Commit 89a59f88 authored by Moreland, Ken's avatar Moreland, Ken
Browse files

Convert detailed atom data set 

This data set comes in multiple atom files, so I needed to
loop over all of them.

I discovered that one of them had some lines truncated. This
corrupted one of the time steps (94750). That said, the timestep
seems repeated in the next file, so I don't think anything
is lost.
parent ed09817e

lammps_atom_convert/LammpsAtomConvert.ipynb

+56 −31
Original line number Diff line number Diff line 
%% Cell type:markdown id:296bffef-9245-4144-b96f-7c86dd250fd2 tags:



Load VTK module.



%% Cell type:code id:a870c2d3-261c-484f-a82e-e21057e950cb tags:



``` python

import sys

sys.version

```



%% Output



    '3.11.4 (main, Jul  5 2023, 08:41:25) [Clang 14.0.6 ]'



%% Cell type:code id:f3a3f2e9-1a0d-45ae-9d58-9e8734b209f7 tags:



``` python

import sys

sys.path.append('/Users/4d5/builds/VTK/Debug/lib/python3.11/site-packages')

import vtk

```



%% Cell type:markdown id:f72ad50b-3132-46e9-9a11-a56f9d0799e6 tags:



Create an object that can read in text LAMMPS atom files and convert them to VTK objects.



%% Cell type:code id:0a559e46-13bb-470c-bbd9-b242c9c9a29d tags:



``` python

class LammpsAtomLoadBase:

    def __init__(self, filename):

        self._file = open(filename, 'r')



    def _lerp_coord(self, x, index):

        return (float(x) * self._coord_scales[index] +

                self._coord_offsets[index])



    def read_next_timestep(self):

        import re

        self.timestep = None

        self.number_of_atoms = None

        self._coord_offsets = None

        self._coord_scales = None

        linenumber = 0

        def read_expected_line():

            line = self._file.readline()

            if line == '':

                raise Exception(

                    'Unexpected EOF at timestep {}. Possible file truncation.'.

                    format(self.timestep))

            return line

        while True:

            linenumber += 1

            line = self._file.readline().strip()

            if line == 'ITEM: TIMESTEP':

                self.timestep = int(self._file.readline())

                self.timestep = int(read_expected_line())

            elif line == 'ITEM: NUMBER OF ATOMS':

                self.number_of_atoms = int(self._file.readline())

                self.number_of_atoms = int(read_expected_line())

            elif line == 'ITEM: BOX BOUNDS pp pp ff':  # Only valid for case from PSI code

                self._coord_offsets = []

                self._coord_scales = []

                for i in range(3):

                    bounds = self._file.readline().split()

                    bounds = read_expected_line().split()

                    min = float(bounds[0])

                    max = float(bounds[1])

                    self._coord_offsets.append(min)

                    self._coord_scales.append(max - min)

            elif line == 'ITEM: ATOMS id type xs ys zs':

                if not self.number_of_atoms:

                    raise RuntimeError(

                        'ITEM: NUMBER OF ATOMS not encountered.')

                    raise Exception(

                        'ITEM: NUMBER OF ATOMS not encountered by {}.'.format(lineno))

                if not self._coord_offsets:

                    raise RuntimeError(

                        'ITEM: BOX BOUNDS not encountered.')

                    raise Exception(

                        'ITEM: BOX BOUNDS not encountered by {}.'.format(lineno))

                self._initialize_data()

                for i in range(self.number_of_atoms):

                    fieldvalues = self._file.readline().split()

                    fieldvalues = read_expected_line().split()

                    fields = {}

                    fields['id'] = int(fieldvalues[0])

                    fields['type'] = int(fieldvalues[1])

                    coords = [ self._lerp_coord(fieldvalues[2], 0),

                               self._lerp_coord(fieldvalues[3], 1),

                               self._lerp_coord(fieldvalues[4], 2),

                             ]

                    self._add_data(coords, fields)

                self._finalize_data()

                return True

            elif line == '':

                return False

            else:

                raise RuntimeError(

                    'Unknown line encountered: `{}`'.format(line))

                raise Exception(

                    'Unknown line encountered: `{}` at {}'.format(line, lineno))



class LammpsAtomLoadVTK(LammpsAtomLoadBase):

    def __init__(self, filename):

        LammpsAtomLoadBase.__init__(self, filename)



    def _initialize_data(self):

        self._points = vtk.vtkPoints()

        self._points.Allocate(self.number_of_atoms)

        self._type_array = vtk.vtkSignedCharArray()

        self._type_array.SetName('type')

        self._type_array.SetNumberOfComponents(1)

        self._type_array.Allocate(self.number_of_atoms)

        self._id_array = vtk.vtkIntArray()

        self._id_array.SetName('id')

        self._id_array.SetNumberOfComponents(1)

        self._id_array.Allocate(self.number_of_atoms)



    def _add_data(self, coords, fields):

        self._points.InsertNextPoint(coords)

        self._type_array.InsertNextValue(fields['type'])

        self._id_array.InsertNextValue(fields['id'])



    def _finalize_data(self):

        self.data = vtk.vtkUnstructuredGrid()

        self.data.SetPoints(self._points)

        self.data.GetPointData().AddArray(self._type_array)

        self.data.GetPointData().AddArray(self._id_array)

```



%% Cell type:code id:521be01e-c970-45c1-b851-ad97026e4a85 tags:



``` python

loader = LammpsAtomLoadVTK(

    '/Users/4d5/data/PSI/karl-hammond-2023/110-25x25nm/dump.110-25x25nm')

```



%% Cell type:code id:26cbe0a8-cc84-4440-9d2e-0ce15295faff tags:



``` python

import glob

targetdir = '/Users/4d5/Downloads/'

targetname = '110-25x25nm'

targetname = '110-25x25nm-detailed'

series_file = open(targetdir + targetname + '.vtk.series', 'w')

series_file.write('{\n')

series_file.write('  "file-series-version" : "1.0",\n')

series_file.write('  "files" : [\n')

while loader.read_next_timestep():

    print('.', end='', flush=True)

    vtkfilename = '{}{:06}.vtk'.format(targetname, loader.timestep)

    writer = vtk.vtkDataSetWriter()

    writer.SetFileTypeToBinary()

    writer.SetFileName(targetdir + vtkfilename)

    writer.SetInputData(loader.data)

    writer.Write()

    series_file.write(

        '    {{ "name" : "{}", "time" : {} }},\n'.format(

            vtkfilename, loader.timestep))

for infilename in sorted(glob.glob(

    '/Users/4d5/data/PSI/karl-hammond-2023/110-25x25nm_detailed/dump.*')):

    print(infilename)

    loader = LammpsAtomLoadVTK(infilename)

    try:

        while loader.read_next_timestep():

            print('.', end='', flush=True)

            vtkfilename = '{}-{:06}.vtk'.format(targetname, loader.timestep)

            writer = vtk.vtkDataSetWriter()

            writer.SetFileTypeToBinary()

            writer.SetFileName(targetdir + vtkfilename)

            writer.SetInputData(loader.data)

            writer.Write()

            series_file.write(

                '    {{ "name" : "{}", "time" : {} }},\n'.format(

                    vtkfilename, loader.timestep))

        print('')

    except Exception as e:

        print('\nEncountered issue when loading file. Might have partial results.')

        print(str(e))

series_file.write('  ]\n')

series_file.write('}\n')

series_file.close()

```



%% Output



    ...................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................

    /Users/4d5/data/PSI/karl-hammond-2023/110-25x25nm_detailed/dump.110-25x25nm-detailed_84001-86499

    ...................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................

    /Users/4d5/data/PSI/karl-hammond-2023/110-25x25nm_detailed/dump.110-25x25nm-detailed_86500-88999

    ....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................

    /Users/4d5/data/PSI/karl-hammond-2023/110-25x25nm_detailed/dump.110-25x25nm-detailed_89000-91999

    ...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................

    /Users/4d5/data/PSI/karl-hammond-2023/110-25x25nm_detailed/dump.110-25x25nm-detailed_92000-to-94750

    ..............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................

    Encountered issue when loading file. Might have partial results.

    Unexpected EOF at timestep 94750. Possible file truncation.

    /Users/4d5/data/PSI/karl-hammond-2023/110-25x25nm_detailed/dump.110-25x25nm-detailed_94750-to-98267

    ..............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................

    /Users/4d5/data/PSI/karl-hammond-2023/110-25x25nm_detailed/dump.110-25x25nm-detailed_98268-to-100724

    .........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................



%% Cell type:code id:27f94099-5e0c-4e58-801c-713822958559 tags:

%% Cell type:code id:c5d2b2e0-4fca-45be-a860-317c2a0f2731 tags:



``` python

```