From 68b957960ae79ab08046bfbbce920c1c592c6d2c Mon Sep 17 00:00:00 2001
From: Sudarsan Surendralal <sudarsan.sl@gmail.com>
Date: Tue, 9 Mar 2021 10:41:36 +0100
Subject: [PATCH] Cosmetic changes to ex_02
---
.../ex_02_creating_structure_databases.ipynb | 1347 +++++------------
1 file changed, 410 insertions(+), 937 deletions(-)
diff --git a/day_1/ex_02_creating_structure_databases.ipynb b/day_1/ex_02_creating_structure_databases.ipynb
index e016483..d746423 100644
--- a/day_1/ex_02_creating_structure_databases.ipynb
+++ b/day_1/ex_02_creating_structure_databases.ipynb
@@ -2,7 +2,7 @@
"cells": [
{
"cell_type": "markdown",
- "id": "appointed-stylus",
+ "id": "previous-lotus",
"metadata": {},
"source": [
"# [**Workflows for atomistic simulations**](http://potentials.rub.de/) "
@@ -10,7 +10,7 @@
},
{
"cell_type": "markdown",
- "id": "straight-bicycle",
+ "id": "solid-explosion",
"metadata": {},
"source": [
"## **Day 1 - Atomistic simulations with [pyiron](https://pyiron.org)**\n",
@@ -29,7 +29,7 @@
},
{
"cell_type": "markdown",
- "id": "durable-leone",
+ "id": "apparent-assembly",
"metadata": {},
"source": [
"## **Importing necessary modules and creating a project**\n",
@@ -40,7 +40,7 @@
{
"cell_type": "code",
"execution_count": 1,
- "id": "novel-wisconsin",
+ "id": "fitting-testing",
"metadata": {},
"outputs": [],
"source": [
@@ -52,7 +52,7 @@
{
"cell_type": "code",
"execution_count": 2,
- "id": "sitting-religious",
+ "id": "mature-bearing",
"metadata": {},
"outputs": [],
"source": [
@@ -62,7 +62,7 @@
{
"cell_type": "code",
"execution_count": 3,
- "id": "technical-newport",
+ "id": "considered-karma",
"metadata": {},
"outputs": [],
"source": [
@@ -71,7 +71,7 @@
},
{
"cell_type": "markdown",
- "id": "based-kentucky",
+ "id": "controlled-david",
"metadata": {},
"source": [
"## Creating a structure \"container\" from the data\n",
@@ -83,8 +83,8 @@
},
{
"cell_type": "code",
- "execution_count": 9,
- "id": "attached-germany",
+ "execution_count": 4,
+ "id": "wrong-pickup",
"metadata": {},
"outputs": [],
"source": [
@@ -94,8 +94,8 @@
},
{
"cell_type": "code",
- "execution_count": 16,
- "id": "filled-natural",
+ "execution_count": 5,
+ "id": "current-vanilla",
"metadata": {},
"outputs": [],
"source": [
@@ -105,7 +105,7 @@
},
{
"cell_type": "markdown",
- "id": "married-storm",
+ "id": "dominican-northwest",
"metadata": {},
"source": [
"## **Add structures from the E-V curves**\n",
@@ -115,8 +115,8 @@
},
{
"cell_type": "code",
- "execution_count": 17,
- "id": "mediterranean-upset",
+ "execution_count": 6,
+ "id": "concrete-background",
"metadata": {},
"outputs": [],
"source": [
@@ -127,7 +127,7 @@
},
{
"cell_type": "markdown",
- "id": "acquired-missile",
+ "id": "worse-scheduling",
"metadata": {},
"source": [
"We can obtain this data as a `pandas` table"
@@ -135,8 +135,8 @@
},
{
"cell_type": "code",
- "execution_count": 18,
- "id": "greatest-person",
+ "execution_count": 7,
+ "id": "changed-shame",
"metadata": {},
"outputs": [
{
@@ -170,326 +170,6 @@
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
- " <td>None</td>\n",
- " <td>(Atom('Cu', [0.0, 0.0, 0.0], index=0))</td>\n",
- " <td>-3.142019</td>\n",
- " <td>[[1.1869253621046177e-16, -1.7429070520896771e-16, -1.397277865277868e-16]]</td>\n",
- " <td>1.0</td>\n",
- " </tr>\n",
- " <tr>\n",
- " <th>1</th>\n",
- " <td>None</td>\n",
- " <td>(Atom('Cu', [0.0, 0.0, 0.0], index=0))</td>\n",
- " <td>-3.338596</td>\n",
- " <td>[[-1.92404082484227e-16, 4.231084758750405e-17, 3.6193775346684653e-17]]</td>\n",
- " <td>1.0</td>\n",
- " </tr>\n",
- " <tr>\n",
- " <th>2</th>\n",
- " <td>None</td>\n",
- " <td>(Atom('Cu', [0.0, 0.0, 0.0], index=0))</td>\n",
- " <td>-3.416929</td>\n",
- " <td>[[-2.9113397169423695e-17, 7.54965057835309e-17, -3.624419431643654e-17]]</td>\n",
- " <td>1.0</td>\n",
- " </tr>\n",
- " <tr>\n",
- " <th>3</th>\n",
- " <td>None</td>\n",
- " <td>(Atom('Cu', [0.0, 0.0, 0.0], index=0))</td>\n",
- " <td>-3.409602</td>\n",
- " <td>[[3.771496125435321e-17, 3.412312546579927e-17, -2.4310047599025677e-17]]</td>\n",
- " <td>1.0</td>\n",
- " </tr>\n",
- " <tr>\n",
- " <th>4</th>\n",
- " <td>None</td>\n",
- " <td>(Atom('Cu', [0.0, 0.0, 0.0], index=0))</td>\n",
- " <td>-3.330215</td>\n",
- " <td>[[-2.0545362501508919e-16, -3.5486130576273854e-17, 3.5486130576273854e-17]]</td>\n",
- " <td>1.0</td>\n",
- " </tr>\n",
- " <tr>\n",
- " <th>5</th>\n",
- " <td>None</td>\n",
- " <td>(Atom('Cu', [0.0, 0.0, 0.0], index=0))</td>\n",
- " <td>-3.195118</td>\n",
- " <td>[[1.6101257219667079e-16, -4.2948421129906387e-17, 4.2948421129906387e-17]]</td>\n",
- " <td>1.0</td>\n",
- " </tr>\n",
- " <tr>\n",
- " <th>6</th>\n",
- " <td>None</td>\n",
- " <td>(Atom('Cu', [0.0, 0.0, 0.0], index=0))</td>\n",
- " <td>-3.035358</td>\n",
- " <td>[[-5.946777565406637e-17, -1.0605082175909553e-16, -1.2946304704347008e-16]]</td>\n",
- " <td>1.0</td>\n",
- " </tr>\n",
- " <tr>\n",
- " <th>7</th>\n",
- " <td>None</td>\n",
- " <td>(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...</td>\n",
- " <td>-347.182406</td>\n",
- " <td>[[-1.2656542480726799e-14, -1.46965772884755e-14, -1.61017033040167e-14], [-1.3905543383430098e-14, 4.5310977192514186e-15, 4.8333732849403796e-15], [4.9682480351975795e-15, -1.4072076837123899e-1...</td>\n",
- " <td>108.0</td>\n",
- " </tr>\n",
- " <tr>\n",
- " <th>8</th>\n",
- " <td>None</td>\n",
- " <td>(Atom('Cu', [0.140426153531212, 11.00934611760493, 10.968207696001379], index=0), Atom('Cu', [10.983357200359302, 1.779939365335074, 1.7146804782560905], index=1), Atom('Cu', [2.1228644677344763, ...</td>\n",
- " <td>-348.253665</td>\n",
- " <td>[[-0.21910202935187897, -0.37573419410584397, 0.43392575377979187], [0.16208168404695897, -0.00671505675904709, 1.03458554920361], [-1.2001630139266497, -0.40207322348963503, -0.45620473735655703]...</td>\n",
- " <td>108.0</td>\n",
- " </tr>\n",
- " <tr>\n",
- " <th>9</th>\n",
- " <td>None</td>\n",
- " <td>(Atom('Cu', [0.1407579358923329, 11.020287239626356, 10.855878337455094], index=0), Atom('Cu', [0.29542104007972325, 1.6514729828183248, 1.7760939949715002], index=1), Atom('Cu', [1.99578258187561...</td>\n",
- " <td>-345.424528</td>\n",
- " <td>[[-0.023031834879881696, 0.042841438691562095, 0.5899774836434479], [-0.5418151518759569, 0.6754733604036028, -0.5582999589284809], [-0.6011411771360858, -0.355590065329821, -0.0035901986306415582...</td>\n",
- " <td>108.0</td>\n",
- " </tr>\n",
- " <tr>\n",
- " <th>10</th>\n",
- " <td>None</td>\n",
- " <td>(Atom('Cu', [0.04675277832683521, 10.951786003502875, 0.20014601215416555], index=0), Atom('Cu', [0.08453269827616121, 1.807218974303731, 1.7664733621606055], index=1), Atom('Cu', [1.9597357123378...</td>\n",
- " <td>-346.758349</td>\n",
- " <td>[[-0.32237334386615796, 0.43406651671724894, -0.5886238546572939], [-0.6295919499998729, 0.07530471384300086, -0.12687342568230403], [-0.06506588733991228, 0.8782024477953109, -0.12243680387297393...</td>\n",
- " <td>108.0</td>\n",
- " </tr>\n",
- " <tr>\n",
- " <th>11</th>\n",
- " <td>None</td>\n",
- " <td>(Atom('Cu', [10.991332780892245, 11.027168829788469, 0.17044757336885022], index=0), Atom('Cu', [10.869778028731718, 1.9053524080340238, 1.7569642307109068], index=1), Atom('Cu', [1.89027128290555...</td>\n",
- " <td>-344.603627</td>\n",
- " <td>[[0.45078377546738896, -0.7167806257867769, -0.320969733282763], [0.5707773027838049, -0.5494069530705199, 0.510256621543289], [-0.36439749359274193, 0.17709586752044496, 0.23127352998569298], [0....</td>\n",
- " <td>108.0</td>\n",
- " </tr>\n",
- " <tr>\n",
- " <th>12</th>\n",
- " <td>None</td>\n",
- " <td>(Atom('Cu', [10.958070767872973, 0.05270018288525903, 11.015795828313184], index=0), Atom('Cu', [0.04540970504125744, 2.0780519854689388, 1.8353871076994486], index=1), Atom('Cu', [1.8285627799497...</td>\n",
- " <td>-346.849801</td>\n",
- " <td>[[-0.38409855462219894, 0.12077975249818296, 0.024465771201292483], [-0.6560764999451358, -1.05845756801878, -0.658182913095082], [-0.5103420261962529, -0.35656271154938, 0.7090309519821769], [-0....</td>\n",
- " <td>108.0</td>\n",
- " </tr>\n",
- " <tr>\n",
- " <th>13</th>\n",
- " <td>None</td>\n",
- " <td>(Atom('Cu', [10.903697402270481, 10.843249424147054, 0.09574490333935876], index=0), Atom('Cu', [10.594918916668115, 1.7187193807013557, 1.957301113531466], index=1), Atom('Cu', [1.676074002401865...</td>\n",
- " <td>-345.015235</td>\n",
- " <td>[[0.22044015995668098, -0.2607278388818459, -0.3855032322190499], [0.7754186544660099, -0.04652340102386694, -0.26232164996063695], [0.43147792874898694, -0.9840256256911009, 0.34987911571105595],...</td>\n",
- " <td>108.0</td>\n",
- " </tr>\n",
- " <tr>\n",
- " <th>14</th>\n",
- " <td>None</td>\n",
- " <td>(Atom('Cu', [0.25841198959969514, 0.07063449316617948, 10.912283030401635], index=0), Atom('Cu', [0.19649020014428978, 1.7891621064498946, 1.803181486480956], index=1), Atom('Cu', [1.7493171890008...</td>\n",
- " <td>-346.569097</td>\n",
- " <td>[[-0.5020206209676749, 0.007307596544171969, 0.24586848661916993], [-1.1645196400331899, 0.1476285180684419, 0.6168850904586589], [0.7183114431792579, -0.5420093171036479, -0.06687387962480258], [...</td>\n",
- " <td>108.0</td>\n",
- " </tr>\n",
- " <tr>\n",
- " <th>15</th>\n",
- " <td>None</td>\n",
- " <td>(Atom('Cu', [0.004994793789590358, 10.985055637636528, 10.904222762438215], index=0), Atom('Cu', [10.941729664004177, 1.8868614122932958, 1.8147512571785023], index=1), Atom('Cu', [1.8438031255437...</td>\n",
- " <td>-344.892954</td>\n",
- " <td>[[0.04806202889719739, 0.48969724353819394, 1.29371057615331], [0.5538169933185199, -0.7855310261714289, -0.033081946412792815], [0.34832740609982993, 0.9937361742308158, 0.30650548838004904], [-0...</td>\n",
- " <td>108.0</td>\n",
- " </tr>\n",
- " <tr>\n",
- " <th>16</th>\n",
- " <td>None</td>\n",
- " <td>(Atom('Cu', [0.03645923830333788, 10.856010693932728, 10.970572990196315], index=0), Atom('Cu', [10.913522535008392, 1.8161914381204696, 1.5447581077411967], index=1), Atom('Cu', [1.77583933019795...</td>\n",
- " <td>-347.628843</td>\n",
- " <td>[[0.24033044872062098, 1.5305792677179897, -0.6791236163119347], [0.05903491332573559, 0.148151392595253, 0.542468964409148], [0.07921843405670739, 0.145966157214324, 0.7342269238916159], [0.77503...</td>\n",
- " <td>108.0</td>\n",
- " </tr>\n",
- " <tr>\n",
- " <th>17</th>\n",
- " <td>None</td>\n",
- " <td>(Atom('Cu', [0.009767181825404037, 0.0071865231528328395, 11.0089023992238], index=0), Atom('Cu', [10.89374596605574, 1.9969194212313586, 1.595578837066423], index=1), Atom('Cu', [2.05442192913884...</td>\n",
- " <td>-345.776979</td>\n",
- " <td>[[-0.13926025211222698, -0.0920021629424733, 0.21001691285267599], [0.6767944835284789, -1.1148612203782198, 1.7165284718417098], [-0.7950973845960859, 0.2356681337270629, 0.13328556064538893], [0...</td>\n",
- " <td>108.0</td>\n",
- " </tr>\n",
- " <tr>\n",
- " <th>18</th>\n",
- " <td>None</td>\n",
- " <td>(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...</td>\n",
- " <td>-342.906251</td>\n",
- " <td>[[-1.3933298959045699e-14, -0.10827842091784899, -0.108278420917849], [-0.10827842091784899, -1.3877479054990188e-14, -0.108278420917849], [-0.10827842091784899, -0.108278420917849, -1.38424758326...</td>\n",
- " <td>107.0</td>\n",
- " </tr>\n",
- " <tr>\n",
- " <th>19</th>\n",
- " <td>None</td>\n",
- " <td>(Atom('Cu', [0.10390109091492504, 1.9580560553035629, 1.779188560767685], index=0), Atom('Cu', [1.3868099266682106, 10.93717630776342, 1.601790948781396], index=1), Atom('Cu', [1.7183987889409966,...</td>\n",
- " <td>-343.569002</td>\n",
- " <td>[[-0.45079778130218695, 0.19236747741170795, 0.23614131969524693], [1.2984317307784499, 0.04751568933291938, 0.005443425577977482], [0.48875760189522893, -0.5765163470127929, -0.5531364786691719],...</td>\n",
- " <td>107.0</td>\n",
- " </tr>\n",
- " <tr>\n",
- " <th>20</th>\n",
- " <td>None</td>\n",
- " <td>(Atom('Cu', [0.2223234793002756, 1.6999920633404135, 1.7623980235259114], index=0), Atom('Cu', [2.122882660879041, 0.18624238423025943, 2.030808683988878], index=1), Atom('Cu', [1.7334689484700414...</td>\n",
- " <td>-343.317892</td>\n",
- " <td>[[-0.6920262907044069, 0.3986975029533409, 0.10738641941643497], [-1.2097205794553298, -2.21423543020926, -0.8363385508172672], [-0.36839592956658596, 0.35919893904268096, 0.09738195090664269], [2...</td>\n",
- " <td>107.0</td>\n",
- " </tr>\n",
- " <tr>\n",
- " <th>21</th>\n",
- " <td>None</td>\n",
- " <td>(Atom('Cu', [10.839434974930338, 1.9008464900018593, 1.6867963294684278], index=0), Atom('Cu', [1.5876598581358559, 0.15447557118789498, 1.715299994817798], index=1), Atom('Cu', [2.148606011735498...</td>\n",
- " <td>-341.057270</td>\n",
- " <td>[[0.5607305368018309, 0.07454461225822963, 0.17092757180402804], [0.7460358156721709, -0.9693709228665989, -0.357775642488428], [-1.4982109077380097, 1.0695224870660298, 0.17016025464137993], [1.1...</td>\n",
- " <td>107.0</td>\n",
- " </tr>\n",
- " <tr>\n",
- " <th>22</th>\n",
- " <td>None</td>\n",
- " <td>(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...</td>\n",
- " <td>-342.067006</td>\n",
- " <td>[[0.7768634672312369, 0.615614277472231, -0.6520778674544528], [0.5196497874591819, -0.7614150189249069, 0.33452284258026094], [1.0185593798470798, 0.11349094338622906, -1.1138567887728799], [0.39...</td>\n",
- " <td>107.0</td>\n",
- " </tr>\n",
- " <tr>\n",
- " <th>23</th>\n",
- " <td>None</td>\n",
- " <td>(Atom('Cu', [0.18579648605077317, 1.6025971043596021, 1.8725196193757527], index=0), Atom('Cu', [2.0480835165906024, 0.055238510607153124, 2.258841094259334], index=1), Atom('Cu', [1.8423446841272...</td>\n",
- " <td>-342.528496</td>\n",
- " <td>[[-1.2511641505681497, 0.045660252990561916, 0.39426999337691987], [-0.4923847861277789, -0.676187288680257, -1.3802167704923], [-0.12072100498159098, 0.5666924914439229, -0.8825937576849239], [0....</td>\n",
- " <td>107.0</td>\n",
- " </tr>\n",
- " <tr>\n",
- " <th>24</th>\n",
- " <td>None</td>\n",
- " <td>(Atom('Cu', [10.902653792490328, 1.9016481867720487, 1.712386801004505], index=0), Atom('Cu', [1.6843656295425262, 0.20454959542790652, 1.4940727709027473], index=1), Atom('Cu', [1.628967729295861...</td>\n",
- " <td>-342.900954</td>\n",
- " <td>[[0.5080309295986539, -0.4875222169174689, 0.46898176405272696], [0.11031309252296198, -0.7243436014688799, 1.2808414836059598], [0.6855285827079979, 0.576817447055947, 0.31599931473888204], [0.50...</td>\n",
- " <td>107.0</td>\n",
- " </tr>\n",
- " <tr>\n",
- " <th>25</th>\n",
- " <td>None</td>\n",
- " <td>(Atom('Cu', [0.2202511036922136, 1.5872348575607442, 1.7623998700282655], index=0), Atom('Cu', [1.8386689358546338, 10.988833155546024, 1.8571406735818983], index=1), Atom('Cu', [1.976390891645592...</td>\n",
- " <td>-340.983380</td>\n",
- " <td>[[-0.6923371397061229, 0.9615117892959398, 0.396261839433264], [0.18083100499512797, -0.47103552335731996, 0.5072798013711759], [-0.22735248831930896, 0.37011177620569996, -1.1740345740817597], [0...</td>\n",
- " <td>107.0</td>\n",
- " </tr>\n",
- " <tr>\n",
- " <th>26</th>\n",
- " <td>None</td>\n",
- " <td>(Atom('Cu', [10.746144724861097, 1.6561216261540705, 1.6676063346982197], index=0), Atom('Cu', [1.8697696006277247, 0.29566102043388925, 1.9071090181664805], index=1), Atom('Cu', [1.82013088394316...</td>\n",
- " <td>-342.479965</td>\n",
- " <td>[[0.46940172398488794, 0.557542533896084, 0.861383405261689], [-0.16043498489103097, -1.0997839627759998, -0.013974118313924476], [-0.13554483762266598, 0.6363641149062679, 0.153788969879775], [1....</td>\n",
- " <td>107.0</td>\n",
- " </tr>\n",
- " <tr>\n",
- " <th>27</th>\n",
- " <td>None</td>\n",
- " <td>(Atom('Cu', [0.17063059290766686, 1.8534187978406447, 1.7423748775395635], index=0), Atom('Cu', [1.8595651370150335, 10.90572322929213, 1.810598025463111], index=1), Atom('Cu', [1.934651223968069,...</td>\n",
- " <td>-340.174298</td>\n",
- " <td>[[-1.1653987834207897, -0.07515193371140247, -0.13414295102360305], [0.17707911646472896, 0.37588362216028093, 0.10312993516925903], [0.6003632691780849, 0.3869695806628, 0.03431754153949555], [-0...</td>\n",
- " <td>107.0</td>\n",
- " </tr>\n",
- " <tr>\n",
- " <th>28</th>\n",
- " <td>None</td>\n",
- " <td>(Atom('Cu', [10.866365842640102, 1.8491297818376022, 2.093244182315977], index=0), Atom('Cu', [1.7536272335648937, 10.898985481755824, 1.8241252890179567], index=1), Atom('Cu', [1.994555230114336,...</td>\n",
- " <td>-343.805462</td>\n",
- " <td>[[0.42819147658911194, -1.3404675072584398, -0.840042992949223], [0.47822853532413195, -0.07949121681390955, -0.36737406099153697], [-0.9172012989939929, 0.3239785862266829, -0.013009375610539234]...</td>\n",
- " <td>107.0</td>\n",
- " </tr>\n",
- " <tr>\n",
- " <th>29</th>\n",
- " <td>None</td>\n",
- " <td>(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...</td>\n",
- " <td>-400.111422</td>\n",
- " <td>[[-8.770761894538741e-15, 1.15657750043852e-09, 0.109956784695642], [-1.0824674490095302e-15, 1.15657515335765e-09, 0.10995678469564], [2.4308896909297503e-15, 1.1565748914144101e-09, 0.1099567846...</td>\n",
- " <td>128.0</td>\n",
- " </tr>\n",
- " <tr>\n",
- " <th>30</th>\n",
- " <td>None</td>\n",
- " <td>(Atom('Cu', [0.4126496185424086, 0.9553642998076769, 0.12158924761653131], index=0), Atom('Cu', [2.831118842513476, 1.0700158216349893, 25.916922304272767], index=1), Atom('Cu', [5.314789299948389...</td>\n",
- " <td>-399.591699</td>\n",
- " <td>[[-0.570999988178131, 1.09833300989089, -0.566585257198732], [-0.0492000252908114, 0.597416506778632, 0.966635869516025], [-0.0024866801464792, -0.0674126479000064, 0.2546322145358], [0.2289085885...</td>\n",
- " <td>128.0</td>\n",
- " </tr>\n",
- " <tr>\n",
- " <th>31</th>\n",
- " <td>None</td>\n",
- " <td>(Atom('Cu', [10.151562776611806, 1.6587733567107183, 26.43035938894712], index=0), Atom('Cu', [2.5212828819853748, 1.9070842851152785, 26.36203940098048], index=1), Atom('Cu', [4.715098279443367, ...</td>\n",
- " <td>-398.422617</td>\n",
- " <td>[[-0.555658749547497, 0.42566314828364993, 0.466167261187443], [-1.39449792316952, -0.5017985009363372, 0.4456531170887249], [1.25410857633035, -0.33111996310077596, -0.24658722383829995], [0.3911...</td>\n",
- " <td>128.0</td>\n",
- " </tr>\n",
- " <tr>\n",
- " <th>32</th>\n",
- " <td>None</td>\n",
- " <td>(Atom('Cu', [0.19573901040697333, 1.051460534941847, 26.530022925039237], index=0), Atom('Cu', [2.995726956631421, 1.1546751485293076, 26.840478692293868], index=1), Atom('Cu', [5.923947432763936,...</td>\n",
- " <td>-395.110340</td>\n",
- " <td>[[0.550884754551829, 0.33865983742272204, 0.12042096866985205], [0.189727589275692, -0.524367356684999, -0.17886090450862402], [-1.6758650723099, -0.31030261483377614, 0.6946509585213989], [0.4453...</td>\n",
- " <td>128.0</td>\n",
- " </tr>\n",
- " <tr>\n",
- " <th>33</th>\n",
- " <td>None</td>\n",
- " <td>(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....</td>\n",
- " <td>-396.833326</td>\n",
- " <td>[[0.235449441284142, 0.601163461325591, 0.04737458109310825], [0.337344266123105, 0.66485729403382, 0.37768738132523805], [-0.171831038530166, -0.11286098093109101, -0.07415135874528352], [-0.1966...</td>\n",
- " <td>128.0</td>\n",
- " </tr>\n",
- " <tr>\n",
- " <th>34</th>\n",
- " <td>None</td>\n",
- " <td>(Atom('Cu', [0.3429326290376805, 1.5170285327525175, 0.14896315086845416], index=0), Atom('Cu', [3.129345868860857, 1.495102964861245, 0.01607848650845961], index=1), Atom('Cu', [5.714332108258016...</td>\n",
- " <td>-400.444368</td>\n",
- " <td>[[1.15453322332565, 0.04603660924771737, -1.21282260887155], [-0.403390913673288, -0.18969536874868004, 0.030526533198225264], [-0.683024325114862, -0.967333273082708, 0.4114320467737619], [-0.867...</td>\n",
- " <td>128.0</td>\n",
- " </tr>\n",
- " <tr>\n",
- " <th>35</th>\n",
- " <td>None</td>\n",
- " <td>(Atom('Cu', [9.95801241508363, 1.4359511579313753, 26.639342243648862], index=0), Atom('Cu', [2.2681416259098204, 1.7861270127574713, 0.0041936446239185], index=1), Atom('Cu', [5.074253116948648, ...</td>\n",
- " <td>-397.843043</td>\n",
- " <td>[[0.742004122721361, 0.22577315893502206, 0.12298868177971806], [0.771069504028052, -0.90014541931557, -0.660403448738781], [-0.462456173466872, 1.24796716628589, -0.4192010350460109], [0.08219110...</td>\n",
- " <td>128.0</td>\n",
- " </tr>\n",
- " <tr>\n",
- " <th>36</th>\n",
- " <td>None</td>\n",
- " <td>(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...</td>\n",
- " <td>-399.776798</td>\n",
- " <td>[[0.552749731038993, -0.46087407707755496, 0.177277816519943], [0.340079509783844, 0.23574679643440802, 0.26784307872713603], [0.388298578408562, 0.331969932822417, 0.34399524632239104], [-0.59826...</td>\n",
- " <td>128.0</td>\n",
- " </tr>\n",
- " <tr>\n",
- " <th>37</th>\n",
- " <td>None</td>\n",
- " <td>(Atom('Cu', [10.188116701703345, 1.3482529143763475, 26.353847647582224], index=0), Atom('Cu', [2.4559442807081986, 1.4757747059762696, 26.57379282025388], index=1), Atom('Cu', [5.077086561123585,...</td>\n",
- " <td>-399.168074</td>\n",
- " <td>[[0.570532228156976, 0.17193739345012202, 0.796311675035985], [0.67297011060888, -0.81773224395498, 0.207420342553107], [0.391385096561351, -0.862073619446019, 0.597813478897486], [-0.270452726779...</td>\n",
- " <td>128.0</td>\n",
- " </tr>\n",
- " <tr>\n",
- " <th>38</th>\n",
- " <td>None</td>\n",
- " <td>(Atom('Cu', [10.165259029706933, 1.7122531598094173, 26.335638965295193], index=0), Atom('Cu', [2.3513330869200098, 1.5487334168655387, 26.34258116233103], index=1), Atom('Cu', [4.95573138146394, ...</td>\n",
- " <td>-396.984690</td>\n",
- " <td>[[-1.11093024791963, -0.6986058376048401, 0.44674121624886787], [0.0416051560041239, -0.0424634970331458, -0.0874515615419252], [-0.135122617155289, -0.778975629913174, -1.04402814519501], [0.8442...</td>\n",
- " <td>128.0</td>\n",
- " </tr>\n",
- " <tr>\n",
- " <th>39</th>\n",
- " <td>None</td>\n",
- " <td>(Atom('Cu', [0.36893784059756035, 1.481831927531004, 26.53504700964859], index=0), Atom('Cu', [2.6965712181950883, 1.488812429574298, 26.730123522873537], index=1), Atom('Cu', [5.668661292604278, ...</td>\n",
- " <td>-399.581912</td>\n",
- " <td>[[-0.645092069902244, 0.04920122139904896, 0.21081031345366397], [1.14893686034324, -0.6114894792387109, -0.40665475671972495], [-0.287092609914331, 0.292443458702414, -0.801010316546939], [-0.184...</td>\n",
- " <td>128.0</td>\n",
- " </tr>\n",
- " <tr>\n",
- " <th>40</th>\n",
" <td>job_a_3_4</td>\n",
" <td>(Atom('Cu', [0.0, 0.0, 0.0], index=0))</td>\n",
" <td>-3.142019</td>\n",
@@ -497,7 +177,7 @@
" <td>1.0</td>\n",
" </tr>\n",
" <tr>\n",
- " <th>41</th>\n",
+ " <th>1</th>\n",
" <td>job_a_3_5</td>\n",
" <td>(Atom('Cu', [0.0, 0.0, 0.0], index=0))</td>\n",
" <td>-3.338596</td>\n",
@@ -505,7 +185,7 @@
" <td>1.0</td>\n",
" </tr>\n",
" <tr>\n",
- " <th>42</th>\n",
+ " <th>2</th>\n",
" <td>job_a_3_6</td>\n",
" <td>(Atom('Cu', [0.0, 0.0, 0.0], index=0))</td>\n",
" <td>-3.416929</td>\n",
@@ -513,7 +193,7 @@
" <td>1.0</td>\n",
" </tr>\n",
" <tr>\n",
- " <th>43</th>\n",
+ " <th>3</th>\n",
" <td>job_a_3_7</td>\n",
" <td>(Atom('Cu', [0.0, 0.0, 0.0], index=0))</td>\n",
" <td>-3.409602</td>\n",
@@ -521,7 +201,7 @@
" <td>1.0</td>\n",
" </tr>\n",
" <tr>\n",
- " <th>44</th>\n",
+ " <th>4</th>\n",
" <td>job_a_3_8</td>\n",
" <td>(Atom('Cu', [0.0, 0.0, 0.0], index=0))</td>\n",
" <td>-3.330215</td>\n",
@@ -529,7 +209,7 @@
" <td>1.0</td>\n",
" </tr>\n",
" <tr>\n",
- " <th>45</th>\n",
+ " <th>5</th>\n",
" <td>job_a_3_9</td>\n",
" <td>(Atom('Cu', [0.0, 0.0, 0.0], index=0))</td>\n",
" <td>-3.195118</td>\n",
@@ -537,7 +217,7 @@
" <td>1.0</td>\n",
" </tr>\n",
" <tr>\n",
- " <th>46</th>\n",
+ " <th>6</th>\n",
" <td>job_a_4_0</td>\n",
" <td>(Atom('Cu', [0.0, 0.0, 0.0], index=0))</td>\n",
" <td>-3.035358</td>\n",
@@ -549,253 +229,35 @@
"</div>"
],
"text/plain": [
- " name \\\n",
- "0 None \n",
- "1 None \n",
- "2 None \n",
- "3 None \n",
- "4 None \n",
- "5 None \n",
- "6 None \n",
- "7 None \n",
- "8 None \n",
- "9 None \n",
- "10 None \n",
- "11 None \n",
- "12 None \n",
- "13 None \n",
- "14 None \n",
- "15 None \n",
- "16 None \n",
- "17 None \n",
- "18 None \n",
- "19 None \n",
- "20 None \n",
- "21 None \n",
- "22 None \n",
- "23 None \n",
- "24 None \n",
- "25 None \n",
- "26 None \n",
- "27 None \n",
- "28 None \n",
- "29 None \n",
- "30 None \n",
- "31 None \n",
- "32 None \n",
- "33 None \n",
- "34 None \n",
- "35 None \n",
- "36 None \n",
- "37 None \n",
- "38 None \n",
- "39 None \n",
- "40 job_a_3_4 \n",
- "41 job_a_3_5 \n",
- "42 job_a_3_6 \n",
- "43 job_a_3_7 \n",
- "44 job_a_3_8 \n",
- "45 job_a_3_9 \n",
- "46 job_a_4_0 \n",
+ " name atoms energy \\\n",
+ "0 job_a_3_4 (Atom('Cu', [0.0, 0.0, 0.0], index=0)) -3.142019 \n",
+ "1 job_a_3_5 (Atom('Cu', [0.0, 0.0, 0.0], index=0)) -3.338596 \n",
+ "2 job_a_3_6 (Atom('Cu', [0.0, 0.0, 0.0], index=0)) -3.416929 \n",
+ "3 job_a_3_7 (Atom('Cu', [0.0, 0.0, 0.0], index=0)) -3.409602 \n",
+ "4 job_a_3_8 (Atom('Cu', [0.0, 0.0, 0.0], index=0)) -3.330215 \n",
+ "5 job_a_3_9 (Atom('Cu', [0.0, 0.0, 0.0], index=0)) -3.195118 \n",
+ "6 job_a_4_0 (Atom('Cu', [0.0, 0.0, 0.0], index=0)) -3.035358 \n",
"\n",
- " atoms \\\n",
- "0 (Atom('Cu', [0.0, 0.0, 0.0], index=0)) \n",
- "1 (Atom('Cu', [0.0, 0.0, 0.0], index=0)) \n",
- "2 (Atom('Cu', [0.0, 0.0, 0.0], index=0)) \n",
- "3 (Atom('Cu', [0.0, 0.0, 0.0], index=0)) \n",
- "4 (Atom('Cu', [0.0, 0.0, 0.0], index=0)) \n",
- "5 (Atom('Cu', [0.0, 0.0, 0.0], index=0)) \n",
- "6 (Atom('Cu', [0.0, 0.0, 0.0], index=0)) \n",
- "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... \n",
- "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, ... \n",
- "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... \n",
- "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... \n",
- "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... \n",
- "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... \n",
- "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... \n",
- "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... \n",
- "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... \n",
- "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... \n",
- "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... \n",
- "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... \n",
- "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,... \n",
- "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... \n",
- "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... \n",
- "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... \n",
- "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... \n",
- "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... \n",
- "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... \n",
- "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... \n",
- "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,... \n",
- "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,... \n",
- "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... \n",
- "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... \n",
- "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, ... \n",
- "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,... \n",
- "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.... \n",
- "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... \n",
- "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, ... \n",
- "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... \n",
- "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,... \n",
- "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, ... \n",
- "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, ... \n",
- "40 (Atom('Cu', [0.0, 0.0, 0.0], index=0)) \n",
- "41 (Atom('Cu', [0.0, 0.0, 0.0], index=0)) \n",
- "42 (Atom('Cu', [0.0, 0.0, 0.0], index=0)) \n",
- "43 (Atom('Cu', [0.0, 0.0, 0.0], index=0)) \n",
- "44 (Atom('Cu', [0.0, 0.0, 0.0], index=0)) \n",
- "45 (Atom('Cu', [0.0, 0.0, 0.0], index=0)) \n",
- "46 (Atom('Cu', [0.0, 0.0, 0.0], index=0)) \n",
+ " forces \\\n",
+ "0 [[1.1869253621046177e-16, -1.7429070520896771e-16, -1.397277865277868e-16]] \n",
+ "1 [[-1.92404082484227e-16, 4.231084758750405e-17, 3.6193775346684653e-17]] \n",
+ "2 [[-2.9113397169423695e-17, 7.54965057835309e-17, -3.624419431643654e-17]] \n",
+ "3 [[3.771496125435321e-17, 3.412312546579927e-17, -2.4310047599025677e-17]] \n",
+ "4 [[-2.0545362501508919e-16, -3.5486130576273854e-17, 3.5486130576273854e-17]] \n",
+ "5 [[1.6101257219667079e-16, -4.2948421129906387e-17, 4.2948421129906387e-17]] \n",
+ "6 [[-5.946777565406637e-17, -1.0605082175909553e-16, -1.2946304704347008e-16]] \n",
"\n",
- " energy \\\n",
- "0 -3.142019 \n",
- "1 -3.338596 \n",
- "2 -3.416929 \n",
- "3 -3.409602 \n",
- "4 -3.330215 \n",
- "5 -3.195118 \n",
- "6 -3.035358 \n",
- "7 -347.182406 \n",
- "8 -348.253665 \n",
- "9 -345.424528 \n",
- "10 -346.758349 \n",
- "11 -344.603627 \n",
- "12 -346.849801 \n",
- "13 -345.015235 \n",
- "14 -346.569097 \n",
- "15 -344.892954 \n",
- "16 -347.628843 \n",
- "17 -345.776979 \n",
- "18 -342.906251 \n",
- "19 -343.569002 \n",
- "20 -343.317892 \n",
- "21 -341.057270 \n",
- "22 -342.067006 \n",
- "23 -342.528496 \n",
- "24 -342.900954 \n",
- "25 -340.983380 \n",
- "26 -342.479965 \n",
- "27 -340.174298 \n",
- "28 -343.805462 \n",
- "29 -400.111422 \n",
- "30 -399.591699 \n",
- "31 -398.422617 \n",
- "32 -395.110340 \n",
- "33 -396.833326 \n",
- "34 -400.444368 \n",
- "35 -397.843043 \n",
- "36 -399.776798 \n",
- "37 -399.168074 \n",
- "38 -396.984690 \n",
- "39 -399.581912 \n",
- "40 -3.142019 \n",
- "41 -3.338596 \n",
- "42 -3.416929 \n",
- "43 -3.409602 \n",
- "44 -3.330215 \n",
- "45 -3.195118 \n",
- "46 -3.035358 \n",
- "\n",
- " forces \\\n",
- "0 [[1.1869253621046177e-16, -1.7429070520896771e-16, -1.397277865277868e-16]] \n",
- "1 [[-1.92404082484227e-16, 4.231084758750405e-17, 3.6193775346684653e-17]] \n",
- "2 [[-2.9113397169423695e-17, 7.54965057835309e-17, -3.624419431643654e-17]] \n",
- "3 [[3.771496125435321e-17, 3.412312546579927e-17, -2.4310047599025677e-17]] \n",
- "4 [[-2.0545362501508919e-16, -3.5486130576273854e-17, 3.5486130576273854e-17]] \n",
- "5 [[1.6101257219667079e-16, -4.2948421129906387e-17, 4.2948421129906387e-17]] \n",
- "6 [[-5.946777565406637e-17, -1.0605082175909553e-16, -1.2946304704347008e-16]] \n",
- "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... \n",
- "8 [[-0.21910202935187897, -0.37573419410584397, 0.43392575377979187], [0.16208168404695897, -0.00671505675904709, 1.03458554920361], [-1.2001630139266497, -0.40207322348963503, -0.45620473735655703]... \n",
- "9 [[-0.023031834879881696, 0.042841438691562095, 0.5899774836434479], [-0.5418151518759569, 0.6754733604036028, -0.5582999589284809], [-0.6011411771360858, -0.355590065329821, -0.0035901986306415582... \n",
- "10 [[-0.32237334386615796, 0.43406651671724894, -0.5886238546572939], [-0.6295919499998729, 0.07530471384300086, -0.12687342568230403], [-0.06506588733991228, 0.8782024477953109, -0.12243680387297393... \n",
- "11 [[0.45078377546738896, -0.7167806257867769, -0.320969733282763], [0.5707773027838049, -0.5494069530705199, 0.510256621543289], [-0.36439749359274193, 0.17709586752044496, 0.23127352998569298], [0.... \n",
- "12 [[-0.38409855462219894, 0.12077975249818296, 0.024465771201292483], [-0.6560764999451358, -1.05845756801878, -0.658182913095082], [-0.5103420261962529, -0.35656271154938, 0.7090309519821769], [-0.... \n",
- "13 [[0.22044015995668098, -0.2607278388818459, -0.3855032322190499], [0.7754186544660099, -0.04652340102386694, -0.26232164996063695], [0.43147792874898694, -0.9840256256911009, 0.34987911571105595],... \n",
- "14 [[-0.5020206209676749, 0.007307596544171969, 0.24586848661916993], [-1.1645196400331899, 0.1476285180684419, 0.6168850904586589], [0.7183114431792579, -0.5420093171036479, -0.06687387962480258], [... \n",
- "15 [[0.04806202889719739, 0.48969724353819394, 1.29371057615331], [0.5538169933185199, -0.7855310261714289, -0.033081946412792815], [0.34832740609982993, 0.9937361742308158, 0.30650548838004904], [-0... \n",
- "16 [[0.24033044872062098, 1.5305792677179897, -0.6791236163119347], [0.05903491332573559, 0.148151392595253, 0.542468964409148], [0.07921843405670739, 0.145966157214324, 0.7342269238916159], [0.77503... \n",
- "17 [[-0.13926025211222698, -0.0920021629424733, 0.21001691285267599], [0.6767944835284789, -1.1148612203782198, 1.7165284718417098], [-0.7950973845960859, 0.2356681337270629, 0.13328556064538893], [0... \n",
- "18 [[-1.3933298959045699e-14, -0.10827842091784899, -0.108278420917849], [-0.10827842091784899, -1.3877479054990188e-14, -0.108278420917849], [-0.10827842091784899, -0.108278420917849, -1.38424758326... \n",
- "19 [[-0.45079778130218695, 0.19236747741170795, 0.23614131969524693], [1.2984317307784499, 0.04751568933291938, 0.005443425577977482], [0.48875760189522893, -0.5765163470127929, -0.5531364786691719],... \n",
- "20 [[-0.6920262907044069, 0.3986975029533409, 0.10738641941643497], [-1.2097205794553298, -2.21423543020926, -0.8363385508172672], [-0.36839592956658596, 0.35919893904268096, 0.09738195090664269], [2... \n",
- "21 [[0.5607305368018309, 0.07454461225822963, 0.17092757180402804], [0.7460358156721709, -0.9693709228665989, -0.357775642488428], [-1.4982109077380097, 1.0695224870660298, 0.17016025464137993], [1.1... \n",
- "22 [[0.7768634672312369, 0.615614277472231, -0.6520778674544528], [0.5196497874591819, -0.7614150189249069, 0.33452284258026094], [1.0185593798470798, 0.11349094338622906, -1.1138567887728799], [0.39... \n",
- "23 [[-1.2511641505681497, 0.045660252990561916, 0.39426999337691987], [-0.4923847861277789, -0.676187288680257, -1.3802167704923], [-0.12072100498159098, 0.5666924914439229, -0.8825937576849239], [0.... \n",
- "24 [[0.5080309295986539, -0.4875222169174689, 0.46898176405272696], [0.11031309252296198, -0.7243436014688799, 1.2808414836059598], [0.6855285827079979, 0.576817447055947, 0.31599931473888204], [0.50... \n",
- "25 [[-0.6923371397061229, 0.9615117892959398, 0.396261839433264], [0.18083100499512797, -0.47103552335731996, 0.5072798013711759], [-0.22735248831930896, 0.37011177620569996, -1.1740345740817597], [0... \n",
- "26 [[0.46940172398488794, 0.557542533896084, 0.861383405261689], [-0.16043498489103097, -1.0997839627759998, -0.013974118313924476], [-0.13554483762266598, 0.6363641149062679, 0.153788969879775], [1.... \n",
- "27 [[-1.1653987834207897, -0.07515193371140247, -0.13414295102360305], [0.17707911646472896, 0.37588362216028093, 0.10312993516925903], [0.6003632691780849, 0.3869695806628, 0.03431754153949555], [-0... \n",
- "28 [[0.42819147658911194, -1.3404675072584398, -0.840042992949223], [0.47822853532413195, -0.07949121681390955, -0.36737406099153697], [-0.9172012989939929, 0.3239785862266829, -0.013009375610539234]... \n",
- "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... \n",
- "30 [[-0.570999988178131, 1.09833300989089, -0.566585257198732], [-0.0492000252908114, 0.597416506778632, 0.966635869516025], [-0.0024866801464792, -0.0674126479000064, 0.2546322145358], [0.2289085885... \n",
- "31 [[-0.555658749547497, 0.42566314828364993, 0.466167261187443], [-1.39449792316952, -0.5017985009363372, 0.4456531170887249], [1.25410857633035, -0.33111996310077596, -0.24658722383829995], [0.3911... \n",
- "32 [[0.550884754551829, 0.33865983742272204, 0.12042096866985205], [0.189727589275692, -0.524367356684999, -0.17886090450862402], [-1.6758650723099, -0.31030261483377614, 0.6946509585213989], [0.4453... \n",
- "33 [[0.235449441284142, 0.601163461325591, 0.04737458109310825], [0.337344266123105, 0.66485729403382, 0.37768738132523805], [-0.171831038530166, -0.11286098093109101, -0.07415135874528352], [-0.1966... \n",
- "34 [[1.15453322332565, 0.04603660924771737, -1.21282260887155], [-0.403390913673288, -0.18969536874868004, 0.030526533198225264], [-0.683024325114862, -0.967333273082708, 0.4114320467737619], [-0.867... \n",
- "35 [[0.742004122721361, 0.22577315893502206, 0.12298868177971806], [0.771069504028052, -0.90014541931557, -0.660403448738781], [-0.462456173466872, 1.24796716628589, -0.4192010350460109], [0.08219110... \n",
- "36 [[0.552749731038993, -0.46087407707755496, 0.177277816519943], [0.340079509783844, 0.23574679643440802, 0.26784307872713603], [0.388298578408562, 0.331969932822417, 0.34399524632239104], [-0.59826... \n",
- "37 [[0.570532228156976, 0.17193739345012202, 0.796311675035985], [0.67297011060888, -0.81773224395498, 0.207420342553107], [0.391385096561351, -0.862073619446019, 0.597813478897486], [-0.270452726779... \n",
- "38 [[-1.11093024791963, -0.6986058376048401, 0.44674121624886787], [0.0416051560041239, -0.0424634970331458, -0.0874515615419252], [-0.135122617155289, -0.778975629913174, -1.04402814519501], [0.8442... \n",
- "39 [[-0.645092069902244, 0.04920122139904896, 0.21081031345366397], [1.14893686034324, -0.6114894792387109, -0.40665475671972495], [-0.287092609914331, 0.292443458702414, -0.801010316546939], [-0.184... \n",
- "40 [[1.1869253621046177e-16, -1.7429070520896771e-16, -1.397277865277868e-16]] \n",
- "41 [[-1.92404082484227e-16, 4.231084758750405e-17, 3.6193775346684653e-17]] \n",
- "42 [[-2.9113397169423695e-17, 7.54965057835309e-17, -3.624419431643654e-17]] \n",
- "43 [[3.771496125435321e-17, 3.412312546579927e-17, -2.4310047599025677e-17]] \n",
- "44 [[-2.0545362501508919e-16, -3.5486130576273854e-17, 3.5486130576273854e-17]] \n",
- "45 [[1.6101257219667079e-16, -4.2948421129906387e-17, 4.2948421129906387e-17]] \n",
- "46 [[-5.946777565406637e-17, -1.0605082175909553e-16, -1.2946304704347008e-16]] \n",
- "\n",
- " number_of_atoms \n",
- "0 1.0 \n",
- "1 1.0 \n",
- "2 1.0 \n",
- "3 1.0 \n",
- "4 1.0 \n",
- "5 1.0 \n",
- "6 1.0 \n",
- "7 108.0 \n",
- "8 108.0 \n",
- "9 108.0 \n",
- "10 108.0 \n",
- "11 108.0 \n",
- "12 108.0 \n",
- "13 108.0 \n",
- "14 108.0 \n",
- "15 108.0 \n",
- "16 108.0 \n",
- "17 108.0 \n",
- "18 107.0 \n",
- "19 107.0 \n",
- "20 107.0 \n",
- "21 107.0 \n",
- "22 107.0 \n",
- "23 107.0 \n",
- "24 107.0 \n",
- "25 107.0 \n",
- "26 107.0 \n",
- "27 107.0 \n",
- "28 107.0 \n",
- "29 128.0 \n",
- "30 128.0 \n",
- "31 128.0 \n",
- "32 128.0 \n",
- "33 128.0 \n",
- "34 128.0 \n",
- "35 128.0 \n",
- "36 128.0 \n",
- "37 128.0 \n",
- "38 128.0 \n",
- "39 128.0 \n",
- "40 1.0 \n",
- "41 1.0 \n",
- "42 1.0 \n",
- "43 1.0 \n",
- "44 1.0 \n",
- "45 1.0 \n",
- "46 1.0 "
+ " number_of_atoms \n",
+ "0 1.0 \n",
+ "1 1.0 \n",
+ "2 1.0 \n",
+ "3 1.0 \n",
+ "4 1.0 \n",
+ "5 1.0 \n",
+ "6 1.0 "
]
},
- "execution_count": 18,
+ "execution_count": 7,
"metadata": {},
"output_type": "execute_result"
}
@@ -806,7 +268,7 @@
},
{
"cell_type": "markdown",
- "id": "imperial-belarus",
+ "id": "ultimate-duncan",
"metadata": {},
"source": [
"## **Add structures from the MD**\n",
@@ -816,8 +278,8 @@
},
{
"cell_type": "code",
- "execution_count": 20,
- "id": "healthy-structure",
+ "execution_count": 8,
+ "id": "disabled-computer",
"metadata": {},
"outputs": [],
"source": [
@@ -827,8 +289,8 @@
},
{
"cell_type": "code",
- "execution_count": 21,
- "id": "outside-bhutan",
+ "execution_count": 9,
+ "id": "aggregate-wilderness",
"metadata": {},
"outputs": [],
"source": [
@@ -843,7 +305,7 @@
},
{
"cell_type": "markdown",
- "id": "minus-blink",
+ "id": "welsh-commercial",
"metadata": {},
"source": [
"## **Add some defect structures (vacancies, surfaces, etc)**\n",
@@ -853,15 +315,15 @@
},
{
"cell_type": "code",
- "execution_count": 22,
- "id": "loaded-sheriff",
+ "execution_count": 10,
+ "id": "continuing-upset",
"metadata": {},
"outputs": [
{
- "name": "stderr",
+ "name": "stdout",
"output_type": "stream",
"text": [
- "2021-03-08 11:55:40,043 - pyiron_log - WARNING - The job lammps_job_vac is being loaded instead of running. To re-run use the argument 'delete_existing_job=True in create_job'\n"
+ "The job lammps_job_vac was saved and received the ID: 303\n"
]
}
],
@@ -877,15 +339,15 @@
},
{
"cell_type": "code",
- "execution_count": 28,
- "id": "billion-shade",
+ "execution_count": 11,
+ "id": "listed-occurrence",
"metadata": {},
"outputs": [
{
- "name": "stderr",
+ "name": "stdout",
"output_type": "stream",
"text": [
- "2021-03-08 11:56:36,874 - pyiron_log - WARNING - The job lammps_job_surf is being loaded instead of running. To re-run use the argument 'delete_existing_job=True in create_job'\n"
+ "The job lammps_job_surf was saved and received the ID: 304\n"
]
}
],
@@ -900,17 +362,17 @@
},
{
"cell_type": "code",
- "execution_count": 29,
- "id": "constitutional-throw",
+ "execution_count": 12,
+ "id": "sound-bathroom",
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
- "{'groups': ['tc'], 'nodes': ['lammps_job_vac', 'lammps_job_surf', 'dataset_example']}"
+ "{'groups': [], 'nodes': ['lammps_job_vac', 'lammps_job_surf']}"
]
},
- "execution_count": 29,
+ "execution_count": 12,
"metadata": {},
"output_type": "execute_result"
}
@@ -921,7 +383,7 @@
},
{
"cell_type": "markdown",
- "id": "alpine-cooking",
+ "id": "processed-liability",
"metadata": {},
"source": [
"We now add these structures to the dataset"
@@ -929,31 +391,42 @@
},
{
"cell_type": "code",
- "execution_count": 33,
- "id": "italian-cleanup",
+ "execution_count": 19,
+ "id": "trained-target",
"metadata": {},
"outputs": [],
"source": [
- "for job_name in [\"lammps_job_vac\", \"lammps_job_surf\"]:\n",
- " job_md = pr.load(job_name)\n",
+ "for job_md in pr.iter_jobs(status=\"finished\"):\n",
" pos = job_md[\"output/generic/positions\"]\n",
- " traj_length = len(pos)\n",
- " stride = 10\n",
- " for i in range(0, traj_length, stride):\n",
- " container.include_job(job_md, iteration_step=i)"
+ " if pos is not None:\n",
+ " traj_length = len(pos)\n",
+ " stride = 10\n",
+ " for i in range(0, traj_length, stride):\n",
+ " container.include_job(job_md, iteration_step=i)"
]
},
{
"cell_type": "code",
- "execution_count": 34,
- "id": "exotic-asset",
+ "execution_count": 14,
+ "id": "attended-drama",
"metadata": {},
"outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "The job dataset_example was saved and received the ID: 306\n"
+ ]
+ },
{
"name": "stderr",
"output_type": "stream",
"text": [
- "2021-03-08 11:59:00,874 - pyiron_log - WARNING - The job dataset_example is being loaded instead of running. To re-run use the argument 'delete_existing_job=True in create_job'\n"
+ "/opt/conda/lib/python3.8/site-packages/pandas/core/generic.py:2606: PerformanceWarning: \n",
+ "your performance may suffer as PyTables will pickle object types that it cannot\n",
+ "map directly to c-types [inferred_type->mixed,key->block1_values] [items->Index(['name', 'atoms', 'forces'], dtype='object')]\n",
+ "\n",
+ " pytables.to_hdf(\n"
]
}
],
@@ -964,8 +437,8 @@
},
{
"cell_type": "code",
- "execution_count": 32,
- "id": "british-kelly",
+ "execution_count": 15,
+ "id": "signal-establishment",
"metadata": {},
"outputs": [
{
@@ -1009,17 +482,17 @@
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
- " <td>4332</td>\n",
+ " <td>303</td>\n",
" <td>finished</td>\n",
" <td>Cu107</td>\n",
" <td>lammps_job_vac</td>\n",
" <td>/lammps_job_vac</td>\n",
- " <td>/home/surendralal/</td>\n",
- " <td>notebooks/pyiron_potentialfit/day_1/creating_datasets/</td>\n",
- " <td>2021-03-04 15:54:10.622737</td>\n",
- " <td>2021-03-04 15:54:15.859551</td>\n",
- " <td>5.0</td>\n",
- " <td>pyiron@cmdell17#1</td>\n",
+ " <td>/home/pyiron/</td>\n",
+ " <td>day_1/creating_datasets/</td>\n",
+ " <td>2021-03-09 09:38:28.337496</td>\n",
+ " <td>2021-03-09 09:38:33.222851</td>\n",
+ " <td>4.0</td>\n",
+ " <td>pyiron@jupyter-sudarsan#1</td>\n",
" <td>Lammps</td>\n",
" <td>0.1</td>\n",
" <td>None</td>\n",
@@ -1027,17 +500,17 @@
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
- " <td>4333</td>\n",
+ " <td>304</td>\n",
" <td>finished</td>\n",
" <td>Cu128</td>\n",
" <td>lammps_job_surf</td>\n",
" <td>/lammps_job_surf</td>\n",
- " <td>/home/surendralal/</td>\n",
- " <td>notebooks/pyiron_potentialfit/day_1/creating_datasets/</td>\n",
- " <td>2021-03-04 15:54:16.720902</td>\n",
- " <td>2021-03-04 15:54:21.579389</td>\n",
- " <td>4.0</td>\n",
- " <td>pyiron@cmdell17#1</td>\n",
+ " <td>/home/pyiron/</td>\n",
+ " <td>day_1/creating_datasets/</td>\n",
+ " <td>2021-03-09 09:38:34.181033</td>\n",
+ " <td>2021-03-09 09:38:39.609826</td>\n",
+ " <td>5.0</td>\n",
+ " <td>pyiron@jupyter-sudarsan#1</td>\n",
" <td>Lammps</td>\n",
" <td>0.1</td>\n",
" <td>None</td>\n",
@@ -1045,17 +518,17 @@
" </tr>\n",
" <tr>\n",
" <th>2</th>\n",
- " <td>4334</td>\n",
+ " <td>306</td>\n",
" <td>finished</td>\n",
" <td>None</td>\n",
" <td>dataset_example</td>\n",
" <td>/dataset_example</td>\n",
- " <td>/home/surendralal/</td>\n",
- " <td>notebooks/pyiron_potentialfit/day_1/creating_datasets/</td>\n",
- " <td>2021-03-04 15:54:23.919785</td>\n",
+ " <td>/home/pyiron/</td>\n",
+ " <td>day_1/creating_datasets/</td>\n",
+ " <td>2021-03-09 09:38:48.660175</td>\n",
" <td>NaT</td>\n",
" <td>NaN</td>\n",
- " <td>pyiron@cmdell17#1</td>\n",
+ " <td>pyiron@jupyter-sudarsan#1</td>\n",
" <td>TrainingContainer</td>\n",
" <td>0.4</td>\n",
" <td>None</td>\n",
@@ -1066,28 +539,28 @@
"</div>"
],
"text/plain": [
- " id status chemicalformula job subjob \\\n",
- "0 4332 finished Cu107 lammps_job_vac /lammps_job_vac \n",
- "1 4333 finished Cu128 lammps_job_surf /lammps_job_surf \n",
- "2 4334 finished None dataset_example /dataset_example \n",
+ " id status chemicalformula job subjob \\\n",
+ "0 303 finished Cu107 lammps_job_vac /lammps_job_vac \n",
+ "1 304 finished Cu128 lammps_job_surf /lammps_job_surf \n",
+ "2 306 finished None dataset_example /dataset_example \n",
"\n",
- " projectpath project \\\n",
- "0 /home/surendralal/ notebooks/pyiron_potentialfit/day_1/creating_datasets/ \n",
- "1 /home/surendralal/ notebooks/pyiron_potentialfit/day_1/creating_datasets/ \n",
- "2 /home/surendralal/ notebooks/pyiron_potentialfit/day_1/creating_datasets/ \n",
+ " projectpath project timestart \\\n",
+ "0 /home/pyiron/ day_1/creating_datasets/ 2021-03-09 09:38:28.337496 \n",
+ "1 /home/pyiron/ day_1/creating_datasets/ 2021-03-09 09:38:34.181033 \n",
+ "2 /home/pyiron/ day_1/creating_datasets/ 2021-03-09 09:38:48.660175 \n",
"\n",
- " timestart timestop totalcputime \\\n",
- "0 2021-03-04 15:54:10.622737 2021-03-04 15:54:15.859551 5.0 \n",
- "1 2021-03-04 15:54:16.720902 2021-03-04 15:54:21.579389 4.0 \n",
- "2 2021-03-04 15:54:23.919785 NaT NaN \n",
+ " timestop totalcputime computer \\\n",
+ "0 2021-03-09 09:38:33.222851 4.0 pyiron@jupyter-sudarsan#1 \n",
+ "1 2021-03-09 09:38:39.609826 5.0 pyiron@jupyter-sudarsan#1 \n",
+ "2 NaT NaN pyiron@jupyter-sudarsan#1 \n",
"\n",
- " computer hamilton hamversion parentid masterid \n",
- "0 pyiron@cmdell17#1 Lammps 0.1 None None \n",
- "1 pyiron@cmdell17#1 Lammps 0.1 None None \n",
- "2 pyiron@cmdell17#1 TrainingContainer 0.4 None None "
+ " hamilton hamversion parentid masterid \n",
+ "0 Lammps 0.1 None None \n",
+ "1 Lammps 0.1 None None \n",
+ "2 TrainingContainer 0.4 None None "
]
},
- "execution_count": 32,
+ "execution_count": 15,
"metadata": {},
"output_type": "execute_result"
}
@@ -1098,7 +571,7 @@
},
{
"cell_type": "markdown",
- "id": "ideal-volunteer",
+ "id": "lyric-blair",
"metadata": {},
"source": [
"## **Reloading the dataset**\n",
@@ -1108,8 +581,8 @@
},
{
"cell_type": "code",
- "execution_count": 35,
- "id": "numeric-museum",
+ "execution_count": 16,
+ "id": "swiss-catering",
"metadata": {},
"outputs": [
{
@@ -1143,7 +616,7 @@
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
- " <td>None</td>\n",
+ " <td>job_a_3_4</td>\n",
" <td>(Atom('Cu', [0.0, 0.0, 0.0], index=0))</td>\n",
" <td>-3.142019</td>\n",
" <td>[[1.1869253621046177e-16, -1.7429070520896771e-16, -1.397277865277868e-16]]</td>\n",
@@ -1151,7 +624,7 @@
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
- " <td>None</td>\n",
+ " <td>job_a_3_5</td>\n",
" <td>(Atom('Cu', [0.0, 0.0, 0.0], index=0))</td>\n",
" <td>-3.338596</td>\n",
" <td>[[-1.92404082484227e-16, 4.231084758750405e-17, 3.6193775346684653e-17]]</td>\n",
@@ -1159,7 +632,7 @@
" </tr>\n",
" <tr>\n",
" <th>2</th>\n",
- " <td>None</td>\n",
+ " <td>job_a_3_6</td>\n",
" <td>(Atom('Cu', [0.0, 0.0, 0.0], index=0))</td>\n",
" <td>-3.416929</td>\n",
" <td>[[-2.9113397169423695e-17, 7.54965057835309e-17, -3.624419431643654e-17]]</td>\n",
@@ -1167,7 +640,7 @@
" </tr>\n",
" <tr>\n",
" <th>3</th>\n",
- " <td>None</td>\n",
+ " <td>job_a_3_7</td>\n",
" <td>(Atom('Cu', [0.0, 0.0, 0.0], index=0))</td>\n",
" <td>-3.409602</td>\n",
" <td>[[3.771496125435321e-17, 3.412312546579927e-17, -2.4310047599025677e-17]]</td>\n",
@@ -1175,7 +648,7 @@
" </tr>\n",
" <tr>\n",
" <th>4</th>\n",
- " <td>None</td>\n",
+ " <td>job_a_3_8</td>\n",
" <td>(Atom('Cu', [0.0, 0.0, 0.0], index=0))</td>\n",
" <td>-3.330215</td>\n",
" <td>[[-2.0545362501508919e-16, -3.5486130576273854e-17, 3.5486130576273854e-17]]</td>\n",
@@ -1183,7 +656,7 @@
" </tr>\n",
" <tr>\n",
" <th>5</th>\n",
- " <td>None</td>\n",
+ " <td>job_a_3_9</td>\n",
" <td>(Atom('Cu', [0.0, 0.0, 0.0], index=0))</td>\n",
" <td>-3.195118</td>\n",
" <td>[[1.6101257219667079e-16, -4.2948421129906387e-17, 4.2948421129906387e-17]]</td>\n",
@@ -1191,7 +664,7 @@
" </tr>\n",
" <tr>\n",
" <th>6</th>\n",
- " <td>None</td>\n",
+ " <td>job_a_4_0</td>\n",
" <td>(Atom('Cu', [0.0, 0.0, 0.0], index=0))</td>\n",
" <td>-3.035358</td>\n",
" <td>[[-5.946777565406637e-17, -1.0605082175909553e-16, -1.2946304704347008e-16]]</td>\n",
@@ -1199,266 +672,266 @@
" </tr>\n",
" <tr>\n",
" <th>7</th>\n",
- " <td>None</td>\n",
- " <td>(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...</td>\n",
- " <td>-347.182406</td>\n",
+ " <td>lammps_job</td>\n",
+ " <td>(Atom('Cu', [0.0, 0.0, 0.0], index=0), Atom('Cu', [0.0, 1.804999999999592, 1.804999999999592], index=1), Atom('Cu', [1.804999999999592, 1.1052437362302367e-16, 1.804999999999592], index=2), Atom('...</td>\n",
+ " <td>-369.311743</td>\n",
" <td>[[-1.2656542480726799e-14, -1.46965772884755e-14, -1.61017033040167e-14], [-1.3905543383430098e-14, 4.5310977192514186e-15, 4.8333732849403796e-15], [4.9682480351975795e-15, -1.4072076837123899e-1...</td>\n",
" <td>108.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>8</th>\n",
- " <td>None</td>\n",
- " <td>(Atom('Cu', [0.140426153531212, 11.00934611760493, 10.968207696001379], index=0), Atom('Cu', [10.983357200359302, 1.779939365335074, 1.7146804782560905], index=1), Atom('Cu', [2.1228644677344763, ...</td>\n",
- " <td>-348.253665</td>\n",
+ " <td>lammps_job</td>\n",
+ " <td>(Atom('Cu', [0.140426153531212, 11.00934611760493, 10.96820769600138], index=0), Atom('Cu', [10.983357200359302, 1.779939365335074, 1.7146804782560903], index=1), Atom('Cu', [2.1228644677344763, 0...</td>\n",
+ " <td>-360.190839</td>\n",
" <td>[[-0.21910202935187897, -0.37573419410584397, 0.43392575377979187], [0.16208168404695897, -0.00671505675904709, 1.03458554920361], [-1.2001630139266497, -0.40207322348963503, -0.45620473735655703]...</td>\n",
" <td>108.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>9</th>\n",
- " <td>None</td>\n",
- " <td>(Atom('Cu', [0.1407579358923329, 11.020287239626356, 10.855878337455094], index=0), Atom('Cu', [0.29542104007972325, 1.6514729828183248, 1.7760939949715002], index=1), Atom('Cu', [1.99578258187561...</td>\n",
- " <td>-345.424528</td>\n",
- " <td>[[-0.023031834879881696, 0.042841438691562095, 0.5899774836434479], [-0.5418151518759569, 0.6754733604036028, -0.5582999589284809], [-0.6011411771360858, -0.355590065329821, -0.0035901986306415582...</td>\n",
+ " <td>lammps_job</td>\n",
+ " <td>(Atom('Cu', [0.1407579358923329, 11.020287239626356, 10.855878337455094], index=0), Atom('Cu', [0.29542104007972325, 1.6514729828183248, 1.7760939949715], index=1), Atom('Cu', [1.9957825818756145,...</td>\n",
+ " <td>-356.403521</td>\n",
+ " <td>[[-0.023031834879864897, 0.04284143869144259, 0.5899774836434099], [-0.5418151518758109, 0.6754733604037649, -0.5582999589285099], [-0.6011411771363389, -0.355590065330048, -0.003590198630652358],...</td>\n",
" <td>108.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>10</th>\n",
- " <td>None</td>\n",
- " <td>(Atom('Cu', [0.04675277832683521, 10.951786003502875, 0.20014601215416555], index=0), Atom('Cu', [0.08453269827616121, 1.807218974303731, 1.7664733621606055], index=1), Atom('Cu', [1.9597357123378...</td>\n",
- " <td>-346.758349</td>\n",
- " <td>[[-0.32237334386615796, 0.43406651671724894, -0.5886238546572939], [-0.6295919499998729, 0.07530471384300086, -0.12687342568230403], [-0.06506588733991228, 0.8782024477953109, -0.12243680387297393...</td>\n",
+ " <td>lammps_job</td>\n",
+ " <td>(Atom('Cu', [0.046752778326835207, 10.951786003502875, 0.20014601215416555], index=0), Atom('Cu', [0.08453269827616121, 1.8072189743037306, 1.7664733621606052], index=1), Atom('Cu', [1.95973571233...</td>\n",
+ " <td>-358.245754</td>\n",
+ " <td>[[-0.32237334386617594, 0.43406651671772695, -0.5886238546573999], [-0.6295919499999019, 0.07530471384292876, -0.12687342568255203], [-0.06506588733974998, 0.8782024477947719, -0.12243680387296693...</td>\n",
" <td>108.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>11</th>\n",
- " <td>None</td>\n",
- " <td>(Atom('Cu', [10.991332780892245, 11.027168829788469, 0.17044757336885022], index=0), Atom('Cu', [10.869778028731718, 1.9053524080340238, 1.7569642307109068], index=1), Atom('Cu', [1.89027128290555...</td>\n",
- " <td>-344.603627</td>\n",
- " <td>[[0.45078377546738896, -0.7167806257867769, -0.320969733282763], [0.5707773027838049, -0.5494069530705199, 0.510256621543289], [-0.36439749359274193, 0.17709586752044496, 0.23127352998569298], [0....</td>\n",
+ " <td>lammps_job</td>\n",
+ " <td>(Atom('Cu', [10.99133278089223, 11.027168829788456, 0.17044757336885], index=0), Atom('Cu', [10.869778028731703, 1.9053524080340212, 1.7569642307109046], index=1), Atom('Cu', [1.8902712829055568, ...</td>\n",
+ " <td>-356.564325</td>\n",
+ " <td>[[0.45078377546780296, -0.7167806257868728, -0.320969733281809], [0.5707773027839779, -0.5494069530720159, 0.510256621543522], [-0.36439749359319995, 0.17709586752113193, 0.23127352998529296], [0....</td>\n",
" <td>108.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>12</th>\n",
- " <td>None</td>\n",
- " <td>(Atom('Cu', [10.958070767872973, 0.05270018288525903, 11.015795828313184], index=0), Atom('Cu', [0.04540970504125744, 2.0780519854689388, 1.8353871076994486], index=1), Atom('Cu', [1.8285627799497...</td>\n",
- " <td>-346.849801</td>\n",
- " <td>[[-0.38409855462219894, 0.12077975249818296, 0.024465771201292483], [-0.6560764999451358, -1.05845756801878, -0.658182913095082], [-0.5103420261962529, -0.35656271154938, 0.7090309519821769], [-0....</td>\n",
+ " <td>lammps_job</td>\n",
+ " <td>(Atom('Cu', [10.958070767873476, 0.05270018288526145, 11.015795828313692], index=0), Atom('Cu', [0.045409705041259525, 2.078051985469034, 1.8353871076995325], index=1), Atom('Cu', [1.8285627799498...</td>\n",
+ " <td>-357.011799</td>\n",
+ " <td>[[-0.38409855462373593, 0.12077975249587695, 0.02446577119927368], [-0.6560764999470009, -1.05845756801682, -0.658182913092867], [-0.5103420261931418, -0.356562711546522, 0.7090309519858399], [-0....</td>\n",
" <td>108.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>13</th>\n",
- " <td>None</td>\n",
- " <td>(Atom('Cu', [10.903697402270481, 10.843249424147054, 0.09574490333935876], index=0), Atom('Cu', [10.594918916668115, 1.7187193807013557, 1.957301113531466], index=1), Atom('Cu', [1.676074002401865...</td>\n",
- " <td>-345.015235</td>\n",
- " <td>[[0.22044015995668098, -0.2607278388818459, -0.3855032322190499], [0.7754186544660099, -0.04652340102386694, -0.26232164996063695], [0.43147792874898694, -0.9840256256911009, 0.34987911571105595],...</td>\n",
+ " <td>lammps_job</td>\n",
+ " <td>(Atom('Cu', [10.903697402270652, 10.843249424146602, 0.09574490333936027], index=0), Atom('Cu', [10.59491891666766, 1.7187193807026324, 1.9573011135302476], index=1), Atom('Cu', [1.676074002401891...</td>\n",
+ " <td>-357.856759</td>\n",
+ " <td>[[0.22044015996419397, -0.26072783887691897, -0.38550323222201893], [0.7754186544628359, -0.04652340102588245, -0.2623216499598349], [0.4314779287479719, -0.9840256256937749, 0.34987911571166197],...</td>\n",
" <td>108.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>14</th>\n",
- " <td>None</td>\n",
- " <td>(Atom('Cu', [0.25841198959969514, 0.07063449316617948, 10.912283030401635], index=0), Atom('Cu', [0.19649020014428978, 1.7891621064498946, 1.803181486480956], index=1), Atom('Cu', [1.7493171890008...</td>\n",
- " <td>-346.569097</td>\n",
- " <td>[[-0.5020206209676749, 0.007307596544171969, 0.24586848661916993], [-1.1645196400331899, 0.1476285180684419, 0.6168850904586589], [0.7183114431792579, -0.5420093171036479, -0.06687387962480258], [...</td>\n",
+ " <td>lammps_job</td>\n",
+ " <td>(Atom('Cu', [0.258411989603464, 0.0706344931649224, 10.912283030397811], index=0), Atom('Cu', [0.1964902001455455, 1.7891621064461172, 1.8031814864809468], index=1), Atom('Cu', [1.7493171890021084...</td>\n",
+ " <td>-358.316140</td>\n",
+ " <td>[[-0.5020206209738959, 0.007307596546447969, 0.24586848662953095], [-1.1645196400318298, 0.14762851807991492, 0.6168850904682569], [0.7183114431738189, -0.5420093170980669, -0.06687387962120929], ...</td>\n",
" <td>108.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>15</th>\n",
- " <td>None</td>\n",
- " <td>(Atom('Cu', [0.004994793789590358, 10.985055637636528, 10.904222762438215], index=0), Atom('Cu', [10.941729664004177, 1.8868614122932958, 1.8147512571785023], index=1), Atom('Cu', [1.8438031255437...</td>\n",
- " <td>-344.892954</td>\n",
- " <td>[[0.04806202889719739, 0.48969724353819394, 1.29371057615331], [0.5538169933185199, -0.7855310261714289, -0.033081946412792815], [0.34832740609982993, 0.9937361742308158, 0.30650548838004904], [-0...</td>\n",
+ " <td>lammps_job</td>\n",
+ " <td>(Atom('Cu', [0.004994793782076363, 10.985055637641707, 10.904222762435255], index=0), Atom('Cu', [10.9417296640056, 1.886861412294462, 1.8147512571859394], index=1), Atom('Cu', [1.8438031255436442...</td>\n",
+ " <td>-356.847816</td>\n",
+ " <td>[[0.04806202890911529, 0.4896972435411299, 1.29371057618316], [0.5538169933312109, -0.7855310261686719, -0.033081946439222513], [0.34832740608971496, 0.9937361742507679, 0.30650548838579206], [-0....</td>\n",
" <td>108.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>16</th>\n",
- " <td>None</td>\n",
- " <td>(Atom('Cu', [0.03645923830333788, 10.856010693932728, 10.970572990196315], index=0), Atom('Cu', [10.913522535008392, 1.8161914381204696, 1.5447581077411967], index=1), Atom('Cu', [1.77583933019795...</td>\n",
- " <td>-347.628843</td>\n",
- " <td>[[0.24033044872062098, 1.5305792677179897, -0.6791236163119347], [0.05903491332573559, 0.148151392595253, 0.542468964409148], [0.07921843405670739, 0.145966157214324, 0.7342269238916159], [0.77503...</td>\n",
+ " <td>lammps_job</td>\n",
+ " <td>(Atom('Cu', [0.03645923831331586, 10.8560106939291, 10.97057299019823], index=0), Atom('Cu', [10.913522535013476, 1.816191438106623, 1.5447581077438086], index=1), Atom('Cu', [1.7758393302091413, ...</td>\n",
+ " <td>-358.626624</td>\n",
+ " <td>[[0.24033044872932896, 1.5305792676779497, -0.6791236163998687], [0.05903491330127059, 0.148151392634253, 0.542468964385662], [0.07921843405774338, 0.145966157230826, 0.7342269239659519], [0.77503...</td>\n",
" <td>108.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>17</th>\n",
- " <td>None</td>\n",
- " <td>(Atom('Cu', [0.009767181825404037, 0.0071865231528328395, 11.0089023992238], index=0), Atom('Cu', [10.89374596605574, 1.9969194212313586, 1.595578837066423], index=1), Atom('Cu', [2.05442192913884...</td>\n",
- " <td>-345.776979</td>\n",
- " <td>[[-0.13926025211222698, -0.0920021629424733, 0.21001691285267599], [0.6767944835284789, -1.1148612203782198, 1.7165284718417098], [-0.7950973845960859, 0.2356681337270629, 0.13328556064538893], [0...</td>\n",
+ " <td>lammps_job</td>\n",
+ " <td>(Atom('Cu', [0.00976718182041884, 0.007186523165377699, 11.008902399259645], index=0), Atom('Cu', [10.89374596607187, 1.9969194212527828, 1.5955788370755422], index=1), Atom('Cu', [2.0544219291027...</td>\n",
+ " <td>-356.796173</td>\n",
+ " <td>[[-0.13926025200196399, -0.0920021630565197, 0.21001691279918497], [0.6767944835632749, -1.1148612202170798, 1.7165284720013199], [-0.7950973844667609, 0.2356681335380539, 0.13328556065954994], [0...</td>\n",
" <td>108.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>18</th>\n",
- " <td>None</td>\n",
- " <td>(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...</td>\n",
- " <td>-342.906251</td>\n",
+ " <td>lammps_job_vac</td>\n",
+ " <td>(Atom('Cu', [0.0, 1.804999999999592, 1.804999999999592], index=0), Atom('Cu', [1.804999999999592, 1.1052437362302367e-16, 1.804999999999592], index=1), Atom('Cu', [1.804999999999592, 1.80499999999...</td>\n",
+ " <td>-364.828772</td>\n",
" <td>[[-1.3933298959045699e-14, -0.10827842091784899, -0.108278420917849], [-0.10827842091784899, -1.3877479054990188e-14, -0.108278420917849], [-0.10827842091784899, -0.108278420917849, -1.38424758326...</td>\n",
" <td>107.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>19</th>\n",
- " <td>None</td>\n",
- " <td>(Atom('Cu', [0.10390109091492504, 1.9580560553035629, 1.779188560767685], index=0), Atom('Cu', [1.3868099266682106, 10.93717630776342, 1.601790948781396], index=1), Atom('Cu', [1.7183987889409966,...</td>\n",
- " <td>-343.569002</td>\n",
- " <td>[[-0.45079778130218695, 0.19236747741170795, 0.23614131969524693], [1.2984317307784499, 0.04751568933291938, 0.005443425577977482], [0.48875760189522893, -0.5765163470127929, -0.5531364786691719],...</td>\n",
+ " <td>lammps_job_vac</td>\n",
+ " <td>(Atom('Cu', [0.10390109091492468, 1.9580560553035562, 1.7791885607676787], index=0), Atom('Cu', [1.3868099266682057, 10.93717630776338, 1.6017909487813904], index=1), Atom('Cu', [1.718398788940990...</td>\n",
+ " <td>-353.817356</td>\n",
+ " <td>[[-0.45079778130212095, 0.19236747741186794, 0.23614131969518395], [1.2984317307785798, 0.047515689332818876, 0.0054434255778954815], [0.48875760189529993, -0.5765163470127389, -0.5531364786691438...</td>\n",
" <td>107.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>20</th>\n",
- " <td>None</td>\n",
- " <td>(Atom('Cu', [0.2223234793002756, 1.6999920633404135, 1.7623980235259114], index=0), Atom('Cu', [2.122882660879041, 0.18624238423025943, 2.030808683988878], index=1), Atom('Cu', [1.7334689484700414...</td>\n",
- " <td>-343.317892</td>\n",
- " <td>[[-0.6920262907044069, 0.3986975029533409, 0.10738641941643497], [-1.2097205794553298, -2.21423543020926, -0.8363385508172672], [-0.36839592956658596, 0.35919893904268096, 0.09738195090664269], [2...</td>\n",
+ " <td>lammps_job_vac</td>\n",
+ " <td>(Atom('Cu', [0.222323479300276, 1.6999920633404162, 1.7623980235259142], index=0), Atom('Cu', [2.1228826608790445, 0.1862423842302597, 2.0308086839888815], index=1), Atom('Cu', [1.733468948470044,...</td>\n",
+ " <td>-353.115830</td>\n",
+ " <td>[[-0.6920262907037699, 0.3986975029534239, 0.10738641941633598], [-1.2097205794551897, -2.2142354302088, -0.8363385508175151], [-0.36839592956672496, 0.3591989390425319, 0.09738195090699889], [2.1...</td>\n",
" <td>107.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>21</th>\n",
- " <td>None</td>\n",
- " <td>(Atom('Cu', [10.839434974930338, 1.9008464900018593, 1.6867963294684278], index=0), Atom('Cu', [1.5876598581358559, 0.15447557118789498, 1.715299994817798], index=1), Atom('Cu', [2.148606011735498...</td>\n",
- " <td>-341.057270</td>\n",
- " <td>[[0.5607305368018309, 0.07454461225822963, 0.17092757180402804], [0.7460358156721709, -0.9693709228665989, -0.357775642488428], [-1.4982109077380097, 1.0695224870660298, 0.17016025464137993], [1.1...</td>\n",
+ " <td>lammps_job_vac</td>\n",
+ " <td>(Atom('Cu', [10.839434974930233, 1.9008464900018414, 1.6867963294684114], index=0), Atom('Cu', [1.587659858135841, 0.1544755711878935, 1.7152999948177818], index=1), Atom('Cu', [2.148606011735478,...</td>\n",
+ " <td>-352.375089</td>\n",
+ " <td>[[0.5607305368014349, 0.07454461225798582, 0.17092757180355503], [0.7460358156722969, -0.9693709228667519, -0.357775642489466], [-1.4982109077379697, 1.0695224870646098, 0.17016025464195195], [1.1...</td>\n",
" <td>107.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>22</th>\n",
- " <td>None</td>\n",
- " <td>(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...</td>\n",
- " <td>-342.067006</td>\n",
- " <td>[[0.7768634672312369, 0.615614277472231, -0.6520778674544528], [0.5196497874591819, -0.7614150189249069, 0.33452284258026094], [1.0185593798470798, 0.11349094338622906, -1.1138567887728799], [0.39...</td>\n",
+ " <td>lammps_job_vac</td>\n",
+ " <td>(Atom('Cu', [10.827044041158409, 1.8148855201981695, 2.124190925175089], index=0), Atom('Cu', [1.6679142700199683, 0.11062408070456453, 1.6294014594257846], index=1), Atom('Cu', [1.294186866136013...</td>\n",
+ " <td>-352.774500</td>\n",
+ " <td>[[0.7768634672242999, 0.615614277463985, -0.6520778674493769], [0.5196497874591279, -0.7614150189291738, 0.33452284258293197], [1.0185593798557397, 0.11349094339204105, -1.1138567887771997], [0.39...</td>\n",
" <td>107.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>23</th>\n",
- " <td>None</td>\n",
- " <td>(Atom('Cu', [0.18579648605077317, 1.6025971043596021, 1.8725196193757527], index=0), Atom('Cu', [2.0480835165906024, 0.055238510607153124, 2.258841094259334], index=1), Atom('Cu', [1.8423446841272...</td>\n",
- " <td>-342.528496</td>\n",
- " <td>[[-1.2511641505681497, 0.045660252990561916, 0.39426999337691987], [-0.4923847861277789, -0.676187288680257, -1.3802167704923], [-0.12072100498159098, 0.5666924914439229, -0.8825937576849239], [0....</td>\n",
+ " <td>lammps_job_vac</td>\n",
+ " <td>(Atom('Cu', [0.18579648603934987, 1.6025971043768155, 1.8725196193702205], index=0), Atom('Cu', [2.048083516582408, 0.05523851059960332, 2.2588410942434316], index=1), Atom('Cu', [1.84234468412923...</td>\n",
+ " <td>-352.466296</td>\n",
+ " <td>[[-1.2511641504900297, 0.045660252979352216, 0.3942699933548249], [-0.49238478619866294, -0.676187288648693, -1.38021677052805], [-0.12072100498243699, 0.5666924914313989, -0.8825937576412469], [0...</td>\n",
" <td>107.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>24</th>\n",
- " <td>None</td>\n",
- " <td>(Atom('Cu', [10.902653792490328, 1.9016481867720487, 1.712386801004505], index=0), Atom('Cu', [1.6843656295425262, 0.20454959542790652, 1.4940727709027473], index=1), Atom('Cu', [1.628967729295861...</td>\n",
- " <td>-342.900954</td>\n",
- " <td>[[0.5080309295986539, -0.4875222169174689, 0.46898176405272696], [0.11031309252296198, -0.7243436014688799, 1.2808414836059598], [0.6855285827079979, 0.576817447055947, 0.31599931473888204], [0.50...</td>\n",
+ " <td>lammps_job_vac</td>\n",
+ " <td>(Atom('Cu', [10.902653792488254, 1.9016481867624628, 1.7123868009764087], index=0), Atom('Cu', [1.684365629566867, 0.20454959543267073, 1.4940727709048371], index=1), Atom('Cu', [1.628967729292809...</td>\n",
+ " <td>-353.659518</td>\n",
+ " <td>[[0.5080309295530009, -0.4875222168854389, 0.46898176419400794], [0.11031309245877298, -0.7243436015235899, 1.2808414835860897], [0.6855285827566528, 0.576817447011234, 0.31599931467165404], [0.50...</td>\n",
" <td>107.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>25</th>\n",
- " <td>None</td>\n",
- " <td>(Atom('Cu', [0.2202511036922136, 1.5872348575607442, 1.7623998700282655], index=0), Atom('Cu', [1.8386689358546338, 10.988833155546024, 1.8571406735818983], index=1), Atom('Cu', [1.976390891645592...</td>\n",
- " <td>-340.983380</td>\n",
- " <td>[[-0.6923371397061229, 0.9615117892959398, 0.396261839433264], [0.18083100499512797, -0.47103552335731996, 0.5072798013711759], [-0.22735248831930896, 0.37011177620569996, -1.1740345740817597], [0...</td>\n",
+ " <td>lammps_job_vac</td>\n",
+ " <td>(Atom('Cu', [0.22025110375749696, 1.5872348575731654, 1.7623998700921586], index=0), Atom('Cu', [1.8386689358494586, 10.988833155464064, 1.8571406735076377], index=1), Atom('Cu', [1.97639089167179...</td>\n",
+ " <td>-352.032412</td>\n",
+ " <td>[[-0.6923371397932379, 0.9615117891395759, 0.396261839405581], [0.18083100479582398, -0.47103552318232994, 0.5072798015385259], [-0.22735248852514198, 0.3701117760834369, -1.1740345739673297], [0....</td>\n",
" <td>107.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>26</th>\n",
- " <td>None</td>\n",
- " <td>(Atom('Cu', [10.746144724861097, 1.6561216261540705, 1.6676063346982197], index=0), Atom('Cu', [1.8697696006277247, 0.29566102043388925, 1.9071090181664805], index=1), Atom('Cu', [1.82013088394316...</td>\n",
- " <td>-342.479965</td>\n",
- " <td>[[0.46940172398488794, 0.557542533896084, 0.861383405261689], [-0.16043498489103097, -1.0997839627759998, -0.013974118313924476], [-0.13554483762266598, 0.6363641149062679, 0.153788969879775], [1....</td>\n",
+ " <td>lammps_job_vac</td>\n",
+ " <td>(Atom('Cu', [10.746144724792629, 1.6561216261325158, 1.6676063346541934], index=0), Atom('Cu', [1.8697696007010116, 0.2956610204486699, 1.9071090181785917], index=1), Atom('Cu', [1.820130883905895...</td>\n",
+ " <td>-352.885609</td>\n",
+ " <td>[[0.4694017239681809, 0.557542533620799, 0.861383405389437], [-0.16043498520491098, -1.0997839630796997, -0.013974118048379877], [-0.13554483753545396, 0.6363641150344139, 0.153788969504449], [1.0...</td>\n",
" <td>107.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>27</th>\n",
- " <td>None</td>\n",
- " <td>(Atom('Cu', [0.17063059290766686, 1.8534187978406447, 1.7423748775395635], index=0), Atom('Cu', [1.8595651370150335, 10.90572322929213, 1.810598025463111], index=1), Atom('Cu', [1.934651223968069,...</td>\n",
- " <td>-340.174298</td>\n",
- " <td>[[-1.1653987834207897, -0.07515193371140247, -0.13414295102360305], [0.17707911646472896, 0.37588362216028093, 0.10312993516925903], [0.6003632691780849, 0.3869695806628, 0.03431754153949555], [-0...</td>\n",
+ " <td>lammps_job_vac</td>\n",
+ " <td>(Atom('Cu', [0.17063059334564, 1.853418797177199, 1.7423748774412284], index=0), Atom('Cu', [1.8595651381460672, 10.905723229638589, 1.810598025743776], index=1), Atom('Cu', [1.9346512242265819, 1...</td>\n",
+ " <td>-352.295316</td>\n",
+ " <td>[[-1.1653987878668197, -0.07515193358861387, -0.13414295175130306], [0.17707911415253696, 0.37588361844850293, 0.10312993216846503], [0.6003632668071709, 0.386969577632806, 0.03431754138154845], [...</td>\n",
" <td>107.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>28</th>\n",
- " <td>None</td>\n",
- " <td>(Atom('Cu', [10.866365842640102, 1.8491297818376022, 2.093244182315977], index=0), Atom('Cu', [1.7536272335648937, 10.898985481755824, 1.8241252890179567], index=1), Atom('Cu', [1.994555230114336,...</td>\n",
- " <td>-343.805462</td>\n",
- " <td>[[0.42819147658911194, -1.3404675072584398, -0.840042992949223], [0.47822853532413195, -0.07949121681390955, -0.36737406099153697], [-0.9172012989939929, 0.3239785862266829, -0.013009375610539234]...</td>\n",
+ " <td>lammps_job_vac</td>\n",
+ " <td>(Atom('Cu', [10.866365841890905, 1.8491297824671196, 2.0932441820713352], index=0), Atom('Cu', [1.7536272327257443, 10.898985480280807, 1.8241252899027136], index=1), Atom('Cu', [1.994555229954278...</td>\n",
+ " <td>-353.959714</td>\n",
+ " <td>[[0.4281914688318719, -1.3404674992878498, -0.840042998895605], [0.4782285361793289, -0.07949121879472046, -0.36737406210665396], [-0.9172013000957939, 0.3239785884620919, -0.013009379648141535], ...</td>\n",
" <td>107.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>29</th>\n",
- " <td>None</td>\n",
- " <td>(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...</td>\n",
- " <td>-400.111422</td>\n",
+ " <td>lammps_job_surf</td>\n",
+ " <td>(Atom('Cu', [0.0, 1.47377632857406, 9.024277317236802e-17], index=0), Atom('Cu', [2.5526554800834376, 1.4737763285740602, 2.4654784132287465e-16], index=1), Atom('Cu', [5.105310960166875, 1.473776...</td>\n",
+ " <td>-426.377084</td>\n",
" <td>[[-8.770761894538741e-15, 1.15657750043852e-09, 0.109956784695642], [-1.0824674490095302e-15, 1.15657515335765e-09, 0.10995678469564], [2.4308896909297503e-15, 1.1565748914144101e-09, 0.1099567846...</td>\n",
" <td>128.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>30</th>\n",
- " <td>None</td>\n",
- " <td>(Atom('Cu', [0.4126496185424086, 0.9553642998076769, 0.12158924761653131], index=0), Atom('Cu', [2.831118842513476, 1.0700158216349893, 25.916922304272767], index=1), Atom('Cu', [5.314789299948389...</td>\n",
- " <td>-399.591699</td>\n",
- " <td>[[-0.570999988178131, 1.09833300989089, -0.566585257198732], [-0.0492000252908114, 0.597416506778632, 0.966635869516025], [-0.0024866801464792, -0.0674126479000064, 0.2546322145358], [0.2289085885...</td>\n",
+ " <td>lammps_job_surf</td>\n",
+ " <td>(Atom('Cu', [0.4126496185424086, 0.9553642998076769, 0.12158924761653131], index=0), Atom('Cu', [2.831118842513476, 1.070015821634989, 25.91692230427277], index=1), Atom('Cu', [5.314789299948389, ...</td>\n",
+ " <td>-412.725659</td>\n",
+ " <td>[[-0.570999988178138, 1.09833300989088, -0.566585257198733], [-0.0492000252908119, 0.59741650677863, 0.966635869516026], [-0.0024866801464869, -0.0674126479000064, 0.2546322145358], [0.22890858859...</td>\n",
" <td>128.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>31</th>\n",
- " <td>None</td>\n",
- " <td>(Atom('Cu', [10.151562776611806, 1.6587733567107183, 26.43035938894712], index=0), Atom('Cu', [2.5212828819853748, 1.9070842851152785, 26.36203940098048], index=1), Atom('Cu', [4.715098279443367, ...</td>\n",
- " <td>-398.422617</td>\n",
- " <td>[[-0.555658749547497, 0.42566314828364993, 0.466167261187443], [-1.39449792316952, -0.5017985009363372, 0.4456531170887249], [1.25410857633035, -0.33111996310077596, -0.24658722383829995], [0.3911...</td>\n",
+ " <td>lammps_job_surf</td>\n",
+ " <td>(Atom('Cu', [10.151562776611796, 1.6587733567107221, 26.430359388947146], index=0), Atom('Cu', [2.521282881985372, 1.9070842851152827, 26.3620394009805], index=1), Atom('Cu', [4.715098279444533, 1...</td>\n",
+ " <td>-412.248744</td>\n",
+ " <td>[[-0.555658749547297, 0.42566314828364293, 0.466167261187242], [-1.39449792316991, -0.5017985009363141, 0.44565311708876987], [1.25410857633047, -0.33111996310053693, -0.24658722383835793], [0.391...</td>\n",
" <td>128.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>32</th>\n",
- " <td>None</td>\n",
- " <td>(Atom('Cu', [0.19573901040697333, 1.051460534941847, 26.530022925039237], index=0), Atom('Cu', [2.995726956631421, 1.1546751485293076, 26.840478692293868], index=1), Atom('Cu', [5.923947432763936,...</td>\n",
- " <td>-395.110340</td>\n",
- " <td>[[0.550884754551829, 0.33865983742272204, 0.12042096866985205], [0.189727589275692, -0.524367356684999, -0.17886090450862402], [-1.6758650723099, -0.31030261483377614, 0.6946509585213989], [0.4453...</td>\n",
+ " <td>lammps_job_surf</td>\n",
+ " <td>(Atom('Cu', [0.19573901040814495, 1.051460534941852, 26.530022925039262], index=0), Atom('Cu', [2.9957269566314313, 1.1546751485293134, -0.001778040455061588], index=1), Atom('Cu', [5.923947432763...</td>\n",
+ " <td>-408.987597</td>\n",
+ " <td>[[0.550884754551255, 0.33865983742361505, 0.12042096866994706], [0.189727589275785, -0.524367356684469, -0.17886090450817402], [-1.6758650723095, -0.3103026148332811, 0.6946509585210929], [0.44535...</td>\n",
" <td>128.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>33</th>\n",
- " <td>None</td>\n",
- " <td>(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....</td>\n",
- " <td>-396.833326</td>\n",
- " <td>[[0.235449441284142, 0.601163461325591, 0.04737458109310825], [0.337344266123105, 0.66485729403382, 0.37768738132523805], [-0.171831038530166, -0.11286098093109101, -0.07415135874528352], [-0.1966...</td>\n",
+ " <td>lammps_job_surf</td>\n",
+ " <td>(Atom('Cu', [9.88837962589013, 1.4968159202602165, 26.58551059472219], index=0), Atom('Cu', [2.2075440570158325, 1.2900742458621188, 26.685466830384563], index=1), Atom('Cu', [4.939145903748459, 1...</td>\n",
+ " <td>-410.603331</td>\n",
+ " <td>[[0.235449441283078, 0.601163461328045, 0.047374581092271446], [0.337344266120139, 0.664857294034072, 0.37768738132641905], [-0.171831038532397, -0.11286098092806901, -0.07415135874388401], [-0.19...</td>\n",
" <td>128.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>34</th>\n",
- " <td>None</td>\n",
- " <td>(Atom('Cu', [0.3429326290376805, 1.5170285327525175, 0.14896315086845416], index=0), Atom('Cu', [3.129345868860857, 1.495102964861245, 0.01607848650845961], index=1), Atom('Cu', [5.714332108258016...</td>\n",
- " <td>-400.444368</td>\n",
- " <td>[[1.15453322332565, 0.04603660924771737, -1.21282260887155], [-0.403390913673288, -0.18969536874868004, 0.030526533198225264], [-0.683024325114862, -0.967333273082708, 0.4114320467737619], [-0.867...</td>\n",
+ " <td>lammps_job_surf</td>\n",
+ " <td>(Atom('Cu', [0.34293262903884986, 1.5170285327525375, 0.1489631508684563], index=0), Atom('Cu', [3.1293458688620657, 1.4951029648602612, 0.016078486508459836], index=1), Atom('Cu', [5.714332108259...</td>\n",
+ " <td>-412.068287</td>\n",
+ " <td>[[1.15453322332514, 0.04603660924936107, -1.21282260886917], [-0.40339091367313, -0.18969536874822704, 0.030526533197075965], [-0.683024325118812, -0.967333273080052, 0.4114320467711059], [-0.8675...</td>\n",
" <td>128.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>35</th>\n",
- " <td>None</td>\n",
- " <td>(Atom('Cu', [9.95801241508363, 1.4359511579313753, 26.639342243648862], index=0), Atom('Cu', [2.2681416259098204, 1.7861270127574713, 0.0041936446239185], index=1), Atom('Cu', [5.074253116948648, ...</td>\n",
- " <td>-397.843043</td>\n",
- " <td>[[0.742004122721361, 0.22577315893502206, 0.12298868177971806], [0.771069504028052, -0.90014541931557, -0.660403448738781], [-0.462456173466872, 1.24796716628589, -0.4192010350460109], [0.08219110...</td>\n",
+ " <td>lammps_job_surf</td>\n",
+ " <td>(Atom('Cu', [9.95801241508353, 1.4359511579323643, 26.639342243648876], index=0), Atom('Cu', [2.2681416259097977, 1.7861270127584556, 0.004193644623918503], index=1), Atom('Cu', [5.074253116948597...</td>\n",
+ " <td>-410.426591</td>\n",
+ " <td>[[0.742004122720721, 0.22577315892753805, 0.12298868178080906], [0.771069504023197, -0.90014541932296, -0.660403448735684], [-0.462456173471762, 1.24796716627208, -0.41920103505081097], [0.0821911...</td>\n",
" <td>128.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>36</th>\n",
- " <td>None</td>\n",
- " <td>(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...</td>\n",
- " <td>-399.776798</td>\n",
- " <td>[[0.552749731038993, -0.46087407707755496, 0.177277816519943], [0.340079509783844, 0.23574679643440802, 0.26784307872713603], [0.388298578408562, 0.331969932822417, 0.34399524632239104], [-0.59826...</td>\n",
+ " <td>lammps_job_surf</td>\n",
+ " <td>(Atom('Cu', [10.225027496778678, 1.7848555655263902, 26.42388292769736], index=0), Atom('Cu', [2.491486993862084, 1.8611191751030531, 26.648267715418335], index=1), Atom('Cu', [4.968442272628866, ...</td>\n",
+ " <td>-413.081270</td>\n",
+ " <td>[[0.552749731039339, -0.46087407706439093, 0.177277816520108], [0.340079509796374, 0.23574679643604202, 0.26784307872275903], [0.38829857840138, 0.331969932800717, 0.34399524631836903], [-0.598269...</td>\n",
" <td>128.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>37</th>\n",
- " <td>None</td>\n",
- " <td>(Atom('Cu', [10.188116701703345, 1.3482529143763475, 26.353847647582224], index=0), Atom('Cu', [2.4559442807081986, 1.4757747059762696, 26.57379282025388], index=1), Atom('Cu', [5.077086561123585,...</td>\n",
- " <td>-399.168074</td>\n",
- " <td>[[0.570532228156976, 0.17193739345012202, 0.796311675035985], [0.67297011060888, -0.81773224395498, 0.207420342553107], [0.391385096561351, -0.862073619446019, 0.597813478897486], [-0.270452726779...</td>\n",
+ " <td>lammps_job_surf</td>\n",
+ " <td>(Atom('Cu', [10.18811670169521, 1.3482529143794337, 26.353847647583958], index=0), Atom('Cu', [2.4559442807083434, 1.4757747059783504, 26.573792820255626], index=1), Atom('Cu', [5.077086561123885,...</td>\n",
+ " <td>-411.270168</td>\n",
+ " <td>[[0.570532228170616, 0.17193739346638104, 0.796311675023456], [0.672970110578221, -0.817732243959863, 0.207420342553793], [0.391385096556072, -0.862073619432422, 0.597813478903035], [-0.2704527267...</td>\n",
" <td>128.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>38</th>\n",
- " <td>None</td>\n",
- " <td>(Atom('Cu', [10.165259029706933, 1.7122531598094173, 26.335638965295193], index=0), Atom('Cu', [2.3513330869200098, 1.5487334168655387, 26.34258116233103], index=1), Atom('Cu', [4.95573138146394, ...</td>\n",
- " <td>-396.984690</td>\n",
- " <td>[[-1.11093024791963, -0.6986058376048401, 0.44674121624886787], [0.0416051560041239, -0.0424634970331458, -0.0874515615419252], [-0.135122617155289, -0.778975629913174, -1.04402814519501], [0.8442...</td>\n",
+ " <td>lammps_job_surf</td>\n",
+ " <td>(Atom('Cu', [10.165259029717141, 1.7122531597864588, 26.335638965282506], index=0), Atom('Cu', [2.351333086964575, 1.5487334167881261, 26.342581162362286], index=1), Atom('Cu', [4.955731381487939,...</td>\n",
+ " <td>-410.951862</td>\n",
+ " <td>[[-1.11093024775332, -0.6986058375434832, 0.4467412161766239], [0.0416051560885089, -0.0424634968511256, -0.0874515614131588], [-0.135122617107614, -0.778975629931571, -1.04402814517475], [0.84425...</td>\n",
" <td>128.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>39</th>\n",
- " <td>None</td>\n",
- " <td>(Atom('Cu', [0.36893784059756035, 1.481831927531004, 26.53504700964859], index=0), Atom('Cu', [2.6965712181950883, 1.488812429574298, 26.730123522873537], index=1), Atom('Cu', [5.668661292604278, ...</td>\n",
- " <td>-399.581912</td>\n",
- " <td>[[-0.645092069902244, 0.04920122139904896, 0.21081031345366397], [1.14893686034324, -0.6114894792387109, -0.40665475671972495], [-0.287092609914331, 0.292443458702414, -0.801010316546939], [-0.184...</td>\n",
+ " <td>lammps_job_surf</td>\n",
+ " <td>(Atom('Cu', [0.3689378411745667, 1.4818319280204475, 26.535047009582307], index=0), Atom('Cu', [2.6965712182140265, 1.4888124298358478, 26.730123523791978], index=1), Atom('Cu', [5.668661293887029...</td>\n",
+ " <td>-411.163952</td>\n",
+ " <td>[[-0.645092069842764, 0.049201221165188956, 0.21081031392484997], [1.14893686212593, -0.6114894802487358, -0.40665475714370897], [-0.287092610235497, 0.292443460035198, -0.801010315713759], [-0.18...</td>\n",
" <td>128.0</td>\n",
" </tr>\n",
" </tbody>\n",
@@ -1466,47 +939,47 @@
"</div>"
],
"text/plain": [
- " name \\\n",
- "0 None \n",
- "1 None \n",
- "2 None \n",
- "3 None \n",
- "4 None \n",
- "5 None \n",
- "6 None \n",
- "7 None \n",
- "8 None \n",
- "9 None \n",
- "10 None \n",
- "11 None \n",
- "12 None \n",
- "13 None \n",
- "14 None \n",
- "15 None \n",
- "16 None \n",
- "17 None \n",
- "18 None \n",
- "19 None \n",
- "20 None \n",
- "21 None \n",
- "22 None \n",
- "23 None \n",
- "24 None \n",
- "25 None \n",
- "26 None \n",
- "27 None \n",
- "28 None \n",
- "29 None \n",
- "30 None \n",
- "31 None \n",
- "32 None \n",
- "33 None \n",
- "34 None \n",
- "35 None \n",
- "36 None \n",
- "37 None \n",
- "38 None \n",
- "39 None \n",
+ " name \\\n",
+ "0 job_a_3_4 \n",
+ "1 job_a_3_5 \n",
+ "2 job_a_3_6 \n",
+ "3 job_a_3_7 \n",
+ "4 job_a_3_8 \n",
+ "5 job_a_3_9 \n",
+ "6 job_a_4_0 \n",
+ "7 lammps_job \n",
+ "8 lammps_job \n",
+ "9 lammps_job \n",
+ "10 lammps_job \n",
+ "11 lammps_job \n",
+ "12 lammps_job \n",
+ "13 lammps_job \n",
+ "14 lammps_job \n",
+ "15 lammps_job \n",
+ "16 lammps_job \n",
+ "17 lammps_job \n",
+ "18 lammps_job_vac \n",
+ "19 lammps_job_vac \n",
+ "20 lammps_job_vac \n",
+ "21 lammps_job_vac \n",
+ "22 lammps_job_vac \n",
+ "23 lammps_job_vac \n",
+ "24 lammps_job_vac \n",
+ "25 lammps_job_vac \n",
+ "26 lammps_job_vac \n",
+ "27 lammps_job_vac \n",
+ "28 lammps_job_vac \n",
+ "29 lammps_job_surf \n",
+ "30 lammps_job_surf \n",
+ "31 lammps_job_surf \n",
+ "32 lammps_job_surf \n",
+ "33 lammps_job_surf \n",
+ "34 lammps_job_surf \n",
+ "35 lammps_job_surf \n",
+ "36 lammps_job_surf \n",
+ "37 lammps_job_surf \n",
+ "38 lammps_job_surf \n",
+ "39 lammps_job_surf \n",
"\n",
" atoms \\\n",
"0 (Atom('Cu', [0.0, 0.0, 0.0], index=0)) \n",
@@ -1516,39 +989,39 @@
"4 (Atom('Cu', [0.0, 0.0, 0.0], index=0)) \n",
"5 (Atom('Cu', [0.0, 0.0, 0.0], index=0)) \n",
"6 (Atom('Cu', [0.0, 0.0, 0.0], index=0)) \n",
- "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... \n",
- "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, ... \n",
- "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... \n",
- "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... \n",
- "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... \n",
- "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... \n",
- "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... \n",
- "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... \n",
- "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... \n",
- "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... \n",
- "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... \n",
- "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... \n",
- "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,... \n",
- "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... \n",
- "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... \n",
- "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... \n",
- "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... \n",
- "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... \n",
- "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... \n",
- "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... \n",
- "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,... \n",
- "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,... \n",
- "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... \n",
- "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... \n",
- "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, ... \n",
- "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,... \n",
- "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.... \n",
- "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... \n",
- "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, ... \n",
- "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... \n",
- "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,... \n",
- "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, ... \n",
- "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, ... \n",
+ "7 (Atom('Cu', [0.0, 0.0, 0.0], index=0), Atom('Cu', [0.0, 1.804999999999592, 1.804999999999592], index=1), Atom('Cu', [1.804999999999592, 1.1052437362302367e-16, 1.804999999999592], index=2), Atom('... \n",
+ "8 (Atom('Cu', [0.140426153531212, 11.00934611760493, 10.96820769600138], index=0), Atom('Cu', [10.983357200359302, 1.779939365335074, 1.7146804782560903], index=1), Atom('Cu', [2.1228644677344763, 0... \n",
+ "9 (Atom('Cu', [0.1407579358923329, 11.020287239626356, 10.855878337455094], index=0), Atom('Cu', [0.29542104007972325, 1.6514729828183248, 1.7760939949715], index=1), Atom('Cu', [1.9957825818756145,... \n",
+ "10 (Atom('Cu', [0.046752778326835207, 10.951786003502875, 0.20014601215416555], index=0), Atom('Cu', [0.08453269827616121, 1.8072189743037306, 1.7664733621606052], index=1), Atom('Cu', [1.95973571233... \n",
+ "11 (Atom('Cu', [10.99133278089223, 11.027168829788456, 0.17044757336885], index=0), Atom('Cu', [10.869778028731703, 1.9053524080340212, 1.7569642307109046], index=1), Atom('Cu', [1.8902712829055568, ... \n",
+ "12 (Atom('Cu', [10.958070767873476, 0.05270018288526145, 11.015795828313692], index=0), Atom('Cu', [0.045409705041259525, 2.078051985469034, 1.8353871076995325], index=1), Atom('Cu', [1.8285627799498... \n",
+ "13 (Atom('Cu', [10.903697402270652, 10.843249424146602, 0.09574490333936027], index=0), Atom('Cu', [10.59491891666766, 1.7187193807026324, 1.9573011135302476], index=1), Atom('Cu', [1.676074002401891... \n",
+ "14 (Atom('Cu', [0.258411989603464, 0.0706344931649224, 10.912283030397811], index=0), Atom('Cu', [0.1964902001455455, 1.7891621064461172, 1.8031814864809468], index=1), Atom('Cu', [1.7493171890021084... \n",
+ "15 (Atom('Cu', [0.004994793782076363, 10.985055637641707, 10.904222762435255], index=0), Atom('Cu', [10.9417296640056, 1.886861412294462, 1.8147512571859394], index=1), Atom('Cu', [1.8438031255436442... \n",
+ "16 (Atom('Cu', [0.03645923831331586, 10.8560106939291, 10.97057299019823], index=0), Atom('Cu', [10.913522535013476, 1.816191438106623, 1.5447581077438086], index=1), Atom('Cu', [1.7758393302091413, ... \n",
+ "17 (Atom('Cu', [0.00976718182041884, 0.007186523165377699, 11.008902399259645], index=0), Atom('Cu', [10.89374596607187, 1.9969194212527828, 1.5955788370755422], index=1), Atom('Cu', [2.0544219291027... \n",
+ "18 (Atom('Cu', [0.0, 1.804999999999592, 1.804999999999592], index=0), Atom('Cu', [1.804999999999592, 1.1052437362302367e-16, 1.804999999999592], index=1), Atom('Cu', [1.804999999999592, 1.80499999999... \n",
+ "19 (Atom('Cu', [0.10390109091492468, 1.9580560553035562, 1.7791885607676787], index=0), Atom('Cu', [1.3868099266682057, 10.93717630776338, 1.6017909487813904], index=1), Atom('Cu', [1.718398788940990... \n",
+ "20 (Atom('Cu', [0.222323479300276, 1.6999920633404162, 1.7623980235259142], index=0), Atom('Cu', [2.1228826608790445, 0.1862423842302597, 2.0308086839888815], index=1), Atom('Cu', [1.733468948470044,... \n",
+ "21 (Atom('Cu', [10.839434974930233, 1.9008464900018414, 1.6867963294684114], index=0), Atom('Cu', [1.587659858135841, 0.1544755711878935, 1.7152999948177818], index=1), Atom('Cu', [2.148606011735478,... \n",
+ "22 (Atom('Cu', [10.827044041158409, 1.8148855201981695, 2.124190925175089], index=0), Atom('Cu', [1.6679142700199683, 0.11062408070456453, 1.6294014594257846], index=1), Atom('Cu', [1.294186866136013... \n",
+ "23 (Atom('Cu', [0.18579648603934987, 1.6025971043768155, 1.8725196193702205], index=0), Atom('Cu', [2.048083516582408, 0.05523851059960332, 2.2588410942434316], index=1), Atom('Cu', [1.84234468412923... \n",
+ "24 (Atom('Cu', [10.902653792488254, 1.9016481867624628, 1.7123868009764087], index=0), Atom('Cu', [1.684365629566867, 0.20454959543267073, 1.4940727709048371], index=1), Atom('Cu', [1.628967729292809... \n",
+ "25 (Atom('Cu', [0.22025110375749696, 1.5872348575731654, 1.7623998700921586], index=0), Atom('Cu', [1.8386689358494586, 10.988833155464064, 1.8571406735076377], index=1), Atom('Cu', [1.97639089167179... \n",
+ "26 (Atom('Cu', [10.746144724792629, 1.6561216261325158, 1.6676063346541934], index=0), Atom('Cu', [1.8697696007010116, 0.2956610204486699, 1.9071090181785917], index=1), Atom('Cu', [1.820130883905895... \n",
+ "27 (Atom('Cu', [0.17063059334564, 1.853418797177199, 1.7423748774412284], index=0), Atom('Cu', [1.8595651381460672, 10.905723229638589, 1.810598025743776], index=1), Atom('Cu', [1.9346512242265819, 1... \n",
+ "28 (Atom('Cu', [10.866365841890905, 1.8491297824671196, 2.0932441820713352], index=0), Atom('Cu', [1.7536272327257443, 10.898985480280807, 1.8241252899027136], index=1), Atom('Cu', [1.994555229954278... \n",
+ "29 (Atom('Cu', [0.0, 1.47377632857406, 9.024277317236802e-17], index=0), Atom('Cu', [2.5526554800834376, 1.4737763285740602, 2.4654784132287465e-16], index=1), Atom('Cu', [5.105310960166875, 1.473776... \n",
+ "30 (Atom('Cu', [0.4126496185424086, 0.9553642998076769, 0.12158924761653131], index=0), Atom('Cu', [2.831118842513476, 1.070015821634989, 25.91692230427277], index=1), Atom('Cu', [5.314789299948389, ... \n",
+ "31 (Atom('Cu', [10.151562776611796, 1.6587733567107221, 26.430359388947146], index=0), Atom('Cu', [2.521282881985372, 1.9070842851152827, 26.3620394009805], index=1), Atom('Cu', [4.715098279444533, 1... \n",
+ "32 (Atom('Cu', [0.19573901040814495, 1.051460534941852, 26.530022925039262], index=0), Atom('Cu', [2.9957269566314313, 1.1546751485293134, -0.001778040455061588], index=1), Atom('Cu', [5.923947432763... \n",
+ "33 (Atom('Cu', [9.88837962589013, 1.4968159202602165, 26.58551059472219], index=0), Atom('Cu', [2.2075440570158325, 1.2900742458621188, 26.685466830384563], index=1), Atom('Cu', [4.939145903748459, 1... \n",
+ "34 (Atom('Cu', [0.34293262903884986, 1.5170285327525375, 0.1489631508684563], index=0), Atom('Cu', [3.1293458688620657, 1.4951029648602612, 0.016078486508459836], index=1), Atom('Cu', [5.714332108259... \n",
+ "35 (Atom('Cu', [9.95801241508353, 1.4359511579323643, 26.639342243648876], index=0), Atom('Cu', [2.2681416259097977, 1.7861270127584556, 0.004193644623918503], index=1), Atom('Cu', [5.074253116948597... \n",
+ "36 (Atom('Cu', [10.225027496778678, 1.7848555655263902, 26.42388292769736], index=0), Atom('Cu', [2.491486993862084, 1.8611191751030531, 26.648267715418335], index=1), Atom('Cu', [4.968442272628866, ... \n",
+ "37 (Atom('Cu', [10.18811670169521, 1.3482529143794337, 26.353847647583958], index=0), Atom('Cu', [2.4559442807083434, 1.4757747059783504, 26.573792820255626], index=1), Atom('Cu', [5.077086561123885,... \n",
+ "38 (Atom('Cu', [10.165259029717141, 1.7122531597864588, 26.335638965282506], index=0), Atom('Cu', [2.351333086964575, 1.5487334167881261, 26.342581162362286], index=1), Atom('Cu', [4.955731381487939,... \n",
+ "39 (Atom('Cu', [0.3689378411745667, 1.4818319280204475, 26.535047009582307], index=0), Atom('Cu', [2.6965712182140265, 1.4888124298358478, 26.730123523791978], index=1), Atom('Cu', [5.668661293887029... \n",
"\n",
" energy \\\n",
"0 -3.142019 \n",
@@ -1558,39 +1031,39 @@
"4 -3.330215 \n",
"5 -3.195118 \n",
"6 -3.035358 \n",
- "7 -347.182406 \n",
- "8 -348.253665 \n",
- "9 -345.424528 \n",
- "10 -346.758349 \n",
- "11 -344.603627 \n",
- "12 -346.849801 \n",
- "13 -345.015235 \n",
- "14 -346.569097 \n",
- "15 -344.892954 \n",
- "16 -347.628843 \n",
- "17 -345.776979 \n",
- "18 -342.906251 \n",
- "19 -343.569002 \n",
- "20 -343.317892 \n",
- "21 -341.057270 \n",
- "22 -342.067006 \n",
- "23 -342.528496 \n",
- "24 -342.900954 \n",
- "25 -340.983380 \n",
- "26 -342.479965 \n",
- "27 -340.174298 \n",
- "28 -343.805462 \n",
- "29 -400.111422 \n",
- "30 -399.591699 \n",
- "31 -398.422617 \n",
- "32 -395.110340 \n",
- "33 -396.833326 \n",
- "34 -400.444368 \n",
- "35 -397.843043 \n",
- "36 -399.776798 \n",
- "37 -399.168074 \n",
- "38 -396.984690 \n",
- "39 -399.581912 \n",
+ "7 -369.311743 \n",
+ "8 -360.190839 \n",
+ "9 -356.403521 \n",
+ "10 -358.245754 \n",
+ "11 -356.564325 \n",
+ "12 -357.011799 \n",
+ "13 -357.856759 \n",
+ "14 -358.316140 \n",
+ "15 -356.847816 \n",
+ "16 -358.626624 \n",
+ "17 -356.796173 \n",
+ "18 -364.828772 \n",
+ "19 -353.817356 \n",
+ "20 -353.115830 \n",
+ "21 -352.375089 \n",
+ "22 -352.774500 \n",
+ "23 -352.466296 \n",
+ "24 -353.659518 \n",
+ "25 -352.032412 \n",
+ "26 -352.885609 \n",
+ "27 -352.295316 \n",
+ "28 -353.959714 \n",
+ "29 -426.377084 \n",
+ "30 -412.725659 \n",
+ "31 -412.248744 \n",
+ "32 -408.987597 \n",
+ "33 -410.603331 \n",
+ "34 -412.068287 \n",
+ "35 -410.426591 \n",
+ "36 -413.081270 \n",
+ "37 -411.270168 \n",
+ "38 -410.951862 \n",
+ "39 -411.163952 \n",
"\n",
" forces \\\n",
"0 [[1.1869253621046177e-16, -1.7429070520896771e-16, -1.397277865277868e-16]] \n",
@@ -1602,37 +1075,37 @@
"6 [[-5.946777565406637e-17, -1.0605082175909553e-16, -1.2946304704347008e-16]] \n",
"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... \n",
"8 [[-0.21910202935187897, -0.37573419410584397, 0.43392575377979187], [0.16208168404695897, -0.00671505675904709, 1.03458554920361], [-1.2001630139266497, -0.40207322348963503, -0.45620473735655703]... \n",
- "9 [[-0.023031834879881696, 0.042841438691562095, 0.5899774836434479], [-0.5418151518759569, 0.6754733604036028, -0.5582999589284809], [-0.6011411771360858, -0.355590065329821, -0.0035901986306415582... \n",
- "10 [[-0.32237334386615796, 0.43406651671724894, -0.5886238546572939], [-0.6295919499998729, 0.07530471384300086, -0.12687342568230403], [-0.06506588733991228, 0.8782024477953109, -0.12243680387297393... \n",
- "11 [[0.45078377546738896, -0.7167806257867769, -0.320969733282763], [0.5707773027838049, -0.5494069530705199, 0.510256621543289], [-0.36439749359274193, 0.17709586752044496, 0.23127352998569298], [0.... \n",
- "12 [[-0.38409855462219894, 0.12077975249818296, 0.024465771201292483], [-0.6560764999451358, -1.05845756801878, -0.658182913095082], [-0.5103420261962529, -0.35656271154938, 0.7090309519821769], [-0.... \n",
- "13 [[0.22044015995668098, -0.2607278388818459, -0.3855032322190499], [0.7754186544660099, -0.04652340102386694, -0.26232164996063695], [0.43147792874898694, -0.9840256256911009, 0.34987911571105595],... \n",
- "14 [[-0.5020206209676749, 0.007307596544171969, 0.24586848661916993], [-1.1645196400331899, 0.1476285180684419, 0.6168850904586589], [0.7183114431792579, -0.5420093171036479, -0.06687387962480258], [... \n",
- "15 [[0.04806202889719739, 0.48969724353819394, 1.29371057615331], [0.5538169933185199, -0.7855310261714289, -0.033081946412792815], [0.34832740609982993, 0.9937361742308158, 0.30650548838004904], [-0... \n",
- "16 [[0.24033044872062098, 1.5305792677179897, -0.6791236163119347], [0.05903491332573559, 0.148151392595253, 0.542468964409148], [0.07921843405670739, 0.145966157214324, 0.7342269238916159], [0.77503... \n",
- "17 [[-0.13926025211222698, -0.0920021629424733, 0.21001691285267599], [0.6767944835284789, -1.1148612203782198, 1.7165284718417098], [-0.7950973845960859, 0.2356681337270629, 0.13328556064538893], [0... \n",
+ "9 [[-0.023031834879864897, 0.04284143869144259, 0.5899774836434099], [-0.5418151518758109, 0.6754733604037649, -0.5582999589285099], [-0.6011411771363389, -0.355590065330048, -0.003590198630652358],... \n",
+ "10 [[-0.32237334386617594, 0.43406651671772695, -0.5886238546573999], [-0.6295919499999019, 0.07530471384292876, -0.12687342568255203], [-0.06506588733974998, 0.8782024477947719, -0.12243680387296693... \n",
+ "11 [[0.45078377546780296, -0.7167806257868728, -0.320969733281809], [0.5707773027839779, -0.5494069530720159, 0.510256621543522], [-0.36439749359319995, 0.17709586752113193, 0.23127352998529296], [0.... \n",
+ "12 [[-0.38409855462373593, 0.12077975249587695, 0.02446577119927368], [-0.6560764999470009, -1.05845756801682, -0.658182913092867], [-0.5103420261931418, -0.356562711546522, 0.7090309519858399], [-0.... \n",
+ "13 [[0.22044015996419397, -0.26072783887691897, -0.38550323222201893], [0.7754186544628359, -0.04652340102588245, -0.2623216499598349], [0.4314779287479719, -0.9840256256937749, 0.34987911571166197],... \n",
+ "14 [[-0.5020206209738959, 0.007307596546447969, 0.24586848662953095], [-1.1645196400318298, 0.14762851807991492, 0.6168850904682569], [0.7183114431738189, -0.5420093170980669, -0.06687387962120929], ... \n",
+ "15 [[0.04806202890911529, 0.4896972435411299, 1.29371057618316], [0.5538169933312109, -0.7855310261686719, -0.033081946439222513], [0.34832740608971496, 0.9937361742507679, 0.30650548838579206], [-0.... \n",
+ "16 [[0.24033044872932896, 1.5305792676779497, -0.6791236163998687], [0.05903491330127059, 0.148151392634253, 0.542468964385662], [0.07921843405774338, 0.145966157230826, 0.7342269239659519], [0.77503... \n",
+ "17 [[-0.13926025200196399, -0.0920021630565197, 0.21001691279918497], [0.6767944835632749, -1.1148612202170798, 1.7165284720013199], [-0.7950973844667609, 0.2356681335380539, 0.13328556065954994], [0... \n",
"18 [[-1.3933298959045699e-14, -0.10827842091784899, -0.108278420917849], [-0.10827842091784899, -1.3877479054990188e-14, -0.108278420917849], [-0.10827842091784899, -0.108278420917849, -1.38424758326... \n",
- "19 [[-0.45079778130218695, 0.19236747741170795, 0.23614131969524693], [1.2984317307784499, 0.04751568933291938, 0.005443425577977482], [0.48875760189522893, -0.5765163470127929, -0.5531364786691719],... \n",
- "20 [[-0.6920262907044069, 0.3986975029533409, 0.10738641941643497], [-1.2097205794553298, -2.21423543020926, -0.8363385508172672], [-0.36839592956658596, 0.35919893904268096, 0.09738195090664269], [2... \n",
- "21 [[0.5607305368018309, 0.07454461225822963, 0.17092757180402804], [0.7460358156721709, -0.9693709228665989, -0.357775642488428], [-1.4982109077380097, 1.0695224870660298, 0.17016025464137993], [1.1... \n",
- "22 [[0.7768634672312369, 0.615614277472231, -0.6520778674544528], [0.5196497874591819, -0.7614150189249069, 0.33452284258026094], [1.0185593798470798, 0.11349094338622906, -1.1138567887728799], [0.39... \n",
- "23 [[-1.2511641505681497, 0.045660252990561916, 0.39426999337691987], [-0.4923847861277789, -0.676187288680257, -1.3802167704923], [-0.12072100498159098, 0.5666924914439229, -0.8825937576849239], [0.... \n",
- "24 [[0.5080309295986539, -0.4875222169174689, 0.46898176405272696], [0.11031309252296198, -0.7243436014688799, 1.2808414836059598], [0.6855285827079979, 0.576817447055947, 0.31599931473888204], [0.50... \n",
- "25 [[-0.6923371397061229, 0.9615117892959398, 0.396261839433264], [0.18083100499512797, -0.47103552335731996, 0.5072798013711759], [-0.22735248831930896, 0.37011177620569996, -1.1740345740817597], [0... \n",
- "26 [[0.46940172398488794, 0.557542533896084, 0.861383405261689], [-0.16043498489103097, -1.0997839627759998, -0.013974118313924476], [-0.13554483762266598, 0.6363641149062679, 0.153788969879775], [1.... \n",
- "27 [[-1.1653987834207897, -0.07515193371140247, -0.13414295102360305], [0.17707911646472896, 0.37588362216028093, 0.10312993516925903], [0.6003632691780849, 0.3869695806628, 0.03431754153949555], [-0... \n",
- "28 [[0.42819147658911194, -1.3404675072584398, -0.840042992949223], [0.47822853532413195, -0.07949121681390955, -0.36737406099153697], [-0.9172012989939929, 0.3239785862266829, -0.013009375610539234]... \n",
+ "19 [[-0.45079778130212095, 0.19236747741186794, 0.23614131969518395], [1.2984317307785798, 0.047515689332818876, 0.0054434255778954815], [0.48875760189529993, -0.5765163470127389, -0.5531364786691438... \n",
+ "20 [[-0.6920262907037699, 0.3986975029534239, 0.10738641941633598], [-1.2097205794551897, -2.2142354302088, -0.8363385508175151], [-0.36839592956672496, 0.3591989390425319, 0.09738195090699889], [2.1... \n",
+ "21 [[0.5607305368014349, 0.07454461225798582, 0.17092757180355503], [0.7460358156722969, -0.9693709228667519, -0.357775642489466], [-1.4982109077379697, 1.0695224870646098, 0.17016025464195195], [1.1... \n",
+ "22 [[0.7768634672242999, 0.615614277463985, -0.6520778674493769], [0.5196497874591279, -0.7614150189291738, 0.33452284258293197], [1.0185593798557397, 0.11349094339204105, -1.1138567887771997], [0.39... \n",
+ "23 [[-1.2511641504900297, 0.045660252979352216, 0.3942699933548249], [-0.49238478619866294, -0.676187288648693, -1.38021677052805], [-0.12072100498243699, 0.5666924914313989, -0.8825937576412469], [0... \n",
+ "24 [[0.5080309295530009, -0.4875222168854389, 0.46898176419400794], [0.11031309245877298, -0.7243436015235899, 1.2808414835860897], [0.6855285827566528, 0.576817447011234, 0.31599931467165404], [0.50... \n",
+ "25 [[-0.6923371397932379, 0.9615117891395759, 0.396261839405581], [0.18083100479582398, -0.47103552318232994, 0.5072798015385259], [-0.22735248852514198, 0.3701117760834369, -1.1740345739673297], [0.... \n",
+ "26 [[0.4694017239681809, 0.557542533620799, 0.861383405389437], [-0.16043498520491098, -1.0997839630796997, -0.013974118048379877], [-0.13554483753545396, 0.6363641150344139, 0.153788969504449], [1.0... \n",
+ "27 [[-1.1653987878668197, -0.07515193358861387, -0.13414295175130306], [0.17707911415253696, 0.37588361844850293, 0.10312993216846503], [0.6003632668071709, 0.386969577632806, 0.03431754138154845], [... \n",
+ "28 [[0.4281914688318719, -1.3404674992878498, -0.840042998895605], [0.4782285361793289, -0.07949121879472046, -0.36737406210665396], [-0.9172013000957939, 0.3239785884620919, -0.013009379648141535], ... \n",
"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... \n",
- "30 [[-0.570999988178131, 1.09833300989089, -0.566585257198732], [-0.0492000252908114, 0.597416506778632, 0.966635869516025], [-0.0024866801464792, -0.0674126479000064, 0.2546322145358], [0.2289085885... \n",
- "31 [[-0.555658749547497, 0.42566314828364993, 0.466167261187443], [-1.39449792316952, -0.5017985009363372, 0.4456531170887249], [1.25410857633035, -0.33111996310077596, -0.24658722383829995], [0.3911... \n",
- "32 [[0.550884754551829, 0.33865983742272204, 0.12042096866985205], [0.189727589275692, -0.524367356684999, -0.17886090450862402], [-1.6758650723099, -0.31030261483377614, 0.6946509585213989], [0.4453... \n",
- "33 [[0.235449441284142, 0.601163461325591, 0.04737458109310825], [0.337344266123105, 0.66485729403382, 0.37768738132523805], [-0.171831038530166, -0.11286098093109101, -0.07415135874528352], [-0.1966... \n",
- "34 [[1.15453322332565, 0.04603660924771737, -1.21282260887155], [-0.403390913673288, -0.18969536874868004, 0.030526533198225264], [-0.683024325114862, -0.967333273082708, 0.4114320467737619], [-0.867... \n",
- "35 [[0.742004122721361, 0.22577315893502206, 0.12298868177971806], [0.771069504028052, -0.90014541931557, -0.660403448738781], [-0.462456173466872, 1.24796716628589, -0.4192010350460109], [0.08219110... \n",
- "36 [[0.552749731038993, -0.46087407707755496, 0.177277816519943], [0.340079509783844, 0.23574679643440802, 0.26784307872713603], [0.388298578408562, 0.331969932822417, 0.34399524632239104], [-0.59826... \n",
- "37 [[0.570532228156976, 0.17193739345012202, 0.796311675035985], [0.67297011060888, -0.81773224395498, 0.207420342553107], [0.391385096561351, -0.862073619446019, 0.597813478897486], [-0.270452726779... \n",
- "38 [[-1.11093024791963, -0.6986058376048401, 0.44674121624886787], [0.0416051560041239, -0.0424634970331458, -0.0874515615419252], [-0.135122617155289, -0.778975629913174, -1.04402814519501], [0.8442... \n",
- "39 [[-0.645092069902244, 0.04920122139904896, 0.21081031345366397], [1.14893686034324, -0.6114894792387109, -0.40665475671972495], [-0.287092609914331, 0.292443458702414, -0.801010316546939], [-0.184... \n",
+ "30 [[-0.570999988178138, 1.09833300989088, -0.566585257198733], [-0.0492000252908119, 0.59741650677863, 0.966635869516026], [-0.0024866801464869, -0.0674126479000064, 0.2546322145358], [0.22890858859... \n",
+ "31 [[-0.555658749547297, 0.42566314828364293, 0.466167261187242], [-1.39449792316991, -0.5017985009363141, 0.44565311708876987], [1.25410857633047, -0.33111996310053693, -0.24658722383835793], [0.391... \n",
+ "32 [[0.550884754551255, 0.33865983742361505, 0.12042096866994706], [0.189727589275785, -0.524367356684469, -0.17886090450817402], [-1.6758650723095, -0.3103026148332811, 0.6946509585210929], [0.44535... \n",
+ "33 [[0.235449441283078, 0.601163461328045, 0.047374581092271446], [0.337344266120139, 0.664857294034072, 0.37768738132641905], [-0.171831038532397, -0.11286098092806901, -0.07415135874388401], [-0.19... \n",
+ "34 [[1.15453322332514, 0.04603660924936107, -1.21282260886917], [-0.40339091367313, -0.18969536874822704, 0.030526533197075965], [-0.683024325118812, -0.967333273080052, 0.4114320467711059], [-0.8675... \n",
+ "35 [[0.742004122720721, 0.22577315892753805, 0.12298868178080906], [0.771069504023197, -0.90014541932296, -0.660403448735684], [-0.462456173471762, 1.24796716627208, -0.41920103505081097], [0.0821911... \n",
+ "36 [[0.552749731039339, -0.46087407706439093, 0.177277816520108], [0.340079509796374, 0.23574679643604202, 0.26784307872275903], [0.38829857840138, 0.331969932800717, 0.34399524631836903], [-0.598269... \n",
+ "37 [[0.570532228170616, 0.17193739346638104, 0.796311675023456], [0.672970110578221, -0.817732243959863, 0.207420342553793], [0.391385096556072, -0.862073619432422, 0.597813478903035], [-0.2704527267... \n",
+ "38 [[-1.11093024775332, -0.6986058375434832, 0.4467412161766239], [0.0416051560885089, -0.0424634968511256, -0.0874515614131588], [-0.135122617107614, -0.778975629931571, -1.04402814517475], [0.84425... \n",
+ "39 [[-0.645092069842764, 0.049201221165188956, 0.21081031392484997], [1.14893686212593, -0.6114894802487358, -0.40665475714370897], [-0.287092610235497, 0.292443460035198, -0.801010315713759], [-0.18... \n",
"\n",
" number_of_atoms \n",
"0 1.0 \n",
@@ -1677,7 +1150,7 @@
"39 128.0 "
]
},
- "execution_count": 35,
+ "execution_count": 16,
"metadata": {},
"output_type": "execute_result"
}
@@ -1689,7 +1162,7 @@
},
{
"cell_type": "markdown",
- "id": "level-dimension",
+ "id": "premier-least",
"metadata": {},
"source": [
"We can now inspect the data in this dataset quite easily"
@@ -1697,8 +1170,8 @@
},
{
"cell_type": "code",
- "execution_count": 36,
- "id": "visible-execution",
+ "execution_count": 17,
+ "id": "difficult-cartoon",
"metadata": {},
"outputs": [],
"source": [
@@ -1707,8 +1180,8 @@
},
{
"cell_type": "code",
- "execution_count": 37,
- "id": "becoming-integral",
+ "execution_count": 18,
+ "id": "analyzed-bargain",
"metadata": {},
"outputs": [],
"source": [
@@ -1717,7 +1190,7 @@
},
{
"cell_type": "markdown",
- "id": "novel-usage",
+ "id": "serious-carry",
"metadata": {},
"source": [
"The datasets used in the potential fitting procedure for day 2 (obtained from accurate DFT calculations) will be accessed in the same way"
@@ -1726,7 +1199,7 @@
{
"cell_type": "code",
"execution_count": null,
- "id": "forced-scotland",
+ "id": "simple-packet",
"metadata": {},
"outputs": [],
"source": []
@@ -1748,7 +1221,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
- "version": "3.8.8"
+ "version": "3.8.6"
}
},
"nbformat": 4,
--
GitLab