Add MDI example
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taylor-a-barnes
29
examples/USER/mdi/README
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examples/USER/mdi/README
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This dir contains scripts that demonstrate how to use LAMMPS as an
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MDI engine. LAMMPS as an engine performs the MD timestepping.
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The driver is a simple Python script. Every timestep the driver
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sends one or more commands to LAMMPS.
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See the MDI package documentation Build_extras.html#mdi and
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Build_extras.html#mdi for more details on how the LAMMPS MDI
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implementation works.
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--------------
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NOTE: the Script.sh file has comands to perform all the
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runs listed below.
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--------------
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File or ZMQ or mpi/two modes of messaging:
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% mpirun -np 1 lmp_mpi -v mode file -log log.client -in in.message.client &
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% mpirun -np 2 lmp_mpi -v mode file -log log.server -in in.message.server
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% mpirun -np 4 lmp_mpi -v mode zmq -log log.client -in in.message.client &
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% mpirun -np 1 lmp_mpi -v mode zmq -log log.server -in in.message.server
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% mpirun -np 2 lmp_mpi -v mode mpitwo -log log.client -in in.message.client &
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% mpirun -np 4 lmp_mpi -v mode mpitwo -log log.server -in in.message.server
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Or run with in.message.tilt.client/server.
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Don't run the tilt files with the "file" mode; they run too slow.
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13
examples/USER/mdi/Script.sh
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examples/USER/mdi/Script.sh
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#!/bin/bash
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# sample launch scripts
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# TCP, running LAMMPS on one proc
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python driver.py -mdi "-name driver -role DRIVER -method TCP -port 8021" &
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../../../src/lmp_mdi -mdi "-name LAMMPS -role ENGINE -method TCP -port 8021 -hostname localhost" -in lammps.in > lammps.out &
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wait
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# MPI, running LAMMPS on one proc
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mpirun -n 1 python driver.py -mdi "-name driver -role DRIVER -method MPI" : -n 1 ../../../src/lmp_mdi -mdi "-name LAMMPS -role ENGINE -method MPI"
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17
examples/USER/mdi/driver.py
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examples/USER/mdi/driver.py
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import sys
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import mdi
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# Initialize the MDI Library
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mdi.MDI_Init(sys.argv[2])
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# Connect to the engine
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comm = mdi.MDI_Accept_communicator()
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# Determine the name of the engine
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mdi.MDI_Send_Command("<NAME", comm)
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name = mdi.MDI_Recv(mdi.MDI_NAME_LENGTH, mdi.MDI_CHAR, comm)
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print("Engine name: " + str(name))
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# Send the "EXIT" command to the engine
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mdi.MDI_Send_Command("EXIT", comm)
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92
examples/USER/mdi/lammps.data
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examples/USER/mdi/lammps.data
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LAMMPS data file for water
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24 atoms
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16 bonds
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8 angles
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0 dihedrals
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0 impropers
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2 atom types
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1 bond types
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1 angle types
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0 dihedral types
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0 improper types
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0.0 4.9325 xlo xhi
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0.0 4.9325 ylo yhi
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0.0 4.9325 zlo zhi
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Masses
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1 15.9994
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2 1.008
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Pair Coeffs
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1 0.102 3.188
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2 0.000 0.000
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Bond Coeffs
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1 450 0.9572
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Angle Coeffs
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1 55.0 104.52
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Atoms
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1 0 1 -0.83400 2.17919 0.196156 4.15513
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2 0 2 0.41700 2.29785 4.8353 0.126003
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3 0 2 0.41700 1.82037 1.07996 4.23498
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4 0 1 -0.83400 4.65839 0.120414 0.305758
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5 0 2 0.41700 4.67446 -0.0220991 4.29186
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6 0 2 0.41700 4.28188 0.994196 0.410515
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7 0 1 -0.83400 3.65045 2.40907 0.344349
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8 0 2 0.41700 3.52052 2.1838 4.35565
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9 0 2 0.41700 4.26579 3.14208 0.327669
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10 0 1 -0.83400 1.21327 2.62177 4.15519
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11 0 2 0.41700 1.47452 3.53837 4.0667
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12 0 2 0.41700 1.20743 2.46396 0.16677
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13 0 1 -0.83400 4.45777 4.47325 2.74192
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14 0 2 0.41700 4.53396 4.49652 1.78804
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15 0 2 0.41700 4.21354 3.56943 2.94119
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16 0 1 -0.83400 2.04119 4.41585 1.64725
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17 0 2 0.41700 2.26934 4.77582 2.50434
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18 0 2 0.41700 1.69079 3.54574 1.83793
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19 0 1 -0.83400 3.73384 1.97964 2.81949
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20 0 2 0.41700 3.41083 2.22014 1.95113
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21 0 2 0.41700 3.91914 1.04272 2.75561
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22 0 1 -0.83400 1.20859 2.09853 1.68186
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23 0 2 0.41700 1.01865 2.25693 2.60655
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24 0 2 0.41700 1.16884 1.14674 1.58832
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Bonds
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1 1 1 2
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2 1 1 3
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3 1 4 5
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4 1 4 6
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5 1 7 8
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6 1 7 9
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7 1 10 11
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8 1 10 12
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9 1 13 14
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10 1 13 15
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11 1 16 17
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12 1 16 18
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13 1 19 20
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14 1 19 21
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15 1 22 23
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16 1 22 24
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Angles
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1 1 2 1 3
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2 1 5 4 6
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3 1 8 7 9
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4 1 11 10 12
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5 1 14 13 15
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6 1 17 16 18
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7 1 20 19 21
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8 1 23 22 24
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28
examples/USER/mdi/lammps.in
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28
examples/USER/mdi/lammps.in
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units real
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neigh_modify delay 0 every 1 check yes
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atom_style full
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bond_style harmonic
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angle_style harmonic
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pair_style lj/cut/coul/long 10.0
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pair_modify mix arithmetic
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kspace_style pppm 1e-4
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special_bonds amber
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atom_modify sort 0 0
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read_data lammps.data
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timestep 1.0
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dump 1 all custom 1 dump.lammpstrj id element xu yu zu
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dump 2 all custom 1 dump.force id element fx fy fz
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dump 3 all xyz 1 dump.xyz
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dump_modify 1 element O H
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dump_modify 2 element O H
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thermo_style multi
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thermo 1
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fix 1 all nvt temp 300.0 300.0 70.0
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mdi_engine
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