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test_lammps.py
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Tue, Mar 11, 19:12

test_lammps.py
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#!/usr/bin/python3
import pylibmultiscale as lm
import numpy as np
import cv2
lm.loadModules()
Dim = 3
comm = lm.Communicator.getCommunicator()
nb_proc = comm.getNumberFreeProcs()
comm.addGroup('md', nb_proc)
md_group = lm.Communicator.getGroup('md')
A = 4.047971240341177
L = 200
class ImageGeom(lm.Geometry):
def __init__(self, center, name, filename):
super().__init__(3, name)
self.center = np.array(center)
self.img = np.array(cv2.imread(filename))
# import matplotlib.pyplot as plt
# print(self.img.shape)
# print(self.img)
# plt.imshow(np.linalg.norm(self.img, axis=2))
# plt.show()
def init(self):
pass
def contains(self, x, y, z):
_x = int((x - self.center[0]))
_y = int((y - self.center[1]))
_x += int(self.img.shape[0]/2)
_y += int(self.img.shape[1]/2)
if _x > self.img.shape[0]-1 or _x < 0:
return False
if _y > self.img.shape[1]-1 or _y < 0:
return False
if (self.img[_x, _y, :] == [255, 255, 255]).all():
return False
return True
gManager = lm.GeometryManager.getManager()
gManager.reset()
pineapple = ImageGeom((0, -100*A, 0), 'pineapple', 'pineapple.png')
pizza = ImageGeom((0, 100*A, 0), 'pizza', 'pizza.png')
gManager.addGeometry(pineapple)
gManager.addGeometry(pizza)
cube = lm.GeomUnion(3, 'md_geom')
cube.params.ids = ['pineapple', 'pizza']
cube.init()
gManager.addGeometry(cube)
lm.FilterManager.destroy()
lm.ActionManager.destroy()
lm.DomainMultiScale.destroy()
dom = lm.DomainLammps3('md', md_group)
open("lammps.in", 'w').write("""
mass * 26.98153860
pair_style lj/cut 6.03863042319
pair_coeff * * 2.4621 2.596037
fix 2 all nve
""")
dom.params.lammps_file = "lammps.in"
dom.params.create_header = True
dom.params.boundary = ['s', 's', 'p']
dom.params.lattice = 'fcc'
dom.params.lattice_size = A
dom.params.domain_geometry = "md_geom"
dom.params.replica = [-3*L, 3*L, -L, L, 0, 1]
dom.params.lattice_origin = [.1, .1, .1]
dom.params.timestep = 1.
dom.init()
lm.DomainMultiScale.getManager().addObject(dom)
atoms_pineapple = lm.FilterGeometry('atoms_pineapple')
atoms_pineapple.params.geometry = 'pineapple'
atoms_pineapple.init()
atoms_pineapple.compute(dom.getContainer())
atoms_pizza = lm.FilterGeometry('atoms_pizza')
atoms_pizza.params.geometry = 'pizza'
atoms_pizza.init()
atoms_pizza.compute(dom.getContainer())
vel = lm.ComputeExtract('vel_pineapple')
vel.params.field = lm.velocity
vel.init()
vel.compute(atoms_pineapple.evalOutput())
imposed_vel = vel.evalOutput().array().copy()
imposed_vel[:] = [0., 10., 0.]
impose = lm.StimulationField('stim_vel')
impose.params.field = lm.velocity
impose.init()
impose.compute(dofs=atoms_pineapple.evalOutput(), field=imposed_vel)
dumper = lm.DumperParaview('dumper')
dumper.params.input = 'md'
dumper.params.force = True
dumper.params.disp = True
dumper.params.vel = True
dumper.init()
dumper.dump()
nb_step = 10000
for current_step in range(nb_step):
lm.current_step.fset(current_step)
current_time += min_dt
if shouldPrintState:
printState()
print('current_stage: ', lm.current_stage.fget())
lm.current_stage.fset(lm.PRE_DUMP)
actions.action()
lm.current_stage.fset(lm.PRE_STEP1)
actions.action()
dom.performStep1()
dom.coupling(lm.COUPLING_STEP1)
lm.current_stage.fset(lm.PRE_STEP2)
actions.action()
dom.performStep2()
dom.coupling(lm.COUPLING_STEP2)
lm.current_stage.fset(lm.PRE_STEP3)
actions.action()
dom.performStep3()
dom.coupling(lm.COUPLING_STEP3)
lm.current_stage.fset(lm.PRE_STEP4)
actions.action()
dom.coupling(lm.COUPLING_STEP4)
comm.Barrier()

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