from ovito.io import import_file
from ovito.modifiers import ConstructSurfaceModifier
from ovito.modifiers import DeleteSelectedParticlesModifier
from ovito.modifiers import SelectParticleTypeModifier
import sys
# Load a particle structure and construct its geometric surface:
fname = sys.argv[1]
node = import_file(fname, columns=["Particle Type", "Position.X", "Position.Y",
"Position.Z"])
mod = ConstructSurfaceModifier(radius = 2.9)
node.modifiers.append(mod)
node.compute()
# Query computed surface properties:
print("Surface area: %f" % node.output.attributes['ConstructSurfaceMesh.surface_area'])
print("Solid volume: %f" % node.output.attributes['ConstructSurfaceMesh.solid_volume'])
fraction = node.output.attributes['ConstructSurfaceMesh.solid_volume'] / node.output.cell.volume
print("Solid volume fraction: %f" % fraction)
# Export the surface triangle mesh to a VTK file.
mesh = node.output.surface
mesh.export_vtk('surface.vtk', node.output.cell)
help="The concentration of surafce TMS in C3H9Si/nm^2")
args = parser.parse_args()
node = import_file(args.filename)
print("... loading %s"%(args.filename) )
print("... %d files"%(node.source.num_frames))
print("... cutoff for core region %d A"%(args.coreCutoff))
#### Create a bonds modifier (mod) and apply it to the system
###################################################################################
rcut = args.bondLength
modbonds = CreateBondsModifier(mode = CreateBondsModifier.Mode.Pairwise)
modbonds.set_pairwise_cutoff("Type 1", "Type 2", rcut)
modmesh = ConstructSurfaceModifier(radius=5.0)
modbondcount = PythonScriptModifier(function = create_bond_count_particle)
modbondnghbr = PythonScriptModifier(function = create_bond_neighbors_particle)
print("")
print("... adding modifiers")
print(" creating Si-O bonds using cutoff = %1.4f"%(rcut))
print(" calculating bond count")
print(" calculating nearest-neighbor bonded atoms")
node.modifiers.append(modmesh)
node.modifiers.append(modbonds)
node.modifiers.append(modbondcount)
node.modifiers.append(modbondnghbr)
node.compute()
import sys
if "ovito.modifiers.crystalanalysis" not in sys.modules: sys.exit()
from ovito.io import import_file
from ovito.data import SurfaceMesh, SimulationCell
from ovito.modifiers import ConstructSurfaceModifier
# Load a particle structure and reconstruct its geometric surface:
pipeline = import_file("simulation.dump")
pipeline.modifiers.append(ConstructSurfaceModifier(radius=2.9))
data = pipeline.compute()
mesh = data.expect(SurfaceMesh)
cell = data.expect(SimulationCell)
# Query computed surface properties:
print("Surface area: %f" %
data.attributes['ConstructSurfaceMesh.surface_area'])
print("Solid volume: %f" %
data.attributes['ConstructSurfaceMesh.solid_volume'])
fraction = data.attributes['ConstructSurfaceMesh.solid_volume'] / cell.volume
print("Solid volume fraction: %f" % fraction)
# Export the surface triangle mesh to a VTK file.
mesh.export_vtk('surface.vtk', cell)
from ovito.io import import_file
from ovito.modifiers import ConstructSurfaceModifier
# Load a particle structure and construct its surface mesh:
node = import_file("simulation.dump")
node.modifiers.append(ConstructSurfaceModifier(radius=2.8))
node.compute()
# Access the computed surface mesh and export it to VTK files for
# visualization with ParaView.
mesh = node.output.surface
mesh.export_vtk('surface.vtk', node.output.cell)
mesh.export_cap_vtk('surface_cap.vtk', node.output.cell)
try:
print(kuttX)
except:
kuttX = 15
#Load dump file
node = import_file(mappenavn + "/" + filnavn_dump, multiple_frames=True)
#makes folder called "data"
#alternative would be to use if/else and shutil.rmtree() to remove folder. I don't wanna do that though
os.chdir(mappenavn)
os.makedirs("area_mesh")
os.chdir("area_mesh")
#makes Surface mesh
r = 3.5
mod = ConstructSurfaceModifier(radius=r)
node.modifiers.append(mod)
totframe = int(node.source.num_frames) #number of frames
k = 0
areas = []
#write surface mesh to surface_nr files
for i in range(totframe):
dataset.anim.current_frame = i
works = False
reset = False
while not works and k < 15:
k += 1
try:
actual = node.compute()