Convergence parameters check

susyexists/README.md

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+# K-point convergence tracker (Materials)
+
+> Ideal candidate: scientists skilled in Density Functional Theory and proficient in python.
+
+# Overview
+
+The aim of this task is to create a python package that implements automatic convergence tracking mechanism for a materials simulations engine. The convergence is tracked with respect to the k-point sampling inside a reciprocal cell of a crystalline compound.
+
+# Requirements
+
+1. automatically find the dimensions of a k-point mesh that satisfy a certain criteria for total energy (eg. total energy is converged within dE = 0.01meV)
+1. the code shall be written in a way that can facilitate easy addition of convergence wrt other characteristics extracted from simulations (forces, pressures, phonon frequencies etc)
+1. the code shall support VASP or Quantum ESPRESSO
+
+# Expectations
+
+- correctly find k-point mesh that satisfies total energy convergence parameters for a set of 10 materials, starting from Si2, as simplest, to a 10-20-atom supercell of your choice
+- modular and object-oriented implementation
+- commit early and often - at least once per 24 hours
+
+# Timeline
+
+We leave exact timing to the candidate. Must fit Within 5 days total.
+
+# User story
+
+As a user of this software I can start it passing:
+
+- path to input data (eg. pw.in / POSCAR, INCAR, KPOINTS) and
+- kinetic energy cutoff
+
+as parameters and get the k-point dimensions (eg. 5 5 5).
+
+# Notes
+
+- create an account at exabyte.io and use it for the calculation purposes
+- suggested modeling engine: Quantum ESPRESSO

susyexists/Si_parameter_test.ipynb

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+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from src import model #Import library\n",
+    "num_core = 8 #Define number of cores"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "#Step 1 - Initialize model\n",
+    "pw = model.pw(project_id=\"Si\") #Define project\n",
+    "pw.from_poscar(directory=\"./Structures/Si.poscar\") #Load structure\n",
+    "pw.get_primitive() #Get primitive cell\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "ecutwfc: 50.0     DeltaE :-0.0006273841728230423 Ry    Time: 0.1938261985778809 seconds\n",
+      "ecutwfc: 60.0     DeltaE :-0.0003047080408862257 Ry    Time: 0.2084970474243164 seconds\n",
+      "ecutwfc: 70.0     DeltaE :-6.351904913692863e-05 Ry    Time: 0.2371938228607178 seconds\n",
+      "ecutwfc: 80.0     DeltaE :-6.302970438909483e-06 Ry    Time: 0.2995648384094238 seconds\n",
+      "ecutwfc: 90.0     DeltaE :-1.8760475342105565e-06 Ry    Time: 0.3129620552062988 seconds\n",
+      "ecutwfc: 100.0     DeltaE :-1.1352211721771255e-06 Ry    Time: 0.3260128498077393 seconds\n",
+      "ecutwfc: 110.0     DeltaE :-5.068481669923131e-07 Ry    Time: 0.4594228267669678 seconds\n",
+      "ecutwfc: 120.0     DeltaE :-3.066274292251592e-07 Ry    Time: 0.4630310535430908 seconds\n",
+      "ecutwfc: 130.0     DeltaE :-2.0733272876327646e-07 Ry    Time: 0.4597089290618896 seconds\n",
+      "ecutwfc: 140.0     DeltaE :-1.7449340994346585e-07 Ry    Time: 0.5133810043334961 seconds\n",
+      "ecutwfc: 150.0     DeltaE :-1.0422343521554467e-07 Ry    Time: 0.5248079299926758 seconds\n",
+      "ecutwfc: 160.0     DeltaE :-2.12823554335273e-07 Ry    Time: 0.5203700065612793 seconds\n",
+      "ecutwfc: 170.0     DeltaE :-1.0274962747303107e-07 Ry    Time: 0.5212390422821045 seconds\n",
+      "ecutwfc: 180.0     DeltaE :-4.080993676325306e-08 Ry    Time: 0.5420069694519043 seconds\n"
+     ]
+    }
+   ],
+   "source": [
+    "res = pw.test('ecutwfc',conv_thr=1e-7,start=40,end=500,step=10,num_core=8,debug=False,out=True)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "kpoints: 3.0     DeltaE :-0.11467918418520107 Ry    Time: 1.894612073898315 seconds\n",
+      "kpoints: 4.0     DeltaE :-0.02549575453173958 Ry    Time: 3.407161951065063 seconds\n",
+      "kpoints: 5.0     DeltaE :-0.006562763616971168 Ry    Time: 2.148712158203125 seconds\n",
+      "kpoints: 6.0     DeltaE :-0.0016181548250191469 Ry    Time: 3.427868127822876 seconds\n",
+      "kpoints: 7.0     DeltaE :-0.00030730358718500383 Ry    Time: 3.61491584777832 seconds\n",
+      "kpoints: 8.0     DeltaE :-2.980461402835033e-05 Ry    Time: 6.036959886550903 seconds\n",
+      "kpoints: 9.0     DeltaE :7.220643169603136e-06 Ry    Time: 7.17269492149353 seconds\n",
+      "kpoints: 10.0     DeltaE :4.551905615102214e-06 Ry    Time: 9.542922973632812 seconds\n",
+      "kpoints: 11.0     DeltaE :1.018306175382122e-06 Ry    Time: 10.97165894508362 seconds\n",
+      "kpoints: 12.0     DeltaE :-2.4028405931630914e-08 Ry    Time: 13.10678911209106 seconds\n"
+     ]
+    }
+   ],
+   "source": [
+    "res = pw.test('kpoints',conv_thr=1e-7,start=2,end=20,step=1,num_core=8,debug=False,out=True)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.10.12"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}

susyexists/Structures/Si.poscar

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+Si8
+1.0
+   5.4437023729394527    0.0000000000000000    0.0000000000000003
+   0.0000000000000009    5.4437023729394527    0.0000000000000003
+   0.0000000000000000    0.0000000000000000    5.4437023729394527
+Si
+8
+direct
+   0.7500000000000000    0.7500000000000000    0.2500000000000000 Si
+   0.0000000000000000    0.5000000000000000    0.5000000000000000 Si
+   0.7500000000000000    0.2500000000000000    0.7500000000000000 Si
+   0.0000000000000000    0.0000000000000000    0.0000000000000000 Si
+   0.2500000000000000    0.7500000000000000    0.7500000000000000 Si
+   0.5000000000000000    0.5000000000000000    0.0000000000000000 Si
+   0.2500000000000000    0.2500000000000000    0.2500000000000000 Si
+   0.5000000000000000    0.0000000000000000    0.5000000000000000 Si

susyexists/config.json

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+{
+  "pw": {
+    "control": {
+      "pseudo_dir": "./pseudos/"
+    },
+    "system": {
+      "degauss": "0.1",
+      "ecutwfc": "20",
+      "occupations": "smearing"
+    },
+    "electrons": {
+      "conv_thr": "1e-6"
+    },
+    "ions": {},
+    "cell": {},
+    "k_points": "1 1 1 0 0 0"
+  },
+  "ph": {
+    "inputph": {
+      "ldisp": "true",
+      "nq1": "1",
+      "nq2": "1",
+      "nq3": "1"
+    }
+  },
+  "q2r": {
+    "input": {
+      "zasr": "simple"
+    }
+  },
+  "matdyn": {
+    "input": {
+      "asr": "simple",
+      "q_in_band_form": "true",
+      "q_in_cryst_coord": "true"
+    }
+  }
+}