From 69deb6169b4e0cf952924c3c2342b937ba56f866 Mon Sep 17 00:00:00 2001
From: Sarath Menon <sarathmenon@mailbox.org>
Date: Thu, 2 Jun 2022 20:44:18 +0200
Subject: [PATCH] clean up
---
phase_diagram/melting_temperature.ipynb | 343 ------------------------
phase_diagram/tutorial.ipynb | 188 -------------
2 files changed, 531 deletions(-)
delete mode 100644 phase_diagram/melting_temperature.ipynb
delete mode 100644 phase_diagram/tutorial.ipynb
diff --git a/phase_diagram/melting_temperature.ipynb b/phase_diagram/melting_temperature.ipynb
deleted file mode 100644
index c640cac..0000000
--- a/phase_diagram/melting_temperature.ipynb
+++ /dev/null
@@ -1,343 +0,0 @@
-{
- "cells": [
- {
- "cell_type": "code",
- "execution_count": 2,
- "id": "98c500c8-36a8-4454-968c-fb74fc8ae9fc",
- "metadata": {},
- "outputs": [],
- "source": [
- "from helpers import potential_list\n",
- "from pyiron_atomistics import Project"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 3,
- "id": "e9e573fa-5e4c-4a73-bd12-a7f16be9273a",
- "metadata": {},
- "outputs": [],
- "source": [
- "import matplotlib.pyplot as plt\n",
- "import numpy as np"
- ]
- },
- {
- "cell_type": "markdown",
- "id": "9a2e82cd-d5a1-4622-80d1-1a53f0d20fa0",
- "metadata": {},
- "source": [
- "## Aluminium"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 4,
- "id": "8b42ae91-191d-4e5f-9520-2bac9a146a0e",
- "metadata": {},
- "outputs": [],
- "source": [
- "pr = Project('lial_thermodynamics')"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 5,
- "id": "da32f2bd-2439-43a0-a8e7-06efe5069ace",
- "metadata": {},
- "outputs": [],
- "source": [
- "al_sol = pr.create.job.Calphy(\"tm_al_sol\")"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 6,
- "id": "ac85de7f-4627-4ad0-9438-129dd02fbcc5",
- "metadata": {},
- "outputs": [],
- "source": [
- "al_sol.potential = potential_list[0]"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 6,
- "id": "29e3f971-e75a-4ba4-a412-f0451c75d6a4",
- "metadata": {},
- "outputs": [],
- "source": [
- "al_sol.structure = pr.create.structure.ase.bulk('Al', cubic=True).repeat(5)"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 7,
- "id": "b06b4bdc-9dd3-423a-9345-3a69774e81f6",
- "metadata": {
- "tags": []
- },
- "outputs": [
- {
- "name": "stderr",
- "output_type": "stream",
- "text": [
- "2022-05-06 07:41:38,943 - pyiron_log - WARNING - The job tm_al_sol is being loaded instead of running. To re-run use the argument 'delete_existing_job=True in create_job'\n"
- ]
- }
- ],
- "source": [
- "al_sol.calc_free_energy(temperature=[800, 1100], \n",
- " pressure=0, \n",
- " reference_phase=\"solid\")\n",
- "al_sol.run()"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 9,
- "id": "930589c1-b404-45d7-a21c-d0f7391b218c",
- "metadata": {},
- "outputs": [],
- "source": [
- "al_lqd = pr.create.job.Calphy(\"tm_al_lqd\")\n",
- "al_lqd.structure = al_sol.structure\n",
- "al_lqd.potential = potential_list[0]"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 10,
- "id": "a123b0e7-592e-4fcb-aaef-9c2c82a9804f",
- "metadata": {},
- "outputs": [],
- "source": [
- "al_lqd.server.cores = 4"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 11,
- "id": "cbc6479e-d65c-446d-b8bc-7f7eccbc36eb",
- "metadata": {
- "tags": []
- },
- "outputs": [
- {
- "name": "stderr",
- "output_type": "stream",
- "text": [
- "2022-05-06 07:45:26,856 - pyiron_log - WARNING - The job tm_al_lqd is being loaded instead of running. To re-run use the argument 'delete_existing_job=True in create_job'\n"
- ]
- }
- ],
- "source": [
- "al_lqd.calc_free_energy(temperature=[800, 1100], \n",
- " pressure=0, \n",
- " reference_phase=\"liquid\")\n",
- "al_lqd.run()"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 12,
- "id": "249f7482-43e7-471c-895b-ec7283986b90",
- "metadata": {},
- "outputs": [
- {
- "data": {
- "text/plain": [
- "Text(0, 0.5, 'Temperature (K)')"
- ]
- },
- "execution_count": 12,
- "metadata": {},
- "output_type": "execute_result"
- },
- {
- "data": {
- "image/png": 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j6PPc+puc5NTVmvUf533HZ6H5vZDPi2l5jTHZYgkESyCBlHrr7+sz4jh0IpFu9cvxRPc61ChTOPMNj+6EiY9B3FSo0AiufNOpr2WMyTFeJxARKQu0BioCp3HKhixT1RR/BOpPlkAC72RiEh8v2Mb7c7dwJimFG5tW5uFOtShbtGDGG6nCup9g8pNw6jC0HATth1pdLWNyyAUnEBHpADwFlARWAgeAgkBtoAbwPTA6zdweQc0SSPA4dCKRt2bG8eVvO8kflo8BbapxT9vqFCmYP+ONTv8JM4bB8s+cMZFer0GtzjkVsjF5ljcJ5FXgLVX9x8xAIhIO9AbCVPUHXwfrL5ZAgs/2Qyd5dVosE1fHU6pQBA92rMktzaOJCM/kjq2/1dW6Drq/bHW1jPEjbxJIMc8Chmk+a6qqv/s4Rr+zBBK8/th1lBGTN7J462GiS0XxWNcYel1cgXz5MrhjKykRFrwO80dB/ihnVkSrq2WMX3hTzn2miJRIZ0ddgR99GZwxl1Quzld3N+fTO5sSmT+MB79eyVVjF7Joy6H0NwgvAO2fhPsWQrn6MOFB+Ky3U2fLGJMjMksg7wOzRaRM6goRucVd38vfgZm8R0ToEFOWiQ+1YdT1l3DoeCK3fPgb/T5Zyob4DIbaytSGfr/ClW/B/jXwbiuYOxKSzuZs8MbkQZnehSUitwNPAF2BG4H7gO6quj1HovMx68IKLWfOJTNu0Xbemb2Z44lJXH1pJYZ0jaFS8cj0N/Csq1WmjlNXq0qLnA3amFwoO7fxXg+8BewEeqjqYf+E6H+WQEJTwqlzjJ2zmU8XbQfgjlZVGdS+BsWjMijWGDcdfn0UEnZC4zuh8zCrq2VMNngziL4GZ8Y/AaKBg8BJ972qakP/hesflkBC256jpxkzbRM/rtxNkQLh3N+hJv1aVaVg/nSeTj97Ema/BEvGQqEyVlfLmGzwJoFEZ7ZDVd3ho9hyjCWQ3GFD/DFembKRObEHqVQ8kiFda3NVo0rp37G1d5Vzy2/8KqjdHXqNhmIX5XTIxoQ0bxKI6Hn6t7LSJphYAsldFm0+xEuTN7B2zzHqVSjK0z3rcnmt0v9smJwES9936mpJGHR+Hpr0h3znqQ5sjAG8u413tog8KCJ/K4MqIhEi0lFExgH9fB2oMVnVqmZpJtx/OW/c1IhjZ85x28e/0feTpazfm+aOrbBwaHk/DFoMFzWBSY/BZz3h4KbABG5MLpHZFUhB4C7gVqAacBSnlEkYMA14R1VX5UiUPmJXILlXYlIyny/ewVuzNnPszDmuufQihnStTcW0d2ypwh/fwNShzjhJ2yeg9WAIz8LsicbkUdmqxisi+YHSwGlVPer78HKGJZDcz/OOLQHubF2NQR1qUDRtja0TB5zijOt+hLL1oc9bUKlxQGI2JthZOXcsgeQlu/88xehpm/hp5R5KROXnwY61uK1FOjW2Nk6CiUPgxD5oPhA6PmNVfo1JwxIIlkDyorV7Enh58gYWbj5MlZJRPN4tht4NK/x9VsQzCTDjBVj2MRSPhitehxodAxazMcHGm0F0Y0Jeg0rF+KJ/c8bd1YyoCLfG1jsLWbLV43nYgsWg9xi4czKE5YfPr4afBsKpI4EL3JgQkNUxkGiglqrOEJFIIFxVj/s9Oh+zK5C8LTlF+XHFbkZP28S+Y2foXLcsT3avQ61yRf5qdO4MzBsJC9+AyBLQYyTUv9oeQDR5WnZKmdwN3AOUVNUaIlILeE9VO/knVP+xBGLAqbH1ycJtvDt7CyfPJnFj08o80rn232dF3LcGxj/gPIAY09N5ALFoxYDFbEwgZSeBrAKaAb+p6qXuujWqerE/AvUnSyDG05GTZ3lrVhxfLNlBeL583N22Ove0rU7hAuFOg+QkpxTK7Jecrq3Ow5zaWvYAosljsjMGkqiq/6uN7c5GmHdG3k2uVbJQBM9fUZ8Zj7ajY92yvDkzjvavzubzJTs4l5ziPIDY+iEYtAgqNoKJj8I4m3PEmFRZSSBzReRpIFJEugDfAb/4Nyxjck50qUK8c8tl/DSoFdVLF+ZfP6+l2+vzmLpuH6oKJatD3wlw5duwfy282xrmjYLkc4EO3ZiAykoXlgADcOYEEWAq8FEo1cBKZV1Y5nxUlRkbDjBi8ga2HDxJk+gSDO1Zl8bR7uScx/fBpMdhwwQo18CZyKrSZYEN2hg/82oMRETyAatVtYE/g8splkBMViUlp/Dtst2Mmb6JQycS6XlxeZ7sXofoUu5Dhht+gYmPwckD0OpBaD8U8mcw0ZUxIS47g+hfAkNVdae/gssplkDMhTqZmMQH87bywbytJKWk0LdlVR7sWNOZzOr0UZj2LKz8HErWgD5vQ3SrQIdsjM9lJ4HMApoCS3EmlAJAVa/0dZD+ZgnEeGv/sTOMmbaJb5fvokiBcB7qVIvbW0ZTIDwMtsyGXx6Cozuh6d1OufgCRc6/U2NCRHYSSLv01qvqXB/FlmMsgZjs2hB/jJcnb2TepoNULhnJk93r0OviCsjZkzDz37D0A2fCqivegJoh96iUMemyWlhYAjG+M3fTQV6etIGN+45zaZXiPNurLo2jS8LOJc4DiIfjoNFt0O0/zhPtxoSw7FyBHOev5z4igPzASVUt6vMo/cwSiPGl5BTlh+W7GTUtlgPHPQbai4bB3BGw8E0oVBp6jYG6vQMdrjFe8/pBQlUtoqpF3VdB4Frg7WwGM1xEVovIKhGZJiLp1ogQkUdEZJ2IrBWRr91JrhCRkiIyXUTi3J/2K57JcWH5hBuaVmb2Y+15uHMtZm88SOcxc/n3lK0cbfU03D0TCpWF/94K390BJw4GOmRjfMqrLiwRWaKqLbw+qEhRVT3mLj8E1FPV+9K0qQQscD87LSLfApNU9TMRGQkcUdURIvIUUEJVnzzfce0KxPjTgWNnGDN9E98u20Xh1IH2ZhUpsOQtp0BjRGGnOOPF11lxRhNSvL4CEZFrPF7XicgIslnKJDV5uAplsr9wnCfgw4EoYK+7vg8wzl0eB1yVnXiM8YWyRQsy4tqGTBrchkurlOA/EzfQ+Y1F/FriVvTeec4T7T8OgK9vgmN7z79DY4JcVsZAPvV4mwRsBz5U1QPZOrDIi0BfIAHooKr/uL4XkcHAi8BpYJqq3uquP6qqxT3a/amq6XZjicg9ONWEqVKlSuMdO3ZkJ2xjsmzepoO85DnQ3qM2jeP/C7P+4xRn7DocLutnVyMm6GVnEL21qi4837p0tpsBlE/no2dUdbxHu6FAQVV9Ps32JYAfgBuBozg1uL5X1S8uJIF4si4sk9PSG2h/pkUBKs1/CrbPh2pt4Yo3oWS1QIdqTIayk0BWqOpl51uXjcCigYlpy6WIyPVAd1Xt777vC7RQ1UEiEgu0V9V4EakAzFHVmPMdyxKICZRTZ5P4cN423p+3hXPJKdzevAqPlV5M1JwXQJOh03PQ7B7IFxboUI35hwseAxGRliIyBCgjIo96vIYB2fpb7k5KlepKYGM6zXYCLUQkyi3o2AnY4H42AejnLvcDxqezvTFBIyoinMGdazHnsfZce9lFfLZ4By2mVeHrpt+SHN0apjwFn3SHg7GBDtWYLMtsED0CKIwzkF3E43UMuC6bxx3h3pq7GqfK72AAEakoIpMAVPU34HtgBbDGjfWD1O2BLiISB3Rx3xsT9NIOtA+d+Sft9wxkZZMR6OE4eO9yKxVvQkZWurCiVTVXjDxbF5YJNp4D7e0vUsYU+oKSOyZD+YuhzztQ4ZJAh2hMtsZAygBPAPWB/00araodfR2kv1kCMcEoOUX5YcVuRk11BtqHVt3EgGPvEHb6CFz+MLR9AvIXPO9+jPGX7Exp+yXOGEU14AWc23h/92l0xuRhYfmEG5pUZs7j7Xmkc23e2FuX5gkvsapkN5g/Gt5vA7uWBjpMY/4hKwmklKp+DJxT1bmqehfg9VPoxpj0eQ60d2lch2v23sZAnubE8WPox11hylA4e/L8OzImh2QlgaSO5sWLSC8RuRS4yI8xGZOnlS1akJevacjkwW05Hd2B5gkv8lN4N1gyFn23FWwNuZkUTC6VlTGQ3sB8oDLwFlAUeEFVJ/g/PN+yMRATiubHHeTFiRsotn8pr0V9TMXkvc4T7F2HQ8FigQ7P5AFejYGISBhQS1UTVHWtqnZQ1cahmDyMCVVtapVh4kNtuPbaG7kp3yjeT+pFyorPSXqrOcROCXR4Jg/LNIGoajLOg37GmABKHWif8ng3Trcfxk3Jw9l6Igy+vpFz3/WHk4cDHaLJg7LShfUiUAz4L3+fE32Ff0PzPevCMrnFvoQzjJm8hkprx3J/+HiSIoqSv/dowi6+xoozGp/LznMgs9NZrfYciDGBt2Z3AuN++pW+B1+lYb5tHLqoC6VvfBuKpFfH1Bjv2JzoWAIxuZOqMm3Nbrb+MpI7z35NclgBTrR7gXJt+9vViPGJ7EwoVU5EPhaRye77eiLS3x9BGmMunIjQrWFl7nrydSa0/I6NKRdRbvYQNo/pytG9WwIdnsnFsvIcyGfAVCB13vJNwMN+iscY46UC4WHc0L0DVYfM4deLHqXCsT+I+KAlC796mcRzVpzR+F5WEkhpVf0WSAFQ1SQg2a9RGWO8VqpIJL0HPM+B2+eytWADWm8awcaX2zJv8SLyUpe18b+sJJCTIlIKd95yEWmBMw2tMSaIVatZlwZPziS2+Qiqp+yg2ZQr+XLMENbstFt+jW9kJYE8ijOBUw0RWQj8H/CgX6MyxviGCDE9BhL58DIOlm/Dbcc/JuWjzrz6fz+yL+FMoKMzIS5Ld2GJSDgQAwgQq6oh2aFqd2GZPE2VU6u+Ryc+Tv5zx/hArybl8kcZ0D6GqIjwQEdnglh2ngMpCAwCLsfpxpoPvKeqIffriyUQY4CThzk54TEKxf7IxpTKvBLxAL179ObqSyuRL5/d9mv+KTvzgfwfzmRSbwFvA/WAz30bnjEmxxQqRaGbP4Wb/0v1wuf4KGkoh356guvfnsXSbUcCHZ0JIVm5AvlDVS8537pQYFcgxqRxJgGd9hyy4jN2SQWGnBlAqfodGNqjLlVKRQU6OhMksnMFstK98yp1R82Bhb4MzhgTIAWLIVe+AX0nUKlYBN8WGE6buBH0GTOFlyZtIOF0SA53mhySlQTSHFgkIttFZDuwGGgnImtEZLVfozPG5Izq7cg3aDG0GMTNMp1ZUU8Ru+AnOoyaw+eLt5OUnBLoCE0QykoXVnRmn6vqDp9G5EfWhWVMFuxaCuMfgEOxzInswkN/Xk/ZsuV5plddOsSUDXR0JgC87sJyE8QxnJLupVJfqrojlJKHMSaLKjeDe+dBmyG0OzOLpcWfpUniUu789Hf6frKUTfuPBzpCEySycgUyHLgD2IL7NDpWzt2YvGHvSvh5EBxYT1yF3twRfw3xiQW5uVkVHulSm9KFCwQ6QpMDsvMcSCxwsaqe9VdwOcUSiDFeSEqEea/C/DGkRJXmm3JD+NfGykTlD+P+jjW5s3VVCoSHBTpK40fZuQtrLVDc5xEZY0JDeAHo+CzcPYt8hUpzy9YnWNngezpUCWfE5I10HjOXSWvirVBjHpSVK5AmwHicRJKYul5VQ26udLsCMSabks7C/FEwfzRElWJ943/z6B8V2bjvOE2rluDZXvW4pHLxQEdpfCw7XVjrgPeBNbgl3QFUda6vg/Q3SyDG+Ej8H87YyP61pFx8Az+Xe4iX5uzn0IlErr60Ek90j6FCschAR2l8JDsJZK6qtvNbZDnIEogxPpR01rkSmT8KIktyuvto3tpTm48WbCOfwD1tqnNvuxoUKmCFGkNddhLIGJyuqwn8vQtrha+D9DdLIMb4Qfxq92pkDVx8PXtbDuPluQf55Y+9lC1SgMe7xXDtZRdZocYQlp0EMjud1XYbrzHmL0lnYcEY526tyJLQ+zWWR7Vm+K/rWbXrKPUrFuVfvevRonqpQEdqvOB1AslNLIEY42f71sDPA52fDa5De7zChLhERk6JZc/R03SrX46hPepStXShQEdqLoDXt/GKSDkR+VhEJrvv64lIf38EaYwJceUvhrtnQ4dnYP14ZGwL+kQsZ+aQdjzeLYYFcYfo8tpchv+6noRTVqgx1GXlOZDPgKlARff9JuBhP8VjjAl1Yfmh3RNwzxwoUgG+vZ2CPw/g/mYlmP14e6697CI+WbiN9qNmM27Rds5ZocaQlWECcaexBSitqt/i3sKrqklAcg7EZowJZeUbwN2zoMOzsOEXeKcZZXdNZcS1DZn4YBvqVSzK8xPW0f31eczauN8eRAxBmV2BLHV/nhSRUrh1sNy5QRL8HZgxJhcIyw/tHod750KxSvBtX/juDuoVO8sX/ZvzUd8mqMJdny2zQo0hKMNBdBFZqaqXishlONPZNsB5Gr0McJ2qhtxcIDaIbkwAJZ+Dha/DnFegYDHoNRrqX8W55BS+WLKD12fEcSIxiduaO4Uai0dFBDpi47rgu7BEZDcwxn2bDygACM6zIMmqOibdDbMWzHCgD0632AHgDlXdm067R4ABOFc/a4A7VfWMiAwD7gYOuk2fVtVJ5zuuJRBjgsD+9c6dWvGroN5V0HMUFC7DnyfP8tqMTXyxZAdFI/PzaJfa3NKsCuFhWRmqNf7kzV1YYUBhoAhQCAh310W567LjVVVtqKqNgF+B59IJuBLwENBEVRu4x77Jo8lrqtrIfZ03eRhjgkS5ejBgJnR6DmInwdjmsPZHShSK4N99GjBpcBvqVSjKc+PX0fPN+SzcfCjQEZsMZFZjIF5V/+2Pg6rqMY+3hfhrnpG0woFIETmHk7j+cZVijAlBYeHQZgjU7gHjB8H3d8L6n6HnaOqUL8OXA5ozbf1+Xpy4gVs/+o2u9crxTK+6RJey50eCSWZXIH6tOyAiL4rILuBW0rkCUdU9wChgJxAPJKjqNI8mD4jIahH5RERKZHKce0RkmYgsO3jwYEbNjDGBUK4e9J8BnZ6H2MnwTjNY+wMCdKtfnmmPtOWJ7jEs2HyILmPmMWLyRk4kJgU6auPKbAykpKoe8XrHIjOA8ul89IyqjvdoNxQoqKrPp9m+BPADcCNwFPgO+F5VvxCRcsAhnCuX4UAFVb3rfDHZGIgxQezARmdsZO8KqHsF9BoDhZ052PcfO8PIKbH8sGI3ZYoU4Amrr5WjgraUiYhEAxPdcQ7P9dcD3VW1v/u+L9BCVQelaVcV+DXt9umxBGJMkEtOgsVvweyXIKIw9HwVGlwL4iSKVbuO8sIv61i58ygNLyrG81fUp3F0hh0QxkeyMyOhP4Kp5fH2SmBjOs12Ai1EJEpEBOgEbHC3r+DR7mqc24uNMaEuLBwufwTunQ8lq8EP/eG/t8Hx/QA0qlycHwe24vUbG7H/2BmufXcRD3+zkviE0wEOPG8KyBWIiPwAxODcxrsDuE9V94hIReAjVe3ptnsBpwsrCVgJDFDVRBH5HGiE04W1HbhXVePPd1y7AjEmhCQnwZJ3YNaLEBEFPV6Fi6/739XIycQk3pu7hffnbSVMhIHta3BP2+oUzG/zs/ta0HZh5SRLIMaEoIOxznwje5ZBnd7O2EiRcv/7eNeRU7w8eQOT1uyjUvFInu5Zl54Xl0fExkd8Jai6sIwxJsvKxED/adBlOMRNd+7UWv0tuL/8Vi4ZxdhbG/PNPS0oGpmf+79awY0fLGHdXqu45G92BWKMCR0HN8H4+2H3UojpCb1fgyJ/3eyZnKL89/ddjJoWy5+nznJT0yoM6Vqb0oULBDDo0GddWFgCMSZXSEmGJWNh1n8gvCD0GAkNb/jf2AhAwulzvDkzjnGLthOZP4zBnWvRt2VVIsKt08UblkCwBGJMrnIozrka2fWb80T7Fa//7WoEYPOBE/xn4nrmxB6keulC/Kt3PTrUKRuYeEOYjYEYY3KX0rXgzsnQ9UXYOhvGtoA13/9vbASgZtnCfHZnMz69oykI3PnZ79zx6VI2HzgRwMBzD7sCMcaEvkNx8NN9zp1ada90n2Iv87cmZ5NS+L/F23ljZhynzybTt2VVBneuRbHI/AEKOnRYFxaWQIzJ1ZKTYNGbMOdlKFAUeo+Ben3+0ezQiURGT9vEN7/vpERUBEO61uamplUIs7IoGbIEgiUQY/KE/evh5/sg/g9ocJ1TDiWq5D+ardubwAu/rGfptiPUrVCU53rXo2WNUgEIOPjZGIgxJm9InW+k/dNOifixLSB2yj+a1a9YjP/e04Kxt17GsdPnuPnDJQz6cjm7jpzK+ZhDlF2BGGNyr/g/4KeBcGAdNLoVur/sTKebxplzyXw4bytj52whWZV721ZnYPsaREVkNmVS3mFdWFgCMSZPSjoLc1+BBe5Dh1e+BTU7pds0PuE0IyZvZPyqvVQoVpCne9ald8MKeb4sinVhGWPypvAI6PQvGDDdKRH/xTXwy8OQePwfTSsUi+SNmy7lu/taUrJQBA9+vZIbP1jC+r3H/rlfY1cgxpg85NwZmP0fWPQ2FK8MfcZCtTbpNk1OUb5dtotXp8Zy9NRZbmlehSFdYihRKCKHgw4868LCEogxxrVziTP74ZGt0Oxe6Pw8RKQ/33rCqXO8NmMTny/ZQeEC4QzpWptbmlUhPCzvdOBYAsESiDHGw9mTMOMFWPo+lKwOV70LVVpk2HzT/uMMm7CORVsOU6d8EZ6/on6eue3XxkCMMcZTRCHoORL6/QIpSfBJd5j2rNPNlY7a5Yrw5YDmvHfbZRw/k8TNHy7h/i9XsPvPvHvbr12BGGNM4nGY9i9Y/imUrg1XvQcXNc6w+ZlzyXwwbytj52xGFQa2r8F97Wrk2tkQrQsLSyDGmPPYPBMmPAjH98HlD0O7JyE847lE9hw9zUuTNjBxdTyVikfyTK+69GiQ+2ZDtC4sY4w5n5qdYOAiuOQmmD8aPugA8aszbF6peCTv3HIZ39zTgiIFwxn05Qpu+fA3Yvf98xbh3MiuQIwxJj2xU+CXh+DUYWj7BLR5FMIyrtyblJzC10t3MmraJk4kJnF7i2ge6VybYlGhX+3XurCwBGKMuUCnjsDkJ2DNd1ChEVz9HpStm+kmf548y5jpm/jytx0Ui8zPY91iQr7ar3VhGWPMhYoqCdd+BDf8HyTshvfbOiVRUpIz3KREoQiGX9WAXx9sQ61yRXjmp7Vc8dYCft9+JAcDzxl2BWKMMVlx4iBMfBQ2TICLmjrPjZSulekmqsrENfG8NHEDexPOcOUlFRnasw4VikXmUNC+YV1YWAIxxmSTKqz9ASYOgaQz0Ok5aD4Q8mXemXPqbBLvzdnCe/O2EibC/R1qMKBN9ZC57dcSCJZAjDE+cnwf/DIYNk2BKq3gqnecp9nPY9eRU7w4cQNT1u2jcslInu1Vj671ygX9bb82BmKMMb5SpDzc/I3TjbV/HbzbGpZ+CCkpmW5WuWQU793emC/6N6dgeBj3fr6cvp8sZfOB0Lzt165AjDEmOxL2wIQHYMssqNYO+rwNxaucd7NzySl8sWQHY6Zv4vTZZPq2rMrgzrUoFhl8t/1aFxaWQIwxfqIKyz9zamkh0O1FuKwvZKFr6vCJREZNi+Wb33dRMiqCJ7rHcH3jyuQLott+LYFgCcQY42d/7oDx98P2+VCzC1z5JhStmKVN1+5J4PkJ61i+408aXlSM56+oT+PoEn4OOGtsDMQYY/ytRDT0nQA9RsL2BTC2BfzxjXOFch4NKhXj+/ta8vqNjdiXcIZr313Eo9+u4sCx9KsDBwO7AjHGGH84vMWZtGrXbxDTC654HQqXzdKmJxKTeGf2Zj6ev438YcJDnWpxZ+tqRIQH5nd+68LCEogxJoelJMOSsTBzuDP/SK/R0OCaLG++/dBJ/jNxPTM2HKB66UL864p6dIjJWhLyJevCMsaYnJYvDFo9CPfNhxJV4fs74dt+cPJwljavWroQH/Vryqd3NgXgzk9/567PfmfboZN+DDrr7ArEGGNyQnISLHwd5oyAyOLQ+3Wo2zvLm59NSuGzRdt4c+ZmEpOS6X95dR7oWJPCBcL9FfH/WBcWlkCMMUFg/zr46T7Ytxoa3gg9XoHIrN9tdeD4GUZOieX75bspW6QAQ3vW4apGlfz6NLt1YRljTDAoVx/ungXtnnLqao1tCXHTs7x52SIFGXX9Jfw0qBUVihXkkf/+wXXvLWbN7gQ/Bp0+SyDGGJPTwvJDh6EwYCYULA5fXgfjH4Azx7K8i0urlOCnQa0ZeV1Ddhw+yZXvLGDoj6s5fCLRf3GnEZAEIiLDRWS1iKwSkWkiku6TNiIyWETWisg6EXnYY31JEZkuInHuz+B42sYYYy5ExUZw71y4/BFY9SW82wq2zsny5vnyCTc0qcysx9rTv3U1vlu2m/aj5vDJgm2cS868LpcvBOoK5FVVbaiqjYBfgefSNhCRBsDdQDPgEqC3iKQW338KmKmqtYCZ7ntjjAk94QWg8zC4a5qz/H99YNLjcDbrd1oVLZifZ3vXY8rDbWhUuTj//nU9Pd+Yz8LNh/wXNwFKIKrqeZ1WCEhvJL8usERVT6lqEjAXuNr9rA8wzl0eB1zlp1CNMSZnVG4K986HFoNg6Qfw3uWwc8kF7aJm2SL8313N+OD2xiQmpXDrR79x3+fL2XXklF9CDthdWCLyItAXSAA6qOrBNJ/XBcYDLYHTOFcay1T1QRE5qqrFPdr+qarpdmOJyD3APQBVqlRpvGPHDn+cjjHG+M62+TB+EBzd5TxH0uEZyF/wgnZx5lwyHy/YxtuzNpOiynu3NaZDHe8eQszx23hFZAZQPp2PnlHV8R7thgIFVfX5dPbRH7gfOAGsB06r6iMXkkA82W28xpiQkXgcpv0Lln8KZeo4c49UuuyCdxOfcJo3ZsTxVI86FI+K8CqUoH0ORESigYmq2uA87V4CdqvqWBGJBdqraryIVADmqGrM+Y5lCcQYE3I2z4DxD8KJ/dBmCLR9HMK9SwTeCqrnQDwGwwGuBDZm0K6s+7MKcA3wtfvRBKCfu9wPp6vLGGNyn5qdYdBiaHgDzBsJH3V0HkYMAoG6C2uEe3vuaqArMBhARCqKyCSPdj+IyHrgF+B+Vf0zdXugi4jEAV3c98YYkztFFoer34ObvnLmY3+/Hcwf7ZRHCaCAd2HlJOvCMsaEvJOHYeKjsP5nqNQYrnoPytT26yGDqgvLGGOMlwqVghvGwXWfwJGt8H4bWPwOpPj/wcG0LIEYY0woanAtDFoC1dvD1KdhXG84si1HQ7AEYowxoapIebj5G+gzFvatgXdbw+8fZ2kKXV+wBGKMMaFMBC69FQYucp5mn/gofHENJOz2+6EtgRhjTG5QvDLc/rMzbe7OJTC2Faz6yq9XI5ZAjDEmtxCBpgNg4EJn3pGfB8LXN8Px/X45nCUQY4zJbUpWhzt+ha4vwpZZMLa5U1/LxyyBGGNMbpQvDFo9APfNh4qXOknFx/w/G7sxxpjAKRMDt//kl13bFYgxxhivWAIxxhjjFUsgxhhjvGIJxBhjjFcsgRhjjPGKJRBjjDFesQRijDHGK5ZAjDHGeCVPzUgoIgeBHV5uXho45MNwAsnOJfjklvMAO5dglZ1ziVbVMmlX5qkEkh0isiy9KR1DkZ1L8Mkt5wF2LsHKH+diXVjGGGO8YgnEGGOMVyyBZN0HgQ7Ah+xcgk9uOQ+wcwlWPj8XGwMxxhjjFbsCMcYY4xVLIMYYY7xiCcQlIo+IyDoRWSsiX4tIQREpKSLTRSTO/VnCo/1QEdksIrEi0i2QsaeVwbkME5E9IrLKffX0aB/M5zLYPY91IvKwuy7kvpcMziMkvhMR+UREDojIWo91F/wdiEhjEVnjfvamiEgwn4uIVBWR0x7fz3shcC7Xu3/HUkSkSZr2vv9eVDXPv4BKwDYg0n3/LXAHMBJ4yl33FPCKu1wP+AMoAFQDtgBhgT6P85zLMOCxdNoH87k0ANYCUTizZ84AaoXa95LJeYTEdwK0BS4D1nqsu+DvAFgKtAQEmAz0CPJzqerZLs1+gvVc6gIxwBygSVb+TmXnXOwK5C/hQKSIhOP8Q98L9AHGuZ+PA65yl/sA36hqoqpuAzYDzXI23Eyldy4ZCeZzqQssUdVTqpoEzAWuJvS+l4zOIyNBdR6qOg84kmb1BX0HIlIBKKqqi9X5X+v/PLbJMRd4LukK5nNR1Q2qGptOc798L5ZAAFXdA4wCdgLxQIKqTgPKqWq82yYeKOtuUgnY5bGL3e66gMvkXAAeEJHV7qVvapdD0J4Lzm/tbUWklIhEAT2ByoTe95LReUDofSepLvQ7qOQup10fDDI6F4BqIrJSROaKSBt3XTCfS0b88r1YAgHcf7h9cC7tKgKFROS2zDZJZ11Q3A+dybm8C9QAGuEkltGpm6Szm6A4F1XdALwCTAem4FyCJ2WySVCeSybnEXLfSRZkFHsonlM8UEVVLwUeBb4SkaKE5rn45XuxBOLoDGxT1YOqeg74EWgF7Hcv8VIvWw+47Xfz12+QABeReTdRTkr3XFR1v6omq2oK8CF/dYkE87mgqh+r6mWq2hbncj2OEPxe0juPUP1OXBf6Hex2l9OuDwbpnovb3XPYXV6OM25Qm+A+l4z45XuxBOLYCbQQkSj3DoROwAZgAtDPbdMPGO8uTwBuEpECIlINZ0B0aQ7HnJF0zyX1H4jrapxuFQjuc0FEyro/qwDXAF8Tgt9LeucRqt+J64K+A7dr6LiItHD/Xvb12CbQ0j0XESkjImHucnWcc9ka5OeSEf98Lzl950CwvoAXgI04/4g/x7lboRQwE+e33plASY/2z+D8RhJLAO7A8OJcPgfWAKvdv0wVQuRc5gPrcbp9OrnrQu57yeA8QuI7wUna8cA5nN9Y+3vzHQBN3L+TW4C3cSthBOu5ANcC69zvbAVwRQicy9XuciKwH5jqz+/FSpkYY4zxinVhGWOM8YolEGOMMV6xBGKMMcYrlkCMMcZ4xRKIMcYYr1gCMSFDRJI9KqOuEpGqgY4pp4jI9+6zCBl9PkxEXk6zrpGIbPB4P1REbs1kH+1FpJVvIgYRmeFRnsXkQpZATCg5raqNPF7bUz8QR9D9fU59EC2b+6iPUzl1aybNvgZuTLPuJuArj/ddgWlkrD1OBQZf+RwY5MP9mSATdP/gjMkqd76GDSIyFudBr8oi8riI/O4WKHzBo+1tIrLUvXJ5P73/2N15EeaKyHIRmepR3mKOiLzibr8ptaieiISJyKsex7vXXd9eRGaLyFfAGhHJJyJjxZmn4VcRmSQi14lIJxH5yeP4XUTkx3RO9VY8ng4Wka4islhEVojIdyJSWJ0KrEdFpLnHdjcA37jbFAUiVPWgiFwhIr+5RQJniEg592ruPuAR98+ojYhEi8hM99xmuk/RIyKfici77jluFZF24hSD3CAin3kcfwJwc5a/UBN6AvmEq73sdSEvIBlY5b5+wpmvIQVo4X7eFfgAp0BcPuBXnDkT6gK/APnddmOBvmn2nR9YBJRx398IfOIuzwFGu8s9gRnu8j3As+5yAWAZThHL9sBJoJr72XXAJDem8sCf7jrBqRiQesyv8Hja2SO2ucDF7nJpYB5QyH3/JPCcu/w48Jq73AL43WMf1wD/dpdLwP8eIh7gcW7D8JifxP0z6+cu3wX87C5/hpOYBKdw5zHgYvf8lgONPPYRB5QK9N8de/nnFZ5OTjEmWJ1W1Uapb9zfmneo6hJ3VVf3tdJ9Xxin5k9DoDHwu1Puh0j+Kv6XKgZn4qfpbpswnDIRqVKvDJbjJK7U4zUUkevc98Xc453FqTO0zV1/OfCdOkUT94nIbABVVRH5HLhNRD7FmdSnbzrnXQE46C63wJkcaKEbZwSw2P3sG2CRiAzB6b762mMf3YFP3eWLgP+6V1gROBOQpaclTuIBpztqpMdnv7jxrwH2q+oaABFZ5/75rHLbHcCpCn04g2OYEGYJxIS6kx7LArysqu97NhCRB4Fxqjo0k/0IsE5VW2bweaL7M5m//t0I8KCqTk1zvPbpxJWRT3F+0z+Dk2TSK1d/Gijosa/pqvqPriFV3SUi24F2OHWcPM+lGTDQXX4LGKOqE9xYh2US398O4bGc+ueR4rGc+t7z/5WCbvwmF7IxEJObTAXuEpHCACJSSZwquDOB6+SvirglRSQ6zbaxQBkRaem2ye8OXp/veANFJL+7TW0RKZROuwXAte5YSDmcLi4AVHUvTvnsZ3G6htKzAajpLi8BWotITfeYUSJS26Pt18BrwBZV3e22qQ9sVNVkt00xYI+73M9j2+NAEY/3i3CuZMAZh1mQQXzpEucSqTyw/UK2M6HDEojJNdSZefErYLHbtfI9UERV1+P8Bz1NRFbjTOxUIc22Z3HGJV4RkT9wumDOd0fSRzgVdleIyFrgfdK/qv8Bp0JqapvfgASPz78EdrlxpmcibtJR1YM4c9x/7Z7LEqCOR9vvgPq4g+euHjgTWaUaBnwnIvOBQx7rfwGuTh1EBx4C7nSPczswOIP4MtIYZyrfzCYBMyHMqvEakwPcO6VOiEgpnLk9WqvqPvezt4GVqvpxBttGArPdbZLTa3OeY0/HuWkg/ryNfUhE3gAmqOrMnDyuyTmWQIzJASIyByiOM2g9UlU/c9cvxxkv6aKqiZls3w3YoKo7/R6sj4jI3ar6YaDjMP5jCcQYY4xXbAzEGGOMVyyBGGOM8YolEGOMMV6xBGKMMcYrlkCMMcZ45f8BSM4X0/8SPHAAAAAASUVORK5CYII=\n",
- "text/plain": [
- "<Figure size 432x288 with 1 Axes>"
- ]
- },
- "metadata": {
- "needs_background": "light"
- },
- "output_type": "display_data"
- }
- ],
- "source": [
- "plt.plot(al_sol.output.temperature, al_sol.output.energy_free, label=\"solid\")\n",
- "plt.plot(al_lqd.output.temperature, al_lqd.output.energy_free, label=\"liquid\")\n",
- "plt.xlabel(\"Free energy (eV/atom)\")\n",
- "plt.ylabel(\"Temperature (K)\")"
- ]
- },
- {
- "cell_type": "markdown",
- "id": "3dbbdf28-ed8d-4ce9-bc11-b4995e3dc20e",
- "metadata": {},
- "source": [
- "## Lithium"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 23,
- "id": "9f33c24c-ae09-4bb0-ba96-4650ab2276b2",
- "metadata": {},
- "outputs": [],
- "source": [
- "li_sol = pr.create.job.Calphy(\"tm_li_sol3\", delete_aborted_job=True, delete_existing_job=True)"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 24,
- "id": "a50a6d95-6d80-412e-992a-c688dc216865",
- "metadata": {},
- "outputs": [],
- "source": [
- "li_sol.potential = potential_list[1]\n",
- "li_sol.structure = pr.create.structure.ase.bulk('Li', cubic=True).repeat(5)\n",
- "li_sol.server.cores = 4"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 25,
- "id": "29b4158b-1753-4342-a801-af29199405ec",
- "metadata": {
- "tags": []
- },
- "outputs": [
- {
- "name": "stderr",
- "output_type": "stream",
- "text": [
- "/home/users/menonsqr/miniconda3/envs/pyiron-dev/lib/python3.10/site-packages/h5io/_h5io.py:56: 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->block0_values] [items->Index(['Name', 'Filename', 'Model', 'Species', 'Config'], dtype='object')]\n",
- "\n",
- " data.to_hdf(fname, rootpath)\n"
- ]
- },
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "The job tm_li_sol3 was saved and received the ID: 82\n"
- ]
- },
- {
- "ename": "MeltedError",
- "evalue": "System melted, increase size or reduce scaling!",
- "output_type": "error",
- "traceback": [
- "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
- "\u001b[0;31mMeltedError\u001b[0m Traceback (most recent call last)",
- "Input \u001b[0;32mIn [25]\u001b[0m, in \u001b[0;36m<cell line: 4>\u001b[0;34m()\u001b[0m\n\u001b[1;32m 1\u001b[0m li_sol\u001b[38;5;241m.\u001b[39mcalc_free_energy(temperature\u001b[38;5;241m=\u001b[39m[\u001b[38;5;241m400\u001b[39m, \u001b[38;5;241m500\u001b[39m], \n\u001b[1;32m 2\u001b[0m pressure\u001b[38;5;241m=\u001b[39m\u001b[38;5;241m0\u001b[39m, \n\u001b[1;32m 3\u001b[0m reference_phase\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124msolid\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[0;32m----> 4\u001b[0m \u001b[43mli_sol\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mrun\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\n",
- "File \u001b[0;32m~/miniconda3/envs/pyiron-dev/lib/python3.10/site-packages/pyiron_base/generic/util.py:213\u001b[0m, in \u001b[0;36mDeprecator.__deprecate_argument.<locals>.decorated\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m 203\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m kw \u001b[38;5;129;01min\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39marguments:\n\u001b[1;32m 204\u001b[0m warnings\u001b[38;5;241m.\u001b[39mwarn(\n\u001b[1;32m 205\u001b[0m message_format\u001b[38;5;241m.\u001b[39mformat(\n\u001b[1;32m 206\u001b[0m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;132;01m{}\u001b[39;00m\u001b[38;5;124m.\u001b[39m\u001b[38;5;132;01m{}\u001b[39;00m\u001b[38;5;124m(\u001b[39m\u001b[38;5;132;01m{}\u001b[39;00m\u001b[38;5;124m=\u001b[39m\u001b[38;5;132;01m{}\u001b[39;00m\u001b[38;5;124m)\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;241m.\u001b[39mformat(\n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 211\u001b[0m stacklevel\u001b[38;5;241m=\u001b[39m\u001b[38;5;241m2\u001b[39m,\n\u001b[1;32m 212\u001b[0m )\n\u001b[0;32m--> 213\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mfunction\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n",
- "File \u001b[0;32m~/miniconda3/envs/pyiron-dev/lib/python3.10/site-packages/pyiron_base/job/generic.py:689\u001b[0m, in \u001b[0;36mGenericJob.run\u001b[0;34m(self, delete_existing_job, repair, debug, run_mode, run_again)\u001b[0m\n\u001b[1;32m 687\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_run_if_repair()\n\u001b[1;32m 688\u001b[0m \u001b[38;5;28;01melif\u001b[39;00m status \u001b[38;5;241m==\u001b[39m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124minitialized\u001b[39m\u001b[38;5;124m\"\u001b[39m:\n\u001b[0;32m--> 689\u001b[0m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_run_if_new\u001b[49m\u001b[43m(\u001b[49m\u001b[43mdebug\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mdebug\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 690\u001b[0m \u001b[38;5;28;01melif\u001b[39;00m status \u001b[38;5;241m==\u001b[39m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mcreated\u001b[39m\u001b[38;5;124m\"\u001b[39m:\n\u001b[1;32m 691\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_run_if_created()\n",
- "File \u001b[0;32m~/miniconda3/envs/pyiron-dev/lib/python3.10/site-packages/pyiron_base/job/generic.py:1399\u001b[0m, in \u001b[0;36mGenericJob._run_if_new\u001b[0;34m(self, debug)\u001b[0m\n\u001b[1;32m 1397\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 1398\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39msave()\n\u001b[0;32m-> 1399\u001b[0m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mrun\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\n",
- "File \u001b[0;32m~/miniconda3/envs/pyiron-dev/lib/python3.10/site-packages/pyiron_base/generic/util.py:213\u001b[0m, in \u001b[0;36mDeprecator.__deprecate_argument.<locals>.decorated\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m 203\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m kw \u001b[38;5;129;01min\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39marguments:\n\u001b[1;32m 204\u001b[0m warnings\u001b[38;5;241m.\u001b[39mwarn(\n\u001b[1;32m 205\u001b[0m message_format\u001b[38;5;241m.\u001b[39mformat(\n\u001b[1;32m 206\u001b[0m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;132;01m{}\u001b[39;00m\u001b[38;5;124m.\u001b[39m\u001b[38;5;132;01m{}\u001b[39;00m\u001b[38;5;124m(\u001b[39m\u001b[38;5;132;01m{}\u001b[39;00m\u001b[38;5;124m=\u001b[39m\u001b[38;5;132;01m{}\u001b[39;00m\u001b[38;5;124m)\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;241m.\u001b[39mformat(\n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 211\u001b[0m stacklevel\u001b[38;5;241m=\u001b[39m\u001b[38;5;241m2\u001b[39m,\n\u001b[1;32m 212\u001b[0m )\n\u001b[0;32m--> 213\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mfunction\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n",
- "File \u001b[0;32m~/miniconda3/envs/pyiron-dev/lib/python3.10/site-packages/pyiron_base/job/generic.py:691\u001b[0m, in \u001b[0;36mGenericJob.run\u001b[0;34m(self, delete_existing_job, repair, debug, run_mode, run_again)\u001b[0m\n\u001b[1;32m 689\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_run_if_new(debug\u001b[38;5;241m=\u001b[39mdebug)\n\u001b[1;32m 690\u001b[0m \u001b[38;5;28;01melif\u001b[39;00m status \u001b[38;5;241m==\u001b[39m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mcreated\u001b[39m\u001b[38;5;124m\"\u001b[39m:\n\u001b[0;32m--> 691\u001b[0m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_run_if_created\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 692\u001b[0m \u001b[38;5;28;01melif\u001b[39;00m status \u001b[38;5;241m==\u001b[39m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124msubmitted\u001b[39m\u001b[38;5;124m\"\u001b[39m:\n\u001b[1;32m 693\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_run_if_submitted()\n",
- "File \u001b[0;32m~/miniconda3/envs/pyiron-dev/lib/python3.10/site-packages/pyiron_base/job/generic.py:1418\u001b[0m, in \u001b[0;36mGenericJob._run_if_created\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m 1416\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mrun_if_manually(_manually_print\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mFalse\u001b[39;00m)\n\u001b[1;32m 1417\u001b[0m \u001b[38;5;28;01melif\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mserver\u001b[38;5;241m.\u001b[39mrun_mode\u001b[38;5;241m.\u001b[39mmodal:\n\u001b[0;32m-> 1418\u001b[0m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mrun_static\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 1419\u001b[0m \u001b[38;5;28;01melif\u001b[39;00m (\n\u001b[1;32m 1420\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mserver\u001b[38;5;241m.\u001b[39mrun_mode\u001b[38;5;241m.\u001b[39mnon_modal\n\u001b[1;32m 1421\u001b[0m \u001b[38;5;129;01mor\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mserver\u001b[38;5;241m.\u001b[39mrun_mode\u001b[38;5;241m.\u001b[39mthread\n\u001b[1;32m 1422\u001b[0m \u001b[38;5;129;01mor\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mserver\u001b[38;5;241m.\u001b[39mrun_mode\u001b[38;5;241m.\u001b[39mworker\n\u001b[1;32m 1423\u001b[0m ):\n\u001b[1;32m 1424\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mrun_if_non_modal()\n",
- "File \u001b[0;32m~/miniconda3/envs/pyiron-dev/lib/python3.10/site-packages/pyiron_atomistics-0.2.37.post0.dev240-py3.10.egg/pyiron_atomistics/calphy/base.py:505\u001b[0m, in \u001b[0;36mCalphyBase.run_static\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m 503\u001b[0m routine_fe(job) \n\u001b[1;32m 504\u001b[0m \u001b[38;5;28;01melif\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39minput\u001b[38;5;241m.\u001b[39mmode \u001b[38;5;241m==\u001b[39m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mts\u001b[39m\u001b[38;5;124m\"\u001b[39m:\n\u001b[0;32m--> 505\u001b[0m \u001b[43mroutine_ts\u001b[49m\u001b[43m(\u001b[49m\u001b[43mjob\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 506\u001b[0m \u001b[38;5;28;01melif\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39minput\u001b[38;5;241m.\u001b[39mmode \u001b[38;5;241m==\u001b[39m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mpscale\u001b[39m\u001b[38;5;124m\"\u001b[39m:\n\u001b[1;32m 507\u001b[0m routine_pscale(job)\n",
- "File \u001b[0;32m~/miniconda3/envs/pyiron-dev/lib/python3.10/site-packages/calphy-0.9.1-py3.10.egg/calphy/routines.py:363\u001b[0m, in \u001b[0;36mroutine_ts\u001b[0;34m(job)\u001b[0m\n\u001b[1;32m 361\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m i \u001b[38;5;129;01min\u001b[39;00m \u001b[38;5;28mrange\u001b[39m(job\u001b[38;5;241m.\u001b[39mcalc\u001b[38;5;241m.\u001b[39mn_iterations):\n\u001b[1;32m 362\u001b[0m ts \u001b[38;5;241m=\u001b[39m time\u001b[38;5;241m.\u001b[39mtime()\n\u001b[0;32m--> 363\u001b[0m \u001b[43mjob\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mreversible_scaling\u001b[49m\u001b[43m(\u001b[49m\u001b[43miteration\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43m(\u001b[49m\u001b[43mi\u001b[49m\u001b[38;5;241;43m+\u001b[39;49m\u001b[38;5;241;43m1\u001b[39;49m\u001b[43m)\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 364\u001b[0m te \u001b[38;5;241m=\u001b[39m (time\u001b[38;5;241m.\u001b[39mtime() \u001b[38;5;241m-\u001b[39m ts)\n\u001b[1;32m 365\u001b[0m job\u001b[38;5;241m.\u001b[39mlogger\u001b[38;5;241m.\u001b[39minfo(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mTS integration cycle \u001b[39m\u001b[38;5;132;01m%d\u001b[39;00m\u001b[38;5;124m finished in \u001b[39m\u001b[38;5;132;01m%f\u001b[39;00m\u001b[38;5;124m s\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;241m%\u001b[39m(i\u001b[38;5;241m+\u001b[39m\u001b[38;5;241m1\u001b[39m, te))\n",
- "File \u001b[0;32m~/miniconda3/envs/pyiron-dev/lib/python3.10/site-packages/calphy-0.9.1-py3.10.egg/calphy/phase.py:355\u001b[0m, in \u001b[0;36mPhase.reversible_scaling\u001b[0;34m(self, iteration)\u001b[0m\n\u001b[1;32m 353\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m (solids\u001b[38;5;241m/\u001b[39mlmp\u001b[38;5;241m.\u001b[39mnatoms \u001b[38;5;241m<\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mcalc\u001b[38;5;241m.\u001b[39mtolerance\u001b[38;5;241m.\u001b[39msolid_fraction):\n\u001b[1;32m 354\u001b[0m lmp\u001b[38;5;241m.\u001b[39mclose()\n\u001b[0;32m--> 355\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m MeltedError(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mSystem melted, increase size or reduce scaling!\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[1;32m 356\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 357\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m (solids\u001b[38;5;241m/\u001b[39mlmp\u001b[38;5;241m.\u001b[39mnatoms \u001b[38;5;241m>\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mcalc\u001b[38;5;241m.\u001b[39mtolerance\u001b[38;5;241m.\u001b[39mliquid_fraction):\n",
- "\u001b[0;31mMeltedError\u001b[0m: System melted, increase size or reduce scaling!"
- ]
- }
- ],
- "source": [
- "li_sol.calc_free_energy(temperature=[400, 500], \n",
- " pressure=0, \n",
- " reference_phase=\"solid\")\n",
- "li_sol.run()"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "id": "8d1cf858-61d4-42a6-aa97-ed967e62c527",
- "metadata": {},
- "outputs": [],
- "source": [
- "li_lqd = pr.create.job.Calphy(\"tm_li_lqd3\")\n",
- "li_lqd.structure = li_sol.structure\n",
- "li_lqd.potential = potential_list[1]\n",
- "li_lqd.server.cores = 4"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "id": "49d6a15f-583a-48b9-a3ab-b47d0f730ee7",
- "metadata": {
- "tags": []
- },
- "outputs": [],
- "source": [
- "li_lqd.calc_free_energy(temperature=[500, 700], \n",
- " pressure=0, \n",
- " reference_phase=\"liquid\")\n",
- "li_lqd.run()"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "id": "2031e3f7-d389-4ed4-b209-4735b48c701a",
- "metadata": {},
- "outputs": [],
- "source": [
- "plt.plot(li_sol.output.temperature, li_sol.output.energy_free, label=\"solid\")\n",
- "plt.plot(li_lqd.output.temperature, li_lqd.output.energy_free, label=\"liquid\")\n",
- "plt.xlabel(\"Free energy (eV/atom)\")\n",
- "plt.ylabel(\"Temperature (K)\")"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "id": "7b8d8933-56ca-4648-8948-d33d072787d9",
- "metadata": {},
- "outputs": [],
- "source": [
- "arg = np.argsort(np.abs(li_sol.output.energy_free-li_lqd.output.energy_free))[0]\n",
- "li_sol.output.temperature[arg]"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "id": "fae37cab-8c31-4005-9d3c-70822cd06633",
- "metadata": {},
- "outputs": [],
- "source": []
- }
- ],
- "metadata": {
- "kernelspec": {
- "display_name": "pyiron-dev",
- "language": "python",
- "name": "pyiron-dev"
- },
- "language_info": {
- "codemirror_mode": {
- "name": "ipython",
- "version": 3
- },
- "file_extension": ".py",
- "mimetype": "text/x-python",
- "name": "python",
- "nbconvert_exporter": "python",
- "pygments_lexer": "ipython3",
- "version": "3.10.2"
- }
- },
- "nbformat": 4,
- "nbformat_minor": 5
-}
diff --git a/phase_diagram/tutorial.ipynb b/phase_diagram/tutorial.ipynb
deleted file mode 100644
index 95f87b4..0000000
--- a/phase_diagram/tutorial.ipynb
+++ /dev/null
@@ -1,188 +0,0 @@
-{
- "cells": [
- {
- "cell_type": "markdown",
- "id": "10444b16-f852-48eb-ab46-b5ce43e962b3",
- "metadata": {},
- "source": [
- "<table border=\"0\">\n",
- " <tr>\n",
- " <td style=\"width:30%\"><img src=\"img/potentials_logo.png\" width=\"100%\" align=\"justify\"></td>\n",
- " <td style=\"width:70%\"> <p style=\"width:100%;color:#B71C1C;font-size:24px;text-align:justify\"> From electrons to phase diagrams </p> <p style=\"width:100%,font-size:16px\">Day 03 Tutorial</td>\n",
- " </tr>\n",
- "</table>"
- ]
- },
- {
- "cell_type": "markdown",
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- "In this notebook, we will use the potentials fitted in the previous days for the calculation of thermodynamic properties such as Helmholtz and Gibbs free energies, which in turn can be used for the calculation of phase diagrams. We will discuss calphy, the tool for automated calculation of free energies, and the methology involved.\n"
- ]
- },
- {
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- "id": "9b8152d6-5edb-4be2-9d7b-2b80017f70bb",
- "metadata": {},
- "source": [
- "---"
- ]
- },
- {
- "cell_type": "markdown",
- "id": "bfdfcbbf-cc13-4b43-8b6e-31bc25cd4212",
- "metadata": {},
- "source": [
- "### <font style=\"color:#B71C1C\" face=\"Helvetica\" > Phase diagrams and how to calculate them </font>"
- ]
- },
- {
- "cell_type": "markdown",
- "id": "c53d510c-cd30-4e38-9a42-1d84132c0e19",
- "metadata": {},
- "source": [
- "<table border=\"0\">\n",
- " <tr>\n",
- " <td style=\"width:40%\"><img src=\"img/phase_dia_1.png\" width=\"100%\" align=\"justify\"></td>\n",
- " <td style=\"width:60%\"> <p style=\"font-size:14px\">Phase diagrams provide a wealth of information such as: coexisting lines, melting temperature, phase stability, nucleation mechanism. </p></td>\n",
- " </tr>\n",
- "</table>"
- ]
- },
- {
- "cell_type": "markdown",
- "id": "61ecb35b-a285-45d8-a8e5-a6a1f62d6459",
- "metadata": {},
- "source": [
- "### <font style=\"color:#B71C1C\" face=\"Helvetica\" > Calculation of phase diagrams: the essential ingredients</font>"
- ]
- },
- {
- "cell_type": "markdown",
- "id": "7d819917-9a56-4589-9627-baff1e4296f3",
- "metadata": {},
- "source": [
- "<table border=\"0\">\n",
- " <tr>\n",
- " <td style=\"width:50%\"><img src=\"img/cimg4.png\" width=\"100%\" align=\"justify\"></td>\n",
- " <td style=\"width:50%\"> <p style=\"font-size:14px\">Phase diagrams can be evaluated from free energy diagrams. <br> <br>\n",
- " The required input are: <br> <br>\n",
- " ● $G(P, T)$ for unary systems <br>\n",
- " ● $G(x, T)$ for binary systems </p></td>\n",
- " </tr>\n",
- "</table>"
- ]
- },
- {
- "cell_type": "markdown",
- "id": "6198fc41-3bc2-4436-a272-1a168e44307a",
- "metadata": {},
- "source": [
- "### <font style=\"color:#B71C1C\" face=\"Helvetica\" > Calculation of free energies: Thermodynamic integration </font>"
- ]
- },
- {
- "cell_type": "markdown",
- "id": "607f3c8d-4e49-4fb6-be8d-39999eba5f7b",
- "metadata": {
- "tags": []
- },
- "source": [
- "<img src=\"img/fig1.png\" width=\"1000\">"
- ]
- },
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- "cell_type": "markdown",
- "id": "8bab199b-a1a0-42eb-a595-cd545d23873a",
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- "- free energy of reference system are known: Einstein crystal, [Uhlenbeck-Ford model](https://doi.org/10.1063/1.4967775)\n",
- "- the two systems are coupled by \n",
- "$$\n",
- "H(\\lambda) = \\lambda H_f + (1-\\lambda)\\lambda H_i\n",
- "$$\n",
- "- Run calculations for each $\\lambda$ and integrate \n",
- "$$\n",
- "G_f = G_i + \\int_{\\lambda=0}^1 d\\lambda \\bigg \\langle \\frac{\\partial H(\\lambda)}{\\partial \\lambda } \\bigg \\rangle\n",
- "$$"
- ]
- },
- {
- "cell_type": "markdown",
- "id": "4756bb61-6a01-48f8-98b1-9d076b7dccc0",
- "metadata": {},
- "source": [
- "To calculate $F$,\n",
- "\n",
- "- for each phase\n",
- " - for each pressure\n",
- " - for each temperature\n",
- " - for each $\\lambda$\n",
- "\n",
- "If we choose 100 different $\\lambda$ values; 100 calculations are needed for each temperature and pressure! \n",
- "\n",
- "**Dimensionality: (phase, $P$, $T$, $\\lambda$)**\n",
- "\n"
- ]
- },
- {
- "cell_type": "markdown",
- "id": "6ab61ee6-2273-408b-aad5-329601bf79a3",
- "metadata": {},
- "source": [
- "### <font style=\"color:#B71C1C\" face=\"Helvetica\" > Speeding things up: Non-equilibrium calculations </font>"
- ]
- },
- {
- "cell_type": "markdown",
- "id": "c4a61c05-3f8c-47ff-b01a-8ae2c3672998",
- "metadata": {},
- "source": [
- "##### Non-Equilibrium Hamiltonian Interpolation\n",
- "\n",
- "<img src=\"img/cimg5.png\" width=\"600\">"
- ]
- },
- {
- "cell_type": "markdown",
- "id": "bb228e05-ae48-4150-a033-9e0004f09db6",
- "metadata": {},
- "source": [
- "In this method:\n",
- "\n",
- "- Discrete $\\lambda$ parameter is replaced by a time dependent $\\lambda(t)$\n",
- "- Instead of running calculations at each $\\lambda$, run a single, short, non-equilibrium calculation"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "id": "7968c6d8-f410-499f-9341-5abb6243f0a2",
- "metadata": {},
- "outputs": [],
- "source": []
- }
- ],
- "metadata": {
- "kernelspec": {
- "display_name": "pyiron-atom-dev",
- "language": "python",
- "name": "pyiron-atom-dev"
- },
- "language_info": {
- "codemirror_mode": {
- "name": "ipython",
- "version": 3
- },
- "file_extension": ".py",
- "mimetype": "text/x-python",
- "name": "python",
- "nbconvert_exporter": "python",
- "pygments_lexer": "ipython3",
- "version": "3.10.4"
- }
- },
- "nbformat": 4,
- "nbformat_minor": 5
-}
--
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