forked from lijiext/lammps
96 lines
2.2 KiB
Python
Executable File
96 lines
2.2 KiB
Python
Executable File
#!/usr/bin/env python -i
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# preceding line should have path for Python on your machine
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# simple.py
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# Purpose: mimic operation of examples/COUPLE/simple/simple.cpp via Python
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# Serial syntax: simple.py in.lammps
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# in.lammps = LAMMPS input script
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# Parallel syntax: mpirun -np 4 simple.py in.lammps
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# in.lammps = LAMMPS input script
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# also need to uncomment either Pypar or mpi4py sections below
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from __future__ import print_function
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import sys
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import numpy as np
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import ctypes
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# parse command line
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argv = sys.argv
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if len(argv) != 2:
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print("Syntax: simple.py in.lammps")
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sys.exit()
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infile = sys.argv[1]
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me = 0
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# uncomment this if running in parallel via Pypar
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#import pypar
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#me = pypar.rank()
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#nprocs = pypar.size()
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# uncomment this if running in parallel via mpi4py
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#from mpi4py import MPI
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#me = MPI.COMM_WORLD.Get_rank()
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#nprocs = MPI.COMM_WORLD.Get_size()
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from lammps import lammps
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lmp = lammps()
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# run infile one line at a time
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lines = open(infile,'r').readlines()
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for line in lines: lmp.command(line)
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# run 10 more steps
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# get coords from LAMMPS
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# change coords of 1st atom
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# put coords back into LAMMPS
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# run a single step with changed coords
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lmp.command("run 10")
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x = lmp.gather_atoms("x",1,3)
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v = lmp.gather_atoms("v",1,3)
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epsilon = 0.1
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x[0] += epsilon
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lmp.scatter_atoms("x",1,3,x)
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lmp.command("run 1");
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# extract force on single atom two different ways
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f = lmp.extract_atom("f",3)
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print("Force on 1 atom via extract_atom: ",f[0][0])
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fx = lmp.extract_variable("fx","all",1)
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print("Force on 1 atom via extract_variable:",fx[0])
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# use commands_string() and commands_list() to invoke more commands
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strtwo = "run 10\nrun 20"
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lmp.commands_string(strtwo)
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cmds = ["run 10","run 20"]
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lmp.commands_list(cmds)
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# delete all atoms
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# create_atoms() to create new ones with old coords, vels
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# initial thermo should be same as step 20
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natoms = lmp.get_natoms()
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type = natoms*[1]
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lmp.command("delete_atoms group all");
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lmp.create_atoms(natoms,None,type,x,v);
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lmp.command("run 10");
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# uncomment if running in parallel via Pypar
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#print("Proc %d out of %d procs has" % (me,nprocs), lmp)
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#pypar.finalize()
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# uncomment if running in parallel via mpi4py
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#print "Proc %d out of %d procs has" % (me,nprocs), lmp
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#MPI.Finalize()
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