Skip to content

GitLab

Commit 18169ae7 authored by Sudarsan Surendralal's avatar Sudarsan Surendralal
Browse files

Final cleanup

parent 90a83e24
Hide whitespace changes
Inline Side-by-side
day_1/ex_02_creating_structure_databases.ipynb
View file @ 18169ae7
%% Cell type:markdown id:naval-truck tags: %% Cell type:markdown id:appointed-stylus tags:
# [**Workflows for atomistic simulations**](http://potentials.rub.de/) # [**Workflows for atomistic simulations**](http://potentials.rub.de/)
%% Cell type:markdown id:pregnant-battery tags: %% Cell type:markdown id:straight-bicycle tags:
## **Day 1 - Atomistic simulations with [pyiron](https://pyiron.org)** ## **Day 1 - Atomistic simulations with [pyiron](https://pyiron.org)**
### **Exercise 2: Creating and working with structure databases** ### **Exercise 2: Creating and working with structure databases**
Before the excercise, you should: Before the excercise, you should:
* Finish exercise 1 * Finish exercise 1
The aim of this exercise is to make you familiar with: The aim of this exercise is to make you familiar with:
* Creating structure databases and working with them for potential fitting (day 2) * Creating structure databases and working with them for potential fitting (day 2)
%% Cell type:code id:roman-wilderness tags: %% Cell type:markdown id:durable-leone tags:
## **Importing necessary modules and creating a project**
This is done the same way as shown in the first exercise
%% Cell type:code id:novel-wisconsin tags:
``` python ``` python
import numpy as np import numpy as np
%matplotlib inline %matplotlib inline
import matplotlib.pylab as plt import matplotlib.pylab as plt
``` ```
%% Cell type:code id:charming-furniture tags: %% Cell type:code id:sitting-religious tags:
``` python ``` python
from pyiron import Project from pyiron import Project
import pyiron_contrib
``` ```
%% Cell type:code id:bibliographic-honey tags: %% Cell type:code id:technical-newport tags:
``` python ``` python
pr = Project("creating_datasets") pr = Project("creating_datasets")
``` ```
%% Cell type:code id:relative-subscriber tags: %% Cell type:markdown id:based-kentucky tags:
## Creating a structure "container" from the data
We now go over the jobs generated in the first notebook to store structures, energies, and forces into a structure container which will later be used for potential fitting
**Note**: Usually these datasets are created using highly accurate DFT calculations. But for practical reasons, we only demonstrate how to do this using data from LAMMPS calculations (the workflow remain the same)
%% Cell type:code id:attached-germany tags:
``` python ``` python
# Access the project created in exercise 1
pr_fs = pr["../first_steps"] pr_fs = pr["../first_steps"]
``` ```
%% Cell type:code id:solved-sight tags: %% Cell type:code id:filled-natural tags:
``` python ``` python
# Create a TrainingContainer job (to store structures and databases)
container = pr.create.job.TrainingContainer('dataset_example') container = pr.create.job.TrainingContainer('dataset_example')
``` ```
%% Cell type:markdown id:falling-spouse tags: %% Cell type:markdown id:married-storm tags:
## **Add structures from the E-V curves** ## **Add structures from the E-V curves**
%% Cell type:code id:secure-tract tags: For starters, we append structures from the energy volume curves we calculated earlier
``` python %% Cell type:code id:mediterranean-upset tags:
``` python
# Iterate over the jobs in this sub-project and append the final structure, potential energy, and forces
for job in pr_fs["E_V_curve"].iter_jobs(status="finished"): for job in pr_fs["E_V_curve"].iter_jobs(status="finished"):
container.include_job(job, iteration_step=-1) container.include_job(job, iteration_step=-1)
``` ```
%% Cell type:code id:wicked-defeat tags: %% Cell type:markdown id:acquired-missile tags:
We can obtain this data as a `pandas` table
%% Cell type:code id:greatest-person tags:
``` python ``` python
container.to_pandas() container.to_pandas()
``` ```
%%%% Output: execute_result %%%% Output: execute_result
name \ name \
0 None 0 None
1 None 1 None
2 None 2 None
3 None 3 None
4 None 4 None
5 None 5 None
6 None 6 None
7 None 7 None
8 None 8 None
9 None 9 None
10 None 10 None
11 None 11 None
12 None 12 None
13 None 13 None
14 None 14 None
15 None 15 None
16 None 16 None
17 None 17 None
18 None 18 None
19 None 19 None
20 None 20 None
21 None 21 None
22 None 22 None
23 None 23 None
24 None 24 None
25 None 25 None
26 None 26 None
27 None 27 None
28 None 28 None
29 None 29 None
30 None 30 None
31 None 31 None
32 None 32 None
33 None 33 None
34 None 34 None
35 None 35 None
36 None 36 None
37 None 37 None
38 None 38 None
39 None 39 None
40 job_a_3_4 40 job_a_3_4
41 job_a_3_5 41 job_a_3_5
42 job_a_3_6 42 job_a_3_6
43 job_a_3_7 43 job_a_3_7
44 job_a_3_8 44 job_a_3_8
45 job_a_3_9 45 job_a_3_9
46 job_a_4_0 46 job_a_4_0
atoms \ atoms \
0 (Atom('Cu', [0.0, 0.0, 0.0], index=0)) 0 (Atom('Cu', [0.0, 0.0, 0.0], index=0))
1 (Atom('Cu', [0.0, 0.0, 0.0], index=0)) 1 (Atom('Cu', [0.0, 0.0, 0.0], index=0))
2 (Atom('Cu', [0.0, 0.0, 0.0], index=0)) 2 (Atom('Cu', [0.0, 0.0, 0.0], index=0))
3 (Atom('Cu', [0.0, 0.0, 0.0], index=0)) 3 (Atom('Cu', [0.0, 0.0, 0.0], index=0))
4 (Atom('Cu', [0.0, 0.0, 0.0], index=0)) 4 (Atom('Cu', [0.0, 0.0, 0.0], index=0))
5 (Atom('Cu', [0.0, 0.0, 0.0], index=0)) 5 (Atom('Cu', [0.0, 0.0, 0.0], index=0))
6 (Atom('Cu', [0.0, 0.0, 0.0], index=0)) 6 (Atom('Cu', [0.0, 0.0, 0.0], index=0))
7 (Atom('Cu', [0.0, 0.0, 0.0], index=0), Atom('Cu', [0.0, 1.8049999999995918, 1.804999999999592], index=1), Atom('Cu', [1.8049999999995918, 1.1052437362302365e-16, 1.804999999999592], index=2), Atom... 7 (Atom('Cu', [0.0, 0.0, 0.0], index=0), Atom('Cu', [0.0, 1.8049999999995918, 1.804999999999592], index=1), Atom('Cu', [1.8049999999995918, 1.1052437362302365e-16, 1.804999999999592], index=2), Atom...
8 (Atom('Cu', [0.140426153531212, 11.00934611760493, 10.968207696001379], index=0), Atom('Cu', [10.983357200359302, 1.779939365335074, 1.7146804782560905], index=1), Atom('Cu', [2.1228644677344763, ... 8 (Atom('Cu', [0.140426153531212, 11.00934611760493, 10.968207696001379], index=0), Atom('Cu', [10.983357200359302, 1.779939365335074, 1.7146804782560905], index=1), Atom('Cu', [2.1228644677344763, ...
9 (Atom('Cu', [0.1407579358923329, 11.020287239626356, 10.855878337455094], index=0), Atom('Cu', [0.29542104007972325, 1.6514729828183248, 1.7760939949715002], index=1), Atom('Cu', [1.99578258187561... 9 (Atom('Cu', [0.1407579358923329, 11.020287239626356, 10.855878337455094], index=0), Atom('Cu', [0.29542104007972325, 1.6514729828183248, 1.7760939949715002], index=1), Atom('Cu', [1.99578258187561...
10 (Atom('Cu', [0.04675277832683521, 10.951786003502875, 0.20014601215416555], index=0), Atom('Cu', [0.08453269827616121, 1.807218974303731, 1.7664733621606055], index=1), Atom('Cu', [1.9597357123378... 10 (Atom('Cu', [0.04675277832683521, 10.951786003502875, 0.20014601215416555], index=0), Atom('Cu', [0.08453269827616121, 1.807218974303731, 1.7664733621606055], index=1), Atom('Cu', [1.9597357123378...
11 (Atom('Cu', [10.991332780892245, 11.027168829788469, 0.17044757336885022], index=0), Atom('Cu', [10.869778028731718, 1.9053524080340238, 1.7569642307109068], index=1), Atom('Cu', [1.89027128290555... 11 (Atom('Cu', [10.991332780892245, 11.027168829788469, 0.17044757336885022], index=0), Atom('Cu', [10.869778028731718, 1.9053524080340238, 1.7569642307109068], index=1), Atom('Cu', [1.89027128290555...
12 (Atom('Cu', [10.958070767872973, 0.05270018288525903, 11.015795828313184], index=0), Atom('Cu', [0.04540970504125744, 2.0780519854689388, 1.8353871076994486], index=1), Atom('Cu', [1.8285627799497... 12 (Atom('Cu', [10.958070767872973, 0.05270018288525903, 11.015795828313184], index=0), Atom('Cu', [0.04540970504125744, 2.0780519854689388, 1.8353871076994486], index=1), Atom('Cu', [1.8285627799497...
13 (Atom('Cu', [10.903697402270481, 10.843249424147054, 0.09574490333935876], index=0), Atom('Cu', [10.594918916668115, 1.7187193807013557, 1.957301113531466], index=1), Atom('Cu', [1.676074002401865... 13 (Atom('Cu', [10.903697402270481, 10.843249424147054, 0.09574490333935876], index=0), Atom('Cu', [10.594918916668115, 1.7187193807013557, 1.957301113531466], index=1), Atom('Cu', [1.676074002401865...
14 (Atom('Cu', [0.25841198959969514, 0.07063449316617948, 10.912283030401635], index=0), Atom('Cu', [0.19649020014428978, 1.7891621064498946, 1.803181486480956], index=1), Atom('Cu', [1.7493171890008... 14 (Atom('Cu', [0.25841198959969514, 0.07063449316617948, 10.912283030401635], index=0), Atom('Cu', [0.19649020014428978, 1.7891621064498946, 1.803181486480956], index=1), Atom('Cu', [1.7493171890008...
15 (Atom('Cu', [0.004994793789590358, 10.985055637636528, 10.904222762438215], index=0), Atom('Cu', [10.941729664004177, 1.8868614122932958, 1.8147512571785023], index=1), Atom('Cu', [1.8438031255437... 15 (Atom('Cu', [0.004994793789590358, 10.985055637636528, 10.904222762438215], index=0), Atom('Cu', [10.941729664004177, 1.8868614122932958, 1.8147512571785023], index=1), Atom('Cu', [1.8438031255437...
16 (Atom('Cu', [0.03645923830333788, 10.856010693932728, 10.970572990196315], index=0), Atom('Cu', [10.913522535008392, 1.8161914381204696, 1.5447581077411967], index=1), Atom('Cu', [1.77583933019795... 16 (Atom('Cu', [0.03645923830333788, 10.856010693932728, 10.970572990196315], index=0), Atom('Cu', [10.913522535008392, 1.8161914381204696, 1.5447581077411967], index=1), Atom('Cu', [1.77583933019795...
17 (Atom('Cu', [0.009767181825404037, 0.0071865231528328395, 11.0089023992238], index=0), Atom('Cu', [10.89374596605574, 1.9969194212313586, 1.595578837066423], index=1), Atom('Cu', [2.05442192913884... 17 (Atom('Cu', [0.009767181825404037, 0.0071865231528328395, 11.0089023992238], index=0), Atom('Cu', [10.89374596605574, 1.9969194212313586, 1.595578837066423], index=1), Atom('Cu', [2.05442192913884...
18 (Atom('Cu', [0.0, 1.8049999999995918, 1.804999999999592], index=0), Atom('Cu', [1.8049999999995918, 1.1052437362302365e-16, 1.804999999999592], index=1), Atom('Cu', [1.8049999999995918, 1.80499999... 18 (Atom('Cu', [0.0, 1.8049999999995918, 1.804999999999592], index=0), Atom('Cu', [1.8049999999995918, 1.1052437362302365e-16, 1.804999999999592], index=1), Atom('Cu', [1.8049999999995918, 1.80499999...
19 (Atom('Cu', [0.10390109091492504, 1.9580560553035629, 1.779188560767685], index=0), Atom('Cu', [1.3868099266682106, 10.93717630776342, 1.601790948781396], index=1), Atom('Cu', [1.7183987889409966,... 19 (Atom('Cu', [0.10390109091492504, 1.9580560553035629, 1.779188560767685], index=0), Atom('Cu', [1.3868099266682106, 10.93717630776342, 1.601790948781396], index=1), Atom('Cu', [1.7183987889409966,...
20 (Atom('Cu', [0.2223234793002756, 1.6999920633404135, 1.7623980235259114], index=0), Atom('Cu', [2.122882660879041, 0.18624238423025943, 2.030808683988878], index=1), Atom('Cu', [1.7334689484700414... 20 (Atom('Cu', [0.2223234793002756, 1.6999920633404135, 1.7623980235259114], index=0), Atom('Cu', [2.122882660879041, 0.18624238423025943, 2.030808683988878], index=1), Atom('Cu', [1.7334689484700414...
21 (Atom('Cu', [10.839434974930338, 1.9008464900018593, 1.6867963294684278], index=0), Atom('Cu', [1.5876598581358559, 0.15447557118789498, 1.715299994817798], index=1), Atom('Cu', [2.148606011735498... 21 (Atom('Cu', [10.839434974930338, 1.9008464900018593, 1.6867963294684278], index=0), Atom('Cu', [1.5876598581358559, 0.15447557118789498, 1.715299994817798], index=1), Atom('Cu', [2.148606011735498...
22 (Atom('Cu', [10.827044041159013, 1.814885520198166, 2.1241909251750846], index=0), Atom('Cu', [1.6679142700199647, 0.1106240807045643, 1.629401459425781], index=1), Atom('Cu', [1.29418686613977, 2... 22 (Atom('Cu', [10.827044041159013, 1.814885520198166, 2.1241909251750846], index=0), Atom('Cu', [1.6679142700199647, 0.1106240807045643, 1.629401459425781], index=1), Atom('Cu', [1.29418686613977, 2...
23 (Atom('Cu', [0.18579648605077317, 1.6025971043596021, 1.8725196193757527], index=0), Atom('Cu', [2.0480835165906024, 0.055238510607153124, 2.258841094259334], index=1), Atom('Cu', [1.8423446841272... 23 (Atom('Cu', [0.18579648605077317, 1.6025971043596021, 1.8725196193757527], index=0), Atom('Cu', [2.0480835165906024, 0.055238510607153124, 2.258841094259334], index=1), Atom('Cu', [1.8423446841272...
24 (Atom('Cu', [10.902653792490328, 1.9016481867720487, 1.712386801004505], index=0), Atom('Cu', [1.6843656295425262, 0.20454959542790652, 1.4940727709027473], index=1), Atom('Cu', [1.628967729295861... 24 (Atom('Cu', [10.902653792490328, 1.9016481867720487, 1.712386801004505], index=0), Atom('Cu', [1.6843656295425262, 0.20454959542790652, 1.4940727709027473], index=1), Atom('Cu', [1.628967729295861...
25 (Atom('Cu', [0.2202511036922136, 1.5872348575607442, 1.7623998700282655], index=0), Atom('Cu', [1.8386689358546338, 10.988833155546024, 1.8571406735818983], index=1), Atom('Cu', [1.976390891645592... 25 (Atom('Cu', [0.2202511036922136, 1.5872348575607442, 1.7623998700282655], index=0), Atom('Cu', [1.8386689358546338, 10.988833155546024, 1.8571406735818983], index=1), Atom('Cu', [1.976390891645592...
26 (Atom('Cu', [10.746144724861097, 1.6561216261540705, 1.6676063346982197], index=0), Atom('Cu', [1.8697696006277247, 0.29566102043388925, 1.9071090181664805], index=1), Atom('Cu', [1.82013088394316... 26 (Atom('Cu', [10.746144724861097, 1.6561216261540705, 1.6676063346982197], index=0), Atom('Cu', [1.8697696006277247, 0.29566102043388925, 1.9071090181664805], index=1), Atom('Cu', [1.82013088394316...
27 (Atom('Cu', [0.17063059290766686, 1.8534187978406447, 1.7423748775395635], index=0), Atom('Cu', [1.8595651370150335, 10.90572322929213, 1.810598025463111], index=1), Atom('Cu', [1.934651223968069,... 27 (Atom('Cu', [0.17063059290766686, 1.8534187978406447, 1.7423748775395635], index=0), Atom('Cu', [1.8595651370150335, 10.90572322929213, 1.810598025463111], index=1), Atom('Cu', [1.934651223968069,...
28 (Atom('Cu', [10.866365842640102, 1.8491297818376022, 2.093244182315977], index=0), Atom('Cu', [1.7536272335648937, 10.898985481755824, 1.8241252890179567], index=1), Atom('Cu', [1.994555230114336,... 28 (Atom('Cu', [10.866365842640102, 1.8491297818376022, 2.093244182315977], index=0), Atom('Cu', [1.7536272335648937, 10.898985481755824, 1.8241252890179567], index=1), Atom('Cu', [1.994555230114336,...
29 (Atom('Cu', [0.0, 1.4737763285740602, 9.024277317236803e-17], index=0), Atom('Cu', [2.5526554800834376, 1.4737763285740604, 2.4654784132287465e-16], index=1), Atom('Cu', [5.105310960166875, 1.4737... 29 (Atom('Cu', [0.0, 1.4737763285740602, 9.024277317236803e-17], index=0), Atom('Cu', [2.5526554800834376, 1.4737763285740604, 2.4654784132287465e-16], index=1), Atom('Cu', [5.105310960166875, 1.4737...
30 (Atom('Cu', [0.4126496185424086, 0.9553642998076769, 0.12158924761653131], index=0), Atom('Cu', [2.831118842513476, 1.0700158216349893, 25.916922304272767], index=1), Atom('Cu', [5.314789299948389... 30 (Atom('Cu', [0.4126496185424086, 0.9553642998076769, 0.12158924761653131], index=0), Atom('Cu', [2.831118842513476, 1.0700158216349893, 25.916922304272767], index=1), Atom('Cu', [5.314789299948389...
31 (Atom('Cu', [10.151562776611806, 1.6587733567107183, 26.43035938894712], index=0), Atom('Cu', [2.5212828819853748, 1.9070842851152785, 26.36203940098048], index=1), Atom('Cu', [4.715098279443367, ... 31 (Atom('Cu', [10.151562776611806, 1.6587733567107183, 26.43035938894712], index=0), Atom('Cu', [2.5212828819853748, 1.9070842851152785, 26.36203940098048], index=1), Atom('Cu', [4.715098279443367, ...
32 (Atom('Cu', [0.19573901040697333, 1.051460534941847, 26.530022925039237], index=0), Atom('Cu', [2.995726956631421, 1.1546751485293076, 26.840478692293868], index=1), Atom('Cu', [5.923947432763936,... 32 (Atom('Cu', [0.19573901040697333, 1.051460534941847, 26.530022925039237], index=0), Atom('Cu', [2.995726956631421, 1.1546751485293076, 26.840478692293868], index=1), Atom('Cu', [5.923947432763936,...
33 (Atom('Cu', [9.888379625890167, 1.4968159202602271, 26.58551059472236], index=0), Atom('Cu', [2.207544057015841, 1.290074245861123, 26.685466830386254], index=1), Atom('Cu', [4.939145903748478, 1.... 33 (Atom('Cu', [9.888379625890167, 1.4968159202602271, 26.58551059472236], index=0), Atom('Cu', [2.207544057015841, 1.290074245861123, 26.685466830386254], index=1), Atom('Cu', [4.939145903748478, 1....
34 (Atom('Cu', [0.3429326290376805, 1.5170285327525175, 0.14896315086845416], index=0), Atom('Cu', [3.129345868860857, 1.495102964861245, 0.01607848650845961], index=1), Atom('Cu', [5.714332108258016... 34 (Atom('Cu', [0.3429326290376805, 1.5170285327525175, 0.14896315086845416], index=0), Atom('Cu', [3.129345868860857, 1.495102964861245, 0.01607848650845961], index=1), Atom('Cu', [5.714332108258016...
35 (Atom('Cu', [9.95801241508363, 1.4359511579313753, 26.639342243648862], index=0), Atom('Cu', [2.2681416259098204, 1.7861270127574713, 0.0041936446239185], index=1), Atom('Cu', [5.074253116948648, ... 35 (Atom('Cu', [9.95801241508363, 1.4359511579313753, 26.639342243648862], index=0), Atom('Cu', [2.2681416259098204, 1.7861270127574713, 0.0041936446239185], index=1), Atom('Cu', [5.074253116948648, ...
36 (Atom('Cu', [10.225027496779227, 1.7848555655274232, 26.42388292769549], index=0), Atom('Cu', [2.4914869938632442, 1.861119175102061, 26.64826771541495], index=1), Atom('Cu', [4.968442272624181, 1... 36 (Atom('Cu', [10.225027496779227, 1.7848555655274232, 26.42388292769549], index=0), Atom('Cu', [2.4914869938632442, 1.861119175102061, 26.64826771541495], index=1), Atom('Cu', [4.968442272624181, 1...
37 (Atom('Cu', [10.188116701703345, 1.3482529143763475, 26.353847647582224], index=0), Atom('Cu', [2.4559442807081986, 1.4757747059762696, 26.57379282025388], index=1), Atom('Cu', [5.077086561123585,... 37 (Atom('Cu', [10.188116701703345, 1.3482529143763475, 26.353847647582224], index=0), Atom('Cu', [2.4559442807081986, 1.4757747059762696, 26.57379282025388], index=1), Atom('Cu', [5.077086561123585,...
38 (Atom('Cu', [10.165259029706933, 1.7122531598094173, 26.335638965295193], index=0), Atom('Cu', [2.3513330869200098, 1.5487334168655387, 26.34258116233103], index=1), Atom('Cu', [4.95573138146394, ... 38 (Atom('Cu', [10.165259029706933, 1.7122531598094173, 26.335638965295193], index=0), Atom('Cu', [2.3513330869200098, 1.5487334168655387, 26.34258116233103], index=1), Atom('Cu', [4.95573138146394, ...
39 (Atom('Cu', [0.36893784059756035, 1.481831927531004, 26.53504700964859], index=0), Atom('Cu', [2.6965712181950883, 1.488812429574298, 26.730123522873537], index=1), Atom('Cu', [5.668661292604278, ... 39 (Atom('Cu', [0.36893784059756035, 1.481831927531004, 26.53504700964859], index=0), Atom('Cu', [2.6965712181950883, 1.488812429574298, 26.730123522873537], index=1), Atom('Cu', [5.668661292604278, ...
40 (Atom('Cu', [0.0, 0.0, 0.0], index=0)) 40 (Atom('Cu', [0.0, 0.0, 0.0], index=0))
41 (Atom('Cu', [0.0, 0.0, 0.0], index=0)) 41 (Atom('Cu', [0.0, 0.0, 0.0], index=0))
42 (Atom('Cu', [0.0, 0.0, 0.0], index=0)) 42 (Atom('Cu', [0.0, 0.0, 0.0], index=0))
43 (Atom('Cu', [0.0, 0.0, 0.0], index=0)) 43 (Atom('Cu', [0.0, 0.0, 0.0], index=0))
44 (Atom('Cu', [0.0, 0.0, 0.0], index=0)) 44 (Atom('Cu', [0.0, 0.0, 0.0], index=0))
45 (Atom('Cu', [0.0, 0.0, 0.0], index=0)) 45 (Atom('Cu', [0.0, 0.0, 0.0], index=0))
46 (Atom('Cu', [0.0, 0.0, 0.0], index=0)) 46 (Atom('Cu', [0.0, 0.0, 0.0], index=0))
energy \ energy \
0 -3.142019 0 -3.142019
1 -3.338596 1 -3.338596
2 -3.416929 2 -3.416929
3 -3.409602 3 -3.409602
4 -3.330215 4 -3.330215
5 -3.195118 5 -3.195118
6 -3.035358 6 -3.035358
7 -347.182406 7 -347.182406
8 -348.253665 8 -348.253665
9 -345.424528 9 -345.424528
10 -346.758349 10 -346.758349
11 -344.603627 11 -344.603627
12 -346.849801 12 -346.849801
13 -345.015235 13 -345.015235
14 -346.569097 14 -346.569097
15 -344.892954 15 -344.892954
16 -347.628843 16 -347.628843
17 -345.776979 17 -345.776979
18 -342.906251 18 -342.906251
19 -343.569002 19 -343.569002
20 -343.317892 20 -343.317892
21 -341.057270 21 -341.057270
22 -342.067006 22 -342.067006
23 -342.528496 23 -342.528496
24 -342.900954 24 -342.900954
25 -340.983380 25 -340.983380
26 -342.479965 26 -342.479965
27 -340.174298 27 -340.174298
28 -343.805462 28 -343.805462
29 -400.111422 29 -400.111422
30 -399.591699 30 -399.591699
31 -398.422617 31 -398.422617
32 -395.110340 32 -395.110340
33 -396.833326 33 -396.833326
34 -400.444368 34 -400.444368
35 -397.843043 35 -397.843043
36 -399.776798 36 -399.776798
37 -399.168074 37 -399.168074
38 -396.984690 38 -396.984690
39 -399.581912 39 -399.581912
40 -3.142019 40 -3.142019
41 -3.338596 41 -3.338596
42 -3.416929 42 -3.416929
43 -3.409602 43 -3.409602
44 -3.330215 44 -3.330215
45 -3.195118 45 -3.195118
46 -3.035358 46 -3.035358
forces \ forces \
0 [[1.1869253621046177e-16, -1.7429070520896771e-16, -1.397277865277868e-16]] 0 [[1.1869253621046177e-16, -1.7429070520896771e-16, -1.397277865277868e-16]]
1 [[-1.92404082484227e-16, 4.231084758750405e-17, 3.6193775346684653e-17]] 1 [[-1.92404082484227e-16, 4.231084758750405e-17, 3.6193775346684653e-17]]
2 [[-2.9113397169423695e-17, 7.54965057835309e-17, -3.624419431643654e-17]] 2 [[-2.9113397169423695e-17, 7.54965057835309e-17, -3.624419431643654e-17]]
3 [[3.771496125435321e-17, 3.412312546579927e-17, -2.4310047599025677e-17]] 3 [[3.771496125435321e-17, 3.412312546579927e-17, -2.4310047599025677e-17]]
4 [[-2.0545362501508919e-16, -3.5486130576273854e-17, 3.5486130576273854e-17]] 4 [[-2.0545362501508919e-16, -3.5486130576273854e-17, 3.5486130576273854e-17]]
5 [[1.6101257219667079e-16, -4.2948421129906387e-17, 4.2948421129906387e-17]] 5 [[1.6101257219667079e-16, -4.2948421129906387e-17, 4.2948421129906387e-17]]
6 [[-5.946777565406637e-17, -1.0605082175909553e-16, -1.2946304704347008e-16]] 6 [[-5.946777565406637e-17, -1.0605082175909553e-16, -1.2946304704347008e-16]]
7 [[-1.2656542480726799e-14, -1.46965772884755e-14, -1.61017033040167e-14], [-1.3905543383430098e-14, 4.5310977192514186e-15, 4.8333732849403796e-15], [4.9682480351975795e-15, -1.4072076837123899e-1... 7 [[-1.2656542480726799e-14, -1.46965772884755e-14, -1.61017033040167e-14], [-1.3905543383430098e-14, 4.5310977192514186e-15, 4.8333732849403796e-15], [4.9682480351975795e-15, -1.4072076837123899e-1...
8 [[-0.21910202935187897, -0.37573419410584397, 0.43392575377979187], [0.16208168404695897, -0.00671505675904709, 1.03458554920361], [-1.2001630139266497, -0.40207322348963503, -0.45620473735655703]... 8 [[-0.21910202935187897, -0.37573419410584397, 0.43392575377979187], [0.16208168404695897, -0.00671505675904709, 1.03458554920361], [-1.2001630139266497, -0.40207322348963503, -0.45620473735655703]...
9 [[-0.023031834879881696, 0.042841438691562095, 0.5899774836434479], [-0.5418151518759569, 0.6754733604036028, -0.5582999589284809], [-0.6011411771360858, -0.355590065329821, -0.0035901986306415582... 9 [[-0.023031834879881696, 0.042841438691562095, 0.5899774836434479], [-0.5418151518759569, 0.6754733604036028, -0.5582999589284809], [-0.6011411771360858, -0.355590065329821, -0.0035901986306415582...
10 [[-0.32237334386615796, 0.43406651671724894, -0.5886238546572939], [-0.6295919499998729, 0.07530471384300086, -0.12687342568230403], [-0.06506588733991228, 0.8782024477953109, -0.12243680387297393... 10 [[-0.32237334386615796, 0.43406651671724894, -0.5886238546572939], [-0.6295919499998729, 0.07530471384300086, -0.12687342568230403], [-0.06506588733991228, 0.8782024477953109, -0.12243680387297393...
11 [[0.45078377546738896, -0.7167806257867769, -0.320969733282763], [0.5707773027838049, -0.5494069530705199, 0.510256621543289], [-0.36439749359274193, 0.17709586752044496, 0.23127352998569298], [0.... 11 [[0.45078377546738896, -0.7167806257867769, -0.320969733282763], [0.5707773027838049, -0.5494069530705199, 0.510256621543289], [-0.36439749359274193, 0.17709586752044496, 0.23127352998569298], [0....
12 [[-0.38409855462219894, 0.12077975249818296, 0.024465771201292483], [-0.6560764999451358, -1.05845756801878, -0.658182913095082], [-0.5103420261962529, -0.35656271154938, 0.7090309519821769], [-0.... 12 [[-0.38409855462219894, 0.12077975249818296, 0.024465771201292483], [-0.6560764999451358, -1.05845756801878, -0.658182913095082], [-0.5103420261962529, -0.35656271154938, 0.7090309519821769], [-0....
13 [[0.22044015995668098, -0.2607278388818459, -0.3855032322190499], [0.7754186544660099, -0.04652340102386694, -0.26232164996063695], [0.43147792874898694, -0.9840256256911009, 0.34987911571105595],... 13 [[0.22044015995668098, -0.2607278388818459, -0.3855032322190499], [0.7754186544660099, -0.04652340102386694, -0.26232164996063695], [0.43147792874898694, -0.9840256256911009, 0.34987911571105595],...
14 [[-0.5020206209676749, 0.007307596544171969, 0.24586848661916993], [-1.1645196400331899, 0.1476285180684419, 0.6168850904586589], [0.7183114431792579, -0.5420093171036479, -0.06687387962480258], [... 14 [[-0.5020206209676749, 0.007307596544171969, 0.24586848661916993], [-1.1645196400331899, 0.1476285180684419, 0.6168850904586589], [0.7183114431792579, -0.5420093171036479, -0.06687387962480258], [...
15 [[0.04806202889719739, 0.48969724353819394, 1.29371057615331], [0.5538169933185199, -0.7855310261714289, -0.033081946412792815], [0.34832740609982993, 0.9937361742308158, 0.30650548838004904], [-0... 15 [[0.04806202889719739, 0.48969724353819394, 1.29371057615331], [0.5538169933185199, -0.7855310261714289, -0.033081946412792815], [0.34832740609982993, 0.9937361742308158, 0.30650548838004904], [-0...
16 [[0.24033044872062098, 1.5305792677179897, -0.6791236163119347], [0.05903491332573559, 0.148151392595253, 0.542468964409148], [0.07921843405670739, 0.145966157214324, 0.7342269238916159], [0.77503... 16 [[0.24033044872062098, 1.5305792677179897, -0.6791236163119347], [0.05903491332573559, 0.148151392595253, 0.542468964409148], [0.07921843405670739, 0.145966157214324, 0.7342269238916159], [0.77503...
17 [[-0.13926025211222698, -0.0920021629424733, 0.21001691285267599], [0.6767944835284789, -1.1148612203782198, 1.7165284718417098], [-0.7950973845960859, 0.2356681337270629, 0.13328556064538893], [0... 17 [[-0.13926025211222698, -0.0920021629424733, 0.21001691285267599], [0.6767944835284789, -1.1148612203782198, 1.7165284718417098], [-0.7950973845960859, 0.2356681337270629, 0.13328556064538893], [0...
18 [[-1.3933298959045699e-14, -0.10827842091784899, -0.108278420917849], [-0.10827842091784899, -1.3877479054990188e-14, -0.108278420917849], [-0.10827842091784899, -0.108278420917849, -1.38424758326... 18 [[-1.3933298959045699e-14, -0.10827842091784899, -0.108278420917849], [-0.10827842091784899, -1.3877479054990188e-14, -0.108278420917849], [-0.10827842091784899, -0.108278420917849, -1.38424758326...
19 [[-0.45079778130218695, 0.19236747741170795, 0.23614131969524693], [1.2984317307784499, 0.04751568933291938, 0.005443425577977482], [0.48875760189522893, -0.5765163470127929, -0.5531364786691719],... 19 [[-0.45079778130218695, 0.19236747741170795, 0.23614131969524693], [1.2984317307784499, 0.04751568933291938, 0.005443425577977482], [0.48875760189522893, -0.5765163470127929, -0.5531364786691719],...
20 [[-0.6920262907044069, 0.3986975029533409, 0.10738641941643497], [-1.2097205794553298, -2.21423543020926, -0.8363385508172672], [-0.36839592956658596, 0.35919893904268096, 0.09738195090664269], [2... 20 [[-0.6920262907044069, 0.3986975029533409, 0.10738641941643497], [-1.2097205794553298, -2.21423543020926, -0.8363385508172672], [-0.36839592956658596, 0.35919893904268096, 0.09738195090664269], [2...
21 [[0.5607305368018309, 0.07454461225822963, 0.17092757180402804], [0.7460358156721709, -0.9693709228665989, -0.357775642488428], [-1.4982109077380097, 1.0695224870660298, 0.17016025464137993], [1.1... 21 [[0.5607305368018309, 0.07454461225822963, 0.17092757180402804], [0.7460358156721709, -0.9693709228665989, -0.357775642488428], [-1.4982109077380097, 1.0695224870660298, 0.17016025464137993], [1.1...
22 [[0.7768634672312369, 0.615614277472231, -0.6520778674544528], [0.5196497874591819, -0.7614150189249069, 0.33452284258026094], [1.0185593798470798, 0.11349094338622906, -1.1138567887728799], [0.39... 22 [[0.7768634672312369, 0.615614277472231, -0.6520778674544528], [0.5196497874591819, -0.7614150189249069, 0.33452284258026094], [1.0185593798470798, 0.11349094338622906, -1.1138567887728799], [0.39...
23 [[-1.2511641505681497, 0.045660252990561916, 0.39426999337691987], [-0.4923847861277789, -0.676187288680257, -1.3802167704923], [-0.12072100498159098, 0.5666924914439229, -0.8825937576849239], [0.... 23 [[-1.2511641505681497, 0.045660252990561916, 0.39426999337691987], [-0.4923847861277789, -0.676187288680257, -1.3802167704923], [-0.12072100498159098, 0.5666924914439229, -0.8825937576849239], [0....
24 [[0.5080309295986539, -0.4875222169174689, 0.46898176405272696], [0.11031309252296198, -0.7243436014688799, 1.2808414836059598], [0.6855285827079979, 0.576817447055947, 0.31599931473888204], [0.50... 24 [[0.5080309295986539, -0.4875222169174689, 0.46898176405272696], [0.11031309252296198, -0.7243436014688799, 1.2808414836059598], [0.6855285827079979, 0.576817447055947, 0.31599931473888204], [0.50...
25 [[-0.6923371397061229, 0.9615117892959398, 0.396261839433264], [0.18083100499512797, -0.47103552335731996, 0.5072798013711759], [-0.22735248831930896, 0.37011177620569996, -1.1740345740817597], [0... 25 [[-0.6923371397061229, 0.9615117892959398, 0.396261839433264], [0.18083100499512797, -0.47103552335731996, 0.5072798013711759], [-0.22735248831930896, 0.37011177620569996, -1.1740345740817597], [0...
26 [[0.46940172398488794, 0.557542533896084, 0.861383405261689], [-0.16043498489103097, -1.0997839627759998, -0.013974118313924476], [-0.13554483762266598, 0.6363641149062679, 0.153788969879775], [1.... 26 [[0.46940172398488794, 0.557542533896084, 0.861383405261689], [-0.16043498489103097, -1.0997839627759998, -0.013974118313924476], [-0.13554483762266598, 0.6363641149062679, 0.153788969879775], [1....
27 [[-1.1653987834207897, -0.07515193371140247, -0.13414295102360305], [0.17707911646472896, 0.37588362216028093, 0.10312993516925903], [0.6003632691780849, 0.3869695806628, 0.03431754153949555], [-0... 27 [[-1.1653987834207897, -0.07515193371140247, -0.13414295102360305], [0.17707911646472896, 0.37588362216028093, 0.10312993516925903], [0.6003632691780849, 0.3869695806628, 0.03431754153949555], [-0...
28 [[0.42819147658911194, -1.3404675072584398, -0.840042992949223], [0.47822853532413195, -0.07949121681390955, -0.36737406099153697], [-0.9172012989939929, 0.3239785862266829, -0.013009375610539234]... 28 [[0.42819147658911194, -1.3404675072584398, -0.840042992949223], [0.47822853532413195, -0.07949121681390955, -0.36737406099153697], [-0.9172012989939929, 0.3239785862266829, -0.013009375610539234]...
29 [[-8.770761894538741e-15, 1.15657750043852e-09, 0.109956784695642], [-1.0824674490095302e-15, 1.15657515335765e-09, 0.10995678469564], [2.4308896909297503e-15, 1.1565748914144101e-09, 0.1099567846... 29 [[-8.770761894538741e-15, 1.15657750043852e-09, 0.109956784695642], [-1.0824674490095302e-15, 1.15657515335765e-09, 0.10995678469564], [2.4308896909297503e-15, 1.1565748914144101e-09, 0.1099567846...
30 [[-0.570999988178131, 1.09833300989089, -0.566585257198732], [-0.0492000252908114, 0.597416506778632, 0.966635869516025], [-0.0024866801464792, -0.0674126479000064, 0.2546322145358], [0.2289085885... 30 [[-0.570999988178131, 1.09833300989089, -0.566585257198732], [-0.0492000252908114, 0.597416506778632, 0.966635869516025], [-0.0024866801464792, -0.0674126479000064, 0.2546322145358], [0.2289085885...
31 [[-0.555658749547497, 0.42566314828364993, 0.466167261187443], [-1.39449792316952, -0.5017985009363372, 0.4456531170887249], [1.25410857633035, -0.33111996310077596, -0.24658722383829995], [0.3911... 31 [[-0.555658749547497, 0.42566314828364993, 0.466167261187443], [-1.39449792316952, -0.5017985009363372, 0.4456531170887249], [1.25410857633035, -0.33111996310077596, -0.24658722383829995], [0.3911...
32 [[0.550884754551829, 0.33865983742272204, 0.12042096866985205], [0.189727589275692, -0.524367356684999, -0.17886090450862402], [-1.6758650723099, -0.31030261483377614, 0.6946509585213989], [0.4453... 32 [[0.550884754551829, 0.33865983742272204, 0.12042096866985205], [0.189727589275692, -0.524367356684999, -0.17886090450862402], [-1.6758650723099, -0.31030261483377614, 0.6946509585213989], [0.4453...
33 [[0.235449441284142, 0.601163461325591, 0.04737458109310825], [0.337344266123105, 0.66485729403382, 0.37768738132523805], [-0.171831038530166, -0.11286098093109101, -0.07415135874528352], [-0.1966... 33 [[0.235449441284142, 0.601163461325591, 0.04737458109310825], [0.337344266123105, 0.66485729403382, 0.37768738132523805], [-0.171831038530166, -0.11286098093109101, -0.07415135874528352], [-0.1966...
34 [[1.15453322332565, 0.04603660924771737, -1.21282260887155], [-0.403390913673288, -0.18969536874868004, 0.030526533198225264], [-0.683024325114862, -0.967333273082708, 0.4114320467737619], [-0.867... 34 [[1.15453322332565, 0.04603660924771737, -1.21282260887155], [-0.403390913673288, -0.18969536874868004, 0.030526533198225264], [-0.683024325114862, -0.967333273082708, 0.4114320467737619], [-0.867...
35 [[0.742004122721361, 0.22577315893502206, 0.12298868177971806], [0.771069504028052, -0.90014541931557, -0.660403448738781], [-0.462456173466872, 1.24796716628589, -0.4192010350460109], [0.08219110... 35 [[0.742004122721361, 0.22577315893502206, 0.12298868177971806], [0.771069504028052, -0.90014541931557, -0.660403448738781], [-0.462456173466872, 1.24796716628589, -0.4192010350460109], [0.08219110...
36 [[0.552749731038993, -0.46087407707755496, 0.177277816519943], [0.340079509783844, 0.23574679643440802, 0.26784307872713603], [0.388298578408562, 0.331969932822417, 0.34399524632239104], [-0.59826... 36 [[0.552749731038993, -0.46087407707755496, 0.177277816519943], [0.340079509783844, 0.23574679643440802, 0.26784307872713603], [0.388298578408562, 0.331969932822417, 0.34399524632239104], [-0.59826...
37 [[0.570532228156976, 0.17193739345012202, 0.796311675035985], [0.67297011060888, -0.81773224395498, 0.207420342553107], [0.391385096561351, -0.862073619446019, 0.597813478897486], [-0.270452726779... 37 [[0.570532228156976, 0.17193739345012202, 0.796311675035985], [0.67297011060888, -0.81773224395498, 0.207420342553107], [0.391385096561351, -0.862073619446019, 0.597813478897486], [-0.270452726779...
38 [[-1.11093024791963, -0.6986058376048401, 0.44674121624886787], [0.0416051560041239, -0.0424634970331458, -0.0874515615419252], [-0.135122617155289, -0.778975629913174, -1.04402814519501], [0.8442... 38 [[-1.11093024791963, -0.6986058376048401, 0.44674121624886787], [0.0416051560041239, -0.0424634970331458, -0.0874515615419252], [-0.135122617155289, -0.778975629913174, -1.04402814519501], [0.8442...
39 [[-0.645092069902244, 0.04920122139904896, 0.21081031345366397], [1.14893686034324, -0.6114894792387109, -0.40665475671972495], [-0.287092609914331, 0.292443458702414, -0.801010316546939], [-0.184... 39 [[-0.645092069902244, 0.04920122139904896, 0.21081031345366397], [1.14893686034324, -0.6114894792387109, -0.40665475671972495], [-0.287092609914331, 0.292443458702414, -0.801010316546939], [-0.184...
40 [[1.1869253621046177e-16, -1.7429070520896771e-16, -1.397277865277868e-16]] 40 [[1.1869253621046177e-16, -1.7429070520896771e-16, -1.397277865277868e-16]]
41 [[-1.92404082484227e-16, 4.231084758750405e-17, 3.6193775346684653e-17]] 41 [[-1.92404082484227e-16, 4.231084758750405e-17, 3.6193775346684653e-17]]
42 [[-2.9113397169423695e-17, 7.54965057835309e-17, -3.624419431643654e-17]] 42 [[-2.9113397169423695e-17, 7.54965057835309e-17, -3.624419431643654e-17]]
43 [[3.771496125435321e-17, 3.412312546579927e-17, -2.4310047599025677e-17]] 43 [[3.771496125435321e-17, 3.412312546579927e-17, -2.4310047599025677e-17]]
44 [[-2.0545362501508919e-16, -3.5486130576273854e-17, 3.5486130576273854e-17]] 44 [[-2.0545362501508919e-16, -3.5486130576273854e-17, 3.5486130576273854e-17]]
45 [[1.6101257219667079e-16, -4.2948421129906387e-17, 4.2948421129906387e-17]] 45 [[1.6101257219667079e-16, -4.2948421129906387e-17, 4.2948421129906387e-17]]
46 [[-5.946777565406637e-17, -1.0605082175909553e-16, -1.2946304704347008e-16]] 46 [[-5.946777565406637e-17, -1.0605082175909553e-16, -1.2946304704347008e-16]]
number_of_atoms number_of_atoms
0 1.0 0 1.0
1 1.0 1 1.0
2 1.0 2 1.0
3 1.0 3 1.0
4 1.0 4 1.0
5 1.0 5 1.0
6 1.0 6 1.0
7 108.0 7 108.0
8 108.0 8 108.0
9 108.0 9 108.0
10 108.0 10 108.0
11 108.0 11 108.0
12 108.0 12 108.0
13 108.0 13 108.0
14 108.0 14 108.0
15 108.0 15 108.0
16 108.0 16 108.0
17 108.0 17 108.0
18 107.0 18 107.0
19 107.0 19 107.0
20 107.0 20 107.0
21 107.0 21 107.0
22 107.0 22 107.0
23 107.0 23 107.0
24 107.0 24 107.0
25 107.0 25 107.0
26 107.0 26 107.0
27 107.0 27 107.0
28 107.0 28 107.0
29 128.0 29 128.0
30 128.0 30 128.0
31 128.0 31 128.0
32 128.0 32 128.0
33 128.0 33 128.0
34 128.0 34 128.0
35 128.0 35 128.0
36 128.0 36 128.0
37 128.0 37 128.0
38 128.0 38 128.0
39 128.0 39 128.0
40 1.0 40 1.0
41 1.0 41 1.0
42 1.0 42 1.0
43 1.0 43 1.0
44 1.0 44 1.0
45 1.0 45 1.0
46 1.0 46 1.0
%% Cell type:markdown id:transsexual-journalist tags: %% Cell type:markdown id:imperial-belarus tags:
## **Add structures from the MD** ## **Add structures from the MD**
Structures sampled every 10 snapshots (we may need to minimize the structures from the MD) We also add some structures obtained from the MD simulations
%% Cell type:code id:earlier-static tags: %% Cell type:code id:healthy-structure tags: