{"cells":[{"metadata":{},"cell_type":"markdown","source":"## Distinction of solid and liquid"},{"metadata":{"trusted":true},"cell_type":"code","source":"import os\nimport pyiron\nfrom ase.io import read\nimport pyscal.core as pc\nimport matplotlib.pyplot as plt\nimport numpy as np","execution_count":1,"outputs":[]},{"metadata":{"trusted":true},"cell_type":"code","source":"pr = pyiron.Project('ADIS')","execution_count":2,"outputs":[]},{"metadata":{"trusted":true},"cell_type":"code","source":"pr.job_table()","execution_count":3,"outputs":[{"output_type":"execute_result","execution_count":3,"data":{"text/plain":" id status chemicalformula job \\\n0 2 finished H8192 Nucleus \n1 4 finished H3980 Si_1400_20 \n2 5 finished H1529 S5_s00_n130_r1024_720_5 \n3 6 finished H1980 Fe_1050_20 \n4 7 finished H1980 Fe_1350_20 \n5 8 finished H3995 Si_1000_5 \n6 9 finished H1980 Cu_720_20 \n7 10 finished H2000 Cu_400_0 \n8 11 finished H4000 Mg_900_0 \n9 12 finished H4000 Mg_500_0 \n10 13 finished H1534 S5_s00_n130_r1024_720_0 \n11 15 finished H3995 Mg_700_5 \n12 16 finished H3980 Si_1000_20 \n13 17 finished H1554 S5_s00_n130_r1024_560_5 \n14 18 finished H1584 S5_s00_n130_r1024_400_0 \n15 19 finished H1980 Cu_400_20 \n16 20 finished H1995 Fe_1350_5 \n17 21 finished H3995 Mg_1000_5 \n18 22 finished H4000 Si_1400_0 \n19 23 finished H2000 Fe_1350_0 \n20 24 finished H4000 Mg_700_0 \n21 26 finished H1995 Fe_1050_5 \n22 27 finished H3980 Mg_1000_20 \n23 28 finished H2000 Cu_560_0 \n24 29 finished H2000 Fe_750_0 \n25 30 finished H1995 Cu_400_5 \n26 31 finished H1579 S5_s00_n130_r1024_400_5 \n27 32 finished H1980 Fe_750_20 \n28 33 finished H1980 Cu_560_20 \n29 34 finished H2000 Cu_720_0 \n30 35 finished H3980 Mg_500_20 \n31 36 finished H3980 Mg_700_20 \n32 38 finished H3995 Mg_500_5 \n33 39 finished H500 Liquid \n34 40 finished H1995 Cu_560_5 \n35 41 finished H1510 S5_s00_n130_r1024_720_20 \n36 42 finished H3980 Mg_900_20 \n37 43 finished H2000 Fe_1050_0 \n38 44 finished H1559 S5_s00_n130_r1024_560_0 \n39 45 finished H4000 Mg_1000_0 \n40 46 finished H1534 S5_s00_n130_r1024_560_20 \n41 47 finished H3995 Si_1400_5 \n42 48 finished H1995 Cu_720_5 \n43 49 finished H1995 Fe_750_5 \n44 50 finished H4000 Si_1000_0 \n45 51 finished H1559 S5_s00_n130_r1024_400_20 \n46 53 finished H3995 Mg_900_5 \n47 56 finished Cu1995 Cu_minimization \n\n subjob projectpath project \\\n0 /Nucleus /home/jovyan/ ADIS/ \n1 /Si_1400_20 /home/jovyan/ ADIS/ \n2 /S5_s00_n130_r1024_720_5 /home/jovyan/ ADIS/ \n3 /Fe_1050_20 /home/jovyan/ ADIS/ \n4 /Fe_1350_20 /home/jovyan/ ADIS/ \n5 /Si_1000_5 /home/jovyan/ ADIS/ \n6 /Cu_720_20 /home/jovyan/ ADIS/ \n7 /Cu_400_0 /home/jovyan/ ADIS/ \n8 /Mg_900_0 /home/jovyan/ ADIS/ \n9 /Mg_500_0 /home/jovyan/ ADIS/ \n10 /S5_s00_n130_r1024_720_0 /home/jovyan/ ADIS/ \n11 /Mg_700_5 /home/jovyan/ ADIS/ \n12 /Si_1000_20 /home/jovyan/ ADIS/ \n13 /S5_s00_n130_r1024_560_5 /home/jovyan/ ADIS/ \n14 /S5_s00_n130_r1024_400_0 /home/jovyan/ ADIS/ \n15 /Cu_400_20 /home/jovyan/ ADIS/ \n16 /Fe_1350_5 /home/jovyan/ ADIS/ \n17 /Mg_1000_5 /home/jovyan/ ADIS/ \n18 /Si_1400_0 /home/jovyan/ ADIS/ \n19 /Fe_1350_0 /home/jovyan/ ADIS/ \n20 /Mg_700_0 /home/jovyan/ ADIS/ \n21 /Fe_1050_5 /home/jovyan/ ADIS/ \n22 /Mg_1000_20 /home/jovyan/ ADIS/ \n23 /Cu_560_0 /home/jovyan/ ADIS/ \n24 /Fe_750_0 /home/jovyan/ ADIS/ \n25 /Cu_400_5 /home/jovyan/ ADIS/ \n26 /S5_s00_n130_r1024_400_5 /home/jovyan/ ADIS/ \n27 /Fe_750_20 /home/jovyan/ ADIS/ \n28 /Cu_560_20 /home/jovyan/ ADIS/ \n29 /Cu_720_0 /home/jovyan/ ADIS/ \n30 /Mg_500_20 /home/jovyan/ ADIS/ \n31 /Mg_700_20 /home/jovyan/ ADIS/ \n32 /Mg_500_5 /home/jovyan/ ADIS/ \n33 /Liquid /home/jovyan/ ADIS/ \n34 /Cu_560_5 /home/jovyan/ ADIS/ \n35 /S5_s00_n130_r1024_720_20 /home/jovyan/ ADIS/ \n36 /Mg_900_20 /home/jovyan/ ADIS/ \n37 /Fe_1050_0 /home/jovyan/ ADIS/ \n38 /S5_s00_n130_r1024_560_0 /home/jovyan/ ADIS/ \n39 /Mg_1000_0 /home/jovyan/ ADIS/ \n40 /S5_s00_n130_r1024_560_20 /home/jovyan/ ADIS/ \n41 /Si_1400_5 /home/jovyan/ ADIS/ \n42 /Cu_720_5 /home/jovyan/ ADIS/ \n43 /Fe_750_5 /home/jovyan/ ADIS/ \n44 /Si_1000_0 /home/jovyan/ ADIS/ \n45 /S5_s00_n130_r1024_400_20 /home/jovyan/ ADIS/ \n46 /Mg_900_5 /home/jovyan/ ADIS/ \n47 /Cu_minimization /home/jovyan/ ADIS/ \n\n timestart timestop totalcputime \\\n0 2020-11-05 21:11:34.985406 NaT NaN \n1 2020-11-05 21:11:40.585864 NaT NaN \n2 2020-11-05 21:11:43.147042 NaT NaN \n3 2020-11-05 21:11:47.255863 NaT NaN \n4 2020-11-05 21:11:53.247038 NaT NaN \n5 2020-11-05 21:11:59.993315 NaT NaN \n6 2020-11-05 21:12:06.132659 NaT NaN \n7 2020-11-05 21:12:11.172906 NaT NaN \n8 2020-11-05 21:12:18.633493 NaT NaN \n9 2020-11-05 21:12:24.458570 NaT NaN \n10 2020-11-05 21:12:26.942533 NaT NaN \n11 2020-11-05 21:12:33.466119 NaT NaN \n12 2020-11-05 21:12:40.492150 NaT NaN \n13 2020-11-05 21:12:43.054725 NaT NaN \n14 2020-11-05 21:12:44.725043 NaT NaN \n15 2020-11-05 21:12:49.268366 NaT NaN \n16 2020-11-05 21:12:54.623718 NaT NaN \n17 2020-11-05 21:13:01.055022 NaT NaN \n18 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2020-11-05 21:15:29.351879 NaT NaN \n44 2020-11-05 21:15:37.769224 NaT NaN \n45 2020-11-05 21:15:39.951420 NaT NaN \n46 2020-11-05 21:15:46.458817 NaT NaN \n47 2020-11-05 21:43:41.296584 2020-11-05 21:43:43.276914 1.0 \n\n computer \\\n0 pyiron@jupyter-pyiron-2dadis-2dworkshop-2d2020-2d3piumz95#1 \n1 pyiron@jupyter-pyiron-2dadis-2dworkshop-2d2020-2d3piumz95#1 \n2 pyiron@jupyter-pyiron-2dadis-2dworkshop-2d2020-2d3piumz95#1 \n3 pyiron@jupyter-pyiron-2dadis-2dworkshop-2d2020-2d3piumz95#1 \n4 pyiron@jupyter-pyiron-2dadis-2dworkshop-2d2020-2d3piumz95#1 \n5 pyiron@jupyter-pyiron-2dadis-2dworkshop-2d2020-2d3piumz95#1 \n6 pyiron@jupyter-pyiron-2dadis-2dworkshop-2d2020-2d3piumz95#1 \n7 pyiron@jupyter-pyiron-2dadis-2dworkshop-2d2020-2d3piumz95#1 \n8 pyiron@jupyter-pyiron-2dadis-2dworkshop-2d2020-2d3piumz95#1 \n9 pyiron@jupyter-pyiron-2dadis-2dworkshop-2d2020-2d3piumz95#1 \n10 pyiron@jupyter-pyiron-2dadis-2dworkshop-2d2020-2d3piumz95#1 \n11 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idstatuschemicalformulajobsubjobprojectpathprojecttimestarttimestoptotalcputimecomputerhamiltonhamversionparentidmasterid
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36finishedH1980Fe_1050_20/Fe_1050_20/home/jovyan/ADIS/2020-11-05 21:11:47.255863NaTNaNpyiron@jupyter-pyiron-2dadis-2dworkshop-2d2020-2d3piumz95#1AtomisticGenericJob0.2.0NoneNone
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58finishedH3995Si_1000_5/Si_1000_5/home/jovyan/ADIS/2020-11-05 21:11:59.993315NaTNaNpyiron@jupyter-pyiron-2dadis-2dworkshop-2d2020-2d3piumz95#1AtomisticGenericJob0.2.0NoneNone
69finishedH1980Cu_720_20/Cu_720_20/home/jovyan/ADIS/2020-11-05 21:12:06.132659NaTNaNpyiron@jupyter-pyiron-2dadis-2dworkshop-2d2020-2d3piumz95#1AtomisticGenericJob0.2.0NoneNone
710finishedH2000Cu_400_0/Cu_400_0/home/jovyan/ADIS/2020-11-05 21:12:11.172906NaTNaNpyiron@jupyter-pyiron-2dadis-2dworkshop-2d2020-2d3piumz95#1AtomisticGenericJob0.2.0NoneNone
811finishedH4000Mg_900_0/Mg_900_0/home/jovyan/ADIS/2020-11-05 21:12:18.633493NaTNaNpyiron@jupyter-pyiron-2dadis-2dworkshop-2d2020-2d3piumz95#1AtomisticGenericJob0.2.0NoneNone
912finishedH4000Mg_500_0/Mg_500_0/home/jovyan/ADIS/2020-11-05 21:12:24.458570NaTNaNpyiron@jupyter-pyiron-2dadis-2dworkshop-2d2020-2d3piumz95#1AtomisticGenericJob0.2.0NoneNone
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2328finishedH2000Cu_560_0/Cu_560_0/home/jovyan/ADIS/2020-11-05 21:13:40.855803NaTNaNpyiron@jupyter-pyiron-2dadis-2dworkshop-2d2020-2d3piumz95#1AtomisticGenericJob0.2.0NoneNone
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2631finishedH1579S5_s00_n130_r1024_400_5/S5_s00_n130_r1024_400_5/home/jovyan/ADIS/2020-11-05 21:13:57.530915NaTNaNpyiron@jupyter-pyiron-2dadis-2dworkshop-2d2020-2d3piumz95#1AtomisticGenericJob0.2.0NoneNone
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3541finishedH1510S5_s00_n130_r1024_720_20/S5_s00_n130_r1024_720_20/home/jovyan/ADIS/2020-11-05 21:14:37.464296NaTNaNpyiron@jupyter-pyiron-2dadis-2dworkshop-2d2020-2d3piumz95#1AtomisticGenericJob0.2.0NoneNone
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4653finishedH3995Mg_900_5/Mg_900_5/home/jovyan/ADIS/2020-11-05 21:15:46.458817NaTNaNpyiron@jupyter-pyiron-2dadis-2dworkshop-2d2020-2d3piumz95#1AtomisticGenericJob0.2.0NoneNone
4756finishedCu1995Cu_minimization/Cu_minimization/home/jovyan/ADIS/2020-11-05 21:43:41.2965842020-11-05 21:43:43.2769141.0pyiron@jupyter-pyiron-2dadis-2dworkshop-2d2020-2d3piumz95#1Lammps0.1NoneNone
\n
"},"metadata":{}}]},{"metadata":{},"cell_type":"markdown","source":"We will start with a small configuration in which a small solid cluster is embedded in a liquid."},{"metadata":{"trusted":true},"cell_type":"code","source":"job = pr.load(\"Nucleus\")\nstruct = job.get_structure()","execution_count":4,"outputs":[]},{"metadata":{},"cell_type":"markdown","source":"One good idea is to get the q6 values."},{"metadata":{},"cell_type":"markdown","source":"Pyiron can calculate the q6 values and cluster them. Let's see how that works."},{"metadata":{"trusted":true},"cell_type":"code","source":"from pyiron.atomistics.structure.pyscal import get_steinhardt_parameter_job","execution_count":5,"outputs":[]},{"metadata":{"trusted":true},"cell_type":"code","source":"q46, cluster = get_steinhardt_parameter_job(job, clustering=True)","execution_count":6,"outputs":[]},{"metadata":{},"cell_type":"markdown","source":"We will switch a bit onto pyscal now. All the features of pyscal are not yet available on pyiron."},{"metadata":{"trusted":true},"cell_type":"code","source":"sys = pc.System()\nsys.read_inputfile(struct, format=\"ase\")\nsys.find_neighbors(method=\"cutoff\", cutoff=0)\nsys.calculate_q(6, averaged=True)","execution_count":7,"outputs":[]},{"metadata":{},"cell_type":"markdown","source":"from the previous example, we saw that the solid structures had average q6 roughly above 0.3"},{"metadata":{"trusted":true},"cell_type":"code","source":"atoms = sys.atoms\nfor count, atom in enumerate(atoms):\n if atom.get_q(6, averaged=True) > 0.3:\n atom.solid = 1\n else:\n atom.solid = 0","execution_count":8,"outputs":[]}],"metadata":{"kernelspec":{"name":"python3","display_name":"Python 3","language":"python"},"language_info":{"name":"python","version":"3.7.8","mimetype":"text/x-python","codemirror_mode":{"name":"ipython","version":3},"pygments_lexer":"ipython3","nbconvert_exporter":"python","file_extension":".py"}},"nbformat":4,"nbformat_minor":4}