40679 0 0 -2068.2722 7.8492321 8000
|
||||
Loop time of 1.90319 on 1 procs for 3 steps with 3 atoms
|
||||
|
||||
Performance: 0.136 ns/day, 176.221 hours/ns, 1.576 timesteps/s
|
||||
0.0% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 3.9274e-06 | 3.9274e-06 | 3.9274e-06 | 0.0 | 0.00
|
||||
Output | 0.00011798 | 0.00011798 | 0.00011798 | 0.0 | 0.01
|
||||
Modify | 1.9031 | 1.9031 | 1.9031 | 0.0 | 99.99
|
||||
Other | | 1.054e-05 | | | 0.00
|
||||
|
||||
Nlocal: 3 ave 3 max 3 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds not checked
|
||||
Total wall time: 0:00:07
|
||||
@ -1,82 +0,0 @@
|
||||
LAMMPS (19 Sep 2019)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# H2O with NWChem
|
||||
|
||||
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 file tmp.couple
|
||||
units metal
|
||||
atom_style atomic
|
||||
atom_modify sort 0 0.0 map yes
|
||||
|
||||
boundary m m m
|
||||
read_data data.h2o
|
||||
orthogonal box = (-10 -10 -10) to (10 10 10)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
3 atoms
|
||||
read_data CPU = 0.000615383 secs
|
||||
|
||||
group one id 2
|
||||
1 atoms in group one
|
||||
displace_atoms one move 0.1 0.2 0.3
|
||||
|
||||
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
|
||||
minimize 1.0e-6 1.0e-6 10 50
|
||||
WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:174)
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:166)
|
||||
Per MPI rank memory allocation (min/avg/max) = 0.0279 | 0.0279 | 0.0279 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
0 300 0 0 -2067.8909 10.354878 8000
|
||||
1 300 0 0 -2068.0707 10.354878 8000
|
||||
2 300 0 0 -2068.252 10.354878 8000
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:166)
|
||||
3 300 0 0 -2068.2797 10.354878 8000
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:166)
|
||||
4 300 0 0 -2068.2799 10.354878 8000
|
||||
Loop time of 5.71024 on 1 procs for 4 steps with 3 atoms
|
||||
|
||||
0.1% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = energy tolerance
|
||||
Energy initial, next-to-last, final =
|
||||
-2067.96847053 -2068.35730416 -2068.35745184
|
||||
Force two-norm initial, final = 4.54685 0.124714
|
||||
Force max component initial, final = 3.48924 0.0859263
|
||||
Final line search alpha, max atom move = 1 0.0859263
|
||||
Iterations, force evaluations = 4 8
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 6.2305e-07 | 6.2305e-07 | 6.2305e-07 | 0.0 | 0.00
|
||||
Comm | 1.1522e-05 | 1.1522e-05 | 1.1522e-05 | 0.0 | 0.00
|
||||
Output | 8.4217e-05 | 8.4217e-05 | 8.4217e-05 | 0.0 | 0.00
|
||||
Modify | 5.7099 | 5.7099 | 5.7099 | 0.0 | 99.99
|
||||
Other | | 0.0002355 | | | 0.00
|
||||
|
||||
Nlocal: 3 ave 3 max 3 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 2
|
||||
Dangerous builds not checked
|
||||
Total wall time: 0:00:10
|
||||
@ -1,626 +0,0 @@
|
||||
argument 1 = nwchem_lammps.nw
|
||||
|
||||
|
||||
|
||||
============================== echo of input deck ==============================
|
||||
echo
|
||||
|
||||
memory global 40 mb stack 23 mb heap 5 mb
|
||||
|
||||
geometry units angstrom noautosym nocenter
|
||||
O 0.00197082 0.0012463 -0.00298048
|
||||
H -0.0432066 0.769363 -0.596119
|
||||
H 0.0119282 -0.789143 -0.528177
|
||||
end
|
||||
|
||||
scf
|
||||
vectors input nwchem_lammps.movecs
|
||||
end
|
||||
|
||||
dft
|
||||
vectors input nwchem_lammps.movecs
|
||||
end
|
||||
|
||||
basis
|
||||
O library 6-31g*
|
||||
H library 6-31g*
|
||||
end
|
||||
|
||||
scf
|
||||
maxiter 100
|
||||
end
|
||||
|
||||
#dft
|
||||
# xc b3lyp
|
||||
#end
|
||||
|
||||
task scf gradient
|
||||
#task dft gradient
|
||||
================================================================================
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
Northwest Computational Chemistry Package (NWChem) 6.8
|
||||
------------------------------------------------------
|
||||
|
||||
|
||||
Environmental Molecular Sciences Laboratory
|
||||
Pacific Northwest National Laboratory
|
||||
Richland, WA 99352
|
||||
|
||||
Copyright (c) 1994-2018
|
||||
Pacific Northwest National Laboratory
|
||||
Battelle Memorial Institute
|
||||
|
||||
NWChem is an open-source computational chemistry package
|
||||
distributed under the terms of the
|
||||
Educational Community License (ECL) 2.0
|
||||
A copy of the license is included with this distribution
|
||||
in the LICENSE.TXT file
|
||||
|
||||
ACKNOWLEDGMENT
|
||||
--------------
|
||||
|
||||
This software and its documentation were developed at the
|
||||
EMSL at Pacific Northwest National Laboratory, a multiprogram
|
||||
national laboratory, operated for the U.S. Department of Energy
|
||||
by Battelle under Contract Number DE-AC05-76RL01830. Support
|
||||
for this work was provided by the Department of Energy Office
|
||||
of Biological and Environmental Research, Office of Basic
|
||||
Energy Sciences, and the Office of Advanced Scientific Computing.
|
||||
|
||||
|
||||
Job information
|
||||
---------------
|
||||
|
||||
hostname = almondjoy
|
||||
program = /home/jboschen/nwchem-6.8.1-release/bin/LINUX64/nwchem
|
||||
date = Fri Jan 31 00:31:00 2020
|
||||
|
||||
compiled = Tue_Oct_01_13:20:43_2019
|
||||
source = /home/jboschen/nwchem-6.8.1-release
|
||||
nwchem branch = Development
|
||||
nwchem revision = N/A
|
||||
ga revision = 5.6.5
|
||||
use scalapack = F
|
||||
input = nwchem_lammps.nw
|
||||
prefix = nwchem_lammps.
|
||||
data base = ./nwchem_lammps.db
|
||||
status = restart
|
||||
nproc = 1
|
||||
time left = -1s
|
||||
|
||||
|
||||
|
||||
Memory information
|
||||
------------------
|
||||
|
||||
heap = 655358 doubles = 5.0 Mbytes
|
||||
stack = 3014651 doubles = 23.0 Mbytes
|
||||
global = 5242880 doubles = 40.0 Mbytes (distinct from heap & stack)
|
||||
total = 8912889 doubles = 68.0 Mbytes
|
||||
verify = yes
|
||||
hardfail = no
|
||||
|
||||
|
||||
Directory information
|
||||
---------------------
|
||||
|
||||
0 permanent = .
|
||||
0 scratch = .
|
||||
|
||||
|
||||
Previous task information
|
||||
-------------------------
|
||||
|
||||
Theory = scf
|
||||
Operation = gradient
|
||||
Status = ok
|
||||
Qmmm = F
|
||||
Ignore = F
|
||||
|
||||
|
||||
Geometries in the database
|
||||
--------------------------
|
||||
|
||||
Name Natoms Last Modified
|
||||
-------------------------------- ------ ------------------------
|
||||
1 geometry 3 Fri Jan 31 00:30:59 2020
|
||||
|
||||
The geometry named "geometry" is the default for restart
|
||||
|
||||
|
||||
|
||||
Basis sets in the database
|
||||
--------------------------
|
||||
|
||||
Name Natoms Last Modified
|
||||
-------------------------------- ------ ------------------------
|
||||
1 ao basis 2 Fri Jan 31 00:30:59 2020
|
||||
|
||||
The basis set named "ao basis" is the default AO basis for restart
|
||||
|
||||
|
||||
|
||||
|
||||
NWChem Input Module
|
||||
-------------------
|
||||
|
||||
|
||||
|
||||
Scaling coordinates for geometry "geometry" by 1.889725989
|
||||
(inverse scale = 0.529177249)
|
||||
|
||||
|
||||
------
|
||||
auto-z
|
||||
------
|
||||
no constraints, skipping 0.0000000000000000
|
||||
no constraints, skipping 0.0000000000000000
|
||||
|
||||
|
||||
Geometry "geometry" -> ""
|
||||
-------------------------
|
||||
|
||||
Output coordinates in angstroms (scale by 1.889725989 to convert to a.u.)
|
||||
|
||||
No. Tag Charge X Y Z
|
||||
---- ---------------- ---------- -------------- -------------- --------------
|
||||
1 O 8.0000 0.00197082 0.00124630 -0.00298048
|
||||
2 H 1.0000 -0.04320660 0.76936300 -0.59611900
|
||||
3 H 1.0000 0.01192820 -0.78914300 -0.52817700
|
||||
|
||||
Atomic Mass
|
||||
-----------
|
||||
|
||||
O 15.994910
|
||||
H 1.007825
|
||||
|
||||
|
||||
Effective nuclear repulsion energy (a.u.) 9.1573270473
|
||||
|
||||
Nuclear Dipole moment (a.u.)
|
||||
----------------------------
|
||||
X Y Z
|
||||
---------------- ---------------- ----------------
|
||||
-0.0293131272 -0.0185374561 -2.1696696942
|
||||
|
||||
|
||||
|
||||
Z-matrix (autoz)
|
||||
--------
|
||||
|
||||
Units are Angstrom for bonds and degrees for angles
|
||||
|
||||
Type Name I J K L M Value
|
||||
----------- -------- ----- ----- ----- ----- ----- ----------
|
||||
1 Stretch 1 2 0.97152
|
||||
2 Stretch 1 3 0.94902
|
||||
3 Bend 2 1 3 108.72901
|
||||
|
||||
|
||||
XYZ format geometry
|
||||
-------------------
|
||||
3
|
||||
geometry
|
||||
O 0.00197082 0.00124630 -0.00298048
|
||||
H -0.04320660 0.76936300 -0.59611900
|
||||
H 0.01192820 -0.78914300 -0.52817700
|
||||
|
||||
==============================================================================
|
||||
internuclear distances
|
||||
------------------------------------------------------------------------------
|
||||
center one | center two | atomic units | angstroms
|
||||
------------------------------------------------------------------------------
|
||||
2 H | 1 O | 1.83591 | 0.97152
|
||||
3 H | 1 O | 1.79339 | 0.94902
|
||||
------------------------------------------------------------------------------
|
||||
number of included internuclear distances: 2
|
||||
==============================================================================
|
||||
|
||||
|
||||
|
||||
==============================================================================
|
||||
internuclear angles
|
||||
------------------------------------------------------------------------------
|
||||
center 1 | center 2 | center 3 | degrees
|
||||
------------------------------------------------------------------------------
|
||||
2 H | 1 O | 3 H | 108.73
|
||||
------------------------------------------------------------------------------
|
||||
number of included internuclear angles: 1
|
||||
==============================================================================
|
||||
|
||||
|
||||
|
||||
Basis "ao basis" -> "" (cartesian)
|
||||
-----
|
||||
O (Oxygen)
|
||||
----------
|
||||
Exponent Coefficients
|
||||
-------------- ---------------------------------------------------------
|
||||
1 S 5.48467170E+03 0.001831
|
||||
1 S 8.25234950E+02 0.013950
|
||||
1 S 1.88046960E+02 0.068445
|
||||
1 S 5.29645000E+01 0.232714
|
||||
1 S 1.68975700E+01 0.470193
|
||||
1 S 5.79963530E+00 0.358521
|
||||
|
||||
2 S 1.55396160E+01 -0.110778
|
||||
2 S 3.59993360E+00 -0.148026
|
||||
2 S 1.01376180E+00 1.130767
|
||||
|
||||
3 P 1.55396160E+01 0.070874
|
||||
3 P 3.59993360E+00 0.339753
|
||||
3 P 1.01376180E+00 0.727159
|
||||
|
||||
4 S 2.70005800E-01 1.000000
|
||||
|
||||
5 P 2.70005800E-01 1.000000
|
||||
|
||||
6 D 8.00000000E-01 1.000000
|
||||
|
||||
H (Hydrogen)
|
||||
------------
|
||||
Exponent Coefficients
|
||||
-------------- ---------------------------------------------------------
|
||||
1 S 1.87311370E+01 0.033495
|
||||
1 S 2.82539370E+00 0.234727
|
||||
1 S 6.40121700E-01 0.813757
|
||||
|
||||
2 S 1.61277800E-01 1.000000
|
||||
|
||||
|
||||
|
||||
Summary of "ao basis" -> "" (cartesian)
|
||||
------------------------------------------------------------------------------
|
||||
Tag Description Shells Functions and Types
|
||||
---------------- ------------------------------ ------ ---------------------
|
||||
O 6-31g* 6 15 3s2p1d
|
||||
H 6-31g* 2 2 2s
|
||||
|
||||
|
||||
NWChem SCF Module
|
||||
-----------------
|
||||
|
||||
|
||||
|
||||
ao basis = "ao basis"
|
||||
functions = 19
|
||||
atoms = 3
|
||||
closed shells = 5
|
||||
open shells = 0
|
||||
charge = 0.00
|
||||
wavefunction = RHF
|
||||
input vectors = ./nwchem_lammps.movecs
|
||||
output vectors = ./nwchem_lammps.movecs
|
||||
use symmetry = F
|
||||
symmetry adapt = F
|
||||
|
||||
|
||||
Summary of "ao basis" -> "ao basis" (cartesian)
|
||||
------------------------------------------------------------------------------
|
||||
Tag Description Shells Functions and Types
|
||||
---------------- ------------------------------ ------ ---------------------
|
||||
O 6-31g* 6 15 3s2p1d
|
||||
H 6-31g* 2 2 2s
|
||||
|
||||
|
||||
|
||||
Forming initial guess at 0.0s
|
||||
|
||||
|
||||
Loading old vectors from job with title :
|
||||
|
||||
|
||||
|
||||
|
||||
Starting SCF solution at 0.0s
|
||||
|
||||
|
||||
|
||||
----------------------------------------------
|
||||
Quadratically convergent ROHF
|
||||
|
||||
Convergence threshold : 1.000E-04
|
||||
Maximum no. of iterations : 100
|
||||
Final Fock-matrix accuracy: 1.000E-07
|
||||
----------------------------------------------
|
||||
|
||||
|
||||
#quartets = 1.540D+03 #integrals = 1.424D+04 #direct = 0.0% #cached =100.0%
|
||||
|
||||
|
||||
Integral file = ./nwchem_lammps.aoints.0
|
||||
Record size in doubles = 65536 No. of integs per rec = 43688
|
||||
Max. records in memory = 2 Max. records in file = 1392051
|
||||
No. of bits per label = 8 No. of bits per value = 64
|
||||
|
||||
|
||||
iter energy gnorm gmax time
|
||||
----- ------------------- --------- --------- --------
|
||||
1 -76.0095751323 4.63D-02 1.64D-02 0.1
|
||||
2 -76.0097628164 8.13D-04 2.83D-04 0.1
|
||||
3 -76.0097629130 3.92D-06 1.55D-06 0.1
|
||||
|
||||
|
||||
Final RHF results
|
||||
------------------
|
||||
|
||||
Total SCF energy = -76.009762913030
|
||||
One-electron energy = -123.002897732381
|
||||
Two-electron energy = 37.835807772101
|
||||
Nuclear repulsion energy = 9.157327047250
|
||||
|
||||
Time for solution = 0.0s
|
||||
|
||||
|
||||
Final eigenvalues
|
||||
-----------------
|
||||
|
||||
1
|
||||
1 -20.5584
|
||||
2 -1.3367
|
||||
3 -0.7128
|
||||
4 -0.5617
|
||||
5 -0.4959
|
||||
6 0.2104
|
||||
7 0.3038
|
||||
8 1.0409
|
||||
9 1.1202
|
||||
10 1.1606
|
||||
11 1.1691
|
||||
12 1.3840
|
||||
13 1.4192
|
||||
14 2.0312
|
||||
15 2.0334
|
||||
|
||||
ROHF Final Molecular Orbital Analysis
|
||||
-------------------------------------
|
||||
|
||||
Vector 2 Occ=2.000000D+00 E=-1.336749D+00
|
||||
MO Center= -2.8D-03, -1.3D-02, -1.7D-01, r^2= 5.1D-01
|
||||
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
|
||||
----- ------------ --------------- ----- ------------ ---------------
|
||||
2 0.476636 1 O s 6 0.442369 1 O s
|
||||
1 -0.210214 1 O s
|
||||
|
||||
Vector 3 Occ=2.000000D+00 E=-7.127948D-01
|
||||
MO Center= -4.9D-03, 3.9D-03, -2.1D-01, r^2= 7.8D-01
|
||||
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
|
||||
----- ------------ --------------- ----- ------------ ---------------
|
||||
4 0.504894 1 O py 8 0.303932 1 O py
|
||||
18 -0.234724 3 H s 16 0.229765 2 H s
|
||||
|
||||
Vector 4 Occ=2.000000D+00 E=-5.617306D-01
|
||||
MO Center= 3.6D-03, 9.0D-03, 5.6D-02, r^2= 6.9D-01
|
||||
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
|
||||
----- ------------ --------------- ----- ------------ ---------------
|
||||
5 0.559565 1 O pz 9 0.410981 1 O pz
|
||||
6 0.315892 1 O s 2 0.157960 1 O s
|
||||
|
||||
Vector 5 Occ=2.000000D+00 E=-4.959173D-01
|
||||
MO Center= 1.4D-03, 6.9D-05, -2.2D-02, r^2= 6.0D-01
|
||||
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
|
||||
----- ------------ --------------- ----- ------------ ---------------
|
||||
3 0.638390 1 O px 7 0.511530 1 O px
|
||||
|
||||
Vector 6 Occ=0.000000D+00 E= 2.103822D-01
|
||||
MO Center= -2.3D-02, 3.5D-02, -7.3D-01, r^2= 2.6D+00
|
||||
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
|
||||
----- ------------ --------------- ----- ------------ ---------------
|
||||
6 1.416869 1 O s 17 -1.068330 2 H s
|
||||
19 -1.014775 3 H s 9 -0.490951 1 O pz
|
||||
5 -0.212990 1 O pz
|
||||
|
||||
Vector 7 Occ=0.000000D+00 E= 3.037943D-01
|
||||
MO Center= -1.8D-02, -8.9D-02, -7.1D-01, r^2= 2.8D+00
|
||||
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
|
||||
----- ------------ --------------- ----- ------------ ---------------
|
||||
19 -1.426837 3 H s 17 1.332767 2 H s
|
||||
8 -0.842141 1 O py 4 -0.327553 1 O py
|
||||
|
||||
Vector 8 Occ=0.000000D+00 E= 1.040852D+00
|
||||
MO Center= -7.4D-03, 1.3D-01, -1.6D-01, r^2= 1.4D+00
|
||||
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
|
||||
----- ------------ --------------- ----- ------------ ---------------
|
||||
16 0.931594 2 H s 18 -0.747590 3 H s
|
||||
8 -0.655817 1 O py 17 -0.523035 2 H s
|
||||
19 0.366407 3 H s 14 -0.357109 1 O dyz
|
||||
|
||||
Vector 9 Occ=0.000000D+00 E= 1.120172D+00
|
||||
MO Center= -6.8D-03, -2.9D-02, -3.1D-01, r^2= 1.5D+00
|
||||
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
|
||||
----- ------------ --------------- ----- ------------ ---------------
|
||||
6 1.145090 1 O s 18 0.841596 3 H s
|
||||
2 -0.727471 1 O s 16 0.684927 2 H s
|
||||
9 0.559191 1 O pz 19 -0.546678 3 H s
|
||||
17 -0.538778 2 H s 10 -0.344609 1 O dxx
|
||||
15 -0.250035 1 O dzz
|
||||
|
||||
Vector 10 Occ=0.000000D+00 E= 1.160603D+00
|
||||
MO Center= 1.2D-02, -4.3D-02, 2.5D-01, r^2= 1.0D+00
|
||||
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
|
||||
----- ------------ --------------- ----- ------------ ---------------
|
||||
6 1.137949 1 O s 5 -0.844233 1 O pz
|
||||
9 0.595088 1 O pz 2 -0.475986 1 O s
|
||||
18 -0.455932 3 H s 16 -0.357325 2 H s
|
||||
13 -0.317117 1 O dyy 15 -0.196968 1 O dzz
|
||||
|
||||
Vector 11 Occ=0.000000D+00 E= 1.169054D+00
|
||||
MO Center= 1.9D-03, 1.2D-03, -6.4D-03, r^2= 1.1D+00
|
||||
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
|
||||
----- ------------ --------------- ----- ------------ ---------------
|
||||
7 -1.034653 1 O px 3 0.962043 1 O px
|
||||
|
||||
Vector 12 Occ=0.000000D+00 E= 1.384034D+00
|
||||
MO Center= 6.0D-04, -2.6D-03, -5.0D-02, r^2= 1.4D+00
|
||||
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
|
||||
----- ------------ --------------- ----- ------------ ---------------
|
||||
8 1.557767 1 O py 4 -1.035829 1 O py
|
||||
17 -0.900920 2 H s 19 0.901756 3 H s
|
||||
|
||||
Vector 13 Occ=0.000000D+00 E= 1.419205D+00
|
||||
MO Center= -1.3D-02, -4.9D-02, -5.2D-01, r^2= 1.4D+00
|
||||
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
|
||||
----- ------------ --------------- ----- ------------ ---------------
|
||||
6 3.605136 1 O s 2 -1.454853 1 O s
|
||||
9 -1.107532 1 O pz 19 -0.874208 3 H s
|
||||
17 -0.757016 2 H s 13 -0.634436 1 O dyy
|
||||
5 0.516593 1 O pz 15 -0.401100 1 O dzz
|
||||
10 -0.319873 1 O dxx 16 -0.260650 2 H s
|
||||
|
||||
Vector 14 Occ=0.000000D+00 E= 2.031234D+00
|
||||
MO Center= 1.9D-03, 2.3D-03, -3.0D-03, r^2= 6.1D-01
|
||||
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
|
||||
----- ------------ --------------- ----- ------------ ---------------
|
||||
11 1.727083 1 O dxy
|
||||
|
||||
Vector 15 Occ=0.000000D+00 E= 2.033369D+00
|
||||
MO Center= 3.4D-03, 3.4D-03, 4.3D-02, r^2= 6.2D-01
|
||||
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
|
||||
----- ------------ --------------- ----- ------------ ---------------
|
||||
15 1.012642 1 O dzz 13 -0.512441 1 O dyy
|
||||
10 -0.438481 1 O dxx 6 -0.226567 1 O s
|
||||
|
||||
|
||||
center of mass
|
||||
--------------
|
||||
x = -0.00000001 y = -0.00000003 z = -0.12388979
|
||||
|
||||
moments of inertia (a.u.)
|
||||
------------------
|
||||
6.378705068992 0.153373998471 -0.069687034145
|
||||
0.153373998471 2.014476065716 0.150739744400
|
||||
-0.069687034145 0.150739744400 4.379134195179
|
||||
|
||||
Mulliken analysis of the total density
|
||||
--------------------------------------
|
||||
|
||||
Atom Charge Shell Charges
|
||||
----------- ------ -------------------------------------------------------
|
||||
1 O 8 8.87 2.00 0.90 2.90 0.92 2.08 0.08
|
||||
2 H 1 0.56 0.46 0.11
|
||||
3 H 1 0.56 0.47 0.10
|
||||
|
||||
Multipole analysis of the density wrt the origin
|
||||
------------------------------------------------
|
||||
|
||||
L x y z total open nuclear
|
||||
- - - - ----- ---- -------
|
||||
0 0 0 0 -0.000000 0.000000 10.000000
|
||||
|
||||
1 1 0 0 -0.026417 0.000000 -0.029313
|
||||
1 0 1 0 -0.023604 0.000000 -0.018537
|
||||
1 0 0 1 -0.846090 0.000000 -2.169670
|
||||
|
||||
2 2 0 0 -5.373227 0.000000 0.007286
|
||||
2 1 1 0 -0.085617 0.000000 -0.152252
|
||||
2 1 0 1 0.038215 0.000000 0.069311
|
||||
2 0 2 0 -2.927589 0.000000 4.337695
|
||||
2 0 1 1 -0.071410 0.000000 -0.149465
|
||||
2 0 0 2 -4.159949 0.000000 2.265483
|
||||
|
||||
|
||||
Parallel integral file used 1 records with 0 large values
|
||||
|
||||
NWChem Gradients Module
|
||||
-----------------------
|
||||
|
||||
|
||||
|
||||
wavefunction = RHF
|
||||
|
||||
|
||||
|
||||
RHF ENERGY GRADIENTS
|
||||
|
||||
atom coordinates gradient
|
||||
x y z x y z
|
||||
1 O 0.003724 0.002355 -0.005632 0.000909 -0.019294 0.007866
|
||||
2 H -0.081649 1.453885 -1.126502 -0.001242 0.025549 -0.011605
|
||||
3 H 0.022541 -1.491264 -0.998110 0.000333 -0.006255 0.003739
|
||||
|
||||
----------------------------------------
|
||||
| Time | 1-e(secs) | 2-e(secs) |
|
||||
----------------------------------------
|
||||
| CPU | 0.00 | 0.03 |
|
||||
----------------------------------------
|
||||
| WALL | 0.00 | 0.03 |
|
||||
----------------------------------------
|
||||
|
||||
Task times cpu: 0.1s wall: 0.1s
|
||||
|
||||
|
||||
NWChem Input Module
|
||||
-------------------
|
||||
|
||||
|
||||
Summary of allocated global arrays
|
||||
-----------------------------------
|
||||
No active global arrays
|
||||
|
||||
|
||||
|
||||
GA Statistics for process 0
|
||||
------------------------------
|
||||
|
||||
create destroy get put acc scatter gather read&inc
|
||||
calls: 182 182 2869 728 468 0 0 68
|
||||
number of processes/call 1.00e+00 1.00e+00 1.00e+00 0.00e+00 0.00e+00
|
||||
bytes total: 6.18e+05 3.56e+05 1.04e+05 0.00e+00 0.00e+00 5.44e+02
|
||||
bytes remote: 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00
|
||||
Max memory consumed for GA by this process: 39432 bytes
|
||||
|
||||
MA_summarize_allocated_blocks: starting scan ...
|
||||
MA_summarize_allocated_blocks: scan completed: 0 heap blocks, 0 stack blocks
|
||||
MA usage statistics:
|
||||
|
||||
allocation statistics:
|
||||
heap stack
|
||||
---- -----
|
||||
current number of blocks 0 0
|
||||
maximum number of blocks 18 28
|
||||
current total bytes 0 0
|
||||
maximum total bytes 1060104 16000888
|
||||
maximum total K-bytes 1061 16001
|
||||
maximum total M-bytes 2 17
|
||||
|
||||
|
||||
CITATION
|
||||
--------
|
||||
Please cite the following reference when publishing
|
||||
results obtained with NWChem:
|
||||
|
||||
M. Valiev, E.J. Bylaska, N. Govind, K. Kowalski,
|
||||
T.P. Straatsma, H.J.J. van Dam, D. Wang, J. Nieplocha,
|
||||
E. Apra, T.L. Windus, W.A. de Jong
|
||||
"NWChem: a comprehensive and scalable open-source
|
||||
solution for large scale molecular simulations"
|
||||
Comput. Phys. Commun. 181, 1477 (2010)
|
||||
doi:10.1016/j.cpc.2010.04.018
|
||||
|
||||
AUTHORS
|
||||
-------
|
||||
E. Apra, E. J. Bylaska, W. A. de Jong, N. Govind, K. Kowalski,
|
||||
T. P. Straatsma, M. Valiev, H. J. J. van Dam, D. Wang, T. L. Windus,
|
||||
J. Hammond, J. Autschbach, K. Bhaskaran-Nair, J. Brabec, K. Lopata,
|
||||
S. A. Fischer, S. Krishnamoorthy, M. Jacquelin, W. Ma, M. Klemm, O. Villa,
|
||||
Y. Chen, V. Anisimov, F. Aquino, S. Hirata, M. T. Hackler, V. Konjkov,
|
||||
D. Mejia-Rodriguez, T. Risthaus, M. Malagoli, A. Marenich,
|
||||
A. Otero-de-la-Roza, J. Mullin, P. Nichols, R. Peverati, J. Pittner, Y. Zhao,
|
||||
P.-D. Fan, A. Fonari, M. J. Williamson, R. J. Harrison, J. R. Rehr,
|
||||
M. Dupuis, D. Silverstein, D. M. A. Smith, J. Nieplocha, V. Tipparaju,
|
||||
M. Krishnan, B. E. Van Kuiken, A. Vazquez-Mayagoitia, L. Jensen, M. Swart,
|
||||
Q. Wu, T. Van Voorhis, A. A. Auer, M. Nooijen, L. D. Crosby, E. Brown,
|
||||
G. Cisneros, G. I. Fann, H. Fruchtl, J. Garza, K. Hirao, R. A. Kendall,
|
||||
J. A. Nichols, K. Tsemekhman, K. Wolinski, J. Anchell, D. E. Bernholdt,
|
||||
P. Borowski, T. Clark, D. Clerc, H. Dachsel, M. J. O. Deegan, K. Dyall,
|
||||
D. Elwood, E. Glendening, M. Gutowski, A. C. Hess, J. Jaffe, B. G. Johnson,
|
||||
J. Ju, R. Kobayashi, R. Kutteh, Z. Lin, R. Littlefield, X. Long, B. Meng,
|
||||
T. Nakajima, S. Niu, L. Pollack, M. Rosing, K. Glaesemann, G. Sandrone,
|
||||
M. Stave, H. Taylor, G. Thomas, J. H. van Lenthe, A. T. Wong, Z. Zhang.
|
||||
|
||||
Total times cpu: 0.1s wall: 0.2s
|
||||
@ -1,626 +0,0 @@
|
||||
argument 1 = nwchem_lammps.nw
|
||||
|
||||
|
||||
|
||||
============================== echo of input deck ==============================
|
||||
echo
|
||||
|
||||
memory global 40 mb stack 23 mb heap 5 mb
|
||||
|
||||
geometry units angstrom noautosym nocenter
|
||||
O -0.00836667 0.0010006 0.0866404
|
||||
H 0.0968795 0.837453 -0.346117
|
||||
H 0.0114839 -0.638453 -0.612122
|
||||
end
|
||||
|
||||
scf
|
||||
vectors input nwchem_lammps.movecs
|
||||
end
|
||||
|
||||
dft
|
||||
vectors input nwchem_lammps.movecs
|
||||
end
|
||||
|
||||
basis
|
||||
O library 6-31g*
|
||||
H library 6-31g*
|
||||
end
|
||||
|
||||
scf
|
||||
maxiter 100
|
||||
end
|
||||
|
||||
#dft
|
||||
# xc b3lyp
|
||||
#end
|
||||
|
||||
task scf gradient
|
||||
#task dft gradient
|
||||
================================================================================
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
Northwest Computational Chemistry Package (NWChem) 6.8
|
||||
------------------------------------------------------
|
||||
|
||||
|
||||
Environmental Molecular Sciences Laboratory
|
||||
Pacific Northwest National Laboratory
|
||||
Richland, WA 99352
|
||||
|
||||
Copyright (c) 1994-2018
|
||||
Pacific Northwest National Laboratory
|
||||
Battelle Memorial Institute
|
||||
|
||||
NWChem is an open-source computational chemistry package
|
||||
distributed under the terms of the
|
||||
Educational Community License (ECL) 2.0
|
||||
A copy of the license is included with this distribution
|
||||
in the LICENSE.TXT file
|
||||
|
||||
ACKNOWLEDGMENT
|
||||
--------------
|
||||
|
||||
This software and its documentation were developed at the
|
||||
EMSL at Pacific Northwest National Laboratory, a multiprogram
|
||||
national laboratory, operated for the U.S. Department of Energy
|
||||
by Battelle under Contract Number DE-AC05-76RL01830. Support
|
||||
for this work was provided by the Department of Energy Office
|
||||
of Biological and Environmental Research, Office of Basic
|
||||
Energy Sciences, and the Office of Advanced Scientific Computing.
|
||||
|
||||
|
||||
Job information
|
||||
---------------
|
||||
|
||||
hostname = almondjoy
|
||||
program = /home/jboschen/nwchem-6.8.1-release/bin/LINUX64/nwchem
|
||||
date = Fri Jan 31 00:33:40 2020
|
||||
|
||||
compiled = Tue_Oct_01_13:20:43_2019
|
||||
source = /home/jboschen/nwchem-6.8.1-release
|
||||
nwchem branch = Development
|
||||
nwchem revision = N/A
|
||||
ga revision = 5.6.5
|
||||
use scalapack = F
|
||||
input = nwchem_lammps.nw
|
||||
prefix = nwchem_lammps.
|
||||
data base = ./nwchem_lammps.db
|
||||
status = restart
|
||||
nproc = 1
|
||||
time left = -1s
|
||||
|
||||
|
||||
|
||||
Memory information
|
||||
------------------
|
||||
|
||||
heap = 655358 doubles = 5.0 Mbytes
|
||||
stack = 3014651 doubles = 23.0 Mbytes
|
||||
global = 5242880 doubles = 40.0 Mbytes (distinct from heap & stack)
|
||||
total = 8912889 doubles = 68.0 Mbytes
|
||||
verify = yes
|
||||
hardfail = no
|
||||
|
||||
|
||||
Directory information
|
||||
---------------------
|
||||
|
||||
0 permanent = .
|
||||
0 scratch = .
|
||||
|
||||
|
||||
Previous task information
|
||||
-------------------------
|
||||
|
||||
Theory = scf
|
||||
Operation = gradient
|
||||
Status = ok
|
||||
Qmmm = F
|
||||
Ignore = F
|
||||
|
||||
|
||||
Geometries in the database
|
||||
--------------------------
|
||||
|
||||
Name Natoms Last Modified
|
||||
-------------------------------- ------ ------------------------
|
||||
1 geometry 3 Fri Jan 31 00:33:40 2020
|
||||
|
||||
The geometry named "geometry" is the default for restart
|
||||
|
||||
|
||||
|
||||
Basis sets in the database
|
||||
--------------------------
|
||||
|
||||
Name Natoms Last Modified
|
||||
-------------------------------- ------ ------------------------
|
||||
1 ao basis 2 Fri Jan 31 00:33:40 2020
|
||||
|
||||
The basis set named "ao basis" is the default AO basis for restart
|
||||
|
||||
|
||||
|
||||
|
||||
NWChem Input Module
|
||||
-------------------
|
||||
|
||||
|
||||
|
||||
Scaling coordinates for geometry "geometry" by 1.889725989
|
||||
(inverse scale = 0.529177249)
|
||||
|
||||
|
||||
------
|
||||
auto-z
|
||||
------
|
||||
no constraints, skipping 0.0000000000000000
|
||||
no constraints, skipping 0.0000000000000000
|
||||
|
||||
|
||||
Geometry "geometry" -> ""
|
||||
-------------------------
|
||||
|
||||
Output coordinates in angstroms (scale by 1.889725989 to convert to a.u.)
|
||||
|
||||
No. Tag Charge X Y Z
|
||||
---- ---------------- ---------- -------------- -------------- --------------
|
||||
1 O 8.0000 -0.00836667 0.00100060 0.08664040
|
||||
2 H 1.0000 0.09687950 0.83745300 -0.34611700
|
||||
3 H 1.0000 0.01148390 -0.63845300 -0.61212200
|
||||
|
||||
Atomic Mass
|
||||
-----------
|
||||
|
||||
O 15.994910
|
||||
H 1.007825
|
||||
|
||||
|
||||
Effective nuclear repulsion energy (a.u.) 9.2881144400
|
||||
|
||||
Nuclear Dipole moment (a.u.)
|
||||
----------------------------
|
||||
X Y Z
|
||||
---------------- ---------------- ----------------
|
||||
0.0782914233 0.3911823503 -0.5009962172
|
||||
|
||||
|
||||
|
||||
Z-matrix (autoz)
|
||||
--------
|
||||
|
||||
Units are Angstrom for bonds and degrees for angles
|
||||
|
||||
Type Name I J K L M Value
|
||||
----------- -------- ----- ----- ----- ----- ----- ----------
|
||||
1 Stretch 1 2 0.94763
|
||||
2 Stretch 1 3 0.94740
|
||||
3 Bend 2 1 3 104.86952
|
||||
|
||||
|
||||
XYZ format geometry
|
||||
-------------------
|
||||
3
|
||||
geometry
|
||||
O -0.00836667 0.00100060 0.08664040
|
||||
H 0.09687950 0.83745300 -0.34611700
|
||||
H 0.01148390 -0.63845300 -0.61212200
|
||||
|
||||
==============================================================================
|
||||
internuclear distances
|
||||
------------------------------------------------------------------------------
|
||||
center one | center two | atomic units | angstroms
|
||||
------------------------------------------------------------------------------
|
||||
2 H | 1 O | 1.79077 | 0.94763
|
||||
3 H | 1 O | 1.79032 | 0.94740
|
||||
------------------------------------------------------------------------------
|
||||
number of included internuclear distances: 2
|
||||
==============================================================================
|
||||
|
||||
|
||||
|
||||
==============================================================================
|
||||
internuclear angles
|
||||
------------------------------------------------------------------------------
|
||||
center 1 | center 2 | center 3 | degrees
|
||||
------------------------------------------------------------------------------
|
||||
2 H | 1 O | 3 H | 104.87
|
||||
------------------------------------------------------------------------------
|
||||
number of included internuclear angles: 1
|
||||
==============================================================================
|
||||
|
||||
|
||||
|
||||
Basis "ao basis" -> "" (cartesian)
|
||||
-----
|
||||
O (Oxygen)
|
||||
----------
|
||||
Exponent Coefficients
|
||||
-------------- ---------------------------------------------------------
|
||||
1 S 5.48467170E+03 0.001831
|
||||
1 S 8.25234950E+02 0.013950
|
||||
1 S 1.88046960E+02 0.068445
|
||||
1 S 5.29645000E+01 0.232714
|
||||
1 S 1.68975700E+01 0.470193
|
||||
1 S 5.79963530E+00 0.358521
|
||||
|
||||
2 S 1.55396160E+01 -0.110778
|
||||
2 S 3.59993360E+00 -0.148026
|
||||
2 S 1.01376180E+00 1.130767
|
||||
|
||||
3 P 1.55396160E+01 0.070874
|
||||
3 P 3.59993360E+00 0.339753
|
||||
3 P 1.01376180E+00 0.727159
|
||||
|
||||
4 S 2.70005800E-01 1.000000
|
||||
|
||||
5 P 2.70005800E-01 1.000000
|
||||
|
||||
6 D 8.00000000E-01 1.000000
|
||||
|
||||
H (Hydrogen)
|
||||
------------
|
||||
Exponent Coefficients
|
||||
-------------- ---------------------------------------------------------
|
||||
1 S 1.87311370E+01 0.033495
|
||||
1 S 2.82539370E+00 0.234727
|
||||
1 S 6.40121700E-01 0.813757
|
||||
|
||||
2 S 1.61277800E-01 1.000000
|
||||
|
||||
|
||||
|
||||
Summary of "ao basis" -> "" (cartesian)
|
||||
------------------------------------------------------------------------------
|
||||
Tag Description Shells Functions and Types
|
||||
---------------- ------------------------------ ------ ---------------------
|
||||
O 6-31g* 6 15 3s2p1d
|
||||
H 6-31g* 2 2 2s
|
||||
|
||||
|
||||
NWChem SCF Module
|
||||
-----------------
|
||||
|
||||
|
||||
|
||||
ao basis = "ao basis"
|
||||
functions = 19
|
||||
atoms = 3
|
||||
closed shells = 5
|
||||
open shells = 0
|
||||
charge = 0.00
|
||||
wavefunction = RHF
|
||||
input vectors = ./nwchem_lammps.movecs
|
||||
output vectors = ./nwchem_lammps.movecs
|
||||
use symmetry = F
|
||||
symmetry adapt = F
|
||||
|
||||
|
||||
Summary of "ao basis" -> "ao basis" (cartesian)
|
||||
------------------------------------------------------------------------------
|
||||
Tag Description Shells Functions and Types
|
||||
---------------- ------------------------------ ------ ---------------------
|
||||
O 6-31g* 6 15 3s2p1d
|
||||
H 6-31g* 2 2 2s
|
||||
|
||||
|
||||
|
||||
Forming initial guess at 0.0s
|
||||
|
||||
|
||||
Loading old vectors from job with title :
|
||||
|
||||
|
||||
|
||||
|
||||
Starting SCF solution at 0.0s
|
||||
|
||||
|
||||
|
||||
----------------------------------------------
|
||||
Quadratically convergent ROHF
|
||||
|
||||
Convergence threshold : 1.000E-04
|
||||
Maximum no. of iterations : 100
|
||||
Final Fock-matrix accuracy: 1.000E-07
|
||||
----------------------------------------------
|
||||
|
||||
|
||||
#quartets = 1.540D+03 #integrals = 1.424D+04 #direct = 0.0% #cached =100.0%
|
||||
|
||||
|
||||
Integral file = ./nwchem_lammps.aoints.0
|
||||
Record size in doubles = 65536 No. of integs per rec = 43688
|
||||
Max. records in memory = 2 Max. records in file = 1392051
|
||||
No. of bits per label = 8 No. of bits per value = 64
|
||||
|
||||
|
||||
iter energy gnorm gmax time
|
||||
----- ------------------- --------- --------- --------
|
||||
1 -76.0107350035 4.75D-05 2.49D-05 0.1
|
||||
|
||||
|
||||
Final RHF results
|
||||
------------------
|
||||
|
||||
Total SCF energy = -76.010735003510
|
||||
One-electron energy = -123.220958992568
|
||||
Two-electron energy = 37.922109549024
|
||||
Nuclear repulsion energy = 9.288114440035
|
||||
|
||||
Time for solution = 0.0s
|
||||
|
||||
|
||||
Final eigenvalues
|
||||
-----------------
|
||||
|
||||
1
|
||||
1 -20.5583
|
||||
2 -1.3466
|
||||
3 -0.7130
|
||||
4 -0.5721
|
||||
5 -0.4985
|
||||
6 0.2129
|
||||
7 0.3068
|
||||
8 1.0286
|
||||
9 1.1338
|
||||
10 1.1678
|
||||
11 1.1807
|
||||
12 1.3845
|
||||
13 1.4334
|
||||
14 2.0187
|
||||
15 2.0311
|
||||
|
||||
ROHF Final Molecular Orbital Analysis
|
||||
-------------------------------------
|
||||
|
||||
Vector 2 Occ=2.000000D+00 E=-1.346587D+00
|
||||
MO Center= 1.1D-02, 3.1D-02, -8.5D-02, r^2= 5.0D-01
|
||||
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
|
||||
----- ------------ --------------- ----- ------------ ---------------
|
||||
2 0.475648 1 O s 6 0.435095 1 O s
|
||||
1 -0.209463 1 O s
|
||||
|
||||
Vector 3 Occ=2.000000D+00 E=-7.129747D-01
|
||||
MO Center= 1.5D-02, 3.8D-02, -1.3D-01, r^2= 7.6D-01
|
||||
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
|
||||
----- ------------ --------------- ----- ------------ ---------------
|
||||
4 0.500246 1 O py 8 0.299047 1 O py
|
||||
16 0.232138 2 H s 18 -0.232195 3 H s
|
||||
|
||||
Vector 4 Occ=2.000000D+00 E=-5.720760D-01
|
||||
MO Center= -1.5D-02, -9.7D-03, 1.5D-01, r^2= 6.8D-01
|
||||
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
|
||||
----- ------------ --------------- ----- ------------ ---------------
|
||||
5 0.545527 1 O pz 9 0.395332 1 O pz
|
||||
6 0.326735 1 O s 2 0.164593 1 O s
|
||||
|
||||
Vector 5 Occ=2.000000D+00 E=-4.984552D-01
|
||||
MO Center= -6.2D-03, 4.4D-03, 6.7D-02, r^2= 6.0D-01
|
||||
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
|
||||
----- ------------ --------------- ----- ------------ ---------------
|
||||
3 0.634559 1 O px 7 0.507891 1 O px
|
||||
|
||||
Vector 6 Occ=0.000000D+00 E= 2.128732D-01
|
||||
MO Center= 7.5D-02, 1.3D-01, -6.6D-01, r^2= 2.6D+00
|
||||
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
|
||||
----- ------------ --------------- ----- ------------ ---------------
|
||||
6 1.437795 1 O s 17 -1.050892 2 H s
|
||||
19 -1.050374 3 H s 9 -0.494696 1 O pz
|
||||
5 -0.208359 1 O pz
|
||||
|
||||
Vector 7 Occ=0.000000D+00 E= 3.067764D-01
|
||||
MO Center= 7.1D-02, 1.3D-01, -6.3D-01, r^2= 2.7D+00
|
||||
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
|
||||
----- ------------ --------------- ----- ------------ ---------------
|
||||
17 1.413885 2 H s 19 -1.414835 3 H s
|
||||
8 -0.824411 1 O py 4 -0.320355 1 O py
|
||||
|
||||
Vector 8 Occ=0.000000D+00 E= 1.028607D+00
|
||||
MO Center= 7.1D-03, 2.6D-02, -5.2D-02, r^2= 1.4D+00
|
||||
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
|
||||
----- ------------ --------------- ----- ------------ ---------------
|
||||
16 0.839269 2 H s 18 -0.838060 3 H s
|
||||
8 -0.692349 1 O py 17 -0.426291 2 H s
|
||||
19 0.425092 3 H s 14 -0.319117 1 O dyz
|
||||
|
||||
Vector 9 Occ=0.000000D+00 E= 1.133833D+00
|
||||
MO Center= -2.7D-02, -2.9D-02, 2.6D-01, r^2= 1.5D+00
|
||||
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
|
||||
----- ------------ --------------- ----- ------------ ---------------
|
||||
6 1.621086 1 O s 2 -0.910150 1 O s
|
||||
9 0.744864 1 O pz 16 0.490586 2 H s
|
||||
18 0.491102 3 H s 5 -0.484186 1 O pz
|
||||
17 -0.426087 2 H s 19 -0.425823 3 H s
|
||||
10 -0.375325 1 O dxx 15 -0.317874 1 O dzz
|
||||
|
||||
Vector 10 Occ=0.000000D+00 E= 1.167849D+00
|
||||
MO Center= -8.0D-03, 1.6D-03, 8.3D-02, r^2= 1.1D+00
|
||||
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
|
||||
----- ------------ --------------- ----- ------------ ---------------
|
||||
7 -1.028149 1 O px 3 0.955686 1 O px
|
||||
|
||||
Vector 11 Occ=0.000000D+00 E= 1.180721D+00
|
||||
MO Center= 1.8D-02, 4.2D-02, -1.5D-01, r^2= 1.1D+00
|
||||
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
|
||||
----- ------------ --------------- ----- ------------ ---------------
|
||||
16 0.710073 2 H s 18 0.711177 3 H s
|
||||
5 0.704677 1 O pz 17 -0.389719 2 H s
|
||||
19 -0.389376 3 H s 6 -0.326170 1 O s
|
||||
9 -0.288739 1 O pz 13 0.229749 1 O dyy
|
||||
|
||||
Vector 12 Occ=0.000000D+00 E= 1.384514D+00
|
||||
MO Center= -7.4D-04, 1.3D-02, 1.8D-02, r^2= 1.4D+00
|
||||
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
|
||||
----- ------------ --------------- ----- ------------ ---------------
|
||||
8 1.510506 1 O py 4 -1.021750 1 O py
|
||||
17 -0.934844 2 H s 19 0.935260 3 H s
|
||||
9 0.272171 1 O pz 5 -0.184286 1 O pz
|
||||
|
||||
Vector 13 Occ=0.000000D+00 E= 1.433397D+00
|
||||
MO Center= 4.7D-02, 8.7D-02, -4.1D-01, r^2= 1.4D+00
|
||||
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
|
||||
----- ------------ --------------- ----- ------------ ---------------
|
||||
6 3.628985 1 O s 2 -1.436467 1 O s
|
||||
9 -1.143870 1 O pz 17 -0.805578 2 H s
|
||||
19 -0.806493 3 H s 13 -0.635948 1 O dyy
|
||||
5 0.489050 1 O pz 15 -0.410417 1 O dzz
|
||||
16 -0.312860 2 H s 18 -0.312722 3 H s
|
||||
|
||||
Vector 14 Occ=0.000000D+00 E= 2.018721D+00
|
||||
MO Center= -1.4D-02, -7.1D-03, 1.3D-01, r^2= 6.2D-01
|
||||
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
|
||||
----- ------------ --------------- ----- ------------ ---------------
|
||||
15 0.947149 1 O dzz 14 -0.531399 1 O dyz
|
||||
13 -0.526961 1 O dyy 10 -0.358371 1 O dxx
|
||||
12 -0.297495 1 O dxz 6 -0.233087 1 O s
|
||||
|
||||
Vector 15 Occ=0.000000D+00 E= 2.031133D+00
|
||||
MO Center= -8.4D-03, 1.0D-03, 8.7D-02, r^2= 6.1D-01
|
||||
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
|
||||
----- ------------ --------------- ----- ------------ ---------------
|
||||
11 1.681563 1 O dxy 12 0.314688 1 O dxz
|
||||
|
||||
|
||||
center of mass
|
||||
--------------
|
||||
x = -0.00258245 y = 0.02272235 z = 0.04407491
|
||||
|
||||
moments of inertia (a.u.)
|
||||
------------------
|
||||
6.155330507195 -0.266185800841 0.185335033231
|
||||
-0.266185800841 2.211585220634 -0.350250164177
|
||||
0.185335033231 -0.350250164177 4.020009073007
|
||||
|
||||
Mulliken analysis of the total density
|
||||
--------------------------------------
|
||||
|
||||
Atom Charge Shell Charges
|
||||
----------- ------ -------------------------------------------------------
|
||||
1 O 8 8.87 2.00 0.90 2.91 0.91 2.06 0.08
|
||||
2 H 1 0.57 0.47 0.10
|
||||
3 H 1 0.57 0.47 0.10
|
||||
|
||||
Multipole analysis of the density wrt the origin
|
||||
------------------------------------------------
|
||||
|
||||
L x y z total open nuclear
|
||||
- - - - ----- ---- -------
|
||||
0 0 0 0 -0.000000 0.000000 10.000000
|
||||
|
||||
1 1 0 0 0.094145 0.000000 0.078291
|
||||
1 0 1 0 0.148179 0.000000 0.391182
|
||||
1 0 0 1 -0.851621 0.000000 -0.500996
|
||||
|
||||
2 2 0 0 -5.338111 0.000000 0.035987
|
||||
2 1 1 0 0.149191 0.000000 0.263306
|
||||
2 1 0 1 -0.084723 0.000000 -0.165556
|
||||
2 0 2 0 -3.114464 0.000000 3.960160
|
||||
2 0 1 1 0.205130 0.000000 0.362991
|
||||
2 0 0 2 -4.329185 0.000000 1.980308
|
||||
|
||||
|
||||
Parallel integral file used 1 records with 0 large values
|
||||
|
||||
NWChem Gradients Module
|
||||
-----------------------
|
||||
|
||||
|
||||
|
||||
wavefunction = RHF
|
||||
|
||||
|
||||
|
||||
RHF ENERGY GRADIENTS
|
||||
|
||||
atom coordinates gradient
|
||||
x y z x y z
|
||||
1 O -0.015811 0.001891 0.163727 -0.000201 -0.000505 0.001671
|
||||
2 H 0.183076 1.582557 -0.654066 0.000065 -0.000505 -0.001056
|
||||
3 H 0.021701 -1.206501 -1.156743 0.000136 0.001011 -0.000616
|
||||
|
||||
----------------------------------------
|
||||
| Time | 1-e(secs) | 2-e(secs) |
|
||||
----------------------------------------
|
||||
| CPU | 0.00 | 0.03 |
|
||||
----------------------------------------
|
||||
| WALL | 0.00 | 0.03 |
|
||||
----------------------------------------
|
||||
|
||||
Task times cpu: 0.1s wall: 0.1s
|
||||
|
||||
|
||||
NWChem Input Module
|
||||
-------------------
|
||||
|
||||
|
||||
Summary of allocated global arrays
|
||||
-----------------------------------
|
||||
No active global arrays
|
||||
|
||||
|
||||
|
||||
GA Statistics for process 0
|
||||
------------------------------
|
||||
|
||||
create destroy get put acc scatter gather read&inc
|
||||
calls: 46 46 2296 477 27 0 0 68
|
||||
number of processes/call 1.00e+00 1.00e+00 1.00e+00 0.00e+00 0.00e+00
|
||||
bytes total: 2.70e+05 1.39e+05 2.27e+04 0.00e+00 0.00e+00 5.44e+02
|
||||
bytes remote: 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00
|
||||
Max memory consumed for GA by this process: 37544 bytes
|
||||
|
||||
MA_summarize_allocated_blocks: starting scan ...
|
||||
MA_summarize_allocated_blocks: scan completed: 0 heap blocks, 0 stack blocks
|
||||
MA usage statistics:
|
||||
|
||||
allocation statistics:
|
||||
heap stack
|
||||
---- -----
|
||||
current number of blocks 0 0
|
||||
maximum number of blocks 18 28
|
||||
current total bytes 0 0
|
||||
maximum total bytes 1060104 16000888
|
||||
maximum total K-bytes 1061 16001
|
||||
maximum total M-bytes 2 17
|
||||
|
||||
|
||||
CITATION
|
||||
--------
|
||||
Please cite the following reference when publishing
|
||||
results obtained with NWChem:
|
||||
|
||||
M. Valiev, E.J. Bylaska, N. Govind, K. Kowalski,
|
||||
T.P. Straatsma, H.J.J. van Dam, D. Wang, J. Nieplocha,
|
||||
E. Apra, T.L. Windus, W.A. de Jong
|
||||
"NWChem: a comprehensive and scalable open-source
|
||||
solution for large scale molecular simulations"
|
||||
Comput. Phys. Commun. 181, 1477 (2010)
|
||||
doi:10.1016/j.cpc.2010.04.018
|
||||
|
||||
AUTHORS
|
||||
-------
|
||||
E. Apra, E. J. Bylaska, W. A. de Jong, N. Govind, K. Kowalski,
|
||||
T. P. Straatsma, M. Valiev, H. J. J. van Dam, D. Wang, T. L. Windus,
|
||||
J. Hammond, J. Autschbach, K. Bhaskaran-Nair, J. Brabec, K. Lopata,
|
||||
S. A. Fischer, S. Krishnamoorthy, M. Jacquelin, W. Ma, M. Klemm, O. Villa,
|
||||
Y. Chen, V. Anisimov, F. Aquino, S. Hirata, M. T. Hackler, V. Konjkov,
|
||||
D. Mejia-Rodriguez, T. Risthaus, M. Malagoli, A. Marenich,
|
||||
A. Otero-de-la-Roza, J. Mullin, P. Nichols, R. Peverati, J. Pittner, Y. Zhao,
|
||||
P.-D. Fan, A. Fonari, M. J. Williamson, R. J. Harrison, J. R. Rehr,
|
||||
M. Dupuis, D. Silverstein, D. M. A. Smith, J. Nieplocha, V. Tipparaju,
|
||||
M. Krishnan, B. E. Van Kuiken, A. Vazquez-Mayagoitia, L. Jensen, M. Swart,
|
||||
Q. Wu, T. Van Voorhis, A. A. Auer, M. Nooijen, L. D. Crosby, E. Brown,
|
||||
G. Cisneros, G. I. Fann, H. Fruchtl, J. Garza, K. Hirao, R. A. Kendall,
|
||||
J. A. Nichols, K. Tsemekhman, K. Wolinski, J. Anchell, D. E. Bernholdt,
|
||||
P. Borowski, T. Clark, D. Clerc, H. Dachsel, M. J. O. Deegan, K. Dyall,
|
||||
D. Elwood, E. Glendening, M. Gutowski, A. C. Hess, J. Jaffe, B. G. Johnson,
|
||||
J. Ju, R. Kobayashi, R. Kutteh, Z. Lin, R. Littlefield, X. Long, B. Meng,
|
||||
T. Nakajima, S. Niu, L. Pollack, M. Rosing, K. Glaesemann, G. Sandrone,
|
||||
M. Stave, H. Taylor, G. Thomas, J. H. van Lenthe, A. T. Wong, Z. Zhang.
|
||||
|
||||
Total times cpu: 0.1s wall: 0.1s
|
||||
@ -1,447 +0,0 @@
|
||||
#!/usr/bin/env python
|
||||
|
||||
# ----------------------------------------------------------------------
|
||||
# LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
# https://www.lammps.org/ Sandia National Laboratories
|
||||
# Steve Plimpton, sjplimp@sandia.gov
|
||||
# ----------------------------------------------------------------------
|
||||
|
||||
# Syntax: nwchem_wrap.py file/zmq ao/pw input_template
|
||||
# file/zmg = messaging mode, must match LAMMPS messaging mode
|
||||
# ao/pw = basis set mode, selects between atom-centered and plane-wave
|
||||
# the input_template file must correspond to the appropriate basis set mode:
|
||||
# the "ao" mode supports the scf and dft modules in NWChem,
|
||||
# the "pw" mode supports the nwpw module.
|
||||
# input_template = NWChem input file used as template, must include a
|
||||
# "geometry" block with the atoms in the simulation, dummy
|
||||
# xyz coordinates should be included (but are not used).
|
||||
# Atom ordering must match LAMMPS input.
|
||||
|
||||
# wrapper on NWChem
|
||||
# receives message with list of coords
|
||||
# creates NWChem inputs
|
||||
# invokes NWChem to calculate self-consistent energy of that config
|
||||
# reads NWChem outputs
|
||||
# sends message with energy, forces, pressure to client
|
||||
|
||||
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 re
|
||||
import os
|
||||
import shutil
|
||||
from cslib import CSlib
|
||||
|
||||
# comment out 2nd line once 1st line is correct for your system
|
||||
|
||||
nwchemcmd = "mpirun -np 1 /usr/bin/nwchem"
|
||||
nwchemcmd = "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 input file to setup problem
|
||||
# return natoms
|
||||
|
||||
def nwchem_setup_ao(input):
|
||||
|
||||
template = open(input,'r')
|
||||
|
||||
geometry_block = False
|
||||
natoms = 0
|
||||
|
||||
while True:
|
||||
line = template.readline()
|
||||
if not line: break
|
||||
|
||||
if geometry_block and re.search("end",line):
|
||||
geometry_block = False
|
||||
if geometry_block and not re.match("#",line) :
|
||||
natoms += 1
|
||||
if re.search("geometry",line):
|
||||
geometry_block = True
|
||||
|
||||
return natoms
|
||||
|
||||
# -------------------------------------
|
||||
# write a new input file for NWChem
|
||||
# assumes the NWChem input geometry is to be specified in angstroms
|
||||
|
||||
def nwchem_input_write_ao(input,coords):
|
||||
|
||||
template = open(input,'r')
|
||||
new_input = open("nwchem_lammps.nw",'w')
|
||||
|
||||
geometry_block = False
|
||||
i = 0
|
||||
|
||||
while True:
|
||||
line = template.readline()
|
||||
if not line: break
|
||||
|
||||
if geometry_block and not re.match("#",line) and re.search("end",line):
|
||||
geometry_block = False
|
||||
if os.path.exists("nwchem_lammps.movecs"):
|
||||
# The below is hacky, but one of these lines will be ignored
|
||||
# by NWChem depending on if the input file is for scf/dft.
|
||||
append = "\nscf\n vectors input nwchem_lammps.movecs\nend\n"
|
||||
append2 = "\ndft\n vectors input nwchem_lammps.movecs\nend\n"
|
||||
line = line + append + append2
|
||||
|
||||
if geometry_block and not re.match("#",line):
|
||||
x = coords[3*i+0]
|
||||
y = coords[3*i+1]
|
||||
z = coords[3*i+2]
|
||||
coord_string = " %g %g %g \n" % (x,y,z)
|
||||
atom_string = line.split()[0]
|
||||
line = atom_string + coord_string
|
||||
i += 1
|
||||
|
||||
if (not re.match("#",line)) and re.search("geometry",line):
|
||||
geometry_block = True
|
||||
line = "geometry units angstrom noautosym nocenter\n"
|
||||
|
||||
print(line,file=new_input,end='')
|
||||
|
||||
new_input.close()
|
||||
|
||||
# -------------------------------------
|
||||
# read a NWChem output nwchem_lammps.out file
|
||||
|
||||
def nwchem_read_ao(natoms, log):
|
||||
|
||||
nwchem_output = open(log, 'r')
|
||||
energy_pattern = r"Total \w+ energy"
|
||||
gradient_pattern = "x y z x y z"
|
||||
|
||||
eout = 0.0
|
||||
fout = []
|
||||
|
||||
while True:
|
||||
line = nwchem_output.readline()
|
||||
if not line: break
|
||||
|
||||
# pattern match for energy
|
||||
if re.search(energy_pattern,line):
|
||||
eout = float(line.split()[4])
|
||||
|
||||
# pattern match for forces
|
||||
if re.search(gradient_pattern, line):
|
||||
for i in range(natoms):
|
||||
line = nwchem_output.readline()
|
||||
forces = line.split()
|
||||
fout += [float(forces[5]), float(forces[6]), float(forces[7])]
|
||||
|
||||
# convert units
|
||||
hartree2eV = 27.21138602
|
||||
bohr2angstrom = 0.52917721092
|
||||
eout = eout * hartree2eV
|
||||
fout = [i * -hartree2eV/bohr2angstrom for i in fout]
|
||||
|
||||
return eout,fout
|
||||
|
||||
# -------------------------------------
|
||||
# read initial planewave input file to setup problem
|
||||
# return natoms,box
|
||||
def nwchem_setup_pw(input):
|
||||
|
||||
template = open(input,'r')
|
||||
|
||||
geometry_block = False
|
||||
system_block = False
|
||||
coord_pattern = r"^\s*\w{1,2}(?:\s+-?(?:\d+.?\d*|\d*.?\d+)){3}"
|
||||
natoms = 0
|
||||
box = []
|
||||
|
||||
while True:
|
||||
line = template.readline()
|
||||
if not line: break
|
||||
|
||||
if geometry_block and re.search("system crystal",line):
|
||||
system_block = True
|
||||
for i in range(3):
|
||||
line = template.readline()
|
||||
line = re.sub(r'd|D', 'e', line)
|
||||
box += [float(line.split()[1])]
|
||||
|
||||
if geometry_block and not system_block and re.match("#",line) and re.search("end",line):
|
||||
geometry_block = False
|
||||
|
||||
if system_block and re.search("end",line):
|
||||
system_block = False
|
||||
|
||||
if geometry_block and not re.match("#",line) and re.search(coord_pattern,line):
|
||||
natoms += 1
|
||||
|
||||
if re.search("geometry",line) and not re.match("#",line):
|
||||
geometry_block = True
|
||||
|
||||
return natoms,box
|
||||
|
||||
# -------------------------------------
|
||||
# write a new planewave input file for NWChem
|
||||
# assumes the NWChem input geometry is to be specified fractional coordinates
|
||||
|
||||
def nwchem_input_write_pw(input,coords,box):
|
||||
|
||||
template = open(input,'r')
|
||||
new_input = open("nwchem_lammps.nw",'w')
|
||||
|
||||
writing_atoms = False
|
||||
geometry_block = False
|
||||
system_block = False
|
||||
coord_pattern = r"^\s*\w{1,2}(?:\s+-?(?:\d+.?\d*|\d*.?\d+)){3}"
|
||||
i = 0
|
||||
|
||||
while True:
|
||||
line = template.readline()
|
||||
if not line: break
|
||||
|
||||
if geometry_block and re.search("system crystal",line):
|
||||
system_block = True
|
||||
|
||||
if geometry_block and not system_block and not re.match("#",line) and re.search("end",line):
|
||||
geometry_block = False
|
||||
if os.path.exists("nwchem_lammps.movecs"):
|
||||
append = "\nnwpw\n vectors input nwchem_lammps.movecs\nend\n"
|
||||
line = line + append
|
||||
|
||||
if system_block and re.search("end",line):
|
||||
system_block = False
|
||||
|
||||
if geometry_block and not re.match("#",line) and re.search(coord_pattern,line):
|
||||
x = coords[3*i+0] / box[0]
|
||||
y = coords[3*i+1] / box[1]
|
||||
z = coords[3*i+2] / box[2]
|
||||
coord_string = " %g %g %g \n" % (x,y,z)
|
||||
atom_string = line.split()[0]
|
||||
line = atom_string + coord_string
|
||||
i += 1
|
||||
|
||||
if re.search("geometry",line) and not re.match("#",line):
|
||||
geometry_block = True
|
||||
|
||||
print(line,file=new_input,end='')
|
||||
|
||||
new_input.close()
|
||||
|
||||
# -------------------------------------
|
||||
# read a NWChem output nwchem_lammps.out file for planewave calculation
|
||||
|
||||
def nwchem_read_pw(log):
|
||||
nw_output = open(log, 'r')
|
||||
|
||||
eout = 0.0
|
||||
sout = []
|
||||
fout = []
|
||||
reading_forces = False
|
||||
|
||||
while True:
|
||||
line = nw_output.readline()
|
||||
if not line: break
|
||||
|
||||
# pattern match for energy
|
||||
if re.search("PSPW energy",line):
|
||||
eout = float(line.split()[4])
|
||||
|
||||
# pattern match for forces
|
||||
if re.search("C\.O\.M", line):
|
||||
reading_forces = False
|
||||
if reading_forces:
|
||||
forces = line.split()
|
||||
fout += [float(forces[3]), float(forces[4]), float(forces[5])]
|
||||
if re.search("Ion Forces",line):
|
||||
reading_forces = True
|
||||
|
||||
# pattern match for stress
|
||||
if re.search("=== total gradient ===",line):
|
||||
stensor = []
|
||||
for i in range(3):
|
||||
line = nw_output.readline()
|
||||
line = line.replace("S ="," ")
|
||||
stress = line.split()
|
||||
stensor += [float(stress[1]), float(stress[2]), float(stress[3])]
|
||||
sxx = stensor[0]
|
||||
syy = stensor[4]
|
||||
szz = stensor[8]
|
||||
sxy = 0.5 * (float(stensor[1]) + float(stensor[3]))
|
||||
sxz = 0.5 * (stensor[2] + stensor[6])
|
||||
syz = 0.5 * (stensor[5] + stensor[7])
|
||||
sout = [sxx,syy,szz,sxy,sxz,syz]
|
||||
|
||||
# convert units
|
||||
hartree2eV = 27.21138602
|
||||
bohr2angstrom = 0.52917721092
|
||||
austress2bar = 294210156.97
|
||||
eout = eout * hartree2eV
|
||||
fout = [i * hartree2eV/bohr2angstrom for i in fout]
|
||||
sout = [i * austress2bar for i in sout]
|
||||
|
||||
return eout,fout,sout
|
||||
|
||||
# -------------------------------------
|
||||
# main program
|
||||
|
||||
# command-line args
|
||||
#
|
||||
if len(sys.argv) != 4:
|
||||
print("Syntax: python nwchem_wrap.py file/zmq ao/pw input_template")
|
||||
sys.exit(1)
|
||||
|
||||
comm_mode = sys.argv[1]
|
||||
basis_type = sys.argv[2]
|
||||
input_template = sys.argv[3]
|
||||
|
||||
if comm_mode == "file": cs = CSlib(1,comm_mode,"tmp.couple",None)
|
||||
elif comm_mode == "zmq": cs = CSlib(1,comm_mode,"*:5555",None)
|
||||
else:
|
||||
print("Syntax: python nwchem_wrap.py file/zmq")
|
||||
sys.exit(1)
|
||||
|
||||
|
||||
natoms = 0
|
||||
box = []
|
||||
if basis_type == "ao":
|
||||
natoms = nwchem_setup_ao(input_template)
|
||||
elif basis_type == "pw":
|
||||
natoms,box = nwchem_setup_pw(input_template)
|
||||
|
||||
# initial message for AIMD 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
|
||||
|
||||
i = 0
|
||||
if not os.path.exists("nwchem_logs"):
|
||||
os.mkdir("nwchem_logs")
|
||||
|
||||
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, PERIODICITY, ORIGIN, BOX,
|
||||
# NATOMS, COORDS
|
||||
# optional fields: others in enum above, but NWChem ignores them
|
||||
|
||||
if msgID == SETUP:
|
||||
|
||||
origin = []
|
||||
box_lmp = []
|
||||
natoms_recv = ntypes_recv = 0
|
||||
types = []
|
||||
coords = []
|
||||
|
||||
for field in fieldID:
|
||||
if field == DIM:
|
||||
dim = cs.unpack_int(DIM)
|
||||
if dim != 3: error("NWChem only performs 3d simulations")
|
||||
elif field == PERIODICITY:
|
||||
periodicity = cs.unpack(PERIODICITY,1)
|
||||
if basis_type == "ao":
|
||||
if periodicity[0] or periodicity[1] or periodicity[2]:
|
||||
error("NWChem AO basis wrapper only currently supports fully aperiodic systems")
|
||||
elif basis_type == "pw":
|
||||
if not periodicity[0] or not periodicity[1] or not periodicity[2]:
|
||||
error("NWChem PW basis wrapper only currently supports fully periodic systems")
|
||||
elif field == ORIGIN:
|
||||
origin = cs.unpack(ORIGIN,1)
|
||||
elif field == BOX:
|
||||
box_lmp = cs.unpack(BOX,1)
|
||||
if (basis_type == "pw"):
|
||||
if (box[0] != box_lmp[0] or box[1] != box_lmp[4] or box[2] != box_lmp[8]):
|
||||
error("NWChem wrapper mismatch in box dimensions")
|
||||
elif field == NATOMS:
|
||||
natoms_recv = cs.unpack_int(NATOMS)
|
||||
if natoms != natoms_recv:
|
||||
error("NWChem wrapper mismatch in number of atoms")
|
||||
elif field == COORDS:
|
||||
coords = cs.unpack(COORDS,1)
|
||||
|
||||
if not origin or not box_lmp or not natoms or not coords:
|
||||
error("Required NWChem 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)
|
||||
|
||||
if not coords: error("Required NWChem wrapper step field not received");
|
||||
|
||||
else: error("NWChem wrapper received unrecognized message")
|
||||
|
||||
# unpack coords from client
|
||||
# create NWChem input
|
||||
|
||||
if basis_type == "ao":
|
||||
nwchem_input_write_ao(input_template,coords)
|
||||
elif basis_type == "pw":
|
||||
nwchem_input_write_pw(input_template,coords,box)
|
||||
|
||||
# invoke NWChem
|
||||
|
||||
i += 1
|
||||
log = "nwchem_lammps.out"
|
||||
archive = "nwchem_logs/nwchem_lammps" + str(i) + ".out"
|
||||
cmd = nwchemcmd + " nwchem_lammps.nw > " + log
|
||||
print("\nLaunching NWChem ...")
|
||||
print(cmd)
|
||||
subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
|
||||
|
||||
shutil.copyfile(log,archive)
|
||||
|
||||
# process NWChem output
|
||||
|
||||
if basis_type == "ao":
|
||||
energy,forces = nwchem_read_ao(natoms,log)
|
||||
virial = [0,0,0,0,0,0]
|
||||
elif basis_type == "pw":
|
||||
energy,forces,virial = nwchem_read_pw(log)
|
||||
|
||||
# return forces, energy 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
|
||||
@ -1,15 +0,0 @@
|
||||
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
|
||||
|
||||
@ -1,34 +0,0 @@
|
||||
# small W unit cell for use with NWChem
|
||||
|
||||
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 $z
|
||||
|
||||
velocity all create 300.0 87287 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 10 check no
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all client/md
|
||||
fix_modify 2 energy yes
|
||||
|
||||
thermo 1
|
||||
run 3
|
||||
|
||||
@ -1,38 +0,0 @@
|
||||
# small W unit cell for use with NWChem
|
||||
|
||||
variable mode index file
|
||||
|
||||
if "${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
|
||||
|
||||
group one id 2
|
||||
displace_atoms one move 0.1 0.2 0.3
|
||||
|
||||
replicate $x $y $z
|
||||
|
||||
velocity all create 300.0 87287 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 10 check no
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all client/md
|
||||
fix_modify 2 energy yes
|
||||
|
||||
dump 1 all custom 1 dump.W.min id type x y z
|
||||
|
||||
thermo 1
|
||||
minimize 1.0e-6 1.0e-6 10 50
|
||||
@ -1,76 +0,0 @@
|
||||
LAMMPS (18 Sep 2018)
|
||||
# small W unit cell for use with NWChem
|
||||
|
||||
variable mode index file
|
||||
|
||||
if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555"
|
||||
message client md file tmp.couple
|
||||
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 1 MPI processor grid
|
||||
reading atoms ...
|
||||
2 atoms
|
||||
mass 1 183.85
|
||||
|
||||
replicate $x $y $z
|
||||
replicate 1 $y $z
|
||||
replicate 1 1 $z
|
||||
replicate 1 1 1
|
||||
orthogonal box = (0 0 0) to (3.16 3.16 3.16)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
2 atoms
|
||||
Time spent = 0.000187325 secs
|
||||
|
||||
velocity all create 300.0 87287 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 10 check no
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all client/md
|
||||
fix_modify 2 energy yes
|
||||
|
||||
thermo 1
|
||||
run 3
|
||||
Per MPI rank memory allocation (min/avg/max) = 1.8 | 1.8 | 1.8 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 300 0 0 -549.75686 36815830
|
||||
1 300 0 0 -549.75686 36815830
|
||||
2 300 0 0 -549.75686 36815830
|
||||
3 300 0 0 -549.75686 36815830
|
||||
Loop time of 0.400933 on 1 procs for 3 steps with 2 atoms
|
||||
|
||||
Performance: 0.646 ns/day, 37.123 hours/ns, 7.483 timesteps/s
|
||||
0.1% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 4.755e-06 | 4.755e-06 | 4.755e-06 | 0.0 | 0.00
|
||||
Output | 0.00010114 | 0.00010114 | 0.00010114 | 0.0 | 0.03
|
||||
Modify | 0.40082 | 0.40082 | 0.40082 | 0.0 | 99.97
|
||||
Other | | 1.232e-05 | | | 0.00
|
||||
|
||||
Nlocal: 2 ave 2 max 2 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 7 ave 7 max 7 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds not checked
|
||||
|
||||
Total wall time: 0:00:09
|
||||
@ -1,78 +0,0 @@
|
||||
LAMMPS (19 Sep 2019)
|
||||
# small W unit cell for use with NWChem
|
||||
|
||||
variable mode index file
|
||||
|
||||
if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555"
|
||||
message client md file tmp.couple
|
||||
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 1 MPI processor grid
|
||||
reading atoms ...
|
||||
2 atoms
|
||||
read_data CPU = 0.0014801 secs
|
||||
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 1 MPI processor grid
|
||||
2 atoms
|
||||
replicate CPU = 0.000123978 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
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:166)
|
||||
Per MPI rank memory allocation (min/avg/max) = 1.801 | 1.801 | 1.801 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 300 0 0 -549.75686 36815830
|
||||
1 298.93216 0 0 -549.75686 36815825
|
||||
2 295.76254 0 0 -549.75687 36814830
|
||||
3 290.55935 0 0 -549.75687 36811865
|
||||
Loop time of 2.60414 on 1 procs for 3 steps with 2 atoms
|
||||
|
||||
Performance: 0.100 ns/day, 241.124 hours/ns, 1.152 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 | 7.1526e-06 | 7.1526e-06 | 7.1526e-06 | 0.0 | 0.00
|
||||
Output | 0.00012779 | 0.00012779 | 0.00012779 | 0.0 | 0.00
|
||||
Modify | 2.604 | 2.604 | 2.604 | 0.0 | 99.99
|
||||
Other | | 9.06e-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: 0:00:05
|
||||
@ -1,92 +0,0 @@
|
||||
LAMMPS (19 Sep 2019)
|
||||
# small W unit cell for use with NWChem
|
||||
|
||||
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 file tmp.couple
|
||||
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 1 MPI processor grid
|
||||
reading atoms ...
|
||||
2 atoms
|
||||
read_data CPU = 0.00183487 secs
|
||||
mass 1 183.85
|
||||
|
||||
group one id 2
|
||||
1 atoms in group one
|
||||
displace_atoms one move 0.1 0.2 0.3
|
||||
|
||||
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 1 MPI processor grid
|
||||
2 atoms
|
||||
replicate CPU = 0.000159979 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
|
||||
|
||||
dump 1 all custom 1 tmp.dump id type x y z
|
||||
|
||||
thermo 1
|
||||
minimize 1.0e-6 1.0e-6 10 50
|
||||
WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (../min.cpp:174)
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:166)
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.676 | 4.676 | 4.676 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 300 0 0 -547.52142 28510277
|
||||
1 300 0 0 -549.43104 35614471
|
||||
2 300 0 0 -549.75661 36815830
|
||||
3 300 0 0 -549.75662 36815830
|
||||
Loop time of 7.71121 on 1 procs for 3 steps with 2 atoms
|
||||
|
||||
0.0% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = energy tolerance
|
||||
Energy initial, next-to-last, final =
|
||||
-547.560202518 -549.795386038 -549.795398827
|
||||
Force two-norm initial, final = 16.0041 0.00108353
|
||||
Force max component initial, final = 9.57978 0.000719909
|
||||
Final line search alpha, max atom move = 1 0.000719909
|
||||
Iterations, force evaluations = 3 5
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 9.5367e-07 | 9.5367e-07 | 9.5367e-07 | 0.0 | 0.00
|
||||
Comm | 1.3113e-05 | 1.3113e-05 | 1.3113e-05 | 0.0 | 0.00
|
||||
Output | 0.00017023 | 0.00017023 | 0.00017023 | 0.0 | 0.00
|
||||
Modify | 7.7109 | 7.7109 | 7.7109 | 0.0 |100.00
|
||||
Other | | 0.0001729 | | | 0.00
|
||||
|
||||
Nlocal: 2 ave 2 max 2 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 1
|
||||
Dangerous builds not checked
|
||||
Total wall time: 0:00:19
|
||||
File diff suppressed because it is too large
Load Diff
@ -1,817 +0,0 @@
|
||||
argument 1 = nwchem_lammps.nw
|
||||
|
||||
|
||||
|
||||
============================== echo of input deck ==============================
|
||||
echo
|
||||
|
||||
#**** Enter the geometry using fractional coordinates ****
|
||||
geometry units angstrom noautosym
|
||||
system crystal
|
||||
lat_a 3.16d0
|
||||
lat_b 3.16d0
|
||||
lat_c 3.16d0
|
||||
end
|
||||
W 0.999335 0.99967 0.998875
|
||||
W 0.500665 0.50033 0.501125
|
||||
end
|
||||
|
||||
nwpw
|
||||
vectors input nwchem_lammps.movecs
|
||||
end
|
||||
|
||||
#***** setup the nwpw gamma point code ****
|
||||
nwpw
|
||||
simulation_cell
|
||||
ngrid 16 16 16
|
||||
end
|
||||
ewald_ncut 8
|
||||
mulliken
|
||||
lcao #old default
|
||||
end
|
||||
|
||||
nwpw
|
||||
tolerances 1.0d-9 1.0d-9
|
||||
end
|
||||
|
||||
task pspw stress
|
||||
================================================================================
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
Northwest Computational Chemistry Package (NWChem) 6.8
|
||||
------------------------------------------------------
|
||||
|
||||
|
||||
Environmental Molecular Sciences Laboratory
|
||||
Pacific Northwest National Laboratory
|
||||
Richland, WA 99352
|
||||
|
||||
Copyright (c) 1994-2018
|
||||
Pacific Northwest National Laboratory
|
||||
Battelle Memorial Institute
|
||||
|
||||
NWChem is an open-source computational chemistry package
|
||||
distributed under the terms of the
|
||||
Educational Community License (ECL) 2.0
|
||||
A copy of the license is included with this distribution
|
||||
in the LICENSE.TXT file
|
||||
|
||||
ACKNOWLEDGMENT
|
||||
--------------
|
||||
|
||||
This software and its documentation were developed at the
|
||||
EMSL at Pacific Northwest National Laboratory, a multiprogram
|
||||
national laboratory, operated for the U.S. Department of Energy
|
||||
by Battelle under Contract Number DE-AC05-76RL01830. Support
|
||||
for this work was provided by the Department of Energy Office
|
||||
of Biological and Environmental Research, Office of Basic
|
||||
Energy Sciences, and the Office of Advanced Scientific Computing.
|
||||
|
||||
|
||||
Job information
|
||||
---------------
|
||||
|
||||
hostname = singsing
|
||||
program = /home/sjplimp/tools/nwchem-6.8.1-release/bin/LINUX64/nwchem
|
||||
date = Thu Oct 3 16:57:17 2019
|
||||
|
||||
compiled = Wed_Oct_02_09:25:27_2019
|
||||
source = /home/sjplimp/tools/nwchem-6.8.1-release
|
||||
nwchem branch = Development
|
||||
nwchem revision = N/A
|
||||
ga revision = 5.6.5
|
||||
use scalapack = F
|
||||
input = nwchem_lammps.nw
|
||||
prefix = nwchem_lammps.
|
||||
data base = ./nwchem_lammps.db
|
||||
status = restart
|
||||
nproc = 1
|
||||
time left = -1s
|
||||
|
||||
|
||||
|
||||
Memory information
|
||||
------------------
|
||||
|
||||
heap = 13107200 doubles = 100.0 Mbytes
|
||||
stack = 13107197 doubles = 100.0 Mbytes
|
||||
global = 26214400 doubles = 200.0 Mbytes (distinct from heap & stack)
|
||||
total = 52428797 doubles = 400.0 Mbytes
|
||||
verify = yes
|
||||
hardfail = no
|
||||
|
||||
|
||||
Directory information
|
||||
---------------------
|
||||
|
||||
0 permanent = .
|
||||
0 scratch = .
|
||||
|
||||
|
||||
Previous task information
|
||||
-------------------------
|
||||
|
||||
Theory = pspw
|
||||
Operation = stress
|
||||
Status = unknown
|
||||
Qmmm = F
|
||||
Ignore = F
|
||||
|
||||
|
||||
Geometries in the database
|
||||
--------------------------
|
||||
|
||||
Name Natoms Last Modified
|
||||
-------------------------------- ------ ------------------------
|
||||
1 geometry 2 Thu Oct 3 16:57:16 2019
|
||||
|
||||
The geometry named "geometry" is the default for restart
|
||||
|
||||
|
||||
|
||||
Basis sets in the database
|
||||
--------------------------
|
||||
|
||||
There are no basis sets in the database
|
||||
|
||||
|
||||
|
||||
NWChem Input Module
|
||||
-------------------
|
||||
|
||||
|
||||
|
||||
!!!!!!!!! geom_3d NEEDS TESTING !!!!!!!!!!
|
||||
|
||||
|
||||
Geometry "geometry" -> ""
|
||||
-------------------------
|
||||
|
||||
Output coordinates in angstroms (scale by 1.889725989 to convert to a.u.)
|
||||
|
||||
No. Tag Charge X Y Z
|
||||
---- ---------------- ---------- -------------- -------------- --------------
|
||||
1 W 74.0000 3.15789860 3.15895720 3.15644500
|
||||
2 W 74.0000 1.58210140 1.58104280 1.58355500
|
||||
|
||||
Lattice Parameters
|
||||
------------------
|
||||
|
||||
lattice vectors in angstroms (scale by 1.889725989 to convert to a.u.)
|
||||
|
||||
a1=< 3.160 0.000 0.000 >
|
||||
a2=< 0.000 3.160 0.000 >
|
||||
a3=< 0.000 0.000 3.160 >
|
||||
a= 3.160 b= 3.160 c= 3.160
|
||||
alpha= 90.000 beta= 90.000 gamma= 90.000
|
||||
omega= 31.6
|
||||
|
||||
reciprocal lattice vectors in a.u.
|
||||
|
||||
b1=< 1.052 0.000 -0.000 >
|
||||
b2=< -0.000 1.052 -0.000 >
|
||||
b3=< 0.000 0.000 1.052 >
|
||||
|
||||
Atomic Mass
|
||||
-----------
|
||||
|
||||
W 183.951000
|
||||
|
||||
|
||||
|
||||
XYZ format geometry
|
||||
-------------------
|
||||
2
|
||||
geometry
|
||||
W 3.15789860 3.15895720 3.15644500
|
||||
W 1.58210140 1.58104280 1.58355500
|
||||
|
||||
==============================================================================
|
||||
internuclear distances
|
||||
------------------------------------------------------------------------------
|
||||
center one | center two | atomic units | angstroms
|
||||
------------------------------------------------------------------------------
|
||||
2 W | 1 W | 5.15689 | 2.72891
|
||||
------------------------------------------------------------------------------
|
||||
number of included internuclear distances: 1
|
||||
==============================================================================
|
||||
|
||||
|
||||
|
||||
>>>> PSPW Parallel Module - stress <<<<
|
||||
****************************************************
|
||||
* *
|
||||
* NWPW PSPW Calculation *
|
||||
* *
|
||||
* [ (Grassmann/Stiefel manifold implementation) ] *
|
||||
* *
|
||||
* [ NorthWest Chemistry implementation ] *
|
||||
* *
|
||||
* version #5.10 06/12/02 *
|
||||
* *
|
||||
* This code was developed by Eric J. Bylaska, *
|
||||
* and was based upon algorithms and code *
|
||||
* developed by the group of Prof. John H. Weare *
|
||||
* *
|
||||
****************************************************
|
||||
>>> JOB STARTED AT Thu Oct 3 16:57:17 2019 <<<
|
||||
================ input data ========================
|
||||
|
||||
input psi filename:./nwchem_lammps.movecs
|
||||
|
||||
initializing pspw_APC data structure
|
||||
------------------------------------
|
||||
nga, ngs: 3 6
|
||||
Gc : 2.5000000000000000
|
||||
APC gamma: 1 0.59999999999999998
|
||||
APC gamma: 2 0.90000000000000002
|
||||
APC gamma: 3 1.3500000000000001
|
||||
|
||||
number of processors used: 1
|
||||
processor grid : 1 x 1
|
||||
parallel mapping :2d hilbert
|
||||
parallel mapping : balanced
|
||||
number of threads : 1
|
||||
parallel io : off
|
||||
|
||||
options:
|
||||
boundary conditions = periodic (version3)
|
||||
electron spin = restricted
|
||||
exchange-correlation = LDA (Vosko et al) parameterization
|
||||
|
||||
elements involved in the cluster:
|
||||
1: W valence charge: 6.0000 lmax= 2
|
||||
comment : Troullier-Martins pseudopotential
|
||||
pseudpotential type : 0
|
||||
highest angular component : 2
|
||||
local potential used : 0
|
||||
number of non-local projections: 8
|
||||
semicore corrections included : 1.800 (radius) 4.538 (charge)
|
||||
cutoff = 2.389 3.185 2.244
|
||||
|
||||
|
||||
total charge: 0.000
|
||||
|
||||
atomic composition:
|
||||
W : 2
|
||||
|
||||
number of electrons: spin up= 6 ( 6 per task) down= 6 ( 6 per task) (Fourier space)
|
||||
number of orbitals : spin up= 6 ( 6 per task) down= 6 ( 6 per task) (Fourier space)
|
||||
|
||||
supercell:
|
||||
cell_name: cell_default
|
||||
lattice: a1=< 5.972 0.000 0.000 >
|
||||
a2=< 0.000 5.972 0.000 >
|
||||
a3=< 0.000 0.000 5.972 >
|
||||
reciprocal: b1=< 1.052 0.000 -0.000 >
|
||||
b2=< -0.000 1.052 -0.000 >
|
||||
b3=< 0.000 0.000 1.052 >
|
||||
lattice: a= 5.972 b= 5.972 c= 5.972
|
||||
alpha= 90.000 beta= 90.000 gamma= 90.000
|
||||
omega= 212.9
|
||||
|
||||
density cutoff= 35.427 fft= 16x 16x 16( 1052 waves 1052 per task)
|
||||
wavefnc cutoff= 35.427 fft= 16x 16x 16( 1052 waves 1052 per task)
|
||||
Ewald summation: cut radius= 1.90 and 8
|
||||
Madelung Wigner-Seitz= 1.76011888 (alpha= 2.83729748 rs= 3.70444413)
|
||||
|
||||
technical parameters:
|
||||
time step= 5.80 fictitious mass= 400000.0
|
||||
tolerance=0.100E-08 (energy) 0.100E-08 (density)
|
||||
maximum iterations = 1000 ( 10 inner 100 outer )
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
== Energy Calculation ==
|
||||
|
||||
|
||||
====== Grassmann conjugate gradient iteration ======
|
||||
>>> ITERATION STARTED AT Thu Oct 3 16:57:17 2019 <<<
|
||||
iter. Energy DeltaE DeltaRho
|
||||
------------------------------------------------------
|
||||
10 -0.2020457267E+02 -0.12753E-06 0.54770E-09
|
||||
20 -0.2020457281E+02 -0.96520E-09 0.65680E-11
|
||||
*** tolerance ok. iteration terminated
|
||||
>>> ITERATION ENDED AT Thu Oct 3 16:57:18 2019 <<<
|
||||
|
||||
|
||||
== Summary Of Results ==
|
||||
|
||||
number of electrons: spin up= 6.00000 down= 6.00000 (real space)
|
||||
|
||||
total energy : -0.2020457281E+02 ( -0.10102E+02/ion)
|
||||
total orbital energy: 0.5093546150E+01 ( 0.84892E+00/electron)
|
||||
hartree energy : 0.2903382088E+00 ( 0.48390E-01/electron)
|
||||
exc-corr energy : -0.9445078100E+01 ( -0.15742E+01/electron)
|
||||
ion-ion energy : -0.2193939674E+02 ( -0.10970E+02/ion)
|
||||
|
||||
kinetic (planewave) : 0.1441586264E+02 ( 0.24026E+01/electron)
|
||||
V_local (planewave) : 0.1156111351E+02 ( 0.19269E+01/electron)
|
||||
V_nl (planewave) : -0.1508741234E+02 ( -0.25146E+01/electron)
|
||||
V_Coul (planewave) : 0.5806764176E+00 ( 0.96779E-01/electron)
|
||||
V_xc. (planewave) : -0.6376694082E+01 ( -0.10628E+01/electron)
|
||||
Virial Coefficient : -0.6466707350E+00
|
||||
|
||||
orbital energies:
|
||||
0.5414291E+00 ( 14.733eV)
|
||||
0.5414285E+00 ( 14.733eV)
|
||||
0.5414070E+00 ( 14.733eV)
|
||||
0.3596871E+00 ( 9.788eV)
|
||||
0.3596781E+00 ( 9.787eV)
|
||||
0.2031433E+00 ( 5.528eV)
|
||||
|
||||
Total PSPW energy : -0.2020457281E+02
|
||||
|
||||
|
||||
=== Spin Contamination ===
|
||||
|
||||
<Sexact^2> = 0.0000000000000000
|
||||
<S^2> = 0.0000000000000000
|
||||
|
||||
|
||||
|
||||
== Center of Charge ==
|
||||
|
||||
spin up ( -0.0030, -0.0015, -0.0050 )
|
||||
spin down ( -0.0030, -0.0015, -0.0050 )
|
||||
total ( -0.0030, -0.0015, -0.0050 )
|
||||
ionic ( -1.4929, -1.4929, -1.4929 )
|
||||
|
||||
|
||||
== Molecular Dipole wrt Center of Mass ==
|
||||
|
||||
mu = ( -17.8792, -17.8970, -17.8547 ) au
|
||||
|mu| = 30.9638 au, 78.6976 Debye
|
||||
|
||||
|
||||
Translation force removed: ( -0.00000 -0.00000 -0.00000)
|
||||
|
||||
|
||||
============= Ion Gradients =================
|
||||
Ion Forces:
|
||||
1 W ( 0.002737 0.001358 0.004631 )
|
||||
2 W ( -0.002737 -0.001358 -0.004631 )
|
||||
C.O.M. ( 0.000000 0.000000 0.000000 )
|
||||
===============================================
|
||||
|F| = 0.784689E-02
|
||||
|F|/nion = 0.392344E-02
|
||||
max|Fatom|= 0.554859E-02 ( 0.285eV/Angstrom)
|
||||
|
||||
|
||||
|
||||
|
||||
======================
|
||||
= Stress calculation =
|
||||
======================
|
||||
|
||||
|
||||
============= total gradient ==============
|
||||
S = ( 0.12512 0.00000 0.00000 )
|
||||
( 0.00000 0.12512 0.00001 )
|
||||
( 0.00000 0.00001 0.12511 )
|
||||
===================================================
|
||||
|S| = 0.21671E+00
|
||||
pressure = 0.125E+00 au
|
||||
= 0.368E+02 Mbar
|
||||
= 0.368E+04 GPa
|
||||
= 0.363E+08 atm
|
||||
|
||||
|
||||
dE/da = 0.12512
|
||||
dE/db = 0.12512
|
||||
dE/dc = 0.12511
|
||||
dE/dalpha = -0.00003
|
||||
dE/dbeta = -0.00002
|
||||
dE/dgamma = -0.00001
|
||||
|
||||
|
||||
|
||||
|
||||
*************************************************************
|
||||
** **
|
||||
** PSPW Mulliken analysis **
|
||||
** **
|
||||
** Population analysis algorithm devloped by Ryoichi Kawai **
|
||||
** **
|
||||
** Thu Oct 3 16:57 **
|
||||
** **
|
||||
*************************************************************
|
||||
|
||||
|
||||
== XYZ OUTPUT ==
|
||||
|
||||
|
||||
2
|
||||
|
||||
W -0.002101 -0.001043 -0.003555
|
||||
W -1.577898 -1.578956 -1.576444
|
||||
|
||||
|
||||
== Atomic Orbital Expansion ==
|
||||
|
||||
W nodamping
|
||||
|
||||
|
||||
=====================================================
|
||||
| POPULATION ANALYSIS OF FILLED MOLECULAR ORBITALS |
|
||||
=====================================================
|
||||
|
||||
|
||||
== Using pseudoatomic orbital expansion ==
|
||||
|
||||
|
||||
------------------------------------------------------------------------------
|
||||
|
||||
|
||||
*** ORBITAL= 1*** SPIN=BOTH SUM= 0.12471E+01 E= 0.54143E+00 ( 14.733eV)
|
||||
|
||||
NO ATOM L POPULATION
|
||||
s
|
||||
1 W 0 0.00000 0.00000
|
||||
px pz py
|
||||
1 W 1 0.00000 -0.00018 -0.00011 0.00005
|
||||
dx2-y2 dzx d3z2-1 dyz dxy
|
||||
1 W 2 0.49999 0.00003 -0.68532 0.00001 0.10591 0.13824
|
||||
fx(x2-3y2) fz(5z2-1) fx(5z2-1) fz(5z2-3) fy(5z2-1) fxyz fy(3x2-y2)
|
||||
1 W 3 0.00001 -0.00003 -0.00187 -0.00238 -0.00028 0.00001 0.00000 -0.00017
|
||||
s
|
||||
2 W 0 0.00000 0.00000
|
||||
px pz py
|
||||
2 W 1 0.00000 0.00018 0.00011 -0.00005
|
||||
dx2-y2 dzx d3z2-1 dyz dxy
|
||||
2 W 2 0.49999 0.00003 -0.68532 0.00001 0.10591 0.13824
|
||||
fx(x2-3y2) fz(5z2-1) fx(5z2-1) fz(5z2-3) fy(5z2-1) fxyz fy(3x2-y2)
|
||||
2 W 3 0.00001 -0.00003 0.00187 0.00238 0.00028 -0.00001 -0.00000 0.00017
|
||||
|
||||
|
||||
=== DISTRIBUTION ===
|
||||
|
||||
1(W ) 0.5000 2(W ) 0.5000
|
||||
|
||||
|
||||
== ANGULAR MOMENTUM POPULATIONS ===
|
||||
|
||||
s p d f
|
||||
0.0000 0.0000 1.0000 0.0000
|
||||
|
||||
|
||||
------------------------------------------------------------------------------
|
||||
|
||||
|
||||
*** ORBITAL= 2*** SPIN=BOTH SUM= 0.12472E+01 E= 0.54143E+00 ( 14.733eV)
|
||||
|
||||
NO ATOM L POPULATION
|
||||
s
|
||||
1 W 0 0.00000 0.00000
|
||||
px pz py
|
||||
1 W 1 0.00000 0.00002 -0.00005 -0.00011
|
||||
dx2-y2 dzx d3z2-1 dyz dxy
|
||||
1 W 2 0.49998 -0.00001 -0.02322 0.00001 -0.61187 0.35363
|
||||
fx(x2-3y2) fz(5z2-1) fx(5z2-1) fz(5z2-3) fy(5z2-1) fxyz fy(3x2-y2)
|
||||
1 W 3 0.00002 -0.00001 0.00071 -0.00049 -0.00015 -0.00283 0.00006 0.00266
|
||||
s
|
||||
2 W 0 0.00000 0.00000
|
||||
px pz py
|
||||
2 W 1 0.00000 -0.00002 0.00005 0.00011
|
||||
dx2-y2 dzx d3z2-1 dyz dxy
|
||||
2 W 2 0.49998 -0.00001 -0.02322 0.00001 -0.61187 0.35363
|
||||
fx(x2-3y2) fz(5z2-1) fx(5z2-1) fz(5z2-3) fy(5z2-1) fxyz fy(3x2-y2)
|
||||
2 W 3 0.00002 -0.00001 -0.00071 0.00049 0.00015 0.00283 -0.00006 -0.00266
|
||||
|
||||
|
||||
=== DISTRIBUTION ===
|
||||
|
||||
1(W ) 0.5000 2(W ) 0.5000
|
||||
|
||||
|
||||
== ANGULAR MOMENTUM POPULATIONS ===
|
||||
|
||||
s p d f
|
||||
0.0000 0.0000 1.0000 0.0000
|
||||
|
||||
|
||||
------------------------------------------------------------------------------
|
||||
|
||||
|
||||
*** ORBITAL= 3*** SPIN=BOTH SUM= 0.12472E+01 E= 0.54141E+00 ( 14.733eV)
|
||||
|
||||
NO ATOM L POPULATION
|
||||
s
|
||||
1 W 0 0.00000 -0.00000
|
||||
px pz py
|
||||
1 W 1 0.00000 0.00010 0.00006 0.00020
|
||||
dx2-y2 dzx d3z2-1 dyz dxy
|
||||
1 W 2 0.49999 0.00000 0.17259 0.00000 0.33820 0.59651
|
||||
fx(x2-3y2) fz(5z2-1) fx(5z2-1) fz(5z2-3) fy(5z2-1) fxyz fy(3x2-y2)
|
||||
1 W 3 0.00001 0.00000 0.00001 -0.00015 0.00015 -0.00033 -0.00325 -0.00033
|
||||
s
|
||||
2 W 0 0.00000 -0.00000
|
||||
px pz py
|
||||
2 W 1 0.00000 -0.00010 -0.00006 -0.00020
|
||||
dx2-y2 dzx d3z2-1 dyz dxy
|
||||
2 W 2 0.49999 0.00000 0.17259 0.00000 0.33820 0.59651
|
||||
fx(x2-3y2) fz(5z2-1) fx(5z2-1) fz(5z2-3) fy(5z2-1) fxyz fy(3x2-y2)
|
||||
2 W 3 0.00001 0.00000 -0.00001 0.00015 -0.00015 0.00033 0.00325 0.00033
|
||||
|
||||
|
||||
=== DISTRIBUTION ===
|
||||
|
||||
1(W ) 0.5000 2(W ) 0.5000
|
||||
|
||||
|
||||
== ANGULAR MOMENTUM POPULATIONS ===
|
||||
|
||||
s p d f
|
||||
0.0000 0.0000 1.0000 0.0000
|
||||
|
||||
|
||||
------------------------------------------------------------------------------
|
||||
|
||||
|
||||
*** ORBITAL= 4*** SPIN=BOTH SUM= 0.14577E+01 E= 0.35969E+00 ( 9.788eV)
|
||||
|
||||
NO ATOM L POPULATION
|
||||
s
|
||||
1 W 0 0.00000 -0.00000
|
||||
px pz py
|
||||
1 W 1 0.00002 0.00162 -0.00440 0.00049
|
||||
dx2-y2 dzx d3z2-1 dyz dxy
|
||||
1 W 2 0.48998 -0.09896 0.00001 0.69296 0.00001 -0.00001
|
||||
fx(x2-3y2) fz(5z2-1) fx(5z2-1) fz(5z2-3) fy(5z2-1) fxyz fy(3x2-y2)
|
||||
1 W 3 0.00999 -0.09993 0.00031 -0.00131 -0.00234 -0.00064 0.00000 0.00022
|
||||
s
|
||||
2 W 0 0.00000 0.00000
|
||||
px pz py
|
||||
2 W 1 0.00002 0.00162 -0.00440 0.00049
|
||||
dx2-y2 dzx d3z2-1 dyz dxy
|
||||
2 W 2 0.48998 0.09896 -0.00001 -0.69296 -0.00001 0.00001
|
||||
fx(x2-3y2) fz(5z2-1) fx(5z2-1) fz(5z2-3) fy(5z2-1) fxyz fy(3x2-y2)
|
||||
2 W 3 0.00999 0.09993 0.00031 -0.00131 -0.00234 -0.00064 0.00000 0.00022
|
||||
|
||||
|
||||
=== DISTRIBUTION ===
|
||||
|
||||
1(W ) 0.5000 2(W ) 0.5000
|
||||
|
||||
|
||||
== ANGULAR MOMENTUM POPULATIONS ===
|
||||
|
||||
s p d f
|
||||
0.0000 0.0000 0.9800 0.0200
|
||||
|
||||
|
||||
------------------------------------------------------------------------------
|
||||
|
||||
|
||||
*** ORBITAL= 5*** SPIN=BOTH SUM= 0.14616E+01 E= 0.35968E+00 ( 9.787eV)
|
||||
|
||||
NO ATOM L POPULATION
|
||||
s
|
||||
1 W 0 0.00000 0.00000
|
||||
px pz py
|
||||
1 W 1 0.00001 0.00206 0.00063 -0.00121
|
||||
dx2-y2 dzx d3z2-1 dyz dxy
|
||||
1 W 2 0.48871 -0.69206 -0.00002 -0.09883 0.00001 0.00000
|
||||
fx(x2-3y2) fz(5z2-1) fx(5z2-1) fz(5z2-3) fy(5z2-1) fxyz fy(3x2-y2)
|
||||
1 W 3 0.01129 -0.10621 0.00214 0.00009 0.00033 0.00014 0.00000 0.00063
|
||||
s
|
||||
2 W 0 0.00000 -0.00000
|
||||
px pz py
|
||||
2 W 1 0.00001 0.00206 0.00063 -0.00121
|
||||
dx2-y2 dzx d3z2-1 dyz dxy
|
||||
2 W 2 0.48871 0.69206 0.00002 0.09883 -0.00001 -0.00000
|
||||
fx(x2-3y2) fz(5z2-1) fx(5z2-1) fz(5z2-3) fy(5z2-1) fxyz fy(3x2-y2)
|
||||
2 W 3 0.01129 0.10621 0.00214 0.00009 0.00033 0.00014 0.00000 0.00063
|
||||
|
||||
|
||||
=== DISTRIBUTION ===
|
||||
|
||||
1(W ) 0.5000 2(W ) 0.5000
|
||||
|
||||
|
||||
== ANGULAR MOMENTUM POPULATIONS ===
|
||||
|
||||
s p d f
|
||||
0.0000 0.0000 0.9774 0.0226
|
||||
|
||||
|
||||
------------------------------------------------------------------------------
|
||||
|
||||
|
||||
*** ORBITAL= 6*** SPIN=BOTH SUM= 0.19540E+01 E= 0.20314E+00 ( 5.528eV)
|
||||
|
||||
NO ATOM L POPULATION
|
||||
s
|
||||
1 W 0 0.49974 -0.70692
|
||||
px pz py
|
||||
1 W 1 0.00000 0.00028 0.00047 0.00014
|
||||
dx2-y2 dzx d3z2-1 dyz dxy
|
||||
1 W 2 0.00000 -0.00000 -0.00000 -0.00000 -0.00000 -0.00000
|
||||
fx(x2-3y2) fz(5z2-1) fx(5z2-1) fz(5z2-3) fy(5z2-1) fxyz fy(3x2-y2)
|
||||
1 W 3 0.00026 0.01609 -0.00000 -0.00007 0.00021 -0.00003 0.00000 -0.00004
|
||||
s
|
||||
2 W 0 0.49974 -0.70692
|
||||
px pz py
|
||||
2 W 1 0.00000 -0.00028 -0.00047 -0.00014
|
||||
dx2-y2 dzx d3z2-1 dyz dxy
|
||||
2 W 2 0.00000 -0.00000 -0.00000 -0.00000 -0.00000 -0.00000
|
||||
fx(x2-3y2) fz(5z2-1) fx(5z2-1) fz(5z2-3) fy(5z2-1) fxyz fy(3x2-y2)
|
||||
2 W 3 0.00026 0.01609 0.00000 0.00007 -0.00021 0.00003 -0.00000 0.00004
|
||||
|
||||
|
||||
=== DISTRIBUTION ===
|
||||
|
||||
1(W ) 0.5000 2(W ) 0.5000
|
||||
|
||||
|
||||
== ANGULAR MOMENTUM POPULATIONS ===
|
||||
|
||||
s p d f
|
||||
0.9995 0.0000 0.0000 0.0005
|
||||
|
||||
|
||||
========================================
|
||||
| POPULATION ANALYSIS ON EACH ATOM |
|
||||
========================================
|
||||
|
||||
|
||||
NO ATOM SPIN TOTAL s p d f
|
||||
1 W UP 3.00000 0.49974 0.00003 2.47866 0.02157
|
||||
1 W DOWN 3.00000 0.49974 0.00003 2.47866 0.02157
|
||||
2 W UP 3.00000 0.49974 0.00003 2.47866 0.02157
|
||||
2 W DOWN 3.00000 0.49974 0.00003 2.47866 0.02157
|
||||
|
||||
|
||||
|
||||
=== TOTAL ANGULAR MOMENTUM POPULATION ===
|
||||
|
||||
SPIN s p d f
|
||||
UP 16.66% 0.00% 82.62% 0.72%
|
||||
UP 16.66% 0.00% 82.62% 0.72%
|
||||
TOTAL 16.66% 0.00% 82.62% 0.72%
|
||||
|
||||
*************************************************************
|
||||
** **
|
||||
** PSPW Atomic Point Charge (APC) Analysis **
|
||||
** **
|
||||
** Point charge analysis based on paper by P.E. Blochl **
|
||||
** (J. Chem. Phys. vol 103, page 7422, 1995) **
|
||||
** **
|
||||
*************************************************************
|
||||
|
||||
pspw_APC data structure
|
||||
-----------------------
|
||||
nga, ngs: 3 6
|
||||
Gc : 2.5000000000000000
|
||||
APC gamma: 1 0.59999999999999998
|
||||
APC gamma: 2 0.90000000000000002
|
||||
APC gamma: 3 1.3500000000000001
|
||||
|
||||
charge analysis on each atom
|
||||
----------------------------
|
||||
|
||||
no atom Qelc Qion Qtotal
|
||||
-- ---- ------- ------- -------
|
||||
1 W -6.000 6.000 -0.000
|
||||
2 W -6.000 6.000 -0.000
|
||||
Total Q -12.000 12.000 -0.000
|
||||
|
||||
|
||||
gaussian coefficients of model density
|
||||
--------------------------------------
|
||||
|
||||
no atom g=0.000 g=0.600 g=0.900 g=1.350
|
||||
-- ---- ------- ------- ------- -------
|
||||
1 W 6.000 -7.235 17.653 -16.419
|
||||
2 W 6.000 -7.235 17.653 -16.419
|
||||
|
||||
|
||||
=== Electric Field at Atoms ===
|
||||
|
||||
1 W Atomic Electric Field =( -0.00022 -0.00011 -0.00038 )
|
||||
(ion) =( 0.00094 0.00047 0.00159 )
|
||||
(electronic) =( -0.00116 -0.00058 -0.00197 )
|
||||
2 W Atomic Electric Field =( 0.00022 0.00011 0.00038 )
|
||||
(ion) =( -0.00094 -0.00047 -0.00159 )
|
||||
(electronic) =( 0.00116 0.00058 0.00197 )
|
||||
|
||||
output psi filename:./nwchem_lammps.movecs
|
||||
|
||||
|
||||
== Timing ==
|
||||
|
||||
cputime in seconds
|
||||
prologue : 0.114428E+00
|
||||
main loop : 0.475396E+00
|
||||
epilogue : 0.316691E-01
|
||||
total : 0.621493E+00
|
||||
cputime/step: 0.559289E-02 ( 85 evalulations, 20 linesearches)
|
||||
|
||||
|
||||
Time spent doing total step percent
|
||||
total time : 0.623259E+00 0.733246E-02 100.0 %
|
||||
i/o time : 0.103071E-01 0.121260E-03 1.7 %
|
||||
FFTs : 0.348712E-01 0.410250E-03 5.6 %
|
||||
dot products : 0.981057E-02 0.115418E-03 1.6 %
|
||||
geodesic : 0.696999E-01 0.819999E-03 11.2 %
|
||||
ffm_dgemm : 0.104145E-02 0.122523E-04 0.2 %
|
||||
fmf_dgemm : 0.565297E-01 0.665055E-03 9.1 %
|
||||
mmm_dgemm : 0.129490E-03 0.152342E-05 0.0 %
|
||||
m_diagonalize : 0.701885E-03 0.825747E-05 0.1 %
|
||||
exchange correlation : 0.764353E-01 0.899239E-03 12.3 %
|
||||
local pseudopotentials : 0.439882E-03 0.517509E-05 0.1 %
|
||||
non-local pseudopotentials : 0.271890E-01 0.319871E-03 4.4 %
|
||||
hartree potentials : 0.202482E-02 0.238214E-04 0.3 %
|
||||
ion-ion interaction : 0.104062E+00 0.122426E-02 16.7 %
|
||||
structure factors : 0.152984E-01 0.179981E-03 2.5 %
|
||||
phase factors : 0.107278E-04 0.126210E-06 0.0 %
|
||||
masking and packing : 0.304392E-01 0.358108E-03 4.9 %
|
||||
queue fft : 0.111536E+00 0.131219E-02 17.9 %
|
||||
queue fft (serial) : 0.708244E-01 0.833228E-03 11.4 %
|
||||
queue fft (message passing): 0.360800E-01 0.424470E-03 5.8 %
|
||||
non-local psp FFM : 0.860008E-02 0.101177E-03 1.4 %
|
||||
non-local psp FMF : 0.111482E-01 0.131155E-03 1.8 %
|
||||
non-local psp FFM A : 0.214632E-02 0.252509E-04 0.3 %
|
||||
non-local psp FFM B : 0.560879E-02 0.659858E-04 0.9 %
|
||||
|
||||
>>> JOB COMPLETED AT Thu Oct 3 16:57:18 2019 <<<
|
||||
|
||||
Task times cpu: 0.6s wall: 0.6s
|
||||
Summary of allocated global arrays
|
||||
-----------------------------------
|
||||
No active global arrays
|
||||
|
||||
|
||||
|
||||
GA Statistics for process 0
|
||||
------------------------------
|
||||
|
||||
create destroy get put acc scatter gather read&inc
|
||||
calls: 0 0 0 0 0 0 0 0
|
||||
number of processes/call 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00
|
||||
bytes total: 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00
|
||||
bytes remote: 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00
|
||||
Max memory consumed for GA by this process: 0 bytes
|
||||
MA_summarize_allocated_blocks: starting scan ...
|
||||
MA_summarize_allocated_blocks: scan completed: 0 heap blocks, 0 stack blocks
|
||||
MA usage statistics:
|
||||
|
||||
allocation statistics:
|
||||
heap stack
|
||||
---- -----
|
||||
current number of blocks 0 0
|
||||
maximum number of blocks 294 17
|
||||
current total bytes 0 0
|
||||
maximum total bytes 4879496 351944
|
||||
maximum total K-bytes 4880 352
|
||||
maximum total M-bytes 5 1
|
||||
|
||||
|
||||
NWChem Input Module
|
||||
-------------------
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
CITATION
|
||||
--------
|
||||
Please cite the following reference when publishing
|
||||
results obtained with NWChem:
|
||||
|
||||
M. Valiev, E.J. Bylaska, N. Govind, K. Kowalski,
|
||||
T.P. Straatsma, H.J.J. van Dam, D. Wang, J. Nieplocha,
|
||||
E. Apra, T.L. Windus, W.A. de Jong
|
||||
"NWChem: a comprehensive and scalable open-source
|
||||
solution for large scale molecular simulations"
|
||||
Comput. Phys. Commun. 181, 1477 (2010)
|
||||
doi:10.1016/j.cpc.2010.04.018
|
||||
|
||||
AUTHORS
|
||||
-------
|
||||
E. Apra, E. J. Bylaska, W. A. de Jong, N. Govind, K. Kowalski,
|
||||
T. P. Straatsma, M. Valiev, H. J. J. van Dam, D. Wang, T. L. Windus,
|
||||
J. Hammond, J. Autschbach, K. Bhaskaran-Nair, J. Brabec, K. Lopata,
|
||||
S. A. Fischer, S. Krishnamoorthy, M. Jacquelin, W. Ma, M. Klemm, O. Villa,
|
||||
Y. Chen, V. Anisimov, F. Aquino, S. Hirata, M. T. Hackler, V. Konjkov,
|
||||
D. Mejia-Rodriguez, T. Risthaus, M. Malagoli, A. Marenich,
|
||||
A. Otero-de-la-Roza, J. Mullin, P. Nichols, R. Peverati, J. Pittner, Y. Zhao,
|
||||
P.-D. Fan, A. Fonari, M. J. Williamson, R. J. Harrison, J. R. Rehr,
|
||||
M. Dupuis, D. Silverstein, D. M. A. Smith, J. Nieplocha, V. Tipparaju,
|
||||
M. Krishnan, B. E. Van Kuiken, A. Vazquez-Mayagoitia, L. Jensen, M. Swart,
|
||||
Q. Wu, T. Van Voorhis, A. A. Auer, M. Nooijen, L. D. Crosby, E. Brown,
|
||||
G. Cisneros, G. I. Fann, H. Fruchtl, J. Garza, K. Hirao, R. A. Kendall,
|
||||
J. A. Nichols, K. Tsemekhman, K. Wolinski, J. Anchell, D. E. Bernholdt,
|
||||
P. Borowski, T. Clark, D. Clerc, H. Dachsel, M. J. O. Deegan, K. Dyall,
|
||||
D. Elwood, E. Glendening, M. Gutowski, A. C. Hess, J. Jaffe, B. G. Johnson,
|
||||
J. Ju, R. Kobayashi, R. Kutteh, Z. Lin, R. Littlefield, X. Long, B. Meng,
|
||||
T. Nakajima, S. Niu, L. Pollack, M. Rosing, K. Glaesemann, G. Sandrone,
|
||||
M. Stave, H. Taylor, G. Thomas, J. H. van Lenthe, A. T. Wong, Z. Zhang.
|
||||
|
||||
Total times cpu: 0.6s wall: 0.7s
|
||||
@ -1,816 +0,0 @@
|
||||
argument 1 = nwchem_lammps.nw
|
||||
|
||||
|
||||
|
||||
============================== echo of input deck ==============================
|
||||
echo
|
||||
|
||||
#**** Enter the geometry using fractional coordinates ****
|
||||
geometry units angstrom noautosym
|
||||
system crystal
|
||||
lat_a 3.16d0
|
||||
lat_b 3.16d0
|
||||
lat_c 3.16d0
|
||||
end
|
||||
W 0.0158218 0.0316436 0.0474661
|
||||
W 0.515824 0.531647 0.547471
|
||||
end
|
||||
|
||||
nwpw
|
||||
vectors input nwchem_lammps.movecs
|
||||
end
|
||||
|
||||
#***** setup the nwpw gamma point code ****
|
||||
nwpw
|
||||
simulation_cell
|
||||
ngrid 16 16 16
|
||||
end
|
||||
ewald_ncut 8
|
||||
mulliken
|
||||
lcao #old default
|
||||
end
|
||||
|
||||
nwpw
|
||||
tolerances 1.0d-9 1.0d-9
|
||||
end
|
||||
|
||||
task pspw stress
|
||||
================================================================================
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
Northwest Computational Chemistry Package (NWChem) 6.8
|
||||
------------------------------------------------------
|
||||
|
||||
|
||||
Environmental Molecular Sciences Laboratory
|
||||
Pacific Northwest National Laboratory
|
||||
Richland, WA 99352
|
||||
|
||||
Copyright (c) 1994-2018
|
||||
Pacific Northwest National Laboratory
|
||||
Battelle Memorial Institute
|
||||
|
||||
NWChem is an open-source computational chemistry package
|
||||
distributed under the terms of the
|
||||
Educational Community License (ECL) 2.0
|
||||
A copy of the license is included with this distribution
|
||||
in the LICENSE.TXT file
|
||||
|
||||
ACKNOWLEDGMENT
|
||||
--------------
|
||||
|
||||
This software and its documentation were developed at the
|
||||
EMSL at Pacific Northwest National Laboratory, a multiprogram
|
||||
national laboratory, operated for the U.S. Department of Energy
|
||||
by Battelle under Contract Number DE-AC05-76RL01830. Support
|
||||
for this work was provided by the Department of Energy Office
|
||||
of Biological and Environmental Research, Office of Basic
|
||||
Energy Sciences, and the Office of Advanced Scientific Computing.
|
||||
|
||||
|
||||
Job information
|
||||
---------------
|
||||
|
||||
hostname = singsing
|
||||
program = /home/sjplimp/tools/nwchem-6.8.1-release/bin/LINUX64/nwchem
|
||||
date = Thu Oct 3 16:58:54 2019
|
||||
|
||||
compiled = Wed_Oct_02_09:25:27_2019
|
||||
source = /home/sjplimp/tools/nwchem-6.8.1-release
|
||||
nwchem branch = Development
|
||||
nwchem revision = N/A
|
||||
ga revision = 5.6.5
|
||||
use scalapack = F
|
||||
input = nwchem_lammps.nw
|
||||
prefix = nwchem_lammps.
|
||||
data base = ./nwchem_lammps.db
|
||||
status = restart
|
||||
nproc = 1
|
||||
time left = -1s
|
||||
|
||||
|
||||
|
||||
Memory information
|
||||
------------------
|
||||
|
||||
heap = 13107200 doubles = 100.0 Mbytes
|
||||
stack = 13107197 doubles = 100.0 Mbytes
|
||||
global = 26214400 doubles = 200.0 Mbytes (distinct from heap & stack)
|
||||
total = 52428797 doubles = 400.0 Mbytes
|
||||
verify = yes
|
||||
hardfail = no
|
||||
|
||||
|
||||
Directory information
|
||||
---------------------
|
||||
|
||||
0 permanent = .
|
||||
0 scratch = .
|
||||
|
||||
|
||||
Previous task information
|
||||
-------------------------
|
||||
|
||||
Theory = pspw
|
||||
Operation = stress
|
||||
Status = unknown
|
||||
Qmmm = F
|
||||
Ignore = F
|
||||
|
||||
|
||||
Geometries in the database
|
||||
--------------------------
|
||||
|
||||
Name Natoms Last Modified
|
||||
-------------------------------- ------ ------------------------
|
||||
1 geometry 2 Thu Oct 3 16:58:53 2019
|
||||
|
||||
The geometry named "geometry" is the default for restart
|
||||
|
||||
|
||||
|
||||
Basis sets in the database
|
||||
--------------------------
|
||||
|
||||
There are no basis sets in the database
|
||||
|
||||
|
||||
|
||||
NWChem Input Module
|
||||
-------------------
|
||||
|
||||
|
||||
|
||||
!!!!!!!!! geom_3d NEEDS TESTING !!!!!!!!!!
|
||||
|
||||
|
||||
Geometry "geometry" -> ""
|
||||
-------------------------
|
||||
|
||||
Output coordinates in angstroms (scale by 1.889725989 to convert to a.u.)
|
||||
|
||||
No. Tag Charge X Y Z
|
||||
---- ---------------- ---------- -------------- -------------- --------------
|
||||
1 W 74.0000 0.04999689 0.09999378 0.14999288
|
||||
2 W 74.0000 1.63000384 1.68000452 1.73000836
|
||||
|
||||
Lattice Parameters
|
||||
------------------
|
||||
|
||||
lattice vectors in angstroms (scale by 1.889725989 to convert to a.u.)
|
||||
|
||||
a1=< 3.160 0.000 0.000 >
|
||||
a2=< 0.000 3.160 0.000 >
|
||||
a3=< 0.000 0.000 3.160 >
|
||||
a= 3.160 b= 3.160 c= 3.160
|
||||
alpha= 90.000 beta= 90.000 gamma= 90.000
|
||||
omega= 31.6
|
||||
|
||||
reciprocal lattice vectors in a.u.
|
||||
|
||||
b1=< 1.052 0.000 -0.000 >
|
||||
b2=< -0.000 1.052 -0.000 >
|
||||
b3=< 0.000 0.000 1.052 >
|
||||
|
||||
Atomic Mass
|
||||
-----------
|
||||
|
||||
W 183.951000
|
||||
|
||||
|
||||
|
||||
XYZ format geometry
|
||||
-------------------
|
||||
2
|
||||
geometry
|
||||
W 0.04999689 0.09999378 0.14999288
|
||||
W 1.63000384 1.68000452 1.73000836
|
||||
|
||||
==============================================================================
|
||||
internuclear distances
|
||||
------------------------------------------------------------------------------
|
||||
center one | center two | atomic units | angstroms
|
||||
------------------------------------------------------------------------------
|
||||
2 W | 1 W | 5.17154 | 2.73666
|
||||
------------------------------------------------------------------------------
|
||||
number of included internuclear distances: 1
|
||||
==============================================================================
|
||||
|
||||
|
||||
|
||||
>>>> PSPW Parallel Module - stress <<<<
|
||||
****************************************************
|
||||
* *
|
||||
* NWPW PSPW Calculation *
|
||||
* *
|
||||
* [ (Grassmann/Stiefel manifold implementation) ] *
|
||||
* *
|
||||
* [ NorthWest Chemistry implementation ] *
|
||||
* *
|
||||
* version #5.10 06/12/02 *
|
||||
* *
|
||||
* This code was developed by Eric J. Bylaska, *
|
||||
* and was based upon algorithms and code *
|
||||
* developed by the group of Prof. John H. Weare *
|
||||
* *
|
||||
****************************************************
|
||||
>>> JOB STARTED AT Thu Oct 3 16:58:54 2019 <<<
|
||||
================ input data ========================
|
||||
|
||||
input psi filename:./nwchem_lammps.movecs
|
||||
|
||||
initializing pspw_APC data structure
|
||||
------------------------------------
|
||||
nga, ngs: 3 6
|
||||
Gc : 2.5000000000000000
|
||||
APC gamma: 1 0.59999999999999998
|
||||
APC gamma: 2 0.90000000000000002
|
||||
APC gamma: 3 1.3500000000000001
|
||||
|
||||
number of processors used: 1
|
||||
processor grid : 1 x 1
|
||||
parallel mapping :2d hilbert
|
||||
parallel mapping : balanced
|
||||
number of threads : 1
|
||||
parallel io : off
|
||||
|
||||
options:
|
||||
boundary conditions = periodic (version3)
|
||||
electron spin = restricted
|
||||
exchange-correlation = LDA (Vosko et al) parameterization
|
||||
|
||||
elements involved in the cluster:
|
||||
1: W valence charge: 6.0000 lmax= 2
|
||||
comment : Troullier-Martins pseudopotential
|
||||
pseudpotential type : 0
|
||||
highest angular component : 2
|
||||
local potential used : 0
|
||||
number of non-local projections: 8
|
||||
semicore corrections included : 1.800 (radius) 4.538 (charge)
|
||||
cutoff = 2.389 3.185 2.244
|
||||
|
||||
|
||||
total charge: 0.000
|
||||
|
||||
atomic composition:
|
||||
W : 2
|
||||
|
||||
number of electrons: spin up= 6 ( 6 per task) down= 6 ( 6 per task) (Fourier space)
|
||||
number of orbitals : spin up= 6 ( 6 per task) down= 6 ( 6 per task) (Fourier space)
|
||||
|
||||
supercell:
|
||||
cell_name: cell_default
|
||||
lattice: a1=< 5.972 0.000 0.000 >
|
||||
a2=< 0.000 5.972 0.000 >
|
||||
a3=< 0.000 0.000 5.972 >
|
||||
reciprocal: b1=< 1.052 0.000 -0.000 >
|
||||
b2=< -0.000 1.052 -0.000 >
|
||||
b3=< 0.000 0.000 1.052 >
|
||||
lattice: a= 5.972 b= 5.972 c= 5.972
|
||||
alpha= 90.000 beta= 90.000 gamma= 90.000
|
||||
omega= 212.9
|
||||
|
||||
density cutoff= 35.427 fft= 16x 16x 16( 1052 waves 1052 per task)
|
||||
wavefnc cutoff= 35.427 fft= 16x 16x 16( 1052 waves 1052 per task)
|
||||
Ewald summation: cut radius= 1.90 and 8
|
||||
Madelung Wigner-Seitz= 1.76011888 (alpha= 2.83729748 rs= 3.70444413)
|
||||
|
||||
technical parameters:
|
||||
time step= 5.80 fictitious mass= 400000.0
|
||||
tolerance=0.100E-08 (energy) 0.100E-08 (density)
|
||||
maximum iterations = 1000 ( 10 inner 100 outer )
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
== Energy Calculation ==
|
||||
|
||||
|
||||
====== Grassmann conjugate gradient iteration ======
|
||||
>>> ITERATION STARTED AT Thu Oct 3 16:58:54 2019 <<<
|
||||
iter. Energy DeltaE DeltaRho
|
||||
------------------------------------------------------
|
||||
10 -0.2020460841E+02 -0.37164E-09 0.13892E-11
|
||||
*** tolerance ok. iteration terminated
|
||||
>>> ITERATION ENDED AT Thu Oct 3 16:58:54 2019 <<<
|
||||
|
||||
|
||||
== Summary Of Results ==
|
||||
|
||||
number of electrons: spin up= 6.00000 down= 6.00000 (real space)
|
||||
|
||||
total energy : -0.2020460841E+02 ( -0.10102E+02/ion)
|
||||
total orbital energy: 0.5093526999E+01 ( 0.84892E+00/electron)
|
||||
hartree energy : 0.2902689593E+00 ( 0.48378E-01/electron)
|
||||
exc-corr energy : -0.9445045626E+01 ( -0.15742E+01/electron)
|
||||
ion-ion energy : -0.2193948849E+02 ( -0.10970E+02/ion)
|
||||
|
||||
kinetic (planewave) : 0.1441573280E+02 ( 0.24026E+01/electron)
|
||||
V_local (planewave) : 0.1156119613E+02 ( 0.19269E+01/electron)
|
||||
V_nl (planewave) : -0.1508727219E+02 ( -0.25145E+01/electron)
|
||||
V_Coul (planewave) : 0.5805379185E+00 ( 0.96756E-01/electron)
|
||||
V_xc. (planewave) : -0.6376667662E+01 ( -0.10628E+01/electron)
|
||||
Virial Coefficient : -0.6466688811E+00
|
||||
|
||||
orbital energies:
|
||||
0.5414223E+00 ( 14.733eV)
|
||||
0.5414201E+00 ( 14.733eV)
|
||||
0.5414174E+00 ( 14.733eV)
|
||||
0.3596809E+00 ( 9.787eV)
|
||||
0.3596804E+00 ( 9.787eV)
|
||||
0.2031424E+00 ( 5.528eV)
|
||||
|
||||
Total PSPW energy : -0.2020460841E+02
|
||||
|
||||
|
||||
=== Spin Contamination ===
|
||||
|
||||
<Sexact^2> = 0.0000000000000000
|
||||
<S^2> = 0.0000000000000000
|
||||
|
||||
|
||||
|
||||
== Center of Charge ==
|
||||
|
||||
spin up ( 0.0106, 0.0203, 0.0283 )
|
||||
spin down ( 0.0106, 0.0203, 0.0283 )
|
||||
total ( 0.0106, 0.0203, 0.0283 )
|
||||
ionic ( -1.3984, -1.3039, -1.2094 )
|
||||
|
||||
|
||||
== Molecular Dipole wrt Center of Mass ==
|
||||
|
||||
mu = ( -16.9083, -15.8910, -14.8528 ) au
|
||||
|mu| = 27.5503 au, 70.0218 Debye
|
||||
|
||||
|
||||
Translation force removed: ( -0.00002 0.00000 0.00002)
|
||||
|
||||
|
||||
============= Ion Gradients =================
|
||||
Ion Forces:
|
||||
1 W ( -0.000001 0.000005 0.000014 )
|
||||
2 W ( 0.000001 -0.000005 -0.000014 )
|
||||
C.O.M. ( -0.000000 0.000000 0.000000 )
|
||||
===============================================
|
||||
|F| = 0.216488E-04
|
||||
|F|/nion = 0.108244E-04
|
||||
max|Fatom|= 0.153080E-04 ( 0.001eV/Angstrom)
|
||||
|
||||
|
||||
|
||||
|
||||
======================
|
||||
= Stress calculation =
|
||||
======================
|
||||
|
||||
|
||||
============= total gradient ==============
|
||||
S = ( 0.12513 0.00001 -0.00003 )
|
||||
( 0.00001 0.12513 -0.00001 )
|
||||
( -0.00003 -0.00001 0.12513 )
|
||||
===================================================
|
||||
|S| = 0.21673E+00
|
||||
pressure = 0.125E+00 au
|
||||
= 0.368E+02 Mbar
|
||||
= 0.368E+04 GPa
|
||||
= 0.363E+08 atm
|
||||
|
||||
|
||||
dE/da = 0.12513
|
||||
dE/db = 0.12513
|
||||
dE/dc = 0.12513
|
||||
dE/dalpha = 0.00006
|
||||
dE/dbeta = 0.00020
|
||||
dE/dgamma = -0.00008
|
||||
|
||||
|
||||
|
||||
|
||||
*************************************************************
|
||||
** **
|
||||
** PSPW Mulliken analysis **
|
||||
** **
|
||||
** Population analysis algorithm devloped by Ryoichi Kawai **
|
||||
** **
|
||||
** Thu Oct 3 16:58 **
|
||||
** **
|
||||
*************************************************************
|
||||
|
||||
|
||||
== XYZ OUTPUT ==
|
||||
|
||||
|
||||
2
|
||||
|
||||
W 0.049997 0.099994 0.149993
|
||||
W -1.529995 -1.479995 -1.429991
|
||||
|
||||
|
||||
== Atomic Orbital Expansion ==
|
||||
|
||||
W nodamping
|
||||
|
||||
|
||||
=====================================================
|
||||
| POPULATION ANALYSIS OF FILLED MOLECULAR ORBITALS |
|
||||
=====================================================
|
||||
|
||||
|
||||
== Using pseudoatomic orbital expansion ==
|
||||
|
||||
|
||||
------------------------------------------------------------------------------
|
||||
|
||||
|
||||
*** ORBITAL= 1*** SPIN=BOTH SUM= 0.12471E+01 E= 0.54142E+00 ( 14.733eV)
|
||||
|
||||
NO ATOM L POPULATION
|
||||
s
|
||||
1 W 0 0.00000 0.00000
|
||||
px pz py
|
||||
1 W 1 0.00000 0.00000 0.00000 0.00000
|
||||
dx2-y2 dzx d3z2-1 dyz dxy
|
||||
1 W 2 0.50000 -0.00001 -0.03953 0.00002 0.50309 0.49532
|
||||
fx(x2-3y2) fz(5z2-1) fx(5z2-1) fz(5z2-3) fy(5z2-1) fxyz fy(3x2-y2)
|
||||
1 W 3 0.00000 -0.00001 -0.00000 -0.00000 0.00000 0.00000 -0.00001 -0.00000
|
||||
s
|
||||
2 W 0 0.00000 0.00000
|
||||
px pz py
|
||||
2 W 1 0.00000 -0.00000 -0.00000 -0.00000
|
||||
dx2-y2 dzx d3z2-1 dyz dxy
|
||||
2 W 2 0.50000 -0.00001 -0.03953 0.00002 0.50309 0.49532
|
||||
fx(x2-3y2) fz(5z2-1) fx(5z2-1) fz(5z2-3) fy(5z2-1) fxyz fy(3x2-y2)
|
||||
2 W 3 0.00000 -0.00001 0.00000 0.00000 -0.00000 -0.00000 0.00001 0.00000
|
||||
|
||||
|
||||
=== DISTRIBUTION ===
|
||||
|
||||
1(W ) 0.5000 2(W ) 0.5000
|
||||
|
||||
|
||||
== ANGULAR MOMENTUM POPULATIONS ===
|
||||
|
||||
s p d f
|
||||
0.0000 0.0000 1.0000 0.0000
|
||||
|
||||
|
||||
------------------------------------------------------------------------------
|
||||
|
||||
|
||||
*** ORBITAL= 2*** SPIN=BOTH SUM= 0.12471E+01 E= 0.54142E+00 ( 14.733eV)
|
||||
|
||||
NO ATOM L POPULATION
|
||||
s
|
||||
1 W 0 0.00000 -0.00000
|
||||
px pz py
|
||||
1 W 1 0.00000 0.00000 0.00000 0.00000
|
||||
dx2-y2 dzx d3z2-1 dyz dxy
|
||||
1 W 2 0.50000 0.00004 0.62658 0.00003 -0.20360 0.25680
|
||||
fx(x2-3y2) fz(5z2-1) fx(5z2-1) fz(5z2-3) fy(5z2-1) fxyz fy(3x2-y2)
|
||||
1 W 3 0.00000 -0.00004 0.00000 0.00000 -0.00000 -0.00000 -0.00001 0.00000
|
||||
s
|
||||
2 W 0 0.00000 -0.00000
|
||||
px pz py
|
||||
2 W 1 0.00000 -0.00000 -0.00000 -0.00000
|
||||
dx2-y2 dzx d3z2-1 dyz dxy
|
||||
2 W 2 0.50000 0.00004 0.62658 0.00003 -0.20360 0.25680
|
||||
fx(x2-3y2) fz(5z2-1) fx(5z2-1) fz(5z2-3) fy(5z2-1) fxyz fy(3x2-y2)
|
||||
2 W 3 0.00000 -0.00004 -0.00000 -0.00000 -0.00000 0.00000 0.00001 -0.00000
|
||||
|
||||
|
||||
=== DISTRIBUTION ===
|
||||
|
||||
1(W ) 0.5000 2(W ) 0.5000
|
||||
|
||||
|
||||
== ANGULAR MOMENTUM POPULATIONS ===
|
||||
|
||||
s p d f
|
||||
0.0000 0.0000 1.0000 0.0000
|
||||
|
||||
|
||||
------------------------------------------------------------------------------
|
||||
|
||||
|
||||
*** ORBITAL= 3*** SPIN=BOTH SUM= 0.12471E+01 E= 0.54142E+00 ( 14.733eV)
|
||||
|
||||
NO ATOM L POPULATION
|
||||
s
|
||||
1 W 0 0.00000 0.00001
|
||||
px pz py
|
||||
1 W 1 0.00000 0.00000 -0.00000 -0.00000
|
||||
dx2-y2 dzx d3z2-1 dyz dxy
|
||||
1 W 2 0.50000 -0.00001 -0.32532 -0.00000 -0.45327 0.43441
|
||||
fx(x2-3y2) fz(5z2-1) fx(5z2-1) fz(5z2-3) fy(5z2-1) fxyz fy(3x2-y2)
|
||||
1 W 3 0.00000 0.00001 0.00000 -0.00000 -0.00000 -0.00000 -0.00000 0.00000
|
||||
s
|
||||
2 W 0 0.00000 0.00001
|
||||
px pz py
|
||||
2 W 1 0.00000 -0.00000 0.00000 0.00000
|
||||
dx2-y2 dzx d3z2-1 dyz dxy
|
||||
2 W 2 0.50000 -0.00001 -0.32532 -0.00000 -0.45327 0.43441
|
||||
fx(x2-3y2) fz(5z2-1) fx(5z2-1) fz(5z2-3) fy(5z2-1) fxyz fy(3x2-y2)
|
||||
2 W 3 0.00000 0.00001 -0.00000 0.00001 0.00000 0.00000 0.00000 -0.00000
|
||||
|
||||
|
||||
=== DISTRIBUTION ===
|
||||
|
||||
1(W ) 0.5000 2(W ) 0.5000
|
||||
|
||||
|
||||
== ANGULAR MOMENTUM POPULATIONS ===
|
||||
|
||||
s p d f
|
||||
0.0000 0.0000 1.0000 0.0000
|
||||
|
||||
|
||||
------------------------------------------------------------------------------
|
||||
|
||||
|
||||
*** ORBITAL= 4*** SPIN=BOTH SUM= 0.14785E+01 E= 0.35968E+00 ( 9.787eV)
|
||||
|
||||
NO ATOM L POPULATION
|
||||
s
|
||||
1 W 0 0.00000 -0.00000
|
||||
px pz py
|
||||
1 W 1 0.00000 -0.00000 0.00001 -0.00000
|
||||
dx2-y2 dzx d3z2-1 dyz dxy
|
||||
1 W 2 0.48310 0.33381 0.00000 -0.60965 0.00000 0.00000
|
||||
fx(x2-3y2) fz(5z2-1) fx(5z2-1) fz(5z2-3) fy(5z2-1) fxyz fy(3x2-y2)
|
||||
1 W 3 0.01690 0.13001 -0.00000 0.00000 0.00000 0.00000 0.00000 -0.00000
|
||||
s
|
||||
2 W 0 0.00000 0.00000
|
||||
px pz py
|
||||
2 W 1 0.00000 -0.00000 0.00001 -0.00000
|
||||
dx2-y2 dzx d3z2-1 dyz dxy
|
||||
2 W 2 0.48310 -0.33381 -0.00000 0.60965 -0.00000 -0.00000
|
||||
fx(x2-3y2) fz(5z2-1) fx(5z2-1) fz(5z2-3) fy(5z2-1) fxyz fy(3x2-y2)
|
||||
2 W 3 0.01690 -0.13001 -0.00000 0.00000 0.00000 0.00000 0.00000 -0.00000
|
||||
|
||||
|
||||
=== DISTRIBUTION ===
|
||||
|
||||
1(W ) 0.5000 2(W ) 0.5000
|
||||
|
||||
|
||||
== ANGULAR MOMENTUM POPULATIONS ===
|
||||
|
||||
s p d f
|
||||
0.0000 0.0000 0.9662 0.0338
|
||||
|
||||
|
||||
------------------------------------------------------------------------------
|
||||
|
||||
|
||||
*** ORBITAL= 5*** SPIN=BOTH SUM= 0.14407E+01 E= 0.35968E+00 ( 9.787eV)
|
||||
|
||||
NO ATOM L POPULATION
|
||||
s
|
||||
1 W 0 0.00000 -0.00000
|
||||
px pz py
|
||||
1 W 1 0.00000 -0.00000 -0.00000 0.00001
|
||||
dx2-y2 dzx d3z2-1 dyz dxy
|
||||
1 W 2 0.49580 0.61761 -0.00000 0.33817 0.00000 -0.00000
|
||||
fx(x2-3y2) fz(5z2-1) fx(5z2-1) fz(5z2-3) fy(5z2-1) fxyz fy(3x2-y2)
|
||||
1 W 3 0.00420 0.06484 -0.00001 0.00000 -0.00000 -0.00000 -0.00000 -0.00000
|
||||
s
|
||||
2 W 0 0.00000 0.00000
|
||||
px pz py
|
||||
2 W 1 0.00000 -0.00000 -0.00000 0.00001
|
||||
dx2-y2 dzx d3z2-1 dyz dxy
|
||||
2 W 2 0.49580 -0.61761 0.00000 -0.33817 -0.00000 0.00000
|
||||
fx(x2-3y2) fz(5z2-1) fx(5z2-1) fz(5z2-3) fy(5z2-1) fxyz fy(3x2-y2)
|
||||
2 W 3 0.00420 -0.06484 -0.00001 0.00000 -0.00000 -0.00000 -0.00000 -0.00000
|
||||
|
||||
|
||||
=== DISTRIBUTION ===
|
||||
|
||||
1(W ) 0.5000 2(W ) 0.5000
|
||||
|
||||
|
||||
== ANGULAR MOMENTUM POPULATIONS ===
|
||||
|
||||
s p d f
|
||||
0.0000 0.0000 0.9916 0.0084
|
||||
|
||||
|
||||
------------------------------------------------------------------------------
|
||||
|
||||
|
||||
*** ORBITAL= 6*** SPIN=BOTH SUM= 0.19540E+01 E= 0.20314E+00 ( 5.528eV)
|
||||
|
||||
NO ATOM L POPULATION
|
||||
s
|
||||
1 W 0 0.49974 -0.70692
|
||||
px pz py
|
||||
1 W 1 0.00000 0.00000 -0.00000 0.00000
|
||||
dx2-y2 dzx d3z2-1 dyz dxy
|
||||
1 W 2 0.00000 0.00000 -0.00000 -0.00000 -0.00000 0.00000
|
||||
fx(x2-3y2) fz(5z2-1) fx(5z2-1) fz(5z2-3) fy(5z2-1) fxyz fy(3x2-y2)
|
||||
1 W 3 0.00026 0.01609 -0.00000 -0.00000 -0.00000 -0.00000 -0.00000 -0.00000
|
||||
s
|
||||
2 W 0 0.49974 -0.70692
|
||||
px pz py
|
||||
2 W 1 0.00000 -0.00000 0.00000 -0.00000
|
||||
dx2-y2 dzx d3z2-1 dyz dxy
|
||||
2 W 2 0.00000 0.00000 -0.00000 -0.00000 -0.00000 0.00000
|
||||
fx(x2-3y2) fz(5z2-1) fx(5z2-1) fz(5z2-3) fy(5z2-1) fxyz fy(3x2-y2)
|
||||
2 W 3 0.00026 0.01609 0.00000 0.00000 -0.00000 0.00000 0.00000 0.00000
|
||||
|
||||
|
||||
=== DISTRIBUTION ===
|
||||
|
||||
1(W ) 0.5000 2(W ) 0.5000
|
||||
|
||||
|
||||
== ANGULAR MOMENTUM POPULATIONS ===
|
||||
|
||||
s p d f
|
||||
0.9995 0.0000 0.0000 0.0005
|
||||
|
||||
|
||||
========================================
|
||||
| POPULATION ANALYSIS ON EACH ATOM |
|
||||
========================================
|
||||
|
||||
|
||||
NO ATOM SPIN TOTAL s p d f
|
||||
1 W UP 3.00000 0.49974 0.00000 2.47889 0.02137
|
||||
1 W DOWN 3.00000 0.49974 0.00000 2.47889 0.02137
|
||||
2 W UP 3.00000 0.49974 0.00000 2.47889 0.02137
|
||||
2 W DOWN 3.00000 0.49974 0.00000 2.47889 0.02137
|
||||
|
||||
|
||||
|
||||
=== TOTAL ANGULAR MOMENTUM POPULATION ===
|
||||
|
||||
SPIN s p d f
|
||||
UP 16.66% 0.00% 82.63% 0.71%
|
||||
UP 16.66% 0.00% 82.63% 0.71%
|
||||
TOTAL 16.66% 0.00% 82.63% 0.71%
|
||||
|
||||
*************************************************************
|
||||
** **
|
||||
** PSPW Atomic Point Charge (APC) Analysis **
|
||||
** **
|
||||
** Point charge analysis based on paper by P.E. Blochl **
|
||||
** (J. Chem. Phys. vol 103, page 7422, 1995) **
|
||||
** **
|
||||
*************************************************************
|
||||
|
||||
pspw_APC data structure
|
||||
-----------------------
|
||||
nga, ngs: 3 6
|
||||
Gc : 2.5000000000000000
|
||||
APC gamma: 1 0.59999999999999998
|
||||
APC gamma: 2 0.90000000000000002
|
||||
APC gamma: 3 1.3500000000000001
|
||||
|
||||
charge analysis on each atom
|
||||
----------------------------
|
||||
|
||||
no atom Qelc Qion Qtotal
|
||||
-- ---- ------- ------- -------
|
||||
1 W -6.000 6.000 -0.000
|
||||
2 W -6.000 6.000 0.000
|
||||
Total Q -12.000 12.000 -0.000
|
||||
|
||||
|
||||
gaussian coefficients of model density
|
||||
--------------------------------------
|
||||
|
||||
no atom g=0.000 g=0.600 g=0.900 g=1.350
|
||||
-- ---- ------- ------- ------- -------
|
||||
1 W 6.000 -7.235 17.654 -16.419
|
||||
2 W 6.000 -7.234 17.651 -16.418
|
||||
|
||||
|
||||
=== Electric Field at Atoms ===
|
||||
|
||||
1 W Atomic Electric Field =( -0.00002 0.00000 0.00001 )
|
||||
(ion) =( 0.00000 0.00000 0.00000 )
|
||||
(electronic) =( -0.00002 -0.00000 0.00001 )
|
||||
2 W Atomic Electric Field =( -0.00002 0.00000 0.00002 )
|
||||
(ion) =( -0.00000 -0.00000 -0.00000 )
|
||||
(electronic) =( -0.00002 0.00000 0.00002 )
|
||||
|
||||
output psi filename:./nwchem_lammps.movecs
|
||||
|
||||
|
||||
== Timing ==
|
||||
|
||||
cputime in seconds
|
||||
prologue : 0.991130E-01
|
||||
main loop : 0.101190E+00
|
||||
epilogue : 0.203540E-01
|
||||
total : 0.220657E+00
|
||||
cputime/step: 0.252975E-01 ( 4 evalulations, 1 linesearches)
|
||||
|
||||
|
||||
Time spent doing total step percent
|
||||
total time : 0.222262E+00 0.555655E-01 100.0 %
|
||||
i/o time : 0.847340E-02 0.211835E-02 3.8 %
|
||||
FFTs : 0.576015E-02 0.144004E-02 2.6 %
|
||||
dot products : 0.157053E-02 0.392634E-03 0.7 %
|
||||
geodesic : 0.203228E-02 0.508070E-03 0.9 %
|
||||
ffm_dgemm : 0.641376E-04 0.160344E-04 0.0 %
|
||||
fmf_dgemm : 0.202988E-02 0.507471E-03 0.9 %
|
||||
mmm_dgemm : 0.286302E-05 0.715756E-06 0.0 %
|
||||
m_diagonalize : 0.101088E-03 0.252721E-04 0.0 %
|
||||
exchange correlation : 0.287819E-02 0.719547E-03 1.3 %
|
||||
local pseudopotentials : 0.346661E-03 0.866652E-04 0.2 %
|
||||
non-local pseudopotentials : 0.268912E-02 0.672280E-03 1.2 %
|
||||
hartree potentials : 0.163791E-03 0.409476E-04 0.1 %
|
||||
ion-ion interaction : 0.699389E-01 0.174847E-01 31.5 %
|
||||
structure factors : 0.889608E-02 0.222402E-02 4.0 %
|
||||
phase factors : 0.102510E-04 0.256275E-05 0.0 %
|
||||
masking and packing : 0.839656E-02 0.209914E-02 3.8 %
|
||||
queue fft : 0.418949E-02 0.104737E-02 1.9 %
|
||||
queue fft (serial) : 0.264608E-02 0.661519E-03 1.2 %
|
||||
queue fft (message passing): 0.136477E-02 0.341193E-03 0.6 %
|
||||
non-local psp FFM : 0.391964E-03 0.979910E-04 0.2 %
|
||||
non-local psp FMF : 0.407219E-03 0.101805E-03 0.2 %
|
||||
non-local psp FFM A : 0.144235E-03 0.360588E-04 0.1 %
|
||||
non-local psp FFM B : 0.216961E-03 0.542402E-04 0.1 %
|
||||
|
||||
>>> JOB COMPLETED AT Thu Oct 3 16:58:54 2019 <<<
|
||||
|
||||
Task times cpu: 0.2s wall: 0.2s
|
||||
Summary of allocated global arrays
|
||||
-----------------------------------
|
||||
No active global arrays
|
||||
|
||||
|
||||
|
||||
GA Statistics for process 0
|
||||
------------------------------
|
||||
|
||||
create destroy get put acc scatter gather read&inc
|
||||
calls: 0 0 0 0 0 0 0 0
|
||||
number of processes/call 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00
|
||||
bytes total: 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00
|
||||
bytes remote: 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00
|
||||
Max memory consumed for GA by this process: 0 bytes
|
||||
MA_summarize_allocated_blocks: starting scan ...
|
||||
MA_summarize_allocated_blocks: scan completed: 0 heap blocks, 0 stack blocks
|
||||
MA usage statistics:
|
||||
|
||||
allocation statistics:
|
||||
heap stack
|
||||
---- -----
|
||||
current number of blocks 0 0
|
||||
maximum number of blocks 294 17
|
||||
current total bytes 0 0
|
||||
maximum total bytes 4879496 351944
|
||||
maximum total K-bytes 4880 352
|
||||
maximum total M-bytes 5 1
|
||||
|
||||
|
||||
NWChem Input Module
|
||||
-------------------
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
CITATION
|
||||
--------
|
||||
Please cite the following reference when publishing
|
||||
results obtained with NWChem:
|
||||
|
||||
M. Valiev, E.J. Bylaska, N. Govind, K. Kowalski,
|
||||
T.P. Straatsma, H.J.J. van Dam, D. Wang, J. Nieplocha,
|
||||
E. Apra, T.L. Windus, W.A. de Jong
|
||||
"NWChem: a comprehensive and scalable open-source
|
||||
solution for large scale molecular simulations"
|
||||
Comput. Phys. Commun. 181, 1477 (2010)
|
||||
doi:10.1016/j.cpc.2010.04.018
|
||||
|
||||
AUTHORS
|
||||
-------
|
||||
E. Apra, E. J. Bylaska, W. A. de Jong, N. Govind, K. Kowalski,
|
||||
T. P. Straatsma, M. Valiev, H. J. J. van Dam, D. Wang, T. L. Windus,
|
||||
J. Hammond, J. Autschbach, K. Bhaskaran-Nair, J. Brabec, K. Lopata,
|
||||
S. A. Fischer, S. Krishnamoorthy, M. Jacquelin, W. Ma, M. Klemm, O. Villa,
|
||||
Y. Chen, V. Anisimov, F. Aquino, S. Hirata, M. T. Hackler, V. Konjkov,
|
||||
D. Mejia-Rodriguez, T. Risthaus, M. Malagoli, A. Marenich,
|
||||
A. Otero-de-la-Roza, J. Mullin, P. Nichols, R. Peverati, J. Pittner, Y. Zhao,
|
||||
P.-D. Fan, A. Fonari, M. J. Williamson, R. J. Harrison, J. R. Rehr,
|
||||
M. Dupuis, D. Silverstein, D. M. A. Smith, J. Nieplocha, V. Tipparaju,
|
||||
M. Krishnan, B. E. Van Kuiken, A. Vazquez-Mayagoitia, L. Jensen, M. Swart,
|
||||
Q. Wu, T. Van Voorhis, A. A. Auer, M. Nooijen, L. D. Crosby, E. Brown,
|
||||
G. Cisneros, G. I. Fann, H. Fruchtl, J. Garza, K. Hirao, R. A. Kendall,
|
||||
J. A. Nichols, K. Tsemekhman, K. Wolinski, J. Anchell, D. E. Bernholdt,
|
||||
P. Borowski, T. Clark, D. Clerc, H. Dachsel, M. J. O. Deegan, K. Dyall,
|
||||
D. Elwood, E. Glendening, M. Gutowski, A. C. Hess, J. Jaffe, B. G. Johnson,
|
||||
J. Ju, R. Kobayashi, R. Kutteh, Z. Lin, R. Littlefield, X. Long, B. Meng,
|
||||
T. Nakajima, S. Niu, L. Pollack, M. Rosing, K. Glaesemann, G. Sandrone,
|
||||
M. Stave, H. Taylor, G. Thomas, J. H. van Lenthe, A. T. Wong, Z. Zhang.
|
||||
|
||||
Total times cpu: 0.2s wall: 0.3s
|
||||
@ -1,28 +0,0 @@
|
||||
echo
|
||||
|
||||
#**** Enter the geometry using fractional coordinates ****
|
||||
geometry units angstrom noautosym
|
||||
system crystal
|
||||
lat_a 3.16d0
|
||||
lat_b 3.16d0
|
||||
lat_c 3.16d0
|
||||
end
|
||||
W 0.0 0.0 0.0
|
||||
W 0.5 0.5 0.5
|
||||
end
|
||||
|
||||
#***** setup the nwpw gamma point code ****
|
||||
nwpw
|
||||
simulation_cell
|
||||
ngrid 16 16 16
|
||||
end
|
||||
ewald_ncut 8
|
||||
mulliken
|
||||
lcao #old default
|
||||
end
|
||||
|
||||
nwpw
|
||||
tolerances 1.0d-9 1.0d-9
|
||||
end
|
||||
|
||||
task pspw stress
|
||||
@ -1,53 +0,0 @@
|
||||
# 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
|
||||
|
||||
@ -1,6 +0,0 @@
|
||||
K-Points
|
||||
0
|
||||
Monkhorst Pack
|
||||
15 15 15
|
||||
0 0 0
|
||||
|
||||
@ -1,11 +0,0 @@
|
||||
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
|
||||
|
||||
@ -1,149 +0,0 @@
|
||||
Sample LAMMPS MD wrapper on VASP quantum DFT via client/server
|
||||
coupling
|
||||
|
||||
See the MESSAGE package documentation Build_extras.html#message
|
||||
and Build_extras.html#message 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 in.client.W
|
||||
% python vasp_wrap.py file POSCAR_W
|
||||
|
||||
% mpirun -np 2 lmp_mpi -v mode file -in in.client.W
|
||||
% python vasp_wrap.py file POSCAR_W
|
||||
|
||||
ZMQ mode of messaging:
|
||||
|
||||
% mpirun -np 1 lmp_mpi -v mode zmq -in in.client.W
|
||||
% python vasp_wrap.py zmq POSCAR_W
|
||||
|
||||
% mpirun -np 2 lmp_mpi -v mode zmq -in in.client.W
|
||||
% python vasp_wrap.py zmq POSCAR_W
|
||||
@ -1,15 +0,0 @@
|
||||
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
|
||||
|
||||
@ -1,35 +0,0 @@
|
||||
# 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 $z
|
||||
|
||||
velocity all create 300.0 87287 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 10 check no
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all client/md
|
||||
fix_modify 2 energy yes
|
||||
|
||||
thermo 1
|
||||
run 3
|
||||
|
||||
message quit
|
||||
@ -1,76 +0,0 @@
|
||||
LAMMPS (22 Aug 2018)
|
||||
# small W unit cell for use with VASP
|
||||
|
||||
variable mode index file
|
||||
|
||||
if "${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
|
||||
@ -1,300 +0,0 @@
|
||||
#!/usr/bin/env python
|
||||
|
||||
# ----------------------------------------------------------------------
|
||||
# LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
# https://www.lammps.org/ 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
|
||||
File diff suppressed because it is too large
Load Diff
@ -1,4 +1,4 @@
|
||||
LAMMPS data file: two oppositely charged ions confined between two walls
|
||||
LAMMPS data file: two oppositely charged ions confined between two walls epsilon1=2 | epsilon2=10 | epsilon1=2
|
||||
|
||||
4002 atoms
|
||||
3 atom types
|
||||
@ -4015,5 +4015,5 @@ Atoms # dielectric: id mol type q x y z normx normy normz area_per_patch ed em e
|
||||
3998 0 1 0 38.5078 42.4438 30.002 0 0 -1 0.866 8 6 6 0
|
||||
3999 0 1 0 39.0079 41.5776 30.002 0 0 -1 0.866 8 6 6 0
|
||||
4000 0 1 0 39.508 42.4438 30.002 0 0 -1 0.866 8 6 6 0
|
||||
4001 0 2 1 15 20 15 0 0 1 0.866 8 6 10 0
|
||||
4002 0 3 -1 25 20 25 0 0 1 0.866 8 6 10 0
|
||||
4001 0 2 1 15 20 15 0 0 1 1.0 8 6 10 0
|
||||
4002 0 3 -1 25 20 25 0 0 1 1.0 8 6 10 0
|
||||
|
||||
@ -4,6 +4,8 @@
|
||||
# top interface: n = (0, 0, -1)
|
||||
# so that ed's are the same for both interfaces
|
||||
|
||||
# Dielectric constants can be set to be different from the input data file
|
||||
|
||||
variable epsilon1 index 20
|
||||
variable epsilon2 index 8
|
||||
|
||||
@ -21,6 +23,8 @@ variable method index gmres # gmres = BEM/GMRES
|
||||
# dof = Direct optimization of the functional
|
||||
# none
|
||||
|
||||
# compute the relevant values for the interface particles
|
||||
|
||||
variable ed equal "v_epsilon2 - v_epsilon1"
|
||||
variable em equal "(v_epsilon2 + v_epsilon1)/2"
|
||||
variable epsilon equal 1.0 # epsilon at the patch, not used for now
|
||||
@ -34,12 +38,10 @@ group ions type 2 3
|
||||
group cations type 2
|
||||
group anions type 3
|
||||
|
||||
# 1.0 = q * epsilon2 = qreal for cations
|
||||
# -1.0 = q * epsilon2 = qreal for anions
|
||||
variable qscale equal "1.0 / v_epsilon2"
|
||||
set group cations charge ${qscale}
|
||||
variable qscale equal "-1.0 / v_epsilon2"
|
||||
set group anions charge ${qscale}
|
||||
# set the dielectric constant of the medium where the ions reside
|
||||
|
||||
set group cations epsilon ${epsilon2}
|
||||
set group anions epsilon ${epsilon2}
|
||||
|
||||
pair_style lj/cut/coul/long/dielectric 1.122 10.0
|
||||
pair_coeff * * 1.0 1.0
|
||||
@ -59,6 +61,8 @@ dump 3 ions custom 100 ions.dump id mol type q x y z fx fy fz #c_ef[1
|
||||
|
||||
fix 1 ions nve
|
||||
|
||||
# fix modify is used to set the properties of the interface particle group
|
||||
|
||||
if "${method} == gmres" then &
|
||||
"fix 3 interface polarize/bem/gmres 1 1.0e-4" &
|
||||
"fix_modify 3 itr_max 50 dielectrics ${ed} ${em} ${epsilon} ${area} NULL" &
|
||||
|
||||
@ -1,10 +1,16 @@
|
||||
Examples for Extended Dissipative Particle Dynamics (DPD)
|
||||
---------------------------------------------------------
|
||||
This directory contains examples for extended DPD simulations
|
||||
Examples for Basic Dissipative Particle Dynamics (DPD)
|
||||
------------------------------------------------------
|
||||
This directory contains examples for DPD simulations using
|
||||
pair styles from the DPD-BASIC package.
|
||||
|
||||
1) 'dpdext' - test case (DPD fluid) for 'dpdext' pair style (in.dpdext) and an initial
|
||||
configuration (dpdext.data)
|
||||
1) 'dpd' - simple example (DPD fluid) for 'dpd' pair style (in.dpd)
|
||||
|
||||
2) 'dpdext_tstat' - test case (coarse-grained SPC/E water) for 'dpdext/tstat' pair style
|
||||
(in.cg_spce), an initial configuration (dpdext.data) and tabulated potential
|
||||
2) 'dpd_tstat' - coarse-grained SPC/E water example for 'dpd/tstat' pair style
|
||||
(in.dpd_tstat), an initial configuration (dpdext.data) and tabulated potential
|
||||
(cg_spce_table.pot) obtained by bottom-up coarse-graining of the atomistic SPC/E water.
|
||||
|
||||
3) 'dpdext' - simple example (DPD fluid) for 'dpd/ext' pair style (in.dpdext)
|
||||
|
||||
4) 'dpdext_tstat' - coarse-grained SPC/E water example for 'dpd/ext/tstat' pair style
|
||||
(in.dpdext_tstat), an initial configuration (dpdext.data) and tabulated potential
|
||||
(cg_spce_table.pot) obtained by bottom-up coarse-graining of the atomistic SPC/E water.
|
||||
|
||||
43
examples/PACKAGES/dpd-basic/dpd/in.dpd
Normal file
43
examples/PACKAGES/dpd-basic/dpd/in.dpd
Normal file
@ -0,0 +1,43 @@
|
||||
# DPD Fluid
|
||||
|
||||
variable T equal 1.0
|
||||
variable rc equal 1.0
|
||||
variable rcD equal 1.2
|
||||
|
||||
units lj
|
||||
boundary p p p
|
||||
atom_style atomic
|
||||
dimension 3
|
||||
newton on
|
||||
comm_modify vel yes
|
||||
|
||||
### create box and configuration
|
||||
variable L equal 5.0
|
||||
lattice fcc 3.0
|
||||
region simBox block 0 ${L} 0 ${L} 0 ${L}
|
||||
create_box 2 simBox
|
||||
#create_atoms 1 region simBox
|
||||
create_atoms 1 random 100 12456 simBox
|
||||
create_atoms 2 random 100 13245 simBox
|
||||
mass 1 1.0
|
||||
mass 2 2.0
|
||||
###
|
||||
|
||||
pair_style dpd ${T} ${rc} 3854262
|
||||
|
||||
pair_coeff 1 1 25.0 4.5 1.2
|
||||
pair_coeff 1 2 25.1 4.51 1.21
|
||||
pair_coeff 2 2 25.2 4.52 1.22
|
||||
|
||||
timestep 0.01
|
||||
run_style verlet
|
||||
|
||||
velocity all create ${T} 68768932
|
||||
|
||||
thermo_style custom step time temp press
|
||||
thermo 100
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
run 5000
|
||||
|
||||
154
examples/PACKAGES/dpd-basic/dpd/log.5Apr22.dpd.g++.1
Normal file
154
examples/PACKAGES/dpd-basic/dpd/log.5Apr22.dpd.g++.1
Normal file
@ -0,0 +1,154 @@
|
||||
LAMMPS (24 Mar 2022)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# DPD Fluid
|
||||
|
||||
variable T equal 1.0
|
||||
variable rc equal 1.0
|
||||
variable rcD equal 1.2
|
||||
|
||||
units lj
|
||||
boundary p p p
|
||||
atom_style atomic
|
||||
dimension 3
|
||||
newton on
|
||||
comm_modify vel yes
|
||||
|
||||
### create box and configuration
|
||||
variable L equal 5.0
|
||||
lattice fcc 3.0
|
||||
Lattice spacing in x,y,z = 1.1006424 1.1006424 1.1006424
|
||||
region simBox block 0 ${L} 0 ${L} 0 ${L}
|
||||
region simBox block 0 5 0 ${L} 0 ${L}
|
||||
region simBox block 0 5 0 5 0 ${L}
|
||||
region simBox block 0 5 0 5 0 5
|
||||
create_box 2 simBox
|
||||
Created orthogonal box = (0 0 0) to (5.5032121 5.5032121 5.5032121)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
#create_atoms 1 region simBox
|
||||
create_atoms 1 random 100 12456 simBox
|
||||
Created 100 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (5.5032121 5.5032121 5.5032121)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
create_atoms 2 random 100 13245 simBox
|
||||
Created 100 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (5.5032121 5.5032121 5.5032121)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
mass 1 1.0
|
||||
mass 2 2.0
|
||||
###
|
||||
|
||||
pair_style dpd ${T} ${rc} 3854262
|
||||
pair_style dpd 1 ${rc} 3854262
|
||||
pair_style dpd 1 1 3854262
|
||||
|
||||
pair_coeff 1 1 25.0 4.5 1.2
|
||||
pair_coeff 1 2 25.1 4.51 1.21
|
||||
pair_coeff 2 2 25.2 4.52 1.22
|
||||
|
||||
timestep 0.01
|
||||
run_style verlet
|
||||
|
||||
velocity all create ${T} 68768932
|
||||
velocity all create 1 68768932
|
||||
|
||||
thermo_style custom step time temp press
|
||||
thermo 100
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
run 5000
|
||||
generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 1.52
|
||||
ghost atom cutoff = 1.52
|
||||
binsize = 0.76, bins = 8 8 8
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair dpd, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.083 | 3.083 | 3.083 Mbytes
|
||||
Step Time Temp Press
|
||||
0 0 1 9.5226009
|
||||
100 1 1.9913643 9.2036029
|
||||
200 2 1.6321732 9.2787957
|
||||
300 3 1.3533438 8.3081433
|
||||
400 4 1.2125884 8.0809065
|
||||
500 5 1.0682216 8.0877925
|
||||
600 6 0.99100473 8.1100319
|
||||
700 7 0.99731243 7.8225195
|
||||
800 8 1.0597693 7.8368218
|
||||
900 9 0.99038588 7.9450569
|
||||
1000 10 1.077129 7.5857015
|
||||
1100 11 0.99070336 7.5138128
|
||||
1200 12 1.013894 7.2794857
|
||||
1300 13 1.0433203 7.7439871
|
||||
1400 14 1.0285528 7.5662235
|
||||
1500 15 0.99180601 7.8376313
|
||||
1600 16 0.98059071 8.0243735
|
||||
1700 17 1.0070947 8.3186893
|
||||
1800 18 0.99507569 7.0786393
|
||||
1900 19 1.0040168 7.8120389
|
||||
2000 20 0.98636164 7.472185
|
||||
2100 21 0.95811165 7.7085985
|
||||
2200 22 0.93568327 6.9424246
|
||||
2300 23 0.92804144 8.1239435
|
||||
2400 24 0.94940276 7.6108611
|
||||
2500 25 1.0535153 8.0772721
|
||||
2600 26 1.0902144 7.5609768
|
||||
2700 27 1.0737336 7.8706755
|
||||
2800 28 0.93074581 7.3699993
|
||||
2900 29 1.0440705 7.6454988
|
||||
3000 30 0.93868164 7.841168
|
||||
3100 31 1.0172025 7.6856163
|
||||
3200 32 1.0405368 7.5325735
|
||||
3300 33 0.96721201 7.8262809
|
||||
3400 34 0.90430758 7.1693921
|
||||
3500 35 0.89938433 7.865845
|
||||
3600 36 0.9907178 7.3462971
|
||||
3700 37 1.0311879 7.8876401
|
||||
3800 38 0.98339132 7.3413929
|
||||
3900 39 1.2111264 8.0968408
|
||||
4000 40 1.062489 7.7315959
|
||||
4100 41 0.94737492 7.3386028
|
||||
4200 42 1.0453816 8.2017304
|
||||
4300 43 0.97024897 7.7379624
|
||||
4400 44 0.9553861 7.8047635
|
||||
4500 45 1.043252 7.7486215
|
||||
4600 46 0.98611474 8.1237053
|
||||
4700 47 0.98624285 8.5801642
|
||||
4800 48 0.97176754 7.1540299
|
||||
4900 49 1.0165401 7.3853841
|
||||
5000 50 0.88359115 7.5541592
|
||||
Loop time of 0.359916 on 1 procs for 5000 steps with 200 atoms
|
||||
|
||||
Performance: 12002788.048 tau/day, 13892.116 timesteps/s
|
||||
99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.24932 | 0.24932 | 0.24932 | 0.0 | 69.27
|
||||
Neigh | 0.068726 | 0.068726 | 0.068726 | 0.0 | 19.10
|
||||
Comm | 0.028691 | 0.028691 | 0.028691 | 0.0 | 7.97
|
||||
Output | 0.00066318 | 0.00066318 | 0.00066318 | 0.0 | 0.18
|
||||
Modify | 0.0078062 | 0.0078062 | 0.0078062 | 0.0 | 2.17
|
||||
Other | | 0.004713 | | | 1.31
|
||||
|
||||
Nlocal: 200 ave 200 max 200 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 546 ave 546 max 546 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 1649 ave 1649 max 1649 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 1649
|
||||
Ave neighs/atom = 8.245
|
||||
Neighbor list builds = 500
|
||||
Dangerous builds = 500
|
||||
|
||||
Total wall time: 0:00:00
|
||||
154
examples/PACKAGES/dpd-basic/dpd/log.5Apr22.dpd.g++.4
Normal file
154
examples/PACKAGES/dpd-basic/dpd/log.5Apr22.dpd.g++.4
Normal file
@ -0,0 +1,154 @@
|
||||
LAMMPS (24 Mar 2022)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# DPD Fluid
|
||||
|
||||
variable T equal 1.0
|
||||
variable rc equal 1.0
|
||||
variable rcD equal 1.2
|
||||
|
||||
units lj
|
||||
boundary p p p
|
||||
atom_style atomic
|
||||
dimension 3
|
||||
newton on
|
||||
comm_modify vel yes
|
||||
|
||||
### create box and configuration
|
||||
variable L equal 5.0
|
||||
lattice fcc 3.0
|
||||
Lattice spacing in x,y,z = 1.1006424 1.1006424 1.1006424
|
||||
region simBox block 0 ${L} 0 ${L} 0 ${L}
|
||||
region simBox block 0 5 0 ${L} 0 ${L}
|
||||
region simBox block 0 5 0 5 0 ${L}
|
||||
region simBox block 0 5 0 5 0 5
|
||||
create_box 2 simBox
|
||||
Created orthogonal box = (0 0 0) to (5.5032121 5.5032121 5.5032121)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
#create_atoms 1 region simBox
|
||||
create_atoms 1 random 100 12456 simBox
|
||||
Created 100 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (5.5032121 5.5032121 5.5032121)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
create_atoms 2 random 100 13245 simBox
|
||||
Created 100 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (5.5032121 5.5032121 5.5032121)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
mass 1 1.0
|
||||
mass 2 2.0
|
||||
###
|
||||
|
||||
pair_style dpd ${T} ${rc} 3854262
|
||||
pair_style dpd 1 ${rc} 3854262
|
||||
pair_style dpd 1 1 3854262
|
||||
|
||||
pair_coeff 1 1 25.0 4.5 1.2
|
||||
pair_coeff 1 2 25.1 4.51 1.21
|
||||
pair_coeff 2 2 25.2 4.52 1.22
|
||||
|
||||
timestep 0.01
|
||||
run_style verlet
|
||||
|
||||
velocity all create ${T} 68768932
|
||||
velocity all create 1 68768932
|
||||
|
||||
thermo_style custom step time temp press
|
||||
thermo 100
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
run 5000
|
||||
generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 1.52
|
||||
ghost atom cutoff = 1.52
|
||||
binsize = 0.76, bins = 8 8 8
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair dpd, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.064 | 3.064 | 3.064 Mbytes
|
||||
Step Time Temp Press
|
||||
0 0 1 8.603339
|
||||
100 1 1.8691059 8.9058297
|
||||
200 2 1.4500635 8.7420141
|
||||
300 3 1.3089453 8.3985981
|
||||
400 4 1.1647803 8.2948808
|
||||
500 5 1.1399445 7.7421817
|
||||
600 6 1.0297918 7.2040397
|
||||
700 7 1.046713 7.6115758
|
||||
800 8 0.93523712 7.6885563
|
||||
900 9 0.94701493 7.9662712
|
||||
1000 10 0.99302416 7.7606189
|
||||
1100 11 0.98975674 7.5207427
|
||||
1200 12 0.98661662 7.3565222
|
||||
1300 13 1.0289377 7.6110453
|
||||
1400 14 0.9982501 7.8065701
|
||||
1500 15 1.0043888 7.3957185
|
||||
1600 16 1.0175816 7.7885955
|
||||
1700 17 1.0252117 7.5076258
|
||||
1800 18 1.0275139 8.1052823
|
||||
1900 19 1.0021054 7.0385989
|
||||
2000 20 1.0489009 7.7138149
|
||||
2100 21 0.91250488 7.3540839
|
||||
2200 22 0.92470996 7.9600233
|
||||
2300 23 0.96932725 7.3106045
|
||||
2400 24 0.93443088 7.4594635
|
||||
2500 25 0.95596038 7.2544715
|
||||
2600 26 1.0368594 7.6229263
|
||||
2700 27 0.94639332 7.4869636
|
||||
2800 28 0.99917354 7.9806636
|
||||
2900 29 0.95048071 7.0086404
|
||||
3000 30 0.95226181 7.7807205
|
||||
3100 31 0.95864429 7.8059442
|
||||
3200 32 0.85678761 7.3416027
|
||||
3300 33 0.95951096 7.3467158
|
||||
3400 34 0.97665772 8.2900991
|
||||
3500 35 0.92885927 7.5385993
|
||||
3600 36 1.0455015 8.0627999
|
||||
3700 37 0.91911809 8.0371736
|
||||
3800 38 0.92022241 7.5803999
|
||||
3900 39 1.0465522 7.6920189
|
||||
4000 40 0.98568475 7.4529825
|
||||
4100 41 1.0389372 7.2273346
|
||||
4200 42 1.0257545 7.6081878
|
||||
4300 43 1.0937573 8.2158237
|
||||
4400 44 1.0908817 7.5021567
|
||||
4500 45 1.0482874 7.5924368
|
||||
4600 46 1.1468439 8.0285157
|
||||
4700 47 1.119683 8.3365123
|
||||
4800 48 1.0963877 7.51772
|
||||
4900 49 1.0766762 7.3137035
|
||||
5000 50 1.0359203 7.7354572
|
||||
Loop time of 0.148597 on 4 procs for 5000 steps with 200 atoms
|
||||
|
||||
Performance: 29071936.422 tau/day, 33648.075 timesteps/s
|
||||
98.8% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.059602 | 0.063397 | 0.068622 | 1.3 | 42.66
|
||||
Neigh | 0.017747 | 0.018193 | 0.018698 | 0.3 | 12.24
|
||||
Comm | 0.055145 | 0.061014 | 0.065369 | 1.5 | 41.06
|
||||
Output | 0.00042708 | 0.00050725 | 0.00071024 | 0.0 | 0.34
|
||||
Modify | 0.0023494 | 0.002532 | 0.0026434 | 0.2 | 1.70
|
||||
Other | | 0.002953 | | | 1.99
|
||||
|
||||
Nlocal: 50 ave 52 max 48 min
|
||||
Histogram: 1 0 1 0 0 0 0 1 0 1
|
||||
Nghost: 292.75 ave 299 max 287 min
|
||||
Histogram: 1 0 1 0 0 0 1 0 0 1
|
||||
Neighs: 413.5 ave 441 max 399 min
|
||||
Histogram: 2 0 0 1 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 1654
|
||||
Ave neighs/atom = 8.27
|
||||
Neighbor list builds = 500
|
||||
Dangerous builds = 500
|
||||
|
||||
Total wall time: 0:00:00
|
||||
@ -1,4 +1,4 @@
|
||||
DPD Fluid
|
||||
Coarse-Grained SPC/E Water
|
||||
|
||||
2180 atoms
|
||||
|
||||
354
examples/PACKAGES/dpd-basic/dpd_tstat/cg_spce_table.pot
Normal file
354
examples/PACKAGES/dpd-basic/dpd_tstat/cg_spce_table.pot
Normal file
@ -0,0 +1,354 @@
|
||||
VOTCA
|
||||
N 351 R 2.0 9.0
|
||||
|
||||
1 2.000000E+00 2.190202E+01 7.229762E+01
|
||||
2 2.020000E+00 2.048957E+01 6.887333E+01
|
||||
3 2.040000E+00 1.915004E+01 6.500604E+01
|
||||
4 2.060000E+00 1.789228E+01 6.069573E+01
|
||||
5 2.080000E+00 1.672516E+01 5.594242E+01
|
||||
6 2.100000E+00 1.565754E+01 5.074609E+01
|
||||
7 2.120000E+00 1.467088E+01 4.787307E+01
|
||||
8 2.140000E+00 1.374450E+01 4.471740E+01
|
||||
9 2.160000E+00 1.288407E+01 4.127908E+01
|
||||
10 2.180000E+00 1.209522E+01 3.755811E+01
|
||||
11 2.200000E+00 1.138363E+01 3.355449E+01
|
||||
12 2.220000E+00 1.072913E+01 3.188695E+01
|
||||
13 2.240000E+00 1.010845E+01 3.017359E+01
|
||||
14 2.260000E+00 9.522496E+00 2.841440E+01
|
||||
15 2.280000E+00 8.972182E+00 2.660938E+01
|
||||
16 2.300000E+00 8.458426E+00 2.475854E+01
|
||||
17 2.320000E+00 8.014166E+00 2.006698E+01
|
||||
18 2.340000E+00 7.639767E+00 1.777244E+01
|
||||
19 2.360000E+00 7.287288E+00 1.787493E+01
|
||||
20 2.380000E+00 6.908790E+00 2.037445E+01
|
||||
21 2.400000E+00 6.456330E+00 2.527099E+01
|
||||
22 2.420000E+00 5.858025E+00 3.384695E+01
|
||||
23 2.440000E+00 5.130955E+00 3.814748E+01
|
||||
24 2.460000E+00 4.360629E+00 3.817257E+01
|
||||
25 2.480000E+00 3.632555E+00 3.392224E+01
|
||||
26 2.500000E+00 3.032242E+00 2.539647E+01
|
||||
27 2.520000E+00 2.547993E+00 2.297813E+01
|
||||
28 2.540000E+00 2.115131E+00 2.025763E+01
|
||||
29 2.560000E+00 1.739702E+00 1.723497E+01
|
||||
30 2.580000E+00 1.427747E+00 1.391013E+01
|
||||
31 2.600000E+00 1.185311E+00 1.028314E+01
|
||||
32 2.620000E+00 9.860176E-01 9.578245E+00
|
||||
33 2.640000E+00 8.048986E-01 8.465708E+00
|
||||
34 2.660000E+00 6.501069E-01 6.945526E+00
|
||||
35 2.680000E+00 5.297952E-01 5.017699E+00
|
||||
36 2.700000E+00 4.521166E-01 2.682227E+00
|
||||
37 2.720000E+00 3.986447E-01 2.615311E+00
|
||||
38 2.740000E+00 3.494900E-01 2.250522E+00
|
||||
39 2.760000E+00 3.106097E-01 1.587859E+00
|
||||
40 2.780000E+00 2.879614E-01 6.273237E-01
|
||||
41 2.800000E+00 2.875026E-01 -6.310851E-01
|
||||
42 2.820000E+00 3.002733E-01 -6.543549E-01
|
||||
43 2.840000E+00 3.140112E-01 -7.277911E-01
|
||||
44 2.860000E+00 3.297194E-01 -8.513935E-01
|
||||
45 2.880000E+00 3.484014E-01 -1.025162E+00
|
||||
46 2.900000E+00 3.710604E-01 -1.249097E+00
|
||||
47 2.920000E+00 3.974884E-01 -1.380483E+00
|
||||
48 2.940000E+00 4.257507E-01 -1.432530E+00
|
||||
49 2.960000E+00 4.542607E-01 -1.405240E+00
|
||||
50 2.980000E+00 4.814314E-01 -1.298611E+00
|
||||
51 3.000000E+00 5.056762E-01 -1.112645E+00
|
||||
52 3.020000E+00 5.266502E-01 -9.832894E-01
|
||||
53 3.040000E+00 5.449492E-01 -8.451544E-01
|
||||
54 3.060000E+00 5.603978E-01 -6.982396E-01
|
||||
55 3.080000E+00 5.728203E-01 -5.425450E-01
|
||||
56 3.100000E+00 5.820411E-01 -3.780706E-01
|
||||
57 3.120000E+00 5.882509E-01 -2.409307E-01
|
||||
58 3.140000E+00 5.915991E-01 -9.190908E-02
|
||||
59 3.160000E+00 5.918481E-01 6.899430E-02
|
||||
60 3.180000E+00 5.887601E-01 2.417794E-01
|
||||
61 3.200000E+00 5.820977E-01 4.264463E-01
|
||||
62 3.220000E+00 5.733491E-01 4.528343E-01
|
||||
63 3.240000E+00 5.638075E-01 5.057356E-01
|
||||
64 3.260000E+00 5.529429E-01 5.851503E-01
|
||||
65 3.280000E+00 5.402248E-01 6.910784E-01
|
||||
66 3.300000E+00 5.251230E-01 8.235199E-01
|
||||
67 3.320000E+00 5.086524E-01 8.236482E-01
|
||||
68 3.340000E+00 4.921725E-01 8.244583E-01
|
||||
69 3.360000E+00 4.756696E-01 8.259503E-01
|
||||
70 3.380000E+00 4.591299E-01 8.281240E-01
|
||||
71 3.400000E+00 4.425400E-01 8.309796E-01
|
||||
72 3.420000E+00 4.259181E-01 8.311861E-01
|
||||
73 3.440000E+00 4.092937E-01 8.312292E-01
|
||||
74 3.460000E+00 3.926700E-01 8.311089E-01
|
||||
75 3.480000E+00 3.760504E-01 8.308252E-01
|
||||
76 3.500000E+00 3.594381E-01 8.303781E-01
|
||||
77 3.520000E+00 3.428394E-01 8.295412E-01
|
||||
78 3.540000E+00 3.262547E-01 8.289646E-01
|
||||
79 3.560000E+00 3.096790E-01 8.286483E-01
|
||||
80 3.580000E+00 2.931071E-01 8.285923E-01
|
||||
81 3.600000E+00 2.765336E-01 8.287966E-01
|
||||
82 3.620000E+00 2.599901E-01 8.254306E-01
|
||||
83 3.640000E+00 2.435212E-01 8.213359E-01
|
||||
84 3.660000E+00 2.271415E-01 8.165124E-01
|
||||
85 3.680000E+00 2.108656E-01 8.109603E-01
|
||||
86 3.700000E+00 1.947080E-01 8.046794E-01
|
||||
87 3.720000E+00 1.790243E-01 7.653050E-01
|
||||
88 3.740000E+00 1.640312E-01 7.356166E-01
|
||||
89 3.760000E+00 1.495351E-01 7.156143E-01
|
||||
90 3.780000E+00 1.353421E-01 7.052980E-01
|
||||
91 3.800000E+00 1.212586E-01 7.046676E-01
|
||||
92 3.820000E+00 1.072429E-01 6.965706E-01
|
||||
93 3.840000E+00 9.340878E-02 6.865180E-01
|
||||
94 3.860000E+00 7.979524E-02 6.745098E-01
|
||||
95 3.880000E+00 6.644142E-02 6.605462E-01
|
||||
96 3.900000E+00 5.338643E-02 6.446270E-01
|
||||
97 3.920000E+00 4.067486E-02 6.268536E-01
|
||||
98 3.940000E+00 2.829935E-02 6.110218E-01
|
||||
99 3.960000E+00 1.622105E-02 5.971317E-01
|
||||
100 3.980000E+00 4.401131E-03 5.851833E-01
|
||||
101 4.000000E+00 -7.199230E-03 5.751764E-01
|
||||
102 4.020000E+00 -1.856170E-02 5.611971E-01
|
||||
103 4.040000E+00 -2.965216E-02 5.479743E-01
|
||||
104 4.060000E+00 -4.048572E-02 5.355079E-01
|
||||
105 4.080000E+00 -5.107752E-02 5.237981E-01
|
||||
106 4.100000E+00 -6.144268E-02 5.128447E-01
|
||||
107 4.120000E+00 -7.151117E-02 4.939504E-01
|
||||
108 4.140000E+00 -8.119856E-02 4.747353E-01
|
||||
109 4.160000E+00 -9.049845E-02 4.551994E-01
|
||||
110 4.180000E+00 -9.940440E-02 4.353427E-01
|
||||
111 4.200000E+00 -1.079100E-01 4.151651E-01
|
||||
112 4.220000E+00 -1.159565E-01 3.900062E-01
|
||||
113 4.240000E+00 -1.235312E-01 3.679865E-01
|
||||
114 4.260000E+00 -1.306969E-01 3.491061E-01
|
||||
115 4.280000E+00 -1.375164E-01 3.333651E-01
|
||||
116 4.300000E+00 -1.440524E-01 3.207633E-01
|
||||
117 4.320000E+00 -1.503014E-01 3.040292E-01
|
||||
118 4.340000E+00 -1.562092E-01 2.866389E-01
|
||||
119 4.360000E+00 -1.617626E-01 2.685925E-01
|
||||
120 4.380000E+00 -1.669485E-01 2.498899E-01
|
||||
121 4.400000E+00 -1.717538E-01 2.305311E-01
|
||||
122 4.420000E+00 -1.760941E-01 2.036400E-01
|
||||
123 4.440000E+00 -1.799054E-01 1.776469E-01
|
||||
124 4.460000E+00 -1.832059E-01 1.525518E-01
|
||||
125 4.480000E+00 -1.860135E-01 1.283546E-01
|
||||
126 4.500000E+00 -1.883461E-01 1.050554E-01
|
||||
127 4.520000E+00 -1.902569E-01 8.558005E-02
|
||||
128 4.540000E+00 -1.917515E-01 6.344105E-02
|
||||
129 4.560000E+00 -1.927768E-01 3.863842E-02
|
||||
130 4.580000E+00 -1.932793E-01 1.117216E-02
|
||||
131 4.600000E+00 -1.932059E-01 -1.895774E-02
|
||||
132 4.620000E+00 -1.926829E-01 -3.331832E-02
|
||||
133 4.640000E+00 -1.918741E-01 -4.753697E-02
|
||||
134 4.660000E+00 -1.907824E-01 -6.161370E-02
|
||||
135 4.680000E+00 -1.894105E-01 -7.554851E-02
|
||||
136 4.700000E+00 -1.877614E-01 -8.934140E-02
|
||||
137 4.720000E+00 -1.859159E-01 -9.580751E-02
|
||||
138 4.740000E+00 -1.839049E-01 -1.058976E-01
|
||||
139 4.760000E+00 -1.816559E-01 -1.196116E-01
|
||||
140 4.780000E+00 -1.790963E-01 -1.369495E-01
|
||||
141 4.800000E+00 -1.761537E-01 -1.579114E-01
|
||||
142 4.820000E+00 -1.728280E-01 -1.744216E-01
|
||||
143 4.840000E+00 -1.691864E-01 -1.895036E-01
|
||||
144 4.860000E+00 -1.652574E-01 -2.031575E-01
|
||||
145 4.880000E+00 -1.610696E-01 -2.153832E-01
|
||||
146 4.900000E+00 -1.566516E-01 -2.261808E-01
|
||||
147 4.920000E+00 -1.521084E-01 -2.290714E-01
|
||||
148 4.940000E+00 -1.474515E-01 -2.375453E-01
|
||||
149 4.960000E+00 -1.425693E-01 -2.516026E-01
|
||||
150 4.980000E+00 -1.373502E-01 -2.712432E-01
|
||||
151 5.000000E+00 -1.316824E-01 -2.964672E-01
|
||||
152 5.020000E+00 -1.257009E-01 -3.016666E-01
|
||||
153 5.040000E+00 -1.196162E-01 -3.067953E-01
|
||||
154 5.060000E+00 -1.134296E-01 -3.118535E-01
|
||||
155 5.080000E+00 -1.071425E-01 -3.168409E-01
|
||||
156 5.100000E+00 -1.007564E-01 -3.217577E-01
|
||||
157 5.120000E+00 -9.430843E-02 -3.230025E-01
|
||||
158 5.140000E+00 -8.783782E-02 -3.240216E-01
|
||||
159 5.160000E+00 -8.134907E-02 -3.248150E-01
|
||||
160 5.180000E+00 -7.484672E-02 -3.253827E-01
|
||||
161 5.200000E+00 -6.833527E-02 -3.257248E-01
|
||||
162 5.220000E+00 -6.171989E-02 -3.350608E-01
|
||||
163 5.240000E+00 -5.496291E-02 -3.398853E-01
|
||||
164 5.260000E+00 -4.815456E-02 -3.401983E-01
|
||||
165 5.280000E+00 -4.138506E-02 -3.359997E-01
|
||||
166 5.300000E+00 -3.474465E-02 -3.272895E-01
|
||||
167 5.320000E+00 -2.866480E-02 -2.819209E-01
|
||||
168 5.340000E+00 -2.341879E-02 -2.439062E-01
|
||||
169 5.360000E+00 -1.885953E-02 -2.132454E-01
|
||||
170 5.380000E+00 -1.483994E-02 -1.899386E-01
|
||||
171 5.400000E+00 -1.121296E-02 -1.739857E-01
|
||||
172 5.420000E+00 -7.974056E-03 -1.497398E-01
|
||||
173 5.440000E+00 -5.229953E-03 -1.245058E-01
|
||||
174 5.460000E+00 -3.000413E-03 -9.828350E-02
|
||||
175 5.480000E+00 -1.305201E-03 -7.107305E-02
|
||||
176 5.500000E+00 -1.640790E-04 -4.287441E-02
|
||||
177 5.520000E+00 6.371635E-04 -3.612657E-02
|
||||
178 5.540000E+00 1.236053E-03 -2.263906E-02
|
||||
179 5.560000E+00 1.497795E-03 -2.411882E-03
|
||||
180 5.580000E+00 1.287597E-03 2.455496E-02
|
||||
181 5.600000E+00 4.706651E-04 5.826147E-02
|
||||
182 5.620000E+00 -7.026386E-04 5.910929E-02
|
||||
183 5.640000E+00 -1.895322E-03 6.019943E-02
|
||||
184 5.660000E+00 -3.112231E-03 6.153190E-02
|
||||
185 5.680000E+00 -4.358213E-03 6.310668E-02
|
||||
186 5.700000E+00 -5.638114E-03 6.492378E-02
|
||||
187 5.720000E+00 -6.949688E-03 6.610584E-02
|
||||
188 5.740000E+00 -8.277238E-03 6.652145E-02
|
||||
189 5.760000E+00 -9.605436E-03 6.617062E-02
|
||||
190 5.780000E+00 -1.091895E-02 6.505335E-02
|
||||
191 5.800000E+00 -1.220246E-02 6.316963E-02
|
||||
192 5.820000E+00 -1.341489E-02 5.820182E-02
|
||||
193 5.840000E+00 -1.453566E-02 5.400257E-02
|
||||
194 5.860000E+00 -1.558012E-02 5.057189E-02
|
||||
195 5.880000E+00 -1.656366E-02 4.790978E-02
|
||||
196 5.900000E+00 -1.750164E-02 4.601622E-02
|
||||
197 5.920000E+00 -1.840088E-02 4.358369E-02
|
||||
198 5.940000E+00 -1.923199E-02 3.920163E-02
|
||||
199 5.960000E+00 -1.995595E-02 3.287003E-02
|
||||
200 5.980000E+00 -2.053379E-02 2.458889E-02
|
||||
201 6.000000E+00 -2.092651E-02 1.435822E-02
|
||||
202 6.020000E+00 -2.120502E-02 1.352840E-02
|
||||
203 6.040000E+00 -2.146907E-02 1.291186E-02
|
||||
204 6.060000E+00 -2.172292E-02 1.250861E-02
|
||||
205 6.080000E+00 -2.197084E-02 1.231865E-02
|
||||
206 6.100000E+00 -2.221709E-02 1.234198E-02
|
||||
207 6.120000E+00 -2.246474E-02 1.237271E-02
|
||||
208 6.140000E+00 -2.270998E-02 1.210114E-02
|
||||
209 6.160000E+00 -2.294677E-02 1.152726E-02
|
||||
210 6.180000E+00 -2.316905E-02 1.065107E-02
|
||||
211 6.200000E+00 -2.337079E-02 9.472569E-03
|
||||
212 6.220000E+00 -2.332237E-02 -1.276224E-02
|
||||
213 6.240000E+00 -2.292243E-02 -2.567822E-02
|
||||
214 6.260000E+00 -2.235736E-02 -2.927535E-02
|
||||
215 6.280000E+00 -2.181354E-02 -2.355364E-02
|
||||
216 6.300000E+00 -2.147734E-02 -8.513096E-03
|
||||
217 6.320000E+00 -2.141633E-02 1.466366E-03
|
||||
218 6.340000E+00 -2.149820E-02 5.775798E-03
|
||||
219 6.360000E+00 -2.160956E-02 4.415202E-03
|
||||
220 6.380000E+00 -2.163701E-02 -2.615423E-03
|
||||
221 6.400000E+00 -2.146714E-02 -1.531608E-02
|
||||
222 6.420000E+00 -2.107402E-02 -2.337955E-02
|
||||
223 6.440000E+00 -2.055660E-02 -2.774728E-02
|
||||
224 6.460000E+00 -1.998877E-02 -2.841924E-02
|
||||
225 6.480000E+00 -1.944446E-02 -2.539546E-02
|
||||
226 6.500000E+00 -1.899759E-02 -1.867591E-02
|
||||
227 6.520000E+00 -1.869042E-02 -1.259095E-02
|
||||
228 6.540000E+00 -1.847196E-02 -9.804901E-03
|
||||
229 6.560000E+00 -1.827623E-02 -1.031775E-02
|
||||
230 6.580000E+00 -1.803726E-02 -1.412951E-02
|
||||
231 6.600000E+00 -1.768906E-02 -2.124018E-02
|
||||
232 6.620000E+00 -1.710949E-02 -3.551655E-02
|
||||
233 6.640000E+00 -1.631641E-02 -4.259122E-02
|
||||
234 6.660000E+00 -1.545385E-02 -4.246419E-02
|
||||
235 6.680000E+00 -1.466585E-02 -3.513545E-02
|
||||
236 6.700000E+00 -1.409644E-02 -2.060502E-02
|
||||
237 6.720000E+00 -1.374966E-02 -1.461056E-02
|
||||
238 6.740000E+00 -1.349054E-02 -1.183851E-02
|
||||
239 6.760000E+00 -1.325464E-02 -1.228886E-02
|
||||
240 6.780000E+00 -1.297750E-02 -1.596163E-02
|
||||
241 6.800000E+00 -1.259469E-02 -2.285680E-02
|
||||
242 6.820000E+00 -1.213049E-02 -2.349903E-02
|
||||
243 6.840000E+00 -1.165728E-02 -2.375897E-02
|
||||
244 6.860000E+00 -1.118268E-02 -2.363664E-02
|
||||
245 6.880000E+00 -1.071436E-02 -2.313203E-02
|
||||
246 6.900000E+00 -1.025995E-02 -2.224514E-02
|
||||
247 6.920000E+00 -9.817276E-03 -2.203990E-02
|
||||
248 6.940000E+00 -9.377653E-03 -2.193988E-02
|
||||
249 6.960000E+00 -8.938979E-03 -2.194508E-02
|
||||
250 6.980000E+00 -8.499148E-03 -2.205550E-02
|
||||
251 7.000000E+00 -8.056057E-03 -2.227113E-02
|
||||
252 7.020000E+00 -7.597830E-03 -2.345789E-02
|
||||
253 7.040000E+00 -7.121492E-03 -2.408210E-02
|
||||
254 7.060000E+00 -6.638296E-03 -2.414376E-02
|
||||
255 7.080000E+00 -6.159492E-03 -2.364288E-02
|
||||
256 7.100000E+00 -5.696331E-03 -2.257946E-02
|
||||
257 7.120000E+00 -5.301441E-03 -1.729553E-02
|
||||
258 7.140000E+00 -4.989070E-03 -1.432759E-02
|
||||
259 7.160000E+00 -4.712898E-03 -1.367562E-02
|
||||
260 7.180000E+00 -4.426605E-03 -1.533964E-02
|
||||
261 7.200000E+00 -4.083872E-03 -1.931964E-02
|
||||
262 7.220000E+00 -3.631995E-03 -2.538390E-02
|
||||
263 7.240000E+00 -3.087883E-03 -2.854317E-02
|
||||
264 7.260000E+00 -2.509635E-03 -2.879748E-02
|
||||
265 7.280000E+00 -1.955351E-03 -2.614680E-02
|
||||
266 7.300000E+00 -1.483130E-03 -2.059115E-02
|
||||
267 7.320000E+00 -1.113389E-03 -1.639767E-02
|
||||
268 7.340000E+00 -8.266321E-04 -1.229279E-02
|
||||
269 7.360000E+00 -6.210869E-04 -8.276492E-03
|
||||
270 7.380000E+00 -4.949818E-04 -4.348786E-03
|
||||
271 7.400000E+00 -4.465449E-04 -5.096684E-04
|
||||
272 7.420000E+00 -5.304321E-04 8.162452E-03
|
||||
273 7.440000E+00 -7.436056E-04 1.241897E-02
|
||||
274 7.460000E+00 -9.977534E-04 1.225988E-02
|
||||
275 7.480000E+00 -1.204563E-03 7.685191E-03
|
||||
276 7.500000E+00 -1.275724E-03 -1.305104E-03
|
||||
277 7.520000E+00 -1.199415E-03 -5.916706E-03
|
||||
278 7.540000E+00 -1.055417E-03 -8.074089E-03
|
||||
279 7.560000E+00 -8.928131E-04 -7.777253E-03
|
||||
280 7.580000E+00 -7.606883E-04 -5.026198E-03
|
||||
281 7.600000E+00 -7.081267E-04 1.790768E-04
|
||||
282 7.620000E+00 -7.213835E-04 1.157786E-03
|
||||
283 7.640000E+00 -7.548855E-04 2.203601E-03
|
||||
284 7.660000E+00 -8.099749E-04 3.316523E-03
|
||||
285 7.680000E+00 -8.879938E-04 4.496550E-03
|
||||
286 7.700000E+00 -9.902843E-04 5.743685E-03
|
||||
287 7.720000E+00 -1.122403E-03 7.421734E-03
|
||||
288 7.740000E+00 -1.285295E-03 8.820936E-03
|
||||
289 7.760000E+00 -1.473382E-03 9.941291E-03
|
||||
290 7.780000E+00 -1.681087E-03 1.078280E-02
|
||||
291 7.800000E+00 -1.902835E-03 1.134546E-02
|
||||
292 7.820000E+00 -2.225281E-03 2.008573E-02
|
||||
293 7.840000E+00 -2.673724E-03 2.394500E-02
|
||||
294 7.860000E+00 -3.150542E-03 2.292328E-02
|
||||
295 7.880000E+00 -3.558115E-03 1.702056E-02
|
||||
296 7.900000E+00 -3.798824E-03 6.236836E-03
|
||||
297 7.920000E+00 -3.844315E-03 -1.142168E-03
|
||||
298 7.940000E+00 -3.774961E-03 -5.247538E-03
|
||||
299 7.960000E+00 -3.656237E-03 -6.079274E-03
|
||||
300 7.980000E+00 -3.553615E-03 -3.637376E-03
|
||||
301 8.000000E+00 -3.532566E-03 2.078155E-03
|
||||
302 8.020000E+00 -3.611956E-03 5.494873E-03
|
||||
303 8.040000E+00 -3.737724E-03 6.716053E-03
|
||||
304 8.060000E+00 -3.865961E-03 5.741694E-03
|
||||
305 8.080000E+00 -3.952755E-03 2.571796E-03
|
||||
306 8.100000E+00 -3.954196E-03 -2.793640E-03
|
||||
307 8.120000E+00 -3.873685E-03 -5.086591E-03
|
||||
308 8.140000E+00 -3.757567E-03 -6.354313E-03
|
||||
309 8.160000E+00 -3.626347E-03 -6.596805E-03
|
||||
310 8.180000E+00 -3.500530E-03 -5.814068E-03
|
||||
311 8.200000E+00 -3.400620E-03 -4.006101E-03
|
||||
312 8.220000E+00 -3.334411E-03 -2.730570E-03
|
||||
313 8.240000E+00 -3.286762E-03 -2.150229E-03
|
||||
314 8.260000E+00 -3.243768E-03 -2.265076E-03
|
||||
315 8.280000E+00 -3.191524E-03 -3.075114E-03
|
||||
316 8.300000E+00 -3.116129E-03 -4.580340E-03
|
||||
317 8.320000E+00 -2.964210E-03 -1.014102E-02
|
||||
318 8.340000E+00 -2.729309E-03 -1.287854E-02
|
||||
319 8.360000E+00 -2.467889E-03 -1.279292E-02
|
||||
320 8.380000E+00 -2.236413E-03 -9.884157E-03
|
||||
321 8.400000E+00 -2.091344E-03 -4.152240E-03
|
||||
322 8.420000E+00 -2.034875E-03 -1.692189E-03
|
||||
323 8.440000E+00 -2.015752E-03 -4.177491E-04
|
||||
324 8.460000E+00 -2.010261E-03 -3.289192E-04
|
||||
325 8.480000E+00 -1.994691E-03 -1.425700E-03
|
||||
326 8.500000E+00 -1.945329E-03 -3.708091E-03
|
||||
327 8.520000E+00 -1.867098E-03 -4.115259E-03
|
||||
328 8.540000E+00 -1.780711E-03 -4.523663E-03
|
||||
329 8.560000E+00 -1.686143E-03 -4.933304E-03
|
||||
330 8.580000E+00 -1.583370E-03 -5.344181E-03
|
||||
331 8.600000E+00 -1.472368E-03 -5.756296E-03
|
||||
332 8.620000E+00 -1.328792E-03 -8.394009E-03
|
||||
333 8.640000E+00 -1.144899E-03 -9.787974E-03
|
||||
334 8.660000E+00 -9.455644E-04 -9.938189E-03
|
||||
335 8.680000E+00 -7.556630E-04 -8.844656E-03
|
||||
336 8.700000E+00 -6.000698E-04 -6.507373E-03
|
||||
337 8.720000E+00 -5.364035E-04 -3.286769E-04
|
||||
338 8.740000E+00 -5.681458E-04 3.033482E-03
|
||||
339 8.760000E+00 -6.389659E-04 3.579102E-03
|
||||
340 8.780000E+00 -6.925330E-04 1.308185E-03
|
||||
341 8.800000E+00 -6.725164E-04 -3.779270E-03
|
||||
342 8.820000E+00 -5.113768E-04 -1.169180E-02
|
||||
343 8.840000E+00 -2.305599E-04 -1.574700E-02
|
||||
344 8.860000E+00 9.278768E-05 -1.594487E-02
|
||||
345 8.880000E+00 3.815195E-04 -1.228542E-02
|
||||
346 8.900000E+00 5.584889E-04 -4.768636E-03
|
||||
347 8.920000E+00 6.079481E-04 -2.335309E-04
|
||||
348 8.940000E+00 5.700798E-04 3.964121E-03
|
||||
349 8.960000E+00 4.516330E-04 7.824320E-03
|
||||
350 8.980000E+00 2.593567E-04 1.134707E-02
|
||||
351 9.000000E+00 0.000000E+00 1.453236E-02
|
||||
31
examples/PACKAGES/dpd-basic/dpd_tstat/in.dpd_tstat
Normal file
31
examples/PACKAGES/dpd-basic/dpd_tstat/in.dpd_tstat
Normal file
@ -0,0 +1,31 @@
|
||||
# Coarse-Grained SPC/E Water
|
||||
|
||||
variable T equal 300.0
|
||||
variable rc equal 9.0
|
||||
variable rcD equal 10.0
|
||||
|
||||
units real
|
||||
boundary p p p
|
||||
atom_style atomic
|
||||
dimension 3
|
||||
newton on
|
||||
comm_modify vel yes
|
||||
|
||||
read_data cg_spce.data
|
||||
|
||||
pair_style hybrid/overlay table spline 1000 dpd/tstat ${T} ${T} ${rc} 385262
|
||||
|
||||
pair_coeff 1 1 table cg_spce_table.pot VOTCA ${rc}
|
||||
pair_coeff 1 1 dpd/tstat 10.0 ${rcD}
|
||||
|
||||
timestep 1.0
|
||||
run_style verlet
|
||||
|
||||
velocity all create ${T} 68768932
|
||||
|
||||
thermo_style custom step time temp press
|
||||
thermo 100
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
run 1000
|
||||
106
examples/PACKAGES/dpd-basic/dpd_tstat/log.5Apr22.dpd_tstat.g++.1
Normal file
106
examples/PACKAGES/dpd-basic/dpd_tstat/log.5Apr22.dpd_tstat.g++.1
Normal file
@ -0,0 +1,106 @@
|
||||
LAMMPS (24 Mar 2022)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Coarse-Grained SPC/E Water
|
||||
|
||||
variable T equal 300.0
|
||||
variable rc equal 9.0
|
||||
variable rcD equal 10.0
|
||||
|
||||
units real
|
||||
boundary p p p
|
||||
atom_style atomic
|
||||
dimension 3
|
||||
newton on
|
||||
comm_modify vel yes
|
||||
|
||||
read_data cg_spce.data
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (40.31 40.31 40.31)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
2180 atoms
|
||||
read_data CPU = 0.003 seconds
|
||||
|
||||
pair_style hybrid/overlay table spline 1000 dpd/tstat ${T} ${T} ${rc} 385262
|
||||
pair_style hybrid/overlay table spline 1000 dpd/tstat 300 ${T} ${rc} 385262
|
||||
pair_style hybrid/overlay table spline 1000 dpd/tstat 300 300 ${rc} 385262
|
||||
pair_style hybrid/overlay table spline 1000 dpd/tstat 300 300 9 385262
|
||||
|
||||
pair_coeff 1 1 table cg_spce_table.pot VOTCA ${rc}
|
||||
pair_coeff 1 1 table cg_spce_table.pot VOTCA 9
|
||||
WARNING: 16 of 351 force values in table VOTCA are inconsistent with -dE/dr.
|
||||
WARNING: Should only be flagged at inflection points (src/pair_table.cpp:465)
|
||||
pair_coeff 1 1 dpd/tstat 10.0 ${rcD}
|
||||
pair_coeff 1 1 dpd/tstat 10.0 10
|
||||
|
||||
timestep 1.0
|
||||
run_style verlet
|
||||
|
||||
velocity all create ${T} 68768932
|
||||
velocity all create 300 68768932
|
||||
|
||||
thermo_style custom step time temp press
|
||||
thermo 100
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
run 1000
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 7 7 7
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair table, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
(2) pair dpd/tstat, perpetual, copy from (1)
|
||||
attributes: half, newton on
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 5.38 | 5.38 | 5.38 Mbytes
|
||||
Step Time Temp Press
|
||||
0 0 300 7459.7935
|
||||
100 100 309.27219 6997.2438
|
||||
200 200 311.23318 9940.3922
|
||||
300 300 300.14145 7970.3486
|
||||
400 400 293.17924 8390.7272
|
||||
500 500 285.9647 7304.1147
|
||||
600 600 291.15512 6605.1675
|
||||
700 700 294.54557 7708.3815
|
||||
800 800 288.72442 8641.2675
|
||||
900 900 294.83288 7145.1684
|
||||
1000 1000 291.12446 8525.4556
|
||||
Loop time of 10.1894 on 1 procs for 1000 steps with 2180 atoms
|
||||
|
||||
Performance: 8.479 ns/day, 2.830 hours/ns, 98.141 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 | 10.02 | 10.02 | 10.02 | 0.0 | 98.34
|
||||
Neigh | 0.087623 | 0.087623 | 0.087623 | 0.0 | 0.86
|
||||
Comm | 0.055526 | 0.055526 | 0.055526 | 0.0 | 0.54
|
||||
Output | 0.00026505 | 0.00026505 | 0.00026505 | 0.0 | 0.00
|
||||
Modify | 0.013958 | 0.013958 | 0.013958 | 0.0 | 0.14
|
||||
Other | | 0.01163 | | | 0.11
|
||||
|
||||
Nlocal: 2180 ave 2180 max 2180 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 6741 ave 6741 max 6741 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 261567 ave 261567 max 261567 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 261567
|
||||
Ave neighs/atom = 119.98486
|
||||
Neighbor list builds = 14
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:10
|
||||
106
examples/PACKAGES/dpd-basic/dpd_tstat/log.5Apr22.dpd_tstat.g++.4
Normal file
106
examples/PACKAGES/dpd-basic/dpd_tstat/log.5Apr22.dpd_tstat.g++.4
Normal file
@ -0,0 +1,106 @@
|
||||
LAMMPS (24 Mar 2022)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Coarse-Grained SPC/E Water
|
||||
|
||||
variable T equal 300.0
|
||||
variable rc equal 9.0
|
||||
variable rcD equal 10.0
|
||||
|
||||
units real
|
||||
boundary p p p
|
||||
atom_style atomic
|
||||
dimension 3
|
||||
newton on
|
||||
comm_modify vel yes
|
||||
|
||||
read_data cg_spce.data
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (40.31 40.31 40.31)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
2180 atoms
|
||||
read_data CPU = 0.003 seconds
|
||||
|
||||
pair_style hybrid/overlay table spline 1000 dpd/tstat ${T} ${T} ${rc} 385262
|
||||
pair_style hybrid/overlay table spline 1000 dpd/tstat 300 ${T} ${rc} 385262
|
||||
pair_style hybrid/overlay table spline 1000 dpd/tstat 300 300 ${rc} 385262
|
||||
pair_style hybrid/overlay table spline 1000 dpd/tstat 300 300 9 385262
|
||||
|
||||
pair_coeff 1 1 table cg_spce_table.pot VOTCA ${rc}
|
||||
pair_coeff 1 1 table cg_spce_table.pot VOTCA 9
|
||||
WARNING: 16 of 351 force values in table VOTCA are inconsistent with -dE/dr.
|
||||
WARNING: Should only be flagged at inflection points (src/pair_table.cpp:465)
|
||||
pair_coeff 1 1 dpd/tstat 10.0 ${rcD}
|
||||
pair_coeff 1 1 dpd/tstat 10.0 10
|
||||
|
||||
timestep 1.0
|
||||
run_style verlet
|
||||
|
||||
velocity all create ${T} 68768932
|
||||
velocity all create 300 68768932
|
||||
|
||||
thermo_style custom step time temp press
|
||||
thermo 100
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
run 1000
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 7 7 7
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair table, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
(2) pair dpd/tstat, perpetual, copy from (1)
|
||||
attributes: half, newton on
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.695 | 3.696 | 3.697 Mbytes
|
||||
Step Time Temp Press
|
||||
0 0 300 7929.9249
|
||||
100 100 305.51763 8531.8105
|
||||
200 200 304.43334 8697.989
|
||||
300 300 292.42805 6865.4712
|
||||
400 400 300.66447 7606.6995
|
||||
500 500 298.43456 8713.2403
|
||||
600 600 298.10981 6913.5475
|
||||
700 700 297.39737 9121.8642
|
||||
800 800 298.23888 7833.1307
|
||||
900 900 293.91793 8423.8417
|
||||
1000 1000 299.65933 7974.9976
|
||||
Loop time of 2.82436 on 4 procs for 1000 steps with 2180 atoms
|
||||
|
||||
Performance: 30.591 ns/day, 0.785 hours/ns, 354.062 timesteps/s
|
||||
99.7% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 2.6238 | 2.644 | 2.6909 | 1.7 | 93.61
|
||||
Neigh | 0.021524 | 0.021958 | 0.022778 | 0.3 | 0.78
|
||||
Comm | 0.10035 | 0.1479 | 0.16842 | 7.2 | 5.24
|
||||
Output | 0.00019058 | 0.00021173 | 0.00026852 | 0.0 | 0.01
|
||||
Modify | 0.0041395 | 0.0041846 | 0.0042798 | 0.1 | 0.15
|
||||
Other | | 0.006091 | | | 0.22
|
||||
|
||||
Nlocal: 545 ave 559 max 536 min
|
||||
Histogram: 1 0 1 1 0 0 0 0 0 1
|
||||
Nghost: 3613.5 ave 3634 max 3604 min
|
||||
Histogram: 1 2 0 0 0 0 0 0 0 1
|
||||
Neighs: 65402 ave 68101 max 63621 min
|
||||
Histogram: 1 1 0 0 1 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 261608
|
||||
Ave neighs/atom = 120.00367
|
||||
Neighbor list builds = 14
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:02
|
||||
@ -4,9 +4,9 @@ variable T equal 1.0
|
||||
variable rc equal 1.0
|
||||
variable rcD equal 1.2
|
||||
|
||||
units lj
|
||||
units lj
|
||||
boundary p p p
|
||||
atom_style atomic
|
||||
atom_style atomic
|
||||
dimension 3
|
||||
newton on
|
||||
comm_modify vel yes
|
||||
@ -16,29 +16,27 @@ variable L equal 5.0
|
||||
lattice fcc 3.0
|
||||
region simBox block 0 ${L} 0 ${L} 0 ${L}
|
||||
create_box 2 simBox
|
||||
#create_atoms 1 region simBox
|
||||
create_atoms 1 random 100 132456 simBox
|
||||
create_atoms 2 random 100 132456 simBox
|
||||
create_atoms 1 random 100 12456 simBox
|
||||
create_atoms 2 random 100 13245 simBox
|
||||
mass 1 1.0
|
||||
mass 2 2.0
|
||||
###
|
||||
|
||||
pair_style dpd/ext ${T} ${rc} 3854262
|
||||
pair_style dpd/ext ${T} ${rc} 3854262
|
||||
|
||||
pair_coeff 1 1 25.0 4.5 4.53 0.5 0.53 1.2 #${rcD}
|
||||
pair_coeff 1 2 25.1 4.51 4.54 0.51 0.54 1.21 #${rcD}
|
||||
pair_coeff 2 2 25.2 4.52 4.55 0.52 0.55 1.22 #${rcD}
|
||||
|
||||
timestep 0.01
|
||||
timestep 0.01
|
||||
run_style verlet
|
||||
|
||||
velocity all create ${T} 68768932
|
||||
|
||||
thermo_style custom step time temp press
|
||||
thermo 500
|
||||
thermo 100
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
run 50000
|
||||
run 5000
|
||||
|
||||
write_data final.data pair ij
|
||||
153
examples/PACKAGES/dpd-basic/dpdext/log.5Apr22.dpdext.g++.1
Normal file
153
examples/PACKAGES/dpd-basic/dpdext/log.5Apr22.dpdext.g++.1
Normal file
@ -0,0 +1,153 @@
|
||||
LAMMPS (24 Mar 2022)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# DPD Fluid
|
||||
|
||||
variable T equal 1.0
|
||||
variable rc equal 1.0
|
||||
variable rcD equal 1.2
|
||||
|
||||
units lj
|
||||
boundary p p p
|
||||
atom_style atomic
|
||||
dimension 3
|
||||
newton on
|
||||
comm_modify vel yes
|
||||
|
||||
### create box and configuration
|
||||
variable L equal 5.0
|
||||
lattice fcc 3.0
|
||||
Lattice spacing in x,y,z = 1.1006424 1.1006424 1.1006424
|
||||
region simBox block 0 ${L} 0 ${L} 0 ${L}
|
||||
region simBox block 0 5 0 ${L} 0 ${L}
|
||||
region simBox block 0 5 0 5 0 ${L}
|
||||
region simBox block 0 5 0 5 0 5
|
||||
create_box 2 simBox
|
||||
Created orthogonal box = (0 0 0) to (5.5032121 5.5032121 5.5032121)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 random 100 12456 simBox
|
||||
Created 100 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (5.5032121 5.5032121 5.5032121)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
create_atoms 2 random 100 13245 simBox
|
||||
Created 100 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (5.5032121 5.5032121 5.5032121)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
mass 1 1.0
|
||||
mass 2 2.0
|
||||
###
|
||||
|
||||
pair_style dpd/ext ${T} ${rc} 3854262
|
||||
pair_style dpd/ext 1 ${rc} 3854262
|
||||
pair_style dpd/ext 1 1 3854262
|
||||
|
||||
pair_coeff 1 1 25.0 4.5 4.53 0.5 0.53 1.2 #${rcD}
|
||||
pair_coeff 1 2 25.1 4.51 4.54 0.51 0.54 1.21 #${rcD}
|
||||
pair_coeff 2 2 25.2 4.52 4.55 0.52 0.55 1.22 #${rcD}
|
||||
|
||||
timestep 0.01
|
||||
run_style verlet
|
||||
|
||||
velocity all create ${T} 68768932
|
||||
velocity all create 1 68768932
|
||||
|
||||
thermo_style custom step time temp press
|
||||
thermo 100
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
run 5000
|
||||
generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 1.52
|
||||
ghost atom cutoff = 1.52
|
||||
binsize = 0.76, bins = 8 8 8
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair dpd/ext, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.083 | 3.083 | 3.083 Mbytes
|
||||
Step Time Temp Press
|
||||
0 0 1 10.864186
|
||||
100 1 1.1314376 7.1955963
|
||||
200 2 1.0058948 8.4574538
|
||||
300 3 0.93292241 7.7033353
|
||||
400 4 0.93599378 7.9649888
|
||||
500 5 1.0390423 7.9498546
|
||||
600 6 1.0750333 7.3594973
|
||||
700 7 1.119325 7.1843859
|
||||
800 8 0.96727219 6.8327896
|
||||
900 9 0.98826001 8.1974994
|
||||
1000 10 1.105819 7.8830702
|
||||
1100 11 0.99559202 7.8295372
|
||||
1200 12 0.9210428 8.2045593
|
||||
1300 13 0.96628584 8.6531905
|
||||
1400 14 1.1808689 7.7659964
|
||||
1500 15 0.96208743 7.9977415
|
||||
1600 16 1.0080123 7.6254557
|
||||
1700 17 0.96910957 8.3643075
|
||||
1800 18 1.0562621 7.5966268
|
||||
1900 19 0.93109173 7.7944606
|
||||
2000 20 1.1126085 9.3753501
|
||||
2100 21 1.1328553 7.6293793
|
||||
2200 22 0.8964042 7.5985061
|
||||
2300 23 1.0043044 8.0016943
|
||||
2400 24 1.0319521 8.1249684
|
||||
2500 25 0.95913468 7.2383318
|
||||
2600 26 0.99480311 7.6491295
|
||||
2700 27 0.9735191 7.5004628
|
||||
2800 28 0.96145308 8.222045
|
||||
2900 29 1.0131071 6.6390842
|
||||
3000 30 0.99463836 7.0147693
|
||||
3100 31 0.96803993 8.2738796
|
||||
3200 32 0.94066026 9.476403
|
||||
3300 33 0.97401823 6.409563
|
||||
3400 34 1.0548493 7.7301555
|
||||
3500 35 0.98567796 8.2949868
|
||||
3600 36 0.86621746 7.4759028
|
||||
3700 37 0.94934175 8.1189998
|
||||
3800 38 0.9626774 7.7986715
|
||||
3900 39 0.95728518 6.8669836
|
||||
4000 40 1.0866412 7.41281
|
||||
4100 41 0.98873564 6.4612262
|
||||
4200 42 0.9109925 7.1806331
|
||||
4300 43 1.0344723 8.4617679
|
||||
4400 44 0.98920584 7.3622901
|
||||
4500 45 0.99386139 6.8002442
|
||||
4600 46 1.0947487 6.8868352
|
||||
4700 47 0.98789482 7.8428621
|
||||
4800 48 1.0035907 8.3878628
|
||||
4900 49 1.0336467 8.1592349
|
||||
5000 50 1.0870964 8.217988
|
||||
Loop time of 0.907286 on 1 procs for 5000 steps with 200 atoms
|
||||
|
||||
Performance: 4761453.941 tau/day, 5510.942 timesteps/s
|
||||
99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.79672 | 0.79672 | 0.79672 | 0.0 | 87.81
|
||||
Neigh | 0.066416 | 0.066416 | 0.066416 | 0.0 | 7.32
|
||||
Comm | 0.029801 | 0.029801 | 0.029801 | 0.0 | 3.28
|
||||
Output | 0.0010415 | 0.0010415 | 0.0010415 | 0.0 | 0.11
|
||||
Modify | 0.0078915 | 0.0078915 | 0.0078915 | 0.0 | 0.87
|
||||
Other | | 0.005414 | | | 0.60
|
||||
|
||||
Nlocal: 200 ave 200 max 200 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 563 ave 563 max 563 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 1624 ave 1624 max 1624 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 1624
|
||||
Ave neighs/atom = 8.12
|
||||
Neighbor list builds = 500
|
||||
Dangerous builds = 500
|
||||
|
||||
Total wall time: 0:00:00
|
||||
153
examples/PACKAGES/dpd-basic/dpdext/log.5Apr22.dpdext.g++.4
Normal file
153
examples/PACKAGES/dpd-basic/dpdext/log.5Apr22.dpdext.g++.4
Normal file
@ -0,0 +1,153 @@
|
||||
LAMMPS (24 Mar 2022)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# DPD Fluid
|
||||
|
||||
variable T equal 1.0
|
||||
variable rc equal 1.0
|
||||
variable rcD equal 1.2
|
||||
|
||||
units lj
|
||||
boundary p p p
|
||||
atom_style atomic
|
||||
dimension 3
|
||||
newton on
|
||||
comm_modify vel yes
|
||||
|
||||
### create box and configuration
|
||||
variable L equal 5.0
|
||||
lattice fcc 3.0
|
||||
Lattice spacing in x,y,z = 1.1006424 1.1006424 1.1006424
|
||||
region simBox block 0 ${L} 0 ${L} 0 ${L}
|
||||
region simBox block 0 5 0 ${L} 0 ${L}
|
||||
region simBox block 0 5 0 5 0 ${L}
|
||||
region simBox block 0 5 0 5 0 5
|
||||
create_box 2 simBox
|
||||
Created orthogonal box = (0 0 0) to (5.5032121 5.5032121 5.5032121)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 random 100 12456 simBox
|
||||
Created 100 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (5.5032121 5.5032121 5.5032121)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
create_atoms 2 random 100 13245 simBox
|
||||
Created 100 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (5.5032121 5.5032121 5.5032121)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
mass 1 1.0
|
||||
mass 2 2.0
|
||||
###
|
||||
|
||||
pair_style dpd/ext ${T} ${rc} 3854262
|
||||
pair_style dpd/ext 1 ${rc} 3854262
|
||||
pair_style dpd/ext 1 1 3854262
|
||||
|
||||
pair_coeff 1 1 25.0 4.5 4.53 0.5 0.53 1.2 #${rcD}
|
||||
pair_coeff 1 2 25.1 4.51 4.54 0.51 0.54 1.21 #${rcD}
|
||||
pair_coeff 2 2 25.2 4.52 4.55 0.52 0.55 1.22 #${rcD}
|
||||
|
||||
timestep 0.01
|
||||
run_style verlet
|
||||
|
||||
velocity all create ${T} 68768932
|
||||
velocity all create 1 68768932
|
||||
|
||||
thermo_style custom step time temp press
|
||||
thermo 100
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
run 5000
|
||||
generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 1.52
|
||||
ghost atom cutoff = 1.52
|
||||
binsize = 0.76, bins = 8 8 8
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair dpd/ext, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.064 | 3.064 | 3.064 Mbytes
|
||||
Step Time Temp Press
|
||||
0 0 1 9.2729849
|
||||
100 1 1.1416138 7.7058466
|
||||
200 2 0.91696292 8.1601454
|
||||
300 3 0.96358166 6.7987934
|
||||
400 4 0.94726377 7.6196059
|
||||
500 5 1.0941462 7.5974711
|
||||
600 6 0.91469027 8.3921536
|
||||
700 7 1.0912559 7.362721
|
||||
800 8 0.96537861 9.2089379
|
||||
900 9 0.9986577 8.0072887
|
||||
1000 10 0.9580071 7.2399027
|
||||
1100 11 0.94763774 7.8075521
|
||||
1200 12 0.9942368 7.5215461
|
||||
1300 13 1.0312465 8.2684258
|
||||
1400 14 0.95133276 7.2734722
|
||||
1500 15 0.97273431 7.1831939
|
||||
1600 16 1.0052028 7.929104
|
||||
1700 17 0.93909435 8.2831308
|
||||
1800 18 1.0647294 8.850861
|
||||
1900 19 1.0268112 7.2828461
|
||||
2000 20 0.91293528 8.208191
|
||||
2100 21 0.94719411 8.3353929
|
||||
2200 22 0.90507637 9.1708397
|
||||
2300 23 1.0663386 7.1415871
|
||||
2400 24 1.0132089 9.2210634
|
||||
2500 25 1.0633849 8.3368039
|
||||
2600 26 0.95803955 8.8247976
|
||||
2700 27 0.95264552 7.3204561
|
||||
2800 28 0.93548595 7.290555
|
||||
2900 29 0.96876322 7.4969147
|
||||
3000 30 0.99554648 8.2055023
|
||||
3100 31 1.0190751 7.907751
|
||||
3200 32 1.0887502 7.7247246
|
||||
3300 33 1.0059692 7.4039814
|
||||
3400 34 1.0055991 7.3469353
|
||||
3500 35 1.0067689 7.2161248
|
||||
3600 36 1.1103667 8.4373236
|
||||
3700 37 1.0668979 7.1922528
|
||||
3800 38 0.97902043 5.5426601
|
||||
3900 39 1.0268733 6.7786635
|
||||
4000 40 1.0036613 7.8078466
|
||||
4100 41 1.0714377 7.4129166
|
||||
4200 42 0.99168608 6.0096099
|
||||
4300 43 1.084818 7.4932992
|
||||
4400 44 0.98348896 8.9950057
|
||||
4500 45 1.045253 6.1309568
|
||||
4600 46 1.0266723 6.3227645
|
||||
4700 47 1.0183525 8.1505786
|
||||
4800 48 1.0527309 8.2824928
|
||||
4900 49 0.96877903 7.6341751
|
||||
5000 50 1.0178917 7.5037327
|
||||
Loop time of 0.320182 on 4 procs for 5000 steps with 200 atoms
|
||||
|
||||
Performance: 13492326.176 tau/day, 15616.118 timesteps/s
|
||||
98.4% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.20185 | 0.21019 | 0.2166 | 1.4 | 65.65
|
||||
Neigh | 0.017652 | 0.018339 | 0.019085 | 0.5 | 5.73
|
||||
Comm | 0.076802 | 0.084707 | 0.094197 | 2.6 | 26.46
|
||||
Output | 0.00057039 | 0.00066408 | 0.00093301 | 0.0 | 0.21
|
||||
Modify | 0.0025036 | 0.0027709 | 0.0030403 | 0.5 | 0.87
|
||||
Other | | 0.003508 | | | 1.10
|
||||
|
||||
Nlocal: 50 ave 53 max 45 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 1 1
|
||||
Nghost: 288.5 ave 300 max 279 min
|
||||
Histogram: 1 1 0 0 0 0 1 0 0 1
|
||||
Neighs: 418.25 ave 438 max 384 min
|
||||
Histogram: 1 0 0 0 0 1 0 0 0 2
|
||||
|
||||
Total # of neighbors = 1673
|
||||
Ave neighs/atom = 8.365
|
||||
Neighbor list builds = 500
|
||||
Dangerous builds = 500
|
||||
|
||||
Total wall time: 0:00:00
|
||||
File diff suppressed because it is too large
Load Diff
1
examples/PACKAGES/dpd-basic/dpdext_tstat/cg_spce.data
Symbolic link
1
examples/PACKAGES/dpd-basic/dpdext_tstat/cg_spce.data
Symbolic link
@ -0,0 +1 @@
|
||||
../dpd_tstat/cg_spce.data
|
||||
@ -1,354 +0,0 @@
|
||||
VOTCA
|
||||
N 351 R 2.0 9.0
|
||||
|
||||
1 2.000000E+00 2.190202E+01 7.229762E+01
|
||||
2 2.020000E+00 2.048957E+01 6.887333E+01
|
||||
3 2.040000E+00 1.915004E+01 6.500604E+01
|
||||
4 2.060000E+00 1.789228E+01 6.069573E+01
|
||||
5 2.080000E+00 1.672516E+01 5.594242E+01
|
||||
6 2.100000E+00 1.565754E+01 5.074609E+01
|
||||
7 2.120000E+00 1.467088E+01 4.787307E+01
|
||||
8 2.140000E+00 1.374450E+01 4.471740E+01
|
||||
9 2.160000E+00 1.288407E+01 4.127908E+01
|
||||
10 2.180000E+00 1.209522E+01 3.755811E+01
|
||||
11 2.200000E+00 1.138363E+01 3.355449E+01
|
||||
12 2.220000E+00 1.072913E+01 3.188695E+01
|
||||
13 2.240000E+00 1.010845E+01 3.017359E+01
|
||||
14 2.260000E+00 9.522496E+00 2.841440E+01
|
||||
15 2.280000E+00 8.972182E+00 2.660938E+01
|
||||
16 2.300000E+00 8.458426E+00 2.475854E+01
|
||||
17 2.320000E+00 8.014166E+00 2.006698E+01
|
||||
18 2.340000E+00 7.639767E+00 1.777244E+01
|
||||
19 2.360000E+00 7.287288E+00 1.787493E+01
|
||||
20 2.380000E+00 6.908790E+00 2.037445E+01
|
||||
21 2.400000E+00 6.456330E+00 2.527099E+01
|
||||
22 2.420000E+00 5.858025E+00 3.384695E+01
|
||||
23 2.440000E+00 5.130955E+00 3.814748E+01
|
||||
24 2.460000E+00 4.360629E+00 3.817257E+01
|
||||
25 2.480000E+00 3.632555E+00 3.392224E+01
|
||||
26 2.500000E+00 3.032242E+00 2.539647E+01
|
||||
27 2.520000E+00 2.547993E+00 2.297813E+01
|
||||
28 2.540000E+00 2.115131E+00 2.025763E+01
|
||||
29 2.560000E+00 1.739702E+00 1.723497E+01
|
||||
30 2.580000E+00 1.427747E+00 1.391013E+01
|
||||
31 2.600000E+00 1.185311E+00 1.028314E+01
|
||||
32 2.620000E+00 9.860176E-01 9.578245E+00
|
||||
33 2.640000E+00 8.048986E-01 8.465708E+00
|
||||
34 2.660000E+00 6.501069E-01 6.945526E+00
|
||||
35 2.680000E+00 5.297952E-01 5.017699E+00
|
||||
36 2.700000E+00 4.521166E-01 2.682227E+00
|
||||
37 2.720000E+00 3.986447E-01 2.615311E+00
|
||||
38 2.740000E+00 3.494900E-01 2.250522E+00
|
||||
39 2.760000E+00 3.106097E-01 1.587859E+00
|
||||
40 2.780000E+00 2.879614E-01 6.273237E-01
|
||||
41 2.800000E+00 2.875026E-01 -6.310851E-01
|
||||
42 2.820000E+00 3.002733E-01 -6.543549E-01
|
||||
43 2.840000E+00 3.140112E-01 -7.277911E-01
|
||||
44 2.860000E+00 3.297194E-01 -8.513935E-01
|
||||
45 2.880000E+00 3.484014E-01 -1.025162E+00
|
||||
46 2.900000E+00 3.710604E-01 -1.249097E+00
|
||||
47 2.920000E+00 3.974884E-01 -1.380483E+00
|
||||
48 2.940000E+00 4.257507E-01 -1.432530E+00
|
||||
49 2.960000E+00 4.542607E-01 -1.405240E+00
|
||||
50 2.980000E+00 4.814314E-01 -1.298611E+00
|
||||
51 3.000000E+00 5.056762E-01 -1.112645E+00
|
||||
52 3.020000E+00 5.266502E-01 -9.832894E-01
|
||||
53 3.040000E+00 5.449492E-01 -8.451544E-01
|
||||
54 3.060000E+00 5.603978E-01 -6.982396E-01
|
||||
55 3.080000E+00 5.728203E-01 -5.425450E-01
|
||||
56 3.100000E+00 5.820411E-01 -3.780706E-01
|
||||
57 3.120000E+00 5.882509E-01 -2.409307E-01
|
||||
58 3.140000E+00 5.915991E-01 -9.190908E-02
|
||||
59 3.160000E+00 5.918481E-01 6.899430E-02
|
||||
60 3.180000E+00 5.887601E-01 2.417794E-01
|
||||
61 3.200000E+00 5.820977E-01 4.264463E-01
|
||||
62 3.220000E+00 5.733491E-01 4.528343E-01
|
||||
63 3.240000E+00 5.638075E-01 5.057356E-01
|
||||
64 3.260000E+00 5.529429E-01 5.851503E-01
|
||||
65 3.280000E+00 5.402248E-01 6.910784E-01
|
||||
66 3.300000E+00 5.251230E-01 8.235199E-01
|
||||
67 3.320000E+00 5.086524E-01 8.236482E-01
|
||||
68 3.340000E+00 4.921725E-01 8.244583E-01
|
||||
69 3.360000E+00 4.756696E-01 8.259503E-01
|
||||
70 3.380000E+00 4.591299E-01 8.281240E-01
|
||||
71 3.400000E+00 4.425400E-01 8.309796E-01
|
||||
72 3.420000E+00 4.259181E-01 8.311861E-01
|
||||
73 3.440000E+00 4.092937E-01 8.312292E-01
|
||||
74 3.460000E+00 3.926700E-01 8.311089E-01
|
||||
75 3.480000E+00 3.760504E-01 8.308252E-01
|
||||
76 3.500000E+00 3.594381E-01 8.303781E-01
|
||||
77 3.520000E+00 3.428394E-01 8.295412E-01
|
||||
78 3.540000E+00 3.262547E-01 8.289646E-01
|
||||
79 3.560000E+00 3.096790E-01 8.286483E-01
|
||||
80 3.580000E+00 2.931071E-01 8.285923E-01
|
||||
81 3.600000E+00 2.765336E-01 8.287966E-01
|
||||
82 3.620000E+00 2.599901E-01 8.254306E-01
|
||||
83 3.640000E+00 2.435212E-01 8.213359E-01
|
||||
84 3.660000E+00 2.271415E-01 8.165124E-01
|
||||
85 3.680000E+00 2.108656E-01 8.109603E-01
|
||||
86 3.700000E+00 1.947080E-01 8.046794E-01
|
||||
87 3.720000E+00 1.790243E-01 7.653050E-01
|
||||
88 3.740000E+00 1.640312E-01 7.356166E-01
|
||||
89 3.760000E+00 1.495351E-01 7.156143E-01
|
||||
90 3.780000E+00 1.353421E-01 7.052980E-01
|
||||
91 3.800000E+00 1.212586E-01 7.046676E-01
|
||||
92 3.820000E+00 1.072429E-01 6.965706E-01
|
||||
93 3.840000E+00 9.340878E-02 6.865180E-01
|
||||
94 3.860000E+00 7.979524E-02 6.745098E-01
|
||||
95 3.880000E+00 6.644142E-02 6.605462E-01
|
||||
96 3.900000E+00 5.338643E-02 6.446270E-01
|
||||
97 3.920000E+00 4.067486E-02 6.268536E-01
|
||||
98 3.940000E+00 2.829935E-02 6.110218E-01
|
||||
99 3.960000E+00 1.622105E-02 5.971317E-01
|
||||
100 3.980000E+00 4.401131E-03 5.851833E-01
|
||||
101 4.000000E+00 -7.199230E-03 5.751764E-01
|
||||
102 4.020000E+00 -1.856170E-02 5.611971E-01
|
||||
103 4.040000E+00 -2.965216E-02 5.479743E-01
|
||||
104 4.060000E+00 -4.048572E-02 5.355079E-01
|
||||
105 4.080000E+00 -5.107752E-02 5.237981E-01
|
||||
106 4.100000E+00 -6.144268E-02 5.128447E-01
|
||||
107 4.120000E+00 -7.151117E-02 4.939504E-01
|
||||
108 4.140000E+00 -8.119856E-02 4.747353E-01
|
||||
109 4.160000E+00 -9.049845E-02 4.551994E-01
|
||||
110 4.180000E+00 -9.940440E-02 4.353427E-01
|
||||
111 4.200000E+00 -1.079100E-01 4.151651E-01
|
||||
112 4.220000E+00 -1.159565E-01 3.900062E-01
|
||||
113 4.240000E+00 -1.235312E-01 3.679865E-01
|
||||
114 4.260000E+00 -1.306969E-01 3.491061E-01
|
||||
115 4.280000E+00 -1.375164E-01 3.333651E-01
|
||||
116 4.300000E+00 -1.440524E-01 3.207633E-01
|
||||
117 4.320000E+00 -1.503014E-01 3.040292E-01
|
||||
118 4.340000E+00 -1.562092E-01 2.866389E-01
|
||||
119 4.360000E+00 -1.617626E-01 2.685925E-01
|
||||
120 4.380000E+00 -1.669485E-01 2.498899E-01
|
||||
121 4.400000E+00 -1.717538E-01 2.305311E-01
|
||||
122 4.420000E+00 -1.760941E-01 2.036400E-01
|
||||
123 4.440000E+00 -1.799054E-01 1.776469E-01
|
||||
124 4.460000E+00 -1.832059E-01 1.525518E-01
|
||||
125 4.480000E+00 -1.860135E-01 1.283546E-01
|
||||
126 4.500000E+00 -1.883461E-01 1.050554E-01
|
||||
127 4.520000E+00 -1.902569E-01 8.558005E-02
|
||||
128 4.540000E+00 -1.917515E-01 6.344105E-02
|
||||
129 4.560000E+00 -1.927768E-01 3.863842E-02
|
||||
130 4.580000E+00 -1.932793E-01 1.117216E-02
|
||||
131 4.600000E+00 -1.932059E-01 -1.895774E-02
|
||||
132 4.620000E+00 -1.926829E-01 -3.331832E-02
|
||||
133 4.640000E+00 -1.918741E-01 -4.753697E-02
|
||||
134 4.660000E+00 -1.907824E-01 -6.161370E-02
|
||||
135 4.680000E+00 -1.894105E-01 -7.554851E-02
|
||||
136 4.700000E+00 -1.877614E-01 -8.934140E-02
|
||||
137 4.720000E+00 -1.859159E-01 -9.580751E-02
|
||||
138 4.740000E+00 -1.839049E-01 -1.058976E-01
|
||||
139 4.760000E+00 -1.816559E-01 -1.196116E-01
|
||||
140 4.780000E+00 -1.790963E-01 -1.369495E-01
|
||||
141 4.800000E+00 -1.761537E-01 -1.579114E-01
|
||||
142 4.820000E+00 -1.728280E-01 -1.744216E-01
|
||||
143 4.840000E+00 -1.691864E-01 -1.895036E-01
|
||||
144 4.860000E+00 -1.652574E-01 -2.031575E-01
|
||||
145 4.880000E+00 -1.610696E-01 -2.153832E-01
|
||||
146 4.900000E+00 -1.566516E-01 -2.261808E-01
|
||||
147 4.920000E+00 -1.521084E-01 -2.290714E-01
|
||||
148 4.940000E+00 -1.474515E-01 -2.375453E-01
|
||||
149 4.960000E+00 -1.425693E-01 -2.516026E-01
|
||||
150 4.980000E+00 -1.373502E-01 -2.712432E-01
|
||||
151 5.000000E+00 -1.316824E-01 -2.964672E-01
|
||||
152 5.020000E+00 -1.257009E-01 -3.016666E-01
|
||||
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|
||||
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|
||||
155 5.080000E+00 -1.071425E-01 -3.168409E-01
|
||||
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|
||||
157 5.120000E+00 -9.430843E-02 -3.230025E-01
|
||||
158 5.140000E+00 -8.783782E-02 -3.240216E-01
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
185 5.680000E+00 -4.358213E-03 6.310668E-02
|
||||
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|
||||
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|
||||
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|
||||
189 5.760000E+00 -9.605436E-03 6.617062E-02
|
||||
190 5.780000E+00 -1.091895E-02 6.505335E-02
|
||||
191 5.800000E+00 -1.220246E-02 6.316963E-02
|
||||
192 5.820000E+00 -1.341489E-02 5.820182E-02
|
||||
193 5.840000E+00 -1.453566E-02 5.400257E-02
|
||||
194 5.860000E+00 -1.558012E-02 5.057189E-02
|
||||
195 5.880000E+00 -1.656366E-02 4.790978E-02
|
||||
196 5.900000E+00 -1.750164E-02 4.601622E-02
|
||||
197 5.920000E+00 -1.840088E-02 4.358369E-02
|
||||
198 5.940000E+00 -1.923199E-02 3.920163E-02
|
||||
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|
||||
200 5.980000E+00 -2.053379E-02 2.458889E-02
|
||||
201 6.000000E+00 -2.092651E-02 1.435822E-02
|
||||
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|
||||
203 6.040000E+00 -2.146907E-02 1.291186E-02
|
||||
204 6.060000E+00 -2.172292E-02 1.250861E-02
|
||||
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|
||||
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|
||||
207 6.120000E+00 -2.246474E-02 1.237271E-02
|
||||
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|
||||
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|
||||
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|
||||
211 6.200000E+00 -2.337079E-02 9.472569E-03
|
||||
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|
||||
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|
||||
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|
||||
215 6.280000E+00 -2.181354E-02 -2.355364E-02
|
||||
216 6.300000E+00 -2.147734E-02 -8.513096E-03
|
||||
217 6.320000E+00 -2.141633E-02 1.466366E-03
|
||||
218 6.340000E+00 -2.149820E-02 5.775798E-03
|
||||
219 6.360000E+00 -2.160956E-02 4.415202E-03
|
||||
220 6.380000E+00 -2.163701E-02 -2.615423E-03
|
||||
221 6.400000E+00 -2.146714E-02 -1.531608E-02
|
||||
222 6.420000E+00 -2.107402E-02 -2.337955E-02
|
||||
223 6.440000E+00 -2.055660E-02 -2.774728E-02
|
||||
224 6.460000E+00 -1.998877E-02 -2.841924E-02
|
||||
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|
||||
226 6.500000E+00 -1.899759E-02 -1.867591E-02
|
||||
227 6.520000E+00 -1.869042E-02 -1.259095E-02
|
||||
228 6.540000E+00 -1.847196E-02 -9.804901E-03
|
||||
229 6.560000E+00 -1.827623E-02 -1.031775E-02
|
||||
230 6.580000E+00 -1.803726E-02 -1.412951E-02
|
||||
231 6.600000E+00 -1.768906E-02 -2.124018E-02
|
||||
232 6.620000E+00 -1.710949E-02 -3.551655E-02
|
||||
233 6.640000E+00 -1.631641E-02 -4.259122E-02
|
||||
234 6.660000E+00 -1.545385E-02 -4.246419E-02
|
||||
235 6.680000E+00 -1.466585E-02 -3.513545E-02
|
||||
236 6.700000E+00 -1.409644E-02 -2.060502E-02
|
||||
237 6.720000E+00 -1.374966E-02 -1.461056E-02
|
||||
238 6.740000E+00 -1.349054E-02 -1.183851E-02
|
||||
239 6.760000E+00 -1.325464E-02 -1.228886E-02
|
||||
240 6.780000E+00 -1.297750E-02 -1.596163E-02
|
||||
241 6.800000E+00 -1.259469E-02 -2.285680E-02
|
||||
242 6.820000E+00 -1.213049E-02 -2.349903E-02
|
||||
243 6.840000E+00 -1.165728E-02 -2.375897E-02
|
||||
244 6.860000E+00 -1.118268E-02 -2.363664E-02
|
||||
245 6.880000E+00 -1.071436E-02 -2.313203E-02
|
||||
246 6.900000E+00 -1.025995E-02 -2.224514E-02
|
||||
247 6.920000E+00 -9.817276E-03 -2.203990E-02
|
||||
248 6.940000E+00 -9.377653E-03 -2.193988E-02
|
||||
249 6.960000E+00 -8.938979E-03 -2.194508E-02
|
||||
250 6.980000E+00 -8.499148E-03 -2.205550E-02
|
||||
251 7.000000E+00 -8.056057E-03 -2.227113E-02
|
||||
252 7.020000E+00 -7.597830E-03 -2.345789E-02
|
||||
253 7.040000E+00 -7.121492E-03 -2.408210E-02
|
||||
254 7.060000E+00 -6.638296E-03 -2.414376E-02
|
||||
255 7.080000E+00 -6.159492E-03 -2.364288E-02
|
||||
256 7.100000E+00 -5.696331E-03 -2.257946E-02
|
||||
257 7.120000E+00 -5.301441E-03 -1.729553E-02
|
||||
258 7.140000E+00 -4.989070E-03 -1.432759E-02
|
||||
259 7.160000E+00 -4.712898E-03 -1.367562E-02
|
||||
260 7.180000E+00 -4.426605E-03 -1.533964E-02
|
||||
261 7.200000E+00 -4.083872E-03 -1.931964E-02
|
||||
262 7.220000E+00 -3.631995E-03 -2.538390E-02
|
||||
263 7.240000E+00 -3.087883E-03 -2.854317E-02
|
||||
264 7.260000E+00 -2.509635E-03 -2.879748E-02
|
||||
265 7.280000E+00 -1.955351E-03 -2.614680E-02
|
||||
266 7.300000E+00 -1.483130E-03 -2.059115E-02
|
||||
267 7.320000E+00 -1.113389E-03 -1.639767E-02
|
||||
268 7.340000E+00 -8.266321E-04 -1.229279E-02
|
||||
269 7.360000E+00 -6.210869E-04 -8.276492E-03
|
||||
270 7.380000E+00 -4.949818E-04 -4.348786E-03
|
||||
271 7.400000E+00 -4.465449E-04 -5.096684E-04
|
||||
272 7.420000E+00 -5.304321E-04 8.162452E-03
|
||||
273 7.440000E+00 -7.436056E-04 1.241897E-02
|
||||
274 7.460000E+00 -9.977534E-04 1.225988E-02
|
||||
275 7.480000E+00 -1.204563E-03 7.685191E-03
|
||||
276 7.500000E+00 -1.275724E-03 -1.305104E-03
|
||||
277 7.520000E+00 -1.199415E-03 -5.916706E-03
|
||||
278 7.540000E+00 -1.055417E-03 -8.074089E-03
|
||||
279 7.560000E+00 -8.928131E-04 -7.777253E-03
|
||||
280 7.580000E+00 -7.606883E-04 -5.026198E-03
|
||||
281 7.600000E+00 -7.081267E-04 1.790768E-04
|
||||
282 7.620000E+00 -7.213835E-04 1.157786E-03
|
||||
283 7.640000E+00 -7.548855E-04 2.203601E-03
|
||||
284 7.660000E+00 -8.099749E-04 3.316523E-03
|
||||
285 7.680000E+00 -8.879938E-04 4.496550E-03
|
||||
286 7.700000E+00 -9.902843E-04 5.743685E-03
|
||||
287 7.720000E+00 -1.122403E-03 7.421734E-03
|
||||
288 7.740000E+00 -1.285295E-03 8.820936E-03
|
||||
289 7.760000E+00 -1.473382E-03 9.941291E-03
|
||||
290 7.780000E+00 -1.681087E-03 1.078280E-02
|
||||
291 7.800000E+00 -1.902835E-03 1.134546E-02
|
||||
292 7.820000E+00 -2.225281E-03 2.008573E-02
|
||||
293 7.840000E+00 -2.673724E-03 2.394500E-02
|
||||
294 7.860000E+00 -3.150542E-03 2.292328E-02
|
||||
295 7.880000E+00 -3.558115E-03 1.702056E-02
|
||||
296 7.900000E+00 -3.798824E-03 6.236836E-03
|
||||
297 7.920000E+00 -3.844315E-03 -1.142168E-03
|
||||
298 7.940000E+00 -3.774961E-03 -5.247538E-03
|
||||
299 7.960000E+00 -3.656237E-03 -6.079274E-03
|
||||
300 7.980000E+00 -3.553615E-03 -3.637376E-03
|
||||
301 8.000000E+00 -3.532566E-03 2.078155E-03
|
||||
302 8.020000E+00 -3.611956E-03 5.494873E-03
|
||||
303 8.040000E+00 -3.737724E-03 6.716053E-03
|
||||
304 8.060000E+00 -3.865961E-03 5.741694E-03
|
||||
305 8.080000E+00 -3.952755E-03 2.571796E-03
|
||||
306 8.100000E+00 -3.954196E-03 -2.793640E-03
|
||||
307 8.120000E+00 -3.873685E-03 -5.086591E-03
|
||||
308 8.140000E+00 -3.757567E-03 -6.354313E-03
|
||||
309 8.160000E+00 -3.626347E-03 -6.596805E-03
|
||||
310 8.180000E+00 -3.500530E-03 -5.814068E-03
|
||||
311 8.200000E+00 -3.400620E-03 -4.006101E-03
|
||||
312 8.220000E+00 -3.334411E-03 -2.730570E-03
|
||||
313 8.240000E+00 -3.286762E-03 -2.150229E-03
|
||||
314 8.260000E+00 -3.243768E-03 -2.265076E-03
|
||||
315 8.280000E+00 -3.191524E-03 -3.075114E-03
|
||||
316 8.300000E+00 -3.116129E-03 -4.580340E-03
|
||||
317 8.320000E+00 -2.964210E-03 -1.014102E-02
|
||||
318 8.340000E+00 -2.729309E-03 -1.287854E-02
|
||||
319 8.360000E+00 -2.467889E-03 -1.279292E-02
|
||||
320 8.380000E+00 -2.236413E-03 -9.884157E-03
|
||||
321 8.400000E+00 -2.091344E-03 -4.152240E-03
|
||||
322 8.420000E+00 -2.034875E-03 -1.692189E-03
|
||||
323 8.440000E+00 -2.015752E-03 -4.177491E-04
|
||||
324 8.460000E+00 -2.010261E-03 -3.289192E-04
|
||||
325 8.480000E+00 -1.994691E-03 -1.425700E-03
|
||||
326 8.500000E+00 -1.945329E-03 -3.708091E-03
|
||||
327 8.520000E+00 -1.867098E-03 -4.115259E-03
|
||||
328 8.540000E+00 -1.780711E-03 -4.523663E-03
|
||||
329 8.560000E+00 -1.686143E-03 -4.933304E-03
|
||||
330 8.580000E+00 -1.583370E-03 -5.344181E-03
|
||||
331 8.600000E+00 -1.472368E-03 -5.756296E-03
|
||||
332 8.620000E+00 -1.328792E-03 -8.394009E-03
|
||||
333 8.640000E+00 -1.144899E-03 -9.787974E-03
|
||||
334 8.660000E+00 -9.455644E-04 -9.938189E-03
|
||||
335 8.680000E+00 -7.556630E-04 -8.844656E-03
|
||||
336 8.700000E+00 -6.000698E-04 -6.507373E-03
|
||||
337 8.720000E+00 -5.364035E-04 -3.286769E-04
|
||||
338 8.740000E+00 -5.681458E-04 3.033482E-03
|
||||
339 8.760000E+00 -6.389659E-04 3.579102E-03
|
||||
340 8.780000E+00 -6.925330E-04 1.308185E-03
|
||||
341 8.800000E+00 -6.725164E-04 -3.779270E-03
|
||||
342 8.820000E+00 -5.113768E-04 -1.169180E-02
|
||||
343 8.840000E+00 -2.305599E-04 -1.574700E-02
|
||||
344 8.860000E+00 9.278768E-05 -1.594487E-02
|
||||
345 8.880000E+00 3.815195E-04 -1.228542E-02
|
||||
346 8.900000E+00 5.584889E-04 -4.768636E-03
|
||||
347 8.920000E+00 6.079481E-04 -2.335309E-04
|
||||
348 8.940000E+00 5.700798E-04 3.964121E-03
|
||||
349 8.960000E+00 4.516330E-04 7.824320E-03
|
||||
350 8.980000E+00 2.593567E-04 1.134707E-02
|
||||
351 9.000000E+00 0.000000E+00 1.453236E-02
|
||||
1
examples/PACKAGES/dpd-basic/dpdext_tstat/cg_spce_table.pot
Symbolic link
1
examples/PACKAGES/dpd-basic/dpdext_tstat/cg_spce_table.pot
Symbolic link
@ -0,0 +1 @@
|
||||
../dpd_tstat/cg_spce_table.pot
|
||||
@ -4,7 +4,7 @@ variable T equal 300.0
|
||||
variable rc equal 9.0
|
||||
variable rcD equal 10.0
|
||||
|
||||
units real
|
||||
units real
|
||||
boundary p p p
|
||||
atom_style atomic
|
||||
dimension 3
|
||||
@ -13,7 +13,7 @@ comm_modify vel yes
|
||||
|
||||
read_data cg_spce.data
|
||||
|
||||
pair_style hybrid/overlay table linear 1000 dpd/ext/tstat ${T} ${T} ${rc} 385262
|
||||
pair_style hybrid/overlay table spline 1000 dpd/ext/tstat ${T} ${T} ${rc} 385262
|
||||
|
||||
pair_coeff 1 1 table cg_spce_table.pot VOTCA ${rc}
|
||||
pair_coeff 1 1 dpd/ext/tstat 20.0 10.0 0.5 0.5 ${rcD}
|
||||
@ -24,8 +24,8 @@ run_style verlet
|
||||
velocity all create ${T} 68768932
|
||||
|
||||
thermo_style custom step time temp press
|
||||
thermo 10
|
||||
thermo 100
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
run 2000
|
||||
run 1000
|
||||
@ -1,293 +0,0 @@
|
||||
LAMMPS (8 Apr 2021)
|
||||
# Coarse-Grained SPC/E Water
|
||||
|
||||
variable T equal 300.0
|
||||
variable rc equal 9.0
|
||||
variable rcD equal 10.0
|
||||
|
||||
units real
|
||||
boundary p p p
|
||||
atom_style atomic
|
||||
dimension 3
|
||||
newton on
|
||||
comm_modify vel yes
|
||||
|
||||
read_data cg_spce.data
|
||||
Reading data file ...
|
||||
orthogonal box = (0.0000000 0.0000000 0.0000000) to (40.310000 40.310000 40.310000)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
2180 atoms
|
||||
read_data CPU = 0.020 seconds
|
||||
|
||||
pair_style hybrid/overlay table linear 1000 dpd/ext/tstat ${T} ${T} ${rc} 385262
|
||||
pair_style hybrid/overlay table linear 1000 dpd/ext/tstat 300 ${T} ${rc} 385262
|
||||
pair_style hybrid/overlay table linear 1000 dpd/ext/tstat 300 300 ${rc} 385262
|
||||
pair_style hybrid/overlay table linear 1000 dpd/ext/tstat 300 300 9 385262
|
||||
|
||||
pair_coeff 1 1 table cg_spce_table.pot VOTCA ${rc}
|
||||
pair_coeff 1 1 table cg_spce_table.pot VOTCA 9
|
||||
WARNING: 16 of 351 force values in table VOTCA are inconsistent with -dE/dr.
|
||||
Should only be flagged at inflection points (../pair_table.cpp:461)
|
||||
pair_coeff 1 1 dpd/ext/tstat 20.0 10.0 0.5 0.5 ${rcD}
|
||||
pair_coeff 1 1 dpd/ext/tstat 20.0 10.0 0.5 0.5 10
|
||||
|
||||
timestep 1.0
|
||||
run_style verlet
|
||||
|
||||
velocity all create ${T} 68768932
|
||||
velocity all create 300 68768932
|
||||
|
||||
thermo_style custom step time temp press
|
||||
thermo 10
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
run 2000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 7 7 7
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair table, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
(2) pair dpd/ext/tstat, perpetual, copy from (1)
|
||||
attributes: half, newton on
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 5.380 | 5.380 | 5.380 Mbytes
|
||||
Step Time Temp Press
|
||||
0 0 300 7368.7186
|
||||
10 10 298.34842 6443.6033
|
||||
20 20 303.36187 9303.0158
|
||||
30 30 301.59356 7533.7912
|
||||
40 40 300.97217 5623.9089
|
||||
50 50 300.31652 9105.8093
|
||||
60 60 296.92173 9213.304
|
||||
70 70 294.36593 12701.327
|
||||
80 80 295.30077 6098.4732
|
||||
90 90 296.35396 8051.719
|
||||
100 100 293.72532 5555.983
|
||||
110 110 290.95711 9001.8346
|
||||
120 120 290.91972 10264.241
|
||||
130 130 294.14911 11450.959
|
||||
140 140 299.11994 7244.1639
|
||||
150 150 301.20082 7675.7516
|
||||
160 160 300.71883 9718.1901
|
||||
170 170 295.47176 8931.1414
|
||||
180 180 290.45284 7381.7674
|
||||
190 190 291.66922 11028.436
|
||||
200 200 294.0543 11897.269
|
||||
210 210 299.17955 8939.2171
|
||||
220 220 298.45193 8047.038
|
||||
230 230 300.48548 10033.64
|
||||
240 240 299.24752 6310.7247
|
||||
250 250 304.51487 8710.5626
|
||||
260 260 303.6513 5230.8162
|
||||
270 270 300.76074 12164.773
|
||||
280 280 302.60275 11145.98
|
||||
290 290 297.22957 9521.4384
|
||||
300 300 297.1365 7446.9006
|
||||
310 310 292.18323 8021.8344
|
||||
320 320 295.03958 9130.8594
|
||||
330 330 293.9622 4647.512
|
||||
340 340 290.77751 8001.486
|
||||
350 350 292.34687 11887.668
|
||||
360 360 295.95968 9262.148
|
||||
370 370 293.50476 4181.549
|
||||
380 380 288.69498 7632.071
|
||||
390 390 289.63957 5130.0205
|
||||
400 400 295.02212 5643.5024
|
||||
410 410 296.3944 7267.235
|
||||
420 420 299.22019 7149.9305
|
||||
430 430 298.36689 8384.595
|
||||
440 440 295.33149 10515.75
|
||||
450 450 294.76959 11569.389
|
||||
460 460 300.141 7272.4453
|
||||
470 470 299.14431 7792.5419
|
||||
480 480 302.3697 5837.8675
|
||||
490 490 301.94692 6999.1059
|
||||
500 500 300.25929 4885.3948
|
||||
510 510 302.50013 8231.0438
|
||||
520 520 300.76412 8445.0349
|
||||
530 530 298.5016 9110.432
|
||||
540 540 301.14513 9348.6421
|
||||
550 550 297.36425 10753.314
|
||||
560 560 296.50046 10476.823
|
||||
570 570 300.57267 9889.7968
|
||||
580 580 300.4868 8377.423
|
||||
590 590 296.65103 6859.32
|
||||
600 600 298.50013 7080.5995
|
||||
610 610 300.28274 9502.5438
|
||||
620 620 298.45508 8819.7846
|
||||
630 630 300.24859 6291.4944
|
||||
640 640 299.38719 7430.2366
|
||||
650 650 297.91915 9435.3218
|
||||
660 660 300.61208 6287.9931
|
||||
670 670 303.59291 8357.7639
|
||||
680 680 301.85511 1697.3038
|
||||
690 690 298.96873 5210.2286
|
||||
700 700 298.09035 7510.4359
|
||||
710 710 303.11692 10129.526
|
||||
720 720 302.65473 10488.388
|
||||
730 730 300.15444 7118.5953
|
||||
740 740 300.19245 10582.032
|
||||
750 750 296.73618 6538.0363
|
||||
760 760 299.72857 7588.9487
|
||||
770 770 299.00347 6633.9983
|
||||
780 780 301.38129 8053.5347
|
||||
790 790 298.54819 8711.4965
|
||||
800 800 305.54197 9717.9727
|
||||
810 810 302.96497 7582.0444
|
||||
820 820 306.81537 9433.6446
|
||||
830 830 309.16373 10088.582
|
||||
840 840 313.53881 9509.8624
|
||||
850 850 310.82992 5366.015
|
||||
860 860 306.49798 8499.9157
|
||||
870 870 308.93421 5690.3242
|
||||
880 880 302.56668 5526.3636
|
||||
890 890 306.72501 7380.8469
|
||||
900 900 308.87199 10388.13
|
||||
910 910 312.7367 6613.0734
|
||||
920 920 308.34508 5903.4291
|
||||
930 930 306.39924 8615.6622
|
||||
940 940 310.37544 6849.4694
|
||||
950 950 310.13051 6188.7605
|
||||
960 960 308.68049 7637.532
|
||||
970 970 302.85465 6448.7926
|
||||
980 980 307.40719 8763.0959
|
||||
990 990 304.02815 8373.6518
|
||||
1000 1000 300.69539 5682.6678
|
||||
1010 1010 299.16385 6012.246
|
||||
1020 1020 305.118 7913.4144
|
||||
1030 1030 304.20382 10580.788
|
||||
1040 1040 302.91134 7698.4548
|
||||
1050 1050 298.08593 8952.6724
|
||||
1060 1060 302.56196 10602.997
|
||||
1070 1070 305.98211 12174.358
|
||||
1080 1080 305.70253 12288.219
|
||||
1090 1090 303.22805 7922.7166
|
||||
1100 1100 301.54879 5031.3836
|
||||
1110 1110 302.57611 8547.4189
|
||||
1120 1120 302.00845 12966.595
|
||||
1130 1130 296.10912 4514.1707
|
||||
1140 1140 295.11601 6543.7239
|
||||
1150 1150 287.29188 6453.3386
|
||||
1160 1160 284.83881 7168.9427
|
||||
1170 1170 289.77871 7895.7434
|
||||
1180 1180 293.48011 7680.6885
|
||||
1190 1190 295.69035 8609.6593
|
||||
1200 1200 296.0653 7343.68
|
||||
1210 1210 302.72922 6973.6048
|
||||
1220 1220 304.11805 7322.7664
|
||||
1230 1230 300.24647 6418.2612
|
||||
1240 1240 293.24074 9039.1214
|
||||
1250 1250 300.56214 7877.4055
|
||||
1260 1260 308.03086 5644.2135
|
||||
1270 1270 311.12289 6875.5126
|
||||
1280 1280 307.83182 7204.9894
|
||||
1290 1290 309.58491 9993.2255
|
||||
1300 1300 305.36536 8626.859
|
||||
1310 1310 304.35084 3471.1205
|
||||
1320 1320 304.40125 2149.2701
|
||||
1330 1330 295.74547 6252.9592
|
||||
1340 1340 293.16034 3407.4408
|
||||
1350 1350 298.6302 10139.977
|
||||
1360 1360 300.46627 7312.9011
|
||||
1370 1370 298.00367 2780.8886
|
||||
1380 1380 300.97807 9403.3451
|
||||
1390 1390 294.32612 12005.453
|
||||
1400 1400 296.13403 5569.4907
|
||||
1410 1410 297.86152 9558.6064
|
||||
1420 1420 303.01992 8678.345
|
||||
1430 1430 298.53849 5544.6316
|
||||
1440 1440 293.60633 12879.765
|
||||
1450 1450 296.28813 9312.4229
|
||||
1460 1460 292.64466 8344.5877
|
||||
1470 1470 295.28975 7689.9396
|
||||
1480 1480 300.10761 7436.7346
|
||||
1490 1490 291.6152 8909.6757
|
||||
1500 1500 286.644 9756.5014
|
||||
1510 1510 294.52064 10383.164
|
||||
1520 1520 297.49618 4972.89
|
||||
1530 1530 295.63379 6192.5729
|
||||
1540 1540 295.04528 4987.7191
|
||||
1550 1550 290.41403 7013.6076
|
||||
1560 1560 295.62326 7222.5009
|
||||
1570 1570 299.90584 4282.5688
|
||||
1580 1580 299.04532 7885.433
|
||||
1590 1590 300.03907 5508.0652
|
||||
1600 1600 298.05683 9262.3744
|
||||
1610 1610 297.50015 9544.6913
|
||||
1620 1620 303.21217 6393.6756
|
||||
1630 1630 304.44383 9674.6583
|
||||
1640 1640 302.68977 9065.4408
|
||||
1650 1650 303.62415 6851.1575
|
||||
1660 1660 306.11103 8592.0481
|
||||
1670 1670 300.84566 8483.551
|
||||
1680 1680 303.92882 10113.096
|
||||
1690 1690 305.02534 7389.9402
|
||||
1700 1700 303.52902 5541.9256
|
||||
1710 1710 299.27905 9547.7344
|
||||
1720 1720 294.14366 7269.2402
|
||||
1730 1730 299.49977 8086.0601
|
||||
1740 1740 298.66942 7026.6067
|
||||
1750 1750 296.94428 9595.2435
|
||||
1760 1760 297.36921 6268.7436
|
||||
1770 1770 299.88423 10598.189
|
||||
1780 1780 293.76868 7405.7641
|
||||
1790 1790 297.19444 10837.102
|
||||
1800 1800 296.46054 8345.699
|
||||
1810 1810 299.06801 5256.5992
|
||||
1820 1820 294.17725 5510.7529
|
||||
1830 1830 286.78527 6310.8881
|
||||
1840 1840 284.89686 8249.1144
|
||||
1850 1850 293.79389 4578.9263
|
||||
1860 1860 298.31279 8752.305
|
||||
1870 1870 295.31087 8401.2736
|
||||
1880 1880 298.13297 4354.8694
|
||||
1890 1890 298.90786 11454.088
|
||||
1900 1900 299.1416 9121.4138
|
||||
1910 1910 296.43134 12157.884
|
||||
1920 1920 292.05445 8613.1522
|
||||
1930 1930 300.3421 7898.3626
|
||||
1940 1940 304.55746 6311.259
|
||||
1950 1950 304.03899 8789.3537
|
||||
1960 1960 305.08259 7243.5622
|
||||
1970 1970 304.0858 8712.4796
|
||||
1980 1980 299.14574 5166.3501
|
||||
1990 1990 300.07254 10019.769
|
||||
2000 2000 301.78176 8789.7968
|
||||
Loop time of 91.2059 on 1 procs for 2000 steps with 2180 atoms
|
||||
|
||||
Performance: 1.895 ns/day, 12.667 hours/ns, 21.928 timesteps/s
|
||||
99.8% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 90.668 | 90.668 | 90.668 | 0.0 | 99.41
|
||||
Neigh | 0.23231 | 0.23231 | 0.23231 | 0.0 | 0.25
|
||||
Comm | 0.20819 | 0.20819 | 0.20819 | 0.0 | 0.23
|
||||
Output | 0.0049558 | 0.0049558 | 0.0049558 | 0.0 | 0.01
|
||||
Modify | 0.052906 | 0.052906 | 0.052906 | 0.0 | 0.06
|
||||
Other | | 0.03904 | | | 0.04
|
||||
|
||||
Nlocal: 2180.00 ave 2180 max 2180 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 6693.00 ave 6693 max 6693 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 261496.0 ave 261496 max 261496 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 261496
|
||||
Ave neighs/atom = 119.95229
|
||||
Neighbor list builds = 25
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:01:31
|
||||
@ -1,293 +0,0 @@
|
||||
LAMMPS (8 Apr 2021)
|
||||
# Coarse-Grained SPC/E Water
|
||||
|
||||
variable T equal 300.0
|
||||
variable rc equal 9.0
|
||||
variable rcD equal 10.0
|
||||
|
||||
units real
|
||||
boundary p p p
|
||||
atom_style atomic
|
||||
dimension 3
|
||||
newton on
|
||||
comm_modify vel yes
|
||||
|
||||
read_data cg_spce.data
|
||||
Reading data file ...
|
||||
orthogonal box = (0.0000000 0.0000000 0.0000000) to (40.310000 40.310000 40.310000)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
2180 atoms
|
||||
read_data CPU = 0.005 seconds
|
||||
|
||||
pair_style hybrid/overlay table linear 1000 dpd/ext/tstat ${T} ${T} ${rc} 385262
|
||||
pair_style hybrid/overlay table linear 1000 dpd/ext/tstat 300 ${T} ${rc} 385262
|
||||
pair_style hybrid/overlay table linear 1000 dpd/ext/tstat 300 300 ${rc} 385262
|
||||
pair_style hybrid/overlay table linear 1000 dpd/ext/tstat 300 300 9 385262
|
||||
|
||||
pair_coeff 1 1 table cg_spce_table.pot VOTCA ${rc}
|
||||
pair_coeff 1 1 table cg_spce_table.pot VOTCA 9
|
||||
WARNING: 16 of 351 force values in table VOTCA are inconsistent with -dE/dr.
|
||||
Should only be flagged at inflection points (../pair_table.cpp:461)
|
||||
pair_coeff 1 1 dpd/ext/tstat 20.0 10.0 0.5 0.5 ${rcD}
|
||||
pair_coeff 1 1 dpd/ext/tstat 20.0 10.0 0.5 0.5 10
|
||||
|
||||
timestep 1.0
|
||||
run_style verlet
|
||||
|
||||
velocity all create ${T} 68768932
|
||||
velocity all create 300 68768932
|
||||
|
||||
thermo_style custom step time temp press
|
||||
thermo 10
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
run 2000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 7 7 7
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair table, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
(2) pair dpd/ext/tstat, perpetual, copy from (1)
|
||||
attributes: half, newton on
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.695 | 3.696 | 3.697 Mbytes
|
||||
Step Time Temp Press
|
||||
0 0 300 5965.5396
|
||||
10 10 303.16391 8779.1574
|
||||
20 20 306.9014 8268.573
|
||||
30 30 305.84291 9976.0547
|
||||
40 40 301.20527 8832.3902
|
||||
50 50 305.72012 8041.0146
|
||||
60 60 305.1676 7118.8042
|
||||
70 70 305.01132 9423.9307
|
||||
80 80 308.10236 10781.423
|
||||
90 90 309.18703 3637.9961
|
||||
100 100 305.11814 7726.7672
|
||||
110 110 298.37346 8575.1602
|
||||
120 120 304.79786 8910.8048
|
||||
130 130 309.05401 6351.4839
|
||||
140 140 304.28367 4805.137
|
||||
150 150 300.28903 7412.6411
|
||||
160 160 299.39358 10183.593
|
||||
170 170 296.80729 5437.1054
|
||||
180 180 295.2755 8317.0414
|
||||
190 190 303.25949 8338.3453
|
||||
200 200 303.24607 9636.5224
|
||||
210 210 298.56684 10288.264
|
||||
220 220 293.42999 9001.0482
|
||||
230 230 293.12497 9083.5194
|
||||
240 240 291.92847 9659.3388
|
||||
250 250 299.2202 6328.759
|
||||
260 260 297.45209 10405.677
|
||||
270 270 292.12257 7273.9369
|
||||
280 280 289.81113 8957.8747
|
||||
290 290 299.06683 6695.3776
|
||||
300 300 300.75468 6298.5705
|
||||
310 310 296.26524 7432.4815
|
||||
320 320 294.21403 9941.7038
|
||||
330 330 293.01776 4750.2993
|
||||
340 340 295.22553 4968.3595
|
||||
350 350 293.95589 9224.5496
|
||||
360 360 297.94278 8792.0395
|
||||
370 370 298.99075 5453.7814
|
||||
380 380 302.1188 6229.2283
|
||||
390 390 298.48943 8517.5273
|
||||
400 400 295.3701 11328.394
|
||||
410 410 287.74238 4058.0382
|
||||
420 420 288.83732 5706.6773
|
||||
430 430 298.8242 6178.7142
|
||||
440 440 304.42682 10138.321
|
||||
450 450 300.28695 9731.3417
|
||||
460 460 300.34539 9249.4691
|
||||
470 470 303.32231 11638.718
|
||||
480 480 301.46777 4186.402
|
||||
490 490 292.56069 9184.8386
|
||||
500 500 297.26162 11766.733
|
||||
510 510 295.34018 6436.33
|
||||
520 520 300.16314 9325.3669
|
||||
530 530 305.00513 5947.6408
|
||||
540 540 300.88805 5222.7384
|
||||
550 550 301.56707 6669.1808
|
||||
560 560 304.89854 10730.053
|
||||
570 570 299.50424 7956.1042
|
||||
580 580 301.23382 10192.246
|
||||
590 590 298.81222 6017.2125
|
||||
600 600 300.57891 4575.433
|
||||
610 610 301.95936 6309.7515
|
||||
620 620 301.09393 5993.6489
|
||||
630 630 300.47565 4388.7137
|
||||
640 640 299.31886 9535.6093
|
||||
650 650 295.06025 7954.5811
|
||||
660 660 298.72666 8630.7466
|
||||
670 670 302.53833 5636.1305
|
||||
680 680 306.32833 12539.149
|
||||
690 690 296.1951 11345.293
|
||||
700 700 297.00325 6352.1448
|
||||
710 710 298.51181 6922.4379
|
||||
720 720 293.80125 4849.4922
|
||||
730 730 296.52677 11141.583
|
||||
740 740 294.15306 3527.8677
|
||||
750 750 294.74737 8454.0815
|
||||
760 760 292.53913 8187.9032
|
||||
770 770 294.37078 7487.5703
|
||||
780 780 297.50085 9198.7697
|
||||
790 790 298.37773 8969.0024
|
||||
800 800 293.29879 6506.6479
|
||||
810 810 296.58266 8805.7872
|
||||
820 820 290.85616 5248.8123
|
||||
830 830 292.29488 5123.8203
|
||||
840 840 292.77623 8263.5675
|
||||
850 850 297.88225 6777.7444
|
||||
860 860 300.01913 10439.087
|
||||
870 870 295.79578 7318.1322
|
||||
880 880 301.5994 8242.4774
|
||||
890 890 306.63208 8090.6106
|
||||
900 900 303.53759 6831.2666
|
||||
910 910 300.70481 3811.0498
|
||||
920 920 299.96274 8351.1573
|
||||
930 930 299.67435 7046.0534
|
||||
940 940 310.81742 6887.6925
|
||||
950 950 305.09984 4811.088
|
||||
960 960 301.33039 4184.851
|
||||
970 970 301.19205 6417.6542
|
||||
980 980 299.6491 7738.2233
|
||||
990 990 297.33655 9264.0874
|
||||
1000 1000 302.33418 7166.2751
|
||||
1010 1010 300.08402 9121.0882
|
||||
1020 1020 302.82225 6405.7109
|
||||
1030 1030 304.01683 6944.0839
|
||||
1040 1040 305.82618 6160.3838
|
||||
1050 1050 308.12518 4356.0931
|
||||
1060 1060 307.64811 6954.7245
|
||||
1070 1070 313.70509 5558.9804
|
||||
1080 1080 316.09239 7250.6147
|
||||
1090 1090 310.2845 5441.3722
|
||||
1100 1100 300.18899 4417.8774
|
||||
1110 1110 304.02471 5609.1668
|
||||
1120 1120 303.46016 10355.031
|
||||
1130 1130 305.68165 6400.913
|
||||
1140 1140 308.78348 7235.1894
|
||||
1150 1150 299.30025 9246.4856
|
||||
1160 1160 302.70799 9866.9536
|
||||
1170 1170 302.0977 8643.5532
|
||||
1180 1180 307.15407 8866.4664
|
||||
1190 1190 305.78146 7562.4911
|
||||
1200 1200 302.54605 7974.9973
|
||||
1210 1210 306.14264 9554.2381
|
||||
1220 1220 308.89843 6219.5361
|
||||
1230 1230 305.71844 7633.9105
|
||||
1240 1240 306.51911 7705.4795
|
||||
1250 1250 304.78473 8590.5595
|
||||
1260 1260 300.82969 9281.5964
|
||||
1270 1270 305.9271 4951.1323
|
||||
1280 1280 310.32728 9446.3989
|
||||
1290 1290 318.27879 9102.5544
|
||||
1300 1300 310.45777 5931.5457
|
||||
1310 1310 304.81268 1214.4291
|
||||
1320 1320 307.08811 10315.961
|
||||
1330 1330 306.86917 8584.9658
|
||||
1340 1340 307.26912 7254.864
|
||||
1350 1350 310.02754 8508.6256
|
||||
1360 1360 306.12763 4912.6641
|
||||
1370 1370 301.67924 6715.8196
|
||||
1380 1380 298.37239 6149.8821
|
||||
1390 1390 299.62894 8181.4761
|
||||
1400 1400 301.60395 6714.4244
|
||||
1410 1410 297.65752 7035.6575
|
||||
1420 1420 297.02817 7510.2637
|
||||
1430 1430 303.59177 10361.937
|
||||
1440 1440 300.10771 8473.2311
|
||||
1450 1450 291.21837 6097.9954
|
||||
1460 1460 291.58663 7729.0841
|
||||
1470 1470 292.52447 6555.8661
|
||||
1480 1480 294.48264 6960.0201
|
||||
1490 1490 298.34869 8044.2321
|
||||
1500 1500 296.8193 11731.289
|
||||
1510 1510 296.52073 5452.8935
|
||||
1520 1520 294.54819 9591.7969
|
||||
1530 1530 297.36394 5148.5383
|
||||
1540 1540 289.08137 6057.0981
|
||||
1550 1550 288.27007 8965.1965
|
||||
1560 1560 294.84398 8316.9487
|
||||
1570 1570 299.79573 8760.7322
|
||||
1580 1580 295.66745 5045.5322
|
||||
1590 1590 298.14356 7161.1834
|
||||
1600 1600 297.10402 6529.9938
|
||||
1610 1610 299.69137 7741.6027
|
||||
1620 1620 304.93043 11222.109
|
||||
1630 1630 302.01322 10893.107
|
||||
1640 1640 295.47422 8400.3124
|
||||
1650 1650 301.93122 7190.2609
|
||||
1660 1660 305.02639 6140.5552
|
||||
1670 1670 302.86047 8651.5366
|
||||
1680 1680 304.82151 9909.407
|
||||
1690 1690 300.48426 8428.8845
|
||||
1700 1700 293.06643 5333.8144
|
||||
1710 1710 295.43687 9103.4353
|
||||
1720 1720 298.77208 8162.1053
|
||||
1730 1730 300.08189 9603.4371
|
||||
1740 1740 303.16004 10693.291
|
||||
1750 1750 303.54199 9151.023
|
||||
1760 1760 300.99281 4641.2985
|
||||
1770 1770 297.36657 3888.5753
|
||||
1780 1780 298.32969 7286.2299
|
||||
1790 1790 297.34183 8975.8956
|
||||
1800 1800 295.83042 6366.7607
|
||||
1810 1810 295.92044 9308.4953
|
||||
1820 1820 298.10087 7117.2369
|
||||
1830 1830 296.13936 4849.3739
|
||||
1840 1840 296.5869 8321.4011
|
||||
1850 1850 296.74513 9530.6806
|
||||
1860 1860 298.57398 8788.0603
|
||||
1870 1870 299.12825 6015.4777
|
||||
1880 1880 301.91639 11706.441
|
||||
1890 1890 309.85968 10909.493
|
||||
1900 1900 302.64998 8779.8967
|
||||
1910 1910 301.62919 9176.3902
|
||||
1920 1920 300.66238 5369.8681
|
||||
1930 1930 297.64499 8185.09
|
||||
1940 1940 296.47852 10188.803
|
||||
1950 1950 297.802 6679.4466
|
||||
1960 1960 299.78754 7316.8198
|
||||
1970 1970 300.09083 6008.9414
|
||||
1980 1980 297.94119 5615.6403
|
||||
1990 1990 298.37687 9727.308
|
||||
2000 2000 296.08394 6400.2746
|
||||
Loop time of 41.5171 on 4 procs for 2000 steps with 2180 atoms
|
||||
|
||||
Performance: 4.162 ns/day, 5.766 hours/ns, 48.173 timesteps/s
|
||||
99.5% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 38.667 | 38.954 | 39.453 | 4.8 | 93.83
|
||||
Neigh | 0.10947 | 0.11039 | 0.11153 | 0.3 | 0.27
|
||||
Comm | 1.8661 | 2.3644 | 2.652 | 19.6 | 5.70
|
||||
Output | 0.0082644 | 0.0094232 | 0.01281 | 2.0 | 0.02
|
||||
Modify | 0.024678 | 0.025206 | 0.025888 | 0.3 | 0.06
|
||||
Other | | 0.05335 | | | 0.13
|
||||
|
||||
Nlocal: 545.000 ave 559 max 531 min
|
||||
Histogram: 1 0 0 0 1 1 0 0 0 1
|
||||
Nghost: 3619.00 ave 3655 max 3594 min
|
||||
Histogram: 1 1 0 0 1 0 0 0 0 1
|
||||
Neighs: 65415.5 ave 66835 max 64310 min
|
||||
Histogram: 1 0 0 2 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 261662
|
||||
Ave neighs/atom = 120.02844
|
||||
Neighbor list builds = 26
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:41
|
||||
@ -0,0 +1,106 @@
|
||||
LAMMPS (24 Mar 2022)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Coarse-Grained SPC/E Water
|
||||
|
||||
variable T equal 300.0
|
||||
variable rc equal 9.0
|
||||
variable rcD equal 10.0
|
||||
|
||||
units real
|
||||
boundary p p p
|
||||
atom_style atomic
|
||||
dimension 3
|
||||
newton on
|
||||
comm_modify vel yes
|
||||
|
||||
read_data cg_spce.data
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (40.31 40.31 40.31)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
2180 atoms
|
||||
read_data CPU = 0.003 seconds
|
||||
|
||||
pair_style hybrid/overlay table spline 1000 dpd/ext/tstat ${T} ${T} ${rc} 385262
|
||||
pair_style hybrid/overlay table spline 1000 dpd/ext/tstat 300 ${T} ${rc} 385262
|
||||
pair_style hybrid/overlay table spline 1000 dpd/ext/tstat 300 300 ${rc} 385262
|
||||
pair_style hybrid/overlay table spline 1000 dpd/ext/tstat 300 300 9 385262
|
||||
|
||||
pair_coeff 1 1 table cg_spce_table.pot VOTCA ${rc}
|
||||
pair_coeff 1 1 table cg_spce_table.pot VOTCA 9
|
||||
WARNING: 16 of 351 force values in table VOTCA are inconsistent with -dE/dr.
|
||||
WARNING: Should only be flagged at inflection points (src/pair_table.cpp:465)
|
||||
pair_coeff 1 1 dpd/ext/tstat 20.0 10.0 0.5 0.5 ${rcD}
|
||||
pair_coeff 1 1 dpd/ext/tstat 20.0 10.0 0.5 0.5 10
|
||||
|
||||
timestep 1.0
|
||||
run_style verlet
|
||||
|
||||
velocity all create ${T} 68768932
|
||||
velocity all create 300 68768932
|
||||
|
||||
thermo_style custom step time temp press
|
||||
thermo 100
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
run 1000
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 7 7 7
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair table, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
(2) pair dpd/ext/tstat, perpetual, copy from (1)
|
||||
attributes: half, newton on
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 5.38 | 5.38 | 5.38 Mbytes
|
||||
Step Time Temp Press
|
||||
0 0 300 7353.4129
|
||||
100 100 303.74025 4964.013
|
||||
200 200 298.35396 8007.7802
|
||||
300 300 298.28547 6291.5807
|
||||
400 400 298.01797 6252.1041
|
||||
500 500 299.88984 3489.931
|
||||
600 600 302.5718 9092.203
|
||||
700 700 305.38722 5909.02
|
||||
800 800 294.81401 10282.286
|
||||
900 900 292.40724 8338.6878
|
||||
1000 1000 293.64788 6951.569
|
||||
Loop time of 28.1058 on 1 procs for 1000 steps with 2180 atoms
|
||||
|
||||
Performance: 3.074 ns/day, 7.807 hours/ns, 35.580 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 | 27.948 | 27.948 | 27.948 | 0.0 | 99.44
|
||||
Neigh | 0.071647 | 0.071647 | 0.071647 | 0.0 | 0.25
|
||||
Comm | 0.058215 | 0.058215 | 0.058215 | 0.0 | 0.21
|
||||
Output | 0.00026724 | 0.00026724 | 0.00026724 | 0.0 | 0.00
|
||||
Modify | 0.014429 | 0.014429 | 0.014429 | 0.0 | 0.05
|
||||
Other | | 0.01283 | | | 0.05
|
||||
|
||||
Nlocal: 2180 ave 2180 max 2180 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 6643 ave 6643 max 6643 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 261826 ave 261826 max 261826 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 261826
|
||||
Ave neighs/atom = 120.10367
|
||||
Neighbor list builds = 12
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:28
|
||||
@ -0,0 +1,106 @@
|
||||
LAMMPS (24 Mar 2022)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Coarse-Grained SPC/E Water
|
||||
|
||||
variable T equal 300.0
|
||||
variable rc equal 9.0
|
||||
variable rcD equal 10.0
|
||||
|
||||
units real
|
||||
boundary p p p
|
||||
atom_style atomic
|
||||
dimension 3
|
||||
newton on
|
||||
comm_modify vel yes
|
||||
|
||||
read_data cg_spce.data
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (40.31 40.31 40.31)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
2180 atoms
|
||||
read_data CPU = 0.003 seconds
|
||||
|
||||
pair_style hybrid/overlay table spline 1000 dpd/ext/tstat ${T} ${T} ${rc} 385262
|
||||
pair_style hybrid/overlay table spline 1000 dpd/ext/tstat 300 ${T} ${rc} 385262
|
||||
pair_style hybrid/overlay table spline 1000 dpd/ext/tstat 300 300 ${rc} 385262
|
||||
pair_style hybrid/overlay table spline 1000 dpd/ext/tstat 300 300 9 385262
|
||||
|
||||
pair_coeff 1 1 table cg_spce_table.pot VOTCA ${rc}
|
||||
pair_coeff 1 1 table cg_spce_table.pot VOTCA 9
|
||||
WARNING: 16 of 351 force values in table VOTCA are inconsistent with -dE/dr.
|
||||
WARNING: Should only be flagged at inflection points (src/pair_table.cpp:465)
|
||||
pair_coeff 1 1 dpd/ext/tstat 20.0 10.0 0.5 0.5 ${rcD}
|
||||
pair_coeff 1 1 dpd/ext/tstat 20.0 10.0 0.5 0.5 10
|
||||
|
||||
timestep 1.0
|
||||
run_style verlet
|
||||
|
||||
velocity all create ${T} 68768932
|
||||
velocity all create 300 68768932
|
||||
|
||||
thermo_style custom step time temp press
|
||||
thermo 100
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
run 1000
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 7 7 7
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair table, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
(2) pair dpd/ext/tstat, perpetual, copy from (1)
|
||||
attributes: half, newton on
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.695 | 3.696 | 3.697 Mbytes
|
||||
Step Time Temp Press
|
||||
0 0 300 5950.2338
|
||||
100 100 301.15012 9090.2244
|
||||
200 200 301.28795 10589.557
|
||||
300 300 293.61974 5971.7781
|
||||
400 400 310.4217 8198.7972
|
||||
500 500 299.89888 9140.3132
|
||||
600 600 305.56607 7783.4481
|
||||
700 700 295.99415 6276.9444
|
||||
800 800 296.50051 5058.1115
|
||||
900 900 288.68499 8637.0269
|
||||
1000 1000 291.17292 6516.4192
|
||||
Loop time of 7.57429 on 4 procs for 1000 steps with 2180 atoms
|
||||
|
||||
Performance: 11.407 ns/day, 2.104 hours/ns, 132.026 timesteps/s
|
||||
99.8% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 7.2745 | 7.3674 | 7.4316 | 2.1 | 97.27
|
||||
Neigh | 0.01863 | 0.018866 | 0.019429 | 0.2 | 0.25
|
||||
Comm | 0.1123 | 0.17708 | 0.27025 | 13.8 | 2.34
|
||||
Output | 0.00019274 | 0.00021224 | 0.00026504 | 0.0 | 0.00
|
||||
Modify | 0.0041691 | 0.0042729 | 0.0043136 | 0.1 | 0.06
|
||||
Other | | 0.006464 | | | 0.09
|
||||
|
||||
Nlocal: 545 ave 552 max 531 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 2 1
|
||||
Nghost: 3620.5 ave 3656 max 3584 min
|
||||
Histogram: 1 0 1 0 0 0 0 1 0 1
|
||||
Neighs: 65419 ave 66338 max 64104 min
|
||||
Histogram: 1 0 0 0 1 0 0 0 1 1
|
||||
|
||||
Total # of neighbors = 261676
|
||||
Ave neighs/atom = 120.03486
|
||||
Neighbor list builds = 12
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:07
|
||||
@ -23,3 +23,5 @@ to the final states.
|
||||
|
||||
* `quicktests` -- very short runs with charged Lennard-Jones atoms to test
|
||||
*compute fep*, *fix adapt/fep* and *pair lj/cut/coul/long/soft*.
|
||||
|
||||
* `ta` -- surface tension of SPCE water without constraints. Test-area method.
|
||||
|
||||
6174
examples/PACKAGES/fep/ta/data.spce
Normal file
6174
examples/PACKAGES/fep/ta/data.spce
Normal file
File diff suppressed because it is too large
Load Diff
49
examples/PACKAGES/fep/ta/in.spce.lmp
Normal file
49
examples/PACKAGES/fep/ta/in.spce.lmp
Normal file
@ -0,0 +1,49 @@
|
||||
|
||||
units real
|
||||
boundary p p p
|
||||
|
||||
atom_style full
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
|
||||
special_bonds lj/coul 0.0 0.0 0.5
|
||||
|
||||
pair_style lj/cut/coul/long 12.0 12.0
|
||||
pair_modify tail no
|
||||
kspace_style pppm 1.0e-5
|
||||
|
||||
read_data data.spce # 8x8x16 SPCE molecules in a 30x30x100 box
|
||||
|
||||
bond_coeff 1 517.630258 1.0
|
||||
angle_coeff 1 37.950526 109.47
|
||||
pair_coeff 1 1 0.1553 3.166 # O O
|
||||
pair_coeff 1 2 0.0 1.0 # O H
|
||||
pair_coeff 2 2 0.0 1.0 # H H
|
||||
|
||||
# don't use fix shake with compute fep/ta
|
||||
# fix SHAKE all shake 0.0001 20 0 b 1
|
||||
|
||||
neighbor 2.0 bin
|
||||
# neigh_modify delay 0 every 1 check yes
|
||||
|
||||
timestep 1.0
|
||||
|
||||
variable TK equal 300.0
|
||||
compute TA all fep/ta ${TK} xy 1.0005
|
||||
|
||||
velocity all create ${TK} 12345
|
||||
|
||||
thermo_style custom step temp press etotal pe c_TA[*]
|
||||
thermo 5000
|
||||
|
||||
fix NVT all nvt temp ${TK} ${TK} 100
|
||||
run 300000
|
||||
|
||||
reset_timestep 0
|
||||
|
||||
variable gamma_v equal 100*(pzz-0.5*(pxx+pyy))/2/100 # surface tension via the mechanical route
|
||||
|
||||
fix FEP all ave/time 100 1000 100000 c_TA[*] v_gamma_v ave running file spce.fep.ta
|
||||
|
||||
run 2000000
|
||||
|
||||
689
examples/PACKAGES/fep/ta/log.spce
Normal file
689
examples/PACKAGES/fep/ta/log.spce
Normal file
@ -0,0 +1,689 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
package gpu 0
|
||||
|
||||
units real
|
||||
boundary p p p
|
||||
|
||||
atom_style full
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
|
||||
special_bonds lj/coul 0.0 0.0 0.5
|
||||
|
||||
pair_style lj/cut/coul/long 12.0 12.0
|
||||
pair_modify tail no
|
||||
kspace_style pppm 1.0e-5
|
||||
|
||||
read_data data.spce # 8x8x16 SPCE molecules in a 30x30x100 box
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (30 30 100)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
3072 atoms
|
||||
scanning bonds ...
|
||||
2 = max bonds/atom
|
||||
scanning angles ...
|
||||
1 = max angles/atom
|
||||
reading bonds ...
|
||||
2048 bonds
|
||||
reading angles ...
|
||||
1024 angles
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0.5
|
||||
special bond factors coul: 0 0 0.5
|
||||
2 = max # of 1-2 neighbors
|
||||
1 = max # of 1-3 neighbors
|
||||
1 = max # of 1-4 neighbors
|
||||
2 = max # of special neighbors
|
||||
special bonds CPU = 0.001 seconds
|
||||
read_data CPU = 0.006 seconds
|
||||
|
||||
bond_coeff 1 517.630258 1.0
|
||||
angle_coeff 1 37.950526 109.47
|
||||
pair_coeff 1 1 0.1553 3.166 # O O
|
||||
pair_coeff 1 2 0.0 1.0 # O H
|
||||
pair_coeff 2 2 0.0 1.0 # H H
|
||||
|
||||
# don't use fix shake with compute fep/ta
|
||||
# fix SHAKE all shake 0.0001 20 0 b 1
|
||||
|
||||
neighbor 2.0 bin
|
||||
# neigh_modify delay 0 every 1 check yes
|
||||
|
||||
timestep 1.0
|
||||
|
||||
variable TK equal 300.0
|
||||
compute TA all fep/ta ${TK} xy 1.0005
|
||||
compute TA all fep/ta 300 xy 1.0005
|
||||
|
||||
velocity all create ${TK} 12345
|
||||
velocity all create 300 12345
|
||||
|
||||
thermo_style custom step temp press etotal pe c_TA[*]
|
||||
thermo 5000
|
||||
|
||||
fix NVT all nvt temp ${TK} ${TK} 100
|
||||
fix NVT all nvt temp 300 ${TK} 100
|
||||
fix NVT all nvt temp 300 300 100
|
||||
run 300000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- GPU package (short-range, long-range and three-body potentials):
|
||||
|
||||
@Article{Brown11,
|
||||
author = {W. M. Brown, P. Wang, S. J. Plimpton, A. N. Tharrington},
|
||||
title = {Implementing Molecular Dynamics on Hybrid High Performance Computers - Short Range Forces},
|
||||
journal = {Comp.~Phys.~Comm.},
|
||||
year = 2011,
|
||||
volume = 182,
|
||||
pages = {898--911}
|
||||
}
|
||||
|
||||
@Article{Brown12,
|
||||
author = {W. M. Brown, A. Kohlmeyer, S. J. Plimpton, A. N. Tharrington},
|
||||
title = {Implementing Molecular Dynamics on Hybrid High Performance Computers - Particle-Particle Particle-Mesh},
|
||||
journal = {Comp.~Phys.~Comm.},
|
||||
year = 2012,
|
||||
volume = 183,
|
||||
pages = {449--459}
|
||||
}
|
||||
|
||||
@Article{Brown13,
|
||||
author = {W. M. Brown, Y. Masako},
|
||||
title = {Implementing Molecular Dynamics on Hybrid High Performance Computers – Three-Body Potentials},
|
||||
journal = {Comp.~Phys.~Comm.},
|
||||
year = 2013,
|
||||
volume = 184,
|
||||
pages = {2785--2793}
|
||||
}
|
||||
|
||||
@Article{Trung15,
|
||||
author = {T. D. Nguyen, S. J. Plimpton},
|
||||
title = {Accelerating dissipative particle dynamics simulations for soft matter systems},
|
||||
journal = {Comput.~Mater.~Sci.},
|
||||
year = 2015,
|
||||
volume = 100,
|
||||
pages = {173--180}
|
||||
}
|
||||
|
||||
@Article{Trung17,
|
||||
author = {T. D. Nguyen},
|
||||
title = {GPU-accelerated Tersoff potentials for massively parallel Molecular Dynamics simulations},
|
||||
journal = {Comp.~Phys.~Comm.},
|
||||
year = 2017,
|
||||
volume = 212,
|
||||
pages = {113--122}
|
||||
}
|
||||
|
||||
@Article{Nikolskiy19,
|
||||
author = {V. Nikolskiy, V. Stegailov},
|
||||
title = {GPU acceleration of four-site water models in LAMMPS},
|
||||
journal = {Proceeding of the International Conference on Parallel Computing (ParCo 2019), Prague, Czech Republic},
|
||||
year = 2019
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:340)
|
||||
G vector (1/distance) = 0.24270009
|
||||
grid = 20 20 50
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0037271514
|
||||
estimated relative force accuracy = 1.1224206e-05
|
||||
using double precision FFTW3
|
||||
3d grid and FFT values/proc = 40824 20000
|
||||
generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
FEP/TA settings ...
|
||||
temperature = 300.000000
|
||||
scale factor = 1.000500
|
||||
tail no
|
||||
Per MPI rank memory allocation (min/avg/max) = 10.59 | 10.59 | 10.59 Mbytes
|
||||
Step Temp Press TotEng PotEng c_TA[1] c_TA[2] c_TA[3]
|
||||
0 300 5742.8831 8061.6965 5315.4762 -10.940045 93249708 0.45
|
||||
5000 301.43029 -118.64017 -7888.4723 -10647.786 -0.13617205 1.2566061 0.45
|
||||
10000 294.49018 -301.44062 -8063.3808 -10759.164 -0.14897537 1.2838851 0.45
|
||||
15000 294.36123 -407.07728 -8189.2912 -10883.894 0.34568257 0.55998421 0.45
|
||||
20000 300.95171 111.50248 -8104.1193 -10859.052 0.11293291 0.82742794 0.45
|
||||
25000 300.28473 388.00598 -8147.8655 -10896.692 0.11270184 0.82774872 0.45
|
||||
30000 306.62229 -113.93849 -8191.7529 -10998.594 0.26068823 0.6457922 0.45
|
||||
35000 303.66349 -426.81556 -8269.8364 -11049.593 0.78191631 0.26939311 0.45
|
||||
40000 291.70214 -50.50854 -8368.0775 -11038.339 0.20120788 0.71354814 0.45
|
||||
45000 299.74326 -289.18081 -8346.2716 -11090.142 0.4163404 0.49739645 0.45
|
||||
50000 300.53193 36.834691 -8367.5726 -11118.662 0.20517137 0.70881996 0.45
|
||||
55000 298.20207 -107.76906 -8274.386 -11004.148 0.7409946 0.2885342 0.45
|
||||
60000 298.32558 -65.20542 -8433.4884 -11164.381 0.16210976 0.76191344 0.45
|
||||
65000 297.3149 -102.87381 -8379.2515 -11100.892 0.21193701 0.70082127 0.45
|
||||
70000 300.78423 -463.75811 -8381.3317 -11134.731 0.32109349 0.58356406 0.45
|
||||
75000 299.53099 -53.264996 -8495.159 -11237.086 0.44828935 0.47144212 0.45
|
||||
80000 295.55879 -590.1244 -8432.3435 -11137.909 0.28788374 0.61699451 0.45
|
||||
85000 298.73289 -234.73297 -8473.8721 -11208.493 -0.11723275 1.2173128 0.45
|
||||
90000 307.02709 -264.9035 -8303.7625 -11114.309 -0.098959935 1.1805672 0.45
|
||||
95000 304.79112 199.8891 -8364.2553 -11154.334 0.036986735 0.93984396 0.45
|
||||
100000 295.49748 -743.18974 -8453.8066 -11158.811 0.249981 0.65749559 0.45
|
||||
105000 303.11352 -163.70166 -8324.4846 -11099.206 -0.012286442 1.0208231 0.45
|
||||
110000 294.30278 -33.731015 -8512.8168 -11206.884 -0.0129379 1.0219392 0.45
|
||||
115000 293.65421 393.24871 -8481.1933 -11169.324 0.75255277 0.28299408 0.45
|
||||
120000 300.56448 16.832298 -8507.3819 -11258.769 0.13389897 0.79883437 0.45
|
||||
125000 297.92506 -398.77893 -8576.4403 -11303.666 0.07292658 0.88485917 0.45
|
||||
130000 303.007 -589.11865 -8560.7259 -11334.472 0.42876446 0.48713794 0.45
|
||||
135000 310.82674 -203.4991 -8565.3181 -11410.647 0.075268046 0.88139064 0.45
|
||||
140000 303.68345 -710.20709 -8570.895 -11350.834 -0.1023741 1.1873476 0.45
|
||||
145000 293.86825 129.05781 -8457.0747 -11147.165 0.39475138 0.51573896 0.45
|
||||
150000 296.93136 -734.03863 -8577.2763 -11295.406 0.73600373 0.29095985 0.45
|
||||
155000 296.67522 -290.20206 -8631.0579 -11346.843 -0.30049664 1.6554154 0.45
|
||||
160000 301.5685 -656.03394 -8646.3196 -11406.898 0.08494101 0.86720512 0.45
|
||||
165000 295.8808 342.45206 -8602.0309 -11310.544 -0.30873864 1.6784606 0.45
|
||||
170000 303.33048 -64.144957 -8580.8446 -11357.552 0.13622456 0.79572423 0.45
|
||||
175000 300.75245 -908.44969 -8566.8005 -11319.909 0.15795135 0.76724659 0.45
|
||||
180000 301.34603 -350.00512 -8489.0111 -11247.553 0.21089487 0.70204744 0.45
|
||||
185000 305.96254 62.840515 -8458.0542 -11258.856 -0.050029338 1.0875408 0.45
|
||||
190000 300.14392 256.935 -8684.6591 -11432.197 0.40144188 0.50998337 0.45
|
||||
195000 299.32366 -218.70113 -8505.3328 -11245.362 -0.19428451 1.3852659 0.45
|
||||
200000 307.89424 -569.89954 -8615.1541 -11433.639 0.55121888 0.39668508 0.45
|
||||
205000 299.34873 334.69765 -8657.6353 -11397.894 0.17751997 0.74247109 0.45
|
||||
210000 298.54619 -261.12193 -8601.2439 -11334.156 0.74219016 0.28795615 0.45
|
||||
215000 304.02395 -306.81112 -8531.9913 -11315.047 0.86987192 0.23244073 0.45
|
||||
220000 299.95916 278.60921 -8682.394 -11428.24 -0.26474202 1.559051 0.45
|
||||
225000 302.839 -226.36906 -8515.0815 -11287.29 0.060381353 0.90367684 0.45
|
||||
230000 299.54085 240.08589 -8636.8991 -11378.916 -0.46699438 2.1887589 0.45
|
||||
235000 297.62792 -138.20813 -8627.0888 -11351.595 -0.035013312 1.0604901 0.45
|
||||
240000 299.15558 442.88999 -8749.2731 -11487.763 0.14696819 0.78151268 0.45
|
||||
245000 291.76323 174.70322 -8597.8808 -11268.701 -0.3979188 1.9492946 0.45
|
||||
250000 308.21961 37.282506 -8603.7127 -11425.176 0.021882894 0.96395922 0.45
|
||||
255000 307.18484 -493.77408 -8459.5942 -11271.585 0.16914044 0.75298079 0.45
|
||||
260000 294.17364 -238.05366 -8677.8379 -11370.723 -0.35710078 1.8202968 0.45
|
||||
265000 289.14461 -304.12454 -8727.2613 -11374.111 0.18045129 0.73882932 0.45
|
||||
270000 301.51228 -255.75558 -8640.9577 -11401.022 0.49252861 0.43772444 0.45
|
||||
275000 294.98349 -351.00974 -8678.3965 -11378.695 -0.31576914 1.6983718 0.45
|
||||
280000 294.37376 279.87325 -8668.9575 -11363.675 0.26328091 0.64298978 0.45
|
||||
285000 295.68351 249.3086 -8748.533 -11455.24 0.6820904 0.31849899 0.45
|
||||
290000 298.74266 -749.43024 -8583.8679 -11318.578 0.030414997 0.95026156 0.45
|
||||
295000 292.67215 -573.39647 -8713.3223 -11392.463 0.25656615 0.65027291 0.45
|
||||
300000 302.48853 186.71329 -8655.8918 -11424.892 0.20319721 0.71117107 0.45
|
||||
Loop time of 706.805 on 1 procs for 300000 steps with 3072 atoms
|
||||
|
||||
Performance: 36.672 ns/day, 0.654 hours/ns, 424.445 timesteps/s
|
||||
95.4% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 149.88 | 149.88 | 149.88 | 0.0 | 21.21
|
||||
Bond | 17.824 | 17.824 | 17.824 | 0.0 | 2.52
|
||||
Kspace | 517.46 | 517.46 | 517.46 | 0.0 | 73.21
|
||||
Neigh | 1.3789 | 1.3789 | 1.3789 | 0.0 | 0.20
|
||||
Comm | 9.412 | 9.412 | 9.412 | 0.0 | 1.33
|
||||
Output | 0.092 | 0.092 | 0.092 | 0.0 | 0.01
|
||||
Modify | 8.3026 | 8.3026 | 8.3026 | 0.0 | 1.17
|
||||
Other | | 2.458 | | | 0.35
|
||||
|
||||
Nlocal: 3072 ave 3072 max 3072 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 8370 ave 8370 max 8370 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 = -1
|
||||
Ave neighs/atom = -0.00032552083
|
||||
Ave special neighs/atom = 2
|
||||
Neighbor list builds = 14698
|
||||
Dangerous builds = 21
|
||||
|
||||
reset_timestep 0
|
||||
|
||||
variable gamma_v equal 100*(pzz-0.5*(pxx+pyy))/2/100 # surface tension via the mechanical route
|
||||
|
||||
fix FEP all ave/time 100 1000 100000 c_TA[*] v_gamma_v ave running file spce.fep.ta
|
||||
|
||||
run 2000000
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:340)
|
||||
G vector (1/distance) = 0.24270009
|
||||
grid = 20 20 50
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0037271514
|
||||
estimated relative force accuracy = 1.1224206e-05
|
||||
using double precision FFTW3
|
||||
3d grid and FFT values/proc = 40824 20000
|
||||
generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 10.61 | 10.61 | 10.61 Mbytes
|
||||
Step Temp Press TotEng PotEng c_TA[1] c_TA[2] c_TA[3]
|
||||
0 302.48853 186.71327 -8655.8918 -11424.892 0.20325452 0.71110271 0.45
|
||||
5000 296.71986 -573.544 -8510.0832 -11226.277 0.43636365 0.48096787 0.45
|
||||
10000 302.58189 314.36295 -8636.8139 -11406.669 0.005932853 0.99009761 0.45
|
||||
15000 296.98096 -950.66627 -8635.9066 -11354.49 0.48058674 0.44658101 0.45
|
||||
20000 297.11923 -474.65836 -8666.9864 -11386.836 0.27933535 0.62590536 0.45
|
||||
25000 302.26474 -621.83271 -8655.4227 -11422.375 0.01931686 0.96811729 0.45
|
||||
30000 300.37645 -358.95128 -8568.7732 -11318.44 0.25415456 0.65290873 0.45
|
||||
35000 296.5436 179.71411 -8665.0335 -11379.614 0.1911473 0.72569185 0.45
|
||||
40000 300.79459 92.193193 -8617.7807 -11371.275 0.27587113 0.629553 0.45
|
||||
45000 298.87827 220.06674 -8695.83 -11431.782 0.28715816 0.61774591 0.45
|
||||
50000 304.4095 -375.31266 -8614.4396 -11401.025 -0.18683272 1.3680584 0.45
|
||||
55000 305.11287 128.51602 -8559.8245 -11352.848 0.24122754 0.66722084 0.45
|
||||
60000 296.56241 302.30371 -8725.6357 -11440.388 -0.27104279 1.5756158 0.45
|
||||
65000 295.78468 -393.18931 -8716.4616 -11424.095 0.39132466 0.51871194 0.45
|
||||
70000 297.67504 155.75977 -8641.2451 -11366.182 0.031194864 0.94901929 0.45
|
||||
75000 298.81381 -207.51201 -8622.9859 -11358.348 -0.11330086 1.2093106 0.45
|
||||
80000 296.17928 -360.65589 -8679.0048 -11390.25 0.68794433 0.31538684 0.45
|
||||
85000 303.90294 488.01134 -8643.2028 -11425.151 0.41330713 0.49993365 0.45
|
||||
90000 296.49425 14.901201 -8636.0539 -11350.182 -0.21538319 1.4351695 0.45
|
||||
95000 308.63505 137.10659 -8570.395 -11395.661 0.51407684 0.42218544 0.45
|
||||
100000 302.56638 -402.80803 -8635.0157 -11404.729 0.1552006 0.77079493 0.45
|
||||
105000 293.79289 -417.74599 -8626.2538 -11315.654 -0.13491963 1.253969 0.45
|
||||
110000 293.52504 -808.94658 -8684.9259 -11371.874 0.20573374 0.70815164 0.45
|
||||
115000 307.6821 132.78071 -8639.817 -11456.36 -0.67060193 3.0798018 0.45
|
||||
120000 303.22974 121.87128 -8714.7295 -11490.515 0.3675961 0.5397742 0.45
|
||||
125000 303.8202 -34.518279 -8625.1384 -11406.329 0.17151619 0.74998608 0.45
|
||||
130000 294.5718 -508.86133 -8684.9608 -11381.491 0.23323323 0.67622827 0.45
|
||||
135000 302.79866 -445.99091 -8627.6163 -11399.456 0.3300839 0.57482965 0.45
|
||||
140000 297.84052 -78.442467 -8621.5234 -11347.976 0.39157424 0.51849484 0.45
|
||||
145000 303.64247 463.89678 -8673.8591 -11453.423 0.39692857 0.51385891 0.45
|
||||
150000 288.38239 28.567607 -8789.6464 -11429.518 -0.045509865 1.0793274 0.45
|
||||
155000 296.02581 -111.35664 -8674.295 -11384.135 0.23313764 0.67633671 0.45
|
||||
160000 307.72004 -410.73956 -8578.8169 -11395.707 0.28485416 0.62013794 0.45
|
||||
165000 300.42279 -483.56039 -8598.0354 -11348.126 0.38342507 0.52563101 0.45
|
||||
170000 302.51326 -150.99512 -8626.2426 -11395.469 0.2439355 0.66419697 0.45
|
||||
175000 295.41161 -554.9058 -8760.0201 -11464.238 0.38186652 0.52700696 0.45
|
||||
180000 296.21987 -194.97724 -8645.4143 -11357.031 0.098453456 0.84777037 0.45
|
||||
185000 296.52352 -186.85833 -8690.0538 -11404.45 0.6348999 0.34473516 0.45
|
||||
190000 304.72799 -60.2868 -8667.2005 -11456.701 0.1885985 0.72880108 0.45
|
||||
195000 306.65221 -871.17267 -8679.3434 -11486.458 0.56138735 0.38997638 0.45
|
||||
200000 301.07509 362.96369 -8616.9867 -11373.048 -0.53126323 2.4379049 0.45
|
||||
205000 303.65587 -216.8767 -8564.3182 -11344.005 0.11046546 0.83085967 0.45
|
||||
210000 296.20891 -474.08356 -8698.3778 -11409.894 -0.11237476 1.2074335 0.45
|
||||
215000 295.37276 422.46284 -8714.4636 -11418.326 0.042757549 0.93079022 0.45
|
||||
220000 301.20663 -202.20616 -8577.1827 -11334.449 0.30387837 0.60066105 0.45
|
||||
225000 306.20481 -90.566175 -8503.5134 -11306.533 0.29188403 0.6128683 0.45
|
||||
230000 303.54253 -24.255163 -8641.8724 -11420.521 -0.38522168 1.9082173 0.45
|
||||
235000 300.29265 -572.08074 -8664.2779 -11413.177 0.48055356 0.44660587 0.45
|
||||
240000 302.90712 -226.88617 -8636.6962 -11409.528 -0.15295452 1.2924832 0.45
|
||||
245000 305.05222 -68.241521 -8591.0885 -11383.557 -0.19850824 1.3951152 0.45
|
||||
250000 300.27784 -46.680162 -8746.7288 -11495.492 -0.0098493376 1.0166585 0.45
|
||||
255000 308.23091 -424.64171 -8573.7405 -11395.307 0.1366107 0.79520901 0.45
|
||||
260000 296.11619 4.6901264 -8742.1916 -11452.859 -0.12450429 1.2322516 0.45
|
||||
265000 301.62359 134.42152 -8565.5323 -11326.615 -0.028534957 1.0490284 0.45
|
||||
270000 306.71999 -62.484213 -8690.7983 -11498.534 0.28432443 0.62068922 0.45
|
||||
275000 292.91982 532.15442 -8779.2684 -11460.676 -0.40898808 1.9858264 0.45
|
||||
280000 306.88024 -339.05165 -8557.2761 -11366.479 0.12573772 0.80984534 0.45
|
||||
285000 303.38798 617.66326 -8630.5787 -11407.813 -0.1310487 1.2458532 0.45
|
||||
290000 299.66094 302.90333 -8692.267 -11435.383 0.65063395 0.33575584 0.45
|
||||
295000 304.49009 656.72392 -8710.7918 -11498.115 -0.16849302 1.3266137 0.45
|
||||
300000 303.80861 -221.66912 -8688.9465 -11470.031 -0.24985266 1.5205954 0.45
|
||||
305000 300.67136 -498.92059 -8669.6648 -11422.031 0.19219443 0.72441833 0.45
|
||||
310000 305.7021 -521.59218 -8505.6751 -11304.093 0.52013748 0.4179152 0.45
|
||||
315000 302.66313 -359.25677 -8682.4925 -11453.091 -0.26135382 1.5502155 0.45
|
||||
320000 304.5646 441.04962 -8610.9569 -11398.962 0.41662005 0.49716319 0.45
|
||||
325000 300.04934 -142.59053 -8698.3246 -11444.997 -0.23029219 1.4715132 0.45
|
||||
330000 305.55522 -212.47771 -8576.3678 -11373.441 0.091594168 0.85758093 0.45
|
||||
335000 294.79439 -151.62761 -8762.4565 -11461.024 0.14345357 0.78613362 0.45
|
||||
340000 302.4373 463.41717 -8643.2588 -11411.79 0.36279978 0.54413438 0.45
|
||||
345000 295.91624 -272.3623 -8678.9725 -11387.81 0.1032874 0.84092407 0.45
|
||||
350000 300.60829 62.418773 -8633.2343 -11385.023 -0.040578988 1.0704371 0.45
|
||||
355000 301.41802 -860.82496 -8573.5867 -11332.788 0.04947461 0.9203617 0.45
|
||||
360000 298.03103 -265.05516 -8619.4232 -11347.619 -0.20903224 1.4199617 0.45
|
||||
365000 298.08727 -359.76277 -8612.4898 -11341.201 0.040109682 0.93493354 0.45
|
||||
370000 301.55162 -339.05976 -8687.3746 -11447.799 0.1705358 0.75122045 0.45
|
||||
375000 299.3933 -290.38029 -8723.9515 -11464.618 -0.1476 1.2809266 0.45
|
||||
380000 303.02442 -1104.7914 -8626.7252 -11400.631 0.3211992 0.58346059 0.45
|
||||
385000 301.49421 -613.53228 -8662.2479 -11422.146 -0.42642873 2.0447796 0.45
|
||||
390000 302.01134 -351.23257 -8662.4664 -11427.099 0.23747904 0.67142935 0.45
|
||||
395000 307.32962 -443.86959 -8624.8646 -11438.181 0.17359502 0.74737541 0.45
|
||||
400000 301.67955 -253.92045 -8690.6143 -11452.209 -0.43779134 2.0841261 0.45
|
||||
405000 302.60773 -97.544471 -8646.8281 -11416.92 0.071259831 0.88733652 0.45
|
||||
410000 302.48853 -630.99507 -8710.4497 -11479.45 0.28763517 0.61725182 0.45
|
||||
415000 296.46562 -443.33457 -8763.0661 -11476.932 0.088532948 0.86199583 0.45
|
||||
420000 295.37803 -70.515081 -8720.0027 -11423.913 0.06359365 0.89882065 0.45
|
||||
425000 299.31069 -48.284153 -8678.6115 -11418.522 0.063520704 0.89893064 0.45
|
||||
430000 296.37918 -651.48627 -8784.4246 -11497.5 -0.0094249768 1.0159351 0.45
|
||||
435000 303.07145 -284.10404 -8558.3149 -11332.651 0.034731239 0.94340646 0.45
|
||||
440000 293.1823 -280.18182 -8707.2432 -11391.054 0.14151034 0.78870025 0.45
|
||||
445000 305.55617 -286.4858 -8646.9315 -11444.013 0.26166889 0.64473078 0.45
|
||||
450000 300.67206 102.89156 -8705.2376 -11457.61 0.88202179 0.2277515 0.45
|
||||
455000 304.23258 9.5792632 -8571.8771 -11356.843 -0.42835558 2.0513992 0.45
|
||||
460000 292.30355 265.8009 -8707.4453 -11383.212 0.20592758 0.70792142 0.45
|
||||
465000 297.62746 193.66269 -8716.5132 -11441.015 0.36938368 0.53815813 0.45
|
||||
470000 292.53483 -75.549804 -8728.3188 -11406.202 0.49993961 0.43231669 0.45
|
||||
475000 296.10181 -202.26042 -8657.5804 -11368.116 -0.29829888 1.6493239 0.45
|
||||
480000 300.24953 249.20038 -8688.6705 -11437.175 0.4372485 0.48025452 0.45
|
||||
485000 296.41241 -73.46156 -8558.9344 -11272.314 -0.15947631 1.3067001 0.45
|
||||
490000 302.51379 -654.60188 -8571.28 -11340.512 0.36608136 0.54114742 0.45
|
||||
495000 300.50497 -127.55361 -8724.7069 -11475.55 0.029571506 0.95160701 0.45
|
||||
500000 303.60879 183.79306 -8568.3539 -11347.609 0.050255275 0.91915729 0.45
|
||||
505000 303.19721 -181.45226 -8614.403 -11389.891 0.32941264 0.57547725 0.45
|
||||
510000 296.74554 -22.844257 -8659.5977 -11376.026 0.017555998 0.97098101 0.45
|
||||
515000 304.94785 184.89151 -8657.5502 -11449.063 0.36892431 0.53857296 0.45
|
||||
520000 297.55996 -618.66865 -8737.5039 -11461.388 0.0057510291 0.99039963 0.45
|
||||
525000 301.79028 298.59479 -8629.0889 -11391.698 0.34316268 0.56235619 0.45
|
||||
530000 309.73127 127.43322 -8551.5448 -11386.846 0.76278829 0.27817682 0.45
|
||||
535000 296.10155 231.50902 -8700.9183 -11411.452 0.44398766 0.47485618 0.45
|
||||
540000 299.71005 -102.1096 -8655.905 -11399.471 0.76085637 0.27907974 0.45
|
||||
545000 300.14982 -206.19313 -8714.8486 -11462.44 0.22627441 0.68416793 0.45
|
||||
550000 294.79885 -643.7432 -8605.2486 -11303.857 -0.057557071 1.1013603 0.45
|
||||
555000 294.17638 -19.930168 -8726.0381 -11418.949 0.40954478 0.50309869 0.45
|
||||
560000 297.03199 -369.45853 -8470.404 -11189.455 -0.6540448 2.9954437 0.45
|
||||
565000 291.48707 -349.3956 -8714.1576 -11382.45 0.16175418 0.76236802 0.45
|
||||
570000 310.66906 -63.356318 -8637.4971 -11481.383 0.025729917 0.95775884 0.45
|
||||
575000 300.62447 -741.10788 -8620.5725 -11372.509 0.16003059 0.76457532 0.45
|
||||
580000 303.7169 -69.625554 -8649.3106 -11429.556 0.13011667 0.80391862 0.45
|
||||
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1485000 297.20205 -166.62152 -8598.691 -11319.299 -0.24681532 1.5128679 0.45
|
||||
1490000 299.73617 -126.47006 -8649.4834 -11393.289 0.47833671 0.44826968 0.45
|
||||
1495000 295.64416 481.3869 -8697.4378 -11403.784 0.1128182 0.82758717 0.45
|
||||
1500000 301.34876 -64.948239 -8570.0291 -11328.596 0.10524924 0.83816132 0.45
|
||||
1505000 297.45753 538.92423 -8678.9073 -11401.854 0.15764246 0.76764423 0.45
|
||||
1510000 304.47978 -609.79308 -8491.9652 -11279.194 0.40940159 0.50321953 0.45
|
||||
1515000 301.26466 -130.2245 -8572.0691 -11329.866 0.89811777 0.22168463 0.45
|
||||
1520000 306.33064 472.83128 -8553.0557 -11357.227 -0.3949103 1.9394824 0.45
|
||||
1525000 303.77309 446.96086 -8658.8797 -11439.639 0.23907939 0.66962936 0.45
|
||||
1530000 305.94257 -462.96121 -8683.4501 -11484.069 -0.29365623 1.6365296 0.45
|
||||
1535000 296.45268 -725.6647 -8564.4464 -11278.194 0.031785638 0.94807932 0.45
|
||||
1540000 297.90338 -418.20316 -8566.3092 -11293.337 0.50491901 0.42872083 0.45
|
||||
1545000 304.3796 -281.11491 -8571.3965 -11357.708 0.26286914 0.64343405 0.45
|
||||
1550000 296.71481 -62.772449 -8680.9078 -11397.055 0.15669974 0.76885909 0.45
|
||||
1555000 297.50225 148.74592 -8754.0913 -11477.447 0.14286636 0.78690833 0.45
|
||||
1560000 300.52393 373.85791 -8638.4601 -11389.477 0.089292836 0.8608978 0.45
|
||||
1565000 295.18741 -197.82529 -8603.6291 -11305.795 0.36113621 0.54565489 0.45
|
||||
1570000 295.50662 -297.43989 -8727.7936 -11432.881 0.24895806 0.65862474 0.45
|
||||
1575000 306.12787 745.92559 -8609.3706 -11411.686 0.42705392 0.48853767 0.45
|
||||
1580000 300.84367 544.00229 -8635.6029 -11389.546 -0.20268104 1.4049145 0.45
|
||||
1585000 293.01964 208.25986 -8624.1146 -11306.436 -0.013645123 1.0231522 0.45
|
||||
1590000 304.09 110.80761 -8602.177 -11385.837 -0.39136115 1.9279703 0.45
|
||||
1595000 289.74205 -521.57012 -8666.417 -11318.735 0.30601242 0.59851474 0.45
|
||||
1600000 297.3494 368.04946 -8684.986 -11406.943 0.079346518 0.87538143 0.45
|
||||
1605000 301.19957 -293.44562 -8521.9202 -11279.121 0.49408391 0.43658396 0.45
|
||||
1610000 299.66627 -592.72965 -8750.1489 -11493.314 -0.20726596 1.415761 0.45
|
||||
1615000 301.32181 329.96166 -8575.077 -11333.397 0.21514479 0.69706049 0.45
|
||||
1620000 297.46259 -575.7077 -8604.3396 -11327.332 0.051950054 0.91654801 0.45
|
||||
1625000 301.143 -578.27016 -8622.6936 -11379.377 0.33929754 0.566014 0.45
|
||||
1630000 301.9449 119.02272 -8744.8752 -11508.899 0.25690123 0.64990753 0.45
|
||||
1635000 292.31769 -256.96526 -8729.3974 -11405.293 0.2041501 0.71003527 0.45
|
||||
1640000 305.17316 -224.04815 -8619.2426 -11412.818 0.61612842 0.35576261 0.45
|
||||
1645000 299.82547 -453.0871 -8601.8345 -11346.457 0.44515417 0.47392794 0.45
|
||||
1650000 300.70213 -184.15313 -8604.5269 -11357.175 0.40413562 0.50768423 0.45
|
||||
1655000 298.34797 241.12842 -8736.9407 -11468.038 0.2219039 0.68920205 0.45
|
||||
1660000 305.65546 522.2866 -8702.2765 -11500.267 -0.093142651 1.1691034 0.45
|
||||
1665000 296.92311 -22.202256 -8648.9808 -11367.035 0.21695848 0.69494306 0.45
|
||||
1670000 293.71721 -216.98365 -8726.8596 -11415.567 0.062675713 0.90020567 0.45
|
||||
1675000 302.06866 69.039243 -8665.567 -11430.724 0.0012561112 0.99789522 0.45
|
||||
1680000 292.51483 -764.83087 -8759.3069 -11437.007 0.0022259364 0.99627318 0.45
|
||||
1685000 300.70748 -239.98915 -8682.5295 -11435.226 0.21854685 0.69309397 0.45
|
||||
1690000 303.31754 36.443117 -8554.7105 -11331.3 0.18904617 0.72825402 0.45
|
||||
1695000 300.96783 -365.40002 -8606.9996 -11362.08 0.21317894 0.69936284 0.45
|
||||
1700000 301.78038 -460.56572 -8703.0763 -11465.594 -0.074311844 1.1327524 0.45
|
||||
1705000 299.08328 224.74817 -8680.6969 -11418.526 0.14954235 0.77814547 0.45
|
||||
1710000 303.24064 298.73582 -8637.4191 -11413.304 -0.11628651 1.2153822 0.45
|
||||
1715000 299.1988 535.86954 -8722.2318 -11461.118 0.51289768 0.42302132 0.45
|
||||
1720000 300.88716 -11.654893 -8624.0905 -11378.432 0.62281958 0.35179195 0.45
|
||||
1725000 306.59581 -286.69581 -8574.7957 -11381.394 0.3964476 0.51427364 0.45
|
||||
1730000 302.58784 590.55523 -8670.9964 -11440.906 -0.28655798 1.6171597 0.45
|
||||
1735000 295.17235 -60.036989 -8631.671 -11333.699 0.72231294 0.29771902 0.45
|
||||
1740000 290.06228 -254.79282 -8715.6619 -11370.912 0.35583392 0.55052961 0.45
|
||||
1745000 306.47487 418.58552 -8590.4226 -11395.914 -0.04975774 1.0870455 0.45
|
||||
1750000 296.74674 -73.367187 -8727.0183 -11443.458 -0.27066543 1.5746188 0.45
|
||||
1755000 299.03541 551.77198 -8712.6905 -11450.081 -0.35865936 1.8250619 0.45
|
||||
1760000 288.98684 -380.17132 -8775.8546 -11421.26 -0.17754854 1.3469184 0.45
|
||||
1765000 300.76459 -662.80282 -8671.5414 -11424.761 0.078118597 0.87718632 0.45
|
||||
1770000 301.47287 -498.34628 -8675.582 -11435.285 0.57886218 0.37871122 0.45
|
||||
1775000 307.18565 -70.676548 -8554.9531 -11366.951 0.38766498 0.52190597 0.45
|
||||
1780000 302.58164 -329.49774 -8638.9781 -11408.831 0.53149245 0.41003059 0.45
|
||||
1785000 307.4086 294.59322 -8586.4793 -11400.518 0.34963097 0.55628768 0.45
|
||||
1790000 295.81491 -366.57154 -8756.8143 -11464.724 0.61653346 0.35552098 0.45
|
||||
1795000 296.46712 18.92361 -8640.9928 -11354.873 0.21158778 0.70123194 0.45
|
||||
1800000 290.9851 -805.74081 -8636.1049 -11299.802 0.36361854 0.54338759 0.45
|
||||
1805000 291.6313 -58.207903 -8707.0768 -11376.689 0.2659117 0.6401586 0.45
|
||||
1810000 299.14324 327.45026 -8613.3385 -11351.716 0.58264334 0.37631684 0.45
|
||||
1815000 295.3441 37.594139 -8747.5577 -11451.158 0.10312363 0.84115511 0.45
|
||||
1820000 297.19616 596.87014 -8601.4315 -11321.985 0.11690702 0.82193051 0.45
|
||||
1825000 305.23709 -229.45704 -8586.9328 -11381.094 -0.070794327 1.1260885 0.45
|
||||
1830000 308.48265 -50.225625 -8595.8609 -11419.732 0.28577292 0.61918297 0.45
|
||||
1835000 301.67215 30.600339 -8561.9509 -11323.478 0.67464985 0.32249901 0.45
|
||||
1840000 297.44022 -46.915689 -8760.5329 -11483.321 0.20308399 0.71130615 0.45
|
||||
1845000 294.56439 121.7989 -8819.2766 -11515.739 -0.13859762 1.2617292 0.45
|
||||
1850000 303.92475 63.511256 -8655.7131 -11437.861 -0.064617898 1.1144821 0.45
|
||||
1855000 302.36347 -403.0262 -8663.1963 -11431.052 0.63223295 0.34628081 0.45
|
||||
1860000 292.88227 124.53259 -8622.4528 -11303.517 0.21782313 0.69393587 0.45
|
||||
1865000 299.49141 1.3922328 -8592.8243 -11334.389 0.024359522 0.95996296 0.45
|
||||
1870000 295.36403 -1.848842 -8534.7607 -11238.543 0.53331666 0.40877784 0.45
|
||||
1875000 299.5254 -303.35635 -8642.4199 -11384.296 0.12049946 0.8169925 0.45
|
||||
1880000 302.15027 -233.4192 -8607.1984 -11373.102 0.42967343 0.48639576 0.45
|
||||
1885000 293.78387 -312.31798 -8576.6303 -11265.948 0.62050206 0.35316217 0.45
|
||||
1890000 296.33987 227.42925 -8675.0988 -11387.814 -0.2387251 1.4924762 0.45
|
||||
1895000 296.4116 -297.41585 -8695.6693 -11409.041 0.1899345 0.72716967 0.45
|
||||
1900000 305.04631 -744.8928 -8495.6073 -11288.022 -0.092917858 1.1686627 0.45
|
||||
1905000 299.13767 -233.05542 -8771.8955 -11510.222 -0.053515786 1.0939196 0.45
|
||||
1910000 301.18529 391.32364 -8594.238 -11351.309 0.17761387 0.74235415 0.45
|
||||
1915000 304.53139 -205.26743 -8615.1863 -11402.887 -0.65441918 2.9973254 0.45
|
||||
1920000 304.46794 75.506851 -8696.0461 -11483.166 0.28757039 0.6173189 0.45
|
||||
1925000 295.83229 -40.226799 -8677.0683 -11385.137 0.34338584 0.56214572 0.45
|
||||
1930000 298.91694 72.305481 -8662.7622 -11399.068 -0.45255095 2.1363683 0.45
|
||||
1935000 297.28693 -277.78411 -8678.223 -11399.608 0.32165864 0.58301111 0.45
|
||||
1940000 295.22194 -153.48885 -8737.0529 -11439.534 0.47753767 0.4488709 0.45
|
||||
1945000 298.41366 0.98105216 -8615.733 -11347.432 0.061208942 0.90242323 0.45
|
||||
1950000 298.47932 -461.39566 -8587.8993 -11320.199 0.41883297 0.49532116 0.45
|
||||
1955000 293.30456 -530.72887 -8712.242 -11397.172 -0.052983042 1.0929425 0.45
|
||||
1960000 307.27812 -609.68084 -8563.1295 -11375.974 0.10863685 0.83341209 0.45
|
||||
1965000 309.21876 -661.65884 -8619.5376 -11450.147 -0.00074060514 1.0012431 0.45
|
||||
1970000 294.16474 130.9219 -8662.5966 -11355.4 -0.048761848 1.0852311 0.45
|
||||
1975000 293.87023 -652.42226 -8587.2681 -11277.376 -0.42701916 2.0468057 0.45
|
||||
1980000 302.66906 -396.94893 -8576.3291 -11346.982 0.55938449 0.39128874 0.45
|
||||
1985000 304.00863 167.22102 -8525.9503 -11308.866 -0.12417188 1.2315647 0.45
|
||||
1990000 299.53376 -234.11494 -8528.8821 -11270.834 0.58392743 0.37550715 0.45
|
||||
1995000 296.20959 -99.022727 -8599.3854 -11310.908 0.10920765 0.83261451 0.45
|
||||
2000000 307.40367 -179.44965 -8545.6064 -11359.6 0.485016 0.44327537 0.45
|
||||
Loop time of 4787.7 on 1 procs for 2000000 steps with 3072 atoms
|
||||
|
||||
Performance: 36.092 ns/day, 0.665 hours/ns, 417.737 timesteps/s
|
||||
95.4% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1015.1 | 1015.1 | 1015.1 | 0.0 | 21.20
|
||||
Bond | 121.19 | 121.19 | 121.19 | 0.0 | 2.53
|
||||
Kspace | 3455.1 | 3455.1 | 3455.1 | 0.0 | 72.17
|
||||
Neigh | 8.7475 | 8.7475 | 8.7475 | 0.0 | 0.18
|
||||
Comm | 58.679 | 58.679 | 58.679 | 0.0 | 1.23
|
||||
Output | 0.60209 | 0.60209 | 0.60209 | 0.0 | 0.01
|
||||
Modify | 81.328 | 81.328 | 81.328 | 0.0 | 1.70
|
||||
Other | | 46.88 | | | 0.98
|
||||
|
||||
Nlocal: 3072 ave 3072 max 3072 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 8395 ave 8395 max 8395 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 = -1
|
||||
Ave neighs/atom = -0.00032552083
|
||||
Ave special neighs/atom = 2
|
||||
Neighbor list builds = 93794
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 1:31:34
|
||||
22
examples/PACKAGES/fep/ta/spce.fep.ta
Normal file
22
examples/PACKAGES/fep/ta/spce.fep.ta
Normal file
@ -0,0 +1,22 @@
|
||||
# Time-averaged data for fix FEP
|
||||
# TimeStep c_TA[1] c_TA[2] c_TA[3] v_gamma_v
|
||||
100000 0.168677 0.863546 0.45 65.7437
|
||||
200000 0.169722 0.861354 0.45 66.6859
|
||||
300000 0.165507 0.868407 0.45 63.1899
|
||||
400000 0.162311 0.875704 0.45 60.7859
|
||||
500000 0.165468 0.872729 0.45 63.2053
|
||||
600000 0.165267 0.873825 0.45 63.1828
|
||||
700000 0.167824 0.869356 0.45 65.1722
|
||||
800000 0.170332 0.866538 0.45 67.0749
|
||||
900000 0.164396 0.875043 0.45 62.4639
|
||||
1000000 0.164738 0.87663 0.45 62.5659
|
||||
1100000 0.168395 0.870496 0.45 65.415
|
||||
1200000 0.170147 0.867104 0.45 66.7132
|
||||
1300000 0.170509 0.866709 0.45 66.9833
|
||||
1400000 0.171152 0.865294 0.45 67.5598
|
||||
1500000 0.172363 0.863433 0.45 68.547
|
||||
1600000 0.171538 0.864062 0.45 67.8359
|
||||
1700000 0.171662 0.864029 0.45 67.9145
|
||||
1800000 0.170202 0.866069 0.45 66.7697
|
||||
1900000 0.171403 0.864162 0.45 67.6313
|
||||
2000000 0.170962 0.864753 0.45 67.2314
|
||||
1
examples/PACKAGES/tmd/data.peptide
Symbolic link
1
examples/PACKAGES/tmd/data.peptide
Symbolic link
@ -0,0 +1 @@
|
||||
../../peptide/data.peptide
|
||||
45
examples/PACKAGES/tmd/in.tmd
Normal file
45
examples/PACKAGES/tmd/in.tmd
Normal file
@ -0,0 +1,45 @@
|
||||
# Solvated 5-mer peptide
|
||||
|
||||
units real
|
||||
atom_style full
|
||||
|
||||
pair_style lj/charmm/coul/long 8.0 10.0 10.0
|
||||
bond_style harmonic
|
||||
angle_style charmm
|
||||
dihedral_style charmm
|
||||
improper_style harmonic
|
||||
kspace_style pppm 0.0001
|
||||
|
||||
read_data data.peptide
|
||||
|
||||
neighbor 2.0 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
timestep 2.0
|
||||
|
||||
thermo_style multi
|
||||
thermo 50
|
||||
|
||||
group tmd id 1:6
|
||||
|
||||
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
|
||||
fix 0 tmd tmd 0.1 tmd.target 100 tmd.log
|
||||
fix 2 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
|
||||
|
||||
group peptide type <= 12
|
||||
|
||||
#dump 1 peptide atom 10 dump.peptide
|
||||
|
||||
#dump 2 peptide image 25 image.*.jpg type type &
|
||||
# axes yes 0.8 0.02 view 60 -30 bond atom 0.5
|
||||
#dump_modify 2 pad 3
|
||||
|
||||
#dump 3 peptide movie 25 movie.mpg type type &
|
||||
# axes yes 0.8 0.02 view 60 -30 bond atom 0.5
|
||||
#dump_modify 3 pad 3
|
||||
|
||||
#compute bnd all property/local btype batom1 batom2
|
||||
#dump 2 peptide local 300 dump.bond index c_bnd[1] c_bnd[2] c_bnd[3]
|
||||
|
||||
run 300
|
||||
|
||||
210
examples/PACKAGES/tmd/log.31Mar22.tmd.g++.1
Normal file
210
examples/PACKAGES/tmd/log.31Mar22.tmd.g++.1
Normal file
@ -0,0 +1,210 @@
|
||||
LAMMPS (24 Mar 2022)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Solvated 5-mer peptide
|
||||
|
||||
units real
|
||||
atom_style full
|
||||
|
||||
pair_style lj/charmm/coul/long 8.0 10.0 10.0
|
||||
bond_style harmonic
|
||||
angle_style charmm
|
||||
dihedral_style charmm
|
||||
improper_style harmonic
|
||||
kspace_style pppm 0.0001
|
||||
|
||||
read_data data.peptide
|
||||
Reading data file ...
|
||||
orthogonal box = (36.840194 41.013691 29.768095) to (64.21156 68.385058 57.139462)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
2004 atoms
|
||||
reading velocities ...
|
||||
2004 velocities
|
||||
scanning bonds ...
|
||||
3 = max bonds/atom
|
||||
scanning angles ...
|
||||
6 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
14 = max dihedrals/atom
|
||||
scanning impropers ...
|
||||
1 = max impropers/atom
|
||||
reading bonds ...
|
||||
1365 bonds
|
||||
reading angles ...
|
||||
786 angles
|
||||
reading dihedrals ...
|
||||
207 dihedrals
|
||||
reading impropers ...
|
||||
12 impropers
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
4 = max # of 1-2 neighbors
|
||||
7 = max # of 1-3 neighbors
|
||||
14 = max # of 1-4 neighbors
|
||||
18 = max # of special neighbors
|
||||
special bonds CPU = 0.001 seconds
|
||||
read_data CPU = 0.011 seconds
|
||||
|
||||
neighbor 2.0 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
timestep 2.0
|
||||
|
||||
thermo_style multi
|
||||
thermo 50
|
||||
|
||||
group tmd id 1:6
|
||||
6 atoms in group tmd
|
||||
|
||||
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
|
||||
fix 0 tmd tmd 0.1 tmd.target 100 tmd.log
|
||||
Reading TMD target file tmd.target ...
|
||||
fix 2 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
|
||||
19 = # of size 2 clusters
|
||||
6 = # of size 3 clusters
|
||||
3 = # of size 4 clusters
|
||||
640 = # of frozen angles
|
||||
find clusters CPU = 0.000 seconds
|
||||
|
||||
group peptide type <= 12
|
||||
84 atoms in group peptide
|
||||
|
||||
#dump 1 peptide atom 10 dump.peptide
|
||||
|
||||
#dump 2 peptide image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 bond atom 0.5
|
||||
#dump_modify 2 pad 3
|
||||
|
||||
#dump 3 peptide movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 bond atom 0.5
|
||||
#dump_modify 3 pad 3
|
||||
|
||||
#compute bnd all property/local btype batom1 batom2
|
||||
#dump 2 peptide local 300 dump.bond index c_bnd[1] c_bnd[2] c_bnd[3]
|
||||
|
||||
run 300
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:340)
|
||||
G vector (1/distance) = 0.26872465
|
||||
grid = 15 15 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.022820853
|
||||
estimated relative force accuracy = 6.872432e-05
|
||||
using double precision FFTW3
|
||||
3d grid and FFT values/proc = 10648 3375
|
||||
generated 91 of 91 mixed pair_coeff terms from arithmetic mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 5 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 5 5 5
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/charmm/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
SHAKE stats (type/ave/delta/count) on step 0
|
||||
Bond: 4 1.111 1.44264e-05 9
|
||||
Bond: 6 0.996998 7.26967e-06 6
|
||||
Bond: 8 1.08 1.32536e-05 9
|
||||
Bond: 10 1.111 1.22749e-05 8
|
||||
Bond: 12 1.08 1.11767e-05 9
|
||||
Bond: 14 0.96 0 1
|
||||
Bond: 18 0.957206 4.37979e-05 1280
|
||||
Angle: 31 104.519 0.00396029 640
|
||||
Per MPI rank memory allocation (min/avg/max) = 19.78 | 19.78 | 19.78 Mbytes
|
||||
------------ Step 0 ----- CPU = 0 (sec) -------------
|
||||
TotEng = -5237.4580 KinEng = 1134.9186 Temp = 282.1005
|
||||
PotEng = -6372.3766 E_bond = 16.5572 E_angle = 36.3726
|
||||
E_dihed = 15.5190 E_impro = 1.9426 E_vdwl = 692.8945
|
||||
E_coul = 26772.2646 E_long = -33907.9271 Press = -837.0112
|
||||
------------ Step 50 ----- CPU = 0.6301453 (sec) -------------
|
||||
TotEng = -5001.6799 KinEng = 1319.3760 Temp = 327.9501
|
||||
PotEng = -6321.0559 E_bond = 17.4415 E_angle = 42.4509
|
||||
E_dihed = 25.0839 E_impro = 4.4025 E_vdwl = 725.7619
|
||||
E_coul = 26771.0015 E_long = -33907.1980 Press = -1.1409
|
||||
SHAKE stats (type/ave/delta/count) on step 100
|
||||
Bond: 4 1.11096 0.000146572 9
|
||||
Bond: 6 0.996997 7.55911e-06 6
|
||||
Bond: 8 1.08 8.22449e-06 9
|
||||
Bond: 10 1.11099 3.00424e-05 8
|
||||
Bond: 12 1.08 6.53505e-06 9
|
||||
Bond: 14 0.95999 0 1
|
||||
Bond: 18 0.957195 4.74892e-05 1280
|
||||
Angle: 31 104.52 0.00446577 640
|
||||
------------ Step 100 ----- CPU = 1.251267 (sec) -------------
|
||||
TotEng = -5114.3221 KinEng = 1168.2996 Temp = 290.3979
|
||||
PotEng = -6282.6217 E_bond = 45.5470 E_angle = 87.5725
|
||||
E_dihed = 26.1332 E_impro = 1.8662 E_vdwl = 791.5291
|
||||
E_coul = 26670.6791 E_long = -33905.9488 Press = -29.3446
|
||||
------------ Step 150 ----- CPU = 1.869158 (sec) -------------
|
||||
TotEng = -5302.3058 KinEng = 1211.4300 Temp = 301.1186
|
||||
PotEng = -6513.7358 E_bond = 51.4069 E_angle = 82.5752
|
||||
E_dihed = 31.1298 E_impro = 4.3390 E_vdwl = 764.0550
|
||||
E_coul = 26461.8974 E_long = -33909.1392 Press = -1204.2714
|
||||
SHAKE stats (type/ave/delta/count) on step 200
|
||||
Bond: 4 1.11094 0.000292869 9
|
||||
Bond: 6 0.996989 3.13206e-05 6
|
||||
Bond: 8 1.07999 4.4723e-05 9
|
||||
Bond: 10 1.111 1.08895e-05 8
|
||||
Bond: 12 1.07999 1.42694e-05 9
|
||||
Bond: 14 0.959976 0 1
|
||||
Bond: 18 0.957195 8.58256e-05 1280
|
||||
Angle: 31 104.52 0.00597861 640
|
||||
------------ Step 200 ----- CPU = 2.48933 (sec) -------------
|
||||
TotEng = -5785.4658 KinEng = 1048.7220 Temp = 260.6751
|
||||
PotEng = -6834.1879 E_bond = 21.7304 E_angle = 48.3249
|
||||
E_dihed = 20.5973 E_impro = 2.0603 E_vdwl = 818.9175
|
||||
E_coul = 26165.9672 E_long = -33911.7854 Press = -1228.5741
|
||||
------------ Step 250 ----- CPU = 3.119859 (sec) -------------
|
||||
TotEng = -6108.4578 KinEng = 828.5247 Temp = 205.9419
|
||||
PotEng = -6936.9825 E_bond = 26.5971 E_angle = 68.2771
|
||||
E_dihed = 36.1232 E_impro = 5.2092 E_vdwl = 884.1147
|
||||
E_coul = 25955.7300 E_long = -33913.0338 Press = -1365.4744
|
||||
SHAKE stats (type/ave/delta/count) on step 300
|
||||
Bond: 4 1.11174 0.0109853 9
|
||||
Bond: 6 0.996999 1.94772e-06 6
|
||||
Bond: 8 1.08 3.97091e-06 9
|
||||
Bond: 10 1.111 2.52635e-06 8
|
||||
Bond: 12 1.08 1.24444e-06 9
|
||||
Bond: 14 0.96 0 1
|
||||
Bond: 18 0.9572 1.22873e-05 1280
|
||||
Angle: 31 104.52 0.00134864 640
|
||||
------------ Step 300 ----- CPU = 3.74524 (sec) -------------
|
||||
TotEng = -5492.5012 KinEng = 1315.6902 Temp = 327.0339
|
||||
PotEng = -6808.1914 E_bond = 88.7967 E_angle = 104.4231
|
||||
E_dihed = 28.2383 E_impro = 43.5062 E_vdwl = 992.5311
|
||||
E_coul = 25849.1502 E_long = -33914.8370 Press = 268.8004
|
||||
Loop time of 3.74527 on 1 procs for 300 steps with 2004 atoms
|
||||
|
||||
Performance: 13.841 ns/day, 1.734 hours/ns, 80.101 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 | 2.9399 | 2.9399 | 2.9399 | 0.0 | 78.50
|
||||
Bond | 0.0069522 | 0.0069522 | 0.0069522 | 0.0 | 0.19
|
||||
Kspace | 0.25203 | 0.25203 | 0.25203 | 0.0 | 6.73
|
||||
Neigh | 0.48624 | 0.48624 | 0.48624 | 0.0 | 12.98
|
||||
Comm | 0.016948 | 0.016948 | 0.016948 | 0.0 | 0.45
|
||||
Output | 0.00023689 | 0.00023689 | 0.00023689 | 0.0 | 0.01
|
||||
Modify | 0.039476 | 0.039476 | 0.039476 | 0.0 | 1.05
|
||||
Other | | 0.003502 | | | 0.09
|
||||
|
||||
Nlocal: 2004 ave 2004 max 2004 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 11242 ave 11242 max 11242 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 710782 ave 710782 max 710782 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 710782
|
||||
Ave neighs/atom = 354.68164
|
||||
Ave special neighs/atom = 2.3403194
|
||||
Neighbor list builds = 32
|
||||
Dangerous builds = 1
|
||||
|
||||
Total wall time: 0:00:03
|
||||
210
examples/PACKAGES/tmd/log.31Mar22.tmd.g++.4
Normal file
210
examples/PACKAGES/tmd/log.31Mar22.tmd.g++.4
Normal file
@ -0,0 +1,210 @@
|
||||
LAMMPS (24 Mar 2022)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Solvated 5-mer peptide
|
||||
|
||||
units real
|
||||
atom_style full
|
||||
|
||||
pair_style lj/charmm/coul/long 8.0 10.0 10.0
|
||||
bond_style harmonic
|
||||
angle_style charmm
|
||||
dihedral_style charmm
|
||||
improper_style harmonic
|
||||
kspace_style pppm 0.0001
|
||||
|
||||
read_data data.peptide
|
||||
Reading data file ...
|
||||
orthogonal box = (36.840194 41.013691 29.768095) to (64.21156 68.385058 57.139462)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
2004 atoms
|
||||
reading velocities ...
|
||||
2004 velocities
|
||||
scanning bonds ...
|
||||
3 = max bonds/atom
|
||||
scanning angles ...
|
||||
6 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
14 = max dihedrals/atom
|
||||
scanning impropers ...
|
||||
1 = max impropers/atom
|
||||
reading bonds ...
|
||||
1365 bonds
|
||||
reading angles ...
|
||||
786 angles
|
||||
reading dihedrals ...
|
||||
207 dihedrals
|
||||
reading impropers ...
|
||||
12 impropers
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
4 = max # of 1-2 neighbors
|
||||
7 = max # of 1-3 neighbors
|
||||
14 = max # of 1-4 neighbors
|
||||
18 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
read_data CPU = 0.017 seconds
|
||||
|
||||
neighbor 2.0 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
timestep 2.0
|
||||
|
||||
thermo_style multi
|
||||
thermo 50
|
||||
|
||||
group tmd id 1:6
|
||||
6 atoms in group tmd
|
||||
|
||||
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
|
||||
fix 0 tmd tmd 0.1 tmd.target 100 tmd.log
|
||||
Reading TMD target file tmd.target ...
|
||||
fix 2 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
|
||||
19 = # of size 2 clusters
|
||||
6 = # of size 3 clusters
|
||||
3 = # of size 4 clusters
|
||||
640 = # of frozen angles
|
||||
find clusters CPU = 0.000 seconds
|
||||
|
||||
group peptide type <= 12
|
||||
84 atoms in group peptide
|
||||
|
||||
#dump 1 peptide atom 10 dump.peptide
|
||||
|
||||
#dump 2 peptide image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 bond atom 0.5
|
||||
#dump_modify 2 pad 3
|
||||
|
||||
#dump 3 peptide movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 bond atom 0.5
|
||||
#dump_modify 3 pad 3
|
||||
|
||||
#compute bnd all property/local btype batom1 batom2
|
||||
#dump 2 peptide local 300 dump.bond index c_bnd[1] c_bnd[2] c_bnd[3]
|
||||
|
||||
run 300
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:340)
|
||||
G vector (1/distance) = 0.26872465
|
||||
grid = 15 15 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.022820853
|
||||
estimated relative force accuracy = 6.872432e-05
|
||||
using double precision FFTW3
|
||||
3d grid and FFT values/proc = 4312 960
|
||||
generated 91 of 91 mixed pair_coeff terms from arithmetic mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 5 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 5 5 5
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/charmm/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
SHAKE stats (type/ave/delta/count) on step 0
|
||||
Bond: 4 1.111 1.44264e-05 9
|
||||
Bond: 6 0.996998 7.26967e-06 6
|
||||
Bond: 8 1.08 1.32536e-05 6
|
||||
Bond: 10 1.111 1.22749e-05 8
|
||||
Bond: 12 1.08 1.11767e-05 9
|
||||
Bond: 14 0.96 0 1
|
||||
Bond: 18 0.957206 4.37979e-05 1280
|
||||
Angle: 31 104.519 0.00396029 640
|
||||
Per MPI rank memory allocation (min/avg/max) = 16.78 | 16.97 | 17.16 Mbytes
|
||||
------------ Step 0 ----- CPU = 0 (sec) -------------
|
||||
TotEng = -5237.4580 KinEng = 1134.9186 Temp = 282.1005
|
||||
PotEng = -6372.3766 E_bond = 16.5572 E_angle = 36.3726
|
||||
E_dihed = 15.5190 E_impro = 1.9426 E_vdwl = 692.8945
|
||||
E_coul = 26772.2646 E_long = -33907.9271 Press = -837.0112
|
||||
------------ Step 50 ----- CPU = 0.1916178 (sec) -------------
|
||||
TotEng = -5001.6799 KinEng = 1319.3760 Temp = 327.9501
|
||||
PotEng = -6321.0559 E_bond = 17.4415 E_angle = 42.4509
|
||||
E_dihed = 25.0839 E_impro = 4.4025 E_vdwl = 725.7619
|
||||
E_coul = 26771.0015 E_long = -33907.1980 Press = -1.1409
|
||||
SHAKE stats (type/ave/delta/count) on step 100
|
||||
Bond: 4 1.11096 0.000146572 9
|
||||
Bond: 6 0.996997 7.55911e-06 6
|
||||
Bond: 8 1.08 8.22449e-06 6
|
||||
Bond: 10 1.11099 3.00424e-05 8
|
||||
Bond: 12 1.08 6.53505e-06 9
|
||||
Bond: 14 0.95999 0 1
|
||||
Bond: 18 0.957195 4.74892e-05 1280
|
||||
Angle: 31 104.52 0.00446577 640
|
||||
------------ Step 100 ----- CPU = 0.3672111 (sec) -------------
|
||||
TotEng = -5114.3221 KinEng = 1168.2996 Temp = 290.3979
|
||||
PotEng = -6282.6217 E_bond = 45.5470 E_angle = 87.5725
|
||||
E_dihed = 26.1332 E_impro = 1.8662 E_vdwl = 791.5291
|
||||
E_coul = 26670.6792 E_long = -33905.9488 Press = -29.3446
|
||||
------------ Step 150 ----- CPU = 0.5543252 (sec) -------------
|
||||
TotEng = -5302.3058 KinEng = 1211.4300 Temp = 301.1186
|
||||
PotEng = -6513.7358 E_bond = 51.4069 E_angle = 82.5752
|
||||
E_dihed = 31.1298 E_impro = 4.3390 E_vdwl = 764.0550
|
||||
E_coul = 26461.8975 E_long = -33909.1392 Press = -1204.2714
|
||||
SHAKE stats (type/ave/delta/count) on step 200
|
||||
Bond: 4 1.11094 0.000292869 9
|
||||
Bond: 6 0.996989 3.13206e-05 6
|
||||
Bond: 8 1.07999 4.4723e-05 6
|
||||
Bond: 10 1.111 1.08895e-05 8
|
||||
Bond: 12 1.07999 1.42694e-05 9
|
||||
Bond: 14 0.959976 0 1
|
||||
Bond: 18 0.957195 8.58257e-05 1280
|
||||
Angle: 31 104.52 0.00597861 640
|
||||
------------ Step 200 ----- CPU = 0.7449468 (sec) -------------
|
||||
TotEng = -5785.4658 KinEng = 1048.7220 Temp = 260.6751
|
||||
PotEng = -6834.1878 E_bond = 21.7304 E_angle = 48.3249
|
||||
E_dihed = 20.5973 E_impro = 2.0603 E_vdwl = 818.9173
|
||||
E_coul = 26165.9673 E_long = -33911.7854 Press = -1228.5754
|
||||
------------ Step 250 ----- CPU = 0.9417257 (sec) -------------
|
||||
TotEng = -6108.4577 KinEng = 828.5246 Temp = 205.9418
|
||||
PotEng = -6936.9823 E_bond = 26.5971 E_angle = 68.2771
|
||||
E_dihed = 36.1232 E_impro = 5.2092 E_vdwl = 884.1146
|
||||
E_coul = 25955.7302 E_long = -33913.0338 Press = -1365.4736
|
||||
SHAKE stats (type/ave/delta/count) on step 300
|
||||
Bond: 4 1.11174 0.0109854 9
|
||||
Bond: 6 0.996999 1.94775e-06 6
|
||||
Bond: 8 1.08 3.97089e-06 6
|
||||
Bond: 10 1.111 2.52634e-06 8
|
||||
Bond: 12 1.08 1.24445e-06 9
|
||||
Bond: 14 0.96 0 1
|
||||
Bond: 18 0.9572 1.22873e-05 1280
|
||||
Angle: 31 104.52 0.0013486 640
|
||||
------------ Step 300 ----- CPU = 1.137003 (sec) -------------
|
||||
TotEng = -5492.5016 KinEng = 1315.6899 Temp = 327.0339
|
||||
PotEng = -6808.1915 E_bond = 88.7968 E_angle = 104.4228
|
||||
E_dihed = 28.2384 E_impro = 43.5061 E_vdwl = 992.5315
|
||||
E_coul = 25849.1499 E_long = -33914.8370 Press = 268.8010
|
||||
Loop time of 1.13706 on 4 procs for 300 steps with 2004 atoms
|
||||
|
||||
Performance: 45.591 ns/day, 0.526 hours/ns, 263.838 timesteps/s
|
||||
99.5% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.75407 | 0.80373 | 0.84144 | 3.6 | 70.68
|
||||
Bond | 0.0010088 | 0.0024668 | 0.0045274 | 2.6 | 0.22
|
||||
Kspace | 0.095468 | 0.13434 | 0.18276 | 8.9 | 11.81
|
||||
Neigh | 0.13509 | 0.13515 | 0.13522 | 0.0 | 11.89
|
||||
Comm | 0.024217 | 0.025086 | 0.026404 | 0.5 | 2.21
|
||||
Output | 0.00020952 | 0.00023591 | 0.00031389 | 0.0 | 0.02
|
||||
Modify | 0.033319 | 0.033374 | 0.033436 | 0.0 | 2.94
|
||||
Other | | 0.00268 | | | 0.24
|
||||
|
||||
Nlocal: 501 ave 530 max 459 min
|
||||
Histogram: 1 0 0 0 0 0 1 1 0 1
|
||||
Nghost: 6562.75 ave 6755 max 6370 min
|
||||
Histogram: 1 0 0 0 1 1 0 0 0 1
|
||||
Neighs: 177696 ave 195050 max 158403 min
|
||||
Histogram: 1 0 0 1 0 0 0 1 0 1
|
||||
|
||||
Total # of neighbors = 710782
|
||||
Ave neighs/atom = 354.68164
|
||||
Ave special neighs/atom = 2.3403194
|
||||
Neighbor list builds = 32
|
||||
Dangerous builds = 1
|
||||
|
||||
Total wall time: 0:00:01
|
||||
4
examples/PACKAGES/tmd/tmd.log.31Mar22.tmd.g++.1
Normal file
4
examples/PACKAGES/tmd/tmd.log.31Mar22.tmd.g++.1
Normal file
@ -0,0 +1,4 @@
|
||||
# Step rho_target rho_old gamma_back gamma_forward lambda work_lambda work_analytical
|
||||
100 11.580338717125848 11.637740410711476 0.00432656530431019 -0.0006058453921097923 1295.0393774041895 -7808.460018545273 562.4687334224966
|
||||
200 5.840169358562925 5.897571052148553 0.009256742629063092 -0.0004765379201060169 1404.114149312145 -15441.509720360129 1352.9255849946983
|
||||
300 0.10000000000000142 0.15740169358562994 -0.030035833473071705 -0.5643261296323345 -121.59623659080042 -22929.738462520727 2299.6676396746325
|
||||
4
examples/PACKAGES/tmd/tmd.log.31Mar22.tmd.g++.4
Normal file
4
examples/PACKAGES/tmd/tmd.log.31Mar22.tmd.g++.4
Normal file
@ -0,0 +1,4 @@
|
||||
# Step rho_target rho_old gamma_back gamma_forward lambda work_lambda work_analytical
|
||||
100 11.580338717125848 11.637740410711476 0.004326565303381905 -0.0006058453930379918 1295.0393771263327 -7808.46001855425 562.4687334073235
|
||||
200 5.840169358562925 5.897571052148553 0.009256742652188668 -0.0004765378969710561 1404.114152819961 -15441.50972264099 1352.9255825827688
|
||||
300 0.10000000000000142 0.15740169358562994 -0.03003651537895091 -0.5643268572640833 -121.59899719968097 -22929.73877163682 2299.6674130478946
|
||||
13
examples/PACKAGES/tmd/tmd.target
Normal file
13
examples/PACKAGES/tmd/tmd.target
Normal file
@ -0,0 +1,13 @@
|
||||
# pull a few peptide atoms across the box
|
||||
36.840194 64.211560 xlo xhi
|
||||
41.013691 68.385058 ylo yhi
|
||||
29.768095 57.139462 zlo zhi # comment
|
||||
# comment
|
||||
1 53.99993 48.52678 46.78550 0 0 0
|
||||
2 55.10395 48.23499 45.86693 0 0 0
|
||||
3 53.81519 49.54928 47.43995 0 0 0
|
||||
4 55.71714 47.34797 46.13434 0 0 0
|
||||
5 55.72261 49.13657 45.67007 0 0 0
|
||||
6 54.66624 48.09539 44.85538 0 0 0
|
||||
7 53.28193 47.47427 46.91953 0 0 0
|
||||
8 52.07157 47.45486 47.62418 0 0 0
|
||||
@ -83,9 +83,9 @@ 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
|
||||
mc: MC package models: GCMC, Widom, fix mol/swap
|
||||
mdi: use of the MDI package and MolSSI MDI code coupling library
|
||||
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
|
||||
mliap: examples for using several bundled MLIAP potentials
|
||||
@ -118,6 +118,7 @@ ttm: two-temeperature model examples
|
||||
vashishta: models using the Vashishta potential
|
||||
voronoi: Voronoi tesselation via compute voronoi/atom command
|
||||
wall: use of reflective walls with different stochastic models
|
||||
yaml: demonstrates use of yaml thermo and dump styles
|
||||
|
||||
Here is how you might run and visualize one of the sample problems:
|
||||
|
||||
|
||||
3173
examples/bpm/impact/brokenDump
Normal file
3173
examples/bpm/impact/brokenDump
Normal file
File diff suppressed because it is too large
Load Diff
51
examples/bpm/impact/in.bpm.impact.rotational
Normal file
51
examples/bpm/impact/in.bpm.impact.rotational
Normal file
@ -0,0 +1,51 @@
|
||||
units lj
|
||||
dimension 3
|
||||
boundary f f f
|
||||
atom_style bpm/sphere
|
||||
special_bonds lj 0.0 1.0 1.0 coul 0.0 1.0 1.0
|
||||
newton on off
|
||||
comm_modify vel yes cutoff 2.6
|
||||
lattice fcc 1.0
|
||||
region box block -25 15 -22 22 -22 22
|
||||
create_box 1 box bond/types 2 extra/bond/per/atom 20 extra/special/per/atom 50
|
||||
|
||||
region disk cylinder x 0.0 0.0 20.0 -0.5 0.5
|
||||
create_atoms 1 region disk
|
||||
group plate region disk
|
||||
|
||||
region ball sphere 8.0 0.0 0.0 6.0
|
||||
create_atoms 1 region ball
|
||||
group projectile region ball
|
||||
|
||||
displace_atoms all random 0.1 0.1 0.1 134598738
|
||||
|
||||
neighbor 1.0 bin
|
||||
pair_style gran/hooke/history 1.0 NULL 0.5 NULL 0.1 1
|
||||
pair_coeff 1 1
|
||||
|
||||
fix 1 all nve/bpm/sphere
|
||||
|
||||
create_bonds many plate plate 1 0.0 1.5
|
||||
create_bonds many projectile projectile 2 0.0 1.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
special_bonds lj 0.0 1.0 1.0 coul 1.0 1.0 1.0
|
||||
|
||||
bond_style bpm/rotational store/local brkbond 100 time id1 id2
|
||||
bond_coeff 1 1.0 0.2 0.02 0.02 0.05 0.01 0.01 0.01 0.1 0.2 0.002 0.002
|
||||
bond_coeff 2 1.0 0.2 0.02 0.02 0.20 0.04 0.04 0.04 0.1 0.2 0.002 0.002
|
||||
|
||||
velocity projectile set -0.05 0.0 0.0
|
||||
compute nbond all nbond/atom
|
||||
compute tbond all reduce sum c_nbond
|
||||
|
||||
timestep 0.05
|
||||
thermo_style custom step ke pe pxx pyy pzz c_tbond
|
||||
thermo 100
|
||||
thermo_modify lost ignore lost/bond ignore
|
||||
#dump 1 all custom 100 atomDump id radius x y z c_nbond
|
||||
|
||||
dump 2 all local 100 brokenDump f_brkbond[1] f_brkbond[2] f_brkbond[3]
|
||||
dump_modify 2 header no
|
||||
|
||||
run 7500
|
||||
53
examples/bpm/impact/in.bpm.impact.spring
Normal file
53
examples/bpm/impact/in.bpm.impact.spring
Normal file
@ -0,0 +1,53 @@
|
||||
units lj
|
||||
dimension 3
|
||||
boundary f f f
|
||||
atom_style bond
|
||||
special_bonds lj 0.0 1.0 1.0 coul 0.0 1.0 1.0
|
||||
newton on off
|
||||
comm_modify vel yes cutoff 2.6
|
||||
lattice fcc 1.0
|
||||
region box block -25 15 -22 22 -22 22
|
||||
create_box 1 box bond/types 2 extra/bond/per/atom 20 extra/special/per/atom 50
|
||||
|
||||
region disk cylinder x 0.0 0.0 20.0 -0.5 0.5
|
||||
create_atoms 1 region disk
|
||||
group plate region disk
|
||||
|
||||
region ball sphere 8.0 0.0 0.0 6.0
|
||||
create_atoms 1 region ball
|
||||
group projectile region ball
|
||||
|
||||
displace_atoms all random 0.1 0.1 0.1 134598738
|
||||
|
||||
mass 1 1.0
|
||||
|
||||
neighbor 1.0 bin
|
||||
pair_style bpm/spring
|
||||
pair_coeff 1 1 1.0 1.0 1.0
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
create_bonds many plate plate 1 0.0 1.5
|
||||
create_bonds many projectile projectile 2 0.0 1.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
special_bonds lj 0.0 1.0 1.0 coul 1.0 1.0 1.0
|
||||
|
||||
bond_style bpm/spring store/local brkbond 100 time id1 id2
|
||||
bond_coeff 1 1.0 0.04 1.0
|
||||
bond_coeff 2 1.0 0.20 1.0
|
||||
|
||||
velocity projectile set -0.05 0.0 0.0
|
||||
compute nbond all nbond/atom
|
||||
compute tbond all reduce sum c_nbond
|
||||
|
||||
timestep 0.1
|
||||
thermo_style custom step ke pe pxx pyy pzz c_tbond
|
||||
thermo 100
|
||||
thermo_modify lost ignore lost/bond ignore
|
||||
#dump 1 all custom 100 atomDump id x y z c_nbond
|
||||
|
||||
dump 2 all local 100 brokenDump f_brkbond[1] f_brkbond[2] f_brkbond[3]
|
||||
dump_modify 2 header no
|
||||
|
||||
run 7500
|
||||
219
examples/bpm/impact/log.17Feb2022.impact.rotational.g++.4
Normal file
219
examples/bpm/impact/log.17Feb2022.impact.rotational.g++.4
Normal file
@ -0,0 +1,219 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
units lj
|
||||
dimension 3
|
||||
boundary f f f
|
||||
atom_style bpm/sphere
|
||||
special_bonds lj 0.0 1.0 1.0 coul 0.0 1.0 1.0
|
||||
newton on off
|
||||
comm_modify vel yes cutoff 2.6
|
||||
lattice fcc 1.0
|
||||
Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011
|
||||
region box block -25 15 -22 22 -22 22
|
||||
create_box 1 box bond/types 2 extra/bond/per/atom 20 extra/special/per/atom 50
|
||||
Created orthogonal box = (-39.685026 -34.922823 -34.922823) to (23.811016 34.922823 34.922823)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
|
||||
region disk cylinder x 0.0 0.0 20.0 -0.5 0.5
|
||||
create_atoms 1 region disk
|
||||
Created 7529 atoms
|
||||
using lattice units in orthogonal box = (-39.685026 -34.922823 -34.922823) to (23.811016 34.922823 34.922823)
|
||||
create_atoms CPU = 0.002 seconds
|
||||
group plate region disk
|
||||
7529 atoms in group plate
|
||||
|
||||
region ball sphere 8.0 0.0 0.0 6.0
|
||||
create_atoms 1 region ball
|
||||
Created 3589 atoms
|
||||
using lattice units in orthogonal box = (-39.685026 -34.922823 -34.922823) to (23.811016 34.922823 34.922823)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
group projectile region ball
|
||||
3589 atoms in group projectile
|
||||
|
||||
displace_atoms all random 0.1 0.1 0.1 134598738
|
||||
Displacing atoms ...
|
||||
|
||||
neighbor 1.0 bin
|
||||
pair_style gran/hooke/history 1.0 NULL 0.5 NULL 0.1 1
|
||||
pair_coeff 1 1
|
||||
|
||||
fix 1 all nve/bpm/sphere
|
||||
|
||||
create_bonds many plate plate 1 0.0 1.5
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2
|
||||
ghost atom cutoff = 2.6
|
||||
binsize = 1, bins = 64 70 70
|
||||
2 neighbor lists, perpetual/occasional/extra = 1 1 0
|
||||
(1) command create_bonds, occasional
|
||||
attributes: full, newton on
|
||||
pair build: full/bin
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
(2) pair gran/hooke/history, perpetual
|
||||
attributes: half, newton on, size, history
|
||||
pair build: half/size/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Added 38559 bonds, new total = 38559
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 1 1
|
||||
special bond factors coul: 0 1 1
|
||||
15 = max # of 1-2 neighbors
|
||||
101 = max # of special neighbors
|
||||
special bonds CPU = 0.001 seconds
|
||||
create_bonds many projectile projectile 2 0.0 1.5
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
WARNING: Bonds are defined but no bond style is set (../force.cpp:192)
|
||||
WARNING: Likewise 1-2 special neighbor interactions != 1.0 (../force.cpp:194)
|
||||
Added 21869 bonds, new total = 60428
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 1 1
|
||||
special bond factors coul: 0 1 1
|
||||
16 = max # of 1-2 neighbors
|
||||
101 = max # of special neighbors
|
||||
special bonds CPU = 0.001 seconds
|
||||
|
||||
neighbor 0.3 bin
|
||||
special_bonds lj 0.0 1.0 1.0 coul 1.0 1.0 1.0
|
||||
|
||||
bond_style bpm/rotational store/local brkbond 100 time id1 id2
|
||||
bond_coeff 1 1.0 0.2 0.02 0.02 0.05 0.01 0.01 0.01 0.1 0.2 0.002 0.002
|
||||
bond_coeff 2 1.0 0.2 0.02 0.02 0.20 0.04 0.04 0.04 0.1 0.2 0.002 0.002
|
||||
|
||||
velocity projectile set -0.05 0.0 0.0
|
||||
compute nbond all nbond/atom
|
||||
compute tbond all reduce sum c_nbond
|
||||
|
||||
timestep 0.05
|
||||
thermo_style custom step ke pe pxx pyy pzz c_tbond
|
||||
thermo 100
|
||||
thermo_modify lost ignore lost/bond ignore
|
||||
#dump 1 all custom 100 atomDump id radius x y z c_nbond
|
||||
|
||||
dump 2 all local 100 brokenDump f_brkbond[1] f_brkbond[2] f_brkbond[3]
|
||||
dump_modify 2 header no
|
||||
|
||||
run 7500
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 1.3
|
||||
ghost atom cutoff = 2.6
|
||||
binsize = 0.65, bins = 98 108 108
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair gran/hooke/history, perpetual
|
||||
attributes: half, newton on, size, history
|
||||
pair build: half/size/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 33.34 | 33.34 | 33.35 Mbytes
|
||||
Step KinEng PotEng Pxx Pyy Pzz c_tbond
|
||||
0 0.00053238861 0 3.8217307e-05 0 0 10.8703
|
||||
100 0.00053238861 0 3.8217307e-05 1.2166373e-20 1.2308212e-20 10.8703
|
||||
200 0.00053238861 0 3.8217307e-05 1.2454467e-20 1.2479589e-20 10.8703
|
||||
300 0.00053238861 0 3.8217307e-05 1.2256702e-20 1.2621091e-20 10.8703
|
||||
400 0.00053238861 0 3.8217307e-05 1.2170534e-20 1.2751666e-20 10.8703
|
||||
500 0.00053093549 0 3.8484194e-05 7.645531e-08 1.4861825e-07 10.8703
|
||||
600 0.00051485902 0 4.0340751e-05 3.8615876e-07 4.8663463e-07 10.869221
|
||||
700 0.00049942978 0 3.8684008e-05 4.5363318e-07 4.4560229e-07 10.85501
|
||||
800 0.00049465262 0 3.6604612e-05 1.4755468e-07 2.0062093e-07 10.820651
|
||||
900 0.00048784775 0 3.5333139e-05 3.5118328e-07 6.6697625e-07 10.769563
|
||||
1000 0.00048345699 0 3.4702137e-05 7.0312998e-07 4.0218318e-07 10.730347
|
||||
1100 0.00047945073 0 3.5065961e-05 6.2813891e-07 7.4640359e-07 10.703184
|
||||
1200 0.00047512604 0 3.4833144e-05 8.5208604e-07 8.7277583e-07 10.686634
|
||||
1300 0.00047401428 0 3.4236869e-05 1.0321827e-06 7.4545242e-07 10.678
|
||||
1400 0.00047619121 0 3.4416549e-05 8.7518021e-07 7.3979503e-07 10.671704
|
||||
1500 0.0004668728 0 3.4495751e-05 1.4077823e-06 1.517373e-06 10.666127
|
||||
1600 0.00045088371 0 3.3264301e-05 1.8499661e-06 1.9842415e-06 10.66073
|
||||
1700 0.00044275099 0 3.2471064e-05 1.9028747e-06 2.2248947e-06 10.6458
|
||||
1800 0.0004424362 0 3.1846336e-05 1.6208492e-06 1.9291602e-06 10.620615
|
||||
1900 0.00043678957 0 3.1260936e-05 1.4673956e-06 1.6120523e-06 10.603166
|
||||
2000 0.00042747562 0 3.0652107e-05 1.6455486e-06 1.53127e-06 10.576003
|
||||
2100 0.0004214344 0 3.0240727e-05 1.8873967e-06 1.5258622e-06 10.539845
|
||||
2200 0.00041712779 0 3.0329566e-05 1.8846152e-06 1.4971471e-06 10.49937
|
||||
2300 0.00041095769 0 3.0000572e-05 2.3585924e-06 1.6773177e-06 10.471668
|
||||
2400 0.00040883568 0 2.9625158e-05 1.9105554e-06 1.8720763e-06 10.45116
|
||||
2500 0.00040762685 0 2.9441541e-05 1.6848938e-06 1.8877532e-06 10.437309
|
||||
2600 0.00040579873 0 2.9255988e-05 1.7523874e-06 1.636423e-06 10.422378
|
||||
2700 0.00040340975 0 2.9035693e-05 1.673158e-06 1.9038932e-06 10.410505
|
||||
2800 0.00040170914 0 2.8829361e-05 1.6711978e-06 1.9776001e-06 10.400792
|
||||
2900 0.00040015113 0 2.8614186e-05 1.5982427e-06 1.7994733e-06 10.393416
|
||||
3000 0.00040029253 0 2.8470718e-05 1.5589166e-06 1.6682302e-06 10.385321
|
||||
3100 0.00040037329 0 2.8483376e-05 1.2831526e-06 1.4788005e-06 10.378485
|
||||
3200 0.00040142612 0 2.8481287e-05 1.1577988e-06 1.3495778e-06 10.373988
|
||||
3300 0.00040105092 0 2.8547009e-05 1.2155138e-06 1.2633439e-06 10.370031
|
||||
3400 0.00039950673 0 2.8340939e-05 1.1182251e-06 1.1624668e-06 10.364274
|
||||
3500 0.00039715236 0 2.824813e-05 1.3086462e-06 1.2029185e-06 10.360496
|
||||
3600 0.00039446552 0 2.8112283e-05 1.1232321e-06 1.0077217e-06 10.353121
|
||||
3700 0.00039263296 0 2.7927975e-05 1.1083636e-06 1.2091857e-06 10.346645
|
||||
3800 0.00039061341 0 2.7819957e-05 1.1836841e-06 1.3566272e-06 10.341069
|
||||
3900 0.00038985051 0 2.7681947e-05 1.3588359e-06 1.4099727e-06 10.329196
|
||||
4000 0.00038815347 0 2.7492102e-05 1.1111719e-06 1.1700718e-06 10.318043
|
||||
4100 0.00038651302 0 2.7444105e-05 9.9563429e-07 1.4085969e-06 10.311027
|
||||
4200 0.00038565809 0 2.7177341e-05 9.5736307e-07 1.0404482e-06 10.299155
|
||||
4300 0.0003847255 0 2.7029216e-05 9.6204756e-07 1.140804e-06 10.292319
|
||||
4400 0.0003844421 0 2.6841047e-05 9.6570404e-07 1.2319818e-06 10.286203
|
||||
4500 0.0003842788 0 2.6633558e-05 9.6452478e-07 1.1954945e-06 10.278287
|
||||
4600 0.00038365139 0 2.6514403e-05 9.6185846e-07 1.2002452e-06 10.270732
|
||||
4700 0.00038271503 0 2.6374349e-05 9.4061833e-07 1.1774211e-06 10.264796
|
||||
4800 0.00038233688 0 2.638398e-05 1.1644119e-06 1.3746239e-06 10.25742
|
||||
4900 0.00038223496 0 2.6279821e-05 1.1345508e-06 1.4709213e-06 10.246987
|
||||
5000 0.00038219402 0 2.6188871e-05 1.0115151e-06 1.2024203e-06 10.240511
|
||||
5100 0.00038195153 0 2.6137945e-05 1.009856e-06 1.1961088e-06 10.236014
|
||||
5200 0.00038170903 0 2.6103563e-05 1.0046761e-06 1.1881008e-06 10.232236
|
||||
5300 0.00038194303 0 2.6111938e-05 1.0533375e-06 1.2621634e-06 10.230617
|
||||
5400 0.00038147407 0 2.6078641e-05 1.082228e-06 1.2915223e-06 10.230098
|
||||
5500 0.00038156894 0 2.6084488e-05 1.1395485e-06 1.3592644e-06 10.227759
|
||||
5600 0.00038169434 0 2.6085704e-05 1.1173618e-06 1.3003599e-06 10.2256
|
||||
5700 0.00038219734 0 2.6095279e-05 1.1026614e-06 1.280455e-06 10.223621
|
||||
5800 0.00038268758 0 2.6113437e-05 1.1096198e-06 1.2565503e-06 10.222902
|
||||
5900 0.00038300658 0 2.6131709e-05 1.1123595e-06 1.235992e-06 10.222182
|
||||
6000 0.00038250316 0 2.606995e-05 1.1590744e-06 1.2888416e-06 10.221123
|
||||
6100 0.0003821526 0 2.6025605e-05 1.1434025e-06 1.3141861e-06 10.219503
|
||||
6200 0.00038185711 0 2.5991255e-05 1.1471391e-06 1.3427373e-06 10.219503
|
||||
6300 0.00038197679 0 2.5996965e-05 1.1338082e-06 1.3315258e-06 10.218604
|
||||
6400 0.00038232311 0 2.6035805e-05 1.1353407e-06 1.3306683e-06 10.217884
|
||||
6500 0.00038255543 0 2.6091572e-05 1.1768703e-06 1.3629611e-06 10.217704
|
||||
6600 0.00038251887 0 2.6068968e-05 1.1808094e-06 1.3969697e-06 10.217344
|
||||
6700 0.00038177389 0 2.6004288e-05 1.1659866e-06 1.423638e-06 10.218084
|
||||
6800 0.00038096291 0 2.5969494e-05 1.1377343e-06 1.4348787e-06 10.218103
|
||||
6900 0.00038090601 0 2.5951546e-05 1.1327767e-06 1.4311663e-06 10.217024
|
||||
7000 0.00038088094 0 2.5946255e-05 1.1652568e-06 1.4567559e-06 10.215944
|
||||
7100 0.00038094624 0 2.5972593e-05 1.1558871e-06 1.4692935e-06 10.214684
|
||||
7200 0.00038168738 0 2.6002e-05 1.1562707e-06 1.4881081e-06 10.212705
|
||||
7300 0.00038200854 0 2.6038768e-05 1.1339903e-06 1.4808455e-06 10.212345
|
||||
7400 0.00038187543 0 2.6044759e-05 1.101743e-06 1.4758679e-06 10.213084
|
||||
7500 0.00038165297 0 2.6004536e-05 1.0892731e-06 1.4872621e-06 10.214742
|
||||
Loop time of 28.804 on 4 procs for 7500 steps with 11111 atoms
|
||||
|
||||
Performance: 1124843.305 tau/day, 260.380 timesteps/s
|
||||
97.5% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.26977 | 0.28058 | 0.2866 | 1.3 | 0.97
|
||||
Bond | 22.742 | 23.598 | 24.671 | 16.6 | 81.92
|
||||
Neigh | 0.54555 | 0.5728 | 0.60272 | 3.2 | 1.99
|
||||
Comm | 1.4024 | 2.5619 | 3.5079 | 54.8 | 8.89
|
||||
Output | 0.025307 | 0.025833 | 0.027022 | 0.4 | 0.09
|
||||
Modify | 1.592 | 1.6506 | 1.7059 | 4.0 | 5.73
|
||||
Other | | 0.1147 | | | 0.40
|
||||
|
||||
Nlocal: 2777.75 ave 2887 max 2682 min
|
||||
Histogram: 1 0 0 0 2 0 0 0 0 1
|
||||
Nghost: 1152.5 ave 1189 max 1125 min
|
||||
Histogram: 1 0 1 0 0 1 0 0 0 1
|
||||
Neighs: 11515.5 ave 12520 max 10831 min
|
||||
Histogram: 1 1 0 0 1 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 46062
|
||||
Ave neighs/atom = 4.1456215
|
||||
Ave special neighs/atom = 10.214742
|
||||
Neighbor list builds = 408
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:28
|
||||
221
examples/bpm/impact/log.17Feb2022.impact.spring.g++.4
Normal file
221
examples/bpm/impact/log.17Feb2022.impact.spring.g++.4
Normal file
@ -0,0 +1,221 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
units lj
|
||||
dimension 3
|
||||
boundary f f f
|
||||
atom_style bond
|
||||
special_bonds lj 0.0 1.0 1.0 coul 0.0 1.0 1.0
|
||||
newton on off
|
||||
comm_modify vel yes cutoff 2.6
|
||||
lattice fcc 1.0
|
||||
Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011
|
||||
region box block -25 15 -22 22 -22 22
|
||||
create_box 1 box bond/types 2 extra/bond/per/atom 20 extra/special/per/atom 50
|
||||
Created orthogonal box = (-39.685026 -34.922823 -34.922823) to (23.811016 34.922823 34.922823)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
|
||||
region disk cylinder x 0.0 0.0 20.0 -0.5 0.5
|
||||
create_atoms 1 region disk
|
||||
Created 7529 atoms
|
||||
using lattice units in orthogonal box = (-39.685026 -34.922823 -34.922823) to (23.811016 34.922823 34.922823)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
group plate region disk
|
||||
7529 atoms in group plate
|
||||
|
||||
region ball sphere 8.0 0.0 0.0 6.0
|
||||
create_atoms 1 region ball
|
||||
Created 3589 atoms
|
||||
using lattice units in orthogonal box = (-39.685026 -34.922823 -34.922823) to (23.811016 34.922823 34.922823)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
group projectile region ball
|
||||
3589 atoms in group projectile
|
||||
|
||||
displace_atoms all random 0.1 0.1 0.1 134598738
|
||||
Displacing atoms ...
|
||||
|
||||
mass 1 1.0
|
||||
|
||||
neighbor 1.0 bin
|
||||
pair_style bpm/spring
|
||||
pair_coeff 1 1 1.0 1.0 1.0
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
create_bonds many plate plate 1 0.0 1.5
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2
|
||||
ghost atom cutoff = 2.6
|
||||
binsize = 1, bins = 64 70 70
|
||||
2 neighbor lists, perpetual/occasional/extra = 1 1 0
|
||||
(1) command create_bonds, occasional
|
||||
attributes: full, newton on
|
||||
pair build: full/bin
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
(2) pair bpm/spring, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Added 38559 bonds, new total = 38559
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 1 1
|
||||
special bond factors coul: 0 1 1
|
||||
15 = max # of 1-2 neighbors
|
||||
101 = max # of special neighbors
|
||||
special bonds CPU = 0.001 seconds
|
||||
create_bonds many projectile projectile 2 0.0 1.5
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
WARNING: Bonds are defined but no bond style is set (../force.cpp:192)
|
||||
WARNING: Likewise 1-2 special neighbor interactions != 1.0 (../force.cpp:194)
|
||||
Added 21869 bonds, new total = 60428
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 1 1
|
||||
special bond factors coul: 0 1 1
|
||||
16 = max # of 1-2 neighbors
|
||||
101 = max # of special neighbors
|
||||
special bonds CPU = 0.001 seconds
|
||||
|
||||
neighbor 0.3 bin
|
||||
special_bonds lj 0.0 1.0 1.0 coul 1.0 1.0 1.0
|
||||
|
||||
bond_style bpm/spring store/local brkbond 100 time id1 id2
|
||||
bond_coeff 1 1.0 0.04 1.0
|
||||
bond_coeff 2 1.0 0.20 1.0
|
||||
|
||||
velocity projectile set -0.05 0.0 0.0
|
||||
compute nbond all nbond/atom
|
||||
compute tbond all reduce sum c_nbond
|
||||
|
||||
timestep 0.1
|
||||
thermo_style custom step ke pe pxx pyy pzz c_tbond
|
||||
thermo 100
|
||||
thermo_modify lost ignore lost/bond ignore
|
||||
#dump 1 all custom 100 atomDump id x y z c_nbond
|
||||
|
||||
dump 2 all local 100 brokenDump f_brkbond[1] f_brkbond[2] f_brkbond[3]
|
||||
dump_modify 2 header no
|
||||
|
||||
run 7500
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 1.3
|
||||
ghost atom cutoff = 2.6
|
||||
binsize = 0.65, bins = 98 108 108
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair bpm/spring, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 17.74 | 17.74 | 17.74 Mbytes
|
||||
Step KinEng PotEng Pxx Pyy Pzz c_tbond
|
||||
0 0.0010167873 0 7.298968e-05 0 0 10.8703
|
||||
100 0.0010167873 0 7.298968e-05 -8.7429897e-20 -8.8470837e-20 10.8703
|
||||
200 0.0010167873 0 7.298968e-05 -7.2809565e-20 -8.0915788e-20 10.8703
|
||||
300 0.0009951439 0 9.9273671e-05 8.1569216e-06 8.0922512e-06 10.868142
|
||||
400 0.00095142792 0 0.00012669557 -1.3413721e-05 -1.4800745e-05 10.849793
|
||||
500 0.00092272662 0 8.1708784e-05 -9.7488701e-06 -1.3603634e-05 10.819752
|
||||
600 0.00088967612 0 6.2587266e-05 -5.1954127e-06 -6.781587e-06 10.797985
|
||||
700 0.00086070919 0 8.8529902e-05 -9.9431205e-06 -7.9905211e-06 10.776579
|
||||
800 0.00083543943 0 7.5920357e-05 3.6381024e-07 3.7747551e-06 10.759309
|
||||
900 0.00081190799 0 6.3678219e-05 5.4158243e-06 1.2751247e-05 10.744199
|
||||
1000 0.00078828988 0 7.3079869e-05 -6.6410613e-06 -1.198683e-06 10.728368
|
||||
1100 0.00075664718 0 6.2976995e-05 -4.7863299e-06 -3.9814556e-06 10.711819
|
||||
1200 0.00072472205 0 4.9680233e-05 9.3093553e-06 4.4426393e-06 10.69401
|
||||
1300 0.00070176532 0 5.4048176e-05 1.3051954e-05 7.5448558e-06 10.671164
|
||||
1400 0.00068599319 0 5.4062404e-05 9.9930199e-06 1.0353154e-05 10.650117
|
||||
1500 0.0006786164 0 4.5038593e-05 8.067571e-06 9.8825461e-06 10.636266
|
||||
1600 0.00067466823 0 4.6733251e-05 9.8595584e-06 1.1551081e-05 10.621335
|
||||
1700 0.00066847126 0 5.1472453e-05 2.1569974e-07 6.0070599e-06 10.6127
|
||||
1800 0.00065711827 0 5.0355189e-05 -8.030203e-06 -3.1395588e-06 10.599568
|
||||
1900 0.00063882539 0 4.7146888e-05 -2.0596242e-05 -1.6494542e-05 10.581939
|
||||
2000 0.00061717894 0 4.6698781e-05 -2.5473048e-05 -2.7703615e-05 10.567188
|
||||
2100 0.00059261327 0 3.7701055e-05 -2.4637803e-05 -3.3919162e-05 10.552617
|
||||
2200 0.00056527158 0 3.2239421e-05 -1.8786685e-05 -2.4202734e-05 10.538406
|
||||
2300 0.00054054919 0 2.7410334e-05 -6.701111e-06 -7.4354974e-06 10.520777
|
||||
2400 0.00051820065 0 2.2997206e-05 1.5623767e-05 1.8687824e-05 10.501889
|
||||
2500 0.00049647925 0 1.746693e-05 2.8814144e-05 3.5569425e-05 10.487498
|
||||
2600 0.00047837258 0 1.4127067e-05 3.4245611e-05 4.0208577e-05 10.472387
|
||||
2700 0.00046626924 0 1.3714876e-05 3.7922196e-05 4.1550346e-05 10.456377
|
||||
2800 0.0004560167 0 1.5260976e-05 3.5632577e-05 3.7885738e-05 10.440007
|
||||
2900 0.00045331059 0 1.5194832e-05 3.1036124e-05 2.8633755e-05 10.427955
|
||||
3000 0.00045227799 0 1.4877378e-05 1.9327028e-05 2.1189487e-05 10.414283
|
||||
3100 0.00044866178 0 2.0424612e-05 -2.7242288e-06 7.7121438e-06 10.40349
|
||||
3200 0.00044336453 0 2.3276121e-05 -1.979069e-05 -4.2311089e-06 10.395575
|
||||
3300 0.00043526526 0 2.3338132e-05 -2.834945e-05 -1.7302033e-05 10.389998
|
||||
3400 0.00042817758 0 2.4374527e-05 -2.9870076e-05 -3.0623264e-05 10.382803
|
||||
3500 0.00042182658 0 2.6120627e-05 -2.9449521e-05 -3.787776e-05 10.378126
|
||||
3600 0.00041794291 0 2.4736957e-05 -2.4098172e-05 -3.0529166e-05 10.373628
|
||||
3700 0.0004156005 0 2.7543305e-05 -1.2431749e-05 -1.8626096e-05 10.37075
|
||||
3800 0.0004141461 0 2.4630482e-05 -6.345489e-06 -1.7375803e-05 10.368771
|
||||
3900 0.00041328832 0 2.2220142e-05 4.1471034e-07 -1.3339476e-05 10.366972
|
||||
4000 0.00041121725 0 2.3491321e-05 1.1284551e-05 -5.8651834e-06 10.364634
|
||||
4100 0.00040761876 0 2.6688248e-05 1.9721625e-05 3.7536871e-06 10.362655
|
||||
4200 0.00040301362 0 2.7601916e-05 1.9212118e-05 9.7175996e-06 10.359417
|
||||
4300 0.00040001545 0 2.7243769e-05 1.6889359e-05 1.1857147e-05 10.3551
|
||||
4400 0.00039654521 0 2.561083e-05 1.3863551e-05 1.0593597e-05 10.351142
|
||||
4500 0.00039435924 0 2.4366458e-05 1.2545563e-05 1.1323962e-05 10.348804
|
||||
4600 0.00039250006 0 2.3719127e-05 1.1015167e-05 8.5964046e-06 10.348444
|
||||
4700 0.00039145496 0 2.2943915e-05 8.7824224e-06 5.0397129e-06 10.346825
|
||||
4800 0.00039105331 0 2.4005757e-05 7.5899773e-06 9.033741e-07 10.344846
|
||||
4900 0.0003898798 0 2.3819433e-05 4.9673894e-06 -2.3466459e-06 10.343587
|
||||
5000 0.00038747508 0 2.3605028e-05 -1.1717437e-06 -6.1096657e-06 10.343047
|
||||
5100 0.00038549022 0 2.3453798e-05 -9.9256693e-06 -9.3584148e-06 10.341788
|
||||
5200 0.00038283936 0 2.5243567e-05 -1.5877598e-05 -9.9474447e-06 10.340169
|
||||
5300 0.00038140888 0 2.5522223e-05 -1.9331435e-05 -1.1067039e-05 10.33873
|
||||
5400 0.00037916674 0 2.5181488e-05 -2.1581255e-05 -1.1252641e-05 10.336931
|
||||
5500 0.00037782932 0 2.691805e-05 -1.5768241e-05 -5.6704695e-06 10.334952
|
||||
5600 0.00037628832 0 2.5851445e-05 -1.4239811e-05 -1.9122536e-06 10.333153
|
||||
5700 0.00037451913 0 2.4758416e-05 -1.3252284e-05 -1.9222041e-06 10.331714
|
||||
5800 0.00037328662 0 2.2507032e-05 -9.6704092e-06 -7.5470215e-06 10.330095
|
||||
5900 0.00037253111 0 2.3303086e-05 -4.2828034e-06 -7.888056e-06 10.328476
|
||||
6000 0.00037171133 0 2.4042456e-05 -4.7684985e-06 -6.5164336e-06 10.327397
|
||||
6100 0.00036986726 0 2.4938695e-05 -4.8738316e-06 -4.5380007e-06 10.327037
|
||||
6200 0.0003675822 0 2.3322229e-05 -4.6333093e-06 -5.7086464e-06 10.327037
|
||||
6300 0.00036552389 0 2.1435354e-05 -4.8971566e-06 -3.5935426e-06 10.327037
|
||||
6400 0.00036488091 0 2.0813994e-05 -3.8333319e-06 -3.6595059e-06 10.327037
|
||||
6500 0.00036447973 0 2.2241876e-05 8.7797361e-08 -4.141203e-06 10.327037
|
||||
6600 0.00036383343 0 2.269485e-05 4.9364593e-06 1.3062133e-06 10.326677
|
||||
6700 0.00036305076 0 2.1838759e-05 6.4587048e-06 4.7758772e-06 10.326318
|
||||
6800 0.00036226601 0 2.2916622e-05 6.044926e-06 5.0291597e-06 10.325598
|
||||
6900 0.00036175279 0 2.2691667e-05 6.9998847e-06 5.8988637e-06 10.324699
|
||||
7000 0.00036143633 0 2.1725813e-05 8.1268152e-06 5.0390503e-06 10.324519
|
||||
7100 0.0003610248 0 2.1799675e-05 8.65795e-06 3.1360368e-06 10.323439
|
||||
7200 0.00036086259 0 2.2198029e-05 5.1764734e-06 5.4798783e-07 10.32308
|
||||
7300 0.00036099757 0 2.4160496e-05 1.0310325e-06 -5.115075e-07 10.32254
|
||||
7400 0.00036129334 0 2.5325018e-05 -9.4918158e-07 -1.7064957e-06 10.32218
|
||||
7500 0.00036136655 0 2.3513198e-05 -3.8618451e-06 -4.4344772e-06 10.321281
|
||||
Loop time of 4.51074 on 4 procs for 7500 steps with 11118 atoms
|
||||
|
||||
Performance: 14365719.597 tau/day, 1662.699 timesteps/s
|
||||
93.8% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.25733 | 0.26952 | 0.28068 | 1.6 | 5.98
|
||||
Bond | 1.9391 | 2.0128 | 2.0851 | 3.7 | 44.62
|
||||
Neigh | 0.56308 | 0.5941 | 0.62077 | 2.8 | 13.17
|
||||
Comm | 0.68282 | 0.80856 | 0.94406 | 10.7 | 17.93
|
||||
Output | 0.19287 | 0.1933 | 0.19426 | 0.1 | 4.29
|
||||
Modify | 0.53239 | 0.55343 | 0.57349 | 2.0 | 12.27
|
||||
Other | | 0.07902 | | | 1.75
|
||||
|
||||
Nlocal: 2779.5 ave 2862 max 2686 min
|
||||
Histogram: 1 0 0 0 0 1 1 0 0 1
|
||||
Nghost: 1183.25 ave 1220 max 1134 min
|
||||
Histogram: 1 0 0 0 1 0 0 0 1 1
|
||||
Neighs: 11828.8 ave 12387 max 11053 min
|
||||
Histogram: 1 0 0 0 1 0 0 0 1 1
|
||||
|
||||
Total # of neighbors = 47315
|
||||
Ave neighs/atom = 4.2557115
|
||||
Ave special neighs/atom = 10.321461
|
||||
Neighbor list builds = 421
|
||||
Dangerous builds = 11
|
||||
Total wall time: 0:00:04
|
||||
35
examples/bpm/pour/in.bpm.pour
Normal file
35
examples/bpm/pour/in.bpm.pour
Normal file
@ -0,0 +1,35 @@
|
||||
units lj
|
||||
dimension 3
|
||||
boundary m m m
|
||||
atom_style bpm/sphere
|
||||
special_bonds lj 0.0 1.0 1.0 coul 1.0 1.0 1.0
|
||||
newton on off
|
||||
comm_modify vel yes cutoff 3.3
|
||||
region box block -15 15 -15 15 0 60.0
|
||||
create_box 1 box bond/types 1 extra/bond/per/atom 15 extra/special/per/atom 50
|
||||
|
||||
molecule my_mol "rect.mol"
|
||||
region wall_cyl cylinder z 0.0 0.0 10.0 EDGE EDGE side in
|
||||
region dropzone cylinder z 0.0 0.0 10.0 40.0 50.0 side in
|
||||
|
||||
pair_style gran/hertz/history 1.0 NULL 0.5 NULL 0.1 1
|
||||
bond_style bpm/rotational
|
||||
pair_coeff 1 1
|
||||
bond_coeff 1 1.0 0.2 0.01 0.01 2.0 0.4 0.02 0.02 0.2 0.04 0.002 0.002
|
||||
|
||||
compute nbond all nbond/atom
|
||||
compute tbond all reduce sum c_nbond
|
||||
compute_modify thermo_temp dynamic/dof yes
|
||||
|
||||
fix 1 all wall/gran hertz/history 1.0 NULL 0.5 NULL 0.1 1 zplane 0.0 NULL
|
||||
fix 2 all wall/gran/region hertz/history 1.0 NULL 0.5 NULL 0.1 1 region wall_cyl
|
||||
fix 3 all gravity 1e-4 vector 0 0 -1
|
||||
fix 4 all deposit 40 0 1500 712511343 mol my_mol region dropzone near 2.0 vz -0.05 -0.05
|
||||
fix 5 all nve/bpm/sphere
|
||||
|
||||
timestep 0.05
|
||||
thermo_style custom step ke pe pxx pyy pzz c_tbond
|
||||
thermo 100
|
||||
#dump 1 all custom 500 atomDump id radius x y z c_nbond mol
|
||||
|
||||
run 100000
|
||||
1091
examples/bpm/pour/log.17Feb2022.pour.g++.4
Normal file
1091
examples/bpm/pour/log.17Feb2022.pour.g++.4
Normal file
File diff suppressed because it is too large
Load Diff
568
examples/bpm/pour/rect.mol
Normal file
568
examples/bpm/pour/rect.mol
Normal file
@ -0,0 +1,568 @@
|
||||
#Made with create_mol.py
|
||||
|
||||
63 atoms
|
||||
297 bonds
|
||||
|
||||
Coords
|
||||
#ID x y z
|
||||
1 0.0 0.0 0.0
|
||||
2 0.7348518971806154 0.7348518971806154 0.0
|
||||
3 0.7348518971806154 0.0 0.7348518971806154
|
||||
4 0.0 0.7348518971806154 0.7348518971806154
|
||||
5 1.4697037943612308 0.0 0.0
|
||||
6 1.4697037943612308 0.7348518971806154 0.7348518971806154
|
||||
7 0.0 1.4697037943612308 0.0
|
||||
8 0.7348518971806154 1.4697037943612308 0.7348518971806154
|
||||
9 1.4697037943612308 1.4697037943612308 0.0
|
||||
10 0.0 0.0 1.4697037943612308
|
||||
11 0.7348518971806154 0.7348518971806154 1.4697037943612308
|
||||
12 0.7348518971806154 0.0 2.204555691541846
|
||||
13 0.0 0.7348518971806154 2.204555691541846
|
||||
14 1.4697037943612308 0.0 1.4697037943612308
|
||||
15 1.4697037943612308 0.7348518971806154 2.204555691541846
|
||||
16 0.0 1.4697037943612308 1.4697037943612308
|
||||
17 0.7348518971806154 1.4697037943612308 2.204555691541846
|
||||
18 1.4697037943612308 1.4697037943612308 1.4697037943612308
|
||||
19 0.0 0.0 2.9394075887224616
|
||||
20 0.7348518971806154 0.7348518971806154 2.9394075887224616
|
||||
21 0.7348518971806154 0.0 3.674259485903077
|
||||
22 0.0 0.7348518971806154 3.674259485903077
|
||||
23 1.4697037943612308 0.0 2.9394075887224616
|
||||
24 1.4697037943612308 0.7348518971806154 3.674259485903077
|
||||
25 0.0 1.4697037943612308 2.9394075887224616
|
||||
26 0.7348518971806154 1.4697037943612308 3.674259485903077
|
||||
27 1.4697037943612308 1.4697037943612308 2.9394075887224616
|
||||
28 0.0 0.0 4.409111383083692
|
||||
29 0.7348518971806154 0.7348518971806154 4.409111383083692
|
||||
30 0.7348518971806154 0.0 5.143963280264308
|
||||
31 0.0 0.7348518971806154 5.143963280264308
|
||||
32 1.4697037943612308 0.0 4.409111383083692
|
||||
33 1.4697037943612308 0.7348518971806154 5.143963280264308
|
||||
34 0.0 1.4697037943612308 4.409111383083692
|
||||
35 0.7348518971806154 1.4697037943612308 5.143963280264308
|
||||
36 1.4697037943612308 1.4697037943612308 4.409111383083692
|
||||
37 0.0 0.0 5.878815177444923
|
||||
38 0.7348518971806154 0.7348518971806154 5.878815177444923
|
||||
39 0.7348518971806154 0.0 6.613667074625538
|
||||
40 0.0 0.7348518971806154 6.613667074625538
|
||||
41 1.4697037943612308 0.0 5.878815177444923
|
||||
42 1.4697037943612308 0.7348518971806154 6.613667074625538
|
||||
43 0.0 1.4697037943612308 5.878815177444923
|
||||
44 0.7348518971806154 1.4697037943612308 6.613667074625538
|
||||
45 1.4697037943612308 1.4697037943612308 5.878815177444923
|
||||
46 0.0 0.0 7.348518971806154
|
||||
47 0.7348518971806154 0.7348518971806154 7.348518971806154
|
||||
48 0.7348518971806154 0.0 8.08337086898677
|
||||
49 0.0 0.7348518971806154 8.08337086898677
|
||||
50 1.4697037943612308 0.0 7.348518971806154
|
||||
51 1.4697037943612308 0.7348518971806154 8.08337086898677
|
||||
52 0.0 1.4697037943612308 7.348518971806154
|
||||
53 0.7348518971806154 1.4697037943612308 8.08337086898677
|
||||
54 1.4697037943612308 1.4697037943612308 7.348518971806154
|
||||
55 0.0 0.0 8.818222766167384
|
||||
56 0.7348518971806154 0.7348518971806154 8.818222766167384
|
||||
57 0.7348518971806154 0.0 9.553074663348
|
||||
58 0.0 0.7348518971806154 9.553074663348
|
||||
59 1.4697037943612308 0.0 8.818222766167384
|
||||
60 1.4697037943612308 0.7348518971806154 9.553074663348
|
||||
61 0.0 1.4697037943612308 8.818222766167384
|
||||
62 0.7348518971806154 1.4697037943612308 9.553074663348
|
||||
63 1.4697037943612308 1.4697037943612308 8.818222766167384
|
||||
|
||||
Types
|
||||
#ID type
|
||||
1 1
|
||||
2 1
|
||||
3 1
|
||||
4 1
|
||||
5 1
|
||||
6 1
|
||||
7 1
|
||||
8 1
|
||||
9 1
|
||||
10 1
|
||||
11 1
|
||||
12 1
|
||||
13 1
|
||||
14 1
|
||||
15 1
|
||||
16 1
|
||||
17 1
|
||||
18 1
|
||||
19 1
|
||||
20 1
|
||||
21 1
|
||||
22 1
|
||||
23 1
|
||||
24 1
|
||||
25 1
|
||||
26 1
|
||||
27 1
|
||||
28 1
|
||||
29 1
|
||||
30 1
|
||||
31 1
|
||||
32 1
|
||||
33 1
|
||||
34 1
|
||||
35 1
|
||||
36 1
|
||||
37 1
|
||||
38 1
|
||||
39 1
|
||||
40 1
|
||||
41 1
|
||||
42 1
|
||||
43 1
|
||||
44 1
|
||||
45 1
|
||||
46 1
|
||||
47 1
|
||||
48 1
|
||||
49 1
|
||||
50 1
|
||||
51 1
|
||||
52 1
|
||||
53 1
|
||||
54 1
|
||||
55 1
|
||||
56 1
|
||||
57 1
|
||||
58 1
|
||||
59 1
|
||||
60 1
|
||||
61 1
|
||||
62 1
|
||||
63 1
|
||||
|
||||
Diameters
|
||||
#ID diameter
|
||||
1 1
|
||||
2 1
|
||||
3 1
|
||||
4 1
|
||||
5 1
|
||||
6 1
|
||||
7 1
|
||||
8 1
|
||||
9 1
|
||||
10 1
|
||||
11 1
|
||||
12 1
|
||||
13 1
|
||||
14 1
|
||||
15 1
|
||||
16 1
|
||||
17 1
|
||||
18 1
|
||||
19 1
|
||||
20 1
|
||||
21 1
|
||||
22 1
|
||||
23 1
|
||||
24 1
|
||||
25 1
|
||||
26 1
|
||||
27 1
|
||||
28 1
|
||||
29 1
|
||||
30 1
|
||||
31 1
|
||||
32 1
|
||||
33 1
|
||||
34 1
|
||||
35 1
|
||||
36 1
|
||||
37 1
|
||||
38 1
|
||||
39 1
|
||||
40 1
|
||||
41 1
|
||||
42 1
|
||||
43 1
|
||||
44 1
|
||||
45 1
|
||||
46 1
|
||||
47 1
|
||||
48 1
|
||||
49 1
|
||||
50 1
|
||||
51 1
|
||||
52 1
|
||||
53 1
|
||||
54 1
|
||||
55 1
|
||||
56 1
|
||||
57 1
|
||||
58 1
|
||||
59 1
|
||||
60 1
|
||||
61 1
|
||||
62 1
|
||||
63 1
|
||||
|
||||
Masses
|
||||
#ID mass
|
||||
1 1
|
||||
2 1
|
||||
3 1
|
||||
4 1
|
||||
5 1
|
||||
6 1
|
||||
7 1
|
||||
8 1
|
||||
9 1
|
||||
10 1
|
||||
11 1
|
||||
12 1
|
||||
13 1
|
||||
14 1
|
||||
15 1
|
||||
16 1
|
||||
17 1
|
||||
18 1
|
||||
19 1
|
||||
20 1
|
||||
21 1
|
||||
22 1
|
||||
23 1
|
||||
24 1
|
||||
25 1
|
||||
26 1
|
||||
27 1
|
||||
28 1
|
||||
29 1
|
||||
30 1
|
||||
31 1
|
||||
32 1
|
||||
33 1
|
||||
34 1
|
||||
35 1
|
||||
36 1
|
||||
37 1
|
||||
38 1
|
||||
39 1
|
||||
40 1
|
||||
41 1
|
||||
42 1
|
||||
43 1
|
||||
44 1
|
||||
45 1
|
||||
46 1
|
||||
47 1
|
||||
48 1
|
||||
49 1
|
||||
50 1
|
||||
51 1
|
||||
52 1
|
||||
53 1
|
||||
54 1
|
||||
55 1
|
||||
56 1
|
||||
57 1
|
||||
58 1
|
||||
59 1
|
||||
60 1
|
||||
61 1
|
||||
62 1
|
||||
63 1
|
||||
|
||||
Bonds
|
||||
#ID type atom1 atom2
|
||||
1 1 1 2
|
||||
2 1 1 3
|
||||
3 1 1 4
|
||||
4 1 1 5
|
||||
5 1 1 7
|
||||
6 1 1 10
|
||||
7 1 2 3
|
||||
8 1 2 4
|
||||
9 1 2 5
|
||||
10 1 2 6
|
||||
11 1 2 7
|
||||
12 1 2 8
|
||||
13 1 2 9
|
||||
14 1 2 11
|
||||
15 1 3 4
|
||||
16 1 3 5
|
||||
17 1 3 6
|
||||
18 1 3 8
|
||||
19 1 3 10
|
||||
20 1 3 11
|
||||
21 1 3 12
|
||||
22 1 3 14
|
||||
23 1 4 6
|
||||
24 1 4 7
|
||||
25 1 4 8
|
||||
26 1 4 10
|
||||
27 1 4 11
|
||||
28 1 4 13
|
||||
29 1 4 16
|
||||
30 1 5 6
|
||||
31 1 5 9
|
||||
32 1 5 14
|
||||
33 1 6 8
|
||||
34 1 6 9
|
||||
35 1 6 11
|
||||
36 1 6 14
|
||||
37 1 6 18
|
||||
38 1 7 8
|
||||
39 1 7 9
|
||||
40 1 7 16
|
||||
41 1 8 9
|
||||
42 1 8 11
|
||||
43 1 8 16
|
||||
44 1 8 17
|
||||
45 1 8 18
|
||||
46 1 9 18
|
||||
47 1 10 11
|
||||
48 1 10 12
|
||||
49 1 10 13
|
||||
50 1 10 14
|
||||
51 1 10 16
|
||||
52 1 10 19
|
||||
53 1 11 12
|
||||
54 1 11 13
|
||||
55 1 11 14
|
||||
56 1 11 15
|
||||
57 1 11 16
|
||||
58 1 11 17
|
||||
59 1 11 18
|
||||
60 1 12 13
|
||||
61 1 12 14
|
||||
62 1 12 15
|
||||
63 1 12 17
|
||||
64 1 12 19
|
||||
65 1 12 20
|
||||
66 1 12 21
|
||||
67 1 12 23
|
||||
68 1 13 15
|
||||
69 1 13 16
|
||||
70 1 13 17
|
||||
71 1 13 19
|
||||
72 1 13 20
|
||||
73 1 13 22
|
||||
74 1 13 25
|
||||
75 1 14 15
|
||||
76 1 14 18
|
||||
77 1 14 23
|
||||
78 1 15 17
|
||||
79 1 15 18
|
||||
80 1 15 20
|
||||
81 1 15 23
|
||||
82 1 15 27
|
||||
83 1 16 17
|
||||
84 1 16 18
|
||||
85 1 16 25
|
||||
86 1 17 18
|
||||
87 1 17 20
|
||||
88 1 17 25
|
||||
89 1 17 27
|
||||
90 1 18 27
|
||||
91 1 19 20
|
||||
92 1 19 21
|
||||
93 1 19 22
|
||||
94 1 19 23
|
||||
95 1 19 25
|
||||
96 1 19 28
|
||||
97 1 20 21
|
||||
98 1 20 22
|
||||
99 1 20 23
|
||||
100 1 20 24
|
||||
101 1 20 25
|
||||
102 1 20 26
|
||||
103 1 20 27
|
||||
104 1 20 29
|
||||
105 1 21 22
|
||||
106 1 21 23
|
||||
107 1 21 24
|
||||
108 1 21 26
|
||||
109 1 21 28
|
||||
110 1 21 29
|
||||
111 1 21 30
|
||||
112 1 21 32
|
||||
113 1 22 24
|
||||
114 1 22 25
|
||||
115 1 22 26
|
||||
116 1 22 28
|
||||
117 1 22 29
|
||||
118 1 22 34
|
||||
119 1 23 24
|
||||
120 1 23 27
|
||||
121 1 23 32
|
||||
122 1 24 26
|
||||
123 1 24 27
|
||||
124 1 24 29
|
||||
125 1 24 32
|
||||
126 1 24 36
|
||||
127 1 25 26
|
||||
128 1 25 27
|
||||
129 1 25 34
|
||||
130 1 26 27
|
||||
131 1 26 29
|
||||
132 1 26 34
|
||||
133 1 26 35
|
||||
134 1 26 36
|
||||
135 1 27 36
|
||||
136 1 28 29
|
||||
137 1 28 30
|
||||
138 1 28 31
|
||||
139 1 28 32
|
||||
140 1 28 34
|
||||
141 1 28 37
|
||||
142 1 29 30
|
||||
143 1 29 31
|
||||
144 1 29 32
|
||||
145 1 29 33
|
||||
146 1 29 34
|
||||
147 1 29 35
|
||||
148 1 29 36
|
||||
149 1 29 38
|
||||
150 1 30 31
|
||||
151 1 30 32
|
||||
152 1 30 33
|
||||
153 1 30 35
|
||||
154 1 30 37
|
||||
155 1 30 38
|
||||
156 1 30 41
|
||||
157 1 31 33
|
||||
158 1 31 34
|
||||
159 1 31 35
|
||||
160 1 31 37
|
||||
161 1 31 38
|
||||
162 1 31 40
|
||||
163 1 31 43
|
||||
164 1 32 33
|
||||
165 1 32 36
|
||||
166 1 32 41
|
||||
167 1 33 35
|
||||
168 1 33 36
|
||||
169 1 33 38
|
||||
170 1 33 41
|
||||
171 1 33 42
|
||||
172 1 33 45
|
||||
173 1 34 35
|
||||
174 1 34 36
|
||||
175 1 34 43
|
||||
176 1 35 36
|
||||
177 1 35 38
|
||||
178 1 35 43
|
||||
179 1 35 45
|
||||
180 1 36 45
|
||||
181 1 37 38
|
||||
182 1 37 39
|
||||
183 1 37 40
|
||||
184 1 37 41
|
||||
185 1 37 43
|
||||
186 1 37 46
|
||||
187 1 38 39
|
||||
188 1 38 40
|
||||
189 1 38 41
|
||||
190 1 38 42
|
||||
191 1 38 43
|
||||
192 1 38 44
|
||||
193 1 38 45
|
||||
194 1 38 47
|
||||
195 1 39 40
|
||||
196 1 39 41
|
||||
197 1 39 42
|
||||
198 1 39 44
|
||||
199 1 39 46
|
||||
200 1 39 47
|
||||
201 1 39 50
|
||||
202 1 40 42
|
||||
203 1 40 43
|
||||
204 1 40 44
|
||||
205 1 40 46
|
||||
206 1 40 47
|
||||
207 1 40 52
|
||||
208 1 41 42
|
||||
209 1 41 45
|
||||
210 1 41 50
|
||||
211 1 42 44
|
||||
212 1 42 45
|
||||
213 1 42 47
|
||||
214 1 42 50
|
||||
215 1 42 51
|
||||
216 1 42 54
|
||||
217 1 43 44
|
||||
218 1 43 45
|
||||
219 1 43 52
|
||||
220 1 44 45
|
||||
221 1 44 47
|
||||
222 1 44 52
|
||||
223 1 44 53
|
||||
224 1 44 54
|
||||
225 1 45 54
|
||||
226 1 46 47
|
||||
227 1 46 48
|
||||
228 1 46 49
|
||||
229 1 46 50
|
||||
230 1 46 52
|
||||
231 1 46 55
|
||||
232 1 47 48
|
||||
233 1 47 49
|
||||
234 1 47 50
|
||||
235 1 47 51
|
||||
236 1 47 52
|
||||
237 1 47 53
|
||||
238 1 47 54
|
||||
239 1 47 56
|
||||
240 1 48 49
|
||||
241 1 48 50
|
||||
242 1 48 51
|
||||
243 1 48 53
|
||||
244 1 48 55
|
||||
245 1 48 56
|
||||
246 1 48 57
|
||||
247 1 48 59
|
||||
248 1 49 51
|
||||
249 1 49 52
|
||||
250 1 49 53
|
||||
251 1 49 55
|
||||
252 1 49 56
|
||||
253 1 49 58
|
||||
254 1 49 61
|
||||
255 1 50 51
|
||||
256 1 50 54
|
||||
257 1 50 59
|
||||
258 1 51 53
|
||||
259 1 51 54
|
||||
260 1 51 56
|
||||
261 1 51 59
|
||||
262 1 51 63
|
||||
263 1 52 53
|
||||
264 1 52 54
|
||||
265 1 52 61
|
||||
266 1 53 54
|
||||
267 1 53 56
|
||||
268 1 53 61
|
||||
269 1 53 62
|
||||
270 1 53 63
|
||||
271 1 54 63
|
||||
272 1 55 56
|
||||
273 1 55 57
|
||||
274 1 55 58
|
||||
275 1 55 59
|
||||
276 1 55 61
|
||||
277 1 56 57
|
||||
278 1 56 58
|
||||
279 1 56 59
|
||||
280 1 56 60
|
||||
281 1 56 61
|
||||
282 1 56 62
|
||||
283 1 56 63
|
||||
284 1 57 58
|
||||
285 1 57 59
|
||||
286 1 57 60
|
||||
287 1 57 62
|
||||
288 1 58 60
|
||||
289 1 58 61
|
||||
290 1 58 62
|
||||
291 1 59 60
|
||||
292 1 59 63
|
||||
293 1 60 62
|
||||
294 1 60 63
|
||||
295 1 61 62
|
||||
296 1 61 63
|
||||
297 1 62 63
|
||||
99
examples/kim/plugin/CMakeLists.txt
Normal file
99
examples/kim/plugin/CMakeLists.txt
Normal file
@ -0,0 +1,99 @@
|
||||
##########################################
|
||||
# CMake build system for plugin examples.
|
||||
# The is meant to be used as a template for plugins that are
|
||||
# distributed independent from the LAMMPS package.
|
||||
##########################################
|
||||
|
||||
cmake_minimum_required(VERSION 3.10)
|
||||
|
||||
# enforce out-of-source build
|
||||
if(${CMAKE_SOURCE_DIR} STREQUAL ${CMAKE_BINARY_DIR})
|
||||
message(FATAL_ERROR "In-source builds are not allowed. You must create and use a build directory. "
|
||||
"Please remove CMakeCache.txt and CMakeFiles first.")
|
||||
endif()
|
||||
|
||||
project(kimplugin VERSION 1.0 LANGUAGES CXX)
|
||||
|
||||
set(LAMMPS_SOURCE_DIR "" CACHE PATH "Location of LAMMPS sources folder")
|
||||
if(NOT LAMMPS_SOURCE_DIR)
|
||||
message(FATAL_ERROR "Must set LAMMPS_SOURCE_DIR")
|
||||
endif()
|
||||
|
||||
# by default, install into $HOME/.local (not /usr/local),
|
||||
# so that no root access (and sudo) is needed
|
||||
if(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)
|
||||
set(CMAKE_INSTALL_PREFIX "$ENV{HOME}/.local" CACHE PATH "Default install path" FORCE)
|
||||
endif()
|
||||
|
||||
# ugly hacks for MSVC which by default always reports an old C++ standard in the __cplusplus macro
|
||||
# and prints lots of pointless warnings about "unsafe" functions
|
||||
if(MSVC)
|
||||
add_compile_options(/Zc:__cplusplus)
|
||||
add_compile_options(/wd4244)
|
||||
add_compile_options(/wd4267)
|
||||
add_compile_definitions(_CRT_SECURE_NO_WARNINGS)
|
||||
endif()
|
||||
|
||||
# C++11 is required
|
||||
set(CMAKE_CXX_STANDARD 11)
|
||||
set(CMAKE_CXX_STANDARD_REQUIRED ON)
|
||||
|
||||
# Need -restrict with Intel compilers
|
||||
if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
|
||||
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -restrict")
|
||||
endif()
|
||||
|
||||
set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR})
|
||||
include(CheckIncludeFileCXX)
|
||||
include(LAMMPSInterfaceCXX)
|
||||
|
||||
##########################
|
||||
# building the plugins
|
||||
|
||||
add_library(kimplugin MODULE kimplugin.cpp ${LAMMPS_SOURCE_DIR}/KIM/pair_kim.cpp
|
||||
${LAMMPS_SOURCE_DIR}/KIM/fix_store_kim.cpp ${LAMMPS_SOURCE_DIR}/KIM/kim_command.cpp
|
||||
${LAMMPS_SOURCE_DIR}/KIM/kim_init.cpp ${LAMMPS_SOURCE_DIR}/KIM/kim_interactions.cpp
|
||||
${LAMMPS_SOURCE_DIR}/KIM/kim_param.cpp ${LAMMPS_SOURCE_DIR}/KIM/kim_property.cpp
|
||||
${LAMMPS_SOURCE_DIR}/KIM/kim_query.cpp ${LAMMPS_SOURCE_DIR}/KIM/kim_units.cpp)
|
||||
target_link_libraries(kimplugin PRIVATE lammps)
|
||||
target_include_directories(kimplugin PRIVATE ${LAMMPS_SOURCE_DIR}/KIM)
|
||||
set_target_properties(kimplugin PROPERTIES PREFIX "" SUFFIX ".so")
|
||||
|
||||
find_package(KIM-API 2.2.0 CONFIG REQUIRED)
|
||||
target_link_libraries(kimplugin PRIVATE KIM-API::kim-api)
|
||||
|
||||
##########################
|
||||
# need libcurl
|
||||
find_package(CURL)
|
||||
if(CURL_FOUND)
|
||||
if(CMAKE_VERSION VERSION_LESS 3.12)
|
||||
target_include_directories(kimplugin PRIVATE ${CURL_INCLUDE_DIRS})
|
||||
target_link_libraries(kimplugin PRIVATE ${CURL_LIBRARIES})
|
||||
else()
|
||||
target_link_libraries(kimplugin PRIVATE CURL::libcurl)
|
||||
endif()
|
||||
target_compile_definitions(kimplugin PRIVATE -DLMP_KIM_CURL)
|
||||
set(LMP_DEBUG_CURL OFF CACHE STRING "Set libcurl verbose mode on/off. If on, it displays a lot of verbose information about its operations.")
|
||||
mark_as_advanced(LMP_DEBUG_CURL)
|
||||
if(LMP_DEBUG_CURL)
|
||||
target_compile_definitions(kimplugin PRIVATE -DLMP_DEBUG_CURL)
|
||||
endif()
|
||||
set(LMP_NO_SSL_CHECK OFF CACHE STRING "Tell libcurl to not verify the peer. If on, the connection succeeds regardless of the names in the certificate. Insecure - Use with caution!")
|
||||
mark_as_advanced(LMP_NO_SSL_CHECK)
|
||||
if(LMP_NO_SSL_CHECK)
|
||||
target_compile_definitions(kimplugin PRIVATE -DLMP_NO_SSL_CHECK)
|
||||
endif()
|
||||
endif()
|
||||
|
||||
# MacOS seems to need this
|
||||
if(CMAKE_SYSTEM_NAME STREQUAL Darwin)
|
||||
set_target_properties(kimplugin PROPERTIES LINK_FLAGS "-Wl,-undefined,dynamic_lookup")
|
||||
elseif(CMAKE_SYSTEM_NAME STREQUAL "Windows")
|
||||
# tell CMake to export all symbols to a .dll on Windows with special case for MinGW cross-compilers
|
||||
set_target_properties(kimplugin.so PROPERTIES WINDOWS_EXPORT_ALL_SYMBOLS TRUE)
|
||||
if(CMAKE_CROSSCOMPILING)
|
||||
set_target_properties(kimplugin PROPERTIES LINK_FLAGS "-Wl,--export-all-symbols")
|
||||
endif()
|
||||
else()
|
||||
set_target_properties(kimplugin PROPERTIES LINK_FLAGS "-rdynamic")
|
||||
endif()
|
||||
88
examples/kim/plugin/LAMMPSInterfaceCXX.cmake
Normal file
88
examples/kim/plugin/LAMMPSInterfaceCXX.cmake
Normal file
@ -0,0 +1,88 @@
|
||||
# Cmake script code to define the LAMMPS C++ interface
|
||||
# settings required for building LAMMPS plugins
|
||||
|
||||
################################################################################
|
||||
# helper function
|
||||
function(validate_option name values)
|
||||
string(TOLOWER ${${name}} needle_lower)
|
||||
string(TOUPPER ${${name}} needle_upper)
|
||||
list(FIND ${values} ${needle_lower} IDX_LOWER)
|
||||
list(FIND ${values} ${needle_upper} IDX_UPPER)
|
||||
if(${IDX_LOWER} LESS 0 AND ${IDX_UPPER} LESS 0)
|
||||
list_to_bulletpoints(POSSIBLE_VALUE_LIST ${${values}})
|
||||
message(FATAL_ERROR "\n########################################################################\n"
|
||||
"Invalid value '${${name}}' for option ${name}\n"
|
||||
"\n"
|
||||
"Possible values are:\n"
|
||||
"${POSSIBLE_VALUE_LIST}"
|
||||
"########################################################################")
|
||||
endif()
|
||||
endfunction(validate_option)
|
||||
|
||||
#################################################################################
|
||||
# LAMMPS C++ interface. We only need the header related parts.
|
||||
add_library(lammps INTERFACE)
|
||||
target_include_directories(lammps INTERFACE ${LAMMPS_SOURCE_DIR})
|
||||
if((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND CMAKE_CROSSCOMPILING)
|
||||
target_link_libraries(lammps INTERFACE ${CMAKE_BINARY_DIR}/../liblammps.dll.a)
|
||||
endif()
|
||||
################################################################################
|
||||
# MPI configuration
|
||||
if(NOT CMAKE_CROSSCOMPILING)
|
||||
set(MPI_CXX_SKIP_MPICXX TRUE)
|
||||
find_package(MPI QUIET)
|
||||
option(BUILD_MPI "Build MPI version" ${MPI_FOUND})
|
||||
else()
|
||||
option(BUILD_MPI "Build MPI version" OFF)
|
||||
endif()
|
||||
|
||||
if(BUILD_MPI)
|
||||
find_package(MPI REQUIRED)
|
||||
option(LAMMPS_LONGLONG_TO_LONG "Workaround if your system or MPI version does not recognize 'long long' data types" OFF)
|
||||
if(LAMMPS_LONGLONG_TO_LONG)
|
||||
target_compile_definitions(lammps INTERFACE -DLAMMPS_LONGLONG_TO_LONG)
|
||||
endif()
|
||||
target_link_libraries(lammps INTERFACE MPI::MPI_CXX)
|
||||
else()
|
||||
target_include_directories(lammps INTERFACE "${LAMMPS_SOURCE_DIR}/STUBS")
|
||||
endif()
|
||||
|
||||
set(LAMMPS_SIZES "smallbig" CACHE STRING "LAMMPS integer sizes (smallsmall: all 32-bit, smallbig: 64-bit #atoms #timesteps, bigbig: also 64-bit imageint, 64-bit atom ids)")
|
||||
set(LAMMPS_SIZES_VALUES smallbig bigbig smallsmall)
|
||||
set_property(CACHE LAMMPS_SIZES PROPERTY STRINGS ${LAMMPS_SIZES_VALUES})
|
||||
validate_option(LAMMPS_SIZES LAMMPS_SIZES_VALUES)
|
||||
string(TOUPPER ${LAMMPS_SIZES} LAMMPS_SIZES)
|
||||
target_compile_definitions(lammps INTERFACE -DLAMMPS_${LAMMPS_SIZES})
|
||||
|
||||
################################################################################
|
||||
# detect if we may enable OpenMP support by default
|
||||
set(BUILD_OMP_DEFAULT OFF)
|
||||
find_package(OpenMP QUIET)
|
||||
if(OpenMP_FOUND)
|
||||
check_include_file_cxx(omp.h HAVE_OMP_H_INCLUDE)
|
||||
if(HAVE_OMP_H_INCLUDE)
|
||||
set(BUILD_OMP_DEFAULT ON)
|
||||
endif()
|
||||
endif()
|
||||
|
||||
option(BUILD_OMP "Build with OpenMP support" ${BUILD_OMP_DEFAULT})
|
||||
|
||||
if(BUILD_OMP)
|
||||
find_package(OpenMP REQUIRED)
|
||||
check_include_file_cxx(omp.h HAVE_OMP_H_INCLUDE)
|
||||
if(NOT HAVE_OMP_H_INCLUDE)
|
||||
message(FATAL_ERROR "Cannot find the 'omp.h' header file required for full OpenMP support")
|
||||
endif()
|
||||
|
||||
if (((CMAKE_CXX_COMPILER_ID STREQUAL "GNU") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 9.0)) OR
|
||||
(CMAKE_CXX_COMPILER_ID STREQUAL "PGI") OR
|
||||
((CMAKE_CXX_COMPILER_ID STREQUAL "Clang") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 10.0)) OR
|
||||
((CMAKE_CXX_COMPILER_ID STREQUAL "Intel") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 19.0)))
|
||||
# GCC 9.x and later plus Clang 10.x and later implement strict OpenMP 4.0 semantics for consts.
|
||||
# Intel 18.0 was tested to support both, so we switch to OpenMP 4+ from 19.x onward to be safe.
|
||||
target_compile_definitions(lammps INTERFACE -DLAMMPS_OMP_COMPAT=4)
|
||||
else()
|
||||
target_compile_definitions(lammps INTERFACE -DLAMMPS_OMP_COMPAT=3)
|
||||
endif()
|
||||
target_link_libraries(lammps INTERFACE OpenMP::OpenMP_CXX)
|
||||
endif()
|
||||
54
examples/kim/plugin/kimplugin.cpp
Normal file
54
examples/kim/plugin/kimplugin.cpp
Normal file
@ -0,0 +1,54 @@
|
||||
|
||||
#include "lammpsplugin.h"
|
||||
#include "version.h"
|
||||
|
||||
#include "pair_kim.h"
|
||||
#include "fix_store_kim.h"
|
||||
#include "kim_command.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
static Pair *pair_kim_creator(LAMMPS *lmp)
|
||||
{
|
||||
return new PairKIM(lmp);
|
||||
}
|
||||
|
||||
static Fix *fix_store_kim_creator(LAMMPS *lmp, int argc, char **argv)
|
||||
{
|
||||
return new FixStoreKIM(lmp, argc, argv);
|
||||
}
|
||||
|
||||
static Command *kim_command_creator(LAMMPS *lmp)
|
||||
{
|
||||
return new KimCommand(lmp);
|
||||
}
|
||||
|
||||
extern "C" void lammpsplugin_init(void *lmp, void *handle, void *regfunc)
|
||||
{
|
||||
lammpsplugin_t plugin;
|
||||
lammpsplugin_regfunc register_plugin = (lammpsplugin_regfunc) regfunc;
|
||||
|
||||
// register kim pair style
|
||||
plugin.version = LAMMPS_VERSION;
|
||||
plugin.style = "pair";
|
||||
plugin.name = "kim";
|
||||
plugin.info = "KIM plugin pair style v1.0";
|
||||
plugin.author = "Axel Kohlmeyer (akohlmey@gmail.com)";
|
||||
plugin.creator.v1 = (lammpsplugin_factory1 *) &pair_kim_creator;
|
||||
plugin.handle = handle;
|
||||
(*register_plugin)(&plugin, lmp);
|
||||
|
||||
// register fix STORE/KIM only need to update changed fields
|
||||
plugin.style = "fix";
|
||||
plugin.name = "STORE/KIM";
|
||||
plugin.info = "Internal settings storage for KIM fix style v1.0";
|
||||
plugin.creator.v2 = (lammpsplugin_factory2 *) &fix_store_kim_creator;
|
||||
(*register_plugin)(&plugin, lmp);
|
||||
|
||||
// register KIM command
|
||||
plugin.style = "command";
|
||||
plugin.name = "kim";
|
||||
plugin.info = "kim command style v1.0";
|
||||
plugin.creator.v1 = (lammpsplugin_factory1 *) &kim_command_creator;
|
||||
(*register_plugin)(&plugin, lmp);
|
||||
}
|
||||
228
examples/mdi/README
Normal file
228
examples/mdi/README
Normal file
@ -0,0 +1,228 @@
|
||||
These are examples that work the MDI package in LAMMPS which uses the
|
||||
MolSSI MDI library for coupling codes together and communicating
|
||||
between them with MDI messages.
|
||||
|
||||
In MDI lingo, one code is the driver and another code is the engine.
|
||||
The 2 codes can be written in any language; C++ (LAMMPS) and Python
|
||||
are illustrated here. The 2 codes can each be stand-alone codes, in
|
||||
which case they can be run on different numbers of processors. The 2
|
||||
codes can communicate either via TCP (sockets) or via MPI. For the
|
||||
TCP case, the driver and engine need to be launched separately,
|
||||
e.g. in 2 windows on your desktop machine. For the MPI case, a single
|
||||
mpirun command launches both codes.
|
||||
|
||||
Alternatively the engine code can be a plugin library which the driver
|
||||
code loads, in which case the driver and engine run on the same
|
||||
processors.
|
||||
|
||||
LAMMPS supports operating in all these MDI modes. It can be an engine
|
||||
operating either as a stand-alone code or as a plugin. It can also be
|
||||
a driver and couple to an engine that is either a stand-alone code or
|
||||
a plugin. Examples for all these use cases are in this directory.
|
||||
The example commands below illustrate how to run all the variants.
|
||||
|
||||
To use LAMMPS as a plugin engine, you must build it as a shared library.
|
||||
Something like this, which also builds the normal LAMMPS executable
|
||||
lmp_mpi:
|
||||
|
||||
cd src
|
||||
make yes-mdi
|
||||
make mode=shlib mpi
|
||||
|
||||
To use the serial_driver.py example you will need Python 3 with Numpy
|
||||
and mpi4py available in your Python. Make sure LAMMPS and Python are
|
||||
using same the same version of MPI.
|
||||
|
||||
-------------------------------------------------
|
||||
-------------------------------------------------
|
||||
|
||||
* Example #1 = run ab inito MD (AIMD)
|
||||
Two instances of LAMMPS operate as a driver and engine
|
||||
As an engine, LAMMPS is a surrogate for a quantum code
|
||||
|
||||
Note that the 2 input scripts in.aimd.alone and in.aimd.driver
|
||||
have an option for running in NVE vs NPT mode. Comment in/out
|
||||
the appropriate line to change modes. Nothing needs to be
|
||||
changed in the in.aimd.engine or in.aimd.engine.plugin scripts.
|
||||
|
||||
---
|
||||
|
||||
Run the entire calculation with a single instance of LAMMPS by itself
|
||||
results should be identical to running this example with MDI
|
||||
|
||||
% lmp_mpi < in.aimd.alone
|
||||
|
||||
With MDI, the thermo output of the driver should match the thermo
|
||||
output of the in.aimd.alone script.
|
||||
|
||||
---
|
||||
|
||||
Run with TCP: 1 proc each
|
||||
|
||||
% lmp_mpi -mdi "-name aimd -role DRIVER -method TCP -port 8021" -log log.aimd.driver -in in.aimd.driver
|
||||
|
||||
% lmp_mpi -mdi "-name LAMMPS -role ENGINE -method TCP -port 8021 -hostname localhost" -log log.aimd.engine -in in.aimd.engine
|
||||
|
||||
---
|
||||
|
||||
Run with TCP: 3 procs + 4 procs
|
||||
|
||||
% mpirun -np 3 lmp_mpi -mdi "-name aimd -role DRIVER -method TCP -port 8021" -log log.aimd.driver -in in.aimd.driver
|
||||
|
||||
% mpirun -np 4 lmp_mpi -mdi "-name LAMMPS -role ENGINE -method TCP -port 8021 -hostname localhost" -log log.aimd.engine -in in.aimd.engine
|
||||
|
||||
---
|
||||
|
||||
Run with MPI: 1 proc each
|
||||
|
||||
% mpirun -np 1 lmp_mpi -mdi "-name aimd -role DRIVER -method MPI" -log log.aimd.driver -in in.aimd.driver : -np 1 lmp_mpi -mdi "-name LAMMPS -role ENGINE -method MPI" -log log.aimd.engine -in in.aimd.engine
|
||||
|
||||
---
|
||||
|
||||
Run with MPI: 3 procs + 4 procs
|
||||
|
||||
% mpirun -np 3 lmp_mpi -mdi "-name aimd -role DRIVER -method MPI" -log log.aimd.driver -in in.aimd.driver : -np 4 lmp_mpi -mdi "-name LAMMPS -role ENGINE -method MPI" -log log.aimd.engine -in in.aimd.engine
|
||||
|
||||
---
|
||||
|
||||
Run in plugin mode: 1 proc
|
||||
|
||||
% lmp_mpi -mdi "-name aimd -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/src" -log log.aimd.driver.plugin -in in.aimd.driver.plugin
|
||||
|
||||
---
|
||||
|
||||
Run in plugin mode: 3 procs
|
||||
|
||||
% mpirun -np 3 lmp_mpi -mdi "-name aimd -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/src" -log log.aimd.driver.plugin -in in.aimd.driver.plugin
|
||||
|
||||
-------------------------------------------------
|
||||
-------------------------------------------------
|
||||
|
||||
* Example #2 = Python driver runs a sequence of unrelated LAMMPS calculations
|
||||
Each calculation can be a single-point evaluation, MD run, or minimization
|
||||
|
||||
The sequence_driver.py code allows for optional switches in addition
|
||||
to -mdi (required) and the -plugin and -plugin_args switches which are
|
||||
used to link to an engine as a plugin library. The example run
|
||||
commands below just use the default values of the optional switches.
|
||||
The switches are also explained at the top of the file; the info is
|
||||
copied here:
|
||||
|
||||
# -n 3
|
||||
# number of calculations to perform, default = 3
|
||||
# -mode eval/run/min
|
||||
# style of calculations: single snapshot evals, dynamics, minimization
|
||||
# default = run
|
||||
# -size Nx Ny Nz
|
||||
# cubic lattice, default = 2 2 2
|
||||
# -rho 0.75 0.1
|
||||
# reduced density and random variation thereof, default = 0.75 0.1
|
||||
# -delta 0.1
|
||||
# randomly perturb atoms initially by this distance, default 0.1
|
||||
# -nsteps 100
|
||||
# number of timesteps in dynamics runs, default = 100
|
||||
# -temp 1.0
|
||||
# initial temperature in dynamics runs, default = 1.0
|
||||
# -tol 0.001
|
||||
# tolerance for minimizations, default = 0.001
|
||||
# -seed 12345
|
||||
# random number seed > 0, default = 12345
|
||||
|
||||
---
|
||||
|
||||
Run with TCP: 1 proc each
|
||||
|
||||
% python3 sequence_driver.py -mdi "-role DRIVER -name sequence -method TCP -port 8021"
|
||||
|
||||
% lmp_mpi -mdi "-role ENGINE -name LAMMPS -method TCP -port 8021 -hostname localhost" -log log.sequence -in in.sequence
|
||||
|
||||
---
|
||||
|
||||
Run with TCP: 2 proc + 4 procs
|
||||
|
||||
% mpirun -np 2 python3 sequence_driver.py -mdi "-role DRIVER -name sequence -method TCP -port 8021"
|
||||
|
||||
% mpirun -np 4 lmp_mpi -mdi "-role ENGINE -name LAMMPS -method TCP -port 8021 -hostname localhost" -log log.sequence -in in.sequence
|
||||
|
||||
---
|
||||
|
||||
Run with MPI: 1 proc each
|
||||
|
||||
% mpirun -np 1 python3 sequence_driver.py -mdi "-role DRIVER -name sequence -method MPI" : -np 1 lmp_mpi -mdi "-role ENGINE -name LAMMPS -method MPI" -log log.sequence -in in.sequence
|
||||
|
||||
---
|
||||
|
||||
Run with MPI: 2 procs + 4 procs
|
||||
|
||||
% mpirun -np 2 python3 sequence_driver.py -mdi "-role DRIVER -name sequence -method MPI" : -np 4 lmp_mpi -mdi "-role ENGINE -name LAMMPS -method MPI" -log log.sequence -in in.sequence
|
||||
|
||||
---
|
||||
|
||||
Run in plugin mode: 1 proc
|
||||
|
||||
% python3 sequence_driver.py -plugin lammps -mdi "-role DRIVER -name sequence -method LINK -plugin_path /home/sjplimp/lammps/git/src" -plugin_args "-log log.sequence -in in.sequence"
|
||||
|
||||
---
|
||||
|
||||
Run in plugin mode: 3 procs
|
||||
|
||||
% mpirun -np 3 python3 sequence_driver.py -plugin lammps -mdi "-role DRIVER -name sequence -method LINK -plugin_path /home/sjplimp/lammps/git/src" -plugin_args "-log log.sequence -in in.sequence"
|
||||
|
||||
-------------------------------------------------
|
||||
-------------------------------------------------
|
||||
|
||||
* Example #3 = run AIMD with Python driver code and 2 LAMMPS instances as engines
|
||||
First LAMMPS instance performs the MD timestepping
|
||||
Second LAMMPS instance is surrogate QM = computes forces
|
||||
|
||||
The aimd_driver.py code allows for an optional switch in addition to
|
||||
-mdi (required) and the -plugin and -plugin_args swiches which are
|
||||
used to link to the 2 engines as a plugin libraries. The example run
|
||||
commands below use the default values of the optional switch. The
|
||||
switch is also explained the top of the file; the info is copied
|
||||
here:
|
||||
|
||||
# -nsteps 5
|
||||
# number of timesteps in dynamics runs, default = 5
|
||||
|
||||
---
|
||||
|
||||
Run the entire calculation with a single instance of LAMMPS by itself
|
||||
results should be identical to running this example with MDI
|
||||
|
||||
% lmp_mpi < in.aimd.alone
|
||||
|
||||
With MDI, the driver prints the QM and Total energies. These should
|
||||
match the PotEng and TotEng output of the in.aimd.alone script.
|
||||
|
||||
---
|
||||
|
||||
Run with TCP: 1 proc each
|
||||
|
||||
% python3 aimd_driver.py -mdi "-role DRIVER -name aimd -method TCP -port 8021"
|
||||
|
||||
% lmp_mpi -mdi "-role ENGINE -name MM -method TCP -port 8021 -hostname localhost" -log log.aimd.mm -in in.aimd.mm
|
||||
|
||||
% lmp_mpi -mdi "-role ENGINE -name QM -method TCP -port 8021 -hostname localhost" -log log.aimd.qm -in in.aimd.qm
|
||||
|
||||
---
|
||||
|
||||
Run with TCP: 2 procs + 2 procs + 3 procs
|
||||
|
||||
% mpirun -np 2 python3 aimd_driver.py -mdi "-role DRIVER -name aimd -method TCP -port 8021"
|
||||
|
||||
% mpirun -np 2 lmp_mpi -mdi "-role ENGINE -name MM -method TCP -port 8021 -hostname localhost" -log log.aimd.mm -in in.aimd.mm
|
||||
|
||||
% mpirun -np 3 lmp_mpi -mdi "-role ENGINE -name QM -method TCP -port 8021 -hostname localhost" -log log.aimd.qm -in in.aimd.qm
|
||||
|
||||
---
|
||||
|
||||
Run with MPI: 1 proc each
|
||||
|
||||
% mpirun -np 1 python3 aimd_driver.py -mdi "-role DRIVER -name aimd -method MPI" : -np 1 lmp_mpi -mdi "-role ENGINE -name MM -method MPI" -log log.aimd.mm -in in.aimd.mm : -np 1 lmp_mpi -mdi "-role ENGINE -name QM -method MPI" -log log.aimd.qm -in in.aimd.qm
|
||||
|
||||
---
|
||||
|
||||
Run with MPI: 2 procs + 2 procs + 3 procs
|
||||
|
||||
% mpirun -np 2 python3 aimd_driver.py -mdi "-role DRIVER -name aimd -method MPI" : -np 2 lmp_mpi -mdi "-role ENGINE -name MM -method MPI" -log log.aimd.mm -in in.aimd.mm : -np 3 lmp_mpi -mdi "-role ENGINE -name QM -method MPI" -log log.aimd.qm -in in.aimd.qm
|
||||
255
examples/mdi/aimd_driver.py
Normal file
255
examples/mdi/aimd_driver.py
Normal file
@ -0,0 +1,255 @@
|
||||
# MDI driver to perform an AIMD simulation
|
||||
# using one instance of LAMMPS as the MD timestepper
|
||||
# using second instance of LAMMPS as a QM surrogate to compute forces
|
||||
|
||||
# NOTE: this script is derived from the MDI_AIMD_Driver.cpp code
|
||||
# included in the MDI distribution
|
||||
# it alters the timestepping to match a velocity Verlet algorithm
|
||||
# forces are computed once before timestepping beings
|
||||
# both the @COORDS and @FORCES nodes are triggered in the MM code
|
||||
# as the appropriate places to extract COORDS and provide FORCES
|
||||
|
||||
# Syntax: python3 aimd_driver.py switch arg switch arg ...
|
||||
# possible switches:
|
||||
# -mdi "-role DRIVER ..."
|
||||
# required switch
|
||||
# example for stand-alone mode:
|
||||
# -mdi "-role DRIVER -name sequence -method TCP -port 8021"
|
||||
# example for plugin mode:
|
||||
# -mdi "-role DRIVER -name sequemce -method LINK
|
||||
# -plugin_path /home/sjplimp/lammps/src/"
|
||||
# -plugin name
|
||||
# name of plugin library, only when using plugin mode
|
||||
# -plugin_args arglist
|
||||
# args to add when launching plugin library, only when using plugin mode
|
||||
# enclose arglist in quotes if multiple words
|
||||
# -nsteps 5
|
||||
# number of timesteps, default = 5
|
||||
|
||||
import sys,math,random
|
||||
import mdi
|
||||
import numpy as np
|
||||
from mpi4py import MPI
|
||||
|
||||
# error message
|
||||
|
||||
def error(txt=None):
|
||||
if txt: raise Exception(txt)
|
||||
raise Exception("Syntax: python3 aimd_driver.py switch arg switch arg ...")
|
||||
|
||||
# run an AIMD simulation
|
||||
|
||||
def perform_aimd(world,mm_comm,qm_comm):
|
||||
|
||||
me = world.Get_rank()
|
||||
nprocs = world.Get_size()
|
||||
|
||||
# receive number of atoms from the MM engine
|
||||
|
||||
mdi.MDI_Send_command("<NATOMS",mm_comm)
|
||||
natoms = mdi.MDI_Recv(1,mdi.MDI_INT,mm_comm)
|
||||
natoms = world.bcast(natoms,root=0)
|
||||
|
||||
# allocate arrays for coordinates and forces
|
||||
|
||||
coords = np.zeros(3*natoms,dtype=np.float64)
|
||||
forces = np.zeros(3*natoms,dtype=np.float64)
|
||||
|
||||
# MM engine initializes a new MD simulation
|
||||
|
||||
mdi.MDI_Send_command("@INIT_MD",mm_comm)
|
||||
|
||||
# -----------------
|
||||
# compute initial forces for Verlet timestepping
|
||||
# and initial energy for output on step 0
|
||||
# -----------------
|
||||
|
||||
# MM engine proceeds to @FORCES node in setup()
|
||||
|
||||
mdi.MDI_Send_command("@FORCES",mm_comm)
|
||||
|
||||
# get coords from MM engine
|
||||
|
||||
mdi.MDI_Send_command("<COORDS",mm_comm)
|
||||
mdi.MDI_Recv(3*natoms,mdi.MDI_DOUBLE,mm_comm,buf=coords)
|
||||
world.Bcast(coords,root=0)
|
||||
|
||||
# send coords to QM engine
|
||||
|
||||
mdi.MDI_Send_command(">COORDS",qm_comm)
|
||||
mdi.MDI_Send(coords,3*natoms,mdi.MDI_DOUBLE,qm_comm)
|
||||
|
||||
# get QM potential energy
|
||||
|
||||
mdi.MDI_Send_command("<PE",qm_comm)
|
||||
qm_pe = mdi.MDI_Recv(1,mdi.MDI_DOUBLE,qm_comm)
|
||||
qm_pe = world.bcast(qm_pe,root=0)
|
||||
|
||||
# get forces from QM engine
|
||||
|
||||
mdi.MDI_Send_command("<FORCES",qm_comm)
|
||||
mdi.MDI_Recv(3*natoms,mdi.MDI_DOUBLE,qm_comm,buf=forces)
|
||||
world.Bcast(forces,root=0)
|
||||
|
||||
# send forces to MM engine
|
||||
|
||||
mdi.MDI_Send_command(">FORCES",mm_comm)
|
||||
mdi.MDI_Send(forces,3*natoms,mdi.MDI_DOUBLE,mm_comm)
|
||||
|
||||
# get MM kinetic energy
|
||||
|
||||
mdi.MDI_Send_command("<KE",mm_comm)
|
||||
mm_ke = mdi.MDI_Recv(1,mdi.MDI_DOUBLE,mm_comm)
|
||||
mm_ke = world.bcast(mm_ke,root=0)
|
||||
|
||||
# output by driver
|
||||
# normalize energies by atom count
|
||||
|
||||
if me == 0:
|
||||
print("Step %d: MM energy %g, QM energy %g, Total energy %g" % \
|
||||
(0,mm_ke/natoms,qm_pe/natoms,(mm_ke+qm_pe)/natoms))
|
||||
|
||||
# -----------------
|
||||
# timestepping loop
|
||||
# -----------------
|
||||
|
||||
for istep in range(nsteps):
|
||||
|
||||
# MM engine proceeds to @FORCES node
|
||||
|
||||
mdi.MDI_Send_command("@FORCES",mm_comm)
|
||||
|
||||
# get coords from MM engine
|
||||
|
||||
mdi.MDI_Send_command("<COORDS",mm_comm)
|
||||
mdi.MDI_Recv(3*natoms,mdi.MDI_DOUBLE,mm_comm,buf=coords)
|
||||
world.Bcast(coords,root=0)
|
||||
|
||||
# send coords to QM engine
|
||||
|
||||
mdi.MDI_Send_command(">COORDS",qm_comm)
|
||||
mdi.MDI_Send(coords,3*natoms,mdi.MDI_DOUBLE,qm_comm)
|
||||
|
||||
# get QM potential energy
|
||||
|
||||
mdi.MDI_Send_command("<PE",qm_comm)
|
||||
qm_pe = mdi.MDI_Recv(1,mdi.MDI_DOUBLE,qm_comm)
|
||||
qm_pe = world.bcast(qm_pe,root=0)
|
||||
|
||||
# get forces from QM engine
|
||||
|
||||
mdi.MDI_Send_command("<FORCES",qm_comm)
|
||||
mdi.MDI_Recv(3*natoms,mdi.MDI_DOUBLE,qm_comm,buf=forces)
|
||||
world.Bcast(forces,root=0)
|
||||
|
||||
# send forces to MM engine
|
||||
|
||||
mdi.MDI_Send_command(">FORCES",mm_comm)
|
||||
mdi.MDI_Send(forces,3*natoms,mdi.MDI_DOUBLE,mm_comm)
|
||||
|
||||
# MM engine proceeds to @ENDSTEP node
|
||||
# so that KE will be for fully updated velocity
|
||||
|
||||
mdi.MDI_Send_command("@ENDSTEP",mm_comm)
|
||||
|
||||
# get MM kinetic energy
|
||||
|
||||
mdi.MDI_Send_command("<KE",mm_comm)
|
||||
mm_ke = mdi.MDI_Recv(1,mdi.MDI_DOUBLE,mm_comm)
|
||||
mm_ke = world.bcast(mm_ke,root=0)
|
||||
|
||||
# output by driver
|
||||
# normalize energies by atom count
|
||||
|
||||
if me == 0:
|
||||
print("Step %d: MM energy %g, QM energy %g, Total energy %g" % \
|
||||
(istep+1,mm_ke/natoms,qm_pe/natoms,(mm_ke+qm_pe)/natoms))
|
||||
|
||||
# send EXIT to each engine
|
||||
|
||||
mdi.MDI_Send_command("EXIT",mm_comm)
|
||||
mdi.MDI_Send_command("EXIT",qm_comm)
|
||||
|
||||
# ------------------------
|
||||
# main program
|
||||
# ------------------------
|
||||
|
||||
args = sys.argv[1:]
|
||||
narg = len(args)
|
||||
|
||||
# defaults for command-line args
|
||||
|
||||
mdiarg = ""
|
||||
plugin = ""
|
||||
plugin_args = ""
|
||||
|
||||
nsteps = 5
|
||||
|
||||
# parse command-line args
|
||||
|
||||
iarg = 0
|
||||
while iarg < narg:
|
||||
if args[iarg] == "-mdi":
|
||||
if iarg+2 > narg: error()
|
||||
mdiarg = args[iarg+1]
|
||||
iarg += 2
|
||||
elif args[iarg] == "-plugin":
|
||||
if iarg+2 > narg: error()
|
||||
plugin = args[iarg+1]
|
||||
iarg += 2
|
||||
elif args[iarg] == "-plugin_args":
|
||||
if iarg+2 > narg: error()
|
||||
plugin_args = args[iarg+1]
|
||||
iarg += 2
|
||||
elif args[iarg] == "-nsteps":
|
||||
if iarg+2 > narg: error()
|
||||
nsteps = int(args[iarg+1])
|
||||
if nsteps < 0: error()
|
||||
iarg += 2
|
||||
else: error()
|
||||
|
||||
if not mdiarg: error()
|
||||
|
||||
# LAMMPS engines are stand-alone codes
|
||||
# world = MPI communicator for just this driver
|
||||
# invoke perform_tasks() directly
|
||||
|
||||
if not plugin:
|
||||
mdi.MDI_Init(mdiarg)
|
||||
world = mdi.MDI_MPI_get_world_comm()
|
||||
|
||||
# connect to 2 engines, determine which is MM vs QM
|
||||
|
||||
mdicomm1 = mdi.MDI_Accept_Communicator()
|
||||
mdicomm2 = mdi.MDI_Accept_Communicator()
|
||||
|
||||
mdi.MDI_Send_command("<NAME",mdicomm1)
|
||||
name1 = mdi.MDI_Recv(mdi.MDI_NAME_LENGTH,mdi.MDI_CHAR,mdicomm1)
|
||||
name1 = world.bcast(name1,root=0)
|
||||
mdi.MDI_Send_command("<NAME",mdicomm2)
|
||||
name2 = mdi.MDI_Recv(mdi.MDI_NAME_LENGTH,mdi.MDI_CHAR,mdicomm2)
|
||||
name2 = world.bcast(name2,root=0)
|
||||
|
||||
if name1 == "MM" and name2 == "QM":
|
||||
mm_comm = mdicomm1
|
||||
qm_comm = mdicomm2
|
||||
elif name1 == "QM" and name2 == "MM":
|
||||
mm_comm = mdicomm2
|
||||
qm_comm = mdicomm1
|
||||
else: error("Two engines have invalid names")
|
||||
|
||||
perform_aimd(world,mm_comm,qm_comm)
|
||||
|
||||
# LAMMPS engines are plugin libraries
|
||||
# launch plugins
|
||||
# NOTE: need to run driver on 2 or more procs
|
||||
# partition driver into 2 MPI comms
|
||||
# launch one plugin on each partition
|
||||
# each with their own callback function
|
||||
|
||||
if plugin:
|
||||
error("Cannot yet run in plugin mode")
|
||||
mdi.MDI_Init(mdiarg)
|
||||
world = MPI.COMM_WORLD
|
||||
plugin_args += " -mdi \"-role ENGINE -name lammps -method LINK\""
|
||||
mdi.MDI_Launch_plugin(plugin,plugin_args,world,perform_tasks,None)
|
||||
@ -1,4 +1,4 @@
|
||||
# 3d Lennard-Jones melt - no client/server mode
|
||||
# 3d Lennard-Jones melt - MDI driver script
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
@ -21,9 +21,12 @@ pair_coeff 1 1 1.0 1.0 2.5
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
# NVE
|
||||
fix 1 all nve
|
||||
# same with NPT
|
||||
#fix 1 all npt temp 1.0 1.0 0.1 iso 1 1 1.0
|
||||
# NPT
|
||||
#fix 1 all npt temp 1.0 1.0 0.1 iso 1.0 1.0 1.0
|
||||
|
||||
thermo 10
|
||||
run 50
|
||||
thermo_style custom step temp pe etotal press vol
|
||||
thermo 1
|
||||
|
||||
run 5
|
||||
32
examples/mdi/in.aimd.driver
Normal file
32
examples/mdi/in.aimd.driver
Normal file
@ -0,0 +1,32 @@
|
||||
# 3d Lennard-Jones melt - MDI driver script
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
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
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
# NVE
|
||||
fix 1 all nve
|
||||
# NPT
|
||||
#fix 1 all npt temp 1.0 1.0 0.1 iso 1.0 1.0 1.0
|
||||
|
||||
fix 2 all mdi/aimd
|
||||
fix_modify 2 energy yes virial yes
|
||||
|
||||
thermo_style custom step temp pe etotal press vol
|
||||
thermo 1
|
||||
|
||||
run 5
|
||||
34
examples/mdi/in.aimd.driver.plugin
Normal file
34
examples/mdi/in.aimd.driver.plugin
Normal file
@ -0,0 +1,34 @@
|
||||
# 3d Lennard-Jones melt - MDI driver script
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
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
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
# NVE
|
||||
fix 1 all nve
|
||||
# NPT
|
||||
#fix 1 all npt temp 1.0 1.0 0.1 iso 1.0 1.0 1.0
|
||||
|
||||
fix 2 all mdi/aimd
|
||||
fix_modify 2 energy yes virial yes
|
||||
|
||||
thermo_style custom step temp pe etotal press vol
|
||||
thermo 1
|
||||
|
||||
mdi plugin lammps mdi "-role ENGINE -name lammps -method LINK" &
|
||||
infile in.aimd.engine extra "-log log.aimd.engine.plugin" &
|
||||
command "run 5"
|
||||
22
examples/mdi/in.aimd.engine
Normal file
22
examples/mdi/in.aimd.engine
Normal file
@ -0,0 +1,22 @@
|
||||
# 3d Lennard-Jones melt - MDI engine script
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
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 1 check yes
|
||||
|
||||
mdi engine
|
||||
23
examples/mdi/in.aimd.mm
Normal file
23
examples/mdi/in.aimd.mm
Normal file
@ -0,0 +1,23 @@
|
||||
# 3d Lennard-Jones melt - LAMMPS as MM engine for aimd_driver.py
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
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
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
mdi engine
|
||||
22
examples/mdi/in.aimd.qm
Normal file
22
examples/mdi/in.aimd.qm
Normal file
@ -0,0 +1,22 @@
|
||||
# 3d Lennard-Jones melt - LAMMPS as surrogate QM engine for aimd_driver.py
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
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 1 check yes
|
||||
|
||||
mdi engine
|
||||
21
examples/mdi/in.sequence
Normal file
21
examples/mdi/in.sequence
Normal file
@ -0,0 +1,21 @@
|
||||
# MDI engine script to process a series of evaulate, run, minimize commands
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
region box block 0 1 0 1 0 1
|
||||
create_box 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 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
thermo 10
|
||||
|
||||
mdi engine
|
||||
Some files were not shown because too many files have changed in this diff Show More
Reference in New Issue
Block a user