testing updates

cf354005 · Thomas Sebastian Bakaj · 44e3cb37 · cf354005
Commit cf354005 authored 1 year ago by Thomas Sebastian Bakaj
--- a/examples/ocp_validation.ipynb
+++ b/examples/ocp_validation.ipynb
 {
 "cells": [
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "import sys\n",
-    "from pathlib import Path\n",
-    "\n",
-    "sys_path = Path('..')\n",
-    "sys.path.append(str(sys_path.resolve()))"
-   ]
-  },
  {
   "cell_type": "code",
   "execution_count": 1,
@@ -21,7 +8,8 @@
   "source": [
    "import tofhed\n",
    "from tofhed.commander import *  \n",
-    "from tofhed.hinuma import *"
+    "from tofhed.hinuma import *\n",
+    "from pathlib import Path"
   ]
  },
  {

 %% Cell type:code id: tags:

 ``` python
-import sys
-from pathlib import Path
-
-sys_path = Path('..')
-sys.path.append(str(sys_path.resolve()))
-```
-
-%% Cell type:code id: tags:
-
-``` python
 import tofhed
 from tofhed.commander import *
 from tofhed.hinuma import *
+from pathlib import Path
 ```

 %% Cell type:code id: tags:

 ``` python
 #path_xyz = Path('_temp/random207.extxyz')
 path_xyz = Path('_temp/010.xyz')
 ```

 %% Cell type:code id: tags:

 ``` python
 frames = tofhed.utils.read(path_xyz)
 ```

 %% Cell type:code id: tags:

 ``` python
 tofhed.utils.view(frames)
 ```

 %% Output

    <Popen: returncode: None args: ['/Users/thomson/MODES/02_venv/.venv/bin/pyth...>

 %% Cell type:code id: tags:

 ``` python
 from tofhed.commander import *


 path_xyz = '700K_CuH2_100.extxyz'
 path_settings = 'settings.toml'

 data = DataBase() # Create new database in memory

 file = data.files.import_ase(path_xyz, init_frame_number=1, note='700K_CuH2_100 Example from Felix', import_positions=False)

 system = file.newest_system()

 # settings = data.settings.new_settings(settings_dict)
 settings = data.settings.new_settings_from_toml(path_settings)

 experiment = data.experiments.new_experiment(settings.setting_id,
                                             system_id=system.system_id,
                                             note='Initial experiment')

 base_types_dict = experiment.set_base_types()  # Using the settings from the experiment (in this case 'chemical_elements')

 # Automatically sets the surfaces based on the base type algorithm in the settings
 surfaces = experiment.set_new_surfaces()
 surfaces
 ```

 %% Output

    ---------------------------------------------------------------------------
    FileNotFoundError                         Traceback (most recent call last)
 Cell     In[1], line 9
          5 path_settings = 'settings.toml'
          7 data = DataBase() # Create new database in memory
    ----> 9 file = data.files.import_ase(path_xyz, init_frame_number=1, note='700K_CuH2_100 Example from Felix', import_positions=False)
         11 system = file.newest_system()
         13 # settings = data.settings.new_settings(settings_dict)
 File     ~/MODES/01_code/tofhed/tofhed/commander/db_files.py:49, in DBFiles.import_ase(self, path, init_frame_number, frame_range, is_sequence, sequence_id, sequence_order, note, write_split, import_positions)
         45 def import_ase(self, path, init_frame_number, frame_range=(0,-1),
         46                is_sequence=False, sequence_id=None, sequence_order=None,
         47                note='', write_split=100000, import_positions=True):
    ---> 49     check_path(path)
         51     frames = read(path)
         52     file_id = self._import_from_frames(frames, path, init_frame_number,
         53                                        frame_range=frame_range, is_sequence=is_sequence,
         54                                        sequence_id=sequence_id, sequence_order=sequence_order,
         55                                        note=note, write_split=write_split,
         56                                        import_positions=import_positions)
 File     ~/MODES/01_code/tofhed/tofhed/functions.py:47, in check_path(path)
         45 def check_path(path):
         46     if not Path(path).exists():
    ---> 47         raise FileNotFoundError(f'File {path} does not exist')
         49     return True
    FileNotFoundError: File 700K_CuH2_100.extxyz does not exist

 %% Cell type:code id: tags:

 ``` python
 settings_dict = {
    'approach_cutoff': 4.0,  # Cutoff for event detection
    'bond_cutoff': 4.0,  # Cutoff for bond detection
    'hinuma_cutoff': 4.2,  # Cutoff for Hinuma algorithm
    'mic': True,  # Using minimum image convention
    'fudge_factor': 1.7,  # Fudge factor for bond/connection detection
    'zero_vec_tolerance': 0.000001,  # Tolerance for zero vector
    'init_frame_number': 5,  # Frame number to use for initialisation
    'xyz_filter': None, #'z_filter',  # Optional filter function for the hinuma algorithm
    'solid_angle_limit': round(3.14 * 0.8, 3),  # Solid angle limit to be considered as a surface atoms
    'duration_cutoff': 5, # Cutoff for duration of events

    # 'base_type_algorithm': 'hinuma',  # Selecting the base type alghoritm
    # 'max_molecule_size': 5,  # Maximum number of atoms in a molecule

    'base_type_algorithm': 'chemical_elements',
    'chemical_elements': 'H C O N',  # String of chemical elements separated by spaces

    #'base_type_algorithm': 'chemical_tag',
    #'chemical_tag': 2,  # String of chemical elements separated by spaces
 }
 ```

 %% Cell type:code id: tags:

 ``` python
 data = DataBase() # Create new database in memory

 file = data.files.import_ase(path_xyz, init_frame_number=1, note='Test', import_positions=False)

 system = file.newest_system()
 settings = data.settings.new_settings(settings_dict)

 experiment = data.experiments.new_experiment(settings.setting_id,
                                             system_id=system.system_id,
                                             note='Initial experiment')

 base_types_dict = experiment.set_base_types()  # Using the settings from the experiment (in this case 'hinuma')

 # Automatically sets the surfaces based on the base type algorithm in the settings
 surfaces = experiment.set_new_surfaces()
 ```

 %% Output

    sequence_ids: []
    long_experiments {}
    [0, 999]
    sequence_ids: []
    long_experiments {}
    all_ids is None at convert_surface_classifier

 %% Cell type:code id: tags:

 ``` python
 tofhed.analysis.debug_view_surfaces(experiment)
 ```

 %% Cell type:code id: tags:

 ``` python
 settings.solid_angle_limit
 ```

 %% Output

    2.512

 %% Cell type:code id: tags:

 ``` python
 hinuma_surface = set(experiment.surface_groups[1].surface_atom_ids)

 surface_tag = 1
 tag_surface = set([atom_id for atom_id, tag in system.init_tags.items() if tag == surface_tag])

 false_positives = hinuma_surface.difference(tag_surface)
 false_negatives = tag_surface.difference(hinuma_surface)
 false_positives, false_negatives
 ```

 %% Output

    (set(), set())

 %% Cell type:code id: tags:

 ``` python
 atom_id = system.atoms.number_to_id[34]
 atom_id
 ```

 %% Output

    35

 %% Cell type:code id: tags:

 ``` python
 experiment.hinumas[1].solid_angles[atom_id]/(3.14)
 ```

 %% Output

    0.7120869817076638

 %% Cell type:code id: tags:

 ``` python
 experiment.hinumas[1].connections[atom_id]
 ```

 %% Output

    {3, 14, 25, 27, 31, 32, 33, 35, 37, 38, 41, 43, 44, 45, 47, 56, 57}

 %% Cell type:code id: tags:

 ``` python
 ```